Hypomethylation of the lncRNA SOX21-AS1 has clinical prognostic value in cervical cancer

Identification of a novel hypermethylation marker, ZSCAN18, and construction of a diagnostic model in cervical cancer

PURPOSE

Cervical cancer (CC), a common female malignancy, has been linked to alterations in DNA methylation. This study employed an integrated "dry-wet lab" strategy combining bioinformatics, machine learning, and experimental validation to identify novel methylation biomarkers for CC.

METHODS

Methylome and transcriptome data from the TCGA and GEO cohorts (n=349 discovery, n=414 validation) were analyzed to identify differentially methylated CpGs. The top candidates were validated by pyrosequencing, methylation-specific PCR, and quantitative assays. Diagnostic models were developed, and functional studies were performed for the target markers.

RESULTS

Eighteen differentially methylated CpGs were identified, with five top candidates (three in the ZSCAN18 promoter) showing diagnostic potential. ZSCAN18 promoter methylation levels and positivity rates were significantly greater in CC tissues than in normal tissues (p<0.05), reaching 77.8% (21/27) in ThinPrep cytology test (TCT) samples. The ridge regression diagnostic model achieved an AUC of 0.9421 in the validation cohort. Similarly, ZSCAN18 overexpression suppressed CC cell proliferation (p<0.05).

CONCLUSIONS

This study established a rapid, effective and systematic systemic research strategy to screen novel methylation markers for CC. ZSCAN18 promoter methylation correlates with cervical lesion severity, and the diagnostic model enhances the diagnostic ability. These findings highlight the dual role of ZSCAN18 as a diagnostic marker and potential therapeutic target.

SOX21-AS1 Augmented Cervical Cancer Growth by Triggering FZD3 to Activate the Wnt/β-Catenin Signaling Pathway

Long non-coding RNA (LncRNA) SOX21-AS1 has been reported that it plays an important role in biological processes of several cancers. However, how it functions in cervical cancer (CC) still remain unclear. This investigation seeks to explore the impact of SOX21-AS1 on CC cell proliferation, invasion and migration and its association to the FZD3 and the Wnt/β-catenin signaling pathway. SOX21-AS1 expression levels were detected using real-time quantitative PCR in 20 cases of cervical cancer together with its adjacent tissues and several cervical cancer cell lines. Transgenic technology and functional experiments were conducted to confirm the carcinogenic properties of SOX21-AS1, and western blot was utilized to analyze the regulatory network composed of SOX21-AS1, FZD3 and the Wnt/β-catenin signaling pathway in CC. Through bioinformatics analysis, we found that the expression of SOX21-AS1 in CC was the highest among 16 kinds of tumor tissues. Moreover, clinical specimens confirmed that both CC tissues and cell lines possessed elevated SOX21-AS1 expressions (P < 0.01). CC cells which stably expressed upregulated SOX21-AS1 were noted to possesses higher rates of metastasis, invasion and proliferation, lower apoptotic rates and higher expression of FZD3,β-catenin and c-myc (P < 0.01). Conversely, the use of small interfering RNA to inhibit the expression of SOX21-AS1 yielded the opposite results (P < 0.01). SOX21-AS1 functions as an oncogenic LncRNA which enhances CC cell metastasis, invasion and proliferation through FZD3 upregulation via Wnt/β-catenin-signaling pathway activation. This LncRNA may represent an important biomarker for CC patients.

Comprehensive insights into human papillomavirus and cervical cancer: Pathophysiology, screening, and vaccination strategies

This article provides an in-depth review of the Human Papillomavirus (HPV), a predominant etiological factor in cervical cancer, exploring its pathophysiology, epidemiology, and mechanisms of oncogenesis. We examine the role of proteins, DNA methylation markers, and non-coding RNAs as predictive biomarkers in cervical cancer, highlighting their potential in refining diagnostic and prognostic practices. The evolution and efficacy of cervical cancer screening methods, including the Papanicolaou smear, HPV testing, cytology and HPV test, and colposcopy techniques, are critically analyzed. Furthermore, the article delves into the current landscape and future prospects of prophylactic HPV vaccines and therapeutic vaccines, underscoring their significance in the prevention and potential treatment of HPV-related diseases. This comprehensive review aims to synthesize recent advances and ongoing challenges in the field, providing a foundation for future research and clinical strategies in the prevention and management of cervical cancer.

Long non-coding RNA SOX21-AS1: A potential tumor oncogene in human cancers

Emerging data have proposed that the aberrant level of long noncoding RNAs (lncRNA) is related to the onset and progression of cancer. Among them, lncRNA SOX21-AS1 was shown to upregulate and seem to be a novel oncogene in various cancer, including ovarian cancer, lung cancer, breast cancer, pancreatic cancer, osteosarcoma, and melanoma. Available data indicated that SRY-box transcription factor 21 antisense divergent transcript 1 (SOX21-AS1) mostly acts as a competing endogenous RNA (ceRNA) to inhibit the level of its target microRNAs (miRNAs), leading to upregulation of their targets. In addition, SOX21-AS1 is engaged in various signaling pathways like transforming growth factor-β (TGF-β) signaling, Wnt signaling, and phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling. Moreover, this lncRNA was revealed to be correlated with the clinicopathological features of affected patients. SOX21-AS1 was also proved to enhance the resistance of ovarian cancer cells to cisplatin chemotherapy. SOX21-AS1 is markedly associated with poor prognosis and low survival of patients, proposing that it may be a prognostic and diagnostic biomarker in cancer. Overexpression of SOX21-AS1 is related to various cancer-related pathways, like epithelial mesenchymal transition (EMT), invasion, migration, apoptosis, and cell cycle arrest. In this work, we aimed to discuss the biogenesis, function, and underlying molecular mechanism of SOX21-AS1 in cancer progression as well as its potential as a prognostic and diagnostic biomarker in human cancers.

LncRNA SOX21-AS1 accelerates endometrial carcinoma progression through the miR-7-5p/RAF1 pathway

BACKGROUND

Endometrial carcinoma (EC) is one of the world's typical female reproductive tract malignancies, mostly occurring in postmenopausal women. Many reports have confirmed that long non-coding RNA SOX21 antisense RNA1 (lncRNA SOX21-AS1) is associated with the progressions of various cancer. However, the mechanism of SOX21-AS1 in EC remains unclear. Our study is intended to probe the mechanisms of SOX21-AS1 on EC progression.

METHODS

The CCK-8 assay and colony formation detected cell proliferation. Cell migration and invasion were assessed by transwell analysis. Apoptosis was measured by flow cytometry assay. Bioinformatics software predicted target binding and confirmed using a luciferase reporter analysis.

RESULTS

SOX21-AS1 expression was upregulated in EC tumor tissues and cells. High expression of SOX21-AS1 was associated with poor overall survival. Silencing of SOX21-AS1 restrained cell proliferation, migration, invasion, and increased apoptosis in HEC-1A and Ishikawa cells. Additionally, bioinformatics analysis demonstrated that SOX21-AS1 modulated RAF1 expression by competitively binding to miR-7-5p. Functionally, silencing of RAF1 reversed the functions of miR-7-5p inhibitor in the proliferation, invasion, and apoptosis of HEC-1A/sh-SOX21-AS1 and Ishikawa/sh-SOX21-AS1 cells.

CONCLUSIONS

SOX21-AS1 promoted the pathological development of EC by regulating the miR-7-5p/RAF1 pathway. This research may provide a novel target for EC therapy.

Long non-coding RNAs as critical regulators and novel targets in cervical cancer: current status and future perspectives

Cervical cancer is among the leading causes of cancer-associated mortality in women. In spite of vaccine availability, improved screening procedures, and chemoradiation therapy, cervical cancer remains the most commonly diagnosed cancer in 23 countries and the leading cause of cancer deaths in 36 countries. There is, therefore, a need to come up with novel diagnostic and therapeutic targets. Long non-coding RNAs (lncRNAs) play a remarkable role in genome regulation and contribute significantly to several developmental and disease pathways. The deregulation of lncRNAs is often observed in cancer patients, where they are shown to affect multiple cellular processes, including cell cycle, apoptosis, angiogenesis, and invasion. Many lncRNAs are found to be involved in the pathogenesis as well as progression of cervical cancer and have shown potency to track metastatic events. This review provides an overview of lncRNA mediated regulation of cervical carcinogenesis and highlights their potential as diagnostic and prognostic biomarkers as well as therapeutic targets for cervical cancer. In addition, it also discusses the challenges associated with the clinical implication of lncRNAs in cervical cancer.

Mutual interaction of lncRNAs and epigenetics: focusing on cancer

Long noncoding RNAs are characterized as noncoding transcripts longer than 200 nucleotides in response to a variety of functions within the cells. They are involved in almost all cellular mechanisms so as epigenetics. Given that epigenetics is an important phenomenon, which participates in the biology of complex diseases, many valuable studies have been performed to demonstrate the control status of lncRNAs and epigenetics. DNA methylation and histone modifications as epigenetic mechanisms can regulate the expression of lncRNAs by affecting their coding genes. Reciprocally, the three-dimensional structure of lncRNAs could mechanistically control the activity of epigenetic-related enzymes. Dysregulation in the mutual interaction between epigenetics and lncRNAs is one of the hallmarks of cancer. These mechanisms are either directly or indirectly involved in various cancer properties such as proliferation, apoptosis, invasion, and metastasis. For instance, lncRNA HOTAIR plays a role in regulating the expression of many genes by interacting with epigenetic factors such as DNA methyltransferases and EZH2, and thus plays a role in the initiation and progression of various cancers. Conversely, the expression of this lncRNA is also controlled by epigenetic factors. Therefore, focusing on this reciprocated interaction can apply to cancer management and the identification of prognostic, diagnostic, and druggable targets. In the current review, we discuss the reciprocal relationship between lncRNAs and epigenetic mechanisms to promote or prevent cancer progression and find new potent biomarkers and targets for cancer diagnosis and therapy.

Exploration of the Immune-Related Long Noncoding RNA Prognostic Signature and Inflammatory Microenvironment for Cervical Cancer

Purpose: Our research developed immune-related long noncoding RNAs (lncRNAs) for risk stratification in cervical cancer (CC) and explored factors of prognosis, inflammatory microenvironment infiltrates, and chemotherapeutic therapies. Methods: The RNA-seq data and clinical information of CC were collected from the TCGA TARGET GTEx database and the TCGA database. lncRNAs and immune-related signatures were obtained from the GENCODE database and the ImPort database, respectively. We screened out immune-related lncRNA signatures through univariate Cox, LASSO, and multivariate Cox regression methods. We established an immune-related risk model of hub immune-related lncRNAs to evaluate whether the risk score was an independent prognostic predictor. The xCell and CIBERSORTx algorithms were employed to appraise the value of risk scores which are in competition with tumor-infiltrating immune cell abundances. The estimation of tumor immunotherapy response through the TIDE algorithm and prediction of innovative recommended medications on the target to immune-related risk model were also performed on the basis of the IC50 predictor. Results: We successfully established six immune-related lncRNAs (AC006126.4, EGFR-AS1, RP4-647J21.1, LINC00925, EMX2OS, and BZRAP1-AS1) to carry out prognostic prediction of CC. The immune-related risk model was constructed in which we observed that high-risk groups were strongly linked with poor survival outcomes. Risk scores varied with clinicopathological parameters and the tumor stage and were an independent hazard factor that affect prognosis of CC. The xCell algorithm revealed that hub immune-related signatures were relevant to immune cells, especially mast cells, DCs, megakaryocytes, memory B cells, NK cells, and Th1 cells. The CIBERSORTx algorithm revealed an inflammatory microenvironment where naive B cells (p < 0.01), activated dendritic cells (p < 0.05), activated mast cells (p < 0.0001), CD8⁺ T cells (p < 0.001), and regulatory T cells (p < 0.01) were significantly lower in the high-risk group, while macrophages M0 (p < 0.001), macrophages M2 (p < 0.05), resting mast cells (p < 0.0001), and neutrophils (p < 0.01) were highly conferred. The result of TIDE indicated that the number of immunotherapy responders in the low-risk group (124/137) increased significantly (p = 0.00000022) compared to the high-risk group (94/137), suggesting that the immunotherapy response of CC patients was completely negatively correlated with the risk scores. Last, we compared differential IC50 predictive values in high- and low-risk groups, and 12 compounds were identified as future treatments for CC patients. Conclusion: In this study, six immune-related lncRNAs were suggested to predict the outcome of CC, which is beneficial to the formulation of immunotherapy.

Signature involved in immune-related lncRNA pairs for predicting the immune landscape of cervical cancer

Background

Immune-related long non-coding RNAs (irlncRNAs) are known to hold great promise as superior biomarkers for cervical cancer-related immunotherapeutic response and the tumor immune microenvironment. Here, we constructed a prognostic signature based on irlncRNA pairs (IRLPs).

Methods

The samples were downloaded from The Cancer Genome Atlas and the Genotype-Tissue Expression databases. The least absolute shrinkage and selection operator Cox regression was performed to construct the prognostic model. Receiver operating characteristic (ROC) curve and nomogram were plotted to validate accuracy of the model. Next, we estimated the immune cell infiltration and the correlation between risk score and the expression of genes related to immune checkpoint. Finally, we calculated the score of the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm and the half maximal inhibitory concentration of the chemotherapeutic agent to evaluate the response to immunotherapy and chemotherapy.

Results

We constructed a prognostic signature that consisted of 11 irlncRNAs. The area under the curve values of the 1-, 3-, and 5-year ROC curves were 0.844, 0.891, and 0.871, respectively. The expression of CTLA-4, HAVCR2, IDO1, LAG3, and PDCD1 were negatively correlated with risk scores. The score of TIDE in the high-risk group was significantly higher than in the low-risk group ( P < 0.01). Patients in the low-risk subgroup were more sensitive to chemotherapeutic agents, such as axitinib and docetaxel, whereas patients in the low-risk subgroup were more sensitive to mitomycin C.

Conclusion

Our study highlighted the value of the 11 IRLPs signatures to predict the prognosis and the response to immunotherapy and chemotherapeutics for patients with cervical cancer.

LncRNAs as the Regulators of Brain Function and Therapeutic Targets for Alzheimer’s Disease

Alzheimer’s disease (AD) is the most common type of dementia and a serious threat to the health and safety of the elderly population. It has become an emerging public health problem and a major economic and social burden. However, there is currently no effective treatment for AD. Although the mechanism of AD pathogenesis has been investigated substantially, the full range of molecular factors that contribute to its development remain largely unclear. In recent years, accumulating evidence has revealed that long non-coding RNAs (lncRNAs), a type of non-coding RNA longer than 200 nucleotides, play important roles in multiple biological processes involved in AD pathogenesis. With the further exploration of genomics, the role of lncRNA in the pathogenesis of AD has been phenotypically or mechanistically studied. Herein, we systematically review the current knowledge about lncRNAs implicated in AD and elaborate on their main regulatory pathways, which may contribute to the discovery of novel therapeutic targets and drugs for AD.

Identification of Immune-Related lncRNA Prognostic Signature and Molecular Subtypes for Glioblastoma

Background

Glioblastoma multiforme (GBM) is extensively genetically and transcriptionally heterogeneous, which poses challenges for classification and management. Long noncoding RNAs (lncRNAs) play a critical role in the development and progression of GBM, especially in tumor-associated immune processes. Therefore, it is necessary to develop an immune-related lncRNAs (irlncRNAs) signature.

Methods

Univariate and multivariate Cox regression analyses were utilized to construct a prognostic model. GBM-specific CeRNA and PPI network was constructed to predict lncRNAs targets and evaluate the interactions of immune mRNAs translated proteins. GO and KEGG pathway analyses were used to show the biological functions and pathways of CeRNA network-related immunity genes. Consensus Cluster Plus analysis was used for GBM gene clustering. Then, we evaluated GBM subtype-specific prognostic values, clinical characteristics, genes and pathways, immune infiltration access single cell RNA-seq data, and chemotherapeutics efficacy. The hub genes were finally validated.

Results

A total of 17 prognostically related irlncRNAs were screened to build a prognostic model signature based on six key irlncRNAs. Based on GBM-specific CeRNAs and enrichment analysis, PLAU was predicted as a target of lncRNA-H19 and mainly enriched in the malignant related pathways. GBM subtype-A displayed the most favorable prognosis, high proportion of genes (IDH1, ATRX, and EGFR) mutation, chemoradiotherapy, and low risk and was characterized by low expression of four high-risk lncRNAs (H19, HOTAIRM1, AGAP2-AS1, and AC002456.1) and one mRNA KRT8. GSs with poor survival were mainly infiltrated by mesenchymal stem cells (MSCs) and astrocyte, and were more sensitive to gefitinib and roscovitine. Among GSs, three hub genes KRT8, NGFR, and TCEA3, were screened and validated to potentially play feasible oncogenic roles in GBM.

Conclusion

Construction of lncRNAs risk model and identification of GBM subtypes based on 17 irlncRNAs, which suggesting that irlncRNAs had the promising potential for clinical immunotherapy of GBM.

A four immune-related long noncoding RNAs signature as predictors for cervical cancer

The progression, metastasis, and prognosis of cervical cancer (CC) is influenced by the tumor immune microenvironment. Studies proved that long non-coding RNAs (lncRNAs) to engage in cervical cancer development, especially immune-related lncRNAs, have emerged crucial in the tumor immune process. This study was set out to identify an immune-related lncRNA signature. In total, 13,838 lncRNA expression profiles and 328 immune genes were acquired from the clnical data of 306 CC tissues and 3 non-CC tissues. From the 433 identified immune-related lncRNAs, 4 candidate immune-related lncRNAs (SOX21-AS1, AC005332.4, NCK1-DT, LINC01871) were considered independent indicators of cervical cancer prognosis through the univariate and multivariate Cox regression analysis, and they were used to construct a prognostic and survival lncRNA signature model followed by the bootstrap method for further verification. Kaplan-Meier curves illustrated that cervical cancer patients could be divided into high-risk and low-risk groups with significant differences (P = 2.052e - 05), and the discrepancy of immune profiles between these two risk groups was illustrated by principal components analysis. Taken together, the novel survival predictive model created by the four immune-related lncRNAs showed promising clinical prediction value in cervical cancer.

ENPP2 Methylation in Health and Cancer

Autotaxin (ATX) encoded by Ectonucleotide Pyrophosphatase/Phosphodiesterase 2 (ENPP2) is a key enzyme in Lysophosphatidic Acid (LPA) synthesis implicated in cancer. Although its aberrant expression has been reported, ENPP2 methylation profiles in health and malignancy are not described. We examined in silico the methylation of ENPP2 analyzing publicly available methylome datasets, to identify Differentially Methylated CpGs (DMCs) which were then correlated with expression at gene and isoform levels. Significance indication was set to be FDR corrected p-value < 0.05. Healthy tissues presented methylation in all gene body CGs and lower levels in Promoter Associated (PA) regions, whereas in the majority of the tumors examined (HCC, melanoma, CRC, LC and PC) the methylation pattern was reversed. DMCs identified in the promoter were located in sites recognized by multiple transcription factors, suggesting involvement in gene expression. Alterations in methylation were correlated to an aggressive phenotype in cancer cell lines. In prostate and lung adenocarcinomas, increased methylation of PA CGs was correlated to decreased ENPP2 mRNA expression and to poor prognosis parameters. Collectively, our results corroborate that methylation is an active level of ATX expression regulation in cancer. Our study provides an extended description of the methylation status of ENPP2 in health and cancer and points out specific DMCs of value as prognostic biomarkers.

Role of long non-coding RNA H19 in the development of osteoporosis

Background

Osteoporosis is a widespread and serious metabolic bone disease. At present, revealing the molecular mechanisms of osteoporosis and developing effective prevention and treatment methods are of great significance to health worldwide. LncRNA is a non-coding RNA peptide chain with more than 200 nucleotides. Researchers have identified many lncRNAs implicated in the development of diseases and lncRNA H19 is an example.

Results

A large amount of evidence supports the fact that long non-coding RNA (lncRNA) genes, such as H19, have multiple, far-reaching effects on various biological functions. It has been found that lncRNA H19 has a role in the regulation of different types of cells in the body including the osteoblasts, osteocytes, and osteoclasts found in bones. Therefore, it can be postulated that lncRNA H19 affects the incidence and development of osteoporosis.

Conclusion

The prospect of targeting lncRNA H19 in the treatment of osteoporosis is promising because of the effects that lncRNA H19 has on the process of osteogenic differentiation. In this review, we summarize the molecular pathways and mechanisms of lncRNA H19 in the pathogenesis of osteoporosis and summarize the research progress of targeting H19 as a treatment option. Research is emerging that explores more effective treatment possibilities for bone metabolism diseases using molecular targets.

Knockdown of LINC01123 inhibits cell viability, migration and invasion via miR-361-3p/TSPAN1 targeting in cervical cancer

Cervical cancer (CC) is a type of gynecological malignancy that poses a significant threat to females. The aim of the present study was to examine the role of long intergenic non-protein coding RNA 1123 (LINC01123) and its underlying molecular mechanism in the development of CC. mRNA expression levels of LINC01123 and microRNA (miR)-361-3p in CC tissue samples and cell lines were evaluated using reverse transcription-quantitative PCR. Cell viability, migration and invasion were detected using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, wound healing and Transwell assays. Moreover, a xenograft tumor model was established for elucidating the influence of LINC01123 knockdown on tumor growth in vivo. A dual-luciferase reporter assay was used to confirm the association between LINC01123 and miR-361-3p, and miR-361-3p and tetraspanin 1 (TSPAN1). Western blot analysis was used to determine TSPAN1 protein expression. LINC01123 expression was upregulated and miR-361-3p expression was reduced in CC tissue samples and cell lines. Knockdown of LINC01123 inhibited cell viability, migration and invasion in vitro, and suppressed tumor growth in vivo. Furthermore, LINC01123 targeted miR-361-3p and negatively regulated miR-361-3p expression. Overexpression of miR-361-3p inhibited cell viability, migration and invasion in HeLa and CaSki cells. Additionally, miR-361-3p targeted TSPAN1 and negatively regulated TSPAN1 expression. Inhibition of miR-361-3p and overexpression of TSPAN1 reversed the effect of LINC01123 knockdown on cell proliferation, migration and invasion in HeLa cells. Knockdown of LINC01123 inhibited cell proliferation, migration and invasion via miR-361-3p/TSPAN1 regulation in CC, which may present an effective target for treatment of CC.

A New Story of the Three Magi: Scaffolding Proteins and lncRNA Suppressors of Cancer

Scaffolding molecules exert a critical role in orchestrating cellular response through the spatiotemporal assembly of effector proteins as signalosomes. By increasing the efficiency and selectivity of intracellular signaling, these molecules can exert (anti/pro)oncogenic activities. As an archetype of scaffolding proteins with tumor suppressor property, the present review focuses on MAGI1, 2, and 3 (membrane-associated guanylate kinase inverted), a subgroup of the MAGUK protein family, that mediate networks involving receptors, junctional complexes, signaling molecules, and the cytoskeleton. MAGI1, 2, and 3 are comprised of 6 PDZ domains, 2 WW domains, and 1 GUK domain. These 9 protein binding modules allow selective interactions with a wide range of effectors, including the PTEN tumor suppressor, the β-catenin and YAP1 proto-oncogenes, and the regulation of the PI3K/AKT, the Wnt, and the Hippo signaling pathways. The frequent downmodulation of MAGIs in various human malignancies makes these scaffolding molecules and their ligands putative therapeutic targets. Interestingly, MAGI1 and MAGI2 genetic loci generate a series of long non-coding RNAs that act as a tumor promoter or suppressor in a tissue-dependent manner, by selectively sponging some miRNAs or by regulating epigenetic processes. Here, we discuss the different paths followed by the three MAGIs to control carcinogenesis.

Understanding Cervical Cancer through Proteomics

Cancer is one of the leading public health issues worldwide, and the number of cancer patients increases every day. Particularly, cervical cancer (CC) is still the second leading cause of cancer death in women from developing countries. Thus, it is essential to deepen our knowledge about the molecular pathogenesis of CC and propose new therapeutic targets and new methods to diagnose this disease in its early stages. Differential expression analysis using high-throughput techniques applied to biological samples allows determining the physiological state of normal cells and the changes produced by cancer development. The cluster of differential molecular profiles in the genome, the transcriptome, or the proteome is analyzed in the disease, and it is called the molecular signature of cancer. Proteomic analysis of biological samples of patients with different grades of cervical intraepithelial neoplasia (CIN) and CC has served to elucidate the pathways involved in the development and progression of cancer and identify cervical proteins associated with CC. However, several cervical carcinogenesis mechanisms are still unclear. Detecting pathologies in their earliest stages can significantly improve a patient's survival rate, prognosis, and recurrence. The present review is an update on the proteomic study of CC.

Roles of lncRNA MAGI2-AS3 in human cancers

Long noncoding RNAs (lncRNAs) are noncoding RNAs more than 200 nucleotides in length. A growing number of reports indicate that lncRNAs play a key role in multiple cancers by serving as oncogenes or tumor suppressor genes. MAGI2 antisense RNA 3 (MAGI2-AS3) is ubiquitously expressed in human cancers, and the level of MAGI2-AS3 expression is associated with the progression and prognosis of cancers. Moreover, dysregulation of MAGI2-AS3 has been found to regulate cancer cell proliferation, cell death, invasion and metastasis and treatment resistance by serving as a competing endogenous RNA (ceRNA), epigenomic regulator, and transcriptional regulator. Moreover, increasing evidence shows that MAGI2-AS3 may be a potential biomarker for cancer prognosis and a potential target for cancer therapy. In this review, we summarize current research on the functions, mechanisms and clinical significance of the lncRNA MAGI2-AS3 in cancer development.

Integrative analysis of the gastric cancer long non-coding RNA-associated competing endogenous RNA network

Gastric cancer (GC) is a common type of cancer, and identification of novel diagnostic biomarkers associated with this disease is important. The present study aimed to identify novel diagnostic biomarkers associated with the prognosis of GC, using an integrated bioinformatics approach. Differentially expressed long non-coding RNAs (lncRNAs) associated with GC were identified using Gene Expression Omnibus datasets (GSE58828, GSE72305 and GSE99416) and The Cancer Genome Atlas database. A competing endogenous RNA network that incorporated five lncRNAs [long intergenic non-protein coding RNA 501 (LINC00501), LINC00365, SOX21 antisense divergent transcript 1 (SOX21-AS1), GK intronic transcript 1 (GK-IT1) and DLEU7 antisense RNA 1 (DLEU7-AS1)], 29 microRNAs and 114 mRNAs was constructed. Gene Ontology and protein-protein interaction network analyses revealed that these lncRNAs may be involved in 'biological regulation', 'metabolic process', 'cell communication', 'developmental process', 'cell proliferation', 'reproduction' and the 'cell cycle'. The results of receiver operating characteristic curve analysis demonstrated that LINC00501 (AUC=0.819), LINC00365 (AUC=0.580), SOX21-AS1 (AUC=0.736), GK-IT1 (AUC=0.823) and DLEU7-AS1 (AUC=0.932) had the potential to become valuable diagnostic biomarkers for GC. Associations with clinicopathological characteristics demonstrated that LINC00501 expression was significantly associated with sex (P=0.015) and tumor grade (P=0.022). Furthermore, LINC00365 expression was significantly associated with lymph node metastasis (P=0.025). Gene set enrichment analysis revealed that LINC00501, LINC00365 and SOX21-AS1 were enriched in signaling pathways associated with GC. Reverse transcription-quantitative PCR analysis demonstrated that LINC00501 expression (P=0.043) was significantly upregulated in GC tissues, whereas the expression levels of LINC00365 (P=0.033) and SOX21-AS1 (P=0.037) were significantly downregulated in GC tissues. Taken together, the results of the present study suggest that LINC00501, LINC00365, SOX21-AS1, GK-IT1 and DLEU7-AS1 may be used as novel diagnostic biomarkers for GC, and may be functionally associated with GC development and progression.

LINC01133 promotes hepatocellular carcinoma progression by sponging miR-199a-5p and activating annexin A2

BACKGROUND

Long noncoding RNAs (lncRNAs) are functionally associated with cancer development and progression. Although gene copy number variation (CNV) is common in hepatocellular carcinoma (HCC), it is not known how CNV in lncRNAs affects HCC progression and recurrence. We aimed to identify a CNV-related lncRNA involved in HCC progression and recurrence and illustrate its underlying mechanisms and prognostic value.

METHODS

We analyzed the whole genome sequencing (WGS) data of matched cancerous and noncancerous liver samples from 49 patients with HCC to identify lncRNAs with CNV. The results were validated in another cohort of 238 paired HCC and nontumor samples by TaqMan copy number assay. We preformed Kaplan-Meier analysis and log-rank test to identify lncRNA CNV with prognostic value. We conducted loss- and gain-of-function studies to explore the biological functions of LINC01133 in vitro and in vivo. The competing endogenous RNAs (ceRNAs) mechanism was clarified by microRNA sequencing (miR-seq), quantitative real-time PCR (qRT-PCR), western blot, and dual-luciferase reporter assays. We confirmed the binding mechanism between lncRNA and protein by RNA pull-down, RNA immunoprecipitation, qRT-PCR, and western blot analyses.

RESULTS

Genomic copy numbers of LINC01133 were increased in HCC, which were positively related with the elevated expression of LINC01133. Increased copy number of LINC01133 predicted the poor prognosis in HCC patients. LINC01133 overexpression in HCC cells promoted proliferation and aggressive phenotypes in vitro, and facilitated tumor growth and lung metastasis in vivo, whereas LINC01133 knockdown had the opposite effects. LINC01133 sponged miR-199a-5p, resulting in enhanced expression of SNAI1, which induced epithelial-to-mesenchymal transition (EMT) in HCC cells. In addition, LINC01133 interacted with Annexin A2 (ANXA2) to activate the ANXA2/STAT3 signaling pathway.

CONCLUSIONS

LINC01133 promotes HCC progression by sponging miR-199a-5p and interacting with ANXA2. LINC01133 CNV gain is predictive of poor prognosis in patients with HCC.

Comprehensive In Silico Analysis of a Novel Serum Exosome-Derived Competitive Endogenous RNA Network for Constructing a Prognostic Model for Glioblastoma

Purpose

Glioblastoma (GBM) is one of the most aggressive brain tumors with high mortality, and tumor-derived exosomes provide new insight into the mechanisms of GBM tumorigenesis, metastasis and therapeutic resistance. We aimed to establish an exosome-derived competitive endogenous RNA (ceRNA) network for constructing a prognostic model for GBM.

Methods

We obtained the expression profiles of long noncoding RNAs (lncRNAs), miRNAs, and mRNAs from the GEO and TCGA databases and identified differentially expressed RNAs in GBM to construct a ceRNA network. By performing lasso and multivariate Cox regression analyses, we identified optimal prognosis-related differentially expressed lncRNAs (DElncRNAs) and generated a risk score model termed the exosomal lncRNA (exo-lncRNA) signature. The exo-lncRNA signature was subsequently validated in the CGGA GBM cohort. Finally, a novel prognostic nomogram was constructed based on the exo-lncRNA signature and clinicopathological parameters and validated in the CGGA external cohort. Based on the ceRNA hypothesis, oncocers were identified based on highly positive correlations between lncRNAs and mRNAs mediated by the same miRNAs. Furthermore, regression analyses were performed to assess correlations between the expression abundances of lncRNAs in tumors and exosomes.

Results

A total of 45 DElncRNAs, six DEmiRNAs, and 38 DEmRNAs were identified, and an exosome-derived ceRNA network was built. Three optimal prognostic-related DElncRNAs, HOTAIR (HR=0.341, P<0.001), SOX21-AS1 (HR=0.30, P<0.001), and STEAP3-AS1 (HR=2.47, P<0.001), were included to construct the exo-lncRNA signature, which was further proven to be an independent prognostic factor. The novel prognostic nomogram was constructed based on the exo-lncRNA signature, patient age, pharmacotherapy, radiotherapy, IDH mutation status, and MGMT promoter status, with a concordance index of 0.878. ROC and calibration plots both suggested that the nomogram had beneficial discrimination and predictive abilities. A total of 11 pairs of prognostic oncocers were identified. Regression analysis suggested excellent consistency of the expression abundance of the three exosomal lncRNAs between exosomes and tumor tissues.

Conclusions

Exosomal lncRNAs may serve as promising prognostic predictors and therapeutic targets. The prognostic nomogram based on the exo-lncRNA signature might provide an intuitive method for individualized survival prediction and facilitate better treatment strategies.

Novel insights for lncRNA MAGI2-AS3 in solid tumors

Long non-coding RNAs (lncRNAs) refer to elements of genomic transcription with more than 200 nucleotides that are not translated into proteins, but have crucial roles in cancer progression. MAGI2-AS3, a novel lncRNA, has been reported to be aberrantly expressed in many solid tumors. Increasingly, studies have demonstrated that MAGI2-AS3 expression is significantly correlated with patient clinical characteristics, and that MAGI2-AS3 can regulate multiple biological processes through target-gene regulation. Furthermore, MAGI2-AS3 may serve as both a diagnostic biomarker and as a promising therapeutic target against solid tumors. In this review, we summarize the current knowledge regarding the biological functions and related molecular mechanisms of MAGI2-AS3 in solid-tumor progression. We conclude that understanding MAGI2-AS3 properties may provide new insights into the diagnoses and treatments of solid tumors.

SOX21-AS1 modulates neuronal injury of MMP+-treated SH-SY5Y cells via targeting miR-7-5p and inhibiting IRS2

Parkinson's disease (PD), caused by the decreased number of dopaminergic neurons in the substantia nigra, is identified as the second most familiar age-dependent neurodegenerative disease to the public. Long non-coding RNAs (lncRNAs) have been reported to participate in the development of PD. In our research, the expression of lncRNA SRY-box transcription factor 21 antisense divergent transcript 1 (SOX21-AS1) was up-regulated in 1-methyl-4-phenylpyridinium (MMP⁺)-treated SH-SY5Y cells. In addition, SOX21-AS1 depletion weakened the cell injury induced by MMP⁺. Moreover, SOX21-AS1 knockdown decreased Reactive Oxygen Species (ROS) generation and levels of TNF-α, IL-1β and IL-6, but increased SOD activity. However, SOX21-AS1 up-regulation led to opposite results. Further, SOX21-AS1 could bind with miR-7-5p, whose overexpression relieved MMP⁺-induced cell injury. Additionally, insulin receptor substrate 2 (IRS2) served as the target gene of miR-7-5p, and its expression was positively modulated by SOX21-AS1. Similarly, IRS2 knockdown also had alleviative effects on cell injury stimulated by MMP⁺ treatment. In sum up, our study demonstrated a new regulatory network consisted of SOX21-AS1, miR-7-5p and IRS2 in SH-SY5Y cells, supplying with a better comprehension about the pathogenic mechanism of PD.

Long-Chain Non-Coding SOX21-AS1 Promotes Proliferation and Migration of Breast Cancer Cells Through the PI3K/AKT Signaling Pathway

Aim

This study aimed to investigate the effect of long-chain non-coding SOX21-AS1 on the proliferation and migration of breast cancer (BC) cells through the PI3K/AKT signaling pathway.

Methods

Eighty-eight BC and adjacent tissues were collected, and BC cells and normal breast epithelial cells were purchased. LncRNA SOX21-AS1 expression in tissues and cells was detected by RT-PCR. miR-NC, si-SOX21-AS1, and Sh-SOX21-AS1 were transfected into BC cells. The PI3K/AKT signaling pathway was interfered with L740Y-P (activator of the PI3K/AKT pathway) and LY294002 (inhibitor of the PI3K/AKT pathway) in BC cells. The SOX21-AS1 expression in BC tissues and cells was tested by qRT-PCR, and the expression levels of p-PI3K, p-AKT, N-cadherin, E-cadherin, and vimentin were detected by WB.

Results

SOX21-AS1 was highly expressed in BC, and the p-PI3K and p-AKT levels were also high. Cell experiments showed that inhibiting SOX21-AS1 expression could inhibit the proliferation, invasion, migration, and EMT of BC cells, and up-regulating its expression could promote the proliferation, invasion, migration, and EMT of ovarian cancer cells. The tumor-forming experiment in nude mice was consistent with the results in vitro. 740Y-P intervention could reverse the inhibition effect of Si-SOX21-AS1 on BC cell proliferation, invasion, migration, and EMT, while LY294002 intervention could reverse the promotion effect of Sh-SOX21-AS1 on BC cell proliferation, invasion, migration, and EMT.

Conclusion

SOX21-AS1 is highly expressed in BC tissues. Silencing BC expression can inhibit the proliferation, invasion, migration, and EMT of cells by inhibiting the PI3K/AKT signaling pathway, which may be a new target for diagnosis and treatment.

Aberrant Methylation of the SOX21-AS1 Promoter Region Promotes Gene Expression and Its Clinical Value in Cervical Cancer

Cervical cancer is the fourth most common female cancer worldwide. Long non-coding RNAs (lncRNAs), such as SOX21-AS1, play pivotal roles in the progression and metastasis of cancer. We previously described that SOX21-AS1 was hypomethylated in cervical cancer (CC) and aimed to further explore the relationship between methylation of the SOX21-AS1 promoter and CC using clinical cervical samples. Pyrosequencing was performed to detect the methylation status of the SOX21-AS1 promoter in 33 cervical specimens. Additionally, expression levels of related genes in 43 clinical cervical specimens were measured using quantitative real-time PCR (qRT-PCR). The SOX21-AS1 promoter was significantly hypomethylated in CC (P < 0.01). SOX21-AS1 hypomethylation was also significantly associated with an advanced Federation of Gynecology and Obstetrics (FIGO) stage (P < 0.01). The expression levels of SOX21-AS1 and SOX21 were noted to be higher in cancer vs. normal cervix (all P < 0.001). Moreover, the expression of SOX21-AS1 was positively correlated with SOX21 in all samples (r = 0.891, P < 0.001). Methylation statue of the SOX21-AS1 promoter region was negatively correlated with the expression levels of SOX21-AS1 and SOX21 (SOX21-AS1, r = - 0.628; SOX21, r = - 0.648; both P < 0.001). The methylation status of SOX21-AS1 displayed promising diagnostic potential for CC, exhibiting good sensitivity (100.0%) and specificity (69.2%), with an area under the curve of 0.846. In addition, bioinformatic analyses identified a potential link between SOX21-AS1 and the Wnt signaling pathway. Furthermore, methylation status of SOX21-AS1 was negatively correlated with β-catenin/c-myc/cyclin D1 mRNA levels (r_s = - 0.529, - 0.462 ,and - 0.383, respectively, P < 0.05). Our findings illuminated that lncRNA SOX21-AS1 showed hypomethylation in cervical cancer and SOX21-AS1 could serve as a novel biomarker for CC diagnosis or a potential therapeutic target.

Interplay between BRCA1 and GADD45A and Its Potential for Nucleotide Excision Repair in Breast Cancer Pathogenesis

A fraction of breast cancer cases are associated with mutations in the BRCA1 (BRCA1 DNA repair associated, breast cancer type 1 susceptibility protein) gene, whose mutated product may disrupt the repair of DNA double-strand breaks as BRCA1 is directly involved in the homologous recombination repair of such DNA damage. However, BRCA1 can stimulate nucleotide excision repair (NER), the most versatile system of DNA repair processing a broad spectrum of substrates and playing an important role in the maintenance of genome stability. NER removes carcinogenic adducts of diol-epoxy derivatives of benzo[α]pyrene that may play a role in breast cancer pathogenesis as their accumulation is observed in breast cancer patients. NER deficiency was postulated to be intrinsic in stage I of sporadic breast cancer. BRCA1 also interacts with GADD45A (growth arrest and DNA damage-inducible protein GADD45 alpha) that may target NER machinery to actively demethylate genome sites in order to change the expression of genes that may be important in breast cancer. Therefore, the interaction between BRCA1 and GADD45 may play a role in breast cancer pathogenesis through the stimulation of NER, increasing the genomic stability, removing carcinogenic adducts, and the local active demethylation of genes important for cancer transformation.

Proneural and mesenchymal glioma stem cells display major differences in splicing and lncRNA profiles

Therapy resistance and recurrence in high-grade gliomas are driven by their populations of glioma stem cells (GSCs). Thus, detailed molecular characterization of GSCs is needed to develop more effective therapies. We conducted a study to identify differences in the splicing profile and expression of long non-coding RNAs in proneural and mesenchymal GSC cell lines. Genes related to cell cycle, DNA repair, cilium assembly, and splicing showed the most differences between GSC subgroups. We also identified genes distinctly associated with survival among patients of mesenchymal or proneural subgroups. We determined that multiple long non-coding RNAs with increased expression in mesenchymal GSCs are associated with poor survival of glioblastoma patients. In summary, our study established critical differences between proneural and mesenchymal GSCs in splicing profiles and expression of long non-coding RNA. These splicing isoforms and lncRNA signatures may contribute to the uniqueness of GSC subgroups, thus contributing to cancer phenotypes and explaining differences in therapeutic responses.