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de Almeida LM, Cortés S, Vilensky M, Valenzuela O, Cortes-Sanabria L, de Souza M, Barbeito RA, Abdelhay E, Artagaveytia N, Daneri-Navarro A, Llera AS, Müller B, Podhajcer OL, Velazquez C, Alcoba E, Alonso I, Bravo AI, Camejo N, Carraro DM, Castro M, Cataldi S, Cayota A, Cerda M, Colombo A, Crocamo S, Del Toro-Arreola A, Delgadillo-Cristerna R, Delgado L, Breitenbach MD, Fernández E, Fernández J, Fernández W, Franco-Topete RA, Gaete F, Gómez J, Gonzalez-Ramirez LP, Guerrero M, Gutierrez-Rubio SA, Jalfin B, Lopez-Vazquez A, Loria D, Míguez S, Moran-Mendoza ADJ, Morgan-Villela G, Mussetti C, Nagai MA, Oceguera-Villanueva A, Reis RM, Retamales J, Rodriguez R, Rosales C, Salas-Gonzalez E, Segovia L, Sendoya JM, Silva-Garcia AA, Viña S, Zagame L, Jones B, Szklo M. Socioeconomic, Clinical, and Molecular Features of Breast Cancer Influence Overall Survival of Latin American Women. Front Oncol 2022; 12:845527. [PMID: 35530311 PMCID: PMC9071365 DOI: 10.3389/fonc.2022.845527] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Molecular profile of breast cancer in Latin-American women was studied in five countries: Argentina, Brazil, Chile, Mexico, and Uruguay. Data about socioeconomic characteristics, risk factors, prognostic factors, and molecular subtypes were described, and the 60-month overall cumulative survival probabilities (OS) were estimated. From 2011 to 2013, 1,300 eligible Latin-American women 18 years or older, with a diagnosis of breast cancer in clinical stage II or III, and performance status ≦̸1 were invited to participate in a prospective cohort study. Face-to-face interviews were conducted, and clinical and outcome data, including death, were extracted from medical records. Unadjusted associations were evaluated by Chi-squared and Fisher's exact tests and the OS by Kaplan-Meier method. Log-rank test was used to determine differences between cumulative probability curves. Multivariable adjustment was carried out by entering potential confounders in the Cox regression model. The OS at 60 months was 83.9%. Multivariable-adjusted death hazard differences were found for women living in Argentina (2.27), Chile (1.95), and Uruguay (2.42) compared with Mexican women, for older (≥60 years) (1.84) compared with younger (≤40 years) women, for basal-like subtype (5.8), luminal B (2.43), and HER2-enriched (2.52) compared with luminal A subtype, and for tumor clinical stages IIB (1.91), IIIA (3.54), and IIIB (3.94) compared with stage IIA women. OS was associated with country of residence, PAM50 intrinsic subtype, age, and tumor stage at diagnosis. While the latter is known to be influenced by access to care, including cancer screening, timely diagnosis and treatment, including access to more effective treatment protocols, it may also influence epigenetic changes that, potentially, impact molecular subtypes. Data derived from heretofore understudied populations with unique geographic ancestry and sociocultural experiences are critical to furthering our understanding of this complexity.
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Affiliation(s)
| | - Sandra Cortés
- Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marta Vilensky
- Instituto de Oncología Angel Roffo, Buenos Aires, Argentina
| | | | | | | | | | | | - Nora Artagaveytia
- Hospital de Clínicas Manuel Quintela, Universidad de la República, Montevideo, Uruguay
| | | | - Andrea S Llera
- Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | | | | | | | - Elsa Alcoba
- Hospital Municipal de Oncología María Curie, Buenos Aires, Argentina
| | - Isabel Alonso
- Centro Hospitalario Pereira Rossell, Montevideo, Uruguay
| | - Alicia I Bravo
- Hospital Regional de Agudos Eva Perón, Buenos Aires, Argentina
| | - Natalia Camejo
- Hospital de Clínicas Manuel Quintela, Universidad de la República, Montevideo, Uruguay
| | | | - Mónica Castro
- Instituto de Oncología Angel Roffo, Buenos Aires, Argentina
| | | | | | | | | | | | | | | | - Lucia Delgado
- Hospital de Clínicas Manuel Quintela, Universidad de la República, Montevideo, Uruguay
| | | | - Elmer Fernández
- Universidad Católica de Córdoba, Centro de Investigaciones en Bioquímica Clínica e Inmunologia-CONICET, Córdoba, Argentina
| | | | | | | | | | - Jorge Gómez
- Texas A&M University, Houston, TX, United States
| | | | | | | | - Beatriz Jalfin
- Hospital Regional de Agudos Eva Perón, Buenos Aires, Argentina
| | | | - Dora Loria
- Instituto de Oncología Angel Roffo, Buenos Aires, Argentina
| | - Silvia Míguez
- Hospital Municipal de Oncología María Curie, Buenos Aires, Argentina
| | | | | | | | | | | | - Rui M Reis
- Hospital de Câncer de Barretos, Barretos, Brazil
| | - Javier Retamales
- Grupo Oncológico Cooperativo Chileno de Investigación, Santiago, Chile
| | | | - Cristina Rosales
- Hospital Municipal de Oncología María Curie, Buenos Aires, Argentina
| | | | | | - Juan M Sendoya
- Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | - Aida A Silva-Garcia
- OPD Hospital Civil de Guadalajara, Universidad de Guadalajara, Guadalajara, Mexico
| | - Stella Viña
- Instituto de Oncología Angel Roffo, Buenos Aires, Argentina
| | - Livia Zagame
- Instituto Jalisciense de Cancerologia, Guadalajara, Mexico
| | - Beth Jones
- Yale School of Public Health, Yale University, New Heaven, CT, United States
| | - Moysés Szklo
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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2
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Takenaka IKTM, Bartelli TF, Defelicibus A, Sendoya JM, Golubicki M, Robbio J, Serpa MS, Branco GP, Santos LBC, Claro LCL, Dos Santos GO, Kupper BEC, da Silva IT, Llera AS, de Mello CAL, Riechelmann RP, Dias-Neto E, Iseas S, Aguiar S, Nunes DN. Exome and Tissue-Associated Microbiota as Predictive Markers of Response to Neoadjuvant Treatment in Locally Advanced Rectal Cancer. Front Oncol 2022; 12:809441. [PMID: 35392220 PMCID: PMC8982181 DOI: 10.3389/fonc.2022.809441] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
The clinical and pathological responses to multimodal neoadjuvant therapy in locally advanced rectal cancers (LARCs) remain unpredictable, and robust biomarkers are still lacking. Recent studies have shown that tumors present somatic molecular alterations related to better treatment response, and it is also clear that tumor-associated bacteria are modulators of chemotherapy and immunotherapy efficacy, therefore having implications for long-term survivorship and a good potential as the biomarkers of outcome. Here, we performed whole exome sequencing and 16S ribosomal RNA (rRNA) amplicon sequencing from 44 pre-treatment LARC biopsies from Argentinian and Brazilian patients, treated with neoadjuvant chemoradiotherapy or total neoadjuvant treatment, searching for predictive biomarkers of response (responders, n = 17; non-responders, n = 27). In general, the somatic landscape of LARC was not capable to predict a response; however, a significant enrichment in mutational signature SBS5 was observed in non-responders (p = 0.0021), as well as the co-occurrence of APC and FAT4 mutations (p < 0.05). Microbiota studies revealed a similar alpha and beta diversity of bacteria between response groups. Yet, the linear discriminant analysis (LDA) of effect size indicated an enrichment of Hungatella, Flavonifractor, and Methanosphaera (LDA score ≥3) in the pre-treatment biopsies of responders, while non-responders had a higher abundance of Enhydrobacter, Paraprevotella (LDA score ≥3) and Finegoldia (LDA score ≥4). Altogether, the evaluation of these biomarkers in pre-treatment biopsies could eventually predict a neoadjuvant treatment response, while in post-treatment samples, it could help in guiding non-operative treatment strategies.
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Affiliation(s)
| | - Thais F Bartelli
- Medical Genomics Laboratory, International Center for Research, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Alexandre Defelicibus
- Laboratory of Bioinformatics and Computational Biology, International Center for Research, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Juan M Sendoya
- Laboratorio de Terapia Molecular y Celular - Genomics Unit, Fundación Instituto Leloir, Buenos Aires, Argentina.,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mariano Golubicki
- Oncology Unit, Hospital de Gastroenterología Carlos Bonorino Udaondo, Buenos Aires, Argentina.,Clinical Oncology, Intergrupo Argentino para el Tratamiento de los Tumores Gastrointestinales (IATTGI), Buenos Aires, Argentina
| | - Juan Robbio
- Clinical Oncology, Intergrupo Argentino para el Tratamiento de los Tumores Gastrointestinales (IATTGI), Buenos Aires, Argentina
| | - Marianna S Serpa
- Medical Genomics Laboratory, International Center for Research, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Gabriela P Branco
- Medical Genomics Laboratory, International Center for Research, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Luana B C Santos
- Medical Genomics Laboratory, International Center for Research, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Laura C L Claro
- Department of Pathology, A.C.Camargo Cancer Center, São Paulo, Brazil
| | | | - Bruna E C Kupper
- Colorectal Cancer Department, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Israel T da Silva
- Laboratory of Bioinformatics and Computational Biology, International Center for Research, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Andrea S Llera
- Laboratorio de Terapia Molecular y Celular - Genomics Unit, Fundación Instituto Leloir, Buenos Aires, Argentina.,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Celso A L de Mello
- Department of Clinical Oncology, A.C.Camargo Cancer Center, São Paulo, Brazil
| | | | - Emmanuel Dias-Neto
- Medical Genomics Laboratory, International Center for Research, A.C.Camargo Cancer Center, São Paulo, Brazil.,Laboratory of Neurosciences (LIM-27) Alzira Denise Hertzog Silva, Institute of Psychiatry, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Soledad Iseas
- Oncology Unit, Hospital de Gastroenterología Carlos Bonorino Udaondo, Buenos Aires, Argentina
| | - Samuel Aguiar
- Colorectal Cancer Department, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Diana Noronha Nunes
- Medical Genomics Laboratory, International Center for Research, A.C.Camargo Cancer Center, São Paulo, Brazil.,National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation (INCITO), São Paulo, Brazil
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Iseas S, Sendoya JM, Robbio J, Coraglio M, Kujaruk M, Mikolaitis V, Rizzolo M, Cabanne A, Ruiz G, Salanova R, Gualdrini U, Méndez G, Antelo M, Carballido M, Rotondaro C, Viglino J, Eleta M, Di Sibio A, Podhajcer OL, Roca E, Llera AS, Golubicki M, Abba MC. Prognostic Impact of An Integrative Landscape of Clinical, Immune, and Molecular Features in Non-Metastatic Rectal Cancer. Front Oncol 2022; 11:801880. [PMID: 35071006 PMCID: PMC8777220 DOI: 10.3389/fonc.2021.801880] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022] Open
Abstract
Rectal Cancer (RC) is a complex disease that involves highly variable treatment responses. Currently, there is a lack of reliable markers beyond TNM to deliver a personalized treatment in a cancer setting where the goal is a curative treatment. Here, we performed an integrated characterization of the predictive and prognostic role of clinical features, mismatch-repair deficiency markers, HER2, CDX2, PD-L1 expression, and CD3-CD8+ tumor-infiltrating lymphocytes (TILs) coupled with targeted DNA sequencing of 76 non-metastatic RC patients assigned to total mesorectal excision upfront (TME; n = 15) or neoadjuvant chemo-radiotherapy treatment (nCRT; n = 61) followed by TME. Eighty-two percent of RC cases displayed mutations affecting cancer driver genes such as TP53, APC, KRAS, ATM, and PIK3CA. Good response to nCRT treatment was observed in approximately 40% of the RC cases, and poor pathological tumor regression was significantly associated with worse disease-free survival (DFS, HR = 3.45; 95%CI = 1.14-10.4; p = 0.028). High neutrophils-platelets score (NPS) (OR = 10.52; 95%CI=1.34-82.6; p = 0.025) and KRAS mutated cases (OR = 5.49; 95%CI = 1.06-28.4; p = 0.042) were identified as independent predictive factors of poor response to nCRT treatment in a multivariate analysis. Furthermore, a Cox proportional-hazard model showed that the KRAS mutational status was an independent prognostic factor associated with higher risk of local recurrence (HR = 9.68; 95%CI = 1.01-93.2; p <0.05) and shorter DFS (HR = 2.55; 95%CI = 1.05-6.21; p <0.05), while high CEA serum levels were associated with poor DFS (HR = 2.63; 95%CI = 1.01-6.85; p <0.05). Integrated clinical and molecular-based unsupervised analysis allowed us to identify two RC prognostic groups (cluster 1 and cluster 2) associated with disease-specific OS (HR = 20.64; 95%CI = 2.63-162.2; p <0.0001), metastasis-free survival (HR = 3.67; 95%CI = 1.22-11; p = 0.012), local recurrence-free survival (HR = 3.34; 95%CI = 0.96-11.6; p = 0.043) and worse DFS (HR = 2.68; 95%CI = 1.18-6.06; p = 0.012). The worst prognosis cluster 2 was enriched by stage III high-risk clinical tumors, poor responders to nCRT, with low TILs density and high frequency of KRAS and TP53 mutated cases compared with the best prognosis cluster 1 (p <0.05). Overall, this study provides a comprehensive and integrated characterization of non-metastatic RC cases as a new insight to deliver a personalized therapeutic approach.
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Affiliation(s)
- Soledad Iseas
- Oncology Unit, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
| | - Juan M. Sendoya
- Laboratorio de Terapia Molecular y Celular, Genocan, Fundación Instituto Leloir, IIBBA (CONICET), Buenos Aires, Argentina
| | - Juan Robbio
- Oncology Unit, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
- Unidad de Investigación Traslacional, Laboratorio de Biología Molecular GENUIT, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
| | - Mariana Coraglio
- Proctology Unit, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
| | - Mirta Kujaruk
- Pathology Unit, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
| | - Vanesa Mikolaitis
- Pathology Unit, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
| | - Mariana Rizzolo
- Pathology Unit, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
| | - Ana Cabanne
- Pathology Unit, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
| | - Gonzalo Ruiz
- Biomakers Molecular Pathology and Research, Buenos Aires, Argentina
| | - Rubén Salanova
- Biomakers Molecular Pathology and Research, Buenos Aires, Argentina
| | - Ubaldo Gualdrini
- Proctology Unit, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
| | - Guillermo Méndez
- Oncology Unit, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
| | - Marina Antelo
- Oncology Unit, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
| | - Marcela Carballido
- Oncology Unit, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
| | - Cecilia Rotondaro
- Laboratorio de Terapia Molecular y Celular, Genocan, Fundación Instituto Leloir, IIBBA (CONICET), Buenos Aires, Argentina
| | - Julieta Viglino
- Laboratorio de Terapia Molecular y Celular, Genocan, Fundación Instituto Leloir, IIBBA (CONICET), Buenos Aires, Argentina
| | - Martín Eleta
- Imaxe Image Diagnosis Center, Buenos Aires, Argentina
| | | | - Osvaldo L. Podhajcer
- Laboratorio de Terapia Molecular y Celular, Genocan, Fundación Instituto Leloir, IIBBA (CONICET), Buenos Aires, Argentina
| | - Enrique Roca
- Oncology Unit, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
| | - Andrea S. Llera
- Laboratorio de Terapia Molecular y Celular, Genocan, Fundación Instituto Leloir, IIBBA (CONICET), Buenos Aires, Argentina
| | - Mariano Golubicki
- Oncology Unit, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
- Unidad de Investigación Traslacional, Laboratorio de Biología Molecular GENUIT, Gastroenterology Hospital “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
| | - Martín Carlos Abba
- Basic and Applied Immunological Research Center, School of Medical Sciences, National University of La Plata, La Plata, Argentina
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Mena MD, Moresco AA, Vidal SH, Aguilar-Cortes D, Obregon MG, Fandiño AC, Sendoya JM, Llera AS, Podhajcer OL. Clinical and Genetic Spectrum of Stargardt Disease in Argentinean Patients. Front Genet 2021; 12:646058. [PMID: 33841504 PMCID: PMC8033171 DOI: 10.3389/fgene.2021.646058] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/05/2021] [Indexed: 12/11/2022] Open
Abstract
Purpose To describe the clinical and molecular spectrum of Stargardt disease (STGD) in a cohort of Argentinean patients. Methods This retrospective study included 132 subjects comprising 95 probands clinically diagnosed with STGD and relatives from 16 of them. Targeted next-generation sequencing of the coding and splicing regions of ABCA4 and other phenocopying genes (ELOVL4, PROM1, and CNGB3) was performed in 97 STGD patients. Results We found two or more disease-causing variants in the ABCA4 gene in 69/95 (73%) probands, a single ABCA4 variant in 9/95 (9.5%) probands, and no ABCA4 variants in 17/95 (18%) probands. The final analysis identified 173 variants in ABCA4. Seventy-nine ABCA4 variants were unique, of which nine were novel. No significant findings were seen in the other evaluated genes. Conclusion This study describes the phenotypic and genetic features of STGD1 in an Argentinean cohort. The mutations p.(Gly1961Glu) and p.(Arg1129Leu) were the most frequent, representing almost 20% of the mutated alleles. We also expanded the ABCA4 mutational spectrum with nine novel disease-causing variants, of which eight might be associated with South American natives.
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Affiliation(s)
- Marcela D Mena
- Laboratorio de Terapia Molecular y Celular (Genocan), Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | - Angélica A Moresco
- Servicio de Genética, Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Sofía H Vidal
- Servicio de Oftalmología, Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Diana Aguilar-Cortes
- Laboratorio de Terapia Molecular y Celular (Genocan), Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | - María G Obregon
- Servicio de Genética, Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Adriana C Fandiño
- Servicio de Oftalmología, Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Juan M Sendoya
- Laboratorio de Terapia Molecular y Celular (Genocan), Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | - Andrea S Llera
- Laboratorio de Terapia Molecular y Celular (Genocan), Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | - Osvaldo L Podhajcer
- Laboratorio de Terapia Molecular y Celular (Genocan), Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
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5
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Sendoya JM, Iseas S, Golubicki M, Robbio J, Coraglio MF, Gualdrini U, Cabanne A, Kujaruk M, Mikolaitis V, Rizzolo M, Salanova R, Rotondaro C, Abba M, Podhajcer O, Roca E, Llera A. Abstract LB-374: Transcriptome-based inference of immune cell subsets and pathway deregulation in rectal cancer reveals biological processes related to therapy response. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-lb-374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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
Purpose: Colorectal cancer is the second most frequent cancer and the second and third cause of cancer-related mortality in Argentina for men and women respectively. For locally advanced rectal cancer (LARC), preoperative chemoradiotherapy (CRT) ± induction chemotherapy (iCT) comprises the standard treatment. However, only 15-27% of patients achieve a pathological complete response, while 40-60% respond variably. This scenario poses a strong need for biomarkers able to predict response to CRT and provide guidance towards optimal treatment for each patient. Here we explore LARC gene expression data to identify baseline immune populations and pathways that might be associated with response to CRT.
Methods: Using Agilent Human Genome Microarrays, we analyzed gene expression in pre-treatment tumor biopsies of 26 LARC patients as part of an ongoing prospective translational study in Argentina. After treatment with CRT (capecitabine + radiotherapy) ± iCT (capecitabine + oxaliplatin) and surgery, pathological response was assessed according to College of American Pathologists (CAP) guidelines. We grouped CAP scores 0-1 as responders and 2-3 as nonresponders. We estimated cellular heterogeneity of the microenvironment from transcriptomic data by applying two independent computational methods: GSVA and xCell, and inferred patient-specific pathway deregulation with PARADIGM. To elucidate differential features between both patient groups, we performed Two-sample t-Tests for GSVA and xCell, and Rank Product test for PARADIGM. All tests were adjusted for FDR<0.01.
Results: Of 26 analyzed patients, we focused on 16 with currently available response data. T-test yielded 98 differentially expressed genes. From the cell type estimators, among the responder group we observed upmodulation of genes related to B-cells (p-GSVA: 0.0001; p-xCell: 0.004), mast cells (p-GSVA: 0.038; p-xCell: 0.029), activated dendritic cells (p-GSVA: 0.035) and effector memory CD8+cells (p-xCell: 0.034). PARADIGM revealed upmodulated activities in responders such as ‘DNA damage', miR34A (regulation of tumor suppression), and TP73 (apoptotic response to DNA damage). Downmodulated pathways included E2F1/3 (transcriptional/cell cycle activation), PARP1 (DNA repair) and IL8 (tumorigenic/proangiogenic chemokine). For all cases, FDR-adjusted p < 0.0001.
Conclusions: Considering the caveats regarding our current sample size, we could detect higher involvement of adaptive immunity cell populations, upmodulation of proapoptotic features, and downmodulation of DNA repair and proliferation activities in baseline biopsies of responders when compared to nonresponders. Overall, a cell cycle-decelerated tumor with poor DNA repair abilities immersed in a proapoptotic environment seems to be the one in which CRT would be more effective. With necessary validation of these analyses underway, we envision this effort as the basis on which we will evaluate genomic biomarkers for response prediction in our LARC population.
Citation Format: Juan M. Sendoya, Soledad Iseas, Mariano Golubicki, Juan Robbio, Mariana F. Coraglio, Ubaldo Gualdrini, Ana Cabanne, Mirta Kujaruk, Vanesa Mikolaitis, Mariana Rizzolo, Ruben Salanova, Cecilia Rotondaro, Martin Abba, Osvaldo Podhajcer, Enrique Roca, Andrea Llera. Transcriptome-based inference of immune cell subsets and pathway deregulation in rectal cancer reveals biological processes related to therapy response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-374.
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Affiliation(s)
- Juan M. Sendoya
- 1Laboratory of Molecular and Cellular Therapy, Fundacion Instituto Leloir, Buenos Aires, Argentina
| | - Soledad Iseas
- 2Hospital de Gastroenterología Dr. Carlos Bonorino Udaondo, Buenos Aires, Argentina
| | - Mariano Golubicki
- 2Hospital de Gastroenterología Dr. Carlos Bonorino Udaondo, Buenos Aires, Argentina
| | - Juan Robbio
- 2Hospital de Gastroenterología Dr. Carlos Bonorino Udaondo, Buenos Aires, Argentina
| | - Mariana F. Coraglio
- 2Hospital de Gastroenterología Dr. Carlos Bonorino Udaondo, Buenos Aires, Argentina
| | - Ubaldo Gualdrini
- 2Hospital de Gastroenterología Dr. Carlos Bonorino Udaondo, Buenos Aires, Argentina
| | - Ana Cabanne
- 2Hospital de Gastroenterología Dr. Carlos Bonorino Udaondo, Buenos Aires, Argentina
| | - Mirta Kujaruk
- 2Hospital de Gastroenterología Dr. Carlos Bonorino Udaondo, Buenos Aires, Argentina
| | - Vanesa Mikolaitis
- 2Hospital de Gastroenterología Dr. Carlos Bonorino Udaondo, Buenos Aires, Argentina
| | - Mariana Rizzolo
- 2Hospital de Gastroenterología Dr. Carlos Bonorino Udaondo, Buenos Aires, Argentina
| | - Ruben Salanova
- 2Hospital de Gastroenterología Dr. Carlos Bonorino Udaondo, Buenos Aires, Argentina
| | - Cecilia Rotondaro
- 1Laboratory of Molecular and Cellular Therapy, Fundacion Instituto Leloir, Buenos Aires, Argentina
| | - Martin Abba
- 3Centro de Investigaciones Inmunologicas Basicas y Aplicadas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Osvaldo Podhajcer
- 1Laboratory of Molecular and Cellular Therapy, Fundacion Instituto Leloir, Buenos Aires, Argentina
| | - Enrique Roca
- 2Hospital de Gastroenterología Dr. Carlos Bonorino Udaondo, Buenos Aires, Argentina
| | - Andrea Llera
- 1Laboratory of Molecular and Cellular Therapy, Fundacion Instituto Leloir, Buenos Aires, Argentina
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6
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Merino GA, Murua YA, Fresno C, Sendoya JM, Golubicki M, Iseas S, Coraglio M, Podhajcer OL, Llera AS, Fernández EA. TarSeqQC: Quality control on targeted sequencing experiments in R. Hum Mutat 2017; 38:494-502. [DOI: 10.1002/humu.23204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 02/06/2017] [Accepted: 02/19/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Gabriela A. Merino
- Ua Area Cs. Agr. Ing. Bio. Y S, Conicet; Universidad Católica de Córdoba; Córdoba Argentina
- Facultad de Ciencias Exactas; Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
| | - Yanina A. Murua
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Cristóbal Fresno
- Ua Area Cs. Agr. Ing. Bio. Y S, Conicet; Universidad Católica de Córdoba; Córdoba Argentina
| | - Juan M. Sendoya
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Mariano Golubicki
- Intergrupo Argentino para el Tratamiento de los Tumores Gastrointestinales; Buenos Aires Argentina
| | - Soledad Iseas
- Hospital de Gastroenterología “Dr. Carlos Bonorino Udaondo”; Buenos Aires Argentina
| | - Mariana Coraglio
- Hospital de Gastroenterología “Dr. Carlos Bonorino Udaondo”; Buenos Aires Argentina
| | - Osvaldo L. Podhajcer
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Andrea S. Llera
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Elmer A. Fernández
- Ua Area Cs. Agr. Ing. Bio. Y S, Conicet; Universidad Católica de Córdoba; Córdoba Argentina
- Facultad de Ciencias Exactas; Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
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