HOTAIR beyond repression: In protein degradation, inflammation, DNA damage response, and cell signaling

Abstract

Long noncoding RNAs (lncRNAs) are pervasively transcribed from the mammalian genome as transcripts that are usually >200 nucleotides long. LncRNAs generally do not encode proteins but are involved in a variety of physiological processes, principally as epigenetic regulators. HOX transcript antisense intergenic RNA (HOTAIR) is a well-characterized lncRNA that has been implicated in several cancers and in various other diseases. HOTAIR is a repressor lncRNA and regulates various repressive chromatin modifications. However, recent studies have revealed additional functions of HOTAIR in regulation of protein degradation, microRNA (miRNA) sponging, NF-κB activation, inflammation, immune signaling, and DNA damage response. Herein, we have summarized the diverse functions and modes of action of HOTAIR in protein degradation, inflammation, DNA repair, and diseases, beyond its established functions in gene silencing.

Introduction

The human genome is huge with 3 billion base pairs, and the vast majority of this DNA does not code for protein but rather for transcripts that are mostly non-translated, called non-coding RNA (ncRNAs).¹ Long ncRNAs (lncRNAs) are pervasively transcribed from the genome as transcription products usually >200 nucleotides long and, like protein-coding transcripts, lncRNAs may be capped and polyadenylated.² To date, approximately 60,000 lncRNAs have been identified, many of which affect the transcription of various proteins and non-coding genes, such as microRNAs (miRNAs).³ LncRNAs play post-transcriptional roles in the cell to regulate dosage compensation, imprinting, and developmental gene expression.⁴ LncRNAs modulate various aspects of the epigenetic machinery, and their dysregulation impacts several aspects of cellular homeostasis, including proliferation, mobility, chromatin remodeling, gene expression, post-synthetic processing, and differentiation.⁵

HOX transcript antisense intergenic RNA (HOTAIR) is a noncoding transcript encoded from chromosome 12 within the HOXC gene cluster and acts in trans to silence the HOXD locus of chromosome 2, as well as genes on other chromosomes.^6–7 HOTAIR is transcribed from the antisense strand by RNA polymerase II and is 2.2 kb long, spliced, and polyadenylated.⁸ It is overexpressed in a wide variety of cancers and is associated with the promotion of oncogenesis and metastasis,⁹ and is one of the most well-characterized lncRNAs implicated in gene silencing. HOTAIR interacts with chromatin-modifying enzymes such as polycomb repressive complex 2 (PRC2) and lysine specific demethylase 1 (LSD1), multi-protein complexes that are major players in gene silencing.¹⁰ HOTAIR recruits these chromatin-modifying enzymes to gene promoters and suppresses the expression of tumor suppressors, thereby facilitating tumor growth. However, several recent studies revealed that HOTAIR may have additional roles beyond its well-known functions in gene repression, including modulatory roles in certain neurological,¹¹ orthopedic,¹² and metabolic¹³ conditions through several mechanisms, including protein degradation,^14–15 NF-κB activation,^16–17 microRNA sponging,^18–19 and immune signaling.^20–21 This review will focus on the functions of HOTAIR beyond repression and will describe its diverse roles in protein degradation, inflammation, DNA damage response, cell signaling, mechanisms of action, and roles in various diseases.

HOTAIR overexpression in cancer

HOTAIR is an oncogenic lncRNA that is overexpressed in a variety of solid tumors, including breast cancer,²² esophageal cancer,²³ hepatocellular carcinoma,¹⁹ lung cancer,²⁴ colorectal cancer,²⁵ and others.^26–28 HOTAIR overexpression is positively correlated with tumorigenesis, angiogenesis, cancer stem cell differentiation, progression, invasion, drug resistance, metastasis, and poor prognosis in a wide array of human malignancies via various signaling pathways.^28–32 For example, in lung cancers, an increased HOTAIR level is associated with cell motility and invasion, and contributes to chemoresistance in small-cell lung cancer and lung adenocarcinoma, at least partly by regulating the expression of the tumor-suppressor p21.^{24, 33–34} HOTAIR overexpression is associated with distant metastasis and poor prognosis in colon cancer²⁵ and with malignant proliferation, invasion, and metastasis in breast cancer.³⁵ HOTAIR was found to be highly expressed in lymph node metastases from primary melanoma, and its knockdown reduced cell motility and invasion in human melanoma.³⁶ By shortening the cell cycle and promoting malignant cell proliferation, HOTAIR has been found to play a role in the development and progression of adrenocortical carcinoma.³⁷ Independent of other prognostic variables, HOTAIR levels in glioma patients are associated with higher grade and significantly shortened survival.³⁸ HOTAIR deregulation has been identified in various gynecologic cancers, including endometrial and cervical cancers.³⁹ It has been shown to act as an oncogene in gastric cancer, possibly by de-repressing HER2, and a functional single nucleotide polymorphism (SNP) in the HOTAIR gene may affect the risk of this malignancy.^40–41 HOTAIR is significantly upregulated in cancerous gastric tissues and there is evidence for an inverse relationship between HOTAIR and poly r(C)-binding protein 1 (PCBP-1), which is an inhibitor of gastric cancer pathogenesis.⁴² Elevated HOTAIR levels in esophageal squamous cell carcinoma (ESCC) tissues are positively associated with ESCC metastases, higher stage, and significantly reduced overall survival in human patients, and its knockdown diminishes tumor cell invasiveness and migration potential.⁴³ Specific HOTAIR SNPs have also been strongly associated with susceptibility to pancreatic cancer and with malignant cell proliferation.^44–45

HOTAIR in non-malignant disorders

Besides its well-known associations with a multitude of cancers, HOTAIR overexpression has been associated with various neurological,¹¹ musculoskeletal,⁴⁶ and metabolic¹³ disorders. Increased activity of leucine-rich repeat kinase 2 (LRRK2) is strongly implicated in the pathogenesis of Parkinson’s disease (PD); in a mouse model of PD, HOTAIR upregulated this enzyme and specifically increased the stability of its mRNA transcript.⁴⁷ PD mice-model-based studies demonstrated that disease progression could be significantly suppressed by inhibition of HOTAIR, which binds miR-126–5p to indirectly upregulate its target RAB3IP, a guanine nucleotide exchange factor that may suppress neuronal autophagy, and to promote apoptosis in PD cells.⁴⁸ Deregulation of the p35/CDK5 (cyclin-dependent kinase 5) complex is closely associated with the onset and progression of Alzheimer’s disease, and HOTAIR negatively regulates mRNA levels of the gene that encodes for p35, cyclin-dependent kinase 5 regulatory subunit 1 (CDK5R1).⁴⁹ HOTAIR was found to be upregulated in vitamin D-deficient patients with multiple sclerosis, suggesting a possible role in the pathogenesis of this disease specifically through a vitamin D-mediated immune process.⁵⁰

HOTAIR appears to play roles in the most common types of arthritis. Its overexpression was identified in the blood mononuclear cells and serum exosomes of patients with rheumatoid arthritis, possibly indicating its involvement in delivering inflammatory components to nearby cells or through the circulatory system, and the same study showed that HOTAIR contributed to rheumatoid arthritis pathogenesis by upregulating matrix metalloproteinase (MMP)-2 and MMP-13 in osteoclasts and synoviocytes, promoting joint destruction.⁵¹ The pathogenesis of osteoarthritis is associated with HOTAIR overexpression, possibly through a HOTAIR/miR-17–5p/FUT2/β-catenin axis,⁴⁶ with high HOTAIR levels being shown to induce apoptosis and to diminish chondrocyte viability.⁵²

HOTAIR is also involved in disorders of energy metabolism. It is significantly upregulated in patients with type II diabetes¹³ and was found to participate in hepatic insulin resistance by inhibiting SIRT1, a protein deacetylase necessary for maintaining metabolic homeostasis in hepatocytes.⁵³ Likely via promoter methylation, HOTAIR suppresses SIRT1 expression in liver cells exposed to hepatitis C virus core protein, contributing to dysregulation of several genes related to glucose and lipid metabolism.⁵⁴ Interestingly, a study on nasopharyngeal carcinoma showed that knockdown of HOTAIR led to downregulation of fatty acid synthase and inhibition of de novo synthesis of cellular free fatty acids in cancer cells.⁵⁵ A non-comprehensive list of diseases with demonstrated HOTAIR activity and some of its functions and modes of action is presented in Table 1.

Table 1.

HOTAIR’s functions and modes of action in various diseases.

Disease type	Factors linked to HOTAIR overexpression	Proposed mechanism of action	REFs
Lung cancer	Invasion, metastasis, 5FU chemoresistance, poor prognosis	Epigenetic downregulation of tumor suppressors; promotion of EMT via derepression of Snail by sponging miR-34a-5p; promotion of cell cycle progression	18–20, 45,46
Colorectal cancer	Distant metastasis, poor prognosis, 5FU resistance	Suppression of miR-34a, miR-214, and miR-218; EMT induction	21,47–49
Breast cancer	Proliferation, invasion, metastasis, resistance to radiotherapy	Sponging miR-218; EMT promotion	22, 50, 51
Liver cancer	Tumorigenesis, proliferation, metastasis	Suppression of miR-217; upregulation of CCL2; EMT promotion via sponging miR-23b-3p; repression of miR-1	52–57
Esophageal cancer	Metastasis, progression, poor prognosis	Derepression of CCND1 by sponging miR-1	30, 58
Nasopharyngeal carcinoma	Oncogenesis, angiogenesis, tumor progression, poor prognosis	Activation of VEGFA	44, 59, 60
Glioma	Higher tumor grade, progression, shortened survival	Sponging of miR-141 and miR-148b-3p	25, 61, 62
Head and neck squamous cell carcinoma	Proliferation, invasion, migration	Derepression of PI3K/AKT pathway by sponging miR-206	63
Renal cell carcinoma	Tumorigenesis, progression, poor prognosis	HIF-1α/AXL signaling by sponging miR-217; upregulation of IGFBP2	64, 65
Melanoma	Lymph node metastasis, invasion	Unknown	23
Gastric carcinoma	Pathogenesis, larger tumor size, extensive metastasis, poor prognosis	Derepression of HER2 by sponging miR-331–3p; activation of EMT via Snail derepression by sponging of miR-34a and epigenetic suppression of E-cadherin	27–29, 66, 67
Ovarian cancer	Proliferation, invasion, tumor size, metastasis, platinum chemoresistance	Inhibition of cell cycle arrest via upregulation of CCND1 and 2 by miR-206 sponging; miR-373 sponging; NF-κB pathway activation	68
Cervical cancer	Advanced stage, lymph node invasion, metastasis, tumor progression, poor prognosis	Repression of tumor-suppressor miR-206; derepression of HLA-G by sponging miR-148a	26, 69, 70
Pancreatic cancer	Increased risk, proliferation, poor prognosis	Inhibition of cell cycle arrest via sponging miR-613	31, 32, 71
Prostate cancer	Malignant cell growth and invasion	Epigenetic AR suppression in non-CRPC; AR stabilization via blocking ubiquitination in CRPC; repression of tumor suppressor miR-193a	72–74
Adrenocortical carcinoma	Tumorigenesis, progression	Promotion of cell cycle progression by upregulation of CCND1	24
Chromic myeloid leukemia	Acquired multidrug resistance	Activation of PI3K/AKT signaling	75, 76
Acute myeloid leukemia	Poor prognosis	Upregulation of proto-oncogene c-KIT via sponging miR-193a	77
Chondrosarcoma	Higher tumor grade, poor prognosis	Silencing of anti-oncogene miR-454–3p	78
Type 2 diabetes	Hepatic insulin resistance	Inhibition of SIRT1	35, 42, 43
Parkinson’s disease	Pathogenesis	Upregulation of LRRK2, sponging of MiR-126–5p	36, 37
Alzheimer’s disease	Onset and progression	Downregulation of p35 (activator of CDK5)	38
Multiple sclerosis with vitamin D deficiency	Pathogenesis	Unknown	39
Rheumatoid arthritis	Pathogenesis	Upregulation of MMP-2 and −13	40
Osteoarthritis	Increased apoptosis and reduced chondrocyte viability	Sponging miR-130a-3p	41
Sepsis	Activation of NF-κB pathway and upregulation of inflammatory cytokines	Recruitment of coactivators and transcription factors to NF-κB binding sites on IL-6 and iNOS promoters; induced expression of IL-6R by sponging miR-211	70, 79, 80

Abbreviations: AR, androgen receptor; CCL2, chemokine (C-C motif) ligand 2; CCND1 & 2, cyclin D1 and D2; CDK5, cyclin-dependent kinase 5; CRPC, castration-resistant prostate cancer; EMT, epithelial-to-mesenchymal transition; HER2, human epidermal growth factor receptor 2; HLA-G, human leukocyte antigen-G; IGFBP2, insulin growth factor-binding protein 2; IL-6R, interleukin-6R; iNOS, inducible nitric oxide synthase; LRRK2, leucine-rich repeat kinase 2; MMP, matrix metalloproteinase; NF-κB, nuclear factor κB; SIRT1, sirtuin 1; VEGFA, vascular endothelial growth factor A.

HOTAIR in chromatin modification and transcriptional control

HOTAIR is classically known as repressor lncRNA.⁸ It can function as a scaffold by interacting via its 5’ end with EZH2, a subunit of polycomb repressive complex 2 (PRC2), an epigenetic silencing complex that binds to approximately 20% of all lncRNAs and exerts H3K27 tri-methylase activity via its catalytic EZH2 subunit to act as a transcription repressor.⁸ In addition, HOTAIR interacts with lysine-specific demethylase 1A (LSD1), a histone modifier that suppresses transcription via H3K4 demethylation via its 3’ end (Figure 1).⁴ HOTAIR and PRC2 were shown to be functionally interdependent in cancer invasiveness, and the genome-wide silencing of metastasis-suppressor genes via HOTAIR’s targeted recruitment of PRC2 to those genes’ promoters has been demonstrated.⁹ Portoso et al. reported that HOTAIR overexpression was able to repress a limited number of target genes independently of PRC2, suggesting that there are multiple mechanisms through which HOTAIR induces transcriptional repression of other genes.⁵⁶

Figure 1.

HOTAIR recruits and binds PRC2 and LSD1, acting as a transcription-suppressing scaffold. PRC2, bound to the 5’ end of HOTAIR, epigenetically represses gene expression via H3K27me3, while 3’-bound LSD1 does so via H3K4 demethylation.

HOTAIR has also been demonstrated to exert transcriptional control via mechanisms that do not involve the PRC2/LSD1 complex. For example, in a study on liver cancer stem cells, HOTAIR blocked the recruitment of CREB, P300, and RNA polymerase II to the promoter region of SETD2, a histone methyltransferase specific for H3K36me3, which is associated with transcription activation.⁵⁷ In contrast, HOTAIR promoted angiogenesis in nasopharyngeal carcinoma by directly activating the transcription of angiogenic factor VEGFA via binding to HOTAIR-responsive elements in the VEGFA promoter.⁵⁸

Regulation of miRNA by HOTAIR: epigenetic silencing and competitive binding

In addition to epigenetically regulating various protein-coding genes via epigenomic modulations, HOTAIR silences many microRNA (miRNAs). MiRNAs are highly conserved small non-coding RNAs of 17–25 nt in length that play a major regulatory role in cells by binding directly to the 3’-UTR of target messenger RNAs (mRNAs) and causing mRNA cleavage and/or translational repression.⁵⁹ Some miRNAs are considered proto-oncogenes while others act as tumor suppressors by inhibiting the translation of oncogenic proteins. Indeed, perturbations in the expression levels of specific miRNAs have been found to be associated with the vast majority of human malignancies.^60–61 Over half of the 140 lncRNAs analyzed in one study affected their targets in a miRNA-dependent manner.⁶² HOTAIR is no exception, silencing its target miRNAs in various ways. For example, in gastric cancer, miR-34a modulates targets that accelerate metastasis by contributing to epithelial-to-mesenchymal transition (EMT); HOTAIR contributes to EMT in this system by recruiting PRC2 to the miR-34a promoter, where the EZH2 subunit directly binds and mediates repression via H3K27 trimethylation.⁶³ In pancreatic cancer, HOTAIR silences miR-663b by disrupting the balance between H3K27me3 and H3K4me3 at its promoter; this miRNA targets insulin-like growth factor 2, the overexpression of which is closely associated with worse prognosis.⁴⁵ Studies on chondrosarcoma cell lines showed that the HOTAIR/EZH2 complex epigenetically silenced miR-454–3p via CpG-island methylation; this miRNA acts as an anti-oncogene by targeting STAT3 and ATG12 (involved in cell growth and autophagosome formation, respectively).⁶⁴

Besides being transcriptionally repressed via histone modification, miRNAs can be sponged by HOTAIR acting as a competitive endogenous RNA (ceRNA), indirectly causing the de-repression of miRNA targets.⁶⁵ An example of this is shown in Figure 2. Several studies have demonstrated that HOTAIR acts as ceRNA to upregulate specific tumorigenic genes. For example, HOTAIR acts as a sink for miR-331–3p in gastric cancer cells, leading to de-repression of its direct target, human epithelial growth factor receptor (HER2), which oncogenically activates cellular networks involved in proliferation, motility, and angiogenesis.⁴⁰ By competitively binding miR-193a, HOTAIR modulates the expression of the proto-oncogene c-KIT in acute myeloid leukemia cells,⁶⁶ and in ovarian cancer, it acts as a sink for miR-373 to de-repress Rab22a, a small GTPase that modulates cancer cell proliferation.⁶⁷ Overexpression of the transcription factor ZEB1 is involved in malignant transformation and is targeted by miR-23b-3p for suppression; HOTAIR sponges miR-23b-3p in hepatocellular carcinoma (HCC) cells, thus promoting invasion and migration.^{19, 68} MiR-218 is sponged by HOTAIR in breast cancer, inhibiting cell apoptosis and DNA damage from radiotherapy.⁶⁹ SKA2, overexpressed in glioma tissues, is a direct target of miR-141 but is de-repressed by HOTAIR sponging of this miRNA.⁷⁰ Also in glioma, an in vitro model showed that HOTAIR knockdown increased the permeability of the blood-tumor barrier (BTB) by binding to miR-148b-3p and thereby reducing the expression of several proteins related to tight junctions.⁷¹ HOTAIR competitively binds to miR-206, which directly targets STC2 to inhibit activation of the PI3K/AKT signaling pathway in head and neck squamous cell carcinoma (HNSCC), and knockdown of HOTAIR reduced tumor growth in an HNSCC mouse model.⁷²

Figure 2.

Mechanism of competing endogenous (ceRNA) functionality of HOTAIR. HOTAIR contains miRNA response elements (MREs) that can bind to various miRNAs, and can therefore sponge multiple different miRNAs. (B) When HOTAIR is upregulated, more miRNAs are bound by it, freeing the miRNA target genes from miRNA-mediated suppression and resulting in their increased expression.

Renal cell carcinoma tumorigenesis was promoted by HOTAIR functioning as a ceRNA for miR-217, thus de-repressing HIF-1α,⁷³ and researchers have identified an aberrantly activated autoregulatory feedback loop involving HOTAIR’s interference with tumor-suppressing miR-193a in a prostate cancer study.⁷⁴ Knockdown of HOTAIR in a HeLa cervical cancer cell line enhanced the expression of the tumor suppressor miR-206, which targets MKL1, a transcription factor involved in inducing cancer cell migration and invasion.⁷⁵ Antagonistic expression of miR-217 and HOTAIR in HCC has been observed, suggesting that overexpression of HOTAIR leads to tumorigenesis and proliferation via downregulation of miR-217,⁷⁶ a miRNA that directly targets E2F3 protein, which is found at high levels in HCC metastatic tissues.⁷⁷ HOTAIR’s ability to promote malignant progression in colon cancer may be partly due to interactions with miR-34a²⁵ and miR-214.⁷⁸ The latter mechanism may involve a direct target of miR-214 known as ST6GAL1, which restructures sialylated glycoproteins on the surface of colorectal cancer cells to enhance malignancy.⁷⁸ It has been suggested that HOTAIR may be capable of sequestering several miRNAs at once, and since a single miRNA can control multiple genes, this may help explain why HOTAIR has multiple properties in malignances.⁴⁰

It should be noted that HOTAIR/miRNA interactions are not limited to malignant processes, and the effects of HOTAIR overexpression are not always deleterious (see Table 2). HOTAIR protectively influences the proliferative and apoptotic properties of vascular smooth muscle cells by targeting the nuclear transcription factor PPARα via sponging miR-130b-3p.⁷⁹ In intervertebral disc degeneration, HOTAIR expression is decreased; this is undesirable because HOTAIR is able to suppress the TNF-α-induced apoptosis of nucleus pulposus cells by modulating the miR-34a/Bcl-2 axis and sponging miR-34a-5p with the result of downregulating genes involved in apoptosis via the Notch signaling pathway.^80–81 HOTAIR also has a protective function in acute myocardial infarction (AMI) partly via negative modulation of miR-1, which is markedly increased post-AMI.⁸² HOTAIR overexpression also protected against cell injury due to oxidative stress in a cardiomyocyte cell line (H9C2) by sponging miR-125, de-repressing its protein target MMP2, a matrix metalloproteinase important in extracellular matrix homeostasis.⁸³ Interestingly, HOTAIR can also modulate miRNA levels at the transcriptional level. Cheng et al. showed that HOTAIR transcriptionally inhibits miR-122 via CpG island methylation, mediated by DNMTs.⁸⁴

Table 2.

Protective functions and proposed modes of action of HOTAIR in certain conditions and cell types.

Condition or cell type	Role of HOTAIR	Proposed mechanism of action	REFs
Vascular smooth muscle cells	Protection of apoptotic and proliferative properties	Upregulation of PPARα via sponging miR-130b-3p	90
Intervertebral disc degeneration	Prevents apoptosis of nucleus pulposus cells	Downregulation of apoptosis-related genes (Notch signaling pathway) via sponging miR-34a-5p	91, 92
Acute myocardial infarction	Protective factor for cardiomyocytes and biomarker for human AMI	Suppression of miR-1	93
Oxidatively stressed cardiomyocytes	Protection against cell injury	Sponging miR-125	94
Rheumatoid arthritis	Anti-inflammatory effect on LPS-treated chondrocytes	Inhibition of NF-κB	104

HOTAIR modulation of the NF-κB inflammatory pathway and immune signaling

The pro-inflammatory transcription factor NF-κB is a master regulator of hundreds of genes involved in the proliferation and survival of cells, and its prompt activation and termination are crucial for appropriate inflammatory response. Dysregulation of NF-κB is found in many diseases, including almost all malignancies, where constitutively activated NF-κB promotes tumor cell proliferation, angiogenesis, and EMT while suppressing apoptosis.^85–86 Recent studies from our laboratory demonstrate that HOTAIR promotes NF-κB activation by downregulating its inhibitor, IκBα, while HOTAIR itself appears to be transcriptionally regulated by NF-κB in response to lipopolysaccharide (LPS) treatment in macrophages.⁸⁷ SiRNA-mediated knockdown of HOTAIR suppressed the LPS-induced activation of cytokines and pro-inflammatory genes including IL-6 and iNOS, and this was mediated via downregulation of NF-κB activation.⁸⁷ Though the exact mechanism is not clear, we predict that HOTAIR functionally modulates the ubiquitin ligases and/or kinases for the NF-κB inhibitor, IκBα, and thus controls IκBα degradation and hence NF-κB activation (Figure 3). Additionally, metabolic reprogramming plays a central role in macrophage activation, inflammation, and immune response. In a recent study, our laboratory demonstrated that HOTAIR regulates expression of glucose transporter Glut1 and metabolism in macrophages during inflammation.⁸⁸ LPS induces NF-κB binding and enrichment at the Glut1 promoter but this was reduced upon HOTAIR knockdown, which also caused a significant reduction in the otherwise 10-fold increase in glucose uptake under LPS stimulation.⁸⁸ We also found that HOTAIR suppresses gene expression of PTEN (a tumor suppressor that blocks PI3K/AKT activation) during LPS-induced inflammation in macrophages.⁸⁸ These findings suggest a critical regulatory role for HOTAIR in in glucose metabolism via modulation of Glut1 expression and glucose uptake during inflammation. Importantly, in addition to HOTAIR, we have discovered a series of long-noncoding RNAs (we termed them as LinfRNAs – long noncoding inflammation-associated RNAs) that are associated with inflammation and immune response in higher eukaryotes, including humans (manuscripts in preparation). An independent study also demonstrated that HOTAIR regulates NF-κB activation and cytokine expression during DNA damage such as that induced by platinum chemotherapy, creating a positive feedback loop cascade (Figure 3) that sustains an activated DNA damage response, thus reducing chemotherapeutic efficacy and contributing to cellular senescence.⁸⁹ HOTAIR was upregulated via activation of NF-κB in gluteofemoral fat in a mouse model of obesity and sedentary lifestyle, pointing to a possible mechanism by which those co-morbidities are correlated to risk of colorectal cancer.⁹⁰

Figure 3.

HOTAIR modulation of the NF-κB inflammatory pathway in a macrophage. Upon LPS signaling, IκBα is phosphorylated, ubiquitinated, and degraded, releasing NF-κB for translocation into the nucleus. Activated NF-κB binds to promoters of pro-inflammatory cytokines to induce their expression and that of HOTAIR. HOTAIR moves to the cytoplasm, where it facilitates further IκBα degradation so that a positive feedback loop is generated to sustain the pro-inflammatory response.^{87, 89}

In LPS-induced sepsis, HOTAIR was found to regulate TNF-α production via activation of the NF-κB pathway in cardiomyocytes.⁹¹ In UVB-treated keratinocytes, overexpressed HOTAIR promotes the expression of PKR (double-stranded RNA-dependent protein kinase), which is involved in activating the NF-κB pathway.⁹² HOTAIR appears to be linked to the significant upregulation of the inflammatory cytokines IFN-γ, IL-6, IL-17, TNF-α, IL-1β, and IL-6R in monocytes via sponging of miR-211.⁹³ HOTAIR was found to promote colorectal cancer cell viability and 5FU chemotherapy resistance by epigenetically silencing miR-218, which targets VOPP1, an activator of NF-κB signaling.⁹⁴ In a rat model of acute myocardial infarction, HOTAIR upregulated the receptor of advanced glycation end-products (RAGE) in cardiomyocytes, activating NF-κB signaling.⁹⁵ In contrast, in certain cells or conditions, HOTAIR can inactivate the NF-κB pathway and act in an anti-inflammatory manner. For example, it was found to significantly inhibit NF-κB expression in LPS-treated chondrocytes, leading to decreased IL-1β and TNF-α and thereby conferring a protective effect in rheumatoid arthritis.⁹⁶

Recent studies have also revealed novel roles of HOTAIR in immune signaling, both as a target and as a regulator of various immunity factors. HCC cells with HOTAIR overexpression secrete higher levels of chemokine (C-C motif) ligand 2 (CCL2), a humoral immunity factor that is required for recruitment of tumor-associated macrophages and accumulation of myeloid-derived suppressor cells, both of which are critical components of the tumor microenvironment and promote tumor growth and metastasis.⁹⁷ The cause of this CCL2 upregulation may be due to upregulation of its transcriptional factor SP1; it has been shown that miR-326 targets SP1, and that HOTAIR suppresses miR-326.⁹⁸ Human leukocyte antigen-G (HLA-G) is expressed by tumor cells to help them evade the host’s immune surveillance; this antigen is targeted for downregulation by miR-148a, which is downregulated by HOTAIR via competitive binding in cervical cancer cells.⁹⁹ A study using cell cultures with overexpressed HOTAIR in rheumatoid arthritis exosomes showed that HOTAIR may attract active macrophages.⁵¹ HOTAIR may also indirectly promote the progression of sepsis by sponging miR-211, which induces the expression of IL-6R and contributes to initiation of the host immune response.⁹³ HOTAIR itself may also be a target of certain inflammatory immune cells. Data from a study on prostate cancer showed that infiltrating mast cells suppress androgen receptor (AR) expression by upregulating HOTAIR, which then promotes binding of the PRC2 complex to the AR promoter.¹⁰⁰ In addition, HOTAIR is induced in primary macrophages upon stimulation with lipopolysaccharide (LPS) and it is required for the LPS-induced proteasomal degradation of IκBα and subsequent NF-κB activation, causing the downregulation of IL-6 and iNOS.⁸⁷

HOTAIR in DNA repair

Systematic in vivo and in vitro studies from various laboratories, including ours, have established that HOTAIR is an oncogenic lncRNA, playing diverse roles in promoting carcinogenesis.^101–102 In addition to the conventional role of HOTAIR in altering the epigenomic landscape, recent studies have reported that HOTAIR expression significantly modulates the DNA damage response (DDR), which in turn aids in oncogenesis, malignant transformation, and chemotherapeutic resistance.^17,103–104 However, the underlying molecular mechanisms through which HOTAIR modulates the DDR remain elusive. HOTAIR has been shown to induce apoptosis and inflammation in UVB-exposed keratinocytes.⁹² DNA damage was shown to induce the expression of HOTAIR in a p53-dependent manner, which indicates that HOTAIR plays a role in p53-regulated DDR.¹⁰⁵ HOTAIR was also shown to modulate the DNA damage response pathway through suppression of p21 and p5310. Recently, Özeş et. al. not only observed overexpression of HOTAIR in recurrent platinum-resistant ovarian tumors compared to primary ovarian tumors but also demonstrated that HOTAIR activates the NF-κB signaling cascade during platinum-induced DDR, and the DDR-mediated activation of NF-κB induces HOTAIR.⁸⁹ It thus establishes a positive feedback loop with sustained NF-κB activation and persistent DNA-damage signaling, resulting in cellular senescence and chemotherapy resistance in ovarian and other cancers (see Figure 4).⁸⁹ In vitro RNAi-based HOTAIR depletion studies using breast cancer lines that highly overexpress HOTAIR showed that HOTAIR-depleted breast adenocarcinoma cells became significantly sensitized to ionizing radiation, leading to augmented DNA damage through avoiding sponging of miR-218.⁶⁹ This suggests that a HOTAIR-miR-218 axis plays a role in preventing DNA damage, but the mechanism through which this axis might regulate the DDR remains elusive. A recent report showed that HOTAIR promotes malignant growth of human liver cancer stem cells via inhibiting the recruitment of CREB, P300, and RNA polymerase II onto the SETD2 promoter region, in turn inhibiting SETD2 expression and subsequently its phosphorylation (Figure 4).⁵⁷ SETD2 binding capacity to its cognate substrate histone H3 is reduced, leading to consequent reduction of trimethyl histone H3 lysine-36 marks, which prevents mismatch DNA repair.⁵⁷

Figure 4.

Top: In human liver cancer stem cells, HOTAIR blocks the recruitment of transcription factor CREB, the coactivator P300, and RNA polymerase II to the SETD2 promoter region, resulting in repressed transcription of this important H3K36 methylator and thus impairing DNA damage response. Bottom: Platinum chemotherapy for ovarian cancer initiates the DDR, leading to activation of NF-κB, which induces HOTAIR. In the platinum-induced DDR reaction, HOTAIR also activates the NF-κB signaling cascade. This results in a positive feedback loop of sustained NF-κB activation and DNA-damage signaling, promoting cellular senescence and chemoresistance.

Dysregulated HOTAIR expression has thus been demonstrated to unequivocally alter the epigenomic landscape and to affect gene expression and contribute to tumorigenesis. However, the mere modulation of HOTAIR expression can also modulate signaling pathways that play a critical role in regulating the DDR, enabling a signaling cascade that aids in the malignant transformation of various tumors. Therefore, knockdown of HOTAIR in combination with blocking DNA-damaging agents might represent a promising treatment strategy for targeting tumors that show HOTAIR overexpression.

It is interesting to note that HOTAIR is not alone among the lncRNAs as master regulators of cellular DNA damage and repair processes (see Table 3).¹⁰³ This role is reflected in the names given to some of these lncRNAs, such as NORAD (noncoding RNA activated by DNA damage).¹⁰⁶ Some are also classified as damage-induced lncRNAs (dilncRNAs) and for example may be synthesized by RNA polymerase II (RNAPII) after binding to the MRE11–RAD50–NBS1 complex and being recruited to double-strand breaks (DSBs).¹⁰⁷ LncRNAs employ an array of mechanisms to mediate DSB repair.¹⁰⁸ DilncRNAs are transcribed from broken DNA ends and help to recruit the homologous recombination (HR) proteins BRCA1, BRCA2, and RAD51,¹⁰⁹ and the lncRNA BGL3 regulates the HR pathway via recruitment by PARP1 to DSBs, where it enhances the accumulation of the BRCA1/BARD1 complex and controls DNA end resection.¹¹⁰ The recombinase RAD51 is crucial for the high-fidelity repair of DSBs, and its formation is increased by overexpression of the lncRNA TODRA (transcribed in the opposite direction of RAD51).¹¹¹ LncRNA- JADE induces histone H4 acetylation in the DDR by transcriptionally activating Jade1, a key component in the HBO1 (human acetylase binding to ORC1) histone acetylation complex.¹¹² CCND1-upstream intergenic DNA repair lncRNAs 1 and 2 (CUPID1 and CUPID2), which are induced by estrogen stimulation, modulate DDR by affecting the choice of DDR pathway.¹¹³ The lncRNA DDSR1 (DNA damage- sensitive RNA1) is induced by various DSB agents and interferes with DDR signaling.¹¹⁴ The transcription factor E2F1 upregulates ANRIL in response to DNA damage, and this lncRNA in turn inhibits certain CDK inhibitors at the late stage of the DDR, which promotes the cell’s ability to return to normal after necessary DNA repair has been accomplished.¹¹⁵

Table 3.

LncRNAs beyond HOTAIR involved in DNA repair.

LncRNA	Role in DDR	REFS
ANRIL	CDK inhibition in late-stage DDR	117
APTR	PRC2 recruitment for p21 repression	125
BGL3	Recruitment of PARP1 to DSBs; accumulation of BRCA1/BARD1	112
CUPID1 and CUPID2	Influence choice of DDR pathway	115
DilncRNA	Recruitment of HR proteins (BRCA1, BRCA2, and RAD51)	109, 110
DDSR1	Interference with DDR signaling	116
DINO	Required for p53-dependent gene expression; triggers cell cycle arrest and amplifies damage signaling	118
DNM3OS	Inhibition of DNA-repair proteins following irradiation in esophageal cancer cells	132
GUARDIN	Sequestration of mRNA-23a to prevent end-to-end chromosomal fusion by maintaining TRF2	127
JADE	Activation of HBO1 to promote H4 acetylation	114
lincRNA-p21	Activation of tumor suppressor p21	121–123
Meg3	Interaction with PTBP3 to interfere with p53 activation in epithelium	131
NEAT1	Promotion of replication-stress-induced ATR signaling	129
NORAD	Sequestration of proteins (e.g., PUMILIO) that drive chromosomal instability	108
PANDA	Pro-apoptotic via interaction with NF-YA	124
PR-lncRNA-1 and PR-lncRNA-10	Required for efficient binding of p53, transcriptional activation of p53 targets	119
RP11–624C23.1, RP11–203E8, and RP11–446E9	Increased apoptosis after DNA-damaging chemotherapy in childhood leukemia cells	133
TERRA	Protection against damage to telomeres and other chromosomal sites	134
TODRA	Enhanced synthesis of RAD51 for DSB repair	113
TP53TG1	Suppression of tumorigenic protein YBX1	128
WRAP53	p53 induction	130

Unsurprisingly, many of the lncRNAs that play roles in DDR mechanisms do so by either inducing or being induced by p53. For example, DINO (damage-induced noncoding) lncRNA is transcriptionally activated by p53 in the context of DNA damage and is necessary for p53-dependent gene expression, and its expression is sufficient to activate cell cycle arrest and damage signaling even without DNA damage being present.¹¹⁶ Sánchez et al. defined a set of 18 lncRNAs that are bona fide p53 transcriptional targets, two of which (PR-lncRNA-1 and PR-lncRNA-10) were observed to be required for p53’s efficient binding to, and transcriptional activation of, some of its other direct transcriptional targets.¹¹⁷ Another study found 39 lncRNAs associated with p53, and approximately half of these were specifically associated with the induction of DNA damage.¹¹⁸ Several lncRNAs that participate in, or interfere with, p53 pathways do so via links to p21, which is induced by p53 in response to DNA damage. For example, lincRNA-p21 has been found to affect global gene expression in a variety of ways by serving to activate p21.¹¹⁹ P53 transcriptionally activates lincRNA-p21 promoters in response to DNA damage, and lincRNA-p21 inhibition allows the expression of hundreds of genes that p53 represses under normal circumstances.¹²⁰ DNA damage and overexpression of the tumor suppressor ING1b also induces lincRNA-p21.¹²¹ PANDA (p21-associated ncRNA DNA-damage-activated) interacts with NF-YA, a transcription factor involved in pro-apoptotic gene expression.¹²² The lncRNA APTR (Alu-mediated p21 transcriptional regulator) recruits PRC2 to repress the transcription of p21.¹²³

LncRNAs have been shown to be induced by UVC-induced DDR, with the suggestion of involvement in regulation of p53 signaling pathways.¹²⁴ The lncRNA GUARDIN responds to p53 by sequestering mRNA-23a to prevent end-to-end chromosomal fusion by maintaining TRF2 (telomeric repeat-binding factor 2) expression.¹²⁵ Epigenetic loss of lncRNA TP53TG1 by methylation-mediated silencing enriches the nuclear content of RNA binding protein YBX1; this tumorigenic protein activates PI3K and its oncogenic target, AKT, a kinase that promotes the degradation of p53.¹²⁶ NEAT1 helps to attenuate p53 activation as part of a negative feedback loop in which it promotes replication-stress-induced ATR signaling.¹²⁷ WRAP53 is required for DNA-damage-related p53 induction,¹²⁸ and p53 activation induces Meg3 (maternally expressed gene 3) in epithelial cells, where this lncRNAs interacts with RNA binding protein polypyrimidine tract binding protein 3, thus contributing to regulation of gene expression related to DDR.¹²⁹

Various lncRNAs have demonstrated DDR roles in specific cancers. DNM3OS is a fibroblast-promoted lncRNA that confers radioresistance in esophageal squamous cell carcinoma by promoting the expression of DNA damage markers but also inhibiting the expression of several DNA-repair proteins following irradiation.¹³⁰ Three lncRNAs (RP11–624C23.1, RP11–203E8, and RP11–446E9) were found to significantly increase apoptosis after exposure to a DNA-damaging chemotherapeutic agent (camptothecin) in childhood leukemia cells.¹³¹ A single-telomere, long noncoding member of a group of telomeric repeat-containing RNAs (TERRA) was shown to be involved in maintaining genomic integrity in a stomach adenocarcinoma cell line, as its depletion led to increased damage in telomeres and other chromosomal sites.¹³²

HOTAIR promotion of epithelial-to-mesenchymal transition

HOTAIR has been shown to promote epithelial-to-mesenchymal transition (EMT), a process associated with tumor progression, invasion, and metastasis. EMT is regulated via many signaling pathways and transcription factors as well as by many miRNAs.¹³³ Loss of the protein E-cadherin induces EMT, and E-cadherin was found to be lost in 37.1% of invasive ductal breast malignancies.¹³⁴ In human lung cancer cells, HOTAIR sponges miR-34a-5p, leading to de-repression of the transcription factor Snail that in turn is a repressor of E-cadherin.¹³⁵ Snail is also de-repressed by HOTAIR in gastric cancer via repression of miR-34a by recruiting PRC2 to its promoter region, to which the EZH2 subunit directly binds for mediation of H3K27me3.⁶³ Snail was also demonstrated, in TGFβ-treated human hepatoma cells, to form an epithelial-gene-repressing complex with EZH2 by using HOTAIR as a bridge, and this complex promoted EMT.¹³⁶ Carcinoma-associated fibroblasts transactivated HOTAIR in breast cancer cells via TGF-β1 paracrine secretion, promoting EMT and consequential metastatic activity.¹³⁷ HOTAIR knockdown significantly reversed EMT in gastric cancer by increasing E-cadherin expression in a PRC2-dependent manner,¹³⁸ and ablation of HOTAIR expression prevented the induction of EMT and the arising of cancer stem cells in colon and breast cancer cell lines, demonstrating a requirement of HOTAIR for EMT.¹³⁹

HOTAIR involvement in ubiquitination and proteasomal degradation

In addition to its epigenomic, transcriptional, and translational modulation functions, various studies have also elucidated novel post-translational functions of cytoplasmic HOTAIR. Yoon et al. demonstrated that HOTAIR can induce ubiquitin-mediated proteolysis by acting as a scaffold transcript that enhances E3-mediated ubiquitination of substrate proteins and targets them for proteasomal degradation.¹⁴⁰ In brief, HOTAIR interacts with E3 ubiquitin ligases Dzip3 and Mex3b to facilitate the degradation of their respective substrates, Ataxin-1 and Snurportin-1 (Figure 5). Therefore, in the context of senescent cells, human antigen R (HuR) associates with HOTAIR and lowers its stability by recruiting the let7-Ago2 complex (during the normal cell cycle); however, in the cellular senescence state, when HuR levels are alleviated, let7-Ago2-complex-mediated degradation of HOTAIR decreases and HOTAIR is stabilized, leading to rapid degradation of Ataxin-1 and Snurportin-1, thus preventing premature senescence.¹⁴⁰ This HOTAIR-mediated mechanism is also oncogenic because Ataxin-1 activates the promoter of E-cadherin, which is a key tumor suppressor.¹⁴¹

Figure 5.

Ubiquitination and subsequent proteasomal degradation can be both promoted and suppressed by HOTAIR. Left: HOTAIR interacts with E3 ligases Dzip3 and Mex3b at their RNA-binding domains while also associating with their respective protein substrates, Ataxin-1 and Snurportin-1. The resulting complex formation accelerates the ubiquitination and degradation of these senescence-related proteins.¹⁴⁰ Right: HOTAIR competitively binds to the N-terminal domain (NTD) of androgen receptor (AR) to prevent its interaction with E3 ligase MDM2, blocking AR ubiquitination and proteasomal degradation.¹⁴⁴

HOTAIR acts as a ubiquitination scaffold between PLK1 and its substrates, such as the transcription repression factors SUZ12 and ZNF198, in hepatitis B-virus-induced liver carcinogenesis. Mex3b has been identified as the E3 ligase that binds to HOTAIR before ubiquitinating SUZ12 for degradation.¹⁴² HOTAIR was recently shown to also interact with RUNX3, inducing its proteasome-mediated degradation via ubiquitination dependent on MEX3B (an E3 ubiquitin ligase), thus providing a novel regulatory mechanism responsible for silencing the expression of RUNX3 in gastric cancer.¹⁴³ This HOTAIR–RUNX3 interaction might work as a new therapeutic target for metastatic gastric cancer. Other studies have determined that HOTAIR can also block ubiquitination. For example, Zhang et al. demonstrated that HOTAIR promoted castration-resistant prostate cancer by binding to the androgen receptor (AR) protein, stabilizing AR and blocking its degradation by preventing it from interacting with E3 ligase MDM2 (Figure 5).¹⁴⁴

HOTAIR inhibition of cell cycle arrest

One of the myriad ways through which HOTAIR overexpression promotes malignancy is by inhibiting cell cycle arrest of tumor cells. For example, two major positive regulators of the cell cycle that are associated with metastasis, cyclin D1 and D2 (CCND1 and CCND2), are targeted for downregulation by miR-206, which is negatively modulated by HOTAIR in ovarian cancer.⁶⁷ CCND1 is also de-repressed by HOTAIR binding to miR-1 in esophageal squamous cell carcinoma.¹⁴⁵ HOTAIR overexpression in adrenocortical carcinoma cells causes upregulation of cyclin D1 and other genes related to the cell cycle, with the effect of promoting cell cycle progression and cell proliferation.³⁷ In lung cancer, HOTAIR was found to regulate the Rb-E2F pathway, promoting cell cycle passage through the G1-S phase restriction point.¹⁴⁶ In yet another example of miRNA sponging, HOTAIR suppresses miR-613 in pancreatic cancer cells, contributing to malignant growth since miR-613 normally induces cell cycle arrest at the G0/G1 phase.¹⁴⁷

Regulation of HOTAIR

As an oncogenic lncRNA, transcription regulation of HOTAIR is critical for its cellular functions and disease implications. Indeed, multiple studies, including ours, demonstrate that HOTAIR expression is influenced in a variety of ways; for example, studies from our laboratory demonstrated that HOTAIR expression is elevated in breast cancer cells and that estradiol activates HOTAIR transcription in estrogen-receptor (ER)-positive breast cancer cells in an estradiol-dependent manner.¹⁴⁸ ERs and ER co-regulators such as those belonging to the mixed lineage leukemia (MLL) family of histone methyltransferases play critical roles in regulation of HOTAIR expression in an estradiol environment. Additionally, studies from our laboratory also demonstrate that the endocrine disruptors bisphenol-A and diethylstilbestrol regulate HOTAIR expression by inducing estrogen-response elements (EREs) in its promoter; these EREs are bound by ERs and ER co-regulators including MLL-histone methyltransferases and CBP/p300 histone acetylases.¹⁴⁹ Since HOTAIR is an oncogenic lncRNA, its upregulation by estrogen-mimicking endocrine-disrupting chemicals is indicative of the potential risk of such EDCs in cancer and other endocrine regulated diseases. Additionally, HOTAIR expression is elevated in hypoxia,¹⁵⁰ which is a major driving force for tumor cell proliferation¹⁵¹ and angiogenesis.¹⁵² Our recent studies demonstrate that MLL1 histone methylase, which is a crucial player in hypoxia signaling and angiogenesis, coordinates with hypoxia inducible factor, HIF-1α, to regulate hypoxia-induced HOTAIR expression.¹⁵⁰ These observations further suggest a pro-oncogenic functionality of HOTAIR and its potential interplay with other tumorigenic factors, such as HIF and MLL-histone methylases. Cancer-associated fibroblasts secrete the cytokine TGF-β1, which activates SMADs in a paracrine manner; the activated SMADs then directly bind to HOTAIR’s promoter site to induce its transcription.¹³⁷ Other transcription factors that directly bind the HOTAIR promoter region include c-Myc in gallbladder cancer,¹⁵³ FOXC1 in HCC,¹⁵⁴ and HOXA9 in glioma.¹⁵⁵ HOTAIR is also upregulated by overexpression of the hepatitis C virus core protein.⁵⁴

In addition to the transcriptional induction of HOTAIR via epigenetic alteration of its promoter, HOTAIR expression is post-transcriptionally altered by various miRNAs. Genistein, a soy isoflavone studied for its cancer-inhibition effects in prostate cancer cells, was shown to upregulate miR-34a and miR-141, both of which directly target HOTAIR for repression.^156–157 Interestingly, there is evidence that HOTAIR may also be mechanoresponsive. For example, its levels are decreased in certain heart valvular cells exposed to cyclic stretch, with data suggesting that the repression occurs via β-catenin in a stretch-responsive signaling pathway.¹⁵⁸

CONCLUSION

A sizeable body of literature presently exists on the multitude of roles played by HOTAIR in human physiology through varied modes of action. Beyond its well-known role as a regulator of chromatin modification and gene repression, HOTAIR exhibits much more dynamic roles in the regulation of various signaling pathways, microRNA sponging, NF-κB activation, inflammation, immune signaling, modulation of proteasomal degradation via regulation of ubiquitin ligase activity, and DNA damage response. Most reports have focused on its roles in malignancy, but some studies have also demonstrated its involvement in neurodegenerative disorders such as Alzheimer’s and Parkinson’s, inflammatory and immune diseases, arthritis, and diabetes. In general, HOTAIR appears to exhibit two major modes of action: a) Gene silencing via recruitment of chromatin-modifying enzymes (histone methylases and demethylases and DNA methylases) and epigenetic alterations; and b) modulation of inflammatory response via regulation of NF-kB pathway. We predict that there may be unifying mechanisms of action of HOTAIR in most inflammatory and metabolic diseases, where it is found to be up-regulated. In addition to gene repression, HOTAIR-mediated modulation of the NF-kB pathway-mediated inflammatory process might be the central and one of the common mechanisms in cancer, neurodegenerative diseases, diabetes, arthritis, and other inflammatory diseases.

Along with critical roles of HOTAIR in gene regulation and cell signaling, HOTAIR has been implicated as a diagnostic and therapeutic target. Similar to proteins, most lncRNAs are expressed in a cell-and-tissue-type-specific manner and in far greater amounts,^159–160 and many cell-free lncRNAs that were originally only detected in tissues are detectable and stable in various bodily fluids.¹⁶¹ For these reasons, lncRNAs, including HOTAIR, show great promise as novel, non-invasive, and specific biomarkers for diagnosis and prognosis of cancer and other diseases. In NSCLC patients, HOTAIR is detectable in plasma, where its levels are not only elevated but also associated with histology subtype and tumor-node-metastasis (TNM) stage, with greater diagnostic accuracy than CEA levels alone and even greater accuracy when used in combination with that traditional serum biomarker.¹⁶² Clinical data show that serum HOTAIR levels also correlate to TNM stage in esophageal squamous cell carcinoma.¹⁶³ Computational analysis revealed that plasma HOTAIR levels could diagnose gastric cancer with 88% sensitivity and 84% specificity, and higher levels were associated with higher tumor grade, advanced stage, and metastasis.¹⁶⁴ Serum HOTAIR is significantly higher in patients with glioblastoma multiforme compared to healthy controls, with 86.1% sensitivity and 87.5% specificity, and is significantly correlated with high-grade brain tumors.¹⁶⁵ Plasma HOTAIR has also been suggested as a viable biomarker for diagnosis of acute myocardial infarction.⁸² Beyond detection in the blood, lncRNAs can also be found in the urine; for example, HOTAIR is enriched in urinary exosomes in bladder cancer patients and correlates with disease progression.¹⁶⁶ Remarkably, HOTAIR and other lncRNAs can even be detected in the saliva; for example, salivary levels of HOTAIR are significantly higher in pancreatic cancer patients (with sensitivity and specificity of 60–97%) compared to patients with benign pancreatic tumors and a healthy cohort, and are significantly decreased after curative pancreatectomy.¹⁶⁷ Thus, HOTAIR indeed holds potential as a therapeutic target and biomarker for various human diseases, including cancer. Overall, HOTAIR is one of the most well-studied lncRNAs, and is a critical regulator of gene expression, epigenetics, and cell signaling. A vast number of functional studies on HOTAIR indeed suggest that lncRNAs are functional, not mere transcriptional noise. Although further research is necessary before a full understanding of HOTAIR’s functions, mechanisms, and regulation will be achieved, studies so far have highlighted potential uses for HOTAIR as a therapeutic target and biomarker for various human diseases, including cancer.

Research highlights.

HOTAIR is a well-characterized lncRNA that has been implicated in several cancers and other diseases. HOTAIR is a well-known as a repressor lncRNA and regulates various repressive chromatin modifications. However, recent studies have revealed additional functions of HOTAIR in regulation of protein degradation, microRNA (miRNA) sponging, NF-κB activation, inflammation, immune signaling, and DNA damage response. Herein, we have summarized diverse functions and modes of action of HOTAIR, with an emphasis on the following.

1. Roles in cancer

2. Roles in chromatin modification and gene silencing

3. Implications in protein degradation, inflammation and immune signaling.

4. Implications in DNA repair

5. Potential implications in diagnosis and therapeutics