Dataset Information

Transcriptome and proteome analysis of the human corneal endothelium and aqueous humor reveal endothelial cell dysfunction markers

ABSTRACT: Background: The underlying mechanism as well as diagnostic molecular biomarkers for corneal endothelial cell dysfunction (CECD) remain elusive. This study aimed to elucidate molecular mechanism of CECD via proteomic and transcriptomic approaches and identify novel biomarkers in aqueous humor (AH) directly associated with changes in CECs. Methods: We carried out an in-depth proteomic analysis of patient-derived AH as well as transcriptomic analysis of CECs from the same patients with bullous keratopathy (BK) resulting from CECD. Selected candidate proteins were further verified by individual data-independent acquisition and immunoassay using further AH samples from CECD patients. Findings: Using integrated multi-omics analysis, systematic alterations of proteins in AH and mRNA in CECs were mainly associated with the immune mechanism during BK development. Through individual proteomic verification via DIA analysis, three AH proteins were determined as potential predictive markers including TIMP1, FCGBP, and ANGPTL7. Finally, we confirmed these biomarkers using immunoassay in individual AH samples of CECD. Interpretation: Our multi-omics analysis may provide valuable insights into the disease-specific process as well as possibility of biofluid biomarkers in CECD. Further investigation with large scale is required to determine whether AH biomarkers are useful as liquid biopsy targets for the assessment of CEC function

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Jae Hun Jung

LAB HEAD: Jae Hun Jung

PROVIDER: PXD023772 | Pride | 2024-01-26

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	CECD_DIA_Spectronaut_results_median_normalization.csv	Csv
	CECD_DIA_peptide_01_2_rep1.raw	Raw
	CECD_DIA_peptide_02_2_rep1.raw	Raw
	CECD_DIA_peptide_03_2_rep1.raw	Raw
	CECD_DIA_peptide_04_2_rep1.raw	Raw

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Publications

Integrated Analysis of Transcriptome and Proteome of the Human Cornea and Aqueous Humor Reveal Novel Biomarkers for Corneal Endothelial Cell Dysfunction.

Moon Chae-Eun CE Kim Chang Hwan CH Jung Jae Hun JH Cho Young Joo YJ Choi Kee Yong KY Han Kyusun K Seo Kyoung Yul KY Lee Hyung Keun HK Ji Yong Woo YW

International journal of molecular sciences 20231019 20

Earlier studies have reported that elevated protein levels in the aqueous humor (AH) are associated with corneal endothelial cell dysfunction (CECD), but the details of the underlying mechanism as well as specific biomarkers for CECD remain elusive. In the present study, we aimed to identify protein markers in AH directly associated with changes to corneal endothelial cells (CECs), as AH can be easily obtained for analysis. We carried out an in-depth proteomic analysis of patient-derived AH as w ...[more]

PMID: 37895034

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