Integrated multi-omics analysis reveals genomic features, MES-like states, and immune microenvironment characteristics in NF1-mutant glioblastoma
Abstract
MethodsA total of 497 patients with GBM from the MSK cohort were analyzed to evaluate the associations of NF1 mutation with overall survival (OS), progression-free survival (PFS), tumor mutational burden (TMB), temozolomide (TMZ)-associated hypermutation, and DNA repair-related gene alterations. Single-cell transcriptomic data from the GEO dataset were used to analyze tumor cell states, myeloid cell subsets, and T cell-related subsets. Gene set enrichment analysis (GSEA), gene set scoring, and CellChat analysis were applied to evaluate transcriptional programs and potential ligand-receptor communication. MES-like transcriptional features were further validated in a TCGA-GBM bulk RNA-seq cohort of 160 patients, followed by weighted gene co-expression network analysis (WGCNA), ligand-receptor scoring, and immune-related scoring. In addition, an NF1-knockout U87-MG cell line (U87_sgNF1) was generated using CRISPR/Cas9 technology, and Western blot and real-time fluorescence quantitative polymerase chain reaction (RTFQ-PCR) were performed to validate NF1 protein depletion and selected transcriptional changes.ResultsNF1-mutant GBM showed higher TMB and enrichment of TMZ-associated hypermutation. After adjustment for background mutational burden and TMZ-associated hypermutation, NF1 mutation remained significantly associated with mismatch repair (MMR)-related gene alterations. Single-cell analysis showed an enhanced MES-like tumor cell state in NF1-mutant GBM, accompanied by increased TNF-α/NF-κB, hypoxia, inflammatory response, and KRAS-related transcriptional programs. The TCGA-GBM cohort further validated the MES-like transcriptional phenotype and showed that NF1 mutation was associated with multiple co-expression modules involving extracellular matrix organization, TGF-β signaling, and cell-cycle/genome-maintenance processes. RTFQ-PCR analysis of U87_sgNF1 cells showed that representative genes associated with MES-like and other transcriptional programs exhibited expression changes broadly consistent with gene set scores from public single-cell datasets. Immune cell analysis showed increased proportions of M2-like and hypoxic myeloid subpopulations, as well as inflammatory and Treg subpopulations, in NF1-mutant GBM. CellChat analysis suggested enhanced inferred communication involving SPP1-CD44 and SPP1-integrin axes between immune cells and MES-like tumor cells. In the reverse direction, MES-like tumor cells also showed increased potential communication with M2-like myeloid cells and T cells through SPP1/CD44-, FN1/CD44-, COL1A1/CD44- and COL6A1/CD44-related axes. In the TCGA-GBM cohort, corresponding ligand-receptor scores were positively correlated with MES scores and multiple immune-related transcriptional scores.ConclusionNF1-mutant GBM is characterized by higher TMB, TMZ-associated hypermutation, and specific DNA repair-related alterations, together with enhanced MES-like transcriptional states, co-expression network changes, and immune microenvironment-associated features. Potential communication involving SPP1/CD44 and other extracellular matrix-CD44-related axes may exist between MES-like tumor cells and M2-like myeloid cells, as well as between MES-like tumor cells and T cells. This study further delineates the biological features of NF1-mutant GBM across genomic, tumor cell state, and immune microenvironmental levels and provides candidate directions for subsequent mechanistic validation and potential therapeutic investigation.Background and purposeGlioblastoma (GBM) is one of the most common and most malignant tumors of the central nervous system. It is characterized by marked heterogeneity, therapeutic resistance, and a highly immunosuppressive microenvironment. Precision diagnosis and treatment based on molecular classification represents an important research direction for improving patient prognosis. NF1 is an important negative regulator of the RAS/MAPK pathway, and its mutations have been closely associated with the mesenchymal/MES-like phenotype of GBM. However, the relationships among NF1 mutation-associated genomic features, tumor cell states, and alterations in the immune microenvironment remain incompletely integrated. This study aimed to characterize the tumor cell features and tumor microenvironment-associated molecular relationships of NF1-mutant GBM and to provide a basis for further investigation of precision therapeutic and immune microenvironment-targeted strategies.
Related
- Integrated Transcriptomic Analysis Reveals Distinct Molecular and Immune Microenvironment Features of Peutz–Jeghers Syndrome-Associated Lobular Endocervical Glandular Hyperplasia and Gastric-Type Endocervical Adenocarcinoma
- An Immune-Metabolic Signature Reveals Prognostic Stratification and Tumor Microenvironment Features in Breast Cancer.
- Integrated multi-omics analysis reveals that tumour cell-intrinsic DCLK1 is associated with an angiogenic tumour microenvironment in cholangiocarcinoma via NF-κB/CXCL5
- Integrated single-cell and bulk RNA sequencing analysis reveals paraptosis-related biomarkers and immune microenvironment regulation in triple-negative breast cancer
- Stabilizing the CHI3L1-Gal3BP complex remodels the glioblastoma immune microenvironment and synergizes with PD-1 blockade
BibTeX
@article{yueying2026integrated,
title = {{Integrated multi-omics analysis reveals genomic features, MES-like states, and immune microenvironment characteristics in NF1-mutant glioblastoma}},
author = {YAO Yueying and CHEN Guoyu and LI Yanxin and GAO Yijin},
journal = {Zhongguo aizheng zazhi},
year = {2026},
month = sep,
url = {http://www.china-oncology.com/zh/article/doi/10.19401/j.cnki.1007-3639.2026.09.005/},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Integrated multi-omics analysis reveals genomic features, MES-like states, and immune microenvironment characteristics in NF1-mutant glioblastoma
AU - YAO Yueying
AU - CHEN Guoyu
AU - LI Yanxin
AU - GAO Yijin
PY - 2026
DA - 2026/09/01
JO - Zhongguo aizheng zazhi
UR - http://www.china-oncology.com/zh/article/doi/10.19401/j.cnki.1007-3639.2026.09.005/
AB - MethodsA total of 497 patients with GBM from the MSK cohort were analyzed to evaluate the associations of NF1 mutation with overall survival (OS), progression-free survival (PFS), tumor mutational burden (TMB), temozolomide (TMZ)-associated hypermutation, and DNA repair-related gene alterations. Single-cell transcriptomic data from the GEO dataset were used to analyze tumor cell states, myeloid cell subsets, and T cell-related subsets. Gene set enrichment analysis (GSEA), gene set scoring, and CellChat analysis were applied to evaluate transcriptional programs and potential ligand-receptor communication. MES-like transcriptional features were further validated in a TCGA-GBM bulk RNA-seq cohort of 160 patients, followed by weighted gene co-expression network analysis (WGCNA), ligand-receptor scoring, and immune-related scoring. In addition, an NF1-knockout U87-MG cell line (U87_sgNF1) was generated using CRISPR/Cas9 technology, and Western blot and real-time fluorescence quantitative polymerase chain reaction (RTFQ-PCR) were performed to validate NF1 protein depletion and selected transcriptional changes.ResultsNF1-mutant GBM showed higher TMB and enrichment of TMZ-associated hypermutation. After adjustment for background mutational burden and TMZ-associated hypermutation, NF1 mutation remained significantly associated with mismatch repair (MMR)-related gene alterations. Single-cell analysis showed an enhanced MES-like tumor cell state in NF1-mutant GBM, accompanied by increased TNF-α/NF-κB, hypoxia, inflammatory response, and KRAS-related transcriptional programs. The TCGA-GBM cohort further validated the MES-like transcriptional phenotype and showed that NF1 mutation was associated with multiple co-expression modules involving extracellular matrix organization, TGF-β signaling, and cell-cycle/genome-maintenance processes. RTFQ-PCR analysis of U87_sgNF1 cells showed that representative genes associated with MES-like and other transcriptional programs exhibited expression changes broadly consistent with gene set scores from public single-cell datasets. Immune cell analysis showed increased proportions of M2-like and hypoxic myeloid subpopulations, as well as inflammatory and Treg subpopulations, in NF1-mutant GBM. CellChat analysis suggested enhanced inferred communication involving SPP1-CD44 and SPP1-integrin axes between immune cells and MES-like tumor cells. In the reverse direction, MES-like tumor cells also showed increased potential communication with M2-like myeloid cells and T cells through SPP1/CD44-, FN1/CD44-, COL1A1/CD44- and COL6A1/CD44-related axes. In the TCGA-GBM cohort, corresponding ligand-receptor scores were positively correlated with MES scores and multiple immune-related transcriptional scores.ConclusionNF1-mutant GBM is characterized by higher TMB, TMZ-associated hypermutation, and specific DNA repair-related alterations, together with enhanced MES-like transcriptional states, co-expression network changes, and immune microenvironment-associated features. Potential communication involving SPP1/CD44 and other extracellular matrix-CD44-related axes may exist between MES-like tumor cells and M2-like myeloid cells, as well as between MES-like tumor cells and T cells. This study further delineates the biological features of NF1-mutant GBM across genomic, tumor cell state, and immune microenvironmental levels and provides candidate directions for subsequent mechanistic validation and potential therapeutic investigation.Background and purposeGlioblastoma (GBM) is one of the most common and most malignant tumors of the central nervous system. It is characterized by marked heterogeneity, therapeutic resistance, and a highly immunosuppressive microenvironment. Precision diagnosis and treatment based on molecular classification represents an important research direction for improving patient prognosis. NF1 is an important negative regulator of the RAS/MAPK pathway, and its mutations have been closely associated with the mesenchymal/MES-like phenotype of GBM. However, the relationships among NF1 mutation-associated genomic features, tumor cell states, and alterations in the immune microenvironment remain incompletely integrated. This study aimed to characterize the tumor cell features and tumor microenvironment-associated molecular relationships of NF1-mutant GBM and to provide a basis for further investigation of precision therapeutic and immune microenvironment-targeted strategies.
SN - 1007-3639
ER -