Integrated miRNA and mRNA expression profiling to identify mRNA targets of dysregulated miRNAs in pulmonary tuberculosis

Unlocking the potential of miRNAs in detecting pulmonary tuberculosis: prospects and pitfalls

Tuberculosis (TB) is one of the deadliest infectious diseases globally, ranking as 13th leading cause of mortality and morbidity. According to the Global Tuberculosis Report 2022, TB claimed the lives of 1.6 million people worldwide in 2021. Among the casualties, 1 870 000 individuals with HIV co-infections contributed to 6.7% of the total fatalities, accounting TB as the second most lethal infectious disease following COVID-19. In the quest to identify biomarkers for disease progression and anti-TB therapy, microRNAs (miRNAs) have gained attention due to their precise regulatory role in gene expression in disease stages and their ability to distinguish latent and active TB, enabling the development of early TB prognostic signatures. miRNAs are stable in biological fluids and therefore will be useful for non-invasive and broad sample collection. However, their inherent lack of specificity and experimental variations may lead to false-positive outcomes. These limitations can be overcome by integrating standard protocols with machine learning, presenting a novel tool for TB diagnostics and therapeutics. This review summarizes, discusses and highlights the potential of miRNAs as a biomarker, particularly their differential expression at disease stages. The review assesses the advantages and obstacles associated with miRNA-based diagnostic biomarkers in pulmonary TB and facilitates rapid, point-of-care testing.

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.

Downregulation of monocyte miRNAs: implications for immune dysfunction and disease severity in drug-resistant tuberculosis

Background

Monocyte miRNAs govern both protective and pathological responses during tuberculosis (TB) through their differential expression and emerged as potent targets for biomarker discovery and host-directed therapeutics. Thus, this study examined the miRNA profile of sorted monocytes across the TB disease spectrum [drug-resistant TB (DR-TB), drug-sensitive TB (DS-TB), and latent TB] and in healthy individuals (HC) to understand the underlying pathophysiology and their regulatory mechanism.

Methods

We sorted total monocytes including three subsets (HLA-DR⁺CD14⁺, HLA-DR⁺CD14⁺CD16⁺, and HLA-DR⁺CD16⁺cells) from peripheral blood mononuclear cells (PBMCs) of healthy and TB-infected individuals through flow cytometry and subjected them to NanoString-based miRNA profiling.

Results

The outcome was the differential expression of 107 miRNAs particularly the downregulation of miRNAs in the active TB groups (both drug-resistant and drug-sensitive). The miRNA profile revealed differential expression signatures: i) decline of miR-548m in DR-TB alone, ii) decline of miR-486-3p in active TB but significant elevation only in LTB iii) elevation of miR-132-3p only in active TB (DR-TB and DS-TB) and iv) elevation of miR-150-5p in DR-TB alone. The directionality of functions mediated by monocyte miRNAs from Gene Set Enrichment Analysis (GSEA) facilitated two phenomenal findings: i) a bidirectional response between active disease (activation profile in DR-TB and DS-TB compared to LTB and HC) and latent infection (suppression profile in LTB vs HC) and ii) hyper immune activation in the DR-TB group compared to DS-TB.

Conclusion

Thus, monocyte miRNA signatures provide pathological clues for altered monocyte function, drug resistance, and disease severity. Further studies on monocyte miRNAs may shed light on the immune regulatory mechanism for tuberculosis.

Dysregulated expression of microRNAs in aqueous humor from intraocular tuberculosis patients

BACKGROUND

Systemic Mycobacterium tuberculosis (Mtb) infection alters microRNA's expression that controls cellular processes and modulates host defense mechanisms. However, the role of miRNAs in intraocular tuberculosis (IOTB) remains unknown. Therefore, this study aims to identify dysregulated miRNAs in the aqueous humor (AH) of patients with IOTB.

METHODS

AH from intraocular tuberculosis patients (n = 2) and cataract controls (n = 2) were used for small RNA deep sequencing using HiSeq Illumina sequencing platform. Differentially expressed miRNAs and their targets were identified by the bioinformatics approach, and their regulatory functions were predicted by pathway enrichment analysis. The expression of selected miRNAs and their binding targets were further validated by real-time quantitative PCR (RT-qPCR).

RESULTS

In total, we identified 56 differentially expressed miRNAs in the AH of intraocular tuberculosis (IOTB) patients compared to controls. We selected four significantly dysregulated miRNAs (miR-423-5p, miR-328-3p, miR-21-5p, and miR-16-5p) based on the RT-qPCR validation and predicted their gene targets. We developed a miRNA-targets regulatory network by combining pathways of interest and genes associated with TB. We identified that these four miRNAs might play an important role in IOTB pathogenesis via tuberculosis-associated pathways; PI3K-Akt signaling, autophagy and MAPK pathway.

CONCLUSIONS

For the first time, this study identifies the dysregulation of four miRNAs in the AH of IOTB patients using the ultra-low input small-RNA sequencing approach. Further target prediction and validation identify the role of these miRNAs in tuberculosis pathogenesis via tuberculosis-related pathways. This study identifies miRNAs as potentially ideal biomarkers in the aqueous humor of IOTB patients.

MicroRNA‑502‑3p promotes Mycobacterium tuberculosis survival in macrophages by modulating the inflammatory response by targeting ROCK1

Tuberculosis (TB) is caused by Mycobacterium tuberculosis (M. tuberculosis) infection and has the highest mortality rate of any single infectious disease worldwide. The aim of the present study was to investigate the function of microRNA (miR)-502-3p in M. tuberculosis-infected macrophages. The Gene Expression Omnibus database was used to analyze miR-502-3p expression in patients with TB and healthy individuals. THP-1 and RAW 264.7 cells were transfected with miR-502-3p mimic, miR-502-3p inhibitor, pcDNA3.1-ROCK1 or their negative controls. The expression levels of miR-502-3p and inflammatory cytokines were evaluated using reverse transcription-quantitative PCR. The colony-forming unit assay was performed to assess the survival of M. tuberculosis in macrophages, and Toll-like receptor (TLR)4/NF-κB signaling pathway-associated protein expression levels were detected by western blotting. The nuclear translocation of NF-κB p65 was detected via immunocytochemistry. TargetScan was used to predict the binding sites between miR-502-3p and ROCK1. The interaction between miR-502-3p and Rho-associated coiled-coil-forming protein kinase 1 (ROCK1) was confirmed using a dual-luciferase reporter assay; ROCK1 was demonstrated to be a direct target gene of miR-502-3p. Results from the present study demonstrated that miR-502-3p expression was significantly increased during M. tuberculosis infection in macrophages. Upregulation of miR-502-3p expression levels significantly enhanced the survival of intracellular M. tuberculosis. IL-6, TNF-α, and IL-1β mRNA expression levels were significantly upregulated during M. tuberculosis infection but were downregulated by miR-502-3p overexpression. Moreover, miR-502-3p mimics transfection significantly downregulated TLR4/NF-κB signaling pathway-associated protein expression and significantly reduced nuclear transcription of NF-κB in M. tuberculosis-infected macrophages. ROCK1 overexpression reversed the miR-502-3p inhibitory effect on cytokine production in M. tuberculosis-infected macrophages. In conclusion, miR-502-3p/ROCK1 may serve an anti-inflammatory role and may improve the survival of M. tuberculosis within macrophages, which may provide a promising therapeutic target for TB.

Identification and comparison of circular RNAs in preeclampsia

Background

Preeclampsia (PE) is a pregnancy-specific syndrome, belongs to the gestational hypertension diseases category and is considered among the causes of maternal and perinatal mortality and morbidity. However, the pathogenesis of PE is still vague.

Methods

In the present study, the circular RNA (circRNA) expression patterns of normal pregnant women and PE patients were investigated using whole RNA sequencing.

Results

A total of 151 differential expressed circRNAs were identified including 121 upregulated and 30 downregulated ones. Functional and pathway enrichment analysis was conducted on the differentially expressed circRNAs using Gene Ontology and KEGG databases. The results of this analysis indicated that several crucial biological processes and pathways were enriched in PE patients. circRNA–microRNA (miRNA) interaction analysis indicated that the reported differentially expresse circRNAs may be associated with some regulatory functions through miRNAs in PE patients. Two ceRNAs networks were constructed according to the targeting relationship between circRNAs/miRNAs and miRNAs/mRNAs. One sub-network contained one upregulated circRNA, four downregulated miRNAs and five upregulated mRNAs, and another sub-network contained 10 downregulated circRNAs, 21 upregulated miRNAs and 15 downregulated mRNAs.

Conclusion

CircRNA expression patterns have been investigated and this analysis revealed their potential regulatory mechanisms in PE patients. We constructed the ceRNAs (competing endogenous RNA) to reveal the potential molecular roles of dysregulated circRNAs in the PE patients using RNA sequencing data. circRNA_13301 was the only one upregulated circRNA in ceRNA being targeted by four miRNAs.

Tuberculosis-Associated MicroRNAs: From Pathogenesis to Disease Biomarkers

Tuberculosis (TB) caused by Mycobacterium tuberculosis is one of the most lethal infectious diseases with estimates of approximately 1.4 million human deaths in 2018. M. tuberculosis has a well-established ability to circumvent the host immune system to ensure its intracellular survival and persistence in the host. Mechanisms include subversion of expression of key microRNAs (miRNAs) involved in the regulation of host innate and adaptive immune response against M. tuberculosis. Several studies have reported differential expression of miRNAs during active TB and latent tuberculosis infection (LTBI), suggesting their potential use as biomarkers of disease progression and response to anti-TB therapy. This review focused on the miRNAs involved in TB pathogenesis and on the mechanism through which miRNAs induced during TB modulate cell antimicrobial responses. An attentive study of the recent literature identifies a group of miRNAs, which are differentially expressed in active TB vs. LTBI or vs. treated TB and can be proposed as candidate biomarkers.

Respiratory syncytial virus infection-induced mucus secretion by down-regulation of miR-34b/c-5p expression in airway epithelial cells

Severe RSV infection is the main cause of hospitalization to children under the age of five. The regulation of miRNAs on the severity of RSV infection is unclear. The aim of the study was to identify the critical differential expression miRNAs (DE miRNAs) that can regulate the pathological response in RSV‐infected airway epithelial cells. In this study, miRNA and mRNA chips of RSV‐infected airway epithelia from Gene Expression Omnibus (GEO) were screened and analysed, separately. DE miRNAs‐targeted genes were performed for further pathway and process enrichment analysis. DE miRNA‐targeted gene functional network was constructed on the basis of miRNA‐mRNA interaction. The screened critical miRNA was also investigated by bioinformatics analysis. Then, RSV‐infected human bronchial epithelial cells (HBECs) were constructed to verify the expression of the DE miRNAs. Finally, specific synthetic DE miRNAs mimics were used to confirm the effect of DE miRNAs on the RSV‐infected HBECs. 45 DE miRNAs were identified from GEO62306 dataset. Our results showed that hsa‐mir‐34b‐5p and hsa‐mir‐34c‐5p decreased significantly in HBECs after RSV infection. Consistent with the biometric analysis, hsa‐mir‐34b/c‐5p is involved in the regulation of mucin expression gene MUC5AC. In RSV‐infected HBECs, the inducement of MUC5AC production by decreased hsa‐mir‐34b/c‐5p was partly mediated through activation of c‐Jun. These findings provide new insights into the mechanism of mucus obstruction after RSV infection and represent valuable targets for RSV infection and airway obstruction treatment.

Specific PIWI-interacting small noncoding RNA expression patterns in pulmonary tuberculosis patients

Aim: PIWI-interacting RNAs (piRNAs) play crucial roles in germline development and carcinogenesis. The expression patterns of piRNAs in pulmonary tuberculosis (PTB) are still unclear. Materials & methods: Small RNA sequencing was applied to investigate peripheral blood piRNA expression patterns in PTB patients and healthy individuals. Results: A total of 428 upregulated and 349 downregulated piRNAs were identified from PTB patients. Target genes of dysregulated piRNAs were mainly involved in transcription and protein binding. Dysregulated piRNAs were enriched in many pathways related with immunity. Many target genes were regulated by the same piRNAs. Nucleotide bias of these piRNAs showed that piRNAs in peripheral blood may be formed from the primary biogenesis pathway. Conclusion: Findings demonstrated that the PIWI-piRNA pathway is active in human peripheral blood, where it may represent a new player in the PTB pathogenesis.

Comprehensive analysis of long non-coding RNAs expression pattern in the pathogenesis of pulmonary tuberculosis

BACKGROUND

Long non-coding RNAs (lncRNAs) play crucial roles in the progression and pathogenesis of cancer. Right now, less is known about the association between the expression of lncRNAs and the pathogenesis of pulmonary tuberculosis (PTB).

METHODS

In present study, the expression profiles of lncRNAs were investigated by transcriptome sequencing from PTB patients vs. healthy individuals.

RESULTS

A total of 449 differentially expressed (DE) (fold change ≥2, false discovery rate ≤ 0.05) lncRNAs were screened out from the PTB patients. Lnc-HNRNPU-1:7 and lnc-FAM76B-4:1 was found the most upregulated lncRNAs and downregulated lncRNAs in PTB patients, respectively. GO annotation and KEGG analysis were used to explore the potential roles of these DE lncRNAs. The JAK/STAT and TGF-β signaling pathways related to PTB pathogenesis were enriched in PTB patients. The co-expressed of a few lncRNAs and mRNAs on chromosome were shown by cis-regulatory gene analysis. Trans analysis indicated that STAT1, STAT2 and TAF7 transcription factors regulated the expression of lncRNA and mRNA. The constructed lncRNA ceRNA network suggested that lncRNAs regulating mRNAs expression may mediate by sponged miRNAs.

CONCLUSION

We comprehensively analyzed the expression profiles of lncRNAs in PTB patients, thus providing new clues for exploring the regulatory mechanisms of dysregulated lncRNAs in the pathogenesis of PTB.

Identification and characterization of novel type of RNAs, circRNAs in crucian carp Carassius auratus gibelio

Circular RNAs (circRNAs) with regulatory potency activity was identified from varieties of species. Crucian carp (Carassius auratus gibelio) is one of the most freshwater aquaculture species in China. Every year, huge economic damage to the farming was caused by the virus and bacterial infection. Until now, there is any information about circRNA reported from the Crucian carp. In this study, the expression pattern of circRNA in Crucian carp was investigated with transcriptomic analysis. The results showed that only 37 circRNAs were identified from the Crucian carp, and these circRNAs biogenesis was formed with canonical GU-AG splicing mechanism with unevenly distributed on the chromosomes. Wherein, most of the circRNAs were derived from the sense overlapping strategy. Reverse transcript PCR and Sanger sequencing data indicated that these circRNAs were existed authenticity in Crucian carp. The bioinformatics analysis indicated that circRNAs identified from the Crucian carp with potential miRNA sponge regulate the expression level of mRNAs. GO annotation and KEGG pathway analysis of these circRNAs showed that more than 20% circRNAs were related with catalytic activity and binding in the category of molecular function, and these circRNAs were enriched in 9 signaling pathways, such as, Wnt signaling pathway, MAPK signaling pathway, Ubiquitin mediated proteolysis et al. 220 mRNAs would be regulated by the circRNAs via miRNAs mediation. These target mRNAs were further analyzed with functional annotation and KEGG analysis. GO annotation analysis showed that several genes were related with function of nucleotide binding, transcription regulatory activity. KEGG pathway analysis showed that 5 genes were enriched in the pathway of Endocytosis. The circRNA-miRNA-mRNA regulation network indicated that one miRNA can link one or more circRNA and one or more mRNA. Overall, these results will not only help us to further understand the novel RNA transcripts in Crucian carp, but also provide the novel clue to investigate the interaction between host and pathogens from this novel circRNA molecule.