In the current study, we showed that the two latent TB groups (LTBL, LTBH) did not cluster closely. Among detected genes, LTBL and HD clustered as a category, but LTBH is more close to active Tuberculosis. These results suggest that LTBL and HD participants have similar gene expression profiles in their peripheral CD4+ T cells. Although LTBL and LTBH are both latent TB classes, their transcription profiles are actually quite distinct. The TB group did not cluster with any other group directly, which indicates that the peripheral CD4+ T cells of these patients have unique gene expression profiles, and these characteristics help us to well understand TB patients from healthy and latent participants.
With regard to ranked GO terms or KEGG Pathways, the significantly altered expression of genes in the LTBL group were mainly associated with stimulus responses, suggesting that the CD4+ T cells of the LTBL participants might easily respond to M.tb-antigen stimulation. The CD4+ T cells of the LTBH group could easily alternate between their roles in movement and metabolism because many migration- and metabolism-related GO terms were ranked in the LTBH group. The TB group has the largest number of genes ranked by GO terms and KEGG pathways. This is reasonable to assume that the CD4+ T cells of TB patients do not appear to be functionally impaired and may possess the most protective potential and act for alterations in metabolism, migration, adhesion, apoptosis and respond to stimulus.
Although many studies have confirmed the indispensability of IFN-γ in the prevention of TB development, correlation of IFN-γ levels and protection ability still debate 
. Therefore, it is essential to identify other tuberculosis-specific signatures. In this study, TNFSF and TNFRSF genes were screened for further validation because some of them have previously been confirmed to have effects on TB development. TNF-α promotes granuloma formation, which is involved in preventing the dissemination of bacilli 
, and anti-TNF-α treatment for rheumatoid arthritis increases the risk of active tuberculosis development 
. FAS, FASLG and CD30 have also been shown to be related to disease development 
. In our study, soluble CD30 and FASLG were also markedly up-regulated in the plasma of tuberculosis patients (data not shown).
Furthermore, our results indicate that BAFF and APRIL expression is significantly elevated during active tuberculosis infections. And, a stronger secretion of soluble BAFF and APRIL was observed in the pleural effusion of TP patients, which suggests that the two cytokines are involved in pulmonary and extraplumonary Tuberculosis and may reflect disease exacerbation. Although the levels of sAPRIL were lower in the M.tb
antigen-stimulated supernatants than in un-stimulated supernatants of TB patients, we hypothesize that the down-regulation of sAPRIL is caused by its consumption during stimulation because it has been shown to play an anti-apoptotic role through an autocrine pathway 
BAFF and APRIL previously reported as two important mediators of B cells 
, also affect the survival and activation of T cells 
. In particular, BAFF also promotes the Th1 response 
. Certain cytokines, such as IFN-γ, IL-10 and IFN-α, can induce various cells to augment BAFF production 
. However, IL-4 can inhibit BAFF expression 
. Similar to BAFF, APRIL has been shown to be up-regulated in response to IFN-γ and IFN-α treatment 
. In our study, TB and TP patients secreted high antigen specific IFN-γ level detected by ELISPOT (SFCs>110), and plasma level of IFN-γ were markedly increased in the pleural effusion of TP patients but with low IL-4 level (Figure S1
). Therefore, the dramatic enhancement of sBAFF and sAPRIL levels in patients might be caused by the stronger IFN-γ-mediated effects that outweigh the inhibitory effects of IL-4. The exact mechanisms of sBAFF and sAPRIL production require further examination. BAFF has two forms: membrane-bound and soluble 
. An analysis by flow cytometry revealed that the frequency of BAFF+
T cells is increased in TB patients (.C). Some studies have suggested that only immobilized BAFF can enhance the human T cell response to anti-CD3/TCR activation 
. Thus, it appears that sBAFF might act as a suppressor and inhibit the binding of membrane-bound BAFF to its receptors.
shows there are forty-five known genes that interact with BAFF
. An IPA analysis was employed to analyze the interactions and RT-PCR results indicated that a largest number of pathways emanate from apoptosis-related genes, such as BCL2 (data not shown). Therefore, network-regulated apoptosis is important for the fate of CD4+
T cells and might indirectly affect tuberculosis outcome. As an autocrine factor 
, BAFF has also been reported to induce BCL2 up-regulation through BAFFR-mediated signaling 
and to promote T cell survival 
. The cytoplasmic tail of BAFFR has TNF receptor-associated factor (TRAF)-interacting motifs (TIMs) 
, which are involved in mediating cell survival, activation and differentiation. Thus, BAFF might prevent peripheral CD4+
T cells from apoptosis in patients and this mechanism might be related to the induction of BCL2
also shows the intimate association between the Th1 response and the BAFF/APRIL system. The Th1 response plays an indispensable role in M.tb
control and elimination 
. In particular, sufficient macrophage activation is produced by IFN-γ and IL-12, thus permitting more efficient bacilli destruction 
. Deficiencies in IL-12 or IFN-γ or their receptors render individuals more susceptible to mycobacterial infections 
. TNF-α is important for establishing granulomas and the localized control of M.tb
. A few publications revealed that BAFF is expressed on activated T cells and promotes the Th1 response 
. BAFF and IFN-γ have also been shown to establish an inflammatory loop between T and myeloid cells that exacerbates autoimmunity 
. To our knowledge, no direct relation between APRIL and the Th1 response has been reported. However, among the TNFSF-related genes, APRIL is most closely related to BAFF; they share ~30% sequence identity in their TNF homology domains (THDs) 
. APRIL may play a similar role in disease of Tuberculosis. Moreover, we found strong positive correlations between Th1 cytokines (IFN-γ, IL-12p70 and IL-2) and sAPRIL in the pleural effusion of TP patients. Thus, these studies suggest a reciprocal relationship between the BAFF/APRIL system and the Th1 response in pulmonary and extrapulmonary TB patients. In our study, we found effects of the BAFF/APRIL system on tuberculosis to be intriguing. Future studies involving novel ideas and participants are necessary to discern the role of the BAFF/APRIL system in the pathogenesis of tuberculosis.
In summary, our results herein suggest that the elevated expression levels of BAFF and APRIL are associated with active pulmonary and extrapulmonary tuberculosis and that the BAFF/APRIL system is intimately correlated with the Th1 response. These results implicate a potential use for the combination of BAFF and/or APRIL with IFN-γ in the diagnosis of tuberculosis. Moreover, the CD4+ T cell-derived transcriptional signatures of distinct latency populations might be helpful to identify subsets of latent individuals that produce protective responses against tuberculosis. However, longitudinal studies must be performed to assess this hypothesis.