Master Regulatory Transcription Factor Research Articles

Transcriptional regulatory network of the light signaling pathways.

The developmental program by which plants respond is tightly controlled by a complex cascade in which photoreceptors perceive and transduce the light signals that drive signaling processes and direct the transcriptional reprogramming, yielding specific cellular responses. The molecular mechanisms involved in the transcriptional regulation include light-regulated nuclear localization (the phytochromes and UVR8) and nuclear accumulation (the cryptochrome, cry2) of photoreceptors. This regulatory cascade also includes master regulatory transcription factors (TFs) that bridge photoreceptor activation with chromatin remodeling and regulate the expression of numerous light-responsive genes. Light signaling-related TFs often function as signal convergence points in concert with TFs in other signaling pathways to integrate complex endogenous and environmental cues that help the plant adapt to the surrounding environment. Increasing evidence suggests that chromatin modifications play a critical role in regulating light-responsive gene expression and provide an additional layer of light signaling regulation. Here, we provide an overview of our current knowledge of the transcriptional regulatory network involved in the light response, particularly the roles of TFs and chromatin in regulating light-responsive gene expression.

Glycogen synthase kinase-3 promotes T helper type 17 differentiation by promoting interleukin-9 production.

T helper type 17 (Th17) cells are recognized as important contributors to the deleterious effects of several neurological and psychiatric diseases. Clarifying mechanisms that control the production of Th17 cells may therefore provide new strategies for developing novel interventions in a broad spectrum of disorders. Th17 cell differentiation is promoted by glycogen synthase kinase-3 (GSK3), but the mechanisms for this are only beginning to be understood. Using T-cell-selective depletion of GSK3β and multiple selective pharmacological GSK3 inhibitors, we found that GSK3 inhibition decreased C-C motif chemokine (ccl)20, C-C motif chemokine receptor (ccr)6, interleukin (IL)-9, Runt-related transcription factor (Runx)1, interferon regulatory factor (Irf)4 and c-maf mRNA expression after 2days of Th17 cell differentiation in vitro. These effects were found to be independent of the master regulator transcription factor retinoic acid receptor-related orphan receptor γT (RORγT), as GSK3 inhibition still reduced Th17 cell differentiation in RORγT-depleted cells. Because IL-9 was approximately ninefold down-regulated in GSK3β-/- CD4 cells, we tested if reintroduction of IL-9 during Th17 cell differentiation abolished the inhibition by GSK3 deficiency of Th17 cell differentiation. We found that IL-9 over-expression was sufficient to reverse the inhibition of Th17 cell differentiation by GSK3 inhibition or depletion. We found that IL-9 enhances Th17 cell differentiation in part through signal transducer and activator of transcription 3 (STAT3) activation, and IL-9 also enhances STAT3 binding to the IL-17a promoter. Altogether, these findings suggest that IL-9 might be an important mediator of GSK3β-dependent enhancement of Th17 cell differentiation.

Contributions of HOX genes to cancer hallmarks: Enrichment pathway analysis and review.

Homeobox genes function as master regulatory transcription factors during development, and their expression is often altered in cancer. The HOX gene family was initially studied intensively to understand how the expression of each gene was involved in forming axial patterns and shaping the body plan during embryogenesis. More recent investigations have discovered that HOX genes can also play an important role in cancer. The literature has shown that the expression of HOX genes may be increased or decreased in different tumors and that these alterations may differ depending on the specific HOX gene involved and the type of cancer being investigated. New studies are also emerging, showing the critical role of some members of the HOX gene family in tumor progression and variation in clinical response. However, there has been limited systematic evaluation of the various contributions of each member of the HOX gene family in the pathways that drive the common phenotypic changes (or "hallmarks") and that underlie the transformation of normal cells to cancer cells. In this review, we investigate the context of the engagement of HOX gene targets and their downstream pathways in the acquisition of competence of tumor cells to undergo malignant transformation and tumor progression. We also summarize published findings on the involvement of HOX genes in carcinogenesis and use bioinformatics methods to examine how their downstream targets and pathways are involved in each hallmark of the cancer phenotype.

Integrated DNA methylation analysis reveals a potential role for ANKRD30B in Williams syndrome

Williams syndrome (WS) is a rare genetic disorder, caused by a microdeletion at the 7q11.23 region. WS exhibits a wide spectrum of features including hypersociability, which contrasts with social deficits typically associated with autism spectrum disorders. The phenotypic variability in WS likely involves epigenetic modifications; however, the nature of these events remains unclear. To better understand the role of epigenetics in WS phenotypes, we integrated DNA methylation and gene expression profiles in blood from patients with WS and controls. From these studies, 380 differentially methylated positions (DMPs), located throughout the genome, were identified. Systems-level analysis revealed multiple co-methylation modules linked to intermediate phenotypes of WS, with the top-scoring module related to neurogenesis and development of the central nervous system. Notably, ANKRD30B, a promising hub gene, was significantly hypermethylated in blood and downregulated in brain tissue from individuals with WS. Most CpG sites of ANKRD30B in blood were significantly correlated with brain regions. Furthermore, analyses of gene regulatory networks (GRNs) yielded master regulator transcription factors associated with WS. Taken together, this systems-level approach highlights the role of epigenetics in WS, and provides a possible explanation for the complex phenotypes observed in patients with WS.

A Novel Genetically Defined Mouse Model of Hypertensive Nephropathy

The molecular pathways that drive hypertensive nephropathy remain poorly understood. Hypertension (HTN) and chronic kidney disease are comorbid disorders with a correlation as high as 70% in African‐Americans over 65 years old. Because impaired kidney function can be the cause or consequence of HTN, identification of causal hypertensive nephropathy pathways has been especially difficult. Here, we overcome the roadblock with a new genetically‐defined mouse model of HTN that exhibit a low‐renin salt‐sensitive form of the disease, similar to HTN in individuals of sub‐Saharan African descent. The mice, created by introducing activating mutations in the Ste20p‐related proline alanine‐rich kinase (SPAK) in a distal convoluted tubule cell‐specific manner, become hypertensive solely as a consequence of constitutive activation of the thiazide‐sensitive sodium chloride cotransporter (NCC) and salt retention.For these studies, the constitutively active (CA)‐SPAK and control (C57BL/6J) mice were fed control or high salt diet (HSD), and renal function was evaluated over 40 weeks, together with telemetric measurements of blood pressure. RNA‐Seq was performed to evaluate changes in the transcriptional profile in the renal cortex, and corroborated biochemically.Renal function in CA‐SPAK mice began to deteriorate at 20 weeks as evidenced by significant elevation of BUN, creatinine, and frank albuminuria, which gradually increased over the next 20 weeks. HSD consumption exacerbated hypertension in CA‐SPAK mice, and accelerated the decline in renal function. Microscopic evaluation of trichrome‐stained specimens revealed no significant changes in the kidney parenchyma. Thus hypertension appears to drive kidney insufficiency long before the development of nephroangiosclerosis.By contrast, a significant change in the transcription profile was observed between CA‐SPAK mice and controls at an early stage when microalbuminuria begins to develop. 1905 differentially expressed (DE) genes were identified (modified TREAT method, FDR < 0.05 for genes > 10% change). Remarkably, the DE profile was enriched in 26% of the known genes associated with albuminuria in humans (Chi Square test, p = 0.00031). Significant downregulation of key components of the glomerular filtration barrier slit diaphragm genes (nephrin, podocalyxin, synaptopodin, actinin a4, phospholipase C ɛ1) and the proximal tubule protein scavenger, Cubilin, were also observed in the CA‐SPAK. Pathway analysis was especially enriched in proinflammatory responses. Signature genes associated with Major Histocompatibility Complex class II, T helper 17 lymphocytes master regulator transcription factors and B lymphocytes markers were up‐regulated in the CA‐SPAK mice.In conclusion, progression of renal insufficiency in CA‐SPAK mice indicates a causal role of hypertension in nephropathy, and incriminates an inflammatory component as a key driver of early damage to the glomerular filtration barrier and tubular protein reabsorption.Support or Funding InformationThis study was supported by NIH.

RUNX1: an emerging therapeutic target for cardiovascular disease.

Runt-related transcription factor-1 (RUNX1), also known as acute myeloid leukaemia 1 protein (AML1), is a member of the core-binding factor family of transcription factors which modulate cell proliferation, differentiation, and survival in multiple systems. It is a master-regulator transcription factor, which has been implicated in diverse signalling pathways and cellular mechanisms during normal development and disease. RUNX1 is best characterized for its indispensable role for definitive haematopoiesis and its involvement in haematological malignancies. However, more recently RUNX1 has been identified as a key regulator of adverse cardiac remodelling following myocardial infarction. This review discusses the role RUNX1 plays in the heart and highlights its therapeutic potential as a target to limit the progression of adverse cardiac remodelling and heart failure.

Engineered Deregulation of Expression in Yeast with Designed Hybrid-Promoter Architectures in Coordination with Discovered Master Regulator Transcription Factor.

Engineered promoters are key components in the cell-factory design, allowing precise and enhanced expression of genes. Promoters having exceptional strength are attractive candidates for designing metabolic engineering strategies for tailoring de novo production strategies that require directed evolution methods by engineering with de novo synthetic biology tools. Here, the custom-designed AOX1 hybrid-promoter architectures in coordination with targeted transcription factors are shown, transcriptionally rewired the expression over methanol-free substrate-utilization pathway(s) and converted methanol-dependent Pichia pastoris alcohol oxidase 1(AOX1) promoter (PAOX1 ) expression into a non-toxic carbon-source-regulated system. AOX1 promoter variants are engineered by replacing specified cis-regulatory DNA elements with synthetic Adr1, Cat8, and Aca2 cis-acting DNA elements for Mxr1, Cat8, and Aca1 binding, respectively. Applications of the engineered-promoters are validated for eGFP expression and extracellular human serum albumin production. The hybrid-promoter architecture designed with single Cat8 cis-acting DNA element deregulates the expression on ethanol. Compared with PAOX1 on methanol, the expression on ethanol is increased with i) PAOX1/Cat8-L3 (designed with single Cat8 cis-acting element) to 74%, ii) PAOX1/Adr1-L3/Cat8-L3 (designed with single- Cat8 and Adr1 cis-acting elements) to 85%, and for further consolidation of deregulated expression iii) PeAOX1 (designed with triplet- Cat8 and Adr1 cis-acting elements) 1.30-fold, at t = 20 h of batch cultivations.

T cells and their function in the immune response to viruses.

The development of CD4+ T helper cells is determined by the set of transcription factors and the genes these transcription factors transcribe. In this review, we describe the basic nature of Th1, Th2, Th9, Th17, T-follicular helper (Tfh), gamma delta (γδ) T cells, and T-regulatory (Treg) cells subsets, their master regulator transcription factors and their corresponding signature cytokine production profiles. Cellular immunity plays important role during virus infection. Optimal immune response to viral infections require a gentle balance of effector responses to clear the infected cells and regulatory mechanism to prevent immunopathology. The behavior of the helper cells differs with each virus - while in some cases, the response is beneficial; in other cases, it is harmful. We discuss the protective and pathological role of T cell immunity against influenza A virus (IAV), respiratory syncytial virus (RSV), immunodeficiency virus type 1 (HIV-1), and hepatitis B virus (HBV) infection. Keywords: T cell; cytokine; influenza virus; respiratory syncytial virus; hepatitis B virus; human immunodeficiency virus type 1.

In Vitro Direct Reprogramming of Mouse and Human Astrocytes to Induced Neurons.

Direct neuronal reprogramming, rewiring the epigenetic and transcriptional network of a differentiated cell type to neuron, apart from being a very promising approach for the treatment of brain injury and neurodegeneration, also offers a prime opportunity to investigate the molecular underpinnings of neuronal cell fate determination, as the precise molecular mechanisms that establish neuronal fate and diversity at the transcriptional and epigenetic level are incompletely understood. Recent studies from a number of groups, including ours, have shown that astrocytes can be directly reprogrammed into functional neurons in vitro and in vivo following ectopic overexpression of combinations of transcription factors, neurogenic proteins, miRNAs, and small chemical molecules.In this chapter we describe the protocols for in vitro converting primary cortical astrocytes of mouse and human origin to induced neurons, through forced expression of two neurogenic molecules, either each one alone or in combination: the master regulatory bHLH proneural transcription factor NEUROGENIN-2 (NEUROG2) and the neurogenic protein CEND1. Forced expression of each one of the two neurogenic proteins in primary astrocytes via retroviral gene transfer results in their direct conversion to subtype-specific induced neurons, while simultaneous coexpression of both molecules drives them predominantly toward acquisition of a neural precursor cell (NPC) state. Although mouse and human astrocytes exhibit differences in their reprogramming rate and particular characteristics, they can both get efficiently in vitro transdifferentiated to NPCs and induced neurons upon NEUROG2 or/and CEND1 forced expression using the reprogramming protocols described in the chapter, presenting valuable cellular platforms for mechanistic studies and in vivo applications to restore neurodegeneration.

Abstract B124: ERG mediated transcriptional regulation of DLX1 homeobox gene represents a novel mechanism underlying prostate cancer progression

Abstract Homeobox genes are the master regulatory transcription factors involved in the embryonic development and their deregulation in homeostatic biological processes can lead to cancer initiation and progression. A member of Distal less homeobox gene family (DLX), namely DLX1 plays pivotal role in the craniofacial, jaw and GABAergic (gamma aminobutyric acid) interneuron development. Higher expression levels of DLX1 has been associated with primary and metastatic prostate tumor. Moreover, DLX1 and HOXC6 are well-established diagnostic biomarkers for the early detection of prostate cancer (PCa). However, the mechanism involved in DLX1 up-regulation and functional significance in metastatic castration-resistant prostate cancer (mCRPC) progression remains unexplored. Here, we show that benign prostate epithelial cells acquire several oncogenic properties upon ectopic overexpression of DLX1. Similarly, CRISPR/Cas9 mediated DLX1 knockout in castrate-resistant 22RV1 cells show reduced proliferation, invasion, foci formation in cell-based assays, and a remarkable reduction (~80%) in tumor burden in mouse xenograft model, confirming its role in tumor progression. Moreover, our global gene expression profiling data established the role of DLX1 in regulating critical cancer hallmarks such as epithelial-to-mesenchymal transition (EMT), apoptosis and cell cycle regulation. We also demonstrate positive association between DLX1 and the most recurrent TMPRSS2-ERG gene fusion in many independent PCa cohorts, wherein, ~96% of the TMPRSS2-ERG fusion positive patients also harbour higher level of DLX1. Our ChIP-qPCR and luciferase-reporter assay data show that ERG occupies the DLX1 promoter region, and orchestrate its transcriptional control. Nevertheless, a subset of ERG-fusion negative patients also exhibits a higher DLX1 expression, where androgen receptor (AR) and AR variant 7 (AR-V7) plays critical role in transcriptional regulation of DLX1 in an ERG-independent manner. Since, Bromodomain and extra-terminal domain inhibitors (BETi) are known to inhibit the transcriptional activity of AR, AR-V7 and ERG, we examined the effect of BETi on DLX1. Interestingly, a significant decrease in the expression of DLX1 in BETi treated PCa cell lines with a concomitant loss of their oncogenic potential was observed. Taken together, our findings reveal that DLX1 serves as an oncogene thereby regulating several oncogenic properties associated with PCa progression. We discovered a novel transcriptional regulatory network involving ERG dependent up-regulation of DLX1 in TMPRSS2-ERG fusion positive PCa, while AR and AR-V7 governed expression in ERG-independent manner in CRPC cells. Conclusively, our findings suggest that BET domain inhibitors can be used as an adjuvant therapy for DLX1-positive subset of metastatic castration resistant prostate cancer patients. Citation Format: Sakshi Goel, Vipul Bhatia, Mahendra Shyamlal Palecha, Shannon Carskadon, Nallasivam Palanisamy, Bushra Ateeq. ERG mediated transcriptional regulation of DLX1 homeobox gene represents a novel mechanism underlying prostate cancer progression [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B124. doi:10.1158/1535-7163.TARG-19-B124

Randomized Open-Labeled Academic Trial Comparing Standard AZA Therapy with Combination of G-CSF with AZA in High Risk MDS Patients - Interim Analysis

Introduction: Myelodysplastic syndrome (MDS) is characterized by differentiation blockade, cytopenias with commontransfusion dependency and immune defects. Upon progression the myeloblasts accumulate and the patients become vulnerable to severe infection complications. Based on the Prague Charles University General Hospital registry (N=164, median age 73), the AZA therapy in higher-risk MDS patients results in median OS 13.8 Mo with ORR 48.5%. We also noted from our retrospective data that AZA-treated patients with higher G-CSF consumption had significantly reduced occurrence of Grade 4 neutropenias and longer OS (19 vs 16 Mo, p value 0.039). Rationale: To improve poor clinical outcomes we initiated a randomized open labeled academic trial that compares standard AZA therapy (A) with novel AZA-based therapy combination involving use of G-CSF added prior AZA (GA). Both AZA and also decitabine were preclinically shown to induce myeloid differentiation upon G-CSF preincubation. G-CSF binds its receptor in granulocytic precursors and neutrophils to stimulate their survival, proliferation, and differentiation via myeloid master regulator transcription factor and leukemia-suppressor PU.1. We also have previously shown that AZA increases PU.1. expression. Study design & Methods: GA/MDS-2013 (EudraCT No 2013-001639-38). Expected for enrollment are 134 patients, currently enrolled 53 patients (GA arm N=29, A arm N=24) with median age 74 years, M:F ratio 32:21 (GA 16:16, A 13:8),median IPSS-R 6, median follow up 11.2 Mo, median cycles of therapy 6. Diagnosis included:MDS (EB1, EB 2) with IPSS int-2/high (75%), MDS/AML<30% MB (22.5%), and CMML II (2.5%). Transplant candidates were excluded. Randomization is 2:1 for GA vs A arm. Primary endpoints: OS, PFS, time to AML transformation, ORR, infections & QoL. Secondary endpoints: biomarkers. Therapy schedule: 75mg/m2 of AZA 5-2-2, in GA: G-CSF s.c. injected 48 hrs before dose 1 and dose 6. G-CSF is measured in patient sera (prior therapy), myeloid surface markers are determined by flow cytometry (day -2, day 1, and day 9 of cycle 1). Genomic libraries from whole bone marrow are prepared by NEBNext Direct Kit involving 33 gene panel, sequencing runs are performed on Illumina platform. Statistics involved longitudinal multivariate data analysis including the joint models for the OS and response. Results: The presented data include 2.5 years since the beginning of the trial. Median survival for GA arm was 11 vs 6 Mo in the A arm. ORR (CR, CRm, PR, HI) was 56% in GA arm vs 33% in the A arm. Transformation to AML for both arms was comparable. The stratified longitudinal Cox proportional hazards model containing time-varying covariates together with the ordinal multilevel logistic mixed model were utilized. From this joint fitted model, a negative coefficient for the G-AZA treatment (significant p-value 0.0442) can be noticed in the case of the Cox Proportional Hazard part of the model. This means that G-AZA treatment improves patient survival. The estimated odds for the GA arm that responded to the therapy with remission rather than progression is 12.4x higher than for the A arm, controlling for the remaining patients' characteristics (p-value 0.0016).Both the GA and A arms are comparably tolerated. Data on serious infections and neutropenia gr4 were not yet available. The levels of G-CSF in sera prior the study in both arms (GA vs A) were comparable. Flow cytometry revealed G-CSF mediated upregulation of FCgRI (CD64) in the GA but not in the A arm. Multivariate analysis indicates the following: mutated genes: DNMT3A (p-value 0.0157), EZH2 (p-value 0.0091), TP53 (borderline p-value 0.0510), & CSF3R (p-value 0.0057) shorten the overall survival. The significant negative effects on response was noted for mutated EZH2 (p-value 0.0208) and CSF3R (p-value 0.0424) genes. Conclusions: The current results supported by different methods and statistics indicates a beneficial effect of G-CSF pre-treatment to standard AZA therapy in higher risk MDS patients. G-CSF pre-treatment to AZA increases OS and ORR. In addition, we identified biomarkers that are negatively associated with patient survival and response including EZH2, DNMT3A, TP53, & CSF3R. Grant Support: Ministry of Health, #16-27790A. Institutional resources: Progres Q49 & Q26, UNCE/MED/016, LQ1604, SVV 260374/2017, RVO-64165. Disclosures No relevant conflicts of interest to declare.

Reprogramming of Fibroblasts to Oligodendrocyte Progenitor-like Cells Using CRISPR/Cas9-Based Synthetic Transcription Factors.

SummaryCell lineage reprogramming via transgene overexpression of key master regulatory transcription factors has been well documented. However, the poor efficiency and lack of fidelity of this approach is problematic. Synthetic transcription factors (sTFs)—built from the repurposed CRISPR/Cas9 system—can activate endogenous target genes to direct differentiation or trigger lineage reprogramming. Here we explored whether sTFs could be used to steer mouse neural stem cells and mouse embryonic fibroblasts toward the oligodendrocyte lineage. We developed a non-viral modular expression system to enable stable multiplex delivery of pools of sTFs capable of transcriptional activation of three key oligodendrocyte lineage master regulatory genes (Sox10, Olig2, and Nkx6-2). Delivery of these sTFs could enhance neural stem cell differentiation and initiated mouse embryonic fibroblast direct reprograming toward oligodendrocyte progenitor-like cells. Our findings demonstrate the value of sTFs as tools for activating endogenous genes and directing mammalian cell-type identity.

Chemotherapy-Induced Distal Enhancers Drive Transcriptional Programs to Maintain the Chemoresistant State in Ovarian Cancer.

Chemoresistance is driven by unique regulatory networks in the genome that are distinct from those necessary for cancer development. Here, we investigate the contribution of enhancer elements to cisplatin resistance in ovarian cancers. Epigenome profiling of multiple cellular models of chemoresistance identified unique sets of distal enhancers, super-enhancers (SE), and their gene targets that coordinate and maintain the transcriptional program of the platinum-resistant state in ovarian cancer. Pharmacologic inhibition of distal enhancers through small-molecule epigenetic inhibitors suppressed the expression of their target genes and restored cisplatin sensitivity in vitro and in vivo. In addition to known drivers of chemoresistance, our findings identified SOX9 as a critical SE-regulated transcription factor that plays a critical role in acquiring and maintaining the chemoresistant state in ovarian cancer. The approach and findings presented here suggest that integrative analysis of epigenome and transcriptional programs could identify targetable key drivers of chemoresistance in cancers. SIGNIFICANCE: Integrative genome-wide epigenomic and transcriptomic analyses of platinum-sensitive and -resistant ovarian lines identify key distal regulatory regions and associated master regulator transcription factors that can be targeted by small-molecule epigenetic inhibitors.

Restriction of Cellular Plasticity of Differentiated Cells Mediated by Chromatin Modifiers, Transcription Factors and Protein Kinases.

Ectopic expression of master regulatory transcription factors can reprogram the identity of specific cell types. The effectiveness of such induced cellular reprogramming is generally greatly reduced if the cellular substrates are fully differentiated cells. For example, in the nematode C. elegans, the ectopic expression of a neuronal identity-inducing transcription factor, CHE-1, can effectively induce CHE-1 target genes in immature cells but not in fully mature non-neuronal cells. To understand the molecular basis of this progressive restriction of cellular plasticity, we screened for C. elegans mutants in which ectopically expressed CHE-1 is able to induce neuronal effector genes in epidermal cells. We identified a ubiquitin hydrolase, usp-48, that restricts cellular plasticity with a notable cellular specificity. Even though we find usp-48 to be very broadly expressed in all tissue types, usp-48 null mutants specifically make epidermal cells susceptible to CHE-1-mediated activation of neuronal target genes. We screened for additional genes that allow epidermal cells to be at least partially reprogrammed by ectopic che-1 expression and identified many additional proteins that restrict cellular plasticity of epidermal cells, including a chromatin-related factor (H3K79 methyltransferase, DOT-1.1), a transcription factor (nuclear hormone receptor NHR-48), two MAPK-type protein kinases (SEK-1 and PMK-1), a nuclear localized O-GlcNAc transferase (OGT-1) and a member of large family of nuclear proteins related to the Rb-associated LIN-8 chromatin factor. These findings provide novel insights into the control of cellular plasticity.

Master regulator analysis of paragangliomas carrying SDHx, VHL, or MAML3 genetic alterations

BackgroundSuccinate dehydrogenase (SDH) loss and mastermind-like 3 (MAML3) translocation are two clinically important genetic alterations that correlate with increased rates of metastasis in subtypes of human paraganglioma and pheochromocytoma (PPGL) neuroendocrine tumors. Although hypotheses propose that succinate accumulation after SDH loss poisons dioxygenases and activates pseudohypoxia and epigenomic hypermethylation, it remains unclear whether these mechanisms account for oncogenic transcriptional patterns. Additionally, MAML3 translocation has recently been identified as a genetic alteration in PPGL, but is poorly understood. We hypothesize that a key to understanding tumorigenesis driven by these genetic alterations is identification of the transcription factors responsible for the observed oncogenic transcriptional changes.MethodsWe leverage publicly-available human tumor gene expression profiling experiments (N = 179) to reconstruct a PPGL tumor-specific transcriptional network. We subsequently use the inferred transcriptional network to perform master regulator analyses nominating transcription factors predicted to control oncogenic transcription in specific PPGL molecular subtypes. Results are validated by analysis of an independent collection of PPGL tumor specimens (N = 188). We then perform a similar master regulator analysis in SDH-loss mouse embryonic fibroblasts (MEFs) to infer aspects of SDH loss master regulator response conserved across species and tissue types.ResultsA small number of master regulator transcription factors are predicted to drive the observed subtype-specific gene expression patterns in SDH loss and MAML3 translocation-positive PPGL. Interestingly, although EPAS1 perturbation is detectible in SDH-loss and VHL-loss tumors, it is by no means the most potent factor driving observed patterns of transcriptional dysregulation. Analysis of conserved SDH-loss master regulators in human tumors and MEFs implicated ZNF423, a known modulator of retinoic acid response in neuroblastoma. Subsequent functional analysis revealed a blunted cell death response to retinoic acid in SDH-loss MEFs and blunted differentiation response in SDH-inhibited SH-SY5Y neuroblastoma cells.ConclusionsThe unbiased analyses presented here nominate specific transcription factors that are likely drivers of oncogenic transcription in PPGL tumors. This information has the potential to be exploited for targeted therapy. Additionally, the observation that SDH loss or inhibition results in blunted retinoic acid response suggests a potential developmental etiology for this tumor subtype.

Molecular Modeling of the PTF‐J and PTF‐L Heterotrimeric Complexes, 3‐D Printing, Overexpression, Purification and Structural Analysis of the Complexes using Cryo‐Electron Microscopy and Ptf1a gene Expression Patterns During Pancreas Development in Zebrafish

Dallas Independent School District biomedical research students study the master regulatory transcription factor heterotrimeric complexes PTF‐J and PTF‐L that are required for the early and late developmental cascade of the pancreas. The PTF‐J and PTF‐L complexes are composed of a common E‐box protein E12/47, Ptf1a. and either RbpJ or RbpL. The PTF‐J complex is required for the early developmental stage of the pancreas and during the secondary transition of pancreas development, RbpJ is replaced by RbpL generating the PTF‐L complex, which is required for the final maturation steps for the development of the exocrine pancreas. In the current studies biomedical research student utilized the known structures for RbpJ, RpbL, the MyoD bHLH domain and E12/47 bHLH domain to generate molecular models bound to the enhancer sequence found in genes regulated by the heterotrimeric complexes during pancreas development. The PTF‐J and PTF‐L enhancer sequence is composed of an E‐box sequence separated by one to three helical turns from a TC‐box sequence. Biomedical research students performed energy minimization of the complexes and generate a model using 3‐D printing technology. Biomedical research students also study the temporal and spatial expression patterns of the PTF‐J and PTF‐L complexes during pancreas development in Zebrafish using immunofluorescence. The overall goals the program are threefold: first, to expose enthusiastic high school students to an authentic hands‐on biomedical research project, second, to solve the structure of the complexes using Cryo‐Electron Microscopy and third to identify the temporal and spatial expression pattern of the Ptf1a protein during pancreas development in Zebrafish.Support or Funding InformationJunior League of DallasThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Epigenetical Targeting of the FOXP3 Gene by S-Adenosylmethionine Diminishes the Suppressive Capacity of Regulatory T Cells Ex Vivo and Alters the Expression Profiles.

Regulatory T cells (Treg cells), a subgroup of CD4 lymphocytes, play a crucial role in serving as an immune suppressor and in maintaining peripheral tolerance. As the accumulation of Treg cells in the tumor microenvironment is significantly associated with a decreased survival time of patients, they are considered as an important therapeutic target in the immunotherapy of human cancers. These cells are either derived from the thymus, which are called (CD4CD25CD127) natural Treg cells (nTreg cells), or they are generated from CD4CD25 naive T cells by transforming growth factor-beta 1 and interleukin 2 (IL-2) in the periphery, which are called induced Treg cells (iTreg cells). Although iTreg cells are unstable, nTreg cells stably express forkhead box P3 (FOXP3) protein. Moreover, nTreg cells can be classified as memory (CD45RA) and naive (CD45RA) Treg cells, and this classification is based on the expression of CD45RA. FOXP3, which is a master regulator transcription factor, is essential for the functions of Treg cells, and it is mainly controlled by epigenetic mechanisms. The cyclooxygenase 2 (COX2)/prostaglandin E2 (PGE2) pathway is also reported to contribute to the regulatory functions of tumor-infiltrating Treg cells. As a new approach, we investigated whether S-adenosylmethionine (SAM), a substrate of DNA methyltransferase, attenuates the immune-suppressive capacity of the naive subtype of nTreg cells (CD4CD25CD127CD45RA). Moreover, we examined the effects of PGE2/COX2 pathway blockers on the suppressive capacity of Treg cells. We found that SAM diminished the suppression competency of Treg cells by decreasing the FOXP3 mRNA and protein levels in a dose-dependent manner. SAM increased the DNA methylation of FOXP3 at the first intron site. In addition, SAM decreased the mRNA and protein levels of the IL-10 cytokine, which has suppressive roles in the immune system. Moreover, mRNA levels of interferon gamma (IFNG) were found to be increased. COX2 inhibition and blockage of PGE2 receptors also reduced the protein and mRNA levels of IL-10, but they did not exhibit any significant effect on Treg cells' suppression in the coculture system. Our results show that SAM might be considered and investigated as a promising agent for immunotherapy in the future.

Cinnamic acid activates PPARα to stimulate Lysosomal biogenesis and lower Amyloid plaque pathology in an Alzheimer's disease mouse model

The response of the lysosomes, the waste clearance machinery of the cell, to different environmental stimuli is coordinated by a gene network with a master regulator Transcription factor EB (TFEB) at the core. Disruption of multiple facets of the lysosomal and autophagic network has been linked to various neurodegenerative and lysosomal storage disorders, making TFEB an attractive therapeutic target to rescue or augment lysosomal function under pathological scenario. In this study, we demonstrate that cinnamic acid, a naturally occurring plant-based product, induces lysosomal biogenesis in mouse primary brain cells via upregulation of TFEB. We delineate that cinnamic acid activates the nuclear hormone receptor PPARα to transcriptionally upregulate TFEB and stimulate lysosomal biogenesis. Moreover, using in-silico and biochemical approaches we established that cinnamic acid serves as a potent ligand for peroxisome proliferator-activated receptor α (PPARα). Finally, cinnamic acid treatment in male and female 5× Familial Alzheimer's disease (5XFAD) mice remarkably reduced cerebral amyloid-beta plaque burden and improved memory via PPARα. Therefore, stimulation of lysosomal biogenesis by cinnamic acid may have therapeutic implications for treatment of Alzheimer's disease and other lysosomal disorders originating from accumulation of toxic protein aggregates.

Precise Modeling of IKZF1 Alterations in Human B-Cell Acute Lymphoblastic Leukemia Cell Lines Reveals Distinct Chemosensitivity, Homing, and Engraftment Properties

Around 20% of pediatric and the majority of adults with B-cell acute lymphoblastic leukemia (B-ALL) suffer relapse, and prognosis after relapse is very poor. Therefore, identifying those at risk for treatment failure and improving their outcome is imperative. In B-ALL, deletions and mutations of the gene IKAROS family zinc finger 1 (IKZF1) are associated with an increased risk of relapse. IKZF1 encodes the IKAROS protein, which is a master lymphoid regulatory transcription factor and chromatin remodeler. Somatic IKZF1 lesions are thought to be secondarily acquired, arising in lymphoblasts with existing driver genetic lesions, most commonly co-occurring with BCR-ABL1 fusion, activating kinase fusions of Ph-like disease and deregulated DUX4 and ERG. In B-ALL, mono- or bi-allelic deletions of the entire gene, as well as intragenic deletions occur. One of the most common perturbations of IKZF1 in B-ALL is an intragenic deletion of a 50-kilobase (kb) region containing exons 4-7, resulting in the expression of a dominant-negative isoform, IK6. Recently published clinical data show potentially conflicting results over the benefits of therapy intensification in IKZF1-mutant cases (Clappier et al., 2015; Hinze et al., 2017; & Yeoh, et al., 2018). Human cell models of these deletions are needed, as there may be unknown functional differences among mutation types, and the available body of data relies on clinical statistical associations, in vitro RNA interference, viral overexpression of IK6, and mouse models.We used the CRISPR/Cas9 system in the human B-ALL cell lines Nalm-6 and REH by electroporation with sgRNA-Cas9 ribonucleoprotein complexes (RNPs) to generate IKZF1-mutant clones. We identified single cell-derived clonal lines with IKZF1 frameshift mutations in one or both alleles by Sanger sequencing and TIDE decomposition. We confirmed ablation of protein expression by immunoblotting. We treated the IKZF1-mutant clonal cell lines with chemotherapeutic agents commonly used to treat B-ALL and calculated the IC50 by Annexin V/7-AAD double-negative population after 48-72 hour treatment. Compared to IKZF1-wild type Nalm-6 cells, Nalm-6 IKZF1-/- clones exhibited profound resistance to dexamethasone and modest but significant resistance to most other chemotherapeutics tested including vincristine, asparaginase, and daunorubicin. In contrast, these cell lines were more sensitive to the nucleoside analog, cytarabine (Panel A). We next analyzed gene expression profiles by RNA-seq and observed that IKZF1-/- clones are characterized by a stem cell-like gene expression signature and activation of the JAK/STAT pathway (Panel B). Transplantation into immunodeficient NOD scid gamma (NSG) mice demonstrated that IKZF1 deletion leads to enhanced engraftment, significantly increased bone marrow homing, and reduced survival time (Panel D).We also employed a novel CRISPR/Cas9 homology-directed repair (HDR) strategy to generate clonal cell lines expressing IK6 under control of the endogenous promoter, which represents a significant advantage to many previous studies utilizing viral overexpression. We electroporated the cells with sgRNA-Cas9 RNPs along with a 3kb commercially synthesized double-stranded DNA HDR template that knocks-in exon 8 with a GFP tag directly following exon 3. Using this strategy, we were able to isolate heterozygous clones (IKZF1IK6/+) from both Nalm-6 (Panel C) and REH cell lines using flow cytometry sorting for GFP-positive cells. We confirmed precise HDR by Sanger sequencing and immunoblotting. When transplanted into immunodeficient mice, IKZF1IK6/+ cells showed delayed engraftment and disease onset, but profound splenic infiltration, consistent with a more indolent, infiltrative disease phenotype (Panels D & E). Ongoing drug treatment assays suggest the chemosensitivity profiles of IKZF1IK6/+ and IKZF1IK6/- clonal cell lines are distinct from their isogenic IKZF1-/- counterparts.Our data support clinical studies reporting that IKZF1-mutated B-ALL is an aggressive, infiltrative, and treatment-resistant disease. Notable differences in drug response and in vivo dynamics in xenografts exist between IKZF1-/- cells and IKZF1IK6/+ cells. Detailed delineation of the exact IKZF1 status in ALL patients at diagnosis may be informative in more accurately determining risk stratification and the most effective therapeutic regimen. DisclosuresNo relevant conflicts of interest to declare.

Role of TLR4 in the Activation of a Pro-Tumor Phenotype of Mesenchymal Stromal Cells in Mutiple Myeloma

Introduction We have already demonstrated that myeloma mesenchymal stromal cells (MM-MSC) promote cancer immune evasion through the activation of myeloid derived suppressor cells and we hypothesized that MM-MSC could be polarized stromal cells to better ‘serve’ cancer (Giallongo et al, Oncotarget 2016). Since it has been demonstrated that specific Toll-like receptors (TLR) can drive MSC activation status, including two distinct phenotypes defined MSC1 (TLR4-dependent) or MSC2 (TLR3-dependent), we evaluated the effect of TLR activation on MM-MSCMethods Healthy Peripheral blood mononucleated cells (PBMC) were cultured with MSC for 6 days; then neutrophils were isolated using magnetic microbeads and their immunosuppressive activity was evaluated by their ability to suppress activation of CFSE+ T cells. Immunocompetent adult Zebrafish was used as in vivo model for myeloma cells engraftment. Tumor xenograft was measured by tomography 6 days post-injection.Results Using specific agonists for TLR4 (LPS) or TLR3 (poly(I:C)) for 24 h, we observed that healthy MSC acquired the same immunological alteration of MM-MSC after a pre-treatment with LPS. Indeed, MSC1 polarization of HC-MSC induced neutrophils to become immunosuppressive. Moreover, wester blotting analysis confirmed the activation of TLR4/MyD88 pathway in MM-MSC but not in healthy control-MSC (HC-MSC).To investigate if the polarization status of MM-MSC could promote tumor-growth in vivo, a mixtures of fluorescently labeled MM cells plus HC- or MM-MSC were implanted in zebrafish. After six days, the animals co-injected with plasma cells (PC) and MM-MSC showed enhanced tumor colonization and growth (calculated as tumor area) compared with zebrafish injected with PC and HC-MSC (control) (p<0.05). Flow cytometry detection of hCD138+ cells confirmed less MM cells in zebrafish injected with PC and HC-MSC (p=0.001). Therefore, we analyzed the expression of the master regulator transcription factors for Th1/Th2 (tbx21 and gata3) and Th1- and Th2-type cytokines to better assess in vivo the involvement of the immune escape mechanisms promoted by co-injection of PC with MM-MSC. As compared to control animals, gata3, IL-4 and IL-13 were significantly up-regulated in zebrafish injected with PC plus MM-MSC, revealing a Th2 responce. Next, we used TAK-242, a blocker of signaling transduction mediated by the intracellular domain of TLR4, to inhibit its signaling in MM-MSC before injection in zebrafish. Animals co-injected with PC and MM-MSC pre-treated with TAK-242 showed a reduction of 41% of tumor area compared to zebrafish injected with PC and MM-MSC (p<0.001). Moreover, the same animals showed the up-regulation of tbx21 and INFγ (Th1 response).To examine if PC play a role in MSC polarization, before performing co-cultures with PBMC, we pre-treated HC-MSC with MM cell lines (U266, H929, MM1S). PC pre-treatment drove healthy MSC to activate neutrophils in immunosuppressive cells in vitro. Therefore, we investigated if PC activated TLR4 pathway in healthy MSC and found that PC induced nuclear translocation of NFkB and subsequently of IRF3 in HC-MSC, indicating the involvement of TLR4-MyD88-dependent and independent pathways in MSC commitment. Injecting zebrafish with MM cells and HC-MSC co-cultured or not for 24h with PC, we observed that animals injected with HC-MSC pre-treated with PC showed more tumor engraftment (p=0.001) and 15±2,8% more hCD138 (p=0.001). Inhibition of TLR4 signaling during co-culture in vitro of HC-MSC with MM cells led to a reduction of tumor growth (p=0.001) and hCD138 infiltrate (from 17,9±7% to 2,8±1,2%; p=0.0006).Conclusion: TLR4 signaling plays a key role in MSC transformation by inducing a pro-tumor phenotype associated with a permissive microenvironment that circumvents the immune response and allows a better tumor engraftment. DisclosuresPalumbo:Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees. Di Raimondo:Takeda: Honoraria, Research Funding; Celgene: Honoraria.