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Garrido J, Bernal Y, González E, Blanco A, Sepúlveda-Hermosilla G, Freire M, Oróstica K, Rivas S, Marcelain K, Owen G, Ibañez C, Corvalan A, Garrido M, Assar R, Lizana R, Cáceres-Molina J, Ampuero D, Ramos L, Pérez P, Aren O, Chernilo S, Fernández C, Spencer ML, Aguila JF, Dossetto GB, Olea MA, Rasse G, Sánchez C, de Amorim MG, Bartelli TF, Nunes DN, Dias-Neto E, Freitas HC, Armisén R. Beyond tobacco: genomic disparities in lung cancer between smokers and never-smokers. BMC Cancer 2024; 24:951. [PMID: 39097719 PMCID: PMC11297669 DOI: 10.1186/s12885-024-12737-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024] Open
Abstract
BACKGROUND Tobacco use is one of the main risk factors for Lung Cancer (LC) development. However, about 10-20% of those diagnosed with the disease are never-smokers. For Non-Small Cell Lung Cancer (NSCLC) there are clear differences in both the clinical presentation and the tumor genomic profiles between smokers and never-smokers. For example, the Lung Adenocarcinoma (LUAD) histological subtype in never-smokers is predominately found in young women of European, North American, and Asian descent. While the clinical presentation and tumor genomic profiles of smokers have been widely examined, never-smokers are usually underrepresented, especially those of a Latin American (LA) background. In this work, we characterize, for the first time, the difference in the genomic profiles between smokers and never-smokers LC patients from Chile. METHODS We conduct a comparison by smoking status in the frequencies of genomic alterations (GAs) including somatic mutations and structural variants (fusions) in a total of 10 clinically relevant genes, including the eight most common actionable genes for LC (EGFR, KRAS, ALK, MET, BRAF, RET, ERBB2, and ROS1) and two established driver genes for malignancies other than LC (PIK3CA and MAP2K1). Study participants were grouped as either smokers (current and former, n = 473) or never-smokers (n = 200) according to self-report tobacco use at enrollment. RESULTS Our findings indicate a higher overall GA frequency for never-smokers compared to smokers (58 vs. 45.7, p-value < 0.01) with the genes EGFR, KRAS, and PIK3CA displaying the highest prevalence while ERBB2, RET, and ROS1 the lowest. Never-smokers present higher frequencies in seven out of the 10 genes; however, smokers harbor a more complex genomic profile. The clearest differences between groups are seen for EGFR (15.6 vs. 21.5, p-value: < 0.01), PIK3CA (6.8 vs 9.5) and ALK (3.2 vs 7.5) in favor of never-smokers, and KRAS (16.3 vs. 11.5) and MAP2K1 (6.6 vs. 3.5) in favor of smokers. Alterations in these genes are comprised almost exclusively by somatic mutations in EGFR and mainly by fusions in ALK, and only by mutations in PIK3CA, KRAS and MAP2K1. CONCLUSIONS We found clear differences in the genomic landscape by smoking status in LUAD patients from Chile, with potential implications for clinical management in these limited-resource settings.
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Affiliation(s)
- Javiera Garrido
- Centro Genética y Genómica, Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Yanara Bernal
- Centro Genética y Genómica, Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Evelin González
- Centro Genética y Genómica, Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Alejandro Blanco
- Centro Genética y Genómica, Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Gonzalo Sepúlveda-Hermosilla
- Centro Genética y Genómica, Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- CORFO Center of Excellence in Precision Medicine Pfizer, Santiago, Chile
| | - Matías Freire
- CORFO Center of Excellence in Precision Medicine Pfizer, Santiago, Chile
| | - Karen Oróstica
- Instituto de Investigación Interdisciplinario, Vicerrectoría Académica, Universidad de Talca, Talca, Chile
| | - Solange Rivas
- Centro Genética y Genómica, Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Katherine Marcelain
- Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Centro Para La Prevención y el Control del Cáncer, Universidad de Chile, Santiago, Chile
| | - Gareth Owen
- Departamento de Hematología y Oncología and Advanced Center for Chronic Diseases, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Institute for Immunology and Immunotherapy, Santiago, Chile
| | - Carolina Ibañez
- Departamento de Hematología y Oncología and Advanced Center for Chronic Diseases, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro Corvalan
- Departamento de Hematología y Oncología and Advanced Center for Chronic Diseases, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcelo Garrido
- Centro de Oncología de Precisión, Universidad Mayor, Santiago, Chile
| | - Rodrigo Assar
- CORFO Center of Excellence in Precision Medicine Pfizer, Santiago, Chile
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Rodrigo Lizana
- CORFO Center of Excellence in Precision Medicine Pfizer, Santiago, Chile
| | | | - Diego Ampuero
- CORFO Center of Excellence in Precision Medicine Pfizer, Santiago, Chile
| | - Liliana Ramos
- CORFO Center of Excellence in Precision Medicine Pfizer, Santiago, Chile
| | - Paola Pérez
- NIDCR, National Institute of Health, Bethesda, USA
| | - Osvaldo Aren
- Centro de Investigación Clínica Bradford Hill, Santiago, Chile
| | | | | | - María Loreto Spencer
- Departamento de Patología, Hospital Clínico Regional de Concepción Dr. Guillermo Grant Benavente Chile, Concepcion, Chile
| | - Jacqueline Flores Aguila
- Departamento de Salud Pública, Facultad de Medicina, Universidad Católica del Norte, La Serena, Chile
| | - Giuliano Bernal Dossetto
- Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad Católica Del Norte, La Serena, Chile
| | - Mónica Ahumada Olea
- Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Centro Para La Prevención y el Control del Cáncer, Universidad de Chile, Santiago, Chile
- Departamento de Medicina Interna, Servicio de Oncología, Hospital Clínico de La Universidad de Chile, Santiago, Chile
| | | | - Carolina Sánchez
- Centro de Genómica y Bioinformática, Universidad Mayor, Santiago, Chile
| | | | - Thais F Bartelli
- Laboratory of Medical Genomics, A. C. Camargo Cancer Center, Sao Paulo, Brazil
| | - Diana Noronha Nunes
- Laboratory of Medical Genomics, A. C. Camargo Cancer Center, Sao Paulo, Brazil
| | - Emmanuel Dias-Neto
- Laboratory of Medical Genomics, A. C. Camargo Cancer Center, Sao Paulo, Brazil
- Department of Radiation Oncology, Cancer Institute of New Jersey, Rutgers University, Newark, NJ, USA
| | - Helano C Freitas
- Laboratory of Medical Genomics, A. C. Camargo Cancer Center, Sao Paulo, Brazil
- Department of Clinical Oncology, A.C. Camargo Cancer Center, Sao Paulo, Brazil
| | - Ricardo Armisén
- Centro Genética y Genómica, Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile.
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Parra-Medina R, Castañeda-González JP, Montoya L, Gómez-Gómez MP, Clavijo Cabezas D, Plazas Vargas M. PD-L1 expression in non-small cell lung carcinoma in Latin America: a systematic review and meta-analysis. Transl Lung Cancer Res 2024; 13:1660-1671. [PMID: 39118886 PMCID: PMC11304153 DOI: 10.21037/tlcr-24-223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/27/2024] [Indexed: 08/10/2024]
Abstract
Background Programmed cell death ligand 1 (PD-L1) expression in non-small cell lung carcinoma (NSCLC) is a crucial factor in predicting responses to immunotherapy. This systematic review and meta-analysis focuses on the prevalence of PD-L1 expression and clinicopathological features among Hispanic/Latino (H/L) populations. Methods Embase, LILACS, Medline, and Virtual Health Library were searched for studies that evaluated the prevalence of PD-L1 in H/L patients. The protocol was submitted to PROSPERO with ID CRD42023488547. We employed the Joanna Briggs Institute Checklist for Systematic Reviews and Research Syntheses to assess the methodological quality and applicability of the included studies. Meta-analyses were done to determine the prevalence using a random effects model. Results The meta-analysis, encompassing 21 articles with 16,486, revealed that 80.2% of patients had PD-L1 expression data available (n=13,222). The prevalence calculated of PD-L1 expression in Latino NSCLC patients was 55% [95% confidence interval (CI): 0.54-0.55], with 31% (95% CI: 0.27-0.36) showing a tumoral proportion score (TPS) of 1-49%, and 23% (95% CI: 0.16-0.30) registering a TPS ≥50%. Higher expression was observed in male gender, smoking, adenocarcinoma subtypes, poor tumor differentiation, and advanced stages. PD-L1 expression was most frequent in EGFR wild-type status (82.5%) with a odds ratio (OR) 1.54 (95% CI: 1.24-1.92) and PD-L1 expression was associated with ALK positive (OR =1.54; 95% CI: 1.24-1.92). Conclusions This meta-analysis provides a comprehensive overview of PD-L1 expression in NSCLC in the H/L population. The findings underscore the significant prevalence of PD-L1 expression and emphasize the relevance of immunotherapy in this population. Understanding the clinicopathological features associated with PD-L1 expression can contribute to tailored treatment strategies for NSCLC in Latin America.
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Affiliation(s)
- Rafael Parra-Medina
- Research Institute, Fundación Universitaria de Ciencias de la Salud (FUCS), Bogotá, Colombia
- Department of Pathology, Fundación Universitaria de Ciencias de la Salud (FUCS), Bogotá, Colombia
- Department of Pathology, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Juan Pablo Castañeda-González
- Research Institute, Fundación Universitaria de Ciencias de la Salud (FUCS), Bogotá, Colombia
- Department of Pathology, Fundación Universitaria de Ciencias de la Salud (FUCS), Bogotá, Colombia
| | - Luisa Montoya
- Department of Clinical Epidemiology and Biostatistics, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - María Paula Gómez-Gómez
- Department of Pathology, Fundación Universitaria de Ciencias de la Salud (FUCS), Bogotá, Colombia
| | - Daniel Clavijo Cabezas
- Department of Pathology, Fundación Universitaria de Ciencias de la Salud (FUCS), Bogotá, Colombia
| | - Merideidy Plazas Vargas
- Department of Epidemiology, Fundación Universitaria de Ciencias de la Salud (FUCS), Bogotá, Colombia
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An immune-related nomogram model that predicts the overall survival of patients with lung adenocarcinoma. BMC Pulm Med 2022; 22:114. [PMID: 35354459 PMCID: PMC8969384 DOI: 10.1186/s12890-022-01902-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/14/2022] [Indexed: 11/20/2022] Open
Abstract
Background Lung adenocarcinoma accounts for approximately 40% of all primary lung cancers; however, the mortality rates remain high. Successfully predicting progression and overall (OS) time will provide clinicians with more options to manage this disease.
Methods We analyzed RNA sequencing data from 510 cases of lung adenocarcinoma from The Cancer Genome Atlas database using CIBERSORT, ImmuCellAI, and ESTIMATE algorithms. Through these data we constructed 6 immune subtypes and then compared the difference of OS, immune infiltration level and gene expression between these immune subtypes. Also, all the subtypes and immune cells infiltration level were used to evaluate the relationship with prognosis and we introduced lasso-cox method to constructe an immune-related prognosis model. Finally we validated this model in another independent cohort. Results The C3 immune subtype of lung adenocarcinoma exhibited longer survival, whereas the C1 subtype was associated with a higher mutation rate of MUC17 and FLG genes compared with other subtypes. A multifactorial correlation analysis revealed that immune cell infiltration was closely associated with overall survival. Using data from 510 cases, we constructed a nomogram prediction model composed of clinicopathologic factors and immune signatures. This model produced a C-index of 0.73 and achieved a C-index of 0.844 using a validation set. Conclusions Through this study we constructed an immune related prognosis model to instruct lung adenocarcinoma’s OS and validated its value in another independent cohost. These results will be useful in guiding treatment for lung adenocarcinoma based on tumor immune profiles. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-022-01902-6.
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Dalurzo ML, Avilés-Salas A, Soares FA, Hou Y, Li Y, Stroganova A, Öz B, Abdillah A, Wan H, Choi YL. Testing for EGFR Mutations and ALK Rearrangements in Advanced Non-Small-Cell Lung Cancer: Considerations for Countries in Emerging Markets. Onco Targets Ther 2021; 14:4671-4692. [PMID: 34511936 PMCID: PMC8420791 DOI: 10.2147/ott.s313669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/08/2021] [Indexed: 12/24/2022] Open
Abstract
The treatment of patients with advanced non-small-cell lung cancer (NSCLC) in recent years has been increasingly guided by biomarker testing. Testing has centered on driver genetic alterations involving the epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) rearrangements. The presence of these mutations is predictive of response to targeted therapies such as EGFR tyrosine kinase inhibitors (TKIs) and ALK TKIs. However, there are substantial challenges for the implementation of biomarker testing, particularly in emerging countries. Understanding the barriers to testing in NSCLC will be key to improving molecular testing rates worldwide and patient outcomes as a result. In this article, we review EGFR mutations and ALK rearrangements as predictive biomarkers for NSCLC, discuss a selection of appropriate tests and review the literature with respect to the global uptake of EGFR and ALK testing. To help improve testing rates and unify procedures, we review our experiences with biomarker testing in China, South Korea, Russia, Turkey, Brazil, Argentina and Mexico, and propose a set of recommendations that pathologists from emerging countries can apply to assist with the diagnosis of NSCLC.
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Affiliation(s)
- Mercedes L Dalurzo
- Department of Pathology, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Yuan Li
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, People’s Republic of China
| | - Anna Stroganova
- N.N. Blokhin National Medical Research Centre of Oncology, Russian Academy of Medical Sciences, Moscow, Russia
| | - Büge Öz
- Cerrahpaşa School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Arif Abdillah
- Takeda Pharmaceuticals International AG – Singapore Branch, Singapore, Singapore
| | - Hui Wan
- Takeda Pharmaceuticals International AG – Singapore Branch, Singapore, Singapore
| | - Yoon-La Choi
- Department of Pathology and Translational Genomics, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Cavagna R, Escremim de Paula F, Sant'Anna D, Santana I, da Silva VD, da Silva ECA, Bacchi CE, Miziara JE, Dias JM, De Marchi P, Leal LF, Reis RM. Frequency of KRAS p.Gly12Cys Mutation in Brazilian Patients With Lung Cancer. JCO Glob Oncol 2021; 7:639-645. [PMID: 33956502 PMCID: PMC8162527 DOI: 10.1200/go.20.00615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/08/2021] [Accepted: 03/17/2021] [Indexed: 12/14/2022] Open
Affiliation(s)
- Rodrigo Cavagna
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Débora Sant'Anna
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Iara Santana
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
- Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | - José E. Miziara
- Department of Thoracic Surgery, Barretos Cancer Hospital, Barretos, Brazil
| | - Josiane M. Dias
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil
| | - Pedro De Marchi
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil
- Oncoclinicas, Rio de Janeiro, Brazil
| | - Leticia F. Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Barretos School of Health Sciences, Dr Paulo Prata—FACISB, Barretos, Brazil
| | - Rui M. Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga/Guimarães, Portugal
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Vieira IA, Andreis TF, Fernandes BV, Achatz MI, Macedo GS, Schramek D, Ashton-Prolla P. Prevalence of the Brazilian TP53 Founder c.1010G>A (p.Arg337His) in Lung Adenocarcinoma: Is Genotyping Warranted in All Brazilian Patients? Front Genet 2021; 12:606537. [PMID: 33603772 PMCID: PMC7885268 DOI: 10.3389/fgene.2021.606537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
In Southern and Southeastern Brazil, there is a germline pathogenic variant with incomplete penetrance located in the oligomerization domain of TP53, c.1010G>A (p.Arg337His). Due to a founder effect, the variant is present in 0.3% of the general population of the region. Recently, this variant was identified in 4.4 and 8.9% of two apparently unselected, single center case series of Brazilian lung adenocarcinoma (LUAD) patients from the Southeastern and Central regions of the country, respectively. In the present study, our aim was to examine TP53 c.1010G>A allele and genotype frequencies in LUAD samples obtained from patients diagnosed in Southern Brazil. A total of 586 LUAD samples (tumor DNA) recruited from multiple centers in the region were tested, and the mutant allele was identified using TaqMan® assays in seven cases (7/586, 1.2%) which were submitted to next generation sequencing analyses for confirmation. Somatic EGFR mutations were more frequent in TP53 c.1010G>A carriers than in non-carriers (57.1 vs. 17.6%, respectively). Further studies are needed to confirm if TP53 c.1010G>A is a driver in LUAD carcinogenesis and to verify if there is a combined effect of EGFR and germline TP53 c.1010G>A. Although variant frequency was higher than observed in the general population, it is less than previously reported in LUAD patients from other Brazilian regions. Additional data, producing regional allele frequency information in larger series of patients and including cost-effectiveness analyses, are necessary to determine if TP53 c.1010G>A screening in all Brazilian LUAD patients is justified.
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Affiliation(s)
- Igor Araujo Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Tiago Finger Andreis
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Bruna Vieira Fernandes
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Curso de Graduação em Biomedicina, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | | | - Gabriel S. Macedo
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Programa de Medicina Personalizada, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Patricia Ashton-Prolla
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Programa de Medicina Personalizada, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
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Novaes LAC, Sussuchi da Silva L, De Marchi P, Cavagna RDO, de Paula FE, Zanon MF, Evangelista AF, Albino da Silva EC, Duval da Silva V, Leal LF, Reis RM. Simultaneous analysis of ALK, RET, and ROS1 gene fusions by NanoString in Brazilian lung adenocarcinoma patients. Transl Lung Cancer Res 2021; 10:292-303. [PMID: 33569313 PMCID: PMC7867767 DOI: 10.21037/tlcr-20-740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background Gene fusions have been successfully employed as therapeutic targets for lung adenocarcinoma. However, tissue availability for molecular testing of multiples alterations is frequently unfeasible. We aimed to detect the presence of ALK, RET, and ROS1 rearrangements by a RNA-based single assay in Brazilian lung adenocarcinomas and to associate with clinicopathological features and genetic ancestry. Methods From a FFPE series of 444 molecularly characterized lung adenocarcinomas, 253 EGFR/KRAS wild-type cases were eligible for gene rearrangement analysis. Following RNA isolation, ALK, RET, and ROS1 rearrangements were simultaneously analyzed employing the ElementsXT Custom panel (NanoString Technologies). Rearrangements were further associated with clinicopathological features and genetic ancestry of the patients. Results The NanoString platform was performed in subset of 142 cases. Gene fusion results were conclusive for 94.4% (n=134) cases (failure rate =5.6%). ALK rearrangements were observed in 21 out of 134 cases, and associated with younger, never smokers, metastatic disease, and metastases in the central nervous system. RET and ROS1 fusions were detected in two and one out of 134 cases, respectively. Genetic ancestry was not associated with gene fusions. Overall, considering all cases for which a molecular analysis was conclusive (EGFR/KRAS/ALK/RET/ROS1), ALK fusions frequency was observed in 6.5% (21/325), RET in 0.6% (2/325), and ROS1 in 0.3% (1/325). Conclusions This study successfully used a RNA-based single assay for the simultaneous analysis of ALK, RET, and ROS1 fusions employing routine biopsies from Brazilian patients lung adenocarcinoma allowing an extensive molecular testing for actionable rearrangements contributing to guide clinical strategies.
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Affiliation(s)
| | | | - Pedro De Marchi
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil.,Oncoclinicas Group, Rio de Janeiro, Brazil
| | - Rodrigo de Oliveira Cavagna
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Maicon Fernando Zanon
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | - Vinícius Duval da Silva
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil.,Barretos School of Medicine Dr. Paulo Prata - FACISB, Barretos, Brazil
| | - Letícia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Barretos School of Medicine Dr. Paulo Prata - FACISB, Barretos, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
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8
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Mascarenhas E, Gelatti AC, Araújo LH, Baldotto C, Mathias C, Zukin M, Werutsky G, Pacheco P, Gomes R, de Castro G, Cordeiro de Lima VC. Comprehensive genomic profiling of Brazilian non-small cell lung cancer patients (GBOT 0118/LACOG0418). Thorac Cancer 2020; 12:580-587. [PMID: 33314759 PMCID: PMC7919136 DOI: 10.1111/1759-7714.13777] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 01/18/2023] Open
Abstract
Background The aim of this study was to carry out a descriptive analysis of the somatic genetic profile and co‐occurring mutations of non‐small cell lung cancer (NSCLC) samples from patients tested with comprehensive genomic profiling (CGP). Methods This was a retrospective cross‐sectional study of patients diagnosed with NSCLC from 2013 to 2018 in Brazil and whose samples were submitted to CGP (FoundationOne or FoundationACT) using either tumor or circulating tumor DNA (ctDNA) from plasma. Results We recovered 513 CGP results from patients, 457 (89.1%) of which were from tumors and 56 (10.9%) from plasma. The median age of patients was 64 years old, of which 51.6% were males. TP53 mutations were identified in 53.6% of tumor samples, KRAS mutations in 24.2%, EGFR activating mutations were detected in 22.5%, STK11 mutations in 11.6%, PIK3CA mutations in 8.8%, ALK rearrangements in 5.4%, BRAF mutations in 5.2%, and ERBB2 alterations in 4.9%. The most commonly comutated gene was TP53. TP53 p.R337H was observed in 4.3% of samples and was associated with somatic mutations in EGFR and ERBB2 (P < 0.00001). Tumor mutational burden (TMB) analysis was available for 80.5% of samples tested, and 5.5% of samples had high TMB (≥ 20 mutations/Mb). In conclusion, this retrospective analysis of genomic data from NSCLC patients obtained by CGP showed that common abnormalities such as EGFR mutations and ALK rearrangements had similar frequency to those previously described by other groups using others strategies. Additionally, our data confirm an association between TP53 p.R337H, supposedly germline in nature, and somatic mutations in genes of the HER family. Key points Significant findings of the study This is the first report of the prevalence of driver mutations in Brazilian NSCLC patients using comprehensive genomic profiling (CGP). The frequency of the most common driver mutations in this population was similar to that previously described in Brazil.
What this study adds TP53 was the most commonly comutated gene across samples. TP53 p.R337H was associated with somatic mutations in EGFR and ERBB2. Most samples had low TMB; only 5.5% of samples had high TMB.
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Affiliation(s)
- Eldsamira Mascarenhas
- Grupo Brasileiro de Oncologia Torácica, Porto Alegre, Brazil.,Oncologia D'or, Salvador, Brazil
| | - Ana Caroline Gelatti
- Grupo Brasileiro de Oncologia Torácica, Porto Alegre, Brazil.,Latin American Cooperative Oncology Group, Porto Alegre, Brazil.,Grupo Oncoclínicas, Porto Alegre, Brazil
| | - Luiz Henrique Araújo
- Grupo Brasileiro de Oncologia Torácica, Porto Alegre, Brazil.,Instituto COI de Educação e Pesquisa, Rio De Janeiro, Brazil.,Instituto Nacional do Câncer, Rio De Janeiro, Brazil
| | - Clarissa Baldotto
- Grupo Brasileiro de Oncologia Torácica, Porto Alegre, Brazil.,Oncologia D'or, Rio De Janeiro, Brazil
| | - Clarissa Mathias
- Grupo Brasileiro de Oncologia Torácica, Porto Alegre, Brazil.,NOB/Oncoclínicas, Salvador, Brazil
| | - Mauro Zukin
- Grupo Brasileiro de Oncologia Torácica, Porto Alegre, Brazil.,Oncologia D'or, Rio De Janeiro, Brazil
| | | | | | - Rafaela Gomes
- Latin American Cooperative Oncology Group, Porto Alegre, Brazil
| | - Gilberto de Castro
- Grupo Brasileiro de Oncologia Torácica, Porto Alegre, Brazil.,Instituto do Câncer do Estado de São Paulo, São Paulo, Brazil
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9
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Souza CP, Cinegaglia NC, Felix TF, Evangelista AF, Oliveira RA, Hasimoto EN, Cataneo DC, Cataneo AJM, Scapulatempo Neto C, Viana CR, de Paula FE, Drigo SA, Carvalho RF, Marques MMC, Reis RM, Reis PP. Deregulated microRNAs Are Associated with Patient Survival and Predicted to Target Genes That Modulate Lung Cancer Signaling Pathways. Cancers (Basel) 2020; 12:E2711. [PMID: 32971741 PMCID: PMC7563870 DOI: 10.3390/cancers12092711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/05/2020] [Accepted: 09/09/2020] [Indexed: 12/24/2022] Open
Abstract
(1) Background: Although the advances in diagnostic and treatment strategies, lung cancer remains the leading cause of cancer-related deaths, worldwide, with survival rates as low as 16% in developed countries. Low survival rates are mainly due to late diagnosis and the lack of effective treatment. Therefore, the identification of novel, clinically useful biomarkers is still needed for patients with advanced disease stage and poor survival. Micro(mi)RNAs are non-coding RNAs and potent regulators of gene expression with a possible role as diagnostic, prognostic and predictive biomarkers in cancer. (2) Methods: We applied global miRNA expression profiling analysis using TaqMan® arrays in paired tumor and normal lung tissues (n = 38) from treatment-naïve patients with lung adenocarcinoma (AD; n = 23) and lung squamous cell carcinoma (SCC; n = 15). miRNA target genes were validated using The Cancer Genome Atlas (TCGA) lung AD (n = 561) and lung SCC (n = 523) RNA-Seq datasets. (3) Results: We identified 33 significantly deregulated miRNAs (fold change, FC ≥ 2.0 and p < 0.05) in tumors relative to normal lung tissues, regardless of tumor histology. Enrichment analysis confirmed that genes targeted by the 33 miRNAs are aberrantly expressed in lung AD and SCC, and modulate known pathways in lung cancer. Additionally, high expression of miR-25-3p was significantly associated (p < 0.05) with poor patient survival, when considering both tumor histologies. (4) Conclusions: miR-25-3p may be a potential prognostic biomarker in non-small cell lung cancer. Genes targeted by miRNAs regulate EGFR and TGFβ signaling, among other known pathways relevant to lung tumorigenesis.
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Affiliation(s)
- Cristiano P. Souza
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (C.P.S.); (E.N.H.); (D.C.C.); (A.J.M.C.); (S.A.D.)
- Experimental Research Unity (UNIPEX), São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (N.C.C.); (T.F.F.)
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
| | - Naiara C. Cinegaglia
- Experimental Research Unity (UNIPEX), São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (N.C.C.); (T.F.F.)
| | - Tainara F. Felix
- Experimental Research Unity (UNIPEX), São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (N.C.C.); (T.F.F.)
| | - Adriane F. Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
| | - Rogério A. Oliveira
- Department of Biostatistics, Plant Biology, Parasitology, and Zoology, Institute of Biosciences, São Paulo State University UNESP, Botucatu 18618-689, SP, Brazil;
| | - Erica N. Hasimoto
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (C.P.S.); (E.N.H.); (D.C.C.); (A.J.M.C.); (S.A.D.)
| | - Daniele C. Cataneo
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (C.P.S.); (E.N.H.); (D.C.C.); (A.J.M.C.); (S.A.D.)
| | - Antônio J. M. Cataneo
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (C.P.S.); (E.N.H.); (D.C.C.); (A.J.M.C.); (S.A.D.)
| | - Cristovam Scapulatempo Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
| | - Cristiano R. Viana
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
| | - Flávia E. de Paula
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
| | - Sandra A. Drigo
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (C.P.S.); (E.N.H.); (D.C.C.); (A.J.M.C.); (S.A.D.)
- Experimental Research Unity (UNIPEX), São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (N.C.C.); (T.F.F.)
| | - Robson F. Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, UNESP, Botucatu 18618-689, SP, Brazil;
| | - Márcia M. C. Marques
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
- Barretos School of Health Sciences, Barretos 14785-002, SP, Brazil
| | - Rui M. Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s-PT Government Associate Laboratory, 410-057 Braga/Guimarães, Portugal
| | - Patricia P. Reis
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (C.P.S.); (E.N.H.); (D.C.C.); (A.J.M.C.); (S.A.D.)
- Experimental Research Unity (UNIPEX), São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (N.C.C.); (T.F.F.)
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10
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Freitas HC, Torrezan GT, da Cunha IW, Macedo MP, Karen de Sá V, Corassa M, Ferreira ENE, Saito AO, Dal Molin GZ, Cordeiro de Lima VC, Carraro DM. Mutational Portrait of Lung Adenocarcinoma in Brazilian Patients: Past, Present, and Future of Molecular Profiling in the Clinic. Front Oncol 2020; 10:1068. [PMID: 32714871 PMCID: PMC7343968 DOI: 10.3389/fonc.2020.01068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 05/28/2020] [Indexed: 12/23/2022] Open
Abstract
Objectives: Approximately 60% of lung adenocarcinomas (LAs) carry mutations that can guide treatment with tyrosine-kinase inhibitors (TKI) and other targeted therapies. Data on activating mutations in EGFR and other tyrosine-kinase receptor (TKR) genes in highly admixed populations, such as that of Brazil, are scarce. In this study, we comprehensively analyzed the actionable alteration profile of LA in Brazilian patients. Materials and Methods:EGFR driver mutation data were collected from a large Brazilian LA cohort covering an 8-year period of molecular testing in a single institution. Tests were performed using three distinct methods, and demographic and histopathological data were analyzed. For a subset of patients, driver mutations in KRAS, NRAS, and BRAF and gene fusions involving TKR genes (before TKI treatment) and EGFR T790M (after TKI treatment) were assessed. Results:EGFR mutations were detected in 25% of 1,316 LAs evaluated, with exon 19 deletions and exon 21 L858R TKI sensitizing mutations representing 72.5% of all mutations. Mutation rates were higher in women and non-smokers (p < 0.001). Next-generation sequencing was very sensitive, with a lower rate of inconclusive results compared with Sanger sequencing and pyrosequencing. EGFR/RAS/BRAF hotspot gene panels were applied in 495 LA cases and detected oncogenic mutations in 51.3% of samples, most frequently in EGFR (22.4%) and KRAS (26.9%). In subgroups of 36 and 35 patients, gene fusions were detected in 11.1% of tumors and EGFR T790M resistance mutations were detected in 59% of plasma samples from patients previously treated with TKI, respectively. Conclusion: This report provides the first comprehensive actionable alteration portrait of LA in Brazil. The high rate of actionable alterations in EGFR and other driver genes in LA reinforces the need to incorporate TKI guided by molecular diagnostics into clinical routines for patients in both public and private healthcare systems.
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Affiliation(s)
- Helano C Freitas
- Medical Oncology Department, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Giovana Tardin Torrezan
- Genomics and Molecular Biology Group, International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil.,Genomic Diagnostic Laboratory, Anatomic Pathology Department, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Isabela Werneck da Cunha
- Anatomic Pathology Department, A.C. Camargo Cancer Center, São Paulo, Brazil.,Pathology Department, Rede D'OR-São Luiz, São Paulo, Brazil
| | | | | | - Marcelo Corassa
- Medical Oncology Department, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Elisa Napolitano E Ferreira
- Genomics and Molecular Biology Group, International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil.,Research and Development, Fleury Group, São Paulo, Brazil
| | | | - Graziela Zibetti Dal Molin
- Medical Oncology Department, A.C. Camargo Cancer Center, São Paulo, Brazil.,Hospital Beneficencia Portuguesa, São Paulo, Brazil
| | - Vladmir C Cordeiro de Lima
- Medical Oncology Department, A.C. Camargo Cancer Center, São Paulo, Brazil.,Translational Immuno-oncology Laboratory, International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Dirce Maria Carraro
- Genomics and Molecular Biology Group, International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil.,Genomic Diagnostic Laboratory, Anatomic Pathology Department, A.C. Camargo Cancer Center, São Paulo, Brazil
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