1
|
Pomella S, Melaiu O, Cifaldi L, Bei R, Gargari M, Campanella V, Barillari G. Biomarkers Identification in the Microenvironment of Oral Squamous Cell Carcinoma: A Systematic Review of Proteomic Studies. Int J Mol Sci 2024; 25:8929. [PMID: 39201614 PMCID: PMC11354375 DOI: 10.3390/ijms25168929] [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: 06/28/2024] [Revised: 07/30/2024] [Accepted: 08/05/2024] [Indexed: 09/02/2024] Open
Abstract
An important determinant for oral squamous cell carcinoma (OSCC) onset and outcome is the composition of the tumor microenvironment (TME). Thus, the study of the interactions occurring among cancer cells, immune cells, and cancer-associated fibroblasts within the TME could facilitate the understanding of the mechanisms underlying OSCC development and progression, as well as of its sensitivity or resistance to the therapy. In this context, it must be highlighted that the characterization of TME proteins is enabled by proteomic methodologies, particularly mass spectrometry (MS). Aiming to identify TME protein markers employable for diagnosing and prognosticating OSCC, we have retrieved a total of 119 articles spanning 2001 to 2023, of which 17 have passed the selection process, satisfying all its criteria. We have found a total of 570 proteins detected by MS-based proteomics in the TME of OSCC; among them, 542 are identified by a single study, while 28 are cited by two or more studies. These 28 proteins participate in extracellular matrix remodeling and/or energy metabolism. Here, we propose them as markers that could be used to characterize the TME of OSCC for diagnostic/prognostic purposes. Noteworthy, most of the 28 individuated proteins share one feature: being modulated by the hypoxia that is present in the proliferating OSCC mass.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Giovanni Barillari
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Via Montpellier, 00133 Rome, Italy; (S.P.); (O.M.); (L.C.); (R.B.); (M.G.); (V.C.)
| |
Collapse
|
2
|
He Q, Xu S, He F, Wu Z, Wu F, Zhou R, Zhou B, Li F, Yang X. Combined Proteomic and Phosphoproteomic Characterization of the Molecular Regulators and Functional Modules During Pancreatic Progenitor Cell Development. J Proteome Res 2024; 23:40-51. [PMID: 37993262 DOI: 10.1021/acs.jproteome.3c00309] [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: 11/24/2023]
Abstract
Differentiated multipotent pancreatic progenitors have major advantages for both modeling pancreas development and preventing or treating diabetes. Despite significant advancements in inducing the differentiation of human pluripotent stem cells into insulin-producing cells, the complete mechanism governing proliferation and differentiation remains poorly understood. This study used large-scale mass spectrometry to characterize molecular processes at various stages of human embryonic stem cell (hESC) differentiation toward pancreatic progenitors. hESCs were induced into pancreatic progenitor cells in a five-stage differentiation protocol. A high-performance liquid chromatography-mass spectrometry platform was used to undertake comprehensive proteome and phosphoproteome profiling of cells at different stages. A series of bioinformatic explorations, including coregulated modules, gene regulatory networks, and phosphosite enrichment analysis, were then conducted. A total of 27,077 unique phosphorylated sites and 8122 proteins were detected, including several cyclin-dependent kinases at the initial stage of cell differentiation. Furthermore, we discovered that ERK1, a member of the MAPK cascade, contributed to proliferation at an early stage. Finally, Western blotting confirmed that the phosphosites from SIRT1 and CHEK1 could inhibit the corresponding substrate abundance in the late stage. Thus, this study extends our understanding of the molecular mechanism during pancreatic cell development.
Collapse
Affiliation(s)
- Qian He
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology; the Second Clinical Medical College of Jinan University), Shenzhen 518055, China
- School of Food and Drug, Shenzhen Polytechnic, Shenzhen 518055, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen 518020, China
- Institute of Health Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shaohang Xu
- Deepxomics Co., Ltd., Shenzhen 518000, China
| | - Fei He
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology; the Second Clinical Medical College of Jinan University), Shenzhen 518055, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen 518020, China
- Institute of Health Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zubiao Wu
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology; the Second Clinical Medical College of Jinan University), Shenzhen 518055, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen 518020, China
- Institute of Health Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Fujian Wu
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology; the Second Clinical Medical College of Jinan University), Shenzhen 518055, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen 518020, China
- Post-doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou 510632, China
- Institute of Health Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruo Zhou
- Deepxomics Co., Ltd., Shenzhen 518000, China
| | - Baojin Zhou
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Furong Li
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology; the Second Clinical Medical College of Jinan University), Shenzhen 518055, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen 518020, China
- Institute of Health Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiaofei Yang
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology; the Second Clinical Medical College of Jinan University), Shenzhen 518055, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen 518020, China
- Institute of Health Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
3
|
Bai Z, Yan C, Nie Y, Zeng Q, Xu L, Wang S, Chang D. Glucose metabolism-based signature predicts prognosis and immunotherapy strategies for colon adenocarcinoma. J Gene Med 2024; 26:e3620. [PMID: 37973153 DOI: 10.1002/jgm.3620] [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: 08/30/2023] [Revised: 09/25/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The global prevalence and metastasis rates of colon adenocarcinoma (COAD) are high, and therapeutic success is limited. Although previous research has primarily explored changes in gene phenotypes, the incidence rate of COAD remains unchanged. Metabolic reprogramming is a crucial aspect of cancer research and therapy. The present study aims to develop cluster and polygenic risk prediction models for COAD based on glucose metabolism pathways to assess the survival status of patients and potentially identify novel immunotherapy strategies and related therapeutic targets. METHODS COAD-specific data (including clinicopathological information and gene expression profiles) were sourced from The Cancer Genome Atlas (TCGA) and two Gene Expression Omnibus (GEO) datasets (GSE33113 and GSE39582). Gene sets related to glucose metabolism were obtained from the MSigDB database. The Gene Set Variation Analysis (GSVA) method was utilized to calculate pathway scores for glucose metabolism. The hclust function in R, part of the Pheatmap package, was used to establish a clustering system. The mutation characteristics of identified clusters were assessed via MOVICS software, and differentially expressed genes (DEGs) were filtered using limma software. Signature analysis was performed using the least absolute shrinkage and selection operator (LASSO) method. Survival curves, survival receiver operating characteristic (ROC) curves and multivariate Cox regression were analyzed to assess the efficacy and accuracy of the signature for prognostic prediction. The pRRophetic program was employed to predict drug sensitivity, with data sourced from the Genomics of Drug Sensitivity in Cancer (GDSC) database. RESULTS Four COAD subgroups (i.e., C1, C2, C3 and C4) were identified based on glucose metabolism, with the C4 group having higher survival rates. These four clusters were bifurcated into a new Clust2 system (C1 + C2 + C3 and C4). In total, 2175 DEGs were obtained (C1 + C2 + C3 vs. C4), from which 139 prognosis-related genes were identified. ROC curves predicting 1-, 3- and 5-year survival based on a signature containing nine genes showed an area under the curve greater than 0.7. Meanwhile, the study also found this feature to be an important predictor of prognosis in COAD and accordingly assessed the risk score, with higher risk scores being associated with a worse prognosis. The high-risk and low-risk groups responded differently to immunotherapy and chemotherapeutic agents, and there were differences in functional enrichment pathways. CONCLUSIONS This unique signature based on glucose metabolism may potentially provide a basis for predicting patient prognosis, biological characteristics and more effective immunotherapy strategies for COAD.
Collapse
Affiliation(s)
- Zilong Bai
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Chunyu Yan
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Yuanhua Nie
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Qingnuo Zeng
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Longwen Xu
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Shilong Wang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Dongmin Chang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| |
Collapse
|
4
|
Choi DJ, Armstrong G, Lozzi B, Vijayaraghavan P, Plon SE, Wong TC, Boerwinkle E, Muzny DM, Chen HC, Gibbs RA, Ostrom QT, Melin B, Deneen B, Bondy ML, Bainbridge MN. The genomic landscape of familial glioma. SCIENCE ADVANCES 2023; 9:eade2675. [PMID: 37115922 PMCID: PMC10146888 DOI: 10.1126/sciadv.ade2675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Glioma is a rare brain tumor with a poor prognosis. Familial glioma is a subset of glioma with a strong genetic predisposition that accounts for approximately 5% of glioma cases. We performed whole-genome sequencing on an exploratory cohort of 203 individuals from 189 families with a history of familial glioma and an additional validation cohort of 122 individuals from 115 families. We found significant enrichment of rare deleterious variants of seven genes in both cohorts, and the most significantly enriched gene was HERC2 (P = 0.0006). Furthermore, we identified rare noncoding variants in both cohorts that were predicted to affect transcription factor binding sites or cause cryptic splicing. Last, we selected a subset of discovered genes for validation by CRISPR knockdown screening and found that DMBT1, HP1BP3, and ZCH7B3 have profound impacts on proliferation. This study performs comprehensive surveillance of the genomic landscape of familial glioma.
Collapse
Affiliation(s)
- Dong-Joo Choi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Georgina Armstrong
- Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Brittney Lozzi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | | | - Sharon E. Plon
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Terence C. Wong
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
| | - Eric Boerwinkle
- The University of Texas Health Science Center School of Public Health, Houston, TX, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hsiao-Chi Chen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Quinn T. Ostrom
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Benjamin Deneen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Melissa L. Bondy
- Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - The Gliogene Consortium
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
- The University of Texas Health Science Center School of Public Health, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Genomics England Research Consortium
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
- The University of Texas Health Science Center School of Public Health, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | | |
Collapse
|
5
|
Patel B, Zhou Y, Babcock RL, Ma F, Zal MA, Kumar D, Medik YB, Kahn LM, Pineda JE, Park EM, Tang X, Raso MG, Zal T, Clise-Dwyer K, Giancotti FG, Colla S, Watowich SS. STAT3 protects HSCs from intrinsic interferon signaling and loss of long-term blood-forming activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.528069. [PMID: 36798265 PMCID: PMC9934695 DOI: 10.1101/2023.02.10.528069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
STAT3 function in hematopoietic stem and progenitor cells (HSPCs) has been difficult to discern as Stat3 deficiency in the hematopoietic system induces systemic inflammation, which can impact HSPC activity. To address this, we established mixed bone marrow (BM) chimeric mice with CreER-mediated Stat3 deletion in 20% of the hematopoietic compartment. Stat3-deficient HSPCs had impaired hematopoietic activity and failed to undergo expansion in BM in contrast to Stat3-sufficient (CreER) controls. Single-cell RNA sequencing of Lin-ckit+Sca1+ BM cells revealed altered transcriptional responses in Stat3-deficient hematopoietic stem cells (HSCs) and multipotent progenitors, including intrinsic activation of cell cycle, stress response, and interferon signaling pathways. Consistent with their deregulation, Stat3-deficient Lin-ckit+Sca1+ cells accumulated γH2AX over time. Following secondary BM transplantation, Stat3-deficient HSPCs failed to reconstitute peripheral blood effectively, indicating a severe functional defect in the HSC compartment. Our results reveal essential roles for STAT3 in HSCs and suggest the potential for using targeted synthetic lethal approaches with STAT3 inhibition to remove defective or diseased HSPCs.
Collapse
Affiliation(s)
- Bhakti Patel
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yifan Zhou
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rachel L. Babcock
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Feiyang Ma
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Division of Rheumatology, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Malgorzata A. Zal
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dhiraj Kumar
- Herbert Irving Cancer Center and Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Yusra B. Medik
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Laura M. Kahn
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Josué E. Pineda
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Elizabeth M. Park
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tomasz Zal
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Karen Clise-Dwyer
- Department of Stem Cell Transplantation and Hematopoietic Biology and Malignancy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Filippo G. Giancotti
- Herbert Irving Cancer Center and Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Simona Colla
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie S. Watowich
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Program for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX, US
| |
Collapse
|
6
|
EZH2 interacts with HP1BP3 to epigenetically activate WNT7B that promotes temozolomide resistance in glioblastoma. Oncogene 2023; 42:461-470. [PMID: 36517590 DOI: 10.1038/s41388-022-02570-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Glioblastoma (GBM) is the most lethal primary brain tumor in adults and harbors a subpopulation of glioma stem cells (GSCs). Enhancer of Zeste Homolog 2 (EZH2), a histone lysine methyltransferase, deeply involves in the stemness maintenance of GSC. However, the precise mechanism and therapeutic potential remain elusive. We postulated that the interactome of EZH2 in GSC is unique. Therefore, we performed proteomic and transcriptomic research to unveil the oncogenic mechanism of EZH2. Immunoprecipitation and mass spectrometry were used to identify proteins that co-precipitate with EZH2. We show that EZH2 binds to heterochromatin protein 1 binding protein 3 (HP1BP3) in GSCs and impairs the methylation of H3K9. Overexpression of HP1BP3 enhances the proliferation, self-renewal and temozolomide (TMZ) resistance of GBM cells. Furthermore, EZH2 and HP1BP3 co-activate WNT7B expression thereby increasing TMZ resistance and stemness of GBM cells. Importantly, inhibition of WNT7B autocrine via LGK974 effectively reverses the TMZ resistance. Our work clarifies a new oncogenic mechanism of EZH2 by which it interacts with HP1BP3 and epigenetically activates WNT7B thereby promoting TMZ resistance in GSCs. Our results provide a rationale for targeting WNT/β-catenin pathway as a promising strategy to overcome TMZ resistance in GSCs.
Collapse
|
7
|
ITRAQ-based quantitative proteomic analysis reveals that VPS35 promotes the expression of MCM2-7 genes in HeLa cells. Sci Rep 2022; 12:9700. [PMID: 35690672 PMCID: PMC9188599 DOI: 10.1038/s41598-022-13934-3] [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: 11/18/2021] [Accepted: 05/13/2022] [Indexed: 11/25/2022] Open
Abstract
Vacuolar protein sorting 35 (VPS35) is a major component of the retromer complex that regulates endosomal trafficking in eukaryotic cells. Recent studies have shown that VPS35 promotes tumor cell proliferation and affects the nuclear accumulation of its interacting partner. In this study, isobaric tags for relative and absolute quantitation (iTRAQ)-based mass spectrometry were used to measure the changes in nuclear protein abundance in VPS35-depleted HeLa cells. A total of 47 differentially expressed proteins were identified, including 27 downregulated and 20 upregulated proteins. Gene ontology (GO) analysis showed that the downregulated proteins included several minichromosome maintenance (MCM) proteins described as cell proliferation markers, and these proteins were present in the MCM2-7 complex, which is essential for DNA replication. Moreover, we validated that loss of VPS35 reduced the mRNA and protein expression of MCM2-7 genes. Notably, re-expression of VPS35 in VPS35 knockout HeLa cells rescued the expression of these genes. Functionally, we showed that VPS35 contributes to cell proliferation and maintenance of genomic stability of HeLa cells. Therefore, these findings reveal that VPS35 is involved in the regulation of MCM2-7 gene expression and establish a link between VPS35 and cell proliferation.
Collapse
|
8
|
Current Analytical Strategies in Studying Chromatin-Associated-Proteome (Chromatome). Molecules 2021; 26:molecules26216694. [PMID: 34771102 PMCID: PMC8588255 DOI: 10.3390/molecules26216694] [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: 10/07/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 11/25/2022] Open
Abstract
Chromatin is a dynamic structure comprising of DNA and proteins. Its unique nature not only help to pack the DNA tightly within the cell but also is pivotal in regulating gene expression DNA replication. Furthermore it also protects the DNA from being damaged. Various proteins are involved in making a specific complex within a chromatin and the knowledge about these interacting partners is helpful to enhance our understanding about the pathophysiology of various chromatin associated diseases. Moreover, it could also help us to identify new drug targets and design more effective remedies. Due to the existence of chromatin in different forms under various physiological conditions it is hard to develop a single strategy to study chromatin associated proteins under all conditions. In our current review, we tried to provide an overview and comparative analysis of the strategies currently adopted to capture the DNA bounded protein complexes and their mass spectrometric identification and quantification. Precise information about the protein partners and their function in the DNA-protein complexes is crucial to design new and more effective therapeutic molecules against chromatin associated diseases.
Collapse
|
9
|
Alsagaby SA, Brewis IA, Vijayakumar R, Alhumaydhi FA, Alwashmi AS, Alharbi NK, Al Abdulmonem W, Premanathan M, Pratt G, Fegan C, Pepper C, Brennan P. Proteomics-based identification of cancer-associated proteins in chronic lymphocytic leukaemia. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
|
10
|
Shang M, Weng L, Wu S, Liu B, Yin X, Wang Z, Mao A. HP1BP3 promotes tumor growth and metastasis by upregulating miR-23a to target TRAF5 in esophageal squamous cell carcinoma. Am J Cancer Res 2021; 11:2928-2943. [PMID: 34249436 PMCID: PMC8263663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/01/2021] [Indexed: 06/13/2023] Open
Abstract
HP1BP3, an ubiquitously expressed nuclear protein belonging to the H1 histone family of proteins, plays an important role in cell growth and viability. Recently, it was reported that HP1BP3 exclusively regulates miRNA biogenesis by enhancing transcriptional miRNA processing. Although HP1BP3 has previously been implicated in common cancer types, the mechanistic functions and effects of HP1BP3 and its role in the prognosis of esophageal squamous cell carcinoma (ESCC) remain unclear. Here, we report that ESCC tissues and cell lines show increased endogenous expression of HP1BP3. Knockdown of HP1BP3 in TE-1 cells significantly inhibited tumor growth and metastasis in vivo emphasizing its role in cell proliferation and invasion. In contrast, overexpression of HP1BP3 significantly enhanced tumor growth and metastasis in Eca-109 cells. Further, we found that HP1BP3 regulates these functions by upregulating miR-23a, which directly binds to the 3'UTR region of TRAF5 downstream to alter cell survival and proliferation. Our findings describe a role for HP1BP3 in promoting tumor growth and metastasis by upregulating miR-23a to target TRAF5 in esophageal cancer. This study provides novel insights into the potential of targeting miRNAs for therapy and as clinical markers for cancer progression.
Collapse
Affiliation(s)
- Mingyi Shang
- Department of Interventional Radiology, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
- Clinical Research Center, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Li Weng
- Department of Interventional Radiology, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
- Clinical Research Center, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Shaoqiu Wu
- Department of Interventional Radiology, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Bingyan Liu
- Department of Interventional Radiology, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Xiang Yin
- Department of Interventional Radiology, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Zhongmin Wang
- Clinical Research Center, Shanghai Jiao Tong University School of MedicineShanghai, China
- Department of Interventional Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Aiwu Mao
- Department of Interventional Radiology, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
- Clinical Research Center, Shanghai Jiao Tong University School of MedicineShanghai, China
| |
Collapse
|
11
|
Xie J, Lou Q, Zeng Y, Liang Y, Xie S, Xu Q, Yuan L, Wang J, Jiang L, Mou L, Lin D, Zhao M. Single-Cell Atlas Reveals Fatty Acid Metabolites Regulate the Functional Heterogeneity of Mesenchymal Stem Cells. Front Cell Dev Biol 2021; 9:653308. [PMID: 33912565 PMCID: PMC8075002 DOI: 10.3389/fcell.2021.653308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/09/2021] [Indexed: 12/28/2022] Open
Abstract
Bone marrow mesenchymal stem cells (MSCs) are widely used clinically due to their versatile roles in multipotency, immunomodulation, and hematopoietic stem cell (HSC) niche function. However, cellular heterogeneity limits MSCs in the consistency and efficacy of their clinical applications. Metabolism regulates stem cell function and fate decision; however, how metabolites regulate the functional heterogeneity of MSCs remains elusive. Here, using single-cell RNA sequencing, we discovered that fatty acid pathways are involved in the regulation of lineage commitment and functional heterogeneity of MSCs. Functional assays showed that a fatty acid metabolite, butyrate, suppressed the self-renewal, adipogenesis, and osteogenesis differentiation potential of MSCs with increased apoptosis. Conversely, butyrate supplement significantly promoted HSC niche factor expression in MSCs, which suggests that butyrate supplement may provide a therapeutic approach to enhance their HSC niche function. Overall, our work demonstrates that metabolites are essential to regulate the functional heterogeneity of MSCs.
Collapse
Affiliation(s)
- Jiayi Xie
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Qi Lou
- Shenzhen Lansi Institute of Artificial Intelligence in Medicine, Shenzhen, China.,The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People's Hospital, Shenzhen, China
| | - Yunxin Zeng
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yingying Liang
- Shenzhen Lansi Institute of Artificial Intelligence in Medicine, Shenzhen, China.,The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People's Hospital, Shenzhen, China
| | - Siyu Xie
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Quanhui Xu
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, China
| | - Lisha Yuan
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, China
| | - Jin Wang
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, China
| | - Linjia Jiang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lisha Mou
- Shenzhen Lansi Institute of Artificial Intelligence in Medicine, Shenzhen, China
| | - Dongjun Lin
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Meng Zhao
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.,Shenzhen Lansi Institute of Artificial Intelligence in Medicine, Shenzhen, China.,Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, China
| |
Collapse
|
12
|
Vinaiphat A, Low JK, Yeoh KW, Chng WJ, Sze SK. Application of Advanced Mass Spectrometry-Based Proteomics to Study Hypoxia Driven Cancer Progression. Front Oncol 2021; 11:559822. [PMID: 33708620 PMCID: PMC7940826 DOI: 10.3389/fonc.2021.559822] [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: 05/07/2020] [Accepted: 01/07/2021] [Indexed: 12/24/2022] Open
Abstract
Cancer is one of the largest contributors to the burden of chronic disease in the world and is the second leading cause of death globally. It is associated with episodes of low-oxygen stress (hypoxia or ischemia/reperfusion) that promotes cancer progression and therapeutic resistance. Efforts have been made in the past using traditional proteomic approaches to decipher oxygen deprivation stress-related mechanisms of the disease initiation and progression and to identify key proteins as a therapeutic target for the treatment and prevention. Despite the potential benefits of proteomic in translational research for the discovery of new drugs, the therapeutic outcome with this approach has not met expectations in clinical trials. This is mainly due to the disease complexity which possess a multifaceted molecular pathology. Therefore, novel strategies to identify and characterize clinically important sets of modulators and molecular events for multi-target drug discovery are needed. Here, we review important past and current studies on proteomics in cancer with an emphasis on recent pioneered labeling approaches in mass spectrometry (MS)-based systematic quantitative analysis to improve clinical success. We also discuss the results of the selected innovative publications that integrate advanced proteomic technologies (e.g. MALDI-MSI, pSILAC/SILAC/iTRAQ/TMT-LC-MS/MS, MRM-MS) for comprehensive analysis of proteome dynamics in different biosystems, including cell type, cell species, and subcellular proteome (i.e. secretome and chromatome). Finally, we discuss the future direction and challenges in the application of these technological advancements in mass spectrometry within the context of cancer and hypoxia.
Collapse
Affiliation(s)
- Arada Vinaiphat
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jee Keem Low
- Department of Surgery, Tan Tock Seng Hospital, Singapore, Singapore
| | - Kheng Wei Yeoh
- Department of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Wee Joo Chng
- Department of Hematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
13
|
Roles of HIF and 2-Oxoglutarate-Dependent Dioxygenases in Controlling Gene Expression in Hypoxia. Cancers (Basel) 2021; 13:cancers13020350. [PMID: 33477877 PMCID: PMC7832865 DOI: 10.3390/cancers13020350] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that such dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. Abstract Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. We highlight the relevance of HIF and 2-OGDs in the control of gene expression in response to hypoxia and their relevance to human biology and health.
Collapse
|
14
|
Shi G, Hu Y, Zhu X, Jiang Y, Pang J, Wang C, Huang W, Zhao Y, Ma W, Liu D, Huang J, Songyang Z. A critical role of telomere chromatin compaction in ALT tumor cell growth. Nucleic Acids Res 2020; 48:6019-6031. [PMID: 32379321 PMCID: PMC7293046 DOI: 10.1093/nar/gkaa224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/17/2020] [Accepted: 04/18/2020] [Indexed: 01/15/2023] Open
Abstract
ALT tumor cells often contain abundant DNA damage foci at telomeres and rely on the alternative lengthening of telomeres (ALT) mechanism to maintain their telomeres. How the telomere chromatin is regulated and maintained in these cells remains largely unknown. In this study, we present evidence that heterochromatin protein 1 binding protein 3 (HP1BP3) can localize to telomeres and is particularly enriched on telomeres in ALT cells. HP1BP3 inhibition led to preferential growth inhibition of ALT cells, which was accompanied by telomere chromatin decompaction, increased presence of C-circles, more pronounced ALT-associated phenotypes and elongated telomeres. Furthermore, HP1BP3 appeared to participate in regulating telomere histone H3K9me3 epigenetic marks. Taken together, our data suggest that HP1BP3 functions on telomeres to maintain telomere chromatin and represents a novel target for inhibiting ALT cancer cells.
Collapse
Affiliation(s)
- Guang Shi
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yang Hu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xing Zhu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanling Jiang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Junjie Pang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chuanle Wang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenjun Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenbin Ma
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Dan Liu
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA 77030
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA 77030.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| |
Collapse
|
15
|
Belrose JL, Prasad A, Sammons MA, Gibbs KM, Szaro BG. Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons. BMC Genomics 2020; 21:540. [PMID: 32758133 PMCID: PMC7430912 DOI: 10.1186/s12864-020-06954-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The South African claw-toed frog, Xenopus laevis, is uniquely suited for studying differences between regenerative and non-regenerative responses to CNS injury within the same organism, because some CNS neurons (e.g., retinal ganglion cells after optic nerve crush (ONC)) regenerate axons throughout life, whereas others (e.g., hindbrain neurons after spinal cord injury (SCI)) lose this capacity as tadpoles metamorphose into frogs. Tissues from these CNS regions (frog ONC eye, tadpole SCI hindbrain, frog SCI hindbrain) were used in a three-way RNA-seq study of axotomized CNS axons to identify potential core gene expression programs for successful CNS axon regeneration. RESULTS Despite tissue-specific changes in expression dominating the injury responses of each tissue, injury-induced changes in gene expression were nonetheless shared between the two axon-regenerative CNS regions that were not shared with the non-regenerative region. These included similar temporal patterns of gene expression and over 300 injury-responsive genes. Many of these genes and their associated cellular functions had previously been associated with injury responses of multiple tissues, both neural and non-neural, from different species, thereby demonstrating deep phylogenetically conserved commonalities between successful CNS axon regeneration and tissue regeneration in general. Further analyses implicated the KEGG adipocytokine signaling pathway, which links leptin with metabolic and gene regulatory pathways, and a novel gene regulatory network with genes regulating chromatin accessibility at its core, as important hubs in the larger network of injury response genes involved in successful CNS axon regeneration. CONCLUSIONS This study identifies deep, phylogenetically conserved commonalities between CNS axon regeneration and other examples of successful tissue regeneration and provides new targets for studying the molecular underpinnings of successful CNS axon regeneration, as well as a guide for distinguishing pro-regenerative injury-induced changes in gene expression from detrimental ones in mammals.
Collapse
Affiliation(s)
- Jamie L Belrose
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Aparna Prasad
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Morgan A Sammons
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Kurt M Gibbs
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, 40351, USA
| | - Ben G Szaro
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.
| |
Collapse
|
16
|
Tahir MS, Nguyen LT, Schulz BL, Boe-Hansen GA, Thomas MG, Moore SS, Lau LY, Fortes MRS. Proteomics Recapitulates Ovarian Proteins Relevant to Puberty and Fertility in Brahman Heifers ( Bos indicus L.). Genes (Basel) 2019; 10:E923. [PMID: 31726744 PMCID: PMC6895798 DOI: 10.3390/genes10110923] [Citation(s) in RCA: 9] [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: 10/22/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022] Open
Abstract
High fertility and early puberty in Bos indicus heifers are desirable and genetically correlated traits in beef production. The hypothalamus-pituitary-ovarian (HPO) axis synthesizes steroid hormones, which contribute to the shift from the pre-pubertal state into the post-pubertal state and influence subsequent fertility. Understanding variations in abundance of proteins that govern steroid synthesis and ovarian signaling pathways remains crucial to understanding puberty and fertility. We used whole ovaries of six pre-pubertal and six post-pubertal Brahman heifers to conduct differential abundance analyses of protein profiles between the two physiological states. Extracted proteins were digested into peptides followed by identification and quantification with massspectrometry (MS) by sequential window acquisition of all instances of theoretical fragment ion mass spectrometry (SWATH-MS). MS and statistical analysis identified 566 significantly differentially abundant (DA) proteins (adjusted p < 0.05), which were then analyzed for gene ontology and pathway enrichment. Our data indicated an up-regulation of steroidogenic proteins contributing to progesterone synthesis at luteal phase post-puberty. Proteins related to progesterone signaling, TGF-β, retinoic acid, extracellular matrix, cytoskeleton, and pleiotrophin signaling were DA in this study. The DA proteins probably relate to the formation and function of the corpus luteum, which is only present after ovulation, post-puberty. Some DA proteins might also be related to granulosa cells signaling, which regulates oocyte maturation or arrest in ovaries prior to ovulation. Ten DA proteins were coded by genes previously associated with reproductive traits according to the animal quantitative trait loci (QTL) database. In conclusion, the DA proteins and their pathways were related to ovarian activity in Bos indicus cattle. The genes that code for these proteins may explain some known QTLs and could be targeted in future genetic studies.
Collapse
Affiliation(s)
- Muhammad S. Tahir
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia; (M.S.T.); (B.L.S.); (L.Y.L.)
| | - Loan T. Nguyen
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Queensland, Australia; (L.T.N.); (S.S.M.)
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia; (M.S.T.); (B.L.S.); (L.Y.L.)
| | - Gry A. Boe-Hansen
- School of Veterinary Sciences, University of Queensland, Brisbane 4343, Queensland, Australia;
| | - Milton G. Thomas
- Department of Animal Science, Colorado State University, Fort Collins, CO 80523, USA;
| | - Stephen S. Moore
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Queensland, Australia; (L.T.N.); (S.S.M.)
| | - Li Yieng Lau
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia; (M.S.T.); (B.L.S.); (L.Y.L.)
| | - Marina R. S. Fortes
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia; (M.S.T.); (B.L.S.); (L.Y.L.)
| |
Collapse
|
17
|
van Mierlo G, Wester RA, Marks H. A Mass Spectrometry Survey of Chromatin-Associated Proteins in Pluripotency and Early Lineage Commitment. Proteomics 2019; 19:e1900047. [PMID: 31219242 DOI: 10.1002/pmic.201900047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/07/2019] [Indexed: 12/12/2022]
Abstract
Pluripotency can be captured in vitro in the form of Embryonic Stem Cells (ESCs). These ESCs can be either maintained in the unrestricted "naïve" state of pluripotency, adapted to developmentally more constrained "primed" pluripotency or differentiated towards each of the three germ layers. Epigenetic protein complexes and transcription factors have been shown to specify and instruct transitions from ESCs to distinct cell states. In this study, proteomic profiling of the chromatin landscape by chromatin enrichment for proteomics (ChEP) is used in mouse naive pluripotent ESCs, primed pluripotent Epiblast stem cells (EpiSCs), and cells in early stages of differentiation. A comprehensive overview of epigenetic protein complexes associated with the chromatin is provided and proteins associated with the maintenance and loss of pluripotency are identified. The data reveal major compositional alterations of epigenetic complexes during priming and differentiation of naïve pluripotent ESCs. These results contribute to the understanding of ESC differentiation and provide a framework for future studies of lineage commitment of ESCs.
Collapse
Affiliation(s)
- Guido van Mierlo
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands.,Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Roelof Alexander Wester
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands
| |
Collapse
|
18
|
Irmak D, Fatima A, Gutiérrez-Garcia R, Rinschen MM, Wagle P, Altmüller J, Arrigoni L, Hummel B, Klein C, Frese CK, Sawarkar R, Rada-Iglesias A, Vilchez D. Mechanism suppressing H3K9 trimethylation in pluripotent stem cells and its demise by polyQ-expanded huntingtin mutations. Hum Mol Genet 2019; 27:4117-4134. [PMID: 30452683 DOI: 10.1093/hmg/ddy304] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023] Open
Abstract
Pluripotent stem cells are invaluable resources to study development and disease, holding a great promise for regenerative medicine. Here we use human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) from patients with Huntington's disease (HD-iPSCs) to shed light into the normal function of huntingtin (HTT) and its demise in disease. We find that HTT binds ATF7IP, a regulator of the histone H3 methyltransferase SETDB1. HTT inhibits the interaction of the ATF7IP-SETDB1 complex with other heterochromatin regulators and transcriptional repressors, maintaining low levels of H3K9 trimethylation (H3K9me3) in hESCs. Loss of HTT promotes global increased H3K9me3 levels and enrichment of H3K9me3 marks at distinct genes, including transcriptional regulators of neuronal differentiation. Although these genes are normally expressed at low amounts in hESCs, HTT knockdown (KD) reduces their induction during neural differentiation. Notably, mutant expanded polyglutamine repeats in HTT diminish its interaction with ATF7IP-SETDB1 complex and trigger H3K9me3 in HD-iPSCs. Conversely, KD of ATF7IP in HD-iPSCs reduces H3K9me3 alterations and ameliorates gene expression changes in their neural counterparts. Taken together, our results indicate ATF7IP as a potential target to correct aberrant H3K9me3 levels induced by mutant HTT.
Collapse
Affiliation(s)
- Dilber Irmak
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Azra Fatima
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Ricardo Gutiérrez-Garcia
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Markus M Rinschen
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Prerana Wagle
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Janine Altmüller
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Strasse 21, Cologne, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Corinna Klein
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Christian K Frese
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| | - Ritwick Sawarkar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Alvaro Rada-Iglesias
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Strasse 21, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany
| |
Collapse
|
19
|
Neuner SM, Ding S, Kaczorowski CC. Knockdown of heterochromatin protein 1 binding protein 3 recapitulates phenotypic, cellular, and molecular features of aging. Aging Cell 2019; 18:e12886. [PMID: 30549219 PMCID: PMC6351847 DOI: 10.1111/acel.12886] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/25/2018] [Accepted: 11/10/2018] [Indexed: 12/12/2022] Open
Abstract
Identifying genetic factors that modify an individual's susceptibility to cognitive decline in aging is critical to understanding biological processes involved and mitigating risk associated with a number of age‐related disorders. Recently, heterochromatin protein 1 binding protein 3 (Hp1bp3) was identified as a mediator of cognitive aging. Here, we provide a mechanistic explanation for these findings and show that targeted knockdown of Hp1bp3 in the hippocampus by 50%–75% is sufficient to induce cognitive deficits and transcriptional changes reminiscent of those observed in aging and Alzheimer's disease brains. Specifically, neuroinflammatory‐related pathways become activated following Hp1bp3 knockdown in combination with a robust decrease in genes involved in synaptic activity and neuronal function. To test the hypothesis that Hp1bp3 mediates susceptibility to cognitive deficits via a role in neuronal excitability, we performed slice electrophysiology demonstrate transcriptional changes after Hp1bp3 knockdown manifest functionally as a reduction in hippocampal neuronal intrinsic excitability and synaptic plasticity. In addition, as Hp1bp3 is a known mediator of miRNA biogenesis, here we profile the miRNA transcriptome and identify mir‐223 as a putative regulator of a portion of observed mRNA changes, particularly those that are inflammatory‐related. In summary, work here identifies Hp1bp3 as a critical mediator of aging‐related changes at the phenotypic, cellular, and molecular level and will help inform the development of therapeutics designed to target either Hp1bp3 or its downstream effectors in order to promote cognitive longevity.
Collapse
Affiliation(s)
- Sarah M. Neuner
- The Jackson Laboratory Bar Harbor Maine
- Neuroscience Institute University of Tennessee Health Science Center Memphis Tennessee
| | | | | |
Collapse
|
20
|
Voigt J, Malone DFG, Dias J, Leeansyah E, Björkström NK, Ljunggren HG, Gröbe L, Klawonn F, Heyner M, Sandberg JK, Jänsch L. Proteome analysis of human CD56 neg NK cells reveals a homogeneous phenotype surprisingly similar to CD56 dim NK cells. Eur J Immunol 2018; 48:1456-1469. [PMID: 29999523 DOI: 10.1002/eji.201747450] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/07/2018] [Accepted: 07/03/2018] [Indexed: 12/30/2022]
Abstract
NK cells lacking CD56 (CD56neg ) were first identified in chronic HIV-1 infection. However, CD56neg NK cells also exist in healthy individuals, albeit in significantly lower numbers. Here, we provide an extensive proteomic characterisation of human CD56neg peripheral blood NK cells of healthy donors and compare them to their CD56dim and CD56bright counterparts. Unbiased large-scale surface receptor profiling clustered CD56neg cells as part of the main NK cell compartment and indicated an overall CD56dim -like phenotype. Total proteome analyses of CD56neg NK cells further confirmed their similarity with CD56dim NK cells, and revealed a complete cytolytic inventory with high levels of perforin and granzyme H and M. In the present study, twelve proteins discriminated CD56neg NK cells from CD56dim NK cells with nine up-regulated and three down-regulated proteins in the CD56neg NK cell population. Those proteins were functionally related to lytic granule composition and transport, interaction with the extracellular matrix, DNA transcription or repair, and proliferation. Corroborating these results, CD56neg NK cells showed modest cytotoxicity, degranulation, and IFN-ɣ secretion as compared to CD56dim NK cells. In conclusion, CD56neg NK cells constitute functionally competent cells sharing many features of bona fide CD56dim NK cells in healthy individuals, but with some distinct characteristics.
Collapse
Affiliation(s)
- Jenny Voigt
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - David F G Malone
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Joana Dias
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Edwin Leeansyah
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lothar Gröbe
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Frank Klawonn
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Department of Computer Science, Ostfalia University of Applied Sciences, Wolfenbuettel, Germany
| | - Maxi Heyner
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lothar Jänsch
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| |
Collapse
|
21
|
Dutta B, Park JE, Qing ITY, Kon OL, Sze SK. Soy-Derived Phytochemical Genistein Modifies Chromatome Topology to Restrict Cancer Cell Proliferation. Proteomics 2018; 18:e1700474. [PMID: 29963755 DOI: 10.1002/pmic.201700474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/22/2018] [Indexed: 12/18/2022]
Abstract
Epidemiological data indicate that human cancer risk is significantly reduced by the consumption of soy-based foods containing the "phytoestrogen" genistein, which can signal via host cell estrogen receptors. While additional chemoprotective effects of genistein induced by epigenetic factors have also been reported, the key molecules and mechanisms involved are poorly defined. We therefore investigated genistein effects on chromatin-bound proteins in the estrogen receptor-deficient cell line MDA-MB-231 which is insensitive to phytoestrogen signaling. After exposure to low-dose genistein for >1 month, MDA-MB-231 cells exhibited stable epigenetic alterations that are analyzed via partial MNase digestion and TMT-based quantitative proteomics. 3177 chromatin-bound proteins are identified with high confidence, including 882 molecules that displayed altered binding topology after cell conditioning with genistein. Prolonged phytochemical exposure conferred heritable changes in the binding topology of key epigenetic regulators including ATRX, SUV39H1/H2, and HP1BP3 that are preserved in untreated progeny, resulting in sustained downregulation of proliferation genes and reduced cell growth. These data indicate that soy derivative genistein exerts complex estrogen receptor-independent effects on the epigenome likely to influence tumorigenesis by restricting cell growth.
Collapse
Affiliation(s)
- Bamaprasad Dutta
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jung Eun Park
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Ivan Toh Yi Qing
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Oi Lian Kon
- Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| |
Collapse
|
22
|
Serra A, Gallart-Palau X, Dutta B, Sze SK. Online Removal of Sodium Dodecyl Sulfate via Weak Cation Exchange in Liquid Chromatography–Mass Spectrometry Based Proteomics. J Proteome Res 2018; 17:2390-2400. [DOI: 10.1021/acs.jproteome.8b00156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Aida Serra
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Xavier Gallart-Palau
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Bamaprasad Dutta
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| |
Collapse
|
23
|
King BL, Rosenstein MC, Smith AM, Dykeman CA, Smith GA, Yin VP. RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa. NPJ Regen Med 2018; 3:10. [PMID: 29872545 PMCID: PMC5973935 DOI: 10.1038/s41536-018-0049-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/17/2018] [Accepted: 05/04/2018] [Indexed: 12/16/2022] Open
Abstract
Regeneration is an endogenous process of tissue repair that culminates in complete restoration of tissue and organ function. While regenerative capacity in mammals is limited to select tissues, lower vertebrates like zebrafish and salamanders are endowed with the capacity to regenerate entire limbs and most adult tissues, including heart muscle. Numerous profiling studies have been conducted using these research models in an effort to identify the genetic circuits that accompany tissue regeneration. Most of these studies, however, are confined to an individual injury model and/or research organism and focused primarily on protein encoding transcripts. Here we describe RegenDbase, a new database with the functionality to compare and contrast gene regulatory pathways within and across tissues and research models. RegenDbase combines pipelines that integrate analysis of noncoding RNAs in combination with protein encoding transcripts. We created RegenDbase with a newly generated comprehensive dataset for adult zebrafish heart regeneration combined with existing microarray and RNA-sequencing studies on multiple injured tissues. In this current release, we detail microRNA-mRNA regulatory circuits and the biological processes these interactions control during the early stages of heart regeneration. Moreover, we identify known and putative novel lncRNAs and identify their potential target genes based on proximity searches. We postulate that these candidate factors underscore robust regenerative capacity in lower vertebrates. RegenDbase provides a systems-level analysis of tissue regeneration genetic circuits across injury and animal models and addresses the growing need to understand how noncoding RNAs influence these changes in gene expression.
Collapse
Affiliation(s)
- Benjamin L. King
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469 USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469 USA
| | - Michael C. Rosenstein
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Present Address: RockStep Solutions, Portland, ME 04101 USA
| | - Ashley M. Smith
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
| | - Christina A. Dykeman
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
| | - Grace A. Smith
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469 USA
- University of Maine Honors College, University of Maine, Orono, ME 04469 USA
| | - Viravuth P. Yin
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469 USA
| |
Collapse
|
24
|
Batie M, Del Peso L, Rocha S. Hypoxia and Chromatin: A Focus on Transcriptional Repression Mechanisms. Biomedicines 2018; 6:biomedicines6020047. [PMID: 29690561 PMCID: PMC6027312 DOI: 10.3390/biomedicines6020047] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/26/2018] [Accepted: 04/19/2018] [Indexed: 12/20/2022] Open
Abstract
Hypoxia or reduced oxygen availability has been studied extensively for its ability to activate specific genes. Hypoxia-induced gene expression is mediated by the HIF transcription factors, but not exclusively so. Despite the extensive knowledge about how hypoxia activates genes, much less is known about how hypoxia promotes gene repression. In this review, we discuss the potential mechanisms underlying hypoxia-induced transcriptional repression responses. We highlight HIF-dependent and independent mechanisms as well as the potential roles of dioxygenases with functions at the nucleosome and DNA level. Lastly, we discuss recent evidence regarding the involvement of transcriptional repressor complexes in hypoxia.
Collapse
Affiliation(s)
- Michael Batie
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L697ZB, UK.
| | - Luis Del Peso
- Department of Biochemistry, Institute of Biomedical Research, Autonomous Madrid University, Arturo Duperier, 4. 28029 Madrid, Spain.
| | - Sonia Rocha
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L697ZB, UK.
| |
Collapse
|
25
|
Liu H, Zhang L, Wei Q, Shi Z, Shi X, Du J, Huang C, Zhang Y, Guo Z. Comprehensive Proteomic Analysis of PGC7-Interacting Proteins. J Proteome Res 2017; 16:3113-3123. [PMID: 28712289 DOI: 10.1021/acs.jproteome.6b00883] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Primordial germ cell 7 (PGC7), a maternal factor essential for early development, plays a critical role in the regulation of DNA methylation, transcriptional repression, chromatin condensation, and cell division and the maintenance of cell pluripotentiality. Despite the fundamental roles of PGC7 in these cellular processes, only a few molecular and functional interactions of PGC7 have been reported. Here, a streptavidin-biotin affinity purification technique combined with LC-MS/MS was used to analyze potential proteins that interact with PGC7. In total, 291 potential PGC7-interacting proteins were identified. Through an in-depth bioinformatic analysis of potential interactors, we linked PGC7 to critical cellular processes including translation, RNA processing, cell cycle, and regulation of heterochromatin structure. To better understand the functional interactions of PGC7 with its potential interactors, we constructed a protein-protein interaction network using the STRING database. In addition, we discussed in detail the interactions between PGC7 and some of its newly validated partners. The identification of these potential interactors of PGC7 expands our knowledge on the PGC7 interactome and provides a valuable resource for understanding the diverse functions of this protein.
Collapse
Affiliation(s)
- Hongliang Liu
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Lei Zhang
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Qing Wei
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Zhaopeng Shi
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Xiaoyan Shi
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China.,Medical Experiment Center of Shaanxi University of Chinese Medicine , Xianyang, Shaanxi 712000, China
| | - Juan Du
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China.,Medicine School of Yan'an University , Yan'an, Shaanxi 716000, China
| | - Chenyang Huang
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Zekun Guo
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| |
Collapse
|
26
|
Xu D, Yang Q, Cui M, Zhang Q. The novel transcriptional factor HP1BP3 negatively regulates Hsp70 transcription in Crassostrea hongkongensis. Sci Rep 2017; 7:1401. [PMID: 28469151 PMCID: PMC5431216 DOI: 10.1038/s41598-017-01573-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/29/2017] [Indexed: 11/29/2022] Open
Abstract
ChHP1BP3, a chromatin complex-related protein known with dynamic features, was identified as a ChHsp70 promoter-associated factor in Crassostrea hongkongensis by DNA-affinity purification and mass spectrometry analysis. Direct interaction between purified ChHP1BP3 and the ChHsp70 promoter region was demonstrated using EMSA. ChHp1bp3 depletion led to clear enhancements in ChHsp70 mRNA expression in C. hongkongensis hemocytes. However, ChHp1bp3 overexpression in heterologous HEK293T cells correlated with fluctuations in ChHsp70 transcription. Quantitative RT-PCR analysis showed that both ChHsp70 and ChHp1bp3 transcription were responsive to external physical/chemical stresses by heat, CdCl2 and NP. This indicated a plausible correlation between ChHsp70 and ChHp1bp3 in the stress-induced genetic regulatory pathway. While, the distinctive ChHp1bp3 expression patterns upon physical and chemical stresses suggest that the mechanisms that mediate ChHp1bp3 induction might be stress-specific. This study discovered a novel role for HP1BP3 as a negative regulator in controlling Hsp70 transcription in C. hongkongensis, and contributed to better understanding the complex regulatory mechanisms governing Hsp70 transcription.
Collapse
Affiliation(s)
- Delin Xu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China
| | - Qin Yang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China
| | - Miao Cui
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China.
| | - Qizhong Zhang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China.
| |
Collapse
|
27
|
Hollerer I, Curk T, Haase B, Benes V, Hauer C, Neu-Yilik G, Bhuvanagiri M, Hentze MW, Kulozik AE. The differential expression of alternatively polyadenylated transcripts is a common stress-induced response mechanism that modulates mammalian mRNA expression in a quantitative and qualitative fashion. RNA (NEW YORK, N.Y.) 2016; 22:1441-1453. [PMID: 27407180 PMCID: PMC4986898 DOI: 10.1261/rna.055657.115] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
Stress adaptation plays a pivotal role in biological processes and requires tight regulation of gene expression. In this study, we explored the effect of cellular stress on mRNA polyadenylation and investigated the implications of regulated polyadenylation site usage on mammalian gene expression. High-confidence polyadenylation site mapping combined with global pre-mRNA and mRNA expression profiling revealed that stress induces an accumulation of genes with differentially expressed polyadenylated mRNA isoforms in human cells. Specifically, stress provokes a global trend in polyadenylation site usage toward decreased utilization of promoter-proximal poly(A) sites in introns or ORFs and increased utilization of promoter-distal polyadenylation sites in intergenic regions. This extensively affects gene expression beyond regulating mRNA abundance by changing mRNA length and by altering the configuration of open reading frames. Our study highlights the impact of post-transcriptional mechanisms on stress-dependent gene regulation and reveals the differential expression of alternatively polyadenylated transcripts as a common stress-induced mechanism in mammalian cells.
Collapse
Affiliation(s)
- Ina Hollerer
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| | - Tomaz Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana 1001, Slovenia
| | - Bettina Haase
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Vladimir Benes
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Christian Hauer
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| | - Gabriele Neu-Yilik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| | - Madhuri Bhuvanagiri
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| |
Collapse
|
28
|
King BL, Yin VP. A Conserved MicroRNA Regulatory Circuit Is Differentially Controlled during Limb/Appendage Regeneration. PLoS One 2016; 11:e0157106. [PMID: 27355827 PMCID: PMC4927183 DOI: 10.1371/journal.pone.0157106] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/24/2016] [Indexed: 01/25/2023] Open
Abstract
Background Although regenerative capacity is evident throughout the animal kingdom, it is not equally distributed throughout evolution. For instance, complex limb/appendage regeneration is muted in mammals but enhanced in amphibians and teleosts. The defining characteristic of limb/appendage regenerative systems is the formation of a dedifferentiated tissue, termed blastema, which serves as the progenitor reservoir for regenerating tissues. In order to identify a genetic signature that accompanies blastema formation, we employ next-generation sequencing to identify shared, differentially regulated mRNAs and noncoding RNAs in three different, highly regenerative animal systems: zebrafish caudal fins, bichir pectoral fins and axolotl forelimbs. Results These studies identified a core group of 5 microRNAs (miRNAs) that were commonly upregulated and 5 miRNAs that were commonly downregulated, as well as 4 novel tRNAs fragments with sequences conserved with humans. To understand the potential function of these miRNAs, we built a network of 1,550 commonly differentially expressed mRNAs that had functional relationships to 11 orthologous blastema-associated genes. As miR-21 was the most highly upregulated and most highly expressed miRNA in all three models, we validated the expression of known target genes, including the tumor suppressor, pdcd4, and TGFβ receptor subunit, tgfbr2 and novel putative target genes such as the anti-apoptotic factor, bcl2l13, Choline kinase alpha, chka and the regulator of G-protein signaling, rgs5. Conclusions Our extensive analysis of RNA-seq transcriptome profiling studies in three regenerative animal models, that diverged in evolution ~420 million years ago, reveals a common miRNA-regulated genetic network of blastema genes. These comparative studies extend our current understanding of limb/appendage regeneration by identifying previously unassociated blastema genes and the extensive regulation by miRNAs, which could serve as a foundation for future functional studies to examine the process of natural cellular reprogramming in an injury context.
Collapse
Affiliation(s)
- Benjamin L. King
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island, Biological Laboratory, Salisbury Cove, Maine, United States of America
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine, United States of America
| | - Viravuth P. Yin
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island, Biological Laboratory, Salisbury Cove, Maine, United States of America
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine, United States of America
- * E-mail:
| |
Collapse
|
29
|
Neuner SM, Garfinkel BP, Wilmott LA, Ignatowska-Jankowska BM, Citri A, Orly J, Lu L, Overall RW, Mulligan MK, Kempermann G, Williams RW, O'Connell KMS, Kaczorowski CC. Systems genetics identifies Hp1bp3 as a novel modulator of cognitive aging. Neurobiol Aging 2016; 46:58-67. [PMID: 27460150 DOI: 10.1016/j.neurobiolaging.2016.06.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/07/2016] [Accepted: 06/11/2016] [Indexed: 12/13/2022]
Abstract
An individual's genetic makeup plays an important role in determining susceptibility to cognitive aging. Identifying the specific genes that contribute to cognitive aging may aid in early diagnosis of at-risk patients, as well as identify novel therapeutics targets to treat or prevent development of symptoms. Challenges to identifying these specific genes in human studies include complex genetics, difficulty in controlling environmental factors, and limited access to human brain tissue. Here, we identify Hp1bp3 as a novel modulator of cognitive aging using a genetically diverse population of mice and confirm that HP1BP3 protein levels are significantly reduced in the hippocampi of cognitively impaired elderly humans relative to cognitively intact controls. Deletion of functional Hp1bp3 in mice recapitulates memory deficits characteristic of aged impaired mice and humans, further supporting the idea that Hp1bp3 and associated molecular networks are modulators of cognitive aging. Overall, our results suggest Hp1bp3 may serve as a potential target against cognitive aging and demonstrate the utility of genetically diverse animal models for the study of complex human disease.
Collapse
Affiliation(s)
- Sarah M Neuner
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Benjamin P Garfinkel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Lynda A Wilmott
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Bogna M Ignatowska-Jankowska
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ami Citri
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Joseph Orly
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Lu Lu
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Rupert W Overall
- CRTD-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden 01307, Germany
| | - Megan K Mulligan
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Gerd Kempermann
- CRTD-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden 01307, Germany; German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden 01307, Germany
| | - Robert W Williams
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Kristen M S O'Connell
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Catherine C Kaczorowski
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| |
Collapse
|
30
|
Osborne L, Clive M, Kimmel M, Gispen F, Guintivano J, Brown T, Cox O, Judy J, Meilman S, Braier A, Beckmann MW, Kornhuber J, Fasching PA, Goes F, Payne JL, Binder EB, Kaminsky Z. Replication of Epigenetic Postpartum Depression Biomarkers and Variation with Hormone Levels. Neuropsychopharmacology 2016; 41:1648-58. [PMID: 26503311 PMCID: PMC4832028 DOI: 10.1038/npp.2015.333] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/02/2015] [Accepted: 09/18/2015] [Indexed: 11/09/2022]
Abstract
DNA methylation variation at HP1BP3 and TTC9B is modified by estrogen exposure in the rodent hippocampus and was previously shown to be prospectively predictive of postpartum depression (PPD) when modeled in antenatal blood. The objective of this study was to replicate the predictive efficacy of the previously established model in women with and without a previous psychiatric diagnosis and to understand the effects of changing hormone levels on PPD biomarker loci. Using a statistical model trained on DNA methylation data from N=51 high-risk women, we prospectively predicted PPD status in an independent N=51 women using first trimester antenatal gene expression levels of HP1BP3 and TTC9B, with an area under the receiver operator characteristic curve (AUC) of 0.81 (95% CI: 0.69-0.92, p<5 × 10(-4)). Modeling DNA methylation of these genes in N=240 women without a previous psychiatric diagnosis resulted in a cross-sectional prediction of PPD status with an AUC of 0.81 (95% CI: 0.68-0.93, p=0.01). TTC9B and HP1BP3 DNA methylation at early antenatal time points showed moderate evidence for association to the change in estradiol and allopregnanolone over the course of pregnancy, suggesting that epigenetic variation at these loci may be important for mediating hormonal sensitivity. In addition both loci showed PPD-specific trajectories with age, possibly mediated by age-associated hormonal changes. The data add to the growing body of evidence suggesting that PPD is mediated by differential gene expression and epigenetic sensitivity to pregnancy hormones and that modeling proxies of this sensitivity enable accurate prediction of PPD.
Collapse
Affiliation(s)
- Lauren Osborne
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Makena Clive
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mary Kimmel
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fiona Gispen
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jerry Guintivano
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tori Brown
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olivia Cox
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer Judy
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Samantha Meilman
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aviva Braier
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Johannes Kornhuber
- Department of Psychiatry, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Fernando Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer L Payne
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Zachary Kaminsky
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA,The Mood Disorder Center, Johns Hopkins University, 720 Rutland Avenue, Ross Research Building 1070, Baltimore, MD 21205, USA, Tel: +1 443 287 0093, Fax: +1 410 502 0065,E-mail:
| |
Collapse
|
31
|
Maekawa R, Lee L, Okada M, Asada H, Shinagawa M, Tamura I, Sato S, Tamura H, Sugino N. Changes in gene expression of histone modification enzymes in rat granulosa cells undergoing luteinization during ovulation. J Ovarian Res 2016; 9:15. [PMID: 26979106 PMCID: PMC4793631 DOI: 10.1186/s13048-016-0225-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/09/2016] [Indexed: 12/20/2022] Open
Abstract
Background The ovulatory LH surge rapidly alters the expression of steroidogenesis-related genes such as steroidogenic acute regulatory protein (StAR) in granulosa cells (GCs) undergoing luteinization. We recently reported that histone modifications contribute to these changes. Histone modifications are regulated by a variety of histone modification enzymes. This study investigated the changes in gene expression of histone modification enzymes in rat GCs undergoing luteinization after the induction of ovulation. The extracellular regulated kinase (ERK)-1/2 is a mediator in the intracellular signaling pathway stimulated by the ovulatory LH surge and regulates the expression of a number of genes in GCs. We further investigated whether ERK-1/2 is involved in the regulation of the histone modification at the StAR promoter region in GCs undergoing luteinization. Results GCs were obtained from rats treated with equine chorionic gonadotropin (CG) before (0 h) and after human (h) CG injection. The expressions of 84 genes regulating histone modifications or DNA methylation were measured using a PCR array. Five genes (HDAC4, HDAC10, EZH2, SETDB2, and CIITA) were identified as histone acetylation- or histone methylation-related genes, and were significantly altered after hCG injection. None of the genes were related to DNA methylation. mRNA levels of EZH2, SETDB2, HDAC4, and HDAC10 decreased and CIITA mRNA levels increased 4 or 12 h after hCG injection. GCs isolated after eCG injection were incubated with hCG for 4 h to induce luteinization. StAR mRNA levels were significantly increased by hCG accompanied by the increase in H3K4me3 of the StAR promoter region. StAR mRNA expression was inhibited by the ERK inhibitor with the significant decrease of H3K4me3. These results suggest that hCG increases StAR gene expression through the ERK-1/2-mediated signaling which is also associated with histone modification of the promoter region. Conclusions Gene expressions of histone modification enzymes change in GCs undergoing luteinization after ovulation induction. This change may play important roles in regulating the expression of various genes during the early stage of luteinization, which may be critical for the subsequent corpus luteum formation.
Collapse
Affiliation(s)
- Ryo Maekawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Lifa Lee
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Maki Okada
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Hiromi Asada
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Masahiro Shinagawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Isao Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Shun Sato
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Hiroshi Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Norihiro Sugino
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan.
| |
Collapse
|
32
|
Berthelot V, Mouta-Cardoso G, Hégarat N, Guillonneau F, François JC, Giovannangeli C, Praseuth D, Rusconi F. The human DNA ends proteome uncovers an unexpected entanglement of functional pathways. Nucleic Acids Res 2016; 44:4721-33. [PMID: 26921407 PMCID: PMC4889927 DOI: 10.1093/nar/gkw121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/17/2016] [Indexed: 01/06/2023] Open
Abstract
DNA ends get exposed in cells upon either normal or dysfunctional cellular processes or molecular events. Telomeres need to be protected by the shelterin complex to avoid junctions occurring between chromosomes while failing topoisomerases or clustered DNA damage processing may produce double-strand breaks, thus requiring swift repair to avoid cell death. The rigorous study of the great many proteins involved in the maintenance of DNA integrity is a challenging task because of the innumerous unspecific electrostatic and/or hydrophobic DNA—protein interactions that arise due to the chemical nature of DNA. We devised a technique that discriminates the proteins recruited specifically at DNA ends from those that bind to DNA because of a generic affinity for the double helix. Our study shows that the DNA ends proteome comprises proteins of an unexpectedly wide functional spectrum, ranging from DNA repair to ribosome biogenesis and cytoskeleton, including novel proteins of undocumented function. A global mapping of the identified proteome on published DNA repair protein networks demonstrated the excellent specificity and functional coverage of our purification technique. Finally, the native nucleoproteic complexes that assembled specifically onto DNA ends were shown to be endowed with a highly efficient DNA repair activity.
Collapse
Affiliation(s)
- Vivien Berthelot
- Laboratoire de chimie physique, UMR CNRS 8000, University of Paris-Sud, F-91400 Orsay, France
| | - Gildas Mouta-Cardoso
- Structure et Instabilité des Génomes, INSERM U1154, UMR CNRS/MNHN 7196, F-75005 Paris, France
| | - Nadia Hégarat
- Structure et Instabilité des Génomes, INSERM U1154, UMR CNRS/MNHN 7196, F-75005 Paris, France
| | - François Guillonneau
- Plateforme de spectrométrie de masse 3P5, Institut Cochin, F-75014 Paris, France
| | - Jean-Christophe François
- Inserm and Sorbonne Universities, UPMC, UMR_S 938, Research Center Saint-Antoine, F-75012 Paris, France
| | - Carine Giovannangeli
- Structure et Instabilité des Génomes, INSERM U1154, UMR CNRS/MNHN 7196, F-75005 Paris, France
| | - Danièle Praseuth
- Structure et Instabilité des Génomes, INSERM U1154, UMR CNRS/MNHN 7196, F-75005 Paris, France
| | - Filippo Rusconi
- Laboratoire de chimie physique, UMR CNRS 8000, University of Paris-Sud, F-91400 Orsay, France
| |
Collapse
|
33
|
Porter LF, Galli GG, Williamson S, Selley J, Knight D, Elcioglu N, Aydin A, Elcioglu M, Venselaar H, Lund AH, Bonshek R, Black GC, Manson FD. A role for repressive complexes and H3K9 di-methylation in PRDM5-associated brittle cornea syndrome. Hum Mol Genet 2015; 24:6565-79. [PMID: 26395458 PMCID: PMC4634368 DOI: 10.1093/hmg/ddv345] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 07/29/2015] [Accepted: 08/18/2015] [Indexed: 12/11/2022] Open
Abstract
Type 2 brittle cornea syndrome (BCS2) is an inherited connective tissue disease with a devastating ocular phenotype caused by mutations in the transcription factor PR domain containing 5 (PRDM5) hypothesized to exert epigenetic effects through histone and DNA methylation. Here we investigate clinical samples, including skin fibroblasts and retinal tissue from BCS2 patients, to elucidate the epigenetic role of PRDM5 and mechanisms of its dysregulation in disease. First we report abnormal retinal vascular morphology in the eyes of two cousins with BCS2 (PRDM5 Δ exons 9-14) using immunohistochemistry, and mine data from skin fibroblast expression microarrays from patients with PRDM5 mutations p.Arg590* and Δ exons 9-14, as well as from a PRDM5 ChIP-sequencing experiment. Gene ontology analysis of dysregulated PRDM5-target genes reveals enrichment for extracellular matrix (ECM) genes supporting vascular integrity and development. Q-PCR and ChIP-qPCR confirm upregulation of critical mediators of ECM stability in vascular structures (COL13A1, COL15A1, NTN1, CDH5) in patient fibroblasts. We identify H3K9 di-methylation (H3K9me2) at these PRDM5-target genes in fibroblasts, and demonstrate that the BCS2 mutation p.Arg83Cys diminishes interaction of PRDM5 with repressive complexes, including NuRD complex protein CHD4, and the repressive chromatin interactor HP1BP3, by co-immunoprecipitation combined with mass spectrometry. We observe reduced heterochromatin protein 1 binding protein 3 (HP1BP3) staining in the retinas of two cousins lacking exons 9-14 by immunohistochemistry, and dysregulated H3K9me2 in skin fibroblasts of three patients (p.Arg590*, p.Glu134* and Δ exons 9-14) by western blotting. These findings suggest that defective interaction of PRDM5 with repressive complexes, and dysregulation of H3K9me2, play a role in PRDM5-associated disease.
Collapse
Affiliation(s)
- Louise F Porter
- Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK, Manchester Royal Eye Hospital, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK, Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Giorgio G Galli
- Stem Cell Program, Boston Children's Hospital, Harvard Stem Cell and Regenerative Biology Department and Harvard Stem Cell Institute, Harvard University, Boston, MA, USA, Biotech Research and Innovation Centre and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Sally Williamson
- Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Julian Selley
- Faculty of Life Sciences, Michael Smith Building, Manchester, UK
| | - David Knight
- Faculty of Life Sciences, Michael Smith Building, Manchester, UK
| | - Nursel Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul, Turkey
| | - Ali Aydin
- Department of Ophthalmology, University of Medipol Medical Faculty, Istanbul, Turkey
| | - Mustafa Elcioglu
- Department of Ophthalmology, Okmeydani Research and Training Hospital, Istanbul, Turkey
| | - Hanka Venselaar
- Centre of Molecular and Biomolecular Informatics, Radboudumc Institute for Molecular Life Sciences, Nijmegen, The Netherlands and
| | - Anders H Lund
- Biotech Research and Innovation Centre and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Richard Bonshek
- Manchester Royal Eye Hospital, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK, National Ophthalmic Pathology Service Laboratory, Department of Histopathology, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Graeme C Black
- Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK, Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK
| | - Forbes D Manson
- Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| |
Collapse
|
34
|
Garfinkel BP, Melamed-Book N, Anuka E, Bustin M, Orly J. HP1BP3 is a novel histone H1 related protein with essential roles in viability and growth. Nucleic Acids Res 2015; 43:2074-90. [PMID: 25662603 PMCID: PMC4344522 DOI: 10.1093/nar/gkv089] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/17/2014] [Accepted: 01/23/2015] [Indexed: 12/28/2022] Open
Abstract
The dynamic architecture of chromatin is vital for proper cellular function, and is maintained by the concerted action of numerous nuclear proteins, including that of the linker histone H1 variants, the most abundant family of nucleosome-binding proteins. Here we show that the nuclear protein HP1BP3 is widely expressed in most vertebrate tissues and is evolutionarily and structurally related to the H1 family. HP1BP3 contains three globular domains and a highly positively charged C-terminal domain, resembling similar domains in H1. Fluorescence recovery after photobleaching (FRAP) studies indicate that like H1, binding of HP1BP3 to chromatin depends on both its C and N terminal regions and is affected by the cell cycle and post translational modifications. HP1BP3 contains functional motifs not found in H1 histones, including an acidic stretch and a consensus HP1-binding motif. Transcriptional profiling of HeLa cells lacking HP1BP3 showed altered expression of 383 genes, suggesting a role for HP1BP3 in modulation of gene expression. Significantly, Hp1bp3(-/-) mice present a dramatic phenotype with 60% of pups dying within 24 h of birth and the surviving animals exhibiting a lifelong 20% growth retardation. We suggest that HP1BP3 is a ubiquitous histone H1 like nuclear protein with distinct and non-redundant functions necessary for survival and growth.
Collapse
Affiliation(s)
- Benjamin P Garfinkel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Naomi Melamed-Book
- Bio-Imaging Unit, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Eli Anuka
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph Orly
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| |
Collapse
|
35
|
Gallart-Palau X, Serra A, Qian J, Chen CP, Kalaria RN, Sze SK. Temporal lobe proteins implicated in synaptic failure exhibit differential expression and deamidation in vascular dementia. Neurochem Int 2014; 80:87-98. [PMID: 25497727 DOI: 10.1016/j.neuint.2014.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/26/2014] [Accepted: 12/02/2014] [Indexed: 12/20/2022]
Abstract
Progressive synaptic failure precedes the loss of neurons and decline in cognitive function in neurodegenerative disorders, but the specific proteins and posttranslational modifications that promote synaptic failure in vascular dementia (VaD) remain largely unknown. We therefore used an isobaric tag for relative and absolute proteomic quantitation (iTRAQ) to profile the synapse-associated proteome of post-mortem human cortex from vascular dementia patients and age-matched controls. Brain tissue from VaD patients exhibited significant down-regulation of critical synaptic proteins including clathrin (0.29; p < 1.0⋅10(-3)) and GDI1 (0.51; p = 3.0⋅10(-3)), whereas SNAP25 (1.6; p = 5.5⋅10(-3)), bassoon (1.4; p = 1.3⋅10(-3)), excitatory amino acid transporter 2 (2.6; p = 9.2⋅10(-3)) and Ca(2+)/calmodulin dependent kinase II (1.6; p = 3.0⋅10(-2)) were substantially up-regulated. Our analyses further revealed divergent patterns of protein modification in the dementia patient samples, including a specific deamidation of synapsin1 predicted to compromise protein structure. Our results reveal potential molecular targets for intervention in synaptic failure and prevention of cognitive decline in VaD.
Collapse
Affiliation(s)
| | - Aida Serra
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jingru Qian
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Christopher P Chen
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Memory, Aging and Cognition Centre, National University Health System, Singapore
| | - Raj N Kalaria
- Institute for Ageing and Health, NIHR Biomedical Research Building, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, United Kingdom
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore.
| |
Collapse
|
36
|
Dutta B, Yan R, Lim SK, Tam JP, Sze SK. Quantitative profiling of chromatome dynamics reveals a novel role for HP1BP3 in hypoxia-induced oncogenesis. Mol Cell Proteomics 2014; 13:3236-49. [PMID: 25100860 DOI: 10.1074/mcp.m114.038232] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In contrast to the intensely studied genetic and epigenetic changes that induce host cell transformation to initiate tumor development, those that promote the malignant progression of cancer remain poorly defined. As emerging evidence suggests that the hypoxic tumor microenvironment could re-model the chromatin-associated proteome (chromatome) to induce epigenetic changes and alter gene expression in cancer cells, we hypothesized that hypoxia-driven evolution of the chromatome promotes malignant changes and the development of therapy resistance in tumor cells. To test this hypothesis, we isolated chromatins from tumor cells treated with varying conditions of normoxia, hypoxia, and re-oxygenation and then partially digested them with DNase I and analyzed them for changes in euchromatin- and heterochromatin-associated proteins using an iTRAQ-based quantitative proteomic approach. We identified a total of 1446 proteins with a high level of confidence, including 819 proteins that were observed to change their chromatin association topology under hypoxic conditions. These hypoxia-sensitive proteins included key mediators of chromatin organization, transcriptional regulation, and DNA repair. Furthermore, our proteomic and functional experiments revealed a novel role for the chromatin organizer protein HP1BP3 in mediating chromatin condensation during hypoxia, leading to increased tumor cell viability, radio-resistance, chemo-resistance, and self-renewal. Taken together, our findings indicate that HP1BP3 is a key mediator of tumor progression and cancer cell acquisition of therapy-resistant traits, and thus might represent a novel therapeutic target in a range of human malignancies.
Collapse
Affiliation(s)
- Bamaprasad Dutta
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr., Singapore 637551
| | - Ren Yan
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr., Singapore 637551
| | - Sai Kiang Lim
- §Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, Singapore 138648
| | - James P Tam
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr., Singapore 637551
| | - Siu Kwan Sze
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr., Singapore 637551;
| |
Collapse
|