京都大学 / 新制・課程博士 / 博士(医科学) / 甲第25008号 / 医科博第155号 / 新制||医科||10(附属図書館) / 京都大学大学院医学研究科医科学専攻 / (主査)教授 伊藤 貴浩, 教授 藤田 恭之, 教授 伊藤 能永 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Aim: This study aims to identify pyroptosis-related genes (PRGs), their functional immune characteristics, and distinct pyroptosis-related clusters in periodontitis. Methods: Differentially expressed (DE)-PRGs were determined by merging the expression profiles of GSE10334, GSE16134, and PRGs obtained from previous literatures and Molecular Signatures Database (MSigDB). Least absolute shrinkage and selection operator (LASSO) regression was applied to screen the prognostic PRGs and develop a prognostic model. Consensus clustering was applied to determine the pyroptosisrelated clusters. Functional analysis and single-sample gene set enrichment analysis (ssGSEA) were performed to explore the biological characteristics and immune activities of the clusters. The hub pyroptosis-related modules were defined using weighted correlation network analysis (WGCNA). Results: Of the 26 periodontitis-related DE-PRGs, the highest positive relevance was for High-Mobility Group Box 1 (HMGB1) and SR-Related CTD Associated Factor 11 (SCAF11). A 14-PRG-based signature was developed through the LASSO model. In addition, three pyroptosis-related clusters were obtained based on the 14 prognostic PRGs. Caspase 3 (CASP3), Granzyme B (GZMB), Interleukin 1 Alpha (IL1A), IL1Beta (B), IL6, Phospholipase C Gamma 1 (PLCG1) and PYD And CARD Domain Containing (PYCARD) were dysregulated in the three clusters. Distinct biological functions and immune activities, including human leukocyte antigen (HLA) gene expression, immune cell infiltration, and immune pathway activities, were identified in the three pyroptosisrelated clusters of periodontitis. Furthermore, the pink module associated with endoplasmic stress-related functions was found to be correlated with cluster 2 and was suggested as the hub pyroptosis-related module. Conclusion: The study identified 14 key pyroptosis-related genes, three distinct pyroptosis-related clusters, and one pyroptosis-related gene module describing several molecular aspects of pyroptosis in the pathogenesis and immune micro-environment regulation of periodontitis and also highlighted functional heterogeneity in pyroptosisrelated mechanisms.

Simple Summary Soft tissue sarcomas (STS) are a group of rare malignant tumors with high tissue heterogeneity and poor prognosis, and which are still without effective individualized immunotherapy approaches. In this study, four potential tumor antigens, six STS immune subtypes, and six functional gene modules were identified. The different immune subtypes have different molecular, cellular, and clinical characteristics. The superiority of mRNA vaccine therapies has been demonstrated during the current pandemic as well as in tumor vaccine studies, and the present study provides guidance for future mRNA vaccine development. Furthermore, in future individualized immunotherapies for STS, it is possible to select different immunotherapies based on the different immune subtypes identified in this study. In fact, the immune subtypes identified in this study explain, to some extent, the failure of immunotherapy for certain STS subtypes in previous clinical trials, and facilitate further understanding of strategy selection for the immunotherapy of STS. To our knowledge, this is the first study to address STS mRNA vaccine development and immunophenotyping. This study provides a theoretical framework for STS mRNA vaccine development and the selection of patients for vaccination and provides a reference for promoting individualized immunotherapy. Abstract Soft tissue sarcomas (STS) are a rare disease with high recurrence rates and poor prognosis. Missing therapy options together with the high heterogeneity of this tumor type gives impetus to the development of individualized treatment approaches. This study identifies potential tumor antigens for the development of mRNA tumor vaccines for STS and explores potential immune subtypes, stratifying patients for immunotherapy. RNA-sequencing data and clinical information were extracted from 189 STS samples from The Cancer Genome Atlas (TCGA) and microarray data were extracted from 103 STS samples from the Gene Expression Omnibus (GEO). Potential tumor antigens were identified using cBioportal, the Oncomine database, and prognostic analyses. Consensus clustering was used to define immune subtypes and immune gene modules, and graph learning-based dimensionality reduction analysis was used to depict the immune landscape. Finally, four potential tumor antigens were identified, each related to prognosis and antigen-presenting cell infiltration in STS: HLTF, ITGA10, PLCG1, and TTC3. Six immune subtypes and six gene modules were defined and validated in an independent cohort. The different immune subtypes have different molecular, cellular, and clinical characteristics. The immune landscape of STS reveals the immunity-related distribution of patients and intra-cluster heterogeneity of immune subtypes. This study provides a theoretical framework for STS mRNA vaccine development and the selection of patients for vaccination, and provides a reference for promoting individualized immunotherapy.

Au cours de ma thèse, je me suis intéressée à une population cellulaire rare et peu étudiée de l’épithélium intestinal ; les cellules tuft. La fonction de ces cellules fut longtemps débattue dans la littérature, jusqu’à ce que nous découvrions leur fonction dans l’initiation de la réponse immune de type II en réponse à une infection parasitaire. De manière intéressante, ces cellules sont présentes de manière massive et transitoire au sein des lésions adénomateuses précoces et certains groupes ont suggéré l’implication de ces cellules en tant que cellules souches tumorales. Les principaux objectifs de ma thèse ont été de déterminer le rôle des cellules tuft au cours de la tumorigenèse intestinale et colorectale.Nous avons montré que l’absence de cellules tuft impacte le processus de tumorigenèse à la fois dans l’intestin grêle, dans des souris de la lignée Apc14/+, et au niveau du colon, après traitement avec un agent carcinogène. Nos données indiquent que si les cellules tuft n’agissent pas en tant que cellules souches tumorales, leur absence impacte certaines populations de cellules immunitaires. Afin de déterminer les mécanismes permettant aux cellules tuft de moduler le microenvironnement immunitaire, nous avons identifié par analyse transcriptomique de cellules tuft isolées par cytométrie en flux, des gènes codant pour des médiateurs connus pour être impliqués dans la communication avec le système immunitaire. Des analyses in-vivo, permettront de valider d’un point de vue fonctionnel l’implication de ces médiateurs immunitaires dans la fonction immuno-régulatrice des cellules tuft ainsi que dans le développement tumoral.L’ensemble de ces travaux a permis d’identifier une fonction immuno-régulatrice des cellules tuft au cours d’une infection parasitaire, mais aussi très probablement lors du développement tumoral. La compréhension des mécanismes permettant aux cellules tuft de moduler certaines populations de cellules immunitaires permettra d’identifier des cibles d’intérêt thérapeutique potentiel pour le traitement de patients atteints d’un cancer colorectal. / I focused my PhD project on a scare epithelial cell population referred as tuft cells. Their function has been debated for decades in the literature, until we discovered their crucial role in the initiation of the so-called type-2 immune response following parasitic infection. Interestingly, tuft cells are present in early adenomatous intestinal lesions and literature suggested that these cells could act as cancer stem cells. The main objective of my PhD was to determine the tuft cell function during intestinal and colorectal cancer.We showed that tuft cells deficiency impacts both intestinal and colorectal tumorigenesis process, using Apc14/+ mouse strain and chemically induced carcinogenesis model, respectively. Our data indicate that tuft cells are not cancer stem cells, but that these cells are able to regulate immune cell populations. To get more insights into mechanisms allowing tuft cells to modulate the immune microenvironment, we identified, by transcriptomic analysis of FACS-isolated tuft cells, specific genes encoding mediators involved in the crosstalk with the immune system. Functional in-vivo validation of the most relevant candidates will identify tuft cells derived factors crucial for the immune-regulatory tuft cell function and for tumor development.This work allowed to highlight the immune-regulatory function of tuft cells during parasitic infection and likely during tumor development. A better knowledge of the mechanisms allowing tuft cells to shape either a pro- or an anti-tumoral microenvironment, will potentially paves the way for new therapeutic strategies regarding intestinal and colorectal tumorigenesis.

Le carcinome hépatocellulaire (CHC) est la deuxième cause de mortalité par cancer dans le monde. Plusieurs études attestent du rôle du microenvironnement tumoral (MET) comme acteur fondamental de la carcinogenèse. A l’aide de modèles murins mimant un sous groupe de CHC fréquent, notre équipe avait identifié la molécule LECT2 comme un effecteur moléculaire important du MET dans le contrôle de l’agressivité tumorale.L'objectif de ma thèse a été d’adresser le rôle fonctionnel de LECT2 dans le microenvironnement immunitaire au cours du CHC.A l’aide de modèles murins, nous observons que l’absence de LECT2 entraine une accumulation importante de cellules myéloïdes dans le MET. Nous montrons que ces cellules myéloïdes sont immatures, arborent des capacités immunosuppressives puissantes vis-à-vis des lymphocytes T et ont un programme transcriptionnel permettant une action promotrice de tumeurs. De façon intéressante, l’accumulation de ces acteurs dans le microenvironnement est associée à l’émergence de nodules tumoraux indifférenciés exprimant des marqueurs de transition épithélio-mésenchymateuse/cellules progénitrices/métastases.D’un point de vue mécanistique, nous avons démontré une perte de différenciation plus importante des hépatocytes en absence de LECT2 dans des conditions d’activation de la signalisation β-caténine. Nous montrons également par des expériences de co-culture que les cellules myéloïdes infiltrant les tumeurs en absence de LECT2 ont une forte capacité à induire une perte de différenciation des hépatocytes.Enfin, nous avons analysé l'expression de LECT2 dans une vaste cohorte d’échantillons humains de CHC. Nous montrons que la diminution d’expression de LECT2 corrèle fortement avec 1)- la présence d’invasion vasculaire, 2)- la perte de différenciation des hépatocytes tumoraux et 3)- la présence d’infiltrats inflammatoires.L’ensemble de ces données démontre que LECT2 agit comme un régulateur essentiel dans la cancérogénèse hépatique à travers son action double sur les hépatocytes et sur la fonction des cellules myéloïdes infiltrant les tumeurs. Ainsi, ces travaux identifient LECT2 comme un biomarqueur potentiel ouvrant de nouvelles perspectives de traitement du CHC. / Hepatocellular carcinoma (HCC) is the second cause of cancer-rel ated death worldwide. Several studies highlighted the tumor microenvironment (TEM) as a key player in cancer from initiation to progression steps of tumorigenesis. Using relevant HCC mouse models, our team identified the chemokine-like LECT2 as a critical actor of liver TEM in the control of tumor aggressiveness.The aim of my thesis was to address functionally the role of LECT2 in the immune microenvironment during HCC.Using mouse models, we observed that the absence of LECT2 induces a significant accumulation of myeloid cells in the TEM. We showed that these myeloid cells were immature, harbored strong immunosuppressive capabilities on T cells and expressed a transcriptional program sustaining tumor progression. Interestingly, the accumulation of these actors in the microenvironment is associated with the emergence of poorly differentiated tumor nodules expressing epithelial-to-mesenchymal transition / progenitor / metastasis markers.Mechanistically, we demonstrated that LECT2-deficient hepatocytes in the context of β-catenin activation were able to perform EMT like WT hepatocytes do after TGF-β1 challenge. In co-culture experiments, we demonstrated that tumor-infiltrating myeloid cells in the absence of LECT2 have a strong ability to induce hepatocyte EMT.Finally, we analyzed the expression of LECT2 in a vast cohort of HCC liver samples and found that downregulation of LECT2 expression strongly correlates with 1) - the presence of vascular invasion, 2) – histological grade and 3) - the presence of inflammatory infiltrates.Altogether, our data demonstrate that LECT2 acts as a strong regulator of liver tumor aggressiveness through its dual action on hepatocytes and impact on the function of tumor infiltrating myeloid cells. This work identifies LECT2 as a new biomarker for HCC and pave the way to new therapeutic strategies.

Cancer remains the second most common cause of death worldwide affecting around 10 million patients every year. Among the therapeutic options, chemotherapeutic drugs are widely used but often associated with side effects. In addition, toxicity against immune cells may hamper anti-tumor immune responses. Some chemotherapeutic drugs, however, preserve immune functions and some can even stimulate anti-tumor immune responses through the induction of immunogenic cell death (ICD) rather than apoptosis. ICD stimulates the immune system by several mechanisms including the release of damage-associated molecular patterns (DAMPs) from dying cells. In this review, we will discuss the consequences of inducing two recently characterized forms of ICD, i.e., pyroptosis and necroptosis, in the tumor microenvironment (TME) and the perspectives they may offer to increase the immunogenicity of the so-called cold tumors and to stimulate effective anti-tumor immune responses.

La morbi-mortalité élevée des carcinomes épidermoïdes de la cavité orale (CECO), qui peuvent se développer à partir de lésions orales à potentiel malin (LOPM), rend indispensable le développement de nouvelles stratégies thérapeutiques. Le décryptage de l’hétérogénéité moléculaire aux différentes étapes de la carcinogénèse orale pourrait permettre de personnaliser les stratégies thérapeutiques de prévention et de traitement de ces cancers. Notre objectif était de caractériser l’hétérogénéité transcriptomique des LOPM et des CECO.Nous avons d’abord défini des signatures transcriptomiques associées aux changements histologiques de la carcinogénèse orale observés dans le modèle murin induit par le 4-NQO, montrant la pertinence de l’analyse de la dynamique temporelle du transcriptome pour améliorer la prévention des CECO. Cependant, ce modèle ne représentant qu’un sous-groupe particulier des CECO, nous avons ensuite étudié l’hétérogénéité inter-lésionnelle des LOPM en identifiant deux sous-types transcriptomiques principaux nommés « classical » et « immunological », qui sont caractérisés par différents biomarqueurs de risque de CECO.Au stade invasif, nous avons également étudié l’hétérogénéité transcriptomique des CECO HPV-négatifs entre les patients non-fumeurs non-buveurs (NFNB) et les patients fumeurs buveurs (FB). Le microenvironnement immunitaire était la principale différence biologique entre NFNB et FB, suggérant un bénéfice accru des immunothérapies chez les NFNB. Le profil transcriptomique de réponse antivirale observé dans les CECO des NFNB pourrait être en faveur de leur origine virale. En conclusion, l’hétérogénéité transcriptomique des LOPM et CECO suggère de personnaliser les stratégies thérapeutiques des patients porteurs de ces lésions / Oral squamous cell carcinomas (OSCC), which may develop from oral premalignant lesions (OPL), are associated with a substantial morbidity and mortality. A better understanding of the molecular heterogeneity at different steps of oral carcinogenesis may help to refine prevention and treatment strategies of patients suffering from OPL and OSCC. Our goal was to decipher transcriptomic hetereogeneity of OPL as well as OSCC. Using the 4-NQO murine model of oral carcinogenesis, we first identified transcriptomic signatures that characterized the dynamics of gene expression changes through different stages of disease progression, and that could be relevant for refining prevention strategies. Because this model represents only a subgroup of patients suffering from OSCC, we then investigated inter-OPL molecular heterogeneity. We identified two distinct gene expression subtypes, which were named classical and immunological and were characterized by different biomarkers of cancer risk. At invasive steps, we investigated transcriptomic heterogeneity between HPV-negative OSCC from never-smoker never-drinker (NSND) and smoker drinker (SD) patients. The immune microenvironment was the main biological difference between OSCC from NSND and SD, suggesting higher clinical benefit of immunotherapies in OSCC from NSND. The antiviral gene expression profile of OSCC from NSND could suggest a viral origin.In conclusion, we investigated transcriptomic heterogeneity of OPL as well as OSCC, that could help to refine their prevention and treatment strategies