Using one–to–many urine proteome comparisons to provide clues for fever of unknown origin

ObjectiveTo provide diagnostic evidence and clues for patients with fever of unknown origin (FUO) through urine proteomics analysis.MethodsUrine samples of FUO were one–to–many analysed by using liquid chromatography tandem mass spectrometry(LC–MS/MS) to identify differential proteins and related biological pathways. One–to–many analysis means a comparative analysis of one sample to many controls.ResultsWe observed biological pathways related to fever, such as LXR/RXR activation, FXR/RXR activation and acute phase response signaling, etc., which indicates that urine can obviously distinguish disease from health status. In addition, we found that the results of each sample were different, which highlight the necessity of one–to–many analysis.ConclusionsThe combined method of urine proteomics and one–to–many analysis can provide clues for FUO, and might also be applied to the exploration of any unknown disease.

Urine Proteomics Differentiate Primary Thrombotic Antiphospholipid Syndrome From Obstetric Antiphospholipid Syndrome

Antiphospholipid syndrome (APS) is a multisystem disorder characterized by thrombosis and/or recurrent fetal loss. This clinical phenotype heterogeneity may result in differences in response to treatment and prognosis. In this study, we aimed to identify primary thrombotic APS (TAPS) from primary obstetric APS (OAPS) using urine proteomics as a non-invasive method. Only patients with primary APS were enrolled in this study from 2016 to 2018 at a single clinical center in Shanghai. Urine samples from 15 patients with TAPS, 9 patients with OAPS, and 15 healthy controls (HCs) were collected and analyzed using isobaric tags for relative and absolute quantification (iTRAQ) labeling combined with liquid chromatography-tandem mass spectrometry analysis to identify differentially expressed proteins. Cluster analysis of urine proteomics identified differentiated proteins among the TAPS, OAPS, and HC groups. Urinary proteins were enriched in cytokine and cytokine receptor pathways. Representative secreted cytokines screened out (fold change >1.20, or <0.83, p<0.05) in these differentiated proteins were measured by enzyme-linked immunosorbent assay in a validation cohort. The results showed that the levels of C-X-C motif chemokine ligand 12 (CXCL12) were higher in the urine of patients with TAPS than in those with OAPS (p=0.035), while the levels of platelet-derived growth factor subunit B (PDGFB) were lower in patients with TAPS than in those with OAPS (p=0.041). In addition, correlation analysis showed that CXCL12 levels were positively correlated with immunoglobulin G anti-β2-glycoprotein I antibody (r=0.617, p=0.016). Our results demonstrated that urinary CXCL12 and PDGFB might serve as potential non-invasive markers to differentiate primary TAPS from primary OAPS.

Molecular analysis of prostate cancer: prostate tissue and urine proteomics based approach

Benign prostatic hyperplasia (BPH) and prostate cancer are the most frequently diagnosed conditions in men above 60 years. BPH manifests as benign enlargement of the prostate gland causing pain and difficulty in micturition, often associated with other lower urinary tract symptoms. On the other hand, prostate cancer might initially set in as a tumor of no clinical significance, but can ultimately develop into an aggressively metastatic cancer at later stages. Due to overlapping symptomatic manifestations with BPH, it might be difficult to diagnose prostate cancer and differentiate it from BPH. Screening for prostate cancer is based on examining the levels of prostate specific antigen (PSA), a clinical biomarker for prostate cancer in blood. However, several reported cases indicate that PSA might lack the sensitivity and specificity required to differentiate between the cancerous and benign conditions of prostate. Therefore, in the absence of non-invasive biomarkers in a diagnostic setup, an intensely invasive surgical removal of a part of the tissue and subsequent histopathologial examination is the only available procedure to confirm the cancer. In this study, we used tissue and urine proteomics platforms to profile respective proteomes in both clinical conditions. We observed that latent transforming growth factor binding protein was significantly under-expressed in the both tissue and urine proteome of prostate cancer. We propose that the down-regulation of the latent transforming growth factor binding protein 4 might be explored in a large set of patients with prostate cancer to develop a non-invasive urine based biomarker for the diagnosis of prostate cancer.

Integration of urine proteomics and renal single-cell genomics identifies an interferon-gamma response gradient in lupus nephritis

Lupus nephritis, one of the most serious manifestations of systemic lupus erythematosus (SLE), has both a heterogeneous clinical and pathological presentation. For example, proliferative nephritis identifies a more aggressive disease class that requires immunosuppression. However, the current classification system relies on the static appearance of histopathological morphology which does not capture differences in the inflammatory response. Therefore, a biomarker grounded in the disease biology is needed to understand the molecular heterogeneity of lupus nephritis and identify immunologic mechanism and pathways. Here, we analyzed the patterns of 1000 urine protein biomarkers in 30 patients with active lupus nephritis. We found that patients stratify over a chemokine gradient inducible by interferon-gamma. Higher values identified patients with proliferative lupus nephritis. After integrating the urine proteomics with the single-cell transcriptomics of kidney biopsies, it was observed that the urinary chemokines defining the gradient were predominantly produced by infiltrating CD8 T cells, along with natural killer and myeloid cells. The urine chemokine gradient significantly correlated with the number of kidney-infiltrating CD8 cells. These findings suggest that urine proteomics can capture the complex biology of the kidney in lupus nephritis. Patient-specific pathways may be noninvasively tracked in the urine in real time, enabling diagnosis and personalized treatment.