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Sun J, Li J, He Y, Kang W, Ye X. Identification and validation of protein biomarkers for predicting gastrointestinal stromal tumor recurrence. Comput Struct Biotechnol J 2024; 23:1065-1075. [PMID: 38455069 PMCID: PMC10918489 DOI: 10.1016/j.csbj.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
We conducted a proteomic analysis using mass spectrometry to identify and validate protein biomarkers for accurately predicting recurrence risk in gastrointestinal stromal tumors (GIST) patients, focusing on differentially expressed proteins in metastatic versus primary GIST tissues. We selected five biomarkers-GPX4, RBM4, TPM3, PFKFB2, and PGAM5-and validated their expressions in primary tumors of recurrent and non-recurrent GIST patients via immunohistochemistry. Our analysis of the association between these biomarkers with recurrence-free survival (RFS) and overall survival (OS), along with their interrelationships, revealed that immunohistochemistry confirmed significantly higher expressions of these biomarkers in primary GIST tissues of recurrent patients. Kaplan-Meier survival analysis showed that high expressions of GPX4, RBM4, TPM3, PFKFB2, and PGAM5 correlated with lower RFS, and GPX4 and RBM4 with lower OS. All biomarker pairs showed positive associations, with high expressions correlating with increased recurrence rates, and GPX4 and RBM4 with higher mortality rates. In conclusion, the biomarkers GPX4, RBM4, TPM3, PFKFB2, and PGAM5 are clinically relevant for predicting GIST recurrence, with their high expressions in primary tumors linked to poorer RFS and OS. They serve as potential prognostic indicators, enabling early treatment and improved outcomes. The observed interrelationships among these biomarkers further validate their accuracy in predicting GIST recurrence.
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Affiliation(s)
| | | | - Yixuan He
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weiming Kang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Ye
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Li Y, Yue L, Zhang S, Wang X, Zhu YN, Liu J, Ren H, Jiang W, Wang J, Zhang Z, Liu T. Proteomic, single-cell and bulk transcriptomic analysis of plasma and tumor tissues unveil core proteins in response to anti-PD-L1 immunotherapy in triple negative breast cancer. Comput Biol Med 2024; 176:108537. [PMID: 38744008 DOI: 10.1016/j.compbiomed.2024.108537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Anti-PD-1/PD-L1 treatment has achieved durable responses in TNBC patients, whereas a fraction of them showed non-sensitivity to the treatment and the mechanism is still unclear. METHODS Pre- and post-treatment plasma samples from triple negative breast cancer (TNBC) patients treated with immunotherapy were measured by tandem mass tag (TMT) mass spectrometry. Public proteome data of lung cancer and melanoma treated with immunotherapy were employed to validate the findings. Blood and tissue single-cell RNA sequencing (scRNA-seq) data of TNBC patients treated with or without immunotherapy were analyzed to identify the derivations of plasma proteins. RNA-seq data from IMvigor210 and other cancer types were used to validate plasma proteins in predicting response to immunotherapy. RESULTS A random forest model constructed by FAP, LRG1, LBP and COMP could well predict the response to immunotherapy. The activation of complement cascade was observed in responders, whereas FAP and COMP showed a higher abundance in non-responders and negative correlated with the activation of complements. scRNA-seq and bulk RNA-seq analysis suggested that FAP, COMP and complements were derived from fibroblasts of tumor tissues. CONCLUSIONS We constructe an effective plasma proteomic model in predicting response to immunotherapy, and find that FAP+ and COMP+ fibroblasts are potential targets for reversing immunotherapy resistance.
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Affiliation(s)
- Yingpu Li
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China; NHC Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, 150001, China
| | - Liang Yue
- Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, 310030, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, 310030, China; Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310030, China
| | - Sifan Zhang
- Department of Neurobiology, Harbin Medical University, Harbin, 150081, Heilongjiang Province, China
| | - Xinxuan Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China
| | - Yu-Nan Zhu
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China
| | - Jianyu Liu
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China
| | - He Ren
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China
| | - Wenhao Jiang
- Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, 310030, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, 310030, China; Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310030, China
| | - Jingxuan Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China.
| | - Zhiren Zhang
- NHC Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, 150001, China; Institute of Metabolic Disease, Heilongjiang Academy of Medical Science, Heilongjiang Key Laboratory for Metabolic Disorder and Cancer Related Cardiovascular Diseases, Harbin, 150001, China.
| | - Tong Liu
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China; NHC Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, 150001, China.
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Feng W, Lv C, Cheng L, Song X, Li X, Xie H, Chen S, Wang X, Xue L, Zhang C, Kou J, Wang L, Zhao H. Targeting ERS-mitophagy in hippocampal neurons to explore the improvement of memory by tea polyphenols in aged type 2 diabetic rats. Free Radic Biol Med 2024; 213:293-308. [PMID: 38286317 DOI: 10.1016/j.freeradbiomed.2024.01.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/15/2024] [Accepted: 01/26/2024] [Indexed: 01/31/2024]
Abstract
Increasing evidence demonstrated that mitophagy and endoplasmic reticulum stress (ERS) was closely associated with memory decline in elderly type 2 diabetes mellitus (T2DM). Tea polyphenols (TP), an excellent natural antioxidant, has been reported to have neuroprotective properties in aging and diabetes, but the underlying mechanisms are still not fully understood. This study targets ERS-mitophagy in hippocampal neurons to investigate the improvement effect of memory in aged T2DM rats by TP. Rats were randomly divided into the control group, the aged group, the aged T2DM model group, the TP 75, 150, 300 mg/kg groups. TP 300 mg/kg ameliorated mitophagy by decreasing the levels of p-mTOR (S2448), P62 and HSP60 and increasing the levels of PINK1 and Parkin, the ratio of LC3Ⅱ/LC3Ⅰ, co-localization of LC3 and HSP60 and the number of autophagosomes and autolysosomes. TP 300 mg/kg attenuated ERS by downregulating the levels of p-PERK, p-eIF2α, ATF4, GRP78 and restoring the ER structure. To further verify epigallocatechin gallate (EGCG), which is the main active component of TP, enhanced mitophagy by inhibiting ERS, PC12 cells were pretreated with ERS activator tunicamycin (TM) or ERS inhibitor 4-phenylbutyric acid (4-PBA). The results showed that the improvement of mitophagy by EGCG was inhibited by TM and promoted by 4-PBA. Collectively, ERS-mitophagy in hippocampal neurons plays a key role in the improvement of memory by TP in aged T2DM rats. This study will provide a new perspective and strategy for the prevention of memory decline in elderly with T2DM.
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Affiliation(s)
- Wenjuan Feng
- Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Chenhui Lv
- Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Le Cheng
- Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Xin Song
- Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Xuemin Li
- Center for Disease Control and Prevention in Shanxi Province, Taiyuan, Shanxi, 030012, PR China
| | - Haoran Xie
- Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Shuangzhi Chen
- Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Xi Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Lushan Xue
- Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Cheng Zhang
- Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Jie Kou
- Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Lili Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Haifeng Zhao
- Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China; Key Laboratory of Coal Environmental Pathogenicity and Prevention (Shanxi Medical University), Ministry of Education, PR China.
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Lu W, Xu J, Chen Y, Huang J, Shen Q, Sun F, Zhang Y, Ji D, Xue B, Li J. Identication and validation of cell senescence biomarkers in idiopathic pulmonary hypertension via integrated transcriptome analyses and machine learning. Exp Gerontol 2023; 182:112303. [PMID: 37776984 DOI: 10.1016/j.exger.2023.112303] [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: 08/03/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Idiopathic pulmonary hypertension (IPAH) is a rare and severe disease that affects the pulmonary vasculature. As the diagnosis of IPAH requires invasive right heart catheterization surgery, early detection of this condition is notoriously challenging. Therefore, it is of utmost importance to investigate biomarkers present in peripheral blood that could aid physicians in the early identification and management of IPAH. METHOD We speculate that cellular senescence may be involved in the occurrence and development of IPAH through various pathways. In this study, we utilized integrated transcriptome analyses and machine learning-based approach to develop a diagnostic model for IPAH cell senescence. To select genetic features, we employed two machine learning algorithms: the Least Absolute Shrinkage and Selection Operator (LASSO) and Random Forest (RF). Additionally, we validated our findings through both external data sets and qRT-PCR experiments. RESULTS The resulting diagnostic nomogram was able to identify five important biomarkers that can aid in the diagnosis of IPAH, including TNFRSF1B, CCL16, GCLM, IL15, and SOD1. These genes are primarily associated with the immune system, as well as with cell senescence and apoptosis. CONCLUSION Our study demonstrates the utility of machine learning algorithms in making accurate diagnoses of IPAH, providing clinicians with a more directed approach to the diagnosis and treatment of this disease.
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Affiliation(s)
- Wenzhang Lu
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Jiayi Xu
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Yanrong Chen
- Department of Operating Room, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Jinbo Huang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Qin Shen
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Fei Sun
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Yan Zhang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Daojun Ji
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Bijuan Xue
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Jun Li
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China.
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