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Wang FA, Zhuang Z, Gao F, He R, Zhang S, Wang L, Liu J, Li Y. TMO-Net: an explainable pretrained multi-omics model for multi-task learning in oncology. Genome Biol 2024; 25:149. [PMID: 38845006 PMCID: PMC11157742 DOI: 10.1186/s13059-024-03293-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
Cancer is a complex disease composing systemic alterations in multiple scales. In this study, we develop the Tumor Multi-Omics pre-trained Network (TMO-Net) that integrates multi-omics pan-cancer datasets for model pre-training, facilitating cross-omics interactions and enabling joint representation learning and incomplete omics inference. This model enhances multi-omics sample representation and empowers various downstream oncology tasks with incomplete multi-omics datasets. By employing interpretable learning, we characterize the contributions of distinct omics features to clinical outcomes. The TMO-Net model serves as a versatile framework for cross-modal multi-omics learning in oncology, paving the way for tumor omics-specific foundation models.
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Affiliation(s)
- Feng-Ao Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
- Guangzhou National Laboratory, Guangzhou, 510005, China
| | - Zhenfeng Zhuang
- Department of Computer Science at the School of Informatics, Xiamen University, Xiamen, 361005, China
| | - Feng Gao
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200433, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Ruikun He
- BYHEALTH Institute of Nutrition & Health, Guangzhou, 510000, China
| | - Shaoting Zhang
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200433, China
| | - Liansheng Wang
- Department of Computer Science at the School of Informatics, Xiamen University, Xiamen, 361005, China.
| | - Junwei Liu
- Guangzhou National Laboratory, Guangzhou, 510005, China.
| | - Yixue Li
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
- Guangzhou National Laboratory, Guangzhou, 510005, China.
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200030, China.
- GZMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, 511436, China.
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200433, China.
- Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200032, China.
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Liu L, Xiao H, Yang G. SPARC Controls Migration and Invasion of Hepatocellular Carcinoma Cells Via Regulating GPD2-Mediated Mitochondrial Respiration. Biochem Genet 2024:10.1007/s10528-024-10682-z. [PMID: 38334876 DOI: 10.1007/s10528-024-10682-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/03/2024] [Indexed: 02/10/2024]
Abstract
Mitochondrial respiration and metabolism play a pivotal role in facilitating the migratory and invasive capacities of cancer cells. In this study, we aimed to explore the potential influence of glycoprotein SPARC on mitochondrial respiration and its subsequent influence on the migration and invasion of hepatocellular carcinoma (HCC) cells. Lentivirus-mediated shRNA delivery was employed to deplete SPARC in HCC cell lines. The mitochondria localization of SPARC was validated using cellular fractionation followed by Western blot analysis, as well as immunofluorescence staining and Proteinase K protection assay. Co-immunoprecipitation was employed to investigate the interaction between SPARC and GPD2. Seahorse XF Cell Mito Stress Test was conducted to assess the mitochondrial respiration and functionality of HCC cells. Our study identifies an active pool of SPARC within the mitochondria of HCC cells, with the mitochondrial subset proving crucial for the regulation of migration and invasion. The mitochondrial SPARC interacts with GPD2, influencing its expression levels and subsequently modulating GPD2-mediated mitochondrial respiration. This regulatory mechanism orchestrates the migratory and invasive phenotypes of HCC cells. Notably, SPARC and GPD2 exhibit upregulated expression in HCC tissues compared to normal liver tissues. High expression levels of both SPARC and GPD2 in HCC patients are associated with a poorer prognosis. Our study unveils a novel role for SPARC in governing HCC cell migration and invasion through regulating GPD2-mediated mitochondrial respiration. These findings underscore the importance of mitochondrial processes in cancer progression and propose the SPARC/GPD2 axis as a promising target for HCC interventions.
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Affiliation(s)
- Lei Liu
- Department of Medical Oncology, Yantaishan Hospital, Yantai, Shandong Province, China
| | - Huawei Xiao
- Department of Medical Oncology, Yantaishan Hospital, Yantai, Shandong Province, China
| | - Guiqing Yang
- Department of Medical Oncology, Yantai Traditional Chinese Medicine Hospital, Yantai, Shandong Province, China.
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Park SY, Hwang BO, Song NY. The role of myokines in cancer: crosstalk between skeletal muscle and tumor. BMB Rep 2023; 56:365-373. [PMID: 37291054 PMCID: PMC10390289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/02/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023] Open
Abstract
Loss of skeletal muscle mass is a primary feature of sarcopenia and cancer cachexia. In cancer patients, tumor-derived inflammatory factors promote muscle atrophy via tumor-to-muscle effects, which is closely associated with poor prognosis. During the past decade, skeletal muscle has been considered to function as an autocrine, paracrine, and endocrine organ by releasing numerous myokines. The circulating myokines can modulate pathophysiology in the other organs, as well as in the tumor microenvironment, suggesting myokines function as muscleto-tumor signaling molecules. Here, we highlight the roles of myokines in tumorigenesis, particularly in terms of crosstalk between skeletal muscle and tumor. Better understanding of tumor-to-muscle and muscle-to-tumor effects will shed light on novel strategies for the diagnosis and treatment of cancer. [BMB Reports 2023; 56(7): 365-373].
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Affiliation(s)
- Se-Young Park
- Department of Applied Life Science, The Graduate School, Yonsei University, Seoul 03722, Korea
- BK21 Four Project, Yonsei University College of Dentistry, Seoul 03722, Korea
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Byeong-Oh Hwang
- Department of Applied Life Science, The Graduate School, Yonsei University, Seoul 03722, Korea
- BK21 Four Project, Yonsei University College of Dentistry, Seoul 03722, Korea
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Na-Young Song
- Department of Applied Life Science, The Graduate School, Yonsei University, Seoul 03722, Korea
- BK21 Four Project, Yonsei University College of Dentistry, Seoul 03722, Korea
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul 03722, Korea
- Oral Cancer Research Institute, Yonsei University College of Dentistry, Seoul 03722, Korea
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Park SY, Hwang BO, Song NY. The role of myokines in cancer: crosstalk between skeletal muscle and tumor. BMB Rep 2023; 56:365-373. [PMID: 37291054 PMCID: PMC10390289 DOI: 10.5483/bmbrep.2023-0064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/02/2023] [Accepted: 06/01/2023] [Indexed: 09/22/2023] Open
Abstract
Loss of skeletal muscle mass is a primary feature of sarcopenia and cancer cachexia. In cancer patients, tumor-derived inflammatory factors promote muscle atrophy via tumor-to-muscle effects, which is closely associated with poor prognosis. During the past decade, skeletal muscle has been considered to function as an autocrine, paracrine, and endocrine organ by releasing numerous myokines. The circulating myokines can modulate pathophysiology in the other organs, as well as in the tumor microenvironment, suggesting myokines function as muscleto-tumor signaling molecules. Here, we highlight the roles of myokines in tumorigenesis, particularly in terms of crosstalk between skeletal muscle and tumor. Better understanding of tumor-to-muscle and muscle-to-tumor effects will shed light on novel strategies for the diagnosis and treatment of cancer. [BMB Reports 2023; 56(7): 365-373].
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Affiliation(s)
- Se-Young Park
- Department of Applied Life Science, The Graduate School, Yonsei University, Seoul 03722, Korea
- BK21 Four Project, Yonsei University College of Dentistry, Seoul 03722, Korea
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Byeong-Oh Hwang
- Department of Applied Life Science, The Graduate School, Yonsei University, Seoul 03722, Korea
- BK21 Four Project, Yonsei University College of Dentistry, Seoul 03722, Korea
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Na-Young Song
- Department of Applied Life Science, The Graduate School, Yonsei University, Seoul 03722, Korea
- BK21 Four Project, Yonsei University College of Dentistry, Seoul 03722, Korea
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul 03722, Korea
- Oral Cancer Research Institute, Yonsei University College of Dentistry, Seoul 03722, Korea
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SPARC promotes fibroblast proliferation, migration, and collagen production in keloids by inactivation of p53. J Dermatol Sci 2023; 109:2-11. [PMID: 36642579 DOI: 10.1016/j.jdermsci.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/20/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
BACKGROUND Keloid, an aggressive fibroproliferative disease of the skin, is usually caused by infectious skin diseases, burns, and trauma. OBJECTIVE This study aimed to assess the effect of SPARC on the keloid pathogenesis. METHODS In normal skin and keloid scar tissues, changes in SPARC expression were analysed by qRT-PCR, western blotting, and immunohistochemistry. Keloid fibroblasts were isolated from human keloid tissue. GSEA was performed to investigate the signalling pathways related to SPARC. Cell Counting Kit-8, 5-Ethynyl-2'-deoxyuridine, transwell assay, and scratching assays were used to assess fibroblast proliferation and migration. Changes in α-SMA, fibronectin, collagen I, and collagen III levels were examined in fibroblasts by western blotting. RESULTS SPARC expression was upregulated in keloid scar tissues. In fibroblasts, cell proliferation, migration, collagen production, and extracellular matrix (ECM) synthesis were promoted by SPARC overexpression, whereas SPARC knockdown resulted a converse result. GSEA showed that SPARC regulates the p53 pathway. In keloid scar tissues, there was a negative correlation between SPARC and p53 expression. p53 expression was decreased by SPARC overexpression, whereas SPARC knockdown increased p53 expression. Furthermore, the effects of SPARC on the fibroblast phenotype were reversed by p53 overexpression. CONCLUSIONS Fibroblast proliferation, migration, and ECM synthesis were promoted by SPARC overexpression, which was achieved by regulating the p53 pathway. Our findings provide new therapeutic targets for keloids.
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Deng S, Zhang L, Li J, Jin Y, Wang J. Activation of the PI3K-AKT signaling pathway by SPARC contributes to the malignant phenotype of cholangiocarcinoma cells. Tissue Cell 2022; 76:101756. [PMID: 35217388 DOI: 10.1016/j.tice.2022.101756] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 12/22/2022]
Abstract
Cholangiocarcinoma (CCA) is a primary biliary epithelium malignancy with limited therapies, poor prognosis and high mortality rate. Nowadays, the molecular mechanisms of CCA remain elusive. SPARC has been proposed to be highly expressed in clinical CCA tissues, but few studies has been elucidated its functions in CCA. In the current study, we aimed to investigate the functional role of SPARC in the progression of CCA. In this study, a significantly increased expression of SPARC was observed in CCA tissues and cells. Knockdown of SPARC by RNA interference significantly impeded the proliferation of CCA cells. Moreover, SPARC silencing hampered the migration and invasion of CCA cells by inhibiting EMT. In parallel, overexpression of SPARC in RBE cells had the opposite effects. Mechanically, SPARC promoted proliferation, migration, invasion, and EMT of CCA cells in vitro via activating the PI3K-AKT signaling. Overall, our integrated analysis revealed that SPARC plays a crucial role in CCA progression via the PI3K-AKT signaling pathway, which suggests that targeting SPARC might represent a promising approach for improving CCA patient's clinical outcome.
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Affiliation(s)
- Shikang Deng
- Medical School, Kunming University of Science and Technology, Kumming, Yunnan, China; Department of Hepatobiliary and Pancreatic Surgery, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kumming, Yunnan, China
| | - Li Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kumming, Yunnan, China
| | - Jiao Li
- Department of Hepatobiliary and Pancreatic Surgery, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kumming, Yunnan, China
| | - Yan Jin
- Department of Hepatobiliary and Pancreatic Surgery, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kumming, Yunnan, China
| | - Junfeng Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kumming, Yunnan, China.
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