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Kolipaka R, Magesh I, Bharathy MA, Karthik S, Saranya I, Selvamurugan N. A potential function for MicroRNA-124 in normal and pathological bone conditions. Noncoding RNA Res 2024; 9:687-694. [PMID: 38577015 PMCID: PMC10990750 DOI: 10.1016/j.ncrna.2024.02.018] [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: 01/07/2024] [Revised: 02/22/2024] [Accepted: 02/25/2024] [Indexed: 04/06/2024] Open
Abstract
Cells produce short single-stranded non-coding RNAs (ncRNAs) called microRNAs (miRNAs), which actively regulate gene expression at the posttranscriptional level. Several miRNAs have been observed to exert significant impacts on bone health and bone-related disorders. One of these, miR-124, is observed in bone microenvironments and is conserved across species. It affects bone cell growth and differentiation by activating different transcription factors and signaling pathways. In-depth functional analyses of miR-124 have revealed several physiological and pathological roles exerted through interactions with other ncRNAs. Deciphering these RNA-mediated signaling networks and pathways is essential for understanding the potential impacts of dysregulated miRNA functions on bone biology. In this review, we aim to provide a comprehensive analysis of miR-124's involvement in bone physiology and pathology. We highlight the importance of miR-124 in controlling transcription factors and signaling pathways that promote bone growth. This review reveals therapeutic implications for the treatment of bone-related diseases.
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Affiliation(s)
- Rushil Kolipaka
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - Induja Magesh
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - M.R. Ashok Bharathy
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - S. Karthik
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - I. Saranya
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - N. Selvamurugan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
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2
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Liang M, An B, Deng T, Du L, Li K, Cao S, Du Y, Xu L, Zhang L, Gao X, Cao Y, Zhao Y, Li J, Gao H. Incorporating genome-wide and transcriptome-wide association studies to identify genetic elements of longissimus dorsi muscle in Huaxi cattle. Front Genet 2023; 13:982433. [PMID: 36685878 PMCID: PMC9852892 DOI: 10.3389/fgene.2022.982433] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/07/2022] [Indexed: 01/07/2023] Open
Abstract
Locating the genetic variation of important livestock and poultry economic traits is essential for genetic improvement in breeding programs. Identifying the candidate genes for the productive ability of Huaxi cattle was one crucial element for practical breeding. Based on the genotype and phenotype data of 1,478 individuals and the RNA-seq data of 120 individuals contained in 1,478 individuals, we implemented genome-wide association studies (GWAS), transcriptome-wide association studies (TWAS), and Fisher's combined test (FCT) to identify the candidate genes for the carcass trait, the weight of longissimus dorsi muscle (LDM). The results indicated that GWAS, TWAS, and FCT identified seven candidate genes for LDM altogether: PENK was located by GWAS and FCT, PPAT was located by TWAS and FCT, and XKR4, MTMR3, FGFRL1, DHRS4, and LAP3 were only located by one of the methods. After functional analysis of these candidate genes and referring to the reported studies, we found that they were mainly functional in the progress of the development of the body and the growth of muscle cells. Combining advanced breeding techniques such as gene editing with our study will significantly accelerate the genetic improvement for the future breeding of Huaxi cattle.
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Affiliation(s)
- Mang Liang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingxing An
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyu Deng
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lili Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Keanning Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sheng Cao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yueying Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Cao
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yuming Zhao
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Huijiang Gao,
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3
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Role of miRNAs in the regulation of cancer-associated signaling pathways. Noncoding RNA Res 2022. [DOI: 10.1016/j.ncrna.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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4
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Natterson-Horowitz B, Baccouche BM, Mary J, Shivkumar T, Bertelsen MF, Aalkjær C, Smerup MH, Ajijola OA, Hadaya J, Wang T. Did giraffe cardiovascular evolution solve the problem of heart failure with preserved ejection fraction? EVOLUTION MEDICINE AND PUBLIC HEALTH 2021; 9:248-255. [PMID: 34447575 PMCID: PMC8385250 DOI: 10.1093/emph/eoab016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 06/04/2021] [Indexed: 11/18/2022]
Abstract
The evolved adaptations of other species can be a source of insight for novel biomedical innovation. Limitations of traditional animal models for the study of some pathologies are fueling efforts to find new approaches to biomedical investigation. One emerging approach recognizes the evolved adaptations in other species as possible solutions to human pathology. The giraffe heart, for example, appears resistant to pathology related to heart failure with preserved ejection fraction (HFpEF)—a leading form of hypertension-associated cardiovascular disease in humans. Here, we postulate that the physiological pressure-induced left ventricular thickening in giraffes does not result in the pathological cardiovascular changes observed in humans with hypertension. The mechanisms underlying this cardiovascular adaptation to high blood pressure in the giraffe may be a bioinspired roadmap for preventive and therapeutic strategies for human HFpEF.
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Affiliation(s)
- Barbara Natterson-Horowitz
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Basil M Baccouche
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jennifer Mary
- Zoobiquity Research Initiative at UCLA, Los Angeles, CA 90024, USA
| | | | | | | | - Morten H Smerup
- Department of Cardiothoracic Surgery, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Olujimi A Ajijola
- UCLA Cardiac Arrhythmia Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Joseph Hadaya
- UCLA Cardiac Arrhythmia Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Molecular, Cellular and Integrative Physiology Program, UCLA, Los Angeles, CA, USA
| | - Tobias Wang
- Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
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5
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Liu C, Gao J, Cui X, Li Z, Chen L, Yuan Y, Zhang Y, Mei L, Zhao L, Cai D, Hu M, Zhou B, Li Z, Qin T, Si H, Li G, Lin Z, Xu Y, Zhu C, Yin Y, Zhang C, Xu W, Li Q, Wang K, Gilbert MTP, Heller R, Wang W, Huang J, Qiu Q. A towering genome: Experimentally validated adaptations to high blood pressure and extreme stature in the giraffe. SCIENCE ADVANCES 2021; 7:7/12/eabe9459. [PMID: 33731352 PMCID: PMC7968835 DOI: 10.1126/sciadv.abe9459] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/02/2021] [Indexed: 05/02/2023]
Abstract
The suite of adaptations associated with the extreme stature of the giraffe has long interested biologists and physiologists. By generating a high-quality chromosome-level giraffe genome and a comprehensive comparison with other ruminant genomes, we identified a robust catalog of giraffe-specific mutations. These are primarily related to cardiovascular, bone growth, vision, hearing, and circadian functions. Among them, the giraffe FGFRL1 gene is an outlier with seven unique amino acid substitutions not found in any other ruminant. Gene-edited mice with the giraffe-type FGFRL1 show exceptional hypertension resistance and higher bone mineral density, both of which are tightly connected with giraffe adaptations to high stature. Our results facilitate a deeper understanding of the molecular mechanism underpinning distinct giraffe traits, and may provide insights into the study of hypertension in humans.
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Affiliation(s)
- Chang Liu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Jianbo Gao
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an 710032, China
| | - Xinxin Cui
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yuan Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Liangwei Mei
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an 710032, China
| | - Lan Zhao
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Xi'an 710069, China
| | - Dan Cai
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Mingliang Hu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Botong Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Zihe Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tao Qin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Huazhe Si
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Guangyu Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Zeshan Lin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yicheng Xu
- Jiaxing SynBioLab. Co. Ltd., Jiaxing 314000, China
| | - Chenglong Zhu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yuan Yin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Chenzhou Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Qingjie Li
- Research Center of Traditional Chinese Medicine, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun 130021, China
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350, Denmark
- Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N 2200, Denmark.
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Jinghui Huang
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an 710032, China.
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China.
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6
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Wang Y, Ye W, Liu Y, Mei B, Liu X, Huang Q. Osteoporosis genome-wide association study variant c.3781 C>A is regulated by a novel anti-osteogenic factor miR-345-5p. Hum Mutat 2020; 41:709-718. [PMID: 31883164 DOI: 10.1002/humu.23959] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 12/21/2022]
Abstract
Upstream transcription factor family member 3 (USF3) c.3781C>A (rs1026364) in the 3'-untranslated region (3'-UTR) has been firmly associated with bone mineral density (BMD) in genome-wide association study (GWAS). However, the molecular mechanism by which it influences BMD and osteoporosis is unknown. Bioinformatics analyses suggested that the risk c.3781A allele creates a target site for hsa-miR-345-5p binding. Luciferase assay validated that the c.3781A allele displayed significantly lower luciferase activities than the c.3781C allele in the human osteoblast cell line hFOB1.19, osteosarcoma cell lines U-2OS and Saos-2, and embryonic kidney cell line 293T. Furthermore, hsa-miR-345-5p regulated USF3 expression on both messenger RNA and protein levels in hFOB1.19 and U937 cells with heterozygous A/C genotype. Transfection of hsa-miR-345-5p antagomiR in heterozygous hFOB1.19 cells significantly increased the expression of osteogenic marker genes RUNX2, OSTERIX, COL1A1, ALP, OPN, OCN, and alkaline phosphatase activity and matrix mineralization level. Importantly, we found that hsa-miR-345-5p also inhibits osteoblast maturation in cell lines U-2OS with hsa-miR-345-5p nonbinding C/C genotype by targeting RUNX3 and SMAD1. Our findings uncovered a novel pathogenetic mechanism of osteoporosis by GWAS variant c.3781C>A-mediated disruption of hsa-miR-345-5p binding at the 3'-UTR of USF3 and the functional role of hsa-miR-345-5p in osteogenic differentiation.
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Affiliation(s)
- Ya Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Weiyuan Ye
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Yuyong Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Bing Mei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Xinhong Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Qingyang Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
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7
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Zheng W, Liu C, Lei M, Han Y, Zhou X, Li C, Sun S, Ma X. Evaluation of common variants in the CNR2 gene and its interaction with abdominal obesity for osteoporosis susceptibility in Chinese post-menopausal females. Bone Joint Res 2019; 8:544-549. [PMID: 31832174 PMCID: PMC6888734 DOI: 10.1302/2046-3758.811.bjr-2018-0284.r1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objectives The objective of this study was to investigate the association of four single-nucleotide polymorphisms (SNPs) of the cannabinoid receptor 2 (CNR2) gene, gene-obesity interaction, and haplotype combination with osteoporosis (OP) susceptibility. Methods Chinese patients with OP were recruited between March 2011 and December 2015 from our hospital. In this study, a total of 1267 post-menopausal female patients (631 OP patients and 636 control patients) were selected. The mean age of all subjects was 69.2 years (sd 15.8). A generalized multifactor dimensionality reduction (GMDR) model and logistic regression model were used to examine the interaction between SNP and obesity on OP. For OP patient-control haplotype analyses, the SHEsis online haplotype analysis software (http://analysis.bio-x.cn/) was employed. Results The logistic regression model revealed that the C allele of rs2501431 and the G allele of rs3003336 were associated with increased OP risk, compared with those with wild genotype. However, no significant correlations were found when analyzing the association of rs4237 and rs2229579 with OP risk. The GMDR analysis suggested that the interaction model composed of two factors, rs3003336 and abdominal obesity (AO), was the best model with statistical significance (p-value from sign test (Psign) = 0.012), indicating a potential gene-environment interaction between rs3003336 and AO. Overall, the two-locus models had a cross-validation consistency of 10/10 and had a testing accuracy of 0.641. Abdominally obese subjects with the AG or GG genotype have the highest OP risk, compared with subjects with the AA genotype and normal waist circumference (WC) (odds ratio (OR) 2.23, 95% confidence interval (CI) 1.54 to 3.51). Haplotype analysis also indicated that the haplotype containing the rs3003336-G and rs2501431-C alleles was associated with a statistically increased OP risk. Conclusion Our results suggested that the C allele of rs2501431 and the G allele of rs3003336 of the CNR2 gene, interaction between rs3003336 and AO, and the haplotype containing the rs3003336-G and rs2501431-C alleles were all associated with increased OP risk. Cite this article: Bone Joint Res 2019;8:544–549.
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Affiliation(s)
- W Zheng
- Department of Orthopaedics, Affiliated Hospital of Hebei University, Baoding, China
| | - C Liu
- Department of Pharmacology, Department of Medicine, Hebei University, Baoding, China
| | - M Lei
- Department of Orthopaedics, Affiliated Hospital of Hebei University, Baoding, China
| | - Y Han
- Department of Orthopaedics, Affiliated Hospital of Hebei University, Baoding, China
| | - X Zhou
- Department of Orthopaedics, Affiliated Hospital of Hebei University, Baoding, China
| | - C Li
- Department of Orthopaedics, Affiliated Hospital of Hebei University, Baoding, China
| | - S Sun
- Department of Orthopaedics, Affiliated Hospital of Hebei University, Baoding, China
| | - X Ma
- Department of Orthopaedics, Affiliated Hospital of Hebei University, Baoding, China
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8
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Abstract
PURPOSE OF REVIEW The goal of the review is to provide a comprehensive overview of the current understanding of the mechanisms underlying variation in human stature. RECENT FINDINGS Human height is an anthropometric trait that varies considerably within human populations as well as across the globe. Historically, much research focus was placed on understanding the biology of growth plate chondrocytes and how modifications to core chondrocyte proliferation and differentiation pathways potentially shaped height attainment in normal as well as pathological contexts. Recently, much progress has been made to improve our understanding regarding the mechanisms underlying the normal and pathological range of height variation within as well as between human populations, and today, it is understood to reflect complex interactions among a myriad of genetic, environmental, and evolutionary factors. Indeed, recent improvements in genetics (e.g., GWAS) and breakthroughs in functional genomics (e.g., whole exome sequencing, DNA methylation analysis, ATAC-sequencing, and CRISPR) have shed light on previously unknown pathways/mechanisms governing pathological and common height variation. Additionally, the use of an evolutionary perspective has also revealed important mechanisms that have shaped height variation across the planet. This review provides an overview of the current knowledge of the biological mechanisms underlying height variation by highlighting new research findings on skeletal growth control with an emphasis on previously unknown pathways/mechanisms influencing pathological and common height variation. In this context, this review also discusses how evolutionary forces likely shaped the genomic architecture of height across the globe.
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Affiliation(s)
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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9
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Huang YT. Genome-wide analyses of sparse mediation effects under composite null hypotheses. Ann Appl Stat 2019. [DOI: 10.1214/18-aoas1181] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Cheng VKF, Au PCM, Tan KC, Cheung CL. MicroRNA and Human Bone Health. JBMR Plus 2018; 3:2-13. [PMID: 30680358 PMCID: PMC6339549 DOI: 10.1002/jbm4.10115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 12/19/2022] Open
Abstract
The small non‐coding microRNAs (miRNAs) are post‐transcription regulators that modulate diverse cellular process in bone cells. Because optimal miRNA targeting is essential for their function, single‐nucleotide polymorphisms (SNPs) within or proximal to the loci of miRNA (miR‐SNPs) or mRNA (PolymiRTS) could potentially disrupt the miRNA‐mRNA interaction, leading to changes in bone metabolism and osteoporosis. Recent human studies of skeletal traits using miRNA profiling, genomewide association studies, and functional studies started to decipher the complex miRNA regulatory network. These studies have indicated that miRNAs may be a promising bone marker. This review focuses on human miRNA studies on bone traits and discusses how genetic variants affect bone metabolic pathways. Major ex vivo investigations using human samples supported with animal and in vitro models have shed light on the mechanistic role of miRNAs. Furthermore, studying the miRNAs’ signatures in secondary osteoporosis and osteoporotic medications such as teriparatide (TPTD) and denosumab (DMab) have provided valuable insight into clinical management of the disease. © 2018 The Authors. JBMR Plus Published by Wiley Periodicals, Inc. on behalf of the American Society for Bone and Mineral Research
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Affiliation(s)
- Vincent Ka-Fai Cheng
- Department of Pharmacology and Pharmacy The University of Hong Kong Pokfulam Hong Kong
| | - Philip Chun-Ming Au
- Department of Pharmacology and Pharmacy The University of Hong Kong Pokfulam Hong Kong
| | - Kathryn Cb Tan
- Department of Medicine The University of Hong Kong Pokfulam Hong Kong
| | - Ching-Lung Cheung
- Department of Pharmacology and Pharmacy The University of Hong Kong Pokfulam Hong Kong.,Centre for Genomic Sciences Li Ka Shing Faculty of Medicine The University of Hong Kong Pokfulam Hong Kong
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11
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Piletic K, Kunej T. MicroRNA-Target Interactions Reloaded: Identification of Potentially Functional Sequence Variants Within Validated MicroRNA-Target Interactions. ACTA ACUST UNITED AC 2018; 22:700-708. [DOI: 10.1089/omi.2018.0159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Klara Piletic
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
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12
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Pei YF, Hu WZ, Yan MW, Li CW, Liu L, Yang XL, Hai R, Wang XY, Shen H, Tian Q, Deng HW, Zhang L. Joint study of two genome-wide association meta-analyses identified 20p12.1 and 20q13.33 for bone mineral density. Bone 2018; 110:378-385. [PMID: 29499414 PMCID: PMC6329308 DOI: 10.1016/j.bone.2018.02.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 01/19/2023]
Abstract
In the present study, aiming to identify loci associated with osteoporosis, we conducted a joint association study of 2 independent genome-wide association meta-analyses of femoral neck and lumbar spine bone mineral densities (BMDs): 1) an in-house study of 6 samples involving 7484 subjects, and 2) the GEFOS-seq study of 7 samples involving 32,965 subjects. The in-house samples were imputed by the 1000 genomes project phase 3 reference panel. SNP-based association test was applied to 7,998,108 autosomal SNPs in each meta-analysis, and for each SNP the 2 association signals were then combined for joint analysis and for mutual replication. Combining the evidence from both studies, we identified 2 novel loci associated with BMDs at the genome-wide significance level (α=5.0×10-8): 20p12.1 (rs73100693 p=2.65×10-8, closest gene MACROD2) and 20q13.33 (rs2380128 p=3.44×10-8, OSBPL2). We also replicated 7 loci that were reported by two recent studies on heel and total body BMD. Our findings provide useful insights that enhance our understanding of bone development, osteoporosis and fracture pathogenesis.
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Affiliation(s)
- Yu-Fang Pei
- Department of Epidemiology and Health Statistics, School of Public Health, Medical College of Soochow University, Jiangsu, PR China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Jiangsu, PR China
| | - Wen-Zhu Hu
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Jiangsu, PR China; Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, PR China
| | - Min-Wei Yan
- Department of Orthopedic Surgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, PR China
| | - Chang-Wei Li
- Department of Epidemiology and Biostatistics, University of Georgia College of Public Health, Athens, GA, USA
| | - Lu Liu
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Jiangsu, PR China; Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, PR China
| | - Xiao-Lin Yang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Jiangsu, PR China; Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, PR China
| | - Rong Hai
- Inner Mongolia Autonomous Region People's Hospital, Hohhot, Inner Mongolia, PR China
| | - Xiu-Yan Wang
- Inner Mongolia Autonomous Region People's Hospital, Hohhot, Inner Mongolia, PR China
| | - Hui Shen
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Qing Tian
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Hong-Wen Deng
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA.
| | - Lei Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Jiangsu, PR China; Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, PR China.
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13
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Kähkönen TE, Ivaska KK, Jiang M, Büki KG, Väänänen HK, Härkönen PL. Role of fibroblast growth factor receptors (FGFR) and FGFR like-1 (FGFRL1) in mesenchymal stromal cell differentiation to osteoblasts and adipocytes. Mol Cell Endocrinol 2018; 461:194-204. [PMID: 28923346 DOI: 10.1016/j.mce.2017.09.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 08/16/2017] [Accepted: 09/13/2017] [Indexed: 12/13/2022]
Abstract
Fibroblast growth factors (FGF) and their receptors (FGFRs) regulate many developmental processes including differentiation of mesenchymal stromal cells (MSC). We developed two MSC lines capable of differentiating to osteoblasts and adipocytes and studied the role of FGFRs in this process. We identified FGFR2 and fibroblast growth factor receptor like-1 (FGFRL1) as possible actors in MSC differentiation with gene microarray and qRT-PCR. FGFR2 and FGFRL1 mRNA expression strongly increased during MSC differentiation to osteoblasts. FGF2 treatment, resulting in downregulation of FGFR2, or silencing FGFR2 expression with siRNAs inhibited osteoblast differentiation. During adipocyte differentiation expression of FGFR1 and FGFRL1 increased and was down-regulated by FGF2. FGFR1 knockdown inhibited adipocyte differentiation. Silencing FGFR2 and FGFR1 in MSCs was associated with decreased FGFRL1 expression in osteoblasts and adipocytes, respectively. Our results suggest that FGFR1 and FGFR2 regulate FGFRL1 expression. FGFRL1 may mediate or modulate FGFR regulation of MSC differentiation together with FGFR2 in osteoblastic and FGFR1 in adipocytic lineage.
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Affiliation(s)
- T E Kähkönen
- University of Turku, Institute of Biomedicine, Turku, Finland.
| | - K K Ivaska
- University of Turku, Institute of Biomedicine, Turku, Finland
| | - M Jiang
- University of Turku, Institute of Biomedicine, Turku, Finland
| | - K G Büki
- University of Turku, Institute of Biomedicine, Turku, Finland
| | - H K Väänänen
- University of Turku, Institute of Biomedicine, Turku, Finland
| | - P L Härkönen
- University of Turku, Institute of Biomedicine, Turku, Finland
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14
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Abstract
PURPOSE OF REVIEW Osteogenesis is a complex process involving the specification of multiple progenitor cells and their maturation and differentiation into matrix-secreting osteoblasts. Osteogenesis occurs not only during embryogenesis but also during growth, after an injury, and in normal homeostatic maintenance. While much is known about osteogenesis-associated regulatory genes, the role of microRNAs (miRNAs), which are epigenetic regulators of protein expression, is just beginning to be explored. While miRNAs do not abrogate all protein expression, their purpose is to finely tune it, allowing for a timely and temporary protein down-regulation. RECENT FINDINGS The last decade has unveiled a multitude of miRNAs that regulate key proteins within the osteogenic lineage, thus qualifying them as "ostemiRs." These miRNAs may endogenously target an activator or inhibitor of differentiation, and depending on the target, may either lead to the prolongation of a progenitor maintenance state or to early differentiation. Interestingly, cellular identity seems intimately coupled to the expression of miRNAs, which participate in the suppression of previous and subsequent differentiation steps. In such cases where key osteogenic proteins were identified as direct targets of miRNAs in non-bone cell types, or through bioinformatic prediction, future research illuminating the activity of these miRNAs during osteogenesis will be extremely valuable. Many bone-related diseases involve the dysregulation of transcription factors or other proteins found within osteoblasts and their progenitors, and the dysregulation of miRNAs, which target such factors, may play a pivotal role in disease etiology, or even as a possible therapy.
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Affiliation(s)
- Steven R Sera
- Department of Cell Biology and Neuroscience and Stem Cell Center, College of Natural and Agricultural Sciences, University of California Riverside, 1113 Biological Sciences Building, Riverside, CA, 92521, USA
| | - Nicole I Zur Nieden
- Department of Cell Biology and Neuroscience and Stem Cell Center, College of Natural and Agricultural Sciences, University of California Riverside, 1113 Biological Sciences Building, Riverside, CA, 92521, USA.
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15
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Li M, Guan H. Noncoding RNAs Regulating NF-κB Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 927:317-36. [PMID: 27376741 DOI: 10.1007/978-981-10-1498-7_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As transcription factors that regulate expression of a variety of genes essential for diverse physiological and pathological processes, nuclear factor kappa B (NF-κB) family molecules play important roles in the development and progression of malignant tumor, and constitutive activation of NF-κB has been evidenced in various types of tumor tissues. Underlying its pathologic role, deregulated expression and/or transactivating activity of NF-κB usually involves multiple layers of molecular mechanisms. Noncoding RNAs, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are known to modulate expression and biological functions of regulatory proteins in a variety of cancer contexts. In this chapter, the regulatory role of miRNAs and lncRNAs in NF-κB signaling in malignant diseases will be discussed.
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Affiliation(s)
- Mengfeng Li
- Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, China.
| | - Hongyu Guan
- Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, China
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16
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Gan S, Huang Z, Liu N, Su R, Xie G, Zhong B, Zhang K, Wang S, Hu X, Zhang J, Xiang S. MicroRNA-140-5p impairs zebrafish embryonic bone development via targeting BMP-2. FEBS Lett 2017; 590:1438-46. [PMID: 27130837 DOI: 10.1002/1873-3468.12190] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 12/21/2022]
Abstract
MicroRNA-140-5p (miRNA-140-5p) is important for embryonic bone development. In this study, we found that miRNA-140-5p and its binding site in the 3'UTR of bone morphogenetic protein 2 (BMP-2) are highly conserved among vertebrates, and miRNA-140-5p negatively regulates both zebrafish and human BMP-2 genes. Microinjection of miRNA-140-5p or BMP-2b morpholino into zebrafish embryos led to a similar phenotype, including shortened tails, curved trunks, and defects in cranial cartilage. Moreover, miRNA-140-5p injection induced zebrafish embryo malformation that could be significantly rescued by microinjection of BMP-2 mRNA. In conclusion, our results indicated that miRNA-140-5p regulates zebrafish embryonic bone development via targeting BMP-2.
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Affiliation(s)
- Shiquan Gan
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, Department of Biochemistry and Molecular Biology, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486), Changsha, Hunan, China
| | - Zhaoqin Huang
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, Department of Biochemistry and Molecular Biology, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486), Changsha, Hunan, China
| | - Ning Liu
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, Department of Biochemistry and Molecular Biology, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,College of Medicine, Hunan Normal University, Changsha, Hunan, China
| | - Renxiang Su
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, Department of Biochemistry and Molecular Biology, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486), Changsha, Hunan, China
| | - Guie Xie
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, Department of Biochemistry and Molecular Biology, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486), Changsha, Hunan, China
| | - Beibei Zhong
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, Department of Biochemistry and Molecular Biology, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486), Changsha, Hunan, China
| | - Kai Zhang
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, Department of Biochemistry and Molecular Biology, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486), Changsha, Hunan, China
| | - Shang Wang
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, Department of Biochemistry and Molecular Biology, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486), Changsha, Hunan, China
| | - Xiang Hu
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, Department of Biochemistry and Molecular Biology, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486), Changsha, Hunan, China
| | - Jian Zhang
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, Department of Biochemistry and Molecular Biology, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486), Changsha, Hunan, China
| | - Shuanglin Xiang
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, Department of Biochemistry and Molecular Biology, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486), Changsha, Hunan, China
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17
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Zhang X, Chu Q, Guo G, Dong G, Li X, Zhang Q, Zhang S, Zhang Z, Wang Y. Genome-wide association studies identified multiple genetic loci for body size at four growth stages in Chinese Holstein cattle. PLoS One 2017; 12:e0175971. [PMID: 28426785 PMCID: PMC5398616 DOI: 10.1371/journal.pone.0175971] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 04/03/2017] [Indexed: 12/14/2022] Open
Abstract
The growth and maturity of cattle body size affect not only feed efficiency, but also productivity and longevity. Dissecting the genetic architecture of body size is critical for cattle breeding to improve both efficiency and productivity. The volume and weight of body size are indicated by several measurements. Among them, Heart Girth (HG) and Hip Height (HH) are the most important traits. They are widely used as predictors of body weight (BW). Few association studies have been conducted for HG and HH in cattle focusing on single growth stage. In this study, we extended the Genome-wide association studies to a full spectrum of four growth stages (6-, 12-, 18-, and 24-months after birth) in Chinese Holstein heifers. The whole genomic single nucleotide polymorphisms (SNPs) were obtained from the Illumina BovineSNP50 v2 BeadChip genotyped on 3,325 individuals. Estimated breeding values (EBVs) were derived for both HG and HH at the four different ages and analyzed separately for GWAS by using the Fixed and random model Circuitous Probability Unification (FarmCPU) method. In total, 27 SNPs were identified to be significantly associated with HG and HH at different growth stages. We found 66 candidate genes located nearby the associated SNPs, including nine genes that were known as highly related to development and skeletal and muscular growth. In addition, biological function analysis was performed by Ingenuity Pathway Analysis and an interaction network related to development was obtained, which contained 16 genes out of the 66 candidates. The set of putative genes provided valuable resources and can help elucidate the genomic architecture and mechanisms underlying growth traits in dairy cattle.
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Affiliation(s)
- Xu Zhang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P.R. China
| | - Gang Guo
- Beijing Sunlon Livestock Development Co. Ltd, Beijing, P.R. China
| | - Ganghui Dong
- Beijing Sunlon Livestock Development Co. Ltd, Beijing, P.R. China
| | - Xizhi Li
- Beijing Sunlon Livestock Development Co. Ltd, Beijing, P.R. China
| | - Qin Zhang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - Shengli Zhang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Yachun Wang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
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18
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The roles of RNA processing in translating genotype to phenotype. NATURE REVIEWS. MOLECULAR CELL BIOLOGY 2016. [PMID: 27847391 DOI: 10.1038/nrm.2016.139.] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A goal of human genetics studies is to determine the mechanisms by which genetic variation produces phenotypic differences that affect human health. Efforts in this respect have previously focused on genetic variants that affect mRNA levels by altering epigenetic and transcriptional regulation. Recent studies show that genetic variants that affect RNA processing are at least equally as common as, and are largely independent from, those variants that affect transcription. We highlight the impact of genetic variation on pre-mRNA splicing and polyadenylation, and on the stability, translation and structure of mRNAs as mechanisms that produce phenotypic traits. These results emphasize the importance of including RNA processing signals in analyses to identify functional variants.
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19
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Manning KS, Cooper TA. The roles of RNA processing in translating genotype to phenotype. Nat Rev Mol Cell Biol 2016; 18:102-114. [PMID: 27847391 DOI: 10.1038/nrm.2016.139] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A goal of human genetics studies is to determine the mechanisms by which genetic variation produces phenotypic differences that affect human health. Efforts in this respect have previously focused on genetic variants that affect mRNA levels by altering epigenetic and transcriptional regulation. Recent studies show that genetic variants that affect RNA processing are at least equally as common as, and are largely independent from, those variants that affect transcription. We highlight the impact of genetic variation on pre-mRNA splicing and polyadenylation, and on the stability, translation and structure of mRNAs as mechanisms that produce phenotypic traits. These results emphasize the importance of including RNA processing signals in analyses to identify functional variants.
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Affiliation(s)
- Kassie S Manning
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Thomas A Cooper
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.,Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, Texas 77030, USA
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20
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Kitjaroentham A, Hananantachai H, Phonrat B, Preutthipan S, Tungtrongchitr R. Low density lipoprotein receptor-related protein 5 gene polymorphisms and osteoporosis in Thai menopausal women. J Negat Results Biomed 2016; 15:16. [PMID: 27582019 PMCID: PMC5007848 DOI: 10.1186/s12952-016-0059-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 08/17/2016] [Indexed: 11/13/2022] Open
Abstract
Background Osteoporosis, characterized by low bone mineral density (BMD) and high bone fracture risk, is prevalent in Thai menopausal women. Genetic factors are known to play a key role in BMD. Low density lipoprotein receptor-related protein 5 (LRP5), a co-receptor in the Wnt/beta-catenin pathway, is involved in many aspects of bone biology. As coding single nucleotide polymorphisms (cSNPs) of LRP5, including A1330V (rs3736228), and Asian-related Q89R (rs41494349) and N740N (rs2306862), are associated with lowered BMD, this study aimed to determine the relationship between these LRP5 polymorphisms and BMD in 277 Thai menopausal women. Results Only rs3736228 deviated from the Hardy–Weinberg equilibrium of allele frequency (p = 0.022). The median, range and p value for the BMD related to each SNP parameter were compared (Mann–Whitney U test). Significant differences were observed between wild-type and risk alleles for both rs3736228 (total radial, p = 0.011; and radial 33, p = 0.001) and rs2306862 (radial 33: p = 0.015) SNPs, with no significant difference for rs41494349 SNP. Linkage disequilibrium was strong for both rs3736228 and rs2306862 SNPs. Haplotype analysis identified high CC frequency in both normal and osteopenia/osteoporosis groups, with a significant odds ratio for carrying the TT haplotype; however, this was non-significant after adjusting for age. Multivariate binary logistic regression analysis performed for rs3736228 showed that individuals with a body mass index <25 kg/m2 had an increased risk of osteoporosis for each decade, but the polymorphism had no effect. Conclusions This study did not identify LRP5 polymorphisms as a risk factor for osteoporosis in Thai menopausal women. Further studies with larger sample sizes are needed to further clarify the role of LRP5 as a genetic determinant of osteoporosis. Electronic supplementary material The online version of this article (doi:10.1186/s12952-016-0059-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anong Kitjaroentham
- Department of Tropical Nutrition and Food Science, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Hathairad Hananantachai
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Benjaluck Phonrat
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sangchai Preutthipan
- Department of Obstetrics and Gynecology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Rungsunn Tungtrongchitr
- Department of Tropical Nutrition and Food Science, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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21
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Niu T, Liu N, Yu X, Zhao M, Choi HJ, Leo PJ, Brown MA, Zhang L, Pei YF, Shen H, He H, Fu X, Lu S, Chen XD, Tan LJ, Yang TL, Guo Y, Cho NH, Shen J, Guo YF, Nicholson GC, Prince RL, Eisman JA, Jones G, Sambrook PN, Tian Q, Zhu XZ, Papasian CJ, Duncan EL, Uitterlinden AG, Shin CS, Xiang S, Deng HW. Identification of IDUA and WNT16 Phosphorylation-Related Non-Synonymous Polymorphisms for Bone Mineral Density in Meta-Analyses of Genome-Wide Association Studies. J Bone Miner Res 2016; 31:358-68. [PMID: 26256109 PMCID: PMC5362379 DOI: 10.1002/jbmr.2687] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 07/29/2015] [Accepted: 08/06/2015] [Indexed: 11/06/2022]
Abstract
Protein phosphorylation regulates a wide variety of cellular processes. Thus, we hypothesize that single-nucleotide polymorphisms (SNPs) that may modulate protein phosphorylation could affect osteoporosis risk. Based on a previous conventional genome-wide association (GWA) study, we conducted a three-stage meta-analysis targeting phosphorylation-related SNPs (phosSNPs) for femoral neck (FN)-bone mineral density (BMD), total hip (HIP)-BMD, and lumbar spine (LS)-BMD phenotypes. In stage 1, 9593 phosSNPs were meta-analyzed in 11,140 individuals of various ancestries. Genome-wide significance (GWS) and suggestive significance were defined by α = 5.21 × 10(-6) (0.05/9593) and 1.00 × 10(-4), respectively. In stage 2, nine stage 1-discovered phosSNPs (based on α = 1.00 × 10(-4)) were in silico meta-analyzed in Dutch, Korean, and Australian cohorts. In stage 3, four phosSNPs that replicated in stage 2 (based on α = 5.56 × 10(-3), 0.05/9) were de novo genotyped in two independent cohorts. IDUA rs3755955 and rs6831280, and WNT16 rs2707466 were associated with BMD phenotypes in each respective stage, and in three stages combined, achieving GWS for both FN-BMD (p = 8.36 × 10(-10), p = 5.26 × 10(-10), and p = 3.01 × 10(-10), respectively) and HIP-BMD (p = 3.26 × 10(-6), p = 1.97 × 10(-6), and p = 1.63 × 10(-12), respectively). Although in vitro studies demonstrated no differences in expressions of wild-type and mutant forms of IDUA and WNT16B proteins, in silico analyses predicts that WNT16 rs2707466 directly abolishes a phosphorylation site, which could cause a deleterious effect on WNT16 protein, and that IDUA phosSNPs rs3755955 and rs6831280 could exert indirect effects on nearby phosphorylation sites. Further studies will be required to determine the detailed and specific molecular effects of these BMD-associated non-synonymous variants.
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Affiliation(s)
- Tianhua Niu
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Ning Liu
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
| | - Xun Yu
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
| | - Ming Zhao
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Hyung Jin Choi
- Dept of Internal Medicine, College of Medicine, Seoul National University, Seoul, Korea
- Dept of Internal Medicine, Chungbuk National University Hospital, Cheongju, Korea
| | - Paul J. Leo
- University of Queensland Diamantina Inst, Translat Res Inst, Brisbane, Queensland, Australia
| | - Matthew A. Brown
- University of Queensland Diamantina Inst, Translat Res Inst, Brisbane, Queensland, Australia
| | - Lei Zhang
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
- Ctr of Syst Biomed Sci, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Yu-Fang Pei
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Hui Shen
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Hao He
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Xiaoying Fu
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Shan Lu
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
| | - Xiang-Ding Chen
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
| | - Li-Jun Tan
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
| | - Tie-Lin Yang
- School of Life Sci & Tech, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Yan Guo
- School of Life Sci & Tech, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Nam H. Cho
- Dept of Prev Med, Ajou University School of Medicine, Youngtong-Gu, Suwon, Korea
| | - Jie Shen
- Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Yan-Fang Guo
- Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, P. R. China
| | | | - Richard L. Prince
- School of Medicine and Pharmacology, University of Western Australia, Perth, Australia
- Dept of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Perth, Australia
| | - John A. Eisman
- Garvan Inst of Medical Research, University of New South Wales, Sydney, Australia
| | - Graeme Jones
- Menzies Res Inst, University of Tasmania, Hobart, Australia
| | - Philip N. Sambrook
- Kolling Inst, Royal North Shore Hospital, University of Sydney, Sydney, Australia
| | - Qing Tian
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
| | - Xue-Zhen Zhu
- School of Life Sci & Tech, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | | | - Emma L. Duncan
- University of Queensland Diamantina Inst, Translat Res Inst, Brisbane, Queensland, Australia
- Endocrinology, Royal Brisbane and Women’s Hospital, Brisbane, Queensland, Australia
| | - André G. Uitterlinden
- Dept of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Dept of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - Chan Soo Shin
- Dept of Internal Medicine, College of Medicine, Seoul National University, Seoul, Korea
| | - Shuanglin Xiang
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
| | - Hong-Wen Deng
- Dept of Biostat & Bioinfo, Tulane University Schl of Pub Hlth & Trop Med, New Orleans, LA 70112, USA
- College of Life Sci, Hunan Normal University, Changsha, Hunan 410081, P. R. China
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