Leukemia-initiating cells (LICs) are regarded as the origin of leukemia relapse and therapeutic resistance. Identifying direct stemness determinants that fuel LIC self-renewal is critical for ...developing targeted approaches. Here, we show that the RNA-editing enzyme ADAR1 is a crucial stemness factor that promotes LIC self-renewal by attenuating aberrant double-stranded RNA (dsRNA) sensing. Elevated adenosine-to-inosine editing is a common attribute of relapsed T cell acute lymphoblastic leukemia (T-ALL) regardless of molecular subtype. Consequently, knockdown of ADAR1 severely inhibits LIC self-renewal capacity and prolongs survival in T-ALL patient-derived xenograft models. Mechanistically, ADAR1 directs hyper-editing of immunogenic dsRNA to avoid detection by the innate immune sensor melanoma differentiation-associated protein 5 (MDA5). Moreover, we uncover that the cell-intrinsic level of MDA5 dictates the dependency on the ADAR1-MDA5 axis in T-ALL. Collectively, our results show that ADAR1 functions as a self-renewal factor that limits the sensing of endogenous dsRNA. Thus, targeting ADAR1 presents an effective therapeutic strategy for eliminating T-ALL LICs.
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•Elevated A-to-I RNA modifications are associated with increased risk of relapse•Loss of ADAR1 impairs LIC self-renewal partly via ADAR1-MDA5 axis•Cell-intrinsic level of MDA5 dictates the dependence of LICs on ADAR1-MDA5 axis•RNA-editing-independent activity suppresses ISGs
Rivera et al. showed that widespread adenosine-to-inosine RNA editing by the RNA-editing enzyme ADAR1 is associated with leukemia relapse in patients with T-ALL. ADAR1 promotes LIC stemness via regulation of stem cell gene expression and suppression of MDA5-directed dsRNA sensing by RNA hyper-editing and RNA-editing-independent mechanisms.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Bispecific anti-CD33×anti-CD64 antibody (BsAb) directly inhibited proliferation and colony formation of human acute myeloid leukemia cell lines, without affecting the function of normal monocytes. ...Addition of BsAb to normal monocytes induced tyrosine phosphorylation of Cbl and Vav, association of these molecules with CD33, and downstream signaling. In leukemia cells that were insensitive to BsAb treatment, Vav and Cbl were constitutively phosphorylated and, therefore, constitutively associated with CD33. Direct growth inhibition is an additional mechanism by which BsAb may be useful in the therapy of AML.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Post-transcriptional adenosine-to-inosine RNA editing mediated by adenosine deaminase acting on RNA1 (ADAR1) promotes cancer progression and therapeutic resistance. However, ADAR1 editase-dependent ...mechanisms governing leukemia stem cell (LSC) generation have not been elucidated. In blast crisis chronic myeloid leukemia (BC CML), we show that increased JAK2 signaling and BCR-ABL1 amplification activate ADAR1. In a humanized BC CML mouse model, combined JAK2 and BCR-ABL1 inhibition prevents LSC self-renewal commensurate with ADAR1 downregulation. Lentiviral ADAR1 wild-type, but not an editing-defective ADAR1E912A mutant, induces self-renewal gene expression and impairs biogenesis of stem cell regulatory let-7 microRNAs. Combined RNA sequencing, qRT-PCR, CLIP-ADAR1, and pri-let-7 mutagenesis data suggest that ADAR1 promotes LSC generation via let-7 pri-microRNA editing and LIN28B upregulation. A small-molecule tool compound antagonizes ADAR1’s effect on LSC self-renewal in stromal co-cultures and restores let-7 biogenesis. Thus, ADAR1 activation represents a unique therapeutic vulnerability in LSCs with active JAK2 signaling.
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•JAK2 signaling activates ADAR1-mediated A-to-I RNA editing•JAK2 and BCR-ABL1 signaling converge on ADAR1 activation through STAT5a•ADAR1-mediated microRNA editing impairs let-7 biogenesis and enhances LSC self-renewal•JAK2 and BCR-ABL1 inhibition reduces ADAR1 expression and prevents LSC self-renewal
Zipeto, Court, and colleagues show a pivotal role for let-7 microRNA editing in leukemia stem cell self-renewal. Impairment of let-7 is dependent on JAK2 and BCR-ABL-mediated activation of ADAR1 editing. This provides a novel mechanism of malignant reprogramming that can be targeted through combined JAK2 and BCR-ABL or ADAR1 inhibition.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Secondary acute myeloid leukemia (sAML) is the most therapeutically recalcitrant form of AML with a life expectancy of less than 12 months. Secondary AML evolves from relatively prevalent ...myeloproliferative neoplasms (MPNs), myelodysplastic syndrome (MDS), or after chemotherapy, radiation therapy, or hematopoietic cell transplantation (HCT) that together confer a 14% risk of sAML at 15 years. Cumulative sequencing studies show that human splicing factor mutations, epigenetic spliceosome deregulation, RNA editing-induced splicing alterations, and pro-survival splice isoform switching drive dormant leukemia stem cell (LSC) generation and sAML resistance to chemotherapy and molecularly targeted agents resulting in high rates of relapse. LSC are immunologically silent in part because they activate adenosine deaminase acting on dsRNA (ADAR1), which attenuates the innate immune response. In addition, therapeutic splicing modulation has the potential to induce neoepitope formation and augment checkpoint inhibitor therapy. Thus, there is a pressing need for clinical development of splicing modulatory agents that eradicate therapy resistant LSC and reduce sAML drug resistance and relapse. Rebecsinib (17 S-FD-895) is a pharmacologically stable, potent, and selective small molecule splicing modulator that targets the SF3B core of the spliceosome at the interface of SF3B1, SF3B3 and PHF5A. We previously showed that Rebecsinib inhibits human LSC maintenance in sAML models at doses that spare normal hematopoietic stem and progenitor cells (HSPCs). In IND-enabling studies, we now demonstrate that splicing modulation with this potent agent is a pre-clinical tox-proven strategy to eradicate LSC with the potential to overcome immune checkpoint resistance via inhibition of ADAR1 splicing and activity. We further describe targeted LSC eradication that correlates with detection of unique intron-retained and exon-skipped transcripts that can be quantified by splice isoform-specific qRT-PCR and RNA-sequencing analyses and can be used as predictive biomarkers to monitor molecular responses to Rebecsinib treatment. Mechanistically, the therapeutic effects were accompanied by on-target splicing modulatory effects, including reductions in pro-survival MCL1L transcripts and splicing factor gene products such as SF3B1 and SF3B3, which form part of the splicing modulator binding pocket as well as alterations in self-renewal promoting ADAR1 and STAT3beta transcripts. In multi-species toxicology and pharmacokinetic/pharmacodynamic studies, Rebecsinib induced splicing modulation and was well-tolerated over a broad range of doses. Because of disrupted spliceosome function, SF3B1 overexpression and increased dependence on pro-survival splice isoform expression, Rebecsinib-mediated induction of pro-survival to pro-apoptotic splice isoform switching inhibits sAML LSC survival and self-renewal at doses that spare normal HSPCs in vitro and in humanized mouse models commensurate with dose-dependent changes in splicing reporter exon skipping and SF3B1, MCL1, BCL2 and CD44 isoform levels. Together, this potent and selective agent along with biomarkers of response to splicing modulation provide a sensitive method of detecting activity and mechanism of action of Rebecsinib, and demonstrate its LSC selectivity in humanized stromal co-cultures and humanized mouse models, which will have utility in future clinical development of this novel therapeutic agent.
Crews: Ionis Pharmaceuticals: Research Funding. Burkart: Algenesis: Other: Co-founder. Jamieson: Forty Seven Inc.: Patents & Royalties.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Age-related human hematopoietic stem cell (HSC) exhaustion and myeloid-lineage skewing promote oncogenic transformation of hematopoietic progenitor cells into therapy-resistant leukemia stem cells ...(LSCs) in secondary acute myeloid leukemia (AML). While acquisition of clonal DNA mutations has been linked to increased rates of secondary AML for individuals older than 60 years, the contribution of RNA processing alterations to human hematopoietic stem and progenitor aging and LSC generation remains unclear. Comprehensive RNA sequencing and splice-isoform-specific PCR uncovered characteristic RNA splice isoform expression patterns that distinguished normal young and aged human stem and progenitor cells (HSPCs) from malignant myelodysplastic syndrome (MDS) and AML progenitors. In splicing reporter assays and pre-clinical patient-derived AML models, treatment with a pharmacologic splicing modulator, 17S-FD-895, reversed pro-survival splice isoform switching and significantly impaired LSC maintenance. Therapeutic splicing modulation, together with monitoring splice isoform biomarkers of healthy HSPC aging versus LSC generation, may be employed safely and effectively to prevent relapse, the leading cause of leukemia-related mortality.
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•Splice isoform signatures distinguish normal and malignant progenitor cell aging•Pro-survival splice isoform switching is a feature of secondary AML LSC•Splice isoform biomarkers provide diagnostic and therapeutic targets for AML•Spliceosome modulators impair AML LSC maintenance in humanized pre-clinical models
Crews et al. show that unique splice isoform signatures distinguish normal human HSC and progenitor cell aging from AML and MDS progenitors. Widespread deregulation of splicing factor gene expression typified AML progenitors and sensitized them to small-molecule splicing-targeted agents, supporting the utility of spliceosome modulation in leukemia stem cell eradication and anti-aging strategies.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Adenosine deaminase acting on RNA1 (ADAR1) preserves genomic integrity by preventing retroviral integration and retrotransposition during stress responses. However, ...inflammatory-microenvironment-induced ADAR1p110 to p150 splice isoform switching drives cancer stem cell (CSC) generation and therapeutic resistance in 20 malignancies. Previously, predicting and preventing ADAR1p150-mediated malignant RNA editing represented a significant challenge. Thus, we developed lentiviral ADAR1 and splicing reporters for non-invasive detection of splicing-mediated ADAR1 adenosine-to-inosine (A-to-I) RNA editing activation; a quantitative ADAR1p150 intracellular flow cytometric assay; a selective small-molecule inhibitor of splicing-mediated ADAR1 activation, Rebecsinib, which inhibits leukemia stem cell (LSC) self-renewal and prolongs humanized LSC mouse model survival at doses that spare normal hematopoietic stem and progenitor cells (HSPCs); and pre-IND studies showing favorable Rebecsinib toxicokinetic and pharmacodynamic (TK/PD) properties. Together, these results lay the foundation for developing Rebecsinib as a clinical ADAR1p150 antagonist aimed at obviating malignant microenvironment-driven LSC generation.
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•ADAR1p150 isoform-mediated A-to-I RNA editing fuels human LSC generation•Lentiviral ADAR1 and splicing reporters enable detection of ADAR1p150 activation•Rebecsinib inhibits ADAR1p150-driven LSC self-renewal while sparing normal HSCs•Rebecsinib pre-IND studies show scalable chemistry and favorable pharmacokinetics
Jamieson and colleagues demonstrate that splicing-mediated activation of the inflammation-responsive RNA editase ADAR1 can be inhibited by Rebecsinib, a selective splicing modulator with favorable safety, pharmacokinetic, and pharmacodynamic properties in pre-IND studies. These findings support Rebecsinib development as a potent ADAR1p150 antagonist aimed at preventing leukemia stem cell generation.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Bi-specific anti-CD33 × anti-CD64 antibodies (BsAb) mediated more potent and longer-lasting inhibition of proliferation of human leukemia cell lines and primary acute myeloid leukemia (AML) samples ...compared to mono-specific anti-CD33 mAb. There were no differences between these two antibodies in cellular internalization over time. The inhibitory effect of BsAb was mimicked by a mouse IgG2a subclass mono-specific anti-CD33 mAb. These findings indicate that enhanced inhibition of proliferation was caused by simultaneous ligation of both CD33 and CD64 molecules. We conclude that inhibition of leukemia cell growth initiated by BsAb during prolonged exposure may have therapeutic value for the treatment of AML.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Abstract
Dysregulation of inflammatory cytokine responsive APOBEC3 cytosine deaminases has been shown to be a contributing factor in cancer evolution, presenting as gene expression changes and ...inclusion of distinct C-to-T mutation patterns. However, the context specificity and mechanisms by which APOBEC3 enzymes promote cancer initiation and progression require further elucidation. Lentiviral overexpression of APOBEC3C and an editase deficient APOBEC3C mutant in healthy cord blood, bone marrow and MPN patient hematopoietic stem/progenitor cells (HSPCs) allows us to study the effects of innate immune deaminase dysregulation in the hematopoietic niche. We are focusing on the upregulation of APOBEC3C and adenosine deaminase acting on RNA1 (ADAR1), as we have previously shown them to be contemporaneously upregulated in the high-risk myelofibrosis (MF) stem cell population compared to normal aged bone marrow. We can compare these novel differential gene expression changes, RNA hyper-editing sites, and DNA mutation signatures induced by APOBEC3 mutagenesis to abnormalities seen in both hematopoietic malignancies and solid tumor cancers. Gene set enrichment analysis (GSEA) performed on this dataset has exposed numerous deregulated pathways brought on by exaggerated levels of APOBEC3, including changes in splicing pathways. To further investigate the complex relationship between splicing and deaminase deregulation, we treated myeloproliferative neoplasm patient samples and normal HPSCs with Rebecsinib (also known as 17S-FD-895), a pharmacologically stable, potent, and selective small molecule splicing modulator, which interestingly caused significant downregulation of APOBEC3C. We will continue to investigate these findings as a potential target to correct the dysregulation seen in MPN progression. Consequently, we aim to use these findings to identify predictive biomarkers and druggable targets of leukemic initiation progression.
Citation Format: Jane Marie Isquith, Jessica Pham, Thomas Whisenant, Larisa Balaian, Catriona Jamieson. Molecular mechanisms of RNA and DNA editing in leukemic transformation of hemopoietic stem and progenitor cells abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 123.
In view of the single-agent activity of azacitidine and gemtuzumab ozogamicin (GO) in patients with relapsed acute myeloid leukemia, we studied a combination strategy in a phase I/II trial to ...potentially further improve outcomes. GO/azacitidine therapy was relatively well tolerated and resulted in response rates similar to those with GO used as monotherapy at higher doses.
Treatment with hypomethylating agent therapy might enhance anti-CD33 monoclonal antibody-mediated cytotoxicity against acute myeloid leukemia (AML) blasts through epigenetic effects on Syk and SHP-1 expression.
In the present phase I/II study, we treated patients with relapsed or refractory AML with azacitidine, followed by 2 doses of gemtuzumab ozogamicin (GO) at 6 mg/m2, the Food and Drug Administration-approved dose and schedule at study initiation. We sought to determine the maximum tolerated dose and clinical activity of this combination therapy. Secondarily, we aimed to determine whether baseline Syk and SHP-1 expression can be used as predictive biomarkers of treatment response.
The established maximum tolerated dose was azacitidine 75 mg/m2 daily for 6 consecutive days, followed by GO 6 mg/m2 on days 7 and 21. Of the 50 evaluable patients, 12 (24%) obtained complete remission (CR) or CR with incomplete peripheral blood recovery (CRp). No dose-limiting toxicities were observed in phase I, and no patient developed hepatic sinusoidal obstructive syndrome. Although no significant correlation was found between Syk and SHP-1 expression and the clinical response to combination therapy, in vitro studies repeatedly demonstrated that azacitidine-treated AML cells had an increased response to GO treatment.
Our study found that the combination of GO with azacitidine is relatively well tolerated, with response rates similar to those with GO monotherapy at higher doses. Differences in the GO drug schedule, dose level, and frequency might explain the discrepant response rates between our study and others, suggesting that the optimal GO dose remains unclear, especially when combined with hypomethylating agent therapy.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Abstract
While 5 year survival rates for acute lymphoblastic leukemia (ALL) in childhood are 90% (https://www.cancer.org/cancer/leukemia-in-children/detection-diagnosis-staging/survival-rates.html), ...acute myeloid leukemia survival rates have lagged behind at 65 to 70%. Thus, AML is the leading cause of childhood leukemic mortality and is a heterogeneous disease characterized by diverse mutations many occurring at low frequencies. Whole exome sequencing analyses have not been sufficient to predict relapse in many pediatric patients at least in part because of transcriptomic and epitranscriptomic alterations that drive therapy resistant leukemia stem cell (LSC) propagation. Recent results reported by ourselves and others suggest that LSC in AML harbor unique mRNA splicing profiles characterized by intron retention and exon skipping. In adult AML, whole transcriptome RNA sequencing data revealed global spliceosome disruption that uniquely distinguished LSCs from normal age-matched hematopoietic stem and progenitor cells (Crews et al Cell Stem Cell 2016). However, the role of splicing deregulation in LSC propagation in human pediatric AML had not been clearly elucidated. Recently, we have developed 17S-FD-895, a small molecule compound targeting SF3B1, which modulates mRNA splicing. To date, we have evaluated the effects of this splicing modulator on both self-renewal as well as pro-survival splice variants in CD34+ cells derived from both peripheral blood as well as bone marrow of pediatric AML patients. Splice isoform specific qRT-PCR demonstrated a dose-dependent increase in SF3B1 intron retention following treatment. Furthermore, splicing modulation induced MCL1 exon 2 skipping, producing pro-apoptotic MCL1-S transcripts. Hematopoietic progenitor assays demonstrated a dose-dependent reduction in LSC clonogenicity and self-renewal. In these assays, LSC were found to be sensitive to nanomolar concentrations that spared normal hematopoietic stem and progenitor cells. To further dissect the role of pre-mRNA splicing in pediatric AML, we developed a lentiviral fluorescent splicing reporter that switches from GFP to RFP expression following an exon skipping or intron retention event. In addition, whole transcriptome RNA sequencing (RNA-seq) was performed on FACS purified stem cells (CD34+/CD38-/Lin-) as well as progenitor cells (CD34+/CD38+/Lin-) from both pediatric AML as well as aged-matched normal bone marrow samples and samples were transplanted into immunocompromised mice followed by 17S-FD-895 treatment to assess sensitivity to splicing modulation in vivo. As a result of these studies, we have demonstrated LSC splicing patterns in pediatric AML that may inform novel biomarker identification as well as development of 17S-FD-895 for pediatric AML.
Citation Format: Inge Van der Werf, Phoebe Mondala, Raymond Diep, Larisa Balaian, Cayla Mason, Gertjan Kaspers, Jacqueline Cloos, Jim La Clair, Peggy Wentworth, Tom Whisenant, Katie Fisch, Michael Burkart, Catriona Jamieson. Selective targeting of splicing deregulation in pediatric acute myeloid leukemia stem cells abstract. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 469.
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