Publications for All Faculty - 2021

  • Jiang W, Bush J, Sheen J A Versatile and Efficient Plant Protoplast Platform for Genome Editing by Cas9 RNPs. Front Genome Ed. 2021;3:719190 - PMID: 35005700 - PMCID: PMC8729822 - DOI: 10.3389/fgeed.2021.719190

  • Chrissy Bolton ∗ Christopher S. Smillie ∗ Sumeet Pandey ∗ Rasa Elmentaite Gabrielle Wei Carmen Argmann Dominik Aschenbrenner Kylie R. James Dermot P.B. McGovern Marina Macchi Judy Cho Dror S. Shouval Jochen Kammermeier Sibylle Koletzko Krithika Bagalopal Melania Capitani Athena Cavounidis Elisabete Pires Carl Weidinger James McCullagh Peter D. Arkwright Wolfram Haller Britta Siegmund Lauren Peters Luke Jostins Simon P.L. Travis Carl A. Anderson Scott Snapper Christoph Klein Eric Schadt Matthias Zilbauer Ramnik Xavier Sarah Teichmann Aleixo M. Muise Aviv Regev Holm H. Uhlig An integrated taxonomy for monogenic inflammatory bowel disease. Gastroenterology. 2021;:ePub - DOI: https://doi.org/10.1053/j.gastro.2021.11.014

  • Charlesworth AG, Seroussi U, Lehrbach NJ, Renaud MS, Sundby AE, Molnar RI, Lao RX, Willis AR, Woock JR, Aber MJ, Diao AJ, Reinke AW, Ruvkun G, Claycomb JM Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility. Nucleic Acids Res. 2021;49(15):8836-8865 - PMID: 34329465 - PMCID: PMC8421154 - DOI: 10.1093/nar/gkab619

  • Tak YE, Horng JE, Perry NT, Schultz HT, Iyer S, Yao Q, Zou LS, Aryee MJ, Pinello L, Joung JK Augmenting and directing long-range CRISPR-mediated activation in human cells. Nat Methods. 2021;18(9):1075-1081 - PMID: 34354266 - PMCID: PMC8446310 - DOI: 10.1038/s41592-021-01224-1

  • Pelka K, Hofree M, Chen JH, Sarkizova S, Pirl JD, Jorgji V, Bejnood A, Dionne D, Ge WH, Xu KH, Chao SX, Zollinger DR, Lieb DJ, Reeves JW, Fuhrman CA, Hoang ML, Delorey T, Nguyen LT, Waldman J, Klapholz M, Wakiro I, Cohen O, Albers J, Smillie CS, Cuoco MS, Wu J, Su MJ, Yeung J, Vijaykumar B, Magnuson AM, Asinovski N, Moll T, Goder-Reiser MN, Applebaum AS, Brais LK, DelloStritto LK, Denning SL, Phillips ST, Hill EK, Meehan JK, Frederick DT, Sharova T, Kanodia A, Todres EZ, Jané-Valbuena J, Biton M, Izar B, Lambden CD, Clancy TE, Bleday R, Melnitchouk N, Irani J, Kunitake H, Berger DL, Srivastava A, Hornick JL, Ogino S, Rotem A, Vigneau S, Johnson BE, Corcoran RB, Sharpe AH, Kuchroo VK, Ng K, Giannakis M, Nieman LT, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N Spatially organized multicellular immune hubs in human colorectal cancer. Cell. 2021;184(18):4734-4752.e20 - PMID: 34450029 - PMCID: PMC8772395 - DOI: 10.1016/j.cell.2021.08.003

  • Stražar M, Temba GS, Vlamakis H, Kullaya VI, Lyamuya F, Mmbaga BT, Joosten LAB, van der Ven AJAM, Netea MG, de Mast Q, Xavier RJ Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations. Nat Commun. 2021;12(1):4845 - PMID: 34381036 - PMCID: PMC8357928 - DOI: 10.1038/s41467-021-25213-2

  • Brown EM, Arellano-Santoyo H, Temple ER, Costliow ZA, Pichaud M, Hall AB, Liu K, Durney MA, Gu X, Plichta DR, Clish CA, Porter JA, Vlamakis H, Xavier RJ Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors. Cell Host Microbe. 2021;29(9):1351-1365.e11 - PMID: 34403684 - PMCID: PMC8429246 - DOI: 10.1016/j.chom.2021.07.011

  • Sato Y, Atarashi K, Plichta DR, Arai Y, Sasajima S, Kearney SM, Suda W, Takeshita K, Sasaki T, Okamoto S, Skelly AN, Okamura Y, Vlamakis H, Li Y, Tanoue T, Takei H, Nittono H, Narushima S, Irie J, Itoh H, Moriya K, Sugiura Y, Suematsu M, Moritoki N, Shibata S, Littman DR, Fischbach MA, Uwamino Y, Inoue T, Honda A, Hattori M, Murai T, Xavier RJ, Hirose N, Honda K Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians. Nature. 2021;599(7885):458-464 - PMID: 34325466 - DOI: 10.1038/s41586-021-03832-5

  • Liu K, Kong L, Graham DB, Carey KL, Xavier RJ SAC1 regulates autophagosomal phosphatidylinositol-4-phosphate for xenophagy-directed bacterial clearance. Cell Reports. 2021;36(4):109434 - PMID: 34320354 - PMCID: PMC8327279 - DOI: https://doi.org/10.1016/j.celrep.2021.109434

  • Lee JWJ, Plichta D, Hogstrom L, Borren NZ, Lau H, Gregory SM, Tan W, Khalili H, Clish C, Vlamakis H, Xavier RJ, Ananthakrishnan AN Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease. Cell Host Microbe. 2021;29(8):1294-1304.e4 - PMID: 34297922 - PMCID: PMC8366279 - DOI: 10.1016/j.chom.2021.06.019

  • Vadaq N, Schirmer M, Tunjungputri RN, Vlamakis H, Chiriac C, Ardiansyah E, Gasem MH, Joosten L, de Groot PG, Xavier RJ, Netea MG, van der Ven AJAM, de Mast Q Untargeted plasma metabolome and gut microbiome profiling provide novel insights in the regulation of platelet reactivity in healthy individuals. Thromb Haemost. 2021;122(4):529-539 - PMID: 34192775 - DOI: 10.1055/a-1541-3706

  • Xie L, McKenzie CI, Qu X, Mu Y, Wang Q, Bing N, Naidoo K, Alam MJ, Yu D, Gong F, Ang C, Robert R, Marques FZ, Furlotte N, Hinds D, Gasser O, 23andMe Research Team, Xavier RJ, Mackay CR pH and Proton Sensor GPR65 Determine Susceptibility to Atopic Dermatitis. J Immunol. 2021;207(1):101-109 - PMID: 34135065 - PMCID: PMC8674371 - DOI: 10.4049/jimmunol.2001363

  • Arnett A, Moo KG, Flynn KJ, Sundberg TB, Johannessen L, Shamji AF, Gray NS, Decker T, Zheng Y, Gersuk VH, Rahman ZS, Levy DE, Marié IJ, Linsley PS, Xavier RJ, Khor B The CDK8 inhibitor DCA promotes a tolerogenic chemical immunophenotype in CD4+ T cells via a novel CDK8-GATA3-FOXP3 pathway. Mol Cell Biol. 2021;41(9):e0008521 - PMID: 34124936 - PMCID: PMC8384069 - DOI: 10.1128/MCB.00085-21

  • Gligorijević V, Renfrew PD, Kosciolek T, Leman JK, Berenberg D, Vatanen T, Chandler C, Taylor BC, Fisk IM, Vlamakis H, Xavier RJ, Knight R, Cho K, Bonneau R Structure-based protein function prediction using graph convolutional networks. Nat Commun. 2021;12(1):3168 - PMID: 34039967 - PMCID: PMC8155034 - DOI: 10.1038/s41467-021-23303-9

  • Scheid JF, Barnes CO, Eraslan B, Hudak A, Keeffe JR, Cosimi LA, Brown EM, Muecksch F, Weisblum Y, Zhang S, Delorey T, Woolley AE, Ghantous F, Park SM, Phillips D, Tusi B, Huey-Tubman KE, Cohen AA, Gnanapragasam PNP, Rzasa K, Hatziioanno T, Durney MA, Gu X, Tada T, Landau NR, West AP, Rozenblatt-Rosen O, Seaman MS, Baden LR, Graham DB, Deguine J, Bieniasz PD, Regev A, Hung D, Bjorkman PJ, Xavier RJ B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV. Cell. 2021;184(12):3205-3221.e24 - PMID: 34015271 - PMCID: PMC8064835 - DOI: 10.1016/j.cell.2021.04.032

  • Xavier RJ Translating the human microbiome: a path to improving health. Genome Med. 2021;13(1):78 - PMID: 33952319 - PMCID: PMC8097784 - DOI: 10.1186/s13073-021-00896-w

  • Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB Longitudinal proteomic analysis of plasma from patients with severe COVID-19 reveal patient survival-associated signatures, tissue-specific cell death, and cell-cell interactions. Cell Rep Med. 2021;2(5):100287 - PMID: 33969320 - PMCID: PMC8091031 - DOI: 10.1016/j.xcrm.2021.100287

  • Henke MT, Brown EM, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J Capsular polysaccharide correlates with immune response to the human gut microbe Ruminococcus gnavus. Proc Natl Acad Sci U S A. 2021;118(20):ePub - PMID: 33972416 - PMCID: PMC8157926 - DOI: 10.1073/pnas.2007595118

  • Ma P, He LL, Pironti A, Laibinis HH, Ernst CM, Manson AL, Bhattacharyya RP, Earl AM, Livny J, Hung DT Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics. Elife. 2021;10:ePub - PMID: 33871353 - PMCID: PMC8079144 - DOI: 10.7554/eLife.67310

  • Penaranda C, Chumbler NM, Hung DT Dual transcriptional analysis reveals adaptation of host and pathogen to intracellular survival of Pseudomonas aeruginosa associated with urinary tract infection. PLoS Pathog. 2021;17(4):e1009534 - PMID: 33901267 - PMCID: PMC8102004 - DOI: 10.1371/journal.ppat.1009534

  • Petri K, Zhang W, Ma J, Schmidts A, Lee H, Horng JE, Kim DY, Kurt IC, Clement K, Hsu JY, Pinello L, Maus MV, Joung JK, Yeh JJ CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells. Nat Biotechnol. 2021;40(2):189-193 - PMID: 33927418 - PMCID: PMC8553808 - DOI: 10.1038/s41587-021-00901-y

  • Petersen AØ, Jokinen M, Plichta DR, Liebisch G, Gronwald W, Oefner PJ, Vlamakis H, Chung DC, Ranki A, Xavier RJ Cytokine-specific autoantibodies shape the gut microbiome in autoimmune polyendocrine syndrome type 1. J Allergy Clin Immunol. 2021;148(3):876-888 - PMID: 33819509 - PMCID: PMC8429070 - DOI: 10.1016/j.jaci.2021.03.025

  • Nasser J, Bergman DT, Fulco CP, Guckelberger P, Doughty BR, Patwardhan TA, Jones TR, Nguyen TH, Ulirsch JC, Lekschas F, Mualim K, Natri HM, Weeks EM, Munson G, Kane M, Kang HY, Cui A, Ray JP, Eisenhaure TM, Collins RL, Dey K, Pfister H, Price AL, Epstein CB, Kundaje A, Xavier RJ, Daly MJ, Huang H, Finucane HK, Hacohen N, Lander ES, Engreitz JM Genome-wide enhancer maps link risk variants to disease genes. Nature. 2021;593(7858):238-243 - PMID: 33828297 - DOI: 10.1038/s41586-021-03446-x

  • Duzdevich D, Carr CE, Ding D, Zhang SJ, Walton TS, Szostak JW Competition between bridged dinucleotides and activated mononucleotides determines the error frequency of nonenzymatic RNA primer extension. Nucleic Acids Res. 2021;49(7):3681-3691 - PMID: 33744957 - PMCID: PMC8053118 - DOI: 10.1093/nar/gkab173

  • Jaeger N, Gamini R, Cella M, Schettini JL, Bugatti M, Zhao S, Rosadini CV, Esaulova E, Di Luccia B, Kinnett B, Vermi W, Artyomov MN, Wynn TA, Xavier RJ, Jelinsky SA, Colonna M Single-cell analyses of Crohn's disease tissues reveal intestinal intraepithelial T cells heterogeneity and altered subset distributions. Nat Commun. 2021;12(1):1921 - PMID: 33771991 - PMCID: PMC7997960 - DOI: 10.1038/s41467-021-22164-6

  • Groussin M, Poyet M, Sistiaga A, Kearney SM, Moniz K, Noel M, Hooker J, Gibbons SM, Segurel L, Froment A, Mohamed RS, Fezeu A, Juimo VA, Lafosse S, Tabe FE, Girard C, Iqaluk D, Nguyen LTT, Shapiro BJ, Lehtimäki J, Ruokolainen L, Kettunen PP, Vatanen T, Sigwazi S, Mabulla A, Domínguez-Rodrigo M, Nartey YA, Agyei-Nkansah A, Duah A, Awuku YA, Valles KA, Asibey SO, Afihene MY, Roberts LR, Plymoth A, Onyekwere CA, Summons RE, Xavier RJ, Alm EJ Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell. 2021;184(8):2053-2067.e18 - PMID: 33794144 - DOI: 10.1016/j.cell.2021.02.052

  • Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Triglia ET, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams T, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo ASE, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CGK, NHLBI LungMap Consortium, Human Cell Atlas Lung Biological Network Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nat Med. 2021;27(3):546-559 - PMID: 33654293 - DOI: 10.1038/s41591-020-01227-z

  • Sullivan ZA, Khoury-Hanold W, Lim J, Smillie C, Biton M, Reis BS, Zwick RK, Pope SD, Israni-Winger K, Parsa R, Philip NH, Rashed S, Palm N, Wang A, Mucida D, Regev A, Medzhitov R γδ T cells regulate the intestinal response to nutrient sensing. Science. 2021;371(6535):ePub - PMID: 33737460 - DOI: 10.1126/science.aba8310

  • Plichta DR, Somani J, Pichaud M, Wallace ZS, Fernandes AD, Perugino CA, Lähdesmäki H, Stone JH, Vlamakis H, Chung DC, Khanna D, Pillai S, Xavier RJ Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis. Genome Med. 2021;13(1):35 - PMID: 33648559 - PMCID: PMC7919092 - DOI: 10.1186/s13073-021-00853-7

  • Kim SC, O'Flaherty DK, Giurgiu C, Zhou L, Szostak JW The Emergence of RNA from the Heterogeneous Products of Prebiotic Nucleotide Synthesis. J Am Chem Soc. 2021;143(9):3267-3279 - PMID: 33636080 - DOI: 10.1021/jacs.0c12955

  • Mojarro A, Jin L, Szostak JW, Head JW, Zuber MT In search of the RNA world on Mars. Geobiology. 2021;19(3):307-321 - PMID: 33565260 - PMCID: PMC8248371 - DOI: 10.1111/gbi.12433

  • Annas GJ, Beisel CL, Clement K, Crisanti A, Francis S, Galardini M, Galizi R, Grünewald J, Immobile G, Khalil AS, Müller R, Pattanayak V, Petri K, Paul L, Pinello L, Simoni A, Taxiarchi C, Joung JK A Code of Ethics for Gene Drive Research. CRISPR J. 2021;4(1):19-24 - PMID: 33571044 - PMCID: PMC7898401 - DOI: 10.1089/crispr.2020.0096

  • Radakovic A, Wright TH, Lelyveld VS, Szostak JW A Potential Role for Aminoacylation in Primordial RNA Copying Chemistry. Biochemistry. 2021;60(6):477-488 - PMID: 33523633 - DOI: 10.1021/acs.biochem.0c00943

  • Tanes C, Bittinger K, Gao Y, Friedman ES, Nessel L, Paladhi UR, Chau L, Panfen E, Fischbach MA, Braun J, Xavier RJ, Clish CB, Li H, Bushman FD, Lewis JD, Wu GD Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Cell Host Microbe. 2021;29(3):394-407.e5 - PMID: 33440171 - PMCID: PMC8022197 - DOI: 10.1016/j.chom.2020.12.012

  • Zabaleta N, Dai W, Bhatt U, Chichester JA, Estelien R, Sanmiguel J, Michalson KT, Diop C, Maciorowski D, Qi W, Hudspeth E, Cucalon A, Dyer CD, Pampena MB, Knox JJ, LaRocque RC, Charles RC, Li D, Kim M, Sheridan A, Storm N, Johnson RI, Feldman J, Hauser BM, Ryan A, Kobayashi DT, Chauhan R, McGlynn M, Ryan ET, Schmidt AG, Price B, Honko A, Griffiths A, Yaghmour S, Hodge R, Betts MR, Freeman MW, Wilson JM, Vandenberghe LH Immunogenicity of an AAV-based, room-temperature stable, single dose COVID-19 vaccine in mice and non-human primates. bioRxiv. 2021;:ePub - PMID: 33442684 - PMCID: PMC7805441 - DOI: 10.1101/2021.01.05.422952

  • Warnhoff K, Hercher TW, Mendel RR, Ruvkun G Protein-bound molybdenum cofactor is bioavailable and rescues molybdenum cofactor-deficient C. elegans. Genes Dev. 2021;35(3-4):212-217 - PMID: 33446569 - PMCID: PMC7849362 - DOI: 10.1101/gad.345579.120

  • You K, Wang L, Chou CH, Liu K, Nakata T, Jaiswal A, Yao J, Lefkovith A, Omar A, Perrigoue JG, Towne JE, Regev A, Graham DB, Xavier RJ QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis. Science. 2021;371(6524):ePub - PMID: 33384352 - PMCID: PMC8315080 - DOI: 10.1126/science.abb6896

  • Zhang W, Kim SC, Tam CP, Lelyveld VS, Bala S, Chaput JC, Szostak JW Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization. Nucleic Acids Res. 2021;49(2):646-656 - PMID: 33347562 - PMCID: PMC7826252 - DOI: 10.1093/nar/gkaa1215

  • Dong X, Yang Y, Zou Z, Zhao Y, Ci B, Zhong L, Bhave M, Wang L, Kuo YC, Zang X, Zhong R, Aguilera ER, Richardson RB, Simonetti B, Schoggins JW, Pfeiffer JK, Yu L, Zhang X, Xie Y, Schmid SL, Xiao G, Gleeson PA, Ktistakis NT, Cullen PJ, Xavier RJ, Levine B Sorting nexin 5 mediates virus-induced autophagy and immunity. Nature. 2021;589(7842):456-461 - PMID: 33328639 - PMCID: PMC7856200 - DOI: 10.1038/s41586-020-03056-z

  • Efron PA, Darden DB, Wang Z, Nacionales DC, Lopez MC, Hawkins RB, Cox MC, Rincon JC, Ungaro R, Dirain ML, Ghita GL, Chen T, Billiar TR, Delano MJ, Leeuwenburgh C, Bihorac A, Brakenridge SC, Moore FA, Mohr AM, Tompkins RG, Brumback BA, Baker HV, Upchurch GR, Moldawer LL Transcriptomic responses from improved murine sepsis models can better mimic human surgical sepsis. FASEB J. 2021;35(2):e21156 - PMID: 33140449 - PMCID: PMC7855423 - DOI: 10.1096/fj.202002150R

  • Zhou L, Ding D, Szostak JW The Virtual Circular Genome Model for Primordial RNA Replication. RNA. 2021;27(1):1-11 - PMID: 33028653 - PMCID: PMC7749632 - DOI: 10.1261/rna.077693.120

  • Hu S, Vich Vila A, Gacesa R, Collij V, Stevens C, Fu JM, Wong I, Talkowski ME, Rivas MA, Imhann F, Bolte L, van Dullemen H, Dijkstra G, Visschedijk MC, Festen EA, Xavier RJ, Fu J, Daly MJ, Wijmenga C, Zhernakova A, Kurilshikov A, Weersma RK Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD. Gut. 2021;70(2):285-296 - PMID: 32651235 - PMCID: PMC7815889 - DOI: 10.1136/gutjnl-2019-319706

  • Kurt IC, Zhou R, Iyer S, Garcia SP, Miller BR, Langner LM, Grünewald J, Joung JK CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells. Nat Biotechnol. 2021;39(1):41-46 - PMID: 32690971 - PMCID: PMC7854778 - DOI: 10.1038/s41587-020-0609-x

  • Borren NZ, Plichta D, Joshi AD, Bonilla G, Peng V, Colizzo FP, Luther J, Khalili H, Garber JJ, van der Woude CJ, Sadreyev R, Vlamakis H, Xavier RJ, Ananthakrishnan AN Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases. Clin Gastroenterol Hepatol. 2021;19(3):519-527.e5 - PMID: 32184182 - DOI: 10.1016/j.cgh.2020.03.013