Molecular genetic analysis of DNA obtained from fixed, air dried or paraffin embedded sources

Acquired genomic copy number changes in CML patients with the Philadelphia chromosome (Ph+)

Chronic myeloid leukemia (CML) is characterized by the BCR-ABL1 fusion gene; this fusion gene is usually a consequence of the Philadelphia (Ph(+)) chromosome, which results from the t(9;22)(q34;q11.2). Patients newly diagnosed with CML are routinely treated with tyrosine kinase inhibitors; however, the clinical course of the disease can vary, and this variance may be associated with genetic heterogeneity. Array comparative genomic hybridization (CGH) technology is a powerful tool for identifying subtle genomic segmental alterations, which can result from either losses or gains of chromosomal material. These changes may reveal the presence of genes that play important roles in disease initiation or progression or in treatment outcomes. To investigate whether subtle somatic copy number changes (CNCs) are commonly present in CML patients, a pilot study of 19 patients with the Ph(+) chromosome, but who were negative for common secondary chromosomal anomalies [+der(22), +8, i(17q), and +19], was conducted using a high-density whole genomic oligonucleotide array CGH analysis. Four of the 19 cases had somatic segmental CNCs, including the loss of 9q34, 15q25.3, and 15q13 and a gain of 7p21.1-p15.3. The findings demonstrate that subtle genomic changes are relatively common in CML patients with a Ph(+) chromosome and that the clinical significance of these findings, especially the newly discovered regions, must be determined in large patient population studies.

Evaluation of microRNA expression in patient bone marrow aspirate slides

Like formalin fixed paraffin embedded (FFPE) tissues, archived bone marrow aspirate slides are an abundant and untapped resource of biospecimens that could enable retrospective molecular studies of disease. Historically, RNA obtained from slides is limited in utility because of their low quality and highly fragmented nature. MicroRNAs are small (≈22 nt) non-coding RNA that regulate gene expression, and are speculated to preserve well in FFPE tissue. Here we investigate the use of archived bone marrow aspirate slides for miRNA expression analysis in paediatric leukaemia. After determining the optimal method of miRNA extraction, we used TaqMan qRT-PCR to identify reference miRNA for normalisation of other miRNA species. We found hsa-miR-16 and hsa-miR-26b to be the most stably expressed between lymphoblastoid cell lines, primary bone marrow aspirates and archived samples. We found the average fold change in expression of hsa-miR-26b and two miRNA reportedly dysregulated in leukaemia (hsa-miR-128a, hsa-miR-223) was <0.5 between matching archived slide and bone marrow aspirates. Differential expression of hsa-miR-128a and hsa-miR-223 was observed between leukaemic and non-leukaemic bone marrow from archived slides or flash frozen bone marrow. The demonstration that archived bone marrow aspirate slides can be utilized for miRNA expression studies offers tremendous potential for future investigations into the role miRNA play in the development and long term outcome of hematologic, as well as non-hematologic, diseases.

Molecular cytogenetic characterization of epithelioid hemangioendothelioma

Epithelioid hemangioendothelioma (EHE) is a rare vascular tumor whose pathological diagnosis can be difficult. In the literature two cases of EHE were found to harbor a balanced t(1;3)(p36.3;q25) translocation, suggesting a characteristic chromosomal rearrangement as cause for the development of EHE. In this study, 14 cases of EHE were investigated by interphase fluorescence in situ hybridization (FISH) directed against the translocation breakpoint 1p36.3. A subset of cases was also analyzed by comparative genomic hybridization (CGH) and image cytometry. Five out of eight cases that could be successfully analyzed by FISH harbored a chromosomal break in the 1p36.3 region. The break-apart signals were present in diploid nuclei, and less frequently also in tetraploid nuclei. In the latter, the chromosomal break was present twice, suggesting that polyploidy occurred after the chromosomal alteration. DNA cytometry confirmed that tetraploid cells were present in most examined cases with one case indicating almost equal amounts of diploid and tetraploid tumor cells. CGH revealed single chromosomal imbalances of unclear significance. We could confirm that EHE may harbor a recurrent mutation involving the 1p36.3 chromosomal region thus supporting the notion that the t(1;3)(p36.3;q25) translocation is a relevant genetic finding in this tumor entity.

Detection of submicroscopic disease in the bone marrow and unaffected testis of a child with T-cell acute lymphoblastic leukemia who experienced "isolated" testicular relapse

Testicular relapse has an impact on the prognosis of boys with acute lymphoblastic leukemia (ALL). Because isolated testicular relapse often precedes hematological relapse, systemic therapy is required in addition to local therapy. However, a rationale for the use of a combination of systemic chemotherapy and local therapy is unclear. A 12-year-old boy with T-ALL suffered from isolated testicular relapse at 27 months after diagnosis. He was successfully treated with systemic chemotherapy with orchiectomy and prophylactic irradiation to the contralateral testis. We retrospectively estimated the minimal residual disease in the bone marrow (BM) and the testis by detection of clone-specific T-cell receptor rearrangement of leukemic cells. We detected leukemic cells in the affected testis at relapse, as well as in the BM at initial diagnosis. In addition, we confirmed submicroscopic disease in the unaffected testis and the BM at relapse. We conclude that molecular analysis could reveal the submicroscopic disease in the patient with apparently isolated testicular relapse. This finding may provide a rationale for intensified systemic treatment of patients with isolated testicular relapse.

Ancillary techniques in bone marrow pathology: molecular diagnostics on bone marrow trephine biopsies

Pathologic examination of trephine bone marrow (BM) biopsies plays a central role in the diagnosis and staging of haematological neoplasms and other disorders affecting haematopoiesis. Haematopathology has been profoundly influenced by the advent of molecular genetic techniques suitable for paraffin-embedded tissues, and certain applications, such as the determination of B- and T-cell clonality, belong to its standard diagnostic repertoire. Many of these molecular tests can be performed successfully with nucleic acids extracted from BM trephine biopsies, if some technical aspects specific to this template source such as various fixation and decalcification procedures are taken into consideration. The current indications for molecular BM diagnostics range from the confirmation of lymphoma involvement with gene rearrangement analysis, demonstration of tumor-specific translocations in lymphoid and chronic myeloproliferative disorders along to the detection of microorganisms or marrow involvement by soft tissue sarcomas. The availability of quantitative polymerase chain reaction techniques for the investigation of allelic imbalances and gene expression levels in paraffin-embedded material also open new avenues for research and advanced diagnostics. The molecular detection of minimal residual disease in haematological neoplasms, especially in the context of new treatment strategies, will provide future challenges. This article summarizes the current state of the art in molecular diagnostics applied to paraffin-embedded BM biopsies.

Single cell PCR from archival stained bone marrow slides: a method for molecular diagnosis and characterization

Molecular analysis of isolated single cells is a powerful tool for clarifying issues of cell origin and clonality. Previous reports have described PCR amplifications from total DNA and RNA extracted from archival bone marrow and peripheral blood smears and have also shown the feasibility of amplifications from single cells, microdissected from stained histological sections. In this study, a method is described for performing PCR from morphologically defined single cells isolated from archival May-Gruenwald-Giemsa-stained bone-marrow and blood smears. Using three DNA extraction procedures, the organic lysis showed reproducible high efficiencies of amplifications. With this method, we were able to amplify long range amplicons up to 14.5 kb from mitochondrial DNA as well as PCR products of conventional length. The usability of such products for molecular diagnosis is demonstrated by restriction fragment length polymorphism (RFLP)characterization of a mitochondrial disorder. In conclusion, this method has the power to perform molecular diagnosis and characterization of diseases on the single cell level, and should provide valuable information to aid disease treatment and prognosis of hematological disorders.

Recurrence of acute myelogenous leukemia with the same AML1/ETO breakpoint as at diagnosis after complete remission lasting 15 years: analysis of stored bone marrow smears

The AML1/ETO fusion gene is expressed in virtually all patients with t(8;21)(q22;q22) acute myelogenous leukemia (AML). Long-term complete remission (CR) of AML with t(8;21) has been observed despite the presence of residual AML1/ ETO fusion transcripts, although detection may depend on the sensitivity of the methods used. We examined a patient with recurrent AML who showed the t(8;21)(q22;q22) chromosomal abnormality following a CR of 15 years. The blast cells at the time of recurrence expressed the AML1/ETO fusion transcript, and the breakpoint of the AML1 gene was located on intron 5. Southern blot analysis of the DNA extracted from bone marrow slides that had been made and stored for 15 years revealed the same rearrangement pattern of the AML1 gene. Furthermore, the junction sequences between the AML1 and the ETO genes, analyzed by long-distance inverse polymerase chain reaction, proved to be completely identical. These findings can be interpreted in two ways: (1) The initial leukemia clone persisted and finally relapsed after 15 years in the dormant state. (2) AML developed in different subclones having the same AML1/ETO junctional sequences but with additional genetic changes (second hit).

Minimal residual disease in early phase of chemotherapy reflects poor outcome in children with acute lymphoblastic leukemia--a retrospective study by the Children's Cancer and Leukemia Study Group in Japan

We analyzed the minimal residual disease (MRD) in 50 children with acute lymphoblastic leukemia (ALL) by amplifying the clonally rearranged T-cell receptor (TCR) gamma/delta chain and/or immunoglobulin (Ig) kappa chain gene using the allele-specific-PCR method. All children were treated according to the protocols of the Children's Cancer and Leukemia Study Group of Japan (CCLSG). The patients were stratified into four risk-groups according to the leukocyte count and age at diagnosis. We prospectively sampled the patients' bone marrow at 1 month (point 1) and 3 months (point 2) after the initiation of chemotherapy and quantitated the MRD retrospectively. The results of MRD were closely related with the clinical outcome. The relapse rate of the patients MRD-positive at points 1 and 2 was 46% (6/13) and 86% (6/7), respectively, whereas those MRD-negative results at point 1 and 2 were 13% (3/13) and 3% (3/30), respectively. We found significant differences in the event-free survival between MRD-positive children and MRD-negative children like the reports, which have been made by BFM and EORTC groups. We conclude that MRD in an early phase of chemotherapy can be a good predictor of the prognosis of childhood ALL regardless of the protocol of chemotherapy or race.

Molecular detection of acute lymphoblastic leukaemia in boys with testicular relapse

AIMS

To determine the role of polymerase chain reaction (PCR) based minimal residual disease (MRD) detection of leukaemia specific DNA in testicular relapse in childhood acute lymphoblastic leukaemia.

METHODS

DNA was obtained from archival testicular and bone marrow samples from boys with acute lymphoblastic leukaemia who relapsed in the testes. Overlapping DJH clone specific primers derived from clonal immunoglobulin heavy chain (IgH) gene rearrangement in each case were used to analyse testicular or bone marrow DNA.

RESULTS

Histologically normal end of treatment testicular biopsies in the five patients in longterm remission were all MRD negative, but MRD positive in three of six boys with subsequent testicular relapse. Histologically normal bone marrow samples taken at the end of treatment were MRD negative in five of seven cases, but MRD positive in all cases at the time of isolated testicular relapse. Three boys with unilateral testicular relapse underwent unilateral orchidectomy, rather than bilateral testicular irradiation, as part of their treatment. Two of these boys were MRD positive in the histologically uninvolved testes, and both had subsequent relapses either in the testes or the bone marrow, while the MRD negative patient has not had a testicular relapse.

CONCLUSIONS

The presence of MRD in testicular tissue can be assayed with a PCR based method to detect clone specific antigen receptor gene rearrangements. In this setting, PCR is more sensitive than conventional testicular histology for predicting clinical outcomes. MRD assays might be useful in the management of boys at the time of isolated testicular relapse, to confirm the presence of unilateral testicular disease.

DNA extraction from archival Giemsa-stained bone-marrow slides: comparison of six rapid methods

The ability of six rapid DNA extraction procedures to provide DNA for the polymerase chain reaction from archival Giemsa-stained bone marrow slides was tested on 120 samples. Boiling in distilled water, freeze-thaw method, boiling in 10% Chelex-100 resin solution, proteinase K/Tween 20/NP-40 method coupled with simplified phenol/ chloroform/isoamyl alcohol protocol or salting-out procedure using saturated NaCl and modification of commercial QIAamp procedure (Qiagen. Chatsworth, Calif.) gave DNA extraction efficiencies of 50%, 70%, 85%, 95%, 100% and 100%, respectively. Our results demonstrate that rough DNA extraction methods have decreased efficiencies compared to complete DNA extraction protocols and that the latter are required to ensure highly reproducible results from archival Giemsa-stained bone marrow slides.

On the role of human herpesvirus 6 in viral latency in nervous tissue and in cerebral lymphoma

Latent infections by human herpesvirus 6 (HHV6) in nervous tissue and its role in human disease are poorly understood. For the present study, an improved PCR method has been applied to brain tissue samples from 5 different brain regions from 20 forensic post-mortem cases without neurologic involvement. Spleen tissue from these cases as well as 5 cerebral lymphoma tissue samples were also examined. HHV6 DNA was detected in 3 of 20 brains. The viral sequences could be amplified from cortical brain tissue from these 3 cases. In one of these cases, HHV6 DNA was detectable in two separate tissue samples. PCR was negative in brain lymphoma and spleen tissue. These findings point toward HHV6 latency in brain tissue and might thus support the reported glial tropism of this virus. No role could be found for HHV6 in the pathogenesis of cerebral lymphoma.

Improved technique for analysis of formalin-fixed, paraffin-embedded tumors by fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) and specific DNA probes for peri-centromeric repeat regions and unique sequence loci have made it possible to study chromosomal aberrations from interphase tumor nuclei. Large-scale retrospective studies on the prognostic value of interphase cytogenetics would become feasible if these techniques were readily applicable to nuclei from archival formalin-fixed tumor tissues. We describe here an improved technique for interphase FISH analysis of tumors that have been extensively fixed in formalin. The protocol aims at improving probe penetration and hybridization efficiency by inducing chromatin decondensation and swelling of the nuclei with a heat treatment in a 90 degrees C glycerol solution prior to hybridization. Using this cell pretreatment, FISH results on the detection of chromosome copy number aberrations and amplification of the c-erbB-2 oncogene from formalin-fixed, paraffin-embedded tissues were highly concordant with those from fresh tissues. In contrast to previously described methods, separate adjustments of denaturation or proteinase K digestion are not required for each sample. This method facilitates retrospective analyses of large series of tumors and is also useful for applying FISH to routine diagnostic purposes using formalin-fixed material.

Analysis of delta F508 mutation in cystic fibrosis pathology specimens

Incidence of delta F508, a severe mutation of the CFTR gene is found to be 36.3% in paraffin block cystic fibrosis liver tissues. Samples are histologically grouped according to severity of pancreatic involvement. Two families where delta F508 was detected postmortem and who have no living children, will have the chance for a prenatal diagnosis in the future pregnancies.

Immunoglobulin gene rearrangement in plasma cell dyscrasias: detection of small clonal cell populations in peripheral blood and bone marrow

The bone marrow (BM) and peripheral blood (PB) samples of 71 patients with plasma cell dyscrasias were analysed by the Southern blot technique for the presence of clonal immunoglobulin (Ig) gene rearrangements. 53% of BM samples examined were archival material such as air dried BM slides or frozen trephine biopsies. The results were related to bone marrow plasmacytosis as determined by cytology and flow cytometry, and other clinical parameters. Clonal Ig gene rearrangements were found in BM samples of 45 (83%) of 54 MM patients and in 3 of 6 patients with monoclonal gammopathy of unknown significance (MGUS). Clonal cell populations in the PB were detected in 11 (30%) of 37 examined MM patients, but in none of the patients with MGUS or solitary plasmacytoma of bone. PB involvement was associated with progressive disease. Circulating monoclonal cells were significantly associated with higher M-protein levels (p < 0.05). Thus, circulating clonal precursor cells are encountered more frequently in active MM.

Long-term follow-up of patients with hairy cell leukaemia treated with pentostatin: lymphocyte subpopulations and residual bone marrow infiltration

Peripheral blood lymphocyte (PBL) subsets and bone marrow biopsies were analysed in six patients with hairy cell leukaemia (HCL) treated with 2'-deoxycoformycin (pentostatin, DCF) according to a phase II trial of the EORTC Leukemia Cooperative Group. All patients responded to DCF with four complete and two partial remissions according to conventional criteria. Within the PBL subsets, major changes concerned the CD4+ T cells, which during DCF therapy were distinctly suppressed to nadir values of 0.038-0.18 (median 0.126) x 10(9)/l. In five patients these cells returned to normal 3.0-49.5 (median 14.5) months after the last DCF injection. CD8+ cells were decreased to a lesser extent, and NK cell numbers improved during treatment. Bone marrow immunohistology applying the MoAb B-ly7 demonstrated residual hairy cells (HCs) in all of the six patients following DCF treatment with nadir HC numbers of 0.2-3.0% of bone marrow cells. Immunoglobulin gene rearrangement analysis of DNA obtained from these biopsies showed only germline bands, whereas rearranged bands had been present on the pretreatment specimens. Within the observation period of 15.5-54.0 (median 47.0) months after discontinuation of DCF therapy, immunohistology demonstrated a continuous increase in HC numbers in five of the six patients with clonal rearrangement detectable in bone marrow specimens from three of these patients at last follow-up date. Although established on the basis of a small number of patients, these data suggest that DCF treatment as currently employed in HCL is unable to eradicate the malignant B cell clone.