1
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Rahman R, Rahaman MH, Hanson AR, Choo N, Xie J, Townley SL, Shrestha R, Hassankhani R, Islam S, Ramm S, Simpson KJ, Risbridger GP, Best G, Centenera MM, Balk SP, Kichenadasse G, Taylor RA, Butler LM, Tilley WD, Conn SJ, Lawrence MG, Wang S, Selth LA. CDK9 inhibition inhibits multiple oncogenic transcriptional and epigenetic pathways in prostate cancer. Br J Cancer 2024:10.1038/s41416-024-02810-8. [PMID: 39117800 DOI: 10.1038/s41416-024-02810-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 07/18/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Cyclin-dependent kinase 9 (CDK9) stimulates oncogenic transcriptional pathways in cancer and CDK9 inhibitors have emerged as promising therapeutic candidates. METHODS The activity of an orally bioavailable CDK9 inhibitor, CDKI-73, was evaluated in prostate cancer cell lines, a xenograft mouse model, and patient-derived tumor explants and organoids. Expression of CDK9 was evaluated in clinical specimens by mining public datasets and immunohistochemistry. Effects of CDKI-73 on prostate cancer cells were determined by cell-based assays, molecular profiling and transcriptomic/epigenomic approaches. RESULTS CDKI-73 inhibited proliferation and enhanced cell death in diverse in vitro and in vivo models of androgen receptor (AR)-driven and AR-independent models. Mechanistically, CDKI-73-mediated inhibition of RNA polymerase II serine 2 phosphorylation resulted in reduced expression of BCL-2 anti-apoptotic factors and transcriptional defects. Transcriptomic and epigenomic approaches revealed that CDKI-73 suppressed signaling pathways regulated by AR, MYC, and BRD4, key drivers of dysregulated transcription in prostate cancer, and reprogrammed cancer-associated super-enhancers. These latter findings prompted the evaluation of CDKI-73 with the BRD4 inhibitor AZD5153, a combination that was synergistic in patient-derived organoids and in vivo. CONCLUSION Our work demonstrates that CDK9 inhibition disrupts multiple oncogenic pathways and positions CDKI-73 as a promising therapeutic agent for prostate cancer, particularly aggressive, therapy-resistant subtypes.
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Affiliation(s)
- Razia Rahman
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Muhammed H Rahaman
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Adrienne R Hanson
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Nicholas Choo
- Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Jianling Xie
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Scott L Townley
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Raj Shrestha
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
- Flinders University, Freemasons Centre for Male Health and Wellbeing, Bedford Park, SA, Australia
| | - Ramin Hassankhani
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Saiful Islam
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Susanne Ramm
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Gail P Risbridger
- Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Cabrini Institute, Cabrini Health, Malvern, Melbourne, VIC, Australia
- Melbourne Urological Research Alliance (MURAL), Monash Biomedicine Discovery Institute Cancer Program, Monash University, Clayton, VIC, Australia
| | - Giles Best
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Margaret M Centenera
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Steven P Balk
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Ganessan Kichenadasse
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
- Department of Medical Oncology, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, SA, South Australia
| | - Renea A Taylor
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Cabrini Institute, Cabrini Health, Malvern, Melbourne, VIC, Australia
- Melbourne Urological Research Alliance (MURAL), Monash Biomedicine Discovery Institute Cancer Program, Monash University, Clayton, VIC, Australia
- Biomedicine Discovery Institute Cancer Program, Department of Physiology, Monash University, Clayton, VIC, Australia
| | - Lisa M Butler
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Wayne D Tilley
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Simon J Conn
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Mitchell G Lawrence
- Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Cabrini Institute, Cabrini Health, Malvern, Melbourne, VIC, Australia
- Melbourne Urological Research Alliance (MURAL), Monash Biomedicine Discovery Institute Cancer Program, Monash University, Clayton, VIC, Australia
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Luke A Selth
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia.
- Flinders University, Freemasons Centre for Male Health and Wellbeing, Bedford Park, SA, Australia.
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia.
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2
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Li M, Yang J, Xiao R, Liu Y, Hu J, Li T, Wu P, Zhang M, Huang Y, Sun Y, Li C. The effect of trisomic chromosomes on spatial genome organization and global transcription in embryonic stem cells. Cell Prolif 2024; 57:e13639. [PMID: 38553796 PMCID: PMC11294443 DOI: 10.1111/cpr.13639] [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: 06/20/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 08/03/2024] Open
Abstract
Aneuploidy frequently occurs in cancer and developmental diseases such as Down syndrome, with its functional consequences implicated in dosage effects on gene expression and global perturbation of stress response and cell proliferation pathways. However, how aneuploidy affects spatial genome organization remains less understood. In this study, we addressed this question by utilizing the previously established isogenic wild-type (WT) and trisomic mouse embryonic stem cells (mESCs). We employed a combination of Hi-C, RNA-seq, chromosome painting and nascent RNA imaging technologies to compare the spatial genome structures and gene transcription among these cells. We found that trisomy has little effect on spatial genome organization at the level of A/B compartment or topologically associating domain (TAD). Inter-chromosomal interactions are associated with chromosome regions with high gene density, active histone modifications and high transcription levels, which are confirmed by imaging. Imaging also revealed contracted chromosome volume and weakened transcriptional activity for trisomic chromosomes, suggesting potential implications for the transcriptional output of these chromosomes. Our data resources and findings may contribute to a better understanding of the consequences of aneuploidy from the angle of spatial genome organization.
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Affiliation(s)
- Mengfan Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Junsheng Yang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC)Peking UniversityBeijingChina
| | - Rong Xiao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical GeneticsInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical CollegeBeijingChina
| | - Yunjie Liu
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Jiaqi Hu
- School of Health HumanitiesPeking UniversityBeijingChina
| | - Tingting Li
- State Key Laboratory of ProteomicsInstitute of Basic Medical Sciences, National Center of Biomedical AnalysisBeijingChina
| | - Pengze Wu
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Meili Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical GeneticsInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical CollegeBeijingChina
| | - Yue Huang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical GeneticsInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical CollegeBeijingChina
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC)Peking UniversityBeijingChina
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
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3
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Gupta A, Avadhanula S, Bashyam MD. Evaluation of the gene fusion landscape in early onset sporadic rectal cancer reveals association with chromatin architecture and genome stability. Oncogene 2024; 43:2449-2462. [PMID: 38937601 DOI: 10.1038/s41388-024-03088-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/29/2024]
Abstract
Gene fusions represent a distinct class of structural variants identified frequently in cancer genomes across cancer types. Several gene fusions exhibit gain of oncogenic function and thus have been the focus of development of efficient targeted therapies. However, investigation of fusion landscape in early-onset sporadic rectal cancer, a poorly studied colorectal cancer subtype prevalent in developing countries, has not been performed. Here, we present a comprehensive landscape of gene fusions in EOSRC and CRC using patient derived tumor samples and data from The Cancer Genome Atlas, respectively. Gene Ontology analysis revealed enrichment of unique biological process terms associated with 5'- and 3'- fusion partner genes. Extensive network analysis highlighted genes exhibiting significant promiscuity in fusion formation and their association with chromosome fragile sites. Investigation of fusion formation in the context of global chromatin architecture unraveled a novel mode of gene activation that arose from fusion between genes located in orthogonal chromatin compartments. The study provides novel evidence linking fusions to genome stability and architecture and unearthed a hitherto unidentified mode of gene activation in cancer.
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Affiliation(s)
- Asmita Gupta
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Sumedha Avadhanula
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Murali Dharan Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.
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4
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Abewe H, Richey A, Vahrenkamp JM, Ginley-Hidinger M, Rush CM, Kitchen N, Zhang X, Gertz J. Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598690. [PMID: 38915540 PMCID: PMC11195280 DOI: 10.1101/2024.06.12.598690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Transcriptional enhancers can regulate individual or multiple genes through long-range three-dimensional (3D) genome interactions, and these interactions are commonly altered in cancer. Yet, the functional relationship between changes in 3D interactions associated with regulatory regions and differential gene expression appears context-dependent. In this study, we used HiChiP to capture changes in 3D genome interactions between active regulatory regions of endometrial cancer cells in response to estrogen treatment and uncovered significant differential long-range interactions that are strongly enriched for estrogen receptor α (ER) bound sites (ERBS). The ERBS anchoring differential loops with either a gene's promoter or distal regions were correlated with larger transcriptional responses to estrogen compared to ERBS not involved in differential interactions. To functionally test this observation, CRISPR-based Enhancer-i was used to deactivate specific ERBS, which revealed a wide range of effects on the transcriptional response to estrogen. However, these effects are only subtly and not significantly stronger for ERBS in differential loops. In addition, we observed an enrichment of 3D interactions between the promoters of estrogen up-regulated genes and found that looped promoters can work together cooperatively. Overall, our work suggests that changes in 3D genome structure upon estrogen treatment identify some functionally important regulatory regions; however, these changes aren't required for a transcriptional response to E2 in endometrial cancer cells.
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Affiliation(s)
- Hosiana Abewe
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Alexandra Richey
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Jeffery M Vahrenkamp
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Matthew Ginley-Hidinger
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Craig M Rush
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Noel Kitchen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Xiaoyang Zhang
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Gertz
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
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5
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Chen M, Wu B, Huang Y, Wang W, Zheng Y, Shabbir S, Liu P, Dai Y, Xia M, Hu G, He M. Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation. Nucleic Acids Res 2024; 52:5643-5657. [PMID: 38716861 PMCID: PMC11162768 DOI: 10.1093/nar/gkae318] [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: 10/25/2023] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 06/11/2024] Open
Abstract
Genomic mutations allow bacteria to adapt rapidly to adverse stress environments. The three-dimensional conformation of the genome may also play an important role in transcriptional regulation and environmental adaptation. Here, using chromosome conformation capture, we investigate the high-order architecture of the Zymomonas mobilis chromosome in response to genomic mutation and ambient stimuli (acetic acid and furfural, derived from lignocellulosic hydrolysate). We find that genomic mutation only influences the local chromosome contacts, whereas stress of acetic acid and furfural restrict the long-range contacts and significantly change the chromosome organization at domain scales. Further deciphering the domain feature unveils the important transcription factors, Ferric uptake regulator (Fur) proteins, which act as nucleoid-associated proteins to promote long-range (>200 kb) chromosomal communications and regulate the expression of genes involved in stress response. Our work suggests that ubiquitous transcription factors in prokaryotes mediate chromosome organization and regulate stress-resistance genes in bacterial adaptation.
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Affiliation(s)
- Mao Chen
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
- Graduate School of Chinese Academy of Agricultural Sciences; Beijing 100081, PR China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Yuhuan Huang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
- Graduate School of Chinese Academy of Agricultural Sciences; Beijing 100081, PR China
| | - Weiting Wang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Yudi Zheng
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
- Graduate School of Chinese Academy of Agricultural Sciences; Beijing 100081, PR China
| | - Samina Shabbir
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Panting Liu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Yonghua Dai
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Mengli Xia
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs; Chengdu 610041, PR China
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6
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Xu J, Xu X, Huang D, Luo Y, Lin L, Bai X, Zheng Y, Yang Q, Cheng Y, Huang A, Shi J, Bo X, Gu J, Chen H. A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains. Nat Commun 2024; 15:4376. [PMID: 38782890 PMCID: PMC11116433 DOI: 10.1038/s41467-024-48593-7] [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: 09/18/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the inner and smaller subTADs not only manifest cell-to-cell variability, but also precisely regulate transcription and differentiation. Although over 20 TAD callers are able to detect TAD, their usability in biomedicine is confined by a disagreement of outputs and a limit in understanding TAD hierarchy. We compare 13 computational tools across various conditions and develop a metric to evaluate the similarity of TAD hierarchy. Although outputs of TAD hierarchy at each level vary among callers, data resolutions, sequencing depths, and matrices normalization, they are more consistent when they have a higher similarity of larger TADs. We present comprehensive benchmarking of TAD hierarchy callers and operational guidance to researchers of life science researchers. Moreover, by simulating the mixing of different types of cells, we confirm that TAD hierarchy is generated not simply from stacking Hi-C heatmaps of heterogeneous cells. Finally, we propose an air conditioner model to decipher the role of TAD hierarchy in transcription.
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Affiliation(s)
- Jingxuan Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiang Xu
- Academy of Military Medical Science, Beijing, 100850, China
| | - Dandan Huang
- Department of Oncology, Peking University Shougang Hospital, Beijing, China
- Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Diseases, Peking University Health Science Center, Beijing, China
| | - Yawen Luo
- Academy of Military Medical Science, Beijing, 100850, China
| | - Lin Lin
- Academy of Military Medical Science, Beijing, 100850, China
- School of Computer Science and Information Technology& KLAS, Northeast Normal University, Changchun, China
| | - Xuemei Bai
- Academy of Military Medical Science, Beijing, 100850, China
| | - Yang Zheng
- Academy of Military Medical Science, Beijing, 100850, China
| | - Qian Yang
- Academy of Military Medical Science, Beijing, 100850, China
| | - Yu Cheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - An Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jingyi Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiaochen Bo
- Academy of Military Medical Science, Beijing, 100850, China.
| | - Jin Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
- Department of Oncology, Peking University Shougang Hospital, Beijing, China.
- Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Diseases, Peking University Health Science Center, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Peking University International Cancer Institute, Beijing, China.
| | - Hebing Chen
- Academy of Military Medical Science, Beijing, 100850, China.
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7
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Conway JR, Gillani R, Crowdis J, Reardon B, Park J, Han S, Titchen B, Benamar M, Haq R, Van Allen EM. Somatic structural variants drive distinct modes of oncogenesis in melanoma. J Clin Invest 2024; 134:e177270. [PMID: 38758740 PMCID: PMC11213511 DOI: 10.1172/jci177270] [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: 11/07/2023] [Accepted: 05/07/2024] [Indexed: 05/19/2024] Open
Abstract
The diversity of structural variants (SVs) in melanoma and how they impact oncogenesis are incompletely known. We performed harmonized analysis of SVs across melanoma histologic and genomic subtypes, and we identified distinct global properties between subtypes. These included the frequency and size of SVs and SV classes, their relation to chromothripsis events, and the impact on cancer-related genes of SVs that alter topologically associated domain (TAD) boundaries. Following our prior identification of double-stranded break repair deficiency in a subset of triple-wild-type cutaneous melanoma, we identified MRE11 and NBN loss-of-function SVs in melanomas with this mutational signature. Experimental knockouts of MRE11 and NBN, followed by olaparib cell viability assays in melanoma cells, indicated that dysregulation of each of these genes may cause sensitivity to PARP inhibitors in cutaneous melanomas. Broadly, harmonized analysis of melanoma SVs revealed distinct global genomic properties and molecular drivers, which may have biological and therapeutic impact.
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Affiliation(s)
- Jake R. Conway
- Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Riaz Gillani
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Jett Crowdis
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Brendan Reardon
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jihye Park
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Seunghun Han
- Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Breanna Titchen
- Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Rizwan Haq
- Center for Cancer Precision Medicine and
| | - Eliezer M. Van Allen
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Center for Cancer Precision Medicine and
- Parker Institute for Cancer Immunotherapy, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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8
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Guo J, Chen Y, Zhu H, Tong X, Cao L, Zhang Y, Xie W, Li C. Three-dimensional chromatin landscapes in somatotroph tumour. Clin Transl Med 2024; 14:e1682. [PMID: 38769659 PMCID: PMC11106515 DOI: 10.1002/ctm2.1682] [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: 11/17/2023] [Revised: 04/01/2024] [Accepted: 04/19/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND The three-dimensional (3D) genome architecture plays a critical role inregulating gene expression. However, the specific alterations in thisarchitecture within somatotroph tumors and their implications for gene expression remain largely unexplored. METHODS We employed Hi-C and RNA-seq analyses to compare the 3D genomic structures of somatotroph tumors with normal pituitary tissue. This comprehensive approachenabled the characterization of A/B compartments, topologically associateddomains (TADs), and chromatin loops, integrating these with gene expression patterns. RESULTS We observed a decrease in both the frequency of chromosomal interactions andthe size of TADs in tumor tissue compared to normal tissue. Conversely, the number of TADs and chromatin loops was found to be increased in tumors. Integrated analysis of Hi-C and RNA-seq data demonstrated that changes inhigher-order chromat in structure were associated with alterations in gene expression. Specifically, genes in A compartments showed higher density and increased expression relative to those in B compartments. Moreover, the weakand enhanced insulation boundaries were identified, and the associated genes were enriched in the Wnt/β-Catenin signaling pathway. We identified the gainedand lost loops in tumor and integrated these differences with transcriptional changes to examine the functional relevance of the identified loops. Notably, we observed an enhanced insulation boundary and a greater number of loops in the TCF7L2 gene region within tumors, which was accompanied by an upregulation of TCF7L2 expression. Subsequently, TCF7L2 expression was confirmed through qRT-PCR, and upregulated TCF7L2 prompted cell proliferation and growth hormone (GH) secretion in vitro. CONCLUSION Our results provide comprehensive 3D chromatin architecture maps of somatotroph tumors and offer a valuable resource for furthering the understanding of the underlying biology and mechanisms of gene expression regulation.
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Affiliation(s)
- Jing Guo
- Department of NeurosurgeryBeijing Tiantan Hospital affiliated to Capital Medical UniversityBeijingChina
- Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
| | - Yiyuan Chen
- Department of NeurosurgeryBeijing Tiantan Hospital affiliated to Capital Medical UniversityBeijingChina
- Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
| | - Haibo Zhu
- Department of NeurosurgeryBeijing Tiantan Hospital affiliated to Capital Medical UniversityBeijingChina
| | - Xinyu Tong
- Annoroad Gene Technology Co., LtdBeijingChina
| | - Lei Cao
- Department of NeurosurgeryBeijing Tiantan Hospital affiliated to Capital Medical UniversityBeijingChina
| | - Yazhuo Zhang
- Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Beijing Institute for Brain Disorders Brain Tumor CenterBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
| | - Weiyan Xie
- Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
| | - Chuzhong Li
- Department of NeurosurgeryBeijing Tiantan Hospital affiliated to Capital Medical UniversityBeijingChina
- Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Beijing Institute for Brain Disorders Brain Tumor CenterBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
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9
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Kanaoka S, Okabe A, Kanesaka M, Rahmutulla B, Fukuyo M, Seki M, Hoshii T, Sato H, Imamura Y, Sakamoto S, Ichikawa T, Kaneda A. Chromatin activation with H3K36me2 and compartment shift in metastatic castration-resistant prostate cancer. Cancer Lett 2024; 588:216815. [PMID: 38490329 DOI: 10.1016/j.canlet.2024.216815] [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: 12/04/2023] [Revised: 03/03/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
Epigenetic modifiers are upregulated during the process of prostate cancer, acquiring resistance to castration therapy and becoming lethal metastatic castration-resistant prostate cancer (CRPC). However, the relationship between regulation of histone modifications and chromatin structure in CRPC has yet not fully been validated. Here, we reanalyzed publicly available clinical transcriptome and clinical outcome data and identified NSD2, a histone methyltransferase that catalyzes H3K36me2, as an epigenetic modifier that was upregulated in CRPC and whose increased expression in prostate cancer correlated with higher recurrence rate. We performed ChIP-seq, RNA-seq, and Hi-C to conduct comprehensive epigenomic and transcriptomic analyses to identify epigenetic reprogramming in CRPC. In regions where H3K36me2 was increased, H3K27me3 was decreased, and the compartment was shifted from inactive to active. In these regions, 68 aberrantly activated genes were identified as candidate downstream genes of NSD2 in CRPC. Among these genes, we identified KIF18A as critical for CRPC growth. Under NSD2 upregulation in CRPC, epigenetic alteration with H3K36me2-gain and H3K27me3-loss occurs accompanying with an inactive-to-active compartment shift, suggesting that histone modification and chromatin structure cooperatively change prostate carcinogenesis.
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Affiliation(s)
- Sanji Kanaoka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Department of Urology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Health and Disease Omics Center, Chiba University, Chiba, Japan
| | - Manato Kanesaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Department of Urology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Motoaki Seki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroaki Sato
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Department of Urology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yusuke Imamura
- Department of Urology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shinichi Sakamoto
- Department of Urology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomohiko Ichikawa
- Department of Urology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan; Health and Disease Omics Center, Chiba University, Chiba, Japan.
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10
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Cornejo-Páramo P, Petrova V, Zhang X, Young RS, Wong ES. Emergence of enhancers at late DNA replicating regions. Nat Commun 2024; 15:3451. [PMID: 38658544 PMCID: PMC11043393 DOI: 10.1038/s41467-024-47391-5] [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: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Enhancers are fast-evolving genomic sequences that control spatiotemporal gene expression patterns. By examining enhancer turnover across mammalian species and in multiple tissue types, we uncover a relationship between the emergence of enhancers and genome organization as a function of germline DNA replication time. While enhancers are most abundant in euchromatic regions, enhancers emerge almost twice as often in late compared to early germline replicating regions, independent of transposable elements. Using a deep learning sequence model, we demonstrate that new enhancers are enriched for mutations that alter transcription factor (TF) binding. Recently evolved enhancers appear to be mostly neutrally evolving and enriched in eQTLs. They also show more tissue specificity than conserved enhancers, and the TFs that bind to these elements, as inferred by binding sequences, also show increased tissue-specific gene expression. We find a similar relationship with DNA replication time in cancer, suggesting that these observations may be time-invariant principles of genome evolution. Our work underscores that genome organization has a profound impact in shaping mammalian gene regulation.
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Affiliation(s)
- Paola Cornejo-Páramo
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, Sydney, NSW, Australia
| | - Veronika Petrova
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, Sydney, NSW, Australia
| | - Xuan Zhang
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Robert S Young
- Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, United Kingdom
- Zhejiang University - University of Edinburgh Institute, Zhejiang University, 718 East Haizhou Road, 314400, Haining, PR China
| | - Emily S Wong
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.
- School of Biotechnology and Biomolecular Sciences, Sydney, NSW, Australia.
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11
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Wall BPG, Nguyen M, Harrell JC, Dozmorov MG. Machine and deep learning methods for predicting 3D genome organization. ARXIV 2024:arXiv:2403.03231v1. [PMID: 38495565 PMCID: PMC10942493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution. Machine learning methods have emerged as an alternative to obtain missing 3D interactions and/or improve resolution. Such methods frequently use genome annotation data (ChIP-seq, DNAse-seq, etc.), DNA sequencing information (k-mers, Transcription Factor Binding Site (TFBS) motifs), and other genomic properties to learn the associations between genomic features and chromatin interactions. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, TAD boundaries) and analyze their pros and cons. We also point out obstacles of computational prediction of 3D interactions and suggest future research directions.
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Affiliation(s)
- Brydon P. G. Wall
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - My Nguyen
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - J. Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
- Center for Pharmaceutical Engineering, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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12
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Alaimo A, Genovesi S, Annesi N, De Felice D, Subedi S, Macchia A, La Manna F, Ciani Y, Vannuccini F, Mugoni V, Notarangelo M, Libergoli M, Broso F, Taulli R, Ala U, Savino A, Cortese M, Mirzaaghaei S, Poli V, Bonapace IM, Papotti MG, Molinaro L, Doglioni C, Caffo O, Anesi A, Nagler M, Bertalot G, Carbone FG, Barbareschi M, Basso U, Dassi E, Pizzato M, Romanel A, Demichelis F, Kruithof-de Julio M, Lunardi A. Sterile inflammation via TRPM8 RNA-dependent TLR3-NF-kB/IRF3 activation promotes antitumor immunity in prostate cancer. EMBO J 2024; 43:780-805. [PMID: 38316991 PMCID: PMC10907604 DOI: 10.1038/s44318-024-00040-5] [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: 05/11/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
Inflammation is a common condition of prostate tissue, whose impact on carcinogenesis is highly debated. Microbial colonization is a well-documented cause of a small percentage of prostatitis cases, but it remains unclear what underlies the majority of sterile inflammation reported. Here, androgen- independent fluctuations of PSA expression in prostate cells have lead us to identify a prominent function of the Transient Receptor Potential Cation Channel Subfamily M Member 8 (TRPM8) gene in sterile inflammation. Prostate cells secret TRPM8 RNA into extracellular vesicles (EVs), which primes TLR3/NF-kB-mediated inflammatory signaling after EV endocytosis by epithelial cancer cells. Furthermore, prostate cancer xenografts expressing a translation-defective form of TRPM8 RNA contain less collagen type I in the extracellular matrix, significantly more infiltrating NK cells, and larger necrotic areas as compared to control xenografts. These findings imply sustained, androgen-independent expression of TRPM8 constitutes as a promoter of anticancer innate immunity, which may constitute a clinically relevant condition affecting prostate cancer prognosis.
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Affiliation(s)
- Alessandro Alaimo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
| | - Sacha Genovesi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Nicole Annesi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Dario De Felice
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Saurav Subedi
- Department for BioMedical Research, Urology Research Laboratory, University of Bern, Bern, Switzerland
| | - Alice Macchia
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Federico La Manna
- Department for BioMedical Research, Urology Research Laboratory, University of Bern, Bern, Switzerland
| | - Yari Ciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Federico Vannuccini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Vera Mugoni
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michela Notarangelo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michela Libergoli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesca Broso
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Riccardo Taulli
- Department of Oncology, University of Torino, Torino, Italy
- Center for Experimental Research and Medical Studies (CeRMS), AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Ugo Ala
- Department of Veterinary Sciences, University of Torino, Torino, Italy
| | - Aurora Savino
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Martina Cortese
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Somayeh Mirzaaghaei
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
- Molecular Biotechnology Center (MBC) "Guido Tarone", University of Torino, Torino, Italy
| | - Valeria Poli
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
- Molecular Biotechnology Center (MBC) "Guido Tarone", University of Torino, Torino, Italy
| | - Ian Marc Bonapace
- Department of Biotechnology and Life Sciences, University of Insubria, Busto Arsizio, VA, Italy
| | - Mauro Giulio Papotti
- Department of Pathology, University of Torino and AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Luca Molinaro
- Department of Pathology, University of Torino and AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Claudio Doglioni
- Division of Pathology, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS Vita Salute, San Raffaele University, Milano, Italy
| | - Orazio Caffo
- Medical Oncology Department, Santa Chiara Hospital-APSS, Trento, Italy
| | - Adriano Anesi
- Operative Unit of Clinical Pathology, Santa Chiara Hospital-APSS, Trento, Italy
| | - Michael Nagler
- Department of Urology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Giovanni Bertalot
- Operative Unit of Anatomy Pathology, Santa Chiara Hospital-APSS, Trento, Italy
- Centre for Medical Sciences-CISMed, University of Trento, Trento, Italy
| | | | - Mattia Barbareschi
- Operative Unit of Anatomy Pathology, Santa Chiara Hospital-APSS, Trento, Italy
- Centre for Medical Sciences-CISMed, University of Trento, Trento, Italy
| | - Umberto Basso
- Oncology 1 Unit, Department of Oncology, Istituto Oncologico Veneto IOV IRCCS, Padova, Italy
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Massimo Pizzato
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Marianna Kruithof-de Julio
- Department for BioMedical Research, Urology Research Laboratory, University of Bern, Bern, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Andrea Lunardi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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13
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Wani SA, Hussain S, Gray JS, Nayak D, Tang H, Perez LM, Long MD, Siddappa M, McCabe CJ, Sucheston-Campbell LE, Freeman MR, Campbell MJ. Epigenetic disruption of the RARγ complex impairs its function to bookmark AR enhancer interactions required for enzalutamide sensitivity in prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.15.571947. [PMID: 38168185 PMCID: PMC10760102 DOI: 10.1101/2023.12.15.571947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The current study in prostate cancer (PCa) focused on the genomic mechanisms at the cross-roads of pro-differentiation signals and the emergence of lineage plasticity. We explored an understudied cistromic mechanism involving RARγ's ability to govern AR cistrome-transcriptome relationships, including those associated with more aggressive PCa features. The RARγ complex in PCa cell models was enriched for canonical cofactors, as well as proteins involved in RNA processing and bookmarking. Identifying the repertoire of miR-96 bound and regulated gene targets, including those recognition elements marked by m6A, revealed their significant enrichment in the RARγ complex. RARγ significantly enhanced the AR cistrome, particularly in active enhancers and super-enhancers, and overlapped with the binding of bookmarking factors. Furthermore, RARγ expression led to nucleosome-free chromatin enriched with H3K27ac, and significantly enhanced the AR cistrome in G2/M cells. RARγ functions also antagonized the transcriptional actions of the lineage master regulator ONECUT2. Similarly, gene programs regulated by either miR-96 or antagonized by RARγ were enriched in alternative lineages and more aggressive PCa phenotypes. Together these findings reveal an under-investigated role for RARγ, modulated by miR-96, to bookmark enhancer sites during mitosis. These sites are required by the AR to promote transcriptional competence, and emphasize luminal differentiation, while antagonizing ONECUT2.
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Affiliation(s)
- Sajad A Wani
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Shahid Hussain
- Division of Cancer Biology, Cedars Sinai Cancer, and Los Angeles, CA 90048
- Board of Governors Innovation Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Jaimie S Gray
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Debasis Nayak
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Hancong Tang
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Lillian M Perez
- Division of Cancer Therapeutics, Cedars Sinai Cancer, Departments of Urology and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Mark D Long
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263
| | - Manjunath Siddappa
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Christopher J McCabe
- Institute of Metabolism and Systems Research (IMSR), and Centre of Endocrinology, Diabetes and Metabolism (CEDAM), University of Birmingham, Birmingham, UK
| | | | - Michael R Freeman
- Division of Cancer Therapeutics, Cedars Sinai Cancer, Departments of Urology and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Moray J Campbell
- Division of Cancer Biology, Cedars Sinai Cancer, and Los Angeles, CA 90048
- Board of Governors Innovation Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
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14
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Yang Z, Shi M, Liang Y, Zhang F, Li C, Lu Y, Yin T, Wang Z, Li Y, Hao M, Guo R, Yang H, Lei G, Sun F, Zhang Y, Deng Z, Tian Y, Yu L, Bai C, Wang L, Wan C, Wang H, Yang P. Three-dimensional chromatin landscapes in hepatocellular carcinoma associated with hepatitis B virus. J Gastroenterol 2024; 59:119-137. [PMID: 37925679 DOI: 10.1007/s00535-023-02053-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Three-dimensional (3D) chromatin architecture frequently altered in cancer. However, its changes during the pathogenesis of hepatocellular carcinoma (HCC) remained elusive. METHODS Hi-C and RNA-seq were applied to study the 3D chromatin landscapes and gene expression of HCC and ANHT. Hi-C Pro was used to generate genome-wide raw interaction matrices, which were normalized via iterative correction (ICE). Moreover, the chromosomes were divided into different compartments according to the first principal component (E1). Furthermore, topologically associated domains (TADs) were visualized via WashU Epigenome Browser. Furthermore, differential expression analysis of ANHT and HCC was performed using the DESeq2 R package. Additionally, dysregulated genes associated with 3D genome architecture altered were confirmed using TCGA, qRT-PCR, immunohistochemistry (IHC), etc. RESULTS: First, the intrachromosomal interactions of chr1, chr2, chr5, and chr11 were significantly different, and the interchromosomal interactions of chr4-chr10, chr13-chr21, chr15-chr22, and chr16-chr19 are remarkably different between ANHT and HCC, which resulted in the up-regulation of TP53I3 and ZNF738 and the down-regulation of APOC3 and APOA5 in HCC. Second, 49 compartment regions on 18 chromosomes have significantly switched (A-B or B-A) during HCC tumorigenesis, contributing to up-regulation of RAP2A. Finally, a tumor-specific TAD boundary located on chr5: 6271000-6478000 and enhancer hijacking were identified in HCC tissues, potentially associated with the elevated expression of MED10, whose expression were associated with poor prognosis of HCC patients. CONCLUSION This study demonstrates the crucial role of chromosomal structure variation in HCC oncogenesis and potential novel biomarkers of HCC, laying a foundation for cancer precision medicine development.
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Affiliation(s)
- Zhao Yang
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
- College of Life Science and Technology, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, 843300, Xinjiang, China.
| | - Mengran Shi
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Youfeng Liang
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Fuhan Zhang
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Cong Li
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yinying Lu
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Taian Yin
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhaohai Wang
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yongchao Li
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
- College of Life Science and Technology, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, 843300, Xinjiang, China
| | - Mingxuan Hao
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Rui Guo
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Hao Yang
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Guanglin Lei
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Fang Sun
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Yu Zhang
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Zhuoya Deng
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yuying Tian
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Linxiang Yu
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Changqing Bai
- Department of Respiratory, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Lei Wang
- College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Chuanxing Wan
- College of Life Science and Technology, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, 843300, Xinjiang, China
| | - Haifeng Wang
- Department of Urology, Second Affiliated Hospital of Kunming Medical University, Kunming, 650504, China.
| | - Penghui Yang
- The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
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15
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Zhang L, Liu L, Li H, He J, Chao H, Yan S, Yin Y, Zhao W, Li M. 3D genome structural variations play important roles in regulating seed oil content of Brassica napus. PLANT COMMUNICATIONS 2024; 5:100666. [PMID: 37496273 PMCID: PMC10811347 DOI: 10.1016/j.xplc.2023.100666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/01/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023]
Abstract
Dissecting the complex regulatory mechanism of seed oil content (SOC) is one of the main research goals in Brassica napus. Increasing evidence suggests that genome architecture is linked to multiple biological functions. However, the effect of genome architecture on SOC regulation remains unclear. Here, we used high-throughput chromatin conformation capture to characterize differences in the three-dimensional (3D) landscape of genome architecture of seeds from two B. napus lines, N53-2 (with high SOC) and Ken-C8 (with low SOC). Bioinformatics analysis demonstrated that differentially accessible regions and differentially expressed genes between N53-2 and Ken-C8 were preferentially enriched in regions with quantitative trait loci (QTLs)/associated genomic regions (AGRs) for SOC. A multi-omics analysis demonstrated that expression of SOC-related genes was tightly correlated with genome structural variations in QTLs/AGRs of B. napus. The candidate gene BnaA09g48250D, which showed structural variation in a QTL/AGR on chrA09, was identified by fine-mapping of a KN double-haploid population derived from hybridization of N53-2 and Ken-C8. Overexpression and knockout of BnaA09g48250D led to significant increases and decreases in SOC, respectively, in the transgenic lines. Taken together, our results reveal the 3D genome architecture of B. napus seeds and the roles of genome structural variations in SOC regulation, enriching our understanding of the molecular mechanisms of SOC regulation from the perspective of spatial chromatin structure.
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Affiliation(s)
- Libin Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Lin Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan 430075, China
| | - Huaixin Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Jianjie He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Hongbo Chao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shuxiang Yan
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Yontai Yin
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Weiguo Zhao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China.
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16
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Shah A. Rethinking cancer initiation: The role of large-scale mutational events. Genes Chromosomes Cancer 2024; 63:e23213. [PMID: 37950638 DOI: 10.1002/gcc.23213] [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: 06/08/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/13/2023] Open
Abstract
Cancer initiation is revisited in light of recent discoveries in cancer pathogenesis. Of note is the detection of mutated cancer genes in benign conditions. More significantly, somatic clones, which harbor mutations in cancer genes, arise in normal tissues from early development through adulthood, but seldom do they transform into cancer. Further, clustered mutational events-kataegis, chromothripsis and chromoplexy-are widespread in cancer, generating point mutations and chromosomal rearrangements in a single cellular catastrophe. These observations are contrary to the prevailing somatic mutation theory, which states that a cancer is caused by the gradual accumulation of mutations over time. A different perspective is proposed within the framework of Waddington's epigenetic landscape wherein tumorigenesis is viewed primarily as a disruption of cell development. Cell types are defined by their specific gene-expression profiles, determined by the gene regulatory network, and can be regarded as attractor states of the network dynamics: they represent specific, self-stabilizing patterns of gene activities across the genome. However, large-scale mutational events reshape the landscape topology, creating abnormal "unphysiological" attractors. This is the crux of the process of initiation. Initiation primes the cell for conversion into a tumor phenotype by oncogenes and tumor suppressor genes, which drive cell proliferation and clonal diversification. This view of tumorigenesis calls for a different approach to therapy.
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Affiliation(s)
- Amil Shah
- Department of Medicine, University of British Columbia, Vancouver, Canada
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17
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Gray JS, Wani SA, Hussain S, Huang P, Nayak D, Long MD, Yates C, Clinton SK, Bennet CE, Coss CC, Campbell MJ. The MYC axis in advanced prostate cancer is impacted through concurrent targeting of ERβ and AR using a novel ERβ-selective ligand alongside Enzalutamide. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.567282. [PMID: 38014010 PMCID: PMC10680693 DOI: 10.1101/2023.11.15.567282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
We have dissected the role of Estrogen receptor beta (ERβ) in prostate cancer (PCa) with a novel ERβ ligand, OSU-ERb-12. Drug screens revealed additive interactions between OSU-ERB-12 and either epigenetic inhibitors or the androgen receptor antagonist, Enzalutamide (Enza). Clonogenic and cell biolody studies supported the potent additive effects of OSU-ERB-12 (100nM) and Enza (1μM). The cooperative behavior was in PCa cell lines treated with either OSU-ERB-12 plus Enza or combinations involving 17β-estradiol (E2). OSU-ERb-12 plus Enza uniquely impacted the transcriptiome, accessible chromatin, and the AR, MYC and H3K27ac cistromes. This included skewed transcriptional responses including suppression of the androgen and MYC transcriptomes, and repressed MYC protein. OSU-ERb-12 plus Enza uniquely impacted chromatin accessibility at approximately 3000 nucleosome-free sites, enriched at enhancers, enriched for basic Helix-Loop-Helix motifs. CUT&RUN experiments revealed combination treatment targeting of MYC, AR, and H3K27ac again shaping enhancer accessibility. Specifically, it repressed MYC interactions at enhancer regions enriched for bHLH motifs, and overlapped with publicly-available bHLH cistromes. Finally, cistrome-transcriptome analyses identified ~200 genes that distinguished advanced PCa tumors in the SU2C cohort with high androgen and low neuroendocrine scores.
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Affiliation(s)
- Jaimie S. Gray
- College of Pharmacy, Division of Pharmaceutics and Pharmacology; The Ohio State University, Columbus, OH 43210
- College of Medicine; The Ohio State University, Columbus, OH 43210
- Comprehensive Cancer Center; The Ohio State University, Columbus, OH 43210
| | - Sajad A. Wani
- College of Pharmacy, Division of Pharmaceutics and Pharmacology; The Ohio State University, Columbus, OH 43210
- Comprehensive Cancer Center; The Ohio State University, Columbus, OH 43210
| | - Shahid Hussain
- Board of Governors Innovation Center; Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048
- Cedars-Sinai Cancer; Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048
| | - Phoebe Huang
- College of Pharmacy, Division of Pharmaceutics and Pharmacology; The Ohio State University, Columbus, OH 43210
| | - Debasis Nayak
- College of Pharmacy, Division of Pharmaceutics and Pharmacology; The Ohio State University, Columbus, OH 43210
| | - Mark D. Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Clayton Yates
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Oncology Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Steven K. Clinton
- College of Medicine; The Ohio State University, Columbus, OH 43210
- Comprehensive Cancer Center; The Ohio State University, Columbus, OH 43210
| | - Chad E. Bennet
- Drug Development Institute, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210
| | - Christopher C. Coss
- College of Pharmacy, Division of Pharmaceutics and Pharmacology; The Ohio State University, Columbus, OH 43210
- Comprehensive Cancer Center; The Ohio State University, Columbus, OH 43210
- Drug Development Institute, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210
| | - Moray J. Campbell
- College of Pharmacy, Division of Pharmaceutics and Pharmacology; The Ohio State University, Columbus, OH 43210
- Board of Governors Innovation Center; Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048
- Cedars-Sinai Cancer; Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048
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18
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Tigu AB, Bancos A. The Role of Epigenetic Modifier Mutations in Peripheral T-Cell Lymphomas. Curr Issues Mol Biol 2023; 45:8974-8988. [PMID: 37998740 PMCID: PMC10670124 DOI: 10.3390/cimb45110563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
Peripheral T-cell lymphomas (PTCLs) are a group of diseases with a low incidence, high degree of heterogeneity, and a dismal prognosis in most cases. Because of the low incidence of these diseases, there have been few therapeutic novelties developed over time. Nevertheless, this fact is changing presently as epigenetic modifiers have been shown to be recurrently mutated in some types of PTCLs, especially in the cases of PTCLs not otherwise specified (PTCL-NOS), T follicular helper (TFH), and angioimmunoblastic T-cell lymphoma (AITL). These have brought about more insight into PTCL biology, especially in the case of PTCLs arising from TFH lymphocytes. From a biological perspective, it has been observed that ten-eleven translocators (TET2) mutated T lymphocytes tend to polarize to TFH, while Tregs lose their inhibitory properties. IDH2 R172 was shown to have inhibitory effects on TET2, mimicking the effects of TET2 mutations, as well as having effects on histone methylation. DNA methyltransferase 3A (DNMT3A) loss-of-function, although it was shown to have opposite effects to TET2 from an inflammatory perspective, was also shown to increase the number of T lymphocyte progenitors. Aside from bringing about more knowledge of PTCL biology, these mutations were shown to increase the sensitivity of PTCLs to certain epigenetic therapies, like hypomethylating agents (HMAs) and histone deacetylase inhibitors (HDACis). Thus, to answer the question from the title of this review: We found the Achilles heel, but only for one of the Achilles.
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Affiliation(s)
- Adrian-Bogdan Tigu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania;
- Academy of Romanian Scientists, Ilfov 3, 050044 Bucharest, Romania
| | - Anamaria Bancos
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania;
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
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19
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Zhan C, Tang T, Wu E, Zhang Y, He M, Wu R, Bi C, Wang J, Zhang Y, Shen B. From multi-omics approaches to personalized medicine in myocardial infarction. Front Cardiovasc Med 2023; 10:1250340. [PMID: 37965091 PMCID: PMC10642346 DOI: 10.3389/fcvm.2023.1250340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Myocardial infarction (MI) is a prevalent cardiovascular disease characterized by myocardial necrosis resulting from coronary artery ischemia and hypoxia, which can lead to severe complications such as arrhythmia, cardiac rupture, heart failure, and sudden death. Despite being a research hotspot, the etiological mechanism of MI remains unclear. The emergence and widespread use of omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and other omics, have provided new opportunities for exploring the molecular mechanism of MI and identifying a large number of disease biomarkers. However, a single-omics approach has limitations in understanding the complex biological pathways of diseases. The multi-omics approach can reveal the interaction network among molecules at various levels and overcome the limitations of the single-omics approaches. This review focuses on the omics studies of MI, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and other omics. The exploration extended into the domain of multi-omics integrative analysis, accompanied by a compilation of diverse online resources, databases, and tools conducive to these investigations. Additionally, we discussed the role and prospects of multi-omics approaches in personalized medicine, highlighting the potential for improving diagnosis, treatment, and prognosis of MI.
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Affiliation(s)
- Chaoying Zhan
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Tong Tang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Erman Wu
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxin Zhang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- KeyLaboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mengqiao He
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Rongrong Wu
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Cheng Bi
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- KeyLaboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiao Wang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yingbo Zhang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Bairong Shen
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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20
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Abstract
The human genome is organized into multiple structural layers, ranging from chromosome territories to progressively smaller substructures, such as topologically associating domains (TADs) and chromatin loops. These substructures, collectively referred to as long-range chromatin interactions (LRIs), have a significant role in regulating gene expression. TADs are regions of the genome that harbour groups of genes and regulatory elements that frequently interact with each other and are insulated from other regions, thereby preventing widespread uncontrolled DNA contacts. Chromatin loops formed within TADs through enhancer and promoter interactions are elastic, allowing transcriptional heterogeneity and stochasticity. Over the past decade, it has become evident that the 3D genome structure, also referred to as the chromatin architecture, is central to many transcriptional cellular decisions. In this Review, we delve into the intricate relationship between steroid receptors and LRIs, discussing how steroid receptors interact with and modulate these chromatin interactions. Genetic alterations in the many processes involved in organizing the nuclear architecture are often associated with the development of hormone-dependent cancers. A better understanding of the interplay between architectural proteins and hormone regulatory networks can ultimately be exploited to develop improved approaches for cancer treatment.
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Affiliation(s)
- Theophilus T Tettey
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA.
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21
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Lawson HA, Liang Y, Wang T. Transposable elements in mammalian chromatin organization. Nat Rev Genet 2023; 24:712-723. [PMID: 37286742 DOI: 10.1038/s41576-023-00609-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2023] [Indexed: 06/09/2023]
Abstract
Transposable elements (TEs) are mobile DNA elements that comprise almost 50% of mammalian genomic sequence. TEs are capable of making additional copies of themselves that integrate into new positions in host genomes. This unique property has had an important impact on mammalian genome evolution and on the regulation of gene expression because TE-derived sequences can function as cis-regulatory elements such as enhancers, promoters and silencers. Now, advances in our ability to identify and characterize TEs have revealed that TE-derived sequences also regulate gene expression by both maintaining and shaping 3D genome architecture. Studies are revealing how TEs contribute raw sequence that can give rise to the structures that shape chromatin organization, and thus gene expression, allowing for species-specific genome innovation and evolutionary novelty.
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Affiliation(s)
- Heather A Lawson
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Yonghao Liang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO, USA.
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22
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Luo X, Zhang L, Cui J, An Q, Li H, Zhang Z, Sun G, Huang W, Li Y, Li C, Jia W, Zou L, Zhao G, Xiao F. Small extrachromosomal circular DNAs as biomarkers for multi-cancer diagnosis and monitoring. Clin Transl Med 2023; 13:e1393. [PMID: 37649244 PMCID: PMC10468585 DOI: 10.1002/ctm2.1393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Small extrachromosomal circular DNAs (eccDNAs) have the potential to be cancer biomarkers. However, the formation mechanisms and functions of small eccDNAs selected in carcinogenesis are not clear, and whether the small eccDNA profile in the plasma of cancer patients represents that in cancer tissues remains to be elucidated. METHODS A novel sequencing workflow based on the nanopore sequencing platform was used to sequence naturally existing full-length small eccDNAs in tissues and plasma collected from 25 cancer patients (including prostate cancer, hepatocellular carcinoma and colorectal cancer), and from an independent validation cohort (including 7 cancer plasma and 14 healthy plasma). RESULTS Compared with those in non-cancer tissues, small eccDNAs detected in cancer tissues had a significantly larger number and size (P = 0.040 and 2.2e-16, respectively), along with more even distribution and different formation mechanisms. Although small eccDNAs had different general characteristics and genomic annotation between cancer tissues and the paired plasma, they had similar formation mechanisms and cancer-related functions. Small eccDNAs originated from some specific genes had great multi-cancer diagnostic value in tissues (AUC ≥ 0.8) and plasma (AUC > 0.9), especially increasing the accuracy of multi-cancer prediction of CEA/CA19-9 levels. The high multi-cancer diagnostic value of small eccDNAs originated from ALK&ETV6 could be extrapolated from tissues (AUC = 0.804) to plasma and showed high positive predictive value (100%) and negative predictive value (82.35%) in a validation cohort. CONCLUSIONS As independent and stable circular DNA molecules, small eccDNAs in both tissues and plasma can be used as ideal biomarkers for cost-effective multi-cancer diagnosis and monitoring.
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Affiliation(s)
- Xuanmei Luo
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Lili Zhang
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Jian Cui
- Department of General SurgeryBeijing HospitalBeijingChina
| | - Qi An
- Department of General SurgeryBeijing HospitalBeijingChina
| | - Hexin Li
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Zaifeng Zhang
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Gaoyuan Sun
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Wei Huang
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Yifei Li
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Chang Li
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Wenzhuo Jia
- Department of General SurgeryBeijing HospitalBeijingChina
- National Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Lihui Zou
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Gang Zhao
- Department of General SurgeryBeijing HospitalBeijingChina
- National Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Fei Xiao
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
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23
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Kurup JT, Kim S, Kidder BL. Identifying Cancer Type-Specific Transcriptional Programs through Network Analysis. Cancers (Basel) 2023; 15:4167. [PMID: 37627195 PMCID: PMC10453000 DOI: 10.3390/cancers15164167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Identifying cancer type-specific genes that define cell states is important to develop effective therapies for patients and methods for detection, early diagnosis, and prevention. While molecular mechanisms that drive malignancy have been identified for various cancers, the identification of cell-type defining transcription factors (TFs) that distinguish normal cells from cancer cells has not been fully elucidated. Here, we utilized a network biology framework, which assesses the fidelity of cell fate conversions, to identify cancer type-specific gene regulatory networks (GRN) for 17 types of cancer. Through an integrative analysis of a compendium of expression data, we elucidated core TFs and GRNs for multiple cancer types. Moreover, by comparing normal tissues and cells to cancer type-specific GRNs, we found that the expression of key network-influencing TFs can be utilized as a survival prognostic indicator for a diverse cohort of cancer patients. These findings offer a valuable resource for exploring cancer type-specific networks across a broad range of cancer types.
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Affiliation(s)
- Jiji T. Kurup
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (J.T.K.); (S.K.)
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Seongho Kim
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (J.T.K.); (S.K.)
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Benjamin L. Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (J.T.K.); (S.K.)
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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24
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Song T, Yao M, Yang Y, Liu Z, Zhang L, Li W. Integrative Identification by Hi-C Revealed Distinct Advanced Structural Variations in Lung Adenocarcinoma Tissue. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:390-407. [PMID: 37589026 PMCID: PMC10425312 DOI: 10.1007/s43657-023-00103-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 08/18/2023]
Abstract
Advanced three-dimensional structure variations of chromatin in large genome fragments, such as conversion of A/B compartment, topologically associated domains (TADs) and chromatin loops are related closely to occurrence of malignant tumors. However, the structural characteristics of lung cancer still remain uncovered. In this study, we used high-throughput chromosome (Hi-C) conformation capture technology to detect the advanced structural variations in chromatin of two non-smoking lung adenocarcinoma (LUAD) tumor and paired normal tissues. The results indicate that significant chromatin variations are detected in tumor tissues compared with normal tissues. At compartment scale, the main conversion type of compartment is A → B in tumor tissues, which are concentrated mainly on chromosome 3 (Chr3) (33.6%). A total of 216 tumor-specific TADs are identified in tumor tissues, which are distributed mainly in Chr1 (19), Chr2 (15) and Chr3 (17). Forty-one distinct enhancer-promoter loops are observed in tumor tissue, which are associated closely to tumor-related pathways including mitogen-activated protein kinase (MAPK), Phosphatidylinositol-3-kinase-Protein kinase B (PI3K-AKT), Ras, Wnt and Ras1. The most important observation in this study is that we identify five important genes (SYT16, NCEH1, NXPE3, MB21D2, and DZIP1L), which are detected in both A → B compartment, TADs and chromatin loops in tumor samples, and four of these genes (NCEH1, NXPE3, MB21D2, and DZIP1L) locate on q arm of Chr3. Further gene expression and invasion experiment analysis show that NCEH1, MB21D2 and SYT16 are involved in the tumor development. Thus, we provide a comprehensive overview of advanced structures in LUAD for the first time and provide a basis for further research on the genetic variation of this tumor.
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Affiliation(s)
- Tingting Song
- Department of Respiratory and Critical Care Medicine, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Menglin Yao
- Department of Respiratory and Critical Care Medicine, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Ying Yang
- Department of Respiratory and Critical Care Medicine, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Zhiqiang Liu
- Department of Respiratory and Critical Care Medicine, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Li Zhang
- Department of Respiratory and Critical Care Medicine, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
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25
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Li H, He X, Kurowski L, Zhang R, Zhao D, Zeng J. Improving comparative analyses of Hi-C data via contrastive self-supervised learning. Brief Bioinform 2023; 24:bbad193. [PMID: 37287135 DOI: 10.1093/bib/bbad193] [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: 02/06/2023] [Revised: 04/12/2023] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Hi-C is a widely applied chromosome conformation capture (3C)-based technique, which has produced a large number of genomic contact maps with high sequencing depths for a wide range of cell types, enabling comprehensive analyses of the relationships between biological functionalities (e.g. gene regulation and expression) and the three-dimensional genome structure. Comparative analyses play significant roles in Hi-C data studies, which are designed to make comparisons between Hi-C contact maps, thus evaluating the consistency of replicate Hi-C experiments (i.e. reproducibility measurement) and detecting statistically differential interacting regions with biological significance (i.e. differential chromatin interaction detection). However, due to the complex and hierarchical nature of Hi-C contact maps, it remains challenging to conduct systematic and reliable comparative analyses of Hi-C data. Here, we proposed sslHiC, a contrastive self-supervised representation learning framework, for precisely modeling the multi-level features of chromosome conformation and automatically producing informative feature embeddings for genomic loci and their interactions to facilitate comparative analyses of Hi-C contact maps. Comprehensive computational experiments on both simulated and real datasets demonstrated that our method consistently outperformed the state-of-the-art baseline methods in providing reliable measurements of reproducibility and detecting differential interactions with biological meanings.
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Affiliation(s)
- Han Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084 Beijing, China
| | - Xuan He
- Machine Learning Department, Silexon AI Technology Co., Ltd., 210000 Nanjing, China
| | - Lawrence Kurowski
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084 Beijing, China
| | - Ruotian Zhang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084 Beijing, China
| | - Dan Zhao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084 Beijing, China
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084 Beijing, China
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26
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Blatt EB, Parra K, Neeb A, Buroni L, Bogdan D, Yuan W, Gao Y, Gilbreath C, Paschalis A, Carreira S, DeBerardinis RJ, Mani RS, de Bono JS, Raj GV. Critical role of antioxidant programs in enzalutamide-resistant prostate cancer. Oncogene 2023; 42:2347-2359. [PMID: 37355762 PMCID: PMC10752496 DOI: 10.1038/s41388-023-02756-w] [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: 10/10/2022] [Revised: 05/22/2023] [Accepted: 06/13/2023] [Indexed: 06/26/2023]
Abstract
Therapy resistance to second-generation androgen receptor (AR) antagonists, such as enzalutamide, is common in patients with advanced prostate cancer (PCa). To understand the metabolic alterations involved in enzalutamide resistance, we performed metabolomic, transcriptomic, and cistromic analyses of enzalutamide-sensitive and -resistant PCa cells, xenografts, patient-derived organoids, patient-derived explants, and tumors. We noted dramatically higher basal and inducible levels of reactive oxygen species (ROS) in enzalutamide-resistant PCa and castration-resistant PCa (CRPC), in comparison to enzalutamide-sensitive PCa cells or primary therapy-naive tumors respectively. Unbiased metabolomic evaluation identified that glutamine metabolism was consistently upregulated in enzalutamide-resistant PCa cells and CRPC tumors. Stable isotope tracing studies suggest that this enhanced glutamine metabolism drives an antioxidant program that allows these cells to tolerate higher basal levels of ROS. Inhibition of glutamine metabolism with either a small-molecule glutaminase inhibitor or genetic knockout of glutaminase enhanced ROS levels, and blocked the growth of enzalutamide-resistant PCa. The critical role of compensatory antioxidant pathways in maintaining enzalutamide-resistant PCa cells was validated by targeting another antioxidant program driver, ferredoxin 1. Taken together, our data identify a metabolic need to maintain antioxidant programs and a potentially targetable metabolic vulnerability in enzalutamide-resistant PCa.
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Affiliation(s)
- Eliot B Blatt
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
| | - Karla Parra
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
| | - Antje Neeb
- The Institute of Cancer Research, London, UK
| | | | | | - Wei Yuan
- The Institute of Cancer Research, London, UK
| | - Yunpeng Gao
- Department of Pathology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
| | - Collin Gilbreath
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
| | | | | | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Ram S Mani
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
- Department of Pathology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
| | - Johann S de Bono
- The Institute of Cancer Research, London, UK
- Institute of Cancer Research and the Royal Marsden NHS Foundation Trust, London, UK
| | - Ganesh V Raj
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA.
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA.
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA.
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27
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Qiu Y, Feng D, Jiang W, Zhang T, Lu Q, Zhao M. 3D genome organization and epigenetic regulation in autoimmune diseases. Front Immunol 2023; 14:1196123. [PMID: 37346038 PMCID: PMC10279977 DOI: 10.3389/fimmu.2023.1196123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/17/2023] [Indexed: 06/23/2023] Open
Abstract
Three-dimensional (3D) genomics is an emerging field of research that investigates the relationship between gene regulatory function and the spatial structure of chromatin. Chromatin folding can be studied using chromosome conformation capture (3C) technology and 3C-based derivative sequencing technologies, including chromosome conformation capture-on-chip (4C), chromosome conformation capture carbon copy (5C), and high-throughput chromosome conformation capture (Hi-C), which allow scientists to capture 3D conformations from a single site to the entire genome. A comprehensive analysis of the relationships between various regulatory components and gene function also requires the integration of multi-omics data such as genomics, transcriptomics, and epigenomics. 3D genome folding is involved in immune cell differentiation, activation, and dysfunction and participates in a wide range of diseases, including autoimmune diseases. We describe hierarchical 3D chromatin organization in this review and conclude with characteristics of C-techniques and multi-omics applications of the 3D genome. In addition, we describe the relationship between 3D genome structure and the differentiation and maturation of immune cells and address how changes in chromosome folding contribute to autoimmune diseases.
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Affiliation(s)
- Yueqi Qiu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
| | - Delong Feng
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Wenjuan Jiang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
| | - Tingting Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Ming Zhao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
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28
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Zhang Y, Zhang J, Zhang W, Wang M, Wang S, Xu Y, Zhao L, Li X, Li G. Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:573-588. [PMID: 36702236 PMCID: PMC10787015 DOI: 10.1016/j.gpb.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/30/2022] [Accepted: 01/17/2023] [Indexed: 01/25/2023]
Abstract
Studies on the lung cancer genome are indispensable for developing a cure for lung cancer. Whole-genome resequencing, genome-wide association studies, and transcriptome sequencing have greatly improved our understanding of the cancer genome. However, dysregulation of long-range chromatin interactions in lung cancer remains poorly described. To better understand the three-dimensional (3D) genomic interaction features of the lung cancer genome, we used the A549 cell line as a model system and generated high-resolution chromatin interactions associated with RNA polymerase II (RNAPII), CCCTC-binding factor (CTCF), enhancer of zeste homolog 2 (EZH2), and histone 3 lysine 27 trimethylation (H3K27me3) using long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). Analysis showed that EZH2/H3K27me3-mediated interactions further repressed target genes, either through loops or domains, and their distributions along the genome were distinct from and complementary to those associated with RNAPII. Cancer-related genes were highly enriched with chromatin interactions, and chromatin interactions specific to the A549 cell line were associated with oncogenes and tumor suppressor genes, such as additional repressive interactions on FOXO4 and promoter-promoter interactions between NF1 and RNF135. Knockout of an anchor associated with chromatin interactions reversed the dysregulation of cancer-related genes, suggesting that chromatin interactions are essential for proper expression of lung cancer-related genes. These findings demonstrate the 3D landscape and gene regulatory relationships of the lung cancer genome.
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Affiliation(s)
- Yan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingwen Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Mohan Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangqi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Yao Xu
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China.
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29
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Liu J, Li P, Sun J, Guo J. LPAD: using network construction and label propagation to detect topologically associating domains from Hi-C data. Brief Bioinform 2023; 24:7150739. [PMID: 37139561 DOI: 10.1093/bib/bbad165] [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: 01/09/2023] [Revised: 03/06/2023] [Accepted: 04/09/2023] [Indexed: 05/05/2023] Open
Abstract
With the development of chromosome conformation capture technique, the study of spatial conformation of a genome based on Hi-C technique has made a quantum leap. Previous studies reveal that genomes are folded into hierarchy of three-dimensional (3D) structures associated with topologically associating domains (TADs), and detecting TAD boundaries is of great significance in the chromosome-level analysis of 3D genome architecture. In this paper, we propose a novel TAD identification method, LPAD, which first extracts node correlations from global interactions of chromosomes based on the random walk with restart and then builds an undirected graph from Hi-C contact matrix. Next, LPAD designs a label propagation-based approach to discover communities and generates TADs. Experimental results verify the effectiveness and quality of TAD detections compared with existing methods. Furthermore, experimental evaluation of chromatin immunoprecipitation sequencing data shows that LPAD performs high enrichment of histone modifications remarkably nearby the TAD boundaries, and these results demonstrate LPAD's advantages on TAD identification accuracy.
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Affiliation(s)
- Jian Liu
- College of Computer Science, Nankai University, Tianjin 300071, China
| | - Pingjing Li
- College of Computer Science, Nankai University, Tianjin 300071, China
| | - Jialiang Sun
- College of Computer Science, Nankai University, Tianjin 300071, China
- Centre for Bioinformatics and Intelligent Medicine, Nankai University, Tianjin 300071, China
| | - Jun Guo
- College of Software, Northeastern University, Shenyang 110819, China
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30
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Sun Y, Xu X, Lin L, Xu K, Zheng Y, Ren C, Tao H, Wang X, Zhao H, Tu W, Bai X, Wang J, Huang Q, Li Y, Chen H, Li H, Bo X. A graph neural network-based interpretable framework reveals a novel DNA fragility-associated chromatin structural unit. Genome Biol 2023; 24:90. [PMID: 37095580 PMCID: PMC10124043 DOI: 10.1186/s13059-023-02916-x] [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: 01/19/2022] [Accepted: 03/22/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND DNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, and they can cause cancer if improperly repaired. Recent chromosome conformation capture techniques, such as Hi-C, have enabled the identification of relationships between the 3D chromatin structure and DSBs, but little is known about how to explain these relationships, especially from global contact maps, or their contributions to DSB formation. RESULTS Here, we propose a framework that integrates graph neural network (GNN) to unravel the relationship between 3D chromatin structure and DSBs using an advanced interpretable technique GNNExplainer. We identify a new chromatin structural unit named the DNA fragility-associated chromatin interaction network (FaCIN). FaCIN is a bottleneck-like structure, and it helps to reveal a universal form of how the fragility of a piece of DNA might be affected by the whole genome through chromatin interactions. Moreover, we demonstrate that neck interactions in FaCIN can serve as chromatin structural determinants of DSB formation. CONCLUSIONS Our study provides a more systematic and refined view enabling a better understanding of the mechanisms of DSB formation under the context of the 3D genome.
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Affiliation(s)
- Yu Sun
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Xiang Xu
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Lin Lin
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Kang Xu
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Yang Zheng
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Chao Ren
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Huan Tao
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Xu Wang
- 4Paradigm Inc, Beijing, China
| | | | | | - Xuemei Bai
- The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Junting Wang
- The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Qiya Huang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yaru Li
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China.
| | - Hao Li
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China.
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China.
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31
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Zhang S, Shen T, Zeng Y. Epigenetic Modifications in Prostate Cancer Metastasis and Microenvironment. Cancers (Basel) 2023; 15:cancers15082243. [PMID: 37190171 DOI: 10.3390/cancers15082243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
The gradual evolution of prostate tissue from benign tumor to malignant lesion or distant metastasis is driven by intracellular epigenetic changes and the tumor microenvironment remodeling. With the continuous study of epigenetic modifications, these tumor-driving forces are being discovered and are providing new treatments for cancer. Here we introduce the classification of epigenetic modification and highlight the role of epigenetic modification in tumor remodeling and communication of the tumor microenvironment.
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Affiliation(s)
- Shouyi Zhang
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang 110042, China
| | - Tao Shen
- Department of Urology, Second Affiliated Hospital of Shenyang Medical College, No. 20 Beijiu Road, Heping District, Shenyang 110001, China
| | - Yu Zeng
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang 110042, China
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32
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Dozmorov MG, Marshall MA, Rashid NS, Grible JM, Valentine A, Olex AL, Murthy K, Chakraborty A, Reyna J, Figueroa DS, Hinojosa-Gonzalez L, Da-Inn Lee E, Baur BA, Roy S, Ay F, Harrell JC. Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Sci Rep 2023; 13:5420. [PMID: 37012431 PMCID: PMC10070455 DOI: 10.1038/s41598-023-32568-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Changes in the three-dimensional (3D) structure of the genome are an emerging hallmark of cancer. Cancer-associated copy number variants and single nucleotide polymorphisms promote rewiring of chromatin loops, disruption of topologically associating domains (TADs), active/inactive chromatin state switching, leading to oncogene expression and silencing of tumor suppressors. However, little is known about 3D changes during cancer progression to a chemotherapy-resistant state. We integrated chromatin conformation capture (Hi-C), RNA-seq, and whole-genome sequencing obtained from triple-negative breast cancer patient-derived xenograft primary tumors (UCD52) and carboplatin-resistant samples and found increased short-range (< 2 Mb) interactions, chromatin looping, formation of TAD, chromatin state switching into a more active state, and amplification of ATP-binding cassette transporters. Transcriptome changes suggested the role of long-noncoding RNAs in carboplatin resistance. Rewiring of the 3D genome was associated with TP53, TP63, BATF, FOS-JUN family of transcription factors and led to activation of aggressiveness-, metastasis- and other cancer-related pathways. Integrative analysis highlighted increased ribosome biogenesis and oxidative phosphorylation, suggesting the role of mitochondrial energy metabolism. Our results suggest that 3D genome remodeling may be a key mechanism underlying carboplatin resistance.
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Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
| | - Maggie A Marshall
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Narmeen S Rashid
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biology, University of Richmond, Richmond, VA, 23173, USA
| | - Jacqueline M Grible
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Aaron Valentine
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biochemistry, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Amy L Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Kavita Murthy
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Abhijit Chakraborty
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Joaquin Reyna
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Daniela Salgado Figueroa
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Laura Hinojosa-Gonzalez
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Erika Da-Inn Lee
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Brittany A Baur
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Ferhat Ay
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
- Department of Pediatrics, UC San Diego-School of Medicine, La Jolla, CA, 92093, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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33
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Siddappa M, Hussain S, Wani SA, White J, Tang H, Gray JS, Jafari H, Wu HC, Long MD, Elhussin I, Karanam B, Wang H, Morgan R, Hardiman G, Adelani IB, Rotimi SO, Murphy AR, Nonn L, Davis MB, Kittles RA, Hughes Halbert C, Sucheston-Campbell LE, Yates C, Campbell MJ. African American Prostate Cancer Displays Quantitatively Distinct Vitamin D Receptor Cistrome-transcriptome Relationships Regulated by BAZ1A. CANCER RESEARCH COMMUNICATIONS 2023; 3:621-639. [PMID: 37082578 PMCID: PMC10112383 DOI: 10.1158/2767-9764.crc-22-0389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/12/2023] [Accepted: 03/07/2023] [Indexed: 04/22/2023]
Abstract
African American (AA) prostate cancer associates with vitamin D3 deficiency, but vitamin D receptor (VDR) genomic actions have not been investigated in this context. We undertook VDR proteogenomic analyses in European American (EA) and AA prostate cell lines and four clinical cohorts. Rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) analyses revealed that nonmalignant AA RC43N prostate cells displayed the greatest dynamic protein content in the VDR complex. Likewise, in AA cells, Assay for Transposase-Accessible Chromatin using sequencing established greater 1α,25(OH)2D3-regulated chromatin accessibility, chromatin immunoprecipitation sequencing revealed significant enhancer-enriched VDR cistrome, and RNA sequencing identified the largest 1α,25(OH)2D3-dependent transcriptome. These VDR functions were significantly corrupted in the isogenic AA RC43T prostate cancer cells, and significantly distinct from EA cell models. We identified reduced expression of the chromatin remodeler, BAZ1A, in three AA prostate cancer cohorts as well as RC43T compared with RC43N. Restored BAZ1A expression significantly increased 1α,25(OH)2D3-regulated VDR-dependent gene expression in RC43T, but not HPr1AR or LNCaP cells. The clinical impact of VDR cistrome-transcriptome relationships were tested in three different clinical prostate cancer cohorts. Strikingly, only in AA patients with prostate cancer, the genes bound by VDR and/or associated with 1α,25(OH)2D3-dependent open chromatin (i) predicted progression from high-grade prostatic intraepithelial neoplasia to prostate cancer; (ii) responded to vitamin D3 supplementation in prostate cancer tumors; (iii) differentially responded to 25(OH)D3 serum levels. Finally, partial correlation analyses established that BAZ1A and components of the VDR complex identified by RIME significantly strengthened the correlation between VDR and target genes in AA prostate cancer only. Therefore, VDR transcriptional control is most potent in AA prostate cells and distorted through a BAZ1A-dependent control of VDR function. Significance Our study identified that genomic ancestry drives the VDR complex composition, genomic distribution, and transcriptional function, and is disrupted by BAZ1A and illustrates a novel driver for AA prostate cancer.
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Affiliation(s)
- Manjunath Siddappa
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Shahid Hussain
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Sajad A. Wani
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Jason White
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
| | - Hancong Tang
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Jaimie S. Gray
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Hedieh Jafari
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Hsu-Chang Wu
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Mark D. Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Isra Elhussin
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
| | - Balasubramanyam Karanam
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
| | - Honghe Wang
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
| | - Rebecca Morgan
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
| | - Gary Hardiman
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | | | - Solomon O. Rotimi
- Department of Biochemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Adam R. Murphy
- Department of Urology, Northwestern Medicine, Chicago, Illinois
| | - Larisa Nonn
- Department of Pathology, University of Illinois at Chicago, Chicago, Illinois
| | - Melissa B. Davis
- Department of Surgery, Weill Cornell Medicine, New York City, New York
| | - Rick A. Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope, Duarte, California
| | - Chanita Hughes Halbert
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Lara E. Sucheston-Campbell
- Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, Ohio
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio
| | - Clayton Yates
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Moray J. Campbell
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
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34
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Dang D, Zhang SW, Duan R, Zhang S. Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome. Genome Res 2023; 33:386-400. [PMID: 36894325 PMCID: PMC10078287 DOI: 10.1101/gr.277187.122] [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: 08/08/2022] [Accepted: 02/23/2023] [Indexed: 03/11/2023]
Abstract
Topologically associating domains (TADs) have emerged as basic structural and functional units of genome organization and have been determined by many computational methods from Hi-C contact maps. However, the TADs obtained by different methods vary greatly, which makes the accurate determination of TADs a challenging issue and hinders subsequent biological analyses about their organization and functions. Obvious inconsistencies among the TADs identified by different methods indeed make the statistical and biological properties of TADs overly depend on the chosen method rather than on the data. To this end, we use the consensus structural information captured by these methods to define the TAD separation landscape for decoding the consensus domain organization of the 3D genome. We show that the TAD separation landscape could be used to compare domain boundaries across multiple cell types for discovering conserved and divergent topological structures, decipher three types of boundary regions with diverse biological features, and identify consensus TADs (ConsTADs). We illustrate that these analyses could deepen our understanding of the relationships between the topological domains and chromatin states, gene expression, and DNA replication timing.
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Affiliation(s)
- Dachang Dang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China;
| | - Ran Duan
- Department of Software Engineering, Yunnan University, Kunming 650500, China
| | - Shihua Zhang
- NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China;
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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Yeo SJ, Ying C, Fullwood MJ, Tergaonkar V. Emerging regulatory mechanisms of noncoding RNAs in topologically associating domains. Trends Genet 2023; 39:217-232. [PMID: 36642680 DOI: 10.1016/j.tig.2022.12.003] [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: 08/15/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023]
Abstract
Topologically associating domains (TADs) are integral to spatial genome organization, instructing gene expression, and cell fate. Recently, several advances have uncovered roles for noncoding RNAs (ncRNAs) in the regulation of the form and function of mammalian TADs. Phase separation has also emerged as a potential arbiter of ncRNAs in the regulation of TADs. In this review we discuss the implications of these novel findings in relation to how ncRNAs might structurally and functionally regulate TADs from two perspectives: moderating loop extrusion through interactions with architectural proteins, and facilitating TAD phase separation. Additionally, we propose future studies and directions to investigate these phenomena.
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Affiliation(s)
- Samuel Jianjie Yeo
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University (NTU), Singapore 308232, Singapore
| | - Chen Ying
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore 117599, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Vinay Tergaonkar
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Department of Pathology and the Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore.
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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Labani M, Beheshti A, Argha A, Alinejad-Rokny H. A Comprehensive Investigation of Genomic Variants in Prostate Cancer Reveals 30 Putative Regulatory Variants. Int J Mol Sci 2023; 24:ijms24032472. [PMID: 36768794 PMCID: PMC9916892 DOI: 10.3390/ijms24032472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Prostate cancer (PC) is the most frequently diagnosed non-skin cancer in the world. Previous studies have shown that genomic alterations represent the most common mechanism for molecular alterations responsible for the development and progression of PC. This highlights the importance of identifying functional genomic variants for early detection in high-risk PC individuals. Great efforts have been made to identify common protein-coding genetic variations; however, the impact of non-coding variations, including regulatory genetic variants, is not well understood. Identification of these variants and the underlying target genes will be a key step in improving the detection and treatment of PC. To gain an understanding of the functional impact of genetic variants, and in particular, regulatory variants in PC, we developed an integrative pipeline (AGV) that uses whole genome/exome sequences, GWAS SNPs, chromosome conformation capture data, and ChIP-Seq signals to investigate the potential impact of genomic variants on the underlying target genes in PC. We identified 646 putative regulatory variants, of which 30 significantly altered the expression of at least one protein-coding gene. Our analysis of chromatin interactions data (Hi-C) revealed that the 30 putative regulatory variants could affect 131 coding and non-coding genes. Interestingly, our study identified the 131 protein-coding genes that are involved in disease-related pathways, including Reactome and MSigDB, for most of which targeted treatment options are currently available. Notably, our analysis revealed several non-coding RNAs, including RP11-136K7.2 and RAMP2-AS1, as potential enhancer elements of the protein-coding genes CDH12 and EZH1, respectively. Our results provide a comprehensive map of genomic variants in PC and reveal their potential contribution to prostate cancer progression and development.
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Affiliation(s)
- Mahdieh Labani
- BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
- Data Analytic Lab, Department of Computing, Macquarie University, Sydney, NSW 2109, Australia
| | - Amin Beheshti
- Data Analytic Lab, Department of Computing, Macquarie University, Sydney, NSW 2109, Australia
| | - Ahmadreza Argha
- The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
- UNSW Data Science Hub, The University of New South Wales, Sydney, NSW 2052, Australia
- Health Data Analytics Program, Centre for Applied AI, Macquarie University, Sydney, NSW 2109, Australia
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Zhang L, Xu M, Zhang W, Zhu C, Cui Z, Fu H, Ma Y, Huang S, Cui J, Liang S, Huang L, Wang H. Three-dimensional genome landscape comprehensively reveals patterns of spatial gene regulation in papillary and anaplastic thyroid cancers: a study using representative cell lines for each cancer type. Cell Mol Biol Lett 2023; 28:1. [PMID: 36609218 PMCID: PMC9825046 DOI: 10.1186/s11658-022-00409-6] [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: 04/11/2022] [Accepted: 11/21/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Spatial chromatin structure is intricately linked with somatic aberrations, and somatic mutations of various cancer-related genes, termed co-mutations (CoMuts), occur in certain patterns during cancer initiation and progression. The functional mechanisms underlying these genetic events remain largely unclear in thyroid cancer (TC). With discrepant differentiation, papillary thyroid cancer (PTC) and anaplastic thyroid cancer (ATC) differ greatly in characteristics and prognosis. We aimed to reveal the spatial gene alterations and regulations between the two TC subtypes. METHODS We systematically investigated and compared the spatial co-mutations between ATC (8305C), PTC (BCPAP and TPC-1), and normal thyroid cells (Nthy-ori-3-1). We constructed a framework integrating whole-genome sequencing (WGS), high-throughput chromosome conformation capture (Hi-C), and transcriptome sequencing, to systematically detect the associations between the somatic co-mutations of cancer-related genes, structural variations (SVs), copy number variations (CNVs), and high-order chromatin conformation. RESULTS Spatial co-mutation hotspots were enriched around topologically associating domains (TADs) in TC. A common set of 227 boundaries were identified in both ATC and PTC, with significant overlaps between them. The spatial proximities of the co-mutated gene pairs in the two TC types were significantly greater than in the gene-level and overall backgrounds, and ATC cells had higher TAD contact frequency with CoMuts > 10 compared with PTC cells. Compared with normal thyroid cells, in ATC the number of the created novel three-dimensional chromatin structural domains increased by 10%, and the number of shifted TADs decreased by 7%. We found five TAD blocks with CoMut genes/events specific to ATC with certain mutations in genes including MAST-NSUN4, AM129B/TRUB2, COL5A1/PPP1R26, PPP1R26/GPSM1/CCDC183, and PRAC2/DLX4. For the majority of ATC and PTC cells, the HOXA10 and HIF2α signals close to the transcription start sites of CoMut genes within TADs were significantly stronger than those at the background. CNV breakpoints significantly overlapped with TAD boundaries in both TC subtypes. ATCs had more CNV losses overlapping with TAD boundaries, and noncoding SVs involved in intrachromosomal SVs, amplified inversions, and tandem duplication differed between ATC and PTC. TADs with short range were more abundant in ATC than PTC. More switches of A/B compartment types existed in ATC cells compared with PTC. Gene expression was significantly synchronized, and orchestrated by complex epigenetics and regulatory elements. CONCLUSION Chromatin interactions and gene alterations and regulations are largely heterogeneous in TC. CNVs and complex SVs may function in the TC genome by interplaying with TADs, and are largely different between ATC and PTC. Complexity of TC genomes, which are highly organized by 3D genome-wide interactions mediating mutational and structural variations and gene activation, may have been largely underappreciated. Our comprehensive analysis may provide key evidence and targets for more customized diagnosis and treatment of TC.
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Affiliation(s)
- Linlin Zhang
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Miaomiao Xu
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Wanchun Zhang
- grid.470966.aDepartment of Nuclear Medicine, Shanxi Bethune Hospital (Shanxi Academy of Medical Sciences), Taiyuan, 03003 China
| | - Chuanying Zhu
- grid.16821.3c0000 0004 0368 8293Department of Oncology, Xin Hua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, 200092 China
| | - Zhilei Cui
- grid.412987.10000 0004 0630 1330Department of Respiratory Medicine, XinHua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Hongliang Fu
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Yufei Ma
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Shuo Huang
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Jian Cui
- BioGenius Bioinformatics Institute, Shanghai, 200050 People’s Republic of China
| | - Sheng Liang
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Lei Huang
- grid.16821.3c0000 0004 0368 8293Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China ,grid.16821.3c0000 0004 0368 8293Medical Center on Aging of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Hui Wang
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
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Ling X, Liu X, Jiang S, Fan L, Ding J. The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases. CELL REGENERATION (LONDON, ENGLAND) 2022; 11:42. [PMID: 36539553 PMCID: PMC9768101 DOI: 10.1186/s13619-022-00145-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022]
Abstract
Cell fate transition is a fascinating process involving complex dynamics of three-dimensional (3D) chromatin organization and phase separation, which play an essential role in cell fate decision by regulating gene expression. Phase separation is increasingly being considered a driving force of chromatin folding. In this review, we have summarized the dynamic features of 3D chromatin and phase separation during physiological and pathological cell fate transitions and systematically analyzed recent evidence of phase separation facilitating the chromatin structure. In addition, we discuss current advances in understanding how phase separation contributes to physical and functional enhancer-promoter contacts. We highlight the functional roles of 3D chromatin organization and phase separation in cell fate transitions, and more explorations are required to study the regulatory relationship between 3D chromatin organization and phase separation. 3D chromatin organization (shown by Hi-C contact map) and phase separation are highly dynamic and play functional roles during early embryonic development, cell differentiation, somatic reprogramming, cell transdifferentiation and pathogenetic process. Phase separation can regulate 3D chromatin organization directly, but whether 3D chromatin organization regulates phase separation remains unclear.
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Affiliation(s)
- Xiaoru Ling
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Xinyi Liu
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Shaoshuai Jiang
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Lili Fan
- grid.258164.c0000 0004 1790 3548Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong China
| | - Junjun Ding
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.410737.60000 0000 8653 1072Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436 China ,grid.13291.380000 0001 0807 1581West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041 China
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Shao D, Yang Y, Shi S, Tong H. Three-Dimensional Organization of Chicken Genome Provides Insights into Genetic Adaptation to Extreme Environments. Genes (Basel) 2022; 13:genes13122317. [PMID: 36553584 PMCID: PMC9778438 DOI: 10.3390/genes13122317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
The high-throughput chromosome conformation capture (Hi-C) technique is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. However, the knowledge of the 3D genome structure and its dynamics during extreme environmental adaptations remains poor. Here, we characterized 3D genome architectures using the Hi-C technique for chicken liver cells. Upon comparing Lindian chicken (LDC) liver cells with Wenchang chicken (WCC) liver cells, we discovered that environmental adaptation contributed to the switching of A/B compartments, the reorganization of topologically associated domains (TADs), and TAD boundaries in both liver cells. In addition, the analysis of the switching of A/B compartments revealed that the switched compartmental genes (SCGs) were strongly associated with extreme environment adaption-related pathways, including tight junction, notch signaling pathway, vascular smooth muscle contraction, and the RIG-I-like receptor signaling pathway. The findings of this study advanced our understanding of the evolutionary role of chicken 3D genome architecture and its significance in genome activity and transcriptional regulation.
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Affiliation(s)
- Dan Shao
- Laboratory of Poultry Production, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
| | - Yu Yang
- Laboratory of Poultry Production, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China
- Correspondence: (Y.Y.); (S.S.)
| | - Shourong Shi
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
- Correspondence: (Y.Y.); (S.S.)
| | - Haibing Tong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
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Feng Y, Wang P, Cai L, Zhan M, He F, Wang J, Li Y, Gega E, Zhang W, Zhao W, Xin Y, Chen X, Ruan Y, Lu L. 3D-Epigenomic Regulation of Gene Transcription in Hepatocellular Carcinoma. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2100010. [PMID: 36911294 PMCID: PMC9993472 DOI: 10.1002/ggn2.202100010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 05/03/2022] [Indexed: 11/10/2022]
Abstract
The fundamental cause of transcription dysregulation in hepatocellular carcinoma (HCC) remains elusive. To investigate the underlying mechanisms, comprehensive 3D-epigenomic analyses are performed in cellular models of THLE2 (a normal hepatocytes cell line) and HepG2 (a hepatocellular carcinoma cell line) using integrative approaches for chromatin topology, genomic and epigenomic variation, and transcriptional output. Comparing the 3D-epigenomes in THLE2 and HepG2 reveal that most HCC-associated genes are organized in complex chromatin interactions mediated by RNA polymerase II (RNAPII). Incorporation of genome-wide association studies (GWAS) data enables the identification of non-coding genetic variants that are enriched in distal enhancers connecting to the promoters of HCC-associated genes via long-range chromatin interactions, highlighting their functional roles. Interestingly, CTCF binding and looping proximal to HCC-associated genes appear to form chromatin architectures that overarch RNAPII-mediated chromatin interactions. It is further demonstrated that epigenetic variants by DNA hypomethylation at a subset of CTCF motifs proximal to HCC-associated genes can modify chromatin topological configuration, which in turn alter RNAPII-mediated chromatin interactions and lead to dysregulation of transcription. Together, the 3D-epigenomic analyses provide novel insights of multifaceted interplays involving genetics, epigenetics, and chromatin topology in HCC cells.
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Affiliation(s)
- Yuliang Feng
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China.,The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Liuyang Cai
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Meixiao Zhan
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
| | - Fan He
- Department of Interventional Radiology Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology) Shenzhen Guangdong 518020 P. R. China
| | - Jiahui Wang
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Yong Li
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
| | - Eva Gega
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Wei Zhang
- Department of Interventional Radiology Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology) Shenzhen Guangdong 518020 P. R. China
| | - Wei Zhao
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
| | - Yongjie Xin
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
| | - Xudong Chen
- Department of Interventional Radiology Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology) Shenzhen Guangdong 518020 P. R. China
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Ligong Lu
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
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Tay KY, Wu KX, Chioh FWJ, Autio MI, Pek NMQ, Narmada BC, Tan SH, Low AFH, Lian MM, Chew EGY, Lau HH, Kao SL, Teo AKK, Foo JN, Foo RSY, Heng CK, Chan MYY, Cheung C. Trans-interaction of risk loci 6p24.1 and 10q11.21 is associated with endothelial damage in coronary artery disease. Atherosclerosis 2022; 362:11-22. [PMID: 36435092 DOI: 10.1016/j.atherosclerosis.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS Single nucleotide polymorphism rs6903956 has been identified as one of the genetic risk factors for coronary artery disease (CAD). However, rs6903956 lies in a non-coding locus on chromosome 6p24.1. We aim to interrogate the molecular basis of 6p24.1 containing rs6903956 risk alleles in endothelial disease biology. METHODS AND RESULTS We generated induced pluripotent stem cells (iPSCs) from CAD patients (AA risk genotype at rs6903956) and non-CAD subjects (GG non-risk genotype at rs6903956). CRISPR-Cas9-based deletions (Δ63-89bp) on 6p24.1, including both rs6903956 and a short tandem repeat variant rs140361069 in linkage disequilibrium, were performed to generate isogenic iPSC-derived endothelial cells. Edited CAD endothelial cells, with removal of 'A' risk alleles, exhibited a global transcriptional downregulation of pathways relating to abnormal vascular physiology and activated endothelial processes. A CXC chemokine ligand on chromosome 10q11.21, CXCL12, was uncovered as a potential effector gene in CAD endothelial cells. Underlying this effect was the preferential inter-chromosomal interaction of 6p24.1 risk locus to a weak promoter of CXCL12, confirmed by chromatin conformation capture assays on our iPSC-derived endothelial cells. Functionally, risk genotypes AA/AG at rs6903956 were associated significantly with elevated levels of circulating damaged endothelial cells in CAD patients. Circulating endothelial cells isolated from patients with risk genotypes AA/AG were also found to have 10 folds higher CXCL12 transcript copies/cell than those with non-risk genotype GG. CONCLUSIONS Our study reveals the trans-acting impact of 6p24.1 with another CAD locus on 10q11.21 and is associated with intensified endothelial injury.
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Affiliation(s)
- Kai Yi Tay
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Kan Xing Wu
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Florence Wen Jing Chioh
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Matias Ilmari Autio
- Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Balakrishnan Chakrapani Narmada
- Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore; Experimental Drug Development Centre, A*STAR, 10 Biopolis Road, Singapore, 138670
| | - Sock-Hwee Tan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; National University Heart Centre, National University Health System, Singapore
| | - Adrian Fatt-Hoe Low
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; National University Heart Centre, National University Health System, Singapore
| | - Michelle Mulan Lian
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Elaine Guo Yan Chew
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Hwee Hui Lau
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Proteos, 138673, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Shih Ling Kao
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Medicine, National University Hospital and National University Health System, Singapore
| | - Adrian Kee Keong Teo
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR, Proteos, 138673, Singapore
| | - Jia Nee Foo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore; Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore
| | - Roger Sik Yin Foo
- Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore; National University Heart Centre, National University Health System, Singapore
| | - Chew Kiat Heng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Khoo Teck Puat, National University Children's Medical Institute, National University Health System, Singapore
| | - Mark Yan Yee Chan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; National University Heart Centre, National University Health System, Singapore
| | - Christine Cheung
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR, Proteos, 138673, Singapore.
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Rittenbruch M, Vella K, Brereton M, Hogan JM, Johnson D, Heinrich J, O'Donoghue S. Collaborative Sense-Making in Genomic Research: The Role of Visualisation. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2022; 28:4477-4489. [PMID: 34156943 DOI: 10.1109/tvcg.2021.3090746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Genomic research emerges from collaborative work within and across different scientific disciplines. A diverse range of visualisation techniques has been employed to aid this research, yet relatively little is known as to how these techniques facilitate collaboration. We conducted a case study of collaborative research within a biomedical institute to learn more about the role visualisation plays in genomic mapping. Interviews were conducted with molecular biologists (N = 5) and bioinformaticians (N = 6). We found that genomic research comprises a variety of distinct disciplines engaged in complex analytic tasks that each resist simplification, and their complexity influences how visualisations were used. Visualisation use was impacted by group-specific interactions and temporal work patterns. Visualisations were also crucial to the scientific workflow, used for both question formation and confirmation of hypotheses, and acted as an anchor for the communication of ideas and discussion. In the latter case, two approaches were taken: providing collaborators with either interactive or static imagery representing a viewpoint. The use of generic software for simplified visualisations, and quick production and curation was also noted. We discuss these findings with reference to group-specific interactions and present recommendations for improving collaborative practices through visual analytics.
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44
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Xu Z, Lee DS, Chandran S, Le VT, Bump R, Yasis J, Dallarda S, Marcotte S, Clock B, Haghani N, Cho CY, Akdemir K, Tyndale S, Futreal PA, McVicker G, Wahl GM, Dixon JR. Structural variants drive context-dependent oncogene activation in cancer. Nature 2022; 612:564-572. [PMID: 36477537 PMCID: PMC9810360 DOI: 10.1038/s41586-022-05504-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
Higher-order chromatin structure is important for the regulation of genes by distal regulatory sequences1,2. Structural variants (SVs) that alter three-dimensional (3D) genome organization can lead to enhancer-promoter rewiring and human disease, particularly in the context of cancer3. However, only a small minority of SVs are associated with altered gene expression4,5, and it remains unclear why certain SVs lead to changes in distal gene expression and others do not. To address these questions, we used a combination of genomic profiling and genome engineering to identify sites of recurrent changes in 3D genome structure in cancer and determine the effects of specific rearrangements on oncogene activation. By analysing Hi-C data from 92 cancer cell lines and patient samples, we identified loci affected by recurrent alterations to 3D genome structure, including oncogenes such as MYC, TERT and CCND1. By using CRISPR-Cas9 genome engineering to generate de novo SVs, we show that oncogene activity can be predicted by using 'activity-by-contact' models that consider partner region chromatin contacts and enhancer activity. However, activity-by-contact models are only predictive of specific subsets of genes in the genome, suggesting that different classes of genes engage in distinct modes of regulation by distal regulatory elements. These results indicate that SVs that alter 3D genome organization are widespread in cancer genomes and begin to illustrate predictive rules for the consequences of SVs on oncogene activation.
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Affiliation(s)
- Zhichao Xu
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA,These authors contributed equally
| | - Dong-Sung Lee
- Department of Life Sciences, University of Seoul, Seoul, South Korea,These authors contributed equally
| | - Sahaana Chandran
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Victoria T. Le
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Rosalind Bump
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Jean Yasis
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Sofia Dallarda
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Samantha Marcotte
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Benjamin Clock
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Nicholas Haghani
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Chae Yun Cho
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Kadir Akdemir
- Department of Genomic Medicine; UT MD Anderson Cancer Center; Houston, TX, 77030; USA
| | - Selene Tyndale
- Integrative Biology Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - P. Andrew Futreal
- Department of Genomic Medicine; UT MD Anderson Cancer Center; Houston, TX, 77030; USA
| | - Graham McVicker
- Integrative Biology Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Geoffrey M. Wahl
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Jesse R. Dixon
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA,Correspondence:
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Li N, Meng G, Yang C, Li H, Liu L, Wu Y, Liu B. Changes in epigenetic information during the occurrence and development of gastric cancer. Int J Biochem Cell Biol 2022; 153:106315. [DOI: 10.1016/j.biocel.2022.106315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/22/2022] [Accepted: 10/18/2022] [Indexed: 11/24/2022]
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46
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Gridina M, Fishman V. Multilevel view on chromatin architecture alterations in cancer. Front Genet 2022; 13:1059617. [PMID: 36468037 PMCID: PMC9715599 DOI: 10.3389/fgene.2022.1059617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/31/2022] [Indexed: 12/25/2023] Open
Abstract
Chromosomes inside the nucleus are not located in the form of linear molecules. Instead, there is a complex multilevel genome folding that includes nucleosomes packaging, formation of chromatin loops, domains, compartments, and finally, chromosomal territories. Proper spatial organization play an essential role for the correct functioning of the genome, and is therefore dynamically changed during development or disease. Here we discuss how the organization of the cancer cell genome differs from the healthy genome at various levels. A better understanding of how malignization affects genome organization and long-range gene regulation will help to reveal the molecular mechanisms underlying cancer development and evolution.
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Affiliation(s)
- Maria Gridina
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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47
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Golloshi R, Playter C, Freeman TF, Das P, Raines TI, Garretson JH, Thurston D, McCord RP. Constricted migration is associated with stable 3D genome structure differences in cancer cells. EMBO Rep 2022; 23:e52149. [PMID: 35969179 PMCID: PMC9535800 DOI: 10.15252/embr.202052149] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 07/01/2022] [Accepted: 07/12/2022] [Indexed: 01/14/2023] Open
Abstract
To spread from a localized tumor, metastatic cancer cells must squeeze through constrictions that cause major nuclear deformations. Since chromosome structure affects nucleus stiffness, gene regulation, and DNA repair, here, we investigate the relationship between 3D genome structure and constricted migration in cancer cells. Using melanoma (A375) cells, we identify phenotypic differences in cells that have undergone multiple rounds of constricted migration. These cells display a stably higher migration efficiency, elongated morphology, and differences in the distribution of Lamin A/C and heterochromatin. Hi-C experiments reveal differences in chromosome spatial compartmentalization specific to cells that have passed through constrictions and related alterations in expression of genes associated with migration and metastasis. Certain features of the 3D genome structure changes, such as a loss of B compartment interaction strength, are consistently observed after constricted migration in clonal populations of A375 cells and in MDA-MB-231 breast cancer cells. Our observations suggest that consistent types of chromosome structure changes are induced or selected by passage through constrictions and that these may epigenetically encode stable differences in gene expression and cellular migration phenotype.
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Affiliation(s)
- Rosela Golloshi
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Christopher Playter
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Trevor F Freeman
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Priyojit Das
- UT‐ORNL Graduate School of Genome Science and TechnologyUniversity of TennesseeKnoxvilleTNUSA
| | - Thomas Isaac Raines
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Joshua H Garretson
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Delaney Thurston
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Rachel Patton McCord
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
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Wang X, Yan J, Ye Z, Zhang Z, Wang S, Hao S, Shen B, Wei G. Reorganization of 3D chromatin architecture in doxorubicin-resistant breast cancer cells. Front Cell Dev Biol 2022; 10:974750. [PMID: 36003143 PMCID: PMC9393755 DOI: 10.3389/fcell.2022.974750] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Doxorubicin resistance remains a major therapeutic challenge leading to poor survival prognosis and treatment failure in breast cancer. Although doxorubicin induces massive changes in the transcriptional landscape are well known, potential diagnostic or therapeutic targets associated with the reorganization of three-dimensional (3D) chromatin architecture have not yet been systematically investigated. Methods: Here we performed in situ high-throughput chromosome conformation capture (Hi-C) on parental and doxorubicin-resistant MCF7 (MCF7-DR) human breast cancer cells, followed by integrative analysis of HiC, ATAC-seq, RNA-seq and TCGA data. Results: It revealed that A/B compartment switching was positively correlated to genome-wide differential gene expression. The genome of MCF7-DR cells was spatially reorganized into smaller topologically associating domains (TADs) and chromatin loops. We also revealed the contribution of increased chromatin accessibility and potential transcription factor families, including CTCF, AP-1 and bHLH, to gained TADs or loops. Intriguingly, we observed two condensed genomic regions (∼20 kb) with decreased chromatin accessibility flanking TAD boundaries, which might play a critical role in the formation or maintenance of TADs. Finally, combining data from TCGA, we identified a number of gained and lost enhancer-promoter interactions and their corresponding differentially expressed genes involved in chromatin organization and breast cancer signaling pathways, including FA2H, FOXA1 and JRKL, which might serve as potential treatment targets for breast cancer. Conclusion: These data uncovered a close connection between 3D genome reorganization, chromatin accessibility as well as gene transcription and provide novel insights into the epigenomic mechanisms involving doxorubicin resistance in breast cancer.
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Affiliation(s)
- Xuelong Wang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jizhou Yan
- Department of Developmental Biology, Institute for Marine Biosystem and Neurosciences, Shanghai Ocean University, Shanghai, China
| | - Zhao Ye
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Zhang
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Sheng Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shuang Hao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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Neuropilin-2 promotes lineage plasticity and progression to neuroendocrine prostate cancer. Oncogene 2022; 41:4307-4317. [PMID: 35986103 PMCID: PMC9464715 DOI: 10.1038/s41388-022-02437-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/08/2022]
Abstract
Neuroendocrine prostate cancer (NEPC), a lethal subset of prostate cancer, is characterized by loss of AR signaling and resulting resistance to AR-targeted therapy during neuroendocrine transdifferentiation, for which the molecular mechanisms remain unclear. Here, we report that neuropilin 2 (NRP2) is upregulated in both de novo and therapy-induced NEPC, which induces neuroendocrine markers, neuroendocrine cell morphology, and NEPC cell aggressive behavior. NRP2 silencing restricted NEPC tumor xenograft growth. Mechanistically, NRP2 engages in reciprocal crosstalk with AR, where NRP2 is transcriptionally inhibited by AR, and in turn suppresses AR signaling by downregulating the AR transcriptional program and confers resistance to enzalutamide. Moreover, NRP2 physically interacts with VEGFR2 through the intracellular SEA domain to activate STAT3 phosphorylation and subsequently SOX2, thus driving NEPC differentiation and growth. Collectively, these results characterize NRP2 as a driver of NEPC and suggest NRP2 as a potential therapeutic target in NEPC.
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50
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Zhou T, Feng Q. Androgen receptor signaling and spatial chromatin organization in castration-resistant prostate cancer. Front Med (Lausanne) 2022; 9:924087. [PMID: 35966880 PMCID: PMC9372301 DOI: 10.3389/fmed.2022.924087] [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: 04/20/2022] [Accepted: 07/12/2022] [Indexed: 12/03/2022] Open
Abstract
Prostate cancer is one of the leading causes of cancer death and affects millions of men in the world. The American Cancer Society estimated about 34,500 deaths from prostate cancer in the United States in year 2022. The Androgen receptor (AR) signaling is a major pathway that sustains local and metastatic prostate tumor growth. Androgen-deprivation therapy (ADT) is the standard of care for metastatic prostate cancer patient and can suppress the tumor growth for a median of 2–3 years. Unfortunately, the malignancy inevitably progresses to castration-resistant prostate cancer (CRPC) which is more aggressive and no longer responsive to ADT. Surprisingly, for most of the CPRC patients, cancer growth still depends on androgen receptor signaling. Accumulating evidence suggests that CRPC cells have rewired their transcriptional program to retain AR signaling in the absence of androgens. Besides AR, other transcription factors also contribute to the resistance mechanism through multiple pathways including enhancing AR signaling pathway and activating other complementary signaling pathways for the favor of AR downstream genes expression. More recent studies have shown the role of transcription factors in reconfiguring chromatin 3D structure and regulating topologically associating domains (TADs). Pioneer factors, transcription factors and coactivators form liquid-liquid phase separation compartment that can modulate transcriptional events along with configuring TADs. The role of AR and other transcription factors on chromatin structure change and formation of condensate compartment in prostate cancer cells has only been recently investigated and appreciated. This review intends to provide an overview of transcription factors that contribute to AR signaling through activation of gene expression, governing 3D chromatin structure and establishing phase to phase separation. A more detailed understanding of the spatial role of transcription factors in CRPC might provide novel therapeutic targets for the treatment of CRPC.
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