For optimal growth, plants have evolved strategies to integrate environmental signals to coordinate complex developmental and defensive processes to cope with the changing surroundings. Under challenges, plants prioritize their defense over growth. This trade-off involves complex interactions between multiple hormonal pathways and developmental networks. We discovered that JACKDAW (JKD), the core component of the SHORTROOT (SHR)-SCARECROW (SCR)- JKD plant developmental regulatory network is linking defense responses to the developmental programming. Unlike the well-studied function of JKD in root development, its function in leaves is yet to be understood. We found that JKD is expressed on the abaxial side of the leaf ground tissue. It has conserved functions in promoting SHR nuclear retention and restricting cyclinD6 expression in the leaf. Additionally, JKD has a function in leaf internal architecture establishment, including suppression of the bundle sheath cell division and shaping of the leaf ground tissue. We also found that SHR is a universal asymmetric cell division (ACD) activator, as ectopic SHR expression in the leaf ground tissue promotes stomata development via promoting the ACD to produce more stomata precursor cells. We showed that the knockout mutant of JKD has larger rosettes and better photosynthesis capacity, while the basal defense level and resistance to Botrytis cinerea, a necrotrophic pathogen, are enhanced. Our transcriptome and transcription studies revealed that JKD suppresses the expression of the plant defense hormone Jasmonic acid (JA) response genes and is itself downregulated by JA. This suggests that JKD is involved in the JA signaling, which mediates defense responses for wounding and herbivore attacks. Together, our study indicates that the loss of JKD uncoupled the plant growth-defense trade-off. JKD is a new link between plant development and defense. To verify whether this function of JKD is conserved in crops, JKD orthologues in tomatoes are identified, CRISPR-Cas9 and TILLING mutants are created and analyzed. The results showed that the functions of JKD in root development and resistance to botrytis are conserved. The broad presence of JKD orthologs makes them a great target for molecular breeding to generate crops that do not have to sacrifice their normal growth to defense response.

Mutations in the telomere length maintenance pathway can lead to a spectrum of diseases called telomere syndromes, however, the pathway is not fully understood and there may still be unknown components. We designed a forward genetic screen to identify new genes involved in telomere length maintenance. Of the top ranked genes, ZNF827, a zinc finger protein, is the most promising candidate gene. The possible discovery of a new component involved in telomere length maintenance increases our understanding of the pathway and opens new avenues of research. Recent advances in molecular biology techniques, such as the use of RNA-guided nuclease CRISPR associated protein 9 (Cas9), have made screens like this possible. Cas9 is a nuclease that uses a guide RNA(gRNA) to direct its endonuclease activity. The use of Cas9 has revolutionized the field of genome engineering, providing scientists with more efficient methods to knockout and modify genomes. We sought to optimize CRISPR-Cas9 genome editing to make it as widely accessible as possible. We compared plasmid, ribonucleoprotein (RNP), and RNA only lipid-mediated transfection of CRISPR-Cas9 into cell lines using a novel reporter system to measure genome editing efficiency. All methods were successful to some extent, however, RNP lipofection was the most efficient and has many advantages over other methods. We also found that short homology arms of 30-35bp on donor templates was able to mediate site specific editing. These methods should broaden the accessibility of CRISPR-Cas9 genome editing.

The world of precision medicine was revolutionized by the discovery of CRISPR-Cas systems. In particular, the capabilities of the programmable nuclease Cas9 and its derivatives have unlocked a world in which applied genome engineering to cure human disease is a reality being pursued in patient clinical trials. Gene editing via the induction of programmable, site-specific double strand breaks (DSBs) has been revolutionary for the precision medicine field. However, there are many safety concerns centered on the induction of DSBs causing potential undesirable on- and off-target consequences, particularly for in vivo CRISPR applications. To circumvent these warranted concerns, many groups have attempted to repurpose recombinases or engineer new fusion systems to perform programmable genome engineering without the induction of DSBs. This dissertation will first highlight the development of recombinases for programmable DNA insertions over the course of decades, including efforts to evolve novel DNA recognition sequences, efforts to tether recombinases to programmable DNA-binding proteins, and the recent discovery of naturally occurring RNA-guided DNA transposition systems. This dissertation will then highlight the development of CRISPR-associated transposases (CASTs) as DSB-independent programmable mammalian gene editing tools capable of integrating large DNA cargos, as well as the future directions that may further enhance CAST activity in human cells. The works in this dissertation detail the initial efforts to engineer and optimize a new class of genome manipulation tools that were previously absent from the gene editing toolkit.

<p dir="ltr"><i>Legionella pneumophila</i> strains harboring wild-type <i>rpsL</i> such as Lp02<i>rpsL</i>_WT cannot replicate in mouse bone marrow-derived macrophages (BMDMs) due to induction of extensive lysosome damage and apoptosis. The mechanism of this unique infection-induced cell death remains unknown. Using a genome-wide CRISPR/Cas9 screening, we identified <i>Hmg20a </i>and <i>Nol9</i> as host factors important for restricting strain Lp02<i>rpsL</i>_WT in BMDMs. Depletion of <i>Hmg20a</i> protects macrophages from infection-induced lysosomal damage and apoptosis, allowing productive bacterial replication. The restriction imposed by <i>Hmg20a</i> was mediated by repressing the expression of several endo-lysosomal proteins, including the small GTPase Rab7. We found that SUMOylated Rab7 is recruited to the bacterial phagosome via SulF, a Dot/Icm effector that harbors a SUMO-interacting motif (SIM). Moreover, overexpression of Rab7 rescues intracellular growth of strain Lp02<i>rpsL</i>_WT in BMDMs. Our results establish that <i>L. pneumophila</i> exploits the lysosomal network for the biogenesis of its phagosome in BMDMs.</p>

京都大学 / 新制・課程博士 / 博士(医科学) / 甲第24843号 / 医科博第151号 / 新制||医科||10(附属図書館) / 京都大学大学院医学研究科医科学専攻 / (主査)教授 齋藤, 潤, 教授 遊佐, 宏介, 教授 松田, 秀一 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Le syndrome périodique lié à NLRP12 (NLRP12-AD) est une maladie rare appartenant au groupe des maladies auto-inflammatoires systémiques héréditaires. Ces maladies sont causées par des anomalies du système immunitaire inné. Les cryopyrinopathies (CAPS) sont une famille de maladie auto-inflammatoire liées à des mutations gain de fonction du gène NLRP3. NLRP3 fait partie d’un composant central de l’inflammation, l’inflammasome. En 2007, Jéru et al. ont décrit un premier patient présentant des symptômes évocateurs d’un CAPS qui n’était pas porteur de mutation de NLRP3 mais présentait une mutation de NLRP12. Depuis, 33 patients pédiatriques atteints de NLRP12-AD ont été décrits dans la littérature. Les signes cliniques de la maladie sont variables et ne permettent pas d’établir de critères cliniques diagnostics fiables. La pathogénicité des mutations observées chez les patients est difficile à établir. Les patients atteints de NLRP12-AD représentent également un défi thérapeutique, un certain nombre d’entre eux ne répondant pas aux anti-IL1, un traitement pourtant efficace dans la plupart des inflammasomopathies. De nombreuses études se sont intéressées au rôle de NLPR12, qui posséderait à la fois des propriétés pro et anti-inflammatoires par sa capacité à inhiber les voies canoniques et non canoniques de NFkb mais aussi à former un inflammasome. Le rôle exact de NLRP12 reste controversé, avec des résultats différents selon les cellules ou les stimuli utilisés lors des expériences. L’objectif de notre étude est de créer un modèle in vitro fiable et reproductible afin de mieux comprendre la physiopathologie de NLRP12. Il permettra ensuite d’étudier les mutations de NLRP12 retrouvées chez des patients présentant des symptômes de maladie auto-inflammatoire pour améliorer les performances et la fiabilité du diagnostic et proposer des traitements personnalisés aux patients concernés. Nous avons créé un modèle de cellules THP1 NLRP12 KO en utilisant la technologie de CRISPR/Cas9 qui a permis d’induire une délétion homozygote à la jonction entre le 2ème intron et le 3ème exon de NLRP12, qui code pour le domaine fonctionnel de la protéine. Nos cellules KO semblent sécréter moins de cytokine pro-inflammatoire (IL-1β et TNFα) que les cellules WT, suggérant un rôle pro-inflammatoire de NLRP12 dans notre modèle. Nous avons par ailleurs décrit une cohorte nord-américaine de 17 patients porteurs de mutations de NLRP12 afin d’étudier leurs mutations et produit des vecteurs lentiviraux contenant ces mutations. Nous prévoyons d’explorer le rôle de NLRP12 sur l’activation de la voie NFkB et la formation d’un inflammasome puis de transduire nos cellules KO avec les différentes mutations de nos patients et d’analyser leurs conséquences sur ces mêmes voies et sur la sécrétion cytokinique. / NLRP12-AD is part of a new group of rheumatics’ diseases: the systemic autoinflammatory diseases. Those diseases are caused by defect or dysfunction in the innate immune system. Cryopyrin-associated periodic syndromes (CAPS) is a family of systemic autoinflammatory disease initially linked to NLRP3 gain-of-function heterozygous mutations. NLRP3 is part of a key component of inflammation, the inflammasome. In 2007, Jeru et al. described the first patient with CAPS phenotype, but without NLRP3 mutations. This patient had NLRP12 mutations. Since then, 33 pediatric patients with NLRP12-AD have been published. There is no specific clinical presentation that allow homogenous diagnosis. Determination of the causality of the mutations remains tricky. Lastly, some patients have shown resistance to anti-IL1 treatment, a medication that is highly effective in other inflammasomopathies such as CAPS, a puzzling observation as to the role of NLRP12. NLRP12 has been described with both anti- and pro- inflammatory roles, by its ability to inhibit the canonical and non-canonical NFkB pathways, but also through its hypothetic capacity to form an inflammasome. Hence, the exact role of NLRP12 remains controversial and its role might be stimuli- or cell-dependant. Our objective is to create a reliable and reproductible in vitro model to better understand the role of NLRP12. This model will then allow us to study NLRP12 mutations found in patients with auto-inflammatory symptoms. This will improve our diagnostic performance and help to offer to patients the most suitable therapy. We created NLRP12 knockout THP-1 cells by using the CRPISP-Cas 9 gene editing technology. We were able to induce a homozygous deletion at the intron 2/exon 3 junction that encodes the protein functional domain. Our KO cells seems to secrete less pro-inflammatory cytokines (IL-1β and TNFα) than WT cells. This suggests a pro-inflammatory role of NLRP12. We described a North American cohort of 17 pediatric patients with NLRP12 mutations to study their mutations in our model and produced lentiviral vectors containing those mutations. We planned to study the effects of NLRP12 on NFkB activation and on inflammasome formation. Then, we will transduce our KO cells with the patient’s mutations and compare their consequences on inflammation pathways and cytokine secretion.

Although the understanding of genetic predisposition to prostate cancer (PCa) has been improved through genome-wide association studies (GWAS), little is known about the biological implication of germline variants residing in coding or non-coding regions in cancer development and progression. Our hypothesis is that inherited variants may predispose to specific early recurrent genomic events observed in PCa adenocarcinomas, possibly in the context of variable androgen receptor (AR) signaling that changes during a man’s lifetime. Recent in silico analysis by our group on potential association between germline variants and PCa specific somatic lesions identified a non-coding polymorphic regulatory element at the 7p14.3 locus associated with DNA repair and hormone regulated transcript levels and with an early recurrent prostate cancer specific somatic mutation in the Speckle-Type POZ protein (SPOP) gene (OR=5.54, P=1.22e-08) in human prostate tissue data. In order to functionally characterize the polymorphic 7p14.3 locus (rs1376350, single nucleotide polymorphism, G&gt;A), we set up to establish isogenic cell lines harboring the minor allele by using the CRISPR/Cas9 system. In parallel, CRISPR/Cas9 system was used to knock out different portion of the region encompassing the 7p14.3 variant and to eliminate transcription factors (TFs) binding sites that were identified from previous in silico analysis (i.e. AR and CCAAT/Enhancer Binding Protein (C/EBP) beta (CEBPβ)). The transcriptomes of edited pools and edited single clones from macrodeletion (731 bp), microdeletion (50 bp) and alterations of TFs binding sites were analyzed and compared to the transcriptomes of isogenic cells heterozygous (A/G) and homozygous (A/A) for the minor allele A of the risk variant rs1376350 (with or without AR overexpression). These data identified a set of genes scattered throughout the genome with the same pattern of deregulation suggesting the implication of the variant on the regulation of genes residing in different chromosomes. Additionally, ChIP-qPCR experiments for histone modification supported the identification of the 7p14.3 locus with enhancer activity. Furthermore, ChIP-qPCR of histone mark associated with transcriptional activation or repression in isogenic cells harboring the minor allele A upon AR overexpression showed that the activity of the locus is higher for the minor allele A compared to G, independently from AR activation. Despite the limitations of our model and the current lack of validation in other cells, we confirmed that some of the differentially expressed genes that emerged from the comparative analysis of edited cells are deregulated in human normal and tumor prostate samples as well. This work is a proof of concept of germline predisposition to molecularly distinct cancer subclasses and has the potential to nominate new mechanisms of cancer development. Future work aims to elucidate the mechanisms implicated in the deregulation of the transcriptome by combining the information obtained until now with potential new players that we expect to identify by Mass Spectrometry experiments. To clarify the link between the 7p14.3 variant and the somatic mutations in SPOP, we plan to express mutant SPOP in isogenic cells harboring the minor allele and to asses DNA damage response upon overexpression or silencing of TFs binding at and around the rs1376350 variant. My work is an example of how the CRISPR/Cas9 system can be used to develop a technical framework with convergent approaches to functionally characterize polymorphic regulatory regions including but not limited to the establishment of isogenic cells upon single nucleotide editing.

The neurotransmitter dopamine (DA) plays a critical role in regulating cognition, behavior and physiology in humans. Imbalances in DA or damage to the dopaminergic (DAnergic) system can be consequential to neurological health and lead to the progression of psychiatric and neurodegenerative disorders that include but are not limited to schizophrenia and Parkinson’s disease (PD). PD, in particular, is associated with debilitating motor symptoms that result following a considerable loss of midbrain DAnergic neurons. This loss is likely correlated to a combinatory insult of environmental exposures and genetic predisposition, as the majority of cases are idiopathic in nature. To date there remains to be a curative treatment, thus much research has been done to generate models of sporadic PD through the use of neurotoxic exposures in addition to the search for plant-derived chemicals that confer neuroprotection prior to the onset of symptoms to improve the quality of life for those at risk. Here, we established a model to mimic pathologies observed in sporadic PD using both larval and adult zebrafish. The larval model examined the neurotoxic impact of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), 1-methyl-4-phenyl-pyridinium (MPP+), 6-hydroxydopamine (6-OHDA), rotenone, and paraquat to delineate the optimal compound that exerts the largest degree of diencephalic DAnergic cell death and motor perturbance using Tg(dat:eGFP) transgenic zebrafish. Using this model, we also showed that between ascorbic acid (AA), ferulic acid (FA) and vanillic acid (VA), pretreatment of FA elicits that largest neuroprotective effect against MPTP-induced oxidative stress and neurodegeneration. The optimization of a reliable adult model to investigate mitochondrial impacts in vivo was then addressed through introducing MPTP into the cerebroventricular fluid of Tg(dat:tom20 MLS:mCherry) transgenic zebrafish. Gene expression and immunostaining data suggest that MPTP induces DAnergic mitochondrial fragmentation through mitophagy activation. Moreover, we sought to examine the genetic influence over DAnergic production and disorders by targeting nr4a2 paralogs for CRISPR-Cas9 mediated mutagenesis. Despite a similar deleterious effect observed in DAnergic populations, nr4a2a and nr4a2b mutants each possess variable effects on neurotrophins, metabolism, other neurotransmitters and behavior. nr4a2a mutants more closely resemble PD pathologies, whereas nr4a2b mutants exhibit phenotypes reminiscent of psychiatric disorders. Throughout DAnergic regeneration, nr4a2a was also shown to mimic shha expression patterns suggestive of a predominant role over nr4a2b in differentiation. Further gene expression data may also indicate that notch1a drives the proliferative stages of DAnergic progenitors prior to the shift to shha signaling for differentiation. In sum, we believe the sporadic and genetic models of DA deficiencies offer an opportunistic tool to study molecular mechanisms of DAnergic regeneration, potential therapeutics and to gain a better understanding of mitochondrial influence in neurological pathologies.

Hematological cancers account for nearly ten percent of cancer cases diagnosed annually in the United States. Patients who fail to respond to chemotherapy or radiotherapy must often undergo a bone marrow transplant to treat their malignancy. A significant complication following this procedure is Graft versus Host Disease (GvHD), which occurs when donor T cells mount an immune response against recipient tissues. Immunological research has highlighted the role of aberrant T cell metabolism, specifically a shift toward aerobic glycolysis, as a key driver behind the occurrence of this condition. The transcription factor FoxK1 has been revealed to be a key regulator of the cell's ability to induce aerobic glycolysis. Utilizing established GvHD murine models and novel CRISPR-Cas9 techniques, this study investigates how controlling this important pathway by FoxK1 may limit the damage inflicted by GvHD. Our studies reveal that depleting FoxK1 in donor T cells has a protective effect following transplants by promoting an immunosuppressive phenotype in donor T cells. These results suggest that FoxK1 may hold promise as a future cellular target for cellular therapies administered to transplant patients to prevent the occurrence of GvHD. Continued research is needed to ascertain the precise mechanisms that afford FoxK1 this protective role.

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