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J R Downing

Publications and source records attributed to J R Downing.

At least 19 recordsLinked to original sources
PubMed2006

Genome-wide approach to identify risk factors for therapy-related myeloid leukemia.

Using a target gene approach, only a few host genetic risk factors for treatment-related myeloid leukemia (t-ML) have been defined. Gene expression microarrays allow for a more genome-wide approach to assess possible genetic risk factors for t-ML. We assessed gene expression profiles (n=12 625 probe sets) in diagnostic acute lymphoblastic leukemic cells from 228 children treated on protocols that included leukemogenic agents such as etoposide, 13 of whom developed t-ML. Expression of 68 probes, corresponding to 63 genes, was significantly related to risk of t-ML. Hierarchical clustering of these probe sets clustered patients into three groups with 94, 122 and 12 patients, respectively; 12 of the 13 patients who went on to develop t-ML were overrepresented in the latter group (P<0.0001). A permutation test indicated a low likelihood that these probe sets and clusters were obtained by chance (P<0.001). Distinguishing genes included transcription-related oncogenes (v-Myb, Pax-5), cyclins (CCNG1, CCNG2 and CCND1) and histone HIST1H4C. Common transcription factor recognition elements among similarly up- or downregulated genes included several involved in hematopoietic differentiation or leukemogenesis (Maz, PU.1, ARNT). This approach has identified several genes whose expression distinguishes patients at risk of t-ML, and suggests targets for assessing germline predisposition to leukemogenesis.

Child↗
PubMed2004

Modern diagnostics in chronic myeloproliferative diseases (CMPDs).

According to the new WHO classification a group of chronic myeloproliferative diseases (CMPDs) were defined: chronic myeloid leukemia (CML), chronic neutrophilic leukemia (CNL), chronic eosinophilic leukemia and hypereosinophilic syndrome (CEL/HES), polycythemia vera (PV), chronic idiopathic myelofibrosis (with extramedullary hematopoiesis, CIMF), essential thrombocythemia (ET), and so called CMPD/unclassifiable. As clinical features and laboratory findings differ widely between these diseases several diagnostic approaches are mandatory at diagnosis for classification and are needed also for follow up studies, especially for the measurement of minimal residual disease (MRD). We here outline the laboratory set up at diagnosis and during follow up in CMPDs with specific focus on the respective therapeutical consequences. Only by using a comprehensive diagnostic panel including cytomorphology, cytogenetics, and molecular genetic methods establishing the correct diagnosis, optimizing treatment as well as evaluating treatment response is possible in CMPDs today.

Blood Cell Count↗
PubMed2004

Expression of the adaptor protein BLNK/SLP-65 in childhood acute lymphoblastic leukemia.

Deficient expression of BLNK, an adaptor molecule crucial for normal B-cell development, is associated with increased pro-B/pre-B-cell expansion in mice. It has been proposed that BLNK deficiency is a primary cause of B-lineage acute lymphoblastic leukemia (ALL). We studied BLNK expression in the leukemic cells from 352 patients with childhood ALL (309 B-lineage; 43 T-lineage). By HG_U95Av2 Affymetrix GeneChip analysis, BLNK was expressed in 275 of 284 (96.8%) B-lineage ALL samples but in only one of 43 (2.3%) T-lineage ALL samples. Of 118 B-lineage ALL samples analyzed with the HG_U133A GeneChip, 117 (99.2%) expressed BLNK. All 30 primary B-lineage ALL samples studied by RT-PCR expressed BLNK transcripts; all 19 samples studied by Western blotting or flow cytometry expressed BLNK protein. Levels of BLNK in B-lineage ALL were as high as those of their normal counterparts; they were not related with genetic subgroups or differentiation stage. These results indicate that BLNK deficiency is a rare occurrence in childhood B-lineage ALL and is unlikely to be a common leukemogenic event as previously proposed.

Adaptor Proteins, Signal Transducing↗
PubMed2003

Acute leukemia: subtype discovery and prediction of outcome by gene expression profiling.

Contemporary treatment of acute leukemia requires the accurate assignment of patients at diagnosis to specific risk groups. 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 and 130 pediatric AML patients. Our analysis demonstrates that the single platform of gene expression profiling can accurately identify the known prognostically important genetic subtypes of ALL, including T-ALL, E2A-PBX1, TEL-AML1, MLL rearrangements, BCR-abl, and hyperdiploid >50 chromosomes, and AML, including t(15;17)[PML-RARalpha], t(8;21)[AML1-ETO], inv(16)[CBFbeta-MYH11], MLL gene rearrangement, and cases with FAB-M7 morphology. In addition, within ALL, a novel subgroup was identified based on its unique expression profile. Examination of the gene expression signatures for the different genetic subtypes of acute leukemia provided important insights into the molecular pathology of these leukemias.

Acute Disease↗
PubMed2002

Characteristics and outcome of t(8;21)-positive childhood acute myeloid leukemia: a single institution's experience.

To elucidate the clinical and biological features of childhood acute myeloid leukemia (AML) with the t(8;21), we reviewed the records of patients with AML treated at St Jude Children's Research Hospital over a 17-year period (1980 to 1996). Of 298 patients with AML, 40 (13%) had blast cells that contained the t(8;21). This translocation was associated with a high frequency of French-American-British M2 morphology (82%) and the presence of granulocytic sarcoma (23%). Molecular analysis detected the AML1-ETO fusion transcript in all 25 cases with the t(8;21) tested, but failed to identify additional cases with AML1-ETO among the 127 cases with other cytogenetic findings. Compared to patients with other genetic abnormalities, those with the t(8;21) were less likely to have internal tandem duplications of the FLT3 gene (none of 10 vs 16 of 68). The 6-year overall survival estimate was 55% +/- 9% and the event-free survival estimate, 33% +/- 7%. Of the clinical and biological features examined, only gender was prognostically significant: the 6-year overall survival estimate for males was 68% +/- 10%, compared to 33% +/- 11 for female patients (P = 0.03). Treatment outcome was not influenced by the chemotherapy regimen used or by the use of autologous hematopoietic stem cell transplantation. These results suggest that t(8;21)-positive AML represents a heterogeneous disease with variable outcome. The reported favorable outcome for t(8;21)-positive AML in other studies may be due to the use of high-dose cytarabine.

Acute Disease↗
PubMed2001

A hematopoietic-specific transmembrane protein, Art-1, is possibly regulated by AML1.

The functions of AML1 in hematopoietic differentiation are repressed by AML1-mutants including the AML1/ETO chimeric protein, which is seen in t(8;21) acute myeloid leukemia. Erythroid progenitors of the patients with t(8;21) AML expressed AML1/ETO. To investigate the effect of AML1/ETO in erythroid cells, we made a tetracycline-regulated AML1/ETO overexpression system in mouse erythroleukemic (MEL) cells. Enforced AML1/ETO repressed the terminal erythroid differentiation. Furthermore, we performed representational difference analysis using this MEL cell system to clone the downstream targets of AML1 in erythroid cell differentiation. We cloned a novel transmembrane protein, Art-1 (AML1-regulated transmembrane protein 1), which is a member of tetramembrane spanning superfamily. Art-1 expression was restricted in hematopoietic cells. It was upregulated by AML1 and downregulated by AML1/ETO in both erythroid and myeloid cells, and increased during erythroid cell differentiation. Art-1 may play an important role in the differentiation of erythroid cells, possibly as a direct downstream target of AML1.

Amino Acid Sequence↗
PubMed2001

The role of the AML1 transcription factor in leukemogenesis.

Chromosomal translocations are one of the hallmarks of human leukemias. These structural abnormalities result in the generation of genetic mutations that play a direct role in the transformation of hematopoietic stem cells. Some of the most common targets of these chromosomal rearrangements are the genes that encode the AML1/CBFbeta transcription factor complex. The AML1/CBFbeta complex plays a critical role in normal hematopoiesis, controlling the initiation of a transcriptional cascade required for the formation of definitive hematopoietic stem cells. Understanding how alterations in the normal biologic activity of this transcription factor complex lead to the initiation of leukemia will provide critical insights in the molecular pathogenesis of this disease. These insights in turn are likely to lead to the development of more rational approaches to the treatment of acute leukemia. In this review, we will summarize our current understanding of the mechanisms by which alterations in the activity of AML1/CBFbeta contribute to the development of leukemia.

Core Binding Factor Alpha 2 Subunit↗
PubMed2001

Multicolor spectral karyotyping identifies novel translocations in childhood acute lymphoblastic leukemia.

We used a recently described molecular cytogenetic method, spectral karyotyping (SKY), to analyze metaphase chromosomes from 30 pediatric patients with acute lymphoblastic leukemia (ALL). This group included 20 patients whose leukemic blast cells lacked chromosomal abnormalities detected by conventional cytogenetics and 10 patients whose blast cells had multiple chromosomal abnormalities that could not be completely identified by G-banding analysis. In two of the 20 patients (10%) with apparently normal karyotypes, SKY identified three cryptic translocations: a t(7;8)(q34-35;q24.1) in one patient and a t(13;17)(q22;q21) and a der(19)t(17;19)(q22;p13) in another. Fluorescence in situ hybridization using subtelomeric probes proved the latter translocation to be a t(17;19). SKY analysis was also successful in defining the nature of the chromosomal abnormalities in four of the 10 patients with marker and derivative chromosomes. The identified abnormalities in the latter group included three novel translocations: a der(X)t(X;5)(p11.4;q31), a der(21)t(X;21)(p11.4;p11.2) and a t(X;9)(p11.4;p13). The presence of the t(X;9) was suggested by conventional cytogenetics. The application of fluorescence in situ hybridization using chromosome-specific painting probes and locus-specific probes complemented the SKY analysis by confirming the nature of the chromosome rearrangements defined by SKY and by identifying the amplification of the AML1/CBFA2 gene in one patient with a duplicated 21q. Our study demonstrates the utility of SKY in identifying novel translocations and in refining the identity of chromosomal abnormalities in leukemias.

Adolescent↗
PubMed2001

Use of reverse transcriptase polymerase chain reaction for diagnosis and staging of alveolar rhabdomyosarcoma, Ewing sarcoma family of tumors, and desmoplastic small round cell tumor.

PURPOSE: To compare the use of reverse transcriptase polymerase chain reaction (RT-PCR) with that of morphology-based methods for diagnosis, staging, and detection of metastatic disease in pediatric alveolar rhabdomyosarcoma (ARMS), Ewing sarcoma family of tumors (ESFT), and desmoplastic small round cell tumors (DSRCT). MATERIALS AND METHODS: RT-PCR assays for the EWS-FLII, EWS-ERG, PAX3-FKHR, PAX7-FKHR, and EWS-WTI fusion transcripts were performed on RNA extracted from the primary tumor tissue, bone marrow, and body fluids obtained at initial presentation and relapse. Molecular findings were compared with original histologic diagnoses and results of staging procedures. RESULTS: Eighty-eight samples from 47 patients with ARMS (n = 13), ESFT (n = 31), or DSRCT (n = 3) were analyzed. The detection rate of metastatic disease was significantly higher with RT-PCR (95%) as compared with the morphologic methods (70%) for the three pediatric sarcomas studied. In primary tumors with characteristic fusion transcript, RT-PCR was positive in all cases with morphologic evidence of metastatic disease. Moreover, in six patients (3 with ARMS, 2 with DSRCT, and 1 with ESFT) with metastatic disease, micrometastases in bone marrow (4) and other sites (2) were detected by RT-PCR alone. Importantly, none of the patients with localized disease diagnosed had micrometastases detected by RT-PCR in bone marrow. CONCLUSIONS: The high sensitivity and specificity of RT-PCR for the characteristic fusion transcripts of pediatric sarcomas make it an ideal method to aid in the routine staging of these patients. In addition, the 100% sensitivity of RT-PCR in detection of micrometastasis makes it useful for follow-up and detection of minimal residual disease. However, the clinical significance of molecularly-detectable disease remains unknown. Further studies should aim to elucidate the therapeutic and prognostic implications of micrometastases detected by RT-PCR alone.

Biomarkers, Tumor↗
PubMed2001

The E2A-HLF oncoprotein activates Groucho-related genes and suppresses Runx1.

The E2A-HLF fusion gene, formed by the t(17;19)(q22;p13) chromosomal translocation in leukemic pro-B cells, encodes a chimeric transcription factor consisting of the transactivation domain of E2A linked to the bZIP DNA-binding and protein dimerization domain of hepatic leukemia factor (HLF). This oncoprotein blocks apoptosis induced by growth factor deprivation or irradiation, but the mechanism for this effect remains unclear. We therefore performed representational difference analysis (RDA) to identify downstream genetic targets of E2A-HLF, using a murine FL5.12 pro-B cell line that had been stably transfected with E2A-HLF cDNA under the control of a zinc-regulated metallothionein promoter. Two RDA clones, designated RDA1 and RDA3, were differentially upregulated in E2A-HLF-positive cells after zinc induction. The corresponding cDNAs encoded two WD40 repeat-containing proteins, Grg2 and Grg6. Both are related to the Drosophila protein Groucho, a transcriptional corepressor that lacks DNA-binding activity on its own but can act in concert with other proteins to regulate embryologic development of the fly. Expression of both Grg2 and Grg6 was upregulated 10- to 50-fold by E2A-HLF. Immunoblot analysis detected increased amounts of two additional Groucho-related proteins, Grg1 and Grg4, in cells expressing E2A-HLF. A mutant E2A-HLF protein with a disabled DNA-binding region also mediated pro-B cell survival and activated Groucho-related genes. Among the transcription factors known to interact with Groucho-related protein, only RUNX1 was appreciably downregulated by E2A-HLF. Our results identify a highly conserved family of transcriptional corepressors that are activated by E2A-HLF, and they suggest that downregulation of RUNX1 may contribute to E2A-HLF-mediated leukemogenesis.

Amino Acid Sequence↗
PubMed2001

ETO, a target of t(8;21) in acute leukemia, makes distinct contacts with multiple histone deacetylases and binds mSin3A through its oligomerization domain.

t(8;21) and t(16;21) create two fusion proteins, AML-1-ETO and AML-1-MTG16, respectively, which fuse the AML-1 DNA binding domain to putative transcriptional corepressors, ETO and MTG16. Here, we show that distinct domains of ETO contact the mSin3A and N-CoR corepressors and define two binding sites within ETO for each of these corepressors. In addition, of eight histone deacetylases (HDACs) tested, only the class I HDACs HDAC-1, HDAC-2, and HDAC-3 bind ETO. However, these HDACs bind ETO through different domains. We also show that the murine homologue of MTG16, ETO-2, is also a transcriptional corepressor that works through a similar but distinct mechanism. Like ETO, ETO-2 interacts with N-CoR, but ETO-2 fails to bind mSin3A. Furthermore, ETO-2 binds HDAC-1, HDAC-2, and HDAC-3 but also interacts with HDAC-6 and HDAC-8. In addition, we show that expression of AML-1-ETO causes disruption of the cell cycle in the G(1) phase. Disruption of the cell cycle required the ability of AML-1-ETO to repress transcription because a mutant of AML-1-ETO, Delta469, which removes the majority of the corepressor binding sites, had no phenotype. Moreover, treatment of AML-1-ETO-expressing cells with trichostatin A, an HDAC inhibitor, restored cell cycle control. Thus, AML-1-ETO makes distinct contacts with multiple HDACs and an HDAC inhibitor biologically inactivates this fusion protein.

Amino Acid Sequence↗
PubMed2001

Lack of BCL10 mutations in multiple myeloma and plasma cell leukemia.

To determine whether the BCL10 mutation plays a role in the oncogenesis of plasma cell dyscrasias, we used polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and direct sequencing analysis and examined the genomic BCL10 mutations in 57 patients with multiple myeloma or plasma cell leukemia and 52 normal bone marrow samples. We found three polymorphic sequence variants, either alone or in combination, at codons 5 and 8, and in intron 1 at base 58 of the BCL10 gene in 37 patients with plasma cell dyscrasia. Identical aberrant band shifts were also observed in 34 normal marrow samples. No polymorphic variants were identified in exon 2 or 3 in either patient or control samples, and no pathogenic mutations were detected. Patients with plasma cell dyscrasias in Taiwan appeared to have a higher frequency of polymorphisms at codon 5 and intron 1 at base 58, and a lower frequency at codons 8 and 213. Our results suggest that BCL10 is not involved in the oncogenesis of plasma cell dyscrasias.

Adaptor Proteins, Signal Transducing↗
PubMed2000

Expression of the AML-1 oncogene shortens the G(1) phase of the cell cycle.

The AML-1-encoded transcription factor, AML-1B, regulates numerous hematopoietic-specific genes. Inappropriate expression of AML-1-family proteins is oncogenic in cell culture systems and in mice. To understand the oncogenic functions of AML-1, we established cell lines expressing AML-1B to examine the role of AML-1 in the cell cycle. DNA content analysis and bromodeoxyuridine pulse-chase studies indicated that entry into the S phase of the cell cycle was accelerated by up to 4 h in AML-1B-expressing 32D.3 myeloid progenitor cells as compared with control cells or cells expressing E2F-1. However, AML-1B was not able to induce continued cell cycle progression in the absence of growth factors. The DNA binding and transactivation domains of AML-1B were required for altering the cell cycle. Thus, AML-1B is the first transcription factor that affects the timing of the mammalian cell cycle.

Animals↗
PubMed2000

Alterations of the AML1 transcription factor in human leukemia.

The identification of clonal chromosomal translocations in human leukemias provided one of the first insights into the underlying pathogenesis of this clinically heterogeneous disease. Over the last decade a large number of these chromosomal rearrangements have been molecularly cloned and the involved genes identified. A surprising finding that has emerged from this work is that many of these chromosomal alterations target the genes encoding the AML1/CBFbeta transcription factor complex, a critical regulator of normal hematopoiesis. In this review, we summarize our present understanding of the mechanisms through which alterations of AML1/CBFbeta contribute to leukemogenesis.

Acute Disease↗
PubMed2000

Biological characteristics of the leukemia-associated transcriptional factor AML1 disclosed by hematopoietic rescue of AML1-deficient embryonic stem cells by using a knock-in strategy.

AML1 is one of the most frequently mutated genes associated with human acute leukemia and encodes the DNA-binding subunit of the heterodimering transcriptional factor complex, core-binding factor (CBF) (or polyoma enhancer binding protein 2 [PEBP2]). A null mutation in either AML1 or its dimerizing partner, CBFbeta, results in embryonic lethality secondary to a complete block in fetal liver hematopoiesis, indicating an essential role of this transcription complex in the development of definitive hematopoiesis. The hematopoietic phenotype that results from the loss of AML1 can be replicated in vitro with a two-step culture system of murine embryonic stem (ES) cells. Using this experimental system, we now demonstrate that this hematopoietic defect can be rescued by expressing the PEBP2alphaB1 (AML1b) isoform under the endogenous AML1-regulatory sequences through a knock-in (targeted insertion) approach. Moreover, we demonstrate that the rescued AML1(-/-) ES cell clones contribute to lymphohematopoiesis within the context of chimeric animals. Rescue requires the transcription activation domain of AML1 but does not require the C-terminal VWRPY motif, which is conserved in all AML1 family members and has been shown to interact with the transcriptional corepressor, Groucho/transducin-like Enhancer of split. Taken together, these data provide compelling evidence that the phenotype seen in AML1-deficient mice is due solely to the loss of transcriptionally active AML1.

Animals↗
PubMed1999

Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.

Although cancer classification has improved over the past 30 years, there has been no general approach for identifying new cancer classes (class discovery) or for assigning tumors to known classes (class prediction). Here, a generic approach to cancer classification based on gene expression monitoring by DNA microarrays is described and applied to human acute leukemias as a test case. A class discovery procedure automatically discovered the distinction between acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) without previous knowledge of these classes. An automatically derived class predictor was able to determine the class of new leukemia cases. The results demonstrate the feasibility of cancer classification based solely on gene expression monitoring and suggest a general strategy for discovering and predicting cancer classes for other types of cancer, independent of previous biological knowledge.

Acute Disease↗