bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2022–10–30
29 papers selected by
Connor Rogerson, University of Cambridge
  1. An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters.
  2. Subtype-specific 3D genome alteration in acute myeloid leukaemia.
  3. Enhancer and super-enhancer landscape in polycystic kidney disease.
  4. Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer.
  5. Spatially resolved epigenomic profiling of single cells in complex tissues.
  6. HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia.
  7. A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas.
  8. A cryptic transactivation domain of EZH2 binds AR and AR's splice variant, promoting oncogene activation and tumorous transformation.
  9. Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI.
  10. Lineage Landscape: a comprehensive database that records lineage commitment across species.
  11. Hypoxia promotes osteogenesis by facilitating acetyl-CoA-mediated mitochondrial-nuclear communication.
  12. scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells.
  13. Yap and Taz promote osteogenesis and prevent chondrogenesis in neural crest cells in vitro and in vivo.
  14. The co-evolution of the genome and epigenome in colorectal cancer.
  15. Retinoblastoma protein as an intrinsic BRD4 inhibitor modulates small molecule BET inhibitor sensitivity in cancer.
  16. A satellite DNA array barcodes chromosome 7 and regulates totipotency via ZFP819.
  17. Epigenome programing by H3.3K27M mutation creates a dependence of pediatric glioma on SMARCA4.
  18. Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases.
  19. FOXO3 regulates a common genomic program in aging and glioblastoma stem cells.
  20. Targeting MYC with modular synthetic transcriptional repressors derived from bHLH DNA-binding domains.
  21. Global DNA Methylation Analysis of Cancer-Associated Fibroblasts Reveals Extensive Epigenetic Rewiring Linked with RUNX1 Upregulation in Breast Cancer Stroma.
  22. A multi-omics approach to visualize early neuronal differentiation from hESCs in 4D.
  23. Transcription factor gene Pea3 regulates erectile function during copulation in mice.
  24. Transient inhibition of p53 enhances prime editing and cytosine base-editing efficiencies in human pluripotent stem cells.
  25. Vitamin C enhances NF-κB-driven epigenomic reprogramming and boosts the immunogenic properties of dendritic cells.
  26. Covalent disruptor of YAP-TEAD association suppresses defective hippo signaling.
  27. Z-REX uncovers a bifurcation in function of Keap1 paralogs.
  28. BAF complex maintains glioma stem cells in pediatric H3K27M-glioma.
  29. CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data.
  1. Genes Dev. 2022 Oct 27.
    An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters.
    Chitvan Mittal, Olivia Lang, William K M Lai, B Franklin Pugh.
      Genome-wide, little is understood about how proteins organize at inducible promoters before and after induction and to what extent inducible and constitutive architectures depend on cofactors. We report that sequence-specific transcription factors and their tethered cofactors (e.g., SAGA [Spt-Ada-Gcn5-acetyltransferase], Mediator, TUP, NuA4, SWI/SNF, and RPD3-L) are generally bound to promoters prior to induction ("poised"), rather than recruited upon induction, whereas induction recruits the preinitiation complex (PIC) to DNA. Through depletion and/or deletion experiments, we show that SAGA does not function at constitutive promoters, although a SAGA-independent Gcn5 acetylates +1 nucleosomes there. When inducible promoters are poised, SAGA catalyzes +1 nucleosome acetylation but not PIC assembly. When induced, SAGA catalyzes acetylation, deubiquitylation, and PIC assembly. Surprisingly, SAGA mediates induction by creating a PIC that allows TFIID (transcription factor II-D) to stably associate, rather than creating a completely TFIID-independent PIC, as generally thought. These findings suggest that inducible systems, where present, are integrated with constitutive systems.
    Keywords:  ChIP-seq; SAGA; Saccharomyces; gene regulation; genomics; transcription preinitiation complex
    DOI:  https://doi.org/10.1101/gad.350026.122
  2. Nature. 2022 Oct 26.
    Subtype-specific 3D genome alteration in acute myeloid leukaemia.
    Jie Xu, Fan Song, Huijue Lyu, Mikoto Kobayashi, Baozhen Zhang, Ziyu Zhao, Ye Hou, Xiaotao Wang, Yu Luan, Bei Jia, Lena Stasiak, Josiah Hiu-Yuen Wong, Qixuan Wang, Qi Jin, Qiushi Jin, Yihao Fu, Hongbo Yang, Ross C Hardison, Sinisa Dovat, Leonidas C Platanias, Yarui Diao, Yue Yang, Tomoko Yamada, Aaron D Viny, Ross L Levine, David Claxton, James R Broach, Hong Zheng, Feng Yue.
      Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases1-5. The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter-enhancer and promoter-silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1, DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases.
    DOI:  https://doi.org/10.1038/s41586-022-05365-x
  3. Kidney Int. 2022 Oct 22. pii: S0085-2538(22)00847-X. [Epub ahead of print]
    Enhancer and super-enhancer landscape in polycystic kidney disease.
    Ronak Lakhia, Abheepsa Mishra, Laurence Biggers, Venkat Malladi, Patricia Cobo-Stark, Sachin Hajarnis, Vishal Patel.
      Widespread aberrant gene expression is a pathological hallmark of polycystic kidney disease (PKD). Numerous pathogenic signaling cascades, including c-Myc, Fos, and Jun are transactivated. However, the underlying epigenetic regulators are poorly defined. Here we show that H3K27ac, an acetylated modification of DNA packing protein histone H3 that marks active enhancers, is elevated in mouse and human samples of autosomal dominant PKD. Using comparative H3K27ac ChIP-Seq analysis, we mapped over 16000 active intronic and intergenic enhancer elements in Pkd1-mutant mouse kidneys. We found that the cystic kidney epigenetic landscape resembles that of a developing kidney, and over 90% of upregulated genes in Pkd1-mutant kidneys are co-housed with activated enhancers in the same topologically associated domains. Furthermore, we identified an evolutionarily-conserved enhancer cluster downstream of the c-Myc gene and super-enhancers flanking both Jun and Fos loci in mouse and human models of autosomal dominant PKD. Deleting these regulatory elements reduced c-Myc, Jun, or Fos abundance and suppressed proliferation and 3D cyst growth of Pkd1-mutant cells. Finally, inhibiting glycolysis and glutaminolysis or activating Ppara in Pkd1-mutant cells lowerd global H3K27ac levels and its abundance on c-Myc enhancers. Thus, our work suggests that epigenetic rewiring mediates the transcriptomic dysregulation in PKD, and the regulatory elements can be targeted to slow cyst growth.
    Keywords:  ChIP-Seq; Fos; H3K27ac; Jun; Polycystic kidney disease; c-Myc; enhancers; epigenetics; super-enhancers
    DOI:  https://doi.org/10.1016/j.kint.2022.08.039
  4. Mol Cell. 2022 Oct 18. pii: S1097-2765(22)00955-8. [Epub ahead of print]
    Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer.
    Lele Song, Xinyi Yao, Hangpeng Li, Bo Peng, Alan P Boka, Yiman Liu, Guochao Chen, Zhenyang Liu, Kaeli M Mathias, Lingbo Xia, Qinglan Li, Mustafa Mir, Yuanyuan Li, Haitao Li, Liling Wan.
      Growing evidence suggests prevalence of transcriptional condensates on chromatin, yet their mechanisms of formation and functional significance remain largely unclear. In human cancer, a series of mutations in the histone acetylation reader ENL create gain-of-function mutants with increased transcriptional activation ability. Here, we show that these mutations, clustered in ENL's structured acetyl-reading YEATS domain, trigger aberrant condensates at native genomic targets through multivalent homotypic and heterotypic interactions. Mechanistically, mutation-induced structural changes in the YEATS domain, ENL's two disordered regions of opposing charges, and the incorporation of extrinsic elongation factors are all required for ENL condensate formation. Extensive mutagenesis establishes condensate formation as a driver of oncogenic gene activation. Furthermore, expression of ENL mutants beyond the endogenous level leads to non-functional condensates. Our findings provide new mechanistic and functional insights into cancer-associated condensates and support condensate dysregulation as an oncogenic mechanism.
    Keywords:  ENL YEATS; IDR; cancer epigenetics; chromatin reader; intrinsically disordered protein region; multivalent interactions; mutations; phase separation; structured domains; transcription elongation; transcriptional condensates/hubs
    DOI:  https://doi.org/10.1016/j.molcel.2022.09.034
  5. Cell. 2022 Oct 14. pii: S0092-8674(22)01254-5. [Epub ahead of print]
    Spatially resolved epigenomic profiling of single cells in complex tissues.
    Tian Lu, Cheen Euong Ang, Xiaowei Zhuang.
      The recent development of spatial omics methods has enabled single-cell profiling of the transcriptome and 3D genome organization with high spatial resolution. Expanding the repertoire of spatial omics tools, a spatially resolved single-cell epigenomics method will accelerate understanding of the spatial regulation of cell and tissue functions. Here, we report a method for spatially resolved epigenomic profiling of single cells using in situ tagmentation and transcription followed by multiplexed imaging. We demonstrated the ability to profile histone modifications marking active promoters, putative enhancers, and silent promoters in individual cells, and generated high-resolution spatial atlas of hundreds of active promoters and putative enhancers in embryonic and adult mouse brains. Our results suggested putative promoter-enhancer pairs and enhancer hubs regulating developmentally important genes. We envision this approach will be generally applicable to spatial profiling of epigenetic modifications and DNA-binding proteins, advancing our understanding of how gene expression is spatiotemporally regulated by the epigenome.
    Keywords:  MERFISH; brain; development; enhancer; enhancer hub; enhancer-promoter interaction; epigenomic MERFISH; promoter; single-cell epigenomics; spatial epigenomic
    DOI:  https://doi.org/10.1016/j.cell.2022.09.035
  6. Blood Adv. 2022 Oct 26. pii: bloodadvances.2022007998. [Epub ahead of print]
    HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia.
    Tzung-Huei Lai, Hatice Gulcin Ozer, Pierluigi Gasparini, Giovanni Nigita, Rosario Distefano, Lianbo Yu, Janani Ravikrishnan, Selen Yilmaz, Juan Jesus Gallegos, Sachet A Shukla, Vinay K Puduvalli, Jennifer A Woyach, Rosa Lapalombella, James S Blachly, John C Byrd, Deepa Sampath.
      Chronic lymphocytic leukemia (CLL) is a quiescent B-cell malignancy that depends on transcriptional dysregulation for survival. The histone deacetylases are transcriptional regulators whose role within the regulatory chromatin and consequence on the CLL transcriptome is poorly characterized. Here, we profiled and integrated the genome wide occupancy of HDAC1, BRD4, H3K27Ac and H3K9Ac signals with chromatin accessibility, Pol2 occupancy and target expression signatures in CLL cells. We identified that when HDAC1 was recruited within super-enhancers marked by acetylated H3K27 and BRD4, it functioned as a transcriptional activator that drove the de novo expression of select genes to facilitate survival and progression in CLL. Targeting HDACs reduced BRD4 and Pol2 engagement to downregulate the transcript and proteins levels of specific oncogenic driver genes in CLL such as BLK, a key mediator of the B-cell receptor pathway, core transcription factors such as PAX5 and IKZF3 and the anti-apoptotic gene, BCL2. Concurrently, HDAC1, when recruited in the absence of super-enhancers repressed target gene expression. HDAC inhibition reversed silencing of a defined set of protein coding and noncoding RNA genes. We focused on a specific set of microRNA genes and show that their upregulation was inversely correlated with the expression of CLL specific survival, transcription factor and signaling genes. Our findings identify that the transcriptional activator and repressor functions of HDACs cooperate within the same tumor to establish the transcriptional dependencies essential for survival in CLL.
    DOI:  https://doi.org/10.1182/bloodadvances.2022007998
  7. J Clin Invest. 2022 Oct 25. pii: e160767. [Epub ahead of print]
    A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas.
    Ja-Young Jang, Inah Hwang, Heng Pan, Jun Yao, Lapo Alinari, Eddie Imada, Claudio Zanettini, Michael Kluk, Yizhe Wang, Yun-Kyoung Lee, Hua V Lin, Xiangao Huang, Maurizio Di Liberto, Zhengming Chen, Karla V Ballman, Lewis C Cantley, Luigi Marchionni, Giorgio Inghirami, Olivier Elemento, Robert Baiocchi, Selina Chen-Kiang, Sandro Belvedere, Hongwu Zheng, Jihye Paik.
      Targeting lineage-defined transcriptional dependencies has emerged as an effective therapeutic strategy in cancer treatment. Through screening for molecular vulnerabilities of mantle cell lymphoma (MCL), we identified a set of transcription factors (TFs) including FOXO1, EBF1, PAX5, and IRF4 that are essential for MCL propagation. Integrated chromatin immunoprecipitation and sequencing (ChIP-seq) with transcriptional network reconstruction analysis revealed FOXO1 as a master regulator that acts upstream in the regulatory TF hierarchy. FOXO1 is both necessary and sufficient to drive MCL lineage commitment through supporting the lineage-specific transcription programs. We further show that FOXO1, but not its close paralog FOXO3, can reprogram myeloid leukemia cells and induce B-lineage gene expression. Finally, we demonstrate that cpd10, a small molecule identified from an enriched FOXO1 inhibitor library, induces a robust cytotoxic response of MCL cells in vitro and suppresses MCL progression in vivo. Our findings establish FOXO1 inhibition as a therapeutic strategy targeting lineage-driven transcriptional addiction in MCL.
    Keywords:  Lymphomas; Oncology
    DOI:  https://doi.org/10.1172/JCI160767
  8. Nucleic Acids Res. 2022 Oct 27. pii: gkac861. [Epub ahead of print]
    A cryptic transactivation domain of EZH2 binds AR and AR's splice variant, promoting oncogene activation and tumorous transformation.
    Jun Wang, Kwang-Su Park, Xufen Yu, Weida Gong, H Shelton Earp, Gang Greg Wang, Jian Jin, Ling Cai.
      Enhancer of Zeste Homolog 2 (EZH2) and androgen receptor (AR) are crucial chromatin/gene regulators involved in the development and/or progression of prostate cancer, including advanced castration-resistant prostate cancer (CRPC). To sustain prostate tumorigenicity, EZH2 establishes non-canonical biochemical interaction with AR for mediating oncogene activation, in addition to its canonical role as a transcriptional repressor and enzymatic subunit of Polycomb Repressive Complex 2 (PRC2). However, the molecular basis underlying non-canonical activities of EZH2 in prostate cancer remains elusive, and a therapeutic strategy for targeting EZH2:AR-mediated oncogene activation is also lacking. Here, we report that a cryptic transactivation domain of EZH2 (EZH2TAD) binds both AR and AR spliced variant 7 (AR-V7), a constitutively active AR variant enriched in CRPC, mediating assembly and/or recruitment of transactivation-related machineries at genomic sites that lack PRC2 binding. Such non-canonical targets of EZH2:AR/AR-V7:(co-)activators are enriched for the clinically relevant oncogenes. We also show that EZH2TAD is required for the chromatin recruitment of EZH2 to oncogenes, for EZH2-mediated oncogene activation and for CRPC growth in vitro and in vivo. To completely block EZH2's multifaceted oncogenic activities in prostate cancer, we employed MS177, a recently developed proteolysis-targeting chimera (PROTAC) of EZH2. Strikingly, MS177 achieved on-target depletion of both EZH2's canonical (EZH2:PRC2) and non-canonical (EZH2TAD:AR/AR-V7:co-activators) complexes in prostate cancer cells, eliciting far more potent antitumor effects than the catalytic inhibitors of EZH2. Overall, this study reports a previously unappreciated requirement for EZH2TAD for mediating EZH2's non-canonical (co-)activator recruitment and gene activation functions in prostate cancer and suggests EZH2-targeting PROTACs as a potentially attractive therapeutic for the treatment of aggressive prostate cancer that rely on the circuits wired by EZH2 and AR.
    DOI:  https://doi.org/10.1093/nar/gkac861
  9. Nat Biotechnol. 2022 Oct 27.
    Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI.
    Cong Liu, Hanxiao Sun, Yunpeng Yi, Weiguo Shen, Kai Li, Ye Xiao, Fei Li, Yuchen Li, Yongkang Hou, Bo Lu, Wenqing Liu, Haowei Meng, Jinying Peng, Chengqi Yi, Jing Wang.
      N6-methyladenosine (m6A) is the most abundant RNA modification in mammalian cells and the best-studied epitranscriptomic mark. Despite the development of various tools to map m6A, a transcriptome-wide method that enables absolute quantification of m6A at single-base resolution is lacking. Here we use glyoxal and nitrite-mediated deamination of unmethylated adenosines (GLORI) to develop an absolute m6A quantification method that is conceptually similar to bisulfite-sequencing-based quantification of DNA 5-methylcytosine. We apply GLORI to quantify the m6A methylomes of mouse and human cells and reveal clustered m6A modifications with differential distribution and stoichiometry. In addition, we characterize m6A dynamics under stress and examine the quantitative landscape of m6A modification in gene expression regulation. GLORI is an unbiased, convenient method for the absolute quantification of the m6A methylome.
    DOI:  https://doi.org/10.1038/s41587-022-01487-9
  10. Nucleic Acids Res. 2022 Oct 28. pii: gkac951. [Epub ahead of print]
    Lineage Landscape: a comprehensive database that records lineage commitment across species.
    Haoteng Yan, Ronghao Wang, Shuai Ma, Daoran Huang, Si Wang, Jie Ren, Changfa Lu, Xin Chen, Xiaoyong Lu, Zikai Zheng, Weiqi Zhang, Jing Qu, Yuanchun Zhou, Guang-Hui Liu.
      Commitment to specific cell lineages is critical for mammalian embryonic development. Lineage determination, differentiation, maintenance, and organogenesis result in diverse life forms composed of multiple cell types. To understand the formation and maintenance of living individuals, including human beings, a comprehensive database that integrates multi-omic information underlying lineage differentiation across multiple species is urgently needed. Here, we construct Lineage Landscape, a database that compiles, analyzes and visualizes transcriptomic and epigenomic information related to lineage development in a collection of species. This landscape draws together datasets that capture the ongoing changes in cell lineages from classic model organisms to human beings throughout embryonic, fetal, adult, and aged stages, providing comprehensive, open-access information that is useful to researchers of a broad spectrum of life science disciplines. Lineage Landscape contains single-cell gene expression and bulk transcriptomic, DNA methylation, histone modifications, and chromatin accessibility profiles. Using this database, users can explore genes of interest that exhibit dynamic expression patterns at the transcriptional or epigenetic levels at different stages of lineage development. Lineage Landscape currently includes over 6.6 million cells, 15 million differentially expressed genes and 36 million data entries across 10 species and 34 organs. Lineage Landscape is free to access, browse, search, and download at http://data.iscr.ac.cn/lineage/#/home.
    DOI:  https://doi.org/10.1093/nar/gkac951
  11. EMBO J. 2022 Oct 24. e111239
    Hypoxia promotes osteogenesis by facilitating acetyl-CoA-mediated mitochondrial-nuclear communication.
    Andromachi Pouikli, Monika Maleszewska, Swati Parekh, Ming Yang, Chrysa Nikopoulou, Juan Jose Bonfiglio, Constantine Mylonas, Tonantzi Sandoval, Anna-Lena Schumacher, Yvonne Hinze, Ivan Matic, Christian Frezza, Peter Tessarz.
      Bone-derived mesenchymal stem cells (MSCs) reside in a hypoxic niche that maintains their differentiation potential. While hypoxia (low oxygen concentration) was reported to critically support stem cell function and osteogenesis, the molecular events triggering changes in stem cell fate decisions in response to normoxia (high oxygen concentration) remain elusive. Here, we study the impact of normoxia on mitochondrial-nuclear communication during stem cell differentiation. We show that normoxia-cultured murine MSCs undergo profound transcriptional alterations which cause irreversible osteogenesis defects. Mechanistically, high oxygen promotes chromatin compaction and histone hypo-acetylation, particularly on promoters and enhancers of osteogenic genes. Although normoxia induces metabolic rewiring resulting in elevated acetyl-CoA levels, histone hypo-acetylation occurs due to the trapping of acetyl-CoA inside mitochondria owing to decreased citrate carrier (CiC) activity. Restoring the cytosolic acetyl-CoA pool remodels the chromatin landscape and rescues the osteogenic defects. Collectively, our results demonstrate that the metabolism-chromatin-osteogenesis axis is perturbed upon exposure to high oxygen levels and identifies CiC as a novel, oxygen-sensitive regulator of the MSC function.
    Keywords:  histone acetylation; hypoxia; mesenchymal stem cells; metabolism; osteogenesis
    DOI:  https://doi.org/10.15252/embj.2022111239
  12. Genome Biol. 2022 Oct 28. 23(1): 229
    scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells.
    Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten, Renée Beekman.
      Single-cell DNA methylation profiling currently suffers from excessive noise and/or limited cellular throughput. We developed scTAM-seq, a targeted bisulfite-free method for profiling up to 650 CpGs in up to 10,000 cells per experiment, with a dropout rate as low as 7%. We demonstrate that scTAM-seq can resolve DNA methylation dynamics across B-cell differentiation in blood and bone marrow, identifying intermediate differentiation states that were previously masked. scTAM-seq additionally queries surface-protein expression, thus enabling integration of single-cell DNA methylation information with cell atlas data. In summary, scTAM-seq is a high-throughput, high-confidence method for analyzing DNA methylation at single-CpG resolution across thousands of single cells.
    Keywords:  DNA methylation; Epigenetics; Hematopoiesis; Multi-omic analysis; Single-cell profiling
    DOI:  https://doi.org/10.1186/s13059-022-02796-7
  13. Sci Signal. 2022 Oct 25. 15(757): eabn9009
    Yap and Taz promote osteogenesis and prevent chondrogenesis in neural crest cells in vitro and in vivo.
    Xiaolei Zhao, Li Tang, Tram P Le, Bao H Nguyen, Wen Chen, Mingjie Zheng, Hiroyuki Yamaguchi, Brian Dawson, Shuangjie You, Idaliz M Martinez-Traverso, Shannon Erhardt, Jianxin Wang, Min Li, James F Martin, Brendan H Lee, Yoshihiro Komatsu, Jun Wang.
      Neural crest cells (NCCs) are multipotent stem cells that can differentiate into multiple cell types, including the osteoblasts and chondrocytes, and constitute most of the craniofacial skeleton. Here, we show through in vitro and in vivo studies that the transcriptional regulators Yap and Taz have redundant functions as key determinants of the specification and differentiation of NCCs into osteoblasts or chondrocytes. Primary and cultured NCCs deficient in Yap and Taz switched from osteogenesis to chondrogenesis, and NCC-specific deficiency for Yap and Taz resulted in bone loss and ectopic cartilage in mice. Yap bound to the regulatory elements of key genes that govern osteogenesis and chondrogenesis in NCCs and directly regulated the expression of these genes, some of which also contained binding sites for the TCF/LEF transcription factors that interact with the Wnt effector β-catenin. During differentiation of NCCs in vitro and NCC-derived osteogenesis in vivo, Yap and Taz promoted the expression of osteogenic genes such as Runx2 and Sp7 but repressed the expression of chondrogenic genes such as Sox9 and Col2a1. Furthermore, Yap and Taz interacted with β-catenin in NCCs to coordinately promote osteoblast differentiation and repress chondrogenesis. Together, our data indicate that Yap and Taz promote osteogenesis in NCCs and prevent chondrogenesis, partly through interactions with the Wnt-β-catenin pathway.
    DOI:  https://doi.org/10.1126/scisignal.abn9009
  14. Nature. 2022 Oct 26.
    The co-evolution of the genome and epigenome in colorectal cancer.
    Timon Heide, Jacob Househam, George D Cresswell, Inmaculada Spiteri, Claire Lynn, Maximilian Mossner, Chris Kimberley, Javier Fernandez-Mateos, Bingjie Chen, Luis Zapata, Chela James, Iros Barozzi, Ketevan Chkhaidze, Daniel Nichol, Vinaya Gunasri, Alison Berner, Melissa Schmidt, Eszter Lakatos, Ann-Marie Baker, Helena Costa, Miriam Mitchinson, Rocco Piazza, Marnix Jansen, Giulio Caravagna, Daniele Ramazzotti, Darryl Shibata, John Bridgewater, Manuel Rodriguez-Justo, Luca Magnani, Trevor A Graham, Andrea Sottoriva.
      Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,370 samples from 30 primary cancers and 8 concomitant adenomas and generated 1,207 chromatin accessibility profiles, 527 whole genomes and 297 whole transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent somatic chromatin accessibility alterations, including in regulatory regions of cancer driver genes that were otherwise devoid of genetic mutations. Genome-wide alterations in accessibility for transcription factor binding involved CTCF, downregulation of interferon and increased accessibility for SOX and HOX transcription factor families, suggesting the involvement of developmental genes during tumourigenesis. Somatic chromatin accessibility alterations were heritable and distinguished adenomas from cancers. Mutational signature analysis showed that the epigenome in turn influences the accumulation of DNA mutations. This study provides a map of genetic and epigenetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology.
    DOI:  https://doi.org/10.1038/s41586-022-05202-1
  15. Nat Commun. 2022 Oct 23. 13(1): 6311
    Retinoblastoma protein as an intrinsic BRD4 inhibitor modulates small molecule BET inhibitor sensitivity in cancer.
    Donglin Ding, Rongbin Zheng, Ye Tian, Rafael Jimenez, Xiaonan Hou, Saravut J Weroha, Liguo Wang, Lei Shi, Haojie Huang.
      Bromodomain and extraterminal (BET) proteins including BRD4 play important roles in oncogenesis and immune inflammation. Here we demonstrate that cancer cells with loss of the retinoblastoma (RB) tumor suppressor became resistant to small molecule bromodomain inhibitors of BET proteins. We find that RB binds to bromodomain-1 (BD1) of BRD4, but binding is impeded by CDK4/6-mediated RB phosphorylation at serine-249/threonine-252 (S249/T252). ChIP-seq analysis shows RB knockdown increases BRD4 occupancy at genomic loci of genes enriched in cancer-related pathways including the GPCR-GNBIL-CREB axis. S249/T252-phosphorylated RB positively correlates with GNBIL protein level in prostate cancer patient samples. BET inhibitor resistance in RB-deficient cells is abolished by co-administration of CREB inhibitor. Our study identifies RB protein as a bona fide intrinsic inhibitor of BRD4 and demonstrates that RB inactivation confers resistance to small molecule BET inhibitors, thereby revealing a regulatory hub that converges RB upstream signaling onto BRD4 functions in diseases such as cancer.
    DOI:  https://doi.org/10.1038/s41467-022-34024-y
  16. Sci Adv. 2022 Oct 28. 8(43): eabp8085
    A satellite DNA array barcodes chromosome 7 and regulates totipotency via ZFP819.
    Liane P Fernandes, Rocio Enriquez-Gasca, Poppy A Gould, James H Holt, Lucia Conde, Gabriela Ecco, Javier Herrero, Robert Gifford, Didier Trono, George Kassiotis, Helen M Rowe.
      Mammalian genomes are a battleground for genetic conflict between repetitive elements and KRAB-zinc finger proteins (KZFPs). We asked whether KZFPs can regulate cell fate by using ZFP819, which targets a satellite DNA array, ZP3AR. ZP3AR coats megabase regions of chromosome 7 encompassing genes encoding ZSCAN4, a master transcription factor of totipotency. Depleting ZFP819 in mouse embryonic stem cells (mESCs) causes them to transition to a 2-cell (2C)-like state, whereby the ZP3AR array switches from a poised to an active enhancer state. This is accompanied by a global erosion of heterochromatin roadblocks, which we link to decreased SETDB1 stability. These events result in transcription of active LINE-1 elements and impaired differentiation. In summary, ZFP819 and TRIM28 partner up to close chromatin across Zscan4, to promote exit from totipotency. We propose that satellite DNAs may control developmental fate transitions by barcoding and switching off master transcription factor genes.
    DOI:  https://doi.org/10.1126/sciadv.abp8085
  17. Cancer Discov. 2022 Oct 28. pii: CD-21-1492. [Epub ahead of print]
    Epigenome programing by H3.3K27M mutation creates a dependence of pediatric glioma on SMARCA4.
    Yan Mo, Shoufu Duan, Xu Zhang, Xu Hua, Hui Zhou, Hong-Jian Wei, Jun Watanabe, Nicholas McQuillan, Zhenyi Su, Wei Gu, Cheng-Chia Wu, Christopher R Vakoc, Rintaro Hashizume, Kenneth Chang, Zhiguo Zhang.
      Patients with diffuse midline gliomas-H3K27-altered (DMG) display a dismal prognosis. However, the molecular mechanisms underlying DMG tumorigenesis remain poorly defined. Here we show that SMARCA4, the catalytic subunit of mammalian SWI/SNF chromatin remodeling complex, is essential for the proliferation, migration and invasion of DMG cells and tumor growth in patient-derived DMG xenograft models. SMARCA4 co-localizes with SOX10 at gene regulatory elements (GRE) to control the expression of genes involved in cell growth and extracellular matrix (ECM). Moreover, SMARCA4 chromatin binding is reduced upon depletion of SOX10 or H3.3K27M, a mutation occurring in about 60% DMG tumors. Furthermore, the SMARCA4 occupancy at enhancers marked by both SOX10 and H3K27 acetylation is reduced the most upon depleting the H3.3K27M mutation. Taken together, our results support a model in which epigenome reprogramming by H3.3K27M creates a dependence on SMARCA4-mediated chromatin remodeling to drive gene expression and the pathogenesis of H3.3K27M DMG.
    DOI:  https://doi.org/10.1158/2159-8290.CD-21-1492
  18. Cell Genom. 2022 Aug 10. pii: 100164. [Epub ahead of print]2(8):
    Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases.
    Sean K Wang, Surag Nair, Rui Li, Katerina Kraft, Anusri Pampari, Aman Patel, Joyce B Kang, Christy Luong, Anshul Kundaje, Howard Y Chang.
      Genome-wide association studies (GWASs) of eye disorders have identified hundreds of genetic variants associated with ocular disease. However, the vast majority of these variants are noncoding, making it challenging to interpret their function. Here we present a joint single-cell atlas of gene expression and chromatin accessibility of the adult human retina with more than 50,000 cells, which we used to analyze single-nucleotide polymorphisms (SNPs) implicated by GWASs of age-related macular degeneration, glaucoma, diabetic retinopathy, myopia, and type 2 macular telangiectasia. We integrate this atlas with a HiChIP enhancer connectome, expression quantitative trait loci (eQTL) data, and base-resolution deep learning models to predict noncoding SNPs with causal roles in eye disease, assess SNP impact on transcription factor binding, and define their known and novel target genes. Our efforts nominate pathogenic SNP-target gene interactions for multiple vision disorders and provide a potentially powerful resource for interpreting noncoding variation in the eye.
    DOI:  https://doi.org/10.1016/j.xgen.2022.100164
  19. Aging Cancer. 2021 Dec;2(4): 137-159
    FOXO3 regulates a common genomic program in aging and glioblastoma stem cells.
    Amanda J Audesse, Galina Karashchuk, Zachary A Gardell, Nelli S Lakis, Sun Y Maybury-Lewis, Abigail K Brown, Dena S Leeman, Yee Voan Teo, Nicola Neretti, Douglas C Anthony, Alexander S Brodsky, Ashley E Webb.
       Background: Glioblastoma (GBM) is an aggressive, age-associated malignant glioma that contains populations of cancer stem cells. These glioma stem cells (GSCs) evade therapeutic interventions and repopulate tumors due to their existence in a slowly cycling quiescent state. Although aging is well known to increase cancer initiation, the extent to which the mechanisms supporting GSC tumorigenicity are related to physiological aging remains unknown.
    Aims: Here, we investigate the transcriptional mechanisms by which Forkhead Box O3 (FOXO3), a transcriptional regulator that promotes healthy aging, affects GSC function and the extent to which FOXO3 transcriptional networks are dysregulated in aging and GBM.
    Methods and results: We performed transcriptome analysis of clinical GBM tumors and observed that high FOXO3 activity is associated with gene expression signatures of stem cell quiescence, reduced oxidative metabolism, and improved patient outcomes. Consistent with these findings, we show that elevated FOXO3 activity significantly reduces the proliferation of GBM-derived GSCs. Using RNA-seq, we find that functional ablation of FOXO3 in GSCs rewires the transcriptional circuitry associated with metabolism, epigenetic stability, quiescence, and differentiation. Since FOXO3 has been implicated in healthy aging, we then investigated the extent to which it regulates common transcriptional programs in aging neural stem cells (NSCs) and GSCs. We uncover a shared transcriptional program and, most strikingly, find that FOXO3-regulated pathways are associated with altered mitochondrial functions in both aging and GBM.
    Conclusions: This work identifies a FOXO-associated transcriptional program that correlates between GSCs and aging NSCs and is enriched for metabolic and stemness pathways connected with GBM and aging.
    Keywords:  aging; glioma; stem cells; transcriptomics
    DOI:  https://doi.org/10.1002/aac2.12043
  20. Nat Biotechnol. 2022 Oct 27.
    Targeting MYC with modular synthetic transcriptional repressors derived from bHLH DNA-binding domains.
    Thomas E Speltz, Zeyu Qiao, Colin S Swenson, Xianghang Shangguan, John S Coukos, Christopher W Lee, Deborah M Thomas, Jesse Santana, Sean W Fanning, Geoffrey L Greene, Raymond E Moellering.
      Despite unequivocal roles in disease, transcription factors (TFs) remain largely untapped as pharmacologic targets due to the challenges in targeting protein-protein and protein-DNA interactions. Here we report a chemical strategy to generate modular synthetic transcriptional repressors (STRs) derived from the bHLH domain of MAX. Our synthetic approach yields chemically stabilized tertiary domain mimetics that cooperatively bind the MYC/MAX consensus E-box motif with nanomolar affinity, exhibit specificity that is equivalent to or beyond that of full-length TFs and directly compete with MYC/MAX protein for DNA binding. A lead STR directly inhibits MYC binding in cells, downregulates MYC-dependent expression programs at the proteome level and inhibits MYC-dependent cell proliferation. Co-crystallization and structure determination of a STR:E-box DNA complex confirms retention of DNA recognition in a near identical manner as full-length bHLH TFs. We additionally demonstrate structure-blind design of STRs derived from alternative bHLH-TFs, confirming that STRs can be used to develop highly specific mimetics of TFs targeting other gene regulatory elements.
    DOI:  https://doi.org/10.1038/s41587-022-01504-x
  21. Cancer Res. 2022 Oct 26. OF1-OF14
    Global DNA Methylation Analysis of Cancer-Associated Fibroblasts Reveals Extensive Epigenetic Rewiring Linked with RUNX1 Upregulation in Breast Cancer Stroma.
    Coral Halperin, Joschka Hey, Dieter Weichenhan, Yaniv Stein, Shimrit Mayer, Pavlo Lutsik, Christoph Plass, Ruth Scherz-Shouval.
      Cancer cells recruit and rewire normal fibroblasts in their microenvironment to become protumorigenic cancer-associated fibroblasts (CAF). These CAFs are genomically stable, yet their transcriptional programs are distinct from those of their normal counterparts. Transcriptional regulation plays a major role in this reprogramming, but the extent to which epigenetic modifications of DNA also contribute to the rewiring of CAF transcription is not clear. Here we address this question by dissecting the epigenetic landscape of breast CAFs. Applying tagmentation-based whole-genome bisulfite sequencing in a mouse model of breast cancer, we found that fibroblasts undergo massive DNA methylation changes as they transition into CAFs. Transcriptional and epigenetic analyses revealed RUNX1 as a potential mediator of this process and identified a RUNX1-dependent stromal gene signature. Coculture and mouse models showed that both RUNX1 and its stromal signature are induced as normal fibroblasts transition into CAFs. In breast cancer patients, RUNX1 was upregulated in CAFs, and expression of the RUNX1 signature was associated with poor disease outcome, highlighting the relevance of these findings to human disease. This work presents a comprehensive genome-wide map of DNA methylation in CAFs and reveals a previously unknown facet of the dynamic plasticity of the stroma.
    SIGNIFICANCE: The first genome-wide map of DNA methylation in breast cancer-associated fibroblasts unravels a previously unknown facet of the dynamic plasticity of the stroma, with far-reaching therapeutic implications.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-0209
  22. iScience. 2022 Nov 18. 25(11): 105279
    A multi-omics approach to visualize early neuronal differentiation from hESCs in 4D.
    Athina Samara, Mari Spildrejorde, Ankush Sharma, Martin Falck, Magnus Leithaug, Stefania Modafferi, Pål Marius Bjørnstad, Ganesh Acharya, Kristina Gervin, Robert Lyle, Ragnhild Eskeland.
      Neuronal differentiation of pluripotent stem cells is an established method to study physiology, disease, and medication safety. However, the sequence of events in human neuronal differentiation and the ability of in vitro models to recapitulate early brain development are poorly understood. We developed a protocol optimized for the study of early human brain development and neuropharmacological applications. We comprehensively characterized gene expression and epigenetic profiles at four timepoints, because the cells differentiate from embryonic stem cells towards a heterogeneous population of progenitors, immature and mature neurons bearing telencephalic signatures. A multi-omics roadmap of neuronal differentiation, combined with searchable interactive gene analysis tools, allows for extensive exploration of early neuronal development and the effect of medications.
    Keywords:  Cell biology; Neuroscience; Omics
    DOI:  https://doi.org/10.1016/j.isci.2022.105279
  23. PLoS One. 2022 ;17(10): e0276069
    Transcription factor gene Pea3 regulates erectile function during copulation in mice.
    Jarret A P Weinrich, Aanchal Tyagi, Megan C Kenney, Richard J DiCasoli, Julia A Kaltschmidt.
      Male mice with homozygous loss of function mutations of the transcription factor gene Pea3 (Pea3 null) are infertile due to their inability to inseminate females, however the specific deficits in male sexual behaviors that drive this phenotype are unknown. Here, the copulatory behavior of male mice (Pea3 null and control) with hormonally primed ovariectomized females was monitored via high-speed and high-resolution digital videography to assess for differences in female-directed social behaviors, gross sexual behaviors (mounting, thrusting), and erectile and ejaculatory function. Pea3 null male mice exhibit greatly reduced erectile function, with 44% of males displaying no visible erections during copulation, and 0% achieving sustained erections. As such, Pea3 null males are incapable of intromission and copulatory plug deposition, despite displaying largely normal female-directed social behaviors, mounting behaviors, and ejaculatory grasping behavior. Additionally, the organization and timing of thrusting behaviors is impaired in Pea3 null males. Our results show that the transcription factor gene Pea3 regulates the ability to achieve and maintain erections during copulation in mice.
    DOI:  https://doi.org/10.1371/journal.pone.0276069
  24. Nat Commun. 2022 Oct 27. 13(1): 6354
    Transient inhibition of p53 enhances prime editing and cytosine base-editing efficiencies in human pluripotent stem cells.
    Mu Li, Aaron Zhong, Youjun Wu, Mega Sidharta, Michael Beaury, Xiaolan Zhao, Lorenz Studer, Ting Zhou.
      Precise gene editing in human pluripotent stem cells (hPSCs) holds great promise for studying and potentially treating human diseases. Both prime editing and base editing avoid introducing double strand breaks, but low editing efficiencies make those techniques still an arduous process in hPSCs. Here we report that co-delivering of p53DD, a dominant negative fragment of p53, can greatly enhance prime editing and cytosine base editing efficiencies in generating precise mutations in hPSCs. We further apply PE3 in combination with p53DD to efficiently create multiple isogenic hPSC lines, including lines carrying GBA or LRRK2 mutations associated with Parkinson disease and a LMNA mutation linked to Hutchinson-Gilford progeria syndrome. We also correct GBA and LMNA mutations in the patient-specific iPSCs. Our data show that p53DD improves PE3 efficiency without compromising the genome-wide safety, making it feasible for safe and routine generation of isogenic hPSC lines for disease modeling.
    DOI:  https://doi.org/10.1038/s41467-022-34045-7
  25. Nucleic Acids Res. 2022 Oct 28. pii: gkac941. [Epub ahead of print]
    Vitamin C enhances NF-κB-driven epigenomic reprogramming and boosts the immunogenic properties of dendritic cells.
    Octavio Morante-Palacios, Gerard Godoy-Tena, Josep Calafell-Segura, Laura Ciudad, Eva M Martínez-Cáceres, José Luis Sardina, Esteban Ballestar.
      Dendritic cells (DCs), the most potent antigen-presenting cells, are necessary for effective activation of naïve T cells. DCs' immunological properties are modulated in response to various stimuli. Active DNA demethylation is crucial for DC differentiation and function. Vitamin C, a known cofactor of ten-eleven translocation (TET) enzymes, drives active demethylation. Vitamin C has recently emerged as a promising adjuvant for several types of cancer; however, its effects on human immune cells are poorly understood. In this study, we investigate the epigenomic and transcriptomic reprogramming orchestrated by vitamin C in monocyte-derived DC differentiation and maturation. Vitamin C triggers extensive demethylation at NF-κB/p65 binding sites, together with concordant upregulation of antigen-presentation and immune response-related genes during DC maturation. p65 interacts with TET2 and mediates the aforementioned vitamin C-mediated changes, as demonstrated by pharmacological inhibition. Moreover, vitamin C increases TNFβ production in DCs through NF-κB, in concordance with the upregulation of its coding gene and the demethylation of adjacent CpGs. Finally, vitamin C enhances DC's ability to stimulate the proliferation of autologous antigen-specific T cells. We propose that vitamin C could potentially improve monocyte-derived DC-based cell therapies.
    DOI:  https://doi.org/10.1093/nar/gkac941
  26. Elife. 2022 Oct 27. pii: e78810. [Epub ahead of print]11
    Covalent disruptor of YAP-TEAD association suppresses defective hippo signaling.
    Mengyang Fan, Wenchao Lu, Jianwei Che, Nicholas P Kwiatkowski, Yang Gao, Hyuk-Soo Seo, Scott B Ficarro, Prafulla C Gokhale, Yao Liu, Ezekiel A Geffken, Jimit Lakhani, Kijun Song, Miljan Kuljanin, Wenzhi Ji, Jie Jiang, Zhixiang He, Jason Tse, Andrew S Boghossian, Matthew G Rees, Melissa M Ronan, Jennifer A Roth, Joseph D Mancias, Jarrod A Marto, Sirano Dhe-Paganon, Tinghu Zhang, Nathanael S Gray.
      The transcription factor TEAD, together with its coactivator YAP/TAZ, is a key transcriptional modulator of the Hippo pathway. Activation of TEAD transcription by YAP has been implicated in a number of malignancies, and this complex represents a promising target for drug discovery. However, both YAP and its extensive binding interfaces to TEAD have been difficult to address using small molecules, mainly due to a lack of druggable pockets. TEAD is post-translationally modified by palmitoylation that targets a conserved cysteine at a central pocket, which provides an opportunity to develop cysteine-directed covalent small molecules for TEAD inhibition. Here, we employed covalent fragment screening approach followed by structure-based design to develop an irreversible TEAD inhibitor MYF-03-69. Using a range of in vitro and cell-based assays we demonstrated that through a covalent binding with TEAD palmitate pocket, MYF-03-69 disrupts YAP-TEAD association, suppresses TEAD transcriptional activity and inhibits cell growth of Hippo signaling defective malignant pleural mesothelioma (MPM). Further, a cell viability screening with a panel of 903 cancer cell lines indicated a high correlation between TEAD-YAP dependency and the sensitivity to MYF-03-69. Transcription profiling identified the upregulation of proapoptotic BMF gene in cancer cells that are sensitive to TEAD inhibition. Further optimization of MYF-03-69 led to an in vivo compatible compound MYF-03-176, which shows strong antitumor efficacy in MPM mouse xenograft model via oral administration. Taken together, we disclosed a story of the development of covalent TEAD inhibitors and its high therapeutic potential for clinic treatment for the cancers that are driven by TEAD-YAP alteration.
    Keywords:  biochemistry; chemical biology; human
    DOI:  https://doi.org/10.7554/eLife.78810
  27. Elife. 2022 Oct 27. pii: e83373. [Epub ahead of print]11
    Z-REX uncovers a bifurcation in function of Keap1 paralogs.
    Alexandra Van Hall-Beauvais, Jesse R Poganik, Kuan-Ting Huang, Saba Parvez, Yi Zhao, Hong-Yu Lin, Xuyu Liu, Marcus John Curtis Long, Yimon Aye.
      Studying electrophile signaling is marred by difficulties in parsing changes in pathway flux attributable to on-target, vis-à-vis off-target, modifications. By combining bolus dosing, knockdown, and Z-REX-a tool investigating on-target/on-pathway electrophile signaling, we document that electrophile labeling of one zebrafish-Keap1-paralog (zKeap1b) stimulates Nrf2- driven antioxidant response (AR) signaling (like the human-ortholog). Conversely, zKeap1a is a dominant-negative regulator of electrophile-promoted Nrf2-signaling, and itself is nonpermissive for electrophile-induced Nrf2-upregulation. This behavior is recapitulated in human cells, wherein following electrophile treatment: (1) zKeap1b-transfected cells are permissive for augmented AR-signaling through reduced zKeap1b-Nrf2 binding; (2) zKeap1a-transfected cells are non-permissive for AR-upregulation, as zKeap1a-Nrf2 binding capacity remains unaltered; (3) 1:1 ZKeap1a:zKeap1b-transfected cells show no Nrf2-release from the Keap1-complex, rendering these cells unable to upregulate AR. We identified a zKeap1a-specific point-mutation (C273I) responsible for zKeap1a's behavior. Human-Keap1(C273I), of known diminished Nrf2-regulatory capacity, dominantly muted electrophile-induced Nrf2-signaling. These studies highlight divergent and interdependent electrophile signaling behaviors, despite conserved electrophile sensing.
    Keywords:  biochemistry; chemical biology; zebrafish
    DOI:  https://doi.org/10.7554/eLife.83373
  28. Cancer Discov. 2022 Oct 28. pii: CD-21-1491. [Epub ahead of print]
    BAF complex maintains glioma stem cells in pediatric H3K27M-glioma.
    Eshini Panditharatna, Joana G Marques, Tingjian Wang, Maria C Trissal, Ilon Liu, Li Jiang, Alexander Beck, Andrew Groves, Neekesh V Dharia, Deyao Li, Samantha E Hoffman, Guillaume Kugener, McKenzie L Shaw, Hafsa M Mire, Olivia A Hack, Joshua M Dempster, Caleb Lareau, Lingling Dai, Logan H Sigua, Michael A Quezada, Ann-Catherine J Stanton, Meghan Wyatt, Zohra Kalani, Amy Goodale, Francisca Vazquez, Federica Piccioni, John G Doench, David E Root, Jamie N Anastas, Kristen L Jones, Amy Saur Conway, Sylwia Stopka, Michael S Regan, Yu Liang, Hyuk-Soo Seo, Kijun Song, Puspalata Bashyal, William P Jerome, Nathan D Mathewson, Sirano Dhe-Paganon, Mario L Suva, Angel M Carcaboso, Cinzia Lavarino, Jaume Mora, Quang-De Nguyen, Keith L Ligon, Yang Shi, Sameer Agnihotri, Nathalie Y R Agar, Kimberly Stegmaier, Charles D Stiles, Michelle Monje, Todd R Golub, Jun Qi, Mariella G Filbin.
      Diffuse midline gliomas are uniformly fatal pediatric central nervous system cancers, refractory to standard of care therapeutic modalities. The primary genetic drivers are a set of recurrent amino acid substitutions in genes encoding histone H3 (H3K27M), which are currently undruggable. These H3K27M oncohistones perturb normal chromatin architecture, resulting in an aberrant epigenetic landscape. To interrogate for epigenetic dependencies, we performed a CRISPR screen and show that patient-derived H3K27M-glioma neurospheres are dependent on core components of the mammalian BAF (SWI/SNF) chromatin remodeling complex. The BAF complex maintains glioma stem cells in a cycling, oligodendrocyte precursor cell (OPC)-like state, where genetic perturbation of the BAF catalytic subunit SMARCA4 (BRG1), as well as pharmacological suppression opposes proliferation, promotes progression of differentiation along the astrocytic lineage, and improves overall survival of patient-derived xenograft models. In summary, we demonstrate that therapeutic inhibition of BAF complex has translational potential for children with H3K27M-gliomas.
    DOI:  https://doi.org/10.1158/2159-8290.CD-21-1491
  29. Front Med (Lausanne). 2022 ;9 919345
    CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data.
    Louisa Hadj Abed, Tamar Tak, Jason Cosgrove, Leïla Perié.
      Single-cell lineage tracing permits the labeling of individual cells with a heritable marker to follow the fate of each cell's progeny. Over the last twenty years, several single-cell lineage tracing methods have emerged, enabling major discoveries in developmental biology, oncology and gene therapies. Analytical tools are needed to draw meaningful conclusions from lineage tracing measurements, which are characterized by high variability, sparsity and technical noise. However, the single cell lineage tracing field lacks versatile and easy-to-use tools for standardized and reproducible analyses, in particular tools accessible to biologists. Here we present CellDestiny, a RShiny app and associated web application developed for experimentalists without coding skills to perform visualization and analysis of single cell lineage-tracing datasets through a graphical user interface. We demonstrate the functionality of CellDestiny through the analysis of (i) lentiviral barcoding datasets of murine hematopoietic progenitors; (ii) published integration site data from Wiskott-Aldrich Symdrome patients undergoing gene-therapy treatment; and (iii) simultaneous barcoding and transcriptomic analysis of murine hematopoietic progenitor differentiation in vitro. In summary, CellDestiny is an easy-to-use and versatile toolkit that enables biologists to visualize and analyze single-cell lineage tracing data.
    Keywords:  bioinformatics; data analysis; gene therapy; lentiviral barcoding; lineage tracing; single-cell
    DOI:  https://doi.org/10.3389/fmed.2022.919345
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