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Vieira IA, Viola GD, Pezzi EH, Kowalski TW, Fernandes BV, Andreis TF, Bom N, Sonnenstrahl G, Rocha YMDA, Corrêa BDS, Donatti LM, Sant’Anna GDS, Corleta HVE, Brum IS, Rosset C, Vianna FSL, Macedo GS, Palmero EI, Ashton-Prolla P. Exploring the frequency of a TP53 polyadenylation signal variant in tumor DNA from patients diagnosed with lung adenocarcinomas, sarcomas and uterine leiomyomas. Genet Mol Biol 2024; 46:e20230133. [PMID: 38252059 PMCID: PMC10802224 DOI: 10.1590/1678-4685-gmb-2023-0133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/16/2023] [Indexed: 01/23/2024] Open
Abstract
The TP53 3'UTR variant rs78378222 A>C has been detected in different tumor types as a somatic alteration that reduces p53 expression through modification of polyadenylation and miRNA regulation. Its prevalence is not yet known in all tumors. Herein, we examine tumor tissue prevalence of rs7837822 in Brazilian cohorts of patients from south and southeast regions diagnosed with lung adenocarcinoma (LUAD, n=586), sarcoma (SARC, n=188) and uterine leiomyoma (ULM, n=41). The minor allele (C) was identified in heterozygosity in 6/586 LUAD tumors (prevalence = 1.02 %) and none of the SARC and ULM samples. Additionally, next generation sequencing analysis revealed that all variant-positive tumors (n=4) with sample availability had additional pathogenic or likely pathogenic somatic variants in the TP53 coding regions. Among them, 3/4 (75 %) had the same pathogenic or likely pathogenic sequence variant (allele frequency <0.05 in tumor DNA) namely c.751A>C (p.Ile251Leu). Our results indicate a low somatic prevalence of rs78378222 in LUAD, ULM and SARC tumors from Brazilian patients, which suggests that no further analysis of this variant in the specific studied regions of Brazil is warranted. However, these findings should not exclude tumor molecular testing of this TP53 3'UTR functional variant for different populations.
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Affiliation(s)
- Igor Araujo Vieira
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade do Vale do Rio dos Sinos (UNISINOS), Escola de Saúde, São Leopoldo, RS, Brazil
| | - Guilherme Danielski Viola
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Eduarda Heidrich Pezzi
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Thayne Woycinck Kowalski
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Laboratório de Genética Médica e Populacional, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INAGEMP), Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Genética Médica, Sistema Nacional de Informações sobre Agentes Teratogênicos (SIAT), Porto Alegre, RS, Brazil
- Complexo de Ensino Superior de Cachoeirinha (CESUCA), Cachoeirinha, RS, Brazil
| | - Bruna Vieira Fernandes
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Tiago Finger Andreis
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Natascha Bom
- Universidade do Vale do Rio dos Sinos (UNISINOS), Curso de Graduação em Biomedicina, São Leopoldo, RS, Brazil
| | - Giulianna Sonnenstrahl
- Universidade do Vale do Rio dos Sinos (UNISINOS), Curso de Graduação em Biomedicina, São Leopoldo, RS, Brazil
| | - Yasminne Marinho de Araújo Rocha
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Bruno da Silveira Corrêa
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Luiza Mezzomo Donatti
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Fisiologia, Laboratório de Biologia Molecular Endócrino e Tumoral, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Porto Alegre, RS, Brazil
| | - Gabriela dos Santos Sant’Anna
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Fisiologia, Laboratório de Biologia Molecular Endócrino e Tumoral, Porto Alegre, RS, Brazil
| | - Helena von Eye Corleta
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Fisiologia, Laboratório de Biologia Molecular Endócrino e Tumoral, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Ginecologia e Obstetrícia, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Ginecologia e Obstetrícia, Porto Alegre, RS, Brazil
| | - Ilma Simoni Brum
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Fisiologia, Laboratório de Biologia Molecular Endócrino e Tumoral, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Porto Alegre, RS, Brazil
| | - Clévia Rosset
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Unidade de Pesquisa Laboratorial (UPL), Porto Alegre, RS, Brazil
| | - Fernanda Sales Luiz Vianna
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Laboratório de Genética Médica e Populacional, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INAGEMP), Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Genética Médica, Sistema Nacional de Informações sobre Agentes Teratogênicos (SIAT), Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Imunobiologia e Imunogenética, Porto Alegre, RS, Brazil
| | - Gabriel S. Macedo
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Programa de Medicina Personalizada, Porto Alegre, RS, Brazil
| | - Edenir Inez Palmero
- Instituto Nacional de Câncer (INCA), Departamento de Genética, Rio de Janeiro, RJ, Brazil
- Hospital de Câncer de Barretos, Centro de Pesquisa em Oncologia Molecular, Barretos, SP, Brazil
| | - Patricia Ashton-Prolla
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Programa de Medicina Personalizada, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Porto Alegre, RS, Brazil
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Voropaeva EN, Orlov YL, Pospelova TI, Gurageva AA, Voevoda MI, Maksimov VN, Seregina OB, Churkina MI. The rs78378222 prevalence and the copy loss of the protective allele A in the tumor tissue of diffuse large B-cell lymphoma. PeerJ 2020; 8:e10335. [PMID: 33240649 PMCID: PMC7666812 DOI: 10.7717/peerj.10335] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/19/2020] [Indexed: 12/22/2022] Open
Abstract
Background Rare single nucleotide polymorphisms (SNPs) are likely to be a crucial genetic factor for human diseases, including cancer. rs78378222 is rare SNP in 3′-untranslated region (UTR) of TP53 gene leading to disturbance of 3′-end mRNA processing. The frequency of rs78378222 varies in several studied populations. The meta-analysis of 34 genome-wide association studies indicated that rs78378222 was significantly associated with an increased risk of cancer overall. Bioinformatic analysis indicates that somatic loss of the protective A allele of rs78378222 occurs in the tumor tissue of some malignant. The goal of the current study is to document the rs78378222 prevalence and evaluate the copy loss status of the protective allele A in the tumor tissue of patients with diffuse large B-cell lymphoma (DLBCL). Methods Total DNA was isolated from FFPE-samples and peripheral blood of patients with DLBCL and comparable in age and sex controls. rs78378222 genotyping was performed by the PCR-RFLP method using restriction endonuclease HindIII. Direct Sanger’s sequencing was used to confirm the presence of C allele of the rs78378222. The search for TP53 gene mutations was carried out by Sanger’s direct sequencing method, according to the IARC protocol. Results The result of genotyping of 136 DNA samples from DLBCL tumor tissue suggested that frequency of the rs78378222 was 11/136 (8.1%). Rare allele C frequency was 11/272 (4.2%). A total of 5/11 DLBCL rs78378222 heterozygous samples had the heterozygosity loss in the TP53 gene. Only one of these cases was combined with TP53 gene mutations which have proven oncogenic potential—p.Arg196Gln, other four cases have not mutations in the coding regions of gene. Conclusions At the stages of DLBCL initiation or progression a loss of the protective allele A of rs78378222 occurs. Further efforts are needed to study possible molecular mechanisms underlying somatic alterations in DLBCL in this region of the TP53 3′-UTR as well as functional studies to illustrate how the presents of rs78378222 may affect tumor progression of lymphoma.
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Affiliation(s)
- Elena N Voropaeva
- Research Institute of Internal and Preventive Medicine, Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yuriy L Orlov
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Tatiana I Pospelova
- Novosibirsk State Medical University of the Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - Anna A Gurageva
- Research Institute of Internal and Preventive Medicine, Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mikhail I Voevoda
- Research Institute of Internal and Preventive Medicine, Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Vladimir N Maksimov
- Research Institute of Internal and Preventive Medicine, Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga B Seregina
- Novosibirsk State Medical University of the Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - Maria I Churkina
- Novosibirsk State Medical University of the Ministry of Health of the Russian Federation, Novosibirsk, Russia
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