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.


Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease

Liu H, Doke T, Guo D, Sheng X, Ma Z, Park J, Vy HMT, Nadkarni GN, Abedini A, Miao Z, Palmer M, Voight BF, Li H, Brown CD, Ritchie MD, Shu Y, Susztak K. Nat Genet. 2022 Jun 16. doi: 10.1038/s41588-022-01097-w. Online ahead of print.

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Implicating effector genes at COVID-19 GWAS loci using promoter-focused Capture-C in disease-relevant immune cell types

Pahl MC, Le Coz C, Su C, Sharma P, Thomas RM, Pippin JA, Cruz Cabrera E, Johnson ME, Leonard ME, Lu S, Chesi A, Sullivan KE, Romberg N, Grant SFA, Wells AD. Genome Biol. 2022 Jun 3;23(1):125. doi: 10.1186/s13059-022-02691-1.

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Spatiotemporal multiplexed immunofluorescence imaging of living cells and tissues with bioorthogonal cycling of fluorescent probes

Ko J, Wilkovitsch M, Oh J, Kohler RH, Bolli E, Pittet MJ, Vinegoni C, Sykes DB, Mikula H, Weissleder R, Carlson JCT. Nat Biotechnol. 2022 Jun 2. doi: 10.1038/s41587-022-01339-6. Online ahead of print.

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Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1

Rodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJ, Marrero Rolon R, Westblade LF, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann AC, Parikh BA, McMillen T, Jani K, Babady NE, Hahn AM, Koch RT, Grubaugh ND; Yale SARS-CoV-2 Genomic Surveillance Initiative, Rhoads DD. J Clin Microbiol. 2022 May 18:e0060022. doi: 10.1128/jcm.00600-22. Online ahead of print. PMID: 35582905

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PSMA-targeting TGFβ-insensitive armored CAR T cells in metastatic castration-resistant prostate cancer: a phase 1 trial

Narayan V, Barber-Rotenberg JS, Jung IY, Lacey SF, Rech AJ, Davis MM, Hwang WT, Lal P, Carpenter EL, Maude SL, Plesa G, Vapiwala N, Chew A, Moniak M, Sebro RA, Farwell MD, Marshall A, Gilmore J, Lledo L, Dengel K, Church SE, Hether TD, Xu J, Gohil M, Buckingham TH, Yee SS, Gonzalez VE, Kulikovskaya I, Chen F, Tian L, Tien K, Gladney W, Nobles CL, Raymond HE; Prostate Cancer Cellular Therapy Program Investigators, Hexner EO, Siegel DL, Bushman FD, June CH, Fraietta JA, Haas NB. Nat Med. 2022 Mar 21. doi: 10.1038/s41591-022-01726-1. Online ahead of print.

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No increase in inflammation in late-life major depression screened to exclude physical illness

Luning Prak ET, Brooks T, Makhoul W, Beer JC, Zhao L, Girelli T, Skarke C, Sheline YI. Transl Psychiatry. 2022 Mar 24;12(1):118. doi: 10.1038/s41398-022-01883-4.

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Potent suppression of neuroendocrine tumors and gastrointestinal cancers by CDH17CAR T cells without toxicity to normal tissues

Feng Z, He X, Zhang X, Wu Y, Xing B, Knowles A, Shan Q, Miller S, Hojnacki T, Ma J, Katona BW, Gade TPF, Schrader J, Metz DC, June CH, Hua X. Nat Cancer. 2022 Mar 21. doi: 10.1038/s43018-022-00344-7. Online ahead of print.

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Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes

Fasolino M, Schwartz GW, Patil AR, Mongia A, Golson ML, Wang YJ, Morgan A, Liu C, Schug J, Liu J, Wu M, Traum D, Kondo A, May CL, Goldman N, Wang W, Feldman M, Moore JH, Japp AS, Betts MR, Faryabi RB, Naji A, Kaestner KH, Vahedi G. Nat Metab; 4, 284–299. Published online: 28 February 2022. doi: 10.1038/s42255-022-00531-x

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Rapid manufacturing of non-activated potent CAR T cells

Ghassemi S, Durgin JS, Nunez-Cruz S, Patel J, Leferovich J, Pinzone M, Shen F, Cummins KD, Plesa G, Cantu VA, Reddy S, Bushman FD, Gill SI, O'Doherty U, O'Connor RS, Milone MC. Nat Biomed Eng. 2022 Feb;6(2):118-128. doi: 10.1038/s41551-021-00842-6. Epub 2022 Feb 21.

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EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells

Zhou Y, Petrovic J, Zhao J, Zhang W, Bigdeli A, Zhang Z, Berger SL, Pear WS, Faryabi RB. Mol Cell. Available online 18 February 2022. doi: 10.1016/j.molcel.2022.01.015

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Subcellular Detection of SARS-CoV-2 RNA in Human Tissue Reveals Distinct Localization in Alveolar Type 2 Pneumocytes and Alveolar Macrophages

Acheampong KK, Schaff DL, Emert BL, Lake J, Reffsin S, Shea EK, Comar CE, Litzky LA, Khurram NA, Linn RL, Feldman M, Weiss SR, Montone KT, Cherry S, Shaffer SM.
mBio. 2022 Feb 8:e0375121. doi: 10.1128/mbio.03751-21. Online ahead of print.

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Pyrimidine inhibitors synergize with nucleoside analogues to block SARS-CoV-2

Schultz DC, Johnson RM, Ayyanathan K, Miller J, Whig K, Kamalia B, Dittmar M, Weston S, Hammond HL, Dillen C, Ardanuy J, Taylor L, Lee JS, Li M, Lee E, Shoffler C, Petucci C, Constant S, Ferrer M, Thaiss CA, Frieman MB, Cherry S. Nature. 2022 Feb 7. doi: 10.1038/s41586-022-04482-x. Online ahead of print.

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Decade-long leukaemia remissions with persistence of CD4+ CAR T cells

Melenhorst JJ, Chen GM, Wang M, Porter DL, Chen C, Collins MA, Gao P, Bandyopadhyay S, Sun H, Zhao Z, Lundh S, Pruteanu-Malinici I, Nobles CL, Maji S, Frey NV, Gill SI, Tian L, Kulikovskaya I, Gupta M, Ambrose DE, Davis MM, Fraietta JA, Brogdon JL, Young RM, Chew A, Levine BL, Siegel DL, Alanio C, Wherry EJ, Bushman FD, Lacey SF, Tan K, June CH. Nature. Published: 02 February 2022. doi: 10.1038/s41586-021-04390-6

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Germinal center responses to SARS-CoV-2 mRNA vaccines in healthy and immunocompromised individuals

Lederer K, Bettini E, Parvathaneni K, Painter MM, Agarwal D, Lundgreen KA, Weirick M, Muralidharan K, Castaño D, Goel RR, Xu X, Drapeau EM, Gouma S, Ort JT, Awofolaju M, Greenplate AR, Le Coz C, Romberg N, Trofe-Clark J, Malat G, Jones L, Rosen M, Weiskopf D, Sette A, Besharatian B, Kaminiski M, Hensley SE, Bates P, Wherry EJ, Naji A, Bhoj V, Locci M. Cell. Published: February 01, 2022. doi: 10.1016/j.cell.2022.01.027

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SARS-CoV-2 Spike-Specific T-Cell Responses in Patients With B-Cell Depletion Who Received Chimeric Antigen Receptor T-Cell Treatments

Parvathaneni K, Torres-Rodriguez K, Meng W, Hwang WT, Frey N, Naji A, Bhoj VG. JAMA Oncol. 2022 Jan 1;8(1):164-167.  doi: 10.1001/jamaoncol.2021.6030.

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A human orthogonal IL-2 and IL-2Rβ system enhances CAR T cell expansion and antitumor activity in a murine model of leukemia

Zhang Q, Hresko ME, Picton LK, Su L, Hollander MJ, Nunez-Cruz S, Zhang Z, Assenmacher CA, Sockolosky JT, Garcia KC, Milone MC. Sci Transl Med. 2021 Dec 22;13(625):eabg6986. doi: 10.1126/scitranslmed.abg6986. Epub 2021 Dec 22.

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Lipid nanoparticles enhance the efficacy of mRNA and protein subunit vaccines by inducing robust T follicular helper cell and humoral responses

Alameh MG, Tombácz I, Bettini E, Lederer K, Sittplangkoon C, Wilmore JR, Gaudette BT, Soliman OY, Pine M, Hicks P, Manzoni TB, Knox JJ, Johnson JL, Laczkó D, Muramatsu H, Davis B, Meng W, Rosenfeld AM, Strohmeier S, Lin PJC, Mui BL, Tam YK, Karikó K, Jacquet A, Krammer F, Bates P, Cancro MP, Weissman D, Luning Prak ET, Allman D, Locci M, Pardi N. Immunity. 2021 Dec 14;54(12):2877-2892.e7. doi: 10.1016/j.immuni.2021.11.001. Epub 2021 Nov 4.

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Development of a fully canine anti-canine CTLA4 monoclonal antibody for comparative translational research in dogs with spontaneous tumors

Mason NJ, Chester N, Xiong A, Rotolo A, Wu Y, Yoshimoto S, Glassman P, Gulendran G, Siegel DL. mAbs. 2021 Jan-Dec;13(1):2004638. doi: 10.1080/19420862.2021.2004638.

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Trivalent nucleoside-modified mRNA vaccine yields durable memory B cell protection against genital herpes in preclinical models

Awasthi S, Knox JJ, Desmond A, Alameh MG, Gaudette BT, Lubinski JM, Naughton A, Hook LM, Egan KP, Tam YK, Pardi N, Allman D, Luning Prak ET, Cancro MP, Weissman D, Cohen GH, Friedman HM. J Clin Invest. 2021 Dec 1;131(23):e152310. doi: 10.1172/JCI152310. J Clin Invest. 2021 Dec 1;131(23):e152310. doi: 10.1172/JCI152310.

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A randomized controlled study of convalescent plasma for individuals hospitalized with COVID-19 pneumonia

Bar KJ, Shaw PA, Choi GH, Aqui N, Fesnak A, Yang JB, Soto-Calderon H, Grajales L, Starr J, Andronov M, Mastellone M, Amonu C, Feret G, DeMarshall M, Buchanan M, Caturla M, Gordon J, Wanicur A, Monroy MA, Mampe F, Lindemuth E, Gouma S, Mullin AM, Barilla H, Pronina A, Irwin L, Thomas R, Eichinger RA, Demuth F, Luning Prak ET, Pascual JL, Short WR, Elovitz MA, Baron J, Meyer NJ, Degnan KO, Frank I, Hensley SE, Siegel DL, Tebas P. J Clin Invest. 2021 Nov 17;e155114. doi: 10.1172/JCI155114. Online ahead of print.

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mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern

Goel RR, Painter MM, Apostolidis SA, Mathew D, Meng W, Rosenfeld AM, Lundgreen KA, Reynaldi A, Khoury DS, Pattekar A, Gouma S, Kuri-Cervantes L, Hicks P, Dysinger S, Hicks A, Sharma H, Herring S, Korte S, Baxter AE, Oldridge DA, Giles JR, Weirick ME, McAllister CM, Awofolaju M, Tanenbaum N, Drapeau EM, Dougherty J, Long S, D'Andrea K, Hamilton JT, McLaughlin M, Williams JC, Adamski S, Kuthuru O; UPenn COVID Processing Unit, Frank I, Betts MR, Vella LA, Grifoni A, Weiskopf D, Sette A, Hensley SE, Davenport MP, Bates P, Luning Prak ET, Greenplate AR, Wherry EJ. Science. 2021 Dec 3;374(6572):abm0829. doi: 10.1126/science.abm0829. Epub 2021 Dec 3.

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Practical Scientific Writing and Publishing in Anatomic Pathology

Levon Katsakhyan, Alec M Jacobson, Anna Budina, Zubair W Baloch. Am J Clin Pathol. 2021 Oct 1;aqab144. doi: 10.1093/ajcp/aqab144. Online ahead of print.

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Resting innate-like B cells leverage sustained Notch2/mTORC1 signaling to achieve rapid and mitosis-independent plasma cell differentiation

Gaudette BT, Roman CJ, Ochoa TA, Gómez Atria D, Jones DD, Siebel CW, Maillard I, Allman D. J Clin Invest. 2021;131(20):e151975. doi: 10.1172/JCI151975

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