Brice Lapin

Comprehensive Study of the Clinical Phenotype of Germline BAP1 Variant-Carrying Families Worldwide.

The BRCA1-associated protein-1 (BAP1) tumor predisposition syndrome (BAP1-TPDS) is a hereditary tumor syndrome caused by germline pathogenic variants in BAP1 encoding a tumor suppressor associated with uveal melanoma, mesothelioma, cutaneous melanoma, renal cell carcinoma, and cutaneous BAP1-inactivated melanocytic tumors. However, the full spectrum of tumors associated with the syndrome is yet to be determined. Improved understanding of the BAP1-TPDS is crucial for appropriate clinical management of BAP1 germline variant carriers and their families, including genetic counseling and surveillance for new tumors.

Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of

T-cell prolymphocytic leukemia (T-PLL) is a rare and poor-prognostic mature T-cell malignancy. Here we integrated large-scale profiling data of alterations in gene expression, allelic copy number (CN), and nucleotide sequences in 111 well-characterized patients. Besides prominent signatures of T-cell activation and prevalent clonal variants, we also identify novel hot-spots for CN variability, fusion molecules, alternative transcripts, and progression-associated dynamics. The overall lesional spectrum of T-PLL is mainly annotated to axes of DNA damage responses, T-cell receptor/cytokine signaling, and histone modulation. We formulate a multi-dimensional model of T-PLL pathogenesis centered around a unique combination of TCL1 overexpression with damaging ATM aberrations as initiating core lesions. The effects imposed by TCL1 cooperate with compromised ATM toward a leukemogenic phenotype of impaired DNA damage processing. Dysfunctional ATM appears inefficient in alleviating elevated redox burdens and telomere attrition and in evoking a p53-dependent apoptotic response to genotoxic insults. As non-genotoxic strategies, synergistic combinations of p53 reactivators and deacetylase inhibitors reinstate such cell death execution.

[Role of MBD4 in hypermutator phenotype and malignant transformation].

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

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.

Evolutionary Routes in Metastatic Uveal Melanomas Depend on Alterations.

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.

PML-Regulated Mitochondrial Metabolism Enhances Chemosensitivity in Human Ovarian Cancers.

High-grade serous ovarian cancer (HGSOC) remains an unmet medical challenge. Here, we unravel an unanticipated metabolic heterogeneity in HGSOC. By combining proteomic, metabolomic, and bioergenetic analyses, we identify two molecular subgroups, low- and high-OXPHOS. While low-OXPHOS exhibit a glycolytic metabolism, high-OXPHOS HGSOCs rely on oxidative phosphorylation, supported by glutamine and fatty acid oxidation, and show chronic oxidative stress. We identify an important role for the PML-PGC-1α axis in the metabolic features of high-OXPHOS HGSOC. In high-OXPHOS tumors, chronic oxidative stress promotes aggregation of PML-nuclear bodies, resulting in activation of the transcriptional co-activator PGC-1α. Active PGC-1α increases synthesis of electron transport chain complexes, thereby promoting mitochondrial respiration. Importantly, high-OXPHOS HGSOCs exhibit increased response to conventional chemotherapies, in which increased oxidative stress, PML, and potentially ferroptosis play key functions. Collectively, our data establish a stress-mediated PML-PGC-1α-dependent mechanism that promotes OXPHOS metabolism and chemosensitivity in ovarian cancer.

ART-DeCo: easy tool for detection and characterization of cross-contamination of DNA samples in

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/ .

Functional classification of ATM variants in ataxia-telangiectasia patients.

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.

Colorectal Cancer: A Prospective Ancillary Study to the Unicancer Prodige-14 Trial.

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.

Efficacy of molecularly targeted agents given in the randomised trial SHIVA01 according to the ESMO

A randomised trial SHIVA01 compared the efficacy of matched molecularly targeted therapy outside their indications based on a prespecified treatment algorithm versus conventional chemotherapy in patients with metastatic solid tumours who had failed standard of care. No statistical difference was reported between the two groups in terms of progression-free survival (PFS), challenging treatment algorithm. The European Society for Medical Oncology (ESMO) Scale for Clinical Actionability of molecular Targets (ESCAT) recently defined criteria to prioritise molecular alterations (MAs) to select anticancer drugs. We aimed to retrospectively evaluate the efficacy of matched molecularly targeted agents (MTAs) given in SHIVA01 according to ESCAT tiers.

Basal aurora kinase B activity is sufficient for histone H3 phosphorylation in prophase.

Histone H3 phosphorylation is the hallmark of mitosis deposited by aurora kinase B. Benzo[e]pyridoindoles are a family of potent, broad, ATP-competitive aurora kinase inhibitors. However, benzo[e]pyridoindole C4 only inhibits histone H3 phosphorylation in prophase but not in metaphase. Under the C4 treatment, the cells enter into mitosis with dephosphorylated histone H3, assemble chromosomes normally and progress to metaphase, and then to anaphase. C4 also induces lagging chromosome in anaphase but we demonstrated that these chromosome compaction defects are not related to the absence of H3 phosphorylation in prophase. As a result of C4 action, mitosis lasts longer and the cell cycle is slowed down. We reproduced the mitotic defects with reduced concentrations of potent pan aurora kinase as well as with a specific aurora B ATP-competitive inhibitor; we therefore propose that histone H3 phosphorylation and anaphase chromosome compaction involve the basal activity of aurora kinase B. Our data suggest that aurora kinase B is progressively activated at mitosis entry and at anaphase onset. The full activation of aurora kinase B by its partners, in prometaphase, induces a shift in the catalytic domain of aurora B that modifies its affinity for ATP. These waves of activation/deactivation of aurora B correspond to different conformations of the chromosomal complex revealed by FRAP. The presence of lagging chromosomes may have deleterious consequences on the daughter cells and, unfortunately, the situation may be encountered in patients receiving treatment with aurora kinase inhibitors.

Histone deposition promotes recombination-dependent replication at arrested forks.

Replication stress poses a serious threat to genome stability. Recombination-Dependent-Replication (RDR) promotes DNA synthesis resumption from arrested forks. Despite the identification of chromatin restoration pathways after DNA repair, crosstalk coupling RDR and chromatin assembly is largely unexplored. The fission yeast Chromatin Assembly Factor-1, CAF-1, is known to promote RDR. Here, we addressed the contribution of histone deposition to RDR. We expressed a mutated histone, H3-H113D, to genetically alter replication-dependent chromatin assembly by destabilizing (H3-H4)2 tetramer. We established that DNA synthesis-dependent histone deposition, by CAF-1 and Asf1, promotes RDR by preventing Rqh1-mediated disassembly of joint-molecules. The recombination factor Rad52 promotes CAF-1 binding to sites of recombination-dependent DNA synthesis, indicating that histone deposition occurs downstream Rad52. Histone deposition and Rqh1 activity act synergistically to promote cell resistance to camptothecin, a topoisomerase I inhibitor that induces replication stress. Moreover, histone deposition favors non conservative recombination events occurring spontaneously in the absence of Rqh1, indicating that the stabilization of joint-molecules by histone deposition also occurs independently of Rqh1 activity. These results indicate that histone deposition plays an active role in promoting RDR, a benefit counterbalanced by stabilizing at-risk joint-molecules for genome stability.

Polymersomes with Aggregation-Induced Emission Based on Amphiphilic Block Copolypeptoids

Biocompatible polymersomes are prepared from amphiphilic block copolypeptoids with aggregation-induced emission, where the hydrophobic block P(TPE-NAG) is a tetraphenylethylene (TPE)-modified poly(N-allylglycine) and the hydrophilic block is polysarcosine. These nanoparticles are non-cytotoxic and show strong fluorescence emission in aqueous solution.

Alexandre Eeckhoutte

The Inaugural QBI/Institut Curie/Q-Life Symposium

Photo: Scientists from San Francisco and Paris gather for a group photo at Institut Curie.
 

The Quantitative Biosciences Institute (QBI) at the University of California, San Francisco (UCSF), Institut Curie and Q-Life held their inaugural symposium in Paris in September titled “Quantitative Approaches to Cancer Research,” where 20 scientists from San Francisco and Paris were brought together to empower cancer research and dive into the possibility of forming promising partnerships.

The collaboration between the institutes was fueled by the desire of bringing together some of the world’s leading scientists and their respective expertise to investigate fundamental biological mechanisms to discover solutions to cancer, as well as other maladies including neurological and infectious diseases.

Ultimately, this collaborative ambition stems from the strong belief that developing and using quantitative approaches to study basic biological and biomedical problems will lead to groundbreaking scientific advances.

“Institut Curie is one of the most famous places in the world for cancer research and QBI is really about collaboration and bringing people together. It would be an honor to collaborate with their scientists as we apply some of our quantitative tools that are developed at QBI to studying cancer. Q-Life is conceptually very similar to QBI in that we try to bring together scientists from diverse backgrounds, like physicists, biologists and mathematicians to tackle important problems. That makes for a very easy partnership,” said Nevan Krogan, director of QBI.

The affiliation between QBI and Institut Curie initially began about a year ago when Krogan was invited to give a seminar in Paris by Aura Carreira, director of research at CNRS (French National Center for Scientific Research). They recognized the value in establishing links between scientists in Paris and San Francisco and discussed ways to ignite effective collaboration through symposia and fundraising strategies.

“We started this effort because we have the belief that we need many quantitative approaches, especially now with the advent of new technologies, where we are sequencing a lot of variants in cancer genes and cancer mutations that are being found. The only way, really, to advance with this challenge is to combine quantitative approaches with our basic science. Combining the two is a need. I think this meeting was a reflection of that,” said Carreira.

The symposium was the first of many steps taken as UCSF and Institut Curie strengthen their alliance moving forward.

“To advance cancer research what we need now is to include people from different fields, starting with computational biologists, as well as physicists, chemists and mathematicians. QBI has outstanding scientists and is very well equipped in mass spectrometry and DNA sequencing and that will be very useful in developing our own research in the future,” said Bruno Goud, former director of the research center at Institut Curie.

Next year, a second symposium will be held in San Francisco to further the collaborative exchange. In the meantime, UCSF and Institut Curie are in the process of finalizing an agreement to each contribute funds to create collaborative grants for scientists on both sides.

The hope is that this seed funding will lead to larger funding from federal agencies in both countries as well as from philanthropic opportunities that are presently being pursued.

View the photo gallery here 
View more details on the symposium here

 

The speakers included UCSF researchers Sourav Bandyopadhyay, Jennifer Grandis, Isha Jain, Natalia Jura, Nevan Krogan, Rushika Perera, Davide Ruggero, Kevan Shokat and Danielle Swaney. Scientists from Institut Curie and Q-Life included Olivier Ayrault, Emmanuel Barillot, Renata Basto, Aura Carreira, Emmanuel Farge, Anne Houdusse, Matthieu Piel, Raphael Rodriguez, Celine Vallot and Danijela Vignjevic. 

 

The Inaugural QBI/Institut Curie/Q-Life Symposium

Photo: Scientists from San Francisco and Paris gather for a group photo at Institut Curie.
 

The Quantitative Biosciences Institute (QBI) at the University of California, San Francisco (UCSF), Institut Curie and Q-Life held their inaugural symposium in Paris in September titled “Quantitative Approaches to Cancer Research,” where 20 scientists from San Francisco and Paris were brought together to empower cancer research and dive into the possibility of forming promising partnerships.

The collaboration between the institutes was fueled by the desire of bringing together some of the world’s leading scientists and their respective expertise to investigate fundamental biological mechanisms to discover solutions to cancer, as well as other maladies including neurological and infectious diseases.

Ultimately, this collaborative ambition stems from the strong belief that developing and using quantitative approaches to study basic biological and biomedical problems will lead to groundbreaking scientific advances.

“Institut Curie is one of the most famous places in the world for cancer research and QBI is really about collaboration and bringing people together. It would be an honor to collaborate with their scientists as we apply some of our quantitative tools that are developed at QBI to studying cancer. Q-Life is conceptually very similar to QBI in that we try to bring together scientists from diverse backgrounds, like physicists, biologists and mathematicians to tackle important problems. That makes for a very easy partnership,” said Nevan Krogan, director of QBI.

The affiliation between QBI and Institut Curie initially began about a year ago when Krogan was invited to give a seminar in Paris by Aura Carreira, director of research at CNRS (French National Center for Scientific Research). They recognized the value in establishing links between scientists in Paris and San Francisco and discussed ways to ignite effective collaboration through symposia and fundraising strategies.

“We started this effort because we have the belief that we need many quantitative approaches, especially now with the advent of new technologies, where we are sequencing a lot of variants in cancer genes and cancer mutations that are being found. The only way, really, to advance with this challenge is to combine quantitative approaches with our basic science. Combining the two is a need. I think this meeting was a reflection of that,” said Carreira.

The symposium was the first of many steps taken as UCSF and Institut Curie strengthen their alliance moving forward.

“To advance cancer research what we need now is to include people from different fields, starting with computational biologists, as well as physicists, chemists and mathematicians. QBI has outstanding scientists and is very well equipped in mass spectrometry and DNA sequencing and that will be very useful in developing our own research in the future,” said Bruno Goud, former director of the research center at Institut Curie.

Next year, a second symposium will be held in San Francisco to further the collaborative exchange. In the meantime, UCSF and Institut Curie are in the process of finalizing an agreement to each contribute funds to create collaborative grants for scientists on both sides.

The hope is that this seed funding will lead to larger funding from federal agencies in both countries as well as from philanthropic opportunities that are presently being pursued.

View the photo gallery here 
View more details on the symposium here

 

The speakers included UCSF researchers Sourav Bandyopadhyay, Jennifer Grandis, Isha Jain, Natalia Jura, Nevan Krogan, Rushika Perera, Davide Ruggero, Kevan Shokat and Danielle Swaney. Scientists from Institut Curie and Q-Life included Olivier Ayrault, Emmanuel Barillot, Renata Basto, Aura Carreira, Emmanuel Farge, Anne Houdusse, Matthieu Piel, Raphael Rodriguez, Celine Vallot and Danijela Vignjevic. 

 

Seminars

All Institut Curie seminars

Planning Seminars in Orsay

nanoparticles in F98 glioma cells: first FTIR studies at the Emira laboratory of the SESAME synchrotron.

One strategy to improve the clinical outcome of radiotherapy is to use nanoparticles as radiosensitizers. Along this line, numerous studies have shown the enhanced effectiveness of tumour cell killing when nanoparticles are exposed to irradiation. However, the mechanisms of action are not clear yet. In addition to the damage due to a possible local radiation dose enhancement, the interaction of nanoparticles with essential biological macromolecules could lead to changes in the cells, such as cell arrest at radiosensitive phases. Within this framework, vibrational spectroscopy was used to investigate the biochemical changes in F98 glioma cells induced by X-ray irradiations combined with gadolinium nanoparticles. Fourier transform infrared (FTIR) microspectroscopy experiments were performed at the Emira laboratory of the SESAME synchrotron (Jordan), allowing the characterisation of spectral signatures of nanoparticle-induced effects in glioma cells. Multivariate analysis of the spectra recorded using principal component analysis reveals clear differences in the DNA, protein and lipid regions in the presence of nanoparticles. Prior to irradiation, results show that nanoparticles induce biochemical modifications in the cells, probably due to changes in the cellular function. Biochemical alterations are amplified in the presence of radiation. In particular, variations in the intensity and in the position of the PO2(-) symmetric and asymmetric modes are observed due to radiation damage to the DNA, which is increased in nanoparticle-treated cells. At 24 hours post-irradiation, biochemical changes related to the hallmark characteristics of cell death are detected. This includes a shift towards low wavenumbers in the amide I and II bands, relative amplitude changes in the CH2 and CH3 stretching modes, along with DNA chromatin condensation indications. Results were confirmed by two complementary cell viability assays.

Offres d’emploi

Poste d’ingénieur / lab manager
en biologie moléculaire et génétique

 

Date de Début Décembre 2019

Notre équipe est à la recherche d’un responsable de laboratoire.

Type de poste : CDD d’ingénieur d’étude (IE) à temps plein

Lieu : Institut Curie, campus principal (Paris 5ème)

Début de contrat : Idéalement Déc. 2019 (peut être repoussé)

Durée : 1 ans, renouvelable

 

PRINCIPALES FONCTIONS ET RESPONSABILITÉS

Gestion du laboratoire : Votre principale responsabilité sera de gérer et d’entretenir un laboratoire C. elegans fonctionnel. L’équipe a été créée en décembre 2018 et l’essentiel du laboratoire a déjà été mis en place. Vous poursuivrez la mise en place du laboratoire et le rendrez plus efficace en contact étroit avec le chef d’équipe et les autres membres de l’équipe.

– Organisation pratique de l’espace du laboratoire et des stocks, santé et sécurité

– Choix/achat d’équipement neuf

– Gestion quotidienne du laboratoire, commandes, suivi des stocks et du budget

Biologie moléculaire et génétique : Vous participerez aux recherches du laboratoire et, idéalement, vous poursuivrez également votre propre projet indépendant. Vous assisterez/formerez des étudiants et des post-doctorants sur des questions techniques liées à la biologie moléculaire et cellulaire et la génétique. Ces missions incluront :

  • Création et gestion de bases de données de laboratoire, commande de réactifs et préparation de solutions
  • Réalisation d’expériences génétiques, de croisements, etc.
  • Clonage moléculaire et génération de souches transgéniques, micro-injections, par exemple en utilisant MosSCI & CRISPR/Cas9

 

PROFIL ET EXPERTISE

Compétences essentielles et expérience

  • Au moins 3 ans d’expérience dans un laboratoire de recherche après un diplôme universitaire (licence, master) en biologie moléculaire et/ou cellulaire ou dans une discipline similaire
  • Maitrise de l’anglais et du français (oral et écrit)
  • Expérience de management d’équipe (commande, sécurité, etc.)
  • Autonomie, dynamisme, sens de l’organisation et des responsabilité, intérêt pour la recherche interdisciplinaire, capacité à travailler dans une équipe diversifiée et multiculturelle.

Compétences souhaitables

  • Expérience avec elegans (entretien et manipulation de base, micro-injections)
  • Expérience en microscopie et en analyse d’images

Nous recherchons activement des candidats avec des profils diversifiés. Nous encourageons les candidats de tous âges, capacités, identités et expressions sexuelles, origines nationales, races et ethnies, croyances religieuses et orientations sexuelles à poser leur candidature.

 

COMMENT DEPOSER SA CANDIDATURE

Merci d’adresser votre dossier de candidature (CV, lettre de motivation et nom/email de 2-3 référents) à wolfgang.keil@curie.fr, en indiquant “Candidature WK-LM1” dans l’objet du mail.