Rogers, Laura M.

Background Genes that enhance T-cell function represent promising targets for improving engineered T-cell therapies for cancer. While extensive CRISPR knockout screens have identified key genes enhancing T-cell persistence, employing Sleeping Beauty ( SB ) insertional mutagenesis, which induces both gain-of-function (GOF) and loss-of-function (LOF) mutations via the generation of fusion transcripts with endogenous genes, may uncover additional critical factors that previous approaches have overlooked. Methods We developed transgenic mice carrying D oxycycline (Dox)- i nducible SB mutag e nesis s y stem (DiSBey) in primary T cells. Using DiSBey, we conducted screens for genetic alterations enhancing T-cell persistence under chronic antigen exposure. Specifically, CD8 + T cells from Dox-fed DiSBey mice were subjected to repeated anti-CD3 stimulation over 18 days to mimic chronic antigenic stimulation. We then identified SB transposon genomic insertion sites and corresponding fusion transcripts from the persistent DiSBey CD8 + T cells using enhanced-specificity tagmentation sequencing and RNA sequencing, respectively. Results Under chronic stimulation, SB -mutagenized CD8 + T cells exhibited improved persistence and reduced terminal exhaustion phenotype. Across six independent screens, we identified 38 genes that were recurrently targeted by the SB transposon T2/Onc2 and differentially expressed under chronic anti-CD3 stimulation. T2/Onc2 insertions into Bach2 and Elmo1 were recurrently identified at the genomic level and were associated with altered nascent transcript expression. Bach2 , known as a key regulator of T-cell memory formation and resistance to chronic viral infection-induced exhaustion but less characterized in engineered T cells for cancer therapy, was found to counteract exhaustion in vitro and enhance in vivo tumor persistence in the B16-Ova tumor model. Further, we showed that ectopic Bach2 expression levels influence engineered T-cell differentiation lineage, as low Bach2 overexpression retained more functional progenitor exhausted T cells and exhibited improved therapeutic efficacy. Finally, in human CART19-28ζ cells, BACH2 overexpression enhanced cytotoxicity and tumor control following chronic cancer stimulation. Conclusions Controllable SB mutagenesis using DiSBey mice provides a novel platform for functional screening of genes that improve T-cell phenotypes important for their use as therapies. Our findings highlight a dose-dependent role of BACH2 in enhancing the function of engineered T cells under conditions of chronic antigenic stimulation.

Cytotoxic T cells produce the cytokine interferon-γ (IFN-γ). We sought to determine whether IFN-γ directly kills target cells and found that T cells used IFN-γ to kill murine melanoma cells lacking the kinases TBK1 and IKKε. In the absence of both kinases, IFN-γ induced the production of TNF receptor 1 (TNFR1) and the sensor Z-DNA binding protein 1 (ZBP1) in the tumor cells to stimulate receptor-interacting protein kinase 1 (RIPK1)–dependent apoptosis in a cell-autonomous manner. IFN-γ also enhanced the activation of nuclear factor κB (NF-κB) signaling in a TNFR1-dependent manner in cells deficient in both TBK1 and IKKε. Because IFN-γ–induced apoptosis occurred in a transcription-dependent manner with slow kinetics, STAT1 and NF-κB cooperated to activate the expression of inflammatory genes in the dying cells. Thus, IFN-γ–induced cell death was accompanied by an inflammatory signature in the absence of TBK1 and IKKε. TBK1 and IKKε not only mediated the induction of type I IFN but also inhibited RIPK1-dependent death and NF-κB–dependent inflammation. Therefore, we propose that these kinases may have gained these intertwined functions so that cells infected by pathogens that produce antagonists of TBK1 and IKKε are eliminated by IFN-γ–secreting T cells in an inflammatory manner to compensate for the inhibition of type I IFN production.

Abstract Forward genetic screens are powerful tools for novel biological discoveries because they do not require a priori knowledge of genes controlling a phenotype of interest. The Sleeping Beauty (SB) transposon system is one of many commonly employed genetic screen tools used to induce both gain and loss of gene function mutations via insertional mutagenesis. In the past, SB screens have been successfully utilized to discover several cancer driver genes that could serve as potential therapeutic targets. More recently, SB technologies have been extended to other applications, including the discovery of mechanisms contributing to drug resistance and novel targets for immunotherapy. Importantly, existing tools for SB screen data analysis do not support data-driven case–control comparisons capable of analyzing screens with this design. To this end, we developed a network-based common insertion site (NetCIS) analysis tool to robustly identify common insertion sites (CISes) in a case–control phenotype selection screen. NetCIS uses an efficient graph-based algorithm for discovering statistically significant CISes that differ between cases and controls. We benchmark NetCIS against other insertional mutagenesis analysis tools using a previously published SB dataset and show that NetCIS is able to prioritize previous biologically validated genes similarly or better than competing methods, is the only method that effectively utilizes a case–control experimental setup, and can identify CISes involving unannotated regions of the genome that are overlooked by existing methods. Code for NetCIS and an accompanying tutorial can be found at https://github.com/RogersLabGroup/NetCIS.

Adoptive cell therapy (ACT) has shown remarkable success in the treatment of some malignancies, particularly leukemia. However, there are multiple factors that limit the durability of ACT in solid tumors, including dose-limiting toxicities, the immunosuppressive tumor microenvironment, and T-cell exhaustion. As the manufacture and preparation of adoptive T-cell therapies allows time and adequate conditions for ex vivo T-cell engineering, forward genetic screens can identify novel genetic targets that could improve their effectiveness. CRISPR is a commonly used functional genomics tool that has been successfully used to both enhance our understanding of mechanisms of resistance and to discover potential genetic edits to improve ACT. A complementary approach, Sleeping Beauty transposon mutagenesis provides additional opportunities to identify novel genetic edits without being constrained by the annotated human genome. Here, we summarize forward genetic screens and their tools to uncover strategies to enhance ACT. Complementary approaches can be combined and improved on to identify translatable genetic editing strategies through studies that accurately recapitulate disease-specific challenges.

Abstract TCR diversity measures are often used to understand the immune response in cancer. Traditional measures of diversity rely on bulk RNA sequencing (RNAseq) of the β-chain variable regions. However, the full αβ TCR repertoire is a combination of both the α- and β-chains, which are encoded by separate genes. In contrast with bulk RNAseq, single-cell RNAseq (scRNAseq) allows paired chain analyses, yielding a more accurate measure of the repertoire. Interestingly, ∼30% of mature peripheral T cells express multiple TCR alleles (e.g., two α-chains) and may exhibit dual Ag specificity. scRNAseq has become increasingly common, and data from both human and animal studies are publicly available. However, routine workflows discard secondary TCR alleles and focus on a single TCR clone per cell. This perspectives piece emphasizes why this may not be good practice and highlights unanswered questions in the field of T cell dual specificity.

Abstract T cell–mediated cancer immunotherapies, including anti–PD-1 and CAR-T cells, are becoming standard treatments for many cancer types. One potential strategy to overcome resistance is to enhance the ability of T cells to traffic into tumors. We recently reported results from an innovative, genome-wide screen to identify endogenous T cell genes that enhance intratumoral accumulation using the Sleeping Beauty (SB) transposon system. We successfully identified many promising candidates with this in vivo approach using immunocompetent models of solid tumors. Others have performed similar independent whole-genome and targeted screens in T cells assessing tissue localization using adoptive T cell transfer approaches. To determine how our gene candidates compared with significant candidates identified in these independent screens, we performed a formal rank aggregation to generate a single, integrated ranked list in descending order of selection strength. Aggregated results yielded approximately 1500 T cell gene candidates whose biological functions are enriched in chemotaxis. We hypothesized that these candidates represent novel therapeutic targets to improve T cell migration into solid tumors. Here, we present in vivo validation of two of the most strongly selected candidates, including AP2-associated protein kinase 1 (Aak1) and Small Proline-Rich Protein 1B (SPRR1B). Importantly, in vivo migration of adoptively transferred T cells into tumors was significantly increased when the T cells overexpressed AAK1DN125 or SPRR1B. Our observations strongly support the strength of genomic screens to identify truly novel candidates for further development as immunotherapies to enhance T cell homing to the tumor microenvironment. Supported by Mayo Clinic Graduate School of Biomedical Sciences, K22 (K22CA225786, PI: LM Rogers), and Cancer Immunology and Immunotherapy Program Pilot Award (PI: LM Rogers)

Abstract T cell mediated cancer immunotherapies, including anti-PD-1 and CAR-T, are becoming standard of care for a variety of cancer types. However, patients with tumors that lack T cell infiltration generally do not respond well to immunotherapy. One potential strategy to overcome immunotherapy resistance is to enhance the ability of T cells to traffic into the tumor. The objective of this study was to develop an in vivo genetic screen in endogenous T cells using the Sleeping Beauty (SB) mutagenesis system to identify candidate genes that drive intratumoral T cell accumulation. Mutations in one candidate gene, Aak1, were identified in intratumoral T cells of multiple tumor models, including those treated with anti-PD-1. Insertions were highly clustered, suggesting that a gain-of-function Aak1 mutation may be favorable for driving T cells into the tumor. This gain-of-function is likely dominant-negative, as inhibition of Aak1 kinase activity enhanced intratumoral T cell infiltration. Surprisingly, inhibition of Aak1 kinase activity also abolished the therapeutic effect of anti-PD-1 in mouse models of lymphoma and melanoma. Our data demonstrates that our SB mutagenesis approach can be used to identify target genes that could be therapeutically modified to enhance T cell infiltration into tumors. Our innovative method can be adapted to other immune cell types. At least one candidate gene we identified (Aak1) deserves further evaluation as a potential therapeutic target, though a better understanding of the antagonistic relationship between anti-PD-1 action and Aak1 kinase activity is needed. Immediate next steps also include assessing the impact of candidate gene modification in CAR-T cells on their ability to traffic into solid tumors.