ProteomesPub Date : 2022-09-13DOI: 10.3390/proteomes10030033
Matthew B O'Rourke, Ben R Roediger, Christopher J Jolly, Ben Crossett, Matthew P Padula, Phillip M Hansbro
{"title":"Viral Biomarker Detection and Validation Using MALDI Mass Spectrometry Imaging (MSI).","authors":"Matthew B O'Rourke, Ben R Roediger, Christopher J Jolly, Ben Crossett, Matthew P Padula, Phillip M Hansbro","doi":"10.3390/proteomes10030033","DOIUrl":"https://doi.org/10.3390/proteomes10030033","url":null,"abstract":"<p><p>(1) Background: MALDI imaging is a technique that still largely depends on time of flight (TOF)-based instrument such as the Bruker UltrafleXtreme. While capable of performing targeted MS/MS, these instruments are unable to perform fragmentation while imaging a tissue section necessitating the reliance of MS1 values for peptide level identifications. With this premise in mind, we have developed a hybrid bioinformatic/image-based method for the identification and validation of viral biomarkers. (2) Methods: Formalin-Fixed Paraffin-Embedded (FFPE) mouse samples were sectioned, mounted and prepared for mass spectrometry imaging using our well-established methods. Peptide identification was achieved by first extracting confident images corresponding to theoretical viral peptides. Next, those masses were used to perform a Peptide Mmass Fingerprint (PMF) searched against known viral FASTA sequences against a background mouse FASTA database. Finally, a correlational analysis was performed with imaging data to confirm pixel-by-pixel colocalization and intensity of viral peptides. (3) Results: 14 viral peptides were successfully identified with significant PMF Scores and a correlational result of >0.79 confirming the presence of the virus and distinguishing it from the background mouse proteins. (4) Conclusions: this novel approach leverages the power of mass spectrometry imaging and provides confident identifications for viral proteins without requiring MS/MS using simple MALDI Time Of Flight/Time Of Flight (TOF/TOF) instrumentation.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9506211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10862284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2022-09-01DOI: 10.3390/proteomes10030031
A D A Shahinuzzaman, Abu Hena Mostafa Kamal, Jayanta K Chakrabarty, Aurchie Rahman, Saiful M Chowdhury
{"title":"Identification of Inflammatory Proteomics Networks of Toll-like Receptor 4 through Immunoprecipitation-Based Chemical Cross-Linking Proteomics.","authors":"A D A Shahinuzzaman, Abu Hena Mostafa Kamal, Jayanta K Chakrabarty, Aurchie Rahman, Saiful M Chowdhury","doi":"10.3390/proteomes10030031","DOIUrl":"https://doi.org/10.3390/proteomes10030031","url":null,"abstract":"<p><p>Toll-like receptor 4 (TLR4) is a receptor on an immune cell that can recognize the invasion of bacteria through their attachment with bacterial lipopolysaccharides (LPS). Hence, LPS is a pro-immune response stimulus. On the other hand, statins are lipid-lowering drugs and can also lower immune cell responses. We used human embryonic kidney (HEK 293) cells engineered to express HA-tagged TLR-4 upon treatment with LPS, statin, and both statin and LPS to understand the effect of pro- and anti-inflammatory responses. We performed a monoclonal antibody (mAb) directed co-immunoprecipitation (CO-IP) of HA-tagged TLR4 and its interacting proteins in the HEK 293 extracted proteins. We utilized an ETD cleavable chemical cross-linker to capture weak and transient interactions with TLR4 protein. We tryptic digested immunoprecipitated and cross-linked proteins on beads, followed by liquid chromatography-mass spectrometry (LC-MS/MS) analysis of the peptides. Thus, we utilized the label-free quantitation technique to measure the relative expression of proteins between treated and untreated samples. We identified 712 proteins across treated and untreated samples and performed protein network analysis using Ingenuity Pathway Analysis (IPA) software to reveal their protein networks. After filtering and evaluating protein expression, we identified macrophage myristoylated alanine-rich C kinase substrate (MARCKSL1) and creatine kinase proteins as a potential part of the inflammatory networks of TLR4. The results assumed that MARCKSL1 and creatine kinase proteins might be associated with a statin-induced anti-inflammatory response due to possible interaction with the TLR4.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9506174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33478569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2022-09-01DOI: 10.3390/proteomes10030030
Fábio Trindade, Ana F Ferreira, Francisca Saraiva, Diana Martins, Vera M Mendes, Carla Sousa, Cristina Gavina, Adelino Leite-Moreira, Bruno Manadas, Inês Falcão-Pires, Rui Vitorino
{"title":"Optimization of a Protocol for Protein Extraction from Calcified Aortic Valves for Proteomics Applications: Development of a Standard Operating Procedure.","authors":"Fábio Trindade, Ana F Ferreira, Francisca Saraiva, Diana Martins, Vera M Mendes, Carla Sousa, Cristina Gavina, Adelino Leite-Moreira, Bruno Manadas, Inês Falcão-Pires, Rui Vitorino","doi":"10.3390/proteomes10030030","DOIUrl":"https://doi.org/10.3390/proteomes10030030","url":null,"abstract":"<p><p>The comprehension of the pathophysiological mechanisms, the identification of druggable targets, and putative biomarkers for aortic valve stenosis can be pursued through holistic approaches such as proteomics. However, tissue homogenization and protein extraction are made difficult by tissue calcification. The reproducibility of proteome studies is key in clinical translation of the findings. Thus, we aimed to optimize a protocol for aortic valve homogenization and protein extraction and to develop a standard operating procedure (SOP), which researchers can use to maximize protein yield while reducing inter-laboratory variability. We have compared the protein yield between conventional tissue grinding in nitrogen followed by homogenization with a Potter apparatus with a more advanced bead-beating system. Once we confirmed the superiority of the latter, we further optimized it by testing the effect of beads size, the number of homogenization cycles, tube capacity, lysis buffer/tissue mass ratio, and two different lysis buffers. Optimal protein extraction was achieved with 2.8 mm zirconium dioxide beads, in two homogenization cycles, in the presence of 20 µL RIPA buffer/mg tissue, using 2 mL O-ring cryotubes. As a proof of concept of the usefulness of this SOP for proteomics, the AV proteome of men and women with aortic stenosis was characterized, resulting in the quantification of proteins across six orders of magnitude and uncovering some putative proteins dysregulated by sex.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9505568/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33478568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Proteomic Applications in Aquatic Environment Studies.","authors":"Nadeeka Thushari Gajahin Gamage, Rina Miyashita, Kazutaka Takahashi, Shuichi Asakawa, Jayan Duminda Mahesh Senevirathna","doi":"10.3390/proteomes10030032","DOIUrl":"https://doi.org/10.3390/proteomes10030032","url":null,"abstract":"<p><p>Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9505238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33478570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2022-08-15DOI: 10.3390/proteomes10030028
Timo Längrich, Kaya Bork, Rüdiger Horstkorte, Veronika Weber, Britt Hofmann, Matt Fuszard, Heidi Olzscha
{"title":"Disturbance of Key Cellular Subproteomes upon Propofol Treatment Is Associated with Increased Permeability of the Blood-Brain Barrier.","authors":"Timo Längrich, Kaya Bork, Rüdiger Horstkorte, Veronika Weber, Britt Hofmann, Matt Fuszard, Heidi Olzscha","doi":"10.3390/proteomes10030028","DOIUrl":"https://doi.org/10.3390/proteomes10030028","url":null,"abstract":"<p><strong>Background: </strong>Propofol is a short-acting anesthetic, which is often used for induction and maintenance of general anesthesia, sedation for mechanically ventilated adults and procedural sedation. Several side effects of propofol are known and a substantial number of patients suffer from post-operative delirium after propofol application. In this study, we analyzed the effect of propofol on the function and protein expression profile on a proteome-wide scale.</p><p><strong>Methods: </strong>We cultured human brain microvascular endothelial cells in absence and presence of propofol and analyzed the permeability of the blood-brain barrier (BBB) by fluorescein passage and protein abundance on a proteome-wide scale by mass spectrometry.</p><p><strong>Results: </strong>Propofol interfered with the function of the blood-brain barrier. This was not due to decreased adhesion of propofol-treated human brain microvascular endothelial cells. The proteomic analysis revealed that some key pathways in these cells were disturbed, such as oxygen metabolism, DNA damage recognition and response to stress.</p><p><strong>Conclusions: </strong>Propofol has strong effects on protein expression which could explain several side effects of propofol.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9397097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40649131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Metabolomics in Team-Sport Athletes: Current Knowledge, Challenges, and Future Perspectives.","authors":"Tindaro Bongiovanni, Mathieu Lacome, Vassilios Fanos, Giulia Martera, Erika Cione, Roberto Cannataro","doi":"10.3390/proteomes10030027","DOIUrl":"https://doi.org/10.3390/proteomes10030027","url":null,"abstract":"<p><p>Metabolomics is a promising tool for studying exercise physiology and exercise-associated metabolism. It has recently been defined with the term \"sportomics\" due to metabolomics' capability to characterize several metabolites in several biological samples simultaneously. This narrative review on exercise metabolomics provides an initial and brief overview of the different metabolomics technologies, sample collection, and further processing steps employed for sport. It also discusses the data analysis and its biological interpretation. Thus, we do not cover sample collection, preparation, and analysis paragraphs in detail here but outline a general outlook to help the reader to understand the metabolomics studies conducted in team-sports athletes, alongside endeavoring to recognize existing or emergent trends and deal with upcoming directions in the field of exercise metabolomics in a team-sports setting.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9396992/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40649130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2022-08-01DOI: 10.3390/proteomes10030026
Shivangi Awasthi, Daniel S Spellman, Nathan G Hatcher
{"title":"Proteomic Discovery and Validation of Novel Fluid Biomarkers for Improved Patient Selection and Prediction of Clinical Outcomes in Alzheimer's Disease Patient Cohorts.","authors":"Shivangi Awasthi, Daniel S Spellman, Nathan G Hatcher","doi":"10.3390/proteomes10030026","DOIUrl":"https://doi.org/10.3390/proteomes10030026","url":null,"abstract":"<p><p>Alzheimer's disease (AD) is an irreversible neurodegenerative disease characterized by progressive cognitive decline. The two cardinal neuropathological hallmarks of AD include the buildup of cerebral β amyloid (Aβ) plaques and neurofibrillary tangles of hyperphosphorylated tau. The current disease-modifying treatments are still not effective enough to lower the rate of cognitive decline. There is an urgent need to identify early detection and disease progression biomarkers that can facilitate AD drug development. The current established readouts based on the expression levels of amyloid beta, tau, and phospho-tau have shown many discrepancies in patient samples when linked to disease progression. There is an urgent need to identify diagnostic and disease progression biomarkers from blood, cerebrospinal fluid (CSF), or other biofluids that can facilitate the early detection of the disease and provide pharmacodynamic readouts for new drugs being tested in clinical trials. Advances in proteomic approaches using state-of-the-art mass spectrometry are now being increasingly applied to study AD disease mechanisms and identify drug targets and novel disease biomarkers. In this report, we describe the application of quantitative proteomic approaches for understanding AD pathophysiology, summarize the current knowledge gained from proteomic investigations of AD, and discuss the development and validation of new predictive and diagnostic disease biomarkers.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9397030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40649129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2022-07-20DOI: 10.3390/proteomes10030025
Donatella Pia Spanò, Simone Bonelli, Matteo Calligaris, Anna Paola Carreca, Claudia Carcione, Giovanni Zito, Aldo Nicosia, Sergio Rizzo, Simone Dario Scilabra
{"title":"High-Resolution Secretome Analysis of Chemical Hypoxia Treated Cells Identifies Putative Biomarkers of Chondrosarcoma.","authors":"Donatella Pia Spanò, Simone Bonelli, Matteo Calligaris, Anna Paola Carreca, Claudia Carcione, Giovanni Zito, Aldo Nicosia, Sergio Rizzo, Simone Dario Scilabra","doi":"10.3390/proteomes10030025","DOIUrl":"https://doi.org/10.3390/proteomes10030025","url":null,"abstract":"<p><p>Chondrosarcoma is the second most common bone tumor, accounting for 20% of all cases. Little is known about the pathology and molecular mechanisms involved in the development and in the metastatic process of chondrosarcoma. As a consequence, there are no approved therapies for this tumor and surgical resection is the only treatment currently available. Moreover, there are no available biomarkers for this type of tumor, and chondrosarcoma classification relies on operator-dependent histopathological assessment. Reliable biomarkers of chondrosarcoma are urgently needed, as well as greater understanding of the molecular mechanisms of its development for translational purposes. Hypoxia is a central feature of chondrosarcoma progression. The hypoxic tumor microenvironment of chondrosarcoma triggers a number of cellular events, culminating in increased invasiveness and migratory capability. Herein, we analyzed the effects of chemically-induced hypoxia on the secretome of SW 1353, a human chondrosarcoma cell line, using high-resolution quantitative proteomics. We found that hypoxia induced unconventional protein secretion and the release of proteins associated to exosomes. Among these proteins, which may be used to monitor chondrosarcoma development, we validated the increased secretion in response to hypoxia of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme well-known for its different functional roles in a wide range of tumors. In conclusion, by analyzing the changes induced by hypoxia in the secretome of chondrosarcoma cells, we identified molecular mechanisms that can play a role in chondrosarcoma progression and pinpointed proteins, including GAPDH, that may be developed as potential biomarkers for the diagnosis and therapeutic management of chondrosarcoma.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40634434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2022-07-02DOI: 10.3390/proteomes10030024
Luís M Ramalhete, Rúben Araújo, Aníbal Ferreira, Cecília R C Calado
{"title":"Proteomics for Biomarker Discovery for Diagnosis and Prognosis of Kidney Transplantation Rejection.","authors":"Luís M Ramalhete, Rúben Araújo, Aníbal Ferreira, Cecília R C Calado","doi":"10.3390/proteomes10030024","DOIUrl":"https://doi.org/10.3390/proteomes10030024","url":null,"abstract":"<p><p>Renal transplantation is currently the treatment of choice for end-stage kidney disease, enabling a quality of life superior to dialysis. Despite this, all transplanted patients are at risk of allograft rejection processes. The gold-standard diagnosis of graft rejection, based on histological analysis of kidney biopsy, is prone to sampling errors and carries high costs and risks associated with such invasive procedures. Furthermore, the routine clinical monitoring, based on urine volume, proteinuria, and serum creatinine, usually only detects alterations after graft histologic damage and does not differentiate between the diverse etiologies. Therefore, there is an urgent need for new biomarkers enabling to predict, with high sensitivity and specificity, the rejection processes and the underlying mechanisms obtained from minimally invasive procedures to be implemented in routine clinical surveillance. These new biomarkers should also detect the rejection processes as early as possible, ideally before the 78 clinical outputs, while enabling balanced immunotherapy in order to minimize rejections and reducing the high toxicities associated with these drugs. Proteomics of biofluids, collected through non-invasive or minimally invasive analysis, e.g., blood or urine, present inherent characteristics that may provide biomarker candidates. The current manuscript reviews biofluids proteomics toward biomarkers discovery that specifically identify subclinical, acute, and chronic immune rejection processes while allowing for the discrimination between cell-mediated or antibody-mediated processes. In time, these biomarkers will lead to patient risk stratification, monitoring, and personalized and more efficient immunotherapies toward higher graft survival and patient quality of life.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10704787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2022-06-28DOI: 10.3390/proteomes10030023
Ang Luo, Rongrong Hao, Xia Zhou, Yangfan Jia, Haiyang Tang
{"title":"Integrative Proteomic and Phosphoproteomic Analyses of Hypoxia-Treated Pulmonary Artery Smooth Muscle Cells.","authors":"Ang Luo, Rongrong Hao, Xia Zhou, Yangfan Jia, Haiyang Tang","doi":"10.3390/proteomes10030023","DOIUrl":"https://doi.org/10.3390/proteomes10030023","url":null,"abstract":"<p><p>Abnormal proliferation of pulmonary artery smooth muscle cells (PASMCs) is one of the main causes of pulmonary vascular remodeling in pulmonary arterial hypertension (PAH). Hypoxia is an important factor related to PAH and can induce the excessive proliferation of PASMCs and inhibit apoptosis. To explore the possible mechanism of hypoxia-related PAH, human PASMCs are exposed to hypoxia for 24 h and tandem mass tag (TMT)-based quantitative proteomic and phosphoproteomic analyses are performed. Proteomic analysis revealed 134 proteins are significantly changed (p < 0.05, |log2 (fold change)| > log2 [1.1]), of which 48 proteins are upregulated and 86 are downregulated. Some of the changed proteins are verified by using qRT-PCR and Western blotting. Phosphoproteomic analysis identified 404 significantly changed (p < 0.05, |log2 (fold change)| > log2 [1.1]) phosphopeptides. Among them, 146 peptides are upregulated while 258 ones are downregulated. The kinase-substrate enrichment analysis revealed kinases such as P21 protein-activated kinase 1/2/4 (PAK1/2/4), protein-kinase cGMP-dependent 1 and 2 (PRKG1/2), and mitogen-activated protein-kinase 4/6/7 (MAP2K4/6/7) are significantly enriched and activated. For all the significantly changed proteins or phosphoproteins, a comprehensive pathway analysis is performed. In general, this study furthers our understanding of the mechanism of hypoxia-induced PAH.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10872396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}