Only a small proportion of our genome is transcribed into mRNAs to produce protein. In contrast, most of our genome consists of ncRNAs that are not translated into proteins [10, 11]. In the past, there was a belief that the most important genetic material product were protein-encoding sequences, and that the remaining genome that does not encode proteins had unknown or obscure less important roles, such as ncRNAs and other gene products that were involved in gene expression and message transfer. But, more recently, it has been determined that ncRNA plays critical roles in diverse cellular and physiological processes including gene regulation, chromatin packaging, cell differentiation and development [10, 11, 12, 13, 14]. NcRNAs can be classified based on the number of nucleotides (nt) into lncRNAs that are greater than 200 nt long, and small ncRNAs that have no more than 200 nt. Small ncRNAs include microRNAs (miRNAs), small nuclear RNAs (snRNAs), small interfering RNAs (siRNAs), small nucleolar RNAs (snoRNAs), and Piwi-interacting RNAs (piRNAs) [15, 16, 17]. These different types of ncRNAs are illustrated in Fig. 2. In contrast to the short-lived miRNAs that have been extensively discussed in the literature, lncRNAs are stable and easily detectable in body fluids including plasma, and usually have higher tissue-specificity, thus these are a promising new class of biomarkers deserving of attention [18, 19, 20].

Fig. 2.

Categorization of types of non-coding RNAs (ncRNAs). NcRNAs are classified based on nucleotide number (nt) into long non-coding RNAs (lncRNAs) and small ncRNAs. Small ncRNAs are further classified based on their functions into many types: miRNAs (microRNAs), snRNAs (small nuclear RNAs), siRNAs (small interfering RNAs), snoRNAs (small nucleolar RNAs), piRNAs (Piwi-interacting RNAs).

LncRNAs are non-protein coding RNA transcripts that are greater than 200 nt in length [21]. These play important roles in tumor proliferation and progression via regulating the expression of oncogenes, tumor suppressor genes, and other cancer-associated genes through epigenetic control, and through transcriptional, posttranscriptional, and translational regulation [22, 23]. Although most research has focused on the intracellular roles of lncRNAs, there is a growing interest in the diagnostic and prognostic role of circulating lncRNAs as potential non-invasive biomarkers for a variety of diseases and tumors. Specific lncRNAs have been shown to be survival predictors in patients with heart failure [24], mortality predictors in patients with acute kidney injury [25], and novel biomarkers for diagnosis of coronary artery disease [26], esophageal squamous cell carcinoma [27], and gastric cancer [28].

The HOTAIR gene is located within a HOXC gene cluster on chromosome 12 between the HOXC11 and HOXC12 genes [36, 37]. This gene encodes a long noncoding RNA (lncRNA) molecule called HOTAIR that stretches for nearly 2200 nucleotides [38]. As illustrated in Fig. 3, the HOTAIR-PRC2-LSD1 complex attaches to the promoters of many tumor suppressor genes enabling HOTAIR to silence those genes through methylation of H3K27me3 and demethylation of H3K4me2 [39, 40]. Because of HOTAIR’s role in carcinogenesis, HOTAIR has an important diagnostic or prognostic role in multiple tumors. For example, it acts as a potential biomarker to diagnose breast cancer [41]. It also correlates with disease progression in bladder cancer [42]. It is considered a novel diagnostic biomarker for esophageal squamous cell carcinoma [36], and generally, its aberrant expression is associated with the metastatic progression of many malignancies [43]. Regarding the level of HOTAIR expression in GBM tissues, in a study that used glioma samples to elucidate the correlation between HOTAIR and glioma, Zhang et al. [44] found a significant increase in HOTAIR transcript levels in GBM, compared with that observed in normal tissues and low-grade gliomas. This study also shows that overall survival was inversely correlated with HOTAIR levels in GBM [44]. In another study, Zhou et al. [45] measured HOTAIR levels in gliomas and normal brain tissues and found a higher expression of HOTAIR in GBM tissues than in low-grade gliomas and normal brain tissues. Thus HOTAIR has potential for use as a serum biomarker for GBM diagnosis and prognosis since it appears to enable a correlation between HOTAIR expression and glioma grade.

Fig. 3.

HOTAIR role in epigenetic modifications. PRC2 is a target that HOTAIR can bind to and induce changes. The PRC2 complex then induces lysine methylation on histone H3. This H3K27-methylation is a form of gene silencing and is induced by histone methyltransferase EZH2, a component of PRC2. The LSD1 demethylase creates a repressor complex with REST and CoREST, that together have a pivotal role in gene silencing through mediating enzymatic demethylation of H3K4. HOTAIR interacts with both PRC2 and LSD1. The HOTAIR-PRC2-LSD1 complex attaches to the promoters of many tumor suppressor genes enabling HOTAIR to silence those genes. This histone methylation and demethylation is a dynamic process of epigenetic modification that regulates gene transcription, chromatin packaging, and cellular differentiation. Abbreviations: HOTAIR, HOX transcript antisense RNA; lncRNA, long non-coding RNA; PRC2, polycomb repressive complex 2; SUZ12, suppressor of zeste 12 protein homolog; EED, embryonic ectoderm development; EZH2, enhancer of zeste homolog 2; REST, RE1-silencing transcription factor; LSD1, lysine-specific histone demethylase 1; coREST, REST corepressor 1; H3K27me3, trimtethylated lysine 27 of histone H3; H3K4deme, demethylated lysine 4 of histone H3.

Another mechanism by which lncRNAs can indirectly alter gene expression is by acting as miRNA sponges or as competitive endogenous RNAs (ceRNA) by binding to miRNAs [48]. A single miRNA molecule can directly affect the expression of hundreds of genes by targeting hundreds of mRNAs so miRNAs can repress protein synthesis [49, 50]. As shown in Fig. 4, lncRNA binding to miRNAs can de-repress the expression of all target genes that were acted upon tumor suppressor genes or oncogenes [51].

Fig. 4.

Long noncoding RNA acts as a competitive endogenous RNA. LncRNAs (1) bind to miRNAs. This prevents miRNAs (2) from binding to mRNA (3) thus allowing mRNA translation (4).

LncRNA NEAT1 acts as a ceRNA, as discussed above. LncRNA NEAT1 binds to many miRNAs that have a suppressive effect on glioma cells growth and proliferation, including miR-139-5p, miR-132, miR-128-3p, miR-98-5p, and miR-107 [52, 53, 54, 55, 56, 57]. Subsequently, this leads to tumor cell proliferation and metastasis. Using qRT-PCR to measure NEAT1 expression in cultured tumor tissues from patients with gliomas and non-tumorous tissues, He et al. [58] found significantly higher NEAT 1 expression in glioma tissues. They also reported larger tumor sizes, higher WHO grade, and recurrence were strongly correlated with high levels of NEAT1 upregulation. Further, unfavorable prognoses were associated with patients receiving postoperative chemoradiotherapy with high NEAT1 expression [58]. This suggests a role for lncRNA NEAT1 expression in high-grade gliomas cell proliferation and metastasis, and hence the potential for novel treatments by targeting lncRNA NEAT1. Clinically, Wu et al. [59] found high expression of lncRNA NEAT1 in the plasma of GBM patients.

LncRNA GAS5 gene is located on chromosome 1q12.1 [60]. LncRNA GAS5 is considered an antioncogenic lncRNA and is downregulated in many tumors including ovarian and breast cancers, non-small cell lung cancers, large B‑cell lymphoma, and gastric and laryngeal cancers [60, 61, 62, 63, 64, 65]. In contrast, lncRNA GAS5 acts as an oncogenic lncRNA and is overexpressed in other tumors such as hepatocellular carcinoma and cholangiocarcinoma [66, 67]. LncRNA GAS5 suppresses glioma proliferation and growth by acting as a ceRNA through targeting multiple miRNAs including miRNA-222, miRNA-10b, and miR-196a-5p [68, 69, 70].

In GBM tissues, Toraih et al. [71] found that lncRNA GAS5 was significantly under-expressed. Clinically, Shen et al. [47] found that high serum levels of GAS5 were associated with a 56% decrease in the likelihood of death in GBM patients. This indicates the possibility of using LncRNA GAS5 as a prognostic and diagnostic biomarker for GBM patients.

LncRNA SAMMSON gene is located on chromosome 3p13–3p14 and is known to act as an oncogene in different tumors, such as melanoma, liver tumor, gastric cancer, papillary thyroid carcinoma, and oral squamous cell carcinoma [72, 73, 74, 75, 76]. In GBM tissues and cells, Ni et al. [77] detected high expression of lncRNA SAMMSOM. SAMMSON acts as a ceRNA through binding to miRNA-622. Through this mechanism, it increases GBM cell proliferation [78]. Clinically, Xie et al. [78] found that lncRNA SAMMSON was overexpressed in GBM patient plasma comparing to normal controls.

By binding to the HOTAIR promoter, Bromodomain Containing 4 (BRD4) protein controls HOTAIR levels and increases its expression. Pastori et al. [92] found that by using small molecule BET inhibitors, which are promising epigenetic modulators currently used in clinical trials, BRD4 activity can be inhibited to decrease BRD4 binding at the HOTAIR promoter. HOTAIR levels have been shown to decrease both in vitro and in vivo [92]. This inhibition of HOTAIR transcription is crucial to induce cell cycle arrest in GBM cells. Pastori et al. [92] suggested that HOTAIR can be used as a biomarker for the responsiveness of GBM cells to BET inhibitors. More research to examine the correlation between serum HOTAIR and GBM resistance to BET inhibitors is thus warranted.

TMZ is an alkylating agent that works by attaching an alkyl group (CnH2n+1) to the purine bases of DNA [103]. TMZ is metabolized finally to the electrophilic alkylating methyldiazonium cation that acts as a donor of a methyl group on the O6 position of guanine. Although the majority of DNA-methyl adducts are on the N7 of guanine and the N3 of adenine, the O6 position methylations accounts for about 5% of DNA adducts and are primarily responsible for the cytotoxic effects of TMZ [104]. The subsequent methyl group transferring to the O6 position of guanine forms O6-methylguanine lesion leading to DNA double-strand breaks. As a result, apoptosis and/or autophagy occur that cause cell death [105, 106]. TMZ was approved by the U.S. Food and Drug Administration for the treatment of glioblastoma [107]. There are many mechanisms of TMZ resistance for GBM [108], but here we will focus on lncRNAs role in developing TMZ resistance, their potential use as a biomarker for TMZ resistance, and their use as a novel therapeutic agent.

In contrast to bacteria that develop antibiotic resistance by acquiring protein-coding DNA pieces from other bacteria, non-coding genomic pieces make GBM resistant to TMZ. Of interest, by transferring those lncRNAs from chemoresistance GBM tissue or culture to a chemo-sensitive one, the chemo-sensitive tissue becomes chemoresistant [33].

Mazor et al. [95] found that lncRNA TP73-AS1 promotes TMZ resistance in GBM cancer stem cells and that there is a significant overexpression of lncRNA TP73-AS1 in GBM biopsies. This suggests a potential for this lncRNA to be used as a biomarker to predict TMZ chemoresistance. LncRNA OIP5-AS1 acts as a ceRNA by binding to miRNA-129-5p. Since miRNA-129-5p targets and downregulates IGF2BP2, lncRNA OIP5-AS1 can cause TMZ sensitivity if it is inhibited [96]. Thus, targeting this lncRNA could provide a novel therapeutic pathway for treating GBM patients with TMZ resistance. Another lncRNA that can cause TMZ sensitivity when it is knocked down is lncRNA CRNDE [97]. In GBM cells, LncRNA LINC00511 can promote TMZ chemoresistance by sponging miRNA-126-5p [98]. In contrast to those lncRNAs, there are other lncRNAs which have a protective role and induce chemosensitivity. For instance, lncRNA TUSC7 targets miRNA-10a in GBM cells which inhibits TMZ resistance [99]. LncRNA AC003092.1 is another lncRNA that promotes TMZ chemosensitivity in GBM cells which it does through binding to miRNA-195 [100].