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Gu J, Li Y, Tian Y, Zhang Y, Cheng Y, Tang Y. Noncanonical functions of microRNAs in the nucleus. Acta Biochim Biophys Sin (Shanghai) 2024; 56:151-161. [PMID: 38167929 PMCID: PMC10984876 DOI: 10.3724/abbs.2023268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/03/2023] [Indexed: 01/05/2024] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs (ncRNAs) that play their roles in the regulation of physiological and pathological processes. Originally, it was assumed that miRNAs only modulate gene expression posttranscriptionally in the cytoplasm by inducing target mRNA degradation. However, with further research, evidence shows that mature miRNAs also exist in the cell nucleus, where they can impact gene transcription and ncRNA maturation in several ways. This review provides an overview of novel models of nuclear miRNA functions. Some of the models remain to be verified by experimental evidence, and more details of the miRNA regulation network remain to be discovered in the future.
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Affiliation(s)
- Jiayi Gu
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Yuanan Li
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Youtong Tian
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Yehao Zhang
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Yongjun Cheng
- Department of Rheumatologythe First People’s Hospital of WenlingWenling317500China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology/Department of RheumatologyRenji HospitalShanghai Jiao Tong University School of MedicineShanghai200001China
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteRenji HospitalShanghai200031China
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2
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Fashina IA, McCoy CE, Furney SJ. In silico prioritisation of microRNA-associated common variants in multiple sclerosis. Hum Genomics 2023; 17:31. [PMID: 36991503 PMCID: PMC10061723 DOI: 10.1186/s40246-023-00478-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have highlighted over 200 autosomal variants associated with multiple sclerosis (MS). However, variants in non-coding regions such as those encoding microRNAs have not been explored thoroughly, despite strong evidence of microRNA dysregulation in MS patients and model organisms. This study explores the effect of microRNA-associated variants in MS, through the largest publicly available GWAS, which involved 47,429 MS cases and 68,374 controls. METHODS We identified SNPs within the coordinates of microRNAs, ± 5-kb microRNA flanking regions and predicted 3'UTR target-binding sites using miRBase v22, TargetScan 7.0 RNA22 v2.0 and dbSNP v151. We established the subset of microRNA-associated SNPs which were tested in the summary statistics of the largest MS GWAS by intersecting these datasets. Next, we prioritised those microRNA-associated SNPs which are among known MS susceptibility SNPs, are in strong linkage disequilibrium with the former or meet a microRNA-specific Bonferroni-corrected threshold. Finally, we predicted the effects of those prioritised SNPs on their microRNAs and 3'UTR target-binding sites using TargetScan v7.0, miRVaS and ADmiRE. RESULTS We have identified 30 candidate microRNA-associated variants which meet at least one of our prioritisation criteria. Among these, we highlighted one microRNA variant rs1414273 (MIR548AC) and four 3'UTR microRNA-binding site variants within SLC2A4RG (rs6742), CD27 (rs1059501), MMEL1 (rs881640) and BCL2L13 (rs2587100). We determined changes to the predicted microRNA stability and binding site recognition of these microRNA and target sites. CONCLUSIONS We have systematically examined the functional, structural and regulatory effects of candidate MS variants among microRNAs and 3'UTR targets. This analysis allowed us to identify candidate microRNA-associated MS SNPs and highlights the value of prioritising non-coding RNA variation in GWAS. These candidate SNPs could influence microRNA regulation in MS patients. Our study is the first thorough investigation of both microRNA and 3'UTR target-binding site variation in multiple sclerosis using GWAS summary statistics.
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Affiliation(s)
- Ifeolutembi A. Fashina
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- SFI Centre for Research Training in Genomics Data Sciences, University of Galway, H91 TK33 Galway, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Claire E. McCoy
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Simon J. Furney
- Genomic Oncology Research Group, Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
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3
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Luo M, Li S, Pang Y, Yao L, Ma R, Huang HY, Huang HD, Lee TY. Extraction of microRNA-target interaction sentences from biomedical literature by deep learning approach. Brief Bioinform 2023; 24:6847797. [PMID: 36440972 DOI: 10.1093/bib/bbac497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/16/2022] [Accepted: 10/19/2022] [Indexed: 11/29/2022] Open
Abstract
MicroRNA (miRNA)-target interaction (MTI) plays a substantial role in various cell activities, molecular regulations and physiological processes. Published biomedical literature is the carrier of high-confidence MTI knowledge. However, digging out this knowledge in an efficient manner from large-scale published articles remains challenging. To address this issue, we were motivated to construct a deep learning-based model. We applied the pre-trained language models to biomedical text to obtain the representation, and subsequently fed them into a deep neural network with gate mechanism layers and a fully connected layer for the extraction of MTI information sentences. Performances of the proposed models were evaluated using two datasets constructed on the basis of text data obtained from miRTarBase. The validation and test results revealed that incorporating both PubMedBERT and SciBERT for sentence level encoding with the long short-term memory (LSTM)-based deep neural network can yield an outstanding performance, with both F1 and accuracy being higher than 80% on validation data and test data. Additionally, the proposed deep learning method outperformed the following machine learning methods: random forest, support vector machine, logistic regression and bidirectional LSTM. This work would greatly facilitate studies on MTI analysis and regulations. It is anticipated that this work can assist in large-scale screening of miRNAs, thereby revealing their functional roles in various diseases, which is important for the development of highly specific drugs with fewer side effects. Source code and corpus are publicly available at https://github.com/qi29.
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Affiliation(s)
- Mengqi Luo
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, China; School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shangfu Li
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen
| | - Yuxuan Pang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, PR China, and also in the School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, PR China
| | - Lantian Yao
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, PR China, and also in the School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, PR China
| | - Renfei Ma
- Warshel Institute for Computational Biology, Chinese University of Hong Kong, Shenzhen; School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Hsi-Yuan Huang
- School of Medicine and the Warshel Institute of Computational Biology, The Chinese University of Hong Kong, Shenzhen
| | - Hsien-Da Huang
- School of Medicine, and the executive director of Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen
| | - Tzong-Yi Lee
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, China
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Li C, Dou P, Wang T, Lu X, Xu G, Lin X. Defining disease-related modules based on weighted miRNA synergistic network. Comput Biol Med 2023; 152:106382. [PMID: 36493730 DOI: 10.1016/j.compbiomed.2022.106382] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022]
Abstract
MicroRNAs (miRNAs) play an important role in the biological process. Their expression and functional changes have been observed in most cancers. Meanwhile, there exists cooperative regulation among miRNAs which is important for studying the mechanisms of complex post-transcriptional regulations. Hence, studying miRNA synergy and identifying miRNA synergistic modules can help understand the development and progression of complex diseases, such as cancers. This work studies miRNA synergy and proposes a new method for defining disease-related modules (DDRM) by combining the knowledge databases and miRNA data. DDRM measures the miRNA synergy not only by the co-regulating target subset but also by the non-common target set to construct the weighted miRNA synergistic network (WMSN). The experiments on twelve the cancer genome atlas (TCGA) datasets showed that the important modules identified by DDRM can well distinguish the cancer samples from the normal samples, and DDRM performed better than the previous method in most cases. An external dataset of prostate cancer was applied to validate the module biomarkers determined by DDRM on the prostate cancer data of TCGA. The area under the receiver operating characteristic curve (AUC) value is 0.92 and the performance is superior. Hence, combining the miRNA synergy networks from the knowledge databases and the miRNA data can determine the important functional modules related to diseases, which is of great significance to the study of disease mechanism.
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Affiliation(s)
- Chao Li
- School of Computer Science & Technology, Dalian University of Technology, 116024, Dalian, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Peng Dou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Tianxiang Wang
- School of Computer Science & Technology, Dalian University of Technology, 116024, Dalian, China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; Liaoning Province Key Laboratory of Metabolomics, Dalian, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; Liaoning Province Key Laboratory of Metabolomics, Dalian, China
| | - Xiaohui Lin
- School of Computer Science & Technology, Dalian University of Technology, 116024, Dalian, China.
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Combination of Circulating miR-125a-5p, miR-223-3p and D-dimer as a Novel Biomarker for Deep Vein Thrombosis. Am J Med Sci 2022; 364:601-611. [PMID: 35588895 DOI: 10.1016/j.amjms.2022.04.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 11/19/2021] [Accepted: 04/08/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND Deep venous thrombosis (DVT) is a thrombus formed in the deep venous cavity and can cause a fatal pulmonary embolism. Since circulating miRNAs are used as molecular markers for the early warning and diagnosis of various diseases, such as tumors and cardiovascular diseases, the purpose of the present study was initially to identify differential expression circulating miRNAs in plasma, and then explore potential biomarkers for DVT. METHODS The plasma of 30 patients with DVT before and after DVT-related endovascular interventions constituted 6 sample pools for miRNA sequencing, and the levels of 22 plasma miRNAs were significantly changed. Then, various bioinformatics tools were utilized to screen out 8 miRNAs with potential DVT diagnostic value. Furthermore, their diagnostic values were evaluated in 120 patients with DVT and 120 healthy individuals. RESULTS The levels of 22 circulating plasma miRNAs (12 up-regulated, 10 down-regulated) were significantly changed in patients with DVT before and after endovascular interventions, especially miR-125a-5p (up-regulation) and miR-223-3p (down-regulation). The values of area under the ROC curve (AUC) of miR-125a-5p and miR-223-3p were both >0.8, indicating that they were valuable in diagnosing DVT. The combination of miR-125a-5p and miR-223-3p with D-dimer significantly improved the efficiency of diagnosing DVT, (AUC >0.97, the sensitivity and specificity >95%), and was better than those of D-dimer alone. CONCLUSIONS The levels of miR-125a-5p and miR-223-3p were the most significantly changed in patients with DVT before and after endovascular interventions; together with the classic biomarker D-dimer, they can be used as a potential biomarker for diagnostic and therapeutic process of DVT.
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Li J, Sang ER, Adeyemi O, Miller LC, Sang Y. Comparative transcriptomics reveals small RNA composition and differential microRNA responses underlying interferon-mediated antiviral regulation in porcine alveolar macrophages. Front Immunol 2022; 13:1016268. [PMID: 36389683 PMCID: PMC9651005 DOI: 10.3389/fimmu.2022.1016268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/03/2022] [Indexed: 09/12/2023] Open
Abstract
Previous studies have shown that interferon-mediated antiviral activity is subtype-dependent. Using a whole transcriptome procedure, we aimed to characterize the small RNA transcriptome (sRNA-Seq) and specifically the differential microRNA (miRNA) responses in porcine alveolar macrophages (PAMs) upon antiviral activation during viral infection and interferon (IFN) stimulation. Data showed that near 90% of the qualified reads of sRNA were miRNAs, and about 10% of the other sRNAs included rRNA, snoRNA, snRNA, and tRNA in order of enrichment. As the majority of sRNA (>98%) were commonly detected in all PAM samples under different treatments, about 2% sRNA were differentially expressed between the different antiviral treatments. Focusing on miRNA, 386 miRNA were profiled, including 331 known and 55 novel miRNA sequences, of which most were ascribed to miRNA families conserved among vertebrates, particularly mammalian species. Of the miRNA profiles comparably generated across the different treatments, in general, significantly differentially expressed miRNA (SEM) demonstrated that: (1) the wild-type and vaccine strains of a porcine arterivirus (a.k.a., PRRSV) induced nearly reversed patterns of up- or down-regulated SEMs; (2) similar SEM patterns were found among the treatments by the vaccine strain and antiviral IFN-α1/-ω5 subtypes; and (3) the weak antiviral IFN-ω1, however, remarked a suppressive SEM pattern as to SEMs upregulated in the antiviral treatments by the vaccine and IFN-α1/-ω5 subtypes. Further articulation identified SEMs commonly or uniquely expressed in different treatments, and experimentally validated that some SEMs including miR-10b and particularly miR-9-1 acted significantly in regulation of differential antiviral reactions stimulated by different IFN subtypes. Therefore, this study provides a general picture of porcine sRNA composition and pinpoints key SEMs underlying antiviral regulation in PAMs correlated to a typical respiratory RNA virus in pigs.
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Affiliation(s)
- Jiuyi Li
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
| | - Eric R. Sang
- USDA, Agricultural Research Service, National Animal Disease Center, Virus and Prion Research Unit, Ames, IA, United States
| | - Oluwaseun Adeyemi
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
| | - Laura C. Miller
- USDA, Agricultural Research Service, National Animal Disease Center, Virus and Prion Research Unit, Ames, IA, United States
| | - Yongming Sang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
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MiR-29a Family as a Key Regulator of Skeletal Muscle Dysplasia in a Porcine Model of Intrauterine Growth Retardation. Biomolecules 2022; 12:biom12091193. [PMID: 36139032 PMCID: PMC9496619 DOI: 10.3390/biom12091193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) play an essential role in many biological processes. In this study, miRNAs in the skeletal muscle of normal and intrauterine growth retardation (IUGR) neonatal piglets were identified by sequencing, and canonical miRNAs were functionally validated in vitro. A total of 403 miRNAs were identified in neonatal piglet skeletal muscle, among them 30 and 46 miRNAs were upregulated and downregulated in IUGR pigs, respectively. Upregulated miRNAs were mainly enriched in propanoate metabolism, endocytosis, beta-Alanine metabolism, gap junction, and tumor necrosis factor signaling pathway. Down-regulated miRNAs were mainly enriched in chemical carcinogenesis—receptor activation, endocytosis, MAPK signaling pathway, insulin resistance, and EGFR tyrosine kinase inhibitor resistance. Co-expression network analysis of umbilical cord blood and skeletal muscle miRNAs showed that the miR-29 family is an essential regulator of IUGR pigs. The dual-luciferase reporter system showed that IGF1 and CCND1 were target genes of the miR-29 family. Transfection of IUGR pig umbilical cord blood exosomes and miR-29a mimic significantly inhibited cell proliferation and promoted the expression of cellular protein degradation marker genes Fbxo32 and Trim63. In summary, these results enrich the regulatory network of miRNAs involved in skeletal muscle development in IUGR animals.
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Song M, Yu J, Li B, Dong J, Gao J, Shang L, Zhou X, Bai Y. Identification of functionally important miRNA targeted genes associated with child obesity trait in genome-wide association studies. BMC Genomics 2022; 23:360. [PMID: 35546387 PMCID: PMC9092671 DOI: 10.1186/s12864-022-08576-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have uncovered thousands of genetic variants that are associated with complex human traits and diseases. miRNAs are single-stranded non-coding RNAs. In particular, genetic variants located in the 3'UTR region of mRNAs may play an important role in gene regulation through their interaction with miRNAs. Existing studies have not been thoroughly conducted to elucidate 3'UTR variants discovered through GWAS. The goal of this study is to analyze patterns of GWAS functional variants located in 3'UTRs about their relevance in the network between hosting genes and targeting miRNAs, and elucidate the association between the genes harboring these variants and genetic traits. METHODS We employed MIGWAS, ANNOVAR, MEME, and DAVID software packages to annotate the variants obtained from GWAS for 31 traits and elucidate the association between their harboring genes and their related traits. We identified variants that occurred in the motif regions that may be functionally important in affecting miRNA binding. We also conducted pathway analysis and functional annotation on miRNA targeted genes harboring 3'UTR variants for a trait with the highest percentage of 3'UTR variants occurring. RESULTS The Child Obesity trait has the highest percentage of 3'UTR variants (75%). Of the 16 genes related to the Child Obesity trait, 5 genes (ETV7, GMEB1, NFIX, ZNF566, ZBTB40) had a significant association with the term DNA-Binding (p < 0.05). EQTL analysis revealed 2 relevant tissues and 10 targeted genes associated with the Child Obesity trait. In addition, Red Blood Cells (RBC), Hemoglobin (HB), and Package Cell Volume (PCV) have overlapping variants. In particular, the PIM1 variant occurred inside the HB Motif region 37,174,641-37,174,660, and LUC7L3 variant occurred inside RBC Motif region 50,753,918-50,753,937. CONCLUSION Variants located in 3'UTR can alter the binding affinity of miRNA and impact gene regulation, thus warranting further annotation and analysis. We have developed a bioinformatics bash pipeline to automatically annotate variants, determine the number of variants in different categories for each given trait, and check common variants across different traits. This is a valuable tool to annotate a large number of GWAS result files.
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Affiliation(s)
- Melinda Song
- University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Jiaqi Yu
- College Preparatory School, 6100 Broadway, Oakland, CA 94618 USA
| | - Binze Li
- Bellaire High School, 5100 Maple St, Bellaire, TX 77401 USA
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Julian Dong
- Northville High School, 45700 Six Mile Road, Northville, MI 48168 USA
- College of Engineering, University of Michigan, Ann Arbor, MI 48109 USA
| | - Jeslyn Gao
- Simsbury High School, 34 Farms Village Rd, Simsbury, CT 06070 USA
| | - Lulu Shang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Yongsheng Bai
- Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197 USA
- Next-Gen Intelligent Science Training, Ann Arbor, MI 48105 USA
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Comprehensive Analysis of the Effect of 20(R)-Ginsenoside Rg3 on Stroke Recovery in Rats via the Integrative miRNA–mRNA Regulatory Network. Molecules 2022; 27:molecules27051573. [PMID: 35268674 PMCID: PMC8911624 DOI: 10.3390/molecules27051573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 02/01/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of small, endogenous, noncoding RNAs. Recent research has proven that miRNAs play an essential role in the occurrence and development of ischemic stroke. Our previous studies confirmed that 20(R)-ginsenosideRg3 [20(R)-Rg3] exerts beneficial effects on cerebral ischemia–reperfusion injury (CIRI), but its molecular mechanism has not been elucidated. In this study, we used high-throughput sequencing to investigate the differentially expressed miRNA and mRNA expression profiles of 20(R)-Rg3 preconditioning to ameliorate CIRI injury in rats and to reveal its potential neuroprotective molecular mechanism. The results show that 20(R)-Rg3 alleviated neurobehavioral dysfunction in MCAO/R-treated rats. Among these mRNAs, 953 mRNAs were significantly upregulated and 2602 mRNAs were downregulated in the model group versus the sham group, whereas 437 mRNAs were significantly upregulated and 35 mRNAs were downregulated in the 20(R)-Rg3 group in contrast with those in the model group. Meanwhile, the expression profile of the miRNAs showed that a total of 283 differentially expressed miRNAs were identified, of which 142 miRNAs were significantly upregulated and 141 miRNAs were downregulated in the model group compared with the sham group, whereas 34 miRNAs were differentially expressed in the 20(R)-Rg3 treatment group compared with the model group, with 28 miRNAs being significantly upregulated and six miRNAs being significantly downregulated. Furthermore, 415 (391 upregulated and 24 downregulated) differentially expressed mRNAs and 22 (17 upregulated and 5 downregulated) differentially expressed miRNAs were identified to be related to 20(R)-Rg3′s neuroprotective effect on stroke recovery. The Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that 20(R)-Rg3 could modulate multiple signaling pathways related to these differential miRNAs, such as the cGMP-PKG, cAMP and MAPK signaling pathways. This study provides new insights into the protective mechanism of 20(R)-Rg3 against CIRI, and the mechanism may be partly associated with the regulation of brain miRNA expression and its target signaling pathways.
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A review of non-coding RNA related to NF-κB signaling pathway in the pathogenesis of osteoarthritis. Int Immunopharmacol 2022; 106:108607. [PMID: 35180625 DOI: 10.1016/j.intimp.2022.108607] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 12/21/2022]
Abstract
Osteoarthritis (OA), often called as "wear and tear" arthritis, is the most common form of degenerative joint arthritis and is a leading cause of disability. The nuclear factor-kappaB (NF-κB) transcription factor has long been recognized as a disease-contributing factor for OA. More and more evidences show that targeting NF-κB signaling could offer novel potential therapeutic options for OA damage and reduce the risk of potential side-effects. In recent years, it has been shown that non-coding RNAs(ncRNAs) can trigger the expression of an array of genes and widely activate NF-κB signaling pathway, which induces destruction of the articular joint, leading to OA onset and progression. In this review, we discuss the involvement of NF-κB in OA pathogenesis and how ncRNAs attend and affect OA incidence and evolution, offering novel potential therapeutic options for OA treatment.
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GWAS identifies candidate susceptibility loci and microRNA biomarkers for acute encephalopathy with biphasic seizures and late reduced diffusion. Sci Rep 2022; 12:1332. [PMID: 35079012 PMCID: PMC8789807 DOI: 10.1038/s41598-021-04576-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/24/2021] [Indexed: 12/28/2022] Open
Abstract
Acute encephalopathy with biphasic seizures and late reduced diffusion (AESD) is a severe encephalopathy preceded by viral infections with high fever. AESD is a multifactorial disease, however, few disease susceptibility genes have previously been identified. Here, we conducted a genome-wide association study (GWAS) and assessed functional variants in non-coding regions to study genetic susceptibility in AESD using 254 Japanese children with AESD and 799 adult healthy controls. We also performed a microRNA enrichment analysis using GWAS statistics to search for candidate biomarkers in AESD. The variant with the lowest p-value, rs1850440, was located in the intron of serine/threonine kinase 39 gene (STK39) on chromosome 2q24.3 (p = 2.44 × 10-7, odds ratio = 1.71). The minor allele T of rs1850440 correlated with the stronger expression of STK39 in peripheral blood. This variant possessed enhancer histone modification marks in STK39, the encoded protein of which activates the p38 mitogen-activated protein kinase (MAPK) pathway. In the replication study, the odds ratios of three SNPs, including rs1850440, showed the same direction of association with that in the discovery stage GWAS. One of the candidate microRNAs identified by the microRNA enrichment analysis was associated with inflammatory responses regulated by the MAPK pathway. This study identified STK39 as a novel susceptibility locus of AESD, found microRNAs as potential biomarkers, and implicated immune responses and the MAPK cascade in its pathogenesis.
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12
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Sonehara K, Sakaue S, Maeda Y, Hirata J, Kishikawa T, Yamamoto K, Matsuoka H, Yoshimura M, Nii T, Ohshima S, Kumanogoh A, Okada Y. Genetic architecture of microRNA expression and its link to complex diseases in the Japanese population. Hum Mol Genet 2021; 31:1806-1820. [PMID: 34919704 PMCID: PMC9169454 DOI: 10.1093/hmg/ddab361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/04/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the genetic effects on non-coding RNA (ncRNA) expression facilitates functional characterization of disease-associated genetic loci. Among several classes of ncRNAs, microRNAs (miRNAs) are key post-transcriptional gene regulators. Despite its biological importance, previous studies on the genetic architecture of miRNA expression focused mostly on the European individuals, underrepresented in other populations. Here, we mapped miRNA expression quantitative trait loci (miRNA-eQTL) for 343 miRNAs in 141 Japanese using small RNA sequencing (sRNA-seq) and whole-genome sequencing (WGS), identifying 1275 cis-miRNA-eQTL variants for 40 miRNAs (false discovery rate < 0.2). Of these, 25 miRNAs having eQTL were unreported in the European studies, including 5 miRNAs with their lead variant monomorphic in the European populations, which demonstrates the value of miRNA-eQTL analysis in diverse ancestral populations. MiRNAs with eQTL effect showed allele-specific expression (ASE) (e.g. miR-146a-3p), and ASE analysis further detected cis-regulatory variants not captured by the conventional miRNA-eQTL mapping (e.g. miR-933). We identified a copy number variation (CNV) associated with miRNA expression (e.g. miR-570-3p, P = 7.2 × 10-6), which contributes to a more comprehensive landscape of miRNA-eQTLs. To elucidate a post-transcriptional modification in miRNAs, we created a catalog of miRNA-editing sites, including ten canonical and six non-canonical sites. Finally, by integrating the miRNA-eQTLs and Japanese genome-wide association studies of 25 complex traits (mean n = 192 833), we conducted a transcriptome-wide association study (TWAS), identifying miR-1908-5p as a potential mediator for adult height, colorectal cancer, and type 2 diabetes (P < 9.1 × 10-5). Our study broadens the population diversity in ncRNA-eQTL studies and contributes to functional annotation of disease-associated loci found in non-European populations.
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Affiliation(s)
- Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, 565-0871, Japan
| | - Saori Sakaue
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Center for Data Sciences, Harvard Medical School, Boston, MA, 02114, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, 565-0871, Japan.,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Jun Hirata
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Pharmaceutical Discovery Research Laboratories, Teijin Pharma Limited, Hino, 191-8512, Japan
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Department of Otorhinolaryngology - Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya, 464-8681, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, 565-0871, Japan
| | - Hidetoshi Matsuoka
- Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, 586-8521, Japan
| | - Maiko Yoshimura
- Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, 586-8521, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Shiro Ohshima
- Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, 586-8521, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, 565-0871, Japan.,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, 565-0871, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, 565-0871, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, 565-0871, Japan.,The Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, 565-0871, Japan.,Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
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13
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Xu Q, Chen X, Chen B. MicroRNA-3148 inhibits glioma by decreasing DCUN1D1 and inhibiting the NF-kB pathway. Exp Ther Med 2021; 23:28. [PMID: 34824636 PMCID: PMC8611494 DOI: 10.3892/etm.2021.10950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 09/27/2021] [Indexed: 11/06/2022] Open
Abstract
Glioma, which originates in the brain, is the most aggressive tumor of the central nervous system. It has been shown that microRNA (miRNA) controls the proliferation, migration and apoptosis of glioma cells. The objective of the present study was to measure microRNA-3148 (miR-3148) expression and investigate its impact on the pathogenetic mechanism of glioma. In the present study, reverse transcription-quantitative real-time PCR was employed to detect miR-3148 expression levels in glioma tissues and cell lines. Cell Counting Kit-8 assay, 5-ethynyl-2'-deoxyuridine assay, and Transwell migration assay were performed to assess the influence of miR-3148 on the malignant biological behavior of glioma cells. The biological functions of miR-3148 in glioma were examined via a xenograft tumor growth assay. Furthermore, the association between miR-3148 and DCUN1D1 was investigated via immunohistochemistry, dual-luciferase reporter assay and western blotting. It was observed that miR-3148 was expressed at low levels in glioma cells, and this represented a poor survival rate. In addition, an increased level of miR-3148 in cells and animal models inhibited glioma cell migration and proliferation. Moreover, miR-3148 decreased DCUN1D1 and curbed the nuclear factor κ enhancer binding protein (NF-κB) signaling pathway, thus decreasing the growth of glioma. Thus, miR-3148 is expressed within glioma tissues at low levels where it suppresses glioma by curbing the NF-κB pathway and lowering DCUN1D1.
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Affiliation(s)
- Qianghua Xu
- Department of Neurosurgery, The First People's Hospital of Jingmen, Jingmen, Hubei 448000, P.R. China
| | - Xiao Chen
- Department of Neurosurgery, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei 441021, P.R. China
| | - Bin Chen
- Department of Neurosurgery, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei 441021, P.R. China
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14
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Hu X, Chen Q, Guo H, Li K, Fu B, Chen Y, Zhao H, Wei M, Li Y, Wu H. Identification of Target PTEN-Based miR-425 and miR-576 as Potential Diagnostic and Immunotherapeutic Biomarkers of Colorectal Cancer With Liver Metastasis. Front Oncol 2021; 11:657984. [PMID: 34490081 PMCID: PMC8418231 DOI: 10.3389/fonc.2021.657984] [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: 01/24/2021] [Accepted: 07/28/2021] [Indexed: 12/19/2022] Open
Abstract
A major complication of colorectal cancer (CRC), one of the most common and fatal types of cancers, is secondary liver metastasis. For patients with this fate, there are very few biomarkers available in clinical application, and the disease remains incurable. Recently, increasing studies demonstrated that tumorigenesis and development are closely related to immune escape, indicating that the roles of immune-related indicators might have been neglected in the past in colorectal cancer liver metastases (CRLM). Here, we unveil that elevated miR-425 and miR-576 promote CRLM through inhibiting PTEN-mediated cellular immune function. Specifically, miR-425 and miR-576 were identified for their significant upregulation in CRLM compared with the primary CRC tissues based on GSE81581 (n = 8) and GSE44121 (n = 18) datasets. Besides, we determined that the two microRNAs (miRNAs) coparticipated in restraining P53 and transforming growth factor beta (TGF-β) signaling pathways associated with tumor metastasis, and both shortened the overall survival of the patients with metastatic susceptibility. Notably, in situ hybridization on relatively large samples of paired CRC tissues (n = 157) not only substantiated that the expression of miR-425 and miR-576 was dramatically upregulated in CRLM but also revealed that they were closely related to tumor deterioration, especially liver metastases. Moreover, we further confirmed that the combination of miR-425 and miR-576 was an effective predictive model for liver metastases and poor clinical outcomes. Mechanically, downregulated PTEN (GSE81558, n = 6) was verified to be a shared target of miR-425 and miR-576 acting as metastasis-related oncogenes, on account of the presence of binding sites (+2928-+2934 and +4371-+4378, respectively) and the collaborative suppression of P53/TGF-β signaling in CRLM, which was further confirmed in CRC cells (HCT116 and SW480) based on systematic molecular biology experiments. Importantly, the target PTEN was strongly associated with microsatellite instability, tumor microenvironment, and immune cell infiltration. Thus, we speculate that miR-425 and miR-576 are novel biomarkers for CRLM prevention and immunotherapy and upstream inhibitors of the PTEN-P53/TGF-β function axis.
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Affiliation(s)
- Xiaoyun Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China.,Department of Gene Detection, Liaoning Medical Diagnosis and Treatment Center, Shenyang, China
| | - Qiuchen Chen
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China.,Department of Gene Detection, Liaoning Medical Diagnosis and Treatment Center, Shenyang, China
| | - Hao Guo
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China.,Department of Gene Detection, Liaoning Medical Diagnosis and Treatment Center, Shenyang, China
| | - Kuo Li
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China.,Department of Gene Detection, Liaoning Medical Diagnosis and Treatment Center, Shenyang, China
| | - Boshi Fu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China.,Department of Gene Detection, Liaoning Medical Diagnosis and Treatment Center, Shenyang, China
| | - Yu Chen
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China.,Department of Gene Detection, Liaoning Medical Diagnosis and Treatment Center, Shenyang, China
| | - Haishan Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China.,Department of Gene Detection, Liaoning Medical Diagnosis and Treatment Center, Shenyang, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China.,Department of Gene Detection, Liaoning Medical Diagnosis and Treatment Center, Shenyang, China
| | - Yalun Li
- Department of Anorectal Surgery, First Hospital of China Medical University, Shenyang, China
| | - Huizhe Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China.,Department of Gene Detection, Liaoning Medical Diagnosis and Treatment Center, Shenyang, China
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15
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Tao L, Pang Y, Wang A, Li L, Shen Y, Xu X, Li J. Functional miR-142a-3p Induces Apoptosis and Macrophage Polarization by Targeting tnfaip2 and glut3 in Grass Carp ( Ctenopharyngodon idella). Front Immunol 2021; 12:633324. [PMID: 34262558 PMCID: PMC8273434 DOI: 10.3389/fimmu.2021.633324] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
In the process of microbial invasion, the inflammation reaction is induced to eliminate the pathogen. However, un-controlled or un-resolved inflammation can lead to tissue damage and death of the host. MicroRNAs (miRNAs) are the signaling regulators that prevent the uncontrolled progress of an inflammatory response. Our previous work strongly indicated that miR-142a-3p is related to the immune regulation in grass carp. In the present study, we found that the expression of miR-142a-3p was down-regulated after infection by Aeromonas hydrophila. tnfaip2 and glut3 were confirmed as be the target genes of miR-142a-3p, which were confirmed by expression correlation analysis, gene overexpression, and dual luciferase reporter assay. The miR-142a-3p can reduce cell viability and stimulate cell apoptosis by targeting tnfaip2 and glut3. In addition, miR-142a-3p also regulates macrophage polarization induced by A. hydrophila. Our results suggest that miR-142a-3p has multiple functions in host antibacterial immune response. Our research provides further understanding of the molecular mechanisms between miRNAs and their target genes, and provides a new insights for the development of pro-resolution strategies for the treatment of complex inflammatory diseases in fish.
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Affiliation(s)
- Lizhu Tao
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China.,Institute of Fisheries of Chengdu Agriculture and Forestry Academy, Chengdu, China
| | - Yifan Pang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Anqi Wang
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Lisen Li
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade Do Algarve, Faro, Portugal
| | - Yubang Shen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
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16
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Yasumizu Y, Sakaue S, Konuma T, Suzuki K, Matsuda K, Murakami Y, Kubo M, Palamara PF, Kamatani Y, Okada Y. Genome-Wide Natural Selection Signatures Are Linked to Genetic Risk of Modern Phenotypes in the Japanese Population. Mol Biol Evol 2021; 37:1306-1316. [PMID: 31957793 PMCID: PMC7182208 DOI: 10.1093/molbev/msaa005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Elucidation of natural selection signatures and relationships with phenotype spectra is important to understand adaptive evolution of modern humans. Here, we conducted a genome-wide scan of selection signatures of the Japanese population by estimating locus-specific time to the most recent common ancestor using the ascertained sequentially Markovian coalescent (ASMC), from the biobank-based large-scale genome-wide association study data of 170,882 subjects. We identified 29 genetic loci with selection signatures satisfying the genome-wide significance. The signatures were most evident at the alcohol dehydrogenase (ADH) gene cluster locus at 4q23 (PASMC = 2.2 × 10−36), followed by relatively strong selection at the FAM96A (15q22), MYOF (10q23), 13q21, GRIA2 (4q32), and ASAP2 (2p25) loci (PASMC < 1.0 × 10−10). The additional analysis interrogating extended haplotypes (integrated haplotype score) showed robust concordance of the detected signatures, contributing to fine-mapping of the genes, and provided allelic directional insights into selection pressure (e.g., positive selection for ADH1B-Arg48His and HLA-DPB1*04:01). The phenome-wide selection enrichment analysis with the trait-associated variants identified a variety of the modern human phenotypes involved in the adaptation of Japanese. We observed population-specific evidence of enrichment with the alcohol-related phenotypes, anthropometric and biochemical clinical measurements, and immune-related diseases, differently from the findings in Europeans using the UK Biobank resource. Our study demonstrated population-specific features of the selection signatures in Japanese, highlighting a value of the natural selection study using the nation-wide biobank-scale genome and phenotype data.
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Affiliation(s)
| | - Saori Sakaue
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takahiro Konuma
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ken Suzuki
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Koichi Matsuda
- Department of Computational Biology and Medical Science, Graduate school of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, The Institute of Medical Sciences, The University of Tokyo, Tokyo, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
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17
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Sonehara K, Okada Y. Genomics-driven drug discovery based on disease-susceptibility genes. Inflamm Regen 2021; 41:8. [PMID: 33691789 PMCID: PMC7944616 DOI: 10.1186/s41232-021-00158-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/26/2021] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies have identified numerous disease-susceptibility genes. As knowledge of gene–disease associations accumulates, it is becoming increasingly important to translate this knowledge into clinical practice. This challenge involves finding effective drug targets and estimating their potential side effects, which often results in failure of promising clinical trials. Here, we review recent advances and future perspectives in genetics-led drug discovery, with a focus on drug repurposing, Mendelian randomization, and the use of multifaceted omics data.
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Affiliation(s)
- Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan. .,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, 565-0871, Japan. .,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, 565-0871, Japan.
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18
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Shirai Y, Okada Y. Elucidation of disease etiology by trans-layer omics analysis. Inflamm Regen 2021; 41:6. [PMID: 33557957 PMCID: PMC7871538 DOI: 10.1186/s41232-021-00155-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/22/2021] [Indexed: 12/18/2022] Open
Abstract
To date, genome-wide association studies (GWASs) have successfully identified thousands of associations between genetic polymorphisms and human traits. However, the pathways between the associated genotype and phenotype are often poorly understood. The transcriptome, proteome, and metabolome, the omics, are positioned along the pathway and can provide useful information to translate from genotype to phenotype. This review shows useful data resources for connecting each omics and describes how they are combined into a cohesive analysis. Quantitative trait loci (QTL) are useful information for connecting the genome and other omics. QTL represent how much genetic variants have effects on other omics and give us clues to how GWAS risk SNPs affect biological mechanisms. Integration of each omics provides a robust analytical framework for estimating disease causality, discovering drug targets, and identifying disease-associated tissues. Technological advances and the rise of consortia and biobanks have facilitated the analyses of unprecedented data, improving both the quality and quantity of research. Proficient management of these valuable datasets allows discovering novel insights into the genetic background and etiology of complex human diseases and contributing to personalized medicine.
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Affiliation(s)
- Yuya Shirai
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, 565-0871, Japan.
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19
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Zhan J, Diao Y, Yin G, Sajjad M, Wei X, Lu Z, Wang Y. Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism of Cotton Response to Salt Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:767984. [PMID: 34956267 PMCID: PMC8695560 DOI: 10.3389/fpls.2021.767984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/09/2021] [Indexed: 05/13/2023]
Abstract
To identify the regulatory network of known and novel microRNAs (miRNAs) and their targets responding to salt stress, a combined analysis of mRNA libraries, small RNA libraries, and degradome libraries were performed. In this study, we used unique molecular identifiers (UMIs), which are more sensitive, accurate, and reproducible than traditional methods of sequencing, to quantify the number of molecules and correct for amplification bias. We identified a total of 312 cotton miRNAs using seedlings at 0, 1, 3, and 6 h after NaCl treatment, including 80 known ghr-miRNAs and 232 novel miRNAs and found 155 miRNAs that displayed significant differential expression under salt stress. Among them, fifty-nine differentially expressed miRNAs were simultaneously induced in two or three tissues, while 66, 11, and 19 were specifically expressed in the roots, leaves, and stems, respectively. It is indicated there were different populations of miRNAs against salt stress in roots, leaves and stems. 399 candidate targets of salt-induced miRNAs showed significant differential expression before and after salt treatment, and 72 targets of 25 miRNAs were verified by degradome sequencing data. Furthermore, the regulatory relationship of miRNA-target gene was validated experimentally via 5'RLM-RACE, proving our data reliability. Gene ontology and KEGG pathway analysis found that salt-responsive miRNA targets among the differentially expressed genes were significantly enriched, and mainly involved in response to the stimulus process and the plant hormone signal transduction pathway. Furthermore, the expression levels of newly identified miRNA mir1 and known miRNAs miR390 and miR393 gradually decreased when subjected to continuous salt stress, while overexpression of these miRNAs both increased sensitivity to salt stress. Those newly identified miRNAs and mRNA pairs were conducive to genetic engineering and better understanding the mechanisms responding to salt stress in cotton.
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Affiliation(s)
- Jingjing Zhan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yangyang Diao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Guo Yin
- Handan Academy of Agricultural Sciences, Handan, China
| | - Muhammad Sajjad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xi Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhengying Lu
- Handan Academy of Agricultural Sciences, Handan, China
- *Correspondence: Zhengying Lu,
| | - Ye Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Ye Wang,
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20
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Li B, Dong J, Yu J, Fan Y, Shang L, Zhou X, Bai Y. Pinpointing miRNA and genes enrichment over trait-relevant tissue network in Genome-Wide Association Studies. BMC Med Genomics 2020; 13:191. [PMID: 33371893 PMCID: PMC7771066 DOI: 10.1186/s12920-020-00830-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Understanding gene regulation is important but difficult. Elucidating tissue-specific gene regulation mechanism is even more challenging and requires gene co-expression network assembled from protein-protein interaction, transcription factor and gene binding, and post-transcriptional regulation (e.g., miRNA targeting) information. The miRNA binding affinity could therefore be changed by SNP(s) located at the 3' untranslated regions (3'UTR) of the target messenger RNA (mRNA) which miRNA(s) interacts with. Genome-wide association study (GWAS) has reported significant numbers of loci hosting SNPs associated with many traits. The goal of this study is to pinpoint GWAS functional variants located in 3'UTRs and elucidate if the genes harboring these variants along with their targeting miRNAs are associated with genetic traits relevant to certain tissues. METHODS By applying MIGWAS, CoCoNet, ANNOVAR, and DAVID bioinformatics software and utilizing the gene expression database (e.g. GTEx data) to study GWAS summary statistics for 43 traits from 28 GWAS studies, we have identified a list of miRNAs and targeted genes harboring 3'UTR variants, which could contribute to trait-relevant tissue over miRNA-target gene network. RESULTS Our result demonstrated that strong association between traits and tissues exists, and in particular, the Primary Biliary Cirrhosis (PBC) trait has the most significant p-value for all 180 tissues among all 43 traits used for this study. We reported SNPs located in 3'UTR regions of genes (SFMBT2, ZC3HAV1, and UGT3A1) targeted by miRNAs for PBC trait and its tissue association network. After employing Gene Ontology (GO) analysis for PBC trait, we have also identified a very important miRNA targeted gene over miRNA-target gene network, PFKL, which encodes the liver subunit of an enzyme. CONCLUSIONS The non-coding variants identified from GWAS studies are casually assumed to be not critical to translated protein product. However, 3' untranslated regions (3'UTRs) of genes harbor variants can often change the binding affinity of targeting miRNAs playing important roles in protein translation degree. Our study has shown that GWAS variants could play important roles on miRNA-target gene networks by contributing the association between traits and tissues. Our analysis expands our knowledge on trait-relevant tissue network and paves way for future human disease studies.
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Affiliation(s)
- Binze Li
- Bellaire High School, 5100 Maple St, Bellaire, TX, 77401, USA
| | - Julian Dong
- Northville High School, 45700 Six Mile Road, Northville, MI, 48168, USA
| | - Jiaqi Yu
- College Preparatory School, 6100 Broadway, Oakland, CA, 94618, USA
| | - Yuqi Fan
- The Master's Academy, 1500 Lukas Ln, Oviedo, FL, 32765, USA
| | - Lulu Shang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.,Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yongsheng Bai
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, 48197, USA. .,Next-Gen Intelligent Science Training, Ann Arbor, MI, 48105, USA.
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21
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Liu W, Sheng L, Nie L, Wen X, Mo X. Functional interaction between long non-coding RNA and microRNA in rheumatoid arthritis. J Clin Lab Anal 2020; 34:e23489. [PMID: 33319382 PMCID: PMC7755821 DOI: 10.1002/jcla.23489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/22/2020] [Accepted: 07/01/2020] [Indexed: 01/07/2023] Open
Abstract
MicroRNA (miRNA) has received widespread attention for its role in several key cellular processes such as cell differentiation, cell proliferation, apoptosis, and autoimmune diseases. Although we now have a good understanding of miRNA expression and function, our knowledge regarding the molecular mechanism of long non‐coding RNA (lncRNA) is still in its infancy. In this review, we will briefly introduce the definition and function of lncRNA and summarize the interactions between lncRNA and miRNA and their research progress in rheumatoid arthritis (RA). The expression of miR‐16, miR‐146a, miR‐155, and miR‐223 and the interactions between HOTAIR and miR138, ZFAS1 and miR‐27a, and GAPLINC and miR‐575 are representative examples that may augment the understanding of the pathogenesis of RA and help in the development of new biomarkers and target therapies.
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Affiliation(s)
- Weiwei Liu
- Medical College of Northwest Minzu University, Lanzhou, China
| | - Li Sheng
- Medical College of Northwest Minzu University, Lanzhou, China
| | - Lei Nie
- Medical College of Northwest Minzu University, Lanzhou, China
| | - Xiaoyun Wen
- Medical College of Northwest Minzu University, Lanzhou, China
| | - Xiaodan Mo
- Medical College of Northwest Minzu University, Lanzhou, China
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22
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Kwok ZH, Zhang B, Chew XH, Chan JJ, Teh V, Yang H, Kappei D, Tay Y. Systematic Analysis of Intronic miRNAs Reveals Cooperativity within the Multicomponent FTX Locus to Promote Colon Cancer Development. Cancer Res 2020; 81:1308-1320. [PMID: 33172934 DOI: 10.1158/0008-5472.can-20-1406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/05/2020] [Accepted: 11/06/2020] [Indexed: 11/16/2022]
Abstract
Approximately half of all miRNA reside within intronic regions and are often cotranscribed with their host genes. However, most studies of intronic miRNA focus on individual miRNA, while conversely most studies of protein-coding and noncoding genes frequently ignore any intron-derived miRNA. We hypothesize that the individual components of such multigenic loci may play cooperative or competing roles in driving disease progression and that examining the combinatorial effect of these components would uncover deeper insights into their functional importance. To address this, we performed systematic analyses of intronic miRNA:host loci in colon cancer. The FTX locus, comprising of a long noncoding RNA FTX and multiple intronic miRNA, was highly upregulated in cancer, and cooperativity within this multicomponent locus promoted cancer growth. FTX interacted with DHX9 and DICER and regulated A-to-I RNA editing and miRNA expression. These results show for the first time that a long noncoding RNA can regulate A-to-I RNA editing, further expanding the functional repertoire of long noncoding RNA. Intronic miR-374b and miR-545 inhibited tumor suppressors PTEN and RIG-I to enhance proto-oncogenic PI3K-AKT signaling. Furthermore, intronic miR-421 may exert an autoregulatory effect on miR-374b and miR-545. Taken together, our data unveil the intricate interplay between intronic miRNA and their host transcripts in the modulation of key signaling pathways and disease progression, adding new perspectives to the functional landscape of multigenic loci. SIGNIFICANCE: This study illustrates the functional relationships between individual components of multigenic loci in regulating cancer progression.See related commentary by Calin, p. 1212.
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Affiliation(s)
- Zhi Hao Kwok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Xiao Hong Chew
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jia Jia Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Velda Teh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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23
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Akiyama M. Multi-omics study for interpretation of genome-wide association study. J Hum Genet 2020; 66:3-10. [PMID: 32948838 DOI: 10.1038/s10038-020-00842-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/30/2020] [Accepted: 08/31/2020] [Indexed: 12/23/2022]
Abstract
Genome-wide association studies (GWASs) have identified thousands of genetic loci associated with complex traits, including a wide variety of diseases. Despite the successful identification of associated loci, interpreting GWAS findings remains challenging and requires other biological resources. Omics, including genomics, transcriptomics, proteomics, metabolomics, and epigenomics, are increasingly used in a broad range of research fields. Integrative analyses applying GWAS with these omics data are expected to expand our knowledge of complex traits and provide insight into the pathogenesis of complex diseases and their causative factors. Recently, associations between genetic variants and omics data have been comprehensively evaluated, providing new information on the influence of genetic variants on omics. Furthermore, recent advances in analytic methods, including single-cell technologies, have revealed previously unknown disease mechanisms. To advance our understanding of complex traits, integrative analysis using GWAS with multi-omics data is needed. In this review, I describe successful examples of integrative analyses based on omics and GWAS, discuss the limitations of current multi-omics analyses, and provide a perspective on future integrative studies.
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Affiliation(s)
- Masato Akiyama
- Department of Ocular Pathology and Imaging Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan. .,Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
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24
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Shirai Y, Honda S, Ikari K, Kanai M, Takeda Y, Kamatani Y, Morisaki T, Tanaka E, Kumanogoh A, Harigai M, Okada Y. Association of the RPA3-UMAD1 locus with interstitial lung diseases complicated with rheumatoid arthritis in Japanese. Ann Rheum Dis 2020; 79:1305-1309. [PMID: 32737115 PMCID: PMC7509520 DOI: 10.1136/annrheumdis-2020-217256] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/22/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022]
Abstract
Objectives The genetic background of rheumatoid arthritis–interstitial lung disease (RA-ILD) has been evaluated in Europeans, but little knowledge has been obtained in non-Europeans. This study aimed to elucidate genome-wide risk of RA-ILD in non-Europeans. Methods We performed an initial genome-wide association study (GWAS) of RA-ILD in the Japanese population. By conducting the meta-analysis of the three GWAS datasets of the RA cohorts and biobank of Japanese, our study included 358 RA-ILD cases and 4550 RA subjects without ILD. We then conducted the stratified analysis of the effect of the GWAS risk allele in each CT image pattern. Results We identified one novel RA-ILD risk locus at 7p21 that satisfied the genome-wide significance threshold (rs12702634 at RPA3-UMAD1, OR=2.04, 95% CI 1.59 to 2.60, p=1.5×10−8). Subsequent stratified analysis based on the CT image patterns demonstrated that the effect size of the RA-ILD risk allele (rs12702634-C) was large with the UIP pattern (OR=1.86, 95% CI 0.97 to 3.58, p=0.062) and the probable UIP pattern (OR=2.26, 95% CI 1.36 to 3.73, p=0.0015). Conclusion We revealed one novel genetic association with RA-ILD in Japanese. The RA-ILD risk of the identified variant at RPA3-UMAD1 was relatively high in the CT image patterns related to fibrosis. Our study should contribute to elucidation of the complicated aetiology of RA-ILD.
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Affiliation(s)
- Yuya Shirai
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita City, Japan
| | - Suguru Honda
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Shinjuku-ku, Japan
| | - Katsunori Ikari
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Shinjuku-ku, Japan
| | - Masahiro Kanai
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita City, Japan
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Minato-ku, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takayuki Morisaki
- Division of Molecular Pathology, The Institute of Medical Science, The University of Tokyo, Minato-ku, Japan.,BioBank Japan, The Institute of Medical Science, The University of Tokyo, Minato-ku, Japan
| | - Eiichi Tanaka
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Shinjuku-ku, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita City, Japan.,Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Masayoshi Harigai
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Shinjuku-ku, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan .,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
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25
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Hu Y, Gu X, Duan Y, Shen Y, Xie X. Bioinformatics analysis of prognosis-related long non-coding RNAs in invasive breast carcinoma. Oncol Lett 2020; 20:113-122. [PMID: 32565939 PMCID: PMC7285808 DOI: 10.3892/ol.2020.11558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/07/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is one of the most common types of cancer among women worldwide and needs more sensitive prognostic biomarkers to improve its treatment. In the present study, differentially expressed long non-coding RNAs (lncRNAs) in invasive breast carcinoma from The Cancer Genome Atlas and cBioPortal database were investigated, identifying 292 differentially expressed lncRNAs in 1,100 cases. By analyzing the overall survival rate, 10 lncRNAs were significantly correlated with poor prognosis. To explore the underlying molecular mechanisms of the 10 prognosis-related lncRNAs, bioinformatic methods were used to predict the potential target miRNAs, mRNAs and proteins, and to construct a lncRNA-miRNA-mRNA regulatory network and lncRNA-protein interaction network. Finally, the functions of the target genes and proteins were insvestigated using Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses. The results showed that these 10 lncRNAs could be novel prognostic markers for invasive breast carcinoma and the present study aimed to provide novel insight into the diagnosis and treatment of breast cancer.
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Affiliation(s)
- Yuanyuan Hu
- Department of Breast Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang 310006, P.R. China
| | - Xidong Gu
- Department of Breast Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang 310006, P.R. China
| | - Yin Duan
- Department of Breast Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang 310006, P.R. China
| | - Yong Shen
- Department of Breast Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang 310006, P.R. China
| | - Xiaohong Xie
- Department of Breast Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang 310006, P.R. China
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26
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Ishikawa Y, Terao C. The Impact of Cigarette Smoking on Risk of Rheumatoid Arthritis: A Narrative Review. Cells 2020; 9:cells9020475. [PMID: 32092988 PMCID: PMC7072747 DOI: 10.3390/cells9020475] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammation and subsequent proliferation of synovial tissues, which eventually leads to cartilage and bone destruction without effective treatments. Anti-citrullinated cyclic peptide/protein antibody (ACPA) and rheumatoid factor (RF) are two main characteristic autoantibodies found in RA patients and are associated with unfavorable disease outcomes. Although etiologies and causes of the disease have not been fully clarified yet, it is likely that interactive contributions of genetic and environmental factors play a main role in RA pathology. Previous works have demonstrated several genetic and environmental factors as risks of RA development and/or autoantibody productions. Among these, cigarette smoking and HLA-DRB1 are the well-established environmental and genetic risks, respectively. In this narrative review, we provide a recent update on genetic contributions to RA and the environmental risks of RA with a special focus on cigarette smoking and its impacts on RA pathology. We also describe gene–environmental interaction in RA pathogenesis with an emphasis on cigarette smoking and HLA-DRB1.
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Affiliation(s)
- Yuki Ishikawa
- Section for Immunobiology, Joslin Diabetes Center, Harvard Medical School, One Joslin Place, Boston, MA 02215, USA;
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Clinical Research Center, Shizuoka General Hospital, 4 Chome-27-1 Kitaando, Aoi Ward, Shizuoka 420-8527, Japan
- Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
- Correspondence: ; Tel.: +81-(0)45-503-9121
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27
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Amariuta T, Luo Y, Knevel R, Okada Y, Raychaudhuri S. Advances in genetics toward identifying pathogenic cell states of rheumatoid arthritis. Immunol Rev 2019; 294:188-204. [PMID: 31782165 DOI: 10.1111/imr.12827] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022]
Abstract
Rheumatoid arthritis (RA) risk has a large genetic component (~60%) that is still not fully understood. This has hampered the design of effective treatments that could promise lifelong remission. RA is a polygenic disease with 106 known genome-wide significant associated loci and thousands of small effect causal variants. Our current understanding of RA risk has suggested cell-type-specific contexts for causal variants, implicating CD4 + effector memory T cells, as well as monocytes, B cells and stromal fibroblasts. While these cellular states and categories are still mechanistically broad, future studies may identify causal cell subpopulations. These efforts are propelled by advances in single cell profiling. Identification of causal cell subpopulations may accelerate therapeutic intervention to achieve lifelong remission.
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Affiliation(s)
- Tiffany Amariuta
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Graduate School of Arts and Sciences, Harvard University, Boston, MA, USA
| | - Yang Luo
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Rachel Knevel
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Yukinori Okada
- Division of Medicine, Osaka University, Osaka, Japan.,Osaka University Graduate School of Medicine, Osaka, Japan
| | - Soumya Raychaudhuri
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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28
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Bastami M, Choupani J, Saadatian Z, Zununi Vahed S, Ouladsahebmadarek E, Mansoori Y, Daraei A, Samadi Kafil H, Yousefi B, Mahdipour M, Masotti A, Nariman-Saleh-Fam Z. Evidences from a Systematic Review and Meta-Analysis Unveil the Role of MiRNA Polymorphisms in the Predisposition to Female Neoplasms. Int J Mol Sci 2019; 20:ijms20205088. [PMID: 31615040 PMCID: PMC6834313 DOI: 10.3390/ijms20205088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/24/2019] [Accepted: 10/10/2019] [Indexed: 12/24/2022] Open
Abstract
Breast (BCa) and gynecological (GCa) cancers constitute a group of female neoplasms that has a worldwide significant contribution to cancer morbidity and mortality. Evidence suggests that polymorphisms influencing miRNA function can provide useful information towards predicting the risk of female neoplasms. Inconsistent findings in the literature should be detected and resolved to facilitate the genetic screening of miRNA polymorphisms, even during childhood or adolescence, and their use as predictors of future malignancies. This study represents a comprehensive systematic review and meta-analysis of the association between miRNA polymorphisms and the risk of female neoplasms. Meta-analysis was performed by pooling odds-ratios (ORs) and generalized ORs while using a random-effects model for 15 miRNA polymorphisms. The results suggest that miR-146a rs2910164 is implicated in the susceptibility to GCa. Moreover, miR-196a2 rs11614913-T had a moderate protective effect against female neoplasms, especially GCa, in Asians but not in Caucasians. MiR-27a rs895819-G might pose a protective effect against BCa among Caucasians. MiR-499 rs3746444-C may slightly increase the risk of female neoplasms, especially BCa. MiR-124 rs531564-G may be associated with a lower risk of female neoplasms. The current evidences do not support the association of the remaining polymorphisms and the risk of female neoplasms.
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Affiliation(s)
- Milad Bastami
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5166614756, Iran.
| | - Jalal Choupani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166614756, Iran.
| | - Zahra Saadatian
- Department of Basic Sciences, Faculty of Medicine, Gonabad University of Medical Sciences, Gonabad 9691793718, Iran.
| | - Sepideh Zununi Vahed
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz 5166614756, Iran.
| | - Elaheh Ouladsahebmadarek
- Women's Reproductive Health Research Center, Tabriz University of Medical Sciences, Tabriz 5138663134, Iran.
| | - Yasser Mansoori
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa 7461686688, Iran.
| | - Abdolreza Daraei
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol 4617647745, Iran.
| | - Hossein Samadi Kafil
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166614756, Iran.
| | - Bahman Yousefi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz 5165665811, Iran.
| | - Mahdi Mahdipour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz 5166614756, Iran.
- Department of Reproductive Biology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz 5166614766, Iran.
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children's Hospital-IRCCS, Rome 00146, Italy.
| | - Ziba Nariman-Saleh-Fam
- Women's Reproductive Health Research Center, Tabriz University of Medical Sciences, Tabriz 5138663134, Iran.
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A novel analysis method for biomarker identification based on horizontal relationship: identifying potential biomarkers from large-scale hepatocellular carcinoma metabolomics data. Anal Bioanal Chem 2019; 411:6377-6386. [DOI: 10.1007/s00216-019-02011-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/03/2019] [Accepted: 07/01/2019] [Indexed: 02/07/2023]
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30
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Rhead B, Shao X, Graves JS, Chitnis T, Waldman AT, Lotze T, Schreiner T, Belman A, Krupp L, Greenberg BM, Weinstock–Guttman B, Aaen G, Tillema JM, Rodriguez M, Hart J, Caillier S, Ness J, Harris Y, Rubin J, Candee MS, Gorman M, Benson L, Mar S, Kahn I, Rose J, Casper TC, Quach H, Quach D, Schaefer C, Waubant E, Barcellos LF. miRNA contributions to pediatric-onset multiple sclerosis inferred from GWAS. Ann Clin Transl Neurol 2019; 6:1053-1061. [PMID: 31211169 PMCID: PMC6562070 DOI: 10.1002/acn3.786] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE Onset of multiple sclerosis (MS) occurs in childhood for approximately 5% of cases (pediatric MS, or ped-MS). Epigenetic influences are strongly implicated in MS pathogenesis in adults, including the contribution from microRNAs (miRNAs), small noncoding RNAs that affect gene expression by binding target gene mRNAs. Few studies have specifically examined miRNAs in ped-MS, but individuals developing MS at an early age may carry a relatively high burden of genetic risk factors, and miRNA dysregulation may therefore play a larger role in the development of ped-MS than in adult-onset MS. This study aimed to look for evidence of miRNA involvement in ped-MS pathogenesis. METHODS GWAS results from 486 ped-MS cases and 1362 controls from the U.S. Pediatric MS Network and Kaiser Permanente Northern California membership were investigated for miRNA-specific signals. First, enrichment of miRNA-target gene network signals was evaluated using MIGWAS software. Second, SNPs in miRNA genes and in target gene binding sites (miR-SNPs) were tested for association with ped-MS, and pathway analysis was performed on associated target genes. RESULTS MIGWAS analysis showed that miRNA-target gene signals were enriched in GWAS (P = 0.038) and identified 39 candidate biomarker miRNA-target gene pairs, including immune and neuronal signaling genes. The miR-SNP analysis implicated dysregulation of miRNA binding to target genes in five pathways, mainly involved in immune signaling. INTERPRETATION Evidence from GWAS suggests that miRNAs play a role in ped-MS pathogenesis by affecting immune signaling and other pathways. Candidate biomarker miRNA-target gene pairs should be further studied for diagnostic, prognostic, and/or therapeutic utility.
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Affiliation(s)
- Brooke Rhead
- Division of EpidemiologySchool of Public HealthUniversity of CaliforniaBerkeleyCalifornia
- Computational Biology Graduate GroupUniversity of CaliforniaBerkeleyCalifornia
| | - Xiaorong Shao
- Division of EpidemiologySchool of Public HealthUniversity of CaliforniaBerkeleyCalifornia
| | - Jennifer S. Graves
- Department of NeurologyUniversity of CaliforniaSan FranciscoCalifornia
- Department of NeurosciencesUniversity of CaliforniaSan DiegoCalifornia
| | - Tanuja Chitnis
- Partners Pediatric Multiple Sclerosis CenterMassachusetts General Hospital for ChildrenBostonMassachusetts
| | - Amy T. Waldman
- Division of NeurologyChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvania
| | - Timothy Lotze
- Blue Bird Circle Multiple Sclerosis CenterBaylor College of MedicineHoustonTexas
| | - Teri Schreiner
- Children's Hospital ColoradoUniversity of ColoradoDenverColorado
| | - Anita Belman
- Lourie Center for Pediatric MSStony Brook Children's HospitalStony BrookNew York
| | - Lauren Krupp
- Lourie Center for Pediatric MSStony Brook Children's HospitalStony BrookNew York
| | - Benjamin M. Greenberg
- Department of Neurology and NeurotherapeuticsUniversity of Texas SouthwesternDallasTexas
| | | | - Gregory Aaen
- Pediatric MS Center at Loma Linda University Children's HospitalLoma LindaCalifornia
| | | | | | - Janace Hart
- University of California, San FranciscoRegional Pediatric MS Center NeurologySan FranciscoCalifornia
| | - Stacy Caillier
- University of California, San FranciscoRegional Pediatric MS Center NeurologySan FranciscoCalifornia
| | - Jayne Ness
- University of Alabama Center for Pediatric–onset Demyelinating DiseaseChildren's Hospital of AlabamaBirminghamAlabama
| | - Yolanda Harris
- University of Alabama Center for Pediatric–onset Demyelinating DiseaseChildren's Hospital of AlabamaBirminghamAlabama
| | - Jennifer Rubin
- Department of Pediatric NeurologyNorthwestern Feinberg School of MedicineChicagoIllinois
| | - Meghan S. Candee
- Division of Pediatric NeurologyUniversity of UtahPrimary Children's HospitalSalt Lake CityUtah
| | - Mark Gorman
- Boston Children's HospitalBostonMassachusetts
| | | | - Soe Mar
- Pediatric–onset Demyelinating Diseases and Autoimmune Encephalitis CenterSt. Louis Children's HospitalWashington University School of MedicineSt. LouisMissouri
| | - Ilana Kahn
- Children's National Medical CenterWashingtonDistrict of Columbia
| | - John Rose
- Department of NeurologyUniversity of Utah School of MedicineSalt Lake CityUtah
| | - T. Charles Casper
- Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUtah
| | - Hong Quach
- Division of EpidemiologySchool of Public HealthUniversity of CaliforniaBerkeleyCalifornia
| | - Diana Quach
- Division of EpidemiologySchool of Public HealthUniversity of CaliforniaBerkeleyCalifornia
| | - Catherine Schaefer
- Kaiser Permanente Division of ResearchOaklandCalifornia
- Research Program on Genes, Environment and HealthKaiser PermanenteOaklandCalifornia
| | | | - Lisa F. Barcellos
- Division of EpidemiologySchool of Public HealthUniversity of CaliforniaBerkeleyCalifornia
- Computational Biology Graduate GroupUniversity of CaliforniaBerkeleyCalifornia
- Kaiser Permanente Division of ResearchOaklandCalifornia
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Abstract
PURPOSE OF REVIEW Autoimmune diseases are of unknown origin, and they represent significant causes of morbidity and mortality. Here, we review new developments in the understanding of their pathogenesis that have led to development of well tolerated and effective treatments. RECENT FINDINGS In addition to the long-recognized genetic impact of the HLA locus, interferon regulatory factors, PTPN22, STAT4, and NOX have been implicated in pathogenesis of systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). Smoking, ultraviolet light, diet, and microbiota exert strong environmental influence on development of RA and SLE. Metabolism has been recognized as a critical integrator of genetic and environmental factors, and it controls immune cell differentiation both under physiological and pathological conditions. SUMMARY With the advent of high-throughput genetic, proteomic, and metabolomic technologies, the field of medicine has been shifting towards systems-based and personalized approaches to diagnose and treat common conditions, including rheumatic diseases. Regulatory checkpoints of metabolism and signal transduction, such as glucose utilization, mitochondrial electron transport, JAK, mTOR, and AMPK pathway activation, and production of pro-inflammatory cytokines IL-1, IL-6, and IL-17 have presented new targets for therapeutic intervention. This review amalgamates recent discoveries in genetics and metabolomics with immunological pathways of pathogenesis in rheumatic diseases.
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Affiliation(s)
- Eric Liu
- Division of Rheumatology, Departments of Medicine, Microbiology and Immunology, Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, College of Medicine, Syracuse, New York, USA
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Urbanek-Trzeciak MO, Jaworska E, Krzyzosiak WJ. miRNAmotif-A Tool for the Prediction of Pre-miRNA⁻Protein Interactions. Int J Mol Sci 2018; 19:ijms19124075. [PMID: 30562930 PMCID: PMC6321451 DOI: 10.3390/ijms19124075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are short, non-coding post-transcriptional gene regulators. In mammalian cells, mature miRNAs are produced from primary precursors (pri-miRNAs) using canonical protein machinery, which includes Drosha/DGCR8 and Dicer, or the non-canonical mirtron pathway. In plant cells, mature miRNAs are excised from pri-miRNAs by the DICER-LIKE1 (DCL1) protein complex. The involvement of multiple regulatory proteins that bind directly to distinct miRNA precursors in a sequence- or structure-dependent manner adds to the complexity of the miRNA maturation process. Here, we present a web server that enables searches for miRNA precursors that can be recognized by diverse RNA-binding proteins based on known sequence motifs to facilitate the identification of other proteins involved in miRNA biogenesis. The database used by the web server contains known human, murine, and Arabidopsis thaliana pre-miRNAs. The web server can also be used to predict new RNA-binding protein motifs based on a list of user-provided sequences. We show examples of miRNAmotif applications, presenting precursors that contain motifs recognized by Lin28, MCPIP1, and DGCR8 and predicting motifs within pre-miRNA precursors that are recognized by two DEAD-box helicases—DDX1 and DDX17. miRNAmotif is released as an open-source software under the MIT License. The code is available at GitHub (www.github.com/martynaut/mirnamotif). The webserver is freely available at http://mirnamotif.ibch.poznan.pl.
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Affiliation(s)
- Martyna O Urbanek-Trzeciak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Edyta Jaworska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Wlodzimierz J Krzyzosiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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Okada Y, Eyre S, Suzuki A, Kochi Y, Yamamoto K. Genetics of rheumatoid arthritis: 2018 status. Ann Rheum Dis 2018; 78:446-453. [PMID: 30530827 DOI: 10.1136/annrheumdis-2018-213678] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 01/08/2023]
Abstract
Study of the genetics of rheumatoid arthritis (RA) began about four decades ago with the discovery of HLA-DRB1 Since the beginning of this century, a number of non-HLA risk loci have been identified through genome-wide association studies (GWAS). We now know that over 100 loci are associated with RA risk. Because genetic information implies a clear causal relationship to the disease, research into the pathogenesis of RA should be promoted. However, only 20% of GWAS loci contain coding variants, with the remaining variants occurring in non-coding regions, and therefore, the majority of causal genes and causal variants remain to be identified. The use of epigenetic studies, high-resolution mapping of open chromatin, chromosomal conformation technologies and other approaches could identify many of the missing links between genetic risk variants and causal genetic components, thus expanding our understanding of RA genetics.
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Affiliation(s)
- Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.,Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Stephen Eyre
- Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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