Identification of Characteristic Genomic Markers in Human Hepatoma HuH-7 and Huh7.5.1-8 Cell Lines

Masaki Kawamoto; Toshiyuki Yamaji; Kyoko Saito; Yoshitaka Shirasago; Kazuhiro Satomura; Toshinori Endo; Masayoshi Fukasawa; Kentaro Hanada; Naoki Osada

doi:10.3389/fgene.2020.546106

Identification of Characteristic Genomic Markers in Human Hepatoma HuH-7 and Huh7.5.1-8 Cell Lines

Front Genet. 2020 Oct 9:11:546106. doi: 10.3389/fgene.2020.546106. eCollection 2020.

Authors

Masaki Kawamoto¹, Toshiyuki Yamaji², Kyoko Saito², Yoshitaka Shirasago², Kazuhiro Satomura³, Toshinori Endo³, Masayoshi Fukasawa², Kentaro Hanada², Naoki Osada^{3

4}

Affiliations

¹ Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan.
² Department of Biochemistry & Cell Biology, National Institute of Infectious Diseases, Tokyo, Japan.
³ Faculty of Information Science and Technology, Hokkaido University, Sapporo, Japan.
⁴ Global Station for Big Data and Cybersecurity, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan.

Abstract

The human hepatoma-derived HuH-7 cell line and its derivatives (Huh7.5 and Huh7.5.1) have been widely used as a convenient experimental substitute for primary hepatocytes. In particular, these cell lines represent host cells suitable for propagating the hepatitis C virus (HCV) in vitro. The Huh7.5.1-8 cell line, a subline of Huh7.5.1, can propagate HCV more efficiently than its parental cells. To provide genomic information for cells' quality control, we performed whole-genome sequencing of HuH-7 and Huh7.5.1-8 and identified their characteristic genomic deletions, some of which are applicable to an in-house test for cell authentication. Among the genes related to HCV infection and replication, 53 genes were found to carry missense or loss-of-function mutations likely specific to the HuH-7 and/or Huh7.5.1-8. Eight genes, including DDX58 (RIG-I), BAX, EP300, and SPP1 (osteopontin), contained mutations observed only in Huh7.5.1-8 or mutations with higher frequency in Huh7.5.1-8. These mutations might be relevant to phenotypic differences between the two cell lines and may also serve as genetic markers to distinguish Huh7.5.1-8 cells from the ancestral HuH-7 cells.

Keywords: Huh7 cell line; cell lines; cell substrate; genome sequencing; hepatitis C virus.