Sign in to edit your profile (add interests, mentoring, photo, etc.)
    Keywords
    Last Name
    Institution

    Scot Wolfe PhD

    TitleAssociate Professor
    InstitutionUniversity of Massachusetts Medical School
    DepartmentMolecular, Cell and Cancer Biology
    AddressUniversity of Massachusetts Medical School
    364 Plantation Street, LRB-619
    Worcester MA 01605
    Phone508-856-3953
      Other Positions
      InstitutionUMMS - School of Medicine
      DepartmentBiochemistry and Molecular Pharmacology

      InstitutionUMMS - School of Medicine
      DepartmentProgram in Molecular Medicine

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentBioinformatics and Integrative Biology

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentChemical Biology

        Overview 
        Narrative

        Academic Background

        Scot Wolfe received his B.S. in Chemistry and Biology from Caltech in 1990, and his Ph.D. from Harvard in Chemistry in 1996. From 1996-2001 he was a post-doctoral fellow at Massachusetts Institute of Technology where his work was supported in part by the Leukemia and Lymphoma Society. In 2001, Dr. Wolfe joined the faculty of UMMS.

         

         

         

        Engineering precise gene editing systems for application in gene therapy and the analysis of gene regulatory networks

        Scot Wolfe My research program is focused on four inter-related areas:

        • Understanding fundamental aspects of protein-DNA recognition
        • Engineering programmable nucleases for the targeted cleavage of a single site within a vertebrate genome for gene therapy
        • Applying programmable nucleases to interrogate gene regulatory networks
         
        Protein-DNA recognition - Our research on protein-DNA recognition is focused primarily on two of the most abundant families of DNA-binding domains in metazoans (see our lab website for more details labs.umassmed.edu/WolfeLab ):

        Cys2His2 Zinc fingers & Homeodomains

        We have recently performed comprehensive analysis of homeodomain and Cys2His2 zinc finger specificities in D. melanogaster – (fruit fly) in collaboration with Michael Brodsky (UMMS-MCCB) & Gary Stormo (Wash. U). We have coupled this data with specificity data from artificial zinc fingers and homeodomains that we have selected using our bacterial one-hybrid system.  Using this information we can build simple qualitative models of recognition that allow the design of homeodomains with novel DNA-binding specificity.  This dataset can also be used to broadly predict the specificity of homeodomains (http://ural.wustl.edu/flyhd) and zinc fingers (http://stormo.wustl.edu/ZFModels/).  We continue to explore aspects of DNA recognition by these DNA-binding domain families to both more broadly and accurately predicting the specificity of naturally-occurring family members in all species and for rationally engineering the specificity of these DNA-binding domains.
         
        ZFNs/TALENs/Cas9 in Zebrafish - We are collaborating with Nathan Lawson (UMMS – MCCB) to develop new and improved tools for genome engineering in zebrafish.  We have used ZFNs, TALENs and Cas9 to make targeted knockouts of a number of genes of interest.  We are currently studying the function of miR-375 in pancreas development in the zebrafish to understand its function in the differentiation of alpha and beta cells of the endocrine pancreas.  
         
        Utilizing CRISPR/Cas9 to understand transcriptional regulatory networks in dendritic cells - We are collaborating with a team lead by Jeremy Luban (UMMS – PMM) and Manuel Garber (UMMS – BIB) to exploit recent technical advances in stem cell biology, reverse-genetic tools for primary human cells, and genome-wide assessment of transcripts, local chromatin features and long-range chromatin interactions to construct a model for the transcriptional regulatory network that underlies pathogen detection and maturation in human dendritic cells. We are utilizing CRISPR/Cas9 to modify transcription factors and regulatory elements that may underlie regulatory responses within these processes.  
         
        Utilizing CRISPR/Cas9 to inactivate latent HIV provirus in reservoir cells - We are collaborating with Jeremy Luban (UMMS – PMM) to lead a team that is investigating the chromatin architecture of latent HIV provirus in reservoir cells.  This data will be used to develop precise Cas9 nucleases and corresponding delivery systems to selectively inactivate provirus in reservoir cells to provide a path toward a functional cure for HIV.  
         
        B1H selection systems - We continue to develop a bacterial one-hybrid system for rapidly characterizing the DNA-binding specificities of sequence-specific transcription factors, both naturally-occurring and engineered. Using this technology have characterized >50% all of the sequence-specific transcription factors in the D. melanogaster genome (FlyFactorSurvey) in collaboration with the laboratory of Michael Brodsky (UMMS – MCCB). This dataset is being used to unravel transcription factor regulatory networks within the fly in collaboration with Saurabh Sinha (UI-Urbana Champaign). We have already begun building computational tools to allow the scientific community to identify cis-regulatory modules using clusters of phylogenetically conserved binding sites for these TFs in the fly genome that we have characterized to date (GenomeSurveyor -biotools.umassmed.edu/genomesurveyor).
         

         

         

         

         

         



        Rotation Projects

         

         

        Potential Rotation Projects

        Improving the Precision of CRISPR/Cas9 nucleases for gene therapy applications:

        We are working to improve the precision of the CRISPR/Cas9 system to generate nucleases that will cleave at only a single site in the genome.  These engineering efforts focus on increasing the DNA-binding precision of Cas9 and incorporating systems that will make cleavage drug-dependent.  These modified nucleases will then be applied to cell-culture systems for the targeted repair or inactivation of disease-causing alleles, or the inactivation of HIV proviral genomes.



        Potential Rotation Projects

        Optimization of the Zinc Finger Nuclease framework and the creation of disease models in zebrafish:

        Zinc finger nucleases hold tremendous potential for site-specifically editing genomes in a variety of organisms. Their utility, however, is predicated on the ability to efficiently create sequence-specific zinc finger proteins (ZFPs) for a wide variety of target sequences. My laboratory is focused on the creation of improved zinc finger modules for DNA recognition, improved chimeric frameworks to broadennuclease activity, and the application of these artificial nucleases to construct disease models in zebrafish.



        Bibliographic 
        selected publications
        List All   |   Timeline
        1. Weicksel SE, Gupta A, Zannino DA, Wolfe SA, Sagerström CG. Targeted germ line disruptions reveal general and species-specific roles for paralog group 1 hox genes in zebrafish. BMC Dev Biol. 2014; 14:25.
          View in: PubMed
        2. Gupta A, Christensen RG, Bell HA, Goodwin M, Patel RY, Pandey M, Enuameh MS, Rayla AL, Zhu C, Thibodeau-Beganny S, Brodsky MH, Joung JK, Wolfe SA, Stormo GD. An improved predictive recognition model for Cys2-His2 zinc finger proteins. Nucleic Acids Res. 2014 Apr 1; 42(8):4800-12.
          View in: PubMed
        3. Kearns NA, Genga RM, Enuameh MS, Garber M, Wolfe SA, Maehr R. Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells. Development. 2014 Jan; 141(1):219-23.
          View in: PubMed
        4. Kok FO, Gupta A, Lawson ND, Wolfe SA. Construction and application of site-specific artificial nucleases for targeted gene editing. Methods Mol Biol. 2014; 1101:267-303.
          View in: PubMed
        5. Cheng Q, Kazemian M, Pham H, Blatti C, Celniker SE, Wolfe SA, Brodsky MH, Sinha S. Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. PLoS Genet. 2013; 9(8):e1003571.
          View in: PubMed
        6. Kazemian M, Pham H, Wolfe SA, Brodsky MH, Sinha S. Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development. Nucleic Acids Res. 2013 Sep; 41(17):8237-52.
          View in: PubMed
        7. Gupta A, Hall VL, Kok FO, Shin M, McNulty JC, Lawson ND, Wolfe SA. Targeted chromosomal deletions and inversions in zebrafish. Genome Res. 2013 Jun; 23(6):1008-17.
          View in: PubMed
        8. Enuameh MS, Asriyan Y, Richards A, Christensen RG, Hall VL, Kazemian M, Zhu C, Pham H, Cheng Q, Blatti C, Brasefield JA, Basciotta MD, Ou J, McNulty JC, Zhu LJ, Celniker SE, Sinha S, Stormo GD, Brodsky MH, Wolfe SA. Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res. 2013 Jun; 23(6):928-40.
          View in: PubMed
        9. Zhu C, Gupta A, Hall VL, Rayla AL, Christensen RG, Dake B, Lakshmanan A, Kuperwasser C, Stormo GD, Wolfe SA. Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases. Nucleic Acids Res. 2013 Feb 1; 41(4):2455-65.
          View in: PubMed
        10. Merlin C, Beaver LE, Taylor OR, Wolfe SA, Reppert SM. Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases. Genome Res. 2013 Jan; 23(1):159-68.
          View in: PubMed
        11. Anderson DM, George R, Noyes MB, Rowton M, Liu W, Jiang R, Wolfe SA, Wilson-Rawls J, Rawls A. Characterization of the DNA-binding properties of the Mohawk homeobox transcription factor. J Biol Chem. 2012 Oct 12; 287(42):35351-9.
          View in: PubMed
        12. Shin J, Padmanabhan A, de Groh ED, Lee JS, Haidar S, Dahlberg S, Guo F, He S, Wolman MA, Granato M, Lawson ND, Wolfe SA, Kim SH, Solnica-Krezel L, Kanki JP, Ligon KL, Epstein JA, Look AT. Zebrafish neurofibromatosis type 1 genes have redundant functions in tumorigenesis and embryonic development. Dis Model Mech. 2012 Nov; 5(6):881-94.
          View in: PubMed
        13. Christensen RG, Enuameh MS, Noyes MB, Brodsky MH, Wolfe SA, Stormo GD. Recognition models to predict DNA-binding specificities of homeodomain proteins. Bioinformatics. 2012 Jun 15; 28(12):i84-9.
          View in: PubMed
        14. Gupta A, Christensen RG, Rayla AL, Lakshmanan A, Stormo GD, Wolfe SA. An optimized two-finger archive for ZFN-mediated gene targeting. Nat Methods. 2012 Jun; 9(6):588-90.
          View in: PubMed
        15. Chu SW, Noyes MB, Christensen RG, Pierce BG, Zhu LJ, Weng Z, Stormo GD, Wolfe SA. Exploring the DNA-recognition potential of homeodomains. Genome Res. 2012 Oct; 22(10):1889-98.
          View in: PubMed
        16. Zhu C, Smith T, McNulty J, Rayla AL, Lakshmanan A, Siekmann AF, Buffardi M, Meng X, Shin J, Padmanabhan A, Cifuentes D, Giraldez AJ, Look AT, Epstein JA, Lawson ND, Wolfe SA. Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish. Development. 2011 Oct; 138(20):4555-64.
          View in: PubMed
        17. Lawson ND, Wolfe SA. Forward and reverse genetic approaches for the analysis of vertebrate development in the zebrafish. Dev Cell. 2011 Jul 19; 21(1):48-64.
          View in: PubMed
        18. Christensen RG, Gupta A, Zuo Z, Schriefer LA, Wolfe SA, Stormo GD. A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity. Nucleic Acids Res. 2011 Jul; 39(12):e83.
          View in: PubMed
        19. Bussmann J, Wolfe SA, Siekmann AF. Arterial-venous network formation during brain vascularization involves hemodynamic regulation of chemokine signaling. Development. 2011 May; 138(9):1717-26.
          View in: PubMed
        20. Zhu LJ, Christensen RG, Kazemian M, Hull CJ, Enuameh MS, Basciotta MD, Brasefield JA, Zhu C, Asriyan Y, Lapointe DS, Sinha S, Wolfe SA, Brodsky MH. FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res. 2011 Jan; 39(Database issue):D111-7.
          View in: PubMed
        21. Gupta A, Meng X, Zhu LJ, Lawson ND, Wolfe SA. Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases. Nucleic Acids Res. 2011 Jan; 39(1):381-92.
          View in: PubMed
        22. Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH, Sinha S. Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol. 2010; 8(8).
          View in: PubMed
        23. Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, Wolfe SA, Giraldez AJ. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science. 2010 Jun 25; 328(5986):1694-8.
          View in: PubMed
        24. Siekmann AF, Standley C, Fogarty KE, Wolfe SA, Lawson ND. Chemokine signaling guides regional patterning of the first embryonic artery. Genes Dev. 2009 Oct 1; 23(19):2272-7.
          View in: PubMed
        25. Marx RG, Fives G, Chu SK, Daluiski A, Wolfe SW. Allograft reconstruction for symptomatic chronic complete proximal hamstring tendon avulsion. Knee Surg Sports Traumatol Arthrosc. 2009 Jan; 17(1):19-23.
          View in: PubMed
        26. Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell. 2008 Jun 27; 133(7):1277-89.
          View in: PubMed
        27. Meng X, Noyes MB, Zhu LJ, Lawson ND, Wolfe SA. Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat Biotechnol. 2008 Jun; 26(6):695-701.
          View in: PubMed
        28. Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA. A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res. 2008 May; 36(8):2547-60.
          View in: PubMed
        29. Meng X, Thibodeau-Beganny S, Jiang T, Joung JK, Wolfe SA. Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method. Nucleic Acids Res. 2007; 35(11):e81.
          View in: PubMed
        30. Meng X, Smith RM, Giesecke AV, Joung JK, Wolfe SA. Counter-selectable marker for bacterial-based interaction trap systems. Biotechniques. 2006 Feb; 40(2):179-84.
          View in: PubMed
        31. Meng X, Wolfe SA. Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system. Nat Protoc. 2006; 1(1):30-45.
          View in: PubMed
        32. Meng X, Brodsky MH, Wolfe SA. A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol. 2005 Aug; 23(8):988-94.
          View in: PubMed
        33. Wolfe SA. Mapping key elements of a protein motif. Chem Biol. 2004 Jul; 11(7):889-91.
          View in: PubMed
        34. Wolfe SA, Grant RA, Pabo CO. Structure of a designed dimeric zinc finger protein bound to DNA. Biochemistry. 2003 Nov 25; 42(46):13401-9.
          View in: PubMed
        For assistance with using Profiles, please refer to the online tutorials or contact UMMS Help Desk or call 508-856-8643.
        Scot's Networks
        Click the "See All" links for more information and interactive visualizations!
        Concepts
        _
        Co-Authors
        _
        Similar People
        _
        Same Department
        Physical Neighbors
        _

        This is an official Page/Publication of the University of Massachusetts Worcester Campus
        Office of the Vice Provost for Research, 55 Lake Ave North, Worcester, Massachusetts 01655
        Questions or Comments? Email: publicaffairs@umassmed.edu Phone: 508-856-1572