Genome-wide fly cell RNAi screen related to Wolbachia infection

White PM, Serbus LR, Debec A, Codina A, Bray W, Guichet A, Lokey RS, Sullivan W. Reliance of Wolbachia on High Rates of Host Proteolysis Revealed by a Genome-Wide RNAi Screen of Drosophila Cells. Genetics. 2017 Feb 3. pii: genetics.116.198903. PMID: 28159754.

From the abstract: "Wolbachia are gram-negative, obligate, intracellular bacteria carried by a majority of insect species worldwide. Here we use a Wolbachia-infected Drosophila cell line and genome-wide RNAi screening to identify host factors that influence Wolbachia titer. .. we identified 36 candidate genes that dramatically reduced Wolbachia titer and 41 that increased Wolbachia titer. ... knockdown of 7 genes in the host ubiquitin and proteolysis pathways significantly reduced Wolbachia titer. To test the in vivo relevance of these results, we found that drug and mutant inhibition of proteolysis reduced levels of Wolbachia in the Drosophila oocyte ... Given Wolbachia lack essential amino acid biosynthetic pathways, the reliance of Wolbachia on high rates of host proteolysis via ubiquitination and the ERAD pathways may be a key mechanism for provisioning Wolbachia with amino acids. In addition, the reliance of Wolbachia on the ERAD pathway and disruption of ER morphology suggests a previously unsuspected mechanism for Wolbachia's potent ability to prevent RNA virus replication."

"ex vivo" fly RNAi screen

Kanoh H, Kuraishi T, Tong LL, Watanabe R, Nagata S, Kurata S. Ex vivo genome-wide RNAi screening of the Drosophila Toll signaling pathway elicited by a larva-derived tissue extract. Biochem Biophys Res Commun. 2015 Sep 28. pii: S0006-291X(15)30654-9. PMID: 26427875.

From the abstract: "... In Drosophila, the Toll pathway confers damage responses during bacterial infection and improper cell-fate control. However, the intrinsic ligands and signaling mechanisms that potentiate innate immune responses remain unknown. Here, we demonstrate that a Drosophila larva-derived tissue extract strongly elicits Toll pathway activation via the Toll receptor. Using this extract, we performed ex vivo genome-wide RNAi screening in Drosophila cultured cells, and identified several signaling factors that are required for host defense and antimicrobial-peptide expression in Drosophila adults. ..."

Transcription factor validated in follow-up to genome-wide RNAi screen related to viral-host cell interactions

Panda D, Gold B, Tartell MA, Rausch K, Casas-Tinto S, Cherry S. The Transcription Factor FoxK Participates with Nup98 To Regulate Antiviral Gene Expression. MBio. 2015 Apr 7;6(2). PMID: 25852164.

Review of model organism RNAi screen contributions to understanding host-pathogen interactions

Abnave P, Conti F, Torre C, Ghigo E. What RNAi screens in model organisms revealed about microbicidal response in mammals? Front Cell Infect Microbiol. 2015 Jan 12;4:184. PMID: 25629007; PMCID: PMC4290690.

From the abstract: "The strategies evolved by pathogens to infect hosts and the mechanisms used by the host to eliminate intruders are highly complex. ... The aim of this mini-review is to highlight and describe recent breakthroughs in the field of host-pathogen interactions using RNAi screens of model organisms. We will focus specifically on the model organisms Drosophila melanogaster, Caenorhabditis elegans, and Danio rerio. Moreover, a recent study examining the immune system of planarian will be discussed."

Review of "breakthroughs" in understanding host-pathogen interactions revealed using RNAi screens

Abnave P, Conti F, Torre C, Ghigo E. What RNAi screens in model organisms revealed about microbicidal response in mammals? Front Cell Infect Microbiol. 2015 Jan 12;4:184. eCollection 2014. PMID: 25629007; PMCID: PMC4290690.

From the abstract: "... The emergence of RNA interference (RNAi) and the ability to apply it toward studies in model organisms have allowed a breakthrough in the elucidation of host-pathogen interactions. The aim of this mini-review is to highlight and describe recent breakthroughs in the field of host-pathogen interactions using RNAi screens of model organisms. We will focus specifically on the model organisms Drosophila melanogaster, Caenorhabditis elegans, and Danio rerio."

The biology of RNAi--recent studies

Bronkhorst AW, van Cleef KW, Venselaar H, van Rij RP. A dsRNA-binding protein of a complex invertebrate DNA virus suppresses the Drosophila RNAi response. Nucleic Acids Res. 2014 Oct 29;42(19):12237-48. PMID: 25274730.

From the abstract: "... Here, we show that RNAi is suppressed in IIV-6-infected cells and we mapped RNAi suppressor activity to the viral protein 340R. ... Together, our findings indicate that, in analogy to RNA viruses, DNA viruses antagonize the antiviral RNAi response."

Gandhi SG, Bag I, Sengupta S, Pal-Bhadra M, Bhadra U. Drosophila oncogene Gas41 is RNAi modulator that intersects heterochromatin and siRNA pathway. FEBS J. 2014 Oct 16. PMID: 25323651.

From the abstract: "... These findings suggest that, Drosophila Gas41 guides the repeat associated gene silencing, and Dicer1 interaction thereby depicting a new role of the Gas41. ... In Drosophila, Gas41 plays a dual role. In one hand, it seems to participate with Dicer 1 in the RNAi pathway and alternatively also participate in repeat-induced gene silencing by accumulating heterochromatin proteins at the mw array promoters. ..."

RNAi screening in fly cells to investigate Brucella infection

Pandey A, Ding SL, Ficht TA, de Figueiredo P. siRNA Screens Using Drosophila Cells to Identify Host Factors Required for Infection. Methods Mol Biol. 2014;1197:229-44. PMID: 25172284.

RNA biology--viruses & RNAi suppression

van Mierlo JT, Overheul GJ, Obadia B, van Cleef KW, Webster CL, Saleh MC, Obbard DJ, van Rij RP. Novel Drosophila Viruses Encode Host-Specific Suppressors of RNAi. PLoS Pathog. 2014 Jul 7;10(7):e1004256. PMID: 25032815.

Genetic manipulation of both host cells and pathogen--"iMAD" protocol

O'Connor TJ, Isberg RR. iMAD, a genetic screening strategy for dissecting complex interactions between a pathogen and its host. Nat Protoc. 2014 Aug;9(8):1916-30. PMID: 25033208.

From the abstract: "... Here we present a protocol for dissecting the interaction between a pathogen (Legionella pneumophila) and its host (cultured Drosophila melanogaster cells) using bacterial mutagenesis and host RNAi. ..."

Genome-wide RNAi screen for host factors related to West Nile Virus

Yasunaga A, Hanna SL, Li J, Cho H, Rose PP, Spiridigliozzi A, Gold B, Diamond MS, Cherry S. Genome-Wide RNAi Screen Identifies Broadly-Acting Host Factors That Inhibit Arbovirus Infection. PLoS Pathog. 2014 Feb 13;10(2):e1003914. PMID: 24550726; PMCID: PMC3923753.

From the abstract:  "Investigation of two newly identified factors that restrict diverse viruses, dXPO1 and dRUVBL1, in the Tip60 complex, demonstrated they contributed to antiviral defense at the organismal level in adult flies, in mosquito cells, and in mammalian cells. These data suggest the existence of broadly acting and functionally conserved antiviral genes and pathways that restrict virus infections in evolutionarily divergent hosts."

Genome-wide screen--Viral replication. Breaking report.

Hopkins KC, McLane LM, Maqbool T, Panda D, Gordesky-Gold B, Cherry S. A genome-wide RNAi screen reveals that mRNA decapping restricts bunyaviral replication by limiting the pools of Dcp2-accessible targets for cap-snatching. Genes Dev. 2013 PMID: 23824541.

Recent review--immune responses

This review appears to have a particular focus on the use of RNAi screening to study Drosophila immune responses.

Valanne S. Functional genomic analysis of the Drosophila immune response. Dev Comp Immunol. 2013 May 21. PMID: 23707784.

New disease-relevant cell-based assay--Yersinia enterocolitica

These authors took advantage of the growth temperature of Drosophila cultured cells to establish a cell model for the GI pathogen Y. enterocolitica.

Walker KA, Maltez V, Hall JD, Vitko NP, Miller VL. A Phenotype at Last: Essential Role for the Yersinia enterocolitica Ysa Type III Secretion System in a Drosophila S2 cell model. Infect Immun. 2013 Apr 29. PMID: 23630961.

S2 cell and RNAi system for exploring phagocytosis of L. donovani

Peltan A, Briggs L, Matthews G, Sweeney ST, Smith DF. Identification of Drosophila Gene Products Required for Phagocytosis of Leishmania donovani. PLoS One. 2012;7(12):e51831. doi: 10.1371/journal.pone.0051831. PMID: 23272175; PMCID: PMC3521716.

From the abstract:  "Utilising the phagocytic capability of Drosophila S2 cells, together with available tools for modulating gene expression by RNAi, we have developed an experimental system in which to identify host proteins of this type on a genome-wide scale ... These observations suggest that this experimental approach has the potential to identify a large number of host effectors required for efficient parasite uptake and maintenance.

iMAD approach to host-pathogen screening. Breaking report.

These authors report a strategy for simultaneous genetic manipulation of both host (Drosophila cells) and pathogen genes.

O'Connor TJ, Boyd D, Dorer MS, Isberg RR. Aggravating genetic interactions allow a solution to redundancy in a bacterial pathogen. Science. 2012 Dec 14;338(6113):1440-4. doi: 10.1126/science.1229556. PubMed PMID: 23239729.

Breaking Report: Review of Host-Pathogen Interaction Interactions

On my desk to read today? A review of work in the field of host-pathogen interactions. Studies at the DRSC and elsewhere using Drosophila cell-based RNAi have had an impact in the field.

Bier and Guichard (2011) Deconstructing host-pathogen interactions in Drosophila.
Dis Model Mech. PMID: 21979942.

New Editorial & Report: Phagocytosis of Bacteria

On my desk this morning? A review by Flannagan and Grinstein on the use of knockdown approaches in Drosophila and zebrafish to study phagocytosis of bacteria. The original article is Ulvila et al. (2011). Info on both below.

Flannagan & Grinsten (2011) Fly fishing with RNAi catches novel effectors of phagocytosis. J. Leukoc. Biol. 89:643-645.

Ulvila et al. (2011) Cofilin regulator 14-3-3[] is an evolutionarily conserved protein required for phagocytosis and microbial resistance. J. Leukoc. Biol. 89:649-659.

Breaking Report: Pathogen Screen

On my desk to read today? A pathogen screen in S2 cells.

Qin et al. (2011) Functional Analysis of Host Factors that Mediate the Intracellular Lifestyle of Cryptococcus neoformans. PLoS Pathog. 7(6):e1002078. PMID: 21698225.

Similar interest in screening a relatively small set of genes? The DRSC will cherry-pick from our collection of high-quality amplicons and make dsRNA for your custom screen.

Methods Reports

There are Drosophila RNAi-related reports in a recent Methods in Molecular Biology series book (volume 721). Can't yet say that I'm reading them (don't have copies yet). But they've shown up in PubMed and I did want to make an announcement. Includes reports from S. Cherry, Obadia & Saleh, Nayak & Andino, Yang & Li, and van Cleef et al.

Breaking Report: Sweet Relief?

Also on my desk today? A report describing the application of RNAi in the field--an effort to address honeybee colony collapse disorder.

Hunter et al. (2010) Large-Scale Field Application of RNAi Technology Reducing Israeli Acute Paralysis Virus Disease in Honey Bees (Apismellifera, Hymenoptera: Apidae). PLoS Pathogens. Open Access.

The authors note that "To our knowledge, this is the first successful large-scale real world use of RNAi for disease control."