Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/TDP43_sample_list_HDX.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS36.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS14.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS08.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20210317_OT_HDXMS70.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20210317_OT_HDXMS72.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS50.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS22.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS39.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20210317_OT_HDXMS100.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS26.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS02.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS30.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS18.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20220207_OT_HDXMS43.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/TDP43_Mascot_Export.mzid.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD041160/20210317_OT_HDXMS70.mgfprimaryOK200oscar.vadas@unige.chOscar VadasMass SpectrometryTop-down proteomicsNot availableAggregationHdx-msOligonucleotidesTar dna binding protein (tdp-43)Neuronal toxicityhttps://www.ebi.ac.uk/pride/archive/projects/PXD041160HDX reactions were done in 50 L volumes with a final protein concentration of 1.6 μM. Briefly, 80 pM of TDP-43S333/342D in 8 μL, in absence or in presence of 50 μM TG12, were pre-incubated on ice for 5 min before the initiation of deuteration with D2O. Deuterium exchange reaction was initiated by adding 42 µL of D2O exchange buffer (10 mM Tris, 300 mM NaCl in D2O, pH 8.0) to the protein sample. For reactions with the TDP-43-TG12 complex, D2O buffer also contained 50 μM TG12. Reactions were carried-out on ice for 3 incubation times (3, 30, 300 s) and quenched by the sequential addition of 20 μL of ice-cold quench buffer 1 (4 M Gdn-HCl / 1 M NaCl / 100 mM NaH2PO4 pH 2.4 / 1% Formic Acid). Samples were immediately frozen in liquid nitrogen and stored at -80 ℃ for up to two weeks. All experiments were repeated in triplicate. To quantify deuterium uptake into the protein, samples were thawed and injected in a UPLC system immersed on ice with 0.1 % FA as liquid phase. The protein was digested via two immobilized pepsin columns (Thermo #23131), and peptides were collected onto a VanGuard precolumn trap (Waters). The trap was subsequently eluted, and peptides separated with a C18, 300Å, 1.7 μm particle size Fortis Bio 100 x 2.1 mm column over a gradient of 8 – 30 % buffer C over 20 min at 150 l/min (Buffer B: 0.1 % formic acid; buffer C: 100 % acetonitrile). Mass spectra were acquired on an Orbitrap Velos Pro (Thermo), for ions from 400 to 2200 m/z using an electrospray ionization source operated at 300 °C, 5 kV of ion spray voltage. Peptides were identified by data-dependent acquisition of a non-deuterated sample after MS/MS and data were analyzed by Mascot.PrideDeuterium incorporation levels were quantified using HD examiner software (Sierra Analytics), and quality of every peptide was checked manually. Results are presented as percentage of maximal deuteration compared to theoretical maximal deuteration. Changes in deuteration level between two states were considered significant if >10% and >1 Da and p< 0.05 (unpaired t-test).ProteomicsOscar VadasUniversity of Geneva, Faculty of Medicine, 1211 Geneva, SwitzerlandCOMPLETEHomo Sapiens (human)Bacteriaoscar.vadas@unige.ch37949836 Yang L, Jasiqi Y, Zettor A, Vadas O, Chiaravalli J, Agou F, Lashuel HA. Effective Inhibition of TDP-43 Aggregation by Native State Stabilization. Angew Chem Int Ed Engl. 2024 63(3):e202314587 10.1002/anie.202314587Hydrogen deuterium exchange (hdx-ms)University of Geneva, Faculty of MedicineSwitzerland10.6019/PXD041160Preventing the misfolding or aggregation of transactive response DNA binding protein with 43 kDa (TDP-43) is the most actively pursued disease-modifying strategy to treat amyotrophic lateral sclerosis and other neurodegenerative diseases. In this work, we provide proof of concept that native state stabilization of TDP-43 is a viable and effective strategy for treating TDP-43 proteinopathies. Firstly, we leveraged the Cryo-EM structures of TDP-43 fibrils to design C-terminal substitutions that disrupt TDP-43 aggregation. Secondly, we showed that these substitutions (S333D/S342D) stabilize monomeric TDP-43 without altering its physiological properties. Thirdly, we demonstrated that binding native oligonucleotide ligands stabilized monomeric TDP-43 and prevented its fibrillization and phase separation in the absence of direct binding to the aggregation-prone C-terminal domain. Fourthly, we showed that the monomeric TDP-43 variant could be induced to aggregate in a controlled manner, which enabled the design and implementation of a high-throughput screening assay to identify native state stabilizers of TDP-43. Altogether, our findings demonstrate that different structural domains in TDP-43 could be exploited and targeted to develop drugs that stabilize the native state of TDP-43 and provide a platform to discover novel drugs to treat TDP-43 proteinopathies.Effective Inhibition of TDP-43 Aggregation by Native State Stabilization.Yang Lixin L, Jasiqi Yllza Y, Zettor Agnès A, Vadas Oscar O, Chiaravalli Jeanne J, Agou Fabrice F, Lashuel Hilal A HAfalseNative State Stabilization is an Effective Strategy to Inhibit TDP-43 Oligomerization and FibrillogenesisTransactive response DNA-binding protein 43 kDa (TDP-43) is a partially disordered nuclear protein that plays essential roles in RNA metabolism to maintain cellular homeostasis. In individuals with neurodegenerative diseases (NDDs), including Amyotrophic lateral Sclerosis (ALS), Alzheimer’s disease, and Parkinson’s disease, TDP-43 misfolds, aggregates, and accumulates in the form of neuronal cytoplasmic inclusions which are one of the primary diagnostic pathological biomarkers of NDDs, and key determinants of disease symptomology and progression. Therefore, preventing TDP-43 misfolding and aggregation has emerged as the most actively pursued therapeutic strategy to treat ALS and other NDDs, with an emphasis on targeting TDP-43 aggregates, neutralizing their activity, or promoting their clearance. We propose that the heterogeneity of the aggregation pathway and structural diversity of TDP-43 aggregates renders targeting TDP-43 pathologies with a single drug or antibody challenging or ineffective. Therefore, the most effective approach remains to prevent TDP-43 misfolding in the first place. In this work, we provide strong proof of concept evidence for native state stabilization of monomeric TDP-43 as a viable therapeutic strategy for treating TDP-43 proteinopathies. Firstly, we used Cryo-EM structures of TDP-43 fibrils to design mutations that mimic native post-translational modifications (TDP-43S333D/S342D) and disrupt TDP-43 self-assembly and phase separation resulting in the stabilization of monomeric TDP-43 for days at 4 ℃ or room temperature. Secondly, we show that the binding of native TDP-43 ligands (UG/TG-rich oligo-nucleotide ligands) stabilizes monomeric TDP-43 and prevents its aggregation, independent of direct binding to the aggregation-forming C-terminal domain. Thirdly, we show that the monomeric TDP-43 mutant could be induced to misfold and aggregate in a controlled manner, thus enabling the design of a high-throughput screening assay to identify native state stabilizers and modulators of TDP-43 aggregation, a goal that remained out of reach because of the high aggregation propensity of TDP-43, which have precluded drug discovery efforts to develop native state stabilizers of TDP-43. Altogether, these advances demonstrate that different structural domains in TDP-43 could be targeted and exploited for developing drugs that stabilize the native state of the protein and provides novel tools and assays that make this goal achievable and pave the way for identifying small molecule drugs to treat ALS and other TDP-43 proteinopathies.2026-06-242023-03-28PXD041160NEWT:3555NEWT:71647NEWT:330879NEWT:35554NCBITaxon:12939NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NCBITaxon:2719036NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:10245NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:351581NEWT:43186NEWT:428146NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:661410NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:1401257NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7719NEWT:7959NEWT:2261NEWT:868565NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:1214915NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:5763NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NEWT:5757NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:347256NEWT:1736231NEWT:5518NEWT:398007NEWT:1527468NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:145458NEWT:633149NEWT:1149786NEWT:10239NEWT:68895NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5744NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1235816NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:270643NEWT:2065263NEWT:1772NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:11988NEWT:284812NEWT:8175NEWT:400667NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:459758NEWT:3702NEWT:1245466NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:586722NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NCBITaxon:287NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:1436733NEWT:460519NEWT:1247411NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:333760NEWT:56636NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:81077NEWT:84588NEWT:1679718NEWT:480NEWT:65349NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NEWT:34613NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:886559NEWT:55521NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:1130798NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:203696NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:5911NEWT:1313NEWT:1218097NCBITaxon:50557NEWT:39251NEWT:39491NEWT:212142NCBITaxon:5811NEWT:29491NEWT:101841NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:318586NCBITaxon:5820NEWT:1547NEWT:272634NEWT:198107NEWT:9031NEWT:1872122NEWT:1308NEWT:7091NEWT:1034015NEWT:760568NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:97477NEWT:7111NEWT:347515NEWT:172269NEWT:9534NEWT:6269NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:536088NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:142615NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:634955NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:13095NEWT:162425NEWT:216257NEWT:102169NEWT:208893NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:8655NEWT:5147NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:1257118NEWT:27448NEWT:40674NEWT:1194669NEWT:51329NEWT:243230NEWT:443906NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:104395NEWT:9557NEWT:9315NEWT:6289NEWT:377586NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:9554NEWT:118562NEWT:725NEWT:7137NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NCBITaxon:10298NEWT:80863NEWT:90675NEWT:105231NEWT:104385NEWT:74649NEWT:52638NEWT:57075NEWT:206672NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:71139NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:97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