Journal Articles

Predicability of PD-L1 expression in cancer cells based solely on H&E-stained sections

PD-L1 expression is an important biomarker for selecting patients who are eligible for immune checkpoint inhibitor (ICI) therapy. However, evaluating PD-L1 through immunohistochemistry often faces significant interobserver variability and requires considerable time and resources. Recent advancements in artificial intelligence (AI) have transformed the field of pathology, leading to more standardized and reproducible methods for biomarker quantification. In this study, we examine the application of AI-driven models, particularly deep learning algorithms, to predict PD-L1 expression directly from hematoxylin and eosin-stained histological slides. Several AI-based approaches have been studied, demonstrating high accuracy in estimating PD-L1 expression and predicting responses to ICIs across various cancer types. AI-driven assessments of PD-L1 have been shown to reduce the subjectivity associated with manual scoring methods, such as the Tumor Proportion Score and the Combined Positive Score. Moreover, integrating AI with multimodal data, including genomics, radiomics, and real-world clinical data, can further enhance predictive accuracy and improve patient stratification for immunotherapy. Finally, AI-driven computational pathology offers a transformative approach to biomarker evaluation, providing a faster, more objective, and cost-effective alternative to traditional methods, with significant implications for personalized oncology and precision medicine. Despite these promising results, several challenges remain to be addressed, such as the need for large-scale validation, standardization of AI models, and regulatory approvals for clinical implementation. Tackling these issues will be crucial for incorporating AI-based PD-L1 assessments into routine pathology workflows.

Author Info: (1) Department of Medical Sciences and Public Health, Universitˆ degli Studi di Cagliari, 09123 Cagliari, Italy. Department of Biology, College of Science and Technology, Temple Un

Author Info: (1) Department of Medical Sciences and Public Health, Universitˆ degli Studi di Cagliari, 09123 Cagliari, Italy. Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA. (2) Department of Electrical and Electronic Engineering, Universitˆ degli Studi di Cagliari, 09123 Cagliari, Italy. (3) Medical Oncology Unit, University Hospital of Cagliari, Universitˆ degli Studi di Cagliari, 09123 Cagliari, Italy. (4) Medical Oncology Unit, University Hospital of Cagliari, Universitˆ degli Studi di Cagliari, 09123 Cagliari, Italy. (5) Department of Pathology, Ospedale Oncologico A. Businco, ARNAS G. Brotzu, Cagliari, Italy. (6) Department of Medical Sciences and Public Health, Universitˆ degli Studi di Cagliari, 09123 Cagliari, Italy. (7) Medical Oncology Unit, University Hospital of Cagliari, Universitˆ degli Studi di Cagliari, 09123 Cagliari, Italy. (8) National Cancer Institute, Kyiv, Ukraine. Associazione "Angela Serra" per la ricerca sul cancro, Modena, Italy. (9) Department of Medicine - DIMED; General Anatomic Pathology and Cytopathology Unit, Universitˆ degli Studi di Padova, 35121 Padova, Italy.

Structure guided analysis of KRAS G12 mutants in HLA-A*11:01 reveals a length encoded immunogenic advantage in G12D

KRAS G12 mutations are frequent oncogenic drivers, yet their differential immunogenicity complicates T cell-based therapies. Here, we integrate structural, biophysical, and functional analyses to examine how KRAS G12 variants remodel peptide-MHC-I (pMHC) architecture and T cell receptor (TCR) recognition. Using HLA-A*11:01, we show that single residue substitutions at position 12 induce distinct conformational changes in the MHC groove, with G12D uniquely destabilizing the complex through a buried aspartate side chain. Notably, G12D peptides adopt two registers, a 9-mer and a 10-mer, that diverge sharply in structure and immunogenicity. The 10-mer forms a compact, stable pMHC with a TCR-accessible surface, while the 9-mer adopts a bent conformation incompatible with recognition. Molecular dynamics and NMR titration confirm the superior stability and binding affinity of the 10-mer. These results highlight how peptide length and conformation critically shape immune visibility, offering mechanistic insight for optimizing TCR-T therapies against elusive neoantigens like KRAS G12D.

Author Info: (1) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. (2) Department of Anesthesiology, Putuo People's Hospital, School

Author Info: (1) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. (2) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. (3) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. (4) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. (5) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. (6) Hangzhou Weizhi Biotechnology Co., Ltd, Hangzhou, China. (7) Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China. (8) Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China. (9) State key laboratory of natural and biomimetic drugs, Peking University Health Science Center, Beijing, China. (10) National Facility for Protein Science in Shanghai, ZhangJiang lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China. (11) Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, China. (12) Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China. kx2129@tongji.edu.cn. (13) Department of Anesthesiology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China. lzhao@tongji.edu.cn.

IL-12 and GM-CSF engineered dendritic cells enhance the enrichment and selection of tumor-reactive T cells for cancer immunotherapy

The use of tumor-reactive T cells in targeted tumor elimination holds significant potential for cancer immunotherapy, such as Tumor-Infiltrating Lymphocyte (TIL) therapy and TCR-T adoptive immunotherapy. Critical aspects of the effective clinical application of these immunotherapies include the enrichment and selection of tumor antigens and their corresponding reactive T cells. However, current in vitro methods for expanding and screening tumor antigen-reactive T cells remain inefficient. One reason for this inefficiency is the dysfunctional state of tumor-reactive T cells, which limits their expansion and activation. To address this challenge, we developed an optimized dendritic cell-based culture system, in which dendritic cells simultaneously express interleukin-12 and granulocyte-macrophage colony-stimulating factor (12GM-DCs), to enhance the expansion of tumor-reactive T cells. We found that 12GM-DCs can enrich reactive T cells targeting various tumor antigens, including virus-associated tumor antigens, tumor-associated antigens, mutant tumor neoantigens, and patient-specific tumor neoantigens. Moreover, 12GM-DCs increased the proportion of antigen-specific T cells, enhanced the activation of those T cells, and promoted the maintenance of a memory phenotype. The cytotoxicity of these antigen-reactive T cells was increased after co-culture with 12GM-DCs, likely due to the increased secretion of interferon-_ and granzyme B. Importantly, these functions and phenotypic advantages of tumor antigen-reactive T cells derived from the 12GM-DC culture system could be effectively maintained and the antitumor activity was also enhanced in tumor-burden mice. Our 12GM-DC coculture system effectively enriches antigen-specific T cells and has the potential to advance the clinical application of cancer immunotherapy by targeting tumor antigens and their reactive T cells.

Author Info: (1) Department of Cell Biology and Stem Cell Research Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China. (2) Depa

Author Info: (1) Department of Cell Biology and Stem Cell Research Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China. (2) Department of Cell Biology and Stem Cell Research Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China. The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China. (3) Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing, China. (4) School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China. (5) School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China. (6) Department of Cell Biology and Stem Cell Research Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China. (7) Department of Cell Biology and Stem Cell Research Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China. (8) Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing, China. (9) School of Life Sciences, Peking University, Beijing, China. (10) Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing, China. (11) Department of Cell Biology and Stem Cell Research Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China. (12) School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China. (13) Department of Cell Biology and Stem Cell Research Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China. (14) Department of Cell Biology and Stem Cell Research Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China. School of Life Sciences, Peking University, Beijing, China. (15) Department of Cell Biology and Stem Cell Research Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China. Department of Cell Biology and Stem Cell Research Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking University, Beijing, China. Changping Laboratory, MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.

Harnessing cuproptosis for pancreatic cancer therapy: From molecular insights to clinical prospects

Pancreatic cancer (PC) remains a high-fatality malignancy with limited clinical progress, characterized by aggressive biology, marked resistance to standard therapies, and dismal outcomes. Even with state-of-the-art resection, radiotherapy, and multidrug chemotherapy, median survival benefits are modest, highlighting an urgent need for mechanism-based interventions. Cuproptosis, a newly delineated modality of regulated cell death initiated by intracellular copper accumulation and mitochondrial stress, presents a biologically coherent therapeutic avenue. Distinct from apoptosis, necroptosis, and ferroptosis, cuproptosis is driven by the direct binding of copper to lipoylated enzymes of the tricarboxylic acid (TCA) cycle, resulting in bioenergetic failure, misfolded protein aggregation, and collapse of cytotoxic proteostasis. Converging studies suggest that copper disequilibrium and metabolic reprogramming are recurrent features of PC, potentially contributing to malignant progression, immune evasion, and chemoresistance. These insights motivate two complementary strategies: first, therapeutic manipulation of copper flux, via chelators, ionophores, or transport modulators, to selectively trigger cuproptosis in tumor cells; and second, sensitization of mitochondrial metabolism, through targeting lipoic-acid pathway components, pyruvate utilization, or TCA load, to lower the threshold for cuproptotic killing. In parallel, multi-omic interrogation of cuproptosis-associated genes, proteins, and metabolites may yield prognostic and predictive biomarkers, enabling risk-adapted treatment selection and rational combinations with cytotoxic, targeted, or immunotherapeutic modalities. This review synthesizes recent advances on cuproptosis in PC and outlines its translational potential as both a therapeutic target and a biomarker framework.

Author Info: (1) School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran. (2) School of Medicine, Ardabil university of medical Sciences, Ardabil, Iran. (3) Student Res

Author Info: (1) School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran. (2) School of Medicine, Ardabil university of medical Sciences, Ardabil, Iran. (3) Student Research Committee, School of Medicine, Gonabad University of Medical Sciences, Gonabad, Iran. (4) School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran. (5) Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran. (6) School of Dentistry, Islamic Azad University of Isfahan, Isfahan, Iran. (7) School of Medicine, Islamic Azad University, Najafabad Branch, Isfahan, Iran. (8) School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran. (9) School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran. Electronic address: Mahlashokouhfarr@gmail.com.

Gut microbial metabolites in cancer immunomodulation

Gut microbiota-derived metabolites are emerging as systemic "remote immunoregulators" that shape tumor immunity across tissues. Integrating evidence across short-chain fatty acids, tryptophan derivatives, secondary bile acids, polyamines and other metabolites, we advance a metabolite-immune pathway-cancer framework that links receptor-mediated signaling, epigenetic remodeling and metabolic reprogramming to context-dependent, bidirectional immune effects. Importantly, in addition to the g protein-coupled receptor / aryl hydrocarbon receptor pathway, the selected microbial small molecule metabolites are the true T-cell receptor ligands of unconventional T cells, directly shaping the tissue resident immune and tumor microenvironment, supplementing the receptor signaling and epigenetic programs in our framework. We synthesize how these metabolites recalibrate the tumor immune microenvironment-modulating antigen presentation, T-cell effector fitness and exhaustion, regulatory T-cell activity, and myeloid polarization-and why the same metabolite can either potentiate immune surveillance or entrench immunosuppression depending on ligand-receptor pairing, dose and tissue niche. We compare tumor-type specific patterns (e.g., colorectal, liver, lung, breast and prostate cancers) to highlight common circuits and organ-restricted idiosyncrasies. Methodologically, we outline how single-cell and spatial multi-omics, imaging mass spectrometry and functional biosensors now enable co-registration of metabolite exposure with immune-cell states in human tumors, providing an actionable basis for biomarker discovery. Given ongoing debate about signals attributed to intratumoral microbiota in low-biomass tumor tissues, we foreground quantifiable, spatially mappable and pharmacologically tractable metabolite-receptor pathways, using microbe-associated molecular patterns / translocation as comparators to judge when chemical signals should be prioritized as intervention targets. Finally, we evaluate precision intervention avenues-including fecal microbiota transplantation, rational bacterial consortia, engineered microbes and nanoparticle-enabled metabolite delivery-and propose stratification rules that pair metabolite/receptor signatures with fit-for-purpose delivery. Together, mapping tissue-specific metabolite-immune circuits and embedding them in robust biomarker frameworks may convert microbial metabolites from correlative markers into therapeutic targets and tools, improving the efficacy and durability of cancer immunotherapy.

Author Info: (1) Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, 610041, People's Republic of China. (2) Department of Urology

Author Info: (1) Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, 610041, People's Republic of China. (2) Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, 610041, People's Republic of China. (3) Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, 610041, People's Republic of China. (4) Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, 610041, People's Republic of China. (5) Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, 610041, People's Republic of China. (6) Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, 610041, People's Republic of China. (7) Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, 610041, People's Republic of China. hangxu@wchscu.cn. (8) Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, 610041, People's Republic of China. wycleflue@scu.edu.cn.

Retargeted oncolytic viruses engineered to remodel the tumor microenvironment for glioblastoma immunotherapy

Glioblastoma (GBM) is an aggressive, immunotherapy-resistant brain tumor. Here, we engineered an oncolytic virus platform based on herpes simplex virus 1 for GBM viroimmunotherapy. We mutated the highly cytopathic MacIntyre strain to increase spread and oncolytic activity, limit genetic drift, prevent neuron infection and enable PET tracing. We incorporated microRNA target cassettes to attenuate replication in healthy brain cells. Moreover, we engineered the gD envelope protein to specifically target GBM using EGFR-specific or integrin-specific binders. Lastly, we incorporated five immunomodulators to remodel the tumor microenvironment (TME) by locally expressing IL-12, anti-PD1, a bispecific T cell engager, 15-hydroxyprostaglandin dehydrogenase and anti-TREM2 to target T cells and myeloid cells in the GBM TME. A single intratumoral injection increased survival in GBM preclinical models, while promoting tumor-specific T cell, natural killer cell and myeloid cell responses in the TME. In summary, we engineered a retargeted, safe and traceable oncolytic virus with strong cytotoxic and immunostimulatory activities for GBM immunotherapy.

Author Info: (1) Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. (2) Oncorus, Inc., Andover, MA, USA. (3) Ann Romney Center for

Author Info: (1) Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. (2) Oncorus, Inc., Andover, MA, USA. (3) Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. Faculty of Biology, University of Freiburg, Freiburg, Germany. (4) Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. Department of Neurology, Veterans Affairs Medical Center, Harvard Medical School, Boston, MA, USA. (5) Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. (6) Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. (7) Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. (8) Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. (9) Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. (10) Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA. (11) Oncorus, Inc., Andover, MA, USA. (12) Oncorus, Inc., Andover, MA, USA. (13) Oncorus, Inc., Andover, MA, USA. (14) Oncorus, Inc., Andover, MA, USA. (15) Oncorus, Inc., Andover, MA, USA. (16) Oncorus, Inc., Andover, MA, USA. (17) Oncorus, Inc., Andover, MA, USA. (18) Oncorus, Inc., Andover, MA, USA. (19) Oncorus, Inc., Andover, MA, USA. (20) Oncorus, Inc., Andover, MA, USA. (21) Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA. (22) Oncorus, Inc., Andover, MA, USA. (23) Oncorus, Inc., Andover, MA, USA. (24) Oncorus, Inc., Andover, MA, USA. (25) Oncorus, Inc., Andover, MA, USA. christophe@ovietx.com. (26) Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. fquintana@rics.bwh.harvard.edu. Broad Institute of MIT and Harvard, Cambridge, MA, USA. fquintana@rics.bwh.harvard.edu. The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. fquintana@rics.bwh.harvard.edu.

mRNA engineering of allogeneic mesenchymal stem cells enables coordinated delivery of T cell engagers and immunotherapeutic cues

Allogeneic cell therapies can enable off-the-shelf products that address limitations of autologous therapies. Mesenchymal stem cells are a robust allogeneic source, but no bioengineered mesenchymal stem cell-based therapies exist. Here we use mRNA engineering to create an off-the-shelf immunotherapy that we term DC-25. DC-25 consists of a mesenchymal stem cell armed with three designed mRNA constructs encoding CXCR4 to direct migration, a T cell engager specific for B cell maturation antigen to target B cell maturation antigen-expressing plasma cells involved in cancer and autoimmunity, and interleukin-12 to potentiate pro-immune responses. DC-25 allows tunable expression of each gene, supporting a predictable pharmacokinetic profile. In vitro, DC-25 exhibits synergistic killing of target cells, and in a preclinical in vivo myeloma model, this therapy exhibits potent efficacy that surpasses T cell engager protein infusion. In a phase 1 safety study in patients with myeloma, DC-25 appears safe and generates interleukin-12 production after each infusion. This study motivates human cell therapies that exploit mRNA to achieve efficacy through induction of secreted or surface-bound therapeutic elements.

Author Info: (1) Cartesian Therapeutics, Frederick, MD, USA. andy.stewart@cartesiantx.com. (2) Cartesian Therapeutics, Frederick, MD, USA. (3) Cartesian Therapeutics, Frederick, MD, USA. (4) Ca

Author Info: (1) Cartesian Therapeutics, Frederick, MD, USA. andy.stewart@cartesiantx.com. (2) Cartesian Therapeutics, Frederick, MD, USA. (3) Cartesian Therapeutics, Frederick, MD, USA. (4) Cartesian Therapeutics, Frederick, MD, USA. (5) Cartesian Therapeutics, Frederick, MD, USA. (6) Cartesian Therapeutics, Frederick, MD, USA. (7) Cartesian Therapeutics, Frederick, MD, USA. (8) Cartesian Therapeutics, Frederick, MD, USA. (9) Cartesian Therapeutics, Frederick, MD, USA. (10) Cartesian Therapeutics, Frederick, MD, USA. (11) Cartesian Therapeutics, Frederick, MD, USA. (12) Cartesian Therapeutics, Frederick, MD, USA. (13) Cartesian Therapeutics, Frederick, MD, USA. (14) Cartesian Therapeutics, Frederick, MD, USA. (15) Cartesian Therapeutics, Frederick, MD, USA. (16) Cartesian Therapeutics, Frederick, MD, USA. (17) Cartesian Therapeutics, Frederick, MD, USA. (18) University of Health Sciences, Dr. Abdurrahman Yurtaslan Ankara Oncology Training and Research Hospital, Ankara, Turkey. (19) University of Health Sciences, Dr. Abdurrahman Yurtaslan Ankara Oncology Training and Research Hospital, Ankara, Turkey. (20) Center for Cancer and Blood Disorders, Bethesda, USA, MD. (21) Sarah Cannon Research Institute and Tennessee Oncology, Nashville, TN, USA. (22) Louisiana State University Health-Shreveport, Shreveport, LA, USA. (23) Cartesian Therapeutics, Frederick, MD, USA. (24) Cartesian Therapeutics, Frederick, MD, USA. (25) Cartesian Therapeutics, Frederick, MD, USA. (26) Cartesian Therapeutics, Frederick, MD, USA. (27) Cartesian Therapeutics, Frederick, MD, USA. (28) Cartesian Therapeutics, Frederick, MD, USA. (29) Cartesian Therapeutics, Frederick, MD, USA. (30) Cartesian Therapeutics, Frederick, MD, USA. chris.jewell@cartesiantx.com.

Targeting peptide-MHC complexes with designed T cell receptors and antibodies

Class I major histocompatibility complexes (MHCs), expressed on the surface of all nucleated cells, present peptides derived from intracellular proteins for surveillance by T cells. The precise recognition of foreign or mutated peptide-MHC (pMHC) complexes by T cell receptors (TCRs) is central to immune defense against pathogens and tumors. Although patient-derived TCRs specific for cancer-associated antigens have been used to engineer tumor-targeting therapies, their reactivity toward self- or near-self antigens may be constrained by negative selection in the thymus. Here, we introduce a structure-based deep learning framework, ADAPT (Antigen-receptor Design Against Peptide-MHC Targets), for the design of TCRs and antibodies that bind to pMHC targets of interest. We evaluate the ADAPT pipeline by designing and characterizing TCRs and antibodies against a diverse panel of pMHCs. Cryogenic electron microscopy structures of two designed antibodies bound to their respective pMHC targets demonstrate atomic-level accuracy at the recognition interface, supporting the robustness of our structure-based approach. Computationally designed TCRs and antibodies targeting pMHC complexes could enable a broad range of therapeutic applications, from cancer immunotherapy to autoimmune disease treatment, and insights gained from TCR-pMHC design should advance predictive understanding of TCR specificity with implications for basic immunology and clinical diagnostics.

Author Info: (1) (2) (3) (4) (5) (6) (7) (8) (9) (10) (11) (12)

Author Info: (1) (2) (3) (4) (5) (6) (7) (8) (9) (10) (11) (12)

Prostaglandin E(2)-EP2/EP4 signaling induces the tumor-infiltrating Treg phenotype for tumor growth

Foxp3(+) regulatory T cells (Tregs) heavily infiltrate malignant tumors and restrict antitumor immunity. These tumor-infiltrating Tregs (TI-Tregs) adopt a distinct phenotype by expressing a unique set of genes. This TI-Treg gene expression signature is conserved in TI-Tregs across species and tumor types and stages, suggesting the presence of a common inducing mechanism in the tumor microenvironment (TME). However, identity of such a mechanism remains elusive. Here, we show that prostaglandin E(2) (PGE(2)) produced in TME directly acts on its receptor EP2/EP4 on Tregs to induce the TI-Treg phenotype. PGE(2) added to TCR-activated Tregs induces a set of genes, many of which are included in the TI-Treg signature, in both induced Tregs (iTregs) and naturally occurring Tregs (nTregs) via EP2/EP4- cAMP-PKA pathway. Concomitantly, PGE(2)-treated Tregs exhibit potent suppressive activity to CD8(+) T cells and strongly inhibit their proliferation in an EP4 dependent manner. Consistently, selective loss of EP2 and EP4 in mouse Tregs reduces expression of those genes in Tregs infiltrating Lewis lung carcinoma 1 (LLC1) mouse tumor and significantly delays the tumor progression. In human FOXP3(+)iTregs, PGE(2)-EP4 signaling upregulated the expression of Treg signature genes, FOXP3, CD25, and CTLA-4 as well as a typical TI-Treg signature gene, 4-1BB, and enhanced suppressive activity. Furthermore, analysis of single-cell RNA sequencing of nasopharyngeal cancer patients demonstrates preferential expression of the TI-Treg signature genes in Tregs infiltrating the PTGS2(hi) tumor group compared to the PTGS2(lo) tumor group. These findings suggest that PGE(2)-EP2/EP4 signaling is one of the core mechanisms inducing the TI-Treg phenotype in TME for tumor growth.

Author Info: (1) Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan. (2) Department of Drug Discovery Medicine, Kyoto University Graduate

Author Info: (1) Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan. (2) Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan. (3) Department of Experimental Pathology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan. Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan. (4) Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan. (5) Department of Experimental Pathology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan. Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan. (6) Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan. AMED-FORCE, Japan Agency for Medical Research and Development, Tokyo 100-0004, Japan. Foundation for Biomedical Research and Innovation at Kobe, Kobe 650-0047, Japan.

pTα enhances mRNA translation and potentiates CAR T cells for solid tumor eradication

Spotlight 

To improve CAR T cell proliferation and persistence for solid tumors, Shi et al. inserted the pre-TCR alpha (pTα) invariant domain 1A, known to stimulate a proliferative burst during thymocyte αβ T cell development, into canonical CD28-based CARs. CARs containing the pTα 1A domain (1A-CARs) resulted in greater expansion, persistence, and cytokine secretion, and enhanced survival in orthotopic RCC and GBM models, with less exhaustion. 1A-CARs showed enhanced mRNA translation via phosphorylation of YBX1, the translation master regulator. In contrast, YBX1 ablation lowered mRNA translation and cell expansion, and accelerated exhaustion.

Contributed by Katherine Turner

To improve CAR T cell proliferation and persistence for solid tumors, Shi et al. inserted the pre-TCR alpha (pTα) invariant domain 1A, known to stimulate a proliferative burst during thymocyte αβ T cell development, into canonical CD28-based CARs. CARs containing the pTα 1A domain (1A-CARs) resulted in greater expansion, persistence, and cytokine secretion, and enhanced survival in orthotopic RCC and GBM models, with less exhaustion. 1A-CARs showed enhanced mRNA translation via phosphorylation of YBX1, the translation master regulator. In contrast, YBX1 ablation lowered mRNA translation and cell expansion, and accelerated exhaustion.

Contributed by Katherine Turner

ABSTRACT: Current chimeric antigen receptor (CAR) therapies are effective against a range of hematological malignancies and autoimmune disorders but have shown limited activity against solid tumors. In searching for effective means to enhance the functional persistence and potency of CAR T cells, we explored the potential of integrating pre-T cell features into canonical CD28-based CARs. Thymocytes undergo a proliferation burst during the β-selection developmental stage, which is driven by the pre-T cell receptor and its unique pTα chain. CARs harboring the pTα 1A domain imparted greater expansion, cytokine production, and in vivo persistence to T cells, accompanied by lowered exhaustion and greater long-term tumor control in multiple liquid and solid tumor models. CARs incorporating the 1A domain showed sustained phosphorylation of the mRNA translation master regulator Y-Box Binding Protein 1 (YBX1), which was required for enhanced tumor eradication. The programming of mRNA translation in T cells opens another avenue for regulating and potentiating immunotherapy.

Author Info: (1) Columbia Initiative in Cell Engineering and Therapy (CICET), Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA. (2) Colum

Author Info: (1) Columbia Initiative in Cell Engineering and Therapy (CICET), Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA. (2) Columbia Initiative in Cell Engineering and Therapy (CICET), Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA. (3) Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA. (4) Columbia Initiative in Cell Engineering and Therapy (CICET), Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA. (5) Columbia Initiative in Cell Engineering and Therapy (CICET), Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA. (6) Columbia Initiative in Cell Engineering and Therapy (CICET), Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA. (7) Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA. (8) Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Cell Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA. (9) Columbia Initiative in Cell Engineering and Therapy (CICET), Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA. (10) Orthopedic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA. (11) Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA. (12) Columbia Initiative in Cell Engineering and Therapy (CICET), Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA. Electronic address: mws2188@cumc.columbia.edu.

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