Identification of Potential Prostate Cancer-Related Pseudogenes Based on Competitive Endogenous RNA Network Hypothesis

Identification and validation of the TRHDE-AS1/hsa-miR-449a/ADAMTS5 axis as a novel prognostic biomarker in prostate cancer

Despite advancements in cancer research, the prognostic implications of competing endogenous RNA (ceRNA) networks in prostate cancer (PCa) remain incompletely understood. This study aimed to elucidate the prognostic relevance of ceRNA networks in PCa, utilizing a comprehensive bioinformatics approach alongside experimental validation. After searching The Cancer Genome Atlas (TCGA) database, RNA sequencing (RNA-Seq) data were extracted to identify differentially expressed RNAs (DERs) between 491 PCa samples and 51 normal prostate tissues, following which a comprehensive bioinformatics strategy was implemented to construct a ceRNA network. An optimal prognostic signature comprising these DERs was then established and validated using TCGA data. In addition, functional validation was performed through RNA pull-down, dual-luciferase reporter assays, quantitative real-time PCR, and western blot analysis conducted in PC-3 and DU145 cell lines, thereby complementing the bioinformatics analysis. A total of 613 DERs, comprising 103 long noncoding RNAs (lncRNAs), 60 microRNAs (miRNAs), and 450 messenger RNAs (mRNAs), were identified and utilized in constructing a ceRNA network, which encompassed 23 lncRNAs, 9 miRNAs, and 52 mRNAs. An optimal prognostic signature was established, including VPS9D1 antisense RNA 1 (VPS9D1-AS1), miR-449a, cyclin-dependent kinase 5 regulatory subunit 1 (CDK5R1), targeting protein for Xklp2 (TPX2), solute carrier family 7 member 11 (SLC7A11), copine7 (CPNE7), and maternal embryonic leucine zipper kinase (MELK), yielding area under the curve (AUC) values exceeding 0.8 across training, validation, and entire datasets. Our experiments results revealed an interaction between lncRNA TRHDE antisense RNA 1 (TRHDE-AS1) and miR-449a and that miR-449a could target the ADAM metallopeptidase with thrombospondin type 1 motif 5 (ADAMTS5) mRNA. Knockdown of miR-449a significantly impeded cell proliferation, G1/S transition, migration and invasion, and promoted apoptosis in PC-3 and DU145 cells. Furthermore, knockdown of miR-449a notably downregulated protein expression of CDK4, cyclin D1, N-cadherin and vimentin, while upregulating protein expression of cleaved caspase-3 and E-cadherin. This study contributes to a deeper understanding of the prognostic-linked ceRNA network in PCa, providing fundamental insights that could improve diagnostic and therapeutic approaches for PCa management.

LINC00355 promotes gastric carcinogenesis by scaffolding p300 to activate CDC42 transcription and enhancing HNRNPA2B1 to stabilize CDC42 mRNA dependent on m6A

LINC00355 is involved in the tumorigenesis of several types of cancer. We verified that LINC00355 is upregulated in gastric cancer (GC) and contributes to GC cells' proliferation and metastasis. RNA sequencing (RNA-seq) and rescue assays suggested that LINC00355 controls gastric carcinogenesis by regulating the expression of cell division cycle 42 (CDC42) guanosine triphosphatase (GTPases), thereby activating their downstream pathways. Most previous studies have shown that LINC00355 acts as a ceRNA by sponging miRNAs to modulate downstream gene expression. Our group focus on epigenetic regulatory potential of LINC00355 in gene expression. Mechanistically, LINC00355 binds to p300 histone acetyltransferase, specifying the histone modification pattern on the CDC42 promoter to activate CDC42 transcription, thereby altering GC cell biology. In addition, HNRNPA2B1, which is upregulated by LINC00355, recognizes the N6-methyladenosine (m6A) sites of CDC42 and enhances the stability of CDC42 mRNA transcripts. Therefore, LINC00355 is mechanistically, functionally, and clinically oncogenic in GC cells.

Pathological roles of miRNAs and pseudogene-derived lncRNAs in human cancers, and their comparison as prognosis/diagnosis biomarkers

This review examines and compares the diagnostic and prognostic capabilities of miRNAs and lncRNAs derived from pseudogenes in cancer patients. Additionally, it delves into their roles in cancer pathogenesis. Both miRNAs and pseudogene-derived lncRNAs have undergone thorough investigation as remarkably sensitive and specific cancer biomarkers, offering significant potential for cancer detection and monitoring. . Extensive research is essential to gain a complete understanding of the precise roles these non-coding RNAs play in cancer, allowing the development of novel targeted therapies and biomarkers for improved cancer detection and treatment approaches.

Current insights into the oncogenic roles of lncRNA LINC00355

Long noncoding RNAs (lncRNAs) are a class of nonprotein-coding transcripts that are longer than 200 nucleotides. LINC00355 is a lncRNA located on chromosome 13q21.31 and is consistently upregulated in various cancers. It regulates the expression of downstream genes at both transcriptional and posttranscriptional levels, including eight microRNAs (miR-15a-5p, miR-34b-5p, miR-424-5p, miR-1225, miR-217-5p, miR-6777-3p, miR-195, and miR-466) and three protein-coding genes (ITGA2, RAD18, and UBE3C). LINC00355 plays a role in regulating various biological processes such as cell cycle progression, proliferation, apoptosis, epithelial-mesenchymal transition, invasion, and metastasis of cancer cells. It is involved in the regulation of the Wnt/β-catenin signaling pathway and p53 signaling pathway. Upregulation of LINC00355 has been identified as a high-risk factor in cancer patients and its increased expression is associated with poorer overall survival, recurrence-free survival, and disease-free survival. LINC00355 upregulation has been linked to several unfavorable clinical characteristics, including advanced tumor node metastasis and World Health Organization stages, reduced Karnofsky Performance Scale scores, increased tumor size, greater depth of invasion, and more extensive lymph node metastasis. LINC00355 induces chemotherapy resistance in cancer cells by regulating five downstream genes, namely HMGA2, ABCB1, ITGA2, WNT10B, and CCNE1 genes. In summary, LINC00355 is a potential oncogene with great potential as a diagnostic marker and therapeutic target for cancer.

Aspartoacylase promotes the process of tumour development and is associated with immune infiltrates in gastric cancer

BACKGROUND

Aspartoacylase (ASPA) is a gene that plays an important role in the metabolic reprogramming of cancer. However, the clinical relevance of ASPA in gastric cancer (GC) has not been demonstrated.

METHODS

The link between ASPA and the clinical features of GC was determined using two public genomic databases. The multivariate Cox proportional hazard model and generalised linear regression model were applied to examine whether the ASPA level is associated with the prognosis and other pathological factors. In addition, the role of specific genes in the infiltration of immune cells in the setting of GC was investigated using a further immunological database. The expression level of various proteins was detected using a western blotting assay. Transwell and methyl thiazolyl tetrazolium tests were applied for the detection of cellular invasion and proliferation, with small hairpin ribonucleic acid used to knockdown ASPA.

RESULTS

According to the multivariate Cox regression results, the down-regulated ASPA expression is a distinct prognostic factor. Furthermore, ASPA has significant positive correlations with the infiltration of immune cells in GC lesions. Compared to the non-cancer tissues, the GC tissues had a significantly lower level of ASPA expression (p < 0.05). Using knockdown and overexpression techniques, it was demonstrated that ASPA affects the capacity of cell lines for GC to both proliferate and invade.

CONCLUSION

Overall, ASPA could promote the occurrence and development of GC and presents a promising predictive biomarker for the disease since it is favourably connected with immune infiltrates and negatively correlated with prognosis.

A systematic method introduced a common lncRNA-miRNA-mRNA network in the different stages of prostate cancer

Introduction

The present study aimed to investigate the interaction of the common lncRNA-miRNA-mRNA network involved in signaling pathways in different stages of prostate cancer (PCa) by using bioinformatics and experimental methods.

Methods

Seventy subjects included sixty PCa patients in Local, Locally Advanced, Biochemical Relapse, Metastatic, and Benign stages, and ten healthy subjects were entered into the current study. The mRNAs with significant expression differences were first found using the GEO database. The candidate hub genes were then identified by analyzing Cytohubba and MCODE software. Cytoscape, GO Term, and KEGG software determined hub genes and critical pathways. The expression of candidate lncRNAs, miRNAs, and mRNAs was then assessed using Real-Time PCR and ELISA techniques.

Results

4 lncRNAs, 5 miRNAs, and 15 common target genes were detected in PCa patients compared with the healthy group. Unlike the tumor suppressors, the expression levels of common onco-lncRNAs, oncomiRNAs, and oncogenes showed a considerable increase in patients with advanced stages; Biochemical Relapse and Metastatic, in comparison to the primary stages; Local and Locally Advanced. Additionally, their expression levels significantly increased with a higher Gleason score than a lower one.

Conclusion

Identifying a common lncRNA-miRNA-mRNA network associated with prostate cancer may be clinically valuable as potential predictive biomarkers. They can also serve as novel therapeutic targets for PCa patients.

Mutator-Derived lncRNA Landscape: A Novel Insight Into the Genomic Instability of Prostate Cancer

Background

Increasing evidence has emerged to reveal the correlation between genomic instability and long non-coding RNAs (lncRNAs). The genomic instability-derived lncRNA landscape of prostate cancer (PCa) and its critical clinical implications remain to be understood.

Methods

Patients diagnosed with PCa were recruited from The Cancer Genome Atlas (TCGA) program. Genomic instability-associated lncRNAs were identified by a mutator hypothesis-originated calculative approach. A signature (GILncSig) was derived from genomic instability-associated lncRNAs to classify PCa patients into high-risk and low-risk groups. The biochemical recurrence (BCR) model of a genomic instability-derived lncRNA signature (GILncSig) was established by Cox regression and stratified analysis in the train set. Then its prognostic value and association with clinical features were verified by Kaplan–Meier (K-M) analysis and receiver operating characteristic (ROC) curve in the test set and the total patient set. The regulatory network of transcription factors (TFs) and lncRNAs was established to evaluate TF–lncRNA interactions.

Results

A total of 95 genomic instability-associated lncRNAs of PCa were identified. We constructed the GILncSig based on 10 lncRNAs with independent prognostic value. GILncSig separated patients into the high-risk (n = 121) group and the low-risk (n = 121) group in the train set. Patients with high GILncSig score suffered from more frequent BCR than those with low GILncSig score. The results were further validated in the test set, the whole TCGA cohort, and different subgroups stratified by age and Gleason score (GS). A high GILncSig risk score was significantly associated with a high mutation burden and a low critical gene expression (PTEN and CDK12) in PCa. The predictive performance of our BCR model based on GILncSig outperformed other existing BCR models of PCa based on lncRNAs. The GILncSig also showed a remarkable ability to predict BCR in the subgroup of patients with TP53 mutation or wild type. Transcription factors, such as FOXA1, JUND, and SRF, were found to participate in the regulation of lncRNAs with prognostic value.

Conclusion

In summary, we developed a prognostic signature of BCR based on genomic instability-associated lncRNAs for PCa, which may provide new insights into the epigenetic mechanism of BCR.

LINC00355 regulates p27KIP expression by binding to MENIN to induce proliferation in late-stage relapse breast cancer

Late-stage relapse (LSR) in patients with breast cancer (BC) occurs more than five years and up to 10 years after initial treatment and has less than 30% 5-year relative survival rate. Long non-coding RNAs (lncRNAs) play important roles in BC yet have not been studied in LSR BC. Here, we identify 1127 lncRNAs differentially expressed in LSR BC via transcriptome sequencing and analysis of 72 early-stage and 24 LSR BC patient tumors. Decreasing expression of the most up-regulated lncRNA, LINC00355, in BC and MCF7 long-term estrogen deprived cell lines decreases cellular invasion and proliferation. Subsequent mechanistic studies show that LINC00355 binds to MENIN and changes occupancy at the CDKN1B promoter to decrease p27Kip. In summary, this is a key study discovering lncRNAs in LSR BC and LINC00355 association with epigenetic regulation and proliferation in BC.

Comparing Urinary Glycoproteins among Three Urogenital Cancers and Identifying Prostate Cancer-Specific Glycoproteins

Prostate cancer, bladder cancer, and renal cancers are major urogenital cancers. Of which, prostate cancer is the most commonly diagnosed and second leading cause of cancer death for men in the United States. For urogenital cancers, urine is considered as proximate body fluid to the tumor site for developing non-invasiveness tests. However, the specific molecular signatures from different urogenital cancers are needed to relate changes in urine to various cancer detections. Herein, we utilized a previously published C4-Tip and C18/MAX-Tip workflow for enrichment of glycopeptides from urine samples and evaluated urinary glycopeptides for its cancer specificity. We analyzed 66 urine samples from bladder cancer (n = 27), prostate cancer (n = 4), clear cell renal cell carcinoma (ccRCC, n = 3), and benign plastic hyperplasia (BPH, n = 32) and then compared them with a previous publication that reported glycopeptides associated with aggressive prostate cancer (Gleason score ≥ 8). We further demonstrated the cancer specificity of the glycopeptides associated with aggressive prostate cancer. In this study, a total of 33 glycopeptides were identified to be specifically differentially expressed in prostate cancer compared to other urogenital cancer types as well as BPH urines. By cross-comparison with our previous urinary glycoproteomic dataset for aggressive prostate cancer, we reported a total of four glycopeptides from glycoproteins DSC2, MGAM, PIK3IP1, and CD55, commonly identified to be prostate cancer-specific. Together, these results deepen our understanding of the urinary glycoproteins associated with urogenital cancer types and expand our knowledge of the cancer specificity of urinary glycoproteins among urogenital cancer progression.

The Crosstalk of Long Non-Coding RNA and MicroRNA in Castration-Resistant and Neuroendocrine Prostate Cancer: Their Interaction and Clinical Importance

Prostate cancer is featured by its heterogeneous nature, which indicates a different prognosis. Castration-resistant prostate cancer (CRPC) is a hallmark of the treatment-refractory stage, and the median survival of patients is only within two years. Neuroendocrine prostate cancer (NEPC) is an aggressive variant that arises from de novo presentation of small cell carcinoma or treatment-related transformation with a median survival of 1–2 years from the time of diagnosis. The epigenetic regulators, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), have been proven involved in multiple pathologic mechanisms of CRPC and NEPC. LncRNAs can act as competing endogenous RNAs to sponge miRNAs that would inhibit the expression of their targets. After that, miRNAs interact with the 3’ untranslated region (UTR) of target mRNAs to repress the step of translation. These interactions may modulate gene expression and influence cancer development and progression. Otherwise, epigenetic regulators and genetic mutation also promote neuroendocrine differentiation and cancer stem-like cell formation. This step may induce neuroendocrine prostate cancer development. This review aims to provide an integrated, synthesized overview under current evidence to elucidate the crosstalk of lncRNAs with miRNAs and their influence on castration resistance or neuroendocrine differentiation of prostate cancer. Notably, we also discuss the mechanisms of lncRNA–miRNA interaction in androgen receptor-independent prostate cancer, such as growth factors, oncogenic signaling pathways, cell cycle dysregulation, and cytokines or other transmembrane proteins. Conclusively, we underscore the potential of these communications as potential therapeutic targets in the future.

Comprehensive analysis of lncRNA-miRNA-mRNA regulatory networks for microbiota-mediated colorectal cancer associated with immune cell infiltration

Recent findings have identified microbiota as crucial participants in many disease conditions, including cancers. Competing endogenous RNA (ceRNA) is regarded as a candidate mechanism involving relevant biological processes. We therefore constructed a ceRNA network using the TCGA and GEO database, to determine the potential mechanisms of microbiota-mediated colorectal carcinogenesis and progression. We found a total of 75 lncRNAs, 8 miRNAs, and 9 mRNAs in the probiotics-mediated ceRNA network and a total of 49 lncRNAs, 4 miRNAs, and 3 mRNA in the pathobiont-mediated ceRNA network, which could induce the microbiota-mediated carcinogenesis and progression. The GO and KEGG analysis indicated that the ceRNA network is mainly enriched in the metabolic process, and two unique pathways (the p53 signaling pathway and microRNA in cancer), respectively. A four-gene signature (FRMD6-AS2, DIRC3, LIFR-AS1, and MRPL23-AS1) was suggested as an independent prognostic factor. Four lncRNAs (LINC00355, KCNQ1OT1, LINC00491, and HOTAIR) were associated with poor survival. Three small molecule candidate anticancer drugs (Pentoxyverine, Rimexolone, and Doxylamine) were identified. A four-gene signature (FAM129A, BCL2, PMAIP1, and RPS6) is significantly correlated with immune infiltration level. This study provides a promising biomarker reservoir to explore the mechanism by which microbiota regulate the ceRNA network involving the immune response, and further participate in colorectal carcinogenesis and progression.

Bioinformatic profiling identifies prognosis-related genes in the immune microenvironment of endometrial carcinoma

Endometrial carcinoma (EC) is a common malignancy of female genital system which exhibits a unique immune profile. It is a promising strategy to quantify immune patterns of EC for predicting prognosis and therapeutic efficiency. Here, we attempted to identify the possible immune microenvironment-related prognostic markers of EC. We obtained the RNA sequencing and corresponding clinical data of EC from TCGA database. Then, 3 immune scores based on the Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithm were computed. Correlation between above ESTIMATE scores and other immune-related scores, molecular subtypes, prognosis, and gene mutation status (including BRCA and TP53) were further analyzed. Afterwards, gene modules associated with the ESTIMATE scores were screened out through hierarchical clustering analysis and weighted gene co-expression network analysis (WGCNA). Differentially expressed analysis was performed and genes shared by the most relevant modules were found out. KEGG pathway enrichment analysis was conducted to explore the biological functions of those genes. Survival analysis was carried out to identify prognostic immune-related genes and GSE17025 database was further used to confirm the correlation between immune-related genes and the ImmuneScore. The immune-related scores based on ESTIMATE algorithm was closely related to the immune microenvironment of EC. 3 gene modules that had the closest correlations with 3 ESTIMATE scores were obtained. 109 immune-related genes were preliminarily found out and 29 pathways were significantly enriched, most of which were associated with immune response. Univariate survival analysis revealed that there were 14 genes positively associated with both OS and PFS. Among which, 11 genes showed marked correlations with ImmuneScore values in GSE17025 database. Our current study profiled the immune status and identified 14 novel immune-related prognostic biomarkers for EC. Our findings may help to investigate the complicated tumor microenvironment and develop novel individualized therapeutic targets for EC.

LINC_00355 promotes gastric cancer progression by upregulating PHF19 expression through sponging miR-15a-5p

Background

Long non-coding RNAs exert vital roles in several types of cancer. The objective of this study was to explore the role of LINC_00355 in gastric cancer (GC) progression and its potential mechanism.

Methods

The expression levels of LINC_00355 in GC tissues and cells were detected by quantitative real-time PCR, followed by assessing the effects of LINC_00355 knockdown or overexpression on cell properties. Dual-luciferase reporter assay was utilized to identify the relationship between LINC_00355 and microRNA (miR)-15a-5p and miR-15a-5p and PHD finger protein 19 (PHF19), followed by the rescue experiments.

Results

The results showed that LINC_00355 was highly expressed in GC tissues and cells compared with the corresponding control. LINC_00355 knockdown decreased the viability, migration, and invasion and increased the accumulation of GC cells in G1 phase and apoptosis. Meanwhile, LINC_00355 downregulation markedly increased cleaved caspase 3 and cleaved poly (ADP-ribose) polymerase protein levels, whereas decreased cyclin D1, cyclin E, matrix metalloproteinase (MMP) 9, MMP2, and N-cadherin protein levels in GC cells. However, LINC_00355 overexpression had the opposite effects. It was verified that LINC_00355 upregulated the expression of PHF19 through sponging miR-15a-5p. Furthermore, PHF19 overexpression reversed the effect of LINC_00355 knockdown on GC cell properties, including cell viability, migration, invasion, and apoptosis.

Conclusions

Collectively, these results suggest that LINC_00355 promotes GC progression by up-regulating PHF19 through sponging miR-15a-5p. Our findings may provide an important clinical basis for reversing the malignant phenotype of GC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08227-3.

Construction of an mRNA-miRNA-lncRNA network prognostic for triple-negative breast cancer

The aim of this study was to establish a novel competing endogenous RNA (ceRNA) network able to predict prognosis in patients with triple-negative breast cancer (TNBC). Differential gene expression analysis was performed using the GEO2R tool. Enrichr and STRING were used to conduct protein-protein interaction and pathway enrichment analyses, respectively. Upstream lncRNAs and miRNAs were identified using miRNet and mirTarBase, respectively. Prognostic values, expression, and correlational relationships of mRNAs, lncRNAs, and miRNAs were examined using GEPIA, starBase, and Kaplan-Meier plotter. It total, 860 upregulated and 622 downregulated differentially expressed mRNAs were identified in TNBC. Ten overexpressed and two underexpressed hub genes were screened. Next, 10 key miRNAs upstream of these key hub genes were predicted, of which six upregulated miRNAs were significantly associated with poor prognosis and four downregulated miRNAs were associated with good prognosis in TNBC. NEAT1 and MAL2 were selected as key lncRNAs. An mRNA-miRNA-lncRNA network in TNBC was constructed. Thus, we successfully established a novel mRNA-miRNA-lncRNA regulatory network, each component of which is prognostic for TNBC.

Identification of key long non-coding RNAs in gastric adenocarcinoma

BACKGROUND

Gastric cancer is the third leading cause of cancer-related deaths worldwide.

OBJECTIVE

The present study aims to identify key long non-coding RNAs (lncRNAs) and their potential roles in the pathogenesis of gastric adenocarcinoma.

METHODS

The lncRNA and mRNA expression profile between gastric adenocarcinoma and adjacent non-tumor tissues were obtained from The Cancer Genome Atlas (TCGA). Differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) between gastric adenocarcinoma and adjacent non-tumor tissues were identified after bioinformatics analysis. DElncRNA-DEmRNA co-expression network and DElncRNA-nearby DEmRNA interaction network were constructed, respectively. Functional annotation for DEmRNAs interacted with DElncRNAs was performed. Receiver operating characteristic (ROC) analysis of selected DElncRNAs was conducted.

RESULTS

Based on TCGA, the mRNA and lncRNA expression profiles of 375 gastric adenocarcinoma and 32 adjacent non-tumor tissues were downloaded. A total of 1502 DEmRNAs and 928 DElncRNAs between gastric adenocarcinoma and adjacent non-tumor tissues were identified. HOXC-AS3 might involve with gastric adenocarcinoma by regulating a set of HOX genes (HOXC8, HOXC9, HOXC10, HOXC11, HOXC12 and HOXC13) with cis-effect. AC115619.1-APOA4/APOB and AP006216.2-APOA1/APOA4 integrations might play roles in gastric adenocarcinoma through regulating pathways of Fat digestion and absorption and Vitamin digestion and absorption. Six lncRNAs including (HOTAIR, C20orf166-AS1, PGM5-AS1, HOXC-AS3, HOXC-AS2 and AC012531.1) have excellent diagnostic value for gastric adenocarcinoma.

CONCLUSIONS

This study identifies key lncRNAs in gastric adenocarcinoma which provides clues for exploring the pathogenesis and developing potential biomarkers for gastric adenocarcinoma.

Integration of transcriptomic, proteomic and metabolomic data to reveal the biological mechanisms of AAI injury in renal epithelial cells

Overexposure to aristolochic acid I (AAI) can induce aristolochic acid nephropathy (AAN). However, the comprehensive mechanisms of AAI-induced nephrotoxicity have not been entirely explicated. To investigate the toxicological mechanisms by which AAI induces renal injury, human kidney cells (HK-2 cells) were subjected to comprehensive transcriptomic, proteomic and metabolomic analyses. The transcriptomic analysis identified a total of 7749 differentially expressed genes (DEGs) after AAI treatment, while the proteomic analysis found 598 differentially expressed proteins (DEPs) after AAI treatment. The metabolomic analysis revealed 49 and 42 differentially expressed metabolites (DEMs) in the positive and negative ion modes, respectively. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed on these DEGs, DEPs and DEMs. The results of the comprehensive analyses of transcripts, proteins, and metabolites indicated that the DEGs, DEPs, and DEMs were jointly regulated in three ways. These genes, proteins and metabolites and their related dysregulated pathways may be promising targets for research on the mechanisms of AAI injury in human renal epithelial cells. This study provides large-scale omics data that can be used to formulate new strategies for the prevention, rapid diagnosis, and treatment of AAI injury.

Identification of novel prognostic markers of survival time in high-risk neuroblastoma using gene expression profiles

Neuroblastoma is the most common extracranial solid tumor in childhood. Patients in high-risk group often have poor outcomes with low survival rates despite several treatment options. This study aimed to identify a genetic signature from gene expression profiles that can serve as prognostic indicators of survival time in patients of high-risk neuroblastoma, and that could be potential therapeutic targets. RNA-seq count data was downloaded from UCSC Xena browser and samples grouped into Short Survival (SS) and Long Survival (LS) groups. Differential gene expression (DGE) analysis, enrichment analyses, regulatory network analysis and machine learning (ML) prediction of survival group were performed. Forty differentially expressed genes (DEGs) were identified including genes involved in molecular function activities essential for tumor proliferation. DEGs used as features for prediction of survival groups included EVX2, NHLH2, PRSS12, POU6F2, HOXD10, MAPK15, RTL1, LGR5, CYP17A1, OR10AB1P, MYH14, LRRTM3, GRIN3A, HS3ST5, CRYAB and NXPH3. An accuracy score of 82% was obtained by the ML classification models. SMIM28 was revealed to possibly have a role in tumor proliferation and aggressiveness. Our results indicate that these DEGs can serve as prognostic indicators of survival in high-risk neuroblastoma patients and will assist clinicians in making better therapeutic and patient management decisions.

LINC00355 promoted the progression of lung squamous cell carcinoma through regulating the miR-466/LYAR axis

LINC00355 has been reported aberrantly over-expressed and associated with poor prognosis in various types of cancer. However, reports regarding the effect of LINC00355 on lung squamous cell carcinoma (SCC) are rare. This study aimed to explore the function of LINC00355 in the development and progression of lung SCC and reveal the underlying mechanism. The expression and subcellular location of LINC00355 were determined by qRT-PCR and RNA-FISH, respectively. The lung SCC cell growth was analyzed by CCK-8 assay, transwell invasion, wound healing, colony formation, and flow cytometry assays. Reactive oxygen species level was evaluated by DCFH-DA probes. Bioinformatics online websites, luciferase reporter assay, RNA binding protein immunoprecipitation (RIP), and RNA pull-down assays were utilized to investigate the interaction among LINC00355, miR-466, and Ly-1 antibody reactive clone (LYAR). The results showed that LINC00355 was upregulated in lung SCC and was positively associated with poor overall survival in lung SCC patients. LINC00355 was mainly located in the cytoplasm of SCC cells. Additionally, LINC0035 functioned as a competing endogenous RNA (ceRNA) to target miR-466, and LYAR was identified as a direct target of miR-466. LINC00355 expression negatively correlated with miR-466 level, and positively correlated with LYAR level. Mechanistically, knockdown of LINC00355 inhibited cell proliferation, migration and invasion, promoted cell apoptosis in vitro, and suppressed tumor growth in vivo through targeting miR-466, and thus down-regulated LYAR expression. These findings provide a new sight for understanding the molecular mechanism of lung SCC and indicate that LINC00355 may serve as a potential biomarker for the diagnosis and treatment of lung SCC.

Investigating the regulatory function of the ANO1-AS2 on the ANO1 gene in infertile men with asthenozoospermia and terato-asthenozoospermia

Long non-coding RNAs (lncRNAs) have a particular expression in the testicular tissue and exhibit a regulatory function on the reproduction system. ANO1-AS2 (linc02584), as an lncRNA is located near the anoctamin1 (ANO1) gene. ANO1 is an important component of the transmembrane system exhibiting expression modifications in the idiopathic infertile men. Therefore, the present study was conducted to investigate the relationship between ANO1-AS2 and ANO1 gene expression with sperm motility and morphology in the patients with asthenozoospermia (AZ) and terato- asthenozoospermia (TAZ). The study population included 32 patients with AZ, 35 patients with TAZ, and 34 people with normozoospermia (NZ, control). The expression levels of ANO1 gene and ANO1-AS2 in the spermatozoa were measured by the quantitative real-time polymerase chain reaction (PCR). Docking analysis was performed to investigate the interactions of the ANO1 gene promoter and intermediate elements with ANO1-AS2. ANO1 gene expression was significantly (P < 0.05) downregulated in the patients however; ANO1-AS2 expression was significantly upregulated (P < 0.05). The subsequent analysis confirmed the inverse correlation between ANO1 and ANO1-AS2. ANO1 gene expression level was significantly positively correlated with sperm motility and morphology (P < 0.05). Moreover, ANO1-AS2 expression showed an inverse correlation with sperm motility and morphology (P < 0.05). Docking analysis confirmed that ANO1-AS2 could stably interact with ANO1 gene promoter. In conclusion, ANO1-AS2 is likely to downregulate the ANO1 gene by interacting with ANO1 gene promoter, which can influence the sperm motility and morphology.

Cataract-Associated New Mutants S175G/H181Q of βΒ2-Crystallin and P24S/S31G of γD-Crystallin Are Involved in Protein Aggregation by Structural Changes

β/γ-Crystallins, the main structural protein in human lenses, have highly stable structure for keeping the lens transparent. Their mutations have been linked to cataracts. In this study, we identified 10 new mutations of β/γ-crystallins in lens proteomic dataset of cataract patients using bioinformatics tools. Of these, two double mutants, S175G/H181Q of βΒ2-crystallin and P24S/S31G of γD-crystallin, were found mutations occurred in the largest loop linking the distant β-sheets in the Greek key motif. We selected these double mutants for identifying the properties of these mutations, employing biochemical assay, the identification of protein modifications with nanoUPLC-ESI-TOF tandem MS and examining their structural dynamics with hydrogen/deuterium exchange-mass spectrometry (HDX-MS). We found that both double mutations decrease protein stability and induce the aggregation of β/γ-crystallin, possibly causing cataracts. This finding suggests that both the double mutants can serve as biomarkers of cataracts.

Systematic Evaluation of the Diagnostic and Prognostic Significance of Competitive Endogenous RNA Networks in Prostate Cancer

Long non-coding RNA (lncRNA)-mediated competitive endogenous RNA (ceRNA) networks act as essential mechanisms in tumor initiation and progression, but their diagnostic and prognostic significance in prostate cancer (PCa) remains poorly understood. Presently, using the RNA expression data derived from multiple independent PCa-related studies, we constructed a high confidence and PCa-specific core ceRNA network by employing three lncRNA-gene inference approaches and key node filter strategies and then established a logistic model and risk score formula to evaluate its diagnostic and prognostic values, respectively. The core ceRNA network consists of 10 nodes, all of which are significantly associated with clinical outcomes. Combination of expression of the 10 ceRNAs with a logistic model achieved AUC of ROC and PR curve up to ∼96 and 99% in excluding normal prostate samples, respectively. Additionally, a risk score formula constructed with the ceRNAs exhibited significant association with disease-free survival. More importantly, utilizing the expression of RNAs in the core ceRNA network as a molecular signature, the TCGA-PRAD cohort was divided into four novel clinically relevant subgroups with distinct expression patterns, highlighting a feasible way for improving patient stratification in the future. Overall, we constructed a PCa-specific core ceRNA network, which provides diagnostic and prognostic value.

Pseudogene-Derived lncRNAs and Their miRNA Sponging Mechanism in Human Cancer

Pseudogenes, abundant in the human genome, are traditionally considered as non-functional “junk genes.” However, recent studies have revealed that pseudogenes act as key regulators at DNA, RNA or protein level in diverse human disorders (including cancer), among which pseudogene-derived long non-coding RNA (lncRNA) transcripts are extensively investigated and has been reported to be frequently dysregulated in various types of human cancer. Growing evidence demonstrates that pseudogene-derived lncRNAs play important roles in cancer initiation and progression by serving as competing endogenous RNAs (ceRNAs) through competitively binding to shared microRNAs (miRNAs), thus affecting both their cognate genes and unrelated genes. Herein, we retrospect those current findings about expression, functions and potential ceRNA mechanisms of pseudogene-derived lncRNAs in human cancer, which may provide us with some crucial clues in developing potential targets for cancer therapy in the future.

Construction for Long Non-Coding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network in Human Retinal Detachment (RD) with Proliferative Vitreoretinopathy (PVR)

Background

The aim of this study was to analyze the long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) network in human retinal tissues following detachment with proliferative vitreoretinopathy (PVR).

Material/Methods

Expression data of 19 human detached retinas with PVR and 19 normal retinas from postmortem donors were downloaded from Gene Expression Omnibust (GEO) database (GSE28133). The R package “limma” was utilized to discriminate the dysregulated lncRNA and mRNA profiles. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of differentially expressed mRNAs were performed using R packages “Clusterprofiler.” The ceRNA network of dysregulated genes was constructed by using mircode, miRDB, miRTarBase and TargetScan databases, and was visualized by Cytoscape v3.6.1.

Results

A total of 23 lncRNAs and 994 mRNAs were identified significantly expressed between the human detached retinas with PVR and the normal retina tissues, with thresholds of |log₂FoldChange| >1.0 and adjusted P-value <0.05. The constructed ceRNA network (lncRNA-miRNA-mRNA regulatory axis) included 9 PVR-specific lncRNAs, as well as 27 miRNAs and 73 mRNAs.

Conclusions

We demonstrated the differential lncRNA expression profile and constructed a lncRNA-associated ceRNA network in human detached retinas with PVR. This may ferret out an unknown ceRNA regulatory network in human retinal detachment with PVR.

Optimisation of cancer classification by machine learning generates an enriched list of candidate drug targets and biomarkers

A novel list of potential biomarkers was generated from RNA-seq expression data and used to optimise cancer classification.

A novel long non-coding RNA LINC00355 promotes proliferation of lung adenocarcinoma cells by down-regulating miR-195 and up-regulating the expression of CCNE1

Lung adenocarcinoma is the most common subtype of non-small-cell lung cancer affecting people all over the globe. Recent studies have indicated that long non-coding RNAs (lncRNAs) possess the ability to regulate gene expression. Initially, we uncovered increased LINC00355 expressions in lung adenocarcinoma tissues and cells. Functionally, our findings demonstrated that LINC00355 silencing suppressed the proliferation in vitro and in vivo. In addition, we found that LINC00355 negatively regulated miR-195 in lung adenocarcinoma cells. Simultaneously, silencing LINC00355 by shRNA resulted in suppressed proliferation, colony formation and promoted cell cycle arrest and apoptosis via miR-195. Moreover, silencing LINC00355 by shRNA inhibited the cyclin E1 (CCNE1) gene expression via miR-195 in lung adenocarcinoma cells. Collectively, this study demonstrates the novel lncRNA LINC00355 in regulatory network of CCNE1 via miR-195 in lung adenocarcinoma, highlighting LINC00355 as a new target for the treatment of lung adenocarcinoma.

Characterization of mRNA Expression and Endogenous RNA Profiles in Bladder Cancer Based on The Cancer Genome Atlas (TCGA) Database

Background

Bladder cancer is a multifactorial disease with increasing incidence and mortality. Genetic alterations and altered expressions of mRNAs, long non-coding RNAs (lncRNAs), and miRNAs have been shown to play important roles in the tumorigenesis of bladder cancer. However, the functions of key RNAs and their regulatory network in bladder cancer are still to be elucidated.

Material/Methods

RNA profiles were downloaded from The Cancer Genome Atlas (TCGA) database. The differentially expressed mRNAs, lncRNAs, and miRNAs in bladder cancer were acquired through analyses of data from 414 bladder cancer tissues and 19 normal bladder tissues. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis was performed by using “DAVID6.8” and the R package “ClusterProfile”. Protein–protein interaction and competing endogenous RNA (ceRNA) networks were constructed by using “STRING” database and Cytoscape 3.6.2. Based on the clinical data and Cox regression, a prognosis model was established, and survival analysis was performed.

Results

A total of 1819 mRNAs, 659 lncRNAs, and 160 miRNAs were identified as significantly differentially expressed in bladder cancer of which 52 mRNAs, 58 lncRNAs, and 22 miRNAs were incorporated in the ceRNA network. CFL2 and TPM2 were found to be downregulated and showed significant correlation to each other in bladder cancer. HOXB5 and 6 lncRNAs (ADAMTS9-AS1, AC112721.1, LINC00460, AC110491.1, LINC00163, and HCG22) were strongly associated with high-grade, disease stages, and overall survival.

Conclusions

In this study, we have identified differentially expressed mRNAs, lncRNAs, and miRNAs in bladder cancer which were strongly associated with oncogenesis and prognosis. Further experimental studies are necessary to validate these results.

microRNA-205 and microRNA-338-3p Reduces Cell Apoptosis in Prostate Carcinoma Tissue and LNCaP Prostate Carcinoma Cells by Directly Targeting the B-Cell Lymphoma 2 (Bcl-2) Gene

Background

The inhibitor of apoptosis, B-cell lymphoma 2 (Bcl-2), is encoded by the BCL2 gene. Previous studies have shown that microRNAs are downregulated in prostate cancer. This study aimed to investigate the role of microRNA-205 and microRNA-338-3p and cell apoptosis in prostate carcinoma tissue and the LNCaP human prostate adenocarcinoma cell line by directly targeting the BCL2 gene and Bcl-2 protein expression.

Material/Methods

Bioinformatics methods predicted the target genes of miR-205 and miR-338-3p, which were validated by a luciferase assay. Immunohistochemistry was used to detect Bcl-2 protein expression in 30 samples of prostate carcinoma tissue and 30 matched samples of normal prostate. The normal prostate epithelial cell line, RWPE-1, and LNCaP human prostate adenocarcinoma cells studied in vitro. BCL2 mRNA expression and Bcl-2 protein expression were determined by quantitative polymerase chain reaction (q-PCR) and Western blot, respectively. Cell apoptosis was measured by flow cytometry using annexin V, fluorescein isothiocyanate, and phycoerythrin (annexin V-FITC/PE).

Results

TargetScan Human 7.2 predicted that the structures of miR-205 and miR-338-3p had a binding site on the proto-oncogene, BCL2, which was verified by a luciferase assay. The expression of miR-205 and miR-338-3p were significantly downregulated in prostate carcinoma tissues and LNCaP cells when compared with normal controls. BCL2 expression was significantly inhibited by overexpression of miR-205 and miR-338-3p in LNCaP cells.

Conclusions

The results of this study showed that miR-205 and miR-338-3p downregulated the expression of the BCL2 gene and decreased apoptosis in prostate carcinoma.

Comprehensive analysis of lncRNA-associated competing endogenous RNA network in tongue squamous cell carcinoma

Background

Increasing evidence has demonstrated that long non-coding RNAs (lncRNAs) play an important role in the competitive endogenous RNA (ceRNA) networks in that they regulate protein-coding gene expression by sponging microRNAs (miRNAs). However, the understanding of the ceRNA network in tongue squamous cell carcinoma (TSCC) remains limited.

Methods

Expression profile data regarding mRNAs, miRNAs and lncRNAs as well as clinical information on 122 TSCC tissues and 15 normal controls from The Cancer Genome Atlas (TCGA) database were collected. We used the edgR package to identify differentially expressed mRNAs (DEmRNAs), lncRNAs (DElncRNAs) and miRNAs (DEmiRNAs) between TSCC samples and normal samples. In order to explore the functions of DEmRNAs, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed. Subsequently, a ceRNA network was established based on the identified DElncRNAs-DEmiRNAs and DEmiRNAs-DEmRNAs interactions. The RNAs within the ceRNA network were analyzed for their correlation with overall disease survival. Finally, lncRNAs were specifically analyzed for their correlation with clinical features in the included TSCC patient samples.

Results

A total of 1867 mRNAs, 828 lncRNAs and 81 miRNAs were identified as differentially expressed in TSCC tissues (-log ₂fold change- ≥ 2; adjusted P value <0.01). The resulting ceRNA network included 16 mRNAs, 56 lncRNAs and 6 miRNAs. Ten out of the 56 lncRNAs were found to be associated with the overall survival in TSCC patients (P < 0.05); 10 lncRNAs were correlated with TSCC progression (P < 0.05).

Conclusion

Our study deepens the understanding of ceRNA network regulatory mechanisms in TSCC. Furthermore, we identified ten lncRNAs (PART1, LINC00261, AL163952.1, C2orf48, FAM87A, LINC00052, LINC00472, STEAP3-AS1, TSPEAR-AS1 and ERVH48-1) as novel, potential prognostic biomarkers and therapeutic targets for TSCC.