ALBERT

Description: Publication date: 15 August 2017 Source: Cell Reports, Volume 20, Issue 7 Author(s): Atsushi Hayashi, Yohei Mikami, Kentaro Miyamoto, Nobuhiko Kamada, Toshiro Sato, Shinta Mizuno, Makoto Naganuma, Toshiaki Teratani, Ryo Aoki, Shinji Fukuda, Wataru Suda, Masahira Hattori, Masayuki Amagai, Manabu Ohyama, Takanori Kanai Metabolism by the gut microbiota affects host physiology beyond the gastrointestinal tract. Here, we find that antibiotic-induced dysbiosis, in particular, overgrowth of Lactobacillus murinus ( L. murinus ), impaired gut metabolic function and led to the development of alopecia. While deprivation of dietary biotin per se did not affect skin physiology, its simultaneous treatment with vancomycin resulted in hair loss in specific pathogen-free (SPF) mice. Vancomycin treatment induced the accumulation of L. murinus in the gut, which consumes residual biotin and depletes available biotin in the gut. Consistently, L. murinus induced alopecia when monocolonized in germ-free mice fed a biotin-deficient diet. Supplementation of biotin can reverse established alopecia symptoms in the SPF condition, indicating that L. murinus plays a central role in the induction of hair loss via a biotin-dependent manner. Collectively, our results indicate that luminal metabolic alterations associated with gut dysbiosis and dietary modifications can compromise skin physiology. Graphical abstract Teaser Gut microbiota metabolism affects host physiology beyond the gastrointestinal tract. Here, Hayashi et al. find that antibiotic-induced gut dysbiosis leads to the development of alopecia in mice on a biotin-deficient diet.

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Fahad A. Somaa, Ting-Yi Wang, Jonathan C. Niclis, Kiara F. Bruggeman, Jessica A. Kauhausen, Haoyao Guo, Stuart McDougall, Richard J. Williams, David R. Nisbet, Lachlan H. Thompson, Clare L. Parish Stem cell transplants offer significant hope for brain repair following ischemic damage. Pre-clinical work suggests that therapeutic mechanisms may be multi-faceted, incorporating bone-fide circuit reconstruction by transplanted neurons, but also protection/regeneration of host circuitry. Here, we engineered hydrogel scaffolds to form “bio-bridges” within the necrotic lesion cavity, providing physical and trophic support to transplanted human embryonic stem cell-derived cortical progenitors, as well as residual host neurons. Scaffolds were fabricated by the self-assembly of peptides for a laminin-derived epitope (IKVAV), thereby mimicking the brain’s major extracellular protein. Following focal ischemia in rats, scaffold-supported cell transplants induced progressive motor improvements over 9 months, compared to cell- or scaffold-only implants. These grafts were larger, exhibited greater neuronal differentiation, and showed enhanced electrophysiological properties reflective of mature, integrated neurons. Varying graft timing post-injury enabled us to attribute repair to both neuroprotection and circuit replacement. These findings highlight strategies to improve the efficiency of stem cell grafts for brain repair. Graphical abstract Teaser Somaa et al. examine the capacity of peptide-based scaffolds to structurally and functionally support human pluripotent stem cell-derived neural transplants in the stroke-injured brain. Scaffolds promoted graft maturation and integration and reduced host tissue atrophy, resulting in improved motor function over a period of 9 months.

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Zheng-Quan Tang, Laurence O. Trussell Many studies have explored how neuromodulators affect synaptic function, yet little is known about how they modify computations at the microcircuit level. In the dorsal cochlear nucleus (DCN), a region that integrates auditory and multisensory inputs from two distinct pathways, serotonin (5-HT) enhances excitability of principal cells, predicting a generalized reduction in sensory thresholds. Surprisingly, we found that when looked at from the circuit level, 5-HT enhances signaling only from the multisensory input, while decreasing input from auditory fibers. This effect is only partially explained by an action on auditory nerve terminals. Rather, 5-HT biases processing for one input pathway by simultaneously enhancing excitability in the principal cell and in a pathway-specific feed-forward inhibitory interneuron. Thus, by acting on multiple targets, 5-HT orchestrates a fundamental shift in representation of convergent auditory and multisensory pathways, enhancing the potency of non-auditory signals in a classical auditory pathway. Graphical abstract Teaser Neuromodulators may alter sensory processing upon changes in behavioral state. Tang and Trussell demonstrate that the neuromodulator serotonin shifts the representation of convergent auditory and multisensory pathways at a microcircuit level, enhancing the potency of non-auditory signals in a classical auditory brain region.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Hanqing He, Jiajia Wang, Ting Liu Replication protein A (RPA) is a multifunctional, single-stranded DNA-binding protein complex and plays a critical role in DNA replication and damage response. Herein, we show that the 70-kDa subunit of RPA (RPA1) is acetylated on lysine 163 by the acetyltransferases GCN5 and PCAF and that such acetylation is reversed principally via the action of the deacetylase HDAC6. UV irradiation promotes cytoplasmic translocation of HDAC6, thereby disrupting the interaction of HDAC6 with RPA1 and increasing RPA1 acetylation. Mutation of the acetylation site of RPA1 specifically impairs the ability of the protein to interact with the key nucleotide excision repair (NER) protein XPA, reduces XPA retention at sites of DNA damage caused by UV, compromises NER, and renders the cell hypersensitive to UV irradiation. Our data suggest that the acetylation status of RPA1 played a crucial role in repair of DNA damage via NER. Graphical abstract Teaser He et al. find that the RPA1 protein becomes acetylated at lysine 163 in response to UV irradiation. Such acetylation specifically enhances interaction between RPA1 and the key NER protein XPA and promotes XPA retention at DNA damage sites. These findings suggest that RPA1 acetylation is a unique NER-related event.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Jia Zhou, Jany Chan, Marie Lambelé, Timur Yusufzai, Jason Stumpff, Patricia L. Opresko, Markus Thali, Susan S. Wallace Oxidative damage to telomere DNA compromises telomere integrity. We recently reported that the DNA glycosylase NEIL3 preferentially repairs oxidative lesions in telomere sequences in vitro. Here, we show that loss of NEIL3 causes anaphase DNA bridging because of telomere dysfunction. NEIL3 expression increases during S phase and reaches maximal levels in late S/G2. NEIL3 co-localizes with TRF2 and associates with telomeres during S phase, and this association increases upon oxidative stress. Mechanistic studies reveal that NEIL3 binds to single-stranded DNA via its intrinsically disordered C terminus in a telomere-sequence-independent manner. Moreover, NEIL3 is recruited to telomeres through its interaction with TRF1, and this interaction enhances the enzymatic activity of purified NEIL3. Finally, we show that NEIL3 interacts with AP Endonuclease 1 (APE1) and the long-patch base excision repair proteins PCNA and FEN1. Taken together, we propose that NEIL3 protects genome stability through targeted repair of oxidative damage in telomeres during S/G2 phase. Graphical abstract Teaser NEIL3 DNA glycosylase activity is critical in highly proliferating cells including cancer cells. Zhou et al. show that NEIL3 is specifically active at telomeres during S/G2, and that depletion of NEIL3 causes telomere dysfunction and thus mitotic defects, revealing its involvement in telomere repair, which prevents genome instability.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Marlen Knobloch, Gregor-Alexander Pilz, Bart Ghesquière, Werner J. Kovacs, Thomas Wegleiter, Darcie L. Moore, Martina Hruzova, Nicola Zamboni, Peter Carmeliet, Sebastian Jessberger Hippocampal neurogenesis is important for certain forms of cognition, and failing neurogenesis has been implicated in neuropsychiatric diseases. The neurogenic capacity of hippocampal neural stem/progenitor cells (NSPCs) depends on a balance between quiescent and proliferative states. Here, we show that the rate of fatty acid oxidation (FAO) regulates the activity of NSPCs. Quiescent NSPCs show high levels of carnitine palmitoyltransferase 1a (Cpt1a)-dependent FAO, which is downregulated in proliferating NSPCs. Pharmacological inhibition and conditional deletion of Cpt1a in vitro and in vivo leads to altered NSPC behavior, showing that Cpt1a-dependent FAO is required for stem cell maintenance and proper neurogenesis. Strikingly, manipulation of malonyl-CoA, the metabolite that regulates levels of FAO, is sufficient to induce exit from quiescence and to enhance NSPC proliferation. Thus, the data presented here identify a shift in FAO metabolism that governs NSPC behavior and suggest an instructive role for fatty acid metabolism in regulating NSPC activity. Graphical abstract Teaser Controlled balance between proliferation and quiescence of neural stem/progenitor cells (NSPCs) is required for lifelong neurogenesis. Knobloch et al. identify a metabolic shift in fatty acid oxidation (FAO) that governs the proliferation of NSPCs. Further, their data suggest an instructive role for FAO in regulating NSPC activity. Thus, Knobloch et al. identify FAO as a key metabolic pathway to regulate NSPC activity.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Xiaowan Wang, Qiao Zhang, Ruisi Bao, Nannan Zhang, Yingzhen Wang, Luis Polo-Parada, Andrew Tarim, Aidan Alemifar, Xianlin Han, Heather M. Wilkins, Russell H. Swerdlow, Xinglong Wang, Shinghua Ding Intracellular nicotinamide phosphoribosyltransferase (iNAMPT) is the rate-limiting enzyme of the mammalian NAD + biosynthesis salvage pathway. Using inducible and conditional knockout (cKO) mice, we show that Nampt gene deletion in adult projection neurons leads to a progressive loss of body weight, hypothermia, motor neuron (MN) degeneration, motor function deficits, paralysis, and death. Nampt deletion causes mitochondrial dysfunction, muscle fiber type conversion, and atrophy, as well as defective synaptic function at neuromuscular junctions (NMJs). When treated with nicotinamide mononucleotide (NMN), Nampt cKO mice exhibit reduced motor function deficits and prolonged lifespan. iNAMPT protein levels are significantly reduced in the spinal cord of amyotrophic lateral sclerosis (ALS) patients, indicating the involvement of NAMPT in ALS pathology. Our findings reveal that neuronal NAMPT plays an essential role in mitochondrial bioenergetics, motor function, and survival. Our study suggests that the NAMPT-mediated NAD + biosynthesis pathway is a potential therapeutic target for degenerative MN diseases. Graphical abstract Teaser Wang et al. find that projection neuron NAMPT is essential for mitochondrial bioenergetics, motor function, and survival of adult mice and that iNAMPT is reduced in ALS patients. NMN improves health and extends the lifespan of Nampt knockout mice. Their findings suggest therapeutic avenues for motor neuron degenerative diseases.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Kazuhiro Takara, Daisuke Eino, Koji Ando, Daisuke Yasuda, Hisamichi Naito, Yohei Tsukada, Tomohiro Iba, Taku Wakabayashi, Fumitaka Muramatsu, Hiroyasu Kidoya, Shigetomo Fukuhara, Naoki Mochizuki, Satoshi Ishii, Haruhiko Kishima, Nobuyuki Takakura Vascular normalization in tumors may improve drug delivery and anti-tumor immunity. Angiogenesis inhibitors induce hypoxia, which may facilitate malignant progression; therefore, we investigated other methods to promote vascular maturation. Here, we show that lysophosphatidic acid (LPA) enhances blood flow by promoting fine vascular networks, thereby improving vascular permeability and suppressing tumor growth when combined with anti-cancer drug treatment. Six different G protein-coupled receptors have been identified as LPA receptors (LPA1–6). In studies using mutant mice, we found that LPA4 is involved in vascular network formation. LPA4 activation induces circumferential actin bundling beneath the cell membrane and enhances linear adherens junction formation by VE-cadherin in endothelial cells. Therefore, we conclude that activation of LPA4 is a promising approach for vascular regulation. Graphical abstract Teaser Takara et al. find that lysophosphatidic acid (LPA) promotes fine capillary network formation and improves drug delivery in tumors. LPA controls localization of VE-cadherin in endothelial cells through LPA receptor 4 (LPA4) signaling.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Laina Freyer, Chih-Wei Hsu, Sonja Nowotschin, Andrea Pauli, Junji Ishida, Keiji Kuba, Akiyoshi Fukamizu, Alexander F. Schier, Pamela A. Hoodless, Mary E. Dickinson, Anna-Katerina Hadjantonakis Apela (also known as Elabela, Ende, and Toddler) is a small signaling peptide that activates the G-protein-coupled receptor Aplnr to stimulate cell migration during zebrafish gastrulation. Here, using CRISPR/Cas9 to generate a null, reporter-expressing allele, we study the role of Apela in the developing mouse embryo. We found that loss of Apela results in low-penetrance cardiovascular defects that manifest after the onset of circulation. Three-dimensional micro-computed tomography revealed a higher penetrance of vascular remodeling defects, from which some mutants recover, and identified extraembryonic anomalies as the earliest morphological distinction in Apela mutant embryos. Transcriptomics at late gastrulation identified aberrant upregulation of erythroid and myeloid markers in mutant embryos prior to the appearance of physical malformations. Double-mutant analyses showed that loss of Apela signaling impacts early Aplnr-expressing mesodermal populations independently of the alternative ligand Apelin, leading to lethal cardiac defects in some Apela null embryos. Graphical abstract Teaser Apela (a.k.a. Elabela, Ende, and Toddler) is a key signaling peptide that activates APLNR in mouse development. Freyer et al. show that lethal developmental defects in Apela mutants may rely on sufficient blood circulation. They suggest that extraembryonic mesoderm derivatives, including endothelial and hematopoietic progenitors, may be the first cell populations impacted by the loss of Apela.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Meimei Zhao, Rui Geng, Xiang Guo, Ruoshi Yuan, Xiao Zhou, Yanyan Zhong, Yanfei Huo, Mei Zhou, Qinjian Shen, Yinglu Li, Weiguo Zhu, Jiadong Wang The RPA complex can integrate multiple stress signals into diverse responses by activating distinct DNA repair pathways. However, it remains unclear how RPA1 elects to activate a specific repair pathway during different types of DNA damage. Here, we report that PCAF/GCN5-mediated K163 acetylation of RPA1 is crucial for nucleotide excision repair (NER) but is dispensable for other DNA repair pathways. Mechanistically, we demonstrate that the acetylation of RPA1 is critical for the steady accumulation of XPA at damaged DNA sites and preferentially activates the NER pathway. DNA-PK phosphorylates and activates PCAF upon UV damage and consequently promotes the acetylation of RPA1. Moreover, the acetylation of RPA1 is tightly regulated by HDAC6 and SIRT1. Together, our results demonstrate that the K163 acetylation of RPA1 plays a key role in the repair of UV-induced DNA damage and reveal how the specific RPA1 modification modulates the choice of distinct DNA repair pathways. Graphical abstract Teaser RPA complex is a central player in multiple DNA repair pathways. Zhao et al. show that PCAF/GCN5-mediated acetylation of RPA1 is crucial for NER repair by promoting stable RPA1/XPA complex.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Ngat T. Tran, Michael T. Laub, Tung B.K. Le The structural maintenance of chromosomes (SMC) complex plays an important role in chromosome organization and segregation in most living organisms. In Caulobacter crescentus , SMC is required to align the left and the right arms of the chromosome that run in parallel down the long axis of the cell. However, the mechanism of SMC-mediated alignment of chromosomal arms remains elusive. Here, using genome-wide methods and microscopy of single cells, we show that Caulobacter SMC is recruited to the centromeric parS site and that SMC-mediated arm alignment depends on the chromosome-partitioning protein ParB. We provide evidence that SMC likely tethers the parS- proximal regions of the chromosomal arms together, promoting arm alignment. Furthermore, we show that highly transcribed genes near parS that are oriented against SMC translocation disrupt arm alignment, suggesting that head-on transcription interferes with SMC translocation. Our results demonstrate a tight interdependence of bacterial chromosome organization and global patterns of transcription. Graphical abstract Teaser Tran et al. investigate the mechanism and function of SMC in the global organization of the Caulobacter chromosome. The findings suggest that SMC functions as a tether to actively cohese the chromosomal arms together and show that head-on transcription profoundly interferes with SMC translocation from the centromeric parS site.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Megan S. Wyeth, Kenneth A. Pelkey, Xiaoqing Yuan, Geoffrey Vargish, April D. Johnston, Steven Hunt, Calvin Fang, Daniel Abebe, Vivek Mahadevan, André Fisahn, Michael W. Salter, Roderick R. McInnes, Ramesh Chittajallu, Chris J. McBain Although Netos are considered auxiliary subunits critical for kainate receptor (KAR) function, direct evidence for their regulation of native KARs is limited. Because Neto KAR regulation is GluK subunit/Neto isoform specific, such regulation must be determined in cell-type-specific contexts. We demonstrate Neto1/2 expression in somatostatin (SOM)-, cholecystokinin/cannabinoid receptor 1 (CCK/CB1)-, and parvalbumin (PV)-containing interneurons. KAR-mediated excitation of these interneurons is contingent upon Neto1 because kainate yields comparable effects in Neto2 knockouts and wild-types but fails to excite interneurons or recruit inhibition in Neto1 knockouts. In contrast, presynaptic KARs in CCK/CB1 interneurons are dually regulated by both Neto1 and Neto2. Neto association promotes tonic presynaptic KAR activation, dampening CCK/CB1 interneuron output, and loss of this brake in Neto mutants profoundly increases CCK/CB1 interneuron-mediated inhibition. Our results confirm that Neto1 regulates endogenous somatodendritic KARs in diverse interneurons and demonstrate Neto regulation of presynaptic KARs in mature inhibitory presynaptic terminals. Graphical abstract Teaser Netos are considered critical kainate receptor (KAR) auxiliary subunits in glutamatergic principal cells, but their roles in GABAergic interneurons remain unexplored. Wyeth et al. find that somatodendritic KARs within diverse interneurons require Neto1, whereas both Neto1 and Neto2 regulate presynaptic KAR-mediated suppression of inhibitory transmission.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Héctor Climente-González, Eduard Porta-Pardo, Adam Godzik, Eduardo Eyras Alternative splicing changes are frequently observed in cancer and are starting to be recognized as important signatures for tumor progression and therapy. However, their functional impact and relevance to tumorigenesis remain mostly unknown. We carried out a systematic analysis to characterize the potential functional consequences of alternative splicing changes in thousands of tumor samples. This analysis revealed that a subset of alternative splicing changes affect protein domain families that are frequently mutated in tumors and potentially disrupt protein-protein interactions in cancer-related pathways. Moreover, there was a negative correlation between the number of these alternative splicing changes in a sample and the number of somatic mutations in drivers. We propose that a subset of the alternative splicing changes observed in tumors may represent independent oncogenic processes that could be relevant to explain the functional transformations in cancer, and some of them could potentially be considered alternative splicing drivers (AS drivers). Graphical abstract Teaser Climente-González et al. show that alternative splicing (AS) changes in tumors are linked to a significant loss of functional domain families that are also frequently mutated in cancer. These domain losses happen independently of somatic mutations and lead to the remodeling of complexes and protein-protein interactions in cancer.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Zeyu Chen, Erietta Stelekati, Makoto Kurachi, Sixiang Yu, Zhangying Cai, Sasikanth Manne, Omar Khan, Xiaolu Yang, E. John Wherry MicroRNAs play an important role in T cell responses. However, how microRNAs regulate CD8 T cell memory remains poorly defined. Here, we found that miR-150 negatively regulates CD8 T cell memory in vivo. Genetic deletion of miR-150 disrupted the balance between memory precursor and terminal effector CD8 T cells following acute viral infection. Moreover, miR-150-deficient memory CD8 T cells were more protective upon rechallenge. A key circuit whereby miR-150 repressed memory CD8 T cell development through the transcription factor c-Myb was identified. Without miR-150, c-Myb was upregulated and anti-apoptotic targets of c-Myb, such as Bcl-2 and Bcl-xL, were also increased, suggesting a miR-150-c-Myb survival circuit during memory CD8 T cell development. Indeed, overexpression of non-repressible c-Myb rescued the memory CD8 T cell defects caused by overexpression of miR-150. Overall, these results identify a key role for miR-150 in memory CD8 T cells through a c-Myb-controlled enhanced survival circuit. Graphical abstract Teaser Memory CD8 T cells are critical for long-term adaptive immune protection. In this study, Chen et al. find that miR-150 negatively regulates CD8 T cell memory formation by targeting the c-Myb-Bcl-2/Bcl-xl survival axis.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Daniel N. Itzhak, Colin Davies, Stefka Tyanova, Archana Mishra, James Williamson, Robin Antrobus, Jürgen Cox, Michael P. Weekes, Georg H.H. Borner We previously developed a mass spectrometry-based method, dynamic organellar maps, for the determination of protein subcellular localization and identification of translocation events in comparative experiments. The use of metabolic labeling for quantification (stable isotope labeling by amino acids in cell culture [SILAC]) renders the method best suited to cells grown in culture. Here, we have adapted the workflow to both label-free quantification (LFQ) and chemical labeling/multiplexing strategies (tandem mass tagging [TMT]). Both methods are highly effective for the generation of organellar maps and capture of protein translocations. Furthermore, application of label-free organellar mapping to acutely isolated mouse primary neurons provided subcellular localization and copy-number information for over 8,000 proteins, allowing a detailed analysis of organellar organization. Our study extends the scope of dynamic organellar maps to any cell type or tissue and also to high-throughput screening. Graphical abstract Teaser Dynamic organellar maps previously provided a proteomic method for capturing protein subcellular localization changes in cultured cells. Itzhak et al. have now adapted the approach to a universal format, extending the method to all cell types. Application to primary mouse neurons provides spatial and quantitative information for more than 8,000 proteins.

Description: Publication date: 15 August 2017 Source: Cell Reports, Volume 20, Issue 7 Author(s): Irene Saugar, Alberto Jiménez-Martín, José Antonio Tercero Structure-specific endonucleases contribute to the maintenance of genome integrity by cleaving DNA intermediates that need to be resolved for faithful DNA repair, replication, or recombination. Despite advances in the understanding of their function and regulation, it is less clear how these proteins respond to genotoxic stress. Here, we show that the structure-specific endonuclease Mus81-Mms4/EME1 relocalizes to subnuclear foci following DNA damage and colocalizes with the endonucleases Rad1-Rad10 (XPF-ERCC1) and Slx1-Slx4. Recruitment takes place into a class of stress foci defined by Cmr1/WDR76, a protein involved in preserving genome stability, and depends on the E2-ubiquitin-conjugating enzyme Rad6 and the E3-ubiquitin ligase Bre1. Foci dynamics show that, in the presence of DNA intermediates that need resolution by Mus81-Mms4, Mus81 foci persist until this endonuclease is activated by Mms4 phosphorylation. Our data suggest that subnuclear relocalization is relevant for the function of Mus81-Mms4 and, probably, of the endonucleases that colocalize with it. Graphical abstract Teaser Saugar et al. find that, under conditions of DNA damage, the structure-specific endonuclease Mus81-Mms4/EME1 relocalizes to subnuclear foci, where it colocalizes with the endonucleases Rad1-Rad10 and Slx1-Slx4. Relocalization takes place to a class of stress-induced foci defined by the Cmr1 protein and correlates with the function of the endonuclease.

Description: Publication date: 15 August 2017 Source: Cell Reports, Volume 20, Issue 7 Author(s): Santosh Narayan, Gene Bryant, Shivangi Shah, Georgina Berrozpe, Mark Ptashne SOX2 and OCT4, in conjunction with KLF4 and cMYC, are sufficient to reprogram human fibroblasts to induced pluripotent stem cells (iPSCs), but it is unclear if they function as transcriptional activators or as repressors. We now show that, like OCT4, SOX2 functions as a transcriptional activator. We substituted SOX2-VP16 (a strong activator) for wild-type (WT) SOX2, and we saw an increase in the efficiency and rate of reprogramming, whereas the SOX2-HP1 fusion (a strong repressor) eliminated reprogramming. We report that, at an early stage of reprogramming, virtually all DNA-bound OCT4, SOX2, and SOX2-VP16 were embedded in putative enhancers, about half of which were created de novo. Those associated with SOX2-VP16 were, on average, stronger than those bearing WT SOX2. Many newly created putative enhancers were transient, and many transcription factor locations on DNA changed as reprogramming progressed. These results are consistent with the idea that, during reprogramming, there is an intermediate state that is distinct from both parental cells and iPSCs. Graphical abstract Teaser Narayan et al. show that substituting SOX2 with the strong activator SOX2-VP16 increases reprogramming efficiency of human fibroblasts, especially those cultured from older donors. Thousands of enhancers are created and destroyed in the course of reprogramming, including many enhancers created at binding sites of OCT4 or SOX2.

Description: Publication date: 15 August 2017 Source: Cell Reports, Volume 20, Issue 7 Author(s): Zhifeng Huang, Yi Tan, Junlian Gu, Yang Liu, Lintao Song, Jianlou Niu, Longwei Zhao, Lakshmi Srinivasan, Qian Lin, Jingjing Deng, Yang Li, Daniel J. Conklin, Thomas A. Neubert, Lu Cai, Xiaokun Li, Moosa Mohammadi The recent discovery of metabolic roles for fibroblast growth factor 1 (FGF1) in glucose homeostasis has expanded the functions of this classically known mitogen. To dissect the molecular basis for this functional pleiotropy, we engineered an FGF1 partial agonist carrying triple mutations (FGF1 ΔHBS ) that diminished its ability to induce heparan sulfate (HS)-assisted FGF receptor (FGFR) dimerization and activation. FGF1 ΔHBS exhibited a severely reduced proliferative potential, while preserving the full metabolic activity of wild-type FGF1 in vitro and in vivo. Hence, suboptimal FGFR activation by a weak FGF1-FGFR dimer is sufficient to evoke a metabolic response, whereas full FGFR activation by stable and sustained dimerization is required to elicit a mitogenic response. In addition to providing a physical basis for the diverse activities of FGF1, our findings will impact ongoing drug discoveries targeting FGF1 and related FGFs for the treatment of a variety of human diseases. Graphical abstract Teaser Huang et al. report that quantitative differences in FGF-FGFR dimer stability give rise to different thresholds of intracellular signals to determine mitogenic versus metabolic activities of FGFs.

Description: Publication date: 15 August 2017 Source: Cell Reports, Volume 20, Issue 7 Author(s): Jessica A. Hicks, Liande Li, Masayuki Matsui, Yongjun Chu, Oleg Volkov, Krystal C. Johnson, David R. Corey In the cytoplasm, small RNAs can control mammalian translation by regulating the stability of mRNA. In the nucleus, small RNAs can also control transcription and splicing. The mechanisms for RNA-mediated nuclear regulation are not understood and remain controversial, hindering the effective application of nuclear RNAi and investigation of its natural regulatory roles. Here, we reveal that the human GW182 paralogs TNRC6A/B/C are central organizing factors critical to RNA-mediated transcriptional activation. Mass spectrometry of purified nuclear lysates followed by experimental validation demonstrates that TNRC6A interacts with proteins involved in protein degradation, RNAi, the CCR4-NOT complex, the mediator complex, and histone-modifying complexes. Functional analysis implicates TNRC6A, NAT10, MED14, and WDR5 in RNA-mediated transcriptional activation. These findings describe protein complexes capable of bridging RNA-mediated sequence-specific recognition of noncoding RNA transcripts with the regulation of gene transcription. Graphical abstract Teaser Nuclear RNAi has the potential to add a previously unrecognized layer of control over mammalian gene expression. Hicks et al. use mass spectrometry to expand identification of protein partners that may play roles in RNA-mediated regulation of transcription and splicing.

Description: Publication date: 15 August 2017 Source: Cell Reports, Volume 20, Issue 7 Author(s): Lorenza Magno, Caswell Barry, Christoph Schmidt-Hieber, Polyvios Theodotou, Michael Häusser, Nicoletta Kessaris The transcription factor NKX2-1 is best known for its role in the specification of subsets of cortical, striatal, and pallidal neurons. We demonstrate through genetic fate mapping and intersectional focal septal deletion that NKX2-1 is selectively required in the embryonic septal neuroepithelium for the development of cholinergic septohippocampal projection neurons and large subsets of basal forebrain cholinergic neurons. In the absence of NKX2-1, these neurons fail to develop, causing alterations in hippocampal theta rhythms and severe deficiencies in learning and memory. Our results demonstrate that learning and memory are dependent on NKX2-1 function in the embryonic septum and suggest that cognitive deficiencies that are sometimes associated with pathogenic mutations in NKX2-1 in humans may be a direct consequence of loss of NKX2-1 function. Graphical abstract Teaser NKX2-1 is a highly conserved patterning gene in the developing forebrain, mutations in which can lead to a spectrum of disorders including cognitive deficiencies. Using genetic fate mapping and intersectional deletion, Magno et al. demonstrate a requirement for embryonic septal NKX2-1 in forebrain cholinergic system development and learning and memory.

Description: Publication date: 15 August 2017 Source: Cell Reports, Volume 20, Issue 7 Author(s): Sara Montagner, Cristina Leoni, Stefan Emming, Giulia Della Chiara, Chiara Balestrieri, Iros Barozzi, Viviana Piccolo, Susan Togher, Myunggon Ko, Anjana Rao, Gioacchino Natoli, Silvia Monticelli

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Ronen Blecher, Sharon Krief, Tal Galili, Eran Assaraf, Tomer Stern, Yoram Anekstein, Gabriel Agar, Elazar Zelzer Successful fracture repair requires restoration of bone morphology and mechanical integrity. Recent evidence shows that fractured bones of neonatal mice undergo spontaneous realignment, dubbed “natural reduction.” Here, we show that natural reduction is regulated by the proprioceptive system and improves with age. Comparison among mice of different ages revealed, surprisingly, that 3-month-old mice exhibited more rapid and effective natural reduction than newborns. Fractured bones of null mutants for transcription factor Runx3 , lacking functional proprioceptors, failed to realign properly. Blocking Runx3 expression in the peripheral nervous system, but not in limb mesenchyme, recapitulated the null phenotype, as did inactivation of muscles flanking the fracture site. Egr3 knockout mice, which lack muscle spindles but not Golgi tendon organs, displayed a less severe phenotype, suggesting that both receptor types, as well as muscle contraction, are required for this regulatory mechanism. These findings uncover a physiological role for proprioception in non-autonomous regulation of skeletal integrity. Graphical abstract Teaser Blecher et al. report that natural reduction, the process whereby fractured bones are realigned, fails in mutant mice lacking functional proprioceptive circuitry. Surprisingly, natural reduction was more rapid and effective in 3-month-old mice than in newborns. These findings suggest a physiological role for proprioception in non-autonomous regulation of skeletal integrity.

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Kristina Petkau, Meghan Ferguson, Silvia Guntermann, Edan Foley Gut innate immune defenses control bacterial populations and protect the host interior from invasion. Although excess intestinal immune activity frequently promotes inflammatory illnesses, we know little about the consequences of chronic innate immune activity exclusively in endodermal gut cells of an otherwise normal animal. To address this question, we examined the consequences of persistent inflammatory signals in adult fly intestinal progenitor cells. We found that constitutive immune activity disrupts expression of homeostatic regulators such as Notch pathway components and induces hyperplasia throughout the gut. Consistent with these observations, we found that persistent immune signals interfere with progenitor cell differentiation and exacerbate the formation of Notch-dependent intestinal tumors. These findings uncover a link between constitutive immune activity and tumorigenesis in intestinal stem cells. Graphical abstract Teaser Petkau et al. show that persistent immune activity in gut progenitor cells promotes tumorigenesis in adult flies.

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Mikkel Roland Holst, Maite Vidal-Quadras, Elin Larsson, Jie Song, Madlen Hubert, Jeanette Blomberg, Magnus Lundborg, Maréne Landström, Richard Lundmark Cellular blebbing, caused by local alterations in cell-surface tension, has been shown to increase the invasiveness of cancer cells. However, the regulatory mechanisms balancing cell-surface dynamics and bleb formation remain elusive. Here, we show that an acute reduction in cell volume activates clathrin-independent endocytosis. Hence, a decrease in surface tension is buffered by the internalization of the plasma membrane (PM) lipid bilayer. Membrane invagination and endocytosis are driven by the tension-mediated recruitment of the membrane sculpting and GTPase-activating protein GRAF1 (GTPase regulator associated with focal adhesion kinase-1) to the PM. Disruption of this regulation by depleting cells of GRAF1 or mutating key phosphatidylinositol-interacting amino acids in the protein results in increased cellular blebbing and promotes the 3D motility of cancer cells. Our data support a role for clathrin-independent endocytic machinery in balancing membrane tension, which clarifies the previously reported role of GRAF1 as a tumor suppressor. Graphical abstract Teaser Holst et al. show that clathrin-independent endocytosis facilitates the rearrangement of the cell surface in response to a decrease in cell volume. This regulation, mediated by the protein GRAF1, suppresses cellular blebbing and the invasiveness of cancer cells, clarifying why GRAF1 acts as a tumor suppressor.

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Fabio Da Silva, Ana Sofia Rocha, Fariba Jian Motamedi, Filippo Massa, Cem Basboga, Harris Morrison, Kay Dietrich Wagner, Andreas Schedl Coronary arteries are essential to support the heart with oxygen, and coronary heart disease is one of the leading causes of death worldwide. The coronary arteries form at highly stereotyped locations and are derived from the primitive vascular plexus of the heart. How coronary arteries are remodeled and the signaling molecules that govern this process are poorly understood. Here, we have identified the Wnt-signaling modulator Rspo3 as a crucial regulator of coronary artery formation in the developing heart. Rspo3 is specifically expressed around the coronary stems at critical time points in their development. Temporal ablation of Rspo3 at E11.5 leads to decreased β-catenin signaling and a reduction in arterial-specific proliferation. As a result, the coronary stems are defective and the arterial tree does not form properly. These results identify a mechanism through which localized expression of RSPO3 induces proliferation of the coronary arteries at their stems and permits their formation. Graphical abstract Teaser Coronary arteries supply the heart with blood, and coronary diseases are one of the leading causes of death worldwide. Da Silva et al. find that RSPO3 is specifically expressed around the developing stems of the left and right coronaries, where it promotes their formation by stimulating arterial-specific proliferation through Wnt/β-catenin signaling.

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Min Xia, Kun Chen, Xiao Yao, Yichi Xu, Jiaying Yao, Jun Yan, Zhen Shao, Gang Wang DNA repair is related to many physiological and pathological processes, including pigmentation. Little is known about the role of the transcriptional cofactor Mediator complex in DNA repair and pigmentation. Here, we demonstrate that Mediator MED23 plays an important role in coupling UV-induced DNA repair to pigmentation. The loss of Med23 specifically impairs the pigmentation process in melanocyte-lineage cells and in zebrafish. Med23 deficiency leads to enhanced nucleotide excision repair (NER) and less DNA damage following UV radiation because of the enhanced expression and recruitment of NER factors to chromatin for genomic stability. Integrative analyses of melanoma cells reveal that MED23 controls the expression of a melanocyte master regulator, Mitf , by modulating its distal enhancer activity, leading to opposing effects on pigmentation and DNA repair. Collectively, the Mediator MED23/MITF axis connects DNA repair to pigmentation, thus providing molecular insights into the DNA damage response and skin-related diseases. Graphical abstract Teaser Xia et al. find that MED23 controls Mitf expression by modulating its enhancer function, thus connecting DNA repair to pigmentation.

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Brian O. Orr, David Gorczyca, Meg A. Younger, Lily Y. Jan, Yuh-Nung Jan, Graeme W. Davis The homeostatic control of presynaptic neurotransmitter release stabilizes information transfer at synaptic connections in the nervous system of organisms ranging from insect to human. Presynaptic homeostatic signaling centers upon the regulated membrane insertion of an amiloride-sensitive degenerin/epithelial sodium (Deg/ENaC) channel. Elucidating the subunit composition of this channel is an essential step toward defining the underlying mechanisms of presynaptic homeostatic plasticity (PHP). Here, we demonstrate that the ppk1 gene encodes an essential subunit of this Deg/ENaC channel, functioning in motoneurons for the rapid induction and maintenance of PHP. We provide genetic and biochemical evidence that PPK1 functions together with PPK11 and PPK16 as a presynaptic, hetero-trimeric Deg/ENaC channel. Finally, we highlight tight control of Deg/ENaC channel expression and activity, showing increased PPK1 protein expression during PHP and evidence for signaling mechanisms that fine tune the level of Deg/ENaC activity during PHP. Graphical abstract Teaser Orr et al. define the subunit composition of an essential Deg/ENaC channel that controls the rapid induction and sustained expression of presynaptic homeostatic plasticity. The demonstration that PPK1 incorporates into DEG/ENaC channels with diverse physiological activities highlights the potential for tremendous DEG/ENaC channel diversity in Drosophila.

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Marco R. Cosenza, Anna Cazzola, Annik Rossberg, Nicole L. Schieber, Gleb Konotop, Elena Bausch, Alla Slynko, Tim Holland-Letz, Marc S. Raab, Taronish Dubash, Hanno Glimm, Sven Poppelreuther, Christel Herold-Mende, Yannick Schwab, Alwin Krämer Chromosomal instability is a hallmark of cancer and correlates with the presence of extra centrosomes, which originate from centriole overduplication. Overduplicated centrioles lead to the formation of centriole rosettes, which mature into supernumerary centrosomes in the subsequent cell cycle. While extra centrosomes promote chromosome missegregation by clustering into pseudo-bipolar spindles, the contribution of centriole rosettes to chromosome missegregation is unknown. We used multi-modal imaging of cells with conditional centriole overduplication to show that mitotic rosettes in bipolar spindles frequently harbor unequal centriole numbers, leading to biased chromosome capture that favors binding to the prominent pole. This results in chromosome missegregation and aneuploidy. Rosette mitoses lead to viable offspring and significantly contribute to progeny production. We further show that centrosome abnormalities in primary human malignancies frequently consist of centriole rosettes. As asymmetric centriole rosettes generate mitotic errors that can be propagated, rosette mitoses are sufficient to cause chromosome missegregation in cancer. Graphical abstract Teaser Extra centrosomes are frequent in human cancers and cause chromosome missegregation via clustering into a pseudo-bipolar mitotic spindle array. Cosenza et al. now demonstrate that centriole rosettes, a transient stage of extra centrosome formation, drive chromosome missegregation in addition to centrosome clustering and are frequently found in primary tumors.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Diletta Edifizi, Hendrik Nolte, Vipin Babu, Laia Castells-Roca, Michael M. Mueller, Susanne Brodesser, Marcus Krüger, Björn Schumacher DNA damage causally contributes to aging and age-related diseases. Mutations in nucleotide excision repair (NER) genes cause highly complex congenital syndromes characterized by growth retardation, cancer susceptibility, and accelerated aging in humans. Orthologous mutations in Caenorhabditis elegans lead to growth delay, genome instability, and accelerated functional decline, thus allowing investigation of the consequences of persistent DNA damage during development and aging in a simple metazoan model. Here, we conducted proteome, lipidome, and phosphoproteome analysis of NER-deficient animals in response to UV treatment to gain comprehensive insights into the full range of physiological adaptations to unrepaired DNA damage. We derive metabolic changes indicative of a tissue maintenance program and implicate an autophagy-mediated proteostatic response. We assign central roles for the insulin-, EGF-, and AMPK-like signaling pathways in orchestrating the adaptive response to DNA damage. Our results provide insights into the DNA damage responses in the organismal context. Graphical abstract Teaser Edifizi et al. provide a comprehensive proteomics, phosphoproteomics, and lipidomics analysis of the response to persistent DNA damage in a metazoan organism. Proteostasis shifts toward autophagy, fatty acid metabolism is attenuated, and the insulin-, EGF-, and AMPK-like signaling pathways form the center of the response network.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Anne Rechtien, Laura Richert, Hadrien Lorenzo, Gloria Martrus, Boris Hejblum, Christine Dahlke, Rahel Kasonta, Madeleine Zinser, Hans Stubbe, Urte Matschl, Ansgar Lohse, Verena Krähling, Markus Eickmann, Stephan Becker, Rodolphe Thiébaut, Marcus Altfeld, Marylyn Addo Predicting vaccine efficacy remains a challenge. We used a systems vaccinology approach to identify early innate immune correlates of antibody induction in humans receiving the Ebola vaccine rVSV-ZEBOV. Blood samples from days 0, 1, 3, 7, and 14 were analyzed for changes in cytokine levels, innate immune cell subsets, and gene expression. Integrative statistical analyses with cross-validation identified a signature of 5 early innate markers correlating with antibody titers on day 28 and beyond. Among those, IP-10 on day 3 and MFI of CXCR6 on NK cells on day 1 were independent correlates. Consistently, we found an early gene expression signature linked to IP-10. This comprehensive characterization of early innate immune responses to the rVSV-ZEBOV vaccine in humans revealed immune signatures linked to IP-10. These results suggest correlates of vaccine-induced antibody induction and provide a rationale to explore strategies for augmenting the effectiveness of vaccines through manipulation of IP-10. Graphical abstract Teaser Rechtien et al. apply a systems vaccinology approach to examine the early innate immune responses elicited by the Ebola vaccine rVSV-ZEBOV. They find that early innate immune responses, with IP-10 as an independent soluble marker, correlate with EBOV-GP-specific antibody induction.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Theodoros I. Roumeliotis, Steven P. Williams, Emanuel Gonçalves, Clara Alsinet, Martin Del Castillo Velasco-Herrera, Nanne Aben, Fatemeh Zamanzad Ghavidel, Magali Michaut, Michael Schubert, Stacey Price, James C. Wright, Lu Yu, Mi Yang, Rodrigo Dienstmann, Justin Guinney, Pedro Beltrao, Alvis Brazma, Mercedes Pardo, Oliver Stegle, David J. Adams, Lodewyk Wessels, Julio Saez-Rodriguez, Ultan McDermott, Jyoti S. Choudhary Assessing the impact of genomic alterations on protein networks is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used isobaric labeling to characterize the proteomic landscapes of 50 colorectal cancer cell lines and to decipher the functional consequences of somatic genomic variants. The robust quantification of over 9,000 proteins and 11,000 phosphopeptides on average enabled the de novo construction of a functional protein correlation network, which ultimately exposed the collateral effects of mutations on protein complexes. CRISPR-cas9 deletion of key chromatin modifiers confirmed that the consequences of genomic alterations can propagate through protein interactions in a transcript-independent manner. Lastly, we leveraged the quantified proteome to perform unsupervised classification of the cell lines and to build predictive models of drug response in colorectal cancer. Overall, we provide a deep integrative view of the functional network and the molecular structure underlying the heterogeneity of colorectal cancer cells. Graphical abstract Teaser Roumeliotis et al. use in-depth proteomics to assess the impact of genomic alterations on protein networks in colorectal cancer cell lines. Cell-line-specific network signatures are inferred de novo by protein quantification profiles and ultimately expose the collateral and transcript-independent effects of detrimental mutations on protein complexes.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Federica F. Morelli, Dineke S. Verbeek, Jessika Bertacchini, Jonathan Vinet, Laura Mediani, Sandra Marmiroli, Giovanna Cenacchi, Milena Nasi, Sara De Biasi, Jeanette F. Brunsting, Jan Lammerding, Elena Pegoraro, Corrado Angelini, Rossella Tupler, Simon Alberti, Serena Carra Small heat shock proteins (HSPBs) contain intrinsically disordered regions (IDRs), but the functions of these IDRs are still unknown. Here, we report that, in mammalian cells, HSPB2 phase separates to form nuclear compartments with liquid-like properties. We show that phase separation requires the disordered C-terminal domain of HSPB2. We further demonstrate that, in differentiating myoblasts, nuclear HSPB2 compartments sequester lamin A. Increasing the nuclear concentration of HSPB2 causes the formation of aberrant nuclear compartments that mislocalize lamin A and chromatin, with detrimental consequences for nuclear function and integrity. Importantly, phase separation of HSPB2 is regulated by HSPB3, but this ability is lost in two identified HSPB3 mutants that are associated with myopathy. Our results suggest that HSPB2 phase separation is involved in reorganizing the nucleoplasm during myoblast differentiation. Furthermore, these findings support the idea that aberrant HSPB2 phase separation, due to HSPB3 loss-of-function mutations, contributes to myopathy. Graphical abstract Teaser Morelli et al. show that, in mammalian cells, HSPB2 forms liquid-like nuclear compartments that affect lamin A localization and mobility, with detrimental consequences for chromatin organization and nuclear integrity. Aberrant compartment formation by HSPB2 is regulated by HSPB3, but not by two identified HSPB3 mutants linked to myopathy.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Chan Zhou, Benoit Molinie, Kaveh Daneshvar, Joshua V. Pondick, Jinkai Wang, Nicholas Van Wittenberghe, Yi Xing, Cosmas C. Giallourakis, Alan C. Mullen N 6 -methyladenosine (m 6 A) is the most abundant internal modification of mRNAs and is implicated in all aspects of post-transcriptional RNA metabolism. However, little is known about m 6 A modifications to circular (circ) RNAs. We developed a computational pipeline (AutoCirc) that, together with depletion of ribosomal RNA and m 6 A immunoprecipitation, defined thousands of m 6 A circRNAs with cell-type-specific expression. The presence of m 6 A circRNAs is corroborated by interaction between circRNAs and YTHDF1/YTHDF2, proteins that read m 6 A sites in mRNAs, and by reduced m 6 A levels upon depletion of METTL3, the m 6 A writer. Despite sharing m 6 A readers and writers, m 6 A circRNAs are frequently derived from exons that are not methylated in mRNAs, whereas mRNAs that are methylated on the same exons that compose m 6 A circRNAs exhibit less stability in a process regulated by YTHDF2. These results expand our understanding of the breadth of m 6 A modifications and uncover regulation of circRNAs through m 6 A modification. Graphical abstract Teaser Zhou et al. find that N 6 -adenosine methylation (m 6 A) is widespread in circular (circ) RNAs and exhibits cell-type-specific patterns of expression. m 6 A modifications are written and read by the same protein complexes that interact with mRNAs, but many sites of m 6 A modifications in circRNAs are distinct from those in mRNAs.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Sebastian Falk, Fabien Bonneau, Judith Ebert, Alexander Kögel, Elena Conti The RNA-degrading exosome mediates the processing and decay of many cellular transcripts. In the yeast nucleus, the ubiquitous 10-subunit exosome core complex (Exo-9–Rrp44) functions with four conserved cofactors (Rrp6, Rrp47, Mtr4, and Mpp6). Biochemical and structural studies to date have shed insights into the mechanisms of the exosome core and its nuclear cofactors, with the exception of Mpp6. We report the 3.2-Å resolution crystal structure of a S. cerevisiae Exo-9–Mpp6 complex, revealing how linear motifs in the Mpp6 middle domain bind Rrp40 via evolutionary conserved residues. In particular, Mpp6 binds near a tryptophan residue of Rrp40 that is mutated in human patients suffering from pontocerebellar hypoplasia. Using biochemical assays, we show that Mpp6 is required for the ability of Mtr4 to extend the trajectory of an RNA entering the exosome core, suggesting that it promotes the channeling of substrates from the nuclear helicase to the processive RNase. Graphical abstract Teaser Falk et al. provide insights into the structure and function of the nuclear RNA exosome. The authors elucidate how the nuclear cofactor Mpp6 is recruited to the exosome core complex and show that it facilitates the threading of RNA substrates from the Mtr4 helicase to the Rrp44 RNase.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Jonathan M. Goodwin, William E. Dowdle, Rowena DeJesus, Zuncai Wang, Philip Bergman, Marek Kobylarz, Alicia Lindeman, Ramnik J. Xavier, Gregory McAllister, Beat Nyfeler, Gregory Hoffman, Leon O. Murphy Iron is vital for many homeostatic processes, and its liberation from ferritin nanocages occurs in the lysosome. Studies indicate that ferritin and its binding partner nuclear receptor coactivator-4 (NCOA4) are targeted to lysosomes by a form of selective autophagy. By using genome-scale functional screening, we identify an alternative lysosomal transport pathway for ferritin that requires FIP200, ATG9A, VPS34, and TAX1BP1 but lacks involvement of the ATG8 lipidation machinery that constitutes classical macroautophagy. TAX1BP1 binds directly to NCOA4 and is required for lysosomal trafficking of ferritin under basal and iron-depleted conditions. Under basal conditions ULK1/2-FIP200 controls ferritin turnover, but its deletion leads to TAX1BP1-dependent activation of TBK1 that regulates redistribution of ATG9A to the Golgi enabling continued trafficking of ferritin. Cells expressing an amyotrophic lateral sclerosis (ALS)-associated TBK1 allele are incapable of degrading ferritin suggesting a molecular mechanism that explains the presence of iron deposits in patient brain biopsies. Graphical abstract Teaser Goodwin et al. employ functional CRISPR screening approaches to show lysosomal ferritin turnover is autophagy-independent, revealing a role for TBK1 in iron homeostasis.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Rasmus Iversen, Omri Snir, Maria Stensland, José E. Kroll, Øyvind Steinsbø, Ilma R. Korponay-Szabó, Knut E.A. Lundin, Gustavo A. de Souza, Ludvig M. Sollid Mucosal antigens induce generation of lamina propria plasma cells (PCs) that secrete dimeric immunoglobulin A (IgA) destined for transport across the epithelium. In addition, blood contains monomeric IgA. To study the relationship between mucosal and systemic antibody responses, we took advantage of celiac disease patient samples for isolation of gut PCs as well as serum IgA and IgG reactive with a gluten-derived peptide or the autoantigen transglutaminase 2. Proteomic analysis of serum IgA revealed antigen-specific V-gene preferences, which matched those found in gut PCs. Further, gut PC CDR-H3 sequences were abundant in serum IgA but also detectable in serum IgG. Our data indicate that the same B cell clones that give rise to gut PCs also contribute to the serum antibody pool. However, serum IgA antibodies had a molecular composition distinct from that of IgA antibodies secreted in the gut, suggesting that individual B cell clones give rise to different PC populations. Graphical abstract Teaser The relationship between mucosal antibody responses and antibodies in blood is not clearly understood. Iversen et al. use proteomics to characterize antibodies in serum and gut biopsy specimens obtained from celiac disease patients. Serum and gut IgA are derived from the same B cell clones but produced by different plasma cells.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Tirtha Kamal Das, Ross Leigh Cagan Gene fusions are increasingly recognized as important cancer drivers. The KIF5B-RET gene has been identified as a primary driver in a subset of lung adenocarcinomas. Targeting human KIF5B-RET to epithelia in Drosophila directed multiple aspects of transformation, including hyperproliferation, epithelial-to-mesenchymal transition, invasion, and extension of striking invadopodia-like processes. The KIF5B-RET-transformed human bronchial cell line showed similar aspects of transformation, including invadopodia-like processes. Through a combination of genetic and biochemical studies, we demonstrate that the kinesin and kinase domains of KIF5B-RET act together to establish an emergent microtubule and RAB-vesicle-dependent RET-SRC-EGFR-FGFR signaling hub. We demonstrate that drugs designed to inhibit RET alone work poorly in KIF5B-RET-transformed cells. However, combining the RET inhibitor sorafenib with drugs that target EGFR, microtubules, or FGFR led to strong efficacy in both Drosophila and human cell line KIF5B-RET models. This work demonstrates the utility of exploring the full biology of fusions to identify rational therapeutic strategies. Graphical abstract Teaser Das and Cagan find that each portion of the KIF5B-RET fusion oncoprotein recruits different components to assemble a multi-kinase oncogenic signaling hub that promotes invadopodia formation. This suggests that multiple kinase components of this KIF5B-RET hub need to be simultaneously targeted therapeutically.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): David A. Brown, Vincenzo Di Cerbo, Angelika Feldmann, Jaewoo Ahn, Shinsuke Ito, Neil P. Blackledge, Manabu Nakayama, Michael McClellan, Emilia Dimitrova, Anne H. Turberfield, Hannah K. Long, Hamish W. King, Skirmantas Kriaucionis, Lothar Schermelleh, Tatiana G. Kutateladze, Haruhiko Koseki, Robert J. Klose Chromatin modifications and the promoter-associated epigenome are important for the regulation of gene expression. However, the mechanisms by which chromatin-modifying complexes are targeted to the appropriate gene promoters in vertebrates and how they influence gene expression have remained poorly defined. Here, using a combination of live-cell imaging and functional genomics, we discover that the vertebrate SET1 complex is targeted to actively transcribed gene promoters through CFP1, which engages in a form of multivalent chromatin reading that involves recognition of non-methylated DNA and histone H3 lysine 4 trimethylation (H3K4me3). CFP1 defines SET1 complex occupancy on chromatin, and its multivalent interactions are required for the SET1 complex to place H3K4me3. In the absence of CFP1, gene expression is perturbed, suggesting that normal targeting and function of the SET1 complex are central to creating an appropriately functioning vertebrate promoter-associated epigenome. Graphical abstract Teaser Brown et al. show that the SET1 complex is driven to active CpG island promoters via the CFP1 protein, which engages in multivalent chromatin binding to recognize both non-methylated DNA and H3K4me3. This is necessary for normal H3K4me3 at active gene promoters and appropriate regulation of gene expression.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Amayra Hernández-Vega, Marcus Braun, Lara Scharrel, Marcus Jahnel, Susanne Wegmann, Bradley T. Hyman, Simon Alberti, Stefan Diez, Anthony A. Hyman Non-centrosomal microtubule bundles play important roles in cellular organization and function. Although many diverse proteins are known that can bundle microtubules, biochemical mechanisms by which cells could locally control the nucleation and formation of microtubule bundles are understudied. Here, we demonstrate that the concentration of tubulin into a condensed, liquid-like compartment composed of the unstructured neuronal protein tau is sufficient to nucleate microtubule bundles. We show that, under conditions of macro-molecular crowding, tau forms liquid-like drops. Tubulin partitions into these drops, efficiently increasing tubulin concentration and driving the nucleation of microtubules. These growing microtubules form bundles, which deform the drops while remaining enclosed by diffusible tau molecules exhibiting a liquid-like behavior. Our data suggest that condensed compartments of microtubule bundling proteins could promote the local formation of microtubule bundles in neurons by acting as non-centrosomal microtubule nucleation centers and that liquid-like tau encapsulation could provide both stability and plasticity to long axonal microtubule bundles. Graphical abstract Teaser Hernández-Vega et al. show that tau forms liquid-like drops in vitro. Tubulin gets enriched in these drops, enabling microtubule bundles polymerization within drops. Microtubule bundles deform tau drops, reshaping them into rod-like structures. Microtubules in these structures remain as stable bundles. The findings have potential implications for tau function in axonal projections.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Florine E.M. Scholte, Marko Zivcec, John V. Dzimianski, Michelle K. Deaton, Jessica R. Spengler, Stephen R. Welch, Stuart T. Nichol, Scott D. Pegan, Christina F. Spiropoulou, Éric Bergeron Antiviral responses are regulated by conjugation of ubiquitin (Ub) and interferon-stimulated gene 15 (ISG15) to proteins. Certain classes of viruses encode Ub- or ISG15-specific proteases belonging to the ovarian tumor (OTU) superfamily. Their activity is thought to suppress cellular immune responses, but studies demonstrating the function of viral OTU proteases during infection are lacking. Crimean-Congo hemorrhagic fever virus (CCHFV, family Nairoviridae) is a highly pathogenic human virus that encodes an OTU with both deubiquitinase and deISGylase activity as part of the viral RNA polymerase. We investigated CCHFV OTU function by inactivating protease catalytic activity or by selectively disrupting its deubiquitinase and deISGylase activity using reverse genetics. CCHFV OTU inactivation blocked viral replication independently of its RNA polymerase activity, while deubiquitinase activity proved critical for suppressing the interferon responses. Our findings provide insights into viral OTU functions and support the development of therapeutics and vaccines. Graphical abstract Teaser Using reverse genetics, Scholte et al. report that OTU catalytic activity is critical for Crimean-Congo hemorrhagic fever virus replication, and deubiquitinase activity suppresses the antiviral response to infection. These findings provide insights in the multifunctional properties of viral OTUs and support development of OTU-specific therapeutics.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Benjamin E. Zalisko, Charlene Chan, Vladimir Denic, Ronald S. Rock, Robert J. Keenan The Get1/2 transmembrane complex drives the insertion of tail-anchored (TA) proteins from the cytosolic chaperone Get3 into the endoplasmic reticulum membrane. Mechanistic insight into how Get1/2 coordinates this process is confounded by a lack of understanding of the basic architecture of the complex. Here, we define the oligomeric state of full-length Get1/2 in reconstituted lipid bilayers by combining single-molecule and bulk fluorescence measurements with quantitative in vitro insertion analysis. We show that a single Get1/2 heterodimer is sufficient for insertion and demonstrate that the conserved cytosolic regions of Get1 and Get2 bind asymmetrically to opposing subunits of the Get3 homodimer. Altogether, our results define a simplified model for how Get1/2 and Get3 coordinate TA protein insertion. Graphical abstract Teaser Tail-anchored membrane proteins are inserted into the endoplasmic reticulum via the post-translational GET pathway. Zalisko et al. combine single-molecule and bulk fluorescence measurements with quantitative in vitro insertion assays to define the architecture of the heterodimeric Get1/2 insertase and its engagement with the soluble chaperone Get3.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Steven Moreira, Enio Polena, Victor Gordon, Solen Abdulla, Sujeivan Mahendram, Jiayi Cao, Alexandre Blais, Geoffrey A. Wood, Anna Dvorkin-Gheva, Bradley W. Doble Co-expression and cross-regulation of the four TCF/LEFs render their redundant and unique functions ambiguous. Here, we describe quadruple-knockout (QKO) mouse ESCs lacking all full-length TCF/LEFs and cell lines rescued with TCF7 or TCF7L1. QKO cells self-renew, despite gene expression patterns that differ significantly from WT, and display delayed, neurectoderm-biased, embryoid body (EB) differentiation. QKO EBs have no contracting cardiomyocytes and differentiate poorly into mesendoderm but readily generate neuronal cells. QKO cells and TCF7L1-rescued cells cannot efficiently activate TCF reporters, whereas TCF7-rescued cells exhibit significant reporter responsiveness. Surprisingly, despite dramatically different transactivation capacities, re-expression of TCF7L1 or TCF7 in QKO cells restores their tri-lineage differentiation ability, with similar lineage marker expression patterns and beating cardiomyocyte frequencies observed in EBs. Both factors also similarly affect the transcriptome of QKO cells. Our data reveal that a single TCF, regardless of its activation capacity, is sufficient for effective trilineage differentiation of ESCs. Graphical abstract Teaser Moreira et al. describe the generation and characterization of mouse ESCs lacking all four full-length TCF/LEF factors. By knocking in single epitope-tagged TCF/LEFs, they reveal redundancies in the abilities of “activating” and “repressive” TCFs to rescue the differentiation deficits of the quadruple-knockout cells.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Min-Hee Oh, Samuel L. Collins, Im-Hong Sun, Ada J. Tam, Chirag H. Patel, Matthew L. Arwood, Yee Chan-Li, Jonathan D. Powell, Maureen R. Horton Tissue-resident macrophages play critical roles in sentinel and homeostatic functions as well as in promoting inflammation and immunity. It has become clear that the generation of these cells is highly dependent upon tissue-specific cues derived from the microenvironment that, in turn, regulate unique differentiation programs. Recently, a role for GATA6 has emerged in the differentiation programming of resident peritoneal macrophages. We identify a critical role for mTOR in integrating cues from the tissue microenvironment in regulating differentiation and metabolic reprogramming. Specifically, inhibition of mTORC2 leads to enhanced GATA6 expression in a FOXO1 dependent fashion. Functionally, inhibition of mTORC2 promotes peritoneal resident macrophage generation in the resolution phase during zymosan-induced peritonitis. Also, mTORC2-deficient peritoneal resident macrophages displayed increased functionality and metabolic reprogramming. Notably, mTORC2 activation distinguishes tissue-resident macrophage proliferation and differentiation from that of M2 macrophages. Overall, our data implicate a selective role for mTORC2 in the differentiation of tissue-resident macrophages. Graphical abstract Teaser Oh et al. identify the mTORC2-FOXO1 axis as playing a critical role in integrating cues from the microenvironment to regulate metabolic reprogramming, differentiation, and function of peritoneal tissue-resident macrophages.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Canjun Zhu, Pingwen Xu, Yanlin He, Yexian Yuan, Tao Wang, Xingcai Cai, Lulu Yu, Liusong Yang, Junguo Wu, Lina Wang, Xiaotong Zhu, Songbo Wang, Ping Gao, Qianyun Xi, Yongliang Zhang, Yong Xu, Qingyan Jiang, Gang Shu Although the widely used anticoagulant drug heparin has been shown to have many other biological functions independent of its anticoagulant role, its effects on energy homeostasis are unknown. Here, we demonstrate that heparin level is negatively associated with nutritional states and that heparin treatment increases food intake and body weight gain. By using electrophysiological, pharmacological, molecular biological, and chemogenetic approaches, we provide evidence that heparin increases food intake by stimulating AgRP neurons and increasing AgRP release. Our results support a model whereby heparin competes with insulin for insulin receptor binding on AgRP neurons, and by doing so it inhibits FoxO1 activity to promote AgRP release and feeding. Heparin may be a potential drug target for food intake regulation and body weight control. Graphical abstract Teaser Zhu et al. demonstrate that heparin competes with insulin for insulin receptor binding on AgRP neurons, and by doing so it inhibits FoxO1 activity to promote AgRP release and feeding. Heparin is identified as a potential drug target for food intake regulation and body weight control.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Chen Zhong, Jinlong Shen, Huibing Zhang, Guangyi Li, Senlin Shen, Fang Wang, Kuan Hu, Longxing Cao, Yongning He, Jianping Ding Summary Unlike cerebellin 1 (Cbln1), which bridges neurexin (Nrxn) receptors and δ-type glutamate receptors in a trans -synaptic triad, Cbln4 was reported to have no or weak binding for the receptors despite sharing ∼70% sequence identity with Cbln1. Here, we report crystal structures of the homotrimers of the C1q domain of Cbln1 and Cbln4 at 2.2 and 2.3 Å resolution, respectively. Comparison of the structures suggests that the difference between Cbln1 and Cbln4 in GluD2 binding might be because of their sequence and structural divergence in loop CD. Surprisingly, we show that Cbln4 binds to Nrxn1β and forms a stable complex with the laminin, nectin, sex-hormone binding globulin (LNS) domain of Nrxn1β. Furthermore, the negative-stain electron microscopy reconstruction of hexameric full-length Cbln1 at 13 Å resolution and that of the Cbln4/Nrxn1β complex at 19 Å resolution suggest that Nrxn1β binds to the N-terminal region of Cbln4, probably through strand β10 of the S4 insert. Graphical abstract Teaser Cbln1 and Cbln4 share high sequence identity but have divergent functions. Zhong et al. find that Cbln4 forms a complex with Nrxn1β. Using crystal structures of the C1q domain of Cbln1 and Cbln4 and negative-stain EM reconstructions of Cbln1 and Cbln4/Nrxn1β, the authors examine similarities and divergence between Cbln1 and Cbln4.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Sandro Goruppi, Maria-Giuseppina Procopio, Seunghee Jo, Andrea Clocchiatti, Victor Neel, G. Paolo Dotto The connection between signaling pathways activating cancer-associated fibroblasts (CAFs) remains to be determined. Metabolic alterations linked to autophagy have also been implicated in CAF activation. CSL/RBPJ, a transcriptional repressor that mediates Notch signaling, suppresses the gene expression program(s), leading to stromal senescence and CAF activation. Deregulated GLI signaling can also contribute to CAF conversion. Here, we report that compromised CSL function depends on GLI activation for conversion of human dermal fibroblasts into CAFs, separately from cellular senescence. Decreased CSL upregulates the expression of the ULK3 kinase, which binds and activates GLI2. Increased ULK3 also induces autophagy, which is unlinked from GLI and CAF activation. ULK3 upregulation occurs in the CAFs of several tumor types, and ULK3 silencing suppresses the tumor-enhancing properties of these cells. Thus, ULK3 links two key signaling pathways involved in CAF conversion and is an attractive target for stroma-focused anti-cancer intervention. Graphical abstract Teaser Goruppi et al. demonstrate that CSL, a transcriptional repressor mediating Notch signaling, suppresses the conversion of fibroblasts into cancer-associated fibroblasts (CAFs) by controlling the expression of autophagy kinase ULK3, which, in turn, activates GLI signaling. Their studies connect two key pathways involved in CAF activation and identify a target for stroma-focused anti-cancer intervention.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Hayao Ohno, Naoko Sakai, Takeshi Adachi, Yuichi Iino Memorizing the intensity of sensory stimuli enables animals to successfully deal with changing environmental conditions and contributes to cognitive functions such as auditory and visual working memory. However, how nervous systems process past and current stimulus intensity is largely unknown at the molecular level. Here, we employ in vivo diacylglycerol (DAG) imaging in the ASER taste neuron of Caenorhabditis elegans and demonstrate that associative learning between ambient salt concentrations and food can be explained by changes in presynaptic DAG. The abundance of DAG is regulated in response to external salt concentration changes via sensory transduction in ASER and can encode differences between past and current salt concentrations. The DAG dynamics are modulated downstream of the synaptic insulin/phosphatidylinositol 3-kinase (PI3K)/Akt pathway, which regulates the behavioral plasticity induced by starvation. These results provide insights into how a single neuron stores past input intensity and generates appropriate behavioral responses. Graphical abstract Teaser Animals adapt to environmental changes by memorizing the intensity of sensory stimuli. By employing diacylglycerol imaging and behavioral analyses, Ohno et al. show the in vivo dynamics of neuronal diacylglycerol and present insights into how a single neuron processes past and current stimulus intensity.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Samuel B. Stephens, Robert J. Edwards, Masato Sadahiro, Wei-Jye Lin, Cheng Jiang, Stephen R. Salton, Christopher B. Newgard The prohormone VGF is expressed in neuroendocrine and endocrine tissues and regulates nutrient and energy status both centrally and peripherally. We and others have shown that VGF-derived peptides have direct action on the islet β cell as secretagogues and cytoprotective agents; however, the endogenous function of VGF in the β cell has not been described. Here, we demonstrate that VGF regulates secretory granule formation. VGF loss-of-function studies in both isolated islets and conditional knockout mice reveal a profound decrease in stimulus-coupled insulin secretion. Moreover, VGF is necessary to facilitate efficient exit of granule cargo from the trans -Golgi network and proinsulin processing. It also functions to replenish insulin granule stores following nutrient stimulation. Our data support a model in which VGF operates at a critical node of granule biogenesis in the islet β cell to coordinate insulin biosynthesis with β cell secretory capacity. Graphical abstract Teaser Stephens et al. find that the granin protein, VGF, regulates key aspects of pancreatic islet β cell function. These studies highlight a role for VGF in the maintenance and replenishment of insulin granules during nutrient stimulation by promoting exit of granule cargo from the trans -Golgi network and facilitating granule formation.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Stephanie Zimmermann, Lennart Pfannkuch, Munir A. Al-Zeer, Sina Bartfeld, Manuel Koch, Jianping Liu, Cindy Rechner, Meike Soerensen, Olga Sokolova, Alla Zamyatina, Paul Kosma, André P. Mäurer, Frithjof Glowinski, Klaus-Peter Pleissner, Monika Schmid, Volker Brinkmann, Alexander Karlas, Michael Naumann, Marion Rother, Nikolaus Machuy, Thomas F. Meyer Activation of transcription factor NF-κB is a hallmark of infection with the gastric pathogen Helicobacter pylori , associated with inflammation and carcinogenesis. Genome-wide RNAi screening revealed numerous host factors involved in H. pylori-, but not IL-1β- and TNF-α-dependent NF-κB regulation. Pathway analysis including CRISPR/Cas9-knockout and recombinant protein technology, immunofluorescence microscopy, immunoblotting, mass spectrometry, and mutant H. pylori strains identified the  H. pylori metabolite D- glycero -β-D- manno -heptose 1,7-bisphosphate (βHBP) as a cag PAI type IV secretion system (T4SS)-dependent effector of NF-κB activation in infected cells. Upon pathogen-host cell contact, TIFA forms large complexes (TIFAsomes) including interacting host factors, such as TRAF2. NF-κB activation, TIFA phosphorylation, and TIFAsome formation depend on a functional ALPK1 kinase, highlighting the ALPK1-TIFA axis as a core innate immune pathway. ALPK1-TIFA-mediated NF-κB activation was independent of CagA protein translocation, indicating that CagA translocation and HBP delivery to host cells are distinct features of the pathogen’s T4SS. Graphical abstract Teaser Zimmermann et al. identify pathogen and host factors involved in NF-κB activation after infection with type IV secretion-proficient Helicobacter pylori . Central hits are ALPK1 and TIFA. ALPK1 is necessary for phosphorylation-dependent formation of TIFA complexes (TIFAsomes) with TRAF2. This yields HBP-ALPK1-TIFA-TRAF2-NF-κB as the core-regulon of H. pylori-induced innate immune activation.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Ryan J. McGinty, Franco Puleo, Anna Y. Aksenova, Julia A. Hisey, Alexander A. Shishkin, Erika L. Pearson, Eric T. Wang, David E. Housman, Claire Moore, Sergei M. Mirkin Expansions of microsatellite repeats are responsible for numerous hereditary diseases in humans, including myotonic dystrophy and Friedreich’s ataxia. Whereas the length of an expandable repeat is the main factor determining disease inheritance, recent data point to genomic trans modifiers that can impact the likelihood of expansions and disease progression. Detection of these modifiers may lead to understanding and treating repeat expansion diseases. Here, we describe a method for the rapid, genome-wide identification of trans modifiers for repeat expansion in a yeast experimental system. Using this method, we found that missense mutations in the endoribonuclease subunit (Ysh1) of the mRNA cleavage and polyadenylation complex dramatically increase the rate of (GAA) n repeat expansions but only when they are actively transcribed. These expansions correlate with slower transcription elongation caused by the ysh1 mutation. These results reveal an interplay between RNA processing and repeat-mediated genome instability, confirming the validity of our approach. Graphical abstract Teaser McGinty et al. developed a genetic screen in S. cerevisiae to identify genes promoting expansions of (GAA) n repeats. The authors uncovered the unexpected involvement of essential RNA-processing gene, YSH1 . Mutation in YSH1 leads to slow transcription elongation, promoting DSBs, whose repair via HR causes repeat expansions.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Aaron Topol, Shijia Zhu, Brigham J. Hartley, Jane English, Mads E. Hauberg, Ngoc Tran, Chelsea Ann Rittenhouse, Anthony Simone, Douglas M. Ruderfer, Jessica Johnson, Ben Readhead, Yoav Hadas, Peter A. Gochman, Ying-Chih Wang, Hardik Shah, Gerard Cagney, Judith Rapoport, Fred H. Gage, Joel T. Dudley, Pamela Sklar, Manuel Mattheisen, David Cotter, Gang Fang, Kristen J. Brennand

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Xiao Ling Li, Murugan Subramanian, Matthew F. Jones, Ritu Chaudhary, Deepak K. Singh, Xinying Zong, Berkley Gryder, Sivasish Sindri, Min Mo, Aaron Schetter, Xinyu Wen, Swetha Parvathaneni, Dickran Kazandjian, Lisa M. Jenkins, Wei Tang, Fathi Elloumi, Jennifer L. Martindale, Maite Huarte, Yuelin Zhu, Ana I. Robles, Susan M. Frier, Frank Rigo, Maggie Cam, Stefan Ambs, Sudha Sharma, Curtis C. Harris, Mary Dasso, Kannanganattu V. Prasanth, Ashish Lal Basal p53 levels are tightly suppressed under normal conditions. Disrupting this regulation results in elevated p53 levels to induce cell cycle arrest, apoptosis, and tumor suppression. Here, we report the suppression of basal p53 levels by a nuclear, p53-regulated long noncoding RNA that we termed PURPL (p53 upregulated regulator of p53 levels). Targeted depletion of PURPL in colorectal cancer cells results in elevated basal p53 levels and induces growth defects in cell culture and in mouse xenografts. PURPL associates with MYBBP1A, a protein that binds to and stabilizes p53, and inhibits the formation of the p53-MYBBP1A complex. In the absence of PURPL , MYBBP1A interacts with and stabilizes p53. Silencing MYBBP1A significantly rescues basal p53 levels and proliferation in PURPL -deficient cells, suggesting that MYBBP1A mediates the effect of PURPL in regulating p53. These results reveal a p53- PURPL auto-regulatory feedback loop and demonstrate a role for PURPL in maintaining basal p53 levels. Graphical abstract Teaser For a cell to divide, the tumor suppressor protein p53 must be kept at low levels. Li et al. find that a long noncoding RNA PURPL allows cancer cells to divide by keeping p53 levels low. PURPL binds to the p53 regulator MYBBP1A to suppress p53 levels and facilitate cell proliferation.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Christopher P. Burgess, Armin Lak, Nicholas A. Steinmetz, Peter Zatka-Haas, Charu Bai Reddy, Elina A.K. Jacobs, Jennifer F. Linden, Joseph J. Paton, Adam Ranson, Sylvia Schröder, Sofia Soares, Miles J. Wells, Lauren E. Wool, Kenneth D. Harris, Matteo Carandini Research in neuroscience increasingly relies on the mouse, a mammalian species that affords unparalleled genetic tractability and brain atlases. Here, we introduce high-yield methods for probing mouse visual decisions. Mice are head-fixed, facilitating repeatable visual stimulation, eye tracking, and brain access. They turn a steering wheel to make two alternative choices, forced or unforced. Learning is rapid thanks to intuitive coupling of stimuli to wheel position. The mouse decisions deliver high-quality psychometric curves for detection and discrimination and conform to the predictions of a simple probabilistic observer model. The task is readily paired with two-photon imaging of cortical activity. Optogenetic inactivation reveals that the task requires mice to use their visual cortex. Mice are motivated to perform the task by fluid reward or optogenetic stimulation of dopamine neurons. This stimulation elicits a larger number of trials and faster learning. These methods provide a platform to accurately probe mouse vision and its neural basis. Graphical abstract Teaser Burgess et al. introduce methods to probe visual discrimination and its neural basis in head-fixed mice. Mice turn a steering wheel to make two alternative choice, and their behavior matches a simple probabilistic observer. The task engages and requires the visual cortex. Optogenetic stimulation of dopaminergic neurons can replace water control.

Description: Publication date: 5 September 2017 Source: Cell Reports, Volume 20, Issue 10 Author(s): Kiho Lee, Eleftherios Mylonakis Adjusting to a continuously changing environment is a key feature of life. For metazoans, environmental changes include alterations in the gut microbiota, which can affect both memory and behavior. The bacteriovorous nematode Caenorhabditis elegans discriminates between pathogenic and non-pathogenic food sources, avoiding the consumption of pathogens. Here, we demonstrate the role of the intestine in regulating C. elegans avoidance to Pseudomonas aeruginosa by an insulin-like neuropeptide encoded by ins-11 . The transcriptional expression of ins-11 is controlled through transcription factor hlh-30 and the p38 mitogen-activated protein kinase (MAPK) pathway. ins-11 negatively controls signal pathways in neurons that regulate aversive learning behavior. Attenuation of ins-11 increased avoidance behavior and survival on pathogenic bacteria but decreased opportunities to find a food source as well as lowered energy storage and the number of viable progeny. Our findings support a role for the intestine in avoidance and identify an advantageous role for negative feedback that allows C. elegans to actively balance noxious and favorable environments. Graphical abstract Teaser Lee and Mylonakis describe the inhibitory role of a neuropeptide that is encoded by ins-11 and is expressed in intestine. The neuropeptide prevents abnormal activation of neurons that stimulate aversive learning behavior in C. elegans . ins-11 allows nematodes to adjust when they move between pathogenic and non-pathogenic microbes.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Johanna Sigl-Glöckner, Michael Brecht In many species, polyploidy, in which an increase in nuclear DNA content is accompanied by an increase in cell size, contributes to cellular diversity. In the rat visual cortex, most neurons are small and homogeneous in size, while layer 5 cells are heterogeneous, containing some very large neurons. To measure DNA content, we quantified nuclear chromocenters and integrated DNA/DAPI fluorescence. The results suggest that most cortical neurons, non-neuronal cells, parvalbumin-positive interneurons, and large entorhinal layer 2 stellate projection neurons are diploid. In contrast, chromocenter counts and integrated fluorescence are ∼2-fold higher for some excitatory neurons in layer 5, suggesting that large Ctip2-negative and Ctip2-positive layer 5 neurons might be tetraploid. The distribution of putatively tetraploid neurons differed between areas and showed sharp borders aligned with functional subdivisions of the somatosensory cortex. Telomere counting and flow cytometry supported layer 5 polyploidy. We conclude that polyploidy contributes to cellular and areal diversity of rat cortex. Graphical abstract Teaser Cortical principal cell diversity is poorly understood. Sigl-Glöckner and Brecht find that very large principal neurons in layer 5 of rat cortex are polyploid. Putatively tetraploid neurons are differentially distributed across cortical areas and functional subdivisions.

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Kaitlyn M. Fonzi, Merridee J. Lefner, Paul E.M. Phillips, Matthew J. Wanat The dopamine system responds to reward-predictive cues to reflect a prospective estimation of reward value, although its role in encoding retrospective reward-related information is unclear. We report that cue-evoked dopamine release in the nucleus accumbens core encodes the time elapsed since the previous reward or rather the wait time. Specifically, a cue that always follows the preceding reward with a short wait time elicits a greater dopamine response relative to a distinct cue that always follows the preceding reward with a long wait time. Differences in the dopamine response between short wait and long wait cues were evident even when these cues were never experienced together within the same context. Conditioned responding updated accordingly with a change in cue-evoked dopamine release but was unrelated to a difference in the dopamine response between cues. Collectively, these findings illustrate that the cue-evoked dopamine response conveys a subjective estimation of the relative reward rate. Graphical abstract Teaser Fonzi et al. demonstrate that cue-evoked dopamine release encodes retrospective time-related information. They find that the dopamine system can discern differences between cues that have never been experienced together in the same context.

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Anne-Julie Lessard, Manon LeBel, Benoit Egarnes, Paul Préfontaine, Peter Thériault, Arnaud Droit, Alexandre Brunet, Serge Rivest, Jean Gosselin The signals that regulate the fate of circulating monocytes remain unknown. In the present study, we demonstrate that triggering of the NOD2 receptor by muramyl dipeptide (MDP) converts inflammatory Ly6C high monocytes into patrolling Ly6C low monocytes. Administration of MDP to Nr4a1 −/− mice, which lack Ly6C low monocytes, or to Ly6C low -depleted mice led to the emergence of blood-patrolling monocytes with a profile similar to that of Ly6C low monocytes, including high expression of CX3CR1 and LFA1. Using intravital microscopy in animal models of inflammatory diseases, we also found that converted Ly6C high monocytes patrol the endothelium of blood vessels and that their presence contributes to a reduction in the inflammatory response following MDP injection. Our results demonstrate that NOD2 contributes to the regulation of blood monocytes and suggest that it could be therapeutically targeted to treat inflammatory diseases. Graphical abstract Teaser The signals that regulate the conversion of inflammatory monocytes into patrolling subset(s) remain unknown. Here, Lessard et al. demonstrate that triggering NOD2 transforms inflammatory Ly6C high monocytes into Ly6C low monocytes that look and function like patrolling cells.

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Margot Martinez-Moreno, Timothy Mark O’Shea, John P. Zepecki, Alexander Olaru, Jennifer K. Ness, Robert Langer, Nikos Tapinos Precise regulation of Egr2 transcription is fundamentally important to the control of peripheral myelination. Here, we describe a long non-coding RNA antisense to the promoter of Egr2 (Egr2-AS-RNA). During peripheral nerve injury, the expression of Egr2-AS-RNA is increased and correlates with decreased Egr2 transcript and protein levels. Ectopic expression of Egr2-AS-RNA in dorsal root ganglion (DRG) cultures inhibits the expression of Egr2 mRNA and induces demyelination. In vivo inhibition of Egr2-AS-RNA using oligonucleotide GapMers released from a biodegradable hydrogel following sciatic nerve injury reverts the EGR2-mediated gene expression profile and significantly delays demyelination. Egr2-AS-RNA gradually recruits H3K27ME3, AGO1, AGO2, and EZH2 on the Egr2 promoter following sciatic nerve injury. Furthermore, expression of Egr2-AS-RNA is regulated through ERK1/2 signaling to YY1, while loss of Ser184 of YY1 regulates binding to Egr2-AS-RNA. In conclusion, we describe functional exploration of an antisense long non-coding RNA in peripheral nervous system (PNS) biology. Graphical abstract Teaser Martinez-Moreno et al. report a role for a long non-coding RNA antisense to the promoter of Egr2 , Egr2-AS-RNA, during the response to peripheral nerve injury. Inhibition of Egr2-AS-RNA following sciatic nerve injury reverts EGR2-mediated gene expression and delays demyelination.

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Alba Torrents de la Peña, Jean-Philippe Julien, Steven W. de Taeye, Fernando Garces, Miklos Guttman, Gabriel Ozorowski, Laura K. Pritchard, Anna-Janina Behrens, Eden P. Go, Judith A. Burger, Edith E. Schermer, Kwinten Sliepen, Thomas J. Ketas, Pavel Pugach, Anila Yasmeen, Christopher A. Cottrell, Jonathan L. Torres, Charlotte D. Vavourakis, Marit J. van Gils, Celia LaBranche, David C. Montefiori, Heather Desaire, Max Crispin, Per Johan Klasse, Kelly K. Lee, John P. Moore, Andrew B. Ward, Ian A. Wilson, Rogier W. Sanders The production of native-like recombinant versions of the HIV-1 envelope glycoprotein (Env) trimer requires overcoming the natural flexibility and instability of the complex. The engineered BG505 SOSIP.664 trimer mimics the structure and antigenicity of native Env. Here, we describe how the introduction of new disulfide bonds between the glycoprotein (gp)120 and gp41 subunits of SOSIP trimers of the BG505 and other genotypes improves their stability and antigenicity, reduces their conformational flexibility, and helps maintain them in the unliganded conformation. The resulting next-generation SOSIP.v5 trimers induce strong autologous tier-2 neutralizing antibody (NAb) responses in rabbits. In addition, the BG505 SOSIP.v6 trimers induced weak heterologous NAb responses against a subset of tier-2 viruses that were not elicited by the prototype BG505 SOSIP.664. These stabilization methods can be applied to trimers from multiple genotypes as components of multivalent vaccines aimed at inducing broadly NAbs (bNAbs). Graphical abstract Teaser Native-like HIV-1 envelope trimers are a platform for efforts to induce broadly neutralizing antibodies. Torrents de la Peña et al. design HIV-1 envelope trimers with enhanced stability and reduced flexibility. These modified trimers improve the induction of neutralizing antibodies and provide new opportunities toward elicitation of broadly neutralizing antibodies.

Description: Publication date: 22 August 2017 Source: Cell Reports, Volume 20, Issue 8 Author(s): Oliver H. Miller, Andreas Bruns, Imen Ben Ammar, Thomas Mueggler, Benjamin J. Hall The NMDA receptor (NMDAR) antagonist ketamine elicits a long-lasting antidepressant response in patients with treatment-resistant depression. Understanding how antagonism of NMDARs alters synapse and circuit function is pivotal to developing circuit-based therapies for depression. Using virally induced gene deletion, ex vivo optogenetic-assisted circuit analysis, and in vivo chemogenetics and fMRI, we assessed the role of NMDARs in the medial prefrontal cortex (mPFC) in controlling depression-related behavior in mice. We demonstrate that post-developmental genetic deletion of the NMDAR subunit GluN2B from pyramidal neurons in the mPFC enhances connectivity between the mPFC and limbic thalamus, but not the ventral hippocampus, and reduces depression-like behavior. Using intersectional chemogenetics, we show that activation of this thalamocortical circuit is sufficient to elicit a decrease in despair-like behavior. Our findings reveal that GluN2B exerts input-specific control of pyramidal neuron innervation and identify a medial dorsal thalamus (MDT)→mPFC circuit that controls depression-like behavior. Graphical abstract Teaser In these experiments, Miller et al. show that GluN2B-containing NMDARs are enriched at synapses between the medial dorsal thalamus and medial prefrontal cortex. They also show that post-developmental deletion of these receptors in the mPFC enhances synaptic connectivity and that direct activation of this circuit in vivo drives strong antidepressant-like behavior in mice.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Debabrata Chakravarti, Tapas K. Hazra Nucleotide excision repair (NER) requires replication protein A (RPA), among others, to respond to DNA damaging agents. In this issue of Cell Reports , He et al. (2017) and Zhao et al. (2017) show acetylation of RPA1 regulates the UV-induced DNA damage response. Teaser Nucleotide excision repair (NER) requires replication protein A (RPA), among others, to respond to DNA damaging agents. In this issue of Cell Reports , He et al. (2017) and Zhao et al. (2017) show acetylation of RPA1 regulates the UV-induced DNA damage response.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Jui-Heng Tseng, Ling Xie, Sheng Song, Youmei Xie, Lauren Allen, Deepa Ajit, Jau-Shyong Hong, Xian Chen, Rick B. Meeker, Todd J. Cohen The initiating events that promote tau mislocalization and pathology in Alzheimer’s disease (AD) are not well defined, partly because of the lack of endogenous models that recapitulate tau dysfunction. We exposed wild-type neurons to a neuroinflammatory trigger and examined the effect on endogenous tau. We found that tau re-localized and accumulated within pathological neuritic foci, or beads, comprised of mostly hypo-phosphorylated, acetylated, and oligomeric tau. These structures were detected in aged wild-type mice and were enhanced in response to neuroinflammation in vivo, highlighting a previously undescribed endogenous age-related tau pathology. Strikingly, deletion or inhibition of the cytoplasmic shuttling factor HDAC6 suppressed neuritic tau bead formation in neurons and mice. Using mass spectrometry-based profiling, we identified a single neuroinflammatory factor, the metalloproteinase MMP-9, as a mediator of neuritic tau beading. Thus, our study uncovers a link between neuroinflammation and neuritic tau beading as a potential early-stage pathogenic mechanism in AD. Graphical abstract Teaser Tau mislocalization and aggregation are implicated in the pathogenesis of Alzheimer’s disease. Tseng et al. report that endogenous neuronal tau re-localizes to distinct neuritic foci, which are active sites of calcium deregulation, leading to aberrant tau accumulation. These findings provide insights into the early-stage tau dysfunction that occurs in vulnerable neurons.

Description: Publication date: 29 August 2017 Source: Cell Reports, Volume 20, Issue 9 Author(s): Yohei Shinmyo, Yukari Terashita, Tung Anh Dinh Duong, Toshihide Horiike, Muneo Kawasumi, Kazuyoshi Hosomichi, Atsushi Tajima, Hiroshi Kawasaki Folds in the cerebral cortex in mammals are believed to be key structures for accommodating increased cortical neurons in the cranial cavity. However, the mechanisms underlying cortical folding remain largely unknown, mainly because genetic manipulations for the gyrencephalic brain have been unavailable. By combining in utero electroporation and the CRISPR/Cas9 system, we succeeded in efficient gene knockout of Cdk5 , which is mutated in some patients with classical lissencephaly, in the gyrencephalic brains of ferrets. We show that Cdk5 knockout in the ferret cerebral cortex markedly impaired cortical folding. Furthermore, the results obtained from the introduction of dominant-negative Cdk5 into specific cortical layers suggest that Cdk5 function in upper-layer neurons is more important for cortical folding than that in lower-layer neurons. Cdk5 inhibition induced severe migration defects in cortical neurons. Taken together, our findings suggest that the appropriate positioning of upper-layer neurons is critical for cortical folding. Graphical abstract Teaser Shinmyo et al. describe a highly efficient gene knockout method for the folded cerebral cortex of ferrets using the CRISPR/Cas9 system. Loss-of-function studies of the Cdk5 gene suggest that appropriate positioning of upper-layer neurons is crucial for cortical folding.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Ni Li, David C. Johnson, Niels Weinhold, Scott Kimber, Sara E. Dobbins, Jonathan S. Mitchell, Ben Kinnersley, Amit Sud, Philip J. Law, Giulia Orlando, Matthew Scales, Christopher P. Wardell, Asta Försti, Phuc H. Hoang, Molly Went, Amy Holroyd, Fadi Hariri, Tomi Pastinen, Tobias Meissner, Hartmut Goldschmidt, Kari Hemminki, Gareth J. Morgan, Martin Kaiser, Richard S. Houlston Multiple myeloma (MM) is a malignancy of plasma cells. Genome-wide association studies have shown that variation at 5q15 influences MM risk. Here, we have sought to decipher the causal variant at 5q15 and the mechanism by which it influences tumorigenesis. We show that rs6877329 G > C resides in a predicted enhancer element that physically interacts with the transcription start site of ELL2 . The rs6877329-C risk allele is associated with reduced enhancer activity and lowered ELL2 expression. Since ELL2 is critical to the B cell differentiation process, reduced ELL2 expression is consistent with inherited genetic variation contributing to arrest of plasma cell development, facilitating MM clonal expansion. These data provide evidence for a biological mechanism underlying a hereditary risk of MM at 5q15. Graphical abstract Teaser Li et al. find that rs6877329 underlies the 5q15 MM risk locus. Functional data demonstrate that rs6877329 resides within an enhancer that physically interacts with the ELL2 promoter. The rs6877329-C risk allele reduces enhancer activity and is associated with reduced ELL2 expression in MM patients.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Bret M. Evers, Carlos Rodriguez-Navas, Rachel J. Tesla, Janine Prange-Kiel, Catherine R. Wasser, Kyoung Shin Yoo, Jeffrey McDonald, Basar Cenik, Thomas A. Ravenscroft, Florian Plattner, Rosa Rademakers, Gang Yu, Charles L. White, Joachim Herz Defective lysosomal function defines many neurodegenerative diseases, such as neuronal ceroid lipofuscinoses (NCL) and Niemann-Pick type C (NPC), and is implicated in Alzheimer’s disease (AD) and frontotemporal lobar degeneration (FTLD-TDP) with progranulin (PGRN) deficiency. Here, we show that PGRN is involved in lysosomal homeostasis and lipid metabolism. PGRN deficiency alters lysosome abundance and morphology in mouse neurons. Using an unbiased lipidomic approach, we found that brain lipid composition in humans and mice with PGRN deficiency shows disease-specific differences that distinguish them from normal and other pathologic groups. PGRN loss leads to an accumulation of polyunsaturated triacylglycerides, as well as a reduction of diacylglycerides and phosphatidylserines in fibroblast and enriched lysosome lipidomes. Transcriptomic analysis of PGRN-deficient mouse brains revealed distinct expression patterns of lysosomal, immune-related, and lipid metabolic genes. These findings have implications for the pathogenesis of FTLD-TDP due to PGRN deficiency and suggest lysosomal dysfunction as an underlying mechanism. Graphical abstract Teaser Lysosomal dysfunction is a central pathogenic mechanism in neurodegenerative diseases. Using unbiased lipidomic analysis, Evers et al. demonstrate that progranulin (PGRN) is involved in lysosomal homeostasis and metabolism of polyunsaturated triacylglycerides (TAGs).

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Michael P. Conlin, Dylan A. Reid, George W. Small, Howard H. Chang, Go Watanabe, Michael R. Lieber, Dale A. Ramsden, Eli Rothenberg Nonhomologous end joining (NHEJ) must adapt to diverse end structures during repair of chromosome breaks. Here, we investigate the mechanistic basis for this flexibility. DNA ends are aligned in a paired-end complex (PEC) by Ku, XLF, XRCC4, and DNA ligase IV (LIG4); we show by single-molecule analysis how terminal mispairs lead to mobilization of ends within PECs and consequent sampling of more end-alignment configurations. This remodeling is essential for direct ligation of damaged and mispaired ends during cellular NHEJ, since remodeling and ligation of such ends both require a LIG4-specific structural motif, insert1. Insert1 is also required for PEC remodeling that enables nucleolytic processing when end structures block direct ligation. Accordingly, cells expressing LIG4 lacking insert1 are sensitive to ionizing radiation. Cellular NHEJ of diverse ends thus identifies the steps necessary for repair through LIG4-mediated sensing of differences in end structure and consequent dynamic remodeling of aligned ends. Graphical abstract Teaser Conlin et al. show that, when DNA double-strand breaks have terminal mispairs or damage, an unstructured loop unique to DNA ligase IV allows for dynamic remodeling of the alignment and end repair; the loop is also required for cellular resistance to ionizing radiation.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Archis Bagati, Anna Bianchi-Smiraglia, Sudha Moparthy, Kateryna Kolesnikova, Emily E. Fink, Brittany C. Lipchick, Masha Kolesnikova, Peter Jowdy, Anthony Polechetti, Amin Mahpour, Jason Ross, Joseph A. Wawrzyniak, Dong Hyun Yun, Gyorgy Paragh, Nadezhda I. Kozlova, Albert E. Berman, Jianmin Wang, Song Liu, Michael J. Nemeth, Mikhail A. Nikiforov Lineage-specific regulation of tumor progression by the same transcription factor is understudied. We find that levels of the FOXQ1 transcription factor, an oncogene in carcinomas, are decreased during melanoma progression. Moreover, in contrast to carcinomas, FOXQ1 suppresses epithelial-to-mesenchymal transition, invasion, and metastasis in melanoma cells. We find that these lineage-specific functions of FOXQ1 largely depend on its ability to activate (in carcinomas) or repress (in melanoma) transcription of the N-cadherin gene ( CDH2 ). We demonstrate that FOXQ1 interacts with nuclear β-catenin and TLE proteins, and the β-catenin/TLE ratio, which is higher in carcinoma than melanoma cells, determines the effect of FOXQ1 on CDH2 transcription. Accordingly, other FOXQ1-dependent phenotypes can be manipulated by altering nuclear β-catenin or TLE proteins levels. Our data identify FOXQ1 as a melanoma suppressor and establish a mechanism underlying its inverse lineage-specific transcriptional regulation of transformed phenotypes. Graphical abstract Teaser Bagati et al. report that the carcinoma oncogene FOXQ1 acts as a tumor suppressor in melanoma cells. Depending on β-catenin levels, which are higher in carcinoma than in melanoma cells, FOXQ1 activates or represses N-cadherin gene, invasion, and metastasis.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): James D.P. Rhodes, Judith H.I. Haarhuis, Jonathan B. Grimm, Benjamin D. Rowland, Luke D. Lavis, Kim A. Nasmyth To ensure disjunction to opposite poles during anaphase, sister chromatids must be held together following DNA replication. This is mediated by cohesin, which is thought to entrap sister DNAs inside a tripartite ring composed of its Smc and kleisin (Scc1) subunits. How such structures are created during S phase is poorly understood, in particular whether they are derived from complexes that had entrapped DNAs prior to replication. To address this, we used selective photobleaching to determine whether cohesin associated with chromatin in G1 persists in situ after replication. We developed a non-fluorescent HaloTag ligand to discriminate the fluorescence recovery signal from labeling of newly synthesized Halo-tagged Scc1 protein (pulse-chase or pcFRAP). In cells where cohesin turnover is inactivated by deletion of WAPL , Scc1 can remain associated with chromatin throughout S phase. These findings suggest that cohesion might be generated by cohesin that is already bound to un-replicated DNA. Graphical abstract Teaser How sister chromatids become entrapped within cohesin rings is not known. Rhodes et al. show that cohesin that is loaded onto DNA before S phase can remain associated with chromatin throughout DNA replication. This is consistent with the conversion of G1-loaded cohesin into its cohesive form.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Nina Kerres, Steffen Steurer, Stefanie Schlager, Gerd Bader, Helmut Berger, Maureen Caligiuri, Christian Dank, John R. Engen, Peter Ettmayer, Bernhard Fischerauer, Gerlinde Flotzinger, Daniel Gerlach, Thomas Gerstberger, Teresa Gmaschitz, Peter Greb, Bingsong Han, Elizabeth Heyes, Roxana E. Iacob, Dirk Kessler, Heike Kölle, Lyne Lamarre, David R. Lancia, Simon Lucas, Moriz Mayer, Katharina Mayr, Nikolai Mischerikow, Katja Mück, Christoph Peinsipp, Oliver Petermann, Ulrich Reiser, Dorothea Rudolph, Klaus Rumpel, Carina Salomon, Dirk Scharn, Renate Schnitzer, Andreas Schrenk, Norbert Schweifer, Diane Thompson, Elisabeth Traxler, Roland Varecka, Tilman Voss, Alexander Weiss-Puxbaum, Sandra Winkler, Xiaozhang Zheng, Andreas Zoephel, Norbert Kraut, Darryl McConnell, Mark Pearson, Manfred Koegl The transcription factor BCL6 is a known driver of oncogenesis in lymphoid malignancies, including diffuse large B cell lymphoma (DLBCL). Disruption of its interaction with transcriptional repressors interferes with the oncogenic effects of BCL6. We used a structure-based drug design to develop highly potent compounds that block this interaction. A subset of these inhibitors also causes rapid ubiquitylation and degradation of BCL6 in cells. These compounds display significantly stronger induction of expression of BCL6-repressed genes and anti-proliferative effects than compounds that merely inhibit co-repressor interactions. This work establishes the BTB domain as a highly druggable structure, paving the way for the use of other members of this protein family as drug targets. The magnitude of effects elicited by this class of BCL6-degrading compounds exceeds that of our equipotent non-degrading inhibitors, suggesting opportunities for the development of BCL6-based lymphoma therapeutics. Graphical abstract Teaser Kerres et al. show that the BTB domain of BCL6 is highly druggable and that potent binders can be derived that cause rapid degradation of BCL6. Inhibitors that induce degradation cause stronger anti-proliferative effects than other BCL6 inhibitors and offer new routes to the development of lymphoma treatments.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Brahma V. Kumar, Wenji Ma, Michelle Miron, Tomer Granot, Rebecca S. Guyer, Dustin J. Carpenter, Takashi Senda, Xiaoyun Sun, Siu-Hong Ho, Harvey Lerner, Amy L. Friedman, Yufeng Shen, Donna L. Farber Tissue-resident memory T cells (TRMs) in mice mediate optimal protective immunity to infection and vaccination, while in humans, the existence and properties of TRMs remain unclear. Here, we use a unique human tissue resource to determine whether human tissue memory T cells constitute a distinct subset in diverse mucosal and lymphoid tissues. We identify a core transcriptional profile within the CD69 + subset of memory CD4 + and CD8 + T cells in lung and spleen that is distinct from that of CD69 − TEM cells in tissues and circulation and defines human TRMs based on homology to the transcriptional profile of mouse CD8 + TRMs. Human TRMs in diverse sites exhibit increased expression of adhesion and inhibitory molecules, produce both pro-inflammatory and regulatory cytokines, and have reduced turnover compared with circulating TEM, suggesting unique adaptations for in situ immunity. Together, our results provide a unifying signature for human TRM and a blueprint for designing tissue-targeted immunotherapies. Graphical abstract Teaser Kumar et al. identify a core transcriptional and phenotypic signature that defines human TRMs for both CD4 + and CD8 + T cells that is preserved across diverse individuals and in mucosal and lymphoid sites.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Shanshan Lang, Jia Xie, Xueyong Zhu, Nicholas C. Wu, Richard A. Lerner, Ian A. Wilson Antibodies that target both group 1 and group 2 influenza A viruses are valuable for therapeutic and vaccine development, but only a few have been reported to date. Here, we describe a new V H 1-69 antibody 27F3 that broadly recognizes heterosubtypic hemagglutinins (HAs) from both group 1 and group 2 influenza A viruses. Structural characterization of 27F3 Fab with A/California/04/2009 (H1N1) hemagglutinin illustrates that 27F3 shares the key binding features observed in other V H 1-69 antibodies to the HA stem. Compared to other V H 1-69 antibodies, the 27F3 V H domain interacts with the HA stem in a distinct orientation, which alters its epitope and may have influenced its breadth. The diverse rotations of V H 1-69 antibodies on the HA stem epitope highlight the different ways that this antibody family can evolve to broadly neutralize influenza A viruses. These results have important implications for understanding how to elicit broad antibody responses against influenza virus. Graphical abstract Teaser Lang et al. discover a human V H 1-69 antibody that neutralizes group 1 and group 2 influenza A viruses and demonstrate the consensus and differences in the mode of binding of antibodies from this class with the HA stem.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Pedro Sousa-Victor, Arshad Ayyaz, Rippei Hayashi, Yanyan Qi, David T. Madden, Victoria V. Lunyak, Heinrich Jasper Sophisticated mechanisms that preserve genome integrity are critical to ensure the maintenance of regenerative capacity while preventing transformation of somatic stem cells (SCs), yet little is known about mechanisms regulating genome maintenance in these cells. Here, we show that intestinal stem cells (ISCs) induce the Argonaute family protein Piwi in response to JAK/STAT signaling during acute proliferative episodes. Piwi function is critical to ensure heterochromatin maintenance, suppress retrotransposon activation, and prevent DNA damage in homeostasis and under regenerative pressure. Accordingly, loss of Piwi results in the loss of actively dividing ISCs and their progenies by apoptosis. We further show that Piwi expression is sufficient to allay age-related retrotransposon expression, DNA damage, apoptosis, and mis-differentiation phenotypes in the ISC lineage, improving epithelial homeostasis. Our data identify a role for Piwi in the regulation of somatic SC function, and they highlight the importance of retrotransposon control in somatic SC maintenance. Graphical abstract Teaser Stem cell function depends on mechanisms that ensure the maintenance of genome integrity. Using the Drosophila intestine as a model, Sousa-Victor et al. identify Piwi as a regulator of somatic stem cell genomic integrity, required for long-term maintenance and function of ISCs, and they find that it can allay age-related stem cell dysfunction.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Patricia Domingues, Benjamin G. Hale Host restriction of influenza A virus limits pandemic emergence. The viral RNA polymerase (vPol) is an essential enzyme that must adapt for avian viruses to replicate in humans. Species differences in host ANP32A dictate adaptation: human ANP32A lacks an uncharacterized 33 amino-acid insertion that is present in avian ANP32A. Here, we uncover important contributions of host SUMOylation to vPol activity, including avANP32A function. We also identify a hydrophobic SUMO interaction motif (SIM)-like sequence unique to avANP32A that critically supports avian-signature vPol. Unrelated SIM sequences partially recapitulate this function when introduced into huANP32A. By investigating ANP32A-vPol interactions, we find that huANP32A interacts weakly with both human- and avian-signature vPols, while the hydrophobic motif of avANP32A promotes stronger interactions. Furthermore, we identify a highly acidic stretch in avANP32A that constitutes a major site of vPol interaction. Our data suggest compensatory mechanisms underlying vPol adaptation to host ANP32A independent of species-specific interactions. Graphical abstract Teaser Species differences in cellular ANP32A dictate influenza A virus polymerase host restriction. Domingues and Hale describe the contribution of host SUMOylation to viral polymerase activity and identify a SUMO interaction motif-like sequence unique to avian ANP32A that promotes interaction with the viral polymerase and is critical for determining host range.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Toni A. Baeumler, Ahmed Ashour Ahmed, Tudor A. Fulga Synthetic receptors provide a powerful experimental tool for generation of designer cells capable of monitoring the environment, sensing specific input signals, and executing diverse custom response programs. To advance the promise of cellular engineering, we have developed a class of chimeric receptors that integrate a highly programmable and portable nuclease-deficient CRISPR/Cas9 (dCas9) signal transduction module. We demonstrate that the core dCas9 synthetic receptor (dCas9-synR) architecture can be readily adapted to various classes of native ectodomain scaffolds, linking their natural inputs with orthogonal output functions. Importantly, these receptors achieved stringent OFF/ON state transition characteristics, showed agonist-mediated dose-dependent activation, and could be programmed to couple specific disease markers with diverse, therapeutically relevant multi-gene expression circuits. The modular dCas9-synR platform developed here provides a generalizable blueprint for designing next generations of synthetic receptors, which will enable the implementation of highly complex combinatorial functions in cellular engineering. Graphical abstract Teaser Using a highly programmable split-dCas9-based signal transduction module, Baeumler et al. have created a novel class of synthetic receptors (dCas9-synRs) capable of coupling biologically relevant input signals with the direct activation of custom user-defined output response programs. dCas9-synRs expand the promise of cellular engineering for research and therapeutic applications.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Ed Reznik, Dimitris Christodoulou, Joshua E. Goldford, Emma Briars, Uwe Sauer, Daniel Segrè, Elad Noor Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of a genome-scale atlas of small molecule-enzyme regulatory interactions. Here, we develop a framework leveraging the vast, but fragmented, biochemical literature to reconstruct and analyze the small molecule regulatory network (SMRN) of the model organism Escherichia coli , including the primary metabolite regulators and enzyme targets. Using metabolic control analysis, we prove a fundamental trade-off between regulation and enzymatic activity, and we combine it with metabolomic measurements and the SMRN to make inferences on the sensitivity of enzymes to their regulators. Generalizing the analysis to other organisms, we identify highly conserved regulatory interactions across evolutionarily divergent species, further emphasizing a critical role for small molecule interactions in the maintenance of metabolic homeostasis. Graphical abstract Teaser Reznik et al. report a computational pipeline for the genome-scale reconstruction of metabolic small molecule regulatory networks. They describe general design principles underlying small molecule regulation, and they prove a fundamental trade-off between the activity of a metabolic enzyme and the extent to which it is regulated.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Chen-Chun Pai, Anastasiya Kishkevich, Rachel S. Deegan, Andrea Keszthelyi, Lisa Folkes, Stephen E. Kearsey, Nagore De León, Ignacio Soriano, Robertus Antonius Maria de Bruin, Antony M. Carr, Timothy C. Humphrey Chromatin modification through histone H3 lysine 36 methylation by the SETD2 tumor suppressor plays a key role in maintaining genome stability. Here, we describe a role for Set2-dependent H3K36 methylation in facilitating DNA replication and the transcriptional responses to both replication stress and DNA damage through promoting Mlu I cell-cycle box (MCB) binding factor (MBF)-complex-dependent transcription in fission yeast. Set2 loss leads to reduced MBF-dependent ribonucleotide reductase (RNR) expression, reduced deoxyribonucleoside triphosphate (dNTP) synthesis, altered replication origin firing, and a checkpoint-dependent S-phase delay. Accordingly, prolonged S phase in the absence of Set2 is suppressed by increasing dNTP synthesis. Furthermore, H3K36 is di- and tri-methylated at these MBF gene promoters, and Set2 loss leads to reduced MBF binding and transcription in response to genotoxic stress. Together, these findings provide new insights into how H3K36 methylation facilitates DNA replication and promotes genotoxic stress responses in fission yeast. Graphical abstract Teaser Pai et al. find that the Set2 methyltransferase facilitates dNTP synthesis and DNA replication through promoting MBF-dependent transcription in fission yeast. Set2 loss results in reduced ribonucleotide reductase expression, reduced dNTP synthesis, altered replication origin firing, and checkpoint-dependent S-phase delay. These findings suggest how H3K36 methylation suppresses replication stress.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Young Ho Ban, Se-Chan Oh, Sang-Hwan Seo, Seok-Min Kim, In-Pyo Choi, Philip D. Greenberg, Jun Chang, Tae-Don Kim, Sang-Jun Ha MicroRNA (miR)-150 is a developmental regulator of several immune-cell types, but its role in CD8 + T cells is largely unexplored. Here, we show that miR-150 regulates the generation of memory CD8 + T cells. After acute virus infection, miR-150 knockout (KO) mice exhibited an accelerated differentiation of CD8 + T cells into memory cells and improved production of effector cytokines. Additionally, miR-150 KO CD8 + T cells displayed an enhanced recall response and improved protection against infections with another virus and bacteria. We found that forkhead box O1 (Foxo1) and T cell-specific transcription factor 1 (TCF1) are upregulated during the early activation phase in miR-150 KO CD8 + T cells and that miR-150 directly targets and suppresses Foxo1. These results suggest that miR-150-mediated suppression of Foxo1 regulates the balance between effector and memory cell differentiation, which might aid in the development of improved vaccines and T cell therapeutics. Graphical abstract Teaser MicroRNAs regulate CD8 + T cell responses, but their targets and function in CD8 + T cell differentiation are unclear. Ban et al. identify miR-150 as a regulator of CD8 + T cell differentiation and show that it represses the expression of Foxo1, an inducer of TCF1 that promotes the memory CD8 + T cells formation.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Yael Gropper, Tali Feferman, Tali Shalit, Tomer-Meir Salame, Ziv Porat, Guy Shakhar Cytotoxic T lymphocytes (CTLs) used in immunotherapy are typically cultured under atmospheric O 2 pressure but encounter hypoxic conditions inside tumors. Activating CTLs under hypoxic conditions has been shown to improve their cytotoxicity in vitro, but the mechanism employed and the implications for immunotherapy remain unknown. We activated and cultured OT-I CD8 T cells at either 1% or 20% O 2 . Hypoxic CTLs survived, as well as normoxic ones, in vitro but killed OVA-expressing B16 melanoma cells more efficiently. Hypoxic CTLs contained similar numbers of cytolytic granules and released them as efficiently but packaged more granzyme-B in each granule without producing more perforin. We imaged CTL distribution and motility inside B16-OVA tumors using confocal and intravital 2-photon microscopy and observed no obvious differences. However, mice treated with hypoxic CTLs exhibited better tumor regression and survived longer. Thus, hypoxic CTLs may perform better in tumor immunotherapy because of higher intrinsic cytotoxicity rather than improved migration inside tumors. Graphical abstract Teaser Gropper et al. show that antigen-specific CD8 T cells activated under hypoxic, rather than normoxic, conditions disperse normally in cognate tumors and do not migrate farther away from blood vessels but package more granzyme-B into their granules, show enhanced cytotoxicity, and reject tumors more efficiently.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Meera C. Viswanathan, William Schmidt, Michael J. Rynkiewicz, Karuna Agarwal, Jian Gao, Joseph Katz, William Lehman, Anthony Cammarato Striated muscle contraction is regulated by the movement of tropomyosin over the thin filament surface, which blocks or exposes myosin binding sites on actin. Findings suggest that electrostatic contacts, particularly those between K326, K328, and R147 on actin and tropomyosin, establish an energetically favorable F-actin-tropomyosin configuration, with tropomyosin positioned in a location that impedes actomyosin associations and promotes relaxation. Here, we provide data that directly support a vital role for these actin residues, termed the A-triad, in tropomyosin positioning in intact functioning muscle. By examining the effects of an A295S α-cardiac actin hypertrophic cardiomyopathy-causing mutation, over a range of increasingly complex in silico, in vitro, and in vivo Drosophila muscle models, we propose that subtle A-triad-tropomyosin perturbation can destabilize thin filament regulation, which leads to hypercontractility and triggers disease. Our efforts increase understanding of basic thin filament biology and help unravel the mechanistic basis of a complex cardiac disorder. Graphical abstract Teaser Viswanathan et al. demonstrate that the conserved actin A-triad, composed of K326, K328, and R147, normally biases tropomyosin to a position that impedes actomyosin associations along resting striated muscle thin filaments. The proximally located actin A295S hypertrophic cardiomyopathy mutation distorts A-triad-tropomyosin associations, which promotes contractile disinhibition, hypercontraction, and disease pathogenesis.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Tadayuki Ogawa, Shinya Saijo, Nobutaka Shimizu, Xuguang Jiang, Nobutaka Hirokawa Microtubules (MTs) are dynamic structures that are fundamental for cell morphogenesis and motility. MT-associated motors work efficiently to perform their functions. Unlike other motile kinesins, KIF2 catalytically depolymerizes MTs from the peeled protofilament end during ATP hydrolysis. However, the detailed mechanism by which KIF2 drives processive MT depolymerization remains unknown. To elucidate the catalytic mechanism, the transitional KIF2-tubulin complex during MT depolymerization was analyzed through multiple methods, including atomic force microscopy, size-exclusion chromatography, multi-angle light scattering, small-angle X-ray scattering, analytical ultracentrifugation, and mass spectrometry. The analyses outlined the conformation in which one KIF2core domain binds tightly to two tubulin dimers in the middle pre-hydrolysis state during ATP hydrolysis, a process critical for catalytic MT depolymerization. The X-ray crystallographic structure of the KIF2core domain displays the activated conformation that sustains the large KIF2-tubulin 1:2 complex. Graphical abstract Teaser Ogawa et al. reveal the mechanism of catalytic microtubule depolymerization by the microtubule-destabilizing kinesin, KIF2. They characterize the transitional conformation of the large KIF2-tubulin dimer 1:2 complex in solution, which is critical for the efficient mechanism of depolymerization at peeled microtubule protofilament ends during ATP hydrolysis.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): James H. Felce, Sarah L. Latty, Rachel G. Knox, Susan R. Mattick, Yuan Lui, Steven F. Lee, David Klenerman, Simon J. Davis The organization of Rhodopsin -family G protein-coupled receptors (GPCRs) at the cell surface is controversial. Support both for and against the existence of dimers has been obtained in studies of mostly individual receptors. Here, we use a large-scale comparative study to examine the stoichiometric signatures of 60 receptors expressed by a single human cell line. Using bioluminescence resonance energy transfer- and single-molecule microscopy-based assays, we found that a relatively small fraction of Rhodopsin -family GPCRs behaved as dimers and that these receptors otherwise appear to be monomeric. Overall, the analysis predicted that fewer than 20% of ∼700 Rhodopsin -family receptors form dimers. The clustered distribution of the dimers in our sample and a striking correlation between receptor organization and GPCR family size that we also uncover each suggest that receptor stoichiometry might have profoundly influenced GPCR expansion and diversification. Graphical abstract Teaser The quaternary organization of Rhodopsin -family GPCRs is controversial. Felce et al. show that 60 receptors are mostly monomeric. They propose a simple explanation for the remarkable asymmetry in GPCR family structure, i.e., that it is underpinned by the lineage expansion of monomers rather than dimers.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Maria Fernanda Forni, Julia Peloggia, Tárcio T. Braga, Jesús Eduardo Ortega Chinchilla, Jorge Shinohara, Carlos Arturo Navas, Niels Olsen Saraiva Camara, Alicia J. Kowaltowski Caloric restriction (CR) is the most effective intervention known to enhance lifespan, but its effect on the skin is poorly understood. Here, we show that CR mice display fur coat remodeling associated with an expansion of the hair follicle stem cell (HFSC) pool. We also find that the dermal adipocyte depot (dWAT) is underdeveloped in CR animals. The dermal/vennule annulus vasculature is enlarged, and a vascular endothelial growth factor (VEGF) switch and metabolic reprogramming in both the dermis and the epidermis are observed. When the fur coat is removed, CR mice display increased energy expenditure associated with lean weight loss and locomotion impairment. Our findings indicate that CR promotes extensive skin and fur remodeling. These changes are necessary for thermal homeostasis and metabolic fitness under conditions of limited energy intake, suggesting a potential adaptive mechanism. Graphical abstract Teaser Caloric restriction significantly increases the lifespan, but its effect on the skin is poorly understood. Forni et al. show that caloric restriction changes the structure and metabolism of the skin; these changes affect whole-body thermoregulation.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Peter J. Arthur-Farraj, Claire C. Morgan, Martyna Adamowicz, Jose A. Gomez-Sanchez, Shaline V. Fazal, Anthony Beucher, Bonnie Razzaghi, Rhona Mirsky, Kristjan R. Jessen, Timothy J. Aitman Repair Schwann cells play a critical role in orchestrating nerve repair after injury, but the cellular and molecular processes that generate them are poorly understood. Here, we perform a combined whole-genome, coding and non-coding RNA and CpG methylation study following nerve injury. We show that genes involved in the epithelial-mesenchymal transition are enriched in repair cells, and we identify several long non-coding RNAs in Schwann cells. We demonstrate that the AP-1 transcription factor C-JUN regulates the expression of certain micro RNAs in repair Schwann cells, in particular miR-21 and miR-34. Surprisingly, unlike during development, changes in CpG methylation are limited in injury, restricted to specific locations, such as enhancer regions of Schwann cell-specific genes (e.g., Nedd4l ), and close to local enrichment of AP-1 motifs. These genetic and epigenomic changes broaden our mechanistic understanding of the formation of repair Schwann cell during peripheral nervous system tissue repair. Graphical abstract Teaser Arthur-Farraj et al. report a combined transcriptome and whole-genome CpG methylation study in repair Schwann cells after nerve injury. They identify Schwann cell-expressed lncRNAs and miRNAs under the control of c-Jun, as well differential methylation of enhancers of repair program genes.

Description: Publication date: 12 September 2017 Source: Cell Reports, Volume 20, Issue 11 Author(s): Kamran Rizzolo, Jennifer Huen, Ashwani Kumar, Sadhna Phanse, James Vlasblom, Yoshito Kakihara, Hussein A. Zeineddine, Zoran Minic, Jamie Snider, Wen Wang, Carles Pons, Thiago V. Seraphim, Edgar Erik Boczek, Simon Alberti, Michael Costanzo, Chad L. Myers, Igor Stagljar, Charles Boone, Mohan Babu, Walid A. Houry A comprehensive view of molecular chaperone function in the cell was obtained through a systematic global integrative network approach based on physical (protein-protein) and genetic (gene-gene or epistatic) interaction mapping. This allowed us to decipher interactions involving all core chaperones (67) and cochaperones (15) of Saccharomyces cerevisiae . Our analysis revealed the presence of a large chaperone functional supercomplex, which we named the naturally joined (NAJ) chaperone complex, encompassing Hsp40, Hsp70, Hsp90, AAA+, CCT, and small Hsps. We further found that many chaperones interact with proteins that form foci or condensates under stress conditions. Using an in vitro reconstitution approach, we demonstrate condensate formation for the highly conserved AAA+ ATPases Rvb1 and Rvb2, which are part of the R2TP complex that interacts with Hsp90. This expanded view of the chaperone network in the cell clearly demonstrates the distinction between chaperones having broad versus narrow substrate specificities in protein homeostasis. Graphical abstract Teaser Rizzolo et al. use a systematic integrative approach combining physical and genetic interaction data to construct a comprehensive chaperone network. This analysis revealed the presence of a large functional chaperone supercomplex, the NAJ complex. Furthermore, many chaperone interactors were found to form condensates.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Nicolas Merienne, Gabriel Vachey, Lucie de Longprez, Cécile Meunier, Virginie Zimmer, Guillaume Perriard, Mathieu Canales, Amandine Mathias, Lucas Herrgott, Tim Beltraminelli, Axelle Maulet, Thomas Dequesne, Catherine Pythoud, Maria Rey, Luc Pellerin, Emmanuel Brouillet, Anselme L. Perrier, Renaud du Pasquier, Nicole Déglon Neurodegenerative disorders are a major public health problem because of the high frequency of these diseases. Genome editing with the CRISPR/Cas9 system is making it possible to modify the sequence of genes linked to these disorders. We designed the KamiCas9 self-inactivating editing system to achieve transient expression of the Cas9 protein and high editing efficiency. In the first application, the gene responsible for Huntington’s disease (HD) was targeted in adult mouse neuronal and glial cells. Mutant huntingtin (HTT) was efficiently inactivated in mouse models of HD, leading to an improvement in key markers of the disease. Sequencing of potential off-targets with the constitutive Cas9 system in differentiated human iPSC revealed a very low incidence with only one site above background level. This off-target frequency was significantly reduced with the KamiCas9 system. These results demonstrate the potential of the self-inactivating CRISPR/Cas9 editing for applications in the context of neurodegenerative diseases. Graphical abstract Teaser Merienne et al. describe the KamiCas9 method, a self-inactivating system for transient genome editing with improved safety. They demonstrate the feasibility and impact in the CNS with the permanent disruption of huntingtin gene in the context of Huntington’s disease.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Tsukasa Sanosaka, Takuya Imamura, Nobuhiko Hamazaki, MuhChyi Chai, Katsuhide Igarashi, Maky Ideta-Otsuka, Fumihito Miura, Takashi Ito, Nobuyuki Fujii, Kazuho Ikeo, Kinichi Nakashima Regulation of the epigenome during in vivo specification of brain stem cells is still poorly understood. Here, we report DNA methylome analyses of directly sampled cortical neural stem and progenitor cells (NS/PCs) at different development stages, as well as those of terminally differentiated cortical neurons, astrocytes, and oligodendrocytes. We found that sequential specification of cortical NS/PCs is regulated by two successive waves of demethylation at early and late development stages, which are responsible for the establishment of neuron- and glia-specific low-methylated regions (LMRs), respectively. The regulatory role of demethylation of the gliogenic genes was substantiated by the enrichment of nuclear factor I (NFI)-binding sites. We provide evidence that de novo DNA methylation of neuron-specific LMRs establishes glia-specific epigenotypes, essentially by silencing neuronal genes. Our data highlight the in vivo implications of DNA methylation dynamics in shaping epigenomic features that confer the differentiation potential of NS/PCs sequentially during development. Graphical abstract Teaser Using freshly sampled cortical cells, Sanosaka et al. reveal sequential changes in genome-wide DNA methylation status in the developing mouse CNS. This resource characterizes stage-dependent differentially methylation regions (DMRs), targeted by specific transcription factors including NFI, for the understanding of cell-intrinsic mechanisms in the CNS.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): John D. Huck, Nanette L. Que, Feng Hong, Zihai Li, Daniel T. Gewirth Hsp90 chaperones undergo ATP-driven conformational changes during the maturation of client proteins, populating a closed state upon ATP binding in which the N-terminal domains of the homodimer form a second inter-protomer dimer interface. A structure of GRP94, the endoplasmic reticulum hsp90, in a closed conformation has not been described, and the determinants that regulate closure are not well understood. Here, we determined the 2.6-Å structure of AMPPNP-bound GRP94 in the closed dimer conformation. The structure includes the pre-N domain, a region preceding the N-terminal domain that is highly conserved in GRP94, but not in other hsp90s. We show that the GRP94 pre-N domain is essential for client maturation, and we identify the pre-N domain as an important regulator of ATPase rates and dimer closure. The structure also reveals a GRP94:polypeptide interaction that partially mimics a client-bound state. The results provide structural insight into the ATP-dependent client maturation process of GRP94. Graphical abstract Teaser Huck et al. determined the structure of the ER hsp90 chaperone GRP94, and they show that it adopts a closed dimer conformation. The non-conserved pre-N-terminal domain is shown to be essential for GRP94 client maturation, but it is structurally distinct. A captured polypeptide fragment in the structure mimics a bound client.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Elodie Villa, Emma Proïcs, Camila Rubio-Patiño, Sandrine Obba, Barbara Zunino, Jozef P. Bossowski, Romain M. Rozier, Johanna Chiche, Laura Mondragón, Joel S. Riley, Sandrine Marchetti, Els Verhoeyen, Stephen W.G. Tait, Jean-Ehrland Ricci Mitophagy is an evolutionarily conserved process that selectively targets impaired mitochondria for degradation. Defects in mitophagy are often associated with diverse pathologies, including cancer. Because the main known regulators of mitophagy are frequently inactivated in cancer cells, the mechanisms that regulate mitophagy in cancer cells are not fully understood. Here, we identified an E3 ubiquitin ligase (ARIH1/HHARI) that triggers mitophagy in cancer cells in a PINK1-dependent manner. We found that ARIH1/HHARI polyubiquitinates damaged mitochondria, leading to their removal via autophagy. Importantly, ARIH1 is widely expressed in cancer cells, notably in breast and lung adenocarcinomas; ARIH1 expression protects against chemotherapy-induced death. These data challenge the view that the main regulators of mitophagy are tumor suppressors, arguing instead that ARIH1-mediated mitophagy promotes therapeutic resistance. Graphical abstract Teaser Clearance of damaged mitochondria (mitophagy) is involved in the resistance to chemotherapeutic-induced death, but the main known regulators of mitophagy are not expressed in cancer cells. Villa et al. show that the RBR E3 ligase ARIH1 is expressed in several cancer cell types. ARIH1 controls PINK1-dependent mitophagy and sensitivity to chemotherapies.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Yuki Hatanaka, Takeshi Tsusaka, Natsumi Shimizu, Kohtaro Morita, Takehiro Suzuki, Shinichi Machida, Manabu Satoh, Arata Honda, Michiko Hirose, Satoshi Kamimura, Narumi Ogonuki, Toshinobu Nakamura, Kimiko Inoue, Yoshihiko Hosoi, Naoshi Dohmae, Toru Nakano, Hitoshi Kurumizaka, Kazuya Matsumoto, Yoichi Shinkai, Atsuo Ogura At fertilization, the paternal genome undergoes extensive reprogramming through protamine-histone exchange and active DNA demethylation, but only a few maternal factors have been defined in these processes. We identified maternal Mettl23 as a protein arginine methyltransferase (PRMT), which most likely catalyzes the asymmetric dimethylation of histone H3R17 (H3R17me2a), as indicated by in vitro assays and treatment with TBBD, an H3R17 PRMT inhibitor. Maternal histone H3.3, which is essential for paternal nucleosomal assembly, is unable to be incorporated into the male pronucleus when it lacks R17me2a. Mettl23 interacts with Tet3, a 5mC-oxidizing enzyme responsible for active DNA demethylation, by binding to another maternal factor, GSE (gonad-specific expression). Depletion of Mettl23 from oocytes resulted in impaired accumulation of GSE, Tet3, and 5hmC in the male pronucleus, suggesting that Mettl23 may recruit GSE-Tet3 to chromatin. Our findings establish H3R17me2a and its catalyzing enzyme Mettl23 as key regulators of paternal genome reprogramming. Graphical abstract Teaser Maternal factors mediate nucleosome assembly and active DNA demethylation of the paternal genome during reprogramming in mouse oocytes; however, the underlying mechanisms are poorly described. Hatanaka et al. show that maternally provided H3R17me2a is responsible not only for H3.3 incorporation but also for active DNA demethylation in the paternal genome.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Irfan J. Lodhi, John M. Dean, Anyuan He, Hongsuk Park, Min Tan, Chu Feng, Haowei Song, Fong-Fu Hsu, Clay F. Semenkovich How the nuclear receptor PPARγ regulates the development of two functionally distinct types of adipose tissue, brown and white fat, as well as the browning of white fat, remains unclear. Our previous studies suggest that PexRAP, a peroxisomal lipid synthetic enzyme, regulates PPARγ signaling and white adipogenesis. Here, we show that PexRAP is an inhibitor of brown adipocyte gene expression. PexRAP inactivation promoted adipocyte browning, increased energy expenditure, and decreased adiposity. Identification of PexRAP-interacting proteins suggests that PexRAP function extends beyond its role as a lipid synthetic enzyme. Notably, PexRAP interacts with importin-β1, a nuclear import factor, and knockdown of PexRAP in adipocytes reduced the levels of nuclear phospholipids. PexRAP also interacts with PPARγ, as well as PRDM16, a critical transcriptional regulator of thermogenesis, and disrupts the PRDM16-PPARγ complex, providing a potential mechanism for PexRAP-mediated inhibition of adipocyte browning. These results identify PexRAP as an important regulator of adipose tissue remodeling. Graphical abstract Teaser Lodhi et al. find that the peroxisomal lipid synthetic enzyme PexRAP is also a nuclear protein that suppresses adipose tissue browning. PexRAP interacts with PPARγ and PRDM16 and inhibits PRDM16-mediated thermogenic gene expression.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Simon Koplev, James Longden, Jesper Ferkinghoff-Borg, Mathias Blicher Bjerregård, Thomas R. Cox, Janine T. Erler, Jesper T. Pedersen, Franziska Voellmy, Morten O.A. Sommer, Rune Linding Signaling networks are nonlinear and complex, involving a large ensemble of dynamic interaction states that fluctuate in space and time. However, therapeutic strategies, such as combination chemotherapy, rarely consider the timing of drug perturbations. If we are to advance drug discovery for complex diseases, it will be essential to develop methods capable of identifying dynamic cellular responses to clinically relevant perturbations. Here, we present a Bayesian dose-response framework and the screening of an oncological drug matrix, comprising 10,000 drug combinations in melanoma and pancreatic cancer cell lines, from which we predict sequentially effective drug combinations. Approximately 23% of the tested combinations showed high-confidence sequential effects (either synergistic or antagonistic), demonstrating that cellular perturbations of many drug combinations have temporal aspects, which are currently both underutilized and poorly understood. Graphical abstract Teaser Therapeutic strategies, such as combination chemotherapy, rarely consider the timing of drug perturbations. Koplev et al. present a Bayesian dose-response framework for the prediction of sequentially effective drug combinations. They find widespread time dependency that is partially conserved between cancer cells of the same tissue origin.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Shashi Kant, Claire L. Standen, Caroline Morel, Dae Young Jung, Jason K. Kim, Wojciech Swat, Richard A. Flavell, Roger J. Davis Obesity is a major risk factor for the development of metabolic syndrome and type 2 diabetes. How obesity contributes to metabolic syndrome is unclear. Free fatty acid (FFA) activation of a non-receptor tyrosine kinase (SRC)-dependent cJun NH 2 -terminal kinase (JNK) signaling pathway is implicated in this process. However, the mechanism that mediates SRC-dependent JNK activation is unclear. Here, we identify a role for the scaffold protein JIP1 in SRC-dependent JNK activation. SRC phosphorylation of JIP1 creates phosphotyrosine interaction motifs that bind the SH2 domains of SRC and the guanine nucleotide exchange factor VAV. These interactions are required for SRC-induced activation of VAV and the subsequent engagement of a JIP1-tethered JNK signaling module. The JIP1 scaffold protein, therefore, plays a dual role in FFA signaling by coordinating upstream SRC functions together with downstream effector signaling by the JNK pathway. Graphical abstract Teaser Kant et al. demonstrate that scaffold protein JIP1 is required for palmitate-stimulated redistribution of SRC to lipid rafts. Phosphorylation of JIP1 on tyrosine mediates SH2 domain interactions with both SRC and the RAC exchange factor VAV. This signaling complex causes RAC-dependent activation of the MLK pathway that activates JNK.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Michihiro Takahama, Mitsunori Fukuda, Norihiko Ohbayashi, Tatsuya Kozaki, Takuma Misawa, Toru Okamoto, Yoshiharu Matsuura, Shizuo Akira, Tatsuya Saitoh Cyclic GMP-AMP synthase (cGAS) is a cytosolic DNA sensor that induces the IFN antiviral response. However, the regulatory mechanisms that mediate cGAS-triggered signaling have not been fully explored. Here, we show the involvement of a small GTPase, RAB2B, and its effector protein, Golgi-associated RAB2B interactor-like 5 (GARIL5), in the cGAS-mediated IFN response. RAB2B-deficiency affects the IFN response induced by cytosolic DNA. Consistent with this, RAB2B deficiency enhances replication of vaccinia virus, a DNA virus. After DNA stimulation, RAB2B colocalizes with stimulator of interferon genes (STING), the downstream signal mediator of cGAS, on the Golgi apparatus. The GTP-binding activity of RAB2B is required for its localization on the Golgi apparatus and for recruitment of GARIL5. GARIL5 deficiency also affects the IFN response induced by cytosolic DNA and enhances replication of vaccinia virus. These findings indicate that the RAB2B-GARIL5 complex promotes IFN responses against DNA viruses by regulating the cGAS-STING signaling axis. Graphical abstract Teaser Takahama et al. show that RAB2B GTPase recruits its effector protein GARIL5 into the Golgi apparatus to positively regulate cytosolic DNA-triggered activation of the cGAS-STING signaling axis and promotes the type I IFN-mediated host defense response to DNA viruses.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Fiona K. Ritchie, Rhianna Knable, Justin Chaplin, Rhiannon Gursanscky, Maria Gallegos, Brent Neumann, Massimo A. Hilliard The disproportionate length of an axon makes its structural and functional maintenance a major task for a neuron. The heterochronic gene lin-14 has previously been implicated in regulating the timing of key developmental events in the nematode C. elegans . Here, we report that LIN-14 is critical for maintaining neuronal integrity. Animals lacking lin-14 display axonal degeneration and guidance errors in both sensory and motor neurons. We demonstrate that LIN-14 functions both cell autonomously within the neuron and non-cell autonomously in the surrounding tissue, and we show that interaction between the axon and its surrounding tissue is essential for the preservation of axonal structure. Furthermore, we demonstrate that lin-14 expression is only required during a short period early in development in order to promote axonal maintenance throughout the animal’s life. Our results identify a crucial role for LIN-14 in preventing axonal degeneration and in maintaining correct interaction between an axon and its surrounding tissue. Graphical abstract Teaser Maintenance of the long and thin axonal compartment is essential for neuronal function. Ritchie et al. found that LIN-14 is critical for maintaining neuronal integrity and preventing axonal degeneration. LIN-14 acts within the neuron as well as in the surrounding tissue to preserve the correct axonal position and structure.

Description: Publication date: 19 September 2017 Source: Cell Reports, Volume 20, Issue 12 Author(s): Charu Mehta, Kirby D. Johnson, Xin Gao, Irene M. Ong, Koichi R. Katsumura, Skye C. McIver, Erik A. Ranheim, Emery H. Bresnick Hematopoietic development requires the transcription factor GATA-2, and GATA-2 mutations cause diverse pathologies, including leukemia. GATA-2-regulated enhancers increase Gata2 expression in hematopoietic stem/progenitor cells and control hematopoiesis. The +9.5-kb enhancer activates transcription in endothelium and hematopoietic stem cells (HSCs), and its deletion abrogates HSC generation. The −77-kb enhancer activates transcription in myeloid progenitors, and its deletion impairs differentiation. Since +9.5 −/− embryos are HSC deficient, it was unclear whether the +9.5 functions in progenitors or if GATA-2 expression in progenitors solely requires −77. We further dissected the mechanisms using −77;+9.5 compound heterozygous (CH) mice. The embryonic lethal CH mutation depleted megakaryocyte-erythrocyte progenitors (MEPs). While the +9.5 suffices for HSC generation, the −77 and +9.5 must reside on one allele to induce MEPs. The −77 generated burst-forming unit-erythroid through the induction of GATA-1 and other GATA-2 targets. The enhancer circuits controlled signaling pathways that orchestrate a GATA factor-dependent blood development program. Graphical abstract Teaser Mutations of GATA2 and its enhancers cause immunodeficiency, myelodysplastic syndrome, and leukemia. Mehta et al. report that enhancers linked to these pathologies function collectively to generate a vital blood precursor, while a single enhancer generates a distinct blood precursor.

Description: Publication date: 15 August 2017 Source: Cell Reports, Volume 20, Issue 7 Author(s): Alexandra Van Keymeulen, Marco Fioramonti, Alessia Centonze, Gaëlle Bouvencourt, Younes Achouri, Cédric Blanpain The mammary gland (MG) is composed of different cell lineages, including the basal and the luminal cells (LCs) that are maintained by distinct stem cell (SC) populations. LCs can be subdivided into estrogen receptor (ER) + and ER − cells. LCs act as the cancer cell of origin in different types of mammary tumors. It remains unclear whether the heterogeneity found in luminal-derived mammary tumors arises from a pre-existing heterogeneity within LCs. To investigate LC heterogeneity, we used lineage tracing to assess whether the ER + lineage is maintained by multipotent SCs or by lineage-restricted SCs. To this end, we generated doxycycline-inducible ER-rtTA mice that allowed us to perform genetic lineage tracing of ER + LCs and study their fate and long-term maintenance. Our results show that ER + cells are maintained by lineage-restricted SCs that exclusively contribute to the expansion of the ER + lineage during puberty and their maintenance during adult life. Graphical abstract Teaser Van Keymeulen et al. performed lineage tracing of estrogen receptor (ER)-expressing cells in the mammary gland. They show that the ER + cells are maintained by lineage-restricted stem cells that exclusively contribute to the expansion of the ER + lineage during puberty and to their maintenance during adult life.

Description: Publication date: 15 August 2017 Source: Cell Reports, Volume 20, Issue 7 Author(s): Brook E. Heaton, Edward M. Kennedy, Rebekah E. Dumm, Alfred T. Harding, Matthew T. Sacco, David Sachs, Nicholas S. Heaton Influenza A virus (IAV) is a pathogen that poses significant risks to human health. It is therefore critical to develop strategies to prevent influenza disease. Many loss-of-function screens have been performed to identify the host proteins required for viral infection. However, there has been no systematic screen to identify the host factors that, when overexpressed, are sufficient to prevent infection. In this study, we used CRISPR/dCas9 activation technology to perform a genome-wide overexpression screen to identify IAV restriction factors. The major hit from our screen, B4GALNT2, showed inhibitory activity against influenza viruses with an α2,3-linked sialic acid receptor preference. B4GALNT2 overexpression prevented the infection of every avian influenza virus strain tested, including the H5, H9, and H7 subtypes, which have previously caused disease in humans. Thus, we have used CRISPR/dCas9 activation technology to identify a factor that can abolish infection by avian influenza viruses. Graphical abstract Teaser Heaton et al. apply CRISPR SAM genome-wide screening technology to find restriction factors for avian and human strains of influenza A virus. The major hit, B4GALNT2, modified a glycan containing the influenza A virus receptor and restricted infection with all avian strains tested.

Description: Publication date: 15 August 2017 Source: Cell Reports, Volume 20, Issue 7 Author(s): Romain Madelaine, Steven A. Sloan, Nina Huber, James H. Notwell, Louis C. Leung, Gemini Skariah, Caroline Halluin, Sergiu P. Paşca, Gill Bejerano, Mark A. Krasnow, Ben A. Barres, Philippe Mourrain In the developing brain, neurons expressing VEGF-A and blood vessels grow in close apposition, but many of the molecular pathways regulating neuronal VEGF-A and neurovascular system development remain to be deciphered. Here, we show that miR-9 links neurogenesis and angiogenesis through the formation of neurons expressing VEGF-A. We found that miR-9 directly targets the transcription factors TLX and ONECUTs to regulate VEGF-A expression. miR-9 inhibition leads to increased TLX and ONECUT expression, resulting in VEGF-A overexpression. This untimely increase of neuronal VEGF-A signal leads to the thickening of blood vessels at the expense of the normal formation of the neurovascular network in the brain and retina. Thus, this conserved transcriptional cascade is critical for proper brain development in vertebrates. Because of this dual role on neural stem cell proliferation and angiogenesis, miR-9 and its downstream targets are promising factors for cellular regenerative therapy following stroke and for brain tumor treatment. Graphical abstract Teaser The coordination of neuronal and vascular cell development is critical to ensure the proper formation of the vertebrate brain. Madelaine et al. show that the microRNA-9 couples neurogenesis and brain angiogenesis through the inhibition of Tlx and Onecut transcription factors regulating neuronal VEGF-A expression.

Description: Publication date: 15 August 2017 Source: Cell Reports, Volume 20, Issue 7 Author(s): Vorrapon Chaikeeratisak, Katrina Nguyen, MacKennon E. Egan, Marcella L. Erb, Anastasia Vavilina, Joe Pogliano We recently demonstrated that the large Pseudomonas chlororaphis bacteriophage 201φ2-1 assembles a nucleus-like structure that encloses phage DNA and segregates proteins according to function, with DNA processing proteins inside and metabolic enzymes and ribosomes outside the nucleus. Here, we investigate the replication pathway of the Pseudomonas aeruginosa bacteriophages φKZ and φPA3. Bacteriophages φKZ and φPA3 encode a proteinaceous shell that assembles a nucleus-like structure that compartmentalizes proteins and DNA during viral infection. We show that the tubulin-like protein PhuZ encoded by each phage assembles a bipolar spindle that displays dynamic instability and positions the nucleus at midcell. Our results suggest that the phage spindle and nucleus play the same functional role in all three phages, 201φ2-1, φKZ, and φPA3, demonstrating that these key structures are conserved among large Pseudomonas phages. Graphical abstract Teaser The nucleus and spindle are defining features of eukaryotic cells that separate them from bacteria and archaea. Chaikeeratisak et al. show that a tubulin-based spindle and a nucleus-like structure are conserved among large Pseudomonas phages, providing insight into the evolution of these key cell biological structures.

Description: Publication date: 15 August 2017 Source: Cell Reports, Volume 20, Issue 7 Author(s): Nathan J. Palpant, Yuliang Wang, Brandon Hadland, Rebecca J. Zaunbrecher, Meredith Redd, Daniel Jones, Lil Pabon, Rajan Jain, Jonathan Epstein, Walter L. Ruzzo, Ying Zheng, Irwin Bernstein, Adam Margolin, Charles E. Murry We analyzed chromatin dynamics and transcriptional activity of human embryonic stem cell (hESC)-derived cardiac progenitor cells (CPCs) and KDR + /CD34 + endothelial cells generated from different mesodermal origins. Using an unbiased algorithm to hierarchically rank genes modulated at the level of chromatin and transcription, we identified candidate regulators of mesodermal lineage determination. HOPX, a non-DNA-binding homeodomain protein, was identified as a candidate regulator of blood-forming endothelial cells. Using HOPX reporter and knockout hESCs, we show that HOPX regulates blood formation. Loss of HOPX does not impact endothelial fate specification but markedly reduces primitive hematopoiesis, acting at least in part through failure to suppress Wnt/β-catenin signaling. Thus, chromatin state analysis permits identification of regulators of mesodermal specification, including a conserved role for HOPX in governing primitive hematopoiesis. Graphical abstract Teaser Palpant et al. analyze gene expression and chromatin dynamics in cardiovascular progenitor cells derived from hPSCs to elucidate genes governing cell fate. HOPX is identified as a regulator of primitive hematopoiesis, providing insight into controlling cell lineages from pluripotency for disease modeling or therapeutic applications.