Detection of lncRNA-mRNA interaction modules by integrating eQTL with weighted gene co-expression network analysis

Identification of important modules and biomarkers in tuberculosis based on WGCNA

Background

Tuberculosis (TB) is a significant public health concern, particularly in China. Long noncoding RNAs (lncRNAs) can provide abundant pathological information regarding etiology and could include candidate biomarkers for diagnosis of TB. However, data regarding lncRNA expression profiles and specific lncRNAs associated with TB are limited.

Methods

We performed ceRNA-microarray analysis to determine the expression profile of lncRNAs in peripheral blood mononuclear cells (PBMCs). Weighted gene co-expression network analysis (WGCNA) was then conducted to identify the critical module and genes associated with TB. Other bioinformatics analyses, including Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and co-expression networks, were conducted to explore the function of the critical module. Finally, real-time quantitative polymerase chain reaction (qPCR) was used to validate the candidate biomarkers, and receiver operating characteristic analysis was used to assess the diagnostic performance of the candidate biomarkers.

Results

Based on 8 TB patients and 9 healthy controls (HCs), a total of 1,372 differentially expressed lncRNAs were identified, including 738 upregulated lncRNAs and 634 downregulated lncRNAs. Among all lncRNAs and mRNAs in the microarray, the top 25% lncRNAs (3729) and top 25% mRNAs (2824), which exhibited higher median expression values, were incorporated into the WGCNA. The analysis generated 16 co-expression modules, among which the blue module was highly correlated with TB. GO and KEGG analyses showed that the blue module was significantly enriched in infection and immunity. Subsequently, considering module membership values (>0.85), gene significance values (>0.90) and fold-change value (>2 or < 0.5) as selection criteria, the top 10 upregulated lncRNAs and top 10 downregulated lncRNAs in the blue module were considered as potential biomarkers. The candidates were then validated in an independent validation sample set (31 TB patients and 32 HCs). The expression levels of 8 candidates differed significantly between TB patients and HCs. The lncRNAs ABHD17B (area under the curve [AUC] = 1.000) and ENST00000607464.1 (AUC = 1.000) were the best lncRNAs in distinguishing TB patients from HCs.

Conclusion

This study characterized the lncRNA profiles of TB patients and identified a significant module associated with TB as well as novel potential biomarkers for TB diagnosis.

An intersectional analysis of LncRNAs and mRNAs reveals the potential therapeutic targets of Bi Zhong Xiao Decoction in collagen-induced arthritis rats

Background

Bi Zhong Xiao decoction (BZXD), a traditional Chinese herbal formula, has been used clinically for many years to treat rheumatoid arthritis (RA). Both clinical and experimental studies have revealed that BZXD is effective in treating RA, but the mechanism remains unclear. In this study, we aimed to explore the mechanism of efficacy of BZXD through transcriptomic analysis of lncRNA and mRNA.

Methods

The combination method of ultra-high performance liquid chromatography-mass spectrometry/mass spectrometry was used to assess the quality of BZXD. The efficacy of BZXD in treating collagen-induced arthritis (CIA) was evaluated by clinical assessment, weight changes, hematoxylin–eosin and safranin o-fast green staining, and Micro-CT. Arraystar rat lncRNA-mRNA chip technology was used to determine the lncRNA and mRNA expression profiles of the Control, CIA and BZXD groups, and to screen gene expression profiles related to the curative effect of BZXD. A lncRNA-mRNA co-expression network was constructed for the therapeutic efficacy genes. Through GO function and KEGG pathway enrichment analysis, the biological functions and signaling pathways of therapeutic efficacy genes were determined. Based on fold change and functional annotation, key differentially expressed lncRNAs and mRNAs were selected for reverse transcription-quantitative polymerase chain reaction (RT-qPCR) validation. The functions of lncRNAs targeting mRNAs were verified in vitro.

Results

We demonstrated that BZXD could effectively reverse bone erosion. After BZXD treatment, up to 33 lncRNAs and 107 mRNAs differentially expressed genes were reversely regulated by BZXD. These differentially expressed lncRNAs are mainly involved in the biological process of the immune response and are closely related to the ECM-receptor interaction, MAPK signaling pathway, Focal adhesion, Ras signaling pathway, Antigen processing and presentation, and Chemokine signaling pathway. We identified four lncRNAs (uc.361−, ENSRNOT00000092834, ENSRNOT00000089244, ENSRNOT00000084631) and three mRNAs (Acvr2a, Cbx2, Morc4) as potential therapeutic targets for BZXD and their microarray data consistent with the RT-qPCR. In vitro experiments confirmed that silencing the lncRNAs ENSRNOT00000092834 and ENSRNOT00000084631 reversed the expression of target mRNAs.

Conclusions

This study elucidates the possible mechanism of BZXD reversing bone erosion in CIA rats from the perspective of lncRNA and mRNA. To provide a basis and direction for further exploration of the mechanism of BZXD in treating RA.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13020-022-00670-z.

Transcriptome profiling of lncRNA and co-expression network in the vaginal epithelial tissue of women with lubrication disorders

Background

Vaginal lubrication is a crucial physiological response that occurs at the beginning of sexual arousal. However, research on lubrication disorders (LD) is still in its infancy, and the role of long non-coding RNAs (lncRNAs) in LD remains unclear. This study aimed to explore the function of lncRNAs in the pathogenesis of vaginal LD.

Methods

The expression profiles of LD and normal control (NC) lncRNAs were examined using next-generation sequencing (NGS), and eight selected differentially expressed lncRNAs were verified by quantitative real-time PCR. We conducted GO annotation and KEGG pathway enrichment analyses to determine the principal functions of significantly deregulated genes. LncRNA-mRNA co-expression and protein-protein interaction (PPI) networks were constructed and the lncRNA transcription factors (TFs) were predicted.

Results

From the results, we identified 181,631 lncRNAs and 145,224 mRNAs in vaginal epithelial tissue. Subsequently, our preliminary judgment revealed a total of 499 up-regulated and 337 down-regulated lncRNAs in LD. The top three enriched GO items of the dysregulated lncRNAs included the following significant terms: “contractile fiber part,” “actin filament-based process,” and “contractile fiber”. The most enriched pathways were “cell-extracellular matrix interactions,” “muscle contraction,” “cell-cell communication,” and “cGMP-PKG signaling pathway”. Our results also showed that the lncRNA-mRNA co-expression network was a powerful platform for predicting lncRNA functions. We determined the three hub genes, ADCY5, CXCL12, and NMU, using PPI network construction and analysis. A total of 231 TFs were predicted with RHOXF1, SNAI2, ZNF354C and TBX15 were suspected to be involved in the mechanism of LD.

Conclusion

In this study, we constructed the lncRNA-mRNA co-expression network, predicted the lncRNA TFs, and comprehensively analyzed lncRNA expression profiles in LD, providing a basis for future studies on LD clinical biomarkers and therapeutic targets. Further research is also needed to fully determine lncRNA’s role in LD development.

LncRNA RHPN1-AS1 promotes the progression of nasopharyngeal carcinoma by targeting CELF2 expression

This study aims to investigate the role of lncRNA RHPN1-AS1 in NPC and its potential regulatory mechanism. The expression of RHPN1-AS1 in tissues and cells was measured by qRT-PCR. The effect of RHPN1-AS1 silencing on biological functions of NPC cells was detected by CCK-8, colony formation, flow cytometry, wound healing, and transwell assays. The protein expression was measured by western blot. The RBPs of RHPN1-AS1 were predicted by Starbase and LncTar, and verify by RIP assay. ESTIMATE was used to analyze the relationship between CELF2 expression and tumor purity. GSEA was used to analyze the downstream signaling pathway of CELF2. In our study, RHPN1-AS1 was up-regulated in NPC tissues and cells. RHPN1-AS1 silencing inhibited cell viability, capacity of proliferation, migration and invasion, promoted apoptosis, decreased protein expression of Bcl-2, MMP2/9, increased protein expression of Bax, caspase-3, and TIMP2 of NPC cells. CELF2 was a target of RHPN1-AS1 and was down-regulated in NPC tissues and cells. CELF2 level was associated with tumor purity negatively. Low expression of CELF2 activated mTORC1 signaling pathway and increased protein expression of p-mTORC1/mTORC1 and p-P70S6K/P70S6K. RHPN1-AS1 silencing eliminated the activating effect of CELF2 silencing on mTORC1 signaling pathway. Moreover, CELF2 silencing reversed the inhibitory effect of RHPN1-AS1 on NPC progression. In conclusion, our findings indicated that RHPN1-AS1 plays an important role in NPC via activating mTORC1 signaling which is modulated by CELF2. RHPN1-AS1 may serve as a potential therapeutic target for NPC treatment.

Multi-omics annotation of human long non-coding RNAs

LncRNAs (long non-coding RNAs) are pervasively transcribed in the human genome and also extensively involved in a variety of essential biological processes and human diseases. The comprehensive annotation of human lncRNAs is of great significance in navigating the functional landscape of the human genome and deepening the understanding of the multi-featured RNA world. However, the unique characteristics of lncRNAs as well as their enormous quantity have complicated and challenged the annotation of lncRNAs. Advances in high-throughput sequencing technologies give rise to a large volume of omics data that are generated at an unprecedented rate and scale, providing possibilities in the identification, characterization and functional annotation of lncRNAs. Here, we review the recent important discoveries of human lncRNAs through analysis of various omics data and summarize specialized lncRNA database resources. Moreover, we highlight the multi-omics integrative analysis as a powerful strategy to efficiently discover and characterize the functional lncRNAs and elucidate their potential molecular mechanisms.

Prognostic potential of lncRNA RHPN1-AS1 in glioma

Expression level of long non-coding RNA (lncRNA) RHPN1-AS1 in glioma tissues was detected to determine potential risk factors influencing prognosis of glioma. This study aimed to clarify the molecular mechanisms underlying tumorigenesis of glioma and thus to improve therapeutic efficacy of glioma. RHPN1-AS1 levels in glioma tissues (n=105) and normal brain tissues (n=105) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). The relationship between RHPN1-AS1 level and pathological indicators of glioma patients was analyzed. Glioma patients were followed up for 5 years. Overall survival (OS) and relapse-free survival (RFS) in glioma patients were tested by Kaplan-Meier and log-rank method. Potential factors influencing prognosis of glioma were analyzed by Cox regression model. RHPN1-AS1 was upregulated in glioma tissues. Its level was correlated to histological grade, Karnofsky (KPS) score and postoperative recurrence of glioma patients, rather than sex, age, pathological and tumor size. Glioma patients expressing high level of RHPN1-AS1 suffered worse OS and RFS than those with low level. Advanced histological grade, KPS score <80 and high level of RHPN1-AS1 were considered to be risk factors influencing postoperative prognosis of glioma. High level of RHPN1-AS1 is an independent risk factor for poor prognosis of glioma, which may be utilized as a prognostic hallmark.

Linc-PINT acted as a tumor suppressor by sponging miR-543 and miR-576-5p in esophageal cancer

This manuscript aimed to investigate linc-PINT's role as a tumor suppressor and its downstream microRNAs (miRNAs) in esophageal cancer. Log-rank, Cox, and nomogram were used for survival analysis. Quantitative real-time polymerase chain reaction was used to evaluate the expression. Cell counting kit-8 was used for proliferation tests. As for in vivo experiments, low expression of linc-PINT was associated with better prognosis; besides, the nomogram indicated that linc-PINT, miR-543, and miR-576-5p served well in predicting the survival rate. As for the in vitro experiments, linc-PINT could directly regulate miR-543 and miR-576-5p to inhibit the proliferation of Eca-109 cell line. In conclusion, linc-PINT-miR-543/miR-576-5p pathway could predict the prognosis and provide novel therapeutic targets for esophageal cancer.

Systematic analysis of lncRNA expression profiles and atherosclerosis-associated lncRNA-mRNA network revealing functional lncRNAs in carotid atherosclerotic rabbit models

Atherosclerosis, a multifactorial and chronic immune inflammatory disorder, is the main cause of multiple cardiovascular diseases. Researchers recently reported that lncRNAs may exert important functions in the progression of atherosclerosis (AS). Some studies found that lncRNAs can act as ceRNAs to communicate with each other by the competition of common miRNA response elements. However, lncRNA-associated ceRNA network in terms of atherosclerosis is limited. In present study, we pioneered to construct and systematically analyze the lncRNA-mRNA network and reveal its potential roles in carotid atherosclerotic rabbit models. Atherosclerosis was induced in rabbits (n = 3) carotid arteries via a high-fat diet and balloon injury, while age-matched rabbits (n = 3) were treated with normal chow as controls. RNA-seq analysis was conducted on rabbits carotid arteries (n = 6) with or without plaque formation. Based on the ceRNA mechanism, a ternary interaction network including lncRNA, mRNA, and miRNA was generated and an AS-related lncRNA-mRNA network (ASLMN) was extracted. Furthermore, we analyzed the properties of ASLMN and discovered that six lncRNAs (MSTRG.10603.16, 5258.4, 12799.3, 5352.1, 12022.1, and 12250.4) were highly related to AS through topological analysis. GO and KEGG enrichment analysis indicated that lncRNA MSTRG.5258.4 may downregulate inducible co-stimulator to perform a downregulated role in AS through T cell receptor signaling pathway and downregulate THBS1 to conduct a upregulated function in AS through ECM-receptor interaction pathway. Finally, our results elucidated the important function of lncRNAs in the origination and progression of AS. We provided an ASLMN of atherosclerosis development in carotid arteries of rabbits and probable targets which may lay the foundation for future research of clinical applications.