Mol Neurobiol DOI 10.1007/s12035-016-9793-6

The Role of Long Noncoding RNAs in Neurodegenerative Diseases Peixing Wan 1 & Wenru Su 1 & Yehong Zhuo 1

Received: 24 November 2015 / Accepted: 11 February 2016 # Springer Science+Business Media New York 2016

Abstract Long noncoding RNAs (lncRNAs) are transcripts with low protein-coding potential but occupy a large part of transcriptional output. Their roles include regulating gene expression at the epigenetic, transcriptional, and posttranscriptional level in cellular homeostasis. However, lncRNA studies are still in their infancy and the functions of the vast majority of lncRNA transcripts remain unknown. It is generally known that the function of the human nervous system largely relies on the precise regulation of gene expression. Various studies have shown that lncRNAs have a significant impact on normal neural development and on the development and progression of neurodegenerative diseases. In this review, we focused on recent studies associated with lncRNAs in neurodegenerative diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), amyotrophic lateral sclerosis (ALS), multiple system atrophy (MSA), frontotemporal lobar degeneration (FTLD), and glaucoma. Glaucoma, caused by unexplained ganglion cell lesion and apoptosis, is now labeled as a chronic neurodegenerative disorder [1], and therefore, we discussed the association of lncRNAs with glaucoma as well. We illustrate the role of some specific lncRNAs, which may provide new insights into our understanding of the etiology and pathophysiology of the neurodegenerative diseases mentioned above.

* Wenru Su [email protected] * Yehong Zhuo [email protected]

1

State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, Guangdong, People’s Republic of China

Keywords Long noncoding RNAs (lncRNAs) . Neurodegenerative diseases . Alzheimer’s disease (AD) . Parkinson’s disease (PD) . Huntington’s disease (HD) . Amyotrophic lateral sclerosis (ALS) . Multiple system atrophy (MSA) . Frontotemporal lobar degeneration (FTLD) . Glaucoma

Introduction Over the past decade, advances in genome-wide analysis have revealed that up to 90 % of the human genome is transcribed. However, approximately only 1 % of RNA transcripts encode proteins, whereas the remaining transcripts are noncoding RNAs (ncRNAs) [2]. Noncoding transcripts are further divided into housekeeping ncRNAs and regulatory ncRNAs. Housekeeping ncRNAs, which are usually constitutively expressed, include ribosomal, transfer, small nuclear, and small nucleolar RNAs. Regulatory ncRNAs are generally divided into two classes based on nucleotide length. Those less than 200 nucleotides are usually referred to as short/small ncRNAs and include microRNAs, small interfering RNAs, and Piwi-associated RNAs, whereas those greater than 200 nucleotides are known as long noncoding RNAs (lncRNAs) [3]. An abundance of studies investigating the dysregulation of lncRNAs in cancer [4, 5], stroke [6, 7], neurological diseases [8], and Hirsch sprung disease [9] suggest that lncRNAs play vital roles in disease pathological progress, diagnosis, and prognosis (Table 1). The human nervous system is the most highly evolved and sophisticated biological system. lncRNAs, which are transcribed from a different location of the genome from that of other RNAs, are highly expressed in the nervous system [10, 11], and their networks are highly adapted to complex neurobiological functions. The roles of lncRNAs in

5; 5

22q12.2

11q13.1

14q32

Abhd11os

TUG1

NEAT1

MEG3

13q21

4p16.3

HTT-AS

ATXN8OS

3

HAR1

9p21.2

13 11p14.1

rs7990916 BDNF-AS

AS C9ORF72

3p25.3

NAT-Rad18

4p14

3; 3 A3

Sox2OT

AS Uchl1

NC_023688.1

17A

22q11

5p13.2

GDNF-AS

1p36.12

2p21

BCYRN1

PINK1-AS

11q23.3

BACE1-AS

DGCR5

Genomic location

Official symbol

SCA8; KLHL1AS; NCRNA00003

NAPINK1; PINK1AS; PINK1-AS1

GTL2; FP504; prebp1; PRO0518; PRO2160; LINC00023; NCRNA00023; onco-lncRNA-83 LINC00037; NCRNA00037

TI-227H; LINC00080; NCRNA00080 VINC; TncRNA; LINC00084; NCRNA00084

Wbscr26; Wnscr26; AI462243; 2010001M06Rik

HTTAS; HTT-AS1

BDNF; BDNFOS; BDNF-AS1; ANTI-BDNF; NCRNA00049

GDNFOS

BC200; BC200a; LINC00004; NCRNA00004

BACE1AS; BACE1-AS1; NCRNA00177

Possible names

HD

HD

HD

HD

HD

HD

AD HD

AD

AD and PD

PD

An antisense transcript at the C9ORF72 locus An antisense transcript to the KLHL1 gene.

SCA and MSA

ALS

An antisense to the mouse Ubiquitin PD carboxy-terminal hydrolase L1 (Uchl1)

Transcribed from the antisense of PINK1 locus

Inhibit GABAB signaling pathway by antagonize GABAB R2 transcription Modulate Sox2 gene expression to down neurogenesis, acting as a biomarker in neurodegeneration NAT-Rad18 impair the capability of neuron suffering DNA damage stress

Regulate the expression of endogenous GDNF in human brain

Increase BACE1 mRNA stability resulting Aβ overexpression through post-transcriptional procession Manipulate local proteins in postsynaptic dendritic micro domains to maintenance of long-term synaptic plasticity

Roles of lncRNAs

Up

Up

Down

Up

Down

Down

Up

Up

Down

Down

Down

Regulate KLHL1 expression and lead to toxic RNA gain-of-function pathologies

Target degradation of the corresponding mRNA

AS Uchl1 induces UchL1 expression by up-regulating its translation

Stabilize the PINK1 resulting disturbed mitochondrial respiratory chain, and vulnerable to apoptosis

DGCR5 is downstream target of REST in HD

It associates with PRC2 complex, and is found in the chromatin compartment of the cell

Its expression is specifically unregulated in the nucleus of heroin users

Indispensable for retinal development

Abhd11os overexpression produces neuroprotection against an N-terminal fragment of mutant huntingtin

HTTAS decreases endogenous HTT transcript levels

Mutated Huntingtin result in the abnormal expression of HAR1

Up regulated then down regulated No significant change Remain unknown Up Decreasing BDNF expression post-transcriptionally

Up

Dysregulated/ differences in tissue expression Up

AD

AD

Down

Up

AD and PD

AD

Relevant Expression level neurodegenerative disorders

DiGeorge syndrome crucial region gene 5 HD

Natural antisense transcript of the HD repeat locus The expression of Abhd11os is accumulated in mouse striatum TUG1 is expressed in the retina as well as brain Forms paraspeckle or act as a transcriptional regulator Interacts with the tumor suppressor p53. Its deletion enhances angiogenesis in vivo

A genetic variant in the lincRNA 01080 An overlapping antisense lncRNA of BDNF gene Overlap the gene of HAR1

Transcribed from the antisense of Rad18 gene

Located in the human G-protein-coupled receptor Affiliated with the antisense RNA class

Transcribed from opposite strand of GDNF gene merely in primate genomes

Generated and recruited into function regulating dendritic protein biosynthesis

Transcribed from the antisense strand of protein-coding BACE1 gene

Detailed information

Brief conclusion of dysregulated lncRNAs in neurodegenerative diseases

Summary of lncRNAs in neurodegenerative diseases

Table 1

Mol Neurobiol

Manipulate the activity of promoter in LOXL1 region Dysregulated

Interacts with polycomb repressive Glaucoma complex-1 (PRC1) and -2 (PRC2), leading to epigenetic silencing of other genes Encoded on the opposite strand of LOXL1 Exfoliation glaucoma

Dysregulated

Interacts directly with ATXN7 mRNA. ATXN7L3B mediate feedback regulation of ATXN7 may contribute to the specific neurodegenerative disease Influence the nearby CDKN2A and CDKN2B genes via regulatory mechanisms, which can influence cell proliferation and senescence Dysregulated

ANRIL; p15AS; PCAT12; CDKN2BAS; CDKN2B-AS; NCRNA00089

SCA 12q21

9p21.3

15q24.1

ATXN7L3B

CDKN2B AS1

LOXL1 -AS1

lnc-SCA7

TAC/TGC expansion interferes with normal antisense function A conserved long noncoding RNA

Definition of lncRNA The earliest identified lncRNAs, for example, X-inactive specific transcript and H19, were discovered by searching cDNA libraries in the 1980s and 1990s [12, 13]. Since then, with the improvement of microarray sensitivity and sequencing technology, various novel lncRNA transcripts have been found [14]. There are limitations to the definition of lncRNAs. The latest definition proposed by the HUGO Gene Nomenclature Committee (HGNC) describes lncRNAs as spliced, capped, and polyadenylated RNAs [15]. lncRNA transcripts are partially similar to messenger RNAs (mRNAs) [16, 17] as they are frequently transcribed by RNA polymerase II, contain classical splice sites (GU/ AG), have similar intron/exon lengths to mRNAs, exhibit alternative splicing, and are associated with the same types of histone modifications as protein-coding genes [18, 19]. However, lncRNAs generally present low protein-coding potential and are devoid of extended open reading frames (ORFs), although some lncRNAs may encode short peptide sequence [20, 21]. Until now, only very few lncRNAs have been validated by experiment, whereas most lncRNAs have been annotated via bioinformatics and still need further experimental verification.

Classification of lncRNAs

Classification Based on Transcript Length of lncRNAs

Genomic location

Possible names

brain development, neuron function, maintenance, and differentiation, as well as neurodegenerative diseases, are becoming increasingly evident. Here, we provide a systematic and comprehensive summary of the existing knowledge of lncRNAs, with the aim of providing a better understanding of this new field of study.

Currently, the classification of lncRNAs remains controversial (Table 2). Therefore, having a comprehensive review of these existing lncRNA classifications are of great importance. The existing classifications of lncRNAs rest on their different properties: from their size, to their localization, and to their function [22].

Official symbol

Summary of lncRNAs in neurodegenerative diseases

Table 1 (continued)

Detailed information

Relevant Expression level neurodegenerative disorders

Roles of lncRNAs

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The length of lncRNAs comes as the most commonly used method for their classification. Classification Based on Association with Protein-Coding Genes and Other Functional DNA Elements These criteria serve as the foundation of the GENCODE classification of lncRNAs [23].

Mol Neurobiol Table 2

Different classifications of lncRNAs

Category

Abbreviation

Classification Based on Subcellular Localization

1. Classification based on transcript length of lncRNAs Long noncoding RNA

lncRNA

Long-intergenic noncoding RNA; large intervening noncoding RNA, long-intervening noncoding RNA Very long intergenic noncoding RNA

lincRNA

vlincRNA

macroRNA 2. Classification based on association with protein-coding genes and other functional DNA elements Enhancers or enhancer-like lncRNAs Promoter-associated RNAs asRNA

Intergenic RNAs Bidirectional RNAs

lincRNA

3′ UTR-associated RNAs Telomeres, telomeric repeat-containing RNA

4. Classification based on subcellular localization Chromatin-associated RNA Chromatin-interlinking RNA Nuclear bodies–associated RNAs

RNA localization can provide important clues to its function. The ENCODE consortium provided detailed profile of three subnuclear compartments (chromatin, nucleolus, and nucleoplasm) to reveal their lncRNA compositions [27]. Analyzing the classification of lncRNAs can help predict their function because their functions are usually closely related to those of their associated protein-coding genes, size, and localization.

Functions of lncRNA and the Possible Mechanisms

Antisense RNAs Intronic RNAs

3. Classification based on function Long noncoding RNAs with enhancer-like function; ncRNA-activating miRNA primary transcripts piRNA primary transcripts Competing endogenous RNA

lncRNAs act as precursors for shorter functional RNAs as mi- and piwi-interacting RNAs (piRNAs).

ncRNA-a

ceRNA

CAR ciRNA

PRC2 associated RNAs

lncRNAs are categorized into three major groups: lncRNAs transcribed from the host Protein Coding Gene (PCG), lncRNAs transcribed from gene regulatory regions, and lncRNAs transcribed from other specific chromosomal regions. In addition, lncRNAs within each of these groups can be further subgrouped (Fig. 1) [24]. In addition, some lncRNAs exhibit mixed characteristics, such as microRNAs, which are transcribed from multi-gene transcripts or even the whole chromosome [25]. Classification Based on Function A large part of lncRNAs can participate in tremendous cellular processes. These lncRNAs are distinguished from others by positively regulating nearby genes. A famous example is competing endogenous RNAs (ceRNAs). They have similar sequence with protein-coding transcripts as mRNAs and function by competing for combination or function [26]. Some

Existing evidence has confirmed diverse functions of lncRNAs; however, not all lncRNAs are functional. Indeed, some lncRNAs have been observed as transcriptional noise [28]. Recently, the heated debate on how many human genes are functional has been raised by scholars worldwide, putting forward the idea that more than 80 % of the human genome is functional [29]. In fact, although only a very small portion of identified lncRNAs have been experimentally examined to date, a group of scientists from the Spector laboratory suggest that lncRNAs function in many biological contexts, from modifying chromatin structure to regulating protein levels (Fig. 2) [29]. Identification of the functions of lncRNAs is a significant challenge for lncRNA investigations, and there is still a long way to go. lncRNA functions attracting the most attention in tumor research are associated with epigenetic changes that affect gene regulation, including DNA methylation, nucleosome positioning, and miRNA expression as well as histone modifications and higher-order chromatin remodeling [30].

The Role of lncRNA in Neurodegenerative Diseases lncRNAs have been found to be dysregulated in many neurodegenerative diseases and lncRNA transcripts that regulate key genes [24, 31, 32]. We present some examples of lncRNAs implicated in neurological disorders below. Alzheimer’s Disease One of the best-known examples of an lncRNA that regulates a key gene in human neurological disease is β-secretase-1 antisense RNA (BACE1-AS) in Alzheimer’s disease. The main pathological change associated with AD is the aggregation of amyloid plaques on neurons that are derived from the proteolytic processing of the amyloid precursor protein (APP) by the β-site amyloid precursor protein-cleaving enzyme (BACE1). Studies by Faghihi and his co-workers identified

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Fig. 1 Origin of lncRNAs. lncRNAs are divided into three major groups. (I) lncRNAs transcribed from gene regulatory regions. (1) Enhancers or enhancer-like lncRNAs (lncRNAs transcribed from enhancer domains or lncRNAs exhibiting enhancer activity); (2) promoter-associated RNAs (lncRNAs transcribed from promoter domains of protein-coding genes). (II) lncRNAs transcribed relative to the host PCG. (3) Antisense RNAs (lncRNA overlaps with one or more exons of another transcript on the opposite strand); (4) intronic RNAs (lncRNA is derived from an intron);

(5) intergenic RNAs (lncRNA is localized between two genes, also called lincRNAs); (6) bidirectional RNAs (lncRNA is expressed upon the initiation of transcription of a neighboring coding transcript on the opposite strand in close genomic proximity). (III) lncRNAs transcribed from other specific chromosomal regions. (7) 3′ UTR associated RNAs (lncRNAs derived from the 3’-untranslated region of a protein-coding transcript); (8) telomeres, telomeric repeat-containing RNA

a conserved antisense transcript, BACE1-AS, at the BACE1 locus [33]. BACE1-AS has been shown to be capable of upregulating BACE1 mRNA by forming a stabilizing duplex with the mRNA that results in an increase in BACE1 protein levels [34, 35]. This finding may be important in the development of therapies for AD. In vivo knockdown of BACE1-AS by the continuous infusion of siRNAs directly into the brain resulted in a downregulation of BACE1-AS and BACE1, as well as a reduction in β-amyloid synthesis and aggregation in the brain [36].. Another lncRNA found to be dysregulated in AD and the aging brain was the brain cytoplasmic (BC) RNA BCYRN1. BCYRN1 levels in Brodmann’s area 9, which is affected in AD, were found to be higher in age-matched AD brains than in those of controls, and the relative levels of BCYRN1 RNA

increased with the severity of AD [37]. BCYRN1 plays an important role in modulating local protein synthesis in dendrites, and overexpression of BCYRN1 in AD and aging brains could be a cause of synaptodendritic deterioration. However, another study showed contrasting results of a 70 % reduction in BCYRN1 RNA levels in AD-afflicted brains compared with control brains [38]. One possible explanation for the differences may stem from variances in the sampling location of the brain or in the severity of disease. GDNF-AS is transcribed from the opposite strand of GDNF gene whose expression levels are impaired in neurodegenerative diseases and is only found in primate genomes [39, 40]. The GDNF-AS gene has four exons that are spliced into different isoforms including the lncRNAs GDNF-AS1 and GDNF-AS2. In AD patients, the mature GDNF peptide

Fig. 2 Functions of lncRNAs. (I) Interaction with replication and transcription machinery. (1) lncRNAs induce chromatin remodeling and histone modification. (II) Interaction with mRNA. lncRNAs hybridize to mRNAs by base pairing with complementary sequences to block splice sites targeted by the spliceosome. This may lead to (2) alternatively spliced transcripts, (3) translation inhibition, (4) mRNA degeneration,

and (5) lncRNA interaction with Dicer to generate endogenous siRNAs. (III) Interaction with other biological molecules. (6) lncRNAs interact with proteins and modulate their activity by binding to specific protein partners, (7) alter protein localization to the target position, (8) serve as scaffolds to allow the formation of larger RNA–protein complexes (9) or act as miRNA sponges

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was downregulated. Further analysis of novel GDNF and GDNF-AS isoforms in AD brains may reveal the role of endogenous GDNF in human brain diseases. 17A is a novel ncRNA located in the human G-proteincoupled receptor 51 genes (GPR51, GABA B2 receptor) that plays a role in tightly controlling the alternative splicing of GPR51. 17A decreases the transcription of GABAB R2 and significantly impairs the GABAB signaling pathway. Inflammation in AD brains can trigger 17A expression, thereby enhancing the secretion of amyloid-β (Aβ) and increasing inflammation in AD brains [41]. Sox2 overlapping transcript (Sox2OT) is a stable transcript in mouse embryonic stem cells associated with embryo differentiation [11]. Interestingly, a study by Arisier analyzed the microarray expression of an anti-NGF AD11 transgenic mouse model and found that Sox2OT could serve as an ideal biomarker of neurodegeneration in both early and late stages [42]. Rad18 is an enzyme involved in the DNA damage repair system. NAT-Rad18 is transcribed from the antisense Rad18 gene. Microarray analysis demonstrated that the gene expression of Aβ-stimulated NAT-Rad18 was upregulated, which led to the downregulation of Rad18 at the posttranscriptional level. These results suggest that NAT-Rad18 can reduce the impact of DNA damage stress to neurons and increase neuron apoptosis [43]. A previous study analyzing human single-nucleotide polymorphisms (SNPs) in lincRNAs at the genome level indicated that a genetic variant, rs7990916, in lincRNA01080 may play an important role in the physiology and pathophysiology of the human brain [44]. To confirm this finding, Chinese scientists Luo X and his coworkers conducted a case–control study investigating the association of AD with rs7990916 in an independent Han Chinese individual. Their results do not support previous findings, suggesting that further studies using large-scale association analyses are required [45]. Tremendous efforts have been put into their translational applications by identifying specific lncRNAs that are changed in Alzheimer’s disease in order to provide biomarkers and to better illustrate molecular pathways [46]. Huntington’s Disease Huntington’s disease (HD) is caused by an expansion of a CAG triplet repeat stretch within the huntingtin gene, resulting in a mutant form of the huntingtin protein. The gene BDNF encodes a secreted growth factor that promotes neuronal maturation and survival. The overlapping antisense lncRNA, BDNF-AS, has been shown to inhibit BDNF expression post-transcriptionally [47, 48]. Patients with HD have reduced levels of BDNF in the brain, and it has been shown that overexpression of BDNF in the forebrain rescues HD phenotypes in a mouse model [49].

Given that BDNF plays such a key role in HD, downregulating BDNF-AS and thereby increasing BDNF levels could be a plausible approach for HD therapy [50]. Johnson’s group investigated lncRNA expression in human HD brain tissues and found that the expression of HAR1 was significantly decreased in the striatum, due to the activation of specific DNA regulatory motifs resulting in transcriptional repression [51]. Additionally, huntingtin antisense (HTT-AS) is a natural antisense transcript at the HD repeat locus. HTTAS v1 (exons 1 and 3) is downregulated in the human HD frontal cortex; however, its function remains unknown. In the present study, scientists focused on Abhd11os (called ABHD11-AS1 in human), which is a lncRNA whose expression is enriched in the mouse striatum. Studies demonstrate that Abhd11os levels are markedly reduced in multiple mouse models of HD. In vivo experiments were performed in mice using lentiviral vectors encoding Abhd11os or a small hairpin RNA targeting Abhd11os. The results show that Abhd11os overexpression produces neuroprotection against an Nterminal fragment of the mutant Huntington protein, whereas Abhd11os knockdown is proteoxic [52]. The expression of an additional four known lncRNAs was found to be dysregulated in the brains of HD patients: TUG1 [47] and NEAT1 are upregulated [53], whereas MEG3 [54] and DGCR5 [55] are downregulated. NEAT1, which is one of the first examples of a transcript necessary for the formation of paraspeckles, may play specific roles in the pathology of the brain as its expression is upregulated in the nucleus of heroin users. Although no functional studies have been carried out with DGCR5, this neural-specific, disease-associated transcript may have an important function within the human nervous system. MEG3 is transcribed into a wide variety of splice isoforms and is found on human chromosome 14. There is evidence that MEG3 is an epigenetic gene regulator associated with the PRC2 complex. Parkinson’s Disease Parkinson’s disease (PD) is a chronic, progressive movement disorder caused by the loss of dopamine-producing cells in the brain. Loss or overexpression of phosphatase and tensin homologue–induced kinase1 ( PINK1) results in impaired dopamine release and motor deficits [56]. NaPINK1 is a human-specific ncRNA transcribed from the antisense orientation of the PINK1 locus that has the ability to stabilize the expression of PINK1. NaPINK1 silencing results in the decreased expression of PINK1 in neurons [57], and studies in mouse brains have demonstrated similar results [58]. AS Uchl1 is a recently identified antisense transcript of the mouse ubiquitin carboxy-terminal hydrolase L1 gene (Uchl1) involved in brain function and neurodegenerative diseases.

Mol Neurobiol

AS Uchl1 increases UCHL1 protein synthesis at a posttranscriptional level, and AS Uchl1 activity depends on the presence of a 5′ overlapping sequence and an embedded inverted short interspersed nuclear elements B2 (SINEB2) element. AS Uchl1 function is under the control of stress signaling pathways as mTORC1 inhibition by rapamycin causes an increase in UCHL1 protein levels that is associated with the shuttling of AS Uchl1 RNA from the nucleus to the cytoplasm [59]. Once in the cytoplasm, AS Uchl1 RNA promotes the association of the overlapping sense protein-coding mRNA with active polysomes for translation. This activity is disrupted in rare cases of familial Parkinson’s disease, and the loss of UCHL1 activity has also been reported in many neurodegenerative diseases. Importantly, the manipulation of Uchl1 expression has been proposed as a tool for therapeutic intervention. We have shown that AS Uchl1 expression is under the regulation of Nurr1, a major transcription factor involved in dopaminergic cell regulation of Nurr1 and maintenance. Furthermore, AS Uchl1 RNA levels are strongly downregulated in neurochemical models of PD in vitro and in vivo. This work positions AS Uchl1 RNA as a component of Nurr1dependent gene network and a target of cellular stress and extends our understanding on the role of antisense transcription in the brain [60]. Amyotrophic Lateral Sclerosis Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease characterized by progressive paralysis of the muscles of the limbs and muscles involved in speech, swallowing, and respiration due to the progressive degeneration of voluntary motor neurons. In 2011, a hexanucleotide (GGGGCC) repeat expansion in the protein-coding gene C9ORF72 (chromosome 9 ORF 72) became the first identified causative mutation for both ALS and front temporal dementia [61, 62]. Noncoding transcripts have now also been identified at the C9ORF72 locus. The C9ORF72 repeat expansion region undergoes bidirectional transcription [63]. Both sense and antisense C9ORF72 transcripts are elevated in the brains of ALS patients where they form nuclear RNA foci [64]. The importance of the antisense C9ORF72 transcript is exemplified by the results of experiments targeting the degradation of the corresponding sense transcript using antisense oligonucleotides. However, correcting the diseaseassociated gene expression in patient-derived fibroblasts is insufficient for treating the disease [65]. Spinocerebellar Ataxia Spinocerebellar ataxia type 8 (SCA8) is caused by a CTG triplet expansion in the brain-expressed ATXN8OS gene.

ATXN8OS is an antisense lncRNA transcript that partially overlaps with the neighboring protein-coding gene, KLHL1 [66]. Although the etiology of the disease is not well understood, the microsatellite expansion of the antisense transcript is believed to function in regulating KLHL1 expression [67]. Microsatellite expansions in noncoding regions are also known to cause toxic RNA gain-of-function pathologies by sequestering factors involved in alternative splicing [68, 69]. Another type of SCA, spinocerebellar ataxia type 7 (SCA7), which is characterized by progressive cerebellar and retinal degeneration, is caused by a CAG-repeat expansion in ATXN7. ATXN7L3B, a conserved long noncoding RNA, interacts directly with ATXN7 mRNA. Mutations in ATXN7 disrupt these regulatory interactions and result in a neuron-specific increase in ATXN7 expression. The results in Tan JY’s lab characterize how ATXN7L3B mediate feedback regulation of ATXN7 may contribute to the specific neurodegenerative disease [69]. Multiple System Atrophy From a clinical standpoint, multiple system atrophy (MSA) and SCA 8 share several features. Scientists from Brazil studied the presence of expanded SCA8 alleles in ten patients with probable MSA. Neuroimaging studies were performed in all ten subjects. All subjects were initially assessed with brain CT scans showing signs of cerebellar and pontine atrophy. Combined CTA/CTG repeats were within normal range for both alleles in nine MSA patients, ranging from 20 to 28 repeats, whereas one patient presented 22/76 repeats. From a clinical standpoint, the latter subject presented no distinctive features that differed from the other subjects carrying smaller repeat sizes [70]. Frontotemporal Lobar Degeneration Frontotemporal lobar degeneration (FTLD) defines a progressive degeneration of the frontal and anterior temporal lobes of the brain. Two major pathologies types, FTLD-TDP and FTLD-FUS, are featured by the abnormal accumulation of RNA-binding proteins (RBPs) TDP-43 and FUS/TLS, respectively. lncRNAs are recently reported to have binding sites for FTLD/ALS-related proteins TDP-43 and FUS/TLS. One possible explanation is that TDP-43 and FUS/TLS regulate lncRNA transcription or transcript stability. It has been demonstrated that lncRNAs are dysregulated when it comes to depletion or unavailability of TDP-43 or FUS/TLS. The second alternative is that the binding to TDP-43 or FUS/TLS would enable lncRNAs to perform their function. It has been experimentally demonstrated that the cellular function of some lncRNAs is strictly dependent on the direct binding to TDP-

Mol Neurobiol

43 or FUS/TLS (Lourenco GF, Janitz M, Huang Y, Halliday GM. Long noncoding RNAs in TDP-43 and FUS/TLS-related frontotemporal lobar degeneration (FTLD)) [62, 65].

The Role of lncRNA in Glaucoma Optic nerve degeneration caused by glaucoma is a leading cause of blindness worldwide. IOP is just one of the risk factors; pathogenesis of glaucoma is found to be similar to that of common neurodegenerative diseases like Alzheimer’s and Parkinson [71]. However, the abnormalities in CNS regions and the optic nerve in glaucoma are distal but similar to each other [72]. The cyclin-dependent kinase inhibitor 2B antisense ncRNA (CDKN2B-AS1) on chromosome 9p21.3 is a genetic susceptibility locus for several age-related diseases. A group of scientists in the USA studied the association between ten CDKN2B-AS1 SNPs and glaucoma features among 976 POAG cases from the Glaucoma Genes and Environment (GLAUGEN) study and 1971 cases from the National Eye Institute Glaucoma Human Genetics Collaboration (NEIGHBOR) consortium. Analysis of nine of the ten protective CDKN2B-AS1 SNPs with minor alleles associated with reduced disease risk demonstrated that primary open-angle glaucoma (POAG) patients carrying these minor alleles had a smaller cup-to-disc ratio despite having higher intraocular pressure (IOP). Analysis of the one adverse SNP for which minor allele A is associated with increased disease risk demonstrated that POAG patients with the A allele had a larger cup-to-disc ratio despite having lower IOP. Alleles of CDKN2B-AS1 SNPs, which influence the risk of developing POAG, also modulate optic nerve degeneration among POAG patients [73]. In addition, a group of Japanese scientists examined genome-wide association studies (GWASs) of the same lncRNA in 2219 Japanese individuals and reported the identification of five variants in CDKN2B-AS1, which was already reported to be a significant locus associated with glaucoma in the Caucasian population [74]. Coding variants in the lysyl oxidase-like 1 (LOXL1) gene are strongly associated with exfoliation glaucoma (XFG). The entire LOXL1 genomic locus from black South African, US Caucasian, German, and Japanese XFS (exfoliation syndrome) patients and age-matched controls was sequenced. LOXL1-AS1, a lncRNA encoded on the opposite strand of LOXL1, was strongly associated with XFS. This region contains a promoter, whose activity was significantly modulated by the associated XFS risk alleles. LOXL1-AS1 expression is also significantly altered in response to oxidative stress in human lens epithelial cells and human Schlemm’s canal endothelial cells [75].

Concluding Remarks Many lncRNAs have been shown to play regulatory roles in the development and function of the nervous system, and dysregulation of this intricate regulatory network could result in the disruption of normal brain development and function. Studying lncRNA mechanisms will provide valuable insight into the molecular basis of neurodegenerative disorders, which may lead to new therapeutics and diagnostics. It is even conceivable that lncRNAs might be suitable as direct therapeutic targets because it is possible to produce antagoNATs that could provide selective treatments for neurological diseases. The essential role of these regulatory RNAs is reflected in almost every aspect in neurodegenerative diseases. lncRNAs are therefore excellent candidates for both disease biomarkers and therapies [76]. There are still some challenges to our review of lncRNAs. One important challenge is the technique used to identify functional lncRNAs involved in pathological effects. This problem turns out to be surprisingly difficult, even in simple pairwise comparisons, due to the significant level of noise in ChIP-seq data. The second challenge lies in the identification of the function of specific lncRNAs using both bioinformatics and experimental approaches. The development of transgenic animal models and genetic engineering techniques for altering the expression level of specific lncRNAs by downregulation or upregulation are classic strategies that can be used for these experiments. In addition, the mechanisms by which lncRNAs operate at the molecular, cellular, and more complex neural network level remain elusive. In summary, the synergy between these new experimental approaches and classical biochemical work could ultimately pave the way to a complete understanding of the functional roles of lncRNAs in neurodegenerative diseases and glaucoma. Compliance with ethical standard Conflict of interest All authors have completed the ICMJE uniform disclosure form at www.icmje.org/coi_disclosure.pdf; the authors have no other financial relationships with any organizations that might have an interest in the submitted work in the previous 3 years; and no other relationships or activities that could appear to have influenced the submitted work. Contribution of authors Doctor Peixing Wan (wrote and revised MS, data analysis); Prof Wenru Su (revised MS); Prof Yehong Zhuo (revised and approved MS) affirms that the manuscript is an honest, accurate, and transparent account of the study being reported; that no important aspects of the study have been omitted; and that any discrepancies from the study as planned (and, if relevant, registered) have been explained. Correspondence and requests for materials should be addressed to Ye h o n g Z h u o ( z h u o y h @ m a i l . s y s u . e d u . c n ) o r We n r u S u ([email protected]). Financial Support Prof. Yehong Zhuo is supported by Guangdong Province National Natural Science Foundation (Grant

Mol Neurobiol No.2014A030308016). The sponsor of the study had no role in the design of the original study protocol, in the collection, analysis, and interpretation of the data, in writing the report, or in the decision to submit the manuscript for publication. Copyright The corresponding author has the right to grant on behalf of all authors and does grant on behalf of all authors, an exclusive license on a worldwide basis to the Neurobiology of Disease Publishing Group Ltd. to permit this article (if accepted) to be published in Neurobiology of Disease editions and any other products and sublicenses such use and exploit all subsidiary rights, as set out in our license.

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