Long noncoding RNAs in cancer: From discovery to therapeutic targets

LncRNA HOXA‑AS2 is a prognostic and clinicopathological predictor in patients with cancer: A meta‑analysis

Elevated expression of long non-coding RNA homeobox A cluster antisense RNA 2 (lncRNA HOXA-AS2) is known to have prognostic value in various solid tumors. The present meta-analysis aimed to comprehensively quantify its prognostic significance across a wider spectrum of malignancies and to provide an updated synthesis of evidence that could refine prognostic models. To achieve this aim, multiple databases were carefully searched for lncRNA HOXA-AS2-related articles published in the past 10 years. Hazard ratios (HRs) or odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to demonstrate the prognostic value of lncRNA HOXA-AS2 using Stata 15.0 software. The function of lncRNA HOXA-AS2 was inferred from its associations with key clinical outcomes such as lymph node metastasis, distant metastasis, tumor stage and tumor size, which may reflect its role in tumor biology. In the present systematic review and meta-analysis of 454 patients across 7 studies, it was found that high lncRNA HOXA-AS2 expression was significantly associated with a shorter overall survival (OS) time in patients with cancer (HR=2.14; 95% CI, 1.40-3.27; P<0.001). High lncRNA HOXA-AS2 expression was also associated with lymph node metastasis [odds ratio (OR)=2.06; 95% CI, 1.07-3.99; P=0.032], distant metastasis (OR=2.11; 95% CI, 1.15-3.88; P=0.016), advanced tumor stage (OR=2.71; 95% CI, 1.50-4.89; P=0.001) and larger tumor size (OR=2.02; 95% CI, 0.86-4.78; P=0.006). However, no significant association was observed with age (OR=1.00; 95% CI, 0.63-1.59; P=0.991) or sex (OR=1.55; 95% CI, 0.72-3.34; P=0.258). In conclusion, elevated expression of lncRNA HOXA-AS2 was significantly related to poor clinical outcomes in various cancer types, such as osteosarcoma, non-small cell lung cancer and papillary thyroid carcinoma, a finding that was further confirmed by the present study. Specifically, the potential of lncRNAHOXA-AS2 as a biomarker in assessing tumor stage, metastasis risk and OS in patients was demonstrated. However, the results of the present study also indicated that the expression of lncRNA HOXA-AS2 was not significantly associated with age or sex, suggesting its role in cancer progression might be independent of these factors. This insight may direct future research to place more focus on the relationship between lncRNA HOXA-AS2 and specific cancer types and clinical characteristics.

LncRNA LOXL1-AS1 promotes proliferation and invasion and inhibits apoptosis in retinoblastoma by regulating the MAPK signaling pathway

Retinoblastoma (RB) is an intraocular malignancy that is most common in children and rare in adults. Addressing novel biomarkers and therapeutic targets for RB to modulate tumor progression has become a challenge. The aim of the present study was to investigate the function of long non-coding RNAs (LncRNAs) LOXL1-AS1 in RB cell proliferation and metastasis. It was found that LOXL1-AS1 was overexpressed in RB tissues and cells. In order to evaluate cell viability and colony formation potential, the knockdown of LOXL1-AS1 has been established. Knockdown of LOXL1-AS1 was also inhibited cells migration and invasion. In addition, the proportion of cells in the G2/M phase of the sh-LOXL1-AS1 group increased significantly, and the proportion of cells in the sh-NC group decreased significantly. In the xenograft model of RB, the tumors in the sh-LOXL1-AS1 group grow slowly compared to the sh-NC group. Western blot analysis revealed that LOXL1-AS1 can regulate the progression of RB cells through MAPK signaling pathway in vitro and in vivo. These results indicated that LncRNA LOXL1-AS1 promotes proliferation, invasion and inhibits apoptosis of retinoblastoma by regulating MAPK signaling pathway, and might be expected to be a novel basis for clinical diagnosis and treatment.

Possible role of lncRNAs in amelioration of Parkinson's disease symptoms by transplantation of dopaminergic cells

Long non-coding RNAs (lncRNAs) are biomarkers for diagnosis and treatment of Parkinson's disease (PD). Since dopaminergic cell transplantation is a clinical method to treat PD, this study investigated the effects of dopaminergic cell therapy on the expression of some lncRNAs and genes related to PD. In this study, Twenty-eight rats were randomly assigned to four experimental groups. The control group (Sal group) received saline injections. The Par group was a PD rat model with 6-hydroxydopamine (6-OHDA) injection in right striatum (ST). PD animals were transplanted by undifferentiated P19 stem cells (Par-E group), and P19-derived dopaminergic cells (Par-N group). Cell transplant effects were evaluated using behavioral tests (cylinder, open field, and rotarod tests), and histological methods (H&E and Nissl staining, and immunohistochemistry). Moreover, the expression of lncRNAs MALAT1, MEG3, and SNHG1, alongside specific neuronal (synaptophysin) and dopaminergic (tyrosine hydroxylase) markers was evaluated by qRT-PCR. Behavioral and histopathological examinations revealed that cell transplantation partially compensated dopaminergic cell degeneration in ST and substantia nigra (SN) of PD rats. The expression of MALAT1, SNHG1, and MEG3 was decreased in the ST of the Par group, while MEG3 and SNHG1 gene expression was increased in PBMC relative to the Sal group. In PBMC of the Par-N group, all three lncRNAs showed a reduction in their expression. Conversely, MALAT1 and SNHG1 expression was increased in ST tissue, while MEG3 gene expression was decreased compared to the Sal group. In conclusion, dopaminergic cell transplantation could change the lncRNAs expression. Furthermore, it partially improves symptoms in PD rats.

Deciphering the oncogenic landscape: Unveiling the molecular machinery and clinical significance of LncRNA TMPO-AS1 in human cancers

The in-depth exploration of long non-coding RNAs (lncRNAs) reveals their pivotal and diverse roles in various disorders, particularly cancer. Within this intricate landscape, thymopoietin-antisense RNA-1 (TMPO-AS1) emerges as a noteworthy instigator of oncogenesis in humans. This exhaustive review seeks to intricately unravel the present understanding of TMPO-AS1, emphasizing its molecular foundations and highlighting its clinical applications in the realm of cancer research. TMPO-AS1 consistently exhibits heightened expression across a spectrum of cancer types, encompassing lung, colorectal, breast, cervical, bladder, pancreatic, hepatocellular, gastric, ovarian, and osteosarcoma. Elevated levels of TMPO-AS1 are intricately linked to unfavorable prognoses, accompanied by distinctive clinical and pathological characteristics. Functionally, TMPO-AS1 showcases its prowess in enhancing cancer cell migration, invasion, proliferation, and orchestrating epithelial-mesenchymal transition (EMT) through a myriad of molecular mechanisms. These mechanisms entail intricate interactions with proteins, microRNAs, and intricate signaling pathways. Furthermore, TMPO-AS1 is intricately involved in regulating critical cellular processes, including apoptosis and the cell cycle. The mounting evidence converges towards the potential of TMPO-AS1 serving as a diagnostic and prognostic biomarker, further entwined with its potential role in influencing chemoresistance in cancer. This potential is underscored by its consistent associations with clinical outcomes and treatment responses. This comprehensive investigation not only consolidates our existing knowledge of TMPO-AS1's multifaceted roles but also sheds illuminating insights on its profound significance in the intricate landscape of cancer biology, paving the way for potential applications in clinical practice.

Long noncoding RNA LINC00921 serves as a predictive biomarker for lung adenocarcinoma: An observational study

Lung adenocarcinoma (LUAD) is usually diagnosed at advanced stages. Hence, there is an urgent need to seek an effective biomarker to predict LUAD status. Long noncoding RNAs (lncRNAs) play key roles in the development of tumors. However, the relationship between LINC00921 and LUAD remains unclear. The gene expression data of LUAD were downloaded from the Cancer Genome Atlas database to investigate the expression level of LINC00921 in LUAD. Diagnostic ability analysis, survival analysis, tumor mutational burden analysis, and immune cell infiltration analysis of LINC00921 in LUAD patients were performed simultaneously. According to the median expression value of LINC00921, patients were divided into LINC00921 high- and low-expression groups. The function of LINC00921 in LUAD was identified through difference analysis and enrichment analysis. Moreover, drugs that may be relevant to LUAD treatment were screened. Finally, blood samples were collected for real-time polymerase chain reaction. LINC00921 was significantly lower in LUAD tumor tissues. Notably, patients with low expression of LINC00921 had a shorter median survival time. Decreased immune cell infiltration in the tumor microenvironment in the low LINC00921 expression group may contribute to poorer patient outcomes. Tumor mutational burden was significantly different in survival between the LINC00921 high- and low-expression groups. In addition, LINC00921 may exert an influence on cancer development through its regulation of target genes transcription. Glyceraldehyde-3-phosphate dehydrogenase-related drugs may be more likely to be therapeutically effective in LUAD. LINC00921 was able to be used as the potential diagnostic indicator for LUAD.

Decoding LINC00052 role in breast cancer by bioinformatic and experimental analyses

LncRNA is a group of transcripts with a length exceeding 200 nucleotides that contribute to tumour development. Our research group found that LINC00052 expression was repressed during the formation of breast cancer (BC) multicellular spheroids. Intriguingly, LINC00052 precise role in BC remains uncertain. We explored LINC00052 expression in BC patients` RNA samples (TCGA) in silico, as well as in an in-house patient cohort, and inferred its cellular and molecular mechanisms. In vitro studies evaluated LINC00052 relevance in BC cells viability, cell cycle and DNA damage. Results. Bioinformatic RNAseq analysis of BC patients showed that LINC00052 is overexpressed in samples from all BC molecular subtypes. A similar LINC00052 expression pattern was observed in an in-house patient cohort. In addition, higher LINC00052 levels are related to better BC patient´s overall survival. Remarkably, MCF-7 and ZR-75-1 cells treated with estradiol showed increased LINC00052 expression compared to control, while these changes were not observed in MDA-MB-231 cells. In parallel, bioinformatic analyses indicated that LINC00052 influences DNA damage and cell cycle. MCF-7 cells with low LINC00052 levels exhibited increased cellular protection against DNA damage and diminished growth capacity. Furthermore, in cisplatin-resistant MCF-7 cells, LINC00052 expression was downregulated. Conclusion. This work shows that LINC00052 expression is associated with better BC patient survival. Remarkably, LINC00052 expression can be regulated by Estradiol. Additionally, assays suggest that LINC00052 could modulate MCF-7 cells growth and DNA damage repair. Overall, this study highlights the need for further research to unravel LINC00052 molecular mechanisms and potential clinical applications in BC.

Breast cancer-derived exosomal lncRNA SNHG14 induces normal fibroblast activation to cancer-associated fibroblasts via the EBF1/FAM171A1 axis

BACKGROUND

Exosomes released from cancer cells can activate normal fibroblasts (NFs) into cancer-associated fibroblasts (CAFs), which promotes cancer development. Our study aims to explore the role and potential mechanisms of breast cancer exosomes-delivered long non-coding RNA (lncRNA) SNHG14 in regulating CAFs transformation.

METHODS

Adjacent normal tissues, cancerous and serum specimens were gathered in breast cancer patients. Exosomes and NFs were separated from breast cancer cells (SKBR-3) and normal tissues of patients, respectively. Cell viability and migration were measured with CCK-8 and Transwell assays. CAFs markers, fibroblast activation protein (FAP) and a-smooth muscle actin (α-SMA) were detected for assessing CAFs activation. The interactions between molecules were evaluated using dual luciferase reporter assay, RNA immunoprecipitation and chromatin immunoprecipitation.

RESULTS

SNHG14 and FAM171A1 were upregulated in breast cancer. Exosomes secreted by SKBR-3 cells induced NFs activation in CAFs, as indicated by upregulating CAFs marker levels and facilitated cell viability and migration. Exosomal SNHG14 silencing in SKBR-3 cells inhibited CAFs activation. SNHG14 positively regulated FAM171A1 expression through EBF1. FAM171A1 overexpression eliminated the inhibition effect of exosomal SNHG14 silencing in CAFs transformation.

CONCLUSION

Breast cancer-derived exosomal SNHG14 contributed to NFs transformation into CAFs by the EBF1/FAM171A1 axis.

JMJD6-BRD4 complex stimulates lncRNA HOTAIR transcription by binding to the promoter region of HOTAIR and induces radioresistance in liver cancer stem cells

BACKGROUND

Long non-coding RNA (lncRNA) HOTAIR acts importantly in liver cancer development, but its effect on radioresistance remains poorly understood. Here, our study probed into the possible impact of HOTAIR in radioresistance in liver cancer stem cells (LCSCs) and to elucidate its molecular basis.

METHODS

Following sorting of stem and non-stem liver cancer cells, LCSCs were identified and subjected to RNA-seq analysis for selecting differentially expressed genes. Expression of HOTAIR was determined in liver cancer tissues and CSCs. The stemness, proliferation, apoptosis and radioresistance of LCSCs were then detected in response to altered expression of HOTAIR-LSD1-JMJD6-BRD4.

RESULTS

Ectopic HOTAIR expression was found to promote radioresistance of LCSCs by maintaining its stemness. Mechanistic investigations indicated that HOTAIR recruited LSD1 to the MAPK1 promoter region and reduced the level of H3K9me2 in the promoter region, thus elevating ERK2 (MAPK1) expression. JMJD6-BRD4 complex promoted HOTAIR transcription by forming a complex and positively regulated ERK2 (MAPK1) expression, maintaining the stemness of LCSCs, and ultimately promoting their radioresistance in vitro and in vivo.

CONCLUSION

Collectively, our work highlights the promoting effect of the JMJD6-BRD4 complex on the radioresistance of LCSCs through a HOTAIR-dependent mechanism.

Pathogenic mycoplasmas of humans regulate the long noncoding RNAs in epithelial cells

Non-coding RNAs (ncRNAs), specifically long ncRNAs (lncRNAs), regulate cellular processes by affecting gene expression at the transcriptional, post-transcriptional, and epigenetic levels. Emerging evidence indicates that pathogenic microbes dysregulate the expression of host lncRNAs to suppress cellular defense mechanisms and promote survival. To understand whether the pathogenic human mycoplasmas dysregulate host lncRNAs, we infected HeLa cells with Mycoplasma genitalium (Mg) and Mycoplasma penumoniae (Mp) and assessed the expression of lncRNAs by directional RNA-seq analysis. HeLa cells infected with these species showed up-and-down regulation of lncRNAs expression, indicating that both species can modulate host lncRNAs. However, the number of upregulated (200 for Mg and 112 for Mp) and downregulated lncRNAs (30 for Mg and 62 for Mp) differ widely between these two species. GREAT analysis of the noncoding regions associated with differentially expressed lncRNAs showed that Mg and Mp regulate a discrete set of lncRNA plausibly related to transcription, metabolism, and inflammation. Further, signaling network analysis of the differentially regulated lncRNAs exhibited diverse pathways such as neurodegeneration, NOD-like receptor signaling, MAPK signaling, p53 signaling, and PI3K signaling, suggesting that both species primarily target signaling mechanisms. Overall, the study's results suggest that Mg and Mp modulate lncRNAs to promote their survival within the host but in distinct manners.

Long non-coding RNA HOTTIP exerts an oncogenic function by regulating HOXA13 in nasopharyngeal carcinoma

BACKGROUND

The long non-coding RNA HOXA transcript at the distal tip (HOTTIP) and homeobox A13 (HOXA13) have been identified as oncogenes that play a pivotal role in tumorigenesis. However, their specific mechanisms of action in nasopharyngeal carcinoma (NPC) progression remain unclear.

METHODS AND RESULTS

In the present study, RT-qPCR was employed to quantify RNA expression in NPC cells and tissues. Flow cytometry, MTT, CCK8 and colony formation assays were utilized to assess cell apoptosis and proliferation. Transwell assay was conducted to evaluate migration and invasion while Western blotting was performed for protein expression analysis. Our findings revealed that the expression of HOTTIP was significantly upregulated in NPC cell lines. Inhibition of HOTTIP could induce apoptosis and suppress proliferation, clonogenicity, invasion and metastasis in NPC cells. Knockdown of HOTTIP led to downregulation of HOXA13 expression, which subsequently inhibited the proliferation and metastasis in NPC cells. The inhibitory effects on cell proliferation and metastasis caused by HOTTIP silencing were rescued by HOXA13 overexpression. Additionally, there was a significant positive correlation between HOTTIP and HOXA13, which were found to be elevated in NPC tissues compared to normal tissues.

CONCLUSIONS

We have determined that LncRNA HOTTIP facilitates tumorigenesis by modulating the expression of HOXA13 in NPC cells. Targeting HOTTIP/HOXA13 may be a promising therapeutic strategy for NPC.

Pyroptosis-related lncRNA prognostic signatures for cutaneous melanoma and tumor microenvironment status

Aims: To explore whether the expression of pyroptosis-related lncRNAs makes a difference in the prognosis and antitumor immunity of cutaneous melanoma (CM) patients. Methods: A series of analyses were conducted to establish a prognostic risk model and validate its accuracy. Immune-related analyses were performed to further assess the associations among immune status, tumor microenvironment and the prognostic risk model. Results: Eight pyroptosis-related lncRNAs relevant to prognosis were ascertained and applied to establish the prognostic risk model. The low-risk group had a higher overall survival rate. Conclusion: The established prognostic risk model presents better prediction ability for the prognosis of CM patients and provides new possible therapeutic targets for CM.

BMP15 Modulates the H19/miR-26b/SMAD1 Axis Influences Yak Granulosa Cell Proliferation, Autophagy, and Apoptosis

Bone morphogenetic protein 15 (BMP15) regulates the growth and development of follicles. In particular, the long non-coding RNA H19 plays an important role in mammalian reproduction. However, the function and regulatory mechanism of the interaction of BMP15 with H19 in yak granulosa cell (GC) proliferation, autophagy, and apoptosis are poorly understood. In our study, quantitative reverse-transcription-polymerase chain reaction analysis showed that H19 were highly expressed in yak healthy follicles. H19 was induced by BMP15 protein in yak GCs. In addition, we confirmed that overexpression of H19 promoted yak GC proliferation and autophagy and inhibited apoptosis. Bioinformatic analysis and luciferase reporter assays demonstrated that H19 directly binds to miR-26b, and SMAD1 was identified as a target of miR-26b. miR-26b overexpression inhibited GC proliferation and autophagy and promoted apoptosis through decreased SMAD1 expression, which was attenuated by H19 overexpression. RNA immunoprecipitation-quantitative polymerase chain reaction and dual-luciferase assays showed that miR-26b was sponged by H19 to preserve SMAD1 expression. Furthermore, SMAD1 mRNA expression was induced and miR-26b expression was reduced after yak GCs were treated with BMP15 protein. In conclusion, our results demonstrated that the H19/miR-26b/SMAD1 axis responds to BMP15 to regulate yack GC proliferation, autophagy, and apoptosis.

High-throughput sequencing approach for the identification of lncRNA biomarkers in hepatocellular carcinoma and revealing the effect of ZFAS1/miR-150-5p on hepatocellular carcinoma progression

Aims

To screen abnormal lncRNAs and diagnostic biomarkers in the progression of hepatocellular carcinoma through high-throughput sequencing and explore the underlying mechanisms of abnormal lncRNAs in the progression of hepatocellular carcinoma.

Methods

The transcriptome sequencing was used to analyze the RNA expression profile and identify differentially expressed RNAs. Hub lncRNAs were screened by combining (WGCNA, ceRNA regulatory network, PPI, GO and KEGG analyses, Kaplan-Meier curve analysis, Cox analysis, risk model construction and qPCR). Thereafter, the correlation between the expression of hub lncRNAs and tumor clinicopathological parameters was analyzed, and the hub lncRNAs were analyzed by GSEA. Finally, the effects of hub RNAs on the proliferation, migration and invasion of HepG2 cells were investigated in vitro.

Results

Compared with the control group, a total of 610 lncRNAs, 2,593 mRNAs and 26 miRNAs were screened in patients with hepatocellular carcinoma. Through miRNA target prediction and WGCNA, a ceRNA was constructed, comprising 324 nodes and 621 edges. Enrichment analysis showed that mRNAs in ceRNA were involved mainly in cancer development progression. Then, the ZFAS1/miR-150-5p interaction pair was screened out by Kaplan Meier curve analysis, Cox analysis and qPCR analysis. Its expression was related to tumor stage, TNM stage and patient age. ROC curve analysis showed that it has a good predictive value for the risk of hepatocellular carcinoma. GSEA showed that ZFAS1 was also enriched in the regulation of immune response, cell differentiation and proliferation. Loss-of-function experiments revealed that ZFAS1 inhibition could remarkably suppress HepG2 cell proliferation, migration and invasion in vitro. Bioinformatic analysis and luciferase reporter assays revealed that ZFAS1 directly interacted with miR-150-5p. Rescue experiments showed that a miR-150-5p inhibitor reversed the cell proliferation, migration and invasion functions of ZFAS1 knockdown in vitro.

Conclusion

ZFAS1 is associated with the malignant status and prognosis of patients with hepatocellular carcinoma, and the ZFAS1/miR-150-5p axis is involved in hepatocellular carcinoma progression.

A novel lipid metabolism-related lncRNA signature predictive of clinical prognosis in cervical cancer

Background: Cervical cancer (CC) is a serious threat to women populations worldwide. Lipid metabolism is believed to have modulating functions in cancer. Long non-coding RNAs (lncRNAs) are potential biomarkers for the different tumor prognosis. Our work aims at investigating the prognostic value of lipid metabolism-related lncRNAs in CC.

Methods: LncRNA expression profiling was conducted in 291 patients from The Cancer Genome Atlas (TCGA). Patient samples were randomly assigned to the training or testing set in a 3:2 ratio. A novel lipid metabolism-related five-lncRNA signature with prognostic value for CC was built through the univariate Cox regression, least absolute contraction and selection operator (LASSO) regression and multivariate Cox regression analyses, and was further evaluated by the Kaplan-Meier methods. Relevant analyses were also applied to identify the independent clinicopathological factors. GO and KEGG analyses were conducted to investigate the biological functions and molecular pathways. Immune infiltration analysis was included to probe the relationship between lncRNA signature and cancer cell microenvironment.

Results: The novel lipid metabolism-related five-lncRNA signature was confirmed to be predictive of overall survival (OS) in CC patients. Risk score, cancer stage, pregnancy, and BMI were validated as independent factors with prognostic value. GO and KEGG indicated that lipid metabolism participated in several tumor associated functions and pathways. Moreover, our results suggested that the five-lncRNA expression has potential link with tumor immune microenvironment.

Conclusion: In conclusion, we built an innovative prognostic risk signature based upon lipid metabolism-related lncRNAs. The five-lncRNA signature may be beneficial to provide novel potential therapeutic targets and improve personalized treatment strategies for CC patients in future clinical treatments.

A novel inflammation-related lncRNAs prognostic signature identifies LINC00346 in promoting proliferation, migration, and immune infiltration of glioma

In this study, a total of 13 inflammation-related lncRNAs with a high prognostic value were identified with univariate, multivariate Cox regression analysis, and LASSO analysis. LINC00346, which is one of the 13 lncRNAs identified, was positively associated with type 2 macrophage activation and the malignant degree of glioma. Fluorescence in situ hybridization (FISH) and immunohistochemical staining showed that LINC00346 was highly expressed in high-grade glioma, while type 2 macrophages key transcription factor STAT3 and surface marker CD204 were also highly expressed simultaneously. LINC00346 high-expression gliomas were more sensitive to the anti–PD-1 and anti-CTLA-4 therapy. LINC00346 was also associated with tumor proliferation and tumor migration validated by EdU, cell colony, formation CCK8, and transwell assays. These findings reveal novel biomarkers for predicting glioma prognosis and outline relationships between lncRNAs inflammation, and glioma, as well as possible immune checkpoint targets for glioma.

Downregulation of SOX21-AS1 alleviated cisplatin resistance in cervical cancer through Epithelial-messenchymal transition (EMT) inhibition

Cisplatin is widely used in chemotherapies in cervical cancer (CC). Nevertheless, drug resistance in cancer patients poses a major threat to efficacy of treatment. To explore the underlying modulatory mechanism of SOX21-AS1 in cisplatin resistance in CC cell and mice models，Gepia database was referred for SOX21-AS1 expression in cancer tissues and normal ones. RT-qPCR was used to measure the differential expression of SOX21-AS1 in parental Siha cells and cisplatin-resistant Siha/DDP cells. Luciferase reporter gene assays were conducted to verify putative bindings between SOX21-AS1 and miR-9-3p. Western blot method was employed to evaluate the changes in cleaved-caspase 7 protein expression. Cisplatin resistance was evaluated in each transfected group using CCK8 method after cells were exposed to cisplatin (0,7.5,15,30,60,120, 240ug/ml) for 24h. Flow cytometry method was used to measure the apoptosis rates. Cell migration and invasion were measured using Transwell assays. Immunofluorescence method was applied to observe EMT markers including E-cadherin, Snail, MMP3 and MMP9. Siha/DDP cell groups stably transfected with sh-NC and sh- SOX21-AS1 were injected through tail vein of Balb/C mice. Lung tissue sections were used for HE staining and IHC analysis. SOX1-AS1 expression was higher in cancer tissues than normal ones and was also higher in Siha/DDP rather than Siha cells. SOX21-AS1 was targeted by miR-9-3p in CC cells. Downregulation of SOX21-AS1 or overexpression of miR-9-3p inhibited cisplatin resistance in Siha/DDP cells and reduced cell invasion and migration and attenuated EMT progression. In vivo, the SOX21-AS1 knockdown led to less severe lung metastasis. Downregulation of SOX21-AS1 alleviated cisplatin resistance in cervical cancer through EMT inhibition.

Long Intergenic Noncoding RNAs Affect Biological Pathways Underlying Autoimmune and Neurodegenerative Disorders

Long intergenic noncoding RNAs (lincRNAs) are a class of independently transcribed molecules longer than 200 nucleotides that do not overlap known protein-coding genes. LincRNAs have diverse roles in gene expression and participate in a spectrum of biological processes. Dysregulation of lincRNA expression can abrogate cellular homeostasis, cell differentiation, and development and can also deregulate the immune and nervous systems. A growing body of literature indicates their important and multifaceted roles in the pathogenesis of several different diseases. Furthermore, certain lincRNAs can be considered potential therapeutic targets and valuable diagnostic or prognostic biomarkers capable of predicting the onset of a disease, its degree of activity, or the progression phase. In this review, we discuss possible mechanisms and molecular functions of lincRNAs in the pathogenesis of selected autoimmune and neurodegenerative disorders: multiple sclerosis, rheumatoid arthritis, systemic lupus erythematosus, Sjögren’s syndrome, Huntington’s disease, Parkinson’s disease, Alzheimer’s disease, and amyotrophic lateral sclerosis. This summary can provide new ideas for future research, diagnosis, and treatment of these highly prevalent and devastating diseases.

Long noncoding RNAs (lncRNAs) in HIV-mediated carcinogenesis: Role in cell homeostasis, cell survival processes and drug resistance

There is accruing data implicating long non-coding RNAs (lncRNAs) in the development and progression of non-communicable diseases such as cancer. These lncRNAs have been implicated in many diverse HIV-host interactions, some of which are beneficial to HIV propagation. The virus-host interactions induce the expression of HIV-regulated long non-coding RNAs, which are implicated in the carcinogenesis process, therefore, it is critical to understand the molecular mechanisms that underpin these HIV-regulated lncRNAs, especially in cancer formation. Herein, we summarize the role of HIV-regulated lncRNAs targeting cancer development-related processes including apoptosis, cell cycle, cell survival signalling, angiogenesis and drug resistance. It is unclear how lncRNAs regulate cancer development, this review also discuss recent discoveries regarding the functions of lncRNAs in cancer biology. Innovative research in this field will be beneficial for the future development of therapeutic strategies targeting long non-coding RNAs that are regulated by HIV, especially in HIV associated cancers.

Comprehensive Analysis of a Ferroptosis-Related lncRNA Signature for Predicting Prognosis and Immune Landscape in Osteosarcoma

Research on the implications of ferroptosis in tumors has increased rapidly in the last decades. There are evidences that ferroptosis is involved in several aspects of cancer biology, including tumor progression, metastasis, immunomodulation, and therapeutic response. Nonetheless, the interaction between ferroptosis-related lncRNAs (FRLs) and the osteosarcoma immune microenvironment is poorly understood. In this study, a risk model composed of FRLs was developed using univariate and LASSO Cox regression analyses. On the basis of this model, FRL scores were calculated to systematically explore the role of the model in predicting the prognosis and immune characteristics of osteosarcoma patients. Survival analysis showed that osteosarcoma samples with lower FRL-score had better overall survival. After predicting the abundance of immune cells in osteosarcoma microenvironment by single-sample gene-set enrichment analysis (ssGSEA) and ESTIMATE analysis, we found that the FRL-score could distinguish immune function, immune score, stromal score, tumor purity, and tumor infiltration of immune cells in different osteosarcoma patients. In addition, FRL-score was also associated with immune checkpoint gene expression and half-maximal inhibitory concentration of chemotherapeutic agents. Finally, we confirmed that knockdown of RPARP-AS1 suppressed the malignant activity of osteosarcoma cells in vitro experiments. In general, the FRL-based prognostic signature could promote our understanding of the immune microenvironment characteristics of osteosarcoma and guide more effective treatment regimens.

LINC01194 recruits NUMA1 to promote ubiquitination of RYR2 to enhance malignant progression in triple-negative breast cancer

Long intergenic nonprotein coding RNA 1194 (LINC01194) has been reported as an oncogene in several cancer types, but its expression and potential role in triple-negative breast cancer (TNBC) are still unclear. We found that LINC01194 was significantly highly expressed in TNBC based on The Cancer Genome Atlas (TCGA) database. Data from in vitro experiments and in vivo assays demonstrated that LINC01194 promoted TNBC progression. Through bioinformatics prediction, mass spectrometry, and mechanical experiments, we found that LINC01194 could recruit nuclear mitotic apparatus protein 1 (NUMA1) to bind to the untranslated region (3'UTR) of ubiquitin-conjugating enzyme E2 C (UBE2C) 3' and stabilize UBE2C mRNA. Moreover, we found that UBE2C acted as an ubiquitin ligase to promote the ubiquitination and degradation of ryanodine receptor type 2 (RYR2) that inhibited the progression of TNBC by inhibiting the Wnt/β-catenin signaling pathway. In summary, LINC01194 activate the Wnt/β-catenin signaling pathway and accelerates the malignant progression of TNBC by recruiting NUMA1 to stabilize UBE2C mRNA and thus promotes RYR2 ubiquitination and degradation. These findings might provide a more effective therapeutic strategy for TNBC patients.

Long Non-Coding RNA MAFG-AS1 as a Potential Biomarker for Hepatocellular Carcinoma: Linkage with Tumor Features, Markers, Liver Functions, and Survival Profile

Purpose

Long non-coding RNAs musculoaponeurotic fibrosarcoma oncogene family, protein G antisense 1 (lnc-MAFG-AS1) regulates hepatocellular carcinoma (HCC) progression and treatment resistance in multiple ways, while its engagement in HCC clinical management remains obscure. The current study aims to explore the relationship of lnc-MAFG-AS1 with tumor features, liver function indexes, tumor markers, and prognosis in HCC patients.

Methods

One hundred and fifty-two surgical HCC patients who underwent tumor resection were retrospectively analyzed. Their tumor and adjacent tissues were acquired and then proposed to reverse transcription-quantitative polymerase chain reaction to detect lnc-MAFG-AS1 expression.

Results

Lnc-MAFG-AS1 expression was increased in HCC tumor tissue than in adjacent tissue [median (interquartile range): 2.730 (1.685–4.198) vs. 0.990 (0.703–1.468), p < 0.001], with a high area under the curve [0.889, 95% confidence interval (CI): 0.854–0.924] to distinguish them via receiver operating characteristic curve analysis. Tumor lnc-MAFG-AS1 was linked with multifocal nodules (p < 0.001), increased Barcelona Clinic Liver Cancer (BCLC) stage (p = 0.018), and elevated China Liver Cancer (CNLC) stage (p = 0.008), which also correlated with an abnormal alpha-fetoprotein (AFP) level (p = 0.004), However, lnc-MAFG-AS1 was not linked with other disease conditions, tumor properties, liver function indexes, or tumor markers (all ps > 0.05). In addition, patients with a high expression of lnc-MAFG-AS1 exhibited worse overall survival than those with a low expression of lnc-MAFG-AS1 [median (95% CI): 34.0 (24.5–43.5) vs. 48.0 (41.5–54.5) months] (p = 0.011), which was further validated by univariate Cox’s analysis [hazard ratio (HR) = 1.827, p = 0.013] and multivariate Cox’s analysis (HR = 1.697, p = 0.040).

Conclusion

Lnc-MAFG-AS1 relates to multifocal nodules, increased BCLC stage, elevated CNLC stage, and abnormal AFP level and predicts pejorative prognosis in HCC patients.

Long non-coding RNAs are involved in alternative splicing and promote cancer progression

Alternative splicing (AS) is a key process in which precursor RNAs produce different mature RNAs, and the disorder of AS is a key factor in promoting cancer development. Compared with coding RNA, studies on the functions of long non-coding RNAs (lncRNAs) are far from enough. In fact, lncRNA is an important participant and regulator in the process of AS. On the one hand, lncRNAs regulate cancer progression as AS products of precursor messenger RNA (mRNA), but on the other hand, precursor lncRNA generates cancer-related abnormal splicing variants through AS. In addition, lncRNAs directly or indirectly regulate the AS events of downstream target genes, thus affecting the occurrence and development of cancer. Here, we reviewed how lncRNAs regulate AS and influence oncogenesis in different ways.

Opportunities and challenges of using high-sensitivity nanobiosensors to detect long noncoding RNAs: A preliminary review

The two types ofncRNAs, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are responsible for several biological processes within cells, such as the immune responses, cell growth and invasion, and regulation of the cell cycle. Rapidly expanding class of ncRNAs, lncRNAsinteract with other molecules to form chromatin-remodeling complexes. These potential hallmarks of diseases contribute to transcriptional and post-transcriptional regulation of several genes, possibly via cross-talk with other RNAs. Aberrant expression of lncRNAshas drawn increasing attention to the pathophysiology of different diseases, includingcancer and cardiovasculardiseases. Unfortunately, circulating lncRNAs are presented in the bloodstream at very low levels, making sensitive detection difficult. Currently, there are few methods for detecting these ncRNAs from which quantitative real-time-polymerase chain reaction (qRT-PCR) is the most routinely used technique. These techniqueslack sensitivity for intracellular detection of lncRNAs. Moreover, they are tedious and require a large sample size. Currently, nanotechnology has taken over the diagnostic field because of the tunable properties and modification opportunities. Furthermore, these conventional techniques can be merged with nanotechnology to improve detection sensitivity.This review highlights some of the most recent findings on nanotechnology-based methods and possible obstacles intheir application for moreaccurate sensing of lncRNAs.

Deciphering the Non-Coding RNA Landscape of Pediatric Acute Myeloid Leukemia

Pediatric acute myeloid leukemia (pedAML) is a heterogeneous blood cancer that affects children. Although survival rates have significantly improved over the past few decades, 20-30% of children will succumb due to treatment-related toxicity or relapse. The molecular characterization of the leukemic stem cell, shown to be responsible for relapse, is needed to improve treatment options and survival. Recently, it has become clear that non-coding RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), play a role in the development of human diseases, including pediatric cancer. Nevertheless, non-coding RNA expression data in pedAML are scarce. Here, we explored lncRNA (n = 30,168) and miRNA (n = 627) expression in pedAML subpopulations (leukemic stem cells (LSCs) and leukemic blasts (L-blasts)) and their normal counterparts (hematopoietic stem cells and control myeloblasts). The potential regulatory activity of differentially expressed lncRNAs in LSCs (unique or shared with the L-blast comparison) on miRNAs was assessed. Moreover, pre-ranked gene set enrichment analyses of (anti-) correlated protein-coding genes were performed to predict the functional relevance of the differentially upregulated lncRNAs in LSCs (unique or shared with the L-blast comparison). In conclusion, this study provides a catalog of non-coding RNAs with a potential role in the pathogenesis of pedAML, paving the way for further translational research studies.

CircRNA circ_0023984 promotes the progression of esophageal squamous cell carcinoma via regulating miR-134-5p/cystatin-s axis

Recent studies have shown that circRNAs can act as oncogenic factors or tumor suppressors by sponging microRNAs (miRNAs). The upregulation of circ_0023984 was reported in esophageal squamous cell carcinoma (ESCC). However, its functional role in ESCC remain unclear. In the present study, circ_0023984 expression in ESCC cells and tissues were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting (WB). Subcellular fraction experiment was performed to determine relative nuclear-cytoplasmic localization. The loss-of-function effects of circ_0023984 in ESCC cell lines were investigated by shRNA-mediated knockdown. Functional assays including cell Counting Kit-8 (CCK-8), 5-Ethynyl-2’-deoxyuridine (EDU) incorporation, colony formation and Transwell migration assays were conducted to assess the malignant phenotype. The interaction between the two molecules was analyzed by RNA pull-down, luciferase reporter assay and RNA immunoprecipitation (RIP). The subcutaneous tumor model in nude mice was used to assess the role of circ-0023984 in tumorigenesis. We found that ESCC patients with high circ_0023984 expression was associated with a poor prognosis. The knockdown of circ_0023984 suppressed cell growth, invasion, and migration in ESCC cells. Circ_0023984 interacted with miR-134-5p and inhibited its activity, which promoted the expression of CST4 (Cystatin-S). Circ_0023984 also regulated tumorigenesis in a CST4-dependent manner. Together, our study indicates that the oncogenic role of Circ_0023984 is mediated by miR-134-5p/CST4 Axis in ESCC, which could serve as potential targets for future therapeutic strategies.

Clinicopathological and prognostic significance of long non-coding RNA EWSAT1 in human cancers: A review and meta analysis

Background

Ewing sarcoma-associated transcript 1 (lncRNA EWSAT1) is reported to have a close relationship with the overall survival in many cancers. However, the role of its prognosis and correlations with the clinicopathological features in different cancers haven’t been explored yet. Herein, we intend to assess the prognostic value and correlations with the clinicopathological features in several cancers.

Methods

PubMed, Embase, Web of Science, and The Cochrane Library were searched for literature review from inception to October 25, 2021. Valid data was extracted to make forest and sensitivity analysis plots using Review Manager 5.4 and Stata software. Hazard ratio (HR) or odds ratio (OR) with 95% confidence interval (CI) was used to evaluate the relationship between different expression of EWSAT1 and patients’ prognosis and clinicopathological features.

Results

7 studies were screened for this review, including 550 samples. Meta-analysis showed that high expression of lncRNA EWSAT1 was associated with poor overall survival (OS) (HR = 2.10, 95% CI, 1.60–2.75, p < 0.0001) in cancers reported. In addition, patients in high expression group of EWAST1 tended to have more metastasis (OR = 2.20, 95% CI 1.47–3.31, p = 0.0001), and higher TNM stage (I+II vs. III: OR = 0.34, 95% CI 0.21–0.56, p < 0.0001), but in the same time with higher differentiation (well + moderate vs. Poor: OR = 2.21, 95% CI 1.02–4.76, p = 0.04). Age (OR = 1.47, 95% CI 0.94–2.30, p = 0.09) was not significantly different in patients with aberrant expression of EWSAT1.

Conclusions

Our study shows that high expression of EWSAT1 may indicate poor overall survival and associated with several clinicopathological features, which can be used as a potential prognosis biomarker for multiple cancers.

Hypoxia-induced long noncoding RNA NR2F1-AS1 maintains pancreatic cancer proliferation, migration, and invasion by activating the NR2F1/AKT/mTOR axis

Accumulating evidence has demonstrated the essential role of long noncoding RNAs (lncRNAs) in various types of human cancer, including pancreatic cancer (PC). However, the functions and regulatory mechanisms of nuclear receptor subfamily 2 group F member 1 antisense RNA 1 (NR2F1-AS1) that are responsible for its role in the malignant progression of PC cells remains to be investigated. In this study, the biological effects of NR2F1-AS1 and NR2F1 in PC were investigated by in vitro and in vivo experiments. The mechanisms of NR2F1-AS1 were monitored by bioinformatic predictive analysis and confirmatory experiments. Our results indicated that NR2F1-AS1 was overexpressed and positively correlated with poor survival in PC. Depletion of NR2F1-AS1 restrained PC cell proliferation, migration, invasion, and suppressed xenograft tumor growth and metastasis in vitro and in vivo. Mechanistic experiments suggested that NR2F1-AS1 positively regulated the neighboring NR2F1 gene, which subsequently activated AKT/mTOR signaling, resulting in the upregulation of hypoxia-inducible factor-1α (HIF-1α). Further investigations elucidated that NR2F1-AS1 expression was transcriptionally regulated by HIF-1α under hypoxia. These findings demonstrated that hypoxia-induced NR2F1-AS1 expression directly increased NR2F1 levels to promote PC cell proliferation, migration, and invasion by activating AKT/mTOR signaling. Together, these findings suggest that NR2F1-AS1 could be a prospective therapeutic target for PC.

Long non-coding RNA CATIP antisense RNA 1 (lncRNA CATIP-AS1) downregulation contributes to the progression and metastasis of thyroid cancer via epithelial-mesenchymal transition (EMT) pathway

Thyroid cancer (THCA) is the most common cancer of the endocrine system across the globe. To date, the mechanism of development of THCA remains scarcely known. In this study, we aim to elucidate the long non-coding RNA CATIP antisense RNA 1 (lncRNA CATIP-AS1/CATIP-AS1) role in the pathogenesis of THCA and its regulatory mechanism. The result shows that the CATIP-AS1 was significantly downregulated in THCA tissues and cells and was associated with a poor prognosis of patients diagnosed with THCA. The overexpression of CATIP-AS1 significantly inhibited THCA cell proliferation, migration, and epithelial–mesenchymal transition (EMT) but increased the THCA cell apoptosis. We found that CATIP-AS1 endogenously sponges miR-515-5p and its overexpression could inhibit miR-515-5p regulatory effect. Moreover, the overexpression of miR-515-5p repressed the Smad4 expression level, consequently reversed the inhibiting effect of overexpressed CATIP-AS1 on the proliferation, and migration of THCA cell. It also reversed the increased THCA cell apoptosis and the downregulated-CATIP-AS1-induced cell EMT inhibition. Summarily, we demonstrated that the CATIP-AS1 promotes the progression and metastasis of THCA via EMT pathway partly through regulating the miR-515-5p and Smad4 expression in THCA cell. The CATIP-AS1 could be a promising biomarker for early THCA detection and prognosis and a possible therapeutic target for its treatment.

Silencing of long chain noncoding RNA paternally expressed gene (PEG10) inhibits the progression of neuroblastoma by regulating microRNA-449a (miR-449a)/ribosomal protein S2 (RPS2) axis

To investigate the mechanism of paternally expressed gene (PEG10) in regulating neuroblastoma (NB) progression. PEG10 expression was detected using quantitative real-time reverse transcription polymerase-chain reaction (qRT-PCR). The interaction of miR-449a and PEG10 or ribosomal protein S2 (RPS2) was employed by starBase, and then proved through RIP and dual-luciferase reporter assays. The NB cell viability, proliferation, invasion, and migration were evaluated by Cell Counting Kit-8 (CCK-8), colony formation, and Transwell assay. The mRNA and protein levels were determined by qRT-PCR and Western blotting, respectively. The levels of PEG10 and RPS2 were remarkably increased in NB tissues and cells, nevertheless the expression of miR-449a was conspicuously declined in NB tissues and cells. Silencing of PEG10 inhibited proliferation, migration, and invasion in SK-N-BE (2) cells, while overexpression of PEG10 promoted proliferation, migration, and invasion in SH-SY5Y cells. We affirmed that PEG10 interacted with miR-449a, and miR-449a could target the 3'UTR of RPS2 and negatively regulate its expression in NB cells. The upregulation of miR-449a inhibited proliferation, migration, and invasion in SK-N-BE (2) cells, while downregulation of miR-449a promoted proliferation, migration, and invasion in SH-SY5Y cells. Moreover, miR-449a overexpression weaken the function of PEG10-mediated on promoting proliferation, migration, and invasion in SH-SY5Y cells, while RPS2 overexpression rescued the effects of miR-449a-mediated on inhibiting those behaviors of SH-SY5Y cells. In conclusion, Silencing of PEG10 could inhibit proliferation, migration, and invasion via the miR-449a/RPS2 axis in NB cells.

SPATS2 is positively activated by long noncoding RNA SNHG5 via regulating DNMT3a expression to promote hepatocellular carcinoma progression

Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors with high mortality worldwide. Spermatogenesis-associated serine-rich 2 (SPATS2) could be a novel diagnostic and prognostic biomarker in HCC. However, the regulatory mechanism of SPATS2 in HCC requires further elucidation. Therefore, the study’s objective was to investigate this process in HCC. In this study, we found that SPATS2 is significantly upregulated in HepG2 cells to promote cell growth and migration. SPATS2 is the target transcript of lncRNA SNHG5. SPATS2 positively affects the proliferation and migration of HepG2 cells caused by the higher expression of SNHG5. Mechanistically, we identified that the elevated of SPATS2 was attributed to SNHG5 related hypomethylation of SPATS2. SNHG5 reduced the expression of DNMT3a to suppress the methylation level of SPATS2. Taken together, our results uncover a novel epigenetic regulatory mechanism of lncRNA SNHG5-DNMT3a axis-related SPATS2 expression underlying HCC progression. This may serve as a novel prognostic marker and a promising therapeutic target for the treatment of HCC.

LncRNA MIR205HG accelerates cell proliferation, migration and invasion in hepatoblastoma through the activation of MAPK signaling pathway and PI3K/AKT signaling pathway

Background

Hepatoblastoma (HB) is identified to be the most common liver malignancy which occurs in children. Long non-coding RNAs (lncRNAs) have been implicated in numerous biological processes and diseases, including HB. LncRNA MIR205 host gene (MIR205HG) has been investigated in multiple cancers, however, its role in HB remains to be elucidated.

Methods

MIR205HG expression was analyzed by RT-qPCR. EdU, colony formation and transwell assays were implemented to measure the biological function of MIR205HG on the progression of HB. Mechanism assays were carried out to probe into the underlying mechanism of MIR205HG in HB cells.

Results

MIR205HG was significantly overexpressed in HB. Moreover, MIR205HG inhibition suppressed the proliferative, migratory and invasive capacities of HB cells. Furthermore, MIR205HG competitively bound to microRNA-514a-5p (miR-514a-5p) and targeted mitogen-activated protein kinase 9 (MAPK9) to stimulate mitogen activated protein kinase (MAPK) signaling pathway. Besides, MIR205HG also served as a sponge for microRNA-205-5p (miR-205-5p) to activate the PI3K/AKT signaling pathway.

Conclusion

MIR205HG drives the progression of HB which might provide an efficient marker and new therapeutic target for HB.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13062-021-00309-3.

The transcriptomic revolution and radiation biology

PURPOSE

This article will briefly review the origins and evolution of functional genomics, first describing the experimental technology, and then some of the approaches applied to data analysis and visualization. It will emphasize application of functional genomics to radiation biology, using examples from the author's work to illustrate several key types of analysis. It concludes with a look at non-coding RNA, alternative reading of the genome, and single-cell transcriptomics, some of the innovative areas that may help to shape future research in radiation biology and oncology.

CONCLUSIONS

Transcriptomic approaches have provided insight into many areas of radiation biology and medicine, and innovations in technology and data analysis approaches promise continued contributions to radiation science in the future.

LncRNA ILF3-AS1 promotes cell migration, invasion and EMT process in hepatocellular carcinoma via the miR-628-5p/MEIS2 axis to activate the Notch pathway

BACKGROUND

Long non-coding RNAs (lncRNAs) are essential indicators for hepatocellular carcinoma. LncRNAs can exert the same functions as their antisense mRNAs. ILF3 is an oncogene in hepatocellular carcinoma. ILF3 divergent transcript (ILF3-AS1) is the antisense RNA of ILF3, and has been reported as an oncogene in various cancers.

AIMS

To explore the role of lncRNA ILF3-AS1 in malignant phenotypes of hepatocellular carcinoma cells.

METHODS AND RESULTS

RT-qPCR analysis revealed that ILF3-AS1 was significantly upregulated in hepatocellular carcinoma cells. The hepatocellular carcinoma cell viability was suppressed by silenced ILF3-AS1. Transwell and wound healing assays showed that ILF3-AS1 downregulation inhibited cell invasion and migration. The levels of proteins associated with epithelial-mesenchymal transition (EMT) process and the Notch pathway were detected by western blot analysis. Luciferase reporter, RNA pull down and RIP assays were used to investigate the relationship between ILF3-AS1 and downstream target genes. ILF3-AS1 competed with meis homeobox 2 (MEIS2) for miR-628-5p in hepatocellular carcinoma cells. ILF3-AS1 elevated the levels of key proteins on the Notch pathway. Rescue assays demonstrated that MEIS2 reversed the antitumor effects of silenced ILF3-AS1 on hepatocellular carcinoma. In vivo assays demonstrated that ILF3-AS1 silencing inhibited the hepatocellular carcinoma tumor growth.

CONCLUSIONS

ILF3-AS1 promoted hepatocellular carcinoma progression via the Notch pathway and miR-628-5p/MEIS2 axis.

Long Non-Coding RNA (lncRNA) in Oral Squamous Cell Carcinoma: Biological Function and Clinical Application

Simple Summary

Increasing evidence has revealed the regulatory roles of long non-coding RNAs (lncRNAs) in the initiation and progress of oral squamous cell carcinoma (OSCC). As some novel lncRNA-targeted techniques combined with immune checkpoint therapies have emerged, they provide a new strategy for OSCC treatment. This review summarizes current knowledge regarding the involvement of lncRNAs in OSCC along with their possible use as diagnostic and prognostic biomarker and therapeutic targets.

Abstract

Oral squamous cell carcinoma (OSCC) is a type of malignancy with high mortality, leading to poor prognosis worldwide. However, the molecular mechanisms underlying OSCC carcinogenesis have not been fully understood. Recently, the discovery and characterization of long non-coding RNAs (lncRNAs) have revealed their regulatory importance in OSCC. Abnormal expression of lncRNAs has been broadly implicated in the initiation and progress of tumors. In this review, we summarize the functions and molecular mechanisms regarding these lncRNAs in OSCC. In addition, we highlight the crosstalk between lncRNA and tumor microenvironment (TME), and discuss the potential applications of lncRNAs as diagnostic and prognostic tools and therapeutic targets in OSCC. Notably, we also discuss lncRNA-targeted therapeutic techniques including CRISPR-Cas9 as well as immune checkpoint therapies to target lncRNA and the PD-1/PD-L1 axis. Therefore, this review presents the future perspectives of lncRNAs in OSCC therapy, but more research is needed to allow the applications of these findings to the clinic.

Characterization of the Testis-specific LINC01016 Gene Reveals Isoform-specific Roles in Controlling Biological Processes

Long noncoding RNAs (lncRNAs) have emerged as critical regulators of biological processes. However, the aberrant expression of an isoform from the same lncRNA gene could lead to RNA with altered functions due to changes in their conformations, leading to diseases. Here, we describe a detailed characterization of the gene that encodes long intergenic non-protein-coding RNA 01016 (LINC01016, also known as LncRNA1195) with a focus on its structure, exon usage, and expression in human and macaque tissues. In this study we show that it is among the highly expressed lncRNAs in the testis, exclusively conserved among nonhuman primates, suggesting its recent evolution and is processed into 12 distinct RNAs in testis, cervix, and uterus tissues. Further, we integrate de novo annotation of expressed LINC01016 transcripts and isoform-dependent gene expression analyses to show that human LINC01016 is a multiexon gene, processed through differential exon usage with isoform-specific roles. Furthermore, in cervical, testicular, and uterine cancers, LINC01016 isoforms are differentially expressed, and their expression is predictive of survival in these cancers. This study has revealed an essential aspect of lncRNA biology, rarely associated with coding RNAs, that lncRNA genes are precisely processed to generate isoforms with distinct biological roles in specific tissues.

The LINC00152/miR-138 Axis Facilitates Gastric Cancer Progression by Mediating SIRT2

Gastric cancer (GC) is the most common gastrointestinal cancer and the main cause of tumor-related death. Exploring markers for early diagnosis and new therapeutic targets is always on the way. In the last 10 years, long noncoding RNAs (lncRNAs) have been widely proved to be involved in the progress of many tumors and are regarded as potential targets for tumor therapy. We found that LINC00152, a newly identified lncRNA, was significantly upregulated in GC tissues and affected clinicopathological characteristics in GC patients. Furthermore, we observed that LINC00152 knockdown can significantly reduce cell proliferation and promote apoptosis in human gastric cancer cells. Further bioinformatic analysis indicated that LINC00152 competitively bound with miR-138 and regulated the expression of miR-138. Moreover, SIRT2 was further proved to be a downstream target of miR-138. Overall, this study elucidates the molecular mechanism of LINC00152 underlying the malignant phenotype of GC cells by mediating miR-138/SIRT2 axis, which provides a new understanding of the role and molecular mechanism of lncRNA in GC and also provides a new way for the treatment of gastric cancer.

Long non-coding RNA HEIH: a novel tumor activator in multiple cancers

The last decade has witnessed the altered expression levels of long non-coding RNA HEIH in different types of cancer. More than half of the HEIH studies in cancer have been published within the last two years. To our knowledge, this is the first review to discuss very recent developments and insights into HEIH contribution to carcinogenesis. The functional role, molecular mechanism, and clinical significance of HEIH in human cancers are described in detail. The expression of HEIH is elevated in a broad spectrum of cancers, and its disorder contributes to cell proliferation, migration, invasion, and drug resistance of cancer cells through different underlying mechanisms. In addition, the high expression of HEIH is significantly associated with advanced tumor stage, tumor size and decreased overall survival, suggesting HEIH may function as a prognostic biomarker and potential therapeutic target for human cancers.

Differential expression of long non-coding RNAs as diagnostic markers for lung cancer and other malignant tumors

Due to advances in chip and sequencing technology, several types and numbers of long non-coding RNAs (lncRNAs) have been identified. LncRNAs are defined as non-protein-coding RNA molecules longer than 200 nucleotides, and are now thought as a new frontier in the study of human malignant diseases including NSCLC. Diagnosis of numerous malignant tumors has been closely linked to the differential expression of certain lncRNAs. LncRNAs are involved in gene expression regulation at multiple levels of epigenetics, transcriptional regulation, and post-transcriptional regulation. Mutations, deletions, or abnormal expression levels lead to physiological abnormalities, disease occurrence and are closely associated with human tumor diseases. LncRNAs play a crucial role in cancerous processes as either oncogenes or tumor suppressor genes. The expression of lncRNAs can regulate tumor cell in the proliferation, migration, apoptosis, cycle, invasion, and metastasis. As such, lncRNAs are potential diagnostic and treatment targets for cancer. And that, tumor biomarkers need to be detectable in easily accessible body samples, should be characterized by high specificity and sufficient sensitivity. Herein, it is significant clinical importance to screen and supplement new biomarkers for early diagnosis of lung cancer. This study aimed at systematically describing lncRNAs from five aspects based on recent studies: concepts, classification, structure, molecular mechanism, signal pathway, as well as review lncRNA implications in malignant tumor.

Development of a long noncoding RNA BC032469-dependent gold nanoparticle molecular beacon for the detection of gastric cancer cells

Aim: Long noncoding RNA (lncRNA) BC032469-dependent gold nanoparticle molecular beacons (AuNP-MB) were constructed for the detection of gastric cancer cells. Materials & methods: The AuNP-MBs were prepared according to well-established procedures based on the Au-S interaction between the gold lattice and thiol functionalized oligonucleotides. More importantly, the stability and targeting ability of AuNP-MB were verified by a series of in vitro and in vivo experiments. Results: The lncRNA-dependent probes were successfully utilized for AuNP-MB-based intracellular imaging, with fluorescence effectively emitted in GC cells, but not in normal cells. Notably, such fluorescent emission was positively correlated with lncRNA BC032469 expression. Conclusion: The authors developed an effective fluorescent imaging probe for the recognition of gastric cancer cells.

LBX2-AS1 as a Novel Diagnostic Biomarker and Therapeutic Target Facilitates Multiple Myeloma Progression by Enhancing mRNA Stability of LBX2

Objective: Multiple myeloma (MM) represents a common age-associated malignancy globally. The function and underlying mechanism of antisense lncRNA LBX2-AS1 remain ambiguous in multiple myeloma (MM). Herein, we aimed to observe the biological implication of this lncRNA in MM.

Methods: RT-qPCR was employed to examine circulating LBX2-AS1 and LBX2 in 60 paired MM and healthy subjects. Correlation between the two was analyzed by Pearson test. Under transfection with shLBX2-AS1, proliferation and apoptosis were evaluated in MM cells through CCK-8, colony formation and flow cytometry. LBX2 expression was examined in MM cells with shLBX2-AS1 or pcDNA3.1-LBX2 transfection. Following treatment with cycloheximide or actinomycin D, LBX2 expression was examined in pcDNA3.1-LBX2-transfected MM cells at different time points. Rescue assays were then presented. Finally, xenograft tumor models were established.

Results: Circulating LBX2-AS1 was up-regulated in MM patients and positively correlated to LBX2 expression. Area under the curve (AUC) of LBX2-AS1 expression was 0.7525. Its up-regulation was also found in MM cells and primarily distributed in cytoplasm. LBX2-AS1 knockdown distinctly weakened proliferative ability and induced apoptosis in MM cells. Overexpressing LBX2-AS1 markedly strengthened LBX2 expression by increasing its mRNA stability. Rescue assays showed that silencing LBX2-AS1 distinctly weakened the pcDNA3.1-LBX2-induced increase in proliferation and decrease in apoptosis for MM cells. Silencing LBX2-AS1 markedly weakened tumor growth.

Conclusion: Our data demonstrated that circulating LBX2-AS1 could be an underlying diagnostic marker in MM. Targeting LBX2-AS1 suppressed tumor progression by affecting mRNA stability of LBX2 in MM. Hence, LBX2-AS1 could be a novel therapeutic marker against MM.

lncRNA DSCR8 mediates miR-137/Cdc42 to regulate gastric cancer cell proliferation, invasion, and cell cycle as a competitive endogenous RNA

lncRNA DSCR8 (Down syndrome critical region 8) is involved in progression of many cancers, but its specific role in gastric cancer (GC) is still unclear. Here, qRT-PCR detected upregulated expression of DSCR8 and Cdc42 and downregulated expression of miR-137 in GC. The protein expression level of Cdc42 in GC was upregulated as tested by western blot. Statistical analysis showed that DSCR8 was closely associated with some malignant clinicopathological features (such as tumor size, metastasis, and stage) in GC patients. Fluorescence in situ hybridization showed that DSCR8 was localized in the nucleus and cytoplasm. Dual-luciferase reporter gene, RNA immunoprecipitation, and biotin pull-down assays showed that DSCR8 could bind to miR-137 could bind to Cdc42. In vitro and in vivo assays showed that DSCR8 could promote proliferation, invasion, and the cycle of GC cells and inhibit cell apoptosis. In addition, a rescue experiment showed that DSCR8 regulated progression of GC cells via miR-137. Furthermore, DSCR8 regulated Cdc42 in GC cells by inhibiting miR-137. Taken together, these data indicated that DSCR8 could adsorb miR-137 to reduce its inhibitory effect on Cdc42 expression, thereby promoting the progression of GC cells and regulating the cell cycle. These results provide a novel direction for DSCR8 as a target of GC.

Integrated Bioinformatic Analysis of Competing Endogenous RNA Network of Choriocarcinoma

Background

Numerous studies have demonstrated that noncoding RNAs are involved in choriocarcinoma (CC). The competing endogenous RNA (ceRNA) network plays an important role in the occurrence and development of carcinoma. However, the involvement of the ceRNA network in CC remains unclear. The current study aimed to investigate the regulatory mechanism of ceRNA in CC.

Material/Methods

We downloaded the messenger RNAs (mRNAs) expression profiles (GSE20510 and GSE65654) and microRNAs (miRNAs) expression profiles (GSE32346 and GSE130489) from GEO datasets. The limma package of R software was used to identify differentially expressed RNAs (DERNAs). Then, we performed functional annotation of the differentially expressed mRNAs (DEmRNAs). TargetScan, miRDB, miRWalk, and Starbase were used to construct a CC-specific ceRNA network and select key molecules.

Results

The results identified a total of 177 DEmRNAs and 189 differentially expressed miRNAs (DEmiRNAs) between the trophoblast and CC cell line samples. Ten differentially expressed lncRNAs (DElncRNAs) were obtained based on experimental studies. The DEmRNAs were mainly enriched in cell proliferation, positive regulation of the apoptotic process, and cell death. A total of 10 genes were ascertained as hub genes. Based on DEmRNAs, DEmiRNAs, and DElncRNAs, a CC-specific ceRNA network was established. Five DElncRNAs, 15 DEmiRNAs, and 45 DEmRNAs were identified. In addition, LINC00261, MEG3, MALAT1, H19, and OGFRP1 were identified as 5 key lncRNAs in choriocarcinoma.

Conclusions

This study provides novel insights into CC mechanisms and identified potential therapeutic targets for CC.

Bioinformatics analysis based on immune-autophagy-related lncRNAs combined with immune infiltration in bladder cancer

Background

To construct a prognostic model based on immune-autophagy-related long noncoding RNA (IArlncRNAs), mainly to predict the overall survival rate (OS) of bladder cancer patients and investigate its possible mechanisms.

Methods

Transcriptome and clinical data were obtained from The Cancer Genome Atlas (TCGA) database. We identified the IArlncRNA by co-expression analysis, differential expression analysis, and Venn analysis. Then, we identified the independent prognostic IArlncRNAs by univariate Cox regression, LASSO regression, and multivariate Cox regression analysis. Moreover, we constructed the prognostic model based on the independent prognostic IArlncRNAs and clinical features. The proportion of 22 immune cell subtypes was analyzed by the CIBERSORT algorithm. Besides, we identified the differential proportion of 22 immune cell subtypes between the high- and low-risk groups. In addition, we identified the correlation between immune-infiltrating cells (screened by univariate Cox regression and multivariate Cox regression analysis) and IArlncRNAs by Pearson correlation analysis. Finally, we estimated the half-maximal inhibitory concentration (IC₅₀) of chemotherapeutic drugs in patients with bladder cancer based on the pRRophetic algorithm.

Results

Four IArlncRNAs were identified as independent prognostic factors, including AL136084.3, AC006270.1, Z84484.1, and AL513218.1. The OS of patients in the high-risk group was significantly worse compared to the low-risk group. The nomogram showed an excellent predictive effect with the C-index of 0.64. The calibration chart showed a good actual vs. predicted probability. B cells naïve, T cells CD8, T cells CD4 memory resting, T cells follicular helper, macrophages M1, dendritic resting and activated cells had higher infiltrations in the low-risk group and lower infiltration of macrophages M2. The fraction of macrophages M2 was positively associated with AL136084.3. The fraction of T cells CD8 was positively associated with Z84484.1. The fraction of M + macrophages M0 was negatively associated with Z84484.1. Further, we identified the differential IC₅₀ of 24 chemotherapeutic drugs between the high- and low-risk groups.

Conclusions

The prognostic model based on 4 IArlncRNAs showed an excellent predictive effect. Furthermore, we reasonably speculated that IArlncRNAs are directly or indirectly involved in the immune regulation of the tumor microenvironment (TME), as well as autophagy.

Identification of Key lncRNA-mRNA Pairs and Functional lncRNAs in Breast Cancer by Integrative Analysis of TCGA Data

Long non-coding RNAs (lncRNAs) play an important role in many diseases and are involved in the post-transcriptional regulatory network of tumors. The purpose of this study is to mine new lncRNA–mRNA regulatory pairs and analyze the new mechanism of lncRNA involvement in breast cancer progression. Using breast cancer miRNA and mRNA expression profiling from The Cancer Genome Atlas (TCGA), we identified 59 differentially expressed lncRNAs, 88 differentially expressed miRNAs, and 1,465 differentially expressed mRNAs between breast cancer tissue and adjacent normal breast cancer. Whereafter, four candidate lncRNAs (FGF14-AS2, LINC01235, AC055854.1, and AC124798.1) were identified by the Kaplan–Meier (K–M) plotter. Furthermore, we screened the hub lncRNA (LINC01235) through univariate Cox analysis, multivariate Cox analysis, and qPCR validation, which was significantly correlated with breast cancer stage, ER status, and pathological N. Subsequently, 107 LINC01235-related mRNAs were obtained by combining differentially expressed miRNAs, differentially expressed mRNAs, and LINC01235 targeting miRNAs and mRNAs. The protein–protein interaction (PPI) network was established by Cytoscape software, and 53 key genes were screened. Function and pathway enrichment showed that LINC01235-related key genes might be involved in the process of cell differentiation, cell proliferation, and p53 signal pathway. In addition, LINC01235 has been confirmed to regulate the proliferation, migration, and invasion of MCF-7 cells in in vitro experiments. Furthermore, we screened three mRNAs (ESR1, ADRA2A, and DTL) associated with breast cancer drug resistance from key genes. Through RNA interference experiments in vitro and correlation analysis, we found that there was a negative feedback mechanism between LINC01235 and ESR1/ADRA2A. In conclusion, our results suggest that LINC01235-ESR1 and LINC01235-ADRA2A could serve as important co-expression pairs in the progression of breast cancer, and LINC01235 plays a key role as an independent prognostic factor in patients with breast cancer. The findings of this work greatly increase our understanding of the molecular regulatory mechanisms of lncRNA in breast cancer.

Immune-Related lncRNAs to Construct Novel Signatures and Predict the Prognosis of Rectal Cancer

Colorectal cancer (CRC) is one of the most common cancers. Almost 1/3 of CRC are rectal cancer, and 95% of rectal cancers are rectal adenocarcinoma (READ). Increasing evidences indicated that long noncoding RNAs (lncRNAs) have important role in the genesis and development of cancers. The purpose of our present study was to identify the differential expression lncRNAs which potentially related with immune cells infiltration and establish a risk assessment model to predict the clinical outcome for READ patients. We obtained three immune-related differential expression lncRNAs (IR-DELs) (C17orf77, GATA2-AS1, and TPT1-AS1) by differential expression analysis following correlation analysis and Cox regression analysis. A risk assessment model were constructed by integrating these analysis results. We then plotted the 1-, 3-, and 5-year ROC curves depending on our risk assessment model, which suggested that all AUC values were over 0.7. In addition, we found that the risk assessment model was correlated with several immune cells and factors. This study suggested that those three signatures (C17orf77, GATA2-AS1, and TPT1-AS1) screened by pairing IR-DELs could be prognosis markers for READ patients and might benefit them from antitumor immunotherapy.

Long non-coding RNA LINC01207 promotes cell proliferation and migration but suppresses apoptosis and autophagy in oral squamous cell carcinoma by the microRNA-1301-3p/lactate dehydrogenase isoform A axis

Long noncoding RNAs (lncRNAs) have been reported to participate in the progression of various cancers, including oral squamous cell carcinoma (OSCC). This study aims to find out whether lncRNA LINC01207 regulates the progression of OSCC. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was conducted to evaluate gene expression in OSCC cells and tissues. Cell viability, proliferation, migration, apoptosis, and autophagy were detected using Cell Counting Kit-8 (CCK-8), colony formation, Transwell assays, flow cytometry, and western blot analysis. Luciferase reporter and RNA immunoprecipitation (RIP) assays were conducted to assess the interactions among genes. We found that LINC01207 was overexpressed in OSCC cells and tissues. LINC01207 silencing inhibited OSCC cell proliferation and migration but promoted apoptosis and autophagy, and LINC01207 overexpression had an opposite result. LINC01207 interacted with microRNA-1301-3p (miR-1301-3p) while lactate dehydrogenase isoform A (LHDA) was targeted by miR1301-3p. Effects caused by LINC01207 downregulation on OSCC cells were reversed by overexpression of LDHA. Overall, LINC01207 promotes OSCC progression via the miR-1301-3p/LDHA axis