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Mou Y, Lv K. Extracellular vesicle-delivered hsa_circ_0090081 regulated by EIF4A3 enhances gastric cancer tumorigenesis. Cell Div 2024; 19:19. [PMID: 38862985 PMCID: PMC11165812 DOI: 10.1186/s13008-024-00123-z] [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: 02/07/2024] [Accepted: 06/03/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Circular RNA (circRNA) and extracellular vesicles (EVs) in tumors are crucial for the malignant phenotype of tumor cells. Nevertheless, the mechanisms and clinical effects of EV-delivered hsa_circ_0090081 in gastric cancer (GC) are unclear. This study aimed to reveal the effect of eukaryotic translation initiation factor 4A3 (EIF4A3)-mediated hsa_circ_0090081 expression and EV-delivered hsa_circ_0090081 on GC progression. METHODS qRT-PCR was conducted to clarify hsa_circ_0090081 and EIF4A3 levels in GC tissues. Transmission electronic microscopy (TEM), nanoparticle tracking analysis (NTA), and Western blotting identified the EVs isolated from GC cells by ultracentrifugation. The roles of hsa_circ_0090081, EIF4A3, and EV-delivered hsa_circ_0090081 in GC cells were analyzed using Transwell, EdU, and CCK-8 assays. The regulatory role between EIF4A3 and hsa_circ_0090081 was investigated using RIP, qRT-PCR, and Pearson's analysis. RESULTS Our study showed that hsa_circ_0090081 and EIF4A3 were highly expressed in GC, and hsa_circ_0090081 was associated with poor prognosis. Data revealed that hsa_circ_0090081 inhibition restrained GC cell proliferation, invasion, and migration. Additionally, EIF4A3 could bind to the pre-mRNA of PHEX (linear form of hsa_circ_0090081) to enhance hsa_circ_0090081 expression in GC cells. Moreover, EIF4A3 overexpression nullified the malignant phenotypic suppression caused by hsa_circ_0090081 silencing in GC cells. Furthermore, EVs secreted by GC cells delivered hsa_circ_0090081 to facilitate the malignant progression of targeted GC cells. CONCLUSION This study showed that hsa_circ_0090081 was enhanced by EIF4A3 to play a promotive role in GC development. The results may help understand the mechanism of EIF4A3 and EV-delivered hsa_circ_0090081 and offer a valuable GC therapeutic target.
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Affiliation(s)
- Yanjie Mou
- Department of Tradition Chinese Medicine, Wuhan Third Hospital (Tongren Hospital of Wuhan University), No. 241, Pengliuyang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Kun Lv
- Department of Tradition Chinese Medicine, Wuhan Third Hospital (Tongren Hospital of Wuhan University), No. 241, Pengliuyang Road, Wuchang District, Wuhan, 430060, Hubei, China.
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2
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Chen JJ, Shi P, Cui ZC, Jiang N, Ma J. CircRNA_0044556 affects the sensitivity of triple-negative breast cancer cells to paclitaxel by regulating miR-665. J Chemother 2024:1-9. [PMID: 38850033 DOI: 10.1080/1120009x.2024.2345028] [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: 12/02/2023] [Accepted: 04/15/2024] [Indexed: 06/09/2024]
Abstract
CircRNAs have been implicated in the development of resistance in triple-negative breast cancer (TNBC). However, the association between circRNA_0044556 and paclitaxel (PTX) resistance in TNBC is still limited. Therefore, the purpose of this study was to investigate the effect of circRNA_0044556 on biological function and PTX resistance in TNBC cells. PTX-resistant TNBC cells (MDA-MB-231/PTX) were obtained by continuously exposing MDA-MB-231 cells to increasing paclitaxel levels. The expression levels of circRNA_0044556 and miR-665 were measured by qRT-PCR. The regulatory relationship between miR-665 and circRNA_0044556 was verified by biological information website analysis and double-luciferase reporter gene detection experiments. MTT assay, clone assay, flow cytometry and Western blot analysis were used to evaluate the influence of cell biological function. Elevated circRNA_0044556 was observed in TNBC, and paclitaxel increased the expression of circRNA_0044556 in TNBC cells. In TNBC, circRNA_0044556 acted as a ceRNA for miR-665. In addition, low expression of circRNA_0044556 combined with miR-665 inhibited the proliferation of TNBC cells and paclitaxel-resistant TNBC cells while inducing cell death. Our study demonstrated that the downregulation of circRNA_0044556 inhibits the malignant progression of TNBC cells and paclitaxel resistance via miR-665. Thus, circRNA_0044556 may be a potential therapeutic target for PTX-resistance TNBC.
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Affiliation(s)
- Jing-Jing Chen
- Department of Breast Surgery (No.1), Tangshan People's Hospital, Tangshan, China
| | - Peng Shi
- Department of Urology, Tangshan People's Hospital, Tangshan, China
| | - Zhi-Chao Cui
- Department of Breast Surgery (No.1), Tangshan People's Hospital, Tangshan, China
| | - Nan Jiang
- Department of Breast Surgery (No.1), Tangshan People's Hospital, Tangshan, China
| | - Jie Ma
- Department of Breast Surgery (No.1), Tangshan People's Hospital, Tangshan, China
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3
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Dergunova LV, Vinogradina MA, Filippenkov IB, Limborska SA, Dergunov AD. Circular RNAs Variously Participate in Coronary Atherogenesis. Curr Issues Mol Biol 2023; 45:6682-6700. [PMID: 37623241 PMCID: PMC10453518 DOI: 10.3390/cimb45080422] [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: 06/29/2023] [Revised: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023] Open
Abstract
Over the past decade, numerous studies have shown that circular RNAs (circRNAs) play a significant role in coronary artery atherogenesis and other cardiovascular diseases. They belong to the class of non-coding RNAs and arise as a result of non-canonical splicing of premature RNA, which results in the formation of closed single-stranded circRNA molecules that lack 5'-end caps and 3'-end poly(A) tails. circRNAs have broad post-transcriptional regulatory activity. Acting as a sponge for miRNAs, circRNAs compete with mRNAs for binding to miRNAs, acting as competing endogenous RNAs. Numerous circRNAs are involved in the circRNA-miRNA-mRNA regulatory axes associated with the pathogenesis of cardiomyopathy, chronic heart failure, hypertension, atherosclerosis, and coronary artery disease. Recent studies have shown that сirc_0001445, circ_0000345, circ_0093887, сircSmoc1-2, and circ_0003423 are involved in the pathogenesis of coronary artery disease (CAD) with an atheroprotective effect, while circ_0002984, circ_0029589, circ_0124644, circ_0091822, and circ_0050486 possess a proatherogenic effect. With their high resistance to endonucleases, circRNAs are promising diagnostic biomarkers and therapeutic targets. This review aims to provide updated information on the involvement of atherogenesis-related circRNAs in the pathogenesis of CAD. We also discuss the main modern approaches to detecting and studying circRNA-miRNA-mRNA interactions, as well as the prospects for using circRNAs as biomarkers and therapeutic targets for the treatment of cardiovascular diseases.
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Affiliation(s)
- Liudmila V. Dergunova
- Laboratory of Human Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia; (M.A.V.); (I.B.F.); (S.A.L.)
| | - Margarita A. Vinogradina
- Laboratory of Human Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia; (M.A.V.); (I.B.F.); (S.A.L.)
| | - Ivan B. Filippenkov
- Laboratory of Human Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia; (M.A.V.); (I.B.F.); (S.A.L.)
| | - Svetlana A. Limborska
- Laboratory of Human Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia; (M.A.V.); (I.B.F.); (S.A.L.)
| | - Alexander D. Dergunov
- Laboratory of Structural Fundamentals of Lipoprotein Metabolism, National Medical Research Center for Therapy and Preventive Medicine, Petroverigsky Street 10, Moscow 101990, Russia;
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4
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Matsuoka T, Yashiro M. Novel biomarkers for early detection of gastric cancer. World J Gastroenterol 2023; 29:2515-2533. [PMID: 37213407 PMCID: PMC10198055 DOI: 10.3748/wjg.v29.i17.2515] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/31/2023] [Accepted: 04/13/2023] [Indexed: 05/23/2023] Open
Abstract
Gastric cancer (GC) remains a leading cause of cancer-related death worldwide. Less than half of GC cases are diagnosed at an advanced stage due to its lack of early symptoms. GC is a heterogeneous disease associated with a number of genetic and somatic mutations. Early detection and effective monitoring of tumor progression are essential for reducing GC disease burden and mortality. The current widespread use of semi-invasive endoscopic methods and radiologic approaches has increased the number of treatable cancers: However, these approaches are invasive, costly, and time-consuming. Thus, novel molecular noninvasive tests that detect GC alterations seem to be more sensitive and specific compared to the current methods. Recent technological advances have enabled the detection of blood-based biomarkers that could be used as diagnostic indicators and for monitoring postsurgical minimal residual disease. These biomarkers include circulating DNA, RNA, extracellular vesicles, and proteins, and their clinical applications are currently being investigated. The identification of ideal diagnostic markers for GC that have high sensitivity and specificity would improve survival rates and contribute to the advancement of precision medicine. This review provides an overview of current topics regarding the novel, recently developed diagnostic markers for GC.
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Affiliation(s)
- Tasuku Matsuoka
- Molecular Oncology and Therapeutics, Osaka Metropolitan University Graduate School of Medicine, Osaka 5458585, Japan
| | - Masakazu Yashiro
- Molecular Oncology and Therapeutics, Osaka Metropolitan University Graduate School of Medicine, Osaka 5458585, Japan
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5
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Hou G, Zuo H, Shi J, Dai D, Wang H, Song X, Xu G, Tao G. EIF4A3 induced circABCA5 promotes the gastric cancer progression by SPI1 mediated IL6/JAK2/STAT3 signaling. Am J Cancer Res 2023; 13:602-622. [PMID: 36895988 PMCID: PMC9989606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/12/2023] [Indexed: 03/11/2023] Open
Abstract
Gastric cancer is one of the most common malignancies of the digestive system with high mortality rates. Recent studies have demonstrated that circRNAs are novel noncoding RNAs that play vital roles in the tumorigenesis and development of gastric cancer. Our study found a novel circRNA, namely, hsa_circ_0107595 (also called circABCA5), that is overexpressed in gastric cancer based on circRNA sequencing. qPCR demonstrated its overexpression in gastric cancer specimens. The overexpression or knockdown of circABCA5 in gastric cancer cell lines was achieved by lentiviral-mediated transfection. All MTS, EdU, Transwell and migration assays and xenograft experiments demonstrated that circABCA5 could promote gastric cancer proliferation, invasion, and migration in vitro and in vivo. Mechanistically, both RIP and RNA pulldown assays confirmed that circABCA5 could bind to the SPI1 protein, upregulate SPI1 expression, and promote its nuclear translocation. SPI1 could further promote the malignant phenotype of gastric cancer by activating IL6/JAK2/STAT3 signaling. In addition, EIF4A3 could directly bind to circABCA5, promoting its stability and expression. Our study reveals that circABCA5 plays a vital role in the diagnosis and prognosis of gastric cancer and may even be developed as a molecular target for the treatment of gastric cancer.
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Affiliation(s)
- Guowei Hou
- Department of General Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University Huaian 223300, Jiangsu, China
| | - Hao Zuo
- Department of General Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University Huaian 223300, Jiangsu, China
| | - Jin Shi
- Department of General Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University Huaian 223300, Jiangsu, China
| | - Dezhu Dai
- Department of General Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University Huaian 223300, Jiangsu, China
| | - Haixiao Wang
- Department of General Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University Huaian 223300, Jiangsu, China
| | - Xudong Song
- Department of General Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University Huaian 223300, Jiangsu, China
| | - Guo Xu
- Department of General Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University Huaian 223300, Jiangsu, China
| | - Guoquan Tao
- Department of General Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University Huaian 223300, Jiangsu, China
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6
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Quirino MWL, Albuquerque APB, De Souza MFD, Da Silva Filho AF, Martins MR, Da Rocha Pitta MG, Pereira MC, De Melo Rêgo MJB. alpha2,3 sialic acid processing enzymes expression in gastric cancer tissues reveals that ST3Gal3 but not Neu3 are associated with Lauren's classification, angiolymphatic invasion and histological grade. Eur J Histochem 2022; 66. [PMID: 36172711 PMCID: PMC9577379 DOI: 10.4081/ejh.2022.3330] [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: 09/16/2021] [Accepted: 08/27/2022] [Indexed: 11/22/2022] Open
Abstract
Gastric cancer (GC) is one of the leading causes of cancer-related deaths worldwide. Despite progress in the last decades, there are still no reliable biomarkers for the diagnosis of and prognosis for GC. Aberrant sialylation is a widespread critical event in the development of GC. Neuraminidases (Neu) and sialyltransferases (STs) regulate the ablation and addition of sialic acid during glycoconjugates biosynthesis, and they are a considerable source of biomarkers in various cancers. This study retrospectively characterized Neu3 and ST3Gal3 expression by immunohistochemistry in 71 paraffin-embedded GC tissue specimens and analyzed the relationship between their expression and the clinicopathological parameters. Neu3 expression was markedly increased in GC tissues compared with non-tumoral tissues (p<0.0001). Intratumoral ST3Gal3 staining was significantly associated with intestinal subtype (p=0.0042) and was negatively associated with angiolymphatic invasion (p=0.0002) and higher histological grade G3 (p=0.0066). Multivariate analysis revealed that ST3Gal3 positivity is able to predict Lauren's classification. No associations were found between Neu3 staining and clinical parameters. The in silico analysis of mRNA expression in GC validation cohorts corroborates the significant ST3Gal3 association with higher histological grade observed in our study. These findings suggest that ST3Gal3 expression may be an indicator for aggressiveness of primary GC.
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Affiliation(s)
- Michael W L Quirino
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for -Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE.
| | - Amanda P B Albuquerque
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for -Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE.
| | - Maria F D De Souza
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for -Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE.
| | - Antônio F Da Silva Filho
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for -Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE.
| | | | - Maira G Da Rocha Pitta
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for -Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE.
| | - Michelly C Pereira
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for -Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE.
| | - Moacyr J B De Melo Rêgo
- Laboratory of Immunomodulation and New Therapeutical Approaches, Research Centre for -Therapeutic Innovation Suely Galdino (NUPIT-SG), Federal University of Pernambuco, Recife, PE.
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7
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Yuan Y, Zhang X, Du K, Zhu X, Chang S, Chen Y, Xu Y, Sun J, Luo X, Deng S, Qin Y, Feng X, Wei Y, Fan X, Liu Z, Zheng B, Ashktorab H, Smoot D, Li S, Xie X, Jin Z, Peng Y. Circ_CEA promotes the interaction between the p53 and cyclin-dependent kinases 1 as a scaffold to inhibit the apoptosis of gastric cancer. Cell Death Dis 2022; 13:827. [PMID: 36167685 PMCID: PMC9515085 DOI: 10.1038/s41419-022-05254-1] [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: 04/11/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 01/23/2023]
Abstract
Circular RNAs (circRNAs) have been reported to play essential roles in tumorigenesis and progression. This study aimed to identify dysregulated circRNAs in gastric cancer (GC) and investigate the functions and underlying mechanism of these circRNAs in GC development. Here, we identify circ_CEA, a circRNA derived from the back-splicing of CEA cell adhesion molecule 5 (CEA) gene, as a novel oncogenic driver of GC. Circ_CEA is significantly upregulated in GC tissues and cell lines. Circ_CEA knockdown suppresses GC progression, and enhances stress-induced apoptosis in vitro and in vivo. Mechanistically, circ_CEA interacts with p53 and cyclin-dependent kinases 1 (CDK1) proteins. It serves as a scaffold to enhance the association between p53 and CDK1. As a result, circ_CEA promotes CDK1-mediated p53 phosphorylation at Ser315, then decreases p53 nuclear retention and suppresses its activity, leading to the downregulation of p53 target genes associated with apoptosis. These findings suggest that circ_CEA protects GC cells from stress-induced apoptosis, via acting as a protein scaffold and interacting with p53 and CDK1 proteins. Combinational therapy of targeting circ_CEA and chemo-drug caused more cell apoptosis, decreased tumor volume and alleviated side effect induced by chemo-drug. Therefore, targeting circ_CEA might present a novel treatment strategy for GC.
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Affiliation(s)
- Yuan Yuan
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Xiaojing Zhang
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Kaining Du
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Xiaohui Zhu
- grid.499351.30000 0004 6353 6136Department of Pharmacology, College of Pharmacy, Shenzhen Technology University, Shenzhen, Guangdong 518118 People’s Republic of China
| | - Shanshan Chang
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Yang Chen
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Yidan Xu
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Jiachun Sun
- grid.453074.10000 0000 9797 0900The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Henan Key Laboratory of Cancer Epigenetics, No. 24, Jinhua Road, Jianxi District, Luoyang, Henan 471003 People’s Republic of China
| | - Xiaonuan Luo
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Shiqi Deng
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Ying Qin
- grid.452847.80000 0004 6068 028XDepartment of Gastrointestinal Surgery, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, Guangdong 518000 People’s Republic of China
| | - Xianling Feng
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Yanjie Wei
- grid.458489.c0000 0001 0483 7922Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Shenzhen, Guangdong 518000 People’s Republic of China
| | - Xinmin Fan
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Ziyang Liu
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Baixin Zheng
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Hassan Ashktorab
- grid.257127.40000 0001 0547 4545Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, DC 20060 USA
| | - Duane Smoot
- Department of Medicine, Meharry Medical Center, Nashville, TN 37208 USA
| | - Song Li
- grid.454883.60000 0004 1788 7648Shenzhen Science & Technology Development Exchange Center, Shenzhen, Guangdong 518055 People’s Republic of China
| | - Xiaoxun Xie
- grid.256607.00000 0004 1798 2653School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021 Guangxi People’s Republic of China
| | - Zhe Jin
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Yin Peng
- grid.508211.f0000 0004 6004 3854Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060 People’s Republic of China
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Identification of key candidate genes for IgA nephropathy using machine learning and statistics based bioinformatics models. Sci Rep 2022; 12:13963. [PMID: 35978028 PMCID: PMC9385868 DOI: 10.1038/s41598-022-18273-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/08/2022] [Indexed: 11/08/2022] Open
Abstract
Immunoglobulin-A-nephropathy (IgAN) is a kidney disease caused by the accumulation of IgAN deposits in the kidneys, which causes inflammation and damage to the kidney tissues. Various bioinformatics analysis-based approaches are widely used to predict novel candidate genes and pathways associated with IgAN. However, there is still some scope to clearly explore the molecular mechanisms and causes of IgAN development and progression. Therefore, the present study aimed to identify key candidate genes for IgAN using machine learning (ML) and statistics-based bioinformatics models. First, differentially expressed genes (DEGs) were identified using limma, and then enrichment analysis was performed on DEGs using DAVID. Protein-protein interaction (PPI) was constructed using STRING and Cytoscape was used to determine hub genes based on connectivity and hub modules based on MCODE scores and their associated genes from DEGs. Furthermore, ML-based algorithms, namely support vector machine (SVM), least absolute shrinkage and selection operator (LASSO), and partial least square discriminant analysis (PLS-DA) were applied to identify the discriminative genes of IgAN from DEGs. Finally, the key candidate genes (FOS, JUN, EGR1, FOSB, and DUSP1) were identified as overlapping genes among the selected hub genes, hub module genes, and discriminative genes from SVM, LASSO, and PLS-DA, respectively which can be used for the diagnosis and treatment of IgAN.
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