Department of Genetics Publications for June 13-26, 2021

Department of Genetics faculty, postdocs, students and collaborators published twenty one papers during June 13-26, 2021.

 

Common genetic variation influencing human white matter microstructure. 

Zhao B, Li T, Yang Y, Wang X, Luo T, Shan Y, Zhu Z, Xiong D, Hauberg ME, Bendl J, Fullard JF, Roussos P, Li Y, Stein JL, Zhu H.

Science. 2021 Jun 18;372(6548):eabf3736. doi: 10.1126/science.abf3736.

PMID: 34140357

 

Landscape and selection of vaccine epitopes in SARS-CoV-2. 

Smith CC, Olsen KS, Gentry KM, Sambade M, Beck W, Garness J, Entwistle S, Willis C, Vensko S, Woods A, Fini M, Carpenter B, Routh E, Kodysh J, O’Donnell T, Haber C, Heiss K, Stadler V, Garrison E, Sandor AM, Ting JPY, Weiss J, Krajewski K, Grant OC, Woods RJ, Heise M, Vincent BG, Rubinsteyn A.

Genome Med. 2021 Jun 14;13(1):101. doi: 10.1186/s13073-021-00910-1.

PMID: 34127050

 

Evaluating the clinical utility of early exome sequencing in diverse pediatric outpatient populations in the North Carolina Clinical Genomic Evaluation of Next-generation Exome Sequencing (NCGENES) 2 study: a randomized controlled trial. 

Staley BS, Milko LV, Waltz M, Griesemer I, Mollison L, Grant TL, Farnan L, Roche M, Navas A, Lightfoot A, Foreman AKM, O’Daniel JM, O’Neill SC, Lin FC, Roman TS, Brandt A, Powell BC, Rini C, Berg JS, Bensen JT.

Trials. 2021 Jun 14;22(1):395. doi: 10.1186/s13063-021-05341-2.

PMID: 34127041

 

Identification of a novel inflamed tumor microenvironment signature as a predictive biomarker of bacillus Calmette-Guerin immunotherapy in non-muscle invasive bladder cancer. 

Damrauer JS, Roell KR, Smith MA, Sun X, Kirk EL, Hoadley KA, Benefield HC, Iyer G, Solit DB, Milowsky MI, Kim WY, Nielsen ME, Wobker SE, Dalbagni G, Al-Ahmadie HA, Olshan AF, Bochner BH, Furberg H, Troester MA, Pietzak EJ.

Clin Cancer Res. 2021 Jun 11:clincanres.0205.2021. doi: 10.1158/1078-0432.CCR-21-0205. Online ahead of print.

PMID: 34117034

 

From base pair to brain. 

Matoba N, Stein JL.

Nat Neurosci. 2021 May;24(5):619-621. doi: 10.1038/s41593-021-00852-2.

PMID: 33875895

 

Targeting Chikungunya Virus Replication by Benzoannulene Inhibitors. 

Ahmed SK, Haese NN, Cowan JT, Pathak V, Moukha-Chafiq O, Smith VJ, Rodzinak KJ, Ahmad F, Zhang S, Bonin KM, Streblow AD, Streblow CE, Kreklywich CN, Morrison C, Sarkar S, Moorman N, Sander W, Allen R, DeFilippis V, Tekwani BL, Wu M, Hirsch AJ, Smith JL, Tower NA, Rasmussen L, Bostwick R, Maddry JA, Ananthan S, Gerdes JM, Augelli-Szafran CE, Suto MJ, Morrison TE, Heise MT, Streblow DN, Pathak AK.

J Med Chem. 2021 Apr 22;64(8):4762-4786. doi: 10.1021/acs.jmedchem.0c02183. Epub 2021 Apr 9.

PMID: 33835811

 

Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol. 

Boschen KE, Ptacek TS, Berginski ME, Simon JM, Parnell SE.

Dis Model Mech. 2021 Jun 1;14(6):dmm049012. doi: 10.1242/dmm.049012. Epub 2021 Jun 17.

PMID: 34137816

 

Generation of an induced pluripotent stem cell line (UNCCi002-A) from a healthy donor using a non-integration system to study Cerebral Cavernous Malformation (CCM). 

Beltran AA, Molina SG, Marquez A, Munoz LJ, Olivares JF, Beltran AS.

Stem Cell Res. 2021 Jun 9;54:102421. doi: 10.1016/j.scr.2021.102421. Online ahead of print.

PMID: 34130156

 

Harnessing ultrasound-stimulated phase change contrast agents to improve antibiotic efficacy against methicillin-resistant Staphylococcus aureus biofilms. 

Durham PG, Sidders AE, Beam JE, Kedziora KM, Dayton PA, Conlon BP, Papadopoulou V, Rowe SE.

Biofilm. 2021 May 11;3:100049. doi: 10.1016/j.bioflm.2021.100049. eCollection 2021 Dec.

PMID: 34124645

 

Systems genetics in diversity outbred mice inform BMD GWAS and identify determinants of bone strength. 

Al-Barghouthi BM, Mesner LD, Calabrese GM, Brooks D, Tommasini SM, Bouxsein ML, Horowitz MC, Rosen CJ, Nguyen K, Haddox S, Farber EA, Onengut-Gumuscu S, Pomp D, Farber CR.

Nat Commun. 2021 Jun 7;12(1):3408. doi: 10.1038/s41467-021-23649-0.

PMID: 34099702

 

A conserved BAH module within mammalian BAHD1 connects H3K27me3 to Polycomb gene silencing. 

Fan H, Guo Y, Tsai YH, Storey AJ, Kim A, Gong W, Edmondson RD, Mackintosh SG, Li H, Byrum SD, Tackett AJ, Cai L, Wang GG.

Nucleic Acids Res. 2021 May 7;49(8):4441-4455. doi: 10.1093/nar/gkab210.

PMID: 33823544

 

Transcriptomic bases of a polyphenism. 

Levis NA, Kelly PW, Harmon EA, Ehrenreich IM, McKay DJ, Pfennig DW.

J Exp Zool B Mol Dev Evol. 2021 Jun 18. doi: 10.1002/jez.b.23066. Online ahead of print.

PMID: 34142757

 

Genome sequencing unveils a regulatory landscape of platelet reactivity. 

Keramati AR, Chen MH, Rodriguez BAT, Yanek LR, Bhan A, Gaynor BJ, Ryan K, Brody JA, Zhong X, Wei Q; NHLBI Trans-Omics for Precision (TOPMed) Consortium, Kammers K, Kanchan K, Iyer K, Kowalski MH, Pitsillides AN, Cupples LA, Li B, Schlaeger TM, Shuldiner AR, O’Connell JR, Ruczinski I, Mitchell BD, Faraday N, Taub MA, Becker LC, Lewis JP, Mathias RA, Johnson AD.

Nat Commun. 2021 Jun 15;12(1):3626. doi: 10.1038/s41467-021-23470-9.

PMID: 34131117

 

DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing. 

Bhattacharya A, Hamilton AM, Troester MA, Love MI.

Nucleic Acids Res. 2021 May 7;49(8):e48. doi: 10.1093/nar/gkab031.

PMID: 33524140

 

Highly metastatic claudin-low mammary cancers can originate from luminal epithelial cells. 

Rädler PD, Wehde BL, Triplett AA, Shrestha H, Shepherd JH, Pfefferle AD, Rui H, Cardiff RD, Perou CM, Wagner KU.

Nat Commun. 2021 Jun 18;12(1):3742. doi: 10.1038/s41467-021-23957-5.

PMID: 34145248

 

Determinants of penetrance and variable expressivity in monogenic metabolic conditions across 77,184 exomes. 

Goodrich JK, Singer-Berk M, Son R, Sveden A, Wood J, England E, Cole JB, Weisburd B, Watts N, Caulkins L, Dornbos P, Koesterer R, Zappala Z, Zhang H, Maloney KA, Dahl A, Aguilar-Salinas CA, Atzmon G, Barajas-Olmos F, Barzilai N, Blangero J, Boerwinkle E, Bonnycastle LL, Bottinger E, Bowden DW, Centeno-Cruz F, Chambers JC, Chami N, Chan E, Chan J, Cheng CY, Cho YS, Contreras-Cubas C, Córdova E, Correa A, DeFronzo RA, Duggirala R, Dupuis J, Garay-Sevilla ME, García-Ortiz H, Gieger C, Glaser B, González-Villalpando C, Gonzalez ME, Grarup N, Groop L, Gross M, Haiman C, Han S, Hanis CL, Hansen T, Heard-Costa NL, Henderson BE, Hernandez JMM, Hwang MY, Islas-Andrade S, Jørgensen ME, Kang HM, Kim BJ, Kim YJ, Koistinen HA, Kooner JS, Kuusisto J, Kwak SH, Laakso M, Lange L, Lee JY, Lee J, Lehman DM, Linneberg A, Liu J, Loos RJF, Lyssenko V, Ma RCW, Martínez-Hernández A, Meigs JB, Meitinger T, Mendoza-Caamal E, Mohlke KL, Morris AD, Morrison AC, Ng MCY, Nilsson PM, O’Donnell CJ, Orozco L, Palmer CNA, Park KS, Post WS, Pedersen O, Preuss M, Psaty BM, Reiner AP, Revilla-Monsalve C, Rich SS, Rotter JI, Saleheen D, Schurmann C, Sim X, Sladek R, Small KS, So WY, Spector TD, Strauch K, Strom TM, Tai ES, Tam CHT, Teo YY, Thameem F, Tomlinson B, Tracy RP, Tuomi T, Tuomilehto J, Tusié-Luna T, van Dam RM, Vasan RS, Wilson JG, Witte DR, Wong TY; AMP-T2D-GENES Consortia, Burtt NP, Zaitlen N, McCarthy MI, Boehnke M, Pollin TI, Flannick J, Mercader JM, O’Donnell-Luria A, Baxter S, Florez JC, MacArthur DG, Udler MS.

Nat Commun. 2021 Jun 9;12(1):3505. doi: 10.1038/s41467-021-23556-4.

PMID: 34108472

 

Phase separation drives aberrant chromatin looping and cancer development. 

Ahn JH, Davis ES, Daugird TA, Zhao S, Quiroga IY, Uryu H, Li J, Storey AJ, Tsai YH, Keeley DP, Mackintosh SG, Edmondson RD, Byrum SD, Cai L, Tackett AJ, Zheng D, Legant WR, Phanstiel DH, Wang GG.

Nature. 2021 Jun 23. doi: 10.1038/s41586-021-03662-5. Online ahead of print.

PMID: 34163069

 

A nadA Mutation Confers Nicotinic Acid Auxotrophy in Pro-carcinogenic Intestinal Escherichia coli NC101. 

Lopez LR, Barlogio CJ, Broberg CA, Wang J, Arthur JC.

Front Microbiol. 2021 Jun 2;12:670005. doi: 10.3389/fmicb.2021.670005. eCollection 2021.

PMID: 34149655

 

Anticipating the ethical, legal, and social implications of human genome research: An ongoing experiment. 

Juengst ET.

Am J Med Genet A. 2021 Jun 22. doi: 10.1002/ajmg.a.62405. Online ahead of print.

PMID: 34155808

 

Statistical Modeling of High Dimensional Counts. 

Love MI.

Methods Mol Biol. 2021;2284:97-134. doi: 10.1007/978-1-0716-1307-8_7.

PMID: 33835440

 

Parasites, niche modification and the host microbiome: A field survey of multiple parasites. 

O’Keeffe KR, Halliday FW, Jones CD, Carbone I, Mitchell CE.

Mol Ecol. 2021 May;30(10):2404-2416. doi: 10.1111/mec.15892. Epub 2021 Apr 12.

PMID: 33740826