| Ciliogenesis and cilium length (1) | 8517
| IKBKG | 139260 |
46.45
|
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:
|
| Ciliogenesis and cilium length (1) | 8517
| IKBKG | 139260 |
31.5
|
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) | 8517
| IKBKG | |
2.09
|
Increased HPV18 LCR reporter activity
| yes |
ReferenceGenome-wide siRNA screen identifies SMCX, EP400, and Brd4 as E2-dependent regulators of human papillomavirus oncogene expression. Smith et al.,
2010
An essential step in the pathogenesis of human papillomavirus (HPV)-associated cancers is the dysregulated expression of the viral oncogenes. The papillomavirus E2 protein can silence the long control region (LCR) promoter that controls viral E6 and E7 oncogene expression. The mechanisms by which E2 represses oncogene expression and the cellular factors through which E2 mediates this silencing are largely unknown. We conducted an unbiased, genome-wide siRNA screen and series of secondary screens that identified 96 cellular genes that contribute to the repression of the HPV LCR. In addition to confirming a role for the E2-binding bromodomain protein Brd4 in E2-mediated silencing, we identified a number of genes that have not previously been implicated in E2 repression, including the demethylase JARID1C/SMCX as well as EP400, a component of the NuA4/TIP60 histone acetyltransferase complex. Each of these genes contributes independently and additively to E2-mediated silencing, indicating that E2 functions through several distinct cellular complexes to repress E6 and E7 expression.
Screen DetailsStable ID:
GR00197-A-1
Screen Title:
Human papillomavirus oncogene expression regulation (1)
Assay:
HPV18 LCR reporter activity
Method:
Luminescence
Scope:
Genome-wide
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
C33A/BE2/18LCR c4
Library:
Dharmacon, Human siGENOME SMARTpool library
Reagent Type:
siRNA
Score Type:
Z-score
Cutoff:
>= 2
Notes:
Author-submitted data; Phenotype strength according to Z-scores: weak: 2 - 3; moderate: 3 - 5; strong: > 5
|
| Combinatorial effect with gemcitabine |
| IKBKG | IKBKG_B |
-0.36
|
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:
|
| HIV-1 infection (1) | 8517
| IKBKG | |
40
|
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:
|
| Salmonella enterica subspecies 1 serovar Typhimurium invasion (1) | 8517
| IKBKG | np |
0.14
|
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:
|
| Apoptosis regulation after Chlamydia trachomatis serovar L2 infection | 8517
| IKBKG | np |
np
|
none
| no |
ReferenceHIF-1α is involved in mediating apoptosis resistance to Chlamydia trachomatis-infected cells. Sharma et al.,
2011
Chlamydiae are obligate intracellular Gram-negative bacteria that cause widespread diseases in humans. Due to the intimate association between bacterium and host, Chlamydia evolved various strategies to protect their host cell against death-inducing stimuli, allowing the bacterium to complete its development cycle. An RNA interference (RNAi)-based screen was used to identify host cell factors required for apoptosis resistance of human epithelial cells infected with Chlamydia trachomatis serovar L2. Among the 32 validated hits, the anti-apoptotic Bcl-2 family member Mcl-1 was identified as a target. Protein network analyses implicated the transcription factor hypoxia-induced factor 1 alpha (HIF-1α) to be central to the regulation of many of the identified targets. Further mechanistic investigations showed that HIF-1α was stabilized within the host cell cytoplasm during early infection time points, followed by its translocation to the nucleus and eventual transcriptional activation of Mcl-1. siRNA-mediated depletion of HIF-1α led to a drastic decrease in Mcl-1, rendering the cell sensitive to apoptosis induction. Taken together, our findings identify HIF-1α as responsible for upregulation of Mcl-1 and the maintenance of apoptosis resistance during Chlamydia infection.
Screen DetailsStable ID:
GR00206-A
Screen Title:
Apoptosis regulation after Chlamydia trachomatis serovar L2 infection
Assay:
Cleaved cytokeratin-18 protein expression
Method:
Fluorescence
Scope:
Apoptosis, cellular trafficking and cell signalling genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Custom-made, Custom-made
Reagent Type:
siRNA
Score Type:
p-value
Cutoff:
<= 0.05
Notes:
Author-reviewed
|
| Combinatorial effect with gemcitabine |
| IKBKG | IKBKG_A |
-0.39
|
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:
|
| Hepatitis C virus replication (1) | 8517
| IKBKG | PL-50017 |
0.74
|
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:
|
| NF-kappaB pathway regulation (2) | 8517
| IKBKG | |
sp
|
Downregulation of NF-kappaB pathway after IL-1beta stimulation
| no |
ReferenceGenome-wide siRNA screen for mediators of NF-κB activation. Gewurz et al.,
2012
Although canonical NFκB is frequently critical for cell proliferation, survival, or differentiation, NFκB hyperactivation can cause malignant, inflammatory, or autoimmune disorders. Despite intensive study, mammalian NFκB pathway loss-of-function RNAi analyses have been limited to specific protein classes. We therefore undertook a human genome-wide siRNA screen for novel NFκB activation pathway components. Using an Epstein Barr virus latent membrane protein (LMP1) mutant, the transcriptional effects of which are canonical NFκB-dependent, we identified 155 proteins significantly and substantially important for NFκB activation in HEK293 cells. These proteins included many kinases, phosphatases, ubiquitin ligases, and deubiquinating enzymes not previously known to be important for NFκB activation. Relevance to other canonical NFκB pathways was extended by finding that 118 of the 155 LMP1 NF-κB activation pathway components were similarly important for IL-1β-, and 79 for TNFα-mediated NFκB activation in the same cells. MAP3K8, PIM3, and six other enzymes were uniquely relevant to LMP1-mediated NFκB activation. Most novel pathway components functioned upstream of IκB kinase complex (IKK) activation. Robust siRNA knockdown effects were confirmed for all mRNAs or proteins tested. Although multiple ZC3H-family proteins negatively regulate NFκB, ZC3H13 and ZC3H18 were activation pathway components. ZC3H13 was critical for LMP1, TNFα, and IL-1β NFκB-dependent transcription, but not for IKK activation, whereas ZC3H18 was critical for IKK activation. Down-modulators of LMP1 mediated NFκB activation were also identified. These experiments identify multiple targets to inhibit or stimulate LMP1-, IL-1β-, or TNFα-mediated canonical NFκB activation.
Screen DetailsStable ID:
GR00199-A-2
Screen Title:
NF-kappaB pathway regulation (2)
Assay:
NF-kappaB pathway reporter
Method:
Fluorescence
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HEK293
Library:
Dharmacon, siArray
Reagent Type:
siRNA
Score Type:
Complex, sp
Cutoff:
Complex criteria
Notes:
Additional information about the primary genome-wide screen
|
| Ciliogenesis and cilium length (1) | 8517
| IKBKG | 139262 |
1.67
|
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 |
| IKBKG | IKBKG 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:
|
| Homologous recombination DNA double-strand break repair (HR-DSBR) (1) | ENSG00000073009
| IKBKG | np |
-0.26
|
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:
|
| Melanogenesis | NM_003639
| IKBKG | np |
0.94
|
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)
|
| Ciliogenesis and cilium length (1) | 8517
| IKBKG | 139262 |
-31.01
|
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:
|
| TNF-induced apoptosis | NM_003639
| IKBKG | np |
1.92
|
Decreased viability after TNF/CHX stimulation
| no |
ReferenceA functional RNAi screen identifies hexokinase 1 as a modifier of type II apoptosis. Schindler and Foley,
2010
Tumor necrosis factor alpha (TNF-alpha) signals through NF-kappaB, JNK, and caspase modules to drive physiological responses that range from inflammation to apoptosis. The balance between the individual modules determines the nature of the response, and deregulated TNF signaling has been implicated in numerous pathological conditions. We used a quantitative high-throughput RNA interference assay to probe the entire complement of human kinases and phosphatases for gene products that tilt the balance of TNF signal transduction in favor of cell death or cell viability. Of all gene products tested, loss of hexokinase 1 resulted in the greatest elevations in TNF-dependent death. In secondary assays, we demonstrated that hexokinase 1 does not alter TNF-dependent activation of NF-kappaB or JNK modules. Instead, hexokinase 1 modifies the induction of caspase-driven cell death. Specifically, we showed that hexokinase 1 inhibits the formation of active, pro-apoptotic caspases in response to extrinsic inducers of apoptosis. These data are the first loss-of-function reports to examine the involvement of hexokinase 1 in the transduction of cell death signals and indicate that hexokinases are critical determinants of the viability of cells in response to extrinsic apoptotic cues.
Screen DetailsStable ID:
GR00228-A
Screen Title:
TNF-induced apoptosis
Assay:
Viability (synthetic lethal)
Method:
Fluorescence
Scope:
Kinases and phosphatases
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Applied Biosystems, Human kinase siRNA library V3 and Human phosphatase siRNA library V3
Reagent Type:
siRNA
Score Type:
Death index
Cutoff:
99% confidence interval: > 2.58 SD; 95% confidence interval: > 1.96 SD
Notes:
|
| Combinatorial effect with gemcitabine |
| IKBKG | IKBKG_B |
-0.47
|
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:
|
| Self-renewal and pluripotency in human embryonic stem cells (1) | NM_003639
| IKBKG | |
0.23
|
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:
|
| Cell division (1) | ENSG00000073009
| IKBKG | ENSG00000073009 |
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:
|
| Ciliogenesis and cilium length (1) | 8517
| IKBKG | 4787 |
50.56
|
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 |
| IKBKG | IKBKG 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:
|
| Combinatorial effect with gemcitabine |
| IKBKG | IKBKG_A |
0.03
|
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:
|
| NF-kappaB pathway regulation (2) | 8517
| IKBKG | |
sp
|
Downregulation of NF-kappaB pathway after TNFalpha stimulation
| no |
ReferenceGenome-wide siRNA screen for mediators of NF-κB activation. Gewurz et al.,
2012
Although canonical NFκB is frequently critical for cell proliferation, survival, or differentiation, NFκB hyperactivation can cause malignant, inflammatory, or autoimmune disorders. Despite intensive study, mammalian NFκB pathway loss-of-function RNAi analyses have been limited to specific protein classes. We therefore undertook a human genome-wide siRNA screen for novel NFκB activation pathway components. Using an Epstein Barr virus latent membrane protein (LMP1) mutant, the transcriptional effects of which are canonical NFκB-dependent, we identified 155 proteins significantly and substantially important for NFκB activation in HEK293 cells. These proteins included many kinases, phosphatases, ubiquitin ligases, and deubiquinating enzymes not previously known to be important for NFκB activation. Relevance to other canonical NFκB pathways was extended by finding that 118 of the 155 LMP1 NF-κB activation pathway components were similarly important for IL-1β-, and 79 for TNFα-mediated NFκB activation in the same cells. MAP3K8, PIM3, and six other enzymes were uniquely relevant to LMP1-mediated NFκB activation. Most novel pathway components functioned upstream of IκB kinase complex (IKK) activation. Robust siRNA knockdown effects were confirmed for all mRNAs or proteins tested. Although multiple ZC3H-family proteins negatively regulate NFκB, ZC3H13 and ZC3H18 were activation pathway components. ZC3H13 was critical for LMP1, TNFα, and IL-1β NFκB-dependent transcription, but not for IKK activation, whereas ZC3H18 was critical for IKK activation. Down-modulators of LMP1 mediated NFκB activation were also identified. These experiments identify multiple targets to inhibit or stimulate LMP1-, IL-1β-, or TNFα-mediated canonical NFκB activation.
Screen DetailsStable ID:
GR00199-A-2
Screen Title:
NF-kappaB pathway regulation (2)
Assay:
NF-kappaB pathway reporter
Method:
Fluorescence
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HEK293
Library:
Dharmacon, siArray
Reagent Type:
siRNA
Score Type:
Complex, sp
Cutoff:
Complex criteria
Notes:
Additional information about the primary genome-wide screen
|
| Combinatorial effect with paclitaxel | NM_003639
| IKBKG | np |
0.92
|
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
|
| Genome stability | NM_003639
| IKBKG | 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)
|
| Ciliogenesis and cilium length (1) | 8517
| IKBKG | 4787 |
35.56
|
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:
|
| TP53 interactions (1) | ENSG00000073009
| | 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:
|