Master Regulator Protein Research Articles

Identification and Targeting of Regulators of SARS-CoV-2-Host interactions in the Airway Epithelium.

Although the impact of SARS-CoV-2 in the lung has been extensively studied, the molecular regulators and targets of the host-cell programs hijacked by the virus in distinct human airway epithelial cell populations remain poorly understood. This is in part ascribed to the use of non-primary cell systems, overreliance on single-cell gene expression profiling that not ultimately reflect protein activity and bias toward the downstream effects rather than their mechanistic determinants. Here we address these issues by network-based analysis of single cell transcriptomic profiles of pathophysiologically relevant human adult basal, ciliated and secretory cells to identify master regulator (MR) protein modules controlling their SARS-CoV-2-mediated reprogramming. This uncovered chromatin remodeling, endosomal sorting, ubiquitin pathway as well as proviral factors identified by CRISPR analyses as components of the host response collectively or selectively activated in these cells. Large-scale perturbation assays, using a clinically-relevant drug library, identified 11 drugs able to invert the entire MR signature activated by SARS-CoV-2 in these cell types. Leveraging MR analysis and perturbational profiles of human primary cells, represents a novel mechanism-based approach and resource that can be directly generalized to interrogate signatures of other airway conditions for drug prioritization.

APE1 is a master regulator of the ATR-/ATM-mediated DNA damage response

To maintain genomic integrity, cells have evolved several conserved DNA damage response (DDR) pathways in response to DNA damage and stress conditions. Apurinic/apyrimidinic endonuclease 1 (APE1) exhibits AP endonuclease, 3′-5′ exonuclease, 3′-phosphodiesterase, and 3′-exoribonuclease activities and plays critical roles in the DNA repair and redox regulation of transcription. However, it remains unclear whether and how APE1 is involved in DDR pathways. In this perspective, we first updated our knowledge of APE1's functional domains and its nuclease activities and their specific associated substrates. We then summarized the newly discovered roles and mechanisms of action of APE1 in the global and nucleolar ATR-mediated DDR pathway. While the ATM-mediated DDR is well known to be activated by DNA double-strand breaks and oxidative stress, here we provided new perspectives as to how ATM DDR signaling is activated by indirect single-strand breaks (SSBs) resulting from genotoxic stress and defined SSB structures, and discuss how ATM kinase is directly activated and regulated by its activator, APE1. Together, accumulating body of new evidence supports the notion that APE1 is a master regulator protein of the ATR- and ATM-mediated DDR pathways. These new findings of APE1 in DDR signaling provide previously uncharacterized but critical functions and regulations of APE1 in genome integrity.

DnaA modulates the gene expression and morphology of the Lyme disease spirochete.

Lyme disease is the most prevalent tick-borne infection in the Northern Hemisphere. Borrelia burgdorferi , the causative spirochete bacteria, has been maintained in nature for millennia in a consistent enzootic cycle between Ixodes ticks and various small vertebrate hosts. During the tick's blood meal, B. burgdorferi substantially increases its replication rate, alters its repertoire of outer surface proteins, and disseminates into the new vertebrate host. Across eubacteria, DnaA is the master regulatory protein that initiates chromosomal replication and acts as a transcription factor to regulate specific pathways. Here, we describe the roles that B. burgdorferi DnaA has on the physiology and gene expression of this medically important pathogen.

Distinct profiles of plant immune resilience revealed by natural variation in warm temperature-modulated disease resistance among Arabidopsis accessions.

Elevated temperature suppresses the plant defence hormone salicylic acid (SA) by downregulating the expression of master immune regulatory genes CALMODULIN BINDING PROTEIN 60-LIKE G (CBP60g) and SYSTEMIC ACQUIRED RESISTANCE DEFICIENT1 (SARD1). However, previous studies in Arabidopsis thaliana plants have primarily focused on the accession Columbia-0 (Col-0), while the genetic determinants of intraspecific variation in Arabidopsis immunity under elevated temperature remain unknown. Here we show that BASIC HELIX LOOP HELIX 059 (bHLH059), a thermosensitive SA regulator at nonstress temperatures, does not regulate immune suppression under warmer temperatures. In agreement, temperature-resilient and -sensitive Arabidopsis accessions based on disease resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000 did not correlate with bHLH059 polymorphisms. Instead, we found that temperature-resilient accessions exhibit varying CBP60g and SARD1 expression profiles, potentially revealing CBP60g/SARD1-dependent and independent mechanisms of immune resilience to warming temperature. We identified thermoresilient accessions that exhibited either temperature-sensitive or -insensitive induction of the SA biosynthetic gene ICS1 (direct target gene of CBP60g and SARD1) and SA hormone levels. Collectively, this study has unveiled the intraspecific diversity of Arabidopsis immune responses under warm temperatures, which could aid in predicting plant responses to climate change and provide foundational knowledge for climate-resilient crop engineering.

ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity.

Tumor heterogeneity complicates patient treatment and can be due to transitioning of cancer cells across phenotypic cell states. This process is associated with the acquisition of independence from an oncogenic driver, such as the estrogen receptor (ER) in breast cancer (BC), resulting in tumor progression, therapeutic failure and metastatic spread. The transcription factor ONECUT2 (OC2) has been shown to be a master regulator protein of metastatic castration-resistant prostate cancer (mCRPC) tumors that promotes lineage plasticity to a drug-resistant neuroendocrine (NEPC) phenotype. Here, we investigate the role of OC2 in the dynamic conversion between different molecular subtypes in BC. We analyze OC2 expression and clinical significance in BC using public databases and immunohistochemical staining. In vitro, we perform RNA-Seq, RT-qPCR and western-blot after OC2 enforced expression. We also assess cellular effects of OC2 silencing and inhibition with a drug-like small molecule in vitro and in vivo. OC2 is highly expressed in a substantial subset of hormone receptor negative human BC tumors and tamoxifen-resistant models, and is associated with poor clinical outcome, lymph node metastasis and heightened clinical stage. OC2 inhibits ER expression and activity, suppresses a gene expression program associated with luminal differentiation and activates a basal-like state at the gene expression level. We also show that OC2 is required for cell growth and survival in metastatic BC models and that it can be targeted with a small molecule inhibitor providing a novel therapeutic strategy for patients with OC2 active tumors. The transcription factor OC2 is a driver of BC heterogeneity and a potential drug target in distinct cell states within the breast tumors.

Endoplasmic reticulum stress response favors cardiomyocyte apoptosis near birth

INTRODUCTION: One-third of cardiomyocyte are lost just before birth in the normally developing heart. The underlying reasons for this cell loss are unknown. We studied the role of the endoplasmic reticulum (ER) stress response in regulation of cardiomyocyte apoptosis in perinatal sheep hearts. We hypothesized that the signaling balance from survival to apoptosis changes just before the cardiomyocyte numbers decline, and that the ER stress response contributes. METHODS: Snap-frozen left ventricular (LV) samples and cultured cardiomyocytes from normally-growing lambs at 135 d of gestational age (dGA; term=147 dGA), 143 dGA and 1 d postnatal age (dPN) were used for this study (n=6 each age).Gene and protein regulation was studied by RT-PCR and western blot analysis. Parameters were compared by age by 1-way ANOVA followed, if justified, by Šídák's multiple comparisons test. RESULTS: In the LV, the ER stress master regulatory protein GRP78 was similar within fetal ages, but declined 32% between 143 dGA and 1 dPN (P= 0.0005), indicating less capacity for responding to misfolded proteins. eIF2α, downstream of GRP78, is critical for deciding the survival/apoptosis outcome following ER stress. Phosphorylation of eIF2α doubled between 135 dGA and 143 dGA (P=0.0015), implying increased ER stress in this period, and declined again at 1 dPN (p<0.0001 vs. 143 dGA). Cleaved apoptosis effector caspase 3 protein peaked after birth; levels at 1 dPN were 1- to 2-fold higher than at other ages (p<0.0001 vs. 135 dGA, P=0.002 vs. 143 dGA). Together, these data suggest that survival signaling in the ER stress pathway may be blunted between 135 and 143 dGA, as evidenced by diminished GRP78 expression and elevated eIF2α phosphorylation, resulting in activation of the apoptosis pathway. To better understand the mechanisms regulating dynamic perinatal changes in the ER stress response pathway, we studied sensitivity to ER stress (thapsigargin: 5 μM, 12 h) in cultured LV cardiomyocytes. In response to thapsigargin, GRP78 protein levels rose ~3-fold higher in cells from 135 dGA compared to 143 dGA or 1 dPN hearts (p<0.0001), supporting diminishing survival signaling closer to the time of birth. Phosphorylation of eIF2α followed a similar pattern and was highest in 135 dGA cells (p<0.0001 vs. 143 dGA and 1 dPN). This contrasts to the greater levels of phospho-eIF2α at 143 dGA in the tissue analysis. Thapsigargin stimulated 2-fold more cleavage of caspase 3 at 1 dPN than 135 dGA (P=0.0243), a similar timing as found in LV tissue. CONCLUSION: Findings suggest that at two weeks before birth, heart and cardiomyocytes are resilient to ER stress and stimulation of apoptosis, whereas nearer the time of birth there is a blunted ER stress response and increased activation of apoptotic pathways. R01HL142483 (Jonker), Collins Foundation (Bose). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

The small RNA PrrH aggravates Pseudomonas aeruginosa-induced acute lung injury by regulating the type III secretion system activator ExsA.

Pseudomonas aeruginosa is a Gram-negative bacterium and the leading cause of nosocomial pneumonia. The pathogenicity of P. aeruginosa is due to the secretion of many virulence factors. Small regulatory RNAs (sRNAs) regulate various bacterial adaptations, especially virulence. Therefore, understanding the mechanism by which sRNAs regulate virulence is necessary for understanding the pathogenicity of P. aeruginosa and the treatment of the related disease. In this study, we demonstrated that PrrH enhances the pathogenicity of P. aeruginosa by binding to the coding sequence regions of the ExsA, the master regulatory protein of type III secretion system, causing severe lung injury and exacerbating the inflammatory response and apoptosis. These findings revealed that PrrH is a crucial molecule that positively regulates ExsA. Type III-positive strains are often associated with a high mortality rate in P. aeruginosa infections in clinical practice. Therefore, this discovery may provide a new target for treating P. aeruginosa infections, especially type III-positive strains.

Stem Cell Protein PIWIL2 Promotes EMT Process and Stem Cell-Like Properties in MCF7 Breast Cancer Cell Line.

Piwi-like RNA-mediated gene silencing 2 (PIWIL2) is a member of AGO/PIWI gene family, which is enriched in cancer stem cells (CSCs). The purpose of this research was to investigate the overexpression of PIWIL2 and its role in the induction of EMT and CSC properties in MCF7 breast cancer cell line. MCF7 cells were transfected with the human gene PIWIL2 (Hili) under the control of CMV promoter utilizing the neon electroporation method. Subsequently, the selection was conducted using G418, and doubling time was calculated in the transformed and control cells. RT and real-time PCR were also performed to analyze the expression of epithelial and mesenchymal genes and those related to CSCs. According to the observations from this study, transfecting MCF7 cells with PIWIL2 triggered the conversion of epithelial cells to mesenchymal cells and induced the genes specific for breast CSCs, which was coincident with 9-h reduction in the doubling time of the transfected cells. Furthermore, the molecular analyses revealed a significant reduction in the expression of epithelial markers, while a significant increase was detected in the expression of mesenchymal genes and many CSC biomarkers. PIWIL2 protein acts as a master regulatory protein that is able to manipulate the transcription through specific signaling pathways, which allow the cells to gain stem cell-like properties.

M6A Regulates the Stability of Cellular Transcripts Required for Efficient KSHV Lytic Replication.

The epitranscriptomic modification N6-methyladenosine (m6A) is a ubiquitous feature of the mammalian transcriptome. It modulates mRNA fate and dynamics to exert regulatory control over numerous cellular processes and disease pathways, including viral infection. Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation from the latent phase leads to the redistribution of m6A topology upon both viral and cellular mRNAs within infected cells. Here we investigate the role of m6A in cellular transcripts upregulated during KSHV lytic replication. Our results show that m6A is crucial for the stability of the GPRC5A mRNA, whose expression is induced by the KSHV latent-lytic switch master regulator, the replication and transcription activator (RTA) protein. Moreover, we demonstrate that GPRC5A is essential for efficient KSHV lytic replication by directly regulating NFκB signalling. Overall, this work highlights the central importance of m6A in modulating cellular gene expression to influence viral infection.

Macrophage inhibitory cytokine-1 aggravates diet-induced gallstone formation via increased ABCG5/ABCG8 expression.

Macrophage inhibitory cytokine 1 (MIC-1), which is overproduced in various human cancers and associated with cachexia, acts on the hypothalamus to suppress appetite and reduce body weight. We investigated the mechanisms through which MIC-1 affects bile acid metabolism and gallstone formation, which are poorly understood. Over 6 weeks, male C57BL/6 mice fed either standard chow or a lithogenic diet were intraperitoneally injected with phosphate-buffered saline (PBS) or MIC-1 (200 μg/kg/week). Among lithogenic diet-fed mice, MIC-1 treatment resulted in increased gallstone formation compared with PBS treatment. Compared with PBS treatment, MIC-1 treatment decreased hepatic cholesterol and bile acid levels and reduced expression of HMG-CoA reductase (HMGCR), the master cholesterol metabolism regulator sterol regulatory element-binding protein 2, cholesterol 7α-hydroxylase (CYP7A1), mitochondrial sterol 27-hydroxylase, and oxysterol 7α-hydroxylase. Compared with PBS treatment, MIC-1 treatment had no effect on small heterodimer partner, farnesoid X receptor, or pregnane X receptor expression, and extracellular signal-related kinase and c-Jun N-terminal kinase phosphorylation decreased, suggesting that these factors do not contribute to the MIC-1-induced reduction in CYP7A1 expression. Compared with PBS treatment, MIC-1 treatment increased AMP-activated protein kinase (AMPK) phosphorylation. Treatment with the AMPK activator 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR) reduced CYP7A1 and HMGCR expression, whereas the AMPK inhibitor Compound C reversed MIC-1-induced reductions in CYP7A1 and HMGCR expression. Furthermore, in MIC-1-treated mice, total biliary cholesterol levels increased together with increased ATP-binding cassette subfamily G (ABCG)5 and ABCG8 expression. Compared with PBS treatment, MIC-1 treatment did not affect expression of liver X receptors α and β, liver receptor homolog 1, hepatocyte nuclear factor 4α, or NR1I3 (also known as constitutive androstane receptor), which are upstream of ABCG5/8; however, MIC-1 treatment increased ABCG5/8 expression and promoter activities. Our study indicates that MIC-1 influences gallstone formation by increasing AMPK phosphorylation, reducing CYP7A1 and HMGCR expression, and increasing ABCG5 and ABCG8 expression.

DIPG-49. A SYSTEMS BIOLOGY APPROACH TO DEFINING AND TARGETING CELL STATE-SPECIFIC MASTER REGULATOR DEPENDENCIES IN DIFFUSE MIDLINE GLIOMA

Abstract Diffuse Midline Glioma (DMG) are fatal pediatric brain tumors. We leveraged network-based methodologies to dissect the heterogeneity of DMG tumors and to discover Master Regulator (MR) proteins representing pharmacologically accessible, mechanistic determinants of molecularly distinct cell states. We produced a DMG regulatory network from 122 publicly available RNAseq profiles with ARACNe, and inferred sample-specific MR protein activity with VIPER. A CRISPR/Cas9 KO screen across 3 DMG patient cell lines identified a set of 73/77 essential genes that were enriched in the MR signature of 80% of patient samples (GSEA p=0.000034). FOXM1 emerged as an essential MR, significantly activated across virtually all patients. We then generated RNAseq profiles following perturbation with ~300 oncology drugs in 2 DMG cell lines most representative of patient MR signatures, and used this to identify drugs that invert patient MR activity profiles using the NYS/CA Dept.of Health approved OncoTreat algorithm. OncoTreat predicted sensitivity to HDAC, MEK, CDK, PI3K, and proteosome inhibitors in subsets of patients. 80%of OncoTreat-predicted drugs (p<10-5) from 3 DMG patient tumor biopsies showed in vitro sensitivity in cultured tumor cells from the respective patients, with overall 68% accuracy among 223 drugs evaluated by both OncoTreat and in vitro (Fisher’s Exact Test p=0.0449). Further analysis of DMG intra-tumor heterogeneity via protein activity inference from published scRNAseq profiles identified 6 tumor clusters with unique MR signatures representing distinct cellular states. Targetable MRs and OncoTreat-predicted drugs were distinct between these states. Bulk RNAseq analysis recapitulated predictions seen in the more prevalent Oligodendrocyte progenitor cell-like states, but failed to capture MR and drug predictions for the Astrocyte-like states. Ongoing validations of cell state-specific drug predictions in vivo in subcutaneous patient-derived xenograft and orthotopic syngeneic DMG models have already shown tumor volume and subpopulation differences (e.g. Trametinib-treated). This provides a platform to nominate much-needed novel drugs to treat DMG.

Abstract 4304: Network-based inference identifies cell state-specific drugs targeting master regulator vulnerabilities in diffuse midline glioma

Abstract Diffuse Midline Glioma (DMG) are fatal pediatric brain tumors with no therapies. We leveraged network-based methodologies to dissect the heterogeneity of DMG tumors and to discover Master Regulator (MR) proteins representing pharmacologically accessible, mechanistic determinants of molecularly distinct cell states. We produced the first DMG regulatory network from 122 publicly available RNAseq profiles with ARACNe (Basso et al. Nat Genet 2005), and inferred sample-specific MR protein activity with VIPER (Alvarez et al. Nat Genet 2016) based on the differential expression of their targets. 7 of the top 25 most active MRs found comprise a well-characterized MR block (MRB2) (Paull et al.Cell 2021), frequently activated across aggressive tumors, and enriched in DMG patient MR signatures (Fisher’s Exact Test p=4.4 × 10−18). A CRISPR/Cas9 KO screen across 3 DMG patient cell lines identified a set of 73/77 essential genes that were enriched in the MR signature of 80% of patient samples (GSEA p=0.000034). FOXM1 emerged as an essential MR, significantly activated across virtually all patients. We then generated RNAseq profiles following perturbation with ~300 oncology drugs in 2 DMG cell lines most representative of patient MR signatures, and used this to identify drugs that invert patient MR activity profiles using the NYS/CA Dept. of Health approved OncoTreat algorithm (Alvarez et al. Nat Genet 2018). OncoTreat predicted sensitivity to HDAC, MEK, CDK, PI3K, and proteosome inhibitors in subsets of patients, overlapping with published DMG drug screens. Importantly, 80% of OncoTreat-predicted drugs (p<10−5) from 3 DMG patient tumor biopsies showed in vitro sensitivity in cultured tumor cells from the respective patients, with overall 68% accuracy among 223 drugs evaluated by both OncoTreat and in vitro (Fisher’s Exact Test p=0.0449). Further analysis of DMG intra-tumor heterogeneity via protein activity inference across DMG single cells from 6 published scRNAseq profiles identified 6 tumor clusters with unique MR signatures co-existing in virtually all patients representing distinct cellular states (2 astrocyte-, 1 oligodendrocyte-, and 3 oligodendrocyte precursor cell-like states). Targetable MRs and OncoTreat-predicted drugs were distinct between these states. Bulk RNAseq analysis recapitulated predictions seen in the more prevalent OPC-like states, but failed to capture MR and drug predictions for the AC-like states (e.g. JAK1/Ruxolitinib and STAT3/Napabucasin). We are currently validating cell state-specific drug predictions in vivo at single-cell resolution in subcutaneous patient-derived xenograft and orthotopic syngeneic DMG models that we have shown recapitulate patient tumor heterogeneity, including with focused ultrasound-mediated drug delivery. This provides a platform to nominate much-needed novel drugs and drug combinations to treat DMG. Citation Format: Ester Calvo Fernandez, Junqiang Wang, Xu Zhang, Hong-Jian Wei, Hanna E. Minns, Aaron T. Griffin, Lukas Vlahos, Timothy J. Martins, Pamela S. Becker, John Crawford, Robyn D. Gartrell, Luca Szalontay, Stergios Zacharoulis, Zhiguo Zhang, Robert Wechsler-Reya, Cheng-Chia Wu, Andrea Califano, Jovana Pavisic. Network-based inference identifies cell state-specific drugs targeting master regulator vulnerabilities in diffuse midline glioma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4304.

ESTABLISHMENT AND TREATMENT OF MURINE COLONOIDS TO STUDY THE EPITHELIAL EFFECTS OF INTESTINAL INFLAMMATION IN VITRO

Abstract BACKGROUND Disruption of the intestinal epithelial barrier is a hallmark of inflammatory bowel disease (IBD). The 3-dimensional colonoid culture system is a useful in vitro model to study intestinal stem cell dynamics and epithelial cell physiology in IBD pathogenesis. However, we have shown that in vivo epithelial changes are not necessarily retained in colonoids established from mice undergoing acute inflammation using a DSS model and primarily reflect stem cell physiology rather than that of terminally differentiated cells. We developed experimental methods to address this limitation. We terminally differentiate colonoids or create 2-D monolayers, and challenge them with a cocktail of inflammatory mediators that are typically elevated during IBD. METHODS Murine colonoids are established by isolating colonic crypts and plating them in basement membrane matrix. Over 3 to 5 days, crypt structures develop into spheroid colonoids 250 μm in diameter, forming a prominent lumen surrounded by a thin layer of epithelial stem cells. They are passaged a minimum of two times and then are either 1) terminally differentiated by incubating the colonoids with Differentiating Media or 2) used to establish intestinal epithelial monolayers. Inflammation is then induced by incubating cells with a cocktail of inflammatory mediators (TNFa, IL-1b, IFNg, H2O2). Protein is collected after 72 hours, and expression of proteins involved in mitochondrial biogenesis were assessed (n=3). RESULTS We found that changes in mitochondrial dynamics, reflective of key metabolic changes in the epithelium that are observed in colonic scrapings of DSS-treated mice are not recapitulated in traditional colonoids derived from mice on the same DSS regimen. We found that changes in expression and protein levels of peroxisome proliferator-activator receptor-gamma coactivator-1a (PGC1a), the master regulator protein of mitochondrial biogenesis, were not maintained in colonoids. After terminally differentiating colonoids and subsequently inducing inflammation, we were able to recapitulate a failure of mitochondrial biogenesis failure that is a hallmark of both human IBD and murine colitis. Protein expression of PGC1a as well as downstream transcription factor A, mitochondria (TFAM) were both decreased when assessed via western blot. DISCUSSION Colonoids are a useful tool for studying colonic physiology in vitro, however are limited in their ability to evaluate the effects of in vivo inflammation on the mitochondrial function and cellular metabolism. When removed from the intestinal milieu, crypt cells demonstrate a recovery of mitochondrial health and reflect stem primarily stem cell physiology. Our strategies provide opportunities for organoid manipulation which, when employed properly, can shed light on key aspects of intestinal epithelial mitochondrial function during inflammation.

DYRK1A (Dual Specificity Tyrosine Phosphorylation Regulated Kinase 1A), a Master Regulatory Protein Involved in Down Syndrome Clinical Neurological Abnormalities and Associated Mental Retardation and a Promising Potential Drug Target for Therapeutics and Treatments

Over-expression of chromosome 21 genes, particularly in Down Syndrome Critical Region (DSCR), is the main cause of Down syndrome (DS) neuropathological features including mental retardation, cognitive impairments and early onset of Alzheimer’s disease. One of DSCR genes, that we studied herein, DYRK1A (Dual-Specificity Tyrosine-Phosphorylation-Regulated Kinase 1A), is a master regulatory protein involved in DS neuropathological features and associated mental retardation. Interestingly, normalization of DYRK1A over-expression by DYRK1A inhibitor, epigalloctechin-3-gallate (EGCG), rescues brain defects, restores cognitive impairments in DS trisomic and DYRK1A transgenic mouse models and in DS patients. These results indicates DYRK1A inhibitor epigalloctechin-3-gallate (EGCG) as an effective treatment and DYRK1A as a key regulatory protein involved in DS clinical neuropathological features suggesting DYRK1A as a valuable potential drug target for therapeutics and Treatments of DS and mental retardation opening new directions for developing new medical preventive and therapeutic treatments.

Dual‐Specificity Tyrosine Phosphorylation‐Regulated Kinase‐1A (DYRK1A), A Master Regulatory Protein Involved in Down Syndrome Brain Alterations and Mental Disability, A Key Contributor to Neurodegenerative Disorders of Alzheimer's Disease and A Potential Therapeutic Target

Down syndrome (DS) is the most frequent genetic disease characterized by several neuropathological features including alteration in neurogenesis, mental disability, cognitive impairments, learning-memory deficits and early onset of Alzheimer's disease (AD). Over expression of chromosome 21 genes, localized in Down Syndrome Critical Region (DSCR), is the main cause of DS neuropathological features.

Epigenomic landscape study reveals molecular subtypes and EBV-associated regulatory epigenome reprogramming in nasopharyngeal carcinoma.

Epstein-Barr virus (EBV) latent infection is associated with genome-wide epigenomic changes in several malignancies, but its role in epigenetic dysregulation remains unclear in nasopharyngeal carcinoma (NPC). To investigate EBV-associated epigenetic dysregulation, we performed a multi-omics study by integrating whole-genome bisulfite sequencing (WGBS), assay for transposase-accessible chromatin using sequencing (ATAC-Seq), whole-exome sequencing (WES), and single-cell RNA sequencing (scRNA-Seq) data. In addition to the known global DNA hypermethylated subtype, we discovered a novel subtype with global hypomethylation in EBV+NPC. The consistent EBV-specific differentially methylated regions (EBV-DMRs) in the human genome were identified from both subtypes and associated with loss of CTCF binding (P<2.2e-16). Importantly, CTCF is a master chromatin regulator and CTCF protein was reduced in 45% of NPC cases, especially in those with advanced NPC (Stage IV vs. others: 62% vs. 38%, P=0.034). This result links EBV with chromatin changes. The ATAC-Seq data suggest regulatory epigenome reprogramming through chromatin accessibility changes in EBV+NPC with altered CTCF binding and the switch of transcription factor binding from differentiation-associated KLF/SP family to the innate and adaptive immunity-related NF-ĸB and IRF families. Detailed chromatin accessibility analysis identified a potential EBV target gene CD74, which mediated EBV-specific cell-cell communications in the tumor microenvironment (TME) and was strongly correlated with Tcell exhaustion (r2=0.55). Our study reveals the unexpected epigenetic heterogeneity, providing insights into NPC pathogenesis and highlighting the involvement of host factors in virus-associated epigenetic changes. EBV infection is associated with epigenome reprogramming and may promote immune evasion. This study was funded by the Hong Kong Research Grants Council grant (AoE/M-06/08) to MLL, General Research Fund (17103218 and 17102619) and seed funding for basic research (201611159158) to WD, and General Research Fund (17119618) to HC.

Abstract 2127: Master regulator analysis of the tumor microenvironment and the distinctive tumor sub-populations in pancreatic ductal adenocarcinoma

Abstract By 2030, pancreatic ductal adenocarcinoma (PDAC) is projected to become the second leading cause of cancer-associated mortality in the United States. However, current strategies in targeting key driver mutations such as KRAS, CDKN2A, TP53, and SMAD4, have found limited translational success. As a result, the standard of care for PDAC patients continues to rely on cytotoxic chemotherapies. Master regulator (MR) proteins integrate upstream genomic alterations to generate a common downstream transcriptional signature characteristic of a tumor cell population. Importantly, aberrant MR protein activity is requisite to implementing and maintaining a pro-tumor state. Therefore, MR proteins serve as critical tumor dependencies and represent a promising class of therapeutic targets for cancer treatment. Here, we propose a novel, network-based approach to identify top MR proteins by utilizing a combination of ARACNe (Margolin et al, 2006) and VIPER (Alvarez et al, 2016) algorithms for the analysis of single-nuclei transcriptomic data. Specifically, we used VIPER to investigate the heterogeneity of the tumor microenvironment (TME) and to characterize the tumor sub-populations that co-exist in a patient PDAC specimen. Clustering analysis based on protein activity revealed six populations in the TME. The SingleR classifier subsequently annotated these clusters as myeloid and lymphoid immune, fibroblast, neuroendocrine, epithelial, and putative tumor cells. Next, we validated the putative tumor cells by performing InferCNV which detected widespread chromosomal copy number variations. We identified two distinct tumor subpopulations which were found to be enriched by the MR signatures of the Oncogenic Precursor (OP) and Lineage subtypes, previously demonstrated to represent more and less differentiated tumor cell populations, respectively (Laise et al, 2020). Interestingly, top MR proteins identified for the putative tumor cells using the single-nuclei transcriptomics closely corresponded with those identified by single-cell and previous bulk transcriptomics, providing orthogonal validation for the inferred protein activities. We characterized the diverse cell populations in the PDAC TME, delineated two distinct tumor cell subtypes, and demonstrated high concordance of inferred MR protein activity at the single-cell, single-nuclei, and bulk levels. These results demonstrate the feasibility of applying systems biology-based methods to identify MR proteins in an N = 1 context and represent a novel precision medicine approach in the treatment of PDAC patients. Future lines of inquiry center on identifying treatments against each tumor subpopulation via OncoTreat, an algorithm that leverages high-throughput drug perturbation data to predict effective therapies based on inferred ability to invert MR protein activity (Alvarez, 2018). Citation Format: Jinjie Ling, Lorenzo Tomassoni, Alvaro Curiel, Kenneth Olive, Andrea Califano. Master regulator analysis of the tumor microenvironment and the distinctive tumor sub-populations in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2127.

Abstract 2359: Identifying synergistic master regulators of pancreatic ductal adenocarcinoma tumorigenesis through CRISPR/Cas9 combinatorial genetic screens

Abstract Pancreatic ductal adenocarcinoma (PDAC) is the third-leading cause of cancer-related mortality and is highly resistant to cytotoxic, targeted, and immune therapies. Compared to other cancers, PDAC is remarkable for its relatively uniform set of DNA alterations; unfortunately, these hallmark events are not currently targetable and other mutations known to confer sensitivity to specific drugs are uncommon. Consequently, cytotoxic combinations remain the standard of care, with most patients quickly exhibiting primary or secondary chemoresistance. Previous studies have shown that transcriptional regulatory proteins can form small, highly interconnected and autoregulated modules that can initiate and maintain malignant tumor cell state, and that the Master Regulator (MR) protein they comprise represent a novel class of non-oncogene dependencies. We used the VIPER algorithm to identify MR proteins representing mechanistic regulators of the transcriptional state for 200 laser microdissected PDAC epithelial compartment samples, collected at Columbia University Irving Medical Center (CUIMC). To systematically identify synergistic pairs of MRs, we designed a combinatorial CRISPR-Cas9 screen based on the Big Papi dual SaCas9/SpCas9 system which was used to systematically target all possible pairs of the top 50 MRs identified by VIPER analysis across 6 PDAC cell lines (KP4, PATU8988S, PANC1, HPAFII, BXPC3, MIAPACA2) with three guide-RNAs per gene, thus differentiating between potentially idiosyncratic, cell line-specific and highly conserved genetic interactions. We also developed a novel nonparametric statistical method for inferring genetic interactions from this data based on the use of conditional Mann-Whitney U tests; our new analytical method significantly improved over a previously developed parametric model of synergy inference, demonstrating increased correlation between genetic interactions inferred from biological replicates of the same cell line while simultaneously prioritizing four established synthetic lethal gene pairs in the top 10 gene pairs following integration across all 6 cell lines: BCL2L1-MCL1, BCL2L1-BCL2L2, MAPK1-MAPK3, and SEC23A-SEC23B. The methods also identified 314 additional highly significant (FDR &amp;lt; 0.05), yet never previously reported synthetic lethal interactions that are being validated using an array-based, low-throughput screening platform. We expect that the results of this screen will help elucidate mechanisms controlling the state of PDAC tumor cells and identify potentially druggable gene pairs. Citation Format: Aaron T. Griffin, Mikko Turunen, Lorenzo Tomassoni, Kenneth P. Olive, Pasquale Laise, Andrea Califano. Identifying synergistic master regulators of pancreatic ductal adenocarcinoma tumorigenesis through CRISPR/Cas9 combinatorial genetic screens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2359.

Abstract 486: A systems biology approach to defining tumor heterogeneity, prognostic and targetable master regulator protein signatures from bulk and single cell RNA-seq in diffuse midline glioma (DMG)

Abstract Despite major advances in molecular profiling and numerous clinical trials, diffuse midline glioma (DMG) remains a fatal disease with median survival of only ~9 months and no identified effective drugs. To address this challenge, we leveraged network-based methodologies to dissect the heterogeneity of DMG tumors and to discover Master Regulator (MR) proteins representing pharmacologically accessible, mechanistic determinants of molecularly distinct DMG cell states. The study has produced the first DMG-specific regulatory network, reverse-engineered from 122 publicly available pediatric DMG RNA-seq profiles with ARACNe (Basso et al. Nat Genet 2005). Using this network, we measured protein activity for each sample via VIPER (Alvarez et al., Nat Genet 2016). Activity-based clustering identified 2 clusters, characterized by significant overall survival difference (&amp;gt;1 year, p-val=0.02 by χ2 analysis). Protein activity signatures were not significantly associated with tumor location and Histone3 mutation status. The most aberrantly activated MR proteins across all DMG patients (i.e., TOP2A, CENPF, BUB1B, FOXM1, GTSE1, MKI67, and E2F8), relative to normal caudate tissue from GTEx, were highly enriched in cell cycle regulation members, with samples in the worst outcome cluster showing significantly higher activity. Pharmacologically accessible MRs found to be significantly activated in subsets of patients (p-val&amp;lt;10E-5) include TOP2A, CHEK1, CDK2, and EZH2. To dissect DMG intra-tumor heterogeneity, we measured protein activity from published single-cell RNA-seq profiles of 6 DMG patients, using single-cell based regulatory networks. Activity-based analysis of tumor cells identified 8 clusters representing distinct differentiation and proliferation stages—i.e. astrocyte-like, oligodendrocyte-like, and multiple oligodendrocyte precursor cell (OPC)-like subpopulations. Consistent with bulk-based findings, these included an OPC-like-cycling population presenting highly aberrant activity of proliferative MRs (i.e. TOP2A, CENPF, FOXM1, E2F8, ZWINT, and CCNA2), suggesting this as a key DMG regulatory module (Tumor Checkpoint). We are working to define targetable MRs in these subpopulations, and generating RNA-seq profiles of SU-DIPG-VI and SF8628, two DMG cell lines showing protein activity similarity to &amp;gt;95% of patient samples by enrichment analysis (p-val &amp;lt; 10E-5), following perturbation with ~400 oncology drugs. This will allow us to identify drugs capable of inducing tumor demise by inverting the activity of the MRs of each tumor subpopulation, using the NY Dept. of Health approved OncoTreat algorithm (Alvarez et al., Nat Genet 2018). We are currently finalizing and validating both MR and drug predictions to nominate novel, much-needed therapeutic strategies. Citation Format: Ester Calvo Fernández, Junqiang Wang, Aaron T. Griffin, Luca Szalontay, Stergios Zacharoulis, Jovana Pavisic, Andrea Califano. A systems biology approach to defining tumor heterogeneity, prognostic and targetable master regulator protein signatures from bulk and single cell RNA-seq in diffuse midline glioma (DMG) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 486.

Abstract 488: A systems biology approach to defining tumor heterogeneity and prognostic and targetable master regulator protein signatures from bulk and single-cell RNAseq in osteosarcoma

Abstract Despite many clinical trials, outcome for osteosarcoma (OS) patients remains poor, especially for those with metastatic or relapsed/refractory disease. We leveraged network-based systems biology approaches to discover Master Regulator (MR) proteins representing pharmacologically accessible, mechanistic determinants of OS cell state, and to dissect tumor transcriptional heterogeneity. MRs were identified by interrogating an OS regulatory network—generated from 87 RNAseq profiles in the TARGET OS cohort—with gene expression signatures from 149 diagnostic OS samples, using the VIPER algorithm. RNAseq profiles were generated in four sarcoma cell lines following perturbation with ~400 oncology drugs, and used to identify drugs capable of inverting MR activity profiles with the OncoTreat algorithm. Unsupervised, protein activity-based clustering of the samples identified two clusters, characterized by a significant overall survival difference (76% vs 38%, log-rank p-val 0.0041). Patients in the high-risk cluster presented aberrant activity of proteins involved in cell cycle (FOXM1, CENPF, TOP2A) and epigenetic remodeling (EZH2, KDM1A), while those in the low-risk cluster had aberrant activity of proteins involved in immune response (VAV1, CD86, CEBPE), interferon gama signaling (IRF5, MNDA), and senescence control (CREG1, TFEC). We further identified patients with metastatic disease and particularly poor outcome (&amp;lt;15% survival) showing high activity in stem cell-related proteins NANOG, ZSCAN4, and LIN28A. To address intra-tumor heterogeneity and immune infiltration (40-60% in the samples) in bulk RNAseq data, we inferred protein activity in previously published single-cell RNAseq profiles from 11 OS patients, using regulatory networks also produced by single-cell analysis. We identified three tumor subpopulations, co-existing in all the samples, with lineage similarity to osteoblasts, chondroblasts, and fibroblasts. The most active MR proteins (p-val &amp;lt; 10E-30) were highly distinct across these subpopulations: NANOG, REL, IGF2, TOP2A (osteoblasts), SSTR3, WNT1, KDM6B, EZH2 (chondroblasts), and NOD1, ERBB3, PRKDC, INSR (fibroblasts). Pharmacologically accessible MRs significantly active across the three subpopulations and in subsets of bulk RNAseq samples included EZH2, CDK2, TOP2A, HDAC5, and PRKDC. OncoTreat analysis predicted sensitivity to camptothecin, seliciclib, galunisertib, and rigosertib in both fibroblast- and chondroblast-like subpopulations. In conclusion, using network-based systems biology approaches in OS, we identified pharmacologically accessible MR subtypes differentiating survival at the bulk tissue level, and defining three distinct tumor subpopulations at the single-cell level with unique predicted drug sensitivities. Citation Format: Somnath Tagore, Jovana Pavisic, Aaron T. Griffin, Katherine Janeway, Andrew L. Kung, Filemon Dela Cruz, Alejandro Sweet-Cordero, Inge Behroozfard, Stanley Leung, Alex Lee, Darrell Yamashiro, Julia Glade Bender, Andrea Califano. A systems biology approach to defining tumor heterogeneity and prognostic and targetable master regulator protein signatures from bulk and single-cell RNAseq in osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 488.