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Ding M, Tyrchan C, Bäck E, Östling J, Schubert S, McCrae C. Combined siRNA and Small-Molecule Phenotypic Screening Identifies Targets Regulating Rhinovirus Replication in Primary Human Bronchial Epithelial Cells. SLAS DISCOVERY 2020; 25:634-645. [PMID: 32189556 DOI: 10.1177/2472555220909726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Human rhinovirus (RV) is the most common cause of acute upper respiratory tract infections and has recently been shown to play a significant role in exacerbations of asthma and chronic obstructive pulmonary disease (COPD). There is a significant unmet medical need for agents for the prevention and/or treatment of exacerbations triggered by human RV infection. Phenotypic drug discovery programs using different perturbation modalities, for example, siRNA, small-molecule compounds, and CRISPR, hold significant value for identifying novel drug targets. We have previously reported the identification of lanosterol synthase as a novel regulator of RV2 replication through a phenotypic screen of a library of siRNAs against druggable genes in normal human bronchial epithelial (NHBE) cells. Here, we describe a follow-up phenotypic screen of small-molecule compounds that are annotated to be pharmacological regulators of target genes that were identified to significantly affect RV2 replication in the siRNA primary screen of 10,500 druggable genes. Two hundred seventy small-molecule compounds selected for interacting with 122 target gene hits were screened in the primary RV2 assay in NHBE cells by quantifying viral replication via in situ hybridization followed by secondary quantitative PCR-based assays for RV2, RV14, and RV16. The described follow-up phenotypic screening allowed us to identify Fms-related tyrosine kinase 4 (FLT4) as a novel target regulating RV replication. We demonstrate that a combination of siRNA and small-molecule compound screening models is a useful phenotypic drug discovery approach for the identification of novel drug targets.
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Affiliation(s)
- Mei Ding
- Discovery Sciences, Research and Early Development, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - Elisabeth Bäck
- Discovery Sciences, Research and Early Development, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - Jörgen Östling
- Bioscience, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | | | - Christopher McCrae
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), R&D BioPharmaceuticals, AstraZeneca, Gaithersburg, MD, USA
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2
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TCEA1 regulates the proliferative potential of mouse myeloid cells. Exp Cell Res 2018; 370:551-560. [PMID: 30009791 DOI: 10.1016/j.yexcr.2018.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 01/15/2023]
Abstract
Leukemia is a malignance with complex pathogenesis and poor prognosis. Discovery of noval regulators amenable to leukemia could be of value to gain insight into the pathogenesis, diagnosis and prognosis of leukemia. Here, we conducted a large-scale shRNA library screening for functional regulators in the development of myeloid cells in primary cells. We identified eighteen candidate regulators in the primary screening. Those genes cover a wide range of cellular functions, including gene expression regulation, intracellular signaling transduction, nucleotide excision repair, cell cycle control and transcription regulation. In both primary screening and validation, shRNAs targeting Tcea1, encoding the transcription elongation factor A (SII) 1, exhibited the greatest influence on the proliferative potential of cells. Knocking down the expression of Tcea1 in the 32Dcl3 myeloid cell line led to enhanced proliferation of myeloid cells and blockage of myeloid differentiation induced by G-CSF. In addition, silence of Tcea1 inhibited apoptosis of myeloid cells. Thus, Tcea1 was identified as a gene which can influence the proliferative potential, survival and differentiation of myeloid cells. These findings have implications for how transcriptional elongation influences myeloid cell development and leukemic transformation.
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Ibáñez G, Calder PA, Radu C, Bhinder B, Shum D, Antczak C, Djaballah H. Evaluation of Compound Optical Interference in High-Content Screening. SLAS DISCOVERY 2017; 23:321-329. [PMID: 28467117 DOI: 10.1177/2472555217707725] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Compound optical interference remains an inherent problem in chemical screening and has been well documented for biochemical assays and less so for automated microscopy-based assays. It has also been the assumption that the latter should not suffer from such interference because of the washing steps involved in the process, thus eliminating the residual nonspecific compound effects. Instead, these compounds may have no relevance to the actual target, and as such, compound optical interference contributes to a number of false-positives, resulting in a high attrition rate during subsequent follow-up studies. In this report, we analyze the outcome of a high-content screen using enhanced green fluorescent protein as a reporter in a gain-of-function cell-based assay in search of modulators of the micro RNA (miRNA) biogenesis pathway. Using a previously validated image-based biosensor, we screened a diverse library collection of ~315,000 compounds covering natural and synthetic derivatives in which 1130 positives were identified to enhance green fluorescence expression. Lateral confirmation and dose-response studies revealed that all of these compounds were the result of optical interference and not specific inhibition of miRNA biogenesis. Here, we highlight the chemical classes that are susceptible to compound optical interference and discuss their implications in automated microscopy-based assays.
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Affiliation(s)
- Glorymar Ibáñez
- 1 Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.,2 HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul A Calder
- 1 Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.,2 HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Constantin Radu
- 3 Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Bhavneet Bhinder
- 2 HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,4 Weill Cornell Medicine, New York, NY, USA
| | - David Shum
- 2 HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,3 Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Christophe Antczak
- 2 HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,5 Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Hakim Djaballah
- 2 HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,6 Keren Therapeutics, Scarsdale, NY, USA
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Validation of Synthetic CRISPR Reagents as a Tool for Arrayed Functional Genomic Screening. PLoS One 2016; 11:e0168968. [PMID: 28030641 PMCID: PMC5193459 DOI: 10.1371/journal.pone.0168968] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/10/2016] [Indexed: 12/03/2022] Open
Abstract
To date, lentiviral-based CRISPR-Cas9 screens have largely been conducted in pooled format. However, numerous assays are not amenable to pooled approaches, and lentiviral screening in arrayed format presents many challenges. We sought to examine synthetic CRISPR reagents in the context of arrayed screening. Experiments were performed using aberrant DNA replication as an assay. Using synthetic CRISPR RNAs targeting the known control gene GMNN in HCT-116 cells stably expressing Cas9, we observed statistically significant phenotype among the majority of transfected cells within 72 hours. Additional studies revealed near complete loss of GMNN protein and editing of GMNN DNA. We next conducted a screen of synthetic CRISPR RNAs directed against 640 ubiquitin-related genes. Screening identified known and novel DNA replication regulators that were also supported by siRNA gene knockdown. Notably, CRISPR screening identified more statistically significant hits than corresponding siRNA screens run in parallel. These results highlight the possibility of using synthetic CRISPR reagents as an arrayed screening tool.
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Bhinder B, Shum D, Li M, Ibáñez G, Vlassov AV, Magdaleno S, Djaballah H. Discovery of a dicer-independent, cell-type dependent alternate targeting sequence generator: implications in gene silencing & pooled RNAi screens. PLoS One 2014; 9:e100676. [PMID: 24987961 PMCID: PMC4079264 DOI: 10.1371/journal.pone.0100676] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/02/2014] [Indexed: 12/20/2022] Open
Abstract
There is an acceptance that plasmid-based delivery of interfering RNA always generates the intended targeting sequences in cells, making it as specific as its synthetic counterpart. However, recent studies have reported on cellular inefficiencies of the former, especially in light of emerging gene discordance at inter-screen level and across formats. Focusing primarily on the TRC plasmid-based shRNA hairpins, we reasoned that alleged specificities were perhaps compromised due to altered processing; resulting in a multitude of random interfering sequences. For this purpose, we opted to study the processing of hairpin TRCN#40273 targeting CTTN; which showed activity in a miRNA-21 gain-of-function shRNA screen, but inactive when used as an siRNA duplex. Using a previously described walk-through method, we identified 36 theoretical cleavage variants resulting in 78 potential siRNA duplexes targeting 53 genes. We synthesized and tested all of them. Surprisingly, six duplexes targeting ASH1L, DROSHA, GNG7, PRKCH, THEM4, and WDR92 scored as active. QRT-PCR analysis on hairpin transduced reporter cells confirmed knockdown of all six genes, besides CTTN; revealing a surprising 7 gene-signature perturbation by this one single hairpin. We expanded our qRT-PCR studies to 26 additional cell lines and observed unique knockdown profiles associated with each cell line tested; even for those lacking functional DICER1 gene suggesting no obvious dependence on dicer for shRNA hairpin processing; contrary to published models. Taken together, we report on a novel dicer independent, cell-type dependent mechanism for non-specific RNAi gene silencing we coin Alternate Targeting Sequence Generator (ATSG). In summary, ATSG adds another dimension to the already complex interpretation of RNAi screening data, and provides for the first time strong evidence in support of arrayed screening, and questions the scientific merits of performing pooled RNAi screens, where deconvolution of up to genome-scale pools is indispensable for target identification.
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Affiliation(s)
- Bhavneet Bhinder
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - David Shum
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Mu Li
- Thermo Fisher Scientific, Austin, Texas, United States of America
| | - Glorymar Ibáñez
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | | | - Susan Magdaleno
- Thermo Fisher Scientific, Austin, Texas, United States of America
| | - Hakim Djaballah
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail:
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Antczak C, Mahida JP, Singh C, Calder PA, Djaballah H. A high content assay to assess cellular fitness. Comb Chem High Throughput Screen 2014; 17:12-24. [PMID: 23957721 DOI: 10.2174/13862073113169990056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 08/14/2013] [Accepted: 08/15/2013] [Indexed: 12/12/2022]
Abstract
A universal process in experimental biology is the use of engineered cells; more often, stably or transiently transfected cells are generated for the purpose. Therefore, it is important that cell health assessment is conducted to check for stress mediated by induction of heat shock proteins (Hsps). For this purpose, we have developed an integrated platform that would enable a direct assessment of transfection efficiency (TE) combined with cellular toxicity and stress response. We make use of automated microscopy and high content analysis to extract from the same well a multiplexed readout to assess and determine optimal chemical transfection conditions. As a proof of concept, we investigated seven commercial reagents, in a matrix of dose and time, to study transfection of an EGFP DNA plasmid into HeLa cells and their consequences on health and fitness; where we scored for cellular proliferation, EGFP positive cells, and induction of Hsp10 and Hsp70 as makers of stress responses. FuGENE HD emerged as the most optimal reagent with no apparent side effects suitable for performing microtiter based miniaturized transfection for both chemical and RNAi screening. In summary, we report on a high content assay method to assess cellular overall fitness upon chemical transfection.
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Affiliation(s)
| | | | | | | | - Hakim Djaballah
- HTS Core Facility, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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Shum D, Bhinder B, Djaballah H. Modulators of the microRNA biogenesis pathway via arrayed lentiviral enabled RNAi screening for drug and biomarker discovery. Comb Chem High Throughput Screen 2014; 16:791-805. [PMID: 23977983 DOI: 10.2174/1386207311301010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 07/23/2013] [Accepted: 07/24/2013] [Indexed: 01/05/2023]
Abstract
MicroRNAs (miRNAs) are small endogenous and conserved non-coding RNA molecules that regulate gene expression. Although the first miRNA was discovered well over sixteen years ago, little is known about their biogenesis and it is only recently that we have begun to understand their scope and diversity. For this purpose, we performed an RNAi screen aimed at identifying genes involved in their biogenesis pathway with a potential use as biomarkers. Using a previously developed miRNA 21 (miR-21) EGFP-based biosensor cell based assay monitoring green fluorescence enhancements, we performed an arrayed short hairpin RNA (shRNA) screen against a lentiviral particle ready TRC1 library covering 16,039 genes in 384-well plate format, and interrogating the genome one gene at a time building a panoramic view of endogenous miRNA activity. Using the BDA method for RNAi data analysis, we nominate 497 gene candidates the knockdown of which increased the EGFP fluorescence and yielding an initial hit rate of 3.09%; of which only 22, with reported validated clones, are deemed high-confidence gene candidates. An unexpected and surprising result was that only DROSHA was identified as a hit out of the seven core essential miRNA biogenesis genes; suggesting that perhaps intracellular shRNA processing into the correct duplex may be cell dependent and with differential outcome. Biological classification revealed several major control junctions among them genes involved in transport and vesicular trafficking. In summary, we report on 22 high confidence gene candidate regulators of miRNA biogenesis with potential use in drug and biomarker discovery.
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Affiliation(s)
- David Shum
- HTS Core Facility, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA.
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Hadji A, Ceppi P, Murmann AE, Brockway S, Pattanayak A, Bhinder B, Hau A, De Chant S, Parimi V, Kolesza P, Richards J, Chandel N, Djaballah H, Peter ME. Death induced by CD95 or CD95 ligand elimination. Cell Rep 2014; 7:208-22. [PMID: 24656822 DOI: 10.1016/j.celrep.2014.02.035] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 10/07/2013] [Accepted: 02/24/2014] [Indexed: 01/07/2023] Open
Abstract
CD95 (Fas/APO-1), when bound by its cognate ligand CD95L, induces cells to die by apoptosis. We now show that elimination of CD95 or CD95L results in a form of cell death that is independent of caspase-8, RIPK1/MLKL, and p53, is not inhibited by Bcl-xL expression, and preferentially affects cancer cells. All tumors that formed in mouse models of low-grade serous ovarian cancer or chemically induced liver cancer with tissue-specific deletion of CD95 still expressed CD95, suggesting that cancer cannot form in the absence of CD95. Death induced by CD95R/L elimination (DICE) is characterized by an increase in cell size, production of mitochondrial ROS, and DNA damage. It resembles a necrotic form of mitotic catastrophe. No single drug was found to completely block this form of cell death, and it could also not be blocked by the knockdown of a single gene, making it a promising way to kill cancer cells.
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Affiliation(s)
- Abbas Hadji
- Division of Hematology/Oncology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Paolo Ceppi
- Division of Hematology/Oncology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrea E Murmann
- Division of Hematology/Oncology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sonia Brockway
- Division of Hematology/Oncology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Abhinandan Pattanayak
- Division of Hematology/Oncology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Bhavneet Bhinder
- HTS Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Annika Hau
- Division of Hematology/Oncology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shirley De Chant
- Division of Hematology/Oncology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Vamsi Parimi
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Piotre Kolesza
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joanne Richards
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Navdeep Chandel
- Division of Pulmonary and Cell and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hakim Djaballah
- HTS Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Marcus E Peter
- Division of Hematology/Oncology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA.
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Stierle AA, Stierle DB, Mitman GG, Snyder S, Antczak C, Djaballah H. Phomopsolides and Related Compounds from the Alga-associated Fungus, Penicillium clavigerum. Nat Prod Commun 2014. [DOI: 10.1177/1934578x1400900126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
For the past fifteen years we have studied the secondary metabolites of extremophilic fungi from the Berkeley Pit, an abandoned acid mine waste lake. Fungi associated with an acid-tolerant alga have also been harvested from the Pit. Penicillium clavigerum Demelius was isolated from the green alga Chlorella vulgaris Beyerinck [Beijerinck]. In culture it produced the known compounds phomfuranone (1), patulin (2), dimethylphthalides (3) and (4), phomopsolide A (5), phomopsolide C (6), phomopsolide B (7), phomopsolide E (8), phomopsolide F (9), and phompyrone (10) and the new compound berkbenzofuran thioester (11). Compounds 5 and 6 were potent inhibitors (IC50 < 10 μM) of specific and established human cancer cell lines.
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Affiliation(s)
- Andrea A. Stierle
- Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, Montana 59812, USA
| | - Donald B. Stierle
- Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, Montana 59812, USA
| | - Grant G. Mitman
- Department of Biological Sciences, Montana Tech of the University of Montana, Butte, Montana 59701, USA
| | - Shea Snyder
- Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, Montana 59812, USA
| | - Christophe Antczak
- HTS Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Hakim Djaballah
- HTS Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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Bhinder B, Djaballah H. Systematic analysis of RNAi reports identifies dismal commonality at gene-level and reveals an unprecedented enrichment in pooled shRNA screens. Comb Chem High Throughput Screen 2013; 16:665-81. [PMID: 23848309 PMCID: PMC3885821 DOI: 10.2174/13862073113169990045] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 07/01/2013] [Accepted: 07/02/2013] [Indexed: 11/22/2022]
Abstract
RNA interference (RNAi) has opened promising avenues to better understand gene function. Though many RNAi screens report on the identification of genes, very few, if any, have been further studied and validated. Data discrepancy is emerging as one of RNAi main pitfalls. We reasoned that a systematic analysis of lethality-based screens, since they score for cell death, would examine the extent of hit discordance at inter-screen level. To this end, we developed a methodology for literature mining and overlap analysis of several screens using both siRNA and shRNA flavors, and obtained 64 gene lists censoring an initial list of 7,430 nominated genes. We further performed a comparative analysis first at a global level followed by hit re-assessment under much more stringent conditions. To our surprise, none of the hits overlapped across the board even for PLK1, which emerged as a strong candidate in siRNA screens; but only marginally in the shRNA ones. Furthermore, EIF5B emerges as the most common hit only in the shRNA screens. A highly unusual and unprecedented result was the observation that 5,269 out of 6,664 nominated genes (~80%) in the shRNA screens were exclusive to the pooled format, raising concerns as to the merits of pooled screens which qualify hits based on relative depletions, possibly due to multiple integrations per cell, data deconvolution or inaccuracies in intracellular processing causing off-target effects. Without golden standards in place, we would encourage the community to pay more attention to RNAi screening data analysis practices, bearing in mind that it is combinatorial in nature and one active siRNA duplex or shRNA hairpin per gene does not suffice credible hit nomination. Finally, we also would like to caution interpretation of pooled shRNA screening outcomes.
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Affiliation(s)
- Bhavneet Bhinder
- HTS Core Facility, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, USA.
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