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Vlahopoulos SA. Divergent Processing of Cell Stress Signals as the Basis of Cancer Progression: Licensing NFκB on Chromatin. Int J Mol Sci 2024; 25:8621. [PMID: 39201306 PMCID: PMC11354898 DOI: 10.3390/ijms25168621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 08/03/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
Inflammation is activated by diverse triggers that induce the expression of cytokines and adhesion molecules, which permit a succession of molecules and cells to deliver stimuli and functions that help the immune system clear the primary cause of tissue damage, whether this is an infection, a tumor, or a trauma. During inflammation, short-term changes in the expression and secretion of strong mediators of inflammation occur, while long-term changes occur to specific groups of cells. Long-term changes include cellular transdifferentiation for some types of cells that need to regenerate damaged tissue, as well as death for specific immune cells that can be detrimental to tissue integrity if they remain active beyond the boundaries of essential function. The transcriptional regulator NFκB enables some of the fundamental gene expression changes during inflammation, as well as during tissue development. During recurrence of malignant disease, cell stress-induced alterations enable the growth of cancer cell clones that are substantially resistant to therapeutic intervention and to the immune system. A number of those alterations occur due to significant defects in feedback signal cascades that control the activity of NFκB. Specifically, cell stress contributes to feedback defects as it overrides modules that otherwise control inflammation to protect host tissue. NFκB is involved in both the suppression and promotion of cancer, and the key distinctive feature that determines its net effect remains unclear. This paper aims to provide a clear answer to at least one aspect of this question, namely the mechanism that enables a divergent response of cancer cells to critical inflammatory stimuli and to cell stress in general.
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Ni Y, Shi M, Liu L, Lin D, Zeng H, Ong C, Wang Y. G9a in Cancer: Mechanisms, Therapeutic Advancements, and Clinical Implications. Cancers (Basel) 2024; 16:2175. [PMID: 38927881 PMCID: PMC11201431 DOI: 10.3390/cancers16122175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
G9a, also named EHMT2, is a histone 3 lysine 9 (H3K9) methyltransferase responsible for catalyzing H3K9 mono- and dimethylation (H3K9me1 and H3K9me2). G9a contributes to various aspects of embryonic development and tissue differentiation through epigenetic regulation. Furthermore, the aberrant expression of G9a is frequently observed in various tumors, particularly in prostate cancer, where it contributes to cancer pathogenesis and progression. This review highlights the critical role of G9a in multiple cancer-related processes, such as epigenetic dysregulation, tumor suppressor gene silencing, cancer lineage plasticity, hypoxia adaption, and cancer progression. Despite the increased research on G9a in prostate cancer, there are still significant gaps, particularly in understanding its interactions within the tumor microenvironment and its broader epigenetic effects. Furthermore, this review discusses the recent advancements in G9a inhibitors, including the development of dual-target inhibitors that target G9a along with other epigenetic factors such as EZH2 and HDAC. It aims to bring together the existing knowledge, identify gaps in the current research, and suggest future directions for research and treatment strategies.
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Affiliation(s)
- Yuchao Ni
- Department of Urology, West China Hospital, Sichuan University, Chengdu 610041, China;
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (M.S.); (L.L.); (D.L.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Mingchen Shi
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (M.S.); (L.L.); (D.L.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Liangliang Liu
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (M.S.); (L.L.); (D.L.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Dong Lin
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (M.S.); (L.L.); (D.L.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Hao Zeng
- Department of Urology, West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Christopher Ong
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (M.S.); (L.L.); (D.L.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (M.S.); (L.L.); (D.L.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
- Department of Experimental Therapeutics, BC Cancer, Vancouver, BC V5Z 1L3, Canada
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3
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Joosten SEP, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Yavuz K, Donaldson Collier M, Morova T, Altintaş UB, Kim Y, Canisius S, Moelans CB, van Diest PJ, Korkmaz G, Lack NA, Vermeulen M, Linn SC, Zwart W. Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions. Genome Res 2024; 34:539-555. [PMID: 38719469 PMCID: PMC11146591 DOI: 10.1101/gr.278680.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/11/2024] [Indexed: 06/05/2024]
Abstract
Estrogen Receptor 1 (ESR1; also known as ERα, encoded by ESR1 gene) is the main driver and prime drug target in luminal breast cancer. ESR1 chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ESR1 chromatin action, along with its biological implications. Here, we use a large set of ESR1 ChIP-seq data from 70 ESR1+ breast cancers to explore inter-patient heterogeneity in ESR1 DNA binding to reveal a striking inter-tumor heterogeneity of ESR1 action. Of note, commonly shared ESR1 sites show the highest estrogen-driven enhancer activity and are most engaged in long-range chromatin interactions. In addition, the most commonly shared ESR1-occupied enhancers are enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ESR1 and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we can confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ESR1-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ESR1 landscape, with the most common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.
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Affiliation(s)
- Stacey E P Joosten
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Sebastian Gregoricchio
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Suzan Stelloo
- Oncode Institute, The Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands
| | - Elif Yapıcı
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
| | - Chia-Chi Flora Huang
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Kerim Yavuz
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Maria Donaldson Collier
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Tunç Morova
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Umut Berkay Altintaş
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Yongsoo Kim
- Department of Pathology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Sander Canisius
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Cathy B Moelans
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
| | - Paul J van Diest
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
| | - Gozde Korkmaz
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
| | - Nathan A Lack
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Michiel Vermeulen
- Oncode Institute, The Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Sabine C Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
- Department of Medical Oncology, Antoni van Leeuwenhoek Hospital, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Oncode Institute, The Netherlands
- Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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4
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Joosten SE, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Collier MD, Morova T, Altintas B, Kim Y, Canisius S, Korkmaz G, Lack N, Vermeulen M, Linn SC, Zwart W. Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564691. [PMID: 37961147 PMCID: PMC10634999 DOI: 10.1101/2023.10.30.564691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Estrogen Receptor alpha (ERα) is the main driver and prime drug target in luminal breast. ERα chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ERα chromatin action, along with its biological implications. Here, we use a large set of ERα ChIP-seq data from 70 ERα+ breast cancers to explore inter-patient heterogeneity in ERα DNA binding, to reveal a striking inter-tumor heterogeneity of ERα action. Interestingly, commonly-shared ERα sites showed the highest estrogen-driven enhancer activity and were most-engaged in long-range chromatin interactions. In addition, the most-commonly shared ERα-occupied enhancers were enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ERα and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we could confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ERα-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ERα landscape, with the most-common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.
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5
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Karamov DD, Galiev AF, Lachinov AA, Davlyatgareev KI, Salazkin SN, Yakhin AR, Lachinov AN. Non-Conjugated Poly(Diphenylene Phthalide)-New Electroactive Material. Polymers (Basel) 2023; 15:3366. [PMID: 37631421 PMCID: PMC10459138 DOI: 10.3390/polym15163366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
In organic electronics, conjugated conductive polymers are most widely used. The scope of their application is currently very wide. Non-conjugated polymers are used much less in electronics and are usually used as insulation materials or materials for capacitors. However, the potential of non-conjugated polymers is much wider, due to the fact that new electronic materials with unique electronic properties can be created on the basis of non-conjugated polymers, as well as other inorganic dielectrics. This article demonstrates the possibilities of creating electrically conductive materials with unique electronic parameters based on non-conjugated polymers. The results of the study of the sensory properties of humidity are given as examples of the practical application of the structure. The abnormal electronic properties are realized along the interface of two polymer dielectrics with functional polar groups. The submicron films of polydiphenylenephthalide were used as a dielectric. It is shown that a quasi-two-dimensional electronic structure with abnormally large values of conductivity and mobility of charge carriers occurs along the interface. These structures are often called quasi-two-dimensional electron gas (Q2DEG). This article describes the manufacturing processes of multielectrode devices. Polymer films are deposited via the spin-coating method with polymer solutions in cyclohexanone. The metal electrodes were manufactured through thermal deposition in a vacuum. Three types of metal electrodes made of aluminum, copper and chromium were used. The influence of the electron work function of contacting metals on the electronic parameters of the structure was studied. It was established that the work function decrease leads to an increase in the conductivity and mobility of charge carriers. The charge carrier parameters were estimated based on the analysis of the current-voltage characteristics within the space-charge-limited current technique. The Richardson-Schottky thermionic emission model was used to evaluate values a potential barrier at metal/organic interfaces. It was established that the change in ambient humidity strongly affects the electronic transport properties along the polymer/polymer interface. It is demonstrated that the increase in conductivity with an increase in humidity occurs due to an increase in the mobility of charge carriers and a decrease in the height of the potential barrier at the three-dimensional metal contact with two-dimensional polymer interface. The potential barrier between the electrode and the bulk of the polymer film is significantly higher than between the electrode and the quasi-two-dimensional polymer structure.
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Affiliation(s)
- Danfis D. Karamov
- Institute of Molecule and Crystal Physics—Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450075 Ufa, Russia; (A.F.G.); (A.N.L.)
| | - Azat F. Galiev
- Institute of Molecule and Crystal Physics—Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450075 Ufa, Russia; (A.F.G.); (A.N.L.)
| | - Alexey A. Lachinov
- Institute of Molecule and Crystal Physics—Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450075 Ufa, Russia; (A.F.G.); (A.N.L.)
| | - Khalim I. Davlyatgareev
- Institute of Physics, Mathematics, Digital and Nanotechnologies, Akmulla Bashkir State Pedagogical University, 450000 Ufa, Russia
| | - Sergey N. Salazkin
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 119334 Moscow, Russia;
- Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Artur R. Yakhin
- Institute of Physics, Mathematics, Digital and Nanotechnologies, Akmulla Bashkir State Pedagogical University, 450000 Ufa, Russia
| | - Alexey N. Lachinov
- Institute of Molecule and Crystal Physics—Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450075 Ufa, Russia; (A.F.G.); (A.N.L.)
- Institute of Physics, Mathematics, Digital and Nanotechnologies, Akmulla Bashkir State Pedagogical University, 450000 Ufa, Russia
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6
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Chen R, Yang T, Jin B, Xu W, Yan Y, Wood N, Lehmann HI, Wang S, Zhu X, Yuan W, Chen H, Liu Z, Li G, Bowen TS, Li J, Xiao J. CircTmeff1 Promotes Muscle Atrophy by Interacting with TDP-43 and Encoding A Novel TMEFF1-339aa Protein. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206732. [PMID: 37088818 PMCID: PMC10265041 DOI: 10.1002/advs.202206732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/04/2023] [Indexed: 05/03/2023]
Abstract
Skeletal muscle atrophy is a common clinical feature of many acute and chronic conditions. Circular RNAs (circRNAs) are covalently closed RNA transcripts that are involved in various physiological and pathological processes, but their role in muscle atrophy remains unknown. Global circRNA expression profiling indicated that circRNAs are involved in the pathophysiological processes of muscle atrophy. circTmeff1 is identified as a potential circRNA candidate that influences muscle atrophy. It is further identified that circTmeff1 is highly expressed in multiple types of muscle atrophy in vivo and in vitro. Moreover, the overexpression of circTmeff1 triggers muscle atrophy in vitro and in vivo, while the knockdown of circTmeff1 expression rescues muscle atrophy in vitro and in vivo. In particular, the knockdown of circTmeff1 expression partially rescues muscle mass in mice during established atrophic settings. Mechanistically, circTmeff1 directly interacts with TAR DNA-binding protein 43 (TDP-43) and promotes aggregation of TDP-43 in mitochondria, which triggers the release of mitochondrial DNA (mtDNA) into cytosol and activation of the cyclic GMP-AMP synthase (cGAS)/ stimulator of interferon genes (STING) pathway. Unexpectedly, TMEFF1-339aa is identified as a novel protein encoded by circTmeff1 that mediates its pro-atrophic effects. Collectively, the inhibition of circTmeff1 represents a novel therapeutic approach for multiple types of skeletal muscle atrophy.
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Affiliation(s)
- Rui Chen
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Tingting Yang
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Bing Jin
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Wanru Xu
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Yuwei Yan
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Nathanael Wood
- School of Biomedical SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - H. Immo Lehmann
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Siqi Wang
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Xiaolan Zhu
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Weilin Yuan
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Hongjian Chen
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Zhengyu Liu
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - T. Scott Bowen
- School of Biomedical SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Jin Li
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
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Okashita N, Maeda R, Tachibana M. CDYL reinforces male gonadal sex determination through epigenetically repressing Wnt4 transcription in mice. Proc Natl Acad Sci U S A 2023; 120:e2221499120. [PMID: 37155872 PMCID: PMC10193937 DOI: 10.1073/pnas.2221499120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/01/2023] [Indexed: 05/10/2023] Open
Abstract
In mammals, male and female gonads initially develop from bipotential progenitor cells, which can differentiate into either testicular or ovarian cells. The decision to adopt a testicular or ovarian fate relies on robust genetic forces, i.e., activation of the testis-determining gene Sry, as well as a delicate balance of expression levels for pro-testis and pro-ovary factors. Recently, epigenetic regulation has been found to be a key element in activation of Sry. Nevertheless, the mechanism by which epigenetic regulation controls the expression balance of pro-testis and pro-ovary factors remains unclear. Chromodomain Y-like protein (CDYL) is a reader protein for repressive histone H3 methylation marks. We found that a subpopulation of Cdyl-deficient mice exhibited XY sex reversal. Gene expression analysis revealed that the testis-promoting gene Sox9 was downregulated in XY Cdyl-deficient gonads during the sex determination period without affecting Sry expression. Instead, we found that the ovary-promoting gene Wnt4 was derepressed in XY Cdyl-deficient gonads prior to and during the sex-determination period. Wnt4 heterozygous deficiency restored SOX9 expression in Cdyl-deficient XY gonads, indicating that derepressed Wnt4 is a cause of the repression of Sox9. We found that CDYL directly bound to the Wnt4 promoter and maintained its H3K27me3 levels during the sex-determination period. These findings indicate that CDYL reinforces male gonadal sex determination by repressing the ovary-promoting pathway in mice.
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Affiliation(s)
- Naoki Okashita
- Laboratory of Epigenome Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Ryo Maeda
- Laboratory of Epigenome Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Makoto Tachibana
- Laboratory of Epigenome Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
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8
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Hussain I, Alasiri H, Ullah Khan W, Alhooshani K. Advanced electrocatalytic technologies for conversion of carbon dioxide into methanol by electrochemical reduction: Recent progress and future perspectives. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
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9
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Sibuh BZ, Quazi S, Panday H, Parashar R, Jha NK, Mathur R, Jha SK, Taneja P, Jha AK. The Emerging Role of Epigenetics in Metabolism and Endocrinology. BIOLOGY 2023; 12:256. [PMID: 36829533 PMCID: PMC9953656 DOI: 10.3390/biology12020256] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023]
Abstract
Each cell in a multicellular organism has its own phenotype despite sharing the same genome. Epigenetics is a somatic, heritable pattern of gene expression or cellular phenotype mediated by structural changes in chromatin that occur without altering the DNA sequence. Epigenetic modification is an important factor in determining the level and timing of gene expression in response to endogenous and exogenous stimuli. There is also growing evidence concerning the interaction between epigenetics and metabolism. Accordingly, several enzymes that consume vital metabolites as substrates or cofactors are used during the catalysis of epigenetic modification. Therefore, altered metabolism might lead to diseases and pathogenesis, including endocrine disorders and cancer. In addition, it has been demonstrated that epigenetic modification influences the endocrine system and immune response-related pathways. In this regard, epigenetic modification may impact the levels of hormones that are important in regulating growth, development, reproduction, energy balance, and metabolism. Altering the function of the endocrine system has negative health consequences. Furthermore, endocrine disruptors (EDC) have a significant impact on the endocrine system, causing the abnormal functioning of hormones and their receptors, resulting in various diseases and disorders. Overall, this review focuses on the impact of epigenetics on the endocrine system and its interaction with metabolism.
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Affiliation(s)
- Belay Zeleke Sibuh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Knowledge Park III, Greater Noida 201310, India
| | - Sameer Quazi
- GenLab Biosolutions Private Limited, Bangalore 560043, India
- Department of Biomedical Sciences, School of Life Sciences, Anglia Ruskin University, Cambridge CB1 1PT, UK
- Clinical Bioinformatics, School of Health Sciences, The University of Manchester, Manchester M13 9P, UK
- SCAMT Institute, ITMO University, St. Petersburg 197101, Russia
| | - Hrithika Panday
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Knowledge Park III, Greater Noida 201310, India
| | - Ritika Parashar
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Knowledge Park III, Greater Noida 201310, India
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Knowledge Park III, Greater Noida 201310, India
- School of Bioengineering & Biosciences, Lovely Professional University, Phagwara 144411, India
| | - Runjhun Mathur
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Knowledge Park III, Greater Noida 201310, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Knowledge Park III, Greater Noida 201310, India
- Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun 248007, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali 140413, India
| | - Pankaj Taneja
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Knowledge Park III, Greater Noida 201310, India
| | - Abhimanyu Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Knowledge Park III, Greater Noida 201310, India
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10
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Siouda M, Dujardin AD, Dekeyzer B, Schaeffer L, Mulligan P. Chromodomain on Y-like 2 (CDYL2) implicated in mitosis and genome stability regulation via interaction with CHAMP1 and POGZ. Cell Mol Life Sci 2023; 80:47. [PMID: 36658409 PMCID: PMC11072993 DOI: 10.1007/s00018-022-04659-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 01/21/2023]
Abstract
Histone H3 trimethylation on lysine 9 (H3K9me3) is a defining feature of mammalian pericentromeres, loss of which results in genome instability. Here we show that CDYL2 is recruited to pericentromeres in an H3K9me3-dependent manner and is required for faithful mitosis and genome stability. CDYL2 RNAi in MCF-7 breast cancer cells and Hela cervical cancer cells inhibited their growth, induced apoptosis, and provoked both nuclear and mitotic aberrations. Mass spectrometry analysis of CDYL2-interacting proteins identified the neurodevelopmental disease-linked mitotic regulators CHAMP1 and POGZ, which are associated with a central non-conserved region of CDYL2. RNAi rescue assays identified both the CDYL2 chromodomain and the CHAMP1-POGZ interacting region as required and, together, sufficient for CDYL2 regulation of mitosis and genome stability. CDYL2 RNAi caused loss of CHAMP1 localization at pericentromeres. We propose that CDYL2 functions as an adaptor protein that connects pericentromeric H3K9me3 with CHAMP1 and POGZ to ensure mitotic fidelity and genome stability.
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Affiliation(s)
- Maha Siouda
- Centre Léon Bérard, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France
| | - Audrey D Dujardin
- Centre Léon Bérard, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France
| | - Blanche Dekeyzer
- Centre Léon Bérard, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France
| | - Laurent Schaeffer
- Faculté de Médecine, Physiopathology and Genetics of Neurons and Muscles Division, Institut NeuroMyoGène, Université Claude Bernard Lyon 1, Université de Lyon, INSERM U1217, CNRS, UMR5310, 3ème étage, Aile B, 8 Avenue Rockefeller, 69008, Lyon, France
- Centre de Biotechnologie Cellulaire, CBC Biotec, CHU de Lyon - HCL Groupement Est, 59 Bvd Pinel, 69677, Cedex Bron, France
| | - Peter Mulligan
- Centre Léon Bérard, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France.
- Faculté de Médecine, Physiopathology and Genetics of Neurons and Muscles Division, Institut NeuroMyoGène, Université Claude Bernard Lyon 1, Université de Lyon, INSERM U1217, CNRS, UMR5310, 3ème étage, Aile B, 8 Avenue Rockefeller, 69008, Lyon, France.
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11
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Shell DJ, Rectenwald JM, Buttery PH, Johnson RL, Foley CA, Guduru SKR, Uguen M, Rubiano JS, Zhang X, Li F, Norris-Drouin JL, Axtman M, Brian Hardy P, Vedadi M, Frye SV, James LI, Pearce KH. Discovery of hit compounds for methyl-lysine reader proteins from a target class DNA-encoded library. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:428-439. [PMID: 36272689 DOI: 10.1016/j.slasd.2022.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022]
Abstract
Methyl-lysine (Kme) reader domains are prevalent in chromatin regulatory proteins which bind post-translational modification sites to recruit repressive and activating factors; therefore, these proteins play crucial roles in cellular signaling and epigenetic regulation. Proteins that contain Kme domains are implicated in various diseases, including cancer, making them attractive therapeutic targets for drug and chemical probe discovery. Herein, we report on expanding the utility of a previously reported, Kme-focused DNA-encoded library (DEL), UNCDEL003, as a screening tool for hit discovery through the specific targeting of Kme reader proteins. As an efficient method for library generation, focused DELs are designed based on structural and functional features of a specific class of proteins with the intent of novel hit discovery. To broadly assess the applicability of our library, UNCDEL003 was screened against five diverse Kme reader protein domains (53BP1 TTD, KDM7B JmjC-PHD, CDYL2 CD, CBX2 CD, and LEDGF PWWP) with varying structures and functions. From these screening efforts, we identified hit compounds which contain unique chemical scaffolds distinct from previously reported ligands. The selected hit compounds were synthesized off-DNA and confirmed using primary and secondary assays and assessed for binding selectivity. Hit compounds from these efforts can serve as starting points for additional development and optimization into chemical probes to aid in further understanding the functionality of these therapeutically relevant proteins.
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Affiliation(s)
- Devan J Shell
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Justin M Rectenwald
- School of Medicine, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Peter H Buttery
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rebecca L Johnson
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Caroline A Foley
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shiva K R Guduru
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mélanie Uguen
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Juanita Sanchez Rubiano
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xindi Zhang
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Jacqueline L Norris-Drouin
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew Axtman
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - P Brian Hardy
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Stephen V Frye
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lindsey I James
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kenneth H Pearce
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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12
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Feng J, Meng X. Histone modification and histone modification-targeted anti-cancer drugs in breast cancer: Fundamentals and beyond. Front Pharmacol 2022; 13:946811. [PMID: 36188615 PMCID: PMC9522521 DOI: 10.3389/fphar.2022.946811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/15/2022] [Indexed: 12/21/2022] Open
Abstract
Dysregulated epigenetic enzymes and resultant abnormal epigenetic modifications (EMs) have been suggested to be closely related to tumor occurrence and progression. Histone modifications (HMs) can assist in maintaining genome stability, DNA repair, transcription, and chromatin modulation within breast cancer (BC) cells. In addition, HMs are reversible, dynamic processes involving the associations of different enzymes with molecular compounds. Abnormal HMs (e.g. histone methylation and histone acetylation) have been identified to be tightly related to BC occurrence and development, even though their underlying mechanisms remain largely unclear. EMs are reversible, and as a result, epigenetic enzymes have aroused wide attention as anti-tumor therapeutic targets. At present, treatments to restore aberrant EMs within BC cells have entered preclinical or clinical trials. In addition, no existing studies have comprehensively analyzed aberrant HMs within BC cells; in addition, HM-targeting BC treatments remain to be further investigated. Histone and non-histone protein methylation is becoming an attractive anti-tumor epigenetic therapeutic target; such methylation-related enzyme inhibitors are under development at present. Consequently, the present work focuses on summarizing relevant studies on HMs related to BC and the possible mechanisms associated with abnormal HMs. Additionally, we also aim to analyze existing therapeutic agents together with those drugs approved and tested through pre-clinical and clinical trials, to assess their roles in HMs. Moreover, epi-drugs that target HMT inhibitors and HDAC inhibitors should be tested in preclinical and clinical studies for the treatment of BC. Epi-drugs that target histone methylation (HMT inhibitors) and histone acetylation (HDAC inhibitors) have now entered clinical trials or are approved by the US Food and Drug Administration (FDA). Therefore, the review covers the difficulties in applying HM-targeting treatments in clinics and proposes feasible approaches for overcoming such difficulties and promoting their use in treating BC cases.
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13
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De Maio F, Rosa E, Perini G, Augello A, Niccolini B, Ciaiola F, Santarelli G, Sciandra F, Bozzi M, Sanguinetti M, Sali M, De Spirito M, Delogu G, Palmieri V, Papi M. 3D-printed graphene polylactic acid devices resistant to SARS-CoV-2: Sunlight-mediated sterilization of additive manufactured objects. CARBON 2022; 194:34-41. [PMID: 35313599 PMCID: PMC8926154 DOI: 10.1016/j.carbon.2022.03.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 02/21/2022] [Accepted: 03/14/2022] [Indexed: 05/24/2023]
Abstract
Additive manufacturing has played a crucial role in the COVID-19 global emergency allowing for rapid production of medical devices, indispensable tools for hospitals, or personal protection equipment. However, medical devices, especially in nosocomial environments, represent high touch surfaces prone to viral infection and currently used filaments for 3D printing can't inhibit transmission of virus [1]. Graphene-family materials are capable of reinforcing mechanical, optical and thermal properties of 3D printed constructs. In particular, graphene can adsorb near-infrared light with high efficiency. Here we demonstrate that the addition of graphene nanoplatelets to PLA filaments (PLA-G) allows the creation of 3D-printed devices that can be sterilized by near-infrared light exposure at power density analog to sunlight. This method has been used to kill SARS-CoV-2 viral particles on the surface of 3D printed PLA-G by 3 min of exposure. 3D-printed PLA-G is highly biocompatible and can represent the ideal material for the production of sterilizable personal protective equipment and daily life objects intended for multiple users.
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Affiliation(s)
- Flavio De Maio
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli" IRCSS, Largo A. Gemelli, 8 00168, Rome, Italy
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Largo Francesco Vito 1, 00168, Italy
| | - Enrico Rosa
- Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, Rome, Largo Francesco Vito 1, 00168, Italy
| | - Giordano Perini
- Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, Rome, Largo Francesco Vito 1, 00168, Italy
- Fondazione Policlinico Universitario "A. Gemelli" IRCSS, Largo A. Gemelli, 8 00168, Rome, Italy
| | - Alberto Augello
- Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, Rome, Largo Francesco Vito 1, 00168, Italy
- Fondazione Policlinico Universitario "A. Gemelli" IRCSS, Largo A. Gemelli, 8 00168, Rome, Italy
| | - Benedetta Niccolini
- Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, Rome, Largo Francesco Vito 1, 00168, Italy
- Fondazione Policlinico Universitario "A. Gemelli" IRCSS, Largo A. Gemelli, 8 00168, Rome, Italy
| | - Francesca Ciaiola
- Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, Rome, Largo Francesco Vito 1, 00168, Italy
| | - Giulia Santarelli
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Largo Francesco Vito 1, 00168, Italy
| | - Francesca Sciandra
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", (SCITEC)-CNR, Roma, Italy
| | - Manuela Bozzi
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Sezione di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli" IRCSS, Largo A. Gemelli, 8 00168, Rome, Italy
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Largo Francesco Vito 1, 00168, Italy
| | - Michela Sali
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli" IRCSS, Largo A. Gemelli, 8 00168, Rome, Italy
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Largo Francesco Vito 1, 00168, Italy
| | - Marco De Spirito
- Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, Rome, Largo Francesco Vito 1, 00168, Italy
- Fondazione Policlinico Universitario "A. Gemelli" IRCSS, Largo A. Gemelli, 8 00168, Rome, Italy
| | - Giovanni Delogu
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Largo Francesco Vito 1, 00168, Italy
- Mater Olbia Hospital, Olbia, Italy
| | - Valentina Palmieri
- Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, Rome, Largo Francesco Vito 1, 00168, Italy
- Fondazione Policlinico Universitario "A. Gemelli" IRCSS, Largo A. Gemelli, 8 00168, Rome, Italy
- Istituto dei Sistemi Complessi, CNR, Via dei Taurini 19, 00185, Rome, Italy
| | - Massimiliano Papi
- Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, Rome, Largo Francesco Vito 1, 00168, Italy
- Fondazione Policlinico Universitario "A. Gemelli" IRCSS, Largo A. Gemelli, 8 00168, Rome, Italy
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14
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Ang GCK, Gupta A, Surana U, Yap SXL, Taneja R. Potential Therapeutics Targeting Upstream Regulators and Interactors of EHMT1/2. Cancers (Basel) 2022; 14:2855. [PMID: 35740522 PMCID: PMC9221123 DOI: 10.3390/cancers14122855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022] Open
Abstract
Euchromatin histone lysine methyltransferases (EHMTs) are epigenetic regulators responsible for silencing gene transcription by catalyzing H3K9 dimethylation. Dysregulation of EHMT1/2 has been reported in multiple cancers and is associated with poor clinical outcomes. Although substantial insights have been gleaned into the downstream targets and pathways regulated by EHMT1/2, few studies have uncovered mechanisms responsible for their dysregulated expression. Moreover, EHMT1/2 interacting partners, which can influence their function and, therefore, the expression of target genes, have not been extensively explored. As none of the currently available EHMT inhibitors have made it past clinical trials, understanding upstream regulators and EHMT protein complexes may provide unique insights into novel therapeutic avenues in EHMT-overexpressing cancers. Here, we review our current understanding of the regulators and interacting partners of EHMTs. We also discuss available therapeutic drugs that target the upstream regulators and binding partners of EHMTs and could potentially modulate EHMT function in cancer progression.
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Affiliation(s)
- Gareth Chin Khye Ang
- Healthy Longevity Translational Research Program, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; (G.C.K.A.); (A.G.)
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore;
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Amogh Gupta
- Healthy Longevity Translational Research Program, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; (G.C.K.A.); (A.G.)
| | - Uttam Surana
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore;
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Shirlyn Xue Ling Yap
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Reshma Taneja
- Healthy Longevity Translational Research Program, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; (G.C.K.A.); (A.G.)
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15
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Liu Z, Li H, Zhong Z, Jiang S. A Whole Genome Sequencing-Based Genome-Wide Association Study Reveals the Potential Associations of Teat Number in Qingping Pigs. Animals (Basel) 2022; 12:1057. [PMID: 35565484 PMCID: PMC9100799 DOI: 10.3390/ani12091057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/06/2022] [Accepted: 04/14/2022] [Indexed: 02/05/2023] Open
Abstract
Teat number plays an important role in the reproductive performance of sows and the growth of piglets. However, the quantitative trait loci (QTLs) and candidate genes for the teat number-related traits in Qingping pigs remain unknown. In this study, we performed GWAS based on whole-genome single-nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) for the total number of teats and five other related traits in 100 Qingping pigs. SNPs and Indels of all 100 pigs were genotyped using 10× whole genome resequencing. GWAS using General Linear Models (GLM) detected a total of 28 SNPs and 45 Indels as peak markers for these six traits. We also performed GWAS for the absolute difference between left and right teat number (ADIFF) using Fixed and random model Circulating Probability Unification (FarmCPU). The most strongly associated SNP and Indel with a distance of 562,788 bp were significantly associated with ADIFF in both GLM and FarmCPU models. In the 1-Mb regions of the most strongly associated SNP and Indel, there were five annotated genes, including TRIML1, TRIML2, ZFP42, FAT1 and MTNR1A. We also highlighted TBX3 as an interesting candidate gene for SSC14. Enrichment analysis of candidate genes suggested the Wnt signaling pathway may contribute to teat number-related traits. This study expanded significant marker-trait associations for teat number and provided useful molecular markers and candidate genes for teat number improvement in the breeding of sows.
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Affiliation(s)
- Zezhang Liu
- Agricultural Ministry Key Laboratory of Swine Breeding and Genetics & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (Z.L.); (Z.Z.)
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing 100083, China;
| | - Zhuxia Zhong
- Agricultural Ministry Key Laboratory of Swine Breeding and Genetics & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (Z.L.); (Z.Z.)
| | - Siwen Jiang
- Agricultural Ministry Key Laboratory of Swine Breeding and Genetics & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (Z.L.); (Z.Z.)
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16
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Chen X, Wang Z, Zhao X, Zhang L, Zhou L, Li X, Ge C, Zhao F, Chen T, Xie H, Cui Y, Tian H, Li H, Yao M, Li J. STAT5A modulates CDYL2/SLC7A6 pathway to inhibit the proliferation and invasion of hepatocellular carcinoma by targeting to mTORC1. Oncogene 2022; 41:2492-2504. [PMID: 35314791 DOI: 10.1038/s41388-022-02273-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/24/2022] [Accepted: 03/08/2022] [Indexed: 01/29/2023]
Abstract
Chromodomain Y-like 2 (CDYL2), as a member of CDY family known to be involved in spermatogenesis, has been reported to participate in breast cancer development recently, but its exact biological role in hepatocellular carcinoma (HCC) remains unclear. Here, we observed that CDYL2 was down-regulated in human primary HCC tissues and the low levels of CDYL2 expression were correlated with poor survival. Gain- and loss-of-function experiments showed that CDYL2 inhibited the proliferation and metastasis of HCC cells in vitro and in vivo. Mechanistically, CDYL2 down-regulates solute carrier family 7 member 6 (SLC7A6) by decreasing the enrichment of H3K4me3 on the promoter region of SLC7A6. Additionally, we also found that signal transducer and activator of transcription 5A (STAT5A) could directly and positively regulate the expression of CDYL2. Thus, CDYL2 was regulated by STAT5A, and suppressed the amino acid transportation through down-regulation of SLC7A6, and then inhibits the mTORC1/S6K pathway, a master regulator of cell growth. Consistently, CDYL2 expression correlated significantly with STAT5A and SLC7A6 expression in HCC. Collectively, we propose a model for a STAT5A/CDYL2/SLC7A6 axis that provides novel insight into CDYL2, which may serve as a potential factor for predicting prognosis and a therapeutic target for HCC patients.
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Affiliation(s)
- Xiaoxia Chen
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200032, China
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 200032, Shanghai, China
| | - Zhenyu Wang
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 200032, Shanghai, China
| | - Xinge Zhao
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 200032, Shanghai, China
| | - Lili Zhang
- Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Lianer Zhou
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 200032, Shanghai, China
| | - Xianxian Li
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 200032, Shanghai, China
| | - Chao Ge
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 200032, Shanghai, China
| | - Fangyu Zhao
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 200032, Shanghai, China
| | - Taoyang Chen
- Qi Dong Liver Cancer Institute, Qi Dong, 226200, China
| | - Haiyang Xie
- Department of General Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Ying Cui
- Cancer Institute of Guangxi, Nanning, 530027, China
| | - Hua Tian
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 200032, Shanghai, China
| | - Hong Li
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 200032, Shanghai, China
| | - Ming Yao
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 200032, Shanghai, China
| | - Jinjun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200032, China.
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 200032, Shanghai, China.
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17
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Osman N, Shawky AEM, Brylinski M. Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure. BMC Genom Data 2022; 23:13. [PMID: 35176995 PMCID: PMC8851830 DOI: 10.1186/s12863-021-01021-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/23/2021] [Indexed: 12/31/2022] Open
Abstract
Background Numerous genome-wide association studies (GWAS) conducted to date revealed genetic variants associated with various diseases, including breast and prostate cancers. Despite the availability of these large-scale data, relatively few variants have been functionally characterized, mainly because the majority of single-nucleotide polymorphisms (SNPs) map to the non-coding regions of the human genome. The functional characterization of these non-coding variants and the identification of their target genes remain challenging. Results In this communication, we explore the potential functional mechanisms of non-coding SNPs by integrating GWAS with the high-resolution chromosome conformation capture (Hi-C) data for breast and prostate cancers. We show that more genetic variants map to regulatory elements through the 3D genome structure than the 1D linear genome lacking physical chromatin interactions. Importantly, the association of enhancers, transcription factors, and their target genes with breast and prostate cancers tends to be higher when these regulatory elements are mapped to high-risk SNPs through spatial interactions compared to simply using a linear proximity. Finally, we demonstrate that topologically associating domains (TADs) carrying high-risk SNPs also contain gene regulatory elements whose association with cancer is generally higher than those belonging to control TADs containing no high-risk variants. Conclusions Our results suggest that many SNPs may contribute to the cancer development by affecting the expression of certain tumor-related genes through long-range chromatin interactions with gene regulatory elements. Integrating large-scale genetic datasets with the 3D genome structure offers an attractive and unique approach to systematically investigate the functional mechanisms of genetic variants in disease risk and progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-01021-x.
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Affiliation(s)
- Noha Osman
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.,Department of Cell Biology, National Research Centre, Giza, 12622, Egypt.,Department of Medicine, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Abd-El-Monsif Shawky
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA. .,Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, 70803, USA.
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Nachiyappan A, Gupta N, Taneja R. EHMT1/EHMT2 in EMT, Cancer Stemness and Drug Resistance: Emerging Evidence and Mechanisms. FEBS J 2021; 289:1329-1351. [PMID: 34954891 DOI: 10.1111/febs.16334] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/25/2021] [Accepted: 12/23/2021] [Indexed: 11/29/2022]
Abstract
Metastasis, therapy failure and tumor recurrence are major clinical challenges in cancer. The interplay between tumor initiating cells (TICs) and Epithelial-Mesenchymal transition (EMT) drives tumor progression and spread. Recent advances have highlighted the involvement of epigenetic deregulation in these processes. The Euchromatin Histone Lysine Methyltransferase 1 (EHMT1) and Euchromatin Histone Lysine Methyltransferase 2 (EHMT2) that primarily mediate histone 3 lysine 9 di-methylation (H3K9me2), as well as methylation of non-histone proteins, are now recognized to be aberrantly expressed in many cancers. Their deregulated expression is associated with EMT, cellular plasticity and therapy resistance. In this review, we summarize evidence of their myriad roles in cancer metastasis, stemness and drug resistance. We discuss cancer-type specific molecular targets, context-dependent mechanisms and future directions of research in targeting EHMT1/EHMT2 for the treatment of cancer.
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Affiliation(s)
- Alamelu Nachiyappan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117593
| | - Neelima Gupta
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117593
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117593.,Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 117593
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Li W, Wu H, Sui S, Wang Q, Xu S, Pang D. Targeting Histone Modifications in Breast Cancer: A Precise Weapon on the Way. Front Cell Dev Biol 2021; 9:736935. [PMID: 34595180 PMCID: PMC8476812 DOI: 10.3389/fcell.2021.736935] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/16/2021] [Indexed: 12/27/2022] Open
Abstract
Histone modifications (HMs) contribute to maintaining genomic stability, transcription, DNA repair, and modulating chromatin in cancer cells. Furthermore, HMs are dynamic and reversible processes that involve interactions between numerous enzymes and molecular components. Aberrant HMs are strongly associated with tumorigenesis and progression of breast cancer (BC), although the specific mechanisms are not completely understood. Moreover, there is no comprehensive overview of abnormal HMs in BC, and BC therapies that target HMs are still in their infancy. Therefore, this review summarizes the existing evidence regarding HMs that are involved in BC and the potential mechanisms that are related to aberrant HMs. Moreover, this review examines the currently available agents and approved drugs that have been tested in pre-clinical and clinical studies to evaluate their effects on HMs. Finally, this review covers the barriers to the clinical application of therapies that target HMs, and possible strategies that could help overcome these barriers and accelerate the use of these therapies to cure patients.
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Affiliation(s)
- Wei Li
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Hao Wu
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Shiyao Sui
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Qin Wang
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Shouping Xu
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Da Pang
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
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Li X, Wang J, Long H, Lin W, Wang H, Chen Y, Yuan Q, Li X. circCDYL2, Overexpressed in Highly Migratory Colorectal Cancer Cells, Promotes Migration by Binding to Ezrin. Front Oncol 2021; 11:716073. [PMID: 34485151 PMCID: PMC8416158 DOI: 10.3389/fonc.2021.716073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/26/2021] [Indexed: 11/28/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common malignancies with high mortality worldwide, particularly due to metastasis. However, there are no clinically available strategies for treating CRC metastasis. Exploring the mechanisms underlying CRC metastasis is the key to improve the treatment of CRC with metastasis. Methods In this study, we generated the highly migratory CRC cell subline H-RKO using a repeated transwell migration assay to identify circRNAs involved in CRC migration by high-throughput RNA sequencing. Upregulated circRNAs were validated by RT-qPCR to identify the most elevated circRNA. The expression of this circRNA (circCDYL2) was evaluated in 40 pairs of CRC tissues and four CRC cell lines by RT-qPCR. Transwell migration and wound healing assays were performed to verify the function of circCDYL2 in cell migration. The cellular distribution of circCDYL2 was confirmed using PCR. RNA pulldown and RNA immunoprecipitation were used to confirm the interaction between circCDYL2 and Ezrin. Western blotting, immunohistochemistry, and rescue experiments were used to determine the role of circCDYL2 in regulating Ezrin protein expression and AKT phosphorylation. Results Among the candidate circRNAs, circCDYL2 was the highest overexpressed circRNA in H-RKO compared to parental N-RKO cells. Furthermore, circCDYL2 expression was elevated in CRC tissues and cell lines. Gain- and loss-of-function assays indicated that circCDYL2 enhanced the migration of CRC cells. circCDYL2 was located in the cytoplasm of CRC cells and interacted with Ezrin to upregulate its protein levels, resulting in AKT phosphorylation. Ezrin knockdown abrogated the CRC cell migration induced by circCDYL2 overexpression. Conclusions Our study demonstrated for the first time that circCDYL2 promotes CRC migration by binding Ezrin and activating the AKT pathway. CircCDYL2 represents a potential therapeutic target for preventing CRC metastasis.
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Affiliation(s)
- Xiaomin Li
- Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jianjun Wang
- Department of Histology and Embryology, Wannan Medical College, Wuhu, China
| | - Huaicheng Long
- Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Weihao Lin
- Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Haowei Wang
- Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yujia Chen
- Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qinzi Yuan
- Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xuenong Li
- Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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Dual EZH2 and G9a inhibition suppresses multiple myeloma cell proliferation by regulating the interferon signal and IRF4-MYC axis. Cell Death Discov 2021; 7:7. [PMID: 33436557 PMCID: PMC7803977 DOI: 10.1038/s41420-020-00400-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/04/2020] [Accepted: 12/23/2020] [Indexed: 02/06/2023] Open
Abstract
Epigenetic mechanisms such as histone modification play key roles in the pathogenesis of multiple myeloma (MM). We previously showed that EZH2, a histone H3 lysine 27 (H3K27) methyltransferase, and G9, a H3K9 methyltransferase, are potential therapeutic targets in MM. Moreover, recent studies suggest EZH2 and G9a cooperate to regulate gene expression. We therefore evaluated the antitumor effect of dual EZH2 and G9a inhibition in MM. A combination of an EZH2 inhibitor and a G9a inhibitor strongly suppressed MM cell proliferation in vitro by inducing cell cycle arrest and apoptosis. Dual EZH2/G9a inhibition also suppressed xenograft formation by MM cells in vivo. In datasets from the Gene Expression Omnibus, higher EZH2 and EHMT2 (encoding G9a) expression was significantly associated with poorer prognoses in MM patients. Microarray analysis revealed that EZH2/G9a inhibition significantly upregulated interferon (IFN)-stimulated genes and suppressed IRF4-MYC axis genes in MM cells. Notably, dual EZH2/G9a inhibition reduced H3K27/H3K9 methylation levels in MM cells and increased expression of endogenous retrovirus (ERV) genes, which suggests that activation of ERV genes may induce the IFN response. These results suggest that dual targeting of EZH2 and G9a may be an effective therapeutic strategy for MM.
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Osman N, Shawky A, Brylinski M. Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure.. [DOI: 10.1101/2020.10.06.328567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractNumerous genome-wide association studies (GWAS) conducted to date revealed genetic variants associated with various diseases, including breast and prostate cancers. Despite the availability of these large-scale data, relatively few variants have been functionally characterized, mainly because the majority of single-nucleotide polymorphisms (SNPs) map to the non-coding regions of the human genome. The functional characterization of these non-coding variants and the identification of their target genes remain challenging. In this communication, we explore the potential functional mechanisms of non-coding SNPs by integrating GWAS with the high-resolution chromosome conformation capture (Hi-C) data for breast and prostate cancers. We show that more genetic variants map to regulatory elements through the 3D genome structure than the 1D linear genome lacking physical chromatin interactions. Importantly, the association of enhancers, transcription factors, and their target genes with breast and prostate cancers tends to be higher when these regulatory elements are mapped to high-risk SNPs through spatial interactions compared to simply using a linear proximity. Finally, we demonstrate that topologically associating domains (TADs) carrying high-risk SNPs also contain gene regulatory elements whose association with cancer is generally higher than those belonging to control TADs containing no high-risk variants. Our results suggest that many SNPs may contribute to the cancer development by affecting the expression of certain tumor-related genes through long-range chromatin interactions with gene regulatory elements. Integrating large-scale genetic datasets with the 3D genome structure offers an attractive and unique approach to systematically investigate the functional mechanisms of genetic variants in disease risk and progression.
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