Ta-Chih Liu

Abnormal expression of Period 1 (PER1) in endometrial carcinoma

The development of endometrial carcinoma (EC) is a multiple‐step process, which includes inactivation of tumour suppressor genes, activation of oncogenes, and disturbance of cancer‐related genes. Recent studies have shown that the circadian cycle may influence cancer development and prognosis. In this study, the expression of a circadian gene, PER1, was examined in 35 ECs and paired non‐tumour tissues by real‐time quantitative reverse transcription‐polymerase chain reaction (RT‐PCR) and immunohistochemistry. Expression levels of PER1 were significantly decreased in EC, and mutational analysis of the coding regions, together with methylation analysis of cytosine‐phosphate guanosine (CpG) sites in the promoter area, was performed to investigate the possible mechanisms. The analyses detected four single nucleotide polymorphisms in both tumour and non‐tumour tissues, which had no relationship with the expression of PER1. In the promoter area of the PER1 gene, the CpG sites were methylated in 31.4% of ECs, but in 11.4% of paired non‐tumour tissues (p < 0.05). These results suggest that the down‐regulation of PER1 expression in EC was partly due to inactivation of the PER1 gene by DNA methylation of the promoter and partly due to other factors. Analysis of the relationships between the expression of PER1, P53, c‐MYC, cyclin A, cyclin B, and cyclin D1 showed no definite relationship. These results suggest that down‐regulation of the PER1 gene disrupts the circadian rhythm, which may favour the survival of endometrial cancer cells. Copyright

Disturbance of circadian gene expression in hepatocellular carcinoma

Circadian rhythm plays an important role in the regulation of digestive system. The human circadian rhythm is controlled by at least nine circadian genes. The aims of this study are to understand the expression of the circadian genes between hepatocellular carcinoma tissues and nontumor tissues, and to explore the possible mechanism(s) contributing to the difference. We analyzed differential expression of the 9 circadian genes in 46 hepatocellular carcinoma and paired noncancerous tissues by real‐time quantitative RT‐PCR and immunohistochemical detection. We also tested the possible regulatory mechanism(s) by direct sequencing and methylation PCR analysis. Our results showed that decreased expression levels of PER1, PER2, PER3, CRY2, and TIM in hepatocellular carcinomas were observed. Decreased‐expression of these genes was not caused by genetic mutations, but by several factors, such as promoter methylation, overexpression of EZH2 or other factors. The downexpression of more circadian genes may result in disturbance of cell cycle, and it is correlated with the tumor size. Downregulation of circadian genes results in disturbance of circadian rhythm in hepatocellular carcinoma which may disrupt the control of the central pacemaker and benefit selective survival of cancerous cells and promote carcinogenesis.

Downregulation of circadian clock genes in chronic myeloid leukemia : Alternative methylation pattern of hPER3

Disruption of circadian rhythm is believed to play a critical role in cancer development. To gain further insights into the roles of circadian genes in chronic myeloid leukemia (CML), we analyzed peripheral blood from 53 healthy individuals and 35 CML patients for the expression of the nine circadian genes. The expression levels of hPER1, hPER2, hPER3, hCRY1, hCRY2 and hBMAL1 were significantly impaired in both chronic phase and blastic crisis of CML cases compared with those in healthy individuals (P < 0.001). Methylation studies in the promoter areas of these six genes revealed that only the CpG sites of the hPER3 gene were methylated in all of the CML patients, and the methylated CpG frequencies differed significantly in patients at blastic crisis (8.24 ± 0.73) or at chronic phase (4.48 ± 0.48). The CpG sites of the hPER2 gene were also methylated in 40% of the CML patients. No mutation was found within the coding region of hPER3 in CML cases. Our results suggest that the downregulated hPER3 expression in CML is correlated with the inactivation of hPER3 by methylation. (Cancer Sci 2006; 97: 1298–1307)

Mutation analysis of PTEN/MMAC1 in acute myeloid leukemia

Recently, a putative tumor suppressor gene, PTEN/MMAC1, has been identified at chromosome 10q23.3, which encodes a 403 amino acid dual‐specificity phosphatase containing a region of homology to tensin and auxillin. Somatic mutations of the PTEN/MMAC1 gene have been identified in a number of cancer cell lines and primary cancers. Mutations in PTEN/MMAC1 are most frequently found in advanced cancers. To evaluate the role of the PTEN/MMAC1 gene in leukemia, bone marrow and/or peripheral blood from 62 acute myeloid leukemia (AML) patients, 5 hemopoietic cell lines (HL60, U937, Raji, KG‐1, K562), and 30 normal controls were analyzed. The results showed aberrant PTEN/MMAC1 transcripts in 15 of the 62 (24%) AML patients, 4 of the 5 cell lines (80%), and 4 of the 30 (13%) normal controls. As in our previous study of TSG101, the abnormal transcripts may result from aberrant RNA splicing as evidenced by the presence of both these aberrant transcripts and normal full length transcripts in all specimens examined. Loss of heterozygosity (LOH) analysis and PCR‐SSCP of the entire coding region showed that none of the AML cases had LOH or mutation. Only one frameshift mutation at codon 130 (insertion of CCCG) with premature termination of coding sequence was observed in the U937 cell line. Our results indicate that the PTEN/MMAC1 gene may play a role in a small percentage of AML, but its significance needs to be further evaluated. Am. J. Hematol. 63:170–175, 2000.

Epigenetic alteration of the SOCS1 gene in chronic myeloid leukaemia.

Summary.  The expression of the suppressor of cytokine signalling‐1 (SOCS1) protein is induced in response to stimulation by several cytokines. The induced SOCS1 inhibits the signalling pathway through the association with a variety of tyrosine kinase proteins. In this study, the mutation analyses, CpG island methylation status, and the expression of the SOCS1 gene in 112 chronic myeloid leukaemia (CML) samples, five leukaemia cell lines, and 30 normal controls were analysed. No genetic mutations of SOCS1 gene were noted in the CML samples. The SOCS1 gene was hypermethylated in 67% and 46% of the blastic and chronic phase CML samples respectively (P < 0·0001). However, there was no methylation of the SOCS1 gene in normal controls or CML in molecular remission. The methylation status of the SOCS1 gene is consistent with the results of the real‐time quantitative reverse transcription polymerase chain reaction and immunocytochemistry staining. Our results demonstrate that the SOCS1 gene silencing is caused by the methylation of CpG islands in CML and is reversed to an unmethylated status in molecular remission. As SOCS1 has universal activity to negatively regulate several cytokine signalling pathways, the loss of the negative regulation of cytokine signalling by the SOCS1 may play a role in the pathogenesis of CML progression.

Characteristics and prevalence of KRAS, BRAF, and PIK3CA mutations in colorectal cancer by high-resolution melting analysis in Taiwanese population

BACKGROUND The identification of KRAS, BRAF, and PIK3CA mutations before the administration of anti-epidermal growth factor receptor therapy of colorectal cancer has become important. The aim of the present study was to investigate the occurrence of KRAS, BRAF, and PIK3CA mutations in the Taiwanese population with colorectal cancer. This study was undertaken to identify BRAF and PIK3CA mutations in patients with colorectal cancer by high-resolution melting (HRM) analysis. HRM analysis is a new gene scan tool that quickly performs the PCR and identifies sequence alterations without requiring post-PCR treatment. METHODS In the present study, DNAs were extracted from 182 cases of formalin-fixed, paraffin-embedded (FFPE) colorectal cancer samples for clinical KRAS mutational analysis by direct sequencing. All the samples were also tested for mutations within BRAF V600E and PIK3CA (exons 9 and 20) by HRM analysis. RESULTS The results were confirmed by direct sequencing. The frequency of BRAF and PIK3CA mutations is 1.1%, and 7.1%, respectively. Intriguingly, we found that nine patients (4.9%) with the KRAS mutation were coexistent with the PIK3CA mutation. Four patients (2.2%) without the KRAS mutation were existent with the PIK3CA mutation. Two patients (1.1%) without the KRAS mutation were existent with the BRAF mutation. CONCLUSIONS In the current study, we suppose that HRM analysis is rapid, feasible, and powerful diagnostic tool for the detection of BRAF and PIK3CA mutations in a clinical setting. Additionally, our results indicated the prevalence of KRAS, BRAF, and PIK3CA mutational status in the Taiwanese population.

Rapid identification of HBB gene mutations by high-resolution melting analysis

OBJECTIVE This study was undertaken to identify HBB gene mutation. DESIGN AND METHODS Herein we evaluated high-resolution melting analysis in the identification of HBB mutations. RESULTS We have successfully established a diagnostic strategy for identifying HBB gene mutations including c.-78A>G, c.-79A>G, c.2T>G, c.79_80insT, c.84_85insC, c.123_124insT, c.125_128delTCTT, c.130 G>T, c.170G>A, c.216_217ins A and c.316-197 C>T from wild-type DNA using HRM analysis. The results of HRM analysis were confirmed by direct DNA sequencing. CONCLUSIONS In summary, we report that HRM analysis is an appealing technique for the identification of HBB mutations. We also believe that HRM can be used as a method for prenatal diagnosis of beta-thalassemia.

Dihydropyrimidine dehydrogenase pharmacogenetics in the Taiwanese population.

Background/purpose5-Fluorouracil (5-FU) remains the most frequently used chemotherapy agent in various human cancers. Over 80% of the 5-FU administered is metabolized by dihydropyrimidine dehydrogenase (DPD) in the liver. However, mutations in the DPD gene have been found to be associated with low DPD activity causing severe complications. The aim of this study was to determine the frequency of 11 known mutations in Taiwanese subjects and the relationship between mutation and DPD level.MethodsSamples from a total of 300 subjects were investigated in this study. The PCR-RFLP method was used to identify 11 mutations of the DPYD gene, including 62G>A, 74A>G, 85T>C (DPYD*9A), 812delT, 1003G>T, 1156G>T, 1627A>G (DPYD*5), 1714C>G, 1897delC (DPYD*3), 2194G>A (DPYD*6), and IVS14+1G>A (DPYD*2A). DPD protein levels were determined using a DPD ELISA kit.ResultsFour mutations, including 74A>G, 85T>C (DPYD*9A), 1627A>G (DPYD*5), and 2194G>A (DPYD*6), were found in our 300 samples. The following mutations were not detected: 62G>A, 812delT, 1003G>T, 1156G>T, 1714C>G, 1897delC (DPYD*3), and IVS14+1G>A (DPYD*2A). The phenotype analysis by DPD protein level indicated that the 1627A>G (DPYD*5) mutation was not associated with the DPD protein level and might be a polymorphism in the DPD gene. The DPD level was also not correlated with gender.ConclusionNo significant correlations between these 11 mutations and DPD protein level were found indicating that examination of these mutations is insufficient to provide a high-value prediction of the 5-FU pharmacogenetic syndrome in Taiwanese. Genotype and phenotype analysis indicated the 1627A>G (DPYD*5) mutation to be a polymorphism.

Gene frequencies of the HPA-1 to HPA-8w platelet antigen alleles in Taiwanese, Indonesian, and Thai

Abstract. Human platelet antigen (HPA) systems consist of more than eight biallelic antigen polymorphisms in which a base pair substitution leads to change in an amino acid of a glycoprotein expressed on the platelet. HPA typing is essential in the diagnosis and treatment for a variety of diseases. We developed a polymerase chain reaction (PCR)-based method to detect HPA-1 through HPA-8w. In this method, the amplified PCR products were used to recognize the polymorphism after restriction enzyme digestions. Among 295 Taiwanese, 107 Indonesian, and 137 Thai subjects studied, HPA-1a, 2a, 4a, 5a, 6a, 7aw, and 8aw genes were present in every sample tested. HPA-1b, 2b, 4b, 5b, and 6b were rarely found among subjects. Only monomorphic HPA-7aw and 8aw alleles were noted in the samples. HPA-3a and 3b alleles showed frequencies of 0.595/0.405, 0.504/0.496, and 0.507/0.493 in Taiwanese, Indonesian, and Thai subjects, respectively. Our report is the first PCR-based method to detect most of the HPA antigen variants in Taiwanese, Indonesian, and Thai. The genomic typing results were also confirmed by direct sequencing for uncertain and some representative cases. The prevalence rates of HPA-1, 2, 3, 4, and 5 in this study were also consistent with other previous reports using different methods.

Molecular characterization of secretor type α(1,2)-fucosyltransferase gene deficiency in the Philippine population

Abstract We analyzed the seven mutations which are responsible for the deficiency of the secretor type α(1,2)-fucosyltransferase gene product, Se enzyme, in the Philippine population. One hundred and one unrelated Filipinos in Taiwan were studied. A new mutation, a 3-base pair deletion from nt 688 through 690, was found in two (0.1%) of 202 chromosomes. The frequencies of six other mutated alleles were as follows: 71/202 (35.2%) were cDNA 385 A→T missensed mutation (se2), 28/202 (13.9%) were C571T nonsense mutation (se3), 16/202 (7.9%) were G849A nonsense mutation (se4), 4/202 (1.9%) were G428A nonsense mutation (se1), and 81/202 (40.1%) were wild-type allele (Se). No C628T nonsense mutations (se5) or fusion genes of pseudogene and FUT2 gene (se 6) were found in this population. For the molecular basis of phenotype Le(a+ b–): eight cases had se2/se2, six cases had se2/se3, two cases had se3/se4, one case was homozygous of se4, one case was se3/se1, and two cases were se2/se7. For the Le(a+ b+) phenotype: four cases had se2/se2, two cases had se2/se3, one case was se3/se3, and one case was se2/se4. For the Le(a– b+) phenotype: 16 cases were Se/Se, 21 cases were Se/se2, six cases were Se/se3, five cases were Se/se4, and two cases had Se/se1. Our results suggest that the genotypes of the α(1,2)-fucosyltransferase gene in phenotypes Le(a+ b+) and Le(a+ b–) are the same. Other factors that play important roles may cause the differences between these two phenotypes. Several hotspot mutations in the α(1,2)-fucosyltransferase gene are responsible for the nonsecretor phenotype.