News Release
September 10, 2015

Blood Cancers Develop When Immune Cell DNA Editing Enzyme Hits Off-target Spots in the Genome, Penn Animal Study Finds

Team urges consideration of cutting-and-pasting errors when using enzymes for gene modification

PHILADELPHIA - Sometimes when the immune system makes small mistakes, the body amplifies its response in a big way: Editing errors in the DNA of developing T and B cells can cause blood cancers. Now, researchers from the Perelman School of Medicine, University of Pennsylvania have shown that when the enzyme key to cutting and pasting segments of DNA hits so-called “off-target” spots on a chromosome, the development of immune cells can lead to cancer in animal models. Knowing the exact nature of these editing errors will be helpful in designing therapeutic enzymes based on these molecular scissors. The Penn team’s findings appear online this week in Cell Reports ahead of the print issue.

V(D)J recombinase, the editing enzyme that generates specific receptors on the surface of immune cells that match foreign invaders, collectively called antigens, can miss its target from time to time. The lab of senior author David Roth, MD, PhD, chair of the Department of Pathology and Laboratory Medicine, has been working out the cancer-related intricacies of V(D)J recombinase for the last two decades. “Knowledge of the exact nature of these off-target errors could lead to the development of safer versions of tools for genetic engineering,” Roth said.

V(D)J recombinase works only during the early stages of immune cell maturation. From this stage in the bone marrow, the diverse array of antibodies and cell-surface receptors found on immune B cells and T cells, respectively, are made to counteract all the foreign invaders the human body encounters.

Breaks in DNA strands associated with V(D)J cutting are normally repaired with high fidelity by finely tuned molecular machinery. Previous studies from the Roth lab showed that V(D)J recombinase (consisting of the RAG1 and RAG2 proteins) normally sends a break in DNA down the correct repair path by preventing access to other, inappropriate repair mechanisms. This shepherding process can be disabled if the “C” terminus of the RAG2 protein subunit is removed. This causes genomic instability in developing immune cells and, in the absence of a working tumor suppressor protein such as p53, an aggressive form of lymphoma develops in mice.

Genome wide analysis of lymphomas of the thymus in these mice with the truncated Rag2 protein revealed a surprise: numerous off-target DNA rearrangements, causing deletions, noted Roth. Previous work had suggested that a different mistake -- chromosome translocations, or swaps between two chromosomes -- might underlie  the development of lymphoma in these mice, but whole genome sequencing revealed deletions as the main drivers of these cancers.

These rearrangements affected several known and suspected oncogenes and tumor suppressor genes, including Notch1, Pten, Ikzf1, Jak1, Phlda1, Trat1, and Agpat9.

Genomewide analysis of chromatin marks also suggested that normal interactions between the C-terminus of the Rag2 protein subunit and a specific chromatin modification helps maintain the fidelity of DNA target recognition by the enzyme. Gene expression is regulated by epigenetic chemical modifications (including methylation and acetylation) on chromatin – histone proteins tightly associated with DNA. Certain chemical groups on histones allow DNA to open up, and others to tighten the chromatin, and so creating availability to be read and expressed as proteins. 

What’s more, say the researchers, the cancer-causing effects of off-target deletions mistakenly created by the V(D)J enzyme need to be considered in designing site-specific enzymes for genome modification such as zinc-finger nucleases, TALENS, or CRISPRs.

Co-senior author Susanna M. Lewis, Martina Mijušković, Yi-Fan Chou, Vered Gigi, Cory R. Lindsay, and Olga Shestova, all from Penn, are also on the Cell Reports paper.

The work was funded by the National Cancer Institute (CA-104588, PN1EY018244, 1R21AI097825-01)

Penn Medicine is one of the world's leading academic medical centers, dedicated to the related missions of medical education, biomedical research, and excellence in patient care. Penn Medicine consists of the Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania (founded in 1765 as the nation's first medical school) and the University of Pennsylvania Health System, which together form a $5.3 billion enterprise.

The Perelman School of Medicine has been ranked among the top five medical schools in the United States for the past 18 years, according to U.S. News & World Report's survey of research-oriented medical schools. The School is consistently among the nation's top recipients of funding from the National Institutes of Health, with $373 million awarded in the 2015 fiscal year.

The University of Pennsylvania Health System's patient care facilities include: The Hospital of the University of Pennsylvania and Penn Presbyterian Medical Center -- which are recognized as one of the nation's top "Honor Roll" hospitals by U.S. News & World Report -- Chester County Hospital; Lancaster General Health; Penn Wissahickon Hospice; and Pennsylvania Hospital -- the nation's first hospital, founded in 1751. Additional affiliated inpatient care facilities and services throughout the Philadelphia region include Chestnut Hill Hospital and Good Shepherd Penn Partners, a partnership between Good Shepherd Rehabilitation Network and Penn Medicine.

Penn Medicine is committed to improving lives and health through a variety of community-based programs and activities. In fiscal year 2015, Penn Medicine provided $253.3 million to benefit our community.

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