ALBERT

Description: Herbaspirillum seropedicae is a rhizobacteria that occupies a specialized ecological niche in agriculture. As an endophyte and prolific grass root colonizer it has the potential to promote plant growth, enhancing crop yield in many cereal crops. While the mechanisms for plant growth promotion are controversial, the one irrefutable fact is these microorganisms rely heavily on plant-borne carbon as their main energy source in support of their biological functions. Unfortunately, the tools and technology enabling researchers to trace carbon exchange between plants and the microorganisms associating with them has been limiting. Here, we demonstrate that radioactive 11CO2 administered to intact maize leaves with translocation of 11C-photosynthates to roots can provide a ‘traceable’ source of carbon whose assimilation by microbial organisms can be quantified with enormous sensitivity. Fluorescence root imaging of RAM10, a green fluorescent protein (GFP) reporting strain of H. seropedicae, was used to identify regions of high microbial colonization. Microbes were mechanically removed from these regions via sonication in saline solution and extracts were subjected to fluorescence measurement and gamma counting to correlate carbon-11 atoms with numbers of colony forming units. The method has potential to translate to other microorganisms provided they possess an optical reporting trait.

Description: In the struggle to survive herbivory by leaf-feeding insects, plants employ multiple strategies to defend themselves. One mechanism by which plants increase resistance is by intensifying their responsiveness in the production of certain defense agents to create a rapid response. Known as defense priming, this action can accelerate and amplify responses of metabolic pathways, providing plants with long-lasting resistance, especially when faced with waves of attack. In the work presented, short-lived radiotracers of carbon administered as 11CO2 and nitrogen administered as 13NH3 were applied in Nicotiana tabacum, to examine the temporal changes in ‘new’ C/N utilization in the biosynthesis of key amino acids (AAs). Responses were induced by using topical application of the defense hormone jasmonic acid (JA). After a single treatment, metabolic partitioning of recently fixed carbon (designated ‘new’ carbon and reflected as 11C) increased through the shikimate pathway, giving rise to tyrosine, phenylalanine and tryptophan. Amplification in ‘new’ carbon fluxes preceded changes in the endogenous (12C) pools of these AAs. Testing after serial JA treatments revealed that fluxes of ‘new’ carbon were accelerated, amplified and sustained over time at this higher rate, suggesting a priming effect. Similar results were observed with recently assimilated nitrogen (designated ‘new’ nitrogen reflected as 13N) with its partitioning into serine, glycine and glutamine, which play important roles supporting the shikimate pathway and downstream secondary metabolism. Finally, X-ray fluorescence imaging revealed that levels of the element Mn, an important co-factor for enzyme regulation in the shikimate pathway, increased within JA treated tissues, suggesting a link between plant metal ion regulation and C/N metabolic priming.

Description: Abstract Programmable transcriptional regulation is a powerful tool to study gene functions. Current methods to selectively regulate target genes are mainly based on promoter exchange or on overexpressing transcriptional activators. To expand the discovery toolbox, we designed a dCas9-based RNA-guided synthetic transcription activation system for Aspergillus nidulans that uses enzymatically disabled “dead” Cas9 fused to three consecutive activation domains (VPR-dCas9). The dCas9-encoding gene is under the control of an estrogen-responsive promoter to allow induction timing and to avoid possible negative effects by strong constitutive expression of the highly active VPR domains. Especially in silent genomic regions, facultative heterochromatin and strictly positioned nucleosomes can constitute a relevant obstacle to the transcriptional machinery. To avoid this negative impact and to facilitate optimal positioning of RNA-guided VPR-dCas9 to targeted promoters, we have created a genome-wide nucleosome map from actively growing cells and stationary cultures to identify the cognate nucleosome-free regions (NFRs). Based on these maps, different single-guide RNAs (sgRNAs) were designed and tested for their targeting and activation potential. Our results demonstrate that the system can be used to regulate several genes in parallel and, depending on the VPR-dCas9 positioning, expression can be pushed to very high levels. We have used the system to turn on individual genes within two different biosynthetic gene clusters (BGCs) which are silent under normal growth conditions. This method also opens opportunities to stepwise activate individual genes in a cluster to decipher the correlated biosynthetic pathway. Keypoints • An inducible RNA-guided transcriptional regulator based on VPR-dCas9 was established in Aspergillus nidulans. • Genome-wide nucleosome positioning maps were created that facilitate sgRNA positioning. • The system was successfully applied to activate genes within two silent biosynthetic gene clusters.

Description: Atlantic menhaden (Brevoortia tyrannus) are an important forage fish for many predators, and they also support the largest commercial fishery by weight on the U.S. East Coast. Menhaden management has been working toward ecological reference points (ERPs) that account for menhaden’s role in the ecosystem. The goal of this work was to develop menhaden ERPs using ecosystem models. An existing Ecopath with Ecosim model of the Northwest Atlantic Continental Shelf (NWACS) was reduced in complexity from 61 to 17 species/functional groups. The new NWACS model of intermediate complexity for ecosystems (NWACS-MICE) serves to link the dynamics of menhaden with key managed predators. Striped bass (Morone saxatilis) were determined to be most sensitive to menhaden harvest and therefore served as an indicator of ecosystem impacts. ERPs were based on the tradeoff relationship between the equilibrium biomass of striped bass and menhaden fishing mortality (F). The ERPs were defined as the menhaden F rates that maintain striped bass at their biomass target and threshold when striped bass are fished at their Ftarget, and all other modeled species were fished at status quo levels. These correspond to an ERP Ftarget of 0.19 and an ERP Fthreshold of 0.57, which are lower than the single species reference points by 30–40%, but higher than current (2017) menhaden F. The ERPs were then fed back into the age-structured stock assessment model projections to provide information on total allowable catch. The ERPs developed in this study were adopted by the Atlantic menhaden Management Board, marking a shift toward ecosystem-based fishery management for this economically and ecologically important species.

Description: Introduction: Belumosudil (KD025) is a novel oral selective rho-associated coiled-coil kinase 2 (ROCK2) inhibitor specifically designed for the treatment of cGVHD, an immune-mediated inflammatory and fibrotic disorder. In a previous dose-finding study (KD025-208, N=54), two-thirds of patients, including those with fibrotic and inflammatory manifestations, achieved a partial or complete response with belumosudil. Herein, we report on the top-line results (6 months after the last patient in) from the pivotal phase 2 trial (ROCKstar [KD025-213], N=132). Methods: This phase 2, open-label, randomized, multicenter study evaluated belumosudil 200 mg QD (n=66) and BID (n=66) in patients with cGVHD who received 2 to 5 prior lines of therapy (LOT). Treatment continued until clinically significant progression of cGVHD. The primary end point was overall response rate (ORR), defined per the 2014 National Institutes of Health Consensus Criteria. Additional end points included duration of response (DOR), Lee Symptom Scale (LSS) score, failure-free survival (FFS), corticosteroid (CS) dose reductions and overall survival. The study was powered such that the lower bound of the 95% confidence interval (CI) excludes 30%, with appropriate multiplicity adjustment. Results: At enrollment, the median age was 56 years, the median time from cGVHD diagnosis to enrollment was 29 months, 67% of patients had severe cGVHD, 52% had ≥4 organs involved, 72% had received ≥3 prior LOT (including ibrutinib [n=46] or ruxolitinib [n=38]) and 73% were refractory to their last LOT. The baseline characteristics of both arms were well balanced. With a median follow-up of 8 months, the ORR (95% CI) with belumosudil 200 mg QD and BID was 73% (60%-83%) and 74% (62%-84%), respectively (Table 1). In patients who previously received ruxolitinib (29%), the ORR with belumosudil 200 mg QD and BID was 65% (41%-85%) and 72% (47%-90%), respectively. In patients who previously received ibrutinib (35%), the ORR with belumosudil 200 mg QD and BID was 73% (50%-89%) and 71% (49%-87%), respectively. High ORRs were seen in all patient subgroups, regardless of length of time from diagnosis to treatment, including those with severe cGVHD, involvement of ≥4 organs and a refractory response to prior LOT (Figure 1). The response rate was similar across all affected organs. The median time to response was 4 weeks. Of responders, 49% have maintained response for ≥20 weeks. The median DOR has not yet been reached. Clinically meaningful improvement (≥7-point reduction) in LSS score on consecutive assessments was observed in 39% and 33% of patients in the QD and BID groups, respectively. Both responders (43%) and nonresponders (17%) experienced a clinically meaningful improvement in LSS score. FFS was 77% (69%-84%) at 6 months. CS and calcineurin inhibitor discontinuations were seen in 18% and 13% of patients, respectively. Belumosudil was well tolerated, with 〉95% relative dose intensity in 83% of patients. Drug discontinuation occurred in 10% of patients due to possible drug-related adverse events (AEs), 3% due to progression of underlying disease and 12% due to progression of cGVHD. AEs were consistent with those expected in patients with cGVHD receiving CS and other immunosuppressants (Table 2). Common AEs included fatigue (32%), diarrhea (29%), nausea (26%), cough (24%), dyspnea (24%), upper respiratory tract infection (23%), peripheral edema (21%) and headache (20%). At least 1 serious AE occurred in 34% of patients. Twenty-three percent of patients had at least 1 liver-related investigation; the most common was increased gamma-glutamyltransferase (11%), and only 1 patient showed an increase in bilirubin. Eight patients died during the study; 5 due to AEs (1 possibly related to belumosudil) and 3 during long-term follow-up (〉28 days after last dose). There were no reports of cytomegalovirus reactivation or infection. Conclusion: Treatment with belumosudil at both doses resulted in high ORRs across key subgroups, meeting the primary end point of this pivotal randomized trial in cGVHD. Responses were durable and clinically meaningful, irrespective of patient and cGVHD characteristics, and were seen in patients who previously received ruxolitinib and ibrutinib. Belumosudil was well tolerated, with limited and manageable AEs. Further studies will evaluate its use earlier in disease management. The 12-month data analysis will be presented at ASH 2020. Disclosures Cutler: Incyte: Consultancy, Membership on an entity's Board of Directors or advisory committees; Kadmon: Consultancy, Membership on an entity's Board of Directors or advisory committees; Jazz: Consultancy, Membership on an entity's Board of Directors or advisory committees; Medsenic: Consultancy, Membership on an entity's Board of Directors or advisory committees; Generon: Consultancy, Membership on an entity's Board of Directors or advisory committees; Mesoblast: Consultancy, Membership on an entity's Board of Directors or advisory committees. Lee:Pfizer: Consultancy, Research Funding; Incyte: Consultancy, Research Funding; Amgen: Research Funding; Kadmon: Research Funding; AstraZeneca: Research Funding; Novartis: Research Funding; Takeda: Research Funding; Syndax: Research Funding. Rotta:Merck: Speakers Bureau; Jazz Pharma: Speakers Bureau. Ramakrishnan:Amgen: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Cigna: Honoraria. Eiznhamer:Kadmon Corporation, LLC: Current Employment, Current equity holder in publicly-traded company. Schueller:Kadmon Corporation, LLC: Current Employment, Current equity holder in publicly-traded company. Yang:Kadmon Corporation, LLC: Current Employment, Current equity holder in publicly-traded company. Green:Kadmon Corporation, LLC: Current Employment, Current equity holder in publicly-traded company. Aggarwal:Kadmon Corporation, LLC: Consultancy; Angiocrine Bioscience, Inc: Current Employment, Other: stock options. Blazar:BlueRock Therapeutics: Research Funding; BlueRock Therapeuetic: Consultancy; Fate Therapeutics Inc.: Research Funding; Magenta Therapeutics: Consultancy; Childrens' Cancer Research Fund: Research Funding; KidsFirst Fund: Research Funding; Tmunity: Other: Co-founder. Jagasia:Ocugen: Other; Mallinckrodt: Research Funding; Janssen: Research Funding.

Description: Myeloproliferative neoplasms (MPNs) are a group of hematopoietic stem cell disorders driven by mutations that constitutively activate physiologic signal transduction pathways essential for hematopoiesis. The majority of patients with classical MPNs harbor mutations within the Janus activated kinase 2 (JAK2), calreticulin (CALR), or thrombopoietin receptor (MPL) genes. The occurrence of driver mutations among patients is mutually exclusive but rare double positive cases have been reported. Employment of targeted sequencing methods for diagnostics revealed more double positive cases and reviewing published studies we estimate the CALR and JAK2 double positive MPN frequency to be about 0.5% in all MPNs and 2% in essential thrombocythemia. However, the mutual exclusivity of CALR and JAK2 mutations in double positive cases was confirmed at single cell level in few studies where clonogenic assays were performed with subsequent genotyping of colonies. In our MPN biobank of over 800 samples, we identified one case diagnosed with PMF, carrying both in JAK2 and CALR, with allelic burdens of 8% and 41%, respectively. Using a clonogenic assay, we confirmed mutual exclusivity of the mutations at CFU level confirming previous findings. Mutations can be mutually exclusive due to their synthetic lethal interaction. Such synthetic lethal interaction has been recently described in splicing factor mutated MDS, showing that SF3B1 and SRSF2 double mutant hematopoietic cells (HSC) have reduced fitness in vivo providing explanation why such patients are never observed. In this study, we tested the hypothesis that JAK2-V617F and CALR-del52 mutations are synthetic lethal if they occur in the same HSC. We have generated mice that co-expresses both JAK2-V617F and CALR-del52 mutations in hematopoietic lineages and analyzed their phenotype. First, we co-expressed JAK2-V617F and CALR-del52 on the Vav1-Cre backgound in which Cre recombinase activates the floxed transgenes in embryonic HSC. Double positive offspring were born at expected Mendelian frequency compared to single positive littermates, suggesting no signs of synthetic lethality in utero. The phenotype of the JAK2-V617F and CALR-del52 double positive mice was significantly more severe compared to single mutant mice. More specifically, double positive mice showed more pronounced splenomegaly, higher white blood cell, lymphocyte, granulocyte, monocyte, and platelet counts in peripheral blood. In the bone marrow, double positive mice had more prominent megakaryocyte dyspoiesis and altered myeloid to erythroid ratios, without evident myelofibrosis as observed in histological sections. This increase in megakaryocyte numbers was also confirmed by FACS. In addition, double positive mice had more obscured follicular architecture and more signs of enhanced extramedullary hematopoiesis in the spleen, and more pronounced megakaryocytic sequestration in the lungs when compared to the JAK2-V617F histology findings. These mice also had lower overall survival compared to the JAK2-V617F and CALR-del52 mice. Next, we performed competitive bone marrow transplantation (BMT) to examine HSC fitness in primary and secondary transplants. Wild type bone marrow (BM) derived from F1 hybrid CD45.1/CD45.2 mice was mixed with BM form either mice bearing single mutation or double mutations (CD45.2), and ingrafted into CD45.1 recipients. The changes in chimerism were followed in peripheral blood by FACS. Double positive BM engrafted recipients equally well as JAK2-V617F or CALR-del52 cells suggesting no functional defect at HSC level. Same results were seen also in secondary BMT. In summary, double positive mice have an enhanced MPN phenotype with lower overall survival compared to single positive JAK2-V617F and CALR-del52 animals. Our results suggest that the mutual exclusivity of MPN driver mutations JAK2-V617F and CALR-del52 is not due to synthetic lethality or loss of HSC fitness. It is possible that once the second mutation is acquired, JAK2-V617F and CALR-del52 double positive cells do not gain additional competitive advantage over single positive HSCs, and therefore, do not grow out into a significant population. Another reason why we do not observe JAK2-V617F and CALR-del52 double positive colonies in patients is the very low likelihood of such HSC arising. Our data shows that such MPN patients may be found and very likely will have more severe MPN. Disclosures No relevant conflicts of interest to declare.

Description: Sonic hedgehog medulloblastoma encompasses a clinically and molecularly diverse group of cancers of the developing central nervous system. Here, we use unbiased sequencing of the transcriptome across a large cohort of 250 tumors to reveal differences among molecular subtypes of the disease, and demonstrate the previously unappreciated importance of non-coding RNA transcripts. We identify alterations within the cAMP dependent pathway (GNAS, PRKAR1A) which converge on GLI2 activity and show that 18% of tumors have a genetic event that directly targets the abundance and/or stability of MYCN. Furthermore, we discover an extensive network of fusions in focally amplified regions encompassing GLI2, and several loss-of-function fusions in tumor suppressor genes PTCH1, SUFU and NCOR1. Molecular convergence on a subset of genes by nucleotide variants, copy number aberrations, and gene fusions highlight the key roles of specific pathways in the pathogenesis of Sonic hedgehog medulloblastoma and open up opportunities for therapeutic intervention.