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Li W, Han G, Li F, Bu P, Hao Y, Huang L, Bai X. Cancer cell-derived exosomal miR-20a-5p inhibits CD8 + T-cell function and confers anti-programmed cell death 1 therapy resistance in triple-negative breast cancer. Cancer Sci 2024; 115:347-356. [PMID: 38129137 PMCID: PMC10859600 DOI: 10.1111/cas.16036] [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: 07/12/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023] Open
Abstract
Circulating miRNAs (cirmiRNAs) can be packaged into the exosomes, participating in intercellular communication, which affects the malignant progression and therapy resistance of triple-negative breast cancer (TNBC). Currently, immune checkpoint inhibitors that regulate T-cell function, especially antibodies against programmed cell death 1 (PD-1) or its ligand PD-L1, are emerging as new promising therapy for TNBC patients. However, only very limited patients showed complete or partial response to anti-PD-1 treatment. Dysfunction of CD8+ T cells is one of the key reasons for the immune escape of TNBC. The regulation of exosome-derived cirmiRNAs on CD8+ T cells in TNBC deserves more investigation. Here, the cirmiR-20a-5p level was significantly upregulated in the plasma of TNBC patients and culture supernatant of TNBC cells. High abundance of cirmiR-20a-5p was correlated with a worse prognosis of TNBC. cirmiR-20a-5p was secreted in the form of exosomes by TNBC cells. Exosomal cirmiR-20a-5p was internalized into CD8+ T cells and resulted into the dysfunction of CD8+ T. A mechanism study uncovered that cirmiR-20a-5p targeted the nuclear protein ataxia-telangiectasia (NPAT) and decreased NPAT expression in CD8+ T cells. An in vivo xenograft mouse model showed that cirmiR-20a-5p conferred TNBC to anti-PD-1 treatment resistance. Collectively, these findings indicated that cirmiR-20a-5p released by TNBC cells via exosome promotes cancer cell growth and leads to the immunosuppression by inducing CD8+ T cell dysfunction. This study suggests that targeting cirmiR-20a-5p might be a novel strategy for overcoming the resistance of TNBC to anti-PD-1 immunotherapy.
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Affiliation(s)
- Weina Li
- Department of Radiotherapy, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Guohui Han
- Department of Breast Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Feng Li
- Department of Biochemistry and Molecular Biology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Peng Bu
- Department of Pathology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Yating Hao
- Department of Breast Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Li Huang
- Department of Breast Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Xiangdong Bai
- Department of Breast Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
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2
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Wang X, Li H, Li N, Yang H, Bai X. LncRNA BCRT1 depletion suppresses cervical cancer cell growth via sponging miR-432-5p/CCR7 axis. 3 Biotech 2024; 14:17. [PMID: 38130686 PMCID: PMC10730479 DOI: 10.1007/s13205-023-03863-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Breast cancer-related transcript 1 (BCRT1), a lncRNA that is overexpressed in several human cancers, facilitates the progression of breast cancer and osteosarcoma. Nevertheless, the function of BCRT1 in cervical cancer (CC) still remains unknown. In this study, BCRT1 was significantly overexpressed in CC tissues and correlated with the advanced stage of CC patients. BCRT1 depletion dampened CC cell proliferation, and drives cell apoptosis and cell cycle inhibition. Mechanistically, BCRT1 bound miR-432-5p and negatively modulated miR-432-5p's expression in CC cells. Reduced miR-452-3p expression was observed in CC tissues and exerted tumor suppressive function in CC cell growth. Further mechanism study revealed that CCR7 was clarified as a target of miR-432-5p and was inhibited following BCRT1 depletion. CCR7 transfection could recover CC cell growth that was suppressed with BCRT1 down-regulation. These results revealed the novel function of BCRT1/miR-432-5p/CCR7 pathway in CC, suggesting BCRT1 might be a potential biomarker and target for CC treatment. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03863-x.
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Affiliation(s)
- Xiaoli Wang
- Department of Gynaecology, Shanxi Integrated Traditional Chinese and Western Medicine Hospital, Shanxi Medical University, No. 85, Jiefang South Road, Taiyuan, 030001 Shanxi China
| | - Huifang Li
- Department of Gynaecology, Shanxi Integrated Traditional Chinese and Western Medicine Hospital, Shanxi Medical University, No. 85, Jiefang South Road, Taiyuan, 030001 Shanxi China
| | - Naihua Li
- Department of Gynaecology, Shanxi Integrated Traditional Chinese and Western Medicine Hospital, Shanxi Medical University, No. 85, Jiefang South Road, Taiyuan, 030001 Shanxi China
| | - Hailan Yang
- Department of Gynaecology, Shanxi Medical University, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi China
| | - Xiangdong Bai
- Department of Breast Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, No. 3, The New Workers’ Road, Taiyuan, Shanxi China
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3
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MicroRNA-5582-3p alleviates the progression of osteosarcoma via targeting FZD4. Mol Cell Toxicol 2022. [DOI: 10.1007/s13273-022-00267-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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4
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Wu X, Wang W, Wu G, Peng C, Liu J. miR-182-5p Serves as an Oncogene in Lung Adenocarcinoma through Binding to STARD13. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:7074343. [PMID: 34335864 PMCID: PMC8321761 DOI: 10.1155/2021/7074343] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/01/2021] [Indexed: 01/02/2023]
Abstract
Lung cancer as one of the commonest invasive malignancies is featured by high morbidity and mortality, wherein lung adenocarcinoma (LUAD) is the most prevalent subtype. Accumulating evidence exhibited that microRNAs are involved in LUAD occurrence and progression. In this study, miR-182-5p was observed to increase in both LUAD tissue and cell lines. Overexpression of miR-182-5p could prominently facilitate cell proliferation, migration, and invasion in LUAD. Through bioinformatics analysis, STARD13 was theorized as the target gene of miR-182-5p, which was lowly expressed in LUAD. Further molecular experiments manifested that miR-182-5p bound to the 3'-untranslated region of STARD13, and there was an inverse correlation between STARD13 and miR-182-5p in LUAD. Rescue experiments demonstrated that silencing STARD13 conspicuously restored the inhibitory effect of decreased miR-182-5p on cell proliferation, migration, and invasion in LUAD. Together, our findings revealed novel roles of the miR-182-5p/STARD13 axis in LUAD progression.
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Affiliation(s)
- Xuhui Wu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China 330006
| | - Wei Wang
- Department of Emergency and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China 330006
| | - Gongzhi Wu
- Department of Cardiothoracic Surgery, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang Province, China 323000
| | - CongXiong Peng
- Department of Cardiothoracic Surgery, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang Province, China 323000
| | - Jichun Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China 330006
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5
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Chen SY, Su MH, Kremling KA, Lepak NK, Romay MC, Sun Q, Bradbury PJ, Buckler ES, Ku HM. Identification of miRNA-eQTLs in maize mature leaf by GWAS. BMC Genomics 2020; 21:689. [PMID: 33023467 PMCID: PMC7541240 DOI: 10.1186/s12864-020-07073-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/14/2020] [Indexed: 11/28/2022] Open
Abstract
Background MiRNAs play essential roles in plant development and response to biotic and abiotic stresses through interaction with their target genes. The expression level of miRNAs shows great variations among different plant accessions, developmental stages, and tissues. Little is known about the content within the plant genome contributing to the variations in plants. This study aims to identify miRNA expression-related quantitative trait loci (miR-QTLs) in the maize genome. Results The miRNA expression level from next generation sequencing (NGS) small RNA libraries derived from mature leaf samples of the maize panel (200 maize lines) was estimated as phenotypes, and maize Hapmap v3.2.1 was chosen as the genotype for the genome-wide association study (GWAS). A total of four significant miR-eQTLs were identified contributing to miR156k-5p, miR159a-3p, miR390a-5p and miR396e-5p, and all of them are trans-eQTLs. In addition, a strong positive coexpression of miRNA was found among five miRNA families. Investigation of the effects of these miRNAs on the expression levels and target genes provided evidence that miRNAs control the expression of their targets by suppression and enhancement. Conclusions These identified significant miR-eQTLs contribute to the diversity of miRNA expression in the maize penal at the developmental stages of mature leaves in maize, and the positive and negative regulation between miRNA and its target genes has also been uncovered.
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Affiliation(s)
- Shu-Yun Chen
- Department of Life Science, National Cheng Kung University, Tainan, 701, Taiwan
| | - Mei-Hsiu Su
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Karl A Kremling
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, 14850, NY, USA
| | - Nicholas K Lepak
- United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Qi Sun
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Peter J Bradbury
- United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - Edward S Buckler
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, 14850, NY, USA.,United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA.,Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Hsin-Mei Ku
- Advanced Plant Biotechnology Center, National Chung Hsing University, No 145 Xingda Rd, South Dist, Taichung, 402, Taiwan.
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6
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Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4. Proc Natl Acad Sci U S A 2020; 117:26520-26530. [PMID: 33020268 DOI: 10.1073/pnas.2005237117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human genome encodes for over 1,500 RNA-binding proteins (RBPs), which coordinate regulatory events on RNA transcripts. Most studies of RBPs have concentrated on their action on host protein-encoding mRNAs, which constitute a minority of the transcriptome. A widely neglected subset of our transcriptome derives from integrated retroviral elements, termed endogenous retroviruses (ERVs), that comprise ∼8% of the human genome. Some ERVs have been shown to be transcribed under physiological and pathological conditions, suggesting that sophisticated regulatory mechanisms to coordinate and prevent their ectopic expression exist. However, it is unknown how broadly RBPs and ERV transcripts directly interact to provide a posttranscriptional layer of regulation. Here, we implemented a computational pipeline to determine the correlation of expression between individual RBPs and ERVs from single-cell or bulk RNA-sequencing data. One of our top candidates for an RBP negatively regulating ERV expression was RNA-binding motif protein 4 (RBM4). We used photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation to demonstrate that RBM4 indeed bound ERV transcripts at CGG consensus elements. Loss of RBM4 resulted in an elevated transcript level of bound ERVs of the HERV-K and -H families, as well as increased expression of HERV-K envelope protein. We pinpointed RBM4 regulation of HERV-K to a CGG-containing element that is conserved in the LTRs of HERV-K-10, -K-11, and -K-20, and validated the functionality of this site using reporter assays. In summary, we systematically identified RBPs that may regulate ERV function and demonstrate a role for RBM4 in controlling ERV expression.
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7
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Jiang L, Bi D, Ding H, Ren Q, Wang P, Kan X. Identification and comparative profiling of gonadal microRNAs in the adult pigeon ( Columba livia). Br Poult Sci 2019; 60:638-648. [PMID: 31343256 DOI: 10.1080/00071668.2019.1639140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1. MicroRNAs are small noncoding RNA molecules that play crucial roles in gene expression. However, the comparative profiling of testicular and ovarian microRNAs in birds are rarely reported, particularly in pigeon.2. In this study, Illumina next-generation sequencing technology was used to sequence miRNA libraries of the gonads from six healthy adult utility pigeons. A total of 344 conserved known miRNAs and 32 novel putative miRNAs candidates were detected. Compared with those of ovaries, 130 differentially expressed (DE) miRNAs were identified in the testes. Among them, 70 miRNAs showed down-regulation in the ovaries, while another 60 miRNAs were up-regulated.3. Combining the results of the expression of target gene measurements and pathway enrichment analyses, it was revealed that some DEmiRNAs from the gonad samples involved in sexual differentiation and development (such as cli-miR-210-3p and cli-miR-214-3p) could down-regulate AR (androgen receptor). Cli-miR-181b-5p, cli-miR-9622-3p and cli-miR-145-5p were highly expressed in both the ovaries and testes, which could co-target HOXC9, and were related to regulation of primary metabolic processes. KEGG enrichment analysis showed that DEmiRNAs may play biological and sex-related roles in pigeon gonads.4. The expression profiles of testicular and ovarian miRNA in adult pigeon gonads are presented for the first time, and the findings may contribute to a better understanding of gonadal expression in poultry.
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Affiliation(s)
- L Jiang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - D Bi
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - H Ding
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Q Ren
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - P Wang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - X Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China
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8
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Abstract
Gene regulatory network that determines the cellular functions exhibits stochastic fluctuations, or "noise," in different layers. Noise has begun to be appreciated for many previously unrecognized functions in important cellular activities. In fact, molecular noise is unavoidable in both microbial and eukaryotic cells, the feedback system is established evolutionally to reduce noise or optimize the noise for cellular homeostasis. The small noncoding RNAs, particularly, microNRAs, post-transcriptionally and negatively regulate gene expressions. MicroRNAs function as a novel layer to buffer noise level, and stabilize mRNA and protein level to maintain normal cellular function. Furthermore, the changing of microRNA expression levels may increase the stochastic fluctuation leading to abnormal cellular function, even diseases.
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Affiliation(s)
- Wei Wu
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California in San Francisco, 600 16th Street Mission Bay/Genentech Hall, Room N212, San Francisco, CA, 94143, USA.
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9
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Abstract
MicroRNA (miRNA) is a non-protein-coding small RNA molecule that negatively regulates gene expression by degradation of mRNA or suppression of mRNA translation. MiRNAs play important roles in biological processes such as cellular development, differentiation, proliferation, apoptosis and stem cell self-renewal and cancer development. The expression profile of microRNAs is tissue-, cell-type specific. PCR- and microarray-based arrays are the commonly used for differential expression of microRNAs between different diseased conditions. With the next-generation sequencing or massively parallel DNA sequencing technology advanced and the cost is plummeting, microRNAseq approach is widely used for the genome-wide discovery of known and unknown miRNA expression. However, the analysis of microRNAseq is computational expensive, here I provide guidelines and available tools for microRNAseq analysis.
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Affiliation(s)
- Wei Wu
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California in San Francisco, 600 16th Street Mission Bay/Genentech Hall, Room N212, San Francisco, CA, 94143, USA.
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10
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Chen Z, Luo J, Sun S, Cao D, Shi H, Loor JJ. miR-148a and miR-17-5p synergistically regulate milk TAG synthesis via PPARGC1A and PPARA in goat mammary epithelial cells. RNA Biol 2017; 14:326-338. [PMID: 28095188 DOI: 10.1080/15476286.2016.1276149] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
MicroRNA (miRNA) are a class of '18-25' nt RNA molecules which regulate gene expression and play an important role in several biologic processes including fatty acid metabolism. Here we used S-Poly (T) and high-throughput sequencing to evaluate the expression of miRNA and mRNA during early-lactation and in the non-lactating ("dry") period in goat mammary gland tissue. Results indicated that miR-148a, miR-17-5p, PPARGC1A and PPARA are highly expressed in the goat mammary gland in early-lactation and non-lactating periods. Utilizing a Luciferase reporter assay and Western Blot, PPARA, an important regulator of fatty acid oxidation, and PGC1a (PPARGC1A), a major regulator of fat metabolism, were demonstrated to be targets of miR-148a and miR-17-5p in goat mammary epithelial cells (GMECs). It was also revealed that miR-148a expression can regulate PPARA, and miR-17-5p represses PPARGC1A in GMECs. Furthermore, the overexpression of miR-148a and miR-17-5p promoted triacylglycerol (TAG) synthesis while the knockdown of miR-148a and miR-17-5p impaired TAG synthesis in GMEC. These findings underscore the importance of miR-148a and miR-17-5p as key components in the regulation of TAG synthesis. In addition, miR-148a cooperates with miR-17-5p to regulate fatty acid metabolism by repressing PPARGC1A and PPARA in GMECs. Further studies on the functional role of miRNAs in lipid metabolism of ruminant mammary cells seem warranted.
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Affiliation(s)
- Zhi Chen
- a Shaanxi Key Laboratory of Molecular Biology for Agriculture , College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , P.R. China
| | - Jun Luo
- a Shaanxi Key Laboratory of Molecular Biology for Agriculture , College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , P.R. China
| | - Shuang Sun
- a Shaanxi Key Laboratory of Molecular Biology for Agriculture , College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , P.R. China
| | - Duoyao Cao
- a Shaanxi Key Laboratory of Molecular Biology for Agriculture , College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , P.R. China
| | - Huaiping Shi
- a Shaanxi Key Laboratory of Molecular Biology for Agriculture , College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , P.R. China
| | - Juan J Loor
- b Mammalian Nutrition Physiology Genomics, Department of Animal Sciences and Division of Nutritional Sciences , University of Illinois , Urbana , IL , USA
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11
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SNP Variation in MicroRNA Biogenesis Pathway Genes as a New Innovation Strategy for Alzheimer Disease Diagnostics. Alzheimer Dis Assoc Disord 2016; 30:203-9. [DOI: 10.1097/wad.0000000000000135] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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12
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Steinkraus BR, Toegel M, Fulga TA. Tiny giants of gene regulation: experimental strategies for microRNA functional studies. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2016; 5:311-62. [PMID: 26950183 PMCID: PMC4949569 DOI: 10.1002/wdev.223] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/19/2015] [Accepted: 11/28/2015] [Indexed: 12/11/2022]
Abstract
The discovery over two decades ago of short regulatory microRNAs (miRNAs) has led to the inception of a vast biomedical research field dedicated to understanding these powerful orchestrators of gene expression. Here we aim to provide a comprehensive overview of the methods and techniques underpinning the experimental pipeline employed for exploratory miRNA studies in animals. Some of the greatest challenges in this field have been uncovering the identity of miRNA-target interactions and deciphering their significance with regard to particular physiological or pathological processes. These endeavors relied almost exclusively on the development of powerful research tools encompassing novel bioinformatics pipelines, high-throughput target identification platforms, and functional target validation methodologies. Thus, in an unparalleled manner, the biomedical technology revolution unceasingly enhanced and refined our ability to dissect miRNA regulatory networks and understand their roles in vivo in the context of cells and organisms. Recurring motifs of target recognition have led to the creation of a large number of multifactorial bioinformatics analysis platforms, which have proved instrumental in guiding experimental miRNA studies. Subsequently, the need for discovery of miRNA-target binding events in vivo drove the emergence of a slew of high-throughput multiplex strategies, which now provide a viable prospect for elucidating genome-wide miRNA-target binding maps in a variety of cell types and tissues. Finally, deciphering the functional relevance of miRNA post-transcriptional gene silencing under physiological conditions, prompted the evolution of a host of technologies enabling systemic manipulation of miRNA homeostasis as well as high-precision interference with their direct, endogenous targets. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Bruno R Steinkraus
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Markus Toegel
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Tudor A Fulga
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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13
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Menor M, Ching T, Zhu X, Garmire D, Garmire LX. mirMark: a site-level and UTR-level classifier for miRNA target prediction. Genome Biol 2015; 15:500. [PMID: 25344330 PMCID: PMC4243195 DOI: 10.1186/s13059-014-0500-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Indexed: 02/07/2023] Open
Abstract
MiRNAs play important roles in many diseases including cancers. However computational prediction of miRNA target genes is challenging and the accuracies of existing methods remain poor. We report mirMark, a new machine learning-based method of miRNA target prediction at the site and UTR levels. This method uses experimentally verified miRNA targets from miRecords and mirTarBase as training sets and considers over 700 features. By combining Correlation-based Feature Selection with a variety of statistical or machine learning methods for the site- and UTR-level classifiers, mirMark significantly improves the overall predictive performance compared to existing publicly available methods. MirMark is available from https://github.com/lanagarmire/MirMark.
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Affiliation(s)
- Mark Menor
- Department of Information and Computer Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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14
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Kushwaha D, Ramakrishnan V, Ng K, Steed T, Nguyen T, Futalan D, Akers JC, Sarkaria J, Jiang T, Chowdhury D, Carter BS, Chen CC. A genome-wide miRNA screen revealed miR-603 as a MGMT-regulating miRNA in glioblastomas. Oncotarget 2015; 5:4026-39. [PMID: 24994119 PMCID: PMC4147303 DOI: 10.18632/oncotarget.1974] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
MGMT expression is a critical determinant for therapeutic resistance to DNA alkylating agents. We previously demonstrated that MGMT expression is post-transcriptionally regulated by miR-181d and other miRNAs. Here, we performed a genome-wide screen to identify MGMT regulating miRNAs. Candidate miRNAs were further tested for inverse correlation with MGMT expression in clinical specimens. We identified 15 candidate miRNAs and characterized the top candidate, miR-603. Transfection of miR-603 suppressed MGMT mRNA/protein expression in vitro and in vivo; this effect was reversed by transfection with antimiR-603. miR-603 affinity-precipitated with MGMT mRNA and suppressed luciferase activity in an MGMT-3'UTR-luciferase assay, suggesting direct interaction between miR-603 and MGMT 3'UTR. miR-603 transfection enhanced the temozolomide (TMZ) sensitivity of MGMT-expressing glioblastoma cell lines. Importantly, miR-603 mediated MGMT suppression and TMZ resistance were reversed by expression of an MGMT cDNA. In a collection of 74 clinical glioblastoma specimens, both miR-603 and miR-181d levels inversely correlated with MGMT expression. Moreover, a combined index of the two miRNAs better reflected MGMT expression than each individually. These results suggest that MGMT is co-regulated by independent miRNAs. Characterization of these miRNAs should contribute toward strategies for enhancing the efficacy of DNA alkylating agents.
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Affiliation(s)
- Deepa Kushwaha
- Dept. of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA; These authors contributed equally as first authors
| | - Valya Ramakrishnan
- Center for Theoretical and Applied Neuro-Oncology, Moores Cancer Center, Division of Neurosurgery, University of California San Diego, San Diego, CA. These authors contributed equally as first authors
| | - Kimberly Ng
- Dept. of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Tyler Steed
- Center for Theoretical and Applied Neuro-Oncology, Moores Cancer Center, Division of Neurosurgery, University of California San Diego, San Diego, CA
| | - Thien Nguyen
- Center for Theoretical and Applied Neuro-Oncology, Moores Cancer Center, Division of Neurosurgery, University of California San Diego, San Diego, CA
| | - Diahnn Futalan
- Center for Theoretical and Applied Neuro-Oncology, Moores Cancer Center, Division of Neurosurgery, University of California San Diego, San Diego, CA
| | - Johnny C Akers
- Center for Theoretical and Applied Neuro-Oncology, Moores Cancer Center, Division of Neurosurgery, University of California San Diego, San Diego, CA
| | - Jann Sarkaria
- Mayo Clinic, Department of Radiation Oncology, Rochester, MN
| | - Tao Jiang
- Department of Neurosurgery, Tiantan Medical Center, Beijing, China
| | | | - Bob S Carter
- Center for Theoretical and Applied Neuro-Oncology, Moores Cancer Center, Division of Neurosurgery, University of California San Diego, San Diego, CA
| | - Clark C Chen
- Center for Theoretical and Applied Neuro-Oncology, Moores Cancer Center, Division of Neurosurgery, University of California San Diego, San Diego, CA
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15
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Etebari K, Asgari S. Accuracy of microRNA discovery pipelines in non-model organisms using closely related species genomes. PLoS One 2014; 9:e84747. [PMID: 24404190 PMCID: PMC3880327 DOI: 10.1371/journal.pone.0084747] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/19/2013] [Indexed: 01/02/2023] Open
Abstract
Mapping small reads to genome reference is an essential and more common approach to identify microRNAs (miRNAs) in an organism. Using closely related species genomes as proxy references can facilitate miRNA expression studies in non-model species that their genomes are not available. However, the level of error this introduces is mostly unknown, as this is the result of evolutionary distance between the proxy reference and the species of interest. To evaluate the accuracy of miRNA discovery pipelines in non-model organisms, small RNA library data from a mosquito, Aedes aegypti, were mapped to three well annotated insect genomes as proxy references using miRanalyzer with two strict and loose mapping criteria. In addition, another web-based miRNA discovery pipeline (DSAP) was used as a control for program performance. Using miRanalyzer, more than 80% reduction was observed in the number of mapped reads using strict criterion when proxy genome references were used; however, only 20% reduction was recorded for mapped reads to other species known mature miRNA datasets. Except a few changes in ranking, mapping criteria did not make any significant differences in the profile of the most abundant miRNAs in A. aegypti when its original or a proxy genome was used as reference. However, more variation was observed in miRNA ranking profile when DSAP was used as analysing tool. Overall, the results also suggested that using a proxy reference did not change the most abundant miRNAs' differential expression profiles when infected or non-infected libraries were compared. However, usage of a proxy reference could provide about 67% of the original outcome from more extremely up- or down-regulated miRNA profiles. Although using closely related species genome incurred some losses in the number of miRNAs, the most abundant miRNAs along with their differential expression profile would be acceptable based on the sensitivity level of each project.
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Affiliation(s)
- Kayvan Etebari
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sassan Asgari
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
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16
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Mor E, Shomron N. Species-specific microRNA regulation influences phenotypic variability: perspectives on species-specific microRNA regulation. Bioessays 2013; 35:881-8. [PMID: 23864354 DOI: 10.1002/bies.201200157] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Phenotypic divergence among animal species may be due in part to species-specific (SS) regulation of gene expression by small, non-coding regulatory RNAs termed "microRNAs". This phenomenon can be modulated by several variables. First, microRNA genes vary by their level of conservation, many of them being SS, or unique to a particular evolutionary lineage. Second, microRNA expression levels vary spatially and temporally in different species. Lastly, while microRNAs bind the 3'UTR of target genes in order to silence their expression, the binding sites themselves are often non-conserved. The variability of the miRNA-target paradigm between different species is thus multifactorial, and this paradigm has only just started to gain attention from researchers in various fields. Here we present and discuss recent findings regarding the characteristics and implications of SS microRNA regulation.
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Affiliation(s)
- Eyal Mor
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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17
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Venkataraman S, Birks DK, Balakrishnan I, Alimova I, Harris PS, Patel PR, Handler MH, Dubuc A, Taylor MD, Foreman NK, Vibhakar R. MicroRNA 218 acts as a tumor suppressor by targeting multiple cancer phenotype-associated genes in medulloblastoma. J Biol Chem 2012; 288:1918-28. [PMID: 23212916 DOI: 10.1074/jbc.m112.396762] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aberrant expression of microRNAs has been implicated in many cancers. We recently demonstrated differential expression of several microRNAs in medulloblastoma. In this study, the regulation and function of microRNA 218 (miR-218), which is significantly underexpressed in medulloblastoma, was evaluated. Re-expression of miR-218 resulted in a significant decrease in medulloblastoma cell growth, cell colony formation, cell migration, invasion, and tumor sphere size. We used C17.2 neural stem cells as a model to show that increased miR-218 expression results in increased cell differentiation and also decreased malignant transformation when transfected with the oncogene REST. These results suggest that miR-218 acts as a tumor suppressor in medulloblastoma. MicroRNAs function by down-regulating translation of target mRNAs. Targets are determined by imperfect base pairing of the microRNA to the 3'-UTR of the mRNA. To comprehensively identify actual miR-218 targets, medulloblastoma cells overexpressing miR-218 and control cells were subjected to high throughput sequencing of RNA isolated by cross-linking immunoprecipitation, a technique that identifies the mRNAs bound to the RNA-induced silencing complex component protein Argonaute 2. High throughput sequencing of mRNAs identified 618 genes as targets of miR-218 and included both previously validated targets and many targets not predicted computationally. Additional work further confirmed CDK6, RICTOR, and CTSB (cathepsin B) as targets of miR-218 and examined the functional role of one of these targets, CDK6, in medulloblastoma.
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Affiliation(s)
- Sujatha Venkataraman
- Department of Pediatrics, Children’s Hospital Colorado, University of Colorado, Denver, Colorado 80045, USA
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18
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Kapeli K, Yeo GW. Genome-wide approaches to dissect the roles of RNA binding proteins in translational control: implications for neurological diseases. Front Neurosci 2012; 6:144. [PMID: 23060744 PMCID: PMC3462321 DOI: 10.3389/fnins.2012.00144] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 09/12/2012] [Indexed: 12/12/2022] Open
Abstract
Translational control of messenger RNAs (mRNAs) is a key aspect of neurobiology, defects of which can lead to neurological diseases. In response to stimuli, local translation of mRNAs is activated at synapses to facilitate long-lasting forms of synaptic plasticity, the cellular basis for learning, and memory formation. Translation, as well as all other aspects of RNA metabolism, is controlled in part by RNA binding proteins (RBPs) that directly interact with mRNAs to form mRNA-protein complexes. Disruption of RBP function is becoming widely recognized as a major cause of neurological diseases. Thus understanding the mechanisms that govern the interplay between translation control and RBP regulation in both normal and diseased neurons will provide new opportunities for novel diagnostics and therapeutic intervention. As a means of studying translational control, genome-wide methods are emerging as powerful tools that have already begun to unveil mechanisms that are missed by single-gene studies. Here, we describe the roles of RBPs in translational control, review genome-wide approaches to examine translational control, and discuss how the application of these approaches may provide mechanistic insight into the pathogenic underpinnings of RBPs in neurological diseases.
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Affiliation(s)
- Katannya Kapeli
- Department of Cellular and Molecular Medicine, University of California San Diego La Jolla, CA, USA
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19
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Liu CH, Wu DY, Pollock JD. Bioinformatic challenges of big data in non-coding RNA research. Front Genet 2012; 3:178. [PMID: 22973302 PMCID: PMC3438686 DOI: 10.3389/fgene.2012.00178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 08/24/2012] [Indexed: 11/24/2022] Open
Affiliation(s)
- Christina H Liu
- Division of Applied Science and Technology, National Institute of Biomedical Imaging and Bioengineering Bethesda, MD, USA
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20
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Enfield KSS, Pikor LA, Martinez VD, Lam WL. Mechanistic Roles of Noncoding RNAs in Lung Cancer Biology and Their Clinical Implications. GENETICS RESEARCH INTERNATIONAL 2012; 2012:737416. [PMID: 22852089 PMCID: PMC3407615 DOI: 10.1155/2012/737416] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 03/08/2012] [Indexed: 01/07/2023]
Abstract
Lung cancer biology has traditionally focused on genomic and epigenomic deregulation of protein-coding genes to identify oncogenes and tumor suppressors diagnostic and therapeutic targets. Another important layer of cancer biology has emerged in the form of noncoding RNAs (ncRNAs), which are major regulators of key cellular processes such as proliferation, RNA splicing, gene regulation, and apoptosis. In the past decade, microRNAs (miRNAs) have moved to the forefront of ncRNA cancer research, while the role of long noncoding RNAs (lncRNAs) is emerging. Here we review the mechanisms by which miRNAs and lncRNAs are deregulated in lung cancer, the technologies that can be applied to detect such alterations, and the clinical potential of these RNA species. An improved comprehension of lung cancer biology will come through the understanding of the interplay between deregulation of non-coding RNAs, the protein-coding genes they regulate, and how these interactions influence cellular networks and signalling pathways.
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Affiliation(s)
- Katey S. S. Enfield
- British Columbia Cancer Research Center, Vancouver, BC, Canada V5Z 1L3
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada V5Z1L3
| | - Larissa A. Pikor
- British Columbia Cancer Research Center, Vancouver, BC, Canada V5Z 1L3
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada V5Z1L3
| | - Victor D. Martinez
- British Columbia Cancer Research Center, Vancouver, BC, Canada V5Z 1L3
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada V6T2B5
| | - Wan L. Lam
- British Columbia Cancer Research Center, Vancouver, BC, Canada V5Z 1L3
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada V5Z1L3
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada V6T2B5
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21
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Tang F, Zhang R, He Y, Zou M, Guo L, Xi T. MicroRNA-125b induces metastasis by targeting STARD13 in MCF-7 and MDA-MB-231 breast cancer cells. PLoS One 2012; 7:e35435. [PMID: 22693547 PMCID: PMC3365056 DOI: 10.1371/journal.pone.0035435] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Accepted: 03/16/2012] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression by targeting mRNAs to trigger either translation repression or mRNA degradation. miR-125b is down-regulated in human breast cancer cells compared with the normal ones except highly metastatic tumor cells MDA-MB-231. However, few functional studies were designed to investigate metastatic potential of miR-125b. In this study, the effects of miR-125b on metastasis in human breast cancer cells were studied, and the targets of miR-125b were also explored. Transwell migration assay, cell wound healing assay, adhesion assay and nude mice model of metastasis were utilized to investigate the effects of miR-125b on metastasis potential in vitro and in vivo. In addition, it was implied STARD13 (DLC2) was a direct target of miR-125b by Target-Scan analysis, luciferase reporter assay and western blot. Furthermore, activation of STARD13 was identified responsible for metastasis induced by miR-125b through a siRNA targeting STARD13. qRT-PCR, immunofluorescent assay and western blot was used to observe the variation of Vimentin and α-SMA in breast cancer cells. In summary, our study provided new insights into the function of miR-125b during the metastasis of breat cancer cells and also suggested the role of miR-125b in pro-metastasis by targeting STARD13.
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Affiliation(s)
- Feng Tang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People’s Republic of China
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, People’s Republic of China
- * E-mail: (TX); (FT)
| | - Rui Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People’s Republic of China
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, People’s Republic of China
| | - Yunmian He
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People’s Republic of China
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, People’s Republic of China
| | - Meijuan Zou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People’s Republic of China
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, People’s Republic of China
| | - Le Guo
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People’s Republic of China
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, People’s Republic of China
| | - Tao Xi
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People’s Republic of China
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, People’s Republic of China
- * E-mail: (TX); (FT)
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Arnold M, Ellwanger DC, Hartsperger ML, Pfeufer A, Stümpflen V. Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways. PLoS One 2012; 7:e36694. [PMID: 22606281 PMCID: PMC3350471 DOI: 10.1371/journal.pone.0036694] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 04/05/2012] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies (GWAS) have become an effective tool to map genes and regions contributing to multifactorial human diseases and traits. A comparably small number of variants identified by GWAS are known to have a direct effect on protein structure whereas the majority of variants is thought to exert their moderate influences on the phenotype through regulatory changes in mRNA expression. MicroRNAs (miRNAs) have been identified as powerful posttranscriptional regulators of mRNAs. Binding to their target sites, which are mostly located within the 3'-untranslated region (3'-UTR) of mRNA transcripts, they modulate mRNA expression and stability. Until today almost all human mRNA transcripts are known to harbor at least one miRNA target site with an average of over 20 miRNA target sites per transcript. Among 5,101 GWAS-identified sentinel single nucleotide polymorphisms (SNPs) that correspond to 18,884 SNPs in linkage disequilibrium (LD) with the sentinels (r2 ≥ 0.8) we identified a significant overrepresentation of SNPs that affect the 3'-UTR of genes (OR = 2.33, 95% CI = 2.12-2.57, P < 10(-52)). This effect was even stronger considering all SNPs in one LD bin a single signal (OR = 4.27, 95% CI = 3.84-4.74, P < 10(-114)). Based on crosslinking immunoprecipitation data we identified four mechanisms affecting miRNA regulation by 3'-UTR mutations: (i) deletion or (ii) creation of miRNA recognition elements within validated RNA-induced silencing complex binding sites, (iii) alteration of 3'-UTR splicing leading to a loss of binding sites, and (iv) change of binding affinity due to modifications of 3'-UTR folding. We annotated 53 SNPs of a total of 288 trait-associated 3'-UTR SNPs as mediating at least one of these mechanisms. Using a qualitative systems biology approach, we demonstrate how our findings can be used to support biological interpretation of GWAS results as well as to provide new experimentally testable hypotheses.
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Affiliation(s)
- Matthias Arnold
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Daniel C. Ellwanger
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Genome-Oriented Bioinformatics, Technische Universität München, Center of Life and Food Science, Freising-Weihenstephan, Germany
| | - Mara L. Hartsperger
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Arne Pfeufer
- Institute for Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, German National Research Center for Environmental Health, Neuherberg, Germany
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy - Affiliated Institute of the University Lübeck, Germany
| | - Volker Stümpflen
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- * E-mail:
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23
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Pérez-Ortín JE, de Miguel-Jiménez L, Chávez S. Genome-wide studies of mRNA synthesis and degradation in eukaryotes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:604-15. [PMID: 22182827 DOI: 10.1016/j.bbagrm.2011.12.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Revised: 12/01/2011] [Accepted: 12/05/2011] [Indexed: 02/04/2023]
Abstract
In recent years, the use of genome-wide technologies has revolutionized the study of eukaryotic transcription producing results for thousands of genes at every step of mRNA life. The statistical analyses of the results for a single condition, different conditions, different transcription stages, or even between different techniques, is outlining a totally new landscape of the eukaryotic transcription process. Although most studies have been conducted in the yeast Saccharomyces cerevisiae as a model cell, others have also focused on higher eukaryotes, which can also be comparatively analyzed. The picture which emerges is that transcription is a more variable process than initially suspected, with large differences between genes at each stage of the process, from initiation to mRNA degradation, but with striking similarities for functionally related genes, indicating that all steps are coordinately regulated. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain.
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Sun J, Liu HP, Deng JE, Zhou M. Systematic analysis of genomic organization and heterogeneities of miRNA cluster in vertebrates. Mol Biol Rep 2011; 39:5143-9. [DOI: 10.1007/s11033-011-1310-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 11/30/2011] [Indexed: 10/14/2022]
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