Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065451/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065451/Feature_level.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065451/Quantified_Proteins.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065451/abundance.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065451/21780_Marley_20240711_90_183_333893_placenta2_002.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065451/21780_Marley_20240711_90_183_333893_placenta2_001.rawprimaryOK200gpendyala@unmc.eduGurudutt PendyalaMass SpectrometryBottom-up proteomicsMixed Disorder As Reaction To StressNot availableEv biomarkersExtracellular vesicles (evs)Fetal developmentPerinatal exposureCardiomyopathyOxycodoneProteomicsPlacental signalinghttps://www.ebi.ac.uk/pride/archive/projects/PXD065451PlacentaThe placental tissues from rat samples were subjected to a detailed proteomics workflow beginning with cell lysis using a 9.5% SDS buffer containing 50 mM triethylammonium bicarbonate (TEAB), 2 mM MgCl₂, and in some cases, 8 M urea for enhanced protein denaturation. Benzonase nuclease was added to each sample to degrade nucleic acids, followed by incubation at room temperature for five minutes. Mechanical disruption was performed by pipetting and sonication (three 10-second pulses with 10-second intervals, repeated up to three times as needed) using an ice-embedded adapter to prevent heat-induced degradation. Protein concentrations were then determined using the Pierce 660 nm Protein Assay, modified with the Ionic Detergent Compatibility Reagent (IDCR) to account for the presence of SDS. Bovine serum albumin (BSA) standards ranging from 31.25 to 2000 µg/mL were used to construct a standard curve on a Varioskan LUX multimode microplate reader. Each sample was normalized to contain 50 µg of protein. Disulfide bonds were reduced by adding 10 mM TCEP and incubating at 37°C for 30 minutes, followed by alkylation of free cysteines using 40 mM acrylamide for another 30 minutes at the same temperature. Protein precipitation and cleanup were achieved using S-Trap™ microcolumns, which included acidification with 27.5% phosphoric acid and binding in a methanol/TEAB-based buffer. To ensure the removal of lipids and other contaminants, each column was washed three times with both 2:1 chloroform:methanol and S-Trap wash buffer. After trapping and washing, on-column digestion was performed using Trypsin/Lys-C at an enzyme-to-substrate ratio of approximately 1:12. Digestion proceeded at 37°C for 2 hours, after which peptides were sequentially eluted with 50 mM TEAB, 0.2% formic acid in water, and 0.2% formic acid in 50% acetonitrile. The eluted peptides were pooled, vacuum-dried at room temperature, and reconstituted in 2% acetonitrile with 0.1% formic acid. Peptide concentrations were determined using the Pierce Fluorometric Peptide Assay, following a standard curve generated from a serial dilution of a 1 mg/mL peptide digest standard. For LC-MS/MS, peptides were diluted to a final concentration of 0.2 µg/µL and spiked with iRT standards for retention time calibration. Samples (5 µL) were injected onto a µPAC™ NEO 50 cm nanoLC column and separated over a 90-minute gradient using a Thermo Exploris 480 mass spectrometer. The instrument was operated in data-dependent acquisition mode with a spray voltage of 2 kV, MS1 resolution of 60,000, MS2 resolution of 15,000, and HCD activation at 30%. Raw files were processed using Proteome Discoverer 2.4 and Spectronaut, with searches conducted against the Human SwissProt and isoform databases. Static modifications included carbamidomethylation of cysteine, and dynamic modifications included oxidation of methionine and N-terminal acetylation. A target false discovery rate (FDR) of 1% was applied at both peptide and protein levels to ensure high-confidence identifications.PrideProteomic Data Processing and Differential Expression Analysis Quantitative proteomic profiles were obtained and analyzed to identify differentially expressed proteins between experimental and control groups. Proteins were filtered based on their log₂ fold change (log2FC) and statistical significance. Specifically, proteins with log2FC values between +0.58 and +1.00 and p-values < 0.05 were classified as moderately upregulated, while those with log2FC values between –1.00 and –0.58 and p-values < 0.05 were considered moderately downregulated. These thresholds correspond to a fold change range of 1.5–2 (upregulated) and 1–1.5 (downregulated), commonly used in proteomic studies to detect meaningful biological variation while minimizing false positives. Gene Identifier Conversion To enable pathway-based analyses, UniProt protein identifiers were mapped to Entrez Gene IDs. This step ensured compatibility with downstream functional enrichment tools and databases. Only successfully mapped entries were retained for further analysis. Functional Enrichment Analysis Functional characterization of the differentially expressed proteins was performed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. GO analysis was conducted for Biological Process (BP). KEGG pathway enrichment was used to identify overrepresented metabolic and signaling pathways. All enrichment analyses were performed using a hypergeometric test framework with multiple hypothesis testing correction via the Benjamini-Hochberg method. Terms with adjusted p-values (FDR) < 0.05 were considered statistically significant. Data Visualization For each analysis, the top 20 enriched GO terms and KEGG pathways were selected based on adjusted p-value ranking. These were visualized using dot plots and bar plots. In the dot plots, the x-axis represented the negative log10 of the adjusted p-value, the y-axis listed the enriched terms, the color gradient reflected significance, and the point size indicated gene count. In the bar plots, bar lengths represented enrichment significance.ProteomicsDr. Gurudutt PendyalaPARTIALRobert Lieberman Endowed Professor of Anesthesiology University of Nebraska Medical Center College of Medicine, Department of AnesthesiologyRattus Norvegicus (rat)41983059 Foroughi-Nezhad A, Moore D, Schaal VL, Hediyal TA, Stone E, Kolli S, Athota P, Shukri O, Yelamanchili SV, Pendyala G. Chronic in utero oxycodone exposure alters placental small EV proteome and fetal cardiomyopathy-linked pathways. Extracell Vesicles Circ Nucl Acids. 2026 7(1):146-164 10.20517/evcna.2025.138gpendyala@unmc.eduUniversity of Nebraska Medical CenterUnited States<b>Aim:</b> The rising prevalence of opioid use during pregnancy poses serious public health concerns. The placenta is a critical organ during gestation, and opioid exposure can disrupt its function and fetal development. However, the molecular mechanisms through which opioids such as oxycodone affect feto-placental development remain poorly understood. This study aimed to investigate the effects of chronic in-utero oxycodone exposure on the composition and signaling functions of placenta-derived small extracellular vesicles (PSEVs) using a rat model. <b>Methods:</b> Extracellular vesicles (EVs) were isolated from placental tissue and characterized through nanoparticle tracking analysis, transmission electron microscopy, western blotting, and label-free quantitative proteomics. Bioinformatic enrichment analyses were conducted to evaluate changes in EVs biophysical properties and protein cargo. <b>Results:</b> Chronic oxycodone exposure significantly altered PSEV characteristics, including particle size distribution and proteomic composition. Among the 456 identified EV proteins, 107 proteins were significantly dysregulated. We found key downregulatory proteins including Atp2a2, Lmna, Tgfb3, Agt, and Sgce, which are crucial for myocardial calcium cycling, nuclear integrity, extracellular matrix remodeling, and blood pressure regulation. These findings indicate disruptions in fetal cardiac programming, particularly hypertrophic and dilated cardiomyopathy pathways. Additionally, enrichment analyses revealed notable perturbations in metabolic processes (e.g., citrate cycle, fatty acid degradation, N-glycan biosynthesis), along with upregulation of vesicle transport and neurodevelopment-related proteins, indicating broader systemic effects on fetal development. While these proteomic findings are robust, further independent validation (e.g., via targeted assays or Western blotting) will be necessary to confirm individual protein-level changes. <b>Conclusion:</b> These results highlight PSEVs as sensitive molecular indicators linking maternal oxycodone use to disrupted fetal cardiovascular, metabolic, and neurodevelopmental pathways. This study provides a novel systems-level framework for understanding opioid-induced placental signaling alterations and lays the groundwork for developing EV-based diagnostic biomarkers and targeted interventions.Chronic in utero oxycodone exposure alters placental small EV proteome and fetal cardiomyopathy-linked pathways.Foroughi-Nezhad Amin A, Moore Dalia D, Schaal Victoria L VL, Hediyal Tousif Ahmed TA, Stone Elizabeth E, Kolli Sree S, Athota Pranavi P, Shukri Omar O, Yelamanchili Sowmya V SV, Pendyala Gurudutt GfalseChronic Perinatal Oxycodone Exposure Alters Placental EV Proteome and Fetal Cardiomyopathy-Linked PathwaysThe rising prevalence of opioid use during pregnancy poses serious public health concerns, yet the molecular mechanisms by which opioids such as oxycodone impact fetal development remain poorly understood. This study investigates the effects of chronic perinatal oxycodone exposure on the composition and signaling functions of placenta-derived extracellular vesicles (EVs) using a rat model. EVs were isolated and characterized via nanoparticle tracking analysis, transmission electron microscopy, Western blotting, and label-free quantitative proteomics. Bioinformatic enrichment analyses revealed that oxycodone exposure significantly altered EV biophysical properties and protein cargo, with pronounced downregulation of cardiomyopathy-associated pathways—including hypertrophic and dilated cardiomyopathy. Key EV proteins such as Atp2a2, Lmna, Tgfb3, Agt, and Sgce, crucial for myocardial function, calcium homeostasis, and vascular signaling, were suppressed, suggesting impaired fetal cardiac programming. Additional pathway analyses indicated disruption of metabolic and glycosylation processes and upregulation of vesicle transport and neurodevelopment-related proteins. These findings position placental EVs as sensitive indicators of in utero drug exposure and propose a mechanistic link between maternal opioid use and altered fetal cardiovascular development. This work establishes a novel systems-level foundation for developing EV-based diagnostics and interventions targeting opioid-induced developmental risk.2026-04-272025-06-25PXD065451NEWT:3555NEWT:71647NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:96731NEWT:383379NEWT:10029NEWT:913645NEWT:44491NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:4442NEWT:192875NEWT:12637NEWT:59729NEWT:2164133NEWT:108061NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:931281NEWT:4432NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:633149NEWT:10239NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:1436733NEWT:460519NEWT:1247411NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:333760NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:84588NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:644223NEWT:235443NEWT:108458NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:39491NCBITaxon:5811NEWT:29491NEWT:2014887NEWT:33952NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:215402NEWT:272634NEWT:9031NEWT:1872122NEWT:7091NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:7111NEWT:347515NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:185579NEWT:941442NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT: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:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:985076NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:28532NEWT:353152NEWT:8496NEWT:27448NEWT:40674NEWT:1194669NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:105231NEWT:52638NEWT:57075NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:7370NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:714NEWT:295027NEWT:632957NEWT:9925NEWT:89462NCBITaxon:9606NEWT:8839NEWT:90690NEWT:1436183NEWT:4232NEWT:2758385NEWT:11298NEWT:171101NEWT:714NEWT:421932NEWT:312017NEWT:196627NEWT:200308NEWT:553470NEWT:200302NEWT:870435NEWT:284593NEWT:100392NEWT:5315NEWT:9913NEWT:265872NEWT:105841NEWT:337330NEWT:2666255NEWT:2285NEWT:999810NCBITaxon:5693NEWT:1392998NEWT:380394NEWT:981087NEWT:180066NEWT:226900NEWT:231490NEWT:7725NEWT:430615NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1416333NEWT:35024NEWT:135461NEWT:1678078NEWT:749906NEWT:418985NEWT:1817808NEWT:749907NEWT:145263NEWT:69014NEWT:142809NEWT:694569NEWT:27606NEWT:9739NEWT:59202NEWT:9975NEWT:8643NEWT:51953NEWT:3197NEWT:860688NEWT:13443NEWT:8644NEWT:36329NEWT:62615NCBITaxon:3044782NEWT:1333550NEWT:160235NEWT:72407NEWT:8639NEWT:8637NEWT:349741NEWT:409859NEWT:157295NEWT:2096NEWT:192222NEWT:9721NEWT:137221NEWT:9963NEWT:1617910NEWT:565050NEWT:409860NEWT:2785785NEWT:411901NEWT:8626NEWT:105884NCBITaxon:9615NEWT:8621NEWT:58334NEWT:1193501NEWT:58331NEWT:6689NEWT:8624NEWT:5116NEWT:862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