Functional Genomics Publications

Below is a list of publications that have resulted from RNAi screening efforts at ICCB-Longwood. Please notify us of your publications that involve use of the ICCB-Longwood Screening Facility.

Jovanović B, Temko D, Stevens LE, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper NW, Daniels VW, Xiao-Yun H, Ge JY, Alečković M, Pyrdol J, Hinohara K, Egri SB, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram MB, Subedee A, Herbert ZT, Wucherpfennig KW, Letai AG, Jaffe JD, Sicinski P, Brown M, Dillon D, Long HW, Michor F, Polyak K. Heterogeneity and transcriptional drivers of triple-negative breast cancer [Internet]. Cell Rep 2023;42(12):113564. Publisher's Version

Schmaier AA, Anderson PF, Chen SM, El-Darzi E, Aivasovsky I, Kaushik MP, Sack KD, Hartzell HC, Parikh SM, Flaumenhaft R, Schulman S. TMEM16E regulates endothelial cell procoagulant activity and thrombosis [Internet]. J Clin Invest 2023;133(11):e163808. Publisher's Version

Chen D-Y, Chin CV, Kenney D, Tavares AH, Khan N, Conway HL, Liu GQ, Choudhary MC, Gertje HP, O'Connell AK, Adams S, Kotton DN, Herrmann A, Ensser A, Connor JH, Bosmann M, Li JZ, Gack MU, Baker SC, Kirchdoerfer RN, Kataria Y, Crossland NA, Douam F, Saeed M. Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation [Internet]. Nature 2023;615:143-150. Publisher's Version

Durall RT, Huang J, Wojenski L, Huang Y, Gokhale PC, Leeper BA, Nash JO, Ballester PL, Davidson S, Shlien A, Sotirakis E, Bertaux F, Dubus V, Luo J, Wu CJ, Keskin DB, Eagen KP, Shapiro GI, French CA. The BRD4-NUT fusion alone drives malignant transformation of NUT carcinoma [Internet]. Cancer Res 2023;(Oct 11) Publisher's Version

Park DS, Nguyen SC, Isenhart R, Shah PP, Kim W, Barnett RJ, Chandra A, Luppino JM, Harke J, Wai M, Walsh PJ, Abdill RJ, Yang R, Lan Y, Yoon S, Yunker R, Kanemaki MT, Vahedi G, Phillips-Cremins JE, Jain R, Joyce EF. High-throughput Oligopaint screen identifies druggable 3D genome regulators. Nature 2023;620:209–217.

Boekell KL, Brown BJ, Talbot BE, Schlondorff JS. Trpc6 gain-of-function disease mutation enhances phosphatidylserine exposure in murine platelets [Internet]. PLoS One 2022;17(6):e0270431. Publisher's Version

Vora SM, Fontana P, Mao T, Leger V, Zhang Y, Fu T-M, Lieberman J, Gehrke L, Shi M, Wang L, Iwasaki A, Wu H. Targeting stem-loop 1 of the SARS-CoV-2 5' UTR to suppress viral translation and Nsp1 evasion [Internet]. Proc Natl Acad Sci U S A 2022;119(9):e2117198119. Publisher's Version

Coverdell TC, Abraham-Fan R-J, Wu C, Abbott SBG, Campbell JN. Genetic encoding of an esophageal motor circuit [Internet]. Cell Rep 2022;39(11):110962. Publisher's Version

Jutzi JS, Marneth AE, Ciboddo M, Guerra-Moreno A, Jiménez-Santos MJ, Kosmidou A, Dressman JW, Liang H, Hamel R, Lozano P, Rumi E, Doench JG, Gotlib J, Krishnan A, Elf S, Al-Shahrour F, Mullally A. Whole-genome CRISPR screening identifies N-glycosylation as a genetic and therapeutic vulnerability in CALR-mutant MPNs [Internet]. Blood 2022;140(11):1291-1304. Publisher's Version

Martínez-Noël G, Szajner P, Kramer RE, Boyland KA, Sheikh A, Smith JA, Howley PM. Identification of MicroRNAs That Stabilize p53 in Human Papillomavirus-Positive Cancer Cells. J Virol 2022;96(4)

Tasdemir-Yilmaz OE, Druckenbrod NR, Olukoya OO, Dong W, Yung AR, Bastille I, Pazyra-Murphy MF, Sitko AA, Hale EB, Vigneau S, Gimelbrant AA, Kharchenko PV, Goodrich LV, Segal RA. Diversity of developing peripheral glia revealed by single-cell RNA sequencing [Internet]. Dev Cell 2021;56(17):2516-2535. Publisher's Version

Chu V, Feng Q, Lim Y, Shao S. Selective destabilization of polypeptides synthesized from NMD-targeted transcripts [Internet]. Mol Biol Cell 2021;32(22):ar38. Publisher's Version

Egusquiaguirre SP, Liu S, Tošić I, Jiang K, Walker SR, Nicolais M, Saw TY, Xiang M, Bartel K, Nelson EA, Frank DA. CDK5RAP3 is a co-factor for the oncogenic transcription factor STAT3 [Internet]. Neoplasia 2020;22(1):47-59. Publisher's Version

Cruz FM, Colbert JD, Rock KL. The GTPase Rab39a promotes phagosome maturation into MHC-I antigen-presenting compartments [Internet]. EMBO J 2020;39:e102020. Publisher's Version

Tattikota SG, Cho B, Liu Y, Hu Y, Barrera V, Steinbaugh MJ, Yoon S-H, Comjean A, Li F, Dervis F, Hung R-J, Nam J-W, Sui SH, Shim J, Perrimon N. A single-cell survey of Drosophila blood [Internet]. eLife 2020;9:e54818. Publisher's Version

Todd WD, Venner A, Anaclet C, Broadhurst RY, Luca RD, Bandaru SS, Issokson L, Hablitz LM, Cravetchi O, Arrigoni E, Campbell JN, Allen CN, Olson DP, Fuller PM. Suprachiasmatic VIP neurons are required for normal circadian rhythmicity and comprised of molecularly distinct subpopulations [Internet]. Nat Commun 2020;11:4410. Publisher's Version

Takahashi N, Cho P, Selfors LM, Kuiken HJ, Kaul R, Fujiwara T, Harris IS, Zhang T, Gygi SP, Brugge JS. 3D Culture Models with CRISPR Screens Reveal Hyperactive NRF2 as a Prerequisite for Spheroid Formation via Regulation of Proliferation and Ferroptosis [Internet]. Mol Cell 2020;80(5):828-844. Publisher's Version

Iuchi S, Paulo JA. Lysine-specific demethylase 2A enhances binding of various nuclear factors to CpG-rich genomic DNAs by action of its CXXC-PHD domain [Internet]. Sci Rep 2019;9:5496. Publisher's Version

Bodnar NO, Kim KH, Ji Z, Wales TE, Svetlov V, Nudler E, Engen JR, Walz T, Rapoport TA. Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4. Nat Struct Mol Biol 2018;25(7):616-622.

Takahashi N, Chen H-Y, Harris IS, Stover DG, Selfors LM, Bronson RT, Deraedt T, Cichowski K, Welm AL, Mori Y, Mills GB, Brugge JS. Cancer Cells Co-opt the Neuronal Redox-Sensing Channel TRPA1 to Promote Oxidative-Stress Tolerance [Internet]. Cancer Cell 2018;33(6):985-1003. Publisher's Version

Amin P, Florez M, Najafov A, Pan H, Geng J, Ofengeim D, Dziedzic SA, Wang H, Barrett VJ, Ito Y, LaVoie MJ, Yuan J. Regulation of a distinct activated RIPK1 intermediatebridging complex I and complex II inTNFα-mediated apoptosis. PNAS 2018;115(26):E5944-E5953.

Zeid R, Lawlor MA, Poon E, Reyes JM, Fulciniti M, Lopez MA, Scott TG, Nabet B, Erb MA, Winter GE, Jacobson Z, Polaski DR, Karlin KL, Hirsch RA, Munshi NP, Westbrook TF, Chesler L, Lin CY, Bradner JE. Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma. Nat Genet. 2018;Jan 29 doi: 10.1038/s41588-018-0044-9.

Zilionis R, Nainys J, Veres A, Savova V, Zemmour D, Klein AM, Mazutis L. Single-cell barcoding and sequencing using droplet microfluidics [Internet]. Nat Protoc 2017;12(1):44-73. Publisher's Version

Hydbring P, Wang Y, Fassl A, Li X, Matia V, Otto T, Choi YJ, Sweeney KE, Suski JM, Yin H, Bogorad RL, Goel S, Yuzugullu H, Kauffman KJ, Yang J, Jin C, Li Y, Floris D, Swanson R, Ng K, Sicinska E, Anders L, Zhao JJ, Polyak K, Anderson DG, Li C, Sicinski P. Cell-Cycle-Targeting MicroRNAs as Therapeutic Tools against Refractory Cancers [Internet]. Cancer Cell 2017;31(4):576-590. Publisher's Version

Fu B, Zhao M, Wang L, Patil G, Smith JA, Juncadella IJ, Zuvela-Jelaska L, Dorf ME, Li S. RNAi Screen and Proteomics Reveal NXF1 as a Novel Regulator of IRF5 Signaling. Sci Rep 2017;Jun 2; 7(1):2683.

Simpson KJ, Smith JA. Knocking down the obstacles to functional genomics data sharing. Sci Data 2017;4:170019 doi:10.1038/sdata.2017.19.

Nelms B, Dalomba NF, Lencer W. A targeted RNAi screen identifies factors affecting diverse stages of receptor-mediated transcytosis. J Cell Biol 2017;216(2):511-525.

Russo BC, Stamm LM, Raaben M, Kim CM, Kahoud E, Robinson LR, Bose S, Queiroz AL, Herrera BB, Baxt LA, Mor-Vaknin N, Fu Y, Molina G, Markovitz DM, Whelan SP, Goldberg MB. Intermediate filaments enable pathogen docking to trigger type 3 effector translocation [Internet]. Nat Microbiol 2016;1:16025. Publisher's Version

Polachek WS, Moshrif HF, Franti M, Coen DM, Streenu VB, Strang BL. High-Throughput Small Interfering RNA Screening Identifies Phosphatidylinositol 3-Kinase Class II Alpha as Important for Production of Human Cytomegalovirus Virions. J Virol 2016;90(18):8360-71.

Savidis G, McDougall WM, Meraner P, Perreira JM, Portmann JM, Trinucci G, John SP, Aker AM, Renzette N, Robbins DR, Guo Z, Green S, Kowalik TF, Brass AL. Identification of Zika Virus and Dengue Virus Dependency Factors using Functional Genomics. Cell Reports 2016;16(1):232-46.

ICCB-Longwood Screening Facility

Functional Genomics Publications

Acknowledging ICCB-L in Publications

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