Commentary on: The potency of lncRNA MALAT1/miR-155 in altering asthmatic Th1/Th2 balance by modulation of CTLA4

Transcriptomic analysis identified that approximately 80% of our genome is transcribed [1] yet only approximately 1–2% of these transcripts are translated into protein [2]. This indicates that a large pool of non-coding RNA transcripts are present in cells to potentially exercise exquisite control over gene expression. Long non-coding RNAs are transcripts longer than 200 nucleotides that are typically not translated into protein but instead alter cell biology by modifying chromatin structure changes, intracellular trafficking, transcription and post-transcriptional processing [3]. Researchers showed that lnc RNA could alter gene expression by modifying the effects of other non-coding RNA, such as miRNA [4]. Studies suggest that lncRNA modulates miRNA function by acting as a sponge to absorb the miRNA and prevent it from degrading its mRNA target [5,6]. Alternatively, lncRNA may antagonize the actions of miRNA by competing with them for binding to their mRNA targets [7]. As an example, the lncRNA BACE1AS stabilized the β-site amyloid precursor protein cleaving enzyme 1 (BACE1) mRNA by interfering with a specific miR-485-5p site [7]. In addition, some lncRNA are actually processed into miRNA to alter cell function. Indeed, lncRNA H19 regulates insulin signaling by generating miR-675, which targets the insulin growth factor receptor (Igf1r) mRNA [8]. Given their abundance and their ability to influence miRNA function, lncRNA could exert key effects on gene expression and intracellular signaling by controlling mRNA stability and protein translation.

Researchers identified abundant lncRNA expression in T-cell lineages suggesting that these transcripts play an important role in T-cell development and differentiation [9]. This could have important implications for allergic asthma where a Th2 predominant response generates cytokines, like IL-4, IL-5 and IL-13, which trigger IgE production and eosinophilic infiltration into the lung [10]. This allergic inflammation stimulates airway mucus production and smooth muscle contraction to provoke symptoms of breathlessness and respiratory distress in patients [11]. The ability of lncRNA to modulate CD4 differentiation and gene expression could impact significantly on the production of these damaging Th2 cytokines in this disease. Consistent with this theory, distinct lncRNA expression profiles were identified in T cells from subjects with difficult-to-control asthma [12]. Moreover, lncRNA levels correlate with expression of mRNA in these T cells suggesting that they exert a pivotal role in altering the effector function of these cells [13]. Thus, identifying how lncRNA change gene expression to promote Th2 skewing could provide new mechanistic insights and therapeutic targets for this disease.

In their work, Liang and Tang [14] propose that the lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a key determinant that promotes the Th2 phenotype in allergic asthma. Using a large and well-defined cohort of healthy and asthmatic subjects, they show up-regulation of MALAT1 expression in the blood coinciding with the down-regulation of its key target, miR-155 (Figure 1). Importantly, MALAT1 expression correlated negatively with lung function and the Th1/Th2 ratio indicating that its effects were compromising lung function by skewing toward Th2 responses. Researchers showed that the transcription factors T-bet and GATA-3 determine T-cell fate with T-bet inducing genes for Th1 development while GATA-3 turns on genes responsible for Th2 responses [15]. Competitive interactions between these two transcription factors determine gene expression and CD4⁺ differentiation. T-bet interferes with the binding of GATA-3 to its Th2 DNA targets, and GATA-3 significantly interferes with the binding of T-bet to its Th1 promoter regions [16]. Liang et al. showed that miR-155 increased T-bet and Th1 cytokines in CD4⁺ cells but had no effect on MALAT1 expression. This is important since miRNA frequently target lncRNA for degradation [17]. On the other hand, MALAT1 decreased miR-155 levels and this was accompanied by increased GATA-3 and Th2 cytokines in these CD4⁺ cells. Thus, this work establishes MALAT1 as a key orchestrator of Th2 skewing in allergic asthma.

A particularly novel aspect of the Liang et al. [14] study was the role of cytotoxic T-lymphocyte antigen 4 (CTLA-4). This receptor protein typically negatively regulates GATA-3 levels and shifts the cell away from a Th2 phenotype [18]. However, Liang et al. [14] showed that MALAT1 increased CTLA4 expression and CTLA4 countered the Th1 differentiation induced by an miR-155 mimic or MALAT1 siRNA treatment. These findings suggest an intricate role for CTLA4 in T-cell differentiation. Consistent with the findings of Liang et al., a recent study found that CTLA-4 blockade enhanced CD8 T-cell function while limiting Th2 polarization in CD4 cells [19].What these results demonstrate is that cofactors like MALAT1 heavily influence the complex effects of CTLA-4 on T-cell differentiation. It is important to note that MALAT1’s regulation of T-bet and GATA-3 could potentially influence the development of other lymphoid cells, such as innate lymphoid cells. T-bet plays an important role in type 3 innate lymphoid cells (ILC3) [20], which counter infection and maintain epithelial integrity via their expression of IL-17 and IL-22 [21,22]. It is also required for the induction of ILC1, which releases the Th1 cytokines IFN-γ and TNF [23,24]. Conversely, GATA-3 promotes ILC2 development which produces the Th2 cytokines IL-5, IL-6 and IL-13 [25]. Innate lymphoid cells confer protection against infection [26] and promote tissue repair [27] but their aberrant activation induces asthma [28], autoimmune injury [29] and cancer [30]. Future studies will address whether MALAT1 alters innate lymphoid cell differentiation to modulate the development of these biological processes in vivo.

MALAT1 is conserved among species [31] and is highly expressed in normal tissues [32]. Despite its abundance, its precise biological function is not fully understood. It is thought to regulate alternative mRNA splicing in the nucleus [33] but data from Malat1 knockout mice show no developmental abnormalities and no clear changes in mRNA splicing [34]. As indicated by its name, MALAT1 has been associated with poor clinical outcomes in lung cancer [31]. However, gene inactivation studies in mice yielded conflicting results with studies showing both enhanced [35] and decreased [36] metastatic potential. Besides regulating miRNA, MALAT1 directs the polycomb repressor complex (PRC) to methylate and silence key genes [37]. MALAT1 also influences gene expression by binding and inactivating the Tead family of transcription factors [35]. Through its varied effects, MALAT1 regulates PI3K-AKT, MAPK, WNT and NF-κB signaling pathways [38], which influence critical biological processes like proliferation, inflammation, cell survival and metabolic function. While the study of Liang et al. [14] suggests that targeting MALAT1 could ameliorate allergic asthma, MALAT1 manipulation would need to be tightly controlled and directed specifically toward CD4⁺ cells. As indicated above, MALAT1 may exert protective effects depending on the cellular context so systemic inhibition could bring about deleterious off-target outcomes. The efforts of Liang et al. [14] advance the field of RNA biology by identifying a heretofore previously unknown role for MALAT1 in Th2-mediated inflammation. This underscores the importance of further studies to better delineate the biological effects of MALAT1 on inflammatory and metabolic responses implicated in tissue injury and repair.

The author declares that there are no competing interests associated with this manuscript.

This work was supported by the Flight Attendant Medical Research Institute (CIA Award) [grant number CIA160028] and the Alpha One Foundation (Research Grant) [grant number 618117].

BACE 1

β-site amyloid precursor protein cleaving enzyme 1

CTLA-4

cytotoxic T-lymphocyte antigen 4

IFN

interferon

MALAT1

metastasis-associated lung adenocarcinoma transcript 1

Th1/Th2

Thelper1/Thelper2

T-bet

T box protein expressed in T cells