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It is now well established that the immune system can recognize developing cancers and that therapeutic manipulation of immunity can induce tumor regression. The capacity to manifest remarkably durable responses in some patients has been ascribed in part to T cells that can (a) kill tumor cells directly, (b) orchestrate diverse antitumor immune responses, (c) manifest long-lasting memory, and (d) display remarkable specificity for tumor-derived proteins. This specificity stems from fundamental differences between cancer cells and their normal counterparts in that the former develop protein-altering mutations and undergo epigenetic and genetic alterations, resulting in aberrant protein expression. These events can result in formation of tumor antigens. The identification of mutated and aberrantly expressed self-tumor antigens has historically been time consuming and laborious. While mutant antigens are usually expressed in a tumor-specific manner, aberrantly expressed antigens are often shared between cancers and, therefore, in the past, have been the major focus of therapeutic cancer vaccines. However, advances in next-generation sequencing and epitope prediction now permit the rapid identification of mutant tumor neoantigens. This review focuses on a discussion of mutant tumor neoantigens and their use in personalizing cancer immunotherapies.

Mutation load correlates with the response of melanomas to immunotherapy [Also see Report by Van Allen et al. ] Cancer immunotherapy has advanced to the forefront of molecular medicine as a consequence of the success of monoclonal antibodies (mAbs) that block immune checkpoints. Such antibodies, like ipilimumab, reverse cancer-induced immunosuppression and induce durable therapeutic responses in certain cancer patients ( 1 ). However, because only some patients respond to checkpoint blockade therapy, there is a need for reliable biomarkers that identify individuals most likely to respond to such treatment. On page 207 of this issue, Van Allen et al. ( 2 ) report the genomic analyses of tumors from 110 melanoma patients prior to ipilimumab therapy. The study not only validates features of responsive melanomas suggested in smaller-scale analyses, but also refutes claims that associate responsiveness to ipilimumab with tumor antigens that show putative similarities to microbial proteins ( 3 ).

The ability of the immune system to eliminate and shape the immunogenicity of tumours defines the process of cancer immunoediting 1 . Immunotherapies such as those that target immune checkpoint molecules can be used to augment immune-mediated elimination of tumours and have resulted in durable responses in patients with cancer that did not respond to previous treatments. However, only a subset of patients benefit from immunotherapy and more knowledge about what is required for successful treatment is needed 2 – 4 . Although the role of tumour neoantigen-specific CD8 + T cells in tumour rejection is well established 5 – 9 , the roles of other subsets of T cells have received less attention. Here we show that spontaneous and immunotherapy-induced anti-tumour responses require the activity of both tumour-antigen-specific CD8 + and CD4 + T cells, even in tumours that do not express major histocompatibility complex (MHC) class II molecules. In addition, the expression of MHC class II-restricted antigens by tumour cells is required at the site of successful rejection, indicating that activation of CD4 + T cells must also occur in the tumour microenvironment. These findings suggest that MHC class II-restricted neoantigens have a key function in the anti-tumour response that is nonoverlapping with that of MHC class I-restricted neoantigens and therefore needs to be considered when identifying patients who will most benefit from immunotherapy. In a mouse tumour model, immunotherapy-induced rejection of tumour cells requires presentation of both MHC class I and MHC class II antigens, which activate CD4 + and CD8 + T cells, respectively.

Due to poor correlation between steady state mRNA levels and protein product, purely transcriptomic profiling methods may miss genes posttranscriptionally regulated by RNA binding proteins (RBPs) and microRNAs (miRNAs). RNA immunoprecipitation (RIP) methods developed to identify in vivo targets of RBPs have greatly elucidated those mRNAs which may be regulated via transcript stability and translation. The RBP HuR (ELAVL1) and family members are major stabilizers of mRNA. Many labs have identified HuR mRNA targets; however, many of these analyses have been performed in cell lines and oftentimes are not independent biological replicates. Little is known about how HuR target mRNAs behave in conditional knock-out models. In the present work, we performed HuR RIP-Seq and RNA-Seq to investigate HuR direct and indirect targets using a novel conditional knock-out model of HuR genetic ablation during CD4+ T activation and Th2 differentiation. Using independent biological replicates, we generated a high coverage RIP-Seq data set (>160 million reads) that was analyzed using bioinformatics methods specifically designed to find direct mRNA targets in RIP-Seq data. Simultaneously, another set of independent biological replicates were sequenced by RNA-Seq (>425 million reads) to identify indirect HuR targets. These direct and indirect targets were combined to determine canonical pathways in CD4+ T cell activation and differentiation for which HuR plays an important role. We show that HuR may regulate genes in multiple canonical pathways involved in T cell activation especially the CD28 family signaling pathway. These data provide insights into potential HuR-regulated genes during T cell activation and immune mechanisms.

Radionuclide-stimulated dynamic therapy (RaST) utilizes Cerenkov-radiating radiopharmaceuticals to activate light-sensitive drugs and materials, generating reactive oxygen species (ROS) that inhibit cancer progression. However, the underlying cell death mechanisms are not fully understood. Using ROS-regenerative nanophotosensitizers coated with a tumor-targeting transferrin-titanocene complex and radiolabeled 2-fluorodeoxyglucose, we found that RaST induced apoptosis and necroptosis, characterized by the activation of RIPK-1, RIPK-3, nuclear factor kappa B, and mixed lineage kinase domain-like pseudokinase, leading to membrane permeabilization, cytokine release, and the expression of immunogenic damage-associated molecular patterns. In immune-deficient breast tumor-bearing mice with adequate stroma and growth factors, RaST did not prevent tumor growth or lung metastasis. However, in immunocompetent models, RaST induced a partial and complete response (CR) with no metastasis, driven by the recruitment of CD11b+, CD11c+, and CD8b+ effector immune cells. A cancer-imaging agent, LS301, identified latent minimal residual disseminated tumors in the lymph nodes of the CR group. Although cancer cells in CR mice enhanced protumor cytokines and immune checkpoints over time, RaST maintained cancer control through dynamic redistribution of ROS-regenerative titanium dioxide nanoparticles from bones to spleen and lymph nodes, supporting sustained immunity. This study highlights how RaST reprograms tumor immunity, overcoming apoptosis resistance by activating complementary necroptosis. RaST activates complementary apoptotic, necroptotic, and immune pathways to eliminate tumors, prevent metastasis, and achieve long term cancer remission.

Background The discordance between steady-state levels of mRNAs and protein has been attributed to posttranscriptional control mechanisms affecting mRNA stability and translation. Traditional methods of genome wide microarray analysis, profiling steady-state levels of mRNA, may miss important mRNA targets owing to significant posttranscriptional gene regulation by RNA binding proteins (RBPs). Methods The ribonomic approach, utilizing RNA immunoprecipitation hybridized to microarray (RIP-Chip), provides global identification of putative endogenous mRNA targets of different RBPs. HuR is an RBP that binds to the AU-rich elements (ARE) of labile mRNAs, such as proto-oncogenes, facilitating their translation into protein. HuR has been shown to play a role in cancer progression and elevated levels of cytoplasmic HuR directly correlate with increased invasiveness and poor prognosis for many cancers, including those of the breast. HuR has been described to control genes in several of the acquired capabilities of cancer and has been hypothesized to be a tumor-maintenance gene, allowing for cancers to proliferate once they are established. Results We used HuR RIP-Chip as a comprehensive and systematic method to survey breast cancer target genes in both MCF-7 (estrogen receptor positive, ER+) and MDA-MB-231 (estrogen receptor negative, ER-) breast cancer cell lines. We identified unique subsets of HuR-associated mRNAs found individually or in both cell types. Two novel HuR targets, CD9 and CALM2 mRNAs, were identified and validated by quantitative RT-PCR and biotin pull-down analysis. Conclusion This is the first report of a side-by-side genome-wide comparison of HuR-associated targets in wild type ER+ and ER- breast cancer. We found distinct, differentially expressed subsets of cancer related genes in ER+ and ER- breast cancer cell lines, and noted that the differential regulation of two cancer-related genes by HuR was contingent upon the cellular environment.

A carcinogen-induced mouse tumour model is used here to show that mutant tumour-specific antigens are targets for CD8 + T-cell responses, mediating tumour regression after checkpoint blockade immunotherapy, and that these antigens can be used effectively in therapeutic vaccines; this advance potentially opens the door to personalized cancer vaccines. Targetting tumour-specific mutant antigens In many individuals, immunosuppression is mediated by T-lymphocyte associated antigen-4 (CTLA-4) and programmed death-1 (PD-1), immunomodulatory receptors expressed on T cells. Matthew Gubin et al . use the MCA mouse sarcoma model to show that mutant tumour antigens serve as targets for CD8 + T-cell responses, mediating tumour regression after checkpoint blockade immunotherapy with anti-PD-1 and/or anti-CTLA-4. The authors demonstrate that these antigens can be used effectively in therapeutic vaccines, suggesting a possible route to personalized cancer vaccines. The immune system influences the fate of developing cancers by not only functioning as a tumour promoter that facilitates cellular transformation, promotes tumour growth and sculpts tumour cell immunogenicity 1 , 2 , 3 , 4 , 5 , 6 , but also as an extrinsic tumour suppressor that either destroys developing tumours or restrains their expansion 1 , 2 , 7 . Yet, clinically apparent cancers still arise in immunocompetent individuals in part as a consequence of cancer-induced immunosuppression. In many individuals, immunosuppression is mediated by cytotoxic T-lymphocyte associated antigen-4 (CTLA-4) and programmed death-1 (PD-1), two immunomodulatory receptors expressed on T cells 8 , 9 . Monoclonal-antibody-based therapies targeting CTLA-4 and/or PD-1 (checkpoint blockade) have yielded significant clinical benefits—including durable responses—to patients with different malignancies 10 , 11 , 12 , 13 . However, little is known about the identity of the tumour antigens that function as the targets of T cells activated by checkpoint blockade immunotherapy and whether these antigens can be used to generate vaccines that are highly tumour-specific. Here we use genomics and bioinformatics approaches to identify tumour-specific mutant proteins as a major class of T-cell rejection antigens following anti-PD-1 and/or anti-CTLA-4 therapy of mice bearing progressively growing sarcomas, and we show that therapeutic synthetic long-peptide vaccines incorporating these mutant epitopes induce tumour rejection comparably to checkpoint blockade immunotherapy. Although mutant tumour-antigen-specific T cells are present in progressively growing tumours, they are reactivated following treatment with anti-PD-1 and/or anti-CTLA-4 and display some overlapping but mostly treatment-specific transcriptional profiles, rendering them capable of mediating tumour rejection. These results reveal that tumour-specific mutant antigens are not only important targets of checkpoint blockade therapy, but they can also be used to develop personalized cancer-specific vaccines and to probe the mechanistic underpinnings of different checkpoint blockade treatments.

Cancer vaccines can elicit tumor-specific T cells, but sustaining their function via immune checkpoint therapy (ICT) may be required for robust anti-tumor immunity. A new study reveals that neoantigen cancer vaccines synergize with anti-PD-L1 ICT in a preclinical model and provides mechanistic insights into this synergy.

The widespread application of single-cell and spatial omics to models and patient samples has transformed immune cell profiling across physiological conditions. However, knowledge of immune cell states, functions, and gene regulation remains fragmented across publications, limiting our ability to synthesize insights and derive mechanistic understanding from the literature. To address this gap and facilitate literature integration, we constructed Immune Cell Knowledge Graphs (ICKGs)—four cell type-specific graphs derived from over 24,000 cancer immunotherapy-focused PubMed abstracts using large language models (LLMs) with “human verifiable” validation. Unlike conventional databases, which provide context-agnostic pathways, ICKGs capture directed, literature-supported relationships among genes, pathways and immune functions, enabling context-aware reasoning. We validated ICKGs using perturbation datasets from cytokine stimulation and CRISPR experiments, demonstrating that ICKGs contain more accurate and immunologically coherent contexts than canonical databases. As a key application, ICKGs provide interpretable and accurate pathway annotations, including signatures unannotated by canonical databases or used in immuno-oncology. To support community use, we created an interactive portal ( https://kchen-lab.github.io/immune-knowledgegraph.github.io/ ) to perform ICKG-based pathway annotations, allowing researchers to explore immune cell-specific insights grounded in literature. This work establishes ICKGs as a scalable framework for immune-specific functional interpretation and mechanistic hypothesis generation in single-cell and spatial omics.

Due to poor correlation between steady state mRNA levels and protein product, purely transcriptomic profiling methods may miss genes posttranscriptionally regulated by RNA binding proteins (RBPs) and microRNAs (miRNAs). RNA immunoprecipitation (RIP) methods developed to identify in vivo targets of RBPs have greatly elucidated those mRNAs which may be regulated via transcript stability and translation. The RBP HuR (ELAVL1) and family members are major stabilizers of mRNA. Many labs have identified HuR mRNA targets; however, many of these analyses have been performed in cell lines and oftentimes are not independent biological replicates. Little is known about how HuR target mRNAs behave in conditional knock-out models. In the present work, we performed HuR RIP-Seq and RNA-Seq to investigate HuR direct and indirect targets using a novel conditional knock-out model of HuR genetic ablation during CD4+ T activation and Th2 differentiation. Using independent biological replicates, we generated a high coverage RIP-Seq data set (>160 million reads) that was analyzed using bioinformatics methods specifically designed to find direct mRNA targets in RIP-Seq data. Simultaneously, another set of independent biological replicates were sequenced by RNA-Seq (>425 million reads) to identify indirect HuR targets. These direct and indirect targets were combined to determine canonical pathways in CD4+ T cell activation and differentiation for which HuR plays an important role. We show that HuR may regulate genes in multiple canonical pathways involved in T cell activation especially the CD28 family signaling pathway. These data provide insights into potential HuR-regulated genes during T cell activation and immune mechanisms.