Gene expression profiling of tumor-initiating stem cells from mouse Krebs-2 carcinoma using a novel marker of poorly differentiated cells

// Ekaterina A. Potter 1, * , Evgenia V. Dolgova 1, * , Anastasia S. Proskurina 1, * , Yaroslav R. Efremov 1, 2 , Alexandra M. Minkevich 1 , Aleksey S. Rozanov 1 , Sergey E. Peltek 1 , Valeriy P. Nikolin 1 , Nelly A. Popova 1, 2 , Igor A. Seledtsov 3 , Vladimir V. Molodtsov 2, 3 , Evgeniy L Zavyalov 1 , Oleg S. Taranov 4 , Sergey I. Baiborodin 1 , Alexander A. Ostanin 5 , Elena R. Chernykh 5 , Nikolay A. Kolchanov 1 , Sergey S. Bogachev 1 1 Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia 2 Novosibirsk State University, Novosibirsk 630090, Russia 3 Softberry Inc., New York 10549, USA 4 The State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk 630559, Russia 5 Research Institute of Fundamental and Clinical Immunology, Novosibirsk 630099, Russia * These authors contributed equally to this work Correspondence to: Sergey S. Bogachev, email: labmolbiol@mail.ru Keywords: tumor-initiating stem cells, DNA internalization, RNAseq, Real Time PCR, TAMRA Received: August 29, 2016      Accepted: December 15, 2016      Published: December 23, 2016 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.