Female urinary proteomics: New insight into exogenous and physiological hormone-dependent changes

Recent progress in mass spectrometry-based urinary proteomics

Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.

Assessment of Urinary Biomarkers for Infectious Diseases Using Lateral Flow Assays: A Comprehensive Overview

Screening of biomarkers is a powerful approach for providing a holistic view of the disease spectrum and facilitating the diagnosis and prognosis of the state of infectious diseases. Unaffected by the homeostasis mechanism in the human body, urine accommodates systemic changes and reflects the pathophysiological condition of an individual. Easy availability in large volumes and non-invasive sample collection have rendered urine an ideal source of biomarkers for various diseases. Infectious diseases may be communicable, and therefore early diagnosis and treatment are of immense importance. Current diagnostic approaches preclude the timely identification of clinical conditions and also lack portability. Point-of-care (POC) testing solutions have gained attention as alternative diagnostic measures due to their ability to provide rapid and on-site results. Lateral flow assays (LFAs) are the mainstay in POC device development and have attracted interest owing to their potential to provide instantaneous results in resource-limited settings. The discovery and optimization of a definitive biomarker can render POC testing an excellent platform, thus impacting unwarranted antibiotic administration and preventing the spread of infectious diseases. This Review summarizes the importance of urine as an emerging biological fluid in infectious disease research and diagnosis in clinical settings. We review the academic research related to LFAs. Further, we also describe commercial POC devices based on the identification of urinary biomarkers as diagnostic targets for infectious diseases. We also discuss the future use of LFAs in developing more effective POC tests for urinary biomarkers of various infections.

Early disease biomarkers can be found using animal models urine proteomics

INTRODUCTION

Early disease detection is a prerequisite for early intervention. Urine is not subjected to homeostatic control, and therefore, it accumulates very early changes associated with disease processes, some of which may be used as biomarkers. Animal models must be used to identify urinary changes associated with very early stages of diseases to avoid potential interfering factors and obtain urine samples at a sufficiently early time point before pathological or clinical manifestations occur.

AREAS COVERED

We reviewed recent (from 2009-2020) urine proteome studies using animal models of many diseases. We focused on early changes in urine proteome of animal models, particularly changes occurring prior to alterations in blood tests, light microscopy observations and clinical manifestations. Additional studies relevant to the topic were also extracted from the references of the cited papers. Changes in the urine proteome at different disease stages and the ability of the urine proteome to differentiate among different animal models are also discussed in this review.

EXPERT COMMENTARY

Urine proteomes of animal models may reflect early changes that occur even before changes in blood parameters, light microscopy observations and clinical manifestations, suggesting the potential use of urinary biomarkers for the very early detection of human diseases.

Urinary biomarker discovery in gliomas using mass spectrometry-based clinical proteomics

Background

Gliomas are the most common primary malignant brain tumors and have a poor prognosis. Early detection of gliomas is crucial to improve patient outcomes. Urine accumulates systematic body changes and thus serves as an excellent early biomarker source.

Methods

At the biomarker discovery phase, we performed a self-controlled proteomics analysis by comparing urine samples collected from five glioma patients at the time of tumor diagnosis and after surgical removal of the tumor. At the biomarker validation phase, we further validated some promising proteins using parallel reaction monitoring (PRM)-based targeted proteomics in another cohort, including glioma, meningioma, and moyamoya disease patients as well as healthy controls.

Results

Using label-free proteome quantitation (LFQ), we identified twenty-seven urinary proteins that were significantly changed after tumor resection, many of which have been previously associated with gliomas. The functions of these proteins were significantly enriched in the autophagy and angiogenesis, which are associated with glioma development. After targeted proteomics validation, we identified a biomarker panel (AACT, TSP4, MDHM, CALR, LEG1, and AHSG) with an area under the curve (AUC) value of 0.958 for the detection of gliomas. Interestingly, AACT, LEG1, and AHSG are also potential cerebrospinal fluid or blood biomarkers of gliomas.

Conclusions

Using LFQ and PRM proteome quantification, we identified candidate urinary protein biomarkers with the potential to detect gliomas. This study will also provide clues for future biomarker studies involving brain diseases.

Regional Differences of the Urinary Proteomes in Healthy Chinese Individuals

Objective Urine is a promising biomarker source for clinical proteomics studies. Regional physiological differences are common in multi-center clinical studies. In this study, we investigate whether significant differences are present in the urinary proteomes of individuals from different regions in China. Methods In this study, morning urine samples were collected from healthy urban residents in three regions of China (Haikou, Xi'an and Xining) and urinary proteins were preserved using a membrane-based method (Urimem). The urine proteomes of 27 normal samples were analyzed using LC-MS/MS and compared among three regions. Functional annotation of the differential proteins among the three areas was analyzed using the DAVID online database, and pathway enrichment of the differential urinary proteins was analyzed using KEGG. Results We identified 1898 proteins from Urimem samples using label-free proteome quantification, of which 56 urine proteins were differentially expressed among the three regions (P < 0.05). Hierarchical clustering analysis showed that inter-regional differences caused less significant changes in the urine proteome than inter-sex differences. After gender stratification, 16 differential proteins were identified in male samples and 84 differential proteins were identified in female samples. Among these differential proteins, several proteins have been previously reported as urinary disease biomarkers. Conclusions Urimem will facilitate urinary protein storage for large-scale urine sample collection. Regional differences are a confounding factor influencing the urine proteome and should be considered in future multi-center biomarker studies.

Comprehensive Analysis of Individual Variation in the Urinary Proteome Revealed Significant Gender Differences

Disease biomarkers are the measurable changes associated with a pathophysiological process. Without homeostatic control, urine accumulates systematic changes in the body. Thus, urine is an attractive biological material for the discovery of disease biomarkers. One of the major bottlenecks in urinary biomarker discovery is that the concentration and composition of urinary proteins are influenced by many physiological factors. To elucidate the individual variation and related factors influencing the urinary proteome, we comprehensively analyzed the urine samples from healthy adult donors (aged 20-69 years). Co-expression network analysis revealed protein clusters representing the metabolic status, gender-related differences and age-related differences in urinary proteins. In particular, we demonstrated that gender is a crucial factor contributing to individual variation. Proteins that were increased in the male urine samples include prostate-secreted proteins and TIMP1, a protein whose abundance alters under various cancers and renal diseases; however, the proteins that were increased in the female urine samples have known functions in the immune system. Nine gender-related proteins were validated on 85 independent samples by multiple reaction monitoring. Five of these proteins were further used to build a model that could accurately distinguish male and female urine samples with an area under curve value of 0.94. Based on the above results, we strongly suggest that future biomarker investigations should consider gender as a crucial factor in experimental design and data analysis. Finally, reference intervals of each urinary protein were estimated, providing a baseline for the discovery of abnormalities.

Gender proteomics I. Which proteins in non-sexual organs

Differences related to gender have long been neglected but recent investigations show that they are widespread and may be recognized with all types of omics approaches, both in tissues and in biological fluids. Our review compiles evidence collected with proteomics techniques in our species, mainly focusing on baseline parameters in non-sexual organs in healthy men and women. Data from human specimens had to be replaced with information from other mammals every time invasive procedures of sample procurement were involved.

SIGNIFICANCE

As our knowledge, and the methods to build it, get refined, gender differences need to receive more and more attention, as they influence the outcome of all aspects in lifestyle, including diet, exercise and environmental factors. In turn this background modulates a differential susceptibility to some disease, or a different pathogenetic mechanism, depending on gender, and a different response to pharmacological therapy. Preparing this review we meant to raise awareness about the gender issue. We anticipate that more and more often, in the future, separate evaluations will be carried out on male and female subjects as an alternative - and an upgrade - to the current approach of reference and test groups being 'matched for age and sex'.

Current state of the art for enhancing urine biomarker discovery

INTRODUCTION

Urine is a highly desirable biospecimen for biomarker analysis because it can be collected recurrently by non-invasive techniques, in relatively large volumes. Urine contains cellular elements, biochemicals, and proteins derived from glomerular filtration of plasma, renal tubule excretion, and urogenital tract secretions that reflect, at a given time point, an individual's metabolic and pathophysiologic state.

AREAS COVERED

High-resolution mass spectrometry, coupled with state of the art fractionation systems are revealing the plethora of diagnostic/prognostic proteomic information existing within urinary exosomes, glycoproteins, and proteins. Affinity capture pre-processing techniques such as combinatorial peptide ligand libraries and biomarker harvesting hydrogel nanoparticles are enabling measurement/identification of previously undetectable urinary proteins. Expert commentary: Future challenges in the urinary proteomics field include a) defining either single or multiple, universally applicable data normalization methods for comparing results within and between individual patients/data sets, and b) defining expected urinary protein levels in healthy individuals.

Effects of urine composition on epithelial Na+ channel-targeted protease activity

We examined human urinary proteolytic activity toward the Epithelial Sodium Channel (ENaC). We focused on two sites in each of alpha and gamma ENaC that are targets of endogenous and exogenous proteases. We examined the effects of ionic strength, pH and urinary H⁺-buffers, metabolic intermediates, redox molecules, and large urinary proteins. Monoatomic cations caused the largest effect, with sodium inhibiting activity in the 15–515 mEq range. Multivalent cations zinc and copper inhibited urinary proteolytic activity at concentrations below 100 μmol/L. Similar to sodium, urea caused a 30% inhibition in the 0–500 mmol/L range. This was not observed with acetone and ethanol. Modulating urinary redox status modified activity with H₂O₂ stimulated and ascorbate inhibited activity. Minimal effects (<10%) were observed with caffeine, glucose, several TCA cycle intermediates, salicylic acid, inorganic phosphate, albumin, creatinine, and Tamm–Horsfall protein. The cumulative activity of ENaC-cleaving proteases was highest at neutral pH, however, alpha and gamma proteases exhibited an inverse dependence with alpha stimulated at acidic and gamma stimulated at alkaline pH. These data indicate that ENaC-targeting urinary proteolytic activity is sensitive to sodium, urea and pH and changes in these components can modify channel cleavage and activation status, and likely downstream sodium absorption unrelated to changes in protein or channel density.

Physiological conditions can be reflected in human urine proteome and metabolome

Biomarkers are the measurable changes associated with physiological or pathophysiological processes. Urine, unlike blood, lacks mechanisms for maintaining homeostasis: it is therefore an ideal source of biomarkers that can reflect systemic changes. Urinary proteome and metabolome have been studied for their diagnostic capabilities, ability to monitor disease and prognostic utility. In this review, the effects of common physiological conditions such as gender, age, diet, daily rhythms, exercise, hormone status, lifestyle and extreme environments on human urine are discussed. These effects should be considered when biomarker studies of diseases are conducted. More importantly, if physiological changes can be reflected in urine, we have reason to expect that urine will become widely used to detect small and early changes in pathological and/or pharmacological conditions.

Advances in urinary proteome analysis and applications in systems biology

The urinary proteome is the focus of many studies due to the ease of urine collection and the relative proteome stability. Systems biology allows the combination of multiple omics studies, forming a link between proteomics, metabolomics, genomics and transcriptomics. In-depth data interpretation is achieved by bioinformatics analysis of -omics data sets. It is expected that the contribution of systems biology to the study of the urinary proteome will offer novel insights. The main focus of this review is on technical aspects of proteomics studies, available tools for systems biology analysis and the application of urinary proteomics in clinical studies and systems biology.

Hormone-dependent changes in female urinary proteome

Human urine represents a good source for proteomic research for clinically related studies as it can be collected and processed easily and can give information about kidney-related mechanisms. Little is known about the urinary proteomic changes resulting from physiological (normal), pathological, or environmental variations, and there are few reports on hormone-related modifications of urine proteome. In our study, we highlighted the variations of urinary proteins associated with menstrual cycle or estro-progestin pill in females. We also described an association between some urinary proteins and the renin-angiotensin-aldosterone system, which might help to improve the understanding of physiological and pathological processes when a gender-specific pattern such as the menopause-related hypertension or eclampsia is evident. We therefore support the usefulness of urinary proteomics as a valuable tool for clinically related study as it can provide information on candidate biomarkers which, in turn, need to be confirmed by multiple approaches before the use in a clinical setting.