Detection of minimal residual cells carrying the t(14;18) by DNA sequence amplification

Use of the polymerase chain reaction to detect hypermethylation in the calcitonin gene. A new, sensitive approach to monitor tumor cells in acute myelogenous leukemia

Based on the recent observations that, in a majority of patients with acute leukemia, the 5' end of the calcitonin gene was hypermethylated and abnormal DNA fragments were observed following HpaII restriction digestion, we have developed a PCR-based method to sensitively detect this abnormal methylation of the calcitonin gene in AML. Applying the concept of competitive PCR, a semi-quantitative correlation was obtained between the amount of hypermethylation and the amount of leukemic cells present. These results suggest that this method will be useful to monitor the amount of tumor cells in bone marrow from patients with AML.

t(2;18) and t(18;22) variant chromosomal translocations in B cell malignancies

Variant translocations (2;18 and 18;22) are described in this review. The chromosomal and molecular findings of these translocation of BCL2 and their effect on possible BCL2 gene activation is discussed. Unanswered questions still remain and these include why this is so rare compared to the 25% incidence recorded for translocations in Burkitt's lymphoma. Further studies are obviously still needed in order to determine the true frequency of these findings and their distribution in the various B-cell disorders.

Using the polymerase chain reaction to estimate mutation frequencies and rates in human cells

The Polymerase Chain Reaction (PCR) has had a significant impact on molecular studies of human mutagenesis, mainly in the acceleration of molecular characterisation of mutant genes in cells isolated by a phenotypic selection. PCR can also be used to study genetic alterations in cells which have not undergone phenotypic selection. By modifying the standard PCR parameters, the presence of mutations can be assayed in single human cells, creating the potential to determine mutation rates in gametes on a cell-by-cell basis (Section I). Alternatively, PCR can be used to selectively amplify a mutant gene in a pool of normal genomes and thus determine a mutation frequency (Section II). Current applications of these two approaches are summarised and critically reviewed.

Frequency and DNA sequence of tal-1 rearrangement in children with T-cell acute lymphoblastic leukemia

Using nested polymerase chain reaction (PCR) a gene rearrangement named tal-1 deletion was found in five of 56 leukemic bone marrow samples from children with T-cell acute lymphoblastic leukemia (ALL). The DNA sequences of the PCR fragments consisted of the known conserved germline sequences in addition to short DNA insertions at the breakpoint region, which were different in each patient. Moreover, one patient was examined at diagnosis and at relapse 11 months later, revealing identical DNA sequences at the rearrangement site. The recombination site of the tal rearrangement therefore may be used as a genetic marker for detecting minimal residual disease in about 10% of T-cell ALL in childhood.

Molecular biology in medicine

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The polymerase chain reaction and its applications in neuropathology

The polymerase chain reaction (PCR) provides a means of generating large numbers of copies of selected segments of DNA. Once amplified, the DNA can be characterized by determination of its size and sequence. For many applications, routinely-processed biopsy and autopsy material is an adequate substrate for the reaction. PCR can be used to amplify sequences of DNA that are uniquely characteristic of particular micro-organisms, allowing their rapid detection in samples of tissue or cerebrospinal fluid. The technique allows clones of cells with gene rearrangements or translocations to be detected with great sensitivity and is proving a useful way to monitor the effects of tumour therapy, particularly in patients with lymphomas and leukaemias. Further applications include the identification of gene deletions and mutations, and the assessment of cell lineage by amplification and analysis of highly polymorphic gene loci (DNA fingerprinting). Because the degree of amplification resulting from PCR is so great, even a single molecule of contaminating DNa may be detected and its significance misinterpreted. Great care, therefore, should be taken to prevent contamination of samples, particularly by the products of previous reactions, and every series of reactions should include appropriate controls.

Classification and staging of lymphoma by molecular genetics

Recombinant DNA technology has provided a wealth of new observations in the study of lymphoma. Progress has been enhanced by the unique rearrangement of immune-specific genes during normal lymphocyte differentiation. Because these gene rearrangements are irreversible and are inherited in all cellular progeny, lymphoid tumors have a monoclonal genomic structure. Molecular analysis of genomic structure is a powerful new method of assessing clonality and lineage to supplement histologic examination in achieving accurate diagnosis and staging of lymphomas. Furthermore, the frequent occurrence of translocations in lymphoid neoplasms provides a second pathway for genomic analysis. In 57 B-cell lymphomas tested by Southern blot and polymerase chain reaction, the authors found evidence of bc12 gene translocation in 100% of follicular small cleaved cell lymphomas, 67% of diffuse small cleaved cell lymphomas, 33% of mixed lymphomas, 25% of diffuse large cell lymphomas, and 25% of small noncleaved lymphomas. They also describe their experience with immunoglobulin heavy chain and T-cell receptor beta chain genomic analysis as well as review the published literature on the utility of molecular genetics in the classification and staging of lymphoma. Future applications of molecular diagnostics in the clinical management of lymphoma patients are assessed.

Sequence analysis of polymerase chain reaction amplified t(14;18) chromosomal breakpoints in formalin fixed, paraffin wax embedded follicular lymphoma

AIMS

To determine whether junctional sequences of rearranged chromosomes can be amplified by use of the polymerase chain reaction (PCR) and whether direct sequence analysis of the PCR products is possible, using DNA from formalin fixed, paraffin wax embedded biopsy specimens.

METHODS

DNA was extracted from paraffin wax embedded, formalin fixed lymphoma specimens, and junctional sequences of rearranged chromosomes were amplified by the PCR. The products were used as templates for asymmetrical PCR. Subsequently, direct sequence analysis was performed using the chain termination method.

RESULTS

Formalin fixed, paraffin wax embedded biopsy specimens and PCR amplification could be used to determine the nucleotide sequences of junctional regions of rearranged chromosomes t(14;18) from patients with follicular lymphoma.

CONCLUSION

The identification of junctional sequences of the translocation in follicular lymphoma provides a molecular "fingerprint" of t(14;18) of the lymphoma of an individual patient and can be used for the detection of clone specific DNA in any biopsy tissue obtained from the patient. The strategy used for rapid sequence analysis of PCR amplified DNA sequences will be useful in many areas of molecular pathology.

PCR amplification of chromosome-specific DNA isolated from flow cytometry-sorted chromosomes

We have established a method for amplifying and obtaining large quantities of chromosome-specific DNA by linker/adaptor ligation and polymerase chain reaction (PCR). Small quantities of DNA isolated from flow cytometry-sorted chromosomes 17 and 21 were digested with MboI, ligated to a linker/adaptor, and then subjected to 35 cycles of PCR. Using this procedure, 20 micrograms of chromosome-specific DNA can be obtained. Southern blot analysis using several DNA probes previously localized to chromosomes 17 and 21 indicated that these gene sequences were present in the amplified chromosome-specific DNA. A small quantity of the chromosome-specific DNA obtained from the first round of PCR amplification was used to amplify DNA for a second, third, and fourth round of PCR (30 cycles), and specific DNA sequences were still detectable. Fluorescence in situ hybridization using these chromosome-specific DNA probes clearly indicated the hybridization signals to the designated chromosomes. We showed that PCR-amplified chromosome 17-specific DNA can be used to detect nonrandom chromosomal translocation of t(15;17) in acute promyelocytic leukemia by fluorescence in situ hybridization.

Molecular biology in the diagnosis and prognosis of solid and lymphoid tumors

The application of molecular biology to the study of human malignancies has led to tremendous gains in our understanding of their pathogenesis. Although their practical applications are still somewhat limited at this point, the use of molecular diagnostic tools is likely to grow at a very rapid rate as newer and more accurate prognostic markers are identified. The availability of reliable prognostic markers should allow earlier intervention in patients with aggressive disease but exhibiting only limited extent of disease at the time of initial diagnosis. Early intervention in such cases could realistically increase the probability of cure, since highly aggressive tumor cells are more likely to be eliminated by early institution of cytotoxic chemotherapy (4). The p53 tumor suppressor gene clearly represents the most promising potential prognostic marker at present, because of both the multiple phenotypic alterations caused by different p53 mutations and the high frequency of p53 mutations which have been observed in a variety of human cancers. Other prognostic markers related to oncogenes and tumor suppressor genes are almost certain to follow. Validation of new prognostic markers requires a knowledge of both histopathologic diagnostic criteria as well as the consequences for the patient of each diagnosis. There is bound to be some "shake-out" in the field of molecular diagnostics just as there was with other recently introduced techniques such as immunohistochemistry and flow cytometry which were found to provide additional useful information for some tumors and not for others. Since the clinical-pathologic studies needed for verification of putative prognostic markers require relatively long periods of follow up, progress in this area will almost certainly lag behind the ability of molecular biologists to identify new and potentially useful prognostic markers. Our collective ability to reap tangible gains in the clinical arena from our heavy investments in molecular biology and biotechnology depends to a large extent on open channels of communication between clinical and basic scientists. As our ever-increasing insights into oncogenic processes spawn new diagnostic and prognostic markers, our priorities should remain focused on those areas which are inadequately addressed by current methods, and we should avoid the technological trap of devising redundant solutions which increase the expense, but not the efficiency of patient care.

Molecular biology: the polymerase chain reaction

Upper aerodigestive tract (UADT) cancers provide an excellent carcinogenesis model for a number of reasons: they are accessible to observation, are usually associated with a known environmental carcinogen (tobacco by-products), are sometimes associated with a tumorigenic DNA virus (HPV), and fall along a spectrum of progressive disease from normal mucosa through leukoplakia and verrucous carcinoma to invasive and metastatic carcinoma. Despite the presence of this unique model, the field of head and neck oncology, as a whole, has been slow in establishing an efficient 2-way conduit between the bedside and the laboratory. Such open communication is important as current evidence suggests that future staging and therapy of head and neck tumors will depend not only on familiar macroscopic and light microscopic criteria, but also on factors that are currently identifiable only in the basic science laboratory. To have a significant impact on the direction and relevance of basic research, clinicians should become knowledgeable and conversant in the vocabulary and general concepts of basic science. The goal of this section is to facilitate communication between the basic researcher and the clinician, thereby promoting clinically relevant basic research. This is to be achieved by fostering understanding of the power, limitations, scope, and horizons of current basic research concepts and techniques. Subsequent articles will review current research topics germane to head and neck cancer, such as oncogenes and tumor suppressor genes, mechanisms of metastasis, tumor immunology and its modulation, and virology.

How are cancer associated genes activated or inactivated?

Altered behaviour or the transformation of a cell can result from the abnormal expression of some oncogene products. Elevated or inappropriate expression can result from (i) mutations in the regulatory region of the gene, (ii) aberrant expression of a transcription factor involved in the regulation of the gene, (iii) gene amplification, or (iv) the insertion of a viral promoter upstream of the gene. In addition, an alteration in the product of a proto-oncogene can lead to the acquisition of a transforming activity. Such changes have been shown to include (i) point mutation, (ii) deletion, and (iii) the formation of fusion genes. Finally, the loss of activity of a gene product can contribute to transformation. This can come about by (i) small or large deletions, (ii) point mutations which abolish function or expression of an intact protein, or (iii) mutations which lead to a protein with an activity which can inhibit the suppressor activity of the normal allele.

Use of the Polymerase Chain Reaction for the Detection of Tumor Cell Involvement of Bone Marrow and Peripheral Blood: Implications for Purging

Bone marrow purging is being performed increasingly in an effort to deplete residual tumor cells from the graft prior to reinfusion. Several studies have suggested that the removal of tumor cells is an important clinical goal. In this review the utility of the polymerase chain reaction (PCR) for the detection of small numbers of tumor cells in bone marrow and peripheral blood is discussed. Using sensitive assays such as PCR, it is expected that the efficacy of bone marrow purging strategies will be improved and this will hopefully result in decreased relapse rates following autologous bone marrow transplantation.

Specific metaphase and interphase detection of the breakpoint region in 8q24 of Burkitt lymphoma cells by triple-color fluorescence in situ hybridization

Triple fluorescence in situ hybridization with a plasmid DNA library from sorted human chromosomes 8 in combination with bacteriophage clones flanking the breakpoint in 8q24 of the Burkitt lymphoma cell line J1 was used for the specific delineation of this breakpoint in individual tumor cells. With this approach, tumor-specific breakpoints in translocation chromosomes can be detected at all stages of the cell cycle with high specificity.

Comparison of strategies to detect and quantitate uniquely marked cells in intra- and inter-species hemopoietic chimeras

Evaluation of the outcome of successful bone marrow transplantation and indepth studies of transplantation biology rely increasingly upon detection and enumeration of donor hemopoietic cells in the transplanted recipients. The ability to detect and enumerate low levels of donor engraftment in interphase cell subpopulations in hemopoietic chimeras is particularly important for studies of mixed lineage chimerism, early relapse manifestations, and engraftment of subpopulations present at low frequency. We describe and compare the sensitivity and specificity of DNA-based detection strategies (fluorescence in situ hybridization, in vitro DNA amplification using the polymerase chain reaction) and flow cytometric analysis of cell surface markers to detect cells carrying marker DNA or proteins in syngeneic (mouse-to-mouse) and xenogeneic (mouse-to-human, monkey, sheep) backgrounds. DNA-based detection strategies offer advantages of rapid analysis and enumeration of target cell frequencies with detection sensitivities approximating 10(-4). The sensitivity of immunofluorescence-linked flow cytometric-based detection of nucleated leukocytes approached 10(-3), whereas flow cytometric-based detection of fixed human erythrocytes was feasible at cell frequencies of 10(-5). Data described in this manuscript should facilitate selection of appropriate methodologies for assessment of hemopoietic chimerism following transplantation.

Low-grade follicular lymphomas: analysis of prognosis in a series of 281 patients

From 1963 to 1988, 281 patients with newly diagnosed follicular lymphomas were treated and followed at the Foundation Bergonié. Distribution of stages was: 72 I, 61 II, 83 III and 65 IV. Within stage III, two subgroups were retrospectively defined: stages III1 (32 cases) included patients with less than 8 involved sites, only 1 or 2 above diaphragm, and no spleen or mediastinal enlargement. Stage III2 (51 cases) included the remaining stage III cases. Median follow-up was 9 years. Complete remission (CR) rate was 82%. 10-year overall survival (OS) and time to treatment failure (TTF) rates were, respectively 38% and 29.5%. 10-year time to relapse (TTR) rate was 36%. Statistical analyses showed concordant results with two main prognostic factors: age (less than 60/greater than 60) and stage (I to III1/III2 and IV). Age was the most important factor for OS analysis and stage for CR and TTR analysis. This leads to only three prognostic groups with different outcome. The first includes younger patients (less than 60 years) with limited stages (less than or equal to III1); the second, patients either older than 60 or with advanced stages; the last, elderly patients with advanced stages. CR rates of these three groups were, respectively 97%, 75% and 57%. 10-year OS were, respectively 73.5%, 27% and 0%; 10-year TTR were 54%, 22% and 0%. These results have lead to data which are easy to handle and which can help to establish a rationale for further prospective trials.

Molecular monitoring of low grade non-Hodgkin's lymphoma by gene amplification

Molecular monitoring by the polymerase chain reaction was used to detect and follow minimal disease in working formulation category B and C on non-Hodgkin's lymphoma. Rearrangement of the bcl-2 gene served as the target for gene amplification. Thirty patients were studied. Bone marrow histology was compared to PCR analysis of bone marrow aspirate and blood. PCR upstaged disease status in approximately 50% of patients. Results are shown from a patient whose disease was followed with PCR during chemotherapy from initial remission to relapse. We conclude that PCR of bone marrow and blood can be used to upstage disease status in low grade lymphoma and PCR of blood may be used to monitor response to treatment with obvious patient benefit. The general approach of molecular monitoring provides a means for appraising therapies in the setting of subclinical disease.

Immunologic purging of marrow assessed by PCR before autologous bone marrow transplantation for B-cell lymphoma

BACKGROUND

The use of autologous bone marrow transplantation is increasing in the management of advanced cancers. Many investigators have attempted to "purge" autologous marrow of residual tumor cells because of concern that reinfused tumor cells might contribute to relapse. The efficacy of purging remains unproved.

METHODS

We performed clonogenic assays in a tumor cell line in culture to determine the efficiency of immunologic purging. Amplification by the polymerase chain reaction (PCR) was used to detect residual lymphoma cells before and after purging of bone marrow from 114 patients with B-cell non-Hodgkin's lymphoma in whom a translocation (t(14;18] that could be amplified by PCR was detected at the time of their initial evaluation.

RESULTS

Immunologic purging in vitro resulted in a 3-to-6-log destruction of cells in the tumor cell line. Residual lymphoma cells were detected by PCR in the bone marrow of all patients before purging. No lymphoma cells could be detected in the marrow of 57 patients after purging. Disease-free survival was increased in these 57 patients as compared with those whose marrow contained detectable residual lymphoma (P less than 0.00001). The ability to purge residual lymphoma cells was not associated with the degree of bone marrow involvement (P = 0.4494) or the previous response to therapy (P = 0.1298).

CONCLUSIONS

The inability to purge residual lymphoma cells was the most important prognostic indicator in predicting relapse. These results provide evidence of the clinical usefulness of ex vivo purging of autologous bone marrow in the treatment of patients with lymphoma and suggest that the reinfusion of malignant cells in autologous marrow contributes to relapse

Gene amplification by polymerase chain reaction in dermatology

The polymerase chain reaction (PCR) is another new powerful technique in molecular biology that has begun to open new perspectives in modern science and also in dermatology. This brief report will therefore elucidate the general principles of the polymerase chain reaction, as well as its limitations and possible pitfalls. Furthermore an overview will be provided on the impact of PCR on molecular biologic approaches in oncology, immunology, and human genetics. The use of the method as a tool to detect microorganisms particularly viruses and bacteria, in cutaneous tissue and it potential other future applications are described as well. Because PCR is automated and is being more and more established in routine laboratories, physicians and scientists should be familiar with the basic principles and potential uses of this methodology.

The polymerase chain reaction and its potential role in clinical diagnostics and research

In-vitro amplification of deoxyribonucleic acid molecules by means of the polymerase chain reaction (PCR) must be regarded as the most important advance in the life sciences to take place during the last decade. Originally applied to the identification of mutations in well-known and fully sequenced human genes, its applications have now been extended to a wide variety of biological and medical disciplines, accompanied by significant technical improvements and sophisticated variations of the basic principle. Specialized molecular genetics laboratories were the first to employ this new method, and they still are in the process of extending its potential. Due to its unique properties, applications of PCR quickly spread to other areas of research, and numerous clinical studies have already employed PCR. The field is currently still expanding rapidly.

Detection and quantitation of neoplastic cells in acute lymphoblastic leukaemia, by use of the polymerase chain reaction

We report a simple and robust method for sensitive quantitation of leukaemic cells in acute lymphocytic leukaemia. Chain determining region 3 (CDR3) of the immunoglobulin heavy chain gene is a precise genetic marker for a patient's leukaemic clone. Quantitation of the leukaemic lymphocytes was achieved by use of the polymerase chain reaction to detect CDR3 at limiting dilution of DNA samples. Five patients were studied and high levels (1 in 1 to 1 in 10) of leukaemic cells were detected at diagnosis or relapse. Leukaemic cells were detected in remission marrows from three patients, at levels of 1 in 1000 to 1 in 100,000. All five patients showed a 1000 to 100,000-fold reduction in the levels of leukaemic cells after induction therapy. This technique should prove useful for monitoring therapy and may help predict outcome.

Detection of rearrangement of immunoglobulin heavy chain and T-cell receptor beta chain in leukemic cells by restricted polymerase chain reaction

Rearrangement of the immunoglobulin heavy chain and of the T-cell receptor beta subunit was analyzed by using restricted polymerase chain reaction (PCR). To differentiate between the germline configuration and the rearranged genome in a DNA sample extracted from lymphocytes, we compared the ratio of the amplified products. The intensity of amplification of the intron region (JHF) upstream of the first joining region was compared to the intensity of joining region 6 of the immunoglobulin heavy chain. The number of the amplification cycles in the PCR was designated in such a way that the ratio of JHF/JH6 was less than one in the rearranged configuration. As the concentration of clonal B-lymphocytes with the rearranged genome in the sample increased the amplification of the JHF intron proportionally decreased. We used the same approach for the two constant regions of the T-cell receptor beta chain. As one of the intron regions of the constant sequence became depleted by rearrangement so the amplification of the particular region decreased. Therefore, the absence or decreased concentration of a particular product of amplification indicated deletion and thus rearrangement of the genome in the leukemic B- or T-lymphocytes. The threshold of detection of cells with the rearranged genome on a photograph of agarose gel loaded with the particular amplified regions and staining with the ethidium bromide is less than 10% by densitometric tracing and 25-50% by visual evaluation. This novel approach allows the detection of the rearranged DNA sequences in a 2 day span. Hence, it can serve as a diagnostic tool for the identification of clonal expansion of lymphocytes in acute leukemias and lymphomas in particular and for the detection of deleted genomic regions in general.

Goals and rationale of cancer treatment

OBJECTIVE

To provide an overview of the goals and rationale for cancer management.

DATA SOURCES

Primarily the series "Changing concepts in the management of cancer" published in the Journal between December 1987 and September 1990 (see Box).

STUDY SELECTION

Tumour types chosen for the series of articles were those with a high incidence, such as melanoma and tumours of the lung, breast and prostate, or curable tumours, such as acute leukaemias and lymphomas.

DATA SYNTHESIS

Emphasis is placed on primary prevention, with lung cancer related to smoking as a model. Breast cancer serves as a model for secondary prevention and adjuvant therapy. The role of goal setting as the first step in cancer treatment is stressed. Some of the reasons why cure is now possible are discussed, as are criteria for the selection of tumours for adjuvant therapy and indications for starting palliative treatment.

CONCLUSIONS

Cancer cure is no longer a myth but a reality. To overcome present barriers to the cure of some cancers, there is need for a better understanding of the biology of epithelial solid tumours including the mechanisms to overcome multiple drug resistance. The restoration of functional health after cure is attained is paramount. Quality of life as a measure of success should be included in all clinical trials.

Lymphocyte predominance Hodgkin's disease (nodular paragranuloma)--a bcl-2 negative germinal centre lymphoma

Hodgkin's disease, lymphocyte predominance type (nodular paragranuloma), is of germinal centre origin and the tumour cells have a B-cell phenotype. As the T(14;18) translocation, and the subsequent expression of bcl-2 protein by germinal centre cells, is the most characteristic finding of centroblastic-centrocytic lymphoma, we have tested a series of 11 cases of lymphocyte predominance Hodgkin's disease, using Southern blot analysis for the major breakpoint region and the minor breakpoint cluster region, polymerase chain reaction with primers for the major and minor breakpoint cluster region, and immunohistological studies with a monoclonal antibody specific for the bcl-2 protein. All three techniques gave negative results in the cases of Hodgkin's disease, establishing a clear differentiation from centroblastic-centrocytic lymphoma. These findings are useful in the differential diagnosis between the two entities and raise the question of the non-clonal nature of lymphocyte predominance Hodgkin's disease.

Monocytoid B-cell lymphoma: a study of 36 cases

We have studied 36 cases of monocytoid B-cell lymphoma (MBCL). We confirm the predilection for females (30 of 36; ratio, five women to one man). The median age was 65 years (range, 29 to 85 years). Monocytoid B-cell lymphoma characteristically involves peripheral lymph nodes (30 of 36) with a propensity for paraparotid or intraparotid nodes. Salivary glands were affected in five patients. Other extranodal sites of involvement included breast, thyroid, stomach, and soft tissue of chest wall. Eight patients manifested with Sjögren's syndrome, one had systemic lupus erythematosus, one presented initially with Raynaud's phenomenon, and two had a monoclonal gammopathy. "Composite lymphomas" were encountered in seven patients. In addition, association with or progression to a higher-grade lymphoma, ie, mixed small and large cell (one) and large cell (six), was observed in seven patients and was associated with a more aggressive behavior of the lymphoma. Immunohistochemical studies performed on biopsy sections from 20 patients confirmed the B-cell nature of MBCL. An average reactivity of less than 10% of the monocytoid B cells with the proliferation marker Ki-67 was demonstrated, in keeping with the indolent behavior of MBCL. Despite our observation of follicular lymphomas frequently accompanying MBCL, the t(14;18) chromosomal translocation does not appear to play a pathogenetic role for MBCL, as determined by molecular studies for the t(14;18) chromosomal translocation and immunologic studies for the BCL2 protein. Our observations also provide support for the proposal that there is an overlap between MBCL and "MALT lymphomas" (those arising from mucosa-associated lymphoid tissue).

Importance of oncogene research to the cancer clinician

For many years a genetic basis has been postulated for cancers and leukaemias. However, this concept has now been strengthened by the discovery of a group of genes (oncogenes) which are specifically associated with neoplasia. These genes have been identified by studies of animal oncogenic viruses, by in vitro transformation studies of mouse fibroblasts, and by molecular analyses of human tumour cells. The oncogenes are altered forms of normal genes (proto-oncogenes) whose protein products are thought to be involved in the regulation of cell proliferation. It appears that the alteration of proto-oncogenes to form oncogenes results in the inappropriate production of normal proteins or in the production of abnormal proteins. It is suggested, therefore, that the presence of such proteins would allow cells to escape from normal cell growth regulation, and as a result produce uncontrolled proliferation. Oncogene research has to date been primarily concerned with identifying oncogenes and assessing their importance in the development of a number of malignancies. Such research is therefore allowing us to build up a framework of genetic changes which define the development of each type of tumour or leukaemia. Furthermore, information concerning the oncogenes is now beginning to be applied diagnostically to help in determining predisposition of an individual to disease, in aiding the accurate staging of disease, in indicating prognosis and in developing markers to detect residual disease after therapy. It is also possible that in the future we may be able to develop new anticancer therapies, for example, based on oncogene protein inhibitors, or anti-oncogene protein antibodies or even gene therapy.

Altered gene expression and oncogenesis of B-cell neoplasia

B-cell malignancies reveal a number of consistent translocations involving the C-MYC, BCL and IG genes. In common, these rearrangements usually lead to an inability of the involved B-cells to respond to normal regulatory controls for expression of the genes. This usually lead to over-production of the protein products of the genes at inappropriate times of the cell growth cycle and appears to allow a survival advantage to the B-cell. The result of these changes almost certainly plays a prominent role in the development of B-cell neoplasia. Classification of these lymphoma's at a molecular level may be of benefit to determine the prognosis and treatment in addition to providing a useful marker of disease. Determining the molecular basis of these B-cell lymphomas may help our understanding of their pathogenesis. This in turn could lead to more rational treatment aimed at altering the abnormal molecular changes and returning the neoplastic cells to normal cell development.

The effect of temperature and oligonucleotide primer length on the specificity and efficiency of amplification by the polymerase chain reaction

The polymerase chain reaction (PCR) is most effectively performed using a thermostable DNA polymerase such as that isolated from Thermus aquaticus. Since temperature and oligonucleotide length are known to control the specificity of oligonucleotide hybridization, we have investigated the effect of oligonucleotide length, base composition, and the annealing temperature on the specificity and efficiency of amplification by the PCR. Generally, the specificity of PCR is controlled by the length of the oligonucleotide and/or the temperature of annealing of the primer to the template. An empirical relationship between oligonucleotide length and ability to support amplification was determined. This relationship allows for the design of specific oligonucleotide primers. A model is proposed which helps explain the observed dependence of PCR on annealing temperature and length of the primer.

Treatment of high-risk solid tumors of childhood with intensive therapy and autologous bone marrow transplantation

Autologous bone marrow transplantation (ABMT) allows delivery of intensive, marrow-ablative chemotherapy or chemoradiotherapy to children with high-risk solid tumors. Results from several studies of neuroblastoma suggest that outcome is improved by ABMT; however, relapses can occur months to years after complete clinical remission. Other high-risk tumors including peripheral neuroepithelioma, Ewing's sarcoma, rhabdomyosarcoma, Wilms' tumor, and brain tumors also appear to be responsive to intensive marrow-ablative therapy, although few studies have been reported. For tumors that can metastasize to marrow, a sensitive method is necessary for detecting tumor cell contamination. Immunocytologic analysis with monoclonal antibodies can identify one neuroblastoma cell per 10(5) normal marrow cells; this method also is applicable to other tumors with appropriate antibodies. Ex vivo removal (purging) of tumor cells decreases the probability of infusing tumorigenic cells with the ABMT. There is considerable experience in tumor detection and purging for neuroblastoma, but little has been done for other childhood solid tumors. Future investigations of ABMT will aim to further increase disease-free survival by intensifying induction and marrow-ablative regimens and by developing therapies to be given after ABMT that are directed at minimal residual disease. As pilot investigations mature, the efficacy of ABMT and conventional chemotherapy will be compared in multi-institution randomized studies.

Gene rearrangement analysis in lymphoid neoplasia

Current uses for gene rearrangement analysis in clinical dermatology are listed in Table 3. This technique is useful for determining the existence of clonal populations within a background of polyclonal lymphoid cells; therefore, it is helpful in the diagnosis and staging of patients with CTCL and PTCL. Although dual genotypes do occur, this technique is usually capable of determining lineage in a clonal lymphoid infiltrate and elucidating and characterizing the etiopathogenesis of certain neoplasms. On the basis of this review of the literature and our own experience, we conclude that gene rearrangement analysis shows great promise for monitoring response to therapy and detecting progression or relapse in patients with CTCL and PTCL. With the recent technology of PCR, it is possible to amplify specific sequences of DNA, detect molecular alterations in individual malignant T cells, and even identify exogenous retroviral gene sequences in tissues of patients with CTCL. Although gene rearrangement analysis has supported or established the clonal nature of lymphomatoid papulosis, pre-Sézary syndrome, granulomatous slack skin syndrome, and follicular mucinosis, the clinical significance of these findings is not yet clear. In the case of primary cutaneous B-cell lymphoma and its benign counterpart, B-cell pseudolymphoma, further investigation will be needed to determine the clinical significance of clonal rearrangements.

Alfacalcidol is a nontoxic, effective treatment of follicular small-cleaved cell lymphoma

Thirty-four patients with progressive low grade non-Hodgkin's lymphoma were treated with 1 microgram oral alfacalcidol daily. Complete response was seen in four patients and a partial response in four patients with an overall response rate of 24%. Median duration of response was 14 months. Disease stabilised in ten other patients (29%) and 16 patients (47%) had tumour progression. In the sub-group of patients with follicular, small-cleaved cell-lymphoma the overall response to treatment was 29%. Apart from one patient who had a mild transitory elevation of serum calcium there was no recorded toxicity from alfacidol. These results indicate that alfacalcidol has significant antitumour activity in patients with low grade non-Hodgkin's lymphoma of the follicular, small-cleaved cell type.

Immunoglobulin gene 'fingerprinting': an approach to analysis of B lymphoid clonality in lymphoproliferative disorders

Rearrangement of the immunoglobulin heavy chain (IgH) gene is widely exploited as a marker of B cell lineage and clonality in the pathology of lymphoproliferative disorders. We have developed a simple, polymerase chain reaction (PCR) based method for detecting IgH gene rearrangement which relies on the observation that by using a panel of PCR amplimers specific for each of the six heavy chain variable region families in conjunction with a common joining region amplimer, clonal rearrangement can be detected in over 90% of cases of B lymphoid malignancy. By using radiolabelled amplimers and exploiting the size heterogeneity resulting from independent IgH rearrangement events, we show that high resolution gel electrophoresis can be used to generate a 'fingerprint' representing the spectrum of B cell clonality in complex populations of B lymphocytes. The method effectively scans the entire IgH gene rearrangement repertoire and is capable of detecting rare clonal or oligoclonal B lymphoid cell populations. In normal bone marrow mononuclear cells, clonal IgH rearrangement could be readily detected at a sensitivity of 10(-3). We illustrate the application of the method in assessing the spectrum of B cell clonality occurring in an autoimmune condition. Hashimoto's thyroiditis, and in a malignant B cell disorder, chronic lymphocytic leukaemia. In addition, we explore the potential application of the technique in tracking minimal residual disease and for monitoring clonal evolution in acute lymphoblastic leukaemia.

Simplified procedures for applying the polymerase chain reaction to routinely fixed paraffin wax sections

The polymerase chain reaction was applied to the analysis of DNA contained in archival paraffin wax embedded material. DNA suitable for the reaction was obtained from these tissues by simple extraction methods, without previous dewaxing of tissue sections. When compared with unfixed material, the reaction efficiency was compromised, so that an increased number of amplification cycles were required to produce equivalent amounts of amplified product. This in turn led to an increase in amplification artefacts, which can be minimised by a simple modification of the standard reaction. Amplification of relatively large DNA fragments was not always successful, and it seems prudent to bear this in mind when designing oligonucleotide primers which are to be used for the amplification of archival material. The efficiency of the procedure can be improved by dividing the amplification cycles into two parts: this reduces the amount of reagent needed, is relatively simple and inexpensive, and can be performed in one working day.

The significance of B-clonal excess in peripheral blood in patients with non-Hodgkin's lymphoma in remission

By taking advantage of the monoclonal nature of non-Hodgkin's lymphoma (NHL) it has been possible to detect small numbers of lymphoma cells which are not evident by routine morphological methods. These new methods are based on the detection of either a restricted light chain expression - clonal excess analysis (CE) or a monoclonal rearrangement of the Ig or T-cell receptor genes. We have studied the impact on relapse and survival of CE in peripheral blood in 202 patients in remission. The patients were sampled repeatedly during follow-up in remission. Median follow-up was 55 months (range 1-180). CE was found more frequently during remission in patients with low-grade NHL 18% as compared to 8% in high-grade NHL. There was no correlation with initial stage and the occurrence of CE in remission. Survival and time to relapse did not differ in those with CE and those with a normal light chain distribution. The conclusion is that CE in remission does not herald a poor prognosis and that an isolated finding of CE in remission is not an indication to start therapy.

Direct sequence analysis of 14q+ and 18q- chromosome junctions at the MBR and MCR revealing clustering within the MBR in follicular lymphoma

The t(14;18) translocation is a highly consistent feature of follicular lymphoma although the underlying mechanism generating this fusion remains uncertain. The breakpoints on chromosome 18 are at one of two sites, designated mbr and mcr, in the bcl-2 gene. A polymerase chain reaction strategy has been developed for amplification and direct sequencing of the resultant 14q+ and 18q- reciprocal junctions. Sequence analysis of the amplified 14q+ junction established that 21 tumours contained a bcl-2 (mbr) sequence to an immunoglobulin JH region, the majority being J5 or J6. A nonrandom pattern of breakpoints within the mbr region was found. Clustering of the breakpoint occurred with over 60% of the translocations clustering within 10 bases. There was a second cluster within the mbr 50 bases 3' of the first cluster. One of these junctions had an unusual configuration with the bcl-2 and JH sequences separated by a recognisable DH region. This suggests that at least some of the junctional sequences, previously thought of as N insertions, may be fragments of unrecognised DH regions. In one of these tumours it was possible to sequence the reciprocal 18q- junction, showing it to consist of a DH/bcl-2 (mbr) fusion. Analysis of both reciprocal junctions for a translocation in the mcr region of bcl-2, showed that this 18q- junction also consisted of DH fused to a bcl-2 sequence. In contrast to previous analyses, which demonstrated either loss or duplication of bcl-2 sequences at the breakpoints, the bcl-2 sequence was conserved during the mbr and mcr translocations in this study.(ABSTRACT TRUNCATED AT 250 WORDS)