PROJECT SUMMARY – TDP-43 Loss-of-Function: Biology to Biomarkers (Project 2) Biomarkers for frontotemporal dementia (FTD) may be used to confirm the presence of neurodegeneration, predict underlying pathology, demonstrate drug target engagement, or monitor disease progression. Biomarkers for pathology prediction represent a major challenge but also a pressing unmet need. For example, if a tau- or TDP-43-based clinical trial chose to recruit across the full FTD spectrum, ~40% of participants would receive treatment for a condition they do not have. Furthermore, candidate biomarkers for tracking disease progression, such as structural MRI or neurofilament light chain (NfL), do not capture molecule-specific pathobiological changes or quantify engagement of potential treatment targets. Recently, it has been shown that frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) is associated with, and possibly driven by, neuron type- specific loss of TDP-43 function. Additional work has shown that loss of nuclear TDP-43 results in incorporation of non-conserved cryptic exons, creating ripples of downstream dysregulation. Moreover, because TDP-43 normally binds to and represses transposable elements, loss of TDP-43 function leads to de-repression of these highly mobile genetic elements, inducing genomic instability and cellular toxicity. The overarching goal of this project is to pursue tissue-informed, biofluid-based molecular FTD biomarkers, using a systematic discovery and validation approach. Biofluid-based biomarkers represent an attractive development platform, and tissue-derived insights provide important constraint and guidance for such efforts. First, in a biomarker candidate discovery phase, we will conduct transcriptomic (blood) and proteomic (CSF) analysis of banked samples from 60 patients with pathologically diagnosed or genetically predicted FTLD-TDP, 60 with FTLD-tau, and 60 controls. Next, candidate biomarkers will undergo multi-method validation that includes correlations with clinical, neuroimaging, digital pathology, and plasma proteomic measures, followed by biochemical and histological confirmation, to prioritize candidates. Finally, top candidates will be developed into single analyte immunoassays and tested as diagnostic and disease monitoring biomarkers using longitudinal plasma samples from 80 patients with FTLD- TDP, 80 with FTLD-tau, and 30 controls. This project will leverage the extensive resources of this long-running PPG, interact with all seven cores, and utilize the complementary expertise of the participating laboratories. Successful completion of this project would have a major impact on the field by advancing our understanding of TDP-43 loss-of-function biology and by providing urgently needed tools for clinical trial-associated enrollment, stratification, and disease monitoring.