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BMC Complementary Medicine and Therapies

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Open Access 01-12-2016 | Research article

Microarray expression profile analysis of mRNAs and long non-coding RNAs in pulmonary tuberculosis with different traditional Chinese medicine syndromes

Authors: Ting-Ting Jiang, Li-Liang Wei, Li-Ying Shi, Zhong-Liang Chen, Chong Wang, Chang-Ming Liu, Zhong-Jie Li, Ji-Cheng Li

Published in: BMC Complementary Medicine and Therapies | Issue 1/2016

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.

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[Internet] World Health Organization, Fact sheet N°104. http://www.who.int/mediacentre/factsheets/fs104/en/index.html Accessed Mar 2015.

Ramachandran G, Swaminathan S. Role of pharmacogenomics in the treatment of tuberculosis: a review. Pharmacogenomics Pers Med. 2012;5:89–98.

Burman WJ, Reves RR. Hepatotoxicity from rifampin plus pyrazinamide: lessons for policymakers and messages for care providers. Am J Resp Crit CareMed. 2001;164:1112–3.CrossRef

Singla R, Sharma SK, Mohan A, Makharia G, Sreenivas V, Jha B, et al. Evaluation of risk factors for antituberculosis treatment induced hepatotoxicity. Indian J Med Res. 2010;132:81–6.PubMed

Tsuyuguchi K, Wada M. Management of adverse effects with antituberculosis chemotherapy [in Japanese]. Kekkaku. 2011;86:87–99.PubMed

Tripathi RP, Bisht SS, Ajay A, Sharma A, Misra M, Gupt MP. Developments in chemical approaches to treat tuberculosis in the last decade. Curr Med Chem. 2012;19:488–517.CrossRefPubMed

Evans DA, Manley KA, Mc KV. Genetic control of isoniazid metabolism in man. Br Med J. 1960;2:485–91.CrossRefPubMedPubMedCentral

Heyckendorf J, Olaru ID, Ruhwald M, Lange C. Getting personal perspectives on individualized treatment duration in multidrug-resistant and extensively drug-resistant tuberculosis. Am J Respir Crit Care Med. 2014;190:374–83.CrossRefPubMed

Guo Z, Yu S, Guan Y, Li YY, Lu YY, Zhang H, et al. Molecular mechanisms of same TCM syndrome for different diseases and different TCM syndrome for same disease in chronic hepatitis B and liver cirrhosis. Evid Based Complement Alternat Med. 2012;2012:120350.CrossRefPubMedPubMedCentral

10.

Liu J, Li Y, Wei L, Yang X, Xie Z, Jiang T, et al. Screening and identification of potential biomarkers and establishment of the diagnostic serum proteomic model for the traditional Chinese medicine syndromes of tuberculosis. J Ethnopharmacol. 2014;155:1322–31.CrossRefPubMed

11.

Wang X, Zhang A, Sun H, Wang P. Systems biology technologies enable personalized traditional Chinese medicine: a systematic review. Am J Chin Med. 2012;40:1109–22.CrossRefPubMed

12.

Zhang A, Sun H, Wang P, Han Y, Wang X. Future perspectives of personalized medicine in traditional Chinese medicine: a systems biology approach. Complement Ther Med. 2012;20:93–9.CrossRefPubMed

13.

Kanawong R, Obafemi-Ajayi T, Ma T, Xu D, Li S, Duan Y. Automated tongue feature extraction for ZHENG classification in traditional Chinese medicine. Evid Based Complement Alternat Med. 2012;2012:912852.CrossRefPubMedPubMedCentral

14.

Cheung F. TCM: made in China. Nature. 2011;480:S82–83.CrossRefPubMed

15.

Tang JL, Liu BY, Ma KW. Traditional Chinese medicine. Lancet. 2008;372:1938–40.CrossRefPubMed

16.

Dai J, Sun S, Cao H, Zheng N, Wang W, Gou X, et al. Applications of new technologies and new methods in ZHENG differentiation. Evid Based Complement Alternat Med. 2012;2012:298014.CrossRefPubMedPubMedCentral

17.

Wang SS, Zhou J, Zhang YF, Wang L, Feng X, Wang Y. Study on the rule of TCM syndromes in pulmonary tuberculosis [in Chinese]. World J Integ Tradit Western Med. 2014;9:498–500.

18.

Liu Y, He F. Chinese medicine in the treatment of tuberculosis of the status and prospect [in Chinese]. Guiding J Tradit Chin Med Pharmacy. 2010;16:100–2.

19.

Xu HD, You CG, Zhang RL, Gao P, Wang ZR. Effects of Astragalus polysaccharides and astragalosides on the phagocytosis of Mycobacterium tuberculosis by macrophages. J Int Med Res. 2007;35:84–90.CrossRefPubMed

20.

Wang L, Yang CL, Or TC, Chen G, Zhou J, Li JC, et al. Differential effects of Radix Paeoniae Rubra (Chishao) on cytokine and chemokine expression inducible by mycobacteria. Chin Med. 2011;6:14.CrossRefPubMedPubMedCentral

21.

Wang M, Guan X, Chi Y, Robinson N, Liu JP. Chinese herbal medicine as adjuvant treatment to chemotherapy for multidrug-resistant tuberculosis (MDR-TB): a systematic review of randomised clinical trials. Tuberculosis. 2015;95:364–72.CrossRefPubMed

22.

Pace E, Gjomarkaj M, Melis M, Profita M, Spatafora M, Vignola AM, et al. Interleukin-8 induces lymphocyte chemotaxis into the pleural space - role of pleural macrophages. Am J Resp Crit Care. 1999;159:1592–9.CrossRef

23.

Godaly G, Young DB. Mycobacterium bovis bacille calmette Guerin infection of human neutrophils induces CXCL8 secretion by MyD88-dependent TLR2 and TLR4 activation. Cell Microbiol. 2005;7:591–601.CrossRefPubMed

24.

Lu J, Ye S, Qin R, Deng Y, Li CP. Effect of Chinese herbal medicine extracts on cell-mediated immunity in a rat model of tuberculosis induced by multiple drug-resistant bacilli. Mol Med Rep. 2013;8:227–32.PubMed

25.

Lu AP, Jiang M, Zhang C, Chan K. An integrative approach of linking traditional Chinese medicine pattern classification and biomedicine diagnosis. J Ethnopharmacol. 2012;141:549–56.CrossRefPubMed

26.

Wang Y, Gao SG, Liu G, Jia RN, Fan DM, Feng XS. Microarray expression profile analysis of long non-coding RNAs in human gastric cardiac adenocarcinoma. Cell Physiol Biochem. 2014;33:1225–38.CrossRefPubMed

27.

Wang P, Lu SH, Mao HL, Bai YN, Ma TL, Cheng ZL, et al. Identification of biomarkers for the detection of early stage lung adenocarcinoma by microarray profiling of long noncoding RNAs. Lung Cancer. 2015;88:147–53.CrossRefPubMed

28.

McKiernan PJ, Molloy K, Cryan SA, McElvaney NG, Greene CM. Long noncoding RNA are aberrantly expressed in vivo in the cystic fibrosis bronchial epithelium. Int J Biochem Cell B. 2014;52:184–91.CrossRef

29.

Zeng JF, Ouyang JJ. Overview and prospect on treatment of pulmonary tuberculosis with serial prescription of TCM [in Chinese]. Guiding J TCM. 2006;12:70–2.

30.

Wang SS, Zhou J, Fang D, Zhou JM. Research on TCM law of tuberculosis and related to objects indicators [in Chinese]. Clin J Chinese Med. 2011;3:13–4.

31.

Jiang TT, Wang C, Wei LL, Yu XM, Shi LY, Xu DD, et al. Serum protein gamma-glutamyl hydrolase, Ig gamma-3 chain C region, and haptoglobin are associated with the syndromes of pulmonary tuberculosis in traditional Chinese medicine. BMC Complement Altern Med. 2015;15:243.CrossRefPubMedPubMedCentral

32.

Baba Y, Iyama KI, Ikeda K, Ishikawa S, Hayashi N, Miyanari N, et al. The expression of type IV collagen alpha 6 chain is related to the prognosis in patients with esophageal squamous cell carcinoma. Ann Surg Oncol. 2008;15:555–65.CrossRefPubMed

33.

Pals G, Eriksson AW, Pronk JC, Frants RR, Klinkenbergknol EC, Bosma A, et al. Differential expression of pepsinogen isozymogens in a patient with barrett esophagus. Clin Genet. 1988;34:90–7.CrossRefPubMed

34.

Pineda M, Fernandez E, Torrents D, Estevez R, Lopez C, Camps M, et al. Identification of a membrane protein, LAT-2, that co-expresses with 4F2 heavy chain, an L-type amino acid transport activity with broad specificity for small and large zwitterionic amino acids. J Biol Chem. 1999;274:19738–44.CrossRefPubMed

35.

Fonseca-Camarillo G, Yamamoto-Furusho JK. Gene expression of solute carrier family 9 (sodium/hydrogen exchanger) 3, (SLC9A3) is downregulated in patients with ulcerative colitis. Inflamm Bowel Dis. 2012;18:1197–8.CrossRefPubMed

36.

He S, Xu JX, Zhu W, Xiang S, Tang C, Lu TT. The therapy of pulmonary tuberculosis with the relationship of lung and spleen [in Chinese]. Guiding J Tradit Chin Med Pharmacy. 2013;28:7–9.

37.

Zhang Y, Liu Y, Li XP, Li J, Li XF, Chen L, et al. Evidence-based novel changes in prevalence and symptom characteristics of spleen deficiency syndrome in persons of varied health status and different ages: across-sectional observational study. Evid Based Complement Alternat Med. 2014;2014:818235.PubMedPubMedCentral

38.

Gaignard P, Menezes M, Schiff M, Bayot A, Rak M, Ogier de Baulny H, et al. Mutations in CYC1, encoding cytochrome c1subunit of respiratory chain complex III, cause insulin-responsive hyperglycemia. Am J Hum Genet. 2013;93:384–9.CrossRefPubMedPubMedCentral

39.

Crofts AR. The cytochrome bc (1) complex: function in the context of structure. Annu Rev Physiol. 2004;66:689–733.CrossRefPubMed

40.

Li GD, Fu D, Liang WQ, Fan L, Chen K, Shan LC, et al. CYC1 silencing sensitizes osteosarcoma cells to TRAIL-induced apoptosis. Cell Physiol Biochem. 2014;34:2070–80.CrossRefPubMed

41.

Curbo S, Lagier-Tourenne C, Carrozzo R, Palenzuela L, Lucioli S, Hirano M, et al. Human mitochondrial pyrophosphatase: cDNA cloning and analysis of the gene in patients with mtDNA depletion syndromes. Genomics. 2006;87:410–6.CrossRefPubMed

42.

Ravera S, Bartolucci M, Cuccarolo P, Litame E, Illarcio M, Calzia D, et al. Oxidative stress in myelin sheath: The other face of the extramitochondrial oxidative phosphorylation ability. Free Radic Res. 2015;49:1156–64.CrossRefPubMed

43.

Schwenk A, Hodgson L, Rayner CF, Griffin GE, Macallan DC. Leptin and energy metabolism in pulmonary tuberculosis. Am J Clin Nutr. 2003;77:392–8.PubMed

44.

Hunt MC, Rautanen A, Westin MA, Svensson LT, Alexson SE. Analysis of the mouse and human acyl-CoA thioesterase (ACOT) gene clusters shows that convergent, functional evolution results in a reduced number of human peroxisomal ACOTs. Faseb J. 2006;20:1855–64.CrossRefPubMed

45.

Muhammad E, Reish O, Ohno Y, Scheetz T, DeLuca A, Searby C, et al. Congenital myopathy is caused by mutation of HACD1. Hum Mol Genet. 2013;22:5229–36.CrossRefPubMedPubMedCentral

46.

Munoz-Elias EJ, McKinney JD. Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence. Nat Med. 2005;11:638–44.CrossRefPubMedPubMedCentral

47.

Arora P, Goyal A, Natarajan VT, Rajakumara E, Verma P, Gupta R, et al. Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis. Nat Chem Biol. 2009;5:166–73.CrossRefPubMedPubMedCentral

Title: Microarray expression profile analysis of mRNAs and long non-coding RNAs in pulmonary tuberculosis with different traditional Chinese medicine syndromes
Authors: Ting-Ting Jiang
Li-Liang Wei
Li-Ying Shi
Zhong-Liang Chen
Chong Wang
Chang-Ming Liu
Zhong-Jie Li
Ji-Cheng Li
Publication date: 01-12-2016
Publisher: BioMed Central
Published in: BMC Complementary Medicine and Therapies / Issue 1/2016
Electronic ISSN: 2662-7671
DOI: https://doi.org/10.1186/s12906-016-1436-y

Keynote webinar | Spotlight on medication adherence

Springer Medicine

Microarray expression profile analysis of mRNAs and long non-coding RNAs in pulmonary tuberculosis with different traditional Chinese medicine syndromes

Abstract

Background

Methods

Results

Conclusions

Keynote webinar | Spotlight on medication adherence

Springer Medicine

Abstract

Background

Methods

Results

Conclusions

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