{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/SNAI_1-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/SNAI_3-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/SNAI_1-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/Vector_2-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/Vector_1-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/Vector_3-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/SNAI_2-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/Vector_3-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/Vector_2-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/SNAI_1-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/Vector_2-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/SNAI_3-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/Vector_3-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/SNAI_2-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/Vector_1-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/SNAI_2-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/SNAI_3-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/Vector_1-3.raw"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/670228_swp_human.FASTA"],"Mztab":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/mzTab.mzTab"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/allSpectraAPL.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061033/combined.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["vthongbo@yahoo.com"],"submitter":["Visith Thongboonkerd"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"disease":["Renal Fibrosis"],"software":[""],"submitter_keywords":["Senescence","Renal fibrosis","Snail1","Proteomics","Kidney"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD061033"],"tissue":["Epithelial Cell","Kidney"],"sample_protocol":["Generation of SNAI1-overexprssed HK-2 cell lines  A stable SNAI1-overexpressing HK-2 cell line was established by retroviral-mediated pBabe-puro-Snail transduction. The pBabe puro Snail (Addgene #23347), pUMVC (packaging plasmid gag/pol) (Addgene # 8449) and pCMV-VSV-G (packaging plasmid VSV-G) (Addgene #8454) plasmids were generously provided by Bob Weinberg, whereas pBabe-puro (empty/control vector) (Addgene #1764) plasmid was kindly provided by Hartmut Land. To produce virus particles harboring the SNAI1 gene, HEK 293T cells were plated on 100-mm culture dishes (1 × 106 cells/dish) and grown overnight before being transiently co-transfected with packaging plasmids gag/pol and VSV-G, together with the pBabe-puro-Snail plasmid or empty pBabe-puro plasmid. The culture media was then refreshed at 16 h post-transfection. Following 48 h, the supernatant containing released virus particles was collected and filtered through a 0.45 µm syringe filter before applying it to the HK-2 cells (target cells) at 40% confluence. The transduction was done at 37°C for 3 h and then replaced with a fresh complete medium (10 ml/dish) for 48 h. Cell selection was carried out using a selective medium containing 0.6 µg/mL puromycin approximately a week before use.  Preparation of cellular proteins for proteomic analysis The vector-transfected or SNAI1-overexpressed cells were seeded into a 6-well plate (approximately 4 ×105 cells/well). After 24-h incubation, cellular proteins were then extracted with SDT lysis buffer (4% SDS, 100 mM DTT, and 100 mM Tris-HCl; pH 7.6), and protein concentrations were measured using Bio-Rad protein assay (Bio-Rad; Milano, Italy) based on Bradford’s method.   In-solution tryptic digestion and analyses of proteins by nanoflow liquid chromatography coupled to tandem mass spectrometry (nanoLC-ESI-LTQ-Orbitrap MS/MS)  An equal amount (30 µg) of total proteins from each sample was subjected to in-solution tryptic digestion as described previously (1). The digested peptides were then analyzed by nanoLC-ESI-LTQ-Orbitrap MS/MS as previously reported (1, 2). References: 1. Kanlaya R, Subkod C, Nanthawuttiphan S, Thongboonkerd V. Caffeine causes cell cycle arrest at G0/G1 and increases of ubiquitinated proteins, ATP and mitochondrial membrane potential in renal cells. Comput Struct Biotechnol J. 2023;21:4552-66. 2. Wuttimongkolchai N, Kanlaya R, Nanthawuttiphan S, Subkod C, Thongboonkerd V. Chlorogenic acid enhances endothelial barrier function and promotes endothelial tube formation: A proteomics approach and functional validation. Biomed Pharmacother. 2022;153:113471"],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["MS/MS data processing and label-free quantitative analysis  The raw MS/MS files (.RAW) were analyzed by MaxQuant (version 2.1.4.0) integrated with the Andromeda search engine. The following parameters were set up for the identification of proteins against the UniProtKB/Swiss-Prot database (human): carbamidomethylation at cysteine (C) as fixed modification; oxidation at methionine (M) as a variable modification; trypsin as the proteolytic enzyme; only one missed cleavage was allowed; precursor mass tolerance was 4.5 ppm; fragment mass tolerance was 0.5 Da; and charge state ions = +2, +3. A 1% false discovery rate (FDR) cutoff was applied at both the peptide-spectrum match (PSM) and protein levels. The MaxQuant LFQ (MaxLFQ) algorithm, featuring match-between-runs, was used for label-free protein quantification (LFQ). All other MaxQuant settings were maintained at their default values as described in the previous study (3).   The obtained ProteinGroups.text was further analyzed by Perseus (version 2.0.7.0). The protein hits flagged as potential contaminants, corresponding to decoy database entries, and those identified only by site modifications were filtered out. Only proteins detected consistently across all replicates within each group were retained. The generated LFQ intensity was log2 transformed and median normalization.  Reference: 3. Tyanova S, Temu T, Cox J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc. 2016;11(12):2301-19.  Statistical analysis  All quantitative data are reported as mean ± SEM obtained from three independent biological replicates. The mean difference between the two groups was analyzed using the Student’s T-test. P-values < 0.05 were considered statistical significance."],"omics_type":["Proteomics"],"labhead":["Prof. Visith Thongboonkerd"],"instrument_platform":[""],"labhead_affiliation":["Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand"],"submission_type":["COMPLETE"],"species":["Homo Sapiens (human)"],"submitter_mail":["sirirajms@gmail.com"],"publication":["42011480 Kanlaya R, Nonthawong K, Suntivichaya M, Yoodee S, Thongboonkerd V. Deciphering the impact of &lt;i&gt;SNAI1&lt;/i&gt; gene on renal tubular cell proteome, nucleolar stress, ribosome biogenesis, senescence, DNA damage response, and focal adhesion dynamics. Genes Dis. 2026 13(4):101926 10.1016/j.gendis.2025.101926"],"submitter_affiliation":["Mahidol University"],"submitter_country":["Thailand"],"doi":["10.6019/PXD061033"],"pubmed_abstract":["Snail1, encoded by <i>SNAI1</i> gene, is an essential protein that regulates epithelial-mesenchymal transition, which leads to extracellular matrix accumulation and kidney fibrosis, but with unclear cellular and molecular mechanisms. This study compared the cellular proteome of <i>SNAI1</i>-overexpressed renal tubular cells with that of vector-control cells by label-free quantitative proteomics, followed by functional assessments using various assays. A total of 233 proteins showed significant changes in their levels by ectopic <i>SNAI1</i> expression. Of these, immunoblotting confirmed the decreases in HSP60 and HSP70 and the increase in DDX1. Bioinformatic analyses revealed the top 10 transcription factors as key upstream regulators of the altered cellular proteome, and translational regulation, ribosome, cell cycle regulation, and cellular senescence were primarily associated with these altered proteins. Gene ontology enrichment showed that focal adhesion, the structure where cells maintain their interior-extracellular matrix interactions, was one of the major affected cellular components. Experimental validations demonstrated that <i>SNAI1</i>-overexpressed cells displayed increases in nucleophosmin, nucleolar organizer regions, cell size, granularity, p21, γH2AX, MMP-9 secretion, and paxillin expression, confirming the bioinformatic predictions. This study has broadened our knowledge of Snail1 functions beyond its established role as the epithelial-mesenchymal transition regulator. In addition to alterations in the cellular proteome, ectopic <i>SNAI1</i> expression induced nucleolar stress, ribosome biogenesis, senescence, and DNA damage response in renal tubular cells. Moreover, Snail1 also affected the dynamics of focal adhesion, which is imperative for cell migration, by regulating paxillin expression. These findings may offer new therapeutic targets related to Snail1-dependent mechanisms for effective management of kidney fibrosis."],"pubmed_title":["Deciphering the impact of &lt;i&gt;SNAI1&lt;/i&gt; gene on renal tubular cell proteome, nucleolar stress, ribosome biogenesis, senescence, DNA damage response, and focal adhesion dynamics."],"pubmed_authors":["Kanlaya Rattiyaporn R, Nonthawong Kanokwan K, Suntivichaya Mueanchan M, Yoodee Sunisa S, Thongboonkerd Visith V"],"additional_accession":[]},"is_claimable":false,"name":"Deciphering the impact of ectopic SNAI1 expression on renal tubular cell proteome and functions","description":"Snail1 is crucial in regulating epithelial mesenchymal transition (EMT), which leads to excessive extracellular matrix (ECM) production and organ fibrosis including the kidney. Elucidating the roles of snail1 in EMT and kidney fibrosis is thus vital for developing targeted therapies. This study investigated the alterations in the proteome of SNAI1-overexpressed proximal tubular epithelial cells over the vector-transfected cells by label-free quantitative proteomics. Of 670 identified proteins, 233 showed significant changes due to ectopic snail1 expression. Of these, immunoblotting confirmed the decreased HSP60 and HSP70 while increased DDX1. X2K Appyter predicted the top ten transcription factors as key upstream regulators of the altered proteome. KEGG enrichment analysis revealed that these altered proteins were primarily associated with translational regulation, ribosome, cell cycle regulation, and cellular senescence. GO enrichment showed that focal adhesion, the structure where cells maintain cell interior-ECM interactions, was markedly overrepresented. Accordingly, functional validations demonstrated that SNAI1-overexpressed cells displayed aberrant ribosome biogenesis, indicated by increasing nucleophosmin and the nucleolar organizer regions. SNAI1-overexpressed cells exhibited senescent phenotypes including cell enlargement and increased granularity, up-regulated senescent makers p21 and γH2AX, and enhanced MMP-9 secretion. Moreover, SNAI1-overexpressed cells up-regulated paxillin, a scaffold protein located at focal adhesions crucial for their dynamic regulation. These findings provide insights into the molecular processes governed by snail1 during renal tubular cells undergoing EMT.","dates":{"publication":"2026-04-27","submission":"2025-02-21"},"accession":"PXD061033","cross_references":{"TAXONOMY":["NEWT:1773","NEWT:6945","NEWT:3555","NEWT:38783","NEWT:8727","NEWT:1182590","NEWT:8726","NEWT:2","NEWT:157546","NEWT:10090","NEWT:935293","NEWT:749200","NEWT:35554","NEWT:4120","NEWT:5693","NEWT:9417","NEWT:347515","NEWT:8724","NEWT:51511","NEWT:1216979","NEWT:307972","NEWT:92867","NEWT:8723","NEWT:990346","NEWT:544496","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:5180","NEWT:284812","NEWT:115104","NCBITaxon:1313","NEWT:1081927","NEWT:43330","NEWT:67825","NEWT:44544","NEWT:13076","NEWT:1249668","NEWT:373995","NEWT:544404","NEWT:3702","NEWT:8839","NEWT:317","NEWT:4232","NEWT:990119","NEWT:1736309","NEWT:4113","NEWT:7227","NEWT:11298","NEWT:7469","NEWT:885318","NEWT:171101","NEWT:4081","NEWT:876138","NEWT:554","NEWT:5691","NEWT:98334","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:627025","NEWT:400772","NEWT:3708","NEWT:106592","NEWT:237561","NEWT:9913","NEWT:10036","NEWT:4100","NEWT:7574","NEWT:1351","NEWT:1076","NEWT:6763","NEWT:7215","NEWT:803","NEWT:8030","NEWT:380394","NEWT:272563","NEWT:507601","NEWT:1639","NEWT:188229","NEWT:4909","NCBITaxon:79857","NEWT:95648","NEWT:746360","NEWT:6239","NEWT:1589","NEWT:135588","NEWT:470150","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:95486","NEWT:3880","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:5664","NEWT:2157","NEWT:146479","NEWT:1911079","NEWT:1000589","NEWT:145943","NEWT:1902","NEWT:85962","NEWT:160488","NEWT:317447","NEWT:3635","NEWT:7955","NCBITaxon:2","NEWT:1480154","NEWT:7959","NEWT:2261","NEWT:3197","NEWT:9615","NEWT:884019","NEWT:4565","NEWT:1264690","NEWT:169963","NCBITaxon:38727","NEWT:36329","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:9606","NEWT:367830","NEWT:157295","NEWT:243230","NEWT:931281","NEWT:373153","NEWT:7029","NEWT:915099","NEWT:1283300","NEWT:334747","NEWT:470","NCBITaxon:79824","NCBITaxon:4563","NEWT:3218","NEWT:84023","NEWT:5759","NEWT:9838","NCBITaxon:9615","NEWT:1736231","NEWT:1193501","NEWT:3055","NEWT:6287","NEWT:2242","NEWT:6326","NEWT:9796","NEWT:2762","NEWT:5476","NEWT:725","NEWT:1174673","NEWT:562","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:1735272","NEWT:29760","NEWT:260705","NEWT:80863","NEWT:1148","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:3603","NEWT:698936","NEWT:2759","NEWT:39946","NEWT:11676","NEWT:9823","NEWT:100226","NCBITaxon:6073","NEWT:4530","NEWT:4896","NEWT:6279","NEWT:7370","NEWT:573","NEWT:6282","NEWT:7091","NEWT:1134506"],"pubmed":["42011480"]}}