Potential lncRNA diagnostic biomarkers for early gastric cancer

Exosomes: Their role in the diagnosis, progression, metastasis, and treatment of glioblastoma

Exosomes are crucial for the growth and spread of glioblastomas, an aggressive form of brain cancer. These tiny vesicles play a crucial role in the activation of signaling pathways and intercellular communication. They can also transfer a variety of biomolecules such as proteins, lipids and nucleic acids from donor to recipient cells. Exosomes can influence the immune response by regulating the activity of immune cells, and they are crucial for the growth and metastasis of glioblastoma cells. In addition, exosomes contribute to drug resistance during treatment, which is a major obstacle in the treatment of glioblastoma. By studying them, the diagnosis and prognosis of glioblastoma can be improved. Due to their high biocompatibility and lack of toxicity, they have become an attractive option for drug delivery. The development of exosomes as carriers of specific therapeutic agents could overcome some of the obstacles to effective treatment of glioblastoma. In this review, we address the potential of exosomes for the treatment of glioblastoma and show how they can be modified for this purpose.

A transcribed ultraconserved noncoding RNA, uc.285+, promotes colorectal cancer proliferation through dual targeting of CDC42 by directly binding mRNA and protein

The transcribed ultraconserved region (T-UCR) belongs to a new type of lncRNAs that are conserved in homologous regions of the rat, mouse and human genomes. A lot of research has reported that differential expression of T-UCRs can influence the development of various cancers, revealing the ability of T-UCRs as new therapeutic targets or potential cancer biomarkers. Most studies on the molecular mechanisms of T-UCRs in cancer have focused on ceRNA regulatory networks and interactions with target proteins, but the present study reveals an innovative dual-targeted regulatory approach in which T-UCRs bind directly to mRNAs and directly to proteins. We screened T-UCRs that may be related to colorectal cancer (CRC) by performing a whole-genome T-UCR gene microarray and further studied the functional mechanism of T-UCR uc.285+ in the development of CRC. Modulation of uc.285+ affected the proliferation of CRC cell lines and influenced the expression of the CDC42 gene. We also found that uc.285+ promoted the proliferation of CRC cells by directly binding to CDC42 mRNA and enhancing its stability while directly binding to CDC42 protein and affecting its stability. In short, our research on the characteristics of cell proliferation found that uc.285+ has a biological function in promoting CRC proliferation. uc.285+ may have considerable potential as a new diagnostic biomarker for CRC.

Natural products and long noncoding RNA signatures in gallbladder cancer: a review focuses on pathogenesis, diagnosis, and drug resistance

Gallbladder cancer (GBC) is an aggressive and lethal malignancy with a poor prognosis. Long noncoding RNAs (lncRNAs) and natural products have emerged as key orchestrators of cancer pathogenesis through widespread dysregulation across GBC transcriptomes. Functional studies have revealed that lncRNAs interact with oncoproteins and tumor suppressors to control proliferation, invasion, metastasis, angiogenesis, stemness, and drug resistance. Curcumin, baicalein, oleanolic acid, shikonin, oxymatrine, arctigenin, liensinine, fangchinoline, and dioscin are a few examples of natural compounds that have demonstrated promising anticancer activities against GBC through the regulation of important signaling pathways. The lncRNAs, i.e., SNHG6, Linc00261, GALM, OIP5-AS1, FOXD2-AS1, MINCR, DGCR5, MEG3, GATA6-AS, TUG1, and DILC, are key players in regulating the aforementioned processes. For example, the lncRNAs FOXD2-AS1, DILC, and HOTAIR activate oncogenes such as DNMT1, Wnt/β-catenin, BMI1, and c-Myc, whereas MEG3 and GATA6-AS suppress the tumor proteins NF-κB, EZH2, and miR-421. Clinically, specific lncRNAs can serve as diagnostic or prognostic biomarkers based on overexpression correlating with advanced TNM stage, metastasis, chemoresistance, and poor survival. Therapeutically, targeting aberrant lncRNAs with siRNA or antisense oligos disrupts their oncogenic signaling and inhibits GBC progression. Overall, dysfunctional lncRNA regulatory circuits offer multiple avenues for precision medicine approaches to improve early GBC detection and overcome this deadly cancer. They have the potential to serve as novel biomarkers as they are detectable in bodily fluids and tissues. These findings enhance gallbladder treatments, mitigating resistance to chemo- and radiotherapy.

LncRNA BCYRN1 as a Potential Therapeutic Target and Diagnostic Marker in Serum Exosomes in Bladder Cancer

Bladder cancer (BC) is a common genitourinary malignancy that exhibits silent morbidity and high mortality rates because of a lack of diagnostic markers and limited effective treatments. Here, we evaluated the role of the lncRNA brain cytoplasmic RNA 1 (BCYRN1) in BC. We performed loss-of-function assays to examine the effects of BCYRN1 downregulation in T24 and BOY BC cells. We found that BCYRN1 downregulation significantly inhibited the proliferation, migration, invasion, and three-dimensional spheroid formation ability and induced apoptosis in BC cells. Additionally, gene set enrichment analysis (GSEA) using RNA sequences from tumor fractions showed that BCYRN1 downregulation decreased the expression of mRNAs associated with the cell cycle. These findings were supported by observations of G2/M arrest in flow cytometry assays. Finally, we examined the expression of serum exosomal BCYRN1 as a biomarker. Clinically, BCYRN1 expression in serum exosomes from patients with BC (n = 31) was significantly higher than that in healthy donors (n = 19; mean difference: 4.1-fold higher, p < 0.01). Moreover, in patients who had undergone complete resection of BC, serum exosomal BCYRN1 levels were significantly decreased (n = 8). Thus, serum exosomal BCYRN1 may be a promising diagnostic marker and therapeutic target in patients with BC.

Impact of RRP1B Variants on the Phenotype, Progression, and Metastasis of Cervical Cancer

Metastasis is a key determinant of cancer progression, influenced significantly by genetic mechanisms. RRP1B, primarily a nucleolar protein, emerges as a suppressor of metastasis, forming alliances with various cellular components and modulating gene expression. This study investigates the involvement of the ribosomal RNA processing 1 homolog B (RRP1B) gene in metastasis regulation in cervical cancer. Through a comprehensive analysis of 172 cervical cancer patients, we evaluated five RRP1B single nucleotide polymorphisms (SNPs) (rs2838342, rs7276633, rs2051407, rs9306160, and rs762400) for their associations with clinicopathological features and survival outcomes. Significant associations were observed between specific genetic variants and clinicopathological parameters. Notably, the A allele of rs2838342 was associated with reduced odds of advanced tumor size, worse prognosis, and, preliminarily, distant metastasis, while the T allele of rs7276633 correlated with a decreased risk of higher tumor size and worse prognosis. Additionally, the C allele of rs2051407 demonstrated protective effects against larger tumors, metastasis, and adverse prognosis. The rs9306160 C allele exhibited a protective effect against metastasis. The rs762400 G allele was significant for reduced tumor size and metastasis risk. Furthermore, the rs2838342 A allele, rs7276633 T allele, rs2051407 C allele, and rs762400 G allele were associated with improved overall survival, demonstrating their potential significance in predicting prognoses in cervical cancer. Linkage disequilibrium and haplotypes analysis enabled us to evaluate the collective effect of the analyzed SNPs, which was in line with the results of allelic models. Our findings underscore the clinical relevance of RRP1B SNPs as prognostic markers in cervical cancer, shedding light on the intricate interplay between genetic factors and disease-progression dynamics. This research provides critical insights for future investigations and underscores the importance of incorporating RRP1B SNP detection into prognostic-assessment tools for accurate prediction of disease outcomes in cervical cancer.

LncRNA PVT1: as a therapeutic target for breast cancer

A significant number of women are identified with breast cancer (BC) every year, making it among the most prevalent malignancies and one of the leading causes of mortality globally. Despite significant progress in understanding BC pathogenesis and treatment options, there is still a need to identify new therapeutic targets and develop more effective treatments. LncRNAs have been discovered as biomarkers and a promising target for various cancers, including BC. PVT1 is a particular one of these lncRNAs, and research has indicated that it has a significant impact on the appearance and progression of BC.PVT1 is an attractive therapeutic target for BC due to its role in promoting cancer cell growth, metastasis and invasion. In addition to its potential as a treatment strategy, PVT1 may also have diagnostic value in BC. In this article, we will discuss targeting PVT1 as a treatment strategy for BC.

Long non-coding RNAs and gastric cancer: An update of potential biomarkers and therapeutic applications

The frequent metastasis of gastric cancer (GC) complicates the cure and therefore the development of effective diagnostic and therapeutic approaches is urgently necessary. In recent years, lncRNA has emerged as a drug target in the treatment of GC, particularly in the areas of cancer immunity, cancer metabolism, and cancer metastasis. This has led to the demonstration of the importance of these RNAs as prognostic, diagnostic and therapeutic agents. In this review, we provide an overview of the biological activities of lncRNAs in GC development and update the latest pathological activities, prognostic and diagnostic strategies, and therapeutic options for GC-related lncRNAs.

Transforming Diagnosis and Therapeutics Using Cancer Genomics

In past quarter of the century, much has been understood about the genetic variation and abnormal genes that activate cancer in humans. All the cancers somehow possess alterations in the DNA sequence of cancer cell's genome. In present, we are heading toward the era where it is possible to obtain complete genome of the cancer cells for their better diagnosis, categorization and to explore treatment options.

Design the RNA aptamer of PCA3 long non-coding ribonucleic acid by the coarse-grained molecular mechanics

The stochastic tunneling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to predict the tertiary structure of the prostate cancer marker PCA3 using two respective secondary structures predicted by the Vienna RNA package and Mathews lab package. The RNA CG force field with the geometrical restraints for maintaining PCA3 secondary structures is used. For each secondary structure, 5000 PCA3 structures were predicted by using 5000 independent initial structures. These structures were then evaluated by a scoring function, considering the contributions from the radius of gyration, contact energy, and surface fraction of complementary nucleotides to ASO683 and ASO735 used in the related experiment. For each secondary structure, the PCA3 structures with the highest three scores were selected for aptamer design and further adsorption simulation. The ASOs complementary to PCA3 surface segments possessing relatively higher RMSF values are selected to be the potential PCA3 aptamers. After the adsorption simulation, the adsorption energies of ASO961, ASO3181, ASO3533, and ASO3595 are higher than or comparable to those of ASO683 and ASO735 used in the experiment. The NEB method was used to obtain MEPs for the adsorption process of all predicted ASOs onto PCA3. The adsorption barriers range between 29 ∼ 39 kcal/mol, while the desorption barriers range between 112 ∼ 352 kcal/mol, indicating these aptamer/PCA3 complexes are very stable. Using PCA3 surface segments with relatively higher RMSF values, longer ASOs can be also obtained and most longer ASOs possess lower binding energy, ranging between -486.1 and -618.2 kcal/mol.Communicated by Ramaswamy H. Sarma.

MARCKSL1-2 reverses docetaxel-resistance of lung adenocarcinoma cells by recruiting SUZ12 to suppress HDAC1 and elevate miR-200b

Background

Long non-coding RNAs (lncRNAs) are implicated in the development of multiple cancers. In our previous study, we demonstrated that HDAC1/4-mediated silencing of microRNA-200b (miR-200b) enhances docetaxel (DTX)-resistance of human lung adenocarcinoma (LAD) cells.

Methods and results

Herein, we probed the function of LncRNA MARCKSL1–2 (MARCKSL1-transcript variant 2, NR_052852.1) in DTX resistance of LAD cells. It was found that MARCKSL1–2 expression was markedly reduced in DTX-resistant LAD cells. Through gain- or loss- of function assays, colony formation assay, EdU assay, TUNEL assay, and flow cytometry analysis, we found that MARCKSL1–2 suppressed the growth and DTX resistance of both parental and DTX-resistant LAD cells. Moreover, we found that MARCKSL1–2 functioned in LAD through increasing miR-200b expression and repressing HDAC1. Mechanistically, MARCKSL1–2 recruited the suppressor of zeste 12 (SUZ12) to the promoter of histone deacetylase 1 (HDAC1) to strengthen histone H3 lysine 27 trimethylation (H3K27me3) of HDAC1 promoter, thereby reducing HDAC1 expression. MARCKSL1–2 up-regulated miR-200b by blocking the suppressive effect of HDAC1 on the histone acetylation modification at miR-200b promoter. Furthermore, in vivo analysis using mouse xenograft tumor model supported that overexpression of MARCKSL1–2 attenuated the DTX resistance in LAD tumors.

Conclusions

We confirmed that MARCKSL1–2 alleviated DTX resistance in LAD cells by abolishing the inhibitory effect of HDAC1 on miR-200b via the recruitment of SUZ12. MARCKSL1–2 could be a promising target to improve the chemotherapy of LAD.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12943-022-01605-w.

Identification of Immune-Related lncRNA Pairs and Construction and Validation of a New Prognostic Signature of Colon Cancer

BACKGROUND

More and more evidence has shown that immune-related long noncoding ribonucleic acid (irlncRNAs) is a potential prognostic factor for colon cancer. The relevant gene pair pattern can improve the sensitivity of the prognostic model. Therefore, our present study aimed to identify irlncRNA Pairs and construct and validate a new prognostic signature in colon cancer.

METHODS

We downloaded the expression matrix of mRNA and lncRNA of patients with colon cancer and their clinical information from the public TCGA database. We obtained immune genes from the ImmPort database. Coexpression analysis was performed to identify irlncRNAs. We built an irlncRNA pair matrix by comparing the expression levels of each lncRNA pair in a cycle. Univariate Cox regression analysis, LASSO penalized regression analysis, and multivariate Cox regression analysis were performed to determine the final variables to construct the prognostic risk score model (a new signature). We draw the receiver operating characteristic (ROC) curves of the signature and clinical characteristics and determine the optimal cutoff value by the optimal Akaike Information Criterion (AIC) value. Based on the optimal cutoff value of the ROC curve of the signature, colon cancer patients were divided into the high- and low-risk groups. Then, the signature was evaluated by clinicopathological features, tumor-infiltrating immune cells, checkpoint-related biomarkers, targeted therapy, and chemotherapy.

RESULTS

We identified 8 lncRNA pairs including AC103740.1|LEF1-AS1, LINC02391|AC053503.5, WWC2-AS2|AL355916.2, AC104090.1|NEURL1-AS1, AC099524.1|AL161908.1, AC074011.1|AL078601.2, AL355916.2|LINC01723, and AP003392.4|LINC00598 from 71 differently expressed irlncRNAs. We constructed a prognostic risk score model (a new signature) using these optimal eight irlncRNA pairs. ROC curve analysis revealed that the highest AUC value of the signature was 0.776 at 1 year, with the optimal cutoff value of 1.283. Our present study also showed that the constructed signature could accurately identify adverse survival outcomes, prognostic clinicopathological features, and specify tumor invasion status. The expression of immune checkpoint-related genes and chemical drug sensitivity were related to different risk groups.

CONCLUSION

In our present study, we constructed a new irlncRNA signature of colon cancer based on the irlncRNA pairs instead of the special expression level of lncRNA. We found this signature had not only good prognostic value but also certain clinical value, which might provide a new insight into the treatment and prognosis of colon cancer.

LncRNA DRAIR is a novel prognostic and diagnostic biomarker for gastric cancer

LncRNA diabetes regulated anti-inflammatory RNA (DRAIR) has been reported to be involved in diabetes-induced injury. However, its role in other human diseases is unclear. Our preliminary sequencing analysis showed its expression was altered in gastric cancer (GC). Thus, this study aimed to explore its diagnostic and prognostic values in GC. DRAIR expression in paired tumor and non-tumor tissues and plasma of GC patients and control samples was determined by RT-qPCR. The diagnostic value of DRAIR for early-stage GC was analyzed using ROC curve analysis. The prognostic value of DRAIR was explored by performing a follow-up (5-year) study. DRAIR expression was downregulated in GC tissues than in non-tumor tissues and in plasma of GC patients than in plasma of healthy controls. DRAIR expression in tumor tissues was closely and positively correlated with its expression in plasma. Plasma DRAIR effectively separated GC patients from controls. High DRAIR levels in tumor tissues and plasma samples were closely correlated with poor survival of GC patients. DRAIR is overexpressed in GC and may serve as an early diagnostic and prognostic biomarker for GC.

Long noncoding RNAs as diagnostic biomarkers for the early detection of digestive tract cancers: a systematic review and meta-analysis

BACKGROUND

long noncoding RNAs (lncRNAs) have attracted attention recently. However, many inconsistencies frequently appeared for the early diagnosis of digestive tract cancers (DTCs). We performed this meta-analysis to describe the diagnostic performance of lncRNAs in the discrimination of DTCs.

METHODS

data were extracted from PubMed, Web of Science, Embase, and Cochrane Library. Their quality was evaluated using the revised Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2). Such parameters as sensitivity and specificity were included for pooled analyses. The STATA 12.0 and Meta-Disc 1.4 software packages were used to perform the statistical analysis.

RESULTS

sixty-nine papers were included in this meta-analysis. The pooled analysis of DTCs showed that lncRNAs had a sensitivity of 0.78 and a specificity of 0.80. The area under the summary ROC curve (AUC) was 0.86. For gastric cancer (GC), the pooled sensitivity and specificity were 0.77 (95 % CI: 0.72-0.81) and 0.75 (95 % CI: 0.71-0.79), respectively, and the AUC was 0.83. For colorectal cancer (CRC), these three parameters were 0.82 (95 % CI: 0.76-0.86), 0.84 (95 % CI: 0.79-0.88), and 0.90, respectively. For esophageal cancer (EC) sensitivity was 0.74 (95 % CI: 0.67-0.80) and specificity reached 0.86 (95 % CI: 0.72-0.93), with an AUC of 0.82.

CONCLUSIONS

LncRNAs show potential diagnostic value for discrimination between DTCs.

X-Inactive-Specific Transcript: Review of Its Functions in the Carcinogenesis

X-inactive-specific transcript (XIST) is one of the firstly discovered long non-coding RNAs with prominent roles in the process of X inactivation. Moreover, this transcript contributes in the carcinogenic process in different tissues. In addition to interacting with chromatin modifying molecules, XIST can be served as a molecular sponge for miRNAs to modulate expression of miRNA targets. Most of the studies have indicated an oncogenic role for XIST. However, in prostate cancer, a single study has indicated a tumor suppressor role for this lncRNA. Similar result has been reported for XIST in oral squamous cell carcinoma. In hepatocellular carcinoma, breast cancer, ovarian cancer, osteosarcoma, and renal cell carcinoma, different studies have reported inconsistent results. In the present manuscript, we review function of XIST in the carcinogenesis.

Circulating long noncoding RNAs as potential biomarkers for stomach cancer: a systematic review and meta-analysis

Background

Recent researches have suggested that long noncoding RNA (lncRNA) is involved in the tumorigenesis and development of stomach cancer (SC). This meta-analysis aimed to identify the diagnostic performance of circulating lncRNAs in SC.

Methods

All relevant studies were systematically searched through PubMed, Web of Science, Cochrane Library, and EMBASE databases. The diagnostic values of lncRNAs were mainly assessed by pooled sensitivity, specificity, and summary receiver operating characteristic area under the curve (SROC AUC). Meta-DiSc 1.4, Review Manager 5.3, and STATA 12.0 were used for statistical analysis. The protocol for this systematic review was registered on INPLASY (INPLASY202120079) and is available in full on the inplasy.com (10.37766/inplasy2021.2.0079).

Results

A total of 42 eligible studies were included in this meta-analysis. The pooled sensitivity, specificity, and SROC AUC were 0.78 (95%CI 0.75–0.81), 0.75 (95%CI 0.71–0.78), and 0.83 (95%CI 0.80–0.86), respectively, suggesting that the lncRNAs test had a high accuracy for the diagnosis of SC. Obvious heterogeneity might come from the type of lncRNA through subgroup and meta-regression analysis. Fagan diagram shows the clinical value of lncRNAs test in SC.

Conclusions

Abnormal expression of circulating lncRNAs exhibits a high efficacy for diagnosing SC, which is promising in clinical application.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12957-021-02194-6.

Current Achievements and Applications of Transcriptomics in Personalized Cancer Medicine

Over the last decades, transcriptome profiling emerged as one of the most powerful approaches in oncology, providing prognostic and predictive utility for cancer management. The development of novel technologies, such as revolutionary next-generation sequencing, enables the identification of cancer biomarkers, gene signatures, and their aberrant expression affecting oncogenesis, as well as the discovery of molecular targets for anticancer therapies. Transcriptomics contribute to a change in the holistic understanding of cancer, from histopathological and organic to molecular classifications, opening a more personalized perspective for tumor diagnostics and therapy. The further advancement on transcriptome profiling may allow standardization and cost reduction of its analysis, which will be the next step for transcriptomics to become a canon of contemporary cancer medicine.

Association study between KCNQ1 and KCNQ1OT1 genetic polymorphisms and gastric cancer susceptibility and survival in a Chinese Han population: a case-control study

Background

The present study analyzed gene polymorphisms in the potassium voltage-gated channel KQT-like subfamily member 1 (KCNQ1) and the long noncoding RNA, KCNQ1OT1, and their impacts on genetic susceptibility and survival in a Chinese Han population with gastric cancer (GC).

Methods

We designed a case-control study that included 681 patients with GC and 756 healthy controls. Three single-nucleotide polymorphisms (SNPs) in the KCNQ1 gene region and eight SNPs in the KCNQ1OT1 gene region were selected for further research.

Results

Among the 11 SNPs, we found no significant differences in the genotype and allele frequencies between GC patients and the healthy population. Hierarchical analysis by the log-additive model indicated that the KCNQ1 rs231348 CT genotype was significantly associated with an increased GC risk in individuals aged ≥55 years, regardless of gender. The KCNQ1OT1 rs231352 CC and rs7128926 AA genotypes increased the risk of GC in individuals with stage III/IV tumors larger than 5 cm in diameter. On evaluating the genotype polymorphism and survival analysis, we detected that the AA genotypes of the KCNQ1OT1 rs7128926 and rs7939976 polymorphisms presented a significant survival advantage over the GA/GG genotypes, especially in patients with the following characteristics: age >55, Helicobacter pylori infection, BMI >24, tumor in the non-cardia region with a diameter greater than 5 cm, clinical stage II, and postoperative adjuvant chemotherapy.

Conclusions

Our results suggest that the KCNQ1 rs231348 and KCNQ1OT1 rs231352 polymorphisms might be independent predictors of the risk of GC susceptibility depending on certain factors, such as the age of the individual and the tumor stage and diameter. Simultaneously, genotype polymorphism of the rs7128926 and rs7939976 loci of the KCNQ1OT1 gene independently predicted the recurrence-free survival (RFS) and overall survival (OS) of GC patients.

Exosomal lncRNA HEIH promotes cisplatin resistance in tongue squamous cell carcinoma via targeting miR-3619-5p/HDGF axis

BACKGROUND

Accumulating evidence has suggested that long noncoding RNAs (lncRNAs) are involved in the progression of types of human cancers. It has been known that exosomes can mediate cell-cell crosstalk by transferring lncRNAs in tumor progression. This study aimed to investigate the role of exosomal lncRNA HEIH on cisplatin (DDP) resistance in tongue squamous cell carcinoma (TSCC).

METHODS

The expression of HEIH in human oral keratinocytes cell line (HOK), DDP-sensitive TSCC cell line (SCC4/S) and DDP-resistant TSCC cell line (SCC4/DDP) was measured. SCC4/S and SCC4/DDP cells were transfected with sh-HEIH to examine TSCC cell proliferation and apoptosis. The DDP-resistant exosomes were extracted and identified. The expression of miR‑3619-5p and TDGF in DDP-sensitive recipient cells was determined. The binding capacity between HEIH and miR‑3619-5p, along with miR‑3619-5p and TDGF was verified.

RESULTS

HEIH expression was significantly upregulated in SCC4/DDP cells. Downregulation of HEIH inhibited DDP resistance and cell proliferation and promoted cell apoptosis. HEIH acted as a competing endogenous RNA (ceRNA) for miR‑3619-5p to upregulate HDGF expression. Exosomal HEIH promoted cell proliferation and drug resistance and inhibited cell apoptosis by sponging miR‑3169-5p and upregulating HDGF.

CONCLUSION

Exosomal HEIH acted as a ceRNA for miR‑3619-5p to upregulate HDGF, thereby promoting DDP resistance in TSCC cells.

BCYRN1 is correlated with progression and prognosis in gastric cancer

Long non-coding RNA brain cytoplasmic RNA 1 (BCYRN1) has been found to play an important role in tumorigenesis of a variety of tumors including gastric cancer (GC). However, the prognostic significance and molecular mechanism of BCYRN1 was still unknown in GC. In the present study, we found BCYRN1 expression was dramatically elevated in GC tissues and cell lines, and positively associated with tumor depth, lymph node metastasis and clinical stage in patients with GC. Moreover, univariate and multivariate Cox regression analyses demonstrated that high BCYRN1 expression was independent prognostic factor for overall survival in GC patients. In lncRNA-microRNA interactome database, we found that there were putative binding sites between BCYRN1 and miR-204-5p. Furthermore, we confirmed that down-regulation of BCYRN1 inhibited GC cell proliferation, migration and invasion through directly up-regulated miR-204-5p expression. In conclusion, BCYRN1 acts as a promising prognostic predictor in GC patients and regulated GC cell proliferation, cell cycle, migration and invasion through targeting miR-204-5p.

Evaluation of C5orf66-AS1 as a Potential Biomarker for Predicting Early Gastric Cancer and Its Role in Gastric Carcinogenesis

Background

Long non-coding RNAs (lncRNAs) participate in a series of pathological processes in tumorigenesis. Reports show that C5orf66-AS1, an antisense lncRNA, is expressed in various tumors. However, the role of C5orf66-AS1 in gastric cancer (GC) has not been fully clarified. The study focused on the expression patterns and serum level of C5orf66-AS1 in GC to explore its potential application in GC screening and diagnosis. The effects of C5orf66-AS1 on GC cells were also analyzed.

Methods

Tissue and serum samples were used for RNA isolation. Expression levels of C5orf66-AS1 in GC tissues, serum, and cell lines were detected using quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR). CCK-8, transwell, and wound healing assays were performed to determine the effects of C5orf66-AS1 on GC cell behavior.

Results

C5orf66-AS1 expression was downregulated in GC cells compared to that in adjacent normal tissues. Serum C5orf66-AS1 levels were significantly lower in GC patients than in superficial gastritis (GS) and atrophic gastritis (GA) patients. Low serum expression of C5orf66-AS1 was associated with an increased risk of gastric dysplasia (GD) and GC. Receiver operating characteristic curve results showed that the area under curve (AUC) for GC was 0.688, with a sensitivity and specificity of 77.5% and 53.6%, respectively. For the GD + early gastric cancer (ECG) group, the AUC was 0.789, with a sensitivity and specificity of 85.15% and 62.86%, respectively. Correlation analyses of clinicopathological parameters showed that serum C5orf66-AS1 was predominantly associated with Lauren type, TNM stages, pTNM stages, and vessel tumor emboli. Additionally, in vitro overexpression of C5orf66-AS1 in AGS cells inhibited cell proliferation, migration, and invasion.

Conclusion

Decreased expression levels of serum C5orf66-AS1 can be utilized for diagnosis of GC, especially for early diagnosis. The low level of serum C5orf66-AS1 indicated poor biological behavior of tumors in GC patients. In addition, C5orf66-AS1 can inhibit GC cell proliferation, migration, and invasion.

Risk factors of tumor invasion and node metastasis in early gastric cancer with undifferentiated component: a multicenter retrospective study on biopsy specimens and clinical data

Background

Early gastric cancer (EGC) with undifferentiated component (UDC) is a more aggressive entity, where the significance of preoperative data to tumor invasion and lymph node metastasis (LNM) remains unclarified.

Methods

A total of 5,020 GC patients undergoing radical gastrectomy in three centers were reviewed, of which, EGC with UDC in preoperative biopsy specimens were enrolled. The histology of biopsy and surgical specimens was graded according to the proportion of UDC and signet ring cells (SRCs). Risk factors of tumor invasion and LNM were evaluated with histological, clinical and demographic data.

Results

Lower body mass index (BMI), melena and larger tumor size were the independent preoperative risk factors of both LNM and LVI, while ulcerative lesion (UL) and the lower third stomach were only correlated with LNM. No relevance was found between the histological features of biopsy specimens and LNM, but SRC or >50% UDC lowered the risk of lymphovascular invasion (LVI) and/or submucosal (SM) invasion. When surgical data (depth of invasion and LVI included) were added, lower BMI, melena and the lower third stomach were still the independent preoperative risk factors of LNM, and LVI, SRC and SM invasion also showed relevance to LNM. The performance of predictive models using pre- or postoperative histological data was comparable.

Conclusions

The preoperative data were significantly relevant to tumor invasion and LNM, showing comparable risk strength with surgical specimens in histology.

SNHG17 enhances the malignant characteristics of tongue squamous cell carcinoma by acting as a competing endogenous RNA on microRNA-876 and thereby increasing specificity protein 1 expression

A long noncoding RNA called SNHG17 (small nucleolar RNA host gene 17) is aberrantly expressed and plays essential roles in multiple human cancer types. Nevertheless, its expression pattern and specific functions in tongue squamous cell carcinoma (TSCC) have not been well studied until now. Hence, in this study, we aimed to measure SNHG17 expression in TSCC and to examine the actions of SNHG17 on the malignant characteristics of TSCC cells. The regulatory mechanism that mediates the oncogenic effects of SNHG17 on TSCC cells was investigated too. In this study, SNHG17 was found to be upregulated in TSCC, and this overexpression closely correlated with adverse clinical parameters and shorter overall survival among the patients with TSCC. The SNHG17 knockdown significantly decreased TSCC cell proliferation, migration, and invasion in vitro and tumor growth in vivo. Mechanism investigation revealed that SNHG17 acts as a competing endogenous RNA on microRNA-876 (miR-876) in TSCC cells. In addition, specificity protein 1 (SP1) was validated as a direct target gene of miR-876 in TSCC cells. SP1 expression restoration in TSCC cells reversed miR-876 overexpression-induced anticancer effects. MiR-876 downregulation strongly attenuated the actions of the SNHG17 knockdown in TSCC cells. SNHG17 plays an oncogenic part in TSCC cells both in vitro and in vivo via sponging of miR-876 and thereby upregulating SP1, which could be regarded as a promising target for TSCC therapy.

Construction of a prognosis‑associated long noncoding RNA‑mRNA network for multiple myeloma based on microarray and bioinformatics analysis

At present, the association between prognosis-associated long noncoding RNAs (lncRNAs) and mRNAs is yet to be reported in multiple myeloma (MM). The aim of the present study was to construct prognostic models with lncRNAs and mRNAs, and to map the interactions between these lncRNAs and mRNAs in MM. LncRNA and mRNA data from 559 patients with MM were acquired from the Genome Expression Omnibus (dataset GSE24080), and their prognostic values were calculated using the survival package in R. Multivariate Cox analysis was used on the top 20 most significant prognosis-associated mRNAs and lncRNAs to develop prognostic signatures. The performances of these prognostic signatures were tested using the survivalROC package in R, which allows for time-dependent receiver operator characteristic (ROC) curve estimation. Weighted correlation network analysis (WGCNA) was conducted to investigate the associations between lncRNAs and mRNAs, and a lncRNA-mRNA network was constructed using Cytoscape software. Univariate Cox regression analysis identified 39 lncRNAs and 1,445 mRNAs that were significantly associated with event-free survival of MM patients. The top 20 most significant survival-associated lncRNAs and mRNAs were selected as candidates for analyzing independent MM prognostic factors. Both signatures could be used to separate patients into two groups with distinct outcomes. The areas under the ROC curves were 0.739 for the lncRNA signature and 0.732 for the mRNA signature. In the lncRNA-mRNA network, a total of 143 mRNAs were positively or negatively associated with 23 prognosis-associated lncRNAs. NCRNA00201, LOC115110 and RP5-968J1.1 were the most dominant drivers. The present study constructed a model that predicted prognosis in MM and formed a network with the corresponding prognosis-associated mRNAs, providing a novel perspective for the clinical diagnosis and treatment of MM, and suggesting novel directions for interpreting the mechanisms underlying the development of MM.

Regulatory Mechanisms and Clinical Applications of the Long Non-coding RNA PVT1 in Cancer Treatment

Cancer is the second leading cause of death worldwide, and no obvious decline in incidence and mortality has occurred in recent years. It is imperative to further investigate the mechanisms underlying tumor progression. Long non-coding RNAs have received considerable attention in recent years because of their major regulatory roles in gene expression. Among them, PVT1 is well-studied, and substantial evidence indicates that PVT1 plays critical roles in the onset and development of cancers. Normally, PVT1 acts as an oncogenic factor by promoting cancer cell proliferation, invasion, metastasis, and drug resistance. Herein, we summarize current knowledge regarding the regulatory effects of PVT1 in cancer progression, as well as the related underlying mechanisms, such as interaction with Myc, modulation of miRNAs, and regulation of gene transcription and protein expression. In extracellular fluid, PVT1 mainly promotes cancer initiation, and it normally enhances cellular cancer characteristics in the cytoplasm and cell nucleus. Regarding clinical applications, its role in drug resistance and its potential use as a diagnostic and prognostic marker have received increasing attention. We hope that this review will contribute to a better understanding of the regulatory role of PVT1 in cancer progression, paving the way for the development of PVT1-based therapeutic approaches in cancer treatment.

Noncoding RNAs in Extracellular Fluids as Cancer Biomarkers: The New Frontier of Liquid Biopsies

The last two decades of cancer research have been devoted in two directions: (1) understanding the mechanism of carcinogenesis for an effective treatment, and (2) improving cancer prevention and screening for early detection of the disease. This last aspect has been developed, especially for certain types of cancers, thanks also to the introduction of new concepts such as liquid biopsies and precision medicine. In this context, there is a growing interest in the application of alternative and noninvasive methodologies to search for cancer biomarkers. The new frontiers of the research lead to a search for RNA molecules circulating in body fluids. Searching for biomarkers in extracellular body fluids represents a better option for patients because they are easier to access, less painful, and potentially more economical. Moreover, the possibility for these types of samples to be taken repeatedly, allows a better monitoring of the disease progression or treatment efficacy for a better intervention and dynamic treatment of the patient, which is the fundamental basis of personalized medicine. RNA molecules, freely circulating in body fluids or packed in microvesicles, have all the characteristics of the ideal biomarkers owing to their high stability under storage and handling conditions and being able to be sampled several times for monitoring. Moreover, as demonstrated for many cancers, their plasma/serum levels mirror those in the primary tumor. There are a large variety of RNA species noncoding for proteins that could be used as cancer biomarkers in liquid biopsies. Among them, the most studied are microRNAs, but recently the attention of the researcher has been also directed towards Piwi-interacting RNAs, circular RNAs, and other small noncoding RNAs. Another class of RNA species, the long noncoding RNAs, is larger than microRNAs and represents a very versatile and promising group of molecules which, apart from their use as biomarkers, have also a possible therapeutic role. In this review, we will give an overview of the most common noncoding RNA species detectable in extracellular fluids and will provide an update concerning the situation of the research on these molecules as cancer biomarkers.

Long non-coding RNA NKILA serves as a biomarker in the early diagnosis and prognosis of patients with colorectal cancer

Colorectal cancer (CRC) is one of the leading causes of cancer-associated mortality worldwide. The prognosis of patients with CRC at an advanced stage is poor. Biomarkers currently used in clinical practice, including carcinoembryonic antigen (CEA) and cancer antigen (CA) 19-9, lack sufficient sensitivity and specificity for early diagnosis and prediction, therefore there remains a requirement to improve the prognosis of patients with CRC. Long non-coding RNAs (lncRNAs) have been revealed to serve fundamental roles in various pathophysiological processes, including cancer initiation and progression. The present study investigated the expression and clinical significance of the lncRNA nuclear factor-κB interacting long non-coding RNA (NKILA) in CRC. It was identified that NKILA was downregulated in six CRC cell lines and tissues (n=173). Low NKILA expression was significantly associated with a poor differentiation grade, larger tumor size and advanced Tumor-Node-Metastases stages. Further statistical analyses revealed that low NKILA expression predicted poor overall survival (OS) rate and progression-free survival (PFS) rate. In addition, low NKILA expression was determined as an independent risk factor for poor OS and PFS. Furthermore, NKILA exhibited a relatively high sensitivity and specificity compared with CEA and CA19-9 in the early diagnosis of CRC. The serum level of NKILA was positively correlated with the level in tissues. In addition, a decreased NKILA level in serum was revealed to be partially restored post-operatively. In conclusion, low NKILA expression has been demonstrated to accelerate CRC progression and NKILA may be a potential novel biomarker in early diagnosis and prognosis of patients with CRC.

Multiple Linear Regression Analysis of lncRNA-Disease Association Prediction Based on Clinical Prognosis Data

Long noncoding RNAs (lncRNAs) have an important role in various life processes of the body, especially cancer. The analysis of disease prognosis is ignored in current prediction on lncRNA-disease associations. In this study, a multiple linear regression model was constructed for lncRNA-disease association prediction based on clinical prognosis data (MlrLDAcp), which integrated the cancer data of clinical prognosis and the expression quantity of lncRNA transcript. MlrLDAcp could realize not only cancer survival prediction but also lncRNA-disease association prediction. Ultimately, 60 lncRNAs most closely related to prostate cancer survival were selected from 481 alternative lncRNAs. Then, the multiple linear regression relationship between the prognosis survival of 176 patients with prostate cancer and 60 lncRNAs was also given. Compared with previous studies, MlrLDAcp had a predominant survival predictive ability and could effectively predict lncRNA-disease associations. MlrLDAcp had an area under the curve (AUC) value of 0.875 for survival prediction and an AUC value of 0.872 for lncRNA-disease association prediction. It could be an effective biological method for biomedical research.

LncRNA HOXA11-AS drives cisplatin resistance of human LUAD cells via modulating miR-454-3p/Stat3

Over the past several years, long non‐coding RNAs (lncRNAs) have attracted more and more attention due to their special functions. They are vital biomarkers in multiple diseases. LncRNA HOMEOBOX A11 (HOXA11) has been found to be aberrantly expressed in some kinds of malignant tumors. In this study, we mainly discuss the oncogenic role of it in promoting malignant progression and chemoresistance in lung adenocarcinoma (LUAD) cells. The expression of HOXA11‐AS was much stronger in cisplatin‐resistant LUAD cells. Based on The Cancer Genome Atlas database, patients with high expression of HOXA11‐AS had shorter survival time. Additionally, knockdown of HOXA11‐AS caused positive changes in cell activities of LUAD. For example, cell proliferation and migration were weakened, the epithelial mesenchymal transition process was reversed, and apoptosis was induced. These changes were more obvious in cells treated with cisplatin. Next, the HOXA11‐AS/miR‐454‐3p/Stat3 (signal transducer and activator of transcription 3) pathway was found to influence the cisplatin resistance of LUAD cells. HOXA11‐AS specifically acted as a competing endogenous RNA (ceRNA) in LUAD cells. The combinations among these three genes were demonstrated. Finally, rescue assays were applied to demonstrate the ceRNA pattern consisting of HOXA11‐AS, miR‐454‐3p and Stat3. In conclusion, lncRNA HOXA11‐AS acted as a ceRNA to promote cisplatin resistance of human LUAD cells via the miR‐454‐3p/Stat3 axis.

X-inactive-specific transcript: A long noncoding RNA with complex roles in human cancers

The X-inactive-specific transcript (XIST/Xist) is one of the first long non-coding RNAs discovered in mammals and plays an essential role in X chromosome inactivation. XIST is dysregulated and acts as an oncogene or a tumor suppressor in different human malignancies. XIST is implicated in many aspects of carcinogenesis including tumor initiation, invasion, metastasis, apoptosis, cell cycle, stemness, autophagy, and drug resistance. This review focuses on research progress on the roles of XIST in tumor development. The multiple pathological functions of XIST in various cancers are systematically reviewed to elucidate the molecular basis of its biological roles and to provide new directions for future research.