Single-cell transcriptomics reveals IRF7 regulation of the tumor microenvironment in isocitrate dehydrogenase wild-type glioma

Abstract

Mutations in isocitrate dehydrogenase (IDH) are important markers of glioma prognosis. However, few studies have examined the gene expression regulatory network (GRN) in IDH-mutant and wild-type gliomas. In this study, single-cell RNA sequencing and spatial transcriptome sequencing were used to analyze the GRN of cell subsets in patients with IDH-mutant and wild-type gliomas. Through gene transcriptional regulation analysis, we identified the M4 module, whose transcription factor activity is highly expressed in IDH wild-type gliomas compared to IDH-mutants. Enrichment analysis revealed that these genes were predominantly expressed in microglia and macrophages, with significant enrichment in interferon-related signaling pathways. Interferon regulatory factor 7 (IRF7), a transcription factor within this pathway, showed the highest percentage of enrichment and was primarily localized in the core region of wild-type IDH tumors. A machine-learning prognostic model identified novel subgroups within the wild-type IDH population. Additionally, IRF7 was shown to promote the proliferation and migration of T98G and U251 cells in vitro, and its knockdown affected glioma cell proliferation in vivo. This study systematically established the regulatory mechanism of IDH transcriptional activity in gliomas at the single-cell level and drew a corresponding cell map. The study presents a transcriptional regulatory activity map for IDH wild-type gliomas, involving single-cell RNA sequencing and spatial transcriptomics to identify gene regulatory networks, machine learning models for IDH subtyping, and experimental validation, highlighting the role of IRF7 in glioma progression.

Keywords

gene transcription regulation / glioma / interferon regulatory factor 7 / isocitrate dehydrogenase 1 / multi-omics

References

[1] Diplas BH, Liu H, Yang R, et al. Sensitive and rapid detection of TERT promoter and IDH mutations in diffuse gliomas. Neuro Oncol. 2019; 21(4): 440-450.

[2] Louis DN, Perry A, Reifenberger G, et al. The 2016 World Health Organization classification of tumors of the central nervous system: a summary. Acta Neuropathol. 2016; 131(6): 803-820.

[3] Louis DN, Perry A, Wesseling P, et al. The 2021 WHO classification of tumors of the central nervous system: a summary. Neuro-oncology. 2021; 23(8): 1231-1251.

[4] Miller JJ, Gonzalez Castro LN, McBrayer S, et al. Isocitrate dehydrogenase (IDH) mutant gliomas: a Society for Neuro-Oncology (SNO) consensus review on diagnosis, management, and future directions. Neuro-oncology. 2023; 25(1): 4-25.

[5] Vargas López AJ. Glioblastoma in adults: a Society for Neuro-Oncology (SNO) and European Society of Neuro-Oncology (EANO) consensus review on current management and future directions. Neuro-oncology. 2021; 23(3): 502-503.

[6] Chaligne R, Gaiti F, Silverbush D, et al. Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states. Nat Genet. 2021; 53(10): 1469-1479.

[7] Flavahan WA, Gaskell E, Bernstein BE. Epigenetic plasticity and the hallmarks of cancer. Science. 2017; 357(6348): eaal2380.

[8] Lan Y-L, Zou S, Wang W, Chen Q, Zhu Y. Progress in cancer neuroscience. MedComm. 2023; 4: e431.

[9] Johnson KC, Anderson KJ, Courtois ET, et al. Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response. Nat Genet. 2021; 53(10): 1456-1468.

[10] Aibar S, González-Blas CB, Moerman T, et al. SCENIC: single-cell regulatory network inference and clustering. Nat Methods. 2017; 14(11): 1083-1086.

[11] Bhaduri A, Di Lullo E, Jung D, et al. Outer radial glia-like cancer stem cells contribute to heterogeneity of glioblastoma. Cell Stem Cell. 2020; 26(1): 48-63.

[12] Tirosh I, Venteicher AS, Hebert C, et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature. 2016; 539(7628): 309-313.

[13] Venteicher AS, Tirosh I, Hebert C, et al. Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science. 2017; 355(6332): eaai8478.

[14] Kreso A, Dick JE. Evolution of the cancer stem cell model. Cell Stem Cell. 2014; 14(3): 275-291.

[15] Wang L, Babikir H, Müller S, et al. The phenotypes of proliferating glioblastoma cells reside on a single axis of variation. Cancer Discov. 2019; 9(12): 1708-1719.

[16] Ferris HA, Perry RJ, Moreira GV, Shulman GI, Horton JD, Kahn CR. Loss of astrocyte cholesterol synthesis disrupts neuronal function and alters whole-body metabolism. Proc Natl Acad Sci U S A. 2017; 114(5): 1189-1194.

[17] Allen NJ, Eroglu C. Cell biology of astrocyte–synapse interactions. Neuron. 2017; 96(3): 697-708.

[18] Linnerbauer M, Wheeler MA, Quintana FJ. Astrocyte crosstalk in CNS inflammation. Neuron. 2020; 108(4): 608-622.

[19] Perelroizen R, Philosof B, Budick-Harmelin N, et al. Astrocyte immunometabolic regulation of the tumour microenvironment drives glioblastoma pathogenicity. Brain. 2022; 145(9): 3288-3307.

[20] Bowman RL, Klemm F, Akkari L, et al. Macrophage ontogeny underlies differences in tumor-specific education in brain malignancies. Cell Rep. 2016; 17(9): 2445-2459.

[21] Chen Z, Feng X, Herting CJ, et al. Cellular and molecular identity of tumor-associated macrophages in glioblastoma. Cancer Res. 2017; 77(9): 2266-2278.

[22] Hussain SF, Yang D, Suki D, Grimm E, Heimberger AB. Innate immune functions of microglia isolated from human glioma patients. J Transl Med. 2006; 4: 15.

[23] Rock RB, Gekker G, Hu S, et al. Role of microglia in central nervous system infections. Clin Microbiol Rev. 2004; 17(4): 942-964.

[24] Hussain SF, Yang D, Suki D, Aldape K, Grimm E, Heimberger AB. The role of human glioma-infiltrating microglia/macrophages in mediating antitumor immune responses. Neuro Oncol. 2006; 8(3): 261-279.

[25] Gutmann DH, McLellan MD, Hussain I, et al. Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma. Genome Res. 2013; 23(3): 431-439.

[26] Morantz RA, Wood GW, Foster M, Clark M, Gollahon K. Macrophages in experimental and human brain tumors. Part 1: studies of the macrophage content of experimental rat brain tumors of varying immunogenicity. J Neurosurg. 1979; 50(3): 298-304.

[27] Broekman ML, Maas SLN, Abels ER, Mempel TR, Krichevsky AM, Breakefield XO. Multidimensional communication in the microenvirons of glioblastoma. Nat Rev Neurol. 2018; 14(8): 482-495.

[28] Guo X, Qiu W, Li B, et al. Hypoxia-induced neuronal activity in glioma patients polarizes microglia by potentiating RNA m6A demethylation. Clin Cancer Res. 2024; 30(6): 1160-1174.

[29] Ye Z, Ai X, Yang K, et al. Targeting microglial metabolic rewiring synergizes with immune-checkpoint blockade therapy for glioblastoma. Cancer Discov. 2023; 13(4): 974-1001.

[30] Honda K, Taniguchi T. IRFs: master regulators of signalling by Toll-like receptors and cytosolic pattern-recognition receptors. Nat Rev Immunol. 2006; 6(9): 644-658.

[31] Negishi H, Taniguchi T, Yanai H. The interferon (IFN) class of cytokines and the IFN regulatory factor (IRF) transcription factor family. Cold Spring Harb Perspect Biol. 2018; 10(11): a028423.

[32] Taniguchi T, Ogasawara K, Takaoka A, Tanaka N. IRF family of transcription factors as regulators of host defense. Ann Rev Immunol. 2001; 19: 623-655.

[33] Jin X, Kim SH, Jeon HM, et al. Interferon regulatory factor 7 regulates glioma stem cells via interleukin-6 and Notch signalling. Brain. 2012; 135: 1055-1069.

[34] Tanaka T, Murakami K, Bando Y, Yoshida S. Interferon regulatory factor 7 participates in the M1-like microglial polarization switch. Glia. 2015; 63(4): 595-610.

[35] Guo C, Yang Q, Xu P, et al. Adjuvant temozolomide chemotherapy with or without interferon alfa among patients with newly diagnosed high-grade gliomas: a randomized clinical trial. JAMA Netw Open. 2023; 6(1): e2253285.

[36] Qing F, Liu Z. Interferon regulatory factor 7 in inflammation, cancer and infection. Front Immunol. 2023; 14: 1190841.

[37] Yang Q, Li X, Chen H, et al. IRF7 regulates the development of granulocytic myeloid-derived suppressor cells through S100A9 transrepression in cancer. Oncogene. 2017; 36(21): 2969-2980.

[38] Kim JK, Jin X, Ham SW, et al. IRF7 promotes glioma cell invasion by inhibiting AGO2 expression. Tumour Biol. 2015; 36(7): 5561-5569.

[39] Tang F, Wang Y, Zeng Y, Xiao A, Tong A, Xu J. Tumor-associated macrophage-related strategies for glioma immunotherapy. NPJ Precis Oncol. 2023; 7(1): 78.

[40] Eckel-Passow JE, Lachance DH, Molinaro AM, et al. Glioma groups based on 1p/19q, IDH, and TERT promoter mutations in tumors. N Engl J Med. 2015; 372(26): 2499-2508.

[41] Wick W, Weller M, van den Bent M, et al. MGMT testing—the challenges for biomarker-based glioma treatment. Nat Rev Neurol. 2014; 10(7): 372-385.

[42] Hu C, Li T, Xu Y, et al. CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data. Nucleic Acids Res. 2023; 51(D1): D870-d876.

[43] Ren Y, Huang Z, Zhou L, et al. Spatial transcriptomics reveals niche-specific enrichment and vulnerabilities of radial glial stem-like cells in malignant gliomas. Nat Commun. 2023; 14(1): 1028.

[44] Chen Y, Huo R, Kang W, et al. Tumor-associated monocytes promote mesenchymal transformation through EGFR signaling in glioma. Cell Rep Med. 2023; 4(9): 101177.

[45] Van de Sande B, Flerin C, Davie K, et al. A scalable SCENIC workflow for single-cell gene regulatory network analysis. Nat Protoc. 2020; 15(7): 2247-2276.

[46] Ravi VM, Will P, Kueckelhaus J, et al. Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma. Cancer Cell. 2022; 40(6): 639-655.e13.

[47] Greenwald AC, Darnell NG, Hoefflin R, et al. Integrative spatial analysis reveals a multi-layered organization of glioblastoma. Cell. 2024; 187(10): 2485-2501.e26.

[48] Qin H, Abulaiti A, Maimaiti A, et al. Integrated machine learning survival framework develops a prognostic model based on inter-crosstalk definition of mitochondrial function and cell death patterns in a large multicenter cohort for lower-grade glioma. J Transl Med. 2023; 21(1): 588.

[49] He Y, Jiang Z, Chen C, Wang X. Classification of triple-negative breast cancers based on immunogenomic profiling. J Exp Clin Cancer Res. 2018; 37(1): 327.

[50] Liu Z, Liu L, Weng S, et al. Machine learning-based integration develops an immune-derived lncRNA signature for improving outcomes in colorectal cancer. Nat Commun. 2022; 13(1): 816.

[51] Zhang N, Zhang H, Wu W, et al. Machine learning-based identification of tumor-infiltrating immune cell-associated lncRNAs for improving outcomes and immunotherapy responses in patients with low-grade glioma. Theranostics. 2022; 12(13): 5931-5948.

[52] Lindskrog SV, Prip F, Lamy P, et al. An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer. Nat Commun. 2021; 12(1): 2301.

[53] Zou Y, Xie J, Zheng S, et al. Leveraging diverse cell-death patterns to predict the prognosis and drug sensitivity of triple-negative breast cancer patients after surgery. Int J Surg. 2022; 107: 106936.

RIGHTS & PERMISSIONS

2024 The Author(s). MedComm published by Sichuan International Medical Exchange & Promotion Association (SCIMEA) and John Wiley & Sons Australia, Ltd.