Targeted quantification of N-1-(carboxymethyl) valine and N-1-(carboxyethyl) valine peptides of β-hemoglobin for better diagnostics in diabetes

Plasma/Serum Proteomics based on Mass Spectrometry

Human blood is a window of physiology and disease. Examination of biomarkers in blood is a common clinical procedure, which can be informative in diagnosis and prognosis of diseases, and in evaluating treatment effectiveness. There is still a huge demand on new blood biomarkers and assays for precision medicine nowadays, therefore plasma/serum proteomics has attracted increasing attention in recent years. How to effectively proceed with the biomarker discovery and clinical diagnostic assay development is a question raised to researchers who are interested in this area. In this review, we comprehensively introduce the background and advancement of technologies for blood proteomics, with a focus on mass spectrometry (MS). Analyzing existing blood biomarkers and newly-built diagnostic assays based on MS can shed light on developing new biomarkers and analytical methods. We summarize various protein analytes in plasma/serum which include total proteome, protein post-translational modifications, and extracellular vesicles, focusing on their corresponding sample preparation methods for MS analysis. We propose screening multiple protein analytes in the same set of blood samples in order to increase success rate for biomarker discovery. We also review the trends of MS techniques for blood tests including sample preparation automation, and further provide our perspectives on their future directions.

Elevated Level of Glycated KQTALVELVK Peptide of Albumin Is Associated with the Risk of Diabetic Nephropathy

Diabetic nephropathy is a leading cause of end-stage renal disease. Hence, early detection of diabetic nephropathy is essential to mitigate the disease burden. Microalbuminuria, the currently used diagnostic marker of diabetic nephropathy, is not efficient in detecting it at an early stage. Therefore, we explored the utility of glycated human serum albumin (HSA) peptides for risk prediction of diabetic nephropathy. Three glycation-sensitive HSA peptides, namely, FKDLGEENFK, KQTALVELVK, and KVPQVSTPTLVEVSR, with deoxyfructosyllysine (DFL) modification were quantified by targeted mass spectrometry (MS) in a study population comprising healthy and type II diabetes subjects with and without nephropathy. Mass spectrometry, receiver operating characteristic (ROC) curve, and correlation analysis revealed that the DFL-modified KQTALVELVK peptide was better than other glycated HSA peptides and HbA_1c for identifying diabetic nephropathy. DFL-modified KQTALVELVK could be a potential marker for risk prediction of diabetic nephropathy.

Sample Preparation Methods for Targeted Single-Cell Proteomics

We compared three cell isolation and two proteomic sample preparation methods for single-cell and near-single-cell analysis. Whole blood was used to quantify hemoglobin (Hb) and glycated-Hb (gly-Hb) in erythrocytes using targeted mass spectrometry and stable isotope-labeled standard peptides. Each method differed in cell isolation and sample preparation as follows: 1) FACS and automated preparation in one-pot for trace samples (autoPOTS); 2) limited dilution via microscopy and a novel rapid one-pot sample preparation method that circumvented the need for the solid-phase extraction, low-volume liquid handling instrumentation and humidified incubation chamber; and 3) CellenONE-based cell isolation and the same one-pot sample preparation method used for limited dilution. Only the CellenONE device routinely isolated single-cells from which Hb was measured to be 540-660 amol per red blood cell (RBC), which was comparable to the calculated SI reference range for mean corpuscular hemoglobin (390-540 amol/RBC). FACSAria sorter and limited dilution could routinely isolate single-digit cell numbers, to reliably quantify CMV-Hb heterogeneity. Finally, we observed that repeated measures, using 5-25 RBCs obtained from N = 10 blood donors, could be used as an alternative and more efficient strategy than single RBC analysis to measure protein heterogeneity, which revealed multimodal distribution, unique for each individual.

Resistance to glycation in the zebra finch: Mass spectrometry-based analysis and its perspectives for evolutionary studies of aging

In humans, hyperglycemia is associated with protein glycation, which may contribute to aging. Strikingly, birds usually outlive mammals of the same body mass, while exhibiting high plasma glucose levels. However, how birds succeed in escaping pro-aging effects of glycation remains unknown. Using a specific mass spectrometry-based approach in captive zebra finches of known age, we recorded high glycaemia values but no glycated hemoglobin form was found. Still, we showed that zebra finch hemoglobin can be glycated in vitro, albeit only to a limited extent compared to its human homologue. This may be due to peculiar structural features, as supported by the unusual presence of three different tetramer populations with balanced proportions and a still bound cofactor that could be inositol pentaphosphate. High levels of the glycated forms of zebra finch plasma serotransferrin, carbonic anhydrase 2, and albumin were measured. Glucose, age or body mass correlations with either plasma glycated proteins or hemoglobin isoforms suggest that those variables may be future molecular tools of choice to monitor glycation and its link with individual fitness. Our molecular advance may help determine how evolution succeeded in associating flying ability, high blood glucose and long lifespan in birds.

Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives

For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.

Aldh1l2 knockout mouse metabolomics links the loss of the mitochondrial folate enzyme to deregulation of a lipid metabolism observed in rare human disorder

Background

Mitochondrial folate enzyme ALDH1L2 (aldehyde dehydrogenase 1 family member L2) converts 10-formyltetrahydrofolate to tetrahydrofolate and CO₂ simultaneously producing NADPH. We have recently reported that the lack of the enzyme due to compound heterozygous mutations was associated with neuro-ichthyotic syndrome in a male patient. Here, we address the role of ALDH1L2 in cellular metabolism and highlight the mechanism by which the enzyme regulates lipid oxidation.

Methods

We generated Aldh1l2 knockout (KO) mouse model, characterized its phenotype, tissue histology, and levels of reduced folate pools and applied untargeted metabolomics to determine metabolic changes in the liver, pancreas, and plasma caused by the enzyme loss. We have also used NanoString Mouse Inflammation V2 Code Set to analyze inflammatory gene expression and evaluate the role of ALDH1L2 in the regulation of inflammatory pathways.

Results

Both male and female Aldh1l2 KO mice were viable and did not show an apparent phenotype. However, H&E and Oil Red O staining revealed the accumulation of lipid vesicles localized between the central veins and portal triads in the liver of Aldh1l2^-/- male mice indicating abnormal lipid metabolism. The metabolomic analysis showed vastly changed metabotypes in the liver and plasma in these mice suggesting channeling of fatty acids away from β-oxidation. Specifically, drastically increased plasma acylcarnitine and acylglycine conjugates were indicative of impaired β-oxidation in the liver. Our metabolomics data further showed that mechanistically, the regulation of lipid metabolism by ALDH1L2 is linked to coenzyme A biosynthesis through the following steps. ALDH1L2 enables sufficient NADPH production in mitochondria to maintain high levels of glutathione, which in turn is required to support high levels of cysteine, the coenzyme A precursor. As the final outcome, the deregulation of lipid metabolism due to ALDH1L2 loss led to decreased ATP levels in mitochondria.

Conclusions

The ALDH1L2 function is important for CoA-dependent pathways including β-oxidation, TCA cycle, and bile acid biosynthesis. The role of ALDH1L2 in the lipid metabolism explains why the loss of this enzyme is associated with neuro-cutaneous diseases. On a broader scale, our study links folate metabolism to the regulation of lipid homeostasis and the energy balance in the cell.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40246-020-00291-3.

Branched-chain amino acids, history of gestational diabetes, and breastfeeding: The Bogalusa Heart Study

BACKGROUND AND AIMS

To examine the associations between history of gestational diabetes mellitus (GDM) and breastfeeding with branched-chain amino acids (BCAA) and their metabolites in later life.

METHODS AND RESULTS

638 women (mean age 48.0 y) who had participated in the Bogalusa Heart Study and substudies of pregnancy history had untargeted, ultrahigh performance liquid chromatography-tandem mass spectroscopy conducted by Metabolon© on serum samples. Metabolites were identified that were BCAA or associated with BCAA metabolic pathways. History of GDM at any pregnancy (self-reported, confirmed with medical records when possible) as well as breastfeeding were examined as predictors of BCAA using linear models, controlling for age, race, BMI, waist circumference, and menopausal status. None of the BCAA differed statistically by history of either GDM or breastfeeding, although absolute levels of each of the BCAA were higher with GDM and lower with breastfeeding. Of the 27 metabolites on the leucine, isoleucine and valine metabolism subpathway, 1-carboxyethylleucine, 1-carboxyethyvaline, and 3-hydroxy-2-ethylpropionate were higher in women with a history of GDM, but lower in women in women with a history of breastfeeding. Similar results were found for alpha-hydroxyisocaproate, 1-carboxyethylisoleucine, and N-acetylleucine.

CONCLUSIONS

GDM and breastfeeding are associated in opposite directions with several metabolites on the BCAA metabolic pathway.

The development and clinical applications of proteomics: an Indian perspective

INTRODUCTION

Proteomic research has been extensively used to identify potential biomarkers or targets for various diseases. Advances in mass spectrometry along with data analytics have led proteomics to become a powerful tool for exploring the critical molecular players associated with diseases, thereby, playing a significant role in the development of proteomic applications for the clinic.

AREAS COVERED

This review presents recent advances in the development and clinical applications of proteomics in India toward understanding various diseases including cancer, metabolic diseases, and reproductive diseases. Keywords combined with 'clinical proteomics in India' 'proteomic research in India' and 'mass spectrometry' were used to search PubMed.

EXPERT OPINION

The past decade has seen a significant increase in research in clinical proteomics in India. This approach has resulted in the development of proteomics-based marker technologies for disease management in the country. The majority of these investigations are still in the discovery phase and efforts have to be made to address the intended clinical use so that the identified potential biomarkers reach the clinic. To move toward this necessity, there is a pressing need to establish some key infrastructure requirements and meaningful collaborations between the clinicians and scientists which will enable more effective solutions to address health issues specific to India.

The role of mass spectrometry in studies of glycation processes and diabetes management

In the last decade, mass spectrometry has been widely employed in the study of diabetes. This was mainly due to the development of new, highly sensitive, and specific methods representing powerful tools to go deep into the biochemical and pathogenetic processes typical of the disease. The aim of this review is to give a panorama of the scientifically valid results obtained in this contest. The recent studies on glycation processes, in particular those devoted to the mechanism of production and to the reactivity of advanced glycation end products (AGEs, AGE peptides, glyoxal, methylglyoxal, dicarbonyl compounds) allowed to obtain a different view on short and long term complications of diabetes. These results have been employed in the research of effective markers and mass spectrometry represented a precious tool allowing the monitoring of diabetic nephropathy, cardiovascular complications, and gestational diabetes. The same approaches have been employed to monitor the non-insulinic diabetes pharmacological treatments, as well as in the discovery and characterization of antidiabetic agents from natural products. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 38:112-146, 2019.

Albumin Abundance and Its Glycation Status Determine Hemoglobin Glycation

Diabetes diagnosis and management majorly depend upon the measurement of glycated hemoglobin (HbA1c) levels. Various factors influence HbA1c levels such as the use of various analytical methods and the presence of various clinical conditions. Plasma albumin levels were known to be negatively associated with HbA1c. However, the precise mechanism by which they affect HbA1c is not well understood. Therefore, we have studied the influence of albumin levels and its glycation status on hemoglobin glycation using erythrocyte culture experiments. Erythrocytes maintained at low albumin concentration exhibited relatively increased albumin and hemoglobin glycation as compared to that in those maintained at higher albumin concentration. Increase in albumin glycation may decrease its ability to protect hemoglobin glycation. This was demonstrated by treatment of erythrocytes with N(ε)-(carboxymethyl)lysine-modified serum albumin (CMSA), which failed to protect hemoglobin glycation; instead, it increased hemoglobin glycation. The inability of CMSA to reduce hemoglobin glycation was due to the lack of free lysine residues of albumin, which was corroborated by using N(ε)-(acetyl)lysine serum albumin (AcSA) and clinical diabetic plasma. This is the first study which demonstrates that the modification of lysine residues of albumin impairs its ability to inhibit hemoglobin glycation. Furthermore, correlation studies between HbA1c and albumin levels or relative albumin fructosamine from clinical subjects supported our experimental finding that albumin abundance and its glycation status influence hemoglobin glycation. Therefore, we propose albumin level and its glycation status to be quantified in conjunction with HbA1c for better management of diabetes.

Maillard Proteomics: Opening New Pages

Protein glycation is a ubiquitous non-enzymatic post-translational modification, formed by reaction of protein amino and guanidino groups with carbonyl compounds, presumably reducing sugars and α-dicarbonyls. Resulting advanced glycation end products (AGEs) represent a highly heterogeneous group of compounds, deleterious in mammals due to their pro-inflammatory effect, and impact in pathogenesis of diabetes mellitus, Alzheimer's disease and ageing. The body of information on the mechanisms and pathways of AGE formation, acquired during the last decades, clearly indicates a certain site-specificity of glycation. It makes characterization of individual glycation sites a critical pre-requisite for understanding in vivo mechanisms of AGE formation and developing adequate nutritional and therapeutic approaches to reduce it in humans. In this context, proteomics is the methodology of choice to address site-specific molecular changes related to protein glycation. Therefore, here we summarize the methods of Maillard proteomics, specifically focusing on the techniques providing comprehensive structural and quantitative characterization of glycated proteome. Further, we address the novel break-through areas, recently established in the field of Maillard research, i.e., in vitro models based on synthetic peptides, site-based diagnostics of metabolism-related diseases (e.g., diabetes mellitus), proteomics of anti-glycative defense, and dynamics of plant glycated proteome during ageing and response to environmental stress.

Abundance matters: role of albumin in diabetes, a proteomics perspective

INTRODUCTION

Human serum albumin (HSA) is a multifaceted protein with vital physiological functions. It is the most abundant plasma protein with inherent capability to bind to diverse ligands, and thus susceptible to various post-translational modifications (PTMs) which alter its structure and functions. One such PTM is glycation, a non-enzymatic reaction between reducing sugar and protein leading to formation of heterogeneous advanced glycation end products (AGEs). Glycated albumin (GA) concentration increases significantly in diabetes and is implicated in development of secondary complications. Areas covered: In this review, we discuss in depth, formation of GA and its consequences, approaches used for characterization and quantification of GA, milestones in GA proteomics, clinical relevance of GA as a biomarker, significance of maintaining abundant levels of albumin and future perspectives. Expert commentary: Elevated GA levels are associated with development of insulin resistance as well as secondary complications, in healthy and diabetic individuals respectively. Mass spectrometry (MS) based approaches aid in precise characterization and quantification of GA including early and advanced glycated peptides, which can be useful in prediction of the disease status. Thus GA has evolved to be one of the best candidates in the pursuit of diagnostic markers for prediction of prediabetes and diabetic complications.

Targeted Quantification of the Glycated Peptides of Human Serum Albumin

Glycated human serum albumin (HSA) serves as an important marker for monitoring the glycemic status. Developing methods for unambiguous identification and quantification of glycated peptides of HSA using high-throughput technologies such as mass spectrometry has a great clinical significance. The following protocol describes the construction of reference spectral libraries for Amadori-modified lysine (AML), N(ε)-(carboxymethyl) lysine (CML)-, and N(ε)-(carboxyethyl)lysine (CEL)-modified peptides of synthetically modified HSA using high-resolution mass spectrometers. The protocol also describes work flows, for unambiguous identification and quantification of glycated modified peptides of HSA in clinical plasma using standard spectral libraries by various mass spectrometry approaches such as parallel reaction monitoring (PRM), sequential window acquisition of all theoretical fragment ion spectra (SWATH), and MS^E.

Proteomics in India: the clinical aspect

Proteomics has emerged as a highly promising bioanalytical technique in various aspects of applied biological research. In Indian academia, proteomics research has grown remarkably over the last decade. It is being extensively used for both basic as well as translation research in the areas of infectious and immune disorders, reproductive disorders, cardiovascular diseases, diabetes, eye disorders, human cancers and hematological disorders. Recently, some seminal works on clinical proteomics have been reported from several laboratories across India. This review aims to shed light on the increasing use of proteomics in India in a variety of biological conditions. It also highlights that India has the expertise and infrastructure needed for pursuing proteomics research in the country and to participate in global initiatives. Research in clinical proteomics is gradually picking up pace in India and its future seems very bright.