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...