IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-58675-9.html
   My bibliography  Save this article

Multimodal fusion of radio-pathology and proteogenomics identify integrated glioma subtypes with prognostic and therapeutic opportunities

Author

Listed:
  • Zaoqu Liu

    (The First Affiliated Hospital of Zhengzhou University
    Chinese Academy of Medical Sciences and Peking Union Medical College
    Interventional Institute of Zhengzhou University
    Interventional Treatment and Clinical Research Center of Henan Province)

  • Yushuai Wu

    (Shanghai Academy of Artificial Intelligence for Science)

  • Hui Xu

    (The First Affiliated Hospital of Zhengzhou University)

  • Minkai Wang

    (The First Affiliated Hospital of Zhengzhou University)

  • Siyuan Weng

    (The First Affiliated Hospital of Zhengzhou University)

  • Dongling Pei

    (The First Affiliated Hospital of Zhengzhou University)

  • Shuang Chen

    (The First Affiliated Hospital of Zhengzhou University)

  • WeiWei Wang

    (The First Affiliated Hospital of Zhengzhou University)

  • Jing Yan

    (The First Affiliated Hospital of Zhengzhou University)

  • Li Cui

    (The First Affiliated Hospital of Zhengzhou University)

  • Jingxian Duan

    (Chinese Academy of Sciences)

  • Yuanshen Zhao

    (Chinese Academy of Sciences)

  • Zilong Wang

    (The First Affiliated Hospital of Zhengzhou University)

  • Zeyu Ma

    (The First Affiliated Hospital of Zhengzhou University)

  • Ran Li

    (Hangzhou City University)

  • Wenchao Duan

    (The First Affiliated Hospital of Zhengzhou University)

  • Yuning Qiu

    (The First Affiliated Hospital of Zhengzhou University)

  • Dingyuan Su

    (The First Affiliated Hospital of Zhengzhou University)

  • Sen Li

    (The First Affiliated Hospital of Zhengzhou University)

  • Haoran Liu

    (The First Affiliated Hospital of Zhengzhou University)

  • Wenyuan Li

    (The First Affiliated Hospital of Zhengzhou University)

  • Caoyuan Ma

    (The First Affiliated Hospital of Zhengzhou University)

  • Miaomiao Yu

    (The First Affiliated Hospital of Zhengzhou University)

  • Yinhui Yu

    (The First Affiliated Hospital of Zhengzhou University)

  • Te Chen

    (The First Affiliated Hospital of Zhengzhou University)

  • Jing Fu

    (The First Affiliated Hospital of Zhengzhou University)

  • YingWei Zhen

    (The First Affiliated Hospital of Zhengzhou University)

  • Bin Yu

    (The First Affiliated Hospital of Zhengzhou University)

  • Yuchen Ji

    (The First Affiliated Hospital of Zhengzhou University)

  • Hairong Zheng

    (Chinese Academy of Sciences
    State Key Laboratory of Biomedical Imaging Science and System)

  • Dong Liang

    (Chinese Academy of Sciences
    State Key Laboratory of Biomedical Imaging Science and System)

  • Xianzhi Liu

    (The First Affiliated Hospital of Zhengzhou University)

  • Dongming Yan

    (The First Affiliated Hospital of Zhengzhou University)

  • Xinwei Han

    (The First Affiliated Hospital of Zhengzhou University
    Interventional Institute of Zhengzhou University
    Interventional Treatment and Clinical Research Center of Henan Province)

  • Fubing Wang

    (Zhongnan Hospital of Wuhan University
    Zhongnan Hospital of Wuhan University
    Chinese Academy of Medical Sciences)

  • Zhi-Cheng Li

    (Chinese Academy of Sciences
    State Key Laboratory of Biomedical Imaging Science and System)

  • Zhenyu Zhang

    (The First Affiliated Hospital of Zhengzhou University)

Abstract

Integrating multimodal data can uncover causal features hidden in single-modality analyses, offering a comprehensive understanding of disease complexity. This study introduces a multimodal fusion subtyping (MOFS) framework that integrates radiological, pathological, genomic, transcriptomic, and proteomic data from 122 patients with IDH-wildtype adult glioma, identifying three subtypes: MOFS1 (proneural) with favorable prognosis, elevated neurodevelopmental activity, and abundant neurocyte infiltration; MOFS2 (proliferative) with the worst prognosis, superior proliferative activity, and genome instability; MOFS3 (TME-rich) with intermediate prognosis, abundant immune and stromal components, and sensitive to anti-PD-1 immunotherapy. STRAP emerges as a prognostic biomarker and potential therapeutic target for MOFS2, associated with its proliferative phenotype. Stromal infiltration in MOFS3 serves as a crucial prognostic indicator, allowing for further prognostic stratification. Additionally, we develop a deep neural network (DNN) classifier based on radiological features to further enhance the clinical translatability, providing a non-invasive tool for predicting MOFS subtypes. Overall, these findings highlight the potential of multimodal fusion in improving the classification, prognostic accuracy, and precision therapy of IDH-wildtype glioma, offering an avenue for personalized management.

Suggested Citation

  • Zaoqu Liu & Yushuai Wu & Hui Xu & Minkai Wang & Siyuan Weng & Dongling Pei & Shuang Chen & WeiWei Wang & Jing Yan & Li Cui & Jingxian Duan & Yuanshen Zhao & Zilong Wang & Zeyu Ma & Ran Li & Wenchao Du, 2025. "Multimodal fusion of radio-pathology and proteogenomics identify integrated glioma subtypes with prognostic and therapeutic opportunities," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58675-9
    DOI: 10.1038/s41467-025-58675-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-58675-9
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-025-58675-9?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Farshad Nassiri & Jeff Liu & Vikas Patil & Yasin Mamatjan & Justin Z. Wang & Rupert Hugh-White & Andrew M. Macklin & Shahbaz Khan & Olivia Singh & Shirin Karimi & Rosario I. Corona & Lydia Y. Liu & Ca, 2021. "A clinically applicable integrative molecular classification of meningiomas," Nature, Nature, vol. 597(7874), pages 119-125, September.
    2. Yingyao Zhou & Bin Zhou & Lars Pache & Max Chang & Alireza Hadj Khodabakhshi & Olga Tanaseichuk & Christopher Benner & Sumit K. Chanda, 2019. "Metascape provides a biologist-oriented resource for the analysis of systems-level datasets," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    3. David A. Barbie & Pablo Tamayo & Jesse S. Boehm & So Young Kim & Susan E. Moody & Ian F. Dunn & Anna C. Schinzel & Peter Sandy & Etienne Meylan & Claudia Scholl & Stefan Fröhling & Edmond M. Chan & Ma, 2009. "Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1," Nature, Nature, vol. 462(7269), pages 108-112, November.
    4. Min Wu & Tingting Wang & Nan Ji & Ting Lu & Ran Yuan & Lingxiang Wu & Junxia Zhang & Mengyuan Li & Penghui Cao & Jiarui Zhao & Guanzhang Li & Jianyu Li & Yu Li & Yujie Tang & Zhengliang Gao & Xiuxing , 2024. "Multi-omics and pharmacological characterization of patient-derived glioma cell lines," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    5. Laura Cantini & Pooya Zakeri & Celine Hernandez & Aurelien Naldi & Denis Thieffry & Elisabeth Remy & Anaïs Baudot, 2021. "Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    6. Kosuke Yoshihara & Maria Shahmoradgoli & Emmanuel Martínez & Rahulsimham Vegesna & Hoon Kim & Wandaliz Torres-Garcia & Victor Treviño & Hui Shen & Peter W. Laird & Douglas A. Levine & Scott L. Carter , 2013. "Inferring tumour purity and stromal and immune cell admixture from expression data," Nature Communications, Nature, vol. 4(1), pages 1-11, December.
    7. Benoît Schmauch & Alberto Romagnoni & Elodie Pronier & Charlie Saillard & Pascale Maillé & Julien Calderaro & Aurélie Kamoun & Meriem Sefta & Sylvain Toldo & Mikhail Zaslavskiy & Thomas Clozel & Matah, 2020. "A deep learning model to predict RNA-Seq expression of tumours from whole slide images," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
    8. Ruben M. Drews & Barbara Hernando & Maxime Tarabichi & Kerstin Haase & Tom Lesluyes & Philip S. Smith & Lena Morrill Gavarró & Dominique-Laurent Couturier & Lydia Liu & Michael Schneider & James D. Br, 2022. "A pan-cancer compendium of chromosomal instability," Nature, Nature, vol. 606(7916), pages 976-983, June.
    9. Nourhan Abdelfattah & Parveen Kumar & Caiyi Wang & Jia-Shiun Leu & William F. Flynn & Ruli Gao & David S. Baskin & Kumar Pichumani & Omkar B. Ijare & Stephanie L. Wood & Suzanne Z. Powell & David L. H, 2022. "Single-cell analysis of human glioma and immune cells identifies S100A4 as an immunotherapy target," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    10. Osama Al-Dalahmah & Michael G. Argenziano & Adithya Kannan & Aayushi Mahajan & Julia Furnari & Fahad Paryani & Deborah Boyett & Akshay Save & Nelson Humala & Fatima Khan & Juncheng Li & Hong Lu & Yu S, 2023. "Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Yuanyuan Qu & Jinwen Feng & Xiaohui Wu & Lin Bai & Wenhao Xu & Lingli Zhu & Yang Liu & Fujiang Xu & Xuan Zhang & Guojian Yang & Jiacheng Lv & Xiuping Chen & Guo-Hai Shi & Hong-Kai Wang & Da-Long Cao &, 2022. "A proteogenomic analysis of clear cell renal cell carcinoma in a Chinese population," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    2. Wanzun Lin & Li Chen & Haojiong Zhang & Xianxin Qiu & Qingting Huang & Fangzhu Wan & Ziyu Le & Shikai Geng & Anlan Zhang & Sufang Qiu & Long Chen & Lin Kong & Jiade J. Lu, 2023. "Tumor-intrinsic YTHDF1 drives immune evasion and resistance to immune checkpoint inhibitors via promoting MHC-I degradation," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    3. Farhoud Faraji & Sydney I. Ramirez & Lauren M. Clubb & Kuniaki Sato & Valeria Burghi & Thomas S. Hoang & Adam Officer & Paola Y. Anguiano Quiroz & William M. G. Galloway & Zbigniew Mikulski & Kate Med, 2025. "YAP-driven malignant reprogramming of oral epithelial stem cells at single cell resolution," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
    4. Kang Wang & Ioannis Zerdes & Henrik J. Johansson & Dhifaf Sarhan & Yizhe Sun & Dimitris C. Kanellis & Emmanouil G. Sifakis & Artur Mezheyeuski & Xingrong Liu & Niklas Loman & Ingrid Hedenfalk & Jonas , 2024. "Longitudinal molecular profiling elucidates immunometabolism dynamics in breast cancer," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
    5. Brian D. Lehmann & Antonio Colaprico & Tiago C. Silva & Jianjiao Chen & Hanbing An & Yuguang Ban & Hanchen Huang & Lily Wang & Jamaal L. James & Justin M. Balko & Paula I. Gonzalez-Ericsson & Melinda , 2021. "Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    6. Qilin Zhang & Ziyan Xu & Rui Han & Yunzhi Wang & Zhen Ye & Jiajun Zhu & Yixin Cai & Fan Zhang & Jiangyan Zhao & Boyuan Yao & Zhaoyu Qin & Nidan Qiao & Ruofan Huang & Jinwen Feng & Yongfei Wang & Wenti, 2024. "Proteogenomic characterization of skull-base chordoma," Nature Communications, Nature, vol. 15(1), pages 1-32, December.
    7. Zhenmei Yao & Ning Xu & Guoguo Shang & Haixing Wang & Hui Tao & Yunzhi Wang & Zhaoyu Qin & Subei Tan & Jinwen Feng & Jiajun Zhu & Fahan Ma & Sha Tian & Qiao Zhang & Yuanyuan Qu & Jun Hou & Jianming Gu, 2023. "Proteogenomics of different urothelial bladder cancer stages reveals distinct molecular features for papillary cancer and carcinoma in situ," Nature Communications, Nature, vol. 14(1), pages 1-25, December.
    8. Christel F. A. Ramirez & Daniel Taranto & Masami Ando-Kuri & Marnix H. P. Groot & Efi Tsouri & Zhijie Huang & Daniel Groot & Roelof J. C. Kluin & Daan J. Kloosterman & Joanne Verheij & Jing Xu & Seren, 2024. "Cancer cell genetics shaping of the tumor microenvironment reveals myeloid cell-centric exploitable vulnerabilities in hepatocellular carcinoma," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
    9. Yuanyuan Qu & Xiaohui Wu & Aihetaimujiang Anwaier & Jinwen Feng & Wenhao Xu & Xiaoru Pei & Yu Zhu & Yang Liu & Lin Bai & Guojian Yang & Xi Tian & Jiaqi Su & Guo-Hai Shi & Da-Long Cao & Fujiang Xu & Yu, 2022. "Proteogenomic characterization of MiT family translocation renal cell carcinoma," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    10. Khoa A. Tran & Venkateswar Addala & Rebecca L. Johnston & David Lovell & Andrew Bradley & Lambros T. Koufariotis & Scott Wood & Sunny Z. Wu & Daniel Roden & Ghamdan Al-Eryani & Alexander Swarbrick & E, 2023. "Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    11. Lida Iliopoulou & Christos Tzaferis & Alejandro Prados & Fani Roumelioti & Vasiliki Koliaraki & George Kollias, 2025. "Different fibroblast subtypes propel spatially defined ileal inflammation through TNFR1 signalling in murine ileitis," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    12. Fatima Khan & Yiyun Lin & Heba Ali & Lizhi Pang & Madeline Dunterman & Wen-Hao Hsu & Katie Frenis & R. Grant Rowe & Derek A. Wainwright & Kathleen McCortney & Leah K. Billingham & Jason Miska & Craig , 2024. "Lactate dehydrogenase A regulates tumor-macrophage symbiosis to promote glioblastoma progression," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    13. Yin Li & Manling Jiang & Ling Aye & Li Luo & Yong Zhang & Fengkai Xu & Yongqi Wei & Dan Peng & Xiang He & Jie Gu & Xiaofang Yu & Guoping Li & Di Ge & Chunlai Lu, 2024. "UPP1 promotes lung adenocarcinoma progression through the induction of an immunosuppressive microenvironment," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    14. Xiaoping Su & Xiaofan Lu & Sehrish Khan Bazai & Linda Dainese & Arnauld Verschuur & Benoit Dumont & Roger Mouawad & Li Xu & Wenxuan Cheng & Fangrong Yan & Sabine Irtan & Véronique Lindner & Catherine , 2023. "Delineating the interplay between oncogenic pathways and immunity in anaplastic Wilms tumors," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    15. Hailiang Zhang & Lin Bai & Xin-Qiang Wu & Xi Tian & Jinwen Feng & Xiaohui Wu & Guo-Hai Shi & Xiaoru Pei & Jiacheng Lyu & Guojian Yang & Yang Liu & Wenhao Xu & Aihetaimujiang Anwaier & Yu Zhu & Da-Long, 2023. "Proteogenomics of clear cell renal cell carcinoma response to tyrosine kinase inhibitor," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
    16. Hikaru Hayashi & Sayaka Seki & Takeshi Tomita & Masayoshi Kato & Norihiro Ashihara & Tokuhiro Chano & Hideki Sanjo & Miwa Kawade & Chenhui Yan & Hiroki Sakai & Hidenori Tomida & Miyuki Tanaka & Mai Iw, 2025. "Synthetic short mRNA prevents metastasis via innate-adaptive immunity," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    17. Zhongqi Fan & Xinchen Zou & Guangyi Wang & Yahui Liu & Yanfang Jiang & Haoyan Wang & Ping Zhang & Feng Wei & Xiaohong Du & Meng Wang & Xiaodong Sun & Bai Ji & Xintong Hu & Liguo Chen & Peiwen Zhou & D, 2024. "A transcriptome based molecular classification scheme for cholangiocarcinoma and subtype-derived prognostic biomarker," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    18. Xiangwei Li & Thomas Delerue & Ben Schöttker & Bernd Holleczek & Eva Grill & Annette Peters & Melanie Waldenberger & Barbara Thorand & Hermann Brenner, 2022. "Derivation and validation of an epigenetic frailty risk score in population-based cohorts of older adults," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    19. Ahrum Son & Hyunsoo Kim & Jolene K. Diedrich & Casimir Bamberger & Daniel B. McClatchy & Stuart A. Lipton & John R. Yates, 2024. "Using in vivo intact structure for system-wide quantitative analysis of changes in proteins," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    20. Yasuhiko Haga & Yoshitaka Sakamoto & Keiko Kajiya & Hitomi Kawai & Miho Oka & Noriko Motoi & Masayuki Shirasawa & Masaya Yotsukura & Shun-Ichi Watanabe & Miyuki Arai & Junko Zenkoh & Kouya Shiraishi &, 2023. "Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma," Nature Communications, Nature, vol. 14(1), pages 1-19, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58675-9. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.