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Abyadeh M, Kaya A. Application of Multiomics Approach to Investigate the Therapeutic Potentials of Stem Cell-derived Extracellular Vesicle Subpopulations for Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593647. [PMID: 38798317 PMCID: PMC11118424 DOI: 10.1101/2024.05.10.593647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Alzheimer's disease (AD) presents a complex interplay of molecular alterations, yet understanding its pathogenesis remains a challenge. In this study, we delved into the intricate landscape of proteome and transcriptome changes in AD brains compared to healthy controls, examining 788 brain samples revealing common alterations at both protein and mRNA levels. Moreover, our analysis revealed distinct protein-level changes in aberrant energy metabolism pathways in AD brains that were not evident at the mRNA level. This suggests that the changes in protein expression could provide a deeper molecular representation of AD pathogenesis. Subsequently, using a comparative proteomic approach, we explored the therapeutic potential of mesenchymal stem cell-derived extracellular vehicles (EVs), isolated through various methods, in mitigating AD-associated changes at the protein level. Our analysis revealed a particular EV-subtype that can be utilized for compensating dysregulated mitochondrial proteostasis in the AD brain. By using network biology approaches, we further revealed the potential regulators of key therapeutic proteins. Overall, our study illuminates the significance of proteome alterations in AD pathogenesis and identifies the therapeutic promise of a specific EV subpopulation with reduced pro-inflammatory protein cargo and enriched proteins to target mitochondrial proteostasis.
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Affiliation(s)
- Morteza Abyadeh
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284 USA
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284 USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA
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Cui P, Zhang Y, Wang C, Xiao B, Wang Q, Zhang L, Li H, Wu C, Tian W. Crucial role of lncRNA NONHSAG037054.2 and GABPA, and their related functional networks, in ankylosing spondylitis. Exp Ther Med 2024; 27:237. [PMID: 38628657 PMCID: PMC11019654 DOI: 10.3892/etm.2024.12525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 02/09/2024] [Indexed: 04/19/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have been previously researched in ankylosing spondylitis (AS). Nevertheless, there are few studies of lncRNAs and mRNAs associated with the pathogenesis of AS. Differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) between AS and normal samples were assessed using the R limma package. DOSE packages and 'clusterProfiler' were exploited for gene enrichment analysis. The functional association of proteins and protein interactions was assessed using the STRING database. To investigate the important genes and subnetworks in the protein-protein interaction network, the MCODE plug-in in the Cytoscape software was utilized. The gene mRNA was examined via reverse transcription-quantitative PCR. In total, 152 DEmRNAs and 204 DElncRNAs were observed between normal and AS samples. A total of 68 candidate genes related to DElncRNA were identified. These candidate genes were enriched in 30 cellular component terms, 22 molecular functions, 83 biological processes, 9 Kyoto Encyclopedia of Genes and Genomes, and 36 disease ontology pathways. NONHSAG037054.2 was the most related lncRNA to genes, and GABPA was the most connected gene to lncRNA in AS. The NCBI/GenBank accession number of the lncRNA NONHSAG037054.2 was not found because it is not included in NCBI. The information of lncRNA NONHSAG037054.2 can be found at the website (http://www.noncode.org/show_gene.php?id=NONHSAG037054 and https://www.genecards.org/cgi-bin/carddisp.pl?gene=ACAP2-IT1). In total, 13 microRNAs (miRNAs) and 46 miRNAs associated with NONHSAG037054.2 and GABPA, respectively, were found. A total of 173 RNA-binding protein genes were associated with both NONHSAG037054.2 and GABPA. In addition, GABPA was downregulated in AS samples, suggesting it may have diagnostic value in AS. In conclusion, NONHSAG037054.2 and GABPA are associated with AS. GABPA was downregulated in AS, and it could serve as a novel diagnostic factor for AS.
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Affiliation(s)
- Penglei Cui
- Department of Spine Surgery, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Yanzhuo Zhang
- Department of Molecular Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Chao Wang
- Department of Molecular Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Bin Xiao
- Department of Spine Surgery, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Qianqian Wang
- Department of Molecular Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Liang Zhang
- Department of Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Hongchao Li
- Department of Rheumatology and Immunology, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Chengai Wu
- Department of Molecular Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Wei Tian
- Department of Spine Surgery, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
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Yin B, Dong B, Guo X, Wang C, Huo H. GABPA protects against gastric cancer deterioration via negatively regulating GPX1. J Med Biochem 2022; 41:355-362. [PMID: 36042907 PMCID: PMC9375539 DOI: 10.5937/jomb0-35445] [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: 12/18/2021] [Accepted: 01/05/2022] [Indexed: 11/18/2022] Open
Abstract
Background To explore the anti-cancer role of GABPA in the progression of gastric cancer (GC), and the underlying mechanism. Methods Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to detect the expression pattern of GABPA in 45 pairs of GC and non-tumoral tissues. The relationship between GABPA expression and clinic pathological indicators of GC patients was analyzed. In AGS and SGC-7901 cells overexpressing GABPA, their migratory ability was determined by trans well and wound healing assay. The interaction between GABPA and its downstream target GPX1 was explored by dual-luciferase reporter assay, and their synergistical regulation on GC cell migration was finally elucidated. Results GABPA was downregulated in GC tissues in comparison to normal ones. Low level of GABPA predicted high incidences of lymphatic and distant metastasis in GC. Overexpression of GABPA blocked AGS and SGC-7901 cells to migrate. GABPA could target GPX1 via the predicted binding site. GPX1 was upregulated in clinical samples of GC, and negatively correlated to GABPA level. The anticancer effect of GABPA on GC relied on the involvement of GPX1. Conclusions GABPA is downregulated in GC samples, which can be utilized to predict GC metastasis. Serving as a tumor suppressor, GABPA blocks GC cells to migrate by targeting GPX1.
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Affiliation(s)
- Binghua Yin
- Handan Central Hospital, CT Room, Handan, China
| | - Bing Dong
- Handan Central Hospital, Department of Gastroenterology, Handan, China
| | - Xiaohui Guo
- Handan Central Hospital, Department of General Surgery, Handan, China
| | - Can Wang
- Handan Central Hospital, Department of General Surgery, Handan, China
| | - Huazhi Huo
- Handan Central Hospital, Department of General Surgery, Handan, China
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Vellingiri B, Iyer M, Devi Subramaniam M, Jayaramayya K, Siama Z, Giridharan B, Narayanasamy A, Abdal Dayem A, Cho SG. Understanding the Role of the Transcription Factor Sp1 in Ovarian Cancer: from Theory to Practice. Int J Mol Sci 2020; 21:E1153. [PMID: 32050495 PMCID: PMC7038193 DOI: 10.3390/ijms21031153] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/01/2020] [Accepted: 02/04/2020] [Indexed: 12/23/2022] Open
Abstract
Ovarian cancer (OC) is one of the deadliest cancers among women contributing to high risk of mortality, mainly owing to delayed detection. There is no specific biomarker for its detection in early stages. However, recent findings show that over-expression of specificity protein 1 (Sp1) is involved in many OC cases. The ubiquitous transcription of Sp1 apparently mediates the maintenance of normal and cancerous biological processes such as cell growth, differentiation, angiogenesis, apoptosis, cellular reprogramming and tumorigenesis. Sp1 exerts its effects on cellular genes containing putative GC-rich Sp1-binding site in their promoters. A better understanding of the mechanisms underlying Sp1 transcription factor (TF) regulation and functions in OC tumorigenesis could help identify novel prognostic markers, to target cancer stem cells (CSCs) by following cellular reprogramming and enable the development of novel therapies for future generations. In this review, we address the structure, function, and biology of Sp1 in normal and cancer cells, underpinning the involvement of Sp1 in OC tumorigenesis. In addition, we have highlighted the influence of Sp1 TF in cellular reprogramming of iPSCs and how it plays a role in controlling CSCs. This review highlights the drugs targeting Sp1 and their action on cancer cells. In conclusion, we predict that research in this direction will be highly beneficial for OC treatment, and chemotherapeutic drugs targeting Sp1 will emerge as a promising therapy for OC.
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Affiliation(s)
- Balachandar Vellingiri
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, India
| | - Mahalaxmi Iyer
- Department of Zoology, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore 641043, India; (M.I.); (K.J.)
| | - Mohana Devi Subramaniam
- Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, Chennai 600006, India;
| | - Kaavya Jayaramayya
- Department of Zoology, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore 641043, India; (M.I.); (K.J.)
| | - Zothan Siama
- Department of Zoology, School of Life-science, Mizoram University, Aizawl 796004, Mizoram, India;
| | - Bupesh Giridharan
- R&D Wing, Sree Balaji Medical College and Hospital (SBMCH), BIHER, Chromepet, Chennai 600044, Tamil Nadu, India;
| | - Arul Narayanasamy
- Disease Proteomics Laboratory, Department of Zoology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India;
| | - Ahmed Abdal Dayem
- Molecular & Cellular Reprogramming Center, Department of Stem Cell & Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea;
| | - Ssang-Goo Cho
- Molecular & Cellular Reprogramming Center, Department of Stem Cell & Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea;
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Na Rangsee N, Yanatatsaneejit P, Pisitkun T, Somparn P, Jintaridth P, Topanurak S. Host proteome linked to HPV E7-mediated specific gene hypermethylation in cancer pathways. Infect Agent Cancer 2020; 15:7. [PMID: 32025240 PMCID: PMC6998090 DOI: 10.1186/s13027-020-0271-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/08/2020] [Indexed: 12/13/2022] Open
Abstract
Background Human papillomavirus (HPV) infection causes around 90% of cervical cancer cases, and cervical cancer is a leading cause of female mortality worldwide. HPV-derived oncoprotein E7 participates in cervical carcinogenesis by inducing aberrant host DNA methylation. However, the targeting specificity of E7 methylation of host genes is not fully understood but is important in the down-regulation of crucial proteins of the hallmark cancer pathways. In this study, we aim to link E7-driven aberrations in the host proteome to corresponding gene promoter hypermethylation events in the hope of providing novel therapeutic targets and biomarkers to indicate the progression of cervical cancer. Methods HEK293 cells were transfected with pcDNA3.1-E7 plasmid and empty vector and subjected to mass spectrometry-based proteomic analysis. Down-regulated proteins (where relative abundance was determined significant by paired T-test) relevant to cancer pathways were selected as gene candidates for mRNA transcript abundance measurement by qPCR and expression compared with that in SiHa cells (HPV type 16 positive). Methylation Specific PCR was used to determine promoter hypermethylation in genes downregulated in both SiHa and transfected HEK293 cell lines. The FunRich and STRING databases were used for identification of potential regulatory transcription factors and the proteins interacting with transcription factor gene candidates, respectively. Results Approximately 400 proteins totally were identified in proteomics analysis. The transcripts of six genes involved in the host immune response and cell proliferation (PTMS, C1QBP, BCAP31, CDKN2A, ZMYM6 and HIST1H1D) were down-regulated, corresponding to proteomic results. Methylation assays showed four gene promoters (PTMS, C1QBP, BCAP31 and CDKN2A) were hypermethylated with 61, 55.5, 70 and 78% increased methylation, respectively. Those four genes can be regulated by the GA-binding protein alpha chain, specificity protein 1 and ETS-like protein-1 transcription factors, as identified from FunRich database predictions. Conclusions HPV E7 altered the HEK293 proteome, particularly with respect to proteins involved in cell proliferation and host immunity. Down-regulation of these proteins appears to be partly mediated via host DNA methylation. E7 possibly complexes with the transcription factors of its targeting genes and DNMT1, allowing methylation of specific target gene promoters.
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Affiliation(s)
- Nopphamon Na Rangsee
- 1Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
| | | | - Trairak Pisitkun
- 3Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Poorichaya Somparn
- 3Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand.,4Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Pornrutsami Jintaridth
- 5Department of Tropical Nutrition and Food Science, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
| | - Supachai Topanurak
- 1Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
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