{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/160404_NJ_EGFR_GluC__FDR.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/Table_S1.xlsx"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/160404_NJ_EGFR_GluC_ProteinSummary.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/160404_NJ_EGFR_GluC_PeptideSummary.txt"],"Xml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/160404_NJ_EGFR_GluC.xml"],"Wiff":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/170403_NJ_FT_B1.wiff","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/170403_NJ_FT_A1.wiff.scan","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/170403_NJ_GL_B1.wiff","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/170403_NJ_GL_A1.wiff","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/170403_NJ_GL_B1.wiff.scan","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/170403_NJ_FT_B1.wiff.scan","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/160404_NJ_EGFR_GluC.wiff","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/170403_NJ_FT_A1.wiff","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/160404_NJ_EGFR_GluC.wiff.scan","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/170403_NJ_GL_A1.wiff.scan"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/Homo_sapiens_sprot_canonical_170307_MQContam.fasta"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/andromeda.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/txt.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD014766/160404_NJ_EGFR_GluC.group"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["kvido.strisovsky@uochb.cas.cz"],"submitter":["Jana Brezinova"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"software":[""],"submitter_keywords":[""],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD014766"],"tissue":["Cell Culture","Keratinocyte"],"sample_protocol":["The mixture of collected media of differentially labelled proteins were concentrated using 2000 MWCO filters (Vivaspin 15R, Sartorius, Germany) to 1/50 of their starting volume. Glycoprotein enrichment was performed using commercial concanavalin A (ConA) and wheat germ agglutinin (WGA) glycoprotein isolation kits (ThermoFisher Scientific, USA) according to supplier’s protocol with the following modifications; 640 µL of concentrated media was enriched using a mixture of both resins, precisely 100 µL ConA and 100 µL WGA resins, and the flow-through was also collected for proteomic analysis. Additionally, the incubation time before final elution of glycoproteins was increased to 10 minutes in each instance. Both flow through (FT) and the glycoprotein fractions (GL) were subjected to the standard enhanced filter-aided sample preparation protocol without passivation employing below stated adjustments (Erde, Loo et al., 2014). The protocol was followed starting from sample processing steps, the pH of FT and GL sample fractions was adjusted with 40 and 20 ul 1M ammonium bicarbonate, respectively. TCEP was added to final concentration of 5 mM and incubated at 37°C for 30 min followed by 30 min centrifugation at 14,000×g. The subsequent steps such as buffer exchange and alkylation were performed as described previously. GL sample fractions were additionally deglycosylated on filter for 1 hour at 37 °C using 2 units of PNGase F (proteomic grade, Sigma Aldrich) prior to trypsin digestion. The sample assessing EGFR cleavage was reconstituted in 150 µL of 100 mM ammonium bicarbonate, incubated with 5 mM DTT at 65 °C for 30 min and alkylated with 12.5 mM iodoacetic acid (IAA) in dark at room temperature for 30 min. Excess of the alkylating reagent was quenched using 8 mM DTT. The proteins were digested using 0.1 µg GluC protease (Promega) for 14 hours at 37 °C. The detergent RapiGest SF (Waters) was removed according to the supplier’s protocol, sample was desalted and evaporated prior to measurement. Prior to the measurement the peptides were reconstituted in 20 µl of 2% (v/v) acetonitrile/0.1% (v/v) formic acid. The LC-MS/MS analysis was performed on an UltiMate 3000 RSLCnano system (Dionex) coupled to a TripleTOF 5600 mass spectrometer with a NanoSpray III source (AB Sciex). After injection the peptides were trapped and desalted in 2% (v/v) acetonitrile/0.1 % formic acid at a flow rate of 5 μL/min on an Acclaim® PepMap100 column (5 μm, 2 cm × 100 μm ID, Thermo Scientific) for 10 minutes. The separation of peptides was performed on an Acclaim® PepMap100 analytical column (3 μm, 25 cm × 75 μm ID, Thermo Scientific) using a gradient from 2% to 30% of acetonitrile over 95 min with a subsequent rise to 95 % (v/v) of acetonitrile/0.1% formic acid. The sample assessing EGFR cleavage was measured using a shorter liquid chromatography method with only 5 min peptide trapping and a gradient rise from 2% to 30% of acetonitrile over 48 min. TOF MS scans were recorded from 350 to 1250 m/z, up to 25 candidate ions per cycle (or 18 in case of the EGFR cleavage sample) were subjected to fragmentation, dynamic exclusion was set for 12 s after one occurrence. In MS/MS mode the fragmentation spectra were acquired within the mass range of 100 – 1600 m/z."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["The quantitative mass spectrometric data files were processed and analysed using MaxQuant (v1.5.2.8). The search was performed using a Uniprot/Swissprot canonical human (downloaded 17/03/07) with common contaminants included. Enzyme specificity was set to trypsin, with variable modifications, methionine oxidation and protein N-acetylation. Cysteine carbamidomethylation was considered a fixed modification. Heavy labels were set to R10K8, a minimal peptide length to 6, and 2 missed cleavages were allowed. Proteins were considered identified if they had at least one unique peptide, and quantified if they had at least one quantifiable SILAC pair. The resulting MaxQuant (Cox & Mann, 2008) protein table was processed using Perseus 1.5.6.0 (Tyanova, Temu et al., 2016) using Phobius (Käll, Krogh et al., 2004) topology predictions implemented by QARIP (Ivankov, Bogatyreva et al., 2013) (see Table S1 - raw files _A1 and _B1 correspond to wt(H) & RNAi(L) and wt(L) & RNAi(H) experiments, respectively)."],"omics_type":["Proteomics"],"labhead":["Kvido Strisovsky"],"instrument_platform":[""],"labhead_affiliation":["Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Flemingovo n. 2, Prague, 166 10, Czech Republic"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["jana.brezinova@uochb.cas.cz"],"publication":["42771030 Johnson N, Dohnálek J, Březinová J, Čáslavský J, Škarková A, Jobe N, Fliegl M, Trávníčková K, Burbridge E, Canbay V, Christiansen CR, Auf dem Keller U, Lábaj J, Fedosieieva O, Procházka J, Rösel D, Brábek J, Vomastek T, Adrain C, Stříšovský K. Rhomboid protease RHBDL2 is a calcium-activated suppressor of EGFR signalling in keratinocytes. Cell Mol Life Sci. 2026 83(1):342 10.1007/s00018-026-06377-w"],"submitter_affiliation":["Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Flemingovo n. 2,\nPrague, 166 10, Czech Republic"],"submitter_country":["Czech Republic"],"pubmed_abstract":["Signalling via the epidermal growth factor receptor (EGFR) is indispensable for morphogenesis and tissue homeostasis. It is activated by extracellular ligands, typically released from transmembrane precursors by proteolysis. Ligand shedding activity is provided by the conserved rhomboid intramembrane serine proteases in Drosophila, but by the unrelated ADAM family metalloproteases in mammals, leaving the functions of mammalian non-mitochondrial rhomboids underexplored. Using quantitative proteomics, we show that EGFR is the main endogenous substrate of the human rhomboid protease RHBDL2 in keratinocytes. By shedding the EGFR ectodomain, thus producing a decoy receptor, RHBDL2 suppresses EGFR signalling, limiting cell migration and invasion. Conspicuously, RHBDL2 activity is upregulated by elevated intracellular calcium concentration, a condition typical of keratinocyte differentiation. These effects are recapitulated in primary human keratinocytes, and human skin equivalents deficient in RHBDL2 display incomplete differentiation and are morphologically disordered compared to wild-type cells. We propose that context-specific fine-tuning of EGFR signalling and sensitivity to cross-talk from other signalling pathways could be important and hitherto overlooked roles of rhomboid proteases in mammals."],"pubmed_title":["Rhomboid protease RHBDL2 is a calcium-activated suppressor of EGFR signalling in keratinocytes."],"pubmed_authors":["Johnson Nicholas N, Dohnálek Jan J, Březinová Jana J, Čáslavský Josef J, Škarková Aneta A, Jobe Njainday N, Fliegl Monika M, Trávníčková Květa K, Burbridge Emma E, Canbay Vahap V, Christiansen Chatpakorn Rassameena CR, Auf dem Keller Ulrich U, Lábaj Juraj J, Fedosieieva Olha O, Procházka Jan J, Rösel Daniel D, Brábek Jan J, Vomastek Tomáš T, Adrain Colin C, Stříšovský Kvido K"],"additional_accession":[]},"is_claimable":false,"name":"Rhomboid protease RHBDL2 is a calcium-activated suppressor of EGFR signalling in keratinocytes.","description":"Signalling via the epidermal growth factor receptor (EGFR) is indispensable for morphogenesis and tissue homeostasis. It is activated by extracellular ligands, typically released from transmembrane precursors by proteolysis. Ligand shedding activity is provided by the conserved rhomboid intramembrane serine proteases in Drosophila, but by the unrelated ADAM family metalloproteases in mammals, leaving the functions of mammalian non-mitochondrial rhomboids underexplored. Using quantitative proteomics, we show that EGFR is the main endogenous substrate of the human rhomboid protease RHBDL2 in keratinocytes. By shedding the EGFR ectodomain, thus producing a decoy receptor, RHBDL2 suppresses EGFR signalling, limiting cell migration and invasion. Conspicuously, RHBDL2 activity is upregulated by elevated intracellular calcium concentration, a condition typical for keratinocyte differentiation. These effects are recapitulated in primary human keratinocytes, and human skin equivalents deficient in RHBDL2 display incomplete differentiation and are morphologically disordered compared to wild type cells. We propose that context-specific fine-tuning of EGFR signalling and sensitivity to cross-talk from other signalling pathways could be important and hitherto overlooked roles of rhomboid proteases in 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