Human rotavirus (HRV) is a major causative agent of acute gastroenteritis (AGE), which causes severe dehydrating diarrhea in children under the age of five and results in up to 215,000 deaths worldwide each year. There are two live oral attenuated vaccines licensed for use in the United States that are highly effective in high-income countries but much less so in low-and middle-income countries (LMICs). Several factors contributing to decreased efficacy in these areas include chronic malnutrition, gut dysbiosis, and concurrent viral infection. Along with this, currently used vaccines require constant cold-chain storage to maintain vaccine stability, and those resources can be scarce in LMICs. These areas continue to maintain a high burden of HRV morbidity and mortality, and more efficacious vaccines are needed. The gnotobiotic (Gn) pig model of HRV infection and diarrhea has long been used in the evaluation of novel HRV vaccines due to Gn pigs' susceptibility to HRV infection, development of clinical signs, histopathological changes in the intestine, and the infection kinetics that mimic those seen in human infants. The first project in this dissertation used the Gn pig model to evaluate a thermostable live oral attenuated vaccine administered as a dissolvable film. Two doses of the tetravalent dissolvable film vaccine conferred significant protection from virus shedding by delaying its onset and reducing peak titers in feces. It also significantly delayed the onset of diarrhea and reduced the duration and area under the curve (AUC) of diarrhea. The dissolvable film was highly immunogenic, inducing high titers of serum virus neutralizing (VN) antibodies specific to each of the four G-types included in the vaccine formulation, HRV-specific serum IgA and IgG, and intestinal IgA. These data confirm the thermostable platform as a useful alternative to liquid vaccines that require cold-chain. The second project evaluated three mRNA-based nonreplicating vaccine candidates in the Gn pig model. All three mRNA candidates encoded a universal CD4+ T cell epitope, P2, derived from tetanus toxoid, fused with the encoded VP8* from P[4], P[6], and P[8] HRVs. Two candidates also encoded for a lumazine synthase (LS) domain fused with the P2-VP8*. A dose response study of the LS-P2-VP8* candidates was conducted simultaneously. Significant protection against virus shedding was induced by all three candidates, with LS-P2-VP8* candidates inducing significantly higher VP8*-specific serum IgG. All three candidates induced significantly higher numbers of P[8]-VP8*-specific IgG antibody-secreting cells (ASCs) and IFN-γ-producing T cells in the ileum, spleen and blood. These data provide guidance for further development of the relatively new mRNA-based technology for use in HRV vaccine development. In the final study of this dissertation, we used the Gn pig model of both P[8] and P[6] HRV infection to evaluate a cocktail nanoparticle-based HRV vaccine. This vaccine was made up of an S60 nanoparticle, self-assembled from the S domain of the human norovirus capsid protein. The exposed C-termini on the S60 nanoparticle were utilized as an antigen display platform, where VP8* from P[4], P[6] and P[8] HRVs was fused. This vaccine was tested as both a two-dose intramuscular (IM) regimen, or as an IM booster preceded by an oral priming immunization with commercial monovalent Rotarix®. Pigs were challenged with either P[6] or P[8] HRV to evaluate cross-protection of the nanoparticle vaccine. Both regimens were highly immunogenic, inducing high titers of serum VN, IgG and IgA antibodies. Furthermore, the prime-boost regimen conferred significant protection against virus shedding in P[8] HRV-challenged pigs as evidenced by the shortened duration of fecal virus shedding. There was also significant protection in P[6] HRV-challenged pigs vaccinated with the prime-boost regimen, as evidenced by the shortened duration, reduced mean peak titer and AUC of virus shedding. Prime-boost-vaccinated pigs challenged with P[8] HRV had significantly higher P[8]-specific IgG ASCs in the spleen post-challenge. Prime-boost-vaccinated pigs challenged with P[6] HRV had significantly higher numbers of P[6] and P[8]-specific IgG ASCs in the ileum, as well as significantly higher numbers of P[8]-specific IgA ASCs in the spleen post-challenge. Oral priming followed by parenteral boosting appears to be a promising vaccination strategy for HRV and these data warrant further investigation into this regimen. Through these studies, we improved our understanding of the effect of different vaccination routes and formulations in the effectiveness of conferring protection against an enteric virus. The knowledge will facilitate the development of more effective vaccination strategies against HRV, the leading cause of infantile diarrhea in LMICs, as well as other enteric viruses. / Doctor of Philosophy / Human rotavirus (HRV) is a major causative agent of acute gastroenteritis (AGE) in children under the age of five. Acute gastroenteritis is characterized by nausea, vomiting, and potentially deadly dehydrating diarrhea. There are two highly effective vaccines licensed for use in the United States; however, these vaccines are much less effective in low- and middle-income countries (LMICs), where HRV disease burden is the highest. There are several reasons thought to be responsible for the decrease in effectiveness seen in these areas, including chronic malnutrition and gut dysbiosis. Non-biological reasons for decreased efficacy may include the breakdown of cold-chain storage for these vaccines, which require constant low temperature storage that is often unavailable in LMICs. Thermostable vaccines are necessary for increasing vaccine distribution and efficacy in these areas. Because many of the biologic factors thought to interfere with the effectiveness of these vaccines appear to be confined to the gastrointestinal tract, development of next generation HRV vaccines has focused on the parenteral route of administration. The gnotobiotic (Gn) pig model is a highly relevant animal model that has been used for decades to evaluate novel HRV vaccine efficacy. Our first study evaluated a thermostable, dissolvable live oral vaccine administered as a dissolvable film in our Gn pig model. Two doses of this vaccine significantly reduced the severity of diarrhea and virus shedding in the stool. Our second study evaluated three mRNA-based intramuscular (IM) vaccines in the Gn pig model. Three doses of all mRNA candidates provided significant protection from virus shedding in the stool, as well as inducing the production of strong HRV-specific antibodies in the serum and high numbers of virus-specific T cells in the tissues. In our final study, we evaluated a nanoparticle-based vaccine as a two-dose IM regimen or as an IM booster preceded by an oral immunization using the commercially available Rotarix® vaccine. The prime-boost regimen significantly shortened the duration and severity of virus shedding in the stool. We also detected more cross-strain HRV-specific antibody-secreting cells in the tissues. All three vaccines evaluated in this dissertation offer differing novelty in the field of HRV vaccine development, and the Gn pig model has been instrumental in the evaluation of these vaccines.

Le développement de vaccins à ARNm est en plein essor dans le domaine de la vaccinologie. Un des défis majeurs de ces approches est de parvenir à transporter et délivrer les ARNm dans le cytoplasme des cellules dendritiques (DC) pour permettre la production d’antigène et l’activation des réponses immunitaires.L’objectif de ce travail a porté sur la conception et l’évaluation de nouvelles stratégies de vectorisation des ARNm par des nanoparticules de poly(acide lactique) (NP-PLA). Une stratégie basée sur l’adsorption des ARNm à la surface des NP-PLA par l’intermédiaire du LAH4-L1, un peptide cationique amphipathique, a été développée. Des polyplexes formés suite à la condensation de l’ARNm par le LAH4-L1 ont été adsorbés sur les NP-PLA pour former des nanocomplexes. L’intérêt des polyplexes et nanocomplexes pour le ciblage des DC et l’activation des réponses immunitaires in vitro a été évalué. Dans des tests de transfection, ces formulations ont induit une expression efficace d’ARNm modèles dans des DC. La présence des NP-PLA dans les formulations semble favoriser l’expression des ARNm. Le traitement avec des inhibiteurs a révélé que les polyplexes et nanocomplexes semblent internalisés par phagocytose et endocytose clathrine-dépendante, et s’échappent des endosomes par un mécanisme dépendant de la pompe à protons v-ATPase. Suite à la transfection de DC dérivées de monocytes (moDC), nous avons montré que nos formulations stimulent les récepteurs de l’immunité innée et induisent une réponse pro-inflammatoire. Cette activation est associée à la maturation des moDC, à la présentation de peptides antigéniques sur le CMH-I et -II et à la sécrétion de cytokines et chémokines impliquées dans l’immunité adaptative. Ces données soulignent l’intérêt des NP-PLA associées au LAH4-L1 pour vectoriser des ARNm, cibler des DC et activer les réponses immunitaires. Dans le contexte du VIH-1, ce type de réponse pourrait aider le système immunitaire à contrôler la charge virale / MRNA-based vaccines currently raise a growing interest in vaccinology. However, the transport and delivery of mRNAs to DC cytoplasm in order to induce antigen production and immune responses remains challenging. The objective of this thesis concerns the design and evaluation of novel strategies to vectorize vaccine mRNAs by poly(lactic acid) nanoparticles (PLA-NPs). We developed a strategy based on mRNA adsorption onto PLA-NPs using, as intermediate, LAH4-L1, an amphipathic cationic peptide. To do this, mRNAs were condensed by LAH4-L1 to form polyplexes which was then adsorbed onto PLA-NPs in a second step to form nanocomplexes. The LAH4-L1/mRNA polyplexes and PLA-NP/LAH4-L1/mRNA nanocomplexes ability to target DCs and induce immune responses in vitro was evaluated. We showed that formulations induce an efficient transfection of mRNA in DCs in vitro. The addition of PLA-NPs in formulations seems to increase sustained expression of mRNAs. DC treatment by inhibitors revealed that polyplexes and nanocomplexes are taken up by phagocytosis and clathrin-dependent endocytosis, and escape endosomes by a v-ATPase-dependent mechanism. Transfection of monocyte-derived DCs (moDCs) showed that LAH4-L1/mRNA polyplexes and PLA-NP/LAH4-L1/mRNA nanocomplexes trigger innate-sensing activation with pro-inflammatory responses. This activation is associated with moDCs maturation, MHC-I and MHC-II presentation, and the secretion cytokines and chemokines involved in adaptive immunity.These data highlight the interest of these new platform formulations to vectorize mRNAs, target DCs and induce immune responses, which in the context of HIV-1, could help the immune system to control the viral load

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.