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Published on: April 17, 2017
Integrative analysis of serum proteomics and transcriptomics in hepatitis C
Jianqiong Wang1, Andong Xia2, Min Tang1
1Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, No.157 Jinbi Road, Kunming, Yunnan, China.
Insights
This study reveals key serum protein and gene expression differences in hepatitis C (HCV) infection. Identified biomarkers like EIF4A3 may aid in diagnosing and treating HCV.
Area of Science:
- Molecular biology
- Virology
- Biochemistry
Background:
- Hepatitis C is a viral infection transmitted via blood and mother-to-child routes.
- Understanding serum molecular features is crucial for characterizing Hepatitis C Virus (HCV) infection.
Purpose of the Study:
- To characterize the serum molecular profiles of Hepatitis C Virus (HCV) infection using proteomics and transcriptomics.
- To identify differentially expressed proteins and genes (DEPs/DEGs) associated with HCV infection and chronic HCV.
Main Methods:
- Serum samples from control, previous HCV infection, and chronic HCV groups were analyzed.
- Proteomics (TMT) and transcriptomics (RNA-seq) were employed, followed by bioinformatics analysis.
- RT-qPCR and western blot validated key findings.
Main Results:
- Significant differences in serum proteomes and transcriptomes were observed between groups.
- DEPs included immunoglobulins and exosomal proteins; DEGs were involved in extracellular matrix regulation and immunity.
- Key proteins (HSPA4, HSPD1) and genes (KIF11, CENPE) were identified, with interactions involving EIF4A3, MNAT1, and UBE2D1.
Conclusions:
- Proteins EIF4A3, EIF2B1, MNAT1, SNRNP70, and UBE2D1 are implicated in HCV infection and pathogenesis.
- These molecules show potential as biomarkers for hepatitis C diagnosis and treatment.
Object:
Hepatitis C is a contagious disease caused by infection with the hepatitis C virus (HCV) through blood and mother-to-child routes. This study intends to characterize the serum molecular features of hepatitis C using proteomics and transcriptomics.
Methods:
Ctrl (normal population), HCV (population with previous HCV infection), and chronic HCV (patients with persistent HCV infection) groups were set up, and the expression profiles of the proteomes and transcriptomes of serum samples were identified using TMT and RNA-seq. Bioinformatics was applied to perform enrichment analysis and PPI network construction of differentially expressed proteins/genes (DEPs/DEGs). RT-qPCR and western blot verified the expression differences of DEPs/DEGs.
Results:
Compared to the Ctrl group, the HCV group had 356 DEPs in serum; compared to the HCV group, the chronic HCV group had 381 DEPs in serum. DEPs are predominantly immunoglobulins and exosomal proteins that regulate carbon dioxide transport, initiation of transcription, immune responses, and bacterial and viral infections. HSPA4, HSPD1, COPS5, PSMD2 and TCP1 are key HCV-associated proteins in DEPs. The HCV group had 684 DEGs compared to the Ctrl group, and the chronic HCV group had 350 DEGs compared to the HCV group. DEGs primarily encode the extracellular matrix and regulate wound healing, cellular communication, oxidative stress, cell adhesion, viral infection, and immunity. KIF11, CENPE, TTK, CDC20 and ASPM are HCV-related hub genes in DEGs. Combined analyses revealed interactions between DEPs and DEGs, especially EIF4A3, MNAT1, and UBE2D1. Moreover, the expression patterns of EIF4A3, EIF2B1, MNAT1, SNRNP70, and UBE2D1 in DEPs/DEGs from Ctrl, HCV, and chronic HCV groups were consistent with the sequencing results.
Conclusion:
EIF4A3, EIF2B1, MNAT1, SNRNP70, and UBE2D1 are involved in the process of HCV infection and pathogenesis, and they may be potential biomarkers for the treatment of patients with hepatitis C.
