1
|
Li L, Song Q, Zhou J, Ji Q. Controllers of histone methylation-modifying enzymes in gastrointestinal cancers. Biomed Pharmacother 2024; 174:116488. [PMID: 38520871 DOI: 10.1016/j.biopha.2024.116488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/26/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024] Open
Abstract
Gastrointestinal (GI) cancers have been considered primarily genetic malignancies, caused by a series of progressive genetic alterations. Accumulating evidence shows that histone methylation, an epigenetic modification program, plays an essential role in the different pathological stages of GI cancer progression, such as precancerous lesions, tumorigenesis, and tumor metastasis. Histone methylation-modifying enzymes, including histone methyltransferases (HMTs) and demethylases (HDMs), are the main executor of post-transcriptional modification. The abnormal expression of histone methylation-modifying enzymes characterizes GI cancers with complex pathogenesis and progression. Interactions between upstream controllers and histone methylation-modifying enzymes have recently been revealed, and have provided numerous opportunities to elucidate the pathogenesis of GI cancers in depth and clearly. Here we focus on the association between histone methylation-modifying enzymes and their controllers, aiming to provide a new perspective on the molecular research and clinical management of GI cancers.
Collapse
Affiliation(s)
- Ling Li
- Department of Medical Oncology & Cancer Institute of Integrative Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qing Song
- Department of Medical Oncology, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, Jiangsu 215007, China
| | - Jing Zhou
- Department of Medical Oncology & Cancer Institute of Integrative Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Liver Disease Department of Integrative Medicine, Ningbo No.2 Hospital, Ningbo, Zhejiang 315000, China.
| | - Qing Ji
- Department of Medical Oncology & Cancer Institute of Integrative Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| |
Collapse
|
2
|
Deng E, Fan X. Categorizing Extrachromosomal Circular DNA as Biomarkers in Serum of Cancer. Biomolecules 2024; 14:488. [PMID: 38672504 PMCID: PMC11048305 DOI: 10.3390/biom14040488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA), a double-stranded circular DNA molecule found in multiple organisms, has garnered an increasing amount of attention in recent years due to its close association with the initiation, malignant progression, and heterogeneous evolution of cancer. The presence of eccDNA in serum assists in non-invasive tumor diagnosis as a biomarker that can be assessed via liquid biopsies. Furthermore, the specific expression patterns of eccDNA provide new insights into personalized cancer therapy. EccDNA plays a pivotal role in tumorigenesis, development, diagnosis, and treatment. In this review, we comprehensively outline the research trajectory of eccDNA, discuss its role as a diagnostic and prognostic biomarker, and elucidate its regulatory mechanisms in cancer. In particular, we emphasize the potential application value of eccDNA in cancer diagnosis and treatment and anticipate the development of novel tumor diagnosis strategies based on serum eccDNA in the future.
Collapse
Affiliation(s)
- Enze Deng
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Xiaoying Fan
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, China
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510005, China
| |
Collapse
|
3
|
Ding LY, Chang CJ, Chen SY, Chen KL, Li YS, Wu YC, Hsu TY, Ying HY, Wu HY, Hughes MW, Wang CY, Chang CH, Tang MJ, Chuang WJ, Shan YS, Chang CJ, Huang PH. Stromal Rigidity Stress Accelerates Pancreatic Intraepithelial Neoplasia Progression and Chromosomal Instability via Nuclear Protein Tyrosine Kinase 2 Localization. Am J Pathol 2024:S0002-9440(24)00132-9. [PMID: 38631549 DOI: 10.1016/j.ajpath.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/11/2024] [Accepted: 02/21/2024] [Indexed: 04/19/2024]
Abstract
Because the mechanotransduction by stromal stiffness stimulates the rupture and repair of the nuclear envelope in pancreatic progenitor cells, accumulated genomic aberrations are under selection in the tumor microenvironment. Analysis of cell growth, micronuclei, and γH2AX foci links to mechanotransduction pressure in vivo during serial orthotopic passages of mouse KrasLSL-G12D/+;Trp53flox/flox;Pdx1-Cre (KPC) cancer cells in the tumor and in migrating through the size-restricted 3-μm micropores. To search for pancreatic cancer cell of origin, analysis of single-cell data sets revealed that the extracellular matrix shapes an alternate route of acinar-ductal transdifferentiation of acinar cells into a central hub of elegantly restrained topoisomerase II α (TOP2A)-overexpressing cancer cells that spread out as unique cancer clusters with copy number amplifications in MYC-PTK2 (protein tyrosine kinase 2) locus and PIK3CA. High-PTK2 expression is associated with 171 differentially methylated CpG loci, 319 differentially expressed genes, and poor overall survival in patients with The Cancer Genome Atlas-PAAD. Abolished RGD-integrin signaling by disintegrin KG blocked the PTK2 phosphorylation, increased cancer apoptosis, decreased VAV1 expression, and prolonged overall survival in the KPC mice. Decreases of α-smooth muscle actin deposition in the CD248 knockout KPC mice remodel the tissue stroma and down-regulated TOP2A expression in the epithelium. In summary, stromal stiffness induces the onset of cells of origin of cancer by ectopic TOP2A expression, and the genomic amplification of MYC-PTK2 locus via alternative transdifferentiation of pancreatic progenitor cells is the vulnerability useful for disintegrin KG treatment against cells-of-origin cancer.
Collapse
Affiliation(s)
- Li-Yun Ding
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Jung Chang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Szu-Ying Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuan-Lin Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yueh-Shan Li
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yun-Chieh Wu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ting-Yi Hsu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsin-Yu Ying
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsin-Yi Wu
- Instrumentation Center, College of Science, National Taiwan University, Taipei, Taiwan
| | - Michael W Hughes
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Life Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Yih Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Han Chang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan; Medical Device Innovation Center, National Cheng Kung University, Tainan, Taiwan
| | - Ming-Jer Tang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan; Department Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Woei-Jer Chuang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Center of Cell Therapy, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yan-Shen Shan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Center of Cell Therapy, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Division of General Surgery, Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Jung Chang
- Department of Internal Medicine, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Po-Hsien Huang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| |
Collapse
|
4
|
Abu-Zaid A, Fang J, Jin H, Singh S, Pichavaram P, Wu Q, Tillman H, Janke L, Rosikiewicz W, Xu B, Van De Velde LA, Guo Y, Li Y, Shendy NAM, Delahunty IM, Rankovic Z, Chen T, Chen X, Freeman KW, Hatley ME, Durbin AD, Murray PJ, Murphy AJ, Thomas PG, Davidoff AM, Yang J. Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma. Cell Rep Med 2024; 5:101468. [PMID: 38508144 PMCID: PMC10983111 DOI: 10.1016/j.xcrm.2024.101468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/21/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Neuroblastoma with MYCN amplification (MNA) is a high-risk disease that has a poor survival rate. Neuroblastoma displays cellular heterogeneity, including more differentiated (adrenergic) and more primitive (mesenchymal) cellular states. Here, we demonstrate that MYCN oncoprotein promotes a cellular state switch in mesenchymal cells to an adrenergic state, accompanied by induction of histone lysine demethylase 4 family members (KDM4A-C) that act in concert to control the expression of MYCN and adrenergic core regulatory circulatory (CRC) transcription factors. Pharmacologic inhibition of KDM4 blocks expression of MYCN and the adrenergic CRC transcriptome with genome-wide induction of transcriptionally repressive H3K9me3, resulting in potent anticancer activity against neuroblastomas with MNA by inducing neuroblastic differentiation and apoptosis. Furthermore, a short-term KDM4 inhibition in combination with conventional, cytotoxic chemotherapy results in complete tumor responses of xenografts with MNA. Thus, KDM4 blockade may serve as a transformative strategy to target the adrenergic CRC dependencies in MNA neuroblastomas.
Collapse
Affiliation(s)
- Ahmed Abu-Zaid
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA; College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jie Fang
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shivendra Singh
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Qiong Wu
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Heather Tillman
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laura Janke
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lee-Ann Van De Velde
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yian Guo
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yimei Li
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Noha A M Shendy
- Department of Molecular Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ian M Delahunty
- Department of Molecular Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiang Chen
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kevin W Freeman
- Genetics, Genomics & Informatics, The University of Tennessee Health Science Center, Memphis, TN 38103, USA
| | - Mark E Hatley
- Department of Molecular Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Adam D Durbin
- Department of Molecular Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter J Murray
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Andrew J Murphy
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Division of Pediatric Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrew M Davidoff
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Division of Pediatric Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, TN 38105, USA; St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Avenue, Suite 500, Memphis, TN 38163, USA
| | - Jun Yang
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA; St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Avenue, Suite 500, Memphis, TN 38163, USA; College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA.
| |
Collapse
|
5
|
Sadida HQ, Abdulla A, Marzooqi SA, Hashem S, Macha MA, Akil ASAS, Bhat AA. Epigenetic modifications: Key players in cancer heterogeneity and drug resistance. Transl Oncol 2024; 39:101821. [PMID: 37931371 PMCID: PMC10654239 DOI: 10.1016/j.tranon.2023.101821] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/12/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
Cancer heterogeneity and drug resistance remain pivotal obstacles in effective cancer treatment and management. One major contributor to these challenges is epigenetic modifications - gene regulation that does not involve changes to the DNA sequence itself but significantly impacts gene expression. As we elucidate these phenomena, we underscore the pivotal role of epigenetic modifications in regulating gene expression, contributing to cellular diversity, and driving adaptive changes that can instigate therapeutic resistance. This review dissects essential epigenetic modifications - DNA methylation, histone modifications, and chromatin remodeling - illustrating their significant yet complex contributions to cancer biology. While these changes offer potential avenues for therapeutic intervention due to their reversible nature, the interplay of epigenetic and genetic changes in cancer cells presents unique challenges that must be addressed to harness their full potential. By critically analyzing the current research landscape, we identify knowledge gaps and propose future research directions, exploring the potential of epigenetic therapies and discussing the obstacles in translating these concepts into effective treatments. This comprehensive review aims to stimulate further research and aid in developing innovative, patient-centered cancer therapies. Understanding the role of epigenetic modifications in cancer heterogeneity and drug resistance is critical for scientific advancement and paves the way towards improving patient outcomes in the fight against this formidable disease.
Collapse
Affiliation(s)
- Hana Q Sadida
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Alanoud Abdulla
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Sara Al Marzooqi
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Sheema Hashem
- Laboratory of Genomic Medicine, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Jammu & Kashmir, India
| | - Ammira S Al-Shabeeb Akil
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar.
| | - Ajaz A Bhat
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar.
| |
Collapse
|
6
|
Chen Z, Qi Y, Shen J, Chen Z. Histone demethylase KDM6A coordinating with KMT2B regulates self-renewal and chemoresistance of non-small cell lung cancer stem cells. Transl Oncol 2023; 37:101778. [PMID: 37683307 PMCID: PMC10493599 DOI: 10.1016/j.tranon.2023.101778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND AND AIMS Wnt signaling is essential for the maintenance of cancer stem cells (CSCs), but mutations in the β-catenin and APC genes are less common in non-small cell lung carcinoma (NSCLC). Thus, the mechanism underlying the constitutive activation of Wnt signaling in lung CSCs is still unknown. MATERIALS AND METHODS Gene set enrichment analysis and immunohistochemistry were performed to establish the correlation between KDM6A/KM2B and CSC stemness. Human NSCLC cell lines were genetically manipulated for functional studies. Sphere formation assay and stemness gene expression profiling were examined to investigate the role of KDM6A/KMT2B in lung CSCs. Tumor xenograft assay were used to identify the function of KDM6A/KMT2B on tumorigenicity and tumor recurrence in vivo. Western blot analysis, coimmunoprecipitation and chromatin immunoprecipitation were performed to understand KDM6A/KMT2B mediated epigenetic regulation of Histone 3 lysine 4 methylation (H3K4me) on Wnt signaling pathway. RESULTS We discovered that the expression of Histone demethylase KDM6A and methyltransferase KMT2B correlate with the stemness of CSCs in NSCLC. KDM6A coordinates with KMT2B to activate the Wnt/β-catenin signaling pathway by regulating the H3K4me3 level and promotes the tumorigenicity and maintenance of CSC stemness. Furthermore, KDM6A/ KMT2B overexpression promotes the CSC chemoresistance and tumor recurrence both in vitro and in vivo. Inhibition of KDM6A and KMT2B potently suppress tumor initiation and recurrence in xenografted animal models. CONCLUSION Our findings suggest that KDM6A and KMT2B mediate the constitutive activation of Wnt/β-catenin signaling in lung CSCs, potentially providing a therapeutic target for NSCLC.
Collapse
Affiliation(s)
- Zhiwei Chen
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yuwen Qi
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Shen
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhen Chen
- Department of Pathology, Shidong hospital, Yangpu District, Shidong hospital affiliated to University of Shanghai for Science and Technology, China.
| |
Collapse
|
7
|
Gray ZH, Chakraborty D, Duttweiler RR, Alekbaeva GD, Murphy SE, Chetal K, Ji F, Ferman BI, Honer MA, Wang Z, Myers C, Sun R, Kaniskan HÜ, Toma MM, Bondarenko EA, Santoro JN, Miranda C, Dillingham ME, Tang R, Gozani O, Jin J, Skorski T, Duy C, Lee H, Sadreyev RI, Whetstine JR. Epigenetic balance ensures mechanistic control of MLL amplification and rearrangement. Cell 2023; 186:4528-4545.e18. [PMID: 37788669 PMCID: PMC10591855 DOI: 10.1016/j.cell.2023.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 06/01/2023] [Accepted: 09/08/2023] [Indexed: 10/05/2023]
Abstract
MLL/KMT2A amplifications and translocations are prevalent in infant, adult, and therapy-induced leukemia. However, the molecular contributor(s) to these alterations are unclear. Here, we demonstrate that histone H3 lysine 9 mono- and di-methylation (H3K9me1/2) balance at the MLL/KMT2A locus regulates these amplifications and rearrangements. This balance is controlled by the crosstalk between lysine demethylase KDM3B and methyltransferase G9a/EHMT2. KDM3B depletion increases H3K9me1/2 levels and reduces CTCF occupancy at the MLL/KMT2A locus, in turn promoting amplification and rearrangements. Depleting CTCF is also sufficient to generate these focal alterations. Furthermore, the chemotherapy doxorubicin (Dox), which associates with therapy-induced leukemia and promotes MLL/KMT2A amplifications and rearrangements, suppresses KDM3B and CTCF protein levels. KDM3B and CTCF overexpression rescues Dox-induced MLL/KMT2A alterations. G9a inhibition in human cells or mice also suppresses MLL/KMT2A events accompanying Dox treatment. Therefore, MLL/KMT2A amplifications and rearrangements are controlled by epigenetic regulators that are tractable drug targets, which has clinical implications.
Collapse
Affiliation(s)
- Zach H Gray
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Damayanti Chakraborty
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Reuben R Duttweiler
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Gulnaz D Alekbaeva
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Sedona E Murphy
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Kashish Chetal
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin I Ferman
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Madison A Honer
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Zhentian Wang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Cynthia Myers
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Renhong Sun
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Monika Maria Toma
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, 3420 N. Broad Street, MRB 548, Philadelphia, PA 19140, USA
| | - Elena A Bondarenko
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - John N Santoro
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Christopher Miranda
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Megan E Dillingham
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Ran Tang
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA; School of Life Science and Technology, Harbin Institute of Technology, 150000 Harbin, China
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tomasz Skorski
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, 3420 N. Broad Street, MRB 548, Philadelphia, PA 19140, USA
| | - Cihangir Duy
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Hayan Lee
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA.
| |
Collapse
|
8
|
Luo D, Chen M, Li Q, Wang K, Wang K, Li J, Fu G, Shan Z, Liu Q, Yang Y, Liang L, Ma Y, Qin Y, Qin J, Gao D, Li X. CUL4B-DDB1-COP1-mediated UTX downregulation promotes colorectal cancer progression. Exp Hematol Oncol 2023; 12:77. [PMID: 37679762 PMCID: PMC10483726 DOI: 10.1186/s40164-023-00440-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND UTX (encoded by KDM6A), a histone demethylase for H3K27me2/3, is frequently mutated in human cancers. However, its functional and regulatory mechanisms in colorectal cancer (CRC) remain unclear. METHODS Immunohistochemistry staining was used to investigate the clinical relevance of UTX in CRC. Additionally, we generated a spontaneous mouse CRC model with conditional Utx knockout to explore the role of UTX in the colorectal tumorigenesis. Post-translational regulation of UTX was determined by co-immunoprecipitation and immunoblot analyses. RESULTS Herein, we identify that downregulation of UTX, mediated by the Cullin 4B-DNA Damage Binding Protein-1-Constitutive Photomorphogenesis Protein 1 (CUL4B-DDB1-COP1) complex, promotes CRC progression. Utx deletion in intestinal epithelial cells enhanced the susceptibility to tumorigenesis in AOM/DSS-induced spontaneous mouse CRC model. However, this effect is primarily alleviated by GSK126, an inhibitor of histone methyltransferase EZH2. Mechanistically, EMP1 and AUTS2 are identified as putative UTX target genes mediating UTX functions in limiting intestinal tumorigenesis. Notably, the CUL4B-DDB1-COP1 complex is identified as the functional E3 ligase responsible for targeting UTX for degradation in CRC cells. Thus, Cop1 deficiency in mouse intestinal tissue results in UTX accumulation and restricts tumorigenesis. Furthermore, patient cohort analysis reveals that UTX expression is negatively correlated with clinical stage, favorable disease outcomes, and COP1 expression. CONCLUSIONS In the current study, the tumor suppressor function and regulation of UTX in CRC provide a molecular basis and the rationale to target EZH2 in UTX-deficient CRC.
Collapse
Grants
- 82103259, 81972260, 81925029, 82230098, 32221002, 81790253 National Natural Science Foundation of China
- 82103259, 81972260, 81925029, 82230098, 32221002, 81790253 National Natural Science Foundation of China
- 82103259, 81972260, 81925029, 82230098, 32221002, 81790253 National Natural Science Foundation of China
- 2020YFA0803203 and 2019YFA0802102 National Key Research and Development Program of China
- YSBR-014 CAS project for young scientists in basic research
- JCTD-2018-14 CAS Interdisciplinary Innovation Team
- CAS Interdisciplinary Innovation Team and the Shanghai Municipal
Science and Technology Major Project
Collapse
Affiliation(s)
- Dakui Luo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Min Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingguo Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Kangjunjie Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Kaihua Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junqiang Li
- D1 Medical Technology (Shanghai) Co., Ltd, Shanghai, 201802, China
| | - Guoxiang Fu
- D1 Medical Technology (Shanghai) Co., Ltd, Shanghai, 201802, China
| | - Zezhi Shan
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qi Liu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yufei Yang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Lei Liang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yi Qin
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Jun Qin
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Daming Gao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
| | - Xinxiang Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
9
|
Tang D, Lu Y, Zuo N, Yan R, Wu C, Wu L, Liu S, He Y. The H3K27 demethylase controls the lateral line embryogenesis of zebrafish. Cell Biol Toxicol 2023; 39:1137-1152. [PMID: 34716527 PMCID: PMC10406677 DOI: 10.1007/s10565-021-09669-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/11/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Kdm6b, a specific histone 3 lysine 27 (H3K27) demethylase, has been reported to be implicated in a variety of developmental processes including cell differentiation and cell fate determination and multiple organogenesis. Here, we regulated the transcript level of kdm6bb to study the potential role in controlling the hearing organ development of zebrafish. METHODS A morpholino antisense oligonucleotide (MO) strategy was used to induce Kdm6b deficiency; immunohistochemical staining and in situ hybridization analysis were conducted to figure out the morphologic alterations and embryonic mechanisms. RESULTS Kdm6bb is expressed in the primordium and neuromasts at the early stage of zebrafish embryogenesis, suggesting a potential function of Kdm6b in the development of mechanosensory organs. Knockdown of kdm6bb severely influences the cell migration and proliferation in posterior lateral line primordium, abates the number of neuromasts along the trunk, and mRNA-mediated rescue test can partially renew the neuromasts. Loss of kdm6bb might be related to aberrant expressions of chemokine genes encompassing cxcl12a and cxcr4b/cxcr7b in the migrating primordium. Moreover, inhibition of kdm6bb reduces the expression of genes in Fgf signaling pathway, while it increases the axin2 and lef1 expression level of Wnt/β-catenin signaling during the migrating stage. CONCLUSIONS Collectively, our results revealed that Kdm6b plays an essential role in guiding the migration of primordium and in regulating the deposition of zebrafish neuromasts by mediating the gene expression of chemokines and Wnt and Fgf signaling pathway. Since histone methylation and demethylation are reversible, targeting Kdm6b may present as a novel therapeutic regimen for hearing disorders.
Collapse
Affiliation(s)
- Dongmei Tang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, NHC Key Laboratory of Hearing Medicine, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
| | - Yitong Lu
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, 2 Zheshanwest Road, Wuhu, 241001, Anhui, China
| | - Na Zuo
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, 2 Zheshanwest Road, Wuhu, 241001, Anhui, China
| | - Renchun Yan
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, 2 Zheshanwest Road, Wuhu, 241001, Anhui, China
| | - Cheng Wu
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, 2 Zheshanwest Road, Wuhu, 241001, Anhui, China
| | - Lijuan Wu
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, 2 Zheshanwest Road, Wuhu, 241001, Anhui, China
| | - Shaofeng Liu
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, 2 Zheshanwest Road, Wuhu, 241001, Anhui, China.
| | - Yingzi He
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, NHC Key Laboratory of Hearing Medicine, Fudan University, 83 Fenyang Road, Shanghai, 200031, China.
| |
Collapse
|
10
|
Wright GM, Menzel J, Tatman PD, Black JC. Transition from Transient DNA Rereplication to Inherited Gene Amplification Following Prolonged Environmental Stress. bioRxiv 2023:2023.05.08.539886. [PMID: 37214911 PMCID: PMC10197558 DOI: 10.1101/2023.05.08.539886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cells require the ability to adapt to changing environmental conditions, however, it is unclear how these changes elicit stable permanent changes in genomes. We demonstrate that, in response to environmental metal exposure, the metallothionein (MT) locus undergoes DNA rereplication generating transient site-specific gene amplifications (TSSGs). Chronic metal exposure allows transition from MT TSSG to inherited MT gene amplification through homologous recombination within and outside of the MT locus. DNA rereplication of the MT locus is suppressed by H3K27me3 and EZH2. Long-term ablation of EZH2 activity eventually leads to integration and inheritance of MT gene amplifications without the selective pressure of metal exposure. The rereplication and inheritance of MT gene amplification is an evolutionarily conserved response to environmental metal from yeast to human. Our results describe a new paradigm for adaptation to environmental stress where targeted, transient DNA rereplication precedes stable inherited gene amplification.
Collapse
|
11
|
Chen Y, Qiu Q, She J, Yu J. Extrachromosomal circular DNA in colorectal cancer: biogenesis, function and potential as therapeutic target. Oncogene 2023; 42:941-951. [PMID: 36859558 PMCID: PMC10038807 DOI: 10.1038/s41388-023-02640-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/03/2023]
Abstract
Extrachromosomal circular DNA (ecDNA) has gained renewed interest since its discovery more than half a century ago, emerging as critical driver of tumor evolution. ecDNA is highly prevalent in many types of cancers, including colorectal cancer (CRC), which is one of the most deadly cancers worldwide. ecDNAs play an essential role in regulating oncogene expression, intratumor heterogeneity, and resistance to therapy independently of canonical chromosomal alterations in CRC. Furthermore, the existence of ecDNAs is attributed to the patient's prognosis, since ecDNA-based oncogene amplification adversely affects clinical outcomes. Recent understanding of ecDNA put an extra layer of complexity in the pathogenesis of CRC. In this review, we will discuss the current understanding on mechanisms of biogenesis, and distinctive features of ecDNA in CRC. In addition, we will examine how ecDNAs mediate oncogene overexpression, gene regulation, and topological interactions with active chromatin, which facilitates genetic heterogeneity, accelerates CRC malignancy, and enhances rapid adaptation to therapy resistance. Finally, we will discuss the potential diagnostic and therapeutic implications of ecDNAs in CRC.
Collapse
Affiliation(s)
- Yinnan Chen
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Quanpeng Qiu
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Junjun She
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Jun Yu
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
12
|
Abstract
Extrachromosomal DNA (ecDNA) amplification is an important driver alteration in cancer. It has been observed in most cancer types and is associated with worse patient outcome. The functional impact of ecDNA has been linked to its unique properties, such as its circular structure that is associated with altered chromatinization and epigenetic regulatory landscape, as well as its ability to randomly segregate during cell division, which fuels intercellular copy number heterogeneity. Recent investigations suggest that ecDNA is structurally more complex than previously anticipated and that it localizes to specialized nuclear bodies (hubs) and can act in trans as an enhancer for genes on other ecDNAs or chromosomes. In this Review, we synthesize what is currently known about how ecDNA is generated and how its genetic and epigenetic architecture affects proto-oncogene deregulation in cancer. We discuss how recently identified ecDNA functions may impact oncogenesis but also serve as new therapeutic vulnerabilities in cancer.
Collapse
Affiliation(s)
- Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Rocío Chamorro González
- Department of Paediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany
| | - Anton G Henssen
- Department of Paediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany.
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany.
- Berlin Institute of Health, Berlin, Germany.
- German Cancer Consortium (DKTK), partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Neurosurgery, Amsterdam UMC, Amsterdam, the Netherlands.
| |
Collapse
|
13
|
Yang Y, Yang M, Pang H, Qiu Y, Sun T, Wang T, Shen S, Wang W, Bao J. A Macrophage Differentiation-Mediated Gene: DDX20 as a Molecular Biomarker Encompassing the Tumor Microenvironment, Disease Staging, and Prognoses in Hepatocellular Carcinoma. Oxidative Medicine and Cellular Longevity 2022; 2022:1-22. [PMID: 36246406 PMCID: PMC9556188 DOI: 10.1155/2022/9971776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/03/2022] [Accepted: 09/17/2022] [Indexed: 11/18/2022]
Abstract
Background DDX20 involves the mechanism of cell proliferate, mitogenic Ets transcriptional suppressor (METS), which can arrest the cell cycle of macrophages. However, little is known about DDX20 expression, clinical values, and the relationship with tumor microenvironment in HCC. Methods We mined the transcriptional, protein expression and survival data of DDX20 in HCC from online databases. The immunological effects of DDX20 were estimated by bioinformatic algorithms. The RNAi and CRISPR screening were used to assess the gene effect of DDX20 for the EGFR gene in liver tumor cell. Results We found that the DDX20 was highly expressed in HCC. The qRT-PCR result shows a significantly upregulated DDX20 expression in HCC samples from the West China Hospital. The high mRNA expression of DDX20 is associated with a poor survival. DDX20 expression is positively correlated with MDSCs in HCC tissues. Moreover, DDX20 has a high predicted ability for the response to immunotherapy. Furthermore, hsa-mir-324-5p could regulate the macrophage differentiation by interacting with DDX20. Meanwhile, the EGFR gene gets a high dependency score for DDX20. Conclusion In sum, DDX20 may serve as a prognostic marker for worse clinical outcomes with HCC and potentially enable more precise and personalized immunotherapeutic strategies in the future.
Collapse
|
14
|
Abstract
Increasing evidence demonstrates that DNA damage and genome instability play a crucial role in ageing. Mammalian cells have developed a wide range of complex and well‐orchestrated DNA repair pathways to respond to and resolve many different types of DNA lesions that occur from exogenous and endogenous sources. Defects in these repair pathways lead to accelerated or premature ageing syndromes and increase the likelihood of cancer development. Understanding the fundamental mechanisms of DNA repair will help develop novel strategies to treat ageing‐related diseases. Here, we revisit the processes involved in DNA damage repair and how these can contribute to diseases, including ageing and cancer. We also review recent mechanistic insights into DNA repair and discuss how these insights are being used to develop novel therapeutic strategies for treating human disease. We discuss the use of PARP inhibitors in the clinic for the treatment of breast and ovarian cancer and the challenges associated with acquired drug resistance. Finally, we discuss how DNA repair pathway‐targeted therapeutics are moving beyond PARP inhibition in the search for ever more innovative and efficacious cancer therapies.
Collapse
Affiliation(s)
- Thomas L Clarke
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, 02114, Boston, MA, USA.,The Broad Institute of Harvard and MIT, 02142, Cambridge, MA, USA
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, 02114, Boston, MA, USA.,The Broad Institute of Harvard and MIT, 02142, Cambridge, MA, USA
| |
Collapse
|
15
|
Hurník P, Chyra Z, Ševčíková T, Štembírek J, Trtková KS, Gaykalova DA, Buchtová M, Hrubá E. Epigenetic Regulations of Perineural Invasion in Head and Neck Squamous Cell Carcinoma. Front Genet 2022; 13:848557. [PMID: 35571032 PMCID: PMC9091179 DOI: 10.3389/fgene.2022.848557] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
Carcinomas of the oral cavity and oropharynx belong among the ten most common malignancies in the human population. The prognosis of head and neck squamous cell carcinoma (HNSCC) is determined by the degree of invasiveness of the primary tumor and by the extent of metastatic spread into regional and distant lymph nodes. Moreover, the level of the perineural invasion itself associates with tumor localization, invasion's extent, and the presence of nodal metastases. Here, we summarize the current knowledge about different aspects of epigenetic changes, which can be associated with HNSCC while focusing on perineural invasion (PNI). We review epigenetic modifications of the genes involved in the PNI process in HNSCC from the omics perspective and specific epigenetic modifications in OSCC or other neurotropic cancers associated with perineural invasion. Moreover, we summarize DNA methylation status of tumor-suppressor genes, methylation and demethylation enzymes and histone post-translational modifications associated with PNI. The influence of other epigenetic factors on the HNSCC incidence and perineural invasion such as tobacco, alcohol and oral microbiome is overviewed and HPV infection is discussed as an epigenetic factor associated with OSCC and related perineural invasion. Understanding epigenetic regulations of axon growth that lead to tumorous spread or uncovering the molecular control of axon interaction with cancer tissue can help to discover new therapeutic targets for these tumors.
Collapse
Affiliation(s)
- Pavel Hurník
- Department of Clinical and Molecular Pathology and Medical Genetics, Faculty of Medicine and University Hospital Ostrava, Ostrava, Czechia
- Department of Histology and Embryology, Medical Faculty, Masaryk University, Brno, Czechia
| | - Zuzana Chyra
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czechia
| | - Tereza Ševčíková
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czechia
| | - Jan Štembírek
- Department of Maxillofacial Surgery, University Hospital Ostrava, Ostrava, Czechia
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
| | - Kateřina Smešný Trtková
- Department of Clinical and Molecular Pathology and Medical Genetics, Faculty of Medicine and University Hospital Ostrava, Ostrava, Czechia
- Department of Clinical and Molecular Pathology, Faculty of Medicine and University Hospital Olomouc, Olomouc, Czechia
| | - Daria A. Gaykalova
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland Medical Center, Baltimore, MD, United States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, United States
- Institute for Genome Sciences, University of Maryland Medical Center, Baltimore, MD, United States
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States
| | - Marcela Buchtová
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Eva Hrubá
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| |
Collapse
|
16
|
Wu P, Liu Y, Zhou R, Liu L, Zeng H, Xiong F, Zhang S, Gong Z, Zhang W, Guo C, Wang F, Zhou M, Zu X, Zeng Z, Li Y, Li G, Huang H, Xiong W. Extrachromosomal Circular DNA: A New Target in Cancer. Front Oncol 2022; 12:814504. [PMID: 35494014 PMCID: PMC9046939 DOI: 10.3389/fonc.2022.814504] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Genomic instability and amplification are intrinsically important traits determining the development and heterogeneity of tumors. The role of extrachromosomal circular DNA (eccDNA) in tumors has recently been highlighted. EccDNAs are unique genetic materials located off the chromosomal DNA. They have been detected in a variety of tumors. This review analyzes the mechanisms involved in the formation of eccDNAs and their genetic characteristics. In addition, the high-copy number and transcriptional levels of oncogenes located in eccDNA molecules contribute to the acceleration of tumor evolution and drug resistance and drive the development of genetic heterogeneity. Understanding the specific genomic forms of eccDNAs and characterizing their potential functions will provide new strategies for tumor therapy. Further research may yield new targets and molecular markers for the early diagnosis and treatment of human cancer.
Collapse
Affiliation(s)
- Pan Wu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yuhang Liu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ruijia Zhou
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Lingyun Liu
- Cancer Research Institute, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Hongli Zeng
- Cancer Research Institute, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Fang Xiong
- Department of Stomatology, Xiangya Hospital, Central South University, Changsha, China
| | - Shanshan Zhang
- Department of Stomatology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wenling Zhang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Xuyu Zu
- Cancer Research Institute, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Zhaoyang Zeng
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Yong Li
- Department of Medicine, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States
| | - Guiyuan Li
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - He Huang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: He Huang, ; Wei Xiong,
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: He Huang, ; Wei Xiong,
| |
Collapse
|
17
|
Thang NX, Yoo S, La H, Lee H, Park C, Park KS, Hong K. Epigenetic Factors as Etiological Agents, Diagnostic Markers, and Therapeutic Targets for Luminal Breast Cancer. Biomedicines 2022; 10:748. [PMID: 35453496 PMCID: PMC9031900 DOI: 10.3390/biomedicines10040748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022] Open
Abstract
Luminal breast cancer, an etiologically heterogeneous disease, is characterized by high steroid hormone receptor activity and aberrant gene expression profiles. Endocrine therapy and chemotherapy are promising therapeutic approaches to mitigate breast cancer proliferation and recurrence. However, the treatment of therapy-resistant breast cancer is a major challenge. Recent studies on breast cancer etiology have revealed the critical roles of epigenetic factors in luminal breast cancer tumorigenesis and drug resistance. Tumorigenic epigenetic factor-induced aberrant chromatin dynamics dysregulate the onset of gene expression and consequently promote tumorigenesis and metastasis. Epigenetic dysregulation, a type of somatic mutation, is a high-risk factor for breast cancer progression and therapy resistance. Therefore, epigenetic modulators alone or in combination with other therapies are potential therapeutic agents for breast cancer. Several clinical trials have analyzed the therapeutic efficacy of potential epi-drugs for breast cancer and reported beneficial clinical outcomes, including inhibition of tumor cell adhesion and invasiveness and mitigation of endocrine therapy resistance. This review focuses on recent findings on the mechanisms of epigenetic factors in the progression of luminal breast cancer. Additionally, recent findings on the potential of epigenetic factors as diagnostic biomarkers and therapeutic targets for breast cancer are discussed.
Collapse
|
18
|
Van Rechem C, Ji F, Chakraborty D, Black JC, Sadreyev RI, Whetstine JR. Collective regulation of chromatin modifications predicts replication timing during cell cycle. Cell Rep 2021; 37:109799. [PMID: 34610305 PMCID: PMC8530517 DOI: 10.1016/j.celrep.2021.109799] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/16/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022] Open
Abstract
Replication timing (RT) associates with genome architecture, while having a mixed relationship to histone marks. By profiling replication at high resolution and assessing broad histone marks across the cell cycle at the resolution of RT with and without genetic perturbation, we address the causal relationship between histone marks and RT. Four primary chromatin states, including an uncharacterized H3K36me2 state, emerge and define 97% of the mappable genome. RT and local replication patterns (e.g., initiation zones) quantitatively associate with chromatin states, histone mark dynamics, and spatial chromatin structure. Manipulation of broad histone marks and enhancer elements by overexpressing the histone H3 lysine 9/36 tri-demethylase KDM4A impacts RT across 11% of the genome. Broad histone modification changes were strong predictors of the observed RT alterations. Lastly, replication within H3K36me2-enriched neighborhoods is sensitive to KDM4A overexpression and is controlled at a megabase scale. These studies establish a role for collective chromatin mark regulation in modulating RT. Van Rechem et al. establish that collective histone mark dynamics and their associated regulation modulate replication timing (RT). Four primary chromatin states define 97% of the mappable genome and associate with RT patterns. The K9/K36me3 demethylase KDM4A controls 11% of RT genome-wide through broad histone marks, especially H3K36me2, and enhancers.
Collapse
Affiliation(s)
- Capucine Van Rechem
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Stanford Medicine, Stanford, CA 94305, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Damayanti Chakraborty
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Joshua C Black
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA; Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
| |
Collapse
|
19
|
Abstract
Clinical and laboratory studies over recent decades have established branched evolution as a feature of cancer. However, while grounded in somatic selection, several lines of evidence suggest a Darwinian model alone is insufficient to fully explain cancer evolution. First, the role of macroevolutionary events in tumour initiation and progression contradicts Darwin's central thesis of gradualism. Whole-genome doubling, chromosomal chromoplexy and chromothripsis represent examples of single catastrophic events which can drive tumour evolution. Second, neutral evolution can play a role in some tumours, indicating that selection is not always driving evolution. Third, increasing appreciation of the role of the ageing soma has led to recent generalised theories of age-dependent carcinogenesis. Here, we review these concepts and others, which collectively argue for a model of cancer evolution which extends beyond Darwin. We also highlight clinical opportunities which can be grasped through targeting cancer vulnerabilities arising from non-Darwinian patterns of evolution.
Collapse
Affiliation(s)
- Roberto Vendramin
- Cancer Research UK Lung Cancer Centre of ExcellenceUniversity College London Cancer InstituteLondonUK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of ExcellenceUniversity College London Cancer InstituteLondonUK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of ExcellenceUniversity College London Cancer InstituteLondonUK
- Cancer Evolution and Genome Instability LaboratoryThe Francis Crick InstituteLondonUK
| |
Collapse
|
20
|
Luo M, Yang X, Chen HN, Nice EC, Huang C. Drug resistance in colorectal cancer: An epigenetic overview. Biochim Biophys Acta Rev Cancer 2021; 1876:188623. [PMID: 34481016 DOI: 10.1016/j.bbcan.2021.188623] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023]
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. Despite significant progress that has been made in therapies against CRC over the past decades, drug resistance is still a major limitation in CRC treatment. Numerous investigations have unequivocally shown that epigenetic regulation plays an important role in CRC drug resistance because of the high rate of epigenetic alterations in multiple genes during cancer development or drug treatment. Furthermore, the reversibility of epigenetic alterations provides novel therapeutic strategies to overcome drug resistance using small molecules, which can target non-coding RNAs or reverse histone modification and DNA methylation. In this review, we discuss epigenetic regulation in CRC drug resistance and the possible role of preventing or reversing CRC drug resistance using epigenetic therapy in CRC treatment.
Collapse
Affiliation(s)
- Maochao Luo
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang 315020, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Xingyue Yang
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang 315020, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Hai-Ning Chen
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
| | - Canhua Huang
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang 315020, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
| |
Collapse
|
21
|
Ye C, Wang H, Li Z, Xia C, Yuan S, Yan R, Yang X, Ma T, Wen X, Yang D. Comprehensive data analysis of genomics, epigenomics, and transcriptomics to identify specific biomolecular markers for prostate adenocarcinoma. Transl Androl Urol 2021; 10:3030-3045. [PMID: 34430406 PMCID: PMC8350225 DOI: 10.21037/tau-21-576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/15/2021] [Indexed: 12/14/2022] Open
Abstract
Background Multiomics data analysis based on high-throughput sequencing technology has become a hotspot in tumor investigation. The present study aimed to explore prognostic biomarkers via investigating DNA copy number variation (CNV) and methylation variation (MET) data in prostate cancer. Methods We obtained the messenger RNA (mRNA) expression, CNV, and methylated data of prostate adenocarcinoma (PRAD) samples via The Cancer Genome Atlas (TCGA)-PRAD cohort. We calculated and assessed the associations between CNV and RNA sequencing (RNA-seq), and between MET and RNA-seq via Pearson correlation coefficients. We then used the "iCluster" package to perform multigroup cluster analysis with CNVcor gene CNV data, METcor gene methylation data, and CNVcor and METcor gene mRNA data. The univariate Cox analysis was used to screen significant hub genes, and multivariate Cox analysis was used to construct risk a model. The nomogram was constructed based on "rms" package, and the immune infiltrating patterns were compared between high- and low-risk groups. Results A total of 477 PRAD samples with complete CNV, methylation, mRNA, and matched clinical information were included in our study. A list of 10,073 CNVcor genes and 9841 METcor genes were confirmed with a significance level of P<0.01. We found that CNVcor is more likely to appear on chromosome (chr)8, chr17, and chr10, while METcor is more likely to appear on chr1, chr19, and chr17. Based on the core genes, we finally classified the samples into 4 subtypes, incorporating iC1 (iCluster) (92 samples), iC2 (79 samples), iC3 (165 samples), and iC4 (141 samples). Furthermore, we constructed the prognostic model for PRAD based on the 5 genes (IER3, AOX1, PRKCDBP, UBD, and FBLN5). Nomograms incorporating risk score and other clinical variables were further constructed, and these nomograms exhibited superior predictive ability. We further compared the differential immune infiltrating patterns in 2 risk groups and found significantly low levels of infiltrating cluster of differentiation (CD)8+ T cells in high-risk samples. Conclusions Our study integrated the multi-omics data to elucidate the molecular features of PRAD and pivotal genes for predicting prognosis.
Collapse
Affiliation(s)
- Chunwei Ye
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Haifeng Wang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zhipeng Li
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chengxing Xia
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shunhui Yuan
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ruping Yan
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaofang Yang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Tao Ma
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xingqiao Wen
- Department of Urology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Delin Yang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| |
Collapse
|
22
|
Kleszcz R, Skalski M, Krajka-Kuźniak V, Paluszczak J. The inhibitors of KDM4 and KDM6 histone lysine demethylases enhance the anti-growth effects of erlotinib and HS-173 in head and neck cancer cells. Eur J Pharm Sci 2021; 166:105961. [PMID: 34363938 DOI: 10.1016/j.ejps.2021.105961] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/05/2021] [Accepted: 07/27/2021] [Indexed: 12/19/2022]
Abstract
Novel therapeutics are required to improve treatment outcomes in head and neck squamous cell carcinoma (HNSCC) patients. Histone lysine demethylases (KDM) have emerged recently as new potential drug targets for HNSCC therapy. They might also potentiate the action of the inhibitors of EGFR and PI3K signaling pathways. This study aimed at evaluating the anti-cancer effects of KDM4 (ML324) and KDM6 (GSK-J4) inhibitors and their combinations with EGFR (erlotinib) and PI3K (HS-173) inhibitors in HNSCC cells. The effect of the inhibitors on the viability of CAL27 and FaDu cells was evaluated using resazurin assay. The effect of the chemicals on cell cycle and apoptosis was assessed using propidium iodide and Annexin V staining, respectively. The effect of the compounds on gene expression was determined using qPCR and Western blot. The changes in cell cycle distribution upon treatment with the compounds were small to moderate, with the exception of erlotinib, which induced G1 arrest. However, all the compounds and their combinations induced apoptosis in both cell lines. These effects were associated with changes in the level of expression of CDKN1A, CCND1 and BIRC5. The inhibition of KDM4 and KDM6 using ML324 and GSK-J4, respectively, can be regarded as a novel therapeutic strategy in HNSCC.
Collapse
Affiliation(s)
- Robert Kleszcz
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, ul. Święcickiego 4, 60-781 Poznań, Poland
| | - Marcin Skalski
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, ul. Święcickiego 4, 60-781 Poznań, Poland
| | - Violetta Krajka-Kuźniak
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, ul. Święcickiego 4, 60-781 Poznań, Poland
| | - Jarosław Paluszczak
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, ul. Święcickiego 4, 60-781 Poznań, Poland.
| |
Collapse
|
23
|
Abstract
The observation and analysis of intra-tumour heterogeneity (ITH), particularly in genomic studies, has advanced our understanding of the evolutionary forces that shape cancer growth and development. However, only a subset of the variation observed in a single tumour will have an impact on cancer evolution, highlighting the need to distinguish between functional and non-functional ITH. Emerging studies highlight a role for the cancer epigenome, transcriptome and immune microenvironment in functional ITH. Here, we consider the importance of both genetic and non-genetic ITH and their role in tumour evolution, and present the rationale for a broad research focus beyond the cancer genome. Systems-biology analytical approaches will be necessary to outline the scale and importance of functional ITH. By allowing a deeper understanding of tumour evolution this will, in time, encourage development of novel therapies and improve outcomes for patients.
Collapse
Affiliation(s)
- James R M Black
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Center of Excellence, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Center of Excellence, University College London Cancer Institute, London, UK.
| |
Collapse
|
24
|
Biswas A, De S. Drivers of dynamic intratumor heterogeneity and phenotypic plasticity. Am J Physiol Cell Physiol 2021; 320:C750-C760. [PMID: 33657326 PMCID: PMC8163571 DOI: 10.1152/ajpcell.00575.2020] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/08/2021] [Accepted: 02/25/2021] [Indexed: 12/19/2022]
Abstract
Cancer is a clonal disease, i.e., all tumor cells within a malignant lesion trace their lineage back to a precursor somatic cell that acquired oncogenic mutations during development and aging. And yet, those tumor cells tend to have genetic and nongenetic variations among themselves-which is denoted as intratumor heterogeneity. Although some of these variations are inconsequential, others tend to contribute to cell state transition and phenotypic heterogeneity, providing a substrate for somatic evolution. Tumor cell phenotypes can dynamically change under the influence of genetic mutations, epigenetic modifications, and microenvironmental contexts. Although epigenetic and microenvironmental changes are adaptive, genetic mutations are usually considered permanent. Emerging reports suggest that certain classes of genetic alterations show extensive reversibility in tumors in clinically relevant timescales, contributing as major drivers of dynamic intratumor heterogeneity and phenotypic plasticity. Dynamic heterogeneity and phenotypic plasticity can confer resistance to treatment, promote metastasis, and enhance evolvability in cancer. Here, we first highlight recent efforts to characterize intratumor heterogeneity at genetic, epigenetic, and microenvironmental levels. We then discuss phenotypic plasticity and cell state transition by tumor cells, under the influence of genetic and nongenetic determinants and their clinical significance in classification of tumors and therapeutic decision-making.
Collapse
Affiliation(s)
- Antara Biswas
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Subhajyoti De
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| |
Collapse
|
25
|
Young NL, Dere R. Mechanistic insights into KDM4A driven genomic instability. Biochem Soc Trans 2021; 49:93-105. [PMID: 33492339 DOI: 10.1042/BST20191219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022]
Abstract
Alterations in global epigenetic signatures on chromatin are well established to contribute to tumor initiation and progression. Chromatin methylation status modulates several key cellular processes that maintain the integrity of the genome. KDM4A, a demethylase that belongs to the Fe-II dependent dioxygenase family that uses α-ketoglutarate and molecular oxygen as cofactors, is overexpressed in several cancers and is associated with an overall poor prognosis. KDM4A demethylates lysine 9 (H3K9me2/3) and lysine 36 (H3K36me3) methyl marks on histone H3. Given the complexity that exists with these marks on chromatin and their effects on transcription and proliferation, it naturally follows that demethylation serves an equally important role in these cellular processes. In this review, we highlight the role of KDM4A in transcriptional modulation, either dependent or independent of its enzymatic activity, arising from the amplification of this demethylase in cancer. KDM4A modulates re-replication of distinct genomic loci, activates cell cycle inducers, and represses proteins involved in checkpoint control giving rise to proliferative damage, mitotic disturbances and chromosomal breaks, ultimately resulting in genomic instability. In parallel, emerging evidence of non-nuclear substrates of epigenetic modulators emphasize the need to investigate the role of KDM4A in regulating non-nuclear substrates and evaluate their contribution to genomic instability in this context. The existence of promising KDM-specific inhibitors makes these demethylases an attractive target for therapeutic intervention in cancers.
Collapse
|
26
|
Chopra A, Cho WC, Willmore WG, Biggar KK. Hypoxia-Inducible Lysine Methyltransferases: G9a and GLP Hypoxic Regulation, Non-histone Substrate Modification, and Pathological Relevance. Front Genet 2020; 11:579636. [PMID: 33088284 PMCID: PMC7495024 DOI: 10.3389/fgene.2020.579636] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/13/2020] [Indexed: 12/29/2022] Open
Abstract
Oxygen sensing is inherent among most animal lifeforms and is critical for organism survival. Oxygen sensing mechanisms collectively trigger cellular and physiological responses that enable adaption to a reduction in ideal oxygen levels. The major mechanism by which oxygen-responsive changes in the transcriptome occur are mediated through the hypoxia-inducible factor (HIF) pathway. Upon reduced oxygen conditions, HIF activates hypoxia-responsive gene expression programs. However, under normal oxygen conditions, the activity of HIF is regularly suppressed by cellular oxygen sensors; prolyl-4 and asparaginyl hydroxylases. Recently, these oxygen sensors have also been found to suppress the function of two lysine methyltransferases, G9a and G9a-like protein (GLP). In this manner, the methyltransferase activity of G9a and GLP are hypoxia-inducible and thus present a new avenue of low-oxygen signaling. Furthermore, G9a and GLP elicit lysine methylation on a wide variety of non-histone proteins, many of which are known to be regulated by hypoxia. In this article we aim to review the effects of oxygen on G9a and GLP function, non-histone methylation events inflicted by these methyltransferases, and the clinical relevance of these enzymes in cancer.
Collapse
Affiliation(s)
- Anand Chopra
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada.,Department of Biology, Carleton University, Ottawa, ON, Canada
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China
| | - William G Willmore
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada.,Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada.,Department of Biology, Carleton University, Ottawa, ON, Canada
| |
Collapse
|
27
|
Van Rechem C, Ji F, Mishra S, Chakraborty D, Murphy SE, Dillingham ME, Sadreyev RI, Whetstine JR. The lysine demethylase KDM4A controls the cell-cycle expression of replicative canonical histone genes. Biochim Biophys Acta Gene Regul Mech 2020; 1863:194624. [PMID: 32798738 DOI: 10.1016/j.bbagrm.2020.194624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/22/2020] [Accepted: 08/10/2020] [Indexed: 12/27/2022]
Abstract
Chromatin modulation provides a key checkpoint for controlling cell cycle regulated gene networks. The replicative canonical histone genes are one such gene family under tight regulation during cell division. These genes are most highly expressed during S phase when histones are needed to chromatinize the new DNA template. While this fact has been known for a while, limited knowledge exists about the specific chromatin regulators controlling their temporal expression during cell cycle. Since histones and their associated mutations are emerging as major players in diseases such as cancer, identifying the chromatin factors modulating their expression is critical. The histone lysine tri-demethylase KDM4A is regulated over cell cycle and plays a direct role in DNA replication timing, site-specific rereplication, and DNA amplifications during S phase. Here, we establish an unappreciated role for the catalytically active KDM4A in directly regulating canonical replicative histone gene networks during cell cycle. Of interest, we further demonstrate that KDM4A interacts with proteins controlling histone expression and RNA processing (i.e., hnRNPUL1 and FUS/TLS). Together, this study provides a new function for KDM4A in modulating canonical histone gene expression.
Collapse
Affiliation(s)
- Capucine Van Rechem
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Fei Ji
- Massachusetts General Hospital, Department of Molecular Biology, Simches Research Center, Boston, MA 02114, United States of America
| | - Sweta Mishra
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Damayanti Chakraborty
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Sedona E Murphy
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Megan E Dillingham
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Ruslan I Sadreyev
- Massachusetts General Hospital, Department of Molecular Biology, Simches Research Center, Boston, MA 02114, United States of America; Massachusetts General Hospital, Department of Pathology and Harvard Medical School, Simches Research Center, Boston, MA 02114, United States of America.
| | - Johnathan R Whetstine
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America; Fox Chase Cancer Center, 333 Cottman Avenue West 260, Philadelphia, PA 19111, United States of America.
| |
Collapse
|
28
|
Sun Y, Bailey CP, Sadighi Z, Zaky W, Chandra J. Pediatric high-grade glioma: aberrant epigenetics and kinase signaling define emerging therapeutic opportunities. J Neurooncol 2020; 150:17-26. [PMID: 32504402 PMCID: PMC10141680 DOI: 10.1007/s11060-020-03546-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Supratentorial pediatric high-grade gliomas (pHGGs) are aggressive malignancies that lack effective treatment options. Deep genomic sequencing by multiple groups has revealed that the primary alterations unique to pHGGs occur in epigenetic and kinase genes. These mutations, fusions, and deletions present a therapeutic opportunity by use of small molecules targeting epigenetic modifiers and kinases that contribute to pHGG growth. METHODS Using a targeted search of the pre-clinical literature and clinicaltrials.gov for kinase and epigenetic pathways in pHGG, we collectively describe how these mechanisms are being targeted in pre-clinical animal models and in current clinical trials, as well as propose unexplored therapeutic possibilities for future investigations. RESULTS Relevant pHGG kinases are targetable by several FDA-approved or clinical-stage kinase inhibitors, including altered BRAF/MET/NTRK/ALK and wild-type PI3K/EGFR/PDGFR/VEGF/AXL. Epigenetic proteins implicated in pHGG are also clinically targetable and include histone erasers, writers and readers such as HDACs, demethylases LSD1/JMJD3, methyltransferase EZH2, chromatin reader bromodomains, and chromatin remodeler subunit BMI-1. Crosstalk between these pathways can occur involving kinases such as EGFR and AMPK interacting with epigenetic modifiers such as HDACs or EZH2. Single agent trial results of kinase inhibitors or epigenetic targets alone are underwhelming and hampered by poor pharmacokinetics, adaptive resistance, and broad inclusion criteria. CONCLUSIONS The genetic and phenotypic diversity of pHGGs is now well characterized after large-scale sequencing studies on patient tissue. However, clinical treatment paradigms have not yet shifted in response to this information. Combination therapies targeting multiple kinases or epigenetic targets may hold more promise, especially if attempted in selected patient populations with hemispheric pHGG tumors and relevant targeted therapeutic biomarkers.
Collapse
Affiliation(s)
- Yusha Sun
- Department of Pediatrics - Research, MD Anderson Cancer Center, 1515 Holcombe Blvd, Box 853, Houston, TX, 77030, USA
| | - Cavan P Bailey
- Department of Pediatrics - Research, MD Anderson Cancer Center, 1515 Holcombe Blvd, Box 853, Houston, TX, 77030, USA
| | - Zsila Sadighi
- Department of Pediatrics, MD Anderson Cancer Center, Houston, TX, USA
| | - Wafik Zaky
- Department of Pediatrics, MD Anderson Cancer Center, Houston, TX, USA
| | - Joya Chandra
- Department of Pediatrics - Research, MD Anderson Cancer Center, 1515 Holcombe Blvd, Box 853, Houston, TX, 77030, USA. .,Department of Epigenetics and Molecular Carcinogenesis, MD Anderson Cancer Center, 1515 Holcombe Blvd, Box 853, Houston, TX, 77030, USA.
| |
Collapse
|
29
|
Abstract
Background Serine provides important precursors of protein, lipid, and nucleotide synthesis needed for tumor cell growth. Phosphoglycerate dehydrogenase (PHGDH), a key rate-limiting enzyme in the serine de novo synthesis pathway, is highly expressed in many tumor types (including gastric cancer) and negatively correlated with overall survival. Cisplatin is a chemotherapeutic drug commonly used in the treatment of gastric cancer. In this study, we mainly investigated the relationship between serine metabolism and resistance to cisplatin in gastric cancer cells, as well as the regulatory mechanism involved in this process. Materials and Methods We determined the effect of different concentrations of serine or a PHGDH inhibitor combined with cisplatin or oxaliplatin on the viability and apoptosis of SGC7901, BGC823, and MGC803 cells via the Cell Counting Kit-8 and Hoechst 33258 staining, respectively. Western blotting was utilized to detect the relative protein expression. Furthermore, we investigated DNA damage through the micrococcal nuclease sensitivity assay detected using agarose gels. Results We found that reduced concentrations of serine or inhibition of PHGDH hindered the toxicity and pro-apoptotic effects of cisplatin on gastric cancer cells. Moreover, the addition of serine could reverse the sensitivity of gastric cancer cells to cisplatin. Moreover, we found that DNA damage was reduced by treatment with PHGDH inhibitor NCT-503 or CBR-5884. Inhibition of serine metabolism induced a decrease in H3K4 tri-methylation, which was reversed by JIB-04 (inhibitor of H3K4 demethylase). The tolerance of gastric cancer cells to cisplatin was relieved by JIB-04. Through micrococcal nuclease experiments, we further found that inhibiting the activity of PHGDH strengthened chromatin tightness. Conclusion Inhibition of serine metabolism reduced H3K4 tri-methylation and increased the density of chromatin, which leads to decreased toxicity and pro-apoptotic effect of platinum chemotherapeutic drugs on gastric cancer cells.
Collapse
Affiliation(s)
- Xiaoya Zhao
- Central Laboratory, Jinhua Hospital of Zhejiang University, Jinhua 321000, Zhejiang Province, People's Republic of China.,Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou 310000, Zhejiang Province, People's Republic of China
| | - Jianfei Fu
- Department of Medical Oncology, Jinhua Hospital of Zhejiang University, Jinhua 321000, Zhejiang Province, People's Republic of China
| | - Wanfen Tang
- Department of Medical Oncology, Jinhua Hospital of Zhejiang University, Jinhua 321000, Zhejiang Province, People's Republic of China
| | - Liangliang Yu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou 310000, Zhejiang Province, People's Republic of China
| | - Wenxia Xu
- Central Laboratory, Jinhua Hospital of Zhejiang University, Jinhua 321000, Zhejiang Province, People's Republic of China
| |
Collapse
|
30
|
Bailey C, Shoura MJ, Mischel PS, Swanton C. Extrachromosomal DNA-relieving heredity constraints, accelerating tumour evolution. Ann Oncol 2020; 31:884-893. [PMID: 32275948 DOI: 10.1016/j.annonc.2020.03.303] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/26/2020] [Indexed: 12/31/2022] Open
Abstract
Oncogene amplification on extrachromosomal DNA (ecDNA) provides a mechanism by which cancer cells can rapidly adapt to changes in the tumour microenvironment. These circular structures contain oncogenes and their regulatory elements, and, lacking centromeres, they are subject to unequal segregation during mitosis. This non-Mendelian mechanism of inheritance results in increased tumour heterogeneity with daughter cells that can contain increasingly amplified oncogene copy number. These structures also contain favourable epigenetic modifications including transcriptionally active chromatin, further fuelling positive selection. ecDNA drives aggressive tumour behaviour, is related to poorer survival outcomes and provides mechanisms of drug resistance. Recent evidence suggests one in four solid tumours contain cells with ecDNA structures. The concept of tumour evolution is one in which cancer cells compete to survive in a diverse tumour microenvironment under the Darwinian principles of variation and fitness heritability. Unconstrained by conventional segregation constraints, ecDNA can accelerate intratumoral heterogeneity and cellular fitness. In this review, we highlight some of the recent discoveries underpinning this process.
Collapse
Affiliation(s)
- C Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - M J Shoura
- Department of Pathology, Stanford University School of Medicine, Stanford, USA
| | - P S Mischel
- Ludwig Institute for Cancer Research, University of California at San Diego, San Diego, USA; San Diego Moores Cancer Center, University of California, La Jolla, USA; Department of Pathology, University of California San Diego, La Jolla, USA
| | - C Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| |
Collapse
|