Comparative analysis of anticoagulant influence on PMI estimation based on porcine blood metabolomics profile measured using GC-MS.

Introduction: Accurate post-mortem interval (PMI) estimation is essential in forensic investigations. Although various methods for PMI determination have been developed, only an approximate estimation is still achievable, and an accurate PMI indication is still challenging. Therefore, in this study, we employed gas chromatography-mass spectrometry (GC-MS)-based metabolomics to assess post-mortem changes in porcine blood samples collected with and without the addition of anticoagulant (EDTA).

Understanding PACS2 syndrome's pathomechanism by studying E209K and E211K mutations.

Phosphofurin acidic cluster sorting protein 2 (PACS2) plays a vital role in maintaining cellular homeostasis by regulating protein trafficking between cellular membranes. This function impacts crucial processes like apoptosis, mitochondria-endoplasmic reticulum interaction, and subsequently Ca flux, lipid biosynthesis, and autophagy. Missense mutations, particularly E209K and E211K, are linked to developmental and epileptic encephalopathy-66 (DEE66), known as PACS2 syndrome.

New Application of an Old Drug: Anti-Diabetic Properties of Phloroglucinol.

Phloroglucinol (PHG), an analgesic and spasmolytic drug, shows promise in preventing high-fat-diet (HFD)-induced non-alcoholic fatty liver disease (NAFLD) and insulin resistance. In Wistar rats, 10 weeks of PHG treatment did not prevent HFD-induced weight gain but significantly mitigated fasting hyperglycemia, impaired insulin responses, and liver steatosis. This protective effect was not linked to hepatic lipogenesis or AMP-activated protein kinase (AMPK) activation.

Probiotic Lactobacillus plantarum 299v supplementation in patients with major depression in a double-blind, randomized, placebo-controlled trial: A metabolomics study.

Background: Understanding the multifactorial nature of major depressive disorder (MDD) is crucial for tailoring treatments. However, the complex interplay of various factors underlying the development and progression of MDD poses significant challenges. Our previous study demonstrated improvements in cognitive functions in MDD patients undergoing treatment with selective serotonin reuptake inhibitors (SSRIs) supplemented with Lactobacillus plantarum 299v (LP299v).

New insight into primary hyperparathyroidism using untargeted metabolomics.

Primary Hyperparathyroidism (PHPT) is characterized by excessive parathormone (PTH) secretion and disrupted calcium homeostasis. Untargeted metabolomics offers a valuable approach to understanding the complex metabolic alterations associated with different diseases, including PHPT. Plasma untargeted metabolomics was applied to investigate the metabolic profiles of PHPT patients compared to a control group.

Extracellular matrix hyaluronan modulates fat cell differentiation and primary cilia dynamics.

Hyaluronan is an important extracellular matrix component, with poorly documented physiological role in the context of lipid-rich adipose tissue. We have investigated the global impact of hyaluronan removal from adipose tissue environment by in vitro exposure to exogenous hyaluronidase (or heat inactivated enzyme). Gene set expression analysis from RNA sequencing revealed downregulated adipogenesis as a main response to hyaluronan removal from human adipose tissue samples, which was confirmed by hyaluronidase-mediated inhibition of adipocyte differentiation in the 3T3L1 adipose cell line.

imputomics: web server and R package for missing values imputation in metabolomics data.

Motivation: Missing values are commonly observed in metabolomics data from mass spectrometry. Imputing them is crucial because it assures data completeness, increases the statistical power of analyses, prevents inaccurate results, and improves the quality of exploratory analysis, statistical modeling, and machine learning. Numerous Missing Value Imputation Algorithms (MVIAs) employ heuristics or statistical models to replace missing information with estimates.

Metabolomic profile of acute myeloid leukaemia parallels of prognosis and response to therapy.

The heterogeneity of acute myeloid leukemia (AML), a complex hematological malignancy, is caused by mutations in myeloid cells affecting their differentiation and proliferation. Thus, various cytogenetic alterations in AML cells may be characterized by a unique metabolome and require different treatment approaches. In this study, we performed untargeted metabolomics to assess metabolomics differences between AML patients and healthy controls, AML patients with different treatment outcomes, AML patients in different risk groups based on the 2017 European LeukemiaNet (ELN) recommendations for the diagnosis and management of AML, AML patients with and without FLT3-ITD mutation, and a comparison between patients with FLT3-ITD, CBF-AML (Core binding factor acute myelogenous leukemia), and MLL AML (mixed-lineage leukemia gene) in comparison to control subjects.

Serum metabolomics identified specific lipid compounds which may serve as markers of disease progression in patients with Alström and Bardet-Biedl syndromes.

Alström syndrome (ALMS) and Bardet-Biedl syndrome (BBS) are among the so-called ciliopathies and are associated with the development of multiple systemic abnormalities, including early childhood obesity and progressive neurodegeneration. Given the progressive deterioration of patients' quality of life, in the absence of defined causal treatment, it seems reasonable to identify the metabolic background of these diseases and search for their progression markers. The aim of this study was to find metabolites characteristic to ALMS and BBS, correlating with clinical course parameters, and related to the diseases progression.

Glioma and post-translational modifications: A complex relationship.

Post-translational modifications (PTMs) are common covalent processes in biochemical pathways that alter protein function and activity. These modifications occur through proteolytic cleavage or attachment of modifying groups, such as phosphoryl, methyl, glycosyl, or acetyl groups, with one or more amino acid residues of a single protein. Some PTMs also present crosstalk abilities that affect both protein functionality and structure, creating new proteoforms.

A single extraction 96-well method for LC-MS/MS quantification of urinary eicosanoids, steroids and drugs.

Urinary eicosanoid concentrations reflect inflammatory processes in multiple diseases and have been used as biomarkers of disease as well as suggested for patient stratification in precision medicine. However, implementation of urinary eicosanoid profiling in large-scale analyses is restricted due to sample preparation limits. Here we demonstrate a single solid-phase extraction of 300 µL urine in 96-well-format for prostaglandins, thromboxanes, isoprostanes, cysteinyl-leukotriene E and the linoleic acid-derived dihydroxy-octadecenoic acids (9,10- and 12,13-DiHOME).

Searching for Effective Methods of Diagnosing Nervous System Lesions in Patients with Alström and Bardet-Biedl Syndromes.

Bardet-Biedl syndrome (BBS) and Alström syndrome (ALMS) are rare multisystem diseases with an autosomal recessive mode of inheritance and genetic heterogeneity, characterized by visual impairment, hearing impairment, cardiomyopathy, childhood obesity, and insulin resistance. The purpose of our study was to evaluate the indicators of nervous system changes occurring in patients with ALMS and BBS using optical coherence tomography (OCT) and magnetic resonance spectroscopy (MRS) methods compared to a group of healthy subjects. The OCT results showed significantly lower macular thickness in the patient group compared to the control group ( = 0.

Adaptation of the AbsoluteIDQ p180 kit to the analysis of metabolites in the human aqueous humor.

The aim of this study was to use the commercial kit AbsoluteIDQ p180 (Biocrates) for the quantification of metabolites in aqueous humor (AH), as well as to determine the optimal volume of AH that is necessary to obtain reliable and reproducible results. Different volumes of AH (10 µl, 20 µl, and 30 µl) were tested. Of the 188 metabolites measurable with the Biocrates kit, 69 were detected in AH.

Simultaneous Comparison of Aqueous Humor and Serum Metabolic Profiles of Diabetic and Nondiabetic Patients Undergoing Cataract Surgery-A Targeted and Quantitative Metabolomics Study.

The aim of this study was to compare the aqueous humor (AH) and serum concentrations of metabolites in diabetic ( = 36) and nondiabetic ( = 36) senior adults undergoing cataract surgery. Blood samples were collected before surgery and AH during surgery. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS)-based targeted metabolomic and lipidomic analyses of samples were performed using the AbsoluteIDQ p180 kit.

Applied Molecular-Based Quality Control of Biobanked Samples for Multi-Omics Approach.

Biobanks are vital for high-throughput translational research, but the rapid development of novel molecular techniques, especially in omics assays, poses challenges to traditional practices and recommendations. In our study, we used biospecimens from oncological patients in Polish clinics and collaborated with the Indivumed Group. For serum/plasma samples, we monitored hemolysis, controlled RNA extraction, assessed cDNA library quality and quantity, and verified NGS raw data.

A comparison of different machine-learning techniques for the selection of a panel of metabolites allowing early detection of brain tumors.

Metabolomics combined with machine learning methods (MLMs), is a powerful tool for searching novel diagnostic panels. This study was intended to use targeted plasma metabolomics and advanced MLMs to develop strategies for diagnosing brain tumors. Measurement of 188 metabolites was performed on plasma samples collected from 95 patients with gliomas (grade I-IV), 70 with meningioma, and 71 healthy individuals as a control group.

Extent of interocular (a)symmetry based on the metabolomic profile of human aqueous humor.

Interocular comparison of the metabolomic signature of aqueous humor (AH) was performed. The aim of the study was to quantitatively evaluate the symmetry in concentrations of various metabolites belonging to different categories. The study included AH samples from 23 patients, 74.

Evaluation of the Oral Bacterial Genome and Metabolites in Patients with Wolfram Syndrome.

In Wolfram syndrome (WFS), due to the loss of wolframin function, there is increased ER stress and, as a result, progressive neurodegenerative disorders, accompanied by insulin-dependent diabetes. The aim of the study was to evaluate the oral microbiome and metabolome in WFS patients compared with patients with type 1 diabetes mellitus (T1DM) and controls. The buccal and gingival samples were collected from 12 WFS patients, 29 HbA1c-matched T1DM patients ( = 0.

In Vitro Animal Model for Estimating the Time since Death with Attention to Early Postmortem Stage.

Estimating the postmortem interval (PMI) has remained the subject of investigations in forensic medicine for many years. Every kind of death results in changes in metabolites in body tissues and fluids due to lack of oxygen, altered circulation, enzymatic reactions, cellular degradation, and cessation of anabolic production of metabolites. Metabolic changes may provide markers determining the time since death, which is challenging in current analytical and observation-based methods.

The Beneficial Effect of Cinnamon and Red Capsicum Intake on Postprandial Changes in Plasma Metabolites Evoked by a High-Carbohydrate Meal in Men with Overweight/Obesity.

The relationship of high-carbohydrate (HC) meal intake to metabolic syndrome is still not fully explained. Metabolomics has the potential to indicate metabolic pathways altered by HC meals, which may improve our knowledge regarding the mechanisms by which HC meals may contribute to metabolic syndrome development. The fasting and postprandial metabolic response to HC or normo-carbohydrate (NC) meals with/without cinnamon + capsicum intake was evaluated using untargeted metabolomics and compared between normal-weight (NW) and overweight/obese (OW/OB) healthy men.

Optimization of a GC-MS method for the profiling of microbiota-dependent metabolites in blood samples: An application to type 2 diabetes and prediabetes.

Changes in serum or plasma metabolome may reflect gut microbiota dysbiosis, which is also known to occur in patients with prediabetes and type 2 diabetes (T2DM). Thus, developing a robust method for the analysis of microbiota-dependent metabolites (MDMs) is an important issue. Gas chromatography with mass spectrometry (GC-MS) is a powerful approach enabling detection of a wide range of MDMs in biofluid samples with good repeatability and reproducibility, but requires selection of a suitable solvents and conditions.