Three different mutations in codon 61 of the human N-ras gene detected by synthetic oligonucleotide hybridization

From Ras to Rap and Back, a Journey of 35 Years

Our laboratory has studied Ras and Ras-like proteins since the discovery of the Ras oncogene 35 years ago. In this review, I will give an account of what we have done in these 35 years and indicate the main papers that have guided our research. Our efforts started with the early analysis of mutant Ras in human tumors followed by deciphering of the role of Ras in signal transduction pathways. In an attempt to interfere in Ras signaling we turned to Rap proteins. These proteins are the closest relatives of Ras and were initially identified as Ras antagonists. However, our studies revealed that the Rap signaling network primarily is involved in spatiotemporal control of cell adhesion, in part through regulation of the actin cytoskeleton. More recently we returned to Ras, trying to interfere in Ras signaling by combinatorial drug testing using the organoid technology.

Therapeutic Approaches to RAS Mutation

The study of oncogenic RAS mutations has led to crucial discoveries regarding cancer molecular biology and behavior and has been integral in shaping the era of targeted cancer therapy. RAS mutations are one of the most common oncogenic drivers in human cancer, and intense efforts to find a clinically effective inhibitor are ongoing. Despite these efforts, targeting RAS mutations has remained elusive, so much so that some have termed oncogenic RAS mutations as "undruggable." In this review, we will summarize current understanding of RAS biology, explore strategies to inhibit RAS oncoproteins and its downstream effectors, and discuss recently described complexities that have shed new light on this pursuit.

RUNX3 and p53: How Two Tumor Suppressors Cooperate Against Oncogenic Ras?

RUNX family members play pivotal roles in both normal development and neoplasia. In particular, RUNX1 and RUNX2 are essential for determination of the hematopoietic and osteogenic lineages, respectively. RUNX3 is involved in lineage determination of various types of epithelial cells. Analysis of mouse models and human cancer specimens revealed that RUNX3 acts as a tumor suppressor via multiple mechanisms. p53-related pathways play central roles in tumor suppression through the DNA damage response and oncogene surveillance, and RUNX3 is involved in both processes. In response to DNA damage, RUNX3 facilitates p53 phosphorylation by the ATM/ATR pathway and p53 acetylation by p300. When oncogenes are activated, RUNX3 induces ARF, thereby stabilizing p53. Here, we summarize the molecular mechanisms underlying the p53-mediated tumor-suppressor activity of RUNX3.

A two-hybrid approach to identify inhibitors of the RAS-RAF interaction

MCP compounds were developed with the idea to inhibit RAS/RAF interaction. They were identified by carrying out high-throughput screens of chemical compounds for their ability to inhibit RAS/RAF interaction in the yeast two-hybrid assay. A number of compounds including MCP1, MCP53, and MCP110 were identified as active compounds. Their inhibition of the RAS signaling was demonstrated by examining RAF and MEK activities, phosphorylation of ERK as well as characterizing their effects on events downstream of RAF. Direct evidence for the inhibition of RAS/RAF interaction was obtained by carrying out co-IP experiments. MCP compounds inhibit proliferation of a wide range of human cancer cell lines. Combination studies with other drugs showed that MCP compounds synergize with MAPK pathway inhibitors as well as with microtubule-targeting chemotherapeutics. In particular, a strong synergy with paclitaxel was observed. Efficacy to inhibit tumor formation was demonstrated using mouse xenograft models. Combination of MCP110 and paclitaxel was particularly effective in inhibiting tumor growth in a mouse xenograft model of colorectal carcinoma.

Rhabdomyosarcomas: an overview on the experimental animal models

Rhabdomyosarcomas (RMS) are aggressive childhood soft-tissue malignancies deriving from mesenchymal progenitors that are committed to muscle-specific lineages. Despite the histopathological signatures associated with three main histological variants, termed embryonal, alveolar and pleomorphic, a plethora of genetic and molecular changes are recognized in RMS. Over the years, exposure to carcinogens or ionizing radiations and gene-targeting approaches in vivo have greatly contributed to disclose some of the mechanisms underlying RMS onset. In this review, we describe the principal distinct features associated with RMS variants and focus on the current available experimental animal models to point out the molecular determinants cooperating with RMS development and progression.

The GTPase TcRjl of the human pathogen Trypanosoma cruzi is involved in the cell growth and differentiation

The protozoan parasite Trypanosoma cruzi, the etiological agent of Chagas Disease, undergoes through a complex life cycle where rounds of cell division and differentiation occur initially in the gut of triatominae vectors and, after transmission, inside of infected cells in vertebrate hosts. Members of the Ras superfamily of GTPases are molecular switches which play pivotal regulatory functions in cell growth and differentiation. We have previously described a novel GTPase in T. cruzi, TcRjl, which belongs to the RJL family of Ras-related GTP binding proteins. Here we show that most of TcRjl protein is found bound to GTP nucleotides and may be locked in this stage. In addition, we show that TcRjl is located close to the kinetoplast, in a region corresponding possibly to flagellar pocket of the parasite and the expression of a dominant-negative TcRjl construct (TcRjlS37N) displays a significative growth phenotype in reduced serum medium. Remarkably, overexpression of TcRjl inhibits differentiation of epimastigotes to trypomastigote forms and promotes the accumulation of intermediate differentiation stages. Our data suggest that TcRjl might play a role in the control of the parasite growth and differentiation.

Inhibition of MEK/ERK signaling induces apoptosis of acute myelogenous leukemia cells via inhibition of eukaryotic initiation factor 4E-binding protein 1 and down-regulation of Mcl-1

We previously showed that the MEK inhibitor AZD6244 induced apoptosis in acute myelogenous leukemia (AML) HL60 cells. However, the mechanisms of AZD6244 to induce apoptosis remain to be fully elucidated. This study found that exposure of HL60 cells to AZD6244 down-regulated the levels of phosphor (p)-4E-binding protein 1 (4E-BP1), a substrate of mammalian target of rapamycin complex 1 (mTORC1), and anti-apoptotic protein Mcl-1. On the other hand, exposure of EOL-1 and MOLM13 cells to AZD6244 failed to induce apoptosis and levels of p-4E-BP1 and Mcl-1 were not down-regulated in these cells. These observations prompted us to hypothesize that down-regulation od 4E-BP1 and Mcl-1 might play an important role in AZD6244-mediated apoptosis. As expected, down-regulation of 4E-BP1 by an siRNA sensitized EOL-1 cells to AZD6244-mediated apoptosis in parallel with down-regulation of Mcl-1. Moreover, we found that blockade of mTORC1 by RAD001 synergistically enhanced the action of AZD6244 in leukemia cells.

Cytotoxic activity of the third-generation bisphosphonate zoledronic acid in acute myeloid leukemia

The third-generation bisphosphonate zoledronic acid (ZOL) has recently been shown to be active against human tumour and leukemic cell lines. The purpose of this study was to evaluate the antileukemic potential of ZOL in acute myeloid leukemia (AML). We determined the lethal concentration 50% (LC 50) using the WST-1 assay of ZOL as being 287.9 microg/ml after 24 h and 108.3 microg/ml after 96 h in HL 60 cells and to be 382.4 and 43.2 microg/ml, respectively, in nine samples from patients with AML. The ZOL induced inhibition of proliferative activity of HL 60 cells could not be abrogated by the hematopetic growth factors G-CSF and GM-CSF. ZOL was found to by cytotoxic in HL 60 cells without activation of caspase 3. ZOL was not cross resistant with cytarabine as shown by the linear correlation of LC 50s. Both agents, however, exerted an additive cytotoxicity as revealed by isobologram-analysis and combination index. These data warrant further investigation of ZOL in the treatment of AML.

Immunophenotypic changes induced on human HL60 leukaemia cells by 1alpha,25-dihydroxyvitamin D3 and 12-O-tetradecanoyl phorbol-13-acetate

1alpha,25-Dihydroxyvitamin D3 (1,25D3) induces HL60 cells to acquire a monocyte-like phenotype, while cells treated with 12-O-tetradecanoyl phorbol-13-acetate (TPA) resemble macrophages. Using a microarray of 82 CD antibodies, 24 cluster of differentiation (CD) antigens were detected on HL60 cells. 1,25D3 induced the following antigens in decreasing order of the change: CD14, CD11c, CD11b, CD54, CD86, CD38 and CD66c, with repression of CD117, CD71, CD95, CD45 and CD64. TPA induced the following antigens in decreasing order of the change: CD11c, CD9, CD11b, CD54, CD38, CD45RO and CD66c, with repression of CD4, CD117, CD95, CD71 and CD64. The results presented provide a basis for monitoring differentiation therapy of myeloid leukaemias in patients.

RJLs: a new family of Ras-related GTP-binding proteins

The Ras superfamily of GTP binding proteins encompasses several gene families that regulate a plethora of events in the eukaryotic cell. Here we describe a novel branch of this superfamily which we have named RJLs. These are present in many unicellular organisms and also in deuterostomes but apparently missing in some intermediary phyla, suggesting an intriguing possibility of lateral gene transference between lower and higher eukaryotes. RJLs lack classical membrane targeting signals and the conserved glutamine residue that coordinates GTP hydrolysis in other proteins from the Ras superfamily. Interestingly, chordate orthologues are chimeras fused to "J" domains in their C-terminal, suggesting that these proteins recruit Hsc70 to specific sites in the cell. Expression analysis of RJLs from chordates suggests predominant expression in nervous tissues, possibly reflecting a role for RJLs in the development or maintenance of the sophisticated chordate nervous system.

Retroviral insertional mutagenesis: tagging cancer pathways

Slow transforming retroviruses, such as the Moloney murine leukemia virus (M-MuLV), induce tumors upon infection of a host after a relatively long latency period. The underlying mechanism leading to cell transformation is the activation of proto-oncogenes or inactivation of tumor suppressor genes as a consequence of proviral insertions into the host genome. Cells carrying proviral insertions that confer a selective advantage will preferentially grow out. This means that proviral insertions mark genes contributing to tumorigenesis, as was demonstrated by the identification of numerous proto-oncogenes in retrovirally induced tumors in the past. Since cancer is a complex multistep process, the proviral insertions in one clone of tumor cells also represent oncogenic events that cooperate in tumorigenesis. Novel advances, such as the launch of the complete mouse genome, high-throughput isolation of proviral flanking sequences, and genetically modified animals have revolutionized proviral tagging into an elegant and efficient approach to identify signaling pathways that collaborate in cancer.

A more accurate detection of codon 72 polymorphism and LOH of the TP53 gene

The polymorphism at codon 72 of the TP53 gene has been extensively studied for its involvement in cancerogenesis and loss of heterozygosity (LOH) detection. Usually, the exon 4 of the TP53 gene is amplified by polymerase chain reaction (PCR) on DNA extracted from blood and tumor tissues, then digested by AccII. In the case of heterozygosity, the comparison of AccII profile from blood and tumor DNA PCR products allowed the identification of a potential LOH in the TP53 locus. This method can be hindered by a partial AccII digestion and/or DNA contamination of non-tumor cells. To circumvent these problems, we have developed a new approach by using the AccII restriction site between exon 4 and exon 6. The PCR amplification of exon 4-6, followed by AccII digestion allowed us to detect without ambiguity any LOH case.

A homogeneous europium cryptate-based assay for the diagnosis of mutations by time-resolved fluorescence resonance energy transfer

Oligonucleotide ligation assay (OLA) is considered to be a very useful methodology for the detection and characterization of mutations, particularly for clinical purposes. The fluorescence resonance energy transfer between a fluorescent donor and a suitable fluorophore as acceptor has been applied in the past to several scientific fields. This technique is well adapted to nucleic acid analysis such as DNA sequencing, DNA hybridization and polymerase chain reaction. We describe here a homogeneous format based on the use of a rare earth cryptate label as donor: tris-bipyridine-Eu(3+). The long-lived fluorescence of this label makes it possible to reach a high sensitivity by using a time-resolved detection mode. A non-radiative energy transfer technology, known as time-resolved amplification of cryptate emission (TRACE((R))) characterized by a temporal and spectral selectivity has been developed. The TRACE((R)) detection of characterized single nucleotide polymorphism using the OLA for allelic discrimination is proposed. We demonstrate the potentialities of this OLA-TRACE((R)) methodology through the analysis of K-ras oncogene point mutations.

Identification of expressed genes by laser-mediated manipulation of single cells

We describe a rapid noncontact method for the capture of single cells or small tissue areas of any size or shape directly within the cap of a common microfuge tube. Prior to the laser-mediated transfer, the specimen is isolated by laser microbeam microdissection, forming a clear-cut gap around the selected area. Laser treatment does not impair subsequent RNA analysis. We have used this method to isolate a single cell from archival colon adenocarcinoma, and were able to detect point mutations within codon 12 of c-Ki-ras2 mRNA after nested RT-PCR analysis.

Lack of correlation between in vitro and in vivo replication of precisely defined benz-a-anthracene adducted DNAs

Like other polycyclic aromatic hydrocarbons, certain metabolites of benz[a]anthracene have been implicated as potent carcinogens. These effects are thought to be caused by the covalent binding of these species to nucleophilic groups on the bases of DNA. To address the molecular mechanisms by which these molecules induce mutations, this study employed oligonucleotides containing four site-specific N6 adenine-benz[a]anthracene diol epoxide adducts. Using a prokaryotic in vivo replication system, we have shown that both non-bay region anti-trans-benz[a]anthracene adducts are essentially nonmutagenic. In contrast, the bay region anti-trans-benz[a]anthracene lesions do induce point mutations at the adduct site. The mutagenic frequency of these bay region lesions is dependent on the stereochemistry about the adduct-forming bond, as well as the strain of Escherichia coli in which they are replicated. The ability of the bacterial replication machinery to bypass the lesions does not correlate with the differences observed in their mutagenesis. While both non-bay region adducts are readily bypassed in vivo, the bay region adducts are both blocking to approximately the same degree. In vitro studies of the interactions of E. coli DNA polymerase III with these adducts have also been undertaken to further dissect the relationship between adduct structure and biological activity.

Advanced multiplexed analysis with the FlowMetrixTM system

The FlowMetrixTM System is a multiplexed data acquisition and analysis platform for flow cytometric analysis of microsphere-based assays that performs simultaneous measurement of up to 64 different analytes. The system consists of 64 distinct sets of fluorescent microspheres and a standard benchtop flow cytometer interfaced with a personal computer containing a digital signal processing board and Windows95®-based software. Individual sets of microspheres can be modified with reactive components such as antigens, antibodies, or oligonucleotides, and then mixed to form a multiplexed assay set. The digital signal-processing hardware and Windows95-based software provide complete control of the flow cytometer and perform real-time data processing, allowing multiple independent reactions to be analyzed simultaneously. The system has been used to perform qualitative and quantitative immunoassays for multiple serum proteins in both capture and competitive inhibition assay formats. The system has also been used to perform DNA sequence analysis by multiplexed competitive hybridization with 16 different sequence-specific oligonucleotide probes.

H-ras oncogene point mutations in arthritic synovium

OBJECTIVE

To examine mutational activation of ras proto-oncogenes in synovial tissue from patients with rheumatoid arthritis (RA) compared with synovial specimens from patients with osteoarthritis (OA) or other arthropathies. Synovial samples from cadavers, without any signs of joint disease, were used as control material.

METHODS

Using a combination of polymerase chain reaction (PCR) and automated sequencing of the amplified PCR product, regions around codons 12, 13, and 61 of the H-, K-, and N-ras proto-oncogenes were analyzed. Confirmation of mutations was based on restriction fragment length polymorphism analysis and/or oligonucleotide hybridization.

RESULTS

Four (6%) of 72 patients with RA, 2 (13%) of 16 with OA, and 1 (8%) of 12 with other arthropathies harbored mutant H-ras proto-oncogenes, and were heterozygous at codon 13 for the GGT-->GAT (Gly-->Asp) change. An unexpected mutation was found in the H-ras gene, in which a heterozygous GTG-->ATG (Val-->Met) mutation was observed over codon 14. The incidence for this mutation was 39% (28 of 72) in RA patients, 94% (15 of 16) in OA patients, and 42% (5 of 12) in patients with other arthropathies. All samples carrying the codon 13 mutation of H-ras were also codon 14-mutated, i.e., double mutations existed. Identical point mutations were also detected in a few synovial specimens obtained from cadavers (n = 8), including a single case of double mutation. All specimens showed normal K- and N-ras loci.

CONCLUSION

Activation of proto-oncogene H-ras by point mutation in codons 13 and 14 occurred in the synovial tissue of patients with RA, OA, or other arthropathies, as well as, to some extent, in the control synovia, indicating that the phenomenon is not specific for RA. In codon 14, incidence of the H-ras point mutation was highest in OA tissue. The possible significance of this codon 14-mutated H-ras gene needs to be clarified.

Ras p21 protein immunoreactivity and its relationship to p53 expression and prognosis in gallbladder and extrahepatic biliary carcinoma

Ras oncogene mutation is found in many human malignancies. The ras family of genes consists of three functional genes which encode highly similar, guanine nucleotide-binding, proteins (p21) of 21kDa, with GTPase activity. The p21 protein is present on the inner aspect of the plasma membrane of a variety of cells. Using a polyclonal antibody, pan-ras p21 (Oncogene Science), the immunohistochemical expression of the ras oncogene in human gallbladder adenocarcinoma (n = 13) and dysplasia (n = 3), chronic cholecystitis (n = 11), common bile duct carcinoma (n = 6), together with ampullary carcinoma (n = 8) and carcinoma in situ (CIS) (n = 3), was examined. A statistically significant difference in ras p21 immunoreactivity between gallbladder cancers and chronic cholecystitis (P = 0.032; chi 2 test) was demonstrated. Strong ras p21 immunoreactivity was present in most gallbladder carcinomas (n = 8; 62%) but not in the cases of gallbladder dysplasia (n = 1; 33%) or chronic cholecystitis (n = 2; 18%). However, the ras p21 expression was strong in only a minority of the cases of ampullary carcinoma (n = 1; 13%), common bile duct carcinomas (n = 3; 50%), and none of the ampullary CIS, and was not shown to be statistically significant. There was no statistically significant correlation between ras p21 expression and patient survival (r = 0.18, r2 = 0.031, P = 0.56; simple regression analysis), or between ras p21 expression and p53 immunoreactivity (r = 0.13, r2 = 0.017, P = 0.47; simple regression analysis). In conclusion, ras p21 expression is increased in most cases of gallbladder carcinomas with no specific relationship to tumour grade suggesting that it may be important in the development of gallbladder carcinomas but not in its progression. No significant correlation was found between ras p21 expression and p53 immunoreactivity in gallbladder and biliary tract tumours and ras p21 immunoreactivity does not appear to be of any prognostic value. The lower rate of ras p21 overexpression in common bile duct and ampullary carcinomas suggests that these tumours may have a different molecular origin to gallbladder cancers.

Rapid and large-scale method to detect K-ras gene mutations in tumor samples

We have developed a rapid and large-scale method for the detection of K-ras gene mutations in tumors. First, DNA is amplified by an asymmetric PCR; second, the single-strand dinitrophenyl (DNP)-labeled amplified DNA is hybridized specifically to oligonucleotide probes affixed on a tube. Finally, perfectly matched duplexes are easily detected by a monoclonal anti-DNP antibody bearing125I. The usefulness of this technique is illustrated by analyzing K-ras codon 12 mutations in human colorectal samples. This reliable assay procedure can be applied to the rapid screening of virtually any genetic disease caused by previously described point mutations.

12th meeting of the Scientific Group on Methodologies for the Safety Evaluation of Chemicals: susceptibility to environmental hazards

The 12th meeting of the Scientific Group on Methodologies for the Safety Evaluation of Chemicals (SGOMSEC) considered the topic of methodologies for determining human and ecosystem susceptibility to environmental hazards. The report prepared at the meeting describes measurement of susceptibility through the use of biological markers of exposure, biological markers of effect, and biomarkers directly indicative of susceptibility of humans or of ecosystems. The utility and validity of these biological markers for the study of susceptibility are evaluated, as are opportunities for developing newer approaches for the study of humans or of ecosystems. For the first time a SGOMSEC workshop also formally considered the issue of ethics in relation to methodology, an issue of particular concern for studies of susceptibility.

12th meeting of the Scientific Group on Methodologies for the Safety Evaluation of Chemicals: susceptibility to environmental hazards

The 12th meeting of the Scientific Group on Methodologies for the Safety Evaluation of Chemicals (SGOMSEC) considered the topic of methodologies for determining human and ecosystem susceptibility to environmental hazards. The report prepared at the meeting describes measurement of susceptibility through the use of biological markers of exposure, biological markers of effect, and biomarkers directly indicative of susceptibility of humans or of ecosystems. The utility and validity of these biological markers for the study of susceptibility are evaluated, as are opportunities for developing newer approaches for the study of humans or of ecosystems. For the first time a SGOMSEC workshop also formally considered the issue of ethics in relation to methodology, an issue of particular concern for studies of susceptibility.

TP53 mutations in myelodysplastic syndrome

Mutations of the TP53 tumor suppressor gene, contributing to the development and progression of a wide variety of human malignancies, are found in some of the patients with myelodysplastic syndromes (MDS). Previous reports revealed that TP53 mutations were found in 0-25% of patients with MDS and are closely associated with a complex abnormal karyotype including such chromosomal losses as -5/5q-, -7/7q- and/or 17p-, which are known to be frequent in therapy-related leukemias. We have also detected TP53 mutation in 10 (14%) of 70 patients with MDS. All of the mutations were detected at the time of diagnosis, which suggest the TP53 mutation may play a role in the development of MDS. Those patients with a TP53 mutation had a poor prognosis regardless of leukemic transformation or not. The reported mutational spectra of TP53 in MDS and ANLL differ from those of colon and lung cancers. Compared with other hematological disorders, the spectrum of TP53 mutations in MDS and ANLL is assumed to be associated with pathogenic exposure to known or unknown carcinogens, as suggested by the chromosomal findings. Further studies are required to clarify the pathogenesis of this heterogenous disease entity.

Laboratory probing of oncogenes from human liquid and solid specimens as markers of exposure to toxicants

Recent discoveries regarding the mechanistic role of oncogenes and tumor suppressor genes in cancer development have opened a new era of molecular diagnosis. It has been observed repeatedly that genetic lesions serve as tumor markers in a broad variety of human cancers. The ras gene family, consisting of three related genes, H-ras, K-ras, and N-ras, acquires transforming activity through amplification or mutation in many tissues. If not all, then most types of human malignancies have been found to contain an altered ras gene. Because the ras oncogenes actively participate in both early and intermediate stages of cancer, several highly specific and sensitive approaches have been introduced to detect these genetic alterations as biomarkers of exposure to carcinogens. There is also mounting evidence that implicate chemical-specific alterations of the p53 tumor suppressor gene detected in most human tumors. Therefore, it seems a reliable laboratory approach to identify both altered p53 and ras genes as biomarkers of human chronic or intermittent exposure to toxicants in a variety of occupational settings.

Ras oncogene mutations in thyroid tumors: polymerase chain reaction-restriction-fragment-length polymorphism analysis from paraffin-embedded tissues

Ras mutations have been found in thyroid lesions. Different studies have shown different frequencies of mutations among benign and malignant lesions. The presence of point mutations in codons 12 and 13 of the c-K-ras, c-H-ras, and N-ras genes was studied in 58 thyroid lesions (10 nodular goiters, 10 follicular adenomas, and 15 papillary, 10 follicular, and 13 anaplastic carcinomas). DNA was extracted from formalin-fixed paraffin-embedded tissue, and target sequences were amplified in vitro by the polymerase chain reaction. Mutations were detected by the presence of restriction-fragment-length polymorphisms either occurring naturally or introduced artificially by the use of mutant primers. No characterization of the mutations was performed. Results were correlated with clinicopathologic features and patient follow-up. One goiter showed a mutation at codon 13, c-K-ras. All follicular adenomas, including three hyalinizing trabecular adenomas, were negative. Four papillary carcinomas presented mutations (one at codon 13, c-K-ras; three at codon 12, N-ras). Two follicular carcinomas showed mutations at codon 12, N-ras. Five anaplastic carcinomas showed mutations (two at codon 12 and two at codon 13, c-K-ras; one at codon 12, N-ras). In summary, the results confirm that ras oncogenes play a role in thyroid tumorigenesis, probably at an early step. Ras mutations appear not to be related to prognosis.

The SKM-1 leukemic cell line established from a patient with progression to myelomonocytic leukemia in myelodysplastic syndrome (MDS)-contribution to better understanding of MDS

Although molecular and cytogenetic studies strongly point to the role of oncogenes, the mechanisms underlying the development of MDS and their progressive evolution to AML are still largely unknown. It has been postulated that AML has a preleukemic stage and a multi step pathogenesis, with the preleukemic stem cell able to undergo clonal evolution, with the acquisition of karyotypic abnormalities, leading to the development of acute leukemic subclones. The activations of the ras oncogenes or inactivation of the p53 anti-oncogene by point mutations have been described recently in several cases of MDS as well as AML, suggesting a critical role for these alterations in the development of these myelogenous leukemias. We reported previously establishment of a leukemic cell line, SKM-1, from the patient who initially possessed multiple point mutations of ras genes but lost these mutations during disease progression to myelomonocytic leukemia with acquisition of chromosomal abnormalities involving the p53 anti-oncogene. This process is characterized by genetic instabilities probably due to the failure of their DNA repairment leading to abnormal control of cell proliferation and differentiation. Studying this cell line, SKM-1, is a promising approach to understand the mechanisms of the initiation, disease progression, alterations of DNA repairment, and genetic instability in MDS and myelogenous malignancies.

The proliferation of multiple myeloma colonies (MY-CFUc) in vitro is independent of prognosis and is not associated with mutated N- or K-ras alleles in human bone marrow aspirates

During the period September 1987 to March 1993 the proliferation of myeloma cells as colonies (MY-CFUc) in vitro was examined in bone marrow aspirates from 43 patients with multiple myeloma and two patients with Waldenström's macroglobulinaemia. Twenty-four samples from 45 patients, of whom three were at presentation, four were in complete remission (CR), six had achieved a partial response (PR) and 11 had progressive disease (PD), produced MY-CFUc in vitro. The same bone marrow aspirates or one taken within 2 months of that assessed for MY-CFUc were used in the polymerase chain reaction (PCR). Genomic DNA was analysed for mutations in N- and K-ras by slot blotting of the amplified products from the PCR with 32P-labelled probes and by direct sequencing. No mutations were detected in N- or K-ras proto-oncogenes at codons 12, 13 or 61 in any sample. Eleven of the patients from whom MY-CFUc were produced remain alive with a median survival of 73 months (range 15-75 months). MY-CFUc have been cultured from 19 of these 24 patients on subsequent occasions, of whom nine remain alive. Among patients whose cells did not produce MY-CFUc in vitro at the time of sampling for mutated ras alleles, biopsy samples from four patients have produced MY-CFUc in vitro on subsequent occasions, of whom one patient remains alive. The data show that the proliferation of MY-CFUc in vitro occurred independently of disease status and was not indicative of prognosis. The failure to detect mutated N- or K-ras alleles in any sample suggests that if such mutations were present in the cells which form colonies in vitro they represented less than 0.1% of the tumour burden and did not affect the survival of this group of patients.

Polymerase chain reaction-based methods for the detection of mutations in oncogenes and tumor suppressor genes

Altered expression of oncogenes and tumor suppressor genes, the normal function of which is to regulate cell growth and differentiation, represents a central event in the pathogenesis of human cancer. Aberrant expression of these genes is often a result of a mutational event. In vitro amplification of DNA with the polymerase chain reaction (PCR) has enormously increased the sensitivity of the methods to detect mutations. These PCR-based techniques have thus become invaluable in the elucidation of the mechanisms of carcinogenesis as well as in molecular genetics. In addition, the precise definition of a mutation at the molecular level can be a very valuable adjunct to the diagnosis and classification of malignancies as well as to their prognostic assessment. In this article several PCR-based strategies are outlined, their applicability in the detection of different types of mutations is discussed, and finally the application of these techniques in fresh and archival tissues is presented.

Allele loss and point mutation in codons 12 and 61 of the c-Ha-ras oncogene in carcinogen-transformed human breast epithelial cells

There is significant evidence that the ras oncogene plays a role in experimental mammary carcinogenesis; the evidence in human breast cancer, however, is more limited. We induced the expression of transformation phenotypes in the human breast epithelial cell line MCF-10F with the chemical carcinogens 7,12-dimethylbenz[a]anthracene, N-methyl-N-nitrosourea, N-methyl-N-nitro-N'-nitrosoguanidine, and benzo[a]pyrene. This work was designed to clarify whether chemically induced neoplastic transformation correlates with alterations in the ras gene. MCF-10F cells have two c-Ha-ras alleles, identified by 1.0-kb and 1.2-kb restriction fragments. Treatment with carcinogens resulted in the loss of one of the alleles (1.0 kb). Polymerase chain reaction-amplified DNA from all carcinogen-treated cells was analyzed for point mutations in c-Ha-ras at codons 12 and 61. All of the carcinogens induced a mutation of the remaining allele at the first position of codon 12 (GGC-->AGC). Another frequent mutation occurred at the first position of codon 61 (CAG-->GAG). The changes in c-Ha-ras were associated with the emergence of colony formation in agar-methocel, but no specific changes in this gene correlated with the emergence of invasiveness or tumorigenesis, indicating that other genes may be involved in the process.

K-ras oncogene codon 12 point mutations in testicular cancer

A significant association between N-ras oncogene activating point mutations and testicular cancer has recently been reported. We have studied DNA samples from the blood and fresh tumor tissues of 17 Norwegian testicular cancer patients (11 seminomas/6 nonseminomas). Point mutations in K-ras-2 and N-ras exons 1 and 2 were studied by denaturing gradient gel electrophoresis (DGGE) and by oligonucleotide hybridization. No N-ras mutations were detected in these tumor samples, but two K-ras-2 exon 1 mutations were found in two of the seminoma tumors (stage I and II tumors) using the DGGE technique. The mutations were confirmed by dot blotting and oligonucleotide hybridization and identified as a G-->T and a G-->A point mutation in K-ras-2 codon 12, leading to a valine and a serine substitution, respectively. All the white blood cell DNAs were negative. As a positive control for DGGE screening, we ran two plasmid constructs carrying human N-ras exon 2 sequences with mutations. To study the role of ras gene activation in testicular cancer, a larger tumor sample population will be investigated.

Separation of transforming N-ras mutations in codons 12, 13 and 61 by denaturing gradient gel electrophoresis: investigation based on a set of phagemid constructs

In the present study we have introduced 19 activating base pair substitutions into N-ras cDNA by use of an in vitro site-directed mutagenesis system. Six mutants were constructed for N-ras codon 12 (exon 1), six for codon 13 (exon 1), and seven for codon 61 (exon 2). Fifteen out of 19 PCR-amplified mutation sequences showed a clear separation from the wild type on denaturing gradient gel electrophoresis runs as homoduplex band, and the rest could be separated after heteroduplex formation with wild-type DNA. These constructs can be used as controls in many screening systems for analyzing activating point mutations of the N-ras gene.

Genetic analysis using polymerase chain reaction-amplified DNA and immobilized oligonucleotide probes: reverse dot-blot typing

The reverse dot-blot method is a simple and rapid diagnostic procedure that allows screening of sample for a variety of mutations/polymorphisms in a single hybridization reaction. Several methods of immobilizing the oligonucleotide probes are discussed. The reverse dot-blot method has several unique properties that are valuable in a diagnostic setting: (1) the typing results from a single sample can be located on a single strip. This facilitates scanning and interpretation of the probe reactivity patterns and minimizes the potential for user error. (2) The test can utilize premade typing strips. This minimizes user labor as well as error potential and allows the use of standardized reagents. (3) Unlike dot-blot/oligonucleotide typing, only the PCR product is labeled, eliminating the potential problem of probes labeled to different specific activities. This method has already been used in the areas of forensic genetic typing (the HLA-DQ alpha Amplitype test), tissue typing for transplantation (the HLA-DR beta) test, cystic fibrosis screening, as well as in a variety of research applications.

A sensitive restriction fragment length polymorphism method to detect CAA-->AAA mutations at codon 61 of Ha-ras

A rapid and sensitive assay was developed to detect CAA-->AAA mutations at codon 61 of Ha-ras. The region surrounding codon 61 was amplified by the polymerase chain reaction (PCR) using one primer containing a mismatch at the second position of codon 60. Using this primer creates an Msel restriction enzyme site if codon 61 carries the C.G-->A.T transversion. An aliquot of the second PCR primer was 5'-end-labeled with 32P to increase the sensitivity of detection of the PCR product. After cleavage with Msel, DNA was electrophoresed on a nondenaturing polyacrylamide gel, and the products were visualized by autoradiography. The sensitivity of this assay was such that the mutation could be detected when present in only one of 200 alleles. DNA samples from spontaneous Crl:CD-1(ICR)BR mouse liver tumors were analyzed using this method. Nine of 38 samples contained the mutation, and in one of those nine, the mutation had not been previously detected by either direct sequencing of tumor DNA or by sequencing the DNA from NIH 3T3 cells transfected with the tumor DNA.

Simultaneous detection of two cystic fibrosis alleles using dual-label time-resolved fluorometry

A simple dual-label hybridization test for normal and mutant cystic fibrosis (CF) alleles is described. The assay is based on time-resolved fluorometry (TRF), which allows the simultaneous detection of DNA probes labelled with different lanthanides from one hybridization reaction. DNA was liberated from dried blood disks, normally used in neonatal screening programmes, by boiling in alkaline solution. A 138 bp region including the site of deletion, delta F-508, which is present on about 70% of cystic fibrosis chromosomes, was amplified using the polymerase chain reaction (PCR). The presence or absence of normal and mutant alleles was then determined in a solution hybridization using allele specific oligonucleotide probes labelled either with europium (Eu) or with samarium (Sm) chelates. A common biotinylated probe was used for binding the hybrids onto microtitration wells coated with streptavidin. Some 5 x 10(7) molecules of the normal allele (Eu) and 5 x 10(8) molecules of the mutant allele (Sm) could be detected simultaneously in a single hybridization reaction. The assay was simple to perform and made it possible to reduce the number of hybridizations needed to interpret the sample as being normal, carrier or mutant with regard to the mutation, delta F-508.

PCR regimen for enhanced specificity and yield of targeted genomic DNA sequences: ras and p53

By weighting the PCR reaction in favor of specificity for the target sequence in the beginning cycles and for continued efficient amplification of the sequence into later cycles, we were able to show an improvement in the specificity and quantity of amplified ras and p53 sequences. Increased purity and yield of specific products favorably enhanced post-PCR evaluation and interpretation of results using direct sequencing and single-stranded conformation polymorphism (SSCP) analysis when point mutations were present in DNA from tumor cell lines and tissues.

Detection of allele-specific expression of N-RAS oncogenes in human leukaemia cells

We report analysis of allele-specific expression of N-RAS transcripts in myeloid leukaemic cells and cell lines. Expression was assessed by an assay of reverse-transcription/PCR combined with differential hybridization with mutation-specific oligonucleotides. In cells from all patients with acute myeloid leukaemia (AML) and in myeloid cell lines HL-60 and THP-1, expression of both the wild-type allele and the abnormal allele altered by a point mutation could be detected, albeit not always at comparable levels. This might be due for instance to allelic exclusion. The assay described provides a means of analysing the degree of expression of dominant oncogenes.

Molecular genetic study showing that the IN/157 'oligodendroglioma' cell line has been contaminated by rhabdomyosarcoma (RD) cells

The IN/157 cell line was originally isolated from a human oligodendroglioma biopsy and has been used in recent years to study aspects of glioma cell biology. We established that IN/157 cells carry a relatively infrequent mutation at position three of codon 61 of the N-ras gene, suggesting that such a mutation may have contributed towards the genesis of the original tumour. However, the mutation was not detectable within the original paraffin-embedded glioma biopsy from which the cell line was supposedly derived. We thus considered the possibility that the cells had been contaminated by another cell line and, by means of DNA fingerprinting, have demonstrated that the contaminating cell line is the rhabdomyosarcoma line RD. We feel that this study makes several important points regarding experiments which make use of cell lines. We discuss the possible implications of contamination events with regard to erroneous conclusions about the biology of the cell lines and tumour types from which they supposedly derive. We also suggest ways in which future contamination-related errors can be minimized.

An S5 self-incompatibility allele-specific cDNA sequence from Brassica oleracea shows high homology to the SLR2 gene

The sequence is reported of a cDNA molecule homologous to an mRNA from stigma tissue of Brassica oleracea plants homozygous for the S5 self-incompatibility allele. This cDNA is closely related to a previously published sequence designated SLR2, which was obtained from the same stigma cDNA library and is also related to the SLR1 gene, a cDNA for which has also been obtained from this library. Various B. oleracea lines differing in S alleles and of different varieties have been screened for the presence of particular S gene family sequences using a method involving hybridization of sequence-specific oligonucleotide probes to PCR products. The results indicate that a gene homologous to the sequence presented here is absent from a line lacking the S5 allele, though present in other lines containing the S5 allele, regardless of their genetic background. This finding suggests that the sequence represents a transcript of the SLG (S locus glycoprotein) gene. A similar approach has confirmed that a cDNA derived from a Brassica line containing the S29 allele is also S allele-specific. The predicted amino acid sequences derived from a number of S gene family sequences are compared using numerical methods and possible evolutionary relationships between them are discussed.

Invasive human fibrosarcoma DNA mediated induction of a 92 kDa gelatinase/type IV collagenase leads to an invasive phenotype

Proteolytic enzymes, such as gelatinase/type IV collagenase, play a pivotal role in cancer invasion and metastasis. Invasive human fibrosarcoma cells (HT1080) secrete two species of gelatinase/type IV collagenase, 68-72 kDa and 92 kDa enzymes. The purpose of this study is to elucidate which species of gelatinase/type IV collagenase plays a more important role in invasion. We have found that HT1080 x human fibroblast hybrids have reduced ability to invade a reconstituted basement membrane (Matrigel) in vitro compared to HT1080 cells, and abundantly secrete only the 68-72 kDa gelatinase/type IV collagenase. These data suggest that the 92 kDa gelatinase/type IV collagenase may be more important in HT1080 cell invasion. We next transfected HT1080 genomic DNA into non-invasive mouse C3H/10T1/2 fibroblast cells, which secrete only 68-72 kDa gelatinase/type IV collagenase. Four invasive transfectants were established. These invasive transfectants secreted the 92 kDa gelatinase/type IV collagenase in addition to the 68-72 kDa gelatinase/type IV collagenase, whereas non-invasive control DNA transfectants did not secrete the 92 kDa gelatinase/type IV collagenase. These results suggest that the induction of the 92 kDa gelatinase/type IV collagenase is important in the invasive phenotype.

Mutation detection

The detection and characterization of mutations in genes has become a major area of interest in many areas of biology. Such variation may account for speciation, tumour formation, drug resistance, as well as the more obvious nature of inherited disease.

Rat model of the human "Triton" tumor: direct genetic evidence for the myogenic differentiation capacity of schwannoma cells using the mutant neu gene as a cell lineage marker

Spontaneous myogenic differentiation was observed in 2 out of 15 cases when cells from schwannomas induced in the offspring of BDIX rats by transplacental exposure to N-ethyl-N-nitrosourea (EtNU) were grown in monolayer culture following fluorescence-activated cell sorting with monoclonal antibody (Mab) 217c. Myotubes and numerous mononucleated cells no longer expressed the Schwann cell antigens 217c and S-100 protein, but rather revealed the presence of desmin, the alpha-sarcomeric form (alpha-sr) of actin, and the cell surface antigen specified by Mab RB21-7, a 250 kD glycoprotein sharing an epitope with the neural cell adhesion molecule (N-CAM). Subcutaneous reimplantation of such cells into syngeneic animals led to the appearance of tumors composed of both S-100 positive Schwann cells and desmin and alpha-sr-actin positive rhabdomyoblasts, thus closely resembling the human "Triton" tumor. With the use of the polymerase chain reaction and allele-specific oligonucleotide hybridization, DNA isolated from individual myotubes was analyzed for the presence of a T----A transversion mutation at nucleotide 2012 of the neu gene, which is diagnostic of EtNU-induced rat schwannomas. All of the amplified DNA isolates contained the mutant neu allele, thus providing direct genetic proof for the capacity of mammalian neuroectodermal cells for myogenic differentiation.

Cytogenetic and cellular characteristics of a human embryonal rhabdomyosarcoma cell line, RMS-YM

A human tumour cell line, designated RMS-YM, was established from a childhood rhabdomyosarcoma. The monolayer cells were polygonal, round or spindle-shaped. The cells became multilayered and formed many focal piles when confluent. RMS-YM became stable with a doubling time of about 30 h and has been maintained for 104 passages to date. Tumourigenicity of the cells was confirmed by heterotransplantation into nude mice. Morphological features were similar to those of the primary tumour, and myofibrils were found by electron microscopy. The expression of desmin and human myoglobin, and high levels of striated muscle system specific enzymes were recognised. Chromosomal analysis revealed possible gene amplification in the form of homogeneously staining regions. Oncogene analysis was performed on the primary tumour and the cell line, but neither N-myc nor N-ras genes were amplified, nor were Ki-ras, Ha-ras or N-ras genes mutated at the 12th, 13th and 61st codons. The RMS-YM cell line may provide a system to identify novel genes which are amplified in rhabdomyosarcoma.