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Phospho-proteome profiling in human neurons reveals targets of TBK1 in ALS/FTD-associated autophagy networks.

Julie Smeyers·Juan A Oses-Prieto·Lin Yadanar·Man Wang·Marci Iadarola·Serena Lu·Karen S Wang·Taylor H Watanabe·Jayanta Debnath·Alma L Burlingame·Daniel A Mordes
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Abstract

Loss-of-function variants in TBK1, encoding a protein kinase, are strongly associated with familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). However, how haploinsufficiency for TBK1 leads to age-related neurodegeneration remains unresolved. Here, we utilize sets of isogenic induced pluripotent stem cells (iPSCs) with loss of TBK1 or loss of optineurin (OPTN) for quantitative global proteomics and phospho-proteomics in both stem cells and excitatory neurons. We found that TBK1 sustains the abundance and phosphorylation of its interacting adapter proteins, AZI2/NAP1, TANK, and TBKBP1/SINTBAD. Moreover, TBK1 regulates the phosphorylation of endo-lysosomal proteins, such as GABARAPL2, the late-endosome GTPase RAB7A, and selective autophagy cargo receptor proteins-including novel phospho-sites in p62/SQSTM1-in neurons. Finally, we provide a census of the phospho-proteome in nascent human neurons for further studies. Overall, TBK1 serves as a point of convergence in ALS/FTD-linked endo-lysosomal networks that act in a cell-autonomous manner to maintain protein homeostasis in neurons.

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HumansProtein Serine-Threonine KinasesAmyotrophic Lateral SclerosisNeuronsAutophagyInduced Pluripotent Stem CellsPhosphorylationFrontotemporal DementiaProteomeCell Cycle ProteinsProteomicsTranscription Factor TFIIIAMembrane Transport ProteinsPhosphoproteinsALSCP: Molecular biologyCP: NeuroscienceOPTNTBK1autophagydementiaiPSC disease modelingneurodegenerationphospho-proteomicsproteomicsJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov't

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Julie Smeyers, Juan A Oses-Prieto, Lin Yadanar, Man Wang, Marci Iadarola, Serena Lu, Karen S Wang, Taylor H Watanabe, Jayanta Debnath, Alma L Burlingame, Daniel A Mordes. 2025-10-29. Phospho-proteome profiling in human neurons reveals targets of TBK1 in ALS/FTD-associated autophagy networks.. https://doi.org/10.1016/j.celrep.2025.116494

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