title: Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq.
abstract: A central challenge in oncology is how to kill tumors containing heterogeneous cell populations defined by different combinations of mutated genes. Identifying these mutated genes and understanding how they cooperate requires single-cell analysis, but current single-cell analytic methods, such as PCR-based strategies or whole-exome sequencing, are biased, lack sequencing depth or are cost prohibitive. Transposon-based mutagenesis allows the identification of early cancer drivers, but current sequencing methods have limitations that prevent single-cell analysis. We report a liquid-phase, capture-based sequencing and bioinformatics pipeline, Sleeping Beauty (SB) capture hybridization sequencing (SBCapSeq), that facilitates sequencing of transposon insertion sites from single tumor cells in a SB mouse model of myeloid leukemia (ML). SBCapSeq analysis of just 26 cells from one tumor revealed the tumor's major clonal subpopulations, enabled detection of clonal insertion events not detected by other sequencing methods and led to the identification of dominant subclones, each containing a unique pair of interacting gene drivers along with three to six cooperating cancer genes with SB-driven expression changes.
authors.affiliation: Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA.|Institute of Molecular and Cell Biology, Singapore, Republic of Singapore.
authors.forename: Karen M
authors.initials: KM
authors.lastname: Mann
authors.affiliation: Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA.
authors.forename: Justin Y
authors.initials: JY
authors.lastname: Newberg
authors.affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Black
authors.affiliation: Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA.
authors.forename: Devin J
authors.identifier: 0000-0003-4364-1273
authors.initials: DJ
authors.lastname: Jones
authors.affiliation: Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA.
authors.forename: Felipe
authors.initials: F
authors.lastname: Amaya-Manzanares
authors.affiliation: Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA.
authors.forename: Liliana
authors.initials: L
authors.lastname: Guzman-Rojas
authors.affiliation: Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA.
authors.forename: Takahiro
authors.initials: T
authors.lastname: Kodama
authors.affiliation: Institute of Molecular and Cell Biology, Singapore, Republic of Singapore.
authors.forename: Jerrold M
authors.initials: JM
authors.lastname: Ward
authors.affiliation: Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
authors.forename: Alistair G
authors.initials: AG
authors.lastname: Rust
authors.affiliation: Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
authors.forename: Louise
authors.initials: L
authors.lastname: van der Weyden
authors.affiliation: Institute of Molecular and Cell Biology, Singapore, Republic of Singapore.
authors.forename: Christopher Chin Kuan
authors.initials: CC
authors.lastname: Yew
authors.affiliation: Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Jill L
authors.initials: JL
authors.lastname: Waters
authors.affiliation: Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Marco L
authors.initials: ML
authors.lastname: Leung
authors.affiliation: Institute of Molecular and Cell Biology, Singapore, Republic of Singapore.
authors.forename: Keith
authors.initials: K
authors.lastname: Rogers
authors.affiliation: Institute of Molecular and Cell Biology, Singapore, Republic of Singapore.
authors.forename: Susan M
authors.initials: SM
authors.lastname: Rogers
authors.affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand.
authors.forename: Leslie A
authors.initials: LA
authors.lastname: McNoe
authors.affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand.
authors.forename: Luxmanan
authors.initials: L
authors.lastname: Selvanesan
authors.affiliation: Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Navin
authors.affiliation: Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA.|Institute of Molecular and Cell Biology, Singapore, Republic of Singapore.
authors.forename: Nancy A
authors.initials: NA
authors.lastname: Jenkins
authors.affiliation: Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA.|Institute of Molecular and Cell Biology, Singapore, Republic of Singapore.
authors.forename: Neal G
authors.initials: NG
authors.lastname: Copeland
authors.affiliation: Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA.|Institute of Molecular and Cell Biology, Singapore, Republic of Singapore.
authors.forename: Michael B
authors.identifier: 0000-0002-7515-6515
authors.initials: MB
authors.lastname: Mann
mesh_terms: D000465:Algorithms; D000818:Animals; D014408:Biomarkers, Tumor / Q000235:genetics; D004251:DNA Transposable Elements; D004273:DNA, Neoplasm / Q000235:genetics*; D005260:Female; D052138:Genes, Neoplasm / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D017403:In Situ Hybridization / Q000379:methods*; D007951:Leukemia, Myeloid / Q000235:genetics* / Q000473:pathology; D008297:Male; D051379:Mice; D016254:Mutagenesis, Insertional / Q000235:genetics*; D009363:Neoplasm Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D019895:Transposases / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor; D004251:DNA Transposable Elements; D004273:DNA, Neoplasm; D009363:Neoplasm Proteins; D019895:Transposases; C494471:sleeping beauty transposase, human