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

Diagnostic value of lncRNAs LINC00152 and LARS2-AS1 and their regulatory roles in macrophage immune response in tuberculosis

OBJECTIVES

To determine the usefulness of LINC00152 and LARS2-AS1 as potential biomarkers for latent tuberculosis (LTB) and active tuberculosis (ATB), as well as their effect on Mycobacterium (Mtb) infection.

METHODS

The expression levels of LINC00152 and LARS2-AS1 in the health, patients with LTB and ATB were detected by qRT-PCR. The ROC curves were constructed to show their potential as biomarkers. The intracellular survival assays for Mtb and the levels of immune-related cytokines were determined to discover the effect of LINC00152 and LARS2-AS1 on Mtb infection. The relationships of miR-485-5p with LINC00152 and LARS2-AS1 were explored.

RESULTS

LINC00152 and LARS2-AS1 levels were significantly elevated in patients with ATB and LTB, and Mtb-infected macrophages. LINC00152 and LARS2-AS1 can distinguish the LTB from the health and ATB from LTB. LARS2-AS1 and LINC00152 knock-down reduced the intracellular Mtb survival and induced cellular immune response after Mtb challenge. miR-485-5p was a targeting miRNA for LINC00152 and LARS2-AS1.

CONCLUSIONS

LINC00152 and LARS2-AS1 can be considered as potential biomarkers for tuberculosis disease. LINC00152 and LARS2-AS1 have anti-Mtb effects.

Advances of Long Non-Coding RNAs as Potential Biomarkers for Tuberculosis: New Hope for Diagnosis?

Tuberculosis (TB), one of the top ten causes of death globally induced by the infection of Mycobacterium tuberculosis (Mtb), remains a grave public health issue worldwide. With almost one-third of the world's population getting infected by Mtb, between 5% and 10% of these infected individuals are predicted to develop active TB disease, which would not only result in severe tissue damage and necrosis, but also pose serious threats to human life. However, the exact molecular mechanisms underlying the pathogenesis and immunology of TB remain unclear, which significantly restricts the effective control of TB epidemics. Despite significant advances in current detection technologies and treatments for TB, there are still no appropriate solutions that are suitable for simultaneous, early, rapid, and accurate screening of TB. Various cellular events can perturb the development and progression of TB, which are always associated with several specific molecular signaling events controlled by dysregulated gene expression patterns. Long non-coding RNAs (lncRNAs), a kind of non-coding RNA (ncRNA) with a transcript of more than 200 nucleotides in length in eukaryotic cells, have been found to regulate the expression of protein-coding genes that are involved in some critical signaling events, such as inflammatory, pathological, and immunological responses. Increasing evidence has claimed that lncRNAs might directly influence the susceptibility to TB, as well as the development and progression of TB. Therefore, lncRNAs have been widely expected to serve as promising molecular biomarkers and therapeutic targets for TB. In this review, we summarized the functions of lncRNAs and their regulatory roles in the development and progression of TB. More importantly, we widely discussed the potential of lncRNAs to act as TB biomarkers, which would offer new possibilities in novel diagnostic strategy exploration and benefit the control of the TB epidemic.

Diagnostic value of Long non-coding Ribonucleic Acid non-coding activated by Deoxyribonucleic Acid damage in pulmonary tuberculosis and its regulatory role in Mycobacterium tuberculosis infection of macrophages

Pulmonary tuberculosis (PTB) infection is a chronic inflammatory response caused by Mycobacterium tuberculosis (Mtb). The purpose of this study was to confirm the value of Long non-coding RNA (LncRNA) non-coding activated by DNA damage (NORAD) in the diagnosis of PTB and to explore its mechanism in Mtb-infected macrophages. NORAD serum levels were estimated by qRT-PCR in 90 PTB patients and 85 healthy individuals. ROC curves were employed to assess the diagnostic value of NORAD for PTB. Human and murine macrophages were infected with Mtb strain H37Rv. CCK-8 and ELISA detected macrophages viability and inflammatory cytokine secretion. A dual-luciferase reporter assay was performed to analyze the targeting relationship between NORAD and microRNA (miR)-618. NORAD was significantly elevated in patients with PTB, and its positivity was correlated with inflammatory cytokines IL-1 β (r = 0.854), TNF-α (r = 0.617), IL-6 (r = 0.585). With an AUC of 0.918, and sensitivity and specificity of 80.0% and 89.4%, respectively, NORAD remarkedly identified PTB patients from healthy individuals. Furthermore, Mtb infection significantly increased NORAD levels in THP-1 and RAW264.7 and increased their viability and inflammation (P <0.001). However, this increased effect was weakened by reduced NORAD. Dual-luciferase reporter assay confirmed that miR-618 in macrophages was a target miRNA for NORAD and can be negatively regulated by it. Moreover, elevated miR-618 suppressed macrophage viability and inflammation in Mtb infection. NORAD is a potential diagnostic biomarker for PTB and is involved in Mtb infected macrophage activity and inflammation by targeting miR-618. This article is protected by copyright. All rights reserved.

Traditional Chinese Medicine: Role in Reducing β-Amyloid, Apoptosis, Autophagy, Neuroinflammation, Oxidative Stress, and Mitochondrial Dysfunction of Alzheimer's Disease

Alzheimer's disease (AD) is a progressive age-related neurodegenerative disease characterized by memory loss and cognitive impairment. The major characteristics of AD are amyloid β plaques, apoptosis, autophagy dysfunction, neuroinflammation, oxidative stress, and mitochondrial dysfunction. These are mostly used as the significant indicators for selecting the effects of potential drugs. It is imperative to explain AD pathogenesis and realize productive treatments. Although the currently used chemical drugs for clinical applications of AD are effective in managing the symptoms, they are inadequate to achieve anticipated preventive or therapeutic outcomes. There are new strategies for treating AD. Traditional Chinese Medicine (TCM) has accumulated thousands of years of experience in treating dementia. Nowadays, numerous modern pharmacological studies have verified the efficacy of many bioactive ingredients isolated from TCM for AD treatment. In this review, representative TCM for the treatment of AD are discussed, and among these herbal medicines, the Lamiaceae family accounts for the highest proportion. It is concluded that monomers and extracts from TCM have potential therapeutic effect for AD treatment.

Long non-coding RNA molecules in tuberculosis

Tuberculosis (TB), a chronic disease caused by Mycobacterium tuberculosis, is one of the deadliest infectious diseases in the world. Despite significant advances in detection techniques and therapeutic approaches for tuberculosis, there is still no suitable solution for early screening and reducing the number of individuals affected and their effective treatment. Various cellular events can disrupt the development of TB. The basis of these events is dysregulating of genes expression patterns related with specific molecules. Long non-coding RNAs (lncRNAs) are molecules discovered to regulate the expression of protein-coding genes and participate in gene silencing, cell cycle regulation and cellular differentiation processes. Dysregulation of lncRNAs has been found to be associated with many diseases, including cancers and infectious diseases. Thus, the recognition of lncRNAs as novel molecular biomarkers and therapeutic targets for tuberculosis is promising. In the present review, we try to summarize the current findings of lncRNA expression patterns and its role in tuberculosis infection process.

Tanshinone IIA protects lens epithelial cells from H2 O 2 -induced injury by upregulation of lncRNA ANRIL

Tanshinone IIA is a lipophilic diterpene extracted from the Salvia miltiorrhiza bunge, possessing antiapoptotic and antioxidant activities. The purpose of this study was to explore the effects of Tanshinone IIA on age-related nuclear cataract. Human lens epithelial cell line SRA01/04 was subjected to H ₂ O ₂ to mimic a cell model of cataract. Cell Counting Kit-8 assay, flow cytometer, and reactive oxygen species (ROS) detection were performed to evaluate the effect of Tanshinone IIA pretreatment on SRA01/04 cells injured by H ₂ O ₂ . Besides, the real-time quantitative polymerase chain reaction was used to assess the expression of long noncoding RNA (lncRNA) antisense noncoding RNA in the INK4 locus (ANRIL). Western blot analysis was performed to detect the expression of core proteins involved in cell survival and nuclear factor-κB (NF-κB) pathway. H ₂ O ₂ significantly decreased SRA01/04 cells viability, whereas increased apoptosis and ROS generation. This phenomenon was coupled with the upregulated p53, p21, Bax, cleaved caspase-3, and the downregulated cyclinD1, CDK4, and Bcl-2. Tanshinone IIA pretreatment protected SRA01/04 cells against H ₂ O ₂ -induced injury. In the meantime, the expression of lncRNA ANRIL was upregulated by Tanshinone IIA. And, the protective effects of Tanshinone IIA on H ₂ O ₂ -stimulated SRA01/04 cells were abolished when lncRNA ANRIL was silenced. Moreover, the elevated expression of lncRNA ANRIL induced by Tanshinone IIA was abolished by BAY 11-7082 (an inhibitor of NF-κB). To conclude, Tanshinone IIA protects SRA01/04 cells from apoptosis triggered by H ₂ O ₂ . Tanshinone IIA confers its protective effects possibly via modulation of NF-κB signaling and thereby elevating the expression of lncRNA ANRIL.

Downregulation of lncRNA AFAP1-AS1 by oridonin inhibits the epithelial-to-mesenchymal transition and proliferation of pancreatic cancer cells

Recent studies have demonstrated that the expression of the long non-coding RNA (lncRNA) AFAP1-AS1 in pancreatic cancer is negatively correlated with survival and prognosis. However, the effects of oridonin and lncRNA AFAP1-AS1 on the epithelial-to-mesenchymal transition (EMT) and migration of pancreatic cancer cells have not been fully elucidated. Surgery is the only potentially curative method for pancreatic cancer, but postoperative recurrence and metastasis are common. The aim of the present study was to assess the effect of oridonin and lncRNA AFAP1-AS1 silencing on pancreatic cancer cells. The pancreatic cancer cell lines BxPC-3 and PANC-1 cells were transfected with siAFAP1-AS1 and its negative control (siNC). After that, oridonin was used to treat the siAFAP1-AS1-transfected cells. The expression of lncRNA AFAP1-AS1 was downregulated in the pancreatic cancer cell lines BxPC-3 and PANC-1. The apoptosis and cell cycle progression of pancreatic cancer cells were evaluated by flow cytometry and Hoechst 33258 staining. Metastasis and invasion of BxPC-3 and PANC-1 cells were detected by transwell migration assay, real-time cell analysis, and western blot analysis. Cells were transfected with the lentiviral siAFAP1-AS1 and siNC, and tumorigenesis was evaluated in BALB/C nude mice. Immunohistochemical examination was used to verify the effects of oridonin and siAFAP1-AS1 on pancreatic cancer. The results demonstrated that the combination of oridonin and siAFAP1-AS1 inhibited pancreatic cancer cell proliferation, induced apoptosis, arrested cell cycle progression, prevented the migration, regulated EMT-related protein expression in BxPC-3 and PANC-1 cells, and inhibited pancreatic cancer cell tumorigenicity and EMT in nude mice.

Antiapoptosis effect of ZiShen prescription to increase learning and memory abilities of compound Alzheimer's disease model rats

Alzheimer's disease (AD) is a neurodegenerative disease characterized progressive memory loss and cognitive impairment. In previous studies, the activities of extracts of Chinese medicinal herbs to treat brain function disorders caused by AD have already been reported. ZiShen prescription was a traditional Chinese medicine (TCM) compound prescription reformed for AD disease based on the basic theory of TCM. To explore the effect of ZiShen (kidney-reinforcing) prescription on the learning and memory abilities, we made compound AD model rats by injecting d-galactose and ibotenic acid into the abdominal cavity to damage both sides of the nucleus basalis of Meynert with ibotenic acid. The trisected Y-maze was used to test the learning and memory abilities of AD model rats before and after treatment by ZiShen prescription and Piracetam. To investigate the mechanism of ZiShen prescription, the expressions of apoptosis-related genes (Bcl-2/Bax) in the cortex and hippocampus of compound AD model rats were detected in the cortex and hippocampus. The results show that, comparing with Piracetam, a clinical medicine to promote the thinking and memory for AD patients, ZiShen prescription significantly increased the learning and memory abilities of the compound AD model rats. After the treatment of ZiShen prescription, the expression of Bcl-2 was upregulated, along with a downregulation of Bax in the cortex and hippocampus of compound AD model rats. And the results indicated that the clinical benefits of ZiShen prescription were slightly better than Piracetam. Still, further well-designed studies are required to ensure the clinical effect of ZiShen.

Exploring the molecular mechanisms of Traditional Chinese Medicine components using gene expression signatures and connectivity map

BACKGROUND AND OBJECTIVE

Traditional Chinese Medicine (TCM) has been practiced over thousands of years in China and other Asian countries for treating various symptoms and diseases. However, the underlying molecular mechanisms of TCM are poorly understood, partly due to the "multi-component, multi-target" nature of TCM. To uncover the molecular mechanisms of TCM, we perform comprehensive gene expression analysis using connectivity map.

METHODS

We interrogated gene expression signatures obtained 102 TCM components using the next generation Connectivity Map (CMap) resource. We performed systematic data mining and analysis on the mechanism of action (MoA) of these TCM components based on the CMap results.

RESULTS

We clustered the 102 TCM components into four groups based on their MoAs using next generation CMap resource. We performed gene set enrichment analysis on these components to provide additional supports for explaining these molecular mechanisms. We also provided literature evidence to validate the MoAs identified through this bioinformatics analysis. Finally, we developed the Traditional Chinese Medicine Drug Repurposing Hub (TCM Hub) - a connectivity map resource to facilitate the elucidation of TCM MoA for drug repurposing research. TCMHub is freely available in http://tanlab.ucdenver.edu/TCMHub.

CONCLUSIONS

Molecular mechanisms of TCM could be uncovered by using gene expression signatures and connectivity map. Through this analysis, we identified many of the TCM components possess diverse MoAs, this may explain the applications of TCM in treating various symptoms and diseases.

Long Non-Coding RNAs in the Regulation of Gene Expression: Physiology and Disease

The identification of RNAs that are not translated into proteins was an important breakthrough, defining the diversity of molecules involved in eukaryotic regulation of gene expression. These non-coding RNAs can be divided into two main classes according to their length: short non-coding RNAs, such as microRNAs (miRNAs), and long non-coding RNAs (lncRNAs). The lncRNAs in association with other molecules can coordinate several physiological processes and their dysfunction may impact in several pathologies, including cancer and infectious diseases. They can control the flux of genetic information, such as chromosome structure modulation, transcription, splicing, messenger RNA (mRNA) stability, mRNA availability, and post-translational modifications. Long non-coding RNAs present interaction domains for DNA, mRNAs, miRNAs, and proteins, depending on both sequence and secondary structure. The advent of new generation sequencing has provided evidences of putative lncRNAs existence; however, the analysis of transcriptomes for their functional characterization remains a challenge. Here, we review some important aspects of lncRNA biology, focusing on their role as regulatory elements in gene expression modulation during physiological and disease processes, with implications in host and pathogens physiology, and their role in immune response modulation.

Long non-coding PCED1B-AS1 regulates macrophage apoptosis and autophagy by sponging miR-155 in active tuberculosis

Macrophages play a major role in the control and elimination of invading Mycobacterium tuberculosis (Mtb). Emerging studies have demonstrated that long non-coding RNAs (lncRNAs) are involved in resident macrophages in Mtb. However, the regulatory mechanism between lncRNAs and macrophages in tuberculosis (TB) remains unclear. In this study, we sought to investigate the effect of Mtb-associated lncRNA PCED1B-AS1 on macrophage apoptosis and autophagy. Our study first evaluated PCED1B-AS1 expression in the CD14⁺ monocytes from patients with active tuberculosis and from healthy individuals. It was found that PCED1B-AS1 expression was down-regulated in patients with active tuberculosis, accompanied by significant attenuated monocyte apoptosis and enhanced autophagy. In vitro, knockdown of PCED1B-AS1 reduced macrophage apoptosis and promoted autophagy. PCED1B-AS1 serves as an endogenous sponge to block miR-155 expression in macrophages by directly binding to miR-155. Furthermore, we demonstrated that overexpression of FOXO3/Rheb, target genes of miR-155, reversed the PCED1B-AS1-mediated effects on macrophage apoptosis and autophagy. Altogether, our data indicate that PCED1B-AS1 modulates macrophage apoptosis and autophagy by targeting the miR-155 axis in active TB.

FBP2 and Talin-1 are potential protein markers for Mongolian medicine symptom evaluation in viral infectious diseases

BACKGROUND

Influenza, measles, and mumps are common viral infectious diseases in Mongolia. The traditional Mongolian medicine (TMM) classified them as warm disease, and still plays a major role in the diagnoses and treatments.

METHODS

To interpret the connotation of the complex theoretical system in TMM with scientific technique, in this study, a high throughput mass spectrometry was used to identify potential protein markers of TMM symptom types. Fifty venous blood samples were drawn from influenza, measles and mumps patients. Differential proteins between samples of patients diagnosed as immature and mature heat in TMM were detected by mass spectrometry.

RESULTS

After proteomics analysis, 1500 proteins and 7619 polypeptides were identified and 1323 in total showed differential expression between those 2 symptom types; then enrichment analysis of the differentially expressed proteins revealed the significant biological functions related to the differentially expressed proteins, including cardiomyopathy, several bacterial and parasitic infections, bacterial invasion of epithelial cells, insulin signaling pathway, and regulation of actin cytoskeleton. The network analysis showed that FBP2 and Talin-1 were critical points and might determine the evolution directions of TMM warm disease symptom.

CONCLUSIONS

This study suggests that the identified core differential proteins may be regarded as potential biomarkers, and benefit to evaluate the evolutionary tendency of TMM warm disease symptoms.

Profiling analysis of 17β-estradiol-regulated lncRNAs in mouse thymic epithelial cells

Thymus is the primary organ for T cell differentiation and maturation. Many studies have demonstrated that estrogen plays a crucial role in thymic epithelial cell (TEC) proliferation during thymic involution. LncRNAs are involved in various biological processes; however, estrogen-mediated lncRNA expression in TECs has not been yet reported. To address this question, the mouse medullary thymic epithelial cell line 1 (MTEC1) was treated with 17β-estradiol (E2). By using CCK8 assay and flow cytometry, we found that E2 was able to inhibit viability and proliferation of MTEC1 cells. The expression profiles of lncRNAs in MTEC1 cells with or without E2 treatment were then measured by RNA-Seq, and a total of 962 lncRNAs and 2,469 mRNAs were shown to be differentially expressed. The reliability of RNA-Seq was confirmed by quantitative RT-PCR. Correlation analysis was conducted to investigate the potential function of lncRNAs. According to gene ontology (GO) analysis, differentially expressed lncRNAs were mainly related to cell proliferation, cell cycle and cell apoptosis. KEGG pathway analysis indicated that these lncRNAs were associated with several pathways, namely immunological activity, metabolism and cytokine-cytokine receptor interaction. In conclusion, our study provided a novel direction for studying the relationship between lncRNAs and E2 in the thymus.

Deregulated lncRNAs in B Cells from Patients with Active Tuberculosis

Role of lncRNAs in human adaptive immune response to TB infection is largely unexplored. To address this issue, here we characterized lncRNA expression profile in primary human B cell response to TB infection using microarray assay. Several lncRNAs and mRNAs were chosen for RT-qPCR validation. Bioinformatics prediction was applied to delineate function of the deregulated mRNAs. We found that 844 lncRNAs and 597 mRNAs were differentially expressed between B cell samples from individuals with or without TB. KEGG pathway analysis for the deregulated mRNAs indicated a number of pathways, such as TB, TLR signaling pathway and antigen processing and presentation. Moreover, corresponding to the dysregulation of many lncRNAs, we also found that their adjacent protein-coding genes were also deregulated. Functional annotation for the corresponding mRNAs showed that these lncRNAs were mainly associated with TLR signaling, TGF-β signaling. Interestingly, SOCS3, which is a critical negative regulator of cytokine response to TB infection and its nearby lncRNA XLOC_012582, were highly expressed in active TB B cells. Subsequent RT-qPCR results confirmed the changes. Whether upregulated XLOC_012582 causes SOCS3 overexpression and is eventually involved in the context of exacerbations of active TB represents an interesting issue that deserves to be further explored. Taken together, for the first time, we identified a set of deregulated lncRNAs in active TB B cells and their functions were predicted. Such findings provided novel insight into the pathogenesis of TB and further studies should focus on the function and pathogenic mechanisms of the lncRNAs involved in active TB.