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Ong JWJ, Tan KS, Lee JJX, Seet JE, Choi HW, Ler SG, Gunaratne J, Narasaraju T, Sham LT, Patzel V, Chow VT. Differential effects of microRNAs miR-21, miR-99 and miR-145 on lung regeneration and inflammation during recovery from influenza pneumonia. J Med Virol 2023; 95:e29286. [PMID: 38087452 DOI: 10.1002/jmv.29286] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/10/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023]
Abstract
In a mouse model of influenza pneumonia, we previously documented that proliferating alveolar type II (AT2) cells are the major stem cells involved in early lung recovery. Profiling of microRNAs revealed significant dysregulation of specific ones, including miR-21 and miR-99a. Moreover, miR-145 is known to exhibit antagonism to miR-21. This follow-up study investigated the roles of microRNAs miR-21, miR-99a, and miR-145 in the murine pulmonary regenerative process and inflammation during influenza pneumonia. Inhibition of miR-21 resulted in severe morbidity, and in significantly decreased proliferating AT2 cells due to impaired transition from innate to adaptive immune responses. Knockdown of miR-99a culminated in moderate morbidity, with a significant increase in proliferating AT2 cells that may be linked to PTEN downregulation. In contrast, miR-145 antagonism did not impact morbidity nor the proliferating AT2 cell population, and was associated with downregulation of TNF-alpha, IL1-beta, YM1, and LY6G. Hence, a complex interplay exists between expression of specific miRNAs, lung regeneration, and inflammation during recovery from influenza pneumonia. Inhibition of miR-21 and miR-99a (but not miR-145) can lead to deleterious cellular and molecular effects on pulmonary repair and inflammatory processes during influenza pneumonia.
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Affiliation(s)
- Joe Wee Jian Ong
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kai Sen Tan
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Ju Ee Seet
- Department of Pathology, National University of Singapore, Singapore
| | - Hyung Won Choi
- Department of Medicine, National University of Singapore, Singapore
| | | | | | - Teluguakula Narasaraju
- Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, Karnataka, India
| | - Lok-To Sham
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Volker Patzel
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Vincent T Chow
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Gujrati H, Ha S, Wang BD. Deregulated microRNAs Involved in Prostate Cancer Aggressiveness and Treatment Resistance Mechanisms. Cancers (Basel) 2023; 15:3140. [PMID: 37370750 PMCID: PMC10296615 DOI: 10.3390/cancers15123140] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Prostate cancer (PCa) is the most frequently diagnosed cancer and the second leading cause of cancer deaths among American men. Complex genetic and epigenetic mechanisms are involved in the development and progression of PCa. MicroRNAs (miRNAs) are short noncoding RNAs that regulate protein expression at the post-transcriptional level by targeting mRNAs for degradation or inhibiting protein translation. In the past two decades, the field of miRNA research has rapidly expanded, and emerging evidence has revealed miRNA dysfunction to be an important epigenetic mechanism underlying a wide range of diseases, including cancers. This review article focuses on understanding the functional roles and molecular mechanisms of deregulated miRNAs in PCa aggressiveness and drug resistance based on the existing literature. Specifically, the miRNAs differentially expressed (upregulated or downregulated) in PCa vs. normal tissues, advanced vs. low-grade PCa, and treatment-responsive vs. non-responsive PCa are discussed. In particular, the oncogenic and tumor-suppressive miRNAs involved in the regulation of (1) the synthesis of the androgen receptor (AR) and its AR-V7 splice variant, (2) PTEN expression and PTEN-mediated signaling, (3) RNA splicing mechanisms, (4) chemo- and hormone-therapy resistance, and (5) racial disparities in PCa are discussed and summarized. We further provide an overview of the current advances and challenges of miRNA-based biomarkers and therapeutics in clinical practice for PCa diagnosis/prognosis and treatment.
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Affiliation(s)
- Himali Gujrati
- Department of Pharmaceutical Sciences, University of Maryland Eastern Shore School of Pharmacy, Princess Anne, MD 21853, USA
| | - Siyoung Ha
- Department of Pharmaceutical Sciences, University of Maryland Eastern Shore School of Pharmacy, Princess Anne, MD 21853, USA
| | - Bi-Dar Wang
- Department of Pharmaceutical Sciences, University of Maryland Eastern Shore School of Pharmacy, Princess Anne, MD 21853, USA
- Hormone Related Cancers Program, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
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3
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Gao H, Cao H, Li Z, Li L, Guo Y, Chen Y, Peng G, Zeng W, Du J, Dong W, Yang F. Exosome-derived Small RNAs in mouse Sertoli cells inhibit spermatogonial apoptosis. Theriogenology 2023; 200:155-167. [PMID: 36806925 DOI: 10.1016/j.theriogenology.2023.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 02/11/2023] [Accepted: 02/12/2023] [Indexed: 02/16/2023]
Abstract
Spermatogenesis is a highly complicated biological process that occurs in the epithelium of the seminiferous tubules. It is regulated by a complex network of endocrine and paracrine factors. Sertoli cells (SCs) play a key role in spermatogenesis due to their production of trophic, differentiation, and immune-modulating factors. However, many of the molecular pathways of SC action remain controversial and unclear. Recently, many studies have focused on exosomes as an important mechanism of intercellular communication. We found that the exosomes derived from mouse SCs inhibited the apoptosis of primary spermatogonia. A total of 1016 miRNAs in SCs and 556 miRNAs in exosomes were detected using miRNA high-throughput sequencing. A total of 294 miRNAs were differentially expressed between SCs and exosomes. Furthermore, 19 tsRNA families appeared in SCs, while 6 tsRNA families appeared in exosomes. A total of 57 and 1 miRNAs (RPM >4) and 14 and 1 tsRNAs were exclusively expressed in SCs and exosomes, respectively. MiR-10b is one of the top ten exosomes with a relatively large enrichment of miRNA. Overexpression of miR-10b downregulates the expression of the target KLF4 to reduce spermatogonial apoptosis in primary spermatogonia or the C18-4 cell line.
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Affiliation(s)
- Huihui Gao
- Center for Wildlife Biology of Qin-Mountains, Northwest Agriculture and Forestry University, Yangling, China; College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, China.
| | - Heran Cao
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, China.
| | - Zhenpeng Li
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, China.
| | - Long Li
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, China.
| | - Yingjie Guo
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, China.
| | - Yining Chen
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, China.
| | - Guofan Peng
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, China.
| | - Wenxian Zeng
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, China.
| | - Jian Du
- Center for Stem Cell Biology and Regenerative Medicine, Tsinghua University, Beijing, China.
| | - Wuzi Dong
- Center for Wildlife Biology of Qin-Mountains, Northwest Agriculture and Forestry University, Yangling, China; College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, China.
| | - Fangxia Yang
- Center for Wildlife Biology of Qin-Mountains, Northwest Agriculture and Forestry University, Yangling, China; College of Forestry, Northwest Agriculture and Forestry University, Yangling, China.
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4
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Oshi M, Tokumaru Y, Benesch MGK, Sugito N, Wu R, Yan L, Yamada A, Chishima T, Ishikawa T, Endo I, Takabe K. High miR-99b expression is associated with cell proliferation and worse patient outcomes in breast cancer. Am J Cancer Res 2022; 12:4840-4852. [PMID: 36381329 PMCID: PMC9641402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023] Open
Abstract
Although miR-99b is a known suppressive microRNA (miRNA) in several cancers, its role in breast cancer has not been elucidated. In this study, we examined the clinical relevance of miR-99b expression in breast cancer. We analyzed miRNA and mRNA expression and their relationships with clinical parameters in 1,961 breast cancer samples from two independent large cohorts, the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and The Cancer Genome Atlas (TCGA). Several algorithms, including gene set enrichment analysis (GSEA) and xCell, have been used to investigate biological functions and the tumor microenvironment. High miR-99b expression significantly enriched the mTORC1 signaling gene set in breast cancer (NES = 1.63, FDR = 0.03, and NES = 1.58, FDR = 0.10, in METABRIC and TCGA, respectively). No other mechanisms, including the epithelial mesenchymal transition, NFκB, and TGF-β signaling, were consistently enriched in both cohorts. MiR-99b-high breast cancer was associated with high homologous recombination deficiencies, intratumor heterogeneity, and high rates of mutation and neoantigens. In agreement, miR-99b-high breast cancer was associated with increased cell proliferation, correlating with Nottingham histological grade, and significant enrichment of E2F targets, G2/M checkpoint, and mitotic spindle gene sets consistently in both cohorts (P = 0.01, P < 0.001). High miR-99b levels were also associated with low stromal cell fractions in the tumor microenvironment, including adipocytes, keratinocytes, and lymphatic endothelial cells (P < 0.001). However, in both cohorts, miR-99b expression was not associated with significant infiltration of immune cells, except dendritic cells (P = 0.006, 0.020). Finally, in both cohorts, breast cancer with high miR-99b expression was significantly associated with worse disease-free survival (DSS) and overall survival (OS), particularly in estrogen receptor (ER)-positive/human epidermal growth factor (HER)2-negative breast cancer (DSS hazard ratio (HR) 1.29, 95% confidence interval (CI) 1.10-1.51, P < 0.001 in the METABRIC cohort and HR 1.82, 95% CI 1.12-2.98, P = 0.017 in the TCGA cohort). In conclusion, breast cancer with high miR-99b expression was significantly associated with mTORC1 signaling, cell proliferation, and decreased patient survival, particularly in the ER-positive/HER2-negative subtype.
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Affiliation(s)
- Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo 14263, New York, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Yoshihisa Tokumaru
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo 14263, New York, USA
- Department of Surgical Oncology, Graduate School of Medicine, Gifu University1-1 Yanagido, Gifu 501-1194, Japan
| | - Matthew GK Benesch
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo 14263, New York, USA
| | - Nobuhiko Sugito
- Department of Surgical Oncology, Graduate School of Medicine, Gifu University1-1 Yanagido, Gifu 501-1194, Japan
| | - Rongrong Wu
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo 14263, New York, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer CenterBuffalo 14263, New York, USA
| | - Akimitsu Yamada
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Takashi Chishima
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo 14263, New York, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental SciencesNiigata 951-8520, Japan
- Department of Breast Surgery, Fukushima Medical University School of MedicineFukushima 960-1295, Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New YorkBuffalo 14263, New York, USA
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5
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Sadeghi M, Bahrami A, Hasankhani A, Kioumarsi H, Nouralizadeh R, Abdulkareem SA, Ghafouri F, Barkema HW. lncRNA-miRNA-mRNA ceRNA Network Involved in Sheep Prolificacy: An Integrated Approach. Genes (Basel) 2022; 13:genes13081295. [PMID: 35893032 PMCID: PMC9332185 DOI: 10.3390/genes13081295] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023] Open
Abstract
Understanding the molecular pattern of fertility is considered as an important step in breeding of different species, and despite the high importance of the fertility, little success has been achieved in dissecting the interactome basis of sheep fertility. However, the complex mechanisms associated with prolificacy in sheep have not been fully understood. Therefore, this study aimed to use competitive endogenous RNA (ceRNA) networks to evaluate this trait to better understand the molecular mechanisms responsible for fertility. A competitive endogenous RNA (ceRNA) network of the corpus luteum was constructed between Romanov and Baluchi sheep breeds with either good or poor genetic merit for prolificacy using whole-transcriptome analysis. First, the main list of lncRNAs, miRNAs, and mRNA related to the corpus luteum that alter with the breed were extracted, then miRNA−mRNA and lncRNA−mRNA interactions were predicted, and the ceRNA network was constructed by integrating these interactions with the other gene regulatory networks and the protein−protein interaction (PPI). A total of 264 mRNAs, 14 lncRNAs, and 34 miRNAs were identified by combining the GO and KEGG enrichment analyses. In total, 44, 7, 7, and 6 mRNAs, lncRNAs, miRNAs, and crucial modules, respectively, were disclosed through clustering for the corpus luteum ceRNA network. All these RNAs involved in biological processes, namely proteolysis, actin cytoskeleton organization, immune system process, cell adhesion, cell differentiation, and lipid metabolic process, have an overexpression pattern (Padj < 0.01). This study increases our understanding of the contribution of different breed transcriptomes to phenotypic fertility differences and constructed a ceRNA network in sheep (Ovis aries) to provide insights into further research on the molecular mechanism and identify new biomarkers for genetic improvement.
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Affiliation(s)
- Masoumeh Sadeghi
- Environmental Health, Zahedan University of Medical Sciences, Zahedan 98, Iran;
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 31, Iran; (A.H.); (F.G.)
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, 80333 Munich, Germany
- Correspondence: (A.B.); (R.N.); Tel.: +98-9199300065 (A.B.)
| | - Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 31, Iran; (A.H.); (F.G.)
| | - Hamed Kioumarsi
- Department of Animal Science Research, Gilan Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Rasht 43, Iran;
| | - Reza Nouralizadeh
- Department of Food and Drug Control, Faculty of Pharmacy, Jundishapour University of Medical Sciences, Ahvaz 63, Iran
- Correspondence: (A.B.); (R.N.); Tel.: +98-9199300065 (A.B.)
| | - Sarah Ali Abdulkareem
- Department of Computer Science, Al-Turath University College, Al Mansour, Baghdad 10011, Iraq;
| | - Farzad Ghafouri
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 31, Iran; (A.H.); (F.G.)
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N4Z6, Canada;
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6
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Gu Y, Zhou H, Yu H, Yang W, Wang B, Qian F, Cheng Y, He S, Zhao X, Zhu L, Zhang Y, Jin M, Lu E. miR-99a regulates CD4 + T cell differentiation and attenuates experimental autoimmune encephalomyelitis by mTOR-mediated glycolysis. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:1173-1185. [PMID: 34820151 PMCID: PMC8598972 DOI: 10.1016/j.omtn.2021.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 07/13/2021] [Indexed: 12/21/2022]
Abstract
Multiple microRNAs exhibit diverse functions to regulate inflammatory and autoimmune diseases. MicroRNA-99a (miR-99a) has been shown to be involved in adipose tissue inflammation and to be downregulated in the inflammatory lesions of autoimmune diseases rheumatoid arthritis and systemic lupus erythematosus. In this study, we found that miR-99a was downregulated in CD4+ T cells from experimental autoimmune encephalomyelitis (EAE) mice, an animal model of multiple sclerosis. Overexpression of miR-99a alleviated EAE development by promoting regulator T cells and inhibiting T helper type 1 (Th1) cell differentiation. Bioinformatics and functional analyses further revealed that the anti-inflammatory effects of miR-99a was attributable to its role in negatively regulating glycolysis reprogramming of CD4+ T cells by targeting the mTOR pathway. Additionally, miR-99a expression was induced by transforming growth factor β (TGF-β) to regulate CD4+ T cell glycolysis and differentiation. Taken together, our results characterize a pivotal role of miR-99a in regulating CD4+ T cell differentiation and glycolysis reprogramming during EAE development, which may indicate that miR-99a is a promising therapeutic target for the amelioration of multiple sclerosis and possibly other autoimmune diseases.
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Affiliation(s)
- Yuting Gu
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hong Zhou
- Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Hongshuang Yu
- Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wanlin Yang
- Children's Hospital of Soochow University, Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Medical College of Soochow University, Soochow University, Suzhou, Jiangsu 215006, China
| | - Bei Wang
- Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Fengtao Qian
- Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yiji Cheng
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Shan He
- Children's Hospital of Soochow University, Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Medical College of Soochow University, Soochow University, Suzhou, Jiangsu 215006, China
| | - Xiaonan Zhao
- Children's Hospital of Soochow University, Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Medical College of Soochow University, Soochow University, Suzhou, Jiangsu 215006, China
| | - Linqiao Zhu
- Children's Hospital of Soochow University, Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Medical College of Soochow University, Soochow University, Suzhou, Jiangsu 215006, China
| | - Yanyun Zhang
- Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China.,Children's Hospital of Soochow University, Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Medical College of Soochow University, Soochow University, Suzhou, Jiangsu 215006, China
| | - Min Jin
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Eryi Lu
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
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7
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Quan KY, Yap CG, Jahan NK, Pillai N. Review of early circulating biomolecules associated with diabetes nephropathy - Ideal candidates for early biomarker array test for DN. Diabetes Res Clin Pract 2021; 182:109122. [PMID: 34742785 DOI: 10.1016/j.diabres.2021.109122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 07/26/2021] [Accepted: 10/31/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Diabetic nephropathy (DN) is one of the catastrophic complications of type 2 diabetes mellitus (T2DM). 45% of DN patients progressed to End Stage Renal Disease (ESRD) which robs casualties of the quality of live. The challenge in early diagnosis of DN is it is asymptomatic in the early phase. Current gold standard test for screening and diagnosis of DN are nonspecific and are not sensitive in detecting DN early enough and subsequently monitor renal function during management and intervention plans. Recent studies reported various biomolecules which are associated with the onset of DN in T2DM using cutting-edge technologies. These biomolecules could be potential early biomarkers for DN. This review selectively identified potential early serum biomolecules which are potential candidates for developing an Early Biomarker Array Test for DN. METHODS An advanced literature search was conducted on 4 online databases. Search terms used were "Diabetes Mellitus, Type 2", "Diabetic nephropathy", "pathogenesis" and "early biomarker. Filters were applied to capture articles published from 2010 to 2020, written in English, human or animal models and focused on serum biomolecules associated with DN. RESULTS Five serum biomolecules have been evidently described as contributing pivotal roles in the pathophysiology of DN. MiR-377, miR-99b, CYP2E1, TGF-β1 and periostin are potential candidates for designing an early biomarker array for screening and diagnosis of early stages of DN. The five shortlisted biomolecules originates from endogenous biochemical processes which are specific to the progressive pathophysiology of DN. CONCLUSION miR-377, miR-99b, CYP2E1, TGF-β1 and periostin are potential candidate biomolecules for diagnosing DN at the early phases and can be developed into a panel of endogenous biomarkers for early detection of DN in patients with T2DM. The outcomes of this study will be a stepping stone towards planning and developing an early biomarker array test for diabetic nephropathy. The proposed panel of early biomarkers for DN has potential of stratifying the stages of DN because each biomolecule appears at distinct stages in the pathophysiology of DN.
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Affiliation(s)
- Kok Ying Quan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Kuala Lumpur, Malaysia
| | - Christina Gertrude Yap
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Kuala Lumpur, Malaysia.
| | - Nowrozy Kamar Jahan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Kuala Lumpur, Malaysia.
| | - Naganathan Pillai
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Kuala Lumpur, Malaysia.
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8
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Identification of miR-199a-5p, miR-214-3p and miR-99b-5p as Fibrosis-Specific Extracellular Biomarkers and Promoters of HSC Activation. Int J Mol Sci 2021; 22:ijms22189799. [PMID: 34575957 PMCID: PMC8464755 DOI: 10.3390/ijms22189799] [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: 07/28/2021] [Revised: 08/27/2021] [Accepted: 09/07/2021] [Indexed: 12/14/2022] Open
Abstract
Liver fibrosis is characterized by the accumulation of extracellular matrix (ECM) resulting in the formation of fibrous scars. In the clinic, liver biopsies are the standard diagnostic method despite the potential for clinical complications. miRNAs are single-stranded, non-coding RNAs that can be detected in tissues, body fluids and cultured cells. The regulation of many miRNAs has been linked to tissue damage, including liver fibrosis in patients, resulting in aberrant miRNA expression/release. Experimental evidence also suggests that miRNAs are regulated in a similar manner in vitro and could thus serve as translational in vitro–in vivo biomarkers. In this work, we set out to identify and characterize biomarkers for liver fibrosis that could be used in vitro and clinically for research and diagnostic purposes. We focused on miRNAs released from hepatic 3D cultures exposed to methotrexate (MTX), which causes fibrosis, and acetaminophen (APAP), an acute hepatotoxicant with no clinically relevant association to liver fibrosis. Using a 3D in vitro model, we corroborated compound-specific responses as we show MTX induced a fibrotic response, and APAP did not. Performing miRNA-seq of cell culture supernatants, we identified potential miRNA biomarkers (miR-199a-5p, miR-214-3p, niRNA-125a-5p and miR-99b-5p) that were associated with a fibrotic phenotype and not with hepatocellular damage alone. Moreover, transfection of HSC with miR-199a-5p led to decreased expression of caveolin-1 and increased α-SMA expression, suggesting its role in HSC activation. In conclusion, we propose that extracellular miR-214-3p, miR-99b-5p, miR-125a-5p and specifically miR-199a-5p could contribute towards a panel of miRNAs for identifying liver fibrosis and that miR-199a-5p, miR-214-3p and miR-99b-5p are promoters of HSC activation.
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9
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Ari Yuka S, Yilmaz A. Network based multifactorial modelling of miRNA-target interactions. PeerJ 2021; 9:e11121. [PMID: 33777541 PMCID: PMC7983860 DOI: 10.7717/peerj.11121] [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: 12/07/2020] [Accepted: 02/25/2021] [Indexed: 12/26/2022] Open
Abstract
Competing endogenous RNA (ceRNA) regulations and crosstalk between various types of non-coding RNA in humans is an important and under-explored subject. Several studies have pointed out that an alteration in miRNA:target interaction can result in unexpected changes due to indirect and complex interactions. In this article, we defined a new network-based model that incorporates miRNA:ceRNA interactions with expression values. Our approach calculates network-wide effects of perturbations in the expression level of one or more nodes in the presence or absence of miRNA interaction factors such as seed type, binding energy. We carried out the analysis of large-scale miRNA:target networks from breast cancer patients. Highly perturbing genes identified by our approach coincide with breast cancer-associated genes and miRNAs. Our network-based approach takes the sponge effect into account and helps to unveil the crosstalk between nodes in miRNA:target network. The model has potential to reveal unforeseen regulations that are only evident in the network context. Our tool is scalable and can be plugged in with emerging miRNA effectors such as circRNAs, lncRNAs, and available as R package ceRNAnetsim: https://www.bioconductor.org/packages/release/bioc/html/ceRNAnetsim.html.
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Affiliation(s)
- Selcen Ari Yuka
- Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey
| | - Alper Yilmaz
- Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey
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10
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Ivanova E, Le Guillou S, Hue-Beauvais C, Le Provost F. Epigenetics: New Insights into Mammary Gland Biology. Genes (Basel) 2021; 12:genes12020231. [PMID: 33562534 PMCID: PMC7914701 DOI: 10.3390/genes12020231] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/23/2021] [Accepted: 01/28/2021] [Indexed: 12/14/2022] Open
Abstract
The mammary gland undergoes important anatomical and physiological changes from embryogenesis through puberty, pregnancy, lactation and involution. These steps are under the control of a complex network of molecular factors, in which epigenetic mechanisms play a role that is increasingly well described. Recently, studies investigating epigenetic modifications and their impacts on gene expression in the mammary gland have been performed at different physiological stages and in different mammary cell types. This has led to the establishment of a role for epigenetic marks in milk component biosynthesis. This review aims to summarize the available knowledge regarding the involvement of the four main molecular mechanisms in epigenetics: DNA methylation, histone modifications, polycomb protein activity and non-coding RNA functions.
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A risk progression breast epithelial 3D culture model reveals Cx43/hsa_circ_0077755/miR-182 as a biomarker axis for heightened risk of breast cancer initiation. Sci Rep 2021; 11:2626. [PMID: 33514777 PMCID: PMC7846862 DOI: 10.1038/s41598-021-82057-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
mRNA-circRNA-miRNAs axes have been characterized in breast cancer, but not as risk-assessment axes for tumor initiation in early-onset breast cancer that is increasing drastically worldwide. To address this gap, we performed circular RNA (circRNA) microarrays and microRNA (miRNA) sequencing on acini of HMT-3522 S1 (S1) breast epithelial risk-progression culture model in 3D and chose an early-stage population miRNome for a validation cohort. Nontumorigenic S1 cells form fully polarized epithelium while pretumorigenic counterparts silenced for gap junction Cx43 (Cx43-KO-S1) lose epithelial polarity, multilayer and mimic premalignant in vivo mammary epithelial morphology. Here, 121 circRNAs and 65 miRNAs were significantly dysregulated in response to Cx43 silencing in cultured epithelia and 15 miRNAs from the patient cohort were involved in epithelial polarity disruption. Focusing on the possible sponging activity of the validated circRNAs to their target miRNAs, we found all miRNAs to be highly enriched in cancer-related pathways and cross-compared their dysregulation to actual miRNA datasets from the cultured epithelia and the patient validation cohort. We present the involvement of gap junction in post-transcriptional axes and reveal Cx43/hsa_circ_0077755/miR-182 as a potential biomarker signature axis for heightened-risk of breast cancer initiation, and that its dysregulation patterns might predict prognosis along breast cancer initiation and progression.
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Regulators at Every Step-How microRNAs Drive Tumor Cell Invasiveness and Metastasis. Cancers (Basel) 2020; 12:cancers12123709. [PMID: 33321819 PMCID: PMC7763175 DOI: 10.3390/cancers12123709] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Tumor cell invasiveness and metastasis are key processes in cancer progression and are composed of many steps. All of them are regulated by multiple microRNAs that either promote or suppress tumor progression. Multiple studies demonstrated that microRNAs target the mRNAs of multiple genes involved in the regulation of cell motility, local invasion, and metastatic niche formation. Thus, microRNAs are promising biomarkers and therapeutic targets in oncology. Abstract Tumor cell invasiveness and metastasis are the main causes of mortality in cancer. Tumor progression is composed of many steps, including primary tumor growth, local invasion, intravasation, survival in the circulation, pre-metastatic niche formation, and metastasis. All these steps are strictly controlled by microRNAs (miRNAs), small non-coding RNA that regulate gene expression at the post-transcriptional level. miRNAs can act as oncomiRs that promote tumor cell invasion and metastasis or as tumor suppressor miRNAs that inhibit tumor progression. These miRNAs regulate the actin cytoskeleton, the expression of extracellular matrix (ECM) receptors including integrins and ECM-remodeling enzymes comprising matrix metalloproteinases (MMPs), and regulate epithelial–mesenchymal transition (EMT), hence modulating cell migration and invasiveness. Moreover, miRNAs regulate angiogenesis, the formation of a pre-metastatic niche, and metastasis. Thus, miRNAs are biomarkers of metastases as well as promising targets of therapy. In this review, we comprehensively describe the role of various miRNAs in tumor cell migration, invasion, and metastasis.
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Regulators at Every Step—How microRNAs Drive Tumor Cell Invasiveness and Metastasis. Cancers (Basel) 2020. [DOI: 10.3390/cancers12123709
expr 991289423 + 939431153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Tumor cell invasiveness and metastasis are the main causes of mortality in cancer. Tumor progression is composed of many steps, including primary tumor growth, local invasion, intravasation, survival in the circulation, pre-metastatic niche formation, and metastasis. All these steps are strictly controlled by microRNAs (miRNAs), small non-coding RNA that regulate gene expression at the post-transcriptional level. miRNAs can act as oncomiRs that promote tumor cell invasion and metastasis or as tumor suppressor miRNAs that inhibit tumor progression. These miRNAs regulate the actin cytoskeleton, the expression of extracellular matrix (ECM) receptors including integrins and ECM-remodeling enzymes comprising matrix metalloproteinases (MMPs), and regulate epithelial–mesenchymal transition (EMT), hence modulating cell migration and invasiveness. Moreover, miRNAs regulate angiogenesis, the formation of a pre-metastatic niche, and metastasis. Thus, miRNAs are biomarkers of metastases as well as promising targets of therapy. In this review, we comprehensively describe the role of various miRNAs in tumor cell migration, invasion, and metastasis.
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Eniafe J, Jiang S. MicroRNA-99 family in cancer and immunity. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1635. [PMID: 33230974 DOI: 10.1002/wrna.1635] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022]
Abstract
The microRNA (miR)-99 family comprising miR-99a, miR-99b, and miR-100 is an evolutionarily conserved family with existence dating prior to the bilaterians. Members are typically oncogenic in leukemia while their functional roles in other cancers alternate between that of a tumor suppressor and a tumor promoter. Targets of the miR-99 family rank in the lists of oncogenes and tumor suppressors, thereby illustrating the dual role of this miR family as oncogenic miRs (oncomiRs) and tumor suppressing miRs (TSmiRs) in different cellular contexts. In addition to their functional roles in cancers, miR-99 family is implicated in the modulation of macrophage inflammatory responses and T-cell subsets biology, thereby exerting critical roles in the maintenance of tissue homeostasis, establishment of peripheral tolerance as well as resolution of an inflammatory reaction. Here, we review emerging knowledge of this miR family and discuss remaining concerns linked to their activities. A better dissection of the functional roles of miR-99 family members in cancer and immunity will help in the development of novel miR-99-based therapeutics for the treatment of human cancer and immune-related diseases. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Joseph Eniafe
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA
| | - Shuai Jiang
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA
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Garrido-Cano I, Constâncio V, Adam-Artigues A, Lameirinhas A, Simón S, Ortega B, Martínez MT, Hernando C, Bermejo B, Lluch A, Lopes P, Henrique R, Jerónimo C, Cejalvo JM, Eroles P. Circulating miR-99a-5p Expression in Plasma: A Potential Biomarker for Early Diagnosis of Breast Cancer. Int J Mol Sci 2020; 21:ijms21197427. [PMID: 33050096 PMCID: PMC7582935 DOI: 10.3390/ijms21197427] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs have emerged as new diagnostic and therapeutic biomarkers for breast cancer. Herein, we analysed miR-99a-5p expression levels in primary tumours and plasma of breast cancer patients to evaluate its usefulness as a minimally invasive diagnostic biomarker. MiR-99a-5p expression levels were determined by quantitative real-time PCR in three independent cohorts of patients: (I) Discovery cohort: breast cancer tissues (n = 103) and healthy breast tissues (n = 26); (II) Testing cohort: plasma samples from 105 patients and 98 healthy donors; (III) Validation cohort: plasma samples from 89 patients and 85 healthy donors. Our results demonstrated that miR-99a-5p was significantly downregulated in breast cancer tissues compared to healthy breast tissues. Conversely, miR-99a-5p levels were significantly higher in breast cancer patients than in healthy controls in plasma samples from both testing and validation cohorts, and ROC curve analysis revealed that miR-99a-5p has good diagnostic potential even to detect early breast cancer. In conclusion, miR-99a-5p’s deregulated expression distinguished healthy patients from breast cancer patients in two different types of samples (tissues and plasma). Interestingly, expression levels in plasma were significantly lower in healthy controls than in early-stage breast cancer patients. Our findings suggest circulating miR-99a-5p as a novel promising non-invasive biomarker for breast cancer detection.
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Affiliation(s)
- Iris Garrido-Cano
- Biomedical Research Institute INCLIVA, 46010 Valencia, Spain; (I.G.-C.); (A.A.-A.); (A.L.); (S.S.); (B.O.); (M.T.M.); (C.H.); (B.B.)
- Cancer Biology and Epigenetics Group–Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (P.L.); (R.H.)
| | - Vera Constâncio
- Cancer Biology and Epigenetics Group–Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (P.L.); (R.H.)
| | - Anna Adam-Artigues
- Biomedical Research Institute INCLIVA, 46010 Valencia, Spain; (I.G.-C.); (A.A.-A.); (A.L.); (S.S.); (B.O.); (M.T.M.); (C.H.); (B.B.)
| | - Ana Lameirinhas
- Biomedical Research Institute INCLIVA, 46010 Valencia, Spain; (I.G.-C.); (A.A.-A.); (A.L.); (S.S.); (B.O.); (M.T.M.); (C.H.); (B.B.)
| | - Soraya Simón
- Biomedical Research Institute INCLIVA, 46010 Valencia, Spain; (I.G.-C.); (A.A.-A.); (A.L.); (S.S.); (B.O.); (M.T.M.); (C.H.); (B.B.)
- Clinical Oncology Department, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
| | - Belen Ortega
- Biomedical Research Institute INCLIVA, 46010 Valencia, Spain; (I.G.-C.); (A.A.-A.); (A.L.); (S.S.); (B.O.); (M.T.M.); (C.H.); (B.B.)
- Clinical Oncology Department, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
| | - María Teresa Martínez
- Biomedical Research Institute INCLIVA, 46010 Valencia, Spain; (I.G.-C.); (A.A.-A.); (A.L.); (S.S.); (B.O.); (M.T.M.); (C.H.); (B.B.)
- Clinical Oncology Department, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
| | - Cristina Hernando
- Biomedical Research Institute INCLIVA, 46010 Valencia, Spain; (I.G.-C.); (A.A.-A.); (A.L.); (S.S.); (B.O.); (M.T.M.); (C.H.); (B.B.)
- Clinical Oncology Department, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
| | - Begoña Bermejo
- Biomedical Research Institute INCLIVA, 46010 Valencia, Spain; (I.G.-C.); (A.A.-A.); (A.L.); (S.S.); (B.O.); (M.T.M.); (C.H.); (B.B.)
- Clinical Oncology Department, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
| | - Ana Lluch
- Clinical Oncology Department, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Department of Medicine, Universitat de València, 46010 Valencia, Spain
| | - Paula Lopes
- Cancer Biology and Epigenetics Group–Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (P.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group–Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (P.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group–Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (P.L.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
- Correspondence: (C.J.); (J.M.C.); (P.E.); Tel.: +351-962447005 (C.J.); +34-961973517 (J.M.C.); +34-961973517 (P.E.)
| | - Juan Miguel Cejalvo
- Biomedical Research Institute INCLIVA, 46010 Valencia, Spain; (I.G.-C.); (A.A.-A.); (A.L.); (S.S.); (B.O.); (M.T.M.); (C.H.); (B.B.)
- Clinical Oncology Department, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
- Correspondence: (C.J.); (J.M.C.); (P.E.); Tel.: +351-962447005 (C.J.); +34-961973517 (J.M.C.); +34-961973517 (P.E.)
| | - Pilar Eroles
- Biomedical Research Institute INCLIVA, 46010 Valencia, Spain; (I.G.-C.); (A.A.-A.); (A.L.); (S.S.); (B.O.); (M.T.M.); (C.H.); (B.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- COST Action CA15204, 1210 Brussels, Belgium
- Department of Physiology, Universitat de València, 46010 Valencia, Spain
- Correspondence: (C.J.); (J.M.C.); (P.E.); Tel.: +351-962447005 (C.J.); +34-961973517 (J.M.C.); +34-961973517 (P.E.)
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Bahlakeh G, Gorji A, Soltani H, Ghadiri T. MicroRNA alterations in neuropathologic cognitive disorders with an emphasis on dementia: Lessons from animal models. J Cell Physiol 2020; 236:806-823. [PMID: 32602584 DOI: 10.1002/jcp.29908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 06/05/2020] [Accepted: 06/15/2020] [Indexed: 12/11/2022]
Abstract
Cognitive dysfunction is a state of losing or having difficulties in remembering, learning, focusing, or making decisions that impact individual healthy life. Small single-stranded and nonprotein coding RNAs, microRNAs (miRNAs) participate actively in regulatory processes, incorporate cognitive signaling pathways, and intensely affect cognitive evolution. miRNAs exert their modification activities through translational or transcriptional processes. Reportedly, cognitive impairment and dementia are rising, especially in developing countries. Herein we provided a brief review of original studies addressing miRNA changes in the most common neurological diseases with a focus on dementia and Alzheimer's disease. It must be noted that an increase in the level of certain miRNAs but a decrease in other ones deteriorate cognitive performance. The current review revealed that induction of miR-214-3p, miR-302, miR-21, miR- 200b/c, miR-207, miR-132, miR-188-3p and 5p, and miR-873 improved cognitive impairment in various cognitive tasks. On the other hand, intentionally lowering the level of miR-34a, miR-124, miR-574, and miR-191a enhanced cognitive function and memory. Synaptic dysfunction is a core cause of cognitive dysfunction; miRNA-34, miRNA-34-c, miRNA-124, miRNA-188-5p, miRNA-210-5p, miRNA-335-3p, and miRNA-134 strongly influence synaptic-related mechanisms. The downregulation of miRNA-132 aggregates both amyloid and tau in tauopathy. Concerning the massive burden of neurological diseases worldwide, the future challenge is the translation of animal model knowledge into the detection of pathophysiological stages of neurocognitive disorders and designing efficient therapeutic strategies. While the delivery procedure of agomir or antagomir miRNAs into the brain is invasive and only applied in animal studies, finding a safe and specific delivery route is a priority.
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Affiliation(s)
- Gozal Bahlakeh
- Department of Anatomy, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Gorji
- Epilepsy Research Center, Department of Neurology and Institute for Translational Neurology, Westfälische Wilhelms-Universität Münster, Münster, Germany.,Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran.,Neuroscience Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Soltani
- Department of Neurosciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tahereh Ghadiri
- Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran.,Department of Neurosciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
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Zhu P, Liu J, Lu M, Wu G, Lin X, Cai L, Zhang X. Influence and mechanism of miR-99a suppressing development of colorectal cancer (CRC) with diabetes mellitus (DM). Onco Targets Ther 2019; 12:10311-10321. [PMID: 31819515 PMCID: PMC6885593 DOI: 10.2147/ott.s190998] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 07/18/2019] [Indexed: 12/24/2022] Open
Abstract
Objective This study aimed to identify the changes of miRNAs in colorectal cancer (CRC) complicated with diabetes mellitus (DM) (CRC + DM) tissues and their potential effects. Methods The changes of miRNAs in CRC + DM tissues were determined by miRNA microarray. The expression levels of miR-99a in 40 clinical specimens and 6 CRC cell lines were determined by qRT-PCR. The capacity for miR-99a to induce cell proliferation and invasion was examined with miR-99a-overexpressing HCT-116 cells. The relative mTOR mRNA and protein levels were determined by qRT-PCR and Western blotting, respectively, in HCT-116 cells transfected with miR-99a. The dual luciferase assay was performed to confirm the direct regulation of miR-99a on mTOR 3′-UTR. The HCT-116 cells were treated with 100 mg/L advanced glycation end products (AGEs); then, the mTOR expression levels were determined by qRT-PCR, Western blotting, and immunohistochemistry. Results Seventeen miRNAs were found to be differentially expressed among normal tissue, CRC tissue, and CRC with DM tissue, including 15 upregulated and 2 downregulated with fold changs of more than 2 times. qRT-PCR confirmed that miR-99a was downregulated in CRC and CRC + DM tissues. In addition, miR-99a overexpression remarkably impaired CRC cell proliferation and metastasis, and negatively regulated mTOR signaling through direct binding to the 3′-UTR of mTOR. AGEs could suppress miR-99a and stimulate mTOR signaling in CRC cells. Increased mTOR was also identified in CRC with DM tissues. Conclusion Our findings indicate that miR-99a is a potential marker and therapeutic target of CRC complicated with DM, and that AGEs impair miR-99a-overactivated mTOR signaling in CRC with DM patients, which promotes CRC development.
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Affiliation(s)
- Peixuan Zhu
- The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jiahao Liu
- Cancer Center, Traditional Chinese Medicine-Integrated Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Meijuan Lu
- The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Gongfa Wu
- Department of Pathology, Zengcheng District People's Hospital of Guangzhou City, Guangzhou, People's Republic of China
| | - Xutao Lin
- The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Longmei Cai
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Xiaona Zhang
- The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
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18
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Altered expression of miRNAs and mRNAs reveals the potential regulatory role of miRNAs in the developmental process of early weaned goats. PLoS One 2019; 14:e0220907. [PMID: 31393969 PMCID: PMC6687162 DOI: 10.1371/journal.pone.0220907] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/25/2019] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) play pivotal roles in growth, development, and stress responses. However, the regulatory function of miRNAs in early weaned goats remains unclear. Deep sequencing comparison of mRNA and miRNA expression profiles showed that 18 miRNAs and 373 genes were differentially expressed in pre- and post-weaning Chongming white goats. Bioinformatics analysis indicated that these differentially expressed genes are involved in cellular processes, developmental processes, and growth in terms of biological process analysis. KEGG analysis showed that downregulated genes were enriched in salivary secretion, bile secretion, vascular smooth muscle contraction, and calcium signaling pathways. Additionally, a miRNA-mRNA co-expression network of the 18 dysregulated miRNAs and their 107 target mRNAs was constructed using a combination of Pearson’s correlation analysis and prediction by miRanda software. Among the downregulated miRNAs, two (chi-miR-206 and chi-miR-133a/b) were muscle development-related and the others were cell proliferation associated. Further RT-qPCR analysis confirmed that downregulated miRNAs (chi-miR-99b-3p, chi-miR-224, and chi-miR-10b-5p) were highly expressed in muscle tissues (heart, spleen, or kidney) of the rapid growth period (7-month old) in Chongming white goats. The results of the present study suggested that weaning induced cell proliferation repression in post-weaning goats, providing new insight into the mechanism of muscle development of goats, although additional details remain to be elucidated in the future.
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19
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Nziza N, Duroux-Richard I, Apparailly F. MicroRNAs in juvenile idiopathic arthritis: Can we learn more about pathophysiological mechanisms? Autoimmun Rev 2019; 18:796-804. [DOI: 10.1016/j.autrev.2019.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/03/2019] [Indexed: 01/05/2023]
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20
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Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X, Cheng X. Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites. Nucleic Acids Res 2019; 46:3864-3877. [PMID: 29294058 PMCID: PMC5934627 DOI: 10.1093/nar/gkx1274] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/22/2017] [Indexed: 12/14/2022] Open
Abstract
Wilms tumor protein (WT1) is a Cys2-His2 zinc-finger transcription factor vital for embryonic development of the genitourinary system. The protein contains a C-terminal DNA binding domain with four tandem zinc-fingers (ZF1-4). An alternative splicing of Wt1 can add three additional amino acids-lysine (K), threonine (T) and serine (S)-between ZF3 and ZF4. In the -KTS isoform, ZF2-4 determine the sequence-specificity of DNA binding, whereas the function of ZF1 remains elusive. Three X-ray structures are described here for wild-type -KTS isoform ZF1-4 in complex with its cognate DNA sequence. We observed four unique ZF1 conformations. First, like ZF2-4, ZF1 can be positioned continuously in the DNA major groove forming a 'near-cognate' complex. Second, while ZF2-4 make base-specific interactions with one DNA molecule, ZF1 can interact with a second DNA molecule (or, presumably, two regions of the same DNA molecule). Third, ZF1 can intercalate at the joint of two tail-to-head DNA molecules. If such intercalation occurs on a continuous DNA molecule, it would kink the DNA at the ZF1 binding site. Fourth, two ZF1 units can dimerize. Furthermore, we examined a Denys-Drash syndrome-associated ZF1 mutation (methionine at position 342 is replaced by arginine). This mutation enhances WT1 affinity for a guanine base. X-ray crystallography of the mutant in complex with its preferred sequence revealed the interactions responsible for this affinity change. These results provide insight into the mechanisms of action of WT1, and clarify the fact that ZF1 plays a role in determining sequence specificity of this critical transcription factor.
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Affiliation(s)
- Dongxue Wang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yu Zheng
- RGENE, Inc., 953 Indiana Street, San Francisco, CA 94107, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Bahiraee A, Ebrahimi R, Halabian R, Aghabozorgi AS, Amani J. The role of inflammation and its related microRNAs in breast cancer: A narrative review. J Cell Physiol 2019; 234:19480-19493. [PMID: 31025369 DOI: 10.1002/jcp.28742] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/27/2019] [Accepted: 04/10/2019] [Indexed: 12/21/2022]
Abstract
Breast cancer is recognized as the most common type of cancer among women with a high rate of mortality all over the world. Over the past years, growing attention has been regarded to realize more about the mechanisms underlying the disease process. It is revealed that the progression of breast cancer may be strongly linked to chronic inflammation owing to the role of inflammatory factors in genetic instability and subsequent cancer predisposition. Although the association between breast cancer and inflammatory pathways has been well-defined now, only recent evidence pointed towards the inflammation-related microRNAs (miRNAs) as potential biomarkers and therapeutic targets involved in the crosstalk of multiple pathways during breast cancer development. Moreover, the practical interactions between these miRNAs and inflammatory factors are also a little characterized. In this review, we intended to describe the effects of predominant inflammatory pathways such as cytokines, phosphoinositide 3-kinase/protein kinase B, and nuclear factor kappa B in association with tumor promoting and tumor suppressing miRNAs on breast cancer progression. Providing new studies in the field of combining biomarkers for early diagnosis, prognosis, and monitoring breast cancer are very important. Notably, understanding the underlying mechanisms of miRNAs as a possible link between inflammation and tumorigenesis may offer a novel insight for combating this epidemic.
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Affiliation(s)
- Alireza Bahiraee
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reyhane Ebrahimi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Raheleh Halabian
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Amirsaeed Sabeti Aghabozorgi
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Jafar Amani
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Xie J, Cao Y. Expression of TGF-β1 and miR-99a in serum of patients with early spontaneous abortion and correlation with hormone levels during pregnancy. Exp Ther Med 2019; 17:4593-4597. [PMID: 31086590 PMCID: PMC6489008 DOI: 10.3892/etm.2019.7477] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/02/2019] [Indexed: 11/30/2022] Open
Abstract
Expression of TGF-β1 and miR-99a in patients with early spontaneous abortion and correlation with hormone levels during pregnancy were investigated. A total of 70 pregnant women with early spontaneous abortion diagnosed in Jining No. 1 People's Hospital from February 1, 2015 to May 1, 2018 were selected as the study group, and 83 normal pregnant women who chose abortion for non-medical reasons in the same period as the control group. Enzyme-linked immunosorbent assay (ELISA) was used to detect TGF-β1 and the levels of serum β-HCG, progesterone and estrogen during pregnancy in the two groups, and RT-qPCR to detect the expression of miR-99a, and partial correlation analysis to analyze the correlation of TGF-β1 and miR-99a with the levels of serum β-HCG, progesterone and estrogen in the study group of patients. Expression of β-HCG was significantly lower in the study group than that in the control group, with a statistically significant difference (P<0.001), and that of progesterone was significantly lower in the study group than that in the control group, with a statistically significant difference (P<0.001). Expression of estrogen was significantly lower in the study group than that in the control group, with a statistically significant difference (P<0.001). The partial correlation analysis indicated that the levels of serum β-HCG, progesterone and estrogen were positively correlated with TGF-β1 (r=0.944, 0.868, 0.869, P<0.001), negatively correlated with the expression level of miR-99a (r=−0.944, −0.892, −0.891, all P<0.001). miR-99a was highly expressed in the serum of patients with early spontaneous abortion, but TGF-β1 expression was low. The expression levels of the two factors are related to hormone levels during pregnancy, which are expected to be new candidate molecular diagnostic markers in the diagnosis of early spontaneous abortion.
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Affiliation(s)
- Juping Xie
- Department of Obstetrics, Jining No. 1 People's Hospital, Jining, Shandong 272100, P.R. China
| | - Yali Cao
- Department of Obstetrics, Jining No. 1 People's Hospital, Jining, Shandong 272100, P.R. China
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23
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Lin JF, Tsai TF, Lin YC, Chen HE, Chou KY, Hwang TIS. Benzyl isothiocyanate suppresses IGF1R, FGFR3 and mTOR expression by upregulation of miR-99a-5p in human bladder cancer cells. Int J Oncol 2019; 54:2106-2116. [PMID: 30942430 DOI: 10.3892/ijo.2019.4763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/26/2018] [Indexed: 11/06/2022] Open
Abstract
Benzyl isothiocyanate (BITC) is known for its pharmacological properties against malignant neoplasm, including bladder cancer (BC). The current study investigated microRNAs (miRNA or miR) expression profiles with an emphasis on the role of miR‑99a‑5p in BITC‑treated BC cells. A quantitative polymerase chain reaction (qPCR) microarray containing 79 aberrantly expressed miRNAs in BC was used to detect miRNA expression in BITC‑treated cells. Several dysregulated miRNAs were identified and further confirmed using miRNA stem‑loop reverse transcription (RT)‑qPCR in 5637 cells. Insulin‑like growth factor 1 receptor (IGF1R), fibroblast growth factor receptor 3 (FGFR3) and mammalian target of rapamycin (mTOR) expression were determined by RT‑qPCR and western blotting. Cell viability was evaluated using WST‑1 reagent and apoptosis was monitored by determining the levels of cleaved‑poly ADP‑ribose polymerase and cleaved‑caspase‑3. BITC treatment significantly upregulated miR‑99a‑5p levels in a dose‑dependent manner. miR‑99a‑5p overexpression decreased IGF1R, mTOR and FGFR3 expression, predicted targets of miR‑99a‑5p. In addition, antisense miR‑99a‑5p sequences inhibited BITC‑induced miR‑99a‑5p overexpression, resulting in the restoration of protein expression and decreased cell viability. The current study identified multiple miRNAs responsive to BITC treatment, including miR‑99a‑5p. In addition, the induction of miR‑99a‑5p decreased IGF1R, mTOR and FGFR3 expression in BITC‑treated BC cells. The current study provided novel insight into the antitumor mechanism by which BITC restores miR‑99a‑5p expression and decreases cancer cell survival.
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Affiliation(s)
- Ji-Fan Lin
- Central Laboratory, Shin-Kong Wu Ho-Su Memorial Hospital, Taipei 111, Taiwan, R.O.C
| | - Te-Fu Tsai
- Division of Urology, School of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan, R.O.C
| | - Yi-Chia Lin
- Division of Urology, School of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan, R.O.C
| | - Hung-En Chen
- Division of Urology, School of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan, R.O.C
| | - Kuang-Yu Chou
- Division of Urology, School of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan, R.O.C
| | - Thomas I-Sheng Hwang
- Division of Urology, School of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan, R.O.C
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Afshar E, Hashemi-Arabi M, Salami S, Peirouvi T, Pouriran R. Screening of acetaminophen-induced alterations in epithelial-to-mesenchymal transition-related expression of microRNAs in a model of stem-like triple-negative breast cancer cells: The possible functional impacts. Gene 2019; 702:46-55. [PMID: 30898700 DOI: 10.1016/j.gene.2019.02.106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/04/2019] [Accepted: 02/22/2019] [Indexed: 12/21/2022]
Abstract
Current protocols for therapy inefficiently targets triple negative breast cancer and barely eradicate cancer stem cells. Elucidation of the pleiotropic effect of clinically proven therapeutics on cancer cells shed light on novel application of old friends. The pleiotropic effect of acetaminophen (APAP) on breast cancer was previously reported. In a cell model of triple negative breast cancer with stem-like CD44high/CD24low phenotype, we screened the impacts of APAP (1 mM, 72 h) on the Epithelial to mesenchymal transition (EMT)-related expression of miRs. APAP significantly overexpressed hsa-miR-130a-3p, 192-5p, 214-3p, 101-3p, 30d-5p, 10a-5p, 99a-5p, 200c-3p, 143-3p, 30b-5p and let-7f-5p showed significant overexpression, but suppressed the expression of hsa-miR-7-5p, 149-3p, 215, 150-5p, 205-5p, 206, 10b-5p, 20b-5p, 145-5p, 26b-5p, 223-3p, 17-5p, 186-5p, 146a-5p and let-7c. It also altered on the expression of selected EMT-related genes, significantly upregulated the expression of KRT19, AKT2, CD24, and TIMP1; but downregulated the expression of MMP2, ALDH1, MMP9, TWIST, NOTCH1, and AKT1. Such shifts in expression profiles increased the population of the cells with CD44high/CD24high, and CD44low/CD24high phenotypes, significantly reduced the Twist protein and shifted the balance of E-cadherin and Vimentin proteins in favor of differentiation. Treated cells showed a significant reduction of in vitro migration and were significantly chemosensitized to Camptothecin. In conclusion, APAP, at a safe clinical dose, induced a set of targeted alterations in the EMT-related miRs which implicate, even in part, significant mitigation in chemoresistance and in vitro migration. Further studies should also be piloted to elucidate the most crucial miRs and to evaluate its clinical effectiveness.
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Affiliation(s)
- Elham Afshar
- Cell Death and Differentiation Signaling Research Lab, Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Center for Biotechnology, Institute of Science and Technology, Jawaharlal Nehru Technological University, Kukatpally, Hyderabad, Telangana, India
| | - Masoud Hashemi-Arabi
- Cell Death and Differentiation Signaling Research Lab, Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; International Branch, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Siamak Salami
- Cell Death and Differentiation Signaling Research Lab, Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Tahmineh Peirouvi
- Department of Histology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Ramin Pouriran
- International Branch, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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25
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Regmi A, Liu G, Zhong X, Hu S, Ma R, Gou L, Zafar MI, Chen L. Evaluation of Serum microRNAs in Patients with Diabetic Kidney Disease: A Nested Case-Controlled Study and Bioinformatics Analysis. Med Sci Monit 2019; 25:1699-1708. [PMID: 30835718 PMCID: PMC6413564 DOI: 10.12659/msm.913265] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Diabetic kidney disease (DKD) can result in end-stage kidney disease and renal failure. This study aimed to examine the expression of serum microRNAs (miRNAs), miR-20a, miR-99b, miR-122-5p, and miR-486-5p, and to use bioinformatics data to investigate the pathways involved in DKD. MATERIAL AND METHODS Serum miRNAs were obtained from 25 healthy volunteers, 50 patients with non-complicated type 2 diabetes mellitus (T2DM), and 42 patients with T2DM and DKD. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression of serum miRNAs. Specificity and sensitivity of the association between serum miRNAs in DKD were evaluated by analysis of the receiver operating characteristic (ROC) area under the curve (AUC). Serum miRNAs and clinical parameters of the patients were compared. Bioinformatics data analysis accessed the miRNA targets involved in the pathways related to the pathogenesis of DKD. RESULTS Serum levels of miR-99b and miR-122 significantly increased, and mir-20a and miR-486 decreased in the DKD group compared with healthy controls. Serum levels of miR-20a, miR-99b, miR-486-5p, and miR-122-5p were significantly correlated with albuminuria, estimated glomerular filtration rate (eGFR), blood glucose and lipid profiles. ROC curve analysis showed that diagnostic accuracy of serum levels of miR-99b for DKD was superior to miR-486-5p, miR-122-5p, and miR-20a, resulting in AUCs of 0.895, 0.853, 0.80, and 0.697, respectively. These four miRNAs regulate several genes affecting oxidative stress, inflammation, and apoptosis. CONCLUSIONS Serum miR-99b, miR-486-5p, miR-122-5p, and miR-20a were differentially expressed in patients with T2DM and DKD and should be evaluated further as potential biomarkers for DKD.
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Affiliation(s)
- Anita Regmi
- Department of Endocrinology, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
| | - Geng Liu
- Department of Endocrinology, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
| | - Xueyu Zhong
- Department of Endocrinology, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
| | - Shengqing Hu
- Department of Endocrinology, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
| | - Rong Ma
- Department of Endocrinology, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
| | - Luoning Gou
- Department of Endocrinology, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
| | - Mohammad Ishraq Zafar
- Department of Endocrinology, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
| | - LuLu Chen
- Department of Endocrinology, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
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26
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Kenny A, Hernández F, Avila J, Lucas JJ, Henshall DC, Prehn JHM, Jiménez-Mateos EM, Engel T. Profiling of Argonaute-2-loaded microRNAs in a mouse model of frontotemporal dementia with parkinsonism-17. INTERNATIONAL JOURNAL OF PHYSIOLOGY, PATHOPHYSIOLOGY AND PHARMACOLOGY 2018; 10:172-183. [PMID: 30697364 PMCID: PMC6334219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Tauopathies are a group of neurodegenerative diseases characterized by the pathological aggregation of the microtubule-associated protein tau. These include more than 20 diseases, with Alzheimer's disease being the most frequent. While pathological and neurotoxic effects of tau are well documented, the mechanisms by which tau can promote neurodegeneration are less clear. Increasing evidence suggests a functional role for microRNAs in the pathogenesis of tauopathies, with altered expression and function of microRNAs in experimental models and patient brain. To determine whether a pathological expression of tau leads to altered microRNA expression, we investigated a mouse model (VLW), which overexpresses tau carrying three mutations identified in patients suffering from frontotemporal dementia with parkinsonism-17. Argonaute-2-bound microRNAs were co-immunoprecipitated using hippocampal tissue to identify active microRNAs within the model and quantified using a genome-wide high-throughput qPCR-based microRNA platform. While similar numbers of microRNAs are present between wild-type and VLW mice, a prominent increase in Argonaute-2-bound levels of microRNAs could be observed in VLW mice. This included microRNA-134, microRNA-99a and microRNA-101. Subsequent experiments revealed this increase in Argonaute-2 loading of microRNAs to correlate with increased microRNA expression. Our in vivo study suggests that a pathological tau overexpression may lead to an increase in active microRNAs, possibly contributing to dysregulation of gene expression and tau-induced pathology.
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Affiliation(s)
- Aidan Kenny
- Department of Physiology and Medical Physics, Royal College of Surgeons in IrelandDublin 2, Ireland
| | - Félix Hernández
- Department of Molecular Neuropathology, Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Centro Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED)Madrid, Spain
| | - Jesús Avila
- Department of Molecular Neuropathology, Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Centro Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED)Madrid, Spain
| | - José J Lucas
- Department of Molecular Neuropathology, Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Centro Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED)Madrid, Spain
| | - David C Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in IrelandDublin 2, Ireland
- FutureNeuro Research CentreDublin 2, Ireland
| | - Jochen HM Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in IrelandDublin 2, Ireland
- FutureNeuro Research CentreDublin 2, Ireland
| | - Eva M Jiménez-Mateos
- Department of Physiology and Medical Physics, Royal College of Surgeons in IrelandDublin 2, Ireland
- Discipline of Physiology, School of Medicine, Trinity College Dublin, The University of DublinDublin 2, Ireland
| | - Tobias Engel
- Department of Physiology and Medical Physics, Royal College of Surgeons in IrelandDublin 2, Ireland
- FutureNeuro Research CentreDublin 2, Ireland
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27
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Klinge CM. Non-Coding RNAs in Breast Cancer: Intracellular and Intercellular Communication. Noncoding RNA 2018; 4:E40. [PMID: 30545127 PMCID: PMC6316884 DOI: 10.3390/ncrna4040040] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 02/07/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are regulators of intracellular and intercellular signaling in breast cancer. ncRNAs modulate intracellular signaling to control diverse cellular processes, including levels and activity of estrogen receptor α (ERα), proliferation, invasion, migration, apoptosis, and stemness. In addition, ncRNAs can be packaged into exosomes to provide intercellular communication by the transmission of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) to cells locally or systemically. This review provides an overview of the biogenesis and roles of ncRNAs: small nucleolar RNA (snRNA), circular RNAs (circRNAs), PIWI-interacting RNAs (piRNAs), miRNAs, and lncRNAs in breast cancer. Since more is known about the miRNAs and lncRNAs that are expressed in breast tumors, their established targets as oncogenic drivers and tumor suppressors will be reviewed. The focus is on miRNAs and lncRNAs identified in breast tumors, since a number of ncRNAs identified in breast cancer cells are not dysregulated in breast tumors. The identity and putative function of selected lncRNAs increased: nuclear paraspeckle assembly transcript 1 (NEAT1), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), steroid receptor RNA activator 1 (SRA1), colon cancer associated transcript 2 (CCAT2), colorectal neoplasia differentially expressed (CRNDE), myocardial infarction associated transcript (MIAT), and long intergenic non-protein coding RNA, Regulator of Reprogramming (LINC-ROR); and decreased levels of maternally-expressed 3 (MEG3) in breast tumors have been observed as well. miRNAs and lncRNAs are considered targets of therapeutic intervention in breast cancer, but further work is needed to bring the promise of regulating their activities to clinical use.
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Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA.
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28
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Yoshimura A, Sawada K, Nakamura K, Kinose Y, Nakatsuka E, Kobayashi M, Miyamoto M, Ishida K, Matsumoto Y, Kodama M, Hashimoto K, Mabuchi S, Kimura T. Exosomal miR-99a-5p is elevated in sera of ovarian cancer patients and promotes cancer cell invasion by increasing fibronectin and vitronectin expression in neighboring peritoneal mesothelial cells. BMC Cancer 2018; 18:1065. [PMID: 30396333 PMCID: PMC6217763 DOI: 10.1186/s12885-018-4974-5] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022] Open
Abstract
Background microRNAs (miRNAs) stably exist in circulating blood and are encapsulated in extracellular vesicles such as exosomes. The aims of this study were to identify which exosomal miRNAs are highly produced from epithelial ovarian cancer (EOC) cells, to analyze whether serum miRNA can be used to discriminate patients with EOC from healthy volunteers, and to investigate the functional role of exosomal miRNAs in ovarian cancer progression. Methods Exosomes were collected from the culture media of serous ovarian cancer cell lines, namely TYK-nu and HeyA8 cells. An exosomal miRNA microarray revealed that several miRNAs including miR-99a-5p were specifically elevated in EOC-derived exosomes. Expression levels of serum miR-99a-5p in 62 patients with EOC, 26 patients with benign ovarian tumors, and 20 healthy volunteers were determined by miRNA quantitative reverse transcription-polymerase chain reaction. To investigate the role of exosomal miR-99a-5p in peritoneal dissemination, neighboring human peritoneal mesothelial cells (HPMCs) were treated with EOC-derived exosomes and then expression levels of miR-99a-5p were examined. Furthermore, mimics of miR-99a-5p were transfected into HPMCs and the effect of miR-99a-5p on cancer invasion was analyzed using a 3D culture model. Proteomic analysis with the tandem mass tag method was performed on HPMCs transfected with miR-99a-5p and then potential target genes of miR-99a-5p were examined. Results The serum miR-99a-5p levels were significantly increased in patients with EOC, compared with those in benign tumor patients and healthy volunteers (1.7-fold and 2.8-fold, respectively). A receiver operating characteristic curve analysis showed with a cut-off of 1.41 showed sensitivity and specificity of 0.85 and 0.75, respectively, for detecting EOC (area under the curve = 0.88). Serum miR-99a-5p expression levels were significantly decreased after EOC surgeries (1.8 to 1.3, p = 0.002), indicating that miR-99a-5p reflects tumor burden. Treatment with EOC-derived exosomes significantly increased miR-99a-5p expression in HPMCs. HPMCs transfected with miR-99a-5p promoted ovarian cancer invasion and exhibited increased expression levels of fibronectin and vitronectin. Conclusions Serum miR-99a-5p is significantly elevated in ovarian cancer patients. Exosomal miR-99a-5p from EOC cells promotes cell invasion by affecting HPMCs through fibronectin and vitronectin upregulation and may serve as a target for inhibiting ovarian cancer progression. Electronic supplementary material The online version of this article (10.1186/s12885-018-4974-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Akihiko Yoshimura
- Departments of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kenjiro Sawada
- Departments of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Koji Nakamura
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Yasuto Kinose
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Erika Nakatsuka
- Departments of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masaki Kobayashi
- Departments of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mayuko Miyamoto
- Departments of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kyoso Ishida
- Departments of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuri Matsumoto
- Departments of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Michiko Kodama
- Departments of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kae Hashimoto
- Departments of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Seiji Mabuchi
- Departments of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tadashi Kimura
- Departments of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Reza AMMT, Choi YJ, Han SG, Song H, Park C, Hong K, Kim JH. Roles of microRNAs in mammalian reproduction: from the commitment of germ cells to peri-implantation embryos. Biol Rev Camb Philos Soc 2018; 94:415-438. [PMID: 30151880 PMCID: PMC7379200 DOI: 10.1111/brv.12459] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/25/2018] [Accepted: 07/27/2018] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are active regulators of numerous biological and physiological processes including most of the events of mammalian reproduction. Understanding the biological functions of miRNAs in the context of mammalian reproduction will allow a better and comparative understanding of fertility and sterility in male and female mammals. Herein, we summarize recent progress in miRNA‐mediated regulation of mammalian reproduction and highlight the significance of miRNAs in different aspects of mammalian reproduction including the biogenesis of germ cells, the functionality of reproductive organs, and the development of early embryos. Furthermore, we focus on the gene expression regulatory feedback loops involving hormones and miRNA expression to increase our understanding of germ cell commitment and the functioning of reproductive organs. Finally, we discuss the influence of miRNAs on male and female reproductive failure, and provide perspectives for future studies on this topic.
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Affiliation(s)
- Abu Musa Md Talimur Reza
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Research Centre (SRC), Konkuk University, Seoul, 143-701, Republic of Korea
| | - Yun-Jung Choi
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Research Centre (SRC), Konkuk University, Seoul, 143-701, Republic of Korea
| | - Sung Gu Han
- Department of Food Science and Biotechnology of Animal Resources, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Research Centre (SRC), Konkuk University, Seoul, 143-701, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Research Centre (SRC), Konkuk University, Seoul, 143-701, Republic of Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Research Centre (SRC), Konkuk University, Seoul, 143-701, Republic of Korea
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Research Centre (SRC), Konkuk University, Seoul, 143-701, Republic of Korea
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30
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MiR-99b-5p and miR-203a-3p Function as Tumor Suppressors by Targeting IGF-1R in Gastric Cancer. Sci Rep 2018; 8:10119. [PMID: 29973668 PMCID: PMC6031697 DOI: 10.1038/s41598-018-27583-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 04/05/2018] [Indexed: 01/19/2023] Open
Abstract
MicroRNAs (miRNAs) have been explored in many critical cellular processes, including proliferation and apoptosis. The purpose of this study was to detect the biological function and regulation of miR-99b-5p and miR-203a-3p in gastric cancer (GC). Here, we demonstrated that miR-99b-5p/203a-3p were downregulated in both GC tissues and cell lines. MiR-99b-5p/203a-3p overexpression reduced GC cell proliferation and cell cycle progression in vitro. Notably, we combined bioinformatics tools with biological validation assays to demonstrate that insulin-like growth factor 1 receptor (IGF-1R) is a direct co-target and functional mediator of miR-99b-5p/203a-3p in GC cells. Mechanistically, the AKT pathway, which is downstream of IGF-1R, is essential for the functional roles of miR-99b-5p/203a-3p in GC cells. Taken together, our data revealed that IGF-1R is a direct co-target of miR-99b-5p/203a-3p, and miR-99b-5p/203a-3p may function as tumor suppressive miRNAs by negatively regulating IGF-1R expression in GC cells.
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31
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Functional Role of Non-Coding RNAs during Epithelial-To-Mesenchymal Transition. Noncoding RNA 2018; 4:ncrna4020014. [PMID: 29843425 PMCID: PMC6027143 DOI: 10.3390/ncrna4020014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 01/17/2023] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) is a key biological process involved in a multitude of developmental and pathological events. It is characterized by the progressive loss of cell-to-cell contacts and actin cytoskeletal rearrangements, leading to filopodia formation and the progressive up-regulation of a mesenchymal gene expression pattern enabling cell migration. Epithelial-to-mesenchymal transition is already observed in early embryonic stages such as gastrulation, when the epiblast undergoes an EMT process and therefore leads to the formation of the third embryonic layer, the mesoderm. Epithelial-to-mesenchymal transition is pivotal in multiple embryonic processes, such as for example during cardiovascular system development, as valve primordia are formed and the cardiac jelly is progressively invaded by endocardium-derived mesenchyme or as the external cardiac cell layer is established, i.e., the epicardium and cells detached migrate into the embryonic myocardial to form the cardiac fibrous skeleton and the coronary vasculature. Strikingly, the most important biological event in which EMT is pivotal is cancer development and metastasis. Over the last years, understanding of the transcriptional regulatory networks involved in EMT has greatly advanced. Several transcriptional factors such as Snail, Slug, Twist, Zeb1 and Zeb2 have been reported to play fundamental roles in EMT, leading in most cases to transcriptional repression of cell⁻cell interacting proteins such as ZO-1 and cadherins and activation of cytoskeletal markers such as vimentin. In recent years, a fundamental role for non-coding RNAs, particularly microRNAs and more recently long non-coding RNAs, has been identified in normal tissue development and homeostasis as well as in several oncogenic processes. In this study, we will provide a state-of-the-art review of the functional roles of non-coding RNAs, particularly microRNAs, in epithelial-to-mesenchymal transition in both developmental and pathological EMT.
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Cheng H, Xue J, Yang S, Chen Y, Wang Y, Zhu Y, Wang X, Kuang D, Ruan Q, Duan Y, Wang G. Co-targeting of IGF1R/mTOR pathway by miR-497 and miR-99a impairs hepatocellular carcinoma development. Oncotarget 2018. [PMID: 28624790 PMCID: PMC5564620 DOI: 10.18632/oncotarget.18207] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Persistent activation of IGF1R/mTOR signaling pathway plays crucial role in the development of hepatocellular carcinoma (HCC). Therefore, our goal was to elucidate microRNAs (miRNAs) targeting IGF1R/mTOR and the therapeutic potential of single or dual miRNA on HCC development. In this study, we found that miR-497 and miR-99a that target the 3′-UTR of both IGF1R and mTOR were down-regulated in HCC human tissues and cell lines. Functional assay revealed that ectopic expression of miR-497 or miR-99a in HCC cells resulted in a significant inhibition on tumor growth and invasiveness in vitro and tumor development in vivo via repressing the expression of IGF1R and mTOR. Such inhibitory effect on tumor growth is reversed by application of IGF1 ((IGF1R ligand) or MHY1485 (mTOR agonist) in vitro. Furthermore, we found that simultaneous over-expression of both miR-497 and miR-99a exhibited much stronger inhibitory effects on tumor growth than their individual effect, which is still correlated with significantly stronger repression of IGF1R and mTOR. Overall, our results suggest that miR-497 and miR-99a both function as tumor-suppressive miRNAs by suppressing IGF1R/mTOR signaling pathway. The synergistic actions of these two miRNAs partly correlated with IGF1R and mTOR levels, which may represent new strategies for the molecular treatment of HCC.
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Affiliation(s)
- Henghui Cheng
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.,Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Jin Xue
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.,Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Shouhua Yang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Yaobin Chen
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.,Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Yu Wang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.,Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Yuanli Zhu
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.,Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Xiaoyan Wang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.,Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Dong Kuang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.,Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Qiurong Ruan
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.,Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Yaqi Duan
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.,Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Guoping Wang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.,Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
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MicroRNA Expression Analysis of In Vitro Dedifferentiated Human Pancreatic Islet Cells Reveals the Activation of the Pluripotency-Related MicroRNA Cluster miR-302s. Int J Mol Sci 2018; 19:ijms19041170. [PMID: 29649109 PMCID: PMC5979342 DOI: 10.3390/ijms19041170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 12/12/2022] Open
Abstract
β-cell dedifferentiation has been recently suggested as an additional mechanism contributing to type-1 and to type-2 diabetes pathogenesis. Moreover, several studies demonstrated that in vitro culture of native human pancreatic islets derived from non-diabetic donors resulted in the generation of an undifferentiated cell population. Additional evidence from in vitro human β-cell lineage tracing experiments, demonstrated that dedifferentiated cells derive from β-cells, thus representing a potential in vitro model of β-cell dedifferentiation. Here, we report the microRNA expression profiles analysis of in vitro dedifferentiated islet cells in comparison to mature human native pancreatic islets. We identified 13 microRNAs upregulated and 110 downregulated in islet cells upon in vitro dedifferentiation. Interestingly, among upregulated microRNAs, we observed the activation of microRNA miR-302s cluster, previously defined as pluripotency-associated. Bioinformatic analysis indicated that miR-302s are predicted to target several genes involved in the control of β-cell/epithelial phenotype maintenance; accordingly, such genes were downregulated upon human islet in vitro dedifferentiation. Moreover, we uncovered that cell–cell contacts are needed to maintain low/null expression levels of miR-302. In conclusion, we showed that miR-302 microRNA cluster genes are involved in in vitro dedifferentiation of human pancreatic islet cells and inhibits the expression of multiple genes involved in the maintenance of β-cell mature phenotype.
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Nikolic I, Elsworth B, Dodson E, Wu SZ, Gould CM, Mestdagh P, Marshall GM, Horvath LG, Simpson KJ, Swarbrick A. Discovering cancer vulnerabilities using high-throughput micro-RNA screening. Nucleic Acids Res 2018; 45:12657-12670. [PMID: 29156009 PMCID: PMC5728403 DOI: 10.1093/nar/gkx1072] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 10/19/2017] [Indexed: 12/20/2022] Open
Abstract
Micro-RNAs (miRNAs) are potent regulators of gene expression and cellular phenotype. Each miRNA has the potential to target hundreds of transcripts within the cell thus controlling fundamental cellular processes such as survival and proliferation. Here, we exploit this important feature of miRNA networks to discover vulnerabilities in cancer phenotype, and map miRNA-target relationships across different cancer types. More specifically, we report the results of a functional genomics screen of 1280 miRNA mimics and inhibitors in eight cancer cell lines, and its presentation in a sophisticated interactive data portal. This resource represents the most comprehensive survey of miRNA function in oncology, incorporating breast cancer, prostate cancer and neuroblastoma. A user-friendly web portal couples this experimental data with multiple tools for miRNA target prediction, pathway enrichment analysis and visualization. In addition, the database integrates publicly available gene expression and perturbation data enabling tailored and context-specific analysis of miRNA function in a particular disease. As a proof-of-principle, we use the database and its innovative features to uncover novel determinants of the neuroblastoma malignant phenotype.
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Affiliation(s)
- Iva Nikolic
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW 2010, Australia.,Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Benjamin Elsworth
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW 2010, Australia
| | - Eoin Dodson
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW 2010, Australia
| | - Sunny Z Wu
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW 2010, Australia
| | - Cathryn M Gould
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Pieter Mestdagh
- Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent B-9000, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent B-9000, Belgium
| | - Glenn M Marshall
- Sydney Children's Hospital and Children's Cancer Institute, Sydney, NSW 2750, Australia
| | - Lisa G Horvath
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,Chris O'Brien Lifehouse, Camperdown, NSW 2050, Australia.,University of Sydney, Camperdown, NSW 2050, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alexander Swarbrick
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW 2010, Australia
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Rane JK, Erb HHH, Nappo G, Mann VM, Simms MS, Collins AT, Visakorpi T, Maitland NJ. Inhibition of the glucocorticoid receptor results in an enhanced miR-99a/100-mediated radiation response in stem-like cells from human prostate cancers. Oncotarget 2018; 7:51965-51980. [PMID: 27340920 PMCID: PMC5239528 DOI: 10.18632/oncotarget.10207] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/09/2016] [Indexed: 12/21/2022] Open
Abstract
Radiation therapy is a major primary treatment option for both localized early stage prostate cancer, and for advanced, regionally un-resectable, cancer. However, around 30% of patients still experience biochemical recurrence after radiation therapy within 10 years. Thus, identification of better biomarkers and new targets are urgently required to improve current therapeutic strategies. The miR-99 family has been shown to play an important role in the regulation of the DNA damage response, via targeting of the SWI/SNF chromatin remodeling factors, SMARCA5 and SMARCD1 in cell line models. In the present study, we have demonstrated that low expression of miR-99a and miR-100 is present in cell populations which are relatively radiation insensitive, for example in prostate cancer stem cells and in castration-resistant prostate cancer. Additionally, treatment of cells with the synthetic glucocorticoid, Dexamethasone resulted in decreased miR-99a and 100 expression, suggesting a new mechanism of miR-99a and 100 regulation in androgen-independent prostate cells. Strikingly, treatment of prostate cells with the glucocorticoid receptor inhibitor, Mifepristone was found to sensitize prostate cells to radiation by increasing the levels of miR-99a and miR-100. These results qualify the miR99 family as markers of radiation sensitivity and as potential therapeutic targets to improve efficiency of radiotherapy.
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Affiliation(s)
- Jayant K Rane
- The Cancer Research Unit, Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK.,Leukaemia and Stem Cell Biology Group, Department of Haematological Medicine, King's College London, Rayne Institute, London, SE5 9NU, UK
| | - Holger H H Erb
- The Cancer Research Unit, Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK
| | - Giovanna Nappo
- The Cancer Research Unit, Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK.,Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University, 88100, Catanzaro, Italy
| | - Vincent M Mann
- Hull York Medical School, University of Hull, Hull, East Yorkshire, HU6 7RX, UK.,Department of Urology, Castle Hill Hospital, Cottingham, East Yorkshire, HU16 5JQ, UK
| | - Matthew S Simms
- Hull York Medical School, University of Hull, Hull, East Yorkshire, HU6 7RX, UK.,Department of Urology, Castle Hill Hospital, Cottingham, East Yorkshire, HU16 5JQ, UK
| | - Anne T Collins
- The Cancer Research Unit, Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology - BioMediTech, University of Tampere and Tampere University Hospital, Tampere, 33520 Finland
| | - Norman J Maitland
- The Cancer Research Unit, Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK.,Hull York Medical School, University of Hull, Hull, East Yorkshire, HU6 7RX, UK
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Peñarando J, López-Sánchez LM, Mena R, Guil-Luna S, Conde F, Hernández V, Toledano M, Gudiño V, Raponi M, Billard C, Villar C, Díaz C, Gómez-Barbadillo J, De la Haba-Rodríguez J, Myant K, Aranda E, Rodríguez-Ariza A. A role for endothelial nitric oxide synthase in intestinal stem cell proliferation and mesenchymal colorectal cancer. BMC Biol 2018; 16:3. [PMID: 29329541 PMCID: PMC5795284 DOI: 10.1186/s12915-017-0472-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/14/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Nitric oxide (NO) has been highlighted as an important agent in cancer-related events. Although the inducible nitric oxide synthase (iNOS) isoform has received most attention, recent studies in the literature indicate that the endothelial isoenzyme (eNOS) can also modulate different tumor processes including resistance, angiogenesis, invasion, and metastasis. However, the role of eNOS in cancer stem cell (CSC) biology and mesenchymal tumors is unknown. RESULTS Here, we show that eNOS was significantly upregulated in VilCre ERT2 Apc fl/+ and VilCre ERT2 Apc fl/fl mouse intestinal tissue, with intense immunostaining in hyperproliferative crypts. Similarly, the more invasive VilCre ERT2 Apc fl/+ Pten fl/+ mouse model showed an overexpression of eNOS in intestinal tumors whereas this isoform was not expressed in normal tissue. However, none of the three models showed iNOS expression. Notably, when 40 human colorectal tumors were classified into different clinically relevant molecular subtypes, high eNOS expression was found in the poor relapse-free and overall survival mesenchymal subtype, whereas iNOS was absent. Furthermore, Apc fl/fl organoids overexpressed eNOS compared with wild-type organoids and NO depletion with the scavenger carboxy-PTIO (c-PTIO) decreased the proliferation and the expression of stem-cell markers, such as Lgr5, Troy, Vav3, and Slc14a1, in these intestinal organoids. Moreover, specific NO depletion also decreased the expression of CSC-related proteins in human colorectal cancer cells such as β-catenin and Bmi1, impairing the CSC phenotype. To rule out the contribution of iNOS in this effect, we established an iNOS-knockdown colorectal cancer cell line. NO-depleted cells showed a decreased capacity to form tumors and c-PTIO treatment in vivo showed an antitumoral effect in a xenograft mouse model. CONCLUSION Our data support that eNOS upregulation occurs after Apc loss, emerging as an unexpected potential new target in poor-prognosis mesenchymal colorectal tumors, where NO scavenging could represent an interesting therapeutic alternative to targeting the CSC subpopulation.
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Affiliation(s)
- Jon Peñarando
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Avda Menéndez Pidal s/n, Córdoba, Spain
| | - Laura M López-Sánchez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Avda Menéndez Pidal s/n, Córdoba, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Rafael Mena
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Avda Menéndez Pidal s/n, Córdoba, Spain
| | - Silvia Guil-Luna
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Avda Menéndez Pidal s/n, Córdoba, Spain
| | - Francisco Conde
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Avda Menéndez Pidal s/n, Córdoba, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Vanessa Hernández
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Avda Menéndez Pidal s/n, Córdoba, Spain
| | - Marta Toledano
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Avda Menéndez Pidal s/n, Córdoba, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Victoria Gudiño
- The Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Michela Raponi
- The Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Caroline Billard
- The Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Carlos Villar
- Unidad de Gestión Clínica de Anatomía Patológica, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - César Díaz
- Unidad de Gestión Clínica de Cirugía General y del Aparato Digestivo, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - José Gómez-Barbadillo
- Unidad de Gestión Clínica de Cirugía General y del Aparato Digestivo, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Juan De la Haba-Rodríguez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Avda Menéndez Pidal s/n, Córdoba, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Unidad de Gestión Clínica de Oncología Médica, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Kevin Myant
- The Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Enrique Aranda
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Avda Menéndez Pidal s/n, Córdoba, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Unidad de Gestión Clínica de Oncología Médica, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Antonio Rodríguez-Ariza
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Avda Menéndez Pidal s/n, Córdoba, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
- Unidad de Gestión Clínica de Oncología Médica, Hospital Universitario Reina Sofía, Córdoba, Spain.
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Sharma B, Preet Kaur R, Raut S, Munshi A. BRCA1 mutation spectrum, functions, and therapeutic strategies: The story so far. Curr Probl Cancer 2018; 42:189-207. [PMID: 29452958 DOI: 10.1016/j.currproblcancer.2018.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/19/2017] [Accepted: 01/04/2018] [Indexed: 02/07/2023]
Abstract
BRCA1 gene mutations account for about 25-28% of hereditary Breast Cancer as BRCA1 is included in the category of high penetrance genes. Except for few commonmutations, there is a heterogenous spectrum of BRCA1 mutations in various ethnic groups. 185AGdel and 5382ins Care the most common BRCA1 alterations (founder mutations) which have been identified in most of the population. This review has been compiled with an aim to consolidate the information on genetic variants reported in BRCA1 found in various ethnic groups, their functional implications if known; involvement of BRCA1 in various cellular pathways/processes and potential BRCA1 targeted therapies. The pathological variations of BRCA1 vary among different ethical groups. A systematic search in PubMed and Google scholar for the literature on BRCA1 gene was carried out to figure out structure and function of BRCA1 gene. BRCA1 is a large protein having 1863 amino acids with multiple functional domains and interacts with multiple proteins to carry out various crucial cellular processes. BRCA1 plays a major role in maintaining genome integrity, transcription regulation, chromatin remodeling, cell cycle checkpoint control, DNA damage repair, chromosomal segregation, and apoptosis. Studies investigating the phenotypic response of mutant BRCA1 protein and comparing it to wildtype BRCA1 protein are clinically important as they are involved in homologous recombination and other repair mechanisms. These studies may help in developing more targetted therapies, detecting novel interacting partners, identification of new signaling pathways that BRCA1 is a part of or downstream target genes that BRCA1 affects.
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Affiliation(s)
- Babita Sharma
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
| | - Raman Preet Kaur
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
| | - Sonali Raut
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India.
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Genome-wide Profiling of Urinary Extracellular Vesicle microRNAs Associated With Diabetic Nephropathy in Type 1 Diabetes. Kidney Int Rep 2017; 3:555-572. [PMID: 29854963 PMCID: PMC5976846 DOI: 10.1016/j.ekir.2017.11.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/15/2017] [Accepted: 11/27/2017] [Indexed: 01/01/2023] Open
Abstract
Introduction Diabetic nephropathy (DN) is a form of progressive kidney disease that often leads to end-stage renal disease (ESRD). It is initiated by microvascular complications due to diabetes. Although microalbuminuria (MA) is the earliest clinical indication of DN among patients with type 1 diabetes (T1D), it lacks the sensitivity and specificity to detect the early onset of DN. Recently, microRNAs (miRNAs) have emerged as critical regulators in diabetes as well as various forms of kidney disease, including renal fibrosis, acute kidney injury, and progressive kidney disease. Additionally, circulating extracellular miRNAs, especially miRNAs packaged in extracellular vesicles (EVs), have garnered significant attention as potential noninvasive biomarkers for various diseases and health conditions. Methods As part of the University of Pittsburgh Epidemiology of Diabetes Complications (EDC) study, urine was collected from individuals with T1D with various grades of DN or MA (normal, overt, intermittent, and persistent) over a decade at prespecified intervals. We isolated EVs from urine and analyzed the small-RNA using NextGen sequencing. Results We identified a set of miRNAs that are enriched in urinary EVs compared with EV-depleted samples, and identified a number of miRNAs showing concentration changes associated with DN occurrence, MA status, and other variables, such as hemoglobin A1c levels. Conclusion Many of the miRNAs associated with DN occurrence or MA status directly target pathways associated with renal fibrosis (including transforming growth factor-β and phosphatase and tensin homolog), which is one of the major contributors to the pathology of DN. These miRNAs are potential biomarkers for DN and MA.
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Sajja VSSS, Jablonska A, Haughey N, Bulte JWM, Stevens RD, Long JB, Walczak P, Janowski M. Sphingolipids and microRNA Changes in Blood following Blast Traumatic Brain Injury: An Exploratory Study. J Neurotrauma 2017; 35:353-361. [PMID: 29020847 DOI: 10.1089/neu.2017.5009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
At present, accurate and reliable biomarkers to ascertain the presence, severity, or prognosis of blast traumatic brain injury (bTBI) are lacking. There is an urgent need to establish accurate and reliable biomarkers capable of mbTBI detection. Currently, there are no studies that identify changes in miRNA and lipids at varied severities of bTBI. Various biological components such as lipids, circulating mRNA, and miRNA, could potentially be detected using advanced techniques such as next-generation sequencing and mass spectroscopy. Therefore, plasma analysis is an attractive approach with which to diagnose and treat brain injuries. Subacute changes in plasma microRNA (miRNA) and lipid composition for sphingolipids were evaluated in a murine model of mild-to-moderate bTBI using next-generation sequencing and mass spectroscopy respectively. Animals were exposed at 17, 17 × 3, and 20 psi blast intensities using a calibrated blast simulator. Plasma lipid profiling demonstrated decreased C18 fatty acid chains of sphingomyelins and increased ceramide levels when compared with controls. Plasma levels of brain-enriched miRNA, miR-127 were increased in all groups while let-7a, b, and g were reduced in the 17 × 3 and 20 psi groups, but let 7d was increased in the 17 psi group. The majority of the miRs and lipids are highly conserved across different species, making them attractive to explore and potentially employ as diagnostic markers. It is tempting to speculate that sphingolipids, miR-128, and the let-7 family could predict mTBI, while a combination of miR-484, miR-122, miR-148a, miR-130a, and miR-223 could be used to predict the overall status of injury following blast injury.
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Affiliation(s)
- Venkata Siva Sai Sujith Sajja
- 1 Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine , Baltimore, Maryland.,2 Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, Johns Hopkins University , Baltimore, Maryland.,3 Johns Hopkins Military & Veterans Health Institute , Baltimore, Maryland.,4 Blast-Induced Neurotrauma Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research , Silver Spring, Maryland
| | - Anna Jablonska
- 1 Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine , Baltimore, Maryland.,2 Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, Johns Hopkins University , Baltimore, Maryland
| | - Norman Haughey
- 5 Department of Neurology and Neurosurgery, Richard T. Johnson Division of Neuroimmunology and Neurological Infections, Johns Hopkins University School of Medicine , Baltimore, Maryland.,6 Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Jeff W M Bulte
- 1 Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine , Baltimore, Maryland.,2 Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, Johns Hopkins University , Baltimore, Maryland
| | - Robert D Stevens
- 1 Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine , Baltimore, Maryland.,2 Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, Johns Hopkins University , Baltimore, Maryland.,5 Department of Neurology and Neurosurgery, Richard T. Johnson Division of Neuroimmunology and Neurological Infections, Johns Hopkins University School of Medicine , Baltimore, Maryland.,7 Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Joseph B Long
- 4 Blast-Induced Neurotrauma Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research , Silver Spring, Maryland
| | - Piotr Walczak
- 1 Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine , Baltimore, Maryland.,2 Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, Johns Hopkins University , Baltimore, Maryland.,8 Department of Radiology, Faculty of Medical Sciences, University of Warmia and Mazury , Olsztyn, Poland
| | - Miroslaw Janowski
- 1 Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine , Baltimore, Maryland.,2 Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, Johns Hopkins University , Baltimore, Maryland.,9 NeuroRepair Department, Mossakowski Medical Research Centre , Polish Academy of Sciences, Warsaw, Poland
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Luo J, Ding P, Liang C, Cao B, Chen X. Collective Prediction of Disease-Associated miRNAs Based on Transduction Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:1468-1475. [PMID: 27542179 DOI: 10.1109/tcbb.2016.2599866] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The discovery of human disease-related miRNA is a challenging problem for complex disease biology research. For existing computational methods, it is difficult to achieve excellent performance with sparse known miRNA-disease association verified by biological experiment. Here, we develop CPTL, a Collective Prediction based on Transduction Learning, to systematically prioritize miRNAs related to disease. By combining disease similarity, miRNA similarity with known miRNA-disease association, we construct a miRNA-disease network for predicting miRNA-disease association. Then, CPTL calculates relevance score and updates the network structure iteratively, until a convergence criterion is reached. The relevance score of node including miRNA and disease is calculated by the use of transduction learning based on its neighbors. The network structure is updated using relevance score, which increases the weight of important links. To show the effectiveness of our method, we compared CPTL with existing methods based on HMDD datasets. Experimental results indicate that CPTL outperforms existing approaches in terms of AUC, precision, recall, and F1-score. Moreover, experiments performed with different number of iterations verify that CPTL has good convergence. Besides, it is analyzed that the varying of weighted parameters affect predicted results. Case study on breast cancer has further confirmed the identification ability of CPTL.
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Iskandar AR, Titz B, Sewer A, Leroy P, Schneider T, Zanetti F, Mathis C, Elamin A, Frentzel S, Schlage WK, Martin F, Ivanov NV, Peitsch MC, Hoeng J. Systems toxicology meta-analysis of in vitro assessment studies: biological impact of a candidate modified-risk tobacco product aerosol compared with cigarette smoke on human organotypic cultures of the aerodigestive tract. Toxicol Res (Camb) 2017; 6:631-653. [PMID: 30090531 PMCID: PMC6062142 DOI: 10.1039/c7tx00047b] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/26/2017] [Indexed: 12/22/2022] Open
Abstract
Systems biology combines comprehensive molecular analyses with quantitative modeling to understand the characteristics of a biological system as a whole. Leveraging a similar approach, systems toxicology aims to decipher complex biological responses following exposures. This work reports a systems toxicology meta-analysis in the context of in vitro assessment of a candidate modified-risk tobacco product (MRTP) using three human organotypic cultures of the aerodigestive tract (buccal, bronchial, and nasal epithelia). Complementing a series of functional measures, a causal network enrichment analysis of transcriptomic data was used to compare quantitatively the biological impact of aerosol from the Tobacco Heating System (THS) 2.2, a candidate MRTP, with 3R4F cigarette smoke (CS) at similar nicotine concentrations. Lower toxicity was observed in all cultures following exposure to THS2.2 aerosol compared with 3R4F CS. Because of their morphological differences, a smaller exposure impact was observed in the buccal (stratified epithelium) compared with the bronchial and nasal (pseudostratified epithelium). However, the causal network enrichment approach supported a similar mechanistic impact of CS across the three cultures, including the impact on xenobiotic, oxidative stress, and inflammatory responses. At comparable nicotine concentrations, THS2.2 aerosol elicited reduced and more transient effects on these processes. To demonstrate the benefits of additional data modalities, we employed a newly established targeted mass-spectrometry marker panel to further confirm the reduced cellular stress responses elicited by THS2.2 aerosol compared with 3R4F CS in the nasal culture. Overall, this work demonstrates the applicability and robustness of the systems toxicology approach for in vitro inhalation toxicity assessment.
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Affiliation(s)
- A R Iskandar
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - B Titz
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - A Sewer
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - P Leroy
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - T Schneider
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - F Zanetti
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - C Mathis
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - A Elamin
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - S Frentzel
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - W K Schlage
- Biology consultant , Max-Baermann-Str. 21 , 51429 Bergisch Gladbach , Germany
| | - F Martin
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - N V Ivanov
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - M C Peitsch
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - J Hoeng
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
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Maitrias P, Metzinger-Le Meuth V, Nader J, Reix T, Caus T, Metzinger L. The Involvement of miRNA in Carotid-Related Stroke. Arterioscler Thromb Vasc Biol 2017; 37:1608-1617. [PMID: 28775076 DOI: 10.1161/atvbaha.117.309233] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/19/2017] [Indexed: 12/18/2022]
Abstract
Cardiovascular disease is the leading cause of morbidity and mortality in developed countries. Stroke is associated with a marked disability burden and has a major economic impact; this is especially true for carotid artery stroke. Major advances in primary and secondary prevention during the last few decades have helped to tackle this public health problem. However, better knowledge of the physiopathology of stroke and its underlying genetic mechanisms is needed to improve diagnosis and therapy. miRNAs are an important, recently identified class of post-transcriptional regulators of gene expression and are known to be involved in cerebrovascular disease. These endogenous, small, noncoding RNAs may have applications as noninvasive biomarkers and therapeutic tools in practice. Here, we review the involvement of several miRNAs in cell-based and whole-animal models of stroke, with a focus on human miRNA profiling studies of carotid artery stroke. Lastly, we describe the miRNAs' potential role as a biomarker of stroke.
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Affiliation(s)
- Pierre Maitrias
- From the Department of Cardiovascular Surgery, Amiens University Hospital, France (P.M., J.N., T.R., T.C.); University Paris 13, Sorbonne Paris Cite, UFR SMBH, Bobigny, France (V.M.-L.M.); INSERM Unit-1088, Pathophysiological Mechanisms and Consequences of Cardiovascular Calcifications, Centre Universitaire de Recherche en Santé, University Picardie Jules Verne, Amiens, France (P.M., V.M.-L.M., J.N., T.C., L.M.); Medicine College, Jules Verne University of Picardie, Amiens, France (P.M., T.R.); and Department of Biochemistry, Center of Human Biology, Amiens University Hospital, France (L.M.).
| | - Valérie Metzinger-Le Meuth
- From the Department of Cardiovascular Surgery, Amiens University Hospital, France (P.M., J.N., T.R., T.C.); University Paris 13, Sorbonne Paris Cite, UFR SMBH, Bobigny, France (V.M.-L.M.); INSERM Unit-1088, Pathophysiological Mechanisms and Consequences of Cardiovascular Calcifications, Centre Universitaire de Recherche en Santé, University Picardie Jules Verne, Amiens, France (P.M., V.M.-L.M., J.N., T.C., L.M.); Medicine College, Jules Verne University of Picardie, Amiens, France (P.M., T.R.); and Department of Biochemistry, Center of Human Biology, Amiens University Hospital, France (L.M.)
| | - Joseph Nader
- From the Department of Cardiovascular Surgery, Amiens University Hospital, France (P.M., J.N., T.R., T.C.); University Paris 13, Sorbonne Paris Cite, UFR SMBH, Bobigny, France (V.M.-L.M.); INSERM Unit-1088, Pathophysiological Mechanisms and Consequences of Cardiovascular Calcifications, Centre Universitaire de Recherche en Santé, University Picardie Jules Verne, Amiens, France (P.M., V.M.-L.M., J.N., T.C., L.M.); Medicine College, Jules Verne University of Picardie, Amiens, France (P.M., T.R.); and Department of Biochemistry, Center of Human Biology, Amiens University Hospital, France (L.M.)
| | - Thierry Reix
- From the Department of Cardiovascular Surgery, Amiens University Hospital, France (P.M., J.N., T.R., T.C.); University Paris 13, Sorbonne Paris Cite, UFR SMBH, Bobigny, France (V.M.-L.M.); INSERM Unit-1088, Pathophysiological Mechanisms and Consequences of Cardiovascular Calcifications, Centre Universitaire de Recherche en Santé, University Picardie Jules Verne, Amiens, France (P.M., V.M.-L.M., J.N., T.C., L.M.); Medicine College, Jules Verne University of Picardie, Amiens, France (P.M., T.R.); and Department of Biochemistry, Center of Human Biology, Amiens University Hospital, France (L.M.)
| | - Thierry Caus
- From the Department of Cardiovascular Surgery, Amiens University Hospital, France (P.M., J.N., T.R., T.C.); University Paris 13, Sorbonne Paris Cite, UFR SMBH, Bobigny, France (V.M.-L.M.); INSERM Unit-1088, Pathophysiological Mechanisms and Consequences of Cardiovascular Calcifications, Centre Universitaire de Recherche en Santé, University Picardie Jules Verne, Amiens, France (P.M., V.M.-L.M., J.N., T.C., L.M.); Medicine College, Jules Verne University of Picardie, Amiens, France (P.M., T.R.); and Department of Biochemistry, Center of Human Biology, Amiens University Hospital, France (L.M.)
| | - Laurent Metzinger
- From the Department of Cardiovascular Surgery, Amiens University Hospital, France (P.M., J.N., T.R., T.C.); University Paris 13, Sorbonne Paris Cite, UFR SMBH, Bobigny, France (V.M.-L.M.); INSERM Unit-1088, Pathophysiological Mechanisms and Consequences of Cardiovascular Calcifications, Centre Universitaire de Recherche en Santé, University Picardie Jules Verne, Amiens, France (P.M., V.M.-L.M., J.N., T.C., L.M.); Medicine College, Jules Verne University of Picardie, Amiens, France (P.M., T.R.); and Department of Biochemistry, Center of Human Biology, Amiens University Hospital, France (L.M.)
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Song N, Wang X, Gui L, Raza SHA, Luoreng Z, Zan L. MicroRNA-214 regulates immunity-related genes in bovine mammary epithelial cells by targeting NFATc3 and TRAF3. Mol Cell Probes 2017. [PMID: 28627449 DOI: 10.1016/j.mcp.2017.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In human, microRNA-214 (miR-214) plays crucial roles in mechanisms of immunity. However, the potential importance of miR-214 in immune mechanisms in dairy cows has not been investigated. In this study, we assessed potential immunity-related functions of miR-214 in human 293A cells and in bovine mammary epithelial cells (BMECs). We found that NFATc3 and TRAF3 could be targeted by miR-214 in both 293A cells and BMECs. We also found that miR-214 indirectly inhibited the expression of MAP3K14, TBK1 and inflammatory cytokines IL-6 and IL-1β. Taken together, our data revealed miR-214 regulated immunity-related genes by targeting NFATc3 and TRAF3, which provides insight into the molecular basis of immunity.
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Affiliation(s)
- Ning Song
- College of Animal Science and Technology, National Beef Cattle Improvement Center, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Xingping Wang
- College of Animal Science and Technology, National Beef Cattle Improvement Center, Northwest A&F University, Yangling Shaanxi 712100, China; Key Laboratory of Zoology in Hunan Higher Education, College of Life Science, Hunan University of Arts and Science, Changde Hunan 415000, China
| | - Linsheng Gui
- College of Animal Science and Technology, National Beef Cattle Improvement Center, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, National Beef Cattle Improvement Center, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Zhuoma Luoreng
- College of Animal Science and Technology, National Beef Cattle Improvement Center, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Linsen Zan
- College of Animal Science and Technology, National Beef Cattle Improvement Center, Northwest A&F University, Yangling Shaanxi 712100, China.
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Gola JM, Strzałka-Mrozik B, Kruszniewska-Rajs C, Adamska J, Gagoś M, Mazurek U. Differential expression of microRNAs and their predicted targets in renal cells exposed to amphotericin B and its complex with copper (II) ions. Toxicol Mech Methods 2017; 27:537-543. [PMID: 28534445 DOI: 10.1080/15376516.2017.1333554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
MicroRNAs (miRNAs) have been reported to regulate essential biological processes, and their expression was shown to be affected by pathological processes and drug-induced toxicity. Amphotericin B (AmB) can cause liver and kidney injury, but a recently developed complex of AmB with copper (II) ions (AmB-Cu2+) exhibits a lower toxicity to human renal cells while retaining a high antifungal activity. The aim of our study was to assess AmB-Cu2+-induced changes in the miRNA profile of renal cells and examine which biological processes are significantly affected by AmB-Cu2+. We also aimed to predict whether differentially expressed miRNAs would influence observed changes in the mRNA profile. miRNA and mRNA profiles in normal human renal proximal tubule epithelial cells (RPTEC) treated with AmB-Cu2+ or AmB were appointed with the use of microarray technology. For differentially expressed mRNAs, the PANTHER overrepresentation binomial test was performed. miRNA target interactions (MTIs) were predicted using the miRTar tool. The mRNA profile was much more strongly affected than the miRNA profile, in both AmB-Cu2+- and AmB-treated cells. AmB-Cu2+ influenced both the miRNA and mRNA profiles much more strongly than AmB. The most affected biological processes were intracellular signal transduction (AmB-Cu2+) and signal transduction (AmB). Only a few interactions between differentiating miRNAs and mRNAs were found. Changes in the profiles of genes involved in signal transduction and intracellular signal transduction may not result from interactions with differentially expressed miRNAs. Changes in the miRNA profile suggest the possible influence of tested drugs on the regulation of fibrosis via a miRNA-dependent mechanism.
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Affiliation(s)
- Joanna Magdalena Gola
- a Department of Molecular Biology , School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia , Sosnowiec , Poland
| | - Barbara Strzałka-Mrozik
- a Department of Molecular Biology , School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia , Sosnowiec , Poland
| | - Celina Kruszniewska-Rajs
- a Department of Molecular Biology , School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia , Sosnowiec , Poland
| | - Jolanta Adamska
- a Department of Molecular Biology , School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia , Sosnowiec , Poland
| | - Mariusz Gagoś
- b Department of Cell Biology , Institute of Biology and Biotechnology, Maria Curie-Skłodowska University , Lublin , Poland
| | - Urszula Mazurek
- a Department of Molecular Biology , School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia , Sosnowiec , Poland
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Bahrami A, Miraie-Ashtiani SR, Sadeghi M, Najafi A. miRNA-mRNA network involved in folliculogenesis interactome: systems biology approach. Reproduction 2017; 154:51-65. [PMID: 28450315 DOI: 10.1530/rep-17-0049] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/06/2017] [Accepted: 04/24/2017] [Indexed: 01/01/2023]
Abstract
At later phases of folliculogenesis, the mammalian ovarian follicle contains layers of granulosa cells surrounding an antral cavity. To better understand the molecular basis of follicular growth and granulosa cell maturation, we study transcriptome profiling of granulosa cells from small (<5 mm) and large (>10 mm) bovine follicles using simultaneous method of Affymetrix microarrays (24,128 probe sets) and RNA-Seq data sets. This study proposes a computational method to discover the functional miRNA-mRNA regulatory modules, that is, groups of miRNAs and their target mRNAs that are believed to take part cooperatively in post-transcriptional gene regulation under specific conditions. The reconstructed network was named Integrated miRNA-mRNA Bipartite Network. 277 genes and 6 key modules were disclosed through clustering for mRNA master list. The 66 genes are among the genes that belong to at least two modules. All these genes, being involved in at least one of the phenomena, namely cell survival, proliferation, metastasis and apoptosis, have an overexpression pattern (P < 0.01). For miRNA master list, a total of 172 sequences were differentially expressed (P < 0.01) between dominant (large) and each of subordinate (small) follicles. Within the follicle, these miRNAs were predominantly expressed in mural granulosa cells. Finally, predicted and validated targets of these miRNAs enriched in dominant (large) follicles were identified, which are mapped to signaling pathways involved in follicular cell proliferation, steroidogenesis, PI3K/AKT/mTOR and Ras/Raf/MEK/ERK. The identification of miRNAs and their target mRNAs and the construction of their regulatory networks may give new insights into biological procedures.
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Affiliation(s)
- Abolfazl Bahrami
- Department of Animal ScienceUniversity College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Seyed Reza Miraie-Ashtiani
- Department of Animal ScienceUniversity College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mostafa Sadeghi
- Department of Animal ScienceUniversity College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ali Najafi
- Molecular Biology Research CenterBaqiyatallah University of Medical Sciences, Tehran, Iran
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Wu N, Zhu Q, Chen B, Gao J, Xu Z, Li D. High-throughput sequencing of pituitary and hypothalamic microRNA transcriptome associated with high rate of egg production. BMC Genomics 2017; 18:255. [PMID: 28335741 PMCID: PMC5364632 DOI: 10.1186/s12864-017-3644-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/18/2017] [Indexed: 01/21/2023] Open
Abstract
Background MicroRNAs exist widely in viruses, plants and animals. As endogenous small non-coding RNAs, miRNAs regulate a variety of biological processes. Tissue miRNA expression studies have discovered numerous functions for miRNAs in various tissues of chicken, but the regulation of miRNAs in chicken pituitary and hypothalamic development related to high and low egg-laying performance has remained unclear. Results In this study, using high-throughput sequencing technology, we sequenced two tissues (pituitary and hypothalamus) in 3 high- and 3 low-rate egg production Luhua chickens at the age of 300 days. By comparing low- and high-rate egg production chickens, 46 known miRNAs and 27 novel miRNAs were identified as differentially expressed (P < 0.05). Six differentially expressed known miRNAs, which are expressed in both tissues, were used in RT-qPCR validation and SNP detection. Among them, seven SNPs in two miRNA precursors (gga-miR-1684a and gga-miR-1434) were found that might enhance or reduce the production of the mature miRNAs. In addition, 124 and 30 reciprocally expressed miRNA-target pairs were identified by RNA-seq in pituitary and hypothalamic tissues, respectively and randomly selected candidate miRNA and miRNA-target pairs were validated by RT-qPCR in Jiuyuan black fowl. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation illustrated that a large number of egg laying-related pathways were enriched in the high-rate egg production chickens, including ovarian steroidogenesis and steroid hormone biosynthesis. Conclusions These differentially expressed miRNAs and their predicted target genes, especially identified reciprocally expressed miRNA-target pairs, advance the study of miRNA function and egg production associated miRNA identification. The analysis of the miRNA-related SNPs and their effects provided insights into the effects of SNPs on miRNA biogenesis and function. The data generated in this study will further our understanding of miRNA regulation mechanisms in the chicken egg-laying process. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3644-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nan Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Qing Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Binlong Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Jian Gao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Zhongxian Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000.
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47
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Wu N, Gaur U, Zhu Q, Chen B, Xu Z, Zhao X, Yang M, Li D. Expressed microRNA associated with high rate of egg production in chicken ovarian follicles. Anim Genet 2016; 48:205-216. [PMID: 27781291 DOI: 10.1111/age.12516] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2016] [Indexed: 01/28/2023]
Abstract
MicroRNA (miRNA) is a highly conserved class of small noncoding RNA about 19-24 nucleotides in length that function in a specific manner to post-transcriptionally regulate gene expression in organisms. Tissue miRNA expression studies have discovered a myriad of functions for miRNAs in various aspects, but a role for miRNAs in chicken ovarian tissue at 300 days of age has not hitherto been reported. In this study, we performed the first miRNA analysis of ovarian tissues in chickens with low and high rates of egg production using high-throughput sequencing. By comparing low rate of egg production chickens with high rate of egg production chickens, 17 significantly differentially expressed miRNAs were found (P < 0.05), including 11 known and six novel miRNAs. We found that all 11 known miRNAs were involved mainly in pathways of reproduction regulation, such as steroid hormone biosynthesis and dopaminergic synapse. Additionally, expression profiling of six randomly selected differentially regulated miRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR). Some miRNAs, such as gga-miR-34b, gga-miR-34c and gga-miR-216b, were reported to regulate processes such as proliferation, cell cycle, apoptosis and metastasis and were expressed differentially in ovaries of chickens with high rates of egg production, suggesting that these miRNAs have an important role in ovary development and reproductive management of chicken. Furthermore, we uncovered that a significantly up-regulated miRNA-gga-miR-200a-3p-is ubiquitous in reproduction-regulation-related pathways. This miRNA may play a special central role in the reproductive management of chicken, and needs to be further studied for confirmation.
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Affiliation(s)
- N Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - U Gaur
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - Q Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - B Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - Z Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - X Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - M Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - D Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
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miRNA expression patterns in normal breast tissue and invasive breast cancers of BRCA1 and BRCA2 germ-line mutation carriers. Oncotarget 2016; 6:32115-37. [PMID: 26378051 PMCID: PMC4741663 DOI: 10.18632/oncotarget.5617] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/13/2015] [Indexed: 12/11/2022] Open
Abstract
miRNA deregulation has been found to promote carcinogenesis. Little is known about miRNA deregulation in hereditary breast tumors as no miRNA expression profiling studies have been performed in normal breast tissue of BRCA1 and BRCA2 mutation carriers. miRNA profiles of 17 BRCA1- and 9 BRCA2-associated breast carcinomas were analyzed using microarrays. Normal breast tissues from BRCA1 and BRCA2 mutation carriers (both n = 5) and non-mutation carriers (n = 10) were also included. Candidate miRNAs were validated by qRT-PCR. Breast carcinomas showed extensive miRNA alteration compared to normal breast tissues in BRCA1 and BRCA2 mutation carriers. Moreover, normal breast tissue from BRCA1 mutation carriers already showed miRNA alterations compared to non-mutation carriers. Chromosomal distribution analysis showed several hotspots containing down- or up-regulated miRNAs. Pathway analysis yielded many similarities between the BRCA1 and BRCA2 axes with miRNAs involved in cell cycle regulation, proliferation and apoptosis. Lesser known pathways were also affected, including cellular movement and protein trafficking. This study provides a comprehensive insight into the potential role of miRNA deregulation in BRCA1/2-associated breast carcinogenesis. The observed extensive miRNA deregulation is likely the result of genome-wide effects of chromosomal instability caused by impaired BRCA1 or BRCA2 function. This study's results also suggest the existence of common pathways driving breast carcinogenesis in both BRCA1 and BRCA2 germ-line mutation carriers.
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Moustakas A, Heldin CH. Mechanisms of TGFβ-Induced Epithelial-Mesenchymal Transition. J Clin Med 2016; 5:jcm5070063. [PMID: 27367735 PMCID: PMC4961994 DOI: 10.3390/jcm5070063] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 02/07/2023] Open
Abstract
Transitory phenotypic changes such as the epithelial–mesenchymal transition (EMT) help embryonic cells to generate migratory descendants that populate new sites and establish the distinct tissues in the developing embryo. The mesenchymal descendants of diverse epithelia also participate in the wound healing response of adult tissues, and facilitate the progression of cancer. EMT can be induced by several extracellular cues in the microenvironment of a given epithelial tissue. One such cue, transforming growth factor β (TGFβ), prominently induces EMT via a group of specific transcription factors. The potency of TGFβ is partly based on its ability to perform two parallel molecular functions, i.e. to induce the expression of growth factors, cytokines and chemokines, which sequentially and in a complementary manner help to establish and maintain the EMT, and to mediate signaling crosstalk with other developmental signaling pathways, thus promoting changes in cell differentiation. The molecules that are activated by TGFβ signaling or act as cooperating partners of this pathway are impossible to exhaust within a single coherent and contemporary report. Here, we present selected examples to illustrate the key principles of the circuits that control EMT under the influence of TGFβ.
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Affiliation(s)
- Aristidis Moustakas
- Ludwig Cancer Research, Science for Life Laboratory, Uppsala University, Box 595, SE 751 24 Uppsala, Sweden.
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Box 582, SE 751 23 Uppsala, Sweden.
| | - Carl-Henrik Heldin
- Ludwig Cancer Research, Science for Life Laboratory, Uppsala University, Box 595, SE 751 24 Uppsala, Sweden.
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Chen W, Zhou S, Mao L, Zhang H, Sun D, Zhang J, Li JI, Tang JH. Crosstalk between TGF-β signaling and miRNAs in breast cancer metastasis. Tumour Biol 2016; 37:10011-9. [DOI: 10.1007/s13277-016-5060-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 05/01/2016] [Indexed: 12/12/2022] Open
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