Dysregulated mRNAs Research Articles

RNA Landscapes of Brain and Brain-Derived Extracellular Vesicles in Simian Immunodeficiency Virus Infection and Central Nervous System Pathology.

Brain tissue-derived extracellular vesicles (bdEVs) act locally in the central nervous system (CNS) and may indicate molecular mechanisms in human immunodeficiency virus (HIV) CNS pathology. Using brain homogenate (BH) and bdEVs from a simian immunodeficiency virus (SIV) model of HIV disease, we identified RNA networks in SIV infection and neuroinflammation. Postmortem occipital cortex samples were obtained from uninfected controls and SIV-infected subjects (acute and chronic phases with or without CNS pathology [SIV encephalitis]). bdEVs were separated and characterized per international consensus guidelines. RNAs from bdEVs and BH were sequenced and quantitative polymerase chain reaction (qPCR)-amplified to detect levels of small RNAs (sRNAs, including microRNAs [miRNAs]) and longer RNAs including messenger RNAs (mRNAs) and circular RNAs (circRNAs). Dysregulated RNAs in BH and bdEVs were identified in acute and chronic infection with pathology groups, including mRNAs, miRNAs, and circRNAs. Most dysregulated mRNAs in bdEVs reflected dysregulation in source BH. These mRNAs are disproportionately involved in inflammation and immune responses. Based on target prediction, several circRNAs that were differentially abundant in source tissue might be responsible for specific differences in sRNA levels in bdEVs during SIV infection. RNA profiling of bdEVs and source tissues reveals potential regulatory networks in SIV infection and SIV-related CNS pathology.

Hsa_circ_0073453 modulates IL-8 secretion by GC-MSCs to promote gastric cancer progression by sponging miR-146a-5p

Gastric cancer associated mesenchymal stem cells (GC-MSCs) have been demonstrated to promote gastric cancer progression in a paracrine manner. IL-8 is highly secreted by GC-MSCs and is crucial for their oncogenic function. However, the mechanism underlying the modulation of IL-8 secretion by GC-MSCs has not been well elucidated. In this study, Shbio-human ceRNA array was used to identify dysregulated mRNAs and circRNAs between GC-MSCs and bone marrow derived mesenchymal stem cells (BM-MSCs). IL-8 was validated to be a critical paracrine cytokine for GC-MSCs promoting migration and invasion of gastric cancer cells. circ_0073453 was identified as a novel GC-MSC-derived circRNA which acted as a sponge of miR-146a-5p, thus increasing IL-8 expression and secretion to promote gastric cancer cell metastasis. Furthermore, circ_0073453 modulated IL-8 secretion by GC-MSCs to enhance gastric cancer cells PD-L1 expression to resist cytotoxic CD8+ T cell-killing. circ_0073453/miR-146a-5p/IL-8 axis was deregulated in gastric cancer tissues and associated with prognosis depending on MSC abundance in cancer tissues. Taken together, our findings suggest that circ_0073453/miR-146a-5p/IL-8 axis is critical for GC-MSCs promoting gastric cancer progression. Hence, hsa_circ_0073453 may be a potential therapeutic target for gastric cancer.

Construction of a New Immune-Related Competing Endogenous RNA Network with Prognostic Value in Lung Adenocarcinoma.

Tumor microenvironment has significant influence on the gene expression of tumor tissues and on the clinical outcomes in lung adenocarcinoma. Infiltrating immune and stromal cells not only perturb the tumor signal in molecular studies, but also play crucial roles in cancer biology. The competing endogenous RNAs (ceRNAs) are useful to explain the post-transcriptional layer regulated by gene translation and play an important role in the occurrence and progression of lung adenocarcinoma. Therefore, identifying novel molecular markers by constructing ceRNA associated with immune infiltration is of great significance to guide the treatment of lung adenocarcinoma in the future. According to the immune and stromal scores of lung adenocarcinoma samples in The Cancer Genome Atlas (TCGA) database calculated by the ESTIMATE algorithm, we identified differentially expressed lncRNAs, miRNAs and mRNAs associated with immune infiltration, including 60 dysregulated lncRNAs, 38 dysregulated mRNAs, and 29 dysregulated miRNAs. Based on the PPI network and Cox regression analysis, 5 mRNAs including CNR2, P2RY12, ZNF831, RSPO1, and F2 were identified to be related to immune infiltration and prognosis in lung adenocarcinoma, and their differential expression, prognosis and correlation with immune cells were verified. Next, through target binding prediction, pearson correlation analysis and expression analysis, a novel immune-related ceRNA network containing 6 lncRNAs, 4 miRNAs, and 3 mRNAs was finally constructed. The present study constructed a novel immune-associated lncRNA-miRNA-mRNA ceRNA network, which deepens our understanding on the molecular network mechanism of lung adenocarcinoma and provides potential prognostic markers and novel therapeutic targets for the patients with lung adenocarcinoma.

Hepatic gene expression profiles during fed-fasted-refed state in mice.

Background: Regulation of nutrient status during fasting and refeeding plays an important role in maintaining metabolic homeostasis in the liver. Thus, we investigated the impact of the physiological Fed-Fast-Refed cycle on hepatic gene expression in nutrient-sensitive mice. Methods: We performed transcriptomic analysis of liver samples in fed, fasted and refed groups of mice. Through mRNA-sequencing (RNA-Seq) and miRNA-Seq, we compared fasted and fed states (fasted versus fed cohort) as well as refed and fasted states (refed versus fasted cohort) to detect dynamic alterations of hepatic mRNA-miRNA expression during the fed-fasted-refed cycle. Results: We found dozens of dysregulated mRNAs-miRNAs in the transition from fed to fasted and from fasted to refed states. Gene set enrichment analysis showed that gene expression of the two cohorts shared common pathways of regulation, especially for lipid and protein metabolism. We identified eight significant mRNA and three miRNA clusters that were up-downregulated or down-upregulated during the Fed-Fast-Refed cycle. A protein-protein interaction network of dysregulated mRNAs was constructed and clustered into 22 key modules. The regulation between miRNAs and target mRNAs was presented in a network. Up to 42 miRNA-mRNA-pathway pairs were identified to be involved in metabolism. In lipid metabolism, there were significant correlations between mmu-miR-296-5p and Cyp2u1 and between mmu-miR-novel-chr19_16777 and Acsl3. Conclusion: Collectively, our data provide a valuable resource for the molecular characterization of the physiological Fed-Fast-Refed cycle in the liver.

RF04 | PSUN133 Assessment of the Rnf20 Histone Modifier in Regulating Pancreatic Beta-Cell Identity and Function

Abstract Type 1 and Type 2 Diabetes are characterized by a loss of functional pancreatic islet β-cells. With the prevalence of diabetes increasing worldwide, a complete understanding of the gene regulatory mechanisms governing the development and function of insulin-producing β-cells is requisite for improving diabetes therapies. Islet 1 (Isl1) is a LIM-homeodomain class transcription factor (TF) required for the maturation, proliferation, function, and survival of islet cells. In our previous study, we identified Isl1 interactions with the ring finger ubiquitin ligases Ring Finger 20 (Rnf20) and Rnf40 in mouse β-cell extracts, mouse islets, and human islets. Rnf20 and Rnf40, exist as homodimeric or heterodimeric complexes to deposit a mono-ubiquitin epigenetic mark on histone (H)2B (i.e., H2Bub1) and regulate gene transcription as a precursor to active H3K4 trimethylation (H3K4me3) and H3K79 methylation (H3K79me) marks. We demonstrated that Rnf20 and Rnf40 are required for the expression of several important β-cell genes and glucose-stimulated insulin secretion in vitro. Specifically, loss of Rnf20and Rnf40 in MIN6 β-cells resulted in a significant dysregulation of β-cell Slc2a2/Glut2 and MafA expression, target genes which were occupied by Rnf20 and H2Bub1. Additionally, using proximity ligation assay (PLA) in MIN6 β-cells, we demonstrated a robust increase in interactions between Isl1 and Rnf20 under high glucose conditions. Based on this, we hypothesize that Rnf20 and/or Rnf40 are required to establish and maintain β-cell identity in adult islets. To begin addressing this, we disrupted Rnf20/Rnf20 and/or Rnf20/Rnf40 complexes in β-cells via generation of adult inducible Rnf20 β-cell-specific knockout mice. In the adult inducible model, 2 weeks following tamoxifen induction (i.e., by 8 weeks of age) both male and female mice became hyperglycemic and severely glucose intolerant. These 8-week-old Rnf20-deficient mice also had reduced plasma insulin following a glucose challenge yet normal insulin sensitivity. Islet RNA exhibited dysregulated mRNAs encoding islet hormones, glucose-stimulated insulin secretion markers, and β-cell identity markers, including Slc2a2/Glut2, Ucn3, and Hb9 . Our findings of similar phenotypes between Isl1 and Rnf20 adult knockout models, a glucose sensitive interaction between Isl1 and Rnf20, and their occupancy of the Slc2a2/Glut2 locus support mechanisms of Isl1-Rnf driven β-cell regulation. Presentation: Saturday, June 11, 2022 1:12 p.m. - 1:17 p.m., Sunday, June 12, 2022 12:30 p.m. - 2:30 p.m.

Molecular Response of Keloids to Ionizing Radiation: Targeting FOXO1 Radiosensitizes Keloids

Purpose Keloids are benign dermal tumors that arise from abnormal wound healing processes following skin lesions. Surgical excision followed by radiotherapy plays an important role in the treatment of keloids. Nevertheless, radioresistance remains a serious impediment to treatment efficacy. Investigation of the molecular response of keloids to radiation may contribute to radiosensitizing strategies. Materials and Methods Primary keloid fibroblasts from human keloids were isolated and irradiated with X-ray. The expression profiles of messenger RNA (mRNA) in nonradiated and irradiated primary keloid fibroblasts were measured by mRNA sequencing analysis. Then, we identified common motifs and corresponding transcription factors of dysregulated mRNAs by using bioinformatic analysis of the proximal promoters. Whereafter, GO and KEGG were used to analyse the functional enrichment of the differentially expressed genes. Results We found that radiation not only suppressed proliferation but also increased cell senescence of primary keloid fibroblasts. There were 184 mRNAs and 204 mRNAs that showed significant changes in 4 and 8 Gy irradiated primary keloid fibroblasts, respectively. Among them, 8 upregulated and 30 downregulated mRNAs showed consistent alterations in 4 and 8 Gy irradiated primary keloid fibroblasts. More importantly, the forkhead box O1 (FOXO1) signaling pathway was involved in the irradiation response. Pretreatment with the FOXO1 signaling inhibitor AS1842856 significantly promoted LDH release, apoptosis and senescence of primary keloid fibroblasts following irradiation. Conclusion Our findings illustrated the molecular changes in human keloid fibroblasts in response to radiation, and FOXO1 pathway inhibition is expected to provide a novel strategy for the radiosensitization of keloids.

Decoding ceRNA regulatory network in the pulmonary artery of hypoxia-induced pulmonary hypertension (HPH) rat model

BackgroundHypoxia-induced pulmonary hypertension (HPH) is a lethal cardiovascular disease with the characteristic of severe remodeling of pulmonary vascular. Although a large number of dysregulated mRNAs, lncRNAs, circRNAs, and miRNAs related to HPH have been identified from extensive studies, the competitive endogenous RNA (ceRNA) regulatory network in the pulmonary artery that responds to hypoxia remains largely unknown.ResultsTranscriptomic profiles in the pulmonary arteries of HPH rats were characterized through high-throughput RNA sequencing in this study. Through relatively strict screening, a set of differentially expressed RNAs (DERNAs) including 19 DEmRNAs, 8 DElncRNAs, 19 DEcircRNAs, and 23 DEmiRNAs were identified between HPH and normal rats. The DEmRNAs were further found to be involved in cell adhesion, axon guidance, PPAR signaling pathway, and calcium signaling pathway, suggesting their crucial role in HPH. Moreover, a hypoxia-induced ceRNA regulatory network in the pulmonary arteries of HPH rats was constructed according to the ceRNA hypothesis. More specifically, the ceRNA network was composed of 10 miRNAs as hub nodes, which might be sponged by 6 circRNAs and 7 lncRNAs, and directed the expression of 18 downstream target genes that might play important role in the progression of HPH. The expression patterns of selected DERNAs in the ceRNA network were then validated to be consistent with sequencing results in another three independent batches of HPH and normal control rats. The diagnostic effectiveness of several hub mRNAs in ceRNA network was further evaluated through investigating their expression profiles in patients with pulmonary artery hypertension (PAH) recorded in the Gene Expression Omnibus (GEO) dataset GSE117261. Dysregulated POSTN, LTBP2, SPP1, and LSAMP were observed in both the pulmonary arteries of HPH rats and lung tissues of PAH patients.ConclusionsA ceRNA regulatory network in the pulmonary arteries of HPH rats was constructed, 10 hub miRNAs and their corresponding interacting lncRNAs, circRNAs, and mRNAs were identified. The expression patterns of selected DERNAs were further validated to be consistent with the sequencing result. POSTN, LTBP2, SPP1, and LSAMP were suggested to be potential diagnostic biomarkers and therapeutic targets for PAH.

Insights from Dysregulated mRNA Expression Profile of β-Cells in Response to Proinflammatory Cytokines.

Type 1 diabetes mellitus (T1DM) is a chronic autoimmune disease that is characterized by autoimmunity and its mediated β-cell damage. Chronic exposure of β-cells to proinflammatory cytokines is known to regulate the expression of many genes, subsequently resulting in the impairment of some signaling pathways involved with insulin production and secretion and/or β-cell apoptosis. In our study, RNA sequencing technology was applied to identify differentially expressed mRNAs in MIN6 cells treated with a mix of cytokines, including IL-1β, TNF-α, and IFN-γ. The results showed 809 upregulated and 946 downregulated protein-coding mRNAs in MIN6 cells upon the stimulation of cytokines. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analyses were performed to predict the functions of dysregulated genes. The networks of circRNA-mRNA were constructed between differentially mRNAs and dysregulated expressed circRNAs in our previous study. In addition, we selected 8 dysregulated mRNAs for further validation by quantitative real-time PCR. The RNA sequencing data showed 809 upregulated and 946 downregulated protein-coding mRNAs. GO analysis showed that the top 10 significant “biological processes,” “cellular components,” and “molecular functions” for upregulated mRNAs include “immune system process,” “inflammatory response,” and “innate immune response” and the top 10 for downregulated mRNAs include “cell cycle,” “mitotic cytokinesis,” and “cytoplasm.” KEGG analysis showed that these differentially expressed genes were involved with “antigen processing and presentation,” “TNF signaling pathway” and “type 1 diabetes,” “cell cycle,” “necroptosis,” and “Rap1 signaling pathway.” We also constructed the networks of differentially expressed circRNAs and mRNAs. We observed that upregulated circRNA 006029 and downregulated circRNA 000286 and 017277 were associated with the vast majority of selected dysregulated mRNAs, while circRNA 013053 was only related to the protein-coding gene, Slc7a2. To the summary, these data indicated that differentially expressed mRNAs may play key or partial roles in cytokine-mediated β-cell dysfunction and gave us the hint that circRNAs might regulate mRNAs, thereby contributing to the development of T1DM. The current study provided a systematic perspective on the potential functions and possible regulatory mechanisms of mRNAs in proinflammatory cytokine-induced β-cell destruction.

Dexmedetomidine alleviates oxygen and glucose deprivation-induced apoptosis in mesenchymal stem cell via downregulation of MKP-1

Bone marrow mesenchymal stem cell (MSC)-based therapy is a novel candidate for heart repair. But ischemia-reperfusion injury leads to low viability of MSC. Dexmedetomidine (Dex) has been found to protect neurons against ischemia-reperfusion injury. It remains unknown if Dex could increase the viability of MSCs under ischemia. The present study is to observe the potential protective effect of Dex on MSCs under ischemia and its underlying mechanisms. Specific mRNAs related to myocardial ischemia in the GEO database were selected from the mRNA profiles assessed in a previous study using microarray. The most dysregulated mRNAs of the specific ones from the above study were subject to bioinformatics analysis at our laboratory. These dysregulated mRNAs possibly regulated apoptosis of cardiomyocytes and were validated in vitro for their protective effect on MSCs under ischemia. MSCs were pre-treated with Dex at 10 μM concentration for 24 h under oxygen-glucose deprivation (OGD). Flow cytometry and TUNEL assay were carried out to detect apoptosis in Dex-pretreated MSCs under OGD. The relative expressions of mitogen-activated protein kinase phosphatase 1 (MKP-1) and related genes were detected by quantitative polymerase chain reaction and western blotting. Microarray data analysis revealed that Dex regulates MAPK phosphatase activity. Dex significantly reduced in vitro apoptosis of MSCs under OGD, which suppressed the synthesis level of Beclin1 and light chain 3 proteins. Dex down-regulated MKP-1 expression and attenuated an OGD-induced change in the mitogen activated protein kinase 3 (MAPK3) signaling pathway. Dex increases the viability of MSC and improves its tolerance to OGD in association with the MKP-1 signaling pathway, thus suggesting the potential of Dex as a novel strategy for promoting MSCs efficacy under ischemia.

Integrated Analysis of lncRNA-Associated ceRNA Network Identifies Two lncRNA Signatures as a Prognostic Biomarker in Gastric Cancer.

Background Gastric cancer (GC) is a malignant tumour that originates in the gastric mucosal epithelium and is associated with high mortality rates worldwide. Long noncoding RNAs (lncRNAs) have been identified to play an important role in the development of various tumours, including GC. Yet, lncRNA biomarkers in a competing endogenous RNA network (ceRNA network) that are used to predict survival prognosis remain lacking. The aim of this study was to construct a ceRNA network and identify the lncRNA signature as prognostic factors for survival prediction. Methods The lncRNAs with overall survival significance were used to construct the ceRNA network. Function enrichment, protein-protein interaction, and cluster analysis were performed for dysregulated mRNAs. Multivariate Cox proportional hazards regression was performed to screen the potential prognostic lncRNAs. RT-qPCR was used to measure the relative expression levels of lncRNAs in cell lines. CCK8 assay was used to assess the proliferation of GC cells transfected with sh-lncRNAs. Results Differentially expressed genes were identified including 585 lncRNAs, 144 miRNAs, and 2794 mRNAs. The ceRNA network was constructed using 35 DElncRNAs associated with overall survival of GC patients. Functional analysis revealed that these dysregulated mRNAs were enriched in cancer-related pathways, including TGF-beta, Rap 1, calcium, and the cGMP-PKG signalling pathway. A multivariate Cox regression analysis and cumulative risk score suggested that two of those lncRNAs (LINC01644 and LINC01697) had significant prognostic value. Furthermore, the results indicate that LINC01644 and LINC01697 were upregulated in GC cells. Knockdown of LINC01644 or LINC01697 suppressed the proliferation of GC cells. Conclusions The authors identified 2-lncRNA signature in ceRNA regulatory network as prognostic biomarkers for the prediction of GC patient survival and revealed that silencing LINC01644 or LINC01697 inhibited the proliferation of GC cells.

Metabolic Syndrome Is Associated With Altered mRNA and miRNA Content in Human Circulating Extracellular Vesicles.

As mediators of intercellular communication, circulating extracellular vehicles (EVs) can modulate tissue and cellular pathways by altering transcription profiles in recipient cells, and their content may reflect the status of their parent cells. However, whether their cargo is altered in the metabolic syndrome (Mets) remains unclear. We hypothesized that MetS altered mRNAs and miRNAs packed within circulating-EVs. EVs were collected from plasma of patients with MetS or age-matched Lean controls (n=4 each). RNA sequencing was performed to identify dysregulated mRNAs and miRNAs, and analyze genes targeted by miRNAs, top pathways, and diseases associated with MetS-EVs. MetS patients showed elevated body weight, blood pressure, glucose, insulin, and liver injury markers levels. 1,446 mRNAs were downregulated and 32 upregulated in MetS- compared to Lean-EVs, whereas 40 miRNAs were selectively enriched and 10 downregulated in MetS-EVs. MetS upregulated in EVs genes involved in apoptosis, mitochondrial regulation, transport, and lipoproteins, but downregulated vessel and heart development, protein complex biogenesis, and angiogenesis. MetS also upregulated miRNAs targeting genes implicated in cellular processes, including oxidation–reduction, and downregulated miRNAs capable of modulating catalytic activity, as well as heart, blood vessel, and skeletal development, transcriptional regulation, apoptosis, and cell cycle. Our study, thus, indicates that human subjects with MetS show modified cargo of circulating EVs, which in turn may modulate several critical cellular functions and fate. These EVs may reflect the anomalous status of their parent cells, and potentially serve as important regulators, biomarkers, and targets in the progression and treatment of MetS.

LncRNA ENSMUST00000155383 is Involved in the Improvement of DPP-4 Inhibitor MK-626 on Vascular Endothelial Function by Modulating Cacna1c-Mediated Ca2+ Influx in Hypertensive Mice.

Objective: This study investigated the protective effects of dipeptidyl peptidase-4 inhibitor MK-626 on vascular endothelial function by regulating lncRNAs in hypertensive vasculature. Methods: Angiotensin Ⅱ (Ang Ⅱ)-loaded osmotic pumps were implanted in mice with or without MK-626 administration. GLP-1 levels in plasma were measured by ELISA. Aortic rings were suspended in myograph for tension measurement. Microarray was performed to analyze lncRNA and mRNA expression profiles. Protein expression and phosphorylation were examined by Western blot. The differentially expressed (DE)-genes were validated by qRT-PCR. The intracellular Ca2+ concentration was detected by laser confocal system. Results: MK-626 elevated plasma GLP-1 level, increased eNOS phosphorylation, improved endothelium-dependent relaxations, and reduced systolic blood pressure in Ang Ⅱ-induced hypertensive mice. Microarray revealed the dysregulations of 723 lncRNAs and 742 mRNAs were reversed by MK-626 in hypertensive mouse aortae. qRT-PCR validation showed that 13 DE-lncRNAs and eight dysregulated mRNAs in both hypertensive mouse aortae and mouse aortic endothelial cells (MAECs) were rescued by MK-626. Among them, four mRNAs (Cacna1C, Itgav, Itga8, and Npnt) were co-expressed with lncRNA ENSMUST00000155383. Cacna1C protein expression was reduced in the ECs but was elevated in smooth muscle cells from Ang Ⅱ-infused mice, which were both reversed by MK-626. Knockdown of lncRNA ENSMUST00000155383 suppressed the increased Cacna1c protein and mRNA expression, elevated Ca2+ level, and enhanced eNOS phosphorylation induced by MK-626 in the hypertensive mouse ECs. Conclusion: The dysregulations of lncRNA ENSMUST00000155383-associated genes might play crucial roles in hypertension-induced endothelial dysfunction through affecting calcium pathway. MK-626 might ameliorate endothelial dysfunction by upregulating lncRNA ENSMUST00000155383, enhancing Ca2+ concentration, and subsequently restoring eNOS activity in hypertension.

CircRNA-ceRNA Network Revealing the Potential Regulatory Roles of CircRNA in Alzheimer's Disease Involved the cGMP-PKG Signal Pathway.

Background: Alzheimer’s disease (AD) is a chronic progressive neurodegenerative disease. The characteristic pathologies include extracellular senile plaques formed by β-amyloid protein deposition, neurofibrillary tangles formed by hyperphosphorylation of tau protein, and neuronal loss with glial cell hyperplasia. Circular RNAs (circRNAs) are rich in miRNA-binding sites (miRNA response elements, MREs), which serve as miRNA sponges or competitive endogenous RNAs (ceRNAs). Although several research groups have identified dysregulated circRNAs in the cerebral cortex of SAMP8 mice or APP/PS1 mice using deep RNA-seq analysis, we need to further explore circRNA expression patterns, targets, functions and the signaling pathways involved in the pathogenesis of AD and in particular the hippocampal circRNA expression profiles in AD.Methods: We used deep RNA sequencing to investigate circRNA-ceRNA network patterns in the hippocampus of APP/PS1 mice.Results: In our study, 70 dysregulated circRNAs, 39 dysregulated miRNAs and 121 dysregulated mRNAs were identified between the APP/PS1 group and the wild-type group at 8 months in the hippocampus of the mice. Through correlation analysis, we identified 11 dysregulated circRNAs, 7 dysregulated miRNAs and 8 dysregulated mRNAs forming 16 relationships in the circRNA-miRNA-mRNA regulatory network. Gene ontology (GO) analysis indicated that the dysregulated circRNAs were most enriched in biological metabolic processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the dysregulation of circRNAs was enriched in the cGMP-PKG signaling pathway, cAMP signaling pathway, Hippo signaling pathway, platelet activation, long-term potentiation and axon guidance. In addition, our findings preliminarily verified that the novel_circ_0003012/mmu-miR-298-3p/Smoc2 signaling axis may regulate the pathophysiology of AD by affecting the cGMP-PKG signaling pathway.Conclusions: These newly identified circRNAs in networks and signaling pathways reveal potential diagnostic or therapeutic targets for AD.

SLC40A1 Mediates Ferroptosis and Cognitive Dysfunction in Type 1 Diabetes

Cognitive dysfunction often accompanies diabetes. Both hypoglycemia and hyperglycemia cause cognitive dysfunctions. However, the underlying pathophysiology remains unclear. Recent evidence show that ferroptosis primarily triggers nerve cell death, Alzheimer’s disease (AD), Huntington’s disease (HD), and Parkinson’s disease (PD). The present study aimed to investigate whether ferroptosis is a vital pathogenic pathway in diabetes-induced cognitive dysfunction. Type 1 diabetic rat model was created by intraperitoneal injection of streptozotocin (STZ). Significant cognitive dysfunction was observed in the diabetic rats as evidenced by increase in latency period to find a hidden platform and decreased cumulative time spent in the target quadrant (TQ) in the Morris water maze test. We detected the amplitude of low-frequency fluctuation (ALFF) of the BOLD (Blood Oxygenation Level-Dependent) signal using resting-state functional magnetic resonance imaging (rs-fMRI). Consequently, we found that the ALFF values, as well as the T2 relaxation time of the bilateral hippocampus, were reduced in Type 1 diabetic rats. We detected Fe2+ level and lipid peroxidation products (malondialdehyde (MDA) and 4-Hydroxynonenal (4-HNE)) in the hippocampus. Mitochondria and neuron injury in the STZ-induced diabetic rats were determined using a Transmission Electron Microscope and Nissl body staining. Iron overload and ferroptosis were detected in the hippocampus. Furthermore, mRNA microarray analysis revealed 201 dysregulated mRNAs in STZ-induced type 1 diabetes (T1D). Pathway enrichment analyses indicated that differentially expressed mRNAs associated-coding genes were associated with ferroptosis. Among ferroptosis signaling pathway genes, Slc40a1 gene (ferroportin) was downregulated. We show that ferroptosis is associated with diabetic cognitive dysfunction and Slc40a1 mediates ferroptosis in T1D.

Identification of circulating biomarkers for differentiating patients with papillary thyroid cancers from benign thyroid tumors.

This study aimed to identify the potential circulating biomarkers of protein, mRNAs, and long non-coding RNAs (lncRNAs) to differentiate the papillary thyroid cancers from benign thyroid tumors. The study population of 100 patients was classified into identification (10 patients with papillary thyroid cancers and 10 patients with benign thyroid tumors) and validation groups (45 patients with papillary thyroid cancers and 35 patients with benign thyroid tumors). The Sengenics Immunome Protein Array-combined data mining approach using the Open Targets Platform was used to identify the putative protein biomarkers, and their expression validated using the enzyme-linked immunosorbent assay. Next-generation sequencing by Illumina HiSeq was used for the detection of dysregulated mRNAs and lncRNAs. The website Timer v2.0 helped identify the putative mRNA biomarkers, which were significantly over-expressed in papillary thyroid cancers than in adjacent normal thyroid tissue. The mRNA and lncRNA biomarker expression was validated by a real-time polymerase chain reaction. Although putative protein and mRNA biomarkers have been identified, their serum expression could not be confirmed in the validation cohorts. In addition, seven lncRNAs (TCONS_00516490, TCONS_00336559, TCONS_00311568, TCONS_00321917, TCONS_00336522, TCONS_00282483, and TCONS_00494326) were identified and validated as significantly downregulated in patients with papillary thyroid cancers compared to those with benign thyroid tumors. These seven lncRNAs showed moderate accuracy based on the area under the curve (AUC = 0.736) of receiver operating characteristic in predicting the occurrence of papillary thyroid cancers. We identified seven downregulated circulating lncRNAs with the potential for predicting the occurrence of papillary thyroid cancers.

MicroRNA Regulation of TRAIL in Renal Carcinoma: Tiny Juggernauts at Work.

Renal Carcinoma (RC) is the ninth most prevalent cancer in men. Advancements in high- throughput technology have begun to scratch the surface of the complex landscape of renal cancer. Development, progression, invasion and metastasis are the key mechanism modulated by the microRNAs (miRNAs). Recent pieces of evidence have delineated the role of these micro steering wheels in the regulation of vital processes of RC biology, therefore miRNAs can be implemented as a new therapeutic target for RC. MiRNAs also negatively affect the process of apoptosis in cancer cells leading to their survival and growth. The role of dysregulated mRNAs in hindering the TRAIL- mediated apoptotic pathway is also known. Therapeutic interventions targeting tumor-suppressive miRNAs to promote apoptosis through extrinsic/intrinsic pathways seem a promising approach for advanced stage and metastatic renal cancers. This article aims to discuss RC-specific microRNAs, their roles in the TRAIL pathway and highlight the distinguished microRNAs that could serve as a diagnostic biomarker and therapeutic targets for this cancer.

Systematic Analysis of Competing Endogenous RNA Networks in Diffuse Large B-Cell Lymphoma and Hodgkin's Lymphoma.

Lymphoma is a systemic malignancy, originating from the lymphatic system, which accounts for 3 to 4% of all tumors. There are two major subtypes of lymphoma, namely, diffuse large B-cell lymphoma (DLBCL) and Hodgkin’s lymphoma (HL). Elucidation of the pathogenesis of these two lymphoma types is crucial for the identification of potential therapeutic targets. Compared with the corresponding knowledge of other diseases, the understanding of the regulatory networks involved in DLBCL and HL is relatively deficient. To address this, we comprehensively analyzed the mRNAs, lncRNAs, and miRNAs that were differentially expressed between normal and tumor samples of DLBCL and HL. In addition, functional enrichment analysis of the differentially expressed mRNAs was performed. We constructed two specific ceRNA networks of DLBCL and HL. The pathways enriched by dysregulated mRNAs in DLBCL and HL were mainly involved in immune responses, transcription process, and metabolism process. The ceRNA network analysis revealed that 45 ceRNAs were shared between the two ceRNA networks, including five pivotal lncRNAs (MALAT1, CTBP1-AS, THUMPD3-AS, PSMA3-AS1, and NUTM2A-AS1). In addition, we proposed a DLBCL survival risk model based on a DLBCL-specific network constructed by Lasso regression analysis. The model, which is based on eight mRNAs, exhibited excellent performance in regard to predicting outcomes in DLBCL patients, with a p value of 0.0017 and AUC of 0.9783. In summary, although the molecular mechanisms underlying tumorigenesis in DLBCL and HL were quite different, the same pivotal lncRNAs acted as key regulators. Our findings identify novel potential prognostic and therapeutic targets for DLBCL and HL.

Integrated analysis of circRNA-miRNA-mRNA regulatory network identifies potential diagnostic biomarkers in diabetic foot ulcer.

Diabetic foot ulcer (DFU) is a common and serious complication of diabetes mellitus, which influences patients’ quality of life. Recently, circRNA regulated the mRNA levels by functioning as miRNA sponge in various disease, including diabetes mellitus. Nevertheless, the circRNA-miRNA-mRNA regulatory network involved in DFU remains obscure. The aim of this study is to construct a competing endogenous RNA (ceRNA) network and screen biological indicators as diagnostic factors in DFU.All the differentially expressed circRNAs, miRNAs and mRNAs were derived from Gene Expression Omnibus database. Furthermore, circRNAs identified by cytoHubba analysis and miRNAs obtained by human miRNA-disease database were used to construct DFU-specific ceRNA network with intersection of mRNAs. Functional enrichment analysis displayed the function and pathway of dysregulated mRNAs. Hub genes with high diagnostic value were screened by ClusterONE, GO semantic similarity and receiver operating characteristic (ROC) curve.Here, the ceRNA network consisted of 8 circRNAs, 11 miRNAs and 91 mRNAs. Functional enrichment analysis demonstrated diabetic complications-related pathway including TGF-beta, FoxO and Wnt signaling pathway. GO semantic similarity and ROC curve analysis showed 6 hub genes with high diagnostic value (the area under the ROC curve ≥ 0.8) in patients with DFU, including BCL2, CCND1, IRAK4, SMAD4, SP1 and SUFU, which were identified as potential target genes for DFU diagnosis. In conclusion, the present study looked at a circRNA-miRNA-mRNA regulatory network with DFU and screened the potential function of mRNA, then identified novel diagnostic biomarkers and therapeutic targets for patients with DFU.

Analysis of lncRNA, miRNA and mRNA-associated ceRNA networks and identification of potential drug targets for drug-resistant non-small cell lung cancer.

Background: Drug resistance to chemotherapeutic drugs or targeted medicines is an obstacle encountered in the treatment of non-small-cell lung cancer (NSCLC). However, the mechanisms of competing endogenous RNA (ceRNA) on the drug resistance in NSCLC are rarely reported. In this paper, the comprehensive expression profiles of lncRNAs and mRNAs in drug-resistant NSCLC cells were obtained by RNA sequencing.Methods: The dysregulated lncRNAs, miRNAs and mRNAs in drug-resistant NSCLC cell lines were identified by RNA-sequencing and bioinformatics methods.Results: A total of 39 dysregulated lncRNAs and 650 dysregulated mRNAs were identified between drug-resistant NSCLC cell lines and their parental cell lines. Additionally, 33 lncRNA-miRNA-mRNA pathways in the ceRNA network in drug-resistant NSCLC were constructed through bioinformatics methods and ceRNA regulatory rules. These comprised 12 dysregulated lncRNAs, five dysregulated miRNAs, and eight dysregulated mRNAs. In addition, lncRNA ATP2B1/miR-222-5p/TAB2 and lncRNA HUWE1/miR-222-5p/TAB2 were identified as potential ceRNA networks involved in drug resistance to NSCLC.Conclusions: The current study provides a promising therapeutic strategy against the lncRNA-miRNA-mRNA ceRNA regulatory network for NSCLC treatment and deepens our comprehension of the ceRNA regulatory mechanisms related to drug resistance to NSCLC.

Comprehensive Analysis of Therapy-Related Messenger RNAs and Long Noncoding RNAs as Novel Biomarkers for Advanced Colorectal Cancer.

Colorectal cancer (CRC) is one of the most common types of human cancers. However, the mechanisms underlying CRC progression remained elusive. This study identified differently expressed messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs), and small nucleolar RNAs (snoRNAs) between pre-therapeutic biopsies and post-therapeutic resections of locally advanced CRC by analyzing a public dataset, GSE94104. We identified 427 dysregulated mRNAs, 4 dysregulated lncRNAs, and 19 dysregulated snoRNAs between pre- and post-therapeutic locally advanced CRC samples. By constructing a protein–protein interaction network and co-expressing networks, we identified 10 key mRNAs, 4 key lncRNAs, and 7 key snoRNAs. Bioinformatics analysis showed therapy-related mRNAs were associated with nucleosome assembly, chromatin silencing at recombinant DNA, negative regulation of gene expression, and DNA replication. Therapy-related lncRNAs were associated with cell adhesion, extracellular matrix organization, angiogenesis, and sister chromatid cohesion. In addition, therapy-related snoRNAs were associated with DNA replication, nucleosome assembly, and telomere organization. We thought this study provided useful information for identifying novel biomarkers for CRC.