Frederic D. Bushman, Ph.D.

faculty photo
William Maul Measey Professor in Microbiology
Co-Director, PennCHOP Microbiome Program
Chair, Department of Microbiology, University of Pennsylvania
Co-Director, Penn Center for Research on Coronaviruses and Other Emerging Pathogens
Department: Microbiology

Contact information
426 Johnson Pavilion
Department of Microbiology
3610 Hamilton Walk
Philadelphia, PA 19104-6076
Lab: (215) 573-8733
Education:
B.A. (Biology and English)
Amherst College, 1980.
Ph.D. (Cellular and Developmental Biology)
Harvard University, 1988.
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Description of Research Expertise

Research Interests
Human microbiome, human virome, SARS-CoV-2, human gene therapy, HIV.

Keywords
microbiome, virome, gene therapy, SARS-CoV-2, HIV, Clostridioides difficile, integration, integrase, virology.

Description of Research
Our goal is to carry out research on interactions between humans and their microbes that yields the maximum positive effect on human welfare. Often this involves development and implementation of new technology for basic research and biotechnology. One research focus involves studies of the human microbiome, the gigantic community of microbes that live associated with every human. Other research centers on specific viruses, such as SARS-CoV-2 and HIV, and the full populations of viruses in humans—the virome. A third related area involves methods for understanding and improving approaches to human gene therapy, including integration by viral vectors.

Our laboratory supports a core facility that provides genomic analysis for human gene therapy, with particular focus on the consequences of gene modification for the human genome: Viral/ Molecular High Density Sequencing Core.

Honors, Awards, Memberships
Fellow of the American Association for the Advancement of Science, 2014
Pioneer Award, Journal of Human Gene Therapy, 2014
Fellow of the American Academy of Microbiology, 2009
Master of Arts, Honoris Causa, University of Pennsylvania, 2004
Stohlman Scholar, Leukemia and Lymphoma Society of America, 2001
Scholar, Leukemia Society of America, Inc., 1996-2001
Special Fellow, Leukemia Society of America, Inc., 1992-1995
Fellow, Leukemia Society of America, Inc., 1989-1992


Rotation Projects
Rotation projects center on the human microbiome in health and disease, analysis of viral replication, and studies of integration in human gene therapy.

Selected Publications

Bushman FD, Fujiwara T, Craigie R: Retroviral DNA integration directed by HIV integration protein in vitro. Science 249: 1555-1558, 1990.

Schröder AR, Shinn P, Chen H, Berry C, Ecker JR, Bushman F: HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110: 521-529, 2002 Notes: see also cover.

Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD: Linking long-term dietary patterns with gut microbial enterotypes. Science 334: 105-108, 2011.

Bushman FD, Conrad M, Ren Y, Zhao C, Gu C, Petucci C, Kim MS, Abbas A, Downes KJ, Devas N, Mattei LM, Breton J, Kelsen J, Marakos S, Galgano A, Kachelries K, Erlichman J, Hart JL, Moraskie M, Kim D, Zhang H, Hofstaedter CE, Wu GD, Lewis JD, Zackular JP, Li H, Bittinger K, Baldassano R.: Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease. Cell Host Microbe 28: 422-433, Sep 2020.

Abbas AA, Taylor LJ, Dothard MI, Leiby JS, Fitzgerald AS, Khatib LA, Collman RG, Bushman FD: Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness. Cell Host Microbe 25(5): 719-729, May 2019.

Liang G, Zhao C, Zhang H, Mattei L, Sherrill-Mix S, Bittinger K, Kessler LR, Wu GD, Baldassano RN, DeRusso P, Ford E, Elovitz MA, Kelly MS, Patel MZ, Mazhani T, Gerber JS, Kelly A, Zemel BS, Bushman FD.: The stepwise assembly of the neonatal virome is modulated by breastfeeding. Nature 581: 470-474, May 2020.

Gupta K, Turkki V, Sherrill-Mix S, Hwang Y, Eilers G, Taylor L, McDanal C, Wang P, Temelkoff D, Nolte RT, Velthuisen E, Jeffrey J, Van Duyne GD, Bushman FD: Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase. PLoS Biology 14(12): e1002584, Dec 2016.

Fraietta Joseph A, Nobles Christopher L, Sammons Morgan A, Lundh Stefan, Carty Shannon A, Reich Tyler J, Cogdill Alexandria P, Morrissette Jennifer J D, DeNizio Jamie E, Reddy Shantan, Hwang Young, Gohil Mercy, Kulikovskaya Irina, Nazimuddin Farzana, Gupta Minnal, Chen Fang, Everett John K, Alexander Katherine A, Lin-Shiao Enrique, Gee Marvin H, Liu Xiaojun, Young Regina M, Ambrose David, Wang Yan, Xu Jun, Jordan Martha S, Marcucci Katherine T, Levine Bruce L, Garcia K Christopher, Zhao Yangbing, Kalos Michael, Porter David L, Kohli Rahul M, Lacey Simon F, Berger Shelley L, Bushman Frederic D, June Carl H, Melenhorst J Joseph: Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells. Nature 558(7709): 307-312, June 2018.

Stadtmauer EA, Fraietta JA, Davis MM, Cohen AD, Weber KL, Lancaster E, Mangan PA, Kulikovskaya I, Gupta M, Chen F, Tian L, Gonzalez VE, Xu J, Jung IY, Melenhorst JJ, Plesa G, Shea J, Matlawski T, Cervini A, Gaymon AL, Desjardins S, Lamontagne A, Salas-Mckee J, Fesnak A, Siegel DL, Levine BL, Jadlowsky JK, Young RM, Chew A, Hwang WT, Hexner EO, Carreno BM, Nobles CL, Bushman FD, Parker KR, Qi Y, Satpathy AT, Chang HY, Zhao Y, Lacey SF, June CH.: CRISPR-engineered T cells in patients with refractory cancer. Science 367: eaba7365, Feb 2020.

Keeler EL, Merenstein C, Reddy S, Taylor LJ, Cobián-Güemes AG, Zankharia U, Collman RG, Bushman FD.: Widespread, human-associated redondoviruses infect the commensal protozoan Entamoeba gingivalis. Cell Host Microbe Nov 2022.

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Last updated: 03/27/2024
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