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      Murine Leukemias with Retroviral Insertions at Lmo2 Are Predictive of the Leukemias Induced in SCID-X1 Patients Following Retroviral Gene Therapy

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          Abstract

          Five X-linked severe combined immunodeficiency patients (SCID-X1) successfully treated with autologous bone marrow stem cells infected ex vivo with an IL2RG-containing retrovirus subsequently developed T-cell leukemia and four contained insertional mutations at LMO2. Genetic evidence also suggests a role for IL2RG in tumor formation, although this remains controversial. Here, we show that the genes and signaling pathways deregulated in murine leukemias with retroviral insertions at Lmo2 are similar to those deregulated in human leukemias with high LMO2 expression and are highly predictive of the leukemias induced in SCID-X1 patients. We also provide additional evidence supporting the notion that IL2RG and LMO2 cooperate in leukemia induction but are not sufficient and require additional cooperating mutations. The highly concordant nature of the genetic events giving rise to mouse and human leukemias with mutations at Lmo2 are an encouraging sign to those wanting to use mice to model human cancer and may help in designing safer methods for retroviral gene therapy.

          Author Summary

          Twenty patients with X-linked severe combined immunodeficiency (SCID-X1) have been successfully treated by gene therapy. Unfortunately, five of these patients have developed T-cell leukemia two or more years after receiving the therapeutic gene IL2RG on a retroviral vector. The leukemias developed because the vector inserted itself near cancer-causing genes and disrupted their normal regulation. Remarkably, in four patients, the vector inserted near a known T-cell oncogene, LMO2. We have found that in mice, similar retroviruses cause T-cell leukemias by inserting near Lmo2. We have found two leukemias that have retroviral insertions near Lmo2 and Il2rg in the same cell. The probability of these insertions happening by chance is exceedingly small and these results imply that these two genes are deregulated together to induce leukemia. Our data show that Lmo2 and Il2rg cooperate but may not be sufficient for leukemia development and additional mutations contribute to leukemia development. We have also found cooperating retroviral insertions in genes that are abnormally expressed in human T-cell leukemias. The mouse models provide unique insight into the pathogenesis of T-cell leukemia, and they are highly predictive of the leukemias caused by SCID-X1 gene therapy.

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          Most cited references38

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          Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1.

          Gene transfer into hematopoietic stem cells has been used successfully for correcting lymphoid but not myeloid immunodeficiencies. Here we report on two adults who received gene therapy after nonmyeloablative bone marrow conditioning for the treatment of X-linked chronic granulomatous disease (X-CGD), a primary immunodeficiency caused by a defect in the oxidative antimicrobial activity of phagocytes resulting from mutations in gp91(phox). We detected substantial gene transfer in both individuals' neutrophils that lead to a large number of functionally corrected phagocytes and notable clinical improvement. Large-scale retroviral integration site-distribution analysis showed activating insertions in MDS1-EVI1, PRDM16 or SETBP1 that had influenced regulation of long-term hematopoiesis by expanding gene-corrected myelopoiesis three- to four-fold in both individuals. Although insertional influences have probably reinforced the therapeutic efficacy in this trial, our results suggest that gene therapy in combination with bone marrow conditioning can be successfully used to treat inherited diseases affecting the myeloid compartment such as CGD.
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            Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling.

            Treatment of pediatric acute lymphoblastic leukemia (ALL) is based on the concept of tailoring the intensity of therapy to a patient's risk of relapse. To determine whether gene expression profiling could enhance risk assignment, we used oligonucleotide microarrays to analyze the pattern of genes expressed in leukemic blasts from 360 pediatric ALL patients. Distinct expression profiles identified each of the prognostically important leukemia subtypes, including T-ALL, E2A-PBX1, BCR-ABL, TEL-AML1, MLL rearrangement, and hyperdiploid >50 chromosomes. In addition, another ALL subgroup was identified based on its unique expression profile. Examination of the genes comprising the expression signatures provided important insights into the biology of these leukemia subgroups. Further, within some genetic subgroups, expression profiles identified those patients that would eventually fail therapy. Thus, the single platform of expression profiling should enhance the accurate risk stratification of pediatric ALL patients.
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              A random variance model for detection of differential gene expression in small microarray experiments.

              Microarray techniques provide a valuable way of characterizing the molecular nature of disease. Unfortunately expense and limited specimen availability often lead to studies with small sample sizes. This makes accurate estimation of variability difficult, since variance estimates made on a gene by gene basis will have few degrees of freedom, and the assumption that all genes share equal variance is unlikely to be true. We propose a model by which the within gene variances are drawn from an inverse gamma distribution, whose parameters are estimated across all genes. This results in a test statistic that is a minor variation of those used in standard linear models. We demonstrate that the model assumptions are valid on experimental data, and that the model has more power than standard tests to pick up large changes in expression, while not increasing the rate of false positives. This method is incorporated into BRB-ArrayTools version 3.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html). ftp://linus.nci.nih.gov/pub/techreport/RVM_supplement.pdf
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS Genet
                plos
                plosgen
                PLoS Genetics
                Public Library of Science (San Francisco, USA )
                1553-7390
                1553-7404
                May 2009
                May 2009
                22 May 2009
                : 5
                : 5
                : e1000491
                Affiliations
                [1 ]Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
                [2 ]Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
                [3 ]Mouse Cancer Genetics Program, National Cancer Institute, Frederick, Maryland, United States of America
                [4 ]Department of Pathology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
                [5 ]Advanced Biomedical Computing Center, National Cancer Institute, Frederick, Maryland, United States of America
                [6 ]St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
                [7 ]Institute of Molecular and Cell Biology, Biopolis, Singapore, Singapore
                University of Washington, United States of America
                Author notes

                Conceived and designed the experiments: UPD. Performed the experiments: UPD RT SMC. Analyzed the data: UPD NAJ NGC. Contributed reagents/materials/analysis tools: UPD KA MAT MY RS JRD NAJ NGC. Wrote the paper: UPD NAJ NGC.

                Article
                09-PLGE-RA-0225R3
                10.1371/journal.pgen.1000491
                2679194
                19461887
                7467fd1b-e10d-42ad-adf1-b80b41bacc6c
                Davé et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 12 February 2009
                : 22 April 2009
                Page count
                Pages: 13
                Categories
                Research Article
                Genetics and Genomics/Cancer Genetics
                Genetics and Genomics/Disease Models
                Hematology/Acute Lymphoblastic Leukemia
                Oncology/Hematological Malignancies
                Virology/Viruses and Cancer

                Genetics
                Genetics

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