Long non-coding RNAs in immune regulation and their potential as therapeutic targets

Abstract

Long non-coding RNAs (lncRNAs) are potent regulators of immune cell development and function. Their implication in multiple immune-mediated disorders highlights lncRNAs as exciting biomarkers and potential drug targets. Recent technological innovations in oligo-based therapeutics, development of RNA-targeting small molecules, and CRISPR-based approaches, position RNA as the next therapeutic frontier. Here, we review the latest advances made toward understanding the role of lncRNAs in human immunological disorders and further discuss RNA-targeting approaches that could be potentially exploited to manipulate lncRNA function as a clinical intervention.

Introduction

Although the human genome is pervasively transcribed into RNA, less than 2% of our DNA encodes proteins through messenger RNAs (mRNAs)[1,2]. Moreover, non-coding RNAs (ncRNAs) account for up to 97% of the mass of RNA in the cell, with rRNAs and tRNAs being the most abundant transcripts[3]. These ncRNAs show a rich diversity in both form and function, and based on their size, they are broadly classified into small non-coding RNAs (≤ 200 nucleotides reviewed in[4-7]) and long non-coding RNAs (lncRNAs; > 200 nucleotides) [8]. The varied molecular functions of lncRNAs include—but are not limited to—the regulation of transcription, transcript stability, translation, and cell signaling, as well as nuclear scaffolding. Moreover, the NONCODE database currently boasts 96,000 human lncRNA genes, indicating that lncRNAs potentially outnumber protein-coding (PC) genes by as many as five-fold[9]. Although, by definition, lncRNAs do not encode proteins, many have molecular features similar to that of PC mRNAs in that they are spliced, 3’ polyadenylated, and 5’ m⁷G capped. However, it should be noted that a small fraction of transcripts previously annotated as lncRNAs contain small open reading frames that could be translated into small peptides or micropeptides, some of which have biological function[10-12]. Conversely, some PC genes produce transcripts that act similar to ncRNAs, blurring the line between coding and noncoding genes[13-15]. While the functions of most lncRNAs are largely unknown, they play key roles in virtually all major subclasses of immune cells, such as coordinating immune cell differentiation, homeostasis, and effector function[16-28]. (Recent reviews elaborate on the mechanisms of lncRNAs implicated in the biology of immune cells[29-32].) Compared to mRNAs, lncRNAs are generally expressed in a more tissue-, cell type-, and disease-specific manner[33-35], making them attractive therapeutic targets and biomarkers for disease diagnosis. For example, overexpression of the lncRNA PCA3 in prostate cancer cells is currently exploited as a urine-accessible biomarker in the differential diagnosis of prostate cancer[36,37]. Thus, characterizing lncRNAs in immune cells will not only aid in understanding the function of the non-coding portions of the human genome, but may identify biomarkers for immunologic diseases and eventually reveal novel “druggable” targets.

lncRNAs in immunologic diseases

Transcriptome analyses of various immune cells have produced a catalog of lncRNAs that are differentially expressed in a broad range of immune-related diseases. However, in most cases, the function of the lncRNAs are unknown and their contribution to disease pathogenesis have not been tested. In this review, we will describe a selection of the best-characterized immunologic disease-associated lncRNAs (additional examples are listed in Table 1).

Table 1: A selection of lncRNAs associated with various immune disorders.

The lncRNAs reported in this table have been curated based on their association with an immune related disorder, and have undergone additional characterization either in vivo or in vitro. Due to space restraints, the many disease associated lncRNAs that lack functional testing are not listed.

LncRNA	Species Studied	Relevant cell(s)	Disease	Ref
Plasmacytoma variant translocation 1 (PVT1)	Human	Primary airway smooth muscle cells	Asthma	[112]
LNC_000127	Human	PBMCs - Eosinophils	Asthma	[113]
BANCR	Human	Primary esophageal epithelial cells	Eosinophilic esophagitis	[114]
GAS5	Mouse/Human	PBMCs	Rheumatoid arthritis (RA); systemic lupus erythematosus(SLE); multiple sclerosis(MS); sarcoidosis; Inflammatory bowel diseases (IDB)	[115,116]
HOTAIR	Human	PBMC	RA	[117]
H19	Human	Isolated synovial macrophages (in RA) and intestinal epithelial cells (in IBD)	RA; IBD	[118,119]
NEAT1	Human	Monocytes	SLE	[120]
Linc0949, and linc0597	Human	PMBC	SLE	[121]
Psoriasis-associated non-protein coding RNA induced by stress (PRINS)	Human	Epidermal keratinocytes	Psoriasis	[122-124]
PSORS1C3	Human	Tonsils and skin biopsies	Psoriasis	[125]
IFNG-AS1	Human	CD4 T cells	IBD	[126]
CDKN2B-AS1	Human	Intestinal epithelial cells	IBD	[127]
LINC00305	Human	Monocytes	Atherosclerosis	[57]
TMEVPG1 aka NeST aka IFNG-AS1	Human	Th1 cells	Hashimoto’s Thyroiditis	[18,28,128,129]
FlicR	Mouse/Human	Tregs	Diabetes	[130]
Linc-MAF-4	Mouse/Human	Th1	MS	[30,46]
Morrbid	Mouse/Human	Eosinophils, CD8+ T cells, monocytes	Hypereosinophilic Syndrome; Lymphocytic choriomeningitis virus infection; AML	[42,45,105]
Lnc13	Human	Macrophages	CeD	[41]
LncRNA-CD244	Human	CD8+ T cells	MTB infection
NKILA	Human	Tumor infiltrating T cells	Cancer	[51]
THRIL	Human	Macrophages	Kawasaki disease	[26]

Lnc13 in celiac disease

Celiac disease (CeD) is a complex, immune cell-mediated, gluten-sensitive enteropathy with varying clinical manifestations[38,39]. CeD has a strong genetic influence, and while risk variants in the major histocompatibility (MHC) region explain most CeD heritability, single-nucleotide polymorphisms (SNPs) outside of MHC are also implicated. Like other complex diseases, the majority of CeD-associated SNPs fall within non-coding regions[40]. While most complex disease SNPs likely alter the function of DNA regulatory elements, some may impact the function of lncRNAs. Indeed Castellanos-Rubio et al. discovered a novel lncRNA, called lnc13, that is expressed from a CeD-associated haplotype block[41]. Under homeostatic conditions in macrophages, lnc13 repressed expression of inflammatory genes by binding to their transcriptional start sites and recruiting the heterogeneous nuclear ribonucleoprotein hnRNPD. Intestinal biopsies from patients with CeD showed reduced levels of lnc13 RNA, which could potentially render these cells hyperinflammatory. Perhaps most interesting was the finding that lnc13 bound less efficiently to hnRNPD when it contained a CeD-associated SNP, thereby reducing its ability to suppress the inflammatory response. This study provides a lncRNA-based mechanism by which SNPs can contribute to CeD. Moreover, lnc13 serves as a clear example of how genetic changes can increase disease risk by directly impairing lncRNA function.

MORRBID in hypereosinophilic syndrome

The lncRNA Morrbid was first identified in mice as a regulator of short-lived myeloid cell lifespan[42]. In neutrophils, eosinophils, and monocytes, Morrbid represses expression of the pro-apoptotic gene Bcl2l11 (a.k.a Bim), which lies on the same chromosome approximately 150 kilobases away. Kotzin et al. found that Morrbid recruits the EZH2-containing polycomb repressive complex 2 (PRC2) to the Bcl2l11 promoter where it catalyzes deposition of H3K27me3 to maintain Bcl2l11 in a transcriptionally poised state[42]. The observation that Morrbid expression was induced by common β chain cytokines (IL-3, IL-5, and GM-CSF) suggests that Morrbid connects the presence of these external survival factors with the transcriptional program controlling cell lifespan. Morrbid is conserved across multiple species, and similar to mice, human MORRBID is most highly expressed in granulocytes. Moreover, MORRBID is overexpressed in eosinophils from individuals with hypereosinophilic syndrome, highlighting the relevance of MORRBID to human disease[42]. Although likely downstream of the elevated IL-5 levels that are observed in hypereosinophilic syndrome, the increased expression of MORRBID could potentially be increasing the steady-state number of eosinophils in these individuals by extending eosinophil lifespan, thereby promoting hypereosinophilia. If so, pharmacologic inhibition of MORRBID could potentially reduce eosinophil numbers. Indeed, clinical trials blocking IL-5 signaling have shown some efficacy in the treatment of hypereosinophilic syndrome[43,44]. A recent study of how inflammatory stress impacts hematopoiesis in mice has shown that Morrbid is also important in promoting the survival of pre-leukemic hematopoietic stem and progenitor cells (HSPCs)[45]. Interestingly, MORRBID overexpression is observed in a subset of acute myeloid leukemia patients and is associated with poor overall survival (R. Kapur and Z. Cai personal communication).

Linc-MAF-4 in multiple sclerosis

Linc-MAF-4 is a chromatin-associated lncRNA that is transcribed from a locus 139.5 kilobases upstream of the gene MAI, which encodes the C-Maf transcription factor that regulates Th2 cell differentiation[30]. Expression of these two genes is inversely correlated: linc-MAF-4 is expressed in Th1 cells whereas MAF is expressed in Th2 cells. In Th1 cells, Ranzani et al. found that linc-MAF-4 recruits EZH2 and LSD1 to the MAF promoter, leading to deposition of H3K27me3 and silencing of MAF[30]. Knockdown of linc-MAF-4 in Th1 cells resulted in inappropriate expression of MAF, GATA3, and IL4, suggesting that linc-MAF-4 promotes Th1 differentiation by blocking the C-Maf-controlled Th2 transcriptional program. A subsequent study connected linc-MAF-4 to multiple sclerosis (MS)[46]. MS is a disease of the central nervous system in which Th1 and Th17 cells play a critical role. Peripheral blood mononuclear cells (PBMCs) from MS patients exhibit increased expression of linc-MAF-4 and decreased expression of MAF, as compared to healthy controls[46]. Interestingly, higher expression levels of linc-MAF-4 positively correlate with an increased annual relapse rate, indicating that this lncRNA could potentially serve as a biomarker for MS. However, the cause for linc-MAF-4 upregulation in MS has not been established; therefore, determining whether elevated levels of linc-MAF-4 reflect increased numbers of Th1 cells or, alternatively, whether dysregulation of linc-MAF-4 could potentially contribute to MS susceptibility by promoting Th1 differentiation, is an area for further research.

LncRNA-CD244 in Mycobacterium tuberculosis infection

CD8⁺ T cells mount an adaptive immune response during infection with Mycobacterium tuberculosis (MTB)[47]. In humans, CD244 is a marker of CD8⁺ T cell exhaustion in chronic infection, and when highly expressed, it acts as an inhibitory receptor [48]. Wang et al. discovered lncRNA-CD244 as a negative regulator of anti-MTB responses[49]. Patients with an active MTB infection were found to have increased numbers of CD244⁺CD8⁺ T cells, and ex vivo stimulation of these cells with MTB lysates further increased CD244 expression. Blockade of CD244 signaling enhanced production of IFN-γ, TNF-α, and IL-6 by CD8⁺ T cells, confirming that CD244 upregulation impairs anti-MTB responses. In parallel, lncRNA-CD244 was found to be highly expressed in CD244⁺CD8⁺ T cells during active MTB infection, and expression of lncRNA-CD244 was induced by CD244 signaling. Wang et al. further demonstrated that lncRNA-CD244 bound EZH2 and mediated its recruitment to the IFNG and TNFA loci, inducing a repressive chromatin state. This finding provides a mechanism to explain how CD244 signaling suppresses CD8⁺ T cell responses. Finally, they showed that in a humanized mouse model, knockdown of lncRNA-CD244 in adoptively transferred CD8⁺ T cells significantly enhanced IFN-γ and TNF-α expression and improved protective immunity. Given that CD244 expression is implicated in impaired adaptive immune responses in chronic viral infections and cancer[48], lncRNA-CD244 could be a potential therapeutic target to limit CD8⁺ T cell exhaustion.

NKILA in tumor-infiltrating T cells

Discovered in a microarray screen of breast cancer cells treated with inflammatory cytokines, NF-κB interacting lncRNA (NKILA) was found to bind NF-κB/IκB and mask the phosphorylation motifs of IκB, thereby inhibiting NF-κB activation[50]. Low NKILA expression is associated with breast cancer metastasis and poor patient prognosis[51], and a similar association is observed in other cancers[52-55]. Recently, Huang et al. reported a separate role for NKILA in tumor-infiltrating cytotoxic T lymphocytes (CTLs) and type 1 helper T (Th1) cells[51]. They observed that subsets of tumor-infiltrating T cells displayed increased sensitivity to activation-induced cell death (AICD) that was in part due to NF-κB inactivation driven by upregulation of NKILA. Stimulating AICD is one of the many mechanisms tumors can use to evade the immune system[56], and this is the first report connecting this mechanism to a lncRNA. Importantly, Huang et al. found that patients with a greater percentage of tumor-infiltrating CTLs that expressed high levels of NKILA had shorter overall survival and disease-free survival than patients with tumor-infiltrating CTLs that expressed lower levels of NKILA. Using patient-derived breast cancer xenografts in mice, Huang et al. showed that knockdown of NKILA expression in CTLs increased their tumor infiltration, reduced AICD, and concomitantly inhibited cancer growth. These findings highlight the complex roles lncRNAs may play in disease, with increased expression of NKILA in immune cells and cancer cells being associated with opposing clinical outcomes, and moreover, suggest that therapeutic targeting of lncRNAs may necessitate a highly nuanced approach.

LINC00305 in atherosclerosis

By searching GWAS databases. Zhang et al. discovered atherosclerosis-associated SNPs located in the intron of the novel lncRNA LINC00305[57]. Interestingly, they showed that LINC00305 was expressed in monocytes and atherosclerotic plaques, and was overexpressed in PBMCs of individuals with atherosclerosis. Using a cDNA overexpression strategy in the monocytic cell line THP-1, they found that LINC00305 activated inflammation-associated genes through the NF-κB pathway. This suggests that LINC00305 is an immune lncRNA that promotes the inflammation underlying atherosclerosis. The authors next demonstrated that LINC00305 binds the lipocalin-interacting membrane receptor (LIMR) and increases its interaction with the aryl hydrocarbon receptor repressor (AHRR), which in turn is responsible for the augmented NF-κB activation. What remains to be addressed is how these intronic SNPs impact expression of LINC00305, and why this is specifically associated with atherosclerosis.

LncRNAs as therapeutic targets

Given the vast number of lncRNAs and their contribution to disease, development of lncRNA targeting strategies could greatly broaden the landscape of therapeutic interventions. While little has been done with respect to lncRNAs specifically, a number of approaches have been successfully developed to target mRNAs and microRNAs. In general, these approaches can drive RNA degradation, alter splicing patterns, or prevent translation of the target RNA. While lncRNAs do not undergo translation, these approaches may be adapted to prevent lncRNAs from binding to the protein(s) they interact with. Although some lncRNAs can be found in the cytoplasm, many are restricted to the nucleus[58]; therefore, care must be taken to select a targeting approach that is compatible with the subcellular localization of the target lncRNA (see below). Since most in vivo RNA-targeting modalities are currently delivered systemically (Figure 1), this provides a significant challenge in promoting efficient uptake by relevant cell types[59]. However, a unique property of the immune system can be exploited to partially circumvent these restrictions: for example, patient-derived HSPCs can be isolated and genetically modified ex vivo, expanded in number, and returned to the patient (Figure 1). Below, we present examples of different RNA-targeting strategies, as well as highlight some that are already in clinical use.

Figure 1. Potential strategies for therapeutic targeting of immune cell lncRNAs.

For transient targeting, ASOs are delivered systematically in vivo via intravenous or subcutaneous injections, or delivered to specific sites such as the cerebrospinal fluid. Following uptake by relevant cells types, ASOs alter lncRNA function by driving lncRNA degradation, altering splicing or blocking interaction with binding proteins. For long-term targeting, ex vivo editing of patient derived cells will likely be more efficacious. For example, hematopoietic stem cells can be harvested and edited ex vivo to manipulate expression of target lncRNAs, before delivery of corrected cells back to the patient. CRISPR based technologies are particularly amenable to this approach, with CRISPRi being used to silence lncRNA transcription or CasRx to knockdown the lncRNA transcripts. However, as both CRISPRi and CasRx require continued expression or CRISPR proteins special care must be taken to avoid toxicity or off-target effects.

RNA interference (RNAi)

Small interfering RNAs (siRNAs) are 21–23-nucleotide, double-stranded RNA molecules in which one strand is complementary to the target RNA. The antisense strand hybridizes to the target endogenous RNA in the cytoplasm and invokes a degradation pathway that involves dicer, RNA-induced silencing complex (RISC), and the AGO2 endonuclease[60]. Unmodified siRNAs are themselves susceptible to nucleases and have short half lives in vivo. The addition of 2′-O methyl sugar residues and phosphorothioate linkages to the 3′ end of the siRNA can slow enzymatic degradation, thereby increasing pharmacologic potential[61]. To increase the efficiency of delivery and uptake by relevant cell types, siRNAs can be delivered intravenously or intramuscularly with one of three different formulations: lipid nanoparticles[62], GalNAc conjugates[63], or masked endosomolytic compounds[64]. In 2018, the first siRNA drug, Onpattro™, was approved by the FDA to treat hereditary transthyretin amyloidosis[65]. Onpattro™ is formulated with nanoparticles and administered intravenously. Although not yet tested in humans, siRNA-mediated knockdown of the lncRNAs MALAT1 and HOTAIR in animal models has been shown to reduce cancer cell proliferation, growth, and metastasis, suggesting that siRNAs may also be used for lncRNA targeting [66,67].

Antisense oligos (ASOs)

ASOs are short 15–20-nucleotide, single-stranded DNA molecules that hybridize to endogenous target RNAs to initiate a ribonuclease (RNase) H-dependent degradation pathway[61,68,69]. RNA:DNA hybrids are substrates for RNase H1, which is concentrated inside the nucleus[70,71]. Unmodified, single-stranded ASOs are easily degraded, have poor bioavailability, and display suboptimal target binding. These shortcomings have been addressed by multiple advances in the chemical modification of ASOs, as reviewed in Shen et al. [72]. One prime example of a chemically-modified ASO is Spinraza™, an FDA-approved drug used in the treatment of spinal muscular atrophy (SMA). Spinraza™ is a phosphorothioate-linked, 2′-O–2-methoxyethyl-modified, ASO drug[73] that promotes alternative splicing of SMN2 mRNAs by targeting an intron splice silencer, thereby boosting production of the encoded full-length survival motor neuron protein[74]. One of the biggest challenges with developing efficacious ASO-based therapeutics is delivering them to target tissues and cell types. When given systemically, ASOs accumulate in the liver and kidneys [75-78]. Delivery of ASOs directly into target tissues can significantly increase uptake by relevant cell type[79]. Indeed, Spinraza™ must be administered directly into the cerebrospinal fluid. In addition, conjugation of ASOs to different biologic carriers has the potential to promote their uptake by cells of interest [79-82]. Finally, given ASOs ability to target nuclear RNAs, they are preferable to siRNAs for targeting most lncRNAs[70,71]. Indeed, the feasibility of using ASOs for in vivo lncRNA targeting has been demonstrated in different mouse models of cancer[83,84] and immune disorders[85-88].

(i). Gapmer, second generation ASOs

Gapmers are ASOs that contain a core DNA sequence flanked 5’ and 3’ by short RNA sequences consisting of chemically modified, degradation-resistant ribonucleotides. This RNA–DNA–RNA chimera enhances hybridization affinity to target RNA sequences and simultaneously serves as a substrate for RNase H1[89,90]. TEGSEDI™ is a 20-nucleotide, phosphorothioate-linked gapmer that has five 2′-O-–2-methoxyethy ribonucleotides at each terminus flanking a core of ten 2′-deoxyribonucleotides[91]. TEGSEDI™ was recently FDA-approved for the treatment of hereditary transthyretin amyloidosis[92]. In contrast to the siRNA Onpattro™, TEGSEDI™ is water-soluble and is administered subcutaneously without nanoparticle formulation[93,94]. No special delivery mechanisms are required for TEGSEDI™ as the target tissue is the liver.

(ii). Phosphorodiamidate morpholino oligomers and peptide nucleic acid, third generation ASOs

Phosphorodiamidate morpholino oligomers (PMOs) are charge-neutral, 20–25 nucleotide, single-stranded DNA analogs, where the five-membered ribofuranosyl rings of DNA are replaced with six-membered morpholino rings connected by phosphorodiamidate linkages[95]. PMOs effectively bind to target mRNAs to block translation through steric hindrance and thus work independently of RNase H-dependent degradation[96]. PMO-based EXONDYS 51™ is an FDA-approved therapy for Duchenne muscular dystrophy that functions by altering splicing of the dystrophin gene[97].

Peptide nucleic acids (PNAs), like PMOs, are charge-neutral oligomers with an N-(2-aminoethyl) glycine backbone. The neutral amide backbone makes PNAs resistant to both nucleases and proteases; thus PNA–DNA or PNA–RNA duplexes are more stable than the natural homo- or heteroduplexes[98]. Özcş et al. used PNAs to disrupt interactions of the lncRNA HOTAIR with PRC2, thereby reducing tumor progression and improving survival of mice harboring platinum-resistant, patient-derived ovarian tumor xenografts[99]. These initial studies demonstrate the feasibility of PNA-mediated targeting of lncRNAs in vivo.

Small molecules

These represent a diverse class of low-molecular-weight organic compounds that, by virtue of their small size and chemical properties, may easily enter cells where they can interact with and affect host molecules, such as proteins and RNAs. For example, ABX464 is small-molecule inhibitor that has shown efficacy in a phase 2a proof-of-concept study to treat ulcerative colitis. ABX464 binds the cap-binding complex (CBC) to trigger splicing of a lncRNA that houses the anti-inflammatory miR-124, thereby increasing miR-124 expression. In addition, several groups have developed small molecules against the lncRNAs BDNF-AS, HOTAIR, GAS5 and MALAT1, highlighting the lncRNA-targeting potential for this class of molecules[100-102]. While the development of RNA-targeting small molecules is relatively nascent, we predict that this field will flourish in the coming years and lead to the development of therapeutics against currently ‘undruggable’ targets.

CRISPR–Cas systems

CRISPR–Cas9 genome-editing technology depends on the ability to recruit the Cas9 bacterial endonuclease to specific genomic sites via the sequence-complementarity of its associated guide RNAs (gRNA). The gRNAs are designed to the target DNA sequences and bind downstream of a protospacer adjacent motif (PAM; three-nucleotide sequence). Cas9 then recognizes the PAM sequence and generates a double-stranded DNA break three nucleotides upstream[103,104]. Non-homology-directed repair of the double-stranded break by the cell’s intrinsic DNA repair machinery leaves behind mutations in the targeted DNA. While such mutations can effectively silence PC genes by inducing frameshifts in the coding sequence, the impact of non-homology-directed repair on lncRNAs is less predictable. To circumvent this, we and others have used CRISPR–Cas9 to delete either lncRNA promoter sequences or entire lncRNA loci to prevent their expression[105,106]. However, this approach is not without caveats. For example, lncRNA loci could contain DNA regulatory elements that regulate local gene expression. Furthermore, there is substantial crosstalk between promoters of different genes [107-109]. Therefore, for each genomic deletion, it is critical to assess the impact on local gene expression to account for unwanted off-target effects. Alternatively, CRISPR–Cas9-based epigenome-editing methods can be used to modify expression of lncRNAs using CRISPR interference/activation (CRISPRi/a). Using a catalytically inactive Cas9 that is fused to either a transcriptional repressor (KRAB domain) or activators (VP64/P300 domains), a gene promoter can be targeted using gRNAs to achieve specific transcriptional interference or activation[110]. Recently, Konermann et al. identified a Type VI-D CRISPR–Cas system, called CasRx, that allows direct targeting of transcripts[111]. They demonstrated that CasRx was able to efficiently knockdown both mRNA and lncRNA targets[111]. While, both CRISPRi/a and CasRx are still in their infancy, they provide an exciting area to be explored for therapeutic targeting of lncRNAs. As of November 2019, there are five active CRISPR–Cas9 clinical trials in the US, and four on-going and one completed trial in China; of these 10, nine trials are hematopoietic cell-specific. Phase-I/II clinical trials are being actively pursued to treat severe sickle cell disease ( NCT03745287) and transfusion-dependent β-thalassemia ( NCT03655678) by using CRISPR-Cas9 to target a BCL11A gene enhancer in HSPCs. Interestingly, seven Phase 1/2 clinical trials are underway using CRISPR-Cas9-engineered T Cells, notably for treating B-cell malignancies ( NCT03044743, NCT04035434, and NCT03398967), mesothelin-positive solid tumors ( NCT03747965 and NCT03545815), leukemia and lymphoma ( NCT03166878 and NCT03044743), and carcinomas ( NCT03044743 and NCT03081715). These clinical trials highlight the feasibility of applying CRISPR–Cas technology to hematopoietic cells as a therapeutic tool.

Conclusion

The lncRNA field has expanded rapidly over the last decade with lncRNAs emerging as important molecules in immune regulation and diverse diseases. However, for lncRNA therapeutics to be realized, we must first identify those that truly drive pathogenesis. Furthermore, although lncRNAs are often expressed in a cell type-specific manner, some—such as in the case of NKILA—may play opposing roles in different cell types even within a single disease. The biggest challenge will therefore be to develop technologies that will enable delivery of RNA targeting therapeutics in a cell type-selective manner.

Highlights.

More than 97% of transcripts in the cell are categorized as non-coding RNAs.

long non-coding RNAs (lncRNAs) outnumber protein coding genes.

lncRNAs are often expressed in a tissue-, cell type-, and disease-specific manner.

lncRNAs play known roles in virtually all major subclasses of immune cells.

lncRNAs are implicated in multiple immunologic disorders.