Abstract 1958: Developing an online tool to validate survival-associated miRNAs utilizing expression data from 2,061 breast cancer patients

Background. MicroRNAs (miRNAs) are small non-coding RNAs capable of simultaneously regulating multiple gene networks, and affecting breast cancer patients’ outcome. Here we present the development of an online tool for the real-time meta-analysis of published miRNA datasets to identify novel prognostic biomarkers in breast cancer.

Methods. First, a comprehensive database was set up by searching GEO, TCGA, and PubMed repositories to identify datasets with published miRNA expression and clinical data. Due to platform differences, each dataset was processed separately. Kaplan-Meier and Cox regression analyses were performed to investigate the prognostic value of a set of dysregulated miRNAs in breast cancer. The complete analysis tool can be accessed online at: www.kmplot.com/mirna.

Results. Overall, 2,061 samples from four independent datasets were integrated into the tool including the expression signature of 1,302 distinct miRNAs. In addition to overall survival data, ER status (n = 2,039), histological grade (n = 1,396) and lymph node status (n = 1,933) are also available. By using our online tool, we demonstrated the prognostic value of some of the previous reported miRNAs implicated in breast cancer. For instance, miR-29c, miR-34c, miR-101, miR-125, and miR-190b, showed a consistent prognostic value in at least three out of four breast cancer datasets.

Discussion. In summary, we established the first online integrated platform for the rapid identification of the prognostic value of miRNAs in breast cancer.

Citation Format: Balázs Győrffy, András Lánczky, Giulia Bottai, Ádám Nagy, András Szabó, Libero Santarpia. Developing an online tool to validate survival-associated miRNAs utilizing expression data from 2,061 breast cancer patients. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1958.

Comparison of the amount of bioaccessible fumonisin B1 and B2 in maize and rice inoculated with Fusarium verticillioides (MRC 826) and determined by in vitro digestion-preliminary results

In this study the occurrence of hidden fumonisin B1 (FB1) and fumonisin B2 (FB2) was analysed, on two cereal substrates (maize and rice), inoculated with Fusarium verticillioides (MRC 826), in order to determine the ratio of hidden FB1 and FB2. Two parallel methods were applied: an in vitro human digestion sample pre-treatment and the routine extraction procedure, in both cases with subsequent LC-MS analysis. It was found that all samples showed higher concentration of total fumonisin B1 after digestion, as compared to that of free fumonisin analysed only after extraction. The percentage of the hidden form by maize was 18.8 % (±2.4) for FB1 and 36.8 % (±3.8) for FB2, while for rice it was 32.3 % (±11.3) and 58.0 (±6.8), respectively, expressed as the proportion to total fumonisin B1, for the total dataset. Significant differences were found in the FB1 and FB2 concentration measured after the different digestion phases (saliva, gastric and duodenal) in case of both matrixes. The results are useful for human risk assessment, since both humans and animals may be exposed to markedly higher toxin load, as determined merely by conventional analytical methods.

Complex Formation of Human Proelastases with Procarboxypeptidases A1 and A2

The pancreas secretes digestive proenzymes typically in their monomeric form. A notable exception is the ternary complex formed by proproteinase E, chymotrypsinogen C, and procarboxypeptidase A (proCPA) in cattle and other ruminants. In the human and pig pancreas binary complexes of proCPA with proelastases were found. To characterize complex formation among human pancreatic protease zymogens in a systematic manner, we performed binding experiments using recombinant proelastases CELA2A, CELA3A, and CELA3B; chymotrypsinogens CTRB1, CTRB2, CTRC, and CTRL1; and procarboxypeptidases CPA1, CPA2, and CPB1. We found that proCELA3B bound not only to proCPA1 (KD 43 nm) but even more tightly to proCPA2 (KD 18 nm), whereas proCELA2A bound weakly to proCPA1 only (KD 152 nm). Surprisingly, proCELA3A, which shares 92% identity with proCELA3B, did not form stable complexes due to the evolutionary replacement of Ala(241) with Gly. The polymorphic nature of position 241 in both CELA3A (∼4% Ala(241) alleles) and CELA3B (∼2% Gly(241) alleles) points to individual variations in complex formation. The functional effect of complex formation was delayed procarboxypeptidase activation due to increased affinity of the inhibitory activation peptide, whereas proelastase activation was unchanged. We conclude that complex formation among human pancreatic protease zymogens is limited to a subset of proelastases and procarboxypeptidases. Complex formation stabilizes the inhibitory activation peptide of procarboxypeptidases and thereby increases zymogen stability and controls activation.

In vivo confinement promotes collective migration of neural crest cells

Collective cell migration is fundamental throughout development and in many diseases. Spatial confinement using micropatterns has been shown to promote collective cell migration in vitro, but its effect in vivo remains unclear. Combining computational and experimental approaches, we show that the in vivo collective migration of neural crest cells (NCCs) depends on such confinement. We demonstrate that confinement may be imposed by the spatiotemporal distribution of a nonpermissive substrate provided by versican, an extracellular matrix molecule previously proposed to have contrasting roles: barrier or promoter of NCC migration. We resolve the controversy by demonstrating that versican works as an inhibitor of NCC migration and also acts as a guiding cue by forming exclusionary boundaries. Our model predicts an optimal number of cells in a given confinement width to allow for directional migration. This optimum coincides with the width of neural crest migratory streams analyzed across different species, proposing an explanation for the highly conserved nature of NCC streams during development.

A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients

Background

The use of somatic mutations for predicting clinical outcome is difficult because a mutation can indirectly influence the function of many genes, and also because clinical follow-up is sparse in the relatively young next generation sequencing (NGS) databanks. Here we approach this problem by linking sequence databanks to well annotated gene-chip datasets, using a multigene transcriptomic fingerprint as a link between gene mutations and gene expression in breast cancer patients.

Methods

The database consists of 763 NGS samples containing mutational status for 22,938 genes and RNA-seq data for 10,987 genes. The gene chip database contains 5,934 patients with 10,987 genes plus clinical characteristics. For the prediction, mutations present in a sample are first translated into a ‘transcriptomic fingerprint’ by running ROC analysis on mutation and RNA-seq data. Then correlation to survival is assessed by computing Cox regression for both up- and downregulated signatures.

Results

According to this approach, the top driver oncogenes having a mutation prevalence over 5 % included AKT1, TRANK1, TRAPPC10, RPGR, COL6A2, RAPGEF4, ATG2B, CNTRL, NAA38, OSBPL10, POTEF, SCLT1, SUN1, VWDE, MTUS2, and PIK3CA, and the top tumor suppressor genes included PHEX, TP53, GGA3, RGS22, PXDNL, ARFGEF1, BRCA2, CHD8, GCC2, and ARMC4. The system was validated by computing correlation between RNA-seq and microarray data (r² = 0.73, P < 1E-16). Cross-validation using 20 genes with a prevalence of approximately 5 % confirmed analysis reproducibility.

Conclusions

We established a pipeline enabling rapid clinical validation of a discovered mutation in a large breast cancer cohort. An online interface is available for evaluating any human gene mutation or combinations of maximum three such genes (http://www.g-2-o.com).

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-015-0228-1) contains supplementary material, which is available to authorized users.

Cell traction in collective cell migration and morphogenesis: the chase and run mechanism

Directional collective cell migration plays an important role in development, physiology, and disease. An increasing number of studies revealed key aspects of how cells coordinate their movement through distances surpassing several cell diameters. While physical modeling and measurements of forces during collective cell movements helped to reveal key mechanisms, most of these studies focus on tightly connected epithelial cultures. Less is known about collective migration of mesenchymal cells. A typical example of such behavior is the migration of the neural crest cells, which migrate large distances as a group. A recent study revealed that this persistent migration is aided by the interaction between the neural crest and the neighboring placode cells, whereby neural crest chase the placodes via chemotaxis, but upon contact both populations undergo contact inhibition of locomotion and a rapid reorganization of cellular traction. The resulting asymmetric traction field of the placodes forces them to run away from the chasers. We argue that this chase and run interaction may not be specific only to the neural crest system, but could serve as the underlying mechanism for several morphogenetic processes involving collective cell migration.

Cadherin Switch during EMT in Neural Crest Cells Leads to Contact Inhibition of Locomotion via Repolarization of Forces

Contact inhibition of locomotion (CIL) is the process through which cells move away from each other after cell-cell contact, and it contributes to malignant invasion and developmental migration. Various cell types exhibit CIL, whereas others remain in contact after collision and may form stable junctions. To investigate what determines this differential behavior, we study neural crest cells, a migratory stem cell population whose invasiveness has been likened to cancer metastasis. By comparing pre-migratory and migratory neural crest cells, we show that the switch from E- to N-cadherin during EMT is essential for acquisition of CIL behavior. Loss of E-cadherin leads to repolarization of protrusions, via p120 and Rac1, resulting in a redistribution of forces from intercellular tension to cell-matrix adhesions, which break down the cadherin junction. These data provide insight into the balance of physical forces that contributes to CIL in cells in vivo.

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Neural crest cells acquire contact inhibition of locomotion (CIL) during EMT

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An E- to N-cadherin switch controls CIL

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E-cadherin represses CIL by controlling Rac1-dependent protrusions via p120

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During CIL, forces are redistributed from intercellular junctions to cell matrix

Mesotrypsin Signature Mutation in a Chymotrypsin C (CTRC) Variant Associated with Chronic Pancreatitis

Human chymotrypsin C (CTRC) protects against pancreatitis by degrading trypsinogen and thereby curtailing harmful intra-pancreatic trypsinogen activation. Loss-of-function mutations in CTRC increase the risk for chronic pancreatitis. Here we describe functional analysis of eight previously uncharacterized natural CTRC variants tested for potential defects in secretion, proteolytic stability, and catalytic activity. We found that all variants were secreted from transfected cells normally, and none suffered proteolytic degradation by trypsin. Five variants had normal enzymatic activity, whereas variant p.R29Q was catalytically inactive due to loss of activation by trypsin and variant p.S239C exhibited impaired activity possibly caused by disulfide mispairing. Surprisingly, variant p.G214R had increased activity on a small chromogenic peptide substrate but was markedly defective in cleaving bovine β-casein or the natural CTRC substrates human cationic trypsinogen and procarboxypeptidase A1. Mutation p.G214R is analogous to the evolutionary mutation in human mesotrypsin, which rendered this trypsin isoform resistant to proteinaceous inhibitors and conferred its ability to cleave these inhibitors. Similarly to the mesotrypsin phenotype, CTRC variant p.G214R was inhibited poorly by eglin C, ecotin, or a CTRC-specific variant of SGPI-2, and it readily cleaved the reactive-site peptide bonds in eglin C and ecotin. We conclude that CTRC variants p.R29Q, p.G214R, and p.S239C are risk factors for chronic pancreatitis. Furthermore, the mesotrypsin-like CTRC variant highlights how the same natural mutation in homologous pancreatic serine proteases can evolve a new physiological role or lead to pathology, determined by the biological context of protease function.

Exhaled methane concentration profiles during exercise on an ergometer

Exhaled methane concentration measurements are extensively used in medical investigation of certain gastrointestinal conditions. However, the dynamics of endogenous methane release is largely unknown. Breath methane profiles during ergometer tests were measured by means of a photoacoustic spectroscopy based sensor. Five methane-producing volunteers (with exhaled methane level being at least 1 ppm higher than room air) were measured. The experimental protocol consisted of 5 min rest--15 min pedalling (at a workload of 75 W)--5 min rest. In addition, hemodynamic and respiratory parameters were determined and compared to the estimated alveolar methane concentration. The alveolar breath methane level decreased considerably, by a factor of 3-4 within 1.5 min, while the estimated ventilation-perfusion ratio increased by a factor of 2-3. Mean pre-exercise and exercise methane concentrations were 11.4 ppm (SD:7.3) and 2.8 ppm (SD:1.9), respectively. The changes can be described by the high sensitivity of exhaled methane to ventilation-perfusion ratio and are in line with the Farhi equation.

Determination of the amount of bioaccessible fumonisin B1 in different matrices after in vitro digestion

Conventional analytical methods used for the analysis of fumonisin content in animal feeds fail to take into account the fumonisin content bound to the matrix, which is otherwise bioaccessible and can be absorbed from the gastrointestinal tract. Moreover, underestimation of fumonisin content using routine analytical methods can affect animal experiments using cereals contaminated by fungi. In the present study, hidden fumonisin B1 was analysed in two cereal substrates (maize and wheat) which were inoculated with Fusarium verticillioides (MRC 826). The study compared a routine extraction procedure with an in vitro digestion sample pre-treatment. We found that all samples showed a higher content of fumonisin B1 after digestion, compared to the free fumonisin obtained only by extraction. The percentage of the hidden form was 38.6% (±18.5) in maize and 28.3% (±17.8) in wheat, expressed as the proportion of total fumonisin B1. These results indicate that the toxin exposure of the animals determined by the routine fumonisin analysis was underestimated, generally by 40%, as bioaccessibility was not taken into consideration. This is crucial in interpretation (and maybe in re-evaluation) of the results obtained from (other) animal experiments.

Influence of lowland forests on subsurface salt accumulation in shallow groundwater areas

In flat sedimentary plains in areas with a sub-humid climate, tree planting on grasslands and arable lands creates strong hydrological shifts. As a result of deep rooting and high water uptake of trees, groundwater levels drop and subsurface salt accumulation increases. Tree planting has expanded globally and in Hungary it reached rates of 15 000 ha year(-1), being focused mainly in the Great Hungarian Plain where forests replace grasslands and crops in a region with widespread shallow groundwater. We performed soil and groundwater observations in 31 pairs of forest and control plots in the region, including gradients of initial water table depth and salinity, soil layering, and tree species and age. Accumulated tree biomass was positively correlated with soil salinization rates following tree planting, being also affected by species (poplar > common oak > black locust) and stand age. Differences among tree species effects appeared to be related to their growth rates. Due to downward deep percolation and salt leaching episodes during the Hungarian winters, the observed salt accumulation rates were lower than those described under similar settings in the warmer Argentine Pampas.

Individual and combined haematotoxic effects of fumonisin B(1) and T-2 mycotoxins in rabbits

Weaned rabbits were fed diets contaminated with 2 mg/kg diet T-2 toxin alone, or 10 mg/kg diet fumonisin B1 (FB1) alone, and both toxins in combination (2+10 mg/kg, resp.), as compared to a toxin free control. Samplings were performed after 2 and 4 weeks. Bodyweight of the T-2 fed group was lower after 4 weeks; the liver weight increased dramatically. Red blood cell (RBC) Na(+)/K(+) ATPase activity decreased after 4 weeks in the T-2 group, it increased in the FB1 group and antagonism was found by the combined treatment. The RBC membrane fatty acid profile was modified by both toxins similarly during the entire feeding. After 4 weeks T-2 alone and in combination (with FB1) was found to increase mean cell volume (MCV). The time-dependent alterations in the T-2 group were significant for MCV (increase) and the mean cell haemoglobin (increase). The active monovalent cation transport was altered by both mycotoxins. Most probably FB1 exerts its sodium pump activity modification via an altered ceramide metabolism (behenic acid decrease in the RBC membrane), while for T-2 toxin a moderate membrane disruption and enzyme (protein) synthesis inhibition was supposed (ca. 75% decrease of the sodium pump activity).

Tyrosine sulfation of human trypsin steers S2' subsite selectivity towards basic amino acids

Human cationic and anionic trypsins are sulfated on Tyr154, a residue which helps to shape the prime side substrate-binding subsites. Here, we used phage display technology to assess the significance of tyrosine sulfation for the specificity of human trypsins. The prime side residues P1′–P4′ in the binding loop of bovine pancreatic trypsin inhibitor (BPTI) were fully randomized and tight binding inhibitor phages were selected against non-sulfated and sulfated human cationic trypsin. The selection pattern for the two targets differed mostly at the P2′ position, where variants selected against non-sulfated trypsin contained primarily aliphatic residues (Leu, Ile, Met), while variants selected against sulfated trypsin were enriched also for Arg. BPTI variants carrying Arg, Lys, Ile, Leu or Ala at the P2′ position of the binding loop were purified and equilibrium dissociation constants were determined against non-sulfated and sulfated cationic and anionic human trypsins. BPTI variants harboring apolar residues at P2′ exhibited 3–12-fold lower affinity to sulfated trypsin relative to the non-sulfated enzyme, whereas BPTI variants containing basic residues at P2′ had comparable affinity to both trypsin forms. Taken together, the observations demonstrate that the tyrosyl sulfate in human trypsins interacts with the P2′ position of the substrate-like inhibitor and this modification increases P2′ selectivity towards basic side chains.

Sand grain mineralogy and morphology under forest and grassland/arable fields in Eastern Hungary

Related to ongoing (re)forestation in the Great Hungarian Plain the short-term influence of changing land cover was studied on the grains of skeletal sandy soils. In three sampling areas with forest and grassy/arable control plots, the 0.1–0.2 mm grain size fraction of samples taken every 20 cm from the 0–100 cm sandy soil layer (totalling 22,509 grains) were separated and described with optical mineralogical microscope. In order to distinguish sand grains of forest-covered and control areas (grassland/arable land), the results of mineralogical and morphological observations were compared. It was revealed that the amount of feldspar grains is 8–9 times less than the amount of the quartz ones. The increase in the quartz/feldspar (q/fp) ratio is tied to the “consumption” of feldspars: the intense consumption of potassium by trees. Under the forest-covered fields, the number of in-situ crushed grains increased. Grains with etch pits are frequent in samples from the grasslands (except in Hajdúsámson). In samples of forest-covered areas a greatly increased number of brown grains with limonite and/or humus films were observed. The gained results can be useful in proving earlier land use in forested fields.

Percutaneous video choledochoscopic treatment of retained biliary stones via dilated T-tube tract

BACKGROUND

Retained biliary stones is a common clinical problem in patients after surgery for complicated gallstone disease. When postoperative endoscopic retrograde cholangiopancreatography (ERCP) and endoscopic sphincterotomy are unsuccessful, several percutaneous procedures for stone removal can be applied as alternatives to relaparotomy. These procedures are performed either under fluoroscopic control or with the use of choledochoscopy, but it is also possible to combine these methods.

METHODS

Since 1994, we have used the percutaneous video choledochoscopic technique for the removal of difficult retained biliary stones via dilated T-tube tract in 17 patients, applying the technique of percutaneous stone extraction used in urology. While waiting for the T-tube tract to mature and after the removal of the T-tube, the dilatation of its tract was 26-30 Fr. Stone removal was carried out using a flexible video choledochoscope and a rigid renoscope under fluoroscopic control, with the aid of Dormia baskets, rigid forceps, and high-pressure irrigation.

RESULTS

We performed 23 operative procedures, and the clearance of the biliary ducts was successful in all cases. There were no major complications or deaths.

CONCLUSION

Percutaneous video choledochoscopic-assisted removal of large retained biliary stones via the T-tube tract is a highly effective and safe procedure. Its advantages over other procedures include the ability to visualize the stones and noncalculous filling defects; it also guarantees that the stones can be removed under visual video endoscopic control. It has no problems related to tract or stone size.

[Flow cytometry in the diagnosis of hemophagocytic lymphohistiocytosis in a case with fatal outcome]

Hemophagocytic lymphohistiocytosis is a multisystem inflammation, generated by the uncontrolled and excessive activation of cytotoxic T lymphocytes and natural killer cells. Severe immunodeficiency and generalized macrophage activation can often be detected in the background of this life threatening disorder. It is classified as a primary immunodeficiency. Functional abnormalities of the perforin protein or defects in granule secretory mechanisms are caused by gene mutations in most cases. Diagnostic criteria of hemophagocytic lymphohistiocytosis are the following: fever, splenomegaly, cytopenias affecting at least two of the 3 lineages in peripheral blood, hypertriglyceridemia and hyperferritinemia, elevated serum level of soluble interleukin-2 receptor (sCD25), hypofibrinogenemia, hemophagocytosis in bone marrow and decreased cytotoxic T cell and natural killer cell activity. In this case report the authors summarize the utility of functional flow cytometry in the diagnosis of hemophagocytic lymphohistiocytosis. Using flow cytometry, elevated intracellular perforin content, decreased killing activity of cytotoxic T cells and natural killer cells, and impaired cell surface expression of CD107a (LAMP1 protein) from in vitro stimulated blood lymphocytes were detected. Abnormal secretion of perforin was also demonstrated. Genetic testing revealed mutation of the MUNC 13-4 gene, which confirmed the base of the abnormal flow cytometric findings. This case report demonstrates the value of functional flow cytometry in the rapid diagnosis of genetically determined hemophagocytic lymphohistiocytosis, a condition in which early diagnosis is critical for optimal management. The authors emphasize the significance of functional flow cytometry in the differential diagnosis of immunodeficiencies.

Zymogen activation confers thermodynamic stability on a key peptide bond and protects human cationic trypsin from degradation

Human cationic trypsinogen, precursor of the digestive enzyme trypsin, can be rapidly degraded to protect the pancreas when pathological conditions threaten, while trypsin itself is impressively resistant to degradation. For either form, degradation is controlled by two necessary initial proteolytic events: cleavage of the Leu81-Glu82 peptide bond by chymotrypsin C (CTRC) and cleavage of the Arg122-Val123 peptide bond by trypsin. Here we demonstrate that the Leu81-Glu82 peptide bond of human cationic trypsin, but not trypsinogen, is thermodynamically stable, such that cleavage by CTRC leads to an equilibrium mixture containing 10% cleaved and 90% uncleaved trypsin. When cleaved trypsin was incubated with CTRC, the Leu81-Glu82 peptide bond was re-synthesized to establish the same equilibrium. The thermodynamic stability of the scissile peptide bond was not dependent on CTRC or Leu-81, as re-synthesis was also accomplished by other proteases acting on mutated cationic trypsin. The Leu81-Glu82 peptide bond is located within a calcium binding loop, and thermodynamic stability of the bond was strictly dependent on calcium and on the calcium-coordinated residue Glu-85. Trypsinolytic cleavage of the Arg122-Val123 site was also delayed in trypsin relative to trypsinogen in a calcium-dependent manner, but for this bond cleavage was modulated by kinetic rather than thermodynamic control. Our results reveal that the trypsinogen to trypsin conformational switch modulates cleavage susceptibility of nick sites by altering both the thermodynamics and kinetics of cleavage to protect human cationic trypsin from premature degradation.

Comprehensive functional analysis of chymotrypsin C (CTRC) variants reveals distinct loss-of-function mechanisms associated with pancreatitis risk

OBJECTIVE

The digestive enzyme chymotrypsin C (CTRC) protects against pancreatitis by promoting degradation of trypsinogen, thereby curtailing potentially harmful trypsinogen activation. Loss-of-function variants in CTRC increase the risk for chronic pancreatitis. The aim of the present study was to perform comprehensive functional analysis of all missense CTRC variants identified to date.

DESIGN

We investigated secretion, activity and degradation of 27 published and five novel CTRC mutants. We also assessed the effect of five mutants on endoplasmic reticulum (ER) stress.

RESULTS

None of the mutants exhibited a gain of function, such as increased secretion or activity. By contrast, 11 mutants showed marked loss of function, three mutants had moderate functional defects, whereas 18 mutants were functionally similar to wild-type CTRC. The functional deficiencies observed were diminished secretion, impaired catalytic activity and degradation by trypsin. Mutants with a secretion defect caused ER stress that was proportional to the loss in secretion. ER stress was not associated with loss-of-function phenotypes related to catalytic defect or proteolytic instability.

CONCLUSIONS

Pathogenic CTRC variants cause loss of function by three distinct but mutually non-exclusive mechanisms that affect secretion, activity and proteolytic stability. ER stress may be induced by a subset of CTRC mutants, but does not represent a common pathological mechanism of CTRC variants. This phenotypic dataset should aid in the classification of the clinical relevance of CTRC variants identified in patients with chronic pancreatitis.

Body mass related variations in the polar lipid fatty acyl chain composition of the mammalian lung and alveolar surfactant

In nine mammalian species (mouse - cattle: 21.5 g-503 kg) lung total phospholipids (PL), alveolar surfactant phosphatidylcholine (PC) and sphingomyelin (SM) fatty acyl (FA) chain composition was tested relating to body mass (BM) and resting respiratory rate (RRR) associated adaptations. In PL, PC and SM oleic acid (C18:1 n9) provided negative correlations with RRR. Palmitic acid (C16:0) was strongly, positively correlated with RRR in the pulmonary PLs, and myristic (C14:0) acid correlated positively with RRR in the surfactant PCs. In pulmonary PLs negative allometry was found for myristic, palmitic, palmitoleic (C16:1 n7) and docosahexaenoic (C22:6 n3) acids and total saturation, while oleic (C18:1 n9), alpha-linolenic (C18:3 n3) and gondoic (C20:1 n9) acids, total n9 FA s and monounsaturation increased allometrically. In surfactant PC FA s palmitic acid provided negative, while oleic acid and monounsaturation positive allometry; the average FA chain length (ACL) was identical in all species. Surfactant SM FA composition was fully species independent for palmitic and arachidonic acids, total saturation, monounsaturation and ACL. The in vivo lipid peroxidation rate was species independent. The variability of lung PLs was consonant with the "membrane pacemakers theory", while surfactant PC composition was mostly related to RRR.

Age-dependent parathormone levels and different CKD-MBD treatment practices of dialysis patients in Hungary--results from a nationwide clinical audit

Background

Achieving target levels of laboratory parameters of bone and mineral metabolism in chronic kidney disease (CKD) patients is important but also difficult in those living with end-stage kidney disease. This study aimed to determine if there are age-related differences in chronic kidney disease-mineral and bone disorder (CKD-MBD) characteristics, including treatment practice in Hungarian dialysis patients.

Methods

Data were collected retrospectively from a large cohort of dialysis patients in Hungary. Patients on hemodialysis and peritoneal dialysis were also included. The enrolled patients were allocated into two groups based on their age (<65 years and ≥65 years). Characteristics of the age groups and differences in disease-related (epidemiology, laboratory, and treatment practice) parameters between the groups were analyzed.

Results

A total of 5008 patients were included in the analysis and the mean age was 63.4±14.2 years. A total of 47.2% of patients were women, 32.8% had diabetes, and 11.4% were on peritoneal dialysis. Diabetes (37.9% vs 27.3%), bone disease (42.9% vs 34.1%), and soft tissue calcification (56.3% vs 44.7%) were more prevalent in the older group than the younger group (p<0.001 for all). We found an inverse relationship between age and parathyroid hormone (PTH) levels (p<0.001). Serum PTH levels were lower in patients with diabetes compared with those without diabetes below 80 years (p<0.001). Diabetes and age were independently associated with serum PTH levels (interaction: diabetes × age groups, p=0.138). Older patients were more likely than younger patients to achieve laboratory target ranges for each parameter (Ca: 66.9% vs 62.1%, p<0.001; PO₄: 52.6% vs 49.2%, p<0.05; and PTH: 50.6% vs 46.6%, p<0.01), and for combined parameters (19.8% vs 15.8%, p<0.001). Older patients were less likely to receive related medication than younger patients (66.9% vs 79.7%, p<0.001).

Conclusions

The achievement of laboratory target ranges for bone and mineral metabolism and clinical practice in CKD depends on the age of the patients. A greater proportion of older patients met target criteria and received less medication compared with younger patients.

Collective cell streams in epithelial monolayers depend on cell adhesion

We report a spontaneously emerging, randomly oriented, collective streaming behavior within a monolayer culture of a human keratinocyte cell line, and explore the effect of modulating cell adhesions by perturbing the function of calcium-dependent cell adhesion molecules. We demonstrate that decreasing cell adhesion induces narrower and more anisotropic cell streams, reminiscent of decreasing the Taylor scale of turbulent liquids. To explain our empirical findings, we propose a cell-based model that represents the dual nature of cell-cell adhesions. Spring-like connections provide mechanical stability, while a cellular Potts model formalism represents surface-tension driven attachment. By changing the relevance and persistence of mechanical links between cells, we are able to explain the experimentally observed changes in emergent flow patterns.

Cellular potts modeling of tumor growth, tumor invasion, and tumor evolution

Despite a growing wealth of available molecular data, the growth of tumors, invasion of tumors into healthy tissue, and response of tumors to therapies are still poorly understood. Although genetic mutations are in general the first step in the development of a cancer, for the mutated cell to persist in a tissue, it must compete against the other, healthy or diseased cells, for example by becoming more motile, adhesive, or multiplying faster. Thus, the cellular phenotype determines the success of a cancer cell in competition with its neighbors, irrespective of the genetic mutations or physiological alterations that gave rise to the altered phenotype. What phenotypes can make a cell "successful" in an environment of healthy and cancerous cells, and how? A widely used tool for getting more insight into that question is cell-based modeling. Cell-based models constitute a class of computational, agent-based models that mimic biophysical and molecular interactions between cells. One of the most widely used cell-based modeling formalisms is the cellular Potts model (CPM), a lattice-based, multi particle cell-based modeling approach. The CPM has become a popular and accessible method for modeling mechanisms of multicellular processes including cell sorting, gastrulation, or angiogenesis. The CPM accounts for biophysical cellular properties, including cell proliferation, cell motility, and cell adhesion, which play a key role in cancer. Multiscale models are constructed by extending the agents with intracellular processes including metabolism, growth, and signaling. Here we review the use of the CPM for modeling tumor growth, tumor invasion, and tumor progression. We argue that the accessibility and flexibility of the CPM, and its accurate, yet coarse-grained and computationally efficient representation of cell and tissue biophysics, make the CPM the method of choice for modeling cellular processes in tumor development.

A note on the special fillet fatty acid composition of the dwarf carp (Cyprinus carpio carpio) living in thermal Lake Hévíz, Hungary

Fatty acid (FA) composition of the fillet and the intestinal content of dwarf common carp (Cyprinus carpio carpio) living in Lake Hévíz was determined in wintertime collected samples and results were compared to widespread literature data on carp. Fillet FA profile of the thermally adapted (28 °C) Hévíz dwarf carps differed from profiles originated from divergent culture and feeding conditions in the overall level of saturation. Fillet myristic acid proportions largely exceeded all literature data in spite of poor dietary supply. Fillet fatty acid results indicate the effects of thermal adaptation (high saturation level) and the correlative effects of feed components rich in omega-3 fatty acids, with special respect to docosahexaenoic acid. With the application of discriminant factor analysis the Hévíz sample was accurately differentiated from the literature data on carp fillet fatty acid profile, mostly based on C14:0, C18:1 n9, C18:2 n6, C20:1 n9 and C20:4 n6 FAs. In summary, fillet FA profile suggested thermal adaptation, location specificity and the ingestion of algal and bacterial material.

Long-range electrostatic complementarity governs substrate recognition by human chymotrypsin C, a key regulator of digestive enzyme activation

Human chymotrypsin C (CTRC) is a pancreatic serine protease that regulates activation and degradation of trypsinogens and procarboxypeptidases by targeting specific cleavage sites within their zymogen precursors. In cleaving these regulatory sites, which are characterized by multiple flanking acidic residues, CTRC shows substrate specificity that is distinct from that of other isoforms of chymotrypsin and elastase. Here, we report the first crystal structure of active CTRC, determined at 1.9-Å resolution, revealing the structural basis for binding specificity. The structure shows human CTRC bound to the small protein protease inhibitor eglin c, which binds in a substrate-like manner filling the S6-S5' subsites of the substrate binding cleft. Significant binding affinity derives from burial of preferred hydrophobic residues at the P1, P4, and P2' positions of CTRC, although acidic P2' residues can also be accommodated by formation of an interfacial salt bridge. Acidic residues may also be specifically accommodated in the P6 position. The most unique structural feature of CTRC is a ring of intense positive electrostatic surface potential surrounding the primarily hydrophobic substrate binding site. Our results indicate that long-range electrostatic attraction toward substrates of concentrated negative charge governs substrate discrimination, which explains CTRC selectivity in regulating active digestive enzyme levels.

Determinants of chymotrypsin C cleavage specificity in the calcium-binding loop of human cationic trypsinogen

The pancreatic serine protease chymotrypsin C (CTRC) cleaves the Leu81-Glu82 peptide bond in the calcium-binding loop of human cationic trypsinogen and thereby promotes its degradation. This serves as a protective mechanism against ectopic trypsinogen activation in the pancreas. In the present study, we demonstrate that cleavage of the Leu81-Glu82 peptide bond by CTRC is highly specific, and other human pancreatic chymotrypsins (CTRB1, CTRB2 and CTRL1) and elastases (ELA2A, ELA3A and ELA3B) do not catalyze this reaction. To elucidate the mechanistic basis for CTRC specificity, we surveyed the primary (P1) cleavage preference of these pancreatic proteases on peptide substrates. We found that CTRC cleaved after a P1 Leu with at least tenfold higher catalytic efficiency than other enzymes tested. To assess extended sub-site interactions, we introduced Ala mutations into human cationic trypsinogen at the P3, P1' P3' and P4' amino acid positions, where P1-P1' corresponds to Leu81-Glu82. Interestingly, CTRC-mediated cleavage was stimulated threefold by mutation E82A and unaffected by mutations E79A and N84A, but all three mutations compromised specificity and resulted in increased cleavage by ELA2A. Mutation E85A decreased CTRC cleavage by twofold. Remarkably, other chymotrypsins and elastases did not cleave human cationic trypsinogen even with the L81F or L81A mutations, which introduced favorable P1 residues for these enzymes. We conclude that specific cleavage of the Leu81-Glu82 peptide bond in human cationic trypsinogen by CTRC is primarily determined by its distinctively high activity on leucyl peptide bonds, with the P1' Glu82, P3' Asn84 and P4' Glu85 residues serving as additional specificity determinants.

Fatty acid profile of fillet, liver and mesenteric fat in tilapia (<i>Oreochromis niloticus</i>) fed vegetable oil supplementation in the finishing period of fattening

Abstract. Tilapia (Oreochromis niloticus) previously reared on a commercial feed were shifted to 3 experimental diets with added 5 % of soybean, linseed oil or fish oils, for 42 days as a finishing diet, according to literature recommendations. Fillet, liver and mesenteric fat total lipid fatty acid composition was determined and evaluated taking health and dietary recommendations into consideration. It was found that dietary vegetable oil fatty acids are effectively incorporated into tilapia hepatic and muscular total lipids, but have no pronounced effect on further fatty acid metabolism, in particular on the n-3 fatty acids. Liver was found to sensitively indicate elevated dietary lipid intake, as proven by its higher, most probably endogenous palmitate synthesis. Based on our results the application of vegetable oils to partially substitute fish oil for tilapia can be recommended in relation to the most important dietary lipid quality indicators.

[Hungarian consensus regarding the role of vitamin D in the prevention and treatment of diseases]

The metabolism of vitamin D is unique in the human body and its diverse effects are present in almost every organ. Vitamin D deficiency is one of the most prominent health issues in the civilized world. For the solution of this concern an extensive collaboration is imperative. Recognizing this necessity the most prominent Hungarian medical associations fighting with the effects of vitamin D deficiency worked out a collective consensus on the importance, diagnosis, prevention and suggested therapy of vitamin D deficiency. Along with the clinical guidelines of the different associations, the result of this consensus could serve as guidance for the practicing doctors in the prevention and therapy of vitamin D deficiency. In addition the consensus aims to direct the attention of decision-makers and the general public on the significance of this issue.