Gene expression profiling of tumor-initiating stem cells from mouse Krebs-2 carcinoma using a novel marker of poorly differentiated cells
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Ekaterina A. Potter1,*, Evgenia V. Dolgova1,*, Anastasia S. Proskurina1,*, Yaroslav R. Efremov1,2, Alexandra M. Minkevich1, Aleksey S. Rozanov1, Sergey E. Peltek1, Valeriy P. Nikolin1, Nelly A. Popova1,2, Igor A. Seledtsov3, Vladimir V. Molodtsov2,3, Evgeniy L Zavyalov1, Oleg S. Taranov4, Sergey I. Baiborodin1, Alexander A. Ostanin5, Elena R. Chernykh5, Nikolay A. Kolchanov1, Sergey S. Bogachev1
1Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
2Novosibirsk State University, Novosibirsk 630090, Russia
3Softberry Inc., New York 10549, USA
4The State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk 630559, Russia
5Research Institute of Fundamental and Clinical Immunology, Novosibirsk 630099, Russia
*These authors contributed equally to this work
Sergey S. Bogachev, email: [email protected]
Keywords: tumor-initiating stem cells, DNA internalization, RNAseq, Real Time PCR, TAMRA
Received: August 29, 2016 Accepted: December 15, 2016 Published: December 23, 2016
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.
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