Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.

Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding in patient-matched samples. By integrating peptide features associated with presentation and recognition, we developed a model of tumor epitope immunogenicity that filtered out 98% of non-immunogenic peptides with a precision above 0.70. Pipelines prioritizing model features had superior performance, and pipeline alterations leveraging them improved prediction performance. These findings were validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding. This data resource enables identification of parameters underlying effective anti-tumor immunity and is available to the research community.

Impaired mitochondrial oxidative phosphorylation limits the self-renewal of T cells exposed to persistent antigen.

The majority of tumor-infiltrating T cells exhibit a terminally exhausted phenotype, marked by a loss of self-renewal capacity. How repetitive antigenic stimulation impairs T cell self-renewal remains poorly defined. Here, we show that persistent antigenic stimulation impaired ADP-coupled oxidative phosphorylation. The resultant bioenergetic compromise blocked proliferation by limiting nucleotide triphosphate synthesis. Inhibition of mitochondrial oxidative phosphorylation in activated T cells was sufficient to suppress proliferation and upregulate genes linked to T cell exhaustion. Conversely, prevention of mitochondrial oxidative stress during chronic T cell stimulation allowed sustained T cell proliferation and induced genes associated with stem-like progenitor T cells. As a result, antioxidant treatment enhanced the anti-tumor efficacy of chronically stimulated T cells. These data reveal that loss of ATP production through oxidative phosphorylation limits T cell proliferation and effector function during chronic antigenic stimulation. Furthermore, treatments that maintain redox balance promote T cell self-renewal and enhance anti-tumor immunity.

Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer.

Pancreatic ductal adenocarcinoma is a lethal cancer with fewer than 7% of patients surviving past 5 years. T-cell immunity has been linked to the exceptional outcome of the few long-term survivors, yet the relevant antigens remain unknown. Here we use genetic, immunohistochemical and transcriptional immunoprofiling, computational biophysics, and functional assays to identify T-cell antigens in long-term survivors of pancreatic cancer. Using whole-exome sequencing and in silico neoantigen prediction, we found that tumours with both the highest neoantigen number and the most abundant CD8+ T-cell infiltrates, but neither alone, stratified patients with the longest survival. Investigating the specific neoantigen qualities promoting T-cell activation in long-term survivors, we discovered that these individuals were enriched in neoantigen qualities defined by a fitness model, and neoantigens in the tumour antigen MUC16 (also known as CA125). A neoantigen quality fitness model conferring greater immunogenicity to neoantigens with differential presentation and homology to infectious disease-derived peptides identified long-term survivors in two independent datasets, whereas a neoantigen quantity model ascribing greater immunogenicity to increasing neoantigen number alone did not. We detected intratumoural and lasting circulating T-cell reactivity to both high-quality and MUC16 neoantigens in long-term survivors of pancreatic cancer, including clones with specificity to both high-quality neoantigens and predicted cross-reactive microbial epitopes, consistent with neoantigen molecular mimicry. Notably, we observed selective loss of high-quality and MUC16 neoantigenic clones on metastatic progression, suggesting neoantigen immunoediting. Our results identify neoantigens with unique qualities as T-cell targets in pancreatic ductal adenocarcinoma. More broadly, we identify neoantigen quality as a biomarker for immunogenic tumours that may guide the application of immunotherapies.

Probiotics enhance resistance to Streptococcus iniae in Nile tilapia (Oreochromis niloticus) reared in biofloc systems.

Biofloc technology is a rearing technique that maintains desired water quality by manipulating carbon and nitrogen and their inherent mixture of organic matter and microbes. Beneficial microorganisms in biofloc systems produce bioactive metabolites that may deter the growth of pathogenic microbes. As little is known about the interaction of biofloc systems and the addition of probiotics, this study focused on this integration to manipulate the microbial community and its interactions within biofloc systems. The present study evaluated two probiotics (B. velezensis AP193 and BiOWiSH FeedBuilder Syn 3) for use in Nile tilapia (Oreochromis niloticus) culture in a biofloc system. Nine independent 3785 L circular tanks were stocked with 120 juveniles (71.4 ± 4.4 g). Tilapia were fed for 16 weeks and randomly assigned three diets: a commercial control diet or a commercial diet top-coated with either AP193 or BiOWiSH FeedBuilder Syn3. At 14 weeks, the fish were challenged with a low dose of Streptococcus iniae (ARS-98-60, 7.2 × 107 CFU mL-1 , via intraperitoneal injection) in a common garden experimental design. At 16 weeks, the fish were challenged with a high dose of S. iniae (6.6 × 108 CFU mL-1 ) in the same manner. At the end of each challenge trial, cumulative per cent mortality, lysozyme activity and expression of 4 genes (il-1ß, il6, il8 and tnfα) from the spleen were measured. In both challenges, the mortalities of the probiotic-fed groups were significantly lower (p < .05) than in the control diet. Although there were some strong trends, probiotic applications did not result in significant immune gene expression changes related to diet during the pre-trial period and following exposure to S. iniae. Nonetheless, overall il6 expression was lower in fish challenged with a high dose of ARS-98-60, while tnfα expression was lower in fish subjected to a lower pathogen dose. Study findings demonstrate the applicability of probiotics as a dietary supplement for tilapia reared in biofloc systems.

Observations of phase changes in monoolein during high viscous injection.

Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood. The self-assembled structure of the LCP can be affected by pressure, dehydration and temperature changes, all of which occur during continuous flow injection. These changes to the LCP structure may in turn impact the results of X-ray diffraction measurements from membrane protein crystals. To investigate the influence of HVIs on the structure of the LCP we conducted a study of the phase changes in monoolein/water and monoolein/buffer mixtures during continuous flow injection, at both atmospheric pressure and under vacuum. The reservoir pressure in the HVI was tracked to determine if there is any correlation with the phase behaviour of the LCP. The results indicated that, even though the reservoir pressure underwent (at times) significant variation, this did not appear to correlate with observed phase changes in the sample stream or correspond to shifts in the LCP lattice parameter. During vacuum injection, there was a three-way coexistence of the gyroid cubic phase, diamond cubic phase and lamellar phase. During injection at atmospheric pressure, the coexistence of a cubic phase and lamellar phase in the monoolein/water mixtures was also observed. The degree to which the lamellar phase is formed was found to be strongly dependent on the co-flowing gas conditions used to stabilize the LCP stream. A combination of laboratory-based optical polarization microscopy and simulation studies was used to investigate these observations.

Genome and epigenome engineering CRISPR toolkit for in vivo modulation of cis-regulatory interactions and gene expression in the chicken embryo.

CRISPR/Cas9 genome engineering has revolutionised all aspects of biological research, with epigenome engineering transforming gene regulation studies. Here, we present an optimised, adaptable toolkit enabling genome and epigenome engineering in the chicken embryo, and demonstrate its utility by probing gene regulatory interactions mediated by neural crest enhancers. First, we optimise novel efficient guide-RNA mini expression vectors utilising chick U6 promoters, provide a strategy for rapid somatic gene knockout and establish a protocol for evaluation of mutational penetrance by targeted next-generation sequencing. We show that CRISPR/Cas9-mediated disruption of transcription factors causes a reduction in their cognate enhancer-driven reporter activity. Next, we assess endogenous enhancer function using both enhancer deletion and nuclease-deficient Cas9 (dCas9) effector fusions to modulate enhancer chromatin landscape, thus providing the first report of epigenome engineering in a developing embryo. Finally, we use the synergistic activation mediator (SAM) system to activate an endogenous target promoter. The novel genome and epigenome engineering toolkit developed here enables manipulation of endogenous gene expression and enhancer activity in chicken embryos, facilitating high-resolution analysis of gene regulatory interactions in vivo.

Evaluation of Escherichia coli and coliforms in aquaponic water for produce irrigation.

The FDA Produce Safety Rule states that water used for irrigation purposes, likely to come into contact with the edible portion of fruit and vegetables, must not exceed a defined limit of Escherichia coli populations. Although aquaponics has not been included in this guideline, it is worth investigating to establish a baseline for facilities to reference in produce production. Two microbial assays were performed, one a decoupled media-based aquaponics system over one year and another on a decoupled nutrient film technique (NFT) aquaponics system over 16 days. Water was sampled from each system over time to analyze changes of E. coli and coliforms. The geometric mean (GM) and statistical threshold variable (STV) were calculated based on E. coli populations from the irrigation source in each system. From the first experiment, it was determined, based on the FDA Produce Safety Rule, that E. coli must be monitored more closely from June to January as they were above the advised limit. The second experiment determined that E. coli and coliforms in the water significantly decreased over 16 days. Water should be held for 8 d and up to 16 d to reduce the likelihood of foodborne pathogens to contaminate produce.

Tobacco use predicts a more difficult episode of care after anatomic total shoulder arthroplasty.

BACKGROUND: In the current health care environment, it is becoming increasingly important to recognize risks factors that may affect a patient's postoperative outcome. To determine the potential impact of tobacco as a risk factor, we evaluated postoperative pain, narcotic use, length of stay, reoperations, and complications in the global 90-day episode of care for patients undergoing anatomic total shoulder arthroplasty (TSA) who were current tobacco users, former users, or nonusers. METHODS: Database search identified 163 patients with primary anatomic TSA done for glenohumeral arthritis; these were divided into 3 groups: current tobacco users (28), nonusers (88), and former users (47). All surgeries were done with the same technique and implants. RESULTS: Patients in the current tobacco use group had significantly higher visual analog scale scores preoperatively and at 12 weeks postoperatively than nonusers and former users. Mean improvement in visual analog scale scores was significantly less in current tobacco users. Cumulative oral morphine equivalent use at 12 weeks was significantly higher in current tobacco users than in nonusers and former users. The average oral morphine equivalent per day was also significantly higher in the current tobacco users than in nonusers and former users. There were no significant differences in length of stay or complications. CONCLUSIONS: Although length of stay, complication rates, hospital readmissions, and reoperation rates were not significantly different, tobacco users reported increased postoperative pain and narcotic use in the global period after TSA. Former tobacco users were found to have a postoperative course similar to that of nonusers, suggesting that discontinuation of tobacco use can improve a patient's episode of care performance after TSA.

Anisotropic ion diffusion in α-Cr2O3: an atomistic simulation study.

Chromia (α-Cr2O3) is one of the most technologically important oxides, as it is the basis behind the passivation of many structural materials like stainless steel. It both resists oxygen ingress and slows the release of metals from its substrate by its high density and very low diffusivities. Were any further improvement to the protectiveness of chromia to be realized, no matter how small, it would have an enormous impact due to its ubiquitousness. Here we use molecular dynamics (MD) in conjunction with nudged elastic band (NEB) calculations to study the diffusion mechanisms of oxygen and chromium ions in α-Cr2O3. Significant anisotropic diffusion between the ab-plane and the c-axis is observed for both oxygen and chromium ions. We found that vacancy-mediated ion diffusion in the ab-plane is faster than diffusion along the c-axis, while interstitial-mediated diffusion along the c-axis is faster. Vacancy and interstitial defect migration paths unveil the atomistic mechanisms responsible for this anisotropic ion diffusion, as the most energetically favorable diffusion path accounts for the observed anisotropy. The results of this study have profound implications for the reduction and control of corrosion.

Spatial and functional heterogeneities shape collective behavior of tumor-immune networks.

Tumor growth involves a dynamic interplay between cancer cells and host cells, which collectively form a tumor microenvironmental network that either suppresses or promotes tumor growth under different conditions. The transition from tumor suppression to tumor promotion is mediated by a tumor-induced shift in the local immune state, and despite the clinical challenge this shift poses, little is known about how such dysfunctional immune states are initiated. Clinical and experimental observations have indicated that differences in both the composition and spatial distribution of different cell types and/or signaling molecules within the tumor microenvironment can strongly impact tumor pathogenesis and ultimately patient prognosis. How such "functional" and "spatial" heterogeneities confer such effects, however, is not known. To investigate these phenomena at a level currently inaccessible by direct observation, we developed a computational model of a nascent metastatic tumor capturing salient features of known tumor-immune interactions that faithfully recapitulates key features of existing experimental observations. Surprisingly, over a wide range of model formulations, we observed that heterogeneity in both spatial organization and cell phenotype drove the emergence of immunosuppressive network states. We determined that this observation is general and robust to parameter choice by developing a systems-level sensitivity analysis technique, and we extended this analysis to generate other parameter-independent, experimentally testable hypotheses. Lastly, we leveraged this model as an in silico test bed to evaluate potential strategies for engineering cell-based therapies to overcome tumor associated immune dysfunction and thereby identified modes of immune modulation predicted to be most effective. Collectively, this work establishes a new integrated framework for investigating and modulating tumor-immune networks and provides insights into how such interactions may shape early stages of tumor formation.

Diabetes-related mortality in adults with cystic fibrosis. Role of genotype and sex.

RATIONALE: Diabetes is associated with increased mortality in cystic fibrosis. Aggressive screening and early institution of insulin treatment significantly reduced this risk over the period of 1992-2008. OBJECTIVES: To determine if progressive improvement in cystic fibrosis-related diabetes (CFRD) mortality has continued since 2008, and examine associations with CFTR genotypes linked to pancreatic insufficiency and to sex. METHODS: Chart review was performed on 664 patients followed from 2008 to 2012. MEASUREMENTS AND MAIN RESULTS: Overall mortality for patients with CFRD was 1.8 per 100 person-years, compared with 0.5 in patients with CF without diabetes (P = 0.0002); neither rate changed significantly from mortality reported for 2003-2008. Genotype impacted both mortality and diabetes risk: adults with severe CFTR genotypes experienced greater mortality at every age older than 32 years than those with mild genotypes (P = 0.002), and the risk of developing CFRD was also greatly increased in those with severe genotypes (prevalence 60% in adult patients with severe vs. 14% in adults with mild mutations). CFRD had a direct influence on mortality because it was associated with increased risk of death within each genotype category (20 vs. 2%, P = 0.007 for mild; 12 vs. 4%, P = 0.012 for severe). There was also a sex difference in adults with severe CFTR genotypes; both mortality and CFRD prevalence were higher at every age in females than males. CONCLUSIONS: Despite substantial improvement over time, mortality for CFRD patients greater than 30 years remains higher than for patients with CF without diabetes.

Postoperative pneumoperitoneum: is it normal or pathologic?

BACKGROUND: Pneumoperitoneum on computed tomography (CT) after abdominal surgery is common, but its incidence, duration, and clinical significance is widely debated. MATERIALS AND METHODS: A retrospective, cohort study of patients who underwent abdominal CT within 30 days of abdominal surgery. RESULTS: Among 344 patients, pneumoperitoneum was found in 39% (135/344) of patients on postoperative days 0-6 in 53%, 7-13 in 41%, 14-20 in 23%, 21-27 in 13%, and 28-30 in 0%. Pneumoperitoneum was associated with the presence of a drain (P = 0.014) but not with age, gender, body mass index, smoking history, lung disease, or open versus laparoscopic surgery (P > 0.05 for all variables). Eight patients required intervention (6%), most commonly for anastomotic leak (4 patients, 50%). CONCLUSIONS: Postoperative pneumoperitoneum on abdominal CT can be seen in up to 23% of patients 3-weeks postoperatively; however, only 6% of the patients required intervention emphasizing the typically benign consequences of postoperative free air.

Timing of MOG-IgG Testing Is Key to 2023 MOGAD Diagnostic Criteria.

BACKGROUND AND OBJECTIVES: Myelin oligodendrocyte glycoprotein (MOG) antibody-associated disease (MOGAD) is a recently identified autoimmune demyelinating disorder of the CNS affecting both adults and children. Diagnostic criteria for MOGAD have recently been published. We aimed to validate the 2023 MOGAD diagnostic criteria in a real-world cohort of patients with atypical CNS inflammation. METHODS: All patients referred to the National neuromyelitis optica spectrum disorder (NMOSD) specialized service at The Walton Center NHS Foundation Trust between 2012 and 2023 with an atypical demyelinating syndrome were evaluated. We systematically applied the 2023 MOGAD diagnostic criteria and previous 2018 International Diagnostic Recommendations for MOG encephalomyelitis to our retrospective cohort. RESULTS: 474 patients were screened and 66 were excluded for lack of clinical information. Preexisting diagnoses within our cohort included the following: MOGAD, n = 127; AQP4-IgG NMOSD, n = 125; seronegative NMOSD, n = 33; multiple sclerosis (MS), n = 10; and other diagnoses, n = 113. Of patients with preexisting MOGAD, 97% (123/127) fulfilled the 2023 MOGAD diagnostic criteria. Three patients with a low-positive MOG-IgG did not meet supportive features though 2/3 had insufficient investigations. Alternative diagnoses could not be excluded in 1 patient with MS-MOGAD overlap. No patients with a non-MOGAD diagnosis were found to fulfill the 2023 diagnostic criteria. The sensitivity and specificity of the 2023 MOGAD diagnostic criteria were 97% and 100% with no false positives, improving on 2018 International Diagnostic Recommendations for MOG encephalomyelitis. Low-positive MOG-IgG results were more often associated with a longer time from disease onset to sampling (p < 0.001). In addition, in patients with a MOG-IgG1 test within 6 months of clinical onset, approximately 25% can become low positive by 6 months. Of patients with preexisting MOGAD, 9% (12/127) had insufficient investigations and examinations to fully evaluate additional supportive features. However, in those who were completely evaluated, supportive features were fulfilled in 97% (111/115). DISCUSSION: The 2023 MOGAD diagnostic criteria were highly sensitive and specific and closely align with historically established cases of MOGAD. However, because additional supportive features are stipulated for patients with a low-positive MOG-IgG result, missed diagnoses may occur due to delayed testing or insufficient investigations.

Adsorptive removal of iodate oxyanions from water using a Zr-based metal-organic framework.

A Zr6-based metal-organic framework (MOF), MOF-808, is investigated for the adsorptive removal of IO3- from aqueous solutions, due to its high surface area and abundance of open metal sites. The uptake kinetics, adsorption capacity and binding mode are studied, showing a maximum uptake capacity of 233 mg g-1, the highest reported by any material.

Prior anti-CTLA-4 therapy impacts molecular characteristics associated with anti-PD-1 response in advanced melanoma.

Immune checkpoint inhibitors (ICIs), including CTLA-4- and PD-1-blocking antibodies, can have profound effects on tumor immune cell infiltration that have not been consistent in biopsy series reported to date. Here, we analyze seven molecular datasets of samples from patients with advanced melanoma (N = 514) treated with ICI agents to investigate clinical, genomic, and transcriptomic features of anti-PD-1 response in cutaneous melanoma. We find that prior anti-CTLA-4 therapy is associated with differences in genomic, individual gene, and gene signatures in anti-PD-1 responders. Anti-CTLA-4-experienced melanoma tumors that respond to PD-1 blockade exhibit increased tumor mutational burden, inflammatory signatures, and altered cell cycle processes compared with anti-CTLA-4-naive tumors or anti-CTLA-4-experienced, anti-PD-1-nonresponsive melanoma tumors. We report a harmonized, aggregate resource and suggest that prior CTLA-4 blockade therapy is associated with marked differences in the tumor microenvironment that impact the predictive features of PD-1 blockade therapy response.

Anti-GD2 CAR-NKT cells in relapsed or refractory neuroblastoma: updated phase 1 trial interim results.

Vα24-invariant natural killer T cells (NKTs) have anti-tumor properties that can be enhanced by chimeric antigen receptors (CARs). Here we report updated interim results from the first-in-human phase 1 evaluation of autologous NKTs co-expressing a GD2-specific CAR with interleukin 15 (IL15) (GD2-CAR.15) in 12 children with neuroblastoma (NB). The primary objectives were safety and determination of maximum tolerated dose (MTD). The anti-tumor activity of GD2-CAR.15 NKTs was assessed as a secondary objective. Immune response evaluation was an additional objective. No dose-limiting toxicities occurred; one patient experienced grade 2 cytokine release syndrome that was resolved by tocilizumab. The MTD was not reached. The objective response rate was 25% (3/12), including two partial responses and one complete response. The frequency of CD62L+NKTs in products correlated with CAR-NKT expansion in patients and was higher in responders (n = 5; objective response or stable disease with reduction in tumor burden) than non-responders (n = 7). BTG1 (BTG anti-proliferation factor 1) expression was upregulated in peripheral GD2-CAR.15 NKTs and is a key driver of hyporesponsiveness in exhausted NKT and T cells. GD2-CAR.15 NKTs with BTG1 knockdown eliminated metastatic NB in a mouse model. We conclude that GD2-CAR.15 NKTs are safe and can mediate objective responses in patients with NB. Additionally, their anti-tumor activity may be enhanced by targeting BTG1. ClinicalTrials.gov registration: NCT03294954 .

Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade.

Paired single-cell RNA and T cell receptor sequencing (scRNA/TCR-seq) has allowed for enhanced resolution of clonal T cell dynamics in cancer. Here, we report a scRNA/TCR-seq analysis of 187,650 T cells from 31 tissue regions, including tumor, adjacent normal tissues, and lymph nodes (LN), from three patients with non-small cell lung cancer after immune checkpoint blockade (ICB). Regions with viable cancer cells are enriched for exhausted CD8+ T cells, regulatory CD4+ T cells (Treg), and follicular helper CD4+ T cells (TFH). Tracking T cell clonotypes across tissues, combined with neoantigen specificity assays, reveals that TFH and tumor-specific exhausted CD8+ T cells are clonally linked to TCF7+SELL+ progenitors in tumor draining LNs, and progressive exhaustion trajectories of CD8+ T, Treg, and TFH cells with proximity to the tumor microenvironment. Finally, longitudinal tracking of tumor-specific CD8+ and CD4+ T cell clones reveals persistence in the peripheral blood for years after ICB therapy.

Oxidation state of uranium in A6Cu12U2S15 (A = K, Rb, Cs) compounds.

Black single crystals of A(6)Cu(12)U(2)S(15) (A = K, Rb, Cs) have been synthesized by the reactive flux method. These isostructural compounds crystallize in the cubic space group Ia ̅3d at room temperature. The structure comprises a three-dimensional framework built from US(6) octahedra and CuS(3) trigonal planar units with A cations residing in the cavities. There are no S-S bonds in the structure. To elucidate the oxidation state of U in these compounds, various physical property measurements and characterization methods were carried out. Temperature-dependent electrical resistivity measurement on a single crystal of K(6)Cu(12)U(2)S(15) showed it to be a semiconductor. These three A(6)Cu(12)U(2)S(15) (A = K, Rb, Cs) compounds all exhibit small effective magnetic moments, < 0.58 µ(B)/U and band gaps of about 0.55(2) eV in their optical absorption spectra. From X-ray absorption near edge spectroscopy (XANES), the absorption edge of A(6)Cu(12)U(2)S(15) is very close to that of UO(3). Electronic band structure calculations at the density functional theory (DFT) level indicate a strong degree of covalency between U and S atoms, but theory was not conclusive about the formal oxidation state of U. All experimental data suggest that the A(6)Cu(12)U(2)S(15) family is best described as an intermediate U(5+)/U(6+) sulfide system of (A(+))(6)(Cu(+))(12)(U(5+))(2)(S(2-))(13)(S(-))(2) and (A(+))(6)(Cu(+))(12)(U(6+))(2)(S(2-))(15).

Bystander T cells in cancer immunology and therapy.

Cancer-specific T cells are required for effective anti-cancer immunity and have a central role in cancer immunotherapy. However, emerging evidence suggests that only a small fraction of tumor-infiltrating T cells are cancer specific, and T cells that recognize cancer-unrelated antigens (so-called 'bystanders') are abundant. Although the role of cancer-specific T cells in anti-cancer immunity has been well established, the implications of bystander T cells in tumors are only beginning to be understood. It is becoming increasingly clear that bystander T cells are not a homogeneous group of cells but, instead, they differ in their specificities, their activation states and effector functions. In this Perspective, we discuss recent studies of bystander T cells in tumors, including experimental and computational approaches that enable their identification and functional analysis and viewpoints on how these insights could be used to develop new therapeutic approaches for cancer immunotherapy.