High ORM1 Expression Marks a Subset of Genetically Adverse-Risk B-ALL Characterized By MDSC Enrichment, T-Cell Dysfunction, and Inferior Overall Survival

Alterations in the transcriptional activity of certain bone marrow microenvironment populations have been shown to contribute to the pathogenesis of B-lymphoblastic leukemia (B-ALL); however, the precise mechanisms by which neoplastic lymphoblasts shape the gene expression programs of reactive immune and stromal cell populations to support a leukemogenic niche remain incompletely characterized. ORM1 is an acute phase protein with immunomodulatory properties that is overexpressed in a subset of high-risk B-ALL. In an initial exploratory analysis of 1,104 adult and pediatric B-ALL RNA-seq transcriptomes annotated with mature survival outcomes (PMID 30643249), high ORM1 expression was significantly associated with inferior event-free and overall survival and predominantly associated with Ph+, Ph-like, and KMT2A-r B-ALL subtypes. We hypothesized that B-ALL with high ORM1 expression is associated with transcriptionally distinct bone marrow microenvironment immune cell subsets that contribute to its aggressive clinical behavior and sought to delineate these alterations through digital cytometry and analysis of single cell proteogenomic sequencing (CITE-seq) data.

To delineate the tumor microenvironment (TME) features of ORM1 high B-ALL through digital cytometry, we constructed a novel bone marrow signature matrix that recapitulates the native BM cellular landscape, including hematopoietic progenitors and mesenchymal stem cells, and performed de novo transcriptional subtype discovery agnostic to clinical outcomes using the Ecotyper platform on a cohort of 577 B-ALL microarray transcriptomes from the MILE study (GSE13159). Discovery analysis identified 51 transcriptionally defined TME cell states across 17 cell types. ORM1 overexpression significantly correlated with transcriptionally-distinct neutrophil, promyelocyte, monocyte, and macrophage subsets enriched for immunosuppressive gene expression programs as well as CD8+ and γδ T-cell subsets with hallmark transcriptional features of effector dysfunction and exhaustion. To validate the imputed cell states at single-cell resolution and define their immunophenotypic features, we drew upon several B-ALL CITE-seq datasets. Recovery and assignment of discovery cohort transcriptional states to single-cell transcriptomes in KMT2A-r and Ph+ cases confirmed enrichment for multiple myeloid-derived suppressor cell (MDSC) and dysfunctional T-cell transcriptional subsets. MDSCs were predominantly monocytic but also included neutrophilic promyelocytes with surface expression of CD123 and CD155/PVR, which interacts with TIGIT to suppress immune cell activation. Indeed, enrichment for CD8+ cytotoxic lymphocytes with surface expression of PD-1 and TIGIT was also present. Neutrophilic MDSCs were present at diagnosis, in pre-relapse remission samples and at the time of relapse, suggesting that their persistence following frontline therapy may facilitate the immune evasion and expansion of treatment-resistance leukemic clones that drive eventual relapse.

Taken together, high ORM1 expression marks a subset of high-risk B-ALL characterized by enrichment for transcriptionally-distinct immunosuppressive TME cell states which may be targetable with emerging therapeutic strategies aimed at restoring host anti-tumor immunity.