Сайты гликирования белков плазмы крови как перспективные биомаркеры сахарного диабета второго типа тема диссертации и автореферата по ВАК РФ 00.00.00, кандидат наук Соболева Алена Вадимовна

• Соболева Алена Вадимовна
• кандидат наук
• 2023

Оглавление диссертации кандидат наук Соболева Алена Вадимовна

Directory

1. List of abbreviations

2. Introduction

2.1 Diabetes mellitus

2.2 Post-translational modifications of proteins

2.3 Protein glycation

2.4 Physiological role of protein glycation in the mammalian organism

2.5 Analytical approaches to characterize protein glycation

2.5.1 Conventional methods of Maillard analytics

2.5.2 Proteomics in analysis of protein glycation

2.5.3 Chromatographic and mass spectrometric approaches to improve the coverage of glycated proteome

2.5.4 Assessment of modification types and positions in glycated proteins and peptides

2.6 Biomarkers of T2DM

3. Objectives

3.1 Thesis statements to be defended

3.2 Scientific novelty

3.3 Theoretical and practical value

3.4 Reliability of the obtained results

3.4.1 Approbation of the research

3.4.2 Personal contribution of the author

3.4.3 Publications

3.5 Thesis structure

4. Materials and methods

4.1 Reagents

4.2 Equipment

4.3 Laboratory plasticware

4.4 Software

4.5 Peptide synthesis

4.6 Setup of experimental cohorts

4.7 Blood sampling, isolation of plasma and determination of protein contents therein

4.8 SDS-PAGE and precision of protein determination

4.9 Tryptic digestion

4.9.1 Tryptic digestion of proteins from human plasma

4.9.2 Spiking with internal standards

4.10 Boronic acid affinity chromatography

4.12 Liquid chromatography - mass spectrometry (LC-MS) analysis

4.12.1 LC-MS analysis of tryptic digests

4.12.2 LC-MS and MS/MS analysis of tryptic digests with internal standards

4.13 Standardization and validation of method for quantification of glycated peptides

4.14 Peptide identification and primary statistical analysis

4.15 Statistical analysis, generation and validation of the linear discriminant analysis model

5. Results

5.1 Identification of new peptide biomarkers of T2DM in blood plasma

5.1.1 Experimental workflow: sample preparation

5.1.2 Annotation of glycated peptides and specific glycation sites

5.1.3 Label-free relative quantification

5.1.4 Confirmation of amino acid sequence of glycated biomarker peptides

5.2 Absolute quantification of prospective T2DM biomarkers by the standard isotope dilution approach

5.2.1 Standard isotope dilution and tryptic digestion

5.2.2 Annotation of glycated peptides and corresponding internal standards by LC-MS

5.2.3 Standardization and validation of the quantification method

5.2.4 Absolute quantification of plasma protein glycation sites

5.3 Integrated biomarker of T2DM

5.3.1 Search for new glycated sites and relative quantitative analysis without labeled standards

5.3.2 Linear discriminant analysis

6. Discussion

6.1 Experimental setup

6.2 Biomarker potential of glycated proteolytic peptides

6.3 Absolute quantification of individual glycation sites

6.4 Specific set of glycation sites as an integrated biomarker of T2DM

7. Conclusions

8. References

9. Supplementary information

Введение диссертации (часть автореферата) на тему «Сайты гликирования белков плазмы крови как перспективные биомаркеры сахарного диабета второго типа»

2. Introduction

2.1 Diabetes mellitus

Diabetes mellitus (DM) is a group of metabolic diseases underlied by absolute or relative insufficiency of insulin secretion, compromised activity of this hormone, or both, resulting in hyperglycemia [1]. The hyperglycaemic state develops as a result of insulin deficiency, insulin resistance and impaired beta cell function, manifested as a persistent increase in blood glucose content [2, 3]. The disease is characterized by chronic progression and alterations in plethora of metabolic pathways (carbohydrate, fat and protein metabolism, mineral and water equilibrium) which leads to damage and dysfunction of various organs and tissues [4, 5]. Type 2 DM (T2DM) is typically manifested as progressive defect of insulin secretion usually accompanied with resistance to this hormone [6]. To date, T2DM is generally considered to be an incurable disease, although the current state of the diabetes therapy protocols allows efficient suppression of its progression [7]. The global incidence of T2DM doubles during the last 30 years becoming a non-communicable epidemic [8]. According to the World Health Organization (WHO) there are currently more than 463 million people with DM worldwide, but in 2030 this number will increase to 578 million and will reach 700 million in 2045 [9]. On the other hand, the real rate of morbidity growth is far ahead of even such depressing forecasts provided by statisticians. The complete understanding of the reasons behind this dramatic increase in case numbers is still unclear, although such factors as steadily increasing survival rates of diabetic individuals in the human population, continuous improvement of the disease management, reducing premature mortality, diet quality and increasing number of younger adults with T2DM might be the primary contributors in the observed dynamics of diabetes cases [9].

Since the early stages of the disease, as well as and the preceding development of insulin resistance and glucose tolerance, are asymptomatic, T2DM is usually diagnosed only at the stage of well-manifested complications [10]. It is important to note, that in many cases, when T2DM is mediated by environmental and life style-related factors, the progress of the disease can be suppressed or even reversed at the early stages without the use of medication or only by minimal treatment. On the other hand, prediction of the disease onset and correctness of its early diagnosis would reduce the risk of complication development. This requires, however, clear understanding of the molecular mechanisms underlying the pathogenesis of T2DM, the nature of the environmental factors affecting these mechanisms, as well as the availability of highly-sensitive, efficient and reliable methods for early diagnosis of T2DM and prediction of its possible occurrence. Appropriate analytical methods can be based on specific biomarkers, which might rely on key metabolites [11, 12], physiological signals [12], specific proteins [13] or individual modification sites therein [14, 15]. Thereby, the accuracy of

diagnosis and/or prediction critically depends on the number of individual markers, taken in consideration [16].

2.2 Post-translational modifications of proteins

Proteins represent the principal effector molecules in living cells, directly impacting on expression the information encoded in genes. The whole protein complement of a cell, tissue or organism at a given time point is usually referred to as proteome, analogously to the global gene complement, defined as genome [17]. Remarkably, due to the fact that each gene can encode more than one protein, proteome turns to be much more complex than genome [18]. One of the major mechanisms behind this outstanding variability of unique protein structures is underlied by their covalent modifications, occurring either co- or post-translationally [19]. Resulting chemical structures and reactions behind their formation vary essentially in eukaryotes with alkylation, glycosylation, hydroxylation, oxidation, and phosphorylation being the most widely spread. During the last decades, these modifications were shown to play an important role in modulation of the protein structure and function contributing in regulation of cell homeostasis [20].

The majority of these modifications are enzyme-dependent. Thus, reversible phosphorylation of serine, threonine and tyrosine residues in eukaryotic proteins plays an important role in signal transduction, regulation of cellular metabolism and the cell cycle [21]. Indeed, intracellular signal transduction relies on finely tuned activities of specific kinases and phosphatases, thus the patterns of corresponding phosphorylation sites clearly indicate activation or inhibition of these enzymes and, hence, the whole signaling pathways, related to their activity [22]. On the other hand, glycosylation of serine and asparagine residues in membrane and secretory proteins is often involved in cell-cell recognition [23]. Besides, characteristic and structurally unique glycan moieties target corresponding glycoproteins to specific cellular compartments [24]. Not less importantly, acetylation of lysine residues in core histones plays a key role in regulation of the functional state of chromatin [25], whereas hydroxylation of proline residues stabilizes the tertiary structure of collagens [26]. The common features of enzyme-dependent modifications include site and residue specificity and often reversibility. In contrast, non-enzymatic modifications are not site-specific (no consensus sequence required) and are mostly irreversible [27].

These non-enzymatic modifications of cellular and extracellular proteins are represented with oxidation, deamidation, glyco- and lipoxidation. Deamidation occurs at glutamine and asparagine residues and accompanies age-related deleterious alterations in protein structure [28]. Protein oxidation is mediated by reactive oxygen species (ROS), and can occur at the polypeptide backbone [29], or target methionine, cysteine, lysine, tyrosine and tryptophan residues [30]. Oxidative modifications are the markers of protein damage [31] and are known to render proteins for degradation in the proteasome

[32]. On the other hand, reversible oxidation of cysteine residues impacts on the regulation of cellular metabolism and physiology, underlying the phenomenon of ROS-signaling [33, 34]. Glycation, as well as closely related glyco- and lipoxidation [35], represents one of the most structurally heterogeneous non-enzymatic post-translational modification, characterized with an array of biological effects, many of which are still waiting for a thorough study.

2.3 Protein glycation

Glycation is usually referred to as the reaction of proteins with reducing sugars and dicarbonyl products of their degradation [36]. In general, glycation can be considered as a complex process, including degradation of reducing sugars, formation of reactive carbonyl compounds and covalent modification of protein. Therefore, glycation is often termed as Maillard reaction of proteins [37]. The formation of the sugar-protein complex through a series of chemical reactions was described by the French chemist Louis Camille Maillard (1878-1936) in 1912 [38]. Later on Mario Amadori identified N-D-glycosylamine is an intermediate in interaction of D-glucose with amino acids [39, 40], whereas Richard Kuhn und Alfredo Dansi identified 1-amino-1-deoxy-D-fructose as the product of a subsequent double bond migration [41] (Figure 1) [42].

Figure 1 Pathways of early and advanced glycation [42] (oxidative glycosylation [43], Namiki pathway [44], enolization [45], oxidative [46] and non-oxidative (enolization and dehydration stages are not mentioned) [47] degradation of early glycation products, polyol pathway [48] and lipid peroxidation [49].

This event is referred to as Amadori rearrangement and its product is termed as Amadori compound [39]. In 1961 formation of deoxyaldoses (Heyns products) was shown in reaction of amino acids with ketoses [50]. Both reactions rely on formation of corresponding relatively labile Schiff base

intermediates [51] and might take from minutes to weeks depending on temperature and reacting glycation agent (typically sugar) [52, 53].

These early glycation products are readily involved in further oxidation, degradation and rearrangement reactions yielding a heterogeneous group of advanced glycation end-products (AGEs, Figure 2). In mammals, AGEs are formed predominantly via so-called glycoxidative pathway, i.e. degradation of protein-bound early glycation products [54]. On the other hand, AGEs can be generated via the reactions of a-dicarbonyls, like glyoxal (GO), methylglyoxal (MGO) and 3-deoxyglucosone (3-DG), with lysyl and arginyl residues of proteins [55]. These highly-reactive intermediates are continuously generated in living organisms via oxidative degradation of sugars [55, 56], lipid catabolism [57], polyol pathway [58] and non-enzymatic conversion of glycolytic triosephosphate intermediates -glyceraldehyde-3-phosphate and dihydroxyacetone phosphate [59] (Figure 1). The latter mechanism can be judged as one of the principle contributors in a-dicarbonyl generation under stress conditions, when glycolysis is suppressed [60-62]. The second potent source of a-dicarbonyl compounds is metal-catalyzed monosaccharide autoxidation, i.e. of oxidation of sugar hydroperoxides in Fenton reaction [63, 64].

Despite their high heterogeneity (Figure 2), AGEs can be classified according their origin (lysine- or/and arginine-derived) [65, 66], formation pathways (i.e. formed via glycoxidation/Namiki pathway, oxidative glycosylation or non-oxidative pathway) [44, 67, 68], chemical structure (aliphatic, cyclic and heterocyclic) [69] and physical-chemical properties (fluorescent and non-fluorescent) [70,71]. Thus, depending on conditions, at least the half of such lysine-derived AGEs as N-(carboxymethyl)lysine (CML) and N-(carboxyethyl)lysine (CEL) are formed via the glycoxidative pathway [54, 72-75], cyclic pyrraline originates from the non-oxidative pathway [76-78], whereas heterocyclic GO- and MGO-derived hydroimidazolones (Glarg and MG-H, respectively) are formed exclusively by "oxidative glycosylation" - via direct interaction with a-dicarbonyls with arginyl side chains [79-83]. Such modifications, as N^-(carboxymethyl)- and N^-(2-carboxyethyl)arginine (CMA and CEA, respectively) represent the products of hydroimidazolone alkaline hydrolysis [84,85]. Formation of amide AGEs might relay on both glucoxidative and autoxidative pathways [45, 86]. Some AGEs, like pentosidine and vesperlysine (Figure 2) have pronounced fluorescent properties, representing on the group of cross-linking AGEs [87, 88]. Remarkably, some cross-linking AGEs (like, for example, GO-derived lysine dimer, GOLD [89], glucosepane [90] Figure 2) are not fluorescent. Thus, individual pathways advanced glycation reactions clearly differ in respect of the intermediates involved, resulting products and manifested biological effects.

Заключение диссертации по теме «Другие cпециальности», Соболева Алена Вадимовна

207 7. Выводы

1. Для идентификации гликированных пептидов был использован подход восходящей протеомики, основанный на триптическом протеолизе белков плазмы крови, обогащении гликированных пептидов на да-аминофенилбороновой кислоте и последующем анализе с помощью ЖХ-МС (DDA).

2. В общей сложности было идентифицировано 47 фруктозамин (Амадори)-содержащих сайтов гликирования. Соответствующие триптические пептиды уверенно и воспроизводимо детектировались с высокой интенсивностью сигнала.

3. Относительный количественный анализ без добавления меченых стандартов с последующей статистической обработкой выявил 42 гликированных пептида, представляющих 40 индивидуальных сайтов гликирования в девяти белках плазмы крови. Эти пептиды могут рассматриваться в качестве предполагаемых биомаркеров СД2. Среди них 10 ранее описанных биомаркеров были подтверждены, а для 30 сайтов биомаркерное поведение было продемонстрировано впервые.

4. Отдельные биомаркеры были способны предсказывать СД2 с вероятностью не менее 90 %. Более того, индивидуальные сайты гликирования ряда белков плазмы могут рассматриваться в качестве предполагаемых маркеров краткосрочного гликемического контроля.

5. На основании результатов ЛДА, выполненных для когорт пациентов, страдающих СД2, и нормогликемических индивидуумов, был предложен интегрированный биомаркер СД2 (т. е. набор триптических пептидов, содержащих модификацию - продукты Амадори) с точностью предсказания заболевания до 92 %.

6. Абсолютный количественный анализ с применением внутренних стандартов -дважды меченых гликированных пептидов позволил оценить абсолютные количества и молярные концентрации индивидуальных гликированных пептидов в белках плазмы крови.

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