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8. Bioinformatics and system biology approach to identify potential common pathogenesis for COVID-19 infection and osteoarthritis.

Author

Chen, Ziyi, Wang, Wenjuan, Jue, Hao, and Hua, Yinghui

Subjects
*COVID-19, *RECEIVER operating characteristic curves, *GENE expression profiling, *SYSTEMS biology, *GENE regulatory networks, *GENE expression
Abstract

A growing of evidence has showed that patients with osteoarthritis (OA) had a higher coronavirus 2019 (COVID-19) infection rate and a poorer prognosis after infected it. Additionally, scientists have also discovered that COVID-19 infection might cause pathological changes in the musculoskeletal system. However, its mechanism is still not fully elucidated. This study aims to further explore the sharing pathogenesis of patients with both OA and COVID-19 infection and find candidate drugs. Gene expression profiles of OA (GSE51588) and COVID-19 (GSE147507) were obtained from the Gene Expression Omnibus (GEO) database. The common differentially expressed genes (DEGs) for both OA and COVID-19 were identified and several hub genes were extracted from them. Then gene and pathway enrichment analysis of the DEGs were performed; protein–protein interaction (PPI) network, transcription factor (TF)-gene regulatory network, TF-miRNA regulatory network and gene-disease association network were constructed based on the DEGs and hub genes. Finally, we predicted several candidate molecular drugs related to hub genes using DSigDB database. The receiver operating characteristic curve (ROC) was applied to evaluate the accuracy of hub genes in the diagnosis of both OA and COVID-19. In total, 83 overlapping DEGs were identified and selected for subsequent analyses. CXCR4, EGR2, ENO1, FASN, GATA6, HIST1H3H, HIST1H4H, HIST1H4I, HIST1H4K, MTHFD2, PDK1, TUBA4A, TUBB1 and TUBB3 were screened out as hub genes, and some showed preferable values as diagnostic markers for both OA and COVID-19. Several candidate molecular drugs, which are related to the hug genes, were identified. These sharing pathways and hub genes may provide new ideas for further mechanistic studies and guide more individual-based effective treatments for OA patients with COVID-19 infection. [ABSTRACT FROM AUTHOR]

Published
2023
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9. Identification of the novel bacterial blight resistance gene Xa46(t) by mapping and expression analysis of the rice mutant H120

Author

Jianyuan Yang, Wang Congying, Aiqing Feng, Zeng Liexian, Su Jing, Xiaoyuan Zhu, Wang Wenjuan, Bing Chen, and Chen Shen

Subjects
0106 biological sciences, 0301 basic medicine, Agricultural genetics, Candidate gene, Xanthomonas, Mutant, Quantitative Trait Loci, lcsh:Medicine, Biology, Quantitative trait locus, Genes, Plant, 01 natural sciences, Chromosomes, Plant, Article, Plant breeding, 03 medical and health sciences, Xanthomonas oryzae, Gene Expression Regulation, Plant, Blight, Allele, lcsh:Science, Gene, Disease Resistance, Plant Diseases, Genetics, Regulation of gene expression, Multidisciplinary, lcsh:R, food and beverages, Oryza, biology.organism_classification, Plants, Genetically Modified, 030104 developmental biology, lcsh:Q, 010606 plant biology & botany
Abstract

Rice bacterial leaf blight is caused by Xanthomonas oryzae pv. oryzae (Xoo) and produces substantial losses in rice yields. Resistance breeding is an effective method for controlling bacterial leaf blight disease. The mutant line H120 derived from the japonica line Lijiangxintuanheigu is resistant to all Chinese Xoo races. To identify and map the Xoo resistance gene(s) of H120, we examined the association between phenotypic and genotypic variations in two F2 populations derived from crosses between H120/CO39 and H120/IR24. The segregation ratios of F2 progeny consisted with the action of a single dominant resistance gene, which we named Xa46(t). Xa46(t) was mapped between the markers RM26981 and RM26984 within an approximately 65.34-kb region on chromosome 11. The 12 genes predicted within the target region included two candidate genes encoding the serine/threonine-protein kinase Doa (Loc_Os11g37540) and Calmodulin-2/3/5 (Loc_Os11g37550). Differential expression of H120 was analyzed by RNA-seq. Four genes in the Xa46(t) target region were differentially expressed after inoculation with Xoo. Mapping and expression data suggest that Loc_Os11g37540 allele is most likely to be Xa46(t). The sequence comparison of Xa23 allele between H120 and CBB23 indicated that the Xa46(t) gene is not identical to Xa23.

Published
2019

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