The impact and role of identified long noncoding RNAs in nonalcoholic fatty liver disease: A narrative review

Abstract

Background

Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide, but its mechanism and pathophysiology remain unclear. Long noncoding RNAs (lncRNAs) may exert a vital influence on regulating various biological functions in NAFLD.

Methods

The databases such as Google Scholar, PubMed, and Medline were searched using the following keywords: nonalcoholic fatty liver disease, nonalcoholic fatty liver disease, NAFLD, nonalcoholic steatohepatitis, nonalcoholic steatohepatitis, NASH, long noncoding RNAs, and lncRNAs. Considering the titles and abstracts, unrelated studies were excluded. The authors evaluated the full texts of the remaining studies.

Results

We summarized the current knowledge of lncRNAs and the main signaling pathways of lncRNAs involved in NAFLD explored in recent years. As a heterogeneous group of noncoding RNAs (ncRNAs), lncRNAs play crucial roles in biological processes underlying the pathophysiology of NAFLD. The mechanisms, particularly those associated with the regulation of the expression and activities of lncRNAs, play important roles in NAFLD.

Conclusion

A better comprehension of the mechanism controlled by lncRNAs in NAFLD is necessary for the identification of novel therapeutic targets for drug development and improved, noninvasive methods for diagnosis.

LncRNAs play an important role in the regulation of NAFLD biological functions through the interaction of multiple pathways. We summarized the lncRNAs identified in recent years that are mainly involved in regulating NAFLD and possible signaling pathways that mediate their regulatory effects. LncRNAs and various signaling pathways gradually formed an across‐linked network, allowing us to understand the complexity of lncRNAs regulatory mechanism on NAFLD.

1. INTRODUCTION

Nonalcoholic fatty liver disease (NAFLD) is a chronic liver injury characterized by abnormal lipid accumulation in hepatocytes in the absence of excessive alcohol intake or other attributable causes. ¹ With the increasing prevalence of obesity and weight‐related metabolic syndrome, NAFLD has become one of the most prevalent causes of chronic diseases. Although steady progress has been made in understanding the disease epidemiology and pathogenesis, the slowest advancement has been achieved in the therapeutic field. There is no FDA‐approved medication for nonalcoholic steatohepatitis (NASH), and it is urgent to develop effective drugs.

Long noncoding RNAs (lncRNAs) are a subclass of noncoding genes that are more than 200 nucleotides in length and are confirmed to control gene expression at epigenetics, transcription, and translation levels; furthermore, increasing evidence indicates their involvement in various diseases. ² Thousands of expressed lncRNAs are changed in the initiation and progression of NAFLD, but a tiny amount of these has provided evidence in support of causality. It might be of possibility to provide new targets for NAFLD treatment by exploring and identifying the role and mechanism of lncRNAs unconventionally expressed in NAFLD.

2. LNCRNAS INVOLVED IN THE REGULATION OF NAFLD

The hypothesis of multiple hits, including adipose tissue‐derived cytokines, insulin resistance (IR), mitochondrial dysfunction, oxidative stress, endoplasmic reticulum stress (ERS), intestinal flora disturbance, and genetic variations, is the currently approved interpretation of the etiology and pathophysiology of NAFLD. ³ Moreover, epigenetic factors also play critical roles in disease manifestation and progression. ⁴ Epigenetic modifications mainly include DNA methylation alteration, posttranslational histone modification, and noncoding RNA (ncRNA) expression. ⁵ As a heterogeneous group of ncRNAs, lncRNAs participate in epigenetic modifications. LncRNAs have been shown to control hepatic lipid regulation and metabolism in the process of NASH. ⁶ Latest studies on the regulatory roles of lncRNAs indicate that their interactions and regulation with microRNAs (miRNAs) and circular RNAs (circRNAs) extend the current comprehension of the regulatory mechanisms and complexities involved in NAFLD. In the initiation and development of NAFLD, lncRNAs can be divided into upregulated and downregulated lncRNAs according to their altered expression. Some of the identified lncRNAs participating in the regulation of NAFLD are summarized and presented in the tables. (Tables 1 and 2).

TABLE 1.

Upregulated LncRNAs expressed in NAFLD.

Genes	Principal function	Target genes	Molecules and signaling pathways
MAYA	Promoting hepatocyte senescence Promoting Iron overload		YAP
Gm9795	Endoplasmic reticulum stress Promoting inflammatory response		NF‐κB pathway, JNK pathway
Platr4	Promoting inflammatory response		NF‐κB pathway
NEAT1	Promoting lipid accumulation Promoting lipogenesis Promoting lipid metabolism Promoting fibrosis Promoting inflammatory response	miR‐139‐5p miR‐212‐5p miR‐506 miR‐146a‐5p/ ROCK1	c‐Jun/SREBP1c GRIA3 MiR‐140/AMPK/SREBP‐1 pathway Hh signaling pathway mTOR/S6K1 signaling pathway AMPK/SREBP pathway mTOR/S6K1 pathway
HOTAIR	Promoting lipid accumulation	miR‐130b‐3p/ROCK1	ROCK1, AMPK signaling pathway
H19	Hepatic steatosis Lipid accumulation Promoting fibrogenesis	miR‐130a	MLXIPL and mTORC1 networks, PI3K/mTOR pathway PPARγ Collagen alpha‐1(I) chain, α‐SMA
LncTNF	Promoting inflammation		NF‐κB pathway
Gm15622	Promoting lipid accumulation	miR‐742‐3p	SREBP‐1c
Gm10804	Promoting disorder of glucose and lipid metabolism, lipid accumulation		SREBP‐1c
CCAT1	Promoting lipid droplet formation	miR‐613	miR‐613/ LXRα, ChREBP
LncARSR	Promoting lipid accumulation, cell proliferation and invasion Promoting hepatic lipogenesis and hepatic cholesterol biosynthesis		YAP1 and IRS2/AKT pathway PI3K/AKT/ SREBP‐1c AKT/SREBP‐2/HMGCR
HULC	Promoting hepatic fibrosis and hepatocyte apoptosis		MAPK signaling pathway
Uc.372	Promoting lipid accumulation and hepatic steatosis	miR‐195/miR‐4668	miR‐195/miR‐4668
MALAT1	Promoting hepatic insulin resistance and hepatic steatosis		CXCL5, SREBP‐1c
SRA	Promoting adipocytes Differentiation and insulin‐stimulated glucose absorption Prevents FFA oxidation		ATGL, FOXO1, PPARγ

TABLE 2.

Downregulated LncRNAs expressed in NAFLD.

Gene names	Principal function	Target genes	Molecules and signaling pathways
LncHR1	Preventing the accumulation of fatty acids and TG		SREBP‐1c, PDK1/AKT/FOXO1
SRD5A3‐AS1	Promoting cell proliferation, steatosis, inflammation, and fibrosis	miR‐1205	YAP1, NF2
Gm16551	Promoting de novo lipogenesis		Acetyl coenzyme A carboxylase‐1 and stearoyl coenzyme A desaturase‐1
AC012668	Promoting lipid accumulation	miR‐380‐5p	miR‐380‐5p/LRP2
Uc.333	Decreasing insulin sensitivity, promoting IR	miR‐223/Foxo1	miR‐223/FOXO1, PI3K/AKT/GSK
Mirt2	Promoting hepatic steatosis	miR‐34a‐5p	miR‐34a‐5p/USP10
MEG3	Promoting lipid degeneration	miR‐21	LRP6/AKT/ mTOR
FLRL2	Promoting lipogenesis, inflammation, and ER stress		Arnt1/Sirt1
LncSHGL	Promoting hepatic gluconeogenesis/lipogenesis		PI3K/AKT, hnRNPA1/CaM

2.1. Upregulated lncRNAs expressed in NAFLD

2.1.1. MAYA

MAYA has been identified as a new lncRNA that has the ability to mediate the Hippo/YAP signaling pathway. ⁷ MAYA facilitates liver cell senescence through the way of downgraduating YAP protein expression in NAFLD. ⁸ Hepatocyte senescence is pivotal in the pathogenesis and development of NAFLD. ⁹ Loss of MAYA increased YAP expression, which subsequently depressed hepatocyte senescence by regulating iron overload in palmitic acid‐treated hepatocytes. ⁸ Suppression of MAYA was capable of reducing cellular senescence and consequently ameliorating NAFLD. However, the present data did not clarify other underlying signaling pathways involved in hepatocyte senescence in the progression of NAFLD.

2.1.2. Gm9795

Gm9795, an 1170 bp lncRNA, is a pseudogene of the STAR‐related lipid transfer (START) domain located on chromosome 10. A study based on the microarray analysis was performed to compare the profiles of liver lncRNA expression in NASH, NAFLD, and normal mice. ¹⁰ In the study, Gm9795 expression was closely related to NASH severity; more interestingly, Gm9795 did not affect lipid accumulation in the development of NASH; however, it facilitated the expression of inflammatory factors through the NF‐kB/JNK signaling pathway by triggering ERS activation. Hence, Gm9795 accelerates the development and progression of NAFLD depending on inflammation factors.

2.1.3. Platr4

Platr (pluripotency‐associated transcript) was identified as a family consisted of 32 members and involved in maintaining profile of embryonic stem cell (ESC) gene expression. ¹¹ Among Platr family members, Platr4 suppressed the activity of NOD‐like receptor family pyrin domain containing‐3 (NLRP3) inflammasome as a circadian inhibitor by depressing transcription and expression of NLRP3 inflammasome and apoptosis‐associated speck‐like protein containing a CARD (ASC) through inhibiting NF‐κB. ¹² Loss of Platr4 promoted steatohepatitis in mice experimental model, whereas overexpression of Platr4 ameliorated liver pathological conditions. Therefore, Platr4 may be a promising factor that can be regulated to ameliorate steatohepatitis.

2.1.4. NEAT1

NEAT1 is a familial tumor syndrome multiple endocrine neoplasia (MEN) type 1 locus (Chr11q13.1) transcript. ¹³ In NAFLD, by sponging miR‐139‐5p, NEAT1 facilitates hepatic lipid accumulation via activating the c‐Jun/sterol regulatory element binding protein‐1c (SREBP1c) axis. ¹⁴ In addition, miR‐212‐5p was suppressed by interacting with NEAT1, which resulted in GRIA3 (encoding subunit‐3 of glutamate ionotropic AMPA receptor) upregulation and accelerated lipid accumulation in NAFLD. ¹⁵ Moreover, by sponging miR‐506, NEAT1 regulated fibrosis, inflammatory response, and lipid metabolism. ¹⁶ NEAT1 also promoted lipid accumulation by regulating miR‐146a‐5p/ROCK1 and AMPK/SREBP signaling pathways. ¹⁷ In another study, ¹⁸ NEAT1 could exacerbate the progression of NAFLD synergistically with miR‐140 through binding to miR‐140 directly; however, loss of NEAT1 could exert a lipid‐lowering effect in NAFLD. From these studies, we could consider that NEAT1 is a risk factor affecting the progression of NAFLD.

2.1.5. HOTAIR

HOX transcript antisense RNA shortly termed as HOTAIR can interact with diverse chromatin‐modifying complexes, acting as a molecular scaffold to alter the chromatin state and consequently regulate target genes expression. ¹⁹ In mice fed a high‐fat diet (HFD), HOTAIR was dramatically increased, and the upregulated HOTAIR remarkably accelerated hepatic IR through the AKT/GSK pathway. ²⁰ Loss of HOTAIR could suppress the levels of total cholesterol and triglyceride (TG), which indicated that HOTAIR might be a vital target in the process of NAFLD. ²¹ Another research also revealed that HOTAIR upregulated in NAFLD, and inhibition of HOTAIR reversed lipid accumulation in free fatty acid (FFA)‐treated liver cells by miR‐130b‐3p/ROCK1 axis. ²² The current results indicated the important role of HOTAIR by influencing the metabolism of glucose and lipids in NAFLD.

2.1.6. H19

H19 is situated in a conserved imprinted gene cluster containing a neighboring reciprocally imprinted gene for insulin‐like growth factor‐2. ²³ H19 facilitated hepatic steatosis and lipid accumulation in NAFLD by upregulating the mTORC1 signaling axis; however, lipid accumulation induced by H19 was suppressed significantly by PI3K/mTOR inhibitors. ²⁴ In the progression of NAFLD, the expression of H19 increased, while loss of H19 suppressed steatosis and TG release in FFA‐induced hepatocytes; H19 had the ability of sponging miR‐130a, and H19 silencing could alleviate hepatic lipogenesis by controlling the miR‐130a/PPARγ signaling pathway. ²⁵ Meanwhile, H19 promotes liver fibrogenesis in NAFLD by upregulating fibrous substance expression and activating hepatic stellate cells (HSCs). ²⁶ These reported findings indicated that H19 participated in regulating hepatic lipid metabolism and lipogenesis, and it might be a promising therapeutic target of NAFLD.

2.1.7. LncTNF

LncTNF is situated on chromosome 3q26.32, which is a novel intergenic lncRNA involved in liver inflammation with the strongest response to TNF‐α stimulation. Using bioinformatics and RNA sequencing, 109 lncRNAs were identified to participate in NAFLD; meanwhile, researchers verified the involvement of lncTNF in the TNF‐α/NF‐κB pathway. ²⁷ LncTNF was positively correlated with hepatic lobular inflammation, and the expression of lncTNF in hepatocytes increased dramatically after TNF‐α stimulation. ²⁷ It is generally accepted that lncTNF is capable of regulating hepatocyte inflammation and controlling the progression of simple fatty liver disease to steatohepatitis by NF‐κB signaling pathway.

2.1.8. Gm15622

Gm15622 is an antisense lncRNA located in the cytoplasm, as predicted with the MGI database and online iLoc LncRNA software. Gm15622 was expressed at a significantly high level in the liver samples of obese mice and in hepatocytes treated with FFA, and loss of GM15622 contributed to alleviating NAFLD‐associated lipid deposition. ²⁸ Gm15622 facilitates de novo synthesis of lipids by regulating miR‐742‐3p/SREBP‐1c axis in NAFLD. Briefly, Gm15622 overexpression promoted hepatic lipid accumulation by upregulating SREBP‐1c; conversely, Gm15622 inhibition alleviated hepatic lipid accumulation by downregulating SREBP‐1c. ²⁸ The existing materials indicate that Gm15622 is a critical modulator affecting hepatic lipid metabolism in NAFLD.

2.1.9. Gm10804

By comparing the liver lncRNAs expression profiles in NAFLD and normal subjects, researchers found that Gm10804 elevated significantly in NAFLD, suggesting that Gm10804 might be involved in NAFLD. ²⁹ Gm10804 was also observed to be overexpressed in high glucose (HG)‐treated hepatocytes and liver samples from NAFLD mice. ³⁰ Furthermore, Gm10804 overexpression aggravated the HG‐induced intracellular TG content, lipid accumulation, and expression of hepatic lipogenic proteins and gluconeogenesis enzymes, while Gm10804 silencing had the opposite effect. From this published study, we could draw the conclusion that Gm10804 inhibition alleviated hepatic lipid accumulation by ameliorating hepatic glucose and lipid metabolism disorder in NAFLD.

2.1.10. CCAT1

CCAT1, termed as colon cancer‐associated transcript‐1, is located on chromosome 8q24.21 with a length of 2795 bp, which was first observed to be overexpressed in colon cancer. Upregulated CCAT1 exhibits oncogenic properties in various cancer types. ³¹ CCAT1 dramatically upregulated both in oleic acid (OA)‐treated hepatocytes and in NAFLD tissue samples. ³² CCAT1 facilitated the OA‐induced lipogenesis in vitro and the steatosis process in vivo by sponging miR‐613 to regulate LXRα transcription and by enhancing LXRα downstream ChREBP expression. That is to say, CCAT1 enhanced LXRα transcription by serving as a ceRNA to promote NAFLD.

2.1.11. LncARSR

LncARSR is located on chromosome 9q82, with a length of 591 nucleotides. ³³ LncARSR upregulated in NAFLD, and lncARSR silencing ameliorated TG accumulation, while overexpression accelerated lipogenesis. ³⁴ The AKT/SREBP‐1c signaling pathway regulated the effect of lncARSR on lipogenesis. LncARSR overexpression facilitates hepatic cholesterol biosynthesis through the AKT/SREBP‐2/HMGCR signaling pathway. ³⁵ In one study, ³⁶ researchers observed that lncARSR upregulated in NAFLD; in terms of mechanism, lncARSR was capable of binding to YAP1 specifically, which activated the IRS2/AKT pathway and subsequently increased lipid accumulation. Conversely, lncARSR inhibition suppressed the IRS2/AKT signaling pathway and consequently inhibited lipid accumulation by downregulating YAP1. Hence, lncARSR could be a target for NAFLD treatment.

2.1.12. HULC

HULC is located on chromosome 6p24.3, with a length of 1600 nucleotides, participating in organ fibrosis. ³⁷ HULC was also involved in the process of NAFLD. ³⁸ In the study, researchers observed that liver expression of HULC elevated in rats with NAFLD; furthermore, loss of HULC improved the liver pathological findings, alleviated liver lipid deposition, and decreased hepatocyte apoptosis by inhibiting the MAPK signaling pathway. These findings implied that HULC might be a meaningful indicator and a potential molecular marker for NAFLD.

2.1.13. Uc.372

Ultraconserved (uc) RNAs, a class of lncRNAs, are conserved across mammals, but their physiological and pathological roles remain largely uncharacterized. Uc.372 is one of the ucRNAs with 481 segments longer than 200 bp. ³⁹ Uc.372 was identified as a vital lncRNA participating in NAFLD by impairing homeostasis of lipid metabolism. ⁴⁰ The study implied that uc.372 was highly expressed in the liver both in HFD‐fed mice and in NAFLD patients. In terms of mechanism, uc.372 promoted hepatic steatosis and lipid accumulation by suppressing miR‐195/miR‐4668 maturation, consequently relieving the inhibition of target genes such as fatty acid synthase (FAS) and CD36. From the findings, we could consider that uc.372 inhibition might serve as a potential therapeutic approach for NAFLD.

2.1.14. MALAT1

MALAT1, termed as metastasis associated in lung adenocarcinoma transcript‐1, is located at 11q13 with a length of 8.5 kb. ⁴¹ As reported, MALAT1 was involved in the process of fatty liver‐related fibrosis. ⁴² In this study, MALT1 and chemokine ligand‐5 (CXCL‐5) was observed to be upregulated in activated HSCs; meanwhile, loss of hepatic MALAT1 suppressed CXCL‐5 expression. Therefore, CXCL‐5 signaling pathway participated in the development of fibrosis in NAFLD by which functionally relevant differential expression of MALAT1 may play the pivotal role. Moreover, MALAT1 facilitated hepatic steatosis, lipid accumulation, and IR in NAFLD by enhancing nuclear SREBP‐1c protein stability. ⁴³ Thus, MALAT1 inhibitors might be new therapeutic agents in the progression of NAFLD in the future.

2.1.15. SRA

Steroid receptor RNA activator (SRA) is intergenic and has a core sequence with a length of 687 bp in humans. ⁴⁴ SRA promotes adipocyte glucose uptake and differentiation by enhancing the transcriptional activity of PPARγ, decreasing adipocyte‐related inflammatory gene expression or enhancing insulin receptor expression by inhibiting JNK and p38 MAPK phosphorylation, activating IR transcription and increasing downstream pathway activities by IRS‐1 and AKT. ⁴⁵ , ⁴⁶ Furthermore, SRA modulated adipose triglyceride lipase (ATGL) by inhibiting Forkhead box O‐1 (FOXO1) activity to promote ATGL transcription. ⁴⁷ Loss of SRA upregulated ATGL expression principally by enhancing the inductive effect of FOXO1, which promoted FFA β‐oxidation capability and consequently contributed to protection against hepatic steatosis. Therefore, regulating SRA might be one of the possible choices to treat NAFLD.

2.2. Downregulated lncRNAs in NAFLD

2.2.1. LncHR1

LncHR1, also named as hepatitis C virus (HCV) regulated‐1, was first observed to be highly expressed in Huh7 cells infected by HCV. LncHR1 had potential regulatory functions through SREBP‐1c, TG, and lipid droplets (LD) accumulation. ⁴⁸ LncHR1 is a negative regulator of SREBP‐1c. LncHR1 overexpression suppressed SREBP‐1c expression, oleic acid (OA)‐induced TG and LD accumulation in hepatocytes, and it could also reduce TG levels in NAFLD. ⁴⁸ Phosphorylation of PDK1/AKT/FOXO1 is involved in lncHR1 negatively regulating SREBP‐1c and TG accumulation. ⁴⁹ The current studies offer new information regarding therapeutic targets in NAFLD that upregulation of lncHR1 might contribute to NAFLD regression through the SREBP‐1c‐related signaling pathway.

2.2.2. SRD5A3‐AS1

SRD5A3‐AS1 is located on chromosome 4 at position q12 with a length of 31,877 bases. SRD5A3‐AS1 expression declined in NASH. ⁵⁰ The Hippo signaling‐targeted regulatory network (i.e., YAP1, FOXA2, AMOTL2, TEAD2, SMAD4 and NF2)‐miR‐650 and miR‐1205‐SRD5A3‐AS1 participated in NASH. In another study, ⁵¹ SRD5A3‐AS1 was observed to be sharply decreased in NASH group compared with controls. Moreover, amelioration of hepatocyte injury and improvement of lipid metabolism through elevating the level of SRD5A3‐AS1. SRD5A3‐AS1‐miR‐1205‐NF2 axis played critical role in NASH. Briefly, SRD5A3‐AS1 inhibited miR‐1205, subsequently upregulating NF2, a target of miR‐1205. Thereby, the upregulated NF2 negatively regulated YAP1, which inhibited cell proliferation and suppressed IL‐6, TGF‐β1, and α‐SMA expression in NAFLD. Therefore, SRD5A3‐AS1 might be a meaningful molecular agent in the treatment of NAFLD.

2.2.3. Gm16551

Gm16551 was originally identified to be a capped, spliced, and polyadenylated intergenic noncoding transcript. As a liver‐specific lncRNA, Gm16551 expression declined in NAFLD that suppressed SREBP‐1c activity through a negative feedback loop, consequently regulating de novo lipogenesis. ⁵² Downregulation of Gm16551 inhibited SREBP‐1c activity, thereby influencing its action toward lipogenic gene, ATP citrate lyase (ACLY), a target of SREBP‐1c. In NAFLD, Gm16511 expression decreased, while H19 increased that facilitated hepatic steatosis and lipid accumulation. ²⁶ Gm16551 was downregulated by HFD, while coffee administration promoted Gm1655 expression and improved hepatic steatosis. ⁵³ , ⁵⁴ That is to say, decaffeinated coffee upregulates Gm16551 that participated in the onset and progression of NAFLD.

2.2.4. AC012668

AC012668 is located on chromosome 2. In a recent study, AC012668 was sharply downregulated in NAFLD. ⁵⁵ AC012668 overexpression alleviated NAFLD through miR380‐5p/low‐density lipoprotein‐related protein‐2 (LRP2) axis. As ceRNA, AC012668 inhibited miR‐380‐5p, thereby preventing its action toward the target LRP2. Collectively, AC012668/miR‐380‐5p/LRP2 axis participated in NAFLD, which may open up a completely new strategy for the treatment of this disease.

2.2.5. Uc.333

As mentioned above, upregulation of liver uc.372 controlled hepatic steatosis through suppressing miR‐195/miR‐4668 maturation in NAFLD. ⁴⁰ Here, another ucRNA named as uc.33, the expression declined sharply in NAFLD. ⁵⁶ In terms of mechanism, uc.333 improved insulin sensitivity and decreased IR through activating the PI3K/AKT/GSK pathway, an important pathway for regulating IR by sponging miR‐223 and directly targeting FOXO1. Therefore, uc.333 may be a promising agent to treat and prevent NAFLD.

2.2.6. Mirt2

Mirt2, termed as myocardial infarction‐associated transcript 2, is a newfound lncRNA with the activity of anti‐inflammatory. ⁵⁷ Mirt2 decreased in the livers of obese mice, revealing that mirt2 was involved in NAFLD. ⁵⁸ Liver‐specific mirt2 overexpression improved hepatic glucose tolerance and IR, and alleviated lipid deposition in HFD mice; meanwhile, upregulation of mirt2 improved liver function in obese mice. Mirt2 acted as ceRNA by sponging miR‐34a‐5p and consequently upregulated expression of USP10, target gene of miR‐34aa‐5p, and led to inhibition of gluconeogenesis, lipogenesis, hepatic IR, and steatosis. As we know, Mirt2 negatively regulated NAFLD onset and progression that implied it might be a potential pharmacological strategy for NAFLD treatment by upregulating mirt2.

2.2.7. MEG3

Maternally expressed gene‐3 (MEG3) is located in the imprinted DLK1–MEG3 locus on the human chromosome 14q32.3 region. ⁵⁹ MEG3 expression in the liver was sharply downregulated in NAFLD. ⁶⁰ Downregulation of MEG3 showed close relation with lipogenesis‐related genes in NAFLD; upregulation of MEG3 reversed hepatic lipid accumulation induced by FFA. ⁶¹ The axis of MEG3/miR‐21/lipoprotein receptor‐related protein‐6 (LRP6) participated in the FFA‐challenged hepatocytes steatosis. FFAs suppressed MEG3 expression by upregulating miR‐21, which subsequently activated the AKT/mTOR pathway through downregulating LRP6, and eventually resulting in TG release and lipid degeneration. Declined level of MEG3 was in parallel with NAFLD severity; moreover, MEG3 activity was also regulated by destabilizing enhancer of zeste homolog‐2 (EZH2) through degradation mediated by ubiquitin. ⁶² The above findings illustrated that MEG3 might be considered as a molecular marker and a therapeutic target for NAFLD.

2.2.8. FLRL2

Fatty liver‐related lncRNA2 (FLRL2) was reported as a potential key regulator in NAFLD. ⁶³ Interfering with FLRL2 affected the expression of circadian rhythm gene aryl‐hydrocarbon receptor nuclear translocator‐like (Arntl), which was a target of FLR2. That is, FLRL2‐Arntl axis might participate in the pathogenesis of NAFLD. Overexpression of FLRL2 was capable to alleviate hepatic steatosis and lipogenesis through activating the Arntl‐Sirt1 axis and suppressing ER stress and inflammation. Therefore, FLRL2‐mediated gene therapy might be a promising pharmacological strategy in NAFLD. ⁶⁴

2.2.9. LncSHGL

LncSHGL is a nonsecretory lncRNA that highly expresses in the liver and has the ability to suppress hepatic gluconeogenesis and lipogenesis. ⁶⁵ LncSHGL is a novel inhibitor of gluconeogenesis and lipogenesis, while expression of LncSHGL decreased in NAFLD. ⁶⁶ LncSHGL recruited hnRNPA1 to activate PI3K/AKT, elevating protein levels of CaM to inhibit liver gluconeogenesis and lipogenesis independent of insulin. As a novel suppressor of gluconeogenesis and lipogenesis, lncSHGL might represent a promising strategy for the treatment of hepatic steatosis.

2.3. Implications of lncRNAs in NAFLD

A better understanding of the mechanism in the progression of NAFLD and exploring novel intervention targets are of paramount importance to develop medications to reverse NASH. As mentioned above, LncRNAs have been shown to control hepatic lipid regulation and metabolism; importantly, their expression level was relevant to the severity of NAFLD. LncRNAs act as ceRNAs to regulate biological processes by sponging miRNAs in the development and progression of NAFLD. As one of the important epigenetic modifications, lncRNAs are inheritable as well as reversible, this could provide a new way for individualized prevention and therapy in NAFLD. It might be of possibility to provide new targets for NAFLD treatment by exploring and identifying the role and mechanism of lncRNAs unconventionally expressed in NAFLD.

3. SIGNALING PATHWAYS OF LNCRNAS REGULATING NAFLD

As mentioned above, lncRNAs are necessary in the process of epigenetic modification. Accumulating studies have revealed that lncRNAs play a critical role in the regulation of NAFLD through the interaction of multiple pathways. We summarized the latest identified lncRNAs that are mainly involved in regulating NAFLD and possible signaling pathways that mediate their regulatory effects.

3.1. NF‐κB pathway

The NF‐κB signaling pathway is one of the evolutionarily conserved pathways to maintain homeostasis, and its interactions couple energy balance with the immune or inflammatory response. ⁶⁷ The primary agents of regulating NF‐κB pathway involved inhibitory IκB (inhibitor of NF‐κB) proteins and the IκB kinase (IKK) complex. ⁶⁸ After infecting with bacterial and viral, microbial products are recognized by Toll‐like receptors (TLRs) and inflammatory cytokines, which can induce activation of NF‐κB. The NF‐κB pathway can mediate NAFLD by lncRNAs such as Gm9795, Platr4, and lncTNF. ¹⁰ , ²⁷ , ⁶⁹ The regulatory process is mediated through NF‐κB‐dependent transcription of inflammatory factors such as cytokines, chemokines, and cell adhesion molecules.

3.2. MAPK/JNK/JUN pathway

JNK, a member of the MAPK family, can be activated and exerts functions by regulating obesity, IR, and cell death in NAFLD. ⁷⁰ Phosphorylation events in response to stress stimuli can activate MAPK/JNK/JUN pathway. The stress stimuli enforce small GTPases of the Rho family in the cell membrane and guide the activation of MAP3K, and next protein kinase phosphorylation activates MKK4/7 through MAP3K. Phosphorylated MKK7 activates JNKs by phosphorylation on tyrosine and threonine. The MAPK/JNK/JUN pathway is a potential and novel therapeutic target for NAFLD, which participates in the process of liver inflammation and lipid accumulation. Studies have found that Gm9795 and NEAT1 act on the JNK pathway, ¹⁴ , ⁶⁹ and HULC works on the MAPK pathway in the pathogenesis of NAFLD. ³⁸

3.3. AMPK pathway

AMPK, termed as AMP‐activated protein kinase, is a vital enzyme of regulating multiple metabolic pathways. AMPK is considered to have important implications in the treatment of obesity, IR, NAFLD, and cardiovascular disease (CVD). The AMPK/SREBP‐1 pathway and its downstream proteins are closely related to lipid metabolism. ⁷¹ , ⁷² NEAT1 inhibits AMPK pathway activation through different pathways. As reported, miR‐140 can interact with NEAT1 and is capable of promoting its expression. In addition, NEAT1 participates in miR‐140‐induced adipogenesis and consequently regulates hepatic steatosis, that is, the positive regulation of NEAT1 by miR‐140 was imperative for adipogenesis. ⁷³ In NAFLD, NEAT1 influenced lipid accumulation through miR‐146a‐5p/ROCK1 axis and further regulated the AMPK/SREBP pathway. ¹⁷

3.4. Hedgehog pathway

The hedgehog (Hh) pathway is involved in hepatic steatosis, and inhibiting the Hh pathway enhances steatosis. Absence of Hh ligand suppresses another receptor smoothened (Smo) by inhibiting the dissociation of Gli with its inhibitor Sufu and consequently inducing the phosphorylation of Gli. However, in the presence of Hh ligand, the Hh pathway can be activated, and Gli is further transferred to the nucleus to upregulate the target gene transcription. ⁷⁴ , ⁷⁵ , ⁷⁶ As reported, conditional liver‐specific knockout of Smo inhibited the Hh pathway and then induced liver steatosis; the steatogenic suppression effect of Gli originated from a shifting of lipid metabolism toward lipogenesis by SREBP‐1c. ⁷⁷ And more interestingly, altered Hh pathway activity was also involved in the process of liver fibrosis and carcinogenesis. ⁷⁴ , ⁷⁸

3.5. mTOR pathway

The mTOR pathway includes two functionally distinct protein complexes identified as mTORC1 and mTORC2 that regulate cell growth through controlling metabolic pathways. ⁷⁹ As a promising therapeutic target of metabolic diseases, mTORC1 is capable of promoting lipid biogenesis through activating the expression of RNA‐binding SR protein (SRPK2). ⁸⁰ The mTOR/S6K1 pathway is involved in cell growth, proliferation, and differentiation through controlling protein synthesis and lipid metabolism. ⁸¹ In addition, one of the important contributions of the mTOR/S6K1 pathway is to participate in insulin signal transduction in type 2 diabetes. ⁸² Notably, suppression of mTOR/S6K1 presented the similar effect as silencing of NEAT1 on ACC and FAS expression, which implies that hepatic lipid metabolism is regulated by the mTOR pathway.

3.6. AKT pathway

AKT is a serine/threonine kinase and is involved in the PI3K signaling pathway. LncRNAs or pathways regulate the AKT pathway in NAFLD, including the pathways such as YAP1/IRS2/AKT, PI3K/AKT/SREBP‐1c, AKT/SREBP‐2/HMGCR, PDK1/AKT/FOX, PI3K/AKT/GSK, and AKT/mTOR. Specifically, lncARSR works on hepatic cells via the YAP1/IRS2/AKT, PI3K/AKT/SREBP‐1c, and AKT/SREBP‐2/HMGCR pathways, uc.333 regulates hepatic cells through the PI3K/AKT/GSK pathway, and MEG3 acts on NAFLD via the LRP6/AKT/mTOR pathway. ³⁴ , ³⁵ , ³⁶ , ⁵⁶ As both AKT and lncRNAs play important roles in NAFLD, identifying the specific roles that these lncRNAs play within this pathway may represent a completely new avenue for developing targets with better therapeutic properties.

3.7. Arntl/Sirtl pathway

Arntl is a typical agent that regulates circadian rhythm, and its role in metabolic disorders has been revealed in recent years. ⁸³ Sirt1 is a vital metabolic regulator that is controlled by a large number of transcription factors, and Arntl was capable of binding to the E‐box elements in the Sirt1 promoter to upregulate its expression. ⁸⁴ Sirt1 binds to Arntl and deacetylates Arntl, thereby maintaining high‐magnitude circadian transcription of Arntl. ⁸⁵ , ⁸⁶ FLRL2 is able to activate the Arntl/Sirt1 axis, subsequently attenuates hepatocyte steatosis, and inhabits hepatic lipogenesis and inflammation, providing preliminary evidence for the therapeutic benefits of Arntl/Sirt1 in NAFLD. ⁶⁴

4. CONCLUSIONS AND PERSPECTIVES

LncRNAs and the related pathways are building an across‐linked network, giving us an opportunity to explore the regulatory mechanisms in the process of NAFLD. Notably, the regulatory effect of lncRNAs on NAFLD is interrelated and constitutes a relatively complex network (Figure 1). However, the mechanisms and signaling pathways of lncRNAs regulating NAFLD remain unclear and need to be verified in the future. The detail mechanisms regarding the interactions among lncRNAs, molecules and the related pathways, and the positions and roles of lncRNAs involved in NAFLD regulation are still worth investigating. Other lncRNAs, molecular mechanisms, and regulatory pathways have not yet been unveiled. Undoubtedly, research needs to be done to enrich the complex network that regulates NAFLD.

FIGURE 1.

Network regarding lncRNAs and signaling pathways in NAFLD. As a heterogeneous group of noncoding RNAs (ncRNAs), lncRNAs play crucial roles in biological processes underlying the pathophysiology of NAFLD. LncRNAs and the main pathways controlled by lncRNAs are involved in the regulation of NAFLD. The regulation of lncRNAs on NAFLD is not independent but interrelated and constitutes a relatively complex regulatory network.

Prospectively, the study of lncRNAs regulating NAFLD is expected to provide a new promising possibility for NAFLD treatment. LncRNAs might be novel therapeutic targets for drug development and improved, noninvasive methods for diagnosis by exploring the roles and mechanisms of lncRNAs unconventionally expressed in NAFLD.

AUTHOR CONTRIBUTIONS

Na Shi and Kang Sun contributed to bibliographic research, drafting of the paper, critical revision, and final approval of the submitted version. Haiying Tang contributed to critical revision and final approval of the submitted version. Jingwei Mao contributed to study conception and design, critical revision, and final approval of the submitted version. All authors read and approved the final manuscript.

CONFLICT OF INTEREST STATEMENT

The authors declare that they have no conflicts of interest.

Shi N, Sun K, Tang H, Mao J. The impact and role of identified long noncoding RNAs in nonalcoholic fatty liver disease: A narrative review. J Clin Lab Anal. 2023;37:e24943. doi: 10.1002/jcla.24943

DATA AVAILABILITY STATEMENT

The datasets used or analyzed during the current study are available from the corresponding author on reasonable request.