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. 2020 Jul 22;107(2):292-305.e6.
doi: 10.1016/j.neuron.2020.04.011. Epub 2020 May 5.

Chimeric Peptide Species Contribute to Divergent Dipeptide Repeat Pathology in c9ALS/FTD and SCA36

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Chimeric Peptide Species Contribute to Divergent Dipeptide Repeat Pathology in c9ALS/FTD and SCA36

Zachary T McEachin et al. Neuron. .

Abstract

GGGGCC hexanucleotide repeat expansions (HREs) in C9orf72 cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) and lead to the production of aggregating dipeptide repeat proteins (DPRs) via repeat associated non-AUG (RAN) translation. Here, we show the similar intronic GGCCTG HREs that causes spinocerebellar ataxia type 36 (SCA36) is also translated into DPRs, including poly(GP) and poly(PR). We demonstrate that poly(GP) is more abundant in SCA36 compared to c9ALS/FTD patient tissue due to canonical AUG-mediated translation from intron-retained GGCCTG repeat RNAs. However, the frequency of the antisense RAN translation product poly(PR) is comparable between c9ALS/FTD and SCA36 patient samples. Interestingly, in SCA36 patient tissue, poly(GP) exists as a soluble species, and no TDP-43 pathology is present. We show that aggregate-prone chimeric DPR (cDPR) species underlie the divergent DPR pathology between c9ALS/FTD and SCA36. These findings reveal key differences in translation, solubility, and protein aggregation of DPRs between c9ALS/FTD and SCA36.

Keywords: ALS; C9orf72 expansion; FTD; RAN translation; SCA36; antisense oligonucleotide therapy; chimeric DPRs; dipeptide repeats; neurodegeneration.

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Conflict of interest statement

Declaration of Interests The authors declare no competing interests.

Figures

Figure 1:
Figure 1:. Poly(GP) is more abundant in patient-derived cellular models of SCA36 compared to c9ALS/FTD.
(A) Schematic of putative dipeptide repeats in SCA36 and c9ALS/FTD. Red asterisk indicates putative DPRs common to both c9ALS/FTD and SCA36. (B-F) Immunoassay for poly(GP) in SCA36 fibroblast, lymphoblastoid cell lines (LCL), induced pluripotent stem cell (iPS), 3D forebrain organoid (Day 105), and iPS-derived motor neurons (iPS-MNs). (B-F) Adjusted P-values displayed if not significant; *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001; Kruskal-Wallis one way analysis of variance followed by Dunn’s multiple comparison test.
Figure 2:
Figure 2:. Poly(GP) is abundant but does not form insoluble inclusions in SCA36 postmortem tissue.
(A) poly(GP) is detectable throughout the CNS of SCA36 patients. (B-E) poly(GP) is expressed at similar or increased abundance in SCA36 samples compared to c9ALS/FTD samples in disease relevant CNS regions (Cb Ctx: n=7 control, n=11 c9ALS/FTD, n=6 SCA36 cases; Cb DN: n=3 control, n=5 c9ALS/FTD, n=3 SCA36 cases; Ft. Ctx: n=7 control, n=11 c9ALS/FTD, n=6 SCA36 cases; Sp Cd: n=3 control, n=3 c9ALS/FTD, n=4 SCA36 cases). (F) poly(GP) aggregates in c9ALS/FTD but not SCA36 patient postmortem tissue (n=5 SCA36). Scale Bar: 100 μm. (G) poly(GP) is detectable in the urea-soluble fraction of c9ALS/FTD but not SCA36 samples as assessed by dotblot (n=2 control, n=2 c9ALS/FTD, n=4 SCA36 cases). (H) Quantitative immunoassay of sequentially fractionated tissue samples reveals poly(GP) predominately exist as a soluble protein species in SCA36 whereas in c9ALS/FTD a large fraction of poly(GP) exists in the insoluble fraction (Cb Ctx: n=4 c9ALS/FTD, n=4 SCA36 cases; Ft. Ctx: n=5 c9ALS/FTD, n=5 SCA36 cases). (I) Representative images of granule, Purkinje, and molecular cell layer ROI selection (white ouline) for digital spatial profiling of cerebellar samples. Calbindin and DAPI were used to delineate cerebellar architecture. (J) Volcano plots illustrating differentially abundant proteins as determined by digital spatial profiling in the cerebellar granule layer of c9ALS/FTD and SCA36 compared to controls (n=7 c9ALS/FTD, n=5 SCA36, n=7 control cases). Significant proteins (FDR<0.05) are colored. (B to E) *P<0.05, **P<0.005, ***P<0.0005, Kruskal-Wallis one way analysis of variance followed by Dunn’s multiple comparison test.
Figure 3:
Figure 3:. SCA36 produces antisense DPRs but lacks TDP-43 pathology.
(A) The antisense DPR, poly(PR) aggregates in both c9ALS/FTD and SCA36 cerebellar tissue. (B) SCA36 frontal cortex tissue lacks TDP43 pathology characteristic of c9ALS/FTD. Scale bars: 50μm, inset 10μm. (C) pTDP43 is not found in the detergent insoluble, urea soluble fraction of SCA36 patient frontal cortex. #cleavage products, *full-length TDP43, †oligomeric species, ‡high molecular weight species.
Figure 4:
Figure 4:. Expanded TG3C2 repeats impair splicing of NOP56 intron 1 and result in AUG-mediated translation of poly(GP) DPRs in SCA36.
(A) Relative expression of NOP56 using TaqMan probes spanning exon-exon junctions in control and SCA36 patient cerebellar cortex samples (n=20 control, n=5 SCA36). NOP56 expression as detected by exon 3-exon 4 or exon 6-exon 7 junction probes is increased in SCA36 compared to controls. In contrast, NOP56 expression as detected by exon 1-exon 2 junction probes is decreased in SCA36 compared to controls. (B) NOP56 protein is increased in SCA36 patient cerebellar cortex compared to controls (n=4 control, n=3 SCA36). Top: Western blot analysis of NOP56 and ß-actin. Bottom: Quantification of NOP56 protein in control and SCA36 samples relative to ß-actin. (C) Relative expression of NOP56 using a TaqMan probe spanning the intron 1 - exon 2 junction in control and SCA36 patient cerebellar cortex samples (n=9 control, n=6 SCA36). (D) NOP56 transcripts containing a retained intron 1 but not intron 4 or intron 10 is increased in SCA36 compared to control (n=9 control, n=6 SCA36) as detected by Nanostring. (E) Alignment of the 5’ flanking sequence of intron 1 from the expanded allele of SCA36 cases. (F) Schematic figure of (GGCCTG)82 NanoLuc (NLuc) reporter constructs. (G) Expression of ATG (GGCCTG)82 NanoLuc reporter constructs (n=3 biological replicates). Values normalized to co-transected firefly luciferase (FLuc). (H) Expression of 6x Stop and ATG - (GGCCTG)82 NanoLuc reporter constructs for the +1 (GL) and +2 (WA) frame (n=3 biological replicates). Data are presented as mean ± SEM. (A-D) *P<0.05, **P<0.005, ***P<0.0005, ****P<0.0001, Mann-Whitney test. (G) ***P<0.0005, ordinary one-way ANOVA. (H) *P<0.05, unpaired Student’s t-test.
Figure 5:
Figure 5:. Chimeric peptides underlie divergent DPR pathology in c9ALS/FTD and SCA36.
(A) poly(GP) immunohistochemistry in AAV-GFP and AAV-GP80x-GFP; poly(GP) is diffuse throughout the CNS after 2 months in vivo. Scale bars: 100μm, inset 50μm. (B) poly(GA) and poly(GP) colocalize in perinuclear aggregates in the frontal cortex of a c9ALS/FTD patients and c9BAC mice. (C) Schematic illustrating putative mechanisms of poly(GA)-mediated poly(GP) aggregation. (D) Immunofluorescence for GFP 48 hours after transfection in HEK293T cells expressing GP80x-GFP or chimeric GA50xGP50x-GFP to assess the aggregation propensity of a chimeric GAGP peptide. Scale bar: 10μm. (E) Immunoblot for the indicated proteins to determine whether GP80x-GFP, GA80x-GFP, chimeric GA50xGP50-GFP, or 1:1 co-transfection of GP80x-GFP and GA80x-HA is present in the soluble (S) or insoluble (In) fraction. (F) Schematic illustrating the meso-scale discovery (MSD) immunoassay developed to detect chimeric DPRs. (G) A traditional GA/GA MSD assay or a chimeric peptide detecting GA/GP immunoassay was used to detect poly(GA) or chimeric poly(GA:GP) DPRs in the detergent insoluble, urea soluble fraction from control (n=3 cases), c9ALS/FTD (n=4 cases), or SCA36 (n=5 cases) patient frontal cortex and (H) detergent-insoluble, urea-soluble fraction from control (n=3 cases) and c9ALS/FTD (n=6 cases) patient cerebellar cortex. (G, H) *p<0.05, **p<0.005, Kruskal-Wallis one way analysis of variance followed by pairwise one-tailed Mann-Whitney Test.
Figure 6:
Figure 6:. Antisense oligonucleotides reduce poly(GP) in patient derived cellular models of SCA36.
(A-D) Dose-response curves were generated by treating SCA36 fibroblast (n=3 patient cell lines) with described concentrations. UTC=untransfected control. (A) Dose-response curves show robust reduction of poly(GP) by NOP56 intron 1 (ASO-#1) or TG3C2 (ASO-#2) targeting ASOs (see Figure S10A and Table S2). (B) NOP56 mRNA levels as measured by exon 1 – exon 2 junction probes are not reduced at 1nM or 10nM ASO concentrations. (C) NOP56 protein is not significantly reduced at 0.1nM, 1nM, or 10nM ASO concentrations. (D) poly(GP) is reduced at 10nM ASO concentrations relative to a scrambled control. (A) to (D) n=3 SCA36 patient fibroblast cell lines, treated for 48 hours at respective concentrations. (E, F) SCA36 fibroblast (n=2 patient cell lines) and LCLs (n=2 patient cell lines) were treated with 5μM non-targeting control ASO or an ASO targeting intron 1 of NOP56 delivered via gymnosis. Protein lysates were collected 10 days after treatment and poly(GP) levels measured. Data are presented as mean ± SEM; (B) to (E), *P<0.05, **P<0.01, ***P<0.001 one-way analysis of variance (ANOVA) followed by Dunnett’s multiple comparisons test. (G) poly(GP) is detectable in cerebrospinal fluid (CSF) from c9ALS/FTD (n=5), and SCA36 patients (n=5) but not healthy controls (n=5).
Figure 7:
Figure 7:. Model of divergent translation and pathology of dipeptide repeats in c9ALS/FTD and SCA36.
The c9ALS/FTD-associated G4C2 and SCA36-associated TG3C2 repeat expansions are similarly positioned in the first intron of the genes C9orf72 and NOP56, respectively; however, the flanking genetic context of these repeat expansions differ. With respect to C9orf72, the 5’ intron sequence flanking the G4C2 repeat contains a near-cognate CUG start codon. In c9ALS/FTD, translational initiation at this near-cognate start codon, either from a retained mRNA transcript variant or a spliced and exported intron 1 RNA species, would preferentially produce a poly(GA) dipeptide repeat (DPR) protein. In contrast, NOP56 intron 1 is located between two coding exons, thus retention of intron 1 harboring a TG3C2 expansion would produce a novel NOP56 transcript variant that would preferentially produce a poly(GP) DPR protein via canonical AUG-mediated translation. Translational frameshifting and/or genetic aberrations in the respective repeat expansions result in chimeric DPR (cDPR) species. In c9ALS/FTD, these chimeric species would results in homogenous poly(GA) DPRs and/or GA-rich poly(GA:GP) cDPRs that result in poly(GA) and poly(GP) inclusions as seen in c9ALS/FTD patient samples. In SCA36, homogenous poly(GP) DPRs and/or GP-rich cDPRs would result in soluble poly(GP) as seen in SCA36 patient samples.

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