Person: Armisen, Ricardo
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Armisen
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Ricardo
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Publication Advances in machine learning for tumour classification in cancer of unknown primary: A mini-review(2024) OrĆ³stica, Karen; Mardones, Felipe; Bernal, Yanara; Molina, Samuel; Orchard, Marcos; Verdugo, Ricardo; Carvajal-Hausdorf, Daniel; Marcelain, Katherine; Contreras, Seba; Armisen, RicardoCancers of unknown primary (CUP) are a heterogeneous group of aggressive metastatic cancers where standardised diagnostic techniques fail to identify the organ where it originated, resulting in a poor prognosis and resistance to treatment. Recent advances in large-scale sequencing techniques have enabled the identification of mutational signatures specific to particular tumour subtypes, even from liquid biopsy samples such as blood. This breakthrough paves the way for the development of new cost-effective diagnostic strategies. This mini-review explores recent advancements in Machine Learning (ML) and its application to tumour classification methods for CUP patients, identifying its weaknesses and strengths when classifying the tumour type. In the era of multi-omics, integrating several sources of information (e.g., imaging, molecular biomarkers, and family history) requires important theoretical advancements: increasing the dimensionality of the problem can result in lowering the predictive accuracy and robustness when data is scarce. Here, we review and discuss different architectures and strategies for incorporating cutting-edge machine learning into CUP diagnosis, aiming to bridge the gap between theory and clinical practice.Publication SKI regulates rRNA transcription and pericentromeric heterochromatin to ensure centromere integrity and genome stability(2025) Pola, VĆctor; Carrero, David; Sagredo, Eduardo; Inostroza, VĆctor; Cappelli, Claudio; Rivas, Solange; BitrĆ”n, Mirita; Zambrano, Evelyn; Gonzalez, Evelin; Morales, Fernanda; Manterola, Marcia; Montecino, MartĆn; Armisen, Ricardo; Marcelain, KatherineAccurate chromosome segregation and ribosomal gene expression silencing are essential for maintaining genome integrity, and disruptions in these processes are key for oncogenesis and cancer progression. Here, we demonstrate a novel role for the transcriptional co-repressor SKI in regulating rDNA and pericentromeric heterochromatin (PCH) silencing in human cells. We found that SKI localizes to the rDNA promoter on acrocentric chromosomes and is crucial for maintaining H3K9 trimethylation (H3K9me3) and repressing 45S rRNA gene expression. SKI is also associated with BSR and HSATII satellites within PCH, where is necessary for H3K9 methylation and recruitment of SUV39H1 and HP1Ī±, key players for heterochromatin silencing and centromere function. Consequently, SKI deficiency disrupted centromere integrity and resulted in aberrant chromosome segregation, micronuclei formation, and chromosome instability. The identification of SKI as a key participant in the epigenetic-mediated silencing of pericentromeric and ribosomal DNA provides a fundamental insight, paving the way for new research into the intricate relationship between transcriptional regulation and genome instability during cancer progression, and opening novel opportunities for therapeutic intervention.Publication Data Resource Profile: EULAT Eradicate GBC: the European-Latin American Research Consortium towards Eradication of Preventable Gallbladder Cancer(2025) Scherer, Dominique; Barahona, Carol; Mengoa, Claudio; Montenegro, Paola; Losada, Hector; Lineth, Ana; Rojas, Armando; Vera, Allan; Spencer, Loreto; Ortega, Alejandro; Vargas, Karina; Roa, Juan; Inklemona, Cristina; Colombo, Alicia; Kirsten, Romy; Zollner, Linda; Marcelain, Katherine; Rounge, Trine; Langseth, Hilde; Lewis, Sarah; Arroyo, Gerardo; Armisen, Ricardo; Nervi, Bruno; Muller, Bettina; Fernandez, Piga; Kumar, Rajiv; Salinas, Pamela; Kelly, Rachel; Jenab, Mazda; Bermejo, JustoPublication The mutational landscape and actionable targets of gallbladder cancer: an ancestry-informed and comparative analysis of a Chilean population(2025) Erices, JosĆ©; GonzĆ”lez, Evelin; Salgado, Marcela; Barahona, Carol; Freire, MatĆas; SepuĢlveda, Gonzalo; Ampuero, Diego; Blanco, Alejandro; GĆ”rate, Valentina; BĆ”ez, Pablo; Tapia, Camilo; Toro, Jessica; Gallegos, IvĆ”n; Barajas, Olga; Ahumada, MĆ³nica; Sanhueza, VerĆ³nica; Spencer, Loreto; De Toro, Gonzalo; Morales, Erik; GutiĆ©rrez, Lorena; Morales, Fernanda; Marin, Arnaldo; Varela, Nelson; Bermejo, Justo; Armisen, Ricardo; Marcelain, KatherineIntroduction: Gallbladder cancer (GBC) is a highly aggressive malignancy with one of the highest incidence rates reported in Chile. Despite its clinical impact, molecular characterization of GBC in Latin American populations remains limited, and the absence of effective targeted therapies underscores the urgent need for new therapeutic strategies. Methods: We collected 118 tumor samples, of which 56 passed sequencing quality control using the Oncomineā¢ Comprehensive Assay v1. Somatic variants were identified with ANNOVAR and Cancer Genome Interpreter, and ancestry was inferred using ADMIXTURE and PCA with ancestry-informative markers. Comparative analyses were performed with Japanese, Singaporean, and U.S. cohorts. Results: A total of 535 somatic mutations were detected in 43 genes, with TP53 (30%), TSC2 (29%), and NOTCH1 (27%) being the most frequently mutated. We identified 121 clinically actionable variants in ATM, BRCA1/2, EGFR, ERBB2, and other genes. Exploratory analysis suggested an association between higher Mapuche ancestry and TP53 mutations. Comparative analyses revealed distinct mutational patterns in the Chilean cohort relative to Asian and U.S. datasets. Conclusion: This ancestry-informed genomic analysis provides the first comprehensive landscape of Chilean GBC, identifying actionable alterations with potential therapeutic relevance and supporting the development of population-specific precision oncology strategies.Publication Transcription-Coupled Repair Promotes the Retention of Mutations in Coding Regions During Replication Stress(2026) Zambrano, Evelyn; Fierro, Cristopher; Morales, Fernanda; Manterola, Marcia; Marin, Arnaldo; Armisen, Ricardo; Marcelain, KatherineReplication stress (RS) is a primary driver of genomic instability in cancer, yet the contribution of transcription-coupled repair (TC-NER) to this process remains unclear. Here, we investigate how the TC-NER factor ERCC6 (CSB) shapes mutational landscapes under RS. We found that ERCC6 deficiency biases early damage signaling toward a 53BP1-mediated response, ultimately leading to senescence. Conversely, ERCC6-proficient cells prioritize survival and proliferative recovery but at the expense of distinct genomic alterations. Whole-exome sequencing reveals that ERCC6 proficiency is associated with the retention of stress-induced mutations specifically within coding regions of transcriptionally active loci, whereas ERCC6-deficient cells accumulate variants primarily in intergenic regions. These findings suggest that while ERCC6 safeguards transcriptional continuity during RS, its activity is associated with a biased retention of stress-induced mutations within coding regions in the surviving cell population. These findings reveal a previously unrecognized link between transcription-coupled repair and mutation distribution in human cells, linking TC-NER to context-dependent somatic evolution and tumor heterogeneity.