Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/241206report.pg_matrix.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_13.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_17.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_09.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_07.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_04.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_02.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_15.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_14.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_16.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_18.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_05.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_08.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053993/20241118_DrOtsuka_Sup_03.rawprimaryOK200hide0729.bri@niigata-u.ac.jpGodfried DougnonMass SpectrometryBottom-up proteomicsData-independent acquisitionNucleusExtracellular wasteNeurodegenerationAlzheimer's diseaseAmyloid precursor proteinhttps://www.ebi.ac.uk/pride/archive/projects/PXD053993Hela CellTo collect proteins secreted into serum-free medium, cells were seeded on 6-well plates and then treated with or without 5 µM etoposide for 24 hr. Subsequently, the cells were washed with PBS three times and placed in serum-free and phenol red–free DMEM, and the conditioned media was collected after 3 hrs. The conditioned medium was centrifuged at 1,000 g at 4°C for 5 min to remove cell debris and filtered through a 0.22 µm filter. Samples were concentrated using a Vivaspan 20 with a 3000 MWCO (Sartorius Stedim Biotech GmbH, Goettingen, Germany) according to the manufacturer’s instructions. Protein samples were subjected to reduction and alkylation with 2.5 mM TCEP (Thermo Fisher Scientific) and 12.5 mM iodoacetamide (IAA) (Merck), respectively. After acetone precipitation, the pellets were sonicated in 100 mM HEPES (pH 8.0), followed by digestion with trypsin at a protein ratio of 1:50 at 37°C for 16 hrs. The resulting protein digests (equivalent to 5 µg) were desalted using StageTip (SDB-XC, 3M, St. Paul, MN, USA). The desalted peptides were injected (200 ng/sample) into a precolumn (L-column micro, CERI, Tokyo, Japan) and fractionated on an in-house fabricated 20 cm column packed with 2 µm octadecyl silane particles (CERI). Elution was performed with a linear gradient of 5% to 35% solvent B over 70 min at a flow rate of 200 nl/min (solvent A = 0.1% formic acid; solvent B = 0.1% formic acid in acetonitrile) with the use of a Dionex Ultimate 3000 HPLC System (Thermo Fisher Scientific). Eluted peptides were sprayed with a nanoelectrospray source and a column oven set at 42°C (AMR, Tokyo, Japan).PrideNot availableThe Q Exactive Hybrid Quadrupole-Orbitrap mass spectrometer was operated in data-independent acquisition mode. All the data were acquired in profile mode using positive polarity. MS1 spectra were collected in the range of 430–860 m/z at a resolution of 35,000 using an automated gain control (AGC) target value of 1 × 106 ions with a maximum injection time of 50 msec. MS2 spectra were collected in the range of > 200 m/z at a resolution of 17,500 using an AGC target value of 1 × 106 ions and automatic maximum ion injection times. Twenty-one DIA windows of 20 units ranged from 430 to 850 m/z with an overlap of 1 unit. The normalized collision energy was set to 25. All DIA raw data were processed with DIA-NN (ver. 1.8)54 using library-free search mode against human UniProt sequences (https://www.uniprot.org/; accessed 27 April 2021). The enzyme specificity was set to “trypsin”. The precursor m/z range was set from m/z 430 to 850. Carbamidomethylation of cysteine was set as a fixed modification. Samples were prepared in triplicate.ProteomicsHideaki MatsuiDepartment of Neuroscience of Disease, Brain Research Institute, Niigata UniversityPARTIALHomo Sapiens (human)dougnong@bri.niigata-u.ac.jp10.1073/PNAS.2524190123Niigata UniversityJapanfalseA protective role for APP in nuclear waste clearance via lysosomal exocytosisAmyloid precursor protein (APP) is widely known for its role in Alzheimer’s disease (AD) pathogenesis through its proteolytic processing into amyloid-β peptides. However, its physiological function remains incompletely understood. Here, we uncover a protective role for full-length APP in facilitating the disposal of nuclear-derived debris under genotoxic stress. In both cultured cells and in vivo mouse models, loss of APP leads to nuclear waste accumulation, increased inflammation, and cell death, whereas APP overexpression mitigates these effects. Mechanistically, we show that APP supports the extracellular release of nuclear material through lysosomal exocytosis. APP mutants associated with familial AD fail to mediate this process. Consistently, human AD brain tissue exhibits abnormal nuclear morphology, accumulation of nuclear waste in the cytoplasm, and reduced APP levels per neuron. These findings highlight a conserved cellular mechanism by which APP contributes to nuclear and cellular homeostasis, and suggest that impaired nuclear waste clearance may represent an underappreciated contributor to neurodegeneration.2026-06-112024-07-17PXD053993NEWT:6945NEWT:3555NEWT:2NEWT:157546NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:544496NEWT:2042546NEWT:45351NEWT:43179NEWT:4513NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:1211601NEWT:876138NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:1351NEWT:1438992NEWT:2649997NEWT:272563NEWT:224326NCBITaxon:79857NEWT:95648NEWT:3885NEWT:3888NEWT:1589NEWT:135622NEWT:6915NEWT:3649NEWT:101510NEWT:3880NEWT:272559NEWT:3641NEWT:383379NEWT:10029NEWT:1000589NEWT:85962NEWT:317447NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:197NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:1270NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:1148NEWT:580240NEWT:294128NEWT:11676NEWT:55571NEWT:100226NEWT:4530NEWT:4896NEWT:75058NEWT:13616NEWT:1094343NEWT:296543NEWT:1773NEWT:1895NEWT:1182590NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NCBITaxon:1313NEWT:43330NEWT:408169NEWT:44544NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:990119NEWT:408172NEWT:408170NEWT:493760NEWT:260710NEWT:257313NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:106592NEWT:536231NEWT:1432138NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:9598NEWT:8030NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:432359NEWT:46835NEWT:2711NEWT:376686NEWT:95486NEWT:9103NEWT:29159NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:3635NEWT:5811NEWT:235443NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:169963NEWT:499175NEWT:476272NEWT:3747NEWT:367830NEWT:178616NEWT:410289NEWT:373153NEWT:352472NEWT:360094NEWT:470NEWT:1313NEWT:411469NEWT:84023NEWT:559292NCBITaxon:5811NEWT:411464NEWT:411460NEWT:2762NEWT:1174673NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:28038NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:327159NEWT:178876NEWT:327160NEWT:573NEWT:9031NEWT:7091NEWT:241368NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:5180NEWT:256737NEWT:115104NEWT:1081927NEWT:1238993NEWT:67825NEWT:185579NEWT:13076NEWT:1249668NEWT:317NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:415540NEWT:4081NEWT:554NEWT:98334NEWT:426428NEWT:7574NEWT:7215NEWT:575412NEWT:29204NEWT:2172103NEWT:507601NCBITaxon:6157NEWT:746360NEWT:6239NEWT:470150NEWT:216257NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:435590NEWT:1902NEWT:160488NEWT:28104NCBITaxon:2NEWT:985076NEWT:1215323NEWT:52641NEWT:7038NEWT:6192NEWT:28532NCBITaxon:38727NEWT:2829NEWT:216599NEWT:216595NEWT:243230NEWT:8355NEWT:9685NEWT:7029NEWT:1080772NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NEWT:6289NEWT:436486NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:170187NEWT:260707NCBITaxon:6191NEWT:1836NEWT:185431NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NCBITaxon:6073NEWT:884204NEWT:6279NEWT:1123869NEWT:9544NEWT:7370NEWT:83906NEWT:607699NEWT:6282NEWT:208964NEWT:1134506NEWT:575584NEWT:38783NEWT:8727NEWT:4006NEWT:8726NEWT:6426NEWT:6669NEWT:10090NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:5334NEWT:37334NEWT:382352NCBITaxon:10359NEWT:242619NEWT:632957NEWT:373995NEWT:5689NEWT:544404NEWT:9925NEWT:8839NEWT:4232NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:714NEWT:421932NEWT:196627NEWT:5691NEWT:48479NEWT:627025NEWT:1097677NEWT:61674NEWT:1117957NEWT:9913NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:29722NEWT:380394NEWT:1692259NEWT:180066NEWT:135588NEWT:1843183NEWT:58002NEWT:326423NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:418985NEWT:146479NEWT:1911079NEWT:264203NEWT:1480154NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:9612NEWT:38865NEWT:51953NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:72407NEWT:349741NEWT:9605NEWT:9606NEWT:157295NEWT:641501NEWT:7668NEWT:915099NEWT:74940NEWT:9721NEWT:137221NEWT:1450511NEWT:1143193NEWT:411901NEWT:9838NEWT:105884NCBITaxon:9615NEWT:58334NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:5476NEWT:1274432NEWT:1274426NEWT:70448NEWT:9825NEWT:1274423NEWT:393765NEWT:698936NEWT:39946NEWT:9823NEWT:9940NEWT:521001NEWT:39947NEWT:1274420NEWT:578458https://orcid.org/0000-0003-1383-5691