title: Microarray expression profile analysis of mRNAs and long non-coding RNAs in pulmonary tuberculosis with different traditional Chinese medicine syndromes.
abstract: BACKGROUND
  Combination chemotherapy with Western anti-tuberculosis (TB) drugs is the mainstay of TB treatment. Chinese herbal medicines with either heat clearing and detoxifying effects or nourishing Yin and reducing fire effects have been used to treat TB based on the Traditional Chinese Medicine (TCM) syndromes of TB patients. This study analyzed the expression profiles of long non-coding RNAs (lncRNAs) and mRNAs in TB patients with different TCM syndromes.
  
  
  METHODS
  TB patients were classified as pulmonary Yin deficiency (PYD) syndrome, hyperactivity of fire due to Yin deficiency (HFYD) syndrome, and deficiency of Qi and Yin (DQY) syndrome. Total RNA from 44 TB patients and healthy controls was extracted and hybridized with a human lncRNA microarray containing 30586 lncRNAs and 26109 mRNAs probes. Bioinformatics analyses, including gene ontology (GO) and pathways, were performed. Related clinical data were also analyzed.
  
  
  RESULTS
  Differentially expressed mRNAs and lncRNAs were identified (fold change >2, and P < 0.05) in PYD (634 mRNAs and 566 lncRNAs), HFYD (47 mRNAs and 55 lncRNAs), and DQY (63 mRNAs and 60 lncRNAs) patients. The most enriched pathways were the hippo signaling pathway (P = 0.000164) and the protein digestion and absorption pathway (P = 5.89017E-05). Clinical analyses revealed that the lipid indexes of TB patients were abnormal and that the triglyceride concentration was significantly higher in DQY patients (P = 0.0252). Our study is the first to acquire the microarray expression profiles of lncRNAs and mRNAs and analyze pathway enrichment in PYD, HFYD, and DQY patients with TB.
  
  
  CONCLUSIONS
  Our analyses of the expression profiles of lncRNAs and mRNAs may represent a novel method to explore the biological essence of TCM syndromes of TB.
authors.affiliation: Institute of Cell Biology, Zhejiang University, Hangzhou, Zhejiang, China.
authors.forename: Ting-Ting
authors.initials: TT
authors.lastname: Jiang
authors.affiliation: Department of Pneumology, Shaoxing Municipal Hospital, Shaoxing, Zhejiang, China.
authors.forename: Li-Liang
authors.initials: LL
authors.lastname: Wei
authors.affiliation: Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, Zhejiang, China.
authors.forename: Li-Ying
authors.initials: LY
authors.lastname: Shi
authors.affiliation: Institute of Cell Biology, Zhejiang University, Hangzhou, Zhejiang, China.
authors.forename: Zhong-Liang
authors.initials: ZL
authors.lastname: Chen
authors.affiliation: Institute of Cell Biology, Zhejiang University, Hangzhou, Zhejiang, China.
authors.forename: Chong
authors.initials: C
authors.lastname: Wang
authors.affiliation: Institute of Cell Biology, Zhejiang University, Hangzhou, Zhejiang, China.
authors.forename: Chang-Ming
authors.initials: CM
authors.lastname: Liu
authors.affiliation: Institute of Cell Biology, Zhejiang University, Hangzhou, Zhejiang, China.
authors.forename: Zhong-Jie
authors.initials: ZJ
authors.lastname: Li
authors.affiliation: Institute of Cell Biology, Zhejiang University, Hangzhou, Zhejiang, China. lijichen@zju.edu.cn.
authors.forename: Ji-Cheng
authors.initials: JC
authors.lastname: Li
mesh_terms: D000328:Adult; D000368:Aged; D016022:Case-Control Studies; D019295:Computational Biology; D003937:Diagnosis, Differential; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D008297:Male; D008875:Middle Aged; D019413:Qi; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D014397:Tuberculosis, Pulmonary / Q000175:diagnosis / Q000235:genetics* / Q000378:metabolism; D016710:Yin Deficiency / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism; D055815:Young Adult
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger
keywords: Pulmonary tuberculosis; TCM syndrome; lncRNAs; mRNAs