Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut.

BACKGROUND: Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic processes. However, most of the routinely used mutation calling algorithms are not optimised for the simultaneous analysis of multiple samples, or for non-human experimental model systems with no reliable databases of common genetic variations. Most standard tools either require numerous in-house post filtering steps with scarce documentation or take an unpractically long time to run. To overcome these problems, we designed the streamlined IsoMut tool which can be readily adapted to experimental scenarios where the goal is the identification of experimentally induced mutations in multiple isogenic samples. METHODS: Using 30 isogenic samples, reliable cohorts of validated mutations were created for testing purposes. Optimal values of the filtering parameters of IsoMut were determined in a thorough and strict optimization procedure based on these test sets. RESULTS: We show that IsoMut, when tuned correctly, decreases the false positive rate compared to conventional tools in a 30 sample experimental setup; and detects not only single nucleotide variations, but short insertions and deletions as well. IsoMut can also be run more than a hundred times faster than the most precise state of art tool, due its straightforward and easily understandable filtering algorithm. CONCLUSIONS: IsoMut has already been successfully applied in multiple recent studies to find unique, treatment induced mutations in sets of isogenic samples with very low false positive rates. These types of studies provide an important contribution to determining the mutagenic effect of environmental agents or genetic defects, and IsoMut turned out to be an invaluable tool in the analysis of such data.

Predicting protein conformation by statistical methods.

The unique folded structure makes a polypeptide a functional protein. The number of known sequences is about a hundred times larger than the number of known structures and the gap is increasing rapidly. The primary goal of all structure prediction methods is to obtain structure-related information on proteins, whose structures have not been determined experimentally. Besides this goal, the development of accurate prediction methods helps to reveal principles of protein folding. Here we present a brief survey of protein structure predictions based on statistical analyses of known sequence and structure data. We discuss the background of these methods and attempt to elucidate principles, which govern structure formation of soluble and membrane proteins.

The HMMTOP transmembrane topology prediction server.

UNLABELLED: The HMMTOP transmembrane topology prediction server predicts both the localization of helical transmembrane segments and the topology of transmembrane proteins. Recently, several improvements have been introduced to the original method. Now, the user is allowed to submit additional information about segment localization to enhance the prediction power. This option improves the prediction accuracy as well as helps the interpretation of experimental results, i.e. in epitope insertion experiments. AVAILABILITY: HMMTOP 2.0 is freely available to non-commercial users at http://www.enzim.hu/hmmtop. Source code is also available upon request to academic users.

Some aspects of complementarity in the immune system. A bird's eye view.

The burden of this paper is the suggestion that the defence capacity of the immune system is rather limited. It cannot stand in readiness to deal with a practically endless diversity and abundance of microbes. In contrast to conventional thinking the current model proposes: (1) The core idea that cells of the immune system are basically and constantly interconnected with host cells (e.g., through TCR-MHC interactions) and that foreign antigens (peptides) may tend to obstruct such interactions. Peptides presented during a viral infection typically decrease complementarity between the structures that are the products of the major histocompatibility complex (MHC) genes (or other genes related to it) and T cells. The altered MHC profile exposes infected cells to a polyclonal immune attack from other T cells such that tissue destruction occurs in an allograft rejection-like fashion. This may explain why a substantial portion of T cell numbers is activated when only a small number of specific T cells is 'obstructed' from functioning by the presence of nonself peptides. (2) Phagocytes 'see' targets even in a non-immune host because complement distribution associated with polyreactive natural antibodies magnifies sensitization differences between pathogens and host cells. (3) There is only a probability that hypermutation will successfully change the genome in some B cell clones to produce high affinity antibodies that prevent the re-infection of the host by the same pathogen, but cannot conquer primary infections. (4) The history of the development of the immune responses suggests that during prolonged interaction between host and microbes in our natural habitat, carried on over many generations, the adaptive antibody population may facilitate the evolution of the natural antibody repertoire. The model predicts that microbes, which are not a part of the local environment, may invade the organism without significant resistance. The model is discussed in various interactions for survival in the context of infection and tumorigenicity.

Validity and reliability of leonhard's classification of endogenous psychoses: preliminary report on a prospective 25- to 30-year follow-up study.

A 25- to 30-year controlled follow-up investigation of endogenous psychoses started in 1997. The research program labeled "Budapest 2000" was initiated in 1967 as a controlled prospective study. The assessment of 108 patients and 24 normal control persons has so far been completed. With regard to the "middle groups" in the Leonhardian classification, diagnoses of bipolar manic-depressive psychosis, cycloid psychosis, periodic catatonia, systematic paraphrenia, systematic catatonia and hebephrenia proved to be valid in the long term. Revision of the category affect-laden paraphrenia seems to be called for.

Prion protein: evolution caught en route.

The prion protein displays a unique structural ambiguity in that it can adopt multiple stable conformations under physiological conditions. In our view, this puzzling feature resulted from a sudden environmental change in evolution when the prion, previously an integral membrane protein, got expelled into the extracellular space. Analysis of known vertebrate prions unveils a primordial transmembrane protein encrypted in their sequence, underlying this relocalization hypothesis. Apparently, the time elapsed since this event was insufficient to create a "minimally frustrated" sequence in the new milieu, probably due to the functional constraints set by the importance of the very flexibility that was created in the relocalization. This scenario may explain why, in a structural sense, the prion protein is still en route toward becoming a foldable globular protein.

Topology of membrane proteins.

Integral membrane proteins play important roles in living cells. Due to difficulties of experimental techniques, theoretical approaches, i.e., topology prediction methods, are important for structure determination of this class of proteins. Here we show a detailed comparison of transmembrane topology prediction methods. According to this comparison, we conclude that the topology of integral membrane proteins is determined by the maximum divergence of the amino acid composition of sequence segments. These segments are located in different areas of the cell, which can be characterized by different physicochemical properties. The results of these prediction methods compared to the X-ray diffraction data of several transmembrane proteins will also be discussed.

Characterization of the amino-terminal regions in the human multidrug resistance protein (MRP1).

The human multidrug resistance protein (MRP1) contributes to drug resistance in cancer cells. In addition to an MDR1-like core, MRP1 contains an N-terminal membrane-bound (TMD(0)) region and a cytoplasmic linker (L(0)), both characteristic of several members of the MRP family. In order to study the role of the TMD(0) and L(0) regions, we constructed various truncated and mutated MRP1, and chimeric MRP1-MDR1 molecules, which were expressed in insect (Sf9) and polarized mammalian (MDCKII) cells. The function of the various proteins was examined in isolated membrane vesicles by measuring the transport of leukotriene C(4) and other glutathione conjugates, and by vanadate-dependent nucleotide occlusion. Cellular localization, and glutathione-conjugate and drug transport, were also studied in MDCKII cells. We found that chimeric proteins consisting of N-terminal fragments of MRP1 fused to the N terminus of MDR1 preserved the transport, nucleotide occlusion and apical membrane routing of wild-type MDR1. As shown before, MRP1 without TMD(0)L(0) (Delta MRP1), was non-functional and localized intracellularly, so we investigated the coexpression of Delta MRP1 with the isolated L(0) region. Coexpression yielded a functional MRP1 molecule in Sf9 cells and routing to the lateral membrane in MDCKII cells. Interestingly, the L(0) peptide was found to be associated with membranes in Sf9 cells and could only be solubilized by urea or detergent. A 10-amino-acid deletion in a predicted amphipathic region of L(0) abolished its attachment to the membrane and eliminated MRP1 transport function, but did not affect membrane routing. Taken together, these experiments suggest that the L(0) region forms a distinct domain within MRP1, which interacts with hydrophobic membrane regions and with the core region of MRP1.

Functional multidrug resistance protein (MRP1) lacking the N-terminal transmembrane domain.

The human multidrug resistance protein (MRP1) causes drug resistance by extruding drugs from tumor cells. In addition to an MDR-like core, MRP1 contains an N-terminal membrane-bound region (TMD0) connected to the core by a cytoplasmic linker (L0). We have studied truncated MRP1 versions containing either the MDR-like core alone or the core plus linker L0, produced in the baculovirus-insect (Sf9) cell system. Their function was examined in isolated membrane vesicles. Full-length MRP1 showed ATP-dependent, vanadate-sensitive accumulation of leukotriene C4 and N-ethylmaleimide glutathione. In addition, leukotriene C4-stimulated, vanadate-dependent nucleotide occlusion was detected. The MDR-like core was virtually inactive. Co-expression of the core with the N-terminal region including L0 fully restored MRP1 function. Unexpectedly, a truncated MRP1 mutant lacking the entire TMD0 region but still containing L0 behaved like wild-type MRP1 in vesicle uptake and nucleotide trapping experiments. We also expressed the MRP1 constructs in polarized canine kidney derived MDCKII cells. Like wild-type MRP1, the MRP1 protein without the TMD0 region was routed to the lateral plasma membrane and transported dinitrophenyl glutathione and daunorubicin. The TMD0L0 and the MRP1 minus TMD0L0 remained in an intracellular compartment. Taken together, these experiments strongly suggest that the TMD0 region is neither required for the transport function of MRP1 nor for its proper routing to the plasma membrane.

Principles governing amino acid composition of integral membrane proteins: application to topology prediction.

A new method is suggested here for topology prediction of helical transmembrane proteins. The method is based on the hypothesis that the localizations of the transmembrane segments and the topology are determined by the difference in the amino acid distributions in various structural parts of these proteins rather than by specific amino acid compositions of these parts. A hidden Markov model with special architecture was developed to search transmembrane topology corresponding to the maximum likelihood among all the possible topologies of a given protein. The prediction accuracy was tested on 158 proteins and was found to be higher than that found using prediction methods already available. The method successfully predicted all the transmembrane segments in 143 proteins out of the 158, and for 135 of these proteins both the membrane spanning regions and the topologies were predicted correctly. The observed level of accuracy is a strong argument in favor of our hypothesis.

Survival chance in papillary thyroid cancer in Hungary: individual survival probability estimation using the Markov method.

PURPOSE: The typically benign, but occasionally rapidly fatal clinical course of papillary thyroid cancer has raised the need for individual survival probability estimation, to tailor the treatment strategy exclusively to a given patient. MATERIALS AND METHODS: A retrospective study was performed on 400 papillary thyroid cancer patients with a median follow-up time of 7.1 years to establish a clinical database for uni- and multivariate analysis of the prognostic factors related to survival (Kaplan-Meier product limit method and Cox regression). For a more precise prognosis estimation, the effect of the most important clinical events were then investigated on the basis of a Markov renewal model. The basic concept of this approach is that each patient has an individual disease course which (besides the initial clinical categories) is affected by special events, e.g. internal covariates (local/regional/distant relapses). On the supposition that these events and the cause-specific death are influenced by the same biological processes, the parameters of transient survival probability characterizing the speed of the course of the disease for each clinical event and their sequence were determined. The individual survival curves for each patient were calculated by using these parameters and the independent significant clinical variables selected from multivariate studies, summation of which resulted in a mean cause-specific survival function valid for the entire group. On the basis of this Markov model, prediction of the cause-specific survival probability is possible for extrastudy cases, if it is supposed that the clinical events occur within new patients in the same manner and with the similar probability as within the study population. RESULTS: The patient's age, a distant metastasis at presentation, the extent of the surgical intervention, the primary tumor size and extent (pT), the external irradiation dosage and the degree of TSH suppression proved to be statistically significant and independent prognostic factors with regard to cause-specific survival in multivariate studies. During follow-up, 14, 14, 9 and 12% of the patients underwent local/regional/distant relapses or thyroid cancer-related death, respectively. Through use of the above six independent clinical variables and the parameters relating to the four clinical events and their interrelations, mean cause-specific survival probabilities of 88, 83 and 78% were determined at 10, 20 and 30 years, respectively. The survival-predicting software (PATHYPRE) written on the basis of the biostatistical model is available through Internet connections on the home page of the National Institute of Oncology, Budapest (www.oncol.hu). CONCLUSION: Prediction of the individual survival probability for extrastudy cases affords a rationale for individualization of the treatment of papillary thyroid cancer patients.

[PATHYPRE: Pascal program for the estimation of the individual course of patients with papillary thyroid cancer]. / PATHYPRE: Pascal-program a papillaris pajzsmirigyrákos betegek individuális kórlefolyásának becslésére.

Individual survival probability estimation provided by mathematical models based on cases with a known clinical course is of great help as concerns the treatment strategy decision relating to malignant tumours. Data on four hundred Hungarian papillary thyroid cancer patients were used together with the Markov method to construct a survival model (Orv. Hetil. 1996 137: 1067-1078,) for prediction of the individual clinical course of newly diagnosed cases for 30 years following surgical intervention. Input data included the age, the primary tumour size and extent (pT), distant metastasis at presentation, the extent of the surgical intervention, the external irradiation dosage and the degree of TSH suppression. From the input data, the PATHYPRE program can estimate the individual local/regional/distant relapse-free survival probabilities and overall cause-specific survival probability. The survival probabilities may be predicted for variations in the treatment parameters, and thus the model helps in the selection of the most appropriate therapy for the patient. The PATHYPRE software is available through the Internet connections on the home page of the National Institute of Oncology, Budapest (www.oncol.hu).

Membrane topology distinguishes a subfamily of the ATP-binding cassette (ABC) transporters.

A group of ATP-binding cassette (ABC) transporters, including the yeast cadmium transporter (YCF1), the mammalian multidrug resistance-associated protein (MRP), the multispecific organic anion transporter and its congener (MOAT and EBCR), as well as the sulfonylurea receptor (SUR), group into a subfamily by sequence comparison. We suggest that these MRP-related proteins are also characterized by a special, common membrane topology pattern. The most studied ABC transporters, the cystic fibrosis transmembrane conductance regulator (CFTR) and the multidrug resistance (MDR) proteins, were shown to contain a tandem repeat of six transmembrane helices, each set followed by an ATP-binding domain. According to the present study, in contrast to various membrane topology predictions proposed for the different MRP-related proteins, they all seem to have a CFTR/MDR-like core structure, and an additional, large, N-terminal hydrophobic region. This latter domain is predicted to contain 4-6 (most probably 5) transmembrane helices, and is occasionally glycosylated on the cell surface. Since all the MRP-related transporters were shown to interact with anionic compounds, the N-terminal membrane-bound domain may have a key role in these interactions.

[Survival potentials of patients with papillary carcinoma of the thyroid gland in Hungary]. / A papillaris pajzsmirigyrákos betegek túlélési esélyei Magyarországon.

The typically benign, but occasionally rapid fatal clinical course of papillary thyroid cancer has raised the need for individual survival probability estimation, to tailor the treatment strategy exclusively to the given patient. A retrospective study was performed on 400 papillary thyroid cancer patients, with a mean follow-up time of 10.3 years, to establish a clinical database for uni- and multivariate analysis of the survival probability-related prognostic factors (Kaplan-Meier product limit method and Cox regression). For a more precise prognosis estimation, in the next step the most important clinical events were investigated and survival functions for each patient were calculated on the basis of a Markov renewal model. The basic concept of this approach is as follows: each patient has an individual disease course, which (besides the initial clinical categories) is affected by special events, e.g. internal covariates (local/regional/distant relapses), that a patient experiences throughout the course of the disease. On the supposition that these events and the cause-specific death are influenced by the same biological process, the parameters of transient survival probability characterizing the speed of the course of the disease for each sequence of clinical events were determined. The individual survival curves for each patients were calculated by using the former parameters and the independent, significant clinical variables, summation of which resulted in an overall cause-specific survival function valid for the entire group. The patient's age, a distant metastasis at presentation, the extent of the surgical intervention, the primary tumour size, the dosage of the external irradiation and the degree of the TSH suppression proved to be statistically significant (in that sequence) and independent prognostic factors as concerns cause-specific survival in multivariate studies. During follow-up 14%, 14%, 9% and 12% of the patients underwent local/regional/distant relapses and thyroid cancer-related death. Through use of the above six independent clinical variables and the parameters relating to the interrelations of the four clinical events, mean cause-specific survival probabilities of 88%, 83% and 78% were determined at 10, 20 and 30 years, respectively. The 30-year individual survival probability prediction for these study cases showed that no cancer-related death occurred > or = 92% (low-risk group), while the tumour-related deaths were considerable (31%) < or = 78% (high-risk group), and there were only 6% deaths in the intermediate-risk group. The constructed survival function permits a prediction of the individual survival probability of extra-study cases under the given treatment conditions and within the given population, and thus affords a rationale for individualization of the treatment of papillary thyroid cancer patients.

Membrane topology and glycosylation of the human multidrug resistance-associated protein.

The membrane topology of the human multidrug resistance-associated protein (MRP) was examined by flow cytometry phenotyping, immunoblotting, and limited proteolysis in drug-resistant human and baculovirus-infected insect cells, expressing either the glycosylated or the underglycosylated forms of this protein. Inhibition of N-linked glycosylation in human cells by tunicamycin did not inhibit the transport function or the antibody recognition of MRP, although its apparent molecular mass was reduced from 180 kDa to 150 kDa. Extracellular addition of trypsin or chymotrypsin had no effect either on the function or on the molecular mass of MRP, while in isolated membranes limited proteolysis produced three large membrane-bound fragments. These experiments and the alignment of the MRP sequence with the human cystic fibrosis transmembrane conductance regulator (CFTR) suggest that human MRP, similarly to CFTR, contains a tandem repeat of six transmembrane helices, each followed by a nucleotide binding domain, and that the C-terminal membrane-bound region is glycosylated. However, the N-terminal region of MRP contains an additional membrane-bound, glycosylated area with four or five transmembrane helices, which seems to be a characteristic feature of MRP-like ATP-binding cassette transporters.

[Malignant thyroid tumors in Hungary: morbidity and mortality]. / Malignus pajzsmirigytumorok Magyarországon: morbiditás és mortalitás.

In 1993, 181 new cases (36 men and 145 women) of thyroid cancer were diagnosed pathologically in Hungary, i.e. a morbidity of 1.8/100,000 for the total population, and of 0.7/100,000 and 2.7/100,000 for men and women, respectively. The distribution of the histological diagnoses: 61% papillary, 25% follicular, 5% medullary and 3% anaplastic carcinomas, and 6% others. In the same year, 125 patients (31 men and 94 women) died from thyroid cancer, i.e. a mortality rate of 1.2/100,000 for the total population, and of 0.6/100,000 and 1.8/100,000 for men and women, respectively. The relatively low morbidity reflects the fact that no new strong aetiological factor is operative in Hungary. The substantial mortality rate, however, is influenced by the geographically determined aggressivity of the disease, the inadequacy of the diagnostic procedures and therapeutic measures, and lack of the active follow-up. The latter facts are especially prominent in centres with a low patient turnover. In the field of health care, various measures must be introduced to prevent an increase in the morbidity and to diminish the mortality. Reduction of the iodine deficiency, rationalization of the medical use of ionizing irradiation, and implementation of the necessary hormonal medication for all patients operated by resection for thyroid diseases are needed for tumour prophylaxis. Before any medical decision-making, the achievement of complete diagnostic information, including the pathological revision of clinically questionable cases, is of paramount importance. The fundamental goals as concerns the treatment modalities are as follows: increased surgical skill and level of performance of external irradiation, the availability of radionuclide therapy, and guidance of all types of thyroxine medication by endocrine experts.

Independence divergence-generated binary trees of amino acids.

The discovery of the relationship between amino acids is important in terms of the replacement ability, as used in protein engineering homology studies, and gaining a better understanding of the roles which various properties of the residues play in the creation of a unique, stable, 3-D protein structure. Amino acid sequences of proteins edited by evolution are anything but random. The measure of nonrandomness, i.e. the level of editing, can be characterized by an independence divergence value. This parameter is used to generate binary tree relationships between amino acids. The relationships of residues presented in this paper are based on protein building features and not on the physico-chemical characteristics of amino acids. This approach is not biased by the tautology present in all sequence similarity-based relationship studies. The roles which various physico-chemical characteristics play in the determination of the relationships between amino acids are also discussed.

Chaos game representation of protein structures.

Chaos game representation (CGR) was proposed recently to visualize nucleotide sequences as one of the first applications of this technique in the field of biochemistry. In this paper we would like to demonstrate that representations similar to CGR can be generalized and applied for visualizing and analyzing protein databases. Examples of applications will be presented for investigating regularities, and motifs in the primary structure of proteins, and for analyzing possible structural attachments on the super-secondary structure level of proteins. A further application will be presented for testing structure prediction methods using CGR.