多组学整合分析揭示<italic style="font-style: italic">NF1</italic>突变型胶质母细胞瘤的基因组、MES-like状态及免疫微环境特征

姚月影; 陈国玉; 李彦欣; 高怡瑾

doi:10.19401/j.cnki.1007-3639.2026.09.005

您当前的位置：

首页 >

文章列表页 >

多组学整合分析揭示NF1突变型胶质母细胞瘤的基因组、MES-like状态及免疫微环境特征

论著 | 更新时间：2026-10-23

- 多组学整合分析揭示NF1突变型胶质母细胞瘤的基因组、MES-like状态及免疫微环境特征
- Integrated multi-omics analysis reveals genomic features, MES-like states, and immune microenvironment characteristics in NF1-mutant glioblastoma
- 中国癌症杂志 2026年36卷第9期页码：853-871
- 作者机构：
  
  1.上海交通大学医学院附属上海儿童医学中心肿瘤科，血液肿瘤重点实验室，上海 200127
  2.上海交通大学医学院附属仁济医院，肿瘤系统医学全国重点实验室，上海市肿瘤研究所，上海 200032
  3.上海交通大学医学院附属上海儿童医学中心，转化医学研究所，血液肿瘤重点实验室，上海 200127
- 作者简介：
  
  GAO Yijin　E-mail: gaoyijin@scmc.com.cn
- 基金信息：
  
  上海市自然科学基金(23ZR1441000)
- DOI：10.19401/j.cnki.1007-3639.2026.09.005
  中图分类号： R739.41
- 收稿：2026-06-10，
  
  修回：2026-09-23，
  
  录用：2026-09-30，
  
  纸质出版：2026-09-30
- 稿件说明：
移动端阅览
姚月影, 陈国玉, 李彦欣, 等. 多组学整合分析揭示NF1突变型胶质母细胞瘤的基因组、MES-like状态及免疫微环境特征［J］. 中国癌症杂志, 2026, 36（9）: 853-871.

Yao Y Y, Chen G Y, Li Y X, et al. Integrated multi-omics analysis reveals genomic features, MES-like states, and immune microenvironment characteristics in NF1-mutant glioblastoma［J］. Chin Oncol, 2026, 36（9）: 853-871.
姚月影, 陈国玉, 李彦欣, 等. 多组学整合分析揭示NF1突变型胶质母细胞瘤的基因组、MES-like状态及免疫微环境特征［J］. 中国癌症杂志, 2026, 36（9）: 853-871. DOI： 10.19401/j.cnki.1007-3639.2026.09.005.

Yao Y Y, Chen G Y, Li Y X, et al. Integrated multi-omics analysis reveals genomic features, MES-like states, and immune microenvironment characteristics in NF1-mutant glioblastoma［J］. Chin Oncol, 2026, 36（9）: 853-871. DOI： 10.19401/j.cnki.1007-3639.2026.09.005.

摘要

背景与目的

胶质母细胞瘤（glioblastoma，GBM）是中枢神经系统肿瘤中常见且恶性程度最高的类型，具有高度异质性、治疗抵抗及微环境高度免疫抑制等特征，基于分子分型的精准诊疗以改善患者预后是当前重要的研究方向。

NF1

是RAS/MAPK信号通路的重要负调控因子，其突变与GBM mesenchymal/MES-like表型密切相关，但

NF1

突变相关的基因组特征、肿瘤细胞状态及免疫微环境改变之间的联系仍缺乏系统整合。本研究系统分析

NF1

突变型GBM的肿瘤细胞特征与肿瘤微环境间的分子联系，旨在为该类GBM的精准治疗及免疫微环境干预策略研究提供理论依据。

方法

基于MSK队列497例GBM患者，分析比较

NF1

突变与总体生存期（overall survival，OS）、无进展生存期（progression-free survival，PFS）、肿瘤突变负荷（tumor mutational burden，TMB）及替莫唑胺（temozolomide，TMZ）相关高突变特征及DNA修复相关基因改变的关系。利用GEO单细胞转录组数据分析肿瘤细胞状态、髓系细胞和T细胞相关亚群，并结合基因集富集分析（gene set enrichment analysis，GSEA）、基因集评分和CellChat分析评价转录程序及潜在细胞通信。在160例TCGA-GBM bulk RNA-seq队列中验证MES-like转录特征，并进行加权基因共表达网络分析（weighted gene co-expression network analysis，WGCNA）、配体-受体评分及免疫相关评分分析。进一步采用CRISPR/Cas9技术构建

NF1

敲除U87-MG细胞模型（U87_sg

NF1

），通过蛋白质印迹法（Western blot）验证NF1蛋白表达变化，并通过实时荧光定量聚合酶链反应（real-time fluorescence quantitative polymerase chain reaction，RTFQ-PCR）验证转录水平的变化。

结果

NF1

突变型GBM具有更高的TMB水平，并富集TMZ相关高突变特征，校正背景突变负荷及TMZ相关高突变状态后，

NF1

突变仍与MMR相关基因改变显著相关。单细胞分析显示，

NF1

突变型GBM中MES-like肿瘤细胞状态增强，并伴随TNF-α/NF-κB、缺氧、炎症反应及KRAS等相关转录程序激活。TCGA-GBM队列进一步验证了MES-like转录特征，并显示

NF1

突变伴随多个涉及细胞外基质、TGF-β信号及细胞周期/基因组维持过程的共表达模块变化。RTFQ-PCR结果同样显示，U87_sgNF1细胞中MES-like状态及其他相关转录程序的代表性基因表达变化趋势，与公共单细胞数据集的基因集打分结果总体一致。免疫细胞组成分析显示，

NF1

突变型GBM的M2-like和Hypoxic髓系细胞亚群比例升高，Inflammatory及Treg亚群比例升高。CellChat分析提示M2-like髓系细胞指向MES-like肿瘤细胞的SPP1相关潜在通信增强；同时，MES-like肿瘤细胞指向M2-like髓系细胞及T淋巴细胞的SPP1-CD44、FN1-CD44、COL1A1-CD44及COL6A1-CD44等候选通信亦增强。TCGA-GBM队列验证显示，上述通信评分与MES score及多种免疫相关评分呈显著正相关。

结论

NF1

突变型GBM具有较高TMB、TMZ相关高突变及特定DNA修复相关改变，并与MES-like转录状态增强、共表达网络变化及免疫微环境相关特征相伴随。其免疫微环境中MES-like肿瘤细胞与M2-like髓系细胞及T淋巴细胞之间可能存在SPP1/CD44及其他细胞外基质-

CD44相关的潜在通信模式。本研究从基因组、肿瘤细胞状态及免疫微环境等多个层面补充了

NF1

突变型GBM的生物学特征，并为后续机制验证及潜在干预研究提供候选方向。

Abstract

Methods

A 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

NF1

-knockout U87-MG cell line (U87_sg

NF1

) 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.

Results

NF1

-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 w

as 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

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.

Conclusion

NF1

-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 purpose

Glioblastoma (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.

关键词

Keywords

references

Wen P Y , Weller M , Lee E Q , et al . Glioblastoma in adults: a Society for Neuro-Oncology （SNO） and European Society of Neuro-Oncology （EANO） consensus review on current management and future directions ［J］. Neuro Oncol , 2025 , 27 （ 11 ）: 2751 - 2788 .

Costantini S , Di Gennaro E , Fanelli G , et al . Glioblastoma metabolomics: uncovering biomarkers for diagnosis, prognosis and targeted therapy ［J］. J Exp Clin Cancer Res , 2025 , 44 （ 1 ）: 230 .

Horbinski C , Solomon D A , Lukas R V , et al . Molecular testing for the World Health Organization classification of central nervous system tumors: a review ［J］. JAMA Oncol , 2025 , 11 （ 3 ）: 317 - 328 .

Gritsch S , Batchelor T T , Gonzalez Castro L N . Diagnostic, therapeutic, and prognostic implications of the 2021 World Health Organization classification of tumors of the central nervous system ［J］. Cancer , 2022 , 128 （ 1 ）: 47 - 58 .

Ratner N , Miller S J . A RASopathy gene commonly mutated in cancer: the neurofibromatosis type 1 tumour suppressor ［J］. Nat Rev Cancer , 2015 , 15 （ 5 ）: 290 - 301 .

Verhaak R G W , Hoadley K A , Purdom E , et al . Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1 ［J］. Cancer Cell , 2010 , 17 （ 1 ）: 98 - 110 .

Pan S X , Mirchia K , Payne E , et al . Tumor heterogeneity underlies clinical outcome and MEK inhibitor response in somatic NF1-mutant glioblastoma ［J］. JCI Insight , 2025 , 10 （ 18 ）: e192658 .

Schreurs L D , Vom Stein A F , Jünger S T , et al . The immune landscape in brain metastasis ［J］. Neuro Oncol , 2025 , 27 （ 1 ）: 50 - 62 .

Hara T , Chanoch-Myers R , Mathewson N D , et al . Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma ［J］. Cancer Cell , 2021 , 39 （ 6 ）: 779 - 792.e11 .

Pombo Antunes A R , Scheyltjens I , Lodi F , et al . Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization ［J］. Nat Neurosci , 2021 , 24 （ 4 ）: 595 - 610 .

Neftel C , Laffy J , Filbin M G , et al . An integrative model of cellular states, plasticity, and genetics for glioblastoma ［J］. Cell , 2019 , 178 （ 4 ）: 835 - 849.e21 .

Scheer M , Leisz S , Sorge E , et al . Neurofibromatosis type 1 gene alterations define specific features of a subset of glioblastomas ［J］. Int J Mol Sci , 2021 , 23 （ 1 ）: 352 .

Chang M , Sherief M , Ioannou M , et al . NF1 expression profiling in IDH-wildtype glioblastoma: genomic associations and survival outcomes ［J］. Acta Neuropathol Commun , 2024 , 12 （ 1 ）: 172 .

Vizcaíno M A , Shah S , Eberhart C G , et al . Clinicopathologic implications of NF1 gene alterations in diffuse gliomas ［J］. Hum Pathol , 2015 , 46 （ 9 ）: 1323 - 1330 .

Touat M , Li Y Y , Boynton A N , et al . Mechanisms and therapeutic implications of hypermutation in gliomas ［J］. Nature , 2020 , 580 （ 7804 ）: 517 - 523 .

Barthel F P , Johnson K C , Varn F S , et al . Longitudinal molecular trajectories of diffuse glioma in adults ［J］. Nature , 2019 , 576 （ 7785 ）: 112 - 120 .

Marques C , Unterkircher T , Kroon P , et al . NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1 ［J］. eLife , 2021 , 10 : e64846 .

Bhat K P L , Balasubramaniyan V , Vaillant B , et al . Mesenchymal differentiation mediated by NF-κB promotes radiation resistance in glioblastoma ［J］. Cancer Cell , 2013 , 24 （ 3 ）: 331 - 346 .

Pouyan A , Ghorbanlo M , Eslami M , et al . Glioblastoma multiforme: insights into pathogenesis, key signaling pathways, and therapeutic strategies ［J］. Mol Cancer , 2025 , 24 （ 1 ）: 58 .

Rinkenbaugh A L , Cogswell P C , Calamini B , et al . IKK/NF-κB signaling contributes to glioblastoma stem cell maintenance ［J］. Oncotarget , 2016 , 7 （ 43 ）: 69173 - 69187 .

Avci N G , Ebrahimzadeh-Pustchi S , Akay Y M , et al . NF-κB inhibitor with Temozolomide results in significant apoptosis in glioblastoma via the NF-κB（p65） and actin cytoskeleton regulatory pathways ［J］. Sci Rep , 2020 , 10 （ 1 ）: 13352 .

Miller T E , El Farran C A , Couturier C P , et al . Programs, origins and immunomodulatory functions of myeloid cells in glioma ［J］. Nature , 2025 , 640 （ 8060 ）: 1072 - 1082 .

de Groot J , Ott M , Wei J , et al . A first-in-human Phase I trial of the oral p-STAT3 inhibitor WP1066 in patients with recurrent malignant glioma ［J］. CNS Oncol , 2022 , 11 （ 2 ）: CNS87 .

Butowski N , Colman H , de Groot J F , et al . Orally administered colony stimulating factor 1 receptor inhibitor PLX3397 in recurrent glioblastoma: an Ivy Foundation Early Phase Clinical Trials Consortium phase Ⅱ study ［J］. Neuro Oncol , 2016 , 18 （ 4 ）: 557 - 564 .

He X , Guo Y D , Yu C J , et al . Epithelial-mesenchymal transition is the main way in which glioma-associated microglia/macrophages promote glioma progression ［J］. Front Immunol , 2023 , 14 : 1097880 .

He C , Sheng L Y , Pan D S , et al . Single-cell transcriptomic analysis revealed a critical role of SPP1/CD44-mediated crosstalk between macrophages and cancer cells in glioma ［J］. Front Cell Dev Biol , 2021 , 9 : 779319 .

Fan G Y , Xie T J , Li L , et al . Single-cell and spatial analyses revealed the co-location of cancer stem cells and SPP1+ macrophage in hypoxic region that determines the poor prognosis in hepatocellular carcinoma ［J］. NPJ Precis Oncol , 2024 , 8 （ 1 ）: 75 .

Liu F Z , Zhang J F , Gu X W , et al . Single-cell transcriptome sequencing reveals SPP1-CD44-mediated macrophage-tumor cell interactions drive chemoresistance in TNBC ［J］. J Cell Mol Med , 2024 , 28 （ 13 ）: e18525 .

Zhang M X , Li J H , Meng X L , et al . ITGA5 induces mesenchymal transformation to promote gliomas progression via PI3K/AKT/mTORC1 signaling pathway ［J］. Sci Rep , 2025 , 15 : 13539 .

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

Soni N , Rawat K , Chen Z H , et al . Single-cell dissection of the genotype-immunophenotype relationship in glioblastoma ［J］. Brain , 2025 , 148 （ 9 ）: 3153 - 3169 .

Wei J , Marisetty A , Schrand B , et al . Osteopontin mediates glioblastoma-associated macrophage infiltration and is a potential therapeutic target ［J］. J Clin Invest , 2019 , 129 （ 1 ）: 137 - 149 .

浏览量

下载量

CSCD

文章被引用时，请邮件提醒。

提交

工具集

关联资源

氨基酸代谢重编程在结直肠癌肝转移中的研究进展

Y染色体丢失对男性实体肿瘤影响的研究进展与展望

Siglec-15介导肿瘤免疫逃逸的机制与靶向治疗进展及展望

NSMP亚型子宫内膜癌相关研究的最新进展及展望：从分子生物学研究到临床诊治实践

自然杀伤细胞在卵巢癌免疫治疗中的研究现状及展望

多组学整合分析揭示NF1突变型胶质母细胞瘤的基因组、MES-like状态及免疫微环境特征

Integrated multi-omics analysis reveals genomic features, MES-like states, and immune microenvironment characteristics in NF1-mutant glioblastoma

DOI：10.19401/j.cnki.1007-3639.2026.09.005

摘要

Abstract

关键词

Keywords

references