Co-culture model of B-cell acute lymphoblastic leukemia recapitulates a transcription signature of chemotherapy-refractory minimal residual disease

Abstract

B-cell acute lymphoblastic leukemia (ALL) is characterized by accumulation of immature hematopoietic cells in the bone marrow, a well-established sanctuary site for leukemic cell survival during treatment. While standard of care treatment results in remission in most patients, a small population of patients will relapse, due to the presence of minimal residual disease (MRD) consisting of dormant, chemotherapy-resistant tumor cells. To interrogate this clinically relevant population of treatment refractory cells, we developed an in vitro cell model in which human ALL cells are grown in co-culture with human derived bone marrow stromal cells or osteoblasts. Within this co-culture, tumor cells are found in suspension, lightly attached to the top of the adherent cells, or buried under the adherent cells in a population that is phase dim (PD) by light microscopy. PD cells are dormant and chemotherapy-resistant, consistent with the population of cells that underlies MRD. In the current study, we characterized the transcriptional signature of PD cells by RNA-Seq, and these data were compared to a published expression data set derived from human MRD B-cell ALL patients. Our comparative analyses revealed that the PD cell population is markedly similar to the MRD expression patterns from the primary cells isolated from patients. We further identified genes and key signaling pathways that are common between the PD tumor cells from co-culture and patient derived MRD cells as potential therapeutic targets for future studies.

Redox imbalance in COVID-19 pathophysiology

“…NextSeq2000 was used to generate the sequencing data of 36 million clusters (or 72 million F + R reads) per sample with the P3 flow cell at Marshal University Genomics Core (Huntington, WV, USA). RNA-Seq data analysis follows our previous work [ 34 , 35 ]: briefly, RNA-Seq read aligned to human genome by subread [ 36 ], read counts summarized based on RefSeq gene annotation by featurecount [ 37 ], expression level quantification by RPKM [ 38 ] with an in-house script, visualization of gene expression by MeV [ 39 ], prediction of differentially expressed (DE) genes by EdgeR (FDR = 0.05; |log2FC| > 1, and log2(Count Per million) > 0), and gene set enrichment analysis against hallmark gene sets by GSEA [ 40 , 41 ].…”

Bone Marrow Stroma-Induced Transcriptome and Regulome Signatures of Multiple Myeloma

“…Data Analysis 2.6.1. RNA-Seq Data Analysis RNA-Seq data analysis followed our previous work [18]. Briefly, alignment of pairedend short reads to the reference human genome (hg38) was performed with subread v2.0.1 [19].…”

Hypoxia regulates CD9 expression and dissemination of B lymphoblasts

“…Indeed, hypoxia promotes quiescence of hematopoietic progenitor cells and enhance B lymphoid development [25]. Furthermore, BM microenvironment favors quiescence and chemoresistance of ALL cells by changing their gene expression profile, notably with upregulation of genes involved in the hypoxia signaling pathway and cell adhesion [26,27]. Here, our results show that low O 2 levels regulate CD9 expression through HIF1α signaling and favor leukemic cell migration and engraftment in an ALL model.…”