PUBLICATIONS

Faculty members regularly author or co-author publications in high-tiered journals and serve in editorial board positions. Here is a selection of representative Department faculty publications that have been highlighted in the news or otherwise garnered attention.


Seasonal human coronavirus antibodies are boosted upon SARS-CoV-2 infection but not associated with protection

Elizabeth M Anderson, Eileen C Goodwin, Anurag Verma, Claudia P Arevalo, Marcus J Bolton, Madison E Weirick, Sigrid Gouma, Christopher M McAllister, Shannon R Christensen, JoEllen Weaver, Phillip Hicks, Tomaz B Manzoni, Oluwatosin Oniyide, Holly Ramage, Divij Mathew, Amy E Baxter, Derek A Oldridge, Allison R Greenplate, Jennifer E Wu, Cécile Alanio, Kurt D'Andrea, Oliva Kuthuru, Jeanette Dougherty, Ajinkya Pattekar, Justin Kim, Nicholas Han, Sokratis A Apostolidis, Alex C Huang, Laura A Vella, E John Wherry, Nuala J Meyer, Sara Cherry, Paul Bates, Daniel J Rader, Scott E Hensley. Cell. Available online 9 February 2021. doi: https://doi.org/10.1016/j.cell.2021.02.010

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ALC1 links chromatin accessibility to PARP inhibitor response in homologous recombination-deficient cells

Priyanka Verma, Yeqiao Zhou, Zhendong Cao, Peter V Deraska, Moniher Deb, Eri Arai, Weihua Li, Yue Shao, Laura Puentes, Yiwen Li, Sonali Patankar, Robert H Mach, Robert B Faryabi, Junwei Shi, Roger A Greenberg. Nat Cell Biol. 2021 Jan 18. doi: 10.1038/s41556-020-00624-3. Online ahead of print.

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Inhibitory signaling sustains a distinct early memory CD8+ T cell precursor that is resistant to DNA damage

Jonathan B Johnnidis, Yuki Muroyama, Shin Foong Ngiow, Zeyu Chen, Sasikanth Manne, Zhangying Cai, Shufei Song, Jesse M Platt, Jason M Schenkel, Mohamed Abdel-Hakeem, Jean-Christophe Beltra, Allison R Greenplate, Mohammed-Alkhatim A Ali, Kito Nzingha, Josephine R Giles, Christelle Harly, John Attanasio, Kristen E Pauken, Bertram Bengsch, Michael A Paley, Vesselin T Tomov, Makoto Kurachi, Dario A A Vignali, Arlene H Sharpe, Steven L Reiner, Avinash Bhandoola, F Bradley Johnson, E John Wherry. Sci Immunol. 2021 Jan 15;6(55):eabe3702. doi: 10.1126/sciimmunol.abe3702.

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Real-world integration of genomic data into the electronic health record: the PennChart Genomics Initiative

Kelsey S Lau-Min, Stephanie Byers Asher, Jessica Chen, Susan M Domchek, Michael Feldman, Steven Joffe, Jeffrey Landgraf, Virginia Speare, Lisa A Varughese, Sony Tuteja, Christine VanZandbergen, Marylyn D Ritchie, Katherine L Nathanson. Genet Med. 2020 Dec 10. doi: 10.1038/s41436-020-01056-y. Online ahead of print.

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Autosomal dominant VCP hypomorph mutation impairs disaggregation of PHF-tau

Nabil F Darwich, Jessica M Phan, Boram Kim, EunRan Suh, John D Papatriantafyllou, Lakshmi Changolkar, Aivi T Nguyen, Caroline M O'Rourke, Zhuohao He, Sílvia Porta, Garrett S Gibbons, Kelvin C Luk, Sokratis G Papageorgiou, Murray Grossman, Lauren Massimo, David J Irwin, Corey T McMillan, Ilya M Nasrallah, Camilo Toro, Geoffrey K Aguirre, Vivianna M Van Deerlin, Edward B Lee. Science; 2020 Oct 1;eaay8826. doi: 10.1126/science.aay8826. Online ahead of print.

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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

Raffaella Nativio, Yemin Lan, Greg Donahue, Simone Sidoli, Amit Berson, Ananth R Srinivasan, Oksana Shcherbakova, Alexandre Amlie-Wolf, Ji Nie, Xiaolong Cui, Chuan He, Li-San Wang, Benjamin A Garcia, John Q Trojanowski, Nancy M Bonini, Shelley L Berger. Nat Genet. 2020 Oct;52(10):1024-1035. doi: 10.1038/s41588-020-0696-0. Epub 2020 Sep 28.

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Developing an interactive and illustrative laboratory management curriculum for cytopathology trainees

Marcos Lepe, Christopher Preciado, Sharon J Song, Zubair W Baloch. Diagn Cytopathol. 2020 Jul 22. doi: 10.1002/dc.24448. Online ahead of print.

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Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications

Mathew D, Giles JR, Baxter AE, Oldridge DA, Greenplate AR, Wu JE, Alanio C, Kuri-Cervantes L, Pampena MB, D'Andrea K, Manne S, Chen Z, Huang YJ, Reilly JP, Weisman AR, Ittner CAG, Kuthuru O, Dougherty J, Nzingha K, Han N, Kim J, Pattekar A, Goodwin EC, Anderson EM, Weirick ME, Gouma S, Arevalo CP, Bolton MJ, Chen F, Lacey SF, Ramage H, Cherry S, Hensley SE, Apostolidis SA, Huang AC, Vella LA; UPenn COVID Processing Unit, Betts MR, Meyer NJ, Wherry EJ. Science. 2020 Jul 15;eabc8511. doi: 10.1126/science.abc8511. Online ahead of print.
Penn Medicine news release

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Comprehensive mapping of immune perturbations associated with severe COVID-19

Leticia Kuri-Cervantes, M Betina Pampena, Wenzhao Meng, Aaron M Rosenfeld, Caroline A G Ittner, Ariel R Weisman, Roseline S Agyekum, Divij Mathew, Amy E Baxter, Laura A Vella, Oliva Kuthuru, Sokratis A Apostolidis, Luanne Bershaw, Jeanette Dougherty, Allison R Greenplate, Ajinkya Pattekar, Justin Kim, Nicholas Han, Sigrid Gouma, Madison E Weirick, Claudia P Arevalo, Marcus J Bolton, Eileen C Goodwin, Elizabeth M Anderson, Scott E Hensley, Tiffanie K Jones, Nilam S Mangalmurti, Eline T Luning Prak, E John Wherry, Nuala J Meyer, Michael R Betts. Sci Immunol. 2020 Jul 15;5(49):eabd7114. doi: 10.1126/sciimmunol.abd7114.
Penn Medicine news release

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Whole exome and transcriptome analysis of UV-exposed epidermis and carcinoma in situ reveals early drivers of carcinogenesis

Qi Zheng, Brian C Capell, Vishwas Parekh, Conor O'Day, Cem Atillasoy, Hasan M Bashir, Christopher Yeh, Eun-Hee Shim, Stephen M Prouty, Tzvete Dentchev, Vivian Lee, Lily Wushanley, Yerin Kweon, Yoko Suzuki-Horiuchi, Warren Pear, Elizabeth A Grice, John T Seykora. J Invest Dermatol. 2020 Jul 8;S0022-202X(20)31736-X. doi: 10.1016/j.jid.2020.05.116. Online ahead of print.
Read the Penn Medicine news release

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Cytokine release syndrome in severe COVID-19

Moore JB, June, CH. Cytokine release syndrome in severe COVID-19. Science. 2020 May 1; 368:473. doi: 10.1126/science.abb8925.

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c-Rel is a myeloid checkpoint for cancer immunotherapy

Li T, Li X, Zamani A, Wang W, Lee C, Li M, Luo G, Eiler E, Sun H, Ghosh S, Jin J, Murali R, Ruan Q, Shi W, Chen YH. Nat Cancer 1, 507–517(2020). doi: 10.1038/s43018-020-0061-3

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Developmental Relationships of Four Exhausted CD8 + T Cell Subsets Reveals Underlying Transcriptional and Epigenetic Landscape Control Mechanisms

Beltra JC, Manne S, Abdel-Hakeem MS, Kurachi M, Giles JR, Chen Z, Casella V, Ngiow SF, Khan O, Huang YJ, Yan P, Nzingha K, Xu W, Amaravadi RK, Xu X, Karakousis GC, Mitchell TC, Schuchter LM, Huang AC, Wherry EJ. Immunity. 2020 May 19;52(5):825-841.e8. doi: 10.1016/j.immuni.2020.04.014. Epub 2020 May 11.

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Trib1 regulates T cell differentiation during chronic infection by restraining the effector program

Rome KS, Stein SJ, Kurachi M, Petrovic J, Schwartz GW, Mack EA, Uljon S, Wu WW, DeHart AG, McClory SE, Xu L, Gimotty PA, Blacklow SC, Faryabi RB, Wherry EJ, Jordan MS, Pear WS. J Exp Med. 2020 May 4;217(5):e20190888. doi: 10.1084/jem.20190888.

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The Transcription Factor T-bet Resolves Memory B Cell Subsets with Distinct Tissue Distributions and Antibody Specificities in Mice and Humans

Johnson JL, Rosenthal RL, Knox JJ, Myles A, Naradikian MS, Madej J, Kostiv M, Rosenfeld AM, Meng W, Christensen SR, Hensley SE, Yewdell J, Canaday DH, Zhu J, McDermott AB, Dori Y, Itkin M, Wherry EJ, Pardi N, Weissman D, Naji A, Prak ETL, Betts MR, Cancro MP. Immunity. 2020 Apr 22. pii: S1074-7613(20)30133-3. doi: 10.1016/j.immuni.2020.03.020. [Epub ahead of print]

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Complement as a target in COVID-19?

Risitano, AM, Mastellos, DC, Huber-Lang M, Yancopoulou D,Garlanda C, Lambris JD. Nat. Rev. Immunol. 2020 Apr 23; doi: 10.1038/ s41577-020-0320-7.

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4-1BB costimulation promotes CAR T cell survival through noncanonical NF-κB signaling

Philipson BI, O'Connor RS, May MJ, June CH, Albelda SM, Milone MC. Sci Signal. 2020 Mar 31;13(625). pii: eaay8248. doi: 10.1126/scisignal.aay8248.

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Tumor-Derived Retinoic Acid Regulates Intratumoral Monocyte Differentiation to Promote Immune Suppression

Devalaraja S, To TKJ, Folkert IW, Natesan R, Alam MZ, Li M, Tada Y, Budagyan K, Dang MT, Zhai L, Lobel GP, Ciotti GE, Eisinger-Mathason TSK, Asangani IA, Weber K, Simon MC, Haldar M. Cell. 2020 Mar 19;180(6):1098-1114.e16. doi: 10.1016/j.cell.2020.02.042. Epub 2020 Mar 12.

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TooManyCells identifies and visualizes relationships of single-cell clades

Schwartz GW, Zhou Y, Petrovic J, Fasolino M, Xu L, Shaffer SM, Pear WS, Vahedi G, Faryabi RB. Nat Methods. 2020 Apr;17(4):405-413. doi: 10.1038/s41592-020-0748-5. Epub 2020 Mar 2.

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CRISPR-engineered T cells in patients with refractory cancer

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 I, 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. Science  06 Feb 2020. doi: 10.1126/science.aba7365

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Transmission of tauopathy strains is independent of their isoform composition

He Z, McBride JD, Xu H, Changolkar L, Kim SJ, Zhang B, Narasimhan S, Gibbons GS, Guo JL, Kozak M, Schellenberg GD, Trojanowski JQ, Lee VM. Nat Commun. 2020 Jan 7;11(1):7. doi: 10.1038/s41467-019-13787-x.

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Clinical utility of plasma cell-free DNA in adult patients with newly diagnosed glioblastoma - a pilot prospective study

Bagley S, Nabavizadeh SA, Mays J, Till JE, Ware J, Levy S, Sarchiapone W, Hussain J, Prior TJ, Guiry S, Christensen T, Yee SS, Nasrallah M, Morrissette JJD, Zev Binder Z, O'Rourke DM, Cucchiara AJ, Brem S, Arati S, Desai AS, EL Carpenter. Clin Cancer Res. Published online October 30, 2019. doi: 10.1158/1078-0432.CCR-19-2533

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Neoantigen Dissimilarity to the Self-Proteome Predicts Immunogenicity and Response to Immune Checkpoint Blockade

Richman LP, Vonderheide RH, Rech AJ. Cell Syst. 2019 Oct 8. pii: S2405-4712(19)30307-2. doi: 10.1016/j.cels.2019.08.009. [Epub ahead of print]

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Nucleoside-modified mRNA encoding HSV-2 glycoproteins C, D, and E prevents clinical and subclinical genital herpes

Awasthi S, Hook LM, Pardi N, Wang F, Myles A, Cancro MP, Cohen GH, Weissman D, Friedman HM. Sci Immunol. 2019 Sep 20;4(39). pii: eaaw7083. doi: 10.1126/sciimmunol.aaw7083.

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