Machine-learning-based Analysis Identifies miRNA Expression Profile for Diagnosis and Prediction of Colorectal Cancer: A Preliminary Study.

BACKGROUND: The stage of colorectal cancer (CRC) at the day of diagnosis has the greatest influence on survival rate. Thus, for CRC, which is mainly identified as advanced disease, non-invasive, molecular blood or stool tests could boost the diagnosis and lower mortality. Evaluation of miRNA expression levels in serum of patients diagnosed with CRC is a potential tool in early screening. Screening can be supported by machine learning (ML) as a tool for developing a cancer risk predictive model based on genetic data. MATERIALS AND METHODS: miRNA was isolated from the serum of 8 patients diagnosed with CRC and 10 patients from a control group matched for age and sex. The expression of 179 miRNAs was determined using a serum/plasma panel (Exiqon). Determinations were conducted using real-time PCR technique on an Applied Biosystems QuantStudio3 device in 96-well plates. A predictive model was developed through the Azure Machine Learning platform. RESULTS: A wide panel of 29 up-regulated miRNAs in CRC were identified and divided into two subgroups: 1) miRNAs with significantly higher serum level in cancer patients vs. controls (24 miRNAs) and 2) miRNAs detected only in cancer patients and not in controls (5 miRNAs). Re-analysis of published miRNA profiles of CRC tumours or CRC exosomes revealed that only 2 out of 29 miRNAs were up-regulated in all datasets including ours (miR-34a and miR-25-3p). CONCLUSION: Our research suggests the potential role of overexpressed miRNAs as diagnostic or prognostic biomarkers among CRC patients. Such clustering of miRNAs may be a potential direction for discovering new diagnostic panels of cancer (including CRC), especially using ML. The low correspondence between deregulation of miRNAs in serum and tumour tissue revealed in our study confirms previously published reports.

DNA methylation in adipocytes from visceral and subcutaneous adipose tissue influences insulin-signaling gene expression in obese individuals.

OBJECTIVE: Both obesity and insulin resistance are characterized by severe long-term changes in the expression of many genes of importance in the regulation of metabolism. Because these changes occur throughout life, as a result of external factors, the disorders of gene expression could be epigenetically regulated. MATERIALS/METHODS: We analyzed the relationship between obesity and insulin resistance in enrolled patients by means of evaluation of the expression rate of numerous genes involved in the regulation of adipocyte metabolism and energy homeostasis in subcutaneous and visceral adipose tissue depots. We also investigated global and site-specific DNA methylation as one of the main regulators of gene expression. Visceral and subcutaneous adipose tissue biopsies were collected from 45 patients during abdominal surgery in an age range of 40-60 years. RESULTS: We demonstrated hypermethylation of PPARG, INSR, SLC2A4, and ADIPOQ promoters in obese patients with insulin resistance. Moreover, the methylation rate showed a negative correlation with the expression of the investigated genes. More, we showed a correlation between the expression of PPARG and the expression of numerous genes important for proper insulin action. Given the impact of PPARγ on the regulation of the cell insulin sensitivity through modulation of insulin pathway genes expression, hypermethylation in the PPARG promoter region may constitute one of the epigenetic pathways in the development of insulin resistance in obesity. CONCLUSIONS: Our research shows that epigenetic regulation through excessive methylation may constitute a link between obesity and subsequent insulin resistance.

Metabolic Differences between Subcutaneous and Visceral Adipocytes Differentiated with an Excess of Saturated and Monounsaturated Fatty Acids.

Obesity is a major health problem in highly industrialized countries. High-fat diet (HFD) is one of the most common causes of obesity and obesity-related disorders. There are considerable differences between fat depots and the corresponding risks of metabolic disorders. We investigated the various effects of an excess of fatty acids (palmitic 16:0, stearic 18:0, and oleic acids 18:1n-9) on adipogenesis of subcutaneous- and visceral-derived mesenchymal stem cells (MSCs) and phenotypes of mature adipocytes. MSCs of white adipose tissue were acquired from adipose tissue biopsies obtained from subcutaneous and visceral fat depots from patients undergoing abdominal surgery. The MSCs were extracted and differentiated in vitro with the addition of fatty acids. Oleic acid stimulated adipogenesis, resulting in higher lipid content and larger adipocytes. Furthermore, oleic acid stimulated adipogenesis by increasing the expression of CCAAT enhancer binding protein ß (CEBPB) and peroxisome proliferator activated receptor γ (PPARG). All of the examined fatty acids attenuated the insulin-signaling pathway and radically reduced glucose uptake following insulin stimulation. Visceral adipose tissue was shown to be more prone to generate inflammatory stages. The subcutaneous adipose tissue secreted a greater quantity of adipokines. To summarize, oleic acid showed the strongest effect on adipogenesis. Furthermore, all of the examined fatty acids attenuated insulin signaling and secretion of cytokines and adipokines.

High Primary Antibiotic Resistance of Helicobacter pylori Strains Isolated from Pediatric and Adult Patients in Poland during 2016-2018.

Monitoring the antibiotic resistance of H. pylori is an important step in the effective treatment of this bacterium, thus the aim of the present study was to assess the prevalence of antimicrobial resistance of H. pylori strains isolated from pediatric and adult patients with primary infections in 2016-2018. Antral biopsies from 334 treatment-naïve patients (126 children and 208 adults) were obtained. A total of 71 clinical H. pylori strains (22 from children and 49 from adults) were isolated and examined for amoxicillin (AMX), clarithromycin (CLR), metronidazole (MTZ), tetracycline (TET), and levofloxacin (LEV) susceptibility. The activity of the antibiotics was measured by E-tests. Strains were considered as resistant to antibiotics with minimum inhibitory concentrations (MICs) equal to ≥0.125 µg/mL (AMX), ≥0.5 µg/mL (CLR), ≥8 µg/mL (MTZ), and ≥1 µg/mL (TET and LEV). The highest prevalence of antibiotic resistance in H. pylori strains was observed for CLR and MTZ, at frequencies of 54.5% and 31.8% vs. 30.6% and 46.9% for children and adults, respectively. A much lower frequency of isolation of resistant strains was demonstrated for LEV and TET, this being 9.1% and 4.5% vs. 18.4% and 4.1% for pediatric and adult patients, respectively. The presence of AMX-resistant strains was not observed. The H. pylori strains isolated from Polish patients with primary infections showed a high level of antibiotic resistance to CLR and MTZ (>30%).

Obesity-induced insulin resistance via changes in the DNA methylation profile of insulin pathway genes.

BACKGROUND: Obesity has been shown to play a key role in the development of insulin resistance (IR). Abundant data implicate obesity in DNA hypermethylation at global and site-specific levels, including genes regulating insulin sensitivity. Deregulation of epigenetic marks implicates gene expression and changes in cell metabolism. OBJECTIVES: Our previous reports demonstrated that the strongest risk factor in the development of IR is BMI; accordingly, the objective of this study was to investigate the effect of obesity on DNA methylation and insulin sensitivity. MATERIAL AND METHODS: A study was carried out on lymphocytes (N-34) and visceral adipose tissue (VAT; N-35) of insulin-resistant subjects and healthy controls. Genetic material (DNA and RNA) was extracted from cells. Global and site-specific DNA methylation was analyzed with the use of restriction enzymes followed by real-time polymerase chain reaction (PCR). Gene expression was analyzed as relative mRNA level normalized to a housekeeping gene. RESULTS: Global DNA methylation increased in both types of tissue in obese and insulin-resistant individuals and correlated positively with IR. Two of the 3 investigated promoters of insulin pathway genes were hypermethylated, which correlated negatively with gene expression and positively with IR. The DNMT3a gene was upregulated in obese insulin-resistant individuals in both types of tissues and correlated positively with global DNA methylation. CONCLUSIONS: DNA methylation profile changed depending on body mass index (BMI) and influenced glucose metabolism and insulin sensitivity in VAT.

Serum and urine 1H NMR-based metabolomics in the diagnosis of selected thyroid diseases.

Early detection of nodular thyroid diseases including thyroid cancer is still primarily based on invasive procedures such as fine-needle aspiration biopsy. Therefore, there is a strong need for development of new diagnostic methods that could provide clinically useful information regarding thyroid nodular lesions in a non-invasive way. In this study we investigated 1H NMR based metabolic profiles of paired urine and blood serum samples, that were obtained from healthy individuals and patients with nodular thyroid diseases. Estimation of predictive potential of metabolites was evaluated using chemometric methods and revealed that both urine and serum carry information sufficient to distinguish between patients with nodular lesions and healthy individuals. Data fusion allowed to further improve prediction quality of the models. However, stratification of tumor types and their differentiation in relation to each other was not possible.

Ileal pouch morphology and microbiology in ulcerative colitis patients.

BACKGROUND: Ideal pouch created during restorative proctocolectomy is a new gastrointestinal organ--"neorectum". Although it is made from the ileum, it takes over function of the removed rectum. This new function results in significant morphological changes in pouch's mucous membrane, which becomes similar to the large bowel mucosa. The most common pathology of the ileal pouch is its inflammation--pouchitis. One of the suspected causes of pouchitis is bacterial flora disturbance. OBJECTIVES: The aim of the study was to analyze the morphological and microbiological changes in ileal pouches in different time periods after ileostomy closure and to evaluate the influence of certain bacterial strains on the degree of inflammation. MATERIAL AND METHODS: The study involved 47 patients who had been treated surgically; they were investigated before and at different stages after ileostomy closure. They underwent repeated rectoscopies with biopsies of pouch mucosa and swabs for microbiological examination. In total 89 rectoscopies were performed, which provided 70 histopathological results according to the Heidelberg Pouchitis Activity Score and 87 microbiological test results. RESULTS: The assessment of the morphology of intestinal pouches showed increased signs of chronic inflammation as the length of time after the closure of a protective ileostomy increased. There was no correlation between the signs of acute inflammation and the length of time after surgery; there were more signs of acute inflammation in cases of pouchitis. The composition of the bacterial flora of intestinal pouches changed as the length of time after ileostomy closure increased, with significant increases in the number of enterobacteriaceae species. The presence of Staphylococcus aureus significantly correlates with a higher degree of chronic inflammation; this bacterium may be a potential infectious factor in pouchitis. CONCLUSIONS: Microbiological analysis of intestinal pouch lumen is a useful tool that can be used in routine follow-up assessment of intestinal pouches as well as in diagnosing pouchitis.

Serum and urine metabolomic fingerprinting in diagnostics of inflammatory bowel diseases.

AIM: To evaluate the utility of serum and urine metabolomic analysis in diagnosing and monitoring of inflammatory bowel diseases (IBD). METHODS: Serum and urine samples were collected from 24 patients with ulcerative colitis (UC), 19 patients with the Crohn's disease (CD) and 17 healthy controls. The activity of UC was assessed with the Simple Clinical Colitis Activity Index, while the activity of CD was determined using the Harvey-Bradshaw Index. The analysis of serum and urine samples was performed using proton nuclear magnetic resonance (NMR) spectroscopy. All spectra were exported to Matlab for preprocessing which resulted in two data matrixes for serum and urine. Prior to the chemometric analysis, both data sets were unit variance scaled. The differences in metabolite fingerprints were assessed using partial least-squares-discriminant analysis (PLS-DA). Receiver operating characteristic curves and area under curves were used to evaluate the quality and prediction performance of the obtained PLS-DA models. Metabolites responsible for separation in models were tested using STATISTICA 10 with the Mann-Whitney-Wilcoxon test and the Student's t test (α = 0.05). RESULTS: The comparison between the group of patients with active IBD and the group with IBD in remission provided good PLS-DA models (P value 0.002 for serum and 0.003 for urine). The metabolites that allowed to distinguish these groups were: N-acetylated compounds and phenylalanine (up-regulated in serum), low-density lipoproteins and very low-density lipoproteins (decreased in serum) as well as glycine (increased in urine) and acetoacetate (decreased in urine). The significant differences in metabolomic profiles were also found between the group of patients with active IBD and healthy control subjects providing the PLS-DA models with a very good separation (P value < 0.001 for serum and 0.003 for urine). The metabolites that were found to be the strongest biomarkers included in this case: leucine, isoleucine, 3-hydroxybutyric acid, N-acetylated compounds, acetoacetate, glycine, phenylalanine and lactate (increased in serum), creatine, dimethyl sulfone, histidine, choline and its derivatives (decreased in serum), as well as citrate, hippurate, trigonelline, taurine, succinate and 2-hydroxyisobutyrate (decreased in urine). No clear separation in PLS-DA models was found between CD and UC patients based on the analysis of serum and urine samples, although one metabolite (formate) in univariate statistical analysis was significantly lower in serum of patients with active CD, and two metabolites (alanine and N-acetylated compounds) were significantly higher in serum of patients with CD when comparing jointly patients in the remission and active phase of the diseases. Contrary to the results obtained from the serum samples, the analysis of urine samples allowed to distinguish patients with IBD in remission from healthy control subjects. The metabolites of importance included in this case up-regulated acetoacetate and down-regulated citrate, hippurate, taurine, succinate, glycine, alanine and formate. CONCLUSION: NMR-based metabolomic fingerprinting of serum and urine has the potential to be a useful tool in distinguishing patients with active IBD from those in remission.

Follicular adenomas exhibit a unique metabolic profile. ¹H NMR studies of thyroid lesions.

Thyroid cancer is the most common endocrine malignancy. However, more than 90% of thyroid nodules are benign. It remains unclear whether thyroid carcinoma arises from preexisting benign nodules. Metabolomics can provide valuable and comprehensive information about low molecular weight compounds present in living systems and further our understanding of the biology regulating pathological processes. Herein, we applied ¹H NMR-based metabolic profiling to identify the metabolites present in aqueous tissue extracts of healthy thyroid tissue (H), non-neoplastic nodules (NN), follicular adenomas (FA) and malignant thyroid cancer (TC) as an alternative way of investigating cancer lesions. Multivariate statistical methods provided clear discrimination not only between healthy thyroid tissue and pathological thyroid tissue but also between different types of thyroid lesions. Potential biomarkers common to all thyroid lesions were identified, namely, alanine, methionine, acetone, glutamate, glycine, lactate, tyrosine, phenylalanine and hypoxanthine. Metabolic changes in thyroid cancer were mainly related to osmotic regulators (taurine and scyllo- and myo-inositol), citrate, and amino acids supplying the TCA cycle. Thyroid follicular adenomas were found to display metabolic features of benign non-neoplastic nodules and simultaneously displayed a partial metabolic profile associated with malignancy. This finding allows the discrimination of follicular adenomas from benign non-neoplastic nodules and thyroid cancer with similar accuracy. Moreover, the presented data indicate that follicular adenoma could be an individual stage of thyroid cancer development.