| HIV-1 infection (1) | 672
| BRCA1 | np |
sp
|
Decreased HIV-LTR-beta-galactosidase protein expression
| yes |
ReferenceGenome-scale RNAi screen for host factors required for HIV replication. Zhou et al.,
2008
Human immunodeficiency virus (HIV)-1 depends on the host cell machinery to support its replication. To discover cellular factors associated with HIV-1 replication, we conducted a genome-scale siRNA screen, revealing more than 311 host factors, including 267 that were not previously linked to HIV. Surprisingly, there was little overlap between these genes and the HIV dependency factors described recently. However, an analysis of the genes identified in both screens revealed overlaps in several of the associated pathways or protein complexes, including the SP1/mediator complex and the NF-kappaB signaling pathway. cDNAs for a subset of the identified genes were used to rescue HIV replication following knockdown of the cellular mRNA providing strong evidence that the following six genes are previously uncharacterized host factors for HIV: AKT1, PRKAA1, CD97, NEIL3, BMP2K, and SERPINB6. This study highlights both the power and shortcomings of large scale loss-of-function screens in discovering host-pathogen interactions.
Screen DetailsStable ID:
GR00224-A-1
Screen Title:
HIV-1 infection (1)
Assay:
HIV-LTR-beta-galactosidase protein expression
Method:
Luminescence
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Dharmacon, Ambion and Proligo, np
Reagent Type:
siRNA
Score Type:
Complex, sp
Cutoff:
Complex criteria
Notes:
Additional information about a primary genome-wide screen
|
| Homologous recombination DNA double-strand break repair (HR-DSBR) (1) | ENSG00000012048
| BRCA1 | np |
-6,06
|
Decreased homologous recombination repair frequency
| yes |
ReferenceA genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. Słabicki et al.,
2010
DNA repair is essential to maintain genome integrity, and genes with roles in DNA repair are frequently mutated in a variety of human diseases. Repair via homologous recombination typically restores the original DNA sequence without introducing mutations, and a number of genes that are required for homologous recombination DNA double-strand break repair (HR-DSBR) have been identified. However, a systematic analysis of this important DNA repair pathway in mammalian cells has not been reported. Here, we describe a genome-scale endoribonuclease-prepared short interfering RNA (esiRNA) screen for genes involved in DNA double strand break repair. We report 61 genes that influenced the frequency of HR-DSBR and characterize in detail one of the genes that decreased the frequency of HR-DSBR. We show that the gene KIAA0415 encodes a putative helicase that interacts with SPG11 and SPG15, two proteins mutated in hereditary spastic paraplegia (HSP). We identify mutations in HSP patients, discovering KIAA0415/SPG48 as a novel HSP-associated gene, and show that a KIAA0415/SPG48 mutant cell line is more sensitive to DNA damaging drugs. We present the first genome-scale survey of HR-DSBR in mammalian cells providing a dataset that should accelerate the discovery of novel genes with roles in DNA repair and associated medical conditions. The discovery that proteins forming a novel protein complex are required for efficient HR-DSBR and are mutated in patients suffering from HSP suggests a link between HSP and DNA repair.
Screen DetailsStable ID:
GR00151-A-1
Screen Title:
Homologous recombination DNA double-strand break repair (HR-DSBR) (1)
Assay:
(HR-DSBR) DR-GFP reporter
Method:
Flow cytometry
Scope:
Genome-wide
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Custom-made, Custom-made
Reagent Type:
esiRNA
Score Type:
Z-score
Cutoff:
< -2 OR > 2
Notes:
|
| Combinatorial effect with anticancer drugs (4): cisplatin | NM_007294
| BRCA1 | siRNA 1 - chem. modified |
2,5
|
Decreased viability with cisplatin
| yes |
ReferenceSmall interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Bartz et al.,
2006
RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug''s mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53(+/-) matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity approximately 4- to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.
Screen DetailsStable ID:
GR00101-A-4
Screen Title:
Combinatorial effect with anticancer drugs (4): cisplatin
Assay:
Viability (synthetic lethal)
Method:
Alamar Blue
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Sigma-Proligo, rp
Reagent Type:
siRNA
Score Type:
Fold EC50 shift
Cutoff:
>= 2
Notes:
Additional information about the primary genome-wide screen
|
| Proliferation of cells with active beta-catenin (1) |
| BRCA1 | |
1,04
|
none
| yes |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-1
Screen Title:
Proliferation of cells with active beta-catenin (1)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MCF7
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| HIV-1 infection (2) | 672
| BRCA1 | np |
sp
|
none
| no |
ReferenceGenome-scale RNAi screen for host factors required for HIV replication. Zhou et al.,
2008
Human immunodeficiency virus (HIV)-1 depends on the host cell machinery to support its replication. To discover cellular factors associated with HIV-1 replication, we conducted a genome-scale siRNA screen, revealing more than 311 host factors, including 267 that were not previously linked to HIV. Surprisingly, there was little overlap between these genes and the HIV dependency factors described recently. However, an analysis of the genes identified in both screens revealed overlaps in several of the associated pathways or protein complexes, including the SP1/mediator complex and the NF-kappaB signaling pathway. cDNAs for a subset of the identified genes were used to rescue HIV replication following knockdown of the cellular mRNA providing strong evidence that the following six genes are previously uncharacterized host factors for HIV: AKT1, PRKAA1, CD97, NEIL3, BMP2K, and SERPINB6. This study highlights both the power and shortcomings of large scale loss-of-function screens in discovering host-pathogen interactions.
Screen DetailsStable ID:
GR00224-A-2
Screen Title:
HIV-1 infection (2)
Assay:
HIV-Tat and HIV-LTR-beta-galactosidase protein expression
Method:
Luminescence
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Dharmacon, Ambion and Proligo, np
Reagent Type:
siRNA
Score Type:
Percentage
Cutoff:
< 60 %
Notes:
Additional information about a primary genome-wide screen
|
| Combinatorial effect with anticancer drugs (4): cisplatin | NM_007294
| BRCA1 | siRNA 2 - chem. modified |
2,4
|
Decreased viability with cisplatin
| yes |
ReferenceSmall interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Bartz et al.,
2006
RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug''s mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53(+/-) matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity approximately 4- to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.
Screen DetailsStable ID:
GR00101-A-4
Screen Title:
Combinatorial effect with anticancer drugs (4): cisplatin
Assay:
Viability (synthetic lethal)
Method:
Alamar Blue
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Sigma-Proligo, rp
Reagent Type:
siRNA
Score Type:
Fold EC50 shift
Cutoff:
>= 2
Notes:
Additional information about the primary genome-wide screen
|
| Proliferation of cells with active beta-catenin (1) |
| BRCA1 | |
0,59
|
none
| yes |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-1
Screen Title:
Proliferation of cells with active beta-catenin (1)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MCF7
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Cell division (1) | ENSG00000012048
| BRCA1 | ENSG00000012048 |
sp
|
Increased G1 DNA content
| yes |
ReferenceGenome-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 DetailsStable 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:
|
| Proliferation of cells with active beta-catenin (2) |
| BRCA1 | |
-0,09
|
none
| yes |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-2
Screen Title:
Proliferation of cells with active beta-catenin (2)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MDA-MB-231
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Proliferation of cells with active beta-catenin (4) |
| BRCA1 | |
-0,35
|
none
| no |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-4
Screen Title:
Proliferation of cells with active beta-catenin (4)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
T47D
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Combinatorial effect with anticancer drugs (4): cisplatin | NM_007294
| BRCA1 | np pool chem. modified |
1,6
|
none
| yes |
ReferenceSmall interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Bartz et al.,
2006
RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug''s mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53(+/-) matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity approximately 4- to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.
Screen DetailsStable ID:
GR00101-A-4
Screen Title:
Combinatorial effect with anticancer drugs (4): cisplatin
Assay:
Viability (synthetic lethal)
Method:
Alamar Blue
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Sigma-Proligo, rp
Reagent Type:
siRNA
Score Type:
Fold EC50 shift
Cutoff:
>= 2
Notes:
Additional information about the primary genome-wide screen
|
| Homologous recombination DNA double-strand break repair (HR-DSBR) (2) | ENSG00000012048
| BRCA1 | BRCA1 esiRNA 1 |
< -4
|
Decreased homologous recombination repair frequency
| yes |
ReferenceA genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. Słabicki et al.,
2010
DNA repair is essential to maintain genome integrity, and genes with roles in DNA repair are frequently mutated in a variety of human diseases. Repair via homologous recombination typically restores the original DNA sequence without introducing mutations, and a number of genes that are required for homologous recombination DNA double-strand break repair (HR-DSBR) have been identified. However, a systematic analysis of this important DNA repair pathway in mammalian cells has not been reported. Here, we describe a genome-scale endoribonuclease-prepared short interfering RNA (esiRNA) screen for genes involved in DNA double strand break repair. We report 61 genes that influenced the frequency of HR-DSBR and characterize in detail one of the genes that decreased the frequency of HR-DSBR. We show that the gene KIAA0415 encodes a putative helicase that interacts with SPG11 and SPG15, two proteins mutated in hereditary spastic paraplegia (HSP). We identify mutations in HSP patients, discovering KIAA0415/SPG48 as a novel HSP-associated gene, and show that a KIAA0415/SPG48 mutant cell line is more sensitive to DNA damaging drugs. We present the first genome-scale survey of HR-DSBR in mammalian cells providing a dataset that should accelerate the discovery of novel genes with roles in DNA repair and associated medical conditions. The discovery that proteins forming a novel protein complex are required for efficient HR-DSBR and are mutated in patients suffering from HSP suggests a link between HSP and DNA repair.
Screen DetailsStable ID:
GR00151-A-2
Screen Title:
Homologous recombination DNA double-strand break repair (HR-DSBR) (2)
Assay:
(HR-DSBR) DR-GFP reporter
Method:
Flow cytometry
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Custom-made, Custom-made
Reagent Type:
esiRNA
Score Type:
Z-score
Cutoff:
Complex criteria
Notes:
|
| Apoptosis regulation after Chlamydia trachomatis serovar L2 infection | 672
| BRCA1 | np |
np
|
none
| no |
ReferenceHIF-1α is involved in mediating apoptosis resistance to Chlamydia trachomatis-infected cells. Sharma et al.,
2011
Chlamydiae are obligate intracellular Gram-negative bacteria that cause widespread diseases in humans. Due to the intimate association between bacterium and host, Chlamydia evolved various strategies to protect their host cell against death-inducing stimuli, allowing the bacterium to complete its development cycle. An RNA interference (RNAi)-based screen was used to identify host cell factors required for apoptosis resistance of human epithelial cells infected with Chlamydia trachomatis serovar L2. Among the 32 validated hits, the anti-apoptotic Bcl-2 family member Mcl-1 was identified as a target. Protein network analyses implicated the transcription factor hypoxia-induced factor 1 alpha (HIF-1α) to be central to the regulation of many of the identified targets. Further mechanistic investigations showed that HIF-1α was stabilized within the host cell cytoplasm during early infection time points, followed by its translocation to the nucleus and eventual transcriptional activation of Mcl-1. siRNA-mediated depletion of HIF-1α led to a drastic decrease in Mcl-1, rendering the cell sensitive to apoptosis induction. Taken together, our findings identify HIF-1α as responsible for upregulation of Mcl-1 and the maintenance of apoptosis resistance during Chlamydia infection.
Screen DetailsStable ID:
GR00206-A
Screen Title:
Apoptosis regulation after Chlamydia trachomatis serovar L2 infection
Assay:
Cleaved cytokeratin-18 protein expression
Method:
Fluorescence
Scope:
Apoptosis, cellular trafficking and cell signalling genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Custom-made, Custom-made
Reagent Type:
siRNA
Score Type:
p-value
Cutoff:
<= 0.05
Notes:
|
| Proliferation of cells with active beta-catenin (3) |
| BRCA1 | |
1,42
|
none
| yes |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-3
Screen Title:
Proliferation of cells with active beta-catenin (3)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MDA-MB-453
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Salmonella enterica subspecies 1 serovar Typhimurium invasion (1) | 672
| BRCA1 | np |
-0,25
|
none
| no |
ReferenceRNAi 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 DetailsStable 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:
|
| Proliferation of cells with active beta-catenin (3) |
| BRCA1 | |
-0,29
|
none
| yes |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-3
Screen Title:
Proliferation of cells with active beta-catenin (3)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MDA-MB-453
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Self-renewal and pluripotency in human embryonic stem cells (1) | NM_007294
| BRCA1 | |
-0,56
|
none
| no |
ReferenceA 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 DetailsStable 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:
|
| Combinatorial effect with anticancer drugs (4): cisplatin | NM_007294
| BRCA1 | np |
2,3
|
Decreased viability with cisplatin
| yes |
ReferenceSmall interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Bartz et al.,
2006
RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug''s mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53(+/-) matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity approximately 4- to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.
Screen DetailsStable ID:
GR00101-A-4
Screen Title:
Combinatorial effect with anticancer drugs (4): cisplatin
Assay:
Viability (synthetic lethal)
Method:
Alamar Blue
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Sigma-Proligo, rp
Reagent Type:
siRNA
Score Type:
Fold EC50 shift
Cutoff:
>= 2
Notes:
Additional information about the primary genome-wide screen
|
| Genome stability | NM_007294
| BRCA1 | np |
sp
|
none
| no |
ReferenceA 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 DetailsStable 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)
|
| Proliferation of cells with active beta-catenin (4) |
| BRCA1 | |
-0,42
|
none
| no |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-4
Screen Title:
Proliferation of cells with active beta-catenin (4)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
T47D
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Combinatorial effect with anticancer drugs (4): cisplatin | NM_007294
| BRCA1 | siRNA 3 - chem. modified |
1,6
|
none
| yes |
ReferenceSmall interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Bartz et al.,
2006
RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug''s mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53(+/-) matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity approximately 4- to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.
Screen DetailsStable ID:
GR00101-A-4
Screen Title:
Combinatorial effect with anticancer drugs (4): cisplatin
Assay:
Viability (synthetic lethal)
Method:
Alamar Blue
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Sigma-Proligo, rp
Reagent Type:
siRNA
Score Type:
Fold EC50 shift
Cutoff:
>= 2
Notes:
Additional information about the primary genome-wide screen
|
| Proliferation of cells with active beta-catenin (2) |
| BRCA1 | |
-0,42
|
none
| yes |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-2
Screen Title:
Proliferation of cells with active beta-catenin (2)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MDA-MB-231
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Inhibitor of DNA binding 2 (ID2) expression regulation | NM_007294
| BRCA1 | np |
np
|
none
| no |
ReferenceLarge scale RNAi screen reveals that the inhibitor of DNA binding 2 (ID2) protein is repressed by p53 family member p63 and functions in human keratinocyte differentiation. Wu et al.,
2011
The inhibitor of DNA binding 2, dominant negative helix-loop-helix protein, ID2, acts as an oncogene and elevated levels of ID2 have been reported in several malignancies. Whereas some inducers of the ID2 gene have been characterized, little is known regarding the proteins capable to repress its expression. We developed siRNA microarrays to perform a large scale loss-of-function screen in human adult keratinocytes engineered to express GFP under the control of the upstream region of ID2 gene. We screened the effect of siRNA-dependent inhibition of 220 cancer-associated genes on the expression of the ID2::GFP reporter construct. Three genes NBN, RAD21, and p63 lead to a repression of ID2 promoter activity. Strikingly NBN and RAD21 are playing on major role in cell cycle progression and mitosis arrest. These results underline the pregnant need to silence ID2 expression at transcript level to promote cell cycle exit. Central to this inhibitory mechanism we find p63, a key transcription factor in epithelial development and differentiation, which binds specific cis-acting sequence within the ID2 gene promoter both in vitro and in vivo. P63 would not suppress ID2 expression, but would rather prevent excessive expression of that protein to enable the onset of keratinocyte differentiation.
Screen DetailsStable ID:
GR00211-A
Screen Title:
Inhibitor of DNA binding 2 (ID2) expression regulation
Assay:
ID2::GFP protein expression
Method:
Fluorescence
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HaCaT
Library:
Qiagen, Human Cancer siRNA Set v2
Reagent Type:
siRNA
Score Type:
GFP ratio medians ranking
Cutoff:
Top 6 for >= 1 replicate
Notes:
|
| Wnt/beta-catenin pathway regulation | 672
| BRCA1 | np |
2,17
|
Upregulation of Wnt/beta-catenin pathway after WNT3A stimulation
| no |
ReferenceBruton's tyrosine kinase revealed as a negative regulator of Wnt-beta-catenin signaling. James et al.,
2009
Wnts are secreted ligands that activate several receptor-mediated signal transduction cascades. Homeostatic Wnt signaling through beta-catenin is required in adults, because either elevation or attenuation of beta-catenin function has been linked to diverse diseases. To contribute to the identification of both protein and pharmacological regulators of this pathway, we describe a combinatorial screen that merged data from a high-throughput screen of known bioactive compounds with an independent focused small interfering RNA screen. Each screen independently revealed Bruton''s tyrosine kinase (BTK) as an inhibitor of Wnt-beta-catenin signaling. Loss of BTK function in human colorectal cancer cells, human B cells, zebrafish embryos, and cells derived from X-linked agammaglobulinemia patients with a mutant BTK gene resulted in elevated Wnt-beta-catenin signaling, confirming that BTK acts as a negative regulator of this pathway. From affinity purification-mass spectrometry and biochemical binding studies, we found that BTK directly interacts with a nuclear component of Wnt-beta-catenin signaling, CDC73. Further, we show that BTK increased the abundance of CDC73 in the absence of stimulation and that CDC73 acted as a repressor of beta-catenin-mediated transcription in human colorectal cancer cells and B cells.
Screen DetailsStable ID:
GR00016-A
Screen Title:
Wnt/beta-catenin pathway regulation
Assay:
Wnt/beta-catenin pathway reporter
Method:
Luminescence
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
RKO
Library:
rp, rp
Reagent Type:
siRNA
Score Type:
Z-score
Cutoff:
> 2
Notes:
|
| Hepatitis C virus replication (1) | 672
| BRCA1 | PL-50015 |
0,9
|
none
| no |
ReferenceA 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 DetailsStable 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:
|
| Proliferation of cells with active beta-catenin (2) |
| BRCA1 | |
1,21
|
none
| yes |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-2
Screen Title:
Proliferation of cells with active beta-catenin (2)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MDA-MB-231
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Homologous recombination DNA double-strand break repair (HR-DSBR) (2) | ENSG00000012048
| BRCA1 | BRCA1 esiRNA 2 |
< -4
|
Decreased homologous recombination repair frequency
| yes |
ReferenceA genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. Słabicki et al.,
2010
DNA repair is essential to maintain genome integrity, and genes with roles in DNA repair are frequently mutated in a variety of human diseases. Repair via homologous recombination typically restores the original DNA sequence without introducing mutations, and a number of genes that are required for homologous recombination DNA double-strand break repair (HR-DSBR) have been identified. However, a systematic analysis of this important DNA repair pathway in mammalian cells has not been reported. Here, we describe a genome-scale endoribonuclease-prepared short interfering RNA (esiRNA) screen for genes involved in DNA double strand break repair. We report 61 genes that influenced the frequency of HR-DSBR and characterize in detail one of the genes that decreased the frequency of HR-DSBR. We show that the gene KIAA0415 encodes a putative helicase that interacts with SPG11 and SPG15, two proteins mutated in hereditary spastic paraplegia (HSP). We identify mutations in HSP patients, discovering KIAA0415/SPG48 as a novel HSP-associated gene, and show that a KIAA0415/SPG48 mutant cell line is more sensitive to DNA damaging drugs. We present the first genome-scale survey of HR-DSBR in mammalian cells providing a dataset that should accelerate the discovery of novel genes with roles in DNA repair and associated medical conditions. The discovery that proteins forming a novel protein complex are required for efficient HR-DSBR and are mutated in patients suffering from HSP suggests a link between HSP and DNA repair.
Screen DetailsStable ID:
GR00151-A-2
Screen Title:
Homologous recombination DNA double-strand break repair (HR-DSBR) (2)
Assay:
(HR-DSBR) DR-GFP reporter
Method:
Flow cytometry
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Custom-made, Custom-made
Reagent Type:
esiRNA
Score Type:
Z-score
Cutoff:
Complex criteria
Notes:
|
| Release from monastrol-induced mitotic arrest | NM_007298
| BRCA1 | np |
0,82
|
none
| no |
ReferenceUBE2S elongates ubiquitin chains on APC/C substrates to promote mitotic exit. Garnett et al.,
2009
The anaphase-promoting complex (APC/C), a ubiquitin ligase, is the target of the spindle-assembly checkpoint (SAC), and it ubiquitylates protein substrates whose degradation regulates progress through mitosis. The identity of the ubiquitin-conjugating (E2) enzymes that work with the APC/C is unclear. In an RNA interference (RNAi) screen for factors that modify release from drug-induced SAC activation, we identified the E2 enzyme UBE2S as an APC/C auxiliary factor that promotes mitotic exit. UBE2S is dispensable in a normal mitosis, but its depletion prolongs drug-induced mitotic arrest and suppresses mitotic slippage. In vitro, UBE2S elongates ubiquitin chains initiated by the E2 enzymes UBCH10 and UBCH5, enhancing the degradation of APC/C substrates by the proteasome. Indeed, following release from SAC-induced mitotic arrest, UBE2S-depleted cells neither degrade crucial APC/C substrates, nor silence this checkpoint, whereas bypassing the SAC through BUBR1 depletion or Aurora-B inhibition negates the requirement for UBE2S. Thus, UBE2S functions with the APC/C in a two-step mechanism to control substrate ubiquitylation that is essential for mitotic exit after prolonged SAC activation, providing a new model for APC/C function in human cells.
Screen DetailsStable ID:
GR00188-A
Screen Title:
Release from monastrol-induced mitotic arrest
Assay:
Histone H3 serine 10 phosphorylation
Method:
Fluorescence
Scope:
Ubiquitin-proteasome system genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
Cal51
Library:
Dharmacon, Ubiquitin-proteasome system siRNA library
Reagent Type:
siRNA
Score Type:
ΔMI standard score
Cutoff:
> 2 AND p < 0.01
Notes:
|
| Melanogenesis | NM_007294
| BRCA1 | np |
0,92
|
none
| no |
ReferenceGenome-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 DetailsStable 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)
|
| Combinatorial effect with anticancer drugs (4): cisplatin | NM_007294
| BRCA1 | siRNA 1 |
1,9
|
none
| yes |
ReferenceSmall interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Bartz et al.,
2006
RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug''s mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53(+/-) matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity approximately 4- to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.
Screen DetailsStable ID:
GR00101-A-4
Screen Title:
Combinatorial effect with anticancer drugs (4): cisplatin
Assay:
Viability (synthetic lethal)
Method:
Alamar Blue
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Sigma-Proligo, rp
Reagent Type:
siRNA
Score Type:
Fold EC50 shift
Cutoff:
>= 2
Notes:
Additional information about the primary genome-wide screen
|
| Proliferation of cells with active beta-catenin (3) |
| BRCA1 | |
0,1
|
none
| yes |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-3
Screen Title:
Proliferation of cells with active beta-catenin (3)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MDA-MB-453
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Proliferation of cells with active beta-catenin (4) |
| BRCA1 | |
-0,29
|
none
| no |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-4
Screen Title:
Proliferation of cells with active beta-catenin (4)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
T47D
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Cell division (2) | ENSG00000012048
| BRCA1 | ENSG00000012048_2 |
sp
|
none
| yes |
ReferenceGenome-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 DetailsStable ID:
GR00098-A-2
Screen Title:
Cell division (2)
Assay:
Cell number and DNA content
Method:
Laser scanning cytometry
Scope:
Selected genes
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:
|
| Proliferation of cells with active beta-catenin (4) |
| BRCA1 | |
1,29
|
none
| no |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-4
Screen Title:
Proliferation of cells with active beta-catenin (4)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
T47D
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Proliferation of cells with active beta-catenin (2) |
| BRCA1 | |
-1,09
|
Decreased viability
| yes |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-2
Screen Title:
Proliferation of cells with active beta-catenin (2)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MDA-MB-231
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Proliferation of cells with active beta-catenin (1) |
| BRCA1 | |
-0,57
|
none
| yes |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-1
Screen Title:
Proliferation of cells with active beta-catenin (1)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MCF7
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Combinatorial effect with anticancer drugs (2): gemcitabine | NM_007296
| BRCA1 | np |
np
|
none
| yes |
ReferenceSmall interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Bartz et al.,
2006
RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug''s mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53(+/-) matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity approximately 4- to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.
Screen DetailsStable ID:
GR00101-A-2
Screen Title:
Combinatorial effect with anticancer drugs (2): gemcitabine
Assay:
Viability (synthetic lethal)
Method:
Alamar Blue
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Sigma-Proligo, rp
Reagent Type:
siRNA
Score Type:
log2 ratio
Cutoff:
2 standard deviations from mean ratio
Notes:
Additional information about the primary genome-wide screen
|
| Combinatorial effect with anticancer drugs (3): paclitaxel | NM_007296
| BRCA1 | np |
np
|
none
| yes |
ReferenceSmall interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Bartz et al.,
2006
RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug''s mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53(+/-) matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity approximately 4- to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.
Screen DetailsStable ID:
GR00101-A-3
Screen Title:
Combinatorial effect with anticancer drugs (3): paclitaxel
Assay:
Viability (synthetic lethal)
Method:
Alamar Blue
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Sigma-Proligo, rp
Reagent Type:
siRNA
Score Type:
log2 ratio
Cutoff:
1.7 standard deviations from mean ratio
Notes:
Additional information about the primary genome-wide screen
|
| Combinatorial effect with anticancer drugs (4): cisplatin | NM_007294
| BRCA1 | siRNA 2 |
1,9
|
none
| yes |
ReferenceSmall interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Bartz et al.,
2006
RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug''s mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53(+/-) matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity approximately 4- to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.
Screen DetailsStable ID:
GR00101-A-4
Screen Title:
Combinatorial effect with anticancer drugs (4): cisplatin
Assay:
Viability (synthetic lethal)
Method:
Alamar Blue
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Sigma-Proligo, rp
Reagent Type:
siRNA
Score Type:
Fold EC50 shift
Cutoff:
>= 2
Notes:
Additional information about the primary genome-wide screen
|
| TP53 interactions (1) | ENSG00000012048
| | np |
sp
|
Decreased viability of wild-type and TP53 knockout cells
| no |
ReferenceA systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly. Krastev et al.,
2011
TP53 (tumour protein 53) is one of the most frequently mutated genes in human cancer and its role during cellular transformation has been studied extensively. However, the homeostatic functions of p53 are less well understood. Here, we explore the molecular dependency network of TP53 through an RNAi-mediated synthetic interaction screen employing two HCT116 isogenic cell lines and a genome-scale endoribonuclease-prepared short interfering RNA library. We identify a variety of TP53 synthetic interactions unmasking the complex connections of p53 to cellular physiology and growth control. Molecular dissection of the TP53 synthetic interaction with UNRIP indicates an enhanced dependency of TP53-negative cells on small nucleolar ribonucleoprotein (snoRNP) assembly. This dependency is mediated by the snoRNP chaperone gene NOLC1 (also known as NOPP140), which we identify as a physiological p53 target gene. This unanticipated function of TP53 in snoRNP assembly highlights the potential of RNAi-mediated synthetic interaction screens to dissect molecular pathways of tumour suppressor genes.
Screen DetailsStable ID:
GR00196-A-1
Screen Title:
TP53 interactions (1)
Assay:
TP53 protein expression and viability
Method:
Fluorescence
Scope:
Genome-wide
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HCT116 ( wildtype and TP53 knockout)
Library:
Custom-made, rp
Reagent Type:
esiRNA
Score Type:
Complex, sp
Cutoff:
Complex criteria
Notes:
|
| Cell viability |
| BRCA1 | v2HS_254648 |
-1,86
|
Increased cell death HMECs cells
| no |
ReferenceCancer proliferation gene discovery through functional genomics. Schlabach et al.,
2008
Retroviral short hairpin RNA (shRNA)-mediated genetic screens in mammalian cells are powerful tools for discovering loss-of-function phenotypes. We describe a highly parallel multiplex methodology for screening large pools of shRNAs using half-hairpin barcodes for microarray deconvolution. We carried out dropout screens for shRNAs that affect cell proliferation and viability in cancer cells and normal cells. We identified many shRNAs to be antiproliferative that target core cellular processes, such as the cell cycle and protein translation, in all cells examined. Moreover, we identified genes that are selectively required for proliferation and survival in different cell lines. Our platform enables rapid and cost-effective genome-wide screens to identify cancer proliferation and survival genes for target discovery. Such efforts are complementary to the Cancer Genome Atlas and provide an alternative functional view of cancer cells.
Screen DetailsStable ID:
GR00103-A-0
Screen Title:
Cell viability
Assay:
Cell viability
Method:
Micoarray hybridization
Scope:
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
DLD-1, HCT116 (colon cancer); HCC1954 (breast cancer); HMECs (mammary epithelia cells)
Library:
, shRNA-mir (G. Hannon)
Reagent Type:
shRNA
Score Type:
log ratio
Cutoff:
<= -1 (>= 50% cell death)
Notes:
|
| Proliferation of cells with active beta-catenin (3) |
| BRCA1 | |
-1,28
|
Decreased viability
| yes |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-3
Screen Title:
Proliferation of cells with active beta-catenin (3)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MDA-MB-453
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Proliferation of cells with active beta-catenin (1) |
| BRCA1 | |
0,87
|
none
| yes |
ReferenceCK1epsilon is required for breast cancers dependent on beta-catenin activity. Kim et al.,
2010
Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date.
Screen DetailsStable ID:
GR00221-A-1
Screen Title:
Proliferation of cells with active beta-catenin (1)
Assay:
Viability
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MCF7
Library:
The RNAi Consortium (TRC), TRC shRNA Library
Reagent Type:
shRNA
Score Type:
B-score
Cutoff:
< -1
Notes:
Essential gene: gene with B-score < -1 for >= 2 shRNAs
|
| Human papillomavirus oncogene expression regulation (1) | 672
| BRCA1 | |
-0,6
|
none
| no |
ReferenceGenome-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 DetailsStable 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
|
| Combinatorial effect with anticancer drugs (4): cisplatin | NM_007294
| BRCA1 | siRNA 3 |
2
|
Decreased viability with cisplatin
| yes |
ReferenceSmall interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Bartz et al.,
2006
RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug''s mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53(+/-) matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity approximately 4- to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.
Screen DetailsStable ID:
GR00101-A-4
Screen Title:
Combinatorial effect with anticancer drugs (4): cisplatin
Assay:
Viability (synthetic lethal)
Method:
Alamar Blue
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Sigma-Proligo, rp
Reagent Type:
siRNA
Score Type:
Fold EC50 shift
Cutoff:
>= 2
Notes:
Additional information about the primary genome-wide screen
|
| Cell division (3) | ENSG00000012048
| BRCA1 | ENSG00000012048 |
-1,7
|
none
| yes |
ReferenceGenome-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 DetailsStable ID:
GR00098-A-3
Screen Title:
Cell division (3)
Assay:
Histone H3 phosphorylation; alpha-tubulin and pericentrin protein expression
Method:
Fluorescence
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Custom-made, rp
Reagent Type:
esiRNA
Score Type:
Mitotic index
Cutoff:
>= 2
Notes:
|
| Combinatorial effect with paclitaxel | NM_007294
| BRCA1 | np |
1,1
|
none
| no |
ReferenceSynthetic 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 DetailsStable 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
|
| Cell division (4) | ENSG00000012048
| BRCA1 | ENSG00000012048 |
1,5
|
none
| no |
ReferenceGenome-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 DetailsStable ID:
GR00098-A-4
Screen Title:
Cell division (4)
Assay:
Cell size (forward scatter)
Method:
Flow cytometry
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Custom-made, rp
Reagent Type:
esiRNA
Score Type:
Cell size
Cutoff:
>= 2
Notes:
|
| Combinatorial effect with anticancer drugs (1): cisplatin | NM_007296
| BRCA1 | np |
np
|
Synthetic lethal with cisplatin
| yes |
ReferenceSmall interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Bartz et al.,
2006
RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug''s mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53(+/-) matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity approximately 4- to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.
Screen DetailsStable ID:
GR00101-A-1
Screen Title:
Combinatorial effect with anticancer drugs (1): cisplatin
Assay:
Viability (synthetic lethal)
Method:
Alamar Blue
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Sigma-Proligo, rp
Reagent Type:
siRNA
Score Type:
log2 ratio
Cutoff:
2 standard deviations from mean ratio
Notes:
Additional information about the primary genome-wide screen
|