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Vieira IA, Pezzi EH, Bandeira IC, Reis LB, de Araújo Rocha YM, Fernandes BV, Siebert M, Miyamoto KN, Siqueira MB, Achatz MI, Galvão HDCR, Garcia FADO, Campacci N, Carraro DM, Formiga MN, Vianna FSL, Palmero EI, Macedo GS, Ashton-Prolla P. Functional pri-miR-34b/c rs4938723 and KRAS 3'UTR rs61764370 SNPs: Novel phenotype modifiers in Li-Fraumeni Syndrome? Gene 2024; 898:148069. [PMID: 38070788 DOI: 10.1016/j.gene.2023.148069] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/14/2023] [Accepted: 12/06/2023] [Indexed: 12/25/2023]
Abstract
PURPOSE Li-Fraumeni Syndrome (LFS) is a rare cancer predisposing condition caused by germline pathogenic TP53 variants, in which core tumors comprise sarcomas, breast, brain and adrenocortical neoplasms. Clinical manifestations are highly variable in carriers of the Brazilian germline founder variant TP53 p.R337H, possibly due to the influence of modifier genes such as miRNA genes involved in the regulation of the p53 pathway. Herein, we investigated the potential phenotypic effects of two miRNA-related functional SNPs, pri-miR-34b/c rs4938723 and 3'UTR KRAS rs61764370, in a cohort of 273 LFS patients from Southern and Southeastern Brazil. METHODS The genotyping of selected SNPs was performed by TaqMan® allelic discrimination and subsequently custom TaqMan® genotyping results were confirmed by Sanger sequencing in all SNP-positive LFS patients. RESULTS Although the KRAS SNP showed no effect as a phenotype modulator, the rs4938723 CC genotype was significantly associated with development of LFS non-core tumors (first tumor diagnosis) in p.R337H carriers (p = 0.039). Non-core tumors were also more frequently diagnosed in carriers of germline TP53 DNA binding domain variants harboring the rs4938723 C variant allele. Previous studies described pri-miR-34b/c rs4938723 C as a risk allele for sporadic occurrence of thyroid and prostate cancers (non-core tumors of the LFS spectrum). CONCLUSION With this study, we presented additional evidence about the importance of analyzing miRNA genes that could indirectly regulate p53 expression, and, therefore, may modulate the LFS phenotype, such as those of the miR-34 family.
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Affiliation(s)
- Igor Araujo Vieira
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil; Health School, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo 93022-750, Brazil.
| | - Eduarda Heidrich Pezzi
- Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Larissa Brussa Reis
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Yasminne Marinho de Araújo Rocha
- Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Bruna Vieira Fernandes
- Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Marina Siebert
- Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Monique Banik Siqueira
- Health School, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo 93022-750, Brazil
| | - Maria I Achatz
- Centro de Oncologia, Hospital Sírio-Libanês, São Paulo, Brazil
| | | | | | - Natalia Campacci
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil; Genomic Medicine Service from Hospital Beneficência Portuguesa de São Paulo, São Paulo, Brazil
| | | | | | - Fernanda Sales Luiz Vianna
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil; Department of Genetics, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Edenir Inez Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil; Department of Genetics, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Gabriel S Macedo
- Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil; Hospital Moinhos de Vento (HMV), Porto Alegre, Rio Grande do Sul, Brazil; Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Patricia Ashton-Prolla
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil; Department of Genetics, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil; Medical Genetics Service, HCPA, Porto Alegre, Rio Grande do Sul, Brazil
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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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Giacomazzi J, Ziegelmann PK, da Costa S, Bittar CM, Obst FM, Rosset C, Macedo GS, Bock H, Canal T, Paese MI, Benvenuti JL, Buj MC, Ashton-Prolla P, Goldim JR, Pozza R. Cancer Risk Factors in Southern Brazil: Report of a Comprehensive, Matched Case-Control Study. JCO Glob Oncol 2023; 9:e2300006. [PMID: 38060977 PMCID: PMC10723862 DOI: 10.1200/go.23.00006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 06/26/2023] [Accepted: 10/02/2023] [Indexed: 12/17/2023] Open
Abstract
PURPOSE To evaluate cancer risk factors among cancer cases and controls from Southern Brazil, to analyze a multigene hereditary panel testing (MGPT, 26 genes) for breast cancer (BC) and colorectal cancer (CCR) cases diagnosed age younger than 50 years and to characterize them for hereditary cancer syndrome (HCS) phenotypes. METHODS A case-control (matched by age group and sex) study was conducted on regional cancer. Data on exposure factors and first-/second-degree family history of cancer (1/2FHC) were collected. The MGPT was performed using Illumina next-generation sequencing technology. RESULTS A total of 1,007 cases and 1,007 controls were included. The most frequent cancers were BC (n = 311), CCR (n = 147), prostate (n = 132), and lung cancers (n = 89). It was independently associated with cancer, 1/2FHC, tobacco consumption (TC), pesticide exposure (PE), solvent/glue exposure, and BMI <24. BC was associated with 1/2FHC, TC, and hormone replacement therapy use; CCR with 1/2FHC, TC, and BMI <24; prostate cancer with 1/2FHC, TC, and alcohol consumption; and lung cancer with 1/2FHC, TC, PE, and BMI <24. MGPT identified pathogenic/likely pathogenic mutations in 24 (32%) women with BC and in three (18%) women and four (24%) men diagnosed with CCR at under 50 years. Among the tested patients under 50 years with diagnosed BC and CCR, 98.6% and 97% present criteria for HCS, respectively. CONCLUSION This study confirmed the association of several factors associated with BC, CCR, prostate, and lung cancers and reinforced the importance of evaluating FHC and genetic testing, especially for patients under 50 years with diagnosed BC or CCR. A better understanding of population-specific cancer risk factors builds on sustainable data for developing prevention strategies. These efforts increase the commitment to early detection and surveillance.
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Affiliation(s)
- Juliana Giacomazzi
- Instituto Tacchini de Pesquisa em Saúde/Hospital Tacchini, Tacchini Sistema de Saúde, Bento Gonçalves, Brazil
- Programa de Pós-graduação em Epidemiologia, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil
- Latin American Cooperative Oncology Group, Porto Alegre, Brazil
- Hayde Health, Porto Alegre and Bento Gonçalves, Brazil
| | - Patricia Klarmann Ziegelmann
- Programa de Pós-graduação em Epidemiologia, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil
- Departamento de Estatística, UFRGS, Porto Alegre, Brazil
| | - Samanta da Costa
- Instituto Tacchini de Pesquisa em Saúde/Hospital Tacchini, Tacchini Sistema de Saúde, Bento Gonçalves, Brazil
| | - Camila Matzenbacher Bittar
- Instituto Tacchini de Pesquisa em Saúde/Hospital Tacchini, Tacchini Sistema de Saúde, Bento Gonçalves, Brazil
| | - Fernando Mariano Obst
- Instituto do Câncer, Hospital Tacchini, Tacchini Sistema de Saúde, Bento Gonçalves, Brazil
- Oncoclínicas Porto Alegre, Porto Alegre, Brazil
- Hospital São Lucas da Pontifícia Universidade Católica de Porto Alegre, PUCRS, Porto Alegre, Brazil
| | - Clévia Rosset
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Unidade de Pesquisa Laboratorial, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Gabriel S. Macedo
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Hugo Bock
- Unidade de Pesquisa Laboratorial, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Thais Canal
- Instituto Tacchini de Pesquisa em Saúde/Hospital Tacchini, Tacchini Sistema de Saúde, Bento Gonçalves, Brazil
| | - Mari Ines Paese
- Instituto Tacchini de Pesquisa em Saúde/Hospital Tacchini, Tacchini Sistema de Saúde, Bento Gonçalves, Brazil
| | - Jean Lucas Benvenuti
- Instituto Tacchini de Pesquisa em Saúde/Hospital Tacchini, Tacchini Sistema de Saúde, Bento Gonçalves, Brazil
| | - Maria Carolina Buj
- Instituto Tacchini de Pesquisa em Saúde/Hospital Tacchini, Tacchini Sistema de Saúde, Bento Gonçalves, Brazil
- Hayde Health, Porto Alegre and Bento Gonçalves, Brazil
| | - Patricia Ashton-Prolla
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Departamento de Genética, UFRGS, Porto Alegre, Brazil
| | - José Roberto Goldim
- Serviço de Bioética, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Faculdade de Medicina, PUCRS, Porto Alegre, Brazil
| | - Roberta Pozza
- Instituto Tacchini de Pesquisa em Saúde/Hospital Tacchini, Tacchini Sistema de Saúde, Bento Gonçalves, Brazil
- Hayde Health, Porto Alegre and Bento Gonçalves, Brazil
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Lacerda MP, Jr SJ, Oliveira JC, Macedo GS, Tomazelli AP, Dalloglio AC, Gastal GR, Boettcher IS, Tavares FS. LINFOMA DE HODGKIN CLÁSSICO RECÉM-DIAGNOSTICADO NO CONTEXTO DE DESABASTECIMENTO DE BLEOMICINA: TRATAMENTO COM DOXORRUBICINA, ETOPOSÍDEO, VIMBLASTINA E DACARBAZINA (AEVD). Hematol Transfus Cell Ther 2021. [DOI: 10.1016/j.htct.2021.10.097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Matzenbacher Bittar C, de Araújo Rocha YM, Vieira IA, Rosset C, Andreis TF, Sartor ITS, Artigalás O, Netto CBO, Alemar B, Macedo GS, Ashton-Prolla P. Clinical and molecular characterization of patients fulfilling Chompret criteria for Li-Fraumeni syndrome in Southern Brazil. PLoS One 2021; 16:e0251639. [PMID: 34529667 PMCID: PMC8445435 DOI: 10.1371/journal.pone.0251639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 12/09/2020] [Accepted: 04/29/2021] [Indexed: 12/15/2022] Open
Abstract
Li-Fraumeni syndrome (LFS) is an autosomal dominant cancer predisposition syndrome caused by pathogenic germline variants in the TP53 gene, characterized by a predisposition to the development of a broad spectrum of tumors at an early age. The core tumors related to LFS are bone and soft tissue sarcomas, premenopausal breast cancer, brain tumors, adrenocortical carcinomas (ACC), and leukemias. The revised Chompret criteria has been widely used to establish clinical suspicion and support TP53 germline variant testing and LFS diagnosis. Information on TP53 germline pathogenic variant (PV) prevalence when using Chompret criteria in South America and especially in Brazil is scarce. Therefore, the aim of this study was to characterize patients that fulfilled these specific criteria in southern Brazil, a region known for its high population frequency of a founder TP53 variant c.1010G>A (p.Arg337His), as known as R337H. TP53 germline testing of 191 cancer-affected and independent probands with LFS phenotype identified a heterozygous pathogenic/likely pathogenic variant in 26 (13.6%) probands, both in the DNA binding domain (group A) and in the oligomerization domain (group B) of the gene. Of the 26 carriers, 18 (69.23%) were R337H heterozygotes. Median age at diagnosis of the first tumor in groups A and B differed significantly in this cohort: 22 and 2 years, respectively (P = 0.009). The present study shows the clinical heterogeneity of LFS, highlights particularities of the R337H variant and underscores the need for larger collaborative studies to better define LFS prevalence, clinical spectrum and penetrance of different germline TP53 pathogenic variants.
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Affiliation(s)
- Camila Matzenbacher Bittar
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Yasminne Marinho de Araújo Rocha
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Igor Araujo Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Clévia Rosset
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Tiago Finger Andreis
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Osvaldo Artigalás
- Hospital Moinhos de Vento (HMV), Porto Alegre, Rio Grande do Sul, Brazil
| | - Cristina B. O. Netto
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Barbara Alemar
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Gabriel S. Macedo
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Patricia Ashton-Prolla
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
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Scott RJ, Mehta A, Macedo GS, Borisov PS, Kanesvaran R, El Metnawy W. Genetic testing for homologous recombination repair (HRR) in metastatic castration-resistant prostate cancer (mCRPC): challenges and solutions. Oncotarget 2021; 12:1600-1614. [PMID: 34381565 PMCID: PMC8351605 DOI: 10.18632/oncotarget.28015] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 05/19/2021] [Accepted: 06/14/2021] [Indexed: 12/16/2022] Open
Abstract
Patients with metastatic castration-resistant prostate cancer (mCRPC) have an average survival of only 13 months. Identification of novel predictive and actionable biomarkers in the homologous recombination repair (HRR) pathway in up to a quarter of patients with mCRPC has led to the approval of targeted therapies like poly-ADP ribose polymerase inhibitors (PARPi), with the potential to improve survival outcomes. The approval of PARPi has led to guideline bodies such as the National Comprehensive Cancer Network (NCCN) to actively recommend germline and or somatic HRR gene panel testing to identify patients who will benefit from PARPi. However, there are several challenges as genetic testing is still at an early stage especially in low- and middle-income countries, with cost and availability being major impediments. In addition, there are issues such as choice of optimal tissue for genetic testing, archival, storage, retrieval of tissue blocks, interpretation and classification of variants in the HRR pathway, and the need for pretest and post-test genetic counseling. This review provides insights into the HRR gene mutations prevalent in mCRPC and the challenges for a more widespread gene testing to identify actionable germline pathogenic variants and somatic mutations in the HRR pathway, and proposes a clinical algorithm to enhance the efficiency of the gene testing process.
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Affiliation(s)
- Rodney J. Scott
- Laureate Professor, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Anurag Mehta
- Director, Department of Laboratory & Transfusion Services and Director Research, Rajiv Gandhi Cancer Institute, Delhi, India
| | - Gabriel S. Macedo
- Programa de Medicina Personalizada – Coordenador, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Pavel S. Borisov
- Oncologist Urologist, FSBI “N.N. Petrov NMRC of Oncology” of the Ministry Healthcare of the Russian Federation, St Petersburg, Russia
| | - Ravindran Kanesvaran
- Deputy Head and Senior Consultant, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Wafaa El Metnawy
- Professor of Molecular Pathology, Oncology Center School of Medicine, Cairo University, Giza, Egypt
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7
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Schultheis AM, de Bruijn I, Selenica P, Macedo GS, da Silva EM, Piscuoglio S, Jungbluth AA, Park KJ, Klimstra DS, Wardelmann E, Hartmann W, Gerharz CD, von Petersdorff M, Buettner R, Reis-Filho JS, Weigelt B. Genomic characterization of small cell carcinomas of the uterine cervix. Mol Oncol 2021; 16:833-845. [PMID: 33830625 PMCID: PMC8847983 DOI: 10.1002/1878-0261.12962] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/04/2021] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
Small cell carcinoma (SCC) of the uterine cervix is a rare and aggressive form of neuroendocrine carcinoma, which resembles small cell lung cancer (SCLC) in its histology and poor survival rate. Here, we sought to define the genetic underpinning of SCCs of the uterine cervix and compare their mutational profiles with those of human papillomavirus (HPV)‐positive head and neck squamous cell carcinomas, HPV‐positive cervical carcinomas, and SCLCs using publicly available data. Using a combination of whole‐exome and targeted massively parallel sequencing, we found that the nine uterine cervix SCCs, which were HPV18‐positive (n = 8) or HPV16‐positive (n = 1), harbored a low mutation burden, few copy number alterations, and other than TP53 in two cases no recurrently mutated genes. The majority of mutations were likely passenger missense mutations, and only few affected previously described cancer‐related genes. Using RNA‐sequencing, we identified putative viral integration sites on 18q12.3 and on 8p22 in two SCCs of the uterine cervix. The overall nonsilent mutation rate of uterine cervix SCCs was significantly lower than that of SCLCs, HPV‐driven cervical adeno‐ and squamous cell carcinomas, or HPV‐positive head and neck squamous cell carcinomas. Unlike SCLCs, which are reported to harbor almost universal TP53 and RB1 mutations and a dominant tobacco smoke‐related signature 4, uterine cervix SCCs rarely harbored mutations affecting these genes (2/9, 22% TP53; 0% RB1) and displayed a dominant aging (67%) or APOBEC mutational signature (17%), akin to HPV‐driven cancers, including cervical adeno‐ and squamous cell carcinomas and head and neck squamous cell carcinomas. Taken together, in contrast to SCLCs, which are characterized by highly recurrent TP53 and RB1 alterations, uterine cervix SCCs were positive for HPV leading to inactivation of the suppressors p53 and RB, suggesting that these SCCs are convergent phenotypes.
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Affiliation(s)
- Anne M Schultheis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, University Hospital Cologne, Germany
| | - Ino de Bruijn
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gabriel S Macedo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edaise M da Silva
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Visceral Surgery Research Laboratory, Clarunis, Department of Biomedicine, University of Basel, Switzerland
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kay J Park
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David S Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eva Wardelmann
- Department of Pathology, University Hospital Muenster, Germany
| | | | | | | | | | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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8
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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] [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: 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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9
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Reis LB, Bakos RM, Vianna FSL, Macedo GS, Jacovas VC, Ribeiro-Dos-Santos AM, Santos S, Bakos L, Ashton-Prolla P. Skin pigmentation polymorphisms associated with increased risk of melanoma in a case-control sample from southern Brazil. BMC Cancer 2020; 20:1069. [PMID: 33167923 PMCID: PMC7650158 DOI: 10.1186/s12885-020-07485-x] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Melanoma is the most aggressive type of skin cancer and is associated with environmental and genetic risk factors. It originates in melanocytes, the pigment-producing cells. Single nucleotide polymorphisms (SNPs) in pigmentation genes have been described in melanoma risk modulation, but knowledge in the field is still limited. METHODS In a case-control approach (107 cases and 119 controls), we investigated the effect of four pigmentation gene SNPs (TYR rs1126809, HERC2 rs1129038, SLC24A5 rs1426654, and SLC45A2 rs16891982) on melanoma risk in individuals from southern Brazil using a multivariate logistic regression model and multifactor dimensionality reduction (MDR) analysis. RESULTS Two SNPs were associated with an increased risk of melanoma in a dominant model: rs1129038AA and rs1426654AA [OR = 2.094 (95% CI: 1.106-3.966), P = 2.3 10- 2 and OR = 7.126 (95% CI: 1.873-27.110), P = 4.0 10- 3, respectively]. SNP rs16891982CC was associated with a lower risk to melanoma development in a log-additive model when the allele C was inherited [OR = 0.081 (95% CI: 0.008-0.782), P = 3 10- 2]. In addition, MDR analysis showed that the combination of the rs1426654AA and rs16891982GG genotypes was associated with a higher risk for melanoma (P = 3 10- 3), with a redundant effect. CONCLUSIONS These results contribute to the current knowledge and indicate that epistatic interaction of these SNPs, with an additive or correlational effect, may be involved in modulating the risk of melanoma in individuals from a geographic region with a high incidence of the disease.
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Affiliation(s)
- Larissa B Reis
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil.,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Renato M Bakos
- Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Serviço de Dermatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Fernanda S L Vianna
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gabriel S Macedo
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil
| | - Vanessa C Jacovas
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | - Sidney Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Lúcio Bakos
- Serviço de Dermatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Patricia Ashton-Prolla
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil. .,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil. .,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
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10
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Andreis TF, Correa BS, Vianna FS, De-Paris F, Siebert M, Leistner-Segal S, Hahn EC, Ulbrich JM, Rivero LFR, De Oliveira FH, Lorandi V, Ashton-Prolla P, Macedo GS. Analysis of Predictive Biomarkers in Patients With Lung Adenocarcinoma From Southern Brazil Reveals a Distinct Profile From Other Regions of the Country. J Glob Oncol 2020; 5:1-9. [PMID: 31532708 PMCID: PMC6872182 DOI: 10.1200/jgo.19.00174] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Adenocarcinoma is the most common histologic subtype of non–small-cell lung cancer, representing 40% of all diagnoses. Several biomarkers are currently used to determine patient eligibility for targeted treatments, including analysis of molecular alterations in EGFR and ALK, as well as programmed death-ligand 1 (PD-L1) protein expression. Epidemiologic data reporting the frequency of these biomarkers in Brazilian patients with lung adenocarcinoma (LUAD) are limited, and existing studies predominantly included patients from the southeast region of the country. MATERIALS AND METHODS The goal of this study was to investigate the frequency of somatic mutations in the EGFR, KRAS, NRAS, and BRAF genes, ALK, and PD-L1 expression in a series of Brazilian patients diagnosed with LUAD predominantly recruited from centers in southern Brazil. Molecular analysis of the EGFR, KRAS, NRAS, and BRAF genes was performed by next-generation sequencing using DNA extracted from tumor tissue. Immunohistochemistry was used to detect ALK and PD-L1 expression. RESULTS Analysis of 619 tumors identified KRAS mutations in 189 (30.2%), EGFR mutations in 120 (19.16%), and BRAF mutations in 19 (3%). Immunohistochemistry demonstrated ALK and PD-L1 expression in 4% and 35.1% of patients, respectively. CONCLUSION To our knowledge, this is the first study investigating the molecular epidemiology of patients with LUAD from southern Brazil and the largest assessing the frequency of multiple predictive biomarkers for this tumor in the country. The study also reveals a distinct mutation profile compared with data originating from other regions of Brazil.
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Affiliation(s)
- Tiago F Andreis
- Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Bruno S Correa
- Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Fernanda S Vianna
- Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | | | - Marina Siebert
- Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | | | - Eriza C Hahn
- Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jane M Ulbrich
- Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | | | | | | | - Patricia Ashton-Prolla
- Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
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11
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Bittar CM, Vieira IA, Sabato CS, Andreis TF, Alemar B, Artigalás O, Galvão HDCR, Macedo GS, Palmero EI, Ashton-Prolla P. TP53 variants of uncertain significance: increasing challenges in variant interpretation and genetic counseling. Fam Cancer 2020; 18:451-456. [PMID: 31321604 DOI: 10.1007/s10689-019-00140-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Li-Fraumeni syndrome (LFS) and Li-Fraumeni Like (LFL) are autosomal dominant cancer predisposition syndromes caused by pathogenic germline variants in the TP53 gene. Recent studies have shown that the incorporation of next-generation sequencing by using multigene panels in clinical practice has resulted in the frequent identification of variants of uncertain significance (VUS). Given that there is no established medical management for VUS carriers, the identification of these variants may cause confusion and anxiety for both patients and practitioners. Herein, we aimed to verify VUS frequency and review VUS classification and interpretation in 1844 patients submitted for comprehensive germline TP53 testing independent of clinical criteria. Variant characterization was done assessing clinical information whenever available, variant frequency in population databases, pathogenicity predictions using in silico tools and previous functional studies. All variants were classified based on the guidelines proposed by the American College of Medical Genetics and Genomics (2015) and by the Sherloc framework (2017). Of the twelve VUS (0.65%) identified in TP53, two were classified as likely pathogenic and two were classified as likely benign after re-evaluation, potentially resulting in significant management modification for the proband and relatives. This report cases highlights the challenges and impact of TP53 variant interpretation especially when there is no clear LFS/LFL phenotype.
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Affiliation(s)
- Camila Matzenbacher Bittar
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43323 M, Porto Alegre, RS, 91501-970, Brazil.,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil
| | - Igor Araujo Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43323 M, Porto Alegre, RS, 91501-970, Brazil.,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil
| | - Cristina Silva Sabato
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Viléla, 1331 - Dr. Paulo Prata, Barretos, SP, 14784-400, Brazil
| | - Tiago Finger Andreis
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43323 M, Porto Alegre, RS, 91501-970, Brazil.,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil
| | - Bárbara Alemar
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43323 M, Porto Alegre, RS, 91501-970, Brazil.,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil
| | - Osvaldo Artigalás
- Hospital Moinhos de Vento (HMV), Rua Ramiro Barcelos, 910, Porto Alegre, RS, 91790-560, Brazil
| | - Henrique de Campos Reis Galvão
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Viléla, 1331 - Dr. Paulo Prata, Barretos, SP, 14784-400, Brazil
| | - Gabriel S Macedo
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43323 M, Porto Alegre, RS, 91501-970, Brazil.,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil
| | - Edenir Inez Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Viléla, 1331 - Dr. Paulo Prata, Barretos, SP, 14784-400, Brazil.,Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, SP, 14784-400, Brazil
| | - Patricia Ashton-Prolla
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43323 M, Porto Alegre, RS, 91501-970, Brazil. .,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil. .,Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil.
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12
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Bandeira IC, Vieira IA, Andreis TF, Brussa Reis L, Macedo GS, Vianna FSL, Santos-Silva P, Palmero EI, Galvão HDCR, Ramos CRN, Santiago KM, Achatz MI, da Costa AABA, Ashton-Prolla P. MIR605 rs2043556 is associated with the occurrence of multiple primary tumors in TP53 p.(Arg337His) mutation carriers. Cancer Genet 2019; 240:54-58. [PMID: 31778928 DOI: 10.1016/j.cancergen.2019.11.005] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/13/2019] [Accepted: 11/18/2019] [Indexed: 11/26/2022]
Abstract
Li-Fraumeni and Li-Fraumeni-like (LFS/LFL) Syndrome are cancer predisposition syndromes caused by germline pathogenic variants in TP53 and are associated with an increased risk of multiple early-onset cancers. In Southern and Southeastern Brazil, a germline founder variant with partial penetrance located in the oligomerization domain of TP53, c.1010G>A p.(Arg337His, commonly known as R337H), has been detected in 0.3% of the general population. Recently, the functional MIR605 variant rs2043556 (A>G) has been identified as a novel LFS phenotype modifier in families with germline TP53 DNA binding variants. In this study, our goal was to verify MIR605 rs2043556 allele frequencies and further explore its possible effects on the phenotype of 238 Brazilian individuals carrying TP53 p.(Arg337His). The MIR605 rs2043556 G allele was detected in 136 (57.1%) individuals, including 25 homozygotes (10.5%), and although it had been previously associated with an earlier mean age of tumor onset, this effect was not observed in this study (p = 0.8). However, in p.(Arg337His) mutation carriers, the GG genotype was significantly associated with the occurrence of multiple primary tumors (p = 0.005). We provide further evidence of MIR605 rs2043556 G allele's effect as a phenotype modulator in carriers of germline TP53 pathogenic variants.
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Affiliation(s)
- Isabel Cristina Bandeira
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Igor Araujo Vieira
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil.
| | - Tiago Finger Andreis
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Larissa Brussa Reis
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Gabriel S Macedo
- Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil; Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Fernanda Sales Luiz Vianna
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Patricia Santos-Silva
- Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Edenir Inez Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil; Barretos School of Health Sciences, Barretos, São Paulo, Brazil
| | | | | | - Karina Miranda Santiago
- Oncogenetics Department, International Research Center, AC Camargo Cancer Center, National Institute of Oncogenomics, São Paulo city, São Paulo, Brazil
| | - Maria Isabel Achatz
- Oncogenetics Department, International Research Center, AC Camargo Cancer Center, National Institute of Oncogenomics, São Paulo city, São Paulo, Brazil
| | | | - Patricia Ashton-Prolla
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil; Medical Genetics Service, HCPA, Porto Alegre, Rio Grande do Sul, Brazil; Department of Genetics, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
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Macedo GS, Alemar B, Ashton-Prolla P. Reviewing the characteristics of BRCA and PALB2-related cancers in the precision medicine era. Genet Mol Biol 2019; 42:215-231. [PMID: 31067289 PMCID: PMC6687356 DOI: 10.1590/1678-4685-gmb-2018-0104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 05/15/2018] [Accepted: 10/24/2018] [Indexed: 12/24/2022] Open
Abstract
Germline mutations in BRCA1 and BRCA2 (BRCA) genes confer high risk of developing cancer, especially breast and ovarian tumors. Since the cloning of these tumor suppressor genes over two decades ago, a significant amount of research has been done. Most recently, monoallelic loss-of-function mutations in PALB2 have also been shown to increase the risk of breast cancer. The identification of BRCA1, BRCA2 and PALB2 as proteins involved in DNA double-strand break repair by homologous recombination and of the impact of complete loss of BRCA1 or BRCA2 within tumors have allowed the development of novel therapeutic approaches for patients with germline or somatic mutations in said genes. Despite the advances, especially in the clinical use of PARP inhibitors, key gaps remain. Now, new roles for BRCA1 and BRCA2 are emerging and old concepts, such as the classical two-hit hypothesis for tumor suppression, have been questioned, at least for some BRCA functions. Here aspects regarding cancer predisposition, cellular functions, histological and genomic findings in BRCA and PALB2-related tumors will be presented, in addition to an up-to-date review of the evolution and challenges in the development and clinical use of PARP inhibitors.
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Affiliation(s)
- Gabriel S Macedo
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Precision Medicine Program, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Barbara Alemar
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Precision Medicine Program, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
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14
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De Mattos-Arruda L, Ng CKY, Piscuoglio S, Gonzalez-Cao M, Lim RS, De Filippo MR, Fusco N, Schultheis AM, Ortiz C, Viteri S, Arias A, Macedo GS, Oliveira M, Gomez P, Teixidó C, Nuciforo P, Peg V, Saura C, Ramon Y Cajal S, Casas FT, Weigelt B, Cortes J, Seoane J, Reis-Filho JS. Genetic heterogeneity and actionable mutations in HER2-positive primary breast cancers and their brain metastases. Oncotarget 2018; 9:20617-20630. [PMID: 29755676 PMCID: PMC5945519 DOI: 10.18632/oncotarget.25041] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 01/16/2018] [Accepted: 03/12/2018] [Indexed: 12/19/2022] Open
Abstract
Brain metastases constitute a challenge in the management of patients with HER2-positive breast cancer treated with anti-HER2 systemic therapies. Here we sought to define the repertoire of mutations private to or enriched for in HER2-positive brain metastases. Massively parallel sequencing targeting all exons of 254 genes frequently mutated in breast cancers and/or related to DNA repair was used to characterize the spatial and temporal heterogeneity of HER2-positive breast cancers and their brain metastases in six patients. Data were analyzed with state-of-the-art bioinformatics algorithms and selected mutations were validated with orthogonal methods. Spatial and temporal inter-lesion genetic heterogeneity was observed in the HER2-positive brain metastases from an index patient subjected to a rapid autopsy. Genetic alterations restricted to the brain metastases included mutations in cancer genes FGFR2, PIK3CA and ATR, homozygous deletion in CDKN2A and amplification in KRAS. Shifts in clonal composition and the acquisition of additional mutations in the progression from primary HER2-positive breast cancer to brain metastases following anti-HER2 therapy were investigated in additional five patients. Likely pathogenic mutations private to or enriched in the brain lesions affected cancer and clinically actionable genes, including ATR, BRAF, FGFR2, MAP2K4, PIK3CA, RAF1 and TP53. Changes in clonal composition and the acquisition of additional mutations in brain metastases may affect potentially actionable genes in HER2-positive breast cancers. Our observations have potential clinical implications, given that treatment decisions for patients with brain metastatic disease are still mainly based on biomarkers assessed in the primary tumor.
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Affiliation(s)
- Leticia De Mattos-Arruda
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Institute of Pathology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria R De Filippo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicola Fusco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anne M Schultheis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carolina Ortiz
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Alexandra Arias
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Gabriel S Macedo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mafalda Oliveira
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Patricia Gomez
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Vicente Peg
- Vall d'Hebron Institute of Research, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Cristina Saura
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Santiago Ramon Y Cajal
- Vall d'Hebron Institute of Research, Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Javier Cortes
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain.,Ramon y Cajal University Hospital, Madrid, Spain
| | - Joan Seoane
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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15
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Geyer FC, Li A, Papanastasiou AD, Smith A, Selenica P, Burke KA, Edelweiss M, Wen HC, Piscuoglio S, Schultheis AM, Martelotto LG, Pareja F, Kumar R, Brandes A, Lozada J, Macedo GS, Muenst S, Terracciano LM, Jungbluth A, Foschini MP, Wen HY, Brogi E, Palazzo J, Rubin BP, Ng CKY, Norton L, Varga Z, Ellis IO, Rakha E, Chandarlapatty S, Weigelt B, Reis-Filho JS. Abstract PD4-13: Estrogen receptor-negative breast adenomyoepitheliomas are driven by co-occurring HRAS hotspot and PI3K pathway gene mutations: A genetic and functional analysis. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-pd4-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction:Adenomyoepithelioma (AME) of the breast is a rare biphasic tumor, characterized by epithelial and myoepithelial differentiation. Although AMEs have an indolent clinical course, a subset may progress to carcinoma and metastasize. We sought to define the mutational landscape of AMEs and investigate the functional impact of recurrent pathogenic mutations identified in these tumors.
Methods: Thirty-one AMEs were subjected to whole-exome sequencing (WES, n=8) or massively parallel sequencing targeting all coding regions of 410 key cancer genes and intronic and regulatory regions of selected genes (n=23). Somatic genetic alterations were defined using state-of-the-art bioinformatics algorithms. In an additional set of 12 AMEs, Sanger sequencing analysis of HRAS, PIK3CA and AKT1 was performed. Non-tumorigenic estrogen receptor (ER)-negative mammary epithelial cells (i.e. MCF10A, MCF10A with a PIK3CA H1047R mutation knock-in and MCF12A) were utilized for functional studies using both conventional monolayer and three-dimensional (3D) culture assays.
Results: 27 (63%) and 16 (37%) AMEs were ER-positive and ER-negative, respectively. ER-negativity was significantly associated with histologic features predictive of a more aggressive behavior, with a higher number of mutations and copy number alterations, and with a distinct mutational profile as compared to ER-positive AMEs. Of the 27 ER-positive AMEs, 12 cases (44%) harbored PIK3CA hotspot mutations, and 5 PIK3CA wild-type cases displayed E17K AKT1 hotspot mutations. By contrast, of the 16 ER-negative AMEs, 9 (56%), 9 (56%) and 3 (19%) harbored HRAS, PIK3CA (mostly E545K and H1047R hotspots) and PIK3R1 mutations, respectively. Strikingly, all HRAS mutations were restricted to ER-negative AMEs, affected the hotspot codon Q61 (Q61R/K), and all but one co-occurred with PIK3CA or PIK3R1 mutations. In addition, HRAS Q61 hotspot mutations were significantly associated with necrosis (p=0.01) and high mitotic rates (p=0.03). CDKN2A homozygous deletions were also detected only in ER-negative AMEs (19%) and found to be significantly associated with progression to carcinoma (p=0.001). Forced expression of HRAS Q61R in MCF10A and MCF12A cells resulted in i) increased proliferation and transformation, ii) an irregular growth pattern in 3D organotypic cell cultures, iii) partial loss of the epithelial phenotype, and iv) acquisition of myoepithelial differentiation, which was more overt in PIK3CA-mutant MCF10A cells. HRAS Q61Rinduced hyperactivation of the PI3K pathway, but both PI3K and MAPK pathways likely contributed to the RAS-mediated proliferation, which was completely arrested by combined AKT and MEK inhibition.
Conclusion: AMEs are phenotypically and genetically heterogeneous. Whilst pathogenic mutations in PI3K pathway-related genes occur across the spectrum of lesions, HRAS Q61 hotspot mutations are restricted to ER-negative AMEs. Our genomic and functional analyses indicate that HRAS Q61 mutations are driver events in the pathogenesis of ER-negative AMEs and, in conjunction with mutant PIK3CA, may lead to the acquisition of myoepithelial differentiation in breast epithelial cells.
Citation Format: Geyer FC, Li A, Papanastasiou AD, Smith A, Selenica P, Burke KA, Edelweiss M, Wen H-C, Piscuoglio S, Schultheis AM, Martelotto LG, Pareja F, Kumar R, Brandes A, Lozada J, Macedo GS, Muenst S, Terracciano LM, Jungbluth A, Foschini MP, Wen HY, Brogi E, Palazzo J, Rubin BP, Ng CKY, Norton L, Varga Z, Ellis IO, Rakha E, Chandarlapatty S, Weigelt B, Reis-Filho JS. Estrogen receptor-negative breast adenomyoepitheliomas are driven by co-occurring HRAS hotspot and PI3K pathway gene mutations: A genetic and functional analysis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD4-13.
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Affiliation(s)
- FC Geyer
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - A Li
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - AD Papanastasiou
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - A Smith
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - P Selenica
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - KA Burke
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - M Edelweiss
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - H-C Wen
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - S Piscuoglio
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - AM Schultheis
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - LG Martelotto
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - F Pareja
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - R Kumar
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - A Brandes
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - J Lozada
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - GS Macedo
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - S Muenst
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - LM Terracciano
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - A Jungbluth
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - MP Foschini
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - HY Wen
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - E Brogi
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - J Palazzo
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - BP Rubin
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - CKY Ng
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - L Norton
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - Z Varga
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - IO Ellis
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - E Rakha
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - S Chandarlapatty
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - B Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - JS Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
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16
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Geyer FC, Burke KA, Li A, Papanastatiou AD, Pareja F, Schulteis AS, Ng CK, Piscuoglio S, Edelweiss M, Martelotto LG, Selenica P, Filippo MR, Macedo GS, Jungbluth A, Wen HY, Palazzo J, Varga Z, Rakha E, Ellis IO, Rubin B, Weigelt B, Reis-Filho JS. Abstract 3379: Massively parallel sequencing analysis of breast adenomyoepitheliomas reveals the heterogeneity of the disease and identifies a subset driven by HRAS hotspot mutations. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Adenomyoepithelioma (AME) is a rare biphasic proliferative breast lesion, which may resemble salivary gland epithelial-myoepithelial carcinomas (EMCs). Most AMEs have an indolent clinical course, but malignant transformation and local and distant recurrences have been reported. We sought to define the mutational landscape of AMEs and investigate the functional impact of recurrent likely pathogenic mutations identified in these tumors. Nineteen AMEs were subjected to whole-exome massively parallel sequencing (MPS, n=7) or targeted capture MPS using MSK-IMPACT assay (n=12). Somatic genetic alterations and the cancer cell fraction of mutations were defined using state-of-the-art bioinformatics algorithms. Selected genes (i.e. HRAS and PIK3CA) were subjected to Sanger sequencing in a series of 17 additional AMEs (total n=36). Non-tumorigenic mammary epithelial cells (i.e. MCF10A, MCF10A with the PIK3CAH1047R mutation and MCF12A), which are estrogen receptor (ER)-negative, were utilized for 2D and 3D functional studies. Of 36 cases, 22 were ER-positive and 14 were ER-negative. MPS analysis revealed a low mutation burden and HRASQ61 and PIK3CA hotspot mutations in 6/19 (32%) and 11/19 (58%) AMEs, respectively. All HRASQ61 and all but one PIK3CA mutations were clonal. ER-positive and ER-negative AMEs were fundamentally histologically and genetically distinct. Whilst ER-positive AMEs displayed recurrent PIK3CA mutations (50%, 11/22) but lacked HRAS mutations, ER-negative AMEs displayed, in addition to PIK3CA mutations (57%, 8/14), recurrent HRASQ61 mutations (57%, 8/14). HRASQ61 mutations co-occurred with PIK3CA mutations (50%, 4/8), PIK3R1 deletions (12.5%, 1/8) and/or CDKN2A homozygous deletions (25%, 2/8). HRASQ61 mutations, but not PIK3CA mutations, were significantly associated with ER-negativity (100% vs 21%), concurrent carcinoma (50% vs 7%), axillary metastases (38% vs 0%), high proliferation (63% vs 4%), necrosis (63% vs 11%) and nuclear pleomorphism (75% vs 29%). In vitro forced HRASQ61R expression in MCF10A and MCF12A cells resulted in increased proliferation and transformation. In 3D organotypic cell cultures, forced HRASQ61R resulted in a highly disorganized growth pattern, a partial loss of epithelial phenotype and acquisition of aberrant myoepithelial differentiation, which was more overt in PIK3CA-mutant MCF10A cells. In conclusion, AMEs are phenotypically and genetically heterogeneous. Whilst PIK3CA hotspot mutations occur across the spectrum of lesions, HRASQ61 hotspot mutations are restricted to ER-negative AMEs, which should arguably be classified as breast EMCs. Our genomic and functional analyses are consistent with the notion that HRASQ61 mutations are driver events in the pathogenesis of ER-negative AMEs and may be sufficient for the acquisition of myoepithelial differentiation in breast cells.
Citation Format: Felipe C. Geyer, Kathleen A. Burke, Anqi Li, Anastasios D. Papanastatiou, Fresia Pareja, Anne S. Schulteis, Charlotte K. Ng, Salvatore Piscuoglio, Marcia Edelweiss, Luciano G. Martelotto, Pier Selenica, Maria R. Filippo, Gabriel S. Macedo, Achim Jungbluth, Hannah Y. Wen, Juan Palazzo, Zsuzsanna Varga, Emad Rakha, Ian O. Ellis, Brian Rubin, Britta Weigelt, Jorge S. Reis-Filho. Massively parallel sequencing analysis of breast adenomyoepitheliomas reveals the heterogeneity of the disease and identifies a subset driven by HRAS hotspot mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3379. doi:10.1158/1538-7445.AM2017-3379
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Affiliation(s)
| | | | - Anqi Li
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Fresia Pareja
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Pier Selenica
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Hannah Y. Wen
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Juan Palazzo
- 2Thomas Jefferson University Hospital, Philadelphia, Philadelphia, PA
| | | | - Emad Rakha
- 4Nottingham University Hospitals, Nottingham, United Kingdom
| | - Ian O. Ellis
- 4Nottingham University Hospitals, Nottingham, United Kingdom
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Geyer FC, Pareja F, Burke KA, Schultheis AM, Hussein YR, Ye J, De Filippo MR, Marchio C, Macedo GS, Piscuoglio S, Lim RS, Toy E, Murali R, Jungbluth AA, Reis-Filho JS, Soslow RA, Weigelt B. Genetic analysis of a morphologically heterogeneous ovarian endometrioid carcinoma. Histopathology 2017; 71:480-487. [PMID: 28417598 DOI: 10.1111/his.13240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 03/08/2017] [Accepted: 04/12/2017] [Indexed: 12/24/2022]
Abstract
AIMS Low-grade ovarian endometrioid carcinomas may be associated with high-grade components. Whether the latter are clonally related to and originate from the low-grade endometrioid carcinoma remains unclear. The aim of this study was to use massively parallel sequencing to characterize the genomic landscape and clonal relatedness of an ovarian endometrioid carcinoma containing low-grade and high-grade components. METHODS AND RESULTS DNA samples extracted from each tumour component (low-grade endometrioid, high-grade anaplastic and high-grade squamous) and matched normal tissue were subjected to targeted massively parallel sequencing with the 410-gene Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) sequencing assay. Somatic single nucleotide variants, small insertions and deletions, and copy number alterations were detected with state-of-the-art bioinformatics algorithms, and validated with orthogonal methods. The endometrioid carcinoma and the associated high-grade components shared copy number alterations and four clonal mutations, including SMARCA4 mutations, which resulted in loss of BRG1 protein expression. Subclonal mutations and mutations restricted to single components were also identified, such as distinct TP53 mutations restricted to each histological component. CONCLUSIONS Histologically distinct components of ovarian endometrioid carcinomas may show intratumour genetic heterogeneity but be clonally related, harbouring a complex clonal composition. In the present case, SMARCA4 mutations were probably early events, whereas TP53 somatic mutations were acquired later in evolution.
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Affiliation(s)
- Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anne M Schultheis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yaser R Hussein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jiqing Ye
- Department of Pathology, Rochester General Hospital, Rochester, NY, USA
| | - Maria R De Filippo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caterina Marchio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Gabriel S Macedo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eugene Toy
- Department of Obstetrics and Gynecology, Rochester General Hospital, Rochester, NY, USA
| | - Rajmohan Murali
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Geyer FC, Burke KA, Macedo GS, Piscuoglio S, Ng CK, Martelotto LG, Papanastatiou AD, De Filippo MR, Schultheis AM, Brogi E, Robson M, Wen YH, Weigelt B, Schnitt SJ, Tung N, Reis-Filho JS. Abstract S2-02: The landscape of somatic genetic alterations in BRCA1 and BRCA2 breast cancers. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-s2-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Women carrying BRCA1 or BRCA2 germline mutations have a 45-80% lifetime risk of developing breast cancer (BC). BRCA1 and BRCA2 are perceived as bona fide tumor suppressor genes, whereby bi-allelic inactivation in tumor cells is required for tumorigenesis. Recent studies have indicated that loss of heterozygosity (LOH) of the wild-type allele of BRCA1 may be heterogeneous and constitute a late event. Therefore, additional somatic events prior to full BRCA1/2 inactivation may be required for tumorigenesis. Given that the somatic events that result in the development of BRCA1/2-BCs and their chronology are not understood, here we sought to define the genomic landscape of BRCA1/2-BCs and whether LOH of BRCA1/2 wild-type allele and/or mutations affecting additional tumor suppressor genes would be clonal or subclonal in these cancers.
Methods: We retrieved 29 BRCA1-BCs and 10 BRCA2-BCs from the Pathology Departments of the authors' institutions. DNA extracted from microdissected tumor and normal breast samples was subjected to targeted capture massively parallel sequencing using either the MSK-IMPACT assay or an assay targeting all exons of 254 genes recurrently mutated in BC or related to DNA repair. Somatic single nucleotide variants, small insertions and deletions and copy number alterations affecting genes present in both sequencing assays (111 genes) were defined using state-of-the-art bioinformatics algorithms. ABSOLUTE and FACETS were employed to define clonal (i.e. present virtually in 100% of the cancer cells of a given case) and subclonal mutations and the presence of LOH of the BRCA1 and BRCA2 wild-type alleles.
Results: Our analysis revealed bi-allelic inactivation of BRCA1 in 28 of 29 BRCA1-BCs (93% harbored LOH of the BRCA1 wild-type allele and 3% harbored a second somatic BRCA1 pathogenic mutation). The only BRCA1-BC lacking bi-allelic inactivation of BRCA1 was an estrogen receptor-positive lobular carcinoma, lacking genomic features consistent with homologous recombination DNA repair defects, diagnosed at 62 years of age. Bi-allelic inactivation of BRCA2 was found in all cases (100% of harbored LOH of the BRCA2 wild-type allele). A clonal somatic 'second hit' resulting in bi-allelic inactivation of BRCA1 or BRCA2 was detected in 76% and 100% of BRCA1-BCs and BRCA2-BCs, respectively. In BRCA1-BCs, TP53 mutations were detected in 76% of cases, and these mutations were found to be clonal in 58% of cases. The repertoire of somatic mutations affecting BRCA1-BCs included clonal somatic mutations or homozygous deletions of known tumor suppressor genes, such as PTEN, RB1, CDKN2A and NF1. In contrast, only 10% of the BRCA2-BCs harbored TP53 somatic mutations. Though clonal somatic mutations in several cancer genes were detected, 40% of BRCA2-BCs had no mutations affecting the cancer genes analyzed.
Conclusions: Bi-allelic inactivation of BRCA1 and BRCA2 are frequent events in BRCA1-BCs and BRCA2-BCs, respectively. In a subset of BRCA1-BCs, however, the second 'hit' appeared to be subclonal, whereas mutations affecting TP53 and other tumor suppressor genes were clonal, supporting the notion that at least in a subset of these tumors, loss of the wild-type allele of BRCA1 may be preceded by inactivation of another tumor suppressor gene.
Citation Format: Geyer FC, Burke KA, Macedo GS, Piscuoglio S, Ng CK, Martelotto LG, Papanastatiou AD, De Filippo MR, Schultheis AM, Brogi E, Robson M, Wen YH, Weigelt B, Schnitt SJ, Tung N, Reis-Filho JS. The landscape of somatic genetic alterations in BRCA1 and BRCA2 breast cancers [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr S2-02.
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Affiliation(s)
- FC Geyer
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - KA Burke
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - GS Macedo
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - S Piscuoglio
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - CK Ng
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - LG Martelotto
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - AD Papanastatiou
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - MR De Filippo
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - AM Schultheis
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - E Brogi
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - M Robson
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - YH Wen
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - B Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - SJ Schnitt
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - N Tung
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - JS Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
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Geyer FC, Burke KA, Papanastatiou AD, Macedo GS, Brogi E, Norton L, Wen YH, Weigelt B, Reis-Filho JS. Abstract P1-05-04: Intra-tumor genetic heterogeneity and histologic heterogeneity within metaplastic breast cancers: Genotypic-phenotypic correlations. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p1-05-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Metaplastic breast carcinoma (MBC) is characterized by the presence of neoplastic cells displaying squamous and/or mesenchymal differentiation. Morphologic intra-tumor heterogeneity is frequent in MBCs and reported to be reflected at the transcriptomic level: whilst squamous and chondroid MBCs are preferentially of basal-like subtype, spindle cell MBCs are of claudin-low subtype. Likewise, histologically distinct components within MBCs have been shown to display distinct focal copy number alterations. Here we sought to investigate whether histologically distinct components within MBCs would be underpinned by different mutational profiles and mutational signatures.
Methods: Ten MBCs with two histologically distinct components (spindle, chondroid, osseous, squamous and/ or ductal) were retrieved from the Department of Pathology of the authors' institution. The distinct components of each case and, in two cases, two regions of the same component were separately microdissected. DNA extracted from tumor samples (n=22) and matched normal tissues was subjected to whole-exome sequencing. Somatic genetic alterations were identified using state-of-the-art bioinformatics algorithms. Somatic mutations were classified as clonal (i.e., present virtually in all tumor cells) or subclonal using ABSOLUTE and FACETS. Mutational signatures were defined using non-negative matrix factorization.
Results: Medians of 146 (56-290) somatic mutations and 108 non-synonymous somatic mutations (39-222) per tumor component were identified. The histologically distinct components of each case harbored identical clonal TP53 mutations. Additional recurrent mutations in cancer genes included those affecting PI3K pathway genes (PIK3CA, 2 cases; PIK3R1, 2 cases). Shared mutations between components of each case ranged from 34% to 99% of all mutations, with a median of 84%, of which 24% (12%-53%) were truncal (i.e., shared by and clonal in both components). Private mutations (i.e., found in only one component) ranged from 1% to 66%, with a median of 16%, of which 72% (0-100%) were non-synonymous and 1% (0-52%) were clonal. In two cases, the comparison of two histologically similar regions revealed less heterogeneity, with 94% (87%-100%) of shared mutations, whereas in these samples the median of private mutations was 6% (0-13%), of which 70% (0-100%) were non-synonymous and none were clonal. Private non-synonymous mutations affecting cancer genes included those in PIK3R1, MED12 and NOTCH1. The mutational signatures (e.g. aging or BRCA) were concordant between distinct components of each case; however, differences in the mutational signatures were observed between truncal somatic mutations and mutations restricted to individual components.
Conclusions: MBCs display substantial genetic intra-tumor heterogeneity, which is more overt between histologically distinct components than between regions of similar histology. Our data suggest a genotypic-phenotypic correlation and corroborate the notion that distinct components within MBCs, although clonally related, may be driven by distinct somatic genetic alterations.
Citation Format: Geyer FC, Burke KA, Papanastatiou AD, Macedo GS, Brogi E, Norton L, Wen YH, Weigelt B, Reis-Filho JS. Intra-tumor genetic heterogeneity and histologic heterogeneity within metaplastic breast cancers: Genotypic-phenotypic correlations [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-04.
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Affiliation(s)
- FC Geyer
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - KA Burke
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - GS Macedo
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - E Brogi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - L Norton
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - YH Wen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - B Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - JS Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY
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Macedo GS, Burke KA, Piscuoglio S, Ng CKY, Geyer FC, Martelotto LG, Papanastatiou AD, De Filippo MR, Schultheis AM, Brogi E, Robson ME, Wen HY, Weigelt B, Reis-Filho JS. Abstract 100: The landscape of somatic genetic alterations in BRCA1 and BRCA2 breast cancers. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: BRCA1 or BRCA2 germline mutations account for a substantial proportion of hereditary breast cancers. The majority of BRCA1-associated breast cancers are of triple-negative phenotype (estrogen receptor (ER)-, progesterone receptor (PR)- and HER2-negative) and harbor TP53 somatic mutations. BRCA2-associated cancers are less homogeneous and often ER-positive. Systematic analyses of the profiles of somatic genetic alterations in BRCA1- and BRCA2-breast cancers have yet to be reported. Here we sought to determine the repertoire of somatic mutations and copy number alterations (CNAs) in breast cancers occurring in patients with BRCA1 or BRCA2 germline mutations..
Methods: Eleven BRCA1- and five BRCA2-associated breast cancers were microdissected. DNA was extracted from microdissected frozen tumor-normal pairs and subjected to targeted capture massively parallel sequencing using the MSK-IMPACT platform, which includes all exons and selected introns and regulatory regions of 410 key cancer genes. Somatic single nucleotide variants, small insertions and deletions, CNAs and the cancer cell fraction (CCF) of each alteration were defined using state-of-the-art bioinformatics algorithms.
Results: 82% (9/11) and 18% (2/11) of BRCA1-breast cancers were triple-negative and ER-positive/HER2-negative, respectively. All BRCA2-cancers were ER-positive, of which one was HER2-positive. Sequencing analysis revealed a median of four (2-11) and two (0-6) non-synonymous somatic mutations in BRCA1- and BRCA2-breast cancers, respectively. Within BRCA1-breast cancers all but one (10/11, 91%) harbored TP53 clonal somatic mutations, and clonal somatic loss of the BRCA1 wild-type allele was found in 8 of these cases. The BRCA1-breast cancer lacking these alterations was ER-positive and the only case harboring a PIK3CA mutation. Additional clonal mutations identified in BRCA1-breast cancers included somatic mutations affecting EGFR and RB1. Subclonal mutations in known cancer genes (e.g. GATA3 and PTEN) were also identified, suggesting intra-tumor genetic heterogeneity. All BRCA2-breast cancers analyzed displayed clonal loss of the wild-type of BRCA2, but no gene was found to be recurrently mutated.
Conclusions: BRCA1- and BRCA2-breast cancers are both characterized by clonal inactivation of the BRCA1 and BRCA2 wild-type alleles, respectively, which likely constitute early genetic events. Within BRCA1-breast cancers, TP53 mutations are highly recurrent and clonal, and may precede somatic loss of the BRCA1 wild-type allele, as the latter was subclonal in one case harboring a clonal TP53 somatic mutation.
Citation Format: Gabriel S. Macedo, Kathleen A. Burke, Salvatore Piscuoglio, Charlotte K. Y. Ng, Felipe C. Geyer, Luciano G. Martelotto, Anastasios D. Papanastatiou, Maria R. De Filippo, Anne M. Schultheis, Edi Brogi, Mark E. Robson, Hannah Y. Wen, Britta Weigelt, Jorge S. Reis-Filho. The landscape of somatic genetic alterations in BRCA1 and BRCA2 breast cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 100.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Edi Brogi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Hannah Y. Wen
- Memorial Sloan Kettering Cancer Center, New York, NY
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Fitarelli-Kiehl M, Macedo GS, Schlatter RP, Koehler-Santos P, Matte UDS, Ashton-Prolla P, Giacomazzi J. Comparison of multiple genotyping methods for the identification of the cancer predisposing founder mutation p.R337H in TP53. Genet Mol Biol 2016; 39:203-9. [PMID: 27275664 PMCID: PMC4910550 DOI: 10.1590/1678-4685-gmb-2014-0351] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 11/30/2014] [Accepted: 09/22/2015] [Indexed: 01/04/2023] Open
Abstract
Germline mutations in the TP53 gene are associated with Li-Fraumeni and Li-Fraumeni-Like Syndromes, characterized by increased predisposition to early-onset cancers. In Brazil, the prevalence of the TP53-p.R337H germline mutation is exceedingly high in the general population and in cancer-affected patients, probably as result of a founder effect. Several genotyping methods are used for the molecular diagnosis of LFS/LFL, however Sanger sequencing is still considered the gold standard. We compared performance, cost and turnaround time of Sanger sequencing, PCR-RFLP, TaqMan-PCR and HRM in the p.R337H genotyping. The performance was determined by analysis of 95 genomic DNA samples and results were 100% concordant for all methods. Sequencing was the most expensive method followed by TaqMan-PCR, PCR-RFLP and HRM. The overall cost of HRM increased with the prevalence of positive samples, since confirmatory sequencing must be performed when a sample shows an abnormal melting profile, but remained lower than all other methods when the mutation prevalence was less than 2.5%. Sequencing had the highest throughput and the longest turnaround time, while TaqMan-PCR showed the lowest turnaround and hands-on times. All methodologies studied are suitable for the detection of p.R337H and the choice will depend on the application and clinical scenario.
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Affiliation(s)
- Mariana Fitarelli-Kiehl
- Programa de Pós-Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental,
Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Gabriel S. Macedo
- Programa de Pós-Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental,
Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Rosane Paixão Schlatter
- Grupo de Pesquisa e Pós-Graduação (GPPG), Hospital de Clínicas de
Porto Alegre, and Programa de Pós Graduação em Cardiologia, UFRGS Porto Alegre, RS,
Brazil
| | - Patricia Koehler-Santos
- Unidade de Análises Moleculares e de Proteínas (UAMP), Centro de
Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS,
Brazil
| | - Ursula da Silveira Matte
- Programa de Pós-Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Unidade de Análises Moleculares e de Proteínas (UAMP), Centro de
Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS,
Brazil
- Departamento de Genética, Universidade Federal do Rio Grande do Sul
(UFRGS), Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Programa de Pós-Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental,
Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
- Departamento de Genética, Universidade Federal do Rio Grande do Sul
(UFRGS), Porto Alegre, RS, Brazil
| | - Juliana Giacomazzi
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental,
Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
- Departamento de Genética, Universidade Federal do Rio Grande do Sul
(UFRGS), Porto Alegre, RS, Brazil
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Piscuoglio S, Ng CKY, Murray MP, Guerini-Rocco E, Martelotto LG, Geyer FC, Bidard FC, Berman S, Fusco N, Sakr RA, Eberle CA, De Mattos-Arruda L, Macedo GS, Akram M, Baslan T, Hicks JB, King TA, Brogi E, Norton L, Weigelt B, Hudis CA, Reis-Filho JS. The Genomic Landscape of Male Breast Cancers. Clin Cancer Res 2016; 22:4045-56. [PMID: 26960396 DOI: 10.1158/1078-0432.ccr-15-2840] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/29/2016] [Indexed: 01/07/2023]
Abstract
PURPOSE Male breast cancer is rare, and its genomic landscape has yet to be fully characterized. Lacking studies in men, treatment of males with breast cancer is extrapolated from results in females with breast cancer. We sought to define whether male breast cancers harbor somatic genetic alterations in genes frequently altered in female breast cancers. EXPERIMENTAL DESIGN All male breast cancers were estrogen receptor-positive, and all but two were HER2-negative. Fifty-nine male breast cancers were subtyped by immunohistochemistry, and tumor-normal pairs were microdissected and subjected to massively parallel sequencing targeting all exons of 241 genes frequently mutated in female breast cancers or DNA-repair related. The repertoires of somatic mutations and copy number alterations of male breast cancers were compared with that of subtype-matched female breast cancers. RESULTS Twenty-nine percent and 71% of male breast cancers were immunohistochemically classified as luminal A-like or luminal B-like, respectively. Male breast cancers displayed a heterogeneous repertoire of somatic genetic alterations that to some extent recapitulated that of estrogen receptor (ER)-positive/HER2-negative female breast cancers, including recurrent mutations affecting PIK3CA (20%) and GATA3 (15%). ER-positive/HER2-negative male breast cancers, however, less frequently harbored 16q losses, and PIK3CA and TP53 mutations than ER-positive/HER2-negative female breast cancers. In addition, male breast cancers were found to be significantly enriched for mutations affecting DNA repair-related genes. CONCLUSIONS Male breast cancers less frequently harbor somatic genetic alterations typical of ER-positive/HER2-negative female breast cancers, such as PIK3CA and TP53 mutations and losses of 16q, suggesting that at least a subset of male breast cancers are driven by a distinct repertoire of somatic changes. Given the genomic differences, caution may be needed in the application of biologic and therapeutic findings from studies of female breast cancers to male breast cancers. Clin Cancer Res; 22(16); 4045-56. ©2016 AACR.
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Affiliation(s)
- Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Melissa P Murray
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elena Guerini-Rocco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Pathology, European Institute of Oncology, Milan, Italy
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Pathology, Hospital Israelita Albert Einstein, Instituto Israelita de Ensino e Pesquisa, São Paulo, Brazil
| | - Francois-Clement Bidard
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Medical Oncology, Institut Curie, Paris, France
| | - Samuel Berman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicola Fusco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Rita A Sakr
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carey A Eberle
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Gabriel S Macedo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Muzaffar Akram
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timour Baslan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York. Department of Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York. Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James B Hicks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Tari A King
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Clifford A Hudis
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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23
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Schultheis AM, Ng CKY, De Filippo MR, Piscuoglio S, Macedo GS, Gatius S, Perez Mies B, Soslow RA, Lim RS, Viale A, Huberman KH, Palacios JC, Reis-Filho JS, Matias-Guiu X, Weigelt B. Massively Parallel Sequencing-Based Clonality Analysis of Synchronous Endometrioid Endometrial and Ovarian Carcinomas. J Natl Cancer Inst 2016; 108:djv427. [PMID: 26832770 DOI: 10.1093/jnci/djv427] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 12/14/2015] [Indexed: 12/27/2022] Open
Abstract
Synchronous early-stage endometrioid endometrial carcinomas (EECs) and endometrioid ovarian carcinomas (EOCs) are associated with a favorable prognosis and have been suggested to represent independent primary tumors rather than metastatic disease. We subjected sporadic synchronous EECs/EOCs from five patients to whole-exome massively parallel sequencing, which revealed that the EEC and EOC of each case displayed strikingly similar repertoires of somatic mutations and gene copy number alterations. Despite the presence of mutations restricted to the EEC or EOC in each case, we observed that the mutational processes that shaped their respective genomes were consistent. High-depth targeted massively parallel sequencing of sporadic synchronous EECs/EOCs from 17 additional patients confirmed that these lesions are clonally related. In an additional Lynch Syndrome case, however, the EEC and EOC were found to constitute independent cancers lacking somatic mutations in common. Taken together, sporadic synchronous EECs/EOCs are clonally related and likely constitute dissemination from one site to the other.
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Affiliation(s)
- Anne M Schultheis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF)
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF)
| | - Maria R De Filippo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF)
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF)
| | - Gabriel S Macedo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF)
| | - Sonia Gatius
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF)
| | - Belen Perez Mies
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF)
| | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF)
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF)
| | - Agnes Viale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF)
| | - Kety H Huberman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF)
| | - Jose C Palacios
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF)
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF)
| | - Xavier Matias-Guiu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF).
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY (AMS, CKYN, MRDF, SP, GSM, RAS, RSL, JSRF, BW); Department of Pathology, Hospital Universitario Arnau de Vilanova, University of Lleida, Lleida, Spain (SG, XMG); Department of Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain (BPM, JCP); Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY (AV, KHH); Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY (JSRF).
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24
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Piscuoglio S, Ng CK, Murray M, Burke KA, Edelweiss M, Geyer FC, Macedo GS, Inagaki A, Papanastasiou AD, Martelotto LG, Marchio C, Lim RS, Ioris RA, Nahar PK, Bruijn ID, Smyth L, Akram M, Ross D, Petrini JH, Norton L, Solit DB, Baselga J, Brogi E, Ladanyi M, Weigelt B, Reis-Filho JS. Massively parallel sequencing of phyllodes tumours of the breast reveals actionable mutations, and TERT promoter hotspot mutations and TERT gene amplification as likely drivers of progression. J Pathol 2016; 238:508-18. [PMID: 26832993 DOI: 10.1002/path.4672] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [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: 10/12/2015] [Revised: 10/20/2015] [Accepted: 10/21/2015] [Indexed: 12/25/2022]
Abstract
Phyllodes tumours (PTs) are breast fibroepithelial lesions that are graded based on histological criteria as benign, borderline or malignant. PTs may recur locally. Borderline PTs and malignant PTs may metastasize to distant sites. Breast fibroepithelial lesions, including PTs and fibroadenomas, are characterized by recurrent MED12 exon 2 somatic mutations. We sought to define the repertoire of somatic genetic alterations in PTs and whether these may assist in the differential diagnosis of these lesions. We collected 100 fibroadenomas, 40 benign PTs, 14 borderline PTs and 22 malignant PTs; six, six and 13 benign, borderline and malignant PTs, respectively, and their matched normal tissue, were subjected to targeted massively parallel sequencing (MPS) using the MSK-IMPACT sequencing assay. Recurrent MED12 mutations were found in 56% of PTs; in addition, mutations affecting cancer genes (eg TP53, RB1, SETD2 and EGFR) were exclusively detected in borderline and malignant PTs. We found a novel recurrent clonal hotspot mutation in the TERT promoter (-124 C>T) in 52% and TERT gene amplification in 4% of PTs. Laser capture microdissection revealed that these mutations were restricted to the mesenchymal component of PTs. Sequencing analysis of the entire cohort revealed that the frequency of TERT alterations increased from benign (18%) to borderline (57%) and to malignant PTs (68%; p < 0.01), and TERT alterations were associated with increased levels of TERT mRNA (p < 0.001). No TERT alterations were observed in fibroadenomas. An analysis of TERT promoter sequencing and gene amplification distinguished PTs from fibroadenomas with a sensitivity and a positive predictive value of 100% (CI 95.38-100%) and 100% (CI 85.86-100%), respectively, and a sensitivity and a negative predictive value of 39% (CI 28.65-51.36%) and 68% (CI 60.21-75.78%), respectively. Our results suggest that TERT alterations may drive the progression of PTs, and may assist in the differential diagnosis between PTs and fibroadenomas. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Charlotte Ky Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Melissa Murray
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Marcia Edelweiss
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Pathology, Hospital Israelita Albert Einstein, Instituto Israelita de Ensino e Pesquisa, São Paulo, Brazil
| | - Gabriel S Macedo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Akiko Inagaki
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Anastasios D Papanastasiou
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Pathology, Patras General Hospital, Greece
| | | | - Caterina Marchio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Medical Sciences, University of Turin, Italy
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Rafael A Ioris
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Pooja K Nahar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Ino De Bruijn
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Lillian Smyth
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Muzaffar Akram
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Dara Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - John H Petrini
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.,Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Jose Baselga
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
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25
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Alemar B, Izetti P, Gregório C, Macedo GS, Castro MAA, Osvaldt AB, Matte U, Ashton-Prolla P. miRNA-21 and miRNA-34a Are Potential Minimally Invasive Biomarkers for the Diagnosis of Pancreatic Ductal Adenocarcinoma. Pancreas 2016; 45:84-92. [PMID: 26262588 DOI: 10.1097/mpa.0000000000000383] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Pancreatic ductal adenocarcinoma (PDAC) is one of the most deadly cancers, and its diagnosis often requires invasive procedures. Deregulated miRNA expression has been described in patients with PDAC. In this study, we analyzed the expression levels of 6 miRNAs (miR-21, -34a, -155, -196a, -200b, and -376a involved in PDAC tumorigenesis) in serum and salivary samples to assess their potential role as circulating diagnostics biomarkers. METHODS Serum and salivary samples were collected from patients with PDAC and healthy controls, and miRNA levels were quantified using qRT-PCR. Twenty-four patients with PDAC and 10 healthy controls were recruited. RESULTS A significant difference between PDAC and healthy groups was observed for the expression of miR-21 and miR-34a (P < 0.001 and P = 0.001) in serum samples. Both miRNAs accurately discriminated between the 2 groups, with an area under the curve for miR-21 and miR-34a of 0.889 (P = 0.001) and 0.865 (P = 0.002), respectively. In general, the expression of miRNAs between salivary samples did not differ. CONCLUSIONS Serum miR-21 and miR-34a are potentially useful diagnostic biomarkers of PDAC. In addition, our results suggest that these miRNAs are not differentially expressed in saliva, making them unsuitable for use as noninvasive biomarkers for diagnostic purposes.
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Affiliation(s)
- Bárbara Alemar
- From the *Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul; †Laboratório de Medicina Genômica, Centro de Pesquisa Experimental-Hospital de Clínicas de Porto Alegre; ‡Hospital de Clínicas de Porto Alegre; §Laboratório de Bioinformática e Biologia de Sistemas, Universidade Federal do Paraná; ∥Grupo de Vias Biliares e Pâncreas-Cirurgia do Aparelho Digestivo, Hospital de Clínicas de Porto Alegre; ¶Programa de Pós-Graduação em Medicina: Ciências Cirúrgicas; and #Unidade de Análises Moleculares e de Proteínas, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
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26
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Piscuoglio S, Burke KA, Ng CKY, Papanastasiou AD, Geyer FC, Macedo GS, Martelotto LG, de Bruijn I, De Filippo MR, Schultheis AM, Ioris RA, Levine DA, Soslow RA, Rubin BP, Reis-Filho JS, Weigelt B. Uterine adenosarcomas are mesenchymal neoplasms. J Pathol 2015; 238:381-8. [PMID: 26592504 DOI: 10.1002/path.4675] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [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: 10/05/2015] [Revised: 11/10/2015] [Accepted: 11/17/2015] [Indexed: 12/25/2022]
Abstract
Uterine adenosarcomas (UAs) are biphasic lesions composed of a malignant mesenchymal (ie stromal) component and an epithelial component. UAs are generally low-grade and have a favourable prognosis, but may display sarcomatous overgrowth (SO), which is associated with a worse outcome. We hypothesized that, akin to breast fibroepithelial lesions, UAs are mesenchymal neoplasms in which clonal somatic genetic alterations are restricted to the mesenchymal component. To characterize the somatic genetic alterations in UAs and to test this hypothesis, we subjected 20 UAs to a combination of whole-exome (n = 6), targeted capture (n = 13) massively parallel sequencing (MPS) and/or RNA sequencing (n = 6). Only three genes, FGFR2, KMT2C and DICER1, were recurrently mutated, all in 2/19 cases; however, 26% (5/19) and 21% (4/19) of UAs harboured MDM2/CDK4/HMGA2 and TERT gene amplification, respectively, and two cases harboured fusion genes involving NCOA family members. Using a combination of laser-capture microdissection and in situ techniques, we demonstrated that the somatic genetic alterations detected by MPS were restricted to the mesenchymal component. Furthermore, mitochondrial DNA sequencing of microdissected samples revealed that epithelial and mesenchymal components of UAs were clonally unrelated. In conclusion, here we provide evidence that UAs are genetically heterogeneous lesions and mesenchymal neoplasms.
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Affiliation(s)
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Anastasios D Papanastasiou
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Pathology, Patras General Hospital, University of Patras, Greece
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Pathology, Hospital Israelita Albert Einstein, Instituto Israelita de Ensino e Pesquisa, São Paulo, Brazil
| | - Gabriel S Macedo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | | | - Ino de Bruijn
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Maria R De Filippo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Anne M Schultheis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Rafael A Ioris
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Douglas A Levine
- Gynaecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Brian P Rubin
- Department of Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
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27
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Piscuoglio S, Hodi Z, Katabi N, Guerini-Rocco E, Macedo GS, Ng CKY, Edelweiss M, De Mattos-Arruda L, Wen HY, Rakha EA, Ellis IO, Rubin BP, Weigelt B, Reis-Filho JS. Are acinic cell carcinomas of the breast and salivary glands distinct diseases? Histopathology 2015; 67:529-37. [PMID: 25688711 DOI: 10.1111/his.12673] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [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: 01/02/2015] [Accepted: 02/11/2015] [Indexed: 02/04/2023]
Abstract
AIMS Acinic cell carcinomas (AcCC) of the breast have been reported to constitute the breast counterpart of salivary gland AcCCs, based on the similarities of their histological and immunohistochemical features. Breast AcCC is a vanishingly rare form of triple-negative breast cancer (TNBC). Recent studies have demonstrated that in TNBCs, the two driver genes most frequently mutated are TP53 (82%) and PIK3CA (10%). We sought to define whether breast AcCCs would harbour TP53 and PIK3CA somatic mutations, and if so, whether these would be present in salivary gland AcCCs. METHODS AND RESULTS Sanger sequencing of the entire coding region of TP53 and of PIK3CA hotspot mutation sites of 10 breast and 20 salivary gland microdissected AcCCs revealed eight TP53 (80%) and one PIK3CA (10%) somatic mutations in breast AcCCs. No somatic mutations affecting these genes were found in the 20 salivary gland AcCCs analysed. CONCLUSIONS Our findings demonstrate that breast AcCCs display TP53 and PIK3CA mutations at frequencies similar to those of common types of TNBCs, whereas these genes appear not to be altered in salivary gland AcCCs, suggesting that despite their similar histological appearances, AcCCs of the breast and salivary glands probably constitute unrelated diseases.
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Affiliation(s)
- Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsolt Hodi
- Department of Pathology, University of Nottingham, Nottingham, UK
| | - Nora Katabi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elena Guerini-Rocco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,School of Pathology, University of Milan, Milan, Italy
| | - Gabriel S Macedo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marcia Edelweiss
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leticia De Mattos-Arruda
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emad A Rakha
- Department of Pathology, University of Nottingham, Nottingham, UK
| | - Ian O Ellis
- Department of Pathology, University of Nottingham, Nottingham, UK
| | - Brian P Rubin
- Department of Pathology, Robert J Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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28
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Macedo GS, Lisbôa da Motta L, Giacomazzi J, Netto CBO, Manfredini V, S.Vanzin C, Vargas CR, Hainaut P, Klamt F, Ashton-Prolla P. Increased oxidative damage in carriers of the germline TP53 p.R337H mutation. PLoS One 2012; 7:e47010. [PMID: 23056559 PMCID: PMC3467233 DOI: 10.1371/journal.pone.0047010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 09/11/2012] [Indexed: 11/18/2022] Open
Abstract
Germline mutations in TP53 are the underlying defect of Li-Fraumeni Syndrome (LFS) and Li-Fraumeni-like (LFL) Syndrome, autosomal dominant disorders characterized by predisposition to multiple early onset cancers. In Brazil, a variant form of LFS/LFL is commonly detected because of the high prevalence of a founder mutation at codon 337 in TP53 (p.R337H). The p53 protein exerts multiple roles in the regulation of oxidative metabolism and cellular anti-oxidant defense systems. Herein, we analyzed the redox parameters in blood samples from p.R337H mutation carriers (C, n = 17) and non-carriers (NC, n = 17). We identified a significant increase in erythrocyte GPx activity and in plasma carbonyl content,an indicator of protein oxidative damage, in mutation carriers compared to non-carriers (P = 0.048 and P = 0.035, respectively). Mutation carriers also showed a four-fold increase in plasma malondialdehyde levels, indicating increased lipid peroxidation (NC = 40.20±0.71, C = 160.5±0.88, P<0.0001). Finally, carriers showed increased total antioxidant status but a decrease in plasma ascorbic acid content. The observed imbalance could be associated with deregulated cell bioenergetics and/or with increased inflammatory stress, two effects that may result from loss of wild-type p53 function. These findings provide the first evidence that oxidative damage occurs in carriers of a germline TP53 mutation, and these may have important implications regarding our understanding of the mechanisms responsible for germline TP53 p.R337H mutation-associated carcinogenesis.
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Affiliation(s)
- Gabriel S. Macedo
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Leonardo Lisbôa da Motta
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, UFRGS, Porto Alegre, Brazil
- Institutos Nacionais de Ciência e Tecnologia - Translacional em Medicina (MCT/CNPq INCT-TM), Porto Alegre, RS, Brazil
- Rede Gaúcha de Estresse Oxidativo e Sinalização Celular (FAPERGS), Porto Alegre, RS, Brazil
| | - Juliana Giacomazzi
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Médicas: Medicina, UFRGS, Porto Alegre, Brazil
| | | | - Vanusa Manfredini
- Universidade Federal do Pampa (UNIPAMPA), Campus Uruguaiana-RS, Brazil
| | - Camila S.Vanzin
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, UFRGS, Porto Alegre, Brazil
- Serviço de Genética Médica, HCPA, Porto Alegre, Brazil
| | - Carmen Regla Vargas
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, UFRGS, Porto Alegre, Brazil
- Serviço de Genética Médica, HCPA, Porto Alegre, Brazil
| | - Pierre Hainaut
- International Prevention Research Institute, Lyon, France
| | - Fábio Klamt
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, UFRGS, Porto Alegre, Brazil
- Institutos Nacionais de Ciência e Tecnologia - Translacional em Medicina (MCT/CNPq INCT-TM), Porto Alegre, RS, Brazil
- Rede Gaúcha de Estresse Oxidativo e Sinalização Celular (FAPERGS), Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Ciências Médicas: Medicina, UFRGS, Porto Alegre, Brazil
| | - Patricia Ashton-Prolla
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Médicas: Medicina, UFRGS, Porto Alegre, Brazil
- Serviço de Genética Médica, HCPA, Porto Alegre, Brazil
- * E-mail:
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29
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Crispim D, Fagundes NJR, dos Santos KG, Rheinheimer J, Bouças AP, de Souza BM, Macedo GS, Leiria LB, Gross JL, Canani LH. Polymorphisms of the UCP2 gene are associated with proliferative diabetic retinopathy in patients with diabetes mellitus. Clin Endocrinol (Oxf) 2010; 72:612-9. [PMID: 19681913 DOI: 10.1111/j.1365-2265.2009.03684.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND OBJECTIVE Uncoupling protein 2 (UCP2) plays a role in controlling reactive oxygen species (ROS) production by mitochondria. As ROS overproduction is related to diabetic retinopathy (DR), UCP2 gene polymorphisms might be involved in the development of this complication. We investigated whether the -866G/A (rs659366), Ala55Val (rs660339) and 45 bp insertion/deletion (Ins/Del) polymorphisms in the UCP2 gene might be associated with proliferative DR (PDR). DESIGN AND METHODS In this case-control study, we analysed 501 type 2 diabetic patients (242 patients with PDR and 259 subjects without any degree of DR) and 196 type 1 diabetic patients (85 cases with PDR and 111 without DR). Haplotypes constructed from the combination of the three UCP2 polymorphisms were inferred using a Bayesian statistical method. RESULTS In the type 2 diabetic group, multivariate analyses confirmed that the haplotype [A Val Ins] was an independent risk factor for PDR when present in one [adjusted odds ratio (aOR) = 2.12; P = 0.006], at least one (aOR = 2.75; P = 0.00001), or two copies (aOR = 5.30; P = 0.00001), suggesting an additive model of inheritance. Nevertheless, in type 1 diabetic patients, the association of this haplotype with PDR was confirmed only when it was present in at least one (aOR = 2.68; P = 0.014) or two copies (aOR = 6.02; P = 0.005). CONCLUSIONS The haplotype [A Val Ins] seems to be an important risk factor associated with PDR in both type 2 and 1 diabetic groups.
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Affiliation(s)
- Daisy Crispim
- Endocrine Division, Hospital de Clínicas de Porto Alegre.
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