In this study, a Consequential Life Cycle Assessment (CLCA) was conducted on the introduction of a potato protein for human consumption in Sweden. The assessed environmental impact cathegories in the CLCA were the categories global warming potential, eutrophication and land use. Potato protein is a side-stream that occurs during the production of potato starch and is currently used for animal feed (feed-grade). With the use of the new gene-editing technique CRISPR-Cas9, the stability of proteins in a starch potato can be improved to make the potato protein fit for human consumption (food-grade). The food-grade potato protein can be used as an ingredient in the food products: plant-based meat, quiche, sauces, wine and smoothies. When using the potato protein in one of these food products seven protein sources could potentially be substituted: soybean protein, yellow pea protein, beef protein, pork protein, chicken protein, egg protein and milk protein. The results of the CLCA show that when using the potato protein as an ingredient in a food product instead of other protein sources environmental impact can potentially be reduced. Most environmental impact can be reduced by substituting animal proteins by the potato protein. Therefore, from an environmental point of view, the most interesting food products to use the potato protein in as an ingredient are the food products where currently animal products are used in as the main source of protein.

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<p>Stem cell technologies hold great promise in solving problems within fields such as drug development, regenerative medicine, and disease modeling. Stem cell engineering provides a mechanism that will help stem cells achieve this promise. Currently, many applications within tissue engineering are limited by a lack of ability to create accurate micro-physiological structures that recapitulate multicellular tissue patterns <i>in vivo</i>. Precise control of spatial and temporal signaling is desired to perform concurrent differentiation to multiple cell types intentionally. The OptoWnt construct, a novel optogenetic system activating the Wnt signaling pathway, achieves precise spatiotemporal regulation, in pursuit of greater control in stem cell differentiation. We utilize OptoWnt, to differentiate stem cells into cardiovascular cells: endothelial progenitor cells and cardiomyocytes, valuable cell types for designing microtissues. Endothelial cells comprise the luminal lining of blood and lymphatic vessels, providing the integral structure for distribution within the body, separating mobile and stationary tissues. Cardiomyocytes provide the force required to pump blood throughout the human body and are a highly desired cell type in regenerative medicine.</p> <p>In this project, we have applied an optogenetic induced signaling pathway, OptoWnt, to differentiate human pluripotent stem cells (hPSCs) into cardiovascular cells via light-induced activation of Wnt signaling pathway. In the analysis of these cells and comparison to previous small molecule approaches to cardiovascular cell differentiation, we demonstrate the robustness of the optogenetic approach and similar efficiency that it has with the small molecule approach. In short, we have further demonstrated the utility and potential of optogenetic induction of developmental pathways, via the OptoWnt construct.</p>

Recent advances with the bacterial CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) defense system as genome editing tools have opened a new avenue for targeting disease-causing mutations. The programmability of the Cas9 endonuclease by RNA makes it a potentially powerful therapeutic tool to correct such mutations. The CRISPR-Cas9 system consists of a Cas9 endonuclease that is guided by RNA (sgRNA) to create double-stranded breaks in a target DNA segment complementary to the guide. This process is dependent on a 2-8 nucleotide sequence (called PAM) that is adjacent to the target and functions as a Cas9 binding signal. Each Cas9 ortholog recognizes a unique PAM. However, factors such as the size of Cas9 or the frequency of its PAM sequence in the genome have hindered its clinical use. The Cas9 from Streptococcus pyogenes (SpyCas9) is commonly used in research because its PAM (NGG, where “N” symbolizes any nucleotide) is present every ~8 bp in the genome, providing robust targeting potential. However, it is too large to fit into typical viral vectors used for in vivo delivery, namely adeno-associated vectors (AAV). While several Cas9 orthologs have been characterized, none satisfied the need for a compact, accurate Cas9 with a short PAM. In this thesis, we use two approaches to identify new compact Cas9 orthologs with small PAMs, one using anti-CRISPR proteins and one by searching through closely related Cas9s. First, we use the presence of anti-CRISPRs (naturally occurring, phage-encoded peptides that inhibit CRISPR-Cas9 described in chapter 2) in a genome as indicators of Cas9s that may be highly active. These orthologs come with the added advantage of having inhibitors that can be used as off-switches. We characterize four Cas9s that are targeted by anti-CRISPR proteins and show that they recognize diverse PAMs in vitro. One of the four Cas9’s, namely HpaCas9 from Haemophilus parainfluenzae, induces efficient genome editing in mammalian cells. However, its long N4GATTT PAM does not satisfy the short PAM criterion. For our second approach, we asked whether closely related Cas9 orthologs with drastically different PAM-interacting domains (PIDs, the domain responsible for PAM recognition) recognize different PAMs, and if so, can be used for genome editing. To this end, we exploited natural variation in the PID of closely related Cas9s to identify a compact ortholog from Neisseria meningitidis (Nme2Cas9). Nme2Cas9 recognizes a simple dinucleotide PAM (N4CC) that provides a high target site density. All-in-one AAV delivery of Nme2Cas9 with a guide RNA into adult mouse liver produces efficient genome editing and reduced serum cholesterol with exceptionally high specificity. We further expand our single-AAV platform to pre-implanted zygotes for streamlined generation of genome-edited mice. Finally, we show preliminary data on how CRISPR-Cas9 can be used for therapeutic genome editing for Amytrophic Lateral Sclerosis. Our new findings promise to accelerate the development of genome editing tools for biomedical and therapeutic applications.

There has been tremendous amount of effort focused on the development and improvement of genome editing applications over the decades. Particularly, the development of programmable nucleases has revolutionized genome editing with regards to their improvements in mutagenesis efficacy and targeting feasibility. Programmable nucleases are competent for a variety of genome editing applications. There is growing interest in employing the programmable nucleases in therapeutic genome editing applications, such as correcting mutations in genetic disorders. Type II CRISPR-Cas9 bacterial adaptive immunity systems have recently been engineered as RNA-guided programmable nucleases. Native CRISPR-Cas9 nucleases have two stages of sequence-specific target DNA recognition prior to cleavage: the intrinsic binding of the Cas9 nuclease to a short DNA element (the PAM) followed by testing target site complementarity with the programmable guide RNA. The ease of reprogramming CRISPR-Cas9 nucleases for new target sequences makes them favorable genome editing platform for many applications including gene therapy. However, wild-type Cas9 nucleases have limitations: (i) The PAM element requirement restricts the targeting range of Cas9; (ii) despite the presence of two stages of target recognition, wild-type Cas9 can cleave DNA at unintended sites, which is not desired for therapeutic purposes; and (iii) there is a lack of control over the mutagenic editing product that is procuded. In this study, we developed and characterized chimeric Cas9 platforms to provide solutions to these limitations. In these platforms, the DNA-binding affinity of Cas9 protein from S. pyogenes is attenuated such that the target site binding is dependent on a fused programmable DNA-targeting-unit that recognizes a neighboring DNA-sequence. This modification extends the range of usable PAM elements and substantially improves the targeting specify of wild type Cas9. Furthermore, one of the featured chimeric Cas9 variants developed in this study has both robust nuclease activity and ability to generate predictable uniform editing products. These superior properties of the chimeric Cas9 platforms make them favorable for various genome editing applications and bring programmable nucleases one step closer to therapeutic applications.

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京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19401号 / 医博第4052号 / 新制||医||1012(附属図書館) / 32426 / 京都大学大学院医学研究科医学専攻 / (主査)教授 髙田 穣, 教授 平岡 眞寛, 教授 松本 智裕 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

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