1
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Vorreiter C, Robaa D, Sippl W. Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains. J Chem Inf Model 2024; 64:4553-4569. [PMID: 38771194 PMCID: PMC11167732 DOI: 10.1021/acs.jcim.4c00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Cosolvent molecular dynamics (MD) simulations have proven to be powerful in silico tools to predict hotspots for binding regions on protein surfaces. In the current study, the method was adapted and applied to two Tudor domain-containing proteins, namely Spindlin1 (SPIN1) and survival motor neuron protein (SMN). Tudor domains are characterized by so-called aromatic cages that recognize methylated lysine residues of protein targets. In the study, the conformational transitions from closed to open aromatic cage conformations were investigated by performing MD simulations with cosolvents using six different probe molecules. It is shown that a trajectory clustering approach in combination with volume and atomic distance tracking allows a reasonable discrimination between open and closed aromatic cage conformations and the docking of inhibitors yields very good reproducibility with crystal structures. Cosolvent MDs are suitable to capture the flexibility of aromatic cages and thus represent a promising tool for the optimization of inhibitors.
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Affiliation(s)
- Christopher Vorreiter
- Department of Medicinal Chemistry,
Institute of Pharmacy, Martin-Luther-University
of Halle-Wittenberg, 06120 Halle, Saale, Germany
| | - Dina Robaa
- Department of Medicinal Chemistry,
Institute of Pharmacy, Martin-Luther-University
of Halle-Wittenberg, 06120 Halle, Saale, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry,
Institute of Pharmacy, Martin-Luther-University
of Halle-Wittenberg, 06120 Halle, Saale, Germany
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2
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Fan T, Jiang L, Zhou X, Chi H, Zeng X. Deciphering the dual roles of PHD finger proteins from oncogenic drivers to tumor suppressors. Front Cell Dev Biol 2024; 12:1403396. [PMID: 38813086 PMCID: PMC11133592 DOI: 10.3389/fcell.2024.1403396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024] Open
Abstract
PHD (plant homeodomain) finger proteins emerge as central epigenetic readers and modulators in cancer biology, orchestrating a broad spectrum of cellular processes pivotal to oncogenesis and tumor suppression. This review delineates the dualistic roles of PHD fingers in cancer, highlighting their involvement in chromatin remodeling, gene expression regulation, and interactions with cellular signaling networks. PHD fingers' ability to interpret specific histone modifications underscores their influence on gene expression patterns, impacting crucial cancer-related processes such as cell proliferation, DNA repair, and apoptosis. The review delves into the oncogenic potential of certain PHD finger proteins, exemplified by PHF1 and PHF8, which promote tumor progression through epigenetic dysregulation and modulation of signaling pathways like Wnt and TGFβ. Conversely, it discusses the tumor-suppressive functions of PHD finger proteins, such as PHF2 and members of the ING family, which uphold genomic stability and inhibit tumor growth through their interactions with chromatin and transcriptional regulators. Additionally, the review explores the therapeutic potential of targeting PHD finger proteins in cancer treatment, considering their pivotal roles in regulating cancer stem cells and influencing the immune response to cancer therapy. Through a comprehensive synthesis of current insights, this review underscores the complex but promising landscape of PHD finger proteins in cancer biology, advocating for further research to unlock novel therapeutic avenues that leverage their unique cellular roles.
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Affiliation(s)
- Tingyu Fan
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Lai Jiang
- Clinical Medical College, Southwest Medical University, Luzhou, Sichuan, China
| | - Xuancheng Zhou
- Clinical Medical College, Southwest Medical University, Luzhou, Sichuan, China
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, Sichuan, China
| | - Xi Zeng
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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3
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Francois AK, Rohani A, Loftus M, Dochnal S, Hrit J, McFarlane S, Whitford A, Lewis A, Krakowiak P, Boutell C, Rothbart SB, Kashatus D, Cliffe AR. Single-genome analysis reveals a heterogeneous association of the herpes simplex virus genome with H3K27me2 and the reader PHF20L1 following infection of human fibroblasts. mBio 2024; 15:e0327823. [PMID: 38411116 PMCID: PMC11005365 DOI: 10.1128/mbio.03278-23] [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: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
The fate of herpesvirus genomes following entry into different cell types is thought to regulate the outcome of infection. For the Herpes simplex virus 1 (HSV-1), latent infection of neurons is characterized by association with repressive heterochromatin marked with Polycomb silencing-associated lysine 27 methylation on histone H3 (H3K27me). However, whether H3K27 methylation plays a role in repressing lytic gene expression in non-neuronal cells is unclear. To address this gap in knowledge, and with consideration that the fate of the viral genome and outcome of HSV-1 infection could be heterogeneous, we developed an assay to quantify the abundance of histone modifications within single viral genome foci of infected fibroblasts. Using this approach, combined with bulk epigenetic techniques, we were unable to detect any role for H3K27me3 during HSV-1 lytic infection of fibroblasts. By contrast, we could detect the lesser studied H3K27me2 on a subpopulation of viral genomes, which was consistent with a role for H3K27 demethylases in promoting lytic gene expression. In addition, viral genomes co-localized with the H3K27me2 reader protein PHF20L1, and this association was enhanced by inhibition of the H3K27 demethylases UTX and JMJD3. Notably, targeting of H3K27me2 to viral genomes was enhanced following infection with a transcriptionally defective virus in the absence of Promyelocytic leukemia nuclear bodies. Collectively, these studies implicate a role for H3K27me2 in fibroblast-associated HSV genome silencing in a manner dependent on genome sub-nuclear localization and transcriptional activity. IMPORTANCE Investigating the potential mechanisms of gene silencing for DNA viruses in different cell types is important to understand the differential outcomes of infection, particularly for viruses like herpesviruses that can undergo distinct types of infection in different cell types. In addition, investigating chromatin association with viral genomes informs on the mechanisms of epigenetic regulation of DNA processes. However, there is a growing appreciation for heterogeneity in the outcome of infection at the single cell, and even single viral genome, level. Here we describe a novel assay for quantifying viral genome foci with chromatin proteins and show that a portion of genomes are targeted for silencing by H3K27me2 and associate with the reader protein PHF20L1. This study raises important questions regarding the mechanism of H3K27me2-specific targeting to viral genomes, the contribution of epigenetic heterogeneity to herpesvirus infection, and the role of PHF20L1 in regulating the outcome of DNA virus infection.
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Affiliation(s)
- Alison K. Francois
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Ali Rohani
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Matt Loftus
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Sara Dochnal
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Joel Hrit
- Department of Epigenetics, Van Andel Institute, Grand Rapids, USA
| | - Steven McFarlane
- MRC - University of Glasgow, Centre for Virus Research, Glasgow, United Kingdom
| | - Abigail Whitford
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Anna Lewis
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Patryk Krakowiak
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Chris Boutell
- MRC - University of Glasgow, Centre for Virus Research, Glasgow, United Kingdom
| | | | - David Kashatus
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Anna R. Cliffe
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
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4
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Xue H, Han L, Sun H, Piao Z, Cao W, Qian H, Zhao Z, Lang MF, Gu C. Metastasis-associated 1 localizes to the sarcomeric Z-disc and is implicated in skeletal muscle pathology. Cytoskeleton (Hoboken) 2024. [PMID: 38391059 DOI: 10.1002/cm.21841] [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: 07/19/2023] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
Abstract
Metastasis-associated 1 (MTA1), a subunit of the nucleosome remodeling and histone deacetylation (NuRD) corepressor complex, was reported to be expressed in the cytoplasm of skeletal muscles. However, the exact subcellular localization and the functional implications of MTA1 in skeletal muscles have not been examined. This study aims to demonstrate the subcellular localization of MTA1 in skeletal muscles and reveal its possible roles in skeletal muscle pathogenesis. Striated muscles (skeletal and cardiac) from C57BL/6 mice of 4-5 weeks were collected to examine the expression of MTA1 by Western blotting and immunohistochemistry. Immunofluorescence and immunoelectron microscopy were performed for MTA1, α-actinin (a Z-disc marker protein), and SMN (survival of motor neuron) proteins. Gene Expression Omnibus (GEO) data sets were analyzed using the GEO2R online tool to explore the functional implications of MTA1 in skeletal muscles. MTA1 expression was detected by Western blotting and immunohistochemistry in skeletal and cardiac muscles. Subcellular localization of MTA1 was found in the Z-disc of sarcomeres, where α-actinin and SMN were expressed. Data mining of GEO profiles suggested that MTA1 dysregulation is associated with multiple skeletal muscle defects, such as Duchenne muscular dystrophy, Emery-Dreifuss muscular dystrophy, nemaline myopathy, and dermatomyositis. The GEO analysis also showed that MTA1 expression gradually decreased with age in mouse skeletal muscle precursor cells. The subcellular localization of MTA1 in sarcomeres of skeletal muscles implies its biological roles in sarcomere structures and its possible contribution to skeletal muscle pathology.
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Affiliation(s)
- Hongsheng Xue
- Department of Thoracic Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, China
- Department of Thoracic Surgery, the Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Li Han
- Department of Thoracic Surgery, the Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Haidi Sun
- Department of Physiology and Medical Biology, Medical College, Dalian University, Dalian, China
| | - Zhe Piao
- Department of Thoracic Surgery, the Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Wenjun Cao
- Department of Thoracic Surgery, the Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhilong Zhao
- Department of Thoracic Surgery, the Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Ming-Fei Lang
- Department of Physiology and Medical Biology, Medical College, Dalian University, Dalian, China
| | - Chundong Gu
- Department of Thoracic Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, China
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5
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Francois AK, Rohani A, Loftus M, Dochnal S, Hrit J, McFarlane S, Whitford A, Lewis A, Krakowiak P, Boutell C, Rothbart SB, Kashatus D, Cliffe AR. Single-genome analysis reveals heterogeneous association of the Herpes Simplex Virus genome with H3K27me2 and the reader PHF20L1 following infection of human fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.03.569766. [PMID: 38076966 PMCID: PMC10705572 DOI: 10.1101/2023.12.03.569766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The fate of herpesvirus genomes following entry into different cell types is thought to regulate the outcome of infection. For the Herpes simplex virus 1 (HSV-1), latent infection of neurons is characterized by association with repressive heterochromatin marked with Polycomb silencing-associated lysine 27 methylation on histone H3 (H3K27me). However, whether H3K27 methylation plays a role in repressing lytic gene expression in non-neuronal cells is unclear. To address this gap in knowledge, and with consideration that the fate of the viral genome and outcome of HSV-1 infection could be heterogeneous, we developed an assay to quantify the abundance of histone modifications within single viral genome foci of infected fibroblasts. Using this approach, combined with bulk epigenetic techniques, we were unable to detect any role for H3K27me3 during HSV-1 lytic infection of fibroblasts. In contrast, we could detect the lesser studied H3K27me2 on a subpopulation of viral genomes, which was consistent with a role for H3K27 demethylases in promoting lytic gene expression. This was consistent with a role for H3K27 demethylases in promoting lytic gene expression. In addition, viral genomes co-localized with the H3K27me2 reader protein PHF20L1, and this association was enhanced by inhibition of the H3K27 demethylases UTX and JMJD3. Notably, targeting of H3K27me2 to viral genomes was enhanced following infection with a transcriptionally defective virus in the absence of Promyelocytic leukemia nuclear bodies. Collectively, these studies implicate a role for H3K27me2 in fibroblast-associated HSV genome silencing in a manner dependent on genome sub-nuclear localization and transcriptional activity.
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Affiliation(s)
- Alison K Francois
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Ali Rohani
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Matt Loftus
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Sara Dochnal
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Joel Hrit
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503
| | - Steven McFarlane
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland
| | - Abigail Whitford
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Anna Lewis
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Patryk Krakowiak
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Chris Boutell
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland
| | - Scott B. Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503
| | - David Kashatus
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Anna R Cliffe
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
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6
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Liu W, Zeng Y, Hao X, Wang X, Liu J, Gao T, Wang M, Zhang J, Huo M, Hu T, Ma T, Zhang D, Teng X, Yu H, Zhang M, Yuan B, Huang W, Yang Y, Wang Y. JARID2 coordinates with the NuRD complex to facilitate breast tumorigenesis through response to adipocyte-derived leptin. Cancer Commun (Lond) 2023; 43:1117-1142. [PMID: 37658635 PMCID: PMC10565380 DOI: 10.1002/cac2.12479] [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: 09/07/2022] [Revised: 05/21/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Proteins containing the Jumonji C (JmjC) domain participated in tumorigenesis and cancer progression. However, the mechanisms underlying this effect are still poorly understood. Our objective was to investigate the role of Jumonji and the AT-rich interaction domain-containing 2 (JARID2) - a JmjC family protein - in breast cancer, as well as its latent association with obesity. METHODS Immunohistochemistry, The Cancer Genome Atlas, Gene Expression Omnibus, and other databases were used to analyze the expression of JARID2 in breast cancer cells. Growth curve, 5-ethynyl-2-deoxyuridine (EdU), colony formation, and cell invasion experiments were used to detect whether JARID2 affected breast cancer cell proliferation and invasion. Spheroidization-based experiments and xenotumor transplantation in NOD/SCID mice were used to examine the association between JARID2 and breast cancer stemness. RNA-sequencing, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Enrichment Analysis were used to identify the cell processes in which JARID2 participates. Immunoaffinity purification and silver staining mass spectrometry were conducted to search for proteins that might interact with JARID2. The results were further verified using co-immunoprecipitation and glutathione S-transferase (GST) pull-down experiments. Using chromatin immunoprecipitation (ChIP) sequencing, we sought the target genes that JARID2 and metastasis-associated protein 1 (MTA1) jointly regulated; the results were validated by ChIP-PCR, quantitative ChIP (qChIP) and ChIP-reChIP assays. A coculture experiment was used to explore the interactions between breast cancer cells and adipocytes. RESULTS In this study, we found that JARID2 was highly expressed in multiple types of cancer including breast cancer. JARID2 promoted glycolysis, lipid metabolism, proliferation, invasion, and stemness of breast cancer cells. Furthermore, JARID2 physically interacted with the nucleosome remodeling and deacetylase (NuRD) complex, transcriptionally repressing a series of tumor suppressor genes such as BRCA2 DNA repair associated (BRCA2), RB transcriptional corepressor 1 (RB1), and inositol polyphosphate-4-phosphatase type II B (INPP4B). Additionally, JARID2 expression was regulated by the obesity-associated adipokine leptin via Janus kinase 2/signal transducer and activator of transcription 3 (JAK2/STAT3) pathway in the breast cancer microenvironment. Analysis of various online databases also indicated that JARID2/MTA1 was associated with a poor prognosis of breast cancer. CONCLUSION Our data indicated that JARID2 promoted breast tumorigenesis and development, confirming JARID2 as a target for cancer treatment.
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Affiliation(s)
- Wei Liu
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinP. R. China
- Key Laboratory of Cancer and MicrobiomeState Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Yi Zeng
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinP. R. China
- Department of Biochemistry and Molecular BiologySchool of Basic Medical ScienceSouthwest Medical UniversityLuzhouSichuanP. R. China
| | - Xinhui Hao
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinP. R. China
| | - Xin Wang
- Department of Breast Surgical OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Jiaxiang Liu
- Department of Breast Surgical OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Tianyang Gao
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinP. R. China
| | - Mengdi Wang
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinP. R. China
| | - Jingyao Zhang
- Key Laboratory of Cancer and MicrobiomeState Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Miaomiao Huo
- Key Laboratory of Cancer and MicrobiomeState Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Ting Hu
- Key Laboratory of Cancer and MicrobiomeState Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Tianyu Ma
- Key Laboratory of Cancer and MicrobiomeState Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Die Zhang
- Key Laboratory of Cancer and MicrobiomeState Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Xu Teng
- Beijing Key Laboratory of Cancer Invasion and Metastasis ResearchDepartment of Biochemistry and Molecular BiologySchool of Basic Medical SciencesCapital Medical UniversityBeijingP. R. China
| | - Hefen Yu
- Beijing Key Laboratory of Cancer Invasion and Metastasis ResearchDepartment of Biochemistry and Molecular BiologySchool of Basic Medical SciencesCapital Medical UniversityBeijingP. R. China
| | - Min Zhang
- Key Laboratory of Cancer and MicrobiomeState Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Baowen Yuan
- Key Laboratory of Cancer and MicrobiomeState Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Wei Huang
- Beijing Key Laboratory of Cancer Invasion and Metastasis ResearchDepartment of Biochemistry and Molecular BiologySchool of Basic Medical SciencesCapital Medical UniversityBeijingP. R. China
| | - Yunkai Yang
- Key Laboratory of Cancer and MicrobiomeState Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Yan Wang
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinP. R. China
- Key Laboratory of Cancer and MicrobiomeState Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
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7
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Margasyuk S, Kalinina M, Petrova M, Skvortsov D, Cao C, Pervouchine DD. RNA in situ conformation sequencing reveals novel long-range RNA structures with impact on splicing. RNA (NEW YORK, N.Y.) 2023; 29:1423-1436. [PMID: 37295923 PMCID: PMC10573301 DOI: 10.1261/rna.079508.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/22/2023] [Indexed: 06/12/2023]
Abstract
Over recent years, long-range RNA structure has emerged as a factor that is fundamental to alternative splicing regulation. An increasing number of human disorders are now being associated with splicing defects; hence it is essential to develop methods that assess long-range RNA structure experimentally. RNA in situ conformation sequencing (RIC-seq) is a method that recapitulates RNA structure within physiological RNA-protein complexes. In this work, we juxtapose pairs of conserved complementary regions (PCCRs) that were predicted in silico with the results of RIC-seq experiments conducted in seven human cell lines. We show statistically that RIC-seq support of PCCRs correlates with their properties, such as equilibrium free energy, presence of compensatory substitutions, and occurrence of A-to-I RNA editing sites and forked eCLIP peaks. Exons enclosed in PCCRs that are supported by RIC-seq tend to have weaker splice sites and lower inclusion rates, which is indicative of post-transcriptional splicing regulation mediated by RNA structure. Based on these findings, we prioritize PCCRs according to their RIC-seq support and show, using antisense nucleotides and minigene mutagenesis, that PCCRs in two disease-associated human genes, PHF20L1 and CASK, and also PCCRs in their murine orthologs, impact alternative splicing. In sum, we demonstrate how RIC-seq experiments can be used to discover functional long-range RNA structures, and particularly those that regulate alternative splicing.
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Affiliation(s)
- Sergey Margasyuk
- Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Marina Kalinina
- Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Marina Petrova
- Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Dmitry Skvortsov
- Skolkovo Institute of Science and Technology, Moscow 143026, Russia
- Moscow State University, Faculty of Chemistry, Moscow 119991, Russia
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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8
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Kumar S, Alam SS, Bareke E, Beauchamp MC, Dong Y, Chan W, Majewski J, Jerome-Majewska LA. Sf3b4 regulates chromatin remodeler splicing and Hox expression. Differentiation 2023; 131:59-73. [PMID: 37167859 DOI: 10.1016/j.diff.2023.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/13/2023]
Abstract
SF3B proteins form a heptameric complex in the U2 small nuclear ribonucleoprotein, essential for pre-mRNA splicing. Heterozygous pathogenic variants in human SF3B4 are associated with head, face, limb, and vertebrae defects. Using the CRISPR/Cas9 system, we generated mice with constitutive heterozygous deletion of Sf3b4 and showed that mutant embryos have abnormal vertebral development. Vertebrae abnormalities were accompanied by changes in levels and expression pattern of Hox genes in the somites. RNA sequencing analysis of whole embryos and somites of Sf3b4 mutant and control litter mates revealed increased expression of other Sf3b4 genes. However, the mutants exhibited few differentially expressed genes and a large number of transcripts with differential splicing events (DSE), predominantly increased exon skipping and intron retention. Transcripts with increased DSE included several genes involved in chromatin remodeling that are known to regulate Hox expression. Our study confirms that Sf3b4 is required for normal vertebrae development and shows, for the first time, that like Sf3b1, Sf3b4 also regulates Hox expression. We propose that abnormal splicing of chromatin remodelers is primarily responsible for vertebral defects found in Sf3b4 heterozygous mutant embryos.
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Affiliation(s)
- Shruti Kumar
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0G1, Canada
| | | | - Eric Bareke
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0G1, Canada
| | - Marie-Claude Beauchamp
- Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC, H4A 3J1, Canada
| | - Yanchen Dong
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0G1, Canada
| | - Wesley Chan
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, H3A 2B2, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0G1, Canada
| | - Loydie A Jerome-Majewska
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0G1, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, QC, H3A 2B2, Canada; Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC, H4A 3J1, Canada; Department of Pediatrics, McGill University, Montreal, QC, H4A 3J1, Canada.
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9
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Thakur C, Qiu Y, Fu Y, Bi Z, Zhang W, Ji H, Chen F. Epigenetics and environment in breast cancer: New paradigms for anti-cancer therapies. Front Oncol 2022; 12:971288. [PMID: 36185256 PMCID: PMC9520778 DOI: 10.3389/fonc.2022.971288] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/26/2022] [Indexed: 11/27/2022] Open
Abstract
Breast cancer remains the most frequently diagnosed cancer in women worldwide. Delayed presentation of the disease, late stage at diagnosis, limited therapeutic options, metastasis, and relapse are the major factors contributing to breast cancer mortality. The development and progression of breast cancer is a complex and multi-step process that incorporates an accumulation of several genetic and epigenetic alterations. External environmental factors and internal cellular microenvironmental cues influence the occurrence of these alterations that drives tumorigenesis. Here, we discuss state-of-the-art information on the epigenetics of breast cancer and how environmental risk factors orchestrate major epigenetic events, emphasizing the necessity for a multidisciplinary approach toward a better understanding of the gene-environment interactions implicated in breast cancer. Since epigenetic modifications are reversible and are susceptible to extrinsic and intrinsic stimuli, they offer potential avenues that can be targeted for designing robust breast cancer therapies.
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Affiliation(s)
- Chitra Thakur
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, United States
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, United States
| | - Yiran Qiu
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, United States
| | - Yao Fu
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, United States
| | - Zhuoyue Bi
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, United States
| | - Wenxuan Zhang
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, United States
| | - Haoyan Ji
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, United States
| | - Fei Chen
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, United States
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, United States
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10
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XIST loss impairs mammary stem cell differentiation and increases tumorigenicity through Mediator hyperactivation. Cell 2022; 185:2164-2183.e25. [PMID: 35597241 DOI: 10.1016/j.cell.2022.04.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 01/10/2022] [Accepted: 04/27/2022] [Indexed: 12/27/2022]
Abstract
X inactivation (XCI) is triggered by upregulation of XIST, which coats the chromosome in cis, promoting formation of a heterochromatic domain (Xi). XIST role beyond initiation of XCI is only beginning to be elucidated. Here, we demonstrate that XIST loss impairs differentiation of human mammary stem cells (MaSCs) and promotes emergence of highly tumorigenic and metastatic carcinomas. On the Xi, XIST deficiency triggers epigenetic changes and reactivation of genes overlapping Polycomb domains, including Mediator subunit MED14. MED14 overdosage results in increased Mediator levels and hyperactivation of the MaSC enhancer landscape and transcriptional program, making differentiation less favorable. We further demonstrate that loss of XIST and Xi transcriptional instability is common among human breast tumors of poor prognosis. We conclude that XIST is a gatekeeper of human mammary epithelium homeostasis, thus unveiling a paradigm in the control of somatic cell identity with potential consequences for our understanding of gender-specific malignancies.
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11
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Vattem C, Pakala SB. Metastasis-associated protein 1: A potential driver and regulator of the hallmarks of cancer. J Biosci 2022. [DOI: 10.1007/s12038-022-00263-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Zhu QC, Sun JH, Liang MJ, Zhang ZY, Xia Y. PHF20L1 mediates PAX2 expression to promote angiogenesis and liver metastasis in colorectal cancer through regulating HIC1. Biol Chem 2022; 403:917-928. [PMID: 35357096 DOI: 10.1515/hsz-2022-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/10/2022] [Indexed: 11/15/2022]
Abstract
Colorectal cancer (CRC) is a common cancer with poor prognosis. The research was designed to explore the role of PHF20L1 in angiogenesis and liver metastasis in CRC and discuss its molecular mechanism. Expression levels of PHF20L1, HIC1 and PAX2 in CRC tissues collected from CRC patients were detected using qRT-PCR, WB and immunohistochemical staining. CRC cells were transfected with PHF20L1, HIC1 and PAX2 overexpression or knockdown vectors and the proliferation, apoptosis, EMT and angiogenesis of the cells were determined. WB was utilized to assess protein levels of PHF20L1, HIC1, PAX2 and angiogenesis factor (ANGPT2, FGF1, PDGFA and VEGFA). The role of PHF20L1 regulating tumor formation and liver metastasis in vivo was detected as well. PHF20L1 was observed to express at a high level of CRC tissues. PHF20L1 promoted CRC cell growth, EMT and angiogenesis, and inhibited cell apoptosis. Knockdown of PHF20L1 had opposite effects on CRC cells. PHF20L1 negatively regulated HIC1 expression to promote PAX2 expression, thus promoting CRC cell progression. The in vivo results showed that PHF20L1 contributed to tumor formation and liver metastasis. PHF20L1 increases PAX2 expression to promote angiogenesis in CRC by inhibiting HIC1, therefore facilitating CRC cell EMT and liver metastasis. Our finding may provide a novel insight for CRC pathogenesis.
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Affiliation(s)
- Qing-Chao Zhu
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Jian-Hua Sun
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Ming-Jun Liang
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Zheng-Yun Zhang
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Yang Xia
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
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13
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Van HT, Harkins PR, Patel A, Jain AK, Lu Y, Bedford MT, Santos MA. Methyl-lysine readers PHF20 and PHF20L1 define two distinct gene expression-regulating NSL complexes. J Biol Chem 2022; 298:101588. [PMID: 35033534 PMCID: PMC8867114 DOI: 10.1016/j.jbc.2022.101588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 11/16/2022] Open
Abstract
The methyl-lysine readers plant homeodomain finger protein 20 (PHF20) and its homolog PHF20-like protein 1 (PHF20L1) are known components of the nonspecific lethal (NSL) complex that regulates gene expression through its histone acetyltransferase activity. In the current model, both PHF homologs coexist in the same NSL complex, although this was not formally tested; nor have the functions of PHF20 and PHF20L1 regarding NSL complex integrity and transcriptional regulation been investigated. Here, we perform an in-depth biochemical and functional characterization of PHF20 and PHF20L1 in the context of the NSL complex. Using mass spectrometry, genome-wide chromatin analysis, and protein-domain mapping, we identify the existence of two distinct NSL complexes that exclusively contain either PHF20 or PHF20L1. We show that the C-terminal domains of PHF20 and PHF20L1 are essential for complex formation with NSL, and the Tudor 2 domains are required for chromatin binding. The genome-wide chromatin landscape of PHF20–PHF20L1 shows that these proteins bind mostly to the same genomic regions, at promoters of highly expressed/housekeeping genes. Yet, deletion of PHF20 and PHF20L1 does not abrogate gene expression or impact the recruitment of the NSL complex to those target gene promoters, suggesting the existence of an alternative mechanism that compensates for the transcription of genes whose sustained expression is important for critical cellular functions. This work shifts the current paradigm and lays the foundation for studies on the differential roles of PHF20 and PHF20L1 in regulating NSL complex activity in physiological and diseases states.
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Affiliation(s)
- Hieu T Van
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Graduate Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Peter R Harkins
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Avni Patel
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Margarida A Santos
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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14
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Huo M, Zhang J, Huang W, Wang Y. Interplay Among Metabolism, Epigenetic Modifications, and Gene Expression in Cancer. Front Cell Dev Biol 2022; 9:793428. [PMID: 35004688 PMCID: PMC8740611 DOI: 10.3389/fcell.2021.793428] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic modifications and metabolism are two fundamental biological processes. During tumorigenesis and cancer development both epigenetic and metabolic alterations occur and are often intertwined together. Epigenetic modifications contribute to metabolic reprogramming by modifying the transcriptional regulation of metabolic enzymes, which is crucial for glucose metabolism, lipid metabolism, and amino acid metabolism. Metabolites provide substrates for epigenetic modifications, including histone modification (methylation, acetylation, and phosphorylation), DNA and RNA methylation and non-coding RNAs. Simultaneously, some metabolites can also serve as substrates for nonhistone post-translational modifications that have an impact on the development of tumors. And metabolic enzymes also regulate epigenetic modifications independent of their metabolites. In addition, metabolites produced by gut microbiota influence host metabolism. Understanding the crosstalk among metabolism, epigenetic modifications, and gene expression in cancer may help researchers explore the mechanisms of carcinogenesis and progression to metastasis, thereby provide strategies for the prevention and therapy of cancer. In this review, we summarize the progress in the understanding of the interactions between cancer metabolism and epigenetics.
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Affiliation(s)
- Miaomiao Huo
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingyao Zhang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Huang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yan Wang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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15
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Alberto-Aguilar DR, Hernández-Ramírez VI, Osorio-Trujillo JC, Gallardo-Rincón D, Toledo-Leyva A, Talamás-Rohana P. PHD finger protein 20-like protein 1 (PHF20L1) in ovarian cancer: from its overexpression in tissue to its upregulation by the ascites microenvironment. Cancer Cell Int 2022; 22:6. [PMID: 34991589 PMCID: PMC8740351 DOI: 10.1186/s12935-021-02425-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 12/23/2021] [Indexed: 02/08/2023] Open
Abstract
Background Ovarian cancer is the most aggressive gynecological malignancy. Transcriptional regulators impact the tumor phenotype and, consequently, clinical progression and response to therapy. PHD finger protein 20-like protein 1 (PHF20L1) is a transcriptional regulator with several isoforms, and studies on its role in ovarian cancer are limited. We previously reported that PHF20L1 is expressed as a fucosylated protein in SKOV-3 cells stimulated with ascites from patients with ovarian cancer. Methods We decided to analyze the expression of PHF20L1 in ovarian cancer tissues, determine whether a correlation exists between PHF20L1 expression and patient clinical data, and analyze whether ascites can modulate the different isoforms of this protein. Ovarian cancer biopsies from 29 different patients were analyzed by immunohistochemistry, and the expression of the isoforms in ovarian cancer cells with or without exposure to the tumor microenvironment, i.e., the ascitic fluid, was determined by western blotting assays. Results Immunohistochemical results suggest that PHF20L1 exhibits increased expression in sections of tumor tissues from patients with ovarian cancer and that higher PHF20L1 expression correlates with shorter progression-free survival and shorter overall survival. Furthermore, western blotting assays determined that protein isoforms are differentially regulated in SKOV-3 cells in response to stimulation with ascites from patients with epithelial ovarian cancer. Conclusion The results suggest that PHF20L1 could play a relevant role in ovarian cancer given that higher PHF20L1 protein expression is associated with lower overall patient survival. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02425-6.
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Affiliation(s)
- Dulce Rosario Alberto-Aguilar
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, 07360, Mexico City, Mexico
| | - Verónica Ivonne Hernández-Ramírez
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, 07360, Mexico City, Mexico
| | - Juan Carlos Osorio-Trujillo
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, 07360, Mexico City, Mexico
| | - Dolores Gallardo-Rincón
- Instituto Nacional de Cancerología, Av. San Fernando No. 22, Col. Sección XVI, Delegación Tlalpan, 07360, Mexico City, Mexico
| | - Alfredo Toledo-Leyva
- Instituto Nacional de Cancerología, Av. San Fernando No. 22, Col. Sección XVI, Delegación Tlalpan, 07360, Mexico City, Mexico
| | - Patricia Talamás-Rohana
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, 07360, Mexico City, Mexico.
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16
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Mondal P, Tiwary N, Sengupta A, Dhang S, Roy S, Das C. Epigenetic Reprogramming of the Glucose Metabolic Pathways by the Chromatin Effectors During Cancer. Subcell Biochem 2022; 100:269-336. [PMID: 36301498 DOI: 10.1007/978-3-031-07634-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Glucose metabolism plays a vital role in regulating cellular homeostasis as it acts as the central axis for energy metabolism, alteration in which may lead to serious consequences like metabolic disorders to life-threatening diseases like cancer. Malignant cells, on the other hand, help in tumor progression through abrupt cell proliferation by adapting to the changed metabolic milieu. Metabolic intermediates also vary from normal cells to cancerous ones to help the tumor manifestation. However, metabolic reprogramming is an important phenomenon of cells through which they try to maintain the balance between normal and carcinogenic outcomes. In this process, transcription factors and chromatin modifiers play an essential role to modify the chromatin landscape of important genes related directly or indirectly to metabolism. Our chapter surmises the importance of glucose metabolism and the role of metabolic intermediates in the cell. Also, we summarize the influence of histone effectors in reprogramming the cancer cell metabolism. An interesting aspect of this chapter includes the detailed methods to detect the aberrant metabolic flux, which can be instrumental for the therapeutic regimen of cancer.
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Affiliation(s)
- Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Niharika Tiwary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Amrita Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Sinjini Dhang
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Siddhartha Roy
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.
- Homi Bhaba National Institute, Mumbai, India.
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17
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Bhan A, Ansari K, Chen MY, Jandial R. Human induced pluripotent stem cell-derived platelets loaded with lapatinib effectively target HER2+ breast cancer metastasis to the brain. Sci Rep 2021; 11:16866. [PMID: 34654856 PMCID: PMC8521584 DOI: 10.1038/s41598-021-96351-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 08/06/2021] [Indexed: 01/09/2023] Open
Abstract
Prognosis of patients with HER2+ breast-to-brain-metastasis (BBM) is dismal even after current standard-of-care treatments, including surgical resection, whole-brain radiation, and systemic chemotherapy. Radiation and systemic chemotherapies can also induce cytotoxicity, leading to significant side effects. Studies indicate that donor-derived platelets can serve as immune-compatible drug carriers that interact with and deliver drugs to cancer cells with fewer side effects, making them a promising therapeutic option with enhanced antitumor activity. Moreover, human induced pluripotent stem cells (hiPSCs) provide a potentially renewable source of clinical-grade transfusable platelets that can be drug-loaded to complement the supply of donor-derived platelets. Here, we describe methods for ex vivo generation of megakaryocytes (MKs) and functional platelets from hiPSCs (hiPSC-platelets) in a scalable fashion. We then loaded hiPSC-platelets with lapatinib and infused them into BBM tumor-bearing NOD/SCID mouse models. Such treatment significantly increased intracellular lapatinib accumulation in BBMs in vivo, potentially via tumor cell-induced activation/aggregation. Lapatinib-loaded hiPSC-platelets exhibited normal morphology and function and released lapatinib pH-dependently. Importantly, lapatinib delivery to BBM cells via hiPSC-platelets inhibited tumor growth and prolonged survival of tumor-bearing mice. Overall, use of lapatinib-loaded hiPSC-platelets effectively reduced adverse effects of free lapatinib and enhanced its therapeutic efficacy, suggesting that they represent a novel means to deliver chemotherapeutic drugs as treatment for BBM.
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Affiliation(s)
- Arunoday Bhan
- Division of Neurosurgery, Beckman Research Institute, City of Hope Medical Center, 1500 E. Duarte Rd, Duarte, CA, 91010, USA.
| | - Khairul Ansari
- Division of Neurosurgery, Beckman Research Institute, City of Hope Medical Center, 1500 E. Duarte Rd, Duarte, CA, 91010, USA
- Celcuity LLC, Minneapolis, MN, 55446, USA
| | - Mike Y Chen
- Division of Neurosurgery, Beckman Research Institute, City of Hope Medical Center, 1500 E. Duarte Rd, Duarte, CA, 91010, USA
| | - Rahul Jandial
- Division of Neurosurgery, Beckman Research Institute, City of Hope Medical Center, 1500 E. Duarte Rd, Duarte, CA, 91010, USA
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18
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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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19
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De Novo Polycomb Recruitment: Lessons from Latent Herpesviruses. Viruses 2021; 13:v13081470. [PMID: 34452335 PMCID: PMC8402699 DOI: 10.3390/v13081470] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/11/2022] Open
Abstract
The Human Herpesviruses persist in the form of a latent infection in specialized cell types. During latency, the herpesvirus genomes associate with cellular histone proteins and the viral lytic genes assemble into transcriptionally repressive heterochromatin. Although there is divergence in the nature of heterochromatin on latent herpesvirus genomes, in general, the genomes assemble into forms of heterochromatin that can convert to euchromatin to permit gene expression and therefore reactivation. This reversible form of heterochromatin is known as facultative heterochromatin and is most commonly characterized by polycomb silencing. Polycomb silencing is prevalent on the cellular genome and plays a role in developmentally regulated and imprinted genes, as well as X chromosome inactivation. As herpesviruses initially enter the cell in an un-chromatinized state, they provide an optimal system to study how de novo facultative heterochromatin is targeted to regions of DNA and how it contributes to silencing. Here, we describe how polycomb-mediated silencing potentially assembles onto herpesvirus genomes, synergizing what is known about herpesvirus latency with facultative heterochromatin targeting to the cellular genome. A greater understanding of polycomb silencing of herpesviruses will inform on the mechanism of persistence and reactivation of these pathogenic human viruses and provide clues regarding how de novo facultative heterochromatin forms on the cellular genome.
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20
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Zhang Z, Chen B, Zhu Y, Zhang T, Yuan Y, Zhang X, Xu Y. The Jumonji Domain-Containing Histone Demethylase Homolog 1D/lysine Demethylase 7A (JHDM1D/KDM7A) Is an Epigenetic Activator of RHOJ Transcription in Breast Cancer Cells. Front Cell Dev Biol 2021; 9:664375. [PMID: 34249916 PMCID: PMC8262595 DOI: 10.3389/fcell.2021.664375] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
The small GTPase RHOJ is a key regulator of breast cancer metastasis by promoting cell migration and invasion. The prometastatic stimulus TGF-β activates RHOJ transcription via megakaryocytic leukemia 1 (MKL1). The underlying epigenetic mechanism is not clear. Here, we report that MKL1 deficiency led to disrupted assembly of the RNA polymerase II preinitiation complex on the RHOJ promoter in breast cancer cells. This could be partially explained by histone H3K9/H3K27 methylation status. Further analysis confirmed that the H3K9/H3K27 dual demethylase JHDM1D/KDM7A was essential for TGF-β-induced RHOJ transcription in breast cancer cells. MKL1 interacted with and recruited KDM7A to the RHOJ promoter to cooperatively activate RHOJ transcription. KDM7A knockdown attenuated migration and invasion of breast cancer cells in vitro and mitigated the growth and metastasis of breast cancer cells in nude mice. KDM7A expression level, either singularly or in combination with that of RHOJ, could be used to predict prognosis in breast cancer patients. Of interest, KDM7A appeared to be a direct transcriptional target of TGF-β signaling. A SMAD2/SMAD4 complex bound to the KDM7A promoter and mediated TGF-β-induced KDM7A transcription. In conclusion, our data unveil a novel epigenetic mechanism whereby TGF-β regulates the transcription of the prometastatic small GTPase RHOJ. Screening for small-molecule inhibitors of KDM7A may yield effective therapeutic solutions to treat malignant breast cancers.
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Affiliation(s)
- Ziyu Zhang
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, China.,Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, China
| | - Baoyu Chen
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Yuwen Zhu
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Tianyi Zhang
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Yibiao Yuan
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Xiaoling Zhang
- School of Medicine, Nanchang University, Nanchang, China.,Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, China
| | - Yong Xu
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
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21
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Wang X, Wang C, Guan J, Chen B, Xu L, Chen C. Progress of Breast Cancer basic research in China. Int J Biol Sci 2021; 17:2069-2079. [PMID: 34131406 PMCID: PMC8193257 DOI: 10.7150/ijbs.60631] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022] Open
Abstract
Breast cancer is the most commonly diagnosed and the most lethal cancer in females both in China and worldwide. Currently, the origin of cancer stem cells, the heterogeneity of cancer cells, the mechanism of cancer metastasis and drug resistance are the most important issues that need to be addressed. Chinese investigators have recently made new discoveries in basic breast cancer researches, especially regarding cancer stem cells, cancer metabolism, and microenvironments. These efforts have led to a deeper understanding of drug resistance and metastasis and have also indicated new biomarkers and therapeutic targets. These findings emphasized the importance of the cancer stem cells for targeted therapy. In this review, we summarized the latest important findings in this field in China.
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Affiliation(s)
- Xuerong Wang
- Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Chao Wang
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210009, China
| | - Jiaheng Guan
- Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Baoan Chen
- Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Lin Xu
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210009, China
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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22
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Hernández-Fernández J, Pinzón-Velasco A, López EA, Rodríguez-Becerra P, Mariño-Ramírez L. Transcriptional Analyses of Acute Exposure to Methylmercury on Erythrocytes of Loggerhead Sea Turtle. TOXICS 2021; 9:70. [PMID: 33805397 PMCID: PMC8066450 DOI: 10.3390/toxics9040070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 01/09/2023]
Abstract
To understand changes in enzyme activity and gene expression as biomarkers of exposure to methylmercury, we exposed loggerhead turtle erythrocytes (RBCs) to concentrations of 0, 1, and 5 mg L-1 of MeHg and de novo transcriptome were assembled using RNA-seq. The analysis of differentially expressed genes (DEGs) indicated that 79 unique genes were dysregulated (39 upregulated and 44 downregulated genes). The results showed that MeHg altered gene expression patterns as a response to the cellular stress produced, reflected in cell cycle regulation, lysosomal activity, autophagy, calcium regulation, mitochondrial regulation, apoptosis, and regulation of transcription and translation. The analysis of DEGs showed a low response of the antioxidant machinery to MeHg, evidenced by the fact that genes of early response to oxidative stress were not dysregulated. The RBCs maintained a constitutive expression of proteins that represented a good part of the defense against reactive oxygen species (ROS) induced by MeHg.
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Affiliation(s)
- Javier Hernández-Fernández
- Department of Natural and Environmental Science, Marine Biology Program, Faculty of Science and Engineering, Genetics, Molecular Biology and Bioinformatic Research Group–GENBIMOL, Jorge Tadeo Lozano University, Cra. 4 No 22-61, Bogotá 110311, Colombia;
- Faculty of Sciences, Department of Biology, Pontificia Universidad Javeriana, Calle 45, Cra. 7, Bogotá 110231, Colombia
| | - Andrés Pinzón-Velasco
- Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Calle 45, Cra. 30, Bogotá 111321, Colombia;
| | - Ellie Anne López
- IDEASA Research Group-Environment and Sustainability, Institute of Environmental Studies and Services, Sergio Arboleda University, Bogotá 111711, Colombia;
| | - Pilar Rodríguez-Becerra
- Department of Natural and Environmental Science, Marine Biology Program, Faculty of Science and Engineering, Genetics, Molecular Biology and Bioinformatic Research Group–GENBIMOL, Jorge Tadeo Lozano University, Cra. 4 No 22-61, Bogotá 110311, Colombia;
| | - Leonardo Mariño-Ramírez
- NCBI, NLM, NIH Computational Biology Branch, Building 38A, Room 6S614M 8600 Rockville Pike, MSC 6075, Bethesda, MD 20894-6075, USA;
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23
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Li T, Hui W, Halike H, Gao F. RNA Binding Protein-Based Model for Prognostic Prediction of Colorectal Cancer. Technol Cancer Res Treat 2021; 20:15330338211019504. [PMID: 34080453 PMCID: PMC8182183 DOI: 10.1177/15330338211019504] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a kind of gastrointestinal tumor with serious high morbidity and mortality. Several reports have implicated the disorder of RNA-binding proteins (RBPs) in plenty of tumors, associating it to tumorigenesis and disease progression. The study is intended to construct novel prognostic biomarkers associated with CRC patients. METHODS Data of gene expression was acquired from the TCGA database, prognosis-related genes were selected. Besides, we analyzed GO and KEGG pathways. Univariate and multivariate Cox analyses were performed to generate a prognostic-related gene signature, which was evaluated by the Kaplan-Meier (K-M) and the Receiver Operating Characteristic (ROC) curve. The independent prognostic factor was established by survival analysis. GSE38832 dataset was used to validate the signature. Finally, expression of 8 genes was further confirmed by qRT-PCR in SW480 and SW620 cell lines. RESULTS We obtained 224 differentially expressed RBPS in total, of which 78 were downregulated and 146 were upregulated. Univariate COX analysis was conducted in the TCGA cohort to select 13 RBPs with P < 0.005, stepwise multivariate COX regression analysis was used to construct an 8-RBP signature (TERT, PPARGC1A, BRCA1, CELF4, TDRD7, LUZP4, PNLDC1, ZC3H12C). Based on the model, systematic analysis illustrated that a high risk score was obviously connected to a poor prognosis. The prognostic value of the risk score was validated in GSE38832 dataset, indicating that the risk model was accurate and effective. The prognostic signature-based risk score was identified as an independent prognostic indicator for CRC. The expression results of qRT-PCR were consistent with the results of differential expression analysis. CONCLUSIONS The eight-RBP signature can predict the survival of CRC patients and potentially act as CRC prognostic biomarker.
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Affiliation(s)
- Ting Li
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur
Autonomous Region, Urumqi, Xinjiang Province, China
| | - Wenjia Hui
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur
Autonomous Region, Urumqi, Xinjiang Province, China
| | - Halina Halike
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur
Autonomous Region, Urumqi, Xinjiang Province, China
| | - Feng Gao
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur
Autonomous Region, Urumqi, Xinjiang Province, China
- Feng Gao, PhD, Department of
Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi
830000, Xinjiang Province, China.
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24
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Martin CJ, Moorehead RA. Polycomb repressor complex 2 function in breast cancer (Review). Int J Oncol 2020; 57:1085-1094. [PMID: 33491744 PMCID: PMC7549536 DOI: 10.3892/ijo.2020.5122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/07/2020] [Indexed: 11/24/2022] Open
Abstract
Epigenetic modifications are important contributors to the regulation of genes within the chromatin. The polycomb repressive complex 2 (PRC2) is a multi‑subunit protein complex that is involved in silencing gene expression through the trimethylation of lysine 27 at histone 3 (H3K27me3). The dysregulation of this modification has been associated with tumorigenicity through the increased repression of tumour suppressor genes via condensing DNA to reduce access to the transcription start site (TSS) within tumor suppressor gene promoters. In the present review, the core proteins of PRC2, as well as key accessory proteins, will be described. In addition, mechanisms controlling the recruitment of the PRC2 complex to H3K27 will be outlined. Finally, literature identifying the role of PRC2 in breast cancer proliferation, apoptosis and migration, including the potential roles of long non‑coding RNAs and the miR‑200 family will be summarized as will the potential use of the PRC2 complex as a therapeutic target.
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Affiliation(s)
- Courtney J. Martin
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Roger A. Moorehead
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G2W1, Canada
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25
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Lv M, Gao J, Li M, Ma R, Li F, Liu Y, Liu M, Zhang J, Yao X, Wu J, Shi Y, Tang Y, Pan Y, Zhang Z, Ruan K. Conformational Selection in Ligand Recognition by the First Tudor Domain of PHF20L1. J Phys Chem Lett 2020; 11:7932-7938. [PMID: 32885980 DOI: 10.1021/acs.jpclett.0c02039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The first Tudor domain (Tudor1) of PHF20L1 recognizes (non)histone methylation to play versatile roles. However, the underlying ligand-recognition mechanism remains unknown as a closed state revealed in the free-form structure. NMR relaxation dispersion and molecular dynamics simulations suggest a pre-existing low-population conformation with a remarkable rearrangement of aromatic cage residues of PHF20L1 Tudor1. Such an open-form conformation is utilized to recognize lysine 142 methylated DNMT1, a cosolvent, and an NMR fragment screening hit, as revealed by the complex crystal structures. Intriguingly, the ligand binding capacity was enhanced by mutation that tunes up the open-state population only. The recognition of DNMT1 by PHF20L1 was further validated in cancer cells. This conformational selection mechanism will enable the discovery of small molecule inhibitors against the seemingly "undruggable" PHF20L1 Tudor1.
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Affiliation(s)
- Mengqi Lv
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Jia Gao
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Mingwei Li
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Rongsheng Ma
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Fudong Li
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yaqian Liu
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Mingqing Liu
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Jiahai Zhang
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Xuebiao Yao
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Jihui Wu
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yunyu Shi
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yajun Tang
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yueyin Pan
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Zhiyong Zhang
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Ke Ruan
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
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