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1.  Variations in the MHC Region Confer Risk to Esophageal Squamous Cell Carcinoma on the Subjects from High-Incidence Area in Northern China 
PLoS ONE  2014;9(3):e90438.
Background
The human major histocompatibility complex (MHC) is the most important region in vertebrate genome, and is crucial in innate immunity. Recent studies have demonstrated the possible role of polymorphisms in the MHC region to high risk for esophageal squamous cell carcinoma (ESCC). Our previous genome-wide association study (GWAS) has indicated that the MHC region may confer important risk loci for ESCC, but without further fine mapping. The aim of this study is to further identify the risk loci in the MHC region for ESCC in Chinese population.
Methods
Conditional logistic regression analysis (CLRA) was performed on 24 single nucleotide polymorphisms (SNPs) within the MHC region, which were obtained from the genetically matched 937 cases and 692 controls of Chinese Han population. The identified promising SNPs were further correlated with clinical and clinicopathology characteristics. Immunohistochemistry was performed to explore the protein expression pattern of the related genes in ESCC and neighboring normal tissues.
Results
Of the 24 promising SNPs analyzed, we identified three independent SNPs in the MHC region associated with ESCC: rs35399661 (P = 6.07E-06, OR = 1.71, 95%CI = 1.36–2.17), rs3763338 (P = 1.62E-05, OR = 0.63, 95%CI = 0.50–0.78) and rs2844695 (P = 7.60E-05, OR = 0.74, 95%CI = 0.64–0.86). These three SNPs were located at the genes of HLA-DQA1, TRIM27, and DPCR1, respectively. Further analyses showed that rs2844695 was preferentially associated with younger ESCC cases (P = 0.009). The positive immunostaining rates both for HLA-DQA1 and TRIM27 were much higher in ESCC tissues than in neighboring normal tissues (69.4% vs. 26.8% for HLA-DQA1 and 77.6% vs. 47.8% for TRIM27, P<0.001). Furthermore, the overexpression of HLA-DQA1 is correlated significantly with age (P = 0.001) and family history (P<0.001).
Conclusion
This study for the first time provides evidence that multiple genetic factors within the MHC region confer risk to ESCC on the subjects from high-risk area in northern China.
doi:10.1371/journal.pone.0090438
PMCID: PMC3942432  PMID: 24595008
2.  Evaluation of secondary surgery to enlarge the peeling of the internal limiting membrane following the failed surgery of idiopathic macular holes 
The aim of the present study was to evaluate the clinical results of pars plana vitrectomy (PPV) combined with the surgical enlargement of internal limiting membrane (ILM) peeling in patients who had previously undergone failed idiopathic macular hole (IMH) surgery. In the study, 134 eyes from 130 IMH patients who had received PPV combined with ILM peeling surgery (2 disk diameters) were analyzed. Within this cohort, 14 eyes had IMHs that were not closed, of which 13 eyes underwent a second surgery involving enlargement of the ILM peeling. The extent of the ILM peeling was increased to the vascular arcades of the posterior fundus in the secondary surgery. Of the 13 eyes that underwent secondary surgery, five were in stage III and nine were in stage IV. The second surgery successfully achieved IMH closure in 61.5% (8/13) of the eyes. The IMH was completely closed following surgery and the logMAR vision increased from 0.98 to 0.84 (P=0.013) in the 8 successfully treated cases. The surgical enlargement of ILM peeling closed the IMHs and improved vision in the majority of patients. In addition, the procedures were safe. Therefore, the results of the present study indicate that enlargement of ILM peeling may be an effective therapy for patients who have previously undergone the failed surgical correction of an IMH.
doi:10.3892/etm.2014.1477
PMCID: PMC3919896  PMID: 24520279
idiopathic macular holes; internal limiting membrane peeling enlargement surgery; pars plana vitrectomy
3.  Correction: Retrospective Analysis of Prognostic Factors in 205 Patients with Laryngeal Squamous Cell Carcinoma Who Underwent Surgical Treatment 
PLoS ONE  2013;8(12):10.1371/annotation/9c5dbeb2-9990-464e-a05d-72d329f11647.
doi:10.1371/annotation/9c5dbeb2-9990-464e-a05d-72d329f11647
PMCID: PMC3865305
4.  Genome-Wide Copy Number Variations Inferred from SNP Genotyping Arrays Using a Large White and Minzhu Intercross Population 
PLoS ONE  2013;8(10):e74879.
Copy number variations (CNVs) are one of the main contributors to genetic diversity in animals and are broadly distributed in the genomes of swine. Investigating the performance and evolutionary impacts of pig CNVs requires comprehensive knowledge of their structure and function within and between breeds. In the current study, 4 different programs (i.e., GADA, PennCNV, QuantiSNP, and cnvPartition) were used to analyze Porcine SNP60 genotyping data of 585 pigs from one Large White × Minzhu intercross population to detect copy number variant regions (CNVRs). Overlapping CNVRs recalled by at least 2 programs were used to construct a powerful and comprehensive CNVR map, which contained249 CNVRs (i.e., 70 gains, 43 losses, and 136 gains/losses) and covered 26.22% of the regions in the swine genome. Ten CNVRs, representing different predicted statuses, were selected for validation via quantitative real-time PCR (QPCR); 9/10 CNVRs (i.e., 90%) were validated. When being traced back to the F0 generation, 58 events were identified in only Minzhu F0 parents and 2 events were identified in only Large White F0 parents. A series of CNVR function analyses were performed. Some of the CNVRs functions were predicted, and several interesting CNVRs for meat quality traits and hematological parameters were obtained. A comprehensive and lower false rate genome-wide CNV map was constructed for Large White and Minzhu pig genomes in this study. Our results may provide an important basis for determining the relationship between CNVRs and important qualitative and quantitative traits. In addition, it can help to further understand genetic processes in pigs.
doi:10.1371/journal.pone.0074879
PMCID: PMC3787955  PMID: 24098353
5.  Polymorphism of A133S and promoter hypermethylation in Ras association domain family 1A gene (RASSF1A) is associated with risk of esophageal and gastric cardia cancers in Chinese population from high incidence area in northern China 
BMC Cancer  2013;13:259.
Background
The role of tumor suppressor gene RASSF1A in the esophageal and gastric cardia carcinogenesis is still inconclusive. In this study, the polymorphism, promoter methylation and gene expression of RASSF1A were characterized in esophageal squamous cell carcinoma (ESCC) and gastric cardia adenocarcinoma (GCA).
Methods
We firstly analyzed the prevalence of RASSF1A A133S in a total of 228 cancer patients with ESCC (n=112) and GCA (n=116) and 235 normal controls by polymerase chain reaction (PCR) and restriction enzyme-digestion assay. Then, the promoter methylation status of the RASSF1A in ESCC (n=143), GCA (n=92) and corresponding adjacent normal tissues were further investigated using methylation-specific PCR (MSP) approach. Finally, the RASSF1A protein expression were determined in ESCC (n=27), GCA (n=24) and the matched adjacent normal tissues by immunohistochemical method.
Results
The frequency of 133Ala/Se and Ser/Ser genotype was significantly higher in GCA patients than in normal controls (19.0% vs. 10.2%, P=0.02). Compared with Ala/Ala genotype, Ala/Se and Ser/Ser genotype significantly increased susceptibility to GCA (OR=2.06, 95% CI=1.09–3.97). However, this polymorphism had no association with ESCC (P=0.69). The promoter methylation of RASSF1A gene was significantly increased the risk to both ESCC (OR=5.90, 95% CI=2.78–12.52) and GCA (OR=7.50, 95% CI= 2.78–20.23). Promoter methylation of RASSF1A gene in ESCC was also associated with age and cancer cell differentiation (for age: OR=3.11, 95% CI=1.10–8.73; for differentiation: OR=0.29, 95% CI=0.12–0.69). RASSF1A positive expression was significantly decreased the risk of GCA (OR=0.16, 95% CI=0.03–0.83). In contrast, there was no statistical significance between RASSF1A positive expression and ESCC. The expression of RASSF1A protein trend to be positively related with older GCA patients (OR=16.20, 95% CI=1.57–167.74).
Conclusions
The present findings suggest that alterations of RASSF1A may play an important role in gastric cardia carcinogenesis in terms of polymorphism, promoter hypermethylation and protein expression. Whereas, RASSF1A hypermethylation may probably also be involved in esophageal squamous cell carcinogenesis.
doi:10.1186/1471-2407-13-259
PMCID: PMC3668992  PMID: 23705663
Esophageal squamous cell carcinoma; Gastric cardia adenocarcinoma; A133S in RASSF1A; Polymorphism; Methylation; Protein expression
6.  Genotypic variants at 2q33 and risk of esophageal squamous cell carcinoma in China: a meta-analysis of genome-wide association studies 
Abnet, Christian C. | Wang, Zhaoming | Song, Xin | Hu, Nan | Zhou, Fu-You | Freedman, Neal D. | Li, Xue-Min | Yu, Kai | Shu, Xiao-Ou | Yuan, Jian-Min | Zheng, Wei | Dawsey, Sanford M. | Liao, Linda M. | Lee, Maxwell P. | Ding, Ti | Qiao, You-Lin | Gao, Yu-Tang | Koh, Woon-Puay | Xiang, Yong-Bing | Tang, Ze-Zhong | Fan, Jin-Hu | Chung, Charles C. | Wang, Chaoyu | Wheeler, William | Yeager, Meredith | Yuenger, Jeff | Hutchinson, Amy | Jacobs, Kevin B. | Giffen, Carol A. | Burdett, Laurie | Fraumeni, Joseph F. | Tucker, Margaret A. | Chow, Wong-Ho | Zhao, Xue-Ke | Li, Jiang-Man | Li, Ai-Li | Sun, Liang-Dan | Wei, Wu | Li, Ji-Lin | Zhang, Peng | Li, Hong-Lei | Cui, Wen-Yan | Wang, Wei-Peng | Liu, Zhi-Cai | Yang, Xia | Fu, Wen-Jing | Cui, Ji-Li | Lin, Hong-Li | Zhu, Wen-Liang | Liu, Min | Chen, Xi | Chen, Jie | Guo, Li | Han, Jing-Jing | Zhou, Sheng-Li | Huang, Jia | Wu, Yue | Yuan, Chao | Huang, Jing | Ji, Ai-Fang | Kul, Jian-Wei | Fan, Zhong-Min | Wang, Jian-Po | Zhang, Dong-Yun | Zhang, Lian-Qun | Zhang, Wei | Chen, Yuan-Fang | Ren, Jing-Li | Li, Xiu-Min | Dong, Jin-Cheng | Xing, Guo-Lan | Guo, Zhi-Gang | Yang, Jian-Xue | Mao, Yi-Ming | Yuan, Yuan | Guo, Er-Tao | Zhang, Wei | Hou, Zhi-Chao | Liu, Jing | Li, Yan | Tang, Sa | Chang, Jia | Peng, Xiu-Qin | Han, Min | Yin, Wan-Li | Liu, Ya-Li | Hu, Yan-Long | Liu, Yu | Yang, Liu-Qin | Zhu, Fu-Guo | Yang, Xiu-Feng | Feng, Xiao-Shan | Wang, Zhou | Li, Yin | Gao, She-Gan | Liu, Hai-Lin | Yuan, Ling | Jin, Yan | Zhang, Yan-Rui | Sheyhidin, Ilyar | Li, Feng | Chen, Bao-Ping | Ren, Shu-Wei | Liu, Bin | Li, Dan | Zhang, Gao-Fu | Yue, Wen-Bin | Feng, Chang-Wei | Qige, Qirenwang | Zhao, Jian-Ting | Yang, Wen-Jun | Lei, Guang-Yan | Chen, Long-Qi | Li, En-Min | Xu, Li-Yan | Wu, Zhi-Yong | Bao, Zhi-Qin | Chen, Ji-Li | Li, Xian-Chang | Zhuang, Xiang | Zhou, Ying-Fa | Zuo, Xian-Bo | Dong, Zi-Ming | Wang, Lu-Wen | Fan, Xue-Pin | Wang, Jin | Zhou, Qi | Ma, Guo-Shun | Zhang, Qin-Xian | Liu, Hai | Jian, Xin-Ying | Lian, Sin-Yong | Wang, Jin-Sheng | Chang, Fu-Bao | Lu, Chang-Dong | Miao, Jian-Jun | Chen, Zhi-Guo | Wang, Ran | Guo, Ming | Fan, Zeng-Lin | Tao, Ping | Liu, Tai-Jing | Wei, Jin-Chang | Kong, Qing-Peng | Fan, Lei | Wang, Xian-Zeng | Gao, Fu-Sheng | Wang, Tian-Yun | Xie, Dong | Wang, Li | Chen, Shu-Qing | Yang, Wan-Cai | Hong, Jun-Yan | Wang, Liang | Qiu, Song-Liang | Goldstein, Alisa M. | Yuan, Zhi-Qing | Chanock, Stephen J. | Zhang, Xue-Jun | Taylor, Philip R. | Wang, Li-Dong
Human Molecular Genetics  2012;21(9):2132-2141.
Genome-wide association studies have identified susceptibility loci for esophageal squamous cell carcinoma (ESCC). We conducted a meta-analysis of all single-nucleotide polymorphisms (SNPs) that showed nominally significant P-values in two previously published genome-wide scans that included a total of 2961 ESCC cases and 3400 controls. The meta-analysis revealed five SNPs at 2q33 with P< 5 × 10−8, and the strongest signal was rs13016963, with a combined odds ratio (95% confidence interval) of 1.29 (1.19–1.40) and P= 7.63 × 10−10. An imputation analysis of 4304 SNPs at 2q33 suggested a single association signal, and the strongest imputed SNP associations were similar to those from the genotyped SNPs. We conducted an ancestral recombination graph analysis with 53 SNPs to identify one or more haplotypes that harbor the variants directly responsible for the detected association signal. This showed that the five SNPs exist in a single haplotype along with 45 imputed SNPs in strong linkage disequilibrium, and the strongest candidate was rs10201587, one of the genotyped SNPs. Our meta-analysis found genome-wide significant SNPs at 2q33 that map to the CASP8/ALS2CR12/TRAK2 gene region. Variants in CASP8 have been extensively studied across a spectrum of cancers with mixed results. The locus we identified appears to be distinct from the widely studied rs3834129 and rs1045485 SNPs in CASP8. Future studies of esophageal and other cancers should focus on comprehensive sequencing of this 2q33 locus and functional analysis of rs13016963 and rs10201587 and other strongly correlated variants.
doi:10.1093/hmg/dds029
PMCID: PMC3315211  PMID: 22323360
7.  Retrospective Analysis of Prognostic Factors in 205 Patients with Laryngeal Squamous Cell Carcinoma Who Underwent Surgical Treatment 
PLoS ONE  2013;8(4):e60157.
Objectives
To investigate the most important factors affecting the prognosis of the patients with squamous cell carcinoma (SCC) of the larynx.
Methods
Based on the clinical and follow-up data, 205 patients with SCC of the larynx receiving total laryngectomy, partial laryngectomy, or CO2 laser surgery in GuangDong General Hospital were retrospectively analyzed. A survival analysis was performed by the Kaplan-Meier method and a multivariable analysis of prognostic factors was carried out using the Cox proportional hazard model.
Results
Subtypes of carcinoma included 69.8% glottic and 30.2% supraglottic. Most patients were in N0 stage (77.6%), and 22.4% patients were in N1∼N3 stage. Over half of the patients were in T1∼T2 stage (55.1%), 20.0% in T3, and 24.9% in T4. Mean follow-up duration was 49.2 months. The survival rates 1, 2, and 3 years after the surgery were 99.0%, 91.7%, and 81.5%, respectively. The survival rate for those patients with clinical stage IV was significantly lower than for those with clinical stage I and II (p<0.001 and p = 0.013, respectively). The disease-free progression rates 1, 2, and 3 years after the surgery were 83.9%, 74.6%, and 71.2%, respectively. Futhermore, those patients with a Charlson score of 1 to 2 and ≥3 had higher risk of mortality than those with a Charlson score of 0 (hazard ratios of 1.8 and 2.41 p = 0.042 and p = 0.008). Multivariable analysis revealed that clinical stage, surgical margin, and comorbidity were significantly associated with both mortality and disease-free progression.
Conclusion
The surgical resection margin, clinical stage, and comorbidity were independent factors affecting the laryngeal cancer prognosis. The survival rates were lower for patients with advanced laryngeal cancer, positive surgical margins, or severe comorbidity, suggesting the importance of early diagnosis, early treatment, negative surgical margins, and conditions of comorbidity.
doi:10.1371/journal.pone.0060157
PMCID: PMC3617169  PMID: 23593169
8.  Role of Thermal Process on Self-Assembled Structures of 4′-([2,2′:6′,2″-Terpyridin]-4′-Yl)-[1,1′-Biphenyl]-4-Carboxylic Acid on Au(III) 
The role of dynamic processes on self-assembled structures of 4′-([2,2′:6′, 2″-terpyridin]-4′-yl)-[1,1′-biphenyl]-4-carboxylic acid (l) molecules on Au(III) has been studied by scanning tunneling microscopy. The as-deposited monolayer is closed-packed and periodic in a short-range due to dipole forces. A thermal annealing process at 110 degrees drives such disordered monolayer into ordered chain-like structures, determined by the combination of the dipole forces and hydrogen bonding. Further annealing at 130 degrees turns the whole monolayer into a bowknot-like structure in which hydrogen bonding plays the dominant role in the formation of assembled structures. Such dependence of an assembled structure on the process demonstrates that an assembled structure can be regulated and controlled not only by the molecular structure but also by the thermal process to form the assembled structure.
doi:10.3390/ijms14035686
PMCID: PMC3634450  PMID: 23478440
dynamic processes; self-assembled structure; hydrogen bond; dipole
9.  Potentiation of tumor radiotherapy by a radiation-inducible oncolytic and oncoapoptotic adenovirus in cervical cancer xenografts 
The p53 tumor suppressor pathway is impaired in more than 90% of cervical cancers and cancer-derived cell lines as a result of infection by human papillomavirus (HPV). The HPV E6 oncoprotein forms complexes with p53 and promotes its degradation via the ubiquitin-dependent mechanism. In this study, we attempted to improve the clinical outcomes of this combined therapy by modifying the p53-targeted adenovirus to become radiation-responsive. The anti-tumor adenovirus was constructed by inserting a radiation-responsive expression cassette composed of the promoter of early growth response-1 (Egr-1) and the pro-apoptotic protein TRAIL. We showed that the addition of adenovirus containing Egr-1/TRAIL significantly increased cell death and apoptosis caused by radiotherapy. In mice bearing xenograft tumors, intratumoral administration of the Egr-1/TRAIL adenovirus followed by radiation significantly reduced tumor growth and enhanced tumor survival. Our Egr-1/TRAIL adenoviral gene product may offer a novel “one-two punch” tumor therapy for cervical cancers not only by potentiating radiation treatment but also by preserving p53 defect-specific tumor killing of the oncolytic adenovirus.
doi:10.1002/ijc.26013
PMCID: PMC3118272  PMID: 21351100
Egr-1 promoter; TRAIL; gene therapy; radiotherapy; tumor; apoptosis; adenovirus
10.  Risk factors for adverse outcome in low rectal cancer 
AIM: To demonstrate the oncologic outcomes of low rectal cancer and to clarify the risk factors for survival, focusing particularly on the type of surgery performed.
METHODS: Data from patients with low rectal carcinomas who underwent surgery, either sphincter-preserving surgery (SPS) or abdominoperineal resection (APR), at The First Affiliated Hospital of Sun Yat-sen University in China from August 1994 to December 2005 were retrospectively analyzed.
RESULTS: Of 331 patients with low rectal cancer, 159 (48.0%) were treated with SPS. A higher incidence of positive resection margins and a higher 5-year cumulative local recurrence rate (14.7% vs 6.8%, P = 0.041) were observed in patients after APR compared to SPS. The five-year overall survival (OS) was 54.6% after APR and 66.8% after SPS (P = 0.018), and the 5-year disease-free survival (DFS) was 52.9% after APR and 65.5% after SPS (P = 0.013). In multivariate analysis, poor OS and DFS were significantly related to positive resection margins, pT3-4, and pTNM III-IV but not to the type of surgery.
CONCLUSION: Despite a higher rate of positive resection margins after APR, the type of surgery was not identified as an independent risk factor for survival.
doi:10.3748/wjg.v18.i1.64
PMCID: PMC3251807  PMID: 22228972
Abdominoperineal resection; Prognosis; Rectal neoplasms; Sphincter-preserving surgery; Surgery
11.  Data Mining in Networks of Differentially Expressed Genes during Sow Pregnancy 
Small to moderate gains in Pig fertility can mean large returns in overall efficiency, and developing methods to improve it is highly desirable. High fertility rates depend on completion of successful pregnancies. To understand the molecular signals associated with pregnancy in sows, expression profiling experiments were conducted to identify differentially expressed genes in ovary and myometrium at different pregnancy periods using the Affymetrix Porcine GeneChipTM. A total of 974, 1800, 335 and 710 differentially expressed transcripts were identified in the myometrium during early pregnancy (EP) and late pregnancy (LP), and in the ovary during EP and LP, respectively. Self-Organizing Map (SOM) clusters indicated the differentially expressed genes belonged to 7 different functional groups. Based on BLASTX searches and Gene Ontology (GO) classifications, 129 unique genes closely related to pregnancy showed differential expression patterns. GO analysis also indicated that there were 21 different molecular function categories, 20 different biological process categories, and 8 different cellular component categories of genes differentially expressed during sow pregnancy. Gene regulatory network reconstruction provided us with an interaction model of known genes such as insulin-like growth factor 2 (IGF2) gene, estrogen receptor (ESR) gene, retinol-binding protein-4 (RBP4) gene, and several unknown candidate genes related to reproduction. Several pitch point genes were selected for association study with reproduction traits. For instance, DPPA5 g.363 T>C was found to associate with litter born weight at later parities in Beijing Black pigs significantly (p < 0.05). Overall, this study contributes to elucidating the mechanism underlying pregnancy processes, which maybe provide valuable information for pig reproduction improvement.
doi:10.7150/ijbs.4071
PMCID: PMC3334670  PMID: 22532788
gene network; microarray; myometrium; ovary; sow pregnancy
12.  Genome-Wide Association Analysis of Meat Quality Traits in a Porcine Large White × Minzhu Intercross Population 
Pork quality is an economically important trait and one of the main selection criteria for breeding in the swine industry. In this genome-wide association study (GWAS), 455 pigs from a porcine Large White × Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip, and phenotyped for intramuscular fat content (IMF), marbling, moisture, color L*, color a*, color b* and color score in the longissimus muscle (LM). Association tests between each trait and the SNPs were performed via the Genome Wide Rapid Association using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. From the Ensembl porcine database, SNP annotation was implemented using Sus scrofa Build 9. A total of 45 SNPs showed significant association with one or multiple meat quality traits. Of the 45 SNPs, 36 were located on SSC12. These significantly associated SNPs aligned to or were in close approximation to previously reported quantitative trait loci (QTL) and some were located within introns of previously reported candidate genes. Two haplotype blocks ASGA0100525-ASGA0055225-ALGA0067099-MARC0004712-DIAS0000861, and ASGA0085522-H3GA0056170 were detected in the significant region. The first block contained the genes MYH1, MYH2 and MYH4. A SNP (ASGA0094812) within an intron of the USP43 gene was significantly associated with five meat quality traits. The present results effectively narrowed down the associated regions compared to previous QTL studies and revealed haplotypes and candidate genes on SSC12 for meat quality traits in pigs.
doi:10.7150/ijbs.3614
PMCID: PMC3334672  PMID: 22532790
F2 design; genome-wide association study; meat quality trait; pig; SNP.
13.  Genome-wide Association Study of Porcine Hematological Parameters in a Large White × Minzhu F2 Resource Population 
Hematological traits, which are important indicators of immune function in animals, have been commonly examined as biomarkers of disease and disease severity in humans and animals. Genome-wide significant quantitative trait loci (QTLs) provide important information for use in breeding programs of animals such as pigs. QTLs for hematological parameters (hematological traits) have been detected in pig chromosomes, although these are often mapped by linkage analysis to large intervals making identification of the underlying mutation problematic. Single nucleotide polymorphisms (SNPs) are the common form of genetic variation among individuals and are thought to account for the majority of inherited traits. In this study, a genome-wide association study (GWAS) was performed to detect regions of association with hematological traits in a three-generation resource population produced by intercrossing Large White boars and Minzhu sows during the period from 2007 to 2011. Illumina PorcineSNP60 BeadChip technology was used to genotype each animal and seven hematological parameters were measured (hematocrit (HCT), hemoglobin (HGB), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), mean corpuscular volume (MCV), red blood cell count (RBC) and red blood cell volume distribution width (RDW)). Data were analyzed in a three step Genome-wide Rapid Association using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) method. A total of 62 genome-wide significant and three chromosome-wide significant SNPs associated with hematological parameters were detected in this GWAS. Seven and five SNPs were associated with HCT and HGB, respectively. These SNPs were all located within the region of 34.6-36.5 Mb on SSC7. Four SNPs within the region of 43.7-47.0 Mb and fifty-five SNPs within the region of 42.2-73.8 Mb on SSC8 showed significant association with MCH and MCV, respectively. At chromosome-wide significant level, one SNP at 29.2 Mb on SSC1 and two SNPs within the region of 26.0-26.2 Mb were found to be significantly associated with RBC and RDW, respectively. Many of the SNPs were located within previously reported QTL regions and appeared to narrow down the regions compared with previously described QTL intervals. In current research, a total of seven significant SNPs were found within six candidate genes SCUBE3, KDR, TDO, IGFBP7, ADAMTS3 and AFP. In addition, the KIT gene, which has been previously reported to relate to hematological parameters, was located within the region significantly associated with MCH and MCV and could be a candidate gene. These results of this study may lead to a better understanding of the molecular mechanisms of hematological parameters in pigs.
doi:10.7150/ijbs.4027
PMCID: PMC3385009  PMID: 22745577
genome-wide association study; porcine; hematological parameters
14.  Malignant Peripheral Nerve Sheath Tumors: Differentiation Patterns and Immunohistochemical Features - A Mini-Review and Our New Findings 
Journal of Cancer  2012;3:303-309.
Malignant peripheral nerve sheath tumors (MPNST) represent a group of highly heterogeneous human malignancies often with multiple histological origins, divergent differentiation patterns, and diverse immunohistochemical presentations. The differential diagnosis of MPNST from other spindle cell neoplasms poses great challenges for pathologists. This report provides a mini-review of these unique features associated with MPNST and also presents the first cases of MPNST with six differentiation patterns.
doi:10.7150/jca.4179
PMCID: PMC3390600  PMID: 22773934
Malignant peripheral nerve sheath tumor; Liposarcomatous; Glandular; Fibrohistiocytoid; Neuroendocrine differentiation; Cartilage; Triton tumor; Gangliocyte.
15.  Combined Treatment with an Oncolytic Adenovirus and Antitumor Activity of Vincristine against Retinoblastoma Cells 
Treatment trends of retinoblastoma (RB) have gradually evolved from eye enucleation and external radiation to local treatment. Combined treatment with an oncolytic virus and chemotherapy is currently a new method in RB treatment. To investigate the therapeutic effect of oncolytic adenovirus SG600 in combination with vincristine (VCR) on retinoblastoma in vitro, the cell viability, cell cycle effects and apoptotic activity of HXO-RB44 cells treated with SG600, VCR or SG600 plus VCR were measured using a cell counting kit-8-based procedure and flow cytometry. Western blot analysis for Akt, p-Akt, p-p53 and p-Rb protein was performed to investigate the underlying mechanisms of combined therapy. The combination therapy exerted a synergistic antitumor effect via a type of G2/M and S phase arrest rather than the induction of apoptosis. The combination of VCR and SG600 further reduced Akt phosphorylation compared with cells treated with VCR alone, suggesting that SG600 could overcome chemoresistance, perhaps by down-regulating Akt in RB cells. An increase in the expression of p-p53 and decrease in p-Rb expression in HXO-RB44 after co-treatment might be associated with cell cycle block. Western blot examination revealed that VCR might enhance SG600 replication. These results suggest that viro-chemo combination therapy is a feasible and potentially promising approach for the treatment of retinoblastoma.
doi:10.3390/ijms130910736
PMCID: PMC3472711  PMID: 23109819
retinoblastoma; vincristine; oncolytic adenovirus; Akt; drug resistance
16.  Serum Autofluorescence, a Potential Serum Marker for the Diagnosis of Liver Fibrosis in Rats 
Fluctuations in serum autofluorescence (AF) intensity have recently been widely used as markers of certain diseases such as cancer. To determine the diagnostic value of serum AF intensity for liver fibrosis in rats, we induced liver fibrosis by subcutaneous injection of carbon tetrachloride into rats. The rat serum AF intensities were detected at the excitation wavelength of 337 nm and the emission wavelength of 512 nm. The degree of liver fibrosis was evaluated by Van Gieson’s staining. The relationship between serum AF intensity and the degree of liver fibrosis was analyzed by Spearman and Pearson Correlation. The diagnostic sensitivity and specificity of the serum AF was determined by analyzing the receiver operating characteristic (ROC) curves. Our results show that the serum AF intensity in the rat liver fibrosis model increased when compared with control rats eight weeks and twelve weeks post induction of liver fibrosis. However, there was no significant difference in serum AF intensity between fibrotic and control rats at four week post induction. Furthermore, serum AF intensity correlated positively with the severity of the degree of hepatic fibrosis. ROC analysis further suggested that serum AF intensity is a valid marker for staging fibrosis. Therefore, it may potentially be developed as a novel diagnostic tool for hepatic fibrosis.
doi:10.3390/ijms130912130
PMCID: PMC3472797  PMID: 23109905
serum autofluorescence; hepatic fibrosis; diagnosis; noninvasive
17.  Non-Alcoholic Fatty Liver Disease Is not Related to the Incidence of Diabetic Nephropathy in Type 2 Diabetes 
To analyze the association between non-alcoholic fatty liver disease (NAFLD) and the incidence of diabetic nephropathy in patients with type 2 diabetes, the incidence of diabetic nephropathy was assessed in 413 type 2 diabetic patients, by testing the 24 h urinary albumin excretion rate (UAER). The NAFLD was diagnosed based on patient’s medical history and liver ultrasound. The difference in diabetic nephropathy incidence between patients with and without NAFLD was tested by χ2. Multivariate logistic regression analysis was used to assess the factors associated with diabetic nephropathy among type 2 diabetic patients. Total 363 out of 413 type 2 diabetic patients were enrolled in this study. The incidences of NAFLD and diabetic nephropathy in participants were approximately 56% (202/363) and 38% (137/363) respectively, and there was no significant difference in the prevalence of diabetic nephropathy between patients with and without NAFLD (37.1% vs. 38.5%, p = 0.787). The duration of diabetes (odds ratio [OR] 1.065, 95% confidence interval [CI] 1.014–1.120, p = 0.012), waist circumference (OR 1.077, 95% CI 1.040–1.116, p = 0.000), and fasting blood glucose (FBG; OR 1.136, 95% CI 1.023–1.1262, p = 0.017) were significantly associated with diabetic nephropathy, whereas sex, high blood pressure, total cholesterol (TC), triglyceride (TG), and ankle brachial pressure index (ABI) were not significantly associated with the disorder. The present results suggest that NAFLD is not related to the incidence of diabetic nephropathy in type 2 diabetes, but the duration of diabetes, waist circumference, and FBG are important factors for diabetic nephropathy in type 2 diabetes.
doi:10.3390/ijms131114698
PMCID: PMC3509605  PMID: 23203089
non-alcoholic fatty liver disease; diabetic nephropathy; diabetes
18.  Histological origin of pseudomyxoma peritonei in Chinese women: Clinicopathology and immunohistochemistry 
AIM: To investigate the histological origin of pseudomyxoma peritonei (PMP) in Chinese women.
METHODS: The clinical and pathological data were reviewed for 35 women with PMP, and specimens of the peritoneal, appendiceal and ovarian lesions of each patient were examined using the PV-6000 immunohistochemistry method. Antibodies included cytokeratin (CK)7, CK20, mucin (MUC)-1, MUC-2, carbohydrate antigen (CA)-125, estrogen receptor (ER), and progesterone receptor (PR).
RESULTS: Abundant colloidal mucinous tumors were observed in the peritoneum in all 35 cases. Thirty-one patients had a history of appendectomy, 28 of whom had mucinous lesions. There was one patient with appendicitis, one whose appendix showed no apparent pathological changes, and one with unknown surgical pathology. Ovarian mucinous tumors were found in 24 patients. The tumors were bilateral in 13 patients, on the right-side in nine, and on the left side in two. Twenty patients had combined appendiceal and ovarian lesions; 16 of whom had undergone initial surgery for appendiceal lesions. Four patients had undergone initial surgery for ovarian lesions, and relapse occurred in these patients at 1, 11, 32 and 85 mo after initial surgery. Appendiceal mucinous tumors were found in each of these four patients. Thirty-three of the 35 patients showed peritoneal lesions that were positive for CK20 and MUC-2, but negative for CK7, MUC-1, CA125, ER and PR. The expression patterns in the appendix and the ovary were similar to those of the peritoneal lesions. In one of the remaining two cases, CK20, CK7 and MUC-2 were positive, and MUC-1, CA125, ER and PR were negative. The ovaries were not resected. The appendix of one patient was removed at another hospital, and no specimen was evaluated. In the other case, the appendix appeared to be normal during surgery, and was not resected. Peritoneal and ovarian lesions were negative for CK20, MUC-2, CK7, MUC-1, CA125, ER and PR.
CONCLUSION: Most PMP originated from the appendix. Among women with PMP, the ovarian tumors were implanted rather than primary. For patients with PMP, appendectomy should be performed routinely. The ovaries, especially the right ovaries should be explored.
doi:10.3748/wjg.v17.i30.3531
PMCID: PMC3163252  PMID: 21941421
Pseudomyxoma peritonei; Peritoneum; Tumor origin; Ovary; Appendix; Immunohistochemistry
19.  Adult Wilms Tumor with Intracaval and Intracardiac Extension: Report of a Case and Review of Literature 
Journal of Cancer  2011;2:132-135.
Wilms tumor (WT) occurs infrequently in adults. Even rarer is adult WT with extension by direct intravascular spread into the right side of the heart. The present report describes a partially differentiated WT with intracaval and intracardiac extension in a 54-year-old man. The morphologic and immunohistochemical findings confirmed the diagnosis.
PMCID: PMC3072619  PMID: 21479132
Wilms tumor; adult; intracaval extension; intracardiac extension
20.  Primary Solitary Fibrous Tumor of the Thyroid - Report of a Case and Review of the Literature 
Journal of Cancer  2011;2:206-209.
Solitary fibrous tumor (SFT) is a rare spindle-cell neoplasm, especially in the thyroid. We report a case of primary solitary fibrous tumor of the thyroid gland in a 37 year-old Chinese man. The tumor was characterized by bland-looking spindle cells admixed with thin and thick collagen fibers. On immunohistochemistry study indicated that tumor cells were diffusely positive for CD34, Bcl-2 and CD99, and negative for Desmin, NSE, SMA, S-100, and CD68. The patient remains well 16 months after excision. The morphologic and immunohistochemical features of the thyroid SFTs are similar to their reported counterparts in other anatomic sites.
PMCID: PMC3079918  PMID: 21509151
solitary fibrous tumor; thyroid
21.  Human papillomavirus DNA and P16INK4A expression in concurrent esophageal and gastric cardia cancers 
AIM: To investigate the relationship between human papillomavirus (HPV) infection and concurrent esophagus and gastric cardia cancer from the same patient (CC) and examine the significance of P16INK4A protein expression.
METHODS: Polymerase chain reaction was used to detect the presence of HPV type16 (HPV16). The expression of P16INK4A protein was detected using immunohistochemistry.
RESULTS: Among the CC specimens, HPV16-DNA was found in eight cases of esophageal squamous cell carcinoma (ESCC) and five cases of gastric cardia adenocarcinoma (GCA), respectively (47% vs 29%), and two of both ESCC and GCA. P16INK4A was highly expressed in both ESCC and GCA. In the HPV-associated positive CC, higher P16INK4A expression was observed in the GCA than in the ESCC (75% vs 25%, P < 0.05).
CONCLUSION: HPV16 as a correlated risk factor may play an important role in the development of ESCC and GCA. P16INK4A may be a screening index in the HPV-associated carcinoma of gastric cardia.
doi:10.3748/wjg.v16.i46.5901
PMCID: PMC3001984  PMID: 21155014
Esophageal squamous cell carcinoma; Gastric cardia adenocarcinoma; Human papillomavirus; Polymerase chain reaction; Immunohistochemistry
22.  Inhibition of pleural metastasis of collecting duct carcinoma of the kidney by modified cytokine-induced killer cells: A case report and review of the literature 
Oncology Letters  2010;1(6):955-958.
Collecting duct carcinoma (CDC) or Bellini duct carcinoma of the kidney is a rare, but highly aggressive renal epithelial malignancy, with an extremely poor prognosis. Modified cytokine-induced killer (mCIK) cells were injected into the pleural cavity to treat pleural metastasis of CDC. The patient, a 33-year-old male, was admitted to hospital for further treatment for severe pleural metastasis of CDC. We cured the pleural metastasis through intrapleural infusion with mCIK cells. After receiving this innovative treatment, the patient exhibited a positive response: the cough, dyspnea, chest distress and thoracalgia were evidently relieved, while the pleural fluid became clear after exhibiting haematodes and its level decreased significantly. The patient achieved partial success. This novel immunotherapy method is a promising treatment for patients with refractory pleural metastasis.
doi:10.3892/ol.2010.168
PMCID: PMC3412461  PMID: 22870094
collecting duct carcinoma; pleural metastasis; immunotherapy
23.  A two-level structural equation model approach for analyzing multivariate longitudinal responses 
Statistics in medicine  2008;27(16):3017-3041.
SUMMARY
The analysis of longitudinal data to study changes in variables measured repeatedly over time has received considerable attention in many fields. This paper proposes a two-level structural equation model for analyzing multivariate longitudinal responses that are mixed continuous and ordered categorical variables. The first-level model is defined for measures taken at each time point nested within individuals for investigating their characteristics that are changed with time. The second level is defined for individuals to assess their characteristics that are invariant with time. The proposed model accommodates fixed covariates, nonlinear terms of the latent variables, and missing data. A maximum likelihood (ML) approach is developed for the estimation of parameters and model comparison. Results of a simulation study indicate that the performance of the ML estimation is satisfactory. The proposed methodology is applied to a longitudinal study concerning cocaine use.
doi:10.1002/sim.3266
PMCID: PMC2836235  PMID: 18416447
latent variables; longitudinal study on cocaine use; maximum likelihood; MCEM algorithm; model comparison; ordered categorical variables
24.  Bayesian Analysis of Multivariate Latent Curve Models With Nonlinear Longitudinal Latent Effects 
In longitudinal studies, investigators often measure multiple variables at multiple time points and are interested in investigating individual differences in patterns of change on those variables. Furthermore, in behavioral, social, psychological, and medical research, investigators often deal with latent variables that cannot be observed directly and should be measured by 2 or more manifest variables. Longitudinal latent variables occur when the corresponding manifest variables are measured at multiple time points. Our primary interests are in studying the dynamic change of longitudinal latent variables and exploring the possible interactive effect among the latent variables.
Much of the existing research in longitudinal studies focuses on studying change in a single observed variable at different time points. In this article, we propose a novel latent curve model (LCM) for studying the dynamic change of multivariate manifest and latent variables and their linear and interaction relationships. The proposed LCM has the following useful features: First, it can handle multivariate variables for exploring the dynamic change of their relationships, whereas conventional LCMs usually consider change in a univariate variable. Second, it accommodates both first- and second-order latent variables and their interactions to explore how changes in latent attributes interact to produce a joint effect on the growth of an outcome variable. Third, it accommodates both continuous and ordered categorical data, and missing data.
doi:10.1080/10705510902751275
PMCID: PMC2794133  PMID: 20016757
25.  Occurrence of foodborne bacteria in Alberta feedlots 
The Canadian Veterinary Journal  2009;50(2):166-172.
The occurrence of generic Escherichia coli, E. coli O157, Salmonella, and Campylobacter in cattle manure, beef carcasses, catch basin water, and soils receiving manure application was determined in 21 Alberta feedlots. In cattle manure, generic E. coli (98%, 2069/2100) and Campylobacter (76%, 1590/2100) were frequently detected; E. coli O157 (7%, 143/2100) and Salmonella (1%, 20/2100) were less frequently detected. Samples from beef carcasses in the cooler following Hazard Analysis Critical Control Point interventions yielded only 1 isolate each of generic E. coli and Campylobacter (1/1653) and no Salmonella (0/1653). Catch basin water specimens were positive for generic E. coli in both the spring (62%, 13/21) and the fall (52%, 11/21). Other bacteria were detected only in the spring water specimens, including E. coli O157 (29%, 6/21), Salmonella (5%, 1/21), and Campylobacter (52%, 11/21). Generic E. coli was frequently isolated from soil specimens (30%, 27/88), but E. coli O157 was not found in soil samples obtained in the spring and was only occasionally detected in the fall samples (9%, 3/32). Salmonella were occasionally found in the soil specimens collected in the spring (3%, 2/56), but not in the fall season (0/32). Campylobacter jejuni was frequent in cattle manure (66%, 1070/1623), but rare in carcass and environmental samples. E. coli O157 and Salmonella were rarely detected in cattle or the environment. Generic E. coli and Salmonella were rarely detected on carcasses.
PMCID: PMC2629420  PMID: 19412396

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