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Torres-Reyes LA, Gonzalez-Aldaco K, Panduro A, Jose-Abrego A, Roman S. Whole-Exome Sequencing identified Olfactory Receptor genes as a key contributor to extreme obesity with progression to nonalcoholic steatohepatitis in Mexican patients: Olfactory receptor genes in obese NASH patients. Ann Hepatol 2022; 27:100767. [PMID: 36223880 DOI: 10.1016/j.aohep.2022.100767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/21/2022] [Indexed: 02/08/2023]
Abstract
INTRODUCTION AND OBJECTIVES Obesity is a global health problem that triggers fat liver accumulation. The prevalence of obesity and the risk of non-alcoholic steatohepatitis (NASH) among young obese Mexican is high. Furthermore, genetic predisposition is a key factor in weight gain and disrupts metabolism. Herein, we used Whole-Exome Sequencing to identify potential causal variants and the biological processes that lead to obesity with progression to NASH among Mexican patients. MATERIALS AND METHODS Whole-Exome Sequencing was performed in nine obese patients with NASH diagnosis with a BMI ≥30 kg/m2 and one control (BMI=24.2 kg/m2) by using the Ion S5TM platform. Genetic variants were determined by Ion Reporter software. Enriched GO biological set genes were identified by the WebGestalt tool. Genetic variants within ≥2 obese NASH patients and having scores of SIFT 0.0-0.05 and Polyphen 0.85-1.0 were categorized as pathogenic. RESULTS A total of 1359 variants with a probable pathogenic effect were determined in obese patients with NASH diagnosis. After several filtering steps, the most frequent pathogenic variants found were rs25640-HSD17B4, rs8105737-OR1I1, rs998544-OR5R1, and rs4916685, rs10037067, and rs2366926 in ADGRV1. Notably, the primary biological processes affected by these pathogenic variants were the sensory perception and detection of chemical stimulus pathways in which the olfactory receptor gene family was the most enriched. CONCLUSIONS Variants in the olfactory receptor genes were highly enriched in Mexican obese patients that progress to NASH and could be potential targets of association studies.
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Affiliation(s)
- L A Torres-Reyes
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, "Fray Antonio Alcalde," Guadalajara, Jalisco, Mexico; Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - K Gonzalez-Aldaco
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, "Fray Antonio Alcalde," Guadalajara, Jalisco, Mexico; Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - A Panduro
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, "Fray Antonio Alcalde," Guadalajara, Jalisco, Mexico; Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - A Jose-Abrego
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, "Fray Antonio Alcalde," Guadalajara, Jalisco, Mexico; Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - S Roman
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, "Fray Antonio Alcalde," Guadalajara, Jalisco, Mexico; Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico.
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Sepulveda-Villegas M, Roman S, Rivera-Iñiguez I, Ojeda-Granados C, Gonzalez-Aldaco K, Torres-Reyes LA, Jose-Abrego A, Panduro A. High prevalence of nonalcoholic steatohepatitis and abnormal liver stiffness in a young and obese Mexican population. PLoS One 2019; 14:e0208926. [PMID: 30608932 PMCID: PMC6319733 DOI: 10.1371/journal.pone.0208926] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/26/2018] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE To identify nonalcoholic steatohepatitis (NASH) and liver stiffness in Mexican subjects with different body mass index (BMI). METHODS A cross-sectional study was conducted in 505 adults. Risk for NASH was defined as the presence of one or more of the following biochemical and metabolic parameters (BMPs): fasting glucose ≥100 mg/dl, triglycerides (TG) ≥150 mg/dl, homeostatic model assessment of insulin resistance (HOMA-IR) ≥2.5, aspartate aminotransferase (AST) >54 IU/L and alanine aminotransferase (ALT) >42 IU/L. Body mass index measurement and nutritional assessment were performed by standard procedures. Liver fibrosis stage was determined by liver stiffness measurement using transitional elastography (TE) or by liver biopsy (LB). RESULTS Risk for NASH was 57% (290/505). Most BMPs values incremented by BMI category. Among 171 at-risk patients, 106 subjects were evaluated by TE and 65 subjects by LB. Abnormal liver stiffness (≥6.0 kPa) was prevalent in 54% (57/106) of the cases, whereas by LB, 91% (59/65) of patients with obesity had NASH and liver fibrosis. Furthermore, liver fibrosis was prevalent in 46% (6/13) in normal weight individuals, whereas 4.6% (3/65) of patients with a BMI ≥ 35 kg/m2 showed no histopathological abnormalities. Overall, 67.8% (116/171) of the patients had abnormal liver stiffness or NASH. The normal weight patients with liver damage consumed relatively a higher fat-rich diet compared to the other groups whereas the remaining subgroups shared a similar dietary pattern. CONCLUSION Young patients with overweight and obesity showed a high prevalence of altered BMPs related to abnormal liver stiffness assessed by TE and NASH by LB. Early diagnostic strategies are required to detect the risk for NASH and avoid further liver damage in populations with a rising prevalence of obesity by defining the risk factors involved in the onset and progression of NASH.
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Affiliation(s)
- Maricruz Sepulveda-Villegas
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, “Fray Antonio Alcalde,” Guadalajara, Jalisco, Mexico and Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Sonia Roman
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, “Fray Antonio Alcalde,” Guadalajara, Jalisco, Mexico and Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Ingrid Rivera-Iñiguez
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, “Fray Antonio Alcalde,” Guadalajara, Jalisco, Mexico and Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Claudia Ojeda-Granados
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, “Fray Antonio Alcalde,” Guadalajara, Jalisco, Mexico and Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Karina Gonzalez-Aldaco
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, “Fray Antonio Alcalde,” Guadalajara, Jalisco, Mexico and Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Luis Alberto Torres-Reyes
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, “Fray Antonio Alcalde,” Guadalajara, Jalisco, Mexico and Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Alexis Jose-Abrego
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, “Fray Antonio Alcalde,” Guadalajara, Jalisco, Mexico and Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Arturo Panduro
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, “Fray Antonio Alcalde,” Guadalajara, Jalisco, Mexico and Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
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Flores-Miramontes MG, Torres-Reyes LA, Alvarado-Ruíz L, Romero-Martínez SA, Ramírez-Rodríguez V, Balderas-Peña LMA, Vallejo-Ruíz V, Piña-Sánchez P, Cortés-Gutiérrez EI, Jave-Suárez LF, Aguilar-Lemarroy A. Human papillomavirus genotyping by Linear Array and Next-Generation Sequencing in cervical samples from Western Mexico. Virol J 2015; 12:161. [PMID: 26444975 PMCID: PMC4596464 DOI: 10.1186/s12985-015-0391-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Linear Array® (LA) genotyping test is one of the most used methodologies for Human papillomavirus (HPV) genotyping, in that it is able to detect 37 HPV genotypes and co-infections in the same sample. However, the assay is limited to a restricted number of HPV, and sequence variations in the detection region of the HPV probes could give false negatives results. Recently, 454 Next-Generation sequencing (NGS) technology has been efficiently used also for HPV genotyping; this methodology is based on massive sequencing of HPV fragments and is expected to be highly specific and sensitive. In this work, we studied HPV prevalence in cervixes of women in Western Mexico by LA and confirmed the genotypes found by NGS. METHODS Two hundred thirty three cervical samples from women Without cervical lesions (WCL, n = 48), with Cervical intraepithelial neoplasia grade 1 (CIN I, n = 98), or with Cervical cancer (CC, n = 87) were recruited, DNA was extracted, and HPV positivity was determined by PCR amplification using PGMY09/11 primers. All HPV- positive samples were genotyped individually by LA. Additionally, pools of amplicons from the PGMY-PCR products were sequenced using 454 NGS technology. Results obtained by NGS were compared with those of LA for each group of samples. RESULTS We identified 35 HPV genotypes, among which 30 were identified by both technologies; in addition, the HPV genotypes 32, 44, 74, 102 and 114 were detected by NGS. These latter genotypes, to our knowledge, have not been previously reported in Mexican population. Furthermore, we found that LA did not detect, in some diagnosis groups, certain HPV genotypes included in the test, such as 6, 11, 16, 26, 35, 51, 58, 68, 73, and 89, which indicates possible variations at the species level. CONCLUSIONS There are HPV genotypes in Mexican population that cannot be detected by LA, which is, at present, the most complete commercial genotyping test. More studies are necessary to determine the impact of HPV-44, 74, 102 and 114 on the risk of developing CC. A greater number of samples must be analyzed by NGS for the most accurate determination of Mexican HPV variants.
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Affiliation(s)
- María Guadalupe Flores-Miramontes
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340, Guadalajara, Jalisco, Mexico. .,Programa de Doctorado en Ciencias Biomédica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Jalisco, Mexico.
| | - Luis Alberto Torres-Reyes
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340, Guadalajara, Jalisco, Mexico. .,Programa de Doctorado en Ciencias Biomédica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Jalisco, Mexico.
| | - Liliana Alvarado-Ruíz
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340, Guadalajara, Jalisco, Mexico. .,Programa de Doctorado en Ciencias Biomédica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Jalisco, Mexico.
| | | | | | - Luz María Adriana Balderas-Peña
- Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Especialidades, Centro Médico Nacional de Occidente (CMNO)-IMSS, Guadalajara, Jalisco, Mexico.
| | - Verónica Vallejo-Ruíz
- Centro de Investigación Biomédica de Oriente (CIBIOR)-IMSS, Metepec, Puebla, Mexico.
| | - Patricia Piña-Sánchez
- Laboratorio de Oncología Molecular, Unidad de Investigación Médica en Enfermedades Oncológicas (UIMEO)-IMSS, Mexico City, Mexico.
| | | | - Luis Felipe Jave-Suárez
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340, Guadalajara, Jalisco, Mexico.
| | - Adriana Aguilar-Lemarroy
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340, Guadalajara, Jalisco, Mexico.
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