Introduction
Chronic myeloid leukemia (CML) was one of the first malignancies shown to be initiated in hematopoietic stem cells by the BCR-ABL1 oncogene and sustained in blast crisis (BC) by ...progenitor cells that co-opt stem cell properties and behave like leukemia stem cells (BC LSCs). The BCR-ABL fusion oncogene encodes a constitutively active tyrosine kinase BCR-ABL. Although tyrosine kinase inhibitor (TKI) therapy targeting BCR-ABL suppresses CML during the chronic phase (CP), progenitors undergo expansion as a consequence of subsequent genetic and epigenetic alterations that fuel blast crisis transformation, BC LSC generation and TKI resistance. Self-renewing human BC LSCs harbor increased expression of Inflammation responsive adenosine deaminase acting on RNA (ADAR1), which can alter transcript as well as microRNA (miRNA) maturation, splicing and translation by Adenosine (A)-to-Inosine (I) editing of double stranded RNA. miRNAs are a family of small non-coding RNA molecules that regulate gene expression at a post-transcriptional level by inhibiting protein translation and/or reducing mRNA stability. Eukaryotic cells employ miRNAs in diverse biological processes including cell proliferation, differentiation, pluripotency and self-renewal. The stem cell pluripotency RNA binding protein LIN28B plays critical roles in BC transformation of CML. In this study we sought to characterize CML related-oncogenes, such as BCR-ABL, JAK2 and ADAR1, alone or in stromal co-culture in terms of their ability to regulate LSC self-renewal through modulation of let-7 /LIN28B stem cell transcriptional regulatory axis.
Methods
MiRNAs were extracted from purified CD34+ cells derived from CP and BC CML patient samples as well as cord blood by RNeasy microKit (QIAGEN) and let-7 expression was evaluated by qRT-PCR using miScript Primer assay (QIAGEN). CD34+ cord blood (n=3) were transduced with lentiviral human BCR-ABL, JAK2, let-7a, wild type ADAR1 and ADAR1 mutant, which lacks a functional deaminase domain. Then, 72 hours after transduction, lentivirally transduced cells were plated on irradiated SL/M2 cells. After 5 days of culture, cells were collected for RNA and microRNA extraction. Transduction efficiency and LIN28B levels were evaluated by qRT-PCR and let-7 expression was quantified by qRT-PCR using miScript primer assay. Hematopoietic Progenitor and Replating assaywere performed on lenti-let-7a-overexpressing CB cells to assess differentiation, survival and self-renewal capacity.
Results
Lentiviral overexpression of human BCR-ABL in CD34+ CB did not induce any significant change in let-7 family members and LIN28B expression in absence of stromal co-culture. However, stromal co-culture of BCR-ABL overexpressing CB led to the significant downregulation of members of the let-7 family as well as to upregulation of their target gene LIN28B, thus suggesting that extrinsic microenvironmental cues are necessary for modulating let-7 family levels in presence of BCR-ABL. Notably, qRT-PCR of CB transduced with JAK2 showed significant upregulation of ADAR1 in the absence of stroma, thus suggesting that JAK2 might be a mediator of inflammatory cytokine-driven ADAR1 activation. Lentiviral overexpression of both human JAK2 and ADAR1 significantly reduced the expression of let-7 family members and induced up-regulation of LIN28B. Interestingly, lentiviral overexpression of ADAR1 mutant did not induce any significant change in most let-7 family members. Finally, lentiviral overexpression of let-7a induced significant reduction in survival and self-renewal.
Conclusion
These finding suggest that BCR-ABL requires extrinsic signals from the niche to modulate self-renewal of BC LSCs. Conversely, lentiviral JAK2 overexpression induces activation of aberrant RNA editing and subsequent reduction of let-7 family members in the absence of the niche. Interestingly, experiments with ADAR1 mutant, suggest that ADAR1 downregulates most of the let-7 family members in a RNA–editing dependent way manner. In summary these findings suggest a novel mechanism for BC LSC generation that may have utility in prognostication and selective LSCs targeting.
Jamieson:J&J: Research Funding; Sanofi: Research Funding, Travel Support, Travel Support Other; Roche: Research Funding.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
INTRODUCTION
Multiple myeloma is a heterogeneous hematopoietic malignancy that represents 10% of all blood cancers and is characterized by malignant plasma cell expansion in the bone marrow, which is ...rich in pro-inflammatory cytokines such as interleukin-6 (IL-6). The emergence of therapeutically recalcitrant disease even following intensive treatment suggests the existence of a drug-resistant myeloma-initiating population. These myeloma-initiating cells are thought to co-opt stem cell pathways that enhance their capacity to self-renew and become dormant in protective niches. Recently, we and others showed that aberrant RNA editing plays a key role in malignant transformation through activation of the inflammation-responsive RNA editase ADAR1. In human leukemia stem cells, ADAR1 activation is associated with enhanced self-renewal of dormant progenitors, while lentiviral-shRNA ADAR1 knockdown reduces malignant stem cell self-renewal in vivo. Notably, in 30% of multiple myeloma cases copy number amplification of the ADAR locus on chromosome 1q21, which portends a poor prognosis. Thus, the goal of this study was to investigate whether ADAR1-mediated RNA editing in multiple myeloma occurs as a result of chromosome amplification and pro-inflammatory signaling, and to evaluate the effects of prolonged immunomodulatory therapy on ADAR1 activation leading to the emergence of drug-resistant myeloma-initiating cells.
METHODS AND RESULTS
Increased ADAR1 expression in myeloma patient samples
To determine whether gene expression of ADAR1 correlates with chromosome 1q21 amplification, we evaluated existing microarray datasets (Multiple Myeloma Genomics Initiative) from well-characterized patient samples harboring 2 to ≥4 copies of the CKS1B gene, which is located within 500kB adjacent to ADAR as well as the interleukin-6 (IL-6) receptor locus IL6R on chromosome 1q21. Notably, gain of 1q21 copy number is associated with more proliferative disease and poor-risk cytogenetics, which could also be related to ADAR activation. Interestingly, our analysis of ADAR1 gene expression showed increased ADAR1 levels in patients with a CKS1B score of 4 or greater (n=6) compared with patients with a score of 2 (n=18).
IL-6 mediated induction of RNA editing activity
To evaluate the role of pro-inflammatory cytokine stimulation of ADAR1 in the chromosome 1q21-amplified human myeloma cell line H929, cells were exposed to increasing doses (5-20ng/mL) of recombinant human IL-6. ADAR1 activity, evaluated using a novel diagnostic RNA editing site-specific qPCR (RESSq-PCR) assay to detect cancer stem cell generation, showed that IL-6-treated H929 harbored increased ADAR1 activity.
ADAR1 activation after prolonged lenalidomide exposure
To investigate the effects of immunomodulatory drug treatment on ADAR1-dependent RNA editing, drug-resistant human myeloma cell lines were experimentally derived by low-dose treatment (1 mM) of H929 cells over 10 weeks. Further incubation with lenalidomide at 10mM selected a robustly drug-resistant population. These cells showed a marked increase in ADAR1 expression and RNA editing activity, as measured by direct sequencing and RESSq-PCR. Long-term lenalidomide treatment of H929 also expanded the CD138-negative fraction, suggesting the emergence of a previously-identified myeloma-initiating cell population. Stromal co-culture of H929 cells with a 1:1 mixture of previously inactivated human bone marrow stromal cell lines (HS-5 and HS-27a) secreting IL-6 and other cytokines also enriched for CD138-negative and CD138-dim populations.
CONCLUSION
Considering the recently described role for ADAR1 in malignant transformation and cancer stem cell generation, myeloma cells harboring 1q21 amplification could gain a self-renewal advantage through ADAR1 activation. Using RESSq-PCR to detect aberrant RNA editing, we observed increased ADAR1 activity during the evolution of 1q21-amplified human myeloma cells under prolonged drug treatment, coupled with an expansion of the CD138-negative fraction, which was also observed following bone marrow stromal co-culture. Together these data suggest that ADAR1 represents a novel diagnostic and therapeutic target for multiple myeloma. Moreover, this multiple myeloma niche model represents a valuable tool for evaluating novel methods to inhibit aberrant ADAR1 activation in drug-resistant malignancies.
Jamieson:Sanofi: Honoraria; Roche: Honoraria.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Background
In advanced human malignancies, RNA sequencing (RNA-seq) has uncovered deregulation of adenosine deaminase acting on RNA (ADAR) editases that promote therapeutic resistance and leukemia ...stem cell (LSC) generation. Chronic myeloid leukemia (CML), an important paradigm for understanding LSC evolution, is initiated by BCR-ABL1 oncogene expression in hematopoietic stem cells (HSCs) but undergoes blast crisis (BC) transformation following aberrant self-renewal acquisition by myeloid progenitors harboring cytokine-responsive ADAR1 p150 overexpression. Emerging evidence suggests that adenosine to inosine editing at the level of primary (pri) or precursor (pre)-microRNA (miRNA), alters miRNA biogenesis and impairs biogenesis. However, relatively little is known about the role of inflammatory niche-driven ADAR1 miRNA editing in malignant reprogramming of progenitors into self-renewing LSCs.
Methods
Primary normal and CML progenitors were FACS-purified and RNA-Seq analysis as well as qRT-PCR validation were performed according to published methods (Jiang, 2013). MiRNAs were extracted from purified CD34+ cells derived from CP, BC CML and cord blood by RNeasy microKit (QIAGEN) and let-7 expression was evaluated by qRT-PCR using miScript Primer assay (QIAGEN). CD34+ cord blood (n=3) were transduced with lentiviral human JAK2, let-7a, wt-ADAR1 and mutant ADAR1, which lacks a functional deaminase domain. Because STAT signaling triggers ADAR1 transcriptional activation and both BCR-ABL1 and JAK2 activate STAT5a, nanoproteomics analysis of STAT5a levels was performed. Engrafted immunocompromised RAG2-/-γc-/- mice were treated with a JAK2 inhibitor, SAR302503, alone or in combination with a potent BCR-ABL1 TKI Dasatinib, for two weeks followed by FACS analysis of human progenitor engraftment in hematopoietic tissues and serial transplantation.
Results
RNA-seq and qRT-PCR analysis in FACS purified BC CML progenitors revealed an over-representation of inflammatory pathway activation and higher levels of JAK2-dependent inflammatory cytokine receptors, when compared to normal and chronic phase (CP) progenitors. Moreover, RNA-seq and qRT-PCR analysis showed decreased levels of mature let-7 family of stem cell regulatory miRNA in BC compared to normal and CP progenitors. Lentiviral human JAK2 transduction of CD34+ progenitors led to an increase of ADAR1 transcript levels and to a reduction in let-7 family members. Interestingly, lentiviral human JAK2 transduction of normal progenitors enhanced ADAR1 activity, as revealed by RNA editing-specific qRT-PCR and RNA-seq analysis. Moreover, qRT-PCR analysis of CD34+ progenitors transduced with wt-ADAR1, but not mutant ADAR1 lacking functional deaminase activity, reduced let-7 miRNA levels. These data suggested that ADAR1 impairs let-7 family biogenesis in a RNA editing dependent manner. Interestingly, RNA-seq analysis confirmed higher frequency of A-to-I editing events in pri- and pre-let-7 family members in CD34+ BC compared to CP progenitors, as well as normal progenitors transduced with human JAK2 and ADAR1-wt, but not mutant ADAR1. Lentiviral ADAR1 overexpression enhanced CP CML progenitor self-renewal and decreased levels of some members of the let-7 family. In contrast, lentiviral transduction of human let-7a significantly reduced self-renewal of progenitors. In vivo treatments with Dasatinib in combination with a JAK2 inhibitor, significantly reduced self-renewal of BCR-ABL1 expressing BC progenitors in the bone marrow thereby prolonging survival of serially transplanted mice. Finally, a reduction in ADAR1 p150 transcripts was also noted following combination treatment only suggesting a role for ADAR1 in CSC propagation.
Conclusion
This is the first demonstration that intrinsic BCR-ABL oncogenic signaling and extrinsic cytokines signaling through JAK2 converge on activation of ADAR1 that drives LSC generation by impairing let-7 miRNA biogenesis. Targeted reversal of ADAR1-mediated miRNA editing may enhance eradication of inflammatory niche resident cancer stem cells in a broad array of malignancies, including JAK2-driven myeloproliferative neoplasms.
Jamieson:J&J: Research Funding; GSK: Research Funding.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
INTRODUCTION
Representing ten percent of all hematologic malignancies, multiple myeloma (MM) is typified by clonal plasma cell proliferation in the bone marrow (BM) and may progress to a ...therapy-resistant stage characterized by circulating malignant plasma cells, which is termed plasma cell leukemia, (PCL). Notably, copy number amplification involving the myeloid cell leukemia (MCL)-1 locus, and translocations at the BCL2 locus have been described in high-risk MM. Moreover, BCL2 family members, including both MCL1 and BCL2, are highly expressed in relapsed MM. Finally, downregulation of BCL2 family members was reported to increase sensitivity to lenalidomide, a standard treatment for MM, suggesting that BCL2-targeted treatments may obviate therapeutic resistance.Sabutoclax, a potent small molecule inhibitor of 6 anti-apoptotic BCL2 family proteins, was shown to inhibit cancer stem cell (CSC) survival in chronic myeloid leukemia (CML) (Goff et al Cell Stem Cell 2013). Thus, we investigated BCL2 pro-survival splice isoform expression in therapy-resistant MM and PCL and evaluated whether Sabutoclax reduces malignant plasma cell burden in humanized primagraft assays.
METHODS AND RESULTS
BCL2 pro survival expression in primary myeloma samples
Mononuclear cells from MM or PCL samples were isolated by Ficoll-Paque density gradient separation and collected for RNA extraction or FACS Aria purified into CD138+ or CD34-/CD138- cancer stem cells (CSC) subsets. To evaluate BCL2 pro-survival family member expression, splice isoform-specific quantitative PCR was performed to measure expression of pro-survival long isoforms compared with short splice isoforms, which are pro-apoptotic. Interestingly, MM and PCL patients displayed higher levels of BCL2-L, MCL1-L, BCLX-L and BLF1-L compared to normal controls. Moreover, prolonged lenalidomide exposure increased BCL2-L and MCL1-L expression in the myeloma cell line H929, compared to untreated cells.
Sabutoclax Treatment of a Novel Humanized Plasma Cell Leukemia Primagraft Model
Mononuclear cells from three primary PCL patient samples were stably transduced with a GFP-luciferase lentiviral vector and transplanted intrahepatically in newborn RAG2γ-/- c-/- mice. Engraftment was monitored by peripheral blood free light chain ELISA assays. Flow cytometric analyses revealed robust engraftment of PCL cells in bone marrow, spleen, liver and peripheral blood. Once transplanted mice displayed significant tumor burden above background free light chain levels, animals were randomized by ELISA values in vehicle versus Sabutoclax groups. Sabutoclax was selected because this pan-BCL2 targeted compound, unlike related BCL2 inhibitors such as ABT-199, also inhibits MCL1. Sabutoclax (10mg/kg) was administered intravenously twice weekly for two to four doses. Sabutoclax treated PCL mice showed reduced human plasma cell burden in bone marrow and spleen tissues compared to vehicle controls.
CONCLUSION
Expression of pro-survival BCL2 splice isoforms, including BCL2-L and MCL1-L, portends PCL engraftment in immunocompromised mice. Treatment of human PCL engrafted mice with Sabutoclax reduces malignant plasma cell survival in hematopoietic tissues. Thus, selective targeting of pro-survival isoform expressing CSC with a pan-BCL2 inhibitor may abolish BCL2 and MCL1-dependent therapeutic resistance in MM and PCL.
Jamieson:GlaxoSmithKline: Research Funding; Johnson & Johnson: Research Funding.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Introduction
Human bone marrow aging is typified by decreased cellularity, stem cell exhaustion and myeloid lineage bias that may set the stage for development of myeloid malignancies. Secondary AML ...(sAML) arises from prior myelodysplastic syndromes (MDS) or myeloproliferative neoplasms (MPN), and occurs in patients with an average age of >65. Because of the typically advanced age of this population, patients currently have few effective treatment options available after leukemic transformation. We and others have recently identified a key role for enzymatic RNA editing activity in cancer progression, and in particular in leukemia stem cell (LSC) generation. In hematopoietic stem and progenitor cells, adenosine deaminase acting on dsRNA-1 (ADAR1) is the most abundantly expressed RNA editing gene. However, the role of abnormal RNA editing activity has not been elucidated in healthy human bone marrow aging and age-related MDS with a high risk of transforming to sAML. Therefore, we established whole transcriptome-based RNA editing signatures of benign versus malignant bone marrow progenitor cell aging, which provides novel RNA-based functionally relevant biomarkers of aging, MDS and progression to sAML.
Methods
Whole transcriptome sequencing (RNA-Seq) was performed on FACS-purified hematopoietic stem (CD34+CD38-Lin- HSC) and progenitor cells (CD34+CD38+Lin- HPC) from aged (average age = 65.9 y/o) versus young (average age = 25.8 y/o) adult healthy bone marrow samples, and in leukemia stem cells (LSC) from patients with sAML (average age = 71.4 y/o) and MDS (average age = 63.8 y/o). Comparative gene set enrichment analyses (GSEA) and RNA editing profiles were identified for normal and malignant progenitor cell aging.
Results
Aberrant RNA editing activity has recently been shown to be induced in multiple cancers, and has been implicated as a malignant reprogramming factor. Comparative whole transcriptome RNA sequencing (RNA-seq) and single nucleotide variant analyses revealed widespread increases in RNA editing rates in aged versus young HPC, and in human sAML LSC compared with age-matched normal progenitors. Moreover, RNA editing rates, represented as adenosine (A) to inosine/guanosine (G) changes at known RNA editing loci, were increased in sAML compared with MDS progenitors. The differential expression of certain sites is as high as 70%, which can be readily detected by RESS-qPCR. These data suggest that during aging niche-dependent RNA editing deregulation contributes to MDS progression to sAML. Interestingly, the highly edited loci in sAML LSC were distinct from loci that were differentially edited in aged versus young HPC, suggesting that pro-inflammatory conditions in sAML may trigger RNA editing of a unique set of transcripts, including predominantly RNA processing-related gene products and transcription factors. Notably, several loci in transcripts of APOBEC3C/D that we previously found were associated with blast crisis transformation of chronic myeloid leukemia also displayed enhanced editing in sAML LSC, but not aged versus young HPC.
Conclusions
Detection of aberrant RNA processing provides novel biomarkers as well as potential therapeutic targets for sAML LSC eradication with implications for treatment of a variety of human malignancies and other age-related disorders. We have identified commonly RNA-edited transcripts in multiple hematologic malignancies, which could be developed clinically and as companion diagnostic targets for LSC-targeted therapeutics.
Jamieson:CTI Biopharma: Research Funding; Johnson & Johnson: Research Funding; GlaxoSmithKline: Research Funding.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Myelodysplastic syndromes (MDS) result from ineffective hematopoietic stem cell (HSC) maintenance in an aged bone marrow microenvironment and have a proclivity for evolution to acute myeloid leukemia ...(AML). Progression to therapy resistant AML is driven by leukemia stem cells (LSC) harboring enhanced survival, dormancy and self-renewal capacity in supportive niches. Seminal next-generation DNA sequencing Results suggest that MDS evolution is controlled by mutations in splicing related genes and epigenetic modifiers of gene expression. However little is known about the cell type and context specific functional effects of these mutations on LSC transcriptional alterations that have been shown to promote MDS/AML progression and resistance to therapies such as 5-azacytidine (Vidaza). Therefore, we investigated the effect of splicing inhibitors on LSC survival and self-renewal 1) during progression of MSD to AML and 2) before and after clinical Vidaza treatment in a bone-marrow stromal co-cultures that recapitulates key aspects of the human LSC niche.
Mouse bone marrow cell lines, transfected to producehuman SCF,IL3 and G-CSF, were used as a stromal monolayers. Then human CD34+ cellswere selected from MDS (n=1) and AML primary samples (n=6). As normal controls, CD34+cells from cord blood (CB, n=3) or aged bone marrow (n=3) were utilized for the co-culture experiments. Survival and self-renewal of the CD34+ cells were investigated by colony forming and replating assays. Two SF3B1-targeted splicing inhibitors: FD 895 and a FD-analog were added at the initiation of co-culture at concentrations ranging from 0.1 to10 uM.
After 2 weeksof stromal co-culture, none of the compounds demonstrated inhibition of the cell viability. Meanwhile, the splicing inhibitors demonstratedno reduction in survival in cord blood, and minor cytotoxicity toward aged bone marrow, MDS and AML samples showed a dose- and time-dependent significant (up to 80%) inhibition of colony formation. To analyzethe effect of splicing inhibitors on LSC self-renewal, replatingassayswere performed. While compounds at high doses mediated only a slight decrease in colony formation in normal CB and a-BM samples, MDS and AML samples exhibited a dose dependent inhibition of 38.2+/-8.1% of LSC survival (p<0.001) for FD895 and considerably lower 13.8+/-3.6 % of LSC survival for FD analog (p<0.001). Analysis of pre- and post progression samples from the same patient revealed the capacity of splicing inhibitors to diminish LSC survival. In CMML, FD895 induced significantly less cytotoxicity (35% compared with 75%) after progression to AML. Notably, in aged-BM both compounds reduced only CFU-GM survival, but not HSC self-renewal. In sequential primary samples from AML patients collected before and after clinical treatment with Vidaza, naïve samples exhibited similar sensitivity to FD-895 treatment in stromal co-culture models, and LSC survival and self-renewal capacity was reduced following incubation with FD-895. In contrast, following clinical treatment in patients that were responsive to Vidaza, these samples acquired resistance to splicing inhibition. However, patients that were non-responders to Vidaza treatment retained sensitivity to FD-895 treatment.
These data indicate that RNA editing and splicing activities represent novel regulators of LSC self-renewal and survival in LSC supportive niches. These properties can be inhibited using novel splicing inhibitors with minimal toxicity toward normal progenitors.
No relevant conflicts of interest to declare.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Abstract
Introduction
The adenosine deaminase acting on RNA (ADAR) family of RNA editases has been linked to the pathogenesis of diverse malignancies, including leukemia, breast cancer and ...hepatocellular carcinoma. We previously showed that human leukemia stem cells (LSC) from blast crisis (BC) chronic myeloid leukemia (CML) patients harbor increased ADAR1 expression compared with normal and chronic phase (CP) progenitors. Whole transcriptome RNA sequencing (RNA-Seq) revealed increased adenosine to inosine (A-to-I) RNA editing during CML progression concentrated within primate specific Alu-containing transcripts. However, detection of RNA editing by RNA-Seq in rare cell populations can be technically challenging, costly and requires PCR validation. Thus, the objectives of this study were to validate RNA editing of a subset of these LSC-associated transcripts in the context of lentivirally enforced ADAR1 expression, and to develop an RNA editing reporter reporter assay in human leukemia cells and a qPCR-based diagnostic test to rapidly detect CSC-associated aberrant RNA editing.
Methods
The BCR-ABL+ human leukemia cell line K562 was stably transduced with lentiviral human ADAR1 or vector. FACS-purified K562-ADAR1 cells were transfected with a luciferase-based reporter vector to confirm RNA editing activity. Two genes, MDM2 and APOBEC3D, were selected from our previous RNA-Seq studies of BC progenitors (Jiang et al, 2013). Targeted sequencing was performed on high fidelity PCR products using primers flanking each of 2 editing sites in each gene. RNA editing-specific qPCR primers were designed for each editing site using an allele-specific strategy that detects cDNA containing either an A or G(I) representing an RNA editing event. Both targeted sequencing and qPCR were used to detect RNA editing in K562-ADAR1 and primary cord blood-derived hematopoietic stem cells (HSC) lentivirally transduced with ADAR1.
Results
Lentivirally enforced ADAR1 expression promoted RNA editing activity as measured by luciferase reporter activity. Increased A-to-I changes in MDM2 and APOBEC3D were confirmed by targeted sequencing. In independent experiments, RNA editing site-specific qRT-PCR accurately detected RNA editing in K562-ADAR1 cells (n=3) and in primary HSC overexpressing ADAR1 (n=4). Site-specific primers distinguished G(I) bases at RNA editing sites in cDNA and as predicted gave no signal in gDNA. Relative A-to-I RNA editing ratios were increased by 2 to 3 fold in ADAR1-expressing cells at all four sites.
Conclusions
These results set the stage for development of primate-specific RNA editing as a novel diagnostic strategy for clinical LSC detection and identify ADAR1 as a potential therapeutic target in LSC. These data shed new light on the mechanisms of ADAR1-mediated generation of malignant progenitors that drive therapeutic resistance, disease progression and relapse in CML and may be applicable to other CSC-driven malignancies.
Citation Format: Leslie A. Crews, Qingfei Jiang, Maria A. Zipeto, Angela C. Court, Christian L. Barrett, Marco A. Marra, Kelly A. Frazer, Catriona H. M. Jamieson. A novel diagnostic assay for detection of primate-specific RNA editing events in leukemia stem cells. abstract. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 375. doi:10.1158/1538-7445.AM2014-375
Abstract
The molecular etiology of human progenitor reprogramming into self-renewing leukemia stem cells (LSC) has remained elusive. While DNA sequencing has uncovered spliceosome gene mutations that ...promote alternative splicing and portend leukemic transformation, isoform diversity may also be generated by RNA editing mediated by adenosine deaminase acting on RNA (ADAR) enzymes that regulate stem cell maintenance. In this study, whole transcriptome sequencing of normal, chronic phase (CP) and serially transplantable blast crisis (BC) chronic myeloid leukemia (CML) progenitors revealed increased interferon-γ pathway gene expression in concert with BCR-ABL amplification, enhanced expression of the interferon responsive ADAR1 p150 isoform and a propensity for increased A-to-I RNA editing during CML progression. Lentiviral overexpression experiments demonstrate that ADAR1 p150 promoted expression of the myeloid transcription factor PU.1 and induced malignant reprogramming of myeloid progenitors. Moreover, enforced ADAR1 p150 expression was associated with production of a mis-spliced form of GSK3β implicated in LSC self-renewal. Finally, functional serial transplantation and shRNA studies demonstrate that ADAR1 knockdown impaired in vivo self-renewal capacity of BC CML progenitors. Together these data provide a compelling rationale for developing ADAR1-based LSC detection and eradication strategies.
Citation Format: Qingfei Jiang, Leslie A. Crews, Christian L. Barrett, Angela Court-Recart, Daniel Goff, Anil Sadarangani, Jessica Rusert, Sheldon Morris, Lawrence Goldstein, Hye-Jung Chun, Marco Marra, Kelly Fraser, Kim-Hien Dao, Mark Minden, Catriona Jamieson. ADAR1 promotes malignant progenitor reprogramming in chronic myeloid leukemia. abstract. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 247. doi:10.1158/1538-7445.AM2013-247
Chronic myeloid leukemia (CML) represents an important paradigm for identifying the molecular events that promote malignant reprogramming of progenitors into therapeutically recalcitrant leukemia ...stem cells (LSC) during blast crisis (BC) transformation. To elucidate mechanisms of human BC LSC generation, whole transcriptome RNA sequencing (RNA Seq), lentiviral BCR-ABL and JAK2 transduction, quantitative RT-PCR (qRT-PCR) and serial xenotransplantation studies were performed. In human BC LSC, RNA seq revealed extensive upregulation of inflammation-responsive genes in conjunction with JAK/STAT signaling pathway activation and splice isoform specific qRT-PCR uncovered a predilection for selective STAT5a isoform expression. While lentiviral BCR-ABL1 expression in cord blood progenitors enhanced JAK2 activation and expression of specific STAT5a splice isoforms, lentiviral human JAK2 overexpression globally activated inflammation-response genes and expression of adenosine deaminase RNA associated (ADAR1), a primate specific RNA editase previously shown to activate self-renewal in response to inflammation. Notably, inhibition of BC LSC self-renewal with dasatinib, a BCR-ABL inhibitor, combined with a potent JAK2 inhibitor, SAR302503, was associated with reduced STAT5a isoform expression and phospho-STAT5 activation as well as ADAR1 expression and activity. These results highlight a novel JAK/STAT pathway driven niche-responsive mechanism of human BC LSC generation that can be targeted, at least in part, with a selective JAK2 inhibitor and may be utilized as an RNA editing-based biomarker of cancer stem cell generation and therapeutic resistance.
Jamieson:Sanofi: Consultancy.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Abstract
Chronic myeloid leukemia (CML) is the first cancer that was shown to originate from a genetic abnormality - the Philadelphia chromosome translocation, and production of its constitutively ...active protein tyrosine kinase product, BCR-ABL. The disease progresses slowly from chronic phase to accelerated phase, and later transforms to blast crisis (BC) stage. Cancer stem cells (CSCs) are a subset of tumor cells that have acquired certain treatment-resistant stem cell properties. High levels of RNA editing are associated with a primitive transcriptional program typical of human embryonic stem cells, and RNA editing plays an important role in both embryonic hematopoietic cell fate determination and in maintenance of normal hematopoiesis. Human RNA editing occurs primarily in secondary structures created by Alu retroelements and is carried out by enzymes such as the adenosine deaminase acting on RNA (ADAR) family. Among these, ADAR1 was also recently shown to be required for normal hematopoiesis by suppressing interferon-induced apoptosis. Our research focuses on dissecting the role of ADAR-mediated RNA editing in normal human hematopoietic progenitor cell development compared with malignant editing programs that may be activated in leukemia stem cells (LSC) during the progression of human CML. Our data demonstrates that BC LSC harbor increased levels of the interferon-responsive ADAR1 p150 isoform compared with chronic phase (CP) progenitors and normal cord blood progenitors. Expression of this isoform also exhibits a positive correlation with BCR-ABL expression levels - an effect which is specific to BC progenitors, suggesting that ADAR1 expression correlates with disease progression from CP to BC. In vitro hematopoietic progenitor assays with normal cord blood progenitors and CP samples transduced with lentiviral vectors overexpressing human ADAR1 reveals a significant shift in cell differentiation fate towards granulocyte-macrophage progenitor (GMP) colonies, which has been shown to be the initiating LSC population in CML Correspondingly, a progression towards erythroid lineage was observed in BC CML LSC transduced with lentiviral vectors expressing shRNA targeting ADAR1. Further qRT-PCR analyses revealed that the mechanism through which ADAR1 drives LSC and HSC differentiation towards myelopoiesis involves regulation of PU.1, which in turn inhibits GATA1 expression. Moreover, in vivo studies in a robust humanized CML mouse model showed a significant decrease in LSC serial transplantation potential of lentiviral shADAR1-transduced BC progenitors transplanted into neonatal RAG2-/-γc-/- mice. Together, these data support a crucial role for ADAR1 in cell fate determination and self-renewal potential of hematopoietic stem cells in both normal human progenitors and in malignant LSC that drive disease progression and therapeutic resistance.
Citation Format: {Authors}. {Abstract title} abstract. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5217. doi:1538-7445.AM2012-5217
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