The Role of Mitochondrial RNA from B-Precursor Acute Lymphoblastic Leukaemia Cells in Generating a Chemoprotective Bone Marrow Niche

Treatment resistant cells in precursor B-cell Acute Lymphoblastic Leukaemia (B-ALL) likely reside in a protective bone marrow niche with nestin-expressing mesenchymal stromal cells (MSC) (Duan et al Cancer Cell 2014). Previous work from our laboratory demonstrated that an 'activated MSC' niche, in which MSC have acquired features of cancer associated fibroblasts (CAF), develops in response to reactive oxygen species (ROS)-inducing chemotherapy. Mitochondria are actively transferred along tunneling nanotubes from activated MSC to B-ALL cells and can 'rescue' the cells from chemotherapy (Burt, et al Blood 2019). However, work from other groups suggests that chemoresistant ALL sub-clones exist prior to chemotherapy exposure, carrying a gene expression signature enriched for stemness, mitochondrial metabolism, stress responses and chromatin remodelling (Dobson et al Cancer Discovery 2020). We hypothesised that B-ALL cells may themselves directly activate bone marrow stromal cells and induce niche-formation prior to treatment, leading to ab-inito chemoresistance.

To test this hypothesis, we first used our previously-described, in vitro niche model wherein either the HS27a MSC cell line or healthy donor MSCs were co-cultured with either B-ALL cell lines or primary patient B-ALL cells. Three of the five B-ALL cell lines and three of the four primary B-ALL samples that were tested induced activation of the MSCs, as characterised by cytomorphological changes identified by confocal microscopy, up-regulation of CAF-relevant gene expression and increased IL6, IL8 and CCL2 protein secretion. The ability of the B-ALL cell lines to activate MSC correlated directly with the intrinsic ROS level of the cell as determined by CellROX assay. Mitochondrial transfer from the cell-activated MSC to B-ALL cells, as measured by mitotracker dye transfer, occurred exactly as we had seen when we had used chemotherapy to activate the stroma. In vivo, the MSC-activating ALL cell lines also activated murine MSCs when established as xenografts in NOD-SCID gamma (NSG) mice. Immunohistochemistry of NSG murine femora revealed a very significant expansion in nestin+ cells after exposure to niche-induing ALL cells compared to non-niche-inducing controls.

We aimed to determine the mechanism behind the B-ALL induced MSC activation. We determined that it was contact-independent, arising from exposure of MSC to ALL cells in transwell but also from exposure to B-ALL cell conditioned media alone. RNA sequencing of MSC after treatment with conditioned medium from activating B-ALL cells compared with non-activating controls unexpectedly showed that most highly upregulated pathways in the MSC-activating scenario were those involved in RNA sensing. Thus, we sought evidence for the role of mitochondrial dsRNA, as it had been recently shown to activate the anti-viral signalling pathway (Dhir et al, Nature 2018).

Using the J2 anti-double stranded (ds) RNA monoclonal antibody in both confocal and flow cytometric assays, we observed very significantly higher levels of dsRNA in MSC which had been exposed to stromal-activating B-ALL cell conditioned medium than in non-activating B-ALL or MSC alone controls (see panel for image). We used the small molecule VBIT4, a voltage-dependent anion channel oligomerization inhibitor that decreases mitochondrial nucleic acid release to block this phenomenon in B-ALL cells. We quantified expression of a selection of stromal cell activation marker genes as well as genes in the RNA sensing pathway after treatment with VBIT4-exposed B-ALL cell CM or non-treated control. We observed a 2 to 4-fold reduction in expression of IL6 and CCL2 after VBIT4 exposure, compared to control. In the stromal cell RNA sensing pathway, there was a 15-fold reduction in expression of RIG-I and a 2 to 4-fold reduction in the interferon pathway genes MX2, IFIH1, MAVS and OAS1. Experiments to determine whether knock down of components of the antiviral sensing pathway also abrogates stromal activation and further murine experiments are ongoing.

We propose a model in which ROS-induced mitochondrial dysfunction leads to release of dsRNA which in turn activates bone marrow stromal cells leading to protective niche formation and chemoprotection of acute lymphoblastic leukaemia cells despite lack of prior exposure to cytotoxic agents.

Fielding:Amgen: Consultancy; Pfizer: Consultancy; Novartis: Consultancy.