Several human diseases have been associated with mitochondria! voltage-dependent anion channel-1 (VDAC1) due to its role in calcium ion transportation and apoptosis. Recent studies suggest that VDAC1 may interact with endothelium-dependent nitric oxide synthase (eNOS). Decreased VDAC1 expression may limit the physical interaction between VDAC1 and eNOS and thus impair nitric oxide production, leading to cardiovascular diseases, including pulmonary arterial hypertension (PAH). In this report, we conducted meta-analysis of genome-wide expression data to identify VDAC1 influenced genes implicated in PAH pathobiology. First, we identified the genes differentially expressed between wild-type and Vdac1 knockout mouse embryonic fibroblasts in hypoxic conditions. These genes were deemed to be influenced by VDAC1 deficiency. Gene ontology analysis indicates that the VDAC1 influenced genes are significantly associated with PAH pathobiology. Second, a molecular signature derived from the VDAC1 influenced genes was developed. We suggest that, VDAC1 has a protective role in PAH and the gene expression signature of VDAC1 influenced genes can be used to i) predict severity of pulmonary hypertension secondary to pulmonary diseases, ii) differentiate idiopathic pulmonary artery hypertension (IPAH) patients from controls, and iii) differentiate IPAH from connective tissue disease associated PAH.

Bronchopulmonary dysplasia (BPD) is a chronic lung disease and one of the most severe complications that develop in premature infants following mechanical ventilation, exposure to supplemental oxygen, and inflammation. The hallmarks of the lung pathology are arrested lung development, including fewer and larger alveoli with less septation, thickening of alveolar septa, and impaired development of the capillary network. BPD is associated with increased mortality, respiratory morbidity, neurodevelopmental impairment, and increased healthcare costs. Significant advancements in neonatology in the last several decades, including antenatal steroids and exogenous surfactant replacement therapy, more gentle ventilation methods, and judicious oxygen use, have allowed for the survival of more preterm infants. However, the incidence of BPD still remains high and currently, there is no cure for the disease. Novel effective interventions at this stage of life are of exceptional value. Considering their great potential in promoting tissue regeneration and modulating inflammation, mesenchymal stromal cells (MSCs) represent a promising avenue for treating several disorders, including BPD. Umbilical cord-derived MSCs (UC-MSCs) offer biological advantages over other MSC sources (easily available, high proliferative capacity, and better repair efficacy). Pioneering work in our lab showed that MSCs prevent injury to the developing lung in a rat model mimicking BPD. However, there are still considerable challenges that must be overcome before MSCs can be effectively implemented in clinical trials. As such, UC-MSC heterogeneity is poorly understood, with concerns regarding variations from donors and batches. Thus, to improve the reproducibility of basic research and clinical applications, and to identify the optimal therapeutic cell product, better molecular characterization of UC-MSCs and the development of standardized BPD models will be essential in the clinical translation of MSC therapy for BPD. Moreover, considering that BPD is a disease of prematurity, the therapeutic potential of UC-MSCs isolated from preterm birth is of major interest. In the study presented here, using single-cell RNA sequencing (scRNA-seq), we characterized MSCs isolated from the UC of term and preterm pregnancies at delivery (term and preterm donors), as well as non-progenitor control cell line, human neonatal dermal fibroblasts (HNDFs). Moreover, we associated UC-MSC transcriptomic profiles with their therapeutic potential in hyperoxia-induced lung injury in neonatal rats. Finally, we developed and characterized a novel two-hit (2HIT) BPD model in neonatal mice, assessed UC-MSCs' optimal route of injection, timing, and dose, and evaluated their therapeutic effects in that model. We showed that UC-MSCs isolated from the majority of term and preterm donors, including preterm donors with pregnancy-related complications, have limited heterogeneity and possessed a transcriptome enriched in genes related to cell cycle and cell proliferation activity (termed "progenitor-like" cells). In contrast, UC-MSCs isolated from one term and two preterm donors with preeclampsia displayed a unique transcriptome comprised of many genes related to fibroblast activity, including extracellular matrix (ECM) organization (termed "fibroblast-like" cells). In addition, treatment with progenitor-like UC-MSCs, but not with fibroblast-like cells nor HNDFs, significantly improved lung structure, function, and pulmonary hypertension (PH) in hyperoxia-induced lung injury in neonatal rats. We identified marker genes for the therapeutic UC-MSCs (progenitor-like cells) and non-therapeutic cells (fibroblast-like cells and HNDFs). Among them, the high expression of major histocompatibility complex class I (MHCI) is associated with a reduced therapeutic effect. Furthermore, we developed a novel 2HIT BPD mice model with in-depth characterization of the innate immune response and lung injury. 2HIT injury caused a transient type 1 proinflammatory cytokine response and a significant decrease in type 2 anti-inflammatory cytokine lung expression and number of anti-inflammatory M2 type alveolar macrophages. Moreover, 2HIT mice showed impaired lung compliance and growth. Repeated intravenous (i.v.) injections of UC-MSCs at a dose of 20×10⁶ cells/kg body weight (BW) on postnatal day (PD) one and two improved survival, BW, lung compliance, and growth of 2HIT animals. In conclusion, scRNA-seq experimentation provided evidence that UC-MSCs isolated from different donors harbor different transcriptomes with progenitor-like or fibroblast-like characteristics. Only progenitor-like cells provided a therapeutic effect in hyperoxia-induced lung injury in neonatal rats. The development of a novel murine 2HIT BPD model allowed us to characterize the innate immune response and lung pathology and confirm the optimal dose of UCMSCs to provide therapeutic potential in that model. These results will enable better therapeutic selection of UC-MSCs and help improve treatment regimen prior to ultimate clinical translation.

Les adénomes hépatocellulaires (AHC) sont des tumeurs hépatiques bénignes rares se développant chez la femme jeune suite à la prise de contraceptifs oraux et pouvant se compliquer d’hémorragie et de transformation maligne en carcinome hépatocellulaire (CHC). Une classification génotype/phénotype a mise en évidence trois groupes d’AHC : les AHC inactivés pour le facteur de transcription HNF1A, les AHC mutés pour la β-caténine et les AHC dit « inflammatoires » ayant une activation de la voie JAK/STAT. Nous avons identifiés des mutations activatrices du gènes GNAS, codant pour la sous unité alpha de la protéine Gs, dans un sous-groupe d’AHC inflammatoires ainsi que chez des patients avec des AHC et atteints d’un syndrome de McCune Albright, une maladie rare combinant des tumeurs endocriniennes, une dysplasie fibreuse osseuse et des taches cutanés café au lait. Cette découverte confirme les interactions entre la voie de l’AMP cyclique induite par les mutations GNAS et la voie JAK/STAT. Les CHC sont les tumeurs primitives du foie les plus fréquentes, survenant souvent sur un foie cirrhotique exposé à différents facteurs de risque comme l’hépatite B chronique, l’hépatite C chronique, l’alcool ou le syndrome métabolique. Le CHC est le résultat de l’accumulation d’altérations génétiques et épigénétiques. Premièrement, nous avons identifiés les mutations du promoteur de TERT (Telomerase reverse transcriptase) comme les altérations génétiques somatiques les plus fréquentes des CHC. Ces mutations ont été aussi retrouvées dans des lésions prénéoplasiques développées sur cirrhose suggérant leurs rôles précoces dans l’initiation tumorale et la transformation maligne. A l’inverse l’étude des mutations du promoteur de TERT et la réalisation de séquençage haut-débit dans les AHC et les transformation d’adénome en CHC nous a permis de disséquer les mécanismes de transformation maligne sur foie sain avec la présence de manière précoce d’une mutation de la β-caténine et dans un second temps l’apparition d’une mutation dans le promoteur de TERT. Par la suite, nous avons mis en évidence une signature moléculaire pronostique transcriptomique chez les patients avec CHC traités par résection hépatique. Cette signature moléculaire prédisant à la fois la récidive tumorale et le décès a été validée dans des cohortes de patients à l’étranger. Enfin, nous avons mise en évidence le rôle oncogénique de l’adeno-associated virus de type 2 dans la survenue de CHC sur foie sain via un mécanisme de mutagénèse insertionnelle dans des gènes clés de la carcinogénèse comme TERT, CCNA2, MLL4 ou TNFSF10. Ces résultats ont permit de mettre en évidence de nouveaux facteurs de risque viraux de survenue du CHC, d’identifier de nouvelles altérations génétiques impliquées dans la transformation maligne sur cirrhose et sur foie sain et permit de développer une signature moléculaire pronostique qui pourrait être utiliser dans le futur comme une aide à la stratification thérapeutique chez les patients atteint de CHC. / Hepatocellular adenomas (HCA) are rare benign liver tumors occuring in young women taking oral contraception and complications as haemorrhage or malignant transformation in hepatocellular carcinomes (HCC) could occur. A genotype/phenotype classification has defined different subgroups of tumors : HCA with inactivating mutations of HNF1A, HCA with activating mutations of β-catenin and inflammatory HCA with activation of the JAK/STAT pathway. We have identified activation mutations of GNAS, that codes for the alpha subunit of the Gs protein in a subgroup of inflammatory HCA and in patients with HCA and McCune Albright syndrom, a rare disease that combined endocrine tumor, bone fibrous dysplasia and « cafe au lait » skin macula. These findings highlight the crosstalk between the cyclic AMP pathway induced by GNAS mutation with the JAK/STAT pathway. HCC are the most frequent primary liver tumors worldwide and mainly occur on cirrhosis due to various risk factor as hepatitis B and C virus, alcohol consumption and metabolic syndrome. HCC is due to the accumulation of genetic and epigenetic alterations in the malignant hepatocytes. We have identified TERT (telomerase reverse transcriptase) promoter mutations as the most frequent somatic genetic alterations in HCC. These mutations were also found in cirrhotic premalignant nodules underlying their role in tumor initiation and malignant transformation. In contrast, the study of the different steps of malignant transformation of HCA into HCC using next generation sequencing and TERT promoter screening have shown that activatiing mutation of β-catenin is an early genetic alteration whereas TERT promoter mutation is required in a second step to promote a full malignant transformation. We have also identified a prognostic molecular signature, the 5-gene score, in patients with HCC treated by liver resection. The 5-gene score predicts tumor recurrence and disease specific survival and has been validated in different cohorts of patients worldwide. Finally, we have shown that adeno-associated virus type 2 is involved in liver carcinogenesis on normal liver through insertional mutagenesis in key cancer genes as TERT, CCNA2, MLL4 and TNFSF10. These results have underlined a new oncogenic virus involved in HCC development, identified new genetic alterations involved in malignant transformation on cirrhosis and normal liver and a new prognostic molecular signature that will help to guide treatment of patients with HCC in the future.

Nous avons développé un nouveau test de prédiction de l’efficacité de thérapies anti-cancéreuses. Ce concept se base sur la détermination d’une signature moléculaire tumorale par RT-qPCR. Cette signature est issue d’un algorithme de normalisation innovant de comparaison des données d’expression relative des cibles de la tumeur avec celles de tissus de référence. Cette normalisation offre à chaque cible de la signature un rang et un score spécifique permettant de hiérarchiser les voies pro-tumorales afin de trouver la ou les cibles dominantes responsables du développement de la tumeur. La signature comprend des cibles donnant des informations générales sur le statut et l’hétérogénéité de la tumeur, sur l’angiogenèse et la lymphangiogenèse, sur le microenvironnement tumoral et enfin sur l’activité migratoire. Une validation préclinique dans les modèles du cancer colorectal, de la prostate et du glioblastome, a montré que le test est prédictif de l’efficacité thérapeutique. / We developed a new tool for prediction of cancer treatment efficacy. Our process is based on the determination of the molecular signature which is intended to provide a clinician’s decision tool helping to select which tumor signaling pathway(s) has/have to be targeted for best therapeutic effect. This signature representing a scoring obtained by RT-qPCR through a sequential normalization process of the expression level of target genes in the tumor compared to cancer type-specific references. These genes were selected because of a good knowledge of related biological functions, a correlation between expression level and aggressiveness of the tumor, the existence of a therapeutic arsenal already in clinical use. This signature is validated in a preclinical model of colorectal cancer and prostate cancer and glioblastoma. The results obtained show that the test we developed allows to identify the most important signaling pathway implicated in the disease and to choose the best drug.

Náplní této práce je teoretický úvod a následné praktické zpracování tématu Molekulární signatura jako optimální multi-objektivní funkce s aplikací v predikci v onkogenomice. Úvodní kapitoly jsou zaměřeny na téma rakovina, zejména pak rakovina prsu a její podtyp triple negativní rakovinu prsu. Následuje literární přehled z oblasti optimalizačních metod, zejména se zaměřením na metaheuristické metody a problematiku strojového učení. Část se odkazuje na onkogenomiku a principy microarray a také na statistiku a s důrazem na výpočet p-hodnoty a bimodálního indexu. Praktická část je pak zaměřena na konkrétní průběh výzkumu a nalezené závěry, vedoucí k dalším krokům výzkumu. Implementace vybraných metod byla provedena v programech Matlab a R, s využitím dalších programovacích jazyků a to konkrétně programů Java a Python.

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