Intergenic Non-protein Coding RNA Research Articles

Linc01116 Silencing Inhibits the Proliferation and Invasion, Promotes Apoptosis of Chordoma Cells via Regulating the Expression of Mir-9-5p/PKG1.

Long intergenic non-protein coding RNA 1116 (LINC01116) plays a carcinogenic role in a variety of cancers. The study aims to investigate the roles of LINC01116 and hsa-miR-9-5p (miR-9-5p) and fathom their interaction in chordoma. The predicted binding sites between miR-9-5p with LINC01116 and phosphoglycerate kinase 1 (PGK1) by starBase were confirmed through dual-luciferase reporter assay. The behaviors of chordoma cells undergoing transfection with siLINC01116 or miR-9-5p inhibitor were determined by Cell Counting Kit-8 (CCK-8), colony formation, Transwell, and flow cytometry assays. The glucose consumption, lactate production, and adenosine triphosphate (ATP) production of chordoma cells were examined with specific kits. Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were performed to determine relevant gene expressions in chordoma cells. Silencing of LINC01116 facilitated the apoptosis and expressions of Bcl-2- associated X (Bax), cleaved caspase-3 (C caspase-3) and miR-9-5p while repressing the cell cycle, viability, proliferation, invasion, glucose consumption, lactate production, ATP production, and expressions of PGK1 and Bcl-2. Meanwhile, LINC01116 sponged miR-9-5p, which could target PGK1. Moreover, the miR-9-5p inhibitor acted contrarily and reversed the role of siLINC01116 in chordoma cells. Besides, LINC01116 downregulation facilitated apoptosis and attenuated the proliferation and invasion of chordoma cells as well as PGK1 expression by upregulating miR-9-5p expression. LINC01116/miR-9-5p plays a regulatory role in the progression of chordoma cells and is a potential biomarker for chordoma.

LINC00963 Represses Osteogenic Differentiation of hBMSCs via the miR-10b-5p/RAP2A/AKT Axis.

Osteogenic differentiation of human bone marrow-derived mesenchymal stem cells (hBMSCs) is important for human bone formation. Long non-coding RNAs (lncRNAs) are critical regulators in osteogenic differentiation. This study aimed to explore the function and mechanisms of long intergenic non-protein coding RNA 963 (LINC00963) in affecting osteogenesis. Cell differentiation was assessed by alkaline phosphatase (ALP) activity detection and ALP staining assay. Meanwhile, levels of osteogenic marker genes, including RUNX family transcription factor 2 (RUNX2), osteocalcin (OCN), and osteopontin (OPN), were detected by RT-qPCR and western blot. Cell proliferation and apoptosis were measured using CCK-8 assay and flow cytometry analysis. RNA immunoprecipitation (RIP), RNA pull-down and luciferase reporter assays were used to investigate the interaction between genes. LINC00963 expression was down-regulated in hBMSCs treated with osteogenic induction. LINC00963 overexpression inhibited hBMSCs differentiation, proliferation, and elevated apoptosis. LINC00963 acted as a competing endogenous RNA (ceRNA) to interact with miR-10b-5p and thereby regulated the expression level of Ras-related protein Rap-2a (RAP2A). LINC00963 regulated RAP2A to inhibit the level of phosphorylated AKT (p-AKT). LINC00963 inhibited hBMSCs differentiation, proliferation, and elevated apoptosis via the miR-10b-5p/RAP2A/AKT signaling, which might help improve the treatment of osteoporosis.

The lncRNA LINC01605 promotes the progression of pancreatic ductal adenocarcinoma by activating the mTOR signaling pathway

BackgroundThis study investigated the molecular mechanism of long intergenic non-protein coding RNA 1605 (LINC01605) in the process of tumor growth and liver metastasis of pancreatic ductal adenocarcinoma (PDAC).MethodsLINC01605 was filtered out with specificity through TCGA datasets (related to DFS) and our RNA-sequencing data of PDAC tissue samples from Renji Hospital. The expression level and clinical relevance of LINC01605 were then verified in clinical cohorts and samples by immunohistochemical staining assay and survival analysis. Loss- and gain-of-function experiments were performed to estimate the regulatory effects of LINC01605 in vitro. RNA-seq of LINC01605-knockdown PDAC cells and subsequent inhibitor-based cellular function, western blotting, immunofluorescence and rescue experiments were conducted to explore the mechanisms by which LINC01605 regulates the behaviors of PDAC tumor cells. Subcutaneous xenograft models and intrasplenic liver metastasis models were employed to study its role in PDAC tumor growth and liver metastasis in vivo.ResultsLINC01605 expression is upregulated in both PDAC primary tumor and liver metastasis tissues and correlates with poor clinical prognosis. Loss and gain of function experiments in cells demonstrated that LINC01605 promotes the proliferation and migration of PDAC cells in vitro. In subsequent verification experiments, we found that LINC01605 contributes to PDAC progression through cholesterol metabolism regulation in a LIN28B-interacting manner by activating the mTOR signaling pathway. Furthermore, the animal models showed that LINC01605 facilitates the proliferation and metastatic invasion of PDAC cells in vivo.ConclusionsOur results indicate that the upregulated lncRNA LINC01605 promotes PDAC tumor cell proliferation and migration by regulating cholesterol metabolism via activation of the mTOR signaling pathway in a LIN28B-interacting manner. These findings provide new insight into the role of LINC01605 in PDAC tumor growth and liver metastasis as well as its value for clinical approaches as a metabolic therapeutic target in PDAC.

Abstract 2014: Long Non-coding RNA LINC-PINT Regulates Smooth Muscle Cell Plasticity In Developing Abdominal Aortic Aneurysms

Background: Long noncoding RNAs (lncRNAs) play pivotal roles as molecular regulators in diverse vascular biological processes and diseases. This study utilized multi-transcriptomic profiling to investigate the contribution of lncRNAs in Abdominal Aortic Aneurysm (AAA) disease. Materials & Methods: Utilizing bulk and single-cell RNA sequencing, we identified lncRNA long intergenic non-protein coding RNA, p53 induced transcript (LINC-PINT) as a significantly deregulated transcript in AAA compared to non-dilated aortas. Deconvolution of single-cell and bulk RNA-sequencing via the BayesPrism tool identified plasticity of smooth muscle cells (SMCs) as the predominant shifted condition between dilated vs. non-dilated aortas. Hybridization-based RNA in situ sequencing (HybRISS) confirmed the presence of LINC-PINT in de-differentiating SMCs. Results: Experimental knock-down of LINC-PINT , using site-specific antisense oligonucleotides (LNA-GapmeRs) markedly decreased proliferation rates of cultured human aortic smooth muscle cells (AoSMCs), but also increased their apoptosis, whereas overexpression of LINC-PINT had the opposite effect. Transcriptomic profiling of LINC-PINT -silenced AoSMCs indicated down-regulation of contractility markers, accompanied by an increase of inflammation and extracellular matrix (ECM) degradation. In line with this, LINC-PINT knock-down abolished the transforming growth factor beta (TGF-β)- induced AoSMCs polarization towards a contractile phenotype. Notably, RNA immunoprecipitation (RIP) demonstrated an interaction between LINC-PINT and p65, inhibiting its translocation to the promoter region of inflammatory genes. LINC-PINT knock-down increased p65 binding to its coactivator p50, which was confirmed by Co-immunoprecipitation (CO-IP). Combined in silico prediction and luciferase reporter assays further revealed that LINC-PINT expression was controlled by the ZNF93 and ZNF263 transcription factors. Conclusion: We provide evidence of LINC-PINT being a novel regulator influencing SMC dynamics and fate decisions of central importance to AAA pathophysiology. Currently ongoing in vivo studies in Lncpint -deficient mice explore its relevance in experimental AAA development.

Role of Long Intergenic Nonprotein-Coding RNA 00511 in Nod-Like Receptor Protein Pyrin Domain 3-Induced Chondrocyte Pyroptosis via the MicroRNA-9-5p/FUT1 Axis.

This study aimed to determine the function of LINC00511 in Nod-Like Receptor Pyrin Domain 3 inflammasome-mediated chondrocyte pyroptosis via the regulation of miR-9-5p and FUT 1. Chondrocyte inflammatory injury was induced by treating chondrocytes with LPS. Afterwards, the levels of IL-1β and IL-18, the expression of NLRP3, ASC, Caspase-1, and GSDMD, cell viability, and LDH activity in chondrocytes were assessed. LINC00511 expression in LPS-treated chondrocytes was detected, and LINC00511 was subsequently silenced to analyse its role in chondrocyte pyroptosis. The subcellular localization of LINC00511 was predicted and verified. Furthermore, the binding relationships between LINC00511 and miR-9-5p and between miR-9-5p and FUT1 were validated. LINC00511 regulated NLRP3 inflammasome-mediated chondrocyte pyroptosis through the miR-9-5p/FUT1 axis. LPS-treated ATDC5 cells exhibited elevated levels of inflammatory injury; increased levels of NLRP3, ASC, Caspase-1, and GSDMD; reduced cell viability; increased LDH activity; and increased LINC00511 expression, while LINC00511 silencing inhibited the NLRP3 inflammasome to restrict LPS-induced chondrocyte pyroptosis. Next, LINC00511 sponged miR-9-5p, which targeted FUT1. Silencing LINC00511 suppressed FUT1 by upregulating miR-9-5p. Additionally, downregulation of miR-9-5p or overexpression of FUT1 neutralized the suppressive effect of LINC00511 knockdown on LPS-induced chondrocyte pyroptosis. Silencing LINC00511 inhibited the NLRP3 inflammasome to quench Caspase-1-dependent chondrocyte pyroptosis in OA by promoting miR-9-5p and downregulating FUT1.

Linc00958 Promotes Lung Cancer Proliferation and Migration Through Regulating microRNA-490-3p

This study aimed to investigate the role of long intergenic non-protein coding RNA 00958 (Linc00958) in lung cancer (LCa) progression and its underlying mechanism. The study assessed Linc00958 expression in LCa tissues and adjacent tissues using qRT-PCR, and its impact on patient prognosis was analyzed through Kaplan-Meier survival analysis. Additionally, Linc00958 expression in LCa and normal lung cell lines was examined in vitro. Functional assays, including CCK-8, EdU, and transwell assays, were conducted to evaluate the effects of Linc00958 knockdown on LCa cells. To uncover the molecular mechanism, a dual-luciferase reporter assay was used to confirm the binding relationship between Linc00958 and microRNA-490-3p, a downstream gene. Co-transfection experiments were performed to elucidate microRNA-490-3p’s role in Linc00958’s impact on LCa cell functions. The results showed that Linc00958 was overexpressed in LCa tissues and cells, and high Linc00958 expression correlated with reduced patient survival. in vitro experiments revealed that Linc00958 promoted tumor proliferation and migration in LCa cells. Both computational predictions and dual-luciferase reporter assays demonstrated binding sites between microRNA-490-3p and Linc00958. Co-transfection experiments confirmed that Linc00958 facilitated LCa cell proliferation and migration through modulating microRNA-490-3p expression. In summary, Linc00958 promotes LCa cell proliferation and migration by regulating microRNA-490-3p.

Long non-coding RNA LINC-PINT as a novel prognostic biomarker in human cancer: a meta-analysis and machine learning

Long intergenic non-protein coding RNA, P53 induced transcript (LINC-PINT) exhibits different expression patterns in the majority of tumors, yet its relationship with cancer prognosis remains a subject of debate. This study aims to comprehensively investigate the prognostic significance of LINC-PINT in diverse human cancer. A systematic search was conducted in PubMed, Embase, Cochrane Library, and Web of Science databases to identify pertinent studies exploring the correlation between LINC-PINT expression and cancer patients. Moreover, bioinformatics analysis and in vitro validation were used to validate the results of the meta-analysis and to investigate the potential oncogenic mechanism of LINC-PINT. The meta-analysis encompassed 8 studies, involving 911 patients. The pooled analysis demonstrated a significant association between upregulation of LINC-PINT expression and better survival (P = 0.002) during the cancers. Meanwhile, its downregulation was correlated with advanced tumor staging (P = 0.04) and tumor differentiation (P = 0.03). Additionally, bioinformatics analysis showed that LINC-PINT expression was observed to be linked with Tumor Mutational Burden (TMB) and Microsatellite Instability (MSI) in tumors, the results of bioinformatics were verified by qRT-PCR. And functional enrichment analysis hinted at its involvement in tumorigenesis and tumor progression. Dysregulated LICN-PINT expression is associated with the clinical prognostic and pathological features of various cancers, exhibiting substantial potential as a novel prognostic biomarker.

Long noncoding RNA LINC00858 aggravates the progression of esophageal squamous cell carcinoma via regulating the miR-425-5p/ABL2 axis

Esophageal squamous cell carcinoma (ESCC) is one of the most fatal cancers with high morbidity and mortality, which severely affects people's lives. Long intergenic non-protein coding RNA 858 (LINC00858) was confirmed to promote the progression of colorectal cancer and lung cancer. However, the role of lncRNA LINC00858 is still unknown in ESCC. Herein, the main purpose of research was to explore LINC00858 function and its impact on ESCC cell biological behaviors. RT-qPCR was used to test the expression of LINC00858, miR-425-5p and ABL proto-oncogene 2 (ABL2) in ESCC cells. Functional experiments such as EdU assay, CCK-8 assay, transwell assay and Western blot assay were conducted to investigate the biological behaviors of ESCC cells. Luciferase reporter assay and RIP assay were implemented to determine the binding situation among RNAs. LINC00858 expression was abnormally high in ESCC cells and down-regulation of LINC00858 could restrain the proliferation, invasion, migration and EMT process of ESCC cells. Furthermore, miR-425-5p was proved to be sponged by LINC00858 and was down-regulated in ESCC cells. Besides, we discovered that miR-425-5p could target ABL2. Moreover, knockdown of ABL2 reversed the promoting function of miR-425-5p inhibitor on ESCC progression. LINC00858 aggravated ESCC progression via regulating the miR-425-5p/ABL2 axis.

Knockdown of LINC01128 Downregulates FUT8 to Inhibit OxLDL-Induced Vascular Smooth Muscle Cell Apoptosis in Atherosclerosis.

The apoptosis of vascular smooth muscle cells (VSMCs) contributes to the progression of atherosclerosis (AS). Long intergenic non-protein coding RNA 1128 (LINC01128) has been implicated in AS, and this study aims to uncover the role and mechanism of LINC01128 in regulating oxidized low-density lipoprotein (oxLDL)-induced VSMCs. The position of LINC01128 in cells and its target genes were predicted using bioinformatics. The localization of LINC01128 in human VSMCs was determined through fluorescence in situ hybridization. VSMCs were transfected, and the interaction between LINC01128 and fucosyltransferase 8 (FUT8) was validated by chromatin immunoprecipitation assay. The apoptotic VSMC model was established using oxLDL. LINC01128 expression in VSMCs was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), and FUT8 expression was detected by qRT-PCR and western blot. VSMC viability, migration, invasion abilities, and apoptosis were assessed using cell counting kit-8, transwell assay, and flow cytometry, respectively. OxLDL (200 μg/mL) upregulated the expression of LINC01128 and FUT8 mRNA, as well as FUT8 protein, in VSMCs. LINC01128 was expressed in the nucleus of VSMCs and bound to FUT8. Knockdown of LINC01128 alleviated the inhibitory effects of oxLDL (200 μg/mL) on viability, migration, and invasion, and mitigated the promotion of apoptosis and FUT8 expression in VSMCs. On the other hand, FUT8 overexpression enhanced the suppressive effects of oxLDL (200 μg/mL) on viability, migration, and invasion activities, and amplified the facilitating effect of oxLDL on apoptosis in VSMCs. Moreover, FUT8 overexpression reversed the impact of LINC01128 silencing on viability, migration, invasion, and apoptosis in oxLDL-stimulated VSMCs. The knockdown of LINC01128 downregulates FUT8, inhibiting the progression of VSMCs in AS.

Long non-coding RNA LINC00491 accelerates head and neck squamous cell carcinoma progression through regulating miR-508-3p/SATB1 axis and activating Wnt signaling pathway

Head and neck squamous cell carcinoma (HNSCC) is the most common malignancy of the head and neck epidermis. Accumulating long non-coding RNAs (lncRNAs) have been proven to be involved in the occurrence and development of HNSCC. LncRNA long intergenic non-protein coding RNA 491 (LINC00491) has been confirmed to regulate the progression of some cancers. In our study, we aimed to explore the potential biological function of LINC00491 and expound the regulatory mechanism by which LINC00491 affects the progression of HNSCC. RT-qPCR was utilized to analyze the expression of LINC00491 in HNSCC cell lines and the normal cell line. Functionally, we carried out a series of assays to measure cell proliferation, apoptosis, migration and invasion, such as EdU assay, colony formation, wound healing and western blot assays. Also, mechanism assays including RNA pull down and RIP were also implemented to investigate the interaction of LINC00491 and RNAs. As a result, we discovered that LINC00491 was highly expressed in HNSCC cells. In addition, LINC00491 depletion suppressed cell proliferation, migration and EMT process. Furthermore, we discovered that LINC00491 could bind to miR-508-3p. MiR-508-3p overexpression can restrain HNSCC cell growth. Importantly, miR-508-3p can target SATB homeobox 1 (SATB1) in HNSCC cells. Further, Wnt signaling pathway was proved to be activated by LINC00491 through SATB1 in HNSCC cells. In a word, LINC00491 accelerated HNSCC progression through regulating miR-508-3p/SATB1 axis and activating Wnt signaling pathway.

Selected Genomic Structural Variants Refine ELN-Based Prognostic Stratification of Patients with Acute Myeloid Leukemia and Normal Karyotype

Background. Normal karyotype Acute Myeloid Leukemia (nk-AML) accounts for 40% of all AML. Conventionally, nk-AML patients (pts) have been associated with the ELN favorable and intermediate risk category, characterized by extreme prognostic heterogeneity, representing an unmet therapeutic need especially as regards effective positioning of allogeneic transplantation (ASCT) as consolidation treatment. Aim. To improve risk stratification of nk-AML, on top of 2017 ELN criteria, by identification of structural variants (SV) with prognostic significance through the analysis of whole genome sequencing by long reads Nanopore platform. Patients and Methods. A total of 247 nk-AML pts receiving intensive therapy was included. The learning cohort included 95 pts from the prospective NILG 02/06 trial ( Bassan R Blood Adv 2019; 3:1103) comparing standard vs high-dose chemotherapy and 67 pts from the prospective GIMEMA AML1310 trial of risk-adapted, MRD-directed therapy ( Venditti A, Blood 2019;134:935). The validation cohort comprised 85 pts from Florence database. Whole genome long-read nanopore sequencing was performed on GridION platform to a median depth of 5x. After alignment to hgr38 genome, only those SV that had been concurrently identified by 4 independent callers were retained for analysis. Results. In the whole series (WS),197 pts (79.7%) obtained CR, 91 (46.2%) relapsed; 50 pts (20.2%) were primary refractory, 83 (33.6%) underwent ASCT. According to ELN criteria, 56.7%, 29.2% and 14.1% of the pts were in the favorable, intermediate and adverse risk category. Median survival (OS) was 16.9mo (9-24.7) in adverse risk category, 24.1mo (4.5-43.7) intermediate, and not reached in favorable risk category (P= 0.00007). However, adverse and intermediate category did not differ significantly (P=0.63), as expected considering the selection of nk-AML. Extensive filtering against 100 healthy donors and publicly available datasets of genomic variants to remove SV with >0.01% allele frequency resulted in 2,038 SV; after removal of private SV (ie, present in ≤2 pt), 122 SV were finally retained. Univariate regression analysis resulted in 10 SV associated with OS, of which 7 were validated with independent technology (Sanger and high-resolution melting, HRM). Multivariate analysis including all ELN-risk score variables showed that 5 of the 7 SV were independently associated with OS (hence, referred as high-risk variants, HRV). Three HRV affected the locus of coding genes on Chr4 q32.3 (inversion spanning 6,103bp), Chr5 p12 (333bp insertion) and Chr9 q34.3 (57bp deletion); Chr3 q26.1 (64bp insertion) in a Long Intergenic Non-Protein Coding RNA gene; Chr2 p13.2 (64bp deletion), in intergenic region. Presence of HRV impacted on OS with HR of 4.1 (95%CI,2.4-7; P=1.5e-7) in the learning cohort and HR 3.4 (95%CI, 1.5-7.6; P=0.003) in the validation cohort. Censoring at ASCT had no impact in either cohort. In total, 29 pts (11.7%) were HRV+, and their OS was 12.6mo (95%CI, 5.4-19.9) vs not reached (95%CI, 33.5-40.9; P=8.4183e-11) in HRV- pts (HR 3.9, 95%CI, 2.5-6; P=1.6261e-9) (Figure 1). DFS and EFS was 7mo (95%CI: 3.6-10.5) and 14.6mo (95%CI,2.1-27) in HRV+ pts vs not reached (95%CI, 31.7-40) and 30mo (95%CI: 29.9-30.1) (P<0.01 for both). Also, the rate of relapse was higher among HRV+, 58.6% vs 34.4% (P=0.01), with a trend to lower rate of CR attainment (72.4% vs 82.6%). There was no remarkable difference between HRV+ and HRV- pts as regarded frequency and type of ELN molecular variables. We finally evaluated whether integration of HRV within ELN risk score might improve the predictive performance of the latter. The resulting model enlisted 4 tiers, favorable (median OS not reached), intermediate (27.4mo, 95%CI: 3.6-51.1, HR:2.4; 95%CI,1.5-3.8), adverse (21.5mo, 95%CI: 5.4-37.6, HR:2.5; 95%CI,1.4-4.3) and HRV+ (12.6mo, 95%CI: 5.4-19.9, HR:5.9; 95%CI,3.6-9.8) categories (P=1.3395e-12) (Figure 2). Of note, the HRV+ category included 79.3% of pts otherwise categorized as ELN favorable or intermediate. Conclusions. We have identified, by long-read whole genome sequencing, a set of 5 structural variants that marks a subgroup of nk-AML pts with outmost dismal prognosis and may be integrated in ELN-risk score to help therapeutic decisions. Since HRV can be conveniently interrogated by routine approaches such as Sanger sequencing and HRM, further studies on larger cohorts might support these findings.

A comprehensive analysis of LINC00958 as a prognostic biomarker for head and neck squamous cell carcinoma

This work focused on exploring whether the long intergenic non-protein coding RNA LINC00958 is associated with the prognosis of head and neck squamous cell carcinoma (HNSCC). Associations of the LINC00958 expression level with clinicopathological features of HNSCC were investigated by logistic regression and Wilcoxon signed-rank test. The Kaplan–Meier method was applied to evaluate patient survival. Clinical data and expression profiles were obtained from The Cancer Genome Atlas (TCGA). Associations of patient clinical characteristics with overall survival (OS), progression-free interval (PFI), and disease-specific survival (DSS) were assessed by univariate and multivariate analysis using the Cox proportional hazard model. Immune cell infiltration analysis and gene set enrichment analysis (GSEA) were applied to determine any significant effects of LINC00958. High LINC00958 expression was related to early pT stage (P < 0.01), primary therapy outcome (P < 0.01), HPV status (P < 0.001), lymphovascular invasion (P < 0.001), and perineural invasion (P < 0.01). The receiver operating characteristic curve showed strong prognostic power for LINC00958 (area under curve = 0.886). High LINC00958 expression predicted poor OS (P = 0.007), DSS (P = 0.036), and PFI (P = 0.040). LINC00958 was related to signalling pathways and the infiltration of certain immune cells. miR-27b-5p was significantly associated with LINC00958, and downstream NT5E predicted poor survival in HNSCC cases. LINC00958 may affect the prognosis by regulating NT5E via miR-27b-5p, and could serve as a possible factor to predict the prognosis of HNSCC, especially oral squamous cell carcinoma.

Long Intergenic Non-Protein Coding RNA 312 Regulates FRABIN to Inhibit the Occurrence and Development of Pancreatic Cancer

We investigated the role of LINC00312 in pancreatic cancer (PC) and its underlying mechanism. LINC00312 levels were assessed in PC tissues and cell lines using qRT-PCR, and its correlation with clinical indicators was analyzed. Overexpression and knockdown models of LINC00312 were created in PC cell lines. The effects of LINC00312 on PC cell function were evaluated through CCK-8 and Transwell migration assays, and the binding between LINC00312 and the downstream target gene FGD4 was examined using a dual luciferase reporter gene assay. LINC00312 levels were significantly lower in PC tissues compared to adjacent tissues. High LINC00312 levels were associated with increased incidence of lymphatic and distant metastasis. PC cell lines exhibited downregulated LINC00312 expression. LINC00312 overexpression reduced cell proliferation and migration, while knockdown had the opposite effect. Bioinformatics analysis and luciferase reporter assays confirmed that LINC00312 binds to FGD4. Western blot analysis revealed reduced FGD4 levels upon LINC00312 overexpression, and a negative correlation between FGD4 and LINC00312 expression in PC. Moreover, FGD4 promoted PC cell proliferation and migration, its overexpression counteracted the inhibitory effects of LINC00312 overexpression on PC progression. Downregulation of LINC00312 in PC tissues and cell lines. LINC00312 overexpression suppresses PC cell proliferation and migration by negatively regulating FGD4. Thus, LINC00312 represents a potential therapeutic target for PC.

The long non-coding RNA LINC00707 interacts with Smad proteins to regulate TGFβ signaling and cancer cell invasion

BackgroundLong non-coding RNAs (lncRNAs) regulate cellular processes by interacting with RNAs or proteins. Transforming growth factor β (TGFβ) signaling via Smad proteins regulates gene networks that control diverse biological processes, including cancer cell migration. LncRNAs have emerged as TGFβ targets, yet, their mechanism of action and biological role in cancer remain poorly understood.MethodsWhole-genome transcriptomics identified lncRNA genes regulated by TGFβ. Protein kinase inhibitors and RNA-silencing, in combination with cDNA cloning, provided loss- and gain-of-function analyses. Cancer cell-based assays coupled to RNA-immunoprecipitation, chromatin isolation by RNA purification and protein screening sought mechanistic evidence. Functional validation of TGFβ-regulated lncRNAs was based on new transcriptomics and by combining RNAscope with immunohistochemical analysis in tumor tissue.ResultsTranscriptomics of TGFβ signaling responses revealed down-regulation of the predominantly cytoplasmic long intergenic non-protein coding RNA 707 (LINC00707). Expression of LINC00707 required Smad and mitogen-activated protein kinase inputs. By limiting the binding of Krüppel-like factor 6 to the LINC00707 promoter, TGFβ led to LINC00707 repression. Functionally, LINC00707 suppressed cancer cell invasion, as well as key fibrogenic and pro-mesenchymal responses to TGFβ, as also attested by RNA-sequencing analysis. LINC00707 also suppressed Smad-dependent signaling. Mechanistically, LINC00707 interacted with and retained Smad proteins in the cytoplasm. Upon TGFβ stimulation, LINC00707 dissociated from the Smad complex, which allowed Smad accumulation in the nucleus. In vivo, LINC00707 expression was negatively correlated with Smad2 activation in tumor tissues.ConclusionsLINC00707 interacts with Smad proteins and limits the output of TGFβ signaling, which decreases LINC00707 expression, thus favoring cancer cell invasion.EZy4eavcmbb38C5oFYKmkjVideo

LINC00955 suppresses colorectal cancer growth by acting as a molecular scaffold of TRIM25 and Sp1 to Inhibit DNMT3B-mediated methylation of the PHIP promoter

BackgroundLong non-coding RNAs play an important role in the development of colorectal cancer (CRC), while many CRC-related lncRNAs have not yet been identified.MethodsThe relationship between the expression of LINC00955 (Long Intergenic Non-protein Coding RNA 955) and the prognosis of colorectal cancer patients was analyzed using the sequencing results of the TCGA database. LINC00955 expression levels were measured using qRT-PCR. The anti-proliferative activity of LINC00955 was evaluated using CRC cell lines in vitro and xenograft models in nude mice in vivo. The interaction of TRIM25-Sp1-DNMT3B-PHIP-CDK2 was analyzed by western blotting, protein degradation experiment, luciferase, RNA-IP, RNA pull-down assays and immunohistochemically analysis. The biological roles of LINC00955, tripartite motif containing 25 (TRIM25), Sp1 transcription factor (Sp1), DNA methyltransferase 3 beta (DNMT3B), pleckstrin homology domain interacting protein (PHIP), cyclin dependent kinase 2 (CDK2) in colorectal cancer cells were analyzed using ATP assays, Soft agar experiments and EdU assays.ResultsThe present study showed that LINC00955 is downregulated in CRC tissues, and such downregulation is associated with poor prognosis of CRC patients. We found that LINC00955 can inhibit CRC cell growth both in vitro and in vivo. Evaluation of its mechanism of action showed that LINC00955 acts as a scaffold molecule that directly promotes the binding of TRIM25 to Sp1, and promotes ubiquitination and degradation of Sp1, thereby attenuating transcription and expression of DNMT3B. DNMT3B inhibition results in hypomethylation of the PHIP promoter, in turn increasing PHIP transcription and promoting ubiquitination and degradation of CDK2, ultimately leading to G0/G1 growth arrest and inhibition of CRC cell growth.ConclusionsThese findings indicate that downregulation of LINC00955 in CRC cells promotes tumor growth through the TRIM25/Sp1/DNMT3B/PHIP/CDK2 regulatory axis, suggesting that LINC00955 may be a potential target for the therapy of CRC.

Silencing of LINC00707 Alleviates Brain Injury by Targeting miR-30a-5p to Regulate Microglia Inflammation and Apoptosis.

The role of microglia in traumatic brain injury (TBI) has gained considerable attention. The present study aims to elucidate the potential mechanisms of Long intergenic non-protein coding RNA 707 (LINC00707) in TBI-induced microglia activation and inflammatory factor release. An in vivo model of rat TBI and in vitro microglia model was established using Controlled cortex injury (CCI) and lipopolysaccharide (LPS) stimulation. RT-qPCR to detect LINC00707 levels in rat cerebral cortex or cells. Modified Neurological Impairment Score (mNSS) and Morris Water Maze test was conducted to assess the neurological deficits and cognitive impairment. ELISA analysis of pro-inflammatory factors levels. CCK-8 and flow cytometry for cell viability and apoptosis levels. Dual-luciferase report and RIP assay to validate the targeting relationship between LINC00707 and miR-30a-5p. LINC00707 was elevated in the TBI rat cerebral cortex and LPS-induced microglia, while miR-30a-5p was noticeably decreased (P < 0.05). Increased mNSS, cognitive dysfunction, and brain edema in TBI rats were all prominently reversed by silencing of LINC00707, but this reversal was partially abrogated by decreasing miR-30a-5p (P < 0.05). Inhibition of LINC00707 suppressed the overproduction of inflammatory factors in TBI rats (P < 0.05). LPS decreased microglial cell viability, increased apoptosis, and promoted inflammatory overproduction than control, but the silencing of LINC00707 reversed its effect. Suppression of miR-30a-5p attenuated this reversal (P < 0.05). miR-30a-5p was the target miRNA of LINC00707.All in all, the results suggested that inhibiting LINC00707/miR-30a-5p axis could alleviate the progression of TBI by suppressing the inflammation and apoptosis of microglia cells.

LINC-PINT suppresses breast cancer cell proliferation and migration via MEIS2/PPP3CC/NF-κB pathway by sponging miR-576-5p

BackgroundBreast cancer (BCa) is the most frequent malignant tumor in women. Long non-coding RNAs (lncRNAs) have been acknowledged to exert critical regulating functions in various cancers. Long intergenic non-protein coding RNA, p53 induced transcript (LINC-PINT) has been reported to be a chemosensitizer and a tumor suppressor in BCa. However, its downstream molecular mechanism contributing to its tumor-suppressing role remains to be explored in BCa. MethodsLINC-PINT expression in BCa tissues and cells was measured using quantitative real-time polymerase chain reaction (RT-qPCR). The proliferation of transfected BCa cells was examined by counting kit-8 (CCK-8) and EdU assay. The migrating ability of indicate BCa cells was assessed by wound healing assays. Bioinformatics analysis and mechanism experiments such as RNA immunoprecipitation (RIP), RNA pull down assay, and luciferase reporter assay, were applied to demonstrate the downstream targets of LINC-PINT. ResultsLINC-PINT was downregulated in BCa tissues and cell lines. Overexpression of LINC-PINT suppressed BCa cell proliferation and migration. LINC-PINT could interact with miR-576-5p to upregulate Meis homeobox 2 (MEIS2) that positively regulated protein phosphatase 3 catalytic subunit gamma (PPP3CC) by inactivating the nuclear factor-κB (NF-κB) pathway. ConclusionsThese findings elucidated the anti-tumor role of LINC-PINT in BCa via the miR-576-5p/MEIS2/PPP3CC/NF-κB axis, which suggested that LINC-PINT might serve as a potential therapeutic target for BCa.

The p65-LOC727924-miR-26a/KPNA3-p65 regulatory loop mediates vasoactive intestinal peptide effects on osteoarthritis chondrocytes.

Loss and dysfunction of articular chondrocytes, which disrupt the homeostasis of extracellular matrix formation and breakdown, promote the onset of osteoarthritis (OA). Targeting inflammatory pathways is an important therapeutic strategy for OA. Vasoactive intestinal peptide (VIP) is an immunosuppressive neuropeptide with potent anti-inflammatory effects; however, its role and mechanism in OA remain unclear. In this study, microarray expression profiling from the Gene Expression Omnibus database and integrative bioinformatics analyses were performed to identify differentially expressed lncRNAs in OA samples. qRT-PCR validation of the top ten different expressed lncRNAs indicated that the expression level of intergenic non-protein coding RNA 2203 (LINC02203, also named LOC727924) was the highest in OA cartilage compared to normal cartilage. Hence, the LOC727924 function was further investigated. LOC727924 was upregulated in OA chondrocytes, with a dominant sub-localization in the cytoplasm. In OA chondrocytes, LOC727924 knockdown boosted cell viability, suppressed cell apoptosis, reactive oxygen species (ROS) accumulation, increased aggrecan and collagen II, decreased matrix metallopeptidase (MMP)-3/13 and ADAM metallopeptidase with thrombospondin type 1 motif (ADAMTS)-4/5 levels, and reduced the levels of tumor necrosis factor alpha (TNF-α), interleukin 1 beta (IL-1β), and interleukin 6 (IL-6). LOC727924 could interact with the microRNA 26a (miR-26a)/ karyopherin subunit alpha 3 (KPNA3) axis by competitively targeting miR-26a for KPNA3 binding, therefore down-regulating miR-26a and upregulating KPNA3; in OA chondrocytes, miR-26a inhibition partially abolished LOC727924 knockdown effects on chondrocytes. miR-26a inhibited the nuclear translocation of p65 through targeting KPNA3 and p65 transcriptionally activated LOC727924, forming a p65-LOC727924-miR-26a/KPNA3-p65 regulatory loop to modulate OA chondrocyte phenotypes. In vitro, VIP improved OA chondrocyte proliferation and functions, down-regulated LOC727924, KPNA3, and p65 expression, and upregulated miR-26a expression; in vivo, VIP ameliorated destabilization of the medial meniscus (DMM)-induced damages on the mouse knee joint, down-regulated KPNA3, inhibited the nuclear translocation of p65. In conclusion, the p65-LOC727924-miR-26a/KPNA3-p65 regulatory loop modulates OA chondrocyte apoptosis, ROS accumulation, extracellular matrix (ECM) deposition, and inflammatory response in vitro and OA development in vivo, being one of the mechanisms mediating VIP ameliorating OA.

The expression of lncRNAs CASC2, NEAT1, LINC00299 in breast cancer tissues and their relationship with the XBP1 splicing rate in Iranian patients during 2014-2019: A cross-sectional study.

Breast cancer is a leading cause of incidence and mortality in women globally. Identifying new molecular markers can aid in cancer diagnosis, targeted therapy, and treatment monitoring. This study aimed to measure the expression of the X-box binding protein 1 (XBP1) gene, an index of the unfolded protein response (UPR), and long noncoding RNAs (lncRNAs), including Nuclear Enriched Abundant Transcript 1 (NEAT1), Cancer Susceptibility Candidate 2 (CASC2), and Long Intergenic Nonprotein Coding RNA 299 (LINC00299), as possible regulators of the UPR pathway. Total RNA was extracted from 40 samples of breast tumor tissues and their respective controls. The expression level of lncRNAs CASC2, NEAT1, and LINC00299 was quantified using reverse transcription-polymerase chain reaction (RT-PCR). The ratio of the spliced form of XBP1 to its unspliced form (XBP1u) was determined by PCR and electrophoresis. The results showed a 2.8-fold increase in the ratio of XBP1s/u in breast cancer tissues compared to adjacent nonmalignant samples (p < 0.05). Additionally, the level of lncRNAs NEAT1, CASC2, and LINC00299 in breast tumor tissues increased significantly by twofold, 1.5-fold, and 2.3-fold, respectively, compared to adjacent nonmalignant samples (p < 0.05). Based on the association between the expression of lncRNAs CASC2, LINC00299, and NEAT1 and the XBP1s/u ratio, these lncRNAs could be potential regulators of the UPR pathway. Also, CASC2 and NEAT1 genes could be suggested as suitable biomarkers to distinguish cancerous tissue from noncancerous breast tissue due to their significant increase in expression in cancerous samples compared to adjacent noncancerous.

Analysis on EZH2: mechanism identification of related CeRNA and its immunoassay in hepatocellular carcinoma

ObjectiveTo screen the possible potential signaling pathways related to enhancer of zeste homolog 2 (EZH2) based on ceRNA mechanism, and to analyze the correlation between E2H2 and depths of various immune cell infiltration depths. The relationship between different immune checkpoints were also analyzed.MethodsFirst, the expression of EZH2 in pan-cancer (18 malignancies) was analyzed with the TCGA database. Hepatocellular carcinoma (HCC) tissues of 374 cases and normal tissues of 50 cases were analyzed in terms of the differential expression, overall survival (OS) and progression-free-survival (PFS). Then, we conducted GO and KEGG enrichment analysis on target gene. We also analyzed mRNA-miRNA and MicroRNA (miRNA)- long non-coding RNA (lncRNA) correlation with starbase databse, so as to determine the potential ceRNA mechanism associated with EZH2. Finally, immunoassay and drug-sensitivity analysis of EZH2 was performed.ResultsSeven potential EZH2-related ceRNA pathways were screened out, namely lncRNA: Small Nucleolar RNA Host Gene 1 (SNHG1), SNHG 3, and SNHG 6-miR-101-3p-EZH2; and lncRNA: Long Intergenic Non-Protein Coding RNA 1978 (LINC01978), SNHG12, Ring Finger Protein 216 Pseudogene 1 (RNF216P1), and Coiled-coil Domain Containing 18 Antisense RNA 1 (CCDC18-AS1)-let-7c-5p—EZH2. Finally, 4 potential EZH2-related ceRNA pathways were identified through qPCR.According to immune correlation analysis, EZH2 may be positively correlated with T cells follicular helper, T cells Cluster of differentiation (CD)4 memory activated, Macrophages M0, and B cells memory (P < 0.05, cof > 0.2); while be negatively correlated with T cells CD4 + memory resting (P < 0.05, cof < -0.2). And EZH2 is positively correlated with Programmed Cell Death 1 (PDCD1) (R = 0.22), CD274 (R = 0.3) and Cytotoxic T-Lymphocyte Associated Protein 4 (CTLA4) (R = 0.23). According to drug sensitivity analysis, patients in the high expression group were more susceptible to the effects of various drugs including Sorafenib, 5-Fluorouracil, Doxorubicin, Etoposide, Paclitaxel, and Vinorelbine than those with low expression.ConclusionThis study revealed seven potential pathways of Enhancer of Zeste Homolog 2 (EZH2)-related ceRNA mechanisms: lncRNA (SNHG3, 6) -Mir-101-3P-ezh2; lncRNA (SNHG12, RNF216P1)-let-7c-5p—EZH2. We also analyzed the immunity and drug sensitivity of EZH2. Our study proves that EZH2 still has great research prospects in HCC.