Multi-omic dataset of patient-derived tumor organoids of neuroendocrine neoplasms

Background: Organoids are 3-dimensional experimental models that summarize the anatomical and functional structure of an organ. Although a promising experimental model for precision medicine, patient-derived tumor organoids (PDTOs) have currently been developed only for a fraction of tumor types. Results: We have generated the first multi-omic dataset (whole-genome sequencing [WGS] and RNA-sequencing [RNA-seq]) of PDTOs from the rare and understudied pulmonary neuroendocrine tumors (n = 12; 6 grade 1, 6 grade 2) and provide data from other rare neuroendocrine neoplasms: small intestine (ileal) neuroendocrine tumors (n = 6; 2 grade 1 and 4 grade 2) and large-cell neuroendocrine carcinoma (n = 5; 1 pancreatic and 4 pulmonary). This dataset includes a matched sample from the parental sample (primary tumor or metastasis) for a majority of samples (21/23) and longitudinal sampling of the PDTOs (1 to 2 time points), for a total of n = 47 RNA-seq and n = 33 WGS. We here provide quality control for each technique and the raw and processed data as well as all scripts for genomic analyses to ensure an optimal reuse of the data. In addition, we report gene expression data and somatic small variant calls and describe how they were generated, in particular how we used WGS somatic calls to train a random forest classifier to detect variants in tumor-only RNA-seq. We also report all histopathological images used for medical diagnosis: hematoxylin and eosin–stained slides, brightfield images, and immunohistochemistry images of protein markers of clinical relevance. Conclusions: This dataset will be critical to future studies relying on this PDTO biobank, such as drug screens for novel therapies and experiments investigating the mechanisms of carcinogenesis in these understudied diseases

Druggable growth dependencies and tumor evolution analysis in patient-derived organoids of neuroendocrine neoplasms from multiple body sites

Neuroendocrine neoplasms (NENs) comprise well-differentiated neuroendocrine tumors (NETs) and poorly differentiated neuroendocrine carcinomas (NECs). Treatment options for patients with NENs are limited, in part due to lack of accurate models. We establish patient-derived tumor organoids (PDTOs) from pulmonary NETs and derive PDTOs from an understudied subtype of NEC, large cell neuroendocrine carcinoma (LCNEC), arising from multiple body sites. PDTOs maintain the gene expression patterns, intra-tumoral heterogeneity, and evolutionary processes of parental tumors. Through hypothesis-driven drug sensitivity analyses, we identify ASCL1 as a potential biomarker for response of LCNEC to treatment with BCL-2 inhibitors. Additionally, we discover a dependency on EGF in pulmonary NET PDTOs. Consistent with these findings, we find that, in an independent cohort, approximately 50% of pulmonary NETs express EGFR. This study identifies an actionable vulnerability for a subset of pulmonary NETs, emphasizing the utility of these PDTO models

Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids

International audienceThe worldwide incidence of pulmonary carcinoids is increasing, but little is known about their molecular characteristics. Through machine learning and multi-omics factor analysis, we compare and contrast the genomic profiles of 116 pulmonary carcinoids (including 35 atypical), 75 large-cell neuroendocrine carcinomas (LCNEC), and 66 small-cell lung cancers. Here we report that the integrative analyses on 257 lung neuroendocrine neoplasms stratify atypical carcinoids into two prognostic groups with a 10-year overall survival of 88% and 27%, respectively. We identify therapeutically relevant molecular groups of pulmonary car-cinoids, suggesting DLL3 and the immune system as candidate therapeutic targets; we confirm the value of OTP expression levels for the prognosis and diagnosis of these diseases, and we unveil the group of supra-carcinoids. This group comprises samples with carcinoid-like morphology yet the molecular and clinical features of the deadly LCNEC, further supporting the previously proposed molecular link between the low-and high-grade lung neuroendocrine neoplasms

Caractérisation génomique des tumeurs rares thoraciques

Les carcinoïdes pulmonaires (PCs) et les mésothéliomes pleuraux malins (MPMs) représentent les tumeurs rares thoraciques les plus fréquentes avec une incidence mondiale en augmentation. Les PCs comprennent les carcinoïdes typiques (TCs) et atypiques (ACs) de grade inférieur et intermédiaire, mais font tous deux partie du groupe des tumeurs neuroendocrines du poumon (LNETs). Ce groupe inclut aussi les carcinomes pulmonaires neuroendocriniens à grandes cellules (LCNECs) et les cancers du poumon à petites cellules (SCLCs), tous deux classés comme tumeurs de haut grade. Au sein des MPMs sont reconnus : les épithélioïdes, biphasiques et sarcomatoïdes avec un pronostic relativement meilleur, intermédiaire et mauvais, respectivement. Ces différents types tumoraux au sein des LNETs et des MPMs diffèrent par leur malignité et correspondent donc à des pronostics et à des stratégies thérapeutiques différentes. Alors que leur classification appropriée est essentielle, il existe toujours une grande variabilité inter-observateur lors du diagnostic et les opportunités thérapeutiques restent limitées pour ces patients. En effet, les TCs et les ACs sont souvent confondus ainsi que les ACs et les LCNECs. Alors que la plupart des TCs peuvent faire l'objet de résection chirurgicale, certains ACs et la majorité des LCNECs et SCLCs sont déjà trop agressives et requièrent des stratégies thérapeutiques multimodales. Dans le cas des MPMs, les trois types reconnus ont une valeur prédictive limitée de la survie des patients qui meurent souvent deux ans après leur diagnostic devenus réfractaires à tous les traitements conventionnels. De plus, les MPMs semblent montrer des réponses hautement hétérogènes à des thérapies plus innovantes, sans réelle explication pour ces différents comportements. Alors que par leur rareté ces cancers restent sous-étudiés et pauvrement compris, leur survie globale est souvent plus faible que pour des cancers plus communs. De grandes études de caractérisation génomique pourraient promouvoir une meilleure compréhension des mécanismes sous-jacents à leur développement et informer leur classification pour un meilleur diagnostic et ouvrir de nouvelles perspectives thérapeutiques. L’objectif de cette thèse vise à (1) fournir les pièces manquantes à une meilleure caractérisation moléculaires de ces tumeurs thoraciques rares; (2) investiguer les voies moléculaires responsables des liens et les distorsions entre ces différents types tumoraux; et (3) transférer les résultats des points 1 et 2 à un niveau clinique pouvant directement bénéficier aux patients. Lors de cette thèse, nous avons réuni des données omiques pour un total de 63 PCs, 20 LCNECs et 124 MPMs en plus de 74 PCs, 75 LCNECs, 66 SCLCs et 284 MPMs déjà publiées. Des analyses non-supervisées ont permis de comparer la classification histologique avec le profil moléculaire de ces tumeurs mettant en évidence l’existence de trois clusters de PC avec des profils moléculaires très spécifiques et d’un continuum moléculaire des types épithélioïdes jusqu'aux sarcomatoïdes en passant par les biphasiques. De plus, ces groupes et ce continuum ont une valeur pronostique, permettant l'identification des voies sous-jacentes à ces différences d’agressivité. Une analyse intégrant les quatre types de LNET a révélé l’existence d’une nouvelle entité, appelée les “supra-carcinoïdes” correspondant à des tumeurs présentant la morphologie des PCs mais avec les caractéristiques moléculaires et cliniques des LCNECs. Une analyse intégrative des profils génomiques, transcriptomiques et du méthylome des MPMs a révélé quatre axes de variations moléculaires indépendants pouvant expliquer les différences de comportement des MPMs. Ces découvertes ensemble tendent à informer la classification de ces tumeurs basée sur une meilleure compréhension de leurs similarités et différences visant à une meilleure prédiction du pronostic et de nouvelles stratégies thérapeutiques.Pulmonary carcinoids (PCs) and malignant pleural mesothelioma (MPMs) represent the most common rare thoracic tumours with an increasing worldwide incidence. PCs include both low- and intermediate-grade typical (TCs) and atypical carcinoids (ACs) both belonging to the group of the lung neuroendocrine tumours (LNETs). This group also includes large cell neuroendocrine carcinomas (LCNECs) and small cell lung cancers (SCLCs), both classified as high-grade tumours. Among the MPMs are recognised: epithelioid, biphasic and sarcomatoid tumours with a relatively good-, intermediate- and poor-prognosis, respectively. These diverse tumour types among the LNETs and MPMs differ in their malignancy and therefore refer to variable prognoses and therapeutic strategies. While their appropriate classification is essential, inter-observer variations remain common in diagnosis and treatment opportunities are limited for these patients. Indeed, TCs and ACs are often difficult to distinguish and misclassifications occur when ACs and LCNECs need to be separated. While most TCs can be surgically resected, some ACs and the majority of LCNECs and SCLCs are already too aggressive at the time of diagnosis and require multimodal therapeutic strategies. In the case of MPMs, the three recognised types have prognosis but limited predictive value for patients who often die two years after their diagnosis because their tumour has become refractory to all conventional treatments. In addition, MPMs seem to show highly heterogeneous responses to more innovative therapies, with no real explanation for these different behaviours. While, by their rarity, these cancers remain under-studied and poorly understood, their overall survival is lower than more common cancers. Large genomic characterisation studies would promote a better understanding of the mechanisms underlying their development and inform their classification for a better diagnosis and would pave the way to new therapeutic perspectives. The main objectives of this thesis is to (1) provide the missing pieces for a deeper molecular characterisation of these rare thoracic tumours; (2) to investigate the molecular pathways responsible for the interconnections and distortions between these different tumour types; and (3) translate the results of points 1 and 2 to the clinical level that can directly benefit patients. During this thesis, we gathered omics data for a total of 63 PCs, 20 LCNECs and 124 MPMs in addition to 74 PCs, 75 LCNECs, 66 SCLCs and 284 MPMs already published. Unsupervised analyses contrasted the histological classification with the molecular profile of these tumours, revealing three PC clusters with very specific molecular profiles; and a molecular continuum of MPM types from the epithelioids to sarcomatoids thanks to the biphasics binding them together. In addition, these groups and this continuum have prognostic value, allowing the identification of the pathways underlying these differences in aggressiveness. An integrative analysis including the four LNET types unveiled the existence of a new entity, called the “supra-carcinoids” corresponding to tumours with a PC morphology but with molecular and clinical LCNEC characteristics. Integrative analyses of the genomic, transcriptomic and DNA methylation profiles of MPMs revealed four axes of independent molecular variations that could explain the differences in behaviour of the MPMs. Taken together, these findings tend to inform the classification of these tumours based on a better understanding of their similarities and discrepancies aiming at a more accurate prognosis prediction and new therapeutic strategies

Differential Orthopedia Homeobox expression in pulmonary carcinoids is associated with changes in DNA methylation

Limited number of tumor types have been examined for Orthopedia Homeobox (OTP) expression. In pulmonary carcinoids, loss of expression is a strong indicator of poor prognosis. Here, we investigated OTP expression in 37 different tumor types, and the association between OTP expression and DNA methylation levels in lung neuroendocrine neoplasms. We analyzed publicly available multi-omics data (whole-exome-, whole-genome-, RNA sequencing and Epic 850K-methylation array) of 58 typical carcinoids, 27 atypical carcinoids, 69 large cell neuroendocrine carcinoma and 51 small cell lung cancer patients and TCGA (The Cancer Genome Atlas) data of 33 tumor types. 850K-methylation analysis was cross-validated using targeted pyrosequencing on 35 carcinoids. We report bimodality of OTP expression in carcinoids (OTPhigh vs OTPlow group, likelihood-ratio test P = 1.5 × 10−2), with the OTPhigh group specific to pulmonary carcinoids while absent from all other cohorts analyzed. Significantly different DNA methylation levels were observed between OTPhigh and OTPlow carcinoids in 12/34 OTP infinium probes (FDR .2). OTPlow carcinoids harbor high DNA methylation levels as compared to OTPhigh carcinoids. OTPlow carcinoids showed a significantly worse overall survival (log-rank test P =.0052). Gene set enrichment analysis for somatically mutated genes associated with hallmarks of cancer showed robust enrichment of three hallmarks in the OTPlow group, that is, sustaining proliferative signaling, evading growth suppressor and genome instability and mutation. Together our data suggest that high OTP expression is a unique feature of pulmonary carcinoids with a favorable prognosis and that in poor prognostic patients, OTP expression is lost, most likely due to changes in DNA methylation levels

Druggable growth dependencies and tumor evolution analysis in patient-derived organoids of neuroendocrine neoplasms from multiple body sites

Neuroendocrine neoplasms (NENs) comprise well-differentiated neuroendocrine tumors (NETs) and poorly differentiated neuroendocrine carcinomas (NECs). Treatment options for patients with NENs are limited, in part due to lack of accurate models. We establish patient-derived tumor organoids (PDTOs) from pulmonary NETs and derive PDTOs from an understudied subtype of NEC, large cell neuroendocrine carcinoma (LCNEC), arising from multiple body sites. PDTOs maintain the gene expression patterns, intra-tumoral heterogeneity, and evolutionary processes of parental tumors. Through hypothesis-driven drug sensitivity analyses, we identify ASCL1 as a potential biomarker for response of LCNEC to treatment with BCL-2 inhibitors. Additionally, we discover a dependency on EGF in pulmonary NET PDTOs. Consistent with these findings, we find that, in an independent cohort, approximately 50% of pulmonary NETs express EGFR. This study identifies an actionable vulnerability for a subset of pulmonary NETs, emphasizing the utility of these PDTO models.</p

Redefining malignant pleural mesothelioma types as a continuum uncovers immune-vascular interactions

International audienc

Disentangling heterogeneity of Malignant Pleural Mesothelioma through deep integrative omics analyses

Summary Malignant Pleural Mesothelioma (MPM) is an aggressive cancer with rising incidence and challenging clinical management. Using the largest series of whole-genome sequencing data integrated with transcriptomic and epigenomic data using multi-omic factor analysis, we demonstrate that MPM heterogeneity arises from four sources of variation: tumor cell morphology, ploidy, adaptive immune response, and CpG island methylator phenotype. Previous genomic studies focused on describing only the tumor cell morphology factor, although we robustly find the three other sources in all publicly available cohorts. We prove how these sources of variation explain the biological functions performed by the cancer cells, and how genomic events shape MPM molecular profiles. We show how these new sources of variation help understand the heterogeneity of the clinical behavior of MPM and drug responses measured in cell lines. These findings unearth the interplay between MPM functional biology and its genomic history, and ultimately, inform classification, prognostication and treatment. Graphical abstrac

Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity

International audienceAbstract Malignant pleural mesothelioma (MPM) is an aggressive cancer with rising incidence and challenging clinical management. Through a large series of whole-genome sequencing data, integrated with transcriptomic and epigenomic data using multiomics factor analysis, we demonstrate that the current World Health Organization classification only accounts for up to 10% of interpatient molecular differences. Instead, the MESOMICS project paves the way for a morphomolecular classification of MPM based on four dimensions: ploidy, tumor cell morphology, adaptive immune response and CpG island methylator profile. We show that these four dimensions are complementary, capture major interpatient molecular differences and are delimited by extreme phenotypes that—in the case of the interdependent tumor cell morphology and adapted immune response—reflect tumor specialization. These findings unearth the interplay between MPM functional biology and its genomic history, and provide insights into the variations observed in the clinical behavior of patients with MPM