Biomedical subjects

Hui-Yun Wang

Publications and source records attributed to Hui-Yun Wang.

11 recordsLinked to original sources

PubMed2006

AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays.

Microarray-based analysis of single nucleotide polymorphisms (SNPs) has many applications in large-scale genetic studies. To minimize the influence of experimental variation, microarray data usually need to be processed in different aspects including background subtraction, normalization and low-signal filtering before genotype determination. Although many algorithms are sophisticated for these purposes, biases are still present. In the present paper, new algorithms for SNP microarray data analysis and the software, AccuTyping, developed based on these algorithms are described. The algorithms take advantage of a large number of SNPs included in each assay, and the fact that the top and bottom 20% of SNPs can be safely treated as homozygous after sorting based on their ratios between the signal intensities. These SNPs are then used as controls for color channel normalization and background subtraction. Genotype calls are made based on the logarithms of signal intensity ratios using two cutoff values, which were determined after training the program with a dataset of approximately 160,000 genotypes and validated by non-microarray methods. AccuTyping was used to determine >300,000 genotypes of DNA and sperm samples. The accuracy was shown to be >99%. AccuTyping can be downloaded from http://www2.umdnj.edu/lilabweb/publications/AccuTyping.html.

Algorithms↗

PubMed2005

Strong correlation between meiotic crossovers and haplotype structure in a 2.5-Mb region on the long arm of chromosome 21.

Although the haplotype structure of the human genome has been studied in great detail, very little is known about the mechanisms underlying its formation. To investigate the role of meiotic recombination on haplotype block formation, single nucleotide polymorphisms were selected at a high density from a 2.5-Mb region of human chromosome 21. Direct analysis of meiotic recombination by high-throughput multiplex genotyping of 662 single sperm identifies 41 recombinants. The crossovers were nonrandomly distributed within 16 small areas. All, except one, of these crossovers fall in areas where the haplotype structure exhibits breakdown, displaying a strong statistically positive association between crossovers and haplotype block breaks. The data also indicate a particular clustered distribution of recombination hotspots within the region. This finding supports the hypothesis that meiotic recombination makes a primary contribution to haplotype block formation in the human genome.

Chromosome Mapping↗

PubMed2005

Differences in systemic and central nervous system cellular immunity relevant to relapsing-remitting multiple sclerosis.

In order to elucidate the differences between systemic and central nervous system (CNS) immunity that are relevant to exacerbations of multiple sclerosis (MS), paired peripheral blood and cerebrospinal fluid (CSF) samples obtained from 36 non-treated patients with relapsing-remitting MS (RRMS) were simultaneously examined using flow cytometry to determine the percentages of functional lymphocyte subsets, as well as enzyme-linked immunosorbent assays for measuring soluble immune mediators. Active RRMS patients (n = 27) were characterized by an increase in CD4+ CXCR3+ Th1 cells in blood as compared with inactive patients (n = 9), and this parameter was inversely correlated with plasma levels of IL-10 and IL- 12p70. In contrast, an increase in the percentage of CD4+ CD25+ cells and a decrease in the percentage of CD8+ CD11a(high) cells were features of CSF samples from those with active RRMS. Further, CSF CD4+ CD25+ cells had a close association with leukocyte counts as well as albumin and CXCL10 levels in the CSF, and, thus, could be useful as a measure for inflammatory reactions in the CNS. On the other hand, CD8+ CD11a(high) cells may function as immunoregulatory cells, as their percentage in the CSF showed a positive correlation with CSF levels of the anti-inflammatory cytokine IL-4. These findings suggest that MS relapses occur in a combination with altered cell-mediated immunity that differs between the peripheral blood and CSF compartments, while measurement of lymphocyte subsets may be helpful for monitoring disease status.

Antigens, CD↗

PubMed2005

A genotyping system capable of simultaneously analyzing >1000 single nucleotide polymorphisms in a haploid genome.

A high-throughput genotyping system for scoring single nucleotide polymorphisms (SNPs) has been developed. With this system, >1000 SNPs can be analyzed in a single assay, with a sensitivity that allows the use of single haploid cells as starting material. In the multiplex polymorphic sequence amplification step, instead of attaching universal sequences to the amplicons, primers that are unlikely to have nonspecific and productive interactions are used. Genotypes of SNPs are then determined by using the widely accessible microarray technology and the simple single-base extension assay. Three SNP panels, each consisting of >1000 SNPs, were incorporated into this system. The system was used to analyze 24 human genomic DNA samples. With 5 ng of human genomic DNA, the average detection rate was 98.22% when single probes were used, and 96.71% could be detected by dual probes in different directions. When single sperm cells were used, 91.88% of the SNPs were detectable, which is comparable to the level that was reached when very few genetic markers were used. By using a dual-probe assay, the average genotyping accuracy was 99.96% for 5 ng of human genomic DNA and 99.95% for single sperm. This system may be used to significantly facilitate large-scale genetic analysis even if the amount of DNA template is very limited or even highly degraded as that obtained from paraffin-embedded cancer specimens, and to make many unpractical research projects highly realistic and affordable.

Chromosome Mapping↗

PubMed2004

Alteration of p53 and p21 during hepatocarcinogenesis in tree shrews.

AIM: To investigate p53 mutation and p21 expression in hepatocarcinogenesis induced by hepatitis B virus (HBV) and aflatoxin B(1) (AFB(1)) in tree shrews, and to reveal the role of these genes in hepatocarcinogenesis. METHODS: Tree shrews were divided into four groups: group A, those infected with HBV and fed with AFB(1) (n = 39); group B, those infected with HBV alone (n = 28); group C, those fed with AFB(1) alone (n = 29); and group D, normal controls (n = 20). The tree shrews underwent liver biopsies once every 15 wk. Expression of p53 and p21 proteins and genes in the biopsies and tumor tissues of the experimental tree shrews was detected, respectively, by immunohistochemistry, and by Southern blotting and reverse transcription-polymerase chain reaction and sequencing. RESULTS: The incidence of hepatocellular carcinomas (HCC) was higher in group A (66.7%) than that in group B (3.57%) and C (30%). The time of HCC occurrence was also earlier in group A than that in group C (120.0+/-16.6 wk vs 153.3+/-5.8 wk, respectively, P<0.01). p53 protein was not detected by immunohistochemistry in all groups before the 75(th) wk of the experiment. At the 105(th) wk, the positive rates fo p53 were 78.6%, 60% and 71.4% in groups A, B and C, respectively, which were significantly higher than that in group D (10%) (all P<0.05). An abnormal band of p53 gene was observed in groups A and C. The mutation points of p53 gene in tree shrews with HCC were at codons 275, 78 and 13. The nucleotide sequence and amino acid sequence of tree shrew's wild-type p53 showed 91.7% and 93.4% homologies with those of human p53, respectively. The immunopositivity for p21 was found before HCC development. The incidence of HCC was significantly higher in tree shrews that were positive for p21 than those negative for p21 (80.0% vs 11.0%, P<0.001). The incidence of HCC in p21 positive animals in group A was significantly higher than those positive for p21 in group C (P<0.05). CONCLUSION: A remarkable synergistic effect on HCC development exists between HBV and AFB(1). p53 mutation promotes the development of HCC. HBV and AFB(1) may synergistically induce p53 gene mutation, and stimulate ras gene expression. ras gene is activated at the earlier stage during hepatocarcinogenesis. p21 protein may be an early marker, and the alterations of p53 may be a late event in the development of HCC.

Animals↗

PubMed2004

Immunomonitoring measures in relapsing-remitting multiple sclerosis.

Forty-five patients with relapsing-remitting multiple sclerosis (MS) were examined to determine intracellular cytokine profiles and the surface phenotype of circulating lymphocytes during active, recovery, and stable stages. Active stage patients were characterized by decreases in CD4(+)IL-4(+) Th2 as well as CD4(+)IFN-gamma(+) Th1 cells, when compared with stable stage patients and 16 healthy controls. CCR4(+) Th2 cells were persistently decreased at every MS stage as compared to the controls. CD4(+)CD29(+) and CD4(+)CXCR3(+) cells were closely correlated with IFN-gamma-producing cells. These findings suggest that simultaneous flow cytometry for these two types of measurements can provide information concerning current immune status in MS.

Adolescent↗

PubMed2004

[A case of myeloradiculitis as a complication of visceral larva migrans due to Ascaris suum].

A 35-year-old man noticed a tingling sensation and subsequent slight weakness in the distal part of the left lower extremities, which extended to the left thigh over the following 8 months, when he developed a urinary disturbance. He was admitted to a local hospital and diagnosed as having myelitis, because of the presence of a gadolinium (Gd)-enhanced lesion in the lumbar spinal cord corresponding to the tenth thoracic vertebra (Th10) level. The symptoms disappeared along with some residual sensory disturbance following intravenous administration of 1 g of methylprednisolone (IVMP) for 3 days. However, 4 months later, the patient gradually developed gait disturbance, dysuria, impotence, and fecal incontinence, and was admitted to our hospital in May 2001. A neurological examination revealed the presence of myeloradiculopathy causing a slight weakness in the left hamstring muscles, with positive Babinski and Lasegue signs on the same side. In addition, deep tendon reflexes were absent in the 4 extremities and vibration sense was moderately decreased in the lower extremities, though the results of electrophysiological tests of motor and sensory nerves were normal. A magnetic resonance imaging (MRI) study showed a Gd-enhanced lesion in the spinal cord at the Th8-9 vertebrae level, which was 1 to 2 vertebrae above the initially detected lesion. A lumbar puncture yielded cerebrospinal fluid (CSF) containing mononuclear cells at 7/mm3 that were comprised of an increasd number of CD4+CD25+ activated helper T cells; however, no myelin basic protein or oligoclonal IgG band was present. Serological examinations were negative for the presence of collagen/vascular disorders as well as viral infection due to CMV, EBV, HSV, VZV, and HTLV-1, however, positive for specific antibodies against Ascaris suum in both serum and the CSF, confirming the diagnosis of chronic myeloradiculitis due to visceral larva migrans. The patient was first treated with a single course of a daily 600-mg dose of oral albendazole for 4 weeks, which was resulted in restoration of muscle weakness, as well as disappearance of the Lasègue sign. However, in contrast to the clinical improvement, the CSF sample obtained immediately after completing the treatment showed a worsening trend, as the CSF cell count had increased with a manifestation of marked eosinophilia and CD4+CD25+ cells were also increased. Thereafter, 3-day IVMP treatment was performed twice in cojunction with 3 courses of oral albendazole therapy for the subsequent 4 months, which resulted in normalization of all laboratory measurements concerning the CSF along with a decrement trend in serum and CSF antibody titers specific to Ascaris suum. Our results suggest that neurological involvement due to visceral larva migrans can be efficaciously treated with not only helminthic drugs but also intravenous corticosteroids.

Adult↗

PubMed2003

Immune parameters associated with early treatment effects of high-dose intravenous methylprednisolone in multiple sclerosis.

To determine the immunological effects of high-dose intravenous methylprednisolone (IVMP) and elucidate immune measurements used for evaluation of its therapeutic effect, we analyzed lymphocyte subsets and humoral immune parameters in peripheral blood and cerebrospinal fluid (CSF) samples, before and within 2 weeks of treatment during 19 acute exacerbations in 16 relapsing-remitting multiple sclerosis (MS) patients. In addition to decreases in CSF albumin and IgG levels, treatment resulted in an increase of CD8(+)CXCR3(+) cells as well as a decrease in CD4(+) subsets expressing CD25, CD29, and CCR4 in the CSF. Further, the percentage of circulating CD4(+)CXCR3(+) Th1 cells also decreased. Clinical improvement was achieved following 15 of the 19 treatment occasions. Early (<2 weeks of treatment) clinical improvement was significantly associated with a decrease in CSF CD4(+)CD29(+) helper inducer T cells, whereas they were nearly unchanged in four patients who showed no improvement. Changes in other parameters following IVMP treatment were not different between the responder and non-responder groups.

Adult↗

PubMed2003

Alteration of the p53 gene during tree shrews' hepatocarcinogenesis.

OBJECTIVE: To detect the expression and variation of the p53 gene in hepatocarcinogenesis of tree shrews induced by hepatitis B virus (HBV) and aflatoxin B1 (AFB1). METHODS: Tree shrews were divided into four groups: group A, infected with HBV and fed with AFB1; group B, only infected with HBV; group C, fed with AFB1 alone; and group D normal control. The tree shrews underwent liver biopsy every 15 weeks. Liver and tumor tissues were detected by immunohistochemistry and molecular biotechnologies. RESULTS: The incidence of hepatocellular carcinoma (HCC) was higher in group A (66.7%) than in groups B (0) and C (30%). HCC occurrence was earlier in group A than in group C (120.0+/-16.6 wk vs 153.3+/-5.8 wk, t=3.336, P<0.01). Mutated p53 protein was not found in all groups before 75 weeks of experiment. At the 105th week, the expression rates of mutated p53 protein were 78.6%, 60.0% and 71.4% in groups A, B and C respectively, which were significantly higher than that in group D (10%) (chi2> or =5.03, P<0.05). An abnormal band of the p53 gene was detected in groups A and C. The mutational points of the p53 gene in liver cancer of tree shrews were at codon 275, 78 and 13. Nucleotide sequence and amino acids sequence of tree shrew's wild-type p53 were 91.7% and 93.4% in homology compared with those of human p53, respectively. CONCLUSIONS: Remarkable synergistic effect on HCC exists between HBV and AFB1. Mutated p53 protein expressed before occurrence of HCC promotes the development of HCC. HBV and AFB1 may synergistically induce p53 gene mutation.

Animals↗

PubMed2002

Genome-wide scan for familial nasopharyngeal carcinoma reveals evidence of linkage to chromosome 4.

Nasopharyngeal carcinoma (NPC) occurs with high frequency in Asian populations, especially among people of Cantonese ancestry. In areas with high incidence, NPC clusters in families, which suggests that both geography and genetics may influence disease risk. Although the HLA-Bw46 locus is associated with increased risk of NPC, no predisposing genes have been identified so far. Here we report the results of a genome-wide search carried out in families at high risk of NPC from Guangdong Province, China. Parametric analyses provide evidence of linkage to the D4S405 marker on chromosome 4 with a logarithm of odds for linkage (lod) score of 3.06 and a heterogeneity-adjusted lod (hlod) score of 3.21. Fine mapping with additional markers flanking D4S405 resulted in a lod score of 3.54 and hlod score of 3.67 for the region 4p15.1-q12. Multipoint nonparametric linkage analysis gives lod scores of 3.54 at D4S405 (P = 5.4 x 10(-5)) and 4.2 at D4S3002 (P = 1.1 x 10(-5)), which is positioned 4.5 cM away from D4S405. When Epstein Barr virus antibody titer was included as a covariate, the lod scores reached 4.70 (P = 2.0 x 10(-5)) and 5.36 (P = 4.36 x 10(-6)) for D4S405 and D4S3002, respectively. Our findings provide evidence of a major susceptibility locus for NPC on chromosome 4 in a subset of families.

Adult↗

PubMed2002

Chemokine receptors associated with immunity within and outside the central nervous system in early relapsing-remitting multiple sclerosis.

Thirty-four patients with early relapsing-remitting multiple sclerosis (RRMS) were studied to clarify the differences in chemokine receptor usage by blood and cerebrospinal fluid (CSF) lymphocytes relevant to the pathogenesis of MS. A total of 45 examinations (33 active and 12 inactive stages) revealed that circulating CD4+CXCR3+ T helper 1 (Th1) cells were increased in active MS patients and correlated with the number of gadolinium-enhanced lesions on magnetic resonance (MR) images. In contrast, CSF samples obtained during active stages were characterized by a decrease in the percentage of CD8+CXCR3+ T cells, which was inversely correlated with CSF cell count and intra-blood-brain barrier (BBB) IgG production.

Adolescent↗