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      Association of CTH variant with sinusoidal obstruction syndrome in children receiving intravenous busulfan and cyclophosphamide before hematopoietic stem cell transplantation

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          Abstract

          Sinusoidal obstruction syndrome (SOS) is a severe complication of hematopoietic stem cell transplantation (HSCT) that can be fatal, often attributed to the conditioning regimen prior to HSCT. We evaluated the association of SOS risk with gene variants in cystathionase (CTH), an enzyme involved in glutathione synthesis, in 76 children receiving intravenous busulfan (Bu) before HSCT. Our results indicated an association with CTHc.1364 G>T (OR TT=10.6, 95% confidence interval (CI)=2.16, 51.54) and SOS risk, which was sex dependent (female patients, OR TT=21.82, 95% CI=3.590–132.649). The interaction between CTHc.1364 G>T and another risk variant ( GSTA1*B) was explored. A recessive model with the use of GSTA1*B*B and CTH c.1364 TT genotypes proved to be useful at predicting SOS occurrence, indicating the possibility of using these gene variants as markers of SOS occurrence and to further individualize preemptive treatment aimed at reducing SOS incidence.

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          Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

          Simon C. Lovell, Ian W. Davis, W Bryan Arendall … (2003)
          Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cbeta deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new phi,psi plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the gamma-turn conformation near +75 degrees,-60 degrees, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the gamma-turn H-bond. Favored and allowed phi,psi regions are also defined for Pro, pre-Pro, and Gly (important because Gly phi,psi angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of alpha-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage). Copyright 2003 Wiley-Liss, Inc.
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            Veno-occlusive disease of the liver and multiorgan failure after bone marrow transplantation: a cohort study of 355 patients.

            G B McDonald, M Hinds, L Fisher … (1993)
            To determine the incidence and clinical course of veno-occlusive disease of the liver (VOD) after bone marrow transplantation and to analyze risk factors for severe VOD. Cohort study of 355 consecutive patients. A bone marrow transplantation center. Each patient was prospectively evaluated for VOD, and many risk factors for severe VOD were analyzed using logistic regression models. The relation of VOD to renal and cardiopulmonary failure was analyzed using time-dependent proportional hazards models. Veno-occlusive disease developed in 190 of 355 patients (54%; 95% CI, 48% to 59%): Fifty-four patients had severe VOD and 136 had mild or moderate VOD. Independent variables derived from a multivariate model for predicting severe VOD included elevated transaminase values before transplantation (relative risk, 4.6; P < 0.0001); vancomycin therapy during cytoreductive therapy (relative risk, 2.9; P = 0.003); cytoreductive therapy with a high-dose regimen (relative risk, 2.8; P = 0.01); acyclovir therapy before transplantation (relative risk, 4.8; P = 0.02); mismatched or unrelated donor marrow (relative risk, 2.4; P = 0.02); and previous radiation therapy to the abdomen (relative risk, 2.2; P = 0.04). Vancomycin therapy was a marker for persistent fever. Multiorgan failure was more frequent among patients with VOD and usually followed the onset of liver disease. Veno-occlusive disease, which developed in 54% of bone marrow transplant recipients, is frequently associated with renal and cardiopulmonary failure. Pretransplant transaminase elevations, use of high-dose cytoreductive therapy, and persistent fever during cytoreductive therapy are independent predictors of severe VOD.
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              Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions.

              Beth L. Hahn, John Moore, Michael Ritchie (2003)
              Polymorphisms in human genes are being described in remarkable numbers. Determining which polymorphisms and which environmental factors are associated with common, complex diseases has become a daunting task. This is partly because the effect of any single genetic variation will likely be dependent on other genetic variations (gene-gene interaction or epistasis) and environmental factors (gene-environment interaction). Detecting and characterizing interactions among multiple factors is both a statistical and a computational challenge. To address this problem, we have developed a multifactor dimensionality reduction (MDR) method for collapsing high-dimensional genetic data into a single dimension thus permitting interactions to be detected in relatively small sample sizes. In this paper, we describe the MDR approach and an MDR software package. We developed a program that integrates MDR with a cross-validation strategy for estimating the classification and prediction error of multifactor models. The software can be used to analyze interactions among 2-15 genetic and/or environmental factors. The dataset may contain up to 500 total variables and a maximum of 4000 study subjects. Information on obtaining the executable code, example data, example analysis, and documentation is available upon request. All supplementary information can be found at http://phg.mc.vanderbilt.edu/Software/MDR.
              Article 0 comments Cited 176 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Pharmacogenomics J
                Journal ID (iso-abbrev): Pharmacogenomics J
                Title: The Pharmacogenomics Journal
                Publisher: Nature Publishing Group
                ISSN (Print): 1470-269X
                ISSN (Electronic): 1473-1150
                Publication date (Print): January 2018
                Publication date (Electronic): 25 October 2016
                Volume: 18
                Issue: 1
                Pages: 64-69
                Affiliations
                [1 ]Department of Pediatrics, Onco-Haematology Unit, Geneva University Hospital , Geneva, Switzerland
                [2 ]CANSEARCH Research Laboratory, Department of Pediatrics, Faculty of Medicine, University of Geneva , Geneva, Switzerland
                [3 ]UCIBIO@REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , Caparica, Portugal
                [4 ]Charles-Bruneau Cancer Center, CHU Sainte-Justine , Montreal, Quebec, Canada
                [5 ]St Anna Children’s Hospital , Vienna, Austria
                [6 ]University Hospital for Children and Adolescents , Frankfurt/Main, Germany
                [7 ]Department of Pediatrics, University of Montreal , Montreal, Quebec, Canada
                [8 ]Department of Pharmacology, Faculty of Medicine, University of Montreal , Montreal, Quebec, Canada
                Author notes
                [* ]CANSEARCH Research Laboratory, Department of Pediatrics, Faculty of Medicine, University of Geneva , 64, Avenue De La Roseraie, Geneva 1205, Switzerland. E-mail: Patricia.Curtis@ 123456unige.ch
                Article
                Publisher Item ID: tpj201665
                DOI: 10.1038/tpj.2016.65
                PMC ID: 5817388
                PubMed ID: 27779248
                SO-VID: 973d621c-c0a1-4008-b8fd-840fa37a778c
                Copyright © Copyright © 2018 The Author(s)
                License:

                This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/

                History
                Date received : 12 December 2015
                Date revision received : 05 July 2016
                Date accepted : 19 July 2016
                Categories
                Subject: Original Article

                ScienceOpen disciplines: Pharmacology & Pharmaceutical medicine
                Data availability:
                ScienceOpen disciplines: Pharmacology & Pharmaceutical medicine

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