Analysis of Differentially Expressed Proteins Involved in Autoimmune Cirrhosis and Normal Serum by iTRAQ Proteomics

Zheng, Min; Hu, Kunhua; Bao, Yongzhan; Lü, Hongmei; Li, Jing; Shaowen, Wu; Sun, Lina; Duan, Chaohui

doi:10.1002/prca.201700153

Cited by 6 publications

(4 citation statements)

References 39 publications

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“…In hepatitis C, ubiquitylation and proteasomal degradation of retinoblastoma protein (pRb) with concomitant E2F transcription factor release and cellular proliferation can contribute to the disease progression and development of hepatocellular carcinoma [ 22 ]. Our results are also in line with a study, which, after proteomic analysis, revealed a possible implication of dysfunctional vesicle-mediated transport in the pathogenesis of AIH [ 23 ].…”

Section: Resultssupporting

confidence: 92%

Identifying Differentially Expressed MicroRNAs, Target Genes, and Key Pathways Deregulated in Patients with Liver Diseases

Gholizadeh

Szeląg-Pieniek

Post

et al. 2020

IJMS

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Liver diseases are important causes of morbidity and mortality worldwide. The aim of this study was to identify differentially expressed microRNAs (miRNAs), target genes, and key pathways as innovative diagnostic biomarkers in liver patients with different pathology and functional state. We determined, using RT-qPCR, the expression of 472 miRNAs in 125 explanted livers from subjects with six different liver pathologies and from control livers. ANOVA was employed to obtain differentially expressed miRNAs (DEMs), and miRDB (MicroRNA target prediction database) was used to predict target genes. A miRNA–gene differential regulatory (MGDR) network was constructed for each condition. Key miRNAs were detected using topological analysis. Enrichment analysis for DEMs was performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). We identified important DEMs common and specific to the different patient groups and disease progression stages. hsa-miR-1275 was universally downregulated regardless the disease etiology and stage, while hsa-let-7a*, hsa-miR-195, hsa-miR-374, and hsa-miR-378 were deregulated. The most significantly enriched pathways of target genes controlled by these miRNAs comprise p53 tumor suppressor protein (TP53)-regulated metabolic genes, and those involved in regulation of methyl-CpG-binding protein 2 (MECP2) expression, phosphatase and tensin homolog (PTEN) messenger RNA (mRNA) translation and copper homeostasis. Our findings show a novel panel of deregulated miRNAs in the liver tissue from patients with different liver pathologies. These miRNAs hold potential as biomarkers for diagnosis and staging of liver diseases.

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Section: Resultssupporting

confidence: 92%

Identifying Differentially Expressed MicroRNAs, Target Genes, and Key Pathways Deregulated in Patients with Liver Diseases

Gholizadeh

Szeląg-Pieniek

Post

et al. 2020

IJMS

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“…Currently, there are no studies that have investigated the expression of these proteins in tissue biopsies or biological fluids of PSC patients. Nevertheless, an increased liver content of core histone macro-H2A.1 has been identified in murine models of hepatic steatosis [41] and fat-associated hepatocellular carcinoma [42], and an upregulation of immunoglobulin lambda variable 3-19 has been shown in the serum samples of 16 patients with autoimmune cirrhosis compared to the healthy control group [43]. Although saliva is not considered functionally associated with the bile ducts, some of the identified DEPs, such as disulfideisomerase A3, exhibited a clear deregulation in the bile and serum of PSC patients [20], confirming saliva as potential biological fluid in PSC characterization.…”

Section: Discussionmentioning

confidence: 99%

The Clinical Utility of the Saliva Proteome in Rare Diseases: A Pilot Study for Biomarker Discovery in Primary Sclerosing Cholangitis

Ceccherini,

Michelucci,

Signore

et al. 2024

JCM

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Background: Primary sclerosing cholangitis (PSC) is a rare chronic inflammatory liver disease characterized by biliary strictures and cholestasis. Due to the lack of effective serological indicators for diagnosis and prognosis, in the present study, we examined the potentiality of the saliva proteome to comprehensively screen for novel biomarkers. Methods: Saliva samples of PSC patients and healthy controls were processed and subsequently analyzed using a liquid chromatography–tandem mass spectrometry technique. A bioinformatic approach was applied to detect the differentially expressed proteins, their related biological functions and pathways, and the correlation with the clinical evidence in order to identify a possible marker for the PSC group. Results: We identified 25 differentially expressed proteins in PSC patients when compared to the healthy control group. Among them, eight proteins exhibited area under the curve values up to 0.800, suggesting these saliva proteins as good discriminators between the two groups. Multiple positive correlations were also identified between the dysregulated salivary proteins and increased serum alkaline phosphatase levels and the presence of ulcerative colitis. Pathway analysis revealed significant enrichments in the immune system, neutrophil degranulation, and in the interleukine-17 signaling pathway. Conclusion: We demonstrated the potentiality of saliva as a useful biofluid to obtain a fingerprint of the pathology, suggesting disulfide-isomerase A3 and peroxiredoxin-5 as the better discriminating proteins in PSC patients. Hence, analysis of saliva proteins could become, in future, a useful tool in the screening of patients with suspected PSC.

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“…We carried out mass spectrometric analysis as previously reported [ 18 ]. The iTRAQ-tagged peptide was reconstituted and loaded onto Phenomenex columns (Gemini-NX 3u C18 110 A; 150*2.00 mm) using a Dionex UltiMate 3000 HPLC system (A-phase: 20mM HCOONH4, PH 10, B-phase: 20mM HCOONH4, 98%CAN, PH 10).…”

Section: Methodsmentioning

confidence: 99%

ESF1 and MIPEP proteins promote estrogen receptor-positive breast cancer proliferation and are associated with patient prognosis

Yu,

Qu,

Liang

et al. 2024

Clin Proteom

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Background Estrogen receptor-positive (ER+) breast cancer accounts for two-thirds of all breast cancers, and its early and late recurrences still threaten patients’ long-term survival and quality of life. Finding candidate tumor antigens and potential therapeutic targets is critical to addressing these unmet needs. Method The isobaric tags for relative and absolute quantitation (iTRAQ) proteomic analysis was employed to identify the differentially expressed proteins (DEPs) between ER + breast cancer and corresponding adjacent normal tissue. Candidate DEPs were screened by bioinformatic analyses, and their expression was confirmed by immunohistochemical (IHC) staining and western blot. A series of in vitro experiments, including wound healing assay, colony formation, and cell cycle assay, were performed to reveal the functions of selected DEPs. Additionally, their clinical significances were further analyzed. Result A total of 369 DEPs (fold change ≥ 2.0 or ≤ 0.66, P < 0.05) were discovered. Compared with normal tissue, 358 proteins were up-regulated and 11 proteins were down-regulated in ER + breast cancer. GO and KEGG enrichment analysis showed that DEPs were closely associated with RNA regulation and metabolic pathways. STRING analysis found ESF1 and MIPEP were the hub genes in breast cancer, whose increased expressions were verified by the IHC staining and western blot. Knocking down ESF1 and MIPEP inhibited colony formation and increased cell apoptosis. Besides, knocking down ESF1 inhibited wound healing but not MIPEP. In addition, ESF1 and MIPEP expression were negatively associated with patient prognosis. Conclusion The upregulation of ESF1 and MIPEP promoted ER + breast cancer proliferation, which might provide novel targets for the development of new therapies.

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Analysis of Differentially Expressed Proteins Involved in Autoimmune Cirrhosis and Normal Serum by iTRAQ Proteomics

Abstract: These findings offer a comprehensive profile of the AIC proteome about candidate biomarkers and provide a useful basis for further analysis of the pathogenic mechanism of AIC.

Cited by 6 publications

References 39 publications

Identifying Differentially Expressed MicroRNAs, Target Genes, and Key Pathways Deregulated in Patients with Liver Diseases

Identifying Differentially Expressed MicroRNAs, Target Genes, and Key Pathways Deregulated in Patients with Liver Diseases

The Clinical Utility of the Saliva Proteome in Rare Diseases: A Pilot Study for Biomarker Discovery in Primary Sclerosing Cholangitis

ESF1 and MIPEP proteins promote estrogen receptor-positive breast cancer proliferation and are associated with patient prognosis

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