Fotini Gounari, Ph.D.


  • Associate Professor, Department of Medicine, Cancer Research Center, Committee on Cancer Biology, Committee on Immunology


Ph.D.     National Institute for Medical
               Research, London, UK 

H.D.R. (D.Sc.)  Rene Descartes
               University,  Paris, France 


The University of Chicago 
JFK R314
924 East 57th Street 
Chicago, Illinois 60637

Phone:  (773) 702-3912

Webpage (Lab)

Webpage (Knapp Center)


My laboratory studies molecular processes that control the development of T-cells in the thymus and ensure balanced peripheral T-cell responses. For these studies we use human specimens as well as specifically designed genetically engineered mouse models. We have refined molecular and cellular assays to understand mechanisms of natural, as well as pathogenic T-cell development and function. My long-term goal is to better understand the basic biology of T-cells and to learn how deregulation of this biology leads to disease because this will enable developing targeted therapeutic interventions for pathologies, including autoimmunity and cancer. 

Role of β-catenin in regulation of chromatin landscape and gene expression:Studies in my lab focus on understanding the functions of Wnt signaling in T-cell development and function. This evolutionary conserved pathway has been linked with a variety of developmental processes and its uncontrolled activation in epithelial cells has been associated with carcinogenesis. Activation of Wnt signaling induces the translocation of β-catenin to the nucleus, where with the TCF or Lef-1, it binds to genes as a transcription factor complex. How the β-catenin/TCF complex regulated gene transcription was not clear. Furthermore, little was known about the role of this pathway in T cells. Using genome wide approaches, such as chromatin immunoprecipitation coupled to deep sequencing, my lab has demonstrated that in thymocytes, β-catenin in complex with the T-cell specific DNA binding protein TCF-1 regulate the chromatin landscape and gene accessibility. By controlling the accessibility of genes, the β-catenin/TCF-1 complex regulates gene transcription. Furthermore the β-catenin/TCF-1 complex controls the access of DNA recombination and repair proteins to chromatin and thereby regulates these processes. Below, I will briefly outline our findings with regards to the consequences of β-catenin and TCF-1 mediated chromatin and gene expression changes in T-cells.

β-Catenin promotes the preferential expansion of a tumor promoting regulatory T-cell (Treg) subset in colon cancer: Through a collaborative effort my lab has made a paradigm-shifting discovery that could explain how in autoimmunity inflammation becomes chronic and predisposes to cancer. We identified two distinct Treg subsets with protective or pathogenic properties respectively in mouse models of hereditary polyposis and in human colon cancer. The novel pathogenic subset of Tregs (pro-inflammatory Tregs) can suppress activated T-cells but at the same time promotes inflammation and predisposes to tumorigenesis. These Tregs express Foxp3 the hallmark transcription factor of Tregs yet they also express RORγt a transcription factor that marks pro-inflammatory T-helper-17 (TH17) cells. Expression of RORγt, is critical for the pro-inflammatory properties of these Tregs and is controlled by the Wnt/β-catenin pathway. My studies revealed that during polyposis, the Wnt/β-catenin pathway is induced in intestinal T-cells and Tregs thereby altering their chromatin landscape and gene expression. Specifically, activated β-catenin enhances chromatin accessibility near sites bound by TCF-1 throughout the genome and induces the expression of RORγt, which in turn favors an inflammatory over a regulatory phenotype in these cells. In vivo, this is associated with chronic inflammation and predisposition to colon cancer. T cell specific ablation of RORγt in these mice normalizes TH17 responses and restores Treg frequencies. These findings demonstrate that Wnt/β-catenin signaling in T cells regulates inflammation in the gastrointestinal tract. Excessive Wnt/β-catenin signaling in T-cells causes autoimmunity and predisposes to cancer. Thus my findings provide new targets for therapeutic intervention in chronic pathologic inflammation.

Role of β-catenin and TCF-1 in T-cell development: My lab identified β-catenin and TCF-1 as critical determinants of thymic T-cell fate decisions. In my earlier studies I characterized the profile of progenitor cells that migrate from the bone marrow to the thymus to develop into T-cells. My recent studies demonstrated that TCF-1 is essential for commitment of Early Thymic progenitors (ETP) to the T-cell lineage identifying a novel checkpoint in T-cell development. I have established that TCF-1 is one of the first T-cell specific regulators of transcription to become upregulated by Notch in ETPs. In the absence of TCF-1 these cells are unable to differentiate further become abortive and die because they fail to upregulate proteins needed for DNA replication and repair. Thus, TCF-1 functions as a gatekeeper of the T-cell fate.

Early T cell development is absolutely dependent upon expression of the pre-TCR, which transmits signals required for cell survival, proliferation and developmental progression. My earlier studies demonstrated that activation of β-catenin can rescue T cell development of pre-TCR and even TCR deficient cells. These studies indicated that a function of these receptors is to activate β-catenin. Subsequent biochemical tracing of TCR signaling in thymocytes undergoing selection showed that β-catenin is indeed activated by TCR signaling. These studies demonstrated that activation of β-catenin by the TCR favors negative selection and established its central role in shaping T-cell immunity.

To further define how Wnt/β-catenin signals influence thymocyte maturation, my lab has studied additional components and transcriptional targets of the pathway. The adenomatous polyposis coli (APC) protein regulates the levels of β-catenin by promoting its degradation and in its absence β-catenin accumulates. I have generated conditional APC knockout mice. By comparing T-cell specific activation of β-catenin to ablation of APC I discovered unexpected β-catenin independent functions for APC in chromosome segregation during mitosis that are critical for T-cell development. In the absence of APC, proliferation of developing T-cells is compromised and chromosomal abnormalities accumulate. My findings demonstrated that APC has specific developmental functions that are independent of its role in Wnt/β-catenin signaling.

c-Myc is an important transcriptional target of the Wnt/β-catenin pathway. I have demonstrated that c-Myc is critically required for the pre-TCR driven proliferation of immature thymocytes. I also found that c-Myc is activated downstream of the TCR and this is required for the development of iNKT cells, a group T-cells that respond rapidly to infections. Absence of c-Myc impaired a massive proliferative wave during iNKT cell development in the thymus and resulted in iNKT cell deficiency. I conclude that c-Myc is indispensable for the differentiation and expansion of both T and iNKT cells.

Altogether, studies in my lab showed that β-catenin signaling is essential at multiple stages of T cell development.

β-catenin drives genomic instability and susceptibility to hematologic malignancies: My Lab now has evidence that Wnt/β-catenin signaling is directly linked with genomic instability in cancer. This is because β-catenin and TCF-1 maintain genomic integrity during TCR gene rearrangements that are catalyzed by RAG recombinases. Activation of β-catenin promotes genomic instability, in part, by changing the choice of DNA repair mechanism used. In particular, we found that TCF-1 and RAG2 bind to overlapping DNA sites genome-wide. Interestingly, I found that activation of β-catenin, such as is seen in cancer, alters repair of RAG mediated DNA double strand breaks and allows survival of cells with damaged DNA thereby promoting genomic instability. Indeed, constitutive activation of b-catenin in T-cells induces T-cell lymphomas. These lymphomas have recurrent chromosomal translocations involving unrepaired RAG breaks in the TCRα locus and breaks in the Pvt-1 locus downstream of Myc, which lead to constitutive activation of c-Myc. This is a common oncogenic event in leukemia. Identical translocations are found in human T-cell leukemia, Burkitt’s lymphomas, and plasmacytomas. The thymocyte transformation induced by β-catenin provides a unique model to study molecular mechanisms that are responsible for genomic instability and to identify key events that can be targeted to stop instability and render cancer cells vulnerable to therapy. 


Dose M., Sleckman B.P., Han J., Bredemeyer A.L., Bendelac A. and Gounari F. Intrathymic proliferation wave essential for Va14+ natural killer T cell development depends on c-Myc. Proc. Natl. Acad. Sci. USA, 106:8641-8646. doi: 10.1073/pnas.0812255106 (2009).

Kovalovsky D., Yu Y., Dose M., Emmanouilidou A., Konstantinou T., Germar K., Aghajani K., Guo Z., Mandal M. and Gounari F. β-Catenin/TCF determines the outcome of thymic selection in response to αβTCR signaling. J. Immunol., 183: 3873-3884. doi: 10.4049/jimmunol.0901369 (2009).

Kreslavsky T., Savage A.K., Hobbs R., Gounari F., Bronson R., Pereira P., Pandolfi P.P., Bendelac A. and von Boehmer H. TCR-inducible PLZF transcription factor required for innate phenotype of a subset of γδ T cells with restricted TCR diversity. Proc. Natl. Acad. Sci. USA, 106:12453-12458. doi: 10.1073/pnas.0903895106 (2009).

Gounaris E., Blatner N.R., Dennis K., Magnusson F., Gurish M.F., Strom T.B., Beckhove P., Gounari F. and Khazaie K. T-Regulatory Cells Shift from a Protective Anti-Inflammatory to a Cancer-Promoting Proinflammatory Phenotype in Polyposis Cancer Res., 69: 5490-5497. doi: 10.1158/0008-5472 (2009).

de Keersmaecker K., Real P.J., Della Gatta G., Palomero T., Sulis M.L., Tosello V., Van Vlierberghe P., Barnes K., Castillo M., Sole X., Hadler M., Lenz J., Aplan P.D., Kelliher M., Kee B.L., Pandolfi P.P., Kappes D., Gounari F., Petrie H., Van der Meulen J., Speleman F., Paietta E., Racevskis J., Wiernik P.H., Rowe J.M., Soulier J., Avran D., Cavé H., Dastugue N., Raimondi S., Meijerink J.P.P., Cordon-Cardo C., Califano A., and Ferrando A.A. The TLX1 oncogene drives aneuploidy in T cell transformation Nature Med., 16 (11): 1321-1327. doi: 10.1038/nm.2246 (2010).

Driessens G., Zheng Y., Locke F., Cannon J.L., Gounari F. and Gajewski T.F. Beta-catenin inhibits T cell activation by selective interference with linker for activation of T cells-phospholipase C-γ1 phosphorylation J. Immunol., 2011 186 (2): pp. 784-90. doi: 10.4049/jimmunol.1001562 (2011).

Hu M.G., Deshpande A., Schlichting N., Hinds E.A., Mao C., Dose M., Hu G., Van Etten R.A., Gounari F. and Hinds P.W., CDK6 kinase activity is required for thymocyte development. Blood, 117 (23 ): pp. 6120-6131. doi: 10.1182/blood-2010-08-300517 (2011).

Germar K., Dose M., Konstantinou T., Zhang J., Wang H., Lobry C., Arnett K., Blacklow S.C., Aifantis I., Aster J.C. and Gounari F. Tcf-1 is a gatekeeper for T-cell specification in response to Notch signaling. Proc. Natl. Acad. Sci. USA, 108(50): 20060-5. doi:10.1073/pnas. 1110230108 (2011).

Zhang J., Jackson A.F., Naito T., Dose M., Seavitt J., Liu F., Heller E.J., Kashiwagi M., Yoshida T., Gounari F., Petrie H. and Georgopoulos K. Harnessing of the Nucleosome Remodeling Deacetylase complex controls lymphocyte development and prevents leukemogenesis Nature Immunol.,  13(1): 86-94. doi:10.1038/ni.2150 (2012).

Khazaie K., Zadeha M., Khan M.W., Bere P., Gounari F., Dennis K., Blatner N.R., Owen J.L., Klaenhammer T.R. and Mohamadzadeh M. Abating colon cancer polyposis by Lactobacillus acidophilus deficient in lipoteichoic acid.  Proc. Natl. Acad. Sci. USA, 109(26): 10462-7. doi: 10.1073/pnas.1207230109 (2012).

Blatner N.R., Mulcahy M.F., Dennis K.L., Scholtens D., Bentrem D.J., Phillips J.D., Ham S., Sandall B.P., Khan M.W., Mahvi D.M., Halverson A.L., Stryker S.J., Boller A.M., Singal A., Sneed R.K., Sarraj B., Ansari M.J., Oft M., Iwakura Y., Zhou L., Bonertz A., Beckhove P, Gounari F. and Khazaie K. Expression of RORγt marks a pathogenic T-regulatory cell subset in human colon cancer. Science Translational Medicine, 4(164): 164ra159. doi: 10.1126/scitranslmed.3004566 (2012).

Aghajani K., Keerthivasan S., Yu Y. and Gounari F. Generation of CD4CreERT2 transgenic mice to study development of peripheral CD4-T-cells.  Genesis, 50(12): 908-13. doi: 10.1002/dvg.22052. (2012).

Blatner N.R., Gounari F. and Khazaie K. The two faces of regulatory T-cells in cancer.  Oncoimmunology, 1;2(5). doi: 10.4161/oncoi.23852 (2013).

Li L., Zhang J.A., Dose M., Kueh H-Y., Mosadeghi R., Gounari F. and Rothenberg E.V. Long-range looping of a far downstream enhancer to Bcl11b controls its T-cell specific expression. Blood, 122(6): 902-11. doi: 10.1182/blood-2012-08-447839 (2013).

Yoshida T., Landhuis E., Dose M., Hazan I., Zhang J., Naito T., Jackson A.F., Wu J., Perroti E.A., Kaufmann C., Gounari F., Morgan B.A. and Georgopoulos K. Transcriptional regulation of the Ikzf1 locus. Blood, 122(18): 3149-59. doi: 10.1182/blood-2013-01-474916 (2013).

Dose M., Emmanuel A. O., Chaumeil J., Zhang J., Sun T., Germar K., Aghajani K., Davis E.M., Keerthivasan S., Bredemeyer A.L., Sleckman B. P., Rosen S.T., Skok J.A., Le Beau M.M., Georgopoulos K. and Gounari F. β-catenin induces T-cell transformation by promoting genomic instability. Proc. Natl. Acad. Sci. USA, 111(1): 391–6. doi/10.1073/pnas.1315752111 (2014).

Keerthivasan S. *, Aghajani K.* Dose M., Molinero L., Khan M.W., Venkateswaran V., Weber C., Emmanuel A.O., Sun T., Bentrem D. J., Mulcahy M., Keshavarzian A., Ramos E. M., Blatner N., Khazaie K., Gounari F. T-cell specific activation of -catenin induces IL-17 mediated inflammatory bowel disease and dysplasia. Science Translational Medicine, 6(225), 225ra28. doi:10.1126/scitranslmed.3007607 (2014).