The role of hnRNPs in frontotemporal dementia and amyotrophic lateral sclerosis

Abstract

Dysregulated RNA metabolism is emerging as a crucially important mechanism underpinning the pathogenesis of frontotemporal dementia (FTD) and the clinically, genetically and pathologically overlapping disorder of amyotrophic lateral sclerosis (ALS). Heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a family of RNA-binding proteins with diverse, multi-functional roles across all aspects of mRNA processing. The role of these proteins in neurodegeneration is far from understood. Here, we review some of the unifying mechanisms by which hnRNPs have been directly or indirectly linked with FTD/ALS pathogenesis, including their incorporation into pathological inclusions and their best-known roles in pre-mRNA splicing regulation. We also discuss the broader functionalities of hnRNPs including their roles in cryptic exon repression, stress granule assembly and in co-ordinating the DNA damage response, which are all emerging pathogenic themes in both diseases. We then present an integrated model that depicts how a broad-ranging network of pathogenic events can arise from declining levels of functional hnRNPs that are inadequately compensated for by autoregulatory means. Finally, we provide a comprehensive overview of the most functionally relevant cellular roles, in the context of FTD/ALS pathogenesis, for hnRNPs A1-U.

Keywords: Amyotrophic lateral sclerosis; Autoregulation; Frontotemporal dementia; RNA; hnRNP.

Fig. 1

The hnRNP family: composition and structure. The hnRNP family are named alphabetically from A1 to U, with hnRNP U being the largest protein (120 kDa) in the class. The proteins all contain varying combinations and quantities of RNA-binding domains which facilitate their myriad functional roles in pre-mRNA processing. RNA-recognition motifs (RRMs) are by far the most commonly identified domain in this category. Several hnRNPs also possess a nuclear import/export signal to enable them to perform both nuclear and cytoplasmic functions. RRM RNA recognition motif, KH K-homology domain, RGG Arg-Gly-Gly repeat domain, NLS nuclear localisation signal. Number in the bottom right corner of each schematic indicates amino acid length

Fig. 2

IPA analysis of the hnRNP family. Network analyses obtained using ingenuity pathway analysis (IPA) showing the direct, experimentally confirmed interactions of hnRNPs with both each other (a) and superimposed key FTLD/ALS genes and proteins (b): TARDBP (TDP-43), C9orf72, FUS and MAPT (Tau). Half-circle ‘self’ arrows indicate evidence of autoregulation whilst half-circle lines indicates evidence of self-binding only

Fig. 3

HnRNP involvement in cryptic exon repression. Several hnRNP proteins have been known to bind to exonic and intronic regions of pseudo/cryptic 5′ splice sites. Their presence sterically occludes appropriate assembly of the spliceosome, in-turn inhibiting cryptic exon inclusion. HnRNP dysfunction leads to elevated cryptic inclusion in the final mRNA transcript. If a premature termination codon (PTC) is introduced following a frameshift, non-sense mediated decay (NMD) may be activated to destroy the transcript. Alternatively, the transcript may be partially translated into a truncated, aberrant protein isoform. Indeed, if by chance no PTC is introduced upon cryptic splicing then the full-length transcript may be translated

Fig. 4

HnRNP autoregulation mechanisms. HnRNPs autoregulate their expression by several RNA processing mechanisms. HnRNP binding promotes specific splicing events that result in the production of NMD-sensitive mRNAs and/or transcripts confined to the nucleus (blue background). These include the activation of a normally skipped premature termination codon (PTC)-containing ‘poison exon’ (a), the skipping of a normally ‘essential exon’ (EE) (b) or retention of intronic RNA (IR) (c). TDP-43 binds to its 3′UTR TARDBP binding site within intron 7 and inhibits the selection of the proximal poly(A) site (pA1), up-regulating alternative polyadenylation at its more distal sites: pA4 and more rarely pA2 (isoform not shown) (d). The unstable isoform generated is detained in the nucleus and is subject to exosome-mediated degradation. TDP-43-binding and subsequent RNA Pol II stalling can also lead to alternative splicing of 3′ UTR intronic regions (red rectangles) which truncates the final exon, eliminates the true stop signal and exposes an alternative termination codon (ATC). The ATC being > 50 nt from the final exon-junction complex designates the transcript for NMD. This splicing event is not believed to significantly contribute to TDP-43 autoregulation, but is a crucial feature of hnRNP A1 and hnRNP D/DL autoregulatory mechanisms which activate 3′ UTR poison exon/intron events

Fig. 5

Proposed model of hnRNP dysfunction in FTLD-ALS. The upper panel illustrates hnRNPs continuing to perform their homeostatic functions under relatively low levels of stress e.g., at early stages of FTLD-ALS pathogenesis. HnRNP protein levels are reduced as a result of low-level sequestration within cytoplasmic pathological inclusions (nuclear inclusions not shown) and/or recruitment to stress granules. Indeed persistence of stress granules may be the root cause of some of these aggregates. However, autoregulation ensures adequate amounts of hnRNPs are replenished so they may perform their myriad nuclear functions including alternative splicing regulation, cryptic exon repression and DNA damage repair. By contrast, the lower panel illustrates a scenario whereby hnRNP depletion by pathological sequestration breaches a homeostatic ‘tipping point’ that is beyond compensation by autoregulatory means. At this stage, ensuing mRNA metabolic dysfunction from alternative splicing dysregulation and elevated cryptic exon activation in addition to unrepaired DNA damage may rapidly lead to neurotoxicity and accelerated neurodegeneration