Analysis of Differentially Expressed Proteins and Modifications Induced by Formaldehyde Using LC-MS/MS
Ranran Liu,
Yue Han,
Zhiyue Wu,
Jianji Zhang,
Yong Zang,
Lijin Shen,
Shanshan Tian,
Kai Zhang
Affiliations
Ranran Liu
The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Diseases, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
Yue Han
The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Diseases, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
Zhiyue Wu
The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Diseases, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
Jianji Zhang
The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Diseases, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
Yong Zang
The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Diseases, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
Lijin Shen
NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
Shanshan Tian
The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Diseases, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
Kai Zhang
The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Diseases, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
Formaldehyde (FA) is a toxic compound that is considered to have a carcinogenic effect due to its damage to biological macromolecules. However, the influence of FA at the protein level remains to be explored. Here, we used LC-MS/MS to identify the differentially expressed proteins and modifications to proteins between FA-treated and untreated HeLa cells. Among 2021 proteins identified, 196 proteins were significantly down-regulated and 152 up-regulated. The differentially expressed proteins were further analyzed using bioinformatics tools for annotating the characterization of their localizations and functions. To evaluate the interaction of FA with proteins, we performed proteomic analysis for a mass shift of 12 Da on the side chains of lysine, cysteine and tryptophan, which are induced by FA as noticeable signals. We identified the modified proteins and sites, suggesting direct interaction between FA and proteins. Motif analysis further showed the characterization of amino acid sequences that react with FA. Cluster analysis of the modified proteins indicated that the FA-interacting networks are mostly enriched in the nuclei, ribosomes and metabolism. Our study presents the influence of FA on proteomes and modifications, offering a new insight into the mechanisms underlying FA-induced biological effects.
