Publications by authors named "Xufei Zhang"

19 Publications

  • Page 1 of 1

Automated detection of hippocampal sclerosis: Comparison of a composite MRI-based index with conventional MRI measures.

Epilepsy Res 2021 Aug 9;174:106638. Epub 2021 Apr 9.

Department of Radiology, Sanbo Brain Hospital, Capital Medical University, China. Electronic address:

Purpose: This study aims to compare the performance of an MRI-based composite index (HSI) with conventional MRI-based measures in hippocampal sclerosis (HS) detection and postoperative outcome estimation.

Methods: Seventy-two temporal lobe epilepsy (TLE) patients with pathologically confirmed HS and fifteen TLE patients without HS were included retrospectively. The T1-weighted and FLAIR images of these patients were processed with AccuBrain to quantify the hippocampal volume (HV) and the hippocampal FLAIR signal. The HSI index that considered both HV and hippocampal FLAIR signal was also calculated. Two experienced neuropathologists rated the HS severity with the resected tissue and reached an agreement for all cases. The asymmetry indices of the MRI measures were used to lateralize the sclerotic side, and the original MRI measures were applied to detect HS vs. normal hippocampi. Operating characteristic curve (ROC) analyses were performed for these predictions. We also investigated the sensitivity of the ipsilateral MRI measures in characterizing the pathological severity of HS and the associations of the MRI measures with postoperative outcomes (Engel class categories).

Results: With the optimal cutoffs, the asymmetry indices of HSI and HV both achieved excellent performance in differentiating left vs. right HS (accuracy = 100 %), and the absolute value of the asymmetry index of HSI performed best in differentiating unilateral vs. bilateral HS (accuracy = 91.7 %). Regarding the detection of HS, HSI performed better in sensitivity (94.4 % vs. 87.5 %) while HV performed better in specificity (93.6 % vs. 89.4 %) when the contralateral site of unilateral HS and both sides of non-HS patients were considered as the normal reference, and HSI performed even better than HV when only both sides of non-HS patients were considered as the normal reference (AUC: 0.956 vs. 0.934, p = 0.038). The ipsilateral HSI presented the strongest association with the pathological rating of HS severity (r = 0.405, p < 0.001). None of the ipsilateral or contralateral MRI measures was associated with the postoperative outcomes. Among the asymmetry indices, only the absolute value of the asymmetry index of HV presented a significant association with the Engel classifications for the Year 2∼3 visit (r = -0.466, p = 0.004) or the latest visit with >1 year follow-up (r = -0.374, p = 0.003) while controlling for disease duration and follow-up duration.

Conclusion: The HSI index and HV presented comparable good performance in HS detection, and HSI may have better sensitivity than HV in differentiating pathological HS severity. Higher magnitude of HV dissymmetry may indicate better post-surgical outcomes for HS patients.
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http://dx.doi.org/10.1016/j.eplepsyres.2021.106638DOI Listing
August 2021

Iron homeostasis and disorders revisited in the sepsis.

Free Radic Biol Med 2021 Mar 22;165:1-13. Epub 2021 Jan 22.

Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, PR China; Department of General Surgery, BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, 210002, PR China; Research Institute of General Surgery, Jinling Hospital, Nanjing Medical University, Nanjing, 210002, PR China. Electronic address:

Sepsis is a life-threatening condition caused by a dysregulated host-response to inflammation, although it currently lacks a fully elucidated pathobiology. Iron is a crucial trace element that is essential for fundamental processes in both humans and bacteria. During sepsis, iron metabolism is altered, including increased iron transport and uptake into cells and decreased iron export. The intracellular sequestration of iron limits its availability to circulating pathogens, which serves as a conservative strategy against the pathogens. Although iron retention has been showed to have protective protect effects, an increase in labile iron may cause oxidative injury and cell death (e.g., pyroptosis, ferroptosis) as the condition progresses. Moreover, iron disorders are substantial and correlate with the severity of sepsis. This also suggests that iron may be useful as a diagnostic marker for evaluating the severity and predicting the outcome of the disease. Further knowledge about these disorders could help in evaluating how drugs targeting iron homeostasis can be optimally applied to improve the treatment of patients with sepsis. Here, we present a comprehensive review of recent advances in the understanding of iron metabolism, focusing on the regulatory mechanisms and iron-mediated injury in sepsis.
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http://dx.doi.org/10.1016/j.freeradbiomed.2021.01.025DOI Listing
March 2021

Generation of an urine-derived induced pluripotent stem cell line WMUi017-A from a X-linked Renpenning syndrome (X-RSY) patient with the hemizygous PQBP1 gene mutation p.P609A (c.1825C>G).

Stem Cell Res 2021 03 8;51:102159. Epub 2021 Jan 8.

Center of Scientific Research, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Pediatrics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China. Electronic address:

The mutations of polyglutamine binding protein 1 gene (PQBP1) can lead to the rare inherited X-linked Renpenning syndrome (X-RSY). Here, an induced pluripotent stem cell (iPSC) line WMUi017-A was generated through reprogramming the urine cells of a 5-year-old male X-RSY patient with the hemizygous PQBP1 gene mutation p.P609A (c.1825C>G) using the commercial Sendai virus reprogramming system. The established iPSCs can stably express pluripotent stem cell markers OCT4 and NANOG, and can be induced into three germ layers and maintain a normal karyotype (46, XY) in vitro.
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http://dx.doi.org/10.1016/j.scr.2021.102159DOI Listing
March 2021

STING-dependent induction of lipid peroxidation mediates intestinal ischemia-reperfusion injury.

Free Radic Biol Med 2021 Feb 18;163:135-140. Epub 2020 Dec 18.

Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, PR China; Research Institute of General Surgery, Jinling Hospital, Nanjing, 210002, PR China; Research Institute of General Surgery, Jinling Hospital, Nanjing Medical University, Nanjing, 210002, PR China. Electronic address:

Stimulator of interferon genes (STING) is essential for the type I interferon response against DNA pathogens. Recent evidence has indicated that STING also plays a critical role in various diseases such as systemic lupus erythematous, nonalcoholic fatty liver disease, and cancer. However, the exact function and mechanism of STING in ischemia/reperfusion (I/R) injury, especially in the intestine, remains unknown. In the current study, we evaluated the contribution of STING to the intestinal I/R progression. The data indicate a robust STING activation, specifically in the reperfusion period, with the evidence of interferon response and NF-κB pathway activation. The intestinal I/R injury and distant organ damage was absent in STING mice. Mechanically, this detrimental effect relies on excess level of lipid peroxidation, which was proved by the level of 4-hydroxynonenal (4-HNE) and the malondialdehyde (MDA). Additionally, bone marrow derived macrophage (BMDM) was stimulated with mtDNA or STING agonist showed a dose- and time-dependent lipid peroxidation and cell death, which could be reverse by STING or pretreatment of lipid peroxidation inhibitor. Liproxstatin-1 could also ameliorate injury I/R induced multiple-organ damage. Similar results were also identified in the GSE96733 database, which indicated that STING activation was associated with the disbalance of lipid peroxidation and antioxidant system. Collectively, our results indicate a novel role for STING activation in the regulation of lipid peroxidation is closely associated with intestinal I/R injury, and that anti-lipid peroxidation is a unique and effective mechanistic approach for intestinal I/R injury and STING activation associated damage prevention and treatment.
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http://dx.doi.org/10.1016/j.freeradbiomed.2020.12.010DOI Listing
February 2021

mtDNA-STING pathway promotes necroptosis-dependent enterocyte injury in intestinal ischemia reperfusion.

Cell Death Dis 2020 12 11;11(12):1050. Epub 2020 Dec 11.

Research Institute of General Surgery, Jinling Hospital, Nanjing Medical University, Nanjing, 210002, PR China.

Intestinal ischemia reperfusion (I/R) injury is the important pathogenesis for acute intestinal barrier disruption. The STING signaling is associated with gut homeostasis and barrier integrity. However, the biological function and regulation of STING signaling in intestinal I/R injury are not yet fully understood. As the ligand of STING signaling, the mitochondrial DNA (mtDNA) has been found to be associated with necroptosis. It still remains unknown whether mtDNA-STING signaling triggers intestinal necroptosis in intestinal I/R injury. We found that circulating RIPK3 was significantly increased and had a positive correlation with markers of enterocyte injury in critically ill patients with intestinal injury. Moreover, the levels of circulating mtDNA were also associated with the levels of circulating RIPK3. To explore the relationship between mtDNA and intestinal necroptosis, mice were treated with the intraperitoneal injection of mtDNA, and necroptosis signaling was remarkably activated and the inhibition of necroptosis alleviated mtDNA-induced intestinal injury. Furthermore, STING knockout mice showed an alleviated intestinal necroptosis. In intestinal I/R injury, mtDNA was released from IECs and necroptosis was also triggered, companied with a significant decrease of RIPK3 in the intestine. STING knockout mice markedly attenuated intestinal necroptosis and intestinal I/R injury. Finally, we found that mtDNA-mediated STING signaling triggered necroptosis through synergistic IFN and TNF-α signaling in primary IECs. Our results indicated that mtDNA-STING signaling can contribute to intestinal I/R injury by promoting IEC necroptosis. STING-mediated both IFN and TNF-α signaling can trigger intestinal nercroptosis.
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http://dx.doi.org/10.1038/s41419-020-03239-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7732985PMC
December 2020

Incidence and risk factors of surgical site infection following colorectal surgery in China: a national cross-sectional study.

BMC Infect Dis 2020 Nov 12;20(1):837. Epub 2020 Nov 12.

Research Institute of General Surgery, Jinling Hospital, Nanjing Medical University, Nanjing, 210002, People's Republic of China.

Purposes: Surgical site infection (SSI) after colorectal surgery is a frequent complication associated with the increase in morbidity, medical expenses, and mortality. To date, there is no nationwide large-scale database of SSI after colorectal surgery in China. The aim of this study was to determine the incidence of SSI after colorectal surgery in China and to further evaluate the related risk factors.

Methods: Two multicenter, prospective, cross-sectional studies covering 55 hospitals in China and enrolling adult patients undergoing colorectal surgery were conducted from May 1 to June 30 of 2018 and the same time of 2019. The demographic and perioperative characteristics were collected, and the main outcome was SSI within postoperative 30 days. Multivariable logistic regressions were conducted to predict risk factors of SSI after colorectal surgery.

Results: In total, 1046 patients were enrolled and SSI occurred in 74 patients (7.1%). In the multivariate analysis with adjustments, significant factors associated with SSI were the prior diagnosis of hypertension (OR, 1.903; 95% confidence interval [CI], 1.088-3.327, P = 0.025), national nosocomial infection surveillance risk index score of 2 or 3 (OR, 3.840; 95% CI, 1.926-7.658, P < 0.001), laparoscopic or robotic surgery (OR, 0.363; 95% CI, 0.200-0.659, P < 0.001), and adhesive incise drapes (OR, 0.400; 95% CI, 0.187-0.855, P = 0.018). In addition, SSI group had remarkably increased length of postoperative stays (median, 15.0 d versus 9.0d, P < 0.001), medical expenses (median, 74,620 yuan versus 57,827 yuan, P < 0.001), and the mortality (4.1% versus 0.3%, P = 0.006), compared with those of non-SSI group.

Conclusion: This study provides the newest data of SSI after colorectal surgery in China and finds some predictors of SSI. The data presented in our study can be a tool to develop optimal preventive measures and improve surgical quality in China.
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http://dx.doi.org/10.1186/s12879-020-05567-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7663877PMC
November 2020

Bone Growth is Influenced by Fructose in Adolescent Male Mice Lacking Ketohexokinase (KHK).

Calcif Tissue Int 2020 05 29;106(5):541-552. Epub 2020 Jan 29.

Department of Biomedical Engineering, Graduate School, Rutgers University, New Brunswick, NJ, USA.

Fructose is metabolized in the cytoplasm by the enzyme ketohexokinase (KHK), and excessive consumption may affect bone health. Previous work in calcium-restricted, growing mice demonstrated that fructose disrupted intestinal calcium transport. Thus, we hypothesized that the observed effects on bone were dependent on fructose metabolism and took advantage of a KHK knockout (KO) model to assess direct effects of high plasma fructose on the long bones of growing mice. Four groups (n = 12) of 4-week-old, male, C57Bl/6 background, congenic mice with intact KHK (wild-type, WT) or global knockout of both isoforms of KHK-A/C (KHK-KO), were fed 20% glucose (control diet) or fructose for 8 weeks. Dietary fructose increased by 40-fold plasma fructose in KHK-KO compared to the other three groups (p < 0.05). Obesity (no differences in epididymal fat or body weight) or altered insulin was not observed in either genotype. The femurs of KHK-KO mice with the highest levels of plasma fructose were shorter (2%). Surprisingly, despite the long-term blockade of KHK, fructose feeding resulted in greater bone mineral density, percent volume, and number of trabeculae as measured by µCT in the distal femur of KHK-KO. Moreover, higher plasma fructose concentrations correlated with greater trabecular bone volume, greater work-to-fracture in three-point bending of the femur mid-shaft, and greater plasma sclerostin. Since the metabolism of fructose is severely inhibited in the KHK-KO condition, our data suggest mechanism(s) that alter bone growth may be related to the plasma concentration of fructose.
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http://dx.doi.org/10.1007/s00223-020-00663-wDOI Listing
May 2020

MicroRNA‑432 inhibits the aggressiveness of glioblastoma multiforme by directly targeting IGF‑1R.

Int J Mol Med 2020 Feb 16;45(2):597-606. Epub 2019 Dec 16.

Department of TCM Pharmacy, Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang 323000, P.R. China.

MicroRNA‑432 (miR‑432) has been studied in multiple tumors, but the expression status, biological functions and the mechanism of action of miR‑432 in glioblastoma multiforme (GBM) are yet to be elucidated. In the present study, miR‑432 expression in GBM was determined and its clinical significance was evaluated among patients with GBM. The effects on the malignancy of GBM in vitro and in vivo were examined in detail and the interactions between miR‑432 and insulin‑like growth factor 1 receptor (IGF‑1R) mRNA were then explored. miR‑432 expression in GBM tissue samples and cell lines was measured by reverse transcription‑quantitative (RT‑q)PCR. GBM cell proliferation, apoptosis, migration and invasion in vitro and tumor growth in vivo were evaluated by a Cell Counting Kit‑8 assay, flow‑cytometric analysis, Transwell migration and invasion assays, and a tumor xenograft experiment, respectively. Bioinformatic analysis followed by a luciferase reporter assay, RT‑qPCR and western blotting was applied to demonstrate that IGF‑1R is a direct target gene of miR‑432 in GBM cells. It was found that miR‑432 is downregulated in GBM tumors and cell lines. miR‑432 under expression obviously correlated with the Karnofsky Performance Status score and shorter overall survival among patients with GBM. Exogenous miR‑432 expression significantly reduced proliferation and induced apoptosis of GBM cells. In addition, miR‑432 overexpression impaired the migratory and invasive abilities of GBM cells in vitro and decreased their tumor growth in vivo. Furthermore, IGF‑1R was validated as a direct target gene of miR‑432 in GBM cells. IGF‑1R knockdown imitated the tumor‑suppressive actions of miR‑432 overexpression in GBM cells. Rescue experiments proved IGF‑1R downregulation to be essential for the effects of miR‑432 on GBM cells. The results of the present study revealed a tumor‑suppressive role of the miR‑432‑IGF‑1R axis in GBM cells and this axis may have implications for GBM therapy.
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http://dx.doi.org/10.3892/ijmm.2019.4429DOI Listing
February 2020

Comparison of the inhibitory effect of ketoconazole, voriconazole, fluconazole, and itraconazole on the pharmacokinetics of bosentan and its corresponding active metabolite hydroxy bosentan in rats.

Xenobiotica 2020 Mar 3;50(3):280-287. Epub 2019 Jul 3.

Department of Pharmacy, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.

1. This study aimed to investigate the inhibitory effect of azole antifungal agents, including ketoconazole, voriconazole, fluconazole, and itraconazole, on the pharmacokinetics of bosentan (BOS) and its active metabolite hydroxy bosentan (OHBOS) in Sprague-Dawley (SD) rats.2. A total of 25 healthy male SD rats were divided into five groups and treated with various azole antifungal agents by gavage, followed by a single dose of BOS after 30 min.3. The study found that ketoconazole led to a significant increase (5.1-fold) in the AUC of BOS, associated with a 5.8-fold elevation in the , which was greater than that for fluconazole (2.6- and 2.9-fold) and voriconazole (1.1- and 1.7-fold). Accordingly, the Vz/F and CLz/F of BOS reduced by 89.2% and 83.7%, respectively, on administering ketoconazole concomitantly. However, fluconazole caused a decrease in Vz/F and CLz/F by 77.4% and 72.2%, respectively, compared with voriconazole that exhibited a decrease in CLz/F by 51.7% with a negligible change in Vz/F. Also, obvious differences were observed in the pharmacokinetic parameters of OHBOS between the control and treated groups.4. Collectively, treatment with ketoconazole resulted in a prominent inhibitory effect on the metabolism of BOS, followed by treatment with fluconazole, voriconazole, and itraconazole. Therefore, these details of animal studies may help draw more attention to the safety of BOS while combining it with ketoconazole, voriconazole, fluconazole, or itraconazole clinically.
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http://dx.doi.org/10.1080/00498254.2019.1628321DOI Listing
March 2020

Mitochondrial DNA in liver inflammation and oxidative stress.

Life Sci 2019 Nov 9;236:116464. Epub 2019 May 9.

Lab for Trauma and Surgical Infections, Jinling Hospital, Nanjing 210002, PR China.

The function of liver is highly dependent on mitochondria producing ATP for biosynthetic and detoxifying properties. Accumulating evidence indicates that most hepatic disorders are characterized by profound mitochondrial dysfunction. Mitochondrial dysfunction not only exhibits mitochondrial DNA (mtDNA) damage and depletion, but also releases mtDNA. mtDNA is a closed circular molecule encoding 13 of the polypeptides of the oxidative phosphorylation system. Extensive mtDNA lesions could exacerbate mitochondrial oxidative stress and subsequently cause damage to hepatocytes. When mtDNA leaves the confines of mitochondria to the cytosolic and extracellular environment, it can act as damage-associated molecular patterns (DAMPs) to trigger the inflammatory response through the Toll-like receptor 9, inflammasomes, and stimulator of interferon genes (STING) pathways and further exacerbate hepatocellular damage and even remote organs injury. In addition, mtDNA also plays a vital role in hepatitis B virus (HBV)-related liver injury and hepatocellular carcinoma (HCC). In this review, we describe mtDNA alterations during liver injury, focusing on the mechanisms of mtDNA-mediated liver inflammation and oxidative stress injury.
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http://dx.doi.org/10.1016/j.lfs.2019.05.020DOI Listing
November 2019

Fructose malabsorption induces cholecystokinin expression in the ileum and cecum by changing microbiota composition and metabolism.

FASEB J 2019 06 2;33(6):7126-7142. Epub 2019 Apr 2.

Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.

Current fructose consumption levels often overwhelm the intestinal capacity to absorb fructose. We investigated the impact of fructose malabsorption on intestinal endocrine function and addressed the role of the microbiota in this process. To answer this question, a mouse model of moderate fructose malabsorption [ketohexokinase mutant (KHK)] and wild-type (WT) littermate mice were used and received a 20%-fructose (KHK-F and WT-F) or 20%-glucose diet. Cholecystokinin () mRNA and protein expression in the ileum and cecum, as well as preproglucagon () and neurotensin () mRNA expression in the cecum, increased in KHK-F mice. In KHK-F mice, triple-label immunohistochemistry showed major up-regulation of CCK in enteroendocrine cells (EECs) that were glucagon-like peptide-1 (GLP-1)/Peptide YY (PYY) in the ileum and colon and GLP-1/PYY in the cecum. The cecal microbiota composition was drastically modified in the KHK-F in association with an increase in glucose, propionate, succinate, and lactate concentrations. Antibiotic treatment abolished fructose malabsorption-dependent induction of cecal mRNA expression and, in mouse GLUTag and human NCI-H716 cells, mRNA expression levels increased in response to propionate, both suggesting a microbiota-dependent process. Fructose reaching the lower intestine can modify the composition and metabolism of the microbiota, thereby stimulating the production of CCK from the EECs possibly in response to propionate.-Zhang, X., Grosfeld, A., Williams, E., Vasiliauskas, D., Barretto, S., Smith, L., Mariadassou, M., Philippe, C., Devime, F., Melchior, C., Gourcerol, G., Dourmap, N., Lapaque, N., Larraufie, P., Blottière, H. M., Herberden, C., Gerard, P., Rehfeld, J. F., Ferraris, R. P., Fritton, J. C., Ellero-Simatos, S., Douard, V. Fructose malabsorption induces cholecystokinin expression in the ileum and cecum by changing microbiota composition and metabolism.
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http://dx.doi.org/10.1096/fj.201801526RRDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6988857PMC
June 2019

Voxel-based automated detection of focal cortical dysplasia lesions using diffusion tensor imaging and T2-weighted MRI data.

Epilepsy Behav 2018 07 21;84:127-134. Epub 2018 May 21.

Department of Radiology, Sanbo Brain Hospital, Capital Medical University, Beijing, China. Electronic address:

The aim of this study was to automatically detect focal cortical dysplasia (FCD) lesions in patients with extratemporal lobe epilepsy by relying on diffusion tensor imaging (DTI) and T2-weighted magnetic resonance imaging (MRI) data. We implemented an automated classifier using voxel-based multimodal features to identify gray and white matter abnormalities of FCD in patient cohorts. In addition to the commonly used T2-weighted image intensity feature, DTI-based features were also utilized. A Gaussian processes for machine learning (GPML) classifier was tested on 12 patients with FCD (8 with histologically confirmed FCD) scanned at 1.5 T and cross-validated using a leave-one-out strategy. Moreover, we compared the multimodal GPML paradigm's performance with that of single modal GPML and classical support vector machine (SVM). Our results demonstrated that the GPML performance on DTI-based features (mean AUC = 0.63) matches with the GPML performance on T2-weighted image intensity feature (mean AUC = 0.64). More promisingly, GPML yielded significantly improved performance (mean AUC = 0.76) when applying DTI-based features to multimodal paradigm. Based on the results, it can also be clearly stated that the proposed GPML strategy performed better and is robust to unbalanced dataset contrary to SVM that performed poorly (AUC = 0.69). Therefore, the GPML paradigm using multimodal MRI data containing DTI modality has promising result towards detection of the FCD lesions and provides an effective direction for future researches.
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http://dx.doi.org/10.1016/j.yebeh.2018.04.005DOI Listing
July 2018

A meta analysis of genome-wide association studies for limb bone lengths in four pig populations.

BMC Genet 2015 Jul 29;16:95. Epub 2015 Jul 29.

State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.

Background: Limb bone length is an economically important trait in pigs, because it is negatively correlated with backfat thickness, and is also a determinant to the yield of hip and loin. Moreover, abnormal growth of the limb bone leads to leg structural weakness. Until now, the genetic architecture of the pig lime bone length remains poorly understood. The object of this study was to map genomic loci for limb bone length by genome-wide association study (GWAS) on 4 pig populations.

Results: We measured the lengths of five limb bones including scapula, humerus, ulna, femur and tibia that were dissected from the right-side carcass of 925, 331, 314 and 434 animals from White Duroc × Erhualian F2 intercross, Erhualian, Laiwu and Sutai populations, respectively. We genotyped the 2004 pigs for 62,163 single nucleotide polymorphisms (SNPs) on the Porcine SNP60 BeadChip, and performed GWAS and a GWAS meta analysis in the 4 populations. In total, we identified 12 and 4 loci associated with the limb bone lengths at suggestive and genome-wide significant levels respectively, of which 4 loci were reported for the first time. The most prominent locus was identified in a 924-kb (kilo base pairs) linkage disequilibrium block on Sus Scrofa chromosome (SSC) 7, and High Mobility Group AT-hook 1 (HMGA1) appears to be a strong candidate gene in this region. Another promising locus is located in the middle of SSC4, and Pleiomorphic Adenoma Gene 1 (PLAG1) is a functionally plausible candidate gene underlying the locus. Because the lengths of the 5 limb bones are highly correlated to each other, most of significant loci were associated with all of the 5 traits; however, several loci showed specific effect on the length of one limb bone, such as the locus at the proximal end of SSC2 associated with only the scapula length.

Conclusion: To our knowledge, this study was the first GWAS meta analysis for limb bone lengths in pigs. As expected, the meta analysis is more powerful to identify genomic loci. A total of 16 loci were identified in this study, including four novel loci. HMGA1 and PLAG1 are two appearing candidate genes for pig limb bone lengths, which warrant further investigations.
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http://dx.doi.org/10.1186/s12863-015-0257-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4518597PMC
July 2015

Understanding the molecular mechanisms of human microtia via a pig model of HOXA1 syndrome.

Dis Model Mech 2015 Jun 2;8(6):611-22. Epub 2015 Apr 2.

Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, People's Republic of China

Microtia is a congenital malformation of the outer ears. Although both genetic and environmental components have been implicated in microtia, the genetic causes of this innate disorder are poorly understood. Pigs have naturally occurring diseases comparable to those in humans, providing exceptional opportunity to dissect the molecular mechanism of human inherited diseases. Here we first demonstrated that a truncating mutation in HOXA1 causes a monogenic disorder of microtia in pigs. We further performed RNA sequencing (RNA-Seq) analysis on affected and healthy pig embryos (day 14.25). We identified a list of 337 differentially expressed genes (DEGs) between the normal and mutant samples, shedding light on the transcriptional network involving HOXA1. The DEGs are enriched in biological processes related to cardiovascular system and embryonic development, and neurological, renal and urological diseases. Aberrant expressions of many DEGs have been implicated in human innate deformities corresponding to microtia-associated syndromes. After applying three prioritizing algorithms, we highlighted appealing candidate genes for human microtia from the 337 DEGs. We searched for coding variants of functional significance within six candidate genes in 147 microtia-affected individuals. Of note, we identified one EVC2 non-synonymous mutation (p.Asp1174Asn) as a potential disease-implicating variant for a human microtia-associated syndrome. The findings advance our understanding of the molecular mechanisms underlying human microtia, and provide an interesting example of the characterization of human disease-predisposing variants using pig models.
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http://dx.doi.org/10.1242/dmm.018291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457031PMC
June 2015

Predicting linear B-cell epitopes using amino acid anchoring pair composition.

BioData Min 2015 29;8:14. Epub 2015 Apr 29.

Department of Molecular Biology, Hebei University College of Life Sciences, 180 Wusi Road, Baoding, 071002 China.

Background: Accurate identification of linear B-cell epitopes plays an important role in peptide vaccine designs, immunodiagnosis, and antibody productions. Although several prediction methods have been reported, unsatisfied accuracy has limited the broad usages in linear B-cell epitope prediction. Therefore, developing a reliable model with significant improvement on prediction accuracy is highly desirable.

Results: In this study, we developed a novel model for prediction of linear B-cell epitopes, APCpred, which was derived from the combination of amino acid anchoring pair composition (APC) and Support Vector Machine (SVM) methods. Systematic comparisons with the existing prediction models demonstrated that APCpred method significantly improved the prediction accuracy both in fivefold cross-validation of training datasets and in independent blind datasets. In the fivefold cross-validation test with Chen872 dataset at window size of 20, APCpred achieved AUC of 0.809 and accuracy of 72.94%, which was much more accurate than the existing models, e.g., Bayesb, Chen's AAP methods and the enhanced combination method of AAP with five AP scales. For the fivefold cross-validation test with ABC16 dataset, APCpred achieved an improved AUC of 0.794 and ACC of 73.00% at window size of 16, and attained an AUC of 0.748 and ACC of 67.96% on Blind387 dataset after being trained with ABC16 dataset. Trained with Lbtope_Confirm dataset, APCpred achieved an increased Acc of 55.09% on FBC934 dataset. Within sequence window sizes from 12 to 20, APCpred final model on homology-reduced dataset achieved an optimal AUC of 0.748 and ACC of 68.43% in fivefold cross-validation at the window size of 20.

Conclusion: APCpred model demonstrated a significant improvement in predicting linear B-cell epitopes using the features of amino acid anchoring pair composition (APC). Based on our study, a webserver has been developed for on-line prediction of linear B-cell epitopes, which is a free access at: http:/ccb.bmi.ac.cn/APCpred/.
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http://dx.doi.org/10.1186/s13040-015-0047-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449562PMC
June 2015

Emerging roles of lactic acid bacteria in protection against colorectal cancer.

World J Gastroenterol 2014 Jun;20(24):7878-86

Li Zhong, Xufei Zhang, Mihai Covasa, Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, United States.

Colorectal cancer (CRC) is the third leading cause of cancer deaths worldwide and the fourth most common cancer diagnosed among men and women in the United States. Considering the risk factors of CRC, dietary therapy has become one of the most effective approaches in reducing CRC morbidity and mortality. The use of probiotics is increasing in popularity for both the prevention and treatment of a variety of diseases. As the most common types of microbes used as probiotics, lactic acid bacteria (LAB) are comprised of an ecologically diverse group of microorganisms united by formation of lactic acid as the primary metabolite of sugar metabolism. LAB have been successfully used in managing diarrhea, food allergies, and inflammatory bowel disease. LAB also demonstrated a host of properties in preventing colorectal cancer development by inhibiting initiation or progression through multiple pathways. In this review, we discuss recent insights into cellular and molecular mechanisms of LAB in CRC prevention including apoptosis, antioxidant DNA damages, immune responses, and epigenetics. The emerging experimental findings from clinical trials as well as the proposed mechanisms of gut microbiota in carcinogenesis will also be briefly discussed.
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http://dx.doi.org/10.3748/wjg.v20.i24.7878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4069315PMC
June 2014

A novel autoantibody test for the detection of pre-neoplastic lung lesions.

Mol Cancer 2014 Apr 5;13:78. Epub 2014 Apr 5.

British American Tobacco (Investments) Ltd, Group Research and Development, Regents Park Road, Millbrook, Southampton SO15 8TL, UK.

Background: Atypical adenomatous hyperplasia (AAH) and squamous cell dysplasia (SCD) are associated with the development of malignant lesions in the lung. Accurate diagnosis of AAH and SCD could facilitate earlier clinical intervention and provide useful information for assessing lung cancer risk in human populations. Detection of AAH and SCD has been achieved by imaging and bronchoscopy clinically, but sensitivity and specificity remain less than satisfactory. We utilized the ability of the immune system to identify lesion specific proteins for detection of AAH and SCD.

Methods: AAH and SCD tissue was surgically removed from six patients of Chinese descent (3 AAH and 3 SCD) with corresponding serum samples. Total RNA was extracted from the tissues and a cDNA library was generated and incorporated into a T7 bacteriophage vector. Following enrichment to remove "normal" reactive phages, a total of 200 AAH related and 200 SCD related phage clones were chosen for statistical classifier development and incorporation into a microarray. Microarray slides were tested with an independent double-blinded population consisting of 100 AAH subjects, 100 SCD subjects and 200 healthy control subjects.

Results: Sensitivity of 82% and specificity of 70% were achieved in the detection of AAH using a combination of 9 autoantibody biomarkers. Likewise, 86% sensitivity and 78% specificity were achieved in the detection of SCD using a combination of 13 SCD-associated markers. Sequencing analysis identified that most of these 22 autoantibody biomarkers had known malignant associations.

Conclusions: Both diagnostic values showed promising sensitivity and specificity in detection of pre-neoplastic lung lesions. Hence, this technology could be a useful non-invasive tool to assess lung cancer risk in human populations.
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http://dx.doi.org/10.1186/1476-4598-13-78DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992137PMC
April 2014

Identification of novel autoantibodies for detection of malignant mesothelioma.

PLoS One 2013 19;8(8):e72458. Epub 2013 Aug 19.

Department of Cell Biology, Hebei University College of Life Sciences, Baoding, Hebei, PR China.

Background: The malignant mesothelioma (MM) survival rate has been hampered by the lack of efficient and accurate early detection methods. The immune system may detect the early changes of tumor progression by responding with tumor-associated autoantibody production. Hence, in this study, we translated the humoral immune response to cancer proteins into a potential blood test for MM.

Methodology/principal Findings: A T7 phage MM cDNA library was constructed using MM tumor tissues and biopanned for tumor-associated antigens (TAAs) using pooled MM patient and normal serum samples. About 1008 individual phage TAA clones from the biopanned library were subjected to protein microarray construction and tested with 53 MM and 52 control serum samples as a training group. Nine candidate autoantibody markers were selected from the training group using Tclass system and logistic regression statistical analysis, which achieved 94.3% sensitivity and 90.4% specificity with an AUC value of 0.89 in receiver operating characteristic analysis. The classifier was further evaluated with 50 patient and 50 normal serum samples as an independent blind validation, and the sensitivity of 86.0% and the specificity of 86.0% were obtained with an AUC of 0.82. Sequencing and BLASTN analysis of the classifier revealed that five of these nine candidate markers were found to have strong homology to cancer related proteins (PDIA6, MEG3, SDCCAG3, IGHG3, IGHG1).

Conclusions/significance: Our results indicated that using a panel of 9 autoantibody markers presented a promising accuracy for MM detection. Although the results need further validation in high-risk groups, they provided the potentials in developing a serum-based assay for MM diagnosis.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072458PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3747111PMC
January 2015

Serological antibodies against LY6K as a diagnostic biomarker in esophageal squamous cell carcinoma.

Biomarkers 2012 Jun 19;17(4):372-8. Epub 2012 Apr 19.

Department of Cell Biology, Hebei University College of Life Sciences, Baoding, China.

Objectives: To evaluate the diagnostic values of autoantibodies against lymphocyte antigen 6 complex locus K (LY6K) in esophageal squamous cell carcinoma (ESCC).

Methods: After cloning, expressing, and purifying LY6K as fusion proteins, LY6K autoantibodies were measured in 62 patient and 58 control serum samples using enzyme-linked immunosorbent assay (ELISA). Reverse transcription polymerase chain reaction (RT-PCR) was used to measure the LY6K mRNA levels in ESCC and adjacent tissues.

Results: LY6K autoantibodies were found significantly higher in patients than controls. The area under the receiver-operating characteristic (ROC) curve (AUC) was 0.85, and the optimal sensitivity and specificity for ESCC detection were 80.6 and 78.7%, respectively. LY6K mRNA expressions in patients were upregulated.

Conclusions: Autoantibodies against LY6K may be a good diagnostic biomarker for ESCC.
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http://dx.doi.org/10.3109/1354750X.2012.680609DOI Listing
June 2012