title: Gene expression profiling of tumor-initiating stem cells from mouse Krebs-2 carcinoma using a novel marker of poorly differentiated cells.
abstract: Using the ability of poorly differentiated cells to natively internalize fragments of extracellular double-stranded DNA as a marker, we isolated a tumorigenic subpopulation present in Krebs-2 ascites that demonstrated the features of tumor-inducing cancer stem cells. Having combined TAMRA-labeled DNA probe and the power of RNA-seq technology, we identified a set of 168 genes specifically expressed in TAMRA-positive cells (tumor-initiating stem cells), these genes remaining silent in TAMRA-negative cancer cells. TAMRA+ cells displayed gene expression signatures characteristic of both stem cells and cancer cells. The observed expression differences between TAMRA+ and TAMRA- cells were validated by Real Time PCR. The results obtained corroborated the biological data that TAMRA+ murine Krebs-2 tumor cells are tumor-initiating stem cells. The approach developed can be applied to profile any poorly differentiated cell types that are capable of immanent internalization of double-stranded DNA.
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Ekaterina A
authors.initials: EA
authors.lastname: Potter
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Evgenia V
authors.initials: EV
authors.lastname: Dolgova
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Anastasia S
authors.initials: AS
authors.lastname: Proskurina
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.|Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Yaroslav R
authors.initials: YR
authors.lastname: Efremov
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Alexandra M
authors.initials: AM
authors.lastname: Minkevich
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Aleksey S
authors.initials: AS
authors.lastname: Rozanov
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Sergey E
authors.initials: SE
authors.lastname: Peltek
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Valeriy P
authors.initials: VP
authors.lastname: Nikolin
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.|Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Nelly A
authors.initials: NA
authors.lastname: Popova
authors.affiliation: Softberry Inc., New York 10549, USA.
authors.forename: Igor A
authors.initials: IA
authors.lastname: Seledtsov
authors.affiliation: Novosibirsk State University, Novosibirsk 630090, Russia.|Softberry Inc., New York 10549, USA.
authors.forename: Vladimir V
authors.initials: VV
authors.lastname: Molodtsov
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Evgeniy L
authors.initials: EL
authors.lastname: Zavyalov
authors.affiliation: The State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk 630559, Russia.
authors.forename: Oleg S
authors.initials: OS
authors.lastname: Taranov
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Sergey I
authors.initials: SI
authors.lastname: Baiborodin
authors.affiliation: Institute of Clinical Immunology, Siberian Branch of the Russian Academy of Medical Sciences, Novosibirsk 630099, Russia.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Ostanin
authors.affiliation: Institute of Clinical Immunology, Siberian Branch of the Russian Academy of Medical Sciences, Novosibirsk 630099, Russia.
authors.forename: Elena R
authors.initials: ER
authors.lastname: Chernykh
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Nikolay A
authors.initials: NA
authors.lastname: Kolchanov
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Sergey S
authors.initials: SS
authors.lastname: Bogachev
mesh_terms: D020087:Alu Elements; D000818:Animals; D014408:Biomarkers, Tumor / Q000235:genetics* / Q000378:metabolism; D002287:Carcinoma, Krebs 2 / Q000235:genetics* / Q000473:pathology; D002454:Cell Differentiation; D004247:DNA / Q000235:genetics / Q000378:metabolism; D005456:Fluorescent Dyes / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D014411:Neoplastic Stem Cells / Q000378:metabolism / Q000473:pathology; D010641:Phenotype; D060888:Real-Time Polymerase Chain Reaction; D012235:Rhodamines / Q000378:metabolism; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D059467:Transcriptome
chemical_list: C114557:5-carboxytetramethylrhodamine succinimidyl ester; D014408:Biomarkers, Tumor; D005456:Fluorescent Dyes; D012235:Rhodamines; D004247:DNA
keywords: DNA internalization; RNAseq; Real Time PCR; TAMRA; tumor-initiating stem cells