Converging mechanisms in ALS and FTD: disrupted RNA and protein homeostasis

Abstract

Breakthrough discoveries identifying common genetic causes for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) have transformed our view of these disorders. They share unexpectedly similar signatures, including dysregulation in common molecular players including TDP-43, FUS/TLS, ubiquilin-2, VCP, and expanded hexanucleotide repeats within the C9ORF72 gene. Dysfunction in RNA processing and protein homeostasis is an emerging theme. We present the case here that these two processes are intimately linked, with disease-initiated perturbation of either leading to further deviation of both protein and RNA homeostasis through a feedforward loop including cell-to-cell prion-like spread that may represent the mechanism for relentless disease progression.

Figure 1. Clinical, genetic and pathological overlap of ALS and FTD

(A) ALS and FTD represent a continuum of a broad neurodegenerative disorder with each presenting as extremes of a spectrum of overlapping clinical symptoms (ALS in red and FTD in purple). Major known genetic causes for ALS and FTD are plotted according to the ratio of known mutations that give rise to ALS or FTD. (B) Pathological protein inclusions in ALS and FTD, according to the major protein misaccumulated. Inclusions of TDP-43 and FUS/TLS in ALS and FTD reflect the pathological overlap of ALS and FTD.

Figure 2. Physiological roles of TDP-43 and FUS/TLS in RNA processing

Proposed roles for FUS/TLS include 1) association with TBP within the TFIID complex as a participant in the general transcriptional machinery and 2) binding to long introns in a sawtooth-like pattern, consistent with co-transcriptional deposition. Both TDP-43 and FUS/TLS 3) associate with promoter regions. TDP-43 binds single-stranded TG-rich elements in promoter regions thereby blocking transcription of the downstream gene. In response to DNA damage, FUS/TLS is recruited in the promoter region of cyclin D1 (CCND1) by sense and antisense noncoding RNAs (ncRNAs) and represses CCND1 transcription. BothTDP-43 and FUS/TLS 4) bind long intron-containing RNAs, thereby sustaining their levels. 5) TDP-43 and FUS/TLS control the levels of >950 or >370 RNAs, respectively, either via direct binding or indirectly. TDP-43 and FUS/TLS 6) bind long non-coding RNAs, 7) complex with Drosha (consistent with an involvement in miRNA processing), and 8) bind 3′UTRs of a large number of mRNAs. Both TDP-43 and FUS/TLS shuttle between the nucleus and the cytosol and are incorporated into 9) transporting RNA granules and 10) stress granules, in which they form complexes with mRNAs and other RNA binding proteins.

Figure 3. Comparison of TDP-43 and FUS/TLS RNA binding properties

Data are taken from Polymenidou et al (2011), Lagier-Tourenne et al (2012), Tollervey et al (2011), Sephton et al (2011), Colombrita et al (2012), Rogeli et al (2012), Hoell et al (2011), Ishigaki et al (2012), and Nakaya et al (2013).

Figure 4. Potential pathogenic mechanisms for GGGGCC repeat expansion within the C9ORF72 gene

(Top) Schematic representation of the human C9ORF72 gene (yellow: untranslated regions (UTR), blue: coding exons). Hexanucleotide (GGGGCC) repeat expansion is located between alternative exons 1a and 1b. At least three mechanisms may contribute to disease pathogenesis: A) GGGGCC repeat expansions may lead to reduced expression of the allele containing the repeat expansion (haploinsufficiency); B) RNA foci containing transcribed GGGGCC repeats may sequester RNA-binding protein(s); or C) non-AUG (RAN) translation of GGGGCC repeat-containing RNA produces toxic poly-dipeptides in each of three reading frames. Data and images reproduced with permission from A) Gijselinck et al. (2012), B) DeJesus-Hernandez et al. (2011), and C) Mori et al. (2012).

Figure 5. ALS/FTD-associated proteins involved in protein homeostasis

A) Schematic representation of major cellular degradation pathways. Many ALS/FTD-linked proteins are involved in protein clearance pathway, including B) ubiquilin-2 (UBQLN2) and p62/SQSTM1 (which bind to polyubiquitinated proteins and transport them to proteasome for degradation) and C) p62/SQSTM1 and optineurin (OPTN) (which serve as adaptor proteins to bind simultaneously the substrates that are targeted for autophagy and LC3, a component of autophagosomes). D) Fig4 is a lipid phosphatase that converts PI(3,5)P into PI3P. Autophagy is impaired in the neurons and astrocytes missing Fig4, with the disturbance of PIPs expected to disrupt formation or recycling of autolysosomes. E) ALS/FTD-linked mutations in CHMP2B, a core component of endosomal sorting complexes (ESCRT) required for transport, disrupt the normal endosome-lysosome-autophagy morphology and function. ESCRT complexes bind to ubiquitinated cargos and initiate clustering of ubiquitinated cargos and membrane invagination. The internalized cargos, which are cell membrane proteins, are transported into autophagosomes for degradation. F) VCP interacts with a large number of cofactor proteins that act as ubiquitin adaptors, allowing VCP to interact with a large number of ubiquitinated proteins to enable degradation or recycling, including extraction of misfolded proteins from the ER and subsequently targeting them for degradation. G) VAPB is involved in the unfolded protein response (UPR) by modulating activities of different arms of the UPR.

Figure 6. Aggregate assembly and propagation in ALS and FTD

Prion-like phenomena in ALS may include SOD1, TDP-43 or FUS/TLS seeded aggregation and cell-to-cell spreading. A) TDP-43 and FUS/TLS are both primarily nuclear RNA-binding proteins, whose mutations lead to ALS or FTD. Filled blue boxes on TDP-43 and FUS/TLS molecules indicate RNA-recognition motifs and the striped blue box on FUS/TLS refers to the zinc finger domain that can also bind RNA. B) Cellular stress induces TDP-43 and FUS/TLS incorporation into stress granules, which form through the ordered aggregation of several RNA-binding proteins complexed with RNA molecules. This physiologic reaction to cellular stress may be an initial trigger for pathogenic inclusion formation since the increased local protein concentration and RNA scaffolding molecules may facilitate ordered aggregation of TDP-43 and/or FUS/TLS. C) Upon chronic cellular stress and defects in stress granule disassembly occurring with aging, prion-like conformational changes of TDP-43 and FUS/TLS facilitated by disease causing mutations in them and driven by stress granule formation transform into pathogenic self-perpetuating, irreversible aggregates. D) Possible cell to cell spread (not yet tested for TDP-43 or FUS/TLS) of prion-like aggregates may underlie (at contribute to) disease spread from a focal initiation. E) Self-perpetuating seeding of misfolded, mutant SOD1 has been reported in cell cultures (Grad et al., 2011; Münch et al., 2011). Acquired damage to wild type SOD1 may seed similar self-perpetuating aggregates. F) Mutant, misfolded SOD1 can induce misfolding of wild type SOD1, in a template-directed reaction (Chia et al., 2010; Deng et al., 2006), thereby forming a seed of aggregated protein. G) SOD1 aggregates transfer from cell-to-cell to initiate misfolding and aggregation of wild type or mutant SOD1 in neighboring cells (Münch et al., 2011).

Figure 7. Molecular interplay of TDP-43 with other ALS- and FTD-linked genes in protein and RNA homeostasis

Proposed pathogenic mechanisms in TDP-43-mediated neurodegneration converge onto disruption of protein and RNA homeostasis. Proteins involved in protein and RNA homeostasis are labeled as grey and green, respectively. (Upper panel) Normal functions of ALS/FTD-linked proteins. 1) Three ALS-linked genes (VCP, p62 and CHMP2B) are required for proper turnover of TDP-43, which is degraded both by the proteasome and by autophagy. 2) TDP-43 regulates the expression of the same ALS-linked genes that are required for its own degradation as well as 3) a key autophagy induction protein, ATG7. TDP-43 also regulates two other RNA-binding proteins linked to ALS (FUS/TLS and Ataxin-2). TDP-43, FUS/TLS and Ataxin-2 form RNA-protein granules that are degraded through 4) autophagy/granulophagy. Thus, TDP-43 governs both protein and RNA homeostasis and 5) its own level is tightly maintained. (Lower panel) Disrupted protein and RNA homeostasis that fuels a feed-forward loop driving disease progression. An initiating event that triggers disease initiation can occur at multiple points in either protein or RNA homeostasis pathways, including genetic mutations that predispose one pathway to be more error-prone or other non-genetic factors, such as aging. The well-documented 1) decline in proteostasis during aging may lead to elevated accumulation of TDP-43. Subsequently, 2) the genes that are controlled by TDP-43 become de-regulated, including 3) loss of expression of ATG7, which in turn reduces 4) autophagy (and granulophagy). The net result of this produces 5) disrupted autoregulation of TDP-43 with an increased cytoplasmic concentration of TDP-43, which provokes 6) prion-like templating of it followed by propagation and spread. These gain-of-toxic properties induce over-production of “nonfunctional prion-like” TDP-43 that leads to further loss of TDP-43 function. Similar scenarios could operate for prion-like domain-containing RNA binding proteins, such as FUS/TLS and hnRNP A2/B1.