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Data-Independent Acquisition-Based Mass Spectrometry (DIA-MS) for Quantitative Analysis of Human Intestinal Ischemia/Reperfusion

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Abstract

Intestinal ischemia–reperfusion (II/R) injury is a complex pathologic process, which is of great significance to unravel the underlying mechanisms and pathophysiology. Our study represented a comprehensive proteomic analysis in the human intestine with ischemia–reperfusion injury. The proteomics analysis measured a total of 5,230 proteins, and 417 differently expressed proteins (DEPs) were identified between II/R and control samples. GO and KEGG analysis demonstrated that the 290 upregulated DEPs in II/R were significantly involved in immune-related biological process and tight junction, focal adhesion, and cAMP signaling pathway, whereas the 127 downregulated DEPs in II/R were enriched in lipid metabolic process and metabolic pathway. Furthermore, we screened out 20 hub proteins from the protein–protein interaction (PPI) network according to the degree of connectivity, and six clusters were identified. Combined with the result of KEGG analysis, 6 from the 20 hub proteins, ACTB, CAV1, FLNA, MYLK, ACTN1, and MYL9, were identified as the key proteins in the progress of II/R injury. According to the previous studies, FLNA and MYL9 were selected as the novel disease-related proteins for the first time. In conclusion, this study extended our understanding of the alteration in the human intestine during ischemia and reperfusion and highlighted the potential role of FLNA and MYL9 in the progress of II/R injury, which need to be further studied.

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Data Availability

The mass spectrometry proteomics data have been deposited to the Proteome Xchange Consortium (http://proteomecentral.proteomexchange.org) via the iProX partner repository with the dataset identifier PXD033218.

Abbreviations

DDA:

Data-dependent acquisition

DIA:

Data-independent acquisition

II/R:

Intestinal ischemia–reperfusion

LC–MS/MS:

Liquid chromatography–tandem mass spectrometry

DEP:

Differently expressed proteins

PPI:

Protein–protein interaction

KEGG:

Kyoto Encyclopedia of Genes and Genomes

GO:

Gene Ontology

ROS:

Reactive oxygen species

ICU:

Intensive care unit

PCA:

Principal component analysis

STRING:

Search Tool for the Retrieval of Interacting Genes

MCODE:

Molecular Complex Detection

LFQ:

Label-free quantification

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Funding

This study was supported by the National Natural Science Foundation of China (No. 81801943), the Science and Technology Commission of Shanghai Municipality (No.18411970200), the Shanghai Pujiang Program (No. 21PJD009), and the Medical and Health Science and Technology Innovation Fund Project in Jinshan District, Shanghai (No.2020–3-19).

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Author notes

  1. Anzhong Huang and Wei Wu contributed equally to this work

Authors and Affiliations

  1. Department of General Surgery, Jinshan Hospital, Fudan University, Shanghai, 201508, People’s Republic of China

    Anzhong Huang

  2. Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China

    Wei Wu, Song Chen & Ming Zhong

  3. Center of Emergency and Intensive Care Unit, Jinshan Hospital, Fudan University, Shanghai, China

    Hanbing Hu, Jie Shen & Lin Zhang

  4. Key Laboratory of Chemical Injury, Emergency and Critical Medicine of Shanghai Municipal Health Commission, Shanghai, China

    Hanbing Hu, Jie Shen & Lin Zhang

  5. Institutes of Biomedical Sciences, Fudan University, Shanghai, China

    Jingbo Qie

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  1. Anzhong Huang
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Contributions

JBQ, MZ, and LZ conceived and designed the research; AZH collected the data used in our study; AZH and WW analyzed the data; AZH, SC, and HBH draw the figures; WW and JS wrote the manuscript; and MZ and LZ approved the final version of manuscript. All authors have read and agreed to the published version of the manuscript.

Corresponding authors

Correspondence to Jingbo Qie, Ming Zhong or Lin Zhang.

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This study was performed in line with the principles of the Declaration of Helsinki. Approval was granted by the Ethics Committee of Shanghai Medical College of Fudan University.

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Not applicable.

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The authors declare no competing interests.

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Huang, A., Wu, W., Chen, S. et al. Data-Independent Acquisition-Based Mass Spectrometry (DIA-MS) for Quantitative Analysis of Human Intestinal Ischemia/Reperfusion. Appl Biochem Biotechnol 194, 4156–4168 (2022). https://doi.org/10.1007/s12010-022-04005-4

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