Gene expression profiling of pediatric acute myelogenous leukemia

Differentiation Arrest and Leukemogenesis Group Meeting Dvir Netanely - June 21st, 2005 Normal Blood Cells Normal Blood Cells • The bone marrow produces stem cells (immature cells) that develop into mature blood cells. • There are 3 types of mature blood cells: 1. White blood cells (leukocytes) are part of the immune system. 2. Red blood cells (erythrocytes) carry oxygen from the lungs to the body's tissues. 3. Platelets (thrombocytes) form blood clots that control bleeding. • Normally, blood cells are produced in an orderly, controlled way as the body needs them. This process is called hematopoiesis. Hematopoietic Differentiation Hematopoietic Differentiation Hematopoietic Differentiation • Hematopoietic stem cells in the bone marrow can either self-renew or give rise to progenitor cells that generate precursors of the myeloid or the lymphoid lineage. • The commitment process is characterized by massive cell proliferation in the early phase followed by successive restriction to distinct cell lineages and to cell differentiation. • These processes are regulated by trans-acting factors which activate or repress genes • Leukemic mutations interfere with transcription factor functions, abrogate cell differentiation, and support proliferation. As a consequence, the blood is flooded with immature, non-functional cell types. http://www.mdc-berlin.de/englisch/research/research_areas/cancer/leutz.htm Leukemia • The term leukemia refers to cancers of the white blood cells. • Leukemia is a very heterogeneous disease, composed of many subtypes. Leukemia – Acute vs. Chronic • In general, leukemias are classified into acute (rapidly developing) and chronic (slowly developing) forms. Leukemia – ALL vs. AML • Leukemia is also divided by which type of white blood cell is affected: ALL (Acute Lymphoid Leukemia) vs. AML (Acute Myeloid Leukemia). • AML is more difficult to treat in comparison to ALL, overall cure rates for AML remain below 60%. Acute Leukemias - Statistics • Combining childhood and adult cases, there are 11,000 new cases per year in the U.S.A. • Overall, acute leukemia strikes 5 out of 100,000 people each year. • If untreated, 95% of patients will die within one year of diagnosis. • Acute leukemia is the most common cancer of childhood. • AML is 5 times more common than ALL but ALL represents 85% of cases in children. • Thus, the average ALL patient is 4 years old while the average AML patient is 60 years old. AML • Acute myeloid leukemia (AML) is a cancer of the myeloid line of white blood cells. • The malignant myeloid cells, called myeloblasts, fail to mature into the different types of blood cells. • The myeloblasts proliferate rapidly, accumulate and overtake the number of healthy blood cells, spreading into the bloodstream and other vital organs. The lack of healthy blood cells results in symptoms such as anemia and abnormal bleeding. Leukemia subtypes Leukemia Acute Chronic Myeloid AML FAB: M0 M1 M2 M3 M4 M5 M6 Lymphoid (ALL) M7 Myeloid (CML) Lymphoid (CLL) FAB classification system for AML subtypes • Acute myelogenous leukemia have been divided into 8 subtypes, M0 through to M7 under the FAB (French-American-British) classification system based on the type of cell from which the leukemia developed and degree of maturity. • This is done by examining the appearance of the malignant cells under light microscopy or cytogenetically by characterization of the underlying chromosomal abnormality. • Each subtype is characterized by a particular pattern of chromosomal translocations and have varying prognoses and responses to therapy. FAB classification system for AML subtypes • The eight different subtypes are: – M0 (undifferentiated AML) – M1 (myeloblastic, immature) – M2 (myeloblastic, mature) – M3 (promyelocytic), or acute promyelocytic leukemia (APL) – M4 (myelomonocytic) – M5 (monocytic) – M6 (erythroid) – M7 (megakaryoblastic) FAB Classification FAB Classification M0 M1 M2 M3 M4 Undifferentiated leukemia stem cells predominate or cell type unidentified Myeloblastic leukemia without maturation immature white blood cells predominate Myeloblastic leukemia with maturation (98723--acute) with partial differentiation Promyelocytic leukemia (98663--acute) promyelocytes predominate subdivided: M3a without eosinophilia, M3b with eosinophilia Combination myeloblastic-monoblastic leukemia each component constitutes greater than 20% of the blasts in the bone marrow subdivided M4 acute myelomonocytic leukemia M4E0 acute myelomonocytic leukemia with eosinophilia Monoblastic leukemia (98603--monocytic, NOS; 98913--acute; 98603--chronic; 98603 aleukemic) monoblasts predominate subdivided M5a acute monocytic leukemia without differentiation (98913--monoblastic) M5b acute monocytic leukemia with differentiation (promonocytic) Megakayrocytic leukemia (99103--acute) 98603--subacute; M5 M6 M7 Erythroleukemia (98403) immature red and white cells predominate AML subtypes FAB, Translocation and Fusion Proteins “Acute myelogenous leukemias (AMLs) are genetically heterogeneous and characterized by chromosomal rearrangements that produce fusion proteins with aberrant transcriptional regulatory activities.” Myriam Alcalay et. al., 2003 www.med-ed.virginia.edu/. ../wcd/myeloid1.cfm M1 t(9;22) M2 t(8;21) AML1-ETO M3 t(15;17) PML-RARα acute promyelocytic leukemia M5 t(9;11) Genetic Abnormalities Genetic Abnormalities Chromosomal Translocation Major Prognostic AML Sub types “Chromosomal translocations resulting in specific fusion genes are a hallmark of the leukemias” Z Xiao et. al., Leukemia (2001) 15, 1906–1913 KNOW THE SUBTYPES ! t(15;17) – [PML-RAR] • promyelocytic leukemia–retinoic acid receptor • This fusion PML-RAR protein is responsible for preventing immature myeloid cells from differentiating into more mature cells. “Chromosomal translocations resulting in specific fusion genes are a hallmark of the leukemias” Z Xiao et. al., Leukemia (2001) 15, 1906–1913 t(8;21) - [AML1-ETO] • The AML1 gene encodes the DNA-binding subunit of the AML1/CBFb core binding factor transcription complex, whereas ETO encodes the mammalian homologue of the Drosophila protein Nervy. • AML1 and ETO are both involved in transcriptional regulation of genes in hematopoietic precursor cells. • AML1-ETO fusion protein represses genes whose transcription is normally activated by AML/CBFb. British Journal of Haematology, 1999, 106, 296±308 t(8;21) - [AML1-ETO] Inv16 - [CBF-MYH11] • core-binding factor – smooth muscle myosin heavy chain • The fusion protein blocks transcription of differentiation control genes. The AML1-CBFß Transcription Factor In normal cells, heterodimeric AML1-CBFß transcription-factor complex binds to the DNA sequence TGTGGT in the transcriptional regulatory region of AML1-regulated target genes and activates transcription through the recruitment of coactivators. The AML1-CBFß Transcription Factor • In AML cells with the t(8;21) translocation, the N-terminal part of AML1 fuses with the Cterminal portion of ETO. • The resultant chimeric protein continues to interact with CBFß and to bind to the core enhancer sequence; however, ETO recruits a nuclear corepressor complex and results in the dominant repression of AML1-regulated target genes. The AML1-CBFß Transcription Factor • Similarly, the CBFß-MYH11 chimeric protein encoded by the inv(16) mutation continues to interact with AML1; however, instead of allowing AML1 to interact with DNA, this chimeric protein recruits AML1 into functionally inactive complexes in the cytoplasm. MLL fusion genes • Mixed-lineage leukemia (MLL) fusion proteins. • There are more than 40 proteins that have been found fused to MLL in leukemia patients, and different ones can cause leukemia by different mechanisms. • When the transcription factor MLL functions as it should, without a fusion partner, it binds to and controls the expression of Hox genes, which in turn control cell growth and maturation. Proliferation Legend: (A) In a normal resting cell the intracellular signaling proteins and genes that are normally activated by extracellular growth factors are inactive. (B) When the normal cell is stimulated by an extracellular growth factor, these signaling proteins and genes become active and the cell proliferates. (C) In this cancer cell, a mutation in a protooncogene that encodes an intracellular signaling protein that is normally activated by extracellular growth factors has created an oncogene. The oncogene encodes an altered form of the signaling protein that is active even in the absence of growth factor binding. Cooperating mutations in acute leukemia • No single mutation is sufficient to cause acute leukemia. Accumulating experimental and epidemiologic evidence suggests a model of cooperation between two classes of mutations in acute leukemia: 1. Mutations that confer a proliferative and/or survival benefit to hematopoietic progenitors but does not affect differentiation. 2. Mutations that impair hematopoietic differentiation. Acute leukemia, characterized by enhanced proliferation and survival of cells and impaired differentiation, is the consequence of expression of both classes of mutations. Tallman et. Al., Focus on acute leukemias, Cancer Cell, 2002 • • Pathogenesis and treatment of acute leukemias • • As indicated by the yellow star, intensive cytotoxic chemotherapy remains the mainstay of treatment for all acute leukemias. Good prognosis leukemias are indicated in blue, poor prognosis leukemias are in red, and intermediate or unknown are in white. There are two classes of cooperating mutations in acute leukemia, those that confer proliferation and/or survival and those that impair hematopoietic differentiation. Targeted therapies have been developed or are being tested for many of these, such as ATRA. • • Tallman et. Al., Focus on acute leukemias, Cancer Cell, 2002 Pediatric Leukemia • Leukemia is the most common childhood cancer (25% of all childhood cancers in the US are leukemias). • Approximately 60% of children with leukemia have ALL (Acute Lymphoid Leukemia), and about 38% have AML (Acute Myeloid Leukemia). Gene expression profiling of pediatric acute myelogenous leukemia Blood, 1 December 2004, Vol. 104, No. 12, pp. 3679-3687 Mary E. Ross, Rami Mahfouz, Mihaela Onciu, Hsi-Che Liu, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Stanley Pounds, Cheng Cheng, Jing Ma, Raul C. Ribeiro, Jeffrey E. Rubnitz, Kevin Girtman, W. Kent Williams, Susana C. Raimondi, Der-Cherng Liang, Lee-Yung Shih, Ching-Hon Pui, and James R. Downing Pediatric AML subtypes • The reviewed paper focuses on utilizing gene expression technology to identify sub-types of Pediatric Acute Myeloid Leukemia (AML). Gene expression profiling of pediatric acute myelogenous leukemia • Motivation: – Identification of pediatric AML subtypes based on gene expression profiles. – Seek insights regarding the underlying biological process of each subtype. – Sub type identification will enable the development tailored treatment protocols customized to a certain genetic lesion which will hopefully significantly improve AML patient cure rates. Samples (Patients) –130 pediatric –20 adult Major Prognostic sub types •150 samples used: t(15;17)[PML-RAR] t(8;21)[AML1-ETO] inv16[CBF-MYH11] MLL chimeric fusion genes acute megakaryocytic morphology (FAB-M7) Other Total 15 21 14 23 10 47 130 Unsupervised cluster analysis of pediatric AMLs “..relatively tight grouping was observed for the genetic subgroups AML1-ETO, PML-RAR , and MLL chimeric fusion genes, and for the morphologic subgroups FAB-M3, M7, and M4/M5. Unexpectedly, however, AMLs that expressed the inv16-encoded CBF -MYH11 failed to cluster … indicates significant heterogeneity within the gene expression profile of these cases.” Expression profiles of pediatric AMLs • Looking for subtype expression signatures using Supervised analysis – Trying to find genes that discriminate between subtypes. • Applying SAM with FDR=5% yielded only 63 discriminating genes for CBF-MYH11. AML subtype t(15;17)[PML-RAR] t(8;21)[AML1-ETO] inv16[CBF-MYH11] MLL chimeric fusion genes #Discriminating genes, FDR=5% 2521 764 63 2218 acute megakaryocytic morphology (FABM7) 1242 Expression profiles of pediatric AMLs Hierarchical clustering of the top 50 discriminating genes for each subtype – Some clusters are more distinct than others. Similarity plot • Pair-wise comparisons calculated for 130 pediatric AML samples using the top 50-ranked genes for each subgroup as selected by SAM. CBFb-MYH11, MLL Heterogeneity among genes “Observed variation could not be completely explained by differences in the structure of chromosomal rearrangements, extent of differentiation, or presence of specific secondary mutations” Examination of the discriminating genes • Gene annotation may provide biological insights. • Discriminating genes may be used as therapeutic targets, or as unique classspecific diagnostic targets. AML subtype-specific class discriminating genes Representatives of genes significantly characterizing one specific subtype Building a subtype classifier • Randomly divided the samples to TRAINING and TEST sets. • TRAINING set was used to train a neural network in classifying AML subtypes, based on gene expression data for the 250 discriminating genes identified by SAM. • Testing the classifier on the test set, overall Prediction accuracy of 93% achieved (100% on nonMLL samples). Applying the classifier on Adult samples • The 20 adult samples were used to test the classifier, and yielded overall prediction accuracy of 90%. • ->Pediatric and adult samples are similar for these subtypes, and therefore the classifier is useful for adults as well. Prediction of outcome was not significant • “Identifying a gene expression–based outcome predictor that could provide additional prognostic information, either independent of or within a genetic subtype, would be a significant advance.” Gene expression profiles of pediatric acute leukemia with MLL chimeric fusion genes 130 AML 132 ALL 5 T-ALL w. MLL t Identification of expression signatures associated with MLL fusion genes irrespective of lineage (AML/ALL) A – Unsupervised PCA for the 267 samples – samples cluster according to lineage. Gene expression profiles of pediatric acute leukemia with MLL chimeric fusion genes 130 AML 132 ALL 5 T-ALL w. MLL Identification of expression signatures associated with MLL fusion genes irrespective of lineage (AML/ALL) B – same PCA, MLL rearrangements are colored in red C – Supervised DAV analysis – Separation over gene space between MLL and non-MLL Gene expression profiles of pediatric acute leukemia with MLL chimeric fusion genes 130 AML 132 ALL 5 T-ALL w. MLL t Identification of expression signatures associated with MLL fusion genes irrespective of lineage (AML/ALL) D – Top 50 separating genes (MLL vs. non-MLL) ranked by SAM. Summary I • Distinct gene expression signatures associated with the most common AML translocations were identified. • Gene expression–based classifier performs with 93% accuracy in predicting specific • The classifier performs equally well on AML samples obtained from adults. Summary II • The classifier’s inability to correctly classify a few samples appears to be a result of molecular heterogeneity in AMLs with either CBF -MYH11 or MLL translocations. This raises interesting questions for further study. • DAV analysis showed that ALL and AML samples that include MLL rearrangements are clustered together– implying that MLLrearranged T-ALL and AML are biologically more similar to other leukemias of similar lineage. Differentiation Therapy • Differentiation therapies are broadly defined as those that induce malignant reversion (i.e. the malignant phenotype becomes benign). • Clinically, these therapies have been most successful for acute promyelocytic leukemia (APL), with the use of alltrans retinoic acid (ATRA). This treatment has changed a cancer with a previously dismal outcome into one of the most treatable forms of leukemia. • The exact mechanisms of differentiation are unknown — it is unclear if it occurs by inducing terminal differentiation (G0 arrest), by inducing differentiation ‘backwards’ to the non-malignant form of the cell, or by triggering apoptosis. It is likely that it involves all of these pathways Alexander I Spira et. Al., Differentiation therapy, Current Opinion in Pharmacology 2003 Differentiation Therapy •Although there are probably mechanistic differences in how the various agents lead to differentiation, the overall process itself is likely to function by allowing malignant tumor cells to revert to a more benign form, in which their replication rates are lower compared with malignant forms, leading to a decreased tumor burden • They might also have a decreased tendency for distant metastatic spread, and the process may also restore traditional apoptotic pathways, all of which could improve a patient’s prognosis Alexander I Spira et. Al., Differentiation therapy, Current Opinion in Pharmacology 2003 An Optimistic Ending… The AML subtype M3 (APL) Example AML subtype M3 – APL “Acute promyelocytic leukemia (AML M3) is now the most frequently curable acute leukaemia in adults if promptly diagnosed and adequately treated.” Parmar S, Tallman MS. , 2003 acute promyelocytic leukemia M3 t(15;17) www.med-ed.virginia.edu/. ../wcd/myeloid1.cfm PML-RARα A cure for AML M3 subtype… • All-trans retinoic acid (ATRA) is a drug used for the treatment of acute promyelocytic leukemia (AML subtype M3). • It works in AML-M3 because most cases of this involve a chromosomal translocation of chromosomes 15 and 17, which causes genetic fusion of the retinoic acid receptor (RAR) gene to the promyelocytic leukemia (PML) gene. • This fusion PML-RAR protein is responsible for preventing immature myeloid cells from differentiating into more mature cells. • This block in differentiation is thought to cause leukemia. ATRA acts on PML-RAR to lift this block, causing the immature promyelocytes to differentiate to normal mature blood cells. ATRA mechanism Leukemogenic Effects of PML-RARá and Mechanisms of ATRA/Arsenic Trioxide in the Treatment of APL • (A) In the absence of RA, RARα/RXR heterodimers recruit the transcription corepressor (CoR), which mediates transcriptional silencing by mechanisms that include direct inhibition of the basal transcription machinery and recruitment of chromatin-modifying enzymes. Chromatin modification includes histone deacetylation, which leads to a compact chromatin structure that impairs the access of transcriptional activators. In the presence of physiological concentrations of RA, the corepressor is released and the coactivator is recruited to the RARα/RXR heterodimer, resulting in histone acetylation and overcoming of the transcription blockage. • •http://medicine.plosjournals.org/perlserv/?request=slideshow&type=figure&doi=10.1371/journal.pmed.0020012&id=20372 ATRA mechanism Leukemogenic Effects of PML-RARá and Mechanisms of ATRA/Arsenic Trioxide in the Treatment of APL (B) PML-RARα fusion protein binds to RARα target genes either on its own or with RXR and then recruits corepressors, leading to transcriptional repression and myeloid differentiation inhibition. PMLRARα oncoprotein sequesters the normal RXR and PML, inhibits the PML/P53 apoptotic pathway, and delocalizes PML and other proteins from the nuclear body. •http://medicine.plosjournals.org/perlserv/?request=slideshow&type=figure&doi=10.1371/journal.pmed.0020012&id=20372 ATRA mechanism Leukemogenic Effects of PML-RARá and Mechanisms of ATRA/Arsenic Trioxide in the Treatment of APL (C) In the presence of pharmacological doses of ATRA or arsenic trioxide, the PML-RARα fusion is degraded in ways that are dependent on caspases and proteasomes. The degradation of PML-RAα may lead to derepression of transcription suppression and restoration of PML nuclear body structure. The blockade of other signaling pathways is also released, and the anti-apoptotic effect of PML-RARα is lost. ATRA also induces cyclic AMP (cAMP), which reverses the silencing of RXR, induces the expression of RA-induced genes and cyclooxygenase 1 (Cox 1), inhibits angiogenesis, and downregulates tissue factor. Subsequently, ATRA induces terminal cell differentiation, while arsenic trioxide induces partial differentiation and/or apoptosis of APL cells. The effects of ATRA and arsenic trioxide are indicated with red and blue arrows, respectively. •http://medicine.plosjournals.org/perlserv/?request=slideshow&type=figure&doi=10.1371/journal.pmed.0020012&id=20372 SUMMARY • Differentiation arrest is an important component in the pathogenesis of many cancers. • Acute myeloid leukaemia (AML) represents an excellent example of a cancer that is characterized by a differentiation block. • Specific haematopoietic transcription factors are crucial for differentiation to particular lineages during normal differentiation, and are controlled by specific patterns of expression and protein interactions. • These same transcription factors are frequently disrupted in AML. • Some mechanisms of disruption involve the effect of fusion proteins that are generated by chromosomal translocations on haematopoietic transcription factors. • In other cases, in the absence of common translocations, the transcription factors themselves are mutated. • Characterizing these transcription-factor abnormalities has already affected classification schemes based on patient outcome and contributed to the improvement of AML patient survival rates. • These transcription-factor pathways also represent important targets for future therapeutic intervention. THE END PCA – Principle component Analysis - AML Downing2004 - PCA - AML subgroups data1517 data821 dataadult datainv16 dataM7 dataMLL 50 dataother dataTMLL 0 -50 -40 -30 -20 -10 0 10 20 30 40 50 60 -40 -30 -20 -10 0 10 20 30 40 50 Molecular identification of CBF -MYH11 fusion transcripts in an AML M4Eo patient in the absence of inv16 or other abnormality by cytogenetic and FISH analyses - a rare occurrence F Ravandi1, S S Kadkol2, J Ridgeway1, A Bruno2, C Dodge2 and V Lindgren2 • • The prognostic and therapeutic significance of karyotype at diagnosis in patients with AML is now fully established. Two of the most common recurring cytogenetic abnormalities in AML are t(8;21)(q22;q22) and the pericentric inversion of chromosome 16, inv(16)(p13;q22), or its variant t(16;16)(p13;q22). The chromosome 16 abnormalities, which are closely associated with the FAB subtype M4Eo, result in the creation of a fusion gene between the smooth muscle myosin-heavy chain gene (MYH11) at 16p13 and the core binding factor (CBF ) gene at 16q22. The fusion protein product, CBF -MYH11, interacts with nuclear corepressors, leading to dysregulation of transcription. Patients with 'CBF leukemias' including those with inv(16)/t(16;16) account for up to 20% of young adult cases of de novo AML. Such patients have a more favorable prognosis, particularly when treated with intensive postremission therapy including high-dose cytarabine. Therefore, accurate identification of these patients at diagnosis is of therapeutic significance. • http://www.nature.com/cgitaf/DynaPage.taf?file=/leu/journal/v17/n9/full/2403056a.html Comparison of Cytogenetic and Molecular Genetic Detection of t(8;21) and inv(16) in a Prospective Series of Adults With De Novo Acute Myeloid Leukemia: A Cancer and Leukemia Group B Study By Krzysztof Mrózek, Thomas W. Prior, Colin Edwards, Guido Marcucci, Andrew J. Carroll, Pamela J. Snyder, Prasad R.K. Koduru, Karl S. Theil, Mark J. Pettenati, Kellie J. Archer, Michael A. Caligiuri, James W. Vardiman, Jonathan E. Kolitz, Richard A. Larson, Clara D. Bloomfield • • • • • • ACUTE MYELOID leukemia (AML) is a heterogeneous disease with regard to the morphology, immunophenotype, and genetic rearrangements acquired by leukemic blasts. Multiple recurrent chromosome and gene rearrangements have been identified in AML, and these alterations have been correlated with biologic and clinical features of the disease resulting in delineation of prognostically distinct categories of AML.1-6 One such category is core-binding factor (CBF) AML. Leukemic cells of patients with CBF AML most commonly contain either t(8;21)(q22;q22) or inv(16)(p13q22), chromosome aberrations that result in disruption of genes encoding CBF subunits, CBF (also known as AML1) or CBFß, respectively.1,6 Translocation (8;21) leads to the fusion of the AML1 gene, located at 21q22, with the ETO gene at 8q22 and creation of a chimeric gene AML1/ETO. Similarly, a fusion gene CBFß/MYH11 is produced by juxtaposition of bands 16q22 (containing CBFß) and 16p13 (containing MYH11) as a result of inv(16) or, less frequently, t(16;16)(p13;q22).1,6 http://www.jco.org/cgi/content/full/19/9/2482 • 10 September 2001, Volume 20, Number 40, Pages 5695-5707Molecular mechanisms of leukemogenesis mediated by MLL fusion proteins • Figure 3 The minimal transforming domains of MLL fusion partners. MLL fusion proteins are shown schematically with gray shading of the fusion partners. Boxes with red filling delineate the minimal regions of partner proteins necessary and sufficient for in vitro myeloid immortalization. NTC and TA, conserved amino terminal and transactivation domains of ENL; Bromo + HAT, bromodomain and histone acteyltransferase domains of CBP; OM + LZ, octapeptide and leucine zipper motifs of AF10 The French–American–British (FAB) classification, described approximately 25 years ago, remains the foundation on which the morphologic diagnosis of AML and ALL is based SAM – Significance Analysis of BACK Microarray • SAM is a method for identifying genes on a microarray with statistically significant changes in expression. • Developed in a context of an actual biological experiment. • Assign a score to each gene, uses permutations to estimate the percentage of genes identified by chance. • Does not assume normal distribution of the data • SAM works effectively even with small sample size. • Robust, can be adopted to a broad range of experimental situations. Significance analysis of microarrays applied to the ionizing radiation response \ Virginia Goss Tusher,Robert Tibshirani, and Gilbert Chu 2001 SAM- procedure overview Sample genes expression scale Define and calculate a statistic, d(i) Generate permutated samples Estimate attributes of d(i)’s distribution Identify potentially Significant genes Choose Δ Estimate FDR