The genome-wide molecular signature of transcription factors in leukemia

Transcription factors control expression of genes essential for the normal functioning of the hematopoietic system and regulate development of distinct blood cell types. During leukemogenesis, aberrant regulation of transcription factors such as RUNX1, CBFβ, MLL, C/EBPα, SPI1, GATA, and TAL1 is central to the disease. Here, we will discuss the mechanisms of transcription factor deregulation in leukemia and how in recent years next-generation sequencing approaches have helped to elucidate the molecular role of many of these aberrantly expressed transcription factors. We will focus on the complexes in which these factors reside, the role of posttranslational modification of these factors, their involvement in setting up higher order chromatin structures, and their influence on the local epigenetic environment. We suggest that only comprehensive knowledge on all these aspects will increase our understanding of aberrant gene expression in leukemia as well as open new entry points for therapeutic intervention. Transcription factors control expression of genes essential for the normal functioning of the hematopoietic system and regulate development of distinct blood cell types. During leukemogenesis, aberrant regulation of transcription factors such as RUNX1, CBFβ, MLL, C/EBPα, SPI1, GATA, and TAL1 is central to the disease. Here, we will discuss the mechanisms of transcription factor deregulation in leukemia and how in recent years next-generation sequencing approaches have helped to elucidate the molecular role of many of these aberrantly expressed transcription factors. We will focus on the complexes in which these factors reside, the role of posttranslational modification of these factors, their involvement in setting up higher order chromatin structures, and their influence on the local epigenetic environment. We suggest that only comprehensive knowledge on all these aspects will increase our understanding of aberrant gene expression in leukemia as well as open new entry points for therapeutic intervention. In eukaryotes, chromatin structure and interaction between transcription factors (TFs) modulates transcription of genes. TFs initiate transcription and control transcriptional elongation and thereby influence gene expression programs and consequently cell state [1Adelman K. Lis J.T. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans.Nat Rev Genet. 2012; 13: 720-731Crossref PubMed Google Scholar, 2Bai X. Kim J. 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In this way, they exert control over spatial and temporal expression of genes through a variety of regulatory domains, consequently modulating all complex biological processes, such as cell differentiation, proliferation, and apoptosis [6Maston G.A. Evans S.K. Green M.R. Transcriptional regulatory elements in the human genome.Annu Rev Genomics Hum Genet. 2006; 7: 29-59Crossref PubMed Scopus (262) Google Scholar]. Approximately 10% of genes in the human genome are presumed to code for TFs [7Levine M. Tjian R. Transcription regulation and animal diversity.Nature. 2003; 424: 147-151Crossref PubMed Scopus (696) Google Scholar], with different sets of TFs expressed during different developmental stages. In the same cell type, different TFs can co-localize [8Chen X. Xu H. 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Transcriptional regulation and its misregulation in disease.Cell. 2013; 152: 1237-1251Abstract Full Text Full Text PDF PubMed Scopus (85) Google Scholar]. Also hematopoiesis is classically thought to be governed by a small fraction of crucial TFs that are lineage specific and interact among themselves to control cell state [19Iwasaki H. Akashi K. Myeloid lineage commitment from the hematopoietic stem cell.Immunity. 2007; 26: 726-740Abstract Full Text Full Text PDF PubMed Scopus (171) Google Scholar], such as RUNX1, C/EBPα, and SPI1 in myeloid [20Ichikawa M. Asai T. Saito T. et al.AML-1 is required for megakaryocytic maturation and lymphocytic differentiation, but not for maintenance of hematopoietic stem cells in adult hematopoiesis.Nat Med. 2004; 10: 299-304Crossref PubMed Scopus (338) Google Scholar, 21Tenen D.G. Hromas R. Licht J.D. Zhang D.E. Transcription factors, normal myeloid development, and leukemia.Blood. 1997; 90: 489-519Crossref PubMed Google Scholar, 22Vangala R.K. 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Also, how is transcription regulated by differential usage of TF modules and how are other molecular constituents involved? It has become clear that although TFs are key proteins in regulating gene expression, it is further governed through synergistic contributions from several entities, including interaction between the TFs, post-transcriptional modifications, and the structure of the chromatin template (Fig. 1) [18Lee T.I. Young R.A. Transcriptional regulation and its misregulation in disease.Cell. 2013; 152: 1237-1251Abstract Full Text Full Text PDF PubMed Scopus (85) Google Scholar]. For example, chromatin regulators, such as complexes of the SWI/SNF family and histone-modifying enzymes, assist in mobilizing and modifying nucleosomes during gene transcription and silencing [18Lee T.I. Young R.A. Transcriptional regulation and its misregulation in disease.Cell. 2013; 152: 1237-1251Abstract Full Text Full Text PDF PubMed Scopus (85) Google Scholar, 28Clapier C.R. Cairns B.R. 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The last few decades have witnessed enormous advancements in DNA-sequencing technology, from Sanger sequencing to its automation and finally the advent of next-generation sequencing (NGS) methods. Especially NGS has led to the identification of many new regulatory sequences and insight into transcriptional machinery and chromatin regulators and has provided novel insights into gene regulatory mechanisms in normal but also diseased cells. Application of different NGS methods has made great contributions to the field of hematology. For example whole-genome sequencing (WGS) for detection of single nucleotide variants (SNV), insertions, deletions, and copy number variations has facilitated the sequencing of the first cancer genome [30Ley T.J. Mardis E.R. Ding L. et al.DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.Nature. 2008; 456: 66-72Crossref PubMed Scopus (670) Google Scholar] and identification of mutations in several types of leukemia [31Puente X.S. 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Satake N. et al.Whole-exome sequencing identifies a novel somatic mutation in MMP8 associated with a t(1;22)-acute megakaryoblastic leukemia.Leukemia. 2014; 28: 945-948Crossref PubMed Scopus (1) Google Scholar, 34Cancer Genome Atlas Research NetworkGenomic and epigenomic landscapes of adult de novo acute myeloid leukemia.N Engl J Med. 2013; 368: 2059-2074Crossref PubMed Google Scholar], including hairy cell leukemia (HCL) [35Tiacci E. Trifonov V. Schiavoni G. et al.BRAF mutations in hairy-cell leukemia.N Engl J Med. 2011; 364: 2305-2315Crossref PubMed Scopus (326) Google Scholar] and multiple myeloma [36Chapman M.A. Lawrence M.S. Keats J.J. et al.Initial genome sequencing and analysis of multiple myeloma.Nature. 2011; 471: 467-472Crossref PubMed Scopus (519) Google Scholar]. 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Liu J. et al.Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia.Epigenetics. 2012; 7: 567-578Crossref PubMed Scopus (29) Google Scholar]. These NGS technologies facilitate characterization of the molecular pathology of different diseases, and they have also been used to differentiate related diseases on the basis of mutations in genes of driver pathways [43Braggio E. Egan J.B. Fonseca R. Stewart A.K. Lessons from next-generation sequencing analysis in hematological malignancies.Blood Cancer J. 2013; 3: e127Crossref PubMed Scopus (11) Google Scholar], gene expression profiles [34Cancer Genome Atlas Research NetworkGenomic and epigenomic landscapes of adult de novo acute myeloid leukemia.N Engl J Med. 2013; 368: 2059-2074Crossref PubMed Google Scholar], and epigenetic patterns [44Kulis M. Heath S. Bibikova M. et al.Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia.Nat Genet. 2012; 44: 1236-1242Crossref PubMed Scopus (105) Google Scholar]. Next we further discuss what has been learned from these genome-wide analyses, with a specific focus on leukemia-associated TFs and the context in which they operate. TFs control expression of genes essential for the normal functioning of the hematopoietic system and regulate development of distinct blood cell types. In the event of genetic perturbations, including deletions, insertions, and translocations, the molecular roles of these TFs can be altered, resulting in uncontrolled proliferation of immature blood cell lineages and sometimes depletion of one or more blood cell lineage. Throughout the years many TFs important for various stages of hematopoietic development have been discovered and molecularly characterized. Many of these were initially identified as being mutated in hematologic disorders. Given their importance to disease, genome-wide profiles were generated for many of these TFs in recent years aiming to further elucidate their role in normal and aberrant hematopoiesis. These genome-wide datasets were mostly submitted to the Gene Expression Omnibus (GEO) online repository (www.ncbi.nlm.nih.gov/geo/) and can be identified through GSE accession numbers. Examples include the core binding factors, MLL, C/EBPα, SPI1, GATA, and TAL1 (Fig. 2). The core binding factor (CBF) family consists of two types of proteins: CBFα, which represents a variable DNA-binding subunit, and CBFβ, a nonDNA-binding subunit thought to stabilize the DNA binding of the α subunit. The CBFα subunit can in distinct cell lineages be represented by one of three proteins: RUNX1, RUNX2 (CBFα1), or RUNX3 (CBFα3) [45Markova E.N. Kantidze O.L. Razin S.V. Transcriptional regulation and spatial organisation of the human AML1/RUNX1 gene.J Cell Biochem. 2011; 112: 1997-2005Crossref PubMed Scopus (9) Google Scholar]. RUNX1 and CBFβ are needed at several stages of hematopoiesis, such as megakaryocytic differentiation, platelet formation, erythropoiesis, B-cell development, and T-cell development [46de Bruijn M.F.T.R. Speck N.A. Core-binding factors in hematopoiesis and immune function.Oncogene. 2004; 23: 4238-4248Crossref PubMed Scopus (136) Google Scholar]. In addition, RUNX1 and CBFβ are common targets of chromosomal translocations. For example, in acute myeloid leukemia (AML) the translocation t(8; 21) involves a fusion of the AML1 and ETO genes and its expression results in the chimeric protein AML1-ETO [47Meyers S. Lenny N. Hiebert S.W. The t(8;21) fusion protein interferes with AML-1B-dependent transcriptional activation.Mol Cell Biol. 1995; 15: 1974-1982Crossref PubMed Google Scholar], whereas inversion of a part of chromosome 16 results in the fusion of the CBFβ and MYH11 genes, coding the chimeric protein CBFβ-MYH11 [48Lutterbach B. Hou Y. Durst K.L. Hiebert S.W. The inv(16) encodes an acute myeloid leukemia 1 transcriptional corepressor.Proc Natl Acad Sci USA. 1999; 96: 12822-12827Crossref PubMed Scopus (75) Google Scholar]. The two CBFs are reported to be mutated in 5–10% of AMLs and function by interfering with the normal CBF gene program [40Martens J.H.A. Stunnenberg H.G. The molecular signature of oncofusion proteins in acute myeloid leukemia. FEBS Letters.Fed Eur Biochem Soc. 2010; 584: 2662-2669Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar]. MLL fusions are reported in approximately 10% of acute leukemias (AL). 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