Quantifying the impacts of future shoreline modification on biodiversity in a case study of coastal Georgia, United States.

People often modify the shoreline to mitigate erosion and protect property from storm impacts. The 2 main approaches to modification are gray infrastructure (e.g., bulkheads and seawalls) and natural or green infrastructure (NI) (e.g., living shorelines). Gray infrastructure is still more often used for coastal protection than NI, despite having more detrimental effects on ecosystem parameters, such as biodiversity. We assessed the impact of gray infrastructure on biodiversity and whether the adoption of NI can mitigate its loss. We examined the literature to quantify the relationship of gray infrastructure and NI to biodiversity and developed a model with temporal geospatial data on ecosystem distribution and shoreline modification to project future shoreline modification for our study location, coastal Georgia (United States). We applied the literature-derived empirical relationships of infrastructure effects on biodiversity to the shoreline modification projections to predict change in biodiversity under different NI versus gray infrastructure scenarios. For our study area, which is dominated by marshes and use of gray infrastructure, when just under half of all new coastal infrastructure was to be NI, previous losses of biodiversity from gray infrastructure could be mitigated by 2100 (net change of biodiversity of +0.14%, 95% confidence interval -0.10% to +0.39%). As biodiversity continues to decline from human impacts, it is increasingly imperative to minimize negative impacts when possible. We therefore suggest policy and the permitting process be changed to promote the adoption of NI.

Cuantificación del impacto de la futura modificación de la costa sobre la biodiversidad en un estudio de caso de la costa de Georgia, Estados Unidos Resumen Las personas modifican con frecuencia la costa para mitigar la erosión o proteger su propiedad del impacto de las tormentas. Los dos enfoques principales para la modificación son la infraestructura gris (p. ej.: mamparos y malecones) y la infraestructura verde o natural (IN) (p.ej.: costas vivientes). La infraestructura gris es más común que la IN, a pesar de que tiene efectos dañinos sobre los parámetros ambientales, como la biodiversidad. Evaluamos el impacto de la infraestructura gris sobre la biodiversidad y si la adopción de la IN puede mitigar su pérdida. Analizamos la literatura para cuantificar la relación de la infraestructura gris y la IN con la biodiversidad. También desarrollamos un modelo con datos geoespaciales temporales sobre la distribución de los ecosistemas y la modificación de la costa para proyectar la modificación costera en el futuro en nuestra localidad de estudio: la costa de Georgia, Estados Unidos. Aplicamos las relaciones empíricas derivadas de la literatura de los efectos de la infraestructura sobre la biodiversidad a las proyecciones de modificación de la costa para predecir el cambio en la biodiversidad bajo diferentes escenarios de infraestructura gris versus IN. En nuestra área de estudio, que está dominada por marismas y usa infraestructura gris, cuando un poco menos de la mitad de toda la infraestructura costera nueva debería ser IN, las pérdidas previas de biodiversidad a partir de la infraestructura gris podrían mitigarse para 2100 (cambio neto de la biodiversidad de +0.14%, 95% intervalo de confianza ­0.10% a +0.39%). Conforme la biodiversidad siga en declive por el impacto humano, cada vez es más imperativo minimizar el impacto negativo cuando sea posible. Por lo tanto, sugerimos que se modifiquen las políticas y el proceso de permisos para promover la adopción de la IN.

CDK9 inhibition induces epigenetic reprogramming revealing strategies to circumvent resistance in lymphoma.

Diffuse large B-cell lymphoma (DLBCL) exhibits significant genetic heterogeneity which contributes to drug resistance, necessitating development of novel therapeutic approaches. Pharmacological inhibitors of cyclin-dependent kinases (CDK) demonstrated pre-clinical activity in DLBCL, however many stalled in clinical development. Here we show that AZD4573, a selective inhibitor of CDK9, restricted growth of DLBCL cells. CDK9 inhibition (CDK9i) resulted in rapid changes in the transcriptome and proteome, with downmodulation of multiple oncoproteins (eg, MYC, Mcl-1, JunB, PIM3) and deregulation of phosphoinotiside-3 kinase (PI3K) and senescence pathways. Following initial transcriptional repression due to RNAPII pausing, we observed transcriptional recovery of several oncogenes, including MYC and PIM3. ATAC-Seq and ChIP-Seq experiments revealed that CDK9i induced epigenetic remodeling with bi-directional changes in chromatin accessibility, suppressed promoter activation and led to sustained reprograming of the super-enhancer landscape. A CRISPR library screen suggested that SE-associated genes in the Mediator complex, as well as AKT1, confer resistance to CDK9i. Consistent with this, sgRNA-mediated knockout of MED12 sensitized cells to CDK9i. Informed by our mechanistic findings, we combined AZD4573 with either PIM kinase or PI3K inhibitors. Both combinations decreased proliferation and induced apoptosis in DLBCL and primary lymphoma cells in vitro as well as resulted in delayed tumor progression and extended survival of mice xenografted with DLBCL in vivo. Thus, CDK9i induces reprogramming of the epigenetic landscape, and super-enhancer driven recovery of select oncogenes may contribute to resistance to CDK9i. PIM and PI3K represent potential targets to circumvent resistance to CDK9i in the heterogeneous landscape of DLBCL.

Combined inhibition of JAK/STAT pathway and lysine-specific demethylase 1 as a therapeutic strategy in CSF3R/CEBPA mutant acute myeloid leukemia.

Acute myeloid leukemia (AML) is a deadly hematologic malignancy with poor prognosis, particularly in the elderly. Even among individuals with favorable-risk disease, approximately half will relapse with conventional therapy. In this clinical circumstance, the determinants of relapse are unclear, and there are no therapeutic interventions that can prevent recurrent disease. Mutations in the transcription factor CEBPA are associated with favorable risk in AML. However, mutations in the growth factor receptor CSF3R are commonly co-occurrent in CEBPA mutant AML and are associated with an increased risk of relapse. To develop therapeutic strategies for this disease subset, we performed medium-throughput drug screening on CEBPA/CSF3R mutant leukemia cells and identified sensitivity to inhibitors of lysine-specific demethylase 1 (LSD1). Treatment of CSF3R/CEBPA mutant leukemia cells with LSD1 inhibitors reactivates differentiation-associated enhancers driving immunophenotypic and morphologic differentiation. LSD1 inhibition is ineffective as monotherapy but demonstrates synergy with inhibitors of JAK/STAT signaling, doubling median survival in vivo. These results demonstrate that combined inhibition of JAK/STAT signaling and LSD1 is a promising therapeutic strategy for CEBPA/CSF3R mutant AML.

Statistical considerations for design and analysis of stability, comparability and formulation tests.

This article considers designed experiments for stability, comparability, and formulation testing that are analyzed with regression models in which the degradation rate is a fixed effect. In this setting, we investigate how the number of lots, the number of time points and their locations affect the precision of the entities of interest, leverages of the time points, detection of non-linearity and interim analyses. This investigation shows that modifying time point locations suggested by ICH for stability studies can significantly improve these objectives. In addition, we show that estimates of precision can be biased when a regression model that assumes independent measurements is used in the presence of within-assay session correlation. This bias can lead to longer shelf life estimates in stability studies and loss of power in comparability studies. Mixed-effect models that take into account within-assay session correlation are shown to reduce this bias. The findings in this article are obtained from well known statistical theory but provide valuable practical advice to scientists and statisticians designing and interpreting these types of experiments.

Numerical modeling of wave attenuation: implications of representing vegetation found in coastal saltmarshes in the Chesapeake Bay.

Coastal communities are vulnerable to wave and storm surges during extreme events, highlighting the need to increase community resilience. The effectiveness of natural wetlands in attenuating waves is vital to designing strategies for protecting public safety. This study aimed to understand how vegetation attenuates waves and determine the best method for modeling vegetation's impact on wave dynamics. The researchers compared two different vegetation representations in numerical models, implicit and explicit, using SWAN and XBeach at varying spatial resolutions. The study focused on two marshes in the Chesapeake Bay, using field measurements to investigate the accuracy of each method in representing wave attenuation by vegetation and the implications of explicitly representing average characteristics of one vegetation species on a regional level. Results showed that explicit modeling using average vegetation characteristics provided more accurate results than the implicit model, which only showed wave attenuation due to topography. The finer scale resolution and site-specific vegetation characteristics further improved the accuracy of wave attenuation observed. Understanding the trade-offs between different vegetation representations in numerical models is essential to accurately represent wave attenuation and design effective protection strategies for coastal communities.

Quantifying the effects of sea level rise driven marsh migration on wave attenuation.

Sea level rise (SLR) is the most significant climate change-related threat to coastal wetlands, driving major transformations in coastal regions through marsh migration. Landscape transformations due to marsh migration are manifested in terms of horizontal and vertical changes in land cover and elevation, respectively. These processes will have an impact on saltmarsh wave attenuation that is yet to be explored. This study stands as a comprehensive analysis of spatially distributed wave attenuation by vegetation in the context of a changing climate. Our results show that: i) changes in saltmarsh cover have little to no effect on the attenuation of floods, while ii) changes in elevation can significantly reduce flood extents and water depths; iii) overland wave heights are directly influenced by marsh migration, although iv) being indirectly attenuated by the water depth limiting effects of water depth attenuation driven by changes in elevation; v) the influence of saltmarsh accretion on wave attenuation is largely evident near the marsh edge, where the increasing elevations can drive major wave energy losses via wave breaking. Lastly, vi) considering the synergy between SLR, marsh migration, and changes in elevation results in significantly more wave attenuation than considering the eustatic effects of SLR and/or horizontal marsh migration alone, and therefore should be adopted in future studies.

LSD1 activates a lethal prostate cancer gene network independently of its demethylase function.

Medical castration that interferes with androgen receptor (AR) function is the principal treatment for advanced prostate cancer. However, clinical progression is universal, and tumors with AR-independent resistance mechanisms appear to be increasing in frequency. Consequently, there is an urgent need to develop new treatments targeting molecular pathways enriched in lethal prostate cancer. Lysine-specific demethylase 1 (LSD1) is a histone demethylase and an important regulator of gene expression. Here, we show that LSD1 promotes the survival of prostate cancer cells, including those that are castration-resistant, independently of its demethylase function and of the AR. Importantly, this effect is explained in part by activation of a lethal prostate cancer gene network in collaboration with LSD1's binding protein, ZNF217. Finally, that a small-molecule LSD1 inhibitor-SP-2509-blocks important demethylase-independent functions and suppresses castration-resistant prostate cancer cell viability demonstrates the potential of LSD1 inhibition in this disease.

Microwave Thermolysis Reduces Generalized and Social Anxiety in Young Adults With Axillary Hyperhidrosis.

BACKGROUND AND OBJECTIVE: Hyperhidrosis (HH) is associated with impairments in quality of life (QOL) and elevated anxiety. Microwave thermolysis is a newer treatment that reduces sweating, yet effects on QOL and emotional symptoms have not been examined. Two treatment sessions are recommended to achieve 80% amelioration of clinical HH. We hypothesized that microwave thermolysis would reduce sweat severity, improve QOL, and reduce anxiety in young adults suffering from axillary HH in a prospective clinical trial. STUDY DESIGN/MATERIALS AND METHODS: We enrolled 24 young adults (mean age = 23.57 years, 54% female) with elevated scores on the Hyperhidrosis Disease Severity Scale. All participants received one session of microwave thermolysis, and 83% received two sessions. Participants completed measures of sweat severity, QOL, generalized anxiety, social anxiety, social avoidance, and anxious/depressive mood symptoms at baseline; post-first treatment; and following second treatment. RESULTS: At baseline, all participants had severe sweating; 87.5% had impaired QOL, 75% had elevated social anxiety, 50% with generalized anxiety, 48% with social avoidance, and 38% with anxious/depressed mood. Paired samples t tests indicated significant improvements from baseline to first procedure, including decreased sweating (t(21) = 5.68, P < 0.001), improved QOL (t(23) = 4.97, P < 0.001), and decreased generalized anxiety (t(23) = 8.11, P < 0.001), social anxiety (t(22) = 4.55, P < 0.001), mood symptoms (t(21) = 3.81, P = 0.001), and social avoidance (t(22) = 3.12, P = 0.005). After second treatment, further improvements were noted in sweating (t(18) = 3.28, P = 0.004) and QOL (t(18) = 3.83, P = 0.003), and a marginal trend for generalized anxiety (t(19) = 1.96, P = 0.064). CONCLUSION: There were significant improvements in sweat severity, skin-specific QOL, generalized anxiety, social anxiety, anxious/depressive symptoms, and social avoidance. The majority of the psychosocial benefit appears to emerge after one treatment of microwave thermolysis, whereas the level of sweat severity and QOL continued to show further improvements after a second treatment. Results would suggest that although two microwave thermolysis sessions are needed for maximal treatment optimization of axillary HH, patients may experience significant benefits in improving psychosocial functioning after just one session. Lasers Surg. Med. © 2020 Wiley Periodicals, Inc.

Erythrokinetics: quantitative measurements of red cell production and destruction in normal subjects and patients with anemia.

To study erythropoiesis and anemia, one must have a firm foundation of indices that accurately measure red blood cell production and destruction. This paper, authored by hematology legends Arno G. Motulsky and Clement A. Finch, provides that foundation. Using methods that would not be approved in today's environment, the authors studied a cohort of normal healthy patients and an equal number of patients with different forms of anemia. The results confirm a reciprocal model of red cell production and destruction, show that anemia can be the result of either underproduction (a regenerative anemia or ineffective erythropoiesis) or increased destruction, and define parameters for distinguishing these 2 possibilities that are still widely used today.

Retinoid-X-receptors (α/ß) in melanocytes modulate innate immune responses and differentially regulate cell survival following UV irradiation.

Understanding the molecular mechanisms of ultraviolet (UV) induced melanoma formation is becoming crucial with more reported cases each year. Expression of type II nuclear receptor Retinoid-X-Receptor α (RXRα) is lost during melanoma progression in humans. Here, we observed that in mice with melanocyte-specific ablation of RXRα and RXRß, melanocytes attract fewer IFN-γ secreting immune cells than in wild-type mice following acute UVR exposure, via altered expression of several chemoattractive and chemorepulsive chemokines/cytokines. Reduced IFN-γ in the microenvironment alters UVR-induced apoptosis, and due to this, the survival of surrounding dermal fibroblasts is significantly decreased in mice lacking RXRα/ß. Interestingly, post-UVR survival of the melanocytes themselves is enhanced in the absence of RXRα/ß. Loss of RXRs α/ß specifically in the melanocytes results in an endogenous shift in homeostasis of pro- and anti-apoptotic genes in these cells and enhances their survival compared to the wild type melanocytes. Therefore, RXRs modulate post-UVR survival of dermal fibroblasts in a "non-cell autonomous" manner, underscoring their role in immune surveillance, while independently mediating post-UVR melanocyte survival in a "cell autonomous" manner. Our results emphasize a novel immunomodulatory role of melanocytes in controlling survival of neighboring cell types besides controlling their own, and identifies RXRs as potential targets for therapy against UV induced melanoma.

Coibamide A, a natural lariat depsipeptide, inhibits VEGFA/VEGFR2 expression and suppresses tumor growth in glioblastoma xenografts.

Coibamide A is a cytotoxic lariat depsipeptide isolated from a rare cyanobacterium found within the marine reserve of Coiba National Park, Panama. Earlier testing of coibamide A in the National Cancer Institute in vitro 60 human tumor cell line panel (NCI-60) revealed potent anti-proliferative activity and a unique selectivity profile, potentially reflecting a new target or mechanism of action. In the present study we evaluated the antitumor activity of coibamide A in several functional cell-based assays and in vivo. U87-MG and SF-295 glioblastoma cells showed reduced migratory and invasive capacity and underwent G1 cell cycle arrest as, likely indirect, consequences of treatment. Coibamide A inhibited extracellular VEGFA secreted from U87-MG glioblastoma and MDA-MB-231 breast cancer cells with low nM potency, attenuated proliferation and migration of normal human umbilical vein endothelial cells (HUVECs) and selectively decreased expression of vascular endothelial growth factor receptor 2 (VEGFR2). We report that coibamide A retains potent antitumor properties in a nude mouse xenograft model of glioblastoma; established subcutaneous U87-MG tumors failed to grow for up to 28 days in response to 0.3 mg/Kg doses of coibamide A. However, the natural product was also associated with varied patterns of weight loss and thus targeted delivery and/or medicinal chemistry approaches will almost certainly be required to improve the toxicity profile of this unusual macrocycle. Finally, similarities between coibamide A- and apratoxin A-induced changes in cell morphology, decreases in VEGFR2 expression and macroautophagy signaling in HUVECs raise the possibility that both cyanobacterial natural products share a common mechanism of action.

Semisynthetic model calibration for monitoring glucose in mammalian cell culture with in situ near infrared spectroscopy.

Near infrared (NIR) spectroscopy has the capability of providing real-time, multi-analyte monitoring of the complex reaction mixture associated with cell culture processes. However, the development of robust models to predict the concentration of key analytes has proven difficult. In this study, a modeling methodology using semisynthetic process samples was used to predict glucose concentrations in Chinese Hamster Ovary (CHO) cell culture processes. Partial Least Squares (PLS) regression models were built from in situ NIR spectra, and glucose levels between 4.0 and 14.0 g/L. Two models were constructed. The "standard model" used data provided by cell culture production process samples. The "full model" included the data provided from both cell culture production process samples and semisynthetic samples. The semisynthetic samples were generated by titrating cell culture samples with target viable cell density (VCD) and lactate levels to defined glucose concentrations. The robustness of each model was gauged by predicting glucose in a subsequent cell culture process utilizing a media formulation and cell line not contained in the calibration data sets. The "full model" generated glucose predictions with a root mean square error of prediction (RMSEP) of 0.99 g/L while the "standard model" provided glucose predictions with a RMSEP of 2.26 g/L. The modeling approach utilizing semisynthetic samples proved to be faster development and more effective than using just standard cell culture processes.

Quality by design approach for viral clearance by protein a chromatography.

Protein A chromatography is widely used as a capture step in monoclonal antibody (mAb) purification processes. Antibodies and Fc fusion proteins can be efficiently purified from the majority of other complex components in harvested cell culture fluid (HCCF). Protein A chromatography is also capable of removing modest levels of viruses and is often validated for viral clearance. Historical data mining of Genentech and FDA/CDER databases systematically evaluated the removal of model viruses by Protein A chromatography. First, we found that for each model virus, removal by Protein A chromatography varies significantly across mAbs, while remains consistent within a specific mAb product, even across the acceptable ranges of the process parameters. In addition, our analysis revealed a correlation between retrovirus and parvovirus removal, with retrovirus data generally possessing a greater clearance factor. Finally, we describe a multivariate approach used to evaluate process parameter impacts on viral clearance, based on the levels of retrovirus-like particles (RVLP) present among process characterization study samples. It was shown that RVLP removal by Protein A is robust, that is, parameter effects were not observed across the ranges tested. Robustness of RVLP removal by Protein A also correlates with that for other model viruses such as X-MuLV, MMV, and SV40. The data supports that evaluating RVLP removal using process characterization study samples can establish multivariate acceptable ranges for virus removal by the protein A step for QbD. By measuring RVLP instead of a model retrovirus, it may alleviate some of the technical and economic challenges associated with performing large, design-of-experiment (DoE)-type virus spiking studies. This approach could also serve to provide useful insight when designing strategies to ensure viral safety in the manufacturing of a biopharmaceutical product.

Grp1-associated scaffold protein regulates skin homeostasis after ultraviolet irradiation.

Grp1-associated scaffold protein (Grasp), the product of a retinoic acid-induced gene in P19 embryonal carcinoma cells, is expressed primarily in brain, heart, and lung of the mouse. We report herein that Grasp transcripts are also found in mouse skin in which the Grasp gene is robustly induced following acute ultraviolet-B (UVB) exposure. Grasp(-/-) mice were found to exhibit delayed epidermal proliferation and a blunted apoptotic response after acute UVB exposure. Immunohistochemical analyses revealed that the nuclear residence time of the tumor suppressor protein p53 was reduced in Grasp(-/-) mice after UVB exposure. Taken together, our results suggest that a physiological role of Grasp may be to regulate skin homeostasis after UVB exposure, potentially by influencing p53-mediated apoptotic responses in skin.

Tunable quantum emitters on large-scale foundry silicon photonics.

Controlling large-scale many-body quantum systems at the level of single photons and single atomic systems is a central goal in quantum information science and technology. Intensive research and development has propelled foundry-based silicon-on-insulator photonic integrated circuits to a leading platform for large-scale optical control with individual mode programmability. However, integrating atomic quantum systems with single-emitter tunability remains an open challenge. Here, we overcome this barrier through the hybrid integration of multiple InAs/InP microchiplets containing high-brightness infrared semiconductor quantum dot single photon emitters into advanced silicon-on-insulator photonic integrated circuits fabricated in a 300 mm foundry process. With this platform, we achieve single-photon emission via resonance fluorescence and scalable emission wavelength tunability. The combined control of photonic and quantum systems opens the door to programmable quantum information processors manufactured in leading semiconductor foundries.

Pharmacological inhibition of RAS overcomes FLT3 inhibitor resistance in FLT3-ITD+ AML through AP-1 and RUNX1.

AML is characterized by mutations in genes associated with growth regulation such as internal tandem duplications (ITD) in the receptor kinase FLT3. Inhibitors targeting FLT3 (FLT3i) are being used to treat patients with FLT3-ITD+ but most relapse and become resistant. To elucidate the resistance mechanism, we compared the gene regulatory networks (GRNs) of leukemic cells from patients before and after relapse, which revealed that the GRNs of drug-responsive patients were altered by rewiring their AP-1-RUNX1 axis. Moreover, FLT3i induces the upregulation of signaling genes, and we show that multiple cytokines, including interleukin-3 (IL-3), can overcome FLT3 inhibition and send cells back into cycle. FLT3i leads to loss of AP-1 and RUNX1 chromatin binding, which is counteracted by IL-3. However, cytokine-mediated drug resistance can be overcome by a pan-RAS inhibitor. We show that cytokines instruct AML growth via the transcriptional regulators AP-1 and RUNX1 and that pan-RAS drugs bypass this barrier.

Leukemic stem cells activate lineage inappropriate signalling pathways to promote their growth.

Acute Myeloid Leukemia (AML) is caused by multiple mutations which dysregulate growth and differentiation of myeloid cells. Cells adopt different gene regulatory networks specific to individual mutations, maintaining a rapidly proliferating blast cell population with fatal consequences for the patient if not treated. The most common treatment option is still chemotherapy which targets such cells. However, patients harbour a population of quiescent leukemic stem cells (LSCs) which can emerge from quiescence to trigger relapse after therapy. The processes that allow such cells to re-grow remain unknown. Here, we examine the well characterised t(8;21) AML sub-type as a model to address this question. Using four primary AML samples and a novel t(8;21) patient-derived xenograft model, we show that t(8;21) LSCs aberrantly activate the VEGF and IL-5 signalling pathways. Both pathways operate within a regulatory circuit consisting of the driver oncoprotein RUNX1::ETO and an AP-1/GATA2 axis allowing LSCs to re-enter the cell cycle while preserving self-renewal capacity.

Relevance of tributary inflows for driving molecular composition of dissolved organic matter (DOM) in a regulated river system.

River regulation by dams can alter flow regimes and organic matter dynamics, but less is known about how unregulated tributaries regulate organic matter composition and processing in the regulated river below the confluence. This study reports on water chemistry, especially dissolved organic matter (DOM) concentration and composition (dissolved organic carbon (DOC), organic nitrogen (DON), organic phosphorus (DOP) and combined amino acids (DCAA)) along the regulated Tumut and unregulated Goobarragandra (tributary) rivers under different flow conditions (base flow vs storm event) in south-east Australia. The tributary was significantly different from regulated and downstream sites during base flow conditions with higher temperature, pH, buffering capacity, DOC and nutrient concentrations (DON, DOP, DCAA). DOM characterisation by spectrometry and size exclusion chromatography revealed that the tributary contained a higher proportion of terrestrially derived humic-like and fulvic-like DOM. In contrast, regulated and downstream sites contained higher proportion of microbially derived DOM such as low molecular weight neutrals and protein-like components. Storm pulses of tributary flows into the regulated system, influenced both concentration and composition of DOM at the downstream site, which more strongly resembled the tributary site than the regulated site during the storm event. Additionally, we found that the tributary supplied fresh DOM, including small organic molecules to the regulated system during storm events. The presence of these different types of labile DOM can increase primary productivity and ecological functioning within regulated river reaches downstream of tributary junctions. This has important implications for the protection of unregulated tributary inflows within regulated river basins.

Gene regulatory network analysis predicts cooperating transcription factor regulons required for FLT3-ITD+ AML growth.

AML is a heterogenous disease caused by different mutations. We have previously shown that each mutational sub-type develops its specific gene regulatory network (GRN) with transcription factors interacting with multiple gene modules, many of which are transcription factor genes themselves. Here we hypothesized that highly connected nodes within such networks comprise crucial regulators of AML maintenance. We tested this hypothesis using FLT3-ITD mutated AML as a model and conducted an shRNA drop-out screen informed by this analysis. We show that AML-specific GRNs predict identifying crucial regulatory modules required for AML but not normal cellular growth. Furthermore, our work shows that all modules are highly connected and regulate each other. The careful multi-omic analysis of the role of one (RUNX1) module by shRNA and chemical inhibition shows that this transcription factor and its target genes stabilize the GRN of FLT3-ITD AML and that its removal leads to GRN collapse and cell death.

Identification and interrogation of the gene regulatory network of CEBPA-double mutant acute myeloid leukemia.

Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy caused by mutations in genes encoding transcriptional and epigenetic regulators together with signaling genes. It is characterized by a disturbance of differentiation and abnormal proliferation of hematopoietic progenitors. We have previously shown that each AML subtype establishes its own core gene regulatory network (GRN), consisting of transcription factors binding to their target genes and imposing a specific gene expression pattern that is required for AML maintenance. In this study, we integrate gene expression, open chromatin and ChIP data with promoter-capture Hi-C data to define a refined core GRN common to all patients with CEBPA-double mutant (CEBPAN/C) AML. These mutations disrupt the structure of a major regulator of myelopoiesis. We identify the binding sites of mutated C/EBPα proteins in primary cells, we show that C/EBPα, AP-1 factors and RUNX1 colocalize and are required for AML maintenance, and we employ single cell experiments to link important network nodes to the specific differentiation trajectory from leukemic stem to blast cells. Taken together, our study provides an important resource which predicts the specific therapeutic vulnerabilities of this AML subtype in human cells.