Identification of matrix stiffness-related molecular subtypes in HCC via integrating multi-omics analysis and machine learning algorithms
Abstract Background Matrix stiffness is strongly associated with hepatocarcinogenesis and significantly influences the properties of hepatocellular carcinoma (HCC). Investigating matrix stiffness-related signatures provides crucial insights into HCC prognosis and therapeutic response. Methods Multi-...
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BMC
2025-07-01
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| Series: | Journal of Translational Medicine |
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| Online Access: | https://doi.org/10.1186/s12967-025-06733-7 |
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| author | Hanqi Li Jiayi Zhang Yu Shi Huanhuan Wang Ruida Yang Shaobo Wu Yue Li Xue Yang Qingguang Liu Liankang Sun |
| author_facet | Hanqi Li Jiayi Zhang Yu Shi Huanhuan Wang Ruida Yang Shaobo Wu Yue Li Xue Yang Qingguang Liu Liankang Sun |
| author_sort | Hanqi Li |
| collection | DOAJ |
| description | Abstract Background Matrix stiffness is strongly associated with hepatocarcinogenesis and significantly influences the properties of hepatocellular carcinoma (HCC). Investigating matrix stiffness-related signatures provides crucial insights into HCC prognosis and therapeutic response. Methods Multi-omics data from liver hepatocellular carcinoma (LIHC) were integrated using 10 clustering algorithms, identifying three subgroups with distinct survival outcomes and treatment responses. A matrix stiffness-related signature comprising 57 genes was constructed by evaluating 101 machine learning algorithm combinations. PPARG, the key gene with the greatest contribution to the model, was selected for validation. Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) analyses assessed matrix stiffness activity scores across different cell subgroups and examined PPARG spatial localization within tissues. Experimental studies and bioinformatics analyses further explored the role of PPARG in HCC carcinogenesis and the immune microenvironment. Results The matrix stiffness-related signature demonstrated superior prognostic prediction performance in both training and validation cohorts compared to other existing HCC signatures. Distinct immune and mutation landscape characteristics were observed between patients categorized into high and low matrix stiffness groups. PPARG functioned in tumorigenesis through HSC activation and immune suppression. Furthermore, increased matrix stiffness was found to upregulate PPARG expression, promoting cell proliferation, activating lipid metabolism, and enhancing the stemness of HCC cells through the MAPK signaling pathway. Targeting PPARG with trametinib displayed an enhanced therapy response. Conclusions The matrix stiffness-related signature not only serves as a robust prognostic tool but also aids in identifying immune characteristics and optimizing therapeutic strategies, thus advancing personalized medicine for patients with HCC. |
| format | Article |
| id | doaj-art-7c39dd344697443bb6cbd3906e57f8bd |
| institution | Kabale University |
| issn | 1479-5876 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Translational Medicine |
| spelling | doaj-art-7c39dd344697443bb6cbd3906e57f8bd2025-08-20T03:43:02ZengBMCJournal of Translational Medicine1479-58762025-07-0123112510.1186/s12967-025-06733-7Identification of matrix stiffness-related molecular subtypes in HCC via integrating multi-omics analysis and machine learning algorithmsHanqi Li0Jiayi Zhang1Yu Shi2Huanhuan Wang3Ruida Yang4Shaobo Wu5Yue Li6Xue Yang7Qingguang Liu8Liankang Sun9Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong UniversityDepartment of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong UniversityDepartment of Oncology, The First Affiliated Hospital of Xi’an Jiaotong UniversityDepartment of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong UniversityDepartment of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong UniversityDepartment of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong UniversityDepartment of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong UniversityDepartment of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong UniversityDepartment of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong UniversityDepartment of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong UniversityAbstract Background Matrix stiffness is strongly associated with hepatocarcinogenesis and significantly influences the properties of hepatocellular carcinoma (HCC). Investigating matrix stiffness-related signatures provides crucial insights into HCC prognosis and therapeutic response. Methods Multi-omics data from liver hepatocellular carcinoma (LIHC) were integrated using 10 clustering algorithms, identifying three subgroups with distinct survival outcomes and treatment responses. A matrix stiffness-related signature comprising 57 genes was constructed by evaluating 101 machine learning algorithm combinations. PPARG, the key gene with the greatest contribution to the model, was selected for validation. Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) analyses assessed matrix stiffness activity scores across different cell subgroups and examined PPARG spatial localization within tissues. Experimental studies and bioinformatics analyses further explored the role of PPARG in HCC carcinogenesis and the immune microenvironment. Results The matrix stiffness-related signature demonstrated superior prognostic prediction performance in both training and validation cohorts compared to other existing HCC signatures. Distinct immune and mutation landscape characteristics were observed between patients categorized into high and low matrix stiffness groups. PPARG functioned in tumorigenesis through HSC activation and immune suppression. Furthermore, increased matrix stiffness was found to upregulate PPARG expression, promoting cell proliferation, activating lipid metabolism, and enhancing the stemness of HCC cells through the MAPK signaling pathway. Targeting PPARG with trametinib displayed an enhanced therapy response. Conclusions The matrix stiffness-related signature not only serves as a robust prognostic tool but also aids in identifying immune characteristics and optimizing therapeutic strategies, thus advancing personalized medicine for patients with HCC.https://doi.org/10.1186/s12967-025-06733-7Matrix stiffnessMulti-omicsMachine learningSignatureHepatocellular carcinoma |
| spellingShingle | Hanqi Li Jiayi Zhang Yu Shi Huanhuan Wang Ruida Yang Shaobo Wu Yue Li Xue Yang Qingguang Liu Liankang Sun Identification of matrix stiffness-related molecular subtypes in HCC via integrating multi-omics analysis and machine learning algorithms Journal of Translational Medicine Matrix stiffness Multi-omics Machine learning Signature Hepatocellular carcinoma |
| title | Identification of matrix stiffness-related molecular subtypes in HCC via integrating multi-omics analysis and machine learning algorithms |
| title_full | Identification of matrix stiffness-related molecular subtypes in HCC via integrating multi-omics analysis and machine learning algorithms |
| title_fullStr | Identification of matrix stiffness-related molecular subtypes in HCC via integrating multi-omics analysis and machine learning algorithms |
| title_full_unstemmed | Identification of matrix stiffness-related molecular subtypes in HCC via integrating multi-omics analysis and machine learning algorithms |
| title_short | Identification of matrix stiffness-related molecular subtypes in HCC via integrating multi-omics analysis and machine learning algorithms |
| title_sort | identification of matrix stiffness related molecular subtypes in hcc via integrating multi omics analysis and machine learning algorithms |
| topic | Matrix stiffness Multi-omics Machine learning Signature Hepatocellular carcinoma |
| url | https://doi.org/10.1186/s12967-025-06733-7 |
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