Abstract MP12: The
            Mef2c
            Transcription Factor Regulates The Renin Cell Identity

Introduction: The Renin-Angiotensin-System is essential to maintain blood pressure and fluid electrolyte homeostasis. Because precise regulation of expression and release of renin is critical for survival, understanding the molecular regulation of the renin cell identity is a vital area of study. Advances in epigenetics have enabled finer dissection of chromatin factors which maintain the identity of the renin cell. By studying genes with heightened accessibility profiles that are unique to the JG cell, we now have the capacity to unravel the determinants of the renin cell identity. Hypothesis: That transcription factors central to the governance of renin cell identity can be identified through the Assay for Transposase Accessible Chromatin (ATAC-seq) differential accessibility analysis. Methods: Native renin cell ATAC-seq was compared to existing ENCODE ATAC-seq datasets from 40 other cell types to define regions/peaks which characterize the JG program. Peaks with high intensity and ≥2-fold increase in signal were selected for Motif analysis to search for transcription factors (TFs) whose consensus sequence is enriched in those regions. Identified TFs were then selected for validation by in-situ hybridization and conditional deletion in renin cells. Results: 1) The Mef2c transcription factor was identified as having a consensus sequence in regulatory regions unique to the JG cell. It has clear expression in RNA-seq of renin cells (65 transcripts per million, n=3) and a predicted binding site in the renin gene. These results were validated by in-situ hybridization where signal localized at the JG area was detected in concordance with our in-silico results. 2) We generated Mef2c conditional knockout animals using our Ren1d-Cre mouse to study the effect in renin expression and identity. These mice displayed reduced renin immunostaining at the JG area and a 40% reduction in renin mRNA expression by qPCR from kidney cortices relative to wild-type (n=2, preliminary data). Conclusions: Our studies identified Mef2c as a TF target which likely has an essential role in maintaining and preserving renin cell identity. Experiments involving transcriptomics and epigenomics are ongoing to understand the changes wrought by Mef2c deletion in renin cells.

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Abstract 33: Unlocking Reprogramming Capability: Silencing Antiplasticity Gene p63 Enhances the Reprogramming of Fibroblasts into Induced Cardiomyocytes

Circulation Research ◽

10.1161/res.119.suppl_1.33 ◽

2016 ◽

Vol 119 (suppl_1) ◽

Author(s):

Vivekkumar Patel ◽

Austin Cooney ◽

Elsa Flores ◽

Vivek Singh ◽

Megumi Mathison ◽

...

Keyword(s):

Transcription Factors ◽

Troponin T ◽

Cardiac Fibroblasts ◽

Fold Increase ◽

Cellular Reprogramming ◽

Embryonic Fibroblasts ◽

Reprogramming Efficiency ◽

Cardiac Transcription Factors

Objective: In situ cellular reprogramming of cardiac fibroblasts into (induced) cardiomyocytes (iCMs) represents a promising new potential intervention for the treatment of heart failure. Despite encouraging in vivo data in rodent myocardial infarction models, the relative resistance of human cells to reprogramming may be a significant barrier to the clinical application of this new therapy. We hypothesized that knockdown of the anti-plasticity gene p63 could therefore be used to enhance cellular reprogramming efficiency. Methods: p63 knockout (KO) murine embryonic fibroblasts (MEFs) and MEFs treated with p63 silencing shRNA were assessed for expression of the cardiomyocyte marker Cardiac Troponin T (cTnT) and pro-cardiogenic genes, with or without the treatment with known cardiac transcription factors Hand2 and Myocardin (HM). Results: After 3 wks in culture, expression of the cardiomyocyte marker cTnT (FACS) was significantly greater in p63 KO MEFs than in wild-type (WT) MEFs or WT MEFs treated with transcription factors Hand2 and Myocardin (39% ± 8%, 2.0% ± 1% and 2.7 ± 0.3%, respectively, p < 0.05). Treatment of p63 KO MEFs with Hand2 and Myocardin further increased cTnT expression up to 74% ± 3%. Treatment of WT MEFs with p63 shRNA likewise yielded a 20-fold increase in cTnT expression (qPCR) without HM and a 600-fold increase with HM when compared to non-silencing shRNA treated MEFs. Consistent with these findings, p63 KO or p63 shRNA-treated MEFs demonstrated increased expression (qPCR) of pro-cardiogenic genes Gata4, Mef2c and Tbx5 compared to naïve or non-silencing shRNA treated MEFs. After treatment with p63 shRNA, adult human epidermal cells also demonstrated increased expression of cTnT, myosin heavy chain and pro-cardiogenic genes when analyzed by qPCR. Conclusions: Downregulation of the anti-plasticity gene p63 enhances cellular reprogramming efficiency and iCM generation, as reflected in the increased expression of the cardiomyocyte marker cTnT and pro-cardiogenic genes Gata4, Mef2c and Tbx5. Use of such cellular plasticity enhancing strategies may be a useful strategy to overcome barriers to cellular reprogramming in the clinical arena.

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C/ebpα and Pu.1 Are Members of a Critical Regulatory Network Required for Hoxa9-Mediated Immortalization

Blood ◽

10.1182/blood.v120.21.650.650 ◽

2012 ◽

Vol 120 (21) ◽

pp. 650-650

Author(s):

Cailin Collins ◽

Jingya Wang ◽

Joel Bronstein ◽

Jay L. Hess

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Target Genes ◽

De Novo ◽

Conflicts Of Interest ◽

Epigenetic Modifications ◽

Conditional Knockout ◽

Motif Analysis ◽

Myeloid Leukemias

Abstract Abstract 650 HOXA9 is a homeodomain-containing transcription factor that plays important roles in both development and hematopoiesis. Deregulation of HOXA9 occurs in a variety of acute lymphoid and myeloid leukemias and plays a key role in their pathogenesis. More than 50% of acute myeloid leukemia (AML) cases show up-regulation of HOXA9, which correlates strongly with poor prognosis. Nearly all cases of AML with mixed lineage leukemia (MLL) translocations have increased HOXA9 expression, as well as cases with mutation of the nucleophosmin gene NPM1, overexpression of CDX2, and fusions of NUP98. Despite the crucial role that HOXA9 plays in development, hematopoiesis and leukemia, its transcriptional targets and mechanisms of action are poorly understood. Previously we identified Hoxa9 and Meis1 binding sites in myeloblastic cells, profiled their epigenetic modifications, and identified the target genes regulated by Hoxa9. Hoxa9 and Meis1 co-bind at hundreds of promoter distal, highly evolutionarily conserved sites showing high levels of histone H3K4 monomethylation and CBP/p300 binding characteristic of enhancers. Hoxa9 association at these sites correlates strongly with increases in histone H3K27 acetylation and activation of downstream target genes, including many proleukemic gene loci. De novo motif analysis of Hoxa9 binding sites shows a marked enrichment of motifs for the transcription factors in the C/EBP and ETS families, and C/ebpα and the ETS transcription factor Pu.1 were found to cobind at Hoxa9-regulated enhancers. Both C/ebpα and Pu.1 are known to play critical roles in the establishment of functional enhancers during normal myeloid development and are mutated or otherwise deregulated in various myeloid leukemias. To determine the importance of co-association of Hoxa9, C/ebpα and Pu.1 at myeloid enhancers, we generated cell lines from C/ebpα and Pu.1 conditional knockout mice (kindly provided by Dr. Daniel Tenen, Harvard University) by immortalization with Hoxa9 and Meis1. In addition we transformed bone marrow with a tamoxifen-regulated form of Hoxa9. Strikingly, loss of C/ebpα or Pu.1, or inactivation of Hoxa9, blocks proliferation and leads to myeloid differentiation. ChIP experiments show that both C/ebpα and Pu.1 remain bound to Hoxa9 binding sites in the absence of Hoxa9. After the loss of Pu.1, both Hoxa9 and C/ebpα dissociate from Hoxa9 binding sites with a corresponding decrease in target gene expression. In contrast, loss of C/ebpα does not lead to an immediate decrease in either Hoxa9 or Pu.1 binding, suggesting that C/ebpα may be playing a regulatory as opposed to a scaffolding role at enhancers. Current work focuses on performing ChIP-seq analysis to assess how C/ebpα and Pu.1 affect Hoxa9 and Meis1 binding and epigenetic modifications genome-wide, and in vivo leukemogenesis assays to confirm the requirement of both Pu.1 and C/ebpα in the establishment and maintenance of leukemias with high levels of Hoxa9. Collectively, our findings implicate C/ebpα and Pu.1 as members of a critical transcription factor network required for Hoxa9-mediated transcriptional regulation in leukemia. Disclosures: No relevant conflicts of interest to declare.

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Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data

F1000Research ◽

10.12688/f1000research.10041.1 ◽

2017 ◽

Vol 6 ◽

pp. 372 ◽

Cited By ~ 7

Author(s):

Delasa Aghamirzaie ◽

Karthik Raja Velmurugan ◽

Shuchi Wu ◽

Doaa Altarawy ◽

Lenwood S. Heath ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Transcription Factors ◽

Chromatin Immunoprecipitation ◽

Target Genes ◽

Regulation Of Gene Expression ◽

Data Sets ◽

Motif Analysis ◽

Chromatin Immunoprecipitation Sequencing

Motivation: The increasing availability of chromatin immunoprecipitation sequencing (ChIP-Seq) data enables us to learn more about the action of transcription factors in the regulation of gene expression. Even though in vivo transcriptional regulation often involves the concerted action of more than one transcription factor, the format of each individual ChIP-Seq dataset usually represents the action of a single transcription factor. Therefore, a relational database in which available ChIP-Seq datasets are curated is essential. Results: We present Expresso (database and webserver) as a tool for the collection and integration of available Arabidopsis ChIP-Seq peak data, which in turn can be linked to a user’s gene expression data. Known target genes of transcription factors were identified by motif analysis of publicly available GEO ChIP-Seq data sets. Expresso currently provides three services: 1) Identification of target genes of a given transcription factor; 2) Identification of transcription factors that regulate a gene of interest; 3) Computation of correlation between the gene expression of transcription factors and their target genes. Availability: Expresso is freely available at http://bioinformatics.cs.vt.edu/expresso/

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Abstract 611: AP-1 and ETS Family Transcription Factors Co-localize at Enhancers in Human Aortic Endothelial Cells

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvb.35.suppl_1.611 ◽

2015 ◽

Vol 35 (suppl_1) ◽

Author(s):

Nicholas T Hogan ◽

Casey E Romanoski ◽

Michael T Lam ◽

Christopher K Glass

Keyword(s):

Endothelial Cells ◽

Transcription Factor ◽

Transcription Factors ◽

De Novo ◽

Regulatory Elements ◽

Specific Gene ◽

Motif Analysis ◽

Aortic Endothelial Cells ◽

Human Aortic Endothelial Cells ◽

Aortic Endothelial

Introduction: Sequence-specific transcription factors bind DNA regulatory elements and play a key role in establishing cellular identity. Studies comparing macrophages to B cells have revealed that small numbers of such collaborative or lineage-determining transcription factors (LDTF) establish distinct enhancers in each cell type. These factors also allow for the binding of signal dependent transcription factors. Here we present data which suggest members of the AP-1, ETS, and STAT transcription factor families serve as collaborative transcriptional regulators in human aortic endothelial cells (HAEC). Hypothesis: We hypothesize that a set of AP-1 and ETS transcription factors collaborate to establish key endothelial cell enhancers. Methods: Working in HAEC, we measured poised and active enhancers using ChIP-seq for the epigenetic histone modifications H3K4me2 and H3K27Ac, performed motif analysis, and measured transcription factor binding for candidate factors. Knockdowns of JUN, ERG, and STAT3 followed by RNA-seq were used to evaluate altered enhancer function and gene targets of candidate factors. Results: Our de novo motif analysis revealed that motifs for ETS and AP-1 transcription factors are highly enriched at HAEC enhancers. ChIP-seq experiments for JUN, JUNB, ERG, and STAT3 showed between 8,000 and 55,000 intergenic peaks for each factor. Together these peaks bind 50% of poised enhancers, with a subset co-localizing at these sites. Gene ontology analysis showed that gene targets of these enhancers are involved in endothelial-specific functions. Further, knockdown of JUN, ERG, and STAT3 resulted in a twofold or greater change in expression of hundreds of HAEC transcripts. Conclusion: The genome-wide pattern of JUN, JUNB, ERG, and STAT3 co-localization at enhancers in HAEC suggests these factors serve as key regulators that collaboratively modulate endothelial-specific gene expression. Further investigation of candidate lineage-determining transcription factors using pro-atherogenic signals could reveal regulatory mechanisms of disease-relevant endothelial transcriptional programs.

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Pitx2 transcription factor

10.12681/eadd/45754 ◽

2019 ◽

Author(s):

Ισμήνη Ροζάνη

Keyword(s):

Transcription Factor ◽

Superior Colliculus ◽

Subthalamic Nucleus ◽

Conditional Knockout ◽

Knock Out

Η πρωτεΐνη Pitx2 ανήκει στην ομάδα των μεταγραφικών παραγόντων που φέρουν ομοιοεπικράτεια (homeodomain) και οι οποίοι είναι γνωστοί για τη συμμετοχή τους σε σημαντικές αναπτυξιακές λειτουργίες, όπως η νευρογένεση και η δημιουργία προτύπου σώματος. Μεταλλάξεις στο γονίδιο της Pitx2 στον άνθρωπο εμπλέκονται στην εμφάνιση ενός αυτοσωμικού επικρατούς συνδρόμου, του συνδρόμου Axenfeld-Rieger, που επηρεάζει πολλαπλά όργανα, με προεξάρχοντες τους οφθαλμούς, τους οδόντες, την καρδιά και τον ομφαλό. Η βασική έρευνα επίσης υποδεικνύει ότι η πρωτεΐνη Pitx2 παίζει κομβικό ρόλο στην ανάπτυξη των αντίστοιχων οργάνων. Στο νωτιαίο μυελό η Pitx2 εκφράζεται σε ένα μικρό υποσύνολο των V0 διάμεσων νευρώνων που συνολικά προέρχονται από Dbx1+ προγονικούς νευρώνες. Αυτή η ομάδα των Pitx2+ νευρώνων διαχωρίζεται περαιτέρω σε δύο ίσες περίπου σε αριθμό νευρώνων υποομάδες, μια χολινεργική (V0c) και μια γλουταματεργική (V0g). Οι χολινεργικοί Pitx2 νευρώνες δημιουργούν μεγάλες, χολινεργικές συνάψεις στη μεμβράνη του σώματος και των κοντινών στο σώμα δενδριτών των κινητικών νευρώνων. Οι συνάψεις αυτές έχουν ονομαστεί C boutons και η προέλευσή τους παρέμενε άγνωστη μέχρι την ανακάλυψη των Pitx2 χολινεργικών διάμεσων νευρώνων. Διακοπή της χολινεργικής νευροδιαβίβασης μέσω των C boutons οδηγεί σε αδυναμία αύξησης του έργου συγκεκριμένων μυών του ποντικού σε απαιτητικές δοκιμές, όπως η κολύμβηση.Σκοπός της παρούσας διδακτορικής διατριβής είναι ο εντοπισμός της προέλευσης των C boutons που βρίσκονται στους κινητικούς νευρώνες του εγκεφαλικού στελέχους και η ανίχνευση Pitx2 νευρώνων στον εγκέφαλο ποντικών μετά τη γέννηση. Δείξαμε ότι και τα C boutons του στελέχους προέρχονται από Pitx2 νευρώνες κατ’ αναλογία με τους κινητικούς νευρώνες του νωτιαίου μυελού. Αυτό το αποτέλεσμα έρχεται σε αντίθεση με προηγούμενη δημοσίευση, που παρουσίαζε ότι τα C boutons του στελέχους προέρχονται από νευρώνες που εκφράζουν Pitx2 και από νευρώνες που δεν εκφράζουν. Πιστεύουμε ότι οι μοριακές τεχνικές που χρησιμοποιήθηκαν στην παρούσα διδακτορική εργασία είναι καταλληλότερες για την απάντηση αυτού του ερωτήματος. Επιπλέον, κατά την ανάλυση των περιοχών του εγκεφάλου στις οποίες εντοπίζονται Pitx2 νευρώνες, επιβεβαιώσαμε την ύπαρξη τους σε περιοχές που έχουν αναφερθεί στη βιβλιογραφία του εμβρυικού και νεογνικού εγκεφάλου του ποντικού, αλλά εντοπίσαμε και πληθυσμούς Pitx2 νευρώνων σε νέες θέσεις. Ένας από αυτούς τους πληθυσμούς είναι ο χολινεργικός Pitx2 πληθυσμός των μαστίων (mammillary area) του υποθαλάμου, ο οποίος μαζί με το χολινεργικό Pitx2 πληθυσμό του νωτιαίου μυελού και του στελέχους, αποτελούν τους μόνους χολινεργικούς Pitx2 πληθυσμούς του Κεντρικού Νευρικού Συστήματος και επομένως πιθανούς νευρώνες προέλευσης των C boutons του στελέχους.Δεύτερος στόχος της εργασίας αποτέλεσε η διερεύνηση του ρόλου του μεταγραφικού παράγοντα Pitx2 στην ανάπτυξη των νευρώνων του νωτιαίου μυελού. Κατά την μελέτη αυτή διαπιστώθηκαν αρκετοί παραλληλισμοί σε σχέση με το ρόλο του Pitx2 στην ανάπτυξη των Pitx2 νευρώνων του νωτιαίου μυελού και των Pitx2 νευρώνων του υποθαλαμικού πυρήνα (subthalamic nucleus) και του άνω διδυμίου (superior colliculus), όπως αυτοί έχουν περιγραφεί στη βιβλιογραφία. Χρησιμοποιήθηκαν δύο knock out μοντέλα ποντικών: στο πρώτο έλειπε η Pitx2 από όλο το σώμα του ποντικού (Pitx2 null) και παρουσίαζε εμβρυική θνητότητα και στο δεύτερο δεν εκφραζόταν Pitx2 στους νευρώνες που προέρχονται από Dbx1 προγονικούς νευρώνες (Pitx2 conditional knockout), όπως στους Pitx2 νευρώνες του νωτιαίου μυελού. Και στα δύο μοντέλα λείπει η ομοιοεπικράτεια και συντίθεται μόνο ένα μη ολοκληρωμένο και μη λειτουργικό Pitx2 πεπτίδιο, η ανίχνευση του οποίου με ανοσοφθορισμό ή in situ υβριδοποίηση οδηγεί στον εντοπισμό των νευρώνων που θα εξέφραζαν φυσιολογικά Pitx2 (ελλειμματικοί Pitx2 νευρώνες).Η πιο σημαντική παρατήρηση που προέκυψε από τη μελέτη των δύο μοντέλων έλλειψης Pitx2 είναι ότι η παρουσία της Pitx2 είναι απαραίτητη για την απόκτηση της σωστής θέσης στο χώρο, υποδεικνύοντας πιθανό ρόλο της στην μετανάστευση των Pitx2 νευρώνων του νωτιαίου μυελού κατά την ανάπτυξή τους. Επιπλέον, η έλλειψη Pitx2 οδηγεί σε απώλεια του χολινεργικού χαρακτήρα των V0c νευρώνων και κατ’ επέκταση στη μη δημιουργία C boutons στους κινητικούς νευρώνες του νωτιαίου μυελού. Εάν η απώλεια έκφρασης χολινεργικών δεικτών είναι απόρροια της έλλειψης Pitx2 ή συμβαίνει δευτερογενώς, λόγω της μη ορθής θέσης των ελλειμματικών Pitx2 νευρώνων και της προκύπτουσας απώλειας χωροταξικών πληροφοριών (positional cues), είναι ένα ερώτημα που βρίσκεται ακόμα υπό διερεύνηση. Η έλλειψη της Pitx2 επηρεάζει και τον αριθμό των ελλειμματικών Pitx2 νευρώνων με τρόπο που εξαρτάται από την ηλικία που εξετάζεται.Τα αποτελέσματα της παρούσας έρευνας, που εστιάζει στη μελέτη της ανατομίας και της συνδεσιμότητας του κυκλώματος των Pitx2 νευρώνων και στο ρόλο της πρωτεΐνης Pitx2 στην ανάπτυξη διάμεσων νευρώνων του νωτιαίου μυελού, συνεισφέρουν στη διασύνδεση της μοριακής ταυτότητας με τη χαρτογράφηση και τη λειτουργία των νευρωνικών κυκλωμάτων δημιουργώντας μία βάση για την κατανόησης της φυσιολογίας και της παθολογίας του Κεντρικού Νευρικού Συστήματος.

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The transcription factor Zeb2 regulates development of conventional and plasmacytoid DCs by repressing Id2

Journal of Experimental Medicine ◽

10.1084/jem.20151715 ◽

2016 ◽

Vol 213 (6) ◽

pp. 897-911 ◽

Cited By ~ 70

Author(s):

Charlotte L. Scott ◽

Bieke Soen ◽

Liesbet Martens ◽

Nicolas Skrypek ◽

Wouter Saelens ◽

...

Keyword(s):

Dendritic Cells ◽

Transcription Factor ◽

Transcription Factors ◽

Chromatin Immunoprecipitation ◽

Conditional Knockout ◽

Altered Expression ◽

E Box ◽

A Cell ◽

Plasmacytoid Dcs ◽

Direct Target

Plasmacytoid dendritic cells (DCs [pDCs]) develop from pre-pDCs, whereas two lineages of conventional DCs (cDCs; cDC1s and cDC2s) develop from lineage-committed pre-cDCs. Several transcription factors (TFs) have been implicated in regulating the development of pDCs (E2-2 and Id2) and cDC1s (Irf8, Id2, and Batf3); however, those required for the early commitment of pre-cDCs toward the cDC2 lineage are unknown. Here, we identify the TF zinc finger E box–binding homeobox 2 (Zeb2) to play a crucial role in regulating DC development. Zeb2 was expressed from the pre-pDC and pre-cDC stage onward and highly expressed in mature pDCs and cDC2s. Mice conditionally lacking Zeb2 in CD11c+ cells had a cell-intrinsic reduction in pDCs and cDC2s, coupled with an increase in cDC1s. Conversely, mice in which CD11c+ cells overexpressed Zeb2 displayed a reduction in cDC1s. This was accompanied by altered expression of Id2, which was up-regulated in cDC2s and pDCs from conditional knockout mice. Zeb2 chromatin immunoprecipitation analysis revealed Id2 to be a direct target of Zeb2. Thus, we conclude that Zeb2 regulates commitment to both the cDC2 and pDC lineages through repression of Id2.

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Genome-Wide Enhancer Analysis Reveals the Role of AP-1 Transcription Factor in Head and Neck Squamous Cell Carcinoma

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.701531 ◽

2021 ◽

Vol 8 ◽

Author(s):

Chen-Yu Wang ◽

Guang-Tao Yu ◽

Chuan Gao ◽

Ji Chen ◽

Qing-Lan Li ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Transcription Factors ◽

Cell Carcinoma ◽

Head And Neck ◽

Squamous Cell ◽

Conditional Knockout ◽

Neck Squamous Cell Carcinoma ◽

Motif Analysis ◽

Super Enhancer ◽

Genome Wide

Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers in the world, but its epigenomic features have not been determined. Here, we studied the chromatin landscape of active enhancers of HNSCC head tumor tissues by performing H3K27ac and H3K4me1 ChIP-Seq with a Tgfbr1/Pten double conditional knockout HNSCC mouse model. We identified 1,248 gain variant enhancer loci (VELs) and 2,188 lost VELs, as well as 153 gain variant super enhancer loci (VSELs) and 234 lost VSELs. Potentially involved transcription factors were predicted with motif analysis, and we identified AP-1 as one of the critical oncogenic transcription factors in HNSCC and many other types of cancer. Combining transcriptomic and epigenomic data, our analysis also showed that AP-1 and histone modifications coordinately regulate target gene expression in HNSCC. In conclusion, our study provides important epigenomic information for enhancer studies in HNSCC and reveals new mechanism for AP-1 regulating HNSCC.

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Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks

10.1101/2022.01.11.475197 ◽

2022 ◽

Author(s):

Hélène Neyret-Kahn ◽

Jacqueline Fontugne ◽

Xiang-Yu Meng ◽

Clarice S Groeneveld ◽

Luc Cabel ◽

...

Keyword(s):

Bladder Cancer ◽

Transcription Factor ◽

Transcription Factors ◽

Cancer Cell ◽

Muscle Invasive Bladder Cancer ◽

Cell Identity ◽

Transcription Factor Network ◽

Aggressive Disease ◽

Super Enhancer ◽

Muscle Invasive

Background: Muscle-invasive bladder cancer is a common aggressive disease with unmet clinical needs. Recent work established a set of consensus bladder cancer transcriptomic subtypes that distinguishes the cell identity of bladder cancers for improved diagnosis and treatment. However, how these distinct subtypes are regulated remains unclear. Given the link between super-enhancers and the regulation of cell identity, we hypothesized that epigenetic activation of distinct super-enhancers could drive the transcriptional programs of the various bladder cancer subtypes. Results: Through integrated RNA sequencing and epigenomic profiling of histone marks (H3K27ac, H3K27me3, H3K9me3) in a diverse panel of 15 primary bladder tumours, seven bladder cancer cell lines, and two primary cultures from normal human urothelia, we established the first integrated epigenetic map of bladder cancer and demonstrate the link between bladder cancer subtype and epigenetic control. Through H3K27ac analysis, we identify the repertoire of activated super-enhancers in bladder cancer that distinguish molecular subtypes. Building on these findings, we reveal the super-enhancer-regulated networks of candidate master transcription factors for Luminal and Basal bladder cancer subgroups. We find that FOXA1, a key pioneer factor in Luminal bladder cancers identified in our Luminal transcription factor network, binds subgroup-specific bladder super-enhancers and correlates with their activation. Furthermore, CRISPR-Cas9 inactivating mutation of FOXA1 triggers a shift from Luminal to Basal cell identity. This shift is accompanied by an overexpression of ZBED2, one of the newly identified transcriptional regulators in the Basal-specific transcription factor network. Finally, we show that both FOXA1 and ZBED2 play concordant roles in preventing inflammatory response in bladder cancer cells through STAT2 inhibition and promote cancer cell survival. Conclusions: Overall, our study provides new data for understanding epigenetic regulation of muscle-invasive bladder cancer and identifies a coregulated network of super-enhancers and associated transcription factors as new potential targets for the treatment of this aggressive disease.

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HSF1 transcription factor concentrates in nuclear foci during heat shock: relationship with transcription sites

Journal of Cell Science ◽

10.1242/jcs.110.23.2935 ◽

1997 ◽

Vol 110 (23) ◽

pp. 2935-2941 ◽

Cited By ~ 11

Author(s):

C. Jolly ◽

R. Morimoto ◽

M. Robert-Nicoud ◽

C. Vourc'h

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

In Situ Hybridization ◽

Heat Shock ◽

Human Fibroblasts ◽

Relative Distribution ◽

Transcription Sites ◽

Nuclear Foci ◽

Hsp Genes

In this paper, we show that upon heat shock, HSF1 concentrates in the nucleus of diploid human fibroblasts in two large foci. The relative distribution of HSF1 nuclear foci and active heat shock protein (hsp) genes was investigated by combining fluorescence in situ hybridization (FISH) for the detection of hsp nuclear transcripts and immunofluorescence for the detection of HSF1. We show that the HSF1 foci are distinct from the sites of hsp70 and hsp90 genes transcription. This is the second report of ploidy-dependent foci of transcription factors that are independent of their specific transcription sites. However, the correlation between the number of HSF1 foci and the ploidy of the cells strongly supports the existence of a specific chromosomal target for HSF1 foci.

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NUPR1 is a critical repressor of ferroptosis

Nature Communications ◽

10.1038/s41467-021-20904-2 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Jiao Liu ◽

Xinxin Song ◽

Feimei Kuang ◽

Qiuhong Zhang ◽

Yangchun Xie ◽

...

Keyword(s):

Cell Death ◽

Transcription Factor ◽

Transcription Factors ◽

Mouse Models ◽

Iron Metabolism ◽

Knockout Mice ◽

Multiple Roles ◽

Conditional Knockout ◽

Regulated Cell Death ◽

Nanostring Technology

AbstractFerroptosis is a type of iron-dependent regulated cell death, representing an emerging disease-modulatory mechanism. Transcription factors play multiple roles in ferroptosis, although the key regulator for ferroptosis in iron metabolism remains elusive. Using NanoString technology, we identify NUPR1, a stress-inducible transcription factor, as a driver of ferroptosis resistance. Mechanistically, NUPR1-mediated LCN2 expression blocks ferroptotic cell death through diminishing iron accumulation and subsequent oxidative damage. Consequently, LCN2 depletion mimics NUPR1 deficiency with respect to ferroptosis induction, whereas transfection-enforced re-expression of LCN2 restores resistance to ferroptosis in NUPR1-deficient cells. Pharmacological or genetic blockade of the NUPR1-LCN2 pathway (using NUPR1 shRNA, LCN2 shRNA, pancreas-specific Lcn2 conditional knockout mice, or the small molecule ZZW-115) increases the activity of the ferroptosis inducer erastin and worsens pancreatitis, in suitable mouse models. These findings suggest a link between NUPR1-regulated iron metabolism and ferroptosis susceptibility.

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