A potentially crucial role of the PKD1 C-terminal tail in renal prognosis.

BACKGROUND: Autosomal dominant polycystic disease (ADPKD) often results in renal failure. Recently, allelic influences of PKD1 mutation types on renal survival were extensively investigated. Here, we analyzed integrated influences of PKD1 mutation types and positions on renal survival. METHODS: We included 338 (82 pedigrees) and 72 (12 pedigrees) patients with PKD1 and PKD2 mutations, respectively, identified through comprehensive gene analysis of 101 probands with ADPKD. Genetic testing was performed using next-generation sequencing, long-range PCR, and multiplex ligation-dependent probe amplification. Pathogenic mutations were identified by a software package-integrated seven databases and provided access to five cloud-based computing systems. RESULTS: Mean renal survivals of carriers with PKD1 non-truncating-type mutations at positions upstream of G-protein-coupled receptor proteolytic site (GPS-upstream domain), transmembrane domain, or cytoplasmic C-terminal tail (CTT) domain were 70.2, 67.0, and 50.1 years, respectively (P < 0.0001); renal survival was shorter for mutation positions closer to CTT domain, suggesting its crucial role in renal prognosis. Furthermore, in truncating-type mutations, strong inactivation is anticipated on nucleotides downstream from the mutation site, implying CTT domain inactivation irrespective of mutation site. Shorter mean renal survival was found for PKD1 truncating-type than non-truncating-type mutation carriers (P = 0.0348); mean renal survival was not different between PKD1 3'- and 5'-region truncating-type mutation carriers (P = 0.4375), but was shorter in PKD1 3'-region than in 5'-region non-truncating-type mutation carriers (P = 0.0014). Variable strength of CTT domain inactivation might account for these results. CONCLUSIONS: Aforementioned findings indicate that CTT domain's crucial role in renal prognosis needs further investigation by larger studies (ClinicalTrials.gov; NCT02322385).

Two novel CYP2D6*10 haplotypes as possible causes of a poor metabolic phenotype in Japanese.

During the course of sequencing for the CYP2D6 gene, we found a novel single nucleotide polymorphism of g.3318G>A (E383K) associated with CYP2D6*10, termed as CYP2D6*72. We also found a g.1611T>A (F120I) in the CYP2D6*49, which was previously identified as a CYP2D6*10-associated allele in an independent Japanese population. To clarify the effects of these novel CYP2D6*10 haplotypes on the functions of CYP2D6, kinetic analysis for dextromethorphan O-demethylation was performed using the Escherichia coli expression system and human liver microsomes. The V(max)/K(m) values for dextromethorphan O-demethylation catalyzed by recombinant CYP2D6 forms encoded by CYP2D6*10, CYP2D6*49, and CYP2D6*72 were 3.0, 0.5, and 1.3%, respectively, compared with that catalyzed by CYP2D6.1. Liver microsomes from a human subject genotyped as CYP2D6*10/*49 also showed a reduced dextromethorphan O-demethylase activity. CYP2D6.49 formed a 7-hydroxydextromethorphan, with a roughly similar V(max)/K(m) value to that of O-demethylation. These results suggest that these two CYP2D6*10 haplotypes are possible causes of interindividual variation in the activities and the substrate specificity of CYP2D6.

Mitochondrial complex I activity is significantly decreased in a patient with maternally inherited type 2 diabetes mellitus and hypertrophic cardiomyopathy associated with mitochondrial DNA C3310T mutation: a cybrid study.

Mitochondrial respiratory function in a patient with maternally inherited type 2 diabetes mellitus and hypertrophic cardiomyopathy associated with heteroplasmic mitochondrial DNA (mtDNA) C3310T mutation, which replaces the second amino acid of NADH dehydrogenase 1 (ND1) from a hydrophobic Proline to a hydrophilic Serine, was investigated. Mitochondrial respiratory function solely due to mtDNA C3310T mutation was investigated in cybrid system by the fusion of mtDNA-deleted (rho(0)) HeLa cells and exogenous mtDNA either from the proband or from controls. Total oxygen consumption of the proband cybrid cells was significantly decreased compared with those of controls (2.468+/-0.475 versus 2.871+/-0.484 micromol/h/10(7) cells, p=0.0392). Mitochondrial respiratory chain complex I activity of the proband cybrid cells was also significantly decreased compared with those of controls (0.191+/-0.080 versus 0.288+/-0.113 micromol/h/mg protein, p=0.0223). Furthermore, ATP content in the proband cybrid cells was also significantly decreased compared with those in controls (1.119+/-0.344 versus 1.419+/-0.378 pmol/10(5) cells, p=0.044). The present study indicates that mtDNA C3310T mutation may be a pathogenic mutation of maternally inherited type 2 diabetes mellitus and hypertrophic cardiomyopathy in the proband and the family.

Technical Evaluation: Identification of Pathogenic Mutations in PKD1 and PKD2 in Patients with Autosomal Dominant Polycystic Kidney Disease by Next-Generation Sequencing and Use of a Comprehensive New Classification System.

Genetic testing of PKD1 and PKD2 is expected to play an increasingly important role in determining allelic influences in autosomal dominant polycystic kidney disease (ADPKD) in the near future. However, to date, genetic testing is not commonly employed because it is expensive, complicated because of genetic heterogeneity, and does not easily identify pathogenic variants. In this study, we developed a genetic testing system based on next-generation sequencing (NGS), long-range polymerase chain reaction, and a new software package. The new software package integrated seven databases and provided access to five cloud-based computing systems. The database integrated 241 polymorphic nonpathogenic variants detected in 140 healthy Japanese volunteers aged >35 years, who were confirmed by ultrasonography as having no cysts in either kidney. Using this system, we identified 60 novel and 30 known pathogenic mutations in 101 Japanese patients with ADPKD, with an overall detection rate of 89.1% (90/101) [95% confidence interval (CI), 83.0%-95.2%]. The sensitivity of the system increased to 93.1% (94/101) (95% CI, 88.1%-98.0%) when combined with multiplex ligation-dependent probe amplification analysis, making it sufficient for use in a clinical setting. In 82 (87.2%) of the patients, pathogenic mutations were detected in PKD1 (95% CI, 79.0%-92.5%), whereas in 12 (12.8%) patients pathogenic mutations were detected in PKD2 (95% CI, 7.5%-21.0%); this is consistent with previously reported findings. In addition, we were able to reconfirm our pathogenic mutation identification results using Sanger sequencing. In conclusion, we developed a high-sensitivity NGS-based system and successfully employed it to identify pathogenic mutations in PKD1 and PKD2 in Japanese patients with ADPKD.

Reduced ING1b gene expression plays an important role in carcinogenesis of non-small cell lung cancer patients.

PURPOSE: We performed a clinical study on ING1b gene expression and p53 gene status in relation to p53 target genes. EXPERIMENTAL DESIGN: Eighty-eight tumors from surgically treated non-small cell lung cancer (NSCLC) patients were studied. PCR-single-strand conformational polymorphism after sequencing was performed to investigate ING1 and p53 gene status. Quantitative reverse transcription-PCR was performed to evaluate the gene expression of ING1b, p21, and bax. The results of p21 and bax expression were confirmed with immunohistochemistry. RESULTS: Only two carcinomas (2.3%) had nonmissense mutations of ING1b. Thirty-seven carcinomas (42.0%) had reduced ING1b gene expression. Thirty-seven carcinomas (42.0%) had mutations of p53. In total, 63 carcinomas (71.6%) had either reduced ING1b expression or mutant p53. The p21 gene expression ratio was significantly lower in the ING1b-reduced tumors than in the ING1b-positive tumors (P = 0.0029). Similarly, the bax gene expression ratio was significantly lower in the ING1b-reduced tumors than in the ING1b-positive tumors (P < 0.0001), and it was also significantly lower in tumors that had either reduced ING1b expression or mutant p53 than in tumors that had both positive ING1b expression and wild-type p53 (P = 0.0331). CONCLUSIONS: Reduction of ING1b gene expression was associated with reduced p21 and bax gene expression in NSCLCs. The present study is the first clinical report to confirm the positive role of ING1b in regulating p21 and bax gene expression. ING1b might be one of the tumor suppressor genes that could play a role in carcinogenesis in NSCLC patients.

Ki-ras mutations in codon 12 and p53 mutations (biomarkers) and cytology in bile in patients with hepatobiliary-pancreatic carcinoma.

BACKGROUND/AIMS: The differentiation between benign and malignant jaundice is sometimes difficult even with modern diagnostic modalities. With recent advances in molecular biology, Ki-ras point mutation in codon 12 and p53 mutation have been reported as novel biomarkers of hepatobiliary and pancreatic carcinoma. The purpose of this study was to compare exfoliative bile cytology and biomarkers of the bile in patients with hepatobiliary and pancreatic diseases. METHODOLOGY: Cytologic examination and novel biomarkers, point mutations of codon 12 of Ki-ras and p53 mutations, were examined in the biliary tract bile aspirated through percutaneous transhepatic biliary drainage (PTBD) tube in 30 Japanese patients with benign and malignant hepatobiliary and pancreatic diseases. RESULTS: Sensitivity of the exfoliative bile cytology for malignant conditions was 31% and specificity 100%, while sensitivity of molecular markers of the bile was 25% and specificity 93%. When the cytologic examination and genetic study were in conjunction, sensitivity increased to 50% and specificity remained 93%. CONCLUSIONS: These findings suggest that genetic examinations of the bile, when used in conjunction with cytology, may improve the diagnostic yield for suspected malignant tumors of the hepatobiliary and pancreatic system.

Polymorphisms in the CYP1A2 gene and theophylline metabolism in patients with asthma.

BACKGROUND: Cytochrome p450 (CYP) 1A2 gene polymorphisms are thought to be involved in theophylline metabolism. OBJECTIVE: We analyzed the effect of genetic polymorphisms in the 5'-flanking region to the first intron of the CYP1A2 gene on theophylline metabolism in 75 Japanese patients with asthma and 159 healthy Japanese volunteers. METHODS: Genetic polymorphisms were detected at 4 sites of the CYP1A2 gene, -2964(G/A) and -1569(T/del) in the 5'-flanking region and 155(T/G) and 731(A/C) in the first intron. RESULTS: There were no significant differences in the distribution of gene polymorphisms between the asthmatic and control groups. Among asthmatic patients, theophylline clearance was significantly lower in patients with the polymorphism at site -2964(G/A) whose genotype was G/A (0.029 +/- 0.001 L x h(-1) x kg(-1)) or A/A (0.029 +/- 0.002 L x h(-1) x kg(-1)) than in those whose genotype was G/G (0.034 +/- 0.001 L x h(-1) x kg(-1)) (P <.01 and P <.05, respectively). High theophylline clearance levels significantly correlated with age in the G/G subgroup of site -2964(G/A) (P <.05, r = -0.35) but not in the G/A or A/A subgroup. CONCLUSION: Given its potential side effects, theophylline may need to be used with care in patients with the A allele at site -2964(G/A) in the CYP1A2 gene, because theophylline metabolism levels are lower in such patients, particularly in young asthmatic individuals.

Evaluation of a new assay for hepatitis C virus genotyping and viral load determination in patients with chronic hepatitis C.

A new method for hepatitis C virus (HCV) genotyping that analyzes products generated with the HCV Amplicor Monitor Test has been developed. One hundred and sixty-two Japanese patients with chronic hepatitis C, including 59 patients with hemophilia, were tested for HCV genotypes and viral loads with this new test, and the results were compared with those of a genotyping assay that involved direct sequencing of the E1 region. HCV genotypes and viral loads were also compared between patients with and without hemophilia. There were no discrepancies between the two methods in determining genotypes 2a, 2b, and 3a. However, two patients infected with 1a were mistyped as 1b with the new assay. One patient not classified by this assay was genotype 4. Genotypes found in patients without hemophilia were 1b, 2a, and 2b. Genotypes 1a, 3a, and 4, which were minor variants in Japan, were detected only in patients with hemophilia. In addition, J type, which is a subtype of 1b that originated in Japan, was found at low frequency in hemophiliacs. Thus, the HCV genotypes in patients with hemophilia are likely to be of foreign origin. Overall, this new assay was accurate except for genotype 1a and 4, and allowed simultaneous assessment of genotype and viral load.

Endogenous tumor necrosis factor promotes resistance to cellular stresses by inducing the metallothionein-1A gene.

BACKGROUND: Endogenous tumor necrosis factor (enTNF) acts as a resistance factor against anticancer drugs, heat and exogenous TNF via induction of manganous superoxide dismutase (MnSOD) and heat shock protein 72 (HSP72), while the details of interaction with other molecules are not fully understood. We compared mRNA expression of various genes between MIAPaCa-2 human pancreatic cancer cells and M5 cells transduced with nonsecretory-type TNF gene expression vector. MATERIALS AND METHODS: The expression of certain mRNAs between human pancreatic cancer MIAPaCa-2 cells and M5 cells was compared using fluorescent differential display. RESULTS: Of 140 bands obtained by gel electrophoresis, 53 bands showed patterns differing between MIAPaCa-2 and M5 cells. Among these bands, sequence analysis and RT-PCR identified strong mRNA expression for metallothionein-1A, a scavenger of reactive oxygen species, in transduced M5 cells. CONCLUSION: Metallothionein-1A could be induced by enTNF, resulting in resistance against various cellular stresses.

Quantitative analysis of wild-type and precore mutant hepatitis B virus in carriers.

In the present study, we have analyzed the amount of precore wild-type hepatitis B virus (HBV) (wild-type) and precore mutant HBV (nt 1896: G-->A) (precore mutant) of HBV carriers; 31 asymptomatic healthy carriers (ASC) and 28 patients with chronic hepatitis (CH). Wild-type and precore mutant were quantified using sensitive and specific quantification methods: competitive wild-type-sequence-specific assay and competitive mutation-site-specific assay with different sets of specific primers and internal controls. Median serum levels of wild-type and precore mutant were 9.60 and 8.60 log copies/ml (median percentages of precore mutant in total HBV-DNA: 11.7%) in HBeAg(+) ASC, 8.48 and 8.00 (33.3%) in HBeAg(+) CH, and 6.30 and 6.85 (84.7%) in anti-HBe(+) CH, respectively, showing higher levels of the relative amount of precore mutant to wild-type along with HBeAg/anti-HBe status. Only precore mutant, but not wild-type was detected in anti-HBe(+) ASC. Although median percentages of precore mutant at the anti-HBe(+) ASC and CH stages were much higher than those at the HBeAg(+) ASC and CH stages, a substantial amount of precore mutant was found even at the HBeAg(+) stages. Existence of a substantial amount of precore mutant even in HBeAg(+) ASC suggests that the occurrence of precore mutant is not always closely associated with seroconversion from HBeAg to anti-HBe.

Clinical significance of intrahepatic interleukin-8 in chronic hepatitis C patients.

Background/AIM: Interleukin-8 (IL-8) is known as a chemotactic and angiogenetic cytokine and is a potential mediator of host response to injury or inflammation. In order to identify the role of IL-8 in the pathogenesis of chronic hepatitis C (CHC), we assessed semiquantitatively the messenger RNA (mRNA) expression of IL-8 and other cytokines in liver biopsy specimens of CHC patients. METHOD: Liver biopsy specimens were obtained under peritoneoscopy from 35 patients with CHC. The mRNA expression of IL-8 and other cytokines in the liver were determined by real-time PCR and the correlation between the mRNA expression and histological classification of liver were studied. Liver histology was classified by both staging of fibrosis (F0-F4) and grading of activity (A1, mild; A2, moderate and A3, severe). RESULTS: Patients were classified into F1, 8; F2, 9; F3, 9 and F4, 9 and A1, 6; A2, 14 and A3, 15, by staging of fibrosis and grading of activity, respectively. Expression of IL-8 mRNA increased with staging of fibrosis (F1, 0.402+/-0.65; F2, 0.413+/-0.246; F3, 1.388+/-2.166; F4, 1.991+/-1.879) and grading of activity (A1, 0.560+/-0.808; A2, 0.780+/-1.268; A3, 1.548+/-1.957). The mRNA expressions of IL-2, IL-1alpha, IL-1beta, IL-15 and TNF-alpha were found to be closely correlated with IL-8 mRNA (R=0.638; 0.522; 0.487; 0.465 and 0.495, respectively, in all P<0.05). CONCLUSION: In CHC, intra-hepatic expression of both IL-8 and IL-2 increased with fibrosis and inflammatory activity. Positive correlations were found between IL-8 and other cytokines and between cytokines themselves. These findings suggest that these interacting cytokines play an active role in the pathogenesis of CHC, and maybe involved in the upregulation or induction of one and other.

Tailor-made chemotherapy for non-small cell lung cancer patients.

The selection of the most effective chemotherapy treatment based on evaluation of biomarkers, that is, 'tailor-made chemotherapy', can improve the clinical outcome of non-small cell lung cancer patients, including early-stage tumors with a high metastatic potential and advanced-stage tumors with a low proliferation rate. Therefore, treatment would be chosen according to which drugs would be most effective in combating specific tumors. For example: 5-fluorouracil-derived agents would be used for tumors with a low expression of thymidylate synthase; gefitinib and erlotinib for tumors with epidermal growth factor receptor (EGFR) mutations or increased EGFR gene copy numbers; cisplatin and carboplatin for tumors with a low expression of excision repair cross complementing-1; and gemcitabine for tumors with a low expression of ribonucleotide reductase. The remaining populations of non-small cell lung cancers require chemotherapy using other drugs based on an evaluation of other targeted molecules.

Underexpression of mRNA in human hepatocellular carcinoma focusing on eight loci.

Genetic alterations associated with human hepatocellular carcinoma (HCC) have been reported previously, but are not sufficient to specify differences of HCCs from precancerous diseases of the liver, such as hepatitis, hepatic fibrosis, and cirrhosis. In the present study, we performed differential gene display analysis (DGDA) to clarify the specific genetic alterations associated with gene expression changes in the course of development of HCC from chronic viral hepatitis. Four pairs of surgically resected HCCs and hepatitis tissues were investigated. We found 1,028 expression sequence tags (ESTs) that were decreased or increased in HCC tissues compared with hepatitis tissues in the same patient. Nucleotide sequencing showed that they included 55 EST clones in the GenBank database, which were considered candidates for specific messenger RNA (mRNA) expression alterations in HCCs. After excluding 9 ESTs that code mitochondrial DNA, we performed quantitative real-time reverse-transcription polymerase chain reaction (RT-PCR) for the 46 remaining EST clones. We found 8 mRNAs underexpressed in primary HCC tissues in 20 patients in higher percentages than found in previous studies, including 18 cases (90%) for aldolase B (ALDOB), 15 cases (75%) for carbamyl phosphate synthetase 1 (CPS1), albumin (ALB), plasminogen (PLG), and EST 51549, 13 cases (65%) for cytochrome P450 subfamily 2E1 (CYP2E1), 12 cases (60%) for human retinol-binding protein 4 (RBP4), and 11 cases (55%) for human organic anion transporter C (OATP-C) gene. In conclusion, underexpression of key gene products may be important in the development and/or progression of HCC.

Telomerase activity, P53 mutation and Ki-ras codon 12 point mutation of the peripheral blood in patients with hepato pancreato biliary diseases.

BACKGROUND: With progress in molecular biology, the presence of telomerase activity, P53 mutation and Ki-ras codon 12 point mutation has been reported in malignant tumours of the liver, pancreas and biliary tree. The purpose of this paper is to clarify the clinical implications of finding these three biomarkers in the peripheral blood of affected patients. METHODS: Telomerase activity, P53 mutation, and Ki-ras codon 12 point mutation in the peripheral blood were examined among 86 patients with hepato pancreato biliary disease, both benign and malignant, and the results were compared with clinical findings. RESULTS: Of 20 patients with benign conditions, only one patient with intraductal papillary adenoma showing severe dysplasia exhibited a biomarker (telomerase activity) in the peripheral blood. In total, there were 66 patients with various HPB carcinomas. Of 56 cancer patients studied pre-operatively, 16 were positive for more than one biomarker, 13 were positive for telomerase activity, 4 for P53 mutation (three at exon 7 and another at exon 8), and 2 for Kiras codon 12 point mutation (both in the second letter). Twelve of the 16 biomarker-positive patients had stage IV disease as opposed to 23 of 40 biomarker-negative patients. The resectability rate of the cancer was 38% in positive patients and 50% in negative patients. The one-year survival rate after resection was zero in positive patients and 15% in negative patients, but the difference was not significant (P=0.65). Of 32 patients with liver metastasis at the time of the molecular examination, eight were positive and 24 negative. Of 34 patients without liver metastasis, nine were positive and 25 negative. The development of subsequent liver metastases in those without them at the start was not significantly different in those with and without biomarkers (56 vs 36%: P=0.31). CONCLUSIONS: The three novel biomarkers of the peripheral blood seemed to be of little value for screening of early malignant HPB neoplasms but may help to predict liver metastasis.

A new mutation of the fukutin gene in a non-Japanese patient.

Fukuyama-type congenital muscular dystrophy (FCMD), Walker-Warburg syndrome, and muscle-eye-brain disease are clinically similar autosomal recessive disorders characterized by congenital muscular dystrophy, cobblestone lissencephaly, and eye anomalies. FCMD is frequent in Japan, but no FCMD patient with confirmed fukutin gene mutations has been identified in a non-Japanese population. Here, we describe a Turkish CMD patient with severe brain and eye anomalies. Sequence analysis of the patient's DNA identified a homozygous 1bp insertion mutation in exon 5 of the fukutin gene. To our knowledge, this is the first case worldwide in which a fukutin mutation has been found outside the Japanese population. This report emphasizes the importance of considering fukutin mutations for diagnostic purposes outside of Japan.

Diverse p53 gene aberration in hepatocellular carcinoma detected by dual-color fluorescence in situ hybridization.

BACKGROUND AND AIM: In order to evaluate loss of the p53 gene more precisely, we performed dual-color fluorescence in situ hybridization (dual-color FISH) for chromosome 17 and p53 gene together with DNA polymorphism analysis of the p53 gene in hepatocellular carcinoma (HCC). METHODS: Dual-color FISH using probes specific for the centromere of chromosome 17 and the p53 gene was performed for 41 HCC and DNA polymorphism analysis was also performed for them. RESULTS: Of the 34 HCC tested by dual-color FISH, 20 had loss of at least one p53 gene (58.8%). In contrast, of the 32 HCC tested by DNA polymorphism analysis, 23 gave informative results, among which only eight had loss of heterozygosity (LOH) of the p53 gene (34.8%). Notably, among 14 cases positive for loss of the p53 gene by dual-color FISH, seven cases were negative for LOH of the p53 gene. Moreover, dual-color FISH revealed that the percentage of cells that lost at least one p53 gene increased as the HCC became less differentiated (P < 0.01), whereas LOH did not reveal any such correlation. CONCLUSIONS: These data suggest that loss of the p53 gene was present in a considerable number of HCC, and diversity of the p53 gene aberration increases with progression of HCC. Dual-color FISH is an effective method for detection of p53 gene aberration, and it can provide new insight into oncogenesis in HCC.