title: Subclones in B-lymphoma cell lines: isogenic models for the study of gene regulation.
abstract: Genetic heterogeneity though common in tumors has been rarely documented in cell lines. To examine how often B-lymphoma cell lines are comprised of subclones, we performed immunoglobulin (IG) heavy chain hypermutation analysis. Revealing that subclones are not rare in B-cell lymphoma cell lines, 6/49 IG hypermutated cell lines (12%) consisted of subclones with individual IG mutations. Subclones were also identified in 2/284 leukemia/lymphoma cell lines exhibiting bimodal CD marker expression. We successfully isolated 10 subclones from four cell lines (HG3, SU-DHL-5, TMD-8, U-2932). Whole exome sequencing was performed to molecularly characterize these subclones. We describe in detail the clonal structure of cell line HG3, derived from chronic lymphocytic leukemia. HG3 consists of three subclones each bearing clone-specific aberrations, gene expression and DNA methylation patterns. While donor patient leukemic cells were CD5+, two of three HG3 subclones had independently lost this marker. CD5 on HG3 cells was regulated by epigenetic/transcriptional mechanisms rather than by alternative splicing as reported hitherto. In conclusion, we show that the presence of subclones in cell lines carrying individual mutations and characterized by sets of differentially expressed genes is not uncommon. We show also that these subclones can be useful isogenic models for regulatory and functional studies.
authors: Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors: Hilmar
authors: H
authors: Quentmeier
authors: Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors: Claudia
authors: C
authors: Pommerenke
authors: Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany.
authors: Ole
authors: O
authors: Ammerpohl
authors: Genome Analytics Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors: Robert
authors: R
authors: Geffers
authors: Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors: Vivien
authors: V
authors: Hauer
authors: Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors: Roderick A F
authors: RA
authors: MacLeod
authors: Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors: Stefan
authors: S
authors: Nagel
authors: Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors: Julia
authors: J
authors: Romani
authors: Department of Experimental Medicine, Bioscience and Medical Embryology Section, University of Perugia, Perugia, Italy.
authors: Emanuela
authors: E
authors: Rosati
authors: Department of Clinical and Experimental Medicine, Division of Cell Biology, Linköping University, Linköping, Sweden.
authors: Anders
authors: A
authors: Rosén
authors: Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors: Cord C
authors: CC
authors: Uphoff
authors: Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors: Margarete
authors: M
authors: Zaborski
authors: Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors: Hans G
authors: HG
authors: Drexler
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D018956:CD5 Antigens; D045744:Cell Line, Tumor; D002999:Clone Cells; D059472:Exome / Q000235:genetics*; D005786:Gene Expression Regulation; D015321:Gene Rearrangement; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000235:genetics*; D007135:Immunoglobulin Variable Region / Q000235:genetics*; D016393:Lymphoma, B-Cell / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D009154:Mutation
chemical_list: D014408:Biomarkers, Tumor; D018956:CD5 Antigens; D007143:Immunoglobulin Heavy Chains; D007135:Immunoglobulin Variable Region
keywords: CD5; CLL; cell lines; clonal evolution; subclones