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Arafat MY, Narula K, Kumar M, Chakraborty N, Chakraborty S. Proteo-metabolomic Dissection of Extracellular Matrix Reveals Alterations in Cell Wall Integrity and Calcium Signaling Governs Wall-Associated Susceptibility during Stem Rot Disease in Jute. J Proteome Res 2024; 23:3217-3234. [PMID: 38572503 DOI: 10.1021/acs.jproteome.3c00781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
The plant surveillance system confers specificity to disease and immune states by activating distinct molecular pathways linked to cellular functionality. The extracellular matrix (ECM), a preformed passive barrier, is dynamically remodeled at sites of interaction with pathogenic microbes. Stem rot, caused by Macrophomina phaseolina, adversely affects fiber production in jute. However, how wall related susceptibility affects the ECM proteome and metabolome remains undetermined in bast fiber crops. Here, stem rot responsive quantitative temporal ECM proteome and metabolome were developed in jute upon M. phaseolina infection. Morpho-histological examination revealed that leaf shredding was accompanied by reactive oxygen species production in patho-stressed jute. Electron microscopy showed disease progression and ECM architecture remodeling due to necrosis in the later phase of fungal attack. Using isobaric tags for relative and absolute quantitative proteomics and liquid chromatography-tandem mass spectrometry, we identified 415 disease-responsive proteins involved in wall integrity, acidification, proteostasis, hydration, and redox homeostasis. The disease-related correlation network identified functional hubs centered on α-galactosidase, pectinesterase, and thaumatin. Gas chromatography-mass spectrometry analysis pointed toward enrichment of disease-responsive metabolites associated with the glutathione pathway, TCA cycle, and cutin, suberin, and wax metabolism. Data demonstrated that wall-degrading enzymes, structural carbohydrates, and calcium signaling govern rot responsive wall-susceptibility. Proteomics data were deposited in Pride (PXD046937; PXD046939).
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Affiliation(s)
- Md Yasir Arafat
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Kanika Narula
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Mohit Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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La Y, Ma X, Bao P, Chu M, Yan P, Guo X, Liang C. Quantitative Proteomic Analysis Reveals Key Proteins Involved in Testicular Development of Yaks. Int J Mol Sci 2024; 25:8433. [PMID: 39126002 PMCID: PMC11313431 DOI: 10.3390/ijms25158433] [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: 06/24/2024] [Revised: 07/19/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Male reproductive health is largely determined already in the early development of the testis. Although much work has been carried out to study the mechanisms of testicular development and spermatogenesis, there was previously no information on the differences in the protein composition of yak testicles during early development. In this study, the protein profiles in the testicles of 6- (M6), 18- (M18), and 30-month-old (M30) yaks were comparatively analyzed using TMT proteomics. A total of 5521 proteins were identified, with 13, 1295, and 1397 differentially expressed proteins (DEPs) in 30- vs. 18-, 18- vs. 6-, and 30- vs. 6-month-old testes, respectively. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that DEPs were mainly involved in signaling pathways related to testicular development and spermatogenesis, including the MAPK, PI3K-Akt, Wnt, mTOR, TGF-β, and AMPK signaling pathways. Furthermore, we also identified eight potential proteins (TEX101, PDCL2, SYCP2, SYCP3, COL1A1, COL1A2, ADAM10, and ATF1) that may be related to the testicular development and spermatogenesis of yaks. This study may provide new insights into the molecular mechanisms of the testicular development and spermatogenesis of yaks.
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Affiliation(s)
- Yongfu La
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China; (Y.L.); (X.M.); (P.B.); (M.C.); (P.Y.)
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xiaoming Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China; (Y.L.); (X.M.); (P.B.); (M.C.); (P.Y.)
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China; (Y.L.); (X.M.); (P.B.); (M.C.); (P.Y.)
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China; (Y.L.); (X.M.); (P.B.); (M.C.); (P.Y.)
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Ping Yan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China; (Y.L.); (X.M.); (P.B.); (M.C.); (P.Y.)
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China; (Y.L.); (X.M.); (P.B.); (M.C.); (P.Y.)
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Chunnian Liang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China; (Y.L.); (X.M.); (P.B.); (M.C.); (P.Y.)
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
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Larrey EK, Pathak R. Radiation-Induced Intestinal Normal Tissue Toxicity: Implications for Altered Proteome Profile. Genes (Basel) 2022; 13:2006. [PMID: 36360243 PMCID: PMC9689954 DOI: 10.3390/genes13112006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/10/2022] [Accepted: 10/31/2022] [Indexed: 09/12/2023] Open
Abstract
Radiation-induced toxicity to healthy/normal intestinal tissues, especially during radiotherapy, limits the radiation dose necessary to effectively eradicate tumors of the abdomen and pelvis. Although the pathogenesis of intestinal radiation toxicity is highly complex, understanding post-irradiation alterations in protein profiles can provide crucial insights that make radiotherapy safer and more efficient and allow for increasing the radiation dose during cancer treatment. Recent preclinical and clinical studies have advanced our current understanding of the molecular changes associated with radiation-induced intestinal damage by assessing changes in protein expression with mass spectrometry-based approaches and 2-dimensional difference gel electrophoresis. Studies by various groups have demonstrated that proteins that are involved in the inflammatory response, the apoptotic pathway, reactive oxygen species scavenging, and cell proliferation can be targeted to develop effective radiation countermeasures. Moreover, altered protein profiles serve as a crucial biomarkers for intestinal radiation damage. In this review, we present alterations in protein signatures following intestinal radiation damage as detected by proteomics approaches in preclinical and clinical models with the aim of providing a better understanding of how to accomplish intestinal protection against radiation damage.
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Affiliation(s)
- Enoch K. Larrey
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, AR 72205, USA
- Department of Information Science, University of Arkansas at Little Rock, 2801 S University Ave, Little Rock, AR 72204, USA
| | - Rupak Pathak
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, AR 72205, USA
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Liu F, Ye S, Jiang P, Zhang W, Wang Z, Li C. The proteome profiling of EVs originating from senescent cell model using quantitative proteomics and parallel reaction monitoring. J Proteomics 2022; 266:104669. [PMID: 35788408 DOI: 10.1016/j.jprot.2022.104669] [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: 02/21/2022] [Revised: 05/30/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022]
Abstract
Senescence is the inevitable biological processes and is also considered as the biggest risk factor for the development of age - related diseases (ARDs) and geriatric syndrome (GS). Senescence is also known as inflammaging because it is characterized by persistent, long-term, low-grade inflammation named senescence-associated secretory phenotype (SASP). However, the mechanism for the persistence of inflammaging remains largely unclear. To explore the role of extracellular vesicles (EVs) in senescence/inflammaging, we established the cellular senescence model and performed TMT-based comparative quantitative proteomics and parallel reaction monitoring (PRM) to reveal the changes of EVs between young cells and senescent cells. A total of 3966 proteins were quantifiable, of which 132 were up-regulated, 144 were down-regulated, compared with the young cells. Subsequently, we chose 19 proteins involved in inflammation or proliferation to carry out PRM validation analysis. The result indicated that proteins promoting NF-κB signal pathway were up-regulated, and proteins promoting cell proliferation were down-regulated. The study provided a comprehensive altered proteomics profiles of EVs from senescent cells, and the result showed that EVs could serve as information carrier for further research on the pathogenesis and progression of senescence/inflammaging. SIGNIFICANCE: The mechanism of inflammaging occurrence and development has yet been clear. Therefore, this study attempts to provide an improved understanding of inflammaging from the perspective of EVs. The proteomics analysis revealed that the most changed proteins were connected to inflammation signaling pathways, cell growth and cell death, and PRM analysis results showed that proteins involved in NF-κB signal pathway and cell proliferation were more changed. The research systematically analyzed the profiles of proteins in senescence cell model, and the result indicated that further research should focus on the relationship between EVs and senescence/inflammaging.
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Affiliation(s)
- Fengjuan Liu
- Institute of blood transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
| | - Shengliang Ye
- Institute of blood transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
| | - Peng Jiang
- Institute of blood transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
| | - Wei Zhang
- Institute of blood transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China
| | - Zongkui Wang
- Institute of blood transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
| | - Changqing Li
- Institute of blood transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, China.
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Quantitative proteomic analysis of trachea in fatting pig exposed to ammonia. J Proteomics 2021; 247:104330. [PMID: 34302998 DOI: 10.1016/j.jprot.2021.104330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/06/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023]
Abstract
Ammonia (NH3) is considered as the main pollutant in livestock houses and air environment, and its adverse effects on animal and human health have attracted widespread attention. However, trachea proteomics respond to NH3 is lacking, which is crucial to understanding how NH3 induces respiratory damage. In this study, we performed labeled quantitative proteomic (TMT-MS) analysis in the trachea of fatting pigs exposed to NH3 for 30 days. The proteomic results were then validated by Immunohistochemistry (IHC) and Parallel Reaction Monitoring (PRM). The results showed that a total of 126 differentially abundant proteins (DAPs) were identified (fold change <0.83 or > 1.2 and P < 0.05), including 70 differentially up-regulated proteins (DUPs) and 56 differentially down-regulated proteins (DDPs). These proteins were mainly located in intracellular regions and involved in immune response, metabolism and protein synthesis. The results of DAPs (EHHADH, RPL28, SLC25A6, TUBB6, CD14, CTSS, RPS11, RPL19, SLC25A5, RPS8, FABP3, RPL21, RPL34, RPL32, PDIA3, FBP1, HSPH1, SAR1A and SEC24C) verified by IHC and PRM were consistent with the proteomic results. The results of this study provided a basis and a novel insight for understanding the mechanism of NH3-induced tracheal injury. SIGNIFICANCE: Ammonia (NH3) is considered as the main pollutant in livestock houses and air environment, and its adverse effects on animal and human health have attracted widespread attention. However, trachea proteomics respond to NH3 is lacking, which is crucial to understanding how NH3 induces respiratory damage. Therefore, in this study, labeled quantitative proteomics (TMT-MS) was used to detect trachea tissue samples from finishing pigs in NH3 exposure group and control group, and PRM method was used to further verify the highly abundant proteins in NH3 exposure samples, so as to identify new diagnostic markers for NH3 poisoning. The results of this study provided a basis and a novel insight for understanding the molecular pathological mechanism of NH3-induced tracheal injury.
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Liu JC, Chen YT, Hsieh YJ, Wu CC, Huang MC, Hsu YC, Wu CT, Chen CK, Dash S, Yu JS. Association of urinary ketamine and APOA1 levels with bladder dysfunction in ketamine abusers revealed via proteomics and targeted metabolite analyses. Sci Rep 2021; 11:9583. [PMID: 33953300 PMCID: PMC8099891 DOI: 10.1038/s41598-021-89089-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
Chronic ketamine abuse is associated with bladder dysfunction and cystitis. However, the effects of ketamine abuse on the urinary proteome profile and the correlations among urinary proteins, urinary ketamine (and metabolites) and clinicopathological features of ketamine-induced bladder dysfunction remain to be established. Here, we recruited 56 ketamine abusers (KA) and 40 age-matched healthy controls (HC) and applied the iTRAQ-based proteomics approach to unravel quantitative changes in the urine proteome profile between the two groups. Many of the differentially regulated proteins are involved in the complement and coagulation cascades and/or fibrotic disease. Among them, a significant increase in APOA1 levels in KA relative to control samples (392.1 ± 59.9 ng/ml vs. 13.7 ± 32.6 ng/ml, p < 0.0001) was detected via ELISA. Moreover, urinary ketamine, norketamine and dehydronorketamine contents (measured via LC-SRM-MS) were found to be positively correlated with overactive bladder syndrome score (OABSS) and APOA1 levels with urinary RBC, WBC, OABSS and numeric pain rating scale in KA. Collectively, our results may aid in developing new molecular tool(s) for management of ketamine-induced bladder dysfunction. Moreover, information regarding the differentially regulated proteins in urine of KA provides valuable clues to establish the molecular mechanisms underlying ketamine-induced cystitis.
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Affiliation(s)
- Jo-Chuan Liu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Ting Chen
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ya-Ju Hsieh
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Chun Wu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Ming-Chyi Huang
- Department of Addiction Sciences, Taipei City Psychiatric Center, Taipei City Hospital, Taipei, Taiwan.,Department of Psychiatry, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Chao Hsu
- Department of Urology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chun-Te Wu
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Urology, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Chih-Ken Chen
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Psychiatry, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Srinivas Dash
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Jau-Song Yu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan. .,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan. .,Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan. .,Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, 33303, Taiwan.
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