RNA-binding proteins (RBPs) are classically regarded as facilitators of gene expression. In recent years, however, RNA-protein interactions have also emerged as a pervasive force in the regulation of homeostasis. The compendium of proteins with provable RNA-binding function has swelled from the hundreds to the thousands astride the partnership of MS-based proteomics and RNA Sequencing. At the foundation of these advances is the adaptation of RNA-centric capture methods that extract protein that has been crosslinked in its native environment. These methods reveal snapshots in time displaying an extensive network of regulation and a wealth of data that can be used for both the discovery of RNA-binding function and the molecular interfaces at which these interactions occur. This thesis describes the development of an extraction method that purifies RBP-RNA complexes. This method differentiates itself from other RBP-discovery protocols in that it 1) purifies these complexes so completely that RBP identification can be conducted qualitatively and without differential abundance analysis, 2) permits transcript-targeted capture with sequence-specific oligos, 3) permits global, sequence-agnostic capture 4) both RBP and its bound RNA are isolated intact and 5) can reliably interrogate RBPs at depths that exceed present methods without metabolic or molecular labelling. The performance of this method is first assessed with a census of proteins that directly interact with global, or targeted, RNA transcripts from model cell lines. These efforts are then extended to investigate how protein-RNA interactions change during transition from quiescence to proliferation and then contraction in primary murine CD8+ T cells. Finally, these studies demonstrate how cellular responses provoke different proteins to moonlight as RNA binders and sheds light on a network of complex, co-evolved molecular machines.

Apoptosis is a form of programmed cell death. The intrinsic pathway of apoptosis is governed by the BCL2 family proteins. Targeting BCL2 proteins by small molecules that mimicking the BH3-only proteins to induce apoptosis has proven to be a successful strategy for cancer therapy. Venetoclax, a specific inhibitor of BCL2, has exhibited remarkable efficacy in treating cancers that rely on BCL2 for survival. However, the activity of venetoclax is often limited in other cancers whose survival relies on MCL1, another BCL2 family member. Selective MCL1 inhibitors have been developed and are currently being evaluated in clinical trials. However, the clinical development of these agents has been hampered by toxicity, especially cardiac toxicity. Potentially, another strategy to target MCL1 is by modulating NOXA, a BH3-only protein that selectively binds to MCL1 and mediates its degradation. I hypothesised that increased NOXA expression would prime cancer cells to venetoclax killing and that this would reduce their co-dependence on MCL1. In order to identify new targets to modulate NOXA expression, I generated and validated cell lines that report on NOXA transcription and then carried out CRISPR-Cas9 genetic screens in those NOXA reporter cell lines. In CRISPR-Cas9 loss-of-function screens focused on epigenetic regulators, I found several genes whose mutation or loss modulated NOXA expression, including CTBP1, CHTOP, ZMYM3, SPEN, HSPA1A, KEAP1, FOXA1, HDAC3 and SAP30. Some of these factors have been targeted for cancer therapies, for example KEAP1 and HDAC3, while the others have not yet been recognized for their therapeutic possibilities. Subject to their validation, my results have identified interesting novel mechanisms of NOXA regulation, thus providing the rationale basis for the development of new anti-cancer agents. In CRISPR-Cas9 tiling screens that focused on the NOXA promoter region, five cis-regulatory elements were identified that contributed to regulation of NOXA expression. Among them, a hypermethylated element on the NOXA promoter was found to be important for repressing NOXA expression across diverse cell lines derived from blood cancers. Disrupting this region led to NOXA induction. Potentially, the findings could provide a rational basis of combining hypomethylating agents with venetoclax in a range of haematological malignancies. In summary, several potential NOXA regulating proteins and DNA elements were discovered by the CRISPR-Cas9 screening approaches. Once validated, these findings should provide new insights into NOXA regulation.

T-cell acute lymphoblastic leukaemia (T-ALL) is an aggressive T-cell malignancy that is frequently caused by the overexpression of oncogenic transcription factors. Like many cancers, T-ALL is a heterogeneous disease, with the acquisition of many genetic alterations resulting in multiple clones that contribute to cancer progression. This poses a challenge for therapeutic intervention, as different clones within a tumour can possess different genetic signature and thus possess different levels of sensitivity to therapeutic strategies. Therefore, gaining a better understanding of how these clones arise, is crucial to developing more targeted therapies aimed at these cells. LMO2 is a transcription factor that is overexpressed in approximately 9% of T-ALL cases. The CD2-Lmo2 transgenic mouse model overexpress Lmo2 in the thymus, resulting in a developmental block at the DN3 stage of T-cell development, and subsequent development into T-ALL after a long latency (approximately 10 months). Using these mice, our laboratory has shown Lmo2 confers self-renewal capacity to these developmentally blocked DN3 thymocytes many months before the overt presentation of T-ALL. These self-renewing DN3 thymocytes were termed pre-CSCs due to their ability to self-renew, their capacity to still develop into mature functional T-cells, and not initiate leukaemia for many months when transplanted into recipient mice. This thesis will focus on gaining a better understanding of the multi-step pathogenesis of Lmo2 induced murine T-ALL development. In Chapter Three, we explore the role cellular competition for thymic niche space and signals plays in the Lmo2 induced T-cell developmental block, and Lmo2 induced T-ALL. Using competitive bone marrow transplantation experiments we show that the presence of WT thymic progenitors in the thymus severely hinders the development of Lmo2 transgenic thymic progenitors past the DN2 stage of T-cell development, and their subsequent development into T-ALL. Interestingly, we found that overexpression of Bcl2 in Lmo2 transgenic thymocytes severely abrogated the self-renewal capacity of Lmo2 transgenic thymocytes, and hindered their development into T-ALL. Furthermore, we show that Lmo2 downregulates Il7r in DN2 thymocytes. In Chapter Four, we crossed CD2-Lmo2 transgenic mice with CD2-Il7r transgenic mice to create the CD2-Lmo2;CD2-Il7r double-transgenic mouse line, to investigate the role of Il7r overexpression in the Lmo2 induced developmental block. We found that overexpression of Il7r in Lmo2 transgenic thymocytes does not alleviate the Lmo2 induced DN2, or DN3 developmental block, but does increase the engraftment potential of Lmo2 transgenic DN3 thymocytes. Surprisingly, despite the increase in engraftment potential, Il7r overexpression in Lmo2 transgenic thymocytes resulted in a delay in T-ALL induced death, however Il7r overexpression promoted an immature T-ALL immunophenotype. In Chapter Five, we generated an inducible Lmo2 knockin mouse model in which Lmo2 expression can be inhibited by Dox administration. Using this mouse line, we show that while Lmo2 is still required for the self-renewal of Lmo2 transgenic DN3 thymocytes, Lmo2 is not required for T-ALL maintenance in the majority of Lmo2-Induced T-ALLs.

Chimeric antigen receptor (CAR) T cell therapy has revolutionized the treatment of B cell malignancies by redirecting patient T cells to destroy cancer cells using engineered receptors. While CAR T cell therapies hold enormous potential as treatments in a wide range of tumour settings, treatments for non-B cell cancers have largely failed to significantly improve patient outcomes thus far. Furthermore, CAR therapies carry significant risk of inducing cytokine release syndrome (CRS), a potentially deadly toxicity caused by excessive release of inflammatory cytokines. The ability to minimize toxicity whilst maintaining adequate tumour cell-killing is therefore vital to the continued improvement of CAR therapies. We aimed to investigate the currently ill-defined relationship between CAR oligomeric state and potency using a novel protein engineering approach, with the aim of leveraging this knowledge to predictably modulate CAR activity. With de-novo protein design collaborators we identified synthetic transmembrane domain (TM) sequences that predictably formed defined homo-oligomeric structures. In addition to a previously validated trimeric TM sequence, I used X-ray protein crystallography to determine the structure of a dimeric TM peptide that agreed closely with its predicted structure. I inserted these novel oligomeric TM sequences into a well-established anti-HER2 CAR construct (comprising an anti-HER2 scFv attached via stalk/TM to costimulatory and stimulatory tail sequences) and validated their oligomeric state and signalling capacity in a mouse T cell line. When expressed in primary mouse T cells and incubated with HER2+ target cells, dimeric and trimeric CARs exhibited enhanced target cell killing compared to a reference anti-HER2 CAR. Using an in vivo mouse tumour model it was subsequently demonstrated that CAR oligomeric state correlates positively with CAR T cell anti-tumour efficacy. CARs encoding synthetic oligomeric TM’s also demonstrated a dramatic reduction in the release of inflammatory, CRS-associated cytokines within in vitro experiments. Using rational TM sequence mutations I identified lateral interactions between CARs and the endogenous T cell costimulatory molecule CD28 in primary mouse T cells as the key determinant of CAR cytokine release. These findings present an opportunity to improve efficacy and safety of CAR T cell therapies and warrant further validation in other clinically relevant CAR T cell disease models.

The heart is one of the first organs to develop in a vertebrate embryo. The intricate design of the asymmetric four-chambered organ is reflected in both its structures and mechanics. A healthy functional heart is an amalgamation of precisely aligned great vessels, continuous sheets of trilayered tissues that form the chamber walls and septum, a coordinated conduction system, and an uninterrupted supply of oxygenated blood from the coronary vasculature. At a cellular level, heart morphogenesis is a remarkable feat of tightly regulated cell proliferation, apoptosis, migration and differentiation. These events are driven by spatially and temporally coordinated gene expressions. Post-translational modifications of histone proteins such as acetylation and deacetylation are central to gene expression and repression. The genome site-specific activities of enzymes responsible for acetylation and/or deacetylation rely on protein domains that can recognize and bind to modified histone residues. These protein domains are present in either the histone modifying enzyme itself or adaptor proteins that are present within the histone modifying complex, known as histone ‘reader’ proteins. In this thesis, I have used knockout mice to investigate the roles of two histone reader proteins – ING4 and ING5, both present in histone acetyltransferase complexes in vivo, demonstrating the consequences of loss of these histone reader proteins in the patterning and structural development of the heart. In the first part of my thesis, I have demonstrated that loss of both Ing5 alleles alone did not incur any haematopoietic defects, unlike loss of the proposed histone acetyltransferase enzyme subunit present in the ING5 protein complex. Subsequently, I characterised the survival and appearances of mice with deletion of a combination of Ing4 and Ing5 alleles. I showed that ING4 and ING5 are functionally redundant, as mice died in mid-gestation in the absence of both proteins, whereas mice lacking only ING5 developed to term and mice lacking only ING4 were viable, healthy and fertile. However, mice lacking both Ing5 alleles and one Ing4 allele showed heart development abnormalities with full penetrance and died in utero. In the second part of my thesis, I explored mechanisms underlying the heart development defects observed in the compound mutants. I showed that the epicardium was most vulnerable to the loss of Ing4 and Ing5 alleles. I demonstrated that Ing4+/– Ing5–/– mutant mice were incapable of generating epicardium-derived cells and a proper coronary endothelial network. In addition, I have also demonstrated the redundancy of ING4 and ING5 with respect to gene expression changes and changes in global histone acetylation, further explaining how they possibly control heart development via regulating the functions of their associated histone acetyltransferase enzymes. Overall, my studies provide evidence that ING4 and ING5 are important reader proteins during embryonic development, in particular for the development of the heart and specifically in the epicardium tissue. ING4 and ING5 are likely to exert their functions by targeting the histone acetyltransferase activities of a MYST histone acetyltransferase enzyme to specific gene loci.

Cancer is a major public health issue globally, ranking as the second most common cause of death. Molecularly targeted therapies, focused on exploiting tumour cell dependency on certain oncogenic driver mutations for growth and survival, have greatly improved patient outcomes. However, despite these advances, some of the most frequent oncogenic mutations in cancer, such as those found in KRAS, are extremely challenging to target directly. One promising strategy to expand the range of actionable targets for cancer drug development is the exploitation of synthetic lethal interactions. Synthetic lethality is the term used to describe the death of cells in response to the co-existing disruption of two genes, neither of which is lethal alone. In this setting, targeting a gene that is synthetic lethal with a cancer-relevant mutation has the potential to induce the death of vulnerable cancer cells while leaving healthy cells unaffected. With this background in mind, my lab participated in a focused ENU mutagenesis screen in zebrafish with the aim of identifying genes that are essential for high rates of cell proliferation during endodermal organ development but not required by quiescent tissues. This yielded mutants that exhibited either ‘cell death’ or ‘growth arrest’ phenotypes in the liver, intestine and pancreas. I investigated two of the underlying mutant genes, ahctf1 and rnpc3, for their capacity to engage in synthetic lethal interactions with the kras oncogene. In Chapter 3, I investigated the impact of ahctf1 heterozygosity on the growth and survival of KrasG12V-expressing hepatocytes in a zebrafish model of hepatocellular carcinoma (HCC), TO(krasG12V). ahctf1 encodes Elys, a multifunctional nucleoporin with essential roles in nuclear pore assembly and mitosis. I found that ahctf1 heterozygosity impairs nuclear pore formation, mitotic spindle assembly and chromosome segregation, leading to DNA damage and activation of Tp53-dependent and Tp53-independent cell death pathways which reduced tumour burden. Importantly, ahctf1 heterozygosity did not impact normal liver development, advancing ELYS as an attractive target for cancer therapy with a viable therapeutic window. In Chapter 4, I examined if rnpc3 heterozygosity also reduced tumour burden in the TO(krasG12V) model. rnpc3 encodes 65K, a unique protein component of the U12-dependent spliceosome, a specialised splicing machinery required for the correct splicing of a very small percentage (3.7%) of genes. In hepatocytes expressing krasG12V, rnpc3 heterozygosity reduced the number of cells in S phase of the cell cycle and increased cell death, together reducing tumour burden, without affecting normal tissue. In Chapter 5, I demonstrated that the zebrafish model of HCC is a powerful platform for testing novel therapeutics. I evaluated the efficacy of PRMT5 and KAT6A/B inhibitors early in their development, and showed that they were effective in reducing tumour growth and worthy of future investigation. In conclusion, my studies revealed two promising new targets for cancer treatment. I also demonstrated that the zebrafish HCC model is highly amenable to pharmacological inhibition and provides a valuable system for the pre-clinical examination of drug treatments in vivo.

T cells are an essential component of the vertebrate adaptive immune system. In concert with the innate immune system, T cells protect the host from any number of pathogens that could be experienced over an organism’s lifetime. The hallmark of a T cell is its distinctive T cell receptor generated by somatic gene rearrangement. Variability in the T cell receptor repertoire arises during thymic T cell differentiation, which is then subjected to strict selection processes. Mature T cells in the periphery can undergo further differentiation upon the activation of naive cells to mount immune responses to pathogens. These differentiation events are accompanied by significant proliferative bursts, followed by the clearance of defective or superfluous cells. It follows then, that cell death is also an essential component of T cell differentiation and homeostasis. This PhD thesis explores the molecular mechanisms regulating the differentiation, proliferation and death of T cells, and how interplay among these mechanisms gives rise to immune homeostasis. This study examines how distinct cell death pathways, including the intrinsic and extrinsic apoptotic pathways and necroptosis, are differentially regulated through T cell differentiation and in the various subsets of mature T cells. We found that only inhibition of the intrinsic pathway of apoptosis overcomes failure of beta-selection in the absence of preTCR signalling or proliferation, enabling further differentiation. We also discovered that caspase 8 plays an important pro-survival role in inhibiting necroptosis in recent thymic emigrant T cells and regulatory T cells, and that this feature can be exploited in the case of regulatory T cells for therapeutic intervention in infection settings. In summary, this thesis defines context-specific roles of cell death modalities in controlling T cell differentiation and homeostasis, revealing the potential for immune interventions using targeted therapies.

Necroptosis is a form of programmed cell death that is controlled by a defined set of protein effectors, despite displaying the morphological characteristics of unregulated lytic cell death (necrosis). Recently, there has been increasing interest in this type of cell death, ignited by studies demonstrating that necroptosis is involved in the pathophysiology of various diseases – including inflammatory conditions, degenerative conditions, infectious diseases and cancers – and further kindled by the progression of small molecule necroptosis inhibitors into clinical trials. The best studied form of necroptosis is driven by the tumour necrosis factor (TNF) signalling pathway, which is initiated by TNF binding to its cell surface receptor TNFR1. Importantly, TNF-induced necroptosis is regulated by three key proteins: the kinases RIPK1 and RIPK3, and the pseudokinase MLKL, which acts as the cell death executioner. To identify novel inhibitors of necroptotic cell death, several small molecule screens were performed at WEHI. This PhD thesis details the investigation into the mechanism of action of two small molecule necroptosis inhibitors identified from these screens. I employed a suite of chemical biology, biochemistry and cell biology approaches to deduce the cellular targets of these small molecules and investigate their anti-necroptotic activity. Chapter 2 examines the identification and mechanism of action of Compound 2, a more potent necroptosis inhibitor than its parent compound, Compound 1, which was identified from a small molecule screen against MLKL. I determined that Compound 2 targets all three necroptotic effector proteins – MLKL, RIPK1 and RIPK3 – in vitro and in cells, to potently block necroptosis in human and murine cells at nanomolar concentrations. Moreover, this study highlights that necroptosis can be potently inhibited by targeting multiple effectors, suggesting that targeting multiple proteins in the pathway may be an ideal strategy for inhibiting necroptosis in a therapeutic context. Chapter 3 explores the cellular activity and cellular targets of ABT-869, an inhibitor of necroptosis identified from a phenotypic screen using a cell line expressing a constitutively active MLKL mutant. I determined that ABT-869 blocks necroptotic cell death by targeting RIPK1 and possibly RIPK3, although whether ABT-869 targets RIPK3 directly or indirectly, as a result of RIPK1 inhibition, remains to be elucidated. Furthermore, this study raises some interesting questions regarding the involvement of RIPK1 downstream of MLKL activation, which could contribute to an improved understanding of how necroptosis is regulated at the molecular level. Together, these two novel inhibitors of necroptosis identified from small molecule screens were found to block necroptotic cell death by targeting known components of the TNF-induced necroptosis pathway. This research provides insight into how small molecules can modulate necroptotic signalling by interacting with key necroptotic proteins to inhibit cell death.

Background: Acute lymphoblastic leukaemia (ALL) is the most common childhood cancer and early disease eradication is critically important for long-term cure. ALL remains a leading cause of cancer death in children and young adults because of treatment toxicity and relapsed disease. Increased delineation of the key biological drivers in ALL as well as therapeutic response will present new opportunities to rationally combine existing and novel agents to improve outcomes whilst minimising toxicities. Blocks in apoptosis are now widely recognised as a hallmark of ALL but also a mechanism of resistance to standard chemotherapeutic agents. Co-targeting aberrant cell survival pathways, using novel combinations of BH3-mimetics, are an emerging therapeutic option. My thesis centres on translational and mechanistic studies of combining venetoclax (BCL-2 inhibitor) and S63845 (MCL-1 inhibitor) in high-risk (HR) ALL subtypes. Aim: To inform the clinical utility of BH3-mimetic combinations in HR-ALL by identifying synergistic combinations with each other as well as standard and targeted agents in vitro, evaluating the efficacy and tolerability of combination venetoclax (BCL-2 inhibitor) and S63845 (MCL-1 inhibitor) in vivo, and investigating mechanisms of therapeutic resistance. Methods: BH3-mimetics were combined with each other as well as dexamethasone and targeted tyrosine kinase inhibitors (TKI) to identify the most potent combinations across kinase-activated ALL cell lines and patient derived xenografts (PDX) in vitro and in vivo. The tolerability of combinations venetoclax and S63845 was detailed in NOD-SCID-IL7R (NSG) mice as well as healthy donor blood ex vivo. Loss-of-function mutations that confer resistance to TKIs and BH3-mimetics in a Ph+ALL cell line were identified using an unbiased genome-wide CRISPR-Cas9 loss-of-function screen. Differences in cell signalling and survival pathways following treatment with TKI and BH3-mimetics in vivo in PDX models of Ph-like ALL were identified using mass cytometry. Results: BCL-2 and MCL-1 protein expression remained high in kinase-activated B-ALL cell lines treated with targeted TKI despite up-regulation of BIM pro-apoptotic protein expression. Co-inhibition of BCL-2 and MCL-1, with combination venetoclax and S63845, induced synergistic killing in vitro and was comparable or superior to steroid or TKI combined with each BH3-mimetic, across a range of kinase-activated B-ALL cell lines and PDXs, including the Ph+ and Ph-like subtypes. The combination also had potent anti-leukaemia activity in vivo, which was demonstrated by rapid cytoreduction, but also acute tumour lysis syndrome (ATLS) in some PDX models of Ph-like B-ALL. Combining venetoclax and S63845 appeared tolerable, however, histologic evidence of haematopoietic toxicity was observed, at higher doses, in NSG mice, and synergistic cytotoxicity was observed in lymphocytes of healthy donor blood. Loss of function mutations in NOXA and BAX were identified from the CRISPR screen as important causes of resistance to dasatinib and venetoclax in Ph+ALL. Lastly, CyTOF demonstrated distinct single cell variability in response to TKI or BH3-mimetic treatment of Ph-like ALL, including differences in surface marker expression (CD38, CD179a, and CD34), and cell signalling pathways (pSTAT5). Conclusion: Co-inhibition of BCL-2 and MCL-1 induces synergistic killing in vitro and rapid cytoreduction in vivo in a range of HR B-ALL models, including the Ph+ and Ph-like subtypes. The combination of BCL-2 and MCL-1 inhibition was comparable or superior to steroid or TKI combined with each BH3-mimetic. Although this combination of BH3-mimetics was tolerable in vivo at lower doses, histologic evidence of haematopoietic toxicity and tumour lysis syndrome was observed in NSG mice and PDX models, respectively. The expression level of BCL-2 family anti-apoptotic genes (BCL-2 and MCL-1), BH3-only class of pro-apoptotic genes (NOXA and BAX), surface markers (CD38, CD179a, and CD34) and cell signalling pathways (pSTAT5), predicted treatment resistance. Co-targeting BCL-2 and MCL-1 warrants evaluation in clinical trials that incorporate supportive care including infection prophylaxis and tumour lysis precautions. The findings from this research may be exploited for future studies to test novel combinations of drugs, on the basis of their ability to act on non-overlapping mechanisms, which are likely to result in synergistic anti-leukaemia efficacy.

Innate lymphoid cells (ILCs) are a specialized arm of the innate immune system responsible for protecting the mucosal barrier and defending against infection. ILC activation and cytokine production occurs in response to stimuli in the local environment making them an important initiators of the early immune response. However, they also contribute to inflammatory diseases and thus must be tightly regulated. The development and function of ILCs is dependent on the tight regulation of transcription factors. Two transcription factors GFI1 and GFI1B are involved in this differentiation but have been poorly studied and thus how they shape differentiation is not clear. GFI1 and GFI1B was differentially expressed throughout ILC development. GFI1B expression was limited to the early progenitors whereas GFI1 was expressed in both early progenitors and in all mature ILC subsets in the peripheral organs. GFI1B expression identified the early progenitors in the bone marrow with the capacity to give rise to all ILC subsets. GFI1B expression is also required for the development of progenitors in the bone marrow and lung ILC2. This impacted the lung inflammatory response induced in mice treated with papain as the eosinophil recruitment by ILC2s was impaired. In contrast, GFI1 was highly expressed in mature NK cells and was vital for development and maintenance of these cells. GFI1 regulated multiple NK cell pathways, including proliferation, homing to peripheral organs and effector functions. Defects in these functions impaired the protection mediated by NK cells against metastatic melanoma cells. Together, GFI1 and GFI1B are both key regulators of ILC development, although they regulate different stages of ILC development and function. ILCs are enriched at the mucosal barrier, particularly at the gastrointestinal tract. They play an important role in protecting against infections but also have the capacity to promote inflammation when dysregulated. Their role in the development of colorectal cancer (CRC) is unclear as individual ILC subsets have been associated with both protecting against or promoting tumorigenesis. Characterisation of the immune infiltrate of mice with CRC showed that there was an accumulation of IL-5-producing ILC2 within the colon and this was strongly correlated to the tumour burden. ILC2-deficient mice developed a higher tumour burden compared to control mice, which indicated a protective role for ILC2s against colorectal cancer.

Interleukin-1 beta is a potent proinflammatory cytokine that requires inflammasome-associated caspase-1, a cysteine protease, to cleave inactive precursor IL-1beta, to its active secreted p17 fragment. Excessive IL-1beta activation and release promotes autoinflammatory diseases, such as Cryopyrin associated periodic syndromes (CAPS), gout and cancers. Despite this role in inflammatory disease, the post-translational regulation of IL-1beta is poorly understood. This thesis studies the post-translational modifications (PTMs) of IL-1beta, with a particular focus on the ubiquitination of precursor IL-1beta and its role in modulating IL-1beta activity.

T follicular helper cells (TFH) are specialised CD4+ T cells that promote B cells maturation into antibody secreting plasma and memory cells. Most of the current vaccines generate protection via the induction of long-term antibody responses and circulating TFH are reliable predictors of vaccine response. Conversely, dysfunctional TFH cells are associated with the pathogenesis of immunodeficiency, systemic autoimmunity and allergy. Despite their importance, we have an incomplete understanding of how TFH cells differentiate and function in distinct inflammatory settings. Answering this question has broad health implications to stimulate rational development of vaccines and therapeutics against diverse infections, autoimmune and allergic disease. In this thesis, I investigated the transcriptional and migration control of TFH differentiation during viral infection. In this setting, TFH cells differentiate in parallel with T helper 1 (TH1) CD4+ T effector cells. I investigated two canonical TH1 factors, T-bet and CXCR3, to understand their roles in TFH cells differentiation. Comparing two viral infections, I demonstrated a context-dependent role for T-bet in TFH differentiation and identified the cytokine and chemokine factors that underlie distinct T cell differentiation. Combined, this work demonstrates that there are multiple paths that direct TFH differentiation. This study has led to further investigations into pathogen-specific TFH programs, which will help us understand how TFH orchestrate tailored B cell responses in diverse infections.