| Part I Screening and identification of plasma lncRNAs as potential novel biomarkers for cured pulmonary tuberculosis based on lncRNA microarryBackground: Pulmonary tuberculosis（TB）is a chronic infectious disease caused by Mycobacterium tuberculosis（MTB）.The treatment course for TB is long,and there is no gold standard to accurately determine whether the disease is cured.This can lead to early discharge of patients from the hospital,leading to the risk of disease spread and drug resistance.Patients who are not completely cured can spread the disease to healthy people when they leave the hospital,and the disease is prone to relapse and develop into drug-resistant tuberculosis.The study of plasma lncRNAsmay help to establish potential biomarkersfor cured TB.Methods: In this study,plasma samples were collected from the healthy control group,the untreated TB group and the cured TB group,and differentially expressed lncRNAs were screened by lncRNA microarray.The differentially expressed lncRNAs related to TB and their expression levels were further verified by q PCR.The target genes of differentially expressed lncRNAs were predicted by using coding-non-coding gene co-expression network and m RNA-lncRNA-mi RNA interaction network analyses,and the possible role of differential lncRNAs in the occurrence and development of TB were predicted.Results: The results of lncRNA microarray showed that 972 differential lncRNAs were identified in the cured TB group compared with the untreated TB group.Among them 603 differentiallncRNAs were up-regulated and 369 differentiallncRNAs were down-regulated.The expression levels of lncRNAs uc.48+（p<0.001）and NR105053（p=0.03）were found to be significantly different between the untreated TB group and the cured TB group.The predicted target genes for uc.48+ and NR105053 were EP300,BAI1 and TLR9,MYD88,BAI1,respectively.A predictive model for cured TB was established by thecombination of uc.48+ and NR105053 expression with a sensitivity of 90.00% and a specificity of 86.36%,and an area under the curve（AUC）value of 0.945.Moreover,uc.48+ and NR105053 could affect the ability of macrophages to fight against MTB by regulating the related target genes.Conclusions:（1）lncRNA microarray analysis showed that differentially expressed lncRNAs in plasma could be used as potential biomarkers for therapeutic evaluation of TB.（2）lncRNA microarray analysis,q PCR and ROC curve analysis showed that uc.48+ and NR105053 might serve as potential biomarkers for therapeutic evaluation of TB.（3）uc.48+ and NR105053 could affect the ability of macrophages to fight against MTB.（4）This study may provide laboratory basis for the therapeutic evaluation of TB,and may provide new clues to study the pathological mechanisms of TB.Part II Study on potential diagnostic biomarkers for pulmonary tuberculosis based on multi-omics dataBackground:The current burden of tuberculosis（TB）is still serious worldwide.One of the important reasons for global TBburden is thatthe early diagnosis of TB is difficult.At present,the diagnosis of TB mainly depends on sputum smear or sputum culture,the positive rate of detection is low,and the time to get the test results is slow.The difficulty in early diagnosis of TB brings the risk of misdiagnosis and delayed treatment.Therefore,there is an urgent need to develop new diagnostic methods for early diagnosis of TB.At present there have been a large number of studies at the transcriptional,protein,and metabolite level,and a large number of potential molecular markers have been identified in the blood for early diagnosis of TB.However,the existing biomarker studies tend to focus on a certain aspect of transcription,protein,or metabolism,lacking integrated vision and leaving the challenge of accurate diagnosis of TB under many influencing factors.In this study,we aimed to discover the association between different types of differential molecules through the integrated multi-omics analysis and to form the "integrative pattern" in order to distinguish TB more accurately.Methods:In this study,we integrated the data sets of lncRNAs,m RNAs,mi RNAs and metabolites from previous studies,compared the TB group with the healthy control group,screened the differential RNA molecules,and analyzed their functional enrichment.The lncRNA-mi RNA-m RNA interaction network was constructed based on the competitive endogenous RNA（ce RNA）hypothesis by integrating differential RNA molecules.Moreover,the key regulatory axis was established by co-expression analysisand verified at the level of metabolites.Results: A total of 936 differential m RNAs（582 up-regulated and 354 down-regulatedm RNAs）,1600 differential lncRNAs（790 up-regulated and 810 down-regulatedlncRNAs）,and 140 differential mi RNAs（73 up-regulated and 67 down-regulatedmi RNAs）were identified in the TB group,compared with the healthy control group.A ce RNA regulatory network consisting of 23 lncRNAs,10 mi RNAs,and 113 m RNAs was constructed.The results suggested that lncRNA（OSBPL10-AS1）,mi RNA（hsa-mi R-485-5p）,and m RNA（SLC23A2）might be involved in the regulation of vitamin metabolism in patients with TB.Metabolite analysis showed that compared with the healthy control group,TB patients had abnormal vitamin metabolism,and the expression levels of pyridoxal phosphate,pyridoxamine phosphate,and folic acid were significantly different between the two groups（p<0.05）.Conclusions:（1）Compared with single omics data,combined analysis of multi-omics can find the association between different omics data.From this new perspective,it may provides new help for the screening of biomarkers and to study the pathological mechanisms of TB.（2）Integrated multi-omics analysis showed that vitamin metabolism disorder may be one of the characteristic pathological features of TB.（3）OSBPL10-AS1,hsa-mi R-485-5p,SLC23A2,pyridoxal phosphate,pyridoxamine phosphate,and folic acid may collectively constitute the "integrative pattern" of multiple biomarkers,which may provide an accurate diagnosis of TB. |
