Patient classification and attribute assessment based on machine learning techniques in the qualification process for surgical treatment of adrenal tumours.

Adrenal gland incidentaloma is frequently identified through computed tomography and poses a common clinical challenge. Only selected cases require surgical intervention. The primary aim of this study was to compare the effectiveness of selected machine learning (ML) techniques in proper qualifying patients for adrenalectomy and to identify the most accurate algorithm, providing a valuable tool for doctors to simplify their therapeutic decisions. The secondary aim was to assess the significance of attributes for classification accuracy. In total, clinical data were collected from 33 patients who underwent adrenalectomy. Histopathological assessments confirmed the proper selection of 21 patients for surgical intervention according to the guidelines, with accuracy reaching 64%. Statistical analysis showed that Supported Vector Machines (linear) were significantly better than the baseline (p < 0.05), with accuracy reaching 91%, and imaging features of the tumour were found to be the most crucial attributes. In summarise, ML methods may be helpful in qualifying patients for adrenalectomy.

Cardiovascular risk factors in mild adrenal autonomous cortisol secretion in a Caucasian population.

Cardiovascular risk factors could be present in mild adrenal autonomous cortisol secretion (MACS). However, the most frequent cardiovascular risk factors in MACS have not been established. The aim of the presseent study was to analyse the difference in cardiovascular risk factors in patients with MACS in comparison to those with non-functioning adrenal tumour (NFAT). A total of 295 patients with adrenal incidentaloma were included in this retrospective study. We divided our group into those who showed suppression in 1 mg overnight dexamethasone suppression test (DST) (NFAT) (serum cortisol level ≤1.8 µg/dL) and those who did not show suppression in the DST (MACS) (serum concentration of cortisol > 1.8 µg/dL and ≤5 µg/dL). In the studied groups, we analysed the presence of cardiovascular risk factors, such as obesity, prediabetes, type 2 diabetes mellitus (T2DM), hypertension, hyperlipidaemia, chronic kidney disease and cardiovascular events. In our study, 18.9% of patients were defined as MACS. Importantly, T2DM was diagnosed in 41% of MACS vs 23% of NFAT (P < 0.01) and higher frequency of occurrence of hyperlipidaemia in NFAT (72.4%) vs MACS (53.6%) (P = 0.01) was observed. We did not observed differences in the frequency of obesity, hypertension, chronic kidney disease, prediabetes, atrial fibrillation, stroke, ST and non-ST elevation myocardial infarction and coronary angioplasty between patients with MACS and NFAT (all P > 0.05; respectively). In MACS, T2DM is more prevalent than in NFAT; hyperlipidaemia is more prevalent in NFAT. Accordingly, no differences were found in the incidence of obesity, hypertension, prediabetes, chronic kidney disease between studied groups as well as cardiovascular events.

P2RY8 variants in lupus patients uncover a role for the receptor in immunological tolerance.

B cell self-tolerance is maintained through multiple checkpoints, including restraints on intracellular signaling and cell trafficking. P2RY8 is a receptor with established roles in germinal center (GC) B cell migration inhibition and growth regulation. Somatic P2RY8 variants are common in GC-derived B cell lymphomas. Here, we identify germline novel or rare P2RY8 missense variants in lupus kindreds or the related antiphospholipid syndrome, including a "de novo" variant in a child with severe nephritis. All variants decreased protein expression, F-actin abundance, and GPCR-RhoA signaling, and those with stronger effects increased AKT and ERK activity and cell migration. Remarkably, P2RY8 was reduced in B cell subsets from some SLE patients lacking P2RY8 gene variants. Low P2RY8 correlated with lupus nephritis and increased age-associated B cells and plasma cells. By contrast, P2RY8 overexpression in cells and mice restrained plasma cell development and reinforced negative selection of DNA-reactive developing B cells. These findings uncover a role of P2RY8 in immunological tolerance and lupus pathogenesis.

Assessment of different markers of ovarian reserve in women with papillary thyroid cancer treated with radioactive iodine.

Treatment with radioactive iodine (RAI) in women with differentiated thyroid cancer is associated with decreased serum concentrations of anti-Müllerian hormone (AMH); however, other markers have not been investigated. Therefore, this study aimed to evaluate the effect of RAI treatment on antral follicle count (AFC) and the serum concentration of inhibin B, follicle-stimulating hormone (FSH), and AMH in women with papillary thyroid cancer (PTC) treated with RAI. We examined 25 women at a median age of 33 years treated with a single dose of RAI. We divided the participants into women over (n = 11) and under 35 years of age (n = 14). Serum concentrations of inhibin B, FSH, AMH, and AFC were assessed at baseline and 1 year after RAI treatment. We found decreased AFC (P = 0.03), serum levels of AMH (P < 0.01), inhibin B (P = 0.03), but not FSH (P = 0.23), 1 year after RAI treatment in comparison to baseline in the whole group. When we compared serum levels of AMH in younger vs older women separately, we observed a significant reduction of this hormone's serum level after RAI treatment in both groups (P < 0.01; P = 0.04, respectively). We concluded that RAI treatment significantly impacts the functional ovarian reserve in premenopausal women with PTC.

The Association of Serum Levels of Leptin and Ghrelin with the Dietary Fat Content in Non-Obese Women with Polycystic Ovary Syndrome.

Women with polycystic ovary syndrome (PCOS) are at an increased risk of developing insulin resistance and abdominal obesity in the state of an improper diet balance. Leptin is a peptide considered to be a satiety hormone that plays an important role in the long-term energy balance, whereas ghrelin is a hormone that controls short-term appetite regulation and is considered a hunger hormone. The aim of the present study was to assess the relationship between serum leptin and ghrelin concentrations and the dietary macronutrient content in PCOS women. We examined 73 subjects: 39 women diagnosed with PCOS by the Rotterdam criteria and 34 healthy controls, matched by the body mass index. The subjects completed a consecutive three-day dietary diary to identify the macronutrient and micronutrient intake. Serum concentrations of leptin and total ghrelin were measured and homeostasis model assessment of insulin resistance (HOMA-IR) was calculated. The studied groups did not differ significantly in terms of the intake of macronutrients (proteins, fats, and carbohydrates) and serum concentrations of ghrelin and leptin (all p > 0.05). In the PCOS group, the serum leptin concentration positively correlated with the intake of total fat (r = 0.36, p = 0.02), total cholesterol (r = -0.36, p = 0.02), saturated fatty acids (r = 0.43, p < 0.01), and monounsaturated fatty acids (MUFA) (r = 0.37, p = 0.02), whereas the serum ghrelin concentration correlated in an inverse manner with the intake of total fat (r = -0.37, p = 0.02), MUFA (r = -0.37, p = 0.02), polyunsaturated fatty acids (r = -0.34, p = 0.03), and long chain polyunsaturated fatty acids (r = -0.38, p = 0.02). In this group, we also found a negative association of HOMA-IR with serum ghrelin levels (r = -0.4, p = 0.03) and a positive relationship with the serum leptin concentration (r = 0.5, p < 0.01) and relationships between HOMA-IR and total dietary fat (r = 0.38, p = 0.03) and MUFA (r = 0.35, p = 0.04) intake. In PCOS women, dietary components such as the total fat and type of dietary fat and HOMA-IR are positively connected to serum leptin concentrations and negatively connected to serum ghrelin concentrations, which may influence the energy balance.

Ovarian Reserve and Serum Concentration of Thyroid Peroxidase Antibodies in Euthyroid Women With Different Polycystic Ovary Syndrome Phenotypes.

Objective: It has been shown that women with polycystic ovary syndrome (PCOS), as well as Hashimoto's thyroiditis (HT), are characterized by increased incidence of infertility. Serum anti-Müllerian hormone (AMH), which reflects ovarian reserve, is elevated in PCOS women and is decreased in women with HT. The Rotterdam criteria recognize four clinical PCOS phenotypes, i.e., phenotypes A, B, C, and D. The aim of the present study was to investigate the relation between serum concentrations of thyroid peroxidase antibodies (TPOAbs) and ovarian reserve in different PCOS phenotypes. Patients and methods: We examined 141 women with PCOS [phenotype A was diagnosed in 67 (47.5%) women, phenotype B in 30 (21.3%), phenotype C in 28 (19.9%), and phenotype D in 16 (11.3%)] and 88 control subjects of similar age; all women were euthyroid. Serum concentrations of AMH, thyroid-stimulating hormone (TSH), thyroid hormones, and TPOAbs were assessed. Results: We observed positive serum TPOAbs in 21.9% women with PCOS and in 23.9% controls (p = 0.07). We did not find differences in the frequency of detection of positive serum TPOAbs between phenotypes A, B, and C and the control group (p > 0.05). We did not observe a difference in AMH levels between TPOAbs-positive and TPOAbs-negative women, both in the control group and the PCOS women (all p > 0.05). However, serum AMH concentration was markedly higher in the whole PCOS group (p < 0.01) and in phenotype A (p < 0.01) vs. controls when the serum concentration of TPOAbs was negative. In the groups with positive serum levels of TPOAbs, serum concentration of AMH did not differ between PCOS phenotypes and controls (p = 0.23). Additionally, we observed that serum AMH concentration was related to the level of TPOAbs in the PCOS group (r = -0.4, p = 0.02). Conclusions: The frequency of serum detection of positive TPOAbs did not differ between PCOS phenotypes with clinical/biochemical hyperandrogenism and the control group. The observation of the difference in serum AMH between the PCOS and control groups only in TPOAbs negative women together with the inverse relation of TPOAbs with serum AMH only in the PCOS group might suggest that ovarian reserve is influenced by TPOAbs in PCOS.

Decreased deiodinase activity after glucose load could lead to atherosclerosis in euthyroid women with polycystic ovary syndrome.

OBJECTIVE: Glucose and lipid disturbances, as well as higher tendency to atherosclerosis, are observed in women with polycystic ovary syndrome (PCOS). Thyroid hormones action has long been recognized as an important determinant of glucose and lipid homeostasis. Some studies suggest that even in euthyroid subjects, thyroid function may affect atherosclerosis risk factors. The aim of this study was to evaluate the relationships between thyroid hormonal status and glucose and lipid profile before and after oral glucose tolerance test (OGTT) in PCOS women in comparison to the control group. PATIENTS AND METHODS: The study group included 98 women-60 women with PCOS and 38 women matched for age and BMI as a control group. OGTT with estimation of plasma glucose and lipids, as well as serum insulin and thyroid hormones (TH) concentrations was performed. Activity of peripheral deiodinases at baseline (SPINA-GD1) and at the 120 min of OGTT (SPINA-GD2) was calculated according to the formula by Dietrich et al. as a measure of T4-T3 conversion efficiency. Delta GD was estimated as SPINA-GD1-SPINA-GD2, and delta fT3 was calculated as a difference between fT3 before and after OGTT. RESULTS: We did not find differences in TH, SPINA-GDs, and plasma lipid concentrations between PCOS and control group before and after OGTT. Glucose load resulted in a decrease of level TSH, TC, TG, HDL-C, and LDL-C concentrations in women with PCOS, as well as in the control group (all p < 0.05). We found that GD (p = 0.01) and serum fT3 concentration (p = 0.0008) decreased during glucose load only in the PCOS group. We observed a positive relationship between delta fT3 and plasma TG concentration (r = 0.36, p = 0.004), delta GD and plasma TG concentration after glucose load (r = 0.34, p = 0.007), only in the PCOS group. We also found negative relationship between SPINA-GD2 and plasma TC concentration (r = -0.29, p = 0.02) after glucose load and positive relationship between delta GD and insulin at the 60 min of OGTT (r = 0.29, p = 0.02), only in the PCOS women. CONCLUSIONS: These data showed insufficient conversion of fT4 to fT3, as well as a relationship of SPINA-GDs with insulin, TC and TG in PCOS women after glucose load. It may suggest that disturbances in deiodinase activity after glucose load might promote atherosclerosis in PCOS women.

Structure and expression of conserved Wnt pathway components in the demosponge Amphimedon queenslandica.

Wnt-signalling plays a critical role in animal development, and its misregulation results in serious human diseases, including cancer. While the Wnt pathway is well studied in eumetazoan models, little is known about the evolutionary origin of its components and their functions. Here, we have identified key machinery of the Wnt-ß-catenin (canonical)-signalling pathway that is encoded in the Amphimedon queenslandica (Demospongiae; Porifera) genome, namely Wnt, Fzd, SFRP, Lrp5/6, Dvl, Axin, APC, GSK3, ß-catenin, Tcf, and Groucho. Most of these genes are not detected in the choanoflagellate and other nonmetazoan eukaryotic genomes. In contrast, orthologues of some of key components of bilaterian Wnt-planar cell polarity and Wnt/Ca(2+) are absent from the Amphimedon genome, suggesting these pathways evolved after demosponge and eumetazoan lineages diverged. Sequence analysis of the identified proteins of the Wnt-ß-catenin pathway has revealed the presence of most of the conserved motifs and domains responsible for protein-protein and protein-DNA interactions in vertebrates and insects. However, several protein-protein interaction domains appear to be absent from the Amphimedon Axin and APC proteins. These are also missing from their orthologues in the cnidarian Nematostella vectensis, suggesting that they are bilaterian novelties. All of the analyzed Wnt pathway genes are expressed in specific patterns during Amphimedon embryogenesis. Most are expressed in especially striking and highly dynamic patterns during formation of a simple organ-like larval structure, the pigment ring. Overall, our results indicate that the Wnt-ß-catenin pathway was used in embryonic patterning in the last common ancestor of living metazoans. Subsequently, gene duplications and a possible increase in complexity of protein interactions have resulted in the precisely regulated Wnt pathway observed in extant bilaterian animals.

The Amphimedon queenslandica genome and the evolution of animal complexity.

Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization. Comparative analysis enabled by the sequencing of the sponge genome reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion and diversification of pan-metazoan transcription factor, signalling pathway and structural genes. This diverse 'toolkit' of genes correlates with critical aspects of all metazoan body plans, and comprises cell cycle control and growth, development, somatic- and germ-cell specification, cell adhesion, innate immunity and allorecognition. Notably, many of the genes associated with the emergence of animals are also implicated in cancer, which arises from defects in basic processes associated with metazoan multicellularity.

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

BACKGROUND: Defining the location of genes and the precise nature of gene products remains a fundamental challenge in genome annotation. Interrogating tandem mass spectrometry data using genomic sequence provides an unbiased method to identify novel translation products. A six-frame translation of the entire human genome was used as the query database to search for novel blood proteins in the data from the Human Proteome Organization Plasma Proteome Project. Because this target database is orders of magnitude larger than the databases traditionally employed in tandem mass spectra analysis, careful attention to significance testing is required. Confidence of identification is assessed using our previously described Poisson statistic, which estimates the significance of multi-peptide identifications incorporating the length of the matching sequence, number of spectra searched and size of the target sequence database. RESULTS: Applying a false discovery rate threshold of 0.05, we identified 282 significant open reading frames, each containing two or more peptide matches. There were 627 novel peptides associated with these open reading frames that mapped to a unique genomic coordinate placed within the start/stop points of previously annotated genes. These peptides matched 1,110 distinct tandem MS spectra. Peptides fell into four categories based upon where their genomic coordinates placed them relative to annotated exons within the parent gene. CONCLUSION: This work provides evidence for novel alternative splice variants in many previously annotated genes. These findings suggest that annotation of the genome is not yet complete and that proteomics has the potential to further add to our understanding of gene structures.

Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project.

The pilot phase of the HUPO Plasma Proteome Project (PPP) is an international collaboration to catalog the protein composition of human blood plasma and serum by analyzing standardized aliquots of reference serum and plasma specimens using a variety of experimental techniques. Data management for this project included collection, integration, analysis, and dissemination of findings from participating organizations world-wide. Accomplishing this task required a communication and coordination infrastructure specific enough to support meaningful integration of results from all participants, but flexible enough to react to changing requirements and new insights gained during the course of the project and to allow participants with varying informatics capabilities to contribute. Challenges included integrating heterogeneous data, reducing redundant information to minimal identification sets, and data annotation. Our data integration workflow assembles a minimal and representative set of protein identifications, which account for the contributed data. It accommodates incomplete concordance of results from different laboratories, ambiguity and redundancy in contributed identifications, and redundancy in the protein sequence databases. Recommendations of the PPP for future large-scale proteomics endeavors are described.

Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories.

With the human Plasma Proteome Project (PPP) pilot phase completed, the largest and most ambitious proteomics experiment to date has reached its first milestone. The correspondingly impressive amount of data that came from this pilot project emphasized the need for a centralized dissemination mechanism and led to the development of a detailed, PPP specific data gathering infrastructure at the University of Michigan, Ann Arbor as well as the protein identifications database project at the European Bioinformatics Institute as a general proteomics data repository. One issue that crept up while discussing which data to store for the PPP concerns whether the raw, binary data coming from the mass spectrometers should be stored, or rather the more compact and already significantly processed peak lists. As this debate is not restricted to the PPP but relates to the proteomics community in general, we will attempt to detail the relative merits and caveats associated with centralized storage and dissemination of raw data and/or peak lists, building on the extensive experience gained during the PPP pilot phase. Finally, some suggestions are made for both immediate and future storage of MS data in public repositories.