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Lu Y, Jiang J, He Z, Bao Z, Chen X, Cheng J. Molecular characteristics and oncogenic role of CHD family genes: a pan-cancer analysis based on bioinformatic and biological analysis. Sci Rep 2024; 14:18923. [PMID: 39143142 PMCID: PMC11324730 DOI: 10.1038/s41598-024-68644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 07/25/2024] [Indexed: 08/16/2024] Open
Abstract
Chromodomain helicase DNA-binding protein (CHD) gene family, an ATP (adenosine triphosphate) -dependent chromatin remodeler family, is involved in multiple developmental process and tumor development. However, there have been none pan-cancer analyses of this family. The expression levels, survival profiles, mutation profiles and immune infiltration of the CHD family genes from TCGA and TARGET database were analyzed using online tools or R packages. Interestingly, all types of CHD gene expressions were associated with the prognosis of Neuroblastoma, Acute lymphoblastic leukemia-Phase 3 and Acute Myeloid Leukemia (All P < 0.05). Knock down of CHD7 and CHD9 in K562 (human erythromyeloblastoid leukemia) and HEC-1-B (human endometrial adenocarcinoma) cells significantly inhibit cell proliferation and migration (P < 0.05). Proliferation, colony formation and migration assays were performed in CHD7 and CHD9 knockdown K562 and HBC-1-B cell lines. Mechanisms were also analyzed by PPI and GO ontology for our experiments. Histone modification, especially the methylation of H3K4, might be involved in CHD7 and CHD9 related oncogenesis. Through bioinformatic analysis, we showed CHD genes significantly affected the prognosis of different tumor types, including childhood tumor. Our findings provide new insights into the function and mechanism of CHD gene family, especially in CHD7 and CHD9.
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Affiliation(s)
- Yujia Lu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiebang Jiang
- Jiangsu Province Engineering Research Center of Cardiovascular Drugs Targeting, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Zhihong He
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhouzhou Bao
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xin Chen
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.
- Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University, School of Medicine, Shanghai, China.
| | - Jie Cheng
- Center for Reproductive Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China.
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Deng Q, Qiang J, Liu C, Ding J, Tu J, He X, Xia J, Peng X, Li S, Chen X, Ma W, Zhang L, Jiang Y, Shao Z, Chen C, Liu S, Xu J, Zhang L. SOSTDC1 Nuclear Translocation Facilitates BTIC Maintenance and CHD1-Mediated HR Repair to Promote Tumor Progression and Olaparib Resistance in TNBC. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306860. [PMID: 38864559 PMCID: PMC11304230 DOI: 10.1002/advs.202306860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 05/01/2024] [Indexed: 06/13/2024]
Abstract
Breast tumor-initiating cells (BTICs) of triple-negative breast cancer (TNBC) tissues actively repair DNA and are resistant to treatments including chemotherapy, radiotherapy, and targeted therapy. Herein, it is found that a previously reported secreted protein, sclerostin domain containing 1 (SOSTDC1), is abundantly expressed in BTICs of TNBC cells and positively correlated with a poor patient prognosis. SOSTDC1 knockdown impairs homologous recombination (HR) repair, BTIC maintenance, and sensitized bulk cells and BTICs to Olaparib. Mechanistically, following Olaparib treatment, SOSTDC1 translocates to the nucleus in an importin-α dependent manner. Nuclear SOSTDC1 interacts with the N-terminus of the nucleoprotein, chromatin helicase DNA-binding factor (CHD1), to promote HR repair and BTIC maintenance. Furthermore, nuclear SOSTDC1 bound to β-transducin repeat-containing protein (β-TrCP) binding motifs of CHD1 is found, thereby blocking the β-TrCP-CHD1 interaction and inhibiting β-TrCP-mediated CHD1 ubiquitination and degradation. Collectively, these findings identify a novel nuclear SOSTDC1 pathway in regulating HR repair and BTIC maintenance, providing insight into the TNBC therapeutic strategies.
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Affiliation(s)
- Qiaodan Deng
- Fudan University Shanghai Cancer Center & Institutes of Biomedical SciencesState Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Jiankun Qiang
- Fudan University Shanghai Cancer Center & Institutes of Biomedical SciencesState Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai200032China
- Research Center for Translational MedicineShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Cuicui Liu
- Department of Breast SurgeryShanghai Cancer Center and Cancer InstituteFudan UniversityShanghai200032P. R. China
| | - Jiajun Ding
- Department of ThyroidBreast and Vascular SurgeryXijing HospitalThe Fourth Military Medical UniversityXi'an710032P. R. China
| | - Juchuanli Tu
- Fudan University Shanghai Cancer Center & Institutes of Biomedical SciencesState Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Xueyan He
- Fudan University Shanghai Cancer Center & Institutes of Biomedical SciencesState Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Jie Xia
- Fudan University Shanghai Cancer Center & Institutes of Biomedical SciencesState Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Xilei Peng
- Fudan University Shanghai Cancer Center & Institutes of Biomedical SciencesState Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Siqin Li
- Fudan University Shanghai Cancer Center & Institutes of Biomedical SciencesState Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Xian Chen
- Fudan University Shanghai Cancer Center & Institutes of Biomedical SciencesState Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Wei Ma
- Fudan University Shanghai Cancer Center & Institutes of Biomedical SciencesState Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Lu Zhang
- Fudan University Shanghai Cancer Center & Institutes of Biomedical SciencesState Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Yi‐Zhou Jiang
- Department of Breast SurgeryFudan University Shanghai Cancer CenterShanghai200032China
- Key Laboratory of Breast Cancer in ShanghaiDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Zhi‐Ming Shao
- Department of Breast SurgeryFudan University Shanghai Cancer CenterShanghai200032China
- Key Laboratory of Breast Cancer in ShanghaiDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyKunming650201China
- Academy of Biomedical Engineering & The Third Affiliated HospitalKunming Medical UniversityKunming650118China
| | - Suling Liu
- Fudan University Shanghai Cancer Center & Institutes of Biomedical SciencesState Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai200032China
- Jiangsu Key Lab of Cancer BiomarkersPrevention and TreatmentCollaborative Innovation Center for Cancer MedicineNanjing Medical UniversityNanjing211166China
| | - Jiahui Xu
- Fudan University Shanghai Cancer Center & Institutes of Biomedical SciencesState Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Lixing Zhang
- Fudan University Shanghai Cancer Center & Institutes of Biomedical SciencesState Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai200032China
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Tan WY, Nagabhyrava S, Ang-Olson O, Das P, Ladel L, Sailo B, He L, Sharma A, Ahuja N. Translation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology. Curr Issues Mol Biol 2024; 46:6533-6565. [PMID: 39057032 PMCID: PMC11276574 DOI: 10.3390/cimb46070390] [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: 05/27/2024] [Revised: 06/21/2024] [Accepted: 06/23/2024] [Indexed: 07/28/2024] Open
Abstract
Technological advancements in cell-free DNA (cfDNA) liquid biopsy have triggered exponential growth in numerous clinical applications. While cfDNA-based liquid biopsy has made significant strides in personalizing cancer treatment, the exploration and translation of epigenetics in liquid biopsy to clinical practice is still nascent. This comprehensive review seeks to provide a broad yet in-depth narrative of the present status of epigenetics in cfDNA liquid biopsy and its associated challenges. It highlights the potential of epigenetics in cfDNA liquid biopsy technologies with the hopes of enhancing its clinical translation. The momentum of cfDNA liquid biopsy technologies in recent years has propelled epigenetics to the forefront of molecular biology. We have only begun to reveal the true potential of epigenetics in both our understanding of disease and leveraging epigenetics in the diagnostic and therapeutic domains. Recent clinical applications of epigenetics-based cfDNA liquid biopsy revolve around DNA methylation in screening and early cancer detection, leading to the development of multi-cancer early detection tests and the capability to pinpoint tissues of origin. The clinical application of epigenetics in cfDNA liquid biopsy in minimal residual disease, monitoring, and surveillance are at their initial stages. A notable advancement in fragmentation patterns analysis has created a new avenue for epigenetic biomarkers. However, the widespread application of cfDNA liquid biopsy has many challenges, including biomarker sensitivity, specificity, logistics including infrastructure and personnel, data processing, handling, results interpretation, accessibility, and cost effectiveness. Exploring and translating epigenetics in cfDNA liquid biopsy technology can transform our understanding and perception of cancer prevention and management. cfDNA liquid biopsy has great potential in precision oncology to revolutionize conventional ways of early cancer detection, monitoring residual disease, treatment response, surveillance, and drug development. Adapting the implementation of liquid biopsy workflow to the local policy worldwide and developing point-of-care testing holds great potential to overcome global cancer disparity and improve cancer outcomes.
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Affiliation(s)
- Wan Ying Tan
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
- Department of Internal Medicine, Norwalk Hospital, Norwalk, CT 06850, USA
- Hematology & Oncology, Neag Comprehensive Cancer Center, UConn Health, Farmington, CT 06030, USA
| | | | - Olivia Ang-Olson
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Paromita Das
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Luisa Ladel
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
- Department of Internal Medicine, Norwalk Hospital, Norwalk, CT 06850, USA
| | - Bethsebie Sailo
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Linda He
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Anup Sharma
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Nita Ahuja
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520-8000, USA
- Biological and Biomedical Sciences Program (BBS), Yale University, New Haven, CT 06520-8084, USA
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Xu C, Zhao S, Cai L. Epigenetic (De)regulation in Prostate Cancer. Cancer Treat Res 2023; 190:321-360. [PMID: 38113006 DOI: 10.1007/978-3-031-45654-1_10] [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] [Indexed: 12/21/2023]
Abstract
Prostate cancer (PCa) is a heterogeneous disease exhibiting both genetic and epigenetic deregulations. Epigenetic alterations are defined as changes not based on DNA sequence, which include those of DNA methylation, histone modification, and chromatin remodeling. Androgen receptor (AR) is the main driver for PCa and androgen deprivation therapy (ADT) remains a backbone treatment for patients with PCa; however, ADT resistance almost inevitably occurs and advanced diseases develop termed castration-resistant PCa (CRPC), due to both genetic and epigenetic changes. Due to the reversible nature of epigenetic modifications, inhibitors targeting epigenetic factors have become promising anti-cancer agents. In this chapter, we focus on recent studies about the dysregulation of epigenetic regulators crucially involved in the initiation, development, and progression of PCa and discuss the potential use of inhibitors targeting epigenetic modifiers for treatment of advanced PCa.
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Affiliation(s)
- Chenxi Xu
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Shuai Zhao
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Ling Cai
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
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