Urine proteome analysis by C18 plate-matrix-assisted laser desorption/ionization time-of-flight mass spectrometry allows noninvasive differential diagnosis and prediction of diabetic nephropathy

NMT2 alleviates depression-like behavior in a rat model of chronic unpredictable stress: An integrated proteomic and phosphoproteomic analysis

Proteomics has been widely used to investigate multiple diseases. Combining the analyses of proteomics with phosphoproteomics can be used to further explain the pathological mechanisms of depression. In this study, depression-like behavior was induced in a rat model of chronic unpredictable mild stress (CUMS). We subsequently conducted the sucrose preference test, open field experiment, and forced swimming test to assess depressive-like behavior. Proteomic and phosphoproteomic sequencing of the hippocampal tissues from depressive-like behavior and normal rats were analyzed to identify differentially expressed proteins (DEPs) and differentially phosphorylated proteins (DPPs). Differentially expressed phosphorylated proteins (DEPPs) were obtained by intersecting the DEPs and DPPs, and functional enrichment analysis, as well as ingenuity pathway analysis (IPA), were subsequently performed. The study also investigated correlations among the DEPPs and used qRT-PCR to quantify the expression levels of key genes. Five DEPPs were identified, Gys1, Nmt2, Lrp1, Bin1, and Atp1a1, which were found to activate the synaptogenesis signaling pathway, induce mitochondrial dysfunction, and activate the phosphoinositide biosynthesis and degradation pathways. The qRT-PCR results confirmed the proteomic findings for Gys1, Nmt2, Lrp1, and Atp1a1. Importantly, inhibiting Nmt2 was found to alleviate depression-like behavior and alleviate neuronal apoptosis in the hippocampus of CUMS rats. In conclusion, we identified five DEPPs associated with the synaptogenesis signaling pathway, mitochondrial dysfunction, and phosphoinositide biosynthesis and degradation in depression. Furthermore, NMT2 may be a potential target for the treatment or diagnosis of depression. Our findings provide novel insights into the molecular mechanisms of depression.

Mass Spectrometry Analysis for Clinical Applications: A Review

Mass spectrometry (MS) has become an attractive analytical method in clinical analysis due to its comprehensive advantages of high sensitivity, high specificity and high throughput. Separation techniques coupled MS detection (e.g., LC-MS/MS) have shown unique advantages over immunoassay and have developed as golden criterion for many clinical applications. This review summarizes the characteristics and applications of MS, and emphasizes the high efficiency of MS in clinical research. In addition, this review also put forward further prospects for the future of mass spectrometry technology, including the introduction of miniature MS instruments, point-of-care detection and high-throughput analysis, to achieve better development of MS technology in various fields of clinical application. Moreover, as ambient ionization mass spectrometry (AIMS) requires little or no sample pretreatment and improves the flux of MS, this review also summarizes its potential applications in clinic.

Diagnostic value of α1-MG and URBP in early diabetic renal impairment

Aims/Introduction: Diabetic kidney disease (DKD) is defined as diabetes with impaired renal function, elevated urinary albumin excretion, or both. DKD is one of the most common microvascular complications of diabetes and plays an important role in the cause of end-stage renal disease (ESRD). About 5% of people with type 2 diabetes (T2DM) already have kidney damage at the time they are diagnosed, but other triggers of renal insufficiency, such as obesity, hyperlipidemia, glomerular atherosclerosis are often present, making it difficult to define "diabetic kidney disease" or "diabetic nephropathy" precisely in epidemiology or clinical practice. Therefore, the aim of this study is to identify diabetic patients with CKD at an early stage, and evaluate the value of tubular injury markers including α1-microglobulin (α1-MG), β2-microglobulin (β2-MG), N-acetyl-beta-D-glucosaminidase (NAG) and Urinary retinol binding protein (URBP) in the development of diabetes to DKD. Materials and methods: We recruited a total of 182 hospitalized patients with T2DM in the First Affiliated Hospital of Zhengzhou University from February 2018 to April 2023. We collected basic clinical characteristics and laboratory biochemical parameters of the patients. Based on their levels of urinary albumin creatinine ratio (UACR) and glomerular filtration rate (GFR), patients were divided into DM group (UACR≤30 mg/g and eGFR≥90 mL/min/1.73 m2, n = 63) and DKD group (UACR>30 mg/g or eGFR<90 mL/min/1.73 m2, n = 119) excluding other causes of chronic kidney disease. We further developed diagnostic models to improve the ability to predict the risk of developing DKD by screening potential risk factors using univariate and multivariate logistic regression analysis. Calibration plots and curve analysis were used to validate the model and clinical usefulness. Next, we screened patients with relatively normal estimated glomerular filtration rate (eGFR) (≥90 mL/min/1.73 m2) to investigate whether tubular injury markers could accurately predict the risk of DKD in patients with normal renal function. We defined the rate of GFR decline as a prognostic indicator of renal function in patients and collected the information of the re-hospitalized DKD patients to determine whether the relevant indicators had an impact on the renal prognosis. Results: The patients with DKD had higher levels of tubular injury markers than patients with DM. URBP, α1-MG, eGFR were statistically different in both univariate and multivariate logistic regression analyses and displayed great predictive power after modeling with an area under curve of 0.987. The calibration curve showed medium agreement. Decision curve showed it would add more net benefits for clinical decision. After adjusting eGFR and serum creatinine (Scr), URBP was demonstrated to be associated with early renal function impairment. Conclusion: Tubular injury markers play an important role in early diabetic renal function impairment.

Maternal obesity is associated with a higher number of regulatory-T-cells in newborns without affecting suppression

BACKGROUND

Maternal obesity (MO) is associated with a higher risk of immune-mediated diseases in the offspring and higher leptin levels in cord blood (CB). This study evaluates the number and function of lymphocyte subtypes in CB related to MO and its relationship with leptin concentration and leptin receptor expression.

METHODS

Pregnant women with (n = 32) or without obesity (n = 41) were enrolled at delivery. Cord blood mononuclear cells were separated with Ficoll-Hypaque. B and CD4+, regulatory and effector T cells were quantified by Flow Cytometry. Cord blood leptin concentration was measured by ELISA, and the leptin receptor (sLepR) on Treg cells was determined by Flow Cytometry.

RESULTS

MO was associated with higher numbers of CD4+, Treg and effector T cells in the CB of their offspring, without differences in the suppressive function of Tregs. Female offspring had a higher number of these cells and a higher cord leptin concentration. Tregs expressed higher levels of sLepR than effector T cells, without differences between groups.

CONCLUSIONS

MO is associated with changes in the newborn's immune profile, more evident in female newborns with higher leptin concentrations. More studies are needed to identify the mechanisms by which the high levels of cord leptin in the newborn of women with obesity could affect the offspring's immune system.

Molecular Pathways of Diabetic Kidney Disease Inferred from Proteomics

Diabetic kidney disease (DKD) affects an estimated 20-40% of type 2 diabetes patients and is among the most prevalent microvascular complications in this patient population, contributing to high morbidity and mortality rates. Currently, changes in albuminuria status are thought to be a primary indicator of the onset or progression of DKD, yet progressive nephropathy and renal impairment can occur in certain diabetic individuals who exhibit normal urinary albumin levels, emphasizing the lack of sensitivity and specificity associated with the use of albuminuria as a biomarker for detecting diabetic kidney disease and predicting DKD risk. According to the study, a non-invasive method for early detection or prediction of DKD may involve combining proteomic analytical techniques such second generation sequencing, mass spectrometry, two-dimensional gel electrophoresis, and other advanced system biology algorithms. Another category of proteins of relevance may now be provided by renal tissue biomarkers. The establishment of reliable proteomic biomarkers of DKD represents a novel approach to improving the diagnosis, prognostic evaluation, and treatment of affected patients. In the present review, a series of protein biomarkers that have been characterized to date are discussed, offering a theoretical foundation for future efforts to aid patients suffering from this debilitating microvascular complication.

Elevated serum extracellular vesicle arginase 1 in type 2 diabetes mellitus: a cross-sectional study in middle-aged and elderly population

BACKGROUND

Serum extracellular vesicle (EV)-derived arginase 1 (ARG 1) plays a critical role in diabetes-associated endothelial dysfunction. This study was performed to determine the levels of serum EV-derived ARG 1 in T2DM and non-T2DM participants and to examine the association of serum EV-derived ARG 1 with T2DM incidence.

METHODS

We performed a cross-sectional study in 103 Chinese, including 73 T2DM patients and 30 non-T2DM. Serum EVs were prepared via ultracentrifugation. Serum EV-derived ARG 1 levels were measured by enzyme-linked immunosorbent assay. The correlations between serum EV-derived ARG 1 and clinical variables were analyzed. The association of serum EV-derived ARG 1 levels with T2DM was determined by multivariate logistic regression analysis. Interaction subgroup analysis was used to evaluate the interaction of the relevant baselines on the association between serum EV-derived ARG 1 levels and T2DM.

RESULTS

Serum EV-derived ARG 1 levels were significantly higher in T2DM patients compared with non-T2DM patients (p < 0.001). Correlation analysis revealed that serum EV-derived ARG 1 levels were positively associated with fasting plasma glucose (FPG) (r = 0.316, p = 0.001) and glycated hemoglobin (HbA1c) (r = 0.322, p = 0.001). Serum EV-derived ARG 1 levels were significantly associated with T2DM, especially in the subgroup of T2DM for more than 10 years (OR 1.651, 95% CI = 1.066-2.557; P value, 0.025), after adjusting for confounding factors.

CONCLUSIONS

Elevated concentration of serum EV-derived ARG 1 is closely associated with T2DM.

The better, the choosier: A meta-analysis on interindividual variation of male mate choice

Male mate choice occurs in several animal species, but we know little about the factors that influence the expression of this behaviour. Males vary in their capacity to acquire mates (i.e. male quality), which could be crucial to male mate choice expression but it is often overlooked. Using a meta‐analytical approach, we explore interindividual variation in the expression of male mate choice by comparing the mating investment of males of different qualities and phenotypes to high‐ and low‐quality females. We used two datasets that together contained information from 60 empirical studies, comprising 52 species. We found that males of all qualities and phenotypes prefer high‐quality females, but differ in the strength of such preference. High‐ and medium‐quality males are choosier than low‐quality males. Similarly, males that are larger or in greater body condition are choosier than their counterparts. In contrast, male body mass and age are not associated with changes in male mate choice. We also show that experimental design may influence our understanding of male mating investment patterns, which may limit the generalisation of our findings. Nonetheless, we argue that male quality may be an important feature in the expression of male mate choice.

Urinary Protein and Peptide Markers in Chronic Kidney Disease

Chronic kidney disease (CKD) is a non-specific type of kidney disease that causes a gradual decline in kidney function (from months to years). CKD is a significant risk factor for death, cardiovascular disease, and end-stage renal disease. CKDs of different origins may have the same clinical and laboratory manifestations but different progression rates, which requires early diagnosis to determine. This review focuses on protein/peptide biomarkers of the leading causes of CKD: diabetic nephropathy, IgA nephropathy, lupus nephritis, focal segmental glomerulosclerosis, and membranous nephropathy. Mass spectrometry (MS) approaches provided the most information about urinary peptide and protein contents in different nephropathies. New analytical approaches allow urinary proteomic-peptide profiles to be used as early non-invasive diagnostic tools for specific morphological forms of kidney disease and may become a safe alternative to renal biopsy. MS studies of the key pathogenetic mechanisms of renal disease progression may also contribute to developing new approaches for targeted therapy.

The Potential Role of Electronegative High-Density Lipoprotein H5 Subfraction in RA-Related Atherosclerosis

Although the heterogeneity of high-density lipoprotein-cholesterol (HDL-c) composition is associated with atherosclerotic cardiovascular risk, the link between electronegative subfractions of HDL-c and atherosclerosis in rheumatoid arthritis (RA) remains unknown. We examined the association of the percentage of the most electronegative subfraction of HDL-c (H5%) and RA-related atherosclerosis. Using anion-exchange purification/fast-protein liquid chromatography, we demonstrated significantly higher H5% in patients (median, 7.2%) than HC (2.8%, p < 0.005). Multivariable regression analysis revealed H5% as a significant predictor for subclinical atherosclerosis. We subsequently explored atherogenic role of H5 using cell-based assay. The results showed significantly higher levels of IL-1β and IL-8 mRNA in H5-treated (mean ± SD, 4.45 ± 1.22 folds, 6.02 ± 1.43-folds, respectively) than H1-treated monocytes (0.89 ± 0.18-folds, 1.03 ± 0.26-folds, respectively, both p < 0.001). In macrophages, H5 upregulated the mRNA and protein expression of IL-1β and IL-8 in a dose-dependent manner, and their expression levels were significantly higher than H1-treated macrophages (all p < 0.001). H5 induced more foam cell formation compared with H1-treated macrophages (p < 0.005). In addition, H5 has significantly lower cholesterol efflux capacity than H1 (p < 0.005). The results of nanoLC-MS/MS approach reveal that the best discriminator between high-H5% and normal-H5% is Apo(a), the main constituent of Lp(a). Moreover, Lp(a) level is a significant predictor for high-H5%. These observations suggest that H5 is involved in RA-related atherosclerosis.

BoxCar increases the depth and reproducibility of diabetic urinary proteome analysis

PURPOSE

Mass spectrometry-based proteomics performs well in high throughput detection of urinary proteins. Nonetheless, protein identification depth and reproducibility remain the challenges in diabetic urinary proteome with high complexity and broad dynamic range, especially for low-abundant proteins. As a new data acquisition strategy, the BoxCar method was reported to benefit for low-abundant protein identification. Whether it is propitious to diabetic samples with high dynamic range proteomes has not been discussed yet. We aimed to apply BoxCar method to diabetic urine sample analysis, and to compare it with standard data dependent acquisition (DDA) method on protein identification in detail.

EXPERIMENTAL DESIGN

We performed seven technical replicates analysis on two urine samples from healthy individuals and diabetic patients to evaluate protein detection of BoxCar and standard DDA methods on single sample. Further comparison of two methods was made on multiple diabetic urine samples.

RESULTS

BoxCar could increase over 20% of identified proteins and performed better quantitative reproducibility than standard DDA method either in single or multiple diabetic urinary samples. BoxCar also improved the detection of low-abundant proteins. Functional enrichment analysis of normal albuminuria or microalbuminuria samples indicated that BoxCar acquired more diabetes-related biological information.

CONCLUSIONS AND CLINICAL RELEVANCE

The study demonstrates that BoxCar could enhance the depth and reproducibility in diabetic urinary proteome analysis, which provides reference for mass spectrometry approach selection in clinical urinary proteomic research.

The roles of carbonic anhydrases IX and XII in cancer cell adhesion, migration, invasion and metastasis

The main function of carbonic anhydrases (CAs) in cancer cells is the pH regulation through a conversion of H₂ O and CO₂ to H⁺ and HCO₃ ^- . However, the data of in vitro and in vivo studies have demonstrated that transmembrane isoforms of CA IX and CA XII are involved in various steps of cancer cell migration, invasion and metastasis. According to literature, inhibition of these CAs can affect the expression of multiple proteins. Some scientific groups have reported the possible interactions between CA IX and E-cadherin-catenin system, CA IX and integrins, CA IX, CA XII and ion transporters, which all are highly involved in cell-to-cell adhesion, the formation of membrane protrusions and focal adhesions. Nevertheless, CA IX and CA XII have a high impact on tumour growth and metastases formation. The data discussed in this review are quite recent. It highly support the role of CA IX and CA XII in various cancer metastasis processes through their interactions to other invasion proteins. Nevertheless, all findings show the great potential of these CAs in the context of research and application in clinical use.

Lipotoxicity and Diabetic Nephropathy: Novel Mechanistic Insights and Therapeutic Opportunities

Lipotoxicity is characterized by the ectopic accumulation of lipids in organs different from adipose tissue. Lipotoxicity is mainly associated with dysfunctional signaling and insulin resistance response in non-adipose tissue such as myocardium, pancreas, skeletal muscle, liver, and kidney. Serum lipid abnormalities and renal ectopic lipid accumulation have been associated with the development of kidney diseases, in particular diabetic nephropathy. Chronic hyperinsulinemia, often seen in type 2 diabetes, plays a crucial role in blood and liver lipid metabolism abnormalities, thus resulting in increased non-esterified fatty acids (NEFA). Excessive lipid accumulation alters cellular homeostasis and activates lipogenic and glycogenic cell-signaling pathways. Recent evidences indicate that both quantity and quality of lipids are involved in renal damage associated to lipotoxicity by activating inflammation, oxidative stress, mitochondrial dysfunction, and cell-death. The pathological effects of lipotoxicity have been observed in renal cells, thus promoting podocyte injury, tubular damage, mesangial proliferation, endothelial activation, and formation of macrophage-derived foam cells. Therefore, this review examines the recent preclinical and clinical research about the potentially harmful effects of lipids in the kidney, metabolic markers associated with these mechanisms, major signaling pathways affected, the causes of excessive lipid accumulation, and the types of lipids involved, as well as offers a comprehensive update of therapeutic strategies targeting lipotoxicity.

Analytically validated protein biomarkers of chronic pancreatitis and pancreatic cancer for potential clinical diagnosis with mass spectrometry

RATIONALE

Chronic pancreatitis (CP) is a pancreatic disease with poor prognosis and pancreatic cancer (PC) is one of the most lethal types of cancer that is symptomless in the early stage. Because the clinical and image findings of CP can overlap that of pancreatic cancer (PC) which leads to confusion in the diagnosis and treatment of PC, discovery/verification/validation of more accurate protein biomarkers to diagnose CP and PC is in urgent need.

METHODS

The PubMed, Web of Science, and Google Scholar were searched using the keywords: 'biomarker', 'marker', 'chronic pancreatitis', "pancreatic cancer" or "proteomics" for highly related researches. We focused on the articles published after the year 2005 in this review.

RESULTS

We introduce the background to CP and PC and summarize the diagnosis of CP and PC, analytically validated protein biomarkers, and proteomic approaches for discovery/verification/validation. The potential use of mass spectrometry (MS) in clinical diagnosis is also discussed.

CONCLUSIONS

Continuously improving sensitivity of MS can provide deeper proteome for new marker discovery and high reliability for protein marker verification, validation, and clinical diagnosis. The analytically validated protein markers could be considered as targeted protein biomarkers for developing a MS platform in the clinical validation process or clinical diagnosis of CP and PC.

Evaluation of urinary biomarkers for prediction of diabetic kidney disease: a propensity score matching analysis

BACKGROUND

The aim of this study was to evaluate the diagnostic value of six urinary biomarkers for prediction of diabetic kidney disease (DKD).

METHODS

The cross-sectional study recruited 1053 hospitalized patients with type 2 diabetes mellitus (T2DM), who were categorized into the diabetes mellitus (DM) with normoalbuminuria (NA) group (n = 753) and DKD group (n = 300) according to 24-h urinary albumin excretion rate (24-h UAE). Data on the levels of six studied urinary biomarkers [transferrin (TF), immunoglobulin G (IgG), retinol-binding protein (RBP), β-galactosidase (GAL), N-acetyl-beta-glucosaminidase (NAG), and β2-microglobulin (β2MG)] were obtained. The propensity score matching (PSM) method was applied to eliminate the influences of confounding variables.

RESULTS

Patients with DKD had higher levels of all six urinary biomarkers. All indicators demonstrated significantly increased risk of DKD, except for GAL and β2MG. Single RBP yielded the greatest area under the curve (AUC) value of 0.920 compared with the other five markers, followed by TF (0.867) and IgG (0.867). However, GAL, NAG, and β2MG were shown to have a weak prognostic ability. The diagnostic values of the different combinations were not superior to the single RBP.

CONCLUSIONS

RBP, TF, and IgG could be used as reliable or good predictors of DKD. The combined use of these biomarkers did not improve DKD detection.