title: RNA-seq analysis of 2 closely related leukemia clones that differ in their self-renewal capacity.
abstract: The molecular mechanisms regulating self-renewal of leukemia stem cells remain poorly understood. Here we report the generation of 2 closely related leukemias created through the retroviral overexpression of Meis1 and Hoxa9. Despite their apparent common origin, these clonal leukemias exhibit enormous differences in stem cell frequency (from 1 in 1.4, FLA2; to 1 in 347, FLB1), suggesting that one of these leukemias undergoes nearly unlimited self-renewal divisions. Using next-generation RNA-sequencing, we characterized the transcriptomes of these phenotypically similar, but biologically distinct, leukemias, identifying hundreds of differentially expressed genes and a large number of structural differences (eg, alternative splicing and promoter usage). Focusing on ligand-receptor pairs, we observed high expression levels of Sdf1-Cxcr4; Jagged2-Notch2/1; Osm-Gp130; Scf-cKit; and Bmp15-Tgfb1/2. Interestingly, the integrin beta 2-like gene (Itgb2l) is both highly expressed and differentially expressed between our 2 leukemias (∼ 14-fold higher in FLA2 than FLB1). In addition, gene ontology analysis indicated G-protein-coupled receptor had a much higher proportion of differential expression (22%) compared with other classes (∼ 5%), suggesting a potential role regulating subtle changes in cellular behavior. These results provide the first comprehensive transcriptome analysis of a leukemia stem cell and document an unexpected level of transcriptome variation between phenotypically similar leukemic cells.
authors.affiliation: Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Canada.
authors.forename: Brian T
authors.initials: BT
authors.lastname: Wilhelm
authors.forename: Mathieu
authors.initials: M
authors.lastname: Briau
authors.forename: Pamela
authors.initials: P
authors.lastname: Austin
authors.forename: Amélie
authors.initials: A
authors.lastname: Faubert
authors.forename: Geneviève
authors.initials: G
authors.lastname: Boucher
authors.forename: Pierre
authors.initials: P
authors.lastname: Chagnon
authors.forename: Kristin
authors.initials: K
authors.lastname: Hope
authors.forename: Simon
authors.initials: S
authors.lastname: Girard
authors.forename: Nadine
authors.initials: N
authors.lastname: Mayotte
authors.forename: Josette-Renee
authors.initials: JR
authors.lastname: Landry
authors.forename: Josée
authors.initials: J
authors.lastname: Hébert
authors.forename: Guy
authors.initials: G
authors.lastname: Sauvageau
mesh_terms: D000818:Animals; D002999:Clone Cells; D005434:Flow Cytometry; D020869:Gene Expression Profiling; D015973:Gene Expression Regulation, Leukemic; D005822:Genetic Vectors; D018398:Homeodomain Proteins / Q000235:genetics; D015470:Leukemia, Myeloid, Acute / Q000235:genetics*; D051379:Mice; D008810:Mice, Inbred C57BL; D046228:Microarray Analysis; D000075064:Myeloid Ecotropic Viral Integration Site 1 Protein; D009363:Neoplasm Proteins / Q000235:genetics; D014411:Neoplastic Stem Cells; D012190:Retroviridae; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA
chemical_list: D018398:Homeodomain Proteins; C000616392:Meis1 protein, mouse; D000075064:Myeloid Ecotropic Viral Integration Site 1 Protein; D009363:Neoplasm Proteins; C097899:homeobox protein HOXA9