Baeck-Seung Lee, Ph.D.

Education

• Post-doc., Immunology/Pathology, Washington University in St Louis, 2008 - 2014.

                                    

• Ph.D., Molecular Biology, University of Texas at Austin, 2007

Dissertation: Functional Characterization of the B-cell Lymphoma/Leukemia 11A (BCL11A) Transcription Factor

• M.S., Genetic Engineering, Korea University, Seoul, Korea, 1997

Dissertation: Cloning and Sequencing of cDNA Encoding Antibacterial peptides from a Korean Frog

• B.S., Genetic Engineering, Korea University, Seoul, Korea, 1995

                       

Experience

• Research Scientist, since 2014

Bluebirdbio.com (Seattle, Massachusetts)

Project: Genome editing with ZFN, CRISPR and megaTAL and CAR-T cell engineering with AAV and LV

Role: Test refined megaTAL nucleases for cleavage activity and homology directed repair (HDR) in collaboration with protein engineering teams. Design new AAV donors and develop strategies for higher HDR. Collaborate with virus and RNA production teams to enhance mRNA quality and viral titers. Develop the inducible gene expression system in CAR-T cells and transfer it to another team.

• Post-doc and Staff Scientist, 2008 – 2014

Washington University in St Louis

     Project: DNA repair during V(D)J recombination, Genome editing to make an inducible double strand DNA cleavage/repair system,  Double strand DNA damage response, and Immunology for B cell development

    Role: Develop research ideals and carry out experiments. Supervise and guide graduate students and lab technicians.

• Teaching Assistant, 2007, 2004

University of Texas at Austin (Course: General Microbiology Lab)

• Teaching Assistant, 2003

University of Texas at Austin (Course: Molecules to Organisms)

• Research Scientist, 1999

Clinical Research Center at Seoul National University in Korea

Project: Development of Bio-Artificial Liver Using Pig Hepatocytes

Role: Construct in-house the Bio-Artificial Liver based on previous publications. Coordinate the whole processes from cell isolation, construction and running of the unit, operation, and lab assays.

• Research Scientist, 1998

Cell Death Research Center at Korea University in Korea

Project: Study kinase and caspase activation during apoptosis

Publication

1. Malika Hale, Baeckseung Lee,Yuchi Honaker, Wai-Hang Leung, Alexandra E. Grier, Holly M. Jacobs, Karen Sommer, Jaya Sahni, Shaun W. Jackson, Andrew M. Scharenberg, Alexander Astrakhan, and David J. Rawlings. Homology-Directed Recombination for Enhanced Engineering of Chimeric Antigen Receptor T Cells. Molecular Therapy. 2017 Mar. Vol. 4
2. Dorsett Y, Zhou Y, Tubbs AT, Chen BR, Purman C, Lee BS, George R, Bredemeyer AL, Zhao JY, Sodergen E, Weinstock GM, Han ND, Reyes A, Oltz EM, Dorsett D, Misulovin Z, Payton JE, Sleckman BP. HCoDES reveals chromosomal DNA end structures with single-nucleotide resolution. Mol Cell. 2014 Dec 18;56(6):808-18.
3. Tubbs AT, Dorsett Y, Chan E, Helmink B, Lee BS, Hung P, George R, Bredemeyer AL, Mittal A, Pappu RV, Chowdhury D, Mosammaparast N, Krangel MS, Sleckman BP. KAP-1 promotes resection of broken DNA ends not protected by γ-H2AX and 53BP1 in G₁-phase lymphocytes. Mol Cell Biol. 2014 Aug;34(15):2811-21.
4. Ippolito GC, Dekker JD, Wang YH, Lee BK, Shaffer AL 3rd, Lin J, Wall JK, Lee BS, Staudt LM, Liu YJ, Iyer VR, Tucker HO. Dendritic cell fate is determined by BCL11A.  Proc Natl Acad Sci U S A. 2014 Mar 18;111(11).
5. Um JH, Brown AL, Singh SK, Chen Y, Gucek M, Lee BS, Luckey MA, Kim MK, Park JH, Sleckman BP, Gellert M, Chung JH. metabolic sensor AMPK directly phosphorylates RAG1 protein and regulates V(D)J recombination. Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):9873-8.
6. Baeck-Seung Lee, Eric J. Gapud, Shichuan Zhang, Yair Dorsett, Andrea Bredemeyer, Rosmy George, Elsa Callen, Jeremy A. Daniel, Oleg Osipovich, Eugene M. Oltz, Craig H. Bassing, Andere Nussenzweig, Susan Lees-Miller, Michal Hammel. Benjamin P.C. Chen and Barry P. Sleckman. Functional Intersection of ATM and DNA-PKcs Kinase Activities During V(D)J Recombination. tle="Molecular and cellular biology.">Mol Cell Biol. 2013 Sep;33(18):3568-79.
7. Baeck-Seung Lee, Joseph Dekker, Bum-Kyu Lee, Vishwanath Iyer, Barry Sleckman, Arthur Shaffer, Gregory Ippolito, and Philip Tucker. BCL11A Is a Critical Component of a Transcriptional Network That Activates RAG expression and V(D)J Recombination. Mol Cell Biol. 2017 Dec 13;38(1). pii: e00362-17.
8. Natalie C. Steinel*, Baeck-Seung Lee*, Anthony T. Tubbs, Jeffrey J. Bednarski, Emily Schulte, Katherine S. Yang-Iott, David G. Schatz, Barry P. Sleckman, and Craig H. Bassing (* equally contributed).  The Ataxia Telangiectasia Mutated Kinase Controls Igκ Allelic Exclusion by Inhibiting Secondary Vκ-to-Jκ Rearrangement. J Exp Med. Jan 2013.
9. Gapud EJ*, Lee BS*, Mahowald GK, Bassing CH, Sleckman BP (* equally contributed).  Repair of chromosomal RAG-mediated DNA breaks by mutant RAG proteins lacking phosphatidylinositol 3-like kinase consensus phosphorylation sites. J Immunol. 2011 Aug 15;187:1826.
10. Jeremy A. Daniel, Manuela Pellegrini, Baeck-Seung Lee, Zhi Guo, Darius Filsuf, Natalya V. Belkina, Zhongsheng You, Tanya T. Paull, Barry P. Sleckman, Lionel  Feigenbaum and André Nussenzweig.  Loss of ATM kinase activity leads to embryonic lethality in mice.  J Cell Biol. 2012 Aug6;198:295.
    11.    Yin B, Lee BS, Yang-Iott KS, Sleckman BP, Bassing CH. Redundant and nonredundant functions of ATM and H2AX in αβ T-lineage lymphocytes. J Immunol. 2012 Aug 1:189:1372.
     
11. Helmink BA, Bredemeyer AL, Lee BS, Huang CY, Sharma GG, Walker LM, Bednarski JJ, Lee WL, Pandita TK, Bassing CH, Sleckman BP. MRN complex function in the repair of chromosomal Rag-mediated DNA double-strand breaks. J Exp. Med. 2009 Mar 16;206;669.
12. Liu H, Ippolito GC, Wall JK, Niu T, Probst L, Lee BS, Pulford K, Banham AH, Stockwin L, Shaffer AL, Staudt LM, Das C, Dyer MJ, Tucker PW. Functional studies of BCL11A: characterization of the conserved BCL11A-XL splice variant and its interaction with BCL6 in nuclear paraspeckles of germinal center B cells. Mol Cancer. 2006 May 16;5;18.

Patent

1. Main inventor of novel AAV designs for homology directed repair (two patents are filed)
2. Co-inventor for several megaTAL nucleases used for genome editing

Research Skills

Genome Editing and Gene Therapy

 ; Genomic DNA editing or modification using Zinc finger nuclease, Crispr/cas9, and megaTAL

AAV and mRNA production for homology directed repair (HDR)

LV production, purification, and concentration

Screening and subcloning of genome edited cells

DNA and RNA

 ; Gene expression or silencing using plasmid, retrovirus, lentivirus and siRNA.

 RT-PCR, qPCR, In vitro transcription/translation, EMSA, Northern blot and Southern blot, RNase protection assay, and Microarray.

cDAN library construction, DNA fragmentation assays for cell death, Chromatin immunoprecipitation (ChIP).

Inducible protein expressions using Shield, Tet, or Hormone receptors.

Protein

; ELISA, Western blot, whole cell labeling and kinase assay and Co-immunoprecipitation. Cytokine release assay, Tandem affinity purification for Mass-spec, expression of GST, His, MBP fusion proteins and isolation.

Rabbit antibody production, Monoclonal antibody purification from a hybridoma culture. Electroporation and Chemical or Nanoparticle transfection for gene expression.

Cell

 ; Cell line construction using virus or editing, Sterile transformed and primary cell culture, A small bioreactor and 3D cell cultures.

Inhibitor treatments of ATM, DNA-PKcs, Abl kinases, and PARP1 for gene expression, cell death and DNA repair.

In vitro cell differentiation of B and T cells using cytokines and co-culture.

Luciferase assay, Cell isolation and in vitro culture from mouse and pig.

FACS analysis, cell sorting using Aria or Magnetic beads.

Genome editing experience and plan

• Design, cloning, purification (column and ultracentrifugation), and concentration.
• Checking the integrity of viruses using various molecular biology assays, such as sequencing, FACS, WB, Sothern blot and qPCR.
• Stable cell line constructions using LV.
• Apply the purified LV and AAV for genome editing and gene therapy.
• A novel AAV vector construction for more efficient genome editing
• Genome editing ideas of cell line construction to make packaging cell lines
• LV and AAV are produced and used for gene expression and CAR-T experiment.

• I have very extensive hands on experience in molecular biology, genome editing, immunology and gene therapy.
• I would like to expand my expertise into scalable bioprocessing and am interested in novel approaches for virus design and production, because there are unmet problems of AAV such as efficient producer cell line or increasing encoding capacity.

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