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Zhu T, Okabe A, Usui G, Fujiki R, Komiyama D, Huang KK, Seki M, Fukuyo M, Abe H, Ning M, Okada T, Minami M, Matsumoto M, Fan Q, Rahmutulla B, Hoshii T, Tan P, Morikawa T, Ushiku T, Kaneda A. Integrated enhancer regulatory network by enhancer-promoter looping in gastric cancer. NAR Cancer 2024; 6:zcae020. [PMID: 38720882 PMCID: PMC11077903 DOI: 10.1093/narcan/zcae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/07/2024] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
Enhancer cis-regulatory elements play critical roles in gene regulation at many stages of cell growth. Enhancers in cancer cells also regulate the transcription of oncogenes. In this study, we performed a comprehensive analysis of long-range chromatin interactions, histone modifications, chromatin accessibility and expression in two gastric cancer (GC) cell lines compared to normal gastric epithelial cells. We found that GC-specific enhancers marked by histone modifications can activate a population of genes, including some oncogenes, by interacting with their proximal promoters. In addition, motif analysis of enhancer-promoter interacting enhancers showed that GC-specific transcription factors are enriched. Among them, we found that MYB is crucial for GC cell growth and activated by the enhancer with an enhancer-promoter loop and TCF7 upregulation. Clinical GC samples showed epigenetic activation of enhancers at the MYB locus and significant upregulation of TCF7 and MYB, regardless of molecular GC subtype and clinicopathological factors. Single-cell RNA sequencing of gastric mucosa with intestinal metaplasia showed high expression of TCF7 and MYB in intestinal stem cells. When we inactivated the loop-forming enhancer at the MYB locus using CRISPR interference (dCas9-KRAB), GC cell growth was significantly inhibited. In conclusion, we identified MYB as an oncogene activated by a loop-forming enhancer and contributing to GC cell growth.
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Affiliation(s)
- Tianhui Zhu
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
- Health and Disease Omics Center, Chiba University, Chiba 260-8670, Japan
| | - Genki Usui
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Ryoji Fujiki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Daichi Komiyama
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Kie Kyon Huang
- Program in Cancer and Stem Cell Biology, Duke–NUS Medical School, Singapore 169857, Singapore
| | - Motoaki Seki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Hiroyuki Abe
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Meng Ning
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Tomoka Okada
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Mizuki Minami
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Makoto Matsumoto
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Qin Fan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Patrick Tan
- Program in Cancer and Stem Cell Biology, Duke–NUS Medical School, Singapore 169857, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138632, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Teppei Morikawa
- Department of Diagnostic Pathology, NTT Medical Center Tokyo, Tokyo 141-8625, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
- Health and Disease Omics Center, Chiba University, Chiba 260-8670, Japan
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2
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Bohrer C, Varon E, Peretz E, Reinitz G, Kinor N, Halle D, Nissan A, Shav-Tal Y. CCAT1 lncRNA is chromatin-retained and post-transcriptionally spliced. Histochem Cell Biol 2024:10.1007/s00418-024-02294-w. [PMID: 38763947 DOI: 10.1007/s00418-024-02294-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 05/21/2024]
Abstract
Super-enhancers are unique gene expression regulators widely involved in cancer development. Spread over large DNA segments, they tend to be found next to oncogenes. The super-enhancer c-MYC locus forms long-range chromatin looping with nearby genes, which brings the enhancer and the genes into proximity, to promote gene activation. The colon cancer-associated transcript 1 (CCAT1) gene, which is part of the MYC locus, transcribes a lncRNA that is overexpressed in colon cancer cells through activation by MYC. Comparing different types of cancer cell lines using RNA fluorescence in situ hybridization (RNA FISH), we detected very prominent CCAT1 expression in HeLa cells, observed as several large CCAT1 nuclear foci. We found that dozens of CCAT1 transcripts accumulate on the gene locus, in addition to active transcription occurring from the gene. The accumulating transcripts are released from the chromatin during cell division. Examination of CCAT1 lncRNA expression patterns on the single-RNA level showed that unspliced CCAT1 transcripts are released from the gene into the nucleoplasm. Most of these unspliced transcripts were observed in proximity to the active gene but were not associated with nuclear speckles in which unspliced RNAs usually accumulate. At larger distances from the gene, the CCAT1 transcripts appeared spliced, implying that most CCAT1 transcripts undergo post-transcriptional splicing in the zone of the active gene. Finally, we show that unspliced CCAT1 transcripts can be detected in the cytoplasm during splicing inhibition, which suggests that there are several CCAT1 variants, spliced and unspliced, that the cell can recognize as suitable for export.
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Affiliation(s)
- Chaya Bohrer
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Varon
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Eldar Peretz
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Gita Reinitz
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Noa Kinor
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - David Halle
- Biochemistry Laboratory, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Aviram Nissan
- Ziv Medical Center, Safed, Israel
- Surgical Innovation Laboratory, The Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel.
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3
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Peralta-Alvarez CA, Núñez-Martínez HN, Cerecedo-Castillo ÁJ, Poot-Hernández AC, Tapia-Urzúa G, Garza-Manero S, Guerrero G, Recillas-Targa F. A Bidirectional Non-Coding RNA Promoter Mediates Long-Range Gene Expression Regulation. Genes (Basel) 2024; 15:549. [PMID: 38790178 PMCID: PMC11120797 DOI: 10.3390/genes15050549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Recent evidence suggests that human gene promoters display gene expression regulatory mechanisms beyond the typical single gene local transcription modulation. In mammalian genomes, genes with an associated bidirectional promoter are abundant; bidirectional promoter architecture serves as a regulatory hub for a gene pair expression. However, it has been suggested that its contribution to transcriptional regulation might exceed local transcription initiation modulation. Despite their abundance, the functional consequences of bidirectional promoter architecture remain largely unexplored. This work studies the long-range gene expression regulatory role of a long non-coding RNA gene promoter using chromosome conformation capture methods. We found that this particular bidirectional promoter contributes to distal gene expression regulation in a target-specific manner by establishing promoter-promoter interactions. In particular, we validated that the promoter-promoter interactions of this regulatory element with the promoter of distal gene BBX contribute to modulating the transcription rate of this gene; removing the bidirectional promoter from its genomic context leads to a rearrangement of BBX promoter-enhancer interactions and to increased gene expression. Moreover, long-range regulatory functionality is not directly dependent on its associated non-coding gene pair expression levels.
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Affiliation(s)
- Carlos Alberto Peralta-Alvarez
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
- Instituto de Fisiología Celular, Unidad de Bioinformática y Manejo de la Información, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Hober Nelson Núñez-Martínez
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
| | - Ángel Josué Cerecedo-Castillo
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
| | - Augusto César Poot-Hernández
- Instituto de Fisiología Celular, Unidad de Bioinformática y Manejo de la Información, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Gustavo Tapia-Urzúa
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
| | - Sylvia Garza-Manero
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
| | - Georgina Guerrero
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
| | - Félix Recillas-Targa
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
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4
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Freie B, Carroll PA, Varnum-Finney BJ, Ramsey EL, Ramani V, Bernstein I, Eisenman RN. A germline point mutation in the MYC-FBW7 phosphodegron initiates hematopoietic malignancies. Genes Dev 2024; 38:253-272. [PMID: 38565249 PMCID: PMC11065175 DOI: 10.1101/gad.351292.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024]
Abstract
Oncogenic activation of MYC in cancers predominantly involves increased transcription rather than coding region mutations. However, MYC-dependent lymphomas frequently acquire point mutations in the MYC phosphodegron, including at threonine 58 (T58), where phosphorylation permits binding via the FBW7 ubiquitin ligase triggering MYC degradation. To understand how T58 phosphorylation functions in normal cell physiology, we introduced an alanine mutation at T58 (T58A) into the endogenous c-Myc locus in the mouse germline. While MYC-T58A mice develop normally, lymphomas and myeloid leukemias emerge in ∼60% of adult homozygous T58A mice. We found that primitive hematopoietic progenitor cells from MYC-T58A mice exhibit aberrant self-renewal normally associated with hematopoietic stem cells (HSCs) and up-regulate a subset of MYC target genes important in maintaining stem/progenitor cell balance. In lymphocytes, genomic occupancy by MYC-T58A was increased at all promoters compared with WT MYC, while genes differentially expressed in a T58A-dependent manner were significantly more proximal to MYC-bound enhancers. MYC-T58A lymphocyte progenitors exhibited metabolic alterations and decreased activation of inflammatory and apoptotic pathways. Our data demonstrate that a single point mutation stabilizing MYC is sufficient to skew target gene expression, producing a profound gain of function in multipotential hematopoietic progenitors associated with self-renewal and initiation of lymphomas and leukemias.
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Affiliation(s)
- Brian Freie
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA;
| | - Patrick A Carroll
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | | | - Erin L Ramsey
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Vijay Ramani
- Gladstone Institute for Data Science and Biotechnology, University of California, San Francisco, San Francisco, California 94158, USA
| | - Irwin Bernstein
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Robert N Eisenman
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA;
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5
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Li R, He J, Ni Z, Zhang J, Chi X, Kang C, Li Z, Li X. Mining and exploration of rehabilitation nursing targets for colorectal cancer. Aging (Albany NY) 2024; 16:7022-7042. [PMID: 38637125 PMCID: PMC11087124 DOI: 10.18632/aging.205739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/20/2023] [Indexed: 04/20/2024]
Abstract
BACKGROUND There are often subtle early symptoms of colorectal cancer, a common malignancy of the intestinal tract. However, it is not yet clear how MYC and NCAPG2 are involved in colorectal cancer. METHOD We obtained colorectal cancer datasets GSE32323 and GSE113513 from the Gene Expression Omnibus (GEO). After downloading, we identified differentially expressed genes (DEGs) and performed Weighted Gene Co-expression Network Analysis (WGCNA). We then undertook functional enrichment assay, gene set enrichment assay (GSEA) and immune infiltration assay. Protein-protein interaction (PPI) network construction and analysis were undertaken. Survival analysis and Comparative Toxicogenomics Database (CTD) analysis were conducted. A gene expression heat map was generated. We used TargetScan to identify miRNAs that are regulators of DEGs. RESULTS 1117 DEGs were identified. Their predominant enrichment in activities like the cellular phase of the cell cycle, in cell proliferation, in nuclear and cytoplasmic localisation and in binding to protein-containing complexes was revealed by Gene Ontology (GO). When the enrichment data from GSE32323 and GSE113513 colon cancer datasets were merged, the primary enriched DEGs were linked to the cell cycle, protein complex, cell cycle control, calcium signalling and P53 signalling pathways. In particular, MYC, MAD2L1, CENPF, UBE2C, NUF2 and NCAPG2 were identified as highly expressed in colorectal cancer samples. Comparative Toxicogenomics Database (CTD) demonstrated that the core genes were implicated in the following processes: colorectal neoplasia, tumour cell transformation, inflammation and necrosis. CONCLUSIONS High MYC and NCAPG2 expression has been observed in colorectal cancer, and increased MYC and NCAPG2 expression correlates with worse prognosis.
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Affiliation(s)
- Ruipu Li
- Gastrointestinal Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Shijingshan 100144, Beijing, China
| | - Jie He
- Department of Colorectal Surgery, China Aerospace Science and Industry Corporation 731 Hospital, Fengtai, Beijing, China
| | - Zhijie Ni
- Department of Colorectal Surgery, China Aerospace Science and Industry Corporation 731 Hospital, Fengtai, Beijing, China
| | - Jie Zhang
- Gastrointestinal Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Shijingshan 100144, Beijing, China
| | - Xiaoqian Chi
- Gastrointestinal Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Shijingshan 100144, Beijing, China
| | - Chunbo Kang
- Gastrointestinal Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Shijingshan 100144, Beijing, China
| | - Zhongbo Li
- Department of Colorectal Surgery, China Aerospace Science and Industry Corporation 731 Hospital, Fengtai, Beijing, China
| | - Xubin Li
- Gastrointestinal Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Shijingshan 100144, Beijing, China
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6
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Jakobsen ST, Jensen RAM, Madsen MS, Ravnsborg T, Vaagenso CS, Siersbæk MS, Einarsson H, Andersson R, Jensen ON, Siersbæk R. MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch. Nat Genet 2024; 56:663-674. [PMID: 38454021 DOI: 10.1038/s41588-024-01676-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024]
Abstract
The transcription factor MYC is overexpressed in most cancers, where it drives multiple hallmarks of cancer progression. MYC is known to promote oncogenic transcription by binding to active promoters. In addition, MYC has also been shown to invade distal enhancers when expressed at oncogenic levels, but this enhancer binding has been proposed to have low gene-regulatory potential. Here, we demonstrate that MYC directly regulates enhancer activity to promote cancer type-specific gene programs predictive of poor patient prognosis. MYC induces transcription of enhancer RNA through recruitment of RNA polymerase II (RNAPII), rather than regulating RNAPII pause-release, as is the case at promoters. This process is mediated by MYC-induced H3K9 demethylation and acetylation by GCN5, leading to enhancer-specific BRD4 recruitment through its bromodomains, which facilitates RNAPII recruitment. We propose that MYC drives prognostic cancer type-specific gene programs through induction of an enhancer-specific epigenetic switch, which can be targeted by BET and GCN5 inhibitors.
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Affiliation(s)
- Simon T Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Rikke A M Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Maria S Madsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Tina Ravnsborg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Majken S Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hjorleifur Einarsson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robin Andersson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Rasmus Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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7
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Prutsch N, He S, Berezovskaya A, Durbin AD, Dharia NV, Maher KA, Matthews JD, Hare L, Turner SD, Stegmaier K, Kenner L, Merkel O, Look AT, Abraham BJ, Zimmerman MW. STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma. Cell Rep Med 2024; 5:101472. [PMID: 38508140 PMCID: PMC10983107 DOI: 10.1016/j.xcrm.2024.101472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 12/01/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Anaplastic large cell lymphoma (ALCL) is an aggressive, CD30+ T cell lymphoma of children and adults. ALK fusion transcripts or mutations in the JAK-STAT pathway are observed in most ALCL tumors, but the mechanisms underlying tumorigenesis are not fully understood. Here, we show that dysregulated STAT3 in ALCL cooccupies enhancers with master transcription factors BATF3, IRF4, and IKZF1 to form a core regulatory circuit that establishes and maintains the malignant cell state in ALCL. Critical downstream targets of this network in ALCL cells include the protooncogene MYC, which requires active STAT3 to facilitate high levels of MYC transcription. The core autoregulatory transcriptional circuitry activity is reinforced by MYC binding to the enhancer regions associated with STAT3 and each of the core regulatory transcription factors. Thus, activation of STAT3 provides the crucial link between aberrant tyrosine kinase signaling and the core transcriptional machinery that drives tumorigenesis and creates therapeutic vulnerabilities in ALCL.
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Affiliation(s)
- Nicole Prutsch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA
| | - Alla Berezovskaya
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA
| | - Adam D Durbin
- Division of Molecular Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Kelsey A Maher
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jamie D Matthews
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Lucy Hare
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Department of Pediatric Oncology and Hematology, Addenbrooke's Hospital, Cambridge, UK
| | - Suzanne D Turner
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Lukas Kenner
- Department of Pathology, Unit of Experimental and Laboratory Animal Pathology, Medical University of Vienna, Vienna, Austria
| | - Olaf Merkel
- Department of Pathology, Unit of Experimental and Laboratory Animal Pathology, Medical University of Vienna, Vienna, Austria
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA.
| | - Brian J Abraham
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Mark W Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA.
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8
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He L, Sun H, Wang H. 3D organization of enhancers in MuSCs. Curr Top Dev Biol 2024; 158:407-431. [PMID: 38670714 DOI: 10.1016/bs.ctdb.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Skeletal muscle stem cells (MuSCs), also known as satellite cells, are essential for muscle growth and injury induced regeneration. In healthy adult muscle, MuSCs remain in a quiescent state located in a specialized niche beneath the basal lamina. Upon injury, these dormant MuSCs can quickly activate to re-enter the cell cycle and differentiate into new myofibers, while a subset undergoes self-renewal and returns to quiescence to restore the stem cell pool. The myogenic lineage progression is intricately controlled by complex intrinsic and extrinsic cues and coupled with dynamic transcriptional programs. In transcriptional regulation, enhancers are key regulatory elements controlling spatiotemporal gene expression through physical contacting promoters of target genes. The three-dimensional (3D) chromatin architecture is known to orchestrate the establishment of proper enhancer-promoter interactions throughout development and aging. However, studies dissecting the 3D organization of enhancers in MuSCs are just emerging. Here, we provide an overview of the general properties of enhancers and newly developed methods for assessing their activity. In particular, we summarize recent discoveries regarding the 3D rewiring of enhancers during MuSC specification, lineage progression as well as aging.
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Affiliation(s)
- Liangqiang He
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, New Territories, Hong Kong SAR, P.R. China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| | - Huating Wang
- Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, New Territories, Hong Kong SAR, P.R. China; Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China.
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9
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Kimura K, Jackson TLB, Huang RCC. Interaction and Collaboration of SP1, HIF-1, and MYC in Regulating the Expression of Cancer-Related Genes to Further Enhance Anticancer Drug Development. Curr Issues Mol Biol 2023; 45:9262-9283. [PMID: 37998757 PMCID: PMC10670631 DOI: 10.3390/cimb45110580] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/25/2023] Open
Abstract
Specificity protein 1 (SP1), hypoxia-inducible factor 1 (HIF-1), and MYC are important transcription factors (TFs). SP1, a constitutively expressed housekeeping gene, regulates diverse yet distinct biological activities; MYC is a master regulator of all key cellular activities including cell metabolism and proliferation; and HIF-1, whose protein level is rapidly increased when the local tissue oxygen concentration decreases, functions as a mediator of hypoxic signals. Systems analyses of the regulatory networks in cancer have shown that SP1, HIF-1, and MYC belong to a group of TFs that function as master regulators of cancer. Therefore, the contributions of these TFs are crucial to the development of cancer. SP1, HIF-1, and MYC are often overexpressed in tumors, which indicates the importance of their roles in the development of cancer. Thus, proper manipulation of SP1, HIF-1, and MYC by appropriate agents could have a strong negative impact on cancer development. Under these circumstances, these TFs have naturally become major targets for anticancer drug development. Accordingly, there are currently many SP1 or HIF-1 inhibitors available; however, designing efficient MYC inhibitors has been extremely difficult. Studies have shown that SP1, HIF-1, and MYC modulate the expression of each other and collaborate to regulate the expression of numerous genes. In this review, we provide an overview of the interactions and collaborations of SP1, HIF1A, and MYC in the regulation of various cancer-related genes, and their potential implications in the development of anticancer therapy.
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Affiliation(s)
| | | | - Ru Chih C. Huang
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218-2685, USA
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10
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Milevskiy MJ, Coughlan HD, Kane SR, Johanson TM, Kordafshari S, Chan WF, Tsai M, Surgenor E, Wilcox S, Allan RS, Chen Y, Lindeman GJ, Smyth GK, Visvader JE. Three-dimensional genome architecture coordinates key regulators of lineage specification in mammary epithelial cells. CELL GENOMICS 2023; 3:100424. [PMID: 38020976 PMCID: PMC10667557 DOI: 10.1016/j.xgen.2023.100424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/20/2023] [Accepted: 09/20/2023] [Indexed: 12/01/2023]
Abstract
Although lineage-specific genes have been identified in the mammary gland, little is known about the contribution of the 3D genome organization to gene regulation in the epithelium. Here, we describe the chromatin landscape of the three major epithelial subsets through integration of long- and short-range chromatin interactions, accessibility, histone modifications, and gene expression. While basal genes display exquisite lineage specificity via distal enhancers, luminal-specific genes show widespread promoter priming in basal cells. Cell specificity in luminal progenitors is largely mediated through extensive chromatin interactions with super-enhancers in gene-body regions in addition to interactions with polycomb silencer elements. Moreover, lineage-specific transcription factors appear to be controlled through cell-specific chromatin interactivity. Finally, chromatin accessibility rather than interactivity emerged as a defining feature of the activation of quiescent basal stem cells. This work provides a comprehensive resource for understanding the role of higher-order chromatin interactions in cell-fate specification and differentiation in the adult mouse mammary gland.
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Affiliation(s)
- Michael J.G. Milevskiy
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Hannah D. Coughlan
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Serena R. Kane
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Timothy M. Johanson
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Somayeh Kordafshari
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Wing Fuk Chan
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Minhsuang Tsai
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Elliot Surgenor
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Stephen Wilcox
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Rhys S. Allan
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Yunshun Chen
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Geoffrey J. Lindeman
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
- Parkville Familial Cancer Centre and Department of Medical Oncology, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, VIC 3050, Australia
| | - Gordon K. Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jane E. Visvader
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
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11
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Freie B, Carroll PA, Varnum-Finney BJ, Ramani V, Bernstein I, Eisenman RN. A Germline Point Mutation in the MYC-FBW7 Phosphodegron Initiates Hematopoietic Malignancies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563660. [PMID: 37961183 PMCID: PMC10634767 DOI: 10.1101/2023.10.23.563660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Oncogenic activation of MYC in cancers predominantly involves increased transcription rather than coding region mutations. However, MYC-dependent lymphomas frequently contain point mutations in the MYC phospho-degron, including at threonine-58 (T58), where phosphorylation permits binding by the FBW7 ubiquitin ligase triggering MYC degradation. To understand how T58 phosphorylation functions in normal cell physiology, we introduced an alanine mutation at T58 (T58A) into the endogenous c-Myc locus in the mouse germline. While MYC-T58A mice develop normally, lymphomas and myeloid leukemias emerge in ~60% of adult homozygous T58A mice. We find that primitive hematopoietic progenitor cells from MYC-T58A mice exhibit aberrant self-renewal normally associated with hematopoietic stem cells (HSCs) and upregulate a subset of Myc target genes important in maintaining stem/progenitor cell balance. Genomic occupancy by MYC-T58A was increased at all promoters, compared to WT MYC, while genes differentially expressed in a T58A-dependent manner were significantly more proximal to MYC-bound enhancers. MYC-T58A lymphocyte progenitors exhibited metabolic alterations and decreased activation of inflammatory and apoptotic pathways. Our data demonstrate that a single point mutation in Myc is sufficient to produce a profound gain of function in multipotential hematopoietic progenitors associated with self-renewal and initiation of lymphomas and leukemias.
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Affiliation(s)
- Brian Freie
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA, USA
| | - Patrick A Carroll
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA, USA
| | | | - Vijay Ramani
- Gladstone Institute for Data Science and Biotechnology, University of California, San Francisco, San Francisco CA, USA
| | - Irwin Bernstein
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle WA, USA
| | - Robert N Eisenman
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA, USA
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12
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Jha RK, Kouzine F, Levens D. MYC function and regulation in physiological perspective. Front Cell Dev Biol 2023; 11:1268275. [PMID: 37941901 PMCID: PMC10627926 DOI: 10.3389/fcell.2023.1268275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
MYC, a key member of the Myc-proto-oncogene family, is a universal transcription amplifier that regulates almost every physiological process in a cell including cell cycle, proliferation, metabolism, differentiation, and apoptosis. MYC interacts with several cofactors, chromatin modifiers, and regulators to direct gene expression. MYC levels are tightly regulated, and deregulation of MYC has been associated with numerous diseases including cancer. Understanding the comprehensive biology of MYC under physiological conditions is an utmost necessity to demark biological functions of MYC from its pathological functions. Here we review the recent advances in biological mechanisms, functions, and regulation of MYC. We also emphasize the role of MYC as a global transcription amplifier.
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Affiliation(s)
| | | | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, United States
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13
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Illi B, Nasi S. Myc beyond Cancer: Regulation of Mammalian Tissue Regeneration. PATHOPHYSIOLOGY 2023; 30:346-365. [PMID: 37606389 PMCID: PMC10443299 DOI: 10.3390/pathophysiology30030027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
Myc is one of the most well-known oncogenes driving tumorigenesis in a wide variety of tissues. From the brain to blood, its deregulation derails physiological pathways that grant the correct functioning of the cell. Its action is carried out at the gene expression level, where Myc governs basically every aspect of transcription. Indeed, in addition to its role as a canonical, chromatin-bound transcription factor, Myc rules RNA polymerase II (RNAPII) transcriptional pause-release, elongation and termination and mRNA capping. For this reason, it is evident that minimal perturbations of Myc function mirror malignant cell behavior and, consistently, a large body of literature mainly focuses on Myc malfunctioning. In healthy cells, Myc controls molecular mechanisms involved in pivotal functions, such as cell cycle (and proliferation thereof), apoptosis, metabolism and cell size, angiogenesis, differentiation and stem cell self-renewal. In this latter regard, Myc has been found to also regulate tissue regeneration, a hot topic in the research fields of aging and regenerative medicine. Indeed, Myc appears to have a role in wound healing, in peripheral nerves and in liver, pancreas and even heart recovery. Herein, we discuss the state of the art of Myc's role in tissue regeneration, giving an overview of its potent action beyond cancer.
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Affiliation(s)
- Barbara Illi
- Institute of Molecular Biology and Pathology, National Research Council, c/o Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Sergio Nasi
- Institute of Molecular Biology and Pathology, National Research Council, c/o Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
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14
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Pagella P, Söderholm S, Nordin A, Zambanini G, Ghezzi V, Jauregi-Miguel A, Cantù C. The time-resolved genomic impact of Wnt/β-catenin signaling. Cell Syst 2023; 14:563-581.e7. [PMID: 37473729 DOI: 10.1016/j.cels.2023.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 03/24/2023] [Accepted: 06/12/2023] [Indexed: 07/22/2023]
Abstract
Wnt signaling orchestrates gene expression via its effector, β-catenin. However, it is unknown whether β-catenin binds its target genomic regions simultaneously and how this impacts chromatin dynamics to modulate cell behavior. Using a combination of time-resolved CUT&RUN against β-catenin, ATAC-seq, and perturbation assays in different cell types, we show that Wnt/β-catenin physical targets are tissue-specific, β-catenin "moves" on different loci over time, and its association to DNA accompanies changing chromatin accessibility landscapes that determine cell behavior. In particular, Wnt/β-catenin progressively shapes the chromatin of human embryonic stem cells (hESCs) as they undergo mesodermal differentiation, a behavior that we define as "plastic." In HEK293T cells, on the other hand, Wnt/β-catenin drives a transient chromatin opening, followed by re-establishment of the pre-stimulation state, a response that we define as "elastic." Future experiments shall assess whether other cell communication mechanisms, in addition to Wnt signaling, are ruled by time, cellular idiosyncrasies, and chromatin constraints. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Pierfrancesco Pagella
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Simon Söderholm
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Valeria Ghezzi
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Amaia Jauregi-Miguel
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden.
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15
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Vízkeleti L, Spisák S. Rewired Metabolism Caused by the Oncogenic Deregulation of MYC as an Attractive Therapeutic Target in Cancers. Cells 2023; 12:1745. [PMID: 37443779 PMCID: PMC10341379 DOI: 10.3390/cells12131745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
MYC is one of the most deregulated oncogenes on multiple levels in cancer. As a node transcription factor, MYC plays a diverse regulatory role in many cellular processes, including cell cycle and metabolism, both in physiological and pathological conditions. The relentless growth and proliferation of tumor cells lead to an insatiable demand for energy and nutrients, which requires the rewiring of cellular metabolism. As MYC can orchestrate all aspects of cellular metabolism, its altered regulation plays a central role in these processes, such as the Warburg effect, and is a well-established hallmark of cancer development. However, our current knowledge of MYC suggests that its spatial- and concentration-dependent contribution to tumorigenesis depends more on changes in the global or relative expression of target genes. As the direct targeting of MYC is proven to be challenging due to its relatively high toxicity, understanding its underlying regulatory mechanisms is essential for the development of tumor-selective targeted therapies. The aim of this review is to comprehensively summarize the diverse forms of MYC oncogenic deregulation, including DNA-, transcriptional- and post-translational level alterations, and their consequences for cellular metabolism. Furthermore, we also review the currently available and potentially attractive therapeutic options that exploit the vulnerability arising from the metabolic rearrangement of MYC-driven tumors.
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Affiliation(s)
- Laura Vízkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary;
| | - Sándor Spisák
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
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16
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Kravchuk EV, Ashniev GA, Gladkova MG, Orlov AV, Vasileva AV, Boldyreva AV, Burenin AG, Skirda AM, Nikitin PI, Orlova NN. Experimental Validation and Prediction of Super-Enhancers: Advances and Challenges. Cells 2023; 12:cells12081191. [PMID: 37190100 DOI: 10.3390/cells12081191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Super-enhancers (SEs) are cis-regulatory elements of the human genome that have been widely discussed since the discovery and origin of the term. Super-enhancers have been shown to be strongly associated with the expression of genes crucial for cell differentiation, cell stability maintenance, and tumorigenesis. Our goal was to systematize research studies dedicated to the investigation of structure and functions of super-enhancers as well as to define further perspectives of the field in various applications, such as drug development and clinical use. We overviewed the fundamental studies which provided experimental data on various pathologies and their associations with particular super-enhancers. The analysis of mainstream approaches for SE search and prediction allowed us to accumulate existing data and propose directions for further algorithmic improvements of SEs' reliability levels and efficiency. Thus, here we provide the description of the most robust algorithms such as ROSE, imPROSE, and DEEPSEN and suggest their further use for various research and development tasks. The most promising research direction, which is based on topic and number of published studies, are cancer-associated super-enhancers and prospective SE-targeted therapy strategies, most of which are discussed in this review.
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Affiliation(s)
- Ekaterina V Kravchuk
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Leninskiye Gory, MSU, 1-12, 119991 Moscow, Russia
| | - German A Ashniev
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Leninskiye Gory, MSU, 1-12, 119991 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, MSU, 1-73, 119234 Moscow, Russia
| | - Marina G Gladkova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, MSU, 1-73, 119234 Moscow, Russia
| | - Alexey V Orlov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Anastasiia V Vasileva
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Anna V Boldyreva
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Alexandr G Burenin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Artemiy M Skirda
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Petr I Nikitin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Natalia N Orlova
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
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17
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Wei Z, Wang S, Xu Y, Wang W, Soares F, Ahmed M, Su P, Wang T, Orouji E, Xu X, Zeng Y, Chen S, Liu X, Jia T, Liu Z, Du L, Wang Y, Chen S, Wang C, He HH, Guo H. MYC reshapes CTCF-mediated chromatin architecture in prostate cancer. Nat Commun 2023; 14:1787. [PMID: 36997534 PMCID: PMC10063626 DOI: 10.1038/s41467-023-37544-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
MYC is a well characterized oncogenic transcription factor in prostate cancer, and CTCF is the main architectural protein of three-dimensional genome organization. However, the functional link between the two master regulators has not been reported. In this study, we find that MYC rewires prostate cancer chromatin architecture by interacting with CTCF protein. Through combining the H3K27ac, AR and CTCF HiChIP profiles with CRISPR deletion of a CTCF site upstream of MYC gene, we show that MYC activation leads to profound changes of CTCF-mediated chromatin looping. Mechanistically, MYC colocalizes with CTCF at a subset of genomic sites, and enhances CTCF occupancy at these loci. Consequently, the CTCF-mediated chromatin looping is potentiated by MYC activation, resulting in the disruption of enhancer-promoter looping at neuroendocrine lineage plasticity genes. Collectively, our findings define the function of MYC as a CTCF co-factor in three-dimensional genome organization.
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Affiliation(s)
- Zhao Wei
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, 250012, Shandong Province, China
| | - Song Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Yaning Xu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Wenzheng Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Fraser Soares
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Musaddeque Ahmed
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Ping Su
- National Administration of Health Data, Jinan, 250000, China
| | - Tingting Wang
- Institute of Medical Sciences, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
| | - Elias Orouji
- Epigenetics Initiative, Princess Margaret Genomics Centre, Toronto, ON, Canada
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Xu
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Yong Zeng
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Sujun Chen
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Xiaoyu Liu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Tianwei Jia
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Zhaojian Liu
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Lutao Du
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Yunshan Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Shaoyong Chen
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02215, USA
| | - Chuanxin Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Housheng Hansen He
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G 1L7, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 2M9, Canada.
| | - Haiyang Guo
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China.
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China.
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China.
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18
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Koeniger A, Polo P, Brichkina A, Finkernagel F, Visekruna A, Nist A, Stiewe T, Daude M, Diederich W, Gress T, Adhikary T, Lauth M. Tumor-suppressive disruption of cancer subtype-associated super enhancer circuits by small molecule treatment. NAR Cancer 2023; 5:zcad007. [PMID: 36755960 PMCID: PMC9900422 DOI: 10.1093/narcan/zcad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/04/2023] [Accepted: 01/25/2023] [Indexed: 02/09/2023] Open
Abstract
Transcriptional cancer subtypes which correlate with traits such as tumor growth, drug sensitivity or the chances of relapse and metastasis, have been described for several malignancies. The core regulatory circuits (CRCs) defining these subtypes are established by chromatin super enhancers (SEs) driving key transcription factors (TFs) specific for the particular cell state. In neuroblastoma (NB), one of the most frequent solid pediatric cancer entities, two major SE-directed molecular subtypes have been described: A more lineage-committed adrenergic (ADRN) and a mesenchymal (MES) subtype. Here, we found that a small isoxazole molecule (ISX), a frequently used pro-neural drug, reprogrammed SE activity and switched NB cells from an ADRN subtype towards a growth-retarded MES-like state. The MES-like state shared strong transcriptional overlap with ganglioneuroma (GN), a benign and highly differentiated tumor of the neural crest. Mechanistically, ISX suppressed chromatin binding of N-MYC, a CRC-amplifying transcription factor, resulting in loss of key ADRN subtype-enriched components such as N-MYC itself, PHOX2B and ALK, while concomitently, MES subtype markers were induced. Globally, ISX treatment installed a chromatin accessibility landscape typically associated with low risk NB. In summary, we provide evidence that CRCs and cancer subtype reprogramming might be amenable to future therapeutic targeting.
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Affiliation(s)
- Anke Koeniger
- Philipps University Marburg, Dept. of Gastroenterology, Endocrinology and Metabolism, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Pierfrancesco Polo
- Philipps University Marburg, Dept. of Gastroenterology, Endocrinology and Metabolism, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Anna Brichkina
- Philipps University Marburg, Dept. of Gastroenterology, Endocrinology and Metabolism, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Florian Finkernagel
- Philipps University Marburg, Bioinformatics Core Facility, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Alexander Visekruna
- Philipps University Marburg, Institute for Medical Microbiology and Hygiene, 35043 Marburg, Germany
| | - Andrea Nist
- Member of the German Center for Lung Research (DZL), Center for Tumor- and Immune Biology, Genomics Core Facility, Institute of Molecular Oncology, Philipps University Marburg, 35043 Marburg, Germany
| | - Thorsten Stiewe
- Member of the German Center for Lung Research (DZL), Center for Tumor- and Immune Biology, Genomics Core Facility, Institute of Molecular Oncology, Philipps University Marburg, 35043 Marburg, Germany
| | - Michael Daude
- Philipps University Marburg, Core Facility Medical Chemistry, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Wibke E Diederich
- Philipps University Marburg, Dept. of Medicinal Chemistry and Core Facility Medical Chemistry, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Thomas M Gress
- Philipps University Marburg, Dept. of Gastroenterology, Endocrinology and Metabolism, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Till Adhikary
- Philipps University Marburg, Institute for Medical Bioinformatics and Biostatistics and Institute for Molecular Biology and Tumor Research, Marburg, Germany
| | - Matthias Lauth
- Philipps University Marburg, Dept. of Gastroenterology, Endocrinology and Metabolism, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
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19
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The "Superoncogene" Myc at the Crossroad between Metabolism and Gene Expression in Glioblastoma Multiforme. Int J Mol Sci 2023; 24:ijms24044217. [PMID: 36835628 PMCID: PMC9966483 DOI: 10.3390/ijms24044217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The concept of the Myc (c-myc, n-myc, l-myc) oncogene as a canonical, DNA-bound transcription factor has consistently changed over the past few years. Indeed, Myc controls gene expression programs at multiple levels: directly binding chromatin and recruiting transcriptional coregulators; modulating the activity of RNA polymerases (RNAPs); and drawing chromatin topology. Therefore, it is evident that Myc deregulation in cancer is a dramatic event. Glioblastoma multiforme (GBM) is the most lethal, still incurable, brain cancer in adults, and it is characterized in most cases by Myc deregulation. Metabolic rewiring typically occurs in cancer cells, and GBM undergoes profound metabolic changes to supply increased energy demand. In nontransformed cells, Myc tightly controls metabolic pathways to maintain cellular homeostasis. Consistently, in Myc-overexpressing cancer cells, including GBM cells, these highly controlled metabolic routes are affected by enhanced Myc activity and show substantial alterations. On the other hand, deregulated cancer metabolism impacts Myc expression and function, placing Myc at the intersection between metabolic pathway activation and gene expression. In this review paper, we summarize the available information on GBM metabolism with a specific focus on the control of the Myc oncogene that, in turn, rules the activation of metabolic signals, ensuring GBM growth.
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20
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Chung YC, Bisht M, Thuma J, Tu LC. Single-chromosome dynamics reveals locus-dependent dynamics and chromosome territory orientation. J Cell Sci 2023; 136:289470. [PMID: 36718642 PMCID: PMC10022681 DOI: 10.1242/jcs.260137] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 01/19/2023] [Indexed: 02/01/2023] Open
Abstract
Dynamic chromatin organization instantly influences DNA accessibility through modulating local macromolecular density and interactions, driving changes in transcription activities. Chromatin dynamics have been reported to be locally confined but contribute to coherent chromatin motion across the entire nucleus. However, the regulation of dynamics, nuclear orientation and compaction of subregions along a single chromosome are not well-understood. We used CRISPR-based real-time single-particle tracking and polymer models to characterize the dynamics of specific genomic loci and determine compaction levels of large human chromosomal domains. Our studies showed that chromosome compaction changed during interphase and that compactions of two arms on chromosome 19 were different. The dynamics of genomic loci were subdiffusive and dependent on chromosome regions and transcription states. Surprisingly, the correlation between locus-dependent nuclear localization and mobility was negligible. Strong tethering interactions detected at the pericentromeric region implies local condensation or associations with organelles within local nuclear microenvironments, such as chromatin-nuclear body association. Based on our findings, we propose a 'guided radial model' for the nuclear orientation of the long arm of chromosome 19.
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Affiliation(s)
- Yu-Chieh Chung
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Madhoolika Bisht
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Jenna Thuma
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Li-Chun Tu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
- Author for correspondence ()
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21
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Scagnoli F, Palma A, Favia A, Scuoppo C, Illi B, Nasi S. A New Insight into MYC Action: Control of RNA Polymerase II Methylation and Transcription Termination. Biomedicines 2023; 11:biomedicines11020412. [PMID: 36830948 PMCID: PMC9952900 DOI: 10.3390/biomedicines11020412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
MYC oncoprotein deregulation is a common catastrophic event in human cancer and limiting its activity restrains tumor development and maintenance, as clearly shown via Omomyc, an MYC-interfering 90 amino acid mini-protein. MYC is a multifunctional transcription factor that regulates many aspects of transcription by RNA polymerase II (RNAPII), such as transcription activation, pause release, and elongation. MYC directly associates with Protein Arginine Methyltransferase 5 (PRMT5), a protein that methylates a variety of targets, including RNAPII at the arginine residue R1810 (R1810me2s), crucial for proper transcription termination and splicing of transcripts. Therefore, we asked whether MYC controls termination as well, by affecting R1810me2S. We show that MYC overexpression strongly increases R1810me2s, while Omomyc, an MYC shRNA, or a PRMT5 inhibitor and siRNA counteract this phenomenon. Omomyc also impairs Serine 2 phosphorylation in the RNAPII carboxyterminal domain, a modification that sustains transcription elongation. ChIP-seq experiments show that Omomyc replaces MYC and reshapes RNAPII distribution, increasing occupancy at promoter and termination sites. It is unclear how this may affect gene expression. Transcriptomic analysis shows that transcripts pivotal to key signaling pathways are both up- or down-regulated by Omomyc, whereas genes directly controlled by MYC and belonging to a specific signature are strongly down-regulated. Overall, our data point to an MYC/PRMT5/RNAPII axis that controls termination via RNAPII symmetrical dimethylation and contributes to rewiring the expression of genes altered by MYC overexpression in cancer cells. It remains to be clarified which role this may have in tumor development.
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Affiliation(s)
- Fiorella Scagnoli
- IBPM—CNR, Biology and Biotechnology Department, Sapienza University, 00185 Rome, Italy
- Correspondence: (F.S.); (B.I.); (S.N.)
| | - Alessandro Palma
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
| | - Annarita Favia
- IBPM—CNR, Biology and Biotechnology Department, Sapienza University, 00185 Rome, Italy
| | - Claudio Scuoppo
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Barbara Illi
- IBPM—CNR, Biology and Biotechnology Department, Sapienza University, 00185 Rome, Italy
- Correspondence: (F.S.); (B.I.); (S.N.)
| | - Sergio Nasi
- IBPM—CNR, Biology and Biotechnology Department, Sapienza University, 00185 Rome, Italy
- Correspondence: (F.S.); (B.I.); (S.N.)
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22
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Tsai CH, Chuang YM, Li X, Yu YR, Tzeng SF, Teoh ST, Lindblad KE, Di Matteo M, Cheng WC, Hsueh PC, Kao KC, Imrichova H, Duan L, Gallart-Ayala H, Hsiao PW, Mazzone M, Ivanesevic J, Liu X, de Visser KE, Lujambio A, Lunt SY, Kaech SM, Ho PC. Immunoediting instructs tumor metabolic reprogramming to support immune evasion. Cell Metab 2023; 35:118-133.e7. [PMID: 36599297 PMCID: PMC10375941 DOI: 10.1016/j.cmet.2022.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/06/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023]
Abstract
Immunoediting sculpts immunogenicity and thwarts host anti-tumor responses in tumor cells during tumorigenesis; however, it remains unknown whether metabolic programming of tumor cells can be guided by immunosurveillance. Here, we report that T cell-mediated immunosurveillance in early-stage tumorigenesis instructs c-Myc upregulation and metabolic reprogramming in tumor cells. This previously unexplored tumor-immune interaction is controlled by non-canonical interferon gamma (IFNγ)-STAT3 signaling and supports tumor immune evasion. Our findings uncover that immunoediting instructs deregulated bioenergetic programs in tumor cells to empower them to disarm the T cell-mediated immunosurveillance by imposing metabolic tug-of-war between tumor and infiltrating T cells and forming the suppressive tumor microenvironment.
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Affiliation(s)
- Chin-Hsien Tsai
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland; Graduate Institute of Life Sciences, National Defense Medical Center, Taipei City, Taiwan
| | - Yu-Ming Chuang
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Xiaoyun Li
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Yi-Ru Yu
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Sheue-Fen Tzeng
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland; Graduate Institute of Life Sciences, National Defense Medical Center, Taipei City, Taiwan
| | - Shao Thing Teoh
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Katherine E Lindblad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mario Di Matteo
- Laboratory of Tumor Inflammation and angiogenesis, Vesalius Research Center, VIB, Leuven, Belgium; Laboratory of Tumor Inflammation and angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Wan-Chen Cheng
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Pei-Chun Hsueh
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Kung-Chi Kao
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Wien, Austria
| | - Likun Duan
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Hector Gallart-Ayala
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Pei-Wen Hsiao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei City, Taiwan
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and angiogenesis, Vesalius Research Center, VIB, Leuven, Belgium; Laboratory of Tumor Inflammation and angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Julijana Ivanesevic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Wien, Austria
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Karin E de Visser
- Division of Tumor Biology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sophia Y Lunt
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ping-Chih Ho
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland.
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23
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Yamaguchi K, Chen X, Oji A, Hiratani I, Defossez PA. Large-Scale Chromatin Rearrangements in Cancer. Cancers (Basel) 2022; 14:cancers14102384. [PMID: 35625988 PMCID: PMC9139990 DOI: 10.3390/cancers14102384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Cancers have many genetic mutations such as nucleotide changes, deletions, amplifications, and chromosome gains or losses. Some of these genetic alterations directly contribute to the initiation and progression of tumors. In parallel to these genetic changes, cancer cells acquire modifications to their chromatin landscape, i.e., to the marks that are carried by DNA and the histone proteins it is associated with. These “epimutations” have consequences for gene expression and genome stability, and also contribute to tumoral initiation and progression. Some of these chromatin changes are very local, affecting just one or a few genes. In contrast, some chromatin alterations observed in cancer are more widespread and affect a large part of the genome. In this review, we present different types of large-scale chromatin rearrangements in cancer, explain how they may occur, and why they are relevant for cancer diagnosis and treatment. Abstract Epigenetic abnormalities are extremely widespread in cancer. Some of them are mere consequences of transformation, but some actively contribute to cancer initiation and progression; they provide powerful new biological markers, as well as new targets for therapies. In this review, we examine the recent literature and focus on one particular aspect of epigenome deregulation: large-scale chromatin changes, causing global changes of DNA methylation or histone modifications. After a brief overview of the one-dimension (1D) and three-dimension (3D) epigenome in healthy cells and of its homeostasis mechanisms, we use selected examples to describe how many different events (mutations, changes in metabolism, and infections) can cause profound changes to the epigenome and fuel cancer. We then present the consequences for therapies and briefly discuss the role of single-cell approaches for the future progress of the field.
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Affiliation(s)
- Kosuke Yamaguchi
- UMR7216 Epigenetics and Cell Fate, Université Paris Cité, CNRS, F-75006 Paris, France; (K.Y.); (X.C.)
| | - Xiaoying Chen
- UMR7216 Epigenetics and Cell Fate, Université Paris Cité, CNRS, F-75006 Paris, France; (K.Y.); (X.C.)
| | - Asami Oji
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), Kobe 650-0047, Japan; (A.O.); (I.H.)
| | - Ichiro Hiratani
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), Kobe 650-0047, Japan; (A.O.); (I.H.)
| | - Pierre-Antoine Defossez
- UMR7216 Epigenetics and Cell Fate, Université Paris Cité, CNRS, F-75006 Paris, France; (K.Y.); (X.C.)
- Correspondence: ; Tel.: +33-157278916
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