bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2023–01–22
twenty-two papers selected by
Connor Rogerson, University of Cambridge
  1. Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries.
  2. A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification.
  3. Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating CD8+ T cells.
  4. Arabidopsis LSH10 transcription factor and OTLD1 histone deubiquitinase interact and transcriptionally regulate the same target genes.
  5. A temporal in vivo catalogue of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements.
  6. Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution.
  7. Stem cell plasticity, acetylation of H3K14, and de novo gene activation rely on KAT7.
  8. Enhancer-promoter entanglement explains their transcriptional interdependence.
  9. The ETS transcription factor ETV6 constrains the transcriptional activity of EWS-FLI to promote Ewing sarcoma.
  10. Epigenetic resetting in the human germ line entails histone modification remodeling.
  11. Accounting for cis-regulatory constraint prioritizes genes likely to affect species-specific traits.
  12. Mitotic chromosome condensation resets chromatin to safeguard transcriptional homeostasis during interphase.
  13. VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis.
  14. ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation.
  15. Smarcd3 is an epigenetic modulator of the metabolic landscape in pancreatic ductal adenocarcinoma.
  16. ARID1A loss in pancreas leads to islet developmental defect and metabolic disturbance.
  17. Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis.
  18. Enhancement of a prime editing system via optimal recruitment of the pioneer transcription factor P65.
  19. Two target gene activation pathways for orphan ERR nuclear receptors.
  20. SWI/SNF blockade disrupts PU.1-directed enhancer programs in normal hematopoietic cells and acute myeloid leukemia.
  21. VGLL4 and MENIN function as TEAD1 corepressors to block pancreatic β cell proliferation.
  22. Polycomb deficiency drives a FOXP2-high aggressive state targetable by epigenetic inhibitors.
  1. Genome Res. 2023 Jan 17.
    Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries.
    Zubairul Islam, Bharath Saravanan, Kaivalya Walavalkar, Umer Farooq, Anurag Kumar Singh, Radhakrishnan Sabarinathan, Jitendra Thakur, Awadhesh Pandit, Steven Henikoff, Dimple Notani.
      Vertebrate genomes are partitioned into chromatin domains or topologically associating domains (TADs), which are typically bound by head-to-head pairs of CTCF binding sites. Transcription at domain boundaries correlates with better insulation; however, it is not known whether the boundary transcripts themselves contribute to boundary function. Here we characterize boundary-associated RNAs genome-wide, focusing on the disease-relevant INK4a/ARF and MYC TAD. Using CTCF site deletions and boundary-associated RNA knockdowns, we observe that boundary-associated RNAs facilitate recruitment and clustering of CTCF at TAD borders. The resulting CTCF enrichment enhances TAD insulation, enhancer-promoter interactions, and TAD gene expression. Importantly, knockdown of boundary-associated RNAs results in loss of boundary insulation function. Using enhancer deletions and CRISPRi of promoters, we show that active TAD enhancers, but not promoters, induce boundary-associated RNA transcription, thus defining a novel class of regulatory enhancer RNAs.
    DOI:  https://doi.org/10.1101/gr.276643.122
  2. Nat Commun. 2023 Jan 17. 14(1): 267
    A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification.
    B Edginton-White, A Maytum, S G Kellaway, D K Goode, P Keane, I Pagnuco, S A Assi, L Ames, M Clarke, P N Cockerill, B Göttgens, J B Cazier, C Bonifer.
      Developmental control of gene expression critically depends on distal cis-regulatory elements including enhancers which interact with promoters to activate gene expression. To date no global experiments have been conducted that identify their cell type and cell stage-specific activity within one developmental pathway and in a chromatin context. Here, we describe a high-throughput method that identifies thousands of differentially active cis-elements able to stimulate a minimal promoter at five stages of hematopoietic progenitor development from embryonic stem (ES) cells, which can be adapted to any ES cell derived cell type. We show that blood cell-specific gene expression is controlled by the concerted action of thousands of differentiation stage-specific sets of cis-elements which respond to cytokine signals terminating at signalling responsive transcription factors. Our work provides an important resource for studies of hematopoietic specification and highlights the mechanisms of how and where extrinsic signals program a cell type-specific chromatin landscape driving hematopoietic differentiation.
    DOI:  https://doi.org/10.1038/s41467-023-35910-9
  3. Mol Cell. 2023 Jan 11. pii: S1097-2765(22)01212-6. [Epub ahead of print]
    Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating CD8+ T cells.
    Dania Riegel, Elena Romero-Fernández, Malte Simon, Akinbami Raphael Adenugba, Katrin Singer, Roman Mayr, Florian Weber, Mark Kleemann, Charles D Imbusch, Marina Kreutz, Benedikt Brors, Ines Ugele, Jens M Werner, Peter J Siska, Christian Schmidl.
      Despite extensive studies on the chromatin landscape of exhausted T cells, the transcriptional wiring underlying the heterogeneous functional and dysfunctional states of human tumor-infiltrating lymphocytes (TILs) is incompletely understood. Here, we identify gene-regulatory landscapes in a wide breadth of functional and dysfunctional CD8+ TIL states covering four cancer entities using single-cell chromatin profiling. We map enhancer-promoter interactions in human TILs by integrating single-cell chromatin accessibility with single-cell RNA-seq data from tumor-entity-matching samples and prioritize cell-state-specific genes by super-enhancer analysis. Besides revealing entity-specific chromatin remodeling in exhausted TILs, our analyses identify a common chromatin trajectory to TIL dysfunction and determine key enhancers, transcriptional regulators, and deregulated genes involved in this process. Finally, we validate enhancer regulation at immunotherapeutically relevant loci by targeting non-coding regulatory elements with potent CRISPR activators and repressors. In summary, our study provides a framework for understanding and manipulating cell-state-specific gene-regulatory cues from human tumor-infiltrating lymphocytes.
    Keywords:  CRISPR activation; CRISPR interference; T cell exhaustion; cancer immunology; chromatin accessibility; enhancer; gene regulation; single-cell ATAC-seq; tumor-infiltrating T cells
    DOI:  https://doi.org/10.1016/j.molcel.2022.12.029
  4. Commun Biol. 2023 Jan 17. 6(1): 58
    Arabidopsis LSH10 transcription factor and OTLD1 histone deubiquitinase interact and transcriptionally regulate the same target genes.
    Mi Sa Vo Phan, Ido Keren, Phu Tri Tran, Moshe Lapidot, Vitaly Citovsky.
      Histone ubiquitylation/deubiquitylation plays a major role in the epigenetic regulation of gene expression. In plants, OTLD1, a member of the ovarian tumor (OTU) deubiquitinase family, deubiquitylates histone 2B and represses the expression of genes involved in growth, cell expansion, and hormone signaling. OTLD1 lacks the intrinsic ability to bind DNA. How OTLD1, as well as most other known plant histone deubiquitinases, recognizes its target genes remains unknown. Here, we show that Arabidopsis transcription factor LSH10, a member of the ALOG protein family, interacts with OTLD1 in living plant cells. Loss-of-function LSH10 mutations relieve the OTLD1-promoted transcriptional repression of the target genes, resulting in their elevated expression, whereas recovery of the LSH10 function results in down-regulated transcription of the same genes. We show that LSH10 associates with the target gene chromatin as well as with DNA sequences in the promoter regions of the target genes. Furthermore, without LSH10, the degree of H2B monoubiquitylation in the target promoter chromatin increases. Hence, our data suggest that OTLD1-LSH10 acts as a co-repressor complex potentially representing a general mechanism for the specific function of plant histone deubiquitinases at their target chromatin.
    DOI:  https://doi.org/10.1038/s42003-023-04424-x
  5. Genome Res. 2023 Jan 17. pii: gr.277037.122. [Epub ahead of print]
    A temporal in vivo catalogue of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements.
    Salam Idriss, Mohammad Hallal, Abdullah El-Kurdi, Hasan Zalzali, Inaam El-Rassi, Erik A Ehli, Christel M Davis, Philip E D Chung, Deena M A Gendoo, Eldad Zacksenhaus, Raya Saab, Pierre Khoueiry.
      Pediatric pineoblastomas (PBs) are rare and aggressive tumors of grade IV histology. Although some oncogenic drivers are characterized, including germline mutations in RB1 and DICER1, the role of epigenetic deregulation and cis-regulatory regions in PB pathogenesis and progression is largely unknown. Here, we generated genome-wide gene expression, chromatin accessibility, and H3K27ac profiles covering key time-points of PB initiation and progression from pineal tissues of a mouse model of Ccnd1-driven pineoblastoma. We identified PB-specific enhancers and super-enhancers and found that, in some cases, the accessible genome dynamic precedes the transcriptome, a characteristic that is underexplored in tumor progression. During progression of PB, newly acquired open chromatin regions lacking H3K27ac signal become enriched for repressive state elements and harbor motifs of repressor transcription factors like HINFP, GLI2, and YY1. Copy number variant analysis identified deletion events specific to the tumorigenic stage, affecting among others the histone genes cluster and Gas1, the growth arrest specific gene. Gene set enrichment analysis and gene expression signatures positioned the model used here close to human PB samples demonstrating the potential of our findings for exploring new avenues in PB management and therapy. Overall, this study reports the first temporal and in vivo cis-regulatory, expression, and accessibility maps in PB.
    DOI:  https://doi.org/10.1101/gr.277037.122
  6. Nat Commun. 2023 Jan 17. 14(1): 268
    Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution.
    Laureano Tomás-Daza, Llorenç Rovirosa, Paula López-Martí, Andrea Nieto-Aliseda, François Serra, Ainoa Planas-Riverola, Oscar Molina, Rebecca McDonald, Cedric Ghevaert, Esther Cuatrecasas, Dolors Costa, Mireia Camós, Clara Bueno, Pablo Menéndez, Alfonso Valencia, Biola M Javierre.
      Long-range interactions between regulatory elements and promoters are key in gene transcriptional control; however, their study requires large amounts of starting material, which is not compatible with clinical scenarios nor the study of rare cell populations. Here we introduce low input capture Hi-C (liCHi-C) as a cost-effective, flexible method to map and robustly compare promoter interactomes at high resolution. As proof of its broad applicability, we implement liCHi-C to study normal and malignant human hematopoietic hierarchy in clinical samples. We demonstrate that the dynamic promoter architecture identifies developmental trajectories and orchestrates transcriptional transitions during cell-state commitment. Moreover, liCHi-C enables the identification of disease-relevant cell types, genes and pathways potentially deregulated by non-coding alterations at distal regulatory elements. Finally, we show that liCHi-C can be harnessed to uncover genome-wide structural variants, resolve their breakpoints and infer their pathogenic effects. Collectively, our optimized liCHi-C method expands the study of 3D chromatin organization to unique, low-abundance cell populations, and offers an opportunity to uncover factors and regulatory networks involved in disease pathogenesis.
    DOI:  https://doi.org/10.1038/s41467-023-35911-8
  7. Cell Rep. 2023 Jan 13. pii: S2211-1247(22)01884-8. [Epub ahead of print]42(1): 111980
    Stem cell plasticity, acetylation of H3K14, and de novo gene activation rely on KAT7.
    Andrew J Kueh, Maria I Bergamasco, Anna Quaglieri, Belinda Phipson, Connie S N Li-Wai-Suen, Ingrid M Lönnstedt, Yifang Hu, Zhi-Ping Feng, Chris Woodruff, Rose E May, Stephen Wilcox, Alexandra L Garnham, Michael P Snyder, Gordon K Smyth, Terence P Speed, Tim Thomas, Anne K Voss.
      In the conventional model of transcriptional activation, transcription factors bind to response elements and recruit co-factors, including histone acetyltransferases. Contrary to this model, we show that the histone acetyltransferase KAT7 (HBO1/MYST2) is required genome wide for histone H3 lysine 14 acetylation (H3K14ac). Examining neural stem cells, we find that KAT7 and H3K14ac are present not only at transcribed genes but also at inactive genes, intergenic regions, and in heterochromatin. KAT7 and H3K14ac were not required for the continued transcription of genes that were actively transcribed at the time of loss of KAT7 but indispensable for the activation of repressed genes. The absence of KAT7 abrogates neural stem cell plasticity, diverse differentiation pathways, and cerebral cortex development. Re-expression of KAT7 restored stem cell developmental potential. Overexpression of KAT7 enhanced neuron and oligodendrocyte differentiation. Our data suggest that KAT7 prepares chromatin for transcriptional activation and is a prerequisite for gene activation.
    Keywords:  CP: Neuroscience; CP: Stem cell research; HBO1; KAT7; MYST2; gene activation; heterochromatin; histone H3 lysine 14; histone acetylation; replication initiation; repressed genes; transcriptional initiation
    DOI:  https://doi.org/10.1016/j.celrep.2022.111980
  8. Proc Natl Acad Sci U S A. 2023 Jan 24. 120(4): e2216436120
    Enhancer-promoter entanglement explains their transcriptional interdependence.
    Anil K Panigrahi, David M Lonard, Bert W O'Malley.
      Enhancers not only activate target promoters to stimulate messenger RNA (mRNA) synthesis, but they themselves also undergo transcription to produce enhancer RNAs (eRNAs), the significance of which is not well understood. Transcription at the participating enhancer-promoter pair appears coordinated, but it is unclear why and how. Here, we employ cell-free transcription assays using constructs derived from the human GREB1 locus to demonstrate that transcription at an enhancer and its target promoter is interdependent. This interdependence is observable under conditions where direct enhancer-promoter contact (EPC) takes place. We demonstrate that transcription activation at a participating enhancer-promoter pair is dependent on i) the mutual availability of the enhancer and promoter, ii) the state of transcription at both the enhancer and promoter, iii) local abundance of both eRNA and mRNA, and iv) direct EPC. Our results suggest transcriptional interdependence between the enhancer and the promoter as the basis of their transcriptional concurrence and coordination throughout the genome. We propose a model where transcriptional concurrence, coordination and interdependence are possible if the participating enhancer and promoter are entangled in the form of EPC, reside in a proteinaceous bubble, and utilize shared transcriptional resources and regulatory inputs.
    Keywords:  eRNA; enhancer–promoter contact; transcription activation
    DOI:  https://doi.org/10.1073/pnas.2216436120
  9. Nat Cell Biol. 2023 Jan 19.
    The ETS transcription factor ETV6 constrains the transcriptional activity of EWS-FLI to promote Ewing sarcoma.
    Diana Y Lu, Jana M Ellegast, Kenneth N Ross, Clare F Malone, Shan Lin, Nathaniel W Mabe, Neekesh V Dharia, Ashleigh Meyer, Amy Conway, Angela H Su, Julia Selich-Anderson, Cenny Taslim, Andrea K Byrum, Bo Kyung A Seong, Biniam Adane, Nathanael S Gray, Miguel N Rivera, Stephen L Lessnick, Kimberly Stegmaier.
      Transcription factors (TFs) are frequently mutated in cancer. Paediatric cancers exhibit few mutations genome-wide but frequently harbour sentinel mutations that affect TFs, which provides a context to precisely study the transcriptional circuits that support mutant TF-driven oncogenesis. A broadly relevant mechanism that has garnered intense focus involves the ability of mutant TFs to hijack wild-type lineage-specific TFs in self-reinforcing transcriptional circuits. However, it is not known whether this specific type of circuitry is equally crucial in all mutant TF-driven cancers. Here we describe an alternative yet central transcriptional mechanism that promotes Ewing sarcoma, wherein constraint, rather than reinforcement, of the activity of the fusion TF EWS-FLI supports cancer growth. We discover that ETV6 is a crucial TF dependency that is specific to this disease because it, counter-intuitively, represses the transcriptional output of EWS-FLI. This work discovers a previously undescribed transcriptional mechanism that promotes cancer.
    DOI:  https://doi.org/10.1038/s41556-022-01059-8
  10. Sci Adv. 2023 Jan 18. 9(3): eade1257
    Epigenetic resetting in the human germ line entails histone modification remodeling.
    Wolfram H Gruhn, Walfred W C Tang, Sabine Dietmann, João P Alves-Lopes, Christopher A Penfold, Frederick C K Wong, Navin B Ramakrishna, M Azim Surani.
      Epigenetic resetting in the mammalian germ line entails acute DNA demethylation, which lays the foundation for gametogenesis, totipotency, and embryonic development. We characterize the epigenome of hypomethylated human primordial germ cells (hPGCs) to reveal mechanisms preventing the widespread derepression of genes and transposable elements (TEs). Along with the loss of DNA methylation, we show that hPGCs exhibit a profound reduction of repressive histone modifications resulting in diminished heterochromatic signatures at most genes and TEs and the acquisition of a neutral or paused epigenetic state without transcriptional activation. Efficient maintenance of a heterochromatic state is limited to a subset of genomic loci, such as evolutionarily young TEs and some developmental genes, which require H3K9me3 and H3K27me3, respectively, for efficient transcriptional repression. Accordingly, transcriptional repression in hPGCs presents an exemplary balanced system relying on local maintenance of heterochromatic features and a lack of inductive cues.
    DOI:  https://doi.org/10.1126/sciadv.ade1257
  11. Genome Biol. 2023 Jan 19. 24(1): 11
    Accounting for cis-regulatory constraint prioritizes genes likely to affect species-specific traits.
    Alexander L Starr, David Gokhman, Hunter B Fraser.
      Measuring allele-specific expression in interspecies hybrids is a powerful way to detect cis-regulatory changes underlying adaptation. However, it remains difficult to identify genes most likely to explain species-specific traits. Here, we outline a simple strategy that leverages population-scale allele-specific RNA-seq data to identify genes that show constrained cis-regulation within species yet show divergence between species. Applying this strategy to data from human-chimpanzee hybrid cortical organoids, we identify signatures of lineage-specific selection on genes related to saccharide metabolism, neurodegeneration, and primary cilia. We also highlight cis-regulatory divergence in CUX1 and EDNRB that may shape the trajectory of human brain development.
    Keywords:  Brain; Chimpanzee; Development; Evolution; Gene expression; Human; Hybrid; Primate
    DOI:  https://doi.org/10.1186/s13059-023-02846-8
  12. Proc Natl Acad Sci U S A. 2023 Jan 24. 120(4): e2210593120
    Mitotic chromosome condensation resets chromatin to safeguard transcriptional homeostasis during interphase.
    Lucía Ramos-Alonso, Petter Holland, Stéphanie Le Gras, Xu Zhao, Bernard Jost, Magnar Bjørås, Yves Barral, Jorrit M Enserink, Pierre Chymkowitch.
      Mitotic entry correlates with the condensation of the chromosomes, changes in histone modifications, exclusion of transcription factors from DNA, and the broad downregulation of transcription. However, whether mitotic condensation influences transcription in the subsequent interphase is unknown. Here, we show that preventing one chromosome to condense during mitosis causes it to fail resetting of transcription. Rather, in the following interphase, the affected chromosome contains unusually high levels of the transcription machinery, resulting in abnormally high expression levels of genes in cis, including various transcription factors. This subsequently causes the activation of inducible transcriptional programs in trans, such as the GAL genes, even in the absence of the relevant stimuli. Thus, mitotic chromosome condensation exerts stringent control on interphase gene expression to ensure the maintenance of basic cellular functions and cell identity across cell divisions. Together, our study identifies the maintenance of transcriptional homeostasis during interphase as an unexpected function of mitosis and mitotic chromosome condensation.
    Keywords:  cell cycle; chromatin; chromosomes; mitosis; transcription
    DOI:  https://doi.org/10.1073/pnas.2210593120
  13. Cell Rep. 2023 Jan 18. pii: S2211-1247(23)00024-4. [Epub ahead of print]42(1): 112013
    VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis.
    Sarah Watson, Collette A LaVigne, Lin Xu, Didier Surdez, Joanna Cyrta, Delia Calderon, Matthew V Cannon, Matthew R Kent, Katherine M Silvius, Jack P Kucinski, Emma N Harrison, Whitney Murchison, Dinesh Rakheja, Franck Tirode, Olivier Delattre, James F Amatruda, Genevieve C Kendall.
      Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the fusion of transcriptional coactivators, VGLL2-NCOA2, found in infantile rhabdomyosarcoma. To delineate VGLL2-NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities, we implement a cross-species comparative oncology approach with zebrafish, mouse allograft, and patient samples. We find that VGLL2-NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2-NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2-NCOA2 developmental programs, including a RAS family GTPase, ARF6. In VGLL2-NCOA2 zebrafish, mouse, and patient tumors, ARF6 is highly expressed. ARF6 knockout suppresses VGLL2-NCOA2 oncogenic activity in cell culture, and, more broadly, ARF6 is overexpressed in adult and pediatric sarcomas. Our data indicate that VGLL2-NCOA2 is an oncogene that leverages developmental programs for tumorigenesis and that reactivation or persistence of ARF6 could represent a therapeutic opportunity.
    Keywords:  CP: Cancer; cross-species comparative oncology; developmental biology; functional genomics; fusion oncogene; pediatric cancer; rhabdomyosarcoma
    DOI:  https://doi.org/10.1016/j.celrep.2023.112013
  14. Nat Cell Biol. 2023 Jan 19.
    ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation.
    Yuan Gao, Xue-Yan He, Xiaoli S Wu, Yu-Han Huang, Shushan Toneyan, Taehoon Ha, Jonathan J Ipsaro, Peter K Koo, Leemor Joshua-Tor, Kelly M Bailey, Mikala Egeblad, Christopher R Vakoc.
      The EWS-FLI1 fusion oncoprotein deregulates transcription to initiate the paediatric cancer Ewing sarcoma. Here we used a domain-focused CRISPR screen to implicate the transcriptional repressor ETV6 as a unique dependency in this tumour. Using biochemical assays and epigenomics, we show that ETV6 competes with EWS-FLI1 for binding to select DNA elements enriched for short GGAA repeat sequences. Upon inactivating ETV6, EWS-FLI1 overtakes and hyper-activates these cis-elements to promote mesenchymal differentiation, with SOX11 being a key downstream target. We show that squelching of ETV6 with a dominant-interfering peptide phenocopies these effects and suppresses Ewing sarcoma growth in vivo. These findings reveal targeting of ETV6 as a strategy for neutralizing the EWS-FLI1 oncoprotein by reprogramming of genomic occupancy.
    DOI:  https://doi.org/10.1038/s41556-022-01060-1
  15. Nat Commun. 2023 Jan 18. 14(1): 292
    Smarcd3 is an epigenetic modulator of the metabolic landscape in pancreatic ductal adenocarcinoma.
    L Paige Ferguson, Jovylyn Gatchalian, Matthew L McDermott, Mari Nakamura, Kendall Chambers, Nirakar Rajbhandari, Nikki K Lytle, Sara Brin Rosenthal, Michael Hamilton, Sonia Albini, Martin Wartenberg, Inti Zlobec, José A Galván, Eva Karamitopoulou, Vera Vavinskaya, Alexis Wascher, Andrew M Lowy, Christian M Schürch, Pier Lorenzo Puri, Benoit G Bruneau, Diana C Hargreaves, Tannishtha Reya.
      Pancreatic cancer is characterized by extensive resistance to conventional therapies, making clinical management a challenge. Here we map the epigenetic dependencies of cancer stem cells, cells that preferentially evade therapy and drive progression, and identify SWI/SNF complex member SMARCD3 as a regulator of pancreatic cancer cells. Although SWI/SNF subunits often act as tumor suppressors, we show that SMARCD3 is amplified in cancer, enriched in pancreatic cancer stem cells and upregulated in the human disease. Diverse genetic mouse models of pancreatic cancer and stage-specific Smarcd3 deletion reveal that Smarcd3 loss preferentially impacts established tumors, improving survival especially in context of chemotherapy. Mechanistically, SMARCD3 acts with FOXA1 to control lipid and fatty acid metabolism, programs associated with therapy resistance and poor prognosis in cancer. These data identify SMARCD3 as an epigenetic modulator responsible for establishing the metabolic landscape in aggressive pancreatic cancer cells and a potential target for new therapies.
    DOI:  https://doi.org/10.1038/s41467-023-35796-7
  16. iScience. 2023 Jan 20. 26(1): 105881
    ARID1A loss in pancreas leads to islet developmental defect and metabolic disturbance.
    Tzu-Lei Kuo, Kuang-Hung Cheng, Li-Tzong Chen, Wen-Chun Hung.
      ARID1A is a tumor suppressor gene mutated in 7-10% of pancreatic cancer patients. However, its function in pancreas development and endocrine regulation is unclear. We generated mice that lack Arid1a expression in the pancreas. Our results showed that deletion of the Arid1a gene in mice caused a reduction in islet numbers and insulin production, both of which are associated with diabetes mellitus (DM) phenotype. RNA sequencing of isolated islets confirmed DM gene signature and decrease of developmental lineage genes. We identified neurogenin3, a transcription factor that controls endocrine fate specification, is a direct target of Aird1a. Gene set enrichment analysis indicated the enhancement of histone deacetylase (HDAC) pathway after Arid1a depletion and a clinically approved HDAC inhibitor showed therapeutic benefit by suppressing disease onset. Our data suggest that Arid1a is required for the development of pancreatic islets by regulating Ngn3+-mediated transcriptional program and is important in maintaining endocrine function.
    Keywords:  Diabetology; Endocrine regulation; Endocrinology; Omics; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2022.105881
  17. Genome Res. 2023 Jan 18. pii: gr.277015.122. [Epub ahead of print]
    Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis.
    Shreya Mishra, Neetesh Pandey, Smriti Chawla, Madhu Sharma, Omkar Chandra, Indra Prakash Jha, Debarka Sengupta, Kedar Nath Natrajan, Vibhor Kumar.
      The true benefits of large datasets of the single-cell transcriptome and epigenome profiles can be availed only with their inclusion and search for annotating individual cells. Matching a single-cell epigenome profile to a large pool of reference cells remains a major challenge. Here, we present scEpiSearch, which enables searching, comparison and independent classification of single-cell open-chromatin profiles against a large reference of single-cell expression and open-chromatin datasets. Across performance benchmarks, scEpiSearch outperformed multiple methods in accuracy of search and low-dimensional coembedding of single-cell profiles, irrespective of platforms and species. Here, we also demonstrate the unconventional utilities of scEpiSearch by applying it on single-cell epigenome profiles of K562 cells and samples from patients with acute leukaemia to reveal different aspects of their heterogeneity, multipotent behavior and dedifferentiated states. Applying scEpiSearch on our single-cell open-chromatin profiles from embryonic stem cells (ESCs), we identified ESC subpopulations with more activity and poising for endoplasmic reticulum stress and unfolded protein response. Thus, scEpiSearch solves the nontrivial problem of amalgamating information from a large pool of single cells to identify and study the regulatory states of cells using their single-cell epigenomes.
    DOI:  https://doi.org/10.1101/gr.277015.122
  18. Nat Commun. 2023 Jan 17. 14(1): 257
    Enhancement of a prime editing system via optimal recruitment of the pioneer transcription factor P65.
    Ronghao Chen, Yu Cao, Yajing Liu, Dongdong Zhao, Ju Li, Zhihui Cheng, Changhao Bi, Xueli Zhang.
      Prime editing is a versatile gene editing tool that enables precise sequence changes of all types in the genome, but its application is rather limited by the editing efficiency. Here, we first apply the Suntag system to recruit the transcription factor P65 and enhance the desired editing outcomes in the prime editing system. Next, MS2 hairpins are used to recruit MS2-fused P65 and confirmed that the recruitment of the P65 protein could effectively improve the prime editing efficiency in both the PE3 and PE5 systems. Moreover, this suggests the increased editing efficiency is most likely associated with the induction of chromatin accessibility change by P65. In conclusion, we apply different systems to recruit P65 and enhance the prime editing efficiency of various PE systems. Furthermore, our work provides a variety of methods to work as protein scaffolds for screening target factors and thus supports further optimization of prime editing systems.
    DOI:  https://doi.org/10.1038/s41467-023-35919-0
  19. Cell Res. 2023 Jan 16.
    Two target gene activation pathways for orphan ERR nuclear receptors.
    Tomoyoshi Nakadai, Miho Shimada, Keiichi Ito, Murat Alper Cevher, Chi-Shuen Chu, Kohei Kumegawa, Reo Maruyama, Sohail Malik, Robert G Roeder.
      Estrogen-related receptors (ERRα/β/γ) are orphan nuclear receptors that function in energy-demanding physiological processes, as well as in development and stem cell maintenance, but mechanisms underlying target gene activation by ERRs are largely unknown. Here, reconstituted biochemical assays that manifest ERR-dependent transcription have revealed two complementary mechanisms. On DNA templates, ERRs activate transcription with just the normal complement of general initiation factors through an interaction of the ERR DNA-binding domain with the p52 subunit of initiation factor TFIIH. On chromatin templates, activation by ERRs is dependent on AF2 domain interactions with the cell-specific coactivator PGC-1α, which in turn recruits the ubiquitous p300 and MED1/Mediator coactivators. This role of PGC-1α may also be fulfilled by other AF2-interacting coactivators like NCOA3, which is shown to recruit Mediator selectively to ERRβ and ERRγ. Importantly, combined genetic and RNA-seq analyses establish that both the TFIIH and the AF2 interaction-dependent pathways are essential for ERRβ/γ-selective gene expression and pluripotency maintenance in embryonic stem cells in which NCOA3 is a critical coactivator.
    DOI:  https://doi.org/10.1038/s41422-022-00774-z
  20. Cancer Res. 2023 Jan 20. pii: CAN-22-2129. [Epub ahead of print]
    SWI/SNF blockade disrupts PU.1-directed enhancer programs in normal hematopoietic cells and acute myeloid leukemia.
    Courtney Chambers, Katerina Cermakova, Yuen San Chan, Kristen Kurtz, Katharina Wohlan, Andrew Henry Lewis, Christiana Wang, Anh Pham, Milan Dejmek, Michal Sala, Mario Loeza Cabrera, Rogelio Aguilar, Radim Nencka, Daniel Lacorazza, Rachel E Rau, H Courtney Hodges.
      In acute myeloid leukemia (AML), SWI/SNF chromatin remodeling complexes sustain leukemic identity by driving high levels of MYC. Previous studies have implicated the hematopoietic transcription factor PU.1 (SPI1) as an important target of SWI/SNF inhibition, but PU.1 is widely regarded to have pioneer-like activity. As a result, many questions have remained regarding the interplay between PU.1 and SWI/SNF in AML as well as normal hematopoiesis. Here we found that PU.1 binds to most of its targets in a SWI/SNF-independent manner and recruits SWI/SNF to promote accessibility for other AML core regulatory factors, including RUNX1, LMO2, and MEIS1. SWI/SNF inhibition in AML cells reduced DNA accessibility and binding of these factors at PU.1 sites and redistributed PU.1 to promoters. Analysis of non-tumor hematopoietic cells revealed that similar effects also impair PU.1-dependent B cell and monocyte populations. Nevertheless, SWI/SNF inhibition induced profound therapeutic response in an immunocompetent AML mouse model as well as in primary human AML samples. In vivo, SWI/SNF inhibition promoted leukemic differentiation and reduced the leukemic stem cell burden in bone marrow but also induced leukopenia. These results reveal a variable therapeutic window for SWI/SNF blockade in AML and highlight important off-tumor effects of such therapies in immunocompetent settings.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-2129
  21. Cell Rep. 2023 Jan 18. pii: S2211-1247(22)01803-4. [Epub ahead of print]42(1): 111904
    VGLL4 and MENIN function as TEAD1 corepressors to block pancreatic β cell proliferation.
    Feng Li, Ruya Liu, Vinny Negi, Ping Yang, Jeongkyung Lee, Rajaganapathi Jagannathan, Mousumi Moulik, Vijay K Yechoor.
      TEAD1 and the mammalian Hippo pathway regulate cellular proliferation and function, though their regulatory function in β cells remains poorly characterized. In this study, we demonstrate that while β cell-specific TEAD1 deletion results in a cell-autonomous increase of β cell proliferation, β cell-specific deletion of its canonical coactivators, YAP and TAZ, does not affect proliferation, suggesting the involvement of other cofactors. Using an improved split-GFP system and yeast two-hybrid platform, we identify VGLL4 and MENIN as TEAD1 corepressors in β cells. We show that VGLL4 and MENIN bind to TEAD1 and repress the expression of target genes, including FZD7 and CCN2, which leads to an inhibition of β cell proliferation. In conclusion, we demonstrate that TEAD1 plays a critical role in β cell proliferation and identify VGLL4 and MENIN as TEAD1 corepressors in β cells. We propose that these could be targeted to augment proliferation in β cells for reversing diabetes.
    Keywords:  CP: Cell biology; CP: Metabolism; Hippo pathway; MENIN; TAZ; TEAD1; VGLL4; YAP; beta cell; diabetes; islet; proliferation; split-GPF
    DOI:  https://doi.org/10.1016/j.celrep.2022.111904
  22. Nat Commun. 2023 Jan 20. 14(1): 336
    Polycomb deficiency drives a FOXP2-high aggressive state targetable by epigenetic inhibitors.
    Fan Chen, Aria L Byrd, Jinpeng Liu, Robert M Flight, Tanner J DuCote, Kassandra J Naughton, Xiulong Song, Abigail R Edgin, Alexsandr Lukyanchuk, Danielle T Dixon, Christian M Gosser, Dave-Preston Esoe, Rani D Jayswal, Stuart H Orkin, Hunter N B Moseley, Chi Wang, Christine Fillmore Brainson.
      Inhibitors of the Polycomb Repressive Complex 2 (PRC2) histone methyltransferase EZH2 are approved for certain cancers, but realizing their wider utility relies upon understanding PRC2 biology in each cancer system. Using a genetic model to delete Ezh2 in KRAS-driven lung adenocarcinomas, we observed that Ezh2 haplo-insufficient tumors were less lethal and lower grade than Ezh2 fully-insufficient tumors, which were poorly differentiated and metastatic. Using three-dimensional cultures and in vivo experiments, we determined that EZH2-deficient tumors were vulnerable to H3K27 demethylase or BET inhibitors. PRC2 loss/inhibition led to de-repression of FOXP2, a transcription factor that promotes migration and stemness, and FOXP2 could be suppressed by BET inhibition. Poorly differentiated human lung cancers were enriched for an H3K27me3-low state, representing a subtype that may benefit from BET inhibition as a single therapy or combined with additional EZH2 inhibition. These data highlight diverse roles of PRC2 in KRAS-driven lung adenocarcinomas, and demonstrate the utility of three-dimensional cultures for exploring epigenetic drug sensitivities for cancer.
    DOI:  https://doi.org/10.1038/s41467-023-35784-x
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