Carboxyl-terminal fragments (CTFs) of TDP-43 aggregate to form the diagnostic signature inclusions of frontotemporal lobar degeneration and amyotrophic lateral sclerosis, but the biological significance of these CTFs and how they are generated remain enigmatic. To address these issues, we engineered mammalian cells with an inducible tobacco etch virus (TEV) protease that cleaves TDP-43 containing a TEV cleavage site. Regions of TDP-43 flanking the second RNA recognition motif (RRM2) are efficiently cleaved by TEV, whereas sites within this domain are more resistant to cleavage. CTFs containing RRM2 generated from de novo cleavage of nuclear TDP-43 are transported to the cytoplasm and efficiently cleared, indicating that cleavage alone is not sufficient to initiate CTF aggregation. However, CTFs rapidly aggregated into stable cytoplasmic inclusions following de novo cleavage when dynein-mediated microtubule transport was disrupted, RNA was depleted, or natively misfolded CTFs were introduced into these cells. Our data support a "two-hit" mechanism of CTF aggregation dependent on TDP-43 cleavage.The heterogeneous nuclear ribonucleoprotein (hnRNP) 2 TDP-43 (TAR DNA-binding protein of 43 kDa) forms pathological inclusions that are diagnostic hallmarks of amyotrophic lateral sclerosis (ALS) and the major form of frontotemporal lobar degeneration (FTLD-TDP) (1). Missense mutations in TDP-43 provide a genetic link between hnRNP functions and motor neuron disease (2, 3). TDP-43 is predominantly localized to the nucleus, where it regulates RNA splicing, mRNA stability, microRNA processing, and transcription (4 -6). However, in neurodegenerative TDP-43 proteinopathies like ALS and FTLD-TDP, a loss of nuclear TDP-43 coincides with cytoplasmic TDP-43 inclusions (1). These inclusions contain full-length TDP-43 and TDP-43 C-terminal fragments (CTFs) that are hyperphosphorylated and ubiquitinated. However, it is unclear how each of these species of TDP-43 contributes to inclusion formation or disease pathogenesis.TDP-43 is a typical 2XRRM-gly hnRNP composed of two tandem RNA recognition motifs (RRM1 and RRM2) followed by a glycine-rich carboxyl terminus ( Fig. 1) (7). Both RRMs retain nucleic acid binding properties, yet only RRM1 appears essential for RNA splicing (8). The glycine-rich domain is proposed to interact with other hnRNPs to synergistically affect alternative splicing of specific RNA transcripts (9, 10). A common feature of shuttling hnRNPs involved in RNA splicing is that their nuclear export is coupled to the export and maturation of mRNA in distinct ribonucleoprotein (RNP) complexes (11,12). In this respect, the nucleocytoplasmic shuttling of TDP-43 is dependent on its bipartite importin-␣ nuclear localization signal, a chromosome maintenance region 1 (CRM-1) nuclear export signal in RRM2, and undefined aspects of the carboxyl-terminal glycine-rich domain (13,14).CTFs are signatures of disease exclusively associated with TDP-43 pathology, and CTFs cleaved in the middle of RRM2 extending from amino acid 208 to t...