LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers

Longitudinal serum proteomics analyses identify unique and overlapping host response pathways in Lyme disease and West Nile virus infection

Advancement in proteomics methods for interrogating biological samples has helped identify disease biomarkers for early diagnostics and unravel underlying molecular mechanisms of disease. Herein, we examined the serum proteomes of 23 study participants presenting with one of two common arthropod-borne infections: Lyme disease (LD), an extracellular bacterial infection or West Nile virus infection (WNV), an intracellular viral infection. The LC/MS based serum proteomes of samples collected at the time of diagnosis and during convalescence were assessed using a depletion-based high-throughput shotgun proteomics (dHSP) pipeline as well as a non-depleting blotting-based low-throughput platform (MStern). The LC/MS integrated analyses identified host proteome responses in the acute and recovery phases shared by LD and WNV infections, as well as differentially abundant proteins that were unique to each infection. Notably, we also detected proteins that distinguished localized from disseminated LD and asymptomatic from symptomatic WNV infection. The proteins detected in both diseases with the dHSP pipeline identified unique and overlapping proteins detected with the non-depleting MStern platform, supporting the utility of both detection methods. Machine learning confirmed the use of the serum proteome to distinguish the infection from healthy control sera but could not develop discriminatory models between LD and WNV at current sample numbers. Our study is the first to compare the serum proteomes in two arthropod-borne infections and highlights the similarities in host responses even though the pathogens and the vectors themselves are different.

Simultaneous determination of capsid proteins in nine-valent human papilloma virus vaccines by liquid chromatography tandem mass spectrometry

A liquid chromatography-tandem mass spectrometry method was developed to determine nine types of capsid proteins simultaneously in nine-valent human papillomavirus vaccines. Signature peptides were optimized in terms of specificity, repeatability, determination accuracy and sensitivity. As a result, three signature peptides per capsid protein were obtained. The linear calibration curves were achieved in the range of 11.6-373.6 nmol/L (R²  > 0.998). Compared to our previous liquid chromatography-tandem mass spectrometry method, the current method was more sensitive (3.18-fold) and it can be used for quality evaluation of nine-valent human papillomavirus vaccines, unlike the previous method, which could only be used for bivalent human papillomavirus vaccines. Then, they were utilized to determine nine types of capsid proteins in nine-valent human papillomavirus vaccines from four different manufactures. Intraday and interday precision values for the determination of capsid proteins in nine-valent human papillomavirus vaccines were less than 6.8 and 9.1%, respectively. Recovery rates of all capsid proteins investigated were in the range of 80-120%. In addition, the current assay was used for determination of free capsid protein in nine-valent human papilloma virus vaccines, and the results were used to evaluate the adsorption rate of the adjuvant.

Quantitative Proteomics for Monitoring Renal Transplant Injury

PURPOSE

This study is aimed at developing a molecular diagnostics platform to enhance the interpretation of renal allograft biopsies using quantitative proteomic profiling of formalin-fixed and paraffin-embedded (FFPE) specimens.

EXPERIMENTAL DESIGN

A quantitative proteomics platform composed of 1) an optimized FFPE protein sample preparation method, 2) a tandem mass tag TMT10-plex-based proteomic workflow, and 3) a systematic statistical analysis pipeline to reveal differentially expressed proteins has been developed. This platform is then tested on a small sample set (five samples per phenotype) to reveal proteomic signatures that can differentiate T-cell mediated rejection (TCMR) and polyomavirus BK nephropathy (BKPyVN) from healthy functionally stable kidney tissue (STA).

RESULTS

Among 2798 quantified proteins, the expression levels of 740 BKPyVN and 638 TCMR associated proteins are significantly changed compared to STA specimens. Principal component analysis demonstrated good segregation of all three phenotypes investigated. Protein detection and quantitation are highly reproducible: replicate comparative analyses demonstrated 71-84% overlap of detected proteins, and the coefficient of variation for protein measurements is <15% in triplicate liquid chromatography-tandem mass spectrometry runs.

CONCLUSIONS AND CLINICAL RELEVANCE

Quantitative proteomics can be applied to archived FFPE specimens to differentiate different causes of renal allograft injury.

Reduction of hospital stay at maternity unit: an evaluation of the impact on maternal and neonatal readmission

In June 2015, the Belgian federal minister of public health imposed a reduction of 1 day in hospital stay at the maternity unit. This retrospective cohort study evaluated data of all patients who delivered between January 01 2010 and November 30 2015. Neonatal readmissions during the first 28 days postpartum and maternal readmissions during the first 6 weeks postpartum were studied. In total, 6009 births were included. The neonatal readmissions significantly increased (4.8% versus 6.9%, p value = .04) after June 2015. There was no significant difference in maternal readmissions between groups. In conclusion, hospital stay reduction at the maternity unit was linked with an increase of neonatal readmissions in the first 28 days postpartum, but did not have an effect on the maternal readmissions.Impact StatementWhat is already known on this subject? Many studies have evaluated the impact of early discharge on maternal and neonatal morbidity since 1950. Nevertheless, there are still concerns regarding the advantages and inconveniences of this policy. This retrospective cohort study took place in a tertiary referral centre in Belgium (CHU Tivoli) and evaluated data of all patients who delivered between January 01 2010 and November 30 2015.What the results of this study add? The readmissions for icterus increased significantly after the introduction of the reduced stay. There was no significant difference in maternal readmissions between groups.What the implications are of these findings for clinical practice and/or further research? A shorter hospital may be linked with an increase of neonatal readmissions in the first 28 days postpartum, but does not seem to have an effect on the maternal readmissions. Further prospective studies are needed in order to validate this hypothesis and also elucidate the reasons leading to a higher neonatal readmission rate.