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Villegas-Mirón P, Gallego A, Bertranpetit J, Laayouni H, Espinosa-Parrilla Y. Signatures of genetic variation in human microRNAs point to processes of positive selection and population-specific disease risks. Hum Genet 2022; 141:1673-1693. [PMID: 35249174 PMCID: PMC9522702 DOI: 10.1007/s00439-021-02423-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 12/19/2021] [Indexed: 12/11/2022]
Abstract
The occurrence of natural variation in human microRNAs has been the focus of numerous studies during the last 20 years. Most of them have been focused on the role of specific mutations in disease, while a minor proportion seek to analyse microRNA diversity in the genomes of human populations. We analyse the latest human microRNA annotations in the light of the most updated catalogue of genetic variation provided by the 1000 Genomes Project. By means of the in silico analysis of microRNA genetic variation we show that the level of evolutionary constraint of these sequences is governed by the interplay of different factors, like their evolutionary age or genomic location. The role of mutations in the shaping of microRNA-driven regulatory interactions is emphasized with the acknowledgement that, while the whole microRNA sequence is highly conserved, the seed region shows a pattern of higher genetic diversity that appears to be caused by the dramatic frequency shifts of a fraction of human microRNAs. We highlight the participation of these microRNAs in population-specific processes by identifying that not only the seed, but also the loop, are particularly differentiated regions among human populations. The quantitative computational comparison of signatures of population differentiation showed that candidate microRNAs with the largest differences are enriched in variants implicated in gene expression levels (eQTLs), selective sweeps and pathological processes. We explore the implication of these evolutionary-driven microRNAs and their SNPs in human diseases, such as different types of cancer, and discuss their role in population-specific disease risk.
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Affiliation(s)
- Pablo Villegas-Mirón
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Alicia Gallego
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
- Bioinformatics Studies, ESCI-UPF, Pg. Pujades 1, 08003, Barcelona, Spain.
| | - Yolanda Espinosa-Parrilla
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas, Chile.
- Laboratorio de Medicina Molecular-LMM, Centro Asistencial, Docente Y de Investigación-CADI, Universidad de Magallanes, Punta Arenas, Chile.
- Interuniversity Center on Healthy Aging, Punta Arenas, Chile.
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Landeros N, Corvalan AH, Musleh M, Quiñones LA, Varela NM, Gonzalez-Hormazabal P. Novel Risk Associations between microRNA Polymorphisms and Gastric Cancer in a Chilean Population. Int J Mol Sci 2021; 23:ijms23010467. [PMID: 35008894 PMCID: PMC8745138 DOI: 10.3390/ijms23010467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
Gastric cancer (GC) is the fifth leading cause of cancer deaths in the world, with variations across geographical regions and ethnicities. Emerging evidence indicates that miRNA expression is dysregulated in GC and its polymorphisms may contribute to these variations, which has yet to be explored in Latin American populations. In a case-control study of 310 GC patients and 311 healthy donors from Chile, we assessed the association of 279 polymorphisms in 242 miRNA genes. Two novel polymorphisms were found to be associated with GC: rs4822739:C>G (miR-548j) and rs701213:T>C (miR-4427). Additionally, rs1553867776:T>TCCCCA (miR-4274) and rs12416605:C>T (miR-938) were associated with intestinal-type GC, and rs4822739:C>G (miR-548j) and rs1439619:T>G (miR-3175) with TNM I-II stage. The polymorphisms rs6149511:T> TGAAGGGCTCCA (miR-6891), rs404337:G>A (miR-8084), and rs1439619:T>G (miR-3175) were identified among H.pylori-infected GC patients and rs7500280:T>C (miR-4719) and rs1439619:T>G (miR-3175) were found among H. pylori cagPAI+ infected GC cases. Prediction analysis suggests that seven polymorphisms could alter the secondary structure of the miRNA, and the other one is located in the seed region of miR-938. Targets of miRNAs are enriched in GC pathways, suggesting a possible biological effect. In this study, we identified seven novel associations and replicated one previously described in Caucasian population. These findings contribute to the understanding of miRNA genetic polymorphisms in the GC pathogenesis.
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Affiliation(s)
- Natalia Landeros
- Advanced Center for Chronic Diseases, Pontificia Universidad Católica de Chile, Santiago 8330034, Chile; (N.L.); (A.H.C.)
- Department of Hematology-Oncology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330034, Chile
| | - Alejandro H. Corvalan
- Advanced Center for Chronic Diseases, Pontificia Universidad Católica de Chile, Santiago 8330034, Chile; (N.L.); (A.H.C.)
- Department of Hematology-Oncology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330034, Chile
| | - Maher Musleh
- Department of Surgery, University of Chile Clinical Hospital, Santiago 8380456, Chile;
| | - Luis A. Quiñones
- Department of Basic-Clinical Oncology, School of Medicine, University of Chile, Santiago 8380453, Chile; (L.A.Q.); (N.M.V.)
- Latin American Network for the Implementation and Validation of Pharmacogenomic Clinical Guidelines (RELIVAF-CYTED), 28015 Madrid, Spain
| | - Nelson M. Varela
- Department of Basic-Clinical Oncology, School of Medicine, University of Chile, Santiago 8380453, Chile; (L.A.Q.); (N.M.V.)
- Latin American Network for the Implementation and Validation of Pharmacogenomic Clinical Guidelines (RELIVAF-CYTED), 28015 Madrid, Spain
| | - Patricio Gonzalez-Hormazabal
- Human Genetics Program, Institute of Biomedical Sciences (ICBM), School of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Correspondence:
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Meng F, Chen Y, Yang M, Zhang H, Wang W. Concomitant inhibition of B7-H3 and PD-L1 expression by a novel and synthetic microRNA delivers potent antitumor activities in colorectal tumor models. Invest New Drugs 2021; 39:1267-1274. [PMID: 33909231 DOI: 10.1007/s10637-021-01123-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/21/2021] [Indexed: 02/07/2023]
Abstract
The families of miR-34 and miR-449 share the same seed region. However, the members showed differential effects on the expression of B7-H3 and PD-L1 in HCT-116 cells. Using miR-34a as a template, the non-seed region was modified by nucleotide alteration, yielding four synthetic microRNA (miRNA) analogs. Among those, NS-MX3, with a base alteration from G to C at the 18th locus of miR-34a, showed the most potent inhibition on both B7-H3 and PD-L1 expression. Subsequent investigations demonstrated that NS-MX3 had a broad anti-proliferation activity against several colorectal tumor cell lines and its antitumor effect was consistently reflected by tumor growth inhibition (TGI) in the HCT-116 xenograft model. In addition, NS-MX3 displayed a synergistic effect on TGI when combined with bevacizumab or regorafenib. Further analysis revealed that the superior antitumor activity of NS-MX3 was correlated to concomitant suppression of both B7-H3 and PD-L1 expression in tumor tissues. Taken together, the present study indicates that the non-seed region of miRNAs plays an important role in the regulation of checkpoint genes, thus showcasing single nucleotide alteration of the non-seed region as a promising approach to discover and develop novel immunotherapies.
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Affiliation(s)
- Fanyi Meng
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Yinshuang Chen
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Man Yang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Hongjian Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
| | - Weipeng Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
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de Souza TP, de Carvalho DC, Wanderley AV, Fernandes SM, Rodrigues JCG, Cohen-Paes A, Fernandes MR, Mello Junior FAR, Pastana LF, Vinagre LWMS, Silva ALDC, de Assumpção PP, Santos S, Khayat AS, dos Santos NPC. Influence of variants of the drosha, mir499a, and mir938 genes on susceptibility to acute lymphoblastic leukemia in an admixed population from the brazilian amazon. Am J Transl Res 2020; 12:8216-8224. [PMID: 33437394 PMCID: PMC7791525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/25/2020] [Indexed: 06/12/2023]
Abstract
Acute Lymphoblastic Leukemia (ALL) is the most common type of cancer in children. Polymorphisms that alter the normal function of the microRNAs involved in the development of ALL have been widely investigated, although published data on these polymorphisms in admixed populations are scarce. We investigated the role of 10 polymorphisms in the microRNA and protein-coding genes of the microRNA synthesis complex in susceptibility to pediatric B-cell ALL. The study includes 100 pediatric ALL patients and 180 healthy individuals. The statistical analyses were run in SPSS v.25.0. In the case of the microRNA synthesizing genes, a significant pattern was found in only gene, that is, the rs3805500 polymorphism of DROSHA, in which the homozygous mutant (AA) genotype was associated with a threefold increase in the risk of developing ALL when compared to other genotypes (P=0.004, OR=2.913, CI=1.415-5.998). In the microRNA coding genes, the homozygous mutant rs3746444 genotype of the MIR499A gene was associated with a 17-fold increase in the risk of development of ALL (P<0.001, OR=17.797, CI=5.55-57.016). A protective effect against the development of ALL was also observed in the carriers of the wild homozygous rs2505901 genotype in the MIR938 gene. Our findings highlight the potential of these polymorphisms in the genes involving in the coding of microRNAs for the evaluation of the risk of contracting ALL in the population of the Brazilian Amazon region. These findings contribute to a more complete understanding of the complex etiology of ALL.
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Affiliation(s)
- Tatiane Piedade de Souza
- Laboratory of Human and Medical Genetics, Institute of Biological SciencesBelém, Pará, PA, Brazil
| | | | - Alayde Viera Wanderley
- Research Center of Oncology, Federal University of ParáBelém, Pará, PA, Brazil
- Otávio Lobo Children’s Cancer Hospital-HOIOL-BelémPará, PA, Brazil
| | - Sweny Marinho Fernandes
- Research Center of Oncology, Federal University of ParáBelém, Pará, PA, Brazil
- Otávio Lobo Children’s Cancer Hospital-HOIOL-BelémPará, PA, Brazil
| | | | - Amanda Cohen-Paes
- Research Center of Oncology, Federal University of ParáBelém, Pará, PA, Brazil
| | | | | | | | | | | | | | - Sidney Santos
- Research Center of Oncology, Federal University of ParáBelém, Pará, PA, Brazil
- Laboratory of Human and Medical Genetics, Institute of Biological SciencesBelém, Pará, PA, Brazil
| | - André Salim Khayat
- Research Center of Oncology, Federal University of ParáBelém, Pará, PA, Brazil
| | - Ney Pereira Carneiro dos Santos
- Research Center of Oncology, Federal University of ParáBelém, Pará, PA, Brazil
- Laboratory of Human and Medical Genetics, Institute of Biological SciencesBelém, Pará, PA, Brazil
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Torruella-Loran I, Ramirez Viña MK, Zapata-Contreras D, Muñoz X, Garcia-Ramallo E, Bonet C, Gonzalez CA, Sala N, Espinosa-Parrilla Y. rs12416605:C>T in MIR938 associates with gastric cancer through affecting the regulation of the CXCL12 chemokine gene. Mol Genet Genomic Med 2019; 7:e832. [PMID: 31273931 PMCID: PMC6687864 DOI: 10.1002/mgg3.832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/23/2019] [Accepted: 05/31/2019] [Indexed: 12/11/2022] Open
Abstract
Background MicroRNAs are small regulatory RNAs with important roles in carcinogenesis. Genetic variants in these regulatory molecules may contribute to disease. We aim to identify allelic variants in microRNAs as susceptibility factors to gastric cancer using association studies and functional approaches. Methods Twenty‐one single nucleotide variants potentially functional, because of their location in either the seed, mature or precursor region of 22 microRNAs, were selected for association studies. Genetic association with gastric cancer in 365 cases and 1,284 matched controls (European Prospective Investigation into Cancer and Nutrition Cohort) was analysed using logistic regression. MicroRNA overexpression, transcriptome analysis, and target gene validation experiments were performed for functional studies. Results rs3746444:T>C, in the seed of MIR499A and mature MIR499B, associated with the cardia adenocarcinoma location; rs12416605:C>T, in the seed of MIR938, associated with the diffuse subtype; and rs2114358:T>C, in the precursor MIR1206, associated with the noncardia phenotype. In all cases, the association was inverse, indicating a protective affect against gastric cancer of the three minor allelic variants. MIR499 rs3746444:T>C and MIR1206 rs2114358:T>C are reported to affect the expression of these miRNAs, but the effect of MIR938 rs12416605:C>T is unknown yet. Functional approaches showed that the expression of MIR938 is affected by rs12416605:C>T and revealed that MIR938 could regulate a subset of cancer‐related genes in an allele‐specific fashion. Furthermore, we demonstrated that CXCL12, a chemokine participating in gastric cancer metastasis, is specifically regulated by only one of the rs12416605:C>T alleles. Conclusion rs12416605 appears to be involved in gastric cancer by affecting the regulatory function of MIR938 on genes related to this cancer type, particularly on CXCL12 posttranscriptional regulation.
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Affiliation(s)
- Ignasi Torruella-Loran
- Department of Experimental and Health Sciences, IBE, Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), Barcelona, Spain
| | - María Karla Ramirez Viña
- School of Medicine, Universidad de Magallanes, Punta Arenas, Chile.,Laboratory of Molecular Medicine LMM, Center for Education, Healthcare and Investigation CADI, Universidad de Magallanes, Punta Arenas, Chile
| | - Daniela Zapata-Contreras
- School of Medicine, Universidad de Magallanes, Punta Arenas, Chile.,Laboratory of Molecular Medicine LMM, Center for Education, Healthcare and Investigation CADI, Universidad de Magallanes, Punta Arenas, Chile
| | - Xavier Muñoz
- Molecular Epidemiology Group, Translational Research Laboratory, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Eva Garcia-Ramallo
- Department of Experimental and Health Sciences, IBE, Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), Barcelona, Spain
| | - Catalina Bonet
- Unit of Nutrition, Environment and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL), Barcelona, Spain
| | - Carlos A Gonzalez
- Unit of Nutrition, Environment and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL), Barcelona, Spain
| | - Núria Sala
- Molecular Epidemiology Group, Translational Research Laboratory, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain.,Unit of Nutrition, Environment and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL), Barcelona, Spain
| | - Yolanda Espinosa-Parrilla
- Department of Experimental and Health Sciences, IBE, Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), Barcelona, Spain.,School of Medicine, Universidad de Magallanes, Punta Arenas, Chile.,Laboratory of Molecular Medicine LMM, Center for Education, Healthcare and Investigation CADI, Universidad de Magallanes, Punta Arenas, Chile
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