1: Leukemia. 2005 Jun;19(6):1042-50. Gene expression profiling of leukemic cell lines reveals conserved molecular signatures among subtypes with specific genetic aberrations. Andersson A, Eden P, Lindgren D, Nilsson J, Lassen C, Heldrup J, Fontes M, Borg A, Mitelman F, Johansson B, Hoglund M, Fioretos T. Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden. anna.andersson@klingen.lu.se Hematologic malignancies are characterized by fusion genes of biological/clinical importance. Immortalized cell lines with such aberrations are today widely used to model different aspects of leukemogenesis. Using cDNA microarrays, we determined the gene expression profiles of 40 cell lines as well as of primary leukemias harboring 11q23/MLL rearrangements, t(1;19)[TCF3/PBX1], t(12;21)[ETV6/RUNX1], t(8;21)[RUNX1/CBFA2T1], t(8;14)[IGH@/MYC], t(8;14)[TRA@/MYC], t(9;22)[BCR/ABL1], t(10;11)[PICALM/MLLT10], t(15;17)[PML/RARA], or inv(16)[CBFB/MYH11]. Unsupervised classification revealed that hematopoietic cell lines of diverse origin, but with the same primary genetic changes, segregated together, suggesting that pathogenetically important regulatory networks remain conserved despite numerous passages. Moreover, primary leukemias cosegregated with cell lines carrying identical genetic rearrangements, further supporting that critical regulatory pathways remain intact in hematopoietic cell lines. Transcriptional signatures correlating with clinical subtypes/primary genetic changes were identified and annotated based on their biological/molecular properties and chromosomal localization. Furthermore, the expression profile of tyrosine kinase-encoding genes was investigated, identifying several differentially expressed members, segregating with primary genetic changes, which may be targeted with tyrosine kinase inhibitors. The identified conserved signatures are likely to reflect regulatory networks of importance for the transforming abilities of the primary genetic changes and offer important pathogenetic insights as well as a number of targets for future rational drug design. PMID: 15843827 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 2: Leuk Lymphoma. 2003 Jul;44(7):1187-99. Transcriptional profiling during the early differentiation of granulocyte and monocyte progenitors controlled by conditional versions of the E2a-Pbx1 oncoprotein. Sykes DB, Scheele J, Pasillas M, Kamps MP. Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0612, USA. The E2a-Pbx1 oncoprotein of human pre-B cell leukemia prevents differentiation and maintains continued cell division in cultured myeloid progenitors. Previously, estrogen-dependent forms of E2a-Pbx1 were generated that immortalized neutrophil (ECoM-G cells) or monocyte (ECoM-M cells) progenitors and that permitted their terminal differentiation upon estrogen withdrawal. Here, representational difference analysis (RDA) and Affymetrix array analysis are used to identify changes in gene expression that accompany the early differentiation of these cells. The promoters of these genes, whose expression changes upon E2a-Pbx1 inactivation, integrate the biochemical mechanism through which E2a-Pbx1 arrests differentiation and maintains cell division. Inactivation of E2a-Pbx1 caused the 10- to 80-fold up regulation of a small subset of myeloid differentiation genes (MRP8, Cnlp, NB1, Bactenecin, YM1, Stefin 1, Lipocortin, Lactoferrin, gp91 phox and Ly6-G) and a 10-fold down regulation of the TLE1 corepressor gene, as well as of a group of genes expressed in dividing cells (c-Myc, Nucleophosmin, Spermidine synthase, NOP56, Hnrpa1). Transcription of 97% of cellular genes, including 300 other transcription factor genes (21 Hox genes) and other myeloid genes, varied less than 3-fold, with most varying less than 50%. Therefore, E2a-Pbx1 prevents transcription and maintains the cell cycle by a specific rather than a global transcriptional mechanism. Monocyte progenitors were distinguished by persistent expression of IRF8 and of a category of other genes characterized as "interferon-stimulated" (ISG15, ISG20, Ifit1, Ifi202a, Ifi203, IfiS204, Ifi204-related, IRF7 and Ly6-E.1), as well as by the upregulation of the Lrg21 bZip transcription factor gene during late differentiation. The synchronous expression of stage-specific and cell cycle genes regulated by E2a-Pbx1 in these cell lines comprises a model system in which analysis of their promoters can be used as a starting point to backtrack to the transcriptional mechanisms of oncogenesis by E2a-Pbx1. PMID: 12916872 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 3: Leukemia. 2002 Jul;16(7):1233-58. Antigen expression patterns reflecting genotype of acute leukemias. Hrusak O, Porwit-MacDonald A. Institute of Immunology/CLIP, Charles University, Prague, Czech Republic. Multi-parameter flow cytometry, molecular genetics, and cytogenetic studies have all contributed to new classification of leukemia. In this review we discuss immunophenotypic characteristics of major genotypic leukemia categories. We describe immunophenotype of: B-lineage ALL with MLL rearrangements, TEL/AML1, BCR/ABL, E2A/PBX1 translocations, hyperdiploidy, and myc fusion genes; T-ALL with SCL gene aberrations and t(5;14) translocation; and AML with AML1/ETO, PML/RARalpha, OTT/MAL and CBFbeta/MYH11 translocations, trisomies 8 or 11 and aberrations of chromosomes 7 and 5. Whereas some genotypes associate with certain immunophenotypic features, others can present with variable immunophenotype. Single molecules (as NG2, CBFbeta/SMMHC and PML/RARalpha proteins) associated with or derived from specific translocations have been described. More often, complex immunophenotype patterns have been related to the genotype categories. Most known associations between immunophenotype and genotype have been defined empirically. Therefore, these associations should be validated in independent patient cohorts before they can be widely used for prescreening of leukemia. Progress in our knowledge on leukemia will show how the molecular-genetic changes modulate the immunophenotype as well as how the expressed protein molecules further modulate cell behavior. Publication Types: Review PMID: 12094248 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 4: Best Pract Res Clin Haematol. 2001 Sep;14(3):593-607. Acute lymphoblastic leukaemia. Harrison CJ. Leukaemia Research Fund/UK Cancer Cytogenetics Group Karyotype Database in Acute Lymphoblastic Leukaemia, Department of Haematology, Royal Free and University College School of Medicine, Rowland Hill Street, London, NW3 2PF, UK. In acute lymphoblastic leukaemia (ALL) the karyotype provides important prognostic information which is beginning to have an impact on treatment. The most significant structural chromosomal changes include: the poor-risk abnormalities; t(9;22)(q34;q11), giving rise to the BCR/ABL fusion and rearrangements of the MLL gene; abnormalities previously designated as poor-risk; t(1;19)(q23;p13), producing the E2A/PBX1 and rearrangements of MYC with the immunoglobulin genes; and the probable good risk translocation t(12;21)(p13;q22), which results in the ETV6/AML1 fusion. These abnormalities occur most frequently in B-lineage leukaemias, while rearrangements of the T cell receptor genes are associated with T-lineage ALL. Abnormalities of the short arm of chromosome 9, in particular homozygous deletions involving the tumour suppressor gene (TSG) p16(INK4A), are associated with a poor outcome. Numerical chromosomal abnormalities are of particular importance in relation to prognosis. High hyperdiploidy (51-65 chromosomes) is associated with a good risk, whereas the outlook for patients with near haploidy (23-29 chromosomes) is extremely poor. In view of the introduction of risk-adjusted therapy into the UK childhood ALL treatment trials, an interphase FISH screening programme has been developed to reveal chromosomal abnormalities with prognostic significance in childhood ALL. Novel techniques in molecular cytogenetics are identifying new, cryptic abnormalities in small groups of patients which may lead to further improvements in future treatment protocols. Copyright 2001 Harcourt Publishers Ltd. Publication Types: Review Review, Tutorial PMID: 11640871 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 5: Leukemia. 2001 Mar;15(3):362-70. The leukemogenic transcription factor E2a-Pbx1 induces expression of the putative N-myc and p53 target gene NDRG1 in Ba/F3 cells. Rutherford MN, Bayly GR, Matthews BP, Okuda T, Dinjens WM, Kondoh H, LeBrun DP. Department of Pathology, Queen's University, Kingston, Ontario, Canada. The chimeric transcription factor E2a-Pbx1 is expressed as a result of the 1;19 chromosomal translocation in some 5% of cases of pediatric acute lymphoblastic leukemia. We investigated the biological and transcriptional consequences of forced expression of E2a-Pbx1 in the interleukin-3 (IL-3) dependent, bone marrow-derived cell line Ba/F3. We show that forced expression of E2a-Pbx1 induces apoptosis in Ba/F3 cells without apparent effects on cell cycle progression. This pro-apoptotic effect is enhanced on cytokine deprivation. Furthermore, using cDNA representational difference analysis (RDA), we show that these cellular effects are associated with marked induction of the gene NDRG1, which was previously identified as a target of transcriptional repression by N-myc and induction by the tumor suppressor protein p53. We identify a portion of the NDRG1 promoter capable of mediating transcriptional induction by E2a-Pbx1 and show that NDRG1 is also induced on simple IL-3 deprivation of BaF3 cells. Although we show that E2a-Pbx1 induction of NDRG1 is not impaired as a result of targeting p53 using HPV E6, and therefore does not appear to be p53-dependent, our results overall are consistent with the notion that induction of NDRG1 by E2a-Pbx1 may represent part of an apoptotic or cytostatic cellular response to oncogene activation. PMID: 11237058 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 6: Baillieres Best Pract Res Clin Haematol. 2000 Sep;13(3):427-39. The genetics of childhood acute lymphoblastic leukaemia. Harrison CJ. Department of Haematology, Royal Free and University College Medical School, London, UK. In childhood acute lymphoblastic leukaemia (ALL) a number of genetic changes have been identified which provide diagnostic and prognostic information with a direct impact on patient management. The most significant abnormalities include the translocation, t(12;21)(p13;q22), giving rise to the ETV6/AML1 gene fusion; BCR/ABL arising from t(9;22)(q34;q11); re-arrangements of the MLL gene; the E2A/PBX1 from the t(1;19)(q23;p13); re-arrangements of MYC with the immunoglobulin genes and re-arrangements of the T cell receptor genes. Chromosomal deletions, particularly those of the short arms of chromosomes 9 and 12 and the long arm of chromosome 6, have been postulated to be the sites of tumour suppressor genes (TSG). Numerical chromosomal abnormalities are of particular importance in relation to prognosis. High hyperdiploidy (50-65 chromosomes) is associated with a good risk, whereas the outlook for patients with near haploidy (23-29 chromosomes) is extremely poor. In view of the introduction of risk-adjusted therapy into the UK childhood ALL treatment trials, an interphase FISH screening programme has been developed to reveal chromosomal abnormalities with prognostic significance in childhood ALL. Publication Types: Review Review, Tutorial PMID: 11030043 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 7: Biochim Biophys Acta. 1999 Jul 29;1424(1):R21-36. Transcriptional deregulation in hereditary disorders and cancer: the 12th annual CABM symposium, October 21-22, 1998, Piscataway, NJ. Rabson AB. Center for Advanced Biotechnology and Medicine, Cancer Institute of New Jersey, UMDNJ-Robert Wood Johnson Medical School, Piscataway 08854, USA. rabson@mbcl.rutgers.edu As can be seen from the above descriptions, the presentations at the CABM symposium provided an extraordinarily rich and diverse panorama of some of the most exciting science in current molecular biology. The presentations provided both a general overview and a detailed analysis of multiple biological systems, which despite their specific differences, also generated insights into important common themes. The success of any meeting is most appropriately measured by the kinds of questions that are provoked for future study, not merely by the recitation of past discoveries. In fact, the different presentations often raised highly similar questions for future study. At the most fundamental levels of transcriptional regulation, what are the signals that provide specificity of gene expression? What is the structural basis of specific protein-protein interactions, such as those between homeodomain proteins and beta-catenin-Lef1 interactions, and how are these determinants altered in transcriptional regulation in oncogenesis and in genetic diseases? How is specificity achieved in transcriptional repression, given that the fundamental biochemical reactions often involve modifications of relatively ubiquitous components such as histones? To what extent do changes in specificity of gene activation and repression or in chromosomal architecture mediate the kinds of developmental and oncogenic signals mediated through transcriptional regulators such as Myc, BCL6 and other basic helix-loop-helix proteins and the HMGI proteins? How do altered signaling pathways affect diseases of development and differentiation such as cardiovascular disorders and aging itself? What are the pathways that integrate extracellular signals and transcription during the process of organogenesis? How do fundamental cellular structures such as adhesion junctions, and the interactions of a cell with other cells and extracellular matrix impact on normal and abnormal development and on malignancy, and how do these levels of structure and function alter nuclear regulation of transcription and cell division? These are some of the recurrent questions raised in talk after talk at this symposium, questions that undoubtedly will provide the impetus for important discoveries that will be presented at future CABM symposia. Publication Types: Congresses PMID: 10456033 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 8: Oncogene. 1998 Sep 3;17(9):1149-57. Fli-1b is generated by usage of differential splicing and alternative promoter. Dhulipala PD, Lee L, Rao VN, Reddy ES. Department of Human Genetics, Allegheny University of the Health Sciences, Philadelphia, Pennsylvania 19102, USA. The proto-oncogene Fli-1, a member of Ets family is rearranged or activated through proviral integration in erythroleukemias, induced by Friends' Murine Leukemia Virus. The DNA binding domain (ETS domain) of Fli-1 is fused to the RNA binding domain of EWS by t(11q24:22q12) chromosomal translocation in Ewing's sarcoma and primitive neuroectodermal tumors. Screening of human cDNA libraries has identified two different 5'-termini and alternatively spliced forms of the human Fli-1 gene (Fli-1b), suggesting the possible existence of two independent promoters. The genomic sequence adjacent to the alternate exon of human Fli-1b gene shows functional promoter activity when cloned in promoter-less CAT expression vector and transfected into QT-6 cells. The transcription initiation (CAP) site and minimum promoter region necessary for function were localized. The 5'-flanking regions of human Fli-1b and mouse Fli-1 show 80% homology suggesting conserved promoter regulatory elements. The Fli-1b 5'-flanking sequence lacks canonical TATA or CCAAT boxes but contains a partially conserved TATA-like sequence at position 242. Several transcription factor binding sequences like ATF/CREB, E2A-PBX1, EBP, PEA-3, ETS-2, Sp-1, c-Myc, TBP, GATA-1 and Oct-3 were conserved in the promoter sequence. Functional promoter assays revealed that Fli-1b promoter shows very strong transcriptional activation compared to Fli-1 promoter. We also showed that variant Fli-1b has transcriptional activation properties similar to those of Fli-1. Fli-1b and Fli-1 show differential expression in various hematopoietic cell lines. This differential expression and promoter activities of Fli-1 and Fli-1b suggests that several mechanisms are involved in Fli-1 gene regulation which are mediated by many transcription factors. PMID: 9764825 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 9: Oncogene. 1997 Nov 27;15(22):2735-42. Pim1 cooperates with E2a-Pbx1 to facilitate the progression of thymic lymphomas in transgenic mice. Feldman BJ, Reid TR, Cleary ML. Department of Pathology, Stanford University Medical Center, California 94305, USA. Mice transgenic for the leukemia oncogene E2A-PBX1 invariably develop lethal, high-grade T-cell lymphomas by 5 months of age. In this study, retroviral insertional mutagenesis was employed to identify oncogenes that cooperate with the E2A-PBX1 transgene in lymphomagenesis. Neonatal retroviral infection substantially reduced length of survival due to accelerated development of lymphomas (81 versus 130 days). The Pim1 gene was targeted by retroviral insertions in 48% of accelerated lymphomas whereas less than 5% contained activated c-Myc and none contained activated Pim2. However, Pim1 DNA rearrangements were frequently sub-stoichiometric and not present at all sites of involvement in an otherwise monoclonal lymphoma indicating that Pim1 activation occurred late in the course of lymphomagenesis. Tumor subpopulations containing activated Pim1 alleles displayed a substantial growth advantage over Pim1 negative cells following serial transfer to secondary, syngeneic recipients. Cooperative interactions were observed in intercrossed Pim1 and E2A-PBX1 transgenic mice in which all double transgenic progeny developed lethal, diffuse T lineage lymphomas by 3 months of age, whereas only 13% of E2A-PBX1 and none of Pim1 single transgenic intercross progeny developed lymphomas by 1 year. Tumors from double transgenic mice were monoclonal providing evidence that additional genetic events were required for transformation. Therefore, Pim1 and E2a-Pbx1 cooperate in T lineage lymphomagenesis but they are not sufficient and the role of Pim1 is more likely to be associated with tumor progression. PMID: 9401000 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 10: Leukemia. 1995 Jun;9(6):955-9. p53 gene inactivation in acute lymphoblastic leukemia of B cell lineage associates with chromosomal breakpoints at 11q23 and 8q24. Lanza C, Gaidano G, Cimino G, Lo Coco F, Basso G, Sainati L, Pastore C, Nomdedeu J, Volpe G, Parvis G, et al. Dipartimento di Scienze Biomediche e Oncologia Umana, Ospedale San Luigi Gonzaga, Torino, Italy. The clinical heterogeneity of acute lymphoblastic leukemia (ALL) of B cell lineage reflects the presence of distinct molecular pathways leading to well-defined ALL molecular subtypes. These molecular pathways include the formation of the fusion transcripts BCR/ABL and E2A/PBX1, due to t(9;22) and t(1;19), respectively, as well as rearrangements of the MLL gene at 11q23 and of c-MYC at 8q24. Hyperdiploid ALL in the absence of chromosomal structural abnormalities is an additional ALL molecular subtype. Mutations of the RAS family genes and of the p53 tumor suppressor gene represent additional genetic lesions detected in a fraction (10-20%) of ALL cases. RAS activation in ALL may be detected in all molecular subtypes of ALL and denotes poor prognosis. Conversely, little is known regarding the clinical and biological features of ALL cases carrying p53 mutations. In order to help clarify the role of p53 inactivation in ALL development, we have determined the frequency of p53 mutations throughout the molecular spectrum of B cell lineage ALL. We report that p53 inactivation in ALL of B cell lineage is restricted to cases carrying a rearrangement of MLL or c-MYC, whereas it is consistently negative in other molecular subgroups. These data underline the molecular heterogeneity of ALL of B cell lineage and indicate that at least some of the molecular pathways involved in ALL pathogenesis require more than one genetic lesion. PMID: 7596184 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 11: Br J Haematol. 1995 Mar;89(3):516-26. Heterogeneity of t(1;19)(q23;p13) acute leukaemias. French Haematological Cytology Group. Troussard X, Rimokh R, Valensi F, Leboeuf D, Fenneteau O, Guitard AM, Manel AM, Schillinger F, Leglise C, Brizard A, et al. Laboratoire d'Hematologie, Hopital Necker-Enfants Malades, Paris, France. The t(1;19)(q23;p13) translocation occurs commonly in B-lineage ALL. Previous reports have demonstrated a predominance of cases with expression of cytoplasmic Ig mu (C mu+), and FAB L1/L2 phenotype, a poor prognosis and expression of a fusion transcript involving the E2A and PBX1 genes in C mu+ but not in C mu- cases. Of 38 patients with karyotypically proven t(1;19) (q23;p13) leukaemias, we extensively analysed 18 patients with acute leukaemia including 16 B-lineage ALLs, one T-ALL and one AML M4. The AML was associated with a classic E2A-PBX1 fusion transcript and may represent the human counterpart of the AMLs induced by E2A-PBX1 retroviral infection of murine marrow progenitors. The T-ALL was E2A-PBX1 negative and neither the E2A nor the LYL-1 genes, both situated at chromosome 19 p13, were rearranged. Of the 16 B-lineage ALLs, four had cytological features resembling an 'L3-like' phenotype classically associated with Burkitt's lymphoma, two at diagnosis and relapse and two exclusively at relapse. E2A-PBX1 fusion transcripts were detected by RT-PCR in all 13 C mu+ patients and in 2/3 C mu- cases. The 'L3-like' phenotype did not correlate with a particular stage of maturation arrest (one sIg+, one C mu+, one C mu-) or type of E2A-PBX1 transcript, but was associated in all cases with a trisomy 8. Translocation, rearrangement, amplification or over-expression of the c-myc gene was not observed in these cases, demonstrating that the apparent association with trisomy 8 is not due to deregulation of this gene. We therefore show that the E2A-PBX1 transcript, although occurring predominantly in C mu+ pre-B ALL, also occurs in C mu- early pre-B ALL, sIg+ B-ALL and even in AML. These results suggest that the stage of maturation arrest, and indirectly the prognosis, are not solely due to the type of fusion transcript associated with the t(1;19). PMID: 7734349 [PubMed - indexed for MEDLINE] ---------------------------------------------------------------