Fig. 4: UNC13A risk haplotype associated with ALS or FTD susceptibility potentiates CE inclusion when TDP-43 is dysfunctional.
From: TDP-43 represses cryptic exon inclusion in the FTD–ALS gene UNC13A
a, LocusZoom plot showing SNPs associated with ALS or FTD in UNC13A. SNPs are coloured on the basis of levels of linkage equilibrium; SNPs rs12608932 and rs12973192 are in strong linkage disequilibrium (LD). b, There is a higher percentage inclusion of the risk allele (G) at rs12973192 in the UNC13A splice variant (n = 3 biologically independent samples; two-sided paired t-test; mean ± s.e.m.). Quantification in Extended Data Fig. 7c. c, Location of rs56041637 relative to the two known FTD–ALS GWAS hits and UNC13A CE. d, Design of UNC13A CE minigene reporter constructs and location of the primer pair used for RT–PCR. Black (reference alleles) and blue (risk alleles) triangles represent the genetic variants as shown in c. e, Splicing of minigene reporters was assessed in wild-type (WT) and TDP-43−/− HEK 293T cells. In addition to the inclusion of CE (2), some splice variants showed inclusion of one of the other two cryptic splicing products (3 and 4) (Extended Data Figs. 1a–e, 3a, Supplementary Note 2). The risk haplotype-carrying minigene showed an almost complete loss of canonical splicing product (1) and an increase in alternatively spliced products (2, 3 and 4). n = 2 independent cell culture experiments for each condition. f, Top, survival curves of FTLD-TDP patients stratified on the basis of the number of risk haplotypes. Heterozygous (1) and homozygous (2) patients had shorter survival time after disease onset (n = 205, Mayo Clinic Brain Bank; score (log-rank) test, P = 0.004). Dashed lines mark median survival for each genotype. Risk haplotype effect is modelled additively using Cox multivariable analysis adjusted for genetic mutations, sex and age at onset. Bottom, risk table. Summary results of the analysis are shown in Extended Data Fig. 10b.
