Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response

Yukie Kashima, Ayako Suzuki, Ying Liu, Masahito Hosokawa, Hiroko Matsunaga, Masataka Shirai, Kohji Arikawa, Sumio Sugano, Takashi Kohno, Haruko Takeyama, Katsuya Tsuchihara, Yutaka Suzuki

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Single-cell RNA-seq is a powerful tool for revealing heterogeneity in cancer cells. However, each of the current single-cell RNA-seq platforms has inherent advantages and disadvantages. Here, we show that combining the different single-cell RNA-seq platforms can be an effective approach to obtaining complete information about expression differences and a sufficient cellular population to understand transcriptional heterogeneity in cancers. We demonstrate that it is possible to estimate missing expression information. We further demonstrate that even in the cases where precise information for an individual gene cannot be inferred, the activity of given transcriptional modules can be analyzed. Interestingly, we found that two distinct transcriptional modules, one associated with the Aurora kinase gene and the other with the DUSP gene, are aberrantly regulated in a minor population of cells and may thus contribute to the possible emergence of dormancy or eventual drug resistance within the population.

Original languageEnglish
Article number3482
JournalScientific Reports
Volume8
Issue number1
DOIs
Publication statusPublished - 2018 Dec 1

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Transcriptome
RNA
Aurora Kinases
Population
Genes
Drug Resistance
Neoplasms

ASJC Scopus subject areas

  • General

Cite this

Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response. / Kashima, Yukie; Suzuki, Ayako; Liu, Ying; Hosokawa, Masahito; Matsunaga, Hiroko; Shirai, Masataka; Arikawa, Kohji; Sugano, Sumio; Kohno, Takashi; Takeyama, Haruko; Tsuchihara, Katsuya; Suzuki, Yutaka.

In: Scientific Reports, Vol. 8, No. 1, 3482, 01.12.2018.

Research output: Contribution to journalArticle

Kashima, Y, Suzuki, A, Liu, Y, Hosokawa, M, Matsunaga, H, Shirai, M, Arikawa, K, Sugano, S, Kohno, T, Takeyama, H, Tsuchihara, K & Suzuki, Y 2018, 'Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response', Scientific Reports, vol. 8, no. 1, 3482. https://doi.org/10.1038/s41598-018-21161-y
Kashima, Yukie ; Suzuki, Ayako ; Liu, Ying ; Hosokawa, Masahito ; Matsunaga, Hiroko ; Shirai, Masataka ; Arikawa, Kohji ; Sugano, Sumio ; Kohno, Takashi ; Takeyama, Haruko ; Tsuchihara, Katsuya ; Suzuki, Yutaka. / Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response. In: Scientific Reports. 2018 ; Vol. 8, No. 1.
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