| Proliferation of cells with active beta-catenin (2) |
| AKT1 | |
-0,21
|
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
|
| Ciliogenesis and cilium length (1) | 207
| AKT1 | 42811 |
109,18
|
none
| no |
ReferenceFunctional 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 DetailsStable 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:
|
| Wnt/beta-catenin pathway regulation | 207
| AKT1 | np |
0,68
|
none
| 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:
|
| Wnt signaling |
| AKT1 | AKT1_siRNA-Single-2 |
25,03
|
Wnt reporter downregulated
| no |
ReferenceNew regulators of Wnt/beta-catenin signaling revealed by integrative molecular screening. Major et al.,
2008
The identification and characterization of previously unidentified signal transduction molecules has expanded our understanding of biological systems and facilitated the development of mechanism-based therapeutics. We present a highly validated small interfering RNA (siRNA) screen that functionally annotates the human genome for modulation of the Wnt/beta-catenin signal transduction pathway. Merging these functional data with an extensive Wnt/beta-catenin protein interaction network produces an integrated physical and functional map of the pathway. The power of this approach is illustrated by the positioning of siRNA screen hits into discrete physical complexes of proteins. Similarly, this approach allows one to filter discoveries made through protein-protein interaction screens for functional contribution to the phenotype of interest. Using this methodology, we characterized AGGF1 as a nuclear chromatin-associated protein that participates in beta-catenin-mediated transcription in human colon cancer cells.
Screen DetailsStable ID:
GR00017-A-0
Screen Title:
Wnt signaling
Assay:
Wnt signaling
Method:
Dual luciferase
Scope:
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
DLD1 colon adenocarcinoma cells
Library:
, Custom-made library
Reagent Type:
siRNA
Score Type:
Percentage Wnt reporter activity
Cutoff:
np
Notes:
|
| Proliferation of cells with active beta-catenin (4) |
| AKT1 | |
-1,75
|
Decreased viability
| 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 (3) |
| AKT1 | |
-0,45
|
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
|
| HIV-1 infection (2) | 207
| AKT1 | |
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
|
| Proliferation of cells with active beta-catenin (1) |
| AKT1 | |
-0,47
|
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
|
| Proliferation of cells with active beta-catenin (3) |
| AKT1 | |
-0,96
|
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
|
| Ciliogenesis and cilium length (1) | 207
| AKT1 | 42811 |
87,51
|
none
| no |
ReferenceFunctional 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 DetailsStable 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) | 207
| AKT1 | |
0,3
|
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
|
| Proliferation of cells with active beta-catenin (1) |
| AKT1 | |
-1,9
|
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-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 gemcitabine |
| AKT1 | AKT1_B |
-0,89
|
none
| no |
ReferenceSynthetic lethal RNAi screening identifies sensitizing targets for gemcitabine therapy in pancreatic cancer. Azorsa et al.,
2009
Pancreatic cancer retains a poor prognosis among the gastrointestinal cancers. It affects 230,000 individuals worldwide, has a very high mortality rate, and remains one of the most challenging malignancies to treat successfully. Treatment with gemcitabine, the most widely used chemotherapeutic against pancreatic cancer, is not curative and resistance may occur. Combinations of gemcitabine with other chemotherapeutic drugs or biological agents have resulted in limited improvement.
Screen DetailsStable ID:
GR00225-A
Screen Title:
Combinatorial effect with gemcitabine
Assay:
Viability (synthetic lethal)
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MIA PaCa-2
Library:
Qiagen, Validated kinase siRNA library version 1.0
Reagent Type:
siRNA
Score Type:
log2 ratio
Cutoff:
1.65 SD below mean ratio level
Notes:
|
| Melanogenesis | NM_005163
| AKT1 | np |
0,85
|
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)
|
| Proliferation of cells with active beta-catenin (4) |
| AKT1 | |
-2,75
|
Decreased viability
| 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
|
| tau phosphorylation |
| AKT1 | AKT1 s1 |
sp
|
none
| no |
ReferenceHigh-content siRNA screening of the kinome identifies kinases involved in Alzheimer's disease-related tau hyperphosphorylation. Azorsa et al.,
2010
Neurofibrillary tangles (NFT), a cardinal neuropathological feature of Alzheimer''s disease (AD) that is highly correlated with synaptic loss and dementia severity, appear to be partly attributable to increased phosphorylation of the microtubule stabilizing protein tau at certain AD-related residues. Identifying the kinases involved in the pathologic phosphorylation of tau may provide targets at which to aim new AD-modifying treatments.
Screen DetailsStable ID:
GR00143-A
Screen Title:
tau phosphorylation
Assay:
Total tau and 12E8 tau protein expression
Method:
Fluorescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
H4 overexpressing 4RON tau
Library:
Qiagen, Validated human kinase siRNA Set 2.0
Reagent Type:
siRNA
Score Type:
p-value
Cutoff:
Complex criteria
Notes:
|
| Therapeutic kinase targets in neuroblastoma (3) | 207
| AKT1 | AKT1 |
1,02
|
none
| yes |
ReferenceRNAi screen of the protein kinome identifies checkpoint kinase 1 (CHK1) as a therapeutic target in neuroblastoma. Cole et al.,
2011
Neuroblastoma is a childhood cancer that is often fatal despite intense multimodality therapy. In an effort to identify therapeutic targets for this disease, we performed a comprehensive loss-of-function screen of the protein kinome. Thirty kinases showed significant cellular cytotoxicity when depleted, with loss of the cell cycle checkpoint kinase 1 (CHK1/CHEK1) being the most potent. CHK1 mRNA expression was higher in MYC-Neuroblastoma-related (MYCN)-amplified (P < 0.0001) and high-risk (P = 0.03) tumors. Western blotting revealed that CHK1 was constitutively phosphorylated at the ataxia telangiectasia response kinase target site Ser345 and the autophosphorylation site Ser296 in neuroblastoma cell lines. This pattern was also seen in six of eight high-risk primary tumors but not in control nonneuroblastoma cell lines or in seven of eight low-risk primary tumors. Neuroblastoma cells were sensitive to the two CHK1 inhibitors SB21807 and TCS2312, with median IC(50) values of 564 nM and 548 nM, respectively. In contrast, the control lines had high micromolar IC(50) values, indicating a strong correlation between CHK1 phosphorylation and CHK1 inhibitor sensitivity (P = 0.0004). Furthermore, cell cycle analysis revealed that CHK1 inhibition in neuroblastoma cells caused apoptosis during S-phase, consistent with its role in replication fork progression. CHK1 inhibitor sensitivity correlated with total MYC(N) protein levels, and inducing MYCN in retinal pigmented epithelial cells resulted in CHK1 phosphorylation, which caused growth inhibition when inhibited. These data show the power of a functional RNAi screen to identify tractable therapeutical targets in neuroblastoma and support CHK1 inhibition strategies in this disease.
Screen DetailsStable ID:
GR00193-A-3
Screen Title:
Therapeutic kinase targets in neuroblastoma (3)
Assay:
Substrate adherent cell growth
Method:
rp
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
SKNAS
Library:
Thermo Scientific, Kinase siGenome library
Reagent Type:
siRNA
Score Type:
Relative growth
Cutoff:
0.5 standard deviations below mean
Notes:
|
| Focal adhesion formation | 207
| AKT1 | np |
sp
|
none
| no |
ReferenceMultiparametric analysis of focal adhesion formation by RNAi-mediated gene knockdown. Winograd-Katz et al.,
2009
Cell adhesion to the extracellular matrix is mediated by elaborate networks of multiprotein complexes consisting of adhesion receptors, cytoskeletal components, signaling molecules, and diverse adaptor proteins. To explore how specific molecular pathways function in the assembly of focal adhesions (FAs), we performed a high-throughput, high-resolution, microscopy-based screen. We used small interfering RNAs (siRNAs) to target human kinases, phosphatases, and migration- and adhesion-related genes. Multiparametric image analysis of control and of siRNA-treated cells revealed major correlations between distinct morphological FA features. Clustering analysis identified different gene families whose perturbation induced similar effects, some of which uncoupled the interfeature correlations. Based on these findings, we propose a model for the molecular hierarchy of FA formation, and tested its validity by dynamic analysis of FA formation and turnover. This study provides a comprehensive information resource on the molecular regulation of multiple cell adhesion features, and sheds light on signaling mechanisms regulating the formation of integrin adhesions.
Screen DetailsStable ID:
GR00210-A
Screen Title:
Focal adhesion formation
Assay:
paxillin protein expression
Method:
Fluorescence
Scope:
Kinases, phosphatases and selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Thermo Fisher Scientific, SMARTpool siARRAY siRNA Libraries
Reagent Type:
siRNA
Score Type:
Z-score
Cutoff:
> 3.5 OR < -3.5
Notes:
|
| TP53 interactions (1) | ENSG00000142208
| | np |
sp
|
none
| 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:
|
| Wnt signaling |
| AKT1 | AKT1_siRNA-Single-1 |
39
|
Wnt reporter downregulated
| no |
ReferenceNew regulators of Wnt/beta-catenin signaling revealed by integrative molecular screening. Major et al.,
2008
The identification and characterization of previously unidentified signal transduction molecules has expanded our understanding of biological systems and facilitated the development of mechanism-based therapeutics. We present a highly validated small interfering RNA (siRNA) screen that functionally annotates the human genome for modulation of the Wnt/beta-catenin signal transduction pathway. Merging these functional data with an extensive Wnt/beta-catenin protein interaction network produces an integrated physical and functional map of the pathway. The power of this approach is illustrated by the positioning of siRNA screen hits into discrete physical complexes of proteins. Similarly, this approach allows one to filter discoveries made through protein-protein interaction screens for functional contribution to the phenotype of interest. Using this methodology, we characterized AGGF1 as a nuclear chromatin-associated protein that participates in beta-catenin-mediated transcription in human colon cancer cells.
Screen DetailsStable ID:
GR00017-A-0
Screen Title:
Wnt signaling
Assay:
Wnt signaling
Method:
Dual luciferase
Scope:
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
DLD1 colon adenocarcinoma cells
Library:
, Custom-made library
Reagent Type:
siRNA
Score Type:
Percentage Wnt reporter activity
Cutoff:
np
Notes:
|
| Self-renewal and pluripotency in human embryonic stem cells (1) | NM_005163
| AKT1 | |
0,93
|
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:
|
| Proliferation of cells with active beta-catenin (3) |
| AKT1 | |
-1,61
|
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 (3) |
| AKT1 | |
0,97
|
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
|
| Cell migration |
| AKT1 | np |
np
|
Weaker migration
| no |
ReferenceIdentification of genes that regulate epithelial cell migration using an siRNA screening approach. Simpson et al.,
2008
To provide a systematic analysis of genes that regulate epithelial cell migration, we performed a high throughput wound healing screen with MCF-10A breast epithelial cells, using siRNAs targeting 1,081 human genes encoding phosphatases, kinases and proteins predicted to influence cell migration and adhesion. The primary screen identified three categories of hits: those that accelerate, those that inhibit and those that impair migration with associated effects on cell proliferation or metabolism. Extensive validation of all the hits yielded 66 high confidence genes that, when downregulated, either accelerated or impaired migration; 42 of these high confidence genes have not been previously associated with motility or adhesion. Time-lapse video microscopy revealed a broad spectrum of phenotypic changes involving alterations in the extent and nature of disruption of cell-cell adhesion, directionality of motility, cell polarity and shape, and protrusion dynamics. Informatics analysis highlighted three major signalling nodes, beta-catenin, beta1-integrin and actin, and a large proportion of the genes that accelerated migration impaired cell-cell adhesion.
Screen DetailsStable ID:
GR00055-A-0
Screen Title:
Cell migration
Assay:
Cell migration and viability
Method:
High content (microscopy) / fluorescence
Scope:
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MCF-10A (breast epithelium)
Library:
, Metabolell migration/adhesion
Reagent Type:
siRNA
Score Type:
Visual inspection
Cutoff:
np
Notes:
|
| Human papillomavirus oncogene expression regulation (1) | 207
| AKT1 | |
0,91
|
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
|
| Proliferation of cells with active beta-catenin (2) |
| AKT1 | |
0,71
|
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) (1) | ENSG00000142208
| AKT1 | np |
-1,67
|
none
| no |
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:
|
| Proliferation of cells with active beta-catenin (2) |
| AKT1 | |
-0,62
|
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
|
| Therapeutic kinase targets in neuroblastoma (1) | 207
| AKT1 | AKT1 |
0,95
|
none
| yes |
ReferenceRNAi screen of the protein kinome identifies checkpoint kinase 1 (CHK1) as a therapeutic target in neuroblastoma. Cole et al.,
2011
Neuroblastoma is a childhood cancer that is often fatal despite intense multimodality therapy. In an effort to identify therapeutic targets for this disease, we performed a comprehensive loss-of-function screen of the protein kinome. Thirty kinases showed significant cellular cytotoxicity when depleted, with loss of the cell cycle checkpoint kinase 1 (CHK1/CHEK1) being the most potent. CHK1 mRNA expression was higher in MYC-Neuroblastoma-related (MYCN)-amplified (P < 0.0001) and high-risk (P = 0.03) tumors. Western blotting revealed that CHK1 was constitutively phosphorylated at the ataxia telangiectasia response kinase target site Ser345 and the autophosphorylation site Ser296 in neuroblastoma cell lines. This pattern was also seen in six of eight high-risk primary tumors but not in control nonneuroblastoma cell lines or in seven of eight low-risk primary tumors. Neuroblastoma cells were sensitive to the two CHK1 inhibitors SB21807 and TCS2312, with median IC(50) values of 564 nM and 548 nM, respectively. In contrast, the control lines had high micromolar IC(50) values, indicating a strong correlation between CHK1 phosphorylation and CHK1 inhibitor sensitivity (P = 0.0004). Furthermore, cell cycle analysis revealed that CHK1 inhibition in neuroblastoma cells caused apoptosis during S-phase, consistent with its role in replication fork progression. CHK1 inhibitor sensitivity correlated with total MYC(N) protein levels, and inducing MYCN in retinal pigmented epithelial cells resulted in CHK1 phosphorylation, which caused growth inhibition when inhibited. These data show the power of a functional RNAi screen to identify tractable therapeutical targets in neuroblastoma and support CHK1 inhibition strategies in this disease.
Screen DetailsStable ID:
GR00193-A-1
Screen Title:
Therapeutic kinase targets in neuroblastoma (1)
Assay:
Substrate adherent cell growth
Method:
rp
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
EBC1
Library:
Thermo Scientific, Kinase siGenome library
Reagent Type:
siRNA
Score Type:
Relative growth
Cutoff:
0.5 standard deviations below mean
Notes:
|
| Proliferation of cells with active beta-catenin (2) |
| AKT1 | |
-0,55
|
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) |
| AKT1 | |
-0,97
|
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 (4) |
| AKT1 | |
0,18
|
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 paclitaxel | NM_005163
| AKT1 | np |
0,86
|
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
|
| Ciliogenesis and cilium length (1) | 207
| AKT1 | 632 |
16,24
|
none
| no |
ReferenceFunctional 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 DetailsStable 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:
|
| tau phosphorylation |
| AKT1 | AKT1 s2 |
sp
|
none
| no |
ReferenceHigh-content siRNA screening of the kinome identifies kinases involved in Alzheimer's disease-related tau hyperphosphorylation. Azorsa et al.,
2010
Neurofibrillary tangles (NFT), a cardinal neuropathological feature of Alzheimer''s disease (AD) that is highly correlated with synaptic loss and dementia severity, appear to be partly attributable to increased phosphorylation of the microtubule stabilizing protein tau at certain AD-related residues. Identifying the kinases involved in the pathologic phosphorylation of tau may provide targets at which to aim new AD-modifying treatments.
Screen DetailsStable ID:
GR00143-A
Screen Title:
tau phosphorylation
Assay:
Total tau and 12E8 tau protein expression
Method:
Fluorescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
H4 overexpressing 4RON tau
Library:
Qiagen, Validated human kinase siRNA Set 2.0
Reagent Type:
siRNA
Score Type:
p-value
Cutoff:
Complex criteria
Notes:
|
| Proliferation of cells with active beta-catenin (1) |
| AKT1 | |
-0,92
|
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 gemcitabine |
| AKT1 | AKT1_A |
-0,21
|
none
| no |
ReferenceSynthetic lethal RNAi screening identifies sensitizing targets for gemcitabine therapy in pancreatic cancer. Azorsa et al.,
2009
Pancreatic cancer retains a poor prognosis among the gastrointestinal cancers. It affects 230,000 individuals worldwide, has a very high mortality rate, and remains one of the most challenging malignancies to treat successfully. Treatment with gemcitabine, the most widely used chemotherapeutic against pancreatic cancer, is not curative and resistance may occur. Combinations of gemcitabine with other chemotherapeutic drugs or biological agents have resulted in limited improvement.
Screen DetailsStable ID:
GR00225-A
Screen Title:
Combinatorial effect with gemcitabine
Assay:
Viability (synthetic lethal)
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MIA PaCa-2
Library:
Qiagen, Validated kinase siRNA library version 1.0
Reagent Type:
siRNA
Score Type:
log2 ratio
Cutoff:
1.65 SD below mean ratio level
Notes:
|
| Proliferation of cells with active beta-catenin (2) |
| AKT1 | |
-1,19
|
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
|
| Hepatitis C virus replication (1) | 207
| AKT1 | PL-50001 |
0,92
|
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 (3) |
| AKT1 | |
-1,27
|
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 (2) |
| AKT1 | |
0,36
|
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 (1) |
| AKT1 | |
0,08
|
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
|
| Aryl hydrocarbon receptor (AhR) transduction pathway regulation | 207
| AKT1 | AKT1_3 AKT1_2 AKT1_1 |
np
|
none
| no |
ReferenceRNAi-based screening identifies kinases interfering with dioxin-mediated up-regulation of CYP1A1 activity. Gilot et al.,
2011
The aryl hydrocarbon receptor (AhR) is a transcription factor activated by several environmental pollutants, such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and involved in carcinogenesis and various physiological processes, including immune response and endocrine functions. Characterization of kinases-related AhR transduction pathway remains an important purpose.
Screen DetailsStable ID:
GR00155-A
Screen Title:
Aryl hydrocarbon receptor (AhR) transduction pathway regulation
Assay:
TCDD-induced CYP1A1-related EROD activity and cell viability
Method:
Fluorescence and methylene blue
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MCF-7
Library:
Sigma-Genesys, MISSION siRNA Human Kinase Panel library
Reagent Type:
siRNA
Score Type:
Z-score
Cutoff:
Top 150 for >= 2 of 3 siRNAs AND no effect on cell proliferation
Notes:
|
| Genome stability | NM_005163
| AKT1 | 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 (2) |
| AKT1 | |
1,52
|
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) |
| AKT1 | |
-1,6
|
Decreased viability
| 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 (4) |
| AKT1 | |
0
|
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
|
| Ciliogenesis and cilium length (1) | 207
| AKT1 | 118270 |
-77,32
|
none
| no |
ReferenceFunctional 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 DetailsStable 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:
|
| HIV-1 infection (1) | 207
| AKT1 | |
49
|
Decreased p24 protein expression
| no |
ReferenceIdentification of host proteins required for HIV infection through a functional genomic screen. Brass et al.,
2008
HIV-1 exploits multiple host proteins during infection. We performed a large-scale small interfering RNA screen to identify host factors required by HIV-1 and identified more than 250 HIV-dependency factors (HDFs). These proteins participate in a broad array of cellular functions and implicate new pathways in the viral life cycle. Further analysis revealed previously unknown roles for retrograde Golgi transport proteins (Rab6 and Vps53) in viral entry, a karyopherin (TNPO3) in viral integration, and the Mediator complex (Med28) in viral transcription. Transcriptional analysis revealed that HDF genes were enriched for high expression in immune cells, suggesting that viruses evolve in host cells that optimally perform the functions required for their life cycle. This effort illustrates the power with which RNA interference and forward genetics can be used to expose the dependencies of human pathogens such as HIV, and in so doing identify potential targets for therapy.
Screen DetailsStable ID:
GR00163-A-1
Screen Title:
HIV-1 infection (1)
Assay:
p24 protein expression
Method:
Fluorescence
Scope:
Genome-wide
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
TZM-bl
Library:
Dharmacon, siARRAY siRNA Library
Reagent Type:
siRNA
Score Type:
Percentage of infected cells
Cutoff:
>= 2 standard deviations below plate mean AND viability <= 2 standard deviations below plate mean
Notes:
|
| Proliferation of cells with active beta-catenin (4) |
| AKT1 | |
-0,17
|
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 (1) |
| AKT1 | |
0,97
|
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
|
| Hepatitis C virus replication (1) | 207
| AKT1 | PL-50004 |
0,85
|
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:
|
| Ciliogenesis and cilium length (1) | 207
| AKT1 | 118270 |
-41,72
|
none
| no |
ReferenceFunctional 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 DetailsStable 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:
|
| Therapeutic kinase targets in neuroblastoma (4) | 207
| AKT1 | AKT1 |
4,01
|
none
| no |
ReferenceRNAi screen of the protein kinome identifies checkpoint kinase 1 (CHK1) as a therapeutic target in neuroblastoma. Cole et al.,
2011
Neuroblastoma is a childhood cancer that is often fatal despite intense multimodality therapy. In an effort to identify therapeutic targets for this disease, we performed a comprehensive loss-of-function screen of the protein kinome. Thirty kinases showed significant cellular cytotoxicity when depleted, with loss of the cell cycle checkpoint kinase 1 (CHK1/CHEK1) being the most potent. CHK1 mRNA expression was higher in MYC-Neuroblastoma-related (MYCN)-amplified (P < 0.0001) and high-risk (P = 0.03) tumors. Western blotting revealed that CHK1 was constitutively phosphorylated at the ataxia telangiectasia response kinase target site Ser345 and the autophosphorylation site Ser296 in neuroblastoma cell lines. This pattern was also seen in six of eight high-risk primary tumors but not in control nonneuroblastoma cell lines or in seven of eight low-risk primary tumors. Neuroblastoma cells were sensitive to the two CHK1 inhibitors SB21807 and TCS2312, with median IC(50) values of 564 nM and 548 nM, respectively. In contrast, the control lines had high micromolar IC(50) values, indicating a strong correlation between CHK1 phosphorylation and CHK1 inhibitor sensitivity (P = 0.0004). Furthermore, cell cycle analysis revealed that CHK1 inhibition in neuroblastoma cells caused apoptosis during S-phase, consistent with its role in replication fork progression. CHK1 inhibitor sensitivity correlated with total MYC(N) protein levels, and inducing MYCN in retinal pigmented epithelial cells resulted in CHK1 phosphorylation, which caused growth inhibition when inhibited. These data show the power of a functional RNAi screen to identify tractable therapeutical targets in neuroblastoma and support CHK1 inhibition strategies in this disease.
Screen DetailsStable ID:
GR00193-A-4
Screen Title:
Therapeutic kinase targets in neuroblastoma (4)
Assay:
Substrate adherent cell growth
Method:
rp
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
NLF
Library:
Thermo Scientific, Kinase siGenome library
Reagent Type:
siRNA
Score Type:
Relative growth
Cutoff:
0.5 standard deviations below mean
Notes:
|
| Self-renewal and pluripotency in human embryonic stem cells (1) | NM_005163
| AKT1 | M-003000-02 |
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:
|
| Proliferation of cells with active beta-catenin (1) |
| AKT1 | |
-0,5
|
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
|
| TRAIL-induced apoptosis | NM_5163
| AKT1 | np |
0,14
|
Decreased viability with TRAIL
| no |
ReferenceIdentification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Aza-Blanc et al.,
2003
New opportunities in mammalian functional genomics are emerging through the combination of high throughput technology and methods that allow manipulation of gene expression in living cells. Here we describe the application of an RNAi-based forward genomics approach toward understanding the biology and mechanism of TRAIL-induced apoptosis. TRAIL is a TNF superfamily member that induces selective cytotoxicity of tumor cells when bound to its cognate receptors. In addition to detecting well-characterized genes in the apoptosis pathway, we uncover several modulators including DOBI, a gene required for progression of the apoptotic signal through the intrinsic mitochondrial cell death pathway, and MIRSA, a gene that acts to limit TRAIL-induced apoptosis. Moreover, our data suggest a role for MYC and the WNT pathway in maintaining susceptibility to TRAIL. Collectively, these observations offer several insights on how TRAIL mediates the selective killing of tumor cells and demonstrate the utility of large-scale RNAi screens in mammalian cells.
Screen DetailsStable ID:
GR00154-A
Screen Title:
TRAIL-induced apoptosis
Assay:
Viability
Method:
Alamar Blue
Scope:
Kinases and selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Dharmacon, np
Reagent Type:
siRNA
Score Type:
Sensitivity ratio
Cutoff:
Top 20 AND bottom 20
Notes:
|
| Tamoxifen sensitization |
| AKT1 | np |
-4,57
|
Increases Tamoxifen sensitivity
| no |
ReferenceParallel RNAi and compound screens identify the PDK1 pathway as a target for tamoxifen sensitization. Iorns et al.,
2009
Tamoxifen is the most commonly used drug to treat breast cancer and acts by blocking ERalpha (oestrogen receptor alpha) signalling. Although highly effective, its usefulness is limited by the development of resistance. Given this, strategies that limit resistance by sensitizing cells to tamoxifen may be of use in the clinic. To gain insight into how this might be achieved, we used chemical and genetic screens to identify targets and small-molecule inhibitors that cause tamoxifen sensitization. A high-throughput genetic screen, using an RNA interference library targeting 779 kinases and related proteins, identified the PDK1 (phosphoinositide-dependent kinase 1) signalling pathway as a strong determinant of sensitivity to multiple ERalpha antagonists, including tamoxifen. A chemical screen using existing drugs and known kinase inhibitors also identified inhibitors of the PDK1 pathway, including triciribine and tetrandrine. Aside from identifying novel agents and targets for tamoxifen sensitization, this approach also provides evidence that performing chemical and genetic screens in parallel may be useful.
Screen DetailsStable ID:
GR00120-A-0
Screen Title:
Tamoxifen sensitization
Assay:
Cell viability
Method:
ATP levels
Scope:
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MCF-7 (breast cancer)
Library:
, Dharmacon (kinases)
Reagent Type:
siRNA
Score Type:
Z-score
Cutoff:
<= -4
Notes:
|
| Proliferation of cells with active beta-catenin (1) |
| AKT1 | |
-1,15
|
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-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 gemcitabine |
| AKT1 | AKT1_A |
-0,04
|
none
| no |
ReferenceSynthetic lethal RNAi screening identifies sensitizing targets for gemcitabine therapy in pancreatic cancer. Azorsa et al.,
2009
Pancreatic cancer retains a poor prognosis among the gastrointestinal cancers. It affects 230,000 individuals worldwide, has a very high mortality rate, and remains one of the most challenging malignancies to treat successfully. Treatment with gemcitabine, the most widely used chemotherapeutic against pancreatic cancer, is not curative and resistance may occur. Combinations of gemcitabine with other chemotherapeutic drugs or biological agents have resulted in limited improvement.
Screen DetailsStable ID:
GR00225-A
Screen Title:
Combinatorial effect with gemcitabine
Assay:
Viability (synthetic lethal)
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MIA PaCa-2
Library:
Qiagen, Validated kinase siRNA library version 1.0
Reagent Type:
siRNA
Score Type:
log2 ratio
Cutoff:
1.65 SD below mean ratio level
Notes:
|
| Therapeutic kinase targets in neuroblastoma (2) | 207
| AKT1 | AKT1 |
0,92
|
none
| yes |
ReferenceRNAi screen of the protein kinome identifies checkpoint kinase 1 (CHK1) as a therapeutic target in neuroblastoma. Cole et al.,
2011
Neuroblastoma is a childhood cancer that is often fatal despite intense multimodality therapy. In an effort to identify therapeutic targets for this disease, we performed a comprehensive loss-of-function screen of the protein kinome. Thirty kinases showed significant cellular cytotoxicity when depleted, with loss of the cell cycle checkpoint kinase 1 (CHK1/CHEK1) being the most potent. CHK1 mRNA expression was higher in MYC-Neuroblastoma-related (MYCN)-amplified (P < 0.0001) and high-risk (P = 0.03) tumors. Western blotting revealed that CHK1 was constitutively phosphorylated at the ataxia telangiectasia response kinase target site Ser345 and the autophosphorylation site Ser296 in neuroblastoma cell lines. This pattern was also seen in six of eight high-risk primary tumors but not in control nonneuroblastoma cell lines or in seven of eight low-risk primary tumors. Neuroblastoma cells were sensitive to the two CHK1 inhibitors SB21807 and TCS2312, with median IC(50) values of 564 nM and 548 nM, respectively. In contrast, the control lines had high micromolar IC(50) values, indicating a strong correlation between CHK1 phosphorylation and CHK1 inhibitor sensitivity (P = 0.0004). Furthermore, cell cycle analysis revealed that CHK1 inhibition in neuroblastoma cells caused apoptosis during S-phase, consistent with its role in replication fork progression. CHK1 inhibitor sensitivity correlated with total MYC(N) protein levels, and inducing MYCN in retinal pigmented epithelial cells resulted in CHK1 phosphorylation, which caused growth inhibition when inhibited. These data show the power of a functional RNAi screen to identify tractable therapeutical targets in neuroblastoma and support CHK1 inhibition strategies in this disease.
Screen DetailsStable ID:
GR00193-A-2
Screen Title:
Therapeutic kinase targets in neuroblastoma (2)
Assay:
Substrate adherent cell growth
Method:
rp
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
KELLY
Library:
Thermo Scientific, Kinase siGenome library
Reagent Type:
siRNA
Score Type:
Relative growth
Cutoff:
0.5 standard deviations below mean
Notes:
|
| Melanogenesis | NM_005163
| AKT1 | np |
0,99
|
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)
|
| Proliferation of cells with active beta-catenin (2) |
| AKT1 | |
1,45
|
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 (1) |
| AKT1 | |
-0,41
|
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
|
| Proliferation of cells with active beta-catenin (3) |
| AKT1 | |
1,99
|
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
|
| Apoptosis regulation after Chlamydia trachomatis serovar L2 infection | 207
| AKT1 | np |
np
|
Decreased viability after Chlamydia trachomatis serovar L2 infection and TNF-alpha/CHX stimulation
| yes |
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:
|
| Combinatorial effect with gemcitabine |
| AKT1 | AKT1_B |
-0,35
|
none
| no |
ReferenceSynthetic lethal RNAi screening identifies sensitizing targets for gemcitabine therapy in pancreatic cancer. Azorsa et al.,
2009
Pancreatic cancer retains a poor prognosis among the gastrointestinal cancers. It affects 230,000 individuals worldwide, has a very high mortality rate, and remains one of the most challenging malignancies to treat successfully. Treatment with gemcitabine, the most widely used chemotherapeutic against pancreatic cancer, is not curative and resistance may occur. Combinations of gemcitabine with other chemotherapeutic drugs or biological agents have resulted in limited improvement.
Screen DetailsStable ID:
GR00225-A
Screen Title:
Combinatorial effect with gemcitabine
Assay:
Viability (synthetic lethal)
Method:
Luminescence
Scope:
Kinases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MIA PaCa-2
Library:
Qiagen, Validated kinase siRNA library version 1.0
Reagent Type:
siRNA
Score Type:
log2 ratio
Cutoff:
1.65 SD below mean ratio level
Notes:
|
| Cell division (1) | ENSG00000142208
| AKT1 | ENSG00000142208 |
sp
|
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-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:
|
| HIV-1 infection (1) | 207
| AKT1 | |
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
|
| Proliferation of cells with active beta-catenin (3) |
| AKT1 | |
-0,12
|
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
|
| Ciliogenesis and cilium length (1) | 207
| AKT1 | 632 |
67,43
|
none
| no |
ReferenceFunctional 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 DetailsStable 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:
|
| Salmonella enterica subspecies 1 serovar Typhimurium invasion (1) | 207
| AKT1 | np |
-0,15
|
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:
|
| Combinatorial effect with paclitaxel | NM_005163
| AKT1 | np |
0,91
|
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
|
| Proliferation of cells with active beta-catenin (4) |
| AKT1 | |
-2,34
|
Decreased viability
| 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
|