Application of Proteomics and Machine Learning Methods to Study the Pathogenesis of Diabetic Nephropathy and Screen Urinary Biomarkers.

Diabetic nephropathy (DN) has become the main cause of end-stage renal disease worldwide, causing significant health problems. Early diagnosis of the disease is quite inadequate. To screen urine biomarkers of DN and explore its potential mechanism, this study collected urine from 87 patients with type 2 diabetes mellitus (which will be classified into normal albuminuria, microalbuminuria, and macroalbuminuria groups) and 38 healthy subjects. Twelve individuals from each group were then randomly selected as the screening cohort for proteomics analysis and the rest as the validation cohort. The results showed that humoral immune response, complement activation, complement and coagulation cascades, renin-angiotensin system, and cell adhesion molecules were closely related to the progression of DN. Five overlapping proteins (KLK1, CSPG4, PLAU, SERPINA3, and ALB) were identified as potential biomarkers by machine learning methods. Among them, KLK1 and CSPG4 were positively correlated with the urinary albumin to creatinine ratio (UACR), and SERPINA3 was negatively correlated with the UACR, which were validated by enzyme-linked immunosorbent assay (ELISA). This study provides new insights into disease mechanisms and biomarkers for early diagnosis of DN.

iTRAQ proteomics analysis of placental tissue with gestational diabetes mellitus.

BACKGROUND: Gestational diabetes mellitus is an endocrine and metabolic disorder that appears for the first time during pregnancy and causes varying degrees of short- and/or long-term effects on the mother and child. The etiology of the disease is currently unknown and isobaric tags for relative and absolute quantitation proteomics approach, the present study attempted to identify potential proteins in placental tissues that may be involved in the pathogenesis of GDM and adverse foetal pregnancy outcomes. METHODS: Pregnant women with GDM hospitalised were selected as the experimental group, and pregnant women with normal glucose metabolism as the control group. The iTRAQ protein quantification technology was used to screen the differentially expressed proteins between the GDM group and the normal control group, and the differentially expressed proteins were analysed by GO, KEGG, PPI, etc., and the key proteins were subsequently verified by western blot. RESULTS: Based on the proteomics of iTRAQ, we experimented with three different samples of placental tissues from GDM and normal pregnant women, and the total number of identified proteins were 5906, 5959, and 6017, respectively, which were similar in the three different samples, indicating that the results were reliable. Through the Wayne diagram, we found that the total number of proteins coexisting in the three groups was 4475, and 91 differential proteins that could meet the quantification criteria were strictly screened, of which 32 proteins were up-regulated and 59 proteins were down-regulated. By GO enrichment analysis, these differential proteins are widely distributed in extracellular membrane-bounded organelle, mainly in extracellular exosome, followed by intracellular vesicle, extracellular organelle. It not only undertakes protein binding, protein complex binding, macromolecular complex binding, but also involves molecular biological functions such as neutrophil degranulation, multicellular organismal process, developmental process, cellular component organization, secretion, regulated exocytosis. Through the analysis of the KEGG signaling pathway, it is found that these differential proteins are mainly involved in HIF-1 signaling pathway, Glycolysis/Gluconeogenesis, Central carbon metabolism in cancer, AMPK signaling pathway, Proteoglycans in cancer, Protein processing in endoplasmic reticulum, Thyroid cancer, Alcoholism, Glucagon signaling pathway. DISCUSSION: This preliminary study helps us to understand the changes in the placental proteome of GDM patients, and provides new insights into the pathophysiology of GDM.

Proteomic analysis of the effects of Dictyophora polysaccharide on arsenic-induced hepatotoxicity in rats.

Arsenic (As) is a highly toxic environmental toxicant and a known human carcinogen. Long-term exposure to As can cause liver injury. Dictyophora polysaccharide (DIP) is a biologically active natural compound found in the Dictyophora with excellent antioxidation, anti-inflammation, and immune protection properties. In this study, the Sprague-Dawley (SD) rat model of As toxicity was established using a feeding method, followed by DIP treatment in rats with As-induced liver injury. The molecular mechanisms of As toxicity to the rat liver and the protective effect of DIP were investigated by proteomic studies. The results showed that 172, 328 and 191 differentially expressed proteins (DEPs) were identified between the As-exposed rats versus control rats (As/Ctrl), DIP treated rats versus As-exposed rats (DIP+As/As), and DIP treated rats versus control rats (DIP+As /Ctrl), respectively. Among them, the expression of 90 DEPs in the As/Ctrl groups was reversed by DIP treatment. As exposure caused dysregulation of metabolic pathways, mitochondria, oxidative stress, and apoptosis-related proteins in the rat liver. However, DIP treatment changed or restored the levels of these proteins, which attenuated the damage to the livers of rats caused by As exposure. The results provide new insights into the mechanisms of liver injury induced by As exposure and the treatment of DIP in As poisoning.

The effect of the number of conjugated C=C bonds on the ESIPT and ICT reactions of SNCN derivatives.

The electronic structure of the molecule is significantly influenced by the number of conjugated C=C bonds. In this work, the influence of the conjugated C=C bonds of the SNCN derivatives on the excited state intramolecular proton transfer (ESIPT) and intramolecular charge transfer (ICT) properties are studied by density functional theory (DFT) and time-dependent density functional theory (TDDFT). The calculation level is proved to be reasonable by calculating electronic spectra. The hydrogen bond parameters, infrared vibrational frequency (IR), reduction density gradient (RDG) isosurface, topological analysis and potential energy curves of SNCN derivatives in ground state (S0) and the first excited state (S1) are analyzed. According to theoretical research results, ESIPT reaction has a higher likelihood of occurring in the S1 state. Moreover, the ESIPT reaction becomes more challenging to occur with the number of conjugated C=C bonds rising. Finally, the analyses of the frontier molecular orbitals (FMOs), dipole moment and charge transfer transition confirm that the ICT effect is aided by the increased number of conjugated C=C bonds. This work indicates that the number of conjugated C=C bonds can regulate the ESIPT and ICT processes, which provides guidance for the study of fluorescent groups with similar characteristics.

Substituent effects on the ESIPT process and the potential applications in materials transport field of 2'-aminochalcone derivatives.

This work investigates the different charge transfer characteristics and excited state intramolecular proton transfer process (ESIPT) of 2'-aminochalcones derivatives carrying different electron-withdrawing groups. Four new molecules are designed in the experiment and named as 2c, 3c, 4c and 5c, respectively. (Dyes and Pigments, 2022, 202.) Based on these four molecules, the effect of substituents on the ESIPT process and the charge transfer process are discussed in detail in our work. According to the study of the related parameters at the hydrogen bond site, infrared vibration spectrum, interaction region indicator isosurface (IRI) and scatter plots, it is concluded that the hydrogen bond interaction is enhanced under photoexcitation, and the descending order of the excited state hydrogen bond strength is 3c > 5c > 4c > 2c. The hydrogen bond energy is calculated by atoms in moleculs (AIM) topological analysis and core-valence bifurcation (CVB) index. The potential energy curve reveals the ESIPT mechanism. Frontier molecular orbital and electron-hole analyses explain the reasons for the changes in the ESIPT process at the electronic level. In addition, the ionization potentials (IPa and IPv), affinity energies (EAa and EAv) and reorganization energies are calculated to evaluate the potential application value of organic molecules in material transport field.

Regulating and controlling the stepwise ESDPT channel of BP(OH)2DCEt2 using the strategy of solvent polarity and external electric field.

Excited state double proton transfer (ESDPT) has attracted great scientific interest because of its excellent luminescent properties. However, the complex process of ESDPT has plagued theoretical and experimental scientists for a long time and has become a hot issue. In this work, the ESDPT process of 2,2'-bipyridine-3,3'-diol-5,5'-dicarboxylic acid ethyl ester (BP(OH)2DCEt2) is systematically studied and the regulation of the ESDPT process is further realized. The potential energy curves indicate that BP(OH)2DCEt2 shows the characteristics of stepwise ESDPT in different polar solvents. The increase in solvent polarity will be beneficial to the stepwise ESDPT reaction. Regrettably, it is not possible to distinguish the specific stepwise transfer path of the BP(OH)2DCEt2 molecule due to the symmetry of the potential energy surface along the diagonal. On this basis, we proposed a method to control and regulate the stepwise ESDPT path using an external electric field. The results show that the increase of external electric field intensity is favorable to stepwise ESDPT. It is interesting to note that applying an external electric field in a specific direction will effectively distinguish stepwise ESDPT reaction paths. Therefore, this work not only helps to understand the mechanism of ESDPT, but also contributes to regulation and design of new luminescent materials with excellent luminescent properties.

Effects of arsenic exposure on blood trace element levels in rats and sex differences.

Arsenic (As) is a widespread environmental metalloid and human carcinogen, and its exposure is associated with a wide range of toxic effects, leading to serious health hazards. As poisoning is a complex systemic multi-organ and multi-system damage disease. In this study, a rat model of As poisoning was established to investigate the levels of trace elements in the blood of rats and sex differences in the effect of As on every trace elements in rat blood. Twenty 6-week-old SD (Sprague Dawley) rats were randomly divided into the control group and the As-exposed group. After 3 months, the contents of 19 elements including As in the blood were detected in these two groups by inductively coupled plasma mass spectrometry (ICP-MS). As levels in the blood of As-exposed rats were significantly higher than those in the control group, with increased levels of Rb, Sr, Cs and Ce, and decreased levels of Pd. As showed a significant positive correlation with Rb. There were significant sex differences in blood Se, Pd, Eu, Dy, Ho, and Au levels in the As-exposed group. The results showed that As exposure can lead to an increase of As content in blood and an imbalance of some elements. There were sex differences in the concentration and the correlation between elements of some elements. Elemental imbalances may affect the toxic effects of As and play a synergistic or antagonistic role in As toxicity.

Autism spectrum disorder: pathogenesis, biomarker, and intervention therapy.

Autism spectrum disorder (ASD) has become a common neurodevelopmental disorder. The heterogeneity of ASD poses great challenges for its research and clinical translation. On the basis of reviewing the heterogeneity of ASD, this review systematically summarized the current status and progress of pathogenesis, diagnostic markers, and interventions for ASD. We provided an overview of the ASD molecular mechanisms identified by multi-omics studies and convergent mechanism in different genetic backgrounds. The comorbidities, mechanisms associated with important physiological and metabolic abnormalities (i.e., inflammation, immunity, oxidative stress, and mitochondrial dysfunction), and gut microbial disorder in ASD were reviewed. The non-targeted omics and targeting studies of diagnostic markers for ASD were also reviewed. Moreover, we summarized the progress and methods of behavioral and educational interventions, intervention methods related to technological devices, and research on medical interventions and potential drug targets. This review highlighted the application of high-throughput omics methods in ASD research and emphasized the importance of seeking homogeneity from heterogeneity and exploring the convergence of disease mechanisms, biomarkers, and intervention approaches, and proposes that taking into account individuality and commonality may be the key to achieve accurate diagnosis and treatment of ASD.

Investigating metabolic dysregulation in serum of triple transgenic Alzheimer's disease male mice: implications for pathogenesis and potential biomarkers.

Alzheimer's disease (AD) is a multifactorial neurodegenerative disease that lacks convenient and accessible peripheral blood diagnostic markers and effective drugs. Metabolic dysfunction is one of AD risk factors, which leaded to alterations of various metabolites in the body. Pathological changes of the brain can be reflected in blood metabolites that are expected to explain the disease mechanisms or be candidate biomarkers. The aim of this study was to investigate the changes of targeted metabolites within peripheral blood of AD mouse model, with the purpose of exploring the disease mechanism and potential biomarkers. Targeted metabolomics was used to quantify 256 metabolites in serum of triple transgenic AD (3 × Tg-AD) male mice. Compared with controls, 49 differential metabolites represented dysregulation in purine, pyrimidine, tryptophan, cysteine and methionine and glycerophospholipid metabolism. Among them, adenosine, serotonin, N-acetyl-5-hydroxytryptamine, and acetylcholine play a key role in regulating neural transmitter network. The alteration of S-adenosine-L-homocysteine, S-adenosine-L-methionine, and trimethylamine-N-oxide in AD mice serum can served as indicator of AD risk. The results revealed the changes of metabolites in serum, suggesting that metabolic dysregulation in periphery in AD mice may be related to the disturbances in neuroinhibition, the serotonergic system, sleep function, the cholinergic system, and the gut microbiota. This study provides novel insights into the dysregulation of several key metabolites and metabolic pathways in AD, presenting potential avenues for future research and the development of peripheral biomarkers.

Effects of substitution and conjugation on photophysical properties of ESIPT-based fluorophores with the core of 4-aminophthalimide.

4-Aminophthalimide is a highly fluorescent signaling unit with excellent photophysical properties and wide application foregrounds. Based on this, a range of theoretical investigations are conducted on the fluorescent probe (E)-5-((2-hydroxybenzylidene) amino) isoindoline-1, 3-dione (HID) with the core of 4-aminophthalimide using density functional theory (DFT) and time-containing density functional theory (TD-DFT) methods in this paper. The optimized configurations, vertical excitation and emission energies, electronic characteristics and excited-state intramolecular proton transfer (ESIPT) behaviors of the probe HID are discussed in detail. Furthermore, to enhance the luminescent properties of HID, five novel compounds have been designed based on the structure of HID by introducing amino, methoxy and naphthalene groups (-NH2, -OMe and C10H8). Our work thoroughly explores how the property and position of substituents and conjugation affect photophysical characteristics and ESIPT processes. We find that the ESIPT dynamics can be modulated by the substitution and conjugation effects. Specifically, the introduction of amino and methoxy groups at the ortho-position and the introduction of the naphthalene group promote the ESIPT behavior of HID1, whereas the introduction of amino and methoxy groups at the meta-position exhibits the contrary impact. Therefore, we boldly infer that the introduction of electron-donating groups in the ortho-position and the introduction of the conjugated group make the ESIPT process more effortless to occur, whereas the introduction of substituents with opposing natures in the meta-position makes the ESIPT process more difficult to occur. In addition, the ionization potentials (IP), electron affinities (EA) and reorganization energies (λh and λe) of molecules are calculated to assess their potential as luminescent materials. Our work not only reveals the luminescence and ESIPT mechanism of the probe HID1, but also proposes to modulate the ESIPT process through the substitution and conjugation effects. In particular, the designed molecules have better photoelectric properties as a result of their red-shifted absorption and fluorescence spectra, smaller energy gaps, larger transferred charges and greater charge transferred distances, which offers some valuable ideas for the experimental development of more efficient organic luminescent materials with ESIPT properties.

Effects of arsenic exposure on trace element levels in the hippocampus and cortex of rats and their gender differences.

BACKGROUND: Exposure to arsenic (As) is a major public health challenge worldwide. Chronic exposure to As can cause various human health effects, including skin diseases, cardiovascular disease, neurological disorders, and cancer. Studies have shown that As exposure can lead to disturbances in the balance of trace elements in the body. Moreover, As readily crosses the blood-brain barrier and can be enriched in the hippocampus and cortex, causing neurotoxic damage. At present, there are few reports on the effect of As on trace element levels in the central nervous system (CNS). Therefore, we sought to explore As-induced neurotoxicity and the effects of As on CNS trace element levels. METHODS: An As-induced neurological injury model in rats was established by feeding As chow for 90 days of continuous exposure, and 19 elements were detected in the hippocampus and cortex of As-exposed rats by inductively coupled plasma mass spectrometry. RESULTS: The results showed that the As levels in the hippocampus and cortex of As-exposed rats were significantly higher than those in the control group, The As levels in the cortex were significantly higher than in the hippocampus group. The levels of Cd, Ho, and Rb were increased in the hippocampus and decreased in Au, Ba, Ce, Cs, Pd, Se, Sr, and Tl in the As-exposed group, while the levels of Cd and Rb were increased and Se and Au were decreased in the cortex. Significant gender differences in the effects of As on hippocampal Cd, Ba, Rb, and Sr, and cortical Cd and Mo. CONCLUSION: It is suggested that elemental imbalance may be a risk factor for developing As toxicity plays a synergistic or antagonistic role in As-induced toxicity and is closely related to As-induced CNS damage.

A study of genetic heterogeneity in autism spectrum disorders based on plasma proteomic and metabolomic analysis: multiomics study of autism heterogeneity.

Genetic heterogeneity poses a challenge to research and clinical translation of autism spectrum disorder (ASD). In this study, we conducted a plasma proteomic and metabolomic study of children with ASD with and without risk genes (de novo mutation) and controls to explore the impact of genetic heterogeneity on the search for biomarkers for ASD. In terms of the proteomic and metabolomic profiles, the groups of children with ASD carrying and those not carrying de novo mutation tended to cluster and overlap, and integrating them yielded differentially expressed proteins and differential metabolites that effectively distinguished ASD from controls. The mechanisms associated with them focus on several common and previously reported mechanisms. Proteomics results highlight the role of complement, inflammation and immunity, and cell adhesion. The main pathways of metabolic perturbations include amino acid, vitamin, glycerophospholipid, tryptophan, and glutamates metabolic pathways and solute carriers-related pathways. Integrating the two omics analyses revealed that L-glutamic acid and malate dehydrogenase may play key roles in the pathogenesis of ASD. These results suggest that children with ASD may have important underlying common mechanisms. They are not only potential therapeutic targets for ASD but also important contributors to the study of biomarkers for the disease.

Targeted Metabolomic Analysis of the Eye Tissue of Triple Transgenic Alzheimer's Disease Mice at an Early Pathological Stage.

Alzheimer's disease (AD) is a severe neurodegenerative disease in older people. Despite some consensus on pathogenesis of AD established by previous researches, further elucidation is still required for better understanding. This study analyzed the eye tissues of 2- and 6-month-old triple transgenic AD (3 × Tg-AD) male mice and age-sex-matched wild-type (WT) mice using a targeted metabolomics approach. Compared with WT mice, 20 and 44 differential metabolites were identified in 2- and 6-month-old AD mice, respectively. They were associated with purine metabolism, pantothenate and CoA biosynthesis, pyruvate metabolism, lysine degradation, glycolysis/gluconeogenesis, and pyrimidine metabolism pathways. Among them, 8 metabolites presented differences in both the two groups, and 5 of them showed constant trend of change. The results indicated that the eye tissues of 3 × Tg-AD mice underwent changes in the early stages of the disease, with changes in metabolites observed at 2 months of age and more pronounced at 6 months of age, which is consistent with our previous studies on hippocampal targeted metabolomics in 3 × Tg-AD mice. Therefore, a joint analysis of data from this study and previous hippocampal study was performed, and the differential metabolites and their associated mechanisms were similar in eye and hippocampal tissues, but with tissue specificity.

Subcellular proteomics insights into Alzheimer's disease development.

Alzheimer's disease (AD), one of the most common dementias, is a neurodegenerative disease characterized by cognitive impairment and decreased judgment function. The expected number of AD patient is increasing in the context of the world's advancing medical care and increasing human life expectancy. Since current molecular mechanism studies on AD pathogenesis are incomplete, there is no specific and effective therapeutic agent. Mass spectrometry (MS)-based unbiased proteomics studies provide an effective and comprehensive approach. Many advances have been made in the study of the mechanism, diagnostic markers, and drug targets of AD using proteomics. This paper focus on subcellular level studies, reviews studies using proteomics to study AD-associated mitochondrial dysfunction, synaptic, and myelin damage, the protein composition of amyloid plaques (APs) and neurofibrillary tangles (NFTs), changes in tissue extracellular vehicles (EVs) and exosome proteome, and the protein changes in ribosomes and lysosomes. The methods of sample separation and preparation and proteomic analysis as well as the main findings of these studies are involved. The results of these proteomics studies provide insights into the pathogenesis of AD and provide theoretical resource and direction for future research in AD, helping to identify new biomarkers and drugs targets for AD.

A Systematic Investigation of Complement and Coagulation-Related Protein in Autism Spectrum Disorder Using Multiple Reaction Monitoring Technology.

Autism spectrum disorder (ASD) is one of the common neurodevelopmental disorders in children. Its etiology and pathogenesis are poorly understood. Previous studies have suggested potential changes in the complement and coagulation pathways in individuals with ASD. In this study, using multiple reactions monitoring proteomic technology, 16 of the 33 proteins involved in this pathway were identified as differentially-expressed proteins in plasma between children with ASD and controls. Among them, CFHR3, C4BPB, C4BPA, CFH, C9, SERPIND1, C8A, F9, and F11 were found to be altered in the plasma of children with ASD for the first time. SERPIND1 expression was positively correlated with the CARS score. Using the machine learning method, we obtained a panel composed of 12 differentially-expressed proteins with diagnostic potential for ASD. We also reviewed the proteins changed in this pathway in the brain and blood of patients with ASD. The complement and coagulation pathways may be activated in the peripheral blood of children with ASD and play a key role in the pathogenesis of ASD.

Study on the Mechanism of Arsenic-Induced Lung Injury Based on SWATH Proteomics Technology.

Chronic arsenic poisoning is a global health problem that affects millions of people, and studies have found that long-term ingestion of arsenic-containing compounds can lead to lung damage, but the exact mechanism is unknown. In this study, Sprague-Dawley (SD) rats were used as the research object, and the proteomic analysis method based on sequential window acquisition of all theoretical fragment ions (SWATH) was used to detect the changes in the expression levels of related proteins in the lung tissue of arsenic-exposed rats, and to explore the mechanism of arsenic compound-induced lung injury. The results showed that arsenic exposure resulted in the abnormal expression of collagen type III and proteins involved in metabolic, immune, and cellular processes, leading to the dysfunction of important pathways associated with these proteins, resulting in lung injury. It suggested that the underlying mechanism of arsenic-induced lung injury may be related to oxidative stress, immune injury, cell junction, and collagen type III. This result provides a new research idea for revealing the mechanism of lung injury caused by arsenic exposure.

Unveiling the sensing mechanism and luminescence property of a new ESIPT-based fluorescent sensor for detecting Zn2.

Recently, based on the mechanism of excited-state intramolecular proton transfer (ESIPT), a new fluorescent probe named 3-(benzo[d]thiazol-2-yl)-5-bromosalicylaldehyde-4N-phenyl thiosemicarbazone (BTT) was successfully synthesized [Analyst 146 (2021) 4348-4356.]. However, the importance of ESIPT processes of BTT probe and the mechanism of detecting Zn2+ ions have not been studied in detail. In this study, the photochemical behavior of ESIPT-chromophore and the photophysical changes of detecting Zn2+ ions were explained at the molecular level for the first time. The calculated spectral values were in agreement with the experiment. We not only confirmed the excited state hydrogen-bond strengthening by interaction region indicator (IRI), but also scanned the potential energy curves of BTT molecule in different electronic states, which confirmed that the hydrogen proton is easier to transfer in the first excited state. In addition, we had given the reasonable structure of the BTT-Zn2+ complex (L1) by comparing the binding free energies. The hole-electron distribution and interfragment charge transfer (IFCT) methods proved the excitation type of intraligand charge transfer (ILCT). Finally, the photophysical phenomenon of BTT for detecting Zn2+ ions is explained by calculating the electronic spectra and the energy gap (Egap) between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO).