A Gene Expression High-Throughput Screen (GE-HTS) for Coordinated Detection of Functionally Similar Effectors in Cancer
Genome-wide, loss-of-function screening can be used to identify novel vulnerabilities upon which specific tumor cells depend for survival. Functional Signature Ontology (FUSION) is a gene expression-based high-throughput screening (GE-HTS) method that allows researchers to identify functionally simi...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-10-01
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| Series: | Cancers |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2072-6694/12/11/3143 |
| _version_ | 1797549776950001664 |
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| author | Chaitra Rao Dianna H. Huisman Heidi M. Vieira Danielle E. Frodyma Beth K. Neilsen Binita Chakraborty Suzie K. Hight Michael A. White Kurt W. Fisher Robert E. Lewis |
| author_facet | Chaitra Rao Dianna H. Huisman Heidi M. Vieira Danielle E. Frodyma Beth K. Neilsen Binita Chakraborty Suzie K. Hight Michael A. White Kurt W. Fisher Robert E. Lewis |
| author_sort | Chaitra Rao |
| collection | DOAJ |
| description | Genome-wide, loss-of-function screening can be used to identify novel vulnerabilities upon which specific tumor cells depend for survival. Functional Signature Ontology (FUSION) is a gene expression-based high-throughput screening (GE-HTS) method that allows researchers to identify functionally similar proteins, small molecules, and microRNA mimics, revealing novel therapeutic targets. FUSION uses cell-based high-throughput screening and computational analysis to match gene expression signatures produced by natural products to those produced by small interfering RNA (siRNA) and synthetic microRNA libraries to identify putative protein targets and mechanisms of action (MoA) for several previously undescribed natural products. We have used FUSION to screen for functional analogues to Kinase suppressor of Ras 1 (KSR1), a scaffold protein downstream of Ras in the Raf-MEK-ERK kinase cascade, and biologically validated several proteins with functional similarity to KSR1. FUSION incorporates bioinformatics analysis that may offer higher resolution of the endpoint readout than other screens which utilize Boolean outputs regarding a single pathway activation (i.e., synthetic lethal and cell proliferation). Challenges associated with FUSION and other high-content genome-wide screens include variation, batch effects, and controlling for potential off-target effects. In this review, we discuss the efficacy of FUSION to identify novel inhibitors and oncogene-induced changes that may be cancer cell-specific as well as several potential pitfalls within FUSION and best practices to avoid them. |
| first_indexed | 2024-03-10T15:19:16Z |
| format | Article |
| id | doaj.art-eeb7c3c2153f4bf692228d9922603001 |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-10T15:19:16Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-eeb7c3c2153f4bf692228d99226030012023-11-20T18:40:05ZengMDPI AGCancers2072-66942020-10-011211314310.3390/cancers12113143A Gene Expression High-Throughput Screen (GE-HTS) for Coordinated Detection of Functionally Similar Effectors in CancerChaitra Rao0Dianna H. Huisman1Heidi M. Vieira2Danielle E. Frodyma3Beth K. Neilsen4Binita Chakraborty5Suzie K. Hight6Michael A. White7Kurt W. Fisher8Robert E. Lewis9Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USAEppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USAEppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USAEppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USAEppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USAPharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USAMoores Cancer Center, University of California San Diego, La Jolla, CA 92037, USAChief Scientific Officer, Samumed, LLC, San Diego, CA 92121, USADepartment of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USAEppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USAGenome-wide, loss-of-function screening can be used to identify novel vulnerabilities upon which specific tumor cells depend for survival. Functional Signature Ontology (FUSION) is a gene expression-based high-throughput screening (GE-HTS) method that allows researchers to identify functionally similar proteins, small molecules, and microRNA mimics, revealing novel therapeutic targets. FUSION uses cell-based high-throughput screening and computational analysis to match gene expression signatures produced by natural products to those produced by small interfering RNA (siRNA) and synthetic microRNA libraries to identify putative protein targets and mechanisms of action (MoA) for several previously undescribed natural products. We have used FUSION to screen for functional analogues to Kinase suppressor of Ras 1 (KSR1), a scaffold protein downstream of Ras in the Raf-MEK-ERK kinase cascade, and biologically validated several proteins with functional similarity to KSR1. FUSION incorporates bioinformatics analysis that may offer higher resolution of the endpoint readout than other screens which utilize Boolean outputs regarding a single pathway activation (i.e., synthetic lethal and cell proliferation). Challenges associated with FUSION and other high-content genome-wide screens include variation, batch effects, and controlling for potential off-target effects. In this review, we discuss the efficacy of FUSION to identify novel inhibitors and oncogene-induced changes that may be cancer cell-specific as well as several potential pitfalls within FUSION and best practices to avoid them.https://www.mdpi.com/2072-6694/12/11/3143high-throughput screensfunctional signature ontologycancer susceptibility genesRas-driven cancer |
| spellingShingle | Chaitra Rao Dianna H. Huisman Heidi M. Vieira Danielle E. Frodyma Beth K. Neilsen Binita Chakraborty Suzie K. Hight Michael A. White Kurt W. Fisher Robert E. Lewis A Gene Expression High-Throughput Screen (GE-HTS) for Coordinated Detection of Functionally Similar Effectors in Cancer Cancers high-throughput screens functional signature ontology cancer susceptibility genes Ras-driven cancer |
| title | A Gene Expression High-Throughput Screen (GE-HTS) for Coordinated Detection of Functionally Similar Effectors in Cancer |
| title_full | A Gene Expression High-Throughput Screen (GE-HTS) for Coordinated Detection of Functionally Similar Effectors in Cancer |
| title_fullStr | A Gene Expression High-Throughput Screen (GE-HTS) for Coordinated Detection of Functionally Similar Effectors in Cancer |
| title_full_unstemmed | A Gene Expression High-Throughput Screen (GE-HTS) for Coordinated Detection of Functionally Similar Effectors in Cancer |
| title_short | A Gene Expression High-Throughput Screen (GE-HTS) for Coordinated Detection of Functionally Similar Effectors in Cancer |
| title_sort | gene expression high throughput screen ge hts for coordinated detection of functionally similar effectors in cancer |
| topic | high-throughput screens functional signature ontology cancer susceptibility genes Ras-driven cancer |
| url | https://www.mdpi.com/2072-6694/12/11/3143 |
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