Integrated analysis of noncoding RNAs and mRNAs reveals their potential roles in the biological activities of the growth hormone receptor

Identification of growth hormone receptor as a relevant target for precision medicine in low-EGFR expressing glioblastoma

Objective

New therapeutic approaches are needed to improve the prognosis of glioblastoma (GBM) patients.

Methods

With the objective of identifying alternative oncogenic mechanisms to abnormally activated epidermal growth factor receptor (EGFR) signalling, one of the most common oncogenic mechanisms in GBM, we performed a comparative analysis of gene expression profiles in a series of 54 human GBM samples. We then conducted gain of function as well as genetic and pharmocological inhibition assays in GBM patient‐derived cell lines to functionnally validate our finding.

Results

We identified that growth hormone receptor (GHR) signalling defines a distinct molecular subset of GBMs devoid of EGFR overexpression. GHR overexpression was detected in one third of patients and was associated with low levels of suppressor of cytokine signalling 2 (SOCS2) expression due to SOCS2 promoter hypermethylation. In GBM patient‐derived cell lines, GHR signalling modulates the expression of proteins involved in cellular movement, promotes cell migration, invasion and proliferation in vitro and promotes tumourigenesis, tumour growth, and tumour invasion in vivo. GHR genetic and pharmacological inhibition reduced cell proliferation and migration in vitro.

Conclusion

This study pioneers a new field of investigation to improve the prognosis of GBM patients.

The Effect of LncRNA H19 on Human Dental Pulp Cells Through Tumor Growth Factor-β1 (TGF-β1)/Smad Signaling Pathway

The pulp tissue is located in the pulp cavity of tooth and has the ability of nutrition, feeling, and defense. Human dental pulp cells (hDPCs) are the main cells of pulp with the ability to self-renew and multi-directional differentiation. LncRNA H19 is involved in the regulation of human dental pulp stem cells, but the specific mechanism has not been elucidated. hDPCs were isolated and cultured in vitro to measure vimentin expression by immunohistochemistry (IHC). hDPCs were randomly assigned into control group, negative control (NC) group and lncRNA H19 overexpression group followed by measuring lncRNA H19, DSPP, and DMP-1 mRNA expression, cell proliferation, ALP activity, BMP-2 expression by ELISA, TGF-β1, Smad2, and Smad4 expression by Western blot. hDPCs were positive for vimentin staining and confirmed to be derived from mesenchymal. Transfection of pcDNA3.1-LncRNA H19 plasmid significantly increased LncRNA H19 expression, promoted cell proliferation, enhanced ALP activity, upregulated DSPP and DMP-1, elevated BMP-2 expression in cell supernatant, as well as promoted TGF-β1, Smad2, and Smad4 expressions compared with control (P < 0.05). In conclusion, lncRNA H19 facilitates hDPCs differentiation into odontoblasts by promoting cell proliferation and increasing BMP-2 secretion via regulating TGF-β1/Smad signaling pathway.

A Competitive Endogenous RNA Network Based on Differentially Expressed lncRNA in Lipopolysaccharide-Induced Acute Lung Injury in Mice

Non-coding RNAs have remarkable roles in acute lung injury (ALI) initiation. Nevertheless, the significance of long non-coding RNAs (lncRNAs) in ALI is still unknown. Herein, we purposed to identify potential key genes in ALI and create a competitive endogenous RNA (ceRNA) modulatory network to uncover possible molecular mechanisms that affect lung injury. We generated a lipopolysaccharide-triggered ALI mouse model, whose lung tissue was subjected to RNA sequencing, and then we conducted bioinformatics analysis to select genes showing differential expression (DE) and to build a lncRNA-miRNA (microRNA)- mRNA (messenger RNA) modulatory network. Besides, GO along with KEGG assessments were conducted to identify major biological processes and pathways, respectively, involved in ALI. Then, RT-qPCR assay was employed to verify levels of major RNAs. A protein-protein interaction (PPI) network was created using the Search Tool for the Retrieval of Interacting Genes (STRING) database, and the hub genes were obtained with the Molecular Complex Detection plugin. Finally, a key ceRNA subnetwork was built from major genes and their docking sites. Overall, a total of 8,610 lncRNAs were identified in the normal and LPS groups. Based on the 308 DE lncRNAs [p-value < 0.05, |log2 (fold change) | > 1] and 3,357 DE mRNAs [p-value < 0.05, |log2 (fold change) | > 1], lncRNA-miRNA and miRNA-mRNA pairs were predicted using miRanda. The lncRNA-miRNA-mRNA network was created from 175 lncRNAs, 22 miRNAs, and 209 mRNAs in ALI. The RT-qPCR data keep in step with the RNA sequencing data. GO along with KEGG analyses illustrated that DE mRNAs in this network were mainly bound up with the inflammatory response, developmental process, cell differentiation, cell proliferation, apoptosis, and the NF-kappa B, PI3K-Akt, HIF-1, MAPK, Jak-STAT, and Notch signaling pathways. A PPI network on the basis of the 209 genes was established, and three hub genes (Nkx2-1, Tbx2, and Atf5) were obtained from the network. Additionally, a lncRNA-miRNA-hub gene subnetwork was built from 15 lncRNAs, 3 miRNAs, and 3 mRNAs. Herein, novel ideas are presented to expand our knowledge on the regulation mechanisms of lncRNA-related ceRNAs in the pathogenesis of ALI.

Member Domain 3 (LRIG3) Activates Hypoxia-Inducible Factor-1 α/Vascular Endothelial Growth Factor (HIF-1α/VEGF) Pathway to Inhibit the Growth of Bone Marrow Mesenchymal Stem Cells in Glioma

Member domain 3 (LRIG3) of the LRIG gene family is down-regulated in several cancers. However, its role in bone marrow mesenchymal stem cells (BMSCs) in gliomas and the related mechanisms is unknown. The qRT-PCR assessed LRIG3 mRNA level. Rat BMSCs were randomly assigned into glioma group (BMSCs cultured in glioma microenvironment); LRIG3 overexpression group; and si-LRIG3 inhibitor group followed by analysis of LRIG3 expression, cell proliferation, PCNA and Ki-67 apoptosis, TNF-α; and HIF-1α/VEGF mRNA level. LRIG3 mRNA expression was decreased in gliomas patients (P < 0.05). BMSCs cultured in glioma microenvironment showed decreased LRIG3, increased cell proliferation, decreased PCNA, Ki-67 and TNF-α secretion as well as elevated HIF-1α and VEGF level (P < 0.05). Transfection of LRIG3 siRNA further promoted the above changes. Conversely, LRIG3 plasmid transfection significantly promoted its expression in glioma BMSCs (P < 0.05), inhibited cell proliferation, promoted PCNA, Ki-67, and TNF-α secretion, and increased HIF-1α and VEGF level (P < 0.05). LRIG3 in rat BMSCs cultured in the glioma microenvironment is decreased. Down-regulation of LRIG3 inhibits TNF-α secretion by activating HIF-1α/VEGF pathway regulating BMSCs proliferation and apoptosis.

Zinc Finger E-Box Binding Homeobox 1 Regulates the Biological Behavior of Glioma Cells via iNOS/NF-κB Signaling

The gliomas pathogenesis is complex and effective molecular targets are still unclear. ZEB1 regulates epithelial mesenchymal transition (EMT) and participates in tumors. Our study intends to analyze ZEB1’s role in glioma cells. qRT-PCR detected ZEB1 mRNA expression in normal group and tumor group. ZEB1 siRNA was transfected into glioma cells followed by measuring ZEB1, E-cadherin and Vimentin expression, cell proliferation, Capase-3 activity as well as NF-κB and iNOS changes by immunoblotting. Upregulation of ZEB1 was found in glioma tumor tissue and correlated with glioma clinicopathological characteristics. Interfering with ZEB1 by siRNA significantly down-regulated ZEB1, inhibited cell proliferation, increased Capase-3 activity, down regulated NF-κB and iNOS proteins in glioma cells, elevated E-cadherin and decreased Vimentin level (P <0.05). ZEB1 down regulation in glioma cells can change the expression of NF-κB/iNOS, regulate cell apoptosis and inhibit cell proliferation, thereby delaying EMT process.

MicroRNA-710 regulates multiple pathways of carcinogenesis in murine metastatic breast cancer

Prior research has shown that critical differences between non-metastatic and metastatic tumor cells are at the level of microRNA. Consequently, harnessing these molecules for the treatment of metastatic cancer could have significant clinical impact. In the present study, we set out to identify metastasis-specific microRNAs which drive metastatic colonization of distant organs. Using a murine model of metastatic breast cancer, we employed a directed approach in which we screened for microRNAs that are differentially expressed between the primary tumors and metastatic lesions but concordantly expressed in all of the metastatic lesions irrespective of the tissue that is colonized. Of the identified targets, we focused on miR-710, which was consistently and significantly downregulated in the metastatic lesions relative to the primary tumors. The level of downregulation was independent of the distant organ that is involved, suggesting that miR-710 plays a fundamental role in metastatic colonization. Computational target prediction suggested a pleiotropic role for miR-710 in apoptosis, migration and invasion, and stemness. Using a previously validated oligonucleotide delivery system, we introduced miR-710 mimics into 4T1 metastatic breast adenocarcinoma cells and assessed the resultant phenotypic effects. We demonstrated significant inhibition of cell viability, migration, and invasion. We also showed that the treatment profoundly enhanced cell senescence, reduced stemness, and influenced markers of epithelial to mesenchymal transition, as evidenced by enhanced E-cadherin and reduced vimentin expression. This knowledge represents a first step towards harnessing a similar approach to discover novel microRNA targets with therapeutic potential in metastasis.

Growth signaling and longevity in mouse models

Reduction of insulin/insulin-like growth factor 1 (IGF1) signaling (IIS) extends the lifespan of various species. So far, several longevity mouse models have been developed containing mutations related to growth signaling deficiency by targeting growth hormone (GH), IGF1, IGF1 receptor, insulin receptor, and insulin receptor substrate. In addition, p70 ribosomal protein S6 kinase 1 (S6K1) knockout leads to lifespan extension. S6K1 encodes an important kinase in the regulation of cell growth. S6K1 is regulated by mechanistic target of rapamycin (mTOR) complex 1. The v-myc myelocytomatosis viral oncogene homolog (MYC)-deficient mice also exhibits a longevity phenotype. The gene expression profiles of these mice models have been measured to identify their longevity mechanisms. Here, we summarize our knowledge of long-lived mouse models related to growth and discuss phenotypic characteristics, including organ-specific gene expression patterns.

Co-expression network analysis of gene expression profiles of HER2+ breast cancer-associated brain metastasis

Brain metastasis occurs in ~30% of patients with breast cancer, and patients with human epidermal growth factor receptor 2 (HER2)⁺ breast cancer have a particularly high frequency of brain metastasis. Weighted gene co-expression network analysis was conducted to identify the hub differentially expressed genes from patients with HER2⁺ breast cancer between brain metastases and primary tumors. The potential candidate genes were investigated in another set of patient samples to confirm their relevance. The results indicated that a number of pathways altered significantly when breast cancer metastasized to the brain. Cyclophilin A (CypA) and ribosomal protein L17 (RPL17) were overexpressed in breast cancer-associated brain metastases, whereas tumor protein 63 (TP63) and von Willebrand factor A domain-containing 8 (VWA8) were significantly downregulated in breast cancer brain metastases. Furthermore, the expression of CypA and RPL17 in brain metastases were significantly increased compared with that in primary breast tumors, and the expression of TP63 and VWA8 in brain metastases were significantly decreased. This result indicated that the significant differences in expression observed between primary breast tumors and brain metastases were derived from significantly altered systems, including gene modules rather than single genes.

Mitochondria Associated MicroRNA Expression Profiling of Heart Failure

Heart failure (HF) is associated with mitochondrial dysfunction and energy metabolism impairment. MicroRNAs are implicated in the development of heart failure. However, the mitochondria enriched microRNA during heart failure remains elusive. Here, we generated a pressure overload-induced early and late stage heart failure model at 4 weeks and 8 weeks following transverse aortic constriction (TAC) in mice. We found that expression of mitochondrion protein COX4 was highly enriched in isolated mitochondria from cardiac tissues while GAPDH could hardly be detected. Furthermore, small RNA sequencing for mitochondria RNAs from failing hearts was performed. It was found that 69 microRNAs were upregulated and 2 were downregulated in early heart failure, while 16 microRNAs were upregulated and 6 were downregulated in late heart failure. 15 microRNA candidates were measured in both mitochondria and total cardiac tissues of heart failure by real-time PCR. MiR-696, miR-532, miR-690, and miR-345-3p were enriched in mitochondria from the failing heart at early stage. Bioinformatics analysis showed that mitochondria enriched microRNAs in HF were associated with energy metabolism and oxidative stress pathway. For the first time, we demonstrated microRNAs were enriched in mitochondria during heart failure, which established a link between microRNA and mitochondrion in heart failure.

Systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change

BACKGROUND

Long non-coding RNA (lncRNA) is a class of non-coding RNA with important regulatory roles in biological process of organisms. The systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change are still poorly understood. Here we identified 17,610 lncRNAs and calculated their expression levels based on RNA-seq of 80 individuals of Miscanthus lutarioriparius from two environments, the nearly native habitats and transplanted field, respectively.

RESULTS

LncRNAs had significantly higher expression diversity and lower expression frequency in population than protein coding mRNAs in both environments, which suggested that lncRNAs may experience more relaxed selection or divergent evolution in population compared with protein coding RNAs. In addition, the increase of expression diversity for lncRNAs was always significantly higher and the magnitude of fold change of expression in new stress environment was significantly larger than protein-coding mRNAs. These results suggested that lncRNAs may be more sensitive to environmental change than protein-coding mRNAs. Analysis of environment-robust and environment-specific lncRNA-mRNA co-expression network between two environments revealed the characterization of lncRNAs in response to environmental change. Furthermore, candidate lncRNAs contributing to water use efficiency (WUE) identified based on the WUE-lncRNA-mRNA co-expression network suggested the roles of lncRNAs in response to environmental change.

CONCLUSION

Our study provided a comprehensive understanding of expression characterization of lncRNAs in population for M. lutarioriparius under field condition, which would be useful to explore the roles of lncRNAs and could accelerate the process of adaptation in new environment for many plants.

Integrated analysis of long non-coding RNA‑associated ceRNA network reveals potential lncRNA biomarkers in human lung adenocarcinoma

Accumulating evidence has highlighted the important roles of long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) in tumor biology. However, the roles of cancer specific lncRNAs in lncRNA-related ceRNA network of lung adenocarcinoma (LUAD) are still unclear. In the present study, the 465 RNA sequencing profiles in LUAD patients were obtained from the cancer genome atlas (TCGA) database, which provides large sample RNA sequencing data free of charge, and 41 cancer specific lncRNAs, 25 miRNAs and 1053 mRNAs (fold change >2, p<0.05) were identified. Then, the lncRNA-miRNA-mRNA ceRNA network of LUAD was constructed with 29 key lncRNAs, 24 miRNAs and 72 mRNAs. Subsequently, we selected these 29 key lncRNAs to analyze their correlation with clinical features, and 21 of them were aberrantly expressed with tumor pathological stage, TNM staging system, lymph node metastasis and patient outcome assessment, respectively. Furthermore, there were 5 lncRNAs (BCRP3, LINC00472, CHIAP2, BMS1P20 and UNQ6494) positively correlated with overall survival (OS, log-rank p<0.05). Finally, 7 cancer specific lncRNAs were randomly selected to verify the expression in 53 newly diagnosed LUAD patients using qRT-PCR. The expression results between TCGA and qRT-PCR were 100% in agreement. The correlation between AFAP1-AS1 and LINC00472 and clinical features were also confirmed. Thus, our results showed the lncRNA expression profiles and we constructed an lncRNA-miRNA-mRNA ceRNA network in LUAD. The present study provides novel insight for better understanding of lncRNA-related ceRNA network in LUAD and facilitates the identification of potential biomarkers for diagnosis and prognosis.