Antonio Lario

Increased expression and phosphorylation of the two S100A9 isoforms in mononuclear cells from patients with systemic lupus erythematosus: a proteomic signature for circulating low-density granulocytes.

Proteins differentially expressed in peripheral blood mononuclear cells (PBMCs) from systemic lupus erythematosus (SLE) patients versus Normal controls were identified by 2-DE and MALDI-MS. Thus, S100A9 expression was significantly increased in SLE PBMCs relative to Normal PBMCs at both mRNA and protein levels. Increased S100A9 levels in SLE PBMCs correlated positively with the abnormal presence of low-density granulocytes (LDGs) detected by flow-cytometry in the mononuclear cell fractions. Another set of proteins that were differentially expressed in SLE PBMCs formed S100A9-independent clusters, suggesting that these differences in protein expression are in fact reflecting changes in the abundance of specific cell types. In SLE PBMCs spots of the two S100A9 isoforms, S100A9-l and S100A9-s, and their phosphorylated counterparts were identified and confirmed to be phosphorylated at Thr(113) by MS/MS analyses. In addition, the phorbol ester PMA alone or in combination with ionomycin induced a stronger increase in threonine phosphorylation of S100A9 in SLE than in Normal PBMCs, while the same stimuli caused the opposite effect on phosphorylation and activation of Erk1/2, suggesting the existence of an abnormal S100A9 signaling in SLE PBMCs. Therefore, the expansion and activation of LDGs in SLE seems to underlie this prominent S100A9 signature.

Identification of multiple transferrin species in the spleen and serum from mice with collagen-induced arthritis which may reflect changes in transferrin glycosylation associated with disease activity: The role of CD38.

UNLABELLED Collagen type II-induced arthritis (CIA) is an inflammatory and autoimmune disease. Spleen protein extracts were subjected to 2D-DiGE and MS-MALDI-TOF/TOF analysis to identify protein species that differ in abundance in CD38-KO versus B6 WT mice either with arthritis or with inflammation. Using multivariate analyses, in Col-II-immunized mice, 23 distinct spleen protein species were able to discriminate between WT and CD38-KO mice. Among them, several citrullinated proteins and multiple serotransferrin (Tf) species were identified. In contrast, in CFA/IFA-treated mice, the distinct protein profile, which discriminates between CD38-KO and WT mice, was unrelated with Tf, but not with citrullination. Unexpectedly, non-immunized CD38-KO mice showed a distinct proteome profile as compared with that in non-immunized WT mice, and again multiple protein species were identified as Tf. By using a μLC-TOF-MS method to separate and detect Tf glycopeptide glycoforms, increases in fucosylation and glycan branching was observed in sera from mice CIA(+) versus non-immunized, and between WT and CD38-KO with arthritis. Data on 2-DE Tf spots indicated differences in glycosylation related with NeuGc content. Thus, Tf changed significantly in its glycosylation pattern in arthritic mice. The MS data have been deposited to the ProteomeXchange Consortium with the dataset identifiers: PXD002644, PXD002643, PXD003183, and PXD003163. SIGNIFICANCE 2-DE followed by μLC-TOF-MS could be implemented to identify Tf glycoforms linked to specific protein species, and correlate a particular Tf species to a function. To gain insight into the relationship between transferrin glycoforms and its biological function it is particularly interesting to study putative differences in the glycosylation pattern of Tf in specific tissues associated with the disease (i.e.: joints), or in specific compartments such as exosomes/microvesicles, which are highly enriched in Tf receptors.

Distinct serum proteome profiles associated with collagen-induced arthritis and complete Freund's adjuvant-induced inflammation in CD38-/- mice: The discriminative power of protein species or proteoforms

Collagen‐type‐II‐induced arthritis (CIA) is an autoimmune disease, which involves a complex host systemic response including inflammatory and autoimmune reactions. CIA is milder in CD38−/− than in wild‐type (WT) mice. ProteoMiner‐equalized serum samples were subjected to 2D‐DiGE and MS‐MALDI‐TOF/TOF analyses to identify proteins that changed in their relative abundances in CD38−/− versus WT mice either with arthritis (CIA+), with no arthritis (CIA−), or with inflammation (complete Freunds adjuvant (CFA)‐treated mice). Multivariate analyses revealed that a multiprotein signature (n = 28) was able to discriminate CIA+ from CIA− mice, and WT from CD38−/− mice within each condition. Likewise, a distinct multiprotein signature (n = 16) was identified which differentiated CIA+ CD38−/− mice from CIA+ WT mice, and lastly, a third multiprotein signature (n = 18) indicated that CD38−/− and WT mice could be segregated in response to CFA treatment. Further analyses showed that the discriminative power to distinguish these groups was reached at protein species level and not at the protein level. Hence, the need to identify and quantify proteins at protein species level to better correlate proteome changes with disease processes. It is crucial for plasma proteomics at the low‐abundance protein species level to apply the ProteoMiner enrichment. All MS data have been deposited in the ProteomeXchange with identifiers PXD001788, PXD001799 and PXD002071 (http://proteomecentral.proteomexchange.org/dataset/PXD001788, http://proteomecentral.proteomexchange.org/dataset/PXD001799 and http://proteomecentral.proteomexchange.org/dataset/PXD002071).

A multicentric study to evaluate the use of relative retention times in targeted proteomics

Despite the maturity reached by targeted proteomic strategies, reliable and standardized protocols are urgently needed to enhance reproducibility among different laboratories and analytical platforms, facilitating a more widespread use in biomedical research. To achieve this goal, the use of dimensionless relative retention times (iRT), defined on the basis of peptide standard retention times (RT), has lately emerged as a powerful tool. The robustness, reproducibility and utility of this strategy were examined for the first time in a multicentric setting, involving 28 laboratories that included 24 of the Spanish network of proteomics laboratories (ProteoRed-ISCIII). According to the results obtained in this study, dimensionless retention time values (iRTs) demonstrated to be a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups both intra- and inter-laboratories. iRT values also showed very low variability over long time periods. Furthermore, parallel quantitative analyses showed a high reproducibility despite the variety of experimental strategies used, either MRM (multiple reaction monitoring) or pseudoMRM, and the diversity of analytical platforms employed. BIOLOGICAL SIGNIFICANCE From the very beginning of proteomics as an analytical science there has been a growing interest in developing standardized methods and experimental procedures in order to ensure the highest quality and reproducibility of the results. In this regard, the recent (2012) introduction of the dimensionless retention time concept has been a significant advance. In our multicentric (28 laboratories) study we explore the usefulness of this concept in the context of a targeted proteomics experiment, demonstrating that dimensionless retention time values is a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups.