Home » Publications supported by Functional Genomics

Publications supported by Functional Genomics

Anderson DE, Pfeffermann K, Kim SY, Sawatsky B, Pearson J, Kovtun M, Corcoran DL, Krebs Y, Sigmundsson K, Jamison SF, Yeo ZZJ, Rennick LJ, Wang LF, Talbot PJ, Duprex WP, Garcia-Blanco MA, von Messling V. Comparative Loss-of-Function Screens Reveal ABCE1 as an Essential Cellular Host Factor for Efficient Translation of Paramyxoviridae and Pneumoviridae. MBio. 2019 May 14;10(3). pii: e00826-19. doi: 10.1128/mBio.00826-19.

Le T, Jia Z, Le SC, Zhang Y, Chen J, Yang H. An inner activation gate controls TMEM16F phospholipid scrambling. Nat Commun. 2019 Apr 23;10(1):1846. doi: 10.1038/s41467-019-09778-7.

Walens A, DiMarco AV, Lupo R, Kroger BR, Damrauer JS, Alvarez JV. CCL5 promotes breast cancer recurrence through macrophage recruitment in residual tumors. Elife. 2019 Apr 16;8. pii: e43653. doi: 10.7554/eLife.43653.

Choi HW, Chan C, Shterev ID, Lynch HE, Robinette TJ, Johnson-Weaver BT, Shi J, Sempowski GD, Kim SY, Dickson JK, Gooden DM, Abraham SN, Staats HF. Identification of Novel Mast Cell Activators Using Cell-Based High-Throughput Screening. SLAS Discov. 2019 Mar 27:2472555219834699. doi: 10.1177/2472555219834699.

Xu S, Ware KE, Ding Y, Kim SY, Sheth MU, Rao S, Chan W, Armstrong AJ, Eward WC, Jolly MK, Somarelli JA. An Integrative Systems Biology and Experimental Approach Identifies Convergence of Epithelial Plasticity, Metabolism, and Autophagy to Promote Chemoresistance.J Clin Med. 2019 Feb 7;8(2). pii: E205. doi: 10.3390/jcm8020205.

Le T, Le SC, Yang H. Drosophila Subdued is a moonlighting transmembrane protein 16 (TMEM16) that transports ions and phospholipids. J Biol Chem. 2019 Jan 30. pii: jbc.AC118.006530. doi: 10.1074/jbc.AC118.006530. [Epub ahead of print]

Dikshit A, Jin YJ, Degan S, Hwang J, Foster MW, Li CY, Zhang JY. UBE2N Promotes Melanoma Growth via MEK/FRA1/SOX10 Signaling. Cancer Res. 2018 Nov 15;78(22):6462-6472. doi: 10.1158/0008-5472.CAN-18-1040.

Scarneo SA, Mansourati A, Eibschutz LS, Totzke J, Roques JR, Loiselle D, Carlson D, Hughes P, Haystead TAJ. Genetic and pharmacological validation of TAK1 inhibition in macrophages as a therapeutic strategy to effectively inhibit TNF secretion. Sci Rep. 2018 Nov 19;8(1):17058.

Scott WK, Medie FM, Ruffin F, Sharma-Kuinkel BK, Cyr DD, Guo S, Dykxhoorn DM, Skov RL, Bruun NE, Dahl A, Lerche CJ, Petersen A, Larsen AR, Lauridsen TK, Johansen HK, Ullum H, Sørensen E, Hassager C, Bundgaard H, Schønheyder HC, Torp-Pedersen C, Østergaard LB, Arpi M, Rosenvinge F, Erikstrup LT, Chehri M, Søgaard P, Andersen PS, Fowler VG Jr. Human genetic variation in GLS2 is associated with development of complicated Staphylococcus aureus bacteremia. PLoS Genet. 2018 Oct 5;14(10):e1007667. doi: 10.1371/journal.pgen.1007667. [Epub ahead of print]

Mabe NW, Fox DB, Lupo R, Decker AE, Phelps SN, Thompson JW, Alvarez JV. Epigenetic silencing of tumor suppressor Par-4 promotes chemoresistance in recurrent breast cancer. J Clin Invest. 2018 Aug 27. pii: 99481.

Nelson CS, Huffman T, Jenks JA, Cisneros de la Rosa E, Xie G, Vandergrift N, Pass RF, Pollara J, Permar SR. HCMV glycoprotein B subunit vaccine efficacy mediated by nonneutralizing antibody effector functions. Proc Natl Acad Sci U S A. 2018 Jun 12;115(24):6267-6272.

Yoo J, Wu M, Yin Y, Herzik MA Jr, Lander GC, Lee SY. Cryo-EM structure of a mitochondrial calcium uniporter. Science. 2018 Jun 28. pii: eaar4056. doi: 10.1126/science.aar4056. [Epub ahead of print]

Abaffy T, Bain JR, Muehlbauer MJ, Spasojevic I, Lodha S, Bruguera E, O’Neal SK, Kim SY, Matsunami H. A Testosterone Metabolite 19-Hydroxyandrostenedione Induces Neuroendocrine Trans-Differentiation of Prostate Cancer Cells via an Ectopic Olfactory Receptor. Front Oncol. 2018 May 28;8:162.

Diplas BH, He X, Brosnan-Cashman JA, Liu H, Chen LH, Wang Z, Moure CJ, Killela PJ, Loriaux DB, Lipp ES, Greer PK, Yang R, Rizzo AJ, Rodriguez FJ, Friedman AH, Friedman HS, Wang S, He Y, McLendon RE, Bigner DD, Jiao Y, Waitkus MS, Meeker AK, Yan H. The genomic landscape of TERT promoter wildtype-IDH wildtype glioblastoma. Nat Commun. 2018 May 25;9(1):2087.

Lin J, Gresham J, Wang T, Kim SY, Alvarez J, Damrauer JS, Floyd S, Granek J, Allen A, Chan C, Xie J, Owzar K. bcSeq: An R Package for Fast Sequence Mapping in High-throughput shRNA and CRISPR Screens. Bioinformatics. 2018 May 22.

Anderson GR, Wardell SE, Cakir M, Yip C, Ahn YR, Ali M, Yllanes AP, Chao CA, McDonnell DP, Wood KC. Dysregulation of mitochondrial dynamics proteins are a targetable feature of human tumors. Nat Commun. 2018 Apr 26;9(1):1677.

Tarbet HJ, Dolat L, Smith TJ, Condon BM, O’Brien ET 3rd, Valdivia RH, Boyce M. Site-specific glycosylation regulates the form and function of the intermediate filament cytoskeleton. Elife. 2018 Mar 7;7. pii: e31807.

Waitkus MS, Pirozzi CJ, Moure CJ, Diplas BH, Hansen LJ, Carpenter AB, Yang R, Wang Z, Ingram BO, Karoly ED, Mohney RP, Spasojevic I, McLendon RE, Friedman HS, He Y, Bigner DD, Yan H. Adaptive Evolution of the GDH2 Allosteric Domain Promotes Gliomagenesis by Resolving IDH1R132H-Induced Metabolic Liabilities. Cancer Res. 2018 Jan 1;78(1):36-50.

Cox NJ, Unlu G, Bisnett BJ, Meister TR, Condon BM, Luo PM, Smith TJ, Hanna M, Chhetri A, Soderblom EJ, Audhya A, Knapik EW, Boyce M. Dynamic Glycosylation Governs the Vertebrate COPII Protein Trafficking Pathway. Biochemistry. 2018 Jan 9;57(1):91-107.

Singleton KR, Crawford L, Tsui E, Manchester HE, Maertens O, Liu X, Liberti MV, Magpusao AN, Stein EM, Tingley JP, Frederick DT, Boland GM, Flaherty KT, McCall SJ, Krepler C, Sproesser K, Herlyn M, Adams DJ, Locasale JW, Cichowski K, Mukherjee S, Wood KC. Melanoma Therapeutic Strategies that Select against Resistance by Exploiting MYC-Driven Evolutionary Convergence. Cell Rep. 2017 Dec 5;21(10):2796-2812.

Piro AS, Hernandez D, Luoma S, Feeley EM, Finethy R, Yirga A, Frickel EM, Lesser CF, Coers J. Detection of Cytosolic Shigella flexneri via a C-Terminal Triple-Arginine Motif of GBP1 Inhibits Actin-Based Motility. MBio. 2017 Dec 12;8(6). pii: e01979-17.

Grossman L, Chang C, Dai J, Nikitin PA, Jima DD, Dave SS, Luftig MA. Epstein-Barr Virus Induces Adhesion Receptor CD226 (DNAM-1) Expression during Primary B-Cell Transformation into Lymphoblastoid Cell Lines. mSphere. 2017 Nov 29;2(6). pii: e00305-17.

Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct 5;171(2):481-494.

Carpenter V, Chen YS, Dolat L, Valdivia RH. The Effector TepP Mediates Recruitment and Activation of Phosphoinositide 3-Kinase on Early Chlamydia trachomatis Vacuoles. mSphere. 2017 Jul 19;2(4). pii: e00207-17.

Norris JD, Ellison SJ, Baker JG, Stagg DB, Wardell SE, Park S, Alley HM, Baldi RM, Yllanes A, Andreano KJ, Stice JP, Lawrence SA, Eisner JR, Price DK, Moore WR, Figg WD, McDonnell DP. Androgen receptor antagonism drives cytochrome P450 17A1 inhibitor efficacy in prostate cancer. J Clin Invest. 2017 Jun 1;127(6):2326-2338

Price AM, Dai J, Bazot Q, Patel L, Nikitin PA, Djavadian R, Winter PS, Salinas CA, Barry AP, Wood KC, Johannsen EC, Letai A, Allday MJ, Luftig MA. Epstein-Barr virus ensures B cell survival by uniquely modulating apoptosis at early and late times after infection. Elife. 2017 Apr 20;6. pii: e22509.

Shats I, Deng M, Davidovich A, Zhang C, Kwon JS, Manandhar D, Gordân R, Yao G, You L. Expression level is a key determinant of E2F1-mediated cell fate. Cell Death Differ. 2017 Apr;24(4):626-637.

Sixt BS, Bastidas RJ, Finethy R, Baxter RM, Carpenter VK, Kroemer G, Coers J, Valdivia RH. The Chlamydia trachomatis Inclusion Membrane Protein CpoS Counteracts STING-Mediated Cellular Surveillance and Suicide Programs. Cell Host Microbe. 2017 Jan 11;21(1):113-121.

Subramanian S, Gottschalk WK, Kim SY, Roses AD, Chiba-Falek O. The effects of PPARγ on the regulation of the TOMM40-APOE-C1 genes cluster. Biochim Biophys Acta. 2017 Jan 6;1863(3):810-816.

Gokhale NS, McIntyre AB, McFadden MJ, Roder AE, Kennedy EM, Gandara JA, Hopcraft SE, Quicke KM, Vazquez C, Willer J, Ilkayeva OR, Law BA, Holley CL, Garcia-Blanco MA, Evans MJ, Suthar MS, Bradrick SS, Mason CE, Horner SM. N6-Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection. Cell Host Microbe. 2016 Nov 9;20(5):654-665.

Rittiner JE, Caffall ZF, Hernández-Martinez R, Sanderson SM, Pearson JL, Tsukayama KK, Liu AY, Xiao C, Tracy S, Shipman MK, Hickey P, Johnson J, Scott B, Stacy M, Saunders-Pullman R, Bressman S, Simonyan K, Sharma N, Ozelius LJ, Cirulli ET, Calakos N. Functional Genomic Analyses of Mendelian and Sporadic Disease Identify Impaired eIF2α Signaling as a Generalizable Mechanism for Dystonia. Neuron. 2016 Dec 21;92(6):1238-1251.

Hayes HL, Zhang L, Becker TC, Haldeman JM, Stephens SB, Arlotto M, Moss LG, Newgard CB, Hohmeier HE. A Pdx-1-Regulated Soluble Factor Activates Rat and Human Islet Cell Proliferation. Mol Cell Biol. 2016 Nov 14;36(23):2918-2930.

Pollock JA, Wardell SE, Parent AA, Stagg DB, Ellison SJ, Alley HM, Chao CA, Lawrence SA, Stice JP, Spasojevic I, Baker JG, Kim SH, McDonnell DP, Katzenellenbogen JA, Norris JD. Inhibiting androgen receptor nuclear entry in castration-resistant prostate cancer. Nat Chem Biol. 2016 Oct;12(10):795-801.

Keenan M, Liu B, Tang X, Wu J, Cyr D, Stevens R, Ilkayeva, O, Huang Z, Tollini L, Murphy S, Lucas J, Muoio D, Kim SY, Chi JT. ACLY and ACC1 Regulate Hypoxia-Induced Apoptosis by Modulating ETV4 via α-ketoglutarate. PLoS Genet. 2015 Oct 9;11(10):e1005599.

Kokes M, Dunn JD, Granek JA, Nguyen BD, Barker JR, Valdivia RH, Bastidas RJ. Integrating chemical mutagenesis and whole-genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia. Cell Host Microbe. 2015 May 13;17(5):716-25.

Dhindsa RS, Bradrick SS, Yao X, Heinzen EL, Petrovski S, Krueger BJ, Johnson MR, Frankel WN, Petrou S, Boumil RM, Goldstein DB. Epileptic encephalopathy-causing mutations in DNM1 impair synaptic vesicle endocytosis. Neurol Genet. 2015 Apr 17;1(1):e4.

Barrows NJ, Jamison SF, Bradrick SS, Le Sommer C, Kim SY, Pearson J, Garcia-Blanco MA. Functional genomics approach for the identification of human host factors supporting dengue viral propagation. Methods Mol Biol. 2014;1138:285-99.

Serra V, Eichhorn P, Garcia-Garcia C, Ibrahim Y, Prudkin L, Sanchez G, Rodriguez O, Anton P, Parra JL, Marlow S, Scaltriti M, Perez-Garcia J, Prat A, Arribas J, Hahn WC, Kim SY, Baselga J. RSK3/4 mediate resistance to PI3K pathway inhibitors in breast cancer. J Clin Invest, 2013 Jun 3;123(6):2551-63.

Le Sommer C, Barrows NJ, Bradrick SS, Pearson JL, Garcia-Blanco MA. G protein-coupled receptor kinase 2 promotes flaviviridae entry and replication. PLoS Negl Trop Dis. 2012;6(9):e1820.

Thornbrough JM, Hundley T, Valdivia R, Worley MJ. Human genome-wide RNAi screen for host factors that modulate intracellular Salmonella growth. PLoS One. 2012;7(6):e38097.

Panda D, Das A, Dinh PX, Subramaniam S, Nayak D, Barrows NJ, Pearson JL, Thompson J, Kelly DL, Ladunga I, Pattnaik AK. RNAi screening reveals requirement for host cell secretory pathway in infection by diverse families of negative-strand RNA viruses. Proc Natl Acad Sci U S A. 2011 Nov 22;108(47):19036-41.

Barrows NJ, Le Sommer C, Garcia-Blanco MA, Pearson JL. Factors affecting reproducibility between genome-scale siRNA-based screens. J Biomol Screen. 2010 Aug;15(7):735-47.

Sessions OM, Barrows NJ, Souza-Neto JA, Robinson TJ, Hershey CL, Rodgers MA, Ramirez JL, Dimopoulos G, Yang PL, Pearson JL, Garcia-Blanco MA. Discovery of insect and human dengue virus host factors. Nature. 2009 Apr 23;458(7241):1047-50.