Weller M, Wick W, Aldape K, Brada M, Berger M, Pfister SM, et al. Glioma. Nat Rev Dis Prim. 2015;1:15017.
Google ScholarÂ
Stupp R, Taillibert S, Kanner AA, Kesari S, Steinberg DM, Toms SA, et al. Maintenance therapy with tumor-treating fields plus temozolomide vs temozolomide alone for glioblastoma: a randomized clinical trial. JAMA. 2015;314:2535–43.
Google ScholarÂ
Medikonda R, Dunn G, Rahman M, Fecci P, Lim M. A review of glioblastoma immunotherapy. J Neurooncol. 2021;151:41–53.
Google ScholarÂ
Nejo T, Yamamichi A, Almeida ND, Goretsky YE, Okada H. Tumor antigens in glioma. Semin Immunol. 2020;47:101385.
Google ScholarÂ
Sloan AE, Winter K, Gilbert MR, Aldape K, Choi S, Wen PY, et al. NRG-BN002: Phase I study of ipilimumab, nivolumab, and the combination in patients with newly diagnosed glioblastoma. Neuro Oncol. 2024;26:1628–37.
Google ScholarÂ
Majzner RG, Ramakrishna S, Yeom KW, Patel S, Chinnasamy H, Schultz LM, et al. GD2-CAR T cell therapy for H3K27M-mutated diffuse midline gliomas. Nature. 2022;603:934–41.
Google ScholarÂ
Monje M, Mahdi J, Majzner R, Yeom KW, Schultz LM, Richards RM, et al. Intravenous and intracranial GD2-CAR T cells for H3K27M(+) diffuse midline gliomas. Nature. 2025;637:708–15.
Google ScholarÂ
Oliveira G, Stromhaug K, Klaeger S, Kula T, Frederick DT, Le PM, et al. Phenotype, specificity and avidity of antitumour CD8(+) T cells in melanoma. Nature. 2021;596:119–25.
Google ScholarÂ
Mathewson ND, Ashenberg O, Tirosh I, Gritsch S, Perez EM, Marx S, et al. Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis. Cell. 2021;184:1281–98.e26.
Google ScholarÂ
Naulaerts S, Datsi A, Borras DM, Antoranz Martinez A, Messiaen J, Vanmeerbeek I, et al. Multiomics and spatial mapping characterizes human CD8(+) T cell states in cancer. Sci Transl Med. 2023;15:eadd1016.
Google ScholarÂ
Wang AZ, Mashimo BL, Schaettler MO, Sherpa ND, Leavitt LA, Livingstone AJ, et al. Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population. Cancer Discov. 2024;14:1106–31.
Google ScholarÂ
Woroniecka K, Chongsathidkiet P, Rhodin K, Kemeny H, Dechant C, Farber SH, et al. T-cell exhaustion signatures vary with tumor type and are severe in glioblastoma. Clin Cancer Res. 2018;24:4175–86.
Google ScholarÂ
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14:417–9.
Google ScholarÂ
Song L, Cohen D, Ouyang Z, Cao Y, Hu X, Liu XS. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data. Nat Methods. 2021;18:627–30.
Google ScholarÂ
Orenbuch R, Filip I, Comito D, Shaman J, Pe’er I, Rabadan R, et al. arcasHLA: high-resolution HLA typing from RNAseq. Bioinformatics. 2020;36:33–40.
Google ScholarÂ
Ajaib S, Lodha D, Pollock S, Hemmings G, Finetti MA, Gusnanto A, et al. GBMdeconvoluteR accurately infers proportions of neoplastic and immune cell populations from bulk glioblastoma transcriptomics data. Neuro Oncol. 2023;25:1236–48.
Google ScholarÂ
Danaher P, Warren S, Dennis L, D’Amico L, White A, Disis ML, et al. Gene expression markers of Tumor Infiltrating Leukocytes. J Immunother Cancer. 2017;5:18.
Google ScholarÂ
Aran D, Hu Z, Butte AJ. xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol. 2017;18:220.
Google ScholarÂ
Okamoto T, Mizuta R, Takahashi Y, Otani Y, Sasaki E, Horio Y, et al. Genomic landscape of glioblastoma without IDH somatic mutation in 42 cases: a comprehensive analysis using RNA sequencing data. J Neurooncol. 2024;167:489–99.
Google ScholarÂ
Flensburg C, Sargeant T, Oshlack A, Majewski IJ. SuperFreq: Integrated mutation detection and clonal tracking in cancer. PLoS Comput Biol. 2020;16:e1007603.
Google ScholarÂ
Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 2018;28:1747–56.
Google ScholarÂ
Davidson NM, Majewski IJ, Oshlack A. JAFFA: High sensitivity transcriptome-focused fusion gene detection. Genome Med. 2015;7:43.
Google ScholarÂ
Haas BJ, Dobin A, Li B, Stransky N, Pochet N, Regev A. Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome Biol. 2019;20:213.
Google ScholarÂ
Gaonkar KS, Marini F, Rathi KS, Jain P, Zhu Y, Chimicles NA, et al. annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions. BMC Bioinforma. 2020;21:577.
Google ScholarÂ
Zheng GX, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, et al. Massively parallel digital transcriptional profiling of single cells. Nat Commun. 2017;8:14049.
Google ScholarÂ
Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, et al. Integrated analysis of multimodal single-cell data. Cell. 2021;184:3573–87.e29.
Borcherding N, Bormann NL, Kraus G. scRepertoire: An R-based toolkit for single-cell immune receptor analysis. F1000Res. 2020;9:47.
Google ScholarÂ
Komuro H, Shinohara S, Fukushima Y, Demachi-Okamura A, Muraoka D, Masago K, et al. Single-cell sequencing on CD8(+) TILs revealed the nature of exhausted T cells recognizing neoantigen and cancer/testis antigen in non-small cell lung cancer. J Immunother Cancer. 2023;11:e007180.
Google ScholarÂ
Sugita Y, Muraoka D, Demachi-Okamura A, Komuro H, Masago K, Sasaki E, et al. Candidate tumor-specific CD8(+) T cell subsets identified in the malignant pleural effusion of advanced lung cancer patients by single-cell analysis. Oncoimmunology. 2024;13:2371556.
Google ScholarÂ
Tirosh I, Izar B, Prakadan SM, Wadsworth MH 2nd, Treacy D, Trombetta JJ, et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016;352:189–96.
Tan CL, Lindner K, Boschert T, Meng Z, Rodriguez Ehrenfried A, De Roia A, et al. Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy. Nat Biotechnol. 2025;43:134–42.
Google ScholarÂ
Lowery FJ, Krishna S, Yossef R, Parikh NB, Chatani PD, Zacharakis N, et al. Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers. Science. 2022;375:877–84.
Google ScholarÂ
Li X, Zhou C, Chen K, Huang B, Liu Q, Ye H. Benchmarking HLA genotyping and clarifying HLA impact on survival in tumor immunotherapy. Mol Oncol. 2021;15:1764–82.
Google ScholarÂ
Duhen T, Duhen R, Montler R, Moses J, Moudgil T, de Miranda NF, et al. Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors. Nat Commun. 2018;9:2724.
Google ScholarÂ
Hanada KI, Zhao C, Gil-Hoyos R, Gartner JJ, Chow-Parmer C, Lowery FJ, et al. A phenotypic signature that identifies neoantigen-reactive T cells in fresh human lung cancers. Cancer Cell. 2022;40:479–93.e6.
Google ScholarÂ
Kanehisa M, Furumichi M, Sato Y, Ishiguro-Watanabe M, Tanabe M. KEGG: integrating viruses and cellular organisms. Nucleic Acids Res. 2021;49:D545–D51.
Google ScholarÂ
Barakat R, Chatterjee J, Mu R, Qi X, Gu X, Smirnov I, et al. Human single cell RNA-sequencing reveals a targetable CD8(+) exhausted T cell population that maintains mouse low-grade glioma growth. Nat Commun. 2024;15:10312.
Google ScholarÂ
Panda A, Rosenfeld JA, Singer EA, Bhanot G, Ganesan S. Genomic and immunologic correlates of LAG-3 expression in cancer. Oncoimmunology. 2020;9:1756116.
Google ScholarÂ
Mair MJ, Kiesel B, Feldmann K, Widhalm G, Dieckmann K, Wohrer A, et al. LAG-3 expression in the inflammatory microenvironment of glioma. J Neurooncol. 2021;152:533–9.
Google ScholarÂ
Ruffo E, Wu RC, Bruno TC, Workman CJ, Vignali DAA. Lymphocyte-activation gene 3 (LAG3): The next immune checkpoint receptor. Semin Immunol. 2019;42:101305.
Google ScholarÂ
Saraiva DP, Jacinto A, Borralho P, Braga S, Cabral MG. HLA-DR in Cytotoxic T Lymphocytes Predicts Breast Cancer Patients’ Response to Neoadjuvant Chemotherapy. Front Immunol. 2018;9:2605.
Google ScholarÂ
Liu B, Zhang Y, Wang D, Hu X, Zhang Z. Single-cell meta-analyses reveal responses of tumor-reactive CXCL13(+) T cells to immune-checkpoint blockade. Nat Cancer. 2022;3:1123–36.
Google ScholarÂ
Keskin DB, Anandappa AJ, Sun J, Tirosh I, Mathewson ND, Li S, et al. Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial. Nature. 2019;565:234–9.
Google ScholarÂ
Naghavian R, Faigle W, Oldrati P, Wang J, Toussaint NC, Qiu Y, et al. Microbial peptides activate tumour-infiltrating lymphocytes in glioblastoma. Nature. 2023;617:807–17.
Google ScholarÂ
Kwok DW, Stevers NO, Etxeberria I, Nejo T, Colton Cove M, Chen LH, et al. Tumour-wide RNA splicing aberrations generate actionable public neoantigens. Nature. 2025;639:463–73.
Google ScholarÂ
Jang HJ, Shah NM, Maeng JH, Liang Y, Basri NL, Ge J, et al. Epigenetic therapy potentiates transposable element transcription to create tumor-enriched antigens in glioblastoma cells. Nat Genet. 2024;56:1903–13.
Google ScholarÂ
Eckle SB, Birkinshaw RW, Kostenko L, Corbett AJ, McWilliam HE, Reantragoon R, et al. A molecular basis underpinning the T cell receptor heterogeneity of mucosal-associated invariant T cells. J Exp Med. 2014;211:1585–600.
Google ScholarÂ
Godfrey DI, Koay HF, McCluskey J, Gherardin NA. The biology and functional importance of MAIT cells. Nat Immunol. 2019;20:1110–28.
Google ScholarÂ
Nejo T, Krishna S, Yamamichi A, Lakshmanachetty S, Jimenez C, Lee KY, et al. Glioma-neuronal circuit remodeling induces regional immunosuppression. Nat Commun. 2025;16:4770.
Google ScholarÂ
Okamoto T, Mizuta R, Demachi-Okamura A, Muraoka D, Sasaki E, Masago K, et al. Immune prognostic model for glioblastoma based on the ssGSEA enrichment score. Cancer Genet. 2025;294-295:32–41.
Google ScholarÂ
Rosenberg SA, Restifo NP. Adoptive cell transfer as personalized immunotherapy for human cancer. Science. 2015;348:62–8.
Google ScholarÂ

