Literature DB >> 25498789

Integrating phenotypic small-molecule profiling and human genetics: the next phase in drug discovery.

Cory M Johannessen1, Paul A Clemons2, Bridget K Wagner3.   

Abstract

Over the past decade, tremendous progress in high-throughput small molecule-screening methods has facilitated the rapid expansion of phenotype-based data. Parallel advances in genomic characterization methods have complemented these efforts by providing a growing list of annotated cell line features. Together, these developments have paved the way for feature-based identification of novel, exploitable cellular dependencies, subsequently expanding our therapeutic toolkit in cancer and other diseases. Here, we provide an overview of the evolution of phenotypic small-molecule profiling and discuss the most significant and recent profiling and analytical efforts, their impact on the field, and their clinical ramifications. We additionally provide a perspective for future developments in phenotypic profiling efforts guided by genomic science.
Copyright © 2014 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  cell line profiling; genotype–phenotype; small molecule

Mesh:

Substances:

Year:  2014        PMID: 25498789      PMCID: PMC4281276          DOI: 10.1016/j.tig.2014.11.002

Source DB:  PubMed          Journal:  Trends Genet        ISSN: 0168-9525            Impact factor:   11.639


  77 in total

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2.  Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis.

Authors:  Jason W Locasale; Alexandra R Grassian; Tamar Melman; Costas A Lyssiotis; Katherine R Mattaini; Adam J Bass; Gregory Heffron; Christian M Metallo; Taru Muranen; Hadar Sharfi; Atsuo T Sasaki; Dimitrios Anastasiou; Edouard Mullarky; Natalie I Vokes; Mika Sasaki; Rameen Beroukhim; Gregory Stephanopoulos; Azra H Ligon; Matthew Meyerson; Andrea L Richardson; Lynda Chin; Gerhard Wagner; John M Asara; Joan S Brugge; Lewis C Cantley; Matthew G Vander Heiden
Journal:  Nat Genet       Date:  2011-07-31       Impact factor: 38.330

3.  Potent inhibition of DOT1L as treatment of MLL-fusion leukemia.

Authors:  Scott R Daigle; Edward J Olhava; Carly A Therkelsen; Aravind Basavapathruni; Lei Jin; P Ann Boriack-Sjodin; Christina J Allain; Christine R Klaus; Alejandra Raimondi; Margaret Porter Scott; Nigel J Waters; Richard Chesworth; Mikel P Moyer; Robert A Copeland; Victoria M Richon; Roy M Pollock
Journal:  Blood       Date:  2013-06-25       Impact factor: 22.113

4.  Perturbational profiling of a cell-line model of tumorigenesis by using metabolic measurements.

Authors:  Arvind Ramanathan; Connie Wang; Stuart L Schreiber
Journal:  Proc Natl Acad Sci U S A       Date:  2005-04-19       Impact factor: 11.205

5.  Automated Structure-Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles.

Authors:  Mathias J Wawer; David E Jaramillo; Vlado Dančík; Daniel M Fass; Stephen J Haggarty; Alykhan F Shamji; Bridget K Wagner; Stuart L Schreiber; Paul A Clemons
Journal:  J Biomol Screen       Date:  2014-04-07

6.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

7.  Identification of novel antimitotic agents acting at the tubulin level by computer-assisted evaluation of differential cytotoxicity data.

Authors:  K D Paull; C M Lin; L Malspeis; E Hamel
Journal:  Cancer Res       Date:  1992-07-15       Impact factor: 12.701

8.  C-RAF mutations confer resistance to RAF inhibitors.

Authors:  Rajee Antony; Caroline M Emery; Allison M Sawyer; Levi A Garraway
Journal:  Cancer Res       Date:  2013-06-04       Impact factor: 12.701

9.  Multiplex cytological profiling assay to measure diverse cellular states.

Authors:  Sigrun M Gustafsdottir; Vebjorn Ljosa; Katherine L Sokolnicki; J Anthony Wilson; Deepika Walpita; Melissa M Kemp; Kathleen Petri Seiler; Hyman A Carrel; Todd R Golub; Stuart L Schreiber; Paul A Clemons; Anne E Carpenter; Alykhan F Shamji
Journal:  PLoS One       Date:  2013-12-02       Impact factor: 3.240

10.  Importance of collection in gene set enrichment analysis of drug response in cancer cell lines.

Authors:  Alain R Bateman; Nehme El-Hachem; Andrew H Beck; Hugo J W L Aerts; Benjamin Haibe-Kains
Journal:  Sci Rep       Date:  2014-02-13       Impact factor: 4.379

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  6 in total

Review 1.  High content analysis in amyotrophic lateral sclerosis.

Authors:  Federica Rinaldi; Dario Motti; Laura Ferraiuolo; Brian K Kaspar
Journal:  Mol Cell Neurosci       Date:  2016-12-11       Impact factor: 4.314

2.  Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes.

Authors:  Mark-Anthony Bray; Shantanu Singh; Han Han; Chadwick T Davis; Blake Borgeson; Cathy Hartland; Maria Kost-Alimova; Sigrun M Gustafsdottir; Christopher C Gibson; Anne E Carpenter
Journal:  Nat Protoc       Date:  2016-08-25       Impact factor: 13.491

Review 3.  Accelerating glioblastoma drug discovery: Convergence of patient-derived models, genome editing and phenotypic screening.

Authors:  Eoghan O'Duibhir; Neil O Carragher; Steven M Pollard
Journal:  Mol Cell Neurosci       Date:  2016-11-04       Impact factor: 4.314

Review 4.  Mechanisms of Action for Small Molecules Revealed by Structural Biology in Drug Discovery.

Authors:  Qingxin Li; CongBao Kang
Journal:  Int J Mol Sci       Date:  2020-07-24       Impact factor: 5.923

5.  Early Pharmacological Profiling of Antiproliferative Compounds by Live Cell Imaging.

Authors:  Adrián Puerta; Aday González-Bakker; Guido Santos; José M Padrón
Journal:  Molecules       Date:  2022-08-17       Impact factor: 4.927

6.  Image-based compound profiling reveals a dual inhibitor of tyrosine kinase and microtubule polymerization.

Authors:  Kenji Tanabe
Journal:  Sci Rep       Date:  2016-04-27       Impact factor: 4.379

  6 in total

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