Chronic Myeloid Leukemia Stem Cell Biology

Leukemia progression and relapse is fueled by leukemia stem cells (LSC) that are resistant to current treatments. In the progression of chronic myeloid leukemia (CML), blast crisis progenitors are capable of adopting more primitive but deregulated stem cell features with acquired resistance to targeted therapies. This in turn promotes LSC behavior characterized by aberrant self-renewal, differentiation, and survival capacity. Multiple reports suggest that cell cycle alterations, activation of critical signaling pathways, aberrant microenvironmental cues from the hematopoietic niche, and aberrant epigenetic events and deregulation of RNA processing may facilitate the enhanced survival and malignant transformation of CML progenitors. Here we review the molecular evolution of CML LSC that promotes CML progression and relapse. Recent advances in these areas have identified novel targets that represent important avenues for future therapeutic approaches aimed at selectively eradicating the LSC population while sparing normal hematopoietic progenitors in patients suffering from chronic myeloid malignancies

NOTCH1 Signaling Promotes Human T-Cell Acute Lymphoblastic Leukemia Initiating Cell Regeneration in Supportive Niches

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

An instructive role for Interleukin-7 receptor α in the development of human B-cell precursor leukemia

© The Author(s) 2022. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.Kinase signaling fuels growth of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Yet its role in leukemia initiation is unclear and has not been shown in primary human hematopoietic cells. We previously described activating mutations in interleukin-7 receptor alpha (IL7RA) in poor-prognosis "ph-like" BCP-ALL. Here we show that expression of activated mutant IL7RA in human CD34+ hematopoietic stem and progenitor cells induces a preleukemic state in transplanted immunodeficient NOD/LtSz-scid IL2Rγnull mice, characterized by persistence of self-renewing Pro-B cells with non-productive V(D)J gene rearrangements. Preleukemic CD34+CD10highCD19+ cells evolve into BCP-ALL with spontaneously acquired Cyclin Dependent Kinase Inhibitor 2 A (CDKN2A) deletions, as commonly observed in primary human BCP-ALL. CRISPR mediated gene silencing of CDKN2A in primary human CD34+ cells transduced with activated IL7RA results in robust development of BCP-ALLs in-vivo. Thus, we demonstrate that constitutive activation of IL7RA can initiate preleukemia in primary human hematopoietic progenitors and cooperates with CDKN2A silencing in progression into BCP-ALL.This work was supported by the Israel Science Foundation (# 1178/12 to S.I.), Children with Cancer (UK) (S.I. and T.E.), Swiss Bridge Foundation (S.I.), WLBH Foundation (S.I.), Waxman Cancer Research Foundation (S.I.), US–Israel Binational Science Foundation, Israeli health ministry ERA-NET program (#CANCER11-FP-127 to S.I.), Hans Neufeld Stiftung, the International Collaboration Grant from the Jacki and Bruce Barron Cancer Research Scholars’ Program, a partnership of the Israel Cancer Research Fund and City of Hope (S.I. grants # 00161), the Nevzlin Genomic Center for Precision Medicine in Schneider Children’s Medical Center of Israel, The European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 813091 (S.I.) and the Israel Childhood Cancer Foundation (S.I.). I.G. was partially supported by Israeli ministry of Immigrant Absorption.info:eu-repo/semantics/publishedVersio

Core Transcriptional Regulatory Circuit Controlled by the TAL1 Complex in Human T Cell Acute Lymphoblastic Leukemia

The oncogenic transcription factor TAL1/SCL is aberrantly expressed in over 40% of cases of human T cell acute lymphoblastic leukemia (T-ALL), emphasizing its importance in the molecular pathogenesis of T-ALL. Here we identify the core transcriptional regulatory circuit controlled by TAL1 and its regulatory partners HEB, E2A, LMO1/2, GATA3, and RUNX1. We show that TAL1 forms a positive interconnected autoregulatory loop with GATA3 and RUNX1 and that the TAL1 complex directly activates the MYB oncogene, forming a positive feed-forward regulatory loop that reinforces and stabilizes the TAL1-regulated oncogenic program. One of the critical downstream targets in this circuitry is the TRIB2 gene, which is oppositely regulated by TAL1 and E2A/HEB and is essential for the survival of T-ALL cells.National Cancer Institute (U.S.) (Grant 5P01CA109901)National Cancer Institute (U.S.) (Grant 5P01CA68484)National Cancer Institute (U.S.) (Grant 1K99CA157951)Center for Cancer Research (National Cancer Institute (U.S.))National Institutes of Health (U.S.). Intramural Research Progra

Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in <i>SF3B1</i>-mutated Cancers

<div><p>Mutations in the splicing factor <i>SF3B1</i> are found in several cancer types and have been associated with various splicing defects. Using transcriptome sequencing data from chronic lymphocytic leukemia, breast cancer and uveal melanoma tumor samples, we show that hundreds of cryptic 3’ splice sites (3’SSs) are used in cancers with <i>SF3B1</i> mutations. We define the necessary sequence context for the observed cryptic 3’ SSs and propose that cryptic 3’SS selection is a result of <i>SF3B1</i> mutations causing a shift in the sterically protected region downstream of the branch point. While most cryptic 3’SSs are present at low frequency (<10%) relative to nearby canonical 3’SSs, we identified ten genes that preferred out-of-frame cryptic 3’SSs. We show that cancers with mutations in the <i>SF3B1</i> HEAT 5-9 repeats use cryptic 3’SSs downstream of the branch point and provide both a mechanistic model consistent with published experimental data and affected targets that will guide further research into the oncogenic effects of <i>SF3B1</i> mutation.</p></div

Proximal cryptic 3’SSs used significantly more often in cancers with <i>SF3B1</i> hotspot mutations.

<p>log₂ distance in base pairs from associated canonical 3’SSs to (A) 1,117 significantly differentially used novel 3’SSs, (B) 16,673 novel 3’SSs with canonical intron motifs (GT/AG) used more highly in the mutants but not significant, and (C) 18,660 novel 3’SSs with canonical intron motifs (GT/AG) used more highly in the wild-types but not significant. Zero represents the position of the canonical 3’SS. Negative and positive distances indicate that the cryptic 3’SS is respectively upstream or downstream from the canonical 3’SS. Inset in (A) shows base-by-base binning from zero to 50 base pairs upstream of canonical 3’SS. Red and blue histograms represent junctions with significantly higher usage in <i>SF3B1</i> mutants or <i>SF3B1</i> wild-type samples, respectively. (D) Upper red and blue heatmap shows for each sample the log₂ library-normalized count <i>z</i>-score for 619 cryptic 3’SSs used significantly more often in the <i>SF3B1</i> mutants and located 10–30 bp upstream of canonical 3’SSs (DEXSeq, BH-adjusted <i>p</i> < 0.1). Grey bars at left indicate frequency of <i>SF3B1</i> mutant allele in RNA-seq data. Colorbars indicate <i>SF3B1</i> mutation status, cancer type, and whether the <i>SF3B1</i> mutation is located in the HEAT 5–9 repeats. Black and white colorbar indicates whether novel 3’SSs are out-of-frame (black) relative to canonical 3’SSs. Bottom green heatmap shows relative expression levels for the genes containing each cryptic 3’SS. We calculated the average expression of each gene in each cancer type and normalized by the maximum expression for each gene so that the maximum value in each column is one (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004105#sec010" target="_blank">Methods</a>). Cryptic 3’SSs not observed in all cancer types tend to have differing gene expression levels between cancers. (E) Locations and frequency of <i>SF3B1</i> mutations in HEAT repeats 5–9. Mutations observed more than once in COSMIC (upper axis) cluster in ~10 amino acid hotspots in each HEAT repeat; most frequent mutation in each hotspot is labeled. Bottom axis shows locations and frequency of mutations in our study. BRCA samples with A663V and Y765C mutations do not show evidence for cryptic 3’SS selection.</p

Location of predicted branch point relative to cryptic and canonical 3’SSs and model of cryptic 3’SS selection.

<p>(A) Distance from highest scoring BP predicted for associated canonical 3’SSs to the corresponding proximal cryptic 3’SSs. A negative distance indicates that the cryptic 3’SS is upstream of the BP predicted for the canonical 3’SS. The small spike at 2 bp indicates that in a few cases the adenine in the cryptic 3’SS is predicted to be the BP adenine for the canonical 3’SS. (B) Distance from highest scoring BP predicted for control 3’SSs to downstream intronic AG dinucleotides that are not annotated as 3’SSs. (C) Distance from either highest or second highest scoring BP predicted for canonical 3’SSs to their associated cryptic 3’SSs (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004105#sec010" target="_blank">Methods</a>). (D) Model for proximal cryptic 3’SS selection in <i>SF3B1</i> mutants. yTnAy is the human BP motif. AG dinucleotides located at the edge of the sterically protected region can be used as 3’SSs in <i>SF3B1</i> mutants (star). AG dinucleotides located in the protected or competitive regions (X’s) are respectively sterically hindered from being selected as 3’SSs or out-competed by the canonical 3’SS. Distance from predicted BP to 3’SS for (E) associated canonical 3’SSs and (F) control 3’SSs (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004105#sec010" target="_blank">Methods</a>) is significantly different (<i>p</i> < 10^-23, Mann Whitney U).</p