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
Diagnostic radiologists are expected to review and assimilate findings from prior studies when constructing their overall assessment of the current study. Radiology information systems facilitate ...this process by presenting the radiologist with a subset of prior studies that are more likely to be relevant to the current study, usually by comparing anatomic coverage of both the current and prior studies. It is incumbent on the radiologist to review the full text report and/or images from those prior studies, a process that is time-consuming and confers substantial risk of overlooking a relevant prior study or finding. This risk is compounded when patients have dozens or even hundreds of prior imaging studies. Our goal is to assess the feasibility of natural language processing techniques to automatically extract asserted and negated disease entities from free-text radiology reports as a step towards automated report summarization. We compared automatically extracted disease mentions to a gold-standard set of manual annotations for 50 radiology reports from CT abdomen and pelvis examinations. The automated report summarization pipeline found perfect or overlapping partial matches for 86% of the manually annotated disease mentions (sensitivity 0.86, precision 0.66, accuracy 0.59, F1 score 0.74). The performance of the automated pipeline was good, and the overall accuracy was similar to the interobserver agreement between the two manual annotators.
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NUK, OBVAL, SBMB, SBNM, UL, UM, UPUK, VSZLJ
The molecular etiology of human progenitor reprogramming into self-renewing leukemia stem cells (LSC) has remained elusive. Although DNA sequencing has uncovered spliceosome gene mutations that ...promote alternative splicing and portend leukemic transformation, isoform diversity also may 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, and serially transplantable blast crisis chronic myeloid leukemia (CML) progenitors revealed increased IFN-γ pathway gene expression in concert with BCR-ABL amplification, enhanced expression of the IFN-responsive ADAR1 p150 isoform, and a propensity for increased adenosine-to-inosine RNA editing during CML progression. Lentiviral overexpression experiments demonstrate that ADAR1 p150 promotes expression of the myeloid transcription factor PU.1 and induces malignant reprogramming of myeloid progenitors. Moreover, enforced ADAR1 p150 expression was associated with production of a misspliced 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 blast crisis CML progenitors. Together these data provide a compelling rationale for developing ADAR1-based LSC detection and eradication strategies.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
Leukemia initiating cells (LIC) contribute to therapeutic resistance through acquisition of mutations in signaling pathways, such as NOTCH1, that promote self-renewal and survival within supportive ...niches. Activating mutations in NOTCH1 occur commonly in T cell acute lymphoblastic leukemia (T-ALL) and have been implicated in therapeutic resistance. However, the cell type and context specific consequences of NOTCH1 activation, its role in human LIC regeneration, and sensitivity to NOTCH1 inhibition in hematopoietic microenvironments had not been elucidated.
We established humanized bioluminescent T-ALL LIC mouse models transplanted with pediatric T-ALL samples that were sequenced for NOTCH1 and other common T-ALL mutations. In this study, CD34(+) cells from NOTCH1(Mutated) T-ALL samples had higher leukemic engraftment and serial transplantation capacity than NOTCH1(Wild-type) CD34(+) cells in hematopoietic niches, suggesting that self-renewing LIC were enriched within the NOTCH1(Mutated) CD34(+) fraction. Humanized NOTCH1 monoclonal antibody treatment reduced LIC survival and self-renewal in NOTCH1(Mutated) T-ALL LIC-engrafted mice and resulted in depletion of CD34(+)CD2(+)CD7(+) cells that harbor serial transplantation capacity.
These results reveal a functional hierarchy within the LIC population based on NOTCH1 activation, which renders LIC susceptible to targeted NOTCH1 inhibition and highlights the utility of NOTCH1 antibody targeting as a key component of malignant stem cell eradication strategies.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The only therapeutic options that exist for squamous cell lung carcinoma (SCC) are standard radiation and cytotoxic chemotherapy. Cancer stem cells (CSCs) are hypothesized to account for therapeutic ...resistance, suggesting that CSCs must be specifically targeted. Here, we analyze the transcriptome of CSC and non-CSC subpopulations by RNA-seq to identify new potential therapeutic strategies for SCC.
We sorted a SCC into CD133- and CD133+ subpopulations and then examined both by copy number analysis (CNA) and whole genome and transcriptome sequencing. We analyzed The Cancer Genome Atlas (TCGA) transcriptome data of 221 SCCs to determine the generality of our observations.
Both subpopulations highly expressed numerous mRNA isoforms whose protein products are active drug targets for other cancers; 31 (25%) correspond to 18 genes under active investigation as mAb targets and an additional 4 (3%) are of therapeutic interest. Moreover, we found evidence that both subpopulations were proliferatively driven by very high levels of c-Myc and the TRAIL long isoform (TRAILL) and that normal apoptotic responses to high expression of these genes was prevented through high levels of Mcl-1L and Bcl-xL and c-FlipL-isoforms for which drugs are now in clinical development. SCC RNA-seq data (n = 221) from TCGA supported our findings. Our analysis is inconsistent with the CSC concept that most cells in a cancer have lost their proliferative potential. Furthermore, our study suggests how to target both the CSC and non-CSC subpopulations with one treatment strategy.
Our study is relevant to SCC in particular for it presents numerous potential options to standard therapy that target the entire tumor. In so doing, it demonstrates how transcriptome sequencing provides insights into the molecular underpinnings of cancer propagating cells that, importantly, can be leveraged to identify new potential therapeutic options for cancers beyond what is possible with DNA sequencing.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Leukemia stem cells (LSCs) play a pivotal role in the resistance of chronic myeloid leukemia (CML) to tyrosine kinase inhibitors (TKIs) and its progression to blast crisis (BC), in part, through the ...alternative splicing of self-renewal and survival genes. To elucidate splice-isoform regulators of human BC LSC maintenance, we performed whole-transcriptome RNA sequencing, splice-isoform-specific quantitative RT-PCR (qRT-PCR), nanoproteomics, stromal coculture, and BC LSC xenotransplantation analyses. Cumulatively, these studies show that the alternative splicing of multiple prosurvival BCL2 family genes promotes malignant transformation of myeloid progenitors into BC LSCS that are quiescent in the marrow niche and that contribute to therapeutic resistance. Notably, sabutoclax, a pan-BCL2 inhibitor, renders marrow-niche-resident BC LSCs sensitive to TKIs at doses that spare normal progenitors. These findings underscore the importance of alternative BCL2 family splice-isoform expression in BC LSC maintenance and suggest that the combinatorial inhibition of prosurvival BCL2 family proteins and BCR-ABL may eliminate dormant LSCs and obviate resistance.
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► Splice-isoform switching favors prosurvival BCL2 family expression in human BC ► BC LSCs are quiescent and TKI-resistant in the marrow niche ► Sabutoclax, a pan-BCL2 inhibitor, enhances TKI sensitivity of bone marrow BC LSCs
BCL2 isoform switching in human leukemia stem cells contributes to therapeutic resistance but can be overcome by combining tyrosine kinase inhibition with a pan-BCL2 inhibitor.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Dormant leukemia stem cells (LSC) promote therapeutic resistance and leukemic progression as a result of unbridled activation of stem cell gene expression programs. Thus, we hypothesized that 1) ...deregulation of the hedgehog (Hh) stem cell self-renewal and cell cycle regulatory pathway would promote dormant human LSC generation and 2) that PF-04449913, a clinical antagonist of the GLI2 transcriptional activator, smoothened (SMO), would enhance dormant human LSC eradication.
To test these postulates, whole transcriptome RNA sequencing (RNA-seq), microarray, qRT-PCR, stromal co-culture, confocal fluorescence microscopic, nanoproteomic, serial transplantation and cell cycle analyses were performed on FACS purified normal, chronic phase (CP) chronic myeloid leukemia (CML), blast crisis (BC) phase CML progenitors with or without PF-04449913 treatment.
Notably, RNA-seq analyses revealed that Hh pathway and cell cycle regulatory gene overexpression correlated with leukemic progression. While lentivirally enforced GLI2 expression enhanced leukemic progenitor dormancy in stromal co-cultures, this was not observed with a mutant GLI2 lacking a transactivation domain, suggesting that GLI2 expression prevented cell cycle transit. Selective SMO inhibition with PF-04449913 in humanized stromal co-cultures and LSC xenografts reduced downstream GLI2 protein and cell cycle regulatory gene expression. Moreover, SMO inhibition enhanced cell cycle transit and sensitized BC LSC to tyrosine kinase inhibition in vivo at doses that spare normal HSC.
In summary, while GLI2, forms part of a core HH pathway transcriptional regulatory network that promotes human myeloid leukemic progression and dormant LSC generation, selective inhibition with PF-04449913 reduces the dormant LSC burden thereby providing a strong rationale for clinical trials predicated on SMO inhibition in combination with TKIs or chemotherapeutic agents with the ultimate aim of obviating leukemic therapeutic resistance, persistence and progression.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Chronic Myeloid Leukemia (CML) is a progressive hematopoietic malignancy where expression of the oncogenic fusion protein BCR-ABL1 in leukemia stem cells (LSCs) prevents the proper differentiation of ...myeloid progenitor populations, leading to accumulation of undifferentiated blasts. Current treatments target BCR-ABL1 with tyrosine kinase inhibitors (TKIs). Though effective if administered continuously, TKIs generally fail to eradicate the bone marrow niche-residing LSCs responsible for patient relapse or progression of CML to its terminal stage, Blast Crisis (BC), as evidenced by the high molecular relapse rate following TKI discontinuation. Previous studies performed by ourselves and others show that BC progenitors (CD34+CD38+Lin-) exhibit stem-like behaviors, such as quiescence, self-renewal, and induction of pro-survival gene expression through alternative splicing of BCL2 family members, and thus behave like LSCs. Notably, BC CML LSCs co-cultured on LSC (SL/M2) supportive stroma are resistant to TKIs compared to culturing the cells alone, indicating a role of the extracellular matrix (ECM) in promoting LSC survival. We performed RNA-seq and qRT-PCR of CD34+CD38+Lin- progenitor cells in CML patient samples and found a significant increase in CTGF (Connective Tissue Growth Factor) expression in BC CML versus chronic phase (CP). Interestingly, CTGF is an ECM protein that enhances cell adhesion and has been shown to predict therapeutic resistance in cancers, such as acute lymphoblastic leukemia (ALL). Lentiviral overexpression of CTGF in a CML cell line K562 and CD34+ CP CML patient samples caused proliferation and a decrease in apoptosis markers (cleaved caspase-3), as measured by FACS analysis. Moreover, qRT-PCR analysis of mRNA indicated an increase in pro-survival BCL2 family gene expression. These changes were not observed in normal CD34+ cord blood cells. Currently, lentiviral CTGF transduction of CP CML followed by transplantation into RAG2-/-gc-/- and NSG-S mice will be used to determine the effects of CTGF on LSC maintenance in vivo. In conclusion, CTGF promotes CML LSC survival in vitro and thus could be a key factor in BC transformation and TKI resistance.
Jamieson:J&J, 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
Abstract 910
In blast crisis transformation of CML (BC CML), the leukemia stem cells (LSC), via the acquisition of both enhanced survival and self-renewal capacity, become increasingly resistant to ...BCR-ABL targeted tyrosine kinase inhibition and thus often contribute to relapse after treatment, pointing to the need for alternative therapeutic strategies and a better understanding of the molecular mechanisms underlying disease progression.
Janus kinase 2 (JAK2) plays an important role in BCR–ABL + cell survival and has profound effects on self-renewal and lineage commitment of normal and leukemic hematopoietic stem cells, through the activation of the transcription factor signal transducer and activator of transcription 5 (STAT5).
To determine if JAK/STAT signaling pathway activation is related to CML progression, LSC from human Chronic Phase (CP CML) and BC CML samples were sorted using FACS Aria (Lin-CD34+CD38+) and analyzed using splice-isoform specific q-RT-PCR. Our results showed that, compared to CP CML, BC LSC harbor enhanced mRNA expression of BCR-ABL, JAK2 and STAT5A isoforms, confirming that progression of CP to BC, in CML LSC, is marked by activation of JAK/STAT pathway.
Therefore, we investigated the response of BC CML LSC to a clinical grade JAK2 inhibitor, SAR302503 (Sanofi, Cambridge, MA) alone or in combination with a potent BCR-ABL inhibitor, dasatinib, in vivo. After two weeks of treatment, RAG2−/−gc−/− mice intrahepatic transplanted with BC LSC, showed a significant (p<0.05) reduction of engraftment levels, after combination therapy with SAR302503 and dasatinib, compared to vehicle treated mice, in four different patient samples. In all the hematopoietic tissues analyzed, SAR302503 alone (60 mg/kg/b.i.d.) did not have an effect reducing the leukemic burden. Dasatinib alone (50mg/kg/day) reduced the LSC population in the liver, spleen, and peripheral blood, but the bone marrow retained a significant percentage of BC LSC. However, combination treatment was able to reduce the LSC in the BM significantly (p=0.0006) compared to dasatinib alone.
To test whether the combination therapy can impair self-renewal capacity of the BC CML LSC in vivo, we immunomagnetic bead selected CD34+ cells from BM and spleens of treated mice, and serially transplanted an equal number into secondary recipients. We observed a significant (p<0.0001) reduction of engraftment of LSC on the mice transplanted with combination treated cells compared with vehicle treated cells. Interestingly, secondary mice transplanted with cells treated with dasatinib showed 37.5% engraftment in the spleen and 46.4% in BM, while the level of engraftment for mice transplanted with combination treatment was only 1% and 3% for spleen and BM, respectively. Moreover, mice serially transplanted with combination treated cells, had a significant (p=0.0002) increased survival time. BC CML LSC are enriched for the granulocyte macrophage progenitor (GMP) population, which has been shown to harbor LSC serial transplantation potential. Our results showed that secondary recipient transplanted with combination treated cells, presented a significantly lower proportion of the GMP population, compared with vehicle (p<0.0001) and dasatinib (p=0.02) treated cells. Together, these results suggest that the combination therapy, using a Jak2 inhibitor with a BCR-ABL inhibitor, can abolish LSC self-renewal capacity and thereby potentially prevent relapse.
Validation studies, using nanoproteomic analysis, confirmed that LSC sorted cells from mice treated with SAR302503 had lower expression levels of p-JAK2 (Tyr 1007-08) and p-STAT5A (Tyr 694) compared with vehicle treated mice (51% and 64% of reduction, respectively), while no changes are observed for total JAK2 protein or B2M between both conditions.
Full transcriptome sequencing and q-RT-PCR analysis, on sorted CML LSC from mice treated with SAR302503 in combination with dasatinib, confirmed that STAT5A specific isoforms decresed after treatment, suggesting JAK/STAT pathway could be used as biomarker of response and could explain the impairment of self-renewal in the combination therapy.
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
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
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