1
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Pan L, Parini P, Tremmel R, Loscalzo J, Lauschke VM, Maron BA, Paci P, Ernberg I, Tan NS, Liao Z, Yin W, Rengarajan S, Li X. Single Cell Atlas: a single-cell multi-omics human cell encyclopedia. Genome Biol 2024; 25:104. [PMID: 38641842 PMCID: PMC11027364 DOI: 10.1186/s13059-024-03246-2] [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: 11/16/2022] [Accepted: 04/12/2024] [Indexed: 04/21/2024] Open
Abstract
Single-cell sequencing datasets are key in biology and medicine for unraveling insights into heterogeneous cell populations with unprecedented resolution. Here, we construct a single-cell multi-omics map of human tissues through in-depth characterizations of datasets from five single-cell omics, spatial transcriptomics, and two bulk omics across 125 healthy adult and fetal tissues. We construct its complement web-based platform, the Single Cell Atlas (SCA, www.singlecellatlas.org ), to enable vast interactive data exploration of deep multi-omics signatures across human fetal and adult tissues. The atlas resources and database queries aspire to serve as a one-stop, comprehensive, and time-effective resource for various omics studies.
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Affiliation(s)
- Lu Pan
- Institute of Environmental Medicine, Karolinska Institutet, 171 65, Solna, Sweden
| | - Paolo Parini
- Cardio Metabolic Unit, Department of Medicine, and, Department of Laboratory Medicine , Karolinska Institutet, 141 86, Stockholm, Sweden
- Theme Inflammation and Ageing, Medicine Unit, Karolinska University Hospital, 141 86, Stockholm, Sweden
| | - Roman Tremmel
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
- University of Tuebingen, 72076, Tuebingen, Germany
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Volker M Lauschke
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
- University of Tuebingen, 72076, Tuebingen, Germany
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 65, Solna, Sweden
| | - Bradley A Maron
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185, Rome, Italy
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Solna, Sweden
| | - Nguan Soon Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, 308232, Singapore
| | - Zehuan Liao
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Solna, Sweden
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Weiyao Yin
- Institute of Environmental Medicine, Karolinska Institutet, 171 65, Solna, Sweden
| | - Sundararaman Rengarajan
- Department of Physical Therapy, Movement & Rehabilitation Sciences, Northeastern University, Boston, MA, 02115, USA
| | - Xuexin Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65, Solna, Sweden.
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2
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Zhang P, Zhang W, Wang X, Li L, Lin Y, Wu N, Mao R, Lin J, Kang M, Ding C. BCLAF1 drives esophageal squamous cell carcinoma progression through regulation of YTHDF2-dependent SIX1 mRNA degradation. Cancer Lett 2024; 591:216874. [PMID: 38636894 DOI: 10.1016/j.canlet.2024.216874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/01/2024] [Accepted: 04/07/2024] [Indexed: 04/20/2024]
Abstract
Esophageal cancer ranks among the most prevalent malignant tumors, and esophageal squamous cell carcinoma (ESCC) constitutes its predominant histological form. Despite its impact, a thorough insight into the molecular intricacies of ESCC's development is still incomplete, which hampers the advancement of targeted molecular diagnostics and treatments. Recently, B-cell lymphoma-2-associated transcription factor 1 (BCLAF1) has come under investigation for its potential involvement in tumor biology, yet its specific role and mechanism in ESCC remain unclear. In this study, we observed a marked increase in BCLAF1 expression in ESCC tissues, correlating with advanced tumor stages and inferior patient outcomes. Our comprehensive in vitro and in vivo studies show that BCLAF1 augments glycolytic activity and the proliferation, invasion, and spread of ESCC cells. By employing mass spectrometry, we identified YTHDF2 as a key protein interacting with BCLAF1 in ESCC, with further validation provided by colocalization, co-immunoprecipitation, and GST pull-down assay. Further investigations involving MeRIP-seq and RIP-seq, alongside transcriptomic analysis, highlighted SIX1 mRNA as a molecule significantly upregulated and modified by N6-methyladenosine (m6A) in BCLAF1 overexpressing cells. BCLAF1 was found to reduce the tumor-suppressive activities of YTHDF2, and its effects on promoting glycolysis and cancer progression were shown to hinge on SIX1 expression. This research establishes that BCLAF1 fosters glycolysis and tumor progression in ESCC through the YTHDF2-SIX1 pathway in an m6A-specific manner, suggesting a potential target for future therapeutic intervention.
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Affiliation(s)
- Peipei Zhang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Weiguang Zhang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Xiaoqing Wang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Lingling Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Ye Lin
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Ningzi Wu
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Renyan Mao
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Jihong Lin
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Mingqiang Kang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China; Department of Cardiothoracic Surgery, Affiliated Hospital of Putian University, Putian, 351100, China; Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, 350108, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, 200433, China.
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3
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Yan H, Wu X, Li H, Yu Z, Jin X. Pan-Cancer Analysis Identifies BCLAF1 as a Potential Biomarker for Renal Cell Carcinoma. Biochem Genet 2024:10.1007/s10528-024-10773-x. [PMID: 38573525 DOI: 10.1007/s10528-024-10773-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 03/04/2024] [Indexed: 04/05/2024]
Abstract
B-cell lymphoma-2-associated transcription factor 1 (BCLAF1) is a versatile protein involved in the regulation of gene transcription and post-transcriptional processing. Although BCLAF1 exerts a broad tumor suppressor effect or tumor promoter effect in many cancer types, the specific roles concerning its expression levels, and its impact on tumorigenesis in Renal cell carcinoma (RCC) remain unclear. Here, we utilized the Cancer Genome Atlas (TCGA) and Genotype Tissue Expression (GTEx) datasets alongside R software and online tools to unravel the specific roles of BCLAF1 in 33 cancer types, including its expression levels, tumor immune and molecular subtypes, and its correlation with prognosis, diagnosis, DNA methylation, and immune microenvironment. Additionally, we carried out cell biology experiments to independently investigate the expression of BCLAF1 in RCC and its effects on tumor progression. BCLAF1 was differentially expressed in tumor tissues compared to normal tissues across various cancer types and was also differentially expressed in different immune and molecular subtypes. In RCC, patients with high BCLAF1 expression had a better prognosis and BCLAF1 was tightly correlated with the stage, gender, and histological grade of patients. Furthermore, BCLAF1 had higher DNA methylation levels and higher immune infiltration levels in tumor tissues. Additionally, cell functional experiments confirmed the low expression of BCLAF1 in RCC and that BCLAF1 significantly inhibited the proliferation, migration, and invasion, while inducing apoptosis and cell cycle arrest in RCC cells in vitro. Our study under-scored the potential of BCLAF1 as an important actor in tumorigenesis, especially concerning RCC where it may serve as an effective prognostic marker.
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Affiliation(s)
- Huan Yan
- Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Xiang Wu
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Hong Li
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Zongdong Yu
- Department of Neurosurgery, Shangrao People's Hospital, Shangrao, 334099, China.
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China.
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China.
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4
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Zhou Y, Ran X, Han M. BCLAF1 is Expressed as a Potential Anti-oncogene in Bile Duct Cancer. Biochem Genet 2024:10.1007/s10528-023-10616-1. [PMID: 38198022 DOI: 10.1007/s10528-023-10616-1] [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: 08/19/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
Abstract
Validating the role of BCLAF1 in the development of Bile Duct Cancer. Differential expression of BCLAF1 in Bile Duct Cancer and normal tissues was analyzed bioinformatically, and immuno-infiltration analysis was performed by R. We also derived the correlation between the expression of BCLAF1 and HIF-1α by bioinformatics analysis and validated it by Western Blotting, qRT-PCR and scratch assays before and after hypoxia. Through bioinformatics analysis, we found that BCLAF1 mRNA was significantly higher in the tumor tissues of Bile Duct Cancer. The high expression of BCLAF1 implied a more advanced stage but a lower mortality rate. KEGG and GO enrichment analysis showed that BCLAF1 overexpression in Bile Duct Cancer was mainly associated with histone modification, peptidyl lysine modification, and macromolecular methylation. We used the TIMER algorithm to show that BCLAF1 expression in Bile Duct Cancer is associated with immune cell infiltration, which affects tumor progression and patient prognosis. We confirmed by normoxia and hypoxia qRT-PCR, Western Blotting and scratch assays that BCLAF1 and HIF-1α expression are positively correlated and that BCLAF1 may be expressed as anti-oncogene in Bile Duct Cancer. These findings demonstrate that BCLAF1 may act as anti-oncogene in Bile Duct Cancer and may be involved in immune cell infiltration in Bile Duct Cancer, suppressing the expression of HIF-1α.
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Affiliation(s)
- Yutong Zhou
- Department of Postgraduates, Guizhou Medical University, Guizhou, China
| | - Xun Ran
- Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Min Han
- Affiliated Hospital of Guizhou Medical University, Guizhou, China.
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Beijing Road, Guiyang, 550000, Guizhou Province, China.
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5
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Shi Y, Guo Y, Zhou J, Cui G, Cheng J, Wu Y, Zhao Y, Fang L, Han X, Yang Y, Sun Y. A spatiotemporal gene expression and cell atlases of the developing rat ovary. Cell Prolif 2023; 56:e13516. [PMID: 37309718 PMCID: PMC10693188 DOI: 10.1111/cpr.13516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/14/2023] Open
Abstract
Normal ovarian development is necessary for the production of healthy oocytes. However, the characteristics of oocytes development at different stages and the regulatory relationship between oocytes and somatic cells remain to be fully explained. Here, we combined scRNA-seq and spatial transcriptomic sequencing to profile the transcriptomic atlas of developing ovarian of the rat. We identified four components from developing granulosa cells including cumulus, primitive, mural, and luteal cells, and constructed their differential transcriptional regulatory networks. Several novel growth signals from oocytes to cumulus cells were identified, such as JAG1-NOTCH2 and FGF9-FGFR2. Moreover, we observed three cumulus sequential phases during follicle development determined by the key transcriptional factors in each cumulus phase (Bckaf1, Gata6, Cebpb, etc.), as well as the potential pinpointed roles of macrophages in luteal regression. Altogether, the single-cell spatial transcriptomic profile of the ovary provides not only a new research dimension for temporal and spatial analysis of ovary development, but also valuable data resources and a research basis for in-depth excavation of the mechanisms of mammalian ovary development.
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Affiliation(s)
- Yong Shi
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
- Academy of medical sciencesZhengzhou UniversityZhengzhouChina
| | - Yanjie Guo
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Jiayi Zhou
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
- China National Center for BioinformationBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guanshen Cui
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
- China National Center for BioinformationBeijingChina
| | - Jung‐Chien Cheng
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Ying Wu
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
- China National Center for BioinformationBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yong‐Liang Zhao
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
- China National Center for BioinformationBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lanlan Fang
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Xiao Han
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
- China National Center for BioinformationBeijingChina
| | - Yun‐Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
- China National Center for BioinformationBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Institute of Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
| | - Yingpu Sun
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
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Wang J, Zhu X, Wang S, Zhang Y, Hua W, Liu Z, Zheng Y, Lu X. Phosphoproteomic and proteomic profiling in post-infarction chronic heart failure. Front Pharmacol 2023; 14:1181622. [PMID: 37405054 PMCID: PMC10315476 DOI: 10.3389/fphar.2023.1181622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023] Open
Abstract
Background: Post-infarction chronic heart failure is the most common type of heart failure. Patients with chronic heart failure show elevated morbidity and mortality with limited evidence-based therapies. Phosphoproteomic and proteomic analysis can provide insights regarding molecular mechanisms underlying post-infarction chronic heart failure and explore new therapeutic approaches. Methods and results: Global quantitative phosphoproteomic and proteomic analysis of left ventricular tissues from post-infarction chronic heart failure rats were performed. A total of 33 differentially expressed phosphorylated proteins (DPPs) and 129 differentially expressed proteins were identified. Bioinformatic analysis indicated that DPPs were enriched mostly in nucleocytoplasmic transport and mRNA surveillance pathway. Bclaf1 Ser658 was identified after construction of Protein-Protein Interaction Network and intersection with Thanatos Apoptosis Database. Predicted Upstream Kinases of DPPs based on kinase-substrate enrichment analysis (KSEA) app showed 13 kinases enhanced in heart failure. Proteomic analysis showed marked changes in protein expression related to cardiac contractility and metabolism. Conclusion: The present study marked phosphoproteomics and proteomics changes in post-infarction chronic heart failure. Bclaf1 Ser658 might play a critical role in apoptosis in heart failure. PRKAA1, PRKACA, and PAK1 might serve as potential therapeutic targets for post-infarction chronic heart failure.
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Affiliation(s)
| | | | | | | | | | | | - Yu Zheng
- *Correspondence: Yu Zheng, ; Xiao Lu,
| | - Xiao Lu
- *Correspondence: Yu Zheng, ; Xiao Lu,
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7
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Xing J, Wang H, Xie Y, Fan T, Cui C, Li Y, Wang S, Gu W, Wang C, Tang H, Liu L. Novel rare genetic variants of familial and sporadic pulmonary atresia identified by whole-exome sequencing. Open Life Sci 2023; 18:20220593. [PMID: 37215497 PMCID: PMC10199322 DOI: 10.1515/biol-2022-0593] [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: 11/09/2022] [Revised: 02/14/2023] [Accepted: 03/12/2023] [Indexed: 05/24/2023] Open
Abstract
Pulmonary atresia (PA) is a severe cyanotic congenital heart disease. Although some genetic mutations have been described to be associated with PA, the knowledge of pathogenesis is insufficient. The aim of this research was to use whole-exome sequencing (WES) to determine novel rare genetic variants in PA patients. We performed WES in 33 patients (27 patient-parent trios and 6 single probands) and 300 healthy control individuals. By applying an enhanced analytical framework to incorporate de novo and case-control rare variation, we identified 176 risk genes (100 de novo variants and 87 rare variants). Protein‒protein interaction (PPI) analysis and Genotype-Tissue Expression analysis revealed that 35 putative candidate genes had PPIs with known PA genes with high expression in the human heart. Expression quantitative trait loci analysis revealed that 27 genes that were identified as novel PA genes that could be affected by the surrounding single nucleotide polymorphism were screened. Furthermore, we screened rare damaging variants with a threshold of minor allele frequency at 0.5% in the ExAC_EAS and GnomAD_exome_EAS databases, and the deleteriousness was predicted by bioinformatics tools. For the first time, 18 rare variants in 11 new candidate genes have been identified that may play a role in the pathogenesis of PA. Our research provides new insights into the pathogenesis of PA and helps to identify the critical genes for PA.
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Affiliation(s)
- Junyue Xing
- Henan Key Laboratory of Chronic Disease Management, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, Henan, 451464, China
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People’s Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, Henan, 451464, China
| | - Hongdan Wang
- Medical Genetics Institute of Henan Province, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou 450003, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou 450002, China
| | - Yuanyuan Xie
- Department of Pediatrics, The Seventh Medical Center of Chinese PLA General Hospital, Beijing, 100700, China
| | - Taibing Fan
- Department of Children’s Heart Center, Henan Provincial People’s Hospital, Department of Children’s Heart Center of Central China Fuwai Hospital, Henan Key Medical Laboratory of Tertiary Prevention and Treatment for Congenital Heart Disease, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, Henan, 451464, China
| | - Cunying Cui
- Department of Ultrasound, Fuwai Central China Cardiovascular Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, 451464, China
| | - Yanan Li
- Department of Ultrasound, Fuwai Central China Cardiovascular Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, 451464, China
| | - Shuai Wang
- Department of Translational Medicine Center, Chigene (Beijing) Translational Medical Research Center Co., Beijing, 100176, China
| | - Weiyue Gu
- Department of Translational Medicine Center, Chigene (Beijing) Translational Medical Research Center Co., Beijing, 100176, China
| | - Chengzeng Wang
- Department of Ultrasound, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Hao Tang
- Henan Key Laboratory of Chronic Disease Management, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, Henan, 451464, China
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People’s Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, Henan, 451464, China
| | - Lin Liu
- Department of Ultrasound, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
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Zhao S, Pan T, Deng J, Cao L, Vicencio JM, Liu J, Zhou G, Ng T, Zhang J. Exosomal transfer of miR-181b-5p confers senescence-mediated doxorubicin resistance via modulating BCLAF1 in breast cancer. Br J Cancer 2023; 128:665-677. [PMID: 36522479 PMCID: PMC9938221 DOI: 10.1038/s41416-022-02077-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/25/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Doxorubicin resistance represents a major clinical challenge for treating patients with advanced breast cancer (BC). Exosomes, exchanging genetic cargo between heterogeneous populations of tumour cells, have been proposed to mediate drug resistance and cancer progression in other cancer types. However, their specific role in mediating doxorubicin resistance in BC remains unclear. Here, we demonstrate the important role of exosomal miR-181b-5p (exo-miR-181b-5p) in mediating doxorubicin resistance. METHODS Small-RNA sequencing and bioinformatic analyses were used to screen miRNAs mediating doxorubicin resistance in BC, which were further verified by RT-qPCR. SA-β-gal staining assays allowed us to measure cellular senescence. Exosomes from patients' serum before and after neoadjuvant chemotherapy were isolated for exo-miR-181b-5p quantification. RESULTS Doxorubicin-resistant BC cell lines exhibited upregulated exosomal miR-181b-5p. Addition of exo-miR-181b-5p actively fused with recipient cells and transferred a drug-resistant phenotype. Overexpression of miR-181b-5p downregulated p53/p21 levels and inhibited doxorubicin-induced G1 arrest and senescence by suppressing BCLAF1 expression in vitro. Further, in vivo experiments showed treatment of exo-miR-181b-5p inhibitors exhibited superior tumour control and reversed the doxorubicin-resistance phenotype, accompanied with increased tumoral BCLAF1. CONCLUSION Our data suggests exo-miR-181b-5p as a prognostic biomarker and a therapeutic potential for exo-miR-181b-5p inhibitors in the treatment of doxorubicin-resistant BC patients.
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Affiliation(s)
- Shaorong Zhao
- The 3rd Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Teng Pan
- The 3rd Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Jinhai Deng
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
| | - Lixia Cao
- Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Medical College of Nankai University, 300071, Tianjin, China
| | - Jose M Vicencio
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
- Cancer Institute, Paul O'Gorman Building, University College London, London, UK
| | - Jingjing Liu
- The 3rd Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Guanglin Zhou
- The 3rd Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Tony Ng
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
- Cancer Institute, Paul O'Gorman Building, University College London, London, UK
- Cancer Research UK City of London Centre, London, England
| | - Jin Zhang
- The 3rd Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China.
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9
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Tan W, Zhang J, Liu L, Liang M, Li J, Deng Z, Zheng Z, Deng Y, Liu C, Li Y, Xie G, Zhang J, Zou F, Chen X. Hsp90 Inhibitor STA9090 induced VPS35 related extracellular vesicle release and metastasis in hepatocellular carcinoma. Transl Oncol 2022; 26:101502. [PMID: 36137350 PMCID: PMC9493061 DOI: 10.1016/j.tranon.2022.101502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/28/2022] [Indexed: 11/05/2022] Open
Abstract
Heat shock protein 90 (Hsp90) has been an important therapeutic target for cancer therapy for decades. Unexpectedly, the monotherapy of N-terminal Hsp90 inhibitor STA9090 related clinical trials halted in phase III, and metastases were reported in animal models with the treatment of N-terminal Hsp90 inhibitors. Vacuolar protein sorting-associated protein 35 (VPS35) plays a vital role in endosome-derived EV (extracellular vesicle) traffic in neurodegeneration diseases, but no vps35 related EV were reported in tumors till now. Since tumor derived EVs contributes to metastasis and VPS35 is recently found to be involved in the invasion and metastasis of hepatocellular carcinoma (HCC), whether N-terminal Hsp90 inhibitor STA9090 induced EVs generation and the role of VPS35 in it were explored in this study. We found that N-terminal Hsp90 inhibitor STA9090 upregulated Bclaf1 and VPS35 levels, increased the secretion of EVs, and STA9090-induced-EVs promoted the invasion of HepG2 cells. As the clinical data suggested that the increased Bclaf1 and VPS35 levels correlated with increased metastasis and poorer prognosis in HCC, we focused on the Bclaf1-VPS35-EVs axis to further explore the mechanism of VPS35-related metastasis. The results demonstrated that Bclaf1 facilitated the transcription of VPS35 via bZIP domain, and knockdown of Bclaf1 or VPS35 alleviated pro-metastatic capability of STA9090-induced-EVs. All the results revealed the role of Bclaf1-VPS35-EVs axis on metastasis of HCC, and VPS35 knockdown decreased Hsp90 Inhibitor STA9090 induced extracellular vesicle release and metastasis, which provided a new combination therapeutic strategy to inhibit the metastasis of HCC caused by N-terminal Hsp90 inhibitor induced extracellular vesicles.
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Affiliation(s)
- Wenchong Tan
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jinxin Zhang
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Lixia Liu
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Manfeng Liang
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jieyou Li
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Zihao Deng
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Zhenming Zheng
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yaotang Deng
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Chenyang Liu
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yan Li
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Guantai Xie
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jiajie Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Fei Zou
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.
| | - Xuemei Chen
- Department of Occupational Health and Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.
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10
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Rashmi R, Majumdar S. Pan-Cancer Analysis Reveals the Prognostic Potential of the THAP9/THAP9-AS1 Sense-Antisense Gene Pair in Human Cancers. Noncoding RNA 2022; 8:ncrna8040051. [PMID: 35893234 PMCID: PMC9326536 DOI: 10.3390/ncrna8040051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022] Open
Abstract
Human THAP9, which encodes a domesticated transposase of unknown function, and lncRNA THAP9-AS1 (THAP9-antisense1) are arranged head-to-head on opposite DNA strands, forming a sense and antisense gene pair. We predict that there is a bidirectional promoter that potentially regulates the expression of THAP9 and THAP9-AS1. Although both THAP9 and THAP9-AS1 are reported to be involved in various cancers, their correlative roles on each other’s expression has not been explored. We analyzed the expression levels, prognosis, and predicted biological functions of the two genes across different cancer datasets (TCGA, GTEx). We observed that although the expression levels of the two genes, THAP9 and THAP9-AS1, varied in different tumors, the expression of the gene pair was strongly correlated with patient prognosis; higher expression of the gene pair was usually linked to poor overall and disease-free survival. Thus, THAP9 and THAP9-AS1 may serve as potential clinical biomarkers of tumor prognosis. Further, we performed a gene co-expression analysis (using WGCNA) followed by a differential gene correlation analysis (DGCA) across 22 cancers to identify genes that share the expression pattern of THAP9 and THAP9-AS1. Interestingly, in both normal and cancer samples, THAP9 and THAP9-AS1 often co-express; moreover, their expression is positively correlated in each cancer type, suggesting the coordinated regulation of this H2H gene pair.
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11
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Recurrent somatic mutations as predictors of immunotherapy response. Nat Commun 2022; 13:3938. [PMID: 35803911 PMCID: PMC9270330 DOI: 10.1038/s41467-022-31055-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/25/2022] [Indexed: 11/08/2022] Open
Abstract
Immune checkpoint blockade (ICB) has transformed the treatment of metastatic cancer but is hindered by variable response rates. A key unmet need is the identification of biomarkers that predict treatment response. To address this, we analyzed six whole exome sequencing cohorts with matched disease outcomes to identify genes and pathways predictive of ICB response. To increase detection power, we focus on genes and pathways that are significantly mutated following correction for epigenetic, replication timing, and sequence-based covariates. Using this technique, we identify several genes (BCLAF1, KRAS, BRAF, and TP53) and pathways (MAPK signaling, p53 associated, and immunomodulatory) as predictors of ICB response and develop the Cancer Immunotherapy Response CLassifiEr (CIRCLE). Compared to tumor mutational burden alone, CIRCLE led to superior prediction of ICB response with a 10.5% increase in sensitivity and a 11% increase in specificity. We envision that CIRCLE and more broadly the analysis of recurrently mutated cancer genes will pave the way for better prognostic tools for cancer immunotherapy.
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12
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Jiang K, Ding Y, Dong C, Shan F, Guo K, Zhang J, Zhang F. BCLAF1, a functional partner of BACH1, participates in DNA damage response. DNA Repair (Amst) 2022; 118:103371. [DOI: 10.1016/j.dnarep.2022.103371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 07/02/2022] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
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13
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Rykaczewska U, Zhao Q, Saliba-Gustafsson P, Lengquist M, Kronqvist M, Bergman O, Huang Z, Lund K, Waden K, Pons Vila Z, Caidahl K, Skogsberg J, Vukojevic V, Lindeman JHN, Roy J, Hansson GK, Treuter E, Leeper NJ, Eriksson P, Ehrenborg E, Razuvaev A, Hedin U, Matic L. Plaque Evaluation by Ultrasound and Transcriptomics Reveals BCLAF1 as a Regulator of Smooth Muscle Cell Lipid Transdifferentiation in Atherosclerosis. Arterioscler Thromb Vasc Biol 2022; 42:659-676. [PMID: 35321563 DOI: 10.1161/atvbaha.121.317018] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Understanding the processes behind carotid plaque instability is necessary to develop methods for identification of patients and lesions with stroke risk. Here, we investigated molecular signatures in human plaques stratified by echogenicity as assessed by duplex ultrasound. METHODS Lesion echogenicity was correlated to microarray gene expression profiles from carotid endarterectomies (n=96). The findings were extended into studies of human and mouse atherosclerotic lesions in situ, followed by functional investigations in vitro in human carotid smooth muscle cells (SMCs). RESULTS Pathway analyses highlighted muscle differentiation, iron homeostasis, calcification, matrix organization, cell survival balance, and BCLAF1 (BCL2 [B-cell lymphoma 2]-associated transcription factor 1) as the most significant signatures. BCLAF1 was downregulated in echolucent plaques, positively correlated to proliferation and negatively to apoptosis. By immunohistochemistry, BCLAF1 was found in normal medial SMCs. It was repressed early during atherogenesis but reappeared in CD68+ cells in advanced plaques and interacted with BCL2 by proximity ligation assay. In cultured SMCs, BCLAF1 was induced by differentiation factors and mitogens and suppressed by macrophage-conditioned medium. BCLAF1 silencing led to downregulation of BCL2 and SMC markers, reduced proliferation, and increased apoptosis. Transdifferentiation of SMCs by oxLDL (oxidized low-denisty lipoprotein) was accompanied by upregulation of BCLAF1, CD36, and CD68, while oxLDL exposure with BCLAF1 silencing preserved MYH (myosin heavy chain) 11 expression and prevented transdifferentiation. BCLAF1 was associated with expression of cell differentiation, contractility, viability, and inflammatory genes, as well as the scavenger receptors CD36 and CD68. BCLAF1 expression in CD68+/BCL2+ cells of SMC origin was verified in plaques from MYH11 lineage-tracing atherosclerotic mice. Moreover, BCLAF1 downregulation associated with vulnerability parameters and cardiovascular risk in patients with carotid atherosclerosis. CONCLUSIONS Plaque echogenicity correlated with enrichment of distinct molecular pathways and identified BCLAF1, previously not described in atherosclerosis, as the most significant gene. Functionally, BCLAF1 seems necessary for survival and transdifferentiation of SMCs into a macrophage-like phenotype. The role of BCLAF1 in plaque vulnerability should be further evaluated.
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Affiliation(s)
- Urszula Rykaczewska
- Division of Vascular Surgery, Department of Molecular Medicine and Surgery (U.R., M.L., M.K., K.L., K.W., K.C., J.R., A.R., U.H., L.M.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Quanyi Zhao
- Division of Cardiovascular Medicine, Cardiovascular Institute (Q.Z., P.S.-G.), Stanford University School of Medicine, CA
| | - Peter Saliba-Gustafsson
- Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine (P.S.-G., O.B., G.K.H., P.E., E.E.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Division of Cardiovascular Medicine, Cardiovascular Institute (Q.Z., P.S.-G.), Stanford University School of Medicine, CA
| | - Mariette Lengquist
- Division of Vascular Surgery, Department of Molecular Medicine and Surgery (U.R., M.L., M.K., K.L., K.W., K.C., J.R., A.R., U.H., L.M.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Malin Kronqvist
- Division of Vascular Surgery, Department of Molecular Medicine and Surgery (U.R., M.L., M.K., K.L., K.W., K.C., J.R., A.R., U.H., L.M.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Otto Bergman
- Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine (P.S.-G., O.B., G.K.H., P.E., E.E.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Zhiqiang Huang
- Department of Biosciences and Nutrition (Z.H., E.T.), Karolinska Institutet, Stockholm, Sweden
| | - Kent Lund
- Division of Vascular Surgery, Department of Molecular Medicine and Surgery (U.R., M.L., M.K., K.L., K.W., K.C., J.R., A.R., U.H., L.M.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Katarina Waden
- Division of Vascular Surgery, Department of Molecular Medicine and Surgery (U.R., M.L., M.K., K.L., K.W., K.C., J.R., A.R., U.H., L.M.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Zara Pons Vila
- Clinical Chemistry and Blood Coagulation, Department of Molecular Medicine and Surgery (Z.P.V.), Karolinska Institutet, Stockholm, Sweden
| | - Kenneth Caidahl
- Division of Vascular Surgery, Department of Molecular Medicine and Surgery (U.R., M.L., M.K., K.L., K.W., K.C., J.R., A.R., U.H., L.M.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Clinical Physiology, Sahlgrenska University Hospital and Molecular and Clinical Medicine, University of Gothenburg, Sweden (K.C.)
| | - Josefin Skogsberg
- Department of Medical Biochemistry and Biophysics (J.S.), Karolinska Institutet, Stockholm, Sweden
| | - Vladana Vukojevic
- Department of Clinical Neuroscience, Center for Molecular Medicine (V.V.), Karolinska Institutet, Stockholm, Sweden
| | - Jan H N Lindeman
- Department of Vascular Surgery, Leiden University Medical Center, the Netherlands (J.H.N.L.)
| | - Joy Roy
- Division of Vascular Surgery, Department of Molecular Medicine and Surgery (U.R., M.L., M.K., K.L., K.W., K.C., J.R., A.R., U.H., L.M.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Göran K Hansson
- Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine (P.S.-G., O.B., G.K.H., P.E., E.E.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Eckardt Treuter
- Department of Biosciences and Nutrition (Z.H., E.T.), Karolinska Institutet, Stockholm, Sweden
| | - Nicholas J Leeper
- Department of Surgery (N.J.L.), Stanford University School of Medicine, CA.,Department of Medicine (N.J.L.), Stanford University School of Medicine, CA
| | - Per Eriksson
- Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine (P.S.-G., O.B., G.K.H., P.E., E.E.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Ewa Ehrenborg
- Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine (P.S.-G., O.B., G.K.H., P.E., E.E.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Anton Razuvaev
- Division of Vascular Surgery, Department of Molecular Medicine and Surgery (U.R., M.L., M.K., K.L., K.W., K.C., J.R., A.R., U.H., L.M.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Ulf Hedin
- Division of Vascular Surgery, Department of Molecular Medicine and Surgery (U.R., M.L., M.K., K.L., K.W., K.C., J.R., A.R., U.H., L.M.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Ljubica Matic
- Division of Vascular Surgery, Department of Molecular Medicine and Surgery (U.R., M.L., M.K., K.L., K.W., K.C., J.R., A.R., U.H., L.M.), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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14
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Pellegrina D, Bahcheli AT, Krassowski M, Reimand J. Human phospho-signaling networks of SARS-CoV-2 infection are rewired by population genetic variants. Mol Syst Biol 2022; 18:e10823. [PMID: 35579274 PMCID: PMC9112486 DOI: 10.15252/msb.202110823] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/23/2022] Open
Abstract
SARS-CoV-2 infection hijacks signaling pathways and induces protein-protein interactions between human and viral proteins. Human genetic variation may impact SARS-CoV-2 infection and COVID-19 pathology; however, the genetic variation in these signaling networks remains uncharacterized. Here, we studied human missense single nucleotide variants (SNVs) altering phosphorylation sites modulated by SARS-CoV-2 infection, using machine learning to identify amino acid substitutions altering kinase-bound sequence motifs. We found 2,033 infrequent phosphorylation-associated SNVs (pSNVs) that are enriched in sequence motif alterations, potentially reflecting the evolution of signaling networks regulating host defenses. Proteins with pSNVs are involved in viral life cycle and host responses, including RNA splicing, interferon response (TRIM28), and glucose homeostasis (TBC1D4) with potential associations with COVID-19 comorbidities. pSNVs disrupt CDK and MAPK substrate motifs and replace these with motifs of Tank Binding Kinase 1 (TBK1) involved in innate immune responses, indicating consistent rewiring of signaling networks. Several pSNVs associate with severe COVID-19 and hospitalization (STARD13, ARFGEF2). Our analysis highlights potential genetic factors contributing to inter-individual variation of SARS-CoV-2 infection and COVID-19 and suggests leads for mechanistic and translational studies.
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Affiliation(s)
- Diogo Pellegrina
- Computational Biology ProgramOntario Institute for Cancer ResearchTorontoONCanada
| | - Alexander T Bahcheli
- Computational Biology ProgramOntario Institute for Cancer ResearchTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Michal Krassowski
- Medical Sciences DivisionNuffield Department of Women's and Reproductive HealthUniversity of OxfordOxfordUK
| | - Jüri Reimand
- Computational Biology ProgramOntario Institute for Cancer ResearchTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoONCanada
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15
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Sirtuins are crucial regulators of T cell metabolism and functions. Exp Mol Med 2022; 54:207-215. [PMID: 35296782 PMCID: PMC8979958 DOI: 10.1038/s12276-022-00739-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/23/2021] [Indexed: 01/01/2023] Open
Abstract
It is well known that metabolism underlies T cell differentiation and functions. The pathways regulating T cell metabolism and function are interconnected, and changes in T cell metabolic activity directly impact the effector functions and fate of T cells. Thus, understanding how metabolic pathways influence immune responses and ultimately affect disease progression is paramount. Epigenetic and posttranslational modification mechanisms have been found to control immune responses and metabolic reprogramming. Sirtuins are NAD+-dependent histone deacetylases that play key roles during cellular responses to a variety of stresses and have recently been reported to have potential roles in immune responses. Therefore, sirtuins are of significant interest as therapeutic targets to treat immune-related diseases and enhance antitumor immunity. This review aims to illustrate the potential roles of sirtuins in different subtypes of T cells during the adaptive immune response. Sirtuins, enzymes that regulate how cells respond to stress, regulate T cell metabolism and functions, and therefore blocking or boosting sirtuins influences immune responses. As part of the immune system, some types of T cells attack specific targets; others keep the immune response in check. Imene Hamaidi and Sungjune Kim at H. Lee Moffitt Cancer Center, Tampa, USA, have reviewed how sirtuins affect different subsets of T cells to either promote or suppress immune responses. Boosting sirtuins that increase the function of inflammation-suppressing T cells can improve outcomes for transplant recipients or help treat autoimmune diseases. Conversely, stimulating immune-activating sirtuins can help re-energize exhausted antitumor T cells. Understanding the complex web of sirtuin–T cell interactions may help in developing therapeutic strategies for improving transplant outcomes, and for treating autoimmune diseases and cancer.
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16
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Yu Z, Zhu J, Wang H, Li H, Jin X. Function of BCLAF1 in human disease. Oncol Lett 2022; 23:58. [PMID: 34992690 PMCID: PMC8721854 DOI: 10.3892/ol.2021.13176] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/22/2021] [Indexed: 02/06/2023] Open
Abstract
Originally identified as a regulator of apoptosis and transcription, B-cell lymphoma-2-associated transcription factor 1 (BCLAF1) has since been shown to be associated with a multitude of biological processes, such as DNA damage response, splicing and processing of pre-mRNA, T-cell activation, lung development, muscle cell proliferation and differentiation, autophagy, ischemia-reperfusion injury, and viral infection. In recent years, an increasing amount of evidence has shown that BCLAF1 acts as either a tumor promoter or tumor suppressor in tumorigenesis depending on the cellular context and the type of cancer. Even in the same tumor type, BCLAF1 may have opposite effects. In the present review, the subcellular localization, structural features, mutations within BCLAF1 will be described, then the regulation of BCLAF1 and its downstream targets will be analyzed. Furthermore, the different roles and possible mechanisms of BCLAF1 in tumorigenesis will also be highlighted and discussed. Finally, BCLAF1 may be considered as a potential target for cancer therapy in the future.
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Affiliation(s)
- Zongdong Yu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China.,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China.,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Haibiao Wang
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Hong Li
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China.,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Xiaofeng Jin
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China.,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, Zhejiang 315211, P.R. China
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17
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Zhang R, Xue T, Shao A, Lang Y, Qin C, Zhao M, Kuang Y, Yu Z, Geng Y, Zhao C, Tang J. Bclaf1 regulates c-FLIP expression and protects cells from TNF-induced apoptosis and tissue injury. EMBO Rep 2022; 23:e52702. [PMID: 34693625 PMCID: PMC8728627 DOI: 10.15252/embr.202152702] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 09/27/2021] [Accepted: 10/06/2021] [Indexed: 01/07/2023] Open
Abstract
TNF stimulation generates pro-survival signals through activation of NF-κB that restrict the build-in death signaling triggered by TNF. The competition between TNF-induced survival and death signals ultimately determines the fate of a cell. Here, we report the identification of Bclaf1 as a novel component of the anti-apoptotic program of TNF. Bclaf1 depletion in multiple cells sensitizes cells to TNF-induced apoptosis but not to necroptosis. Bclaf1 exerts its anti-apoptotic function by promoting the transcription of CFLAR, a caspase 8 antagonist, downstream of NF-κB activation. Bclaf1 binds to the p50 subunit of NF-κB, which is required for Bclaf1 to stimulate CFLAR transcription. Finally, in Bclaf1 siRNA administered mice, TNF-induced small intestine injury is much more severe than in control mice with aggravated signs of apoptosis and pyroptosis. These results suggest Bclaf1 is a key regulator in TNF-induced apoptosis, both in vitro and in vivo.
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Affiliation(s)
- Rui Zhang
- College of Veterinary MedicineChina Agricultural UniversityBeijingChina
| | - Teng Xue
- College of Veterinary MedicineChina Agricultural UniversityBeijingChina
| | - Anwen Shao
- College of Veterinary MedicineChina Agricultural UniversityBeijingChina
| | - Yue Lang
- College of Veterinary MedicineChina Agricultural UniversityBeijingChina
| | - Chao Qin
- College of Veterinary MedicineChina Agricultural UniversityBeijingChina
| | - Mingliang Zhao
- College of Veterinary MedicineChina Agricultural UniversityBeijingChina
| | - Yu Kuang
- College of Veterinary MedicineChina Agricultural UniversityBeijingChina
| | - Zhengquan Yu
- State Key Laboratories for Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health and, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yunyun Geng
- Hebei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular DiseaseHebei University of Chinese MedicineShijiazhuangHebeiChina
| | - Chenyang Zhao
- School of Medicine and PharmacyOcean University of ChinaQingdaoChina
| | - Jun Tang
- College of Veterinary MedicineChina Agricultural UniversityBeijingChina
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18
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Shen P, Deng X, Chen Z, Ba X, Qin K, Huang Y, Huang Y, Li T, Yan J, Tu S. SIRT1: A Potential Therapeutic Target in Autoimmune Diseases. Front Immunol 2021; 12:779177. [PMID: 34887866 PMCID: PMC8650132 DOI: 10.3389/fimmu.2021.779177] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/08/2021] [Indexed: 12/21/2022] Open
Abstract
The morbidity and mortality of autoimmune diseases (Ads) have been increasing worldwide, and the identification of novel therapeutic strategies for prevention and treatment is urgently needed. Sirtuin 1 (SIRT1), a member of the class III family of nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylases, has been reported to participate in the progression of several diseases. SIRT1 also regulates inflammation, oxidative stress, mitochondrial function, immune responses, cellular differentiation, proliferation and metabolism, and its altered functions are likely involved in Ads. Several inhibitors and activators have been shown to affect the development of Ads. SIRT1 may represent a novel therapeutic target in these diseases, and small molecules or natural products that modulate the functions of SIRT1 are potential therapeutic agents. In the present review, we summarize current studies of the biological functions of SIRT1 and its role in the pathogenesis and treatment of Ads.
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Affiliation(s)
- Pan Shen
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Xuan Deng
- Department of Nephrology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhe Chen
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Xin Ba
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Kai Qin
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Ying Huang
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Yao Huang
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Li
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Jiahui Yan
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Shenghao Tu
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
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Wu YJ, Fang WJ, Pan S, Zhang SS, Li DF, Wang ZF, Chen WG, Yin Q, Zuo J. Regulation of Sirt1 on energy metabolism and immune response in rheumatoid arthritis. Int Immunopharmacol 2021; 101:108175. [PMID: 34689102 DOI: 10.1016/j.intimp.2021.108175] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 12/21/2022]
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease. Synovial hyperplasia and persistent inflammation serve as its typical pathological manifestations, which ultimately lead to joint destruction and function loss. Both clinical observations and metabolomics studies have revealed the prevalence of metabolic disorders in RA. In inflammatory immune microenvironments, energy metabolism is profoundly changed. Increasingly evidences suggest that this abnormality is involved in the occurrence and development of RA-related inflammation. Unsurprisingly, many energy metabolism sensors have been confirmed with immunoregulatory properties. As a representative, silent information regulator type 1 (Sirt1) controls many aspects of immune cells, such as cell lifespan, polarization, and secretion by functioning as a transcriptional regulator. Because of the profound clinical implication, researches on Sirt1 in the regulation of energy metabolism and immune functions under RA conditions have gradually gained momentum. This signaling balances glycolysis, lipid metabolism and insulin secretion orchestrating with other metabolism sensors, and consequently affects immune milieu through a so-called metabolism-immune feedback mechanism. This article reviews the involvement of Sirt1 in RA by discussing its impacts on energy metabolism and immune functions, and specially highlights the potential of Sirt1-targeting anti-rheumatic regimens. It also provides a theoretical basis for clarifying the mystery about the high incidence of metabolic complications in RA patients and identifying new anti-rheumatic reagents.
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Affiliation(s)
- Yi-Jin Wu
- Department of Pharmacy, the Second Affiliated Hospital of Wannan Medical College, Wuhu, China; Xin'An Medicine Research Center, Wannan Medical College, Wuhu, China
| | - Wen-Juan Fang
- The Second People's Hospital of Hefei, Heifei, China
| | - Shu Pan
- Department of Pharmacy, the Second Affiliated Hospital of Wannan Medical College, Wuhu, China; Xin'An Medicine Research Center, Wannan Medical College, Wuhu, China
| | - Sa-Sa Zhang
- Department of Pharmacy, the Second Affiliated Hospital of Wannan Medical College, Wuhu, China; Xin'An Medicine Research Center, Wannan Medical College, Wuhu, China
| | - Dan-Feng Li
- Department of Traditional Chinese Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital), Wuhu, China
| | - Zhong-Fang Wang
- Department of Pharmacy, the Second Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Wen-Gang Chen
- Department of Pharmacy, the Second Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Qin Yin
- Department of Pharmacy, the Second Affiliated Hospital of Wannan Medical College, Wuhu, China.
| | - Jian Zuo
- Department of Traditional Chinese Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital), Wuhu, China; Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, China.
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20
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The Role of Emerin in Cancer Progression and Metastasis. Int J Mol Sci 2021; 22:ijms222011289. [PMID: 34681951 PMCID: PMC8537873 DOI: 10.3390/ijms222011289] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/27/2022] Open
Abstract
It is commonly recognized in the field that cancer cells exhibit changes in the size and shape of their nuclei. These features often serve as important biomarkers in the diagnosis and prognosis of cancer patients. Nuclear size can significantly impact cell migration due to its incredibly large size. Nuclear structural changes are predicted to regulate cancer cell migration. Nuclear abnormalities are common across a vast spectrum of cancer types, regardless of tissue source, mutational spectrum, and signaling dependencies. The pervasiveness of nuclear alterations suggests that changes in nuclear structure may be crucially linked to the transformation process. The factors driving these nuclear abnormalities, and the functional consequences, are not completely understood. Nuclear envelope proteins play an important role in regulating nuclear size and structure in cancer. Altered expression of nuclear lamina proteins, including emerin, is found in many cancers and this expression is correlated with better clinical outcomes. A model is emerging whereby emerin, as well as other nuclear lamina proteins, binding to the nucleoskeleton regulates the nuclear structure to impact metastasis. In this model, emerin and lamins play a central role in metastatic transformation, since decreased emerin expression during transformation causes the nuclear structural defects required for increased cell migration, intravasation, and extravasation. Herein, we discuss the cellular functions of nuclear lamina proteins, with a particular focus on emerin, and how these functions impact cancer progression and metastasis.
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Complete lung agenesis caused by complex genomic rearrangements with neo-TAD formation at the SHH locus. Hum Genet 2021; 140:1459-1469. [PMID: 34436670 PMCID: PMC8460539 DOI: 10.1007/s00439-021-02344-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/10/2021] [Indexed: 11/05/2022]
Abstract
During human organogenesis, lung development is a timely and tightly regulated developmental process under the control of a large number of signaling molecules. Understanding how genetic variants can disturb normal lung development causing different lung malformations is a major goal for dissecting molecular mechanisms during embryogenesis. Here, through exome sequencing (ES), array CGH, genome sequencing (GS) and Hi-C, we aimed at elucidating the molecular basis of bilateral isolated lung agenesis in three fetuses born to a non-consanguineous family. We detected a complex genomic rearrangement containing duplicated, triplicated and deleted fragments involving the SHH locus in fetuses presenting complete agenesis of both lungs and near-complete agenesis of the trachea, diagnosed by ultrasound screening and confirmed at autopsy following termination. The rearrangement did not include SHH itself, but several regulatory elements for lung development, such as MACS1, a major SHH lung enhancer, and the neighboring genes MNX1 and NOM1. The rearrangement incorporated parts of two topologically associating domains (TADs) including their boundaries. Hi-C of cells from one of the affected fetuses showed the formation of two novel TADs each containing SHH enhancers and the MNX1 and NOM1 genes. Hi-C together with GS indicate that the new 3D conformation is likely causative for this condition by an inappropriate activation of MNX1 included in the neo-TADs by MACS1 enhancer, further highlighting the importance of the 3D chromatin conformation in human disease.
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Doan P, Nguyen P, Murugesan A, Subramanian K, Konda Mani S, Kalimuthu V, Abraham BG, Stringer BW, Balamuthu K, Yli-Harja O, Kandhavelu M. Targeting Orphan G Protein-Coupled Receptor 17 with T0 Ligand Impairs Glioblastoma Growth. Cancers (Basel) 2021; 13:cancers13153773. [PMID: 34359676 PMCID: PMC8345100 DOI: 10.3390/cancers13153773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/10/2021] [Accepted: 07/22/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Glioblastoma multiforme (GBM), or glioblastoma chemotherapy, has one of the poorest improvements across all types of cancers. Despite the different rationales explored in targeted therapy for taming the GBM aggressiveness, its phenotypic plasticity, drug toxicity, and adaptive resistance mechanisms pose many challenges in finding an effective cure. Our manuscript reports the expression and prognostic role of orphan receptor GPR17 in glioma, the molecular mechanism of action of the novel ligand of GPR17, and provides evidence how the T0 agonist promotes glioblastoma cell death through modulation of the MAPK/ERK, PI3K–Akt, STAT, and NF-κB pathways. The highlights are as follows: GPR17 expression is associated with greater survival for both low-grade glioma (LGG) and GBM; GA-T0, a potent GPR17 receptor agonist, causes significant GBM cell death and apoptosis; GPR17 signaling promotes cell cycle arrest at the G1 phase in GBM cells; key genes are modulated in the signaling pathways that inhibit GBM cell proliferation; and GA-T0 crosses the blood–brain barrier and reduces tumor volume. Abstract Glioblastoma, an invasive high-grade brain cancer, exhibits numerous treatment challenges. Amongst the current therapies, targeting functional receptors and active signaling pathways were found to be a potential approach for treating GBM. We exploited the role of endogenous expression of GPR17, a G protein-coupled receptor (GPCR), with agonist GA-T0 in the survival and treatment of GBM. RNA sequencing was performed to understand the association of GPR17 expression with LGG and GBM. RT-PCR and immunoblotting were performed to confirm the endogenous expression of GPR17 mRNA and its encoded protein. Biological functions of GPR17 in the GBM cells was assessed by in vitro analysis. HPLC and histopathology in wild mice and an acute-toxicity analysis in a patient-derived xenograft model were performed to understand the clinical implication of GA-T0 targeting GPR17. We observed the upregulation of GPR17 in association with improved survival of LGG and GBM, confirming it as a predictive biomarker. GA-T0-stimulated GPR17 leads to the inhibition of cyclic AMP and calcium flux. GPR17 signaling activation enhances cytotoxicity against GBM cells and, in patient tissue-derived mesenchymal subtype GBM cells, induces apoptosis and prevents proliferation by stoppage of the cell cycle at the G1 phase. Modulation of the key genes involved in DNA damage, cell cycle arrest, and in several signaling pathways, including MAPK/ERK, PI3K–Akt, STAT, and NF-κB, prevents tumor regression. In vivo activation of GPR17 by GA-T0 reduces the tumor volume, uncovering the potential of GA-T0–GPR17 as a targeted therapy for GBM treatment. Conclusion: Our analysis suggests that GA-T0 targeting the GPR17 receptor presents a novel therapy for treating glioblastoma.
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Affiliation(s)
- Phuong Doan
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; (P.D.); (P.N.); (A.M.); (K.S.)
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520 Tampere, Finland
| | - Phung Nguyen
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; (P.D.); (P.N.); (A.M.); (K.S.)
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520 Tampere, Finland
| | - Akshaya Murugesan
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; (P.D.); (P.N.); (A.M.); (K.S.)
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520 Tampere, Finland
- Department of Biotechnology, Lady Doak College, Thallakulam, Madurai 625002, India
| | - Kumar Subramanian
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; (P.D.); (P.N.); (A.M.); (K.S.)
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520 Tampere, Finland
| | | | - Vignesh Kalimuthu
- Department of Animal Science, Bharathidasan University, Tiruchirappalli 620024, India; (V.K.); (K.B.)
| | - Bobin George Abraham
- Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland;
| | - Brett W. Stringer
- College of Medicine and Public Health, Flinders University, Sturt Rd., Bedford Park, SA 5042, Australia;
| | - Kadalmani Balamuthu
- Department of Animal Science, Bharathidasan University, Tiruchirappalli 620024, India; (V.K.); (K.B.)
| | - Olli Yli-Harja
- Computational Systems Biology Group, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland;
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; (P.D.); (P.N.); (A.M.); (K.S.)
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520 Tampere, Finland
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
- Correspondence: ; Tel.: +358-504721724
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Ma Z, Wang H, Meng F, Han Y, Chen Y, Xiao M, Jiang H, Yu Z, Xu B. Role of BCLAF-1 in PD-L1 stabilization in response to ionizing irradiation. Cancer Sci 2021; 112:4064-4074. [PMID: 34251713 PMCID: PMC8486183 DOI: 10.1111/cas.15056] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/30/2021] [Accepted: 07/10/2021] [Indexed: 11/28/2022] Open
Abstract
Programmed cell death ligand 1 (PD-L1) is a major immunosuppressive checkpoint protein expressed by tumor cells to subvert anticancer immunity. Recent studies have shown that ionizing radiation (IR) upregulates the expression of PD-L1 in tumor cells. However, whether an IR-induced DNA damage response (DDR) directly regulates PD-L1 expression and the functional significance of its upregulation are not fully understood. Here, we show that IR-induced upregulation of PD-L1 expression proceeds through both transcriptional and post-translational mechanisms. Upregulated PD-L1 was predominantly present on the cell membrane, resulting in T-cell apoptosis in a co-culture system. Using mass spectrometry, we identified PD-L1 interacting proteins and found that BCLAF1 (Bcl2 associated transcription factor 1) is an important regulator of PD-L1 in response to IR. BCLAF1 depletion decreased PD-L1 expression by promoting the ubiquitination of PD-L1. In addition, we show that CMTM6 is upregulated in response to IR and participates in BCLAF1-dependent PD-L1 upregulation. Finally, we demonstrated that the ATM/BCLAF1/PD-L1 axis regulated PD-L1 stabilization in response to IR. Together, our findings reveal a novel regulatory mechanism of PD-L1 expression in the DDR.
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Affiliation(s)
- Zhao Ma
- Department of Minimally Invasive Esophageal Surgery, Key Laboratory of Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Han Wang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Cancer Research Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Fanbiao Meng
- Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Cancer Research Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yamei Han
- Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Cancer Research Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yefei Chen
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Mingming Xiao
- Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Cancer Research Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Hongjing Jiang
- Department of Minimally Invasive Esophageal Surgery, Key Laboratory of Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhentao Yu
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Bo Xu
- Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Cancer Research Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Center for Intelligent Oncology, Chongqing University Cancer Hospital, Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer, Chongqing University School of Medicine, Chongqing, China
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24
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Shahbaz S, Jovel J, Elahi S. Differential transcriptional and functional properties of regulatory T cells in HIV-infected individuals on antiretroviral therapy and long-term non-progressors. Clin Transl Immunology 2021; 10:e1289. [PMID: 34094548 PMCID: PMC8155695 DOI: 10.1002/cti2.1289] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/09/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Objectives Regulatory T cells (Tregs) are widely recognised as a subset of CD4+CD25+FOXP3+ T cells that have a key role in maintaining immune homeostasis. The impact of HIV‐1 infection on immunological properties and effector functions of Tregs has remained the topic of debate and controversy. In the present study, we investigated transcriptional profile and functional properties of Tregs in HIV‐1‐infected individuals either receiving antiretroviral therapy (ART, n = 50) or long‐term non‐progressors (LTNPs, n = 24) compared to healthy controls (HCs, n = 38). Methods RNA sequencing (RNAseq), flow cytometry‐based immunophenotyping and functional assays were performed to study Tregs in different HIV cohorts. Results Our RNAseq analysis revealed that Tregs exhibit different transcriptional profiles in HIV‐infected individuals. While Tregs from patients on ART upregulate pathways associated with a more suppressive (activated) phenotype, Tregs in LTNPs exhibit upregulation of pathways associated with impaired suppressive properties. These observations may explain a higher propensity for autoimmune diseases in LTNPs. Also, we found substantial upregulation of HLA‐F mRNA and HLA‐F protein in Tregs from HIV‐infected subjects compared to healthy individuals. These observations highlight a potential role for this non‐classical HLA in Tregs in the context of HIV infection, which should be investigated further in other chronic viral infections and cancer. Conclusion Our study has provided a novel insight into Tregs at the transcriptional and functional levels in different HIV‐infected groups.
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Affiliation(s)
- Shima Shahbaz
- School of Dentistry Faculty of Medicine and Dentistry University of Alberta Edmonton AB Canada
| | - Juan Jovel
- School of Dentistry Faculty of Medicine and Dentistry University of Alberta Edmonton AB Canada
| | - Shokrollah Elahi
- School of Dentistry Faculty of Medicine and Dentistry University of Alberta Edmonton AB Canada.,Department of Medical Microbiology and Immunology Faculty of Medicine and Dentistry University of Alberta Edmonton AB Canada.,Department of Oncology Faculty of Medicine and Dentistry University of Alberta Edmonton AB Canada.,Li Ka Shing Institute of Virology Faculty of Medicine and Dentistry University of Alberta Edmonton AB Canada
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25
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Qiu Y, Zhou X, Liu Y, Tan S, Li Y. The Role of Sirtuin-1 in Immune Response and Systemic Lupus Erythematosus. Front Immunol 2021; 12:632383. [PMID: 33981300 PMCID: PMC8110204 DOI: 10.3389/fimmu.2021.632383] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a potentially fatal multisystem inflammatory chronic disorder, the etiology and pathogenesis of which remain unclear. The loss of immune tolerance in SLE patients contributes to the production of autoantibodies that attack multiple organs and tissues, such as the skin, joints, and kidneys. Immune cells play important roles in the occurrence and progression of SLE through amplified immune responses. Sirtuin-1 (SIRT1), an NAD+-dependent histone deacetylase, has been shown to be a pivotal regulator in various physiological processes, including cell differentiation, apoptosis, metabolism, aging, and immune responses, via modulation of different signaling pathways, such as the nuclear factor κ-light-chain-enhancer of activated B cells and activator protein 1 pathways. Recent studies have provided evidence that SIRT1 could be a regulatory element in the immune system, whose altered functions are likely relevant to SLE development. This review aims to illustrate the functions of SIRT1 in different types of immune cells and the potential roles of SIRT1 in the SLE pathogenesis and its therapeutic perspectives.
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Affiliation(s)
- Yueqi Qiu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Xingyu Zhou
- Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Yu Liu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Siqi Tan
- Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Yaping Li
- Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
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26
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The long noncoding RNA lncCIRBIL disrupts the nuclear translocation of Bclaf1 alleviating cardiac ischemia-reperfusion injury. Nat Commun 2021; 12:522. [PMID: 33483496 PMCID: PMC7822959 DOI: 10.1038/s41467-020-20844-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 12/22/2020] [Indexed: 11/08/2022] Open
Abstract
Cardiac ischemia-reperfusion (I/R) injury is a pathological process resulting in cardiomyocyte death. The present study aims to evaluate the role of the long noncoding RNA Cardiac Injury-Related Bclaf1-Inhibiting LncRNA (lncCIRBIL) on cardiac I/R injury and delineate its mechanism of action. The level of lncCIRBIL is reduced in I/R hearts. Cardiomyocyte-specific transgenic overexpression of lncCIRBIL reduces infarct area following I/R injury. Knockout of lncCIRBIL in mice exacerbates cardiac I/R injury. Qualitatively, the same results are observed in vitro. LncCIRBIL directly binds to BCL2-associated transcription factor 1 (Bclaf1), to inhibit its nuclear translocation. Cardiomyocyte-specific transgenic overexpression of Bclaf1 worsens, while partial knockout of Bclaf1 mitigates cardiac I/R injury. Meanwhile, partial knockout of Bclaf1 abrogates the detrimental effects of lncCIRBIL knockout on cardiac I/R injury. Collectively, the protective effect of lncCIRBIL on I/R injury is accomplished by inhibiting the nuclear translocation of Bclaf1. LncCIRBIL and Bclaf1 are potential therapeutic targets for ischemic cardiac disease.
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RAG-Mediated DNA Breaks Attenuate PU.1 Activity in Early B Cells through Activation of a SPIC-BCLAF1 Complex. Cell Rep 2020; 29:829-843.e5. [PMID: 31644907 PMCID: PMC6870970 DOI: 10.1016/j.celrep.2019.09.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/10/2019] [Accepted: 09/09/2019] [Indexed: 11/22/2022] Open
Abstract
Early B cell development is regulated by stage-specific transcription
factors. PU.1, an ETS-family transcription factor, is essential for coordination
of early B cell maturation and immunoglobulin gene (Ig)
rearrangement. Here we show that RAG DNA double-strand breaks (DSBs) generated
during Ig light chain gene (Igl) rearrangement
in pre-B cells induce global changes in PU.1 chromatin binding. RAG DSBs
activate a SPIC/BCLAF1 transcription factor complex that displaces PU.1
throughout the genome and regulates broad transcriptional changes. SPIC recruits
BCLAF1 to gene-regulatory elements that control expression of key B cell
developmental genes. The SPIC/BCLAF1 complex suppresses expression of the SYK
tyrosine kinase and enforces the transition from large to small pre-B cells.
These studies reveal that RAG DSBs direct genome-wide changes in ETS
transcription factor activity to promote early B cell development. ETS-family transcription factors are key regulators of early B cell
development. Soodgupta et al. show that RAG-induced DNA breaks generated during
antigen receptor gene recombination activate a SPIC/BCLAF1 transcription factor
complex that counters PU.1 activity and regulates gene expression changes to
promote transition from large to small pre-B cells.
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Vincent M, Karolak JA, Deutsch G, Gambin T, Popek E, Isidor B, Szafranski P, Le Caignec C, Stankiewicz P. Clinical, Histopathological, and Molecular Diagnostics in Lethal Lung Developmental Disorders. Am J Respir Crit Care Med 2020; 200:1093-1101. [PMID: 31189067 DOI: 10.1164/rccm.201903-0495tr] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Lethal lung developmental disorders are a rare but important group of pediatric diffuse lung diseases presenting with neonatal respiratory failure. On the basis of histopathological appearance at lung biopsy or autopsy, they have been termed: alveolar capillary dysplasia with misalignment of the pulmonary veins, acinar dysplasia, congenital alveolar dysplasia, and other unspecified primary pulmonary hypoplasias. However, the histopathological continuum in these lethal developmental disorders has made accurate diagnosis challenging, which has implications for recurrence risk. Over the past decade, genetic studies in infants with alveolar capillary dysplasia with misalignment of the pulmonary veins have revealed the causative role of the dosage-sensitive FOXF1 gene and its noncoding regulatory variants in the distant lung-specific enhancer at chromosome 16q24.1. In contrast, the molecular bases of acinar dysplasia and congenital alveolar dysplasia have remained poorly understood. Most recently, disruption of the TBX4-FGF10-FGFR2 epithelial-mesenchymal signaling pathway has been reported in patients with these lethal pulmonary dysplasias. Application of next-generation sequencing techniques, including exome sequencing and whole-genome sequencing, has demonstrated their complex compound inheritance. These data indicate that noncoding regulatory elements play a critical role in lung development in humans. We propose that for more precise lethal lung developmental disorder diagnosis, a diagnostic pathway including whole-genome sequencing should be implemented.
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Affiliation(s)
- Marie Vincent
- Service de Genetique Medicale, Centre Hospitalier Universitaire de Nantes, Nantes, France.,Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Nantes, L'institut du Thorax, Nantes, France
| | - Justyna A Karolak
- Department of Molecular and Human Genetics and.,Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Gail Deutsch
- Department of Pathology, Seattle Children's Hospital, Seattle, Washington
| | - Tomasz Gambin
- Department of Molecular and Human Genetics and.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland; and.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Bertrand Isidor
- Service de Genetique Medicale, Centre Hospitalier Universitaire de Nantes, Nantes, France.,Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Nantes, L'institut du Thorax, Nantes, France
| | | | - Cedric Le Caignec
- Service de Genetique Medicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
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Bclaf1 is a direct target of HIF-1 and critically regulates the stability of HIF-1α under hypoxia. Oncogene 2020; 39:2807-2818. [PMID: 32029898 DOI: 10.1038/s41388-020-1185-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 12/10/2019] [Accepted: 01/23/2020] [Indexed: 01/04/2023]
Abstract
Hypoxic stress is intimately connected with tumor progression, with hypoxia-inducible factor-1α (HIF-1α) being a critical regulator in this process. HIF-1α is stabilized in response to hypoxia, which is required for the induction of gene transcriptions important for hypoxic adaptation. Bclaf1 is a multifunctional protein involved in tumorigenesis, however, its role in this process is not well characterized. Here we report Bclaf1 is a direct transcriptional target of HIF-1 and upregulated in multiple cell lines during hypoxia. Importantly, we found Bclaf1 is involved in the stabilization of HIF-1α during long-term hypoxic treatments. Compared with the control cells, the protein level and stability of HIF-1α in Bclaf1 knockdown or knockout cells is greatly compromised after long-term hypoxic treatments, concomitant with the impaired inductions of HIF-1 target gene transcription. Bclaf1 knockout HeLa cells exhibit a reduced tumor growth in mice xenografts, in which the expressions of HIF-1α and its target genes are also decreased. Bclaf1 binds to HIF-1α in the nucleus, and this interaction is required for Bclaf1 to stabilize HIF-1α in hypoxic condition. These results uncover a positive feedback loop, HIF-1-Bclaf1, that sustains HIF-1 activity during long-term hypoxic conditions by binding to and protecting HIF-1α from degradation, and suggest that Bclaf1 may promote tumor progression by enhancing HIF-1α stability.
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BCLAF1 promotes cell proliferation, invasion and drug-resistance though targeting lncRNA NEAT1 in hepatocellular carcinoma. Life Sci 2019; 242:117177. [PMID: 31870774 DOI: 10.1016/j.lfs.2019.117177] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 01/11/2023]
Abstract
AIMS In the present research, we aimed to investigate the effect of Bcl-2-associated transcription factor 1 (BCLAF1) on hepatocellular carcinoma and further explore the special molecular mechanism. MAIN METHODS The expression of BCLAF1 was analyzed in tumor tissues and different hepatocellular cancer cell lines by real-time RT-PCR and Western blot. Cell proliferation and invasion was explored using MTT and Transwell assay respectively. In addition, luciferase reporter assay was performed to determine the binding activity of BCLAF1 and Nuclear enrichment-rich transcription factor 1 (NEAT1) promoter. Finally, the IC50 for 5-Fluorouracil (5-Fu) was measured by MTT assay, and Western blot was used to determine the expression of P-glycoprotein (P-gp) and multidrug resistance protein1 (MRP1). KEY FINDING The result revealed that BCLAF1 was highly expressed in hepatocellular carcinoma tissues and cells. In addition, BCLAF1-siRNA inhibited the proliferation and invasion of hepatocellular carcinoma cells, and overexpression of BCLAF1 promoted proliferation and invasion. Furthermore, luciferase reporter assay demonstrated that BCLAF1 directly interact with lncNEAT1 promoter and improved NEAT1 expression, and BCLAF1 promoted proliferation and invasion through targeting lncRNA NEAT1. What's more, BCLAF1 promoted 5-Fu resistance and the expression of P-gp and MRP1 in hepatocellular carcinoma cells by targeting NEAT1. SIGNIFICANCE The results of the present study suggested that BCLAF1 might be a new gene related to proliferation and drug-resistance of hepatocellular carcinoma. In the future, the search for a deep and reasonable mechanism for the role of BCLAF1 will help us to understand its function more comprehensively, and finally find a new method for the treatment of human cancer.
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Yu S, Wang X, Dou N, Zhou J, Gao Y, Li Y. B-cell lymphoma-2-associated transcription factor 1 is overexpressed and contributes to sorafenib resistance in hepatocellular carcinoma. Hepatol Res 2019; 49:1329-1340. [PMID: 31237058 DOI: 10.1111/hepr.13395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 06/16/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022]
Abstract
AIM B-cell lymphoma-2-associated transcription factor 1 (BCLAF1) is involved in various biological processes including tumorigenesis, but its function and expression in hepatocellular carcinoma (HCC) is little known, and its clinical value in HCC has not yet been defined. METHODS The protein level of BCLAF1 in HCC specimens and paired adjacent normal tissues was examined by immunohistochemical staining. The effects of BCLAF1 on autophagy in HCC cells were detected by confocal microscopy, transmission electron microscopy, and western blot analysis. Cell proliferation and tumorigenicity assays were carried out in vitro and in vivo. Flow cytometry assay was used to determine the apoptosis level of HCC cells. The correlation of BCLAF1 and sorafenib resistance in HCC was analyzed by the Kaplan-Meier survival method. RESULTS High expression of BCLAF1 was found in HCC tissues compared with adjacent normal tissues, and higher BCLAF1 expression was correlated with higher tumor-node-metastasis stage, worse differentiation, and worse prognosis of HCC patients. BCLAF1 could induce autophagy in HCC cells in response to starvation and BCLAF1-mediated autophagy could enhance cell proliferation and impede cell apoptosis under stress conditions. Animal experiments indicated that BCLAF1 promoted tumorigenicity of HCC cells in vivo. More importantly, high expression of BCLAF1 might contribute to sorafenib resistance in HCC patients. CONCLUSIONS BCLAF1 is a potential oncogene in HCC by inducing autophagy to maintain tumor cell growth in response to stress conditions, and it could serve as a potential biomarker for predicting the prognosis of HCC patients and screening patients who are suitable for sorafenib therapy.
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Affiliation(s)
| | | | | | | | | | - Yandong Li
- Department of Oncology.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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Elyahu Y, Hekselman I, Eizenberg-Magar I, Berner O, Strominger I, Schiller M, Mittal K, Nemirovsky A, Eremenko E, Vital A, Simonovsky E, Chalifa-Caspi V, Friedman N, Yeger-Lotem E, Monsonego A. Aging promotes reorganization of the CD4 T cell landscape toward extreme regulatory and effector phenotypes. SCIENCE ADVANCES 2019; 5:eaaw8330. [PMID: 31457092 PMCID: PMC6703865 DOI: 10.1126/sciadv.aaw8330] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/12/2019] [Indexed: 05/29/2023]
Abstract
Age-associated changes in CD4 T-cell functionality have been linked to chronic inflammation and decreased immunity. However, a detailed characterization of CD4 T cell phenotypes that could explain these dysregulated functional properties is lacking. We used single-cell RNA sequencing and multidimensional protein analyses to profile thousands of CD4 T cells obtained from young and old mice. We found that the landscape of CD4 T cell subsets differs markedly between young and old mice, such that three cell subsets-exhausted, cytotoxic, and activated regulatory T cells (aTregs)-appear rarely in young mice but gradually accumulate with age. Most unexpected were the extreme pro- and anti-inflammatory phenotypes of cytotoxic CD4 T cells and aTregs, respectively. These findings provide a comprehensive view of the dynamic reorganization of the CD4 T cell milieu with age and illuminate dominant subsets associated with chronic inflammation and immunity decline, suggesting new therapeutic avenues for age-related diseases.
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Affiliation(s)
- Yehezqel Elyahu
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Zlotowski Neuroscience Center and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Idan Hekselman
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Omer Berner
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Zlotowski Neuroscience Center and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Itai Strominger
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Zlotowski Neuroscience Center and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Maya Schiller
- Departments of Immunology and Neuroscience, Rappaport Faculty of Medicine, and the Integrated Cancer Center, Technion-Israel Institute of Technology, Haifa 3525422, Israel
| | - Kritika Mittal
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Zlotowski Neuroscience Center and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Anna Nemirovsky
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Zlotowski Neuroscience Center and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ekaterina Eremenko
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Zlotowski Neuroscience Center and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Assaf Vital
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Eyal Simonovsky
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Vered Chalifa-Caspi
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Esti Yeger-Lotem
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Alon Monsonego
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Zlotowski Neuroscience Center and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Lowe M, Lage J, Paatela E, Munson D, Hostager R, Yuan C, Katoku-Kikyo N, Ruiz-Estevez M, Asakura Y, Staats J, Qahar M, Lohman M, Asakura A, Kikyo N. Cry2 Is Critical for Circadian Regulation of Myogenic Differentiation by Bclaf1-Mediated mRNA Stabilization of Cyclin D1 and Tmem176b. Cell Rep 2019; 22:2118-2132. [PMID: 29466738 PMCID: PMC5849083 DOI: 10.1016/j.celrep.2018.01.077] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 01/09/2018] [Accepted: 01/25/2018] [Indexed: 12/30/2022] Open
Abstract
Circadian rhythms regulate cell proliferation and differentiation; however, little is known about their roles in myogenic differentiation. Our synchronized differentiation studies demonstrate that myoblast proliferation and subsequent myotube formation by cell fusion occur in circadian manners. We found that one of the core regulators of circadian rhythms, Cry2, but not Cry1, is critical for the circadian patterns of these two critical steps in myogenic differentiation. This is achieved through the specific interaction between Cry2 and Bclaf1, which stabilizes mRNAs encoding cyclin D1, a G1/S phase transition regulator, and Tmem176b, a transmembrane regulator for myogenic cell fusion. Myoblasts lacking Cry2 display premature cell cycle exit and form short myotubes because of inefficient cell fusion. Consistently, muscle regeneration is impaired in Cry2-/- mice. Bclaf1 knockdown recapitulated the phenotypes of Cry2 knockdown: early cell cycle exit and inefficient cell fusion. This study uncovers a post-transcriptional regulation of myogenic differentiation by circadian rhythms.
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Affiliation(s)
- Matthew Lowe
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development , University of Minnesota, Minneapolis, MN 55455, USA
| | - Jacob Lage
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development , University of Minnesota, Minneapolis, MN 55455, USA
| | - Ellen Paatela
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA
| | - Dane Munson
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA
| | - Reilly Hostager
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA
| | - Ce Yuan
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA; Bioinformatics and Computational Biology Graduate Program , University of Minnesota, Minneapolis, MN 55455, USA
| | - Nobuko Katoku-Kikyo
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA; Department of Neurology , University of Minnesota, Minneapolis, MN 55455, USA
| | - Mercedes Ruiz-Estevez
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development , University of Minnesota, Minneapolis, MN 55455, USA
| | - Yoko Asakura
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development , University of Minnesota, Minneapolis, MN 55455, USA
| | - James Staats
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development , University of Minnesota, Minneapolis, MN 55455, USA
| | - Mulan Qahar
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA; Department of Neurology , University of Minnesota, Minneapolis, MN 55455, USA
| | - Michaela Lohman
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA
| | - Atsushi Asakura
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA; Department of Neurology , University of Minnesota, Minneapolis, MN 55455, USA.
| | - Nobuaki Kikyo
- Stem Cell Institute , University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development , University of Minnesota, Minneapolis, MN 55455, USA.
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34
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Karolak JA, Vincent M, Deutsch G, Gambin T, Cogné B, Pichon O, Vetrini F, Mefford HC, Dines JN, Golden-Grant K, Dipple K, Freed AS, Leppig KA, Dishop M, Mowat D, Bennetts B, Gifford AJ, Weber MA, Lee AF, Boerkoel CF, Bartell TM, Ward-Melver C, Besnard T, Petit F, Bache I, Tümer Z, Denis-Musquer M, Joubert M, Martinovic J, Bénéteau C, Molin A, Carles D, André G, Bieth E, Chassaing N, Devisme L, Chalabreysse L, Pasquier L, Secq V, Don M, Orsaria M, Missirian C, Mortreux J, Sanlaville D, Pons L, Küry S, Bézieau S, Liet JM, Joram N, Bihouée T, Scott DA, Brown CW, Scaglia F, Tsai ACH, Grange DK, Phillips JA, Pfotenhauer JP, Jhangiani SN, Gonzaga-Jauregui CG, Chung WK, Schauer GM, Lipson MH, Mercer CL, van Haeringen A, Liu Q, Popek E, Coban Akdemir ZH, Lupski JR, Szafranski P, Isidor B, Le Caignec C, Stankiewicz P. Complex Compound Inheritance of Lethal Lung Developmental Disorders Due to Disruption of the TBX-FGF Pathway. Am J Hum Genet 2019; 104:213-228. [PMID: 30639323 DOI: 10.1016/j.ajhg.2018.12.010] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/13/2018] [Indexed: 12/24/2022] Open
Abstract
Primary defects in lung branching morphogenesis, resulting in neonatal lethal pulmonary hypoplasias, are incompletely understood. To elucidate the pathogenetics of human lung development, we studied a unique collection of samples obtained from deceased individuals with clinically and histopathologically diagnosed interstitial neonatal lung disorders: acinar dysplasia (n = 14), congenital alveolar dysplasia (n = 2), and other lethal lung hypoplasias (n = 10). We identified rare heterozygous copy-number variant deletions or single-nucleotide variants (SNVs) involving TBX4 (n = 8 and n = 2, respectively) or FGF10 (n = 2 and n = 2, respectively) in 16/26 (61%) individuals. In addition to TBX4, the overlapping ∼2 Mb recurrent and nonrecurrent deletions at 17q23.1q23.2 identified in seven individuals with lung hypoplasia also remove a lung-specific enhancer region. Individuals with coding variants involving either TBX4 or FGF10 also harbored at least one non-coding SNV in the predicted lung-specific enhancer region, which was absent in 13 control individuals with the overlapping deletions but without any structural lung anomalies. The occurrence of rare coding variants involving TBX4 or FGF10 with the putative hypomorphic non-coding SNVs implies a complex compound inheritance of these pulmonary hypoplasias. Moreover, they support the importance of TBX4-FGF10-FGFR2 epithelial-mesenchymal signaling in human lung organogenesis and help to explain the histopathological continuum observed in these rare lethal developmental disorders of the lung.
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MESH Headings
- DNA Copy Number Variations/genetics
- Female
- Fibroblast Growth Factor 10/genetics
- Fibroblast Growth Factor 10/metabolism
- Gene Expression Regulation
- Gestational Age
- Humans
- Infant, Newborn
- Infant, Newborn, Diseases/genetics
- Infant, Newborn, Diseases/metabolism
- Infant, Newborn, Diseases/mortality
- Infant, Newborn, Diseases/pathology
- Lung/embryology
- Lung/growth & development
- Lung Diseases/genetics
- Lung Diseases/metabolism
- Lung Diseases/mortality
- Lung Diseases/pathology
- Male
- Maternal Inheritance
- Organogenesis
- Paternal Inheritance
- Pedigree
- Polymorphism, Single Nucleotide/genetics
- Receptor, Fibroblast Growth Factor, Type 2/metabolism
- Signal Transduction/genetics
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
| | - Marie Vincent
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Gail Deutsch
- Department of Pathology, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Tomasz Gambin
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland; Institute of Computer Science, Warsaw University of Technology, 00-665 Warsaw, Poland
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Olivier Pichon
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France
| | | | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jennifer N Dines
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Katie Golden-Grant
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Katrina Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Amanda S Freed
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Kathleen A Leppig
- Genetic Services Kaiser Permanente of Washington, Seattle, WA 98112, USA
| | - Megan Dishop
- Pathology and Laboratory Medicine, Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick Sydney, NSW 2031 Australia; School of Women's and Children's Health, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Bruce Bennetts
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia; Molecular Genetics Department, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Andrew J Gifford
- School of Women's and Children's Health, The University of New South Wales, Sydney, NSW 2052, Australia; Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Martin A Weber
- Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, NSW 2031, Australia; School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Cornelius F Boerkoel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Tina M Bartell
- Department of Genetics, Kaiser Permanente Sacramento Medical Center, Sacramento, CA 95815, USA
| | | | - Thomas Besnard
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Florence Petit
- Service de Génétique Clinique, CHU Lille, 59000 Lille, France
| | - Iben Bache
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 N Copenhagen, Denmark; Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Ø Copenhagen, Denmark
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Copenhagen, Denmark; Deparment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 N, Copenhagen, Denmark
| | | | | | - Jelena Martinovic
- Unit of Fetal Pathology, AP-HP, Antoine Beclere Hospital, 75000 Paris, France
| | - Claire Bénéteau
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Arnaud Molin
- Service de Génétique Médicale, CHU Caen, 14000 Caen, France
| | - Dominique Carles
- Service d'anatomo-pathologie, CHU Bordeaux, 33000 Bordeaux, France
| | - Gwenaelle André
- Service d'anatomo-pathologie, CHU Bordeaux, 33000 Bordeaux, France
| | - Eric Bieth
- Service de génétique médicale, CHU Toulouse, France and UDEAR, UMR 1056 Inserm - Université de Toulouse, 31000 Toulouse, France
| | - Nicolas Chassaing
- Service de génétique médicale, CHU Toulouse, France and UDEAR, UMR 1056 Inserm - Université de Toulouse, 31000 Toulouse, France
| | | | | | | | - Véronique Secq
- Aix Marseille Univ, APHM, Hôpital Nord, Service d'anatomo-pathologie, 13000 Marseille, France
| | - Massimiliano Don
- Sant'Antonio General Hospital, Pediatric Care Unit, San Daniele del Friuli, 33100 Udine, Italy
| | - Maria Orsaria
- Department of Medical and Biological Sciences, Pathology Unit, University of Udine, Udine, Italy
| | - Chantal Missirian
- Aix Marseille Univ, APHM, INSERM, MMG, Marseille, Timone Hospital, 13000 Marseille, France
| | - Jérémie Mortreux
- Aix Marseille Univ, APHM, INSERM, MMG, Marseille, Timone Hospital, 13000 Marseille, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, GHE, Genetics department, and Lyon University, 69000 Lyon, France
| | - Linda Pons
- Hospices Civils de Lyon, GHE, Genetics department, and Lyon University, 69000 Lyon, France
| | - Sébastien Küry
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Stéphane Bézieau
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Jean-Michel Liet
- Service de réanimation pédiatrique, CHU Nantes, 44000 Nantes, France
| | - Nicolas Joram
- Service de réanimation pédiatrique, CHU Nantes, 44000 Nantes, France
| | | | - Daryl A Scott
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chester W Brown
- Department of Pediatrics, Genetics Division, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Fernando Scaglia
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Joint BCM-CUHK Center of Medical Genetics, Prince of Wales Hospital, ShaTin, New Territories, Hong Kong SAR
| | - Anne Chun-Hui Tsai
- Department of Pediatrics, The Children's Hospital, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Dorothy K Grange
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - John A Phillips
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jean P Pfotenhauer
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - Galen M Schauer
- Department of Pathology, Kaiser Permanente Oakland Medical Center, Oakland, CA 94611, USA
| | - Mark H Lipson
- Department of Genetics, Kaiser Permanente Sacramento Medical Center, Sacramento, CA 95815, USA
| | - Catherine L Mercer
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Princess Anne Hospital, Southampton SO16 5YA, UK
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Qian Liu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Przemyslaw Szafranski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | | | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Institute of Mother and Child, 01-211 Warsaw, Poland.
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Qin C, Zhang R, Lang Y, Shao A, Xu A, Feng W, Han J, Wang M, He W, Yu C, Tang J. Bclaf1 critically regulates the type I interferon response and is degraded by alphaherpesvirus US3. PLoS Pathog 2019; 15:e1007559. [PMID: 30682178 PMCID: PMC6364948 DOI: 10.1371/journal.ppat.1007559] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/06/2019] [Accepted: 01/03/2019] [Indexed: 01/12/2023] Open
Abstract
Type I interferon response plays a prominent role against viral infection, which is frequently disrupted by viruses. Here, we report Bcl-2 associated transcription factor 1 (Bclaf1) is degraded during the alphaherpesvirus Pseudorabies virus (PRV) and Herpes simplex virus type 1 (HSV-1) infections through the viral protein US3. We further reveal that Bclaf1 functions critically in type I interferon signaling. Knockdown or knockout of Bclaf1 in cells significantly impairs interferon-α (IFNα) -mediated gene transcription and viral inhibition against US3 deficient PRV and HSV-1. Mechanistically, Bclaf1 maintains a mechanism allowing STAT1 and STAT2 to be efficiently phosphorylated in response to IFNα, and more importantly, facilitates IFN-stimulated gene factor 3 (ISGF3) binding with IFN-stimulated response elements (ISRE) for efficient gene transcription by directly interacting with ISRE and STAT2. Our studies establish the importance of Bclaf1 in IFNα-induced antiviral immunity and in the control of viral infections. Alphaherpesvirus, such as Pseudorabies virus (PRV) and Herpes simplex virus type 1 (HSV-1), can establish persistent infection and cause various diseases in hosts. Interferon (IFN) response is hosts’ first defense system against viral infection. Here, we report alphaherpesvirus induces degradation of a host protein, Bclaf1, via its expressed viral protein US3 upon infection. We further show that Bclaf1 is a novel regulator of IFN pathway by enhancing the IFN induced transcriptions of anti-viral genes. In the absence of Bclaf1, IFN induced anti-viral activity is greatly reduced. Our study highlight the importance of Bclaf1 in IFN mediated antiviral function and reveal a strategy employed by alphaherpesvirus to counteract hosts’ defense.
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Affiliation(s)
- Chao Qin
- State Key Laboratory of Agrobiotechnology and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Rui Zhang
- State Key Laboratory of Agrobiotechnology and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yue Lang
- State Key Laboratory of Agrobiotechnology and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Anwen Shao
- Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Aotian Xu
- State Key Laboratory of Agrobiotechnology and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wenhai Feng
- Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jun Han
- State Key Laboratory of Agrobiotechnology and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Mengdong Wang
- State Key Laboratory of Agrobiotechnology and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wanwei He
- State Key Laboratory of Agrobiotechnology and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Cuilian Yu
- State Key Laboratory of Agrobiotechnology and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jun Tang
- State Key Laboratory of Agrobiotechnology and College of Veterinary Medicine, China Agricultural University, Beijing, China
- * E-mail:
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Warren JL, MacIver NJ. Regulation of Adaptive Immune Cells by Sirtuins. Front Endocrinol (Lausanne) 2019; 10:466. [PMID: 31354630 PMCID: PMC6637536 DOI: 10.3389/fendo.2019.00466] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 06/26/2019] [Indexed: 12/16/2022] Open
Abstract
It is now well-established that the pathways that control lymphocyte metabolism and function are intimately linked, and changes in lymphocyte metabolism can influence and direct cellular function. Interestingly, a number of recent advances indicate that lymphocyte identity and metabolism is partially controlled via epigenetic regulation. Epigenetic mechanisms, such as changes in DNA methylation or histone acetylation, have been found to alter immune function and play a role in numerous chronic disease states. There are several enzymes that can mediate epigenetic changes; of particular interest are sirtuins, protein deacetylases that mediate adaptive responses to a variety of stresses (including calorie restriction and metabolic stress) and are now understood to play a significant role in immunity. This review will focus on recent advances in the understanding of how sirtuins affect the adaptive immune system. These pathways are of significant interest as therapeutic targets for the treatment of autoimmunity, cancer, and transplant tolerance.
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Affiliation(s)
- Jonathan L. Warren
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, United States
| | - Nancie J. MacIver
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, United States
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, United States
- *Correspondence: Nancie J. MacIver
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Su Y, Wang J, Quan M. Novel insights into the molecular mechanisms underlying the beneficial effects of exercise training on pulmonary arterial hypertension. J Sports Med Phys Fitness 2018; 59:1584-1592. [PMID: 30421875 DOI: 10.23736/s0022-4707.18.09204-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BACKGROUND Recent animal and clinical studies report that exercise training exerts positive influences in pulmonary arterial hypertension (PAH); however, the underlying mechanisms are largely unknown. To give insight into the molecular mechanisms of the improvement effects, we performed gene expression analysis. METHODS Three Gene Expression Omnibus (GEO) datasets were analyzed, including peripheral blood mononuclear (PBMC) gene expression profiles of exercise training in men and patients with PAH. Differentially expressed genes (DEGs) in each dataset were identified, and then, the common DEGs positively regulated by PAH and negatively regulated by exercise training, or the opposite, were further identified. Subsequently, biological processes and pathways were analyzed. RESULTS A total of 7229 DEGs with logFC>0.3 and P<0.05 were identified in exercise, whereas 749 and 2207 DEGs were identified in PAH from the two datasets. After overlapping the whole DEGs from all three datasets, total 16 common DEGs were identified, including BCLAF1, SATB1 and ZFP36L2. Seven of them were up-regulated in exercise training and down-regulated in PAH, and the others were opposite. In addition, these common DEGs were mainly enriched in negative regulation of cellular process, negative regulation of biological process and negative regulation of cellular macromolecule biosynthetic process. CONCLUSIONS Some genes have been implicated in the improvement of pulmonary vascular remodeling and PAH. These findings could not only improve the knowledge about the molecular mechanisms underlying the beneficial effects of exercise training on PAH, but also provide clues for further clinical and animal studies.
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Affiliation(s)
- Youcun Su
- School of Sports and Health School of Physical Education and Health Care, East China Normal University, Shanghai, China
| | - Jing Wang
- School of Sports Science and Engineering, East China University of Science and Technology, Shanghai, China
| | - Minghui Quan
- Department of Sport Rehabilitation, School of Kinesiology, Shanghai University of Sport, Shanghai, China -
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Bclaf1 promotes angiogenesis by regulating HIF-1α transcription in hepatocellular carcinoma. Oncogene 2018; 38:1845-1859. [PMID: 30367150 PMCID: PMC6462866 DOI: 10.1038/s41388-018-0552-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/09/2018] [Accepted: 09/28/2018] [Indexed: 02/07/2023]
Abstract
The development of hepatocellular carcinomas (HCC) depends on their local microenvironment and the induction of neovascularization is a decisive step in tumor progression, since the growth of solid tumors is limited by nutrient and oxygen supply. Hypoxia is the critical factor that induces transcription of the hypoxia inducible factor-1α (HIF-1α) encoding gene HIF1A and HIF-1α protein accumulation to promote angiogenesis. However, the basis for the transcriptional regulation of HIF1A expression in HCC is still unclear. Here, we show that Bclaf1 levels are highly correlated with HIF-1α levels in HCC tissues, and that knockdown of Bclaf1 in HCC cell lines significantly reduces hypoxia-induced HIF1A expression. Furthermore, we found that Bclaf1 promotes HIF1A transcription via its bZIP domain, leading subsequently to increased transcription of the HIF-1α downstream targets VEGFA, TGFB, and EPO that in turn promote HCC-associated angiogenesis and thus survival and thriving of HCC cells. Moreover, we demonstrate that HIF-1α levels and microvessel density decrease after the shRNA-mediated Bclaf1 knockdown in xenograft tumors. Finally, we found that Bclaf1 levels increase in hypoxia in a HIF-1α dependent manner. Therefore, our study identifies Bclaf1 as a novel positive regulator of HIF-1α in the hypoxic microenvironment, providing new incentives for promoting Bcalf1 as a potential therapeutic target for an anti-HCC strategy.
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Li X, He Z, Cheng B, Fang Q, Ma D, Lu T, Wei D, Kuang X, Tang S, Xiong J, Wang J. Effect of BCLAF1 on HDAC inhibitor LMK-235-mediated apoptosis of diffuse large B cell lymphoma cells and its mechanism. Cancer Biol Ther 2018; 19:825-834. [PMID: 29969367 DOI: 10.1080/15384047.2018.1472188] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common type of adult lymphoma. It is a group of malignant tumors with a large number of clinical manifestations and prognoses. Therefore, it is necessary to explore its unknown potential therapeutic targets. Histone deacetylase inhibitor (HDACi) is a novel drug for the treatment of DLBCL, however pan-HDACis cannot be ignored because of their clinical efficacy. By contrast, specific HDACi is well-tolerated, and LMK-235 is a novel HDACi that is a specific inhibitor of HDAC4 and HDAC5. In this study, we investigated the up-regulation of BCLAF1 through NF-κB signaling pathways in LMK-235, mediating the apoptosis of two diffuse large B-cell lymphoma cell lines, OCI-LY10 and OCI-LY3. Further studies showed that BCLAF1 expression was increased in DLBCL cells after treatment with the NF-κB inhibitor Bay11-7082. The combination of Bay11-7082 and siRNA si-HDAC4 significantly increased BCLAF1 expression and further increased apoptosis. These results indicate that BCLAF1 plays an important role in LMK-235-mediated apoptosis and may be a potential target for the treatment of diffuse large B-cell lymphoma.
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Affiliation(s)
- Xinyao Li
- a Guizhou Medical University , Guiyang , Guizhou , China.,d Guizhou Province Laboratory of Haematopoietic Stem Cell Transplantation Center , Guiyang , Guizhou , China.,e Department of Hematology , Affiliated Hospital of Guizhou Medical University , Guiyang , Guizhou , China
| | - Zhengchang He
- a Guizhou Medical University , Guiyang , Guizhou , China.,d Guizhou Province Laboratory of Haematopoietic Stem Cell Transplantation Center , Guiyang , Guizhou , China.,e Department of Hematology , Affiliated Hospital of Guizhou Medical University , Guiyang , Guizhou , China
| | - Bingqing Cheng
- b Department of Pharmacy , Guizhou Medical University , Guiyang , Guizhou , China.,d Guizhou Province Laboratory of Haematopoietic Stem Cell Transplantation Center , Guiyang , Guizhou , China.,e Department of Hematology , Affiliated Hospital of Guizhou Medical University , Guiyang , Guizhou , China
| | - Qin Fang
- b Department of Pharmacy , Guizhou Medical University , Guiyang , Guizhou , China.,c Department of Pharmacy , Affiliated BaiYun Hospital of Guizhou Medical University , Guiyang , Guizhou , China
| | - Dan Ma
- a Guizhou Medical University , Guiyang , Guizhou , China.,d Guizhou Province Laboratory of Haematopoietic Stem Cell Transplantation Center , Guiyang , Guizhou , China.,e Department of Hematology , Affiliated Hospital of Guizhou Medical University , Guiyang , Guizhou , China
| | - Tingting Lu
- a Guizhou Medical University , Guiyang , Guizhou , China.,d Guizhou Province Laboratory of Haematopoietic Stem Cell Transplantation Center , Guiyang , Guizhou , China.,e Department of Hematology , Affiliated Hospital of Guizhou Medical University , Guiyang , Guizhou , China
| | - Danna Wei
- a Guizhou Medical University , Guiyang , Guizhou , China.,d Guizhou Province Laboratory of Haematopoietic Stem Cell Transplantation Center , Guiyang , Guizhou , China.,e Department of Hematology , Affiliated Hospital of Guizhou Medical University , Guiyang , Guizhou , China
| | - Xingyi Kuang
- a Guizhou Medical University , Guiyang , Guizhou , China.,d Guizhou Province Laboratory of Haematopoietic Stem Cell Transplantation Center , Guiyang , Guizhou , China.,e Department of Hematology , Affiliated Hospital of Guizhou Medical University , Guiyang , Guizhou , China
| | - Sishi Tang
- a Guizhou Medical University , Guiyang , Guizhou , China.,d Guizhou Province Laboratory of Haematopoietic Stem Cell Transplantation Center , Guiyang , Guizhou , China.,e Department of Hematology , Affiliated Hospital of Guizhou Medical University , Guiyang , Guizhou , China
| | - Jie Xiong
- a Guizhou Medical University , Guiyang , Guizhou , China.,d Guizhou Province Laboratory of Haematopoietic Stem Cell Transplantation Center , Guiyang , Guizhou , China.,e Department of Hematology , Affiliated Hospital of Guizhou Medical University , Guiyang , Guizhou , China
| | - Jishi Wang
- a Guizhou Medical University , Guiyang , Guizhou , China.,d Guizhou Province Laboratory of Haematopoietic Stem Cell Transplantation Center , Guiyang , Guizhou , China.,e Department of Hematology , Affiliated Hospital of Guizhou Medical University , Guiyang , Guizhou , China
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Wang X, Wei X, Yuan Y, Sun Q, Zhan J, Zhang J, Tang Y, Li F, Ding L, Ye Q, Zhang H. Src-mediated phosphorylation converts FHL1 from tumor suppressor to tumor promoter. J Cell Biol 2018; 217:1335-1351. [PMID: 29434030 PMCID: PMC5881501 DOI: 10.1083/jcb.201708064] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/19/2017] [Accepted: 01/16/2018] [Indexed: 02/07/2023] Open
Abstract
FHL1 has been recognized for a long time as a tumor suppressor protein that associates with both the actin cytoskeleton and the transcriptional machinery. We present in this study a paradigm that phosphorylated FHL1 functions as an oncogenic protein by promoting tumor cell proliferation. The cytosolic tyrosine kinase Src interacts with and phosphorylates FHL1 at Y149 and Y272, which switches FHL1 from a tumor suppressor to a cell growth accelerator. Phosphorylated FHL1 translocates into the nucleus, where it binds to the transcription factor BCLAF1 and promotes tumor cell growth. Importantly, the phosphorylation of FHL1 is increased in tissues from lung adenocarcinoma patients despite the down-regulation of total FHL1 expression. Kindlin-2 was found to interact with FHL1 and recruit FHL1 to focal adhesions. Kindlin-2 competes with Src for binding to FHL1 and suppresses Src-mediated FHL1 phosphorylation. Collectively, we demonstrate that FHL1 can either suppress or promote tumor cell growth depending on the status of the sites for phosphorylation by Src.
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Affiliation(s)
- Xiang Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Human Anatomy, Histology and Embryology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Xiaofan Wei
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Human Anatomy, Histology and Embryology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Yang Yuan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Human Anatomy, Histology and Embryology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Qingrui Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Human Anatomy, Histology and Embryology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Jun Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Human Anatomy, Histology and Embryology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Jing Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Human Anatomy, Histology and Embryology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Yan Tang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Human Anatomy, Histology and Embryology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Feng Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Human Anatomy, Histology and Embryology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Lihua Ding
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Collaborative Innovation Center for Cancer Medicine, Beijing, China
| | - Qinong Ye
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Collaborative Innovation Center for Cancer Medicine, Beijing, China
| | - Hongquan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Human Anatomy, Histology and Embryology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
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miR-194-5p/BCLAF1 deregulation in AML tumorigenesis. Leukemia 2017; 31:2315-2325. [PMID: 28216661 PMCID: PMC5668498 DOI: 10.1038/leu.2017.64] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 12/28/2016] [Accepted: 02/14/2017] [Indexed: 02/07/2023]
Abstract
Deregulation of epigenetic mechanisms, including microRNA, contributes to leukemogenesis and drug resistance by interfering with cancer-specific molecular pathways. Here, we show that the balance between miR-194-5p and its newly discovered target BCL2-associated transcription factor 1 (BCLAF1) regulates differentiation and survival of normal hematopoietic progenitors. In acute myeloid leukemias this balance is perturbed, locking cells into an immature, potentially ‘immortal’ state. Enhanced expression of miR-194-5p by treatment with the histone deacetylase inhibitor SAHA or by exogenous miR-194-5p expression re-sensitizes cells to differentiation and apoptosis by inducing BCLAF1 to shuttle between nucleus and cytosol. miR-194-5p/BCLAF1 balance was found commonly deregulated in 60 primary acute myeloid leukemia patients and was largely restored by ex vivo SAHA treatment. Our findings link treatment responsiveness to re-instatement of miR-194-5p/BCLAF1 balance.
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Martin P, McGovern A, Massey J, Schoenfelder S, Duffus K, Yarwood A, Barton A, Worthington J, Fraser P, Eyre S, Orozco G. Identifying Causal Genes at the Multiple Sclerosis Associated Region 6q23 Using Capture Hi-C. PLoS One 2016; 11:e0166923. [PMID: 27861577 PMCID: PMC5115837 DOI: 10.1371/journal.pone.0166923] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/06/2016] [Indexed: 12/21/2022] Open
Abstract
Background The chromosomal region 6q23 has been found to be associated with multiple sclerosis (MS) predisposition through genome wide association studies (GWAS). There are four independent single nucleotide polymorphisms (SNPs) associated with MS in this region, which spans around 2.5 Mb. Most GWAS variants associated with complex traits, including these four MS associated SNPs, are non-coding and their function is currently unknown. However, GWAS variants have been found to be enriched in enhancers and there is evidence that they may be involved in transcriptional regulation of their distant target genes through long range chromatin looping. Aim The aim of this work is to identify causal disease genes in the 6q23 locus by studying long range chromatin interactions, using the recently developed Capture Hi-C method in human T and B-cell lines. Interactions involving four independent associations unique to MS, tagged by rs11154801, rs17066096, rs7769192 and rs67297943 were analysed using Capture Hi-C Analysis of Genomic Organisation (CHiCAGO). Results We found that the pattern of chromatin looping interactions in the MS 6q23 associated region is complex. Interactions cluster in two regions, the first involving the rs11154801 region and a second containing the rs17066096, rs7769192 and rs67297943 SNPs. Firstly, SNPs located within the AHI1 gene, tagged by rs11154801, are correlated with expression of AHI1 and interact with its promoter. These SNPs also interact with other potential candidate genes such as SGK1 and BCLAF1. Secondly, the rs17066096, rs7769192 and rs67297943 SNPs interact with each other and with immune-related genes such as IL20RA, IL22RA2, IFNGR1 and TNFAIP3. Finally, the above-mentioned regions interact with each other and therefore, may co-regulate these target genes. Conclusion These results suggest that the four 6q23 variants, independently associated with MS, are involved in the regulation of several genes, including immune genes. These findings could help understand mechanisms of disease and suggest potential novel therapeutic targets.
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Affiliation(s)
- Paul Martin
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Amanda McGovern
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Jonathan Massey
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Stefan Schoenfelder
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Kate Duffus
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Annie Yarwood
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Anne Barton
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
- NIHR Manchester Musculoskeletal BRU, Manchester Academic Health Sciences Centre, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Jane Worthington
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
- NIHR Manchester Musculoskeletal BRU, Manchester Academic Health Sciences Centre, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Stephen Eyre
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Gisela Orozco
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Siences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
- * E-mail:
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Abstract
The nucleus is separated from the cytosol by the nuclear envelope, which is a double lipid bilayer composed of the outer nuclear membrane and the inner nuclear membrane. The intermediate filament proteins lamin A, lamin B, and lamin C form a network underlying the inner nuclear membrane. This proteinaceous network provides the nucleus with its strength, rigidity, and elasticity. Positioned within the inner nuclear membrane are more than 150 inner nuclear membrane proteins, many of which interact directly with lamins and require lamins for their inner nuclear membrane localization. Inner nuclear membrane proteins and the nuclear lamins define the nuclear lamina. These inner nuclear membrane proteins have tissue-specific expression and diverse functions including regulating cytoskeletal organization, nuclear architecture, cell cycle dynamics, and genomic organization. Loss or mutations in lamins and inner nuclear membrane proteins cause a wide spectrum of diseases. Here, I will review the functions of the well-studied nuclear lamina proteins and the diseases associated with loss or mutations in these proteins. © 2016 American Physiological Society. Compr Physiol 6:1655-1674, 2016.
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Affiliation(s)
- James M. Holaska
- Department of Pharmaceutical Sciences, University of the Sciences, Philadelphia, Pennsylvania, USA
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Bclaf1 is an important NF-κB signaling transducer and C/EBPβ regulator in DNA damage-induced senescence. Cell Death Differ 2016; 23:865-75. [PMID: 26794446 DOI: 10.1038/cdd.2015.150] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 09/11/2015] [Accepted: 10/13/2015] [Indexed: 12/17/2022] Open
Abstract
Inducing senescence in cancer cells is an effective approach to suppress cancer growth, and it contributes significantly to the efficacy of therapeutic drugs. Previous studies indicated that transcription factors NF-κB (nuclear factor κ-light-chain-enhancer of activated B cells) and C/EBPβ (CCAAT/enhancer-binding protein-β) play a critical role in the establishment of senescence by upregulating proinflammatory cytokines, notably interleukin-6 (IL-6) and interleukin-8 (IL-8). However, it is not clear how these two factors are activated in response to senescence-inducing stimuli and subsequently regulate gene transcription. Here, we reveal Bcl-2-associated transcription factor 1 (Bclaf1) as a novel player in the therapeutic drug doxorubicin-induced senescence (TIS) in multiple cancer cells. Bclaf1 is upregulated through the ATM/Nemo/NF-κB pathway during TIS and is a direct target of p65 and c-Rel. The induction of Bclaf1 by NF-κB is essential for C/EBPβ upregulation and IL-6/IL-8 transcription during TIS. Bclaf1 can interact with the leucine zipper region of C/EBPβ and cooperate with C/EBPβ to upregulate IL-8. Furthermore, we show that Bclaf1 is required for the effectiveness of doxorubicin (Dox) treatment-induced tumor suppression in a xenograft tumor model. These finding suggest that Bclaf1 plays a crucial role in transducing the senescence-inducing signal from NF-κB to C/EBPβ during TIS, thus amplifying the signals for the establishment of senescence. Given the recent revelation that Bclaf1 is involved in tumorigenesis, our data indicate that the responsiveness of Bclaf1 to NF-κB may determine the effectiveness of therapeutic drugs.
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Hogquist KA, Xing Y, Hsu FC, Shapiro VS. T Cell Adolescence: Maturation Events Beyond Positive Selection. THE JOURNAL OF IMMUNOLOGY 2015; 195:1351-7. [PMID: 26254267 DOI: 10.4049/jimmunol.1501050] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Single-positive thymocytes that successfully complete positive and negative selection must still undergo one final step, generally termed T cell maturation, before they gain functional competency and enter the long-lived T cell pool. Maturation initiates after positive selection in single-positive thymocytes and continues in the periphery in recent thymic emigrants, before these newly produced T cells gain functional competency and are ready to participate in the immune response as peripheral naive T cells. Recent work using genetically altered mice demonstrates that T cell maturation is not a single process, but a series of steps that occur independently and sequentially after positive selection. This review focuses on the changes that occur during T cell maturation, as well as the molecules and pathways that are critical at each step.
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Affiliation(s)
- Kristin A Hogquist
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455; and
| | - Yan Xing
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455; and
| | - Fan-Chi Hsu
- Department of Immunology, Mayo Clinic, Rochester, MN 55905
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Brown GT, Cash B, Alnabulsi A, Samuel LM, Murray GI. The expression and prognostic significance of bcl-2-associated transcription factor 1 in rectal cancer following neoadjuvant therapy. Histopathology 2015; 68:556-66. [PMID: 26183150 DOI: 10.1111/his.12780] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 07/12/2015] [Indexed: 12/14/2022]
Abstract
AIMS bcl-2-associated transcription factor 1 (BCLAF1) is a nuclear protein that binds to bcl-related proteins and can induce apoptosis and autophagy. The aim of this study was to investigate the expression of BCLAF1 in a series of rectal cancers following neoadjuvant therapy. METHODS AND RESULTS Immunohistochemistry was performed on a post-neoadjuvant therapy rectal cancer tissue microarray. It contained rectal cancers (n = 248), lymph node metastases (n = 76), and non-neoplastic rectal mucosal samples (n = 73). A monoclonal antibody against BCLAF1 that we have developed was used. Non-neoplastic rectal epithelium showed nuclear localization of BCLAF1 in both crypt and surface epithelial cells, whereas rectal cancers showed both nuclear and cytoplasmic BCLAF1 expression. Most rectal cancers showed moderate or strong nuclear immunoreactivity, but showed weak cytoplasmic immunoreactivity. Cytoplasmic BCLAF1 expression was increased in primary rectal cancers as compared with non-neoplastic rectal mucosa (P = 0.008). Negative and weak nuclear BCLAF1 expression was associated with a poor prognosis [hazard ratio (HR) 0.502, 95% confidence interval (CI) 0.269-0.939, χ(2) = 4.876, P = 0.027]. Nuclear BCLAF1 expression was independently prognostic in a multivariate model (HR 0.431, 95% CI 0.221-0.840, P = 0.013). CONCLUSIONS This study has shown that both cytoplasmic BCLAF1 expression and nuclear BCLAF1 expression are increased in post-neoadjuvant therapy rectal cancer, and that negative and weak nuclear BCLAF1 expression are independently associated with a poor prognosis.
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Affiliation(s)
- Gordon T Brown
- Pathology, Division of Applied Medicine, School of Medicine and Dentistry, University of Aberdeen, Aberdeen, UK
| | - Beatriz Cash
- Vertebrate Antibodies, Tillydrone Avenue, Aberdeen, UK
| | | | - Leslie M Samuel
- Department of Clinical Oncology, Aberdeen Royal Infirmary, NHS Grampian, Aberdeen, UK
| | - Graeme I Murray
- Pathology, Division of Applied Medicine, School of Medicine and Dentistry, University of Aberdeen, Aberdeen, UK
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Metsalu T, Viltrop T, Tiirats A, Rajashekar B, Reimann E, Kõks S, Rull K, Milani L, Acharya G, Basnet P, Vilo J, Mägi R, Metspalu A, Peters M, Haller-Kikkatalo K, Salumets A. Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta. Epigenetics 2015; 9:1397-409. [PMID: 25437054 DOI: 10.4161/15592294.2014.970052] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Given the possible critical importance of placental gene imprinting and random monoallelic expression on fetal and infant health, most of those genes must be identified, in order to understand the risks that the baby might meet during pregnancy and after birth. Therefore, the aim of the current study was to introduce a workflow and tools for analyzing imprinted and random monoallelic gene expression in human placenta, by applying whole-transcriptome (WT) RNA sequencing of placental tissue and genotyping of coding DNA variants in family trios. Ten family trios, each with a healthy spontaneous single-term pregnancy, were recruited. Total RNA was extracted for WT analysis, providing the full sequence information for the placental transcriptome. Parental and child blood DNA genotypes were analyzed by exome SNP genotyping microarrays, mapping the inheritance and estimating the abundance of parental expressed alleles. Imprinted genes showed consistent expression from either parental allele, as demonstrated by the SNP content of sequenced transcripts, while monoallelically expressed genes had random activity of parental alleles. We revealed 4 novel possible imprinted genes (LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed the imprinting of 4 genes (AIM1, PEG10, RHOBTB3 and ZFAT-AS1) in human placenta. The major finding was the identification of 4 genes (ABP1, BCLAF1, IFI30 and ZFAT) with random allelic bias, expressing one of the parental alleles preferentially. The main functions of the imprinted and monoallelically expressed genes included: i) mediating cellular apoptosis and tissue development; ii) regulating inflammation and immune system; iii) facilitating metabolic processes; and iv) regulating cell cycle.
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Key Words
- ASE, allele-specific expression
- FDR, false discovery rate
- GEO, Gene Expression Omnibus
- IUGR, intrauterine growth restriction
- MAF, minor allele frequency
- MHC, major histocompatibility complex
- NK cells, natural killer cells
- RNA sequencing
- RNA-Seq, RNA-sequencing
- RPKM, reads per kilobase per million
- UCSC, University of California Santa Cruz
- WT, whole-transcriptome
- allele-specific expression
- imprinting
- placenta
- random monoallelic expression
- short read mapping
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Affiliation(s)
- Tauno Metsalu
- a Institute of Computer Science ; University of Tartu ; Tartu , Estonia
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48
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Chen X, Lu Y, Zhang Z, Wang J, Yang H, Liu G. Intercellular interplay between Sirt1 signalling and cell metabolism in immune cell biology. Immunology 2015; 145:455-67. [PMID: 25890999 DOI: 10.1111/imm.12473] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/11/2015] [Accepted: 04/15/2015] [Indexed: 12/12/2022] Open
Abstract
Sirtuins are evolutionarily conserved class III histone deacetylases that have been the focus of intense scrutiny and interest since the discovery of Sir2 as a yeast longevity factor. Early reports demonstrated an important role of Sirt1 in aging and metabolism, but its critical regulatory role in the immune system has only been unveiled in recent years. In this review we discuss the latest advances in understanding the regulatory role of Sirt1 in immune responses as well as how Sirt1 translates metabolic cues to immune signals, which would bring new insights into both pathogenesis and potential therapeutic strategies of a variety of immune-related diseases, such as cancer, microbial infection, autoimmune diseases and transplantation.
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Affiliation(s)
- Xi Chen
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Biotherapy Research Centre and Institute of Immunobiology, Fudan University, Shanghai, China
| | - Yun Lu
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Biotherapy Research Centre and Institute of Immunobiology, Fudan University, Shanghai, China
| | - Zhengguo Zhang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Biotherapy Research Centre and Institute of Immunobiology, Fudan University, Shanghai, China
| | - Jian Wang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Biotherapy Research Centre and Institute of Immunobiology, Fudan University, Shanghai, China
| | - Hui Yang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Biotherapy Research Centre and Institute of Immunobiology, Fudan University, Shanghai, China
| | - Guangwei Liu
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Biotherapy Research Centre and Institute of Immunobiology, Fudan University, Shanghai, China
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49
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Global characterization of differential gene expression profiles in mouse Vγ1+ and Vγ4+ γδ T cells. PLoS One 2014; 9:e112964. [PMID: 25405356 PMCID: PMC4236085 DOI: 10.1371/journal.pone.0112964] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 10/16/2014] [Indexed: 11/19/2022] Open
Abstract
Peripheral γδ T cells in mice are classified into two major subpopulations, Vγ1+ and Vγ4+, based on the composition of T cell receptors. However, their intrinsic differences remain unclear. In this study, we analyzed gene expression profiles of the two subsets using Illumina HiSeq 2000 Sequencer. We identified 1995 transcripts related to the activation of Vγ1+ γδ T cells, and 2158 transcripts related to the activation of Vγ4+ γδ T cells. We identified 24 transcripts differentially expressed between the two subsets in resting condition, and 20 after PMA/Ionomycin treatment. We found that both cell types maintained phenotypes producing IFN-γ, TNF-α, TGF-β and IL-10. However, Vγ1+ γδ T cells produced more Th2 type cytokines, such as IL-4 and IL-5, while Vγ4+ γδ T cells preferentially produced IL-17. Our study provides a comprehensive gene expression profile of mouse peripheral Vγ1+ and Vγ4+ γδ T cells that describes the inherent differences between them.
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50
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BCLAF1 and its splicing regulator SRSF10 regulate the tumorigenic potential of colon cancer cells. Nat Commun 2014; 5:4581. [PMID: 25091051 DOI: 10.1038/ncomms5581] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 07/02/2014] [Indexed: 12/31/2022] Open
Abstract
Bcl-2-associated transcription factor 1 (BCLAF1) is known to be involved in multiple biological processes. Although several splice variants of BCLAF1 have been identified, little is known about how BCLAF1 splicing is regulated or the contribution of alternative splicing to its developmental functions. Here we find that inclusion of alternative exon5a was significantly increased in colorectal cancer (CRC) samples. Knockdown of the BCLAF1 protein isoform resulting from exon5a inclusion inhibited growth and that its overexpression increased tumorigenic potential. We also found that the splicing factor SRSF10 stimulates inclusion of exon5a and has growth-inducing activity. Importantly, the upregulation of SRSF10 expression observed in clinical CRC samples parallels the increased inclusion of BCLAF1 exon5a, both of which are associated with higher tumour grade. These findings identify SRSF10 as a key regulator of BCLAF1 pre-mRNA splicing and the maintenance of oncogenic features in human colon cancer cells.
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