Haplobank contains over 100,000 mutated, conditional mouse embryonic stem cell lines, targeting about 70% of the protein-coding genome.
Credit: (c)Izabella Kaminski
Scientist at IMBA developed a biobank of revertible, mutant embryonic stem cells, published in the current issue of Nature. This cell bank — called Haplobank — contains over 100,000 mutated, conditional mouse embryonic stem cell lines, targeting about 70% of the protein-coding genome.
Major concerns about scientific reproducibility and rigor have emerged in recent years. Amgen and Bayer, as well as The Reproducibility Initiative, have been unable to replicate many high-profile cancer studies. Indeed, it is not uncommon to obtain different results from experiments with the same cell line in two different laboratories. These inconsistencies can arise for various reasons. Regardless, irreproducible results waste money, damage the credibility of science and scientists, and delay or undo progress, including the development of effective therapies.
To overcome these problems, the Penninger lab at the IMBA developed a biobank of revertible, mutant embryonic stem cells, published in the current issue of Nature. This cell bank — called Haplobank — contains over 100,000 mutated, conditional mouse embryonic stem cell lines, targeting about 70% of the protein-coding genome (almost 17,000 genes). “Haplobank is available to all scientists, and represents the largest ever library of hemizyogous mutant embryonic stem cell lines to date. The resource overcomes issues arising from clonal variability, because mutations can be repaired in single cells and at whole genome scale,” explains Ulrich Elling, first and corresponding author of the current publication in Nature.
Host-pathogen interactions and drug discovery
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As a proof-of-principle, the authors performed a genetic screen to uncover factors required for infection with rhinovirus — the cause of the common cold. They discovered that rhinovirus requires a previously unknown host cell factor, phospholipase A2G16 (PLA2G16), to kill cells. Further, they showed that a specific domain of PLA2G16 is required for infection and may be an attractive drug target. Interestingly, PLA2G16 was also shown recently to be necessary for successful infection by related viruses, including poliovirus.
Novel genes for blood vessel development
In another proof-of-principle screen, the authors leveraged the pluripotent potential of embryonic stem cells by differentiating them into blood vessel organoids. The formation of blood vessels (angiogenesis) is critical for development and for tissue maintenance, as well as for diseases like cancer. The authors screened candidate angiogenesis genes that were represented in Haplobank, and discovered multiple novel factors that affect blood vessel growth in organoids. Importantly, they observed a strong variability between independent clones, highlighting the advantage of repairable mutagenesis for comparing mutants with their genetically repaired sister clones.
“Haplobank can be used for screens to make entirely new insights into biology and health. Importantly — because gene knockouts can be repaired in our embryonic stem clones — this resource also enables well-controlled, robust and reproducible validation experiments. We feel this is a critical point and contribution, given the current efforts to improve the rigor of scientific research.” Says Josef Penninger, IMBA Director and last author.
Story Source: Materials provided by University of Chicago Original written by Whitney Clavin.Note: Content may be edited for style and length.
Ulrich Elling, Reiner A. Wimmer, Andreas Leibbrandt, Thomas Burkard, Georg Michlits, Alexandra Leopoldi, Thomas Micheler, Dana Abdeen, Sergei Zhuk, Irene M. Aspalter, Cornelia Handl, Julia Liebergesell, Maria Hubmann, Anna-Maria Husa, Manuela Kinzer, Nicole Schuller, Ellen Wetzel, Nina van de Loo, Jorge Arturo Zepeda Martinez, David Estoppey, Ralph Riedl, Fengtang Yang, Beiyuan Fu, Thomas Dechat, Zoltán Ivics, Chukwuma A. Agu, Oliver Bell, Dieter Blaas, Holger Gerhardt, Dominic Hoepfner, Alexander Stark, Josef M. Penninger. A reversible haploid mouse embryonic stem cell biobank resource for functional genomics. Nature, 2017; DOI: 10.1038/nature24027