Table 3.
Cell and in vitro model proteomics studies using label-free techniques for mechanistic insight into ALS and FTD.
| Sample | Summary | Remarks | References |
|---|---|---|---|
| Differentiated C2C12 mouse myoblasts | Detected muscle specific kinase activation via phosphorylation, which preserves innervation of neuromuscular junctions | Innervation of neuromuscular junctions insufficient, however, could potentially be used as an adjuvant therapy | Sengupta-Ghosh et al., 2019 |
| HEK239T cells and rat primary cortical neurons infected with GR149 or PR175 | Poly-GR/PR interactome identified RNA-binding proteins (many low-complexity domains), cytoplasmic/mitochondrial ribosomes components, stress granules and splicing factors | Sequestration of ribosomes via interactions with poly-GR/PRs would potentially impair protein translation in FTD pathology | Hartmann et al., 2018 |
| HEK293 and N2A cells transfected with cyclin FWT or S621G | Identified 7 phosphorylation sites on cyclin F | Cyclin F S621 phosphorylation by CK2 regulates Lys48-specific E3 ligase activity | Lee A. et al., 2017 |
| HEK293 cells expressing RBM45 | Identified 132 protein-protein interactors of RBM45 | RBM45 associates with enriched proteins involved in nuclear RNA processing: TDP-43, Matrin-3, hnRNP-A1 and FUS | Li et al., 2016 |
| HEK293A cells expressing TDP-43ΔNLS and 2KQ and CBP | Identified TDP-43 acetylation sites K145/192 | TDP-43 modulation via acetylation could potentially be used therapeutically | Cohen et al., 2015 |
| HEK293E cells expressing TDP-43192-414 or ΔNLS or WT | Removal of 4 lysine ubiquitination sites in CTF TDP-43 = ubiquitination suppression | Indicates interplay between ubiquitination and phosphorylation of TDP-43 in ALS and FTD pathology | Hans et al., 2018 |
| HEK293T and H4 cells treated with various drugs | Identified 28 phosphorylation sites within FUS’s prion-like domain, following DNA-damaging stress | Multiphosphorylation of these sites does not cause cytoplasmic localization | Rhoads et al., 2018 |
| HEK293T cells expressing C9ORF72 DPRs | Interactome of DPRs: RNA-binding proteins and proteins with low complexity sequence domains | DPRs altered phase separation of low complexity domain proteins, suggesting possible mechanism involved in pathogenesis | Lee et al., 2016 |
| HEK293T cells expressing FUSP525L | Mutant FUS ↓ interactions with many metabolic enzymes. Novel interactions between FUS and VCP, PSF, UBA1 and PSMD12. FUS accumulation = ↓ ATP levels and ↑ poly-ubiquitinated proteins | Defective energy metabolism and protein degradation arise as a result of FUS accumulating and interacting with key regulators | Wang et al., 2015 |
| HEK293T cells expressing FUSR521G or P525L | FUS interacting proteins = fALS implicated proteins hnRNPA1 and Matrin-3 | Potential common pathogenic roles between FUS-ALS and fALS. FUS present in exosomes suggesting contribution to cell-to-cell transmission/spread. Interactors also sequestered into inclusions | Kamelgarn et al., 2016 |
| HEK293T cells expressing mPGRN-HA | PGRN interacts with a network of ER chaperones such as BiP, calreticulin, GRP94 and PDI family proteins | PGRN is a substrate of several PDI proteins and ER chaperone network control could be a therapeutic target | Almeida et al., 2011 |
| HEK293T cells transfected with Zfp106 | Zfp106 interacts with hexanucleotide repeat (GGGGCC) RNA-binding protein, other RNA-binding proteins: TDP-43 and FUS. Zfp106 KO mice develop motor neuron degeneration. Zfp106 suppresses neurotoxicity in Drosophila C9orf72 ALS model | Importance and role of Zfp106 in ALS pathology | Celona et al., 2017 |
| HEK293T cells treated with various drugs | Identified 17 phosphorylation sites within FUS low-complexity domain | Phosphorylated/phosphomimetic FUS reduces aggregation, propensity to aggregate, ameliorates cytotoxicity and disrupt phase separation | Monahan et al., 2017 |
| HEL293FT cells expressing C9ORF72 DPRs | Co-aggregators of poly-GA = Unc119, soluble Unc119 ↓ in poly-GA expressing neurons | Loss of function of Unc119 in neurons with DPR-type pathology as seen in C9orf72 ALS/FTD | May et al., 2014 |
| HeLa cells expressing C9ORF72 DPRs | Arginine-rich DPRs undergo liquid-liquid phase separation and induce this effect on proteins involved in RNA and stress granule metabolism | Arginine-rich DPRs derived from C9ORF72 repeat expansions play an important role in the pathogenesis of ALS/FTD | Boeynaems et al., 2017 |
| HeLa cells expressing FUS | FUS forms liquid-like compartments under stress that are crucial for its role in ALS | Propensity for aggregation vs functionality of FUS action in liquid-compartments found in disease | Patel et al., 2015 |
| In vitro (PGRN) | Cathepsin L cleaves intracellular PGRN | Cathepsin L identified as a key intracellular lysosomal protease, therefore demonstrating link between lysosomal dysfunction and FTLD | Lee C.W. et al., 2017 |
| In vitro (SOD1) | SOD1G37R did not have the same propensity to aggregate as SOD1G93A and SOD1V 148G, however, still formed oligomeric aggregates | Slow disease progression in SOD1G37R patients is due to structural limitations associated with the arginine substitution at residue 37 | McAlary et al., 2016 |
| In vitro (SOD1) | Naringin is a strong native interactor of SOD1, demonstrated to stabilize SOD1 dimers and inhibit aggregation | Analytical method for studying interactions between proteins and drug-like molecules, identifying role of naringin | Zhuang et al., 2016 |
| In vitro (tau) | K225,240,257,311,383 residues in tau involved in crosslinking to K336,338 in α-tubulin | Identified how tau stabilizes microtubules through identifying sites of interface | Kadavath et al., 2015 |
| iPSC-derived motor neurons expressing C9ORF72 DPRs and Drosophila brain | Arginine DPRs interact with ribosomal proteins, expression of eIF1A rescued DPR-induced toxicity | Repression of protein translation is involved in C9orf72 hexanucleotide-repeat induced neurodegeneration | Moens et al., 2019 |
| Mouse primary hippocampal neurons expressing scrambled shRNA FUS | Identified PSD-95 interacting proteins: ↓ SynGAP with FUS depletion. FUS, ELAV1 and ELAV4 exert a level of control on SynGAP mRNA stability | FUS depleted dendritic spines associated with internalization of PSD-95 | Yokoi et al., 2017 |
| N2a cells expressing C9ORF72 | Interactors of C9ORF72 = UBQLN2, hnRNPA2/B1, hnRNPA1 and actin. Colocalization with RAB7 and RAB11 suggests dysregulation of trafficking | Demonstrates the role of C9ORF72 in RAB-mediated trafficking | Farg et al., 2014 |
| N2a cells expressing TDP-43 and CTF | Interactome of TDP-43 using BioID identified 254 proteins vs 389 in CTF, many involved in mRNA processing | TDP-43 aggregate associates were involved in nuclear pore complex and transport machinery | Chou et al., 2018 |
| NSC-34 cells expressing C9ORF72 DPRs | Poly-PR peptides interact with mRNA-binding proteins, ribosomal proteins, translation initiation and elongation factors | Alterations via DPRs are potential therapeutic targets and are involved in neurotoxicity | Kanekura et al., 2016 |
| PC12 cells expressing SOD1G93A | PSMC1, PSMC4 and TCP-1 activated by pyrazolones in the absence of exogenous proteasome inhibitor | In the absence of the heat shock response, pyrazolones enhance proteasomal activation and could be a potential therapeutic target | Trippier et al., 2014 |
| S2 cells expressing Xrp1Short or Long and actin5C-GAL4 | ↑ Xrp1 expression in caz mutants, interactors are involved in gene expression regulation | Caz is the ortholog of human FET proteins FUS, EWSR1, and TAF15, all of which implicated in ALS and FTD, dysregulation of gene repair implicated | Mallik et al., 2018 |
| SH-SY5Y cells knockdown TDP-43 | ↓ RanBP1, Dnmt3a and CgB in TDP-43 knockdown. ↓ RanBP1 = ↑ transportin 1 | TDP-43 mediates RNA metabolism and intracellular transport | Stalekar et al., 2015 |
| SKNBE2 cells expressing tau | AnxA2 interacts with tauWT but not mutant tauR406W | TauR406W mechanism involves impaired membrane binding due to functional interaction with AnxA2 | Gauthier-Kemper et al., 2011 |
| SOD1 isolated from yeast | Low molecular weight fractionated SOD1 does not appear to be post-translational modified compared to high molecular weight SOD1, which is oxidized at residues C146 and H71 | Crucial for SOD1 structure, suggesting a role of oxidative damage for protein misfolding | Martins and English, 2014 |
| SOD1WT or G37R or L38V or G41D or G93A or G93S or D101N isolated from yeast | Structure of SOD1 amyloid fibrils and mutants demonstrated that fibrils protected the N-terminus from digestion via proteases | SOD1 and mutants fibrillate through the N-terminal fragment, highlighting potential ALS implications | Chan et al., 2013 |
↑, denotes increase; ↓, denotes decrease; AnxA2, Annexin A2; caz, RNA-binding protein cabeza; CgB, chorionic gonadotropin beta; CK2, casein kinase II subunit alpha; CTF, C-terminal fragment; Dnmt3a, DNA (cytosine-5)-methyltransferase 3A; DPR, dipeptide repeat; EIF1A, eukaryotic translation initiation factor 1A; ELAV1/4, embryonic lethal abnormal vision protein 1/4; EWSR1, RNA-binding protein EWS; FUS, fused-in-sarcoma; GFAP, glial fibrillary acidic protein; GR, glycine arginine; GRP94, 94 kDa glucose regulated protein; hnRNPA1, heterogeneous nuclear ribonucleoprotein A1; iPSC, induced pluripotent stem cell; MTO, methanethiol oxidase; PDI, protein disulphide isomerase; PIN1, peptidyl-prolyl cis-trans isomerase NIMA-interacting 1; PR, proline arginine; PSD-95, post-synaptic density protein 95; PSF, polypyrimidine tract-binding protein-associated-splicing factor; PSMC1/4, 26S proteasome regulatory subunit 1/4; PSMD12, 26S proteasome non-ATPase regulatory subunit 12; RAB7/11, Ras-related protein Rab-7/11; RanBP1, Ran-binding protein 1; RBM45, RNA binding motif protein 45; ROCK2, rho-associated protein kinase 2; SOD1, superoxide dismutase 1; SynGAP, Ras/Rap GTPase-activating protein SynGAP; TAG15, TATA binding associated factor 15; TCP-1, T-complex protein 1; TDP-43, TAR DNA-binding protein of 43 kDa; UBA1, ubiquitin-like modifier-activating enzyme 1; UBQLN2, ubiquilin-2; Unc119, protein unc-119 homolog A; VCP, vasolin-containing protein; and Zfp106, zinc finger protein 106.