A mouse knockout library for secreted and transmembrane proteins (original) (raw)

References

1. Clamp, M. et al. Distinguishing protein-coding and noncoding genes in the human genome. Proc. Natl. Acad. Sci. USA 104, 19428–19433 (2007).
   Article CAS Google Scholar
2. Austin, C.P. et al. The knockout mouse project. Nat. Genet. 36, 921–924 (2004).
   Article CAS Google Scholar
3. Friedel, R.H., Seisenberger, C., Kaloff, C. & Wurst, W. EUCOMM–the European conditional mouse mutagenesis program. Brief. Funct. Genomics Proteomics 6, 180–185 (2007).
   Article CAS Google Scholar
4. Mouse Genome Sequencing Consortium & Waterston, R.H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002).
   Article CAS Google Scholar
5. Zambrowicz, B.P. & Sands, A.T. Knockouts model the 100 best-selling drugs–will they model the next 100? Nat. Rev. Drug Discov. 2, 38–51 (2003).
   Article CAS Google Scholar
6. Clark, H.F. et al. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Genome Res. 13, 2265–2270 (2003).
   Article CAS Google Scholar
7. Zambrowicz, B.P. et al. Disruption and sequence identification of 2,000 genes in mouse embryonic stem cells. Nature 392, 608–611 (1998).
   Article CAS Google Scholar
8. Beltrandelrio, H. et al. Saturation Screening of the Druggable Mammalian Genome. in Model Organisms in Drug Discovery (eds. Carroll, P.M. & Fitzgerald, K.) 251–278, (John Wiley & Sons, Chichester, West Sussex, England, 2003).
9. Brommage, R. Validation and calibration of DEXA body composition in mice. Am. J. Physiol. Endocrinol. Metab. 285, E454–E459 (2003).
   Article CAS Google Scholar
10. Scott, H.S. et al. Insertion of beta-satellite repeats identifies a transmembrane protease causing both congenital and childhood onset autosomal recessive deafness. Nat. Genet. 27, 59–63 (2001).
    Article CAS Google Scholar
11. Guipponi, M., Antonarakis, S.E. & Scott, H.S. TMPRSS3, a type II transmembrane serine protease mutated in non-syndromic autosomal recessive deafness. Front. Biosci. 13, 1557–1567 (2008).
    Article CAS Google Scholar
12. Ben-Yosef, T. et al. Claudin 14 knockout mice, a model for autosomal recessive deafness DFNB29, are deaf due to cochlear hair cell degeneration. Hum. Mol. Genet. 12, 2049–2061 (2003).
    Article CAS Google Scholar
13. Friedman, L.M., Dror, A.A. & Avraham, K.B. Mouse models to study inner ear development and hereditary hearing loss. Int. J. Dev. Biol. 51, 609–631 (2007).
    Article CAS Google Scholar
14. Fan, B. et al. Hepatocyte growth factor activator inhibitor-1 (HAI-1) is essential for the integrity of basement membranes in the developing placental labyrinth. Dev. Biol. 303, 222–230 (2007).
    Article CAS Google Scholar
15. Yan, M. & Plowman, G.D. Delta-like 4/Notch signaling and its therapeutic implications. Clin. Cancer Res. 13, 7243–7246 (2007).
    Article CAS Google Scholar
16. Wilson, L. et al. Random mutagenesis of proximal mouse chromosome 5 uncovers predominantly embryonic lethal mutations. Genome Res. 15, 1095–1105 (2005).
    Article CAS Google Scholar
17. Junge, H.J. et al. TSPAN12 regulates retinal vascular development by promoting Norrin- but not Wnt-induced FZD4/β-catenin signaling. Cell 139, 299–311 (2009).
    Article CAS Google Scholar
18. Beigneux, A.P. et al. Glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1 plays a critical role in the lipolytic processing of chylomicrons. Cell Metab. 5, 279–291 (2007).
    Article CAS Google Scholar
19. Desai, U. et al. Lipid-lowering effects of anti-angiopoietin-like 4 antibody recapitulate the lipid phenotype found in angiopoietin-like 4 knockout mice. Proc. Natl. Acad. Sci. USA 104, 11766–11771 (2007).
    Article CAS Google Scholar
20. Savelieva, K.V. et al. Learning and memory impairment in Eph receptor A6 knockout mice. Neurosci. Lett. 438, 205–209 (2008).
    Article CAS Google Scholar
21. Holst, C.R. et al. Secreted sulfatases Sulf1 and Sulf2 have overlapping yet essential roles in mouse neonatal survival. PLoS ONE 2, e575 (2007).
    Article Google Scholar
22. Colonna, M., Samaridis, J. & Angman, L. Molecular characterization of two novel C-type lectin-like receptors, one of which is selectively expressed in human dendritic cells. Eur. J. Immunol. 30, 697–704 (2000).
    Article CAS Google Scholar
23. Turner, M. et al. Perinatal lethality and blocked B-cell development in mice lacking the tyrosine kinase Syk. Nature 378, 298–302 (1995).
    Article CAS Google Scholar
24. Cheng, A.M. et al. Syk tyrosine kinase required for mouse viability and B-cell development. Nature 378, 303–306 (1995).
    Article CAS Google Scholar
25. Suzuki-Inoue, K. et al. A novel Syk-dependent mechanism of platelet activation by the C-type lectin receptor CLEC-2. Blood 107, 542–549 (2006).
    Article CAS Google Scholar
26. May, F. et al. CLEC-2 is an essential platelet activating receptor in hemostasis and thrombosis. Blood 114, 3464–3472 (2009).
    Article CAS Google Scholar
27. Cordes, S.P. N-ethyl-N-nitrosourea mutagenesis: boarding the mouse mutant express. Microbiol. Mol. Biol. Rev. 69, 426–439 (2005).
    Article CAS Google Scholar
28. Su, A.I. et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. USA 101, 6062–6067 (2004).
    Article CAS Google Scholar
29. The Eumorphia Consortium EMPReSS: standardized phenotype screens for functional annotation of the mouse genome. Nat. Genet. 37, 1155 (2005).
30. Morgan, H. et al. EuroPhenome: a repository for high-throughput mouse phenotyping data. Nucleic Acids Res. 38, D577–D585 (2010).
    Article CAS Google Scholar
31. Zambrowicz, B.P., Holt, K.H., Walke, D.W., Kirkpatrick, L.L. & Eberhart, D.E. Generation of transgenic animals. in Target Validation in Drug Discovery (eds. Metcalf, B.W. & Dillon, S.) 3–26, (Academic Press, Burlington, Massachusetts, USA, 2007).
32. Friddle, C.J. et al. High-throughput mouse knockouts provide a functional analysis of the genome. Cold Spring Harb. Symp. Quant. Biol. 68, 311–315 (2003).
    Article CAS Google Scholar
33. Pogorelov, V.M., Baker, K.B., Malbari, M.M., Lanthorn, T.H. & Savelieva, K.V. A standardized behavioral test battery to identify and validate targets for neuropsychiatric diseases and pain. in Experimental Animal Models in Neurobehavioral Research (eds. Kalueff, A.V. & LaPorte, J.L.) 17–45 (Laboratory of Clinical Science, Nat. Inst. of Mental Health, Bethesda, Maryland, USA, 2008).
34. Brommage, R. et al. High-throughput screening of mouse knockout lines identifies true lean and obese phenotypes. Obesity (Silver Spring) 16, 2362–2367 (2008).
    Article CAS Google Scholar
35. Zambrowicz, B.P. et al. Wnk1 kinase deficiency lowers blood pressure in mice: a gene-trap screen to identify potential targets for therapeutic intervention. Proc. Natl. Acad. Sci. USA 100, 14109–14114 (2003).
    Article Google Scholar
36. Abuin, A., Hansen, G.M. & Zambrowicz, B. Gene trap mutagenesis. in Conditional Mutagenesis: An Approach to Disease Models (eds. Feil, R. & Metzger, D.) 129–147, (Springer, 2007).
37. Wattler, S., Kelly, M. & Nehls, M. Construction of gene targeting vectors from lambda KOS genomic libraries. Biotechniques 26, 1150–1156, 1158, 1160 (1999).
    Article CAS Google Scholar

Download references

Acknowledgements

We thank J. Brennan, S. Bunting, L. Corson, P. Fielder, E. Filvaroff, D. French, J. Junutula, F. Peale, H. Phillips, M. Rohrer, H. Stern, J. Zha, R. Watts, B. Wolf and scientists in the Genentech Immunology Department for critical review of the knockout phenotypes and E. Bierwagen and D. Wan for the bioinformatics infrastructures used to track phenotypic calls. We thank J. Mitchell for analysis and plotting of histograms depicting phenotypic ranges. We also thank M. Tessier-Lavigne, F. Bazan, M. Kong-Beltran, J. Theunissen, S. Warming and Z. Zhang for critical reading of the manuscript.

Author information

Authors and Affiliations

1. Department of Molecular Biology, Genentech, Inc., South San Francisco, California, USA
   Tracy Tang, Deanna Grant, Mark Solloway, Nico Ghilardi, Andrew Peterson & Frederic J de Sauvage
2. Bioinformatics, Genentech, Inc., South San Francisco, California, USA
   Li Li, Jerry Tang & Yun Li
3. Immunology, Genentech, Inc., South San Francisco, California, USA
   Wei Yu Lin, Flavius Martin & Paul Godowski
4. Tumor Biology & Angiogenesis, Genentech, Inc., South San Francisco, California, USA
   Leon Parker & Weilan Ye
5. Nonclinical Biostatistics, Genentech, Inc., South San Francisco, California, USA
   William Forrest
6. Lexicon Pharmaceuticals, Inc., The Woodlands, Texas, USA
   Tamas Oravecz, Kenneth A Platt, Dennis S Rice, Gwenn M Hansen, Alejandro Abuin, Derek E Eberhart, Kathleen H Holt & Brian P Zambrowicz

Authors

1. Tracy Tang
   You can also search for this author inPubMed Google Scholar
2. Li Li
   You can also search for this author inPubMed Google Scholar
3. Jerry Tang
   You can also search for this author inPubMed Google Scholar
4. Yun Li
   You can also search for this author inPubMed Google Scholar
5. Wei Yu Lin
   You can also search for this author inPubMed Google Scholar
6. Flavius Martin
   You can also search for this author inPubMed Google Scholar
7. Deanna Grant
   You can also search for this author inPubMed Google Scholar
8. Mark Solloway
   You can also search for this author inPubMed Google Scholar
9. Leon Parker
   You can also search for this author inPubMed Google Scholar
10. Weilan Ye
    You can also search for this author inPubMed Google Scholar
11. William Forrest
    You can also search for this author inPubMed Google Scholar
12. Nico Ghilardi
    You can also search for this author inPubMed Google Scholar
13. Tamas Oravecz
    You can also search for this author inPubMed Google Scholar
14. Kenneth A Platt
    You can also search for this author inPubMed Google Scholar
15. Dennis S Rice
    You can also search for this author inPubMed Google Scholar
16. Gwenn M Hansen
    You can also search for this author inPubMed Google Scholar
17. Alejandro Abuin
    You can also search for this author inPubMed Google Scholar
18. Derek E Eberhart
    You can also search for this author inPubMed Google Scholar
19. Paul Godowski
    You can also search for this author inPubMed Google Scholar
20. Kathleen H Holt
    You can also search for this author inPubMed Google Scholar
21. Andrew Peterson
    You can also search for this author inPubMed Google Scholar
22. Brian P Zambrowicz
    You can also search for this author inPubMed Google Scholar
23. Frederic J de Sauvage
    You can also search for this author inPubMed Google Scholar

Contributions

F.J.d.S., T.T., A.P. and B.P.Z. designed the project, analyzed data and wrote the manuscript. F.M. and P.G. designed experiments and analyzed data. J.T. and N.G. contributed to the identification of murine orthologs. K.H.H. and N.G. contributed to the design and verification of targeting strategies. T.O., K.A.P., D.S.R., G.M.H., A.A., D.E.E., K.H.H. and B.P.Z. designed, performed and supervised the knockout generation and phenotype screen. T.T., L.L. and W.F. contributed to the statistical analysis and making the phenotype calls. J.T. and Y.L. implemented the database for public access. L.L. compiled the adult tissue calls. L.P. and W.Y. performed the embryonic in situ hybridization screen. W.Y.L., F.M., D.G. and M.S. performed the follow-up characterization of the Clec1b mutant line.

Corresponding author

Correspondence toFrederic J de Sauvage.

Ethics declarations

Competing interests

T.T., L.L., J.T., Y.L., W.Y.L., F.M., D.G., M.S., L.P., W.Y., W.F., N.G., P.G., A.P. and F.J.d.S. are employees of Genentech, a wholly owned subsidiary of Hoffmann-La Roche. T.O., K.A.P., D.S.R., G.M.H., A.A., D.E.E., K.H.H. and B.P.Z. are employees and shareholders of Lexicon Pharmaceuticals.

Supplementary information

Rights and permissions

About this article

Cite this article

Tang, T., Li, L., Tang, J. et al. A mouse knockout library for secreted and transmembrane proteins.Nat Biotechnol 28, 749–755 (2010). https://doi.org/10.1038/nbt.1644

Download citation

• Received: 06 July 2009
• Accepted: 11 May 2010
• Published: 20 June 2010
• Issue Date: July 2010
• DOI: https://doi.org/10.1038/nbt.1644