A novel human fetal liver-derived model reveals that MLL-AF4 drives a distinct fetal gene expression program in infant ALL

Abstract

Although 90% of children with acute lymphoblastic leukemia (ALL) are now cured1, the prognosis of infant-ALL (diagnosis within the first year of life) remains dismal2. Infant-ALL is usually caused by a single genetic hit that arises in utero: rearrangement of the MLL/KMT2A gene (MLL-r). This is sufficient to give rise to a uniquely aggressive and treatment-refractory leukemia compared to older children with the same MLL-r3–5. The reasons for disparate outcomes in patients of different ages with identical driver mutations are unknown. This paper addresses the hypothesis that fetal-specific gene expression programs co-operate with MLL-AF4 to initiate and maintain infant-ALL. Using direct comparison of fetal and adult HSC and progenitor transcriptomes we identify fetal-specific gene expression programs in primary human cells. We show that MLL-AF4-driven infant-ALL, but not MLL-AF4 childhood-ALL, displays expression of fetal-specific genes. In a direct test of this observation, we find that CRISPR-Cas9 gene editing of primary human fetal liver cells to produce a t(4;11)/MLL-AF4 translocation replicates the clinical features of infant-ALL and drives infant-ALL-specific and fetal-specific gene expression programs. These data strongly support the hypothesis that fetal-specific gene expression programs co-operate with MLL-AF4 to initiate and maintain the distinct biology of infant-ALL.

The Origin of B-cells: Human Fetal B Cell Development and Implications for the Pathogenesis of Childhood Acute Lymphoblastic Leukemia

“…These mechanisms of KMT2A-r mediated transformation are difficult to validate without a bona fide model of iALL, which has been very difficult to generate. However, we have recently developed a novel iALL model derived by CRISPR-Cas9 mediated KMT2A-r in primary human FL HSPC ( 136 ). This demonstrates that a human fetal cell context is permissive, and indeed probably required; to give rise to an ALL that recapitulates key features of iALL.…”

“…This demonstrates that a human fetal cell context is permissive, and indeed probably required; to give rise to an ALL that recapitulates key features of iALL. In this model, recruitment of fetal-specific genes by KMT2A-AF4 is demonstrated by KMT2A-N and AF4-C binding and H3K79me2 at these genes by ChIP-seq ( 136 ). Furthermore, maintenance of fetal-specific gene expression programs accounts for the unique molecular profile of iALL, suggesting that it is the specific fetal target cell(s) in which it arises that provide the permissive cellular context ( 136 ).…”

Does lineage plasticity enable escape from CAR-T cell therapy? Lessons from MLL-r leukemia

“…In contrast to these murine systems, both viral transduction of human umbilical cord blood progenitors [ 51 , 52 , 70 , 71 ] and CRISPR/Cas9 editing of human fetal cells [ 72 ] easily produce a B-ALL depending on the cytokines supplied during in vitro culture and on ontogeny [ 71 ] These observations collectively argue that the combination of fusion oncoprotein and the murine micro-environment produce a myeloid bias that does not accurately reflect the conditions found during early human development ( Figure 2 ). Altering the collective conditions such that pediatric-relevant B-ALLs can be reliably and reproducibly generated in a mouse model would contribute significantly to discovering better cellular or immunotherapeutics for the most common MLL -r pediatric leukemia and, importantly, enable discovery of more effective methods for inducing long-term remission following targeted immunotherapy.…”