ALBERT

Description: Genetic and epigenetic heterogeneity of cancer cells fundamentally shapes cancer progression and relapse. In chronic lymphocytic leukemia (CLL), we previously reported that intra-leukemic epigenetic diversity in DNA methylation (DNAme) follows a stochastic pattern reminiscent of genetic 'trial and error' in cancer evolution. We measured stochastic DNAme from bulk sequencing by observing the proportion of discordantly methylated sequencing reads (PDR), and found that higher PDR was associated with greater cell-to-cell transcriptional heterogeneity and adverse clinical outcome. However, bulk DNAme sequencing does not allow to phase stochastic DNAme across distant genomic loci for a single cell, as it is limited to length of a short sequencing read. Thus, it can only provide the average PDR for a population of cells, rather than the cell-to-cell variation in this important epigenetic feature. Therefore, to define stochastic DNAme changes at the single cell level, we optimized a multiplexed single cell reduced representation bisulfite sequencing (MscRRBS) protocol to allow high-throughput single cell DNAme sequencing. This protocol significantly improves scalability by multiplexing cells with shorter inline-barcodes at an early stage and utilizing SPRI beads purification to eliminate adapter-dimers. We applied MscRRBS to 393 single CD19pos B cells from two healthy volunteers and 111 single cells from a CLL sample. 88% of cells were evaluable with greater than 100,000 covered CpGs (average of 436,230 CpGs per cell). We achieved bisulfite conversion rates of 99.7%+/-0.0001 (mean+/- SD), without a significant reduction in coverage. A downsampling analysis showed that 2.1 million reads per cell provided 85% of CpG coverage with only marginal increase in coverage with further sequencing. Biallelic coverage was observed in 4.6+/-2% of germline SNPs. With MscRRBS, we measure the PDR of each individual cell. As expected from our prior bulk RRBS analysis, we found that the average PDR across cells was higher in CLL compared with B cells from healthy adult volunteers (0.39+/-0.01 vs. 0.26+/-0.08, P

Description: Clonal evolution in response to therapy is a central feature of disease relapse. This raises a fundamental question in cancer biology: what enables the relapse clone to replace the pre-treatment clone? In other words, is the increased fitness of the relapse clone due to a lower death rate during therapy (less sensitivity to therapy) or a higher growth rate following therapy (superior ability to compete during repopulation)? We sought to address this question in chronic lymphocytic leukemia (CLL), as its relatively indolent disease kinetics enable the study of serially collected samples from the same patient over time. We recently reported the genetic characterization of 278 samples from patients enrolled in the German CLL Study Group CLL8 trial (Nature, in press). These samples were collected prior to first therapy with FC or FCR, and studied using whole-exome sequencing (WES). From this cohort, we further analyzed by WES 59 patients (FC [n = 28] or FCR [n = 31]) at time of relapse. We found that clonal evolution is the rule rather than the exception (57 / 59 CLLs), with TP53 alterations found in relapse in 15 cases. This series constitutes a unique opportunity to dissect the clonal dynamics of treated CLL. We therefore quantified clone-specific death and growth rates by targeted deep sequencing of serial peripheral blood samples, beginning at pre-treatment and ending at relapse. Given the expected minimal mutation detection sensitivity (0.1-1%) by targeted deep sequencing, we only selected samples with 〉1% CLL cells by flow cytometry. Such samples were available for 23 of 59 patients, with a median of 6 samples/patient (range 3-10). Based on the mutations identified by WES in the pre-treatment and relapse samples, we designed patient-specific multiplexed assays for targeted deep sequencing (median sequencing depth - 6561). A series of normal samples were sequenced together with patient samples to account for sequencing errors. The measurements of the CLL cell fraction in the sample, by sequencing and by flow cytometry, were highly correlated (r=0.89, p

Description: We previously have shown that the zinc finger transcription factor Egr-1 blocked granulocytic differentiation of HL-60 cells, restricting differentiation along the monocytic lineage. Egr-1 also was observed to block granulocyte colony-stimulating factor (G-CSF)–induced differentiation of interleukin-3 (IL-3)–dependent 32Dcl3 hematopoietic precursor cells, endowing the cells with the ability to be induced by granulocyte-macrophage colony-stimulating factor (GM-CSF) for terminal differentiation along the macrophage lineage. To better understand the function of Egr-1 as a positive modulator of monocytic differentiation, in this work we have studied the effect of ectopic expression of Egr-1 on the murine myeloblastic leukemic cell line M1, which is induced for differentiation by the physiological inducer IL-6. It is shown that, unlike in HL-60 and 32Dcl3 cells, ectopic expression of Egr-1 in M1 cells resulted in activation of the macrophage differentiation program in the absence of differentiation inducer. This included the appearance of morphologically differentiated cells, decreased growth rate in mass culture, and cloning efficiency in soft agar, and expression of endogenous c-myb and c-myc mRNAs was markedly downregulated. Untreated M1Egr-1 cells also exhibited cell adherence, expression of Fc and C3 receptors, and upregulation of the myeloid differentiation primary response genes c-Jun, junD, andjunB and the late genetic markers ferritin light-chainand lysozyme. Ectopic expression of Egr-1 in M1 cells also dramatically increased the sensitivity of the cells for IL-6–induced differentiation, allowed a higher proportion of M1 cells to become terminally differentiated under conditions of optimal stimulation for differentiation, and decreased M1 leukemogenicity in vivo. These findings demonstrate that the functions of Egr-1 as a positive modulator of macrophage differentiation vary, depending on the state of lineage commitment for differentiation of the hematopoietic cell type. © 1998 by The American Society of Hematology.

Description: Gadd45 expression, which is stress inducible, has been associated with growth arrest, but the exact role of gadd45 family genes in apoptosis still remains unclear. We have found that myeloid progenitor cells from gadd45a and gadd45b-deficient mice are more sensitive to ultra-violet radiation, VP-16 or daunorubicin induced apoptosis. indicating that gadd45a or gadd45b protect haematopoetic cells from DNA damaging agents. To determine, how gadd45a or gadd45b proteins exert their anti-apoptotic function, bone marrow cells from wild-type and gadd45a or gadd45b deficient mice were exposed to ultraviolet radiation (UV) and analyzed for expression of stress responsive kinases, including JNK and p38. It was observed that P38 and JNK were activated in wt bone marrow cells in response to UV but not in bone marrow cells defecient in gadd45a. Also, the transcription factor NF-kB was activated in wt bone marrow cells, but not in gadd45a−/− cells. The pharmacological inhibitor SB203580 specific for p38, increased apoptosis in reponse to UV, indicating that p38 is implicated in signaling myeloid cell survival. SB203580 was observed also to inhibit the expression of certain NF-kB target genes, including cIAP-1, c-IAP-2, bcl-2 and bcl-xl, in gadd45a+/+ cells but not in gadd45a deficient bone marrow cells. Taken together this data provides first evidence for the role gadd45a plays in the control of hematopoietic cell survival in response to UV, via modulation of P38 MAPK and NF-kB signaling pathways. Unlike in gadd45a−/− bone marrow cells, p38 activation appeared not to be impaired in gadd45b−/− cells, indicating that gadd45b is not involved in p38 activation in myeloid cells. However, UV induced JNK activation was sustained in gadd45b−/− myeloid cells compared to wt cells, indicating that gadd45b is a negative modulator of UV induced JNK signaling in myeloid cells. UV induced activation of MKK4 an upstream regulator of JNK also was impaired in gadd45b−/−. NF-kB was also found activated in wt cells, but not in gadd45b−/− cells. This data indicates that in bone marrow cells exposed to UV, NF-kB induced expression of Gadd45b plays a protective role against UV induced apoptosis via inhibition of MKK4 kinase which in turn results in suppression of JNK activity. Taken together this data provides evidence that Gadd45a and Gadd45b protect haematopoetic cells from genotoxic-stress induced apoptosis via distinct signaling pathways.

Description: Using a variety of differentiation-inducible myeloid cell lines, we previously showed that the zinc-finger transcription factor early growth response gene 1 (Egr-1) is a positive modulator of macrophage differentiation and negatively regulates granulocytic differentiation. In this study, high-efficiency retroviral transduction was used to ectopically express Egr-1 in myeloid-enriched or stem cell–enriched bone marrow cultures to explore its effect on the development of hematopoietic progenitors in vitro and in lethally irradiated mice. It was found that ectopic Egr-1 expression in normal hematopoietic progenitors stimulates development along the macrophage lineage at the expense of development along the granulocyte or erythroid lineages, regardless of the cytokine used. Moreover, Egr-1 accelerated macrophage development by suppressing the proliferative phase of the growth-to-macrophage developmental program. The remarkable ability of Egr-1 to dictate macrophage development at the expense of development along other lineages resulted in failure of Egr-1–infected hematopoietic progenitors to repopulate the bone marrow and spleen, and thereby prevent death, in lethally irradiated mice. These observations further highlight the role Egr-1 plays in monocytic differentiation and growth suppression.

Description: Both deregulated growth and blocks in differentiation cooperate in the multistage process of leukemogenesis. Thus, understanding functional interactions between genes that regulate normal blood cell development, including cell growth and differentiation, and how their altered expression contributes to leukemia, is important for rational drug design. Previously, we have shown that the zinc finger transcription factor Egr-1 plays a role in monocytic differentiation. Ectopic expression of Egr-1 in M1 myeloblastic leukemia cells was observed to activate the macrophage differentiation program in the absence of the differentiation inducer interleukin 6 (IL-6) and to promote terminal differentiation in its presence. In addition, we have shown that deregulated expression of the proto-oncogene c-myc blocks the myeloid terminal differentiation program. Here we show that restoring expression of Egr-1 in M1 cells that express deregulated c-Myc abrogates the c-Myc block in terminal differentiation, resulting in cells that undergo functional macrophage maturation. However, there is an absence of both growth arrest and cell adhesion. In addition, Egr-1 expression diminished M1myc leukemogenicity in vivo. These findings indicate that Egr-1 can act as a tumor suppressor gene and suggest that Egr-1 or Egr-1 targets may provide important tools for differentiation therapy in certain leukemic phenotypes.

Description: Myeloid leukemic cells (M1) proliferate continuously in culture unless induced by Interleukin-6 (IL6) to undergo a terminal differentiation program into macrophages, followed by apoptosis. M1 cells lack the tumor suppressor p53, which is a critical determinant of the cellular decision to either growth arrest and repair DNA damage or to undergo apoptosis. Activation of a temperature sensitive p53 protein (p53 val) at the permissive temperature in M1 cells results in rapid apoptosis. IL6 treatment blocks this p53-mediated apoptosis. Towards understanding the basis for this p53-mediated apoptosis and its abrogation by IL6, we have shown that at the permissive temperature p53 activates the pro-apoptotic Fas/CD95 pathway by up regulating the Fas/CD95 receptor and cleaving antiapoptotic c-FLIP. On the other hand, antagonistic Fas antibody protects against apoptosis. IL6 decreases Fas/CD95 ligand expression and prevents cleavage of FLIP. Treatment of M1p53ts cells with the specific Akt inhibitor Ly294002 abrogated IL6 protection and resulted in Flip cleavage, suggesting that IL-6 blocks apoptosis by phosphorylating and activating P13kinase/Akt, which in turn promotes FLIP stability. Inhibition of the ERK pro-survival pathway did not abrogate IL6 protection against p53 apoptosis like Akt inhibition caused. Nevertheless M1p53ts-Flip cell lines fail to completely protect against p53 mediated apoptosis, suggesting that FLIP is itself insufficient to protect against apoptosis. Therefore we examined what other proteins may synergize with FLIP to protect from apoptosis, and found that that the pro-survival bcl2 protein family member MCL-1 is strongly up regulated by IL6 in our M1p53 cell line. Generation of M1p53-FLIP-MCL1, M1p53-MCL1, and M1p53 -uncleavable FLIP cell lines is underway to determine whether there is synergy between MCL-1 and FLIP in escape from p53 mediated apoptosis of M1p53 cells. Thus far taken together these data support a model for leukemic progression where cells that acquire the ability to produce an autocrine survival factor, such as IL6, can bypass normal p53 surveillance function by targeting downstream inhibitors of apoptosis such Akt, c-Flip and MCL-1.

Description: 3264 Poster Board III-1 The bcr/abl oncogene causes chronic myelogenous leukemia (CML) in human. BCR/ABL induces the transformation of myeloid lineage through MAPK, JNK/SAPK, PI3K signaling pathways. Growth arrest DNA damage 45A (GADD45A) and GADD45B are upregulated during myeloid lineage terminal differentiation. They are involved in G2/M cell cycle arrest and apoptosis in response to exogenous stress stimuli through MAPK and JNK/SAPK pathways. To investigate the effect of GADD45A and GADD45B in the development of CML, syngeneic wild type lethally irradiated mice were reconstituted with wild type, gadd45a or gadd45b null myeloid progenitors transduced with a retrovirally expressed 210-kD BCR/ABL fusion oncoprotein. We found that loss of gadd45a or gadd45b accelerated the development of CML-like disease in wild type recipients. BCR/ABL transformed gadd45a or gadd45b deficient progenitor recipients exhibited a significantly accelerated kinetics of increase in the number of WBC and percentage of myeloid blasts in blood compared to mice reconstituted with the same number of wild type bone marrow cells transduced with BCR/ABL. There was also increase in the rate of accumulation of CD11b+Gr1+ cells in the bone marrow and spleen. Using in vitro and in vivo BrdU assays, enhanced proliferation capacity was observed for both BCR/ABL transduced gadd45a and gadd45b deficient myeloid progenitors. BCR/ABL transduced gadd45a and gadd45b deficient primary myeloid progenitors formed more and bigger colonies compared to BCR/ABL transformed wild type progenitors. Impaired apoptosis was showed in BCR/ABL transduced gadd45a deficient myeloid progenitors. These results indicate that both gadd45a and gadd45b function as suppressors of the development of BCR/ABL driven CML, where gadd45a appears to suppress CML via mechanism involving inhibition of cell proliferation enhancement of apoptosis, whereas gadd45b appears to only inhibit cellular proliferation. Dissecting the molecular nature of signaling paths involved in the suppressive function of gadd45a and gadd45b in BCR/ABL driven CML, as well as analysis of Gadd45 in CML patients, is underway. Disclosures: No relevant conflicts of interest to declare.

Description: Deregulated expression of the proto-oncogenes c-myc, E2F-1 and c-myb in M1 myeloid leukemic cells rendered these cells incapable of undergoing myeloid terminal differentiation and its associated growth arrest, and prevented the loss in leukemogenicity normally observed when M1 cells are induced to differentiate. We recently showed that expressing Egr-1 in M1myc cells abrogated the c-myc-mediated block in terminal myeloid differentiation, with the cells undergoing macrophage maturation in the absence of growth arrest. Importantly, Egr-1 also abrogated c-myc-driven leukemogenicity. In this study, we asked if Egr-1 functions as a tumor suppressor by abrogating the block in differentiation caused by other oncogenes. It was shown that expressing Egr-1 in M1E2F-1 cells completely overrode the block in terminal myeloid cell differentiation, with the cells undergoing macrophage maturation, and unlike in myc/Egr-1 expressing cells, also becoming growth arrested. In contrast, expression of Egr-1 in M1myb cells promoted progression of the differentiation program to an intermediate stage of differentiation, but the cells became neither fully matured nor growth arrested, continuing to proliferate indefinitely. As seen for expression of Egr-1 in M1myc cells, Egr-1 expression in M1E2F-1 cells also abrogated E2F-1 driven leukemogenicity. In contrast, Egr-1 co-expression with c-myb in M1myb cells did not abrogate myb driven leukemia. Taken together, it can be concluded that Egr-1 is dominant to both E2F-1 and c-myc with regard to terminal morphological differentiation and the ability to suppress leukemias, whereas the proto-oncogene c-myb is dominant to Egr-1. These findings indicate that the tumor suppressor Egr-1 provides important tools for differentiation therapy of multiple leukemic phenotypes, dependent on the molecular nature of the activated oncogene.

Description: Cancer cell phenotype is controlled by both genetic composition and gene expression. Recent large-scale cancer sequencing studies have revealed extensive intratumoral genetic heterogeneity and have demonstrated its potential impact on clonal evolution and clinical outcome. The most direct approach to uncovering the impact of genetic heterogeneity on cellular phenotype requires integration of genetic and transcriptomic profiles of single cells. Currently, however, RNA and DNA cannot be reliably isolated from the same cell. Here, we demonstrate the feasibility for linking single-cell somatic mutation data with cellular transcriptional heterogeneity through a targeted RNA-based approach. By leveraging a microfluidic platform (Fluidigm BioMarkTMHD system) to perform multiplexed targeted amplification of RNA derived from hundreds of single cells, we have generated a versatile approach for the integrated detection of somatic mutations in relation to specific gene transcripts. We focused on a series of chronic lymphocytic leukemia (CLL) B cells that were previously characterized by bulk whole-exome (WES) and RNA-sequencing (RNA-Seq). We developed 2 classes of assays. First, we generated multiplexed nested quantitative RT-PCR assays of 96 genes with known involvement in CLL biology. Second, to simultaneously detect patient-specific somatic mutations in the same cell, we devised multiplexed pre-amplification primers targeting transcribed regions containing somatic point mutations. These regions were then amplified using paired nested primers, for detection of the wild-type or mutant alleles. We focused on those somatic mutations with detectable expression in bulk CLL RNA (〉 5 FPKM by RNA-seq). When applied to either artificial oligonucleotide templates or bulk patient cDNA, these paired wild-type and mutant allele detection assays reliably demonstrated consistent differences in DCT values of 〉6 cycles. In total, we designed expression assays for 96 genes and 46 mutation detection applied to 5 CLL samples (median of 9 assays/sample, range 6-13). We examined up to 384 single cells from each of 5 samples and from normal CD19+ B cells. Based on expression of housekeeping genes ACTB and B2M, we observed viable expression in 1951 of 2112 cells (92.4%). We could clearly discern that expression of the 96 genes was heterogeneous across 354 single CLL-B cells and could discriminate CLL from 174 normal B cells by principal component analysis. 32 out of 46 (70%) mutation detection assays successfully distinguished between wild-type and mutant alleles and the mutant allele was consistently observed in the originating CLL cells, but not in unrelated CLL or non-leukemic B cells. Our RNA-based estimates of allele frequency agreed with single-cell targeted DNA-based detection of somatic mutations conducted for 3 of 5 CLL samples as well as with frequencies estimated from bulk WES-based cancer cell fraction (CCF) measurements. We applied our integrated assay design to 2 CLL samples known to harbor mutations in the putative CLL driver SF3B1: Patient 1 with bulk CCF of 17% (G742D) and Patient 2 with 87% (K700E). Mutation of this critical spliceosome component broadly changes RNA splicing profiles although the functional impact of these alternative splice variants on CLL biology remains unknown. We generated multiplex assays for SF3B1 mutation detection and for expression of mutation-associated alternative splice variants. Consistent with the bulk-sequencing results, we detected 50 of 373 (13.4%) single CLL cells from Patient 1 with SF3B1 mutation. Moreover, the subset of cells with SF3B1 mutation demonstrated high expression of splice variants relative to wild-type cells (GCC2 and MAP3K7, p〈 0.000001). This SF3B1 mutated subclone also displayed reduced expression of RNA splicing factors (BTAF1, DDX17, SNW1, SRSF3, U2SURP; all p