{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077909/checksum.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077909/metadata_abundance.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077909/metadata_phospho.txt"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077909/HIV_vector_pNL4_3.fasta","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077909/uniprotkb_human_reviewed_2023_10_06.fasta"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077909/C33A_cells_abundance_proteomics.sne","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077909/Raw_files_abundance.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077909/Raw_files_phospho.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077909/Dnr3_phosphoproteomics_C33A.sne","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077909/Raw_files_phospho_Dnr1_2.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077909/Dn1_2_phosphoproteomics_C33A.sne"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["mehdibouhaddou@gmail.com"],"submitter":["Mehdi Bouhaddou"],"technology_type":["Mass Spectrometry","Bottom-up proteomics","Data-independent acquisition"],"disease":["Human Immunodeficiency Virus Infectious Disease"],"software":[""],"submitter_keywords":["Mapk and pi3k signaling","Network propagation","Hpv-associated cervical cancer"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD077909"],"tissue":["T Cell","Cell Culture","Epithelial Cell Of Cervix"],"sample_protocol":["Proteomics sample processing Abundance: Cells were washed twice with cold PBS, lysed in 6M guanidine hydrochloride (GH, Sigma-Aldrich) and boiled at 95°C for 5 min. The lysed samples were thawed and sonicated using a probe sonicator 1x for 15 seconds at 20% amplitude. Samples were centrifuged at ∼13,000 rpm for 10 minutes. About 500 µg of protein sample was reduced and alkylated using a 1:10 sample volume of tris-(2-carboxyethyl) (TCEP) (10 mM final) and 2-chloroacetamide (4.4mM final) for 5 minutes at 45°C with shaking. Samples were diluted from 6M to 1M GH withTris-HCl (0.1 M, pH 8). Trypsin and LysC were added at a 1:100 (wt/wt) enzyme-substrate ratio and put in a water bath 37°C overnight (∼16 hours). Thereafter, 10% trifluoroacetic acid (TFA) was added to each sample (pH 2). Desalting of the samples was done using 50 mg Sep Pak C18 cartridges (Waters). Activation of each cartridge was done using 1 mL 80% acetonitrile (ACN)/0.1% TFA followed by equilibration with 3 × 1 mL of 0.1% TFA. After loading the samples, we washed the cartridges with 3 × 1 mL of 0.1% TFA. The samples were then eluted with 1 × 0.8 mL 50% ACN/0.25% formic acid (FA). All samples were dried by vacuum centrifugation. Phospho: Cells were lysed, reduced, and alkylated as above. Proteins were digested 1:100 Trypsin and LysC (wt/wt) enzyme-substrate ratio. Peptides were desalted and dried as above. The Ti-IMAC HP beads (Resyn Biosciences) were used according to the manufacturer's instructions for phosphopeptide enrichment. Samples were dried by vacuum centrifugation. Mass spectrometry proteomics acquisition Abundance: Digested samples were analyzed on an Orbitrap Fusion Lumos Tribrid Mass Spectrometer (Thermo Fisher Scientific) equipped with an Easy nLC 1200 ultra-high pressure liquid chromatography system (Thermo Fisher Scientific). We injected samples on a C18 reverse phase column (25 cm × 75 μm packed with ReprosilPur 1.9-μm particles). We equilibrated analytical columns with 6 μL of mobile phase A with a max pressure of 650 bar. The mobile phase A consisted of 0.1% FA whereas mobile phase B consisted of 0.1% FA / 80% ACN. Peptides were separated by an organic gradient from 4% (2%) to 30% (25%) mobile phase B over 62 min followed by an increase to 45% (40%) B over 10 min, then held at 95% B for 8 min at a flow rate of 300 nl min−1. Data-independent analysis (DIA) was performed using an 80-minute gradient. An MS scan at 60,000 resolving power over a scan range of 350–1100 m/z, a normalized AGC target of 300%, and an RF lens setting of 40%. This was followed by DIA scans at 15000 resolving power, using 20 m/z isolation windows over 350–1100 m/z at a normalized HCD collision energy of 30%. Loop control was set to All. To build a spectral library, one sample from each set of biological replicates was acquired in a data-dependent manner. Data-dependent analysis (DDA) was performed by acquiring a full scan over a m/z range of 350–1100 in the Orbitrap at 60,000 resolving power with a normalized AGC target of 300% and an RF lens setting of 40%. Dynamic exclusion was set to 45s, with a 10-ppm exclusion width setting. Peptides with charge states 2–6 were selected for MS/MS interrogation using higher-energy collisional dissociation (HCD), with 20 MS/MS scans per cycle. Phospho: Dried peptides were resuspended in 0.1% FA and analyzed on a timsTOF HT mass spectrometer (Bruker Daltonics) paired with a Vanish Neo UHPLC system (ThermoScientific). Mobile phase A consisted of 0.1% FA, and mobile phase B consisted of 0.1% FA. Liquid chromatography was performed in a trap-and-elute mode. First, peptides were trapped on a PepMap Neo trap column (5 mm, 100 Å pore size, 5 μm particle size). Then, they were separated by reversed-phase chromatography on an Aurora Elite C18 reverse phase column (15 cm length, 75 μm diameter, 1.7 μm particle size for captive spray, IonOptiks). The 45-minute LC gradient was run with a flow rate of 300 nL/min set as follows: 3-30% B over 37 min, then to 45% B over 4 min, then to 60% B over 1 min, and then to 95% B for 30 second. The column was maintained at 50°C using a column oven for Bruker Captive Spray source (Sonation Lab Solutions). Ionization was performed using a CaptiveSpray source (Bruker Daltonics) at 1700 V. The raw data was acquired in data-independent acquisition coupled with parallel accumulation–serial fragmentation (dia-PASEF) mode. Using equal-size windows of 25 Da with an overlap of 1 Da in the m/z vs ion mobility plane, the precursor ion coverage was maximized for further MS/MS. For dia-PASEF, in the ion mobility (1/K0) range 0.60 to 1.50 Vs cm-2, the collision energy was linearly decreased from 59 eV at 1/K0 = 1.60 Vs cm-2 to 20 eV at 1/K0 = 0.60 Vs cm-2 to collect the MS/MS spectra in the mass range 400.2 to 1399.3 Da. The estimated mean cycle time was 1.38 s. The ion accumulation time and ramp times in the dual TIMS analyzer were set to 100 ms each."],"repository":["Pride"],"modification":[""],"quantification_method":["Not available"],"data_protocol":["Mass spectrometry proteomics data analysis Abundance: We built experiment specific libraries using mass spectra from each DDA dataset for DIA searches using the Pulsar search engine integrated into Spectronaut v19.8.250311.62635 (Huggins) by searching against a reference Uniprot Homo sapiens sequences (downloaded 7 October 2024) and an HIV-1 pNL4-3 proteome of 9 viral proteins, including gag polyprotein, pol polyprotein, vif, vpr, tat, rev, vpu, env polyprotein and nef. For protein abundance samples, data were searched using the default Biognosys (BGS) settings, variable modification of methionine oxidation, static modification of carbamidomethyl cysteine, and filtering to a final 1% FDR at the peptide, peptide spectrum match (PSM) and protein level. For phosphopeptide-enriched samples, BGS settings were modified to include phosphorylation of S, T and Y as a variable modification. We used the generated search libraries to search the DIA data. For protein abundance samples, we used default BGS settings with no data normalization. For phosphopeptide-enriched samples, we applied the PTM site localization score in Spectronaut. Imputation was not performed for all the analyses. Phospho: The raw files were processed with Spectronaut (Biognosys, ver. 19.0) with the directDIA+ (Deep) search algorithm. Carbamidomethylation (cysteine) was set as a fixed modification for database search. Acetylation (protein N-term), oxidation (methionine), and phosphorylation (serine, threonine, tyrosine) were set as variable modifications. Reviewed human proteome and HIV-1 pNL4-3 proteome (downloaded from UniProt) were used for spectral matching. The false discovery rates for the PSM, peptide, and protein groups were set to 0.01, and the minimum localization threshold for PTM was set to zero. For MS2-level area-based quantification, the cross-run normalization option was unchecked (normalization was performed later using MSstats), and the probability cutoff was set to zero for the PTM localization. Quantitative analysis was performed in the R statistical programming language. Initial quality control analyses, including inter-run clustering, correlations, principal component analysis (PCA), peptide and protein counts, and intensities were completed using custom R code. Statistical analysis of phosphorylation and protein abundance changes between exposed and control samples were computed in MSstats. MSstats was parameterized to perform normalization by median equalization, no imputation of missing values, and median smoothing (Tukey’s median polish) to combine intensities for multiple peptide ions or fragments into a single intensity for their protein group, and statistical tests of differences in intensity between conditions. Default settings for MSstats were used for adjusted P values. By default, MSstats uses the Student’s t-test for P value calculation and the Benjamini–Hochberg method of FDR estimation to adjust P values."],"omics_type":["Proteomics"],"labhead":["Mehdi Bouhaddou"],"instrument_platform":[""],"labhead_affiliation":["Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, USA  Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, LA, USA  Molecular Biology Institute, University of California, Los Angeles, USA"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["Not available"],"submitter_mail":["bouhaddoulab@gmail.com"],"submitter_affiliation":["UCLA"],"submitter_country":["United States"],"additional_accession":[]},"is_claimable":false,"name":"Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways","description":"Co-infection of human papillomavirus (HPV) and human immunodeficiency virus type 1 (HIV-1) in women have a six-fold higher risk of developing cervical cancer compared to those without HIV. To evaluate how paracrine signals from HIV-infected T-cells remodeled the proteome of cervical epithelial cells in culture, primary CD4+ T cells isolated from PBMC-enriched leukapheresis products (leukopaks) from two healthy donors were infected or uninfected with a replication-competent pNL4-3 HIV-1 strain for 72 hours. Secretome from the CD4+ T cell cultures was used to stimulate the human HPV-negative cervical epithelial cell line, C33A, for 72 hours. Then, C33A cells were harvested, and cell lysates were digested and subjected to global quantitative mass spectrometry (MS) based abundance proteomics and phosphoproteomics analyses. Both proteomics and phosphoproteomics outputs were analysed using bioinformatics approaches. These datasets revealed altered expression of proteins in the MAPK, PI3K-AKT, and β-catenin signaling pathways. Additionally, MS phosphoproteomics analysis confirmed PI3K-AKT pathway activation in cervical cells exposed to conditioned media from HIV-1-infected T cells.","dates":{"publication":"2026-05-05","submission":"2026-05-01"},"accession":"PXD077909","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:1211601","NEWT:876138","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:1589","NEWT:135622","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:286","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1094343","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:2711","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:32644","NEWT:499175","NEWT:476272","NEWT:3747","NEWT:367830","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:357","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:7091","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:5180","NEWT:256737","NEWT:115104","NEWT:1121114","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:98334","NEWT:426428","NEWT:7574","NEWT:7215","NEWT:575412","NEWT:29204","NEWT:2172103","NEWT:507601","NEWT:643680","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NEWT:1908","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:353152","NEWT:2829","NEWT:366581","NEWT:216599","NEWT:216595","NEWT:243230","NEWT:8355","NEWT:9685","NEWT:7029","NEWT:1080772","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:334747","NEWT:61235","NEWT:6289","NEWT:436486","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:170187","NEWT:260707","NCBITaxon:6191","NEWT:1836","NEWT:185431","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:2697049","NEWT:105231","NEWT:1216981","NCBITaxon:6073","NEWT:884204","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NEWT:607699","NEWT:6282","NEWT:208964","NEWT:1134506","NEWT:575584","NEWT:38783","NEWT:8727","NEWT:4006","NEWT:8726","NEWT:6426","NEWT:6669","NEWT:10090","NEWT:4120","NEWT:51515","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:5334","NEWT:37334","NEWT:382352","NCBITaxon:10359","NEWT:242619","NEWT:632957","NEWT:34073","NEWT:373995","NEWT:544404","NEWT:9925","N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