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Pei X, Luo Y, Zeng H, Jamil M, Liu X, Jiang B. Identification and validation of key genes in gastric cancer: insights from in silico analysis, clinical samples, and functional assays. Aging (Albany NY) 2024; 16:205965. [PMID: 38913913 DOI: 10.18632/aging.205965] [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: 12/19/2023] [Accepted: 05/16/2024] [Indexed: 06/26/2024]
Abstract
INTRODUCTION The underlying mechanisms of gastric cancer (GC) remain unknown. Therefore, in this study, we employed a comprehensive approach, combining computational and experimental methods, to identify potential key genes and unveil the underlying pathogenesis and prognosis of GC. METHODS Gene expression profiles from GEO databases (GSE118916, GSE79973, and GSE29272) were analyzed to identify DEGs between GC and normal tissues. A PPI network was constructed using STRING and Cytoscape, followed by hub gene identification with CytoHubba. Investigations included expression and promoter methylation analysis, survival modeling, mutational and miRNA analysis, gene enrichment, drug prediction, and in vitro assays for cellular behaviors. RESULTS A total of 83 DEGs were identified in the three datasets, comprising 41 up-regulated genes and 42 down-regulated genes. Utilizing the degree and MCC methods, we identified four hub genes that were hypomethylated and up-regulated: COL1A1, COL1A2, COL3A1, and FN1. Subsequent validation of their expression and promoter methylation on clinical GC samples through targeted bisulfite sequencing and RT-qPCR analysis further confirmed the hypomethylation and overexpression of these genes in local GC patients. Furthermore, it was observed that these hub genes regulate tumor proliferation and metastasis in in vivo and exhibited mutations in GC patients. CONCLUSION We found four potential diagnostic and prognostic biomarkers, including COL1A1, COL1A2, COL3A1, and FN1 that may be involved in the occurrence and progression of GC.
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Affiliation(s)
- Xiaofeng Pei
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Yuanling Luo
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Huanwen Zeng
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Muhammad Jamil
- PARC Arid Zone Research Center, Dera Ismail Khan 29050, Pakistan
| | - Xiaodong Liu
- Department of Pharmacy, The 922 Hospital of Joint Logistics Support Force, PLA, Hengyang 421002, China
| | - Bo Jiang
- Department of Emergency, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
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Doherty EL, Krohn G, Warren EC, Patton A, Whitworth CP, Rathod M, Biehl A, Aw WY, Freytes DO, Polacheck WJ. Human Cell-Derived Matrix Composite Hydrogels with Diverse Composition for Use in Vasculature-on-chip Models. Adv Healthc Mater 2024:e2400192. [PMID: 38518808 DOI: 10.1002/adhm.202400192] [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: 02/16/2024] [Revised: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Microphysiological and organ-on-chip platforms seek to address critical gaps in human disease models and drug development that underlie poor rates of clinical success for novel interventions. While the fabrication technology and model cells used to synthesize organs-on-chip have advanced considerably, most platforms rely on animal-derived or synthetic extracellular matrix as a cell substrate, limiting mimicry of human physiology and precluding use in modeling diseases in which matrix dynamics play a role in pathogenesis. Here, the development of human cell-derived matrix (hCDM) composite hydrogels for use in 3D microphysiologic models of the vasculature is reported. hCDM composite hydrogels are derived from human donor fibroblasts and maintain a complex milieu of basement membrane, proteoglycans, and nonfibrillar matrix components. The use of hCDM composite hydrogels as 2D and 3D cell culture substrates is demonstrated, and hCDM composite hydrogels are patterned to form engineered human microvessels. Interestingly, hCDM composite hydrogels are enriched in proteins associated with vascular morphogenesis as determined by mass spectrometry, and functional analysis demonstrates proangiogenic signatures in human endothelial cells cultured in these hydrogels. In conclusion, this study suggests that human donor-derived hCDM composite hydrogels could address technical gaps in human organs-on-chip development and serve as substrates to promote vascularization.
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Affiliation(s)
- Elizabeth L Doherty
- The Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, 10010 Mary Ellen Jones Building, 116 Manning Drive, Chapel Hill, NC 27514, USA
| | - Grace Krohn
- The Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, 10010 Mary Ellen Jones Building, 116 Manning Drive, Chapel Hill, NC 27514, USA
| | - Emily C Warren
- The Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, 10010 Mary Ellen Jones Building, 116 Manning Drive, Chapel Hill, NC 27514, USA
| | - Alexandra Patton
- The Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, 10010 Mary Ellen Jones Building, 116 Manning Drive, Chapel Hill, NC 27514, USA
| | - Chloe P Whitworth
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill School of Medicine, 130 Mason Farm Road, Chapel Hill, Carolina, NC 27599, USA
| | - Mitesh Rathod
- The Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, 10010 Mary Ellen Jones Building, 116 Manning Drive, Chapel Hill, NC 27514, USA
| | - Andreea Biehl
- The Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, 10010 Mary Ellen Jones Building, 116 Manning Drive, Chapel Hill, NC 27514, USA
| | - Wen Yih Aw
- The Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, 10010 Mary Ellen Jones Building, 116 Manning Drive, Chapel Hill, NC 27514, USA
| | - Donald O Freytes
- The Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, 10010 Mary Ellen Jones Building, 116 Manning Drive, Chapel Hill, NC 27514, USA
| | - William J Polacheck
- The Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, 10010 Mary Ellen Jones Building, 116 Manning Drive, Chapel Hill, NC 27514, USA
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, 111 Mason Farm Road, Chapel Hill, Carolina, NC 27599, USA
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Domagała D, Data K, Szyller H, Farzaneh M, Mozdziak P, Woźniak S, Zabel M, Dzięgiel P, Kempisty B. Cellular, Molecular and Clinical Aspects of Aortic Aneurysm-Vascular Physiology and Pathophysiology. Cells 2024; 13:274. [PMID: 38334666 PMCID: PMC10854611 DOI: 10.3390/cells13030274] [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: 11/23/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
A disturbance of the structure of the aortic wall results in the formation of aortic aneurysm, which is characterized by a significant bulge on the vessel surface that may have consequences, such as distention and finally rupture. Abdominal aortic aneurysm (AAA) is a major pathological condition because it affects approximately 8% of elderly men and 1.5% of elderly women. The pathogenesis of AAA involves multiple interlocking mechanisms, including inflammation, immune cell activation, protein degradation and cellular malalignments. The expression of inflammatory factors, such as cytokines and chemokines, induce the infiltration of inflammatory cells into the wall of the aorta, including macrophages, natural killer cells (NK cells) and T and B lymphocytes. Protein degradation occurs with a high expression not only of matrix metalloproteinases (MMPs) but also of neutrophil gelatinase-associated lipocalin (NGAL), interferon gamma (IFN-γ) and chymases. The loss of extracellular matrix (ECM) due to cell apoptosis and phenotype switching reduces tissue density and may contribute to AAA. It is important to consider the key mechanisms of initiating and promoting AAA to achieve better preventative and therapeutic outcomes.
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Affiliation(s)
- Dominika Domagała
- Division of Anatomy, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland; (D.D.); (K.D.); (H.S.); (S.W.)
| | - Krzysztof Data
- Division of Anatomy, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland; (D.D.); (K.D.); (H.S.); (S.W.)
| | - Hubert Szyller
- Division of Anatomy, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland; (D.D.); (K.D.); (H.S.); (S.W.)
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran;
| | - Paul Mozdziak
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27607, USA;
- Physiology Graduate Faculty, North Carolina State University, Raleigh, NC 27613, USA
| | - Sławomir Woźniak
- Division of Anatomy, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland; (D.D.); (K.D.); (H.S.); (S.W.)
| | - Maciej Zabel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland; (M.Z.); (P.D.)
- Division of Anatomy and Histology, University of Zielona Góra, 65-046 Zielona Góra, Poland
| | - Piotr Dzięgiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland; (M.Z.); (P.D.)
- Department of Physiotherapy, University School of Physical Education, 51-612 Wroclaw, Poland
| | - Bartosz Kempisty
- Division of Anatomy, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland; (D.D.); (K.D.); (H.S.); (S.W.)
- Physiology Graduate Faculty, North Carolina State University, Raleigh, NC 27613, USA
- Institute of Veterinary Medicine, Nicolaus Copernicus University, 87-100 Torun, Poland
- Department of Obstetrics and Gynecology, University Hospital and Masaryk University, 602 00 Brno, Czech Republic
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