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Murakami Y, Imaizumi T, Hashizume K, Tezuka Y, Oku Y, Nishiya N, Sanbe A, Kurosaka D. Inhibition of Connective Tissue Growth Factor Expression in Adult Retinal Pigment Epithelial-19 Cells by Blocking Yes-Associated Protein/Transcriptional Coactivator with PDZ-Binding Motif Activity. J Ocul Pharmacol Ther 2024; 40:246-252. [PMID: 38517736 DOI: 10.1089/jop.2023.0141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
Purpose: To investigate the effect of yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ) on connective tissue growth factor (CTGF) expression in adult retinal pigment epithelial (ARPE)-19 cells. We also studied the inhibitory effect of K-975, a new pan-transcriptional enhanced associate domain (TEAD) inhibitor, and luteolin, a plant-derived flavonoid on CTGF expression. Methods: ARPE-19 cells were transfected with either YAP or TAZ overexpression plasmid or treated with transforming growth factor (TGF)-β2. The cells were cultured either with or without K-975 or luteolin. The expression of YAP, TAZ, and CTGF was examined using real-time PCR. Results: ARPE-19 cells overexpressing YAP or TAZ exhibited significantly increased CTGF expression. This increase was attenuated by K-975 or luteolin alone. TGF-β2 treatment significantly raised the expression of not just YAP and TAZ, but also CTGF in ARPE-19 cells. TGF-β2 treatment-enhanced CTGF expression was considerably lowered by the addition of K-975 or luteolin. Conclusions: Overexpression of YAP or TAZ and treatment with TGF-β2 led to an increase in the expression of CTGF in ARPE-19 cells. These increases were attenuated by treatment with K-975 and luteolin. These findings suggest that YAP and TAZ may be related to the expression of CTGF in ARPE-19 cells and that K-975 and luteolin can be explored as potential therapeutic agents for preventing CTGF production in vitreoretinal fibrosis.
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Affiliation(s)
- Yoko Murakami
- Department of Ophthalmology, School of Medicine, Iwate Medical University, 2-1-1 Idaitori, Yahaba-Cho, Shiwa-gun, Iwate, Japan
| | - Toshiyasu Imaizumi
- Department of Ophthalmology, School of Medicine, Iwate Medical University, 2-1-1 Idaitori, Yahaba-Cho, Shiwa-gun, Iwate, Japan
| | - Kouhei Hashizume
- Department of Ophthalmology, School of Medicine, Iwate Medical University, 2-1-1 Idaitori, Yahaba-Cho, Shiwa-gun, Iwate, Japan
| | - Yu Tezuka
- Department of Pharmacotherapeutics, School of Pharmacy, Iwate Medical University, Shiwa-gun, Japan
| | - Yusuke Oku
- Department of Integrated Information for Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa-gun, Japan
| | - Naoyuki Nishiya
- Department of Integrated Information for Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa-gun, Japan
| | - Atsushi Sanbe
- Department of Pharmacotherapeutics, School of Pharmacy, Iwate Medical University, Shiwa-gun, Japan
| | - Daijiro Kurosaka
- Department of Ophthalmology, School of Medicine, Iwate Medical University, 2-1-1 Idaitori, Yahaba-Cho, Shiwa-gun, Iwate, Japan
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2
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Zhu HX, Yang SH, Gao CY, Bian ZH, Chen XM, Huang RR, Meng QL, Li X, Jin H, Tsuneyama K, Han Y, Li L, Zhao ZB, Gershwin ME, Lian ZX. Targeting pathogenic CD8 + tissue-resident T cells with chimeric antigen receptor therapy in murine autoimmune cholangitis. Nat Commun 2024; 15:2936. [PMID: 38580644 PMCID: PMC10997620 DOI: 10.1038/s41467-024-46654-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 03/01/2024] [Indexed: 04/07/2024] Open
Abstract
Primary biliary cholangitis (PBC) is a cholestatic autoimmune liver disease characterized by autoreactive T cell response against intrahepatic small bile ducts. Here, we use Il12b-/-Il2ra-/- mice (DKO mice) as a model of autoimmune cholangitis and demonstrate that Cd8a knockout or treatment with an anti-CD8α antibody prevents/reduces biliary immunopathology. Using single-cell RNA sequencing analysis, we identified CD8+ tissue-resident memory T (Trm) cells in the livers of DKO mice, which highly express activation- and cytotoxicity-associated markers and induce apoptosis of bile duct epithelial cells. Liver CD8+ Trm cells also upregulate the expression of several immune checkpoint molecules, including PD-1. We describe the development of a chimeric antigen receptor to target PD-1-expressing CD8+ Trm cells. Treatment of DKO mice with PD-1-targeting CAR-T cells selectively depleted liver CD8+ Trm cells and alleviated autoimmune cholangitis. Our work highlights the pathogenic role of CD8+ Trm cells and the potential therapeutic usage of PD-1-targeting CAR-T cells.
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Affiliation(s)
- Hao-Xian Zhu
- Chronic Disease Laboratory, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), School of Medicine, South China University of Technology, Guangzhou, China
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Shu-Han Yang
- Chronic Disease Laboratory, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), School of Medicine, South China University of Technology, Guangzhou, China
| | - Cai-Yue Gao
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Zhen-Hua Bian
- Chronic Disease Laboratory, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), School of Medicine, South China University of Technology, Guangzhou, China
| | - Xiao-Min Chen
- Chronic Disease Laboratory, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), School of Medicine, South China University of Technology, Guangzhou, China
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Rong-Rong Huang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Qian-Li Meng
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Xin Li
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Haosheng Jin
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Ying Han
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, China
| | - Liang Li
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
| | - Zhi-Bin Zhao
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
| | - M Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California Davis, Davis, CA, USA.
| | - Zhe-Xiong Lian
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
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3
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Ulhaq ZS, Ogino Y, Tse WKF. Transcriptome alterations in sf3b4-depleted zebrafish: Insights into cataract formation in retinitis pigmentosa model. Exp Eye Res 2024; 240:109819. [PMID: 38311285 DOI: 10.1016/j.exer.2024.109819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
Posterior subcapsular cataract (PSC) frequently develops as a complication in patients with retinitis pigmentosa (RP). Despite numerous scientific investigations, the intricate pathomechanisms underlying cataract formation in individuals affected by RP remain elusive. Therefore, our study aims to elucidate the potential pathogenesis of cataracts in an RP model using splicing factor subunit 3b (sf3b4) mutant zebrafish. By analyzing our previously published transcriptome dataset, we identified that, in addition to RP, cataract was listed as the second condition in our transcriptomic analysis. Furthermore, we confirmed the presence of nucleus retention in the lens fiber cells, along with abnormal cytoskeleton expression in both the lens fiber cells and lens epithelial cells in sf3b4-depleted fish. Upon closer examination, we identified 20 differentially expressed genes (DEGs) that played a role in cataract formation, with 95 % of them related to the downregulation of structural lens proteins. Additionally, we also identified that among all the DEGs, 13 % were associated with fibrotic processes. It seems that the significant upregulation of inflammatory mediators, in conjunction with TGF-β signaling, plays a central role in the cellular biology of PSC and posterior capsular opacification (PCO) in sf3b4 mutant fish. In summary, our study provides valuable insights into cataract formation in the RP model of sf3b4 mutants, highlighting its complexity driven by changes in structural lens proteins and increased cytokines/growth factors.
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Affiliation(s)
- Zulvikar Syambani Ulhaq
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan; Research Center for Pre-clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia.
| | - Yukiko Ogino
- Laboratory of Aquatic Molecular Developmental Biology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.
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4
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Nordbø OP, Landolt L, Eikrem Ø, Scherer A, Leh S, Furriol J, Apeland T, Mydel P, Marti H. Transcriptomic analysis reveals partial epithelial-mesenchymal transition and inflammation as common pathogenic mechanisms in hypertensive nephrosclerosis and Type 2 diabetic nephropathy. Physiol Rep 2023; 11:e15825. [PMID: 37813528 PMCID: PMC10562137 DOI: 10.14814/phy2.15825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Hypertensive nephrosclerosis (HN) and Type 2 diabetic nephropathy (T2DN) are the leading causes of chronic kidney disease (CKD). To explore shared pathogenetic mechanisms, we analyzed transcriptomes of kidney biopsies from patients with HN or T2DN. Total RNA was extracted from 10 μm whole kidney sections from patients with HN, T2DN, and normal controls (Ctrl) (n = 6 for each group) and processed for RNA sequencing. Differentially expressed (log2 fold change >1, adjusted p < 0.05) genes (DEG) and molecular pathways were analyzed, and selected results were validated by immunohistochemistry (IHC). ELISA on serum samples was performed on a related cohort consisting of patients with biopsy-proven HN (n = 13) and DN (n = 9), and a normal control group (n = 14). Cluster analysis on RNA sequencing data separated diseased and normal tissues. RNA sequencing revealed that 88% (341 out of 384) of DEG in HN were also altered in T2DN, while gene set enrichment analysis (GSEA) showed that over 90% of affected molecular pathways, including those related to inflammation, immune response, and cell-cycle regulation, were similarly impacted in both HN and T2DN samples. The increased expression of genes tied to interleukin signaling and lymphocyte activation was more pronounced in HN, while genes associated with extracellular matrix organization were more evident in T2DN. Both HN and T2DN tissues exhibited significant upregulation of genes connected with inflammatory responses, T-cell activity, and partial epithelial to mesenchymal transition (p-EMT). Immunohistochemistry (IHC) further confirmed T-cell (CD4+ and CD8+ ) infiltration in the diseased tissues. Additionally, IHC revealed heightened AXL protein expression, a key regulator of inflammation and p-EMT, in both HN and T2DN, while serum analysis indicated elevated soluble AXL levels in patients with both conditions. These findings underline the shared molecular mechanisms between HN and T2DN, hinting at the potential for common therapeutic strategies targeting both diseases.
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Affiliation(s)
- Ole Petter Nordbø
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of Medicine, Haugesund HospitalHelse FonnaHaugesundNorway
| | - Lea Landolt
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of MedicineHaukeland University HospitalBergenNorway
| | - Øystein Eikrem
- Department of Clinical ScienceUniversity of BergenBergenNorway
| | | | - Sabine Leh
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of PathologyHaukeland University HospitalBergenNorway
| | - Jessica Furriol
- Department of Clinical MedicineUniversity of BergenBergenNorway
| | | | - Piotr Mydel
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of MedicineHaukeland University HospitalBergenNorway
| | - Hans‐Peter Marti
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of MedicineHaukeland University HospitalBergenNorway
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5
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Rajeh A, Cornman HL, Gupta A, Szeto MD, Kambala A, Oladipo O, Parthasarathy V, Deng J, Wheelan S, Pritchard T, Kwatra MM, Semenov YR, Gusev A, Yegnasubramanian S, Kwatra SG. Somatic mutations reveal hyperactive Notch signaling and racial disparities in prurigo nodularis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.25.23295810. [PMID: 37808834 PMCID: PMC10557842 DOI: 10.1101/2023.09.25.23295810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Prurigo nodularis (PN) is a chronic inflammatory skin disease that disproportionately affects African Americans and is characterized by pruritic skin nodules of unknown etiology. Little is known about genetic alterations in PN pathogenesis, especially relating to somatic events which are often implicated in inflammatory conditions. We thus performed whole-exome sequencing on 54 lesional and nonlesional skin biopsies from 17 PN patients and 10 atopic dermatitis (AD) patients for comparison. Somatic mutational analysis revealed that PN lesional skin harbors pervasive somatic mutations in fibrotic, neurotropic, and cancer-associated genes. Nonsynonymous mutations were most frequent in NOTCH1 and the Notch signaling pathway, a regulator of cellular proliferation and tissue fibrosis, and NOTCH1 mutations were absent in AD. Somatic copy-number analysis, combined with expression data, showed that recurrently deleted and downregulated genes in PN lesional skin are associated with axonal guidance and extension. Follow-up immunofluorescence validation demonstrated increased NOTCH1 expression in PN lesional skin fibroblasts and increased Notch signaling in PN lesional dermis. Finally, multi-center data revealed a significantly increased risk of NOTCH1-associated diseases in PN patients. In characterizing the somatic landscape of PN, we uncover novel insights into its pathophysiology and identify a role for dysregulated Notch signaling in PN.
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Affiliation(s)
- Ahmad Rajeh
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hannah L Cornman
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anuj Gupta
- The Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Mindy D Szeto
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anusha Kambala
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olusola Oladipo
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Varsha Parthasarathy
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Junwen Deng
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah Wheelan
- Present affiliation: National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA
| | - Thomas Pritchard
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Madan M Kwatra
- Department of Anesthesiology, Duke University School of Medicine, Durham, NC, USA
| | - Yevgeniy R Semenov
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alexander Gusev
- Division of Genetics, Brigham & Women's Hospital, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Srinivasan Yegnasubramanian
- The Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shawn G Kwatra
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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6
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He ZX, Yang WG, Zengyangzong D, Gao G, Zhang Q, Liu HM, Zhao W, Ma LY. Targeting cullin neddylation for cancer and fibrotic diseases. Theranostics 2023; 13:5017-5056. [PMID: 37771770 PMCID: PMC10526667 DOI: 10.7150/thno.78876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 04/12/2023] [Indexed: 09/30/2023] Open
Abstract
Protein neddylation is a post-translational modification, and its best recognized substrates are cullin family proteins, which are the core component of Cullin-RING ligases (CRLs). Given that most neddylation pathway proteins are overactivated in different cancers and fibrotic diseases, targeting neddylation becomes an emerging approach for the treatment of these diseases. To date, numerous neddylation inhibitors have been developed, of which MLN4924 has entered phase I/II/III clinical trials for cancer treatment, such as acute myeloid leukemia, melanoma, lymphoma and solid tumors. Here, we systematically describe the structures and biological functions of the critical enzymes in neddylation, highlight the medicinal chemistry advances in the development of neddylation inhibitors and propose the perspectives concerning targeting neddylation for cancer and fibrotic diseases.
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Affiliation(s)
- Zhang-Xu He
- Pharmacy College, Henan University of Chinese Medicine, 450046, Zhengzhou, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Wei-guang Yang
- Children's hospital affiliated of Zhengzhou university; Henan children's hospital; Zhengzhou children's hospital, Henan Zhengzhou 450000, China
| | - Dan Zengyangzong
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Ge Gao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Qian Zhang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Hong-Min Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Wen Zhao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Li-Ying Ma
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
- China Meheco Topfond Pharmaceutical Co., Zhumadian 463000, China
- Key Laboratory of Cardio-cerebrovascular Drug, Henan Province, Zhumadian 463000, China
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7
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Golec M, Kamdar M, Barteit S. Comprehensive Ontology of Fibroproliferative Diseases: Protocol for a Semantic Technology Study. JMIR Res Protoc 2023; 12:e48645. [PMID: 37566458 PMCID: PMC10457705 DOI: 10.2196/48645] [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: 05/02/2023] [Revised: 06/16/2023] [Accepted: 07/04/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Fibroproliferative or fibrotic diseases (FDs), which represent a significant proportion of age-related pathologies and account for over 40% of mortality in developed nations, are often underrepresented in focused research. Typically, these conditions are studied individually, such as chronic obstructive pulmonary disease or idiopathic pulmonary fibrosis (IPF), rather than as a collective entity, thereby limiting the holistic understanding and development of effective treatments. To address this, we propose creating and publicizing a comprehensive fibroproliferative disease ontology (FDO) to unify the understanding of FDs. OBJECTIVE This paper aims to delineate the study protocol for the creation of the FDO, foster transparency and high quality standards during its development, and subsequently promote its use once it becomes publicly available. METHODS We aim to establish an ontology encapsulating the broad spectrum of FDs, constructed in the Web Ontology Language format using the Protégé ontology editor, adhering to ontology development life cycle principles. The modeling process will leverage Protégé in accordance with a methodologically defined process, involving targeted scoping reviews of MEDLINE and PubMed information, expert knowledge, and an ontology development process. A hybrid top-down and bottom-up strategy will guide the identification of core concepts and relations, conducted by a team of domain experts based on systematic iterations of scientific literature reviews. RESULTS The result will be an exhaustive FDO accommodating a wide variety of crucial biomedical concepts, augmented with synonyms, definitions, and references. The FDO aims to encapsulate diverse perspectives on the FD domain, including those of clinicians, health informaticians, medical researchers, and public health experts. CONCLUSIONS The FDO is expected to stimulate broader and more in-depth FD research by enabling reasoning, inference, and the identification of relationships between concepts for application in multiple contexts, such as developing specialized software, fostering research communities, and enhancing domain comprehension. A common vocabulary and understanding of relationships among medical professionals could potentially expedite scientific progress and the discovery of innovative solutions. The publicly available FDO will form the foundation for future research, technological advancements, and public health initiatives. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) PRR1-10.2196/48645.
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Affiliation(s)
- Marcin Golec
- Heidelberg Institute of Global Health, Faculty of Medicine and University Hospital, Heidelberg University, Heidelberg, Germany
| | - Maulik Kamdar
- Center for Advanced Clinical Solutions, Optum Health, Eden Prairie, MN, United States
| | - Sandra Barteit
- Heidelberg Institute of Global Health, Faculty of Medicine and University Hospital, Heidelberg University, Heidelberg, Germany
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8
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Majid A, Hassan FO, Hoque MM, Gbadegoye JO, Lebeche D. Bioactive Compounds and Cardiac Fibrosis: Current Insight and Future Prospect. J Cardiovasc Dev Dis 2023; 10:313. [PMID: 37504569 PMCID: PMC10380727 DOI: 10.3390/jcdd10070313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023] Open
Abstract
Cardiac fibrosis is a pathological condition characterized by excessive deposition of collagen and other extracellular matrix components in the heart. It is recognized as a major contributor to the development and progression of heart failure. Despite significant research efforts in characterizing and identifying key molecular mechanisms associated with myocardial fibrosis, effective treatment for this condition is still out of sight. In this regard, bioactive compounds have emerged as potential therapeutic antifibrotic agents due to their anti-inflammatory and antioxidant properties. These compounds exhibit the ability to modulate fibrogenic processes by inhibiting the production of extracellular matrix proteins involved in fibroblast to myofibroblast differentiation, or by promoting their breakdown. Extensive investigation of these bioactive compounds offers new possibilities for preventing or reducing cardiac fibrosis and its detrimental consequences. This comprehensive review aims to provide a thorough overview of the mechanisms underlying cardiac fibrosis, address the limitations of current treatment strategies, and specifically explore the potential of bioactive compounds as therapeutic interventions for the treatment and/or prevention of cardiac fibrosis.
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Affiliation(s)
- Abdul Majid
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Fasilat Oluwakemi Hassan
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Md Monirul Hoque
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Joy Olaoluwa Gbadegoye
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Djamel Lebeche
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
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9
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Basta MD, Petruk S, Mazo A, Walker JL. Fibrosis-the tale of H3K27 histone methyltransferases and demethylases. Front Cell Dev Biol 2023; 11:1193344. [PMID: 37476157 PMCID: PMC10354294 DOI: 10.3389/fcell.2023.1193344] [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: 03/24/2023] [Accepted: 06/22/2023] [Indexed: 07/22/2023] Open
Abstract
Fibrosis, or excessive scarring, is characterized by the emergence of alpha-smooth muscle actin (αSMA)-expressing myofibroblasts and the excessive accumulation of fibrotic extracellular matrix (ECM). Currently, there is a lack of effective treatment options for fibrosis, highlighting an unmet need to identify new therapeutic targets. The acquisition of a fibrotic phenotype is associated with changes in chromatin structure, a key determinant of gene transcription activation and repression. The major repressive histone mark, H3K27me3, has been linked to dynamic changes in gene expression in fibrosis through alterations in chromatin structure. H3K27-specific homologous histone methylase (HMT) enzymes, Enhancer of zeste 1 and 2 (EZH1, EZH2), which are the alternative subunits of the Polycomb Repressive Complex 2 (PRC2) and demethylase (KDM) enzymes, Ubiquitously transcribed tetratricopeptide repeat, X chromosome (UTX), and Lysine demethylase 6B (KDM6B), are responsible for regulating methylation status of H3K27me3. In this review, we explore how these key enzymes regulate chromatin structure to alter gene expression in fibrosis, highlighting them as attractive targets for the treatment of fibrosis.
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Affiliation(s)
- Morgan D. Basta
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, United States
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Janice L. Walker
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, United States
- Department of Ophthalmology, Thomas Jefferson University, Philadelphia, PA, United States
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10
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Han C, Leonardo TR, Romana-Souza B, Shi J, Keiser S, Yuan H, Altakriti M, Ranzer MJ, Ferri-Borgogno S, Mok SC, Koh TJ, Hong SJ, Chen L, DiPietro LA. Microfibril-associated protein 5 and the regulation of skin scar formation. Sci Rep 2023; 13:8728. [PMID: 37253753 PMCID: PMC10229580 DOI: 10.1038/s41598-023-35558-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/20/2023] [Indexed: 06/01/2023] Open
Abstract
Many factors regulate scar formation, which yields a modified extracellular matrix (ECM). Among ECM components, microfibril-associated proteins have been minimally explored in the context of skin wound repair. Microfibril-associated protein 5 (MFAP5), a small 25 kD serine and threonine rich microfibril-associated protein, influences microfibril function and modulates major extracellular signaling pathways. Though known to be associated with fibrosis and angiogenesis in certain pathologies, MFAP5's role in wound healing is unknown. Using a murine model of skin wound repair, we found that MFAP5 is significantly expressed during the proliferative and remodeling phases of healing. Analysis of existing single-cell RNA-sequencing data from mouse skin wounds identified two fibroblast subpopulations as the main expressors of MFAP5 during wound healing. Furthermore, neutralization of MFAP5 in healing mouse wounds decreased collagen deposition and refined angiogenesis without altering wound closure. In vitro, recombinant MFAP5 significantly enhanced dermal fibroblast migration, collagen contractility, and expression of pro-fibrotic genes. Additionally, TGF-ß1 increased MFAP5 expression and production in dermal fibroblasts. Our findings suggest that MFAP5 regulates fibroblast function and influences scar formation in healing wounds. Our work demonstrates a previously undescribed role for MFAP5 and suggests that microfibril-associated proteins may be significant modulators of wound healing outcomes and scarring.
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Affiliation(s)
- Chen Han
- Center for Wound Healing and Tissue Regeneration, University of Illinois Chicago, Chicago, IL, USA
| | - Trevor R Leonardo
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Bruna Romana-Souza
- Department of Histology and Embryology, Rio de Janeiro State University, Rio de Janeiro, RJ, Brazil
| | - Junhe Shi
- NMPA Key Laboratory for Clinical Research and Evaluation of Traditional Chinese Medicine, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shalyn Keiser
- Center for Wound Healing and Tissue Regeneration, University of Illinois Chicago, Chicago, IL, USA
| | - Heidi Yuan
- Center for Wound Healing and Tissue Regeneration, University of Illinois Chicago, Chicago, IL, USA
| | - Mohamad Altakriti
- Center for Wound Healing and Tissue Regeneration, University of Illinois Chicago, Chicago, IL, USA
| | - Matthew J Ranzer
- Department of Surgery, University of Illinois Chicago, Chicago, IL, USA
| | - Sammy Ferri-Borgogno
- Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Samuel C Mok
- Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy J Koh
- Center for Wound Healing and Tissue Regeneration, University of Illinois Chicago, Chicago, IL, USA
- Department of Kinesiology and Nutrition, University of Illinois Chicago, Chicago, IL, USA
| | - Seok Jong Hong
- Department of Surgery, Northwestern University-Feinberg School of Medicine, Chicago, IL, USA
| | - Lin Chen
- Center for Wound Healing and Tissue Regeneration, University of Illinois Chicago, Chicago, IL, USA.
| | - Luisa A DiPietro
- Center for Wound Healing and Tissue Regeneration, University of Illinois Chicago, Chicago, IL, USA.
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11
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Saaoud F, Martinez L, Lu Y, Xu K, Shao Y, Zhuo JL, Gillespie A, Wang H, Tabbara M, Salama A, Yang X, Vazquez-Padron RI. Chronic Kidney Disease Transdifferentiates Veins into a Specialized Immune-Endocrine Organ with Increased MYCN-AP1 Signaling. Cells 2023; 12:1482. [PMID: 37296603 PMCID: PMC10252601 DOI: 10.3390/cells12111482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/27/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023] Open
Abstract
Most patients with end-stage renal disease (ESRD) and advanced chronic kidney disease (CKD) choose hemodialysis as their treatment of choice. Thus, upper-extremity veins provide a functioning arteriovenous access to reduce dependence on central venous catheters. However, it is unknown whether CKD reprograms the transcriptome of veins and primes them for arteriovenous fistula (AVF) failure. To examine this, we performed transcriptomic analyses of bulk RNA sequencing data of veins isolated from 48 CKD patients and 20 non-CKD controls and made the following findings: (1) CKD converts veins into immune organs by upregulating 13 cytokine and chemokine genes, and over 50 canonical and noncanonical secretome genes; (2) CKD increases innate immune responses by upregulating 12 innate immune response genes and 18 cell membrane protein genes for increased intercellular communication, such as CX3CR1 chemokine signaling; (3) CKD upregulates five endoplasmic reticulum protein-coding genes and three mitochondrial genes, impairing mitochondrial bioenergetics and inducing immunometabolic reprogramming; (4) CKD reprograms fibrogenic processes in veins by upregulating 20 fibroblast genes and 6 fibrogenic factors, priming the vein for AVF failure; (5) CKD reprograms numerous cell death and survival programs; (6) CKD reprograms protein kinase signal transduction pathways and upregulates SRPK3 and CHKB; and (7) CKD reprograms vein transcriptomes and upregulates MYCN, AP1, and 11 other transcription factors for embryonic organ development, positive regulation of developmental growth, and muscle structure development in veins. These results provide novel insights on the roles of veins as immune endocrine organs and the effect of CKD in upregulating secretomes and driving immune and vascular cell differentiation.
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Affiliation(s)
- Fatma Saaoud
- Center for Cardiovascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Laisel Martinez
- DeWitt Daughtry Family Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Yifan Lu
- Center for Cardiovascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Keman Xu
- Center for Cardiovascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Ying Shao
- Center for Cardiovascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jia L Zhuo
- Tulane Hypertension and Renal Center of Excellence, Department of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Avrum Gillespie
- Section of Nephrology, Hypertension and Kidney Transplantation, Department of Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Hong Wang
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Marwan Tabbara
- DeWitt Daughtry Family Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alghidak Salama
- DeWitt Daughtry Family Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Xiaofeng Yang
- Center for Cardiovascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
- Section of Nephrology, Hypertension and Kidney Transplantation, Department of Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Roberto I. Vazquez-Padron
- DeWitt Daughtry Family Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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12
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Pal D, Ghatak S, Singh K, Abouhashem AS, Kumar M, El Masry MS, Mohanty SK, Palakurti R, Rustagi Y, Tabasum S, Khona DK, Khanna S, Kacar S, Srivastava R, Bhasme P, Verma SS, Hernandez E, Sharma A, Reese D, Verma P, Ghosh N, Gorain M, Wan J, Liu S, Liu Y, Castro NH, Gnyawali SC, Lawrence W, Moore J, Perez DG, Roy S, Yoder MC, Sen CK. Identification of a physiologic vasculogenic fibroblast state to achieve tissue repair. Nat Commun 2023; 14:1129. [PMID: 36854749 PMCID: PMC9975176 DOI: 10.1038/s41467-023-36665-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Tissue injury to skin diminishes miR-200b in dermal fibroblasts. Fibroblasts are widely reported to directly reprogram into endothelial-like cells and we hypothesized that miR-200b inhibition may cause such changes. We transfected human dermal fibroblasts with anti-miR-200b oligonucleotide, then using single cell RNA sequencing, identified emergence of a vasculogenic subset with a distinct fibroblast transcriptome and demonstrated blood vessel forming function in vivo. Anti-miR-200b delivery to murine injury sites likewise enhanced tissue perfusion, wound closure, and vasculogenic fibroblast contribution to perfused vessels in a FLI1 dependent manner. Vasculogenic fibroblast subset emergence was blunted in delayed healing wounds of diabetic animals but, topical tissue nanotransfection of a single anti-miR-200b oligonucleotide was sufficient to restore FLI1 expression, vasculogenic fibroblast emergence, tissue perfusion, and wound healing. Augmenting a physiologic tissue injury adaptive response mechanism that produces a vasculogenic fibroblast state change opens new avenues for therapeutic tissue vascularization of ischemic wounds.
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Affiliation(s)
- Durba Pal
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, 140001, India
| | - Subhadip Ghatak
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Kanhaiya Singh
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Ahmed Safwat Abouhashem
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Manishekhar Kumar
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mohamed S El Masry
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Sujit K Mohanty
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Ravichand Palakurti
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yashika Rustagi
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Saba Tabasum
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Dolly K Khona
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Savita Khanna
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Sedat Kacar
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Rajneesh Srivastava
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Pramod Bhasme
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sumit S Verma
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Edward Hernandez
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Anu Sharma
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Diamond Reese
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Priyanka Verma
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Nandini Ghosh
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Mahadeo Gorain
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jun Wan
- Center for Computational Biology and Bioinformatics (CCBB), Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sheng Liu
- Center for Computational Biology and Bioinformatics (CCBB), Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics (CCBB), Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Natalia Higuita Castro
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Surya C Gnyawali
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - William Lawrence
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Jordan Moore
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Daniel Gallego Perez
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Sashwati Roy
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Mervin C Yoder
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Chandan K Sen
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, 43210, USA.
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13
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Prepared for special issue on thymosins Thymosin β4 and the anti-fibrotic switch. Int Immunopharmacol 2023; 115:109628. [PMID: 36580759 DOI: 10.1016/j.intimp.2022.109628] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022]
Abstract
Wound healing involves a rapid response to the injury by circulating cells, followed by inflammation with an influx of inflammatory cells that release various factors. Soon after, cellular proliferation begins to replace the damaged cells and extracellular matrix, and then tissue remodeling restores normal tissue function. Various factors can lead to pathological wound healing when excessive and irreversible connective tissue/extracellular matrix deposition occurs, resulting in fibrosis. The process is initiated when immune cells, such as macrophages, release soluble factors that stimulate fibroblasts. TGFβ is the most well-characterized macrophage derived pro-fibrotic mediator. Other soluble mediators of fibrosis include connective tissue growth factor (CTGF), platelet-derived growth factor (PDGF), and interleukin 10 (IL-10). Thymosin β4 (Tβ4) has shown therapeutic benefit in preventing fibrosis/scarring in various animal models of fibrosis/scarring. The mechanism of action of Tβ4 appears related, in part, to a reduction in the inflammatory response, including a reduction in macrophage infiltration, decreased levels of TGFβ and IL-10, and reduced CTGF activation, resulting in both prevention of fibroblast conversion to myofibroblasts and production of normally aligned collagen fibers. The amino N-terminal end of Tβ4, SDKP (serine-aspartate-lysine-proline), appears to contain the majority of anti-fibrotic activity and has shown excellent efficacy in many animal models of fibrosis, including liver, lung, heart, and kidney fibrosis. Ac-SDKP not only prevents fibrosis but can reverse fibrosis. Unanswered questions and future directions will be presented with regard to therapeutic uses alone and in combination with already approved drugs for fibrosis.
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14
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Colitti M, Stefanon B, Sandri M, Licastro D. Incubation of canine dermal fibroblasts with serum from dogs with atopic dermatitis activates extracellular matrix signalling and represses oxidative phosphorylation. Vet Res Commun 2023; 47:247-258. [PMID: 35665445 PMCID: PMC9873773 DOI: 10.1007/s11259-022-09947-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/25/2022] [Indexed: 01/28/2023]
Abstract
The aim of this study was to investigate the effects on gene expression in canine fibroblasts after incubation with a medium enriched with atopic dermatitis canine serum (CAD) compared with healthy canine serum (CTRL) and fetal bovine serum (FBS). Differential Expression and Pathway analysis (iDEP94) in R package (v0.92) was used to identify differentially expressed genes (DEGs) with a False Discovery Rate of 0.01. DEGs from fibroblasts incubated with CAD serum were significantly upregulated and enriched in the extracellular matrix (ECM) and focal adhesion signalling but downregulated in the oxidative phosphorylation pathway. Genes involved in profibrotic processes, such as TGFB1, INHBA, ERK1/2, and the downward regulated genes (collagens and integrins), were significantly upregulated after fibroblasts were exposed to CAD serum. The observed downregulation of genes involved in oxidative phosphorylation suggests metabolic dysregulation toward a myofibroblast phenotype responsible for fibrosis. No differences were found when comparing CTRL with FBS. The DEGs identified in fibroblasts incubated with CAD serum suggest activation of signalling pathways involved in gradual differentiation through a myofibroblast precursors that represent the onset of fibrosis. Molecular and metabolic knowledge of fibroblast changes can be used to identify biomarkers of the disease and new potential pharmacological targets.
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Affiliation(s)
- Monica Colitti
- Departement of AgroFood, Environmental and Animal Science, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - Bruno Stefanon
- Departement of AgroFood, Environmental and Animal Science, University of Udine, via delle Scienze 206, 33100, Udine, Italy.
| | - Misa Sandri
- Departement of AgroFood, Environmental and Animal Science, University of Udine, via delle Scienze 206, 33100, Udine, Italy
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15
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Sheibani N. Connective Tissue Growth Factor: A Key Factor Among Mediators of Tissue Fibrosis. J Ophthalmic Vis Res 2022; 17:449-452. [PMID: 36620701 PMCID: PMC9806321 DOI: 10.18502/jovr.v17i4.12294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/27/2022] [Indexed: 12/03/2022] Open
Abstract
This is an Editorial and does not have an abstract. Please download the PDF or view the article HTML.
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Affiliation(s)
- Nader Sheibani
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA,Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA,McPherson Eye Research Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA,Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA
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16
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Single-cell profiling reveals distinct adaptive immune hallmarks in MDA5+ dermatomyositis with therapeutic implications. Nat Commun 2022; 13:6458. [PMID: 36309526 PMCID: PMC9617246 DOI: 10.1038/s41467-022-34145-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 10/16/2022] [Indexed: 12/25/2022] Open
Abstract
Anti-melanoma differentiation-associated gene 5-positive dermatomyositis (MDA5+ DM) is an autoimmune condition associated with rapidly progressive interstitial lung disease and high mortality. The aetiology and pathogenesis of MDA5+ DM are still largely unknown. Here we describe the immune signatures of MDA5+ DM via single-cell RNA sequencing, flow cytometry and multiplex immunohistochemistry in peripheral B and T cells and in affected lung tissue samples from one patient. We find strong peripheral antibody-secreting cell and CD8+ T cell responses as cellular immune hallmarks, and over-stimulated type I interferon signaling and associated metabolic reprogramming as molecular immune signature in MDA5+ DM. High frequency of circulating ISG15+ CD8+ T cells at baseline predicts poor one-year survival in MDA5+ DM patients. In affected lungs, we find profuse immune cells infiltration, which likely contributes to the pro-fibrotic response via type I interferon production. The importance of type I interferons in MDA5+ DM pathology is further emphasized by our observation in a retrospective cohort of MDA5+ DM patients that combined calcineurin and Janus kinase inhibitor therapy show superior efficacy to calcineurin inhibitor monotherapy. In summary, this study reveals key immune-pathogenic features of MDA5+ DM and provides a potential basis for future tailored therapies.
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17
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Cystic Fibrosis: Systems Biology Analysis from Homozygous p.Phe508del Variant Patients' Samples Reveals Perturbations in Tissue-Specific Pathways. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5262000. [PMID: 34901273 PMCID: PMC8660202 DOI: 10.1155/2021/5262000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/08/2021] [Indexed: 11/24/2022]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disorder, caused by diverse genetic variants for the CF transmembrane conductance regulator (CFTR) protein. Among these, p.Phe508del is the most prevalent variant. The effects of this variant on the physiology of each tissue remains unknown. This study is aimed at predicting cell signaling pathways present in different tissues of fibrocystic patients, homozygous for p.Phe508del. The study involved analysis of two microarray datasets, E-GEOD-15568 and E-MTAB-360 corresponding to the rectal and bronchial epithelium, respectively, obtained from the ArrayExpress repository. Particularly, differentially expressed genes (DEGs) were predicted, protein-protein interaction (PPI) networks were designed, and centrality and functional interaction networks were analyzed. The study reported that p.Phe508del-mutated CFTR-allele in homozygous state influenced the whole gene expression in each tissue differently. Interestingly, gene ontology (GO) term enrichment analysis revealed that only “neutrophil activation” was shared between both tissues; however, nonshared DEGs were grouped into the same GO term. For further verification, functional interaction networks were generated, wherein no shared nodes were reported between these tissues. These results suggested that the p.Phe508del-mutated CFTR-allele in homozygous state promoted tissue-specific pathways in fibrocystic patients. The generated data might further assist in prediction diagnosis to define biomarkers or devising therapeutic strategies.
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Yang P, Cao Y, Jian H, Chen H. Identification of Hub mRNAs and lncRNAs in Atrial Fibrillation Using Weighted Co-expression Network Analysis With RNA-Seq Data. Front Cell Dev Biol 2021; 9:722671. [PMID: 34671599 PMCID: PMC8520999 DOI: 10.3389/fcell.2021.722671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/09/2021] [Indexed: 01/28/2023] Open
Abstract
Atrial fibrillation (AF)/paroxysmal AF (PAF) is the main cause of cardiogenic embolism. In recent years, the progression from paroxysmal AF to persistent AF has attracted more and more attention. However, the molecular mechanism of the progression of AF is unclear. In this study, we performed RNA sequencing for normal samples, paroxysmal AF and persistent AF samples to identify differentially expressed gene (DEG) and explore the roles of these DEGs in AF. Totally, 272 differently expressed mRNAs (DEmRNAs) and 286 differentially expressed lncRNAs (DElncRNAs) were identified in paroxysmal AF compared to normal samples; 324 DEmRNAs and 258 DElncRNAs were found in persistent atrial fibrillation compared with normal samples; and 520 DEmRNAs and 414 DElncRNAs were identified in persistent AF compared to paroxysmal AF samples. Interestingly, among the DEGs, approximately 50% were coding genes and around 50% were non-coding RNAs, suggesting that lncRNAs may also have a crucial role in the progression of AF. Bioinformatics analysis demonstrated that these DEGs were significantly related to regulating multiple AF associated pathways, such as the regulation of vascular endothelial growth factor production and binding to the CXCR chemokine receptor. Furthermore, weighted gene co-expression network analysis (WGCNA) was conducted to identify key modules and hub RNAs and lncRNAs to determine their potential associations with AF. Five hub modules were identified in the progression of AF, including blue, brown, gray, turquoise and yellow modules. Interestingly, blue module and turquoise module were significantly negatively and positively correlated to the progression of AF respectively, indicating that they may have a more important role in the AF. Moreover, the hub protein-protein interaction (PPI) networks and lncRNA-mRNA regulatory network were constructed. Bioinformatics analysis on the hub PPI network in turquoise was involved in regulating immune response related signaling, such as leukocyte chemotaxis, macrophage activation, and positive regulation of α-β T cell activation. Our findings could clarify the underlying molecular changes associated fibrillation, and provide a useful resource for identifying AF marker.
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Affiliation(s)
- Pan Yang
- Emergency Department, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Cardiovascular Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, China.,Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yujing Cao
- Department of Cardiovascular Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, China
| | - Huagang Jian
- Emergency Department, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hao Chen
- Department of Cardiovascular Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, China
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Selman M, Pardo A. Fibroageing: An ageing pathological feature driven by dysregulated extracellular matrix-cell mechanobiology. Ageing Res Rev 2021; 70:101393. [PMID: 34139337 DOI: 10.1016/j.arr.2021.101393] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Ageing is a multifactorial biological process leading to a progressive decline of physiological functions. The process of ageing includes numerous changes in the cells and the interactions between cell-cell and cell-microenvironment remaining as a critical risk factor for the development of chronic degenerative diseases. Systemic inflammation, known as inflammageing, increases as a consequence of ageing contributing to age-related morbidities. But also, persistent and uncontrolled activation of fibrotic pathways, with excessive accumulation of extracellular matrix (ECM) and organ dysfunction is markedly more frequent in the elderly. In this context, we introduce here the concept of Fibroageing, that is, the propensity to develop tissue fibrosis associated with ageing, and propose that ECM is a key player underlying this process. During ageing, molecules of the ECM become damaged through many modifications including glycation, crosslinking, and accumulation, leading to matrix stiffness which intensifies ageing-associated alterations. We provide a framework with some mechanistic hypotheses proposing that stiff ECM, in addition to the well-known activation of fibrotic positive feedback loops, affect several of the hallmarks of ageing, such as cell senescence and mitochondrial dysfunction, and in this context, is a key mechanism and a driver thread of Fibroageing.
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20
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Jin H, Wu Z, Tan B, Liu Z, Zhang B. CircITGA7 Suppresses Gastric Cancer Progression Through miR-1471/MTDH Axis. Front Cell Dev Biol 2021; 9:688970. [PMID: 34504842 PMCID: PMC8423148 DOI: 10.3389/fcell.2021.688970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/13/2021] [Indexed: 12/11/2022] Open
Abstract
In recent years, there have been reports about the involvement of circular RNAs (circRNAs) in the pathogenesis of gastric cancer (GC), but the molecular mechanism in cell proliferation, invasion, and migration is still unclear. Based on The Cancer Genome Atlas (TCGA) database, we analyzed differentially expressed circRNAs between GC and non-tumor tissues. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were used to clarify the functional role in GC. Here, we showed that circITGA7 was lowly expressed in GC tissues based on the TCGA database. In vitro, silencing the expression of circITGA7 increased cell proliferation and metastasis, whereas overexpression did the opposite. Mechanistically, miR-1471 has circITGA7 as a sponge, and miR-1471 has metadherin (MTDH) as a target gene. Consequently, functional analysis showed that the tumor suppressor effect of circITGA7 was the result of regulating the miR-1471/MTDH axis. Overall, the circITGA7/miR-1471/MTDH signaling pathway may play a crucial role in GC, providing a new potential mechanism involved in GC progression.
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Affiliation(s)
- Haifeng Jin
- Department of Gastroenterology, The 980th Hospital of the PLA Joint Logistics Support Force (Primary Bethune International Peace Hospital of PLA), Shijiazhuang, China
| | - Zheng Wu
- Department of Immuno-Oncology, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Bibo Tan
- Department of General Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhen Liu
- Department of Gastroenterology, The 980th Hospital of the PLA Joint Logistics Support Force (Primary Bethune International Peace Hospital of PLA), Shijiazhuang, China
| | - Binqian Zhang
- Department of Clinical Medicine, Chongqing Engineering Research Center of Pharmaceutical Sciences, Chongqing Medical and Pharmaceutical College, Chongqing, China
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Qi L, Wang W, Zhao G, Jiang H, Zhang Y, Zhao D, Jin H, Xu H, Yu H. Circular RNA circCCDC66 promotes glioma proliferation by acting as a ceRNA for miR-320a to regulate FOXM1 expression. Aging (Albany NY) 2021; 13:17673-17689. [PMID: 34252882 PMCID: PMC8312454 DOI: 10.18632/aging.203258] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 05/11/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND In this study, we determine the potential roles and uncover the regulatory mechanisms of circCCDC66 in regulating cell growth and cell metastasis of glioma. METHODS qRT-PCR was used to detect the expressions of circCCDC66 in gliomas and tissues. The biological function of circCCDC66 in glioma cell lines was elucidated by functional experiments. Cell counting kit-8 and transwell were used to detect the effect of circCCDC66 on the proliferation, migration and invasion of glioma cells. Bioinformatics analysis was applied to reveal the targets of circCCDC66. RESULTS The results showed circCCDC66 was overexpressed in glioma and acted as an oncogene. CircCCDC66 knockdown suppressed the proliferation, migration, and invasion of glioma cells. We constructed a circCCDC66 regulating miRNA network and revealed miR-320a was a potential target of circCCDC66, which was down-regulated in high-grade gliomas compared to low-grade gliomas. Bioinformatics analysis showed circCCDC66-miR-320a/b axis was involved in regulating multiple cancer-related pathways. Furthermore, we identified FOXM1 as a key target of circCCDC66, which was involved in regulating DNA damage response pathways. In mechanism study, circCCDC66 could sponge miR-320a, thereby increasing the expression of FOXM1. CONCLUSIONS CircCCDC66 could facilitate glioma cells proliferation, invasion and migration by down-regulating miR-320a and up-regulating FOXM1.
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Affiliation(s)
- Ling Qi
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, Guangdong, China
- Department of Pathophysiology, Jilin Medical University, Jilin 132013, Jilin, China
| | - Weiyao Wang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, Guangdong, China
- Department of Pathophysiology, Jilin Medical University, Jilin 132013, Jilin, China
| | - Guifang Zhao
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, Guangdong, China
- Department of Pathology, Jilin Medical University, Jilin 132013, Jilin, China
| | - Hong Jiang
- Department of Ophthalmology, China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin, China
| | - Yu Zhang
- Department of Neurovascular, First Hospital of Jilin University, Changchun 130021, Jilin, China
| | - Donghai Zhao
- Department of Pathology, Jilin Medical University, Jilin 132013, Jilin, China
| | - Hong Jin
- Department of Pathology, Jilin Medical University, Jilin 132013, Jilin, China
| | - Haiyang Xu
- Department of Oncological Neurosurgery, First Hospital of Jilin University, Changchun 130021, Jilin, China
| | - Hongquan Yu
- Department of Oncological Neurosurgery, First Hospital of Jilin University, Changchun 130021, Jilin, China
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Norouzi-Barough L, Bayat A. Validation strategies for identifying drug targets in dermal fibrotic disorders. Drug Discov Today 2021; 26:2474-2485. [PMID: 34229083 DOI: 10.1016/j.drudis.2021.06.014] [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: 11/23/2020] [Revised: 05/19/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022]
Abstract
Fibrotic skin disorders, such as keloid disease (KD), are common clinically challenging disorders with unknown etiopathogenesis and ill-defined treatment strategies that affect millions of people worldwide. Thus, there is an urgent need to discover novel therapeutics. The validation of potential drug targets is an obligatory step in discovering and developing new therapeutic agents for the successful treatment of dermal fibrotic conditions, such as KD. The integration of multi-omics data with traditional and modern technological approaches, such as RNA interference (RNAi) and genome-editing tools, would provide unique opportunities to identify and validate novel targets in KD during early drug development. Thus, in this review, we summarize the current and emerging drug discovery process with a focus on validation strategies of potential drug targets identified in dermal fibrosis.
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Affiliation(s)
- Leyla Norouzi-Barough
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ardeshir Bayat
- Centre for Dermatology Research, NIHR Manchester Biomedical Research Centre, Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK; Medical Research Council-Wound Healing Unit, Division of Dermatology, University of Cape Town, Cape Town, South Africa.
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Altered Gene Expression in the Testis of Infertile Patients with Nonobstructive Azoospermia. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:5533483. [PMID: 34221106 PMCID: PMC8211532 DOI: 10.1155/2021/5533483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/14/2021] [Accepted: 05/28/2021] [Indexed: 11/18/2022]
Abstract
Background The molecular mechanism of nonobstructive azoospermia (NOA) remains unclear. The aim of this study was to identify gene expression changes in NOA patients and to explore potential biomarkers and therapeutic targets. Methods The gene expression profiles of GSE45885 and GSE145467 were collected from the Gene Expression Omnibus (GEO) database, and the differences between NOA and normal spermatogenesis were analyzed. Enrichment analysis was performed to explore biological functions for common differentially expressed genes (DEGs) in GSE45885 and GSE145467. Coexpression analysis of DEGs in GSE45885 was performed, and two modules with the highest correlation with NOA were screened. Key genes were then screened from the intersection genes of the two modules and common DEGs and PPI network. The expression of key genes was validated by quantitative real-time polymerase chain reaction (qRT-PCR) experiments. Finally, through miRTarBase, miRDB, and RAID, the miRNAs were predicted to regulate key genes, respectively. Results A total of 345 common DEGs were identified and they were mainly related to spermatogenesis, insulin signaling pathway. Coexpression analysis of DEGs in GSE45885 yielded eight modules; MEblack and MEturquoise had the highest correlation with NOA. Six genes in MEturquoise and RNF141 in MEblack were identified as key genes. qRT-PCR experiments validated the differential expression of key genes between NOA and control. Furthermore, RNF141 was regulated by the largest number of miRNAs. Conclusion Our findings suggest that the significant change expression of key genes may be potential markers and therapeutic targets of NOA and may have some impact on the development of NOA.
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Chen G, Mo S, Yuan D. Upregulation Mitochondrial Carrier 1 (MTCH1) Is Associated with Cell Proliferation, Invasion, and Migration of Liver Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9911784. [PMID: 34195286 PMCID: PMC8203356 DOI: 10.1155/2021/9911784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022]
Abstract
Among the primary causes of cancer-associated death in the world, liver hepatocellular carcinoma (LIHC) ranks the third. LIHC is defined as the sixth most frequently diagnosed carcinoma. The gene mitochondrial carrier 1 (MTCH1) is a protein-coding gene. Recent research suggests that MTCH1 may be associated with some diseases. Here, our study attempts to explore the role and implication of MTCH1 in LIHC. Kaplan Meier Plotter and GEPIA (Gene Expression Profiling Interactive Analysis) databases were employed to determine the expression of MTCH1 and its correlation with prognostic status in LIHC patients. For the first time, our results suggested that MTCH1 was aberrantly expressed in human pan-cancer and highly expressed in LIHC. Its high expression was closely associated with metastasis of tumor, stage of cancer, and poor survival of patients. Then, through enrichment analysis, MTCH1 was found to be closely related to RNA splicing in LIHC. Subsequently, we conducted a series of functional experiments. PCR data showed that LIHC cell lines and samples are highly expressed MTCH1. CCK-8 (Cell Counting Kit-8) assays and Transwell assays indicated that silencing MTCH1 certainly suppressed cell proliferation, migration, and invasion. These findings shed the clue that MTCH1 could be regarded as the potential prognosis biomarker of LIHC and a promising therapeutic target for LIHC.
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Affiliation(s)
- Guolin Chen
- Department of Infectious Diseases, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shanshan Mo
- Pharmacy Department of Heilongjiang Sailors General Hospital, Harbin, China
| | - Di Yuan
- Clinical Laboratory, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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Marker Genes Change of Synovial Fibroblasts in Rheumatoid Arthritis Patients. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5544264. [PMID: 34195267 PMCID: PMC8203351 DOI: 10.1155/2021/5544264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/14/2021] [Accepted: 05/24/2021] [Indexed: 01/04/2023]
Abstract
Background Rheumatoid arthritis (RA) is a chronic condition that manifests as inflammation of synovial joints, leading to joint destruction and deformity. Methods We identified single-cell RNA-seq data of synovial fibroblasts from RA and osteoarthritis (OA) patients in GSE109449 dataset. RA- and OA-specific cellular subpopulations were identified, and enrichment analysis was performed. Further, key genes for RA and OA were obtained by combined analysis with differentially expressed genes (DEGs) between RA and OA in GSE56409 dataset. The diagnostic role of key genes for RA was predicted using receiver operating characteristic (ROC) curve. Finally, we identified differences in immune cell infiltration between RA and OA patients, and utilized flow cytometry, qRT-PCR, and Western blot were used to examine the immune cell and key genes in RA patients. Results The cluster 0 matched OA and cluster 3 matched RA and significantly enriched for neutrophil-mediated immunity and ECM receptor interaction, respectively. We identified 478 DEGs. In the top 20 degrees of connection in the PPI network, the key genes for RA were obtained by comparing with the gene markers of cluster 0 and cluster 3, respectively. ROC curve showed that CCL2 and MMP13 might be diagnostic markers for RA. We found aberrant levels of CD8+T, neutrophil, and B cells in RA fibroblasts, which were validated in clinical samples. Importantly, we also validated the differential expression of key genes between RA and OA. Conclusion High expression of CCL2 and MMP13 in RA may be a diagnostic and therapeutic target.
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Wang F, Zhang L, Xu Y, Xie Y, Li S. Comprehensive Analysis and Identification of Key Driver Genes for Distinguishing Between Esophageal Adenocarcinoma and Squamous Cell Carcinoma. Front Cell Dev Biol 2021; 9:676156. [PMID: 34124063 PMCID: PMC8194272 DOI: 10.3389/fcell.2021.676156] [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: 03/04/2021] [Accepted: 04/09/2021] [Indexed: 01/01/2023] Open
Abstract
Background: Esophageal cancer (EC) is one of the deadliest cancers in the world. However, the mechanism that drives the evolution of EC is still unclear. On this basis, we identified the key genes and molecular pathways that may be related to the progression of esophageal adenocarcinoma and squamous cell carcinoma to find potential markers or therapeutic targets. Methods: GSE26886 were obtained from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) among normal samples, EA, and squamous cell carcinoma were determined using R software. Then, potential functions of DEGs were determined using the Database for Annotation, Visualization and Integrated Discovery (DAVID). The STRING software was used to identify the most important modules in the protein-protein interaction (PPI) network. The expression levels of hub genes were confirmed using UALCAN database. Kaplan-Meier plotters were used to confirm the correlation between hub genes and outcomes in EC. Results: In this study, we identified 1,098 genes induced in esophageal adenocarcinoma (EA) and esophageal squamous cell carcinoma (ESCC), and 669 genes were reduced in EA and ESCC, suggesting that these genes may play an important role in the occurrence and development of EC tumors. Bioinformatics analysis showed that these genes were involved in cell cycle regulation and p53 and phosphoinositide 3-kinase (PI3K)/Akt signaling pathway. In addition, we identified 147 induced genes and 130 reduced genes differentially expressed in EA and ESCC. The expression of ESCC in the EA group was different from that in the control group. By PPI network analysis, we identified 10 hub genes, including GNAQ, RGS5, MAPK1, ATP1B1, HADHA, HSDL2, SLC25A20, ACOX1, SCP2, and NLN. TCGA validation showed that these genes were present in the dysfunctional samples between EC and normal samples and between EA and ESCC. Kaplan-Meier analysis showed that MAPK1, ACOX1, SCP2, and NLN were associated with overall survival in patients with ESCC and EA. Conclusions: In this study, we identified a series of DEGs between EC and normal samples and between EA and ESCC samples. We also identified 10 key genes involved in the EC process. We believe that this study may provide a new biomarker for the prognosis of EA and ESCC.
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Affiliation(s)
- Feng Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lan Zhang
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yue Xu
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yilin Xie
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Shenglei Li
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
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Zhang X, He Y, Gu H, Liu Z, Li B, Yang Y, Hao J, Hua R. Construction of a Nine-MicroRNA-Based Signature to Predict the Overall Survival of Esophageal Cancer Patients. Front Genet 2021; 12:670405. [PMID: 34093662 PMCID: PMC8170160 DOI: 10.3389/fgene.2021.670405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Esophageal cancer (EC) is a common malignant tumor. MicroRNAs (miRNAs) play a key role in the occurrence and metastasis and are closely related to the prognosis of EC. Therefore, it will provide a powerful tool to predict the overall survival (OS) of EC patients based on miRNAs expression in EC tissues and blood samples. METHODS Five independent databases, TCGA, GSE106817, GSE113486, GSE122497, and GSE112264, were used to construct nine-miRna signature and nomograms for prognosis. The bioinformatics analysis was used to predict the enrichment pathways of targets. RESULTS A total of 132 overexpressed miRNAs and 23 suppressed miRNAs showed significant differential expression in both EC serum and tissue samples compared with normal samples. We also showed that nine miRNAs were related to the prognosis of EC. Higher levels of miR-15a-5p, miR-92a-3p, miR-92a-1-5p, miR-590-5p, miR-324-5p, miR-25-3p, miR-181b-5p, miR-421, and miR-93-5p were correlated to the shorter survival time in patients with EC. In addition, we constructed a risk prediction model based on the levels of nine differentially expressed miRNAs (DEMs) and found that the OS time of EC patients with high-risk score was shorter than that of EC patients with low-risk score. Furthermore, our results showed that the risk prediction scores of EC samples were higher than those of normal samples. Finally, the area under the curve (AUC) was used to analyze the risk characteristics of EC and normal controls. By calculating the AUC and the calibration curve, the RNA signature showed a good performance. Bioinformatics analysis showed that nine DEMs were associated with several crucial signaling, including p53, FoxO, PI3K-Akt, HIF-1, and TORC1 signaling. Finally, 14 messenger RNAs (mRNAs) were identified as hub targets of nine miRNAs, including BTRC, SIAH1, RNF138, CDC27, NEDD4L, MKRN1, RLIM, FBXO11, RNF34, MYLIP, FBXW7, RNF4, UBE3C, and RNF111. TCGA dataset validation showed that these hub targets were significantly differently expressed in EC tissues compared with normal samples. CONCLUSION We have constructed maps and nomograms of nine-miRna risk signals associated with EC prognosis. Bioinformatics analysis revealed that nine DEMs were associated with several crucial signaling, including p53, FoxO, PI3K-Akt, HIF-1, and TORC1 signaling, in EC. We think that this study will provide clinicians with an effective decision-making tool.
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Affiliation(s)
- Xiaobin Zhang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
- Department of Cardiovascular Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yi He
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Haiyong Gu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhichao Liu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Bin Li
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rong Hua
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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Liu D, Zhang P, Zhao J, Yang L, Wang W. Identification of Molecular Characteristics and New Prognostic Targets for Thymoma by Multiomics Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5587441. [PMID: 34104648 PMCID: PMC8159640 DOI: 10.1155/2021/5587441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/16/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Thymoma is a heterogeneous tumor originated from thymic epithelial cells. The molecular mechanism of thymoma remains unclear. METHODS The expression profile, methylation, and mutation data of thymoma were obtained from TCGA database. The coexpression network was constructed using the variance of gene expression through WGCNA. Enrichment analysis using clusterProfiler R package and overall survival (OS) analysis by Kaplan-Meier method were carried out for the intersection of differential expression genes (DEGs) screened by limma R package and important module genes. PPI network was constructed based on STRING database for genes with significant impact on survival. The impact of key genes on the prognosis of thymoma was evaluated by ROC curve and Cox regression model. Finally, the immune cell infiltration, methylation modification, and gene mutation were calculated. RESULTS We obtained eleven coexpression modules, and three of them were higher positively correlated with thymoma. DEGs in these three modules mainly involved in MAPK cascade and PPAR pathway. LIPE, MYH6, ACTG2, KLF4, SULT4A1, and TF were identified as key genes through the PPI network. AUC values of LIPE were the highest. Cox regression analysis showed that low expression of LIPE was a prognostic risk factor for thymoma. In addition, there was a high correlation between LIPE and T cells. Importantly, the expression of LIPE was modified by methylation. Among all the mutated genes, GTF2I had the highest mutation frequency. CONCLUSION These results suggested that the molecular mechanism of thymoma may be related to immune inflammation. LIPE may be the key genes affecting prognosis of thymoma. Our findings will help to elucidate the pathogenesis and therapeutic targets of thymoma.
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Affiliation(s)
- Dazhong Liu
- Department of Thoracic Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Pengfei Zhang
- Department of Thoracic Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Jiaying Zhao
- Department of Thoracic Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Lei Yang
- Department of Thoracic Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Wei Wang
- Department of Thoracic Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
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Lin Y, Yao Y, Wang Y, Wang L, Cui H. PD-L1 and Immune Infiltration of m 6A RNA Methylation Regulators and Its miRNA Regulators in Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5516100. [PMID: 34055974 PMCID: PMC8147529 DOI: 10.1155/2021/5516100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/01/2021] [Indexed: 01/27/2023]
Abstract
BACKGROUND The aim of this study was to systematically evaluate the relationship between the expression of m6A RNA methylation regulators and prognosis in HCC. METHODS We compared the expression of m6A methylation modulators and PD-L1 between HCC and normal in TCGA database. HCC samples were divided into two subtypes by consensus clustering of data from m6A RNA methylation regulators. The differences in PD-L1, immune infiltration, and prognosis between the two subtypes were further compared. The LASSO regression was used to build a risk score for m6A modulators. In addition, we identified miRNAs that regulate m6A regulators. RESULTS We found that fourteen m6A regulatory genes were significantly differentially expressed between HCC and normal. HCC samples were divided into two clusters. Of these, there are higher PD-L1 expression and poorer overall survival (OS) in cluster 1. There was a significant difference in immune cell infiltration between cluster 1 and cluster 2. Through the LASSO model, we obtained 12 m6A methylation regulators to construct a prognostic risk score. Compared with patients with a high-risk score, patients with a low-risk score had upregulated PD-L1 expression and worse prognosis. There was a significant correlation between risk score and tumor-infiltrating immune cells. Finally, we found that miR-142 may be the important regulator for m6A RNA methylation in HCC. CONCLUSION Our results suggest that m6A RNA methylation modulators may affect the prognosis through PD-L1 and immune cell infiltration in HCC patients. In addition, the two clusters may be beneficial for prognostic stratification and improving immunotherapeutic efficacy.
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Affiliation(s)
- Yingxue Lin
- Department of Medicine, Affiliated Hospital of Chengde Medical University, Nanyingzi Road, Shuangqiao District, Chengde, Hebei, China
| | - Yinhui Yao
- Department of Medicine, Affiliated Hospital of Chengde Medical University, Nanyingzi Road, Shuangqiao District, Chengde, Hebei, China
| | - Ying Wang
- Department of Medicine, Affiliated Hospital of Chengde Medical University, Nanyingzi Road, Shuangqiao District, Chengde, Hebei, China
| | - Lingdi Wang
- Department of Medicine, Affiliated Hospital of Chengde Medical University, Nanyingzi Road, Shuangqiao District, Chengde, Hebei, China
| | - Haipeng Cui
- Department of Pathophysiology, Chengde Medical University, Anyuan Road, Shuangqiao District, Chengde, Hebei, China
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Gu C, Chen J, Dang X, Chen C, Huang Z, Shen W, Shi X, Dai C, Chen C. Hippo Pathway Core Genes Based Prognostic Signature and Immune Infiltration Patterns in Lung Squamous Cell Carcinoma. Front Oncol 2021; 11:680918. [PMID: 33996611 PMCID: PMC8117235 DOI: 10.3389/fonc.2021.680918] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND We investigated the prognostic effects and their patterns of immune infiltration of hippo pathway core genes in lung squamous cell carcinoma, in order to find some clues for underlying mechanisms of LUSC tumorigenesis and help developing new therapeutic methods. METHODS The mutational data, transcriptome data and corresponding clinical medical information of LUSC patients were extracted from The Cancer Genome Atlas (TCGA) database. Differential expression genes (DEGs) and Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were explored. Survival analysis for the hippo core genes and the prognostic model were performed. Immune infiltration was estimated by CIBERSORT algorithm and some immune checkpoints-related genes were further investigated. RESULTS Overall, 551 LUSC samples were included in our study, consisting of 502 LUSC tumor samples and 49 adjacent normal samples, respectively. There were 1910 up-regulated DEGs and 2253 down-regulated DEGs were finally identified. The top five mutational hippo pathway core genes were LATS1 (4%), WWC1 (2%), TAOK1 (2%), TAOK3 (2%), and TAOK2 (2%), respectively. the mutation of LATS2 was highly associated with co-mutational NF2 (P <0.05) and TAOK1 (P <0.05). In survival analyses, we found only WWC1 (log-rank p = 0.046, HR = 1.32, 95% CI = 1-1.73) and LATS2 (log-rank p = 0.013, HR = 1.41, 95%CI = 1.08-1.86) had significant prognostic roles. After getting the three subgroups according to the subtyping results, we demonstrated that T cell gamma delta (p = 5.78e-6), B cell memory (p = 4.61e-4) and T cell CD4+ memory resting (p = 2.65e-5) had significant differences among the three groups. SIGLEC15 (P <0.01) and CD274 (P <0.05) also had statistical differences among the three subgroups. CONCLUSIONS Our study verified the prognostic roles of WWC1 and LATS2 in LUSC patients. Immune checkpoints-related genes SIGLEC15 and CD274 had statistical differences among the three subgroups, which may provide new perceptions on the molecular mechanisms in LUSC and maybe helpful for precisely selecting specific LUSC patients with potential immunotherapy benefits.
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Affiliation(s)
- Chang Gu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiafei Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xuening Dang
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Colorectal Cancer Research Center, Shanghai, China
| | - Chunji Chen
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenyu Huang
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Colorectal Cancer Research Center, Shanghai, China
| | - Weidong Shen
- Division of Functional Immunology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
| | - Xin Shi
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Chenyang Dai
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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Lian R, Zhang G, Yan S, Sun L, Zhang G. Identification of Molecular Regulatory Features and Markers for Acute Type A Aortic Dissection. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:6697848. [PMID: 33953793 PMCID: PMC8057891 DOI: 10.1155/2021/6697848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/03/2021] [Accepted: 03/25/2021] [Indexed: 12/03/2022]
Abstract
BACKGROUND Acute type A aortic dissection (ATAAD) is one of the most lethal cardiovascular diseases, and its molecular mechanism remains unclear. METHODS Differentially expressed genes (DEGs) between ATAAD and control were detected by limma R package in GSE52093, GSE153434, GSE98770, and GSE84827, respectively. The coexpression network of DEGs was identified by the WGCNA package. Enrichment analysis was performed for module genes that were positively correlated with ATAAD using clusterProfiler R package. In addition, differentially methylated markers between aortic dissection and control were identified by ChAMP package. After comparing with ATAAD-related genes, a protein-protein interaction (PPI) network was established based on the STRING database. The genes with the highest connectivity were identified as hub genes. Finally, differential immune cell infiltration between ATAAD and control was identified by ssGSEA. RESULTS From GSE52093 and GSE153434, 268 module genes were obtained with consistent direction of differential expression and high correlation with ATAAD. They were significantly enriched in T cell activation, HIF-1 signaling pathway, and cell cycle. In addition, 2060 differentially methylated markers were obtained from GSE84827. Among them, 77 methylation markers were ATAAD-related DEGs. Using the PPI network, we identified MYC, ITGA2, RND3, BCL2, and PHLPP2 as hub genes. Finally, we identified significantly differentially infiltrated immune cells in ATAAD. CONCLUSION The hub genes we identified may be regulated by methylation and participate in the development of ATAAD through immune inflammation and oxidative stress response. The findings may provide new insights into the molecular mechanisms and therapeutic targets for ATAAD.
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Affiliation(s)
- Rui Lian
- Graduate School of Peking Union Medical College, Beijing, China
- Emergency Department, China-Japan Friendship Hospital, Beijing, China
| | - Guochao Zhang
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Shengtao Yan
- Emergency Department, China-Japan Friendship Hospital, Beijing, China
| | - Lichao Sun
- Emergency Department, China-Japan Friendship Hospital, Beijing, China
| | - Guoqiang Zhang
- Graduate School of Peking Union Medical College, Beijing, China
- Emergency Department, China-Japan Friendship Hospital, Beijing, China
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Gu C, Shi X, Qiu W, Huang Z, Yu Y, Shen F, Chen Y, Pan X. Comprehensive Analysis of the Prognostic Role and Mutational Characteristics of m6A-Related Genes in Lung Squamous Cell Carcinoma. Front Cell Dev Biol 2021; 9:661792. [PMID: 33842487 PMCID: PMC8027321 DOI: 10.3389/fcell.2021.661792] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND There have been limited treatment therapies for lung squamous cell carcinoma (LUSC). M6A-related genes may be the next therapeutic targets for LUSC. In this study, we explored the prognostic role and mutational characteristics of m6A-related genes in LUSC. METHODS LUSC gene expression data, mutational data, and corresponding clinical information were extracted from The Cancer Genome Atlas database. Differentially expressed genes (DEGs) were identified, and the mutation characteristics of LUSC patients were explored. Then, m6A-related genes were extracted and the correlations among the genes were detected. Finally, the prognostic roles of the genes were investigated and the nomogram model was developed. Besides, the protein-protein interaction (PPI) network was used to explore the potential interactions among the genes. RESULTS In total, there are 551 LUSC samples enrolled in our study, containing 502 LUSC tumor samples and 49 adjacent normal LUSC samples, respectively. There were 2970 upregulated DEGs and 1806 downregulated DEGs were further explored. IGF2BP1 and RBM15 had significant co-occurrence frequency (p < 0.05). Besides, METTL14 and ZC3H13 or YTHDF3 also had significant co-occurrence frequency (p < 0.05). All the m6A-related genes represent the positive correlation. WTAP was identified as a prognostic gene in the TCGA database while YTHDC1 and YTHDF1 were identified as prognostic genes. In multivariate Cox analysis, YTHDF1, age, pN stage, pTNM stage, and smoking were all identified as significant prognostic factors for OS. CONCLUSION We investigated the expression patterns and mutational characteristics of LUSC patients and identified three potential independent prognostic m6A-related genes (WTAP, YTHDC1, and YTHDF1) for OS in LUSC patients.
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Affiliation(s)
- Chang Gu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xin Shi
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wenli Qiu
- Department of Lab Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zhenyu Huang
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Colorectal Cancer Research Center, Shanghai, China
| | - Yan Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yumei Chen
- Department of Nuclear Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xufeng Pan
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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