Methods to Study Long Noncoding RNA Biology in Cancer

Analysis of lncRNA-related studies of ivermectin-sensitive and -resistant strains of Haemonchus contortus

In this study, 858 novel long non-coding RNAs (lncRNAs) were predicted as sensitive and resistant strains of Haemonchus contortus to ivermectin. These lncRNAs underwent bioinformatic analysis. In total, 205 lncRNAs significantly differed using log2 (difference multiplicity) > 1 or log2 (difference multiplicity) <  - 1 and FDR < 0.05 as the threshold for significant difference analysis. We selected five lncRNAs based on significant differences in expression, cis-regulation, and their association with the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. These expressions of lncRNAs, namely MSTRG.12610.1, MSTRG.8169.1, MSTRG.6355.1, MSTRG.980.1, and MSTRG.9045.1, were significantly downregulated. These findings were consistent with the results of transcriptomic sequencing. We further investigated the relative expression of target gene mRNAs and the regulation of mRNA and miRNA, starting with lncRNA cis-regulation of mRNA, and constructed a lncRNA-mRNA-miRNA network regulation. After a series of statistical analyses, we finally screened out UGT8, Unc-116, Fer-related kinase-1, GGPP synthase 1, and sart3, which may be involved in developing drug resistance under the regulation of their corresponding lncRNAs. The findings of this study provide a novel direction for future studies on drug resistance targets.

ANRIL: A Long Noncoding RNA in Age-related Diseases

The intensification of the aging population is often accompanied by an increase in agerelated diseases, which impair the quality of life of the elderly. The characteristic feature of aging is progressive physiological decline, which is the largest cause of human pathology and death worldwide. However, natural aging interacts in exceptionally complex ways within and between organs, but its underlying mechanisms are still poorly understood. Long non-coding RNA (lncRNA) is a type of noncoding RNA that exceeds 200 nucleotides in length and does not possess protein-coding ability. It plays a crucial role in the occurrence and development of diseases. ANRIL, also known as CDKN2B-AS1, is an antisense ncRNA located at the INK4 site. It can play a crucial role in agerelated disease progression by regulating single nucleotide polymorphism, histone modifications, or post-transcriptional modifications (such as RNA stability and microRNA), such as cardiovascular disease, diabetes, tumor, arthritis, and osteoporosis. Therefore, a deeper understanding of the molecular mechanisms of lncRNA ANRIL in age-related diseases will help provide new diagnostic and therapeutic targets for clinical practice.

Epigenetic mechanisms of lncRNA in response to thermal stress during embryogenesis of allotetraploid Cyprinus carpio

Embryogenesis and epigenetic mechanisms of lncRNA may play an important role in the formation of temperature tolerance in allotetraploid Cyprinus carpio. To investigate the response of lncRNA to thermal stress during embryogenesis of C. carpio, transcriptome sequencing was performed on 81 embryo or larva samples from different early development stages and temperatures. We identified 45,097 lncRNAs and analyzed transcriptome variation during embryogenesis. Stage-specific and temperature-specific DE lncRNAs and DEGs were screened. GO and KEGG analysis identified numerous pathways involved in thermal stress. Temperature-specific regulation of cis-/trans-/antisense lncRNAs was analyzed. Interaction network analysis identified 6 hub lncRNAs and many hub genes, such as cdk1 and hsf1. Decreased expression of many essential genes regulated by lncRNAs may lead to the death of embryos at 33 °C. Our findings provide new insights into the regulation of lncRNA in thermal stress response during embryogenesis and contribute to the understanding of environmental adaptation of allotetraploid species.

Roles of lncRNAs in pancreatic ductal adenocarcinoma: Diagnosis, treatment, and the development of drug resistance

BACKGROUND

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers, primarily due to its late diagnosis, high propensity to metastasis, and the development of resistance to chemo-/radiotherapy. Accumulating evidence suggests that long non-coding RNAs (lncRNAs) are intimately involved in the treatment resistance of pancreatic cancer cells via interacting with critical signaling pathways and may serve as potential diagnostic/prognostic markers or therapeutic targets in PDAC.

DATA SOURCES

We carried out a systematic review on lncRNAs-based research in the context of pancreatic cancer and presented an overview of the updated information regarding the molecular mechanisms underlying lncRNAs-modulated pancreatic cancer progression and drug resistance, together with their potential value in diagnosis, prognosis, and treatment of PDAC. Literature mining was performed in PubMed with the following keywords: long non-coding RNA, pancreatic ductal adenocarcinoma, pancreatic cancer up to January 2022. Publications relevant to the roles of lncRNAs in diagnosis, prognosis, drug resistance, and therapy of PDAC were collected and systematically reviewed.

RESULTS

LncRNAs, such as HOTAIR, HOTTIP, and PVT1, play essential roles in regulating pancreatic cancer cell proliferation, invasion, migration, and drug resistance, thus may serve as potential diagnostic/prognostic markers or therapeutic targets in PDAC. They participate in tumorigenesis mainly by targeting miRNAs, interacting with signaling molecules, and involving in the epithelial-mesenchymal transition process.

CONCLUSIONS

The functional lncRNAs play essential roles in pancreatic cancer cell proliferation, invasion, migration, and drug resistance and have potential values in diagnosis, prognostic prediction, and treatment of PDAC.

An overview of long noncoding RNAs: Biology, functions, therapeutics, analysis methods, and bioinformatics tools

Long noncoding RNAs (lncRNAs) are a diverse class of RNAs whose functions are widespread in all branches of life and have been the focus of attention in the last decade. While a huge number of lncRNAs have been identified, there is still much work to be done and plenty to be learned. In the current review, we begin with the biogenesis and function of lncRNAs as they are involved in the different cellular processes from regulating the architecture of chromosomes to controlling translation and post-translation modifications. Questions on how overexpression, mutations, or deficiency of lncRNAs can affect the cellular status and result in the pathogenesis of various human diseases are responded to. Besides, we allocate an overview of several studies, concerning the application of lncRNAs either as diagnostic and prognostic biomarkers or novel therapeutics. We also introduce the currently available techniques to explore details of lncRNAs such as their function, cellular localization, and structure. In the last section, as exponentially growing data in this area need to be gathered and organized in comprehensive databases, we have a particular focus on presenting general and specialized databases. Taken together, with this review, we aim to provide the latest information on different aspects of lncRNAs to highlight their importance in physiopathologic states and take a step towards helping future studies.

Exploring clinical implications and role of non-coding RNAs in lung carcinogenesis

Lung cancer is the utmost familiar category of cancer with greatest fatality rate worldwide and several regulatory mechanisms exercise cellular control on critical oncogenic trails implicated in lung associated carcinogenesis. The non-coding RNAs (ncRNAs) are shown to play a variety of regulatory roles, including stimulating cell proliferation, inhibiting programmed cell death, enhancing cancer cell metastatic ability and acquiring resistance to drugs. Furthermore, ncRNAs exhibit tissue-specific expression as well as great stability in bodily fluids. As a consequence, they are strong contenders for cancer based theragnostics. microRNA (miRNA) alters gene expression primarily by either degrading or interfering with the translation of targeted mRNA and long non-coding RNAs (lncRNAs) can influence gene expression by targeting transcriptional activators or repressors, RNA polymers and even DNA-duplex. lncRNAs are typically found to be dysregulated in lung cancer and hence targeting ncRNAs could be a viable strategy for developing potential therapies as well as for overcoming chemoresistance in lung cancer. The purpose of this review is to elucidate the role of ncRNAs, revisiting the recent studies in lung cancer.

Non-Coding RNAs in Cancer Diagnosis and Therapy: Focus on Lung Cancer

Over the last several decades, clinical evaluation and treatment of lung cancers have largely improved with the classification of genetic drivers of the disease, such as EGFR, ALK, and ROS1. There are numerous regulatory factors that exert cellular control over key oncogenic pathways involved in lung cancers. In particular, non-coding RNAs (ncRNAs) have a diversity of regulatory roles in lung cancers such that they have been shown to be involved in inducing proliferation, suppressing apoptotic pathways, increasing metastatic potential of cancer cells, and acquiring drug resistance. The dysregulation of various ncRNAs in human cancers has prompted preclinical studies examining the therapeutic potential of restoring and/or inhibiting these ncRNAs. Furthermore, ncRNAs demonstrate tissue-specific expression in addition to high stability within biological fluids. This makes them excellent candidates as cancer biomarkers. This review aims to discuss the relevance of ncRNAs in cancer pathology, diagnosis, and therapy, with a focus on lung cancer.

LncRNA RBM5-AS1 Promotes Osteosarcoma Cell Proliferation, Migration, and Invasion

Purpose

Osteosarcoma (Os) is the most frequent malignant tumor of the bone in the pediatric age group, and accumulating evidences show that lncRNAs play a key role in the development of Os. Thus, we investigated the role of RBM5-AS1 and its molecular mechanism.

Methods

The expression of RBM5-AS1 in Os tissues and cell lines was detected by real-time polymerase chain reaction (QPCR). The effect of RBM5-AS1 on the proliferation of Os cells was detected using CCK8 assays and flow cytometry. The effect of RBM5-AS1 on the migration and invasion of Os cells was detected by transwell assays. And we performed QPCR and western blotting assays to investigate the relationship between RBM5-AS1 and RBM5. Finally, western blotting assays were performed to explore the mechanism of RBM5.

Results

LncRNA RBM5-AS1 was overexpressed in the Os tissues and cell lines. And lncRNA RBM5-AS1 promoted Os cell proliferation, migration, and invasion in vitro and tumor growth in vivo. LncRNA RBM5-AS1 targets RBM5 in Os cells.

Conclusion

To sum up, the results showed that lncRNA RBM5-AS1 promotes cell proliferation, migration, and invasion in Os.

Long Non-Coding RNAs: The Regulatory Mechanisms, Research Strategies, and Future Directions in Cancers

The development and application of whole genome sequencing technology has greatly broadened our horizons on the capabilities of long non-coding RNAs (lncRNAs). LncRNAs are more than 200 nucleotides in length and lack protein-coding potential. Increasing evidence indicates that lncRNAs exert an irreplaceable role in tumor initiation, progression, as well as metastasis, and are novel molecular biomarkers for diagnosis and prognosis of cancer patients. Furthermore, lncRNAs and the pathways they influence might represent promising therapeutic targets for a number of tumors. Here, we discuss the recent advances in understanding of the specific regulatory mechanisms of lncRNAs. We focused on the signal, decoy, guide, and scaffold functions of lncRNAs at the epigenetic, transcription, and post-transcription levels in cancer cells. Additionally, we summarize the research strategies used to investigate the roles of lncRNAs in tumors, including lncRNAs screening, lncRNAs characteristic analyses, functional studies, and molecular mechanisms of lncRNAs. This review will provide a short but comprehensive description of the lncRNA functions in tumor development and progression, thus accelerating the clinical implementation of lncRNAs as tumor biomarkers and therapeutic targets.

Increased levels of long noncoding RNA LINC00691 correlate with poor prognosis in non-small-cell lung cancer patients

Background

Although long intergenic non‐protein coding RNA 691 (LINC00691) has been functionally identified in several tumors, the association between LINC00691 and non–small‐cell lung cancer (NSCLC) has not been reported. The objective of our study was to explore the clinical significance of LINC00691 in NSCLC.

Methods

RT‐PCR was performed to detect LINC00691 levels in 177 pairs of human NSCLC tissues and matched normal lung specimens. A chi‐squared test was used to analyze the possible influence of LINC00691 on the clinical progress of NSCLC. Kaplan‐Meier methods were used to determine differences in patient survival. The prognostic value of survival variables was evaluated using univariate and multivariate analyses.

Results

We found that LINC00691 levels were increased in tumor specimens compared with matched normal lung tissues (P < .01). Increased LINC00691 levels correlated with lymph node metastasis (P = .025) and advanced TNM stage (P = .002) in NSCLC patients. Moreover, clinical investigations revealed that NSCLC patients with high LINC00691 expression had a shorter overall survival than those with low LINC00691 expression (P = .0042). Finally, Cox regression assays confirmed LINC00691 as an independent prognostic factor for NSCLC patients.

Conclusions

The aberrant expression of LINC00691 may function as a reliable marker for the progression and prognosis of NSCLC in patients.

SP1-Mediated Upregulation of lncRNA LINC01614 Functions a ceRNA for miR-383 to Facilitate Glioma Progression Through Regulation of ADAM12

Background

Long non-coding RNAs (lncRNAs) play an imperative role in tumorigenesis, but few lncRNAs have been functionally characterized in glioma. The aim of the present study was to identify the role of long non-coding RNA LINC01614 (LINC01614) in glioma development and explore the underlying mechanisms of LINC01614/miR-383/ADAM12 axis.

Patients and Methods

LncRNA expression in glioma specimens was measured by lncRNA microarray and qRT-PCR. The prognostic value of LINC01614 expression was statistically analyzed in 112 glioma patients. Loss-of-function experiments were conducted to investigate the biological functions of LINC01614 in vitro. Luciferase analyses, ChIP assays, and RNA pull-down were performed to determine the underlying LINC01614 mechanisms.

Results

We identified a novel glioma-related lncRNA LINC01614 by analyzing TCGA datasets. The distinct upregulation of LINC01614 was observed in both glioma specimens and cell lines using RT-PCR. We also observed that LINC01614 upregulation was induced by nuclear transcription factor SP1. Clinical assays revealed that high levels of LINC01614 were associated with KPS, WHO grade and shorter overall survival of glioma patients. Multivariate analysis further confirmed that LINC01614 was an independent prognostic marker for glioma patients. Besides, functional assays displayed that silence of LINC01614 knockdown distinctly inhibited cell growth, migration and invasion and promoted cell apoptosis in glioma cells. LINC01614 expression was enriched in the cytoplasm of glioma cells. Mechanistic investigation revealed that LINC01614 functioned as a competing endogenous RNA to upregulate a disintegrin and metalloproteinase 12 (ADAM12) by sponging miR-383.

Conclusion

Overall, these findings showed that SP1-induced upregulation of LINC01614 promoted glioma malignant progression via modulating the miR-383/ADAM12 axis, which may provide a promising therapy for glioma.

Long Noncoding RNA SNHG1 Contributes to the Promotion of Prostate Cancer Cells Through Regulating miR-377-3p/AKT2 Axis

Background: Long noncoding RNAs could serve as a candidate target for prostate cancer (PCa) diagnosis and treatment. The current study aimed to investigate the role and functions of SNHG1 in PCa cells. Materials and Methods: Abnormal expression of SNHG1, survival analysis, and target gene were determined or predicted by bioinformatics techniques. Gene expressions at transcriptional and translational levels were determined by Quantitative Real-time PCR and Western blotting, respectively. Cell viability, growth, and apoptosis rate were detected by Cell Counting Kit-8, colony formation assay and flow cytometry. Results: The results showed that SNHG1 was highly expressed in PCa tissues, which was accompanied by decreased miR-377-3p expression and poor overall survival rate, and that miR-377-3p was predicted as the target of SNHG1 in PCa cells. Moreover, SNHG1 counteracted the effects of miR-377-3p on inhibiting cell growth and promoting apoptosis of PCa cells. Furthermore, miR-377-3p counteracted the effects of AKT2 on promoting cell viability, growth, and suppressing apoptosis of PCa cells. In addition, AKT2 expression was proved to be regulated by miR-377-3p. Conclusions: The SNHG1/miR-377-3p/AKT2 regulatory axis in PCa cells was disclosed. The upregulated AKT2 might be a result of dysregulated interaction balance between the expressions of miR-377-3p and SNHG1. Based on such discoveries, the intervention of SNHG1/miR-377-3p/AKT2 axis could be further explored in the treatment of PCa.

SOX2-induced upregulation of lncRNA LINC01561 promotes non-small-cell lung carcinoma progression by sponging miR-760 to modulate SHCBP1 expression

Long noncoding RNAs (lncRNAs) have been shown to have critical regulatory roles in tumorigenesis. lncRNA LINC01561 (LINC01561) is a newly identified tumor-related lncRNA and its dysregulation has been demonstrated in several tumors. However, whether LINC01561 is involved in the progression of non-small-cell lung carcinoma (NSCLC) and its underlying mechanisms remain unknown. In this study, we first provided evidence that LINC01561 expressions were distinctly upregulated in NSCLC tissues and cell lines. Combining with bioinformatics assays and mechanism experiments, our group demonstrated that LINC01561 was activated by SOX2 in NSCLC. Clinical research revealed that upregulation of LINC01561 was related to poorer clinicopathologic features and shorter survival time. Functionally, suppression of LINC01561 exhibited tumor-suppressive functions through impairing cell proliferation, migration, and invasion as well as inducing apoptosis. Moreover, we verified that LINC01561 could directly bind to miR-760, isolating miR-760 from its target gene SHC SH2 domain-binding protein 1 (SHCBP1). We also found that SHCBP1 was lowly expressed in NSCLC and served as a tumor promoter. A functional study indicated that LINC01561 regulated SHCBP1 expression by competitively binding to miR-760. In summary, our findings indicated that SOX2-induced overexpression of LINC01561 promoted the proliferation and metastasis by acting as a competing endogenous RNA to modulate SHCBP1 by sponging miR-760.

The interaction of long non-coding RNA MIAT and miR-133 play a role in the proliferation and metastasis of pancreatic carcinoma

Pancreatic cancer (PC) is one of the most aggressive malignancies in humans. Despite advances in early detection and treatment of PC, the prognosis is still limited. LncRNA myocardial infarction-associated transcript (MIAT) is found abnormally expressed in a variety of cancers. However, the role of MIAT in PC is still unknown. This study aimed to explore whether MIAT was related to the progression of PC and the underlying mechanism. Bioinformatics analysis and luciferase reporter assay validated that miR-133 may target MIAT 3'-UTR. MIAT expression was found remarkably increased and miR-133 expression was significantly decreased in PC tissues and PC cell lines (PATU-8988, BxPC-3, PANC-1, SW1990 and AsPC-1 cells). PC patients with high MIAT level had poor prognosis than that with low MITA level. Besides that, PATU-8988 cells transfected with siMIAT and/or miR-133 inhibitor. The results exhibited that the inhibition of miR-133 expression reversed the inhibition effect of MIAT down-regulation in the growth, migration and invasion of PC cells. Moreover, tumor growth was tremendously suppressed in nude rats received injection of PATU-8988 cells transfected with siMIAT. Taken together, our results suggest that the interaction of MIAT and miR-133 play a role in the proliferation and metastasis of pancreatic carcinoma.