TDP-43 repression of nonconserved cryptic exons is compromised in ALS-FTD

Abstract

Cytoplasmic aggregation of TDP-43, accompanied by its nuclear clearance, is a key common pathological hallmark of amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). However, a limited understanding of this RNA-binding protein (RBP) impedes the clarification of pathogenic mechanisms underlying TDP-43 proteinopathy. In contrast to RBPs that regulate splicing of conserved exons, we found that TDP-43 repressed the splicing of nonconserved cryptic exons, maintaining intron integrity. When TDP-43 was depleted from mouse embryonic stem cells, these cryptic exons were spliced into messenger RNAs, often disrupting their translation and promoting nonsense-mediated decay. Moreover, enforced repression of cryptic exons prevented cell death in TDP-43-deficient cells. Furthermore, repression of cryptic exons was impaired in ALS-FTD cases, suggesting that this splicing defect could potentially underlie TDP-43 proteinopathy.

Fig. 1. Identification of Tdp-43–associated cryptic exons (Mus musculus)

(A) iTDPKO cells are depleted of Tdp-43 upon treatment with 4HT. (B) Visualization of the cryptic exon located in Adnp2 (red bar) of chromosome 18 (chr18) (top). Gene annotation is shown below, labeling exons (thick) and introns (thin). RNA-seq reads from iTDPKO untreated (“Control”) and 4HT treated (“Tdp-43 Knockout”) are aligned to the mm9 genome. The cryptic exon (green arrow) is not conserved (vertebrate conservation, bottom). Strand-specific analysis also confirms the incorporation of cryptic exons on the transcribing strand (fig. S11). (C to E) Most cryptic exons have standard 5′ and 3′ splice sites [Adipor2, (C)]. Occasionally, cryptic exons can present as transcriptional start sites [Sptbn4, (C)], polyadenylation sites [Synj2bp, (D)], or exon extensions [Wbscr22, (E)]. (F) Cryptic exons are flanked by UG tandem repeats that exist upstream, downstream, or internally.

Fig. 2. Repression of cryptic exons is associated with the prevention of cell death induced by loss of Tdp-43

(A) Diagram of the green fluorescent protein, N terminus TDP-43, RAVER1 splicing repressor domain chimeric construct (GTR). (B) Immunoblot using an antibody that recognizes mouse/human N terminus of Tdp-43. (C to F) Whereas iTDPKO cells are not viable when depleted of Tdp-43, GTR1 cells are fully viable. GTR represses a variety of cryptic exons; standard cassette [Adipor2, (C)], polyadenylation [Zfp809, (D)], and exon extensions [Wbscr22, (E)]. However, some cryptic exons are only partially rescued [Synj2bp, (F)]. (G) RNA-seq transcript expression levels for Tdp-43 knockout cells and GTR1 rescue cells were compared with untreated iTDPKO cells. The top 124 down-regulated/up-regulated genes in the Tdp-43 knockout cells were mostly restored to normal levels in the GTR1 rescued cells. Full transcript expression data are provided in the supplementary materials (data table S1).

Fig. 3. Identification of TDP-43–associated cryptic exons (Homo sapiens)

(A) TDP-43 protein levels are greatly reduced when HeLa cells are treated with TDP-43 siRNA (asterisk indicates nonspecific band). (B) Visualization of the cryptic exon located in EPB41L4A. Zoom-in of gene annotation demonstrates that the cryptic exon (green arrow) resides in a nonconserved region. Strand-specific analysis also verifies the incorporation of cryptic exons on the transcribing strand (fig. S12). (C to F) IRF9 contains a transcriptional start site (C), KRT7 contains an exon extension (D), GPSM2 contains a standard cryptic exon (E), and INSR contains a polyadenylation site (F). (G) UG repeats are also found adjacent to human cryptic exons.

Fig. 4. Validation of human cryptic exons and their detection in ALS-FTD brain tissue

(A) Diagram of ATG4B reporter construct and potential splicing isoforms. (B) Immunoblots of HeLa transfections under normal or TDP-43–depleted conditions and (C) the associated electrophoretic gel analysis of splicing isoforms were performed in triplicate. Cryptic isoforms B and C only appeared under conditions of TDP-43 depletion and were rescued by the GTR protein. (D) Diagram of RT-PCR detection strategy. Primers were designed to amplify only the cryptic exon splice junction. (E) DNA fragments are detected at 199 base pairs (bp) (GPSM2) and at 215 bp (ATG4B) for all cases that display TDP-43 proteinopathy; control cases do not display these fragments. Full gel images and case demographics are provided in the supplementary materials (fig. S7 and table S5). Cases 1, 7, and 13 are positive for C9ORF72 expansions; the remaining cases are sporadic. MTG, middle temporal gyrus; MC, motor cortex.