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David Wiest, PhD

David Wiest, PhD
About

Deputy Chief Scientific Officer

Professor

Co-Leader, Blood Cell Development and Function

Director, Cell Sorting Facility and Laboratory Animal Facility

Research Program

Lab Overview

The Wiest lab employs genome wide approaches to gain fundamental insights into the molecular control of the development of T lymphocytes and other hematopoietic cells and then exploits that information to improve the efficacy of cancer treatment. The lab focuses on four main areas. Project 1 seeks to identify the causal mutations responsible for previously unsolved immunodeficiency cases, in collaboration with investigators at the University of California at San Francisco (Figure 1). Project 2 intends to establish a three-dimensional model of the genome restructuring responsible for specification of γδ lineage T cells, and then to exploit those insights to edit the genomes of γδ lineage T cells a maximize their potency as anti-cancer immune effectors (Figures 2 and 3). Project 3 focuses on how an understudied class of molecular effectors, ribosomal proteins, control normal hematopoiesis and the potential of hematopoietic progenitors for transformation (Figures 4 and 5). The goal of Project 4 is to devise novel ways to target the Ras/MAPK pathway, which is activated in 85% of human cancers. They have determined that the ERK2 substrate interaction domains have opposing roles in cancer progression and wish to exploit this insight therapeutically (Figure 6).

Figure 1 – Primary human immunodeficiencies disable the bodies system of defense against invading pathogens, leaving those patients vulnerable to attack. These patients also represent an opportunity of learn more about the molecular processes that control immune cell development. We seek to identify the causes of human immunodeficiency by sequencing the patient genomes to find mutations in their genes, an then use the zebrafish model to screen those mutations to determine if they are responsible for disease. The zebrafish model is ideally suited for this because the molecular processes that control development of fish blood are very similar to those in humans, and they occur very rapidly enabling rapid screening of patient variants.
Figure 2 – αβ and γδ lineage T cells arise from a common set of precursors in the thymus. The signals that determine whether they adopt the αβ and γδ fate arise from their T cell receptor complexes, with weak and strong signals specifying the αβ and γδ fate, respectively. The signals of differing strength specify fate through the extent to which the repress the function of a critical set of transcription factors, the E proteins, E2A and HEB.
Figure 3 – While the extent of E protein suppression by the antagonist Id3 is now well established, with mild repression leading to the αβ fate and strong repression leading to the γδ fate; however, it is not clear how these differences in E protein function repression mediate fate choice. To unravel this mystery, we are taking a genome wide approach to identify the specific E protein binding sites (E protein ChiP-Seq), whether those sites are promoters or enhancers (chromatin marks), what transcription factors bind nearby (Homer analysis), what the genomic targets of E protein bound enhancers are (HiC), and ultimately how all of these changes affect gene expression (RNA-Seq). Together, these analyses will produce a comprehensive, genome-wide, three-dimensional model of how the genome is reorganized during γδ lineage commitment.
Figure 4 – Rpl22 is a component of the large (60S) subunit of the ribosome, but Rpl22 is not necessary for ribosome biogenesis or function. Instead, Rpl22 regulates hematopoiesis, transformation, and morphogenesis by leaving the ribosome and binding to RNA targets to regulate their translation or splicing. The ability of Rpl22 to so is dependent upon its association with hnRNP-A1 and is antagonized by the highly homologous paralog of Rpl22, Rpl22-Like1 (Like1).
Rpl22 plays a key role in regulating the transformation potential of hematopoietic progenitors and does so by controlling their metabolism. When Rpl22 is lost or suppressed, its absence results in induction of Alox12 expression, creating an excess of the 12S-HETE ligand that active the master regulator of fatty acid oxidation (FAO), PPARδ. PPARδ activation drives increased dependence on FAO, which promotes self-renewal and blocks differentiation, thereby creating a premalignant state and increasing the risk for development of myeloid malignancies. Targeting FAO may represent an effective approach to treat myeloid cancers in which Rpl22 expression is reduced.
Figure 6 – The ERK kinases interact with substrates via two distinct domains, the D-domain through which it phosphorylates the majority of its substrates, and the DEF-binding pocket (DBP) through which it interacts with the remainder of its substrates. Using mutational approaches, we have demonstrated that the D-domain plays a key role in promoting cancer progression, while the DBP opposes that process through the induction of senescence. We now seek to employ small molecules to selectively attenuate D domain function as a therapeutic strategy to block cancer progression.

 

Education and Training

Educational Background

  • Postdoctoral training, Developmental Immunology, NIH, 1995
  • PhD, Immunology, Duke University, 1991
  • BS, Microbiology, Penn. State University, 1984

Honors & Awards

  • NCI Board of Scientific Counselors
  • Senior Research Excellence Award, Temple Translational Science Symposium
  • American Cancer Society Southeastern Pennsylvania Research Award
  • Bucks County Board of Associates Key to the Chapter Award
  • Elected to Henry Kunkel Society
  • Inspired Leadership Award
  • Member, Program Committee, American Association of Immunologists, 2010-2013
  • Member Faculty of 1000, Leukocyte Development Section
  • Member, CMIB study section
  • Cancer Research Institute Fellow
  • Norman F. Conant Award for Excellence in Research
Research Profile

Research Program

Research Interests

T lymphocyte development and transformation

  • Molecular basis for specification of the two major T lymphocyte lineages, αβ and γδ
  • Regulatory functions of the ribosomal protein Rpl22 in hematopoiesis, lymphoid development, and leukemogenesis
  • Using zebrafish to identify disease-causing genes in immunodeficient humans

Lab Description

Molecular control of T lymphocyte development and function and malignant hematopoiesis

Project 1: Previously, research into the molecular causes of inherited defects in the human human system, so called immunodeficiencies including servere combined immunodeficiency (SCID), have led not only to a better understanding of human immune cell development, but has also led to the discovery of novel therapeutic targets for cancer treatment (e.g., BTX and Ibrutinib). Accordingly, we combine exome and whole genome sequence analysis with screening of candidate genes in zebrafish to identify the gene mutations causing SCID (Figure 1). Using this approach, we have already identified three novel causes of immunodeficiency (STN1, ARPC1B, and BCL11B) and are currently analyzing two more novel immunodeficiency genes. The role of these genes in the etiology, diagnosis or treatment of hematologic malignancies is also being explored.

Project 2: T lymphocytes recognize and destroy invading pathogens through an assembly of proteins called the T cell antigen receptor (TCR) complex. The TCR has protein subunits that are highly variable and responsible for target recognition (either αβ or γδ) and subunits that are invariant proteins and serve to transmit signals (CD3γδε and ζ). This critical protein assembly (the TCR) controls not only the behavior of mature T lymphocytes but also their development in the thymus. My laboratory seeks to understand how T cell development is controlled by the TCR and was the first to demonstrate that this complex plays a critical role in specification of the two majory T lineages, αβ and γδ, which arise from a common immature precursor in the thymus. Importantly, γδ T cells are a long overlooked immune cell population that is increasingly understood to be critically important in immune responses to cancer. We have found that the nature of the signal transduced by the TCR plays a key role in not just specifying the γδ fate, but also influencing the functions they perform. Moreover, we have identified the signaling axis involved, which exerts its effects through the graded reduction of the activity of E box DNA binding proteins (E proteins), which are critical regulators of lymphocyte development (Figure 2). We are currently building a global three-dimensional genomic regulatory network assembled around E protein targets that are differentially occupied during fate specification (Figure 3). Our ultimate goal is the use this information in conjunction with genome editing to produce optimized anti-cancer γδ T cell effectors to deploy in adoptive cellular therapy.

Project 3: Our efforts to understand the molecular basis for αβ/γδ T lineage commitment, led us to identify an unusual molecular effector that plays a critical role in this process, the ribosomal protein, Rpl22. Ribosomal proteins (RP) have historically been viewed as supporting the ribosome’s ability to synthesize proteins; however, emerging evidence suggests that RP, many of which are RNA-binding proteins, can actually play critical regulatory roles that control both normal development and transformation. We have found this to be true for Rpl22. Its function is selectively required for development of certain hematopoietic cells including αβ lineage T cells. Importantly, Rpl22 also regulates the emergence and behavior of hematopoietic stem cells, particularly their potential for transformation. Of note, the function of Rpl22 as a tumor suppressor is antagonized by its highly homologous (73% identical) ribosomal protein paralog, Rpl22-Like1 (Like1), which promotes development and transformation. Accordingly, developmental outcomes and risk for transformation are controlled by the antagonistic balance of Rpl22 to Like1 (Figure 4). These proteins do not appear to regulate development by altering the function of the ribosome, but instead appear to do so by functioning away from the ribosome, by binding particular RNA targets and controlling either their splicing or their translation. Efforts are ongoing to identify the collection of cellular targets through which they function as well as the molecular basis by which such similar proteins as Rpl22 and Like1 exert opposing functions. We have identified one such target, the mRNA encoding the lipoxygenase Alox12, which controls the transformation potential of hematopoietic progenitors by controlling their metabolic dependence on fatty acid oxidation (FAO), a process on which stem cells and cancer stem cells typically depend (Figure 5). These studies should inform the etiology of a number of human cancers including acute lymphoblastic leukemia (ALL), myelodysplastic syndromes (MDS), and acute myelogenous leukemia (AML), and will likely reveal new therapeutic entry points in these difficult diseases. 

Project 4: The Ras/MAPK pathway is activated in ~85% of human cancers, but to date efforts to target this pathway therapeutically by focusing on the active sites of pathway enzymes have had limited success. We seek to develop effective therapeutic interventions for this pathway by taking a different approach, targeting the substrate interaction domains of ERK proteins, specifically ERK2. ERK2 has two different substrate interaction domains, the D domain and the DEF-binding pocket (DBP). Interestingly, we have found that the D and DBP domains of ERK2 have opposing roles in cancer progression, with D supporting progression and DBP antagonizing this process by promoting senescence (Figure 6). Consequently, we seek to understand the molecular basis for the functioning of these domains and how we can block the function of the D domain therapeutically to attenuate cancer progression.

Lab Staff

Bridget Aylward, PhD

Postdoctoral Fellow

Room: R364
215-728-2968

Alejandra Contreras, PhD

Postdoctoral Fellow

Room: R364
215-728-2968

Paul Harvilla, BS

Graduate Student, University of the Sciences

Room: R364
215-728-2968

Robert Sertori, PhD

Postdoctoral Fellow

Room: R364
215-728-2968

Ninnka Tamot, BS

Graduate Student, University of the Sciences

Room: R364
215-728-2968

Billy Truong, BS

Graduate Student, Temple University

Room: R364
215-728-2968

Michele Rhodes, BS

Scientific Assistant

Room: R364
215-728-2968
Publications

Selected Publications

Fahl, S.P*., Contreras, A.V.*, Verma, A., Qiu, X., Harly, C., Radtke, F., Zúñiga-Pflücker, J.C., Murre, C., Xue, H.H., Sen, J.M., and Wiest, D.L. 2021. The E protein-TCF1 axis controls gd T cell development and effector fate. Cell Reports., In Press. *Contributed Equally.

Rao, S., Peri, S., Hoffman, J., Cai, K.Q., Harris, B., Rhodes, M., Connolly, D.C., Testa, J.R., and Wiest, D.L. 2019. Rpl22L1 overexpression confers 5-FU resistance in colorectal cancer. PLOS One 14:e0222392. PMC6776433

Fahl, S.P., Coffey, F., Kain, L., Zarin, P., Teyton, L., Zúñiga-Pflücker, J.C., Kappes, D.J., and Wiest, D.L. 2018.  Role of a selecting ligand in shaping the gd TCR repertoire. PNAS 115:1889-1894. PMC5828614

Fahl SP, Wiest DL. 2018. Reply to Chien: Clarification of the effect of ligand on γδ-TCR repertoire selection. PNAS 115:E3607-E3608. PMC5910880

Tyner, J.W., Tognon, C.E., Bottomly, D., Wilmot, B., Kurtz, S.E., Savage, S.L., Long, N., Schultz, A.R., Traer, E., Abel, M., Agarwal, A., Blucher, A., Borate, U., Bryant, J., Burke, R., Carlos, A., Carpenter, R., Carroll, J., Chang, B.H., Coblentz, C., d'Almeida, A., Cook, R., Danilov, A., Dao, K.T., Degnin, M., Devine, D., Dibb, J., Edwards, D.K. 5th, Eide, C.A., English, I., Glover, J., Henson, R., Ho, H., Jemal, A., Johnson, K., Johnson, R., Junio, B., Kaempf, A., Leonard, J., Lin, C., Liu, S.Q., Lo, P., Loriaux, M.M., Luty, S., Macey, T., MacManiman, J., Martinez, J., Mori, M., Nelson, D., Nichols, C., Peters, J., Ramsdill, J., Rofelty, A., Schuff, R., Searles, R., Segerdell, E., Smith, R.L., Spurgeon, S.E., Sweeney, T., Thapa, A., Visser, C., Wagner, J., Watanabe-Smith, K., Werth, K., Wolf, J., White, L., Yates, A., Zhang, H., Cogle, C.R., Collins, R.H., Connolly, D.C., Deininger, M.W., Drusbosky, L., Hourigan, C.S., Jordan, C.T., Kropf, P., Lin, T.L., Martinez, M.E., Medeiros, B.C., Pallapati, R.R., Pollyea, D.A., Swords, R.T., Watts, J.M., Weir, S.J., Wiest, D.L., Winters, R.M., McWeeney, S.K., Druker, B.J. 2018. Functional genomic landscape of acute myeloid leukaemia. Nature 562:526-531. PMC6280667

Wiest, D.L. 2018. Gadd45 stress sensors in suppression of leukemia. Oncotarget 28:34191-34192. PMC6188131

Isoda, T., Moore, A.J., He, Z., Chandra,V., Aida, M., Denholtz, M., van Hamburg, J.P., Fisch, K.M., Chang, A.N., Fahl, S., Wiest, D.L., Murre, C.  2017. Non-Coding RNA ThymoD Regulates Compartmentalization and Chromatin Folding to Orchestrate T Cell Fate. Cell 171:103-119. PMC5621651

Somech, R., Lev, A., Lee, Y.N., Simon, A.J., Barel, O., Schiby, G., Avivi, C., Barshack, I., Rhodes, M., Yin, J., Wang, M., Yang, Y., Rhodes, J., Marcus, N., Garty, B.-Z., Stein, J., Amariglio, N., Rechavi, G., Wiest, D.L*, and Zhang, Y*. 2017 Disruption of thrombocyte and T lymphocyte development by a mutation in ARPC1B. J. Immunol. 199:4036-4045. * - co-corresponding authors; PMC5726601

Wiest, D.L. 2017. Themis-tery is solved. Nat. Immunol., 18: 368-370. PubMed

Zhang, Y., O’Learly, M.N., Peri, S., Zha, J., Melov, S., Kappes, D.J., Feng, Q., Rhodes, J., Amieux, P.S., Morris, D.R., Kennedy, B.K., and Wiest, D.L. 2017. Ribosomal proteins Rpl22 and Rpl22l1 control morphogenesis by regulating pre-mRNA splicing. Cell Reports 18:545-556. PMC5234864

Fahl, S.P., Coffey, F., MacCormick, D, and Wiest, D.L. 2016. Control of T cell development by TCR signals. Encyclopedia of Immunology Vol. 1:234–241. PubMed

Fahl, S.P., Kappes, D.J., and Wiest, D.L. 2016. TCR signaling circuits in αβ/γδ T lineage choice. In, CRC Methods in Signal Transduction: T cell diversity and function. CRC Press. Editors: Jonathan Soboloff and Dietmar J. Kappes. PubMed

Punwani, D.*, Zhang, Y.*, Yu, J., Cowan, M.J., Kwan, A., Mendelsohn, B.A., Sunderam, U. Srinivasan, R., Brenner, S., Wiest, D.L.*, and Puck, J.M.* 2016. Bcl11b defect in human severe combined immunodeficiency with multisystem anomalies. NEJM 375:2165-2176. PMC5215776 *Contributed equally; Selected for preview; Nominated to F1000. PubMed

Rao, S., Cai, K.Q., Stadanlick, J.E., Greenberg-Kushnir, N., Solanki-Patel, N., Lee, S.-Y., Testa, J.R., and Wiest, D.L. 2016. Ribosomal protein Rpl22 controls the dissemination of T cell Lymphoma. Cancer Research 76:3387-3396. PMC4891229

Simon, A.J., Lev, A., Zhang, Y., Weiss, B., Rylova, A., Eyal, E., Kol, N., Barel, O., Cesarkas, K., Soudack, M., Greenberg-Kushnir, N., Rhodes, N., Wiest, D.L., Schiby, G., Barshack, I., Katz, S., Pras, E., Poran, H., Reznik-Wolf, H., Ribakovsky, E., Simon, C., Hazou, W., Sidi, Y., Lahad, A., Katzir, H., Glousker, G., Amariglio, N., Tzfati, Y., Selig, S., Rechavi, G., and Somech, R. 2016. Mutations in stn1 cause coats plus syndrome and are associated with genomic and telomere defects. J. Exp. Med. 213:1429-1440. PMC4986528

Solanki, N.R., Stadanlick, J.E., Zhang, Y., Duc, A.-C., Lee, S.-Y., Lauritsen, J.P.H., Zhang, Z., and Wiest, D.L. 2016. Rpl22 loss selectively impairs αβ T cell development by dysregulating ER stress signaling. J. Immunol. 197:2280-9. PMC5011012 Highlighted in “In This Issue”. PubMed... Expand

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