Hum Genet DOI 10.1007/s00439-017-1830-7 REVIEW Genetic mutations in RNA‑binding proteins and their roles in ALS Katannya Kapeli1 · Fernando J. Martinez2 · Gene W. Yeo1,2,3 Received: 1 April 2017 / Accepted: 17 July 2017 © The Author(s) 2017. This article is an open access publication Abstract Mutations in genes that encode RNA-binding revealed that two-thirds of RBPs are expressed in a cell- proteins (RBPs) have emerged as critical determinants of type specifc manner (McKee et al. 2005). This specialized neurological diseases, especially motor neuron disorders expression of RBPs is thought to maintain a diverse gene such as amyotrophic lateral sclerosis (ALS). RBPs are expression profle to support the varied and complex func- involved in all aspects of RNA processing, controlling the tions of neurons. An increasing number of RBPs are being life cycle of RNAs from synthesis to degradation. Hallmark recognized as causal drivers or associated with neurological features of RBPs in neuron dysfunction include misregu- diseases (Polymenidou et al. 2012; Belzil et al. 2013; Nuss- lation of RNA processing, mislocalization of RBPs to the bacher et al. 2015), which reinforces the importance of RBPs cytoplasm, and abnormal aggregation of RBPs. Much pro- in maintaining normal physiology in the nervous system. gress has been made in understanding how ALS-associated Mutations in genes that encode RBPs have been observed mutations in RBPs drive pathogenesis. Here, we focus on in patients with motor neuron disorders such as amyotrophic several key RBPs involved in ALS—TDP-43, HNRNP A2/ lateral sclerosis (ALS), spinal muscular atrophy (SMA), B1, HNRNP A1, FUS, EWSR1, and TAF15—and review multisystem proteinopathy (MSP) and frontotemporal lobar our current understanding of how mutations in these proteins degeneration (FTLD). In adults, ALS is the most common cause disease. motor neuron disorder and is characterized by progressive loss of upper and lower motor neurons, which leads to fatal paralysis (Eykens and Robberecht 2015). The causes of ALS Introduction remain largely unknown, with 90% of cases being sporadic and the remaining 10% having a hereditary component RBPs play a central role in mediating post-transcriptional (Pasinelli and Brown 2016). Model organisms (mouse, yeast, gene expression. They directly bind to RNA and control all and drosophila) and human cells [patient tissue or neurons aspects of RNA processing, including RNA synthesis, matu- generated from patient-derived induced pluripotent stem ration, localization, translation, and decay. A genome-wide cells (iPSCs)] have enabled signifcant progress in dissecting survey of RBPs in the developing mouse nervous system the normal and pathological functions of ALS-linked RBPs. There are more than one hundred genes associated with * Gene W. Yeo ALS, a handful of which encode proteins that control RNA [email protected] processing (Wroe et al. 2008). Here, we focus on several 1 RBPs that are known to be mutated in patients with ALS: Department of Physiology, Yong Loo Lin School TAR DNA-binding protein 43 (TDP-43), heterogeneous of Medicine, National University of Singapore, Singapore 117593, Singapore nuclear ribonucleoprotein A1 (hnRNP A1), heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1), fused 2 Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University in sarcoma/translocated in liposarcoma (FUS/TLS, herein of California, San Diego, La Jolla, CA 92093, USA referred to as FUS), Ewing’s sarcoma breakpoint region 1 3 Molecular Engineering Laboratory, A*STAR, (EWSR1), and TAF15 (TATA-box binding protein asso- Singapore 138673, Singapore ciated factor 15) (Fig. 1). There are many commonalities Vol.:(0123456789)1 3 Hum Genet between these proteins. TDP-43, hnRNP A1, and hnRNP by transportin to control nuclear–cytoplasmic shuttling (Lee A2/B1 are structurally similar in that they contain two et al. 2006) (Fig. 1). They are predominantly nuclear, multi- RNA recognition motifs (RRMs) and a Gly-rich C-terminal functional proteins that are widely expressed in most cell and domain (Fig. 1) (He and Smith 2009). FUS, EWSR1 and tissue types and are implicated in a broad range of cellular TAF15, which form the FET family, also share a similar processes. The importance of these proteins is exemplifed structure: a zinc fnger domain and RRM that facilitates by the observations that compete loss of TDP-43 or hnRNP DNA and RNA binding, respectively, an N-terminal low A1 in mice is embryonic lethal (Kraemer et al. 2010; Liu complexity, prion-like domain that mediates protein inter- et al. 2017) while complete loss of FUS or EWSR1 in mice actions and self-assembly (Han et al. 2012; Kato et al. 2012; is postnatal lethal (Hicks et al. 2000; Li et al. 2007). Disease- Kwon et al. 2013; Schwartz et al. 2012), multiple C-terminal related mutations in these RBP have been reported to alter Arg-Gly-Gly (RGG) domains that facilitate non-specifc the normal functions of the protein in various steps of RNA RNA binding and protein interactions, and an atypical Pro- processing (Fig. 2). In this review, we discuss their normal Tyr nuclear localization signal (PY-NLS) that is recognized functions in RNA processing, their connection to ALS, and 1106 176191 262414 A90V G298S N345K G376D N378D/S RRM1 RRM2 Gly-rich D169G M311V G348C/V/R TDP-43 K263E A315T/E N352S/T S379P/C Mutations N267S A321V/G G357S/R A382P/T RNA G287S Q331K M359V I383T/V G290A/V S332N R361S/T G384R S292N G335D P363A W385G G294A/V M337V G368S N390D/S G295R/S/C Q343R Y374X S393L 11497105 184195 317320 HNRNP RRM1 RRM2 Gly-rich D262V/N A1 Mutations N267S RNA P288S P18S G228-G229insG R502WfsX15 S57del G230delG G503WfsX12 N63S G230C G504WfsX12 19 92 100179 190337 341 S96del R234C/L G507D RRM1 RRM2 Gly-rich S115N R244C G509D HNRNP S142N G245V K510WfsX517 A2/B1 Mutations D290V G144-Y149del M254V K510E/R RNA G156E R383C S513P N159Y G399V R514G/S G173-G174del S462F G515C G174-G175del M464I E516V G187S G466VfsX14 H517D/P/Q G191S G472VfsX57 R518G/K/del 1165 267285 371422 453501 526 G206S R487C Q519X Q210H R491C R521S/G/C/H/L FUS QGSY-richGly-rich RRM RGG Zn RGG R216C G492EfsX527 R522G G222-G223insG R495X R524R/S/T/W Mutations G223del R495EfsX527 P525L RNA G225V R495QfsX527 X527YextX G226S G497AfsX527 1250 283348 360 446454 517548 655 EWSR1 QGSY-rich Gly-rich RRM RGG Zn RGG Mutations P552L G511A RNA 1150 171219 234320 325 354386 572592 QGSY-rich Gly-rich RRM RGGZn RGG A31T R395Q TAF15 M368T R408C Mutations R385H G452E G391E G473E RNA ALS mutations RNA recognition motif zinc finger motif (Zn) RNA interactions glycine-rich domain nuclear localization signal (Gly-rich) QGSY-rich domain arginine-glycine-glycine nuclear export signal rich domain (RGG) Fig. 1 Mutation and RNA interaction maps for ALS-associated protein sequence—missense mutations, frame shifts, and deletions— RNA-binding proteins (RBPs). The locations of mutations identi- are reported. Points of contact between RBPs and mRNA are shown fed in familial and sporadic ALS patients are mapped against the (TDP-43, Buratti and Baralle 2001; all others, Castello et al. 2016) domain structure of the RBP. Mutations that cause a change in the 1 3 Hum Genet Fig. 2 ALS-associated mutations in RBPs may disrupt RNA pro- ▸ NormalDisease cessing by several mechanisms. a Wild-type RBPs have roles in transcription. Mutant forms of the proteins may have abnormal inter- actions with transcription factors like TFIID or RNA polymerase II ? that disrupt transcription. b RBPs bind to introns of pre-mRNAs and splicing factors to regulate constitutive and alternative splicing. ALS- WT mutant proteins alter global splicing through events like exon skip- anscription Tr ping. c ALS-associated RBPs predominantly reside in the nucleus. Mutations in the RBPs can cause mislocalization to the cytoplasm ) (a where they bind and regulate diferent sets of RNAs. Some mutant RBPs were found to promote mislocalization of wild-type RBPs to the cytoplasm. d RBPs are involved in RNA trafcking, particularly g to distant axonal and dendritic sites in neurons. Mutations in RBPs, such as FUS and TDP-43, disrupt the protein’s ability to transport WT mRNAs to their proper destinations. e TDP-43, hnRNP A2/B1, and Alt splicin hnRNP A1 are implicated in translation and mutant forms of these ) RBPs may disrupt this function. For example, mutant forms of TDP- (b 43 have a greater propensity to mislocalize to the mitochondria and block translation of specifc mitochondria-transcribed mRNAs (Wang et al. 2016a). f Mutations in ALS-associated RBPs, like FUS and WT TDP-43, cause the protein to be more resistant to proteasome-medi- WT ated degradation. The longer half-lives of mutant proteins results in WT WT their accumulation, which may confer toxicity. g Wild-type RBPs nat- urally form membrane-less organelles through phase transitions into Nuclear export WT liquid droplets. These reversible interactions are mediated by RNA ) and the low-complexity Gly-rich domain of the RBP. The presence of (c ALS-associated mutant RBPs, dipeptide repeats, or RNA repeats alter the biophysical properties of phase transitions and droplet formations. In these cases, droplets may evolve into insoluble structures through WT fbrilization that disrupt membrane-less organelles and kill neurons WT WT Localization ) speculate how ALS-associated mutations in the genes that (d encode these proteins may contribute to pathogenesis. TDP‑43 anslation Tr ) Roles in RNA processing (e Initially described as a transcription factor (Ou et al. 1995), WT TDP-43 is now better known for its role in RNA process- WT t1/2 t ing. Several groups have used crosslinking and immuno- 1/2 precipitation followed by sequencing (CLIP-seq) to identify the global RNA targets of TDP-43 and showed that TDP-43 Protein stability ) binds to thousands of RNAs (Tollervey et al.