FCM marker importance for MRD assessment in T-cell acute lymphoblastic leukemia: An AIEOP-BFM-ALL-FLOW study group report.

T-lineage acute lymphoblastic leukemia (T-ALL) accounts for about 15% of pediatric and about 25% of adult ALL cases. Minimal/measurable residual disease (MRD) assessed by flow cytometry (FCM) is an important prognostic indicator for risk stratification. In order to assess the MRD a limited number of antibodies directed against the most discriminative antigens must be selected. We propose a pipeline for evaluating the influence of different markers for cell population classification in FCM data. We use linear support vector machine, fitted to each sample individually to avoid issues with patient and laboratory variations. The best separating hyperplane direction as well as the influence of omitting specific markers is considered. Ninety-one bone marrow samples of 43 pediatric T-ALL patients from five reference laboratories were analyzed by FCM regarding marker importance for blast cell identification using combinations of eight different markers. For all laboratories, CD48 and CD99 were among the top three markers with strongest contribution to the optimal hyperplane, measured by median separating hyperplane coefficient size for all samples per center and time point (diagnosis, Day 15, Day 33). Based on the available limited set tested (CD3, CD4, CD5, CD7, CD8, CD45, CD48, CD99), our findings prove that CD48 and CD99 are useful markers for MRD monitoring in T-ALL. The proposed pipeline can be applied for evaluation of other marker combinations in the future.

Comparative treatment costs of risk-stratified therapy for childhood acute lymphoblastic leukemia in India.

BACKGROUND: To evaluate the treatment cost and cost effectiveness of a risk-stratified therapy to treat pediatric acute lymphoblastic leukemia (ALL) in India. METHODS: The cost of total treatment duration was calculated for a retrospective cohort of ALL children treated at a tertiary care facility. Children were risk stratified into standard (SR), intermediate (IR) and high (HR) for B-cell precursor ALL, and T-ALL. Cost of therapy was obtained from the hospital electronic billing systems and details of outpatient (OP) and inpatient (IP) from electronic medical records. Cost effectiveness was calculated in disability-adjusted life years. RESULTS: One hundred and forty five patients, SR (50), IR (36), HR (39), and T-ALL (20) were analyzed. Median cost of the entire treatment for SR, IR, HR, and T-ALL was found to be $3900, $5500, $7400, and $8700, respectively, with chemotherapy contributing to 25%-35% of total cost. Out-patient costs were significantly lower for SR (p < 0.0001). OP costs were higher than in-patient costs for SR and IR, while in-patient costs were higher in T-ALL. Costs for non-therapy admissions were significantly higher in HR and T-ALL (p < 0.0001), representing over 50% of costs of in-patient therapy. HR and T-ALL also had longer durations of non-therapy admissions. Based on WHO-CHOICE guidelines, the risk-stratified approach was very cost effective for all categories of patients. CONCLUSIONS: Risk-stratified approach to treat childhood ALL is very cost-effective for all categories in our setting. The cost for SR and IR patients is significantly reduced through decreased IP admissions for both, chemotherapy and non-chemotherapy reasons.

Acute Leukemia Classification Using Transcriptional Profiles From Low-Cost Nanopore mRNA Sequencing.

PURPOSE: Most cases of pediatric acute leukemia occur in low- and middle-income countries, where health centers lack the tools required for accurate diagnosis and disease classification. Recent research shows the robustness of using unbiased short-read RNA sequencing to classify genomic subtypes of acute leukemia. Compared with short-read sequencing, nanopore sequencing has low capital and consumable costs, making it suitable for use in locations with limited health infrastructure. MATERIALS AND METHODS: We show the feasibility of nanopore mRNA sequencing on 134 cryopreserved acute leukemia specimens (26 acute myeloid leukemia [AML], 73 B-lineage acute lymphoblastic leukemia [B-ALL], 34 T-lineage acute lymphoblastic leukemia, and one acute undifferentiated leukemia). Using multiple library preparation approaches, we generated long-read transcripts for each sample. We developed a novel composite classification approach to predict acute leukemia lineage and major B-ALL and AML molecular subtypes directly from gene expression profiles. RESULTS: We demonstrate accurate classification of acute leukemia samples into AML, B-ALL, or T-lineage acute lymphoblastic leukemia (96.2% of cases are classifiable with a probability of > 0.8, with 100% accuracy) and further classification into clinically actionable genomic subtypes using shallow RNA nanopore sequencing, with 96.2% accuracy for major AML subtypes and 94.1% accuracy for major B-lineage acute lymphoblastic leukemia subtypes. CONCLUSION: Transcriptional profiling of acute leukemia samples using nanopore technology for diagnostic classification is feasible and accurate, which has the potential to improve the accuracy of cancer diagnosis in low-resource settings.

Characteristics of white blood cell count in acute lymphoblastic leukemia: A COST LEGEND phenotype-genotype study.

BACKGROUND: White blood cell count (WBC) as a measure of extramedullary leukemic cell survival is a well-known prognostic factor in acute lymphoblastic leukemia (ALL), but its biology, including impact of host genome variants, is poorly understood. METHODS: We included patients treated with the Nordic Society of Paediatric Haematology and Oncology (NOPHO) ALL-2008 protocol (N = 2347, 72% were genotyped by Illumina Omni2.5exome-8-Bead chip) aged 1-45 years, diagnosed with B-cell precursor (BCP-) or T-cell ALL (T-ALL) to investigate the variation in WBC. Spline functions of WBC were fitted correcting for association with age across ALL subgroups of immunophenotypes and karyotypes. The residuals between spline WBC and actual WBC were used to identify WBC-associated germline genetic variants in a genome-wide association study (GWAS) while adjusting for age and ALL subtype associations. RESULTS: We observed an overall inverse correlation between age and WBC, which was stronger for the selected patient subgroups of immunophenotype and karyotypes (ρBCP-ALL  = -.17, ρT-ALL  = -.19; p < 3 × 10-4 ). Spline functions fitted to age, immunophenotype, and karyotype explained WBC variation better than age alone (ρ = .43, p << 2 × 10-6 ). However, when the spline-adjusted WBC residuals were used as phenotype, no GWAS significant associations were found. Based on available annotation, the top 50 genetic variants suggested effects on signal transduction, translation initiation, cell development, and proliferation. CONCLUSION: These results indicate that host genome variants do not strongly influence WBC across ALL subsets, and future studies of why some patients are more prone to hyperleukocytosis should be performed within specific ALL subsets that apply more complex analyses to capture potential germline variant interactions and impact on WBC.

A single assessment of methotrexate levels at 42 hours permits safe administration and early discharge in children with lymphoblastic lymphoma and leukemia receiving high-dose methotrexate.

High-dose methotrexate (HDMTX) is an important component of treatment in pediatric acute lymphoblastic leukemia (ALL) and lymphoblastic lymphoma (LL). Optimal rescue therapy is essential for the safe administration of HDMTX. A cost-effective strategy that does not compromise safety is necessary for low- and middle-income countries. Consecutive admissions for HDMTX in children with ALL and LL over 12 months were analyzed. The dose of HDMTX was 3 g/m2 in B-ALL and B-LL and 5 g/m2 in T-ALL and T-LL. A methotrexate level was measured at 42 hours of starting HDMTX infusion (T42-MTX). Three doses of folinic acid at T42, T48, and T54 and alkalinized hydration till T54 were administered if T42-MTX <1 µM. A total of 282 cycles of HDMTX that were administered in 71 patients were analyzed. T42-MTX was <1 µM in 266 (94.3%) cycles. T42-MTX was ≥1 µM in 12% and 3% of cycles of HDMTX administered at a dose of 5 g/m2 and 3 g/m2, respectively (p = .074). The median duration of hospitalization for HDM was three days and did not differ with the dose of HDMTX administered (p = .427). Mucositis, delayed recovery of blood counts, and hospitalization for reversible toxicity occurred after 21 (7.4%), 28 (9.9%), and 19 (6.7%) cycles of HDMTX, respectively. Mucositis was greater following the administration of 5 g/m2 of HDMTX. A single T42-MTX measurement permits the safe administration of HDMTX and an expedited discharge from the hospital within three days in more than 90% of children with ALL/LL.

Eleven-marker 10-color flow cytometric assessment of measurable residual disease for T-cell acute lymphoblastic leukemia using an approach of exclusion.

Measurable/minimal residual disease (MRD) status has been suggested as a powerful indicator of clinical-outcome in T-cell lymphoblastic leukemia/lymphoma (T-ALL). Multicolor flow cytometric (MFC)-based T-ALL MRD reports are limited and traditionally based on the utilization of markers-of-immaturity like TdT and CD99. Moreover, studies demonstrating the multicolor flow cytometric (MFC) approach for the assessment of T-ALL MRD are sparse. Herein, we describe an 11-marker, 10-color MFC-based T-ALL MRD method using an "approach of exclusion." METHODS: The study included 269 childhood T-ALL patients treated with a modified-MCP841 protocol. An 11-marker, 10-color MFC-based MRD was performed in bone marrow (BM) samples at the end-of-induction (EOI) and end-of-consolidation (EOC) time-points using Kaluza-version-1.3 software. RESULTS: We studied EOI-MRD in 269 and EOC-MRD in 105 childhood T-ALL patients. EOI-MRD was detectable in 125 (46.5%) samples (median, 0.3%; range, 0.0007-66.3%), and EOC-MRD was detectable in 34/105 (32.4%) samples (median, 0.055%; range, 0.0008-27.6%). Leukemia-associated immunophenotypes (LAIPs) found useful for MRD assessment were dual-negative CD4/CD8 (40.9%), dual-positive CD4/CD8 (23.3%) and only CD4 or CD8 expression (35.8%); dim/subset/dim-negative surface-CD3 (39%), dim/subset/dim-negative/negative CD5 (28.3%), dim/dim-negative/negative/heterogeneous CD45 (44.7%) and co-expression of CD5/CD56 (7.5%). EOI-MRD-positive status was found to be the most-relevant independent factor in the prediction of inferior relapse-free and overall survival. CONCLUSION: We described an 11-marker 10-color MFC-based highly sensitive MRD assay in T-ALL using an approach of exclusion. The addition of CD4 and CD8 to the pan-T-cell markers in a 10-color assay is highly useful in T-ALL MRD assessment and extends its applicability to almost all T-ALL patients.

Eficacia y seguridad del uso de nelarabina en pacientes pediátricos con leucemia linfoblástica aguda de células T con recaída o refractariedad a dos líneas de quimioterapia / Efficacy and safety of the use of nelarabine in pediatric patients with acute lymphoblastic leukemia of T-cells with relapse or refractory to two chemotherapy lines

INTRODUCCIÓN: El presente dictamen expone la evaluación de tecnología de la eficacia y seguridad de nelarabina en el tratamiento de pacientes pediátricos con leucemia linfoblástica aguda de células T con recaída o refractariedad a dos líneas de quimioterapia. El tratamiento estándar en el manejo de pacientes pediátricos con leucemia linfoblástica aguda (LLA) con varias recaídas es el trasplante de progenitores hematopoyéticos (TPH), utilizado como terapia de consolidación una vez que el paciente se encuentra en remisión. En la actualidad, EsSalud cuenta con clofarabina como tratamiento que lleva a los pacientes a remisión de manera que puedan ser trasplantados. El uso por fuera del Petitorio Farmacológico de EsSalud de clofarabina para el tratamiento de pacientes con LLA (de linfocitos T [T-LLA] y de linfocitos B [B-LLA]) que han recaído luego de dos líneas de quimioterapia fue aprobado en el 2016 mediante el Dictamen Preliminar de Evaluación de Tecnología Sanitaria N° 001-SDEPFyOTS-DETS-IETSI-2016 y se encuentra vigente a la fecha. Sin embargo, los especialistas de la institución sostienen que, de acuerdo a su experiencia desde la aprobación de clofarabina hace más de dos años, si bien ésta muestra tasas de respuesta moderadas en pacientes con inmunofenotipo B (i.e., B-LLA), esto no se ha logrado en pacientes con inmunofenotipo T (i.e., T-LLA), y que por lo tanto se requiere de otra alternativa terapéutica en este subgrupo especifico de pacientes. Además, afirman que los pacientes no remitirán espontáneamente y que la sobrevida general es de alrededor de tres meses con tratamiento paliativo. TECNOLOGÍA SANITARIA DE INTERÉS: Nelarabina (2-amino-9ß-D-arabinosyl-6-methoxy-9H-guanina), de nombre comercial ARRANON®, es un análogo de purina de cuarta generación. Este es un profármaco del análogo de desoxiguanosina ara-G sintetizado (9-ß-D-arabinofuranosylguanina). Este profármaco es desmetilado rápidamente por la adenosina desaminasa (ADA) a ara-G y una vez dentro de la célula es fosforilado por la desoxiguanosina quinasa y la desoxicitidina quinasa a su metabolito 5´-monofosfato. Dicho metabolito monofosfato es convertido a la forma activa 5´-trifosfato ara-GTP. Ara-GTP se acumula en los blastos leucémicos lo que lleva a la incorporación preferente de ara-GTP en el ácido desoxirribonucleico (ADN), conduciendo a la inhibición de su síntesis. La inhibición de la síntesis de ADN lleva a la muerte de los blastos leucémicos. Es este el mecanismo a través del cual nelarabina podría tener un impacto sobre la proliferación de células cancerosas en pacientes con LLA. METODOLOGÍA: Se llevó a cabo una búsqueda de la literatura con respecto a la eficacia y seguridad de nelarabina en el tratamiento de pacientes pediátricos con LLA de células T con recaída o refractariedad a dos líneas de quimioterapia en las bases de datos de PubMed, Cochrane Library, el metabuscador TRIPdatabase y el sitio web ww.clinicaltrials.gov. Adicionalmente, se realizó una búsqueda de evaluaciones de tecnologías y guías de práctica clínica en las páginas web de grupos dedicados a la investigación y educación en salud en general como The National Institute for Health and Care Excellence (NICE), Canadian Agency for Drugs and Technologies in Health (CADTH), Scottish Medicines Consortium (SMC), Instituto de Evaluación de Efectividad Clínica y Sanitaria (IECS), Instituto de Evaluación de Tecnología en Salud (IETS); así como en organizaciones especializadas en oncología como European Society for Medical Oncology (ESMO), National Comprehensive Cancer Network (NCCN) y American Society of Clinical Oncology (ASCO). RESULTADOS: Se llevó a cabo una búsqueda de evidencia científica relacionada al uso de nelarabina en el tratamiento de pacientes pediátricos con LLA de células T recurrente o refractario a dos líneas de quimioterapia. En la presente sinopsis se describe la evidencia disponible según el tipo de publicación, siguiendo lo indicado en los criterios de elegibilidad (GPC, ETS, RS, MA y ECA fase III). A la fecha, la evidencia disponible relacionada al tratamiento con nelarabina de pacientes pediátricos con T-LLA es muy escasa, y no se ha publicado ningún estudio de la eficacia comparativa entre nelarabina y clofarabina. Con ello, la evidencia identificada en la presente búsqueda sistemática e incluida en el presente dictamen corresponde principalmente a un ensayo de fase IV no controlado del uso de nelarabina, una guía de práctica clínica (GPC) y una evaluación de tecnología sanitaria (ETS). Adicionalmente, en ausencia de estudios comparativos, y frente a la preocupación de los especialistas de una eficacia diferenciada de clofarabina entre inmunofenotipos, se llevó a cabo una búsqueda de la evidencia del uso de clofarabina en la población de pacientes con T-LLA específicamente, con la finalidad de evaluar si se trata de una alternativa factible para dicha subpoblación. De ella se obtuvo únicamente un ensayo de fase II de un solo brazo que explora la respuesta diferenciada al tratamiento con clofarabina/ciclofosfamida/etopósido entre pacientes pediátricos con B-LLA y T-LLA con dos o más recaídas. CONCLUSIONES: La evidencia identificada a la fecha no permite establecer la eficacia comparativa entre nelarabina y clofarabina. A pesar de que la evidencia que apoya el uso de nelarabina en pacientes con T-LLA es escasa y de baja calidad, y la comparación con clofarabina es descriptiva e indirecta, la baja tasa de respuesta y la tasa nula de supervivencia al año observada en la población con T-LLA tras el uso de clofarabina sugieren que este no sería una alternativa de tratamiento factible para dicho inmunofenotipo y, por lo tanto, nos encontraríamos en un escenario de vacío terapéutico. Además, considerando que, de acuerdo a los especialistas de la institución y la historia natural de la enfermedad, los pacientes no remitirán espontáneamente, se tiene entonces que nelarabina podría ofrecer una tasa de respuesta de alrededor de 40 %. el Instituto de Evaluación de Tecnologías en Salud e Investigación (IETSI), aprueba el uso fuera del petitorio de nelarabina en el tratamiento de pacientes pediátricos con diagnóstico de leucemia linfoblástica aguda de células T con recaída o refractariedad a dos líneas de quimioterapia. La vigencia del presente dictamen preliminar es de un año a partir de la fecha de publicación.

Flow cytometric minimal residual disease assessment of peripheral blood in acute lymphoblastic leukaemia patients has potential for early detection of relapsed extramedullary disease.

OBJECTIVES: To evaluate peripheral blood (PB) for minimal residual disease (MRD) assessment in adults with acute lymphoblastic leukaemia (ALL). METHODS: We analysed 76 matched bone marrow (BM) aspirate and PB specimens independently for the presence of ALL MRD by six-colour flow cytometry (FC). RESULTS: The overall rate of BM MRD-positivity was 24% (18/76) and PB was also MRD-positive in 22% (4/18) of BM-positive cases. We identified two cases with evidence of leukaemic cells in PB at the time of the extramedullary relapse that were interpreted as MRD-negative in BM. CONCLUSIONS: The use of PB MRD as a non-invasive method for monitoring of systemic relapse may have added clinical and diagnostic value in patients with high risk of extramedullary disease.

Cost-effective screening of DNMT3A coding sequence identifies somatic mutation in pediatric T-cell acute lymphoblastic leukemia.

BACKGROUND AND OBJECTIVES: In pediatric T-cell acute lymphoblastic leukemia (T-ALL), risk assignment schemes preclude reliable prediction of outcome, and thus, new prognostic factors are needed. Mutations in DNMT3A are candidate prognostic and classification markers in adults with acute myeloid leukemia (AML) and T-ALL and thus were considered as candidates prognostic markers in pediatric T-ALL. PATIENTS AND METHODS: DNMT3A mutational status was investigated in 74 pediatric T-ALL samples collected at diagnosis. We applied high-resolution melt (HRM) analysis and Sanger sequencing to study the hotspot position (R882) within catalytic MTase domain and exons coding for other functional domains of the protein, known to be mutated in the wide spectrum of hematological malignancies. RESULTS: We demonstrate a low frequency of mutations in DNMT3A coding sequence in pediatric T-ALL (1.4%, n = 1/74). We identified missense mutation, p.Ala644Thr, which has not been described previously in pediatric T-ALL, but is recurrent in adults with T-ALL and AML. CONCLUSIONS: Low frequency of DNMT3A mutations in pediatric T-ALL is in striking contrast to adult T-ALL and renders the necessity for the search of other candidate prognostic markers. Combined Sanger sequencing-HRM approach offers a cost-effective option for genotyping DNMT3A coding sequence, with potential clinical application in other hematological malignancies.

In vitro and in vivo assessment of direct effects of simulated solar and galactic cosmic radiation on human hematopoietic stem/progenitor cells.

Future deep space missions to Mars and near-Earth asteroids will expose astronauts to chronic solar energetic particles (SEP) and galactic cosmic ray (GCR) radiation, and likely one or more solar particle events (SPEs). Given the inherent radiosensitivity of hematopoietic cells and short latency period of leukemias, space radiation-induced hematopoietic damage poses a particular threat to astronauts on extended missions. We show that exposing human hematopoietic stem/progenitor cells (HSC) to extended mission-relevant doses of accelerated high-energy protons and iron ions leads to the following: (1) introduces mutations that are frequently located within genes involved in hematopoiesis and are distinct from those induced by γ-radiation; (2) markedly reduces in vitro colony formation; (3) markedly alters engraftment and lineage commitment in vivo; and (4) leads to the development, in vivo, of what appears to be T-ALL. Sequential exposure to protons and iron ions (as typically occurs in deep space) proved far more deleterious to HSC genome integrity and function than either particle species alone. Our results represent a critical step for more accurately estimating risks to the human hematopoietic system from space radiation, identifying and better defining molecular mechanisms by which space radiation impairs hematopoiesis and induces leukemogenesis, as well as for developing appropriately targeted countermeasures.

Using nonrandomized studies to inform complex clinical decisions: the thorny issue of cranial radiation therapy for T-cell acute lymphoblastic leukemia.

BACKGROUND: There are no randomized controlled trials to inform the decision of which cranial radiation therapy (CRT) strategy to apply to pediatric patients with T-cell acute lymphoblastic leukemia (ALL). PROCEDURE: We performed a decision analysis using a Markov model in which we compared the life expectancy and quality-adjusted life expectancy when administering one of three CRT strategies to a cohort of patients with T-cell ALL: (1) omission of CRT for all patients; (2) CRT only for those with evidence of leukemic involvement in the central nervous system at diagnosis (therapeutic strategy); or (3) CRT for all (prophylactic strategy). RESULTS: When considering plausible event-free survival rates and late mortality after cure for groups of pediatric patients with T-cell ALL, the strategies of omitting CRT, administering therapeutic CRT, and administering prophylactic CRT result in similar short-term (7-year) survival. When considering the increased contribution of deaths from late effects, the strategy of prophylactic CRT is associated with lower life expectancy when compared to the other two strategies. The Monte Carlo probabilistic sensitivity analysis demonstrated that the strategy of prophylactic CRT was the preferred strategy only 5% of the time. CONCLUSIONS: Similar short-term survival may be expected when comparing the strategies of total omission of CRT, therapeutic CRT, and prophylactic CRT for patients with T-cell ALL. Long-term survival is likely inferior for the strategy of prophylactic CRT. The synthesis of nonrandomized trials and the application of decision analysis can help inform complex decision making in pediatric oncology.

Assessment of the effect of sphingosine kinase inhibitors on apoptosis,unfolded protein response and autophagy of T-cell acute lymphoblastic leukemia cells; indications for novel therapeutics.

Sphingosine 1-phosphate (S1P) is a bioactive lipid that is formed by the phosphorylation of sphingosine and catalysed by sphingosine kinase 1 (SK1) or sphingosine kinase 2 (SK2). Sphingosine kinases play a fundamental role in many signaling pathways associated with cancer, suggesting that proteins belonging to this signaling network represent potential therapeutic targets. Over the last years, many improvements have been made in the treatment of T-cell acute lymphoblastic leukemia (T-ALL); however, novel and less toxic therapies are still needed, especially for relapsing and chemo-resistant patients. Here, we analyzed the therapeutic potential of SKi and ROMe, a sphingosine kinase 1 and 2 inhibitor and SK2-selective inhibitor, respectively. While SKi induced apoptosis, ROMe initiated an autophagic cell death in our in vitro cell models. SKi treatment induced an increase in SK1 protein levels in Molt-4 cells, whereas it activated the endoplasmic reticulum (ER) stress/unfolded protein response (UPR) pathway in Jurkat and CEM-R cells as protective mechanisms in a sub-population of T-ALL cells. Interestingly, we observed a synergistic effect of SKi with the classical chemotherapeutic drug vincristine. In addition, we reported that SKi affected signaling cascades implicated in survival, proliferation and stress response of cells. These findings indicate that SK1 or SK2 represent potential targets for treating T-ALL.

A rapid and scalable system for studying gene function in mice using conditional RNA interference.

RNA interference is a powerful tool for studying gene function, however, the reproducible generation of RNAi transgenic mice remains a significant limitation. By combining optimized fluorescence-coupled miR30-based shRNAs with high efficiency ES cell targeting, we developed a fast, scalable pipeline for the production of shRNA transgenic mice. Using this system, we generated eight tet-regulated shRNA transgenic lines targeting Firefly and Renilla luciferases, Oct4 and tumor suppressors p53, p16(INK4a), p19(ARF) and APC and demonstrate potent gene silencing and GFP-tracked knockdown in a broad range of tissues in vivo. Further, using an shRNA targeting APC, we illustrate how this approach can identify predicted phenotypes and also unknown functions for a well-studied gene. In addition, through regulated gene silencing we validate APC/Wnt and p19(ARF) as potential therapeutic targets in T cell acute lymphoblastic leukemia/lymphoma and lung adenocarcinoma, respectively. This system provides a cost-effective and scalable platform for the production of RNAi transgenic mice targeting any mammalian gene. PAPERCLIP:

Minimal residual disease assessment in childhood acute lymphoblastic leukaemia: a Swedish multi-centre study comparing real-time polymerase chain reaction and multicolour flow cytometry.

Minimal residual disease (MRD) assessment is a powerful prognostic factor for determining the risk of relapse in childhood acute lymphoblastic leukaemia (ALL). In this Swedish multi-centre study of childhood ALL diagnosed between 2002 and 2006, the MRD levels were analysed in 726 follow-up samples in 228 children using real-time quantitative polymerase chain reaction (RQ-PCR) of rearranged immunoglobulin/T-cell receptor genes and multicolour flow cytometry (FCM). Using an MRD threshold of 0·1%, which was the sensitivity level reached in all analyses, the concordance between RQ-PCR and FCM MRD values at day 29 was 84%. In B-cell precursor ALL, an MRD level of ≥0·1% at day 29 predicted a higher risk of bone marrow relapse (BMR) with both methods, although FCM was a better discriminator. However, considering the higher median MRD values achieved with RQ-PCR, a higher MRD cut-off (≥0·2%) improved the predictive capacity of RQ-PCR. In T-ALL, RQ-PCR was notably superior to FCM in predicting risk of BMR. That notwithstanding, MRD levels of ≥0·1%, detected by either method at day 29, could not predict isolated extramedullary relapse. In conclusion, the concordance between RQ-PCR and FCM was high and hence both methods are valuable clinical tools for identifying childhood ALL cases with increased risk of BMR.

Detection of clonal immunoglobulin and T-cell receptor gene rearrangements in childhood acute lymphoblastic leukemia using a low-cost PCR strategy.

BACKGROUND: Immunoglobulin (Ig) and T-cell receptor (TCR) gene rearrangements function as specific markers for minimal residual disease (MRD), which is one of the best predictors of outcome in childhood acute lymphoblastic leukemia (ALL). We recently reported on the prognostic value of MRD during the induction of remission through a simplified PCR method. Here, we report on gene rearrangement frequencies and offer guidelines for the application of the technique. PROCEDURE: Two hundred thirty-three children had DNA extracted from bone marrow. Ig and TCR gene rearrangements were amplified using consensus primers and conventional PCR. PCR products were submitted to homo/heteroduplex analysis. A computer program was designed to define combinations of targets for clonal detection using a minimum set of primers and reactions. RESULTS: At least one clonal marker could be detected in 98% of the patients, and two markers in approximately 80%. The most commonly rearranged genes in precursor B-cell ALL were IgH (75%), TCRD (59%), IgK (55%), and TCRG (54%). The most commonly rearranged genes for T-ALL were TCRG (100%) and TCRD (24%). The sensitivity of primers was limited to the detection of 1 leukemic cell among 100 normal cells. CONCLUSIONS: We propose that eight PCR reactions per ALL subtype would allow for the detection of two markers in most cases. In addition, these reactions are suitable for MRD monitoring, especially when aiming the selection of patients with high MRD levels (≥ 10(-2)) at the end of induction therapy. Such an approach would be very useful in centers with limited financial resources.

PCR-based clonality assessment in patients with lymphocytic leukaemias: a single-institution experience.

PCR-based clonality testing can be performed in all lymphoproliferations by analysing gene rearrangements of antigen receptors, rearrangements that are unique for each kind of lymphocyte. Reactive lymphoproliferations have polyclonally rearranged Ig/TCR genes, whereas malignant proliferations (leukaemias and lymphomas) show clonal rearrangements. The aim of this study was to assess the clinical benefits of clonality testing with previously evaluated consensus primers in leukaemia patients. The study included peripheral blood and bone marrow samples of 67 leukaemia patients (32 B-CLL, 24 B-ALL and 11 T-ALL). Clonality testing was based on PCR amplification of rearranged IgH and TCR genes. During diagnosis, monoclonal pattern was found in all analysed B-CLL and T-ALL samples. Testing in B-ALL patients showed positive results in all bone marrow and one peripheral blood samples. Results of clonality testing in B-CLL patients during follow-up were concordant between peripheral blood and bone marrow. Obtained results corresponded to clinical course in all but one patient. In B-ALL group, results of molecular testing in peripheral blood and bone marrow confirmed remission estimated according to clinical criteria in all except one patient. Before any clinical sign of relapse, monoclonal pattern was found in six/seven patients by bone marrow and in three/seven patients by peripheral blood analysis, respectively. Results of molecular monitoring in T-ALL patients did not confirme clinical evaluation in two patients. Obtained results indicate high accuracy of re-evaluated primers for clonality assessment in ALL and CLL patients at the time of diagnosis. Results of clonality testing in B-ALL patients indicate that bone marrow analysis has higher sensitivity compared to analysis of peripheral blood.