Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2_secretomes.mzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2_lysates.mzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-100nM-C3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-1uM-C2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-1uM-S2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-Veh-S2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-10uM-S1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-10uM-C4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-10uM-C1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-100nM-S3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-10uM-S4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-Veh-C2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-1uM-S1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-1uM-C3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-10uM-C5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-Veh-C5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-Veh-C1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-10uM-S3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-Veh-S3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-100nM-S2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-100nM-C4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-100nM-C1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-1uM-S4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-100nM-S1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-1uM-C4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-100nM-C5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-10uM-C2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-Veh-S4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-100nM-S5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-Veh-C4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-10uM-S2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-1uM-S5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-1uM-C5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-1uM-S3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-100nM-C2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-Veh-S5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-10uM-C3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-Veh-C3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-Veh-S1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-100nM-S4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-1uM-C1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2-10uM-S5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2_secretomes.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069776/HepG2_lysates.mzidprimaryOK200m.mayr@imperial.ac.ukXIAOKE YINData-dependent acquisitionMass SpectrometryHumanDdaHepg2LcmsLpaHepatoma cellshttps://www.ebi.ac.uk/pride/archive/projects/PXD069776Culture FluidCell LysateHepg2 CellHepG2 human hepatoma cells (ECACC, 85011430) were maintained in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum (FBS, Merck), 2 mM L-alanyl-L-glutamine (Gibco, Glutamax), 100 U/ml penicillin and 100 µg/ml streptomycin. A plasmid encoding LPA (Origene, RC212070) was used to generate the Lp(a)-producing cell lines. DDK and myc tags on LPA were replaced with a HiBiT tag using NEBuilder HiFi DNA Assembly (NEB) and standard cloning procedures. The HiBiT tag allows for easy detection of secreted LPA by a split luciferase assay and therefore quantifiable measurement of Lp(a) release from the cells. HepG2 cells were transfected with the modified vector using Viafect (Promega) according to the manufacturer’s instructions. The plasmid encodes resistance to neomycin. 48 h after transfection, cells were treated with Geneticin (Gibco) at 1,600 µg/ml in the medium used for culturing (see above) devoid of penicillin and streptomycin. Cells were maintained in these conditions for at least a month to allow for selection of cells that stably produce Lp(a). Geneticin concentration was then reduced to 800 µg/ml for maintenance of the polyclonal populations of cells. For atorvastatin treatment, LPA-expressing HepG2 cells were cultured in complete medium containing 0.1, 1, or 10 µM atorvastatin for nine days, followed by incubation in serum-free medium with the same atorvastatin concentration for the final 24 h. Vehicle was dimethyl sulfoxide. Conditioned media and cell lysates were collected for further analyses. Serum-free medium conditioned by HepG2 cells was cleared of debris by centrifugation and concentrated by ultrafiltration (Merck, Amicon regenerated cellulose membrane). Proteins were denatured, reduced, alkylated and subjected to an in-solution digestion with trypsin/Lys-C (Promega). Acidified peptides were desalted using C18 cartridges on an AssayMAP Bravo Liquid Handling Platform (Agilent). Eluted peptides were vacuum centrifuged (Thermo Scientific, Savant SPD131DDA) and resuspended in 2% acetonitrile (ACN), 0.05% trifluoroacetic acid (aq). The data-dependent acquisition–mass spectrometry (DDA–MS) experiments were conducted on a Vanquish Neo ultra high-performance liquid chromatography system that was coupled via an EASY-Spray source to an Orbitrap Eclipse mass spectrometer equipped with a high-field asymmetric waveform ion mobility spectrometry (FAIMS) Pro interface (all Thermo Scientific). A 35-minute gradient with increasing strength of mobile phase B [80% ACN, 0.1% FA (aq)] was used to elute the peptides from a trap cartridge (Thermo Scientific, PepMap Neo, 300 µm inner diameter × 5 mm length, 5 µm particle size, 100 Å pore size) at 0.25 µL/min. The peptides were separated on a reversed-phase analytical column (Thermo Scientific, EASY-Spray PepMap Neo, 75 μm inner diameter × 50 cm length, 2 μm particle size, 100 Å pore size) kept at 60 °C. Loading and washing were performed at 0.45 µL/min (total run time 50 min). FAIMS compensation voltages of -40 V, 60 V, and -80 V were applied. Precursor ions were analyzed in the Orbitrap (resolution 120,000, scan range 375–1,500 m/z). Data-dependent fragment spectra were acquired after HCD and ion trap analysis (Cycle Time mode) using a fixed total cycle time of 3 s and a dynamic exclusion duration of 60 s.PrideDDA–MS raw files were processed using Proteome Discoverer (Thermo Scientific, v3.2.0.450) and Mascot (Matrix Science, v2.999.0). The files were searched against a human database (UniProtKB/Swiss-Prot, release 2025_01, 20,417 proteins) and in-house databases compiled from mass spectrometric analyses of FBS (249 bovine proteins, porcine trypsin, and Lys-C from P. aeruginosa) and tagged human apolipoproteins (23 proteins). Search results were filtered to include human master proteins with a high protein false discovery rate (FDR) confidence, as determined by Proteome Discoverer’s FDR Validator node (FDR confidence threshold of 0.01 for high confidence), and a minimum number of two unique peptides. Only proteins with <20% missing values in at least one atorvastatin dose groups were retained. Missing values were KNN-imputed (K = 5) using the DMwR2 R package (v0.0.2) when ≤30% of values were missing across all samples. When >30% of values were missing across all samples but <20% were missing in at least one group, and >50% were missing in the remaining groups, the missing values were imputed by multiplying the lowest quantified value per protein by 0.2.ProteomicsProf Manuel Mayr MD PhDCOMPLETENational Heart and Lung Institute, Imperial College London, United KingdomHomo Sapiens (human)41664920 Schmidt LE, Burnap SA, Singh B, Takov K, Losdat S, Schrutka L, Galli L, Theofilatos K, Otto GW, Hengstenberg C, Tzoulaki I, Lang IM, Koskinas KC, Speidl WS, Räber L, Mayr M. Integrative Proteomic and Lipidomic Analysis of Patients With Acute Myocardial Infarction Treated With PCSK9 Antibodies and Statins. Circ Genom Precis Med. 2026 19(2):e005345 10.1161/circgen.125.005345xiaoke.yin@imperial.ac.ukNational Heart and Lung Institute, Faculty of Medicine, Imperial College LondonUnited Kingdom10.6019/PXD069776<h4>Background</h4>PCSK9 (proprotein convertase subtilisin/kexin type 9) inhibition is a potent cholesterol-lowering strategy. This study examined the effects of PCSK9 monoclonal antibodies (mAbs) and high-intensity statins beyond low-density lipoprotein cholesterol reduction, which are not fully defined, particularly in patients with acute myocardial infarction (MI).<h4>Methods</h4>Proteomic and lipidomic analyses were conducted on plasma from 265 patients with acute MI from the PACMAN-AMI (Effects of the PCSK9 Antibody Alirocumab on Coronary Atherosclerosis in Patients With Acute Myocardial Infarction) randomized, placebo-controlled PCSK9 mAb trial and 34 patients without MI with hyperlipidemia from the Vienna Lipid Clinic registry, also receiving PCSK9 mAbs.<h4>Results</h4>Discovery proteomics revealed changes in apolipoproteins and increased PCOLCE (procollagen C-endopeptidase enhancer 1) levels in both the PCSK9 mAb and placebo groups after MI. UK Biobank data confirmed PCOLCE and PCSK9 upregulation as associated with statin use. Hepatoma cell experiments demonstrated a dose-dependent PCOLCE induction on statin treatment. Compared with placebo (statins only), PCSK9 mAb therapy resulted in greater reductions in APOB (apolipoprotein B), APOE (apolipoprotein E), APOC2 (apolipoprotein C2), and APOC3 (apolipoprotein C3), as shown by targeted proteomics. Mediation analysis indicated that these changes were largely explained by low-density lipoprotein cholesterol lowering. Lipidomics identified more pronounced reductions in cholesteryl esters, ceramides, sphingomyelins, phosphatidylcholines, triglycerides, and diglycerides in PCSK9 mAb-treated patients with MI. Results were largely consistent in patients without MI. However, levels of LPA (apolipoprotein[a]), the characteristic protein component of lipoprotein(a), remained unchanged in PCSK9 mAb-treated patients with MI, since a rise of LPA was observed in the placebo group post-MI.<h4>Conclusions</h4>Most apolipoprotein changes after PCSK9 mAb therapy following MI were mediated by low-density lipoprotein cholesterol lowering. Statin use is associated with increased circulating PCOLCE, with hepatoma cell experiments supporting a predominant hepatic origin. Combining PCSK9 mAbs with high-intensity statins mitigates post-MI increases in lipoprotein(a).<h4>Registration</h4>URL: https://www.clinicaltrials.gov; Unique identifier: NCT03067844.Integrative Proteomic and Lipidomic Analysis of Patients With Acute Myocardial Infarction Treated With PCSK9 Antibodies and Statins.Schmidt Lukas E LE, Burnap Sean A SA, Singh Bhawana B, Takov Kaloyan K, Losdat Sylvain S, Schrutka Lore L, Galli Lukas L, Theofilatos Konstantinos K, Otto Georg W GW, Hengstenberg Christian C, Tzoulaki Ioanna I, Lang Irene M IM, Koskinas Konstantinos C KC, Speidl Walter S WS, Räber Lorenz L, Mayr Manuel MfalseIntegrative Proteomics and Lipidomics Analysis of Post-Myocardial Infarction Patients Treated With PCSK9 Antibodies and StatinsProprotein convertase subtilisin/kexin type 9 (PCSK9) inhibition is a potent cholesterol-lowering strategy. This study examined effects of statins and PCSK9 monoclonal antibodies (mAbs) beyond low-density lipoprotein cholesterol reduction, which are not fully defined. To complement in vivo plasma proteomic data, we used HepG2 human hepatoma cells stably expressing apolipoprotein(a) (LPA). Cells were exposed to escalating doses of atorvastatin for ten days, followed by collection of conditioned media and cell lysates for quantitative mass spectrometric analysis. Proteomic profiling of cell lysates revealed a dose-dependent effect on HMG-CoA reductase and other enzymes within the mevalonate pathway. Analysis of conditioned media demonstrated a strong, dose-dependent induction of procollagen C-endopeptidase enhancer 1 (PCOLCE) and a modest increase in secreted LPA. These findings corroborate clinical observations that statin therapy can modestly elevate circulating lipoprotein(a) [Lp(a)] and is associated with increased plasma PCOLCE levels. The HepG2 data provide evidence for a predominant hepatic origin of this PCOLCE response, representing a novel mechanistic insight into statin-associated proteomic changes.2026-04-272025-10-22PXD069776NEWT:330879NEWT:377960NEWT:2042546NEWT:259447NEWT:295546NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:1073882NEWT:475174NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:10034NEWT:661410NEWT:638632NEWT:224326NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:3765NEWT:1589NEWT:135622NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:656064NEWT:36630NEWT:383379NEWT:418106NCBITaxon:12721NEWT:10029NEWT:913645NEWT:641809NEWT:38815NEWT:317447NEWT:4688NEWT:7719NEWT:868565NEWT:135674NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:224308NEWT:3347NEWT:160621NEWT:212790NEWT:110368NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:44688NEWT:44689NEWT:498211NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:246196NEWT:246197NEWT:145458NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:3329NEWT:419481NEWT:5507NEWT:410661NEWT:1140NCBITaxon:2157NEWT:1143NEWT:1287689NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:1182590NEWT:3712NEWT:3711NEWT:2065263NEWT:177437NEWT:10418NEWT:118698NEWT:1616117NEWT:118696NEWT:34865NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:44664NEWT:43346NEWT:3702NEWT:1245466NEWT:244366NEWT:1246791NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT:52299NEWT:8165NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:460519NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:55784NEWT:1303443NEWT:485NEWT:56636NEWT:2853422NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:1185650NEWT:216778NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:1883446NEWT:1233435NEWT:109760NEWT:29031NEWT:317047NEWT:491NEWT:460523NEWT:235443NEWT:1757312NEWT:85694NEWT:108458NEWT:5936NEWT:320637NEWT:1078283NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:1255228NEWT:410289NEWT:373153NEWT:472NEWT:940825NEWT:529507NEWT:1071661NEWT:470NEWT:5911NEWT:748693NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:166313NEWT:63366NEWT:63367NEWT:215402NEWT:1547NEWT:906914NEWT:9031NEWT:27292NEWT:1050722NEWT:108931NEWT:1293497NEWT:1055524NEWT:150475NEWT:267872NEWT:381666NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:2903NEWT:185579NEWT:13076NEWT:1006581NEWT:8673NEWT:33940NEWT:550NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:36185NEWT:1054211NEWT:1225786NEWT:51338NEWT:575412NEWT:28112NEWT:6493NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:9983NEWT:8655NEWT:5147NEWT:28108NEWT:28104NEWT:407821NEWT:568703NCBITaxon:2NEWT:568708NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:298176NEWT:227377NEWT:1774284NEWT:40674NEWT:1194669NEWT:443906NEWT:519NEWT:2510939NEWT:7394NEWT:6063NEWT:1328388NEWT:105487NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:300641NEWT:39655NEWT:9554NEWT:475932NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:214053NEWT:80863NEWT:90675NEWT:52638NEWT:57075NEWT:1666905NEWT:8697NEWT:8695NEWT:884204NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:83906NEWT:99488NEWT:1134506NEWT:255470NEWT:38783NEWT:6426NEWT:33090NEWT:9935NEWT:287889NEWT:305959NEWT:13489NEWT:29829NEWT:92867NEWT:92866NCBITaxon:3055NEWT:51750NEWT:202950NEWT:48106NEWT:295027NCBITaxon:11320NEWT:632957NEWT:9925NCBITaxon:9606NEWT:90690NEWT:1436183NEWT:300273NEWT:4232NEWT:416348NEWT:11298NEWT:4236NEWT:7742NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:9913NEWT:9915NEWT:105841NEWT:2666255NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:9909NEWT:9902NEWT:430615NEWT:72664NEWT:563041NEWT:36599NEWT:41949NEWT:249161NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1678078NEWT:749906NEWT:418985NEWT:749907NEWT:150847NEWT:29835NEWT:431947NEWT:69014NEWT:142809NEWT:302409NEWT:130821NEWT:27606NEWT:1519788NEWT:59202NEWT:9975NEWT:8643NEWT:1159899NEWT:502780NEWT:860688NEWT:13443NEWT:35231NEWT:8644NEWT:1125630NEWT:5141NEWT:46360NCBITaxon:3044782NEWT:202914NEWT:160235NEWT:502779NEWT:297246NEWT:8639NEWT:1928434NEWT:8637NEWT:1114970NEWT:2096NEWT:285272NEWT:192222NEWT:9963NEWT:1617910NEWT:637379NEWT:2785785NEWT:411901NEWT:1298722NEWT:8626NEWT:186801NEWT:105884NCBITaxon:9615NEWT:8621NEWT:58334NEWT:58331NEWT:8624NEWT:5116NEWT:8623NEWT:5597NEWT:194439NCBITaxon:12637NEWT:38727NEWT:218496NEWT:8618NEWT:70448NEWT:300251NEWT:9940NEWT:1247190NEWT:118702NEWT:118700NEWT:2126719NEWT:118705NEWT:6945NEWT:2104NEWT:2627626NEWT:6943NEWT:157546NEWT:870726NEWT:91374NEWT:91373NEWT:474186NEWT:54195NEWT:10136NEWT:38942NEWT:4762NEWT:6941NEWT:307972NEWT:2102NEWT:34NEWT:38949NEWT:1299114NEWT:1590841NEWT:1276473NEWT:2282334NEWT:1247NEWT:70667NEWT:869728NEWT:693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