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Liu M, Han Z, Zhi Y, Ruan Y, Cao G, Wang G, Xu X, Mu J, Kang J, Dai F, Wen X, Zhang Q, Li F. Long-read sequencing reveals oncogenic mechanism of HPV-human fusion transcripts in cervical cancer. Transl Res 2023; 253:80-94. [PMID: 36223881 DOI: 10.1016/j.trsl.2022.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/18/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022]
Abstract
Integration of high-risk human papillomavirus (HPV) into the host genome is a crucial event for the development of cervical cancer, however, the underlying mechanism of HPV integration-driven carcinogenesis remains unknown. Here, we performed long-read RNA sequencing on 12 high-grade squamous intraepithelial lesions (HSIL) and cervical cancer patients, including 3 pairs of cervical cancer and corresponding para-cancerous tissue samples to investigate the full-length landscape of cross-species genome integrations. In addition to massive unannotated isoforms, transcriptional regulatory events, and gene chimerism, more importantly, we found that HPV-human fusion events were prevalent in HPV-associated cervical cancers. Combined with the genome data, we revealed the existence of a universal transcription pattern in these fusion events, whereby structurally similar fusion transcripts were generated by specific splicing in E6 and a canonical splicing donor site in E1 linking to various human splicing acceptors. Highly expressed HPV-human fusion transcripts, eg, HPV16 E6*I-E7-E1SD880-human gene, were the key driver of cervical carcinogenesis, which could trigger overexpression of E6*I and E7, and destroy the transcription of tumor suppressor genes CMAHP, TP63 and P3H2. Finally, evidence from in vitro and in vivo experiments demonstrates that the novel read-through fusion gene mRNA, E1-CMAHP (E1C, formed by the integration of HPV58 E1 with CMAHP), existed in the fusion transcript can promote malignant transformation of cervical epithelial cells via regulating downstream oncogenes to participate in various biological processes. Taken together, we reveal a previously unknown mechanism of HPV integration-driven carcinogenesis and provide a novel target for the diagnosis and treatment of cervical cancer.
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Affiliation(s)
- Min Liu
- Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhiqiang Han
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Zhi
- Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yetian Ruan
- Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Guangxu Cao
- Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Guangxue Wang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xinxin Xu
- Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Fangping Dai
- Genome-decoding Biomedical Technology Co., Ltd, Nantong, China
| | - Xuejun Wen
- Department of Chemical and Life Science Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA
| | - Qingfeng Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai, China.
| | - Fang Li
- Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China.
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Debernardi A, Valot B, Almarcha J, Guenat D, Hocquet D, Algros MP, Riethmuller D, Ramanah R, Mougin C, Prétet JL, Lepiller Q. Longitudinal follow-up of HPV16 sequence after cervical infection: Low intrahost variation and no correlation with clinical evolution. J Med Virol 2022; 94:5512-5518. [PMID: 35799409 DOI: 10.1002/jmv.27978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/12/2022] [Accepted: 07/05/2022] [Indexed: 12/15/2022]
Abstract
Human papillomavirus (HPV) 16 exhibits different variants that may differ in their carcinogenic risk. To identify some high-risk variants, we sequenced and compared HPV16 whole genomes obtained from a longitudinal cohort of 34 HPV16-infected women who had either spontaneously cleared their infection (clearance group or "C"), or developed cervical high-grade lesions following a viral persistence (group persistence or "P"). Phylogenetic analysis of paired samples obtained at the beginning (C0 or P0) and at the end (C2 or P2) of the follow-up (median intervals between C0-C2 and between P0-P2 were 16 and 36.5 months, respectively) revealed a low genetic variability within the host compared to the genetic interhost diversity. By comparing our HPV16 sequences to a reference sequence, we observed 301 different substitutions, more often transitions (60.9%) than transversions (39.1%), that occurred throughout the viral genome, but with a low frequency in E6 and E7 oncogenes (10 and 9 substitutions), suggesting a high conservation of these genes. Deletions and insertions were mostly observed in intergenic regions of the virus. The only significant substitution found between the subgroups C2 and P2 was observed in the L2 gene (L330F), with an unclear biological relevance. Our results suggest a low longitudinal intrahost evolution of HPV16 sequences and no correlation between genetic variations and clinical evolution.
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Affiliation(s)
- Alice Debernardi
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Benoit Valot
- Bioinformatique et Big Data au Service de la Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France.,UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Julien Almarcha
- Bioinformatique et Big Data au Service de la Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
| | - David Guenat
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Didier Hocquet
- Bioinformatique et Big Data au Service de la Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France.,UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | | | - Didier Riethmuller
- Department of Gynecology and Obstetrics, Hôpital Couple-Enfant, University Hospital Grenoble Alpes, La Tronche, France
| | - Rajeev Ramanah
- Gynecology Department, CHU de Besançon, Besançon, France
| | - Christiane Mougin
- Centre National de Référence Papillomavirus, CHU de Besançon, Besançon, France.,UMR U1098 RIGHT, Université de Bourgogne Franche-Comté, Besançon, France
| | - Jean-Luc Prétet
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, Université de Bourgogne-Franche-Comté, Besançon, France.,Centre National de Référence Papillomavirus, CHU de Besançon, Besançon, France.,Laboratoire De Biologie Cellulaire, CHU de Besançon, Besançon, France
| | - Quentin Lepiller
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, Université de Bourgogne-Franche-Comté, Besançon, France.,Centre National de Référence Papillomavirus, CHU de Besançon, Besançon, France.,Laboratoire De Virologie, CHU de Besançon, Besançon, France
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Antonio-Véjar V, Ortiz-Sánchez E, Rosendo-Chalma P, Patiño-Morales CC, Guido-Jiménez MC, Alvarado-Ortiz E, Hernández G, García-Carrancá A. New insights into the interactions of HPV-16 E6*I and E6*II with p53 isoforms and induction of apoptosis in cancer-derived cell lines. Pathol Res Pract 2022; 234:153890. [PMID: 35487028 DOI: 10.1016/j.prp.2022.153890] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023]
Abstract
An important characteristic of cancers associated with high-risk human papillomaviruses (HR-HPV) is the inability of p53 to activate apoptosis due to the effect of the oncoprotein E6. However, the effect of HPV-16 E6 splice variant isoforms (namely E6*I and E6*II), their interaction with the existing p53 isoforms, and their influence on apoptosis is unclear. Here, we report the outcome of ectopic expression of HPV-16 E6, E6*I, and E6*II on the relative levels of p53 and p53 isoforms Δ40p53 and Δ133p53 and their interactions with these proteins. Additionally, we evaluated the effect of ectopic expression of p53, Δ40p53, and Δ133p53 on apoptosis in a p53 null pulmonary cell line (H1299) co-transfected with E6 isoforms and p53+/+ cell lines with HR-HPV (SiHa and HeLa), transfected with p53 isoforms and treated with cisplatin, a conventional drug used to treat cervical cancer. Our results show that E6 and E6*II induced a significant decrease in p53, but only E6 triggered a Δ40p53 decrease and that E6*II interacts with p53 but not with Δ40p53 and Δ133p53. On the other hand, E6*I did not show any effect or interaction with the p53 isoforms. We found that apoptosis was elevated in H1299 cells transfected with p53 (p = 0.0001) and Δ40p53 (p = 0.0001). A weak apoptotic effect was observed when Δ133p53 was ectopically expressed (p = 0.0195). We observed that both p53 (p = 0.0006) and Δ40p53 (p = 0.0014) induced apoptosis in cisplatin-treated SiHa cells; however in cisplatin-treated HeLa cells, only p53 induced apoptosis (p = 0.0029). No significant differences in apoptosis were observed upon ectopic expression of p53, Δ40p53, and Δ133p53 in SiHa and HeLa cells. Our findings suggest a possible therapeutic application for the combining of p53 or Δ40p53 with cisplatin to induce an increased apoptosis of cancer cells expressing E6 isoforms from HPV-16.
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Affiliation(s)
- Verónica Antonio-Véjar
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, 10450, Mexico; Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, 39090, Guerrero, Mexico; Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México and Instituto Nacional de Cancerología, Ciudad de México, 14080, Mexico.
| | - Elizabeth Ortiz-Sánchez
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México, 14080, Mexico.
| | - Pedro Rosendo-Chalma
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, 10450, Mexico; Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México and Instituto Nacional de Cancerología, Ciudad de México, 14080, Mexico.
| | - Carlos C Patiño-Morales
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México and Instituto Nacional de Cancerología, Ciudad de México, 14080, Mexico.
| | - Miriam C Guido-Jiménez
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México and Instituto Nacional de Cancerología, Ciudad de México, 14080, Mexico.
| | - Eduardo Alvarado-Ortiz
- Programa de Posgrado en Ciencias Biológicas. Universidad Nacional Autónoma de México (UNAM), Ciudad de México, 04510, Mexico; Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México and Instituto Nacional de Cancerología, Ciudad de México, 14080, Mexico.
| | - Greco Hernández
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México, 14080, Mexico.
| | - Alejandro García-Carrancá
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México and Instituto Nacional de Cancerología, Ciudad de México, 14080, Mexico.
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4
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Repurposing the Hybrid Capture 2 (HC2) screening test for whole-genome sequencing of human papillomaviruses. Arch Virol 2021; 166:3421-3425. [PMID: 34618227 DOI: 10.1007/s00705-021-05259-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Simple and standardized approaches for genome analysis of human papillomavirus (HPV) by next-generation sequencing are needed. The aim of the study was to develop a protocol for direct deep sequencing of high-risk (hr) HPV strains, based on the widely used commercial Hybrid Capture 2 (QIAGEN) test, without any additional probe design. This protocol was applied to 15 HPV-positive and two HPV-negative cervical samples or cell lines and validated at the genotype level by comparing the sequencing results to those obtained using a commercial genotyping kit. The performance of our protocol, presented in this proof-of-principle study, supports its use for accurate characterization of genetic variants of hrHPV.
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Pang J, Nguyen N, Luebeck J, Ball L, Finegersh A, Ren S, Nakagawa T, Flagg M, Sadat S, Mischel PS, Xu G, Fisch K, Guo T, Cahill G, Panuganti B, Bafna V, Califano J. Extrachromosomal DNA in HPV-Mediated Oropharyngeal Cancer Drives Diverse Oncogene Transcription. Clin Cancer Res 2021; 27:6772-6786. [PMID: 34548317 DOI: 10.1158/1078-0432.ccr-21-2484] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/20/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Human papillomavirus (HPV) plays a major role in oncogenesis and circular extrachromosomal DNA (ecDNA) is found in many cancers. However, the relationship between HPV and circular ecDNA in human cancer is not understood. EXPERIMENTAL DESIGN Forty-four primary tumor tissue samples were obtained from a cohort of patients with HPV-positive oropharynx squamous cell carcinoma (OPSCC). Twenty-eight additional HPV oropharyngeal cancer (HPVOPC) tumors from The Cancer Genome Atlas (TCGA) project were analyzed as a separate validation cohort. Genomic, transcriptomic, proteomic, computational, and functional analyses of HPVOPC were applied to these datasets. RESULTS Our analysis revealed circular, oncogenic DNA in nearly all HPVOPC, with circular human and human-viral hybrid ecDNA present in over a third of HPVOPC and viral circular DNA in remaining tumors. Hybrid ecDNA highly express fusion transcripts from HPV promoters and HPV oncogenes linked to downstream human transcripts that drive oncogenic transformation and immune evasion, and splice multiple, diverse human acceptors to a canonical SA880 viral donor site. HPVOPC have high E6*I expression with specific viral oncogene expression pattern related to viral or hybrid ecDNA composition. CONCLUSIONS Nonchromosomal circular oncogenic DNA is a dominant feature of HPVOPC, revealing an unanticipated link between HPV and ecDNA that leverages the power of extrachromosomal inheritance to drive HPV and somatic oncogene expression.
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Affiliation(s)
- John Pang
- UC San Diego School of Medicine, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, La Jolla, California
| | - Nam Nguyen
- UC San Diego Jacobs School of Engineering, Department of Computer Science and Engineering, La Jolla, California
| | - Jens Luebeck
- Bioinformatics & Systems Biology Graduate Program, University of California at San Diego, La Jolla, California
| | - Laurel Ball
- UC San Diego School of Medicine, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, La Jolla, California
| | - Andrey Finegersh
- UC San Diego School of Medicine, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, La Jolla, California
| | - Shuling Ren
- UC San Diego School of Medicine, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, La Jolla, California
| | - Takuya Nakagawa
- UC San Diego School of Medicine, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, La Jolla, California
| | - Mitchell Flagg
- UC San Diego School of Medicine, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, La Jolla, California
| | - Sayed Sadat
- UC San Diego School of Medicine, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, La Jolla, California
| | - Paul S Mischel
- Stanford University School of Medicine, Department of Pathology, ChEM-H, Stanford, California
| | - Guorong Xu
- UC San Diego School of Medicine, Center for Computational Biology and Bioinformatics, La Jolla, California
| | - Kathleen Fisch
- UC San Diego School of Medicine, Center for Computational Biology and Bioinformatics, La Jolla, California
| | - Theresa Guo
- UC San Diego School of Medicine, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, La Jolla, California.,Johns Hopkins University School of Medicine, Otolaryngology-Head and Neck Surgery, Baltimore, Maryland
| | - Gabrielle Cahill
- UC San Diego School of Medicine, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, La Jolla, California
| | - Bharat Panuganti
- UC San Diego School of Medicine, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, La Jolla, California
| | - Vineet Bafna
- UC San Diego Jacobs School of Engineering, Department of Computer Science and Engineering, La Jolla, California.
| | - Joseph Califano
- UC San Diego School of Medicine, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, La Jolla, California. .,Bioinformatics & Systems Biology Graduate Program, University of California at San Diego, La Jolla, California
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Artaza-Irigaray C, Molina-Pineda A, Aguilar-Lemarroy A, Ortiz-Lazareno P, Limón-Toledo LP, Pereira-Suárez AL, Rojo-Contreras W, Jave-Suárez LF. E6/E7 and E6 * From HPV16 and HPV18 Upregulate IL-6 Expression Independently of p53 in Keratinocytes. Front Immunol 2019; 10:1676. [PMID: 31396215 PMCID: PMC6664019 DOI: 10.3389/fimmu.2019.01676] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/04/2019] [Indexed: 12/24/2022] Open
Abstract
Keratinocyte infection with high-risk human papillomavirus genotypes has been linked to cancer development. In cervix, the alpha HPV16 and HPV18 have been reported as the mayor causative agents of cervical cancer. Oncogenic progression and chronic inflammation are closely related processes, with IL-6 as one of the main pro-inflammatory cytokines involved. However, there are limited studies about the regulation of IL-6 by low and high risk HPVs and the HPV proteins implicated in this modulation. In this work, we report the overexpression of IL-6 in HPV infected cervical cancer derived cell lines (HeLa and SiHa) compared to non-tumorigenic keratinocytes (HaCaT), and in Cervical Intraepithelial Neoplasia grade 1 HPV16 and HPV18 positive cervical samples compared to HPV negative samples without lesions. Moreover, we generated HaCaT keratinocytes that express E5, E6, and E7 from high risk (16 or 18) or low risk (62 and 84) HPVs. E5 proteins do not modify IL-6 expression, while E7 modestly increase it. Interestingly, E6 proteins in HaCaT cells upregulate IL-6 mRNA expression and protein secretion. Indeed, in HaCaT cells that express high risk HPV16E6 or HPV18E6 proteins, only the truncated E6* isoforms were expressed, showing the stronger IL-6 overexpression, while in HaCaT cells that express low risk HPV62 and HPV84 full length E6 proteins, IL-6 was also upregulated but not so drastically. Since HaCaT cells have a mutated p53 form that is not degraded by the introduction of E6 or E6/E7, it seems that E6/E7 regulate IL-6 by an additional mechanism independent of p53. In addition, basal keratinocytes showed a strong expression of IL-6R using immunohistochemistry, suggesting an autocrine mechanism over proliferative cells. Altogether, IL-6 cytokine expression in keratinocytes is upregulated by E6 and E7 proteins from HPVs 16, 18, 62, and 84, especially by high risk HPV16 and HPV18 E6*, which may contribute to promote a pro-inflammatory and highly proliferative microenvironment that can persist over time and lead to cervical tumorigenesis.
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Affiliation(s)
- Cristina Artaza-Irigaray
- Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | - Andrea Molina-Pineda
- Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Adriana Aguilar-Lemarroy
- Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | - Pablo Ortiz-Lazareno
- Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | - Laura P Limón-Toledo
- Centro Médico Nacional de Occidente, Instituto Mexicano del Seguro Social, Hospital de Ginecología y Obstetricia, Guadalajara, Mexico
| | - Ana L Pereira-Suárez
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | | | - Luis F Jave-Suárez
- Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
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