Below we share with the community at large the report we provided to the Fly Board in advance of the 2022 Fly Meeting. As always, your feedback on our technologies and services is welcome. We are here to help.
DRSC/TRiP Functional Genomics Resources at Harvard Medical School
We focus on developing and improving technologies, and help other labs use them to study many topics. Specifically, we focus on cell-based and in vivo technologies that can be applied to study Drosophila and mosquitos. In addition, we use our well-established infrastructure to build large-scale in vivo fly stock collections, and to maintain and develop bioinformatics tools that support these technologies and others. Below, we outline what’s new in the past year in our three main areas of focus: cell-based technologies, in vivo technologies, and bioinformatics resources. We then report on our outreach efforts and list recent preprints and publications.
I. DRSC: The DRSC serves as an NIH NIGMS P41-funded Biomedical Technology Research Resource (DRSC-BTRR) with a focus on technology development in Drosophila and mosquitos. Since our last report, the DRSC-BTRR:
- Continued to distribute dsRNA libraries for Drosophila cell screens and share related knowhow and reagents for functional genomics technologies
- Continued to develop new Cas types, libraries, and cell-based assays for CRISPR pooled-format screening in Drosophila cell lines
- Continued to develop libraries, modified cell lines, and cell-based assays for CRISPR pooled-format screening in mosquito cell lines
- Actively engaged in 18 Driving Biomedical Project (DBP) and 7 service collaborations, with labs in CA, IA, MD, MA, PA, RI, TX, NV, NY, and UT in the USA, and in the Czech Republic, France, Slovenia, and the United Kingdom
- Published research and technology-focused papers and preprints (see below)
Of note for the DRSC future: The P41 BTRR mechanism is transitioning to the RM1 Biomedical Technology Development and Dissemination Center mechanism, plus tech-focused R21s and R01s. We expect to apply in early 2023 to become the DRSC-BTDD.
II. TRiP: The TRiP remains focused primarily on building CRISPR-related fly stocks and other stocks for testing and implementing new technologies. Since our last report, we:
- Generated over 500 new fly stocks as part of the TRiP CRISPR-KO, TRiP-CRISPR-OE, and paralog double-knockout collections, and deposited 300 fly stocks to BDSC
- Began a new project to make an RNAi and CRISPR fly stock resource targeting ~300 fly orthologs of human genes identified as SARS-CoV-2-interactors
- Generated >30 LexA and QF tissue-specific driver lines using CRISPR/Cas9-mediated knock-in that will be deposited soon to BDSC
- Tested new applications and versions of CRISPR/Cas
- Deposited 16 lines to BDSC that can be used to detect any nanobody-epitope tagged protein of interest, as described in Xu et al. eLife
- We also note that in 2021, the BDSC sent 62,622 subcultures of TRiP stocks to 1,340 different user groups across the US and in 43 other countries
III. DRSC Bioinformatics:
- Performed routine maintenance and updates to existing tools for reagent design (e.g., Find CRISPRs 3), reagent identification (e.g., UP-TORR), and data view (e.g., RSVP)
- Add more functions and features to existing tool
- added new species and algorithms to our ortholog prediction tool DIOPT
- enhanced visualization and data mining at the scRNA-seq data portal
- expanded mosquito GuildeXpress to cover more species and datasets
- expanded DRscDB with Fly Cell Atlas datasets
- Developed or in the process of developing new tools
- Launched PathOn for analysis of signaling pathways in bulk RNAseq datasets
- Launched FlyPhoneDB for analysis of cell-cell communication in single-cell RNAseq datasets
- Worked with Erika Larschan’s group to develop and launch TIMEOR, a tool of analyzing temporal regulatory mechanisms from bulk RNAseq datasets
- Continued to work with FlyBase on a gene set enrichment tool, which has been expanded to cover more species and more gene sets
IV. Training & Dissemination: We continue to inform the Drosophila community about our technologies in the following ways:
- Held DRSC/TRiP virtual ‘Office Hours’ in fall 2021 (view summaries here)
- Presented on technologies at the 2021 virtual Boston Area Drosophila meeting
- Presented on technologies at several other virtual conferences and workshops
- Continued to update our website with new protocols, publications, and more
- Continued to update Drosophila Models of Human Diseases
- Continued to update community news and events at the Fly Research Portal
- Provided modified Drosophila and mosquito cell lines to the DGRC
- Provided new fly stocks to BDSC
V. Recent preprints and publications from the DRSC/TRiP
New bioinformatics tools:
Conard AM, Goodman N, Hu Y, Perrimon N, Singh R, Lawrence C, Larschan E. TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data. Nucleic Acids Res. 2021 Jul 2;49(W1):W641-W653. PMID: 34125906; PMCID: PMC8262710.
Liu Y, Li JSS, Rodiger J, Comjean A, Attrill H, Antonazzo G, Brown NH, Hu Y, Perrimon N. FlyPhoneDB: an integrated web-based resource for cell-cell communication prediction in Drosophila. Genetics. 2022 Mar 3;220(3):iyab235. doi: 10.1093/genetics/iyab235. PMID: 35100387.
Ding G, Xiang X, Hu Y, Xiao G, Chen Y, Binari R, Comjean A, Li J, Rushworth E, Fu Z, Mohr SE, Perrimon N, Song W. (2021) Coordination of tumor growth and host wasting by tumor-derived Upd3. Cell Rep. 2021 Aug 17;36(7):109553. doi:10.1016/j.celrep.2021.109553. PMID: 34407411; PMCID: PMC8410949.
Cell technologies and their applications:
Hans M. Dalton, Raghuvir Viswanatha, Ricky Brathwaite Jr., Jae Sophia Zuno, Stephanie E. Mohr, Norbert Perrimon, Clement Y. Chow (2021) A genome-wide CRISPR screen identifies the glycosylation enzyme DPM1 as a modifier of DPAGT1 deficiency and ER stress. bioRxiv 2021.12.03.471178; doi: https://doi.org/10.1101/2021.12.03.471178
Feng X, López Del Amo V, Mameli E, Lee M, Bishop AL, Perrimon N, Gantz VM. Optimized CRISPR tools and site-directed transgenesis towards gene drive development in Culex quinquefasciatus mosquitoes. Nat Commun. 2021 May 20;12(1):2960. doi: 10.1038/s41467-021-23239-0. PMID: 34017003; PMCID: PMC8137705.
Jiunn Song, Arda Mizrak, Chia-Wei Lee, Marcelo Cicconet, Zon Weng Lai, Chieh-Han Lu, Stephanie E. Mohr, Robert V. Farese Jr., Tobias C. Walther (2021) Identification of two pathways mediating protein targeting from ER to lipid droplets. bioRxiv 2021.09.14.460330; doi: https://doi.org/10.1101/2021.09.14.460330
Viswanatha R, Mameli E, Rodiger J, Merckaert P, Feitosa-Suntheimer F, Colpitts TM, Mohr SE, Hu Y, Perrimon N. Bioinformatic and cell-based tools for pooled CRISPR knockout screening in mosquitos. Nat Commun. 2021 Nov 24;12(1):6825. doi: 10.1038/s41467-021-27129-3. PMID: 34819517; PMCID: PMC8613219.
Nanobody-based epitope tagging (cells and in vivo):
Xu J, Kim AR, Cheloha RW, Fischer FA, Li JSS, Feng Y, Stoneburner E, Binari R, Mohr SE, Zirin J, Ploegh HL, Perrimon N. Protein visualization and manipulation in Drosophila through the use of epitope tags recognized by nanobodies. Elife. 2022 Jan 25;11:e74326. doi: 10.7554/eLife.74326. PMID: 35076390; PMCID: PMC8853664.
CRISPR-mediated gene tagging (in vivo):
Oguz Kanca, Jonathan Zirin, Yanhui Hu, Burak Tepe, Debdeep Dutta, Wen-Wen Lin, Liwen Ma, Ming Ge, Zhongyuan Zuo, Lu-Ping Liu, Robert W. Levis, Norbert Perrimon, Hugo J. Bellen (2021) An expanded toolkit for Drosophila gene tagging using synthesized homology donor constructs for CRISPR mediated homologous recombination. bioRxiv 2021.12.24.474112; doi: https://doi.org/10.1101/2021.12.24.474112
Zirin J, Bosch J, Viswanatha R, Mohr SE, Perrimon N. State-of-the-art CRISPR for in vivo and cell-based studies in Drosophila. Trends Genet. 2021 Dec 18:S0168-9525(21)00336-X. doi: 10.1016/j.tig.2021.11.006. PMID: 34933779.