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Khorrami M, Pastras C, Haynes PA, Mirzaei M, Asadnia M. The Current State of Proteomics and Metabolomics for Inner Ear Health and Disease. Proteomes 2024; 12:17. [PMID: 38921823 PMCID: PMC11207525 DOI: 10.3390/proteomes12020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 06/27/2024] Open
Abstract
Characterising inner ear disorders represents a significant challenge due to a lack of reliable experimental procedures and identified biomarkers. It is also difficult to access the complex microenvironments of the inner ear and investigate specific pathological indicators through conventional techniques. Omics technologies have the potential to play a vital role in revolutionising the diagnosis of ear disorders by providing a comprehensive understanding of biological systems at various molecular levels. These approaches reveal valuable information about biomolecular signatures within the cochlear tissue or fluids such as the perilymphatic and endolymphatic fluid. Proteomics identifies changes in protein abundance, while metabolomics explores metabolic products and pathways, aiding the characterisation and early diagnosis of diseases. Although there are different methods for identifying and quantifying biomolecules, mass spectrometry, as part of proteomics and metabolomics analysis, could be utilised as an effective instrument for understanding different inner ear disorders. This study aims to review the literature on the application of proteomic and metabolomic approaches by specifically focusing on Meniere's disease, ototoxicity, noise-induced hearing loss, and vestibular schwannoma. Determining potential protein and metabolite biomarkers may be helpful for the diagnosis and treatment of inner ear problems.
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Affiliation(s)
- Motahare Khorrami
- Faculty of Science and Engineering, School of Engineering, Macquarie University, Sydney 2109, NSW, Australia; (M.K.); (C.P.)
| | - Christopher Pastras
- Faculty of Science and Engineering, School of Engineering, Macquarie University, Sydney 2109, NSW, Australia; (M.K.); (C.P.)
| | - Paul A. Haynes
- School of Natural Sciences, Macquarie University, Macquarie Park, Sydney 2109, NSW, Australia;
| | - Mehdi Mirzaei
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney 2109, NSW, Australia;
| | - Mohsen Asadnia
- Faculty of Science and Engineering, School of Engineering, Macquarie University, Sydney 2109, NSW, Australia; (M.K.); (C.P.)
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Wang R, Lu Y, Qi J, Xi Y, Shen Z, Twumasi G, Bai L, Hu J, Wang J, Li L, Liu H. Genome-wide association analysis explores the genetic loci of amino acid content in duck's breast muscle. BMC Genomics 2024; 25:486. [PMID: 38755558 PMCID: PMC11097541 DOI: 10.1186/s12864-024-10287-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Amino acids are the basic components of protein and an important index to evaluate meat quality. With the rapid development of genomics, candidate regions and genes affecting amino acid content in livestock and poultry have been gradually revealed. Hence, genome-wide association study (GWAS) can be used to screen candidate loci associated with amino acid content in duck meat. RESULT In the current study, the content of 16 amino acids was detected in 358 duck breast muscles. The proportion of Glu to the total amino acid content was relatively high, and the proportion was 0.14. However, the proportion of Met content was relatively low, at just 0.03. By comparative analysis, significant differences were found between males and females in 3 amino acids, including Ser, Met, and Phe. In addition, 12 SNPs were significantly correlated with Pro content by GWAS analysis, and these SNPs were annotated by 7 protein-coding genes; 8 significant SNPs were associated with Tyr content, and these SNPs were annotated by 6 protein-coding genes. At the same time, linkage disequilibrium (LD) analysis was performed on these regions with significant signals. The results showed that three SNPs in the 55-56 Mbp region of chromosome 3 were highly correlated with the leader SNP (chr3:55526954) that affected Pro content (r2 > 0.6). Similarly, LD analysis showed that there were three SNPs in the 21.2-21.6 Mbp region of chromosome 13, which were highly correlated with leader SNP (chr13:21421661) (r2 > 0.6). Moreover, Through functional enrichment analysis of all candidate genes. The results of GO enrichment analysis showed that several significant GO items were associated with amino acid transport function, including amino acid transmembrane transport and glutamine transport. The results further indicate that these candidate genes are closely associated with amino acid transport. Among them, key candidate genes include SLC38A1. For KEGG enrichment analysis, CACNA2D3 and CACNA1D genes were covered by significant pathways. CONCLUSION In this study, GWAS analysis found a total of 28 significant SNPs affecting amino acid content. Through gene annotation, a total of 20 candidate genes were screened. In addition, Through LD analysis and enrichment analysis, we considered that SERAC1, CACNA2D3 and SLC38A1 genes are important candidate genes affecting amino acid content in duck breast muscle.
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Affiliation(s)
- Rui Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, P.R. China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Wenjiang District, 611130, Chengdu, Sichuan, P.R. China
- National Key Laboratory for Swine and Poultry Breeding, Chengdu, P.R. China
| | - Yinjuan Lu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, P.R. China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Wenjiang District, 611130, Chengdu, Sichuan, P.R. China
- National Key Laboratory for Swine and Poultry Breeding, Chengdu, P.R. China
| | - Jingjing Qi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, P.R. China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Wenjiang District, 611130, Chengdu, Sichuan, P.R. China
- National Key Laboratory for Swine and Poultry Breeding, Chengdu, P.R. China
| | - Yang Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, P.R. China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Wenjiang District, 611130, Chengdu, Sichuan, P.R. China
- National Key Laboratory for Swine and Poultry Breeding, Chengdu, P.R. China
| | - Zhenyang Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, P.R. China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Wenjiang District, 611130, Chengdu, Sichuan, P.R. China
- National Key Laboratory for Swine and Poultry Breeding, Chengdu, P.R. China
| | - Grace Twumasi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, P.R. China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Wenjiang District, 611130, Chengdu, Sichuan, P.R. China
- National Key Laboratory for Swine and Poultry Breeding, Chengdu, P.R. China
| | - Lili Bai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, P.R. China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Wenjiang District, 611130, Chengdu, Sichuan, P.R. China
- National Key Laboratory for Swine and Poultry Breeding, Chengdu, P.R. China
| | - Jiwei Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, P.R. China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Wenjiang District, 611130, Chengdu, Sichuan, P.R. China
- National Key Laboratory for Swine and Poultry Breeding, Chengdu, P.R. China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, P.R. China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Wenjiang District, 611130, Chengdu, Sichuan, P.R. China
- National Key Laboratory for Swine and Poultry Breeding, Chengdu, P.R. China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, P.R. China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Wenjiang District, 611130, Chengdu, Sichuan, P.R. China
- National Key Laboratory for Swine and Poultry Breeding, Chengdu, P.R. China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, P.R. China.
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Wenjiang District, 611130, Chengdu, Sichuan, P.R. China.
- National Key Laboratory for Swine and Poultry Breeding, Chengdu, P.R. China.
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Yu QQ, Zhang H, Zhao S, Xie D, Zhao H, Chen W, Pang M, Han B, Jiang P. Systematic evaluation of irinotecan-induced intestinal mucositis based on metabolomics analysis. Front Pharmacol 2022; 13:958882. [PMID: 36188576 PMCID: PMC9520243 DOI: 10.3389/fphar.2022.958882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Chemotherapy-induced intestinal mucositis (CIM) is a major dose-limiting side effect of chemotherapy, especially in regimens containing irinotecan (CPT-11). Several studies on the pathologic mechanisms of CIM focused on both the genomics and molecular pathways triggered by chemotherapy. However, systematic evaluation of metabolomic analysis in irinotecan-induced intestinal mucositis (IIM) has not been investigated. This study aimed to comprehensively analyze metabolite changes in main tissues of IIM mouse models. Male ICR mice were assigned to two groups: the model group (n = 11) treated with CPT-11 (20 mg/kg daily; i.p.) and the control group (n= 11) with solvent for 9 days. Gas chromatography-mass spectrometry (GC-MS) was used to investigate the metabolic alterations in the serum, intestinal, colonic, hepatic, and splenic samples of mice between two groups by multivariate statistical analyses, including GC–MS data processing, pattern recognition analysis, and pathway analysis. Forty-six metabolites, including hydrocarbons, amino acids, lipids, benzenoids, hydroxy acids, and amines, had significant changes in levels in tissues and sera of IIM mouse models. The most important pathways related to the identified metabolites were the glycerolipid metabolism in the colon and aminoacyl-tRNA biosynthesis; glycine, serine, and threonine metabolism; and glyoxylate and dicarboxylate metabolism in the liver. Our study firstly provided a comprehensive and systematic view of metabolic alterations of IIM using GC-MS analysis. The characterizations of metabolic changes could offer profound and theoretical insight into exploring new biomarkers for diagnosis and treatment of IIM.
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Affiliation(s)
- Qing-Qing Yu
- Laboratory of Biochemistry and Biomedical Materials, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Heng Zhang
- Department of Laboratory, Shandong Daizhuang Hospital, Jining, China
| | - Shiyuan Zhao
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Dadi Xie
- Department of Endocrine, Tengzhou Central People’s Hospital, Tengzhou, China
| | - Haibo Zhao
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Weidong Chen
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Min Pang
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Baoqin Han
- Laboratory of Biochemistry and Biomedical Materials, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Baoqin Han, ; Pei Jiang,
| | - Pei Jiang
- Jining First People’s Hospital, Jining Medical College, Jining, China
- *Correspondence: Baoqin Han, ; Pei Jiang,
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