A proteome dataset for TLR4 & IL1R activation & inhibition via FDA /EMA -approved drugs in chondrocytes, osteoblasts and synoviocytes
Mendely Data associated with: Title: A transcriptome & proteome dataset for TLR4 & IL1R activation & inhibition in chondrocytes, osteoblasts and synoviocytes Journal Title: Data in Brief Corresponding Author: Dr. Rodolfo Gomez All Authors: Eloi Franco-Trepat; María Guillán-Fresco; Ana Alonso-Pérez; Miriam López-Fagúndez; Andrés Pazos-Pérez; Antia Crespo-Golmar; Oreste Gualillo; Alberto Jorge-Mora; Susana Belén Bravo; Rodolfo Gomez DOI: PENDING The data provided is also associated as Supplementary Data to Title: Repurposing drugs to inhibit innate immune responses associated with TLR4, IL1, and NLRP3 signaling in joint cells Journal Title: Biomedicine & Pharmacotherapy Corresponding Author: Dr. Rodolfo Gomez All Authors: Eloi Franco-Trepat; María Guillán-Fresco; Ana Alonso-Pérez; Miriam López-Fagúndez; Andrés Pazos-Pérez; Antia Crespo-Golmar; Oreste Gualillo; Alberto Jorge-Mora; Susana Belén Bravo; Rodolfo Gomez DOI: doi.org/10.1016/j.biopha.2022.113671 Data Description Table 1 Merged dataset of approved drugs by the Federal Drugs Agency (FDA) & European Medicine Agency (EMA). Synonyms, formulations, and doses were included as individual entries. Table 2 Merged dataset of approved active compounds by the Federal Drugs Agency (FDA) & European Medicine Agency (EMA). Synonyms, formulations, and doses were included as individual entries. Table 3 List of all primers used in the manuscript including sequence, melting temperature and RefSeq. All primers were purchased as “KiCqStart® SYBR® Green Primers” ref. KSPQ12012 (Merck; USA). Table 4 Cellular proteome & secretome qualitative DDA data (n3) obtained by MALDI-TOFF of primary human OA chondrocytes (Control, TLR4 agonist LPS [100ng/ml] and IL1R agonist IL1β [0.1ng/ml]). Table 5 Cellular proteome quantitative SWATH data (n=3) obtained by MALDI-TOFF of primary human OA chondrocytes (Control, TLR4 agonist LPS [100ng/ml] and IL1R agonist IL1β [0.1ng/ml]).
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Data from primary OA chondrocytes were isolated from OA patients who signed informed consent and performed knee or hip arthroplasty at CHUS. Cells were plated in DMEN F12 +10% FBS, +2% Antibiotic /Glutamine, treated, and isolated by RIPA Buffer protocol. To obtain a qualitative and quantitative protein profile of the cellular proteome and secretome, micro-liquid chromatography (micro-LC) & mass spectrometry (MS/MS) was used. Briefly, a 10% SDS-PAGE gel electrophoresis of protein extracts (100 μg) from primary human OA chondrocytes was performed to extract detected protein bands by Sypro-Ruby staining. Each band was incubated (3 x20') in a 60% acetonitrile digestion solution at 0.5% HCOOH. The resulting peptides were concentrated by a lyophilizer and stored at −20 °C until use. The qualitative proteomic profile was obtained by shotgun data-dependent acquisition (DDA) analysis using micro-LC-MS/MS (SCIEX). In addition to the individual analysis of each condition, a library of MS/MS spectra was created from a mixture of all studied conditions at equal volumes. To obtain the DDA data, a microfluidic gradient system (Eksigent Technologies nanoLC 400) coupled to a reverse phase chromatography (MS/MS quadrupole-TOF/TOF 6600 hybrid) with silica-based columns (YMC Technologies, Teknokroma) was used. The shotgun DDA data acquisition (Time of flight or ToF) of the MS/MS phase was performed with “Analyst software” on a TripleTOF 6600 system. This system was externally calibrated every 4 hours using “PepCalMix software”. MS/MS data files were analyzed by “ProteinPilotTM 5.0.1 software” for database search (ParagonTM algorithm), grouping (ProgroupTM), and pairing to human protein database (Uniprot). A global false discovery rate (FDR from fit) ≤5% was set up. The quantitative proteomic profile was obtained by a complementary analysis known as sequential window acquisition of all theoretical mass spectra (SWATH). The DDA spectral library was necessarily used to create the SWATH spectral library. The SWATH data acquisition of the micro-LC MS/MS phase was performed by “PeakView 2.2 + SWATH Acquisition MicroApp 2.0 software”. Specifically, PeakView attributed an FDR to each peptide linked to MS/MS micro-LC data and the SWATH spectral library. The area under the curve was calculated for those peptides identified with an FDR value <1%. In addition, a global normalization was performed considering the total sum of technical replicas area under the curve (arbitrary units) for a specific condition. I At the statistical level, uniformity between replicates and heterogeneity between conditions were verified using an unsupervised and non-scale multivariate principal component analysis (PCA). In addition, a t-Student statistical test was used per protein to ensure statistical significance (p-value) between conditions. Data integration was processed using MarkerView software. Secondary analysis for DDA and SWATH data was performed with FunRich and STITCH software.