Laboratory for Applied Genome Technologies and Regenerative Medicine, www.dream.au.dk
My group focuses on the development and application of applied genome technologies to better decipher the molecular mechanisms of human diseases, including cancers, vascular dysfunctions, diabetes and neurodegenerative diseases. Technologies that have been established and developed in the research group include the cutting-edge CRISPR gene editing technology, stem cell technology, somatic cell nuclear transfer (SCNT), next generation sequencing, single cell RNA/ATAC sequencing and machine learning-based data processing. In application of these technologies, we are working on the identification of biomarkers which can be used for better diagnosis and treatment, as well as the development of regenerative medicine for human degenerative diseases.
Development CRISPR/Cas9-mediated gene editing technology is one of the major focus of my research group. Although the technology has now been broadly used by the whole scientific society, new CRISPR tools are still being developed to achieve gene editing with high efficiency and safety (lower off-targets). Apart from developing molecular tools to facilitate the validation of CRISPR editing efficiency and enrichment of cells with desired mutations, we are also generating new modification Cas9 proteins, large dataset of CRISPR editing outcome and large dataset of CRISPR off-target cleavage to develop better in silico prediction tools for CRISPR activity and off-targets. For example, we have developed a conventional TRAP-seq technology to simultaneous profile CRISPR outcome in 12,000 editing sites in cells. Link to the study: https://www.biorxiv.org/content/10.1101/2020.05.20.103614v1.article-metrics
Another core application of the CRISPR gene editing and SCNT technologies from our group is the generation of genetically tailored pigs that can be used as human disease models and donors for organ transplantation. Shortage of organs is one of the major unmet needs in transplant medicine. Pigs are similar to humans in term of organ size, physiology, anatomy and functions. Whereas, the application of pigs as organ donors has been greatly hampered by two major barriers: the risk of viral transmission and the immune rejection of xenografts. We are working on generating pigs that are safer and suitable for this purpose by eradicating the porcine endogenous viruses (e.g. PERV) and genetically modified xenogeneic genes using CRISPR gene editing and pig cloning. We have demonstrated that PERV can be successfully inactivated in pigs by CRISPR, link to the study: https://science.sciencemag.org/content/357/6357/1303
A third core application of the CRISPR gene editing technology is the perturbation of extrachromosomal circular DNA (eccDNA) in cancer development. The formation of eccDNA, also known as double-minute, has been discovered over decades. These eccDNAs play a key role in driving the progression of tumors from benign to highly aggressive tumors. Many oncogenes amplify via the formation of eccDNA. To study how the presence or appearance of these eccDNA on cancers progression and response to treatment, we have developed CRISPR-based tools for real-time monitoring the eccDNA in human cells. Link to studies: https://academic.oup.com/nar/article/46/22/e131/5078801
Apart from editing the genome, we also work on genome technologies that can be applied to read and understand how our genome and transcriptome work in cells, organisms and diseases. Based on a cataloging strategy, we work together with an international consortium to generate the most systematically and comprehensively mapping of all protein-coding genes in all tissues/organs in mammals. We also develop visualization webtools that enables all researchers without any bioinformatic background to easily explore the data and results. An example outcome of our cataloging projects is the launch of protein-coding gene atlas in the human, pig and mouse brain. Link to the study: https://science.sciencemag.org/content/367/6482/eaay5947
All tissue/organ specimens are highly heterogeneous and comprise a great numbers of cell types in different proportions. Bulk RNA sequencing can capture the molecular changes in the abundant cell types, but fail to capture that in some rare and most frequently and functionally important cells. The best complementary technology to bulk RNA sequencing is the single cell RNA sequencing (scRNA-seq). One example is the endothelial cells which line the lumen of the vasculature systems. Endothelial cells are highly heterogeneous in different levels: organism, tissue, vessel bed, disease. My group is working on applying the single cell RNA sequencing technology in deciphering endothelial cell heterogeneity and functions in both health and diseases. More particularly, we are focusing on better understanding and protecting the porcine endothelial cells from human immune rejections. Link to some previous results: https://www.sciencedirect.com/science/article/pii/S0092867420300623?dgcid=rss_sd_all