Blast cells surviving acute myeloid leukemia induction therapy are in cycle with a signature of FOXM1 activity

• Published in: BMC cancer 2021-10, Vol.21 (1), p.1153-15, Article 1153
• Main Authors: Williams, Mark S, Basma, Naseer J, Amaral, Fabio M R, Wiseman, Daniel H, Somervaille, Tim C P
• Format: Article
• Language: English
• Subjects: Acute myeloid leukemia; Adolescent; Adult; Aged; Apoptosis; Apoptosis - genetics; Biobanks; Blast cells; Blast Crisis - drug therapy; Blast Crisis - genetics; Blast Crisis - metabolism; Blast Crisis - pathology; Cancer; CD34 antigen; Cell cycle; Cell Differentiation; Cell Proliferation - genetics; Cell surface; Cell Survival; Cells; Chemoresistance; Chemotherapy; Clonal selection; Data analysis; Drug resistance; Drug Resistance, Neoplasm - genetics; Female; Flow Cytometry; Fluorescence in situ hybridization; Forkhead Box Protein M1 - genetics; Forkhead Box Protein M1 - metabolism; FOXM1; Gene expression; Gene Silencing; Genes; Genetic analysis; Genetic aspects; Genomes; Genomics; Health aspects; Humans; Immunophenotyping; In Situ Hybridization, Fluorescence; Induction Chemotherapy; Induction therapy; Leukemia; Leukemia stem cell; Leukemia, Myeloid, Acute - drug therapy; Leukemia, Myeloid, Acute - genetics; Leukemia, Myeloid, Acute - metabolism; Leukemia, Myeloid, Acute - pathology; Male; Medical research; Middle Aged; Myeloid leukemia; Neoplastic Stem Cells - pathology; Patient outcomes; Patients; Quiescence; Recurrence; RNA, Small Interfering - metabolism; Stem cells; Transcriptome; Tumor Stem Cell Assay; Young Adult
• ISSN: 1471-2407; 1471-2407
• DOI: 10.1186/s12885-021-08839-9

Disease relapse remains common following treatment of acute myeloid leukemia (AML) and is due to chemoresistance of leukemia cells with disease repopulating potential. To date, attempts to define the characteristics of in vivo resistant blasts have focused on comparisons between leukemic cells at presentation and relapse. However, further treatment responses are often seen following relapse, suggesting that most blasts remain chemosensitive. We sought to characterise in vivo chemoresistant blasts by studying the transcriptional and genetic features of blasts from before and shortly after induction chemotherapy using paired samples from six patients with primary refractory AML. Leukemic blasts were isolated by fluorescence-activated cell sorting. Fluorescence in situ hybridization (FISH), targeted genetic sequencing and detailed immunophenotypic analysis were used to confirm that sorted cells were leukemic. Sorted blasts were subjected to RNA sequencing. Lentiviral vectors expressing short hairpin RNAs were used to assess the effect of FOXM1 knockdown on colony forming capacity, proliferative capacity and apoptosis in cell lines, primary AML cells and CD34+ cells from healthy donors. Molecular genetic analysis revealed early clonal selection occurring after induction chemotherapy. Immunophenotypic characterisation found leukemia-associated immunophenotypes in all cases that persisted following treatment. Despite the genetic heterogeneity of the leukemias studied, transcriptional analysis found concerted changes in gene expression in resistant blasts. Remarkably, the gene expression signature suggested that post-chemotherapy blasts were more proliferative than those at presentation. Resistant blasts also appeared less differentiated and expressed leukemia stem cell (LSC) maintenance genes. However, the proportion of immunophenotypically defined LSCs appeared to decrease following treatment, with implications for the targeting of these cells on the basis of cell surface antigen expression. The refractory gene signature was highly enriched with targets of the transcription factor FOXM1. shRNA knockdown experiments demonstrated that the viability of primary AML cells, but not normal CD34+ cells, depended on FOXM1 expression. We found that chemorefractory blasts from leukemias with varied genetic backgrounds expressed a common transcriptional program. In contrast to the notion that LSC quiescence confers resistance to chemotherapy we find that refractory blasts