The long non-coding RNAs, a new cancer diagnostic and therapeutic gold mine

Background: Long non-coding RNAs may play role in colorectal cancer (CRC) development, however, lncRNA expression profile in the colorectal adenoma-carcinoma sequence (C-ACS) and its relation to the complex epigenetic regulation system still remain incomplete. Aims: We aimed the whole genomic lncRNA expression profiling with up- and downstream epigenetic analyses of the C-ACS in order to explore the underlying mechanisms and consequences of aberrantly expressed lncRNAs. Materials&methods: lncRNA expression levels were analyzed on 60 colonic biopsy samples (20 CRCs, 20 adenomas, 20 normals) by Human Transcriptome Array (HTA) 2.0 (Affymetrix). Data analysis was perfomed using Expression Console and Transcriptome Analysis Console. Expression of certain candidates was verified in silico on HGU133 Plus 2.0 array data and also by qRT-PCR. DNA methylation status of lncRNA promoter regions was studied by methyl-capture sequencing. miRNA targets of lncRNAs were predicted with miRCODE algorithm and miRNA expression was analysed using GeneChip miRNA 3.0 Array. In the respective regulatory networks mRNA expression changes were also evaluated on the basis of the above-mentioned whole genome expression arrays. Results: According to HTA results analyzing 40.914 non-coding transcripts on whole genome level, in adenomas 12 lncRNAs (e.g. CCAT1, LINC00278) were significantly upregulated and 6 lncRNAs (e.g.FLJ22763, RP11.747D18.1) were downregulated compared to the healthy controls, while in CRC samples 1 lncRNA (UCA1) was overexpressed and 8 lncRNAs (e.g. LINC00350, LINC00261) were underexpressed compared to adenomas (p<0.05; -2≥Fold change≥2). In CRC samples 8 lncRNAs (e.g. MACC1, AC123023.1) were upregulated and 11 lncRNAs (e.g. RP13-497K6.1) were downregulated compared to normal controls. Furthermore, 42% of lncRNAs upregulated in CRC samples showed significantly elevated expression (p<0.05) already in adenoma samples (e.g. LINC350, CCAT1 were upregulated and LINC01133, FLJ22763 were downregulated compared to healthy controls). Promoter DNA methylation showed inverse relation with lncRNA expression along the C-ACS (e.g. CCAT1). In line with aberrant lncRNA expression in tumors, miRNA and mRNA targets’ expression showed systematic alterations, e.g. UCA1 upregulation in CRC samples in parallel with miR-1 downregulation accompanied by MET proto-oncogene target mRNA overexpression (p<0.05). Conclusion: The defined lncRNA sets (including MACC1, CCAT1, UCA1) have a central regulatory role in colorectal adenoma development and in tumor cell growth pathways. The underlying DNA methylation changes and miRNA and mRNA target expression alterations were proven using whole genomic array technologies. The identified lncRNA candidate sets can be further investigated as early diagnostic biomarkers and as potential therapeutic molecular targets for CRC. Citation Format: Alexandra Kalmar, Zsofia B. Nagy, Orsolya Galamb, Barnabas Wichmann, Barbara K. Bartak, Zsolt Tulassay, Bela Molnar. Key tumor growth controlling long non-coding RNA (lncRNA) expression alterations in the colorectal adenoma-carcinoma sequence. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 990.

Pan-cancer analysis of non-coding transcripts reveals the prognostic onco-lncRNA HOXA10-AS in gliomas.

Long noncoding RNAs (lncRNAs) are a unique class of messenger RNA-like transcripts of at least 200 nucleotides in length with no significant protein-coding capacity. Aberrant lncRNA expression is emerging as a major component of the cancer transcriptome. Here, we sought to determine if differential lncRNA expression is a feature of the human cervical intraepithelial neoplasia (CIN) transcriptome. Sequence data were derived from 16 long serial analyses of gene expression (L-SAGE) libraries constructed from cervical specimens representing mild (CIN1), moderate (CIN2), and severe (CIN3) histopathologic grades of CIN. A novel lncRNA discovery pipeline was developed to query the expression of lncRNAs within the SAGE data sets. A total of 2,230,370 sequence tags were delineated from the 16 SAGE libraries, representing the expression of 367,482 unique tags at varying abundance. Using a novel stepwise filtering strategy, we analyzed the cervical SAGE libraries and identified the expression profiles of 1056 lncRNAs in the human cervix. We present the first lncRNA expression profile derived from nonneoplastic cervical tissue and establish that changes in lncRNA expression do occur in cervical intraepithelial lesions. Our analysis also shows statistically significant aberrant expression of lncRNAs in the 3 CIN grades, suggesting that these unique noncoding RNA transcripts may contribute to the development and progression of precursor lesions. Through the analysis of L-SAGE libraries constructed from cervical specimens, we provide the first lncRNA expression profile of the cervix and demonstrate aberrant expression in early-stage neoplasia.

The lncRNA DEANR1 facilitates human endoderm differentiation by activating FOXA2 expression.

Long non-coding RNA (lncRNA) is aberrantly expressed in a variety of tumor diseases. To date, its specific role in acute myeloid leukemia (AML) has not been fully elucidated. This study aims to evaluate the association between aberrant lncRNA expression and poor prognosis in AML patients, and to systematically assess the relationship between aberrant lncRNA expression and AML prognosis. We conducted a comprehensive literature search in PubMed, Embase, Cochrane Library, CNKI (China National Knowledge Infrastructure), WanFang (China Wanfang Database), VIP (China VIP Database), and Sinomed (China Biomedical Literature Database) to identify relevant Chinese and English articles. The search period covered from the inception of these databases to 4 August 2024. Articles were screened according to predefined inclusion and exclusion criteria, and meta-analysis was performed using Stata. A total of 25 articles were included in the analysis. Aberrant lncRNA expression was significantly associated with reduced overall survival (univariate HR = 2.46, 95%CI 2.11-2.88, P < 0.001; multivariate HR = 2.46, 95%CI 2.11-2.88, P < 0.001), event-free survival (HR = 1.51, 95%CI 1.19-1.90, P = 0.001), recurrence-free survival (HR = 2.82, 95%CI 2.03-3.91, P < 0.001), and disease-free survival (HR = 2.390, 95%CI 1.037-5.507, P = 0.041). These findings were statistically significant. The 25 articles collectively identified 22 lncRNAs whose aberrant expression was associated with AML prognosis. Notably, multiple studies highlighted the aberrant expression of lncRNA CRNDE, ZEB2-AS1, and TUG1 as being particularly relevant to AML prognosis. Our meta-analysis revealed that high expression of lncRNA CRNDE and TUG1 was associated with reduced overall survival, while high expression of lncRNA ZEB2-AS1 was linked to decreased disease-free survival, both with statistically significant differences. The expression levels of lncRNAs are closely associated with the prognosis of AML patients and may serve as important indicators for monitoring prognosis in the future. However, further high-quality studies are needed to validate these findings.

BackgroundA novel class of transcripts, long non-coding RNAs (lncRNAs), has recently emerged as a key player in several biological processes, and important roles for these molecules have been reported in a number of complex human diseases, such as autoimmune diseases, neurological disorders, and various cancers. However, the aberrant lncRNAs implicated in myasthenia gravis (MG) remain unknown. The aim of the present study was to explore the abnormal expression of lncRNAs in peripheral blood mononuclear cells (PBMCs) and examine mRNA regulatory relationship networks among MG patients with or without thymoma.MethodsMicroarray assays were performed, and the outstanding differences between lncRNAs or mRNA expression were verified through RT-PCR. The lncRNAs functions were annotated for the target genes using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway. The potential regulatory relationships between the lncRNAs and target genes were analyzed using the ‘cis’ and ‘trans’ model. Outstanding lncRNAs were organized to generate a TF-lncRNA-gene network using Cytoscape software.ResultsThe lncRNA and mRNA expression profile analysis revealed subsets of differentially expressed genes in MG patients with or without thymoma. A total of 12 outstanding dysregulated expression lncRNAs, such as lncRNA oebiotech_11933, were verified through real-time PCR. Several GO terms including the cellular response to interferon-γ, platelet degranulation, chemokine receptor binding and cytokine interactions were very important in MG pathogenesis. The chromosome locations of some lncRNAs and associated co-expression genes were demonstrated using ‘cis’ analysis. The results of the ‘trans’ analysis revealed that some TFs (i.e., CTCF, TAF1and MYC) regulate lncRNA and gene expression. The outstanding lncRNAs in each group were implicated in the regulation of the TF-lncRNA-target gene network.ConclusionThe results of the present study provide a perspective on lncRNA expression in MG. We identify a subset of aberrant lncRNAs and mRNAs as potential biomarkers for the diagnosis of MG. The GO and KEGG pathway analysis provides an annotation to determine the functions of these lncRNAs. The results of the ‘cis’ and ‘trans’ analyses provide information concerning the modular regulation of lncRNAs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-015-0087-z) contains supplementary material, which is available to authorized users.

The present study aimed to investigate the implication of long non-coding RNA (lncRNA) expression profiles in post-menopausal osteoporosis (PMOP). A total of 10 patients with PMOP and 10 age-matched healthy post-menopausal females as controls were consecutively enrolled. Their peripheral blood mononuclear cells were obtained and lncRNA as well as mRNA expression profiles were detected by RNA sequencing, followed by bioinformatics analyses. The lncRNA expression profiles were able to distinguish patients with PMOP from controls based on principal component analysis and heatmap analysis. In total, 254 upregulated lncRNAs and 359 downregulated lncRNAs were identified in patients with PMOP vs. controls. The top 5 upregulated lncRNAs were RP11-704M14.1, RP11-754N21.1, RP11-408E5.5, ANKRD26P3 and TPTEP1. The top 5 downregulated lncRNAs were RP11-310E22.4, RP11-326K13.4, FABP5P1, SERPINB9P1 and RPL13P2. Based on the interaction of dysregulated lncRNAs and mRNAs by RNA sequencing, functional annotations were then performed. Gene Ontology enrichment analysis revealed that the dysregulated lncRNAs were enriched in terms including apoptotic process and positive regulation of NF-κB transaction, and Kyoto Encyclopedia of Genes and Genomes analysis suggested enrichment in PMOP-associated signaling pathways, including osteoclast differentiation, tumor necrosis factor signaling pathway and mitogen-activated protein kinase signaling pathway. In addition, the regulatory network and circos graph further indicated the implication of lncRNA expression profiles in PMOP via interactions with mRNAs. In conclusion, the present study suggested that aberrant lncRNA expression is deeply involved in the pathogenesis of PMOP by affecting osteoclast differentiation, inflammation and apoptotic processes.

Recent discovery that much of the mammalian genome does not encode protein-coding genes (PCGs) has brought widespread attention to long noncoding RNAs (lncRNAs) as a novel layer of biological regulation. Enhancer lnc (elnc) RNAs from the enhancer regions of the genome carry the capacity to regulate PCGs in cis or in trans. Spotted fever rickettsioses represent the consequence of host infection with Gram-negative, obligate intracellular bacteria in the Genus Rickettsia. Despite being implicated in the pathways of infection and inflammation, the roles of lncRNAs in host response to Rickettsia species have remained a mystery. We have profiled the expression of host lncRNAs during infection of susceptible mice with R. conorii as a model closely mimicking the pathogenesis of human spotted fever rickettsioses. RNA sequencing on the lungs of infected hosts yielded reads mapping to 74,964 non-coding RNAs, 206 and 277 of which were determined to be significantly up- and down-regulated, respectively, in comparison to uninfected controls. Following removal of short non-coding RNAs and ambiguous transcripts, remaining transcripts underwent in-depth analysis of mouse lung epigenetic signatures H3K4Me1 and H3K4Me3, active transcript markers (POLR2A, p300, CTCF), and DNaseI hypersensitivity sites to identify two potentially active and highly up-regulated elncRNAs NONMMUT013718 and NONMMUT024103. Using Hi-3C sequencing resource, we further determined that genomic loci of NONMMUT013718 and NONMMUT024103 might interact with and regulate the expression of nearby PCGs, namely Id2 (inhibitor of DNA binding 2) and Apol10b (apolipoprotein 10b), respectively. Heterologous reporter assays confirmed the activity of elncRNAs as the inducers of their predicted PCGs. In the lungs of infected mice, expression of both elncRNAs and their targets was significantly higher than mock-infected controls. Induced expression of NONMMUT013718/Id2 in murine macrophages and NONMMUT024103/Apol10b in endothelial cells was also clearly evident during R. conorii infection in vitro. Finally, shRNA mediated knock-down of NONMMUT013718 and NONMMUT024103 elncRNAs resulted in reduced expression of endogenous Id2 and Apl10b, demonstrating the regulatory roles of these elncRNAs on their target PCGs. Our results provide very first experimental evidence suggesting altered expression of pulmonary lncRNAs and elncRNA-mediated regulation of PCGs involved in immunity and during host interactions with pathogenic rickettsiae.

Osteoarthritis (OA) of hand is a common disease, resulting in disability of the hands. The pathogenesis of hand (H) OA remains to be elucidated, and findings from knee and hip joints cannot be simply applied to HOA. To improve knowledge on the specific biology and pathobiology of HOA, the present study performed bioinformatics analyses to analyze the long non-coding (lnc) RNA expression profile in human chondrocytes of proximal interphalangeal (PIP) finger joints and knee joints. Gene expression data were downloaded from the Gene Expression Omnibus database, and PIP and knee chondrocytes were analyzed (n=3/group). Probes of the Affymetrix Human Gene 2.0 ST Microarray were annotated to obtain information about lncRNA expression profile. Compared with chondrocytes from knee joints, chondrocytes derived from PIP joints had significantly different lncRNA expression profiles, and 1,172 lncRNAs were differentially expressed. Compared with chondrocyte from knee joints, 534 lncRNAs were upregulated and 638 lncRNAs were downregulated in chondrocytes from PIP joints. A co-expression network was constructed to analyze the correlation between lncRNAs and protein-coding genes. Function annotation analyses suggested that protein-coding genes that are co-expressed with lncRNAs are enriched in the biological processes of bone morphogenesis, bone development and cartilage development. In conclusion, the present study demonstrated that chondrocytes derived from PIP joints exhibit a significant difference in lncRNA expression compared with chondrocytes derived from knee joints.

High-throughput long noncoding RNA profiling for diagnostic and prognostic markers in cancer: opportunities and challenges.

Preclinical investigations in animal models have consistently demonstrated neurobiological changes and life-long cognitive deficits following exposure to widely used anesthetics early in life. However, the mechanisms by which these exposures affect brain function remain poorly understood, therefore, limiting the efficacy of current diagnostic and therapeutic options in human studies. The human brain exhibits an abundant expression of long noncoding RNAs (lncRNAs). These biologically active transcripts play critical roles in a diverse array of functions, including epigenetic regulation. Changes in lncRNA expression have been linked with brain development, normal CNS processes, brain injuries, and the development of neurodegenerative diseases, and many lncRNAs are known to have brain-specific expression. Aberrant lncRNA expression has also been implicated in areas of growing importance in anesthesia-related research, including anesthetic-induced developmental neurotoxicity (AIDN), a condition defined by neurological changes occurring in patients repeatedly exposed to anesthesia, and the related condition of perioperative neurocognitive disorder (PND). In this review, we detail recent advances in PND and AIDN research and summarize the evidence supporting roles for lncRNAs in the brain under both normal and pathologic conditions. We also discuss lncRNAs that have been linked with PND and AIDN, and conclude with a discussion of the clinical potential for lncRNAs to serve as diagnostic and therapeutic targets for the prevention of these neurocognitive disorders and the challenges facing the identification and characterization of associated lncRNAs.

IntroductionPulmonary thromboembolism (PTE) is a serious complication in patients with lung adenocarcinoma (LUAD), yet its molecular mechanisms remain poorly understood. This study aimed to investigate the expression profiles of long non-coding RNAs (lncRNAs) and mRNAs in LUAD patients complicated by PTE.MethodsPeripheral blood samples were collected from LUAD patients with PTE and from three control groups (LUAD-only, PTE-only, and healthy controls). RNA sequencing was performed to identify differentially expressed lncRNAs and mRNAs among groups.ResultsRNA sequencing revealed significant dysregulation of transcripts. Compared with LUAD-only patients, 725 lncRNAs and 2,052 mRNAs were differentially expressed in the LUAD + PTE group. Compared with PTE-only patients, 932 lncRNAs and 2,206 mRNAs were differentially expressed, while comparison with healthy controls identified 1,190 lncRNAs and 3,001 mRNAs. Key dysregulated transcripts included MERGE.31027.6, ENST00000318988, MERGE.30976.2, and ENST00000397519. Enrichment analyses highlighted immune response–related pathways, cytokine signaling, and the NF-κB signaling pathway.ConclusionThese findings suggest that aberrant lncRNA and mRNA expression may contribute to the pathogenesis of LUAD complicated by PTE and may serve as potential biomarkers and therapeutic targets for prognosis and treatment.

Introduction. Esophageal squamous cell carcinoma is a dangerous oncological disease for which there are no relevant molecular-biological and biochemical markers for diagnosis, monitoring, and prognosis. Non-coding RNAs, whose aberrant expression is characteristic of many neoplasms may be promising candidate markers.Aim. To investigate the clinical significance of the expression of long non-coding RNAs (lncRNAs) SNGH18, LCAL1, IGFL2-AS1, LINC02301 and LINC01508 in esophageal squamous cell carcinoma depending on the phenotype of the tumor stroma.Materials and methods. The study included 17 patients with esophageal squamous cell carcinoma, who were examined and treated at the N.N. Blokhin National Medical Research Center of Oncology. Gene expression levels were assessed using real-time polymerase chain reaction. Immunohistochemical analysis was conducted to evaluate the expression of CD68, CD163 and inducible nitric oxide synthase. Statistical analysis of the obtained results was performed using GraphPad Prizm v. 10. Differences in lncRNA expression between tumor samples and conditionally normal tissues were assessed using the Wilcoxon test for paired samples. Correlation analysis was carried out by calculating Spearman’s correlation coefficient. Survival analysis was conducted using Kaplan–Meier survival curves. A p-value of less than 0.05 was considered statistically significant.Results. Aberrant expression of the lncRNAs LCAL1, LINC01508 and LINC02301 was observed in tumor tissue compared to conditionally normal tissue. Specifically, the expression of LCAL1 and LINC01508 was increased in tumor tissue (p = 0,001 and p = 0,007), while the expression of lncRNA LINC02301 was decreased (p = 0,004). The expression of lncRNAs SNGH18 and IGFL2-AS1 showed no significant changes. ROC-analysis indicated that examining these lncRNA expressions is not suitable for diagnosing esophageal squamous cell carcinoma. Clinical significance analysis revealed no correlation between the studied lncRNA expressions and the clinicopathological characteristics of the disease correlation analysis of the lncRNAs SNGH18, LCAL1, IGFL2-AS1, LINC02301 and LINC01508 with the phenotype of tumor stroma macrophages demonstrated that LINC01508 was significantly and positively correlated with both the total number of macrophages (r = 0.579; p = 0.017) and the number of macrophages with cytotoxic and immunosuppressive phenotypes (r = 0.567; p = 0.004 and r = 0.496; p = 0.045, accordingly). In contrast, LCAL1 expression was inversely correlated with the number of cytotoxic macrophages (r = –0.490; p = 0.037). Prognostic analysis revealed that only lncRNA IGFL2-AS1 expression was associated with favorable prognosis in esophageal squamous cell carcinoma (hazard ratio 0.374; p = 0.039).Conclusion. Long non-coding RNAs are important regulatory elements in both normal and tumor cells, offering certain advantages for the diagnosis of oncological diseases due to their high specificity and stability in both tissues and circulating body fluids. Growing evidence from scientific research highlights the potential clinical application of lncRNA expression analysis as markers for early diagnosis and as potential therapeutic targets. In this study, we conducted a retrospective investigation and determined the clinical significance of lncRNAs SNGH18, LCAL1, IGFL2-AS1, LINC02301, LINC01508 in esophageal squamous cell carcinoma, thereby expanding our understanding of the molecular changes observed in the development of this disease.

The objective of this study was to elucidate the expression of long non-coding RNA (lncRNA) in leiomyomas (Lyo) and paired myometrium (Myo) and explore the impact of race and MED12 mutation. Fold change analysis (Lyo/paired Myo) indicated the expression of 63 lncRNAs was significantly altered in the mutated group but not in the non-mutated Lyo. Additionally, 65 lncRNAs exhibited an over 1.5-fold change in the Black but not the White group. Fifteen differentially expressed lncRNAs identified with next-generation sequencing underwent qRT-PCR confirmation. Compared with Myo, the expression of TPTEP1, PART1, RPS10P7, MSC-AS1, SNHG12, CA3-AS1, LINC00337, LINC00536, LINC01436, LINC01449, LINC02433, and LINC02624 was significantly higher, while the expression of ZEB2-AS1, LINC00957, and LINC01186 was significantly lower. Comparison of normal Myo with diseased Myo showed significant differences in the expression of several lncRNAs. Analysis based on race and Lyo MED12 mutation status indicated a significantly higher expression of RPS10P7, SNHG12, LINC01449, LINC02433, and LINC02624 in Lyo from Black patients. The expression of TPTEP1, PART1, RPS10P7, MSC-AS1, LINC00337, LINC00536, LINC01436, LINC01449, LINC02433, and LINC02624 was higher, while LINC01186 was significantly lower in the MED12-mutated group. These results indicate that Lyo are characterized by aberrant lncRNA expression, which is further impacted by race and Lyo MED12 mutation status.

Bone marrow stem cells (BMSCs) are involved in steroid-induced osteonecrosis of the femoral head (ONFH). Long noncoding RNAs (lncRNAs) have been demonstrated to regulate functions of BMSCs, especially their differentiation, and have been reported to be implicated in diverse bone disorders. However, the roles of lncRNAs in the progression of steroid-induced ONFH remain unknown. BMSCs were isolated from healthy controls or patients with steroid-induced ONFH. RNA-sequencing was used to identify differentially expressed (DE) coding and noncoding transcripts and a lncRNA-messenger RNA coexpression network were created. The function of lncRNA RP11-154D6 in the proliferation, apoptosis, and differentiation of BMSCs was identified by overexpressing or silencing its expression. Altogether, 3114 DE messenger RNAs and 572 DE lncRNAs were identified and the expression of lncRNA RP11-154D6 was significantly decreased in BMSCs of patients with ONFH. Although no effects on proliferation and apoptosis were identified, we proved lncRNA RP11-154D6 promoted osteogenic differentiation while inhibiting adipogenic differentiation in BMSCs. Aberrant expression of lncRNA was identified in BMSCs of steroid-induced patients with ONFH. Our results demonstrated that lncRNA RP11-154D6 might contribute to the progression of steroid-induced ONFH through regulating the behavior of BMSCs and might provide new insights into the pathogenesis as well as treatment for steroid-induced ONFH.