Genome customization is now one of the most exciting, innovative, and quickly evolving areas of biomedical research. With the emergence of new technologies including TALENs and CRISPR/Cas9, mammalian genome editing is within the technical capabilities of the vast majority of skilled scientists. But, deploying the gene editing process is fraught with significant challenges and even the most skilled practitioners must rely on and benefit from proper planning and support to ensure that their experimental approach has a reasonable chance of success.

After 25 years as a pioneering group in the field of genome editing, the Kmiec laboratory has formed the Gene Editing Institute (GEI) and will remain located at the center for translational cancer research within the Helen F Graham Cancer Center. GEI evolved from a genome customization core managed by Eric B. Kmiec, Ph.D. and has already contributed to the development of these technologies with publications in Nature: Scientific Reports and in PLOS ONE in 2014. The Gene Editing Institute is now on the cutting edge of genomic research, both as a research for discovery investigations and as a research for undergraduate and graduate education. For research applications, we can analyze mutagenesis in the human genome as a function of normal cell processes or help evaluate drug action by creating tools to alter specific genes within the mammalian genome. GEI’s approach is to directly consult with research groups in the design, synthesis and optimization of gene editing tools that can be used across a wide array of biomedical applications. While these cutting edge tools are available for purchase, personal collaboration addressing the true capabilities of the technologies and advice on whether they will meet the researchers’ goals are not readily accessible commercially. For educational opportunities, we provide group or individual tutorials on the concepts of gene editing and aid in the experimental design of genetic tools for researchers interested in employing gene editing.

Research Applications

TALEN therapeutics: Scientists evaluating various drugs or molecular treatments often target a particular protein or gene function by utilizing TALENs to disrupt or modify that function in a targeted pathway. These changes in gene expression, for example, broaden the scope of evaluation in studies aimed at discovering the response of cancer cells to action of a new drug. Functional genomics is enabled in an easy fashion, so much so that many research groups can now carry out functional genomic studies within their own laboratories.

TALENs for progenitor/stem cells: Researchers interested in the analysis of stem cells/progenitor cell development and function, order and use our TALENs to alter gene expression patterns that lead to differential, differentiation of certain kinds of cell populations.
TALEs for gene knockdown/gene up regulation: Scientists are using our TALEs (the binding components of the TALEN) to regulate gene expression at the level of DNA. This approach is an extremely efficient way to modulate the levels of gene expression both in cell and animal models. It is particularly efficient in lower eukaryotes such as C. elegans.

Epigenetic TALEs: We are currently developing an innovative strategy to combine the DNA specific binding capacity of the TALE with enzymatic domains such as TET demethylase in order to demethylate very specific sites within promoter regions, an approach that will define the importance of epigenetic markers leading to oncogene expression and changing DNA function.

CRISPR/Cas9 systems I: Scientists interested in creating pure knockouts in cells have engaged us to design and create these systems for them. While clearly easier to make and to produce, CRISPRs are much less specific in their activity profiles than TALENs and often create serious mutagenesis within the genome at random sites. Thus, the design of these CRISPRs is critical and our workshops are proving invaluable to researchers who are evaluating use of this technology. In a new exciting and innovative approach with collaborators, we will help combine the Flox/insertion system with CRISPR technologies to create an insertion/ deletion model so that random genes can be swapped in and out of the genome at chromos specific designated sites within a chromosome. This collaboration could lead to a significant advancement in the technology that could then be offered as a new tool for other clients.

CRISPR/Cas9 systems II: This system is quickly developing as the most popular genome modifier due to its simplicity of design and cloning. Indeed, CRISPR/Cas9 can catalyze all of the actives of TALENs, but with the important caveats described above. With these drawbacks in mind, we tailor the approach for each application and advise our clients as to which tool is most appropriate not only to use, but why it will sidestep the collateral effects. CRISPRs can also be used in epigenetic editing, the next wave of genome modification, and an area in which we are actively engaged.

Educational Applications

We are partnering now with a biotechnology company to develop and produce an undergraduate and graduate student, hands-on instructional laboratory exercise for gene editing. We are in the process of writing an educational module to complement a gene editing kit for laboratory classes in molecular biology, genetics or biotechnology, etc. The kit will contain all of the cells and reagents needed to perform simple gene editing and we will provide a video and/or on-site instruction to the students. The basis of this kit is founded in over 20 years of research and development of a well accepted and well-established gene editing model system developed by the Kmiec laboratory. We are arranging to beta test the kits at several universities. This would be a first for an IDeA state core /institute facility and meets the goals of these programs in establishing more translational and educational work with the biotechnology community, product development and entrepreneurship.
The Gene Editing Institute was selected to present two workshops at prime speaking slots at NISBRE in June 2014. The feedback was overwhelmingly positive and we have been busy ever since responding to inquiries on use of these technologies, producing reagents and providing technical support. We are currently engaged in developing CRISPR and TALENs for multiple clients including the University of Delaware, University of North Dakota, Dartmouth University, Wistar Institute, University of Vermont, and the Mayo Clinic.
This positive response also led to the creation of “Precision in Practice: Success with Gene Editing Technologies” instructional workshops as outlined in the attached brochure. We have already provided a number of workshops and personal consultations, the most amazing and wonderful experience was at the University of North Dakota, where our staff spent two days presenting workshops and meeting with 10 clients, most of whom are now fully engaged with us in production of reagents for their research. Our educational offerings have expanded from simple teleconferences to full-day on-site workshops and multi-day client-site workshops and one-on-one consultations. We expect this trend to continue as it is far more cost-effective for institutions to host workshops with 10 to 12 researchers at their location.

The high-throughput screening and imaging facility at the Centre for Cellular and Molecular Platform (C-CAMP) has been created to assist academic and industry in developing and performing high-throughput assays involving NCEs, siRNA, shRNA and dsRNA
The core also houses a cutting-edge High Content image-based platform for chemical and biology research using both live and fixed cells.

A high level of protein expression and optimal purification is imperative for protein biology research groups in academia as well as industry for broad applications from drug discovery to industrial enzymes. Depending on specific applications, the system chosen for protein expression can be critical for the end point use of the desired protein. All the expression systems available have their strengths and weaknesses concerning yield, proper folding, post-translational modification (PTM), cost, speed and ease of use.
The facility provides assistance in the selection of an optimal recombinant expression system (prokaryotic and eukaryotic), cloning and sub cloning genes of interest into expression vectors, and in optimizing protein expression and purification. The core also assists in the generation of site-directed mutants of the proteins of interest and in scaling up of recombinant protein production. The facility has separate dedicated labs and necessary instrumentation to perform protein expression in bacteria, yeast.

The Imaging facility at C-CAMP provides researchers with access to high-end platform technologies in the Imaging space. Through C-CAMP, these technologies are also being made available to industry and commercial entities.

The facility houses state-of-the-art imaging equipment to allow researchers to observe nano-scale architecture and phenomena in living systems.

NEXT-GENERATION GENOMICS SERVICES

NGS Instruments: Currently we have two NGS systems, which generate both long and short sequence reads.

a) Illumina - HiSeq 1000

The Illumina system uses Sequencing by Synthesis (SBS) technology to sequence DNA fragments. HiSeq1000 generates over a billion reads of 100 bases per week. This system is ideally suitable for re-sequencing of genomes, transcriptome analysis, SNP discovery and structural variation analysis, DNA-protein interaction analysis (ChIP-Seq), sequencing-based methylation analysis, small RNA, etc.

- Whole Genome Sequencing
- Exome Capture & Sequencing
- Transcriptome Sequencing
- Small RNA Sequencing
- ChIP Sequencing
- Metagenome & Metatranscriptome sequencing

b) Roche 454 - GS Titanium FLX / GS FLX +

The Roche 454 Sequencer uses Pyrosequencing technology to sequence DNA fragments. The FLX + system is capable of generating greater than 1 million reads of 500-700 bases in 10 hours. The system is ideally suitable for de novo sequencing of whole genomes, transcriptomes, and metagenomic characterization of complex samples.

- de novo Whole Genome Sequencing
- de novo Transcriptome Sequencing
- Metagenome & Metatranscriptome sequencing
- Targeted resequencing