Correlation between MGMT promoter methylation and response to temozolomide-based therapy in neuroendocrine neoplasms: an observational retrospective multicenter study

Purpose: Temozolomide (TEM) based therapy has been reported being effective in the treatment of metastatic neuroendocrine neoplasms (NEN), with response rates ranging from 30 to 70%. Among patients affected by advanced glioblastoma or melanoma and treated with TEM, loss of tumoral O6-methylguanine DNA methyltransferase (MGMT) is correlated with improved survival. In NEN patients, the role of MGMT deficiency in predicting clinical outcomes of TEM treatment is still under debate. Methods: In this study we evaluated 95 patients with advanced NENs undergoing treatment with TEM-based therapy. MGMT promoter methylation status was evaluated with two techniques: methylation specific-polymerase chain reaction or pyrosequencing. Results: Treatment with TEM-based therapy was associated with an overall response rate of 27.4% according to RECIST criteria (51.8% of patients with and 17.7% without MGMT promoter methylation). Response to therapy, progression free survival and overall survival was correlated to MGMT status at univariate and multivariate analysis. Methylation of MGMT promoter could be a strong predictive factor of objective response and an important prognostic factor of a longer PFS and OS. Conclusion: According to our results, MGMT methylation status, evaluated with methylation specific-polymerase chain reaction or pyrosequencing, should have an important role in patients with metastatic NENs, in order to guide therapeutic options. These results need further confirmation with prospective studies

Study of the androgen receptor in molecular apocrine breast cancer

Les cancers du sein hormono-indépendants et HER2 non amplifiés, dites triples négatives (TN), représentent 30 % des tumeurs du sein. Elles sont de mauvais pronostic et ne bénéficient pas actuellement de thérapeutiques ciblées.Les tumeurs du sein apocrine moléculaire (AM) sont des tumeurs qui se caractérisent par l’absence de récepteurs hormonaux et la présence du récepteur aux androgènes (RA) dont la voie de signalisation est activée. Dans 50 % des cas elles sont HER2 négatives, et entrent alors dans la catégorie des TN.Le rôle de cette signalisation androgénique est mal connu. Cependant elle apparait comme une cible thérapeutique intéressante dans ce groupe de tumeur ne bénéficiant pas des thérapies ciblées. De plus peu de modèles précliniques représentatifs des tumeurs AM ont été publiés.Dans ce projet nous avons exploré le RA et sa signalisation à partir de modèles de lignées cellulaires.Nous avons d’abord caractérisé ces modèles sur le plan mutationnel en séquençant le RA et en recherchant des altérations moléculaires dans les voies de signalisation des récepteurs hormonaux et des facteurs de croissance puis sur le plan transcritpomique en vérifiant la présence d’une signature AM moléculaire et en recherchant des variants d’épissage du RA.Nous avons ensuite pu mettre en évidence une régulation de la prolifération et de la clonogénicité de ces lignées après blocage du RA et de sa voie de signalisation par invalidation de son expression par siRNA.Nous avons finalement pu vérifier dans plusieurs de ces modèles qu’un traitement par différents agonistes et antagonistes ciblant le RA permettait de moduler la prolifération et l’expression des gènes cibles du RA.Hormone-independent and non-amplified HER2 breast cancers, or triple negative (TN), represent 30% of breast tumors. They have a poor prognosis and do not currently benefit from targeted therapies.Molecular apocrine (MA) breast cancers are characterized by the absence of hormone receptors and the presence of the androgen receptor (AR) which signaling pathway is activated. In 50% of cases they are HER2 negative, and then fall into the category of TN.The role of the androgen signaling is poorly understood. However the AR appears as an attractive therapeutic target in this group of tumors without targeted therapies. Moreover few preclinical models of MA have been published.In this project we explored the AR and its signaling in cell lines models.We first characterized these models on the mutational level by sequencing the AR and seeking molecular alterations in the signaling pathways of hormone receptors and growth factors. Then on the transcritpomique level by checking the presence of a molecular MA signature and seeking the AR splice variants.We then could highlight a regulation of cell proliferation and clonogenicity in these cell lines by blocking the AR and its signaling pathway with siRNAs.We were finally able to check in several of these models that treatment with different agonists and antagonists targeting the AR allowed to modulate cell proliferation and the expression of AR target genes

A Unique TGFB1-Driven Genomic Program Links Astrocytosis, Low-Grade Inflammation and Partial Demyelination in Spinal Cord Periplaques from Progressive Multiple Sclerosis Patients

International audienceWe previously reported that, in multiple sclerosis (MS) patients with a progressive form of the disease, spinal cord periplaques extend distance away from plaque borders and are characterized by the co-occurrence of partial demyelination, astrocytosis and low-grade inflammation. However, transcriptomic analyses did not allow providing a comprehensive view of molecular events in astrocytes vs. oligodendrocytes. Here, we re-assessed our transcriptomic data and performed co-expression analyses to characterize astrocyte vs. oligodendrocyte molecular signatures in periplaques. We identified an astrocytosis-related co-expression module whose central hub was the astrocyte gene Cx43/GJA1 (connexin-43, also named gap junction protein α-1). Such a module comprised GFAP (glial fibrillary acidic protein) and a unique set of transcripts forming a TGFB/SMAD1/SMAD2 (transforming growth factor β/SMAD family member 1/SMAD family member 2) genomic signature. Partial demyelination was characterized by a co-expression network whose central hub was the oligodendrocyte gene NDRG1 (N-myc downstream regulated 1), a gene previously shown to be specifically silenced in the normal-appearing white matter (NAWM) of MS patients. Surprisingly, besides myelin genes, the NDRG1 co-expression module comprised a highly significant number of translation/elongation-related genes. To identify a putative cause of NDRG1 downregulation in periplaques, we then sought to identify the cytokine/chemokine genes whose mRNA levels inversely correlated with those of NDRG1. Following this approach, we found five candidate immune-related genes whose upregulation associated with NDRG1 downregulation: TGFB1(transforming growth factor β 1), PDGFC (platelet derived growth factor C), IL17D (interleukin 17D), IL33 (interleukin 33), and IL12A (interleukin 12A). From these results, we propose that, in the spinal cord periplaques of progressive MS patients, TGFB1 may limit acute inflammation but concurrently induce astrocytosis and an alteration of the translation/elongation of myelin genes in oligodendrocytes

An architecture for genomics analysis in a clinical setting using Galaxy and Docker

International audienceNext-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software. Our solution simplifies the deployment of a small-size analytical platform and simplifies the process for the clinician. From the technical point of view, the tools embedded in the platform are isolated and versioned through Docker images. Along the Galaxy platform, we also introduce the AnalysisManager, a solution that allows single-click analysis for biologists and leverages standardized bioinformatics application programming interfaces. We added a Shiny/R interactive environment to ease the visualization of the outputs. The platform relies on containers and ensures the data traceability by recording analytical actions and by associating inputs and outputs of the tools to EDAM ontology through ReGaTe. The source code is freely available on Github at https://github.com/CARPEM/GalaxyDocker

Bevacizumab as Single Agent in Children and Teenagers with Optic Pathway Glioma

This is a retrospective study conducted on patients with OPG, aged less than 19 years, treated with bevacizumab as a single agent, since 2010 at IHOPe (Institute of Pediatric Hematology and Oncology). Efficacy of the treatment was evaluated on the tumor response rate on MRI with a centralized review basing upon RAPNO criteria and with visual assessment basing upon a 0.2 log change in the logMAR scale. Thirty-one patients with OPG have been included. From a radiological point of view, best anytime responses were: 1 major response, 6 partial responses, 7 minor responses and 14 stable diseases; achieving disease control in 28 (96%) out of 29 patients. Ophthalmological response was evaluated in 25 patients and disease control was achieved in 22 (88%) out of 25, with 14 steady states and 8 significant improvements. Among patients treated with chemotherapy after the bevacizumab course, nine relapsed and have been retreated with objective responses. Bevacizumab used as single agent seems effective in children and adolescents with OPG. Our work paves the way for a phase II study in which bevacizumab alone could be used as frontline therapy

Conventional MRI radiomics in patients with suspected early- or pseudo-progression

International audienceAbstract Background After radiochemotherapy, 30% of patients with early worsening MRI experience pseudoprogression (Psp) which is not distinguishable from early progression (EP). We aimed to assess the diagnostic value of radiomics in patients with suspected EP or Psp. Methods Radiomics features (RF) of 76 patients (53 EP and 23 Psp) retrospectively identified were extracted from conventional MRI based on four volumes-of-interest. Subjects were randomly assigned into training and validation groups. Classification model (EP versus Psp) consisted of a random forest algorithm after univariate filtering. Overall (OS) and progression-free survivals (PFS) were predicted using a semi-supervised principal component analysis, and forecasts were evaluated using C-index and integrated Brier scores (IBS). Results Using 11 RFs, radiomics classified patients with 75.0% and 76.0% accuracy, 81.6% and 94.1% sensitivity, 50.0% and 37.5% specificity, respectively, in training and validation phases. Addition of MGMT promoter status improved accuracy to 83% and 79.2%, and specificity to 63.6% and 75%. OS model included 14 RFs and stratified low- and high-risk patients both in the training (hazard ratio [HR], 3.63; P = .002) and the validation (HR, 3.76; P = .001) phases. Similarly, PFS model stratified patients during training (HR, 2.58; P = .005) and validation (HR, 3.58; P = .004) phases using 5 RF. OS and PFS forecasts had C-index of 0.65 and 0.69, and IBS of 0.122 and 0.147, respectively. Conclusions Conventional MRI radiomics has promising diagnostic value, especially when combined with MGMT promoter status, but with moderate specificity. In addition, our results suggest a potential for predicting OS and PFS

Molecular Characterization of Adult Tumors Diagnosed as Cerebellar Glioblastomas Identifies Subgroups Associated With Prognosis

International audienceAdult tumors diagnosed as cerebellar glioblastoma (cGBM) are rare and their optimal classification remains to be determined. The aim of this study was to identify subgroups of cGBM based on targeted molecular analysis. cGBM diagnosed between 2003 and 2017 were identified from the French Brain Tumor Database and reviewed according to the WHO 2021 classification. The following molecular alterations were studied: IDH1/2, H3F3A, FGFR1, BRAF, TERT promoter mutations, EGFR amplification, MGMT promoter methylation, and alternative lengthening of telomere status. DNA methylation profile was assessed in a subset of cases. Eighty-three cGBM were included and could be classified into 6 mutually exclusive subgroups associated with median age at diagnosis (MA) and prognosis: TERT-mutant and/or EGFR-amplified tumors (n=22, 26.5%, MA=62 y, median overall survival [OS]=4 mo), H3K27M-mutant tumors (n=15, 18.1%, MA=48 y, median OS=8 mo), mitogen-activated protein kinases (MAPK) pathway-activated tumors (FGFR1, BRAF mutation, or occurring in neurofibromatosis type I patients, n=15, 18.1%, MA=48 y, median OS=57 mo), radiation-associated tumors (n=5, 6%, MA=47 y, median OS=5 mo), IDH-mutant tumors (n=1), and unclassified tumors (n=25, 30.1%, MA=63 y, median OS=17 mo). Most MAPK pathway-activated tumors corresponded to high-grade astrocytomas with piloid features based on DNA methylation profiling. In multivariate analysis, MAPK pathway-activating alterations, ATRX loss of expression, and alternative lengthening of telomere positivity were independently associated with a better outcome and TERT/EGFR alterations with a worse outcome. cGBM display an important intertumoral heterogeneity. Targeted molecular analysis enables to classify the majority of tumors diagnosed as cGBM into mutually exclusive and clinically relevant subgroups. The presence of MAPK pathway alterations is associated with a much better prognosis

O6-methylguanine-DNA methyltransferase (MGMT) status in neuroendocrine tumors: a randomized phase II study (MGMT-NET)

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Radiological Characteristics and Natural History of Adult IDH-Wildtype Astrocytomas with TERT Promoter Mutations

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