J. Keith Joung, MD, PhD

Joung Laboratory

“Genome-editing nuclease technologies have important applications in biological research and gene therapy…”

Overview

Program Affiliations

Research Resources

J. Keith Joung, MD, PhD

Professor of Pathology, Harvard Medical School
Associate Chief of Pathology (Research) and
The Jim and Ann Orr MGH Research Scholar,
Massachusetts General Hospital

Molecular Pathology Unit
Massachusetts General Hospital
149 13th Street, 6th Floor
Charlestown, MA 02129
Phone: 617-726-9462

Overview

The Joung laboratory is developing strategies to reprogram the genome and epigenome of living cells to better understand biology and treat disease.  We have developed and optimized molecular tools for customized genome editing that enable scientists to alter the DNA sequence of a living cell—from fruit flies to humans—with great precision. These technologies are based on proteins engineered to recognize and cleave specific genomic sequences.  We also use these targeting methodologies to enable activation, repression, or alteration of histone modifications of specific genes. These tools have many potential research uses and may one day lead to more efficient gene therapy capable of correcting disease-related mutations in human cells.

Genome Editing Using Targeted Nucleases


Genome editing technology using CRISPR-Cas9 nucleases was recently named “Breakthrough of the Year” for 2015 by Science magazine. Much of our recent work with genome-editing nucleases has focused on CRISPR-Cas9. We and our collaborators were the first to demonstrate that these nucleases can function in vivo (Hwang & Fu et al., Nat Biotechnol. 2013), modifying endogenous genes in zebrafish embryos and the first to show that they can induce significant off-target mutations in human cells (Fu et al., Nat Biotechnol. 2013). We recently developed GUIDE-seq, an unbiased, genome-wide method for sensitive detection of CRISPR-Cas9-induced off-target mutations in human cells (Tsai et al., Nat Biotechnol. 2015). Using structure-guided design, we have engineered “high-fidelity” Cas9 variants that robustly fail to show detectable genome-wide off-targets as judged by GUIDE-seq (Kleinstiver & Pattanayak et al., Nature 2016). Finally, we used a combination of structure-guided design and molecular evolution to engineer Cas9 variants with novel DNA binding specificities, thereby broadening the targeting range and applications of this platform (Kleinstiver et al., Nature 2015).


Epigenome Editing Using Targeted Transcription Factors


We have also demonstrated that the TALE and CRISPR platforms can also be utilized to create artificial transcription factors that can robustly alter expression of endogenous human genes (Maeder et al., Nat Methods 2013a; Maeder et al., Nat Methods 2013b). In addition, we have collaborated with Brad Bernstein’s group to develop fusions of the histone demethylase LSD1 with TALE domains that can induce targeted histone alterations at endogenous human enhancers (Mendenhall et al., Nat Biotechnol. 2013).  Finally, we have also developed fusions of engineered TALE domains with the catalytic domain of the TET1 enzyme, enabling the targeted demethylation of CpGs in human cells (Maeder et al., Nat Biotechnol. 2013).

Read more about the Joung Lab from Pathology Basic Science Research Brochure.

Read the Bardeesy Lab's Annual Report in Full

Pathology research report

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Group Members

Lab Members

Maggie Bobbin, PhD Fellow
Ben Kleinstiver, PhD Fellow
Yu Gyoung (Esther) Tak, PhD Fellow
Stacy Francis Lab Manager
Jose Malagon-Lopez, PhD  Bioinformatician
James Angstman PhD student, Harvard MCB
Rebecca Cottman PhD student, Harvard BBS
Jason Gehrke PhD student, Harvard MCB
Ibrahim Cagri Kurt PhD student, Harvard School of Public Health
Jingyi Gong MD/PhD student, Harvard/MIT
Alex Sousa Research Technician II
Moira Welch Research Technician I
Jimmy Guo Research Technician I
Oliver Cervantes Research Technician I
Jackson Allen undergraduate student
Stephanie Yeh undergraduate student

 

Research Projects

 

 The Joung Laboratory develops technologies for genome and epigenome engineering of living cells and organisms using engineered zinc finger, transcription activator-like effector (TALE), and RNA-guided CRISPR-Cas9-based systems and explores their applications for biological research and gene therapy.

Genome Editing Using Targeted Nucleases

Genome editing technology was recently named runner-up for "Breakthrough of the Year" for 2012 and 2013 bySciencemagazine and "Method of the Year" for 2011 byNature Methods. We have previously invented two rapid, robust, and publicly available methods for engineering ZFNs known as OPEN (Oligomerized Pool Engineering; Maeder et al.,Mol Cell2008) and CoDA (Context-Dependent Assembly; Sander et al.,Nat Methods2011). In addition, we have also developed and optimized methods for engineering TALENs including an automated, high-throughput method known as FLASH (Fast Ligation-based Automated Solid-phase High-throughput) assembly (Reyon et al.,Nat Biotechnol.2012). We have also recently described reagents that enable the rapid construction of CRISPR-Cas9 nucleases(Hwang et al.,Nat Biotechnol.2013).

Much of our recent work with genome-editing nucleases has focused on CRISPR-Cas9. We and our collaborators were the first to demonstrate that these nucleases can functionin vivo(Hwang & Fu et al.,Nat Biotechnol. 2013), modifying endogenous genes in zebrafish and the first to show that they can induce significant off-target mutations in human cells (Fu et al.,Nat Biotechnol.2013). To improve the specificities of these nucleases, we have developed two platforms that show greatly reduced off-target effects: one based on the use of truncated guide RNAs (Fu & Sander et al.,Nat Biotechnol.2014) and the other in which we engineered dimerization-dependent CRISPR-Cas9 nucleases (Tsai et al.,Nat Biotechnol. 2014). We recently developed GUIDE-seq, an unbiased, genome-wide method for sensitive detection of CRISPR-Cas9-induced off-target mutations (Tsaiet al.,Nat Biotechnol. 2015). We have also evolved Cas9 variants with novel DNA binding specificities, thereby broadening the targeting range and applications of this platform (Kleinstiver et al.,Nature2015).

Epigenome Editing Using Targeted Transcription Factors

We have recently demonstrated that the TALE and CRISPR RGN platforms can also be utilized to create artificial customizable transcription factors that can robustly alter expression of endogenous human genes (Maeder et al.,Nat Methods2013a; Maeder et al.,Nat Methods2013b). In addition, we have collaborated with the group of Brad Bernstein to develop fusions of the histone demethylase LSD1 with TALE domains that can induce targeted histone alterations at endogenous human enhancers (Mendenhall et al.,Nat Biotechnol. 2013). Finally, we have also developed fusions of engineered TALE domains with the catalytic domain of the TET1 enzyme, enabling the targeted demethylation of CpGs in human cells (Maeder et al.,Nat Biotechnol.2013). We are exploring the use of these and other proteins in both a directed fashion as well as with combinatorial libraries to induce specific phenotypes and cellular states in human cells.

For more information about research concepts, co-authors, and to see a timeline, see Dr. Joung's research profile at the Harvard Clinical and Translational Science Center.

 

Research Positions

Find information by visiting the Harvard Medical School Molecular Genetic Pathology Training Program, and other Pathology fellowship programs at the Massachusetts General Hospital.

Selected Publications

Bibliography of J. Keith Joung via PubMed 

Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, Joung JK. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature. 2016; 529(7587): 490-5.
Tsai SQ, Joung JK. Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases. Nat Rev Genet. 2016; 17(5): 300-12. Review

Kleinstiver BP, Prew MS, Tsai SQ, Nguyen NT, Topkar VV, Zheng Z, Joung JK. Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition. Nat Biotechnol. 2015; 33(12): 1293-1298.

Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JR, Aryee MJ, Joung JK. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature. 2015; 523(7561): 481-5.

Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ, Joung JK. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol. 2015; 33(2): 187-97.

Contact

Contact Us

Joung Laboratory

Massachusetts General Hospital

149 13th Street, 6th Floor Charlestown, MA 02129
  • Phone: 617-726-9462
  • Fax: 617-726-5684

Email: jjoung@partners.org

Back to Top