Dissertations / Theses on the topic 'CRISPRko Screening'

Forward genetic screening allows for the identification of any genes important for a particular biological process or phenotype. While the power of this approach is broadly agreed on, the efficacy of currently available tools limits the strength of conclusions drawn from these experiments. This thesis describes a method to optimize molecular tools for high-throughput screening, both for shRNA and sgRNA based reagents. Using large shRNA efficacy datasets, we first designed an algorithm predicting the potency of shRNAs based on sequence determinants. Combined with a novel shRNA backbone that further improves the processing of synthetic shRNAs, we built a library of potent shRNAs to reliably and efficiently knock-down any gene in the human and mouse genomes. We then went on to apply a similar approach to identify sgRNAs with increased activity. We complemented this with conservation and repair prediction to increase the likelihood of generating functional knock-outs. With these tools in hand, we constructed, sequence-verified and validated arrayed shRNA and sgRNA libraries targeting any protein coding gene in the human genome. These resources allow large-scale screens to be performed in a multiplexed or arrayed format in a variety of biological contexts. I have also applied these tools to identify therapeutic targets to circumvent cancer resistance to treatment in two different contexts. To overcome the shortfalls of single target therapy, I have developed multiplexed multidimensional shRNA screening strategy, where two genes are knocked down simultaneously in each cell. This strategy allows the identification of gene pairs that could be targeted in tandem to maximize therapeutic benefits. As a proof of concept, I have used it with a subset of druggable genes in melanoma cell lines. Moreover, we have applied our genome wide shRNA libraries to a different resistance context, stroma-mediated resistance to gemcitabine in PDAC. In this project, we performed screens in a PDAC-CAF coculture setting to try and identify cancer vulnerabilities specifically in the presence of stroma. Overall, the tools developed in this thesis allow for the efficient knockdown or knockout of any gene, both in an individual or combinatorial setting. Apart from providing a resource that will be useful for many fields, we have performed several proof-of-concept studies where we have applied our tools to identify potential cancer drug targets.

Hepatocellular carcinoma (HCC) is an aggressive subtype of liver cancer with a poor prognosis. Currently, prognosis for HCC patients remains poor as few therapies are available. The clinical need for more effective HCC treatments remains unmet partially because HCC is genetically heterogeneous and HCC driver genes amenable to targeted therapy are largely unknown. Mutations in the TP53 gene are found in ~30% of HCC patients and confer poor prognosis to patients. Identifying genes whose depletion can inhibit HCC growth, and determining the mechanisms involved, will aid the development of targeted therapies for HCC patients. Therefore, the first half of this thesis focuses on identifying genes that are required for cell growth in HCC independent of p53 status. We performed a kinome-wide CRISPR screen to identify genes required for cell growth in three HCC cell lines: HepG2 (p53 wild-type), Huh7 (p53-mutant) and Hep3B (p53-null) cells. The kinome screen identified 31 genes that were required for cell growth in 3 HCC cell lines independent of TP53 status. Among the 31 genes, 8 genes were highly expressed in HCC compared to normal tissue and increased expression was associated with poor survival in HCC patients. We focused on TRRAP, a co-factor for histone acetyltransferases. TRRAP function has not been previously characterized in HCC. CRISPR/Cas9 mediated depletion of TRRAP reduced cell growth and colony formation in all three cell lines. Moreover, depletion of TRRAP reduced its histone acetyltransferase co-factors KAT2A and KAT5 at the protein level with no change at the mRNA level. I found that depletion of KAT5, but not KAT2A, reduced cell growth. Notably, inhibition of proteasome- and lysosome-mediated degradation failed to rescue protein levels of KAT2A and KAT5 in the absence of TRRAP. Moreover, tumor initiation in an HCC mouse model failed after CRISPR/Cas9 depletion of TRRAP due to clearance via macrophages and HCC cells depleted of TRRAP and KAT5 failed to grow as subcutaneous xenografts in vivo. RNA-seq and bioinformatic analysis of HCC patient samples revealed that TRRAP positively regulates expression of genes that are involved in mitotic progression. In HCC, this subset of genes is clinically relevant as they are overexpressed compared to normal tissue and high expression confers poor survival to patients. I identified TOP2A as one of the mitotic gene targets of the TRRAP/KAT5 complex whose inhibition greatly reduces proliferation of HCC cells. Given that this was the first time the TRRAP/KAT5 complex has been identified as a therapeutic target in HCC, the second half of this thesis focuses on identifying the mechanism via which depletion of this complex inhibits proliferation of HCC cells. I discovered that depletion of TRRAP, KAT5 and TOP2A reduced proliferation of HCC cells by inducing senescence. Typically, senescence is an irreversible state of cell cycle arrest at G1 that is due to activation of p53/p21 expression, phosphorylation of RB, and DNA damage. Surprisingly, induction of senescence after loss of TRRAP, KAT5 and TOP2A arrested cells during G2/M and senescence was independent of p53, p21, RB and DNA damage. In summary, this thesis identifies TRRAP as a potential oncogene in HCC. I identified a network of genes regulated by TRRAP and its-cofactor KAT5 that promote mitotic progression. Moreover, I demonstrated that disruption of TRRAP/KAT5 and its downstream target gene TOP2A result in senescence of HCC cells independent of p53 status. Taken together, this work suggests that targeting the TRRAP/KAT5 complex and its network of target genes is a potential therapeutic strategy for HCC patients.

Dans ce travail nous avons élaboré une nouvelle méthode de l'analyse de réseau à définir des membres possibles des voies moléculaires qui sont important pour ce phénotype en utilisant la « hit-liste » des expériences « omics » qui travaille dans le réseau intégré (le réseau comprend des interactions protéine-protéine, de transcription, l’acide ribonucléique micro-l’acide ribonucléique messager et celles métaboliques). La méthode tire des sous-réseaux qui sont construit des voies de quatre types les plus courtes (qui ne se composent des interactions protéine-protéine, ayant au minimum une interaction de transcription, ayant au minimum une interaction l’acide ribonucléique micro-l’acide ribonucléique messager, ayant au minimum une interaction métabolique) entre des hit –gènes et des soi-disant « exécuteurs terminaux » - les composants biologiques qui participent à la réalisation du phénotype finale (s’ils sont connus) ou entre les hit-gènes (si « des exécuteurs terminaux » sont inconnus). La méthode calcule la valeur de la centralité de chaque point culminant et de chaque voie dans le sous-réseau comme la quantité des voies les plus courtes trouvées sur la route précédente et passant à travers le point culminant et la voie. L'importance statistique des valeurs de la centralité est estimée en comparaison avec des valeurs de la centralité dans les sous-réseaux construit des voies les plus courtes pour les hit-listes choisi occasionnellement. Il est supposé que les points culminant et les voies avec les valeurs de la centralité statistiquement signifiantes peuvent être examinés comme les membres possibles des voies moléculaires menant à ce phénotype. S’il y a des valeurs expérimentales et la P-valeur pour un grand nombre des points culminant dans le réseau, la méthode fait possible de calculer les valeurs expérimentales pour les voies (comme le moyen des valeurs expérimentales des points culminant sur la route) et les P-valeurs expérimentales (en utilisant la méthode de Fischer et des transpositions multiples).A l'aide de la méthode masterPATH on a analysé les données de la perte de fonction criblage de l’acide ribonucléique micro et l'analyse de transcription de la différenciation terminal musculaire et les données de la perte de fonction criblage du procès de la réparation de l'ADN. On peut trouver le code initial de la méthode si l’on suit le lien https://github.com/daggoo/masterPATH<br>In this work we developed a new exploratory network analysis method, that works on an integrated network (the network consists of protein-protein, transcriptional, miRNA-mRNA, metabolic interactions) and aims at uncovering potential members of molecular pathways important for a given phenotype using hit list dataset from “omics” experiments. The method extracts subnetwork built from the shortest paths of 4 different types (with only protein-protein interactions, with at least one transcription interaction, with at least one miRNA-mRNA interaction, with at least one metabolic interaction) between hit genes and so called “final implementers” – biological components that are involved in molecular events responsible for final phenotypical realization (if known) or between hit genes (if “final implementers” are not known). The method calculates centrality score for each node and each path in the subnetwork as a number of the shortest paths found in the previous step that pass through the node and the path. Then, the statistical significance of each centrality score is assessed by comparing it with centrality scores in subnetworks built from the shortest paths for randomly sampled hit lists. It is hypothesized that the nodes and the paths with statistically significant centrality score can be considered as putative members of molecular pathways leading to the studied phenotype. In case experimental scores and p-values are available for a large number of nodes in the network, the method can also calculate paths’ experiment-based scores (as an average of the experimental scores of the nodes in the path) and experiment-based p-values (by aggregating p-values of the nodes in the path using Fisher’s combined probability test and permutation approach). The method is illustrated by analyzing the results of miRNA loss-of-function screening and transcriptomic profiling of terminal muscle differentiation and of ‘druggable’ loss-of-function screening of the DNA repair process. The Java source code is available on GitHub page https://github.com/daggoo/masterPATH

The ground state naive pluripotency is established in the epiblast of the blastocyst and can be captured by culturing mouse embryonic stem cells (mESCs) with MEK and GSK3 inhibitors (2i). The transcription network that maintains pluripotency has been extensively studied with the indispensable core factors being Oct4, Sox2 and Nanog, together with other ancillary factors reinforcing the network. However, how this network is dissolved at the onset of differentiation is still not fully understood. To identify genes required for differentiation in an unbiased fashion, I conducted a genome-wide CRISPR-Cas9-mediated screen in Rex1GFPd2 mESCs. This cell line expresses GFP specifically in the naive state and rapidly down-regulate upon differentiation. I differentiated mutagenised mESCs for two days and sorted mutants that kept higher GFP expression. gRNA representation was subsequently analysed by sequencing. I identified 563 and 8 genes whose mutants showed delayed and accelerated differentiation, respectively, at a false discovery rate (FDR) cutoff of 10%. The majority of the previously known genes were identified in my screen, suggesting faithful representation of genes regulating differentiation. Detailed screening result analysis revealed a comprehensive picture of pathways involved in the dissolution of naive pluripotency. Amongst the genes identified are 19 mTORC1 regulators and components of the mTORC2 complex. Deficiency in the TSC and GATOR complexes resulted in mTORC1 upregulation in consistent with previous studies. However, they showed opposite phenotype during ESC differentiation: TSC complex knockout cells showed delayed differentiation, whereas GATOR1 deficiency accelerated differentiation I found that the pattern of GSK3b phosphorylation is highly correlated with differentiation phenotype. I conclude that mTORC1 is involved in pluripotency maintenance and differentiation through cross-talk with the Wnt signalling pathway. My screen has demonstrated the power of CRISPR-Cas9-mediated screen and provided further insights in biological pathways involved in regulating differentiation. It would be interesting to explore the remaining unstudied genes for better understanding of the mechanisms underlying mESC differentiation.

In 2006, Kazutoshi Takahashi and Shinya Yamanaka demonstrated the ability of four transcription factors; Oct4, Sox2, Klf4 and c-Myc to 'reprogram' differentiated somatic cells to a pluripotent state. This technology holds huge potential in the field of regenerative medicine, but reprogramming also a model system by which to the common regulators of all forced cell identity changes, for example, transdifferentiation. Despite this, the mechanism underlying reprogramming remains poorly understood and the efficiency of induced pluripotent stem cell (iPSC) generation, inefficient. One powerful method for elucidating the gene components influencing a biological process, such as reprogramming, is screening for a phenotype of interest using genome-wide mutant libraries. Historically, large-scale knockout screens have been challenging to perform in diploid mammalian genomes, while other screening technologies such as RNAi can be disadvantaged by variable knockdown of target transcripts and off-target effects. Components of clustered regularly interspaced short palindromic repeats and associated Cas proteins (CRISPR-Cas) prokaryote adaptive immunity systems have recently been adapted to edit genomic sequences at high efficiency in mammalian systems. Furthermore, the application of CRISPR-Cas components to perform proofof- principle genome-wide KO screens has been successfully demonstrated. I have utilised the CRISPR-Cas9 system to perform genome-wide loss-of-function screening in the context of murine iPSC reprogramming, identifying 18 novel inhibitors of reprogramming, in addition to four known inhibitors, Trp53, Cdkn1a, Jun, Dot1l and Gtf2i. Understanding how these novel reprogramming roadblocks function to inhibit the reprogramming process will provide insight into the molecular mechanisms underpinning forced cell identity changes.

Cell-free systems allow to perform in-vitro transcription-translation reactions without requiring living organisms, revolutionising scientific research over the last decade. This allows to easily synthesise a variety of molecular components for genetic editing applications without requiring expensive and time-consuming procedures such as cell culture, animal maintenance etc. In this work, I aimed to develop a high-throughput platform for the rapid, flexible and scalable in-vitro testing of various genetic editors, such as those part of the CRISPR/Cas repertoire. I used the commercially available E. coli cell extract (MyTXTL) in combination with a fully customisable design to generate fluorescent reporters, that allow standardised testing of various CRISPR components against any predesigned target or protospacer adjacent motif (PAM) sequences. In order to increase the scalability of this screening platform, I utilised automated liquid handling technologies (Echo 525) and explored the possibility to introduce a high throughput cloning method (BASIC assembly). I believe that this approach will be highly valuable for the screening of CRISPR components prior than their final application in in-vivo systems, such as humans or animals. These genetic editors could then be used in many biological and artificial systems, such as gene editing, metabolomics and genetic engineering.

Les alphavirus sont un groupe de virus enveloppés à ARN simple brin positif retrouvés sur la totalité du globe et responsables de nombreuses maladies humaines et animales. Durant la dernière décennie, une réémergence du virus du chikungunya (CHIKV) a été observée causant de nombreuses épidémies sur tous les continents. Malgré les nombreuses études, les mécanismes moléculaires de réplication du CHIKV et les interactions hôte-virus restent peu caractérisées. L’objectif de mon travail était de mieux comprendre et caractériser l’entrée du virus du chikungunya et les facteurs de l’hôte impliqués dans la réplication chez les mammifères. Plusieurs approches distinctes ont été utilisées dans ce projet. Dans un premier temps, nous avons mis en avant une diminution de l’infection du CHIKV après un traitement avec du fer sous forme de citrate d’ammonium ferrique et nous avons étudié le rôle potentiel dans l’entrée virale de NRAMP2 et TFRC, deux protéines impliquées dans le transport cellulaire du fer et connus comme récepteurs d’entrée de plusieurs virus. D’autre part, nous nous sommes intéressés à deux autres protéines, CD46 et TM9SF2, identifiés à travers un criblage par ARNi réalisé en collaboration, dans le but de déterminer si elles sont utilisées comme facteurs d’entrée par le virus du chikungunya. Dans un dernier axe, nous avons mis en place et réaliser un criblage perte de fonction sur le génome entier en utilisant la technologie CRISPR/Cas9 afin d’identifier des facteurs de l’hôte importants pour l’entrée du CHIKV, sa réplication ou la mort viro-induite. Bien qu’il soit apparu que l’approche utilisée pour le criblage devrait être optimisée, nous avons pu identifier des candidats potentiellement nécessaires pour l’infection par le CHIKV. Ces candidats sont testés individuellement afin de confirmer leur implication dans la biologie du virus<br>Alphaviruses are a group of enveloped, positive-sense RNA viruses which are distributed almost worldwide and are responsible for a considerable number of human and animal diseases. Among these viruses, the Chikungunya virus (CHIKV) has recently re-emerged and caused several outbreaks on all continents in the past decade. Despite many studies, molecular mechanisms of chikungunya virus replication and virus-host interactions remain poorly understood. The aim of my project was to better understand and characterize the CHIKV entry and the host factors involved during replication steps in mammals. Several different approaches have been used in this work. As a first step, we have demonstrated a decrease of CHIKV infection after iron treatment in form of ferric ammonium citrate and we have studied the potential role in viral entry of NRAMP2 and TFRC, two proteins involved in iron transport and known receptors for other viruses. On the other hand, we have also focused on two proteins, CD46 and TM9SF2, identified through an RNAi screen in collaboration, in order to determine if they are required as entry factors for chikungunya virus. In a last axis, we have set up and carried out a genome-wide loss of function screen with the CRISPR/Cas9 technology in order to identify host factors important for chikungunya virus entry, replication or virus-induced cell death. Although it appears that screen conditions should be optimized, we have identified potential candidates required for CHIKV infection and we are currently testing them

Pancreatic ductal adenocarcinoma (PDAC) is among the most lethal malignancies because it is often diagnosed at a late disease stage and has a poor response rate to currently available treatments. Therefore, it is critical to develop new therapeutic approaches that will enhance the efficacy and reduce the toxicity of currently used therapies. Here we aimed to evaluate the therapeutic potential and mechanisms of action for piperlongumine (PL), an alkaloid from long pepper, in PDAC models. We postulated that PL causes PDAC cell death through oxidative stress and complements the therapeutic efficacy of chemotherapeutic agents in PDAC cells. First, we determined that PL is one of the most abundant alkaloids with antitumor properties in the long pepper plant. We also showed PL in combination with gemcitabine, a chemotherapy agent used to treat advanced pancreatic cancer, reduced tumor weight and volume compared to vehicle-control and individual treatments. Further, biochemical analysis, including RNA sequencing and immunohistochemistry, suggested that the antitumor activity of PL was associated with decreased cell proliferation, induction of cell cycle arrest, and oxidative stress-induced cell death. Moreover, we identified that c-Jun N-terminal kinase (JNK) inhibition blocks PL-induced cell death, translocation of Nrf2, and transcriptional activation of HMOX1 in PDAC. Finally, high-throughput drug and CRISPR screenings identified potential targets that could be used in combination with PL to treat PDAC cells. Collectively, our data suggests that cell cycle regulators in combination with PL might be an effective approach to combat pancreatic cancer.<br>NIH

PARP inhibitors (PARPi) have received regulatory approval for the treatment of multiple tumor types, including prostate cancer (PCa), and are associated with therapeutic response in metastatic castration-resistant prostate cancer (mCRPC) patients characterized by defects in homologous recombination repair genes. Clinical trials results suggest that further improvements are possible, for instance in terms of patients’ enrolment criteria. Only 50% of BRCA1/2-deficient patients (TRITON2 trial) respond to therapy, variable antitumor activity is observed for the covered non-BRCA DNA repair gene (DRG) aberrations, and the duration of the treatment response is highly heterogeneous among responders. In this scenario, in the present study we aimed at the identification and characterization of novel low-frequency DRG alterations that could represent potential targets or biomarkers for mCRPC therapy. We exploited an interdisciplinary approach based on in vitro studies including CRISPR/Cas9 genotoxic screenings and on in silico analyses focused on mCRPC patients’ genomic and clinical data. The screenings were performed on PCa cell lines and included the use of a custom sgRNA pooled library targeting 356 DRGs and the administration of several drugs, most of which are currently used in the clinic. To characterize the full spectrum of DRG aberrations, the in silico approach included the joint allele-specific level analysis of germline variants and somatic alterations of 302 DRGs involved in the principal repair pathways while querying the SU2C-PCF dataset of 429 mCRPC. Association of identified DRG defects with patient outcome and response to androgen receptor-signalling inhibitors (ARSI) were performed. Multiple genes were validated as predictive biomarkers of PARPi or carboplatin response, while 14 DRG variants linked with worse prognosis or response to therapy were nominated by the in silico analyses. Altogether, this project allowed for the identification of novel DRG biomarkers and potential targets that could eventually improve the therapeutic options for mCRPC patients.

Identification of small molecules against APOBEC3B The APOBECs are deaminases that act on DNA and RNA to restrict exogenous nucleic acids. Yet, the signature of their mutagenic activity –especially that of APOBEC3A and APOBEC3B- has been observed in the cancer genomes and their ability to increase the genetic heterogeneity of tumours has been linked to the onset of drug resistance in cancer. As such inhibition of their enzymatic activity represents a potential target for anticancer therapies. During my PhD I worked at the identification of APOBEC3B small-molecule inhibitors. To this aim, I used a computational approach to perform a virtual screening on large library of molecules to block APOBEC3B enzymatic activity. I then tested selected molecules from the virtual screening using biochemical assays to quantify their effect on APOBEC3B activity and their capacity to interfere with APOBEC3B binding to DNA. Through this, I was able to identify two small molecules that reduce the activity of this protein, which could provide basis for the development of the first drug for anti-APOBEC activity. Engineering ADAR2 to act on DNA Genome editing technologies have revolutionized our ability to target and modify the genomes of living cells and organisms. The fusion of AID/APOBECs to genome editing tools such as Cas9 allowed the development the first base editor, molecules that can be targeted to mutate specific cytosines. The pool of available Base Editors is in constant expansion as new molecules are developed to target DNA with more specificity and efficiency. As the only adenine-targeting Base Editor is based on TadA- an RNA deaminase-, I focused on the development of a A•T base editor based on the catalytic domain of ADAR2. Adenosine Deaminases Acting on RNA (ADARs), are editing enzymes that catalyse the C6 deamination of adenosine (A) to produce inosine (I) in double-stranded RNA. As human ADAR2 is able to target DNA/RNA hybrids, I first tried -without success- to use chimeras of n/dCas9 and the deaminase domain of ADAR2 to induce mutations in a fluorescent reporter. I then used a bacterial screen to select for mutants of ADAR2 that act on DNA. I selected a mutant that induces a mutator phenotype in bacteria and DNA damage in mammalian cells. I am currently working to engineer this mutant into a Base Editor suitable for biotechnological applications such as gene therapy, antiviral treatment and cancer therapy.

The E3 ubiquitin ligase RNF43 (RING finger protein 43) is an important negative modulator of the WNT signalling pathway that acts at the plasma membrane by targeting Frizzled and its co-receptor LRP for degradation. In the small intestine, this prevents uncontrolled expansion of the stem cell compartment and so it is essential to the maintenance of normal tissue homeostasis. However, despite its crucial role in fine-tuning the WNT pathway and its role as a tumour suppressor, it is unclear whether RNF43 has further binding partners and what their functional relevance is to the modulation of WNT signalling. Here, I describe the development of a new screening strategy which combines CRISPR/Cas9 technology with 3D-intestinal organoid culture for the identification of novel molecular interactors of RNF43. Overall, this study and the technology developed provide a tool to enable the detailed description of the mechanism of action of RNF43, which is important not only in order to increase our understanding of WNT pathway regulation but also to gain potential new insights into RNF43 paralogs, by analogy. The investigation of paralogs is crucial as RNF43 belongs to a newly identified family of E3 ubiquitin ligases, named the PA-RING family, whose members are still poorly characterised. The majority of PA-RING family members have not been linked to any signalling pathway, most of their targets are still unknown and in many cases their in vivo function has not been addressed. In this context, my work has specifically focused on the investigation of the potential involvement of additional PA-RING family members in WNT pathway modulation and also on target identification for selected members. The results summarised in this dissertation show that no other PA-RING family member plays a prominent role in WNT pathway modulation aside from Rnf43 and its homologue Znrf3, however, different classes of adhesion molecules are likely to be regulated by certain of these E3 ligases. In conclusion, my work has contributed to unravelling previously unexplored aspects of this protein family, with particular regard to RNF43 and its mechanism of action. Thanks to this original approach, it was possible to identify potential new players involved either in membrane clearance of Frizzled or in RNF43 maturation. In particular, my thesis focuses on the characterisation of the role of DAAM in RNF43-mediated Frizzled internalisation.

Increased expression and activity of the MYC protein is a widespread cancer hallmark and renders tumor cells addicted to sustained activation of a variety of other gene products. Identification of those dependencies can offer new therapeutic approaches against MYC-driven tumors. Previous studies showed that RNA processing events have a critical role in MYC-induced tumorigenesis and survival. Moreover, we and others observed that multiple genes encoding RNABinding Proteins (RBPs) were positively regulated upon MYC activation in various cell types. Hence, we hypothesized that the activity of specific RBPs could become rate-limiting for the growth and/or survival of MYC-overexpressing cells. Toward the identification of those RBPs, we set up high-throughput genetic dropout screens, involving both RNAi and CRISPR/Cas9 technologies. We designed lentiviral shRNA and sgRNA libraries targeting 730 RBPs, which we transduced in cell lines allowing controlled super-activation of MYC, in order to identify genes whose expression was specifically required in this condition. A series of candidates emerged from our screens, including UPF1 and XRN1, two RBPs involved in mRNA turnover and in particular in nonsense-mediated mRNA decay (NMD). Biological validation in different systems confirmed our screening results and allowed us to extend our observations to other NMD factors, thus identifying NMD as a critical pathway in MYC-overexpressing cells. Addressing the mechanisms underlying the synthetic lethality between MYC and NMD shall not only allow us to unravel this unexpected crosstalk, but shall also pave the way toward the development of new therapeutic opportunities against MYC-dependent tumors.

Pseudomonas aeruginosa est un pathogène opportuniste responsable d’infections nosocomiales sévères associées à un taux élevé de mortalité. Le système de sécrétion de Type III (SST3) et les effecteurs qu’il injecte sont considérés comme des facteurs de virulence prépondérants de P. aeruginosa. Récemment nous avons caractérisé, un groupe de souches ne possédant pas les gènes du SST3, mais dont la virulence repose sur la sécrétion d’une nouvelle toxine de 172 kDa, nommée Exolysine (ExlA) qui provoque la perméabilisation de la membrane des cellules hôtes. ExlA est sécrétée dans le milieu par une porine de la membrane externe, nommée ExlB, formant ainsi un nouveau système de sécrétion à deux partenaires (TPS), ExlBA. Outre le domaine TPS du coté N-terminal de la protéine, impliqué dans sa sécrétion, ExlA possède différents domaines ; des répétitions hémagglutinines, cinq motifs Arginine-Glycine-Acide Aspartique (RGD) et un domaine C-Terminal faiblement conservé. Des tests de cytotoxicité sur des cellules eucaryotes ont montrés que la délétion du domaine C-terminal abolissait l’activité toxique d’ExlA. En utilisant un modèle de liposomes et différents types de cellules eucaryotes, comme les globules rouges, nous avons démontré qu’ExlA forme des pores membranaires de 1.6 nm. De plus, par un criblage cellulaire à haut-débit d’une banque de mutants obtenus par une mutagenèse de transposition, nous avons montré qu’un facteur bactérien additionnel était requis dans la toxicité d’ExlA. En effet, parmi les 7 400 mutants, nous avons identifiés 3 transposons insérés dans des gènes codant pour le pili de type IV, démontrant ainsi que cet appendice impliqué dans l’adhésion des bactéries participe à la toxicité d’ExlA, en permettant un contact rapproché entre la bactérie et les cellules hôtes. Un criblage de macrophages primaires de souris KO pour différentes protéines impliquées dans la voie de l’activation de l’inflammasome, nous a permis de démontrer que le pore formé par ExlA est responsable de l’activation de la Caspase-1 par l’inflammasome NLRP3 conduisant à la maturation de l’interleukine-1ß. Une étude bio-informatique a révélé la présence de gènes homologues à exlA chez d’autres espèces de Pseudomonas non pathogènes, comme P. putida, P. protegens, P. entomophila. Nous avons montré que ces bactéries environnementales sont aussi capables de provoquer une mort cellulaire dépendante de la Caspase-1. Finalement, un criblage d’une banque de macrophages dont les gènes ont été invalidés par la technologie CRISPR/cas9 a révélé que plusieurs protéines du système immunitaire, indirectement liées à l’activation de la Caspase-1 sont impliquées dans la mort cellulaire médiée par ExlA. De plus, nous avons montré que plusieurs sgRNAs ciblant un microARN, mir-741, était grandement enrichi dans les macrophages ayant résisté à une infection avec ExlA. Mir-741 régule l’expression d’enzymes (St8sIa1 et Agpat5) impliquées dans la voie de biosynthèse des sphingolipides et des glycérophospholipides, suggérant ainsi que l’activité d’ExlA requiert un environnement lipidique particulier<br>Pseudomonas aeruginosa is a human opportunistic pathogen responsible for nosocomial infections associated with high mortality. The type III secretion system (T3SS) and T3SS-exported toxins have been considered as key infectivity virulence factors. Our team recently characterized a group of strains lacking T3SS, but employing a new pore-forming toxin of 172 kDa, named Exolysin (ExlA) that provokes cell membrane disruption. In this work we demonstrated that the ExlA secretion requires ExlB, a predicted outer membrane protein encoded in the same operon, showing that ExlA-ExlB define a new active Two-Partner Secretion (TPS) system. In addition to the TPS secretion signals, ExlA harbors several distinct domains, which comprise hemagglutinin domains, five Arginine-Glycine-Aspartic acid (RGD) motifs and a non-conserved C-terminal region lacking any identifiable sequence motifs. Cytotoxic assays showed that the deletion of the C-terminal region abolishes host-cell cytolysis. Using liposomes and eukaryotic cells, including red blood cells, we demonstrated that ExlA forms membrane pores of 1.6 nm. Based on a transposon mutagenesis strategy and a high throughput cellular live-dead screen, we identified additional bacterial factors required for ExlA-mediated cell lysis. Among 7 400 mutants, we identified three transposons inserted in genes encoding components of the Type IV pili, which are adhesive extracellular appendices. Type IV pili probably mediate close contact between bacteria and host cells and facilitate ExlA cytotoxic activity. These findings represent the first example of cooperation between a pore-forming toxin of the TPS family and surface appendages to achieve host cell intoxication. Using mice primary bone marrow macrophages we showed that ExlA pores provoke activation of Caspase-1 via the NLRP3-inflamasomme followed by the maturation of the pro-interleukin-1ß. Mining of microbial genomic databases revealed the presence of exlA-like genes in other Pseudomonas species rarely associated with human infections P. putida, P. protegens and P. entomophila. Interestingly, we showed that these environmental bacteria are also able to provoke Caspase-1 cleavage and pro-inflammatory cell death of macrophages. Finally, genome-wide loss-of-function CRISPR/cas9 RAW library screen revealed that several components of the immune system response, indirectly linked to Caspase-1 are involved in the ExlA-mediated cell lysis. Moreover, we found at least three sgRNAs targeting miRNA, mir-741 were highly enriched in resistant macrophages challenged by ExlA. This miRNA regulates enzymes (St8sIa1 and Agpat5) in the sphingolipids and glycerophololipids biosynthesis pathways, suggesting that ExlA activity may require proper lipid environment

ESCRT (Endosomal Sorting Complex Required for Transport) proteins regulate cell surface receptor degradation by sorting and packaging ubiquitinated cargoes into the intraluminal vesicles of multivesicular bodies (MVBs). A range of human diseases including cancer, and neurodegeneration display altered expression or are caused by mutations of ESCRT subunits. Studies have shown that Drosophila tissues lacking ESCRTs display neoplastic-like features like overproliferation and polarity defects, partly due to aberrant signalling including Notch signalling. To understand ESCRT-regulated processes in vivo, we utilised modification of a deformed wing phenotype specifically caused by knockdown (RNAi) of Vps25, an ESCRT-II subunit. We systematically screened chromosomal regions and identified 204 genetic interactors of Vps25 that enhanced/suppressed the phenotype. They include genes that function in trafficking, signalling, transcription, ion transport and many other biological processes; suggesting that ESCRTs influence a wide range of biological processes. We have focused on a subset of these hits that regulate tissue growth with a secondary screen based on modification of a Delta-driven eye overgrowth phenotype, isolating a subset of 43 genes involved in regulating tissue growth, some of which are novel and uncharacterised. Human orthologues of some of these genes are important in cancers; dropout (dop), whose mammalian orthologues are the MAST kinases, have been shown to contribute towards breast cancer development. dop mediates Delta-driven eye overgrowth possibly by upregulating Delta expression. In human cells, MAST2 does not affect Notch signalling but might contribute to tumorigenesis by regulating the NFκB pathway. We have also characterised another interactor, CG12163 which is the homologue of mammalian Cathepsin F. Mutations in Cathepsin F cause a rare form of neuronal ceroid lipofuscinosis (NCL) called Type B Kufs disease. Our Drosophila model which recapitulates aspects of the human disease phenotype suggests that defects in autophagy might underlie the pathogenesis of NCLs.

GWAS (Genome wide association studies) have aided in the discovery of various novel variants associated with diabetes. However, a detailed study is required to uncover the role of these genes and to determine how their dysfunction affects pathophysiology. Previous work in the lab has been successful in establishing zebrafish as an efficient model to characterise the effects of these candidate genes. Consequently, efforts have been also made to establish zebrafish as an efficient model system for drug screening as well. The current POP (Proof of principle) study aims to find whether treatment with tolbutamide drug in zebrafish carrying MODY (Maturity onset diabetes of the young) mutations has the similar effects in humans. The study employed zebrafish carrying five (gck, hnf1a, hnf1ba, hnf1bb, pdx1) CRISPR induced MODY orthologues. The zebrafish larvae were supplemented with tolbutamide drug from 5dpf till 10dpf (day post fertilisation). At 10dpf, larvae were screened for various glycaemic traits, whole body glucose and lipids as well body size. CRISPR-CAS9- induced mutations were quantified using paired end sequencing. The results showed that treatment with tolbutamide had a significant effect on the hyperglycaemic outcome induced by hnf1bb, hnf1a, and pdx1 mutations which was in line with the known effects of the drug in humans. In conclusion, the POP study proved to be successful in leveraging zebrafish as an efficient model system for, in vivo characterisation of drugs and can likely help to identify novel targets for therapeutic interventions.

The highly specialized cells of the eye function in concert to produce clear vision, one of the most valued senses. Visual impairment or blindness can occur as a result of disease or trauma. Age-related macular degeneration, glaucoma, cataracts and diabetic retinopathy are common causes of vision loss in older individuals. This thesis explores the bioinformatics approaches based on the central dogma as a model for exploring the experimental models for human eye diseases including quality control of stem cells to detect chromosomal abnormalities; epigenetic age prediction of ocular tissues; identification of novel genes in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) knockout screening in uveal melanoma; and RNA-Seq analysis to understand the molecular mechanisms in oxygen-induced retinopathy and differentiation of dental pulp mesenchymal stem cells into trabecular meshwork cells. In a virtual karyotyping study, I investigated the utility of a low-density genome-wide SNP array for the karyotypic assessment of human pluripotent stem cells (hPSCs) using the Illumina Infinium HumanCore BeadChip. Specifically, the resolution of these arrays in detecting chromosomal aberrations and their ability to identify clonal variations was determined. It was shown that the SNP array can detect chromosomal abnormalities when at least 25% of the cell population is aberrant. Our data demonstrate that an array-based karyotyping offers an economical and robust sampling method, in the genomic resolution, compared with standard cytogenetic karyotyping of hPSCs. This approach could provide a reliable, rapid and costeffective assessment of hPSCs clonality and virtual karyotype for large-scale generation and maintenance of hPSCs. To investigate the effects of aging among different tissues, we calculated the DNA methylation age of whole peripheral blood and ocular tissue from the same individual and compared it with the person’s chronological age. We found significant differences between chronological and epigenetic ages (p<0.048). Our study showed that there is a significant difference (mean = 44.4 years) between chronological and epigenetic age in neurosensory retinal tissue and the same pattern identified by various tools. Through a CRISPR knockout screening study, we used the Human GeCKOv2 pooled library in OCM1 cell lines (uveal melanoma) to identify novel genes that are associated with tumorigenesis using the CRISPRAnalyzeR tool on next-generation sequencing data. Overall, from our analysis, we found 15 genes that have relatively low expression in the passage 12 as compared to the passage 0 and are associated with the metabolic process, cellular process, primary metabolic process, cellular metabolic process, biological process and organic substance metabolic process. Our study shows that these genes are crucial for cell proliferation; however, further in-vitro and in-vivo validation is required. In RNA-Seq studies, we investigated the miRNA expression in oxygen-induced retinopathy (OIR) rat models through next-generation sequencing (RNA-Seq) data. Our RNA-Seq data suggested that the expression of miR-143 dysregulated and mediated the regulatory networks, leading to retinal neovascularization. Furthermore, miR-143 can influence cellular motion and cell-matrix interaction during vascular formation. We also found that miR-126, miR-150 is significantly down-regulated and directly involved in retinal neovascularization. We also investigated the propensity of mesenchymal stem cells (MSC) populations (dental pulp-derived MSCs) to differentiate into trabecular meshwork (TM) cells. We performed RNA sequencing under two conditions: control (DPMSCs) and treated (with growth factors to differentiate into the TM cells). Overall, we found over 8000 genes that are statistically significant and have an association with tissue development, extracellular matrix development and related pathways, and demonstrated the ability of DPMSCs to differentiate into TM cells. Using bioinformatics techniques to develop models of blinding eye diseases can lead to new and better treatments to preserve vision.

碩士<br>國立臺灣大學<br>分子醫學研究所<br>107<br>Macrophages are crucial players in immune regulation. They have a wide spectrum of activation states depend on the diverse surrounding stimuli they receive. Classical activation (M1) and alternative activation (M2) are described as two extremes of their polarized states, which elicit pro-inflammatory responses and anti-inflammatory responses respectively to maintain tissue homeostasis. Regnase-1 is a ribonuclease essential in controlling immune responses by regulating mRNA decay of proinflammatory cytokines, and it is reported to be important in promoting macrophage M2 polarization in which ER stress, ROS and autophagy are involved. However, detailed regulatory mechanism of this pathway is remained unclear. The goal of our study is to perform a genome-scale CRISPRi-dCas9 screening to explore new regulators in Regnase-1 mediated M2 polarization. By flow cytometry detection of M2 markers expression, we can identify genes that after CRISPRi disruption and Regnase-1 overexpression lead to decreased M2 expression, as potential regulators in this pathway. We have tested and compared the M2 phenotypes of four mice macrophage cell lines and examined the M1/M2 discrimination of several M2 markers by flow cytometry analysis. Our results demonstrated the M2 discriminating ability of Egr2 and CD206, which by flow cytometry detection can together be used to distinguish M2 phenotypes in both BMDMs and immortalized BMDMs. We have also established CRISPRi-Regnase-1 and inducible Regnase-1 overexpression system for further proof-of-principle screening and the preparations of the large-scale screening. Our data also infer a potential relation between ER stress related protein and M2 polarization, which is to be further investigated in the future works.

碩士<br>國立陽明大學<br>藥理學研究所<br>104<br>Fabry disease is a hereditary, X-linked lysosomal storage disease resulting from deficient activity of the lysosomal α-galactosidase A. It leads to progressive accumulation of glycosphingolipids particularly globotriaosylceramide (GL-3) in lysosomes of the heart, kidneys, skin and various tissues. Regular administration of recombinant human alpha Gal A (rh-α-GLA), termed enzyme replacement therapy (ERT) is currently available as the only effective treatment for the Fabry patients with GL-3 accumulation. However, the rh-α-GLA driven GL-3 clearance has the limitations, i.e. rh-α-GLA is physiologically instable and quickly degraded in cells. Moreover, lacking of an appropriate in vitro disease model restricted the pharmaceutical studies for improving the ERT treatment. Therefore, it is worth to establish a cell model of Fabry disease (FD) as the platform to screen the potential candidates for prolonging its potency. By utilizing the CRISPR/Cas9 genome editing system, we generated the GLA disruption in HEK293T cells that was completely devoid of detectable GLA protein expression and enzyme activity, providing a clear background to investigate rh-α-GLA cellular pharmacokinetics. The administrated rh-α-GLA was decreased with time and had a half-life of 24 hrs in the GLA-null cells. Base on the GLA deficient cell line, we applied to discover the potential drug or small molecular to restore rh-α-GLA activity. Co-treatment of chaperone drug, N-butyldeoxygalactonojirimycin (NB-DGJ), and protease inhibitor, E64, with ERT significantly prolonged rh-α-GLA activity by over two-folds compared to ERT alone. In addition, NB-DGJ and E64 significantly decreased GL-3 accumulation in the Fabry patients-derived fibroblast. Next, we expanded the screening range of drug and identified the activity for discovering other potential drugs. We screened 64 drugs combining ERT in GLA-null cells and discovered that Calpain inhibitor II, E64C, 2-NBDG, β-D-Galactose pentapivalate, 2-Deoxy-D-galactose, Finasteride, Diazepam, Theophylline, Trazodone, Benzamidine, 3-Methyladenine, Carbamazepine, Selegiline, Sulpiride and Fluorouracil could prolong rh-α-GLA activity. By creating this model, we provide a novel in vitro tool with which to screen potential compounds to avoid short period of GLA activity in human body.

RUNX1 est un facteur de transcription essentiel pour l’hématopoïèse et joue un rôle important dans la fonction immunitaire. Des mutations surviennent dans ce gène chez 5 à 13% des patients atteints de leucémie myéloïde aiguë (LMA) (RUNX1mut) et définissent un sous-groupe particulier de LMA associé à un pronostic défavorable. En conséquence, il est nécessaire de procéder à une meilleure caractérisation génétique et de concevoir des stratégies thérapeutiques plus efficaces pour ce sousgroupe particulier de LMA. Bien que la plupart des mutations trouvées dans le gène RUNX1 dans la LMA soient supposément acquises, des mutations germinales dans RUNX1 sont observées chez les patients atteints du syndrome plaquettaire familial avec prédisposition aux hémopathies malignes (RUNX1-FPD, FPD/AML). En outre, 44 % des individus atteints évoluent vers le développement d’une LMA. Suite au séquençage du transcriptome (RNA-Seq) d’échantillons de la cohorte Leucégène, nous avons montré que le dosage allélique de RUNX1 influence l’association avec des mutations coopérantes, le profil d’expression génique et la sensibilité aux médicaments dans les échantillons primaires de LMA RUNX1mut. Aussi, la validation des mutations trouvées chez RUNX1 a mené à la découverte que 30% des mutations identifiées dans notre cohorte de LMA étaient d’origine germinale, révélant une proportion plus élevée qu’attendue de cas de mutations RUNX1 familiales. Un crible chimique a, quant à lui, révélé que la plupart des échantillons RUNX1mut sont sensibles aux glucocorticoïdes (GCs) et nous avons confirmé que les GCs inhibent la prolifération des cellules de LMA et ce, via l’interaction avec le récepteur des glucocorticoïdes (Glucocorticoid Receptor, GR). De plus, nous avons observé que les échantillons contenant des mutations RUNX1 censées entraîner une faible activité résiduelle étaient plus sensibles aux GCs. Nous avons aussi observé que la co-association de certaines mutations, SRSF2mut par exemple, et les niveaux de GR contribuaient à la sensibilité aux GCs. Suite à cela, la sensibilité acquise aux GCs a été obtenue en régulant négativement l’expression de RUNX1 dans des cellules LMA humaines, ce qui a été accompagné par une régulation positive de GR. L’analyse de transcriptome induit par GC a révélé que la différenciation des cellules de LMA induite par GCs pourrait être un mécanisme en jeu dans la réponse antiproliférative associée à ces médicaments. Plus important encore, un criblage génomique fonctionnel a identifié le répresseur transcriptionnel PLZF (ZBTB16) comme un modulateur spécifique de la réponse aux GCs dans les cellules LMA sensibles et résistantes. Ces observations fournissent une caractérisation supplémentaire de la LMA RUNX1mut, soulignant l’importance de procéder à des tests germinaux pour les patients porteurs de mutations RUNX1 délétères. Nos résultats ont également identifié un nouveau rôle pour RUNX1 dans le réseau de signalisation de GR et montrent l’importance d’investiguer le repositionnement des GCs pour traiter la LMA RUNX1mut dans des modèles précliniques. Enfin, nous avons fourni des indications sur le mécanisme d’action des GCs, en montrant que PLZF s’avère un facteur important favorisant la résistance aux GCs dans la LMA.<br>RUNX1 is an essential transcription factor for definite hematopoiesis and plays important roles in immune function. Mutations in RUNX1 occur in 5-13% of Acute Myeloid Leukemia (AML) patients (RUNX1mut ) and are associated with adverse outcome, thus highlighting the need for better genetic characterization and for the design of efficient therapeutic strategies for this particular AML subgroup. Although most RUNX1 mutations in AML are believed to be acquired, germline RUNX1 mutations are observed in the familial platelet disorder with predisposition to hematologic malignancies (RUNX1-FPD, FPD/AML) in which about 44% of affected individuals progress to AML. By performing RNA-sequencing of the Leucegene collection, we revealed that RUNX1 allele dosage influences the association with cooperating mutations, gene expression profile, and drug sensitivity in RUNX1mut primary AML specimens. Validation of RUNX1 mutations led to the discovery that 30% of RUNX1 mutations in our AML cohort are of germline origin, indicating a greater than expected proportion of cases with familial RUNX1 mutations. Chemical screening showed that most RUNX1mut specimens are sensitive to glucocorticoids (GC) and we confirmed that GCs inhibit AML cell proliferation via interaction with the Glucocorticoid Receptor (GR). We observed that specimens harboring RUNX1 mutations expected to result in low residual RUNX1 activity were most sensitive to GCs, and that co-associating mutations, such as SRSF2mut, as well as GR levels contribute to GC-sensitivity. Accordingly, acquired GC-sensitivity was achieved by negatively regulating RUNX1 expression in human AML cells, which was accompanied by upregulation of the GR. GC-induced transcriptome analysis revealed that GC-induced differentiation of AML cells might be a mechanism at play in the antiproliferative response to these drugs. Most critically, functional genomic screening identified the transcriptional repressor PLZF (ZBTB16) as a specific modulator of the GC response in sensitive and resistant AML cells. These findings provide additional characterization of RUNX1mut AML, further stressing the importance of germline testing for patients carrying deleterious RUNX1 mutations. Our results also identified a novel role for RUNX1 in the GR signaling network and support the rationale of investigating GC repurposing for RUNX1mut AML in preclinical models. Finally, we provided insights into the mechanism of action of GCs, which positions PLZF as an important factor promoting resistance to glucocorticoids in AML.