Carlota Rubio-Pérez
A5073262254- Cancer Genomics and Diagnostics
- Cancer Immunotherapy and Biomarkers
- Immune cells in cancer
- Genetics, Bioinformatics, and Biomedical Research
- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Genomics and Chromatin Dynamics
- Ferroptosis and cancer prognosis
- Epigenetics and DNA Methylation
- Evolution and Genetic Dynamics
- Monoclonal and Polyclonal Antibodies Research
- Genomics and Rare Diseases
- RNA modifications and cancer
- Immune Cell Function and Interaction
- Gene expression and cancer classification
- Chromosomal and Genetic Variations
- Protein Degradation and Inhibitors
- Immunotherapy and Immune Responses
- Cancer-related molecular mechanisms research
- Chronic Lymphocytic Leukemia Research
- Lymphoma Diagnosis and Treatment
- Genetic factors in colorectal cancer
- Lung Cancer Treatments and Mutations
- Nutrition, Genetics, and Disease
Universitat de Barcelona
2025
Consorci Institut D'Investigacions Biomediques August Pi I Sunyer
2025
Hospital Clínic de Barcelona
2025
Vall d'Hebron Institute of Oncology
2020-2024
Vall d'Hebron Institut de Recerca
2024
Institute for Research in Biomedicine
2017-2023
Universitat Pompeu Fabra
2014-2023
Vall d'Hebron Hospital Universitari
2019-2021
Centro de Investigación Biomédica en Red de Cáncer
2021
Hospital del Mar Research Institute
2016-2018
Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify now exist, but systematic attempts combine and optimize them on large datasets are few. We report a PanCancer PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) using 26 computational tools catalog driver genes mutations. 299 with implications regarding their anatomical sites cancer/cell types. Sequence- structure-based...
While tumor genome sequencing has become widely available in clinical and research settings, the interpretation of somatic variants remains an important bottleneck. Here we present Cancer Genome Interpreter, a versatile platform that automates newly sequenced cancer genomes, annotating potential alterations detected tumors to act as drivers their possible effect on treatment response. The results are organized different levels evidence according current knowledge, which envision can support...
Abstract Purpose: Throughout their development, tumors are challenged by the immune system, and they acquire features to evade its surveillance. A systematic view of these traits, which shed light on how respond immunotherapies, is still lacking. Experimental Design: Here, we computed relative abundance an array cell populations measure infiltration pattern 9,174 29 solid cancers. We then clustered with similar define immunophenotypes. Finally, identified genomic transcriptomic traits...
Extracting relevant information from large-scale data offers unprecedented opportunities in cancerology. We applied independent component analysis (ICA) to bladder cancer transcriptome sets and interpreted the components using gene enrichment tumor-associated molecular, clinicopathological, processing information. identified associated with biological processes of tumor cells or microenvironment, other revealed technical biases. Applying ICA nine types cancer-shared bladder-cancer-specific...
Abstract Cancer response to immunotherapy depends on the infiltration of CD8 + T cells and presence tumor-associated macrophages within tumors. Still, little is known about determinants these factors. We show that LIF assumes a crucial role in regulation cell tumor infiltration, while promoting protumoral macrophages. observe blockade tumors expressing high levels decreases CD206, CD163 CCL2 induces CXCL9 expression The releases epigenetic silencing triggering infiltration. combination...
Tyrosine kinase inhibitors were found to be clinically effective for treatment of patients with certain subsets cancers carrying somatic mutations in receptor tyrosine kinases. However, the duration clinical response is often limited, and ultimately develop drug resistance. Here, we use single-cell RNA sequencing demonstrate existence multiple cancer cell subpopulations within lines, xenograft tumors patient tumors. These exhibit epigenetic changes differential therapeutic sensitivity....
Abstract Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for resource lncRNAs with validated roles. Furthermore, it remains debated whether mutated can drive tumorigenesis, and such functions could be conserved during evolution. Here, as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, we introduce Cancer LncRNA Census (CLC), compilation 122 GENCODE causal roles in phenotypes. In contrast to existing databases, CLC requires...
Multi-omics datasets represent distinct aspects of the central dogma molecular biology. Such high-dimensional profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple using statistical fusion, rationalizes contributing evidence highlights associated genes. As part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing from...
Purpose: Diffuse gliomas are the most common primary tumor of brain and include different subtypes with diverse prognosis. The genomic characterization diffuse facilitates their molecular diagnosis. anatomical localization complicates access to specimens for diagnosis, in some cases incurring high-risk surgical procedures stereotactic biopsies. Recently, cell-free circulating DNA (ctDNA) has been identified cerebrospinal fluid (CSF) patients malignancies.Experimental Design: We performed an...
The tumor immune microenvironment is a main contributor to cancer progression and promising therapeutic target for oncology. However, microenvironments vary profoundly between patients, biomarkers prognosis treatment response lack precision. A comprehensive compendium of cells required pinpoint predictive cellular states their spatial localization. We generated single-cell atlas, jointly analyzing published data sets >500,000 from 217 patients 13 types, providing the basis patient...
Genome studies of diffuse large B-cell lymphoma (DLBCL) have revealed a number somatic mutations and structural alterations. However, the clinical significance these alterations is still not well defined. In this study, we integrated analysis targeted next-generation sequencing 106 genes genomic copy (CNA) in 150 DLBCL. The clinically significant findings were validated an independent cohort 111 patients. Germinal center activated DLBCL had differential profile mutations, altered pathogenic...
The levels of cell free circulating tumor DNA (ctDNA) in plasma correlated with treatment response and outcome systemic lymphomas. Notably, brain tumors, the ctDNA cerebrospinal fluid (CSF) are higher than plasma. Nevertheless, their role central nervous system (CNS) lymphomas remains elusive. We evaluated CSF from 19 patients: 6 restricted CNS lymphomas, 1 lymphoma, 12 performed whole exome sequencing or targeted to identify somatic mutations primary tumor, then variant-specific droplet...
We investigated the value of tumor-infiltrating NK (TI-NK) cells and HLA class I tumor expression as biomarkers response to neoadjuvant anti-HER2 antibody-based treatment in breast cancer.TI-NK HLA-I were determined by IHC pretreatment biopsies from two cohorts patients with HER2-positive cancer [discovery cohort (n = 42) validation 71)]. Tumor-infiltrating lymphocytes (TIL) scored according international guidelines. Biomarker association pathologic complete (pCR) disease-free survival (DFS)...
Abstract The molecular characterisation of medulloblastoma, the most common paediatric brain tumour, is crucial for correct management and treatment this heterogenous disease. However, insufficient tissue sample, presence tumour heterogeneity, or disseminated disease can challenge its diagnosis monitoring. Here, we report that cerebrospinal fluid (CSF) circulating DNA (ctDNA) recapitulates genomic alterations facilitates subgrouping risk stratification, providing valuable information about...
Abstract The catalog of cancer driver mutations in protein-coding genes has greatly expanded the past decade. However, non-coding are less well-characterized and only a handful recurrent mutations, most notably TERT promoter have been reported. Here, as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 across 38 tumor types, we perform multi-faceted pathway network analyses 2583 genomes 27 types compiled by PCAWG...
Background Reliable predictive imaging markers of response to immune checkpoint inhibitors are needed. Purpose To develop and validate a pretreatment CT-based radiomics signature predict in advanced solid tumors. Materials Methods In this retrospective study, was developed patients with tumors (including breast, cervix, gastrointestinal) treated anti-programmed cell death-1 or programmed death ligand-1 monotherapy from August 2012 May 2018 (cohort 1). This tested bladder lung cancer (cohorts...
The effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on the pathophysiology placenta and its impact pregnancy outcome has not yet been fully elucidated. Here, we present a comprehensive clinical, morphological, molecular analysis placental tissues from pregnant women with without SARS-CoV-2 infection. could be detected in half SARS-CoV-2–positive women. presence virus was associated any distinctive pathological, maternal, or neonatal features. tissue load low...
Abstract Brain metastases are the most common tumor of brain with a dismal prognosis. A fraction patients metastasis benefit from treatment immune checkpoint inhibitors (ICI) and degree phenotype cell infiltration has been used to predict response ICI. However, anatomical location lesions limits access material characterize phenotype. Here, we cells present in matched cerebrospinal fluid (CSF) using single-cell RNA sequencing combined T receptor genotyping. Tumor specifically CD8 + can be...
Abstract Motivation: Several computational methods have been developed to identify cancer drivers genes—genes responsible for development upon specific alterations. These alterations can cause the loss of function (LoF) gene product, instance, in tumor suppressors, or increase change its activity function, if it is an oncogene. Distinguishing between these two classes important understand tumorigenesis patients and has implications therapy decision making. Here, we assess capacity multiple...
SUMMARY The advance of personalized cancer medicine requires the accurate identification mutations driving each patient’s tumor. However, to date, we have only been able obtain partial insights into contribution genomic events tumor development. Here, design a comprehensive approach identify driver in and whole-genome panorama across more than 2,500 tumors from 37 types cancer. This includes coding non-coding point mutations, copy number alterations other rearrangements somatic origin,...
Abstract The discovery of driver mutations is one the key motivations for cancer genome sequencing. Here , as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium which aggregated whole sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify in coding non-coding sites within genomes. Using total 1373 genomic features derived public sources, DriverPower’s...