Abstract

HPRTYale proposed as a pathogenic variant for Lesch-Nyhan syndrome: a case report

Author(s): E. Stur, R.S. Reis, L.P. Agostini, A.M.A. Silva-Conforti and I.D. Louro

Table of Contents | Genet. Mol. Res. 2016 (2) Research Article Effect of uric acid on mitochondrial function and oxidative stress in hepatocytes Authors: Y. Yang Y. Zhou S. Cheng J.L. Sun H. Yao L. Ma Here, we investigated the effect of uric acid (UA) on hepatocyte mitochondria. Hepatocytes cultured in vitro were treated with varying concentrations of UA. The change in apoptotic activity was detected by flow cytometry. The DNA damage index 8-hydroxy-deoxy-guanosine (8-OHdG) and mitochondrial function indices succinate dehydrogenase (SDH), cytochrome C oxidase (CCO), and adenosine triphosphate (ATP) were detected by enzyme assays. Reactive oxygen species (ROS) accumulation was confirmed by a dichloro-dihydro-fluorescein diacetate assay. We observed an increase in apoptotic activity, ROS accumulation, and 8-OHdG activity in hepatocytes treated with UA for extended periods, indicating DNA damage; specifically, we observed a significant increase in these activities 48, 72, and 96 h after UA addition, compared to those observed at 24 h (P [ + ] Genet. Mol. Res. 15(2): gmr8644 DOI: 10.4238/gmr.15028644 Research Article Data integration for identification of important transcription factors of STAT6-mediated cell fate decisions Authors: M. Jargosch S. Kröger E. Gralinska U. Klotz Z. Fang W. Chen U. Leser J. Selbig D. Groth R. Baumgrass Data integration has become a useful strategy for uncovering new insights into complex biological networks. We studied whether this approach can help to delineate the signal transducer and activator of transcription 6 (STAT6)-mediated transcriptional network driving T helper (Th) 2 cell fate decisions. To this end, we performed an integrative analysis of publicly available RNA-seq data of Stat6-knockout mouse studies together with STAT6 ChIP-seq data and our own gene expression time series data during Th2 cell differentiation. We focused on transcription factors (TFs), cytokines, and cytokine receptors and delineated 59 positively and 41 negatively STAT6-regulated genes, which were used to construct a transcriptional network around STAT6. The network illustrates that important and well-known TFs for Th2 cell differentiation are positively regulated by STAT6 and act either as activators for Th2 cells (e.g., Gata3, Atf3, Satb1, Nfil3, Maf, and Pparg) or as suppressors for other Th cell subpopulations such as Th1 (e.g., Ar), Th17 (e.g., Etv6), or iTreg (e.g., Stat3 and Hif1a) cells. Moreover, our approach reveals 11 TFs (e.g., Atf5, Creb3l2, and Asb2) with unknown functions in Th cell differentiation. This fact together with the observed enrichment of asthma risk genes among those regulated by STAT6 underlines the potential value of the data integration strategy used here. Thus, our results clearly support the opinion that data integration is a useful tool to delineate complex physiological processes. [ + ] Genet. Mol. Res. 15(2): gmr8493 DOI: 10.4238/gmr.15028493 Research Article Selecting the optimum conditions for two-dimensional difference gel electrophoresis of proteins expressed in Populus euphratica Authors: J.Q. Hao N. Yue C.X. Zheng We selected the optimum conditions for two-dimensional difference gel electrophoresis (2D-DIGE) of proteins expressed in the heteromorphic leaves of Populus euphratica Oliv. by adjusting the isoelectric focusing, the loading quantity, the concentration of the electrophoretic gel, and other parameters. The results of our study showed that protein separation was improved with many clear protein spots observed, and the differentiations were obvious. The findings of this study will be useful for future studies of protein expression in the heteromorphic leaves of P. euphratica. [ + ] Genet. Mol. Res. 15(2): gmr8360 DOI: 10.4238/gmr.15028360 Research Article Identifying significant pathways of hepatitis B virus-related hepatocellular carcinoma based on crosstalk and network pathways Authors: L.M. Wen W.Z. Wu X.C. Peng This study aims to identify significant pathways in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) based on the pathway network strategy. We proposed a pathway network where a protein-protein interaction (PPI) network was integrated with the crosstalk of pathways. Pathway data were first obtained from background PPI network, Reactome pathway database, and common genes between mRNA differentially expressed genes (DEGs), and miRNA target genes of HBV-related HCC. Pathway interactions were subsequently randomly extracted based on gene-gene interactions, and a weight value was assigned to each crosstalk using the Spearman correlation coefficient. Finally, pathways and crosstalk were visualized via Cytoscape to construct the final pathway network. A total of 9 common genes were identified between 396 mRNA DEGs and 400 miRNA target genes, and 17 pathways were identified based on background pathways and common genes. In addition, we constructed a pathway network that included 136 interactions and 17 pathways. The weight value of netrin-1 signaling and regulation of Frizzled proteins (FZD) by ubiquitination was the largest, at 0.228. In conclusion, we identified 17 significant pathways that might act as potential biomarkers of HBV-related HCC. This information may offer some insight into treatment and detection of HBV-related HCC. [ + ] Genet. Mol. Res. 15(2): gmr8343 DOI: 10.4238/gmr.15028343 Research Article Ancestry analysis of locally adapted Crespa goats from southernmost Brazil Authors: D.D. Lopes G.P. Fernández M. Poli G.R.P. Moreira G.L. Gonçalves T.R.O. Freitas Crespa goats are phenotypically similar to the Angora breed, and are traditionally reared in small, low-tech farms in southernmost Brazil. Whether they represent degenerated remnants of pure Angora goats or result from foreign breeds introduced during colonial times and recently mixed with commercial breeds is unknown. Since the degree of relatedness of Crespa in relation to other goats is completely unknown, we performed a comparative assessment of the genetic similarity between Crespa and foreign commercial breeds reared in the region (Angora, Alpine, Anglo-Nubian, Boer, and Saanen), particularly the Angora. We used 11 microsatellites to score alleles in 148 individuals and performed a Bayesian assignment test, which revealed six clusters (K = 6; Ln likelihood = -5047.6). In addition, a segment of the mitochondrial DNA (mtDNA) control region was sequenced to investigate the relatedness of Crespa goats to Portuguese autochthonous breeds (Algarvia, Bravia, Charnequeira, Serpentina, and Serrana). The origin of the Crespa breed could not be ascertained from the mtDNA, but it does not only descend from the Angora. It is probably related to other introduced and autochthonous Portuguese breeds, in particular the Algarvia. Therefore, our results indicate that this distinctive source of genetic diversity is partly a remnant of animals that were introduced during the colonial period. By recognizing it as genetically distinct, we provide further support for the protection of this particular gene pool. [ + ] Genet. Mol. Res. 15(2): gmr8324 DOI: 10.4238/gmr.15028324 Research Article Effect of SNX-2112 on proliferation of esophageal cancer cells via regulation of excision repair cross-complementing 1, epidermal growth factor receptor, and p53 expression Authors: C.Y. Li Y.J. Ren Y.D. Li SNX-2112 is a potential molecular targeted therapeutic drug against esophageal cancer (EC). However, its exact mechanism of action remains to be explained. The aim of this study was to investigate the effect of SNX-2112 on excision repair cross- complementing 1 (ERCC1), epidermal growth factor receptor (EGFR), and p53, to elucidate the mechanism of action of SNX-2112 on EC. Fresh tumor sections were surgically obtained from 65 patients with EC, and the expression of ERCC1, EGFR, and p53 was determined by immunohistochemical staining. Furthermore, the effect of SNX-2112 (0.2 μM) on the proliferation of EC-9706 cells and the expression of ERCC1, EGFR, and p53 in these cells were analyzed by a cell proliferation assay and western blot, respectively. We observed a significant decrease and increase in ERCC1 (P = 0.001) and p53 (P = 0.043) expression, respectively, and no significant difference in EGFR (P = 0.59) expression, with the TNM stage of EC, which suggested that ERCC1 and p53 could be potential markers for the TNM stage of EC. We also observed a significant increase in ERCC1 expression, and decrease in p53 and EGFR expression, in EC-9706 cells treated with SNX-2112 (P [ + ] Genet. Mol. Res. 15(2): gmr8318 DOI: 10.4238/gmr.15028318 Research Article High polymorphism at microsatellite loci in the Chinese donkey Authors: R.F. Zhang W.M. Xie T. Zhang C.Z. Lei To reveal the genetic diversity and phylogenetic relationships between Chinese donkey breeds, 415 individuals representing ten breeds were investigated using ten microsatellite markers. The observed number of alleles, mean effective number of alleles (NE), mean expected heterozygosity (HE), and polymorphic information content (PIC) of each breed and polymorphic locus were analyzed. The results showed that seven (HTG7, HTG10, AHT4, HTG6, HMS6, HMS3, and HMS7) of ten microsatellite loci were polymorphic. The mean PIC, HE, and NE of seven polymorphic loci for the ten donkey breeds were 0.7679, 0.8072, and 6.0275, respectively. These results suggest that domestic Chinese donkey breeds possess higher levels of genetic diversity and heterozygosity than foreign donkeys. A neighbor-joining tree based on Nei’s standard genetic distance showed that there was close genetic distance among Xinjiang, Qingyang, Xiji, and Guanzhong donkey breeds. In addition, Mongolia and Dezhou donkey breeds were placed in the same category. The phylogenetic tree revealed that the genetic relationships between Chinese donkey breeds are consistent with their geographic distribution and breeding history. [ + ] Genet. Mol. Res. 15(2): gmr8291 DOI: 10.4238/gmr.15028291 Research Article HPRTYale proposed as a pathogenic variant for Lesch-Nyhan syndrome: a case report Authors: E. Stur R.S. Reis L.P. Agostini A.M.A. Silva-Conforti I.D. Louro Lesch-Nyhan syndrome (LNS) is an X-linked recessive disorder caused by a deficiency of hypoxanthine-guanine phosphoribosyltransferase (HPRT), an enzyme encoded by the HPRT1 gene. The classic disease phenotype described by Lesch and Nyhan in 1964 includes hyperuricemia, mental retardation, severe motor deficiency, and recurring self-mutilation. Here, we report the case of a family with 4 affected males and several female obligate carriers. In 1989, Fujimori et al. reported on a patient diagnosed with LNS who had an HPRT variant thereafter codenamed HPRTYale. The same patient was studied by Wilson et al. in 1986, who found no detectable HPRT enzymatic activity, even though normal HPRT mRNA and protein levels were observed. Disease severity is closely related to residual enzymatic activity, which fits the phenotype presented for this previously reported case, as well as for the patients we report on herein. As it has been reported in only one patient, this mutation is still considered a variant of unknown significance. The HPRTYale mutation is a G>C transversion that leads to a different amino acid with different biochemical properties at position 71, potentially causing the major lack of function. To evaluate the impact of this variant, we used the PolyPhen-2 software, which classified it as possibly damaging. Furthermore, the frequency of this mutant allele is likely extremely rare, since it has only been reported on twice, and a population frequency is not yet available. In conclusion, we propose that the HPRTYale variant is pathogenic, and should be included on lab reports hereafter.

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