Identification and validation of the high expression of pseudogene TCAM1P in cervical cancer via integrated bioinformatics analysis

Background HPV as the main cause of cervical cancer has long been revealed, but the detailed mechanism has not yet been elucidated. The role of testis/cancer antigen in cervical cancer has been revealed. However, there are no reports about the statement of testis/cancer-specific non-coding RNA. In this study, we first proposed TCAM1P as a testis/cancer-specific pseudogene, and used a series of experimental data to verify its relationship with HPV, and analyzed its diagnosis value of high-grade cervical lesions and the mechanism of their high expression in cervical cancer. This provides a new direction for the prevention and treatment of cervical cancer. Methods The specific expression of pseudogenes in each tissue was calculated by “TAU” formula. ROC curve was used to judge the diagnosed value of TCAM1P for high-grade lesions. The proliferation ability of cells was measured by CCK8. The expression of TCAM1P, HPV E6/E7 were detected by qRT-PCR. The binding for RBPs on TCAM1P was predicted by starbase v2.0 database, then RIP assay was used to verify. Besides, Gene Ontology (GO) and KEGG enrichment analysis were performed with “clusterprofiler” R package. Results TCAM1P was specifically high-expressed in normal testicular tissue and cervical cancer. Interesting, with the severity of cervical lesions increased, the expression of TCAM1P increased, and TCAM1P could effectively diagnose high-grade cervical lesions. Besides, the expression of TCAM1P was HPV dependent, with highest expression in HPV-positive cervical cancer tissues. Furthermore, RIP assay showed that EIF4A3 regulated the expression of TCAM1P through binding with it. CCK8 assay showed that TCAM1P promoted the proliferation and the Gene ontology (GO) and KEGG Pathway enrichment analysis same suggested that TCAM1P is involved in multiple ways in cell proliferation including Cell cycle, DNA replication and etc. Conclusions In this study, we firstly proposed that TCAM1P is cancer/testis pseudogene and is regulated by HPV E6/E7 and EIF4A3. TCAM1P promotes the proliferation of cervical cancer cells and acts as promoter in cervical cancer. Otherwise, TCAM1P promote proliferation through regulating cell cycle and DNA replication, but more evidence needs to be provided to reveal the mechanism by which TCAM1P plays a role in cervical cancer.

METTL3-Mediated DLGAP1 Antisense RNA 2 Promotes Gastric Cancer Tumorigenesis Through Facilitating C-Myc-Dependent Warburg Effect

Background The critical roles of N6-methyladenosine (m6A) modification have been demonstrated by more and more evidence. However, the cross-talking of m6A and long non-coding RNAs (lncRNAs) in gastric cancer (GC) tumorigenesis is still unclear. Here, our work focused on the functions and molecular mechanism of m6A-modified lncRNA DLGAP1 antisense RNA 2 (DLGAP1-AS2) in GC. Methods LncRNA expression profile data was derived from GEO. M6A profile was screened using Methylated RNA immunoprecipitation sequencing (MeRIP-Seq). The metabolism assays were conducted using quantitative analysis of glucose, lactate, ATP and extracellular acidification rate (ECAR). The m6A level of specific RNA was identified using MeRIP-qPCR. The molecular interaction was detected using RIP assay. Results Microarray analysis found that lncRNA DLGAP1-AS2 up-regulated in GC cells. Clinical data showed that DLGAP1-AS2 high-expression was correlated with advanced pathological stage and poor prognosis. Functionally, DLGAP1-AS2 promoted the Warburg effect (aerobic glycolysis) and knockdown of DLGAP1-AS2 suppressed the tumor growth of GC cells. Mechanistically, m6A methyltransferase METTL3 enhanced the stability of DLGAP1-AS2 via m6A site binding. Moreover, DLGAP1-AS2 interacted with YTHDF1 to enhance the stability of c-Myc mRNA through DLGAP1-AS2/m6A/YTHDF1/c-Myc mRNA. Conclusions In conclusion, our work indicates the functions of m6A-modified DLGAP1-AS2 in the GC aerobic glycolysis, disclosing a potential m6A-dependent manner for GC treatment.

Lin28A/CENPE Promoting the Proliferation and Chemoresistance of Acute Myeloid Leukemia

The prognosis of chemoresistant acute myeloid leukemia (AML) is still poor, mainly owing to the sustained proliferation ability of leukemic cells, while the microtubules have a major role in sustaining the continuity of cell cycle. In the present study, we have identified CENPE, a microtubular kinesin-like motor protein that is highly expressed in the peripheral blood of patients with chemoresistant AML. In our in vitro studies, knockdown of CENPE expression resulted in the suppression of proliferation of myeloid leukemia cells and reversal of cytarabine (Ara-C) chemoresistance. Furthermore, Lin28A, one of the RNA-binding oncogene proteins that increase cell proliferation and invasion and contribute to unfavorable treatment responses in certain malignancies, was found to be remarkably correlated with CENPE expression in chemoresistance AML. Overexpression of LIN28A promoted the proliferation and Ara-C chemoresistance of leukemic cells. RIP assay, RNA pull-down, and dual luciferase reporter analyses indicated that LIN28A bound specifically to the promoter region GGAGA of CENPE. In addition, the impacts of LIN28A on cell growth, apoptosis, cell cycle progression, and Ara-C chemoresistance were reverted by the knockdown of CENPE. Hence, Lin28A/CENPE has enhanced the proliferation and chemoresistance of AML, and therefore, it could be a prospective candidate for AML treatment.

LINC00641 contributes to nasopharyngeal carcinoma cell malignancy through FOXD1 upregulation at the post-transcriptional level

Nasopharyngeal carcinoma (NPC) is a common tumor in the head and neck and is prevalent in China, especially in the southern regions. Molecular mechanisms have attracted much attention in NPC research. FOXD1 has been reported to be a tumor promoter in various cancers. The present study was designed to explore the function of FOXD1 in NPC cells. Functional analyses, including the trypan blue staining assay, EdU and JC-1 assay, and flow cytometry analysis, revealed that FOXD1 facilitated NPC cell proliferation and inhibited NPC cell apoptosis. Next, by means of “starBase” database and mechanism analyses, such as RIP assay, RNA pull-down assay and luciferase reporter assay, miR-378a-3p was found to target FOXD1 and negatively regulate FOXD1 expression in NPC cells. Moreover, miR-378a-3p plays a suppressive role in NPC cells. LINC00641 was identified as a sponge of miR-378a-3p and positively modulated FOXD1 expression in NPC cells. Finally, a series of rescue assays indicated that LINC00641 accelerated NPC cell proliferation and hindered NPC cell apoptosis through FOXD1 upregulation. In conclusion, the present study demonstrated an innovative ceRNA mechanism of LINC00641/miR-378a-3p/FOXD1 in NPC cells, which might provide new insights into NPC treatment.

LncRNA RP11-89 facilitates tumorigenesis and ferroptosis resistance through PROM2-activated iron export by sponging miR-129-5p in bladder cancer

Long non-coding RNAs (lncRNAs) act as important regulators of tumorigenesis and development in bladder cancer. However, the underlying molecular mechanisms remain elusive. We previously identified a novel lncRNA signature related to immunity and progression in bladder cancer. Here we further explored the function of RP11-89, a lncRNA discovered in the previous signature. Loss- and gain-of function experiments were performed using CCK-8 assay, flow cytometry, Transwell assays, scratch tests and subcutaneous nude mouse models. High-throughput RNA sequencing was conducted to identify dysregulated genes in bladder cancer cells with RP11-89 knockdown or overexpression. Regulation of RP11-89 on miR-129-5p and PROM2 was explored through luciferase reporter assay, RIP assay and RNA pull-down assay. RP11-89 promoted cell proliferation, migration and tumorigenesis and inhibited cell cycle arrest via the miR-129-5p/PROM2 axis. We found that RP11-89 “sponges” miR-129-5p and upregulates PROM2. Elevated PROM2 in cells was associated with attenuated ferroptosis through iron export, formation of multivesicular bodies and less mitochondrial abnormalities. We demonstrated that RP11-89 is a novel tumorigenic regulator that inhibits ferroptosis via PROM2-activated iron export. RP11-89 may serve as a potential biomarker for targeted therapy in bladder cancer.

N6-methyladenosine Reader YTHDF1-induced lncRNA DLGAP1-AS2 Promotes the c-Myc Mediated Gastric Cancer Aerobic Glycolysis

Background: Emerging data has demonstrated the essential function of N6-methyladenosine (m6A) modification of long non-coding RNAs (lncRNAs) in human tumorigenesis. Nevertheless, the regulation of m6A-lncRNA approach on gastric cancer (GC) tumorigenesis is unclear. Methods: LncRNA expression profile data was derived from GEO. M6A profile was screened using Methylated RNA immunoprecipitation sequencing (MeRIP-Seq). The metabolism assays were conducted using quantitative analysis of glucose, lactate, ATP and extracellular acidification rate (ECAR). The m6A level of specific RNA was identified using MeRIP-qPCR. The molecular interaction was detected using RIP assay.Results: In the findings, results showed that enhanced DLGAP1-AS2 expression was correlated with advanced pathological stage and poor prognosis. Functionally, DLGAP1-AS2 promoted the aerobic glycolysis and knockdown of DLGAP1-AS2 suppressed the tumor growth of GC cells. Mechanistically, m6A reader YTHDF1 accelerated the enrichment of DLGAP1-AS2 in GC. Moreover, DLGAP1-AS2 interacted with YTHDF1 to integrate c-Myc mRNA, thereby enhancing the stability of c-Myc mRNA through DLGAP1-AS2/m6A/YTHDF1/c-Myc mRNA. Conclusions: In conclusion, our work indicates a novel m6A-maintained lncRNA DLGAP1-AS2 in the GC aerobic glycolysis, disclosing a m6A-reader-dependent modality regulation.

RBM45 Promoted HCC Growth and Metastasis by Stabilizing BCL2 and Twist1 mRNA

The post-transcriptional of mRNA expression involved in the hepatocellular carcinoma (HCC) pathogenesis and progression need to be further explored. RBPs, the main undertaker of post-transcriptional regulatory process, has been shown to impact HCC carcinogenesis and progression. However, the role of RBP, RNA-binding motif 45 (RBM45) in hepatocarcinogenesis and its interaction with its potential target mRNA remains entirely unknown. The expression of RBM45 was significantly increased in HCC and was associated with poor clinicopathological features and clinical outcome of HCC patients. RBM45 promoted HCC cells growth, invasion, migration and EMT in vitro and in vivo. Mechanistically, RNA immunoprecipitation sequencing (RIP-seq) approach was utilized to screen the important differentially expressed RBM45 genes in HCC. Furthermore, RIP assay, pull-down assay and mRNA decay assay were carried out to uncover the effect of RBM45 on its downstream genes. And the results revealed that RBM45 mediated the stabilization of BCL2 and Twist1 mRNA via respectively binding to their 3`UTR. Further assay results suggested RBM45 promoted HCC growth and metastasis upon BCL2 and Twist1. In short, we unveiled a novel role of RBM45 in promoting hepatocarcinogenesis via the post-transcriptional regulation of BCL2 and Twist1 expression. The results proposes that RBM45 may serve as a potential therapeutic target for HCC.

Valproic Acid Protects Chondrocytes from LPS-Stimulated Damage via Regulating miR-302d-3p/ITGB4 Axis and Mediating the PI3K-AKT Signaling Pathway

Background: Osteoarthritis (OA) is one of the most common degenerative joint diseases characterized by increased apoptosis and autophagy deficiency. The investigation was performed to examine the effect of valproic acid (VPA) and molecular mechanism related to miR-302d-3p/ITGB4 axis in OA.Methods: The OA clinical samples were obtained from the GEO database to analyze differentially expressed genes. An in vitro OA model was mimicked by LPS in CHON-001 cells. Autophagy-related genes were downloaded from the HADb website, and potential drugs were mined using the CTD website. The upstream factors of ITGB4 were predicted with bioinformatics analysis, which was validated by luciferase activity assay and RIP assay. Cell viability and apoptosis were evaluated using CCK-8 and flow cytometry. The expression levels, including ITGB4, miR-302d-3p, and autophagy-/PI3K-AKT pathway-related markers, were measured by qRT-PCR or/and western blot.Results: Our results showed that miR-302d-3p inhibited cell viability and promoted apoptosis of LPS-treated CHON-001 cells by targeting ITGB4. VPA treatment remarkably alleviated LPS-stimulated injury in CHON-001 cells. The inhibitory effect of VPA on LPS-stimulated damage in CHON-001 cells was weakened by miR-302d-3p overexpression, while it was intensified because of ITGB4 upregulation. Mechanistically, VPA treatment induced a significant decrease in the levels of p-PI3K and p-AKT in LPS-stimulated CHON-001 cells through regulating miR-302d-3p/ITGB4 axis.Conclusion: Overall, VPA treatment may ameliorate LPS-induced injury on chondrocytes via the regulation of miR-302d-3p/ITGB4 pair and the inactivation of the PI3K-AKT pathway.

Effect of LINC00320 Regulating the Expression of PLEKHA1 through the Transcription Factor MYC in Glioma Cell Proliferation, Migration, Invasion and Apoptosis In vivo and In vitro

Aim: This study was carried out to explore the mechanism and function of LINC00320 in the development of glioma by regulating PLEKHA1 expression through transcription factor MYC.Methods: By searching LINCDISEASE database and through difference analysis of glioma chip, glioma related lncRNAs were screened, and lncRNA-transcription factor-mRNA triplet was predicted through lncMAP database. The expressions of LINC00320 and PLEKHA1 were detected in glioma and normal controls, followed by the detection of the proliferation, invasion, migration, and apoptosis of glioma cells by using CCK-8 method, Transwell assay, and flow cytometry, respectively. In addition, the expression patterns of MMP9 and cleaved-Caspase 3 were detected with Western Blot. Furthermore, the possible mechanism of LINC00320 was predicted in gliomas by LncMAP. RIP assay was performed to verify the interaction between LINC00320 and MYC, and ChIP assay was applied to validate the binding of MYC and PLEKHA1 promoter. The existence of binding site between MYC and PLEKHA1 promoter were determined by dual luciferase reporter gene assay. Lastly, in vivo test was conducted by using nude mice as the objects of study for verification of the results obtained by in vitro tests.Results: LINC00320 was found to be significantly down-expressed in glioma, and patients with low expression levels of LINC00320 exhibited an even worse prognostic outcome. Over-expression of LINC00320 in glioma cells brought about a significant reduction in cell proliferation, migration, invasion, and promoted apoptosis. There was a significant decrease in the protein expression of MMP9 but remarkable increase in that of cleaved-Caspase 3 after LINC00320 over-expression. LncRNA-transcription factor-mRNA triplet prediction showed that LINC00320 regulated the expression of PLEKHA1 through MYC. RIP assay demonstrated that MYC could significantly enrich LINC00320, Chip assay showed that MYC bound with the PLEKHA1 promoter, and dual luciferase reporter gene assay further confirmed the presence of binding site between MYC and PLEKHA1 promoter. Cell function experiment verified that PLEKHA1 could reverse the effect of LINC00320 over-expression.Conclusion: Over-expression of LINC00320 can attenuate the binding of MYC with PLEKHA1 by recruiting MYC, and ultimately inhibit the proliferation, migration and invasion, and promote the apoptosis of glioma cells.

LncRNA SNHG11 Promotes Temozolomide Resistance in Glioblastoma via Promoting MGMT Expression

Background Acquired TMZ resistance is considered as the main reason for the poor prognosis of glioblastoma (GBM) patients. However, underlying mechanism remains unknown. Long noncoding RNAs (lncRNAs) have emerged as important regulators in multiple biological processes. Methods SNHG11 expression in cells and GBM tissues was measured using qRT-PCR. In vitro studies, including CCK-8, colony formation assay, flow cytometry and western blot, were employed to measure the role of SNHG11. Interaction between miR-7-5p, SNHG11, and IRS2 was examined by dual luciferase reporter assay, as well as RNA binding protein immunoprecipitation (RIP) assay. CHIP assays were used to measure the role of SNHG11/miR-7-5p/IRS2 axis on modulating the H3K9 acetylation of MGMT. Results SNHG11 overexpression in GBM tissues contributes to TMZ resistance. In vitro and in vivo studies confirmed that SNHG11 promoted TMZ resistance in GBM cells. In addition, SNHG11 conferred TMZ resistance through increasing MGMT expression. Furthermore, SNHG11 could function as ceRNA by sponging miR-7-5p, which led to increased IRS2 expression. SNHG11/miR-7-5p/IRS2 axis increased MGMT expression by promoting the acetylation of H3K9 in MGMT promoter regions. Conclusion Taken together, our results revealed that targeting SNHG11 is a potential therapy to overcome TMZ resistance. And SNHG11 in GBM tissues is a potential biomarker for predicting response to TMZ.