Time-Resolved scRNA-Seq Tracks the Adaptation of a Sensitive MCL Cell Line to Ibrutinib Treatment

Abstract

Since the approval of ibrutinib for relapsed/refractory mantle cell lymphoma (MCL), the treatment of this rare mature B-cell neoplasm has taken a great leap forward. Despite promising efficacy of the Bruton tyrosine kinase inhibitor, resistance arises inevitably and the underlying mechanisms remain to be elucidated. Here, we aimed to decipher the response of a sensitive MCL cell line treated with ibrutinib using time-resolved single-cell RNA sequencing. The analysis uncovered five subpopulations and their individual responses to the treatment. The effects on the B cell receptor pathway, cell cycle, surface antigen expression, and metabolism were revealed by the computational analysis and were validated by molecular biological methods. The observed upregulation of B cell receptor signaling, crosstalk with the microenvironment, upregulation of CD52, and metabolic reprogramming towards dependence on oxidative phosphorylation favor resistance to ibrutinib treatment. Targeting these cellular responses provide new therapy options in MCL.

The Transcriptome of SH-SY5Y at Single-Cell Resolution: A CITE-Seq Data Analysis Workflow

“…We also believe that a deep characterization at single-cell resolution of human cell lines will allow for a better usage of these omnipresent models in molecular/cell biology and pharmacology. Many single-cell datasets measured on cell lines exist beyond the one described here (SY5Y cells) on other cell lines from neuroblastoma [14], breast cancer [48], and lymphoblasts [49,50]. Fueled by current technological advances provided by, e.g., CITE-seq, cell line single-cell datasets can be produced in even higher numbers and for more experimental contexts, towards the generation of an integrated and comprehensive Human Cell Line Atlas.…”

CD52 and OXPHOS—potential targets in ibrutinib-treated mantle cell lymphoma

“…In a prior scRNA-seq analysis, we tracked an ibrutinib-sensitive MCL cell line across 2 d treatment with ibrutinib, as adaptations in gene expression could be associated with higher resistance to the BTK inhibitor [ 7 ]. Although the four surviving subpopulations showed a common response, the existence of two metabolic distinct subgroups indicated that we had not caught the finally resistant cells.…”

“…Here, we performed a bulk RNA-seq analysis to decipher the features of MCL cells that were finally adapted to ibrutinib by prolonging the treatment of REC-1 cells up to 4 days (d). As RNA-seq data corroborated increased activity of oxidative phosphorylation in resisting cells, we focused on OXPHOS and the previously postulated CD52 as potential targets [ 7 ].…”

“…Previously, we elucidated early transcriptomic alterations in cells persisting on 48 h (h) ibrutinib treatment by scRNA-seq using REC-1, an ibrutinib-sensitive mantle cell lymphoma cell line [ 7 ]. Surviving cells upregulated CD52 and separated into two distinct metabolic subgroups.…”

Restoration of the immune function as a complementary strategy to treat Chronic Lymphocytic Leukemia effectively

“…Targeted therapies are especially prone to resistance with relatively simple mutations in the target protein or pathway, but thanks to methodological advances, we are starting to understand much more complex signaling networks that can create forms of resistance beyond classic genetics. Single-cell technologies, immune-phenotyping, single-cell transcriptome profiling, functional studies, and chromatin mapping, all integrated with bioinformatic analytic tools, may help understand the supportive role of the immune microenvironment in CLL progression and the co-evolution of cells involved in the disease, directly or indirectly [5,41,52,[82][83][84].…”