Amanda C. Poholek, Ph.D.

  • Assistant Professor
  • Department of Pediatrics

Education & Training

  • B.S. Biological Sciences, Fordham University, Bronx, NY 2002
  • PhD. Cell Biology, Yale University, New Haven, CT 2009
  • Post-doctoral fellow, NIAMS, NIH 2015

Research Interest Summary

Our lab is interested in exploring how tissue-specific environmental factors alter transcriptomes and epigenomes of T cells that control their differentiation in the context of diseases such as allergic asthma and cancer.

Research Categories

Research Interests


My research focuses on understanding how immune cells integrate signals encountered in the environment to drive functional outcomes at the molecular and epigenetic level in both health and disease. While the basic mechanisms of immune cell differentiation have been defined, the role that transcription factors and metabolism play in shaping the epigenetic landscape during differentiation remains unclear. 

Blimp-1 regulation in function in T cells

As a model transcription factor, we are currently focused on the regulation and function of the transcriptional repressor Blimp-1 across multiple immune cell types. Blimp-1 has been associated with constraining T cell-mediated autoimmune disease and is highly expressed in exhausted T cells present in chronic viral infection and the tumor microenvironment. In addition, Blimp-1 is the master regulator of plasma cell formation in B cells. Therefore, Blimp-1 has wide-ranging functions depending on the cell type, suggesting its role in disease may be context-dependent. Currently, our group is focused on T cells to understand the factors that regulate expression of Blimp-1 in both CD4 and CD8 T cells, and identify the non-coding genetic regulatory elements such as enhancers that are critical for cell-type specific expression of Blimp-1. We are also exploring the genes regulated by Blimp-1 in CD4 T cell subsets using NextGen sequencing technologies such as ChIP-seq, RNA-seq, and ATAC-seq in an effort to understand the function of Blimp-1 in T cells.  Finally, we are extending our in vitro observations to clinically relevant diseases such as allergic asthma to understand the functional consequences of Blimp-1 in disease settings.
        • Regulation of Blimp-1 in immune cells. The long-term goal of this project is to use identify the extracellular signals and genetic elements of the locus that control Blimp-1 expression in various immune cell types in an effort to understand how the regulation of Blimp-1 expression may be key in constraining T cell-mediated autoimmunity or promoting allergic asthma. 
        • Function of Blimp-1 in immune cells. The aims of this project are identify the genes regulated by Blimp-1 both directly and indirectly in various immune cell types to understand the context-dependent and cell-type specific functions of Blimp- 1 in various disease settings.
        • Identify Blimp-1 mediated allergic asthma disease. The aims of this project are to understand why the selective absence of Blimp-1 in T cells results in reduced lung inflammation and development of allergic airway disease.

Metabolic regulation of the epigenome in T cell differentiation and function.

The process of T cell differentiation is controlled by changes to the transcriptome which requires rearrangement of the chromatin and epigenome. In addition to genomic changes, T cells rapidly alter their metabolic pathways and become glycolytic upon activation. It is well understood that the cofactors required for productive epigenetic changes derive from metabolic intermediates produced during glycolysis and other metabolic pathways. Yet how these rapid changes in metabolism contribute to the differentiation and function of T cells is not known. In addition, settings of metabolic dysfunction in T cells underlie several disease states, including lupus, a systemic autoimmune disease, and T cell responses to chronic viral infection and tumor clearance. Our research aims to understand the metabolic control of the epigenome upon T cell activation and in cases of metabolic dysfunction.
    • Metabolic control of the epigenome in CD8 T cell exhaustion in the tumor. Recent successes in immunotherapy have underscored the power of the immune system as a clinical relevant method of cancer treatment. However only a fraction of patients respond to immunotherapy due to multiple immunosuppressive mechanisms employed by the tumor. CD8 T cells are re-activated by immunotherapy but also profoundly exhausted suggesting immunosuppressive mechanisms in the tumor functionally debilitate CD8 T cell responses. Importantly, recent evidence suggests immunosuppression has an epigenetic consequence tumor T cells as PD1 therapy has no effect on the epigenetic landscape of CD8 tumor infiltrating lymphocytes (TIL). Due to technical limitations, only chromatin accessibility has been explored. In collaboration with Dr. Greg Delgoffe at the Hillman Cancer Center, we have adapted a new low cell number ChIP-seq assay termed CUT&RUN to epigenetically profile histone modifications of CD8 T cells from the tumor based on cell surface markers that correlate with level of exhaustion.  These data represent a foundational map of the epigenetic landscape of CD8 TIL. Ongoing studies aim to explore the consequence of metabolically insufficient states such as hypoxia, and immunotherapy treatment of tumors to understand how the integration of many signals contributes to T cell exhaustion in the tumor at the epigenetic level. 
 

Representative Publications

Ford BR#, Vignali PDA#, Rittenhouse NL#, Scharping NE#, Peralta R, Lontos K, Frisch AT, Delgoffe GM*, Poholek AC*. Tumor microenvironmental signals reshape chromatin landscapes to limit the functional potential of exhausted T cell. Sci.Immunol.  Aug 5;7(74):eabj9123. (PMID: 35930654) 2022. *Corresponding author. #Equal contribution.

Vignali PDA, DePeaux KD#, Watson MJ#, Ye C, Ford BR, Lontos K, McGaa NK, Scharping NE, Menk AV, Robson SC, Poholek AC, Rivadeneira DB, Delgoffe GM. “Hypoxia drives CD39-dependent suppressor function in exhausted T cells to limit antitumor immunity”. Nat. Immunol. Dec 21, 2022. (PMID: 36543958) 2022.

Scharping NE, Rivadeneira DB, Menk AV, Vignali PDA, Ford BR, Rittenhouse NL, Peralta R, Wang Y, Wang Y, DePeaux K, Poholek AC, Delgoffe GM. Metabolic stress induced by continuous stimulation under hypoxia rapidly promotes a terminally exhausted T cell state. Nat. Immunol. (22),205–215 (PMID: 33398183) 2021.

He K*, Hettinga A*, Kale SL, Hu S, Xie MM, Dent AL, Ray A, Poholek AC. Blimp-1 is essential for allergen-induced asthma and Th2 cell development in the lung. J. Exp. Med. 217(7):e20190742. (PMID: 32399548) 2020. *Equal Contribution
Poholek AC*, Jankovic D, Villarino A, Villarino A, Petermanm F, Shouval DS, Snapper SB, Kaech SM, Brooks SR, Vahedi G, Sher A, Kanno Y, O’Shea JJ*. IL-10 induces a STAT3-dependent autoreguatory loop in Th2 cells that promotes Blimp-1- restriction of cell expansion via antagonism of STAT5 target genes. Sci. Immunol. Nov. 11;1(5). (PMID:28713870) 2016. *Corresponding authors.

Poholek AC. Tissue-Specific Contributions to Control of T Cell Immunity. Immunohorizons. Jun 8;5(6):410-423. (PMID: 34103371) 2021.

Ford BR, Poholek AC. Regulation and Immunotherapeutic Targeting of the Epigenome in Exhausted CD8 T cell responses. J.Immunol. Invited Review, Special Issue Systems Immunology. In Press.

Vahedi G*, Poholek AC*, Hand TW, Laurence A, Kanno Y, O’Shea JJ, Hirahara K. Helper T Cell Identity and Evolution of Differential Transcriptomes and Epigenomes. Immunol. Rev. Mar;252(1):24-40. (PMID: 23405893) 2013. *Equal Contribution.

Full List of Publications