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Miles Pufall, PhD

Associate Professor of Biochemistry and Molecular Biology

Introduction

Proteins do not typically emerge from ribosomes ready to function. In fact, most proteins require precise signals to direct where, when, and how well to perform multiple functions. In my lab we study the structural and biophysical basis for how the glucocorticoid receptor (GR) responds to cellular signals. GR is a steroid activated transcription factor that is expressed in every tissue of the body. In each of these tissues GR performs a distinct function by binding different regions of the genome to affect regulation of gene programs. We are interested in understanding how signals change the conformation of GR to direct binding to specific genomic sites and expression of key genes. We have learned that once bound, the DNA sequence has a profound impact on GR structure and function, and we are pursuing how this influences recruitment of the correct complement of transcription factors to faithfully regulate genes.

We study GR in particular because its central role in the treatment of childhood acute lymphoblastic leukemia (ALL). ALL is the most common childhood cancer and is highly treatable, with 90% of patients cured by standard chemotherapy. For the remaining 10%, the prognosis is grim. Surprisingly, treatment response is best predicted by whether ALL cells die when treated ex vivo with a single component of chemotherapy – glucocorticoids, suggesting a central role for GR in ALL treatment efficacy. Since both sensitive and resistant patients have normal levels of wild type GR, it is our hypothesis that important signaling pathways have been disrupted in resistant patients that affect the ability of GR to efficiently kill ALL cells.

The long-term goals of my lab are to develop a deep understanding of how GR is fine-tuned by signals so that we can rationally develop compounds that will potently and specifically drive the genes that kill leukemias. Our immediate goals are to identify: all signals that have an impact on glucocorticoid induced cell death; GR regulated genes that induce cell death; and GR binding sites associated with these genes. In addition, we are elucidating how both drugs and DNA sequence change the structure of GR at these crucial genes.

Current Positions

  • Associate Professor of Biochemistry and Molecular Biology

Education

  • BA in Chemistry, Oberlin College, Oberlin, Ohio
  • MS in Toxicology, American University, Washington, District of Columbia
  • PhD in Oncological Sciences, University of Utah, Salt Lake City, Utah,
  • Postdoctoral Fellow in Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, California

Graduate Program Affiliations

Center, Program and Institute Affiliations

Research Interests

  • Lab Projects

Selected Publications

  • Spector BM, Santana JF, Pufall MA, Price DH (2024). DFF-ChIP: a method to detect and quantify complex interactions between RNA polymerase II, transcription factors, and chromatin., Nucleic Acids Res., 2024 Oct 14;52(18):e88. doi: 10.1093/nar/gkae760.
  • Zimmerman JAO, Fang M, Pufall MA (2023). PI3Kδ Inhibition Potentiates Glucocorticoids in B-lymphoblastic Leukemia by Decreasing Receptor Phosphorylation and Enhancing Gene Regulation., Cancers, 2023 Dec 17, 16(1), 143. doi: 10.3390/cancers16010143.
  • Mielko Z, Zhang Y, Sahay H, Liu Y, Schaich MA, Schnable B, Morrison AM, Burdinski D, Adar S, Pufall MA, Van Houten B, Gordân R, Afek A (2023). UV irradiation remodels the specificity landscape of transcription factors., Proc Natl Acad Sci U S A. 2023 Mar 14;120(11):e2217422120. doi: 10.1073/pnas.2217422120.
  • Alexandari AM, Horton CA, Shrikumar A, Shah N, Li E, Weilert M, Pufall MA, Zeitlinger J, Fordyce PM, Kundaje A (2023). De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding., bioRxiv. 2023 May 11:2023.05.11.540401. doi: 10.1101/2023.05.11.540401. Preprint.
  • Lee RA, Chang M, Yiv N, Tsay A, Tian S, Li D, Poulard C, Stallcup MR, Pufall MA, Wang JC (2023). Transcriptional coactivation by EHMT2 restricts glucocorticoid-induced insulin resistance in a study with male mice., Nat Commun. 2023 May 30;14(1):3143. doi: 10.1038/s41467-023-38584-5.
  • Thiel KW, Newtson AM, Devor EJ, Zhang Y, Malmrose PK, Bi J, Losh HA, Davies S, Smith LE, Padilla J, Leiva SM, Grueter CE, Breheny P, Hagan CR, Pufall MA, Gertz J, Guo Y, Leslie KK (2023). Global expression analysis of endometrial cancer cells in response to progesterone identifies new therapeutic targets., J Steroid Biochem Mol Biol. 2023 Nov;234:106399. doi: 10.1016/j.jsbmb.2023.106399. 
  • Pisano MD, Sun F, Cheng Y, Zhou V, Jing X, Sompallae R, Abrudan J, Zimmermann MT, Mathison A, Janz S, Pufall MA (2023). IL6Myc mouse is an immunocompetent model for the development of aggressive multiple myeloma., Haematologica. 2023 Jul 13. doi: 10.3324/haematol.2022.282538.
  • Rush CM, Blanchard Z, Polaski JT, Osborne KS, Osby K, Vahrenkamp JM, Yang CH, Lum DH, Hagan CR, Leslie KK, Pufall MA, Thiel KW, Gertz J (2022). Characterization of HCI-EC-23 a novel estrogen- and progesterone-responsive endometrial cancer cell line. Sci Rep. 2022 Nov 17;12(1):19731. https://www.nature.com/articles/s41598-022-24211-8
  • Zimmerman JAO, Fang M, Doumbia B, Neyman A, Cha JH, Thomas M, Hall B, Wu M, Wilson AM, Pufall MA., Deacylcortivazol-like pyrazole regioisomers reveal a more accommodating expanded binding pocket for the glucocorticoid receptor. RSC Med Chem. 2021 Mar 4;12(2):203-212. eCollection 2021 Mar 4. PubMed PMID: 34046609; PubMed Central PMCID: PMC8127617.DOI: https://doi-org.proxy.lib.uiowa.edu/10.1039/D0MD00278J
  • Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordân R., DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature. 2020 Nov;587(7833):291-296. https://doi-org.proxy.lib.uiowa.edu/10.1038/s41586-020-2843-2