A5065677035- Bladder and Urothelial Cancer Treatments
- Cancer Immunotherapy and Biomarkers
- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Urinary and Genital Oncology Studies
- Immunotherapy and Immune Responses
- Ferroptosis and cancer prognosis
- Radiomics and Machine Learning in Medical Imaging
- Lung Cancer Treatments and Mutations
- Cancer-related molecular mechanisms research
- Epigenetics and DNA Methylation
- Genomics and Rare Diseases
- Lung Cancer Research Studies
- Protist diversity and phylogeny
- Immune cells in cancer
- Esophageal Cancer Research and Treatment
- Computational Drug Discovery Methods
- Microbial Community Ecology and Physiology
- Immune Cell Function and Interaction
- Biomedical Text Mining and Ontologies
- Methane Hydrates and Related Phenomena
- RNA and protein synthesis mechanisms
- Gene expression and cancer classification
- HER2/EGFR in Cancer Research
- Virus-based gene therapy research
Hospital Del Mar
2020-2025
Hospital del Mar Research Institute
2020-2025
Institut de recherche mathématique de Rennes
2023
Municipal Institute for Medical Research
2020-2022
Universitätsmedizin Göttingen
2018-2019
Institut de Ciències del Mar
2015
Institut Català de Ciències del Clima
2015
Abstract Background Contemporary deep learning approaches show cutting-edge performance in a variety of complex prediction tasks. Nonetheless, the application healthcare remains limited since methods are often considered as non-interpretable black-box models. However, machine community made recent elaborations on interpretability explaining data point-specific decisions techniques. We believe that such explanations can assist need personalized precision medicine via patient-specific...
Abstract Background The variability in responses to neoadjuvant treatment with anti-HER2 antibodies prompts personalized clinical management and the development of innovative strategies. Tumor-infiltrating Natural Killer (TI-NK) cells can predict efficacy HER2-targeted independently from clinicopathological factors primary HER2-positive breast cancer patients. Understanding mechanism/s underlying this association would contribute optimizing patient stratification provide rationale for...
The expression of tumor-specific antigens during cancer progression can trigger an immune response against the tumor. Here, we investigate if microproteins encoded by noncanonical open reading frames (ncORFs) are a relevant source antigens. We analyze RNA sequencing data from 117 hepatocellular carcinoma (HCC) tumors and matched healthy tissue together with ribosome profiling immunopeptidomics data. Combining human leukocyte antigen-epitope binding predictions experimental validation...
Abstract Mutations and activation of the PI3K signaling pathway in breast cancer cells have been linked to brain metastases. However, here we describe that some metastases samples protein expression components is restricted metastatic microenvironment. In contrast therapeutic effects inhibition on cells, reaction microenvironment less understood. Therefore aimed quantify activity metastasis investigate central nervous system (CNS) First, systematically metastases, performed a prospective...
Abstract High-grade T1 (HGT1) bladder cancer is the highest risk subtype of non–muscle-invasive with unpredictable outcome and poorly understood factors. Here, we examined association somatic mutation profiles nonrecurrent disease (GO, good outcome), recurrence (R), or progression (PD) in a cohort HGT1 patients. Exome sequencing was performed on 62 15 matched normal tissue samples. Both tumor only (TO) paired analyses were performed, focusing 95 genes known to be mutated cancer. Somatic...
Abstract One of the hallmarks SARS-CoV-2 infection is an induced immune dysregulation, in some cases resulting cytokine storm syndrome and acute respiratory distress (ARDS). Several physiological parameters are altered as a result storm. Among them, microRNAs (miRNAs) might reflect this poor condition since they play significant role cellular performance including inflammatory responses. Circulating miRNAs patients who underwent ARDS needed mechanical ventilation (MV+; n = 15) were analyzed...
RNA-Seq provides an accurate quantification of gene expression levels and it is widely used for molecular subtype classification in cancer, with special importance prognosis. However, the reliability validity these analyses can significantly be influenced by how data are processed. In this study we evaluate preprocessing methods influence bladder cancer. By benchmarking various aligners, quantifiers normalization transformation, stress choices consistent classification. Our findings...
A comprehensive understanding of cancer has been furthered with technological improvements and decreasing costs next-generation sequencing (NGS). However, the complexity interpreting genomic data is hindering implementation high-throughput technologies in clinical context: increasing evidence on gene–drug interactions complicates task assigning significance to variants. Here we present a method that automatically matches patient-specific alterations treatment options. The relies entirely...
ABSTRACT Ewing sarcoma (ES) is an aggressive bone and soft tissue neoplasm characterized by EWSR1/ETS rearrangements whose cellular origin remains unclear. EWS-FLI1 expression in human pediatric mesenchymal stem cells (hpMSCs) induces a quantitatively qualitatively different transcriptional response than its adult MSCs (haMSCs), but fails to form tumors vivo . ES have early developmental lineage signatures distinct from postnatal MSCs. Here, we generated experimental teratomas out of...
Introduction Immunotherapy is firmly established as a treatment regimen in various solid tumors, driven by its exceptional benefits selected group of patients. Despite widespread adoption immune checkpoint blockade (ICB) across diverse the quest for clinically informative biomarker long-term benefit remains unmet.
Platinum-based chemotherapy combined with immunotherapy provides durable disease control in advanced urothelial cancer. However, cisplatin and carboplatin differently impact the tumor immune microenvironment, affecting chemo-immunotherapy response. Here, we evaluate cell populations ecosystems associated overall survival patients treated platinum-based chemotherapy. Our transcriptomic analysis of pretreatment samples from three cohorts (189 patients) cancer showed that lymphoid infiltration...
Immune checkpoint inhibitors (ICI) have revolutionized cancer treatment and can result in complete remissions even at advanced stages of the disease. However, only a small fraction patients respond to treatment. To better understand which factors drive clinical benefit, we generated whole exome RNA sequencing data from 27 urothelial carcinoma treated with anti-PD-(L)1 monoclonal antibodies. We assessed influence on response non-synonymous mutations (tumor mutational burden or TMB), clonal...
The clinical manifestations of SARS-CoV-2 infection vary widely, from asymptomatic to the development acute respiratory distress syndrome (ARDS) and death. host response elicited by plays a key role in determining outcome. We hypothesized that dynamic whole blood transcriptomic profile hospitalized adult COVID-19 patients characterizing subgroup develops severe disease ARDS would broaden our understanding heterogeneity outcomes. recruited 60 with RT-PCR-confirmed infection, among whom 19...
ABSTRACT Advanced bladder cancer patients show very variable responses to immune checkpoint inhibitors (ICIs) and effective strategies predict response are still lacking. Here we integrate mutation gene expression data from 707 advanced treated with anti-PD-1/anti-PD-L1 build highly accurate predictive models. We find that, in addition tumor mutational burden (TMB), enrichment the APOBEC signature, abundance of pro-inflammatory macrophages, major factors associated response. Paradoxically,...
Next-generation sequencing methods continuously provide clinicians and researchers in precision oncology with growing numbers of genomic variants found cancer. However, manually interpreting the list to identify reliable targets is an inefficient cumbersome process that does not scale increasing number cases. Support by computer systems needed for analysis large experiments clinical studies new therapies, user-friendly applications are molecular tumor boards support their decision-making...
Somatic single nucleotide variants (SNVs) are genomic events with increasing implications in cancer treatment. The clinical standard for SNVs detection is whole genome/exome sequencing (WGS/WES) matched tumor-normal samples. Yet, this a very costly approach both economically and biologically often only tumor samples sequenced. On the other hand, RNA (RNA-Seq) most popular technology to study gene expression, has also potential cost-effective identification of as an alternative tumor-only...
Abstract The impact of tumor focality on prostate cancer (PCa) prognosis has been addressed in several studies with conflicting results. Tumor foci from multifocal (MF) PCa can show highly heterogeneous molecular features. Our aim was to analyze the protein expression PTEN, SPOP, SLC45A3, ETV1, ERG and “triple hit” (ERG overexpression, PTEN plus SLC45A3 loss) unifocal (UF) MF PCa, evaluate their value as prognostic markers according focality, role heterogeneity disease. ETV1...
Hyperprogressive disease (HPD) as a consequence of immune checkpoint inhibitors in NSCLC has been reported multiple studies. However, inconsistent results incidence and survival outcomes within studies, together with different assessment methods, have led to increasing controversy regarding the concept HPD.Consecutive patients treated nivolumab (N = 42) or docetaxel 37) were evaluated. HPD was quantified by applying three methods (tumor growth rate [TGR], tumor kinetics [TGK], Response...