Publications by authors named "Keith Robison"

14 Publications

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Adventure of the CRISPR Coronavirus Disease 2019 Diagnostic.

Authors:
Keith Robison

CRISPR J 2020 06;3(3):138-139

Ginkgo Bioworks, Inc., Boston, Massachusetts, USA.

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http://dx.doi.org/10.1089/crispr.2020.29093.kroDOI Listing
June 2020

Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface.

Proc Natl Acad Sci U S A 2020 07 30;117(29):17195-17203. Epub 2020 Jun 30.

Warp Drive Bio, Inc., Redwood City, CA 94063;

The vast majority of intracellular protein targets are refractory toward small-molecule therapeutic engagement, and additional therapeutic modalities are needed to overcome this deficiency. Here, the identification and characterization of a natural product, WDB002, reveals a therapeutic modality that dramatically expands the currently accepted limits of druggability. WDB002, in complex with the FK506-binding protein (FKBP12), potently and selectively binds the human centrosomal protein 250 (CEP250), resulting in disruption of CEP250 function in cells. The recognition mode is unprecedented in that the targeted domain of CEP250 is a coiled coil and is topologically featureless, embodying both a structural motif and surface topology previously considered on the extreme limits of "undruggability" for an intracellular target. Structural studies reveal extensive protein-WDB002 and protein-protein contacts, with the latter being distinct from those seen in FKBP12 ternary complexes formed by FK506 and rapamycin. Outward-facing structural changes in a bound small molecule can thus reprogram FKBP12 to engage diverse, otherwise "undruggable" targets. The flat-targeting modality demonstrated here has the potential to expand the druggable target range of small-molecule therapeutics. As CEP250 was recently found to be an interaction partner with the Nsp13 protein of the SARS-CoV-2 virus that causes COVID-19 disease, it is possible that WDB002 or an analog may exert useful antiviral activity through its ability to form high-affinity ternary complexes containing CEP250 and FKBP12.
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http://dx.doi.org/10.1073/pnas.2006560117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7382241PMC
July 2020

Critical features for biosynthesis, stability, and functionality of a G protein-coupled receptor uncovered by all-versus-all mutations.

Proc Natl Acad Sci U S A 2012 Jun 4;109(25):9810-5. Epub 2012 Jun 4.

Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland.

The structural features determining efficient biosynthesis, stability in the membrane and, after solubilization, in detergents are not well understood for integral membrane proteins such as G protein-coupled receptors (GPCRs). Starting from the rat neurotensin receptor 1, a class A GPCR, we generated a separate library comprising all 64 codons for each amino acid position. By combining a previously developed FACS-based selection system for functional expression [Sarkar C, et al. (2009) Proc Natl Acad Sci USA 105:14808-14813] with ultradeep 454 sequencing, we determined the amino acid preference in every position and identified several positions in the natural sequence that restrict functional expression. A strong accumulation of shifts, i.e., a residue preference different from wild type, is detected for helix 1, suggesting a key role in receptor biosynthesis. Furthermore, under selective pressure we observe a shift of the most conserved residues of the N-terminal helices. This unique data set allows us to compare the in vitro evolution of a GPCR to the natural evolution of the GPCR family and to observe how selective pressure shapes the sequence space covered by functional molecules. Under the applied selective pressure, several positions shift away from the wild-type sequence, and these improve the biophysical properties. We discuss possible structural reasons for conserved and shifted residues.
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http://dx.doi.org/10.1073/pnas.1202107109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3382542PMC
June 2012

Hedgehog pathway inhibitor saridegib (IPI-926) increases lifespan in a mouse medulloblastoma model.

Proc Natl Acad Sci U S A 2012 May 1;109(20):7859-64. Epub 2012 May 1.

Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

The Sonic Hedgehog (Shh) pathway drives a subset of medulloblastomas, a malignant neuroectodermal brain cancer, and other cancers. Small-molecule Shh pathway inhibitors have induced tumor regression in mice and patients with medulloblastoma; however, drug resistance rapidly emerges, in some cases via de novo mutation of the drug target. Here we assess the response and resistance mechanisms to the natural product derivative saridegib in an aggressive Shh-driven mouse medulloblastoma model. In this model, saridegib treatment induced tumor reduction and significantly prolonged survival. Furthermore, the effect of saridegib on tumor-initiating capacity was demonstrated by reduced tumor incidence, slower growth, and spontaneous tumor regression that occurred in allografts generated from previously treated autochthonous medulloblastomas compared with those from untreated donors. Saridegib, a known P-glycoprotein (Pgp) substrate, induced Pgp activity in treated tumors, which likely contributed to emergence of drug resistance. Unlike other Smoothened (Smo) inhibitors, the drug resistance was neither mutation-dependent nor Gli2 amplification-dependent, and saridegib was found to be active in cells with the D473H point mutation that rendered them resistant to another Smo inhibitor, GDC-0449. The fivefold increase in lifespan in mice treated with saridegib as a single agent compares favorably with both targeted and cytotoxic therapies. The absence of genetic mutations that confer resistance distinguishes saridegib from other Smo inhibitors.
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http://dx.doi.org/10.1073/pnas.1114718109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356655PMC
May 2012

Translating cancer 'omics' to improved outcomes.

Genome Res 2012 Feb;22(2):188-95

British Columbia Cancer Research Centre, Vancouver V5Z 1L3, Canada.

The genomics era has yielded great advances in the understanding of cancer biology. At the same time, the immense complexity of the cancer genome has been revealed, as well as a striking heterogeneity at the whole-genome (or omics) level that exists between even histologically similar tumors. The vast accrual and public availability of multi-omics databases with associated clinical annotation including tumor histology, patient response, and outcome are a rich resource that has the potential to lead to rapid translation of high-throughput omics to improved overall survival. We focus on the unique advantages of a multidimensional approach to genomic analysis in this new high-throughput omics age and discuss the implications of the changing cancer demographic to translational omics research.
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http://dx.doi.org/10.1101/gr.124354.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266027PMC
February 2012

The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis.

Nucleic Acids Res 2012 Jan 15;40(Database issue):D1313-7. Epub 2011 Nov 15.

School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR.

Recent advances in sequencing technology have created unprecedented opportunities for biological research. However, the increasing throughput of these technologies has created many challenges for data management and analysis. As the demand for sophisticated analyses increases, the development time of software and algorithms is outpacing the speed of traditional publication. As technologies continue to be developed, methods change rapidly, making publications less relevant for users. The SEQanswers wiki (SEQwiki) is a wiki database that is actively edited and updated by the members of the SEQanswers community (http://SEQanswers.com/). The wiki provides an extensive catalogue of tools, technologies and tutorials for high-throughput sequencing (HTS), including information about HTS service providers. It has been implemented in MediaWiki with the Semantic MediaWiki and Semantic Forms extensions to collect structured data, providing powerful navigation and reporting features. Within 2 years, the community has created pages for over 500 tools, with approximately 400 literature references and 600 web links. This collaborative effort has made SEQwiki the most comprehensive database of HTS tools anywhere on the web. The wiki includes task-focused mini-reviews of commonly used tools, and a growing collection of more than 100 HTS service providers. SEQwiki is available at: http://wiki.SEQanswers.com/.
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http://dx.doi.org/10.1093/nar/gkr1058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245082PMC
January 2012

Semiconductors charge into sequencing.

Authors:
Keith Robison

Nat Biotechnol 2011 Sep 8;29(9):805-7. Epub 2011 Sep 8.

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http://dx.doi.org/10.1038/nbt.1965DOI Listing
September 2011

Engineering enzyme specificity using computational design of a defined-sequence library.

Chem Biol 2010 Dec;17(12):1306-15

Codon Devices, Inc., 99 Erie Street, Cambridge, MA 02139, USA.

Engineered biosynthetic pathways have the potential to produce high-value molecules from inexpensive feedstocks, but a key limitation is engineering enzymes with high activity and specificity for new reactions. Here, we developed a method for combining structure-based computational protein design with library-based enzyme screening, in which inter-residue correlations favored by the design are encoded into a defined-sequence library. We validated this approach by engineering a glucose 6-oxidase enzyme for use in a proposed pathway to convert D-glucose into D-glucaric acid. The most active variant, identified after only one round of diversification and screening of only 10,000 wells, is approximately 400-fold more active on glucose than is the wild-type enzyme. We anticipate that this strategy will be broadly applicable to the discovery of new enzymes for engineered biological pathways.
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http://dx.doi.org/10.1016/j.chembiol.2010.10.012DOI Listing
December 2010

Editorial: Second-generation sequencing.

Authors:
Keith Robison

Brief Bioinform 2010 Sep;11(5):455-6

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http://dx.doi.org/10.1093/bib/bbq066DOI Listing
September 2010

Application of second-generation sequencing to cancer genomics.

Authors:
Keith Robison

Brief Bioinform 2010 Sep 28;11(5):524-34. Epub 2010 Apr 28.

Infinity Pharmaceuticals Inc., Cambridge, MA 02139, USA.

New generations of DNA sequencing technologies are enabling the systematic study of genetic derangement in cancers. Sequencing of cancer exomes or transcriptomes or even entire cancer genomes are now possible, though technical and economic challenges remain. Cancer samples are inherently heterogeneous and are often contaminated with normal DNA, placing additional demands on informatics tools for detecting genetic variation. However, even low coverage sequencing data can provide valuable information on genetic rearrangements, amplifications and losses in tumor genomes. Novel recurrent oncogenic mutations and fusion transcripts have been discovered with these technologies. In some sequenced cancer genomes, tens of thousands of genetic alterations have been discovered. While this enables the detailed dissection of mutation classes, it also presents a formidable informatics problem of sorting active 'driver' mutations from inactive 'passenger' mutations in order to prioritize these for further experimental characterization.
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http://dx.doi.org/10.1093/bib/bbq013DOI Listing
September 2010

Re-examination of chimp protein kinases suggests "novel architectures" are gene prediction artifacts.

Authors:
Keith Robison

BMC Genomics 2010 Jan 27;11:66. Epub 2010 Jan 27.

Background: Anamika et al recently published in this journal a sequence alignment analysis of protein kinases encoded by the chimpanzee genome in comparison to those in the human genome. From this analysis they concluded that several chimpanzee kinases have unusual domain arrangements.

Results: Re-examination of these kinases reveals claimed novel arrangements cannot withstand scrutiny; each is either not novel or represents over-analysis of weakly confident computer generated gene models. Additional sequence evidence available at the time of the paper's submission either directly contradict the gene models or suggest alternate gene models. These alternate models would minimize or eliminate the observed differences between human and chimp kinases.

Conclusion: None of the proposed novel chimpanzee kinase architectures are supported by experiment evidence. Guidelines to prevent such erroneous conclusions in similar papers are proposed.
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http://dx.doi.org/10.1186/1471-2164-11-66DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2823696PMC
January 2010

The completion of the Mammalian Gene Collection (MGC).

Authors:
Gary Temple Daniela S Gerhard Rebekah Rasooly Elise A Feingold Peter J Good Cristen Robinson Allison Mandich Jeffrey G Derge Jeanne Lewis Debonny Shoaf Francis S Collins Wonhee Jang Lukas Wagner Carolyn M Shenmen Leonie Misquitta Carl F Schaefer Kenneth H Buetow Tom I Bonner Linda Yankie Ming Ward Lon Phan Alex Astashyn Garth Brown Catherine Farrell Jennifer Hart Melissa Landrum Bonnie L Maidak Michael Murphy Terence Murphy Bhanu Rajput Lillian Riddick David Webb Janet Weber Wendy Wu Kim D Pruitt Donna Maglott Adam Siepel Brona Brejova Mark Diekhans Rachel Harte Robert Baertsch Jim Kent David Haussler Michael Brent Laura Langton Charles L G Comstock Michael Stevens Chaochun Wei Marijke J van Baren Kourosh Salehi-Ashtiani Ryan R Murray Lila Ghamsari Elizabeth Mello Chenwei Lin Christa Pennacchio Kirsten Schreiber Nicole Shapiro Amber Marsh Elizabeth Pardes Troy Moore Anita Lebeau Mike Muratet Blake Simmons David Kloske Stephanie Sieja James Hudson Praveen Sethupathy Michael Brownstein Narayan Bhat Joseph Lazar Howard Jacob Chris E Gruber Mark R Smith John McPherson Angela M Garcia Preethi H Gunaratne Jiaqian Wu Donna Muzny Richard A Gibbs Alice C Young Gerard G Bouffard Robert W Blakesley Jim Mullikin Eric D Green Mark C Dickson Alex C Rodriguez Jane Grimwood Jeremy Schmutz Richard M Myers Martin Hirst Thomas Zeng Kane Tse Michelle Moksa Merinda Deng Kevin Ma Diana Mah Johnson Pang Greg Taylor Eric Chuah Athena Deng Keith Fichter Anne Go Stephanie Lee Jing Wang Malachi Griffith Ryan Morin Richard A Moore Michael Mayo Sarah Munro Susan Wagner Steven J M Jones Robert A Holt Marco A Marra Sun Lu Shuwei Yang James Hartigan Marcus Graf Ralf Wagner Stanley Letovksy Jacqueline C Pulido Keith Robison Dominic Esposito James Hartley Vanessa E Wall Ralph F Hopkins Osamu Ohara Stefan Wiemann

Genome Res 2009 Dec 18;19(12):2324-33. Epub 2009 Sep 18.

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide.
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http://dx.doi.org/10.1101/gr.095976.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2792178PMC
December 2009

Correlation of serpin-protease expression by comparative analysis of real-time PCR profiling data.

Genomics 2006 Aug 18;88(2):173-84. Epub 2006 May 18.

Millennium Pharmaceuticals, Inc., 40 Landsdowne Street, Cambridge, MA 02139, USA.

Imbalanced protease activity has long been recognized in the progression of disease states such as cancer and inflammation. Serpins, the largest family of endogenous protease inhibitors, target a wide variety of serine and cysteine proteases and play a role in a number of physiological and pathological states. The expression profiles of 20 serpins and 105 serine and cysteine proteases were determined across a panel of normal and diseased human tissues. In general, expression of serpins was highly restricted in both normal and diseased tissues, suggesting defined physiological roles for these protease inhibitors. A high correlation in expression for a particular serpin-protease pair in healthy tissues was often predictive of a biological interaction. The most striking finding was the dramatic change observed in the regulation of expression between proteases and their cognate inhibitors in diseased tissues. The loss of regulated serpin-protease matched expression may underlie the imbalanced protease activity observed in pathological states.
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http://dx.doi.org/10.1016/j.ygeno.2006.03.017DOI Listing
August 2006

Edge-count probabilities for the identification of local protein communities and their organization.

Proteins 2006 Mar;62(3):800-18

Computational Sciences, Informatics, Millennium Pharmaceuticals Inc., Cambridge, Massachusetts 02139, USA.

We present a computational approach based on a local search strategy that discovers sets of proteins that preferentially interact with each other. Such sets are referred to as protein communities and are likely to represent functional modules. Preferential interaction between module members is quantified via an analytical framework based on a network null model known as the random graph with given expected degrees. Based on this framework, the concept of local protein community is generalized to that of community of communities. Protein communities and higher-level structures are extracted from two yeast protein interaction data sets and a network of published interactions between human proteins. The high level structures obtained with the human network correspond to broad biological concepts such as signal transduction, regulation of gene expression, and intercellular communication. Many of the obtained human communities are enriched, in a statistically significant way, for proteins having no clear orthologs in lower organisms. This indicates that the extracted modules are quite coherent in terms of function.
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http://dx.doi.org/10.1002/prot.20799DOI Listing
March 2006