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Amy E Baxter, D.Phil
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Research Assistant Professor of Systems Pharmacology and Translational Therapeutics
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Director of Research and Development, Immune Health
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Department: Systems Pharmacology and Translational Therapeutics
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Contact information
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3600 Civic Center Blvd.
Philadelphia, PA 19104
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Philadelphia, PA 19104
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Publications
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Education:
21 7 BA 31 (Natural Sciences Tripos Biochemistry) c
30 University of Cambridge, 2009.
21 a M.Sci 31 (Natural Sciences Tripos Biochemistry) c
30 University of Cambridge, 2009.
21 b D.Phil 3d (Infection, Immunology and Translational Medicine) c
2d University of Oxford, 2013.
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21 7 BA 31 (Natural Sciences Tripos Biochemistry) c
30 University of Cambridge, 2009.
21 a M.Sci 31 (Natural Sciences Tripos Biochemistry) c
30 University of Cambridge, 2009.
21 b D.Phil 3d (Infection, Immunology and Translational Medicine) c
2d University of Oxford, 2013.
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Links
b4 Search PubMed for articles
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Permanent linkb4 Search PubMed for articles
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14d In my laboratory and as part of the Immune Health group, one major focus is to identify and characterize immune diversity in large populations to understand 1) how and why an individual’s immune health changes over time and 2) how immune health impacts responses to cancer, infection, autoimmune conditions and therapeutics.
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Description of Research Expertise
142 I am an internationally trained scientist, with expertise in immune oncology, immunology, and virology. The overarching goal of my work has been to define how the immune system responds to persistent threats, from chronic viral infections to tumor cells, by taking advantage of cutting-edge technologies.8
14d In my laboratory and as part of the Immune Health group, one major focus is to identify and characterize immune diversity in large populations to understand 1) how and why an individual’s immune health changes over time and 2) how immune health impacts responses to cancer, infection, autoimmune conditions and therapeutics.
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29e Painter MM, Johnston TS, Lundgreen KA, Santos JJS, Qin JS, Goel RR, Apostolidis SA, Mathew D, Fulmer B, Williams JC, McKeague ML, Pattekar A, Goode A, Nasta S, Baxter AE, Giles JR, Skelly AN, Felley LE, McLaughlin M, Weaver J; Penn Medicine BioBank; Kuthuru O, Dougherty J, Adamski S, Long S, Kee M, Clendenin C, da Silva Antunes R, Grifoni A, Weiskopf D, Sette A, Huang AC, Rader DJ, Hensley SE, Bates P, Greenplate AR, Wherry EJ.: Prior vaccination promotes early activation of memory T cells and enhances immune responses during SARS-CoV-2 breakthrough infection. Nat Immunol 24(10), Sept 2023.
162 Wu JE, Manne S, Ngiow SF, Baxter AE, Huang H, Freilich E, Clark ML, Lee JH, Chen Z, Khan O, Staupe RP, Huang YJ, Shi J, Giles JR, Wherry EJ.: In vitro modeling of CD8(+) T cell exhaustion enables CRISPR screening to reveal a role for BHLHE40. Sci Immunol 8(86): eade3369, Aug 2023.
1bb Baxter AE, Huang H, Giles JR, Chen Z, Wu JE, Drury S, Dalton K, Park SL, Torres L, Simone BW, Klapholz M, Ngiow SF, Freilich E, Manne S, Alcalde V, Ekshyyan V, Berger SL, Shi J, Jordan MS, Wherry EJ.: The SWI/SNF chromatin remodeling complexes BAF and PBAF differentially regulate epigenetic transitions in exhausted CD8(+) T cells. Immunity 56(6): 1320-1340, Jun 2023.
1d8 Giles JR, Ngiow SF, Manne S, Baxter AE, Khan O, Wang P, Staupe R, Abdel-Hakeem MS, Huang H, Mathew D, Painter MM, Wu JE, Huang YJ, Goel RR, Yan PK, Karakousis GC, Xu X, Mitchell TC, Huang AC, Wherry EJ.: Shared and distinct biological circuits in effector, memory and exhausted CD8(+) T cells revealed by temporal single-cell transcriptomics and epigenetics. Nat Immunol 23(11): 1600-1613, Nov 2022.
1d0 Giles JR, Manne S, Freilich E, Oldridge DA, Baxter AE, George S, Chen Z, Huang H, Chilukuri L, Carberry M, Giles L, Weng NP, Young RM, June CH, Schuchter LM, Amaravadi RK, Xu X, Karakousis GC, Mitchell TC, Huang AC, Shi J, Wherry EJ.: Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers. Immunity 55(3): 557-574, Mar 2022.
2bf Vella LA, Giles JR, Baxter AE, Oldridge DA, Diorio C, Kuri-Cervantes L, Alanio C, Pampena MB, Wu JE, Chen Z, Huang YJ, Anderson EM, Gouma S, McNerney KO, Chase J, Burudpakdee C, Lee JH, Apostolidis SA, Huang AC, Mathew D, Kuthuru O, Goodwin EC, Weirick ME, Bolton MJ, Arevalo CP, Ramos A, Jasen CJ, Conrey PE, Sayed S, Giannini HM, D'Andrea K; UPenn COVID Processing Unit; Meyer NJ, Behrens EM, Bassiri H, Hensley SE, Henrickson SE, Teachey DT, Betts MR, Wherry EJ.: Deep immune profiling of MIS-C demonstrates marked but transient immune activation compared to adult and pediatric COVID-19. Sci Immunol 6(57): eabf7570, Mar 2021.
29f 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.: Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications. Science 369(6508): eabc8511, Sep 2020.
16b Niessl J, Baxter AE, Mendoza P, Jankovic M, Cohen YZ, Butler AL, Lu CL, Dubé M, Shimeliovich I, Gruell H, Klein F, Caskey M, Nussenzweig MC, Kaufmann DE.: Combination anti-HIV-1 antibody therapy is associated with increased virus-specific T cell immunity. Nat Med 26(2): 222-227, Feb 2020.
188 Baxter AE, Niessl J, Fromentin R, Richard J, Porichis F, Charlebois R, Massanella M, Brassard N, Alsahafi N, Delgado GG, Routy JP, Walker BD, Finzi A, Chomont N, Kaufmann DE.: Single-Cell Characterization of Viral Translation-Competent Reservoirs in HIV-Infected Individuals. Cell Host Microbe 20(3): 368-380, Sep 2016.
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Selected Publications
115 Huang YJ, Ngiow SF, Baxter AE, Manne S, Park SL, Wu JE, Khan O, Giles JR, Wherry EJ.: Continuous expression of TOX safeguards exhausted CD8 T cell epigenetic fate. Sci Immunol 10(105): eado3032, Mar 2025.29e Painter MM, Johnston TS, Lundgreen KA, Santos JJS, Qin JS, Goel RR, Apostolidis SA, Mathew D, Fulmer B, Williams JC, McKeague ML, Pattekar A, Goode A, Nasta S, Baxter AE, Giles JR, Skelly AN, Felley LE, McLaughlin M, Weaver J; Penn Medicine BioBank; Kuthuru O, Dougherty J, Adamski S, Long S, Kee M, Clendenin C, da Silva Antunes R, Grifoni A, Weiskopf D, Sette A, Huang AC, Rader DJ, Hensley SE, Bates P, Greenplate AR, Wherry EJ.: Prior vaccination promotes early activation of memory T cells and enhances immune responses during SARS-CoV-2 breakthrough infection. Nat Immunol 24(10), Sept 2023.
162 Wu JE, Manne S, Ngiow SF, Baxter AE, Huang H, Freilich E, Clark ML, Lee JH, Chen Z, Khan O, Staupe RP, Huang YJ, Shi J, Giles JR, Wherry EJ.: In vitro modeling of CD8(+) T cell exhaustion enables CRISPR screening to reveal a role for BHLHE40. Sci Immunol 8(86): eade3369, Aug 2023.
1bb Baxter AE, Huang H, Giles JR, Chen Z, Wu JE, Drury S, Dalton K, Park SL, Torres L, Simone BW, Klapholz M, Ngiow SF, Freilich E, Manne S, Alcalde V, Ekshyyan V, Berger SL, Shi J, Jordan MS, Wherry EJ.: The SWI/SNF chromatin remodeling complexes BAF and PBAF differentially regulate epigenetic transitions in exhausted CD8(+) T cells. Immunity 56(6): 1320-1340, Jun 2023.
1d8 Giles JR, Ngiow SF, Manne S, Baxter AE, Khan O, Wang P, Staupe R, Abdel-Hakeem MS, Huang H, Mathew D, Painter MM, Wu JE, Huang YJ, Goel RR, Yan PK, Karakousis GC, Xu X, Mitchell TC, Huang AC, Wherry EJ.: Shared and distinct biological circuits in effector, memory and exhausted CD8(+) T cells revealed by temporal single-cell transcriptomics and epigenetics. Nat Immunol 23(11): 1600-1613, Nov 2022.
1d0 Giles JR, Manne S, Freilich E, Oldridge DA, Baxter AE, George S, Chen Z, Huang H, Chilukuri L, Carberry M, Giles L, Weng NP, Young RM, June CH, Schuchter LM, Amaravadi RK, Xu X, Karakousis GC, Mitchell TC, Huang AC, Shi J, Wherry EJ.: Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers. Immunity 55(3): 557-574, Mar 2022.
2bf Vella LA, Giles JR, Baxter AE, Oldridge DA, Diorio C, Kuri-Cervantes L, Alanio C, Pampena MB, Wu JE, Chen Z, Huang YJ, Anderson EM, Gouma S, McNerney KO, Chase J, Burudpakdee C, Lee JH, Apostolidis SA, Huang AC, Mathew D, Kuthuru O, Goodwin EC, Weirick ME, Bolton MJ, Arevalo CP, Ramos A, Jasen CJ, Conrey PE, Sayed S, Giannini HM, D'Andrea K; UPenn COVID Processing Unit; Meyer NJ, Behrens EM, Bassiri H, Hensley SE, Henrickson SE, Teachey DT, Betts MR, Wherry EJ.: Deep immune profiling of MIS-C demonstrates marked but transient immune activation compared to adult and pediatric COVID-19. Sci Immunol 6(57): eabf7570, Mar 2021.
29f 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.: Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications. Science 369(6508): eabc8511, Sep 2020.
16b Niessl J, Baxter AE, Mendoza P, Jankovic M, Cohen YZ, Butler AL, Lu CL, Dubé M, Shimeliovich I, Gruell H, Klein F, Caskey M, Nussenzweig MC, Kaufmann DE.: Combination anti-HIV-1 antibody therapy is associated with increased virus-specific T cell immunity. Nat Med 26(2): 222-227, Feb 2020.
188 Baxter AE, Niessl J, Fromentin R, Richard J, Porichis F, Charlebois R, Massanella M, Brassard N, Alsahafi N, Delgado GG, Routy JP, Walker BD, Finzi A, Chomont N, Kaufmann DE.: Single-Cell Characterization of Viral Translation-Competent Reservoirs in HIV-Infected Individuals. Cell Host Microbe 20(3): 368-380, Sep 2016.
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