Complex intrachromosomal rearrangement in the process of amplification of the L-myc gene in small-cell lung cancer.

The L-myc gene was first isolated from a human small-cell lung cancer (SCLC) cell line on the basis of its amplification and sequence similarity to c-myc and N-myc. A new mechanism of L-myc activation which results from the production of rlf-L-myc fusion protein was recently reported. On the basis of our earlier observation of a rearrangement involving amplified L-myc in an SCLC cell line, ACC-LC-49, we decided to investigate this rearrangement in detail along with the structure of L-myc amplification units in five additional SCLC cell lines. We report here the identification of a novel genomic region, termed jal, which is distinct from rlf and is juxtaposed to and amplified with L-myc during the process of DNA amplification of the region encompassing L-myc. Long-range analysis using pulsed-field gel electrophoresis revealed that the amplified L-myc locus is involved in highly complex intrachromosomal rearrangements with jal and/or rlf. Our results also suggest that the simultaneous presence of rearrangements both in rlf intron 1 and in regions immediately upstream of L-myc may be necessary for the expression of rlf-L-myc chimeric transcripts.

PAI-1 expression levels in esophageal and colorectal cancers are closely correlated to those in corresponding normal tissues.

To investigate the mechanism of PAI-1 overexpression in esophageal and colorectal cancers, PAI-1 expression levels in these cancers were compared to those in corresponding normal tissues. Quantitative RT-PCR was performed for the PAI-1 gene in esophageal and colorectal cancer tissues and in the corresponding normal tissues and the association between PAI-1 expression levels in these tissues was evaluated. There was a significant correlation between esophageal and colorectal cancer and the corresponding normal PAI-1 expressions with a Spearman's rank correlation coefficient of 0.77 (p < 0.0001) and 0.81 (p < 0.0001), respectively. In previous studies, PAI-1 overexpression was found to be significantly associated with the malignancy of esophageal and colorectal cancers. Taken together, PAI-1 overexpression in esophageal and colorectal cancers might originate from higher PAI-1 expression in corresponding normal tissues and result in a malignant phenotype of these cancers.

Detecting colorectal cancer in stool with the use of multiple genetic targets.

BACKGROUND: Colorectal cancer cells are shed into the stool, providing a potential means for the early detection of the disease using noninvasive approaches. Our goal was to develop reliable, specific molecular genetic tests for the detection of colorectal cancer in stool samples. METHODS: Stool DNA was isolated from paired stools and primary tumor samples from 51 colorectal cancer patients. Three genetic targets-TP53, BAT26, and K-RAS-were used to detect tumor-associated mutations in the stool prior to or without regard to the molecular analyses of the paired tumors. TP53 gene mutations were detected with a mismatch-ligation assay that detects nine common p53 gene mutations. Deletions within the BAT26 locus were detected by a modified solid-phase minisequencing method. Mutations in codons 12 and 13 of K-RAS were detected with a digital polymerase chain reaction-based method. RESULTS: TP53 gene mutations were detected in the tumor DNA of 30 patients, all of whom had the identical TP53 mutation in their stools. Tumors from three patients contained a noninherited deletion at the BAT26 locus, and the same alterations were identified in these patients' stool specimens. Nineteen of 50 tumors tested had a K-RAS mutation; identical mutations were detected in the paired stool DNA samples from eight patients. In no case was a mutation found in stool that was not also present in the primary tumor. Thus, the three genetic markers together detected 36 (71%) of 51 patients (95% confidence interval [CI] = 56% to 83%) with colorectal cancer and 36 (92%) of 39 patients (95% CI = 79% to 98%) whose tumors had an alteration. CONCLUSION: We were able to detect the majority of colorectal cancers by analyzing stool DNA for just three genetic markers. Additional work is needed to determine the specificity of these genetic tests for detecting colorectal neoplasia in asymptomatic patients and to more precisely estimate the prevalence of the mutations and sensitivity of the assay.

Molecular analysis of the protein tyrosine phosphatase gamma gene in human lung cancer cell lines.

The protein tyrosine phosphatase gamma (PTP gamma) gene has recently been suggested as a candidate tumor suppressor gene involved in the oncogenesis of human lung and renal cancers, although no direct evidence for PTP gamma mutations has been demonstrated thus far. We explored the status of PTP gamma in 31 human lung cancer cell lines as well as in various other types of human tumor cell lines. Northern blot analysis revealed that two independent cell lines expressed PTP gamma mRNAs with sizes distinct from those in human fetal and adult normal lung. However, our extensive search for mutations in the PTP gamma gene failed to identify any abnormalities in the cytoplasmic region, which contains two protein tyrosine phosphatase-like domains. These results warrant further examination of genetic alterations in the extracellular and transmembrane domains of PTP gamma, which had not been cloned at the time of the present study.

Molecular detection of genetic alterations in the serum of colorectal cancer patients.

We have searched for the presence of genetic alterations in serum DNA obtained from 44 colorectal cancer patients. Microsatellite analysis using highly polymorphic markers revealed loss of heterozygosity and/or microsatellite instability in 35 of 44 (80%) primary tumors. No alterations were detected in the paired serum DNA. We next used an oligonucleotide-mediated mismatch ligation assay to detect tumor specific gene mutations in the serum. Among the 16 cases with a K-ras gene mutation in the tumor, the same mutation was detected in three paired serum samples. In the 10 cases with a p53 mutation in the tumor, the identical mutation was detected in seven corresponding serum samples. Comparison of the molecular analysis with clinical diagnosis of these patients revealed that none of the seven Dukes' stage B patients with a K-ras mutation in their tumors demonstrated a mutation in the serum. In contrast, five of seven stage B patients with a p53 mutation in the tumor demonstrated a mutation in the paired serum (P = 0.01, Fisher's exact test). Taken together, either a K-ras or p53 mutation was detected in the serum in 40% of the 25 patients (95% confidence interval, 21-61%), whose primary tumors contained a mutation and in 23% of the 44 patients (95% confidence interval, 12-38%) with colorectal cancer. The frequent detection of p53 mutation in the serum of patients with early stage tumors suggests a possible use of this approach for clinical prognosis and cancer monitoring of colorectal cancer patients.

Loss of H19 imprinting in esophageal cancer.

Recent articles have reported that loss of imprinting (LOI) of the endogenous gene H19 was frequently found in lung cancer and chorio-carcinoma, common adulthood cancers. Consequently, we examined the status of genomic imprinting of H19 in 29 esophageal and 48 colorectal cancer specimens, and studied its relation to the expression of H19. Of 12 esophageal cancer specimens heterozygous for the RsaI polymorphism, 6 (50%) exhibited LOI of H19, but none of the 18 colorectal cancer specimens heterozygous for the RsaI polymorphism exhibited LOI of H19. The present study suggests that LOI of H19 may play an important role in the pathogenesis of esophageal cancer. Moreover, H19 expression was frequently abundant in both cancers, and all six esophageal cancers carried LOI with overexpressed H19. Therefore, this overexpression of H19 seems to be an important phenomenon for the development of esophageal and colorectal cancer cells.

Prognostic significance of p53 mutations and 3p deletions in primary resected non-small cell lung cancer.

We evaluated the prognostic significance of p53 mutations and an allelic loss of chromosome 3p in 71 patients with non-small cell lung cancer who underwent potentially curative resection. p53 mutations were detected in 35 cases (49%), while 3p deletions were observed in 34 of 70 informative cases (49%). The presence of the p53 mutation was associated with a shortened survival in all patients (P = 0.014 by log rank test), including those in early stages of the disease (stage I or II, n = 48) (P = 0.016 by log rank test). Multivariate analysis by the Cox proportional hazards model also revealed that p53 mutation was an independent yet unfavorable prognostic factor (P = 0.013). Patients with 3p deletion tended to have a poorer prognosis, but not to a statistically significant extent.

Serial analysis of gene expression in non-small cell lung cancer.

We used the serial analysis of gene expression (SAGE) method to systematically analyze transcripts present in non-small cell lung cancer. Over 226,000 SAGE tags were sequence analyzed from two independent primary lung cancers and two normal human bronchial/tracheal epithelial cell cultures. A total of 226,000 SAGE tags were sequence identified, representing 43,254 unique transcripts. Comparison of the tags present in the tumor with those identified in the normal tissue revealed 175 transcript tags that were overrepresented in the normal tissue and 142 tags that were overexpressed in the tumor by 10-fold or more. Northern hybridization was performed on 15 of the most abundantly expressed tags identified in the tumors. These tags were derived from either a known gene or a matched expressed sequence tag clone. The transcripts for 3 of the 15 genes, PGP 9.5, B-myb, and human mutT, were abundantly expressed in primary lung cancers (10 of 18, 15 of 18, and 6 of 12 tumors, respectively). In contrast, the presence of PGP9.5 and B-myb was much less frequent in primary tumors derived from other tissue origins. These results suggest that at least a portion of the transcripts identified by SAGE are frequently associated with lung cancer, and that their overexpression may contribute to lung tumorigenesis. The identification and further characterization of genes generated by SAGE should provide potential new targets for the diagnosis, prognosis, and therapy of lung cancer.

Coexpression of the stem cell factor and the c-kit genes in small-cell lung cancer.

Stem cell factor (SCF) is a pluripotent growth factor which is suggested to play an important role in proliferation and differentiation in various types of fetal and adult tissues as the ligand of the c-kit proto-oncogene product. However, very little is known about expression of the SCF gene in human malignancies. We analysed DNA and RNA extracted from 28 cell lines and 16 fresh tumor specimens of lung cancer as well as 24 cancer cell lines of various origin for SCF expression. Now we report that the SCF gene is expressed in a wide variety of human cancers including lung cancer, in marked contrast to c-kit, which is expressed in very few types of cancers. As a consequence, coexpression of both the ligand and the receptor is seen only in small-cell lung cancer, suggesting possible involvement of autocrine stimulation via this ligand-receptor system in the pathogenesis of this aggressive cancer. In addition, this study revealed that the human SCF gene is transcribed into two major forms of alternatively spliced mRNAs with different molar ratio in fetal, adult and malignant tissues.

Aberrant upregulation of a novel integrin alpha subunit gene at 3p21.3 in small cell lung cancer.

Our recent identification of homozygous deletions at 3p21.3 in lung cancer has provided further support for the presence of a tumor suppressor gene in this chromosomal region. As a part of our efforts for positional cloning of a tumor suppressor gene at 3p21.3, we have characterized a transcriptional unit within this region using genomic fragments with interspecies conservation. The identified gene was found to encode a novel integrin alpha subunit, termed alpha RLC, which is closely related to alpha 4 in structure but clearly different from alpha 4 in its expression pattern in the physiological and pathological setting of the lung. This finding and the exact localization of the gene suggest that it is a good candidate for a tumor suppressor gene in lung cancer, but our extensive search covering one third of the gene did not reveal any somatic mutations within the coding region. Interestingly, however, alpha RLC was abundantly expressed in fetal lung and lung cancers, particularly small cell lung cancers (SCLC). Its aberrant upregulation in the SCLC samples, both cell lines and primary tumors, which might have been caused by a yet unidentified mutations or by deletions of other gene, and its homology to alpha 4, which is thought to play a role in metastasis, suggest that altered alpha RLC expression may contribute to the acquisition of malignant phenotypes of this type of lung cancer.

Frequent homozygous deletions in lung cancer cell lines detected by a DNA marker located at 3p21.3-p22.

Frequent allelic losses of chromosome 3p in lung cancer have been reported in a number of studies, and we previously demonstrated that 3p21.3 is one of the common regions of deletion in lung cancers and renal cell carcinomas. To further define a region containing the putative tumor suppressor gene, we performed Southern-blot analysis of 26 small cell lung cancer (SCLC) cell lines and ten non-small cell lung cancer (NSCLC) cell lines with 40 cosmid markers located at 3p21.3-p22. One marker detected homozygous deletions of four SCLC cell lines and one NSCLC cell line. None of the other markers revealed homozygous deletions or chromosomal rearrangements in these cell lines. The region of homozygous deletion described here is estimated to consist of less than 1 megabase of DNA, and it is very likely to contain at least one of the tumor suppressor genes associated with carcinogenesis of lung cancer and, possibly, renal cell carcinoma.

Three distinct regions involved in 3p deletion in human lung cancer.

The 3p deletion was first noted by cytogenetic analysis and was later confirmed by several independent studies using restriction fragment length polymorphism (RFLP) probes. As an initial step towards positional cloning (reverse genetics) of the tumor-suppressor gene(s) on 3p, a detailed analysis of the minimum deleted region(s) on 3p was performed with 13 RFLP probes and 48 paired human lung cancer samples. All nine small-cell lung cancer cases (100%) and 31 of 39 non-small-cell lung cancer cases (79%) showed allelic loss at one or more loci mapped on 3p. We show here that three distinct regions on 3p appear to be frequently deleted in lung cancer. These regions include 3p25, 3p21.3 and 3p14-cen. The present study should warrant future work focusing on these chromosomal regions on 3p, and may ultimately lead to the isolation of tumor-suppressor genes involved in the pathogenesis of lung cancer.

Feasibility of a novel blood noise reduction algorithm to enhance reproducibility of ultra-high-frequency intravascular ultrasound images.

BACKGROUND: Ultra-high-frequency (40- to 50-MHz) intravascular ultrasound (IVUS) improves image quality compared with conventional 20- to 30-MHz IVUS. However, as the frequency of IVUS increases, high-intensity backscatter from blood components may cause visual difficulties in discrimination between the lumen and arterial wall structure. The purpose of this study was to evaluate the effect of a novel blood noise reduction algorithm (BNR) on quantitative coronary ultrasound measurements. METHODS AND RESULTS: IVUS studies using a 40-MHz transducer were performed in 35 patients with coronary artery disease. A total of 620 gray-scale images (310 pairs) were processed with and without the BNR, and lumen cross-sectional area (CSA) was determined by 2 independent observers. With the BNR, the intraobserver and interobserver correlation coefficients for lumen CSA were significantly improved (0.85 to 0.99 and 0.80 to 0.98, respectively). In the 270 images (135 pairs) in which vessel wall measurements were possible, the BNR significantly improved the intraobserver and interobserver correlation coefficients for plaque plus media CSA (0.83 to 0.99 and 0.76 to 0.97, respectively), whereas no influence was observed for external elastic membrane CSA (1.00 to 1.00 and 0.99 to 0.99, respectively). CONCLUSIONS: This study demonstrates the feasibility of this novel algorithm to reduce blood noise, thereby enabling accurate lumen border delineation and providing reproducible measurements of both the lumen and plaque plus media CSAs. Incorporating a digital BNR may serve as an important adjunct to ultra-high-frequency IVUS imaging for improving accurate quantitative evaluation of vessel dimensions.

PGP9.5 as a prognostic factor in pancreatic cancer.

The expression of PGP9.5 was evaluated using immunohistochemistry in 69 resected ductal carcinomas of the pancreas and in normal pancreatic tissue. Overexpression did not seem to differ with histological type or pathological stage. A significant negative correlation was found between overexpression of PGP9.5 and postoperative survival. Multivariate analysis also suggested PGP9.5 along with tumor stage and extrapancreatic plexus invasion as strong predictors of the outcome. This study suggests that PGP9.5 expression may be used as a marker for predicting the outcome of resection-treated pancreatic cancer patients.

Molecular detection of p16 promoter methylation in the serum of patients with esophageal squamous cell carcinoma.

PURPOSE AND EXPERIMENTAL DESIGN: Recent evidence shows that the presence of promoter hypermethylation of tumor suppressor genes has been demonstrated in the serum DNA of patients with various cancers such as lung, liver, and head and neck cancer. We have examined promoter hypermethylation of the p16 gene in esophageal squamous cell carcinoma (SCC) using methylation-specific PCR to detect tumor DNA in the serum. RESULTS: Aberrant promoter methylation of the p16 gene was detected in 31 of 38 (82%) esophageal SCCs. Subsequently, we tested for promoter methylation in the paired serum DNA of 31 patients with a p16 alteration in the primary tumor. We found that 7 of these 31 (23%) patients had the same methylation changes in the serum DNA. CONCLUSIONS: This result indicates that promoter methylation present in the tumors of esophageal SCC patients can be detected in the serum of the same patient and that this approach can potentially be used for the screening and monitoring of the disease.

AIS overexpression in advanced esophageal cancer.

We examined AIS status in digestive tract cancers and found that all eight esophageal cancer cell lines (100%) showed AIS/TA-AIS gene overexpression, whereas 1 of 12 (8%) gastric cancer and 0 of 14 (0%) colon cancer cell lines showed AIS/TA-AIS gene expression. We then confirmed that the AIS gene, not the TA-AIS gene, was dominantly expressed in esophageal cancers by reverse transcription-PCR. AIS protein was also expressed in AIS gene-positive cell lines. Subsequently, we tested AIS gene expression in paired esophageal normal tissues and cancers. Twenty-five of 39 (64%) primary esophageal cancers demonstrated an obviously higher expression of AIS gene compared to paired normal tissues. Moreover, high AIS gene expression was significantly associated with lymph node metastases in esophageal cancer (P = 0.0271). These results suggested that AIS may be useful as a marker for advanced esophageal cancer.

Molecular detection of neoplastic cells in lymph nodes of metastatic colorectal cancer patients predicts recurrence.

Disseminated disease, especially to the liver, constitutes the major risk of recurrence for colorectal cancer patients. However, successful resection can still be achieved in 25-35% of colorectal cancer patients with isolated metastases. To evaluate the clinical value of occult micrometastatic disease detection in lymph nodes, we tested genetic (K-ras and p53 gene mutations) and epigenetic (p16 promoter hypermethylation) molecular markers in the perihepatic lymph nodes from colorectal cancer patients with isolated liver metastases. DNA was extracted from 21 paraffin-embedded liver metastases and 80 lymph nodes from 21 colorectal cancer patients. K-ras and p53 gene mutations were identified in DNA from liver metastases by PCR amplification followed by cycle sequencing. A sensitive oligonucleotide-mediated mismatch ligation assay was used to search for the presence of K-ras and p53 mutations to detect occult disease in 68 lymph nodes from tumors positive for these gene mutations. Promoter hypermethylation at the p16 tumor suppressor gene was examined in both liver lesions and lymph nodes by methylation-specific PCR. Sixteen of the 21 (76%) liver metastases harbored either gene point mutations or p16 promoter hypermethylation. Twelve of the 68 lymph nodes were positive for tumor cells by molecular evaluation and negative for tumor cells by histopathology and cytokeratin immunohistochemistry, whereas none were positive for tumor cells by histopathology or negative for tumor cells by molecular analysis (P = 0.0005, McNemar's test). Moreover, in three patients with lymph nodes that were histologically negative at all sites, molecular screening detected tumor DNA at one or more lymph nodes. Survival analysis showed a median survival of 1056 days for patients without evidence of lymph node involvement by molecular analysis and 165 days for patients with positive lymph nodes by this approach (P = 0.0005). These results indicate that lymph node metastasis screening in colorectal cancer patients by molecular-based techniques increases the sensitivity of tumor cell detection and can be a good predictor of recurrence in colorectal cancer patients with resectable liver metastases.

Essential hypertension and 5' upstream core promoter region of human angiotensinogen gene.

The angiotensinogen (AGT) gene M235T variant is associated with essential hypertension and elevated plasma AGT concentrations, although the underlying mechanisms are unknown. Recent studies have suggested that AGCE 1 (human AGT gene core promoter element 1) located in the 5' upstream core promoter region (position -25 to -1) of the human AGT gene has an important part in the expression of AGT mRNA by binding with transcription factor AGCF 1 (human AGT gene core promoter element binding factor 1), and a mutation at -20 from adenine to cytosine (A-20C) increases the level of expression of this transcript. We therefore examined subjects with this mutation to study the association with increased plasma AGT concentrations and with essential hypertension. One hundred eighty-eight subjects receiving no antihypertensive medication were examined with regard to the correlation between A-20C and plasma AGT concentrations, and 234 subjects were studied with respect to the association between A-20C and essential hypertension. A-20C was determined by polymerase chain reaction-restriction fragment length polymorphism analysis with EcoOR 109I. Multiple regression analysis showed a weak but significant correlation between A-20C and plasma AGT concentrations (P=.047) and essential hypertension (P=.049). The results suggest that A-20C may underlie the increase in plasma AGT concentrations and be involved in the development of essential hypertension.

Angiotensin-converting enzyme gene I/D polymorphism and carotid plaques in Japanese.

To clarify the role of genetic factors in atherosclerotic plaque formation in the carotid artery and magnetic resonance imaging abnormalities in the brain, we investigated the association of these abnormalities with the angiotensin-converting enzyme (ACE) genotype. One hundred sixty-nine subjects (age, 59.2+/-0.8 years, mean+/-SE) admitted to our hospital for health checkups underwent brain magnetic resonance imaging to evaluate lacunar infarction. B-mode ultrasound examinations of the carotid arteries were performed to detect atherosclerotic plaque. The I/D polymorphism of the ACE gene was determined by the polymerase chain reaction method. Multivariate regression analysis was performed to assess the effects of the following variables on the presence of plaque, mean plaque thickness, and number of plaques: fibrinogen, sex, age, body mass index, mean blood pressure, glycosylated hemoglobin, LDL cholesterol, HDL cholesterol, hematocrit, and the D allele of the ACE gene. The frequency of carotid atherosclerotic plaque was significantly (P=.034) higher in subjects with the D allele than in those without this allele. However, the frequency of lacunar stroke was similar in these groups. A multivariate regression analysis showed that the presence of plaque was independently associated with the D allele (odds ratio=3.27, P=.016). However, mean plaque thickness and the number of plaques were not associated with the D allele. The D allele of the ACE gene may be involved in the presence of carotid plaque but not in the extent of this plaque or asymptomatic lacunar stroke in Japanese subjects.

Angiotensin-converting enzyme gene polymorphism adds risk for the severity of coronary atherosclerosis in smokers.

To investigate the relation between the angiotensin-converting enzyme (ACE) gene polymorphism and acute coronary syndromes with respect to environmental factors, we analyzed the association of genotype with the coronary angiographic findings of patients with acute myocardial infarction or unstable angina pectoris, and we examined the linkage of each genotype with established risk factors for coronary artery disease. We determined the ACE genotype in 152 Japanese patients with acute coronary syndromes and 399 healthy individuals. The genotype distributions were not different between the two groups (P=.74, chi2 test). In the former group, coronary angiograms were evaluated by criteria based on the number of diseased vessels, the number of stenotic lesions (> or = 50%), and the relative abnormal arterial portion (extent index). Although the number of stenotic lesions was higher in patients with the DD genotype than in those with the ID or II genotype (P=.006), there were no differences in the number of diseased vessels or the extent index. When only smokers were analyzed, the number of diseased vessels (P=.032), number of stenotic lesions (P=.003), and extent index (P=.019) were all higher in patients with the DD genotype than in those with the ID or II genotype. In contrast, these differences in the respective parameters did not exist in nonsmokers. The results indicate smoking-associated effects of the ACE genotype on the severity of coronary atherosclerosis.