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Lin J, Liu P, Sun K, Jiang L, Liu Y, Huang Y, Liu J, Shi M, Zhang J, Wang T, Shen B. Comprehensive analysis of KLF family reveals KLF6 as a promising prognostic and immune biomarker in pancreatic ductal adenocarcinoma. Cancer Cell Int 2024; 24:177. [PMID: 38773440 PMCID: PMC11106939 DOI: 10.1186/s12935-024-03369-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 05/11/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest tumors worldwide, with extremely aggressive and complicated biology. Krüppel-like factors (KLFs) encode a series of transcriptional regulatory proteins and play crucial roles in a variety of processes, including tumor cell differentiation and proliferation. However, the potential biological functions and possible pathways of KLFs in the progression of PDAC remain elusive. METHODS We systematically evaluated the transcriptional variations and expression patterns of KLFs in pancreatic cancer from the UCSC Xena. Based on difference analysis, the non-negative matrix factorization (NMF) algorithm was utilized to identify the immune characteristics and clinical significance of two different subtypes. The multivariate Cox regression was used to construct the risk model and then explore the differences in tumor immune microenvironment (TIME) and drug sensitivity between high and low groups. Through single-cell RNA sequencing (scRNA-seq) analysis, we screened KLF6 and further investigated its biological functions in pancreatic cancer and pan-cancer. RESULTS The KLFs exhibited differential expression and mutations in the transcriptomic profile of PDAC. According to the expression of KLFs, patients were classified into two distinct subtypes, each exhibiting significant differences in prognosis and TIME. Moreover, the KLF signature was developed using univariate Cox and Lasso regression, which proved to be a reliable and effective prognostic model. Furthermore, the KLF_Score was closely associated with immune infiltration, response to immunotherapy, and drug sensitivity and we screened small molecule compounds targeting prognostic genes separately. Through scRNA-seq analysis, KLF6 was selected to further demonstrate its role in the malignance of PC in vitro. Finally, pan-cancer analysis emphasized the biological significance of KLF6 in multiple types of tumors and its clinical utility in assessing cancer prognosis. CONCLUSION This study elucidated the pivotal role of KLF family genes in the malignant development of PC through comprehensive analysis and revealed that KLF6 would be a novel diagnostic biomolecule marker and potential therapeutic target for PDAC.
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Affiliation(s)
- Jiayu Lin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Pengyi Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Keyan Sun
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Lingxi Jiang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yang Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yishu Huang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jia Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Minmin Shi
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jun Zhang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Ting Wang
- Department of Pathology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, People's Republic of China.
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Chen ACY, Jaiswal S, Martinez D, Yerinde C, Ji K, Miranda V, Fung ME, Weiss SA, Zschummel M, Taguchi K, Garris CS, Mempel TR, Hacohen N, Sen DR. The aged tumor microenvironment limits T cell control of cancer. Nat Immunol 2024:10.1038/s41590-024-01828-7. [PMID: 38745085 DOI: 10.1038/s41590-024-01828-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/27/2024] [Indexed: 05/16/2024]
Abstract
The etiology and effect of age-related immune dysfunction in cancer is not completely understood. Here we show that limited priming of CD8+ T cells in the aged tumor microenvironment (TME) outweighs cell-intrinsic defects in limiting tumor control. Increased tumor growth in aging is associated with reduced CD8+ T cell infiltration and function. Transfer of T cells from young mice does not restore tumor control in aged mice owing to rapid induction of T cell dysfunction. Cell-extrinsic signals in the aged TME drive a tumor-infiltrating age-associated dysfunctional (TTAD) cell state that is functionally, transcriptionally and epigenetically distinct from canonical T cell exhaustion. Altered natural killer cell-dendritic cell-CD8+ T cell cross-talk in aged tumors impairs T cell priming by conventional type 1 dendritic cells and promotes TTAD cell formation. Aged mice are thereby unable to benefit from therapeutic tumor vaccination. Critically, myeloid-targeted therapy to reinvigorate conventional type 1 dendritic cells can improve tumor control and restore CD8+ T cell immunity in aging.
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Affiliation(s)
- Alex C Y Chen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Sneha Jaiswal
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniela Martinez
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Cansu Yerinde
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Keely Ji
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Velita Miranda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Megan E Fung
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sarah A Weiss
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Maria Zschummel
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Kazuhiro Taguchi
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher S Garris
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Thorsten R Mempel
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Nir Hacohen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Debattama R Sen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
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3
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Chen L, Li H, Liu X, Zhang N, Wang K, Shi A, Gao H, Akdis D, Saguner AM, Xu X, Osto E, Van de Veen W, Li G, Bayés-Genís A, Duru F, Song J, Li X, Hu S. PBX/Knotted 1 homeobox-2 (PKNOX2) is a novel regulator of myocardial fibrosis. Signal Transduct Target Ther 2024; 9:94. [PMID: 38644381 PMCID: PMC11033280 DOI: 10.1038/s41392-024-01804-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 02/08/2024] [Accepted: 03/13/2024] [Indexed: 04/23/2024] Open
Abstract
Much effort has been made to uncover the cellular heterogeneities of human hearts by single-nucleus RNA sequencing. However, the cardiac transcriptional regulation networks have not been systematically described because of the limitations in detecting transcription factors. In this study, we optimized a pipeline for isolating nuclei and conducting single-nucleus RNA sequencing targeted to detect a higher number of cell signal genes and an optimal number of transcription factors. With this unbiased protocol, we characterized the cellular composition of healthy human hearts and investigated the transcriptional regulation networks involved in determining the cellular identities and functions of the main cardiac cell subtypes. Particularly in fibroblasts, a novel regulator, PKNOX2, was identified as being associated with physiological fibroblast activation in healthy hearts. To validate the roles of these transcription factors in maintaining homeostasis, we used single-nucleus RNA-sequencing analysis of transplanted failing hearts focusing on fibroblast remodelling. The trajectory analysis suggested that PKNOX2 was abnormally decreased from fibroblast activation to pathological myofibroblast formation. Both gain- and loss-of-function in vitro experiments demonstrated the inhibitory role of PKNOX2 in pathological fibrosis remodelling. Moreover, fibroblast-specific overexpression and knockout of PKNOX2 in a heart failure mouse model induced by transverse aortic constriction surgery significantly improved and aggravated myocardial fibrosis, respectively. In summary, this study established a high-quality pipeline for single-nucleus RNA-sequencing analysis of heart muscle. With this optimized protocol, we described the transcriptional regulation networks of the main cardiac cell subtypes and identified PKNOX2 as a novel regulator in suppressing fibrosis and a potential therapeutic target for future translational studies.
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Affiliation(s)
- Liang Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Haotong Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Xiaorui Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Ningning Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Kui Wang
- School of Statistics and Data Science, Nankai University, Tianjin, China
| | - Anteng Shi
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Hang Gao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Deniz Akdis
- Department of Cardiology, University Heart Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Ardan M Saguner
- Department of Cardiology, University Heart Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Xinjie Xu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Elena Osto
- Department of Cardiology, University Heart Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Institute for Clinical Chemistry, University Hospital Zurich and University of Zürich, Zurich, Switzerland
| | - Willem Van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Guangyu Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Antoni Bayés-Genís
- Heart Institute, Hospital Universitari Germans Trias i Pujol, Badalona, CIBERCV, Spain
| | - Firat Duru
- Department of Cardiology, University Heart Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China.
| | - Xiangjie Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China.
| | - Shengshou Hu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China.
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4
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Shi Y, Yao M, Shen S, Wang L, Yao D. Abnormal expression of Krüppel-like transcription factors and their potential values in lung cancer. Heliyon 2024; 10:e28292. [PMID: 38560274 PMCID: PMC10979174 DOI: 10.1016/j.heliyon.2024.e28292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Lung cancer still is one of the most common malignancy tumors in the world. However, the mechanisms of its occurrence and development have not been fully elucidated. Zinc finger protein family (ZNFs) is the largest transcription factor family in human genome. Recently, the more and more basic and clinical evidences have confirmed that ZNFs/Krüppel-like factors (KLFs) refer to a group of conserved zinc finger-containing transcription factors that are involved in lung cancer progression, with the functions of promotion, inhibition, dual roles and unknown classifications. Based on the recent literature, some of the oncogenic KLFs are promising molecular biomarkers for diagnosis, prognosis or therapeutic targets of lung cancer. Interestingly, a novel computational approach has been proposed by using machine learning on features calculated from primary sequences, the XGBoost-based model with accuracy of 96.4 % is efficient in identifying KLF proteins. This paper reviews the recent some progresses of the oncogenic KLFs with their potential values for diagnosis, prognosis and molecular target in lung cancer.
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Affiliation(s)
- Yang Shi
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University & Department of Medical Immunology, Medical School of Nantong University, Nantong 226001, China
- Department of Thoracic Surgery, First People's Hospital of Yancheng, Yancheng 224001, China
| | - Min Yao
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University & Department of Medical Immunology, Medical School of Nantong University, Nantong 226001, China
| | - Shuijie Shen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University & Department of Medical Immunology, Medical School of Nantong University, Nantong 226001, China
| | - Li Wang
- Research Center for Intelligent Information Technology, Nantong University, Nantong 226019, Jiangsu, China
| | - Dengfu Yao
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University & Department of Medical Immunology, Medical School of Nantong University, Nantong 226001, China
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Malgulwar PB, Danussi C, Dharmaiah S, Johnson W, Singh A, Rai K, Rao A, Huse JT. Sirtuin 2 inhibition modulates chromatin landscapes genome-wide to induce senescence in ATRX-deficient malignant glioma. Neuro Oncol 2024; 26:55-67. [PMID: 37625115 PMCID: PMC10769000 DOI: 10.1093/neuonc/noad155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Functional inactivation of ATRX characterizes large subgroups of malignant gliomas in adults and children. ATRX deficiency in glioma induces widespread chromatin remodeling, driving transcriptional shifts and oncogenic phenotypes. Effective strategies to therapeutically target these broad epigenomic sequelae remain undeveloped. METHODS We utilized integrated multiomics and the Broad Institute Connectivity Map (CMAP) to identify drug candidates that could potentially revert ATRX-deficient transcriptional changes. We then employed disease-relevant experimental models to evaluate functional phenotypes, coupling these studies with epigenomic profiling to elucidate molecular mechanism(s). RESULTS CMAP analysis and transcriptional/epigenomic profiling implicated the Class III HDAC Sirtuin2 (SIRT2) as a central mediator of ATRX-deficient cellular phenotypes and a driver of unfavorable prognosis in ATRX-deficient glioma. SIRT2 inhibitors reverted Atrx-deficient transcriptional signatures in murine neuroepithelial progenitor cells (mNPCs), impaired cell migration in Atrx/ATRX-deficient mNPCs and human glioma stem cells (GSCs), and increased expression of senescence markers in glioma models. Moreover, SIRT2 inhibition impaired growth and increased senescence in ATRX-deficient GSCs in vivo. These effects were accompanied by genome-wide shifts in enhancer-associated H3K27ac and H4K16ac marks, with the latter in particular demonstrating compelling transcriptional links to SIRT2-dependent phenotypic reversals. Motif analysis of these data identified the transcription factor KLF16 as a mediator of phenotype reversal in Atrx-deficient cells upon SIRT2 inhibition. CONCLUSIONS Our findings indicate that SIRT2 inhibition selectively targets ATRX-deficient gliomas for senescence through global chromatin remodeling, while demonstrating more broadly a viable approach to combat complex epigenetic rewiring in cancer.
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Affiliation(s)
- Prit Benny Malgulwar
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Carla Danussi
- Sanofi, Research and Development, Cambridge, Massachusetts, USA
| | - Sharvari Dharmaiah
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - William Johnson
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anand Singh
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kunal Rai
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Arvind Rao
- Departments of Biostatistics, Computational Medicine and Bioinformatics, and Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason T Huse
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gordân R, Zeitlinger J, Kundaje A, Fordyce PM. Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science 2023; 381:eadd1250. [PMID: 37733848 DOI: 10.1126/science.add1250] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/26/2023] [Indexed: 09/23/2023]
Abstract
Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter gene expression, yet how they regulate transcription remains unknown. We found that STRs modulate transcription factor (TF)-DNA affinities and apparent on-rates by about 70-fold by directly binding TF DNA-binding domains, with energetic impacts exceeding many consensus motif mutations. STRs maximize the number of weakly preferred microstates near target sites, thereby increasing TF density, with impacts well predicted by statistical mechanics. Confirming that STRs also affect TF binding in cells, neural networks trained only on in vivo occupancies predicted effects identical to those observed in vitro. Approximately 90% of TFs preferentially bound STRs that need not resemble known motifs, providing a cis-regulatory mechanism to target TFs to genomic sites.
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Affiliation(s)
- Connor A Horton
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Amr M Alexandari
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Michael G B Hayes
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Emil Marklund
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julia M Schaepe
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Arjun K Aditham
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Nilay Shah
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Peter H Suzuki
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Avanti Shrikumar
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Ariel Afek
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Computer Science, Duke University, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- The University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Polly M Fordyce
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94110, USA
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7
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Salma M, Andrieu-Soler C, Deleuze V, Soler E. High-throughput methods for the analysis of transcription factors and chromatin modifications: Low input, single cell and spatial genomic technologies. Blood Cells Mol Dis 2023; 101:102745. [PMID: 37121019 DOI: 10.1016/j.bcmd.2023.102745] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023]
Abstract
Genome-wide analysis of transcription factors and epigenomic features is instrumental to shed light on DNA-templated regulatory processes such as transcription, cellular differentiation or to monitor cellular responses to environmental cues. Two decades of technological developments have led to a rich set of approaches progressively pushing the limits of epigenetic profiling towards single cells. More recently, disruptive technologies using innovative biochemistry came into play. Assays such as CUT&RUN, CUT&Tag and variations thereof show considerable potential to survey multiple TFs or histone modifications in parallel from a single experiment and in native conditions. These are in the path to become the dominant assays for genome-wide analysis of TFs and chromatin modifications in bulk, single-cell, and spatial genomic applications. The principles together with pros and cons are discussed.
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Affiliation(s)
- Mohammad Salma
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France
| | - Charlotte Andrieu-Soler
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France
| | - Virginie Deleuze
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France
| | - Eric Soler
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France.
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8
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Sweet DR, Padmanabhan R, Liao X, Dashora HR, Tang X, Nayak L, Jain R, De Val S, Vinayachandran V, Jain MK. Krüppel-Like Factors Orchestrate Endothelial Gene Expression Through Redundant and Non-Redundant Enhancer Networks. J Am Heart Assoc 2023; 12:e024303. [PMID: 36789992 PMCID: PMC10111506 DOI: 10.1161/jaha.121.024303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Background Proper function of endothelial cells is critical for vascular integrity and organismal survival. Studies over the past 2 decades have identified 2 members of the KLF (Krüppel-like factor) family of proteins, KLF2 and KLF4, as nodal regulators of endothelial function. Strikingly, inducible postnatal deletion of both KLF2 and KLF4 resulted in widespread vascular leak, coagulopathy, and rapid death. Importantly, while transcriptomic studies revealed profound alterations in gene expression, the molecular mechanisms underlying these changes remain poorly understood. Here, we seek to determine mechanisms of KLF2 and KLF4 transcriptional control in multiple vascular beds to further understand their roles as critical endothelial regulators. Methods and Results We integrate chromatin occupancy and transcription studies from multiple transgenic mouse models to demonstrate that KLF2 and KLF4 have overlapping yet distinct binding patterns and transcriptional targets in heart and lung endothelium. Mechanistically, KLFs use open chromatin regions in promoters and enhancers and bind in context-specific patterns that govern transcription in microvasculature. Importantly, this occurs during homeostasis in vivo without additional exogenous stimuli. Conclusions Together, this work provides mechanistic insight behind the well-described transcriptional and functional heterogeneity seen in vascular populations, while also establishing tools into exploring microvascular endothelial dynamics in vivo.
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Affiliation(s)
- David R Sweet
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute University Hospitals Cleveland Medical Center Cleveland OH.,Department of Pathology Case Western Reserve University Cleveland OH
| | - Roshan Padmanabhan
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute University Hospitals Cleveland Medical Center Cleveland OH
| | - Xudong Liao
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute University Hospitals Cleveland Medical Center Cleveland OH
| | - Himanshu R Dashora
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute University Hospitals Cleveland Medical Center Cleveland OH
| | - Xinmiao Tang
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute University Hospitals Cleveland Medical Center Cleveland OH
| | - Lalitha Nayak
- Division of Hematology and Oncology University Hospitals Cleveland Medical Center Cleveland OH
| | - Rajan Jain
- Department of Cell and Developmental Biology, Perelman School of Medicine University of Pennsylvania Philadelphia PA
| | - Sarah De Val
- Department of Physiology, Anatomy and Genetics University of Oxford UK
| | - Vinesh Vinayachandran
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute University Hospitals Cleveland Medical Center Cleveland OH
| | - Mukesh K Jain
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute University Hospitals Cleveland Medical Center Cleveland OH.,Division of Biology and Medicine Warren Alpert Medical School of Brown University Providence RI
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9
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CTLA4 +CD4 +CXCR5 -FOXP3 + T cells associate with unfavorable outcome in patients with chronic HBV infection. BMC Immunol 2023; 24:3. [PMID: 36635631 PMCID: PMC9835316 DOI: 10.1186/s12865-022-00537-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/27/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND A major barrier to achieving a favorable outcome of chronic HBV infection is a dysregulated HBV-specific immune response resulting from immunosuppressive features of FOXP3+ T cells. A better definition of FOXP3+ T cells is essential for improving the prognosis of HBV infection. We aimed to investigate the role of CD4+CXCR5-FOXP3+ T cells with CTLA4 expression in patients with chronic HBV infection. METHODS Treatment-naïve chronic HBV-infected patients, HBV-related hepatic failure, and a longitudinal cohort of chronic hepatitis B (CHB) patients with nucleos(t)ide analogue treatment were enrolled for analysis of CD4+CXCR5-FOXP3+ T cell responses by flow cytometry and single-cell RNA sequencing (scRNA-seq). RESULTS ScRNA-seq revealed that circulating CD4+CXCR5-FOXP3+ T cells presented distinct inhibitory features compared to spleen tissue. Meanwhile, patients with treatment-naïve chronic HBV infection or with HBV-related hepatic failure showed an upregulation of immune-suppressive features (PD-1, CTLA4, GITR) on CD4+CXCR5-FOXP3+T cells; in vitro analysis found HBeAg and HBcAg stimulation induced elevated levels of inhibitory molecules. Notably, the frequency of CTLA4+CD4+CXCR5-FOXP3+ T cells was positively correlated with HBV DNA levels, and longitudinal analysis demonstrated a high frequency of this subset at 12 weeks of antiviral treatment predicted unfavorable outcome in CHB patients. CONCLUSIONS CTLA4+CD4+CXCR5-FOXP3+ T cells are related to unfavorable outcomes in HBV-infected patients; these data indicated that alleviating CTLA4+CD4+CXCR5-FOXP3+ T cells may improve the prognosis of HBV infection.
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10
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Malgulwar PB, Danussi C, Dharmaiah S, Johnson WE, Rao A, Huse JT. Sirtuin 2 inhibition modulates chromatin landscapes genome-wide to induce senescence in ATRX-deficient malignant glioma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523324. [PMID: 36711727 PMCID: PMC9882017 DOI: 10.1101/2023.01.09.523324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Inactivating mutations in ATRX characterize large subgroups of malignant gliomas in adults and children. ATRX deficiency in glioma induces widespread chromatin remodeling, driving transcriptional shifts and oncogenic phenotypes. Effective strategies to therapeutically target these broad epigenomic sequelae remain undeveloped. We utilized integrated mulit-omics and the Broad Institute Connectivity Map (CMAP) to identify drug candidates that could potentially revert ATRX-deficient transcriptional changes. We then employed disease-relevant experimental models to evaluate functional phenotypes, coupling these studies with epigenomic profiling to elucidate molecular mechanim(s). CMAP analysis and transcriptional/epigenomic profiling implicated the Class III HDAC Sirtuin2 (Sirt2) as a central mediator of ATRX-deficient cellular phenotypes and a driver of unfavorable prognosis in ATRX-deficient glioma. Sirt2 inhibitors reverted Atrx-deficient transcriptional signatures in murine neuroprogenitor cells (mNPCs) and impaired cell migration in Atrx/ATRX-deficient mNPCs and human glioma stem cells (GSCs). While effects on cellular proliferation in these contexts were more modest, markers of senescence significantly increased, suggesting that Sirt2 inhibition promotes terminal differentiation in ATRX-deficient glioma. These phenotypic effects were accompanied by genome-wide shifts in enhancer-associated H3K27ac and H4K16ac marks, with the latter in particular demonstrating compelling transcriptional links to Sirt2-dependent phenotypic reversals. Motif analysis of these data identified the transcription factor KLF16 as a mediator of phenotype reversal in Atrx-deficient cells upon Sirt2 inhibition. Finally, Sirt2 inhibition impaired growth and increased senescence in ATRX-deficient GSCs in vivo . Our findings indicate that Sirt2 inhibition selectively targets ATRX-deficient gliomas through global chromatin remodeling, while demonstrating more broadly a viable approach to combat complex epigenetic rewiring in cancer. One Sentence Summary Our study demonstrates that SIRT2 inhibition promotes senescence in ATRX-deficient glioma model systems through global epigenomic remodeling, impacting key downstream transcriptional profiles.
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11
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Liu SZ, Xu YC, Tan XY, Zhao T, Zhang DG, Yang H, Luo Z. Transcriptional Regulation and Protein Localization of Zip10, Zip13 and Zip14 Transporters of Freshwater Teleost Yellow Catfish Pelteobagrus fulvidraco Following Zn Exposure in a Heterologous HEK293T Model. Int J Mol Sci 2022; 23:ijms23148034. [PMID: 35887381 PMCID: PMC9321221 DOI: 10.3390/ijms23148034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/04/2022] Open
Abstract
Zip family proteins are involved in the control of zinc (Zn) ion homeostasis. The present study cloned the promoters and investigated the transcription responses and protein subcellular localizations of three LIV-1 subfamily members (zip10, zip13, and zip14) from common freshwater teleost yellow catfish, Pelteobagrus fulvidraco, using in vitro cultured HEK293T model cells. The 2278 bp, 1917 bp, and 1989 bp sequences of zip10, zip13, and zip14 promoters, respectively, were subcloned into pGL3-Basic plasmid for promoter activity analysis. The pcDNA3.1 plasmid coding EGFP tagged pfZip10, pfZip13, and pfZip14 were generated for subsequent confocal microscope analysis. Several potential transcription factors’ binding sites were predicted within the promoters. In vitro promoter analysis in the HEK293T cells showed that high Zn administration significantly reduced the transcriptional activities of the zip10, zip13, and zip14 promoters. The −2017 bp/−2004 bp MRE in the zip10 promoter, the −360 bp/−345 bp MRE in the zip13 promoter, and the −1457 bp/−1442 bp MRE in the zip14 promoter were functional loci that were involved in the regulation of the three zips. The −606 bp/−594 bp KLF4 binding site in the zip13 promoter was a functional locus responsible for zinc-responsive regulation of zip13. The −1383 bp/−1375 bp STAT3 binding site in the zip14 promoter was a functional locus responsible for zinc-responsive regulation of zip14. Moreover, confocal microscope analysis indicated that zinc incubation significantly reduced the fluorescence intensity of pfZip10-EGFP and pfZip14-EGFP but had no significant influence on pfZip13-EGFP fluorescence intensity. Further investigation found that pfZip10 localizes on cell membranes, pfZip14 colocalized with both cell membranes and lysosome, and pfZip13 colocalized with intracellular ER and Golgi. Our research illustrated the transcription regulation of zip10, zip13, and zip14 from P. fulvidraco under zinc administration, which provided a reference value for the mechanisms involved in Zip-family-mediated control of zinc homeostasis in vertebrates.
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Affiliation(s)
- Sheng-Zan Liu
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China; (S.-Z.L.); (Y.-C.X.); (X.-Y.T.); (T.Z.); (D.-G.Z.); (H.Y.)
| | - Yi-Chuang Xu
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China; (S.-Z.L.); (Y.-C.X.); (X.-Y.T.); (T.Z.); (D.-G.Z.); (H.Y.)
| | - Xiao-Ying Tan
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China; (S.-Z.L.); (Y.-C.X.); (X.-Y.T.); (T.Z.); (D.-G.Z.); (H.Y.)
| | - Tao Zhao
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China; (S.-Z.L.); (Y.-C.X.); (X.-Y.T.); (T.Z.); (D.-G.Z.); (H.Y.)
| | - Dian-Guang Zhang
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China; (S.-Z.L.); (Y.-C.X.); (X.-Y.T.); (T.Z.); (D.-G.Z.); (H.Y.)
| | - Hong Yang
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China; (S.-Z.L.); (Y.-C.X.); (X.-Y.T.); (T.Z.); (D.-G.Z.); (H.Y.)
| | - Zhi Luo
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China; (S.-Z.L.); (Y.-C.X.); (X.-Y.T.); (T.Z.); (D.-G.Z.); (H.Y.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence: ; Tel.: +86-27-8728-2113; Fax: +86-27-8728-2114
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12
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Wang Z, Zhou Z, Zhang Y, Zuo F, Du J, Wang M, Hu M, Sun Y, Wang X, Liu M, Zhang Y, Tang W, Yi F. Diacylglycerol kinase epsilon protects against renal ischemia/reperfusion injury in mice through Krüppel-like factor 15/klotho pathway. Ren Fail 2022; 44:902-913. [PMID: 35616094 PMCID: PMC9154760 DOI: 10.1080/0886022x.2022.2079524] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Although recent studies have indicated that mutations in the gene encoding diacylglycerol kinase epsilon (DGKE) result in some proteinuria related hereditary kidney diseases, the DGKE expression pattern in the kidney and its contribution to acute kidney injury (AKI) remain unknown. Therefore, the present study was designed to detect the role of DGKE in mice with AKI. DGKE expression was time-dependently altered in the kidneys of mice with renal ischemia/reperfusion injury (IRI). Compared with wild-type (WT) mice, DGKE- overexpressing mice (Rosa26-Dgke+/+) exhibited protective effects against renal IRI, including reduced serum creatinine, blood urea concentration, tubular cell death and inflammatory responses as well as improved morphological injuries. Consistently, in vitro, DGKE overexpression in human renal proximal tubule (HK-2) cells also protected against oxygen-glucose deprivation (OGD)/reoxygenation-induced cell death. Mechanistically, DGKE regulated Klotho expression, at least partly via the transcription factor Krüppel-like factor (KLF) 15. Moreover, a significant reduction in DGKE was also found in kidneys from patients with ischemia-associated acute tubular necrosis (ATN). Collectively, our studies demonstrate that DGKE protects against AKI in mice at least partly through KLF15/Klotho signaling pathway, indicating that DGKE may present an innovative therapeutic strategy for treating patients with AKI.
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Affiliation(s)
- Ziying Wang
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Zhuanli Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Yanan Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Fuwen Zuo
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Junyao Du
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Mingwei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Muchen Hu
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Yu Sun
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Xiaojie Wang
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Min Liu
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Yan Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Wei Tang
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Fan Yi
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
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Krüppel-like Transcription Factor 7 Is a Causal Gene in Autism Development. Int J Mol Sci 2022; 23:ijms23063376. [PMID: 35328799 PMCID: PMC8949233 DOI: 10.3390/ijms23063376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/13/2022] [Accepted: 03/18/2022] [Indexed: 01/27/2023] Open
Abstract
Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental disease. To date, more than 1000 genes have been shown to be associated with ASD, and only a few of these genes account for more than 1% of autism cases. Klf7 is an important transcription factor of cell proliferation and differentiation in the nervous system, but whether klf7 is involved in autism is unclear. Methods: We first performed ChIP-seq analysis of klf7 in N2A cells, then performed behavioral tests and RNA-seq in klf7+/− mice, and finally restored mice with adeno-associated virus (AAV)-mediated overexpression of klf7 in klf7+/− mice. Results: Klf7 targeted genes are enriched with ASD genes, and 631 ASD risk genes are also differentially expressed in klf7+/− mice which exhibited the core symptoms of ASD. When klf7 levels were increased in the central nervous system (CNS) in klf7+/− adult mice, deficits in social interaction, repetitive behavior and majority of dysregulated ASD genes were rescued in the adults, suggesting transcriptional regulation. Moreover, knockdown of klf7 in human brain organoids caused dysregulation of 517 ASD risk genes, 344 of which were shared with klf7+/− mice, including some high-confidence ASD genes. Conclusions: Our findings highlight a klf7 regulation of ASD genes and provide new insights into the pathogenesis of ASD and promising targets for further research on mechanisms and treatments.
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Characterization of a genomic region 8 kb downstream of GFI1B associated with myeloproliferative neoplasms. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166259. [PMID: 34450246 DOI: 10.1016/j.bbadis.2021.166259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/07/2021] [Accepted: 08/23/2021] [Indexed: 11/23/2022]
Abstract
A genomic locus 8 kb downstream of the transcription factor GFI1B (Growth Factor Independence 1B) predisposes to clonal hematopoiesis and myeloproliferative neoplasms. One of the most significantly associated polymorphisms in this region is rs621940-G. GFI1B auto-represses GFI1B, and altered GFI1B expression contributes to myeloid neoplasms. We studied whether rs621940-G affects GFI1B expression and growth of immature cells. GFI1B ChIP-seq showed clear binding to the rs621940 locus. Preferential binding of various hematopoietic transcription factors to either the rs621940-C or -G allele was observed, but GFI1B showed no preference. In gene reporter assays the rs621940 region inhibited GFI1B promoter activity with the G-allele having less suppressive effects compared to the C-allele. However, CRISPR-Cas9 mediated deletion of the locus in K562 cells did not alter GFI1B expression nor auto-repression. In healthy peripheral blood mononuclear cells GFI1B expression did not differ consistently between the rs621940 alleles. Long range and targeted deep sequencing did not detect consistent effects of rs621940-G on allelic GFI1B expression either. Finally, we observed that myeloid colony formation was not significantly affected by either rs621940 allele in 193 healthy donors. Together, these findings show no evidence that rs621940 or its locus affect GFI1B expression, auto-repression or growth of immature myeloid cells.
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15
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Gans IM, Grendler J, Babich R, Jayasundara N, Coffman JA. Glucocorticoid-Responsive Transcription Factor Krüppel-Like Factor 9 Regulates fkbp5 and Metabolism. Front Cell Dev Biol 2021; 9:727037. [PMID: 34692682 PMCID: PMC8526736 DOI: 10.3389/fcell.2021.727037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/15/2021] [Indexed: 12/30/2022] Open
Abstract
Krüppel-like factor 9 (Klf9) is a feedforward regulator of glucocorticoid receptor (GR) signaling. Here we show that in zebrafish klf9 is expressed with GR-dependent oscillatory dynamics in synchrony with fkbp5, a GR target that encodes a negative feedback regulator of GR signaling. We found that fkbp5 transcript levels are elevated in klf9 -/- mutants and that Klf9 associates with chromatin at the fkbp5 promoter, which becomes hyperacetylated in klf9 -/ - mutants, suggesting that the GR regulates fkbp5 via an incoherent feedforward loop with klf9. As both the GR and Fkbp5 are known to regulate metabolism, we asked how loss of Klf9 affects metabolic rate and gene expression. We found that klf9 -/- mutants have a decreased oxygen consumption rate (OCR) and upregulate glycolytic genes, the promoter regions of which are enriched for potential Klf9 binding motifs. Our results suggest that Klf9 functions downstream of the GR to regulate cellular glucocorticoid responsivity and metabolic homeostasis.
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Affiliation(s)
- Ian M. Gans
- MDI Biological Laboratory, Bar Harbor, ME, United States
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, United States
| | | | - Remy Babich
- The School of Marine Sciences, University of Maine, Orono, ME, United States
| | - Nishad Jayasundara
- Nicholas School of the Environment, Duke University, Durham, NC, United States
| | - James A. Coffman
- MDI Biological Laboratory, Bar Harbor, ME, United States
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, United States
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16
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Li X, Pan X, Zhou H, Wang P, Gao Y, Shang S, Guo S, Sun J, Xiong Z, Ning S, Zhi H, Li X. Comprehensive characterization genetic regulation and chromatin landscape of enhancer-associated long non-coding RNAs and their implication in human cancer. Brief Bioinform 2021; 23:6375264. [PMID: 34581409 DOI: 10.1093/bib/bbab401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/19/2021] [Accepted: 09/02/2021] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) that emanate from enhancer regions (defined as enhancer-associated lncRNAs, or elncRNAs) are emerging as critical regulators in disease progression. However, their biological characteristics and clinical relevance have not been fully portrayed. Here, based on the traditional expression quantitative loci (eQTL) and our optimized residual eQTL method, we comprehensively described the genetic effect on elncRNA expression in more than 300 lymphoblastoid cell lines. Meanwhile, a chromatin atlas of elncRNAs relative to the genetic regulation state was depicted. By applying the maximum likelihood estimate method, we successfully identified causal elncRNAs for protein-coding gene expression reprogramming and showed their associated single nucleotide polymorphisms (SNPs) favor binding of transcription factors. Further epigenome analysis revealed two immune-associated elncRNAs AL662844.4 and LINC01215 possess high levels of H3K27ac and H3K4me1 in human cancer. Besides, pan-cancer analysis of 3D genome, transcriptome, and regulatome data showed they potentially regulate tumor-immune cell interaction through affecting MHC class I genes and CD47, respectively. Moreover, our study showed there exist associations between elncRNA and patient survival. Finally, we made a user-friendly web interface available for exploring the regulatory relationship of SNP-elncRNA-protein-coding gene triplets (http://bio-bigdata.hrbmu.edu.cn/elncVarReg). Our study provides critical mechanistic insights for elncRNA function and illustrates their implications in human cancer.
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Affiliation(s)
- Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Xu Pan
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Hanxiao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Shuang Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Jie Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Zhiying Xiong
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, China
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17
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Presnell JS, Browne WE. Krüppel-like factor gene function in the ctenophore Mnemiopsis leidyi assessed by CRISPR/Cas9-mediated genome editing. Development 2021; 148:272041. [PMID: 34373891 DOI: 10.1242/dev.199771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022]
Abstract
The Krüppel-like factor (Klf) gene family encodes transcription factors that play an important role in the regulation of stem cell proliferation, cell differentiation and development in bilaterians. Although Klf genes have been shown to specify functionally various cell types in non-bilaterian animals, their role in early-diverging animal lineages has not been assessed. Thus, the ancestral activity of these transcription factors in animal development is not well understood. The ctenophore Mnemiopsis leidyi has emerged as an important non-bilaterian model system for understanding early animal evolution. Here, we characterize the expression and functional role of Klf genes during M. leidyi embryogenesis. Zygotic Klf gene function was assessed with both CRISPR/Cas9-mediated genome editing and splice-blocking morpholino oligonucleotide knockdown approaches. Abrogation of zygotic Klf expression during M. leidyi embryogenesis resulted in abnormal development of several organs, including the pharynx, tentacle bulbs and apical organ. Our data suggest an ancient role for Klf genes in regulating endodermal patterning, possibly through regulation of cell proliferation.
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Affiliation(s)
- Jason S Presnell
- Department of Biology, University of Miami, Cox Science Center, 1301 Memorial Drive, Miami, FL 33146, USA
| | - William E Browne
- Department of Biology, University of Miami, Cox Science Center, 1301 Memorial Drive, Miami, FL 33146, USA
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18
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Leylek R, Alcántara-Hernández M, Granja JM, Chavez M, Perez K, Diaz OR, Li R, Satpathy AT, Chang HY, Idoyaga J. Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity. Cell Rep 2021; 32:108180. [PMID: 32966789 PMCID: PMC7546547 DOI: 10.1016/j.celrep.2020.108180] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/18/2020] [Accepted: 09/01/2020] [Indexed: 12/16/2022] Open
Abstract
Human dendritic cells (DCs) comprise subsets with distinct phenotypic and functional characteristics, but the transcriptional programs that dictate their identity remain elusive. Here, we analyze global chromatin accessibility profiles across resting and stimulated human DC subsets by means of the assay for transposase-accessible chromatin using sequencing (ATAC-seq). We uncover specific regions of chromatin accessibility for each subset and transcriptional regulators of DC function. By comparing plasmacytoid DC responses to IFN-I-producing and non-IFN-I-producing conditions, we identify genetic programs related to their function. Finally, by intersecting chromatin accessibility with genome-wide association studies, we recognize DC subset-specific enrichment of heritability in autoimmune diseases. Our results unravel the basis of human DC subset heterogeneity and provide a framework for their analysis in disease pathogenesis. Human dendritic cells (DCs) orchestrate immune responses by a division of labor between functionally specialized subsets; however, the transcriptional basis of this heterogeneity is poorly understood. Using ATAC-seq, Leylek et al. profile the chromatin landscape of human DC subsets, providing insight into the underlying regulatory mechanisms that modulate their function.
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Affiliation(s)
- Rebecca Leylek
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcela Alcántara-Hernández
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeffrey M Granja
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Chavez
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kimberly Perez
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oscar R Diaz
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Juliana Idoyaga
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Perrotta L, Giordo R, Francis D, Rogers HJ, Albani D. Molecular Analysis of the E2F/DP Gene Family of Daucus carota and Involvement of the DcE2F1 Factor in Cell Proliferation. FRONTIERS IN PLANT SCIENCE 2021; 12:652570. [PMID: 33777085 PMCID: PMC7994507 DOI: 10.3389/fpls.2021.652570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
E2F transcription factors are key components of the RB/E2F pathway that, through the action of cyclin-dependent kinases, regulates cell cycle progression in both plants and animals. Moreover, plant and animal E2Fs have also been shown to regulate other cellular functions in addition to cell proliferation. Based on structural and functional features, they can be divided into different classes that have been shown to act as activators or repressors of E2F-dependent genes. Among the first plant E2F factors to be reported, we previously described DcE2F1, an activating E2F which is expressed in cycling carrot (Daucus carota) cells. In this study, we describe the identification of the additional members of the E2F/DP family of D. carota, which includes four typical E2Fs, three atypical E2F/DEL genes, and three related DP genes. Expression analyses of the carrot E2F and DP genes reveal distinctive patterns and suggest that the functions of some of them are not necessarily linked to cell proliferation. DcE2F1 was previously shown to transactivate an E2F-responsive promoter in transient assays but the functional role of this protein in planta was not defined. Sequence comparisons indicate that DcE2F1 could be an ortholog of the AtE2FA factor of Arabidopsis thaliana. Moreover, ectopic expression of the DcE2F1 cDNA in transgenic Arabidopsis plants is able to upregulate AtE2FB and promotes cell proliferation, giving rise to polycotyly with low frequency, effects that are highly similar to those observed when over-expressing AtE2FA. These results indicate that DcE2F1 is involved in the control of cell proliferation and plays important roles in the regulation of embryo and plant development.
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Affiliation(s)
- Lara Perrotta
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
| | - Roberta Giordo
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
| | - Dennis Francis
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Hilary J. Rogers
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Diego Albani
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
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Dolmatov IY. Molecular Aspects of Regeneration Mechanisms in Holothurians. Genes (Basel) 2021; 12:250. [PMID: 33578707 PMCID: PMC7916379 DOI: 10.3390/genes12020250] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 02/07/2023] Open
Abstract
Holothurians, or sea cucumbers, belong to the phylum Echinodermata. They show good regenerative abilities. The present review provides an analysis of available data on the molecular aspects of regeneration mechanisms in holothurians. The genes and signaling pathways activated during the asexual reproduction and the formation of the anterior and posterior parts of the body, as well as the molecular mechanisms that provide regeneration of the nervous and digestive systems, are considered here. Damage causes a strong stress response, the signs of which are recorded even at late regeneration stages. In holothurian tissues, the concentrations of reactive oxygen species and antioxidant enzymes increase. Furthermore, the cellular and humoral components of the immune system are activated. Extracellular matrix remodeling and Wnt signaling play a major role in the regeneration in holothurians. All available morphological and molecular data show that the dedifferentiation of specialized cells in the remnant of the organ and the epithelial morphogenesis constitute the basis of regeneration in holothurians. However, depending on the type of damage, the mechanisms of regeneration may differ significantly in the spatial organization of regeneration process, the involvement of different cell types, and the depth of reprogramming of their genome (dedifferentiation or transdifferentiation).
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Affiliation(s)
- Igor Yu Dolmatov
- A.V. Zhirmunsky National Scientifc Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevsky 17, 690041 Vladivostok, Russia
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21
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Unravelling Structure, Localization, and Genetic Crosstalk of KLF3 in Human Breast Cancer. BIOMED RESEARCH INTERNATIONAL 2021; 2020:1354381. [PMID: 33490232 PMCID: PMC7803292 DOI: 10.1155/2020/1354381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 01/12/2023]
Abstract
Breast cancer is the most prevailing disease among women. It actually develops from breast tissue and has heterogeneous and complex nature that constitutes multiple tumor quiddities. These features are associated with different histological forms, distinctive biological characteristics, and clinical patterns. The predisposition of breast cancer has been attributed to a number of genetic factors, associated with the worst outcomes. Unfortunately, their behavior with relevance to clinical significance remained poorly understood. So, there is a need to further explore the nature of the disease at the transcriptome level. The focus of this study was to explore the influence of Krüppel-like factor 3 (KLF3), tumor protein D52 (TPD52), microRNA 124 (miR-124), and protein kinase C epsilon (PKCε) expression on breast cancer. Moreover, this study was also aimed at predicting the tertiary structure of KLF3 protein. Expression of genes was analyzed through real-time PCR using the delta cycle threshold method, and statistical significance was calculated by two-way ANOVA in Graphpad Prism. For the construction of a 3D model, various bioinformatics software programs, Swiss Model and UCSF Chimera, were employed. The expression of KLF3, miR-124, and PKCε genes was decreased (fold change: 0.076443, 0.06969, and 0.011597, respectively). However, there was 2-fold increased expression of TPD52 with p value < 0.001 relative to control. Tertiary structure of KLF3 exhibited 80.72% structure conservation with its template KLF4 and was 95.06% structurally favored by a Ramachandran plot. These genes might be predictors of stage, metastasis, receptor, and treatment status and used as new biomarkers for breast cancer diagnosis. However, extensive investigations at the tissue level and in in vivo are required to further strengthen their role as a potential biomarker for prognosis of breast cancer.
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O'Connor T, Grant CE, Bodén M, Bailey TL. T-Gene: improved target gene prediction. Bioinformatics 2020; 36:3902-3904. [PMID: 32246829 DOI: 10.1093/bioinformatics/btaa227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/04/2020] [Accepted: 03/30/2020] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Identifying the genes regulated by a given transcription factor (TF) (its 'target genes') is a key step in developing a comprehensive understanding of gene regulation. Previously, we developed a method (CisMapper) for predicting the target genes of a TF based solely on the correlation between a histone modification at the TF's binding site and the expression of the gene across a set of tissues or cell lines. That approach is limited to organisms for which extensive histone and expression data are available, and does not explicitly incorporate the genomic distance between the TF and the gene. RESULTS We present the T-Gene algorithm, which overcomes these limitations. It can be used to predict which genes are most likely to be regulated by a TF, and which of the TF's binding sites are most likely involved in regulating particular genes. T-Gene calculates a novel score that combines distance and histone/expression correlation, and we show that this score accurately predicts when a regulatory element bound by a TF is in contact with a gene's promoter, achieving median precision above 60%. T-Gene is easy to use via its web server or as a command-line tool, and can also make accurate predictions (median precision above 40%) based on distance alone when extensive histone/expression data is not available for the organism. T-Gene provides an estimate of the statistical significance of each of its predictions. AVAILABILITY AND IMPLEMENTATION The T-Gene web server, source code, histone/expression data and genome annotation files are provided at http://meme-suite.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Charles E Grant
- Department of Genome Sciences, University of Washington, Seattle, WA 98195-5065
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Timothy L Bailey
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
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23
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Discover novel disease-associated genes based on regulatory networks of long-range chromatin interactions. Methods 2020; 189:22-33. [PMID: 33096239 DOI: 10.1016/j.ymeth.2020.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/29/2020] [Accepted: 10/18/2020] [Indexed: 02/01/2023] Open
Abstract
Identifying genes and non-coding genetic variants that are genetically associated with complex diseases and the underlying mechanisms is one of the most important questions in functional genomics. Due to the limited statistical power and the lack of mechanistic modeling, traditional genome-wide association studies (GWAS) is restricted to fully address this question. Based on multi-omics data integration, cell-type specific regulatory networks can be built to improve GWAS analysis. In this study, we developed a new computational infrastructure, APRIL, to incorporate 3D chromatin interactions into regulatory network construction, which can extend the networks to include long-range cis-regulatory links between non-coding GWAS SNPs and target genes. Combinatorial transcription factors that co-regulate groups of genes are also inferred to further expand the networks with trans-regulation. A suite of machine learning predictions and statistical tests are incorporated in APRIL to predict novel disease-associated genes based on the expanded regulatory networks. Important features of non-coding regulatory elements and genetic variants are prioritized in network-based predictions, providing systems-level insights on the mechanisms of transcriptional dysregulation associated with complex diseases.
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Jones J, Chen Y, Tiwari M, Li J, Ling J, Sen GL. KLF3 Mediates Epidermal Differentiation through the Epigenomic Writer CBP. iScience 2020; 23:101320. [PMID: 32659720 PMCID: PMC7358749 DOI: 10.1016/j.isci.2020.101320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/02/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
Impairments in the differentiation process can lead to skin diseases that can afflict ∼20% of the population. Thus, it is of utmost importance to understand the factors that promote the differentiation process. Here we identify the transcription factor KLF3 as a regulator of epidermal differentiation. Knockdown of KLF3 results in reduced differentiation gene expression and increased cell cycle gene expression. Over half of KLF3's genomic binding sites occur at active enhancers. KLF3 binds to active enhancers proximal to differentiation genes that are dependent upon KLF3 for expression. KLF3's genomic binding sites also highly overlaps with CBP, a histone acetyltransferase necessary for activating enhancers. Depletion of KLF3 causes reduced CBP localization at enhancers proximal to differentiation gene clusters, which leads to loss of enhancer activation but not priming. Our results suggest that KLF3 is necessary to recruit CBP to activate enhancers and drive epidermal differentiation gene expression.
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Affiliation(s)
- Jackson Jones
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Yifang Chen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Manisha Tiwari
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Jingting Li
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Ji Ling
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - George L Sen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA.
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Gillespie MA, Palii CG, Sanchez-Taltavull D, Shannon P, Longabaugh WJR, Downes DJ, Sivaraman K, Espinoza HM, Hughes JR, Price ND, Perkins TJ, Ranish JA, Brand M. Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis. Mol Cell 2020; 78:960-974.e11. [PMID: 32330456 PMCID: PMC7344268 DOI: 10.1016/j.molcel.2020.03.031] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/20/2020] [Accepted: 03/25/2020] [Indexed: 12/11/2022]
Abstract
Dynamic cellular processes such as differentiation are driven by changes in the abundances of transcription factors (TFs). However, despite years of studies, our knowledge about the protein copy number of TFs in the nucleus is limited. Here, by determining the absolute abundances of 103 TFs and co-factors during the course of human erythropoiesis, we provide a dynamic and quantitative scale for TFs in the nucleus. Furthermore, we establish the first gene regulatory network of cell fate commitment that integrates temporal protein stoichiometry data with mRNA measurements. The model revealed quantitative imbalances in TFs' cross-antagonistic relationships that underlie lineage determination. Finally, we made the surprising discovery that, in the nucleus, co-repressors are dramatically more abundant than co-activators at the protein level, but not at the RNA level, with profound implications for understanding transcriptional regulation. These analyses provide a unique quantitative framework to understand transcriptional regulation of cell differentiation in a dynamic context.
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Affiliation(s)
| | - Carmen G Palii
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada
| | - Daniel Sanchez-Taltavull
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada; Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland
| | - Paul Shannon
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Karthi Sivaraman
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada
| | | | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Theodore J Perkins
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada.
| | - Jeffrey A Ranish
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada.
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26
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Yang M, Li CJ, Xiao Y, Guo Q, Huang Y, Su T, Luo XH, Jiang TJ. Ophiopogonin D promotes bone regeneration by stimulating CD31 hi EMCN hi vessel formation. Cell Prolif 2020; 53:e12784. [PMID: 32080957 PMCID: PMC7106967 DOI: 10.1111/cpr.12784] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/02/2020] [Accepted: 02/04/2020] [Indexed: 12/11/2022] Open
Abstract
Objectives CD31hiEMCNhi vessels (CD31, also known as PECAM1 [platelet and endothelial cell adhesion molecule 1]; EMCN, endomucin), which are strongly positive for CD31 and endomucin, couple angiogenesis and osteogenesis. However, the role of CD31hiEMCNhi vessels in bone regeneration remains unknown. In the present study, we investigated the role of CD31hiEMCNhi vessels in the process of bone regeneration. Materials and Methods We used endothelial‐specific Krüppel like factor 3 (Klf3) knockout mice and ophiopogonin D treatment to interfere with CD31hiEMCNhi vessel formation. We constructed a bone regeneration model by surgical ablation of the trabecular bone. Immunofluorescence and micro‐computed tomography (CT) were used to detect CD31hiEMCNhi vessels and bone formation. Results CD31hiEMCNhi vessels participate in the process of bone regeneration, such that endothelial‐specific Klf3 knockout mice showed increased CD31hiEMCNhi vessels and osteoprogenitors in the bone regeneration area, and further accelerated bone formation. We also demonstrated that the natural compound, ophiopogonin D, acts as a KLF3 inhibitor to promote vessels formation both in vitro and in vivo. Administration of ophiopogonin D increased the abundance of CD31hiEmcnhi vessels and accelerated bone healing. Conclusions Our findings confirmed the important role of CD31hiEmcnhi vessels in bone regeneration and provided a new target to treat bone fracture or promote bone regeneration.
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Affiliation(s)
- Mi Yang
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Chang-Jun Li
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Ye Xiao
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Qi Guo
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Yan Huang
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Tian Su
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Xiang-Hang Luo
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Tie-Jian Jiang
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
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The Eupentacta fraudatrix transcriptome provides insights into regulation of cell transdifferentiation. Sci Rep 2020; 10:1522. [PMID: 32001787 PMCID: PMC6992634 DOI: 10.1038/s41598-020-58470-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
The holothurian Eupentacta fraudatrix is a unique organism for studying regeneration mechanisms. Moreover, E. fraudatrix can quickly restore parts of its body and entire organ systems, yet at the moment, there is no data on the participation of stem cells in the process. To the contrary, it has been repeatedly confirmed that this process is only due to the transformation of terminally differentiated cells. In this study, we examine changes in gene expression during gut regeneration of the holothurian E. fraudatrix. Transcriptomes of intestinal anlage of the three stages of regeneration, as well as the normal gut, were sequenced with an Illumina sequencer (San Diego, CA, USA). We identified 14,617 sea urchin protein homologs, of which 308 were transcription factors. After analysing the dynamics of gene expression during regeneration and the map of biological processes in which they participate, we identified 11 factors: Ef-EGR1, Ef-ELF, Ef-GATA3, Ef-ID2, Ef-KLF1/2/4, Ef-MSC, Ef-PCGF2, Ef-PRDM9, Ef-SNAI2, Ef-TBX20, and Ef-TCF24. With the exception of TCF24, they are all involved in the regeneration, development, epithelial-mesenchymal transition, and immune response in other animals. We suggest that these transcription factors may also be involved in the transdifferentiation of coelomic epithelial cells into enterocytes in holothurians.
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28
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Hodges AJ, Hudson NO, Buck-Koehntop BA. Cys 2His 2 Zinc Finger Methyl-CpG Binding Proteins: Getting a Handle on Methylated DNA. J Mol Biol 2019:S0022-2836(19)30567-4. [PMID: 31628952 DOI: 10.1016/j.jmb.2019.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022]
Abstract
DNA methylation is an essential epigenetic modification involved in the maintenance of genomic stability, preservation of cellular identity, and regulation of the transcriptional landscape needed to maintain cellular function. In an increasing number of disease conditions, DNA methylation patterns are inappropriately distributed in a manner that supports the disease phenotype. Methyl-CpG binding proteins (MBPs) are specialized transcription factors that read and translate methylated DNA signals into recruitment of protein assemblies that can alter local chromatin architecture and transcription. MBPs thus play a key intermediary role in gene regulation for both normal and diseased cells. Here, we highlight established and potential structure-function relationships for the best characterized members of the zinc finger (ZF) family of MBPs in propagating DNA methylation signals into downstream cellular responses. Current and future investigations aimed toward expanding our understanding of ZF MBP cellular roles will provide needed mechanistic insight into normal and disease state functions, as well as afford evaluation for the potential of these proteins as epigenetic-based therapeutic targets.
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Affiliation(s)
- Amelia J Hodges
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Nicholas O Hudson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Bethany A Buck-Koehntop
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA.
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29
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Yang M, Guo Q, Peng H, Xiao YZ, Xiao Y, Huang Y, Li CJ, Su T, Zhang YL, Lei MX, Chen HL, Jiang TJ, Luo XH. Krüppel-like factor 3 inhibition by mutated lncRNA Reg1cp results in human high bone mass syndrome. J Exp Med 2019; 216:1944-1964. [PMID: 31196982 PMCID: PMC6683986 DOI: 10.1084/jem.20181554] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 02/27/2019] [Accepted: 05/16/2019] [Indexed: 12/11/2022] Open
Abstract
The authors report a mutation in the long noncoding RNA Reg1cp that induces osteogenesis via vascular induction in humans. This mutation affects angiogenesis by blocking Klf3’s repressing activity. The Klf3 antagonist Ophiopogonin D could promote CD31hiEmcnhi vessel formation and osteogenesis in osteoporosis mice. High bone mass (HBM) is usually caused by gene mutations, and its mechanism remains unclear. In the present study, we identified a novel mutation in the long noncoding RNA Reg1cp that is associated with HBM. Subsequent analysis in 1,465 Chinese subjects revealed that heterozygous Reg1cp individuals had higher bone density compared with subjects with WT Reg1cp. Mutant Reg1cp increased the formation of the CD31hiEmcnhi endothelium in the bone marrow, which stimulated angiogenesis during osteogenesis. Mechanistically, mutant Reg1cp directly binds to Krüppel-like factor 3 (KLF3) to inhibit its activity. Mice depleted of Klf3 in endothelial cells showed a high abundance of CD31hiEmcnhi vessels and increased bone mass. Notably, we identified a natural compound, Ophiopogonin D, which functions as a KLF3 inhibitor. Administration of Ophiopogonin D increased the abundance of CD31hiEmcnhi vessels and bone formation. Our findings revealed a specific mutation in lncRNA Reg1cp that is involved in the pathogenesis of HBM and provides a new target to treat osteoporosis.
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Affiliation(s)
- Mi Yang
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Qi Guo
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China
| | - Hui Peng
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Yu-Zhong Xiao
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China
| | - Ye Xiao
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Yan Huang
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Chang-Jun Li
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Tian Su
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Yun-Lin Zhang
- Department of Metabolic Endocrinology, The Second People's Hospital of Xiangxiang, Xiangxiang, China
| | - Min-Xiang Lei
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Hui-Ling Chen
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Tie-Jian Jiang
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Xiang-Hang Luo
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, China
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30
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Quintana-Urzainqui I, Kozić Z, Mitra S, Tian T, Manuel M, Mason JO, Price DJ. Tissue-Specific Actions of Pax6 on Proliferation and Differentiation Balance in Developing Forebrain Are Foxg1 Dependent. iScience 2018; 10:171-191. [PMID: 30529950 PMCID: PMC6287089 DOI: 10.1016/j.isci.2018.11.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/02/2018] [Accepted: 11/16/2018] [Indexed: 12/12/2022] Open
Abstract
Differences in the growth and maturation of diverse forebrain tissues depend on region-specific transcriptional regulation. Individual transcription factors act simultaneously in multiple regions that develop very differently, raising questions about the extent to which their actions vary regionally. We found that the transcription factor Pax6 affects the transcriptomes and the balance between proliferation and differentiation in opposite directions in the diencephalon versus cerebral cortex. We tested several possible mechanisms to explain Pax6's tissue-specific actions and found that the presence of the transcription factor Foxg1 in the cortex but not in the diencephalon was most influential. We found that Foxg1 is responsible for many of the differences in cell cycle gene expression between the diencephalon and cortex and, in cortex lacking Foxg1, Pax6's action on the balance of proliferation versus differentiation becomes diencephalon like. Our findings reveal a mechanism for generating regional forebrain diversity in which one transcription factor completely reverses the actions of another.
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Affiliation(s)
- Idoia Quintana-Urzainqui
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK.
| | - Zrinko Kozić
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Soham Mitra
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Tian Tian
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Martine Manuel
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - John O Mason
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - David J Price
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
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Zhao Y, Yu J, Zhao J, Chen X, Xiong N, Wang T, Qing H, Lin Z. Intragenic Transcriptional cis-Antagonism Across SLC6A3. Mol Neurobiol 2018; 56:4051-4060. [PMID: 30259411 DOI: 10.1007/s12035-018-1357-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/18/2018] [Indexed: 12/29/2022]
Abstract
A promoter can be regulated by various cis-acting elements so that delineation of the regulatory modes among them may help understand developmental, environmental and genetic mechanisms in gene activity. Here we report that the human dopamine transporter gene SLC6A3 carries a 5' distal 5-kb super enhancer (5KSE) which upregulated the promoter by 5-fold. Interestingly, 5KSE is able to prevent 3' downstream variable number tandem repeats (3'VNTRs) from silencing the promoter. This new enhancer consists of a 5'VNTR and three repetitive sub-elements that are conserved in primates. Two of 5KSE's sub-elements, E-9.7 and E-8.7, upregulate the promoter, but only the later could continue doing so in the presence of 3'VNTRs. Finally, E-8.7 is activated by novel dopaminergic transcription factors including SRP54 and Nfe2l1. Together, these results reveal a multimodal regulatory mechanism in SLC6A3.
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Affiliation(s)
- Ying Zhao
- Laboratory of Psychiatric Neurogenomics, Basic Neuroscience Division, McLean Hospital, Belmont, MA, 02478, USA.,School of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China
| | - Jinlong Yu
- Laboratory of Psychiatric Neurogenomics, Basic Neuroscience Division, McLean Hospital, Belmont, MA, 02478, USA
| | - Juan Zhao
- Laboratory of Psychiatric Neurogenomics, Basic Neuroscience Division, McLean Hospital, Belmont, MA, 02478, USA.,College of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaowu Chen
- Laboratory of Psychiatric Neurogenomics, Basic Neuroscience Division, McLean Hospital, Belmont, MA, 02478, USA.,Department of Neurology, Shenzhen University General Hospital, Shenzhen, Guangzhou, 518060, China
| | - Nian Xiong
- Laboratory of Psychiatric Neurogenomics, Basic Neuroscience Division, McLean Hospital, Belmont, MA, 02478, USA.,Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Wang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hong Qing
- College of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Zhicheng Lin
- Laboratory of Psychiatric Neurogenomics, Basic Neuroscience Division, McLean Hospital, Belmont, MA, 02478, USA.
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Fibroblast growth factor 10 (FGF10) promotes the adipogenesis of intramuscular preadipocytes in goat. Mol Biol Rep 2018; 45:1881-1888. [PMID: 30250994 DOI: 10.1007/s11033-018-4334-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/25/2018] [Indexed: 02/06/2023]
Abstract
Fibroblast growth factor 10 (FGF10) is an adipokine that is found to participate in the regulation of adipogenesis. However, its function remains to be elucidated in intramuscular fat (IMF) deposition of goat. The purpose of this study was to explore the role of FGF10 in goat IMF deposition. Here, we investigated the expression of FGF10 in goat intramuscular adipocytes inducing 0, 2, 4, 6 and 8 days. Effect of FGF10 on adipogenesis was investigated by gaining and losing function of FGF10 in vitro. And then, we examined several lipid metabolism-related genes, including peroxisome proliferator activated receptor γ (PPARγ), sterol regulatory element binding protein 1 (SREBP1), preadipocyte factor-1 (Pref-1), CCAAT/enhancer binding protein-α (C/EBPα) and CCAAT/enhancer binding protein-β (C/EBPβ), as well as, Krüppel-like factor (KLF) family. We found that the sharp expression of FGF10 appeared at 2 days. Overexpression of FGF10 mediated by adenovirus promotes lipid accumulation, accompanied by up-regulating of LPL and C/EBPα with the down-regulating of C/EBPβ. Conversely, the expression of LPL, C/EBPα and SREBP1 was significantly decreased by the siRNAs of FGF10. Meanwhile, we showed that FGF10 regulated the expression of many KLFs members and interacted synergistically or antagonistically with them. Thus, our results demonstrated a key role of FGF10 as a positively factor in the regulation of adipogenic differentiation of intramuscular preadipocyte in goat.
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EPO does not promote interaction between the erythropoietin and beta-common receptors. Sci Rep 2018; 8:12457. [PMID: 30127368 PMCID: PMC6102255 DOI: 10.1038/s41598-018-29865-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 07/19/2018] [Indexed: 12/13/2022] Open
Abstract
A direct interaction between the erythropoietin (EPOR) and the beta-common (βc) receptors to form an Innate Repair Receptor (IRR) is controversial. On one hand, studies have shown a functional link between EPOR and βc receptor in tissue protection while others have shown no involvement of the βc receptor in tissue repair. To date there is no biophysical evidence to confirm a direct association of the two receptors either in vitro or in vivo. We investigated the existence of an interaction between the extracellular regions of EPOR and the βc receptor in silico and in vitro (either in the presence or absence of EPO or EPO-derived peptide ARA290). Although a possible interaction between EPOR and βc was suggested by our computational and genomic studies, our in vitro biophysical analysis demonstrates that the extracellular regions of the two receptors do not specifically associate. We also explored the involvement of the βc receptor gene (Csf2rb) under anaemic stress conditions and found no requirement for the βc receptor in mice. In light of these studies, we conclude that the extracellular regions of the EPOR and the βc receptor do not directly interact and that the IRR is not involved in anaemic stress.
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Hao JS, Zhu CJ, Yan BY, Yan CY, Ling R. Stimulation of KLF14/PLK1 pathway by thrombin signaling potentiates endothelial dysfunction in Type 2 diabetes mellitus. Biomed Pharmacother 2018; 99:859-866. [PMID: 29710485 DOI: 10.1016/j.biopha.2018.01.151] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 12/11/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) promotes a high oxidative stress and hypercoagulable state that drives microvascular injury and multiple-organ abnormality. Elevated thrombin activity underlies T2DM-linked endothelial dysfunction, but the mechanistic links between T2DM/oxidative stress axis and thrombin-associated endothelial pathologies are incompletely understood. In this work, immunohistochemical studies and quantitative analysis using isolated endothelial cells (ECs) identified accumulated Kru¨ppel-like family of transcription factor 14 (KLF14) deposits in ECs from multiple organs as distinct features of T2DM mice. KLF14 upregulation in ECs, which was stimulated by thrombin treatment, was dependent on multiple pathways including calcium mobilization, activation of PKC and AMPK pathways. Functionally, inhibition of endogenous KLF14 expression significantly attenuated thrombin-induced endotheliocyte proliferation, endothelial cell migration and oxidative stress. Molecularly, by directly binding the promoter, KLF14 functions as a transcriptional activator of PLK1, a polo-like kinase whose overexpression induced excessive reactive oxygen species (ROS) production. Transient knockdown of PLK1 was sufficient to suppress KLF14 overexpression-potentiated endothelial dysfunction. Collectively, these data provide proof of concept that deregulation of KLF14/PLK1 cascade plays a key role in thrombin-induced endothelial dysfunction and targeting KLF14 or PLK1 may limit thrombin-associated pathologies in T2DM patients.
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Affiliation(s)
- Jun-Sheng Hao
- Department of Thyroid Gland and Breast Vascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, PR China
| | - Chao-Juan Zhu
- Department of Emergency Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, PR China
| | - Bin-Yuan Yan
- Department of Epidemiology, School of Public Health, Fourth Military Medical University, Xi'an 710032, PR China
| | - Chang-You Yan
- Family Planning Service Stations of Health and Family Planning Commission of Chengcheng County, Weinan City 714000, PR China.
| | - Rui Ling
- Department of Thyroid Gland and Breast Vascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, PR China.
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