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

Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues

Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS). We therefore tested the two most commonly used WGA methods, multiple displacement amplification (MDA-Qiagen REPLI-g kit) and the hybrid or modified PCR-based method (Sigma/Rubicon Genomics Inc. GenomePlex kit) in FFPE normal and tumor tissue specimens. For the normalized copy number analysis, the FFPE process caused none or very minimal bias. Variations in copy number were minimal in samples amplified using the GenomePlex kit, but they were statistically significantly higher in samples amplified using the REPLI-g kit. The pattern was similar for variant allele frequencies across the samples, which was minimal for the GenomePlex kit but highly variable for the REPLI-g kit. These findings suggest that each WGA method should be tested thoroughly before using it for clinical cancer samples.

Mobile Genome Express (MGE): A comprehensive automatic genetic analyses pipeline with a mobile device

The development of next-generation sequencing (NGS) technology allows to sequence whole exomes or genome. However, data analysis is still the biggest bottleneck for its wide implementation. Most laboratories still depend on manual procedures for data handling and analyses, which translates into a delay and decreased efficiency in the delivery of NGS results to doctors and patients. Thus, there is high demand for developing an automatic and an easy-to-use NGS data analyses system. We developed comprehensive, automatic genetic analyses controller named Mobile Genome Express (MGE) that works in smartphones or other mobile devices. MGE can handle all the steps for genetic analyses, such as: sample information submission, sequencing run quality check from the sequencer, secured data transfer and results review. We sequenced an Actrometrix control DNA containing multiple proven human mutations using a targeted sequencing panel, and the whole analysis was managed by MGE, and its data reviewing program called ELECTRO. All steps were processed automatically except for the final sequencing review procedure with ELECTRO to confirm mutations. The data analysis process was completed within several hours. We confirmed the mutations that we have identified were consistent with our previous results obtained by using multi-step, manual pipelines.

The Evolution of the Polymerase Chain Reaction to Diagnose Childhood Infections

Children's healthcare has evolved over the years, and the pediatric laboratory has contributed to the clinical understanding of childhood disease through the application of new technology and knowledge. This article highlights the evolution of PCR technology to aid in the diagnosis of pediatric infections, from the discovery of the PCR, through the subsequent years when the clinical need exceeded the capability of the technology, until the current day, when application of the PCR is becoming commonplace.

High-dose thiotepa, etoposide and carboplatin as conditioning regimen for autologous stem cell transplantation in patients with high-risk non-Hodgkin lymphoma

High-dose chemotherapy conditioning regimens followed by autologous stem cell transplantation generally provide good results in non-Hodgkin lymphoma. We have evaluated the effects of a high-dose regimen comprising thiotepa, etoposide and carboplatin. After debulking and mobilization with high-dose cyclophosphamide or other schedules, forty-five patients at various disease stages were conditioned with thiotepa, etoposide and carboplatin prior to autologous stem cell transplantation. The overall response rate was 77.8% (30 CR, 66.7%; 5 PR, 11.1%). Ten patients (22.2%) did not respond. Two patients (4.4%) died from transplant-related complications. The mean 5-year overall survival was 71.1%: 12 patients relapsed within the first 5 years of follow-up. The overall response rate and 5-year overall survival were better for patients with an International Prognostic Index (IPI) 1 at diagnosis than for those with IPI 2 and IPI 3 (P<0.005 for all). The thiotepa, etoposide and carboplatin conditioning regimen for autologous stem cell transplantation in non-Hodgkin lymphoma has a good anti-lymphoma effect and provides encouraging results in terms of response to treatment and 5-year overall survival. Its good tolerance and acceptable toxicity suggest that it may a very useful in the management of non-Hodgkin lymphoma.

Biology and treatment of follicular lymphoma

Follicular lymphoma (FL) is the second most common lymphoid tumor. It is composed of elements resembling those of normal germinal centers. In particular, it is constituted by small centrocytes and large centroblasts, typically CD10+, CD19+, CD20+, CD79a+ and BCL6+, with follicular growth pattern. The molecular hallmark of FL is the t(14;18)(q32;q21) translocation, which leads to inappropriate BCL2 expression. This feature, other than representing a pathogenetic primary event, constitutes a suitable diagnostic marker, as well as a target for minimal residual disease monitoring and, hopefully, future therapies. Clinically, FL presents with indolent behavior, characterized by prompt response to initial therapy but almost invariably subsequent relapses. Novel approaches, including stem cell transplantation, monoclonal antibodies and innovative agents, should be then considered for improving long-term results.

Prognostic Factors in Follicular Lymphoma

Follicular lymphoma (FL) is one of the most common types of non-Hodgkin's lymphoma. It is usually diagnosed at an advanced stage, for which many treatment options exist, however, no curative standard therapy has been identified. The outcome is highly variable with a median survival of approximately 10 years. The life expectancy of patients with FL has been extended with the use of rituximab, a monoclonal antibody targeting the CD20 antigen on FL cells, but there remains a group of patients who fail to respond to chemoimmunotherapy and die early of their disease. Transformation of FL to an aggressive histology is an important event with high morbidity and mortality. The Follicular Lymphoma International Prognostic Index has become the clinically useful prognostic tool, but gives only a rough estimate of expected outcome. There is a need for useful biomarkers for prediction of the disease course of single patients to individualize therapy, especially in the new era of chemoimmunotherapy.

Genomic and proteomic biomarkers for cancer: a multitude of opportunities

Biomarkers are molecular indicators of a biological status, and as biochemical species can be assayed to evaluate the presence of cancer and therapeutic interventions. Through a variety of mechanisms cancer cells provide the biomarker material for their own detection. Biomarkers may be detectable in the blood, other body fluids, or tissues. The expectation is that the level of an informative biomarker is related to the specific type of disease present in the body. Biomarkers have potential both as diagnostic indicators and monitors of the effectiveness of clinical interventions. Biomarkers are also able to stratify cancer patients to the most appropriate treatment. Effective biomarkers for the early detection of cancer should provide a patient with a better outcome which in turn will translate into more efficient delivery of healthcare. Technologies for the early detection of cancer have resulted in reductions in disease-associated mortalities from cancers that are otherwise deadly if allowed to progress. Such screening technologies have proven that early detection will decrease the morbidity and mortality from cancer. An emerging theme in biomarker research is the expectation that panels of biomarker analytes rather than single markers will be needed to have sufficient sensitivity and specificity for the presymptomatic detection of cancer. Biomarkers may provide prognostic information of disease enabling interventions using targeted therapeutic agents as well as course-corrections in cancer treatment. Novel genomic, proteomic and metabolomic technologies are being used to discover and validate tumor biomarkers individually and in panels.

Rituximab based therapy followed by autologous stem cell transplantation leads to superior outcome and high rates of PCR negativity in patients with indolent B-cell lymphoproliferative disorders

Autologous stem cell transplantation (ASCT) and rituximab based therapy represent effective treatments of indolent B-cell lymphoproliferative disorders (B-LPDs) that often induce molecular remission (MR). We assessed the impact of MR after treatment on prognosis of 57 patients with indolent B-LPDs. We also evaluated the impact of therapy on patients' outcome. Failure to achieve MR was identified as an independent risk factor regardless of treatment modality. PCR positive patients had shorter progression free survival (PFS) in contrast with patients in MR after rituximab (median 0.75 and 2.5 years respectively; p=0.006) or patients in MR after rituximab followed by ASCT (median 3.3 years; p=0.0032). PCR positive patients had a 5-year overall survival (OS) of only 40% compared to a 5-year OS of 76% for PCR negative patients after rituximab (p=0.0186) and 86% PCR negative patients after rituximab with ASCT (p=0.003). All nine patients transplanted with PCR positive graft relapsed (p=0.0023) with shorter PFS (p=0.0008). Rituximab based therapy induced MR in 25 (64%) compared to 18 (100%) patients after rituximab followed by ASCT (p=0.0025). We observed no difference in PFS between the transplant group (3.3 years) and rituximab based treatment (1.9 years), but the 5-year OS of patients with transplant was 85 and 59% respectively (p=0.0271). Patients with indolent B-LPDs who achieve MR have better prognosis. Rituximab based therapy induces MR in high number of patients, which can be further improved by ASCT and patients have an excellent outcome. PCR positive harvest represents a high risk of relapse after ASCT.

Malignant cells are not found in ovarian cortex from breast cancer patients undergoing ovarian cortex cryopreservation

BACKGROUND

Breast cancer is a frequent indication for ovarian cortex cryopreservation due to its high incidence. The main concern of this procedure is the possibility of reintroducing metastatic cells within the implant, an issue that has not been addressed systematically. Thus, a study was designed to analyse the presence of ovarian metastases in breast cancer patients undergoing ovarian tissue cryopreservation.

METHODS

Morphological and immunohistochemical studies following the concept of the sentinel lymph node (SLN) were performed on 100 cortical ovarian biopsies obtained from 63 patients and on six frozen-thawed entire cortex from patients with the diagnosis of infiltrating ductal breast carcinoma undergoing ovarian cortex extraction and cryopreservation. The antibody panel included Cytokeratin CAM 5.2, Gross Cystic Disease Fluid Protein-15 (GCDFP15), Wilms' tumour antigen-1 (WT1) and Mammaglobin 1.

RESULTS

Employing only morphologic criteria, suspicious neoplastic cells were detected in five biopsies, but in none of the six entire cortex analysed. These five cases were reclassified as hyperplasic surface epithelium-inclusion cysts (CAM 5.2+, WT1+) or apoptotic granulosa cells (CAM 5.2-, GCDFP15+, WT1-).

CONCLUSIONS

Using the methodology of the SLN our data suggest the absence of tumour cells in biopsies obtained from patients undergoing ovarian cortex cryopreservation to preserve their fertility potential, although future methods of cancer screening may change our perception of this procedure.

Commercial LightCycler-based quantitative real-time PCR compared to nested PCR for monitoring of Bcl-2/IgH rearrangement in patients with follicular lymphoma

Translocation of chromosomes 14 and 18 [t(14;18)] for detection of minimal residual disease in follicular lymphoma patients can be analyzed by nested polymerase chain reaction (PCR) or by quantitative PCR like LightCycler-based assays. We have compared both methods in blood and bone marrow samples of 28 patients enrolled in a clinical study on immunochemotherapy. In 42% of samples, the bcl2-IgH rearrangement was detectable by nested PCR, but not by LightCycler PCR. Nested PCR was able to reveal a significant drop in positive bone marrow or peripheral blood samples after therapy. In contrast, with LightCycler PCR, the detected drop in t(14;18)-positive cells did not reach statistical significance. The majority of patients showed positive results with nested PCR of peripheral blood or bone marrow without any associations to presence or absence of histological bone marrow (BM) infiltration by lymphoma cells. With LightCycler PCR, the numbers of positive cells were higher in samples from patients with BM infiltration of lymphoma cells (1.9 x 10(-2)) compared to samples from patients without involvement (4.08 x 10(-5)). A similar trend was seen in samples derived from the peripheral blood. Positivity for t(14;18) after therapy in two patients correlated with clinical relapse 6 months later. The data shown here demonstrate a lower sensitivity of LightCycler vs. nested PCR for detection of t(14;18). The usefulness of nested PCR for t(14;18) for risk stratification after primary therapy has to be validated in larger trials.

Combined molecular diagnosis of B-cell lymphomas with t(11;14)(q13;q32) or t(14;18)(q32;q21) using multiplex- and long distance inverse-polymerase chain reaction

Translocations t(14;18)(q32;q21) and t(11;14)(q13;q32) are recurrent findings in follicular lymphoma (FL) and mantle cell lymphoma (MCL), respectively. However, the molecular counterparts of these translocations can only be detected in up to 75% of FL and 50% of MCL cases using routine techniques. To improve the efficiency of detection, we first devised a single-tube multiplex-polymerase chain reaction (PCR) assay with primers located within a conserved immunoglobulin heavy chain (IGH) sequence and 5' to the main breakpoint cluster regions of BCL2 and CCND1. Using this assay in 17 FL and 11 MCL diagnostic DNA samples, we readily identified a BCL2-IGH fusion in 65% of FL patients and a CCND1-IGH fusion in 55% of MCL patients. In the remaining cases, we used long distance inverse-PCR to detect BCL2-IGH and CCND1-IGH fusion genes with different BCL2 and CCND1 breakpoint locations. We found additional translocations in 3 patients (17%) with FL and in 4 patients (36%) with MCL. Taken together, we show that multiplex-PCR combined with long distance inverse-PCR detected a t(14;18) in 82% of FL patients and a t(11;14) in 91% of MCL patients, demonstrating that this 2-step protocol is an effective approach for molecular detection of t(11;14) and t(14;18) in B-cell lymphomas.

Ovarian tissue cryostorage and grafting: an option to preserve fertility in pediatric patients with malignancies

Fertility preservation in childhood cancer has become an important area of investigation due to increasing survival rates after cancer therapy. For these patients with an increased risk of infertility and premature ovarian failure, cryopreservation of ovarian tissue is a promising tool to preserve at least part of the reproductive potential. In recent years significant improvements have been achieved in this area, and 2 live births after autografting of frozen-thawed ovarian tissue have been reported. However, further research is needed to assess the clinical effectiveness of ovarian cryopreservation, to optimize the technique, and to limit the risk of reintroducing cancer cells in the patient with the graft.

The detection and significance of minimal residual disease in acute and chronic leukemia

Minimal residual disease (MRD) can be detected in many patients with leukemia who have achieved complete remission as defined by conventional pathology examination. The detection of MRD, be it by flow cytometry or by polymerase chain reaction assays, has now been found to be associated with subsequent relapses in most leukemia subtypes, either following chemotherapy or following hematopoietic stem cell transplantation. These assays are now increasingly used in clinical trial design to optimize therapy and provide a novel way to assess treatment efficacy.

Prognostic significance of circulating tumour cells enumerated after filtration enrichment in early and metastatic breast cancer patients

BACKGROUND

We previously found a higher incidence of circulating tumour cells (CTCs) in women with metastatic breast cancer compared to early disease. In this study, we present follow-up data to explore the prognostic significance of these findings.

METHODS

CTCs were quantified by immunostaining and direct visualization after centrifugation and filtration enrichment of peripheral blood from 131 patients. Time to progression (TTP) and overall survival (OS) were defined as interval from first blood sampling to first documented disease progression, or death respectively. Lifetime data was analysed using Kaplan-Meier method, log-rank test and Cox proportional hazards model.

RESULTS

Follow-up data is available for 123 patients. In early disease, median CTC>or=4 best distinguished patients with shorter TTP (p=0.05, log-rank test). In univariate analysis, tumour size, grade, lymphovascular invasion (LVI) and receptor status significantly related to TTP but none of the covariates related to OS. In multivariate analysis, T stage was the only independent predictor of TTP. In metastatic disease, median CTC>or=13 optimally identified patients with shorter TTP (p=0.01). In univariate analysis, median CTC level >or=13 and prior lines of chemotherapy predicted for TTP while in multivariate analysis, median CTC level >or=13 was the only significant independent prognostic factor (p=0.02). No relationship between CTC level and OS was found in this subgroup.

CONCLUSION

Median CTC level determined in the course of treatment predicts for TTP in metastatic breast cancer. In early breast cancer, an association was found between CTC level and TTP although this did not reach statistical significance (p=0.05).

High-dose carmustine, etoposide, and cyclophosphamide followed by allogeneic hematopoietic cell transplantation for non-Hodgkin lymphoma

Allogeneic hematopoietic cell transplantation (HCT) has been shown to be curative in a group of patients with aggressive non-Hodgkin lymphoma (NHL). A previous study has demonstrated equivalent outcomes with a conditioning regimen based on total body irradiation and another not based on total body irradiation with preparative therapy using cyclophosphamide, carmustine, and etoposide (CBV) in autologous HCT. We investigated the safety and efficacy of using CBV in an allogeneic setting. Patients were required to have relapsed or be at high risk for subsequent relapse of NHL. All patients had a fully HLA-matched sibling donor. Patients received carmustine (15 mg/kg), etoposide (60 mg/kg), and cyclophosphamide (100 mg/kg) on days -6, -4, and -2, respectively, followed by allogeneic HCT. All patients were treated with cyclosporine and methylprednisolone as prophylaxis for graft-versus-host disease (GVHD). Thirty-one patients (median age, 46 years) who were felt to be inappropriate candidates for autologous transplantation were enrolled. Each subject had a median of 3 previous chemotherapy regimens. All patients engrafted. Fifteen of 31 patients are alive. Median follow-up time was 11.5 months (range, .4-126). There were 8 deaths due to relapse. Nonrelapse mortality (n = 8) included infection (n = 3), GVHD (n = 2), diffuse alveolar hemorrhage (n = 1), veno-occlusive disease in the setting of concurrent acute GVHD of the liver (n = 1), and leukoencephalopathy (n = 1). Probabilities of event-free survival and overall survival were, respectively, 44% (95% confidence interval, 26%-62%) and 51% (33%-69%) at 1 year and 44% (26%-62%) and 47% (29%-65%) at 5 years. Probability of relapse was 33% (15%-51%) at 1 year and 5 years. Probability of nonrelapse mortality was 31% (13%-49%) at 1 year and 5 years. Incidences were 29% for acute GVHD and 39% for chronic GVHD. None of the 12 patients who developed chronic GVHD has disease recurrence. Patients who had required >3 previous chemotherapy regimens before HCT had an increased probability of relapse. CBV is an effective preparative regimen for patients with aggressive NHL who undergo allogeneic HCT.

Improvement of Overall and Failure-Free Survival in Stage IV Follicular Lymphoma: 25 Years of Treatment Experience at The University of Texas M.D. Anderson Cancer Center

Purpose

Advanced-stage follicular lymphoma is considered incurable. The pace of improvements in treatment has been slow. This article analyzes five sequential cohorts of patients with stage IV follicular lymphoma treated between 1972 and 2002.

Methods

Five consecutive studies (two were randomized trials) involving 580 patients were analyzed for overall survival (OS), failure-free survival (FFS), and survival after first relapse. A proportional hazards analysis, and subset analyses using the follicular lymphoma international prognostic index (FLIPI) score were performed. Treatment regimens included: cyclophosphamide, doxorubicin, vincristine, prednisone, bleomycin (CHOP-Bleo); CHOP-Bleo followed by interferon alfa (IFN-α); a rotation of three regimens (alternating triple therapy), followed by IFN-α; fludarabine, mitoxantrone, dexamethasone (FND) followed by IFN-α; and FND plus delayed versus concurrent rituximab followed by IFN-α.

Results

Improvements in 5-year OS (from 64% to 95%) and FFS (from 29% to 60%) indicate steady progress, perhaps partly due to more effective salvage therapies, but the FFS data also indicate improved front-line therapies; these observations held true after controlling for differences in prognostic factors among the cohorts. The FLIPI model adds rigor to and facilitates comparisons among the different cohorts. An unexpected finding in this study was a trend toward an apparent FFS plateau.

Conclusion

Evolving therapy, including the incorporation of biologic agents, has led to stepwise significant outcome improvements for patients with advanced-stage follicular lymphoma. The apparent plateau in the FFS curve, starting approximately 8 to 10 years from the beginning of treatment, raises the issue of the potential curability of these patients.

A prospective randomized study to compare the molecular response rates between central lymphatic irradiation and intensive alternating triple chemotherapy in the treatment of stage I–III follicular lymphoma

PURPOSE

This study was undertaken to compare the molecular response (MR) rates of 2 regimens, central lymphatic irradiation (CLI) and alternating triple therapy (ATT), in the treatment of Stage I-III follicular lymphoma. MR was defined as disappearance of t(14;18) (q32;q21) amplified by polymerase chain reaction (PCR).

PATIENTS AND METHODS

Sixty-five patients with Stage I to III follicular lymphoma were randomized. CLI consisted of the mantle, abdomen, and pelvic radiation fields. ATT alternated among CHOD-Bleo, ESHAP, and NOPP for 12 courses. Bone marrow (BM) and peripheral blood (PB) samples were obtained before treatment for PCR analysis. PCR-positive patients were followed by PCR analysis. The random-effects logistic model was fitted to the data from the posttreatment PCRs. The factors included in the model were treatment arm, type of PCR (BM vs. PB), and time to PCR sample procurement from the date of registration.

RESULTS

At a median follow-up of 71 months, the 5-year relapse-free survival (RFS) rates were 45% and 54% for CLI and ATT, respectively (p = 0.42). The probability of attaining an MR increased with time after registration (p = 0.007), was lower for BM compared with PB (p = 0.012), and was higher for ATT than for CLI (p = 0.020).

CONCLUSION

ATT regimen achieved a higher MR than CLI, although both arms had similar 5-year RFS.

Detection of BCL2-IGH Using Single-Round PCR Assays

The translocation t(14;18) resulting in fusion of the BCL2 and the immunoglobulin heavy chain genes (BCL2-IGH) is present in 80% to 90% of follicular lymphomas and 20% to 30% of diffuse large B-cell lymphomas. Polymerase chain reaction (PCR) analysis for the translocation products suffers from low analytic specificity. As a result, either nested PCR or probe hybridization is required to aid in the identification of the specific translocation products. These added procedures are undesirable in clinical laboratories because nested procedures increase the possibility of contamination and probe hybridization increases assay turnaround time. To simplify the BCL2-IGH assay procedure, we attempted to eliminate the nonspecific PCR products by optimizing the annealing temperatures of the PCR assays using a gradient thermocycler. We showed that gradually increasing the annealing temperature from 55 degrees C to 67 degrees C significantly enhanced the intensity of the specific PCR products while eliminating the nonspecific ones. We compared the simplified procedure with a PCR-probe hybridization method on 68 patient specimens. The simplified procedure had increased analytic and diagnostic specificities with comparable sensitivities. With significantly improved analytic specificity, one round of PCR is sufficient to detect the BCL2-IGH gene rearrangements without further confirmation.

Detection of Circulating Prostate Cancer Cells Using Real Time Rt – Pcr: Our Experience

PCR (Polymerase Chain Reaction) has revolutionized molecular genetics and continues to be applied to many fields of medicine and biology. We used nested real time RT – PCR to detect circulating prostate cells in patients affected by prostate cancer, in order to evaluate a possible clinical role of this technique. We present our initial experience.

Ovarian transplantation in humans: indications, techniques and the risk of reseeding cancer

Laboratory research on ovarian cryopreservation and transplantation began in the 1950s leading to clinical studies in the 2000s. The research that was performed during this half century indicated that cryopreserved ovarian tissue has the potential to restore fertility in women who face premature ovarian failure due to chemotherapy, radiotherapy or surgery. To date, ovarian function has been restored in at least four women. Even though no pregnancies have been reported so far from these clinical studies, animal studies indicate that this is a valid prospect for humans. Future clinical trials will determine on a larger number of patients the longevity of ovarian grafts, normality of hormone production and ovarian follicle development, possibility and safety of pregnancy, and the safety of auto-transplantation in cancer patients. However, the major improvement in the efficiency of ovarian transplantation is anticipated to come from research exploring the revascularization process.

Molecular response of follicular lymphoma to cyclophosphamide, doxorubicin, vincristine, prednisone C(H)OP or COP-based therapy as measured by polymerase chain reaction evidence of translocation (14;18)(q32;q21)

PURPOSE

Existing data suggest that conventional C(H)OP (cyclophosphamide, doxorubicin, vincristine, prednisone) regimen may not be intensive enough to achieve molecular response, as measured by polymerase chain reaction (PCR) evidence of translocation (14;18)(q32:q21) for follicular lymphoma. This study was undertaken to study the molecular response rate of follicular lymphoma to C(H)OP-based therapy and to analyze prognostic factors for molecular response.

PATIENTS AND METHODS

Twenty patients with pretreatment PCR evidence of t(14;18)(q32; q21) and at least one posttreatment PCR analysis after the initiation of the treatment with C(H)OP with or without radiation therapy constituted the basis for this analysis. The random effects logistic model was used to analyze the data. The following factors were investigated for their relationship to molecular response: gender, age, beta2-microglobulin, use of radiation therapy, Ann Arbor stage, and international Prognostic Index for malignant lymphoma.

RESULTS

Median follow-up was 56 months (range, 23-153 months). A total of 135 PCR results were available, 33 from bone marrow and 102 from peripheral blood. Overall, there was a clear and steady decreasing trend toward loss of PCR positivity with increasing time aftertreatment. By univariate analysis, stage > or = 3, stage = 4, International Prognostic Index > or = 2, and no radiation therapy were adverse factors for molecular response. On multivariate analysis, Ann Arbor stage IV and no radiation therapy were independent risk factors for PCR positivity, both for the peripheral blood data analyzed alone and for all data combined.

DISCUSSION

It is possible to achieve molecular response with C(H)OP with or without radiation therapy in patients with follicular lymphoma. Response rate depends on the Ann Arbor stage and radiation therapy.

Quantitative Assessment of Disease Involvement by Follicular Lymphoma Using Real-Time Polymerase Chain Reaction Measurement of t(14;18)-Carrying Cells

Chromosomal translocation t(14:18)(q32;q21) is one of the most common karyotypic abnormalities in non-Hodgkin's lymphomas. It occurs in more than 85% of follicular lymphoma (FL) cases. Real-time polymerase chain reaction (Q-Rt-PCR) analysis using double-labeled fluorogenic probes is a new tool in the detection and quantification of t(14;18)-carrying cells. We analyzed 239 specimens with Q-Rt-PCR to detect and quantify t(14;18)-carrying cells. To investigate the clinical usefulness of the quantitative assessment, we analyzed the clinical correlation with 92 FL patients of varying clinical status. Of 59 previously untreated patients, patients with stage IV disease had significantly higher quantities of t(14;18)-carrying cells measurable in the bone marrow or the peripheral blood than patients in clinical stages I to III (P = .003 and .043, respectively). Moreover, of the 33 posttherapy patients. the patients in complete remission appeared to have lower detectable levels of t(14;18)-carrying cells than patients in partial remission or with recurrent disease. Q-Rt-PCR permits a sensitive and quantitative assessment of the extent of disease involvement in patients with t(14;18)-carrying FL. The technique has the potential to be a useful tool in the diagnosis of FL, disease assessment, and prognosticating patients' clinical outcomes.

Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936

In a European BIOMED-2 collaborative study, multiplex PCR assays have successfully been developed and standardized for the detection of clonally rearranged immunoglobulin (Ig) and T-cell receptor (TCR) genes and the chromosome aberrations t(11;14) and t(14;18). This has resulted in 107 different primers in only 18 multiplex PCR tubes: three VH-JH, two DH-JH, two Ig kappa (IGK), one Ig lambda (IGL), three TCR beta (TCRB), two TCR gamma (TCRG), one TCR delta (TCRD), three BCL1-Ig heavy chain (IGH), and one BCL2-IGH. The PCR products of Ig/TCR genes can be analyzed for clonality assessment by heteroduplex analysis or GeneScanning. The detection rate of clonal rearrangements using the BIOMED-2 primer sets is unprecedentedly high. This is mainly based on the complementarity of the various BIOMED-2 tubes. In particular, combined application of IGH (VH-JH and DH-JH) and IGK tubes can detect virtually all clonal B-cell proliferations, even in B-cell malignancies with high levels of somatic mutations. The contribution of IGL gene rearrangements seems limited. Combined usage of the TCRB and TCRG tubes detects virtually all clonal T-cell populations, whereas the TCRD tube has added value in case of TCRgammadelta(+) T-cell proliferations. The BIOMED-2 multiplex tubes can now be used for diagnostic clonality studies as well as for the identification of PCR targets suitable for the detection of minimal residual disease.

[Application of molecular biology techniques to malignant haematology]

Malignant hemopathies, although heterogeneous in their prognosis and oncogenesis, represent an interesting model for studying cancer genesis mechanisms in man through the recurrent presence of genetic abnormalities involved in oncogenesis and the availability of tumour material. Nowadays, molecular biology techniques are very much used for the diagnosis, the treatment and the follow-up of these diseases. Firstly used for research, the new techniques have completely changed our ability to characterise malignant hemopathies and to understand the cancer-inducing processes, permitting us to perform the biological assessment of patients with malignant hemopathies, the diagnosis, and to estimate and follow the outcome of patients after treatment. At a more fundamental level, the structural and functional analysis of the deregulated genes implied in leukaemia and lymphoma has improved our knowledge and understanding of oncogenic and physiologic mechanisms significantly.

Gynaecologic concerns for young women exposed to gonadotoxic chemotherapy

PURPOSE OF REVIEW

Due to the improved long-term survival of adolescents and young women with systemic malignancies such as lymphomas and leukaemia undergoing gonadotoxic chemotherapy, preservation of future fertility has been the focus of recent ubiquitous interest. This review summarizes, in brief, the recent progress in the various attempts to prevent premature ovarian failure in these young women with unconsumed fertility potential.

RECENT FINDINGS

The investigational endeavours of ovarian cryopreservation await the clinical experience of auto- or xenotransplantation, or in-vitro maturation of thawed primordial follicles, and in-vitro fertilization. Although promising, this procedure is not available yet. Moreover, the risk of possible reimplantation of malignant stem cells with the thawed cryopreserved ovary has been highlighted following experimental animal observations. The gonadotropin-releasing hormone agonist has been efficient in primates in a prospective study, and in young women in several nonrandomized series. The disruption of the acid sphingomyelinase gene, or sphingosine-1-phosphate, in rodents can prevent follicle destruction by ionizing radiation, possibly indicating in-vivo protection in cancer patients at risk of iatrogenic sterilization.

SUMMARY

The recent enormous scientific advance lends hope that the future may hold answers to the questions regarding safety and efficiency of oocyte, follicle, or ovarian tissue cryopreservation, and the most efficient means of using the thawed tissue - auto-, hetero-, or xenotransplantation versus IVM on the one hand, and in-vivo pharmacological attempts to minimize follicle depletion by gonadotropin-releasing hormone agonist or other modalities on the other hand. Until then, a combination of all the clinically available modalities should be offered to these young women with unconsumed fertility potential who face gonadotoxic therapy.

Minimal residual disease (MRD) in follicular lymphoma in the era of immunotherapy with rituximab

The t(14;18)-translocation can be detected by PCR analysis in more than 90% of cytogenetically t(14;18)-positive follicular lymphomas (FLs), thus providing an easily accessible marker for molecular disease monitoring. Various technical aspects of the detection of residual lymphoma cells as well as the prognostic and clinical significance of the detection of minimal residual disease (MRD) after radiotherapy, chemotherapy and therapy with the monoclonal antibody rituximab are discussed. Up to now the comparability of the different studies investigating minimal residual disease in follicular lymphoma patients is hampered by the use of a variety of PCR techniques. A more standardized quantitative approach based on the real-time PCR technique will provide a powerful tool for the evaluation and optimization of therapy for each individual patient.

The role of molecular staging in malignant melanoma

AIMS

To review the role of tyrosinase RT-PCR in the detection of clinically occult metastatic disease, both within the regional lymph nodes and peripheral blood of patients with malignant melanoma. Secondly, to assess whether the detection of such minimal disease has clinical implications for patients with melanoma.

METHODS

A review of the literature was undertaken by searching the MEDLINE database for the period 1966-2002 without any language restrictions. Keywords included 'Molecular staging of melanoma', 'Reverse transcription polymerase chain reaction', 'Malignant melanoma' and 'Tyrosinase'.

CONCLUSIONS

Detection of tyrosinase RT-PCR positive cells within the peripheral blood correlates with the clinical stage of malignant melanoma, the primary tumour thickness and other known prognostic indicators. Positive tyrosinase RT-PCR is associated with a reduction of disease-free survival and overall survival. Current studies demonstrate a higher rate of recurrence in RT-PCR positive patients with clinical stage II and III disease. Implications of a positive result within the regional lymph nodes are less well defined. A significant correlation has been demonstrated between positive results and increasing primary melanoma thickness. However, a large number of false-positive results have been demonstrated, due to benign naevi and schwann cells, which may hamper any statistically significant conclusions being reached.

Cancer vaccines

Although cancer immunotherapy was initiated by William Coley more than a century ago, the field of cancer vaccines is in an early stage of development. Only recently, major advances in cellular and molecular immunology have allowed a comprehensive understanding of the complex and high rate of interactions between the immune system and tumor cells. We have learned that these tumor-immune system interactions may result either in strong immune antitumor response or tolerance to tumor-associated antigens. This article will discuss the profound interest in cancer vaccines derived from their potential to induce antitumor responses in vivo. Substantial data from several preclinical models and early human clinical trials have confirmed the ability of cancer vaccines to induce immune responses that are tumor-specific and, in some cases, associated with clinical responses. One future challenge will be to determine how to appropriately stimulate the pathways leading to effective interaction among antigen-presenting cells, T lymphocytes, and tumor cells. It also is critical to develop monitoring strategies that may allow the identification of patients who may benefit from cancer vaccines.

Fludarabine, mitoxantrone, dexamethasone (FND) compared with an alternating triple therapy (ATT) regimen in patients with stage IV indolent lymphoma

Treatment for patients with stage IV indolent lymphoma ranges from watchful waiting to intensive chemotherapy and stem cell transplantation. In this trial we compared 2 induction regimens followed by 1 year of interferon maintenance therapy. Fludarabine, mitoxantrone (Novantrone), and dexamethasone (FND) were compared with an alternating triple therapy (ATT) regimen (CHOD-Bleo, ESHAP, and NOPP). Maintenance interferon/dexamethasone was given for 1 year in both treatment arms. Endpoints were comparisons of remission rates, survival, failure-free survival (FFS), molecular response rates, and toxicities. One hundred forty-two patients with previously untreated stage IV indolent lymphoma were evaluable (73 on FND; 69 on ATT). The overall response rates were 97% for FND and 97% for ATT (P =.9). The median follow-up is 5.9 years. The 5-year survival rates were 84% with FND and 82% with ATT (P =.9); the 5-year FFS rates were 41% with FND and 50% with ATT (P =.02). In a multivariate analysis, factors predicting for longer FFS were beta(2)-microglobulin less than 3 mg/L (P =.01) and ATT treatment (P =.03). ATT was associated with a substantially higher rate of grade 3-4 toxicities than FND. In conclusion, both regimens were associated with high rates of response and survival. ATT was associated with substantially longer FFS, but it was more toxic than FND.

Quantitative real-time polymerase chain reaction for detection of circulating cells with t(14;18) in volunteer blood donors and patients with follicular lymphoma

The chromosomal rearrangement t(14;18)(q32;21) involves the major (MBR) or minor (mcr) breakpoint cluster regions and the immunoglobulin heavy chain joining regions (JH) in most follicular lymphomas. As a first step towards determining the clinical significance of circulating cells with t(14;18), we detected and quantitated circulating cells in samples obtained from volunteer blood donors and follicular lymphoma patients. The t(14;18) was co-amplified with beta-actin with real-time quantitative PCR (QRT-PCR) in reactions containing 1 microg of DNA from peripheral blood or bone marrow aspirates. The cell number was quantitated using linear regression and an external standard of serially diluted DNA from cell lines with MBR/JH or mcr/JH rearrangements. At dilutions of 10(5) and 106, sensitivity was 100 and 55% for MBR/JH, and 100 and 10% for mcr/JH rearrangements. Among 102 volunteer blood donors MBR/JH vs. mcr/JH amplicons were detected in 22 vs. 4% with duplicate 1 microg DNA reactions, and in 41 vs. 6% with a total 10 microg DNA analyzed in multiple reactions. Among volunteer blood donors the mean number of circulating cells with MBR/JH vs. mcr/JH rearrangements were 0.8 vs. 0.1/microg DNA, and exceeded the upper normal limit (defined as the mean of all volunteer samples plus two standard deviations) in 3% vs. 2%, respectively. Analysis for MBR/JH rearrangements revealed that follicular lymphoma patients vs. volunteer blood donors were positive in 76% vs. 22% (p = 0.008 by Fisher's exact test); that the mean number of MBR/JH cells per microg of DNA was 91 vs. 0.8 (p = 0.0002 by Mann-Whitney test); and the number of the MBR/JH cells exceeded the upper normal limit in 32% vs. 3% of subjects (p = 0.0001 by Fisher's exact test). Circulating cells with mcr/JH were not detected among any of these 25 lymphoma patients. We conclude that patients with follicular lymphoma are more frequently positive, have higher numbers of circulating cells with t(14;18), which exceed upper normal limit more frequently than in volunteer blood donors.

Progress and promise in the treatment of indolent lymphomas

In the era of conventional alkylating agent-based chemotherapy, advanced stage indolent lymphoma has been considered incurable. The failure of our traditional therapies to cure these patients, coupled with the indolent course of the disease and the elderly population affected, has fostered a nihilistic attitude about the treatment of these diseases. Twenty years ago, in the absence of interesting alternatives to alkylating agents, judicious use and reuse of alkylators was perhaps the best we could do. There are now many reasons for optimism and excitement in the treatment of these diseases, including the availability of promising agents such as interferon-alpha, the nucleoside analogues, and rituximab. Radioimmunotherapy will also likely play a role in future therapy programs. Allogeneic stem cell transplantation is a high-risk approach that is not an option for all patients, but it has the potential to cure patients, even in the setting of relapse. Mini-allogeneic transplantation may permit an approach to allogeneic transplantation that is better tolerated than standard transplant strategies. In addition to these therapy options, biological insights have provided new options for monitoring patients. Molecular monitoring (polymerase chain reaction for bcl-2) is a stringent measure of short-term treatment efficacy, and one that correlates with durability of remission, i.e., it is a surrogate marker by which to judge treatment efficacy. There used to be a limited number of conventional treatment approaches, which consistently failed. The pendulum has swung. There are now many promising new options. It is time to plan and conduct trials that are geared for success.

Insights into the molecular pathogenesis of follicular lymphoma arising from analysis of geographic variation

Incidence rates of follicular lymphoma (FL) inexplicably vary markedly between Western and Asian countries. A hallmark of FL is the bcl-2 translocation, characterized by 1 of 2 common breakpoints known as major breakpoint region (MBR) and minor cluster region (mcr). We analyzed previously published data to compare rates of bcl-2 translocation in FL across geographic regions. Available data from the literature suggest that the incidence of bcl-2 in healthy persons in the absence of FL may be as high as 50% in Western and Asian populations. However, in FL our results show that the frequency of bcl-2 positivity was significantly higher for US than for Asian populations (P <.0001). This pattern persisted for MBR and mcr subgroups. We conclude that a significant gradient exists in the bcl-2 frequency between these FL populations. We therefore suggest that the relatively low incidence of FL in Asian populations is caused not by a lower frequency of bcl-2 rearrangements in healthy populations but by distinct molecular pathways developing in different geographic regions that nonetheless culminate in FL, which is morphologically similar but molecularly distinct. Studies demonstrating differences in clinical characteristics according to the presence or absence of bcl-2 rearrangements support this concept. Thus we hypothesize that FL may in fact be a heterogeneous malignancy encompassing entities with distinct molecular pathogenesis and potentially distinct clinical manifestations. If these findings were confirmed in prospective studies, it would imply that different etiologic or genetic factors might influence the development of FL across separate regions.

Monitoring disease in lymphoma and CLL patients using molecular techniques

Over the past decade considerable advances have been made in the sensitivity of detection of residual lymphoma and leukaemia cells. Assays based on the polymerase chain reaction (PCR) can detect one tumour cell in up to 10(5) to 10(6) normal cells. The identification and cloning of breakpoints associated with specific chromosomal translocations has made possible the application of these techniques to a variety of lymphoid malignancies. In parallel, B cell malignancies exhibit rearrangements of their immunoglobulin genes that are also suitable targets for PCR amplification to identify residual cells. Although these techniques provide a useful adjunct to standard methods of detection and diagnosis, their role in determining disease outcome remains investigational. There is confusion as to whether it is necessary to eradicate PCR-detectable lymphoma cells for cure, so it is not yet possible to determine whether the detection of residual lymphoma cells by PCR is an indication to continue therapy.

Detection of minimal residual disease

A high percentage of patients with leukemia, lymphoma, and solid tumors achieve a complete clinical remission after initial treatment, but the majority of these patients will finally relapse from residual tumor cells detectable in clinical remission only by the most sensitive methods. The in vitro amplification of tumor-specific DNA or RNA sequences by polymerase chain reaction (PCR) allows identification of a few neoplastic cells in 10(4) to 10(6) normal cells. Depending on the underlying malignant disease and therapeutic treatment, the presence of residual tumor cells in an individual patient may herald relapse, but a long-term stable situation or slowly vanishing tumor cells are also possible. Molecular monitoring of residual leukemia and lymphoma cells by quantitative PCR techniques has provided important information about the effectiveness of treatment and the risk of recurrent disease as shown by minimal residual disease (MRD) analysis in patients with various malignant diseases. Such diseases include childhood acute lymphoblastic leukemia, after induction therapy; acute promyelocytic leukemia, during and after chemotherapy; and chronic myelogenous leukemia, during treatment with alpha-interferon and after allogeneic bone marrow transplantation. Evaluation of the predictive value of the detection of MRD has to take into account its evolution and course, the pathogenesis, biology, and natural course of the underlying malignant disease, the molecular genetic lesion, and finally, the type of treatment. Quantification of minimal residual cells by the recently developed real-time quantitative PCR technique will surely have a major impact on our therapeutic strategies for patients with leukemia, lymphomas, and solid tumors. Based on quantitative PCR data, the terms molecular remission and molecular relapse have to be exactly defined and validated in prospective clinical trials to assess the biological and clinical significance of MRD in various types of malignancies.

Use of novel t(11;14) and t(14;18) dual-fusion fluorescence in situ hybridization probes in the differential diagnosis of lymphomas of small lymphocytes

Increasingly, molecular biologic techniques have become important in the diagnosis of non-Hodgkin lymphomas. In the differential diagnosis of lymphoma(s) of small lymphocytes (LSL), reliable detection of t(11;14) or t(14;18) would confirm the diagnosis of mantle cell lymphoma (MCL) or follicle center lymphoma (FCL), respectively. A total of 87 LSL cases (27 MCL, 39 FCL, 17 small lymphocytic lymphoma [SLL], 3 marginal zone lymphomas, and 1 paraimmunoblastic variant of SLL) were diagnosed by a combination of light microscopy, immunohistochemistry, and flow cytometric immunophenotyping. Interphase fluorescence in situ hybridization (FISH) for t(11;14) and t( 14;18) using dual-fusion probes (Vysis, Downers Grove, IL) was performed on touch (n = 69) or gravity (n = 18) preparations from these cases. Of 27 MCL cases tested, 25 (93%) had demonstrable t(11;14), none had t(14;18), and 2 were negative for t(11;14) and t(14;18). Twenty-five of 39 (64%) FCL cases had t(14;18), none had t(11;14), and the remaining FCL cases (14 cases [35%]) had neither t(11;14) nor t(14;18). All 17 (100%) SLL cases had neither t(11;14) nor t(14;18). All 3 (100%) marginal zone lymphoma cases had neither t(11;14) nor t(14;18). The case of paraimmunoblastic variant of SLL had t(11;14) and was negative for t(14;18). No discrepant [i.e., positive for both t(11;14) and t(14;18)] or false-positive cases were noted. Interphase FISH using these commercially available probes is a useful adjunct to light microscopy, immunohistochemistry, and flow cytometric immunophenotyping in the diagnosis of LSL. FISH can be performed successfully on archival single-cell preparations (touch preparations or gravity preparations) when fresh tissue is unavailable. No discordant or false-positive cases were identified.

A framework for the molecular classification of circulating tumor markers

New molecular biological technologies, especially polymerase chain reaction (PCR) and mass spectroscopy, have expanded the pool of molecular targets for cancer diagnosis, monitoring, and prognosis using plasma or serum as the substrate. In this review, a framework is described following the "life history" of a protein--starting with DNA [endogenous (nuclear or mitochondrial) or exogenous (viral)], followed by RNA [endogenous (cell-based or cell-free) or exogenous (viral)], and culminating in protein (either the native protein or the glycan portion of glycoproteins). Each of these levels provides unique opportunities to achieve specificity for cancer diagnosis.

The significance of molecular response of follicular lymphoma to central lymphatic irradiation as measured by polymerase chain reaction for t(14;18)(q32;q21)

BACKGROUND

More than 80% of the patients with follicular lymphoma have a characteristic chromosomal translocation, t(14;18)(q32;q21), at the major breakpoint region (MBR) or minor cluster region (MCR) involving the bcl-2 oncogene. This study was undertaken to assess the significance of the molecular response rate measured by the polymerase chain reaction (PCR) evidence of translocation among patients with Stage I to III follicular lymphoma treated with central lymphatic irradiation (CLI).

METHODS AND MATERIALS

Thirty-three patients with Stage I-III follicular lymphoma were treated with CLI on a prospective protocol. Bone marrow and peripheral blood samples were obtained before CLI for PCR analysis of t(14;18)(q32; q21). PCR-positive patients were followed by PCR analysis at regular intervals during and after CLI, and the results were correlated with clinical outcome. The following pretreatment factors were also investigated for their relationship to relapse and molecular response: gender, age, lactate dehydrogenase (LDH) and beta-2 microglobulin (beta2M) levels, Ann Arbor stage, and International Prognostic Index (IPI) for malignant lymphoma.

RESULTS

The subjects were 19 men and 14 women, with a median age of 52 years (range 30-69), who started CLI between January 1993 and February 1998. Median follow-up was 44 months (range 12-67), and all but 2 patients were still alive at the last follow-up. Four patients were Stage IA, 8 were Stage IIA, 19 were Stage IIIA, and 2 were Stage IIIB. Two patients had abnormal LDH levels (> 618 U/dL) and 7 patients had abnormal beta2M levels (> 2 mg/dL). Nine patients had IPI = 0, 16 had IPI = 1, and 8 had IPI = 2. All patients achieved complete response (CR). Twelve patients have relapsed to date. The median overall time to relapse was 54 months. The actuarial proportion of patients free from relapse at 3 years was 87% (95% confidence interval [CI] 69-95%). A total of 287 PCR results were available, 64 from bone marrow and 223 from peripheral blood. Pretreatment PCR data were available for 27 patients, of whom 21 were positive and 3 were unambiguously negative (in blood and bone marrow for both MBR and MCR). For the 19 PCR positive patients for whom we had post-treatment results, there was a clear and steady decreasing trend toward loss of PCR positivity (49% positive for bone marrow and 32% positive for peripheral blood at 3 years). There was a clear trend for increasing PCR positivity with increasing IPI: 10% for IPI = 0, 31% for IPI = 1, and 63% for IPI = 2 at 3 years for blood. The same trend was also observed for bone marrow. The IPI was the only statistically significant predictor for relapse with a relapse-free survival of 91% at 3 years for IPI < 2 and 75% for IPI = 2 (p = 0.024, log-rank test).

CONCLUSION

Molecular response to CLI occurs gradually over years. High IPI is a negative predictor for molecular response and relapse-free survival.

Differential mobilization of CD34+ cells and lymphoma cells in non-Hodgkin's lymphoma patients mobilized with different growth factors

Co-mobilization of CD34(+) cells and tumor has been documented in patients with different types of cancer undergoing peripheral blood stem cell transplantation (PBSCT). Conflicting reports were published regarding the role of various growth factors in tumor cells mobilization, hence we studied the extent of CD34(+) cells and lymphoma cell mobilization in 35 non-Hodgkin's (NHL) patients primed by cyclophosphamide (Cy) in combination with granulocyte colony-stimulating factor (GCSF) (A, 13 patients), granulocyte-macrophage (GM)-CSF (B, 10 patients), or GM-CSF followed by G-CSF (C, 12 patients). CD34(+) cells were quantitated by flow cytometry and lymphoma cells by the TaqMan Real Time PCR for bcl-2 gene rearrangement. Successful collection in 4 days of > or = 2 x 10(6) CD34(+) cells/kg needed for prompt engraftment was obtained in 76%, 60%, and 58% of patients in arms A, B, and C, respectively. Lymphoma cell mobilization was detected in 35% patients tested, 78% of which had follicular lymphoma. Lymphoma cell mobilization was similar in the three arms of the study, however, presence of lymphoma cells was prevalent in patients who failed to mobilize the amount of 0.4 x 10(6) CD34(+) cells/kg in 2 days ("poor mobilizers") and reached 42%, compared to 17% in the "successful mobilizers" group of patients. Lymphoma cell contamination in PBSCs was detected proportionately in the peripheral blood and in the bone marrow. We conclude that bcl-2 gene rearrangement is prevalent in patients with follicular histology, and, in these patients, an inverse relationship was observed between mobilization of CD34(+) cells and lymphoma cells. Our results explain the high relative risk (1.98) for mobilization in patients with follicular histology.