ALBERT

Description: In this paper, we propose a boosting synthetic aperture radar (SAR) image despeckling method based on non-local weighted group low-rank representation (WGLRR). The spatial structure information of SAR images leads to the similarity of the patches. Furthermore, the data matrix grouped by the similar patches within the noise-free SAR image is often low-rank. Based on this, we use low-rank representation (LRR) to recover the noise-free group data matrix. To maintain the fidelity of the recovered image, we integrate the corrupted probability of each pixel into the group LRR model as a weight to constrain the fidelity of recovered noise-free patches. Each single patch might belong to several groups, so different estimations of each patch are aggregated with a weighted averaging procedure. The residual image contains signal leftovers due to the imperfect denoising, so we strengthen the signal by leveraging on the availability of the denoised image to suppress noise further. Experimental results on simulated and actual SAR images show the superior performance of the proposed method in terms of objective indicators and of perceived image quality.

Description: The application of current channelrhodopsin-based optogenetic tools is limited by the lack of strict ion selectivity and the inability to extend the spectra sensitivity into the near-infrared (NIR) tissue transmissible range. Here we present an NIR-stimulable optogenetic platform (termed 'Opto-CRAC') that selectively and remotely controls Ca2+ oscillations and Ca2+-responsive gene expression to regulate the function of non-excitable cells, including T lymphocytes, macrophages and dendritic cells. When coupled to upconversion nanoparticles, the optogenetic operation window is shifted from the visible range to NIR wavelengths to enable wireless photoactivation of Ca2+-dependent signaling and optogenetic modulation of immunoinflammatory responses. In a mouse model of melanoma by using ovalbumin as surrogate tumor antigen, Opto-CRAC has been shown to act as a genetically-encoded 'photoactivatable adjuvant' to improve antigen-specific immune responses to specifically destruct tumor cells. Our study represents a solid step forward towards the goal of achieving remote and wireless control of Ca2+-modulated activities with tailored function.

Description: Background: Clonal hematopoiesis of indeterminate potential (CHIP) is often observed during aging[1]. CHIP is characterized by a clonal expansion of subset blood-cell clones without other hematological abnormalities. Recent studies reported a strong connection between CHIP and cardiovascular disease (CVD). Individuals with mutations in epigenetic regulators (e.g., DNMT3A, TET2, ASXL1 and JAK2) have a higher risk for CVD[2]. In vivo studies using mouse models confirmed that Tet2-deficient HSPCs exhibited clonal expansion. Furthermore, mice transferred with Tet2-deficient HSPCs showed increased risk of atherosclerosis and worse outcome after permanent left anterior descending artery (LAD) ligation induced myocardial infarction (MI)[3,4]. Macrophages were found to be one of the most affected cell types in Tet2 deficient hematopoietic system associated with increased CVD risk[3,4]. Tet2 deficiency in macrophages is known to cause aberrant innate immune response[5]. Tet2 knockout (KO) macrophages provide a protective microenvironment to prevent melanoma progression[6], suggesting the pivotal role of Tet2 in regulating macrophage function in different context. In this study, we aim to dissect the molecular mechanism on how Tet2 deficiency disrupts normal macrophage function during heart repair. Methods: We crossed Tet2f/f mice with lysMCre mice to yield macrophage specific Tet2 deficient mice (Tet2f/f-lysMCre). We performed LAD ligation in Tet2f/f-lysMCre mice to induce MI. Age and gender matched lysMCre mice were used as controls. Cardiac function was monitored by echocardiogram every week after MI for 4 weeks. Then we sacrificed mice and performed histological analysis to evaluate heart damage and repairs in lysMCre and Tet2f/f-lysMCre mice. During the course of the experiments, we collected peripheral blood and bone marrows to examine the impact of Tet2 loss on macrophages in response to heart damage and repair. In parallel, we also collected heart tissue from lysMCre and Tet2f/f-lysMCre mice at 1 and 4 weeks after LAD ligation followed by single-cell RNA-seq analysis to further dissect the underlying molecular mechanism. Results: Prior to MI, no significant difference in heart function and macrophage numbers were observed between lysMCre and Tet2f/f-lysMCre mice at the age of 6-8 weeks old. Upon LAD-induced MI, we observed worse heart function in Tet2f/f-lysMCre mice compared to lysMCre mice. Tet2f/f-lysMCre mice showed ~40% reduction in ejection fraction and ~50% decrease in fraction shortening compared to lysMCre mice (n = 15). Further histological analysis revealed 〉2-fold increase in scar areas and infarcted areas in Tet2f/f-lysMCre compared to lysMCre mice. Single cell analysis confirmed a substantial increase of the fibroblast population in Tet2f/f-lysMCre mice upon LAD ligation. Furthermore, we also observed altered expression of a large fraction of genes related to macrophage activation and tissue repair capability, suggesting that Tet2 plays important roles in regulating macrophages function within damaged heart tissues. Further epigenomic analysis on sorted cardiac-specific macrophages is anticipated provide more valuable mechanistic information. Conclusion: Taken together, our data suggest that Tet2 deficient macrophages play an important role during heart damage and repair. Inactivation mutations of TET2 detected in CHIP patients might lead to impaired macrophage function during heart damage and therefore increase the CVD risk. References 1. Jaiswal, S., Fontanillas, P., Flannick, J. et al. (2014). N Engl J Med 371, 2488-2498. 2. Jaiswal, S., Natarajan, P., Silver, A. J. et al. (2017). N Engl J Med 377, 111-121. 3. Fuster, J. J., MacLauchlan, S., Zuriaga, M. A. et al. (2017). Science 355, 842-847. 4. Sano, S., Oshima, K., Wang, Y. et al. (2018). J Am Coll Cardiol 71, 875-886. 5. Zhang, Q., Zhao, K., Shen, Q. et al. (2015). Nature 525, 389-393. 6. Pan, W., Zhu, S., Qu, K. et al. (2017). Immunity 47, 284-297 e285. Disclosures No relevant conflicts of interest to declare.

Description: Bromodomain and extra terminal proteins (BETs) act as non-oncogene addiction targets1,2. BET inhibitors (BETi) are epigenetic drugs being explored as a promising therapeutic avenue in cancer, especially acute myeloid leukemia (AML)3,4,5. Although early clinical trials have highlighted the efficacy of this first-in-class therapy, chemotherapy resistance, which is commonly emerged during drug treatment, still hurdle the prevalence of BETi6,7. To seek for a strategy to overcome this hurdle, we carried out a combinatorial drug screening and discovered a synthetic lethality via combined inhibition of BRD4 and CDK7. Cyclin-dependent kinase 7 (CDK7), acting as a member of the general transcription factor H (TFIIH), can directly target the carboxyl-terminal domain (CTD) of the Rpb1 subunit of RNAPII for phosphorylation at serine 5 (Ser5) and serine 7 (Ser7), which is critical for transcription initiation. Recently, CDK7 has also been implicated in super-enhancer (SE) regulation8. Dual pharmacological inhibition of BRD4 and CDK7 caused a synergistic effect on the growth and apoptosis of K562 cells. Knockdown of BRD4 and CDK7 in the same cell line showed similar results as drug treatment, thus ruling out the off-target effects of inhibitors used in this study. Furthermore, we confirmed this synergistic effect in vivo using a xenograft mouse model. After 2 weeks of treatment, mice bearing BET-resistant cells showed prolonged lifespan with less leukemic burden and reduced leukemic blast infiltration in spleen, liver, and bone marrow when treated with combinatorial regimen compared with control and single agent groups. Furthermore, RNA-seq analysis showed that genes involved in cell cycle and proliferation were significantly down-regulated, while genes associated with apoptosis were up-regulated. Myc-associated genes were prominently altered, suggesting that c-Myc is one of the top targets of BRD4 and CDK7 inhibition. Ectopically expressing c-Myc partially rescued the synthetic lethality induced by BRD4 and CDK7 treatment, a finding further confirmed that Myc is potential targets of inhibition of BRD4 and CDK7. Further molecular analysis showed that BRD4 and CDK7 inhibition altered the RNAPII activity at actively transcribed genes. Interestingly, we also observed a strong reduction of RNAPII enrichment, but not H3K27Ac enrichment, at super-enhancers (SE). Loci-specific experiment on c-Myc SE regions will further reveal detailed mechanisms on how BRD4 and CDK7 inhibition affect RNAPII activity at SE to influence gene transcription. Congruently, by adopting a combinatorial drug screen approach, we identified the synthetic lethality of BRD4 and CDK7 inhibition in BRDi resistant leukemia cells both in vitro and in vivo. Our findings identify a new strategy that may enhance the clinical utility of BET inhibitors, especially for the treatment of BETi resistance. Refereneces 1. Dawson, M. A., Kouzarides, T. & Huntly, B. J. Targeting epigenetic readers in cancer. N. Engl. J. Med. 367, 647-657 (2012) 2. Shi, J. & Vakoc, C. R. The mechanisms behind the therapeutic activity of BET bromodomain inhibition. Mol. Cell 54, 728-736 (2014) 3. Herait, P. E. et al. BET-bromodomain inhibitor OTX015 shows clinically meaningful activity at nontoxic doses: interim results of an ongoing phase I trial in hematologic malignancies. Cancer Res.74, CT231 (2014) 4. Zuber, J. et al. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 478, 524-528 (2011) 5. Delmore, J. E. et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 146, 904-917 (2011) 6. Rathert, P. et al. Transcriptional plasticity promotes primary and acquired resistance to BET inhibition. Nature 525, 543-547 (2015) 7. Fong, C. Y. et al. BET inhibitor resistance emerges from leukaemia stem cells. Nature 525, 538-542 (2015) 8. E. Chipumuro, E. Marco, C.L. Christensen, et al. CDK7 inhibition suppresses super-enhancer-linked oncogenic transcription in MYCN-driven cancer. Cell, 159, 1126-1139 (2014) Disclosures No relevant conflicts of interest to declare.

Description: Tet-mediated DNA demethylation plays an important role in shaping the epigenetic landscape and chromatin accessibility to control gene expression. While several studies demonstrated pivotal roles of Tet in regulating embryonic development, little is known about their functions in heart development. Here we analyze DNA methylation and hydroxymethylation dynamics during early cardiac development in both human and mice. We find that cardiac-specific deletion of Tet2 and Tet3 in mice (Tet2/3-DKO) leads to ventricular non-compaction cardiomyopathy (NCC) with embryonic lethality. Single-cell RNA-seq analyses reveal a reduction in cardiomyocyte numbers and transcriptional reprogramming in cardiac tissues upon Tet2/3 depletion. Impaired DNA demethylation and reduced chromatin accessibility in Tet2/3-DKO mice further compromised Ying-yang1 (YY1) binding to its genomic targets, and perturbed high-order chromatin organization at key genes involved in heart development. Our studies provide evidence of the physiological role of Tet in regulating DNA methylation dynamics and chromatin organization during early heart development.

Description: Inactivation of tumor infiltrating lymphocytes (TILs) is one of the mechanisms mitigating anti-tumor immunity during tumor onset and progression. Epigenetic abnormalities are regarded as a major culprit contributing to the dysfunction of TILs within tumor microenvironments. In this study, we used a murine model of melanoma to discover that Tet2 inactivation significantly enhances the anti-tumor activity of TILs, with the efficacy comparable to immune checkpoint inhibition imposed by anti-PD-L1 treatment. Single-cell RNA-seq analysis further revealed that Tet2-deficient TILs exhibit effector-like features. Transcriptomic and ATAC-seq analysis further demonstrated that Tet2 deletion reshapes the chromatin accessibility and favors the binding of transcription factors geared toward CD8+ T cell activation. In summary, our study establishes that Tet2 constitutes one of the epigenetic barriers contributing to dysfunction of TILs, and that Tet2 inactivation could benefit anti-tumor immunity to boost tumor suppression. Disclosures No relevant conflicts of interest to declare.

Description: Ageing is accompanied by a significant reduction of hematopoietic competence driven by various causes including epigenetic alternations [1-4]. Ten-eleven translocation 2 (TET2) has been well delineated as a critical epigenetic regulator that affects hematopoietic progenitor and stem cells (HSPCs) function. Tet2 deficiency confers advantages in clonal expansion of HSPCs and skews myeloid lineage differentiation, giving rise to increased risk of hematological malignancy transformation [5-8]. TET2 loss-of-function mutations are frequently detected in aged HSPCs [10-11], thereby raising the question of how Tet2 deficiency affects HSPCs self-renewal and lineage specification during ageing. To address this question, we harvested HSPCs from wild-type (WT) or Tet2KO young and aged donor mice, followed by competitive bone marrow transplantations to monitor age-dependent functional alterations. Despite the enlargement of the HSC pool size (the number of cells with regenerative potential) in aged mice, the aged WT HSPCs exhibited lower self-renewal capability and displayed impaired hematopoietic differentiation when competed against young stem cells. However, we found that both aged and young Tet2-deficient HSPCs shared comparable peripheral blood reconstitution, indicating no engraftment defects were caused by age for Tet2-deficient HSPCs. In parallel, scRNA-seq analysis revealed that Tet2 deficiency and age promoted the expansion of HSC compartment in a synergistic manner, leading to the largely augmented pool size of Tet2-deficient aged HSCs. But unlike aged WT stem cells, these expanded aged Tet2-null stem cells retained high self-renewal potential and possessed a competitive advantage of lineage outputs both in vitro and in vivo. Overall, through conducting repopulation assays and single-cell transcriptomes analysis, we have demonstrated that Tet2 ablation alters age-dependent HSC functional decline, revealing a disparate ageing process in the Tet2-deficient haemopoietic system. Disclosures No relevant conflicts of interest to declare.