Diagnostic application of a capture based NGS test for the concurrent detection of variants in sequence and copy number as well as LOH

Whole exome sequencing (WES) has made the identification of causative SNVs/InDels associated with rare Mendelian conditions increasingly accessible. Incorporation of softwares allowing CNVs detection into the WES bioinformatics pipelines may increase the diagnostic yield. However, no standard protocols for this analysis are so far available and CNVs in non-coding regions are totally missed by WES, in spite of their possible role in the regulation of the flanking genes expression. So, in a number of cases the diagnostic workflow contemplates an initial investigation by genomic arrays followed, in the negative cases, by WES. The opposite workflow may also be applied, according to the familial segregation of the disease. We show preliminary results for a diagnostic application of a single next generation sequencing panel permitting the concurrent detection of LOH and variations in sequences and copy number. This approach allowed us to highlight compound heterozygosity for a CNV and a sequence variant in a number of cases, the duplication of a non-coding region responsible for sex reversal, and a whole-chromosome isodisomy causing reduction to homozygosity for a WFS1 variant. Moreover, the panel enabled us to detect deletions, duplications, and amplifications with sensitivity comparable to that of the most widely used array-CGH platforms.

Genetics of colorectal polyps

Currently, genetic investigation of human tumours starts from the analysis of advanced cancers. Once a given genetic alteration has been found in advanced tumours, this same alteration is investigated in the pre-neoplastic lesions. The aim of this approach is to assess the significance of the genetic alteration during the carcinogenic process. This review is focused on alterations that have proven to be present in pre-neoplastic lesions that are associated to colorectal cancer (ACF and early adenoma). Alterations that are present at the early stages are likely to play a crucial role in colorectal tumorigenesis. Colorectal tumorigenesis is extremely heterogeneous from a genetic point of view: tumours follow alternative molecular pathways and show different phenotypes (CIN, MIN and CIMP). Tumours are genetically heterogeneous from their early stages: the sequence of genetic events that accumulate within cells during progression to malignancy appears to be determined by the first events. These events have been investigated in ACF and in early adenomas. The understanding of the molecular mechanisms underlying genesis and progression of colorectal tumours will allow the development of new tools for cancer prevention and early diagnosis, as well as for therapeutic approaches specific for different molecular targets.

Cytokine gene polymorphisms in gastric cancer patients from two Italian areas at high and low cancer prevalence

Polymorphisms of interleukin-1beta (IL-1beta), IL-1 receptor antagonist (IL1-RN), and tumor necrosis factor-alpha (TNF-alpha) genes are supposed to be key determinants of gastric cancer risk. Our aim was to study the association between these polymorphisms and gastric cancer in two areas characterized by high (Pavia/Bologna, North Italy) and low (San Giovanni Rotondo, South Italy) gastric cancer prevalence. Genomic DNA was obtained from 216 healthy donors and 98 gastric cancer patients from Pavia and Bologna, and 146 healthy donors and 86 gastric cancer patients from San Giovanni Rotondo. Two SNP in IL-1beta (-511 C/T) and TNF-alpha (-308 G/A) as well as the VNTR polymorphism of IL-1RN locus were studied. A significant linkage disequilibrium was found between IL-1beta -511 and IL-1RN. Genotype and allele frequencies at the IL-1beta, IL-1RN, and TNF-alpha loci in gastric cancer cases were not significantly different from controls. An epistatic effect between IL-1beta -511 and IL-1RN was found with the IL-1beta -511C/IL-1RN*2 haplotype conferring a significant protection against the intestinal-type of gastric cancer in the Southern population. In conclusion, IL-1beta, IL1-RN, and TNF-alpha genotypes are not associated with gastric cancer in Italian patients. An epistatic interrelationship between IL-1beta -511 and IL-1RN confers protection against gastric cancer in low-risk Italian population.

Loss of heterozygosity at 18q21 region in gastric cancer involves a number of cancer-related genes and correlates with stage and histology, but lacks independent prognostic value

Several studies support a role of 18q21 LOH, involving the DCC locus, in colorectal cancer progression; however, its contribution to the natural history of gastric cancer is less clear. Recently, a number of cancer-related genes have been mapped in the 18q21 region, either centromeric or telomeric to DCC. This study searched for 18q21 LOH in 161 gastric cancers representative of all tumour stages and main histological types. To this purpose, seven highly polymorphic markers were used flanking the 18q21 band and spanning the entire region. Thirty-four out of 147 (23.1%) informative cases showed LOH. In 27 of 34 cases (79%), LOH involved all the informative loci. The remaining seven cases showed LOH at more telomeric sites and retained heterozygosity at more centromeric markers, mostly those proximal to the DCC gene. A strong correlation between 18q21 LOH and level of gastric wall invasion, lymph node metastases, or stage was found in cohesive (glandular+solid) and mixed tumours, but not in diffuse cancers. Cox univariate and multivariate analysis showed that invasion level, lymph node metastases, distant metastases, TNM stage, and histology were effective predictors of survival, whereas 18q21 LOH did not show predictive power. The simultaneous deletion of a variety of cancer-related genes with different and even opposite roles might explain why, apparently, 18q21 LOH does not per se contribute significantly to the natural history of gastric cancer, despite strong correlation with stage.

Molecular mechanisms involved in the pathogenesis of gastric carcinoma: interactions between genetic alterations, cellular phenotype and cancer histotype

Gastric cancer develops through the accumulation of multiple genetic lesions that involve oncogenes, tumor suppressor genes and DNA mismatch repair genes. Lauren's classification of gastric carcinoma does not correlate with cellular phenotypes expressed by neoplastic cells and gastric and intestinal cell differentiation markers are widely expressed in both types (intestinal and diffuse) of gastric carcinoma. In contrast, the study of the correlation between morphologic events and genetic alterations, which come about in the cancerogenetic process, seems to indicate the existence of distinct cancerogenetic pathways for the intestinal (or glandular) and diffuse type carcinoma, both originating from a HP-positive gastritis. In particular there seem to be three different profiles of cancerogenesis: 1) p53 mutations which accompany the onset of dysplasia and intestinal-type carcinoma; 2) DNA repair mechanism alterations conditioning microsatellite instability, seem mutually exclusive with regards to p53 mutations. Microsatellite instability correlates with antrally located intestinal-type carcinoma, with little metastatic tendency and a better prognosis; microsatellite instability frequently involves the TGF beta RII, IGF II R genes or the BAX proapoptotic gene, in as much as these contain microsatellite sequences; 3) alterations of E-cadherin, both with regards to mutations and abnormal expression. These lead to junctional and cell polarity loss and are primarily associated with diffuse type carcinoma, which is characterized by poorly cohesive neoplastic cells. Some tumors, initially arising as intestinal-type (glandular structure), acquire a mixed histotype during neoplastic progression, in which both the typical alterations of the intestinal cancerogenesis (p53, microsatellite instability) and those of the diffuse carcinoma (E-cadherin) coexist. The identification of a mixed histotype could have importance both in epidemiologic, pathogenetic and prognostic terms.

Effects of topoisomerase II inhibitors on gastric cancer cells characterized by different genetic lesions

Gastric cancer is poorly-responsive to widely used antitumour drugs, the efficacy of which is thought to be related to the capacity of triggering apoptosis. This process requires a series of gene products including a functional p53 protein. We tested the effects of two DNA topoisomerase II poisons, etoposide and doxorubicin, on gastric cancer cell lines with different genetic lesions. We characterised MKN74 and MKN28 cells for p53 gene status and for the expression of p53 and p21 proteins, as well as of topoisomerase II alpha and beta isoforms. After drug treatments, the cells were analysed for drug cytotoxicity, colony forming ability, cell cycle distribution and presence of apoptotic features. Our findings demonstrated that both etoposide and doxorubicin have a potent anti-proliferative effect on gastric cancer cells. Cell death kinetics was different in the two cell lines, MKN74 cells being more sensitive than MKN28 to the drugs. MKN74 cells, although harboring a wt p53 gene, were unable to undergo a massive apoptosis following etoposide treatment. The response of this cell line might be related to the topoisomerase II beta isozyme, the expression of which proved to be undetectable.

Rb and TP53 pathway alterations in sporadic and NF1-related malignant peripheral nerve sheath tumors

SUMMARY

Karyotypic complexities associated with frequent loss or rearrangement of a number of chromosome arms, deletions, and mutations affecting the TP53 region, and molecular alterations of the INK4A gene have been reported in sporadic and/or neurofibromatosis type I (NF1)-related malignant peripheral nerve sheath tumors (MPNSTs). However, no investigations addressing possible different pathogenetic pathways in sporadic and NF1-associated MPNSTs have been reported. This lack is unexpected because, despite similar morphologic and immunophenotypic features, NF1-related cases are, by definition, associated with NF1 gene defects. Thus, we investigated the occurrence of TP53 and p16(INK4A) gene deregulation and the presence of microsatellite alterations at markers located at 17p, 17q, 9p21, 22q, 11q, 1p, or 2q loci in MPNSTs and neurofibromas either related (14 cases) or unrelated (14 cases) to NF1. Our results indicate that, in MPNSTs, p16(INK4A) inactivation almost equally affects both groups. However, TP53 mutations and loss of heterozygosity involving the TP53 locus (43% versus 9%), and p53 wild type overexpression, related or not to mdm2 overexpression (71% versus 25%), seem to mainly be restricted to sporadic MPNSTs. In NF1-associated MPNSTs, our microsatellite results are consistent with the occurrence of somatic inactivation by loss of heterozygosity of the second NF1 allele.

Detection of microsatellite alterations in the spectrum of melanocytic nevi in patients with or without individual or family history of melanoma

We studied a group of patients with or without individual or family history of melanoma for the occurrence of genetic alterations at microsatellite DNA sequences, usually referred to as microsatellite instability (MSI), and loss of heterozygosity (LOH). Microsatellite analysis of 3 markers located on chromosome 9p21-22 was performed for 88 melanocytic lesions, including 27 melanomas and 35 dysplastic and 26 common nevi, from 48 patients. Three additional markers, on 11q23, 17q21 and 5q22, were investigated in 16 melanomas. Overall, microsatellite alterations of the type usually considered low-level instability at 9p21-22 were observed in 22% of melanomas and 31% of dysplastic and 23% of common nevi. LOH at the same loci was found in 15% of melanomas and 8% of dysplastic nevi but never in common nevi. Cases with a positive family history of melanoma compared to those with a negative family history showed a higher microsatellite alteration frequency (43% vs. 20%), and the same was observed in melanoma compared to non-melanoma carriers (31% vs. 16%). Our results show that (i) MSI is common in all melanocytic lesions, though with differences in the group of patients which could have clinical relevance if confirmed, whereas LOH is restricted to melanomas and dysplastic nevi; (ii) various melanocytic lesions from the same patient represent clonally distinct tumors; (iii) the phenotype suggestive of DNA repair deficiency is influenced by a family or an individual history of melanoma; (iv) the microsatellite alteration frequency correlates with patient groups ordered according to increasing melanoma risk.

p53 codon 72 polymorphism does not affect the risk of cervical cancer in patients from northern Italy

A case-control study was performed to investigate the risk of cervical cancer associated with p53 polymorphism at codon 72, encoding either arginine or proline. It has been recently suggested that the arginine isoform increases the susceptibility to invasive cervical cancer; however, data remain controversial. The polymorphism was examined by both allele-specific PCR and RFLP analysis in 101 patients with primary cervical cancer and in 140 healthy women of the same age and from the same geographical area. The distribution of p53 genotypes in cervical cancer patients and in controls was not significantly different (P = 0.445), and homozygosity for arginine at residue 72 was not associated with an increased risk for cervical cancer (odds ratio, 0.81; 95% confidence interval, 0.47-1.42; P = 0.52). Similarly, different genotype distribution and increased risk were not observed when patients versus controls were analyzed according to human papillomavirus status and cancer histotype. Therefore, no evidence of association between homozygosity for p53 arginine and cervical cancer was found in our population sample.

Microsatellite instability in colorectal-cancer patients with suspected genetic predisposition

Hereditary non-polyposis colorectal cancer (HNPCC) is a dominantly inherited syndrome linked to DNA-mismatch-repair (MMR) gene defects, which also account for microsatellite instability (MSI) in tumour tissues. Diagnosis is based mainly on family history, according to widely accepted criteria (Amsterdam Criteria: AC). Aim of this work was to assess MSI in colorectal-cancer patients with suspected genetic predisposition, and to verify whether MSI represents a tool to manage MMR gene (hMSH2 and hMLH1) mutation analysis. We investigated 13 microsatellites (including the 5 NCI/ICG-HNPCC markers) in 45 patients with suspected hereditary predisposition (including 16 subjects from HNPCC families fulfilling the AC). We found MSI-H (high frequency of instability, i.e., in > or =30% of the markers) in 85% of the HNPCC patients and in 16% of the non-HNPCC subjects. The 5 NCI/ICG-HNPCC microsatellites proved to be the most effective in detecting MSI, being mononucleotide repeats the most unstable markers. We investigated the association between hMSH2- and hMLH1 gene mutations and MSI. Our results indicate that AC are highly predictive both of tumour instability and of MMR-gene mutations. Therefore, as the most likely mutation carriers, HNPCC subjects might be directly analyzed for gene mutations, while to test for MSI in selected non-HNPCC patients and to further investigate MMR genes in MSI-H cases, appears to be a cost-effective way to identify subjects, other than those from kindred fulfilling AC, who might benefit from genetic testing.

Microsatellite instability in colorectal-cancer patients with suspected genetic predisposition

Hereditary non-polyposis colorectal cancer (HNPCC) is a dominantly inherited syndrome linked to DNA-mismatch-repair (MMR) gene defects, which also account for microsatellite instability (MSI) in tumour tissues. Diagnosis is based mainly on family history, according to widely accepted criteria (Amsterdam Criteria: AC). Aim of this work was to assess MSI in colorectal-cancer patients with suspected genetic predisposition, and to verify whether MSI represents a tool to manage MMR gene (hMSH2 and hMLH1) mutation analysis. We investigated 13 microsatellites (including the 5 NCI/ICG-HNPCC markers) in 45 patients with suspected hereditary predisposition (including 16 subjects from HNPCC families fulfilling the AC). We found MSI-H (high frequency of instability, i.e., in > or =30% of the markers) in 85% of the HNPCC patients and in 16% of the non-HNPCC subjects. The 5 NCI/ICG-HNPCC microsatellites proved to be the most effective in detecting MSI, being mononucleotide repeats the most unstable markers. We investigated the association between hMSH2- and hMLH1 gene mutations and MSI. Our results indicate that AC are highly predictive both of tumour instability and of MMR-gene mutations. Therefore, as the most likely mutation carriers, HNPCC subjects might be directly analyzed for gene mutations, while to test for MSI in selected non-HNPCC patients and to further investigate MMR genes in MSI-H cases, appears to be a cost-effective way to identify subjects, other than those from kindred fulfilling AC, who might benefit from genetic testing.

Surname as 'cancer risk' in extreme isolates: example from the island of Lastovo, Croatia

The aim of this study was to analyze whether there are surnames which appear more frequently among the ancestors of cancer cases in a small isolate, in comparison to the ancestral surnames of the healthy controls, using the classic case-control design. The chosen setting was the island of Lastovo, Croatia, located more than 100 kilometers from the nearest coastal region. The period of study was 1970-1995, during which a total of 76 cancer cases were recorded in a population of approximately 800. The comparison of surname frequencies was performed in current and in five ancestral generations. The leading hypothesis was that, if inbreeding and common ancestry contributed to the development of the disease, then those phenomena should be reflected in increasing frequency of some surnames among ancestors, identifying the 'hidden' consanguinity, or 'following' cancer-promoting genes on the Y-chromosome. The results imply that there are surnames representing a classic "risk" for cancer, but also those "protecting" from its development, which all underscores the importance of founder effect and genetic predisposition to the disease in a small, reproductively isolated population. All of the results become more evident and increasingly significant when analyzed in more distant ancestral generations.

Cancer incidence in eastern Adriatic isolates, Croatia: examples from the islands of Krk, Cres, Losinj, Rab and Pag

As an extension of previous research this study investigates the incidence of cancer in five genetic isolate island populations of the Eastern Adriatic, Croatia. Thorough anthropological research over the past three decades has established some of those populations as outstanding examples of genetic isolates. A previous study which found higher cancer incidence in 5 Eastern Adriatic islands than in a control population supported a hypothesis that among the founders of these populations there were genetic variants (especially with recessive inheritance) responsible for genetic susceptibility to certain types of cancer. This study sought to investigate cancer incidence in 5 further island populations. All cancer cases in five island populations (Krk, Cres, Losinj, Rab and Pag) over the 20-year period (1971 to 1990) was extracted from the data of the Croatian Cancer Registry. The mainland populations of Istrian and Primorsko-Goranska County, characterized by similar environmental factors but an outbred genetic structure, represented a control population. After standardization by by sex and age, cancer incidence was higher in the island populations than in the control population in both sexes. The cancer sites primarily responsible for the excess incidence were prostate, stomach and pancreatic cancer in males, and ovarian, breast, stomach, bowel, and brain cancer in females. The reasons for the increased cancer incidence are uncertain and may be due to different environmental exposure between the two populations. However, it is possible that genetic isolation and inbreeding are important factors. Further investigations of cancer in these isolate populations are warranted to explore these findings further.

Variable mutation frequencies in coding repeats of TCF-4 and other target genes in colon, gastric and endometrial carcinoma showing microsatellite instability

Frameshift mutations in genes containing mononucleotide repeats are often observed in cancers exhibiting a high frequency of microsatellite instability (MSI-H). Several tumor types, including colorectal, gastric, and endometrial carcinomas, display this phenotype in a significant proportion of cases. We recently showed in a large series of MSI-H colorectal tumors that approximately 40% of them exhibited frameshift mutations in an (A)9 tract within the coding region of the TCF-4 gene, a crucial member of the APC/beta-catenin/TCF pathway. In the present study, we have examined MSI-H cancers from other primary tumor sites for mutations in this new target gene. Two of 22 (9%) MSI-H primary gastric cancers and none of 23 MSI-H endometrial primary tumors and cell lines were found to have a 1 bp deletion in the TCF-4 repeat. In the same series of tumors we also looked for frameshift mutations in other coding repeats localized within the TGF beta-RII, BAX, IGFIIR, hMSH3 and hMSH6 genes. Our results suggest that the TCF-4 gene, in a similar manner to some of these latter genes, is differentially altered in MSI-H tumors from different primary sites.

Ki-ras and p53 gene mutations in pancreatic ductal carcinoma: a relationship with tumor phenotype and survival

We investigated a series of clinically well documented pancreatic ductal adenocarcinomas for the presence of molecular alterations of the p53 and Ki-ras genes and their correlations with p53 nuclear immunohistochemical expression. The results were evaluated in comparison with cellular expression, by ductal cancer cells, of gastric (PGII) and intestinal (CAR-5) antigens and with several clinicopathologic parameters such as grade, stage, size and lymph-node status. Ki-ras gene mutation at codon 12 was detected in 77.7% of cases with no relationship with tumor grade, stage, and survival of the patients. p53 gene mutations were found in 18/31 (58%) cases and p53 immunohistochemical overexpression was detected in 51/104 (49%) of cases. Both Ki-ras and p53 gene mutations were found in 13/31 (41.9%) of adenocarcinomas examined, while Ki-ras and p53 overexpression was detected in 19/45 (42.2%). A positive correlation between p53 overexpression and tumour grade was found (p0.0001) but no relationship was found between p53 overexpression, tumor stage, lymph-node status and size of the tumors. A trend toward an association of p53 overexpression with poorer survival was found in patients with pancreatic cancers of the same grade, stage or with the same immunophenotype, but the data did not reach statistical significance. The expression of gastric and intestinal antigenic markers in pancreatic adenocarcinomas and the presence of molecular abnormalities analogous to those found in gastric and colorectal cancers suggest common genetic pathways in gastrointestinal and pancreatic carcinogenesis.

Absence of microsatellite instability in breast carcinomas with both p53 and c-erbB-2 alterations

Based on a previous finding that amplification of the c-erbB-2 oncogene and alteration of p53 are strongly associated in most aggressive breast tumours, the present study investigated whether microsatellite instability (MI) might also be associated with this tumour phenotype. Nine polymorphic microsatellite markers, including six dinucleotide, one trinucleotide, and two tetranucleotide repeats, were amplified from paired normal and tumour DNA samples of 15 breast tumours that overexpressed both c-erbB-2 and p53 and of 15 control breast tumours that overexpressed neither protein. All 30 breast tumours analysed exhibited a replication error-negative phenotype, with only one sample showing MI in one of the nine loci. This suggests that the genetic events underlying MI, which are critical in colorectal and gastric tumours, are not involved in the pathogenesis of c-erbB-2/p53 double-altered breast tumours and do not play a central role in breast tumour formation.

A National Cancer Institute Workshop on Microsatellite Instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer

In December 1997, the National Cancer Institute sponsored "The International Workshop on Microsatellite Instability and RER Phenotypes in Cancer Detection and Familial Predisposition," to review and unify the field. The following recommendations were endorsed at the workshop. (a) The form of genomic instability associated with defective DNA mismatch repair in tumors is to be called microsatellite instability (MSI). (b) A panel of five microsatellites has been validated and is recommended as a reference panel for future research in the field. Tumors may be characterized on the basis of: high-frequency MSI (MSI-H), if two or more of the five markers show instability (i.e., have insertion/deletion mutations), and low-frequency MSI (MSI-L), if only one of the five markers shows instability. The distinction between microsatellite stable (MSS) and low frequency MSI (MSI-L) can only be accomplished if a greater number of markers is utilized. (c) A unique clinical and pathological phenotype is identified for the MSI-H tumors, which comprise approximately 15% of colorectal cancers, whereas MSI-L and MSS tumors appear to be phenotypically similar. MSI-H colorectal tumors are found predominantly in the proximal colon, have unique histopathological features, and are associated with a less aggressive clinical course than are stage-matched MSI-L or MSS tumors. Preclinical models suggest the possibility that these tumors may be resistant to the cytotoxicity induced by certain chemotherapeutic agents. The implications for MSI-L are not yet clear. (d) MSI can be measured in fresh or fixed tumor specimens equally well; microdissection of pathological specimens is recommended to enrich for neoplastic tissue; and normal tissue is required to document the presence of MSI. (e) The "Bethesda guidelines," which were developed in 1996 to assist in the selection of tumors for microsatellite analysis, are endorsed. (f) The spectrum of microsatellite alterations in noncolonic tumors was reviewed, and it was concluded that the above recommendations apply only to colorectal neoplasms. (g) A research agenda was recommended.

Genetic pattern, histological structure, and cellular phenotype in early and advanced gastric cancers: evidence for structure-related genetic subsets and for loss of glandular structure during progression of some tumors

Gastric cancer shows remarkable heterogeneity in histological pattern, cellular phenotype, and genotype. Tumor subsets identified by varying procedures have shown limited reciprocal correlation and have failed to provide a sound rationale for the characterization and classification of all tumors. Based on a case series of 130 gastric cancers that covered both early (70 cases) and advanced (60 cases) stages and that represented most histological types and structural patterns, this study investigated (1) microsatellite instability and p53 gene mutation by means of PCR-based molecular techniques and (2) p53 protein accumulation or tumor cell immunophenotype by means of immunoperoxidase procedures. It was found that microsatellite instability and p53 gene mutation involve two distinct subsets of both early and advanced-stage glandular (intestinal) cancer, and that, contrastingly, they leave purely diffuse cancers unaffected. Mixed cancers, namely, those in which glandular admixed with diffuse growths, showed scarce microsatellite instability at all stages, whereas prominent p53 gene mutation and p53 protein accumulation was limited to the advanced stage alone. No significant correlation was found between tumor cell immunophenotype and either genotype or histotype, although some correlation with particular structural patterns was detected. Comparison of intramucosal with invasive growths within any given tumor suggested that invasive cancers with diffuse-type growth arise in part from mucosal cancers of glandular or mixed structure through progressive loss of intercellular junctional systems. It is concluded that at least two genetically distinct subsets of glandular cancer, one with microsatellite instability and the other with p53 lesions, should be separated both from purely diffuse cancer and, at least in the advanced stage, from mixed cancer. Available evidence suggests distinct clinicopathologic profiles for such tumor entities.

Rapid assessment of replication error phenotype in gastric cancer

Forty gastric tumors were investigated for microsatellite instability at the D2S119 and L-myc loci. These tumors and 143 other gastrointestinal cancers were previously analyzed for instability at several different microsatellites. By evaluating previous and present results, repeated sequences were selected that frequently underwent replication errors (RERs). To coamplify these sequences, the following multiplex polymerase chain reactions (PCRs) were performed: 1) D2S119/L-myc/D18S59; 2) D2S119/L-myc/D3S1076; and 3) D2S177/L-myc/BAT-RII. Therefore, the 40 gastric tumors in the present survey were rescreened using multiplex PCRs. Each multiplex allowed detection of nearly all RER+ tumors (80% for multiplex 3 and 87% for multiplexes 1 and 2) that had been previously identified by amplifying 9 different loci with independent reactions. Moreover, for multiplexes 1 and 2, the size differences between normal and RER alleles were sufficient to be detected by electrophoresis on conventional polyacrylamide gels after DNA staining with ethidium bromide. This approach allows a rapid and easy assessment of RER phenotype in gastric tumors.

Analysis and clinical implications of p53 gene mutations and human papillomavirus type 16 and 18 infection in primary adenocarcinoma of the uterine cervix

Mutant p53 is frequently detected in endometrial and ovarian carcinoma, but it is rare in cervical cancers. Previous reports focused on cervical squamous cell carcinoma, whereas cervical adenocarcinoma was given little attention. We searched for p53 gene mutations in 74 primary cervical adenocarcinomas with known human papillomavirus (HPV) status. Our aim was to evaluate the prevalence of p53 mutations and to investigate their possible role as an independent prognostic factor. We found mutations in 13.5% with a high rate of G:C --> A:T transitions as observed in endometrial adenocarcinoma. As p53 mutations are more frequently detected in malignancies of high grade, high stage, and large size, this molecular event seems to play a role in the progression rather than in the induction of cervical adenocarcinoma. In our series, patients with HPV-negative tumors and patients with mutated neoplasms, irrespective of HPV infection, had a shorter survival. Yet the absence of HPV infection and presence of p53 mutations are not independent risk factors for tumor-related death after adjustment for clinicopathological confounders. The only significant and independent predictors of survival are age of patient, stage of disease, tumor grade, and presence of lymph node metastases.

Mean age of tumor onset in hereditary nonpolyposis colorectal cancer (HNPCC) families correlates with the presence of mutations in DNA mismatch repair genes

Fourteen Italian families affected with hereditary nonpolyposis colorectal cancer (HNPCC) were screened for germline mutations at three DNA mismatch repair (MMR) genes, MSH2, MLHI, and GTBP, by using a combination of different methods that included an in vitro synthesized protein assay, single-strand conformation polymorphism analysis, and direct sequencing. DNA alterations were observed in six instances, including a single base deletion in MSH2 exon 14, an A-to-G transition in the splice donor site of MLHI exon 6, and two missense mutations in MLHI exons 5 and 9. A previously reported common mutation affecting the splice donor site of MSH2 exon 5 was identified in two families. No mutations were detected in the GTBP gene. In total, eight of 16 Italian HNPCC families (50%), including two previously reported kindreds, were found to carry a mutation in MMR genes. We compared the mean age of colorectal cancer onset in the index cases (three patients for each family) between the two groups of kindreds, those with identified mutation vs. those without, and found that the first had a significantly lower value (43.0 vs. 53.7 years, P = 0.014). This finding suggests that HNPCC families with a more advanced age of tumor onset are less likely to be associated with known MMR genes.

Microsatellite instability in intestinal- and diffuse-type gastric carcinoma

To investigate the role of genetic instability in the development of intestinal- and diffuse-type gastric cancers, six microsatellite loci were analysed in 98 carcinomas of the two main histotypes, at both early and advanced stages of progression, and in five preneoplastic lesions. RER+ phenotype frequency proved to be significantly higher (P = 0.013) in intestinal (23 per cent) than in diffuse cancers (5 per cent) and slightly higher in advanced (19 per cent) than in early (12 per cent) tumours. When comparing early and advanced tumours of the same histotype, a similar frequency was found for diffuse tumours (4 per cent vs. 6 per cent), and an increase from 19 to 30 per cent for intestinal cancers. Instability at more than one locus was limited to intestinal tumours and replication errors were also detected in an intestinal dysplasia. On the whole, these data suggest that genetic instability has an important and early role in gastric carcinogenesis of the intestinal type and a less important role in gastric carcinogenesis of the diffuse type. Most tumours of this panel had previously been characterized for p53 gene mutations. p53 screening was extended to all samples, to investigate the possible association between gene mutations and microsatellite instability. Analysis showed a trend (P = 0.07, Fisher's exact test) towards a negative association between these two genetic lesions in tumours of the intestinal type.

Gene amplification and proliferative kinetics in relation to prognosis of patients with gastric carcinoma

BACKGROUND

The differences in survival of gastric carcinoma patients who have identical clinical or pathologic stages prompted the authors to investigate the prognostic significance of biologic features that are known to affect the clinical aggressiveness of other tumor types.

METHODS

One hundred twenty-four tumor samples from patients who had received radical or palliative surgery were analyzed for c-myc, c-K-ras, hst, and c-erb B-2 gene amplification by means of the Southern blot technique. Of these tumors, 70 were also examined for cell kinetics by means of the thymidine labeling index (TLI).

RESULTS

The analysis of associations between gene amplification and the anatomicopathologic variables (TNM classification, site of tumor, and histology) showed that amplification represents a late event in the natural history of gastric carcinoma. Gene amplification showed a slight, statistically insignificant, negative impact on overall survival (OS) (P = 0.09). Amplification of c-erb B-2 correlated in a statistically significant way with reduced OS (P = 0.03). Cox multiple regression analysis revealed that neither c-erb B-2 amplification nor TLI had prognostic significance in relation to OS.

CONCLUSIONS

These data indicate that amplification of the examined oncogenes did not reveal a new independent prognostic factor for patients with gastric carcinoma. However, the authors' results did show a strong correlation between gene amplification and tumor progression, which warrants further study involving larger series of patients. At the same time, the TLI results underlined the need to identify the most suitable biologic material for use in the estimation of proliferative indexes in gastric carcinoma.

Gene amplification and proliferative kinetics in relation to prognosis of patients with gastric carcinoma

BACKGROUND

The differences in survival of gastric carcinoma patients who have identical clinical or pathologic stages prompted the authors to investigate the prognostic significance of biologic features that are known to affect the clinical aggressiveness of other tumor types.

METHODS

One hundred twenty-four tumor samples from patients who had received radical or palliative surgery were analyzed for c-myc, c-K-ras, hst, and c-erb B-2 gene amplification by means of the Southern blot technique. Of these tumors, 70 were also examined for cell kinetics by means of the thymidine labeling index (TLI).

RESULTS

The analysis of associations between gene amplification and the anatomicopathologic variables (TNM classification, site of tumor, and histology) showed that amplification represents a late event in the natural history of gastric carcinoma. Gene amplification showed a slight, statistically insignificant, negative impact on overall survival (OS) (P = 0.09). Amplification of c-erb B-2 correlated in a statistically significant way with reduced OS (P = 0.03). Cox multiple regression analysis revealed that neither c-erb B-2 amplification nor TLI had prognostic significance in relation to OS.

CONCLUSIONS

These data indicate that amplification of the examined oncogenes did not reveal a new independent prognostic factor for patients with gastric carcinoma. However, the authors' results did show a strong correlation between gene amplification and tumor progression, which warrants further study involving larger series of patients. At the same time, the TLI results underlined the need to identify the most suitable biologic material for use in the estimation of proliferative indexes in gastric carcinoma.

Microsatellite instability and mutations of p53 and TGF-beta RII genes in gastric cancer

To investigate the molecular mechanism of gastric carcinogenesis, we analyzed genetic instability and p53 gene mutations in 40 primary gastric carcinomas. Tumor samples were from untreated patients with no family history suggestive of genetic predisposition to cancer. We screened six microsatellite loci by the polymerase chain reaction (PCR) method, and exons 5-8 of the p53 gene by the PCR-based denaturing gradient gel electrophoresis and sequencing techniques. Microsatellite instability was detected in 32.5% (13/40), and gene mutations in 40% (16/40), of the tumors analyzed. No statistically significant associations were found between genetic alterations and clinico-pathological variables (with the exception of diffusion of lymph node metastases, which was inversely associated with the presence of microsatellite alterations; P < 0.01). Interestingly, a negative association was found between genetic instability and p53 gene mutations: 11 out of 13 tumors showing instability proved to carry a nonmutated p53 gene versus 2/13 carrying a mutated gene (P = 0.03). These observations suggest that genetic instability and p53 gene mutations play a crucial role in the gastric carcinogenic process, but likely act through distinct pathways during cancer development. However, genetic instability is not in and of itself neoplastic. Therefore, we investigated whether insertion/deletion mutations of the polyadenine tract within the transforming growth factor-beta type II receptor gene (TGF-beta RII) were frequently present in gastric tumors with an RER+ (replication error) phenotype. We found RII mutations in 8/40 (20%) samples: mutations were present in 7/13 (54%) RER+ tumors versus 1/27 (4%) RER- cases (P < 0.001).

Study on aneuploidy and p53 mutations in astrocytomas

To determine whether a correlation exists between aneuploidy and p53 status in astrocytic tumors we analyzed 48 astrocytomas with different grades of malignancy for the presence of p53 mutations and aneuploidy of chromosomes 10 and 17 (Ch10, Ch17), known to be particularly involved with this type of tumor. We used polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) analysis on exons 5-8 of the p53 gene, and fluorescence in situ hybridization (FISH) analysis on interphase nuclei using chromosome specific pericentromeric probes, respectively. Our results showed that Ch10/Ch17 aneuploidy is a common early event in astrocytomas (90% of low grade tumors are aneuploid). p53 mutations and Ch17 aneuploidy are early events, but their incidence is not dependent on tumor grade. Loss of Ch10 is the only alteration that significantly correlates with tumor progression. No significant correlation between the presence of Ch10/Ch17 aneuploidy and p53 mutations was found. However, the coexistence of p53 mutations and aneuploidy, was observed in a subset of cases. The presence of p53 mutations appeared to be a significant predictor of a poor prognosis. In conclusion, genomic instability may or may not be associated with p53 mutations in astrocytomas, thus suggesting that other cellular determinants can also be responsible for the aneuploidy observed.

Loss of heterozygosity for chromosome 11 in adenocarcinoma of the stomach

Loss of heterozygosity (LOH) at several chromosomal loci is a common feature of the malignant progression of human tumors. In the case of chromosome 11, LOH has been well documented in several types of solid neoplasms, including gastric carcinoma, suggesting the presence of suppressor gene(s) at 11p15 and 11q22-23. Little is currently known about the molecular events occurring during the development of gastric cancer. To define the regions of chromosome 11 involved in gastric cancer progression, we used high-density polymorphic markers to screen for LOH in matched normal and tumor tissue DNA from 60 primary gastric carcinomas. We found that 21% of the tumors showed LOH simultaneously at 11p15 and 11q22-23, 41% had LOH at 11p15, and 30% had LOH at 11q22-23. We confirm that the minimal critical area of LOH for 11p15.5 is the approximately 2-Mb region between loci D11S1318 and D11S988. However, when we analyzed the pattern of LOH according to the country of origin of the patient, LOH for 11q22-23 alone was found only in cases from Italy. The minimal critical region of LOH at 11q22-23 is identical to that identified for other solid tumors, suggesting that the same putative tumor suppressor gene(s) contained within this region is involved in the pathogenesis of several common human tumors.

Intestinal and diffuse gastric cancers arise in a different background of Helicobacter pylori gastritis through different gene involvement

Investigation of extensively sampled nontumor gastric mucosa from 205 early gastric cancers showed Helicobacter pylori colonization in 85% of cases, including 100% of diffuse and 78% (83% in 97 cases with Swiss rolls) of glandular or mixed cancers. Intestinal metaplasia, including its type III variant, was prominent in the mucosa associated with glandular and mixed (but not diffuse) early cancers. Both glandular (usually called "intestinal") and diffuse-type cancers showed admixtures of intestinal and gastric tumor cell phenotypes. Both p53 gene mutations and p53 protein immunostaining were essentially restricted to glandular or mixed cancers and associated dysplastic lesions. Their appearance in the advanced stage of diffuse cancer was partly due to a change of the histologic pattern from glandular to diffuse during progression of some tumors. Loss of laminin, beta I integrin, or zonula adherens junctions was a common finding in both early and advanced diffuse cancer. It is concluded that two main pathways operate in gastric carcinogenesis, both starting from H. pylori gastritis and both leading to phenotypically variable, often mixed gastric/intestinal tumor growth. However, only one of the two pathways involves intestinal metaplasia, its type III variant, p53 gene alteration, and dysplasia to end in glandular cancer. In the other pathway, diffuse cancer apparently arises directly from hyperplastic, sometimes atypical necks of mostly nonmetaplastic gastric glands, through primary involvement of genes affecting cell-cell and cell-matrix junctional proteins.

p53 gene mutations and protein nuclear accumulation are early events in intestinal type gastric cancer but late events in diffuse type

We screened for p53 alterations in 71 early gastric cancers of differing histological types and growth patterns, 18 advanced cancers of diffuse type, 19 dysplastic lesions, and 12 extensive intestinal metaplasia cases. Tumors were investigated for gene mutations (exons 5-8) with PCR-based denaturing gradient gel electrophoresis and sequencing techniques, and for protein accumulation with immunohistochemical methods. Nontumor samples were studied with immunohistochemistry alone. Of the early cancers, intestinal tumors showed a much higher p53 mutation frequency (41%) than did diffuse cancers (4%). When comparing early and advanced tumors of the same type, we observed a similarity in mutation frequency (41 versus about 50%) for intestinal tumors, and a significant increase for diffuse tumors (from 4 to 33%). Immunopositive case distribution between tumor types and stages paralleled that of mutated cases. Immunohistochemical and genetic analysis gave concordant results for all samples with gene mutations. Eighteen of the 65 (28%) nonmutated tumors displayed significant immunoreactivity. Early tumors that massively penetrated the submucosa, i.e., the early tumors for which prognosis is worst, showed the highest frequency both of p53 gene mutation and of nonmutated protein accumulation. Twelve of 19 dysplastic lesions showed significant immunoreactivity, whereas intestinal metaplasias proved unreactive in all but a few cells. Our results yield two implications: that p53 alterations have a crucial and early role in gastric carcinogenesis of intestinal type, likely acting at the transition step between metaplasia and dysplasia; and that the alterations are mainly associated with tumor progression in cancer of diffuse type.

Analysis and clinical implications of K-ras gene mutations and infection with human papillomavirus types 16 and 18 in primary adenocarcinoma of the uterine cervix

Experimental models indicate that activated ras genes and HPV oncogenic sequences may cooperate in inducing a completely transformed phenotype in epithelial cells. We searched for K-ras gene mutations and HPV type-16 and -18 sequences in 67 primary adenocarcinomas of the uterine cervix by analyzing DNAs from formalin-fixed, paraffin-embedded tissue samples. Target sequences were amplified by PCR and analyzed by denaturing gradient gel electrophoresis (DGGE) and sequencing for the detection of K-ras gene mutations and by Southern blotting for the detection of HPV infection. We found 16 mutations in 15 cases; 14 were at codon 12 and 2 at codon 13; 11 were base transitions and 5 were transversions. Mutations were more frequent in mucin-secreting than in non-mucinous tumors. HPV oncogenic sequences were detected in 58 cases with no significant difference between K-ras-mutated and wild-type tumors. HPV oncogenic sequences were also more frequent in mucin-secreting than in non-mucinous tumors. Both molecular events were present simultaneously in 13 out of 58 cases, all of which had histologically grade-2 and grade-3 tumors. Clinico-pathological parameters of the disease and the overall survival, however, were independent of K-ras mutations and of HPV-16 and -18 infection, as shown by univariate and multivariate analysis. In contrast, stage of disease, lymph-node metastases, deep infiltration, clear-cell histology and low grade of differentiation were risk factors for tumor-related death.

Intraductal papillary-mucinous tumours represent a distinct group of pancreatic neoplasms: an investigation of tumour cell differentiation and K-ras, p53 and c-erbB-2 abnormalities in 26 patients

Intraductal papillary growth of mucin producing hypersecreting, columnar cells characterizes a group of rare pancreatic exocrine neoplasms which we propose to call intraductal papillary-mucinous tumors (IPMT). We analysed the histopathology of 26 IPMT in relation to gastro-enteropancreatic marker expression, genetic changes and biology. Four IPMT showing only mild dysplasia were considered to be adenomas. Nine tumours displayed moderate dysplasia and were regarded as borderline. Severe dysplasia-carcinoma in situ changes were found in 13 IPMT which were therefore classified as intraductal carcinomas. Six of these carcinomas were frankly invasive and two of these had lymph node metastases. The invasive component resembled mucinous non-cystic carcinoma in all but one tumour which showed a ductal invasion pattern. Immunohistochemically, an intestinal marker type was found in most carcinomas, while gastric type differentiation prevailed among adenomas or borderline tumours. K-ras mutations (seven at codon 12 and one at codon 13) were found in 31% of IPMT (2 adenomas, 1 borderline, 5 carcinomas). Nuclear p53 overexpression was detected in 31% of IPMT (6 carcinomas and 2 borderline IPMT) and correlated with p53 mutations (one at exon 8 and the other at exon 5) in two carcinomas. p53 abnormalities were unrelated to K-ras mutation. c-erbB-2 overexpression was observed in 65% of IPMT, with various grades of dysplasia. Twenty-two of 24 patients are alive and well after a mean post-operative follow-up of 41 months. Only two patients, both with invasive cancer at the time of surgery, died of tumour disease. It is concluded that pancreatic IPMT encompass neoplasms which, in general, have a favorable prognosis, but are heterogeneous in regard to grade of dysplasia and marker expression. Adenoma, borderline tumour, intraductal carcinoma and invasive carcinoma can be differentiated. p53 changes but not K-ras mutation or c-erbB-2 overexpression are related to the grade of malignancy. Most IPMT differ in histological structure, marker expression and behaviour from ductal adenocarcinoma.

K-ras gene mutations: an unfavorable prognostic marker in stage I lung adenocarcinoma

Activation of K-ras gene by point mutations, a common finding in lung adenocarcinomas, has been suggested to decrease patient survival. We investigated 109 lung adenocarcinomas, mostly small, peripheral, stage I tumours (81/109) for presence of K-ras gene mutations at codons 12 and 13. Mutations were detected by denaturing gradient gel electrophoresis analysis of specific sequences amplified by polymerase chain reaction from DNA extracted from archival pathological material. Thirty-three of 109 (30.3%) tumours showed mutations at codon 12 (28/33, 84.8%) or 13 (5/33, 15.2%) of the gene. Mutations and type of nucleotide substitutions were differently distributed among cytological subtypes, being more prevalent among less differentiated (G2 and G3) tumours and among bronchial than bronchiolo-alveolar type adenocarcinomas. Survival analysis showed an adverse effect of K-ras mutation on survival, restricted to stage I tumours. Median survival for 81 stage I patients was 30 months for non-mutated tumours versus 20 months for mutated tumours (p = 0.016). Multivariate analysis showed that age of patient (p = 0.001) and K-ras mutation status (p = 0.04) were the only independent factors influencing survival significantly. These data strengthen the hypothesis that K-ras gene mutations may be useful in identifying a subgroup of patients with poor outcome.

K-ras and p53 gene mutations in pancreatic cancer: ductal and nonductal tumors progress through different genetic lesions

We studied K-ras and p53 gene mutations in a panel of 57 primary pancreatic cancers including ductal and nonductal tumors. DNAs were obtained from formalin-fixed, paraffin-embedded material. Target sequences were amplified by polymerase chain reaction and analyzed by denaturing gradient gel electrophoresis and sequencing. Both K-ras and p53 genes were frequently mutated in ductal cancers (25 of 35, 71.4%; 18 of 35, 51.4%, respectively). K-ras mutations were confined to the second position of codon 12 where base transitions and transversions were equally observed. p53 changes were mainly missense mutations. Transitions and transversions were found equally with a prevalence of G:C-->A:T changes among transitions. No gene alterations were present in the 6 exocrine nonductal tumors and (with one exception) in the 12 endocrine tumors analyzed. Our results indicate that mutated K-ras and p53 genes can cooperate in the establishment of ductal pancreatic cancers, whereas other genetic events have to be present in nonductal tumors. Moreover, K-ras alterations may represent an early event in ductal tumorigenesis, as suggested both by the high gene mutation frequency and by the presence of mutations in low-grade tumors. On the contrary, p53 gene changes seem to represent an event required for the malignancy progression of ductal tumors from lower to higher grades.

Primary retroperitoneal mucinous cystoadenocarcinomas: an immunohistochemical and molecular study

Special immunohistochemical stains for the identification of gastroenteropancreatic antigens in two cases of primary retroperitoneal mucinous cystoadenocarcinomas (PRMC) show that these tumours have patterns similar to ovarian mucinous tumours. Markers of pyloric type gastric mucosa differentiation (M1, cathepsin E, concavavalin A, pepsinogen II) are mostly positive in benign and borderline areas with endocervical type differentiation, while immunoreactivity for intestinal cell markers (M3SI and CAR-5) and for DU-PAN-2 is present mainly in frankly malignant areas, regardless of differentiation type. DNA analysis shows a point mutation of K-ras oncogene at codon 12 (GGT to CGT) in one case. The immunohistochemical and genotypic similarity of PRMC and ovarian mucinous tumours may indicate similar mechanisms in their histogenesis.

Loss of heterozygosity and K-ras gene mutations in gastric cancer

In order to identify relevant genetic lesions in gastric carcinoma, we searched for tumor suppressor gene inactivation and K-ras gene mutations by analyzing tumor and control DNAs from 34 patients. These were from an epidemiologically defined area of Italy characterized by one of the world's highest incidences of stomach cancer. Allele losses were investigated by the Southern blotting procedure at 16 polymorphic loci on 11 different chromosomes. Our data demonstrate that chromosomal regions 5q, 11p, 17p and 18q are frequently deleted, and that 7q and 13q chromosome arms are also involved, although at a lower frequency. Loss of heterozygosity (LOH) at region 11p was not found during other surveys carried out on patients of different geographic origins. No specific combination of allelic losses could be recognized in the samples analyzed, the only exception being that tumors with 17p allelic loss also showed LOH on the 18q region. When matching frequent LOH events and the stage of progression of the tumors, we observed a trend of association between advanced stages and allelic losses on 17p and 18q chromosome arms. The analysis of K-ras, carried out by the polymerase chain reaction and denaturing gradient gel electrophoresis, demonstrated transforming mutations in only 3 out of 32 cases. Colorectal tumorigenesis proceeds by the accumulation of genetic alterations, including K-ras mutations and inactivation of tumor suppressor genes on the 5q, 17p and 18q regions. Our data indicate that, although gastric and colorectal neoplasias share common genetic alterations, they probably progress through different pathways.

Base transitions are the most frequent genetic changes at P53 in gastric cancer

We searched for P53 mutations in gastric carcinoma by analyzing tumor DNAs from 29 patients. We detected 13 different somatic mutations in 15 patients (52%) and a biallelic polymorphism in exon 6 (5 heterozygous subjects). The somatic mutations were mainly localized in the sequences corresponding to the highly conserved domains of the protein. Twelve samples showed a single base change: 11 missense and 1 nonsense mutations. Three samples showed deletions leading to a frame shift, to the in-frame loss of 2 amino acids, and to the deletion of a splicing site. All point mutations, except one, were transitions, and 91% of them were G:C-->A:T changes. We previously analyzed this panel of tumors for allelic loss at the 17p13 chromosomal region, where the P53 gene had previously been located: the results showed an increasing incidence of allelic loss in late-stage tumors. On the contrary, in the present study no trend between P53 mutations and tumor stages was found. This observation indicates that mutation events precede allelic loss in gastric cancer. Half (54%) of the mutations occurred in samples without allelic loss, suggesting that specific mutated alleles, acting in a dominant negative fashion, can alter in vivo the P53 protein function.

DNA amplification in human gastric carcinomas

We recently identified a genomic domain at chromosome 10q26 that is highly amplified in the gastric carcinoma cell lines KATO III and SNU-16 and contains the BEK/K-sam gene, which encodes several growth factor receptors. A contiguous segment of 200 kb spanning this gene was amplified in five of 139 (3.6%) primary gastric carcinomas, all of them classified as poorly differentiated tumors. There was no amplification of this genomic region in a variety of other solid tumors. The overall frequency of gene amplification among the gastric carcinomas rose to 19.4% when MYC, ERBB2, and INT2 were included in the analysis, with significant association with advanced tumor stage. Amplification of various genomic regions in solid tumors may be more frequent than previously estimated.

Detection of K-ras mutations by denaturing gradient gel electrophoresis (DGGE): a study on pancreatic cancer

In pancreatic neoplasias mutations in the first exon (codon 12) of K-ras gene occur at high frequency and seem to have a diagnostic significance. We set up the DGGE conditions to search for these mutations in pancreatic tumor sample DNAs. All samples were directly classified by simply comparing their DGGE patterns with those of control cell lines carrying known K-ras base substitutions. We found a mutation frequency of 73% in pancreatic adenocarcinoma, whereas no mutations were observed in benign lesions. The non-isotopic method we used turned out to be rapid and sensitive. DGGE could therefore be utilized for the detection of K-ras mutations in pancreatic lesions, to evaluate their actual or potential malignancy. In general, DGGE could be useful for K-ras gene screening on pathological tissue samples.

DNA sequences amplified in cancer cells: an interface between tumor biology and human genome analysis

There is growing evidence that amplification of specific genes is associated with tumor progression. While several proto-oncogenes are known to be activated by amplification, it is clear that not all the genes involved in DNA amplification in human tumors have been discovered. Our approach to the identification of such genes is based on the 'reverse genetics' methodology. Anonymous amplified DNA fragments are cloned by virtue of their amplification in a given tumor. These sequences are mapped in the normal genome and hence define a new genetic locus. The amplified domain is isolated by long-range cloning and analyzed along three lines of investigation: new genes are sought that can explain the biological significance of the amplification; the structure of the domain is studied in normal cells and in the amplification unit in the cancer cell; attempts are made to identify molecular probes of diagnostic value within the amplified domain. This application of genome technology to cancer biology is demonstrated in our study of a new genomic domain at chromosome 10q26 which is amplified specifically in human gastric carcinomas.

A 5'-truncated c-myc gene variant not associated with a risk of cancer

By analyzing c-myc specific fragments from white blood cell DNAs of 98 gastric cancer patients and 46 control subjects, we observed 6 unexpected patterns due to presence of a variant c-myc gene in addition to the normal gene. Restriction enzyme mapping indicated that the variant c-myc gene was the result of a 5' deletion including the first exon and part of the first intron. The deleted region, non-coding for the functional c-myc protein, contains sequences involved in the regulation of transcription. We therefore analyzed the c-myc mRNAs from a subject carrying the truncated gene and from a subject homozygous for the normal gene in Northern blotting experiments: the mRNAs were indistinguishable, both qualitatively and quantitatively. Family analysis demonstrated that the truncated gene is inherited in a Mendelian fashion. Population studies showed that the allele, both in patients and in control subjects, reaches a polymorphic frequency (2.1% for the whole sample) and that it is not associated with a risk of cancer.

Heterogeneous protooncogene amplification correlates with tumor progression and presence of metastases in gastric cancer patients

In order to evaluate the relevance of protooncogene alterations in gastric cancer and to specifically relate these alterations to types and stages of the neoplasia, we studied oncogenes of possible interest in gastric tumors with different clinical parameters. Fifty DNAs from primary gastric adenocarcinoma were analyzed, by the Southern blotting technique, for the presence of amplification or rearrangements of seven different protooncogenes: c-myc, c-erbB2, c-Ki-ras, c-Ha-ras, c-N-ras, hst, and c-mos. All the tumors analyzed were histologically classified and staged. Amplification of the following genes was found: c-myc (2 of 50), hst (3 of 50), c-erbB2 (3 of 50), and c-Ki-ras (5 of 50). The simultaneous amplification of hst (3 cases), c-myc (1 of 3), or c-Ki-ras (2 of 3) was observed. Analysis of DNAs from atrophic and metaplastic gastric mucosa (which can be regarded as preneoplastic lesions) of the 10 patients showing gene amplification demonstrated that this was limited to neoplastic cells. Considering protooncogene amplification in general (i.e., involving different genes and occurring to different degrees) and clinical parameters of tumors, we found a statistically significant association between amplification and both tumor progression and presence of metastases. Therefore, at least for the genes analyzed, amplification is a relatively infrequent phenomenon and represents a late event in the temporal development of gastric cancer.

Red cell and serum polymorphisms in the Oltrepò Pavese population (northern Italy)

A sample of about 300 subjects from the Italian population of the Oltrepò Pavese, in Lombardy, was studied for 6 polymorphic genetic markers: ACP1, ADA, ESD, GLO1, PGM1 subtyping and HP. The observed gene frequencies were: ACP1*A = .267, ACP1*B = .697, ACP1*C = .036; ADA*2 = .060; ESD*2 = .119; GLO1*1 = .375; PGM1*1S = .688, PGM1*1F = .095, PGM1*2S = .175, PGM1*2F = .042; HP*1 = .362.

Study of the c-Ha-ras-1 locus polymorphism in an Italian population with high incidence of gastric cancer

The c-Ha-ras-1 proto-oncogene locus is characterized by a restriction fragment length polymorphism resulting from length variation in a variable tandem repetition (VTR) region downstream from the structural part of the gene. The presence of uncommon alleles at this region has been suggested to be an informative marker for the development of different malignancies, including solid tumours. In order to identify possible genetic markers of cancer risk, we studied the c-Ha-ras-1 locus polymorphism in an Italian population characterized by a high incidence of stomach tumours. Gastric cancer patients, some having first-degree relatives affected by the same malignancy, and control subjects were studied. A total of 176 DNAs was analysed by the Southern blotting technique with TaqI restriction enzyme. This yields a fragment containing the sequence of variable length (VTR) and also allows detection of a cleavage site polymorphism. Thirteen different alleles were detected and some new common and rare variants were found. Our results do not provide evidence that the inheritance of any allele may predispose to gastric malignancies. Segregation analysis carried out on 13 patients' families demonstrated, without exception, a Mendelian inheritance of patterns.

Migration pattern and genetic marker distribution of the Afro-American population of Bluefields, Nicaragua

On a sample of the population of mixed African ancestry living in Bluefields, Nicaragua, the pattern of migration and the distribution of red cell and serum genetic markers have been studied. It is concluded that, in spite of a considerable level of internal and external migration, a distinctive genetic structure is maintained by the population. Moreover, a strongly negative assortative mating can be observed between people inhabiting the western and eastern areas of Nicaragua. It is estimated that most, if not all, of the genetic pool of the population is accounted for by a process of admixture between African and Indian peoples.

A study of several red cell enzyme markers in two samples of the Italian population. Report of new CA1 and PGD variant phenotypes

Gene frequencies for 17 red cell enzymatic markers have been determined in two samples of the Italian population (Lombardy and Tuscany regions). A significant difference was found between the two samples for the AK1 and PGM1 systems (AK1*2 .028 and .044, PGM1*2 .254 and .301 in Lombardy and Tuscany respectively). Variant phenotypes, for PEPA, PEPB, CA2, PGM2, PGD and GPT markers, have been observed; some of these are due to new alleles occurring at the CA2 and PGD loci.

Electrophoretic subtyping of phosphoglucomutase locus 1 (PGM1) polymorphism in the Italian and Czechoslovakian populations

About 3,500 subjects from Italy and Czechoslovakia have been analyzed by acid starch gel electrophoresis for the subtyping of PGM1 polymorphism. The Italian sample included three different subgroups, from Northern, Central and Southern Italy. The allele frequencies found in the three groups do not differ significantly from each other; the observed values in the pooled sample are: PGM1S1 = 0.594, PGM1F1 = 0.118, PGM2S1 = 0.231, PGM2F1 = 0.057. In the Czechoslovakian group, which differs significantly from the Italian population, the following allele frequencies were found: PGM1S1 = 0.639, PGM1F1 = 0.118, PGM2S1 = 0.180, PGM2F1 = 0.063. The analysis of 217 families did not show any exception to Mendelian inheritance of the patterns.

Inheritance of rDNA spacer length variants in man

We studied the rDNA spacer length polymorphism in a sample of 121 individuals belonging to families of 2-3 generations. Our data, obtained by restriction pattern analysis of genomic DNA, confirmed the limited and discrete nature of this polymorphism. Using the pattern as a genetic marker, we analyzed the segregation of length variants in the different families and we investigated the possible occurrence of unequal crossing-over events among homologous and nonhomologous rDNA clusters. No direct evidence of recombination in the spacer region that we analyzed emerged from our study. All the differences in the restriction patterns observed among individuals from the same family could be explained as resulting from meiotic segregation. Family data showed a multichromosomal distribution of NTS length variants and demonstrated a direct correspondence between the frequency of a variant in the population and its degree of spreading on the different rDNA clusters.

A study of ten red cell enzymatic markers in the Naples' population. Report of a new GPT variant phenotype

A sample of the population of Naples has been examined for several red cell enzyme markers. About 2,000 newborn have been analyzed for ACP, GLO I, and UMPK; 1,000 of them were also analyzed for PepA and PepB, and 500 for PGM1 and PGM2. In addition about 400 school children have been typed for the PGD and PGP polymorphisms. The observed gene frequencies for the polymorphic systems are: ACPA = 0.293, ACPB = 0.667 and ACPC = 0.040; GLO1 = 0.372; GPT2 = 0.462; UMPK2 = 0.029; PGM21 = 0.279; PGDC = 0.037; PGP1 = 0.953, PGP2 = 0.038 and PGP3 = 0.009. Moreover during the screening of PepA, PepB and GPT markers, some rare alleles have been encountered, one of which, at the GPT locus, has never been reported before. We propose for it the name GPT10.

Subtyping of phosphoglucomutase locus 1 (PGM1) polymorphism in some populations of Rwanda: description of variant phenotypes, "haplotype" frequencies, and linkage disequilibrium data

Some populations of Rwanda (South Twa Pygmies, Hutu, and Tutsi) have been analyzed by acid starch gel electrophoresis for the subtyping of PGM1 polymorphism. The new polymorphic third PGM11 allele, the PGM1(1Twa), which we recently detected in Twa Pygmies from North Rwanda, has not been found in this survey, whereas the rare PGM1(6) allele attains subpolymorphic frequencies in all groups. Comparison between the various populations of Rwanda shows that they differ significantly from each other with the exception of South Twa Pygmies and Tutsi. A relatively low frequency (9.6%) of the PGM1(2S) allele appears to be typical of North Twa Pygmies; a low frequency of PGM1(2F) (1.2%-3.6%) has been found in all these groups but not in the Hutu (6.4%); and a particularly high incidence of the PGM1(1F) allele (the highest so far reported) has been observed in the South Twa Pygmies (20%) and in the Tutsi (18%). The PGM1(1Twa) and PGM1(6) enzymes, which in acid starch gel are not distinguishable, can be clearly differentiated by isoelectric focusing. In addition, the same technique has shown that the rare PGM1(7) allele observed in one Hutu is different from that found at polymorphic frequency in the Japanese and from a rare PGM1(7) allele found in Germany. On the very likely hypothesis that the PGM1(1S), PGM1(1F), PGM1(2S), and PGM1(2F) result from variations at two different polymorphic sites, 1/2 and F/S, within the PGM1 structural gene, all the available population data have been analyzed to investigate whether preferential combinations (haplotypes) were identifiable. Whereas Caucasians show a prevalence of 2F and 1S combination with an 8.02% mean value of linkage disequilibrium expressed as % Dmax, from the very few and scattered African data, it is impossible to draw any inference at present.