Participants
To perform this study, we included a control group of 66 volunteer normal-weight women (BMI = 19-25kg/m2) and 129 women with MO (BMI > 40kg/m2) scheduled to undergo laparoscopic bariatric surgery. Only women were included to avoid heterogeneity, as men and women present differences in metabolic parameters [13,14].
Of the 129 patients with MO, 54 were metabolically healthy, meaning they did not present metabolic alterations such as T2DM, dyslipidemia or hypertension, despite having MO. On the other hand, 75 had been diagnosed with T2DM, meeting the diagnostic criteria of the American Diabetes Association (ADA) [15]. Subjects without T2DM but presenting other metabolic alterations were excluded from this study since they comprised a small and heterogeneous group.
Using the GRANMO sample size calculator (v.7.04), accepting an alpha risk of 0.05 and a beta risk less than 0.2 in a bilateral contrast, we need at least 174 cases (MO) and 57 controls (normal-weight) to detect a minimum odds ratio of 0.25. It is assumed that the exposure rate in the control group will be 0.25. A loss of follow-up rate of 0 has been estimated. The POISSON approximation was used.
Exclusion criteria included acute illness, acute or chronic inflammatory or infective diseases, end-stage malignant disease, menopausal status, contraceptive treatment, alcohol intake exceeding 20 g per day and recurrent smoking.
This study was approved by the Ethics Committee of IISPV (CEIm; 23c/2015). All participants gave written informed consent. This study was conducted retrospectively by accessing the patient data collected from 2014 until 2023. During data collection and analysis, the authors did not have access to patient identifiers, working with blind and encrypted data in a RedCap database.
Biochemical, Anthropometric and Clinical parameters
Anthropometrical variables such as weight, height, BMI, waist-hip ratio, systolic blood pressure (SBP) and diastolic blood pressure (DBP) were obtained from each participant. Biochemical variables were measured from blood samples obtained by specialized nurses using a BD Vacutainer® system after overnight fasting and just before bariatric surgery in subjects with MO. Blood samples were collected and processed into plasma and serum aliquots. Serum aliquots were obtained using tubes without anticoagulant after allowing the blood to clot and stored at −80°C until proteomics processing. Plasma aliquots were obtained from EDTA tubes via centrifugation at 3500 rpm for 15 min at 4 °C. Biochemical variables included glucose, insulin, glycosylated hemoglobin A1c (HbA1c), triglycerides, total cholesterol, high density lipoprotein-cholesterol (HDL-C) and low density lipoprotein-cholesterol (LDL-C) measured using a conventional automated analyzer.
Proteomic Analysis
Protein Extraction and Quantification for Serum Samples:
Before proteomic analysis, the most abundant plasma proteins (albumin, immunoglobulin (Ig)G, antitrypsin, IgA, transferrin, haptoglobin, fibrinogen, alpha2-macroglobulin, alpha1-acid glycoprotein, IgM, apolipoprotein AI, apolipoprotein AII, complement C3 and transthyretin) were depleted to increase the number of identified/quantified proteins. Ten microliters of each sample were passed twice through the Human-14 Multiple Affinity Removal Spin (MARS) cartridge (Agilent Technologies, Catalog Number 5188-6560) following the manufacturer’s protocol. Flow-through fractions were concentrated and buffer exchanged to about 100 μl of 6M urea in 50 mM ammonium bicarbonate (ABC) using 5K MWCO spin columns (Agilent 5185-5991).
Protein Digestion and Peptide 11-plex TMT Labelling:
Twenty-five micrograms of total protein (quantified by Bradford’s method) were reduced with 4 mM 1,4-dithiothreitol (DTT) for 1 hour at 37°C and alkylated with 8 mM iodoacetamide (IAA) for 30 minutes at 25°C in the dark. Samples were then digested overnight (pH 8.0, 37°C) with sequencing-grade Trypsin/Lys-C Protease Mix (ThermoFisher Scientific, CA, USA) at an enzyme ratio of 1:50. Digestion was quenched by acidification with 1% (v/v) formic acid, and peptides were desalted on Oasis HLB SPE columns (Waters, Massachusetts, USA) before TMT 11-plex labelling (ThermoFisher Scientific, CA, USA) following the manufacturer’s instructions. Briefly, samples were resuspended with triethyl ammonium bicarbonate (TEAB) 100 mM, then each TMT channel, previously prepared with CAN, was added to each sample according to Supplementary Table 1.
To normalize all samples across different TMT-multiplexed batches, a pool containing all samples was labelled with the TMT-126 tag and included in each TMT batch. Then, each plex of samples was mixed also according to Supplementary Table 1 and the different TMT 11-plex batches were desalted on Oasis HLB SPE columns before nanoLC-MS analysis.
NanoLC-(Orbitrap)MS/MS Analysis:
Labelled and multiplexed peptides were loaded on a trap nano-column (75 μm I.D.; 1.5 cm length; 3 μm particle diameter, ThermoFisher Scientific, CA, USA) and separated onto a C-18 reversed phase (RP) μPAC™ Neo HPLC column (180 μm bed; 50 cm length; 2.5 x 16 μm pillar diameter, ThermoFisher Scientific, CA, USA) on a Vanquish Neo VN-S10 System (ThermoFisher Scientific). Chromatographic separation was performed with a 180-minute gradient using water LC-MS grade (0.1% formic acid) and acetonitrile (0.1% formic acid) as mobile phases at a flow rate of 300 nL/min.
Mass spectrometry (MS) analyses were performed on an Orbitrap Eclipse from ThermoFisher Scientific by an enhanced FT-resolution MS spectrum (R=60,000 FHMW) followed by data-dependent FT-MS/MS acquisition (R=50,000 FHMW, 30% NCE HCD) from the ten most intense parent ions with a charge state acquisition from two to six and dynamic exclusion of 0.7 min.
Protein Identification and Quantification:
Protein identification and quantification were performed using Proteome Discoverer software v.2.5 (ThermoFisher Scientific, CA, USA) with the Mascot search engine (v2.8, Matrix Science) combining raw data files obtained from each plex. For protein identification, the workflow used the Mascot node combining Homo sapiens and contaminants databases, assuming trypsin digestion. The fragment ion mass tolerance assumed an error of 20 mmu for FT-MS/MS fragmentation mass and 10 ppm for FT-MS precursor ion mass. Oxidation of methionine and acetylation of the N-terminal were set as dynamic modifications, carbamidomethylation as a static modification, and TMT-11plex as a quantitation method. The false discovery rate (FDR) and protein probabilities were calculated by Percolator, with peptide identification set to a maximum of 1%. Peptide quantitation data were retrieved from the ‘Reporter ions quantifier’ node in Proteome Discoverer, using the area of unique and razor peptides and total peptide amount as normalization. Peptide and protein results are expressed in abundance area and are dimensionless.
Statistical analysis
Descriptive data of the patients (anthropometric and biochemical variables) were analyzed using the SPSS/PC+ for Windows statistical package (version 27.0; SPSS, Chicago, Illinois, USA). The Kolmogorov-Smirnov test assessed the distribution of variables. Variables were presented as the median and interquartile range because they exhibited a non-normal distribution. Comparative analyses were conducted using the nonparametric Mann-Whitney U test. P-values <0.05 were considered statistically significant.
For the proteomics data obtained, only proteins identified in >60% of samples in at least one of the experimental groups were considered. Missing value estimation after data filtering was performed using the KNN (k-nearest neighbors) algorithm from MetaboAnalyst software v5.0 for univariate and multivariate statistical analysis. For statistical analysis of the proteomics data, a log base 2 data transformation was applied, and one-way ANOVA with Tukey HSD post hoc and Benjamini-Hochberg FDR correction was performed between groups, with a p-value cut-off of <0.05. Hierarchical clustering heatmaps for the top 25 proteins in each comparison were performed with Euclidean distance measure and Ward clustering method using MetaboAnalyst software v5.0.
Cytoscape software v3.10.2, with the ClueGO plugin, was used to perform gene enrichment analysis and pathway clustering. STRING was used as the database to obtain information on the included proteins, focusing exclusively on Homo sapiens, and for conducting the gene enrichment analysis. ClueGO served as the plugin to perform functional analysis of the proteins and their interactions. We selected the Reactome database to identify pathways developed by the included proteins, setting a medium network specificity and displaying only pathways with a p-value less than 0.05, with Benjamini-Hochberg p-value correction applied. The remaining parameters were kept at their default settings, including GO term grouping and preferred layout.