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SUMMARY: We developed BIODICA, an integrated computational environment for application of independent component analysis (ICA) to bulk and single-cell molecular profiles, interpretation of the results in terms of biological functions and correlation with metadata. The computational core is the novel Python package stabilized-ica which provides interface to several ICA algorithms, a stabilization procedure, meta-analysis and component interpretation tools. BIODICA is equipped with a user-friendly graphical user interface, allowing non-experienced users to perform the ICA-based omics data analysis. The results are provided in interactive ways, thus facilitating communication with biology experts. AVAILABILITY AND IMPLEMENTATION: BIODICA is implemented in Java, Python and JavaScript. The source code is freely available on GitHub under the MIT and the GNU LGPL licenses. BIODICA is supported on all major operating systems. URL: https://sysbio-curie.github.io/biodica-environment/.
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Algoritmos , Programas Informáticos , Biología Computacional/métodos , MetadatosRESUMEN
Ewing sarcoma (EwS) is a highly aggressive pediatric bone cancer that is defined by a somatic fusion between the EWSR1 gene and an ETS family member, most frequently the FLI1 gene, leading to expression of a chimeric transcription factor EWSR1-FLI1. Otherwise, EwS is one of the most genetically stable cancers. The situation when the major cancer driver is well known looks like a unique opportunity for applying the systems biology approach in order to understand the EwS mechanisms as well as to uncover some general mechanistic principles of carcinogenesis. A number of studies have been performed revealing the direct and indirect effects of EWSR1-FLI1 on multiple aspects of cellular life. Nevertheless, the emerging picture of the oncogene action appears to be highly complex and systemic, with multiple reciprocal influences between the immediate consequences of the driver mutation and intracellular and intercellular molecular mechanisms, including regulation of transcription, epigenome, and tumoral microenvironment. In this chapter, we present an overview of existing molecular profiling resources available for EwS tumors and cell lines and provide an online comprehensive catalogue of publicly available omics and other datasets. We further highlight the systems biology studies of EwS, involving mathematical modeling of networks and integration of molecular data. We conclude that despite the seeming simplicity, a lot has yet to be understood on the systems-wide mechanisms connecting the driver mutation and the major cellular phenotypes of this pediatric cancer. Overall, this chapter can serve as a guide for a systems biology researcher to start working on EwS.
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Neoplasias Óseas/etiología , Neoplasias Óseas/metabolismo , Sarcoma de Ewing/etiología , Sarcoma de Ewing/metabolismo , Biología de Sistemas , Neoplasias Óseas/patología , Bases de Datos Genéticas , Genómica/métodos , Humanos , Metabolómica/métodos , Modelos Teóricos , Proteómica/métodos , Sarcoma de Ewing/patología , Biología de Sistemas/métodos , Navegador WebRESUMEN
PURPOSE: Diffuse intrinsic pontine gliomas (DIPG) are the most severe pediatric brain tumors. Although accepted as the standard therapeutic, radiotherapy is only efficient transiently and not even in every patient. The goal of the study was to identify the underlying molecular determinants of response to radiotherapy in DIPG. EXPERIMENTAL DESIGN: We assessed in vitro response to ionizing radiations in 13 different DIPG cellular models derived from treatment-naïve stereotactic biopsies reflecting the genotype variability encountered in patients at diagnosis and correlated it to their principal molecular alterations. Clinical and radiologic response to radiotherapy of a large cohort of 73 DIPG was analyzed according to their genotype. Using a kinome-wide synthetic lethality RNAi screen, we further identified target genes that can sensitize DIPG cells to ionizing radiations. RESULTS: We uncover TP53 mutation as the main driver of increased radioresistance and validated this finding in four isogenic pairs of TP53WT DIPG cells with or without TP53 knockdown. In an integrated clinical, radiological, and molecular study, we show that TP53MUT DIPG patients respond less to irradiation, relapse earlier after radiotherapy, and have a worse prognosis than their TP53WT counterparts. Finally, a kinome-wide synthetic lethality RNAi screen identifies CHK1 as a potential target, whose inhibition increases response to radiation specifically in TP53MUT cells. CONCLUSIONS: Here, we demonstrate that TP53 mutations are driving DIPG radioresistance both in patients and corresponding cellular models. We suggest alternative treatment strategies to mitigate radioresistance with CHK1 inhibitors. These findings will allow to consequently refine radiotherapy schedules in DIPG.
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Neoplasias del Tronco Encefálico/metabolismo , Glioma Pontino Intrínseco Difuso/metabolismo , Tolerancia a Radiación , Transducción de Señal , Proteína p53 Supresora de Tumor/metabolismo , Neoplasias del Tronco Encefálico/genética , Neoplasias del Tronco Encefálico/mortalidad , Neoplasias del Tronco Encefálico/radioterapia , Ciclo Celular/genética , Ciclo Celular/efectos de la radiación , Línea Celular Tumoral , Supervivencia Celular/efectos de la radiación , Glioma Pontino Intrínseco Difuso/genética , Glioma Pontino Intrínseco Difuso/mortalidad , Glioma Pontino Intrínseco Difuso/radioterapia , Relación Dosis-Respuesta en la Radiación , Técnicas de Silenciamiento del Gen , Histonas/genética , Histonas/metabolismo , Humanos , Mutación , Células Madre Neoplásicas/metabolismo , Células Madre Neoplásicas/efectos de la radiación , Pronóstico , Interferencia de ARN , ARN Interferente Pequeño/genética , Tolerancia a Radiación/genética , Proteína p53 Supresora de Tumor/genéticaRESUMEN
Diffuse intrinsic pontine glioma (or DIPG) are pediatric high-grade gliomas associated with a dismal prognosis. They harbor specific substitution in histone H3 at position K27 that induces major epigenetic dysregulations. Most clinical trials failed so far to increase survival, and radiotherapy remains the most efficient treatment, despite only transient tumor control. We conducted the first lentiviral shRNA dropout screen in newly diagnosed DIPG to generate a cancer-lethal signature as a basis for the development of specific treatments with increased efficacy and reduced side effects compared to existing anticancer therapies. The analysis uncovered 41 DIPG essential genes among the 672 genes of human kinases tested, for which several distinct interfering RNAs impaired cell expansion of three different DIPG stem-cell cultures without deleterious effect on two control neural stem cells. Among them, PLK1, AURKB, CHEK1, EGFR, and GSK3A were previously identified by similar approach in adult GBM indicating common dependencies of these cancer cells and pediatric gliomas. As expected, we observed an enrichment of genes involved in proliferation and cell death processes with a significant number of candidates belonging to PTEN/PI3K/AKT and EGFR pathways already under scrutiny in clinical trials in this disease. We highlighted VRK3, a gene involved especially in cell cycle regulation, DNA repair, and neuronal differentiation, as a non-oncogenic addiction in DIPG. Its repression totally blocked DIPG cell growth in the four cellular models evaluated, and induced cell death in H3.3-K27M cells specifically but not in H3.1-K27M cells, supporting VRK3 as an interesting and promising target in DIPG.
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Neoplasias del Tronco Encefálico/genética , Glioma Pontino Intrínseco Difuso/genética , Fosfotransferasas/genética , Proteínas Serina-Treonina Quinasas/fisiología , ARN Interferente Pequeño/fisiología , Análisis de Secuencia de ARN/métodos , Neoplasias del Tronco Encefálico/diagnóstico , Neoplasias del Tronco Encefálico/patología , Supervivencia Celular/genética , Células Cultivadas , Glioma Pontino Intrínseco Difuso/diagnóstico , Glioma Pontino Intrínseco Difuso/patología , Genes Esenciales , Células HEK293 , Humanos , Fosfatidilinositol 3-Quinasas/análisis , Fosfatidilinositol 3-Quinasas/genética , Fosfotransferasas/análisis , Pronóstico , Proteínas Serina-Treonina Quinasas/análisis , Proteínas Serina-Treonina Quinasas/genética , ARN Interferente Pequeño/análisisRESUMEN
Diffuse midline glioma (DMG), H3 K27M-mutant, is a new entity in the updated WHO classification grouping together diffuse intrinsic pontine gliomas and infiltrating glial neoplasms of the midline harboring the same canonical mutation at the Lysine 27 of the histones H3 tail.Two hundred and fifteen patients younger than 18 years old with centrally-reviewed pediatric high-grade gliomas (pHGG) were included in this study. Comprehensive transcriptomic (n = 140) and methylation (n = 80) profiling was performed depending on the material available, in order to assess the biological uniqueness of this new entity compared to other midline and hemispheric pHGG.Tumor classification based on gene expression (GE) data highlighted the similarity of K27M DMG independently of their location along the midline. T-distributed Stochastic Neighbor Embedding (tSNE) analysis of methylation profiling confirms the discrimination of DMG from other well defined supratentorial tumor subgroups. Patients with diffuse intrinsic pontine gliomas (DIPG) and thalamic DMG exhibited a similarly poor prognosis (11.1 and 10.8 months median overall survival, respectively). Interestingly, H3.1-K27M and H3.3-K27M primary tumor samples could be distinguished based both on their GE and DNA methylation profiles, suggesting that they might arise from a different precursor or from a different epigenetic reorganization.These differences in DNA methylation profiles were conserved in glioma stem-like cell culture models of DIPG which mimicked their corresponding primary tumor. ChIP-seq profiling of H3K27me3 in these models indicate that H3.3-K27M mutated DIPG stem cells exhibit higher levels of H3K27 trimethylation which are correlated with fewer genes expressed by RNAseq. When considering the global distribution of the H3K27me3 mark, we observed that intergenic regions were more trimethylated in the H3.3-K27M mutated cells compared to the H3.1-K27M mutated ones.H3 K27M-mutant DMG represent a homogenous group of neoplasms compared to other pediatric gliomas that could be further separated based on the type of histone H3 variant mutated and their respective epigenetic landscapes. As these characteristics drive different phenotypes, these findings may have important implication for the design of future trials in these specific types of neoplasms.
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Neoplasias Encefálicas/genética , Epigenómica , Glioma/genética , Histonas/genética , Mutación/genética , Transcriptoma/fisiología , Adolescente , Encéfalo/patología , Neoplasias Encefálicas/patología , Niño , Preescolar , Metilación de ADN/genética , Femenino , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica/genética , Glioma/patología , Humanos , Lisina/genética , Masculino , Metionina/genética , Análisis de Componente Principal , Células Tumorales CultivadasRESUMEN
The cytidine analogues azacytidine and 5-aza-2'-deoxycytidine (decitabine) are commonly used to treat myelodysplastic syndromes, with or without a myeloproliferative component. It remains unclear whether the response to these hypomethylating agents results from a cytotoxic or an epigenetic effect. In this study, we address this question in chronic myelomonocytic leukaemia. We describe a comprehensive analysis of the mutational landscape of these tumours, combining whole-exome and whole-genome sequencing. We identify an average of 14±5 somatic mutations in coding sequences of sorted monocyte DNA and the signatures of three mutational processes. Serial sequencing demonstrates that the response to hypomethylating agents is associated with changes in DNA methylation and gene expression, without any decrease in the mutation allele burden, nor prevention of new genetic alteration occurence. Our findings indicate that cytosine analogues restore a balanced haematopoiesis without decreasing the size of the mutated clone, arguing for a predominantly epigenetic effect.
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Antimetabolitos Antineoplásicos/farmacología , Azacitidina/análogos & derivados , Azacitidina/farmacología , Supervivencia Celular/efectos de los fármacos , Metilación de ADN/efectos de los fármacos , Epigénesis Genética/efectos de los fármacos , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Leucemia Mielomonocítica Crónica/genética , Mutación , Anciano , Anciano de 80 o más Años , Alelos , Antimetabolitos Antineoplásicos/uso terapéutico , Azacitidina/uso terapéutico , Decitabina , Femenino , Células HEK293 , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Leucemia Mielomonocítica Crónica/tratamiento farmacológico , Masculino , Persona de Mediana Edad , Análisis de Secuencia de ADN , Análisis de Secuencia de ARNRESUMEN
No major predisposition gene for familial myeloproliferative neoplasms (MPN) has been identified. Here we demonstrate that the autosomal dominant transmission of a 700-kb duplication in four genetically related families predisposes to myeloid malignancies, including MPN, frequently progressing to leukemia. Using induced pluripotent stem cells and primary cells, we demonstrate that overexpression of ATG2B and GSKIP enhances hematopoietic progenitor differentiation, including of megakaryocytes, by increasing progenitor sensitivity to thrombopoietin (TPO). ATG2B and GSKIP cooperate with acquired JAK2, MPL and CALR mutations during MPN development. Thus, the germline duplication may change the fitness of cells harboring signaling pathway mutations and increases the probability of disease development.