Equipe DRUM (Réparation de l’ADN et Mélanome Uvéal)

Publications de l’équipe

Année de publication : 2020

Samar Alsafadi, Stephane Dayot, Malcy Tarin, Alexandre Houy, Dorine Bellanger, Michele Cornella, Michel Wassef, Joshua J Waterfall, Erik Lehnert, Sergio Roman-Roman, Marc-Henri Stern, Tatiana Popova (2020 Oct 15)

Genetic alterations of SUGP1 mimic mutant-SF3B1 splice pattern in lung adenocarcinoma and other cancers.

Oncogene : 85-96 : DOI : 10.1038/s41388-020-01507-5 En savoir plus
Résumé

Genes involved in 3′-splice site recognition during mRNA splicing constitute an emerging class of oncogenes. SF3B1 is the most frequently mutated splicing factor in cancer, and SF3B1 mutants corrupt branchpoint recognition leading to usage of cryptic 3′-splice sites and subsequent aberrant junctions. For a comprehensive determination of alterations leading to this splicing pattern, we performed a pan-TCGA screening for SF3B1-specific aberrant acceptor usage. While the most of aberrant 3′-splice patterns were explained by SF3B1 mutations, we also detected nine SF3B1 wild-type tumors (including five lung adenocarcinomas). Genomic profile analysis of these tumors identified somatic mutations combined with loss-of-heterozygosity in the splicing factor SUGP1 in five of these cases. Modeling of SUGP1 loss and mutations in cell lines showed that both alterations induced mutant-SF3B1-like aberrant splicing. Our study provides definitive evidence that genetic alterations of SUGP1 genocopy SF3B1 mutations in lung adenocarcinoma and other cancers.

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Alexandre Eeckhoutte, Alexandre Houy, Elodie Manié, Manon Reverdy, Ivan Bièche, Elisabetta Marangoni, Oumou Goundiam, Anne Vincent-Salomon, Dominique Stoppa-Lyonnet, François-Clément Bidard, Marc-Henri Stern, Tatiana Popova (2020 Apr 22)

ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing.

Bioinformatics (Oxford, England) : 3888-3889 : DOI : 10.1093/bioinformatics/btaa261 En savoir plus
Résumé

We introduce shallowHRD, a software tool to evaluate tumor homologous recombination deficiency (HRD) based on whole genome sequencing (WGS) at low coverage (shallow WGS or sWGS; ∼1X coverage). The tool, based on mining copy number alterations profile, implements a fast and straightforward procedure that shows 87.5% sensitivity and 90.5% specificity for HRD detection. shallowHRD could be instrumental in predicting response to poly(ADP-ribose) polymerase inhibitors, to which HRD tumors are selectively sensitive. shallowHRD displays efficiency comparable to most state-of-art approaches, is cost-effective, generates low-storable outputs and is also suitable for fixed-formalin paraffin embedded tissues.

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Martine J Jager, Carol L Shields, Colleen M Cebulla, Mohamed H Abdel-Rahman, Hans E Grossniklaus, Marc-Henri Stern, Richard D Carvajal, Rubens N Belfort, Renbing Jia, Jerry A Shields, Bertil E Damato (2020 Apr 11)

Uveal melanoma.

Nature reviews. Disease primers : 24 : DOI : 10.1038/s41572-020-0158-0 En savoir plus
Résumé

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. UMs are usually initiated by a mutation in GNAQ or GNA11, unlike cutaneous melanomas, which usually harbour a BRAF or NRAS mutation. The annual incidence in Europe and the USA is ~6 per million population per year. Risk factors include fair skin, light-coloured eyes, congenital ocular melanocytosis, ocular melanocytoma and the BAP1-tumour predisposition syndrome. Ocular treatment aims at preserving the eye and useful vision and, if possible, preventing metastases. Enucleation has largely been superseded by various forms of radiotherapy, phototherapy and local tumour resection, often administered in combination. Ocular outcomes are best with small tumours not extending close to the optic disc and/or fovea. Almost 50% of patients develop metastatic disease, which usually involves the liver, and is usually fatal within 1 year. Although UM metastases are less responsive than cutaneous melanoma to chemotherapy or immune checkpoint inhibitors, encouraging results have been reported with partial hepatectomy for solitary metastases, with percutaneous hepatic perfusion with melphalan or with tebentafusp. Better insight into tumour immunology and metabolism may lead to new treatments.

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Anne-Céline Derrien, Manuel Rodrigues, Alexandre Eeckhoutte, Stéphane Dayot, Alexandre Houy, Lenha Mobuchon, Sophie Gardrat, Delphine Lequin, Stelly Ballet, Gaëlle Pierron, Samar Alsafadi, Odette Mariani, Ahmed El-Marjou, Alexandre Matet, Chrystelle Colas, Nathalie Cassoux, Marc-Henri Stern (2020 Apr 3)

Germline MBD4 Mutations and Predisposition to Uveal Melanoma.

Journal of the National Cancer Institute : 80-87 : DOI : 10.1093/jnci/djaa047 En savoir plus
Résumé

Uveal melanoma (UM) arises from malignant transformation of melanocytes in the uveal tract of the eye. This rare tumor has a poor outcome with frequent chemo-resistant liver metastases. BAP1 is the only known predisposing gene for UM. UMs are generally characterized by low tumor mutation burden, but some UMs display a high level of CpG>TpG mutations associated with MBD4 inactivation. Here, we explored the incidence of germline MBD4 variants in a consecutive series of 1093 primary UM case patients and a series of 192 UM tumors with monosomy 3 (M3).

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Amanda Bortolini Silveira, François-Clément Bidard, Amélie Kasperek, Samia Melaabi, Marie-Laure Tanguy, Manuel Rodrigues, Guillaume Bataillon, Luc Cabel, Bruno Buecher, Jean-Yves Pierga, Charlotte Proudhon, Marc-Henri Stern (2020 Mar 17)

High-Accuracy Determination of Microsatellite Instability Compatible with Liquid Biopsies.

Clinical chemistry : 606-613 : DOI : 10.1093/clinchem/hvaa013 En savoir plus
Résumé

Microsatellite instability (MSI) has recently emerged as a predictive pan-tumor biomarker of immunotherapy efficacy, stimulating the development of diagnostic tools compatible with large-scale screening of patients. In this context, noninvasive detection of MSI from circulating tumor DNA stands as a promising diagnostic and posttreatment monitoring tool.

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Alexandre Eeckhoutte, Mathilde Saint-Ghislain, Manon Reverdy, Virginie Raynal, Sylvain Baulande, Guillaume Bataillon, Lisa Golmard, Dominique Stoppa-Lyonnet, Tatiana Popova, Claude Houdayer, Elodie Manié, Marc-Henri Stern (2020 Mar 16)

Lack of evidence for CDK12 as an ovarian cancer predisposing gene.

Familial cancer : 203-209 : DOI : 10.1007/s10689-020-00169-2 En savoir plus
Résumé

CDK12 variants were investigated as a genetic susceptibility to ovarian cancer in a series of 416 unrelated and consecutive patients with ovarian carcinoma and who carry neither germline BRCA1 nor BRCA2 pathogenic variant. The presence of CDK12 variants was searched in germline DNA by massive parallel sequencing on pooled DNAs. The lack of detection of deleterious variants and the observed proportion of missense variants in the series of ovarian carcinoma patients as compared with all human populations strongly suggests that CDK12 is not an ovarian cancer predisposing gene.

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Année de publication : 2019

Linus Wahnschaffe, Till Braun, Sanna Timonen, Anil K Giri, Alexandra Schrader, Prerana Wagle, Henrikki Almusa, Patricia Johansson, Dorine Bellanger, Cristina López, Claudia Haferlach, Marc-Henri Stern, Jan Dürig, Reiner Siebert, Satu Mustjoki, Tero Aittokallio, Marco Herling (2019 Nov 27)

JAK/STAT-Activating Genomic Alterations Are a Hallmark of T-PLL.

Cancers : DOI : E1833 En savoir plus
Résumé

T-cell prolymphocytic leukemia (T-PLL) is a rare and poor-prognostic mature T-cell leukemia. Recent studies detected genomic aberrations affecting and genes in T-PLL. Due to the limited number of primary patient samples available, genomic analyses of the JAK/STAT pathway have been performed in rather small cohorts. Therefore, we conducted-via a primary-data based pipeline-a meta-analysis that re-evaluated the genomic landscape of T-PLL. It included all available data sets with sequence information on or gene loci in 275 T-PLL. We eliminated overlapping cases and determined a cumulative rate of 62.1% of cases with mutated or genes. Most frequently, (6.3%), (36.4%), and (18.8%) carried somatic single-nucleotide variants (SNVs), with missense mutations in the SH2 or pseudokinase domains as most prevalent. Importantly, these lesions were predominantly subclonal. We did not detect any strong association between mutations of a or gene with clinical characteristics. Irrespective of the presence of gain-of-function (GOF) SNVs, basal phosphorylation of STAT5B was elevated in all analyzed T-PLL. Fittingly, a significant proportion of genes encoding for potential negative regulators of STAT5B showed genomic losses (in 71.4% of T-PLL in total, in 68.4% of T-PLL without any or mutations). They included and . Overall, considering such losses of negative regulators and the GOF mutations in and genes, a total of 89.8% of T-PLL revealed a genomic aberration potentially explaining enhanced STAT5B activity. In essence, we present a comprehensive meta-analysis on the highly prevalent genomic lesions that affect genes encoding JAK/STAT signaling components. This provides an overview of possible modes of activation of this pathway in a large cohort of T-PLL. In light of new advances in JAK/STAT inhibitor development, we also outline translational contexts for harnessing active JAK/STAT signaling, which has emerged as a ‘secondary’ hallmark of T-PLL.

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Petros Tsantoulis, Mauro Delorenzi, Ivan Bièche, Sophie Vacher, Pascale Mariani, Nathalie Cassoux, Alexandre Houy, Marc-Henri Stern, Sergio Roman-Roman, Pierre-Yves Dietrich, Arnaud Roth, Wulfran Cacheux (2019 Nov 22)

Prospective validation in epithelial tumors of a gene expression predictor of liver metastasis derived from uveal melanoma.

Scientific reports : 17178 : DOI : 10.1038/s41598-019-52841-y En savoir plus
Résumé

Predicting the risk of liver metastasis can have important prognostic and therapeutic implications, given the availability of liver-directed therapy. Uveal melanoma has a striking predisposition for liver metastasis despite the absence of anatomical proximity. Understanding its biology may uncover factors promoting liver metastasis in other malignancies. We quantified gene expression by RNAseq in 76 uveal melanomas and combined with public data in a meta-analysis of 196 patients. The meta-analysis of uveal melanoma gene expression identified 63 genes which remained prognostic after adjustment for chromosome 3 status. Two genes, PTP4A3 and JPH1, were selected by L1-penalized regression and combined in a prognostic score. The score predicted liver-specific relapse in a public pan-cancer dataset and in two public colorectal cancer datasets. The score varied between colorectal consensus molecular subtypes (CMS), as did the risk of liver relapse, which was lowest in CMS1. Additional prospective validation was done by real-time PCR in 463 breast cancer patients. The score was significantly correlated with liver relapse in hormone receptor positive tumors. In conclusion, the expression of PTP4A3 and JPH1 correlates with risk of liver metastasis in colorectal cancer and breast cancer. The underlying biological mechanism is an interesting area for further research.

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Alice Fiévet, Dorine Bellanger, Laila Zahed, Lydie Burglen, Anne-Céline Derrien, Catherine Dubois d'Enghien, James Lespinasse, Béatrice Parfait, Jean-Michel Pedespan, Guillaume Rieunier, Dominique Stoppa-Lyonnet, Marc-Henri Stern (2019 Nov 16)

DNA repair functional analyses of NBN hypomorphic variants associated with NBN-related infertility.

Human mutation : 608-618 : DOI : 10.1002/humu.23955 En savoir plus
Résumé

Nijmegen breakage syndrome caused by biallelic pathogenic variants of the DNA-damage response gene NBN, is characterized by severe microcephaly, cancer proneness, infertility, and karyotype abnormalities. We previously reported NBN variants in siblings suffering from fertility defects. Here, we identify a new founder NBN variant (c.442A>G, p.(Thr148Ala)) in Lebanese patients associated with isolated infertility. Functional analyses explored preserved or altered functions correlated with their remarkably mild phenotype. Transcript and protein analyses supported the use of an alternative transcript with in-frame skipping of exons 4-5, leading to p84-NBN protein with a preserved forkhead-associated (FHA) domain. The level of NBN was dramatically reduced and the MRN complex delocalized to the cytoplasm. Interestingly, ataxia-elangiectasia mutated (ATM) also shifted from the nucleus to the cytoplasm, suggesting some interaction between ATM and the MRN complex at a steady state. The ATM pathway activation, attenuated in typical patients with NBS, appeared normal under camptothecin treatment in these new NBN-related infertile patients. Cell cycle checkpoint defect was present in these atypical patients, although to a lesser extent than in typical patients with NBS. In conclusion, we report three new NBN-related infertile patients and we suggest that preserved FHA domain could be responsible for the mild phenotype and intermediate DNA-damage response defects.

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Manuel Rodrigues, Leanne de Koning, Sarah E Coupland, Aart G Jochemsen, Richard Marais, Marc-Henri Stern, André Valente, Raymond Barnhill, Nathalie Cassoux, Andrew Evans, Iain Galloway, Martine J Jager, Ellen Kapiteijn, Bozena Romanowska-Dixon, Bettina Ryll, Sergio Roman-Roman, Sophie Piperno-Neumann, (2019 Jul 25)

So Close, yet so Far: Discrepancies between Uveal and Other Melanomas. A Position Paper from UM Cure 2020.

Cancers : DOI : E1032 En savoir plus
Résumé

Despite much progress in our understanding of uveal melanoma (UM) over the past decades, this rare tumour is still often misclassified. Although UM, like other melanomas, is very probably derived from melanocytes, it is drastically different from cutaneous melanoma and most other melanoma subtypes in terms of epidemiology, aetiology, biology and clinical features, including an intriguing metastatic hepatotropism. UM carries distinctive prognostic chromosome alterations, somatic mutations and gene expression profiles, allowing an active tailored surveillance strategy and dedicated adjuvant clinical trials. There is no standard systemic treatment for disseminated UM at present. In contrast to cutaneous melanoma, UMs are not -mutated, thus curtailing the use of B-Raf inhibitors. Although these tumours are characterised by some immune infiltrates, immune checkpoint inhibitors are rarely effective, possibly due to a low mutation burden. UM patients across the world not only face rare cancer-related issues (e.g., specific management strategies, access to information and to expert centres), but also specific UM problems, which can be exacerbated by the common misconception that it is a subtype of cutaneous melanoma. As a European Consortium dedicated to research on UM and awareness on the disease, « UM Cure 2020 » participants urge medical oncologists, pharmaceutical companies, and regulatory agencies to acknowledge UM as a melanoma with specific issues, in order to accelerate the development of new therapies for patients.

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Manuel Rodrigues, Lenha Mobuchon, Alexandre Houy, Samar Alsafadi, Sylvain Baulande, Odette Mariani, Benjamin Marande, Khadija Ait Rais, Monique K Van der Kooij, Ellen Kapiteijn, Sieta Gassama, Sophie Gardrat, Raymond L Barnhill, Vincent Servois, Rémi Dendale, Marc Putterman, Sarah Tick, Sophie Piperno-Neumann, Nathalie Cassoux, Gaëlle Pierron, Joshua J Waterfall, Sergio Roman-Roman, Pascale Mariani, Marc-Henri Stern (2019 Jun 23)

Evolutionary Routes in Metastatic Uveal Melanomas Depend on Alterations.

Clinical cancer research : an official journal of the American Association for Cancer Research : 5513-5524 : DOI : 10.1158/1078-0432.CCR-19-1215 En savoir plus
Résumé

Uveal melanomas (UM) are genetically simple tumors carrying few copy number alterations (CNA) and a low mutation burden, except in rare -deficient, hypermutated cases. The genomics of uveal melanoma metastatic progression has not been described. We assessed the genetic heterogeneity of primary and metastatic -proficient and -deficient uveal melanomas. We prospectively collected 75 metastatic and 16 primary samples from 25 consecutive uveal melanoma patients, and performed whole-exome sequencing.

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François-Clément Bidard, Nicolas Kiavue, Marc Ychou, Luc Cabel, Marc-Henri Stern, Jordan Madic, Adrien Saliou, Aurore Rampanou, Charles Decraene, Olivier Bouché, Michel Rivoire, François Ghiringhelli, Eric Francois, Rosine Guimbaud, Laurent Mineur, Faiza Khemissa-Akouz, Thibault Mazard, Driffa Moussata, Charlotte Proudhon, Jean-Yves Pierga, Trevor Stanbury, Simon Thézenas, Pascale Mariani (2019 May 31)

Circulating Tumor Cells and Circulating Tumor DNA Detection in Potentially Resectable Metastatic Colorectal Cancer: A Prospective Ancillary Study to the Unicancer Prodige-14 Trial.

Cells : DOI : E516 En savoir plus
Résumé

The management of patients with colorectal cancer (CRC) and potentially resectable liver metastases (LM) requires quick assessment of mutational status and of response to pre-operative systemic therapy. In a prospective phase II trial (NCT01442935), we investigated the clinical validity of circulating tumor cell (CTC) and circulating tumor DNA (ctDNA) detection. CRC patients with potentially resectable LM were treated with first-line triplet or doublet chemotherapy combined with targeted therapy. CTC (Cellsearch) and Kirsten RAt Sarcoma (KRAS) ctDNA (droplet digital polymerase chain reaction (PCR)) levels were assessed at inclusion, after 4 weeks of therapy and before LM surgery. 153 patients were enrolled. The proportion of patients with high CTC counts (≥3 CTC/7.5mL) decreased during therapy: 19% (25/132) at baseline, 3% (3/108) at week 4 and 0/57 before surgery. ctDNA detection sensitivity at baseline was 91% (N=42/46) and also decreased during treatment. Interestingly, persistently detectable KRAS ctDNA (p=0.01) at 4 weeks was associated with a lower R0/R1 LM resection rate. Among patients who had a R0/R1 LM resection, those with detectable ctDNA levels before liver surgery had a shorter overall survival (p<0.001). In CRC patients with limited metastatic spread, ctDNA could be used as liquid biopsy tool. Therefore, ctDNA detection could help to select patients eligible for LM resection.

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Alice Fiévet, Dorine Bellanger, Guillaume Rieunier, Catherine Dubois d'Enghien, Julia Sophie, Patrick Calvas, Jean-Paul Carriere, Mathieu Anheim, Anna Castrioto, Olivier Flabeau, Bertrand Degos, Claire Ewenczyk, Nizar Mahlaoui, Fabien Touzot, Felipe Suarez, Marie Hully, Agathe Roubertie, Nathalie Aladjidi, François Tison, Hélène Antoine-Poirel, Karine Dahan, Diane Doummar, Marie-Christine Nougues, Christine Ioos, Christelle Rougeot, Alice Masurel, Caroline Bourjault, Emmanuelle Ginglinger, Fabienne Prieur, Aurélie Siri, Pierre Bordigoni, Karine Nguyen, Noel Philippe, Céline Bellesme, François Demeocq, Cecilia Altuzarra, Michèle Mathieu-Dramard, Fanny Couderc, Thilo Dörk, Nathalie Auger, Béatrice Parfait, Khadija Abidallah, Virginie Moncoutier, Agnès Collet, Dominique Stoppa-Lyonnet, Marc-Henri Stern (2019 May 4)

Functional classification of ATM variants in ataxia-telangiectasia patients.

Human mutation : 1713-1730 : DOI : 10.1002/humu.23778 En savoir plus
Résumé

Ataxia-telangiectasia (A-T) is a recessive disorder caused by biallelic pathogenic variants of ataxia-telangiectasia mutated (ATM). This disease is characterized by progressive ataxia, telangiectasia, immune deficiency, predisposition to malignancies, and radiosensitivity. However, hypomorphic variants may be discovered associated with very atypical phenotypes, raising the importance of evaluating their pathogenic effects. In this study, multiple functional analyses were performed on lymphoblastoid cell lines from 36 patients, comprising 49 ATM variants, 24 being of uncertain significance. Thirteen patients with atypical phenotype and presumably hypomorphic variants were of particular interest to test strength of functional analyses and to highlight discrepancies with typical patients. Western-blot combined with transcript analyses allowed the identification of one missing variant, confirmed suspected splice defects and revealed unsuspected minor transcripts. Subcellular localization analyses confirmed the low level and abnormal cytoplasmic localization of ATM for most A-T cell lines. Interestingly, atypical patients had lower kinase defect and less altered cell-cycle distribution after genotoxic stress than typical patients. In conclusion, this study demonstrated the pathogenic effects of the 49 variants, highlighted the strength of KAP1 phosphorylation test for pathogenicity assessment and allowed the establishment of the Ataxia-TeLangiectasia Atypical Score to predict atypical phenotype. Altogether, we propose strategies for ATM variant detection and classification.

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Alice Fiévet, Dorine Bellanger, Stéphanie Valence, Lenha Mobuchon, Alexandra Afenjar, Fabienne Giuliano, Catherine Dubois d'Enghien, Béatrice Parfait, Jean-Michel Pedespan, Nathalie Auger, Guillaume Rieunier, Agnès Collet, Lydie Burglen, Dominique Stoppa-Lyonnet, Marc-Henri Stern (2019 Apr 30)

Three new cases of ataxia-telangiectasia-like disorder: No impairment of the ATM pathway, but S-phase checkpoint defect.

Human mutation : 1690-1699 : DOI : 10.1002/humu.23773 En savoir plus
Résumé

Ataxia-telangiectasia-like disorder (ATLD) is a rare genomic instability syndrome caused by biallelic variants of MRE11 (meiotic recombination 11) characterized by progressive cerebellar ataxia and typical karyotype abnormalities. These symptoms are common to those of ataxia-telangiectasia, which is consistent with the key role of MRE11 in ataxia-telangiectasia mutated (ATM) activation after DNA double-strand breaks. Three unrelated French patients were referred with ataxia. Only one had typical karyotype abnormalities. Unreported biallelic MRE11 variants were found in these three cases. Interestingly, one variant (c.424G>A) was present in two cases and haplotype analysis strongly suggested a French founder variant. Variants c.544G>A and c.314+4_314+7del lead to splice defects. The level of MRE11 in lymphoblastoid cell lines was consistently and dramatically reduced. Functional consequences were evaluated on activation of the ATM pathway via phosphorylation of ATM targets (KAP1 and CHK2), but no consistent defect was observed. However, an S-phase checkpoint activation defect after camptothecin was observed in these patients with ATLD. In conclusion, we report the first three French ATLD patients and a French founder variant, and propose an S-phase checkpoint activation study to evaluate the pathogenicity of MRE11 variants.

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Alice Fiévet, Virginie Bernard, Henrique Tenreiro, Catherine Dehainault, Elodie Girard, Vivien Deshaies, Philippe Hupe, Olivier Delattre, Marc-Henri Stern, Dominique Stoppa-Lyonnet, Lisa Golmard, Claude Houdayer (2019 Jan 27)

ART-DeCo: easy tool for detection and characterization of cross-contamination of DNA samples in diagnostic next-generation sequencing analysis.

European journal of human genetics : EJHG : 792-800 : DOI : 10.1038/s41431-018-0317-x En savoir plus
Résumé

Next-generation sequencing (NGS) is routinely used for constitutional genetic analysis. However, cross-contamination between samples constitutes a major risk that could impact the results of the analysis. We have developed ART-DeCo, a tool using the allelic ratio (AR) of the Single Nucleotide Polymorphisms sequenced with regions of interest. When a sample is contaminated by DNA with a different genotype, unexpected ARs are obtained, which are in turn used for detection of contamination with a screening test, followed by identification and quantification of the contaminant. Following optimization, ART-DeCo was applied to 2222 constitutional DNA samples. The screening test was positive for 191 samples. In 33 cases (contamination percentages: 1.3% to 29.2%), the contaminant was identified and was mostly located in adjacent wells. Three other positive cases were due to barcoding errors or mixture of two DNA samples. Interestingly, the last contaminated sample corresponded to a bone marrow transplant recipient. Lastly, no contaminant was identified in 154 weakly positive ( < 4%) samples that were considered to be irrelevant to constitutional genetic analysis. ART-DeCo lends itself to mandatory quality control procedures, also highlighting the delicate steps of library preparation, resulting in practice improvement. Importantly, ART-DeCo can be implemented in any NGS workflow, from gene panel to genome-wide analyses. https://sourceforge.net/projects/ngs-art-deco/ .

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