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Qadri S, Sohail MU, Akhtar N, Pir GJ, Yousif G, Pananchikkal SV, Al-Noubi M, Choi S, Shuaib A, Haik Y, Parray A, Schmidt F. Mass spectrometry-based proteomic profiling of extracellular vesicle proteins in diabetic and non-diabetic ischemic stroke patients: a case-control study. Front Mol Biosci 2024; 11:1387859. [PMID: 38948080 PMCID: PMC11211575 DOI: 10.3389/fmolb.2024.1387859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/23/2024] [Indexed: 07/02/2024] Open
Abstract
Acute ischemic stroke is the most common cause of neurologic dysfunction caused by focal brain ischemia and tissue injury. Diabetes is a major risk factor of stroke, exacerbating disease management and prognosis. Therefore, discovering new diagnostic markers and therapeutic targets is critical for stroke prevention and treatment. Extracellular vesicles (EVs), with their distinctive properties, have emerged as promising candidates for biomarker discovery and therapeutic application. This case-control study utilized mass spectrometry-based proteomics to compare EVs from non-diabetic stroke (nDS = 14), diabetic stroke (DS = 13), and healthy control (HC = 12) subjects. Among 1288 identified proteins, 387 were statistically compared. Statistical comparisons using a general linear model (log2 foldchange ≥0.58 and FDR-p≤0.05) were performed for nDS vs HC, DS vs HC, and DS vs nDS. DS vs HC and DS vs nDS comparisons produced 123 and 149 differentially expressed proteins, respectively. Fibrinogen gamma chain (FIBG), Fibrinogen beta chain (FIBB), Tetratricopeptide repeat protein 16 (TTC16), Proline rich 14-like (PR14L), Inhibitor of nuclear factor kappa-B kinase subunit epsilon (IKKE), Biorientation of chromosomes in cell division protein 1-like 1 (BD1L1), and protein PR14L exhibited significant differences in the DS group. The pathway analysis revealed that the complement system pathways were activated, and blood coagulation and neuroprotection were inhibited in the DS group (z-score ≥2; p ≤ 0.05). These findings underscore the potential of EVs proteomics in identifying biomarkers for stroke management and prevention, warranting further clinical investigation.
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Affiliation(s)
- Shahnaz Qadri
- Department of Pharmaceutical Sciences, Irma Lerma Rangel School of Pharmacy, Texas A&M University, Kingsville, TX, United States
- Sustainability Division, College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Naveed Akhtar
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Ghulam Jeelani Pir
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Ghada Yousif
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Muna Al-Noubi
- Proteomics Core, Weill Cornell Medicine, Doha, Qatar
| | - Sunkyu Choi
- Proteomics Core, Weill Cornell Medicine, Doha, Qatar
| | - Ashfaq Shuaib
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Yousef Haik
- Department of Mechanical and Nuclear Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Aijaz Parray
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Frank Schmidt
- Proteomics Core, Weill Cornell Medicine, Doha, Qatar
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Zamani M, Ebrahimtabar F, Alizadeh-Tabari S, Kasner SE, Elkind MSV, Ananthakrishnan AN, Choden T, Rubin DT, Malekzadeh R. Risk of Common Neurological Disorders in Adult Patients with Inflammatory Bowel Disease: A Systematic Review and Meta-analysis. Inflamm Bowel Dis 2024:izae012. [PMID: 38271615 DOI: 10.1093/ibd/izae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Indexed: 01/27/2024]
Abstract
BACKGROUND Several studies investigated the risks of neurological conditions in patients with inflammatory bowel disease (IBD), with some variability in findings. We aimed to perform a systematic review and meta-analysis of available evidence to elucidate the association between IBD and the risks of common neurological disorders. METHODS We conducted a literature search through Embase, PubMed, Scopus, and ProQuest databases from inception to June 30, 2023, to identify cohort studies assessing the risk of developing stroke, all-cause dementia, Parkinson's disease (PD), multiple sclerosis (MS), seizure/epilepsy, and peripheral neuropathy in adult IBD patients compared with non-IBD population. We combined hazard ratios (HRs) with 95% confidence intervals (CIs) to compute pooled estimates using a random-effects model. RESULTS In total, 22 cohort studies were included, of which 9 studies reported 7074 stroke events in 202 460 IBD patients, 5 studies reported 3783 all-cause dementia diagnoses in 109 602 IBD patients, 7 studies reported 932 PD diagnoses in 354 792 IBD patients, and 1 study reported 6 MS events in 35 581 IBD patients. We observed increased risks of incident stroke (pooled HR = 1.19; 95% CI, 1.06-1.31), all-cause dementia (pooled HR = 1.22; 95% CI, 1.05-1.38), PD (pooled HR = 1.39; 95% CI, 1.20-1.58), and MS (HR = 2.89; 95% CI, 1.02-8.42). No eligible studies were found on peripheral neuropathy and seizure/epilepsy. CONCLUSIONS Inflammatory bowel disease may be modestly associated with increased risks of stroke, all-cause dementia, and PD. Further longitudinal studies are warranted to investigate potential links with MS, seizure/epilepsy, and peripheral neuropathy, as well as their clinical significance.
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Affiliation(s)
- Mohammad Zamani
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Shaghayegh Alizadeh-Tabari
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Scott E Kasner
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Mitchell S V Elkind
- Department of Neurology, Vagelos College of Physicians and Surgeons, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Tenzin Choden
- Inflammatory Bowel Disease Center, University of Chicago Medicine, Chicago, IL, USA
| | - David T Rubin
- Inflammatory Bowel Disease Center, University of Chicago Medicine, Chicago, IL, USA
| | - Reza Malekzadeh
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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Abd ELhafeez AS, Ghanem HM, Swellam M, Taha AM. Involvement of FAM170B-AS1, hsa-miR-1202, and hsa-miR-146a-5p in breast cancer. Cancer Biomark 2024; 39:313-333. [PMID: 38250762 DOI: 10.3233/cbm-230396] [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: 01/23/2024]
Abstract
BACKGROUND FAM170B-AS1 is usually expressed low in all organs except for testicular tissues. No study was performed to explore its role in breast cancer (BC). Contradictory results were reported about hsa-miR-1202 and hsa-miR-146a-5p in BC. OBJECTIVE The present study aimed to explore the involvement of FAM170B-AS1 in BC using bioinformatics predictive tools, followed by a practical validation besides exploring the impact of hsa-miR-1202 and hsa-miR-146a-5p in BC. METHODS This study enrolled 96 female patients with BC, 30 patients with benign breast diseases (BBD), and 25 control subjects. The expressions of circulating FAM170B-AS1, hsa-miR-1202, and hsa-miR-146a-5p were quantified using qRT-PCR. These ncRNAs' associations, predictive, and diagnostic roles in BC were statistically tested. The underlying miRNA/mRNA targets of FAM170B-AS1 in BC were bioinformatically predicted followed by confirmation based on the GEPIA and TCGA databases. RESULTS The expression of FAM170B-AS1 was upregulated in sera of BC patients and hsa-miR-1202 was upregulated in sera of BBD and BC patients while that of hsa-miR-146a-5p was downregulated in BC. These FAM170B-AS1 was significantly associated with BC when compared to BBD. FAM170B-AS1 and hsa-miR-1202 were statistically associated with the BC's stage, grade, and LN metastasis. FAM170B-AS1 and hsa-miR-146a-5p gave the highest specificity and sensitivity for BC. KRAS and EGFR were predicted to be targeted by FAM170B-AS1 through interaction with hsa-miR-143-3p and hsa-miR-7-5p, respectively. Based on the TCGA database, cancer patients having mutations in FAM170B show good overall survival. CONCLUSIONS The present study reported that for the first time, FAM170B-AS1 may be a potential risk factor, predictive, and diagnostic marker for BC. In addition, FAM170B-AS1 might be involved in BC by interacting with hsa-miR-143-3p/KRAS and hsa-miR-7-5p/EGFR through enhancement or repression that may present a new therapeutic option for BC.
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Affiliation(s)
| | - Hala Mostafa Ghanem
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Menha Swellam
- Biochemistry Department, Biotechnology Research Institute, National Research Centre, Dokki, Giza, Egypt
- High Throughput Molecular and Genetic laboratory, Central Laboratories Network and the Centers of Excellence, National Research Centre, Dokki, Giza, Egypt
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Wang M, Gao Y, Chen H, Shen Y, Cheng J, Wang G. Bioinformatics strategies to identify differences in molecular biomarkers for ischemic stroke and myocardial infarction. Medicine (Baltimore) 2023; 102:e35919. [PMID: 37986378 PMCID: PMC10659606 DOI: 10.1097/md.0000000000035919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 11/22/2023] Open
Abstract
Ischemic strokes (ISs) are commonly treated by intravenous thrombolysis using a recombinant tissue plasminogen activator; however, successful treatment can only occur within 3 hours after the stroke. Therefore, it is crucial to determine the causes and underlying molecular mechanisms, identify molecular biomarkers for early diagnosis, and develop precise preventive treatments for strokes. We aimed to clarify the differences in gene expression, molecular mechanisms, and drug prediction approaches between IS and myocardial infarction (MI) using comprehensive bioinformatics analysis. The pathogenesis of these diseases was explored to provide directions for future clinical research. The IS (GSE58294 and GSE16561) and MI (GSE60993 and GSE141512) datasets were downloaded from the Gene Expression Omnibus database. IS and MI transcriptome data were analyzed using bioinformatics methods, and the differentially expressed genes (DEGs) were screened. A protein-protein interaction network was constructed using the STRING database and visualized using Cytoscape, and the candidate genes with high confidence scores were identified using Degree, MCC, EPC, and DMNC in the cytoHubba plug-in. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the DEGs were performed using the database annotation, visualization, and integrated discovery database. Network Analyst 3.0 was used to construct transcription factor (TF) - gene and microRNA (miRNA) - gene regulatory networks of the identified candidate genes. The DrugBank 5.0 database was used to identify gene-drug interactions. After bioinformatics analysis of IS and MI microarray data, 115 and 44 DEGS were obtained in IS and MI, respectively. Moreover, 8 hub genes, 2 miRNAs, and 3 TFs for IS and 8 hub genes, 13 miRNAs, and 2 TFs for MI were screened. The molecular pathology between IS and MI presented differences in terms of GO and KEGG enrichment pathways, TFs, miRNAs, and drugs. These findings provide possible directions for the diagnosis of IS and MI in the future.
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Affiliation(s)
- Min Wang
- School of Clinical Medicine, Dali University, Dali, Yunnan, P.R. China
| | - Yuan Gao
- School of Clinical Medicine, Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Huaqiu Chen
- Xichang People’s Hospital, Xichang, Sichuan, P.R. China
| | - Ying Shen
- The First Hospital of Liangshan, Xichang, Sichuan, P.R. China
| | - Jianjie Cheng
- The First Affiliated Hospital of Dali University, Yunnan, P.R. China
| | - Guangming Wang
- School of Clinical Medicine, Dali University, Dali, Yunnan, P.R. China
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan, P.R. China
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