RAGs (Recombination Activating Genes) are responsible for generation of antigen receptor diversity in case of B-cells and T-cells, through the process of combinatorial joining of different V (variable), D (diversity) and J (joining) gene segments. Each of these segments are flanked by recombination signal sequences (RSS), which consist of a conserved heptamer and nonamer separated by a less conserved spacer of 12 or 23 bp. RAGs recognize and cleave at the 5’ end of heptamer, leading to the formation of hairpin coding ends and blunt signal ends. The coding ends are joined through the process of no homologous DNA end joining (NHEJ), leading to the rearrangement of variable region of antigen receptors. Apart from its physiological property, RAGs can also act as a structure-specific nuclease. Previously, it has been shown that inadvertent action of RAGs on cryptic RSS and non B-DNA structures can lead to the generation of genomic instability and cancer. A very coordinated expression of RAGs has been observed in pro- and pre-B cells of the lymphoid system, which overlaps with the window of productive rearrangement during V(D)J recombination. Besides, studies by us and others have shown that RAG cleavage at altered DNA structures and cryptic RSS leads to chromosomal translocations resulting into cancer. However, several questions related to regulation of RAG expression and its activity in lymphoid cells remains to be answered. Previous studies have suggested regulation of RAG expression at different levels, such as methylation, ubiquitination, phosphorylation and by coordinate action of various transcription factors. In the present study, we evaluate the potential role of miRNAs in the regulation of RAG expression and its function in lymphoid cells. miRNAs are small, single-stranded non-coding RNAs, which play an important role in the regulation of gene expression. They play a critical role in the regulation of different cellular functions. Although there are miRNAs identified to play critical role during development of immune system, several key questions such as its role in the regulation of RAGs is yet to be addressed. In the current study, we have used bioinformatics approach to extract potential miRNAs that bind to 3’UTR of RAG1 and RAG2. miRNA expression datasets were downloaded from NCBI SRA database and extensive evaluation was done using various bioinformatics tools such as Bowtie, Sam tools, Bam tools, Bed tools and R package. We screened the miRNA expression profile across different stages of B-cell development (pro, pre, immature and mature B-cells), which overlap with the narrow window of RAG expression. The shortlisted miRNAs were further analyzed using miRNA databases such as miRBase, Targetscan and EMBL. Results showed that 33 miRNAs were specific to RAG1, among that one (miRNA1) followed RAG expression profile in B-cells. Besides miRNA2, which is a novel miRNA, was selected only on the basis of RAGs expression profile in a stage specific manner and the complementarity of the seed sequence of miRNA2 to the 3’UTR of RAG1 was checked manually. Interestingly, we observed that RAG1 expression was significantly down regulated in the presence of these miRNAs. However, there was no significant difference in the levels of other genes analysed. Further, semi-quantitative RT-PCR analysis confirmed the endogenous processing of pre-miRNA into mature miRNA using the cellular machinery. Besides, enrichment of 3’UTR of seed region of these miRNAs, enhanced the expression level of RAG1. Importantly, the enhancement in RAG1 expression level was limited in case of mature B-cells, where RAG expression is normally not observed. Further, transfection of lymphoid cells with miRNA inhibitors, specific to the miRNAs under study, showed the enhancement in RAG1 expression in lymphoid cells. In addition to this, specificity of selected miRNAs was confirmed by performing 3’UTR reporter assays, where enhanced luciferase expression was observed in case of mutant 3’UTR, while it was minimal in case of wild type constructs. Endogenous expression levels of selected miRNAs were evaluated in both lymphoid and nonlymphoid normal tissues and cancer cells using RT-PCR. Interestingly, we observed inverse correlation of expression levels of miRNA and RAG expression in all the cells tested. Besides, miRNA expression levels were less in pre-B cells and T-cells, owing to the increased expression of RAGs. Apart from this, recombinogenic potential of candidate miRNAs was assessed using episomal based V(D)J recombination assays. Interestingly we observed significant decrease (2-4 fold) in the V(D)J recombination efficiency when miRNA1 or 2 constructs were transfected in Nalm6 cells, as compared to that of controls, where no miRNAs were used. However, in case of Reh cells upon transfection with miRNA1construct, the decrease in recombination potential was upto 9 fold. Hence, we identify two miRNAs that can play an important role in the regulation of RAG1 expression and its physiological activity. Further, studies are being carried out to confirm their role in the regulation of RAG1 during different developmental stages of lymphoid cells in mice. As stated above, in addition to the sequence-specific activity, RAG possesses structure-specific nuclease activity as well. It has been shown that RAGs can cleave different types of altered DNA structures. Studies from our laboratory showed that even when RAGs act as a structure-specific nuclease there is a sequence bias. Presence of cytosine and thymine at the single-stranded region of heteroduplex DNA is important for RAG nicking and double-strand break (DSB) formation. In addition, proximity of a nonamer to bubble structures can enhance RAG cleavage. However, the role of immediate flanking sequences in the RAG mediated cleavage at heteroduplex regions is not understood. We investigated the role of flanking double-stranded DNA sequences in the regulation of RAG cleavage on non-B DNA structures. We found that RAG binding and cleavage on heteroduplex DNA is dependent on the length of double-stranded flanking region. Besides, immediate flanking regions of the heteroduplex DNA affected the RAG binding and cleavage in a sequence dependent manner. Interestingly, we also observed that the cleavage efficiency of RAGs at heteroduplex region was influenced by the phasing of DNA. Thus, our results suggest that sequence, length and phase positions of the DNA can affect the efficiency of RAG cleavage when it acts as a structure-specific nuclease. These findings provide novel insights into regulation of the pathological action of RAGs. Previous studies have shown that in addition to formation of coding and signal joints during V(D)J recombination, nonstandard V(D)J recombination products known as hybrid joints and open-shut joints may be formed, particularly in certain aberrant conditions such as defective NHEJ machinery. Interestingly, the hybrid and open-shut joints closely resemble the transposition mechanisms associated with transposons oretroviruses. Studies have also shown that RAGs possess structural similarity with integrases in domain organization. Both the proteins have Zinc Finger Binding domain (ZFB) which helps in multimerization of the protein, a central catalytic core domain comprising three acidic amino acids D, D and E essential for enzymatic activity and C-terminal domain (CTD) responsible for nonspecific binding to the DNA. Previous studies from our laboratory showed that, Elvitegravir, an inhibitor of integrase could interfere with the biochemical functions of the RAGs in vitro. Specifically, it inhibited the RAG binding and cleavage at RSS, hairpin formation, post-cleavage complex formation involving 12RSS and 23RSS. Using the episomal assay system that mimics signal joints (pGG49) and coding joints (pGG51), we show that Elvitegravir can inhibit V(D)J recombination inside cells. Interestingly we observed 3-6 fold decrease in the recombination frequency in signal ends joining, when treated with increasing concentrations (100, 500 and 1000 nM) of Elvitegravir. A 5-8 fold decrease in coding joints formation was also observed upon treatment with the inhibitor. The presence of recombination was confirmed by restriction digestion followed by sequencing analysis. Further analysis of recombination junctions revealed extensive deletion before joining in the case of Elvitegravir treated samples. Insertions or substitutions near to the recombination junctions were also prominent in treated samples. In depth analysis of sequenced junctions showed the presence of sequence having the features to form hairpins both upstream and downstream to the RSS sequences and was the site of cleavage in cases were higher deletion was observed. The analyzed recombinants did not show any signal joints or coding joints formation in treated samples. This suggests that Elvitegravir affects the physiological function, the V(D)J recombination of RAGs inside the cells. Thus, in the present study, we show that RAGs can be regulated by specific miRNAs. We have identified two potential miRNAs, which can regulate the RAG expression as well as its function in different stages of B- and T-cell development. Further, we also identify a novel regulatory mechanism for the structure-specific activity of the RAG complex. In addition to this, we find that integrase inhibitor, Elvitegravir, affects V(D)J recombination within B-cells, indicating its potential deleterious impact in HIV patients, which needs to be further evaluated.

IgA is the dominant antibody isotype found at mucosal surfaces during homeostasis. However, genetic variation in Fcγ receptors (FcγRs), a family of receptors that mediate immune cell activation by IgG, influences susceptibility to inflammatory bowel disease (IBD), suggesting that IgG may be important during gut inflammation. IBD is a chronic relapsing condition with two major subtypes, Crohn’s disease (CD) and ulcerative colitis (UC), both driven by aberrant immune responses to commensals. In the first part of this thesis, we sought to investigate anti-commensal IgG responses in patients with UC and to determine the mechanism by which local IgG might contribute to intestinal inflammation. We found that UC and murine dextran sodium sulfate (DSS)-induced colitis are associated with a significant increase in anti-commensal IgG and local enrichment of FcγR signalling pathway genes. The genes most robustly correlated with FCGR2A, an activating FcγR associated with UC susceptibility, were IL1B andCXCL8. Ex vivo stimulation of human and murine lamina propria mononuclear cells with IgG immune complexes (IC) resulted in an increase in these cytokines/chemokines. In vivo manipulation of the macrophage FcγR A/I ratio in transgenic mice determined IL-1β and Th17 cell induction. Finally, IL-1β blockade in mice with a high FcγR A/I ratio reduced IL-17 and IL-22-producing T cells and the severity of colitis. Our data reveal that commensal-specific IgG contributes to intestinal inflammation via FcγR-dependent, IL-1β-mediated Th17 activation. In this thesis, we have also addressed the interplay between IgG and group 3 innate lymphoid cells (ILC3s). ILC3s are closely related to natural killer cells, which are known to express FcγRs, and are characterised by their production of Th17 cytokines. Here, we have shown that ILC3s express FcγRs, that ICs drive IL-22 production and MHC class II expression by ILC3s, and FcγR signalling induces a transcriptional programme that reinforces ILC3 maintenance and functionality. These results represent a new paradigm for ILC activation, with direct regulation by the adaptive immune response. Finally, we have begun to address the role played by ILC3-derived cytokines in the regulation of local tissue-resident immune cells. We have demonstrated that ILC depletion significantly alters the activation state of intestinal macrophages, resulting in detrimental bacterial outgrowth following C. rodentium infection but protection from overwhelming DSS-induced inflammation. We have shown that GM-CSF promotes macrophage IL-1β and IL-23 production, which in turn act to reinforce ILC3-derived GM-CSF and IL-22 secretion in vitro, respectively. Therefore, ILC3s are essential coordinators of the local inflammatory response within the gut through activation and possible recruitment of immune cells, and their modulation may be beneficial in the treatment of IBD.

No description available.

Primär myelofibros (PMF) är en typ av myeloproliferativ neoplasm (MPN) som leder till en progressiv och irreversibel benmärgsfibros. En somatisk mutation, Jak2V617F, har hittats hos 50 % av patienterna med MPN i hematopoetiska stamceller. Nyligen har man upptäckt grupp 2 av medfödda lymfoida celler (ILC2) som tillhör det medfödda systemet. De är T-cellernas motsvarighet men saknar TCR-receptorn. ILC2 reagerar på IL-33 och producerar Il-13. Under de senaste åren har man upptäckt att dessa två cytokiner är inblandade i PMF. För att undersöka ILC2:s roll i utvecklingen av benmärgsfibros in vivo producerade vi retrovirus som uttrycker Jak2 vildtyp (JAK2_WT) eller Jak2V617F (JAK2_V617F) och transducerade benmärg vildtyp (BM_WT) eller benmärg ILC2KO (BM_ILC2KO). Benmärgen transplanterades till subletalt bestrålade immunbristande möss (NOG). Klinikopatologiska drag som är karakteristiska för sjukdomens första stadier, som förhöjda hemoglobinnivåer, megakaryocythyperplasi och betydande trombocytos, uppstod inte under studieperioden. Ökade vita blodkroppar uppstod dock på grund av avsaknaden av ILC2 i JAK2_V617F-expressiva möss. Flödescytometeranalys visade ursprunget till den markerade leukocytosen som ett resultat av expansionen från lymfocytlinjen, mer specifikt B-celler, men resultaten är inte entydiga eftersom de förhöjda nivåerna av B-celler kan vara en följd av ILC2 knock-out fenotypen som förvärras av närvaron av mutationen. Granulocytnivåerna från de inympade cellerna hölls låga till följd av att stamcellerna i värdens benmärg var inblandade på grund av subletal bestrålning. Vi drar slutsatsen att frånvaron av ILC2 i JAK2_V617F-uttryckta benmärgsprogenitorer har en tendens att förvärra den myeloproliferativa fenotypen i sjukdomens tidiga skeden, vilket tyder på en möjlig skyddande roll för ILC2 vid utvecklingen av MPN. / Primary myelofibrosis (PMF) is one type of myeloproliferative neoplasm (MPN) that leads to a progressive and irreversible bone marrow fibrosis. A somatic mutation, Jak2V617F has been found in 50% of patients with MPN in hematopoietic stem cells. Group 2 innate lymphoid cells (ILC2) belonging to the innate system has been recently discovered. They are the counter part of T cells but lacking the TCR receptor. ILC2 response to IL-33 producing Il-13. In recent years, the involvement of these two cytokines in the PMF has been uncovered. To investigate the role of ILC2 in the progression of bone marrow fibrosis in vivo we produced retrovirus expressing Jak2 wild-type (JAK2_WT) or Jak2V617F (JAK2_V617F) and transduced bone marrow wild type (BM_WT) or bone marrow ILC2KO (BM_ILC2KO). The bone marrow was transplanted into sub-lethally irradiated immunodeficient mice (NOG). Clinicopathologic features characteristic from the first stages of the disease, as elevated hemoglobin levels, megakaryocyte hyperplasia and significant thrombocytosis did not emerge during the study period. However, increased in white blood cells arise from the absence of ILC2 in JAK2_V617F expressing mice. Flow cytometer analysis revealed the origin of the marked leukocytosis as a result of the expansion from the lymphocyte lineage, more specifically B cells, but the results are inconclusive as the elevated levels of B-cells could be a consequence of the ILC2 knock-out phenotype aggravated by the presence of the mutation. Granulocyte levels from engrafted cells were kept low because of the involvement of host bone marrow stem cells due to sublethal irradiation. We conclude that the absence of ILC2 in JAK2_V617F-express bone marrow progenitors has a tendency to aggravate the myeloproliferative phenotype in the early stages of the disease, indicating a possible protective role of ILC2 in the development of MPNs.

Recombination Activating Genes (RAGs) orchestrate the process called V (D) J recombination, which enables the vertebrate adaptive immune system to specifically recognize millions of antigens. During this recombination process, V (variable), D (diversity) and J (joining) gene segments of antibody (B cell receptor) and TCR (T cell receptor) join by different possible combinations to generate antigen receptor diversity. This unique site specific recombination process is actuated by lymphoid specific proteins called RAG1 and RAG2 (RAGs or RAG complex). RAGs recognize a conserved sequence motif flanking the above subexons called Recombination Signal Sequence (RSS). There are two types of RSS known as 12-RSS and 23-RSS, where a conserved heptamer sequence and nonameric sequence is separated by 12 or 23 bp, respectively. RAGs specifically bind to RSS by RAG1 Nonamer Binding Domain (NBD) and generate nicks which are converted to DSBs via a hairpin intermediate and finally repaired by Non-Homologous DNA End Joining (NHEJ), a major DSB repair pathway in eukaryotes. Thus, RAGs act as a sequence specific endonuclease, and is unique to higher eukaryotes. Therefore, reduced or loss of RAG activity could result in immune deficiency syndromes like Omenn Syndrome (OS) and Severe Combined Immunodeficiency (SCID). Apart from acting as a sequence specific nuclease, RAGs have been shown to cleave on altered DNA structures like mismatches (bubbles), hairpins, flaps, gaps, triplexes and 3’ overhangs. This structure specific nuclease activity is implicated in causing genomic instability in B and T cells, particularly leading to generation of chromosomal translocations in certain lymphoid cancers. However, unlike the sequence- specific cleavage activity, this novel property of RAGs is poorly understood. Structure-specific nuclease activity of RAGs was characterized by using heteroduplex DNA substrate containing bubble region. RAG proteins were overexpressed and purified from human cell line and used for the assay. Results showed that RAGs cleave different bubble substrates with different efficiency. The role of DNA sequence at single-stranded region of heteroduplex DNA on RAG cleavage was investigated by synthesizing the substrate DNA having either adenineguanine/ thymine/ cytosine in the bubble sequence. Interestingly, efficient RAG cleavage was observed only when cytosines were present at single-stranded region, while thymine bubbles were cleaved with much lower efficiency. Adenine and guanine containing bubbles were not cleaved by RAGs. This was the first observation showing sequence specificity during structure-specific nuclease activity of RAGs. Besides, it was observed that RAG cleavage on bubbles with cytosines resulted in DSB formation, which is essential for generation of chromosomal translocations. Further, such specificity and cytosine preference was observed, even when RAGs acted on other altered DNA substrates like hairpin loops, 3’ overhangs and gaps. When the role of flanking duplex region on RAG cleavage was tested, only the 5’ duplex nucleotide was critical for RAG cleavage reaction and cytosine was the most preferred nucleotide. By systematic mutation of bubble region, it was observed that the two cytosines present at the double strand-single strand junction are critical for RAG cleavage. A single nucleotide bubble (mismatch) with cytosines was cleaved by RAGs with low but detectable efficiency. A bubble with at least 2 nt length possessing cytosine was cleaved with higher efficiency resulting in both single-stranded nicks and DSBs. Based on these studies, “C(d)C(s)C(s)” was proposed as a novel recognition motif for RAG cleavage, on altered DNA structures, where“d” and “s” represent double- and single-strand region, respectively. To be targeted by RAGs in vivo, the altered DNA substrates have to compete with RSS, the physiological substrate. It is not known whether such structures will be cleaved by RAGs, when present along with RSS. Besides, the regulation of the both structure and sequence specific nuclease activities are not studied. To address the above questions, RAG cleavage on bubble substrates was performed in presence of RSS either in cis or trans configuration. Results showed that both bubble substrates and RSS were cleaved with similar efficiency by RAGs. In fact, they can compete out each other in a concentration dependent manner. When kinetics of RSS and bubble cleavage were performed, RSS cleavage reaction was faster and saturated within 10-15 min, while bubbles cleavage started slow and went on increasing with time. This difference in kinetics persisted when both substrates were present together. This could be a regulatory mechanism for targeting RAGs to RSS sites and limiting bubble cleavage which can be deleterious to cells. HMGB1, a DNA binding protein which is shown to enhance RSS binding and synapsis, does not affect RAG action on bubble substrates. RAG postcleavage complex is formed during V(D)J recombination process where RAGs remain bound to cleaved RSS after cleavage, which limits further RAG action on other sites. Such cleavage complex was not detected on bubble substrates, which suggests that after cleavage RAGs were not associated to DSBs of bubble cleavage. Finally, the nonamer binding domain of RAG1 involved in RSS binding in V(D)J recombination, was found to be dispensable for the structure-specific nuclease activity and it appears that RAGs bind to bubble substrates using a different domain. In summary, in this study, the structure-specific nuclease activity of RAGs was characterized. A novel sequence motif that can regulate this activity of RAGs was identified. Though altered structures can be equally favored substrates as RSS, differences in reaction kinetics, cleavage complex formation and separate DNA binding domains regulate RAG cleavage, when it acts as a structure-specific nuclease. Thus, this study may help in the better understanding of RAG induced genomic instabilities in lymphoid tissues.

Les modèles animaux ont largement contribué à notre compréhension de l’immunologie humaine et des mécanismes pathologiques associés au développement des maladies. Cependant, les modèles murins ne permettent pas de reproduire toute la complexité des pathologies humaines. Les souris à système immunitaire humain (HIS), par leur capacité à récapituler l’hématopoïèse humaine et à être infectées par des pathogènes humains, constituent une solution de choix pour combler ce fossé inter-espèce. Après greffe de cellules souches hématopoïétiques humaines, des souris hôtes sévèrement immunodéprimées permettent un haut niveau de développement du système hémato-lymphoïde humain tout au long de leur vie. Cependant, certains types cellulaires, comme les cellules lymphoïdes innées, ne parviennent pas à se différencier et à fonctionner normalement dans les modèles murins HIS actuels. Ici, nous décrivons le développement d’un modèle souris HIS original, nommé BRGSF, montrant une amélioration de la maturation, de la fonction et de l’homéostasie des cellules natural killer (NK) humaines et des autres ILCs. De plus, en récapitulant les différentes étapes du développement des ILCs humaines, ce modèle souris BRGSF nous a permis d’identifier pour la première fois un précurseur d’ILC (ILCP) présent à la fois dans notre modèle HIS ainsi que dans le sang périphérique et plusieurs organes lymphoïdes et non-lymphoïdes humains. Cette population circulante d’ILCPs pourrait constituer un substrat pour la production d’ILCs matures dans les tissus périphériques en réponse à des stress environnementaux, inflammatoires et/ou infectieux. Dans une seconde partie de ce travail de thèse, nous avons utilisé ces souris BRGS afin de tester l’efficacité de deux immunothérapies reposant sur les lymphocytes innés pour le traitement d’un carcinome colorectal exprimant EGFR et muté pour KRAS. La première approche a consisté en la co-administration des cellules NK dérivées de sang de cordon ombilical et d'anticorps monoclonal cetuximab afin de promouvoir le mécanisme de cytotoxicité cellulaire dépendante des anticorps (ADCC) contre la tumeur. La seconde stratégie a reposé sur l’injection de nanobodies VHH combinant l’inhibition de l’EGFR et l’activation spécifique du récepteur Vγ9Vδ2 des cellules T effectrices. Les résultats de cette étude soulignent l’importance des modèles murins HIS pour la compréhension du développement des lymphocytes innés humains et pour mieux les mettre à profit dans les thérapies anti-tumeurs / Animal models have extensively contributed to our understanding of human immunobiology and to uncover the underlying pathological mechanisms occurring in the development of the disease. However, mouse models do not always reproduce the genetic complexity inherent in human disease conditions. Human immune system (HIS) mouse models that are susceptible to human pathogens and can recapitulate human hematopoiesis provide one means to bridge the interspecies gap. Severely immunodeficient host mice support life-long, high level human hematolymphoid development after engraftment with human hematopoietic stem cells (HSC). However, the differentiation and function of some blood cell types, including innate lymphoid cells (ILCs), is poorly characterized in current HIS mice. Here we describe the development of a novel HIS mouse model, named BRGSF, which demonstrate enhanced maturation, function and homeostasis of human natural killer (NK) cells and other ILCs. Furthermore, the BRGSF-based HIS mouse model recapitulated the developmental stages of human ILCs. We could identify for the first time an ILC precursor (ILCP) population that is present both in HIS mice and in human peripheral blood as well as in several lymphoid and non-lymphoid human tissues. This circulating human ILCP population may provide a substrate to generate mature ILCs in tissues in response to environmental stressors, inflammation and infection. In a second part of the thesis we used BRGS immunodeficient mice to assess two innate lymphocyte-based immunotherapeutic approaches for treating EGFR-expressing KRAS-mutated colorectal carcinoma in vivo. The first model used a combination of umbilical cord blood (UCB)-derived NK cells and the monoclonal antibody cetuximab to promote antibody dependent cell cytotoxicity (ADCC) against the tumors. In a second model, we evaluated the therapeutic suitability of novel bispecific VHH constructs that combine inhibition of the EGFR with the target-specific activation of effector Vγ9Vδ2-T cells. These studies highlight the utility for HIS-based mouse models to understand human innate lymphocyte development and to harness these potent effectors for anti-tumor therapies.

Dans la première partie de cette thèse, nous avons cherché à déterminer le rôle de l’éosinophile circulant dans l’asthme par une approche transcriptomique. Nos résultats suggèrent que l’éosinophile recruté sur un site inflammatoire présente des fonctions immunomodulatrices, importantes dans la réparation tissulaire et le retour à l’homéostasie. Dans la deuxième partie de cette thèse, nous avons étudié le rôle des cellules NK et des cellules lymphoïdes innées de type 2 (ILC2) dans l’inflammation asthmatique. Les cellules NK circulantes sont fortement activées dans l’asthme sévère et ont la capacité d’induire l’apoptose d’éosinophiles autologues in vitro. La PGD2 induit la production d’IL-13 par les ILC2 en synergie avec les cytokines épithéliales IL-25 et IL-33. Enfin, ces fonctions sont régulées par la LXA4. En conclusion, notre travail de thèse met en lumière de nouveaux rôles pour l’éosinophile et les cellules lymphoïdes innées dans l’immunopathologie de l’asthme. / In the first part of the thesis, we adopted a transcriptomic-based approach to investigate the activation state of circulating eosinophils in patients with asthma and other unrelated hypereosinophilic diseases. Taken together, our results, which suggest that esoinophils, recruited to inflammatory sites exhibit non-specific immunomodulatory functions important for tissue repair and homeostasis. In the second part of the thesis, we investigated the role of NK cells and type 2 innate lymphoid cells (ILC2) in asthma inflammation. Circulating NK cells are highly activated in severe asthma and promote apoptosis of autologous eosinophils in vitro. ILC2 generate interleukin-13 in response to prostaglandin D2 alone and in a synergistic manner with the airway epithelial cytokines IL-25 and IL-33. Finally, these functions are regulated by lipoxine A4. In conclusion, this thesis highlights new roles for eosinophils and innate lymphoid cells in asthma immunopathology.

Health is often defined in terms of absence of disease or pathological processes, but this is a definition of exclusion and incomplete. For example, SARS-CoV-2 viral load does not reliably predict disease severity, and so individuals must vary in their ability to control inflammation and maintain normal tissue homeostasis. This host defense strategy is called disease tolerance, and better understanding of disease tolerance mechanisms could change the way that we treat disease and work to maintain health. The first project presented in this dissertation found that after accounting for effects of age and sex, innate lymphoid cells (ILCs), but not T cells, were lower in adults and children sick with COVID-19 or MIS-C, independent of lymphopenia. Furthermore, abundance of ILCs, but not of T cells, correlated inversely with disease severity. These blood ILCs were shown to produce amphiregulin, a protein implicated in disease tolerance and tissue homeostasis, and the percentage of amphiregulin-producing ILCs was lower in males. These results suggest that, by promoting disease tolerance, homeostatic ILCs decrease morbidity and mortality associated with SARS-CoV-2 infection, and that lower ILC abundance accounts for increased COVID-19 severity with age and in males. The second project describes a novel mouse model of epigenetic inheritance wherein paternal influenza A virus (IAV) infection results in less severe influenza disease in IAV infected offspring. This offspring phenotype was not attributable to differences in viral load, indicating a possible difference in disease tolerance. Paternal caloric deprivation decreased, and influenza B virus infection increased, offspring influenza disease severity, and in vitro fertilization demonstrated sperm are sufficient to transfer IAV-associated epigenetic inheritance phenotypes. These findings represent a foundation for further work that, by continuing to elucidate the mechanisms of disease tolerance and epigenetic inheritance, could provide novel therapeutic interventions to help promote and maintain health.

The Tec kinase ITK is activated by TCR stimulation and also required for TCR downstream signaling. Previous studies have reported differential roles of ITK and another Tec family kinase RLK in CD4+ TH differentiation and effector function. However, these findings are confounded by the complex T cell developmental defects in Itk-/- mice. Furthermore, the function of ITK in tissue-resident T cells in the intestine and anti-viral immune response to a persistent infection has not been studied previously. In addition to T cells, recent studies have indicated an expression of ITK in ILC2, but not in other ILC subsets. Yet, the role of ITK in ILC2 has not been characterized. Here, I have examined the role of ITK and RLK in CD4+ TH subsets using a small molecule inhibitor PRN694. I found that PRN694 impaired TH1 differentiation in vitro, and PRN694 administration prevented TH1-mediated colitis progression in vivo. In an MHV68 infection model, Itk-/- mice failed to control viral replication in the intestine, while gut-homing of CD8+ T cells was greatly impaired. Finally, I found that ILC2 number was markedly reduced in the intestine of Itk-/- mice. Gut-specific defect of Itk-/- ILC2 is associated with a low availability of IL-2 in the intestine of Itk-/- mice. Collectively, these data suggest that ITK is important in T cell migration to the intestine and ILC2 homeostasis in the intestine, thereby contributing to the protective response to a latent virus and intestinal tissue homeostasis.

Angeborene lymphoide Zellen (ILCs) bilden eine Familie von Effektorzellen des angeborenen Immunsystems, denen somatisch rekombinierte Antigenrezeptoren fehlen und die in drei Hauptgruppen eingeteilt werden. In der Embryonalentwicklung spielen Typ 3 ILCs, sogenannte LTi (Lymphoid Tissue inducer) Zellen, eine zentrale Rolle in der Entwicklung von Lymphknoten. ILC3, einschließlich LTi Zellen sind abhängig von dem Master-Transkriptionsfaktor RORgt, was sich in RORgt-defizienten Mäuse durch die Abwesenheit aller ILC3, und auch durch fehlende Lymphknoten äußert. Während postnatale Ko-expression der Transkriptionsfaktoren T-bet und RORgt in ILC3-Subpopulationen fest etabliert ist, ist der Einfluss von T-bet in fötalen ILC3 und auf die Generation von Lymphknoten noch unbekannt. Um diese Mechanismen genau zu untersuchen, wurden fötale ILCs mittels Einzelzell-RNA-Sequenzierung charakterisiert, wodurch eine unerwartete Heterogenität innerhalb der ILC3 mit T-bet-exprimierenden Zellen aufgedeckt wurde. Außerdem wurden PLZF+ ILC-Vorläufer (ILCP) im sich entwickelnden Darm nachgewiesen. Weiterhin, bestätigen diverse Mausmodelle eine Schlüsselrolle für T bet in der Regulation der ILC-Differenzierung und der Entstehung von Lymphknoten. Die zusätzliche genetische Ablation von T-bet in RORgt-defizienten Mäusen beeinflusste Differenzierungsentscheidungen in fötalen ILCP und ermöglichte die Akkumulation von ILCP mit LTi-Aktivität, wodurch die Organogenese von Lymphknoten, unabhängig von RORgt wiederhergestellt wurde. PLZF+ ILCP von RORgt/T-bet-Doppeldefizienten Mäusen bestanden bis ins Erwachsenenalter, wo diese Zellen die Darmbarrierefunktionen durch Produktion von IL-22 wiederherstellten. Darüber hinaus erwies sich RORa als entscheidend für die Entwicklung von PLZF+ ILCP und die damit verbundene Bildung von Lymphknoten. / Innate lymphoid cells (ILCs) represent a family of innate effector cells lacking rearranged antigen receptors, which are classified into three main groups based on their lineage-specifying transcription factors (TF) and effector functions. During embryonic development, the formation of lymphoid organs critically relies on a specific member of group 3 innate lymphoid cells (ILC3), expressing the master transcription factor RORgt and exhibiting lymphoid tissue inducer (LTi) functions. Accordingly, RORgt-deficient mice lack ILC3 and do not generate lymph nodes (LN). While it is established that T-bet is co-expressed with RORgt in a subset of ILC3 emerging postnatally and influencing their differentiation, phenotype and functions, the effect of T-bet on fetal ILC3 biology and its impact on LN generation remains completely unknown. In order to study the role of T-bet in fetal ILC3 differentiation and functions as well as in LN formation, single-cell RNA sequencing and flow cytometry were applied to characterize fetal ILC subsets revealing an unanticipated heterogeneity within embryonic ILC3 and identifying T-bet+ ILC3 subsets within the fetal intestine and mesenteric LN anlage for the first time. Furthermore, PLZF+ ILC progenitors (ILCP) were exposed in the developing mouse intestine. Importantly, using multiple mouse models, a key role for T-bet in regulating ILC differentiation and LN formation was discovered. Specifically, additional deficiency of T-bet in RORgt-deficient mice skewed lineage fate decisions in differentiating fetal ILCP and allowed accumulation of ILCP with LTi activity, thereby rescuing LN organogenesis in a RORgt-independent fashion. PLZF+ ILCP of RORgt/T-bet double deficient mice persisted into adulthood where these cells restored intestinal barrier functions through reinstalled IL-22 production. Moreover, RORa was found to be critical for the development of PLZF+ ILCP and associated LN formation.