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1.
Atherosclerosis ; 384: 117123, 2023 11.
Artículo en Inglés | MEDLINE | ID: mdl-37127497

RESUMEN

BACKGROUND AND AIMS: This study aims to identify sex-specific transcriptional differences and signaling pathways in circulating monocytes contributing to cardiovascular disease. METHODS AND RESULTS: We generated sex-biased gene expression signatures by comparing male versus female monocytes of coronary artery disease (CAD) patients (n = 450) from the Center for Translational Molecular Medicine-Circulating Cells Cohort. Gene set enrichment analysis demonstrated that monocytes from female CAD patients carry stronger chemotaxis and migratory signature than those from males. We then inferred cytokine signaling activities based on CytoSig database of 51 cytokine and growth factor regulation profiles. Monocytes from females feature a higher activation level of EGF, IFN1, VEGF, GM-CSF, and CD40L pathways, whereas IL-4, INS, and HMGB1 signaling was seen to be more activated in males. These sex differences were not observed in healthy subjects, as shown for an independent monocyte cohort of healthy subjects (GSE56034, n = 485). More pronounced GM-CSF signaling in monocytes of female CAD patients was confirmed by the significant enrichment of GM-CSF-activated monocyte signature in females. As we show these effects were not due to increased plasma levels of the corresponding ligands, sex-intrinsic differences in monocyte signaling regulation are suggested. Consistently, regulatory network analysis revealed jun-B as a shared transcription factor activated in all female-specific pathways except IFN1 but suppressed in male-activated IL-4. CONCLUSIONS: We observed overt CAD-specific sex differences in monocyte transcriptional profiles and cytokine- or growth factor-induced responses, which provide insights into underlying mechanisms of sex differences in CVD.


Asunto(s)
Enfermedades Cardiovasculares , Enfermedad de la Arteria Coronaria , Humanos , Masculino , Femenino , Monocitos/metabolismo , Factor Estimulante de Colonias de Granulocitos y Macrófagos , Enfermedades Cardiovasculares/genética , Enfermedades Cardiovasculares/metabolismo , Caracteres Sexuales , Interleucina-4 , Citocinas/metabolismo , Transducción de Señal
2.
Nat Genet ; 54(11): 1690-1701, 2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-36303074

RESUMEN

Adult kidney organoids have been described as strictly tubular epithelia and termed tubuloids. While the cellular origin of tubuloids has remained elusive, here we report that they originate from a distinct CD24+ epithelial subpopulation. Long-term-cultured CD24+ cell-derived tubuloids represent a functional human kidney tubule. We show that kidney tubuloids can be used to model the most common inherited kidney disease, namely autosomal dominant polycystic kidney disease (ADPKD), reconstituting the phenotypic hallmark of this disease with cyst formation. Single-cell RNA sequencing of CRISPR-Cas9 gene-edited PKD1- and PKD2-knockout tubuloids and human ADPKD and control tissue shows similarities in upregulation of disease-driving genes. Furthermore, in a proof of concept, we demonstrate that tolvaptan, the only approved drug for ADPKD, has a significant effect on cyst size in tubuloids but no effect on a pluripotent stem cell-derived model. Thus, tubuloids are derived from a tubular epithelial subpopulation and represent an advanced system for ADPKD disease modeling.


Asunto(s)
Quistes , Riñón Poliquístico Autosómico Dominante , Adulto , Humanos , Riñón Poliquístico Autosómico Dominante/genética , Canales Catiónicos TRPP/genética , Organoides , Riñón , Antígeno CD24/genética
3.
Acta Neuropathol ; 144(5): 987-1003, 2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-36112223

RESUMEN

Multiple sclerosis (MS) is a multifocal and progressive inflammatory disease of the central nervous system (CNS). However, the compartmentalized pathology of the disease affecting various anatomical regions including gray and white matter and lack of appropriate disease models impede understanding of the disease. Utilizing single-nucleus RNA-sequencing and multiplex spatial RNA mapping, we generated an integrated transcriptomic map comprising leukocortical, cerebellar and spinal cord areas in normal and MS tissues that captures regional subtype diversity of various cell types with an emphasis on astrocytes and oligodendrocytes. While we found strong cross-regional diversity among glial subtypes in control tissue, regional signatures become more obscure in MS. This suggests that patterns of transcriptomic changes in MS are shared across regions and converge on specific pathways, especially those regulating cellular stress and immune activation. In addition, we found evidence that a subtype of white matter oligodendrocytes appearing across all three CNS regions adopt pro-remyelinating gene signatures in MS. In summary, our data suggest that cross-regional transcriptomic glial signatures overlap in MS, with different reactive glial cell types capable of either exacerbating or ameliorating pathology.


Asunto(s)
Esclerosis Múltiple , Sustancia Blanca , Astrocitos/patología , Humanos , Esclerosis Múltiple/patología , Neuroglía/patología , Oligodendroglía/metabolismo , ARN/metabolismo , Sustancia Blanca/patología
4.
Nephrol Dial Transplant ; 37(4): 628-637, 2022 03 25.
Artículo en Inglés | MEDLINE | ID: mdl-33332571

RESUMEN

The field of single-cell technologies, in particular single-cell genomics with transcriptomics and epigenomics, and most recently single-cell proteomics, is rapidly growing and holds promise to advance our understanding of organ homoeostasis and disease, and facilitate the identification of novel therapeutic targets and biomarkers. This review offers an introduction to these technologies. In addition, as the size and complexity of the data require sophisticated computational methods for analysis and interpretation, we will also provide an overview of these methods and summarize the single-cell literature specifically pertaining to the kidney.


Asunto(s)
Epigenómica , Genómica , Biología Computacional/métodos , Epigenómica/métodos , Genómica/métodos , Humanos , Riñón , Metabolómica/métodos , Proteómica/métodos , Transcriptoma
5.
Cardiovasc Res ; 118(5): 1232-1246, 2022 03 25.
Artículo en Inglés | MEDLINE | ID: mdl-33913468

RESUMEN

AIMS: Atherosclerotic plaque hypoxia is detrimental for macrophage function. Prolyl hydroxylases (PHDs) initiate cellular hypoxic responses, possibly influencing macrophage function in plaque hypoxia. Thus, we aimed to elucidate the role of myeloid PHDs in atherosclerosis. METHODS AND RESULTS: Myeloid-specific PHD knockout (PHDko) mice were obtained via bone marrow transplantation (PHD1ko, PHD3ko) or conditional knockdown through lysozyme M-driven Cre recombinase (PHD2cko). Mice were fed high cholesterol diet for 6-12 weeks to induce atherosclerosis. Aortic root plaque size was significantly augmented 2.6-fold in PHD2cko, and 1.4-fold in PHD3ko compared to controls but was unchanged in PHD1ko mice. Macrophage apoptosis was promoted in PHD2cko and PHD3ko mice in vitro and in vivo, via the hypoxia-inducible factor (HIF) 1α/BNIP3 axis. Bulk and single-cell RNA data of PHD2cko bone marrow-derived macrophages (BMDMs) and plaque macrophages, respectively, showed enhanced HIF1α/BNIP3 signalling, which was validated in vitro by siRNA silencing. Human plaque BNIP3 mRNA was positively associated with plaque necrotic core size, suggesting similar pro-apoptotic effects in human. Furthermore, PHD2cko plaques displayed enhanced fibrosis, while macrophage collagen breakdown by matrix metalloproteinases, collagen production, and proliferation were unaltered. Instead, PHD2cko BMDMs enhanced fibroblast collagen secretion in a paracrine manner. In silico analysis of macrophage-fibroblast communication predicted SPP1 (osteopontin) signalling as regulator, which was corroborated by enhanced plaque SPP1 protein in vivo. Increased SPP1 mRNA expression upon PHD2cko was preferentially observed in foamy plaque macrophages expressing 'triggering receptor expressed on myeloid cells-2' (TREM2hi) evidenced by single-cell RNA, but not in neutrophils. This confirmed enhanced fibrotic signalling by PHD2cko macrophages to fibroblasts, in vitro as well as in vivo. CONCLUSION: Myeloid PHD2cko and PHD3ko enhanced atherosclerotic plaque growth and macrophage apoptosis, while PHD2cko macrophages further activated collagen secretion by fibroblasts in vitro, likely via paracrine SPP1 signalling through TREM2hi macrophages.


Asunto(s)
Aterosclerosis , Placa Aterosclerótica , Animales , Apoptosis , Aterosclerosis/metabolismo , Colágeno/metabolismo , Fibrosis , Hipoxia/metabolismo , Macrófagos/metabolismo , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Placa Aterosclerótica/metabolismo , ARN/metabolismo , ARN Mensajero/metabolismo
6.
Front Cell Dev Biol ; 9: 695684, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34458258

RESUMEN

BACKGROUND: The protein 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 (PFKFB3) is a key stimulator of glycolytic flux. Systemic, partial PFKFB3 inhibition previously decreased total plaque burden and increased plaque stability. However, it is unclear which cell type conferred these positive effects. Myeloid cells play an important role in atherogenesis, and mainly rely on glycolysis for energy supply. Thus, we studied whether myeloid inhibition of PFKFB3-mediated glycolysis in Ldlr-/-LysMCre+/-Pfkfb3 fl/fl (Pfkfb3 fl/fl ) mice confers beneficial effects on plaque stability and alleviates cardiovascular disease burden compared to Ldlr-/-LysMCre+/-Pfkfb3 wt/wt control mice (Pfkfb3 wt/wt ). METHODS AND RESULTS: Analysis of atherosclerotic human and murine single-cell populations confirmed PFKFB3/Pfkfb3 expression in myeloid cells, but also in lymphocytes, endothelial cells, fibroblasts and smooth muscle cells. Pfkfb3 wt/wt and Pfkfb3 fl/fl mice were fed a 0.25% cholesterol diet for 12 weeks. Pfkfb3 fl/fl bone marrow-derived macrophages (BMDMs) showed 50% knockdown of Pfkfb3 mRNA. As expected based on partial glycolysis inhibition, extracellular acidification rate as a measure of glycolysis was partially reduced in Pfkfb3 fl/fl compared to Pfkfb3 wt/wt BMDMs. Unexpectedly, plaque and necrotic core size, as well as macrophage (MAC3), neutrophil (Ly6G) and collagen (Sirius Red) content were unchanged in advanced Pfkfb3 fl/fl lesions. Similarly, early lesion plaque and necrotic core size and total plaque burden were unaffected. CONCLUSION: Partial myeloid knockdown of PFKFB3 did not affect atherosclerosis development in advanced or early lesions. Previously reported positive effects of systemic, partial PFKFB3 inhibition on lesion stabilization, do not seem conferred by monocytes, macrophages or neutrophils. Instead, other Pfkfb3-expressing cells in atherosclerosis might be responsible, such as DCs, smooth muscle cells or fibroblasts.

7.
Mol Cancer Ther ; 20(6): 1029-1038, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-33846235

RESUMEN

Glioblastoma (GBM) is the most frequent and aggressive primary tumor type in the central nervous system in adults. Resistance to chemotherapy remains one of the major obstacles in GBM treatment. Identifying and overcoming the mechanisms of therapy resistance is instrumental to develop novel therapeutic approaches for patients with GBM. To determine the major drivers of temozolomide (TMZ) sensitivity, we performed shRNA screenings in GBM lines with different O6-methylguanine-DNA methyl-transferase (MGMT) status. We then evaluated dianhydrogalactitol (Val-083), a small alkylating molecule that induces interstrand DNA crosslinking, as a potential treatment to bypass TMZ-resistance mechanisms. We found that loss of mismatch repair (MMR) components and MGMT expression are mutually exclusive mechanisms driving TMZ resistance in vitro Treatment of established GBM cells and tumorsphere lines with Val-083 induces DNA damage and cell-cycle arrest in G2-M phase, independently of MGMT or MMR status, thus circumventing conventional resistance mechanisms to TMZ. Combination of TMZ and Val-083 shows a synergic cytotoxic effect in tumor cells in vitro, ex vivo, and in vivo We propose this combinatorial treatment as a potential approach for patients with GBM.


Asunto(s)
Dianhidrogalactitol/uso terapéutico , Resistencia a Antineoplásicos/efectos de los fármacos , Glioblastoma/tratamiento farmacológico , Temozolomida/farmacología , Animales , Línea Celular Tumoral , Dianhidrogalactitol/farmacología , Humanos , Ratones , Transfección , Ensayos Antitumor por Modelo de Xenoinjerto
8.
Kidney Int ; 99(5): 1127-1139, 2021 05.
Artículo en Inglés | MEDLINE | ID: mdl-33417998

RESUMEN

Understanding why certain patients with IgA nephropathy progress to kidney failure while others maintain normal kidney function remains a major unanswered question. To help answer this, we performed miRNome profiling by next generation sequencing of kidney biopsies in order to identify microRNAs specifically associated with the risk of IgA nephropathy progression. Following sequencing and validation in independent cohorts, four microRNAs (-150-5p, -155-5p, -146b-5p, -135a-5p) were found to be differentially expressed in IgA nephropathy progressors compared to non-progressors, and patients with thin membrane nephropathy, lupus nephritis and membranous nephropathy, and correlated with estimated glomerular filtration rate, proteinuria, and the Oxford MEST-C scores (five histological features that are independent predictors of clinical outcome). Each individual microRNA increased the discrimination score of the International IgAN Prediction Tool, although due to the small number of samples the results did not reach statistical significance. miR-150-5p exhibited the largest amplitude of expression between cohorts and displayed the best discrimination between IgA nephropathy progressors and non-progressors by receiver operating curve analysis (AUC: 0.8). However, expression was similarly upregulated in kidneys with established fibrosis and low estimated glomerular filtration rates at the time of biopsy. Consistent with a more generic role in kidney fibrosis, in situ hybridization revealed that miR-150-5p was found in lymphoid infiltrates, and areas of proliferation and fibrosis consistent with the known drivers of progression. Thus, miR-150-5p may be a potential functional mediator of kidney fibrosis that may add value in predicting risk of progression in IgA nephropathy and other kidney diseases.


Asunto(s)
Glomerulonefritis por IGA , MicroARNs , Biomarcadores , Progresión de la Enfermedad , Tasa de Filtración Glomerular , Glomerulonefritis por IGA/genética , Humanos , Riñón , MicroARNs/genética
9.
Nature ; 589(7841): 281-286, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33176333

RESUMEN

Kidney fibrosis is the hallmark of chronic kidney disease progression; however, at present no antifibrotic therapies exist1-3. The origin, functional heterogeneity and regulation of scar-forming cells that occur during human kidney fibrosis remain poorly understood1,2,4. Here, using single-cell RNA sequencing, we profiled the transcriptomes of cells from the proximal and non-proximal tubules of healthy and fibrotic human kidneys to map the entire human kidney. This analysis enabled us to map all matrix-producing cells at high resolution, and to identify distinct subpopulations of pericytes and fibroblasts as the main cellular sources of scar-forming myofibroblasts during human kidney fibrosis. We used genetic fate-tracing, time-course single-cell RNA sequencing and ATAC-seq (assay for transposase-accessible chromatin using sequencing) experiments in mice, and spatial transcriptomics in human kidney fibrosis, to shed light on the cellular origins and differentiation of human kidney myofibroblasts and their precursors at high resolution. Finally, we used this strategy to detect potential therapeutic targets, and identified NKD2 as a myofibroblast-specific target in human kidney fibrosis.


Asunto(s)
Linaje de la Célula , Fibrosis/patología , Túbulos Renales/patología , Miofibroblastos/patología , Insuficiencia Renal Crónica/patología , Proteínas Adaptadoras Transductoras de Señales/metabolismo , Animales , Proteínas de Unión al Calcio/metabolismo , Estudios de Casos y Controles , Diferenciación Celular , Matriz Extracelular/metabolismo , Matriz Extracelular/patología , Femenino , Fibroblastos/citología , Fibroblastos/metabolismo , Humanos , Masculino , Mesodermo/citología , Mesodermo/patología , Ratones , Miofibroblastos/metabolismo , Pericitos/citología , Pericitos/patología , RNA-Seq , Receptor alfa de Factor de Crecimiento Derivado de Plaquetas/metabolismo , Receptor beta de Factor de Crecimiento Derivado de Plaquetas/metabolismo , Análisis de la Célula Individual , Transcriptoma
10.
Mol Cancer Ther ; 19(8): 1751-1760, 2020 08.
Artículo en Inglés | MEDLINE | ID: mdl-32499301

RESUMEN

Metastasis development is the leading cause of cancer-related mortality in pancreatic ductal adenocarcinoma (PDAC) and yet, few preclinical systems to recapitulate its full spreading process are available. Thus, modeling of tumor progression to metastasis is urgently needed. In this work, we describe the generation of highly metastatic PDAC patient-derived xenograft (PDX) mouse models and subsequent single-cell RNA-sequencing (RNA-seq) of circulating tumor cells (CTC), isolated by human HLA sorting, to identify altered signaling and metabolic pathways, as well as potential therapeutic targets. The mouse models developed liver and lung metastasis with a high reproducibility rate. Isolated CTCs were highly tumorigenic, had metastatic potential, and single-cell RNA-seq showed that their expression profiles clustered separately from those of their matched primary and metastatic tumors and were characterized by low expression of cell-cycle and extracellular matrix-associated genes. CTC transcriptomics identified survivin (BIRC5), a key regulator of mitosis and apoptosis, as one of the highest upregulated genes during metastatic spread. Pharmacologic inhibition of survivin with YM155 or survivin knockdown promoted cell death in organoid models as well as anoikis, suggesting that survivin facilitates cancer cell survival in circulation. Treatment of metastatic PDX models with YM155 alone and in combination with chemotherapy hindered the metastatic development resulting in improved survival. Metastatic PDX mouse model development allowed the identification of survivin as a promising therapeutic target to prevent the metastatic dissemination in PDAC.


Asunto(s)
Biomarcadores de Tumor/genética , Neoplasias Hepáticas/secundario , Neoplasias Pulmonares/secundario , Células Neoplásicas Circulantes/patología , Neoplasias Pancreáticas/patología , Análisis de la Célula Individual/métodos , Transcriptoma , Animales , Apoptosis , Carcinoma Ductal Pancreático/sangre , Carcinoma Ductal Pancreático/genética , Carcinoma Ductal Pancreático/patología , Proliferación Celular , Regulación Neoplásica de la Expresión Génica , Humanos , Neoplasias Hepáticas/sangre , Neoplasias Hepáticas/genética , Neoplasias Pulmonares/sangre , Neoplasias Pulmonares/genética , Ratones , Ratones Endogámicos NOD , Ratones SCID , Neoplasias Pancreáticas/sangre , Neoplasias Pancreáticas/genética , Células Tumorales Cultivadas , Ensayos Antitumor por Modelo de Xenoinjerto
11.
Genome Biol ; 21(1): 36, 2020 02 12.
Artículo en Inglés | MEDLINE | ID: mdl-32051003

RESUMEN

BACKGROUND: Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events and low library sizes. It is thus not clear if functional TF and pathway analysis tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way. RESULTS: To address this question, we perform benchmark studies on simulated and real scRNA-seq data. We include the bulk-RNA tools PROGENy, GO enrichment, and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq. For the in silico study, we simulate single cells from TF/pathway perturbation bulk RNA-seq experiments. We complement the simulated data with real scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on simulated and real data reveal comparable performance to the original bulk data. Additionally, we show that the TF and pathway activities preserve cell type-specific variability by analyzing a mixture sample sequenced with 13 scRNA-seq protocols. We also provide the benchmark data for further use by the community. CONCLUSIONS: Our analyses suggest that bulk-based functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq data, partially outperforming dedicated single-cell tools. Furthermore, we find that the performance of functional analysis tools is more sensitive to the gene sets than to the statistic used.


Asunto(s)
RNA-Seq/métodos , Análisis de la Célula Individual/métodos , Programas Informáticos/normas , Animales , Benchmarking , Redes Reguladoras de Genes , Humanos , RNA-Seq/normas , Análisis de la Célula Individual/normas , Factores de Transcripción/metabolismo , Transcriptoma
12.
Bioinformatics ; 35(22): 4846-4848, 2019 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-31173067

RESUMEN

MOTIVATION: Genetic alterations lead to tumor progression and cell survival but also uncover cancer-specific vulnerabilities on gene dependencies that can be therapeutically exploited. RESULTS: vulcanSpot is a novel computational approach implemented to expand the therapeutic options in cancer beyond known-driver genes unlocking alternative ways to target undruggable genes. The method integrates genome-wide information provided by massive screening experiments to detect genetic vulnerabilities associated to tumors. Then, vulcanSpot prioritizes drugs to target cancer-specific gene dependencies using a weighted scoring system based on well known drug-gene relationships and drug repositioning strategies. AVAILABILITY AND IMPLEMENTATION: http://www.vulcanspot.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Neoplasias , Biología Computacional , Reposicionamiento de Medicamentos , Humanos , Mutación , Programas Informáticos
13.
Cancer Cell ; 35(4): 573-587.e6, 2019 04 15.
Artículo en Inglés | MEDLINE | ID: mdl-30975481

RESUMEN

Five-year survival for pancreatic ductal adenocarcinoma (PDAC) patients remains below 7% due to the lack of effective treatments. Here, we report that combined ablation of EGFR and c-RAF expression results in complete regression of a significant percentage of PDAC tumors driven by Kras/Trp53 mutations in genetically engineered mice. Moreover, systemic elimination of these targets induces toxicities that are well tolerated. Response to this targeted therapy correlates with transcriptional profiles that resemble those observed in human PDACs. Finally, inhibition of EGFR and c-RAF expression effectively blocked tumor progression in nine independent patient-derived xenografts carrying KRAS and TP53 mutations. These results open the door to the development of targeted therapies for PDAC patients.


Asunto(s)
Carcinoma Ductal Pancreático/tratamiento farmacológico , Receptores ErbB/metabolismo , Clorhidrato de Erlotinib/farmacología , Gefitinib/farmacología , Neoplasias Pancreáticas/tratamiento farmacológico , Inhibidores de Proteínas Quinasas/farmacología , Proteínas Proto-Oncogénicas c-raf/antagonistas & inhibidores , Animales , Apoptosis/efectos de los fármacos , Carcinoma Ductal Pancreático/enzimología , Carcinoma Ductal Pancreático/genética , Carcinoma Ductal Pancreático/patología , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , Receptores ErbB/antagonistas & inhibidores , Receptores ErbB/genética , Regulación Neoplásica de la Expresión Génica , Humanos , Ratones de la Cepa 129 , Ratones Endogámicos C57BL , Ratones Transgénicos , Mutación , Neoplasias Pancreáticas/enzimología , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/patología , Proteínas Proto-Oncogénicas c-raf/genética , Proteínas Proto-Oncogénicas c-raf/metabolismo , Proteínas Proto-Oncogénicas p21(ras)/genética , Proteínas Proto-Oncogénicas p21(ras)/metabolismo , Transducción de Señal , Carga Tumoral/efectos de los fármacos , Proteína p53 Supresora de Tumor/genética , Ensayos Antitumor por Modelo de Xenoinjerto
14.
Sci Rep ; 9(1): 975, 2019 01 30.
Artículo en Inglés | MEDLINE | ID: mdl-30700761

RESUMEN

Chronic lymphocytic leukaemia is the most prevalent leukaemia in Western countries. It is an incurable disease characterized by a highly variable clinical course. Chronic lymphocytic leukaemia is an ideal model for studying clonal heterogeneity and dynamics during cancer progression, response to therapy and/or relapse because the disease usually develops over several years. Here we report an analysis by deep sequencing of sequential samples taken at different times from the affected organs of two patients with 12- and 7-year disease courses, respectively. One of the patients followed a linear pattern of clonal evolution, acquiring and selecting new mutations in response to salvage therapy and/or allogeneic transplantation, while the other suffered loss of cellular tumoral clones during progression and histological transformation.


Asunto(s)
Evolución Clonal , Leucemia Linfocítica Crónica de Células B/patología , Células Clonales , Resultado Fatal , Frecuencia de los Genes/genética , Humanos , Leucemia Linfocítica Crónica de Células B/genética , Masculino , Persona de Mediana Edad , Mutagénesis/genética , Mutación/genética , Secuenciación del Exoma
15.
Genome Med ; 10(1): 41, 2018 05 31.
Artículo en Inglés | MEDLINE | ID: mdl-29848362

RESUMEN

BACKGROUND: Large-sequencing cancer genome projects have shown that tumors have thousands of molecular alterations and their frequency is highly heterogeneous. In such scenarios, physicians and oncologists routinely face lists of cancer genomic alterations where only a minority of them are relevant biomarkers to drive clinical decision-making. For this reason, the medical community agrees on the urgent need of methodologies to establish the relevance of tumor alterations, assisting in genomic profile interpretation, and, more importantly, to prioritize those that could be clinically actionable for cancer therapy. RESULTS: We present PanDrugs, a new computational methodology to guide the selection of personalized treatments in cancer patients using the variant lists provided by genome-wide sequencing analyses. PanDrugs offers the largest database of drug-target associations available from well-known targeted therapies to preclinical drugs. Scoring data-driven gene cancer relevance and drug feasibility PanDrugs interprets genomic alterations and provides a prioritized evidence-based list of anticancer therapies. Our tool represents the first drug prescription strategy applying a rational based on pathway context, multi-gene markers impact and information provided by functional experiments. Our approach has been systematically applied to TCGA patients and successfully validated in a cancer case study with a xenograft mouse model demonstrating its utility. CONCLUSIONS: PanDrugs is a feasible method to identify potentially druggable molecular alterations and prioritize drugs to facilitate the interpretation of genomic landscape and clinical decision-making in cancer patients. Our approach expands the search of druggable genomic alterations from the concept of cancer driver genes to the druggable pathway context extending anticancer therapeutic options beyond already known cancer genes. The methodology is public and easily integratable with custom pipelines through its programmatic API or its docker image. The PanDrugs webtool is freely accessible at http://www.pandrugs.org .


Asunto(s)
Antineoplásicos/uso terapéutico , Biología Computacional/métodos , Genómica , Neoplasias/tratamiento farmacológico , Neoplasias/genética , Medicina de Precisión , Simulación por Computador , Genoma Humano , Humanos
16.
Public Health Genomics ; 20(2): 81-91, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28858862

RESUMEN

Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer-related death among solid malignancies. Unfortunately, PDAC lethality has not substantially decreased over the past 20 years. This aggressiveness is related to the genomic complexity and heterogeneity of PDAC, but also to the absence of an effective screening for the detection of early-stage tumors and a lack of efficient therapeutic options. Therefore, there is an urgent need to improve the arsenal of anti-PDAC drugs for an effective treatment of these patients. Patient-derived xenograft (PDX) mouse models represent a promising strategy to personalize PDAC treatment, offering a bench testing of candidate treatments and helping to select empirical treatments in PDAC patients with no therapeutic targets. Moreover, bioinformatics-based approaches have the potential to offer systematic insights into PDAC etiology predicting putatively actionable tumor-specific genomic alterations, identifying novel biomarkers and generating disease-associated gene expression signatures. This review focuses on recent efforts to individualize PDAC treatments using PDX models. Additionally, we discuss the current understanding of the PDAC genomic landscape and the putative druggable targets derived from mutational studies. PDAC molecular subclassifications and gene expression profiling studies are reviewed as well. Finally, latest bioinformatics methodologies based on somatic variant detection and prioritization, in silico drug response prediction, and drug repositioning to improve the treatment of advanced PDAC tumors are also covered.


Asunto(s)
Antineoplásicos/uso terapéutico , Carcinoma Ductal Pancreático , Neoplasias Pancreáticas , Medicina de Precisión/métodos , Ensayos Antitumor por Modelo de Xenoinjerto , Animales , Carcinoma Ductal Pancreático/tratamiento farmacológico , Carcinoma Ductal Pancreático/genética , Biología Computacional , Modelos Animales de Enfermedad , Perfilación de la Expresión Génica/métodos , Regulación de la Expresión Génica/efectos de los fármacos , Genómica , Humanos , Ratones , Neoplasias Pancreáticas/tratamiento farmacológico , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas
17.
Nat Genet ; 49(6): 866-875, 2017 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-28436985

RESUMEN

The identity of the RNA-binding proteins (RBPs) that govern cancer stem cells remains poorly characterized. The MSI2 RBP is a central regulator of translation of cancer stem cell programs. Through proteomic analysis of the MSI2-interacting RBP network and functional shRNA screening, we identified 24 genes required for in vivo leukemia. Syncrip was the most differentially required gene between normal and myeloid leukemia cells. SYNCRIP depletion increased apoptosis and differentiation while delaying leukemogenesis. Gene expression profiling of SYNCRIP-depleted cells demonstrated a loss of the MLL and HOXA9 leukemia stem cell program. SYNCRIP and MSI2 interact indirectly though shared mRNA targets. SYNCRIP maintains HOXA9 translation, and MSI2 or HOXA9 overexpression rescued the effects of SYNCRIP depletion. Altogether, our data identify SYNCRIP as a new RBP that controls the myeloid leukemia stem cell program. We propose that targeting these RBP complexes might provide a novel therapeutic strategy in leukemia.


Asunto(s)
Regulación Leucémica de la Expresión Génica , Ribonucleoproteínas Nucleares Heterogéneas/genética , Leucemia Mieloide/genética , Proteínas de Unión al ARN/metabolismo , Animales , Supervivencia Celular , Femenino , Hematopoyesis/genética , Ribonucleoproteínas Nucleares Heterogéneas/metabolismo , Proteínas de Homeodominio/genética , Humanos , Leucemia Bifenotípica Aguda/genética , Leucemia Bifenotípica Aguda/patología , Leucemia Mieloide/patología , Ratones Endogámicos C57BL , Ratones Noqueados , Células Progenitoras Mieloides/metabolismo , Células Progenitoras Mieloides/patología , ARN Interferente Pequeño , Proteínas de Unión al ARN/genética , Ensayos Antitumor por Modelo de Xenoinjerto
18.
Clin Cancer Res ; 23(5): 1334-1345, 2017 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-27620278

RESUMEN

Purpose: Medullary thyroid carcinoma (MTC) is a rare disease with few genetic drivers, and the etiology specific to each known susceptibility mutation remains unknown. Exploiting multilayer genomic data, we focused our interest on the role of aberrant DNA methylation in MTC development.Experimental Design: We performed genome-wide DNA methylation profiling assessing more than 27,000 CpGs in the largest MTC series reported to date, comprising 48 molecularly characterized tumors. mRNA and miRNA expression data were available for 33 and 31 tumors, respectively. Two human MTC cell lines and 101 paraffin-embedded MTCs were used for validation.Results: The most distinctive methylome was observed for RETM918T-related tumors. Integration of methylation data with mRNA and miRNA expression data identified genes negatively regulated by promoter methylation. These in silico findings were confirmed in vitro for PLCB2, DKK4, MMP20, and miR-10a, -30a, and -200c. The mutation-specific aberrant methylation of PLCB2, DKK4, and MMP20 was validated in 25 independent MTCs by bisulfite pyrosequencing. The methylome and transcriptome data underscored JAK/Stat pathway involvement in RETM918T MTCs. Immunostaining [immunohistochemistry (IHC)] for the active form of signaling effector STAT3 was performed in a series of 101 MTCs. As expected, positive IHC was associated with RETM918T-bearing tumors (P < 0.02). Pharmacologic inhibition of STAT3 activity increased the sensitivity to vandetanib of the RETM918T-positive MTC cell line, MZ-CRC-1.Conclusions: Multilayer OMIC data analysis uncovered methylation hallmarks in genetically defined MTCs and revealed JAK/Stat signaling effector STAT3 as a potential therapeutic target for the treatment of RETM918T MTCs. Clin Cancer Res; 23(5); 1334-45. ©2016 AACR.


Asunto(s)
Carcinoma Neuroendocrino/genética , Metilación de ADN/genética , Proteínas Proto-Oncogénicas c-ret/genética , Factor de Transcripción STAT3/genética , Neoplasias de la Tiroides/genética , Carcinoma Neuroendocrino/tratamiento farmacológico , Carcinoma Neuroendocrino/patología , Femenino , Regulación Neoplásica de la Expresión Génica/genética , Genoma Humano , Genómica , Humanos , Masculino , Mutación , Piperidinas/administración & dosificación , Quinazolinas/administración & dosificación , Transducción de Señal/genética , Neoplasias de la Tiroides/tratamiento farmacológico , Neoplasias de la Tiroides/patología
19.
Cancer Discov ; 6(4): 368-81, 2016 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-26951227

RESUMEN

UNLABELLED: Somatic mutations in calreticulin (CALR) are present in approximately 40% of patients with myeloproliferative neoplasms (MPN), but the mechanism by which mutant CALR is oncogenic remains unclear. Here, we demonstrate that expression of mutant CALR alone is sufficient to engender MPN in mice and recapitulates the disease phenotype of patients with CALR-mutant MPN. We further show that the thrombopoietin receptor MPL is required for mutant CALR-driven transformation through JAK-STAT pathway activation, thus rendering mutant CALR-transformed hematopoietic cells sensitive to JAK2 inhibition. Finally, we demonstrate that the oncogenicity of mutant CALR is dependent on the positive electrostatic charge of the C-terminus of the mutant protein, which is necessary for physical interaction between mutant CALR and MPL. Together, our findings elucidate a novel paradigm of cancer pathogenesis and reveal how CALR mutations induce MPN. SIGNIFICANCE: The mechanism by which CALR mutations induce MPN remains unknown. In this report, we show that the positive charge of the CALR mutant C-terminus is necessary to transform hematopoietic cells by enabling binding between mutant CALR and the thrombopoietin receptor MPL.


Asunto(s)
Calreticulina/genética , Transformación Celular Neoplásica/genética , Mutación , Dominios y Motivos de Interacción de Proteínas/genética , Receptores de Trombopoyetina/genética , Animales , Secuencia de Bases , Trasplante de Médula Ósea , Calreticulina/química , Calreticulina/metabolismo , Línea Celular , Transformación Celular Neoplásica/metabolismo , Modelos Animales de Enfermedad , Femenino , Mutación del Sistema de Lectura , Células Madre Hematopoyéticas/metabolismo , Células Madre Hematopoyéticas/patología , Humanos , Quinasas Janus/antagonistas & inhibidores , Quinasas Janus/metabolismo , Ratones , Trastornos Mieloproliferativos/genética , Trastornos Mieloproliferativos/metabolismo , Trastornos Mieloproliferativos/patología , Fenotipo , Unión Proteica , Inhibidores de Proteínas Quinasas/farmacología , Receptores de Trombopoyetina/metabolismo , Factores de Transcripción STAT/metabolismo , Transducción de Señal , Colapso de la Estructura
20.
Cancer Res ; 75(19): 4119-30, 2015 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-26282166

RESUMEN

The presence of differentiated thyroid cells in thyroid cancer is critical for the antitumor response to radioactive iodide treatment, and loss of the differentiated phenotype is a key hallmark of iodide-refractory metastatic disease. The role of microRNAs (miRNA) in fine-tuning gene expression has become a major regulatory mechanism by which developmental and pathologic processes occur. In this study, we performed next-generation sequencing and expression analysis of eight papillary thyroid carcinomas (PTC) to comprehensively characterize miRNAs involved in loss of differentiation. We found that only a small set of abundant miRNAs is differentially expressed between PTC tissue and normal tissue from the same patient. In addition, we integrated computational prediction of potential targets and mRNA sequencing and identified a master miRNA regulatory network involved in essential biologic processes such as thyroid differentiation. Both mature products of mir-146b (miR-146b-5p and -3p) were among the most abundantly expressed miRNAs in tumors. Specifically, we found that miR-146b-3p binds to the 3'-untranslated region of PAX8 and sodium/iodide symporter (NIS), leading to impaired protein translation and a subsequent reduction in iodide uptake. Furthermore, our findings show that miR-146b and PAX8 regulate each other and share common target genes, thus highlighting a novel regulatory circuit that governs the differentiated phenotype of PTC. In conclusion, our study has uncovered the existence of a miR-146b-3p/PAX8/NIS regulatory circuit that may be exploited therapeutically to modulate thyroid cell differentiation and iodide uptake for improved treatment of advanced thyroid cancer.


Asunto(s)
Carcinoma Papilar/metabolismo , Regulación Neoplásica de la Expresión Génica , Redes Reguladoras de Genes , Yoduros/metabolismo , MicroARNs/fisiología , Proteínas de Neoplasias/fisiología , Factores de Transcripción Paired Box/fisiología , ARN Neoplásico/fisiología , Simportadores/fisiología , Neoplasias de la Tiroides/metabolismo , Regiones no Traducidas 3' , Transporte Biológico , Carcinoma Papilar/patología , Diferenciación Celular , Línea Celular Tumoral , Transformación Celular Neoplásica , Femenino , Humanos , MicroARNs/genética , Factor de Transcripción PAX8 , Factores de Transcripción Paired Box/antagonistas & inhibidores , Factores de Transcripción Paired Box/genética , Fenotipo , ARN/metabolismo , Interferencia de ARN , Glándula Tiroides/metabolismo , Neoplasias de la Tiroides/patología , Transfección
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