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Shannon Patrick Hilchey, Ph.D.

Shannon Patrick Hilchey, Ph.D.


About Me

Faculty Appointments

Research Associate Professor - Department of Medicine, Nephrology (SMD)



PhD | SUNY Coll at Buffalo. Biological Science. 1997

BS | SUNY Coll at Buffalo. Biological Science. 1992


Porter Anderson Immunobiology Fellow. 2003

Recipient of a 2002 Wyeth Above and Beyond Award for Research Excellence 2002

Nominated for the 2002 Wyeth Eagles Leadership Development Program 2002

NIH Postdoctoral Fellowship Recipient, 2000 2000

NYS Breast Cancer Research and Educational Postdoctoral Fellowship Recipient, 1998 1998


My research for the last 17 years has been in the immunobiology of regulatory T cells, T follicular helper cells, and B cell differentiation, in both mice and human subjects. My specific expertise includes developing and applying innovative immunological research methods to study immunobiology in pr...
My research for the last 17 years has been in the immunobiology of regulatory T cells, T follicular helper cells, and B cell differentiation, in both mice and human subjects. My specific expertise includes developing and applying innovative immunological research methods to study immunobiology in primary human samples, especially normal lymphocytes and lymphomas. My research has included genotypic-phenotypic characterization of lymphocyte cellular subsets by combined transcriptomics and flow cytometry. I have specific expertise in research human B and T cell research where cell numbers are typically limiting. In particular, as the Technical Director of the Lymphoma Lab at the James P. Wilmot Cancer Center from 2004-2013, I have published several key studies using novel T cell functional assays with single cell RNAseq from fine needle aspirate (FNA) lymph node biopsies of lymphoma patients. Over the last 5 years, I have developed my own independent research work, with a focus on multidisciplinary transcriptomic and proteomic analysis of B cell differentiation and migration. This work has evolved from collaborations with Drs. Juilee Thakar and Martin Zand, including an RO1 (R01-AI134058-01A1) in which we propose to characterize and model the molecular mechanisms by which changes in oxygen levels modulate human B cell migration. The work involves defining and modeling how human B cells respond to infection or vaccination upon encountering different oxygen levels as they are activated/differentiate within the developing germinal center of the draining lymph node and migrate from the lymph node (1-5% oxygen) to the peripheral blood (5-13% oxygen) ultimately ending up in the bone marrow (5-7%). These studies will fill a critical gap in our understanding of human B cell responses, specifically the effects differing oxygen levels have on human B cells as they migrate within and from one anatomical compartment to another. We are now extending this work into HIV vaccination. My prior work involved studies directly related to the current proposal, including complex parallel flow cytometry, ELISpot, ELISA, RNAseq, and proteomics analysis. Lastly, throughout my tenure at the University of Rochester, I have successfully collaborated with a number of other researchers and produced several peer-reviewed publications, including publications with Dr. Thakar performing high-resolution proteomics and transcriptomics studies.


Journal Articles

Executable Network Models of Integrated Multiomics Data.

Palshikar MG, Min X, Crystal A, Meng J, Hilchey SP, Zand MS, Thakar J

Journal of proteome research.. 2023 March 31 Epub 03/31/2023.

First Impressions Matter: Immune Imprinting and Antibody Cross-Reactivity in Influenza and SARS-CoV-2.

King SM, Bryan SP, Hilchey SP, Wang J, Zand MS

Pathogens.. 2023 January 2112 (2)Epub 01/21/2023.

Anamnestic broadly reactive antibodies induced by H7N9 virus more efficiently bind to seasonal H3N2 strains.

Chen Y, Hilchey SP, Wang J, Garigen J, Zand MS, Huang J

Human vaccines & immunotherapeutics.. 2022 October 5 :2128014. Epub 10/05/2022.

Cyclosporine A Modulates LSP1 Protein Levels in Human B Cells to Attenuate B Cell Migration at Low O Levels.

Hilchey SP, Palshikar MG, Mendelson ES, Shen S, Rasam S, Emo JA, Qu J, Thakar J, Zand MS

Life.. 2022 August 2212 (8)Epub 08/22/2022.

WikiNetworks: translating manually created biological pathways for topological analysis.

Palshikar MG, Hilchey SP, Zand MS, Thakar J

Bioinformatics.. 2021 October 12 Epub 10/12/2021.

Broadly Reactive IgG Responses to Heterologous H5 Prime-Boost Influenza Vaccination Are Shaped by Antigenic Relatedness to Priming Strains.

Wang J, Li D, Perry S, Hilchey SP, Wiltse A, Treanor JJ, Sangster MY, Zand MS

mBio.. 2021 July 6 :e0044921. Epub 07/06/2021.

Cyclosporine a directly affects human and mouse b cell migration in vitro by disrupting a hIF-1 ?dependent, o sensing, molecular switch.

Hilchey SP, Palshikar MG, Emo JA, Li D, Garigen J, Wang J, Mendelson ES, Cipolla V, Thakar J, Zand MS

BMC immunology.. 2020 March 1821 (1):13. Epub 03/18/2020.

Application of volumetric absorptive microsampling (VAMS) to measure multidimensional anti-influenza IgG antibodies by the mPlex-Flu assay.

Wang J, Li D, Wiltse A, Emo J, Hilchey SP, Zand MS

Journal of clinical and translational science.. 2019 December 3 (6):332-343. Epub 09/26/2019.

Surfactant Cocktail-Aided Extraction/Precipitation/On-Pellet Digestion Strategy Enables Efficient and Reproducible Sample Preparation for Large-Scale Quantitative Proteomics.

Shen S, An B, Wang X, Hilchey SP, Li J, Cao J, Tian Y, Hu C, Jin L, Ng A, Tu C, Qu M, ZAnd M, Qu J

Analytical chemistry.. 2018 September 490 (17):10350-10359. Epub 08/21/2018.

Broad cross-reactive IgG responses elicited by adjuvanted vaccination with recombinant influenza hemagglutinin (rHA) in ferrets and mice.

Wang J, Hilchey SP, DeDiego M, Perry S, Hyrien O, Nogales A, Garigen J, Amanat F, Huertas N, Krammer F, Martinez-Sobrido L, Topham DJ, Treanor JJ, Sangster MY, Zand MS

PloS one.. 2018 13 (4):e0193680. Epub 04/11/2018.

IL-15 enhances cross-reactive antibody recall responses to seasonal H3 influenza viruses .

Huang J, Hilchey SP, Wang J, Gerigan J, Zand MS

F1000Research.. 2017 6 :2015. Epub 11/15/2017.

Follicular Lymphoma Tregs Have a Distinct Transcription Profile Impacting Their Migration and Retention in the Malignant Lymph Node.

Nedelkovska H, Rosenberg AF, Hilchey SP, Hyrien O, Burack WR, Quataert SA, Baker CM, Azadniv M, Welle SL, Ansell SM, Kim M, Bernstein SH

PloS one.. 2016 11 (5):e0155347. Epub 05/26/2016.

Dual targeting of the thioredoxin and glutathione antioxidant systems in malignant B cells: a novel synergistic therapeutic approach.

Kiebala M, Skalska J, Casulo C, Brookes PS, Peterson DR, Hilchey SP, Dai Y, Grant S, Maggirwar SB, Bernstein SH

Experimental hematology.. 2015 February 43 (2):89-99. Epub 10/22/2014.

Multi-Dimensional Measurement of Antibody-Mediated Heterosubtypic Immunity to Influenza.

Wang J, Hilchey SP, Hyrien O, Huertas N, Perry S, Ramanunninair M, Bucher D, Zand MS

PloS one.. 2015 10 (6):e0129858. Epub 06/23/2015.

Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice.

Qiu X, Wu S, Hilchey SP, Thakar J, Liu ZP, Welle SL, Henn AD, Wu H, Zand MS

PloS one.. 2015 10 (9):e0138110. Epub 09/28/2015.

Mesenchymal stromal cells support the viability and differentiation of follicular lymphoma-infiltrating follicular helper T-cells.

Brady MT, Hilchey SP, Hyrien O, Spence SA, Bernstein SH

PloS one.. 2014 9 (5):e97597. Epub 05/16/2014.

Modeling the dynamics and migratory pathways of virus-specific antibody-secreting cell populations in primary influenza infection.

Miao H, Sangster MY, Livingstone AM, Hilchey SP, Zhang L, Topham DJ, Mosmann TR, Holden-Wiltse J, Perelson AS, Wu H, Zand MS

PloS one.. 2014 9 (8):e104781. Epub 08/29/2014.

The mitochondrial ATP-dependent Lon protease: a novel target in lymphoma death mediated by the synthetic triterpenoid CDDO and its derivatives.

Bernstein SH, Venkatesh S, Li M, Lee J, Lu B, Hilchey SP, Morse KM, Metcalfe HM, Skalska J, Andreeff M, Brookes PS, Suzuki CK

Blood.. 2012 April 5119 (14):3321-9. Epub 02/08/2012.

Follicular lymphoma tumor-infiltrating T-helper (T(H)) cells have the same polyfunctional potential as normal nodal T(H) cells despite skewed differentiation.

Hilchey SP, Rosenberg AF, Hyrien O, Secor-Socha S, Cochran MR, Brady MT, Wang JC, Sanz I, Burack WR, Quataert SA, Bernstein SH

Blood.. 2011 September 29118 (13):3591-602. Epub 08/05/2011.

Modulation of cell surface protein free thiols: a potential novel mechanism of action of the sesquiterpene lactone parthenolide.

Skalska J, Brookes PS, Nadtochiy SM, Hilchey SP, Jordan CT, Guzman ML, Maggirwar SB, Briehl MM, Bernstein SH

PloS one.. 2009 December 24 (12):e8115. Epub 12/02/2009.

Human follicular lymphoma CD39+-infiltrating T cells contribute to adenosine-mediated T cell hyporesponsiveness.

Hilchey SP, Kobie JJ, Cochran MR, Secor-Socha S, Wang JC, Hyrien O, Burack WR, Mosmann TR, Quataert SA, Bernstein SH

The Journal of immunology : official journal of the American Association of Immunologists.. 2009 November 15183 (10):6157-66. Epub 10/28/2009.

Rituximab immunotherapy results in the induction of a lymphoma idiotype-specific T-cell response in patients with follicular lymphoma: support for a "vaccinal effect" of rituximab.

Hilchey SP, Hyrien O, Mosmann TR, Livingstone AM, Friedberg JW, Young F, Fisher RI, Kelleher RJ, Bankert RB, Bernstein SH

Blood.. 2009 April 16113 (16):3809-12. Epub 02/04/2009.

Follicular lymphoma intratumoral CD4+CD25+GITR+ regulatory T cells potently suppress CD3/CD28-costimulated autologous and allogeneic CD8+CD25- and CD4+CD25- T cells.

Hilchey SP, De A, Rimsza LM, Bankert RB, Bernstein SH

The Journal of immunology : official journal of the American Association of Immunologists.. 2007 April 1178 (7):4051-61. Epub 1900 01 01.

The triterpenoid 2-cyano-3,12-dioxooleana-1,9-dien-28-oic acid and its derivatives elicit human lymphoid cell apoptosis through a novel pathway involving the unregulated mitochondrial permeability transition pore.

Brookes PS, Morse K, Ray D, Tompkins A, Young SM, Hilchey S, Salim S, Konopleva M, Andreeff M, Phipps R, Bernstein SH

Cancer research.. 2007 February 1567 (4):1793-802. Epub 1900 01 01.

The novel triterpenoid 2-cyano-3,12-dioxooleana-1,9-dien-28-oic acid (CDDO) induces apoptosis of human diffuse large B-cell lymphoma cells through a peroxisome proliferator-activated receptor gamma-independent pathway.

Ray DM, Morse KM, Hilchey SP, Garcia TM, Felgar RE, Maggirwar SB, Phipps RP, Bernstein SH

Experimental hematology.. 2006 September 34 (9):1202-11. Epub 1900 01 01.

Increased rejection of primary tumors in mice lacking B cells: inhibition of anti-tumor CTL and TH1 cytokine responses by B cells.

Shah S, Divekar AA, Hilchey SP, Cho HM, Newman CL, Shin SU, Nechustan H, Challita-Eid PM, Segal BM, Yi KH, Rosenblatt JD

International journal of cancer.. 2005 November 20117 (4):574-86. Epub 1900 01 01.

Increased rejection of primary tumors in mice lacking B cells: Inhibition of anti-tumor CTL and TH1 cytokine responses by B cells.

Shah, S., Divekar A.A., Hilchey, S.P., Cho, H.M., Newman, C.L., Shin, S.U., Nechustan, H., Challita-Eid, P.M., Segal, B.M., Yi, K.H., Rosenblatt, J.D.

International Journal of Cancer. 2005; 117: 574-586.

Development of herpes simplex virus-1 amplicon-based immunotherapy for chronic lymphocytic leukemia.

Tolba KA, Bowers WJ, Hilchey SP, Halterman MW, Howard DF, Giuliano RE, Federoff HJ, Rosenblatt JD

Blood.. 2001 July 1598 (2):287-95. Epub 1900 01 01.

A RANTES-antibody fusion protein retains antigen specificity and chemokine function.

Challita-Eid PM, Abboud CN, Morrison SL, Penichet ML, Rosell KE, Poles T, Hilchey SP, Planelles V, Rosenblatt JD

The Journal of immunology : official journal of the American Association of Immunologists.. 1998 October 1161 (7):3729-36. Epub 1900 01 01.

Recognition of nonconserved bases in the P22 operator by P22 repressor requires specific interactions between repressor and conserved bases.

Hilchey SP, Wu L, Koudelka GB

The Journal of biological chemistry.. 1997 August 8272 (32):19898-905. Epub 1900 01 01.

DNA-based loss of specificity mutations. Effects of DNA sequence on the contacted and non-contacted base preferences of bacteriophage P22 repressor.

Hilchey SP, Koudelka GB

The Journal of biological chemistry.. 1997 January 17272 (3):1646-53. Epub 1900 01 01.

Indirect Effects of DNA Sequence of Protein-DNA Interactions.

Koudelka, G.B., Bell, A.C., Hilchey, S.P.

Biological Structure and Dynamics. 1996; 1: 1-19.


Nucleic Acids & Molecular Biology (1997)

Chapter: Indirect Effects of DNA Sequence on Transcriptional Activation by Prokaryotic DNA Binding Proteins.

Authors: Hilchey, S.P., Xu, J., Koudelka, G.B.

Publisher: Mechanisms in Transcription 1997