ADAR1 promotes malignant progenitor reprogramming in chronic myeloid leukemia

Jiang, Qingfei; Crews, Leslie; Barrett, Christian; Chun, Hye Jung; Court, Angela C.; Isquith, Jane; Zipeto, M; Goff, Daniel; Minden, Mark D.; Sadarangani, Anil; Rusert, Jessica M.; Dao, Kim; Morris, Sheldon R.; Goldstein, Lawrence S.B.; Marra, Marco A.; Frazer, Kelly A.; Jamieson, Catriona

doi:10.1073/pnas.1213021110

Cited by 157 publications

(207 citation statements)

References 49 publications

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“…Like AS, mRNA editing is known to contribute to a variety of mammalian phenotypes (Jiang et al 2013). However, to the best of our knowledge, the genetic basis and variability of mRNA editing in genetically diverse individuals is currently unknown.…”

Section: Discussionmentioning

confidence: 99%

The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages

2013

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Alternative splicing and mRNA editing are known to contribute to transcriptome diversity. Although alternative splicing is pervasive and contributes to a variety of pathologies, including cancer, the genetic context for individual differences in isoform usage is still evolving. Similarly, although mRNA editing is ubiquitous and associated with important biological processes such as intracellular viral replication and cancer development, individual variations in mRNA editing and the genetic transmissibility of mRNA editing are equivocal. Here, we have used linkage analysis to show that both mRNA editing and alternative splicing are regulated by the macrophage genetic background and environmental cues. We show that distinct loci, potentially harboring variable splice factors, regulate the splicing of multiple transcripts. Additionally, we show that individual genetic variability at the Apobec1 locus results in differential rates of C-to-U(T) editing in murine macrophages; with mouse strains expressing mostly a truncated alternative transcript isoform of Apobec1 exhibiting lower rates of editing. As a proof of concept, we have used linkage analysis to identify 36 high-confidence novel edited sites. These results provide a novel and complementary method that can be used to identify C-to-U editing sites in individuals segregating at specific loci and show that, beyond DNA sequence and structural changes, differential isoform usage and mRNA editing can contribute to intra-species genomic and phenotypic diversity. [Supplemental material is available for this article.]Splicing is an obligatory step in the processing of both coding and noncoding RNA precursors (pre-RNA) to mature RNA, and is executed by a ribonucleoprotein megaparticle known as the spliceosome. Even though the sequential assembly of the spliceosome (Kornblihtt et al. 2013) can occur around any splice site that consists of consensus sequences recognized by the spliceosomal components, splice sites that conform better to a consensus sequence are strongly recognized and favored by the spliceosome complex. Besides the consensus sequences, the selection of optimal splice sites is regulated, in part, by a minimal set of conserved cis-acting GU and AG sequences at the 59 and 39 splice sites, respectively , and sequence elements known as intronic/exonic splicing enhancers and silencers

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Section: Discussionmentioning

confidence: 99%

The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages

2013

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“…Recent studies have shown that ADAR plays a major role in chronic myeloid leukemia (CML) tumor progression. In these studies, most cells underwent apoptosis following ADAR reduction (Steinman et al 2012;Jiang et al 2013). We used RT-PCR in order to verify AS of HNRNPR in HepG2 ADAR KD cells (Supplement 1, Supplemental Fig.…”

Section: Cells and Transfectionsmentioning

confidence: 99%

Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR)

Solomon

Oren

Safran

et al. 2013

RNA

111

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Alternative mRNA splicing is a major mechanism for gene regulation and transcriptome diversity. Despite the extent of the phenomenon, the regulation and specificity of the splicing machinery are only partially understood. Adenosine-to-inosine (A-to-I) RNA editing of pre-mRNA by ADAR enzymes has been linked to splicing regulation in several cases. Here we used bioinformatics approaches, RNA-seq and exon-specific microarray of ADAR knockdown cells to globally examine how ADAR and its A-to-I RNA editing activity influence alternative mRNA splicing. Although A-to-I RNA editing only rarely targets canonical splicing acceptor, donor, and branch sites, it was found to affect splicing regulatory elements (SREs) within exons. Cassette exons were found to be significantly enriched with A-to-I RNA editing sites compared with constitutive exons. RNAseq and exon-specific microarray revealed that ADAR knockdown in hepatocarcinoma and myelogenous leukemia cell lines leads to global changes in gene expression, with hundreds of genes changing their splicing patterns in both cell lines. This global change in splicing pattern cannot be explained by putative editing sites alone. Genes showing significant changes in their splicing pattern are frequently involved in RNA processing and splicing activity. Analysis of recently published RNA-seq data from glioblastoma cell lines showed similar results. Our global analysis reveals that ADAR plays a major role in splicing regulation. Although direct editing of the splicing motifs does occur, we suggest it is not likely to be the primary mechanism for ADAR-mediated regulation of alternative splicing. Rather, this regulation is achieved by modulating trans-acting factors involved in the splicing machinery.

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“…Sequencing analysis of BC LSCs revealed GSK3β missplicing (16), ADAR1 RNA editase activation (17), and BCL2 splice isoform switching (18). Although similarities between hESC and LSC transcriptional programs had previously been reported in a mouse model of AML, embryonic splice isoform patterns were not examined (19,20).…”

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confidence: 99%

Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal

Holm

Hellqvist

Mason

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Formative research suggests that a human embryonic stem cellspecific alternative splicing gene regulatory network, which is repressed by Muscleblind-like (MBNL) RNA binding proteins, is involved in cell reprogramming. In this study, RNA sequencing, splice isoform-specific quantitative RT-PCR, lentiviral transduction, and in vivo humanized mouse model studies demonstrated that malignant reprogramming of progenitors into self-renewing blast crisis chronic myeloid leukemia stem cells (BC LSCs) was partially driven by decreased MBNL3. Lentiviral knockdown of MBNL3 resulted in reversion to an embryonic alternative splice isoform program typified by overexpression of CD44 transcript variant 3, containing variant exons 8-10, and BC LSC proliferation. Although isoform-specific lentiviral CD44v3 overexpression enhanced chronic phase chronic myeloid leukemia (CML) progenitor replating capacity, lentiviral shRNA knockdown abrogated these effects. Combined treatment with a humanized pan-CD44 monoclonal antibody and a breakpoint cluster region -ABL proto-oncogene 1, nonreceptor tyrosine kinase (BCR-ABL1) antagonist inhibited LSC maintenance in a niche-dependent manner. In summary, MBNL3 down-regulationrelated reversion to an embryonic alternative splicing program, typified by CD44v3 overexpression, represents a previously unidentified mechanism governing malignant progenitor reprogramming in malignant microenvironments and provides a pivotal opportunity for selective BC LSC detection and therapeutic elimination.S ince the discovery of induction of stem cell characteristics in somatic cells by enforced expression of four transcription factors (1, 2), human pluripotent stem cell research has provided key insights into human development. Comparative DNA and RNA sequencing (RNAseq) studies have revealed that humanspecific distal regulatory elements, RNA editing, and alternative splicing play key roles in human embryonic stem cell (hESC) self-renewal and cell fate determination (3-6). Several of the phosphoproteins regulated during differentiation are components of the posttranscriptional RNA modification machinery, including double-stranded RNA-specific adenosine deaminase (ADAR) and serine/arginine-rich splicing factor 7 (SFRS7), thereby highlighting the importance of RNA processing alterations in hESC cell fate determination (5). Another key stem cell regulatory protein, β-catenin, is involved in hESC pluripotency and in the transcriptional regulation of adhesion molecules such as CD44 (5).Increased CD44 expression and splice isoform switching have been linked to enhanced metastatic potential and a poor prognosis in several types of cancer (7,8). Alternative splicing of 9 out of 19 exons in human CD44 pre-mRNA results in expression of different transcript variants, leading to variation in the length and function of the extracellular domain [for National Center for Biotechnology Information (NCBI)-designated CD44 nomenclature, see SI Materials and Methods and Fig. 1E]. Binding of CD44 to stem cell niche-related extracellular ma...

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ADAR1 promotes malignant progenitor reprogramming in chronic myeloid leukemia

Cited by 157 publications

References 49 publications

The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages

The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages

Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR)

Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal

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