TDP-43 dysfunction leads to the accumulation of cryptic transposable element-derived exons in iPSC derived neurons and ALS/FTD patient tissues [brain isoseq]

TDP-43 is an RNA and DNA binding protein that plays major roles in regulating RNA processing. In particular, TDP-43 dysfunction leads to the accumulation of cryptic splice isoforms that result from improperly spliced mRNAs. In addition to its role in regulating splicing, TDP-43 is also known to regulate the expression of transposable elements (TEs). TEs are mobile genetic elements which comprise a significant proportion of the human genome, but are normally silenced in healthy somatic cells. TEs are interspersed throughout the genome, both in gene-depleted regions and interspersed within gene introns and gene regulatory sequences. We used optimized long-read RNA sequencing assays to generate catalogs of mis-spliced and mis-expressed genes and TEs in human neurons depleted for TDP-43. In addition to known TDP-43 driven cryptic isoforms, we identified hundreds of TDP-43 dependent spliced RNAs formed as part of cryptic gene-TE fusion events that result from mis-splicing of TE sequences into gene transcripts. Among these TDP-43 dependent gene-TE cryptic transcripts (crypTEs), we found: TEs that provide alternate gene promoters/5’UTRs, TEs that act as cassette exons inside host gene mRNAs, as well as TEs that provide alternate transcript 3’ ends. These cryptic gene-TE fusions are predicted to induce: aberrant expression of ALS relevant genes, nonsense mediated decay (NMD) products, as well as novel peptides from gene-TE fusions within the gene coding sequence. We further verified that many of these crypTE transcripts are detected in ALS/FTD cortical tissues with TDP-43 pathology. In short, TDP-43 dependent CrypTE events represent a large reservoir of ALS/FTD relevant transcripts and peptides that are not captured by standard assays and analyses.