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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. Fil: Mena, Marcela Daniela C. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Moresco, Angélica A.. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina Fil: Vidal, Sofía H.. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina Fil: Aguilar Cortes, Diana Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Obregon, María G.. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina Fil: Fandiño, Adriana Cristina. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina Fil: Sendoya, Juan Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Llera, Andrea Sabina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Podhajcer, Osvaldo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina

Locally advanced rectal cancer (LARC) remains a medical challenge. Reliable biomarkers to predict which patients will significantly respond to neoadjuvant chemoradiotherapy (nCRT) have not been identified. We evaluated baseline genomic and transcriptomic features to detect differences that may help predict response to nCRT. Eligible LARC patients received nCRT (3D-LCRT 50.4 Gy plus capecitabine 825 mg/m2/bid), preceded by three cycles of CAPOX in high systemic-relapse risk tumors, and subsequent surgery. Frozen tumor biopsies at diagnosis were sequenced using a colorectal cancer panel. Transcriptomic data was used for pathway and cell deconvolution inferential algorithms, coupled with immunohistochemical validation. Clinical and molecular data were analyzed according to nCRT outcome. Pathways related to DNA repair and proliferation (p < 0.005), and co-occurrence of RAS and TP53 mutations (p = 0.001) were associated with poor response. Enrichment of expression signatures related to enhanced immune response, particularly B cells and interferon signaling (p < 0.005), was detected in good responders. Immunohistochemical analysis of CD20⁺ cells validated the association of good response with B cell infiltration (p = 0.047). Findings indicate that the presence of B cells is associated with successful tumor regression following nCRT in LARC. The prevalence of simultaneous RAS and TP53 mutations along with a proficient DNA repair system that may counteract chemoradio-induced DNA damage was associated with poor response., Facultad de Ciencias Médicas, Centro de Investigaciones Inmunológicas Básicas y Aplicadas

Targeted sequencing (TS) is growing as a screening methodology used in research and medical genetics to identify genomic alterations causing human diseases. In general, a list of possible genomic variants is derived from mapped reads through a variant calling step. This processing step is usually based on variant coverage, although it may be affected by several factors. Therefore, undercovered relevant clinical variants may not be reported, affecting pathology diagnosis or treatment. Thus, a prior quality control of the experiment is critical to determine variant detection accuracy and to avoid erroneous medical conclusions. There are several quality control tools, but they are focused on issues related to whole-genome sequencing. However, in TS, quality control should assess experiment, gene, and genomic region performances based on achieved coverages. Here, we propose TarSeqQC R package for quality control in TS experiments. The tool is freely available at Bioconductor repository. TarSeqQC was used to analyze two datasets; low-performance primer pools and features were detected, enhancing the quality of experiment results. Read count profiles were also explored, showing TarSeqQC's effectiveness as an exploration tool. Our proposal may be a valuable bioinformatic tool for routinely TS experiments in both research and medical genetics.

Importance: Comprehensive understanding of the genomic and gene-expression differences between retinoblastoma tumors from patients with bilateral disease may help to characterize risk and optimize treatment according to individual tumor characteristics. Objective: To compare the genomic features between each eye and a specimen from an orbital relapse in patients with bilateral retinoblastoma. Design, Setting, and Participants: In this case, 2 patients with retinoblastoma underwent upfront bilateral enucleation. Tumor samples were subjected to genomic and gene-expression analysis. Primary cell cultures were established from both of the tumors of 1 patient and were used for gene-expression studies. Main Outcomes and Measures: Whole-exome sequencing was performed on an Illumina platform for fresh tumor samples and DNA arrays (CytoScan or OncoScan) were used for paraffin-embedded samples and cell lines. Gene-expression analysis was performed using Agilent microarrays. Germinal and somatic alterations, copy number alterations, and differential gene expression were assessed. Results: After initial bilateral enucleation, patient 1 showed massive choroidal and laminar optic nerve infiltration, while patient 2 showed choroidal and laminar optic nerve invasion. Patient 1 developed left-eye orbital recurrence and bone marrow metastasis less than 1 year after enucleation. Both ocular tumors showed gains on 1q and 6p but presented other distinct genomic alterations, including an additional gain in 2p harboring the N-myc proto-oncogene (MYCN) in the left tumor and orbital recurrence. Similar copy number alterations between the orbital recurrence and the left eye supported the origin of the relapse, with an additional 11q loss only detected in the orbital relapse. Specimens from patient 2 showed common copy number gains and losses, but further evolution rendered a 2p gain spanningMYCNin the left tumor. For this patient, microarray expression analysis showed differential expression of theMYCNand the forkhead box protein G1 (FOXG1) gene pathways between the left and right tumors. Conclusions and Relevance: Differential genomic and gene expression features were observed between tumors in 2 patients with bilateral disease, confirming intereye heterogeneity that might be considered if targeted therapies are used in such patients. Chromosomal alteration profile supported the origin of the orbital recurrence from the homolateral eye in 1 patient. Loss in chromosome 11q may have been associated with extraocular relapse in this patient., Centro de Investigaciones Inmunológicas Básicas y Aplicadas

Although gene expression-derived PAM50 intrinsic subtypes (LumA, LumB, HER2E and Basal) were reported in Latin American breast cancer, most studies did not adequately represent the unique and diverse genetic admixture of the Latin American population and/or included a small number of individuals. As a result of these limitations, confirmation of the prognostic value of available intrinsic subtype classification signatures in a diverse cohort of Latin American women is of utmost importance. We assessed the general distribution and prognostic performance of PAM50-based intrinsic and immunohistochemistry (IHC)-based surrogate subtype classifications in Latin American women included in the Molecular Profile of Breast Cancer Study (MPBCS), an initiative of the US-Latin America Cancer Research Network (US-LACRN) comprising institutions of Argentina, Brazil, Chile, Mexico and Uruguay. MPBCS focused on stage II-III breast cancer in Latin American women. Eligible enrolled patients (n=1300) were characterized clinically, pathologically and epidemiologically and followed-up for 5 years. IHC subtypes were assessed according to St Gallen's 2013 criteria, using Ki67 to discriminate LumB from LumA tumors. A total of 1071 tumors were characterized by gene-expression microarrays. PAM50 classification defined 45% of tumors as LumA, 19.7% as LumB, 13.8% as HER2E and 17.5% as Basal. Normal-like tumors (6.3%) were excluded from the analysis. The 5-year prognostic ability of PAM50 and IHC classifications, both at the cancer-specific (OS) and progression-free survival (PFS), was tested. The prognosis for LumA tumors was significantly better than for other subtypes, while Basal-like tumors had the worst prognosis. The prognostic power of IHC-based subtypes (C-index 0.698 for OS, 0.635 for PFS) was very similar to that of PAM50 (C-index 0.678 for OS, 0.639 for PFS), indicating that in US-LACRN-MPBCS, contrary to other cohorts, surrogate subtypes are as useful as PAM50 for discriminating recurrence risk. PAM50-derived risks of recurrence (RORs), in particular ROR-S (C-index 0.699 for OS, 0.649 for PFS), clearly discriminated risk into low, intermediate and high-risk groups. Transcriptomic pathway analysis showed high proliferation (i.e. cell cycle control and DNA damage repair) associated with LumB, HER2E and Basal tumors, and a strong dependency on the estrogen pathway for LumA. Overall, a general concordance of the molecular features of US-LACRN-MPBCS breast cancer tumors with those of other cohorts was confirmed. The shift towards non-luminal subtypes could be partly attributable to the recruitment bias towards advanced stages. Further refinement of analyses using molecular ancestry assignation may help to reveal more subtle differences in this heterogeneously admixed population. Citation Format: Andrea S. Llera, Eliana Abdelhay, Osvaldo Podhajcer, Nora Artagaveytia, Adrián Daneri-Navarro, Bettina Müller, Carlos Velázquez Contreras, Darío Rocha, Juan Martín Sendoya, Renata Binato, Elmer Fernández, Elsa Alcoba, Isabel Alonso, Alicia I. Bravo, Natalia Camejo, Dirce Carraro, Mónica Castro, Juan M. Castro-Cervantes, Sandra Cataldi, Alfonso Cayota, Mauricio Cerda, Susanne Crocamo, Raul Delgadillo-Cisterna, Lucía Delgado, Alicia del Toro Arreola, Marisa Dreyer Breitenbach, Jorge Fernández, Wanda Fernández, Ramon A. Franco-Topete, Fancy Gaete, Jorge Gómez, Gonzalo Greif, Marisol Guerrero, Marianne Marianne Henderson, Andres de J Moran-Mendoza, María Aparecida Nagai, Antonio Oceguera-Villanueva, Antonio Quintero-Ramos, Rui Reis, Javier Retamales, Robinson Rodríguez, Cristina Rosales, Efrain Salas-González, Laura Segovia, Araceli Silva-García, Vidya Vedham, Livia Zagame, The US-Latin American Cancer Research Network. Molecular features of breast cancer involved in classification and prognosis of a multi-country Latin American cohort: The US-LACRN-MPBCS breast cancer cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 608.

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 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.