A5040764164- Ubiquitin and proteasome pathways
- Single-cell and spatial transcriptomics
- Lymphoma Diagnosis and Treatment
- Epigenetics and DNA Methylation
- Multiple Myeloma Research and Treatments
- Genomics and Chromatin Dynamics
- Immune Cell Function and Interaction
- Chronic Lymphocytic Leukemia Research
- Cancer-related gene regulation
- T-cell and B-cell Immunology
- Protein Degradation and Inhibitors
- RNA modifications and cancer
- Genetic Syndromes and Imprinting
- RNA Research and Splicing
- CAR-T cell therapy research
- Proteoglycans and glycosaminoglycans research
- Immune cells in cancer
- Cancer Cells and Metastasis
- Viral-associated cancers and disorders
- Sarcoma Diagnosis and Treatment
- Monoclonal and Polyclonal Antibodies Research
- Glycosylation and Glycoproteins Research
- Cancer Genomics and Diagnostics
- 14-3-3 protein interactions
- Immune responses and vaccinations
Wellcome Sanger Institute
2022-2024
Universitat de Barcelona
2015-2021
Consorci Institut D'Investigacions Biomediques August Pi I Sunyer
2015-2021
Institut d'Investigació Biomédica de Bellvitge
2014
Abstract To investigate the three-dimensional (3D) genome architecture across normal B cell differentiation and in neoplastic cells from different subtypes of chronic lymphocytic leukemia mantle lymphoma patients, here we integrate situ Hi-C nine additional omics layers. Beyond conventional active (A) inactive (B) compartments, uncover a highly-dynamic intermediate compartment enriched poised polycomb-repressed chromatin. During development, 28% compartments change, mostly involving...
The epigenomic landscape of Parkinson's disease (PD) remains unknown. We performed a genomewide DNA methylation and transcriptome studies in induced pluripotent stem cell (iPSC)-derived dopaminergic neurons (DAn) generated by reprogramming somatic skin cells from patients with monogenic LRRK2-associated PD (L2PD) or sporadic (sPD), healthy subjects. observed extensive changes DAn, RNA expression, which were common L2PD sPD. No significant differences present parental cells, undifferentiated...
The multikinase inhibitor sorafenib is the only effective drug in advanced cases of hepatocellular carcinoma (HCC). However, response differs among patients and effectiveness implies a delay. We have recently described that sensitizes HCC cells to apoptosis. In this work, we explored six different liver tumor cell lines define phenotypic signature may predict lack patients. Results indicated show mesenchymal-like phenotype, resistance suppressor effects transforming growth factor beta...
Assessment of single-cell gene expression (single-cell RNA sequencing) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here we introduce Dandelion, a computational pipeline for scVDJ-seq analysis. It enables the application standard V(D)J analysis workflows to datasets, delivering improved contig annotation identification nonproductive partially spliced contigs. We devised strategy create an AIR feature space that can be used both...
Multiple myeloma (MM) is a plasma cell neoplasm associated with broad variety of genetic lesions. In spite this heterogeneity, MMs share characteristic malignant phenotype whose underlying molecular basis remains poorly characterized. the present study, we examined cells from MM using multi-epigenomics approach and demonstrated that, when compared to normal B cells, showed an extensive activation regulatory elements, in part affecting coregulated adjacent genes. Among target genes...
Deubiquitinases are proteases with a wide functional diversity that profoundly impact multiple biological processes. Among them, the ubiquitin-specific protease 36 (USP36) has been implicated in regulation of nucleolar activity. However, its relevance vivo not yet fully described. Here, we report generation an Usp36-deficient mouse model to examine function this enzyme. We show Usp36 depletion is lethal preimplantation embryos, where it blocks transition from morula blastocyst during...
Abstract Myeloid cells are central to homeostasis and immunity. Characterising in vitro myelopoiesis protocols is imperative for their use research, immunotherapies, understanding human myelopoiesis. Here, we generate a >470K molecular map of induced pluripotent stem (iPSC) differentiation into macrophages. Integration with vivo single-cell atlases shows recapitulates features yolk sac hematopoiesis, before definitive hematopoietic (HSC) emerge. The diversity myeloid generated, including...
Abstract Assessment of single-cell gene expression (scRNA-seq) and adaptive immune receptor sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here, we introduce Dandelion , a computational pipeline for scVDJ-seq analysis. It enables the application standard V(D)J analysis workflows to datasets, delivering improved contig annotation identification non-productive partially spliced contigs. We devised novel strategy create an feature space that can be used both...
Abstract T cells develop from multi-potent hematopoietic progenitors in the thymus and provide adaptive protection against pathogens cancer. However, emergence of human cell-competent blood progenitors, their subsequent specification to lineage, has been challenging capture real time. Here, we leveraged a pluripotent stem cell differentiation system understand transcriptional dynamics fate restriction events that underlie this critical developmental process. Time-resolved single RNA...
Abstract Common approaches to characterize the structure of DNA in nucleus, such as different Chromosome Conformation Capture methods, have not currently been widely applied tissue types due several practical difficulties including requirement for intact cells start sample preparation. In contrast, techniques based on sodium bisulfite conversion assay methylation, many a variety organisms. Recent work has shown possibility inferring some aspects three dimensional from methylation data,...
Abstract Despite recent advances, the dynamics of genome architecture and chromatin function during human cell differentiation its potential reorganization upon neoplastic transformation remains poorly characterized. Here, we integrate in situ Hi-C nine additional omic layers to define biologically characterize dynamic changes three-dimensional (3D) across normal B cells from different subtypes chronic lymphocytic leukemia (CLL) mantle lymphoma (MCL) patients. Beyond conventional active (A)...
T cells develop from hematopoietic progenitors in the thymus and protect against pathogens cancer. However, emergence of human cell-competent blood their subsequent specification to lineage have been challenging capture real time. Here, we leveraged a pluripotent stem cell differentiation system understand transcriptional dynamics fate restriction events that underlie this critical developmental process. Time-resolved single-cell RNA sequencing revealed downregulation multipotent program,...
ABSTRACT Multiple myeloma (MM) is a plasma cell neoplasm associated with broad variety of genetic lesions. In spite this heterogeneity, MMs share characteristic malignant phenotype whose underlying molecular basis remains poorly characterized. the present study, we examined cells from MM using multi-epigenomics approach and demonstrated that when compared to normal B cells, showed an extensive activation regulatory elements, in part affecting co-regulated adjacent genes. Among target genes...
Background: How a quiescent, terminally differentiated plasma cell transforms into an aggressive and lethal disease such as multiple myeloma (MM) remains scientific puzzle. The abnormal genomic landscape of MM patients has been previously characterized but not fully capable explaining the pathogenesis disease. Furthermore, is remarkably heterogeneous with no unifying transforming mechanism. Recently, breakthrough discoveries in epigenetics field have transformed our understanding neoplastic...