Bone marrow fibrosis is associated with non‐response to CD19 CAR T‐cell therapy in B‐acute lymphoblastic leukemia

Abstract CD19 directed CAR T‐cell therapy is used to treat relapsed/refractory B‐cell acute lymphoblastic leukemia. The role of the pre‐CAR bone marrow (BM) stromal microenvironment in determining response to CAR T‐cell therapy has been understudied. We performed whole transcriptome analysis, reticulin fibrosis assessment and CD3 T‐cell infiltration on BM core biopsies from pre‐ and post‐CAR timepoints for 61 patients, as well as on a cohort of 54 primary B‐ALL samples. Pathways of fibrosis, extracellular matrix development, and associated transcription factors AP1 and TGF‐β3 , were enriched and upregulated in nonresponders (NR) even prior to CAR T cell therapy. NR showed significantly higher levels of BM fibrosis compared to complete responders by both clinical reticulin assessment and AI‐assisted digital image scoring. CD3+ T cells showed a trend toward lower infiltration in NR. NR had significantly higher levels of pre‐CAR fibrosis compared to primary B‐ALL. High levels of fibrosis were associated with lower overall survival after CAR T‐cell therapy. In conclusion, BM fibrosis is a novel mechanism mediating nonresponse to CD19‐directed CAR T‐cell therapy in B‐ALL. A widely used clinically assay for quantitating myelofibrosis can be repurposed to determine patients at high risk of non‐response. Genes and pathways associated with BM fibrosis are a potential target to improve response.