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1. Comprehensive Genomic Profile of Heterogeneous Long Follow-Up Triple-Negative Breast Cancer and Its Clinical Characteristics Shows DNA Repair Deficiency Has Better Prognostic.

Author

Rojas-Jiménez E, Mejía-Gómez JC, Díaz-Velásquez C, Quezada-Urban R, Martínez Gregorio H, Vallejo-Lecuona F, de la Cruz-Montoya A, Porras Reyes FI, Pérez-Sánchez VM, Maldonado-Martínez HA, Robles-Estrada M, Bargalló-Rocha E, Cabrera-Galeana P, Ramos-Ramírez M, Chirino YI, Alonso Herrera L, Terrazas LI, Oliver J, Frecha C, Perdomo S, and Vaca-Paniagua F

Subjects
Adult, Aged, DNA Repair-Deficiency Disorders genetics, Female, Humans, Kaplan-Meier Estimate, Lymphocytes, Tumor-Infiltrating pathology, Middle Aged, Triple Negative Breast Neoplasms drug therapy, Triple Negative Breast Neoplasms pathology, Exome Sequencing, Mutation, Triple Negative Breast Neoplasms genetics, Triple Negative Breast Neoplasms mortality
Abstract

Triple-negative breast cancer (TNBC) presents a marked diversity at the molecular level, which promotes a clinical heterogeneity that further complicates treatment. We performed a detailed whole exome sequencing profile of 29 Mexican patients with long follow-up TNBC to identify genomic alterations associated with overall survival (OS), disease-free survival (DFS), and pathologic complete response (PCR), with the aim to define their role as molecular predictive factors of treatment response and prognosis. We detected 31 driver genes with pathogenic mutations in TP53 (53%), BRCA1/2 (27%), CDKN1B (9%), PIK3CA (9%), and PTEN (9%), and 16 operative mutational signatures. Moreover, tumors with mutations in BRCA1/2 showed a trend of sensitivity to platinum salts. We found an association between deficiency in DNA repair and surveillance genes and DFS. Across all analyzed tumors we consistently found a heterogeneous molecular complexity in terms of allelic composition and operative mutational processes, which hampered the definition of molecular traits with clinical utility. This work contributes to the elucidation of the global molecular alterations of TNBC by providing accurate genomic data that may help forthcoming studies to improve treatment and survival. This is the first study that integrates genomic alterations with a long follow-up of clinical variables in a Latin American population that is an underrepresented ethnicity in most of the genomic studies.

Published
2020
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2. Comprehensive genomic profile of heterogeneous long follow-up triple-negative breast cancer and its clinical characteristics shows DNA repair deficiency has better prognostic

Author

Enrique Bargallo-Rocha, Luis I. Terrazas, Clara Díaz-Velásquez, Fernando Vallejo-Lecuona, Fany Iris Porras Reyes, Aldo de la Cruz-Montoya, Javier Oliver, Javier César Mejía-Gómez, Sandra Perdomo, Víctor Pérez-Sánchez, Héctor Martínez Gregorio, Paula Cabrera-Galeana, Cecilia Frecha, Maritza Ramos-Ramírez, Yolanda I. Chirino, Rosalía Quezada-Urban, Felipe Vaca-Paniagua, Luis A. Herrera, Ernesto Rojas-Jiménez, Maybelline Robles-Estrada, Héctor Maldonado-Martinez, [Rojas-Jiménez,E, Díaz-Velásquez,C, Quezada-Urban,R, Martínez Gregorio,H, Vallejo-Lecuona,F, Terrazas,LI, Vaca-Paniagua,F] Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México, Mexico. [Rojas-Jiménez,E, de la Cruz-Montoya,A, Chirino,YI, Vaca-Paniagua,F] Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, Estado de México, Mexico. [Mejía-Gómez,JC] Division of Breast Cancer, Department of Medical Oncology, Mt. Sinai Hospital, University of Toronto, Toronto, ON, Canada. [Quezada-Urban,R] Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia. [Quezada-Urban,R] Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. [Porras Reyes,FI, Pérez-Sánchez,VM, Maldonado-Martínez,HA, Bargalló-Rocha,E, Cabrera-Galeana,P, Ramos-Ramírez,M, Alonso Herrera,L, Vaca-Paniagua,F] Instituto Nacional de Cancerología, CDMX, Mexico. [Robles-Estrada,M] Hospital General de Pachuca SSA, Pachuca, Mexico. [Alonso Herrera,L] Instituto Nacional de Medicina Genómica, CDMX, Mexico. [Alonso Herrera,L] Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas-Instituto Nacional de Cancerología, CDMX, Mexico. [Oliver,J] Medical Oncology Service, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga, CIMES, University of Málaga, Málaga, Spain. [Frecha,C] Unidad de Producción Celular del Hospital Regional Universitario de Málaga—IBIMA—Málaga, Málaga, Spain. [Perdomo,S] Instituto de Nutrición, Genética y Metabolismo, Facultad de Medicina, Universidad El Bosque, Bogotá, Colombia. [Perdomo,S] International Agency for Research on Cancer, World Health Organization, Lyon, France., This study was funded by grants from UNAM PAPIIT IN219217 and CONACyT Fondo Sectorial 272573., and Perdomo Lara, Sandra Janneth [0000-0002-4429-3760]

Subjects
0301 basic medicine, Oncology, Terapéutica, Triple Negative Breast Neoplasms, Kaplan-Meier Estimate, whole exome sequencing, Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans [Medical Subject Headings], 0302 clinical medicine, Diseases::Nutritional and Metabolic Diseases::Metabolic Diseases::DNA Repair-Deficiency Disorders [Medical Subject Headings], somatic mutation, Genetics (clinical), Triple-negative breast cancer, Exome sequencing, Persons::Persons::Age Groups::Adult::Aged [Medical Subject Headings], education.field_of_study, biology, treatment, Middle Aged, Diseases::Neoplasms::Neoplasms by Site::Breast Neoplasms::Triple Negative Breast Neoplasms [Medical Subject Headings], 030220 oncology & carcinogenesis, Neoplasias de la mama, triple-negative breast cancer, WES, Female, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Sequence Analysis::Sequence Analysis, DNA [Medical Subject Headings], Adult, medicine.medical_specialty, Phenomena and Processes::Genetic Phenomena::Genetic Variation::Mutation [Medical Subject Headings], lcsh:QH426-470, DNA repair, Population, Mutational signatures, mutational signatures, Article, 03 medical and health sciences, Breast cancer, Germline mutation, Lymphocytes, Tumor-Infiltrating, Internal medicine, Exome Sequencing, Genetics, medicine, PTEN, Humans, education, Persons::Persons::Age Groups::Adult [Medical Subject Headings], Diseases::Neoplasms::Neoplasms by Site::Breast Neoplasms [Medical Subject Headings], Aged, Secuenciación del exoma completo, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Statistics as Topic::Survival Analysis::Kaplan-Meier Estimate [Medical Subject Headings], Somatic mutation, México, Whole exome sequencing, Persons::Persons::Age Groups::Adult::Middle Aged [Medical Subject Headings], Neoplasias de la mama triple negativas, medicine.disease, DNA Repair-Deficiency Disorders, Treatment, lcsh:Genetics, 030104 developmental biology, Geographical Locations::Geographic Locations::Americas::North America::Mexico [Medical Subject Headings], Check Tags::Female [Medical Subject Headings], Genomic Profile, Mutation, biology.protein, Anatomy::Hemic and Immune Systems::Immune System::Leukocytes::Leukocytes, Mononuclear::Lymphocytes::Lymphocytes, Tumor-Infiltrating [Medical Subject Headings]
Abstract

Triple-negative breast cancer (TNBC) presents a marked diversity at the molecular level, which promotes a clinical heterogeneity that further complicates treatment. We performed a detailed whole exome sequencing profile of 29 Mexican patients with long follow-up TNBC to identify genomic alterations associated with overall survival (OS), disease-free survival (DFS), and pathologic complete response (PCR), with the aim to define their role as molecular predictive factors of treatment response and prognosis. We detected 31 driver genes with pathogenic mutations in TP53 (53%), BRCA1/2 (27%), CDKN1B (9%), PIK3CA (9%), and PTEN (9%), and 16 operative mutational signatures. Moreover, tumors with mutations in BRCA1/2 showed a trend of sensitivity to platinum salts. We found an association between deficiency in DNA repair and surveillance genes and DFS. Across all analyzed tumors we consistently found a heterogeneous molecular complexity in terms of allelic composition and operative mutational processes, which hampered the definition of molecular traits with clinical utility. This work contributes to the elucidation of the global molecular alterations of TNBC by providing accurate genomic data that may help forthcoming studies to improve treatment and survival. This is the first study that integrates genomic alterations with a long follow-up of clinical variables in a Latin American population that is an underrepresented ethnicity in most of the genomic studies.

Published
2020

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