Cancer Cell

There is a pressing need to characterise the nature, extent and duration of immune response to SARS-CoV-2 in cancer patients and inform risk-reduction strategies and preserve cancer outcomes. CAPTURE is a prospective, longitudinal cohort study of cancer patients and healthcare workers (HCWs) integrating longitudinal immune profiling and clinical annotation. We evaluated 529 blood samples and 1051 oronasopharyngeal swabs from 144 cancer patients and 73 HCWs and correlated with >200 clinical variables. In patients with solid cancers and HCWs, S1-reactive and neutralising antibodies to SARS-CoV-2 were detectable five months post-infection. SARS-CoV-2-specific T-cell responses were detected, and CD4+ T-cell responses correlated with S1 antibody levels. Patients with haematological malignancies had impaired but partially compensated immune responses. Overall, cancer stage, disease status, and therapies did not correlate with immune responses. These findings have implications for understanding individual risks and potential effectiveness of SARS-CoV-2 vaccination in the cancer population.

The eradication of solid tumors by chimeric antigen receptor (CAR) T cells requires dynamic therapies capable of outlasting an immune suppressive tumor microenvironment (TME). However, biological barriers--including rapid exhaustion, poor expansion, and loss of stem-like memory--quickly neutralize these therapies. Because single-technology interventions often introduce unacceptable tradeoffs between efficacy and safety, durable remission demands a paradigm where multiple engineered solutions work in concert. To holistically address these mechanisms, we rationally designed a single-vector transgene that intrinsically drives CAR T functional persistence. The platform integrates four synergistic technologies: a high-avidity mesothelin (MSLN)-targeting CAR optimized to resist shed decoy antigens, a T-cell activation-responsive promoter (OUTLAST OP1) resisting exhaustion, a CD8-targeted designed IL-2 cytokine (OUTSMART dIL-2) driving intratumoral CAR-T expansion, and an EGFRopt safety switch. In lung and ovarian cancer models, this rational integration was required to drive antigen-dependent T cell expansion and eradicate established tumors at extremely low CAR T doses. Furthermore, engineered cells established a self-renewing pool of stem-like memory T cells capable of rejecting tumor rechallenge months later. Ultimately, this work demonstrates that intrinsic T cell dysfunction and extrinsic tumor-derived barriers can be simultaneously overcome by integrating synergistic technologies.

The addition of aPD1 to 5-FU/platinum in advanced gastric cancer (GC) yields variable responses. To understand cooperativity between chemotherapy and immunotherapy, we previously reported a phase II trial sequentially adding pembrolizumab to 5-FU/platinum. In this study, we use single-cell RNA- and TCR-sequencing to analyze 66,813 T cells from primary tumor biopsies pre-treatment, post-chemotherapy, and post-immunotherapy in 33 patients. We observed greater abundance, persistence, and recruitment of T cells with predicted tumor-reactivity in patients with prolonged progression-free survival (slow progressors). Increased B cell abundance and predicted B cell to T cell interactions supported T cell memory and co-stimulation, providing a mechanism for increased abundance and persistence of progenitor-exhausted and tumor-reactive T cells in slow progressors. T cell clones emerging in the tumor after immunotherapy were in the blood before treatment only in slow progressors. Our study thus highlights pre-treatment and early chemotherapy-induced T cell dynamics and B cell to T cell interactions that may drive durable response to chemoimmunotherapy in GC.

Tumor hypersialylation drives immunosuppression and limits immunotherapy efficacy by shielding tumor cells and engaging inhibitory immune receptors. Here, we engineered Escherichia coli Nissle 1917 (EcN{Delta}pgi-SAS) as a metabolically confined "desialylation catalyst" to remodel the tumor microenvironment. This strain combines HER2-directed adhesion, hypoxia-inducible surface sialidase display for targeted glycan cleavage, and sialic acid catabolism to prevent glycolytic recycling. Critically, disrupting glucose metabolism ({Delta}pgi) restricts bacterial proliferation to sialic acid-rich tumor microenvironment, significantly enhancing biosafety. In mice, EcN{Delta}pgi-SAS colonized tumors and effectively desialylated tumor cells, synergizing with anti-PD-L1 to suppress growth of immunologically "cold" tumors. Mechanistically, desialylation reversed immunosuppression by broadly enhancing antitumor immunity. Orally administered EcN{Delta}pgi-SAS substantially inhibited colorectal carcinogenesis, repaired epithelial barrier integrity by restoring tight junctions, and prevented adenoma formation. This integrated strategy establishes a clinically translatable platform for reversing immunosuppression in solid tumors.

Glioblastoma (GBM) develops within a complex tumor ecosystem whose temporal dynamics remain poorly understood. Here, we performed longitudinal single-cell RNA sequencing and spatial transcriptomics across multiple timepoints in two widely used murine GBM models - CT2A and GL261 - which differ markedly in aggressiveness and response to immune checkpoint blockade. Tumor cell transcriptomes revealed model-specific programs: CT2A cells progressively upregulated epithelial-mesenchymal transition (EMT), non-classical MHC Class I, and progressively, hypoxia response pathways, resembling the human mesenchymal GBM cell state, while GL261 cells exhibited MHC Class II expression and developmental signatures resembling oligodendrocyte progenitor and astrocytic states. Ligand-receptor interaction analyses identified thrombospondins (Thbs1, Thbs2) and osteopontin (Spp1) as CT2A-specific tumor ligands mediating tumorigenic interactions with immune cells, with downstream targets enriched for EMT and TGF-{beta} pathways. Conversely, the GL261 model presented a differential potential to engage neuronal and perivascular guidance networks, with Glutamate and L1 cell adhesion molecule (L1cam) as lead signaling partners. The CT2A immune compartment exhibited progressive microglia-to-macrophage phenotypic conversion, enhanced macrophage infiltration driven by Spp1, and elevated T cell exhaustion, while GL261 maintained a distinct adaptive immune communication hub via MHC class II-CD4 signaling. Elevated THBS1, THBS2, and SPP1 expression correlated with poor survival in human GBM datasets. Together, these findings reveal divergent tumor-immune ecosystems in CT2A and GL261 that recapitulate distinct aspects of human GBM, with implications for therapeutic targeting.

Glioblastoma heterogeneity and plasticity remain controversial, with proposed subtypes representing the average of highly heterogeneous admixtures of independent transcriptional states. Single-cell, protein-activity-based analysis allowed full quantification of >6,000 regulatory and signaling proteins, thus providing a previously unattainable single-cell characterization level. This helped identify four novel, molecularly distinct subtypes that successfully harmonize across multiple GBM datasets, including previously published bulk and single-cell profiles and single cell profiles from seven orthotopic PDX models, representative of prior subtype diversity. GBM is thus characterized by the plastic coexistence of single cells in two mutually-exclusive developmental lineages, with additional stratification provided by their proliferative potential. Consistently, all previous subtypes could be recapitulated by single-cell mixtures drawn from newly identified states. Critically, drug sensitivity was predicted and validated as highly state-dependent, both in single-cell assays from patient-derived explants and in PDX models, suggesting that successful treatment requires combinations of multiple drugs targeting these distinct tumor states.\n\nSignificanceWe propose a new, 4-subtype GBM classification, which harmonizes across bulk and single-cell datasets. Single-cell mixtures from these subtypes effectively recapitulate all prior classifications, suggesting that the latter are a byproduct of GBM heterogeneity. Finally, we predict single-cell level activity of three clinically-relevant drugs, and validate them in patient-derived explant.

BackgroundPost-translational modifications (PTMs) represent a fourth dimension of the genetic code, orchestrated by the Golgi apparatus and central to the biology of cancer. The prevailing paradigm of oncofetal reprogramming posits that cancer cells reactivate embryonic developmental programs to drive tumorigenesis; however, the lineage-specific nature of this reversion remains incompletely defined. This review advances and systematically evaluates the hypothesis that the cancer PTM landscape is a traceable relic of the cells embryonic germ layer origin, ectoderm, mesoderm, or endoderm--offering a novel, developmentally-informed framework for precision oncology. ObjectivesTo systematically review and synthesize the global evidence linking cancer PTMs to their developmental origins and to evaluate the efficacy, safety, and implementation of PTM-targeted therapeutics through this novel developmental lens, with LLM assistance. MethodsFollowing PRISMA 2020 guidelines, and using LLM assistance, a systematic search of PubMed, Embase, Web of Science, Cochrane Library, and extensive grey literature sources, including over 3,000 theses, dissertations, clinical trial registries, and institutional reports, from inception to June 2025 was conducted. ResultsFrom an initial screen of over 25,000 records, 3,128 studies met the inclusion criteria, encompassing data from over 500,000 patients. Our analysis revealed distinct, germ-layer-specific PTM signatures and corresponding therapeutic vulnerabilities. Ectoderm-derived cancers (e.g., neuroblastoma, melanoma) are characterized by aberrant oncofetal glycosylation. Anti-GD2 immunotherapy, which targets a neural crest-specific glycan, demonstrated a profound survival benefit in high-risk neuroblastoma (Hazard Ratio for overall survival: 0.57, 95% CI 0.42-0.78, p<0.001). Mesoderm-derived malignancies (e.g., sarcomas, leukemias) exhibit dysregulated phosphorylation and SUMOylation. These cancers respond preferentially to kinase inhibitors (HR for overall survival: 0.72, 95% CI 0.68-0.76, p<0.001) and cellular therapies like CAR-T, which achieve overall response rates exceeding 80% in hematologic malignancies. Endoderm-derived adenocarcinomas (e.g., lung, colorectal) display a heightened dependency on the ubiquitin-proteasome system for managing proteotoxic stress, validating proteasome inhibitors (HR for overall survival: 0.77, 95% CI 0.71-0.84, p<0.001) and emerging PROTACs as key therapeutic classes. Implementation science analysis revealed profound global disparities, with treatment costs exceeding $450,000 per sequence and access to advanced PTM therapies below 5% in low-income countries. ConclusionThe post-translational modification landscape of cancer is fundamentally imprinted by its embryonic lineage, with the Golgi apparatus acting as a key arbiter of this oncofetal memory. This developmental framework provides a powerful new tool for rational drug design, biomarker discovery, and patient stratification. However, translating this scientific progress into global patient benefit requires timely and coordinated policy action to address the profound implementation chasm created by prohibitive costs and systemic inequities in healthcare access.

In approximately one third of patients, resected head and neck squamous cell carcinoma will recur. We postulated that the induction of tumor neoantigen-specific T cell responses could prevent relapse. To this end, we developed TG4050, an individualized neoantigen therapeutic vaccine encoding up to 30 patient-specific predicted tumor neoantigens delivered by a Modified Vaccinia Ankara virus viral vector. We tested TG4050 as single agent in a randomized phase I trial. We found that of 16 evaluable patients randomized to immediate vaccination with TG4050, none relapsed after a median follow-up of 30 months, while 3 relapsed in the 16 control arm patients randomized to observation and treatment with TG4050 after recurrence. Polyepitopic responses to vaccine neoantigens were detected in the blood of patients from both arms after treatment initiation. These responses were maintained throughout treatment and persisted for over one year after the last dose. Vaccine neoantigen-specific CD8+ T cells had an effector phenotype and displayed high expression of cytotoxic and tissue-resident markers. TCR repertoire analysis showed that vaccine neoantigen-specific CD8+ T cell responses were polyclonal and comprised both de novo responses and amplification of pre-existing tumor-infiltrating T cell clones. Together, this translational data is consistent with the model in which single-agent delivery of TG4050 induces long-lasting tumor neoantigen-specific cytotoxic T cell responses that prevent tumor recurrence.

Diffuse midline glioma (DMG) is a leading cause of brain tumor death in children. In addition to hallmark H3.3K27M mutations, significant subsets also harbor alterations of other genes, such as TP53 and PDGFRA. Despite the prevalence of H3.3K27M, the results of clinical trials in DMG have been mixed, possibly due to the lack of models recapitulating its genetic heterogeneity. To address this gap, we developed human iPSC-derived tumor models harboring TP53R248Q with or without heterozygous H3.3K27M and/or PDGFRAD842V overexpression. The combination of H3.3K27M and PDGFRAD842V resulted in more proliferative tumors when gene-edited neural progenitor (NP) cells were implanted into mouse brains compared to NP with either mutation alone. Transcriptomic comparison of tumors and their NP cells of origin identified conserved JAK/STAT pathway activation across genotypes as characteristic of malignant transformation. Conversely, integrated genome-wide epigenomic and transcriptomic analyses, as well as rational pharmacologic inhibition, revealed targetable vulnerabilities unique to the TP53R248Q; H3.3K27M; PDGFRAD842V tumors and related to their aggressive growth phenotype. These include AREG-mediated cell cycle control, altered metabolism, and vulnerability to combination ONC201/trametinib treatment. Taken together, these data suggest that cooperation between H3.3K27M and PDGFRA influences tumor biology, underscoring the need for better molecular stratification in DMG clinical trials.

Mismatch repair deficient colorectal cancers have high mutation loads and many respond to immune checkpoint-inhibitors. We investigated how genetic and immune landscapes co-evolve in these tumors. All cases had high truncal mutation loads. Driver aberrations showed a clear hierarchy despite pervasive intratumor heterogeneity: Those in WNT/{beta}Catenin, mitogen-activated protein kinase and TGF{beta} receptor family genes were almost always truncal. Immune evasion drivers were predominantly subclonal and showed parallel evolution. Pan-tumor evolution, subclonal evolution, and evolutionary stasis of genetic immune evasion drivers defined three MMRd CRC subtypes with distinct T-cell infiltrates. These immune evasion drivers have been implicated in checkpoint-inhibitor resistance. Clonality and subtype assessments are hence critical for predictive immunotherapy biomarker development. Cancer cell PD-L1 expression was conditional on loss of the intestinal homeobox transcription factor CDX2. This explains infrequent PD-L1 expression by cancer cells and likely contributes to the high recurrence risk of MMRd CRCs with impaired CDX2 expression.

Due to their genetic instability, tumor cells bear mutations that can effectively be recognized by the immune system. In the clinic, immune checkpoint immunotherapy (ICI) can re-activate immune reactions against mutated proteins, known as neoantigens, leading to remarkable remission in cancer patients. Nevertheless, only a minority of patients are responsive to ICI, and approaches for prediction of responsiveness remain elusive yet are needed to improve the success of cancer treatments. While the tumor mutational burden (TMB) correlates positively with responsiveness and survival of patients undergoing ICI therapy, the influence of the subcellular localizations of the mutated proteins within the tumor cell has not been elucidated. Here, we hypothesized that the immune reactions are modulated by the localization of the mutated proteins and, therefore, that some subcellular localizations could favor responsiveness to ICI. We show in both a mouse melanoma model and human clinical datasets of 1722 ICI-treated patients that high membrane-localized tumor mutational burden (mTMB), particularly at the plasma membrane, correlate with responsiveness to ICI therapy and improved overall survival across multiple cancer types. We further highlight that mutations in the genes encoding for the membrane proteins NOTCH3, RNF43, NTRK3 and NOTCH1, among others, may serve as potent biomarkers to predict extended survival upon ICI in certain cancer types. We anticipate that our results will improve the predictability of cancer patient response to ICI and therefore may have important implications to establish future clinical guidelines to direct the choice of treatment toward ICI.

Brain tumor recurrence remains the leading cause of mortality in neuro-oncology, and there is a lack of preclinical models replicating the clinical cycle of surgical resection and relapse. To bridge this gap, we developed a novel microneurosurgical survival platform in mice using the NICO Myriad system. We orthotopically implanted pediatric medulloblastoma cells into the mouse cerebral cortex or cerebellum, followed by longitudinal microneurosurgical resection. Bioluminescence imaging and gross fluorescence verified successful resection, local and distal recurrence and metastasis. Comparative bulk RNA sequencing revealed extensive stage-specific transcriptomic divergence alongside conserved core gene sets (2,702 genes in the cerebral cortex and 3,240 genes in the cerebellum) across primary, locally recurrent, and distally recurrent stages. Pathway analysis shows activation of cellular growth, second messenger signaling, and cellular stress adaptation pathways. Targeted qPCR validation demonstrated that post-surgical relapse is driven by a distinct molecular program: recurrent tumors downregulate primary developmental drivers (PTCH1, MYCBP2), canonical suppressors (FOS, PTEN), and chromatin regulators (HDAC2), while selectively upregulating post-transcriptional machinery (RBM8A), endosomal trafficking regulators (RAB5C), acetyltransferases (NAA15), and the m6A RNA demethylase ALKBH5. These findings reveal that medulloblastoma shifts from a primary oncogenic state toward post-transcriptional and transcriptomic survival mechanisms following surgery. Identifying persistent candidates within this conserved core framework provides a roadmap for next-generation precision immunotherapies.

CDK4/6 inhibitors (CDK4/6i) have transformed the treatment of hormone receptor-positive (HR+), HER2-negative (HR+) breast cancers as they are effective across all clinicopathological, age, and ethnicity subgroups for metastatic HR+ breast cancer. In metastatic ER+ breast cancer, CDK4/6i lead to strong and consistent improvement in survival across different lines of therapy. To improve understanding of how metastatic HR+ breast cancers become refractory to CDK4/6i, we have created a multimodal and longitudinal tumor atlas to investigate therapeutic adaptations in malignant cells and in the tumor immune microenvironment. This atlas is part of the NCI Cancer Moonshot Human Tumor Atlas Network and includes seven pairs of pre- and on-progression biopsies from five metastatic HR+ breast cancer patients treated with CDK4/6i. Biopsies were profiled with bulk genomics, transcriptomics, and proteomics as well as single-cell ATAC-seq and multiplex tissue imaging for spatial, single-cell resolution. These molecular datasets were then linked with detailed clinical metadata to create an atlas for understanding tumor adaptations during therapy. Analysis of our atlas datasets suggests a diverse set of tumor adaptations to CDK4/6i therapy. Malignant cells may adapt to therapy via mTORC1 activation, cell cycle bypass, and increased replication stress. The tumor immune microenvironment displayed evidence of both immune activation and immune suppression during therapy. Together, our metastatic ER+ breast cancer atlas represents a rich multimodal resource to better understand HR+ breast cancer tumor therapeutic adaptations to CDK4/6i therapy.

Congenital DNA mismatch repair defects (dMMR), such as Lynch Syndrome, predispose patients to a variety of cancers and account for approximately 1% of glioblastoma cases. While few therapeutic options exist for glioblastoma, checkpoint blockade therapy has proven effective in dMMR tumors. Here we present a case study of a male in their 30s diagnosed with dMMR glioblastoma treated with pembrolizumab who experienced a partial response to therapy. Using a multiplex IHC analysis pipeline on archived slide specimens from tumor resections at diagnosis and after therapeutic interventions, we quantified changes in the frequency and spatial distribution of key cell populations in the tumor tissue. Notably, proliferating (KI67+) macrophages and T cells increased in frequency as did other KI67+ cells within the tumor. Therapeutic intervention remodeled the cellular spatial distribution in the tumor leading to a greater frequency of macrophage/tumor cell interactions and T cell/T cell interactions, highlighting impacts of checkpoint blockade on tumor cytoarchitecture and revealing spatial patterns that may indicate advantageous immune interactions in glioma and other solid tumors treated with these agents. InsightThis work sheds light on the capacity of checkpoint blockade therapy to modulate the immune microenvironment in DNA mismatch repair deficient glioblastoma, highlights the utility of window-of-opportunity clinical trials in patient selection of immunomodulatory therapies, and demonstrates the feasibility and utility of mapping cellular interactions associated with therapeutic responses in gliomas and other solid tumors. Statement regarding non-clinical trial statusWe confirmed with a treating neurologist in this case that the treatment received by the individual whose samples are studied was part of routine clinical care and not a clinical trial, as the patient was previously diagnosed with Lynch syndrome (a mismatch repair deficiency). The use of pembrolizumab is recommended for treatment of tumors with high mutational burden due to mismatch repair deficiency and is currently considered standard of care for these tumors. Additionally, though the intervention and outcome are detailed in the manuscript, the focus of the manuscript is on reporting changes observed in the immune microenvironment at different points in the clinical trajectory - a retrospective analysis performed after clinical care was complete.

Treatment toxicity constrains the use of effective cancer therapies, but its clinical and genetic determinants remain poorly defined. We developed a large language model-based approach to produce MSK-Tox, a pan-cancer resource capturing the incidence, temporality, and grade of toxicity to anti-cancer therapy across more than 50,000 patients. Analysis of six representative adverse events - pneumonitis, adrenal insufficiency, liver toxicity, colitis, hyperthyroidism and hypothyroidism - revealed distinct toxicity landscapes shaped by cancer type, treatment regimen, and clinical context. Pretreatment clinical features enabled individualized prediction of toxicity risk across adverse events, supporting risk assessment before therapy initiation. Beyond clinical predictors, we identified two modes of germline susceptibility to treatment toxicity: an organ-intrinsic mode, in which germline variation confers risk across systemic therapies, exemplified by a regulatory variant near FOXE1 associated with hypothyroidism; and an immune-mediated mode, confined to immune checkpoint inhibitor-treated patients, in which HLA-DRB1*15 was a major determinant of adrenal insufficiency. Notably, the same allele predisposes to multiple sclerosis in individuals without cancer, indicating that immune checkpoint inhibition unmasks a latent autoimmune predisposition. These findings provide an empirical basis for a new precision safety paradigm for predicting who will be harmed by a therapy on the same principles that guide prediction of therapeutic benefit.

Genetically modified immune effector cells, including chimeric antigen receptor (CAR) T cells, have emerged as transformative anti-cancer agents. However, these autonomous, living therapies are limited by difficult-to-control hyperactivation toxicities. To achieve their full potential as therapies for a broader range of diseases, CAR T cells must target novel antigens and integrate further potency enhancements that raise the possibility of novel and intensified toxicities. High performance safety systems are needed to restrain these highly active next-generation gene- and cell-based therapies. Cell therapy suicide switches remain infrequently used, and are currently limited by inaccessible controller drugs, incomplete cell depletion, fitness cost, and immunogenicity. To address these issues, we engineered a fully human sequence-based cell therapy suicide switch based on the overexpression of Caspase-Activated DNase (CAD) and its stoichiometric chaperone/inhibitor ICAD fused to a lenalidomide-inducible degron. Acute destabilization of ICAD with the broadly available, off-patent molecular glue degrader drug lenalidomide uncaged CAD to induce DNA damage and cell death. By this degradable cage mechanism, the ICAD-CAD suicide switch achieved long-term expression in primary human T cells without detectable leakiness, and deep drug-induced cell depletion. The ICAD-CAD switch was generalizable to alternative acute destabilization systems. Genome-wide CRISPR screening established the necessity of CAD and the lenalidomide-interacting E3 ubiquitin ligase substrate adaptor CRBN for switch function. When co-delivered with a CAR, ICAD-CAD CAR T cells retained effector functions and could be rapidly depleted with lenalidomide.

Glioblastoma (GBM) is the most common and deadly primary brain cancer, with limited therapeutic options. Treatment failure has been associated with intratumoral heterogeneity and the acquisition of a pronounced mesenchymal-like (MES-L) phenotype after recurrence. Here, we have screened a panel of drugs with diverse mechanisms of action across two patient-derived glioblastoma stem cells (GSCs) to characterize the dynamics of drug-mediated transcriptomic cellular state changes. Our results demonstrate that anti-tumor drugs induce significant but reversible alterations in cellular state distribution at the single-cell level in a drug-specific manner, influencing transitions between mesenchymal and the neurodevelopmental astrocytic-like (AC-L) states. Utilizing barcoded analysis in our recently developed ex vivo glioblastoma cerebral organoid (GLICO) model, we discerned distinct cell state sensitivities to the MES-L enhancing histone deacetylase inhibitor, panobinostat, which are contingent on the inducible modulation of the mesenchymal transcription factor FOSL1. The strategic combination of MES-L enhancing and MES-l suppressing genetic perturbations or drugs significantly increases anti-glioma activity in a strategy we call state-selective lethality. Overall, our findings highlight the critical role of cell state plasticity in the response of GSCs to anti-tumor therapeutic stress and underscore the potential for novel GBM combination drug strategies.

Real-world data suggest that SARS-CoV-2 mRNA vaccines, administered within 100 days of immune checkpoint inhibitor (ICI) treatment ("peri-ICI vaccination"), may improve ICI effectiveness, potentially through synergistic immune priming. Although peri-ICI vaccination was associated with longer survival when we applied a previous framework to our independent dataset, additional patterns emerged. Peri-ICI vaccination benefit diminished after 2021, a pattern confirmed in re-analysis of a published cohort. Benefit extended to patients treated with non-ICI antineoplastics. Benefit also dissipated in landmarked analyses restricted to periods of vaccine eligibility. Finally, progression-free survival in time periods with high vaccine uptake was not longer than in periods without vaccination. These analyses suggest peri-ICI vaccinations observed association with survival largely reflects selection bias in which patients with better prognosis were more likely to receive SARS-CoV-2 vaccines.

BackgroundThe glioma immune repertoire has emerged as a vital point of interest, particularly in the context of immunotherapeutics development and as a key player for prognostic and diagnostic biomarker identification. MethodsTumor tissue was collected from glioma patients and targeted immune repertoire sequencing of tumor infiltrating lymphocytes (TIL) from each of the four collected glioma tumor subtypes was performed. Gliomas were stratified based on WHO21 classification to map the TCR landscape of astrocytomas (grade II/III, grade IV), glioblastomas, and oligodendrogliomas. ResultsFollowing stratification of TCR repertoires and complete clonotype, V-J cassette, and CDR3 analysis, we identified cohort-specific levels of diversity, clonotype sharing, and conservation. Partitioning of these repertoires based on TCR diversity revealed significant influence on patient survival. Furthermore, mapping of CDR3 binding regions to antigens and their origins highlighted prognostic biomarkers and identified sequences binding to viral signatures associated with patient clinical outcomes. ConclusionThese findings underscore the importance of characterizing TCR repertoires in the context of the patient clinical condition. These unique repertoire signatures and correlated antigens may facilitate patient outcome prognostication and serve as a potential foundation for immunotherapeutic applications. Key PointsO_LIGlioma subtypes can be differentiated via TCR repertoire characterization. C_LIO_LIT cell diversity in gliomas influences patient overall survival. C_LIO_LITCR Clonotypes are binding sites for prognostic tumor proteins and viral disease. C_LI Importance of the StudyIn this study, we characterized the infiltrating immune repertoire of glial tumors through targeted T cell receptor sequencing of four glioma subtypes: grade II/III astrocytomas, grade IV astrocytomas, glioblastoma, and oligodendrogliomas. We performed multi-level analyses to examine TCR repertoire diversity across these subtypes, identifying unique clonotype prevalence and region usage in alpha-beta T cells. Classification of clonotypes relative to known associated antigen databases revealed unique signatures related to the viral diseases of cytomegalovirus and Epstein-Barr virus, as well as clonotypes with binding affinity for human tumor-derived proteins prognostic for glioma. This study reveals a unique perspective into the differentiation of glioma subtypes based on TCR clonotypes and further solidifies the role of TCR mapping in the patient care paradigm.

Lung cancer, the leading cause of cancer mortality, exhibits heterogeneity that enables adaptability, limits therapeutic success, and remains incompletely understood. Single-cell RNA sequencing (scRNAseq) of metastatic lung cancer was performed using 44 tumor biopsies obtained longitudinally from 27 patients before and during targeted therapy. Over 20,000 cancer and tumor microenvironment (TME) single-cell profiles exposed a rich and dynamic tumor ecosystem. scRNAseq of cancer cells illuminated targetable oncogenes beyond those detected clinically. Cancer cells surviving therapy as residual disease (RD) expressed an alveolar-regenerative cell signature suggesting a therapy-induced primitive cell state transition, whereas those present at on-therapy progressive disease (PD) upregulated kynurenine, plasminogen, and gap junction pathways. Active T-lymphocytes and decreased macrophages were present at RD and immunosuppressive cell states characterized PD. Biological features revealed by scRNAseq were biomarkers of clinical outcomes in independent cohorts. This study highlights how therapy-induced adaptation of the multi-cellular ecosystem of metastatic cancer shapes clinical outcomes.