{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/proteinGroups.txt"],"Csv":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/IP_ORF1_iRT_metadata.csv"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210601_SOiRTN_37_ORF1_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210601_SOiRTN_41_ORF1_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210602_SOiRTN_43_ORF1_03.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210602_SOiRTN_45_ORF1_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210601_SOiRTN_36_ORF1_04.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210601_SOiRTN_34_ORF1_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210602_SOiRTN_47_ORF1_03.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210601_SOiRTN_33_ORF1_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210601_SOiRTN_38_ORF1_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210602_SOiRTN_42_ORF1_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210602_SOiRTN_44_ORF1_04.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210601_SOiRTN_35_ORF1_03.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210601_SOiRTN_39_ORF1_03.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210602_SOiRTN_46_ORF1_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210601_SOiRTN_40_ORF1_04.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD082586/20210602_SOiRTN_48_ORF1_04.raw"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["jlacava@unmc.edu"],"submitter":["Omar Guillermo Rosas Bringas"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":["Not available"],"submitter_keywords":["Human","orf1p","ip-ms","Human; ip-ms; line-1; orf1p","line-1"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD082586"],"tissue":["Permanent Cell Line Cell","Cell Culture"],"sample_protocol":["Cryomilled N2102Ep cell powder was used for affinity purification of LINE-1 ribonucleoprotein complexes (RNPs) using Dynabeads M-270 Epoxy (Invitrogen) coupled to an anti-LINE-1 ORF1p antibody (clone 4H1). Protein extraction was performed in a buffer containing 20 mM HEPES-Na (pH 7.4), 50 mM MgCl₂, and 0.1% (v/v) Tween-20. Immunoprecipitation (IP) eluates were processed using S-Trap columns as described by Zougman et al. (2014). Samples were resuspended in 25 µL of lysis buffer containing 5% (w/v) SDS, 8 M urea, 100 mM glycine (pH 7.55), and MMTS. Proteins were digested with a Trypsin/Lys-C mix (Promega, #V5071) for 1 h at 47°C. Peptides eluted from the S-Trap columns were dried and resuspended in 25 µL of water:methanol:formic acid (94.9:5.0:0.1, v/v/v) before to LC-MS/MS analysis. Raw data were acquired in data-dependent acquisition (DDA) mode. A total of 5 µL of each final sample was injected onto a 75 µm × 50 cm Acclaim PepMap RSLC nanoViper column packed with 2 µm C18 particles using a Dionex Ultimate 3000 HPLC system interfaced with an Orbitrap Exploris 480 mass spectrometer. The column temperature was maintained at 40°C. Peptides were eluted at a flow rate of 300 nL/min using a gradient of increasing acetonitrile concentration. Solvent A consisted of 0.1% formic acid in water, and solvent B consisted of 0.1% formic acid in acetonitrile. Peptides were ionized by electrospray at 1.8 kV as they eluted from the column. The 60-min elution gradient was as follows: 3% B for 3 min; 3–50% B over 45 min; 50–80% B over 2 min; 80% B for 5 min; 80–3% B over 2 min; followed by column equilibration at 3% B for 3 min. Full MS scans were acquired in profile mode at a resolution of 120,000. The 25 most intense precursor ions with charge states of +2 to +6 from each full scan were selected for fragmentation by higher-energy collisional dissociation (HCD)."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Cryomilled N2102Ep cell powder was used for affinity purification of LINE-1 ribonucleoprotein complexes (RNPs) using Dynabeads M-270 Epoxy (Invitrogen) coupled to an anti-LINE-1 ORF1p antibody (clone 4H1). Protein extraction was performed in a buffer containing 20 mM HEPES-Na (pH 7.4), 50 mM MgCl₂, and 0.1% (v/v) Tween-20. Immunoprecipitation (IP) eluates were processed using S-Trap columns as described by Zougman et al. (2014). Samples were resuspended in 25 µL of lysis buffer containing 5% (w/v) SDS, 8 M urea, 100 mM glycine (pH 7.55), and MMTS. Proteins were digested with a Trypsin/Lys-C mix (Promega, #V5071) for 1 h at 47°C. Peptides eluted from the S-Trap columns were dried and resuspended in 25 µL of water:methanol:formic acid (94.9:5.0:0.1, v/v/v) before to LC-MS/MS analysis. Raw data were acquired in data-dependent acquisition (DDA) mode. A total of 5 µL of each final sample was injected onto a 75 µm × 50 cm Acclaim PepMap RSLC nanoViper column packed with 2 µm C18 particles using a Dionex Ultimate 3000 HPLC system interfaced with an Orbitrap Exploris 480 mass spectrometer. The column temperature was maintained at 40°C. Peptides were eluted at a flow rate of 300 nL/min using a gradient of increasing acetonitrile concentration. Solvent A consisted of 0.1% formic acid in water, and solvent B consisted of 0.1% formic acid in acetonitrile. Peptides were ionized by electrospray at 1.8 kV as they eluted from the column. The 60-min elution gradient was as follows: 3% B for 3 min; 3–50% B over 45 min; 50–80% B over 2 min; 80% B for 5 min; 80–3% B over 2 min; followed by column equilibration at 3% B for 3 min. Full MS scans were acquired in profile mode at a resolution of 120,000. The 25 most intense precursor ions with charge states of +2 to +6 from each full scan were selected for fragmentation by higher-energy collisional dissociation (HCD)."],"omics_type":["Proteomics"],"labhead":["John LaCava"],"instrument_platform":[""],"labhead_affiliation":["University of Nebraska Medical Center"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["orosasbringas@rockefeller.edu"],"publication":["40832305 Damizia M, Baranzini M, Sciamanna I, Altieri L, Rovella P, Rosas Bringa OG, Hozeifi S, Saba LJ, Mourtzinos A, O'Shea A, Ansari MSZ, Andreola F, Cirilli R, Sbardella G, Serafino A, Schumann GG, Trisciuoglio D, LaCava J, Lavia P, Spadafora C. Reverse transcriptase inhibitors induce autophagy in a LINE-1 ORF1p-dependent manner. bioRxiv. 2025:2025.08.07.669170 10.1101/2025.08.07.669170"],"submitter_affiliation":["PhD"],"submitter_country":["Mexico"],"pubmed_abstract":["Human L ong Interspersed N uclear E lement-1 (LINE-1) retrotransposons propagate throughout the genome via reverse-transcribed RNA intermediates. LINE-1 expression is pervasive in cancer. Functional LINE-1s encode two proteins: ORF1p, an RNA-binding protein, and ORF2p, harboring reverse transcriptase and endonuclease activities. Reverse transcriptase inhibitors, including non-nucleoside (NNRTI) and nucleoside (NRTI) inhibitors, inhibit cancer cell proliferation and antagonize cancer progression. We previously found that two NNRTIs induced DNA damage, nuclear lamin rupture, micronuclei formation, and autophagy in prostate cancer cells. We now find that two different RTIs up-regulate LINE-1 mRNA expression and ORF1p abundance in nuclei, triggering ORF1p interactions with lamin B1 and with DNA damage factors. ORF1p accumulates within micronuclei with damaged DNA and with the autophagy receptor p62. We further demonstrate that inhibiting autophagy, or decreasing ORF1p levels, prevent DNA damage and preserve lamin B1 integrity, uncoverig a role of LINE-1-ORF1p in the autophagy response of cancer cells, independent on retrotranscription events."],"pubmed_title":["Reverse transcriptase inhibitors induce autophagy in a LINE-1 ORF1p-dependent manner."],"pubmed_authors":["Damizia Michela M, Baranzini Mirko M, Sciamanna Ilaria I, Altieri Ludovica L, Rovella Paola P, Rosas Bringa Omar G OG, Hozeifi Samira S, Saba Leila J LJ, Mourtzinos Apostolos A, O'Shea Anna A, Ansari Mohammad Salik Zeya MSZ, Andreola Federica F, Cirilli Roberto R, Sbardella Gianluca G, Serafino Annalucia A, Schumann Gerald G GG, Trisciuoglio Daniela D, LaCava John J, Lavia Patrizia P, Spadafora Corrado C"],"additional_accession":[]},"is_claimable":false,"name":"Reverse Transcriptase Inhibitors regulate LINE-1 expresion, modulate ORF1p protein interactions, and activate autophagy in cancer cells","description":"Long Interspersed Element-1 (LINE-1; L1) is an autonomous retrotransposon whose expression is frequently dysregulated in cancer. L1 encodes two proteins, ORF1p and ORF2p, which are essential for retrotransposition. Reverse transcriptase inhibitors (RTIs), including nucleoside (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs), have been reported to exert anti-cancer effects; however, the molecular mechanisms underlying these effects remain incompletely understood. This project investigates the cellular response to RTI treatment and its relationship with LINE-1 expression and activity. RTI treatment also promoted the association of ORF1p with proteins involved in transcriptional regulation, DNA damage, and nuclear architecture.","dates":{"publication":"2026-08-17","submission":"2026-08-14"},"accession":"PXD082586","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:6819","NEWT:475174","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:1589","NEWT:135622","NEWT:67352","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:36630","NEWT:383379","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:410658","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:244366","NEWT:1246791","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2853422","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:491","NEWT:460523","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:470","NEWT:5911","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:906914","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:227377","NEWT:1774284","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:105487","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:7375","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:475932","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:2925","NEWT:214053","NEWT:28550","NEWT:80863","NEWT:90675","NEWT:52638","NEWT:57075","NEWT:1666905","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:99488","NEWT:1134506","NEWT:255470","NEWT:38783","NEWT:6426","NEWT:33090","NEWT:9935","NEWT:287889","NEWT:305959","NEWT:13489","NEWT:29829","NEWT:92867","NEWT:92866","NCBITaxon:3055","NEWT:51750","NEWT:202950","NEWT:441772","NEWT:48106","NEWT:295027","NCBITaxon:11320","NEWT:632957","NEWT:992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