GenomeRNAi - a database for RNAi phenotypes and reagents

Phenotype information for gene 6514 (SLC2A2)

Screen TitleGene IDGene SymbolReagent IDScorePhenotypeComment
hepcidin regulation
NM_000340
SLC2A2
np
2.24
Increased hepcidin::fluc mRNA expression

Reference

Unbiased RNAi screen for hepcidin regulators links hepcidin suppression to proliferative Ras/RAF and nutrient-dependent mTOR signaling. Mleczko-Sanecka et al., 2014

The hepatic hormone hepcidin is a key regulator of systemic iron metabolism. Its expression is largely regulated by 2 signaling pathways: the "iron-regulated" bone morphogenetic protein (BMP) and the inflammatory JAK-STAT pathways. To obtain broader insights into cellular processes that modulate hepcidin transcription and to provide a resource to identify novel genetic modifiers of systemic iron homeostasis, we designed an RNA interference (RNAi) screen that monitors hepcidin promoter activity after the knockdown of 19 599 genes in hepatocarcinoma cells. Interestingly, many of the putative hepcidin activators play roles in signal transduction, inflammation, or transcription, and affect hepcidin transcription through BMP-responsive elements. Furthermore, our work sheds light on new components of the transcriptional machinery that maintain steady-state levels of hepcidin expression and its responses to the BMP- and interleukin-6-triggered signals. Notably, we discover hepcidin suppression mediated via components of Ras/RAF MAPK and mTOR signaling, linking hepcidin transcriptional control to the pathways that respond to mitogen stimulation and nutrient status. Thus using a combination of RNAi screening, reverse phase protein arrays, and small molecules testing, we identify links between the control of systemic iron homeostasis and critical liver processes such as regeneration, response to injury, carcinogenesis, and nutrient metabolism.

Screen Details

Stable ID: GR00253-A
Screen Title: hepcidin regulation
Assay: hepcidin::fluc mRNA expression
Method: Luminescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: Huh7
Library: ThermoFisher, siGenome siARRAY SMARTpool
Reagent Type: siRNA
Score Type: Z-score
Cutoff: >= 1.755 OR <= -1.389
Notes: Cutoff <= -1.389 defined based on hepcidin promotor activity. Additional information about secondary siRNA screens.

Cell viability
SLC2A2
np
10
Decreased viability

Reference

Highly parallel identification of essential genes in cancer cells. Luo et al., 2008

More complete knowledge of the molecular mechanisms underlying cancer will improve prevention, diagnosis and treatment. Efforts such as The Cancer Genome Atlas are systematically characterizing the structural basis of cancer, by identifying the genomic mutations associated with each cancer type. A powerful complementary approach is to systematically characterize the functional basis of cancer, by identifying the genes essential for growth and related phenotypes in different cancer cells. Such information would be particularly valuable for identifying potential drug targets. Here, we report the development of an efficient, robust approach to perform genome-scale pooled shRNA screens for both positive and negative selection and its application to systematically identify cell essential genes in 12 cancer cell lines. By integrating these functional data with comprehensive genetic analyses of primary human tumors, we identified known and putative oncogenes such as EGFR, KRAS, MYC, BCR-ABL, MYB, CRKL, and CDK4 that are essential for cancer cell proliferation and also altered in human cancers. We further used this approach to identify genes involved in the response of cancer cells to tumoricidal agents and found 4 genes required for the response of CML cells to imatinib treatment: PTPN1, NF1, SMARCB1, and SMARCE1, and 5 regulators of the response to FAS activation, FAS, FADD, CASP8, ARID1A and CBX1. Broad application of this highly parallel genetic screening strategy will not only facilitate the rapid identification of genes that drive the malignant state and its response to therapeutics but will also enable the discovery of genes that participate in any biological process.

Screen Details

Stable ID: GR00106-A-0
Screen Title: Cell viability
Assay: Cell viability
Method: Micoarray hybridization
Scope:
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: 12 cancer cell lines
Library: , TRC shRNA library
Reagent Type: shRNA
Score Type: Essentiality
Cutoff: >= 8/12 cancer cell lines
Notes:

Influenza A virus infection (2)
6514
SLC2A2
0.58
none

Reference

The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Brass et al., 2009

Influenza viruses exploit host cell machinery to replicate, resulting in epidemics of respiratory illness. In turn, the host expresses antiviral restriction factors to defend against infection. To find host cell modifiers of influenza A H1N1 viral infection, we used a functional genomic screen and identified over 120 influenza A virus-dependency factors with roles in endosomal acidification, vesicular trafficking, mitochondrial metabolism, and RNA splicing. We discovered that the interferon-inducible transmembrane proteins IFITM1, 2, and 3 restrict an early step in influenza A viral replication. The IFITM proteins confer basal resistance to influenza A virus but are also inducible by interferons type I and II and are critical for interferon''s virustatic actions. Further characterization revealed that the IFITM proteins inhibit the early replication of flaviviruses, including dengue virus and West Nile virus. Collectively this work identifies a family of antiviral restriction factors that mediate cellular innate immunity to at least three major human pathogens.

Screen Details

Stable ID: GR00147-A-2
Screen Title: Influenza A virus infection (2)
Assay: rp
Method: rp
Scope: Selected genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: rp
Biomodel: rp
Library: rp, rp
Reagent Type: siRNA
Score Type: Percentage of infected cells
Cutoff: Complex criteria
Notes:

Influenza A virus infection (2)
6514
SLC2A2
0.58
none

Reference

The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Brass et al., 2009

Influenza viruses exploit host cell machinery to replicate, resulting in epidemics of respiratory illness. In turn, the host expresses antiviral restriction factors to defend against infection. To find host cell modifiers of influenza A H1N1 viral infection, we used a functional genomic screen and identified over 120 influenza A virus-dependency factors with roles in endosomal acidification, vesicular trafficking, mitochondrial metabolism, and RNA splicing. We discovered that the interferon-inducible transmembrane proteins IFITM1, 2, and 3 restrict an early step in influenza A viral replication. The IFITM proteins confer basal resistance to influenza A virus but are also inducible by interferons type I and II and are critical for interferon''s virustatic actions. Further characterization revealed that the IFITM proteins inhibit the early replication of flaviviruses, including dengue virus and West Nile virus. Collectively this work identifies a family of antiviral restriction factors that mediate cellular innate immunity to at least three major human pathogens.

Screen Details

Stable ID: GR00147-A-2
Screen Title: Influenza A virus infection (2)
Assay: rp
Method: rp
Scope: Selected genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: rp
Biomodel: rp
Library: rp, rp
Reagent Type: siRNA
Score Type: Percentage of infected cells
Cutoff: Complex criteria
Notes:

Influenza A virus infection (1)
6514
SLC2A2
np
np
Decreased influenza A virus infection

Reference

The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Brass et al., 2009

Influenza viruses exploit host cell machinery to replicate, resulting in epidemics of respiratory illness. In turn, the host expresses antiviral restriction factors to defend against infection. To find host cell modifiers of influenza A H1N1 viral infection, we used a functional genomic screen and identified over 120 influenza A virus-dependency factors with roles in endosomal acidification, vesicular trafficking, mitochondrial metabolism, and RNA splicing. We discovered that the interferon-inducible transmembrane proteins IFITM1, 2, and 3 restrict an early step in influenza A viral replication. The IFITM proteins confer basal resistance to influenza A virus but are also inducible by interferons type I and II and are critical for interferon''s virustatic actions. Further characterization revealed that the IFITM proteins inhibit the early replication of flaviviruses, including dengue virus and West Nile virus. Collectively this work identifies a family of antiviral restriction factors that mediate cellular innate immunity to at least three major human pathogens.

Screen Details

Stable ID: GR00147-A-1
Screen Title: Influenza A virus infection (1)
Assay: Viral hemagglutinin protein surface expression
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: U2OS
Library: Dharmacon, siARRAY siRNA Library
Reagent Type: siRNA
Score Type: Percentage of viral hemagglutinin positive cells
Cutoff: Complex criteria
Notes:

Regulation of FOXO1 nuclear localization (1)
SLC2A2
np
sp
none rank: 4018

Reference

Whole genome siRNA cell-based screen links mitochondria to Akt signaling network through uncoupling of electron transport chain. Senapedis et al., 2011

Forkhead transcription factors (FOXOs) alter a diverse array of cellular processes including the cell cycle, oxidative stress resistance, and aging. Insulin/Akt activation directs phosphorylation and cytoplasmic sequestration of FOXO away from its target genes and serves as an endpoint of a complex signaling network. Using a human genome small interfering RNA (siRNA) library in a cell-based assay, we identified an extensive network of proteins involved in nuclear export, focal adhesion, and mitochondrial respiration not previously implicated in FOXO localization. Furthermore, a detailed examination of mitochondrial factors revealed that loss of uncoupling protein 5 (UCP5) modifies the energy balance and increases free radicals through up-regulation of uncoupling protein 3 (UCP3). The increased superoxide content induces c-Jun N-terminal kinase 1 (JNK1) kinase activity, which in turn affects FOXO localization through a compensatory dephosphorylation of Akt. The resulting nuclear FOXO increases expression of target genes, including mitochondrial superoxide dismutase. By connecting free radical defense and mitochondrial uncoupling to Akt/FOXO signaling, these results have implications in obesity and type 2 diabetes development and the potential for therapeutic intervention.

Screen Details

Stable ID: GR00247-A-1
Screen Title: Regulation of FOXO1 nuclear localization (1)
Assay: EGFP-FOXO1a protein expression and DNA content
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: U2OS
Library: Dharmacon, Human Genome library
Reagent Type: siRNA
Score Type: Complex, sp
Cutoff: Complex criteria
Notes:

Influenza A virus infection (2)
6514
SLC2A2
0.44
Decreased influenza A virus infection

Reference

The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Brass et al., 2009

Influenza viruses exploit host cell machinery to replicate, resulting in epidemics of respiratory illness. In turn, the host expresses antiviral restriction factors to defend against infection. To find host cell modifiers of influenza A H1N1 viral infection, we used a functional genomic screen and identified over 120 influenza A virus-dependency factors with roles in endosomal acidification, vesicular trafficking, mitochondrial metabolism, and RNA splicing. We discovered that the interferon-inducible transmembrane proteins IFITM1, 2, and 3 restrict an early step in influenza A viral replication. The IFITM proteins confer basal resistance to influenza A virus but are also inducible by interferons type I and II and are critical for interferon''s virustatic actions. Further characterization revealed that the IFITM proteins inhibit the early replication of flaviviruses, including dengue virus and West Nile virus. Collectively this work identifies a family of antiviral restriction factors that mediate cellular innate immunity to at least three major human pathogens.

Screen Details

Stable ID: GR00147-A-2
Screen Title: Influenza A virus infection (2)
Assay: rp
Method: rp
Scope: Selected genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: rp
Biomodel: rp
Library: rp, rp
Reagent Type: siRNA
Score Type: Percentage of infected cells
Cutoff: Complex criteria
Notes:

Hepatitis C virus replication (1)
6514
SLC2A2
PL-50019
0.92
none

Reference

A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Tai et al., 2009

Hepatitis C virus (HCV) chronically infects 3% of the world''s population, and complications from HCV are the leading indication for liver transplantation. Given the need for better anti-HCV therapies, one strategy is to identify and target cellular cofactors of the virus lifecycle. Using a genome-wide siRNA library, we identified 96 human genes that support HCV replication, with a significant number of them being involved in vesicle organization and biogenesis. Phosphatidylinositol 4-kinase PI4KA and multiple subunits of the COPI vesicle coat complex were among the genes identified. Consistent with this, pharmacologic inhibitors of COPI and PI4KA blocked HCV replication. Targeting hepcidin, a peptide critical for iron homeostasis, also affected HCV replication, which may explain the known dysregulation of iron homeostasis in HCV infection. The host cofactors for HCV replication identified in this study should serve as a useful resource in delineating new targets for anti-HCV therapies.

Screen Details

Stable ID: GR00180-A-1
Screen Title: Hepatitis C virus replication (1)
Assay: HCV replicon RNA copy number
Method: Luminescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: Huh7/Rep-Feo
Library: Dharmacon, siARRAY Human Genome siRNA Library
Reagent Type: siRNA
Score Type: q-value
Cutoff: Complex criteria
Notes:

Genome stability
NM_000340
SLC2A2
np
sp
none

Reference

A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability. Paulsen et al., 2009

Signaling pathways that respond to DNA damage are essential for the maintenance of genome stability and are linked to many diseases, including cancer. Here, a genome-wide siRNA screen was employed to identify additional genes involved in genome stabilization by monitoring phosphorylation of the histone variant H2AX, an early mark of DNA damage. We identified hundreds of genes whose downregulation led to elevated levels of H2AX phosphorylation (gammaH2AX) and revealed links to cellular complexes and to genes with unclassified functions. We demonstrate a widespread role for mRNA-processing factors in preventing DNA damage, which in some cases is caused by aberrant RNA-DNA structures. Furthermore, we connect increased gammaH2AX levels to the neurological disorder Charcot-Marie-Tooth (CMT) syndrome, and we find a role for several CMT proteins in the DNA-damage response. These data indicate that preservation of genome stability is mediated by a larger network of biological processes than previously appreciated.

Screen Details

Stable ID: GR00053-A
Screen Title: Genome stability
Assay: gamma-H2AX phosphorylation and DNA content
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: ThermoFisher Scientific, siARRAY human genome siRNA library
Reagent Type: siRNA
Score Type: p-value
Cutoff: Complex criteria
Notes: Confidence groupings from 4 to 1 (highest level of confidence in group 4)

Influenza A virus infection (2)
6514
SLC2A2
0.41
Decreased influenza A virus infection

Reference

The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Brass et al., 2009

Influenza viruses exploit host cell machinery to replicate, resulting in epidemics of respiratory illness. In turn, the host expresses antiviral restriction factors to defend against infection. To find host cell modifiers of influenza A H1N1 viral infection, we used a functional genomic screen and identified over 120 influenza A virus-dependency factors with roles in endosomal acidification, vesicular trafficking, mitochondrial metabolism, and RNA splicing. We discovered that the interferon-inducible transmembrane proteins IFITM1, 2, and 3 restrict an early step in influenza A viral replication. The IFITM proteins confer basal resistance to influenza A virus but are also inducible by interferons type I and II and are critical for interferon''s virustatic actions. Further characterization revealed that the IFITM proteins inhibit the early replication of flaviviruses, including dengue virus and West Nile virus. Collectively this work identifies a family of antiviral restriction factors that mediate cellular innate immunity to at least three major human pathogens.

Screen Details

Stable ID: GR00147-A-2
Screen Title: Influenza A virus infection (2)
Assay: rp
Method: rp
Scope: Selected genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: rp
Biomodel: rp
Library: rp, rp
Reagent Type: siRNA
Score Type: Percentage of infected cells
Cutoff: Complex criteria
Notes:

Negative genetic interactions (1)
6514
SLC2A2
0.15
none

Reference

A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Vizeacoumar et al., 2013

Improved efforts are necessary to define the functional product of cancer mutations currently being revealed through large-scale sequencing efforts. Using genome-scale pooled shRNA screening technology, we mapped negative genetic interactions across a set of isogenic cancer cell lines and confirmed hundreds of these interactions in orthogonal co-culture competition assays to generate a high-confidence genetic interaction network of differentially essential or differential essentiality (DiE) genes. The network uncovered examples of conserved genetic interactions, densely connected functional modules derived from comparative genomics with model systems data, functions for uncharacterized genes in the human genome and targetable vulnerabilities. Finally, we demonstrate a general applicability of DiE gene signatures in determining genetic dependencies of other non-isogenic cancer cell lines. For example, the PTEN(-/-) DiE genes reveal a signature that can preferentially classify PTEN-dependent genotypes across a series of non-isogenic cell lines derived from the breast, pancreas and ovarian cancers. Our reference network suggests that many cancer vulnerabilities remain to be discovered through systematic derivation of a network of differentially essential genes in an isogenic cancer cell model.

Screen Details

Stable ID: GR00255-A-1
Screen Title: Negative genetic interactions (1)
Assay: shRNA abundance
Method: Microarray
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HCT116
Library: TRC lentiviral library, np
Reagent Type: shRNA
Score Type: differential Gene Activity Ranking Profile (dGARP)
Cutoff: < -1.0
Notes: HCT116 BLM-/- and HCT116 BLM+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells)

Selective autophagy regulation (1)
NM_000340
SLC2A2
np
sp
none

Reference

Image-based genome-wide siRNA screen identifies selective autophagy factors. Orvedahl et al., 2011

Selective autophagy involves the recognition and targeting of specific cargo, such as damaged organelles, misfolded proteins, or invading pathogens for lysosomal destruction. Yeast genetic screens have identified proteins required for different forms of selective autophagy, including cytoplasm-to-vacuole targeting, pexophagy and mitophagy, and mammalian genetic screens have identified proteins required for autophagy regulation. However, there have been no systematic approaches to identify molecular determinants of selective autophagy in mammalian cells. Here, to identify mammalian genes required for selective autophagy, we performed a high-content, image-based, genome-wide small interfering RNA screen to detect genes required for the colocalization of Sindbis virus capsid protein with autophagolysosomes. We identified 141 candidate genes required for viral autophagy, which were enriched for cellular pathways related to messenger RNA processing, interferon signalling, vesicle trafficking, cytoskeletal motor function and metabolism. Ninety-six of these genes were also required for Parkin-mediated mitophagy, indicating that common molecular determinants may be involved in autophagic targeting of viral nucleocapsids and autophagic targeting of damaged mitochondria. Murine embryonic fibroblasts lacking one of these gene products, the C2-domain containing protein, SMURF1, are deficient in the autophagosomal targeting of Sindbis and herpes simplex viruses and in the clearance of damaged mitochondria. Moreover, SMURF1-deficient mice accumulate damaged mitochondria in the heart, brain and liver. Thus, our study identifies candidate determinants of selective autophagy, and defines SMURF1 as a newly recognized mediator of both viral autophagy and mitophagy.

Screen Details

Stable ID: GR00242-A-1
Screen Title: Selective autophagy regulation (1)
Assay: Sindbis virus (SIN) capsid SIN-mCherry.capsid and autophagosome GFP–LC3 protein expression
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa/GFP-LC3
Library: Dharmacon, siGenome
Reagent Type: siRNA
Score Type: Z-score
Cutoff: Complex criteria
Notes:

Vaccinia virus (VACV) infection
6514
SLC2A2
J-007515-06
-1.56
Decreased vaccinia virus (VACV) infection number of cells compared to control (%): 59.17

Reference

Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. Sivan et al., 2013

Poxviruses are considered less dependent on host functions than other DNA viruses because of their cytoplasmic site of replication and large genomes, which encode enzymes for DNA and mRNA synthesis. Nevertheless, RNAi screens with two independent human genome-scale libraries have identified more than 500 candidate genes that significantly inhibited and a similar number that enhanced replication and spread of infectious vaccinia virus (VACV). Translational, ubiquitin-proteosome, and endoplasmic reticulum-to-Golgi transport functions, known to be important for VACV, were enriched in the siRNA-inhibiting group, and RNA polymerase II and associated functions were enriched in the siRNA-enhancing group. Additional findings, notably the inhibition of VACV spread by siRNAs to several nuclear pore genes, were unanticipated. Knockdown of nucleoporin 62 strongly inhibited viral morphogenesis, with only a modest effect on viral gene expression, recapitulating and providing insight into previous studies with enucleated cells.

Screen Details

Stable ID: GR00249-S
Screen Title: Vaccinia virus (VACV) infection
Assay: Vaccinia virus VACV IHD-J/GFP protein expression and DNA content
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: Ambion and Dharmacon, Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus
Reagent Type: siRNA
Score Type: Z-score
Cutoff: >= 1 OR <= -1.5
Notes: Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %.

Negative genetic interactions (4)
6514
SLC2A2
-0.7
none

Reference

A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Vizeacoumar et al., 2013

Improved efforts are necessary to define the functional product of cancer mutations currently being revealed through large-scale sequencing efforts. Using genome-scale pooled shRNA screening technology, we mapped negative genetic interactions across a set of isogenic cancer cell lines and confirmed hundreds of these interactions in orthogonal co-culture competition assays to generate a high-confidence genetic interaction network of differentially essential or differential essentiality (DiE) genes. The network uncovered examples of conserved genetic interactions, densely connected functional modules derived from comparative genomics with model systems data, functions for uncharacterized genes in the human genome and targetable vulnerabilities. Finally, we demonstrate a general applicability of DiE gene signatures in determining genetic dependencies of other non-isogenic cancer cell lines. For example, the PTEN(-/-) DiE genes reveal a signature that can preferentially classify PTEN-dependent genotypes across a series of non-isogenic cell lines derived from the breast, pancreas and ovarian cancers. Our reference network suggests that many cancer vulnerabilities remain to be discovered through systematic derivation of a network of differentially essential genes in an isogenic cancer cell model.

Screen Details

Stable ID: GR00255-A-4
Screen Title: Negative genetic interactions (4)
Assay: shRNA abundance
Method: Microarray
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HCT116
Library: TRC lentiviral library, np
Reagent Type: shRNA
Score Type: differential Gene Activity Ranking Profile (dGARP)
Cutoff: < -1.2
Notes: HCT116 PTTG1-/- and HCT116 PTTG1+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells)

Melanogenesis
NM_000340
SLC2A2
np
1.04
none

Reference

Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells. Ganesan et al., 2008

Melanin protects the skin and eyes from the harmful effects of UV irradiation, protects neural cells from toxic insults, and is required for sound conduction in the inner ear. Aberrant regulation of melanogenesis underlies skin disorders (melasma and vitiligo), neurologic disorders (Parkinson''s disease), auditory disorders (Waardenburg''s syndrome), and opthalmologic disorders (age related macular degeneration). Much of the core synthetic machinery driving melanin production has been identified; however, the spectrum of gene products participating in melanogenesis in different physiological niches is poorly understood. Functional genomics based on RNA-mediated interference (RNAi) provides the opportunity to derive unbiased comprehensive collections of pharmaceutically tractable single gene targets supporting melanin production. In this study, we have combined a high-throughput, cell-based, one-well/one-gene screening platform with a genome-wide arrayed synthetic library of chemically synthesized, small interfering RNAs to identify novel biological pathways that govern melanin biogenesis in human melanocytes. Ninety-two novel genes that support pigment production were identified with a low false discovery rate. Secondary validation and preliminary mechanistic studies identified a large panel of targets that converge on tyrosinase expression and stability. Small molecule inhibition of a family of gene products in this class was sufficient to impair chronic tyrosinase expression in pigmented melanoma cells and UV-induced tyrosinase expression in primary melanocytes. Isolation of molecular machinery known to support autophagosome biosynthesis from this screen, together with in vitro and in vivo validation, exposed a close functional relationship between melanogenesis and autophagy. In summary, these studies illustrate the power of RNAi-based functional genomics to identify novel genes, pathways, and pharmacologic agents that impact a biological phenotype and operate outside of preconceived mechanistic relationships.

Screen Details

Stable ID: GR00056-A
Screen Title: Melanogenesis
Assay: Melanin protein expression and viability
Method: Absorbance and luminescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: MNT-1
Library: Dharmacon, rp
Reagent Type: siRNA
Score Type: Normalized absorbance ratio
Cutoff: > 2 standard deviations below mean
Notes: Additional information about a secondary screen (retest to determine false-positive rate)

Vaccinia virus (VACV) infection
6514
SLC2A2
M-007515-02
-1.5
Decreased vaccinia virus (VACV) infection number of cells compared to control (%): 50.72

Reference

Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. Sivan et al., 2013

Poxviruses are considered less dependent on host functions than other DNA viruses because of their cytoplasmic site of replication and large genomes, which encode enzymes for DNA and mRNA synthesis. Nevertheless, RNAi screens with two independent human genome-scale libraries have identified more than 500 candidate genes that significantly inhibited and a similar number that enhanced replication and spread of infectious vaccinia virus (VACV). Translational, ubiquitin-proteosome, and endoplasmic reticulum-to-Golgi transport functions, known to be important for VACV, were enriched in the siRNA-inhibiting group, and RNA polymerase II and associated functions were enriched in the siRNA-enhancing group. Additional findings, notably the inhibition of VACV spread by siRNAs to several nuclear pore genes, were unanticipated. Knockdown of nucleoporin 62 strongly inhibited viral morphogenesis, with only a modest effect on viral gene expression, recapitulating and providing insight into previous studies with enucleated cells.

Screen Details

Stable ID: GR00249-S
Screen Title: Vaccinia virus (VACV) infection
Assay: Vaccinia virus VACV IHD-J/GFP protein expression and DNA content
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: Ambion and Dharmacon, Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus
Reagent Type: siRNA
Score Type: Z-score
Cutoff: >= 1 OR <= -1.5
Notes: Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %.

Vaccinia virus (VACV) infection
6514
SLC2A2
0.35
none number of cells compared to control (%): 86.63

Reference

Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. Sivan et al., 2013

Poxviruses are considered less dependent on host functions than other DNA viruses because of their cytoplasmic site of replication and large genomes, which encode enzymes for DNA and mRNA synthesis. Nevertheless, RNAi screens with two independent human genome-scale libraries have identified more than 500 candidate genes that significantly inhibited and a similar number that enhanced replication and spread of infectious vaccinia virus (VACV). Translational, ubiquitin-proteosome, and endoplasmic reticulum-to-Golgi transport functions, known to be important for VACV, were enriched in the siRNA-inhibiting group, and RNA polymerase II and associated functions were enriched in the siRNA-enhancing group. Additional findings, notably the inhibition of VACV spread by siRNAs to several nuclear pore genes, were unanticipated. Knockdown of nucleoporin 62 strongly inhibited viral morphogenesis, with only a modest effect on viral gene expression, recapitulating and providing insight into previous studies with enucleated cells.

Screen Details

Stable ID: GR00249-S
Screen Title: Vaccinia virus (VACV) infection
Assay: Vaccinia virus VACV IHD-J/GFP protein expression and DNA content
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: Ambion and Dharmacon, Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus
Reagent Type: siRNA
Score Type: Z-score
Cutoff: >= 1 OR <= -1.5
Notes: Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %.

Non-small cell lung cancer (NSCLC) cytotoxicity (2)
SLC2A2
np
-1
Decreased shRNA abundance

Reference

Proteasome inhibitors block DNA repair and radiosensitize non-small cell lung cancer. Cron et al., 2013

Despite optimal radiation therapy (RT), chemotherapy and/or surgery, a majority of patients with locally advanced non-small cell lung cancer (NSCLC) fail treatment. To identify novel gene targets for improved tumor control, we performed whole genome RNAi screens to identify knockdowns that most reproducibly increase NSCLC cytotoxicity. These screens identified several proteasome subunits among top hits, including the topmost hit PSMA1, a component of the core 20 S proteasome. Radiation and proteasome inhibition showed synergistic effects. Proteasome inhibition resulted in an 80-90% decrease in homologous recombination (HR), a 50% decrease in expression of NF-κB-inducible HR genes BRCA1 and FANCD2, and a reduction of BRCA1, FANCD2 and RAD51 ionizing radiation-induced foci. IκBα RNAi knockdown rescued NSCLC radioresistance. Irradiation of mice with NCI-H460 xenografts after inducible PSMA1 shRNA knockdown markedly increased murine survival compared to either treatment alone. Proteasome inhibition is a promising strategy for NSCLC radiosensitization via inhibition of NF-κB-mediated expression of Fanconi Anemia/HR DNA repair genes.

Screen Details

Stable ID: GR00251-A-2
Screen Title: Non-small cell lung cancer (NSCLC) cytotoxicity (2)
Assay: shRNA abundance
Method: Microarray
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: NCI-H460
Library: Hannon-Elledge whole genome pooled shRNA, np
Reagent Type: shRNA
Score Type: Complex, sp
Cutoff: Complex criteria
Notes: All listed genes are final hits. Final hit: >= 1 shRNA with >= 2-fold abundance decrease in both cell lines (A549 and NCI-H460)

Ciliogenesis and cilium length (1)
6514
SLC2A2
116829
-16.32
none

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Influenza A virus infection (2)
6514
SLC2A2
0.45
Decreased influenza A virus infection

Reference

The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Brass et al., 2009

Influenza viruses exploit host cell machinery to replicate, resulting in epidemics of respiratory illness. In turn, the host expresses antiviral restriction factors to defend against infection. To find host cell modifiers of influenza A H1N1 viral infection, we used a functional genomic screen and identified over 120 influenza A virus-dependency factors with roles in endosomal acidification, vesicular trafficking, mitochondrial metabolism, and RNA splicing. We discovered that the interferon-inducible transmembrane proteins IFITM1, 2, and 3 restrict an early step in influenza A viral replication. The IFITM proteins confer basal resistance to influenza A virus but are also inducible by interferons type I and II and are critical for interferon''s virustatic actions. Further characterization revealed that the IFITM proteins inhibit the early replication of flaviviruses, including dengue virus and West Nile virus. Collectively this work identifies a family of antiviral restriction factors that mediate cellular innate immunity to at least three major human pathogens.

Screen Details

Stable ID: GR00147-A-2
Screen Title: Influenza A virus infection (2)
Assay: rp
Method: rp
Scope: Selected genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: rp
Biomodel: rp
Library: rp, rp
Reagent Type: siRNA
Score Type: Percentage of infected cells
Cutoff: Complex criteria
Notes:

Negative genetic interactions (3)
6514
SLC2A2
2.14
none

Reference

A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Vizeacoumar et al., 2013

Improved efforts are necessary to define the functional product of cancer mutations currently being revealed through large-scale sequencing efforts. Using genome-scale pooled shRNA screening technology, we mapped negative genetic interactions across a set of isogenic cancer cell lines and confirmed hundreds of these interactions in orthogonal co-culture competition assays to generate a high-confidence genetic interaction network of differentially essential or differential essentiality (DiE) genes. The network uncovered examples of conserved genetic interactions, densely connected functional modules derived from comparative genomics with model systems data, functions for uncharacterized genes in the human genome and targetable vulnerabilities. Finally, we demonstrate a general applicability of DiE gene signatures in determining genetic dependencies of other non-isogenic cancer cell lines. For example, the PTEN(-/-) DiE genes reveal a signature that can preferentially classify PTEN-dependent genotypes across a series of non-isogenic cell lines derived from the breast, pancreas and ovarian cancers. Our reference network suggests that many cancer vulnerabilities remain to be discovered through systematic derivation of a network of differentially essential genes in an isogenic cancer cell model.

Screen Details

Stable ID: GR00255-A-3
Screen Title: Negative genetic interactions (3)
Assay: shRNA abundance
Method: Microarray
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HCT116
Library: TRC lentiviral library, np
Reagent Type: shRNA
Score Type: differential Gene Activity Ranking Profile (dGARP)
Cutoff: < -1.2
Notes: HCT116 PTEN-/- and HCT116 PTEN+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells)

Combinatorial effect with EMD534085, a Kinesin-5 inhibitor (2)
6514
SLC2A2
np
Decreased number of cells in monopolar arrest with EMD534085 (a Kinesin-5 inhibitor) number of confimed duplexes: 3

Reference

An intermittent live cell imaging screen for siRNA enhancers and suppressors of a kinesin-5 inhibitor. Tsui et al., 2009

Kinesin-5 (also known as Eg5, KSP and Kif11) is required for assembly of a bipolar mitotic spindle. Small molecule inhibitors of Kinesin-5, developed as potential anti-cancer drugs, arrest cell in mitosis and promote apoptosis of cancer cells. We performed a genome-wide siRNA screen for enhancers and suppressors of a Kinesin-5 inhibitor in human cells to elucidate cellular responses, and thus identify factors that might predict drug sensitivity in cancers. Because the drug''s actions play out over several days, we developed an intermittent imaging screen. Live HeLa cells expressing GFP-tagged histone H2B were imaged at 0, 24 and 48 hours after drug addition, and images were analyzed using open-source software that incorporates machine learning. This screen effectively identified siRNAs that caused increased mitotic arrest at low drug concentrations (enhancers), and vice versa (suppressors), and we report siRNAs that caused both effects. We then classified the effect of siRNAs for 15 genes where 3 or 4 out of 4 siRNA oligos tested were suppressors as assessed by time lapse imaging, and by testing for suppression of mitotic arrest in taxol and nocodazole. This identified 4 phenotypic classes of drug suppressors, which included known and novel genes. Our methodology should be applicable to other screens, and the suppressor and enhancer genes we identified may open new lines of research into mitosis and checkpoint biology.

Screen Details

Stable ID: GR00198-A-2
Screen Title: Combinatorial effect with EMD534085, a Kinesin-5 inhibitor (2)
Assay: H2B protein expression
Method: Fluorescence
Scope: Selected genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: Dharmacon, siARRAY siRNA Library
Reagent Type: siRNA
Score Type: Ratio monopolar to total nuclei
Cutoff: > 2 standard deviations below mean for >= 1 siRNA
Notes: Additional information about the primary genome-wide screen

Ciliogenesis and cilium length (1)
6514
SLC2A2
8315
-34.22
none

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Synthetic lethal interaction with Ras
SLC2A2
-0.95 (0.09)
Synthetic lethal with Ras

Reference

A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Luo et al., 2009

Oncogenic mutations in the small GTPase Ras are highly prevalent in cancer, but an understanding of the vulnerabilities of these cancers is lacking. We undertook a genome-wide RNAi screen to identify synthetic lethal interactions with the KRAS oncogene. We discovered a diverse set of proteins whose depletion selectively impaired the viability of Ras mutant cells. Among these we observed a strong enrichment for genes with mitotic functions. We describe a pathway involving the mitotic kinase PLK1, the anaphase-promoting complex/cyclosome, and the proteasome that, when inhibited, results in prometaphase accumulation and the subsequent death of Ras mutant cells. Gene expression analysis indicates that reduced expression of genes in this pathway correlates with increased survival of patients bearing tumors with a Ras transcriptional signature. Our results suggest a previously underappreciated role for Ras in mitotic progression and demonstrate a pharmacologically tractable pathway for the potential treatment of cancers harboring Ras mutations.

Screen Details

Stable ID: GR00018-A-0
Screen Title: Synthetic lethal interaction with Ras
Assay: Synthetic lethal interaction with Ras
Method: Micoarray hybridization
Scope:
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: DLD1 colon adenocarcinoma cells (Ras mutant and wildtype)
Library: , shRNA-mir (G. Hannon)
Reagent Type: shRNA
Score Type: Log2 diff MUT-WT (and P-value)
Cutoff: -0.7 (0.3)
Notes:

Influenza A virus infection (2)
6514
SLC2A2
0.52
Decreased influenza A virus infection

Reference

The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Brass et al., 2009

Influenza viruses exploit host cell machinery to replicate, resulting in epidemics of respiratory illness. In turn, the host expresses antiviral restriction factors to defend against infection. To find host cell modifiers of influenza A H1N1 viral infection, we used a functional genomic screen and identified over 120 influenza A virus-dependency factors with roles in endosomal acidification, vesicular trafficking, mitochondrial metabolism, and RNA splicing. We discovered that the interferon-inducible transmembrane proteins IFITM1, 2, and 3 restrict an early step in influenza A viral replication. The IFITM proteins confer basal resistance to influenza A virus but are also inducible by interferons type I and II and are critical for interferon''s virustatic actions. Further characterization revealed that the IFITM proteins inhibit the early replication of flaviviruses, including dengue virus and West Nile virus. Collectively this work identifies a family of antiviral restriction factors that mediate cellular innate immunity to at least three major human pathogens.

Screen Details

Stable ID: GR00147-A-2
Screen Title: Influenza A virus infection (2)
Assay: rp
Method: rp
Scope: Selected genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: rp
Biomodel: rp
Library: rp, rp
Reagent Type: siRNA
Score Type: Percentage of infected cells
Cutoff: Complex criteria
Notes:

Salmonella enterica subspecies 1 serovar Typhimurium invasion (1)
6514
SLC2A2
np
0.07
none

Reference

RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42. Misselwitz et al., 2011

The pathogen Salmonella Typhimurium is a common cause of diarrhea and invades the gut tissue by injecting a cocktail of virulence factors into epithelial cells, triggering actin rearrangements, membrane ruffling and pathogen entry. One of these factors is SopE, a G-nucleotide exchange factor for the host cellular Rho GTPases Rac1 and Cdc42. How SopE mediates cellular invasion is incompletely understood. Using genome-scale RNAi screening we identified 72 known and novel host cell proteins affecting SopE-mediated entry. Follow-up assays assigned these ''hits'' to particular steps of the invasion process; i.e., binding, effector injection, membrane ruffling, membrane closure and maturation of the Salmonella-containing vacuole. Depletion of the COPI complex revealed a unique effect on virulence factor injection and membrane ruffling. Both effects are attributable to mislocalization of cholesterol, sphingolipids, Rac1 and Cdc42 away from the plasma membrane into a large intracellular compartment. Equivalent results were obtained with the vesicular stomatitis virus. Therefore, COPI-facilitated maintenance of lipids may represent a novel, unifying mechanism essential for a wide range of pathogens, offering opportunities for designing new drugs.

Screen Details

Stable ID: GR00133-A-1
Screen Title: Salmonella enterica subspecies 1 serovar Typhimurium invasion (1)
Assay: Gentamycin protection invasion assay
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: Qiagen, Druggable genome library V2.0
Reagent Type: siRNA
Score Type: log2 median
Cutoff: Complex criteria
Notes:

Influenza A virus infection (2)
6514
SLC2A2
0.52
Decreased influenza A virus infection

Reference

The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Brass et al., 2009

Influenza viruses exploit host cell machinery to replicate, resulting in epidemics of respiratory illness. In turn, the host expresses antiviral restriction factors to defend against infection. To find host cell modifiers of influenza A H1N1 viral infection, we used a functional genomic screen and identified over 120 influenza A virus-dependency factors with roles in endosomal acidification, vesicular trafficking, mitochondrial metabolism, and RNA splicing. We discovered that the interferon-inducible transmembrane proteins IFITM1, 2, and 3 restrict an early step in influenza A viral replication. The IFITM proteins confer basal resistance to influenza A virus but are also inducible by interferons type I and II and are critical for interferon''s virustatic actions. Further characterization revealed that the IFITM proteins inhibit the early replication of flaviviruses, including dengue virus and West Nile virus. Collectively this work identifies a family of antiviral restriction factors that mediate cellular innate immunity to at least three major human pathogens.

Screen Details

Stable ID: GR00147-A-2
Screen Title: Influenza A virus infection (2)
Assay: rp
Method: rp
Scope: Selected genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: rp
Biomodel: rp
Library: rp, rp
Reagent Type: siRNA
Score Type: Percentage of infected cells
Cutoff: Complex criteria
Notes:

Negative genetic interactions (5)
6514
SLC2A2
-0.79
none

Reference

A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Vizeacoumar et al., 2013

Improved efforts are necessary to define the functional product of cancer mutations currently being revealed through large-scale sequencing efforts. Using genome-scale pooled shRNA screening technology, we mapped negative genetic interactions across a set of isogenic cancer cell lines and confirmed hundreds of these interactions in orthogonal co-culture competition assays to generate a high-confidence genetic interaction network of differentially essential or differential essentiality (DiE) genes. The network uncovered examples of conserved genetic interactions, densely connected functional modules derived from comparative genomics with model systems data, functions for uncharacterized genes in the human genome and targetable vulnerabilities. Finally, we demonstrate a general applicability of DiE gene signatures in determining genetic dependencies of other non-isogenic cancer cell lines. For example, the PTEN(-/-) DiE genes reveal a signature that can preferentially classify PTEN-dependent genotypes across a series of non-isogenic cell lines derived from the breast, pancreas and ovarian cancers. Our reference network suggests that many cancer vulnerabilities remain to be discovered through systematic derivation of a network of differentially essential genes in an isogenic cancer cell model.

Screen Details

Stable ID: GR00255-A-5
Screen Title: Negative genetic interactions (5)
Assay: shRNA abundance
Method: Microarray
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HCT116
Library: TRC lentiviral library, np
Reagent Type: shRNA
Score Type: differential Gene Activity Ranking Profile (dGARP)
Cutoff: < -0.8
Notes: HCT116 KRASG13D/- and HCT116 KRAS+/- cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells)

Influenza A virus infection (2)
6514
SLC2A2
0.48
Decreased influenza A virus infection

Reference

The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Brass et al., 2009

Influenza viruses exploit host cell machinery to replicate, resulting in epidemics of respiratory illness. In turn, the host expresses antiviral restriction factors to defend against infection. To find host cell modifiers of influenza A H1N1 viral infection, we used a functional genomic screen and identified over 120 influenza A virus-dependency factors with roles in endosomal acidification, vesicular trafficking, mitochondrial metabolism, and RNA splicing. We discovered that the interferon-inducible transmembrane proteins IFITM1, 2, and 3 restrict an early step in influenza A viral replication. The IFITM proteins confer basal resistance to influenza A virus but are also inducible by interferons type I and II and are critical for interferon''s virustatic actions. Further characterization revealed that the IFITM proteins inhibit the early replication of flaviviruses, including dengue virus and West Nile virus. Collectively this work identifies a family of antiviral restriction factors that mediate cellular innate immunity to at least three major human pathogens.

Screen Details

Stable ID: GR00147-A-2
Screen Title: Influenza A virus infection (2)
Assay: rp
Method: rp
Scope: Selected genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: rp
Biomodel: rp
Library: rp, rp
Reagent Type: siRNA
Score Type: Percentage of infected cells
Cutoff: Complex criteria
Notes:

Ciliogenesis and cilium length (1)
6514
SLC2A2
116827
94.64
none

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Human papillomavirus oncogene expression regulation (1)
6514
SLC2A2
0.95
none

Reference

Genome-wide siRNA screen identifies SMCX, EP400, and Brd4 as E2-dependent regulators of human papillomavirus oncogene expression. Smith et al., 2010

An essential step in the pathogenesis of human papillomavirus (HPV)-associated cancers is the dysregulated expression of the viral oncogenes. The papillomavirus E2 protein can silence the long control region (LCR) promoter that controls viral E6 and E7 oncogene expression. The mechanisms by which E2 represses oncogene expression and the cellular factors through which E2 mediates this silencing are largely unknown. We conducted an unbiased, genome-wide siRNA screen and series of secondary screens that identified 96 cellular genes that contribute to the repression of the HPV LCR. In addition to confirming a role for the E2-binding bromodomain protein Brd4 in E2-mediated silencing, we identified a number of genes that have not previously been implicated in E2 repression, including the demethylase JARID1C/SMCX as well as EP400, a component of the NuA4/TIP60 histone acetyltransferase complex. Each of these genes contributes independently and additively to E2-mediated silencing, indicating that E2 functions through several distinct cellular complexes to repress E6 and E7 expression.

Screen Details

Stable ID: GR00197-A-1
Screen Title: Human papillomavirus oncogene expression regulation (1)
Assay: HPV18 LCR reporter activity
Method: Luminescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: C33A/BE2/18LCR c4
Library: Dharmacon, Human siGENOME SMARTpool library
Reagent Type: siRNA
Score Type: Z-score
Cutoff: >= 2
Notes: Author-submitted data. Phenotype strength according to Z-scores: weak: 2 - 3; moderate: 3 - 5; strong: > 5

Wnt/beta-catenin pathway regulation (2)
NM_000340
SLC2A2
sp
none

Reference

A genome-wide RNAi screen for Wnt/beta-catenin pathway components identifies unexpected roles for TCF transcription factors in cancer. Tang et al., 2008

The Wnt family of secreted proteins coordinate cell fate decision-making in a broad range of developmental and homeostatic contexts. Corruption of Wnt signal transduction pathways frequently results in degenerative diseases and cancer. We have used an iterative genome-wide screening strategy that employs multiple nonredundant RNAi reagents to identify mammalian genes that participate in Wnt/beta-catenin pathway response. Among the genes that were assigned high confidence scores are two members of the TCF/LEF family of DNA-binding proteins that control the transcriptional output of the pathway. Surprisingly, we found that the presumed cancer-promoting gene TCF7L2 functions instead as a transcriptional repressor that restricts colorectal cancer (CRC) cell growth. Mutations in TCF7L2 identified from cancer genome sequencing efforts abolish its ability to function as a transcriptional regulator and result in increased CRC cell growth. We describe a growth-promoting transcriptional program that is likely activated in CRC tumors with compromised TCF7L2 function. Taken together, the results from our screen and studies focused on members of the TCF/LEF gene family refine our understanding of how aberrant Wnt pathway activation sustains CRC growth.

Screen Details

Stable ID: GR00057-A-2
Screen Title: Wnt/beta-catenin pathway regulation (2)
Assay: Wnt pathway reporter
Method: Luminescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: Dharmacon, Human siArray siRNA library
Reagent Type: siRNA
Score Type: Complex, SP
Cutoff: Complex criteria
Notes: Screen with Wnt3A stimulation. Additional information about secondary screens (Dharmacon and Qiagen libraries).

Wnt/beta-catenin pathway regulation (1)
NM_000340
SLC2A2
-0.73
none

Reference

A genome-wide RNAi screen for Wnt/beta-catenin pathway components identifies unexpected roles for TCF transcription factors in cancer. Tang et al., 2008

The Wnt family of secreted proteins coordinate cell fate decision-making in a broad range of developmental and homeostatic contexts. Corruption of Wnt signal transduction pathways frequently results in degenerative diseases and cancer. We have used an iterative genome-wide screening strategy that employs multiple nonredundant RNAi reagents to identify mammalian genes that participate in Wnt/beta-catenin pathway response. Among the genes that were assigned high confidence scores are two members of the TCF/LEF family of DNA-binding proteins that control the transcriptional output of the pathway. Surprisingly, we found that the presumed cancer-promoting gene TCF7L2 functions instead as a transcriptional repressor that restricts colorectal cancer (CRC) cell growth. Mutations in TCF7L2 identified from cancer genome sequencing efforts abolish its ability to function as a transcriptional regulator and result in increased CRC cell growth. We describe a growth-promoting transcriptional program that is likely activated in CRC tumors with compromised TCF7L2 function. Taken together, the results from our screen and studies focused on members of the TCF/LEF gene family refine our understanding of how aberrant Wnt pathway activation sustains CRC growth.

Screen Details

Stable ID: GR00057-A-1
Screen Title: Wnt/beta-catenin pathway regulation (1)
Assay: Wnt pathway reporter
Method: Luminescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: Dharmacon, Human siArray siRNA library
Reagent Type: siRNA
Score Type: Z-score
Cutoff: > 4
Notes: Screen without Wnt3A stimulation. Additional information about secondary screens (Dharmacon and Qiagen libraries).

TRAIL-induced apoptosis (1)
NM_000340
SLC2A2
2.4
none

Reference

A synthetic lethal screen identifies FAT1 as an antagonist of caspase-8 in extrinsic apoptosis. Kranz and Boutros, 2014

The extrinsic apoptosis pathway is initiated by binding of death ligands to death receptors resulting in the formation of the death-inducing signaling complex (DISC). Activation of procaspase-8 within the DISC and its release from the signaling complex is required for processing executor caspases and commiting cell death. Here, we report that the atypical cadherin FAT1 interacts with caspase-8 preventing the association of caspase-8 with the DISC. We identified FAT1 in a genome-wide siRNA screen for synthetic lethal interactions with death receptor-mediated apoptosis. Knockdown of FAT1 sensitized established and patient-derived glioblastoma cell lines for apoptosis transduced by cell death ligands. Depletion of FAT1 resulted in enhanced procaspase-8 recruitment to the DISC and increased formation of caspase-8 containing secondary signaling complexes. In addition, FAT1 knockout cell lines generated by CRISPR/Cas9-mediated genome engineering were more susceptible for death receptor-mediated apoptosis. Our findings provide evidence for a mechanism to control caspase-8-dependent cell death by the atypical cadherin FAT1. These results contribute towards the understanding of effector caspase regulation in physiological conditions.

Screen Details

Stable ID: GR00240-S-1
Screen Title: TRAIL-induced apoptosis (1)
Assay: Viability
Method: Luminescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: U251MG
Library: Dharmacon, SMART-pool siRNA
Reagent Type: siRNA
Score Type: Z-score
Cutoff: > 4
Notes: Author-submitted data

TRAIL-induced apoptosis (2)
NM_000340
SLC2A2
-0.1
none Z-score 2.519

Reference

A synthetic lethal screen identifies FAT1 as an antagonist of caspase-8 in extrinsic apoptosis. Kranz and Boutros, 2014

The extrinsic apoptosis pathway is initiated by binding of death ligands to death receptors resulting in the formation of the death-inducing signaling complex (DISC). Activation of procaspase-8 within the DISC and its release from the signaling complex is required for processing executor caspases and commiting cell death. Here, we report that the atypical cadherin FAT1 interacts with caspase-8 preventing the association of caspase-8 with the DISC. We identified FAT1 in a genome-wide siRNA screen for synthetic lethal interactions with death receptor-mediated apoptosis. Knockdown of FAT1 sensitized established and patient-derived glioblastoma cell lines for apoptosis transduced by cell death ligands. Depletion of FAT1 resulted in enhanced procaspase-8 recruitment to the DISC and increased formation of caspase-8 containing secondary signaling complexes. In addition, FAT1 knockout cell lines generated by CRISPR/Cas9-mediated genome engineering were more susceptible for death receptor-mediated apoptosis. Our findings provide evidence for a mechanism to control caspase-8-dependent cell death by the atypical cadherin FAT1. These results contribute towards the understanding of effector caspase regulation in physiological conditions.

Screen Details

Stable ID: GR00240-S-2
Screen Title: TRAIL-induced apoptosis (2)
Assay: Viability (synthetic lethal)
Method: Luminescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: U251MG
Library: Dharmacon, SMART-pool siRNA
Reagent Type: siRNA
Score Type: Differential score
Cutoff: > 3.6 AND viability Z-score < 4
Notes: Author-submitted data. Z-scores from viability screen (1) are considered in score interpretation for this screen.

Negative genetic interactions (2)
6514
SLC2A2
0.59
none

Reference

A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Vizeacoumar et al., 2013

Improved efforts are necessary to define the functional product of cancer mutations currently being revealed through large-scale sequencing efforts. Using genome-scale pooled shRNA screening technology, we mapped negative genetic interactions across a set of isogenic cancer cell lines and confirmed hundreds of these interactions in orthogonal co-culture competition assays to generate a high-confidence genetic interaction network of differentially essential or differential essentiality (DiE) genes. The network uncovered examples of conserved genetic interactions, densely connected functional modules derived from comparative genomics with model systems data, functions for uncharacterized genes in the human genome and targetable vulnerabilities. Finally, we demonstrate a general applicability of DiE gene signatures in determining genetic dependencies of other non-isogenic cancer cell lines. For example, the PTEN(-/-) DiE genes reveal a signature that can preferentially classify PTEN-dependent genotypes across a series of non-isogenic cell lines derived from the breast, pancreas and ovarian cancers. Our reference network suggests that many cancer vulnerabilities remain to be discovered through systematic derivation of a network of differentially essential genes in an isogenic cancer cell model.

Screen Details

Stable ID: GR00255-A-2
Screen Title: Negative genetic interactions (2)
Assay: shRNA abundance
Method: Microarray
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HCT116
Library: TRC lentiviral library, np
Reagent Type: shRNA
Score Type: differential Gene Activity Ranking Profile (dGARP)
Cutoff: < -1.0
Notes: HCT116 MUS81-/- and HCT116 MUS81+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells)

Ciliogenesis and cilium length (1)
6514
SLC2A2
116829
-27.23
none

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Vaccinia virus (VACV) infection
6514
SLC2A2
-0.75
none number of cells compared to control (%): 73.43

Reference

Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. Sivan et al., 2013

Poxviruses are considered less dependent on host functions than other DNA viruses because of their cytoplasmic site of replication and large genomes, which encode enzymes for DNA and mRNA synthesis. Nevertheless, RNAi screens with two independent human genome-scale libraries have identified more than 500 candidate genes that significantly inhibited and a similar number that enhanced replication and spread of infectious vaccinia virus (VACV). Translational, ubiquitin-proteosome, and endoplasmic reticulum-to-Golgi transport functions, known to be important for VACV, were enriched in the siRNA-inhibiting group, and RNA polymerase II and associated functions were enriched in the siRNA-enhancing group. Additional findings, notably the inhibition of VACV spread by siRNAs to several nuclear pore genes, were unanticipated. Knockdown of nucleoporin 62 strongly inhibited viral morphogenesis, with only a modest effect on viral gene expression, recapitulating and providing insight into previous studies with enucleated cells.

Screen Details

Stable ID: GR00249-S
Screen Title: Vaccinia virus (VACV) infection
Assay: Vaccinia virus VACV IHD-J/GFP protein expression and DNA content
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: Ambion and Dharmacon, Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus
Reagent Type: siRNA
Score Type: Z-score
Cutoff: >= 1 OR <= -1.5
Notes: Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %.

Vaccinia virus (VACV) infection
6514
SLC2A2
0.52
none number of cells compared to control (%): 94.58

Reference

Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. Sivan et al., 2013

Poxviruses are considered less dependent on host functions than other DNA viruses because of their cytoplasmic site of replication and large genomes, which encode enzymes for DNA and mRNA synthesis. Nevertheless, RNAi screens with two independent human genome-scale libraries have identified more than 500 candidate genes that significantly inhibited and a similar number that enhanced replication and spread of infectious vaccinia virus (VACV). Translational, ubiquitin-proteosome, and endoplasmic reticulum-to-Golgi transport functions, known to be important for VACV, were enriched in the siRNA-inhibiting group, and RNA polymerase II and associated functions were enriched in the siRNA-enhancing group. Additional findings, notably the inhibition of VACV spread by siRNAs to several nuclear pore genes, were unanticipated. Knockdown of nucleoporin 62 strongly inhibited viral morphogenesis, with only a modest effect on viral gene expression, recapitulating and providing insight into previous studies with enucleated cells.

Screen Details

Stable ID: GR00249-S
Screen Title: Vaccinia virus (VACV) infection
Assay: Vaccinia virus VACV IHD-J/GFP protein expression and DNA content
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: Ambion and Dharmacon, Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus
Reagent Type: siRNA
Score Type: Z-score
Cutoff: >= 1 OR <= -1.5
Notes: Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %.

Combinatorial effect with paclitaxel
NM_000340
SLC2A2
np
0.94
none

Reference

Synthetic lethal screen identification of chemosensitizer loci in cancer cells. Whitehurst et al., 2007

Abundant evidence suggests that a unifying principle governing the molecular pathology of cancer is the co-dependent aberrant regulation of core machinery driving proliferation and suppressing apoptosis. Anomalous proteins engaged in support of this tumorigenic regulatory environment most probably represent optimal intervention targets in a heterogeneous population of cancer cells. The advent of RNA-mediated interference (RNAi)-based functional genomics provides the opportunity to derive unbiased comprehensive collections of validated gene targets supporting critical biological systems outside the framework of preconceived notions of mechanistic relationships. We have combined a high-throughput cell-based one-well/one-gene screening platform with a genome-wide synthetic library of chemically synthesized small interfering RNAs for systematic interrogation of the molecular underpinnings of cancer cell chemoresponsiveness. NCI-H1155, a human non-small-cell lung cancer line, was employed in a paclitaxel-dependent synthetic lethal screen designed to identify gene targets that specifically reduce cell viability in the presence of otherwise sublethal concentrations of paclitaxel. Using a stringent objective statistical algorithm to reduce false discovery rates below 5%, we isolated a panel of 87 genes that represent major focal points of the autonomous response of cancer cells to the abrogation of microtubule dynamics. Here we show that several of these targets sensitize lung cancer cells to paclitaxel concentrations 1,000-fold lower than otherwise required for a significant response, and we identify mechanistic relationships between cancer-associated aberrant gene expression programmes and the basic cellular machinery required for robust mitotic progression.

Screen Details

Stable ID: GR00054-A
Screen Title: Combinatorial effect with paclitaxel
Assay: Viability (synthetic lethal)
Method: ATP level
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: NCI-H1155
Library: Dharmacon, # G-005000-01
Reagent Type: siRNA
Score Type: Paclitaxel/control ratio
Cutoff: Complex criteria
Notes: Additional information about 87 high-confidence hits

Proliferation and survival of human cancer cell lines
SLC2A2
np
np
Decreased viability in colon lineage colon: no filter, top shRNA

Reference

Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer. Cheung et al., 2011

A comprehensive understanding of the molecular vulnerabilities of every type of cancer will provide a powerful roadmap to guide therapeutic approaches. Efforts such as The Cancer Genome Atlas Project will identify genes with aberrant copy number, sequence, or expression in various cancer types, providing a survey of the genes that may have a causal role in cancer. A complementary approach is to perform systematic loss-of-function studies to identify essential genes in particular cancer cell types. We have begun a systematic effort, termed Project Achilles, aimed at identifying genetic vulnerabilities across large numbers of cancer cell lines. Here, we report the assessment of the essentiality of 11,194 genes in 102 human cancer cell lines. We show that the integration of these functional data with information derived from surveying cancer genomes pinpoints known and previously undescribed lineage-specific dependencies across a wide spectrum of cancers. In particular, we found 54 genes that are specifically essential for the proliferation and viability of ovarian cancer cells and also amplified in primary tumors or differentially overexpressed in ovarian cancer cell lines. One such gene, PAX8, is focally amplified in 16% of high-grade serous ovarian cancers and expressed at higher levels in ovarian tumors. Suppression of PAX8 selectively induces apoptotic cell death of ovarian cancer cells. These results identify PAX8 as an ovarian lineage-specific dependency. More generally, these observations demonstrate that the integration of genome-scale functional and structural studies provides an efficient path to identify dependencies of specific cancer types on particular genes and pathways.

Screen Details

Stable ID: GR00235-A
Screen Title: Proliferation and survival of human cancer cell lines
Assay: Viability
Method: Microarray
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: 786-O, A-204, A549, A2058, A2780, AGS, AsPC-1, BxPC-3, C2BBe1, Caov-3, Caov-4, CFPAC-1, CH-157MN, COLO 205, COLO-704, COLO 741, COV362, COV434, COV504, DLD-1, EFO-21, EFO-27, F5, GP2d, HCC70, HCC364, HCC827, HCC2814, HEC-1-A, Hey-A8, HL-60, HLF, HPAC, Hs
Library: The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type: shRNA
Score Type: Rank
Cutoff: Complex criteria
Notes: Additional information about competition assays. Lineages: colon: C2BBe1, COLO 205, DLD-1, GP2d, HT-29, HT55, HuTu 80, KM12, LoVo, LS411N, LS513, NCI-H508, RKO, SK-CO-1, SNU-C1, SNU-C2A, SW48, SW480; esophageal: KYSE-30, KYSE-150, KYSE-450, KYSE-510, TE-9, TE-15, T.T; glioblastoma multiforme (GBM): LN-215, LN-229, LN-319, LN-464, SF767, U-251 MG; non-small-cell lung cancer (NSCLC): A549, HCC2814, HCC364, HCC827, NCI-H1650, NCI-H1975, NCI-H2122, NCI-H661; ovarian: A2780, Caov-3, Caov-4, COLO-704, COV362, COV434, COV504, EFO-21, EFO-27, Hey-A8, IGROV1, JHOC-5, KURAMOCHI, NIH:OVCAR-3, OV-90, OVCAR-4, OVCAR-8, OVISE, OVMANA, RKN, RMG-I, SNU-840, TOV-112D, TOV-21G, TYK-nu; pancreas: AsPC-1, BxPC-3, CFPAC-1, HPAC, KP-1NL, KP4, L3.3, MIA PaCa-2, Panc 03.27, Panc 08.13, Panc 10.05, QGP-1, SU.86.86

Homologous recombination DNA double-strand break repair (HR-DSBR) (1)
6514
SLC2A2
0.87
none

Reference

A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Adamson et al., 2012

Repair of DNA double-strand breaks is critical to genomic stability and the prevention of developmental disorders and cancer. A central pathway for this repair is homologous recombination (HR). Most knowledge of HR is derived from work in prokaryotic and eukaryotic model organisms. We carried out a genome-wide siRNA-based screen in human cells. Among positive regulators of HR we identified networks of DNA-damage-response and pre-mRNA-processing proteins, and among negative regulators we identified a phosphatase network. Three candidate proteins localized to DNA lesions, including RBMX, a heterogeneous nuclear ribonucleoprotein that has a role in alternative splicing. RBMX accumulated at DNA lesions through multiple domains in a poly(ADP-ribose) polymerase 1-dependent manner and promoted HR by facilitating proper BRCA2 expression. Our screen also revealed that off-target depletion of RAD51 is a common source of RNAi false positives, raising a cautionary note for siRNA screens and RNAi-based studies of HR.

Screen Details

Stable ID: GR00236-A-1
Screen Title: Homologous recombination DNA double-strand break repair (HR-DSBR) (1)
Assay: (HR-DSBR) DR-GFP reporter and DNA content
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: DR-U2OS
Library: Dharmacon, Human siGENOME siRNA (G-005000-05)
Reagent Type: siRNA
Score Type: Relative HR ratio
Cutoff: < ~0.4 OR > 1.88
Notes: Cutoff values correspond 2 standard deviations from the screen-wide mean

Ciliogenesis and cilium length (1)
6514
SLC2A2
116827
79.74
none

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Self-renewal and pluripotency in human embryonic stem cells (1)
NM_000340
SLC2A2
-0.89
none

Reference

A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al., 2010

The derivation of human ES cells (hESCs) from human blastocysts represents one of the milestones in stem cell biology. The full potential of hESCs in research and clinical applications requires a detailed understanding of the genetic network that governs the unique properties of hESCs. Here, we report a genome-wide RNA interference screen to identify genes which regulate self-renewal and pluripotency properties in hESCs. Interestingly, functionally distinct complexes involved in transcriptional regulation and chromatin remodelling are among the factors identified in the screen. To understand the roles of these potential regulators of hESCs, we studied transcription factor PRDM14 to gain new insights into its functional roles in the regulation of pluripotency. We showed that PRDM14 regulates directly the expression of key pluripotency gene POU5F1 through its proximal enhancer. Genome-wide location profiling experiments revealed that PRDM14 colocalized extensively with other key transcription factors such as OCT4, NANOG and SOX2, indicating that PRDM14 is integrated into the core transcriptional regulatory network. More importantly, in a gain-of-function assay, we showed that PRDM14 is able to enhance the efficiency of reprogramming of human fibroblasts in conjunction with OCT4, SOX2 and KLF4. Altogether, our study uncovers a wealth of novel hESC regulators wherein PRDM14 exemplifies a key transcription factor required for the maintenance of hESC identity and the reacquisition of pluripotency in human somatic cells.

Screen Details

Stable ID: GR00184-A-1
Screen Title: Self-renewal and pluripotency in human embryonic stem cells (1)
Assay: POU5F1 protein expression
Method: Fluorescence
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: hESC H1
Library: Dharmacon, SMARTpool siRNA library
Reagent Type: siRNA
Score Type: Z-score
Cutoff: < -2
Notes:

Cell division (1)
ENSG00000163581
SLC2A2
ENSG00000163581
sp
Increased G1 DNA content

Reference

Genome-scale RNAi profiling of cell division in human tissue culture cells. Kittler et al., 2007

Cell division is fundamental for all organisms. Here we report a genome-scale RNA-mediated interference screen in HeLa cells designed to identify human genes that are important for cell division. We have used a library of endoribonuclease-prepared short interfering RNAs for gene silencing and have used DNA content analysis to identify genes that induced cell cycle arrest or altered ploidy on silencing. Validation and secondary assays were performed to generate a nine-parameter loss-of-function phenoprint for each of the genes. These phenotypic signatures allowed the assignment of genes to specific functional classes by combining hierarchical clustering, cross-species analysis and proteomic data mining. We highlight the richness of our dataset by ascribing novel functions to genes in mitosis and cytokinesis. In particular, we identify two evolutionarily conserved transcriptional regulatory networks that govern cytokinesis. Our work provides an experimental framework from which the systematic analysis of novel genes necessary for cell division in human cells can begin.

Screen Details

Stable ID: GR00098-A-1
Screen Title: Cell division (1)
Assay: Cell number and DNA content
Method: Laser scanning cytometry
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: HeLa
Library: Custom-made, rp
Reagent Type: esiRNA
Score Type: Complex, sp
Cutoff: Complex criteria
Notes:

Non-small cell lung cancer (NSCLC) cytotoxicity (1)
SLC2A2
np
-1
Decreased shRNA abundance

Reference

Proteasome inhibitors block DNA repair and radiosensitize non-small cell lung cancer. Cron et al., 2013

Despite optimal radiation therapy (RT), chemotherapy and/or surgery, a majority of patients with locally advanced non-small cell lung cancer (NSCLC) fail treatment. To identify novel gene targets for improved tumor control, we performed whole genome RNAi screens to identify knockdowns that most reproducibly increase NSCLC cytotoxicity. These screens identified several proteasome subunits among top hits, including the topmost hit PSMA1, a component of the core 20 S proteasome. Radiation and proteasome inhibition showed synergistic effects. Proteasome inhibition resulted in an 80-90% decrease in homologous recombination (HR), a 50% decrease in expression of NF-κB-inducible HR genes BRCA1 and FANCD2, and a reduction of BRCA1, FANCD2 and RAD51 ionizing radiation-induced foci. IκBα RNAi knockdown rescued NSCLC radioresistance. Irradiation of mice with NCI-H460 xenografts after inducible PSMA1 shRNA knockdown markedly increased murine survival compared to either treatment alone. Proteasome inhibition is a promising strategy for NSCLC radiosensitization via inhibition of NF-κB-mediated expression of Fanconi Anemia/HR DNA repair genes.

Screen Details

Stable ID: GR00251-A-1
Screen Title: Non-small cell lung cancer (NSCLC) cytotoxicity (1)
Assay: shRNA abundance
Method: Microarray
Scope: Genome-wide
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: A549
Library: Hannon-Elledge whole genome pooled shRNA, np
Reagent Type: shRNA
Score Type: Complex, sp
Cutoff: Complex criteria
Notes: All listed genes are final hits. Final hit: >= 1 shRNA with >= 2-fold abundance decrease in both cell lines (A549 and NCI-H460)

Ciliogenesis and cilium length (1)
6514
SLC2A2
8315
-27.25
none

Reference

Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al., 2010

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. However, regulatory molecules that coordinate the biogenesis of primary cilia with other cellular processes, including cytoskeletal organization, vesicle trafficking and cell-cell adhesion, remain to be identified. Here we report the results of a functional genomic screen using RNA interference (RNAi) to identify human genes involved in ciliogenesis control. The screen identified 36 positive and 13 negative ciliogenesis modulators, which include molecules involved in actin dynamics and vesicle trafficking. Further investigation demonstrated that blocking actin assembly facilitates ciliogenesis by stabilizing the pericentrosomal preciliary compartment (PPC), a previously uncharacterized compact vesiculotubular structure storing transmembrane proteins destined for cilia during the early phase of ciliogenesis. The PPC was labelled by recycling endosome markers. Moreover, knockdown of modulators that are involved in the endocytic recycling pathway affected the formation of the PPC as well as ciliogenesis. Our results uncover a critical regulatory step that couples actin dynamics and endocytic recycling with ciliogenesis, and also provides potential target molecules for future study.

Screen Details

Stable ID: GR00149-A-1
Screen Title: Ciliogenesis and cilium length (1)
Assay: Smoothed protein expression
Method: Fluorescence
Scope: Druggable genes
Screen Type: Cell-based
Species: Homo sapiens
Biosource: Cell line
Biomodel: htRPE
Library: Ambion, Human druggable genome siRNA library V3.1
Reagent Type: siRNA
Score Type: Normalized percent inhibition
Cutoff: > 1.5 OR < -1.5 standard deviations from mean
Notes:

Reagent information for gene 6514 (SLC2A2)

Reagent IDTypeLibrary
D-007515-05 siRNA
siGENOME|Thermo Scientific Dharmacon|1|RefSeq release 5-7|84206 siRNAs in pools of four|siRNA|http://www.dharmacon.com/
D-007515-03 siRNA
siGENOME|Thermo Scientific Dharmacon|1|RefSeq release 5-7|84206 siRNAs in pools of four|siRNA|http://www.dharmacon.com/
D-007515-01 siRNA
siGENOME|Thermo Scientific Dharmacon|1|RefSeq release 5-7|84206 siRNAs in pools of four|siRNA|http://www.dharmacon.com/
M-007515-01 siRNA_Pool
siGENOME|Thermo Scientific Dharmacon|1|RefSeq release 5-7|84206 siRNAs in pools of four|siRNA|http://www.dharmacon.com/
D-007515-02 siRNA
siGENOME|Thermo Scientific Dharmacon|1|RefSeq release 5-7|84206 siRNAs in pools of four|siRNA|http://www.dharmacon.com/
SI00007476 siRNA
Druggable and whole genome supplement|Qiagen|1, 3|RefSeq|70308 siRNAs in pools of four|siRNA|http://www.qiagen.com/
SI03070487 siRNA
Druggable and whole genome supplement|Qiagen|1, 3|RefSeq|70308 siRNAs in pools of four|siRNA|http://www.qiagen.com/
SI00007455 siRNA
Druggable and whole genome supplement|Qiagen|1, 3|RefSeq|70308 siRNAs in pools of four|siRNA|http://www.qiagen.com/
SI03049795 siRNA
Druggable and whole genome supplement|Qiagen|1, 3|RefSeq|70308 siRNAs in pools of four|siRNA|http://www.qiagen.com/
SP00002773 siRNA_Pool
Druggable and whole genome supplement|Qiagen|1, 3|RefSeq|70308 siRNAs in pools of four|siRNA|http://www.qiagen.com/
TRCN0000043601 shRNA
TRC shRNA Library|The RNAi Consortium (TRC)|1|RefSeq|81054|shRNA|http://www.broadinstitute.org/rnai/public/
TRCN0000043602 shRNA
TRC shRNA Library|The RNAi Consortium (TRC)|1|RefSeq|81054|shRNA|http://www.broadinstitute.org/rnai/public/
TRCN0000043600 shRNA
TRC shRNA Library|The RNAi Consortium (TRC)|1|RefSeq|81054|shRNA|http://www.broadinstitute.org/rnai/public/
TRCN0000043599 shRNA
TRC shRNA Library|The RNAi Consortium (TRC)|1|RefSeq|81054|shRNA|http://www.broadinstitute.org/rnai/public/
TRCN0000043598 shRNA
TRC shRNA Library|The RNAi Consortium (TRC)|1|RefSeq|81054|shRNA|http://www.broadinstitute.org/rnai/public/
v2HS_92464 siRNA
shRNAmir|OpenBiosystems|1|RefSeq|2120|shRNA|http://www.openbiosystems.com/
s12928 siRNA
Ambion Silencer Select|Ambion|1|RefSeq|64781|siRNA|http://www.invitrogen.com/site/us/en/home/brands/ambion.html?CID=fl-ambion
s12929 siRNA
Ambion Silencer Select|Ambion|1|RefSeq|64781|siRNA|http://www.invitrogen.com/site/us/en/home/brands/ambion.html?CID=fl-ambion
s12930 siRNA
Ambion Silencer Select|Ambion|1|RefSeq|64781|siRNA|http://www.invitrogen.com/site/us/en/home/brands/ambion.html?CID=fl-ambion

Gene information for gene 6514 (SLC2A2)

Gene:
Alternate gene names:GLUT2
Description:solute carrier family 2 (facilitated glucose transporter), member 2
Chromosome:3
Start:170996347
Stop:171026978
Strand:negative
Locus:3q26.1-q26.2
Biotype:protein-coding
Status:live
Entrez Gene:
GeneCards:
Ensembl:
Hgnc:
Hprd:
Mim:
Uniprot:
Vega:
RefSeq:

Genome browser for gene 6514 (SLC2A2)

Homo sapiens GRCh38
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