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Hire Dr. Josephine G.

United States

USD 100 /hr

PhD in immunology from Yale University | Expert in T cell exhaustion, single cell genomics, CRISPR, R analysis

Profile Summary

I am currently a senior research investigator at the University of Pennsylvania. My overall research goal is to elucidate the epigenetic and transcriptional networks that control CD8 T cell differentiation. Specifically, my work focuses on CD8 T cell exhaustion in cancer and chronic infection. These studies combine mouse models of T cell differentiation and human immunology with next-generation sequencing, single cell genomics, high dimensional cytometry, CRISPR technologies, and computational analysis. I graduated from Mount Holyoke College summa cum laude in 2007, then earned a PhD from Yale University. My graduate work in the laboratory of Mark J. Shlomchik investigated T cell - B cell interaction in systemic autoimmune disease and resulted in a novel method for identifying and studying autoreactive T cells. In my postdoctoral position, I was awarded a Cancer Research Institute-Mark Foundation Fellow and published papers in Science, Immunity, Nature Immunology, Science Immunology, and others. I am available to consult at all stages for scientific projects: overall project conception and development, experimental design, assay development and optimization, analysis (flow cytometry, bulk and single cell genomics, R analysis), data visualization (R coding and Illustrator), manuscript writing/editing, and scientific presentations.

Subject Matter Expertise

• ★ Omics
• ★ Basic Immunology
• ★ Data Analysis
• ☆ Molecular Biology
• ☆ Transcriptomics
• ☆ Genomics
• ☆ Chromatin
• ☆ Epigenetics
• ☆ PCR
• ☆ Molecular Cloning
• ☆ Next Generation Sequencing (NGS)
• ☆ ATAC-Seq
• ☆ Gene Expression Analysis
• ☆ RNA Sequencing
• ☆ Cell Biology
• ☆ Data Processing
• ☆ Data Exploration
• ☆ Data Visualization
• ☆ Bioinformatics
• ☆ Gene & Protein Expression Analysis
• ☆ Systems Biology
• ☆ Cytometry
• ☆ R
• ☆ Clinical Immunology
• ☆ Cancer Research
• ☆ Presentation Design
• ☆ Technical & Scientific Writing
• ☆ Manuscript & Journal Article Writing
• ☆ Experimental Protocols
• ☆ SOP & Protocol Writing

Services

• Writing
• Research
• Consulting
• Data & AI

Writing Technical Writing

Research Scientific and Technical Research

Consulting Scientific and Technical Consulting

Data & AI Data Visualization, Data Processing

Work Experience

Trainee

University of Pennsylvania

- Present

Senior Research Investigator

University of Pennsylvania

December 2021 - Present

Education

PhD in Immunology

University of Pennsylvania

August 2007 - May 2015

Bachelors

Mount Holyoke College

August 2002 - May 2005

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Goel, R.R., Painter, M.M., Lundgreen, K.A., Apostolidis, S.A., Baxter, A.E., Giles, J.R., Mathew, D., Pattekar, A., Reynaldi, A., Khoury, D.S., et al.(2022). Efficient recall of Omicron-reactive B cell memory after a third dose of SARS-CoV-2 mRNA vaccine . Cell. 185. (11). p. 1875-1887.e8.

Bucktrout, S.L., Banovich, N.E., Butterfield, L.H., Cimen-Bozkus, C., Giles, J.R., Good, Z., Goodman, D., Jonsson, V.D., Lareau, C., Marson, A., et al.(2022). Advancing T cell-based cancer therapy with single-cell technologies . Nature medicine. 28. (9). p. 1761-1764.

Daniel, B., Yost, K.E., Hsiung, S., Sandor, K., Xia, Y., Qi, Y., Hiam-Galvez, K.J., Black, M., J. Raposo, C., Shi, Q., et al.(2022). Divergent clonal differentiation trajectories of T cell exhaustion . Nature Immunology. 23. (11). p. 1614-1627.

Merenstein, C., Liang, G., Whiteside, S.A., Cobián-Güemes, A.G., Merlino, M.S., Taylor, L.J., Glascock, A., Bittinger, K., Tanes, C., Graham-Wooten, J., et al.(2022). Erratum: Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome(mBio 12:4 (e01777-21) DOI: 10.1128/mBio.01777-21) . mBio. 13. (5).

Giles, J.R., Manne, S., Freilich, E., Oldridge, D.A., Baxter, A.E., George, S., Chen, Z., Huang, H., Chilukuri, L., Carberry, M., et al.(2022). Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers . Immunity. 55. (3). p. 557-574.e7.

Giles, J.R., Ngiow, S.F., Manne, S., Baxter, A.E., Khan, O., Wang, P., Staupe, R., Abdel-Hakeem, M.S., Huang, H., Mathew, D., et al.(2022). Shared and distinct biological circuits in effector, memory and exhausted CD8⁺ T cells revealed by temporal single-cell transcriptomics and epigenetics . Nature Immunology. 23. (11). p. 1600-1613.

Apostolidis, S.A., Sarkar, A., Giannini, H.M., Goel, R.R., Mathew, D., Suzuki, A., Baxter, A.E., Greenplate, A.R., Alanio, C., Abdel-Hakeem, M., et al.(2022). Signaling Through FcγRIIA and the C5a-C5aR Pathway Mediate Platelet Hyperactivation in COVID-19 . Frontiers in Immunology. 13.

Abdel-Hakeem, M.S., Manne, S., Beltra, J.-C., Stelekati, E., Chen, Z., Nzingha, K., Ali, M.-A., Johnson, J.L., Giles, J.R., Mathew, D., et al.(2021). Author Correction: Epigenetic scarring of exhausted T cells hinders memory differentiation upon eliminating chronic antigenic stimulation (Nature Immunology, (2021), 22, 8, (1008-1019), 10.1038/s41590-021-00975-5) . Nature Immunology. 22. (11). p. 1465.

Bange, E.M., Han, N.A., Wileyto, P., Kim, J.Y., Gouma, S., Robinson, J., Greenplate, A.R., Hwee, M.A., Porterfield, F., Owoyemi, O., et al.(2021). CD8⁺ T cells contribute to survival in patients with COVID-19 and hematologic cancer . Nature Medicine. 27. (7). p. 1280-1289.

Vella, L.A., Giles, J.R., Baxter, A.E., Oldridge, D.A., Diorio, C., Kuri-Cervantes, L., Alanio, C., Pampena, M.B., Wu, J.E., Chen, Z., et al.(2021). Deep immune profiling of MIS-C demonstrates marked but transient immune activation compared to adult and pediatric COVID-19 . Science Immunology. 6. (57).

Goel, R.R., Apostolidis, S.A., Painter, M.M., Mathew, D., Pattekar, A., Kuthuru, O., Gouma, S., Hicks, P., Meng, W., Rosenfeld, A.M., et al.(2021). Distinct antibody and memory B cell responses in SARSCoV-2 naïve and recovered individuals following mRNA vaccination . Science Immunology. 6. (58). p. 1-19.

Abdel-Hakeem, M.S., Manne, S., Beltra, J.-C., Stelekati, E., Chen, Z., Nzingha, K., Ali, M.-A., Johnson, J.L., Giles, J.R., Mathew, D., et al.(2021). Epigenetic scarring of exhausted T cells hinders memory differentiation upon eliminating chronic antigenic stimulation . Nature Immunology. 22. (8). p. 1008-1019.

Chen, Z., Arai, E., Khan, O., Zhang, Z., Ngiow, S.F., He, Y., Huang, H., Manne, S., Cao, Z., Baxter, A.E., et al.(2021). In vivo CD8⁺ T cell CRISPR screening reveals control by Fli1 in infection and cancer . Cell. 184. (5). p. 1262-1280.e22.

Johnnidis, J.B., Muroyama, Y., Ngiow, S.F., Chen, Z., Manne, S., Cai, Z., Song, S., Platt, J.M., Schenkel, J.M., Abdel-Hakeem, M., et al.(2021). Inhibitory signaling sustains a distinct early memory CD8⁺ T cell precursor that is resistant to DNA damage . Science Immunology. 6. (55).

Diorio, C., Shraim, R., Vella, L.A., Giles, J.R., Baxter, A.E., Oldridge, D.A., Canna, S.W., Henrickson, S.E., McNerney, K.O., Balamuth, F., et al.(2021). Proteomic profiling of MIS-C patients indicates heterogeneity relating to interferon gamma dysregulation and vascular endothelial dysfunction . Nature Communications. 12. (1).

Painter, M.M., Mathew, D., Goel, R.R., Apostolidis, S.A., Pattekar, A., Kuthuru, O., Baxter, A.E., Herati, R.S., Oldridge, D.A., Gouma, S., et al.(2021). Rapid induction of antigen-specific CD4⁺ T cells is associated with coordinated humoral and cellular immunity to SARS-CoV-2 mRNA vaccination . Immunity. 54. (9). p. 2133-2142.e3.

Merenstein, C., Liang, G., Whiteside, S.A., Cobián-Güemes, A.G., Merlino, M.S., Taylor, L.J., Glascock, A., Bittinger, K., Tanes, C., Graham-Wooten, J., et al.(2021). Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome . mBio. 12. (4).

Goel, R.R., Painter, M.M., Apostolidis, S.A., Mathew, D., Meng, W., Rosenfeld, A.M., Lundgreen, K.A., Reynaldi, A., Khoury, D.S., Pattekar, A., et al.(2021). mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern . Science. 374. (6572).

Mathew, D., Giles, J.R., Baxter, A.E., Oldridge, D.A., Greenplate, A.R., Wu, J.E., Alanio, C., Kuri-Cervantes, H., Pampena, M.B., D'Andrea, K., et al.(2020). Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications . Science. 369. (6508).

Beltra, J.-C., Manne, S., Abdel-Hakeem, M.S., Kurachi, M., Giles, J.R., Chen, Z., Casella, V., Ngiow, S.F., Khan, O., Huang, Y.J., et al.(2020). Developmental Relationships of Four Exhausted CD8⁺ T Cell Subsets Reveals Underlying Transcriptional and Epigenetic Landscape Control Mechanisms . Immunity. 52. (5). p. 825-841.e8.

Vella, L.A., Buggert, M., Manne, S., Herati, R.S., Sayin, I., Kuri-Cervantes, L., Brody, I.B., O’Boyle, K.C., Kaprielian, H., Giles, J.R., et al.(2019). T follicular helper cells in human efferent lymph retain lymphoid characteristics . Journal of Clinical Investigation. 129. (8). p. 3185-3200.

Chen, Z., Ji, Z., Ngiow, S.F., Manne, S., Cai, Z., Huang, A.C., Johnson, J., Staupe, R.P., Bengsch, B., Xu, C., et al.(2019). TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision . Immunity. 51. (5). p. 840-855.e5.

Khan, O., Giles, J.R., McDonald, S., Manne, S., Ngiow, S.F., Patel, K.P., Werner, M.T., Huang, A.C., Alexander, K.A., Wu, J.E., et al.(2019). TOX transcriptionally and epigenetically programs CD8⁺ T cell exhaustion . Nature. 571. (7764). p. 211-218.

Giles, J.R., Neves, A.T., Marshak-Rothstein, A., Shlomchik, M.J.(2017). Autoreactive helper T cells alleviate the need for intrinsic TLR signaling in autoreactive B cell activation . JCI Insight. 2. (4).

Huang, A.C., Postow, M.A., Orlowski, R.J., Mick, R., Bengsch, B., Manne, S., Xu, W., Harmon, S., Giles, J.R., Wenz, B., et al.(2017). T-cell invigoration to tumour burden ratio associated with anti-PD-1 response . Nature. 545. (7652). p. 60-65.

Ols, M.L., Cullen, J.L., Turqueti-Neves, A., Giles, J., Shlomchik, M.J.(2016). Dendritic Cells Regulate Extrafollicular Autoreactive B Cells via T Cells Expressing Fas and Fas Ligand . Immunity. 45. (5). p. 1052-1065.

Giles, J.R., Kashgarian, M., Koni, P.A., Shlomchik, M.J.(2015). B cell-specific MHC class II deletion reveals multiple nonredundant roles for B cell antigen presentation in murine lupus . Journal of Immunology. 195. (6). p. 2571-2579.

OTHER

Goel, R.R., Painter, M.M., Lundgreen, K.A., Apostolidis, S.A., Baxter, A.E., Giles, J.R., Mathew, D., Pattekar, A., Reynaldi, A., Khoury, D.S., et al.(2022). Efficient recall of Omicron-reactive B cell memory after a third dose of SARS-CoV-2 mRNA vaccine . bioRxiv.

Gustafson, C.E., Thomson, Z., He, Z., Swanson, E., Henderson, K., Pebworth, M.-P., Okada, L.Y., Heubeck, A.T., Roll, C.R., Hernandez, V., et al.(2022). Distinct Heterogeneity in the Naive T cell Compartments of Children and Adults . bioRxiv.

Beltra, J.-C., Abdel-Hakeem, M.S., Manne, S., Zhang, Z., Huang, H., Kurachi, M., Su, L., Picton, L., Muroyama, Y., Casella, V., et al.(2022). Enhanced STAT5a activation rewires exhausted CD8 T cells during chronic stimulation to acquire a hybrid durable effector like state . bioRxiv.

Giles, J.R., Ngiow, S.F., Manne, S., Baxter, A.E., Khan, O., Wang, P., Staupe, R., Abdel-Hakeem, M.S., Huang, H., Mathew, D., et al.(2022). Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates . bioRxiv.

Daniel, B., Yost, K.E., Sandor, K., Xia, Y., Qi, Y., Hiam-Galvez, K.J., Meier, S.L., Belk, J.A., Giles, J.R., Wherry, E.J., et al.(2021). Divergent clonal differentiation trajectories of T cell exhaustion . bioRxiv.

Diorio, C., Shraim, R., Vella, L.A., Giles, J.R., Baxter, A.E., Oldridge, D.A., Canna, S.W., Henrickson, S.E., McNerney, K.O., Balamuth, F., et al.(2021). Proteomic profiling of MIS-C patients reveals heterogeneity relating to interferon gamma dysregulation and vascular endothelial dysfunction . medRxiv.

Apostolidis, S.A., Sarkar, A., Giannini, H.M., Goel, R.R., Mathew, D., Suzuki, A., Baxter, A.E., Greenplate, A.R., Alanio, C., Abdel-Hakeem, M., et al.(2021). Signaling through FcgRIIA and the C5a-C5aR pathway mediates platelet hyperactivation in COVID-19 . bioRxiv.

Merenstein, C., Liang, G., Whiteside, S.A., Cobián-Güemes, A.G., Merlino, M.S., Taylor, L.J., Glascock, A., Bittinger, K., Tanes, C., Graham-Wooten, J., et al.(2021). Signatures of COVID-19 severity and immune response in the respiratory tract microbiome . medRxiv.

Goel, R.R., Apostolidis, S.A., Painter, M.M., Mathew, D., Pattekar, A., Kuthuru, O., Gouma, S., Kuri-Cervantes, L., Meng, W., Adamski, S., et al.(2021). Longitudinal analysis reveals distinct antibody and memory B cell responses in SARS-CoV2 Naïve and recovered individuals following mRNA vaccination . medRxiv.

Goel, R.R., Painter, M.M., Apostolidis, S.A., Mathew, D., Meng, W., Rosenfeld, A.M., Lundgreen, K.A., Reynaldi, A., Khoury, D.S., Pattekar, A., et al.(2021). mRNA vaccination induces durable immune memory to SARS-CoV-2 with continued evolution to variants of concern . bioRxiv.

Vella, L.A., Giles, J.R., Baxter, A.E., Oldridge, D.A., Diorio, C., Kuri-Cervantes, L., Alanio, C., Pampena, M.B., Wu, J.E., Chen, Z., et al.(2020). Deep Immune Profiling of MIS-C demonstrates marked but transient immune activation compared to adult and pediatric COVID-19 . medRxiv.

Mathew, D., Giles, J.R., Baxter, A.E., Greenplate, A.R., Wu, J.E., Alanio, C., Oldridge, D.A., Kuri-Cervantes, L., Pampena, M.B., D’Andrea, K., et al.(2020). Deep immune profiling of COVID-19 patients reveals patient heterogeneity and distinct immunotypes with implications for therapeutic interventions . bioRxiv.

Chen, Z., Arai, E., Khan, O., Zhang, Z., Ngiow, S.F., He, Y., Huang, H., Manne, S., Cao, Z., Baxter, A.E., et al.(2020). In vivo CRISPR screening identifies Fli1 as a transcriptional safeguard that restrains effector CD8 T cell differentiation during infection and cancer . bioRxiv.

Chen, Z., Arai, E., Khan, O., Zhang, Z., Ngiow, S.F., He, Y., Huang, H., Manne, S., Cao, Z., Baxter, A.E., et al.(2020). In vivo CRISPR Screening Identifies Fli1 as a Transcriptional Safeguard that Restrains Effector CD8 T Cell Differentiation during Infection and Cancer . SSRN.

Staupe, R.P., Vella, L.A., Manne, S., Giles, J.R., Meng, W., Herati, R.S., Khan, O., Wu, J.E., Baxter, A.E., Luning Prak, E.T., et al.(2019). Chronic viral infection promotes early germinal center exit of B cells and impaired antibody development . bioRxiv.