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Wang YY, Yang WX, Cai JY, Wang FF, You CG. Comprehensive molecular characteristics of hepatocellular carcinoma based on multi-omics analysis. BMC Cancer 2025; 25:573. [PMID: 40159482 PMCID: PMC11956240 DOI: 10.1186/s12885-025-13952-0] [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: 10/17/2024] [Accepted: 03/17/2025] [Indexed: 04/02/2025] Open
Abstract
BACKGROUND The high heterogeneity of hepatocellular carcinoma (HCC) poses challenges for precision treatment strategies. This study aims to use multi-omics methodologies to better understand its pathogenesis and discover biomarkers. METHODS Quantitative proteomics was used to investigate hepatocellular carcinoma tissues (HCT) and their corresponding adjacent non-tumor tissues (DNT), obtained from six HCC patients. Untargeted metabolomics was applied to analyze the metabolic profiles of HCT and DNT of ten HCC patients. Statistical analyses, such as the Student's t-test, were performed to identify differentially expressed proteins (DEPs) and metabolites (DEMs) between the two groups. The functions and metabolic pathways involving DEPs and DEMs were annotated and enriched using the gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) databases. Bioinformatics methods were then utilized to analyze consistency between proteomics and metabolomics results, leading to identification of potential biomarkers along with key altered pathways associated with HCC. RESULTS This study identified 1556 DEPs between HCT and DNT samples. These DEPs were primarily enriched in crucial biological pathways such as amino acid degradation, fatty acid metabolism, and DNA replication. Subsequently, the analysis of metabolomics identified 500 DEMs that mainly participated in glycerophospholipid metabolism, the phospholipase D signaling pathway, and choline metabolism related to cancer. Integrated analysis of proteomics and metabolomics data unveiled significant dysfunctions in bile secretion, multiple amino acid and fatty acid metabolic pathways among HCC patients. Further investigation revealed that five proteins (PTP4A3, B4GALT5, GAB1, ME2, and PKM) along with seven metabolites (PI(6 keto-PGF1alpha/16:0), 13, 16, 19-docosatrienoic acid, PA(18:2(9Z, 12Z)/20:1(11Z)), Citric Acid, PG(20:3(6, 8, 11)-OH(5)/18:2(9Z, 12Z)), Spermidine, and N2-Acetylornithine) exhibited excellent diagnostic efficiency for HCC and could serve as its potential biomarkers. CONCLUSION Our integrated proteome and metabolome analysis revealed 10 key HCC-related pathways and proposed 12 potential biomarkers, which may enhance our understanding of HCC pathophysiology and be helpful in facilitating early diagnosis and treatment strategies.
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Affiliation(s)
- Ying-Ying Wang
- Laboratory Medicine Center, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, Gansu Province, 730030, China
| | - Wan-Xia Yang
- Laboratory Medicine Center, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, Gansu Province, 730030, China
| | - Jiang-Ying Cai
- Laboratory Medicine Center, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, Gansu Province, 730030, China
| | - Fang-Fang Wang
- Laboratory Medicine Center, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, Gansu Province, 730030, China
| | - Chong-Ge You
- Laboratory Medicine Center, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, Gansu Province, 730030, China.
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He L, Meng F, Chen R, Qin J, Sun M, Fan Z, Du J. Precise Regulations at the Subcellular Level through Intracellular Polymerization, Assembly, and Transformation. JACS AU 2024; 4:4162-4186. [PMID: 39610726 PMCID: PMC11600172 DOI: 10.1021/jacsau.4c00849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2024] [Revised: 10/18/2024] [Accepted: 10/22/2024] [Indexed: 11/30/2024]
Abstract
A living cell is an intricate machine that creates subregions to operate cell functions effectively. Subcellular dysfunction has been identified as a potential druggable target for successful drug design and therapy. The treatments based on intracellular polymerization, self-assembly, or transformation offer various advantages, including enhanced blood circulation of monomers, long-term drug delivery pharmacokinetics, low drug resistance, and the ability to target deep tissues and organelles. In this review, we discuss the latest developments of intracellular synthesis applied to precisely control cellular functions. First, we discuss the design and applications of endogenous and exogenous stimuli-triggered intracellular polymerization, self-assembly, and dynamic morphology transformation of biomolecules at the subcellular level. Second, we highlight the benefits of these strategies applied in cancer diagnosis and treatment and modulating cellular states or cell metabolism of living systems. Finally, we conclude the recent progress in this field, discuss future perspectives, analyze the challenges of the intracellular functional reactions for regulation, and find future opportunities.
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Affiliation(s)
- Le He
- School
of Materials Science and Engineering, East
China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Department
of Gynaecology and Obstetrics, Shanghai Key Laboratory of Anesthesiology
and Brain Functional Modulation, Clinical Research Center for Anesthesiology
and Perioperative Medicine, Translational Research Institute of Brain
and Brain-Like Intelligence, Shanghai Fourth People’s Hospital,
School of Medicine, Tongji University, Shanghai 200434, China
| | - Fanying Meng
- Department
of Polymeric Materials, School of Materials Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai 201804, China
| | - Ran Chen
- Department
of Polymeric Materials, School of Materials Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai 201804, China
| | - Jinlong Qin
- Department
of Gynaecology and Obstetrics, Shanghai Key Laboratory of Anesthesiology
and Brain Functional Modulation, Clinical Research Center for Anesthesiology
and Perioperative Medicine, Translational Research Institute of Brain
and Brain-Like Intelligence, Shanghai Fourth People’s Hospital,
School of Medicine, Tongji University, Shanghai 200434, China
| | - Min Sun
- Department
of Gynaecology and Obstetrics, Shanghai Key Laboratory of Anesthesiology
and Brain Functional Modulation, Clinical Research Center for Anesthesiology
and Perioperative Medicine, Translational Research Institute of Brain
and Brain-Like Intelligence, Shanghai Fourth People’s Hospital,
School of Medicine, Tongji University, Shanghai 200434, China
| | - Zhen Fan
- Department
of Gynaecology and Obstetrics, Shanghai Key Laboratory of Anesthesiology
and Brain Functional Modulation, Clinical Research Center for Anesthesiology
and Perioperative Medicine, Translational Research Institute of Brain
and Brain-Like Intelligence, Shanghai Fourth People’s Hospital,
School of Medicine, Tongji University, Shanghai 200434, China
- Department
of Polymeric Materials, School of Materials Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai 201804, China
| | - Jianzhong Du
- School
of Materials Science and Engineering, East
China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Department
of Gynaecology and Obstetrics, Shanghai Key Laboratory of Anesthesiology
and Brain Functional Modulation, Clinical Research Center for Anesthesiology
and Perioperative Medicine, Translational Research Institute of Brain
and Brain-Like Intelligence, Shanghai Fourth People’s Hospital,
School of Medicine, Tongji University, Shanghai 200434, China
- Department
of Polymeric Materials, School of Materials Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai 201804, China
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