Page 61 - Haematologica Vol. 109 - July 2024

ARTICLE - Leukemia-induced interferon signature in stroma M.W.E. Smeets et al.
after exposure to primary BCP-ALL patients’ samples (n=15; Figure 1A) for 40 hours, a co-culture condition for which we previously established that a leukemic niche is created by the interaction of BCP-ALL cells with MSC.14 Pathway analysis of RNA-sequencing data revealed enrichment for IFN-pathway-activated genes in the MSC after co-culture with BCP-ALL cells (Online Supplementary Figure S3). The
A
induction of IFN-related genes could not be attributed to other cell types, e.g., T-lymphocytes, present in the samples (Online Supplementary Table S2). All three tested origins of bone marrow-derived MSC (MSC#1-3) had similar levels of increased IFN-related gene expression in co-culture with BCP-ALL cells, suggesting that the leukemia-induced change in expression is independent from the origin of
B
Figure 1. B-cell precursor acute lymphoblastic leukemia cells induce an interferon-related gene signature in mesenchymal stro- mal cells. (A) Diagram of the experimental setup. RNA sequencing was performed on sorted viable mesenchymal stromal cells (MSC) and acute lymphoblastic leukemia (ALL) fractions after mono-culture and after MSC/ALL co-culture; for the gating strat- egy see Online Supplementary Figure S1. Secreted interferon levels were measured in equal volumes of supernatant of mono-cul- tures and MSC/ALL co-cultures (Figure 6A). (B) IFI6 mRNA levels expressed in paired samples of MSC sorted after mono-culture (squares; MSC#1-3 indicated in red, blue, and green, respectively.) and MSC sorted after co-culture with BCP-ALL cells from 15 individual patients (#1, ETV6-RUNX1-like; #2-6, B-other; #7, high hyperdiploid; #8-15, ETV6-RUNX1; circles). Boxplots represent the interquartile range, the median is depicted by a line. IFN: interferon; FDR: P value for the false discovery rate; FPKM: fragments per kilobase million; HD: high hyperdiploid.
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