RNA expression profiling from the liquid fraction of synovial fluid in knee joint osteoarthritis patients

被引:0
作者
Jiang, Peng [1 ,2 ]
Sun, Shui [1 ,2 ,5 ]
Zhang, Ju [3 ]
Li, Cuidan [3 ]
Ma, Guannan [3 ]
Wang, Jian [2 ]
Chen, Fei [3 ]
Liao, Dezhong Joshua [4 ]
机构
[1] Shandong Univ, Sch Clin Med, Jinan 250100, Shandong, Peoples R China
[2] Shandong Univ, Shandong Prov Hosp, Dept Orthopaed, Jinan 250021, Shandong, Peoples R China
[3] Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genom Sci & Informat, Beijing 100101, Peoples R China
[4] Guizhou Med Univ, Dept Pathol, Key Lab Endem & Ethn Dis, Minist Educ China, Guiyang 550004, Guizhou, Peoples R China
[5] Shandong Univ, Shandong Prov Hosp, Dept Orthopaed, 324 FIve Weft Seven Rd, Jinan 250021, Shandong, Peoples R China
来源
AMERICAN JOURNAL OF TRANSLATIONAL RESEARCH | 2022年 / 14卷 / 09期
关键词
Osteoarthritis; knee joint; synovial fluid; transcriptome; second-generation sequencing; RHEUMATOID-ARTHRITIS; TRANSCRIPTOME; BIOMARKERS; ARTIFACTS; DIAGNOSIS; GENES;
D O I
暂无
中图分类号
R73 [肿瘤学];
学科分类号
100214 ;
摘要
Objective: To investigate the RNA profile of synovial fluid (SF) from osteoarthritis (OA) patients and carry out cluster analysis of OA-related genes. Methods: RNA of SF from OA patients was isolated using RNA-specific Trizol. A cDNA library was built and subjected to the second-generation sequencing using HisSeq4000 with a data size of 8G. The sequencing reads were aligned to the UCSC human reference genome (hg38) using Tophat with default parameters. Gene function enrichment was generated using DAVID. Results: The minimum weight 0.096 mu g RNA of SF sample was used for sequencing analysis, which produced 66,154,562 clean reads, 91.28% of which were matched to the reference with 2,682 genes identified. Some of the unmatchable reads matched RNAs of bacteria, mainly Pseudomonas. The detected human RNAs in samples fell into different categories of genes, including protein-coding ones, processed and unprocessed pseudogenes, and long noncoding, antisense and miscellaneous RNAs that mediate various biological functions. Interestingly, 80% of the expressed genes belonged to the mitochondrial genome. Conclusion: These results suggest that less than 0.1 mu g RNA is sufficient for establishing a cDNA library and deep sequencing, and that the liquid fraction of SF contains a whole RNA repertoire that may reflect a history of previous microorganism infections.
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收藏
页码:6782 / 6791
页数:10
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