Identification of latent tuberculosis infection-related microRNAs in human U937 macrophages expressing Mycobacterium tuberculosis Hsp16.3

Diagnostic value of microRNAs in active tuberculosis based on quantitative and enrichment analyses

BACKGROUND

Tuberculosis (TB) infection remains a crucial global health challenge, with active tuberculosis (ATB) representing main infection source. MicroRNA (miRNA) has emerged as a potential diagnostic tool in this context. This study aims to identify candidate miRNAs for ATB diagnosis and explore their possible mechanisms.

METHODS

Differentially expressed miRNAs in ATB were summarized in qualitative analysis. The diagnostic values of miRNAs for ATB subtypes were assessed by overall sensitivity, specificity, and area under the curve. Additionally, we conducted enrichment analysis on miRNAs and target genes.

RESULTS

Over 100 differentially expressed miRNAs were identified, with miR-29 family being the most extensively studied. The miR-29 family demonstrated sensitivity, specificity, and area under the curve of 80 %, 80 % and 0.86 respectively for active pulmonary TB (PTB). The differentially expressed miR-29-target genes in PTB were enriched in immune-related pathways.

CONCLUSIONS

The miR-29 family exhibits good diagnostic value for active PTB and shows association with immune process.

NOS2/miR-493-5p Signaling Regulates in the LPS-Induced Inflammatory Response in the RAW264.7 Cells

Tuberculosis (TB) is a fatal infectious disease; however, the molecular mechanisms underlying the pathogenicity of TB remain elusive. The present study aims to identify potential biomarkers associated with Mycobacterium tuberculosis (M.tb) infection by using integrated bioinformatics and in vitro validation studies. GSE50050, GSE78706, and GSE108844 data from the gene expression omnibus (GEO) database were downloaded to identify differentially expressed genes (DEGs). The functions of DEGs were further subjected to gene ontology (GO) and KEGG pathway analysis. The hub genes from the DEGs were determined based on the protein-protein interaction (PPI) network analysis. Finally, the hub genes were experimentally validated using the in vitro functional studies. A total of 26 common DEGs were identified among GSE50050, GSE78706, and GSE108844. The functional enrichment analysis showed that the common DEGs were associated with cytokines response and TB pathways. The PPI network analysis identified nine hub genes. Further in vitro studies showed that nitric oxide synthase 2 (NOS2) was up-regulated in RAW264.7 cells upon lipopolysaccharides (LPS) stimulation, which was accompanied by increased inflammatory cytokines release. Furthermore, NOS2 was found to be a target of miR-493-5p, which was confirmed by luciferase reporter assay. NOS2 was repressed by miR-493-5p overexpression and was up-regulated after miR-493-5p inhibition in RAW264.7 cells. The rescue experiments showed that LPS-induced increase in the inflammatory cytokines of the RAW264.7 cells was significantly attenuated by NOS2 knockdown and miR-493-5p overexpression. Collectively, our results for the first time demonstrated that NOS2/miR-493-5p signaling pathway may potentially involve in the inflammatory response during bacterial infection such as M. tb infection.

The exploitation of host autophagy and ubiquitin machinery by Mycobacterium tuberculosis in shaping immune responses and host defense during infection

Intracellular pathogens have evolved various efficient molecular armaments to subvert innate defenses. Cellular ubiquitination, a normal physiological process to maintain homeostasis, is emerging one such exploited mechanism. Ubiquitin (Ub), a small protein modifier, is conjugated to diverse protein substrates to regulate many functions. Structurally diverse linkages of poly-Ub to target proteins allow enormous functional diversity with specificity being governed by evolutionarily conserved enzymes (E3-Ub ligases). The Ub-binding domain (UBD) and LC3-interacting region (LIR) are critical features of macroautophagy/autophagy receptors that recognize Ub-conjugated on protein substrates. Emerging evidence suggests that E3-Ub ligases unexpectedly protect against intracellular pathogens by tagging poly-Ub on their surfaces and targeting them to phagophores. Two E3-Ub ligases, PRKN and SMURF1, provide immunity against Mycobacterium tuberculosis (M. tb). Both enzymes conjugate K63 and K48-linked poly-Ub to M. tb for successful delivery to phagophores. Intriguingly, M. tb exploits virulence factors to effectively dampen host-directed autophagy utilizing diverse mechanisms. Autophagy receptors contain LIR-motifs that interact with conserved Atg8-family proteins to modulate phagophore biogenesis and fusion to the lysosome. Intracellular pathogens have evolved a vast repertoire of virulence effectors to subdue host-immunity via hijacking the host ubiquitination process. This review highlights the xenophagy-mediated clearance of M. tb involving host E3-Ub ligases and counter-strategy of autophagy inhibition by M. tb using virulence factors. The role of Ub-binding receptors and their mode of autophagy regulation is also explained. We also discuss the co-opting and utilization of the host Ub system by M. tb for its survival and virulence.Abbreviations: APC: anaphase promoting complex/cyclosome; ATG5: autophagy related 5; BCG: bacille Calmette-Guerin; C2: Ca²⁺-binding motif; CALCOCO2: calcium binding and coiled-coil domain 2; CUE: coupling of ubiquitin conjugation to ER degradation domains; DUB: deubiquitinating enzyme; GABARAP: GABA type A receptor-associated protein; HECT: homologous to the E6-AP carboxyl terminus; IBR: in-between-ring fingers; IFN: interferon; IL1B: interleukin 1 beta; KEAP1: kelch like ECH associated protein 1; LAMP1: lysosomal associated membrane protein 1; LGALS: galectin; LIR: LC3-interacting region; MAPK11/p38: mitogen-activated protein kinase 11; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAPK8/JNK: mitogen-activated protein kinase 8; MHC-II: major histocompatibility complex-II; MTOR: mechanistic target of rapamycin kinase; NBR1: NBR1 autophagy cargo receptor; NFKB1/p50: nuclear factor kappa B subunit 1; OPTN: optineurin; PB1: phox and bem 1; PE/PPE: proline-glutamic acid/proline-proline-glutamic acid; PknG: serine/threonine-protein kinase PknG; PRKN: parkin RBR E3 ubiquitin protein ligase; RBR: RING-in between RING; RING: really interesting new gene; RNF166: RING finger protein 166; ROS: reactive oxygen species; SMURF1: SMAD specific E3 ubiquitin protein ligase 1; SQSTM1: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1; TNF: tumor necrosis factor; TRAF6: TNF receptor associated factor 6; Ub: ubiquitin; UBA: ubiquitin-associated; UBAN: ubiquitin-binding domain in ABIN proteins and NEMO; UBD: ubiquitin-binding domain; UBL: ubiquitin-like; ULK1: unc-51 like autophagy activating kinase 1.

MicroRNAs as immune regulators and biomarkers in tuberculosis

Tuberculosis (TB), which is caused by Mycobacterium tuberculosis (Mtb), is one of the most lethal infectious disease worldwide, and it greatly affects human health. Some diagnostic and therapeutic methods are available to effectively prevent and treat TB; however, only a few systematic studies have described the roles of microRNAs (miRNAs) in TB. Combining multiple clinical datasets and previous studies on Mtb and miRNAs, we state that pathogens can exploit interactions between miRNAs and other biomolecules to avoid host mechanisms of immune-mediated clearance and survive in host cells for a long time. During the interaction between Mtb and host cells, miRNA expression levels are altered, resulting in the changes in the miRNA-mediated regulation of host cell metabolism, inflammatory responses, apoptosis, and autophagy. In addition, differential miRNA expression can be used to distinguish healthy individuals, patients with TB, and patients with latent TB. This review summarizes the roles of miRNAs in immune regulation and their application as biomarkers in TB. These findings could provide new opportunities for the diagnosis and treatment of TB.

Dexmedetomidine reduces propofol-induced hippocampal neuron injury by modulating the miR-377-5p/Arc pathway

BACKGROUND

Propofol and dexmedetomidine (DEX) are widely used in general anesthesia, and exert toxic and protective effects on hippocampal neurons, respectively. The study sought to investigate the molecular mechanisms of DEX-mediated neuroprotection against propofol-induced hippocampal neuron injury in mouse brains.

METHODS

Hippocampal neurons of mice and HT22 cells were treated with propofol, DEX, and propofol+DEX. In addition, transfection of miR-377-5p mimics or inhibitors was performed in HT22 cells. Neuronal apoptosis was evaluated by a means of terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick end labeling (TUNEL) or Hochest 33,258 staining; Arc positive expression in hippocampus tissues was detected using a microscope in immunohistochemistry assays; miRNA-377-5p expression was quantified by RT-qPCR; the protein levels of Arc, DNMT3A, and DNMT3B were determined using western blot; Cell Counting Kit-8 (CCK-8) assay was used to detect the viability and apoptotic rate of the neurons; methylation analysis in the miR-377-5p promoter was performed through methylated DNA immunoprecipitation (MeDIP) assay; dual luciferase reporter assay was performed to confirm whether Arc was under targeted regulation of miR-377-5p.

RESULTS

In the current study, both in vitro and in vivo, propofol treatment induced hippocampal neuron apoptosis and suppressed cell viability. DNMT3A and DNMT3B expression levels were decreased following propofol treatment, resulting in lowered methylation in the miR-377-5p promoter region and then enhanced expression of miR-377-5p, leading to a decrease in the expression of downstream Arc. Conversely, the expression levels of DNMT3A and DNMT3B were increased following DEX treatment, thus methylation in miR-377-5p promoter region was improved, and miR-377-5p expression was decreased, leading to an increase in the expression of downstream Arc. Eventually, DEX pretreatment protected hippocampal neurons against propofol-induced neurotoxicity by recovering the expression levels of DNMT3A, miR-377-5p, and Arc to the normal levels. Additionally, DNMT3A knockdown improved miR-377-5p expression but reduced Arc expression, and DNMT3A overexpression exerted the opposite effects. Dual luciferase reporter assay revealed a binding target between miR-377-5p and Arc 3'UTR. The neuroprotective effect of DEX against propofol-induced neuronal apoptosis was diminished after Arc knockdown. Silencing Arc independently triggered the apoptosis of HT22 cells, which was alleviated through transfection of miR-377-5p inhibitors.

CONCLUSIONS

DEX reduced propofol-induced hippocampal neuron injury via the miR-377-5p/Arc signaling pathway.

Cathepsins and Their Endogenous Inhibitors in Host Defense During Mycobacterium tuberculosis and HIV Infection

The moment a very old bacterial pathogen met a young virus from the 80's defined the beginning of a tragic syndemic for humanity. Such is the case for the causative agent of tuberculosis and the human immunodeficiency virus (HIV). Syndemic is by definition a convergence of more than one disease resulting in magnification of their burden. Both pathogens work synergistically contributing to speed up the replication of each other. Mycobacterium tuberculosis (Mtb) and HIV infections are in the 21st century among the leaders of morbidity and mortality of humankind. There is an urgent need for development of new approaches for prevention, better diagnosis, and new therapies for both infections. Moreover, these approaches should consider Mtb and HIV as a co-infection, rather than just as separate problems, to prevent further aggravation of the HIV-TB syndemic. Both pathogens manipulate the host immune responses to establish chronic infections in intracellular niches of their host cells. This includes manipulation of host relevant antimicrobial proteases such as cathepsins or their endogenous inhibitors. Here we discuss recent understanding on how Mtb and HIV interact with cathepsins and their inhibitors in their multifactorial functions during the pathogenesis of both infections. Particularly we will address the role on pathogen transmission, during establishment of intracellular chronic niches and in granuloma clinical outcome and tuberculosis diagnosis. This area of research will open new avenues for the design of innovative therapies and diagnostic interventions so urgently needed to fight this threat to humanity.

Monocyte and Macrophage miRNA: Potent Biomarker and Target for Host-Directed Therapy for Tuberculosis

The end TB strategy reinforces the essentiality of readily accessible biomarkers for early tuberculosis diagnosis. Exploration of microRNA (miRNA) and pathway analysis opens an avenue for the discovery of possible therapeutic targets. miRNA is a small, non-coding oligonucleotide characterized by the mechanism of gene regulation, transcription, and immunomodulation. Studies on miRNA define their importance as an immune marker for active disease progression and as an immunomodulator for innate mechanisms, such as apoptosis and autophagy. Monocyte research is highly advancing toward TB pathogenesis and biomarker efficiency because of its innate and adaptive response connectivity. The combination of monocytes/macrophages and their relative miRNA expression furnish newer insight on the unresolved mechanism for Mycobacterium survival, exploitation of host defense, latent infection, and disease resistance. This review deals with miRNA from monocytes, their relative expression in different disease stages of TB, multiple gene regulating mechanisms in shaping immunity against tuberculosis, and their functionality as biomarker and host-mediated therapeutics. Future collaborative efforts involving multidisciplinary approach in various ethnic population with multiple factors (age, gender, mycobacterial strain, disease stage, other chronic lung infections, and inflammatory disease criteria) on these short miRNAs from body fluids and cells could predict the valuable miRNA biosignature network as a potent tool for biomarkers and host-directed therapy.

Targets and regulation of microRNA-652-3p in homoeostasis and disease

microRNA are small non-coding RNA molecules which inhibit gene expression by binding mRNA, preventing its translation. As important regulators of gene expression, there is increasing interest in microRNAs as potential diagnostic biomarkers and therapeutic targets. Studies investigating the role of one of the miRNA-miR-652-3p-detail diverse roles for this miRNA in normal cell homoeostasis and disease states, including cancers, cardiovascular disease, mental health, and central nervous system diseases. Here, we review recent literature surrounding miR-652-3p, discussing its known target genes and their relevance to disease progression. These studies demonstrate that miR-652-3p targets LLGL1 and ZEB1 to modulate cell polarity mechanisms, with impacts on cancer metastasis and asymmetric cell division. Inhibition of the NOTCH ligand JAG1 by miR-652-3p can have diverse effects on angiogenesis and immune cell regulation. Investigation of miR-652-3p and other dysregulated miRNAs identified a number of pathways potentially regulated by miR-652-3p. This review demonstrates that miR-652-3p has great promise as a diagnostic or therapeutic target due to its activity across multiple cellular systems.

Neutrophil-derived trail is a proinflammatory subtype of neutrophil-derived extracellular vesicles

Aims: Extracellular vesicles (EVs) are membrane-derived vesicles that mediate intercellular communications. Neutrophils produce different subtypes of EVs during inflammatory responses. Neutrophil-derived trails (NDTRs) are generated by neutrophils migrating toward inflammatory foci, whereas neutrophil-derived microvesicles (NDMVs) are thought to be generated by neutrophils that have arrived at the inflammatory foci. However, the physical and functional characteristics of neutrophil-derived EVs are incompletely understood. In this study, we aimed to investigate the differences between NDTRs and NDMVs. Methods: The generation of neutrophil-derived EVs were visualized by live-cell fluorescence images and the physical characteristics were further analyzed using nanotracking analysis assay, scanning electron microscopic analysis, and marker expressions. Functional characteristics of neutrophil-derived EVs were analyzed using assays for bactericidal activity, monocyte chemotaxis, phenotype polarization of macrophages, and miRNA sequencing. Finally, the effects of neutrophil-derived EVs on the acute and chronic inflammation were examined in vivo. Results: Both EVs share similar characteristics including stimulators, surface marker expression, bactericidal activity, and chemoattractive effect on monocytes via MCP-1. However, the integrin-mediated physical interaction was required for generation of NDTRs whereas NDMV generation was dependent on PI3K pathway. Interestingly, NDTRs contained proinflammatory miRNAs such as miR-1260, miR-1285, miR-4454, and miR-7975, while NDMVs contained anti-inflammatory miRNAs such as miR-126, miR-150, and miR-451a. Although both EVs were easily uptaken by monocytes, NDTRs enhanced proinflammatory macrophage polarization whereas NDMVs induced anti-inflammatory macrophage polarization. Moreover, NDTRs showed protective effects against lethality in a murine sepsis model and pathological changes in a murine chronic colitis model. Conclusion: These results suggest that NDTR is a proinflammatory subtype of neutrophil-derived EVs distinguished from NDMV.

MicroRNA research: The new dawn of Tuberculosis

Tuberculosis (TB) is global, one of the most fatal communicable diseases and leading cause of worldwide mortality. One-third of the global population is latently affected by Mtb (Mycobacterium tuberculosis) due to its ability to circumvent the host's immune response for its own survival. MicroRNAs (miRNAs) are small, non-coding RNAs which function at the post-transcriptional level and are critical in fine-tuning immune responses regulating the repertoire of genes expressed in immune cells. Recent studies have established their crucial role against TB. Furthermore, the differential expression pattern of miRNAs has revealed the potential role of miRNAs as biomarkers which could be utilized to differentiate between healthy controls and active TB patients or between active and latent TB. The recent advancements made in the field of miRNA regulation of the host responses against TB, as well as the potential of miRNAs as biomarkers for TB diagnosis are discussed here in this review.

Reprogramming of Small Noncoding RNA Populations in Peripheral Blood Reveals Host Biomarkers for Latent and Active Mycobacterium tuberculosis Infection

Tuberculosis is the infectious disease with the worldwide largest disease burden and there remains a great need for better diagnostic biomarkers to detect latent and active M. tuberculosis infection. RNA molecules hold great promise in this regard, as their levels of expression may differ considerably between infected and uninfected subjects. We have measured expression changes in the four major classes of small noncoding RNAs in blood samples from patients with different stages of TB infection. We found that, in addition to miRNAs (which are known to be highly regulated in blood cells from TB patients), expression of piRNA and snoRNA is greatly altered in both latent and active TB, yielding promising biomarkers. Even though the functions of many sncRNA other than miRNA are still poorly understood, our results strongly suggest that at least piRNA and snoRNA populations may represent hitherto underappreciated players in the different stages of TB infection.

In tuberculosis (TB), as in other infectious diseases, studies of small noncoding RNAs (sncRNA) in peripheral blood have focused on microRNAs (miRNAs) but have neglected the other major sncRNA classes in spite of their potential functions in host gene regulation. Using RNA sequencing of whole blood, we have therefore determined expression of miRNA, PIWI-interacting RNA (piRNA), small nucleolar RNA (snoRNA), and small nuclear RNA (snRNA) in patients with TB (n = 8), latent TB infection (LTBI; n = 21), and treated LTBI (LTBItt; n = 6) and in uninfected exposed controls (ExC; n = 14). As expected, sncRNA reprogramming was greater in TB than in LTBI, with the greatest changes seen in miRNA populations. However, substantial dynamics were also evident in piRNA and snoRNA populations. One miRNA and 2 piRNAs were identified as moderately accurate (area under the curve [AUC] = 0.70 to 0.74) biomarkers for LTBI, as were 1 miRNA, 1 piRNA, and 2 snoRNAs (AUC = 0.79 to 0.91) for accomplished LTBI treatment. Logistic regression identified the combination of 4 sncRNA (let-7a-5p, miR-589-5p, miR-196b-5p, and SNORD104) as a highly sensitive (100%) classifier to discriminate TB from all non-TB groups. Notably, it reclassified 8 presumed LTBI cases as TB cases, 5 of which turned out to have features of Mycobacterium tuberculosis infection on chest radiographs. SNORD104 expression decreased during M. tuberculosis infection of primary human peripheral blood mononuclear cells (PBMC) and M2-like (P = 0.03) but not M1-like (P = 0.31) macrophages, suggesting that its downregulation in peripheral blood in TB is biologically relevant. Taken together, the results demonstrate that snoRNA and piRNA should be considered in addition to miRNA as biomarkers and pathogenesis factors in the various stages of TB.

Genome-Wide miRNA Analysis Identifies Potential Biomarkers in Distinguishing Tuberculous and Viral Meningitis

Tuberculous meningitis (TBM) is the most common and severe form of central nervous system tuberculosis. Due to the non-specific clinical presentation and lack of efficient diagnosis methods, it is difficult to discriminate TBM from other frequent types of meningitis, especially viral meningitis (VM). In order to identify the potential biomarkers for discriminating TBM and VM and to reveal the different pathophysiological processes between TBM and VM, a genome-wide miRNA screening of PBMCs from TBM, VM, and healthy controls (HCs) using microarray assay was performed (12 samples). Twenty-eight differentially expressed miRNAs were identified between TBM and VM, and 11 differentially expressed miRNAs were identified between TBM and HCs. The 6 overlapping miRNAs detected in both TBM vs. VM and TBM vs. HCs were verified by qPCR analysis and showed a 100% consistent expression patterns with that in microarray test. Statistically significant differences of 4 miRNAs (miR-126-3p, miR-130a-3p, miR-151a-3p, and miR-199a-5p) were further confirmed in TBM compared with VM and HCs in independent PBMCs sample set (n = 96, P < 0.01). Three of which were also showed significantly different between TBM and VM in CSF samples (n = 70, P < 0.05). The receiver operating characteristic curve (ROC) analysis showed that the area under the ROC curve (AUC) of these 4 miRNAs in PBMCs were more than 0.70 in discriminating TBM from VM. Combination of these 4 miRNAs could achieve better discriminative capacity [AUC = 0.893 (0.788-0.957)], with a sensitivity of 90.6% (75.0-98.0%), and a specificity of 86.7% (69.3-96.2%). Additional validation was performed to evaluate the diagnostic panel in another independent sample set (n = 49), which yielded a sensitivity of 81.8% (9/11), and specificity of 90.0% (9/10) in distinguishing TBM and VM, and a sensitivity of 81.8% (9/11), and a specificity of 84.6% (11/13) in discriminating TBM from other non-TBM patients. This study uncovered the miRNA profiles of TBM and VM patients, which can facilitate better understanding of the pathogenesis involved in these two diseases and identified 4 novel miRNAs in distinguishing TBM and VM.

Small RNA Profiles of Serum Exosomes Derived From Individuals With Latent and Active Tuberculosis

Tuberculosis (TB) has been the leading lethal infectious disease worldwide since 2014, and about one third of the world’s population has a latent TB infection (LTBI). This is largely attributed to the difficulties in diagnosis and treatment of TB and LTBI patients. Exosomes offer a new perspective on investigation of the process of TB infection. In this study, we performed small RNA sequencing to explore small RNA profiles of serum exosomes derived from LTBI and TB patients and healthy controls (HC). Our results revealed distinct miRNA profile of the exosomes in the three groups. We screened 250 differentially expressed miRNAs including 130 specifically expressed miRNAs. Some miRNAs were further validated to be specifically expressed in LTBI (hsa-let-7e-5p, hsa-let-7d-5p, hsa-miR-450a-5p, and hsa-miR-140-5p) and TB samples (hsa-miR-1246, hsa-miR-2110, hsa-miR-370-3P, hsa-miR-28-3p, and hsa-miR-193b-5p). Additionally, we demonstrated four expression panels in LTBI and TB groups, and six expression patterns among the three groups. These specifically expressed miRNAs and differentially expressed miRNAs in different panels and patterns provide potential biomarkers for detection/diagnosis of latent and active TB using exosomal miRNAs. Additionally, we also discovered plenty of small RNAs derived from genomic repetitive sequences, which might play roles in host immune responses along with Mtb infection progresses. Overall, our findings provide important reference and an improved understanding about miRNAs and repetitive region-derived small RNAs in exosomes during the Mtb infectious process, and facilitate the development of potential molecular targets for detection/diagnosis of latent and active tuberculosis.

MiR-377 inhibits wear particle-induced osteolysis via targeting RANKL

Periprosthetic osteolysis caused by wear particles is the main factor that affects the long-term efficacy of artificial joint replacement, and macrophages play a vital role in the pathogenesis of periprosthetic osteolysis, while the potential mechanism underlying this is still unclear. To investigate the underlying role of miR-377 in wear particle-induced osteolysis (PIO), blood samples from patients undergoing arthroplasty were collected for analyzing the correlation between miR-377 expression and the clinicopathological parameters of PIO. Peripheral blood macrophages were obtained to compare the miR-377 and receptor activator of NF-κB ligand (RANKL) expressions. Bone marrow macrophages (BMMs) following titanium (Ti) particle treatment and/or miR-377 mimic transfection were used. The expressions of RANKL, pro-inflammatory cytokines interleukin 6 (IL-6) and tumor necrosis factor-α (TNF-α) and the osteoclast-related molecules tartrate-resistant acid phosphatase (TRAP) and cathepsin K (CTSK) were determined using real-time polymerase chain reaction or western blotting or enzyme-linked immunosorbent assay or TRAP staining, when appropriate. The interaction between miR-377 and RANKL was assessed by luciferase reporter assay. The in vivo role of miR-377 in PIO was evaluated using a mouse calvarial osteolysis model. There were significant differences in downregulated miR-377 expression between the different numbers of particles in the joint prostheses. The Ti particle treatment increased pro-inflammatory cytokine levels, downregulated RANKL and increased osteoclast activity in BMMs, while miR-377 overexpression led to the opposite effect. Taken together, miR-377 downregulated the target gene RANKL, resulting in PIO inhibition. MiR-377 relieved PIO by negatively regulating RANKL.

Bioinformatics analysis of microRNA expression between patients with and without latent tuberculosis infections

Tuberculosis (TB) is a globally prevalent infectious disease. The mechanisms of latent TB infection (LTBI) remain to be fully elucidated and may provide novel approaches for diagnosis. As therapeutic targets and molecular diagnostic markers, microRNAs (miRs) have been studied and utilized in various diseases. In the present study, the differentially expressed miRs (DEMs) in LTBI were screened and analyzed to determine the underlying mechanisms and identify potential biomarkers, thereby contributing to the diagnosis of LTBI. The GSE25435 and GSE29190 datasets from Gene Expression Omnibus were selected for analysis. The 2 datasets were analyzed individually using the Bioconductor package to screen the DEMs with specific cut-off criteria [P<0.01 and |log (fold change)|≥1]. Target gene prediction and interaction network construction were performed using Targetscan, the Search Tool for the Retrieval of Interacting Genes and Proteins and Cytoscape individually, and were merged using the latter tool. The hub genes were finally selected based on their degree of connectivity (DC). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using the KEGG and GENCLIP. A total of 144 DEMs were identified from the 2 datasets. By exploring the overlapping miRs in the two datasets, Homo sapiens (hsa)-miR-29a and hsa-miR-15b were identified to be decreased, while hsa-miR-576-5p, hsa-miR-500 and hsa-miR-155 were identified to be upregulated. hsa-miR-500a-3p and hsa-miR-29a-3p, as well as 4 genes, namely cell division cycle (CDC)42, actin α1, skeletal muscle (ACTA1), phosphatase and tensin homolog (PTEN) and fos proto-oncogene (FOS), were selected as the key factors in this regulatory network. A total of 9 signaling pathways, including phosphoinositide-3 kinase (PI3K)/AKT and 11 biological processes, were identified to be associated with LTBI. In conclusion, the present analysis identified hsa-miR-500a-3p and hsa-miR-29a-3p, as well as CDC42, ACTA1, PTEN and FOS, as the most promising biomarkers and therapeutic candidates for LTBI. The PI3K/AKT signaling pathway is the key signaling pathway implicated in LTBI, and an in-depth investigation of the efficiency of PI3K/AKT signaling inhibitors may be used to prevent a chronic state of infection in LTBI.

Signature of circular RNAs in peripheral blood mononuclear cells from patients with active tuberculosis

The study was to characterize the expression profiles of circular RNAs (circRNAs) in peripheral blood mononuclear cells (PBMCs) from active tuberculosis (TB) patients and to investigate their function. Microarray was applied to detect circRNA expression and reverse transcription‐quantitative polymerase chain reaction was conducted to validate the microarray results. Meanwhile, receiver operating characteristic curve (ROC) curve was calculated to evaluate the predictive power of the selected circRNAs for TB diagnosis. Additionally, circRNA/miRNA interaction was predicted based on miRNA target prediction software, and gene ontology as well as Kyoto Encyclopedia of Genes and Genomes pathway analysis were used to predict their biological function. In total, 171 circRNAs were found to be dysregulated in TB samples. Specifically, circRNA_103017, circRNA_059914 and circRNA_101128 were confirmed to be increased, while circRNA_062400 was decreased in TB samples. ROC analysis revealed that circRNA_103017 had potential value for TB diagnosis, followed by circRNA_059914 and circRNA_101128. Moreover, circRNA_101128 expression in TB samples was negatively correlated with the level of its possible target let‐7a and bioinformatics analysis showed that circRNA_101128 was potentially involved in MAPK and P13K‐Akt pathway possibly via modulation of let‐7a. Taken together, our results indicated that some dysregulated circRNAs were potential biomarkers for the diagnosis of TB and circRNA_101128‐let‐7a interplay may play considerable role in PBMCs response to Mtb infection.

Downregulation of miR-20b-5p facilitates Mycobacterium tuberculosis survival in RAW 264.7 macrophages via attenuating the cell apoptosis by Mcl-1 upregulation

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb). The interaction between Mtb and macrophages, which is regulated by microRNAs, determines the development of TB. However, the function of microRNA-20b-5p (miR-20b-5p) in RAW 264.7 macrophages against Mtb remains unknown. In this study, we analyzed the expression level of miR-20b-5p in macrophage responses to Mtb infection and exosomes derived from macrophages after Mtb infection. MiR-20b-5p mimics and inhibitor were, respectively, transfected to evaluate the effect of miR-20b-5p on Mtb and macrophages. In addition, the targets of miR-20b-5p were predicted by a bioinformatics analysis. The macrophages were respectively transfected with miR-20b-5p mimics and inhibitor to determine the messenger RNA expression levels of the targets by reverse transcription-polymerase chain reaction assay. The results revealed that the miR-20b-5p expression level was decreased in the infected macrophages at different times. MiR-20b-5p was shown in the exosomes released from macrophages infected with Mtb. Upregulation of the miR-20b-5p level suppressed the survival of Mtb in macrophages, while downregulation of the miR-20b-5p level enhanced the survival of Mtb in macrophages. Overexpression of miR-20b-5p decreased the cell viability and induced apoptosis in Mtb-infected macrophages, while underexpression of miR-20b-5p increased the cell vitality and attenuated apoptosis in Mtb-infected macrophages. The bioinformatics analysis revealed that Mcl-1 was a target of miR-20b-5p. MiR-20b-5p negatively regulated the expression of Mcl-1. Overall, this study is the first to demonstrate the effect of miR-20b-5p on Mtb infection and present miR-20b-5p and exosomes as the potential therapeutic targets of TB.

miRNAs in immune responses to Mycobacterium tuberculosis infection

Tuberculosis (TB) is one of the most fatal infectious diseases, affecting one third of the world's population. The causative agent, Mycobacterium tuberculosis (Mtb), has a well-established ability to circumvent the host's immune system for its long-term intracellular survival. MicroRNAs (miRNAs) are crucial post-transcriptional regulators of immune response. They act by negatively regulating the expression levels of important genes in both innate and adaptive immunity. It has been established in recent studies that the host immune response against Mtb is regulated by many miRNAs, most of which are induced by Mtb infection. Moreover, differential expression of miRNA in tuberculosis (TB) patients may help distinguish between TB patients and healthy individuals or latent TB. In this review, we present the recent advancements on the miRNA regulation of the host responses against Mtb infection, as well as the potential of miRNAs to as biomarkers for TB diagnosis.

Anionic nanoliposomes reduced atherosclerosis progression in Low Density Lipoprotein Receptor (LDLR) deficient mice fed a high fat diet

Atherosclerosis is a systemic disease characterized by the deposition of cholesterol and inflammatory cells within the arterial wall. Removal of cholesterol from the vessel wall may have an impact on the size and composition of atherosclerotic lesions. Anionic phospholipids or liposome vesicles composed of a lipid bilayer such as nanoliposomes have been suggested as treatments for dyslipidemia. In this study, we investigated the effect of anionic nanoliposomes on atherosclerosis in a mouse model. Low-density lipoprotein receptor knockout mice (Ldlr^-/- ) were fed with an atherosclerosis promoting high fat and cholesterol (HFC) diet for 12 weeks. Anionic nanoliposomes including hydrogenated soy phosphatidylcholine (HSPC) and distearoyl phosphatidylglycerol (DSPG) (molar ratio: 1:3) were injected intravenously into HFC-fed Ldlr^-/- mice once a week for 4 weeks. Mice receiving nanoliposomes had significantly reduced atherosclerosis within the aortic arch as assessed by Sudan IV staining area (p = 0.007), and reduced intima/media ratio (p = 0.030) and greater collagen deposition within atherosclerosis plaques within the brachiocephalic artery (p = 0.007), compared to control mice. Administration of nanoliposomes enhanced markers of reverse cholesterol transport (RCT) and increased markers of plaque stability in HFC-fed Ldlr^-/- mice. Reduced cholesterol accumulation was observed in the liver along with the up-regulation of the major genes involved in the efflux of cholesterol such as hepatic ATP-binding cassette transporters (ABC) including Abc-a1, Abc-g1, Abc-g5, and Abc-g8, Scavenger receptor class B, member 1 (Scarb1), and Liver X receptor alpha (Lxr)-α. Lecithin Cholesterol Acyltransferase activity within the plasma was also increased in mice receiving nanoliposomes. Anionic nanoliposome administration reduced atherosclerosis in HFC-fed Ldlr^-/- mice by promoting RCT and upregulating the ABC-A1/ABC-G1 pathway.

miRNAs in Tuberculosis: New Avenues for Diagnosis and Host-Directed Therapy

Tuberculosis (TB) is one of the most fatal infectious diseases and a leading cause of mortality, with 95% of these deaths occurring in developing countries. The causative agent, Mycobacterium tuberculosis (Mtb), has a well-established ability to circumvent the host's immune system for its intracellular survival. microRNAs (miRNAs) are small, non-coding RNAs having an important function at the post-transcriptional level and are involved in shaping immunity by regulating the repertoire of genes expressed in immune cells. It has been established in recent studies that the innate immune response against TB is significantly regulated by miRNAs. Moreover, differential expression of miRNA in Mtb infection can reflect the disease progression and may help distinguish between active and latent TB infection (LTBI). These findings encouraged the application of miRNAs as potential biomarkers. Similarly, active participation of miRNAs in modulation of autophagy and apoptosis responses against Mtb opens an exciting avenue for the exploitation of miRNAs as host directed therapy (HDT) against TB. Nanoparticles mediated delivery of miRNAs to treat various diseases has been reported and this technology has a great potential to be used in TB. In reality, this exploitation of miRNAs as biomarkers and in HDT is still in its infancy stage, and more studies using animal models mimicking human TB are advocated to assess the role of miRNAs as biomarkers and therapeutic targets. In this review, we attempt to summarize the recent advancements in the role of miRNAs in TB as immune modulator, miRNAs' capability to distinguish between active and latent TB and, finally, usage of miRNAs as therapeutic targets against TB.

MicroRNA-296: a promising target in the pathogenesis of atherosclerosis?

Atherosclerosis has been recognized as an inflammatory disease involving the vascular wall. MicroRNAs are a group of small noncoding RNAs to regulate gene expression at the transcriptional level through mRNA degradation or translation repression. Recent studies suggest that miR-296 may play crucial roles in the regulation of angiogenesis, inflammatory response, cholesterol metabolism, hypertension, cellular proliferation and apoptosis. In this review, we primarily discussed the molecular targets of miR-296 involved in the development of atherosclerosis, which may provide a basis for future investigation and a better understanding of the biological functions of miR-296 in atherosclerosis.

Changed immune and miRNA response in RAW264.7 cells infected with cell wall deficient mycobacterium tuberculosis

Cell wall deficient (CWD) forms of Mycobacterium tuberculosis (Mtb) confers a marked resistance to immune system of the host. However, there is limit data on the effect of intracellular CWD-Mtb infection on macrophages. In the study, effects of CWD-Mtb on cell viability, cytokine response and miRNA expression of macrophages were analyzed. Cell viability was reduced, levels of interleukin-1α (IL-1α), IL-1β, IL-6, IL-10 and interferon-γ (IFN-γ) were also significantly changed after infection of RAW264.7 cells with CWD-Mtb. A total of 105 miRNAs were deregulated between CWD-Mtb and wild Mtb group, and among them, miR-29b was upregulated in CWD-Mtb group. Downregulation of miR-29b resulted in significant elevation level of IFN-γ mRNA. Involved signaling pathways of potential target genes of differentially expressed miRNAs mainly focused on T cell receptor signaling pathway, MAPK signaling pathway, neurotrophin signaling pathway, and regulation of actin cytoskeleton. Taken together, the results showed that cytokine production of CWD-Mtb infected macrophages was altered and many miRNAs were involved in regulation of macrophage response to CWD-Mtb infection, which probably determined the differential outcome following different phenotype Mtb infection. These findings open up a new and interesting avenue for an improved understanding of pathogenesis of CWD-Mtb.

MicroRNA 27a-3p Regulates Antimicrobial Responses of Murine Macrophages Infected by Mycobacterium avium subspecies paratuberculosis by Targeting Interleukin-10 and TGF-β-Activated Protein Kinase 1 Binding Protein 2

Mycobacterium avium subspecies paratuberculosis (MAP) persistently survive and replicate in mononuclear phagocytic cells by adopting various strategies to subvert host immune response. Interleukin-10 (IL-10) upregulation via inhibition of macrophage bactericidal activity is a critical step for MAP survival and pathogenesis within the host cell. Mitogen-activated protein kinase p38 signaling cascade plays a crucial role in the elevation of IL-10 and progression of MAP pathogenesis. The contribution of microRNAs (miRNAs) and their influence on the activation of macrophages during MAP pathogenesis are still unclear. In the current study, we found that miRNA-27a-3p (miR-27a) expression is downregulated during MAP infection both in vivo and in vitro. Moreover, miR-27a is also downregulated in toll-like receptor 2 (TLR2)-stimulated murine macrophages (RAW264.7 and bone marrow-derived macrophage). ELISA and real-time qRT-PCR results confirm that overexpression of miR-27a inhibited MAP-induced IL-10 production in macrophages and upregulated pro-inflammatory cytokines, while miR-27a inhibitor counteracted these effects. Luciferase reporter assay results revealed that IL-10 and TGF-β-activated protein kinase 1 binding protein 2 (TAB 2) are potential targets of miR-27a. In addition, we demonstrated that miR-27a negatively regulates TAB 2 expression and diminishes TAB 2-dependent p38/JNK phosphorylation, ultimately downregulating IL-10 expression in MAP-infected macrophages. Furthermore, overexpression of miR-27a significantly inhibited the intracellular survival of MAP in infected macrophages. Our data show that miR-27a augments antimicrobial activities of macrophages and inhibits the expression of IL-10, demonstrating that miR-27a regulates protective innate immune responses during MAP infection and can be exploited as a novel therapeutic target in the control of intracellular pathogens, including paratuberculosis.

Mycobacterium tuberculosis Modulates miR-106b-5p to Control Cathepsin S Expression Resulting in Higher Pathogen Survival and Poor T-Cell Activation

The success of tuberculosis (TB) bacillus, Mycobacterium tuberculosis (Mtb), relies on the ability to survive in host cells and escape to immune surveillance and activation. We recently demonstrated that Mtb manipulation of host lysosomal cathepsins in macrophages leads to decreased enzymatic activity and pathogen survival. In addition, while searching for microRNAs (miRNAs) involved in posttranscriptional gene regulation during mycobacteria infection of human macrophages, we found that selected miRNAs such as miR-106b-5p were specifically upregulated by pathogenic mycobacteria. Here, we show that miR-106b-5p is actively manipulated by Mtb to ensure its survival in macrophages. Using an in silico prediction approach, we identified miR-106b-5p with a potential binding to the 3'-untranslated region of cathepsin S (CtsS) mRNA. We demonstrated by luminescence-based methods that miR-106b-5p indeed targets CTSS mRNA resulting in protein translation silencing. Moreover, miR-106b-5p gain-of-function experiments lead to a decreased CtsS expression favoring Mtb intracellular survival. By contrast, miR-106b-5p loss-of-function in infected cells was concomitant with increased CtsS expression, with significant intracellular killing of Mtb and T-cell activation. Modulation of miR-106b-5p did not impact necrosis, apoptosis or autophagy arguing that miR-106b-5p directly targeted CtsS expression as a way for Mtb to avoid exposure to degradative enzymes in the endocytic pathway. Altogether, our data suggest that manipulation of miR-106b-5p as a potential target for host-directed therapy for Mtb infection.

IFN-β: A Contentious Player in Host-Pathogen Interaction in Tuberculosis

Tuberculosis (TB) is a major health threat to the human population worldwide. The etiology of the disease is Mycobacterium tuberculosis (Mtb), a highly successful intracellular pathogen. It has the ability to manipulate the host immune response and to make the intracellular environment suitable for its survival. Many studies have addressed the interactions between the bacteria and the host immune cells as involving many immune mediators and other cellular players. Interferon-β (IFN-β) signaling is crucial for inducing the host innate immune response and it is an important determinant in the fate of mycobacterial infection. The role of IFN-β in protection against viral infections is well established and has been studied for decades, but its role in mycobacterial infections remains much more complicated and debatable. The involvement of IFN-β in immune evasion mechanisms adopted by Mtb has been an important area of investigation in recent years. These advances have widened our understanding of the pro-bacterial role of IFN-β in host–pathogen interactions. This pro-bacterial activity of IFN-β appears to be correlated with its anti-inflammatory characteristics, primarily by antagonizing the production and function of interleukin 1β (IL-1β) and interleukin 18 (IL-18) through increased interleukin 10 (IL-10) production and by inhibiting the nucleotide-binding domain and leucine-rich repeat protein-3 (NLRP3) inflammasome. Furthermore, it also fails to provoke a proper T helper 1 (Th1) response and reduces the expression of major histocompatibility complex II (MHC-II) and interferon-γ receptors (IFNGRs). Here we will review some studies to provide a paradigm for the induction, regulation, and role of IFN-β in mycobacterial infection. Indeed, recent studies suggest that IFN-β plays a role in Mtb survival in host cells and its downregulation may be a useful therapeutic strategy to control Mtb infection.

Effects of Mycobacterium tuberculosis Mutant Strain Hsp16.3 Gene on Murine RAW 264.7 Macrophage Autophagy

Heat shock protein Hsp16.3 is closely related to latent Mycobacterium tuberculosis (MTB) infection and plays an important role in sustained survival when MTB is dormant. In this study, the Hsp16.3 gene mutant MTB H37Rv strain (Hsp16.3ΔMTB) was obtained through gene recombination and infected into murine RAW 264.7 macrophages. Western blotting and immunofluorescence showed increased expression of the autophagy-related protein LC3, and transmission electron microscopy showed significantly increased macrophage autophagosomes, suggesting that Hsp16.3ΔMTB facilitates murine macrophage autophagy. These findings have implications for preventing and controlling tuberculosis.

IL-10 down-regulates the expression of survival associated gene hspX of Mycobacterium tuberculosis in murine macrophage

Mycobacterium tuberculosis (MTB) adopts a special survival strategy to overcome the killing mechanism(s) of host immune system. Amongst the many known factors, small heat shock protein 16.3 (sHSP16.3) of MTB encoded by gene hspX has been reported to be critical for the survival of MTB. In the present study, the effect of recombinant murine interferon-gamma (rmIFN-γ) and recombinant murine interleukin-10 (rmIL-10) on the expression of gene hspX of MTB in murine macrophage RAW264.7 has been investigated. By real-time RT-PCR, it was observed that three increasing concentrations (5, 25 and 50 ng/ml) of rmIFN-γ significantly up-regulated the expression of hspX whereas similar concentrations of rmIL-10 (5, 25 and 50 ng/ml) significantly down-regulated the hspX expression. This effect was not only dependent on the concentration of the stimulus but this was time-dependent as well. A contrasting pattern of hspX expression was observed against combinations of two different concentrations of rmIFN-γ and rmIL-10. The study results suggest that rIL-10 mediated down-regulation of hspX expression, in the presence of low concentration of rIFN-γ, could be used as an important strategy to decrease the dormancy of MTB in its host and thus making MTB susceptible to the standard anti-mycobacterial therapy used for treating tuberculosis. However, as these are only preliminary results in the murine cell line model, this hypothesis needs to be first validated in human cell lines and subsequently in animal models mimicking the latent infection using clinical isolates of MTB before considering the development of modified regimens for humans.

Promising landscape for regulating macrophage polarization: epigenetic viewpoint

Macrophages are critical myeloid cells with the hallmark of phenotypic heterogeneity and functional plasticity. Macrophages phenotypes are commonly described as classically-activated M1 and alternatively-activated M2 macrophages which play an essential role in the tissues homeostasis and diseases pathogenesis. Alternations of macrophage polarization and function states require precise regulation of target-gene expression. Emerging data demonstrate that epigenetic mechanisms and transcriptional factors are becoming increasingly appreciated in the orchestration of macrophage polarization in response to local environmental signals. This review is to focus on the advanced concepts of epigenetics changes involved with the macrophage polarization, including microRNAs, DNA methylation and histone modification, which are responsible for the altered cellular signaling and signature genes expression during M1 or M2 polarization. Eventually, the persistent investigation and understanding of epigenetic mechanisms in tissue macrophage polarization and function will enhance the potential to develop novel therapeutic targets for various diseases.

Increased miR-424-5p expression in peripheral blood mononuclear cells from patients with pemphigus

Pemphigus is an autoimmune disease that causes blisters and erosions in the skin and mucous membranes. The development of pemphigus is associated with the imbalance of T‑cell and humoral responses. MicroRNAs (miRNAs) can regulate many cell functions. However, whether miRNA expression is altered in peripheral blood mononuclear cells (PBMCs) during the pathogenesis of pemphigus has not been clarified. The aim of the present study was to examine the miRNA expression profiles of PBMCs from patients with pemphigus. The expression profiles of miRNAs in PBMCs from patients with active pemphigus (n=3) and healthy subjects (n=3) were analyzed by microarray. The relative levels of miR-424-5p expression in PBMCs from 9 patients and controls were validated by RT-qPCR. The functional and biological processes of the differentially expressed miRNAs were analyzed by bioinformatics. There were 124 differentially expressed miRNAs in PBMCs from the patients with pemphigus, compared with healthy controls, including 71 that were upregulated (P<0.05, fold change >2), and 53 that were downregulated (P<0.05, fold change <0.5). miR-424-5p was highly expressed in patients with pemphigus. Bioinformatics analysis indicated that the genes targeted by miR-424-5p were involved in intracellular signaling cascades, phosphate metabolism and regulation of kinase activity. The predicted target genes were associated with the T-cell receptor and mitogen-activated protein kinase signaling pathways as well as others. In conclusion, the results have demonstrated the miRNA expression profile, and verified that miR-424-5p was upregulated in PBMCs from patients with pemphigus. The biological function and potential pathways of miR-424-5p in pemphigus were predicted. Thus, miR-424-5p may contribute to the pathogenesis of pemphigus.

Differentially expressed miR-3680-5p is associated with parathyroid hormone regulation in peritoneal dialysis patients

Mineral and bone disorder (MBD) is observed universally in patients with chronic kidney disease (CKD). Detrimental MBD-related skeletal changes include increased prevalence of fracture, cardiovascular disease, and mortality. MicroRNAs (miRNAs) have been identified as useful biomarkers in various diseases, and the aim of this study was to identify miRNAs associated with parathyroid hormone level in peritoneal dialysis (PD) patients. Fifty-two PD patients were enrolled and grouped by their intact parathyroid hormone (iPTH) level; 11 patients had low iPTH (<150 pg/mL) and 41 patients had high iPTH (≥150 pg/mL). Total RNA was extracted from whole blood samples. Total RNA from 15 patients (7 and 8 patients in the low and high iPTH groups, respectively) underwent miRNA microarray analysis, and three differentially upregulated (>2-fold change) miRNAs previously associated with human disease were selected for real-time quantitative PCR (qPCR) analysis. Interaction analyses between miRNAs and genes were performed by using TargetScan and the KEGG pathway database. Microarray results revealed 165 miRNAs were differentially expressed between patients with high iPTH levels and low iPTH levels. Of those miRNAs, 81 were upregulated and 84 were downregulated in patients with high iPTH levels. Expression levels of miR-1299, miR-3680-5p, and miR-548b-5p (previously associated with human disease) in 52 patients were analyzed by using qPCR. MiR-3680-5p was differentially expressed in low and high iPTH patients (P < 0.05). The predicted target genes of miR-3680-5p were USP6, USP32, USP46, and DLT, which are involved in the ubiquitin proteolysis pathway. This pathway has roles in PTH and parathyroid hormone related protein degradation and proteolysis. The mechanisms involved in the associations among low PTH, adynamic bone disease, miR-3680-5p, and the target genes should be explored further in order to elucidate their roles in CKD-MBD development.

microRNA-20a Inhibits Autophagic Process by Targeting ATG7 and ATG16L1 and Favors Mycobacterial Survival in Macrophage Cells

Autophagy plays important roles in the host immune response against mycobacterial infection. Mycobacterium tuberculosis (M. tuberculosis) can live in macrophages owing to its ability to evade attacks by regulating autophagic response. MicroRNAs (miRNAs) are small noncoding, endogenously encoded RNA which plays critical roles in precise regulation of macrophage functions. Whether miRNAs specifically influence the activation of macrophage autophagy during M. tuberculosis infection are largely unknown. In this study, we demonstrate that BCG infection of macrophages resulted in enhanced expression of miRNA-20a, which inhibits autophagic process by targeting ATG7 and ATG16L1 and promotes BCG survival in macrophages. Forced overexpression of miR-20a decreased the expression levels of LC3-II and the number of LC3 puncta in macrophages, and promoted BCG survival in macrophages, while transfection with miR-20a inhibitor had the opposite effect. Moreover, the inhibitory effect of miR-20a on autophagy was further confirmed by transmission electron microscopy (TEM) analysis. Quantification of autophagosomes per cellular cross-section revealed a significant reduction upon transfection with miR-20a mimic, but transfection with miR-20a inhibitor increased the number of autophagosomes per cellular cross-section. Moreover, silencing of ATG7 significantly inhibited autophagic response, and transfection with ATG7 siRNA plus miR-20a mimic could further decrease autophagic response. Collectively, our data reveal that miR-20a inhibits autophagic response and promotes BCG survival in macrophages by targeting ATG7 and ATG16L1, which may have implications for a better understanding of pathogenesis of M. tuberculosis infection.

High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants

Background

Mycobacterium abscessus (MAB) is an emerging pathogen causing pulmonary infections in those with inflammatory lung disorders, such as Cystic Fibrosis (CF), and is associated with the highest fatality rate among rapidly growing mycobacteria (RGM). Phenotypically, MAB manifests as either a Smooth (MAB-S) or a Rough (MAB-R) morphotype, which differ in their levels of cell wall glycopeptidolipids (GPLs) and in their pathogenicity in vivo. As one of the primary immune cells encountered by MAB, we sought to examine the early transcriptional events within macrophages, following infection with both MAB-S or MAB-R.

Results

We sampled the transcriptomes (mRNA and miRNA) of THP-1-derived macrophages infected with both MAB-R and MAB-S at 1, 4 and 24 h post-infection (hpi) using RNA-seq. A core set of 606 genes showed consistent expression profiles in response to both morphotypes, corresponding to the early transcriptional response to MAB. The core response is type I Interferon (IFN)-driven, involving the NF-κB and MAPK signaling pathways with concomitant pro-inflammatory cytokine production, and network analysis identified STAT1, EGR1, and SRC as key hub and bottleneck genes. MAB-S elicited a more robust transcriptional response at both the mRNA and miRNA levels, which was reflected in higher cytokine levels in culture supernatants. The transcriptional profiles of macrophages infected with both morphotypes were highly correlated, however, and a direct comparison identified few genes to distinguish them. Most of the induced miRNAs have previously been associated with mycobacterial infection and overall miRNA expression patterns were similarly highly correlated between the morphotypes.

Conclusions

The report here details the first whole transcriptome analysis of the early macrophage response to MAB infection. The overall picture at the early stages of macrophage infection is similar to that of other mycobacteria, reflected in a core type I IFN and pro-inflammatory cytokine response. Large-scale transcriptional differences in the host response to the different MAB morphotypes are not evident in the early stages of infection, however the subset of genes with distinct expression profiles suggest potentially interesting differences in internal trafficking of MAB within macrophages.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2246-1) contains supplementary material, which is available to authorized users.

Construction of a Semisynthetic Human VH Single-Domain Antibody Library and Selection of Domain Antibodies against α-Crystalline of Mycobacterium tuberculosis

The use of human variable heavy (VH) domain antibodies has been on the rise due to their small scaffold size and simple folding mechanism. A highly diverse library is largely dependent on the diversity introduced within the complementarity-determining region (CDR) cassettes. Here we introduced diversity with the use of a single framework diversifying all three CDRs using tailored codons consisting of degenerate trinucleotides (NNK). The length of the degeneracy in the CDRs was also taken into consideration based on the most frequently occurring length of CDRs and the canonical confirmation for each antibody subfamily. The semisynthetic human VH domain genes were assembled in a single pot using a temperature cascading process. The affinity selection process with Mycobacterium tuberculosis (MTb) α-crystalline was done using a semiautomated process. Enrichment of target-specific clones was observed with successful identification of monoclonal VH domain antibodies for MTb α-crystalline. In short, the semisynthetic library generated was able to select monoclonal VH domain antibodies against full MTb α-crystalline protein with complete semisynthetic CDRs displayed on a single scaffold. The library has the potential to be applied for the isolation of antibodies against other pathogenic proteins.

From Single Cells to Engineered and Explanted Tissues: New Perspectives in Bacterial Infection Biology

Cell culture techniques are essential for studying host-pathogen interactions. In addition to the broad range of single cell type-based two-dimensional cell culture models, an enormous amount of coculture systems, combining two or more different cell types, has been developed. These systems enable microscopic visualization and molecular analyses of bacterial adherence and internalization mechanisms and also provide a suitable setup for various biochemical, immunological, and pharmacological applications. The implementation of natural or synthetical scaffolds elevated the model complexity to the level of three-dimensional cell culture. Additionally, several transwell-based cell culture techniques are applied to study bacterial interaction with physiological tissue barriers. For keeping highly differentiated phenotype of eukaryotic cells in ex vivo culture conditions, different kinds of microgravity-simulating rotary-wall vessel systems are employed. Furthermore, the implementation of microfluidic pumps enables constant nutrient and gas exchange during cell cultivation and allows the investigation of long-term infection processes. The highest level of cell culture complexity is reached by engineered and explanted tissues which currently pave the way for a more comprehensive view on microbial pathogenicity mechanisms.

Systematic expression profiling analysis identifies specific microRNA-gene interactions that may differentiate between active and latent tuberculosis infection

Tuberculosis (TB) is the second most common cause of death from infectious diseases. About 90% of those infected are asymptomatic—the so-called latent TB infections (LTBI), with a 10% lifetime chance of progressing to active TB. To further understand the molecular pathogenesis of TB, several molecular studies have attempted to compare the expression profiles between healthy controls and active TB or LTBI patients. However, the results vary due to diverse genetic backgrounds and study designs and the inherent complexity of the disease process. Thus, developing a sensitive and efficient method for the detection of LTBI is both crucial and challenging. For the present study, we performed a systematic analysis of the gene and microRNA profiles of healthy individuals versus those affected with TB or LTBI. Combined with a series of in silico analysis utilizing publicly available microRNA knowledge bases and published literature data, we have uncovered several microRNA-gene interactions that specifically target both the blood and lungs. Some of these molecular interactions are novel and may serve as potential biomarkers of TB and LTBI, facilitating the development for a more sensitive, efficient, and cost-effective diagnostic assay for TB and LTBI for the Taiwanese population.

Role of host- and pathogen-associated lipids in directing the immune response in mycobacterial infections, with emphasis on Mycobacterium avium subsp. paratuberculosis

Mycobacteria have a complex cell wall with a high lipid content that confers unique advantages for bacterial survival in the hostile host environment, leading to long-term infection. There is a wealth of evidence suggesting the role cell wall-associated lipid antigens play at the host-pathogen interface by contributing to bacterial virulence. One pathway that pathogenic mycobacteria use to subvert host immune pathways to their advantage is host cholesterol/lipid homeostasis. This review focuses on the possible role of pathogen- and host-associated lipids in the survival and persistence of pathogenic mycobacteria with emphasis on Mycobacterium avium subsp. paratuberculosis. We draw upon literature in diverse areas of infectious and metabolic diseases and explain a mechanism by which mycobacterial-induced changes in the host cellular energy state could account for phenomena that are a hallmark of chronic mycobacterial diseases.

Identification and comparative analysis of the Pseudosciaena crocea microRNA transcriptome response to poly(I:C) infection using a deep sequencing approach

Two sRNA libraries with or without poly(I:C) infection of large yellow croaker Pseudosciaena crocea were constructed and sequenced using the high-throughput Illumina/Solexa deep sequencing technology. The high-throughput sequencing pipeline yielded 163,79,272 and 217,07,070 raw reads corresponding to 132,27,594 and 206,86,409 clean reads for the normal and infected libraries, respectively. Bioinfromatic analysis identified 534 miRNAs, of which, 158 miRNAs were known in miRBase 20.0 and the remaining 376 were not found homology to any known metazoan miRNAs, suggesting a possible species-specificity. We analyzed the significance of differently expressed miRNAs between two libraries using pairwise comparison. There was significant differential expression of 112 miRNAs (p < 0.001) between two libraries. Thereinto, a number of known miRNAs were identified immune-related. Real-time quantitative PCR experiments (RT-qPCR) were preformed for 6 miRNAs of the two samples, and agreement was found between the sequencing and RT-qPCR data. To our knowledge, this is the first comprehensive study of miRNAs in P. crocea and of expression analysis of P. crocea miRNAs in response to poly(I:C) infection, and many miRNAs were differentially regulated under normal and infection conditions. These findings deepened our understanding of the role of miRNAs in the intricate host's immune system, and should be useful to develop new control strategies for host immune defense against various foreign infection in P. crocea.