Poholek Lab

Technologies in genomic sequencing (NextGen Sequencing technologies) have greatly expanded our ability to study complex traits and assess how genetics and epigenetics contribute to health and disease. In addition, we can leverage these technologies to interrogate cellular differentiation and function at the chromatin and transcriptome level. Amanda C. Poholek, Ph.D. laboratory explores the intersection of chromatin accessibility, epigenetics, and transcription factor networks contributing to immune cell differentiation and function. 


Immune cells play a critical role in establishing and maintaining whole organism health. Aberrant immune cell function underlies a host of diseases ranging from immunodeficiency to autoimmunity. As a model system for cellular differentiation, immune cells have the unique task of existing in a naïve state during homeostasis and have the capability to further differentiate after exposure to pathogens or immune insults. Intriguingly, many immune cells possess inherent flexibility in their naïve state so that upon insult they can choose a variety of functional outcomes that are appropriately tailored to the needed response. The most well-studied cell that exhibits these properties is the CD4 T cell, which upon activation can differentiate into several subsets that have unique functions. These fates are determined by appropriate activation and expression of specific transcription factors. Currently, our lab is focused on understanding how the transcriptional repressor Blimp-1 contributes to T cell differentiation and function using novel model systems and NextGen Sequencing technologies as a model system for how transcription factors can alter immune cell differentiation and function.

Current Research Projects

Identification of enhancers controlling cell-type dependent expression of Blimp-1

Using ChIP-seq to identify enhancers and a genetic reporter of Blimp-1 expression, we are exploring the factors that are required to drive Blimp-1 expression and determining which non-coding enhancers are relevant to control expression of Blimp-1 in different cell types.

Determining cell-type specific function of Blimp-1

Using RNA-seq and ChIP-seq, we are exploring how Blimp-1 functions in different immune cell types. Genetic tools allow us to delete Blimp-1 in specific cell types (constitutively or inducibly) or overexpress Blimp-1 in a dose-dependent cell type specific manner.

Blimp-1 mediated Th2 cell development in the lung impacting allergic airway inflammation

Using a murine model of allergic asthma, we are exploring the requirement of Blimp-1 in asthma disease.

Epigenetic regulation of tumor-infiltrating T cells

Using a new low-cell number ChIPseq assay (CUT&RUN) we are exploring the epigenetics of T cells in murine tumors in collaboration with Dr. Greg Delgoffe at the Hillman Cancer Center.

Current Lab members

Amanda Poholek, Ph.D. - Principal Investigator 

Angela Hettinga - Technician

Kun He, Ph.D. - Postdoc

Rhodes Ford - PMI Graduate Student

Elizabeth Schmitz - Undergraduate Student

Shivani Pandya - Undergraduate Student

 Lab Alumni

Natalie Rittenhouse - Technician

Samantha Grimes - Undergraduate Student

Selected Publications

Poholek AC, Jankovic D, Villarino AV, Petermann F, Hettinga A, Shouval DS, Snapper SB, Kaech SM, Brooks SR, Vahedi G, Sher A, Kanno Y, O'Shea JJ. IL-10 induces a STAT3-dependent autoregulatory loop in Th2 cells that promotes Blimp-1 restriction of cell expansion via antagonism of STAT5 target genes. Science Immunology. Nov 11, Vol.1 Issue 5. 2016. 

Shih HY, Sciume G, Poholek AC, Vahedi G, Hirahara K, Villarino A, Bonelli M, Bosselut R, Kanno Y, Muljo S, O’Shea JJ. Transcriptional and epigenetic networks of helper T cells and innate lymphoid cells. Immunological Reviews. Sept;261(1):23-49. 2014. 

Nakayamada S*, Poholek AC*, Lu KT, Takahashi H, Hirahara K, Kato, M, Iwata S, Cannons JL, Schwartzberg PL, Vahedi G, Sun H, Kanno Y, O’Shea JJ. Type I Interferon induces binding of STAT1 to Bcl6: Divergent Roles of STAT-family transcription factors in the TFH cell genetic program. The Journal of Immunology. Mar 1;192(5):2156-66. 2014. 

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. Immunological Reviews. Mar;252(1):24-40. 2013. 

Poholek AC, Hansen K, Hernandez S, Eto D, Chandele A, Weinstein JS, Dong X, Odegard J, Kaech SM, Dent AL, Crotty S, Craft J. In vivo regulation of Bcl6 and T follicular helper cell development. The Journal of Immunology, 185(1):313-26, 2010.

Johnston R*, Poholek AC*, DiToro D, Yusuf I, Eto D, Barnett B, Dent A, Craft J, and Crotty S. Bcl6 and Blimp-1 are reciprocal and antagonist regulators of T follicular helper cell differentiation. Science. 325(5943):1006-10, 2009 

A full list of Amanda Poholek, Ph.D. publication can be found on NCBI.