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Wang W, Shi W, Wang Y, Yang Y, Li P, Zeng Z, Hu W, Chen Y, Tang D, Dai Y. Systematic proteomics profiling of lysine crotonylation of the lung at Pseudoglandular and Canalicular phases in human fetus. Proteome Sci 2023; 21:22. [PMID: 38041078 PMCID: PMC10691156 DOI: 10.1186/s12953-023-00215-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/28/2023] [Indexed: 12/03/2023] Open
Abstract
Lung tissue is an important organ of the fetus, and genomic research on its development has improved our understanding of the biology of this tissue. However, the proteomic research of developing fetal lung tissue is still very scarce. We conducted comprehensive analysis of two developmental stages of fetal lung tissue of proteomics. It showed the developmental characteristics of lung tissue, such as the down-regulation of metabolism-related protein expression, the up-regulation of cell cycle-related proteins, and the regulation in proteins and pathways related to lung development. In addition, we also discovered some key core proteins related to lung development, and provided some key crotonylation modification sites that regulation during lung tissue development. Our comprehensive analysis of lung proteomics can provide a more comprehensive understanding of the developmental status of lung tissue, and provide a certain reference for future research and epigenetics of lung tissue.
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Affiliation(s)
- Wei Wang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China
| | - Wei Shi
- Department of Obstetrics and Gynecology, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern, University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China
| | - Yinglan Wang
- Department of Obstetrics and Gynecology, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern, University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China
| | - Yane Yang
- Shenzhen Far East Women & Children Hospital, Shenzhen, 518000, Guangdong, China
| | - Ping Li
- Shenzhen Far East Women & Children Hospital, Shenzhen, 518000, Guangdong, China
| | - Zhipeng Zeng
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China
| | - Wenlong Hu
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China
| | - Yumei Chen
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China
| | - Donge Tang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China.
| | - Yong Dai
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China.
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Hwang M, Assassi S, Zheng J, Castillo J, Chavez R, Vanarsa K, Mohan C, Reveille J. Quantitative proteomic screening uncovers candidate diagnostic and monitoring serum biomarkers of ankylosing spondylitis. Arthritis Res Ther 2023; 25:57. [PMID: 37041650 PMCID: PMC10088143 DOI: 10.1186/s13075-023-03044-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/30/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND We sought to discover serum biomarkers of ankylosing spondylitis (AS) for diagnosis and monitoring disease activity. METHODS We studied biologic-treatment-naïve AS and healthy control (HC) patients' sera. Eighty samples matched by age, gender, and race (1:1:1 ratio) for AS patients with active disease, inactive disease, and HC were analyzed with SOMAscan™, an aptamer-based discovery platform. T-tests tests were performed for high/low-disease activity AS patients versus HCs (diagnosis) and high versus low disease activity (Monitoring) in a 2:1 and 1:1 ratio, respectively, to identify differentially expressed proteins (DEPs). We used the Cytoscape Molecular Complex Detection (MCODE) plugin to find clusters in protein-protein interaction networks and Ingenuity Pathway Analysis (IPA) for upstream regulators. Lasso regression analysis was performed for diagnosis. RESULTS Of the 1317 proteins detected in our diagnosis and monitoring analyses, 367 and 167 (317 and 59, FDR-corrected q < .05) DEPs, respectively, were detected. MCODE identified complement, IL-10 signaling, and immune/interleukin signaling as the top 3 diagnosis PPI clusters. Complement, extracellular matrix organization/proteoglycans, and MAPK/RAS signaling were the top 3 monitoring PPI clusters. IPA showed interleukin 23/17 (interleukin 22, interleukin 23A), TNF (TNF receptor-associated factor 3), cGAS-STING (cyclic GMP-AMP synthase, Stimulator of Interferon Gene 1), and Jak/Stat (Signal transducer and activator of transcription 1), signaling in predicted upstream regulators. Lasso regression identified a Diagnostic 13-protein model predictive of AS. This model had a sensitivity of 0.75, specificity of 0.90, a kappa of 0.59, and overall accuracy of 0.80 (95% CI: 0.61-0.92). The AS vs HC ROC curve was 0.79 (95% CI: 0.61-0.96). CONCLUSION We identified multiple candidate AS diagnostic and disease activity monitoring serum biomarkers using a comprehensive proteomic screen. Enrichment analysis identified key pathways in AS diagnosis and monitoring. Lasso regression identified a multi-protein panel with modest predictive ability.
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Affiliation(s)
- Mark Hwang
- McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin MSB.5270, TX, 77030, Houston, USA.
| | - Shervin Assassi
- McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin MSB.5270, TX, 77030, Houston, USA
| | - Jim Zheng
- School of Biomedical Informatics, UTHealth Houston, Houston, TX, USA
| | | | - Reyna Chavez
- McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin MSB.5270, TX, 77030, Houston, USA
| | - Kamala Vanarsa
- Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Chandra Mohan
- Biomedical Engineering, University of Houston, Houston, TX, USA
| | - John Reveille
- McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin MSB.5270, TX, 77030, Houston, USA
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Yu Z, Hong X, Zhang X, Zheng F, Liu F, Xu H, Zhu C, Cai W, Liu D, Yin L, Hu B, Tang D, Dai Y. Global Proteomic Analyses Reveals Abnormal Immune Regulation in Patients With New Onset Ankylosing Spondylitis. Front Immunol 2022; 13:838891. [PMID: 35371008 PMCID: PMC8967996 DOI: 10.3389/fimmu.2022.838891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundAnkylosing spondylitis (AS) is a chronic inflammatory disease with serious consequences and a high rate of morbidity and mortality, In our previous work, we reveal the key features of proteins in new-onset ankylosing spondylitis patients.Material and MethodsAnkylosing spondylitis (AS) is a chronic inflammatory condition that affects the spine, and inflammation plays an essential role in AS pathogenesis. The inflammatory process in AS, however, is still poorly understood due to its intricacy. Systematic proteomic and phosphorylation analyses of peripheral blood mononuclear cells (PBMCs) were used to investigate potential pathways involved in AS pathogenesis.ResultsLiquid chromatography-tandem mass spectrometry (LC–MS/MS) analysis was performed and discovered 782 differentially expressed proteins (DEPs) and 122 differentially phosphorylated proteins (DPPs) between 9 new-onset AS patients and 9 healthy controls. The DEPs were further verified using parallel reaction monitoring (PRM) analysis. PRM analysis verified that 3 proteins (HSP90AB1, HSP90AA1 and HSPA8) in the antigen processing and presentation pathway, 6 proteins (including ITPR1, MYLK and STIM1) in the platelet activation pathway and 10 proteins (including MYL12A, MYL9 and ROCK2) in the leukocyte transendothelial migration pathway were highly expressed in the PBMCs of AS patients.ConclusionThe key proteins involved in antigen processing and presentation, platelet activation and leukocyte transendothelial migration revealed abnormal immune regulation in patients with new-onset AS. These proteins might be used as candidate markers for AS diagnosis and new therapeutic targets, as well as elucidating the pathophysiology of AS.
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Affiliation(s)
- Zongchao Yu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Xiaoping Hong
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Xiaoli Zhang
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Fengping Zheng
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Fanna Liu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Huixuan Xu
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Chengxin Zhu
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Wanxia Cai
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Dongzhou Liu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Lianghong Yin
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Bo Hu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
- *Correspondence: Yong Dai, ; Bo Hu, ; Donge Tang,
| | - Donge Tang
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
- *Correspondence: Yong Dai, ; Bo Hu, ; Donge Tang,
| | - Yong Dai
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
- *Correspondence: Yong Dai, ; Bo Hu, ; Donge Tang,
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Shangguan Y, Wang Y, Shi W, Guo R, Zeng Z, Hu W, Cai W, Yan Q, Xu Y, Tang D, Dai Y. Systematic proteomics analysis of lysine acetylation reveals critical features of placental proteins in pregnant women with preeclampsia. J Cell Mol Med 2021; 25:10614-10626. [PMID: 34697885 PMCID: PMC8581308 DOI: 10.1111/jcmm.16997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/01/2021] [Accepted: 09/30/2021] [Indexed: 12/14/2022] Open
Abstract
Preeclampsia (PE) is a dangerous hypertensive disorder that occurs during pregnancy. The specific aetiology and pathogenesis of PE have yet to be clarified. To better reveal the specific pathogenesis of PE, we characterized the proteome and acetyl proteome (acetylome) profile of placental tissue from PE and normal-term pregnancy by label-free quantification proteomics technology and PRM analysis. In this research, 373 differentially expressed proteins (DEPs) were identified by proteome analysis. Functional enrichment analysis revealed significant enrichment of DEPs related to angiogenesis and the immune system. COL12A1, C4BPA and F13A1 may be potential biomarkers for PE diagnosis and new therapeutic targets. Additionally, 700 Kac sites were identified on 585 differentially acetylated proteins (DAPs) by acetylome analyses. These DAPs may participate in the occurrence and development of PE by affecting the complement and coagulation cascades pathway, which may have important implications for better understand the pathogenesis of PE. In conclusion, this study systematically analysed the reveals critical features of placental proteins in pregnant women with PE, providing a resource for exploring the contribution of lysine acetylation modification to PE.
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Affiliation(s)
- Yu Shangguan
- Clinical Medical Research CenterGuangdong Provincial Engineering Research Center of Autoimmune Disease Precision MedicineShenzhen Engineering Research Center of Autoimmune DiseaseThe Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and TechnologyShenzhen People's HospitalShenzhenChina
- Guangxi Key Laboratory of Metabolic Disease ResearchNephrology Department924st HospitalGuilinChina
- College of Life ScienceGuangxi Normal UniversityGuilinChina
| | - Yinglan Wang
- Clinical Medical Research CenterGuangdong Provincial Engineering Research Center of Autoimmune Disease Precision MedicineShenzhen Engineering Research Center of Autoimmune DiseaseThe Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and TechnologyShenzhen People's HospitalShenzhenChina
| | - Wei Shi
- Clinical Medical Research CenterGuangdong Provincial Engineering Research Center of Autoimmune Disease Precision MedicineShenzhen Engineering Research Center of Autoimmune DiseaseThe Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and TechnologyShenzhen People's HospitalShenzhenChina
| | - Ruonan Guo
- Clinical Medical Research CenterGuangdong Provincial Engineering Research Center of Autoimmune Disease Precision MedicineShenzhen Engineering Research Center of Autoimmune DiseaseThe Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and TechnologyShenzhen People's HospitalShenzhenChina
| | - Zhipeng Zeng
- Clinical Medical Research CenterGuangdong Provincial Engineering Research Center of Autoimmune Disease Precision MedicineShenzhen Engineering Research Center of Autoimmune DiseaseThe Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and TechnologyShenzhen People's HospitalShenzhenChina
| | - Wenlong Hu
- Clinical Medical Research CenterGuangdong Provincial Engineering Research Center of Autoimmune Disease Precision MedicineShenzhen Engineering Research Center of Autoimmune DiseaseThe Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and TechnologyShenzhen People's HospitalShenzhenChina
| | - Wanxia Cai
- Clinical Medical Research CenterGuangdong Provincial Engineering Research Center of Autoimmune Disease Precision MedicineShenzhen Engineering Research Center of Autoimmune DiseaseThe Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and TechnologyShenzhen People's HospitalShenzhenChina
| | - Qiang Yan
- Guangxi Key Laboratory of Metabolic Disease ResearchNephrology Department924st HospitalGuilinChina
- College of Life ScienceGuangxi Normal UniversityGuilinChina
| | - Yong Xu
- Clinical Medical Research CenterGuangdong Provincial Engineering Research Center of Autoimmune Disease Precision MedicineShenzhen Engineering Research Center of Autoimmune DiseaseThe Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and TechnologyShenzhen People's HospitalShenzhenChina
| | - Donge Tang
- Clinical Medical Research CenterGuangdong Provincial Engineering Research Center of Autoimmune Disease Precision MedicineShenzhen Engineering Research Center of Autoimmune DiseaseThe Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and TechnologyShenzhen People's HospitalShenzhenChina
| | - Yong Dai
- Clinical Medical Research CenterGuangdong Provincial Engineering Research Center of Autoimmune Disease Precision MedicineShenzhen Engineering Research Center of Autoimmune DiseaseThe Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and TechnologyShenzhen People's HospitalShenzhenChina
- Guangxi Key Laboratory of Metabolic Disease ResearchNephrology Department924st HospitalGuilinChina
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