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Jamil MA, Al-Rifai R, Nuesgen N, Altmüller J, Oldenburg J, El-Maarri O. The role of microRNAs in defining LSECs cellular identity and in regulating F8 gene expression. Front Genet 2024; 15:1302685. [PMID: 38440189 PMCID: PMC10910020 DOI: 10.3389/fgene.2024.1302685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/03/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction: Coagulation Factor VIII (FVIII) plays a pivotal role in the coagulation cascade, and deficiencies in its levels, as seen in Hemophilia A, can lead to significant health implications. Liver sinusoidal endothelial cells (LSECs) are the main producers and contributors of FVIII in blood, a fact we have previously elucidated through mRNA expression profiling when comparing these cells to other endothelial cell types. Methods: Our current investigation focuses on small microRNAs, analyzing their distinct expression patterns across various endothelial cells and hepatocytes. Results: The outcome of this exploration underscores the discernible microRNAs expression differences that set LSECs apart from both hepatocytes (193 microRNAs at p < 0.05) and other endothelial cells (72 microRNAs at p < 0.05). Notably, the 134 and 35 overexpressed microRNAs in LSECs compared to hepatocytes and other endothelial cells, respectively, shed light on the unique functions of LSECs in the liver. Discussion: Our investigation identified a panel of 10 microRNAs (miR-429, miR-200b-3p, miR-200a-3p, miR-216b-5p, miR-1185-5p, miR-19b-3p, miR-192-5p, miR-122-5p, miR-30c-2-3p, and miR-30a-5p) that distinctly define LSEC identity. Furthermore, our scrutiny extended to microRNAs implicated in F8 regulation, revealing a subset (miR-122-5p, miR-214-3p, miR-204-3p, and miR-2682-5p) whose expression intricately correlates with F8 expression within LSECs. This microRNA cohort emerges as a crucial modulator of F8, both directly through suppression and indirect effects on established F8-related transcription factors. The above microRNAs emerged as potential targets for innovative therapies in Hemophilia A patients.
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Affiliation(s)
- Muhammad Ahmer Jamil
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Rawya Al-Rifai
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Nicole Nuesgen
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Osman El-Maarri
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
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Xing XW, Shi HY, Liu S, Feng SX, Feng SQ, Gong BQ. miR-496/MMP10 Is Involved in the Proliferation of IL-1β-Induced Fibroblast-Like Synoviocytes Via Mediating the NF-κB Signaling Pathway. Inflammation 2021; 44:1359-1369. [PMID: 33548006 DOI: 10.1007/s10753-021-01421-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 12/18/2022]
Abstract
Rheumatoid arthritis (RA) is a common chronic autoimmune disease featured by synovial inflammation. miR-496 is closely involved in various pathologic conditions. However, its role in RA has not yet been elucidated. Expression of miR-496 and MMP10 was determined based on the clinical samples with RA retrieved from the Gene Expression Omnibus (GEO) datasets. In vitro model of RA was constructed in MH7A cells stimulated by IL-1β (10 ng/mL). Cell counting kit 8 (CCK-8) and flow cytometry experiments were implemented to investigate the cell viability and apoptosis rate of MH7A cells. TargetScan was applied to identify the targets of miR-496, and the regulation of miR-496 on MMP10 expression was validated by a dual-luciferase reporter gene assay. qRT-PCR and western blot analyses were conducted to examine the expression. miR-496 expression was decreased in RA tissues and MH7A cells after IL-1β treatment. Overexpression of miR-496 significantly inhibited IL-1β-treated MH7A cell viability. MMP10 was identified as a target of miR-496 and its expression was negatively regulated by miR-496. The effects of miR-496 on MH7A cell proliferation and apoptosis were reversed by MMP10. The activity of NF-κB pathway was associated with the miR-496/MMP10 axis in IL-1β-stimulated MH7A cells. To summarize, this study demonstrated that miR-496 can impair the proliferative ability and facilitate the apoptosis of IL-1β-treated MH7A through regulating MMP10 expression and NF-κB signaling pathway.
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Affiliation(s)
- Xue-Wu Xing
- Department of Orthopedics, Tianjin First Central Hospital, No.24 FuKang Road, Nankai District, Tianjin, 300192, China
| | - Hong-Yu Shi
- Department of Orthopedics, Tianjin Medical University General Hospital, No.154 Anshan Road, Heping District, Tianjin, 300052, China
| | - Shen Liu
- Department of Orthopedics, Tianjin Medical University General Hospital, No.154 Anshan Road, Heping District, Tianjin, 300052, China
| | - Shu-Xin Feng
- Department of Orthopedics, Tianjin First Central Hospital, No.24 FuKang Road, Nankai District, Tianjin, 300192, China
| | - Shi-Qing Feng
- Department of Orthopedics, Tianjin Medical University General Hospital, No.154 Anshan Road, Heping District, Tianjin, 300052, China.
| | - Bao-Qi Gong
- Department of Rheumatology, Tianjin First Central Hospital, No.24 FuKang Road, Nankai District, Tianjin, 300192, China.
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Urbanek-Trzeciak MO, Galka-Marciniak P, Nawrocka PM, Kowal E, Szwec S, Giefing M, Kozlowski P. Pan-cancer analysis of somatic mutations in miRNA genes. EBioMedicine 2020; 61:103051. [PMID: 33038763 PMCID: PMC7648123 DOI: 10.1016/j.ebiom.2020.103051] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/16/2020] [Accepted: 09/16/2020] [Indexed: 02/08/2023] Open
Abstract
Background miRNAs are considered important players in oncogenesis, serving either as oncomiRs or suppressormiRs. Although the accumulation of somatic alterations is an intrinsic aspect of cancer development and many important cancer-driving mutations have been identified in protein-coding genes, the area of functional somatic mutations in miRNA genes is heavily understudied. Methods Here, based on the analysis of large genomic datasets, mostly the whole-exome sequencing of over 10,000 cancer/normal sample pairs deposited within the TCGA repository, we undertook an analysis of somatic mutations in miRNA genes. Findings We identified and characterized over 10,000 somatic mutations and showed that some of the miRNA genes are overmutated in Pan-Cancer and/or specific cancers. Nonrandom occurrence of the identified mutations was confirmed by a strong association of overmutated miRNA genes with KEGG pathways, most of which were related to specific cancer types or cancer-related processes. Additionally, we showed that mutations in some of the overmutated genes correlate with miRNA expression, cancer staging, and patient survival. Interpretation Our study is the first comprehensive Pan-Cancer study of cancer somatic mutations in miRNA genes. It may help to understand the consequences of mutations in miRNA genes and the identification of miRNA functional mutations. The results may also be the first step (form the basis and provide the resources) in the development of computational and/or statistical approaches/tools dedicated to the identification of cancer-driver miRNA genes. Funding This work was supported by research grants from the Polish National Science Centre 2016/22/A/NZ2/00184 and 2015/17/N/NZ3/03629.
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Affiliation(s)
| | | | - Paulina M Nawrocka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Ewelina Kowal
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Sylwia Szwec
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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Singh NN, Ottesen EW, Singh RN. A survey of transcripts generated by spinal muscular atrophy genes. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194562. [PMID: 32387331 PMCID: PMC7302838 DOI: 10.1016/j.bbagrm.2020.194562] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/01/2020] [Accepted: 04/13/2020] [Indexed: 02/07/2023]
Abstract
Human Survival Motor Neuron (SMN) genes code for SMN, an essential multifunctional protein. Complete loss of SMN is embryonic lethal, while low levels of SMN lead to spinal muscular atrophy (SMA), a major genetic disease of children and infants. Reduced levels of SMN are associated with the abnormal development of heart, lung, muscle, gastro-intestinal system and testis. The SMN loci have been shown to generate a vast repertoire of transcripts, including linear, back- and trans-spliced RNAs as well as antisense long noncoding RNAs. However, functions of the majority of these transcripts remain unknown. Here we review the nature of RNAs generated from the SMN loci and discuss their potential functions in cellular metabolism.
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Affiliation(s)
- Natalia N Singh
- Department of Biomedical Science, Iowa State University, Ames, IA, 50011, United States of America
| | - Eric W Ottesen
- Department of Biomedical Science, Iowa State University, Ames, IA, 50011, United States of America
| | - Ravindra N Singh
- Department of Biomedical Science, Iowa State University, Ames, IA, 50011, United States of America.
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Zhu G, Lin C, Cheng Z, Wang Q, Hoffman RM, Singh SR, Huang Y, Zheng W, Yang S, Ye J. TRAF6-Mediated Inflammatory Cytokines Secretion in LPS-induced Colorectal Cancer Cells Is Regulated by miR-140. Cancer Genomics Proteomics 2020; 17:23-33. [PMID: 31882548 DOI: 10.21873/cgp.20164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/03/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND/AIM Colorectal cancer (CRC) cells secrete inflammatory cytokines that affect CRC progression. The aim of the present study was to determine if micro-RNA-140(miR-140) regulates inflammatory cytokine secretion induced by lipopolysaccharide (LPS) in colorectal cancer cells by targeting tumor necrosis factor receptor (TNFR)-associated factor 6 (TRAF6). MATERIALS AND METHODS Fifty fresh colon-cancer specimens and normal colorectal tissues were collected from patients with CRC and tested for the expression miR-140. Human CRC cell lines SW480 and HCT116 were treated with various concentrations and times with LPS. miR-140 and mRNA expression of potentially related genes were analyzed by qPCR. Protein expression was analyzed using western blot or ELISA. Overexpression plasmids with pcDNA3.1-TRAF6, pGL4.10-wtTRAF6 and pGL4.10-mutTRAF6 were constructed. miRNA target gene prediction and a dual luciferase assay were used to analyze miR-140-targeted TRAF6. RESULTS miR-140 expression was up-regulated in CRC tissues. In CRC cells, LPS could increase miR-140 expression in a time- and concentration-dependent manner. LPS increased inflammatory cytokine mRNA expression levels in SW480 and HCT116 human colon-cancer cells. miRNA-140 suppressed TRAF6 expression via targeting the 3'UTR. TRAF6 affected miR-140-mediated inflammatory cytokine expression of SW480 and HCT116 cells under LPS treatment. CONCLUSION miR-140 regulates inflammatory cytokine secretion of LPS-induced colorectal cancer cells by targeting TRAF6.
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Affiliation(s)
- Guangwei Zhu
- Department of Gastrointestinal Surgery 2 Section, The First Hospital Affiliated to Fujian Medical University, Fuzhou, P.R. China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, P.R. China
| | - Chunlin Lin
- Department of Gastrointestinal Surgery 2 Section, The First Hospital Affiliated to Fujian Medical University, Fuzhou, P.R. China
| | - Zhibin Cheng
- Department of Gastrointestinal Surgery 2 Section, The First Hospital Affiliated to Fujian Medical University, Fuzhou, P.R. China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, P.R. China
| | - Qin Wang
- Department of Gastrointestinal Surgery 2 Section, The First Hospital Affiliated to Fujian Medical University, Fuzhou, P.R. China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, P.R. China
| | - Robert M Hoffman
- AntiCancer, Inc., San Diego, CA, U.S.A.,Department of Surgery, University of California, San Diego, CA, U.S.A
| | - Shree Ram Singh
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, U.S.A.
| | - Yongjian Huang
- Department of Gastrointestinal Surgery 2 Section, The First Hospital Affiliated to Fujian Medical University, Fuzhou, P.R. China
| | - Wei Zheng
- Department of Gastrointestinal Surgery 2 Section, The First Hospital Affiliated to Fujian Medical University, Fuzhou, P.R. China
| | - Shugang Yang
- Department of Gastrointestinal Surgery 2 Section, The First Hospital Affiliated to Fujian Medical University, Fuzhou, P.R. China
| | - Jianxin Ye
- Department of Gastrointestinal Surgery 2 Section, The First Hospital Affiliated to Fujian Medical University, Fuzhou, P.R. China .,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, P.R. China
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Wu D, Zhang T, Wang J, Zhou J, Pan H, Qu P. Long noncoding RNA NNT-AS1 enhances the malignant phenotype of bladder cancer by acting as a competing endogenous RNA on microRNA-496 thereby increasing HMGB1 expression. Aging (Albany NY) 2019; 11:12624-12640. [PMID: 31848324 PMCID: PMC6949093 DOI: 10.18632/aging.102591] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/26/2019] [Indexed: 12/12/2022]
Abstract
The long noncoding RNA nicotinamide nucleotide transhydrogenase antisense RNA 1 (NNT-AS1) is a key malignancy regulator in a variety of human cancers. In this study, we first measured the expression of NNT-AS1 in bladder cancer and examined its role in cancer progression. The mechanisms behind the oncogenic functions of NNT-AS1 in bladder cancer were explored. We found that NNT-AS1 was upregulated in bladder cancer tissues and cell lines. This increased expression demonstrated a significant correlation with advanced clinical stage, lymph node metastasis, and shorter overall survival. NNT-AS1 knockdown suppressed bladder cancer cell proliferation, migration, and invasion and facilitated apoptosis in vitro and hindered tumor growth in vivo. NNT-AS1 functioned as a competing endogenous RNA for microRNA-496 (miR-496), and the suppressive effects of NNT-AS1 knockdown on malignant characteristics were abrogated by miR-496 silencing. HMGB1 was identified as a direct target gene of miR-496 in bladder cancer, and HMGB1 expression was enhanced by NNT-AS1 via sponging of miR-496. In conclusion, the NNT-AS1–miR-496–HMGB1 pathway plays a significant role in the aggressive behavior of bladder cancer and may lead to new NNT-AS1–based diagnostics and therapeutics.
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Affiliation(s)
- Deyao Wu
- Department of Urology, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng People's Hospital, Yancheng 224001, China
| | - Tielong Zhang
- Department of Urology, Jianhu Hospital Affiliated to Nantong University, Yancheng 224700, China
| | - Jie Wang
- Department of Urology, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng People's Hospital, Yancheng 224001, China
| | - Jian Zhou
- Department of Urology, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng People's Hospital, Yancheng 224001, China
| | - Huixing Pan
- Department of Urology, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng People's Hospital, Yancheng 224001, China
| | - Ping Qu
- Department of Urology, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng People's Hospital, Yancheng 224001, China
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