Renal biomarker qualification submission: A dialog between the FDA-EMEA and Predictive Safety Testing Consortium

Frank Dieterle; Frank Sistare; Federico Goodsaid; Marisa Papaluca; Josef S. Ozer; Craig P. Webb; William Baer; Anthony Senagore; Matthew J. Schipper; Jacky Vonderscher; Stefan Sultana; David L. Gerhold; Jonathan A. Phillips; Gérard Maurer; Kevin Carl; David Laurie; Ernie Harpur; Manisha Sonee; Daniela Ennulat; Dan Holder; Dina Andrews-Cleavenger; Yi Zhong Gu; Karol L. Thompson; Peter L. Goering; Jean Marc Vidal; Eric Abadie; Romaldas MacIulaitis; David Jacobson-Kram; Albert F. Defelice; Elizabeth A. Hausner; Melanie Blank; Aliza Thompson; Patricia Harlow; Douglas Throckmorton; Shen Xiao; Nancy Xu; William Taylor; Spiros Vamvakas; Bruno Flamion; Beatriz Silva Lima; Peter Kasper; Markku Pasanen; Krishna Prasad; Sean Troth; Denise Bounous; Denise Robinson-Gravatt; Graham Betton; Myrtle A. Davis; Jackie Akunda; James Eric McDuffie; Laura Suter; Leslie Obert; Magalie Guffroy; Mark Pinches; Supriya Jayadev; Eric A. Blomme; Sven A. Beushausen; Valérie G. Barlow; Nathaniel Collins; Jeff Waring; David Honor; Sandra Snook; Jinhe Lee; Phil Rossi; Elizabeth Walker; William Mattes

doi:10.1038/nbt.1625

Renal biomarker qualification submission: A dialog between the FDA-EMEA and Predictive Safety Testing Consortium

Frank Dieterle, Frank Sistare, Federico Goodsaid, Marisa Papaluca, Josef S. Ozer, Craig P. Webb, William Baer, Anthony Senagore, Matthew J. Schipper, Jacky Vonderscher, Stefan Sultana, David L. Gerhold, Jonathan A. Phillips, Gérard Maurer, Kevin Carl, David Laurie, Ernie Harpur, Manisha Sonee, Daniela Ennulat, Dan HolderDina Andrews-Cleavenger, Yi Zhong Gu, Karol L. Thompson, Peter L. Goering, Jean Marc Vidal, Eric Abadie, Romaldas MacIulaitis, David Jacobson-Kram, Albert F. Defelice, Elizabeth A. Hausner, Melanie Blank, Aliza Thompson, Patricia Harlow, Douglas Throckmorton, Shen Xiao, Nancy Xu, William Taylor, Spiros Vamvakas, Bruno Flamion, Beatriz Silva Lima, Peter Kasper, Markku Pasanen, Krishna Prasad, Sean Troth, Denise Bounous, Denise Robinson-Gravatt, Graham Betton, Myrtle A. Davis, Jackie Akunda, James Eric McDuffie, Laura Suter, Leslie Obert, Magalie Guffroy, Mark Pinches, Supriya Jayadev, Eric A. Blomme, Sven A. Beushausen, Valérie G. Barlow, Nathaniel Collins, Jeff Waring, David Honor, Sandra Snook, Jinhe Lee, Phil Rossi, Elizabeth Walker, William Mattes

Research output: Contribution to journal › Review article › peer-review

313 Scopus citations

Abstract

Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis and human, demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

Original language	English (US)
Pages (from-to)	455-462
Number of pages	8
Journal	Nature Biotechnology
Volume	28
Issue number	5
DOIs	https://doi.org/10.1038/nbt.1625
State	Published - May 2010
Externally published	Yes

ASJC Scopus subject areas

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Molecular Medicine
Biomedical Engineering

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Dieterle, F., Sistare, F., Goodsaid, F., Papaluca, M., Ozer, J. S., Webb, C. P., Baer, W., Senagore, A., Schipper, M. J., Vonderscher, J., Sultana, S., Gerhold, D. L., Phillips, J. A., Maurer, G., Carl, K., Laurie, D., Harpur, E., Sonee, M., Ennulat, D., ... Mattes, W. (2010). Renal biomarker qualification submission: A dialog between the FDA-EMEA and Predictive Safety Testing Consortium. Nature Biotechnology, 28(5), 455-462. https://doi.org/10.1038/nbt.1625

Dieterle, F, Sistare, F, Goodsaid, F, Papaluca, M, Ozer, JS, Webb, CP, Baer, W, Senagore, A, Schipper, MJ, Vonderscher, J, Sultana, S, Gerhold, DL, Phillips, JA, Maurer, G, Carl, K, Laurie, D, Harpur, E, Sonee, M, Ennulat, D, Holder, D, Andrews-Cleavenger, D, Gu, YZ, Thompson, KL, Goering, PL, Vidal, JM, Abadie, E, MacIulaitis, R, Jacobson-Kram, D, Defelice, AF, Hausner, EA, Blank, M, Thompson, A, Harlow, P, Throckmorton, D, Xiao, S, Xu, N, Taylor, W, Vamvakas, S, Flamion, B, Lima, BS, Kasper, P, Pasanen, M, Prasad, K, Troth, S, Bounous, D, Robinson-Gravatt, D, Betton, G, Davis, MA, Akunda, J, McDuffie, JE, Suter, L, Obert, L, Guffroy, M, Pinches, M, Jayadev, S, Blomme, EA, Beushausen, SA, Barlow, VG, Collins, N, Waring, J, Honor, D, Snook, S, Lee, J, Rossi, P, Walker, E & Mattes, W 2010, 'Renal biomarker qualification submission: A dialog between the FDA-EMEA and Predictive Safety Testing Consortium', Nature Biotechnology, vol. 28, no. 5, pp. 455-462. https://doi.org/10.1038/nbt.1625

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abstract = "Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis and human, demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.",

author = "Frank Dieterle and Frank Sistare and Federico Goodsaid and Marisa Papaluca and Ozer, {Josef S.} and Webb, {Craig P.} and William Baer and Anthony Senagore and Schipper, {Matthew J.} and Jacky Vonderscher and Stefan Sultana and Gerhold, {David L.} and Phillips, {Jonathan A.} and G{\'e}rard Maurer and Kevin Carl and David Laurie and Ernie Harpur and Manisha Sonee and Daniela Ennulat and Dan Holder and Dina Andrews-Cleavenger and Gu, {Yi Zhong} and Thompson, {Karol L.} and Goering, {Peter L.} and Vidal, {Jean Marc} and Eric Abadie and Romaldas MacIulaitis and David Jacobson-Kram and Defelice, {Albert F.} and Hausner, {Elizabeth A.} and Melanie Blank and Aliza Thompson and Patricia Harlow and Douglas Throckmorton and Shen Xiao and Nancy Xu and William Taylor and Spiros Vamvakas and Bruno Flamion and Lima, {Beatriz Silva} and Peter Kasper and Markku Pasanen and Krishna Prasad and Sean Troth and Denise Bounous and Denise Robinson-Gravatt and Graham Betton and Davis, {Myrtle A.} and Jackie Akunda and McDuffie, {James Eric} and Laura Suter and Leslie Obert and Magalie Guffroy and Mark Pinches and Supriya Jayadev and Blomme, {Eric A.} and Beushausen, {Sven A.} and Barlow, {Val{\'e}rie G.} and Nathaniel Collins and Jeff Waring and David Honor and Sandra Snook and Jinhe Lee and Phil Rossi and Elizabeth Walker and William Mattes",

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AU - Papaluca, Marisa

AU - Ozer, Josef S.

AU - Webb, Craig P.

AU - Baer, William

AU - Senagore, Anthony

AU - Schipper, Matthew J.

AU - Vonderscher, Jacky

AU - Sultana, Stefan

AU - Gerhold, David L.

AU - Phillips, Jonathan A.

AU - Maurer, Gérard

AU - Carl, Kevin

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AU - Gu, Yi Zhong

AU - Thompson, Karol L.

AU - Goering, Peter L.

AU - Vidal, Jean Marc

AU - Abadie, Eric

AU - MacIulaitis, Romaldas

AU - Jacobson-Kram, David

AU - Defelice, Albert F.

AU - Hausner, Elizabeth A.

AU - Blank, Melanie

AU - Thompson, Aliza

AU - Harlow, Patricia

AU - Throckmorton, Douglas

AU - Xiao, Shen

AU - Xu, Nancy

AU - Taylor, William

AU - Vamvakas, Spiros

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AU - Honor, David

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Renal biomarker qualification submission: A dialog between the FDA-EMEA and Predictive Safety Testing Consortium

Abstract

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