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Le carcinome séreux de haut grade (CSHG) est le sous-type histologique le plus courant du cancer de l'ovaire et demeure le cancer le plus meurtrier de l'appareil reproducteur féminin. Les récents progrès de l'immunothérapie contre le cancer ont mis en évidence un énorme potentiel thérapeutique pour les patientes confrontées à des besoins non satisfaits de soins de santé pour le traitement des CSHG. Une étape cruciale pour le développement de nouvelles stratégies thérapeutiques consiste à identifier les antigènes spécifiques des tumeurs (TSA), c’est-à-dire des antigènes majeurs d'histocompatibilité de classe I présents à la surface des cellules cancéreuses mais absents des cellules normales. Ces TSA peuvent être reconnus par les cellules T et sont des éléments essentiels dans la conception de vaccins destinés à stimuler les réponses immunitaires anticancéreuses. Les travaux menés dans le cadre de mon programme de doctorat ont porté sur l'identification et la caractérisation des TSAs dans les CSHG. Les premières études sur les TSAs ont été dirigées uniquement vers l’identification de TSAs dérivés de mutations dans les régions codantes, menant à l’identification d’antigènes très rares et privés dans les CSHG. Dans notre première étude, nous avons analysé 23 échantillons de cancer de l'ovaire en utilisant une approche protéogénomique nous permettant d'étudier à la fois les régions génomiques codantes et non codantes. Ce faisant, nous avons identifié un total de 103 TSAs, dont 91 qui ne portaient pas de mutations et dérivaient de séquences présumées non-codantes. Nous appelons ces antigènes « TSAs exprimés de manière aberrante (aeTSAs) » puisqu’ils sont exprimés de manière aberrante dans les échantillons de cancer mais absents dans les tissus normaux. Contrairement aux TSAs mutés, qui sont davantage patient- spécifiques, l’ARN codant pour les aeTSAs est exprimé par plusieurs patientes atteints d’un CSHG, celles-ci exprimant individuellement une médiane de 5 aeTSAs. De par leur nombre élevé et du fait que leur expression soit partagée dans une large population de patientes atteints de CSHG, les aeTSAs représentent des cibles intéressantes pour l'immunothérapie du cancer. En raison de leur origine principalement non codante, la nature et la régulation des aeTSAs sont peu connues. Notre seconde étude a donc porté sur la régulation de la biogenèse des aeTSAs. L’analyse de données de séquençage de l'ARN de CSHG en cellule unique a montré une expression enrichie et spécifique des gènes sources des aeTSAs dans les cellules cancéreuses. Grâce à une analyse transcriptomique plus poussée, nous avons identifié de nouveaux transcrits récurrents codant pour les aeTSAs et avons déterminé que ces transcrits sont largement surexprimés dans les CSHG. De plus, nous avons déterminé que les aeTSAs issus d'événements de traduction non canonique sont codés préférentiellement par des cadres de lecture ouverts courts et générés à partir de régions près de l'extrémité C-terminale. Finalement, nos analyses sur l'accessibilité de la chromatine et les modifications des histones supportent l’hypothèse que les transcrits codant pour les aeTSAs ont recourt à des promoteurs alternatifs, ce qui suggère un rôle important de l'épigénome du cancer dans la genèse du paysage antigénique. Nos travaux représentent la première analyse complète des antigènes provenant des régions codantes et non codantes dans les tumeurs ovariennes. Nous avons pu dresser une liste exhaustive de cibles thérapeutiques potentielles et mieux comprendre leur biogenèse. Nos travaux portant sur la découverte et la caractérisation des aeTSAs favoriseront la conception de nouvelles immunothérapies ciblant ces antigènes et ce qui sera bénéfique pour un plus grand nombre de patientes atteintes de CSHG., High-grade serous carcinoma (HGSC) is the most common histologic subtype of ovarian cancer and the most lethal cancer in the female reproductive system. Recent advances in cancer immunotherapy have highlighted enormous therapeutical potential for patients facing unmet clinical needs in HGSC treatment. A crucial step for developing new therapeutic strategies is identifying targetable tumor-specific antigens (TSAs), namely the major histocompatibility class I antigens presented on the cancer cell surface but absent from normal cells. These TSAs can be recognized by T cells and are essential elements in designing vaccines to stimulate anti-cancer immune responses. The goal of my Ph.D. thesis was to identify and characterize TSAs in HGSC. In early studies of TSAs, most groups focused solely on TSAs derived from mutations in coding regions, which reported very rare and private antigens in HGSCs. In our first study, we used a proteogenomic workflow that enabled us to survey both coding and noncoding sequences to analyse 23 ovarian cancer samples. We uncovered 103 TSAs, 91 of which were not mutated and derived mainly from allegedly noncoding sequences. We call these antigens aberrantly expressed TSAs (aeTSAs), for their lack of expression in normal tissues while being aberrantly expressed in cancer samples. Unlike the mutated TSAs unique to individual tumors, the aeTSAs have shared RNA expression in HGSC tumors, with an estimated median presentation of five per patient. Because of their number and shared expression in a large population, we consider aeTSAs attractive targets for immunotherapy. Due to their primarily noncoding origin, little is known about the nature and regulation of aeTSAs. In our second study, we explored the biogenesis of the aeTSAs. HGSC single-cell RNA sequencing data showed a malignant cell-specific/enriched expression of aeTSA source genes. Further transcriptomic profiling identified novel recurrent transcripts coding for aeTSAs and revealed broad overexpression of aeTSA-coding transcripts in HGSC. Moreover, we showed that aeTSAs derived from noncanonical translation events are coded preferably by short open reading frames and generated from regions close to the C-terminus. Our analysis of chromatin accessibility and histone modifications support a differential promoter activity for aeTSA-coding transcripts, suggesting an important role of cancer epigenome in shaping the antigen landscape. Our work is the first comprehensive analysis of ovarian tumor antigens derived from both coding and noncoding regions. We reported an extensive list of potential therapeutic targets and provided insights into their biogenesis. Our work on discovering and characterizing shared TSAs shall promote the design of new antigen-targeting immunotherapy that benefits more HGSC patients.

Background: Despite toxic side effects and limited durable response, the current standard-of-care treatment for high grade serous ovarian cancer (HGSOC) remains platinum/taxane-based chemotherapy. Given that the overall prognosis has not improved drastically over the past several decades, there is a critical need to understand the underlying mechanisms that lead to tumour development and progression. Methods: We utilized an integrative proteogenomic analysis of HGSOC tumours applying a poor prognosis gene expression signature (PPS) as a conceptual framework to analyse orthogonal genomic and proteomic data from the TCGA (n = 488) and CPTAC (n = 169) studies. Genes identified through in silico analyses were assessed in vitro studies to demonstrate their impact on proliferation and cell cycle progression. Findings: These analyses identified DNA amplification and overexpression of the transcription factor ADNP (Activity Dependent Neuroprotector Homeobox) in poorly prognostic tumours. Validation studies confirmed the prognostic capacity of ADNP and suggested an oncogenic role for this protein given the association between ADNP expression and pro-proliferative signalling. In vitro studies confirmed ADNP as a novel and essential mediator of cell proliferation through dysregulation of cell cycle checkpoints. Interpretation: We identified ADNP as being amplified and overexpressed in poor prognosis HGSOC in silico analyses and demonstrated that ADNP is a novel and essential oncogene in HGSOC which mediates proliferation through dysregulation of cell cycle checkpoints in vitro. Funding: The National Cancer Institute of the National Institutes of Health, the V Foundation for Cancer Research and the New Jersey Commission for Cancer Research. Keywords: High-grade serous ovarian cancer, HGSOC, Proteogenomic, ADNP, Poor prognostic marker

Studies on small quantity, highly complex protein samples, such as salivary pellicle, have been enabled by recent major technological and analytical breakthroughs. Advances in mass spectrometry-based computational proteomics such as Multidimensional Protein Identification Technology have allowed precise identification and quantification of complex protein samples on a proteome-wide scale, which has enabled the determination of corresponding genes and cellular functions at the protein level. The latter was achieved via protein-protein interaction mapping with Gene Ontology annotation. In recent years, the application of these technologies has broken various barriers in small-quantity-complex-protein research such as salivary pellicle. This review provides a concise summary of contemporary proteomic techniques contributing to (1) increased complex protein (up to hundreds) identification using minute sample sizes (µg level), (2) precise protein quantification by advanced stable isotope labelling or label-free approaches and (3) the emerging concepts and techniques regarding computational integration, such as the Gene Ontology Consortium and protein-protein interaction mapping. The latter integrates the structural, genomic, and biological context of proteins and genes to predict protein interactions and functional connections in a given biological context. The same technological breakthroughs and computational integration concepts can also be applied to other low-volume oral protein complexes such as gingival crevicular or peri-implant sulcular fluids.

Glioblastoma (GBM) is the most aggressive nervous system cancer. Understanding its molecular pathogenesis is crucial to improving diagnosis and treatment. Integrated analysis of genomic, proteomic, post-translational modification and metabolomic data on 99 treatment-naive GBMs provides insights to GBM biology. We identify key phosphorylation events (e.g., phosphorylated PTPN11 and PLCG1) as potential switches mediating oncogenic pathway activation, as well as potential targets for EGFR-, TP53-, and RB1-altered tumors. Immune subtypes with distinct immune cell types are discovered using bulk omics methodologies, validated by snRNA-seq, and correlated with specific expression and histone acetylation patterns. Histone H2B acetylation in classical-like and immune-low GBM is driven largely by BRDs, CREBBP, and EP300. Integrated metabolomic and proteomic data identify specific lipid distributions across subtypes and distinct global metabolic changes in IDH-mutated tumors. This work highlights biological relationships that could contribute to stratification of GBM patients for more effective treatment. Wang et al. perform integrated proteogenomic analysis of adult glioblastoma (GBM), including metabolomics, lipidomics, and single nuclei RNA-Seq, revealing insights into the immune landscape of GBM, cell-specific nature of EMT signatures, histone acetylation in classical GBM, and the existence of signaling hubs which could provide therapeutic vulnerabilities.

Summary Resistance to platinum compounds is a major determinant of patient survival in high-grade serous ovarian cancer (HGSOC). To understand mechanisms of platinum resistance and identify potential therapeutic targets in resistant HGSOC, we generated a data resource composed of dynamic (±carboplatin) protein, post-translational modification, and RNA sequencing (RNA-seq) profiles from intra-patient cell line pairs derived from 3 HGSOC patients before and after acquiring platinum resistance. These profiles reveal extensive responses to carboplatin that differ between sensitive and resistant cells. Higher fatty acid oxidation (FAO) pathway expression is associated with platinum resistance, and both pharmacologic inhibition and CRISPR knockout of carnitine palmitoyltransferase 1A (CPT1A), which represents a rate limiting step of FAO, sensitize HGSOC cells to platinum. The results are further validated in patient-derived xenograft models, indicating that CPT1A is a candidate therapeutic target to overcome platinum resistance. All multiomic data can be queried via an intuitive gene-query user interface (https://sites.google.com/view/ptrc-cell-line)., Graphical abstract, Highlights • Multi-omic profiles of platinum-resistant and sensitive ovarian cancer models • Significant alterations in multiomic profiles after carboplatin exposure • Oxidative phosphorylation and fatty acid oxidation (FAO) implicated in resistance • FAO/CPT1A may be a candidate druggable pathway to overcome platinum resistance, Huang et al. report extensive multiomic profiling of preclinical models of high-grade serous ovarian cancer and identify molecular features associated with resistance to standard-of-care, platinum-based chemotherapy. Functional data are presented, demonstrating that CPT1A is a candidate therapeutic target to overcome platinum resistance.

Adhesive secretion has a fundamental role in barnacles&rsquo, survival, keeping them in an adequate position on the substrate under a variety of hydrologic regimes. It arouses special interest for industrial applications, such as antifouling strategies, underwater industrial and surgical glues, and dental composites. This study was focused on the goose barnacle Pollicipes pollicipes adhesion system, a species that lives in the Eastern Atlantic strongly exposed intertidal rocky shores and cliffs. The protein composition of P. pollicipes cement multicomplex and cement gland was quantitatively studied using a label-free LC-MS high-throughput proteomic analysis, searched against a custom transcriptome-derived database. Overall, 11,755 peptide sequences were identified in the gland while 2880 peptide sequences were detected in the cement, clustered in 1616 and 1568 protein groups, respectively. The gland proteome was dominated by proteins of the muscle, cytoskeleton, and some uncharacterized proteins, while the cement was, for the first time, reported to be composed by nearly 50% of proteins that are not canonical cement proteins, mainly unannotated proteins, chemical cues, and protease inhibitors, among others. Bulk adhesive proteins accounted for one-third of the cement proteome, with CP52k being the most abundant. Some unannotated proteins highly expressed in the proteomes, as well as at the transcriptomic level, showed similar physicochemical properties to the known surface-coupling barnacle adhesive proteins while the function of the others remains to be discovered. New quantitative and qualitative clues are provided to understand the diversity and function of proteins in the cement of stalked barnacles, contributing to the whole adhesion model in Cirripedia.

Adhesive secretion has a fundamental role in barnacles’ survival, keeping them in an adequate position on the substrate under a variety of hydrologic regimes. It arouses special interest for industrial applications, such as antifouling strategies, underwater industrial and surgical glues, and dental composites. This study was focused on the goose barnacle Pollicipes pollicipes adhesion system, a species that lives in the Eastern Atlantic strongly exposed intertidal rocky shores and cliffs. The protein composition of P. pollicipes cement multicomplex and cement gland was quantitatively studied using a label-free LC-MS high-throughput proteomic analysis, searched against a custom transcriptome-derived database. Overall, 11,755 peptide sequences were identified in the gland while 2880 peptide sequences were detected in the cement, clustered in 1616 and 1568 protein groups, respectively. The gland proteome was dominated by proteins of the muscle, cytoskeleton, and some uncharacterized proteins, while the cement was, for the first time, reported to be composed by nearly 50% of proteins that are not canonical cement proteins, mainly unannotated proteins, chemical cues, and protease inhibitors, among others. Bulk adhesive proteins accounted for one-third of the cement proteome, with CP52k being the most abundant. Some unannotated proteins highly expressed in the proteomes, as well as at the transcriptomic level, showed similar physicochemical properties to the known surface-coupling barnacle adhesive proteins while the function of the others remains to be discovered. New quantitative and qualitative clues are provided to understand the diversity and function of proteins in the cement of stalked barnacles, contributing to the whole adhesion model in Cirripedia.

The exploitation of omics data combining transcriptomic and proteomic enables the detailed study of the molecular mechanisms of non-model organisms exposed to an environmental stress. The assembly of data from the RNA-seq of non-model organism enables to produce the protein database for the interpretation of spectra generated in shotgun proteomics. In this context, the aim of the PhD work was to optimize the interpretation and analysis of proteomic data through the development of innovative concepts for the construction of protein databases and the exploration of biodiversity. The first step focused on the development of a pretreatment method for RNA-seq data based on proteomic attribution results. The second step was to work on reducing the size of the databases by optimizing the parameters of the automated coding region search. The optimized method enabled the analysis of 7 taxonomic groups of Gammarids representative of the diversity found in natura. The proteomic databases thus produced enabled the inter-population analysis of 40 individual Gammarus pulex proteomes from two sampling sites (polluted vs reference). Statistical analysis based on an "individual" approach has shown an heterogeneity of the biological response within a population of organisms induced by an environmental stress. Different subclusters of molecular mechanisms response have been identified. Finally, the study of the transversality of the biomarkers peptides identified with Gammarus fossarum revealed which are the common ones using both proteomic and transcriptomic data. For this purpose, a software for the exploration of peptide sequences has been developed suggesting potential substitute biomarkers when the defined peptides are not available for some species of gammarids. All these concepts aim to improve the interpretation of data by proteogenomics. This work opens the door to the multi-omic analysis of individuals collected in natura by considering inter-species and intra-population biodiversity., L’exploitation conjointe des données transcriptomiques et protéomiques permet l’étude détaillée des mécanismes moléculaires induits lors de perturbations environnementales. L’assemblage de données issues du séquençage des ARNs d’organismes dit « non-modèle » permet de produire la base de données pour l’interprétation des spectres générés en protéomique shotgun. Dans ce contexte, les travaux de thèse avaient pour objectif d’optimiser l’interprétation et l’analyse des données protéomiques par le développement de concepts innovants pour la construction de bases de données protéiques et l’exploration de la biodiversité. La première étape s’est concentrée sur la mise au point d’une méthode de pré-traitement des données de séquençage basée sur les résultats d’attribution protéomique. La deuxième étape a consisté à travailler sur la réduction de la taille des bases de données en optimisant les paramètres de la recherche automatisée des régions codantes. La méthode optimisée a permis l’analyse de 7 groupes taxonomiques de Gammaridés représentatifs de la diversité retrouvée in natura. Les bases de données protéomiques ainsi produites ont permis l’analyse inter-population de 40 protéomes individuels de Gammarus pulex répartis sur deux sites de prélèvement (pollué vs référence). L’analyse statistique basée sur une approche « individu-centré » a montré une hétérogénéité de la réponse biologique au sein d’une population d’organismes suite à une perturbation environnementale. Différents sous-groupes de mécanismes moléculaires induits ont été identifiés. Enfin, l’étude de la transversalité de biomarqueurs peptidiques identifiés chez Gammarus fossarum a permis de définir les peptides communs à l’aide de l’ensemble des données protéomiques et transcriptomiques. Pour cela, un logiciel d’exploration des séquences peptidiques a été développé permettant de proposer de potentiels biomarqueurs substituts dans le cas où les peptides définis ne sont pas applicables à certaines espèces de gammare. Tous ces concepts s’intègrent dans une démarche pour améliorer et approfondir l’interprétation des données par protéogénomique. Ces travaux entrouvrent la porte à l’analyse multi-omique d’individus prélevés in natura en considérant la biodiversité inter-espèce et intra-population.

Dans un contexte où le transfert adoptif de lymphocytes T (ATC) représente l’avenir de l’immunothérapie du cancer, l’identification des meilleurs antigènes associés aux molécules de classe I du CMH (MAP) à cibler sur les cellules cancéreuses est d’une importance capitale. Plusieurs types de MAP sont des cibles potentielles pour l’ATC : 1) les antigènes mineurs d’histocompatibilité (MiHA) qui dérivent de polymorphismes génétiques entre un donneur et un receveur lors d’un ATC, 2) les antigènes associés aux tumeurs (TAA) qui peuvent dériver de transcrits surexprimés et 3) les antigènes spécifiques aux tumeurs (TSA) qui dérivent de mutations somatiques ou de transcrits exprimés de façon aberrante. Des centaines d’essais cliniques ont mis en évidence un potentiel thérapeutique pour chacune de ces classes de MAP. Néanmoins, les ATC ciblant ces antigènes sont utilisés en contextes largement différents: des lymphocytes T MiHA-spécifiques provenant d’un donneur compatible sont utilisés pour le traitement de cancers hématologiques tandis que des lymphocytes T TAA- ou TSA-spécifiques provenant du patient sont utilisés pour traiter des tumeurs solides. De fait, jamais ces différents types de MAP n’ont été comparés pour leur potentiel thérapeutique dans un même modèle tumoral. L’objectif de cette thèse était donc de mesurer et de comparer le potentiel thérapeutique de MiHA, TAA et TSA exprimés dans la lignée cellulaire EL4 afin de mieux comprendre les mécanismes dictant leur immunogénicité. Nous avons donc sélectionné des MiHA et des TAA rapportés dans la littérature, puis avons développé une approche protéogénomique permettant d’identifier tous les types de TSA présentés sur ces cellules. Nous avons ainsi déterminé que : 1) Seuls les MAP perçus comme du non-soi (MiHA et TSA) peuvent induire de fortes réponses anti-cancéreuses, 2) Leur immunogénicité dépend de l’abondance et de l’avidité fonctionnelle des lymphocytes T antigène-spécifiques et 3) La clonalité des antigènes et la nature de leurs altérations génétique dictent également l’immunogénicité des TSA. En résumé, nous avons développé une plateforme permettant l’identification de MAP présentés par les cellules cancéreuses et identifié des paramètres permettant la priorisation de ceux-ci en contexte clinique., In a context where adoptive transfer of T lymphocytes (ATC) represents the future of cancer immunotherapy, the identification of the best antigens associated to major histocompatibility complex class I (MAPs) to target on cancer cells is of capital importance. Several types of MAPs expressed at the surface of cancer cells can be targeted for ATC: 1) minor histocompatibility antigens (MiHAs), that derive from germline polymorphisms between a donor and a recipient during an ATC, 2) tumor associated antigens (TAAs) that include antigens that derive from overexpressed transcripts in cancer cells compared to their normal counterpart and 3) tumor specific antigens (TSAs) that derive from somatic mutations or from aberrantly expressed transcripts in cancer cells. Hundreds of clinical trials have highlighted the therapeutic potential of each of these classes of antigens. Nonetheless, ATCs targeting these antigens have been studied in dramatically different contexts: donor-derived T cells targeting MiHAs are used for treating hematologic malignancies while patient-derived T cells targeting TAAs or TSAs are used for the treatment of solid tumors. As such, the therapeutic potential of these MAPs has never been assessed in a single tumor model. Thus, the goal of this thesis was to evaluate and compare the therapeutic potential of MiHAs, TAAs and TSAs expressed on the EL4 cell line to better understand the mechanisms dictating their immunogenicity. We first selected MiHAs and TAAs previously reported in the literature, then developed a proteogenomic approach that enabled us to identify all types of TSAs presented by EL4 cells. By doing so, we found that : 1) Only MAPs that are seen as non-self by T cells (MiHAs and TSAs) can induce strong antitumor responses, 2) Both the abundance and functional avidity of MiHA- or TSA-specific T cells dictated the immunogenicity of these antigens, and 3) The clonality of the antigen and the nature of their genetic alterations also represented an important parameter dictating TSAs’ immunogenicity. In conclusion, we developed a proteogenomic platform that will enable the identification of all types of cancer antigens and identified metrics that will guide the priorization of MiHAs and TSAs in a clinical setting.

Among dinitrogen (N2)-fixing some cyanobacteria can establish symbiosis with a broad range of host plants from all plant lineages including bryophytes, ferns, gymnosperms, and angiosperms. In the boreal forests, the symbiosis between epiphytic cyanobacteria and feathermosses Hylocomium splendens and Pleurozium schreberi is ecologically important. The main input of biological N to the boreal forests is through these cyanobacteria, and thus, they greatly contribute to the productivity of this ecosystem. Despite the ecological relevance of the feathermoss symbiosis, our knowledge about the establishment and maintenance of cyanobacterial-plant partnerships in general is limited, and particularly our understanding of the feathermoss symbiosis is rudimentary. The first aim of this thesis was to gain insight on the genomic rearrangements that enabled cyanobacteria to form a symbiosis with feathermosses, and their genomic diversity and similarities with other plant-symbiotic cyanobacteria partnerships. Genomic comparison of the feathermoss isolates with the genomes of free-living cyanobacteria highlighted that functions such as chemotaxis and motility, the transport and metabolism of organic sulfur, and the uptake of phosphate and amino acids were enriched in the genome of plant-symbiotic cyanobacteria. The second aim of this PhD study was to identify cyanobacterial molecular pathways involved in forming the feathermoss symbiosis and the regulatory rewiring needed to maintain it. Global transcriptional and post-transcriptional regulation in cyanobacteria during the early phase of establishment of the feathermoss symbiosis, and after colonization of the moss were investigated. The results revealed that the putative symbiotic gene repertoire includes pathways never before associated with cyanobacteria-plant symbioses, such as nitric-oxide sensing and regulation, and the transport and metabolism of aliphatic sulfonate. The third aim was to explore the role of the cyanobacterial community in contributing to the temporal variability of N2-fixation activity. Results from a field-study showed that temporal variation in N2-fixation rates could be explained to a high degree by changes in cyanobacterial community composition and activity. In particular, the cyanobacteria belonging to the genus Stigonema - although not dominating the community- appeared to be the main contributors to the N2-fixation activities. Based on this result, it is suggested that this genus is responsible for the main input of N in the boreal forest ecosystems. The last aim was to understand how the relationship between cyanobacterial community composition and N2-fixation activity will be affected by climatic changes such as, increased temperature (11oC compared to 19oC) and CO2 level (500 ppm compared to 1000 ppm). Laboratory experiments highlighted that 30 weeks of combined elevation of temperature and CO2 resulted in increased N2-fixation activity and moss growth rates. The observed increases were suggested to be allocated to reduced cyanobacterial diversity and changes in community composition, resulting in the dominance of cyanobacteria adapted to the future abiotic condition. At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 4: Manuscript.

Mutations of the SHANK3 gene have been associated with autism spectrum disorder. Individuals harboring different SHANK3 mutations display considerable heterogeneity in their cognitive impairment, likely due to the high SHANK3 transcriptional diversity. In this study, we report a novel interaction between the Mutated in colorectal cancer (MCC) protein and a newly identified SHANK3 protein isoform in human colon cancer cells and mouse brain tissue. Hence, our proteogenomic analysis identifies a new human long isoform of the key synaptic protein SHANK3 that was not predicted by the human reference genome. Taken together, our findings describe a potential new role for MCC in neurons, a new human SHANK3 long isoform and, importantly, highlight the use of proteomic data towards the re-annotation of GC-rich genomic regions.

In autoimmune diseases, specific autoantibodies detected in patients’ sera areusually investigated by techniques using purified self-antigens and/or relevantpeptides from preselected targets. Such a restrictive view may be overcome by usingnew biological techniques to improve the diagnostic procedure. In a first step, weevaluated the impact of slight changes in target self-antigens related to posttranslationalmodifications, such as citrullination. In view of the weak resultsobtained, we further focused on some properties of the humoral response. Westudied the global self-reactive IgG antibody patterns against a large panel ofantigens derived from different target tissue extracts, especially brain antigens.Despite inter-individual differences, some reactivities allowed us to discriminatebetween the immune profiles of healthy individuals and those of patients. The selfreactivefootprints can also differentiate distinct autoimmune diseases and theirclinical forms. When we induced experimental autoimmune diseases, dynamicchanges occurred at the early phases with significant patterns related to pathogenicor protective events. A pathological distortion of the self-reactive antibodyrepertoire was also found in clinically isolated syndromes predictive of multiplesclerosis. Despite the predominant organ-specific symptoms in the clinical andexperimental situations studied, discriminant self-IgG reactivities mostly involvedubiquitous antigens rather than organ specific targets. Interestingly, discriminantIgM reactivities targeting both tissue-specific and ubiquitous antigens were alsospecifically observed in a T-dependent autoimmune disease (autoimmunepolyendocrinopathy syndrome), suggesting that T-cell-dependent but also T-cellindependentmechanisms might be involved in pathological changes in the selfreactiverepertoire. Although these footprints have allowed the identification ofuseful new biomarkers, their pathophysiological relevance remains to be defined.The molecular characterization of specific antigenic targets in autoimmune disease isa critical step towards understanding the pathological mechanisms and developinguseful diagnostic and therapeutic tools. In this perspective, we emphasize the needfor accurate methodological approaches. Our analysis of self-reactive footprintshighlights the potent role of complementary events related to putative dysfunctionin the innate/natural immune response in autoimmune diseases.; Dans le cadre du diagnostic biologique des maladies auto-immunes, les autoanticorpssont généralement recherchés par des méthodes qui utilisent des antigènes(ou peptides) présélectionnés. De telles techniques ont des limites qui pourraient êtrecontournées par de nouvelles approches. Dans le premier temps de ce travail, nousrapportons l'intérêt d’évaluer les réactivités d'auto-anticorps vis-à-vis de ciblesmodifiées par des processus post traductionnels, comme la citrullination dans lecadre diagnostique de la polyarthrite rhumatoïde. Cette approche ne peut toutefoispas être transposée à toutes les pathologies auto-immunes, et notamment lasclérose en plaques. Dans un deuxième temps, notre démarche s’est élargie àl’analyse globale de la réactivité des immunoglobulines G sériques dirigée contredifférents extraits d’antigènes tissulaires, notamment issus du cerveau. Malgré lagrande hétérogénéité des réponses interindividuelles, il a été possible d’observer desprofils de réactivités distinguant les sujets sains de patients souffrant de différentespathologies à composantes auto-immunes. Cette signature sérologique permetégalement de distinguer les profils auto-immuns associés à différentes maladies etmême de distinguer leurs formes cliniques. Dans le modèle expérimental développéau laboratoire, nous avons observé que des modifications de ces profils apparaissentde façon précoce et peuvent être liés à une évolution péjorative ou favorable de lamaladie auto-immune. Ces résultats ont été confirmés dans la sclérose en plaques,où l’étude menée chez des patients ne présentant qu’un syndrome clinique isolé, amontré que les profils de réactivité sérique des IgG sont déjà marqués de l’empreintede la maladie qui se révèlera cliniquement en moyenne trois ans plus tard. De façonintéressante, d'autres travaux ont montré que le répertoire des IgM pouvaitégalement être perturbé au cours d’un processus auto-immun dont la pathogénierepose sur un dysfonctionnement des lymphocytes T (syndrome APECED). Cesrésultats suggèrent que des mécanismes T dépendants mais aussi T indépendantspèsent sur la constitution et l’entretien du répertoire auto-immun pathologique.Pour identifier les cibles des réactivités discriminantes révélées par cette premièreapproche, nous avons développé une technique de caractérisation moléculairefaisant appel à la technique immunoprotéomique. Alors que les pathologieshumaines et les modèles animaux étudiés sont principalement des pathologiesspécifiques d’organe, les antigènes tissulaires qui ont été identifiés comme cibles desréactivités spécifiquement associées à ces pathologies sont des antigènesubiquitaires, et non des antigènes spécifiques d’organe. Ces résultats posent laquestion de l’implication réelle de ces cibles dans la physiopathologie des maladiesauto-immunes. Ils illustrent également l’impérative nécessité de connaître les limitesdes résultats apportés par les méthodes d’immunoprotéomique.La caractérisation de la signature sérologique d’un processus pathologique, autravers de l’analyse des perturbations globales des réactivités sériques qui lui sontassociées, offre des perspectives intéressantes tant en termes de prise en charge dupatient qu’en termes de compréhension physiopathologique des maladies autoimmunes.Elle pourrait aboutir à d’utiles débouchés thérapeutiques. Ces attentesjustifient pleinement l’investissement qui a été mis en place par notre laboratoiredans le cadre de sa validation méthodologique.

In autoimmune diseases, specific autoantibodies detected in patients’ sera areusually investigated by techniques using purified self-antigens and/or relevantpeptides from preselected targets. Such a restrictive view may be overcome by usingnew biological techniques to improve the diagnostic procedure. In a first step, weevaluated the impact of slight changes in target self-antigens related to posttranslationalmodifications, such as citrullination. In view of the weak resultsobtained, we further focused on some properties of the humoral response. Westudied the global self-reactive IgG antibody patterns against a large panel ofantigens derived from different target tissue extracts, especially brain antigens.Despite inter-individual differences, some reactivities allowed us to discriminatebetween the immune profiles of healthy individuals and those of patients. The selfreactivefootprints can also differentiate distinct autoimmune diseases and theirclinical forms. When we induced experimental autoimmune diseases, dynamicchanges occurred at the early phases with significant patterns related to pathogenicor protective events. A pathological distortion of the self-reactive antibodyrepertoire was also found in clinically isolated syndromes predictive of multiplesclerosis. Despite the predominant organ-specific symptoms in the clinical andexperimental situations studied, discriminant self-IgG reactivities mostly involvedubiquitous antigens rather than organ specific targets. Interestingly, discriminantIgM reactivities targeting both tissue-specific and ubiquitous antigens were alsospecifically observed in a T-dependent autoimmune disease (autoimmunepolyendocrinopathy syndrome), suggesting that T-cell-dependent but also T-cellindependentmechanisms might be involved in pathological changes in the selfreactiverepertoire. Although these footprints have allowed the identification ofuseful new biomarkers, their pathophysiological relevance remains to be defined.The molecular characterization of specific antigenic targets in autoimmune disease isa critical step towards understanding the pathological mechanisms and developinguseful diagnostic and therapeutic tools. In this perspective, we emphasize the needfor accurate methodological approaches. Our analysis of self-reactive footprintshighlights the potent role of complementary events related to putative dysfunctionin the innate/natural immune response in autoimmune diseases., Dans le cadre du diagnostic biologique des maladies auto-immunes, les autoanticorpssont généralement recherchés par des méthodes qui utilisent des antigènes(ou peptides) présélectionnés. De telles techniques ont des limites qui pourraient êtrecontournées par de nouvelles approches. Dans le premier temps de ce travail, nousrapportons l'intérêt d’évaluer les réactivités d'auto-anticorps vis-à-vis de ciblesmodifiées par des processus post traductionnels, comme la citrullination dans lecadre diagnostique de la polyarthrite rhumatoïde. Cette approche ne peut toutefoispas être transposée à toutes les pathologies auto-immunes, et notamment lasclérose en plaques. Dans un deuxième temps, notre démarche s’est élargie àl’analyse globale de la réactivité des immunoglobulines G sériques dirigée contredifférents extraits d’antigènes tissulaires, notamment issus du cerveau. Malgré lagrande hétérogénéité des réponses interindividuelles, il a été possible d’observer desprofils de réactivités distinguant les sujets sains de patients souffrant de différentespathologies à composantes auto-immunes. Cette signature sérologique permetégalement de distinguer les profils auto-immuns associés à différentes maladies etmême de distinguer leurs formes cliniques. Dans le modèle expérimental développéau laboratoire, nous avons observé que des modifications de ces profils apparaissentde façon précoce et peuvent être liés à une évolution péjorative ou favorable de lamaladie auto-immune. Ces résultats ont été confirmés dans la sclérose en plaques,où l’étude menée chez des patients ne présentant qu’un syndrome clinique isolé, amontré que les profils de réactivité sérique des IgG sont déjà marqués de l’empreintede la maladie qui se révèlera cliniquement en moyenne trois ans plus tard. De façonintéressante, d'autres travaux ont montré que le répertoire des IgM pouvaitégalement être perturbé au cours d’un processus auto-immun dont la pathogénierepose sur un dysfonctionnement des lymphocytes T (syndrome APECED). Cesrésultats suggèrent que des mécanismes T dépendants mais aussi T indépendantspèsent sur la constitution et l’entretien du répertoire auto-immun pathologique.Pour identifier les cibles des réactivités discriminantes révélées par cette premièreapproche, nous avons développé une technique de caractérisation moléculairefaisant appel à la technique immunoprotéomique. Alors que les pathologieshumaines et les modèles animaux étudiés sont principalement des pathologiesspécifiques d’organe, les antigènes tissulaires qui ont été identifiés comme cibles desréactivités spécifiquement associées à ces pathologies sont des antigènesubiquitaires, et non des antigènes spécifiques d’organe. Ces résultats posent laquestion de l’implication réelle de ces cibles dans la physiopathologie des maladiesauto-immunes. Ils illustrent également l’impérative nécessité de connaître les limitesdes résultats apportés par les méthodes d’immunoprotéomique.La caractérisation de la signature sérologique d’un processus pathologique, autravers de l’analyse des perturbations globales des réactivités sériques qui lui sontassociées, offre des perspectives intéressantes tant en termes de prise en charge dupatient qu’en termes de compréhension physiopathologique des maladies autoimmunes.Elle pourrait aboutir à d’utiles débouchés thérapeutiques. Ces attentesjustifient pleinement l’investissement qui a été mis en place par notre laboratoiredans le cadre de sa validation méthodologique.

Summary The liver is the largest solid organ in the body, yet it remains incompletely characterized. Here we present a spatial proteogenomic atlas of the healthy and obese human and murine liver combining single-cell CITE-seq, single-nuclei sequencing, spatial transcriptomics, and spatial proteomics. By integrating these multi-omic datasets, we provide validated strategies to reliably discriminate and localize all hepatic cells, including a population of lipid-associated macrophages (LAMs) at the bile ducts. We then align this atlas across seven species, revealing the conserved program of bona fide Kupffer cells and LAMs. We also uncover the respective spatially resolved cellular niches of these macrophages and the microenvironmental circuits driving their unique transcriptomic identities. We demonstrate that LAMs are induced by local lipid exposure, leading to their induction in steatotic regions of the murine and human liver, while Kupffer cell development crucially depends on their cross-talk with hepatic stellate cells via the evolutionarily conserved ALK1-BMP9/10 axis., Graphical abstract, Highlights • Spatial proteogenomic single-cell atlas of healthy and obese murine and human liver • Validated flow cytometry and microscopy panels for all hepatic cells • LAMs are differentially located in the lean and obese liver • Evolutionary conserved BMP9/10-ALK1 axis is essential for KC development, By combining single-cell and -nucleus sequencing with spatial mapping of RNA and proteins, this vast spatial proteogenomic atlas of healthy and obese human and mouse livers presents methods to identify and localize all hepatic cells and provides insights into hepatic myeloid cells, including identification of reliable surface markers for isolation and localization of hepatic macrophages, characterization of lipid-associated macrophages in both healthy and steatotic livers, determination of a key regulatory axis of Kupffer cell development, and identification of a conserved core gene expression signature of Kupffer cells across 7 species, including chickens and zebrafish.