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Proliferative stem cell-like population of blasts in KMT2A-rearranged infant ALL [scRNA-seq]

ABSTRACT: Among pediatric acute lymphoblastic leukemias (ALL), KMT2A-rearranged infant ALL (KMT2Ar iALL) carries a uniquely poor prognosis due to high rates of treatment-refractory or relapsing disease. It is important to understand how KMT2A mutations drive such aggressive disease in order to develop more effective and less toxic therapies. The PROM1 gene, encoding the pentaspan glycoprotein prominin-1/CD133, is activated by the direct action of the most common KMT2A fusion protein; KMT2A::AFF1 (MLL-AF4). CD133 expression is essential for proliferation of KMT2A::AFF1+ cell lines but its role in primary disease remains unclear with heterogenous expression seen in iALL patient samples. To clarify the role of CD133 in KMT2Ar iALL we have used a highly physiological primary human fetal liver derived model (CRISPRKMT2A::AFF1 ALL) which recapitulates CD133 heterogeneity. We show that CD133 expression marks a highly proliferative subset of CRISPRKMT2A::AFF1 blasts with a stem-cell gene expression profile capable of causing more aggressive disease in vivo. CRISPR inactivation of PROM1 limits leukemic proliferation, suggesting a functional role in our model and providing a strong rationale for targeting therapies against CD133.

ORGANISM(S): Homo sapiens

PROVIDER: GSE296245 | GEO | 2025/06/26

REPOSITORIES: GEO

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PROLIFERATIVE STEM CELL LIKE POPULATION OF BLASTS IN KMT2A REARRANGED INFANT ALL

Project description:Among pediatric acute lymphoblastic leukemias (ALL), KMT2A-rearranged infant ALL (KMT2Ar iALL) carries a uniquely poor prognosis due to high rates of treatment-refractory or relapsing disease. It is important to understand how KMT2A mutations drive such aggressive disease in order to develop more effective and less toxic therapies. The PROM1 gene, encoding the pentaspan glycoprotein prominin-1/CD133, is activated by the direct action of the most common KMT2A fusion protein; KMT2A::AFF1 (MLL-AF4). CD133 expression is essential for proliferation of KMT2A::AFF1+ cell lines but its role in primary disease remains unclear with heterogenous expression seen in iALL patient samples. To clarify the role of CD133 in KMT2Ar iALL we have used a highly physiological primary human fetal liver derived model (CRISPRKMT2A::AFF1 ALL) which recapitulates CD133 heterogeneity. We show that CD133 expression marks a highly proliferative subset of CRISPRKMT2A::AFF1 blasts with a stem-cell gene expression profile capable of causing more aggressive disease in vivo. CRISPR inactivation of PROM1 limits leukemic proliferation, suggesting a functional role in our model and providing a strong rationale for targeting therapies against CD133.

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