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1.
Mol Cell ; 82(13): 2458-2471.e9, 2022 07 07.
Article in English | MEDLINE | ID: mdl-35550257

ABSTRACT

Many cancers are characterized by gene fusions encoding oncogenic chimeric transcription factors (TFs) such as EWS::FLI1 in Ewing sarcoma (EwS). Here, we find that EWS::FLI1 induces the robust expression of a specific set of novel spliced and polyadenylated transcripts within otherwise transcriptionally silent regions of the genome. These neogenes (NGs) are virtually undetectable in large collections of normal tissues or non-EwS tumors and can be silenced by CRISPR interference at regulatory EWS::FLI1-bound microsatellites. Ribosome profiling and proteomics further show that some NGs are translated into highly EwS-specific peptides. More generally, we show that hundreds of NGs can be detected in diverse cancers characterized by chimeric TFs. Altogether, this study identifies the transcription, processing, and translation of novel, specific, highly expressed multi-exonic transcripts from otherwise silent regions of the genome as a new activity of aberrant TFs in cancer.


Subject(s)
Carcinogenesis , Gene Expression Regulation, Neoplastic , Oncogene Proteins, Fusion , Proto-Oncogene Protein c-fli-1 , Transcription Factors , Carcinogenesis/genetics , Cell Line, Tumor , Gene Expression Regulation, Neoplastic/genetics , Gene Silencing , Genome/genetics , Genomics , Humans , Oncogene Proteins, Fusion/genetics , Oncogene Proteins, Fusion/metabolism , Oncogenes/genetics , Proto-Oncogene Protein c-fli-1/genetics , Proto-Oncogene Protein c-fli-1/metabolism , Sarcoma, Ewing/genetics , Sarcoma, Ewing/metabolism , Sarcoma, Ewing/pathology , Transcription Factors/genetics , Transcription, Genetic/genetics
2.
Cell ; 153(5): 1064-79, 2013 May 23.
Article in English | MEDLINE | ID: mdl-23706743

ABSTRACT

Metabolic adaptation is essential for cell survival during nutrient deprivation. We report that eukaryotic elongation factor 2 kinase (eEF2K), which is activated by AMP-kinase (AMPK), confers cell survival under acute nutrient depletion by blocking translation elongation. Tumor cells exploit this pathway to adapt to nutrient deprivation by reactivating the AMPK-eEF2K axis. Adaptation of transformed cells to nutrient withdrawal is severely compromised in cells lacking eEF2K. Moreover, eEF2K knockdown restored sensitivity to acute nutrient deprivation in highly resistant human tumor cell lines. In vivo, overexpression of eEF2K rendered murine tumors remarkably resistant to caloric restriction. Expression of eEF2K strongly correlated with overall survival in human medulloblastoma and glioblastoma multiforme. Finally, C. elegans strains deficient in efk-1, the eEF2K ortholog, were severely compromised in their response to nutrient depletion. Our data highlight a conserved role for eEF2K in protecting cells from nutrient deprivation and in conferring tumor cell adaptation to metabolic stress. PAPERCLIP:


Subject(s)
Caenorhabditis elegans/metabolism , Elongation Factor 2 Kinase/metabolism , Neoplasms/physiopathology , Peptide Chain Elongation, Translational , Signal Transduction , AMP-Activated Protein Kinases/metabolism , Animals , Brain Neoplasms/physiopathology , Caenorhabditis elegans/genetics , Cell Survival , Cell Transformation, Neoplastic , Elongation Factor 2 Kinase/genetics , Food Deprivation , Glioblastoma/physiopathology , HeLa Cells , Humans , Mice , Mice, Nude , NIH 3T3 Cells , Neoplasm Transplantation , Peptide Elongation Factor 2/metabolism , Transplantation, Heterologous
3.
Nature ; 609(7929): 1021-1028, 2022 09.
Article in English | MEDLINE | ID: mdl-36131014

ABSTRACT

Medulloblastoma (MB) comprises a group of heterogeneous paediatric embryonal neoplasms of the hindbrain with strong links to early development of the hindbrain1-4. Mutations that activate Sonic hedgehog signalling lead to Sonic hedgehog MB in the upper rhombic lip (RL) granule cell lineage5-8. By contrast, mutations that activate WNT signalling lead to WNT MB in the lower RL9,10. However, little is known about the more commonly occurring group 4 (G4) MB, which is thought to arise in the unipolar brush cell lineage3,4. Here we demonstrate that somatic mutations that cause G4 MB converge on the core binding factor alpha (CBFA) complex and mutually exclusive alterations that affect CBFA2T2, CBFA2T3, PRDM6, UTX and OTX2. CBFA2T2 is expressed early in the progenitor cells of the cerebellar RL subventricular zone in Homo sapiens, and G4 MB transcriptionally resembles these progenitors but are stalled in developmental time. Knockdown of OTX2 in model systems relieves this differentiation blockade, which allows MB cells to spontaneously proceed along normal developmental differentiation trajectories. The specific nature of the split human RL, which is destined to generate most of the neurons in the human brain, and its high level of susceptible EOMES+KI67+ unipolar brush cell progenitor cells probably predisposes our species to the development of G4 MB.


Subject(s)
Cell Differentiation , Cerebellar Neoplasms , Medulloblastoma , Metencephalon , Cell Differentiation/genetics , Cell Lineage , Cerebellar Neoplasms/classification , Cerebellar Neoplasms/genetics , Cerebellar Neoplasms/pathology , Cerebellum/embryology , Cerebellum/pathology , Core Binding Factor alpha Subunits/genetics , Hedgehog Proteins/metabolism , Histone Demethylases , Humans , Ki-67 Antigen/metabolism , Medulloblastoma/classification , Medulloblastoma/genetics , Medulloblastoma/pathology , Metencephalon/embryology , Metencephalon/pathology , Muscle Proteins , Mutation , Otx Transcription Factors/deficiency , Otx Transcription Factors/genetics , Repressor Proteins , T-Box Domain Proteins/metabolism , Transcription Factors
4.
Am J Hum Genet ; 108(9): 1590-1610, 2021 09 02.
Article in English | MEDLINE | ID: mdl-34390653

ABSTRACT

Our study investigated the underlying mechanism for the 14q24 renal cell carcinoma (RCC) susceptibility risk locus identified by a genome-wide association study (GWAS). The sentinel single-nucleotide polymorphism (SNP), rs4903064, at 14q24 confers an allele-specific effect on expression of the double PHD fingers 3 (DPF3) of the BAF SWI/SNF complex as assessed by massively parallel reporter assay, confirmatory luciferase assays, and eQTL analyses. Overexpression of DPF3 in renal cell lines increases growth rates and alters chromatin accessibility and gene expression, leading to inhibition of apoptosis and activation of oncogenic pathways. siRNA interference of multiple DPF3-deregulated genes reduces growth. Our results indicate that germline variation in DPF3, a component of the BAF complex, part of the SWI/SNF complexes, can lead to reduced apoptosis and activation of the STAT3 pathway, both critical in RCC carcinogenesis. In addition, we show that altered DPF3 expression in the 14q24 RCC locus could influence the effectiveness of immunotherapy treatment for RCC by regulating tumor cytokine secretion and immune cell activation.


Subject(s)
Carcinoma, Renal Cell/genetics , Chromosomes, Human, Pair 14 , DNA-Binding Proteins/genetics , Genetic Loci , Kidney Neoplasms/genetics , STAT3 Transcription Factor/genetics , Transcription Factors/genetics , Carcinogenesis/genetics , Carcinogenesis/immunology , Carcinogenesis/pathology , Carcinoma, Renal Cell/immunology , Carcinoma, Renal Cell/pathology , Carcinoma, Renal Cell/therapy , Cell Line, Tumor , Chromatin/chemistry , Chromatin/immunology , Chromatin Assembly and Disassembly/immunology , Cytokines/genetics , Cytokines/immunology , DNA-Binding Proteins/immunology , Gene Expression Regulation , Genetic Predisposition to Disease , Genome, Human , Genome-Wide Association Study , High-Throughput Nucleotide Sequencing , Humans , Immunotherapy/methods , Kidney Neoplasms/immunology , Kidney Neoplasms/pathology , Kidney Neoplasms/therapy , Polymorphism, Single Nucleotide , STAT3 Transcription Factor/immunology , T-Lymphocytes, Cytotoxic , Transcription Factors/immunology
5.
J Med Genet ; 60(12): 1206-1209, 2023 Nov 27.
Article in English | MEDLINE | ID: mdl-37263769

ABSTRACT

BRCA1 and BRCA2 are tumour suppressor genes that have been characterised as predisposition genes for the development of hereditary breast and ovarian cancers among other malignancies. The molecular diagnosis of this predisposition syndrome is based on the detection of inactivating variants of any type in those genes. But in the case of structural variants, functional consequences can be difficult to assess using standard molecular methods, as the precise resolution of their sequence is often impossible with short-read next generation sequencing techniques. It has been recently demonstrated that Oxford Nanopore long-read sequencing technology can accurately and rapidly provide genetic diagnoses of Mendelian diseases, including those linked to pathogenic structural variants. Here, we report the accurate resolution of a germline duplication event of exons 18-20 of BRCA1 using Nanopore sequencing with adaptive sampling target enrichment. This allowed us to classify this variant as pathogenic within a short timeframe of 10 days. This study provides a proof-of-concept that nanopore adaptive sampling is a highly efficient technique for the investigation of structural variants of tumour suppressor genes in a clinical context.


Subject(s)
Breast Neoplasms , Nanopore Sequencing , Female , Humans , Virulence , Genetic Predisposition to Disease , BRCA1 Protein/genetics , BRCA2 Protein/genetics , Genes, BRCA2 , Exons , Breast Neoplasms/genetics , Germ-Line Mutation/genetics , High-Throughput Nucleotide Sequencing/methods
6.
Pediatr Blood Cancer ; 70(4): e30228, 2023 04.
Article in English | MEDLINE | ID: mdl-36722003

ABSTRACT

BACKGROUND: Alveolar rhabdomyosarcoma (ARMS) is an aggressive pediatric cancer and cases with fusion PAX3-FOXO1 and PAX7-FOXO1 seem to have a poor prognosis. The aim is to evaluate whether PAX-FOXO1 alterations influence clinical outcome in childhood and adolescence population with ARMS. PROCEDURE: A population-based study was conducted between 2011 and 2016 in patients less than 17 years with a diagnosis of ARMS. Overall survival (OS) depending on fusion status with clinical factors was analyzed. RESULTS: Out of 111 ARMS patients recorded in the French National Childhood Cancer Registry during the 2011-2016 period, 61% expressed PAX3-FOXO1, 15% expressed PAX7-FOXO1, 13% were FOXO1 fusion-positive without PAX specification, and 7% were PAX-FOXO1 negative (n = 4 missing data). Compared to patients with PAX7-FOXO1 positive ARMS, those with PAX3-FOXO1 positive tumor were significantly older (10-17 years: 57.4% vs. 29.4%), and had more often a metastatic disease (54.4% vs. 23.5%). Poorer 5-year OS for patients with PAX3-FOXO1 and PAX not specified FOXO1-positive tumor were observed (44.0% [32.0-55.4] and 35.7% [13.1-59.4], respectively). After adjustment for stage at diagnosis, patients with positive tumor for PAX3-FOXO1 were 3.6-fold more likely to die than those with positive tumor for PAX7-FOXO1. CONCLUSION: At the population level, PAX3-FOXO1 was associated with a significant higher risk of death compared to PAX7-FOXO1-positive and PAX-FOXO1-negative tumors, and could explain poorer 5-year OS observed in adolescence population diagnosed with ARMS. A continuous risk score derived from the combination of clinical parameters with PAX3-FOXO1 fusion status represents a robust approach to improving current risk-adapted therapy for ARMS.


Subject(s)
Rhabdomyosarcoma, Alveolar , Rhabdomyosarcoma , Child , Humans , Adolescent , Rhabdomyosarcoma, Alveolar/pathology , Paired Box Transcription Factors , PAX7 Transcription Factor , PAX3 Transcription Factor , Forkhead Transcription Factors , Forkhead Box Protein O1 , Oncogene Proteins, Fusion
8.
Nucleic Acids Res ; 49(9): 5038-5056, 2021 05 21.
Article in English | MEDLINE | ID: mdl-34009296

ABSTRACT

ERG family proteins (ERG, FLI1 and FEV) are a subfamily of ETS transcription factors with key roles in physiology and development. In Ewing sarcoma, the oncogenic fusion protein EWS-FLI1 regulates both transcription and alternative splicing of pre-messenger RNAs. However, whether wild-type ERG family proteins might regulate splicing is unknown. Here, we show that wild-type ERG proteins associate with spliceosomal components, are found on nascent RNAs, and induce alternative splicing when recruited onto a reporter minigene. Transcriptomic analysis revealed that ERG and FLI1 regulate large numbers of alternative spliced exons (ASEs) enriched with RBFOX2 motifs and co-regulated by this splicing factor. ERG and FLI1 are associated with RBFOX2 via their conserved carboxy-terminal domain, which is present in EWS-FLI1. Accordingly, EWS-FLI1 is also associated with RBFOX2 and regulates ASEs enriched in RBFOX2 motifs. However, in contrast to wild-type ERG and FLI1, EWS-FLI1 often antagonizes RBFOX2 effects on exon inclusion. In particular, EWS-FLI1 reduces RBFOX2 binding to the ADD3 pre-mRNA, thus increasing its long isoform, which represses the mesenchymal phenotype of Ewing sarcoma cells. Our findings reveal a RBFOX2-mediated splicing regulatory function of wild-type ERG family proteins, that is altered in EWS-FLI1 and contributes to the Ewing sarcoma cell phenotype.


Subject(s)
Alternative Splicing , Oncogene Proteins, Fusion/metabolism , Proto-Oncogene Protein c-fli-1/metabolism , RNA Splicing Factors/metabolism , RNA-Binding Protein EWS/metabolism , Repressor Proteins/metabolism , Calmodulin-Binding Proteins/genetics , Calmodulin-Binding Proteins/metabolism , Cell Line , Cell Line, Tumor , HeLa Cells , Human Umbilical Vein Endothelial Cells/metabolism , Humans , Protein Domains , Sarcoma, Ewing/genetics , Sarcoma, Ewing/metabolism , Transcriptional Regulator ERG/chemistry , Transcriptional Regulator ERG/metabolism
9.
Genes Chromosomes Cancer ; 61(4): 200-205, 2022 04.
Article in English | MEDLINE | ID: mdl-34877752

ABSTRACT

Over the last decade, the development of next-generation sequencing techniques has led to the molecular dismantlement of adult and pediatric sarcoma, with the identification of multiple gene fusions associated with specific subtypes and currently integrated into diagnostic classifications. In this report, we describe and discuss the identification of a novel EWSR1-UBP1 gene fusion in an adult patient presenting with multi-metastatic sarcoma. Extensive pathological, transcriptomic, and genomic characterization of this tumor in comparison with a cohort of different subtypes of pediatric and adult sarcoma revealed that this fusion represents a novel variant of spindle cell rhabdomyosarcoma with features of TFCP2-rearranged subfamily.


Subject(s)
DNA-Binding Proteins/genetics , Liver Neoplasms/secondary , Lung Neoplasms/genetics , Oncogene Proteins, Fusion/genetics , RNA-Binding Protein EWS/genetics , Rhabdomyosarcoma/genetics , Transcription Factors/genetics , Bone Neoplasms/secondary , Female , Humans , Liver Neoplasms/genetics , Lung Neoplasms/pathology , Middle Aged , Rhabdomyosarcoma/classification , Rhabdomyosarcoma/pathology , Rhabdomyosarcoma/secondary , Skin Neoplasms/secondary
10.
Haematologica ; 107(1): 268-283, 2022 Jan 01.
Article in English | MEDLINE | ID: mdl-33241676

ABSTRACT

The gene CXXC5, encoding a Retinoid-Inducible Nuclear Factor (RINF), is located within a region at 5q31.2 commonly deleted in myelodysplastic syndrome (MDS) and adult acute myeloid leukemia (AML). RINF may act as an epigenetic regulator and has been proposed as a tumor suppressor in hematopoietic malignancies. However, functional studies in normal hematopoiesis are lacking, and its mechanism of action is unknow. Here, we evaluated the consequences of RINF silencing on cytokineinduced erythroid differentiation of human primary CD34+ progenitors. We found that RINF is expressed in immature erythroid cells and that RINF-knockdown accelerated erythropoietin-driven maturation, leading to a significant reduction (~45%) in the number of red blood cells (RBCs), without affecting cell viability. The phenotype induced by RINF-silencing was TGFß-dependent and mediated by SMAD7, a TGFß- signaling inhibitor. RINF upregulates SMAD7 expression by direct binding to its promoter and we found a close correlation between RINF and SMAD7 mRNA levels both in CD34+ cells isolated from bone marrow of healthy donors and MDS patients with del(5q). Importantly, RINF knockdown attenuated SMAD7 expression in primary cells and ectopic SMAD7 expression was sufficient to prevent the RINF knockdowndependent erythroid phenotype. Finally, RINF silencing affects 5'-hydroxymethylation of human erythroblasts, in agreement with its recently described role as a Tet2- anchoring platform in mouse. Altogether, our data bring insight into how the epigenetic factor RINF, as a transcriptional regulator of SMAD7, may fine-tune cell sensitivity to TGFß superfamily cytokines and thus play an important role in both normal and pathological erythropoiesis.


Subject(s)
DNA-Binding Proteins , Leukemia, Myeloid, Acute , Myelodysplastic Syndromes , Smad7 Protein , Transcription Factors , Adult , Animals , Cell Cycle , Epigenesis, Genetic , Humans , Leukemia, Myeloid, Acute/genetics , Mice , Myelodysplastic Syndromes/genetics , RNA, Messenger , Smad7 Protein/genetics
11.
J Pathol ; 255(1): 1-15, 2021 09.
Article in English | MEDLINE | ID: mdl-33999421

ABSTRACT

Extracranial rhabdoid tumours (ECRTs) are an aggressive malignancy of infancy and early childhood. The vast majority of cases demonstrate inactivation of SMARCB1 (ECRTSMARCB1 ) on a background of a remarkably stable genome, a low mutational burden, and no other recurrent mutations. Rarely, ECRTs can harbour the alternative inactivation of SMARCA4 (ECRTSMARCA4 ) instead of SMARCB1. However, very few ECRTSMARCA4 cases have been published to date, and a systematic characterization of ECRTSMARCA4 is missing from the literature. In this study, we report the clinical, pathological, and genomic features of additional cases of ECRTSMARCA4 and show that they are comparable to those of ECRTSMARCB1. We also assess whether ECRTSMARCB1 , ECRTSMARCA4 , and small cell carcinomas of the ovary, hypercalcaemic type (SCCOHT) represent distinct or overlapping entities at a molecular level. Using DNA methylation and transcriptomics-based tumour classification approaches, we demonstrate that ECRTSMARCA4 display molecular features intermediate between SCCOHT and ECRTSMARCB1 ; however, ECRTSMARCA4 appear to be more closely related to SCCOHT by DNA methylation. Conversely, both transcriptomics and DNA methylation show a larger gap between SCCOHT and ECRTSMARCB1 , potentially supporting their continuous separate classification. Lastly, we show that ECRTSMARCA4 display concomitant lack of SMARCA4 (BRG1) and SMARCA2 (BRM) expression at the protein level, similar to what is seen in SCCOHT. Overall, these results expand our knowledge on this rare tumour type and explore the similarities and differences among entities from the 'rhabdoid tumour' spectrum. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.


Subject(s)
DNA Helicases/deficiency , Nuclear Proteins/deficiency , Rhabdoid Tumor/genetics , Rhabdoid Tumor/pathology , Transcription Factors/deficiency , Carcinoma, Small Cell/genetics , Carcinoma, Small Cell/pathology , Child, Preschool , DNA Helicases/genetics , Female , Humans , Infant , Male , Nuclear Proteins/genetics , Ovarian Neoplasms/genetics , Ovarian Neoplasms/pathology , SMARCB1 Protein/deficiency , SMARCB1 Protein/genetics , Transcription Factors/genetics
12.
Nucleic Acids Res ; 48(5): 2676-2693, 2020 03 18.
Article in English | MEDLINE | ID: mdl-31943118

ABSTRACT

Besides analyses of specific alternative splicing (AS) variants, little is known about AS regulatory pathways and programs involved in anticancer drug resistance. Doxorubicin is widely used in breast cancer chemotherapy. Here, we identified 1723 AS events and 41 splicing factors regulated in a breast cancer cell model of acquired resistance to doxorubicin. An RNAi screen on splicing factors identified the little studied ZRANB2 and SYF2, whose depletion partially reversed doxorubicin resistance. By RNAi and RNA-seq in resistant cells, we found that the AS programs controlled by ZRANB2 and SYF2 were enriched in resistance-associated AS events, and converged on the ECT2 splice variant including exon 5 (ECT2-Ex5+). Both ZRANB2 and SYF2 were found associated with ECT2 pre-messenger RNA, and ECT2-Ex5+ isoform depletion reduced doxorubicin resistance. Following doxorubicin treatment, resistant cells accumulated in S phase, which partially depended on ZRANB2, SYF2 and the ECT2-Ex5+ isoform. Finally, doxorubicin combination with an oligonucleotide inhibiting ECT2-Ex5 inclusion reduced doxorubicin-resistant tumor growth in mouse xenografts, and high ECT2-Ex5 inclusion levels were associated with bad prognosis in breast cancer treated with chemotherapy. Altogether, our data identify AS programs controlled by ZRANB2 and SYF2 and converging on ECT2, that participate to breast cancer cell resistance to doxorubicin.


Subject(s)
Alternative Splicing/genetics , Breast Neoplasms/drug therapy , Doxorubicin/therapeutic use , Drug Resistance, Neoplasm , Proto-Oncogene Proteins/metabolism , RNA-Binding Proteins/metabolism , Adult , Aged , Aged, 80 and over , Alternative Splicing/drug effects , Animals , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Cell Line, Tumor , Cell Proliferation/drug effects , Doxorubicin/pharmacology , Drug Resistance, Neoplasm/drug effects , Drug Resistance, Neoplasm/genetics , Epithelial-Mesenchymal Transition/drug effects , Epithelial-Mesenchymal Transition/genetics , Exons/genetics , Female , Gene Expression Regulation, Neoplastic/drug effects , Humans , MCF-7 Cells , Mice, Nude , MicroRNAs/genetics , MicroRNAs/metabolism , Middle Aged , Protein Isoforms/metabolism , RNA Splice Sites/genetics , S Phase/drug effects , Spliceosomes/metabolism
13.
EMBO Rep ; 20(12): e48375, 2019 12 05.
Article in English | MEDLINE | ID: mdl-31668005

ABSTRACT

Outcomes for metastatic Ewing sarcoma and osteosarcoma are dismal and have not changed for decades. Oxidative stress attenuates melanoma metastasis, and melanoma cells must reduce oxidative stress to metastasize. We explored this in sarcomas by screening for oxidative stress sensitizers, which identified the class I HDAC inhibitor MS-275 as enhancing vulnerability to reactive oxygen species (ROS) in sarcoma cells. Mechanistically, MS-275 inhibits YB-1 deacetylation, decreasing its binding to 5'-UTRs of NFE2L2 encoding the antioxidant factor NRF2, thereby reducing NFE2L2 translation and synthesis of NRF2 to increase cellular ROS. By global acetylomics, MS-275 promotes rapid acetylation of the YB-1 RNA-binding protein at lysine-81, blocking binding and translational activation of NFE2L2, as well as known YB-1 mRNA targets, HIF1A, and the stress granule nucleator, G3BP1. MS-275 dramatically reduces sarcoma metastasis in vivo, but an MS-275-resistant YB-1K81-to-alanine mutant restores metastatic capacity and NRF2, HIF1α, and G3BP1 synthesis in MS-275-treated mice. These studies describe a novel function for MS-275 through enhanced YB-1 acetylation, thus inhibiting YB-1 translational control of key cytoprotective factors and its pro-metastatic activity.


Subject(s)
Antineoplastic Agents/therapeutic use , Benzamides/therapeutic use , Bone Neoplasms/drug therapy , Histone Deacetylase Inhibitors/therapeutic use , Pyridines/therapeutic use , Sarcoma, Ewing/drug therapy , Transcription Factors/metabolism , Acetylation , Animals , Bone Neoplasms/metabolism , Bone Neoplasms/pathology , Cell Line, Tumor , Cells, Cultured , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Mice , NF-E2-Related Factor 2/metabolism , Neoplasm Metastasis , Oxidative Stress , Sarcoma, Ewing/metabolism , Sarcoma, Ewing/pathology
14.
Int J Cancer ; 144(1): 68-79, 2019 01 01.
Article in English | MEDLINE | ID: mdl-29923174

ABSTRACT

Circulating tumor DNA (ctDNA) is a powerful tool for the molecular characterization of cancer. The most frequent pediatric kidney tumors (KT) are Wilms' tumors (WT), but other diagnoses may occur. According to the SIOP strategy, in most countries pediatric KT have a presumptive diagnosis of WT if they are clinically and radiologically compatible. The histologic confirmation is established after post-chemotherapy nephrectomy. Thus, there is a risk for a small fraction of patients to receive neoadjuvant chemotherapy that is not adapted to the disease. The aim of this work is to perform molecular diagnosis of pediatric KT by tumor genetic characterization based on the analysis of ctDNA. We analyzed ctDNA extracted from plasma samples of 18 pediatric patients with KT by whole-exome sequencing and compared the results to their matched tumor and germline DNA. Copy number alterations (CNAs) and single nucleotide variations (SNVs) were analyzed. We were able to detect tumor cell specific genetic alterations-CNAs, SNVs or both-in ctDNA in all patients except in one (for whom the plasma sample was obtained long after nephrectomy). These results open the door to new applications for the study of ctDNA with regards to the molecular diagnosis of KT, with a possibility of its usefulness for adapting the treatment early after diagnosis, but also for disease monitoring and follow up.


Subject(s)
Biomarkers, Tumor/genetics , Circulating Tumor DNA/genetics , Kidney Neoplasms/genetics , Wilms Tumor/genetics , Biomarkers, Tumor/blood , Child , Child, Preschool , Circulating Tumor DNA/blood , DNA Copy Number Variations , Female , Humans , Infant , Kidney Neoplasms/diagnosis , Kidney Neoplasms/therapy , Male , Neoadjuvant Therapy , Nephrectomy , Retrospective Studies , Sensitivity and Specificity , Whole Genome Sequencing/methods , Wilms Tumor/diagnosis , Wilms Tumor/therapy
15.
Int J Cancer ; 145(10): 2781-2791, 2019 11 15.
Article in English | MEDLINE | ID: mdl-31018240

ABSTRACT

In neuroblastoma (NB), genetic alterations in chromatin remodeling (CRGs) and epigenetic modifier genes (EMGs) have been described. We sought to determine their frequency and clinical impact. Whole exome (WES)/whole genome sequencing (WGS) data and targeted sequencing (TSCA®) of exonic regions of 33 CRGs/EMGs were analyzed in tumor samples from 283 NB patients, with constitutional material available for 55 patients. The frequency of CRG/EMG variations in NB cases was then compared to the Genome Aggregation Database (gnomAD). The sequencing revealed SNVs/small InDels or focal CNAs of CRGs/EMGs in 20% (56/283) of all cases, occurring at a somatic level in 4 (7.2%), at a germline level in 12 (22%) cases, whereas for the remaining cases, only tumor material could be analyzed. The most frequently altered genes were ATRX (5%), SMARCA4 (2.5%), MLL3 (2.5%) and ARID1B (2.5%). Double events (SNVs/small InDels/CNAs associated with LOH) were observed in SMARCA4 (n = 3), ATRX (n = 1) and PBRM1 (n = 1). Among the 60 variations, 24 (8.4%) targeted domains of functional importance for chromatin remodeling or highly conserved domains but of unknown function. Variations in SMARCA4 and ATRX occurred more frequently in the NB as compared to the gnomAD control cohort (OR = 4.49, 95%CI: 1.63-9.97, p = 0.038; OR 3.44, 95%CI: 1.46-6.91, p = 0.043, respectively). Cases with CRG/EMG variations showed a poorer overall survival compared to cases without variations. Genetic variations of CRGs/EMGs with likely functional impact were observed in 8.4% (24/283) of NB. Our case-control approach suggests a role of SMARCA4 as a player of NB oncogenesis.


Subject(s)
Carcinogenesis/genetics , Chromatin Assembly and Disassembly/genetics , DNA Helicases/genetics , Neuroblastoma/genetics , Nuclear Proteins/genetics , Transcription Factors/genetics , Adolescent , Case-Control Studies , Child , Child, Preschool , DNA Copy Number Variations , Exons/genetics , Female , Germ-Line Mutation , Humans , INDEL Mutation , Infant , Infant, Newborn , Kaplan-Meier Estimate , Male , Neuroblastoma/mortality , Neuroblastoma/pathology , Polymorphism, Single Nucleotide , Progression-Free Survival , Exome Sequencing , X-linked Nuclear Protein/genetics
17.
Bioinformatics ; 34(11): 1808-1816, 2018 06 01.
Article in English | MEDLINE | ID: mdl-29342233

ABSTRACT

Motivation: In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering [reducing dispersion in variant allele frequency estimates (VAFs)] and using all biologically relevant variants. Results: We present a framework for defining cancer clones using most reliable variants of high depth of coverage and assigning functional mutations to the detected clones. The key element of our framework is QuantumClone, a method for variant clustering into clones based on VAFs, genotypes of corresponding regions and information about tumor purity. We validated QuantumClone and our framework on simulated data. We then applied our framework to whole genome sequencing data for 19 neuroblastoma trios each including constitutional, diagnosis and relapse samples. We confirmed an enrichment of damaging variants within such pathways as MAPK (mitogen-activated protein kinases), neuritogenesis, epithelial-mesenchymal transition, cell survival and DNA repair. Most pathways had more damaging variants in the expanding clones compared to shrinking ones, which can be explained by the increased total number of variants between these two populations. Functional mutational rate varied for ancestral clones and clones shrinking or expanding upon treatment, suggesting changes in clone selection mechanisms at different time points of tumor evolution. Availability and implementation: Source code and binaries of the QuantumClone R package are freely available for download at https://CRAN.R-project.org/package=QuantumClone. Contact: gudrun.schleiermacher@curie.fr or valentina.boeva@inserm.fr. Supplementary information: Supplementary data are available at Bioinformatics online.


Subject(s)
Clonal Evolution , DNA Copy Number Variations , Molecular Typing/methods , Neoplasms/genetics , Software , Whole Genome Sequencing/methods , Cluster Analysis , DNA Mutational Analysis/methods , Gene Frequency , High-Throughput Nucleotide Sequencing/methods , Humans , Mutation , Neoplasms/diagnosis
18.
Am J Pathol ; 188(10): 2378-2391, 2018 10.
Article in English | MEDLINE | ID: mdl-30075151

ABSTRACT

Medullary breast carcinoma (MBC) is a rare subtype of triple-negative breast cancer with specific genomic features within the spectrum of basal-like carcinoma (BLC). In this study of 19 MBCs and 36 non-MBC BLCs, we refined the transcriptomic and genomic knowledge about this entity. Unsupervised and supervised analysis of transcriptomic profiles confirmed that MBC clearly differs from non-MBC BLC, with 92 genes overexpressed and 154 genes underexpressed in MBC compared with non-MBC BLC. Immunity-related pathways are the most differentially represented pathways in MBC compared with non-MBC BLC. The proapoptotic gene BCLG (official name BCL2L14) is by far the most intensely overexpressed gene in MBC. A quantitative RT-PCR validation study conducted in 526 breast tumors corresponding to all molecular subtypes documented the specificity of BCLG overexpression in MBC, which was confirmed at the protein level by immunohistochemistry. We also found that most MBCs belong to the immunomodulatory triple-negative breast cancer subtype. Using pan-genomic analysis, it was found that MBC harbors more losses of heterozygosity than non-MBC BLC. These observations corroborate the notion that MBC remains a distinct entity that could benefit from specific treatment strategies (such as deescalation or targeted therapy) adapted to this rare tumor type.


Subject(s)
Carcinoma, Medullary/genetics , Proto-Oncogene Proteins c-bcl-2/genetics , Triple Negative Breast Neoplasms/genetics , BRCA2 Protein/genetics , DNA, Neoplasm/metabolism , Female , Gene Expression Profiling , Genes, Neoplasm/genetics , Humans , Loss of Heterozygosity/genetics , RNA, Neoplasm/metabolism , Retrospective Studies , Reverse Transcriptase Polymerase Chain Reaction , Ubiquitin-Protein Ligases/genetics
19.
J Pathol ; 245(1): 29-40, 2018 05.
Article in English | MEDLINE | ID: mdl-29431183

ABSTRACT

Sarcoma represents a highly heterogeneous group of tumours. We report here the first unbiased and systematic search for gene fusions combined with unsupervised expression analysis of a series of 184 small round cell sarcomas. Fusion genes were detected in 59% of samples, with half of them being observed recurrently. We identified biologically homogeneous groups of tumours such as the CIC-fused (to DUX4, FOXO4 or NUTM1) and BCOR-rearranged (BCOR-CCNB3, BCOR-MAML3, ZC3H7B-BCOR, and BCOR internal duplication) tumour groups. VGLL2-fused tumours represented a more biologically and pathologically heterogeneous group. This study also refined the characteristics of some entities such as EWSR1-PATZ1 spindle cell sarcoma or FUS-NFATC2 bone tumours that are different from EWSR1-NFATC2 tumours and transcriptionally resemble CIC-fused tumour entities. We also describe a completely novel group of epithelioid and spindle-cell rhabdomyosarcomas characterized by EWSR1- or FUS-TFCP2 fusions. Finally, expression data identified some potentially new therapeutic targets or pathways. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.


Subject(s)
Bone Neoplasms/genetics , Oncogene Proteins, Fusion/genetics , Sarcoma, Small Cell/genetics , Transcriptome/genetics , Biomarkers, Tumor/genetics , DNA-Binding Proteins/genetics , Gene Fusion/genetics , Humans , Muscle Proteins/genetics , Repressor Proteins/genetics , Transcription Factors/genetics
20.
Brain ; 141(5): 1300-1319, 2018 05 01.
Article in English | MEDLINE | ID: mdl-29490009

ABSTRACT

Genetic modifications during development of paediatric groups 3 and 4 medulloblastoma are responsible for their highly metastatic properties and poor patient survival rates. PRUNE1 is highly expressed in metastatic medulloblastoma group 3, which is characterized by TGF-ß signalling activation, c-MYC amplification, and OTX2 expression. We describe the process of activation of the PRUNE1 signalling pathway that includes its binding to NME1, TGF-ß activation, OTX2 upregulation, SNAIL (SNAI1) upregulation, and PTEN inhibition. The newly identified small molecule pyrimido-pyrimidine derivative AA7.1 enhances PRUNE1 degradation, inhibits this activation network, and augments PTEN expression. Both AA7.1 and a competitive permeable peptide that impairs PRUNE1/NME1 complex formation, impair tumour growth and metastatic dissemination in orthotopic xenograft models with a metastatic medulloblastoma group 3 cell line (D425-Med cells). Using whole exome sequencing technology in metastatic medulloblastoma primary tumour cells, we also define 23 common 'non-synonymous homozygous' deleterious gene variants as part of the protein molecular network of relevance for metastatic processes. This PRUNE1/TGF-ß/OTX2/PTEN axis, together with the medulloblastoma-driver mutations, is of relevance for future rational and targeted therapies for metastatic medulloblastoma group 3.10.1093/brain/awy039_video1awy039media15742053534001.


Subject(s)
Carrier Proteins/metabolism , Cerebellar Neoplasms/metabolism , Gene Expression Regulation, Neoplastic/physiology , Medulloblastoma/metabolism , Neoplasm Metastasis/physiopathology , PTEN Phosphohydrolase/metabolism , Adolescent , Animals , Carrier Proteins/genetics , Cell Line, Tumor , Cell Movement/drug effects , Cell Proliferation/drug effects , Cerebellar Neoplasms/pathology , Child , Child, Preschool , Female , Gene Expression Regulation, Neoplastic/drug effects , Gene Regulatory Networks , Humans , Infant , Male , Medulloblastoma/pathology , Mice , Mice, Inbred BALB C , Models, Molecular , Neoplasm Metastasis/genetics , PTEN Phosphohydrolase/genetics , Phosphoric Monoester Hydrolases , Pyrimidinones/chemistry , Pyrimidinones/pharmacology , Signal Transduction/drug effects , Signal Transduction/genetics , Snail Family Transcription Factors/metabolism , Transforming Growth Factor beta/metabolism
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