HuH-7 reference genome profile: complex karyotype composed of massive loss of heterozygosity

Human Cell
Fumio KasaiArihiro Kohara

Abstract

Human cell lines represent a valuable resource as in vitro experimental models. A hepatoma cell line, HuH-7 (JCRB0403), has been used extensively in various research fields and a number of studies using this line have been published continuously since it was established in 1982. However, an accurate genome profile, which can be served as a reliable reference, has not been available. In this study, we performed M-FISH, SNP microarray and amplicon sequencing to characterize the cell line. Single cell analysis of metaphases revealed a high level of heterogeneity with a mode of 60 chromosomes. Cytogenetic results demonstrated chromosome abnormalities involving every chromosome in addition to a massive loss of heterozygosity, which accounts for 55.3% of the genome, consistent with the homozygous variants seen in the sequence analysis. We provide empirical data that the HuH-7 cell line is composed of highly heterogeneous cell populations, suggesting that besides cell line authentication, the quality of cell lines needs to be taken into consideration in the future use of tumor cell lines.

References

Nov 3, 2001·Journal of Molecular Medicine : Official Organ of the Gesellschaft Deutscher Naturforscher Und Ärzte·M VolkmannW J Hofmann
Nov 20, 2002·Journal of Virology·Keril J BlightCharles M Rice
Aug 19, 2003·Nature Genetics·Donna G AlbertsonJoe W Gray
Jan 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Toru KondoTetsuya Taga
Mar 9, 2004·Cell Cycle·Takao SetoguchiToru Kondo
Oct 6, 2007·Cancer Biomarkers : Section a of Disease Markers·Toru Kondo
Jul 23, 2008·Molecular Cancer Research : MCR·Stephanie MaXin-Yuan Guan
Dec 31, 2010·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Sarah L Thompson, Duane A Compton
Mar 8, 2011·Cell·Douglas Hanahan, Robert A Weinberg
Aug 21, 2012·International Journal of Biological Sciences·Yi ChenRong-Guang Shao
Dec 19, 2012·Cell Stem Cell·Qiurong DingChad A Cowan
Feb 26, 2013·Journal of the National Cancer Institute·Jean-Pierre GilletMichael M Gottesman
Nov 29, 2013·Nature·Benjamin Haibe-KainsJohn Quackenbush
May 29, 2015·Nature Methods·Leonard P FreedmanYvonne A Reid
Aug 2, 2015·BMC Medical Genomics·Georgina L RylandKylie L Gorringe
Aug 8, 2015·Molecular Cancer Research : MCR·Andrew GoodspeedJames C Costello
Oct 3, 2015·Genome Research·Nicholas E Navin
Dec 3, 2016·Nucleic Acids Research·Simon A ForbesPeter J Campbell
Jan 26, 2017·In Vitro Cellular & Developmental Biology. Animal·Melanie ArulSwee Hung Cheah
Aug 16, 2017·In Vitro Cellular & Developmental Biology. Animal·John M BaustFrank Simione
Oct 8, 2017·In Vitro Cellular & Developmental Biology. Animal·Yvonne A Reid
Dec 3, 2017·In Vitro Cellular & Developmental Biology. Animal·Raymond W Nims, Yvonne Reid
Mar 9, 2018·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Fumio KasaiMalcolm A Ferguson-Smith

❮ Previous
Next ❯

Citations

Dec 28, 2019·Journal of Clinical Medicine·Katie MorganJohn N Plevris
Sep 29, 2020·Frontiers in Immunology·Inmaculada Sanclemente-AlamanUlises Gómez-Pinedo
Feb 15, 2020·Biochimica Et Biophysica Acta. Molecular and Cell Biology of Lipids·Camilla PramfalkPaolo Parini
May 15, 2021·Mutation Research. Genetic Toxicology and Environmental Mutagenesis·Fotini PapachristouAlexandra Tsaroucha

❮ Previous
Next ❯

Methods Mentioned

BETA
chip
flow cytometry

Software Mentioned

Affymetrix
Ion Torrent Variant Caller Plugin
Metafer
Ion Reporter
Chromosome Analysis Suite
Isis

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.