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Creating stem cell 'twins' to study disease
Researchers led by Dr. Knut Woltjen report a new gene editing technique that can modify a single DNA base on our human genome with absolute precision. This on a human genome containing approximately 3 billion base pairs, all crowded into the nucleus of a cell.
The technique is described in the journal Nature Communications. It is unique in that it guides the cell's own repair mechanisms to do the cutting, in order to provide scientists with pairs of genetically identical cells so that they can study gene mutations found in diseases.
Single mutations in DNA, known as single nucleotide polymorphisms - or SNPs for short - are the most common type of alteration found in our human genome. More than 10 million SNPs have been identified, many associated with disorders such as Alzheimer's, heart disease, and diabetes. In order to understand the role of SNPs in hereditary disease, scientists at the Kyoto University Center for iPS cell Research and Application (CiRA) create induced pluripotent stem cells from patient donors with these diseases.
iPS cells retain their original genetic makeup from their donor, and can be converted into any cell type in the body. So, cells from tissues such as the brain, heart, or pancreas can be created and observed in the laboratory to enable safe testing for disease treatments before use on patients in clinical trials.
Proving that a SNP causes disease requires very strict comparisons to genetically matched, or isogenic, iPS cells. These ideal cells are described as isogenic "twins" — cells whose genomes differ only by one SNP. But, according to Shin-Il Kim PhD, in the Woltjen lab and co-first author on the study, creating these twins is not easy. "Usually we need to add a gene for antibiotic resistance along with the SNP to overcome low efficiency [caused by the change]. Since that adds another change to the genome, we also need a way to remove it."
To create isogenic twins, the Woltjen team has developed new genome editing technology that inserts a SNP modification along with a fluorescent reporter gene, which acts as a signal to detect the modification. They also engineered a short duplicated DNA sequence, known as a microhomology, on the left and right sides of this fluorescent reporter gene, creating unique targets for the enzyme CRISPR to cut the DNA.
These features allow researchers to exploit an endogenous DNA repair system in the cell called microhomology-mediated end joining (MMEJ). MMEJ removes only the the fluorescent reporter gene, leaving the modified SNP behind.
By arranging the mutant SNP in one microhomology and the normal SNP in the other, the method efficiently generates isogenic twins.
CiRA Associate Professor Knut Woltjen PhD, calls the new gene editing method MhAX short for Microhomology-Assisted eXcision after observing naturally occurring MMEJ repair in response to DNA damage. Woltjen: "To make MhAX work, we duplicate DNA sequences which are already present in the genome. We then let the cells resolve this duplication. At the same time, the cells decide which SNPs will remain after repair. One experiment results in the full spectrum of possible SNP genotypes." The paper "Microhomology-assisted scarless genome editing in human iPSCs" appeared March 5, 2018 in Nature Communications
In collaboration with Dr. Takashi Yamamoto at Hiroshima University, and Dr. Tomoyoshi Soga of Keio University, the Woltjen lab used MhAX to create SNPs in the HPRT and APRT genes, mutations that are respectively associated with gout and kidney disease.
Biochemical analyses showed cells with the HPRT mutant SNP had altered metabolism similar to that observed in patients, while the isogenic twin control cells, derived in the same experiment, acted normally. The APRT*J mutation, often found in a population of Japanese patients with acute kidney failure, demonstrated the high efficiency of MhAX, as both gene copies (one from the mother and one from the father) required gene editing to study the mutation's effects.
Woltjen's lab has already begun applying their procedure to the creation and correction of SNPs in genes associated with other diseases. Collaborating with researchers in Japan and Canada, they are investigating the genetic cause of severe diabetes in juvenile patients.
Diabetes clinical trials using embryonic stem cells are currently underway, but chronic immune suppression is required for the use of these cells. Gene correction of the patient's own iPS cells could lead to a source of healthy insulin-producing pancreatic cells with a reduced chance of rejection following transplantation.
"Our goal is to generate gene editing technologies which improve our understanding of disease mechanisms, and ultimately lead to therapies. We're confident that MhAX will have broad applicability in current human disease research, and beyond."
Gene-edited induced pluripotent stem cells (iPSCs) provide relevant isogenic human disease models in patient-specific or healthy genetic backgrounds. Towards this end, gene targeting using antibiotic selection along with engineered point mutations remains a reliable method to enrich edited cells. Nevertheless, integrated selection markers obstruct scarless transgene-free gene editing. Here, we present a method for scarless selection marker excision using engineered microhomology-mediated end joining (MMEJ). By overlapping the homology arms of standard donor vectors, short tandem microhomologies are generated flanking the selection marker. Unique CRISPR-Cas9 protospacer sequences nested between the selection marker and engineered microhomologies are cleaved after gene targeting, engaging MMEJ and scarless excision. Moreover, when point mutations are positioned unilaterally within engineered microhomologies, both mutant and normal isogenic clones are derived simultaneously. The utility and fidelity of our method is demonstrated in human iPSCs by editing the X-linked HPRT1 locus and biallelic modification of the autosomal APRT locus, eliciting disease-relevant metabolic phenotypes.
Authors: Shin-Il Kim, Tomoko Matsumoto, Harunobu Kagawa, Michiko Nakamura, Ryoko Hirohata, Ayano Ueno, Maki Ohishi, Tetsushi Sakuma, Tomoyoshi Soga, Takashi Yamamoto & Knut Woltjen
About Center for iPS Cell Research and Application (CiRA)
CiRA was founded in 2008 and is devoted to the study of induced pluripotent stem cells (iPS cells) and other forms of cell reprogramming along with their medical applications. Since its inception, CiRA has been directed by Shinya Yamanaka, who earned the Nobel Prize in 2012 for his discovery of induced pluripotent stem cells (iPS cells). For more information, please see: https://www.cira.kyoto-u.ac.jp/e/index.html
Kyoto University is one of Japan and Asia's premier research institutions, founded in 1897 and responsible for producing numerous Nobel laureates and winners of other prestigious international prizes. A broad curriculum across the arts and sciences at both undergraduate and graduate levels is complemented by numerous research centers, as well as facilities and offices around Japan and the world. For more information please see: http://www.kyoto-u.ac.jp/en
Hiroshima University, which was established in 1874 as Hakushima School, comprises 11 faculties, 11 graduate schools, an attached research institute, a university hospital, and 11 attached schools. Based on its founding principle of "a single unified university, free and pursuing peace" and its five guiding principles, the University is committed to promoting advanced scientific research that benefits the future of humankind while fostering excellent human resources. For more information please see: https://www.hiroshima-u.ac.jp/en
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Artistic representation of stem cells with shared genetic information being 'cut' to aid study of human disease. Image credit: Kyoto University Neda Bagheri, Justin Finkle, and Jia Wu