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>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.

Il Fusarium verticillioides (Fv) causa il marciume rosa della spiga e contamina le cariossidi con fumonisine, una famiglia di micotossine che colpisce mangimi e alimenti considerata cancerogena per l'uomo e gli animali. Sono stati condotti diversi studi per identificare i geni del mais associati alla resistenza della pianta ospite all'infezione da Fv e l'accumulo di fumonisina. È noto che le ossilipine regolano la difesa contro i patogeni e che il cross-talk lipidico ospite-patogeno influenza la patogenesi. A questo proposito, i mutanti di mais trasposonici del gene ZmLOX4, la linea suscettibile W22 e la resistente TZI18 sono stati testati per la resistenza a Fv mediante il saggio biologico Rolled Towel Assay (RTA). Inoltre, sono stati studiati i profili di espressione di 16 geni coinvolti nella via LOX e volatili verdi (GLV) e l'attività della lipossigenasi è stata analizzata nelle stesse linee. Inoltre, è stata applicata la tecnologia di modifica del genoma di Clustered Shortspeed Palindromic Repeat / Cas9 associato (CRISPR / Cas9) regolarmente esaminata per indagare le possibili implicazioni del gene ZmLOX6 e del fattore di trascrizione ZmWRKY125 nei meccanismi di resistenza contro Fv. L'espressione di questi geni è stata precedentemente osservata dagli esperimenti di RNA - Seq in genotipi resistenti al mais e Studi di Genome Wide Association (GWAS) che hanno portato a un SNP significativamente associato a ZmWRKY125. Inoltre, il gene ZmLOX4 è stato overespresso nella linea A188 per valutare un possibile miglioramento della resistenza alla malattia verso Fv. Il lavoro molecolare del CRISPR si basa su una doppia clonazione utilizzando due diverse single guide RNA (sgRNA) per un bersaglio genico. I costrutti sotto il promotore ZmpUBI nel vettore binario p1609 sono stati trasformati nella linea A188 utilizzando la trasformazione mediata da Agrobacterium tumefaciens. Le piante di mais modificate nei geni ZmLOX6 e ZmWRKY125 e ZmLOX4 che sovraesprimono saranno caratterizzate per RTA, prove sperimentali in campo e per il loro contenuto di fumonisina. Inoltre, saranno testati l’attività lipossigenasica totale, i suoi metaboliti derivati ​​e le osslipine, oltre all'analisi dell'espressione dei principali geni coinvolti nella via dell'acido jasmonico. / Fusarium verticillioides (Fv) causes ear rot in maize and contaminates the kernels with fumonisins, a family of mycotoxins that affects feed and food and considered carcinogenic for humans and animals. Several studies were conducted to identify maize genes associated with host plant resistance to Fv infection and fumonisin accumulation. It is known that plant lipoxygenase (LOX)-derived oxylipins regulate defense against pathogens and that the host-pathogen lipid cross-talk influences the pathogenesis. In this regard, maize mutants carrying Mu insertions in the ZmLOX4 gene, the susceptible W22 and the resistant TZI18 lines were tested for Fv resistance by the screening method rolled towel assay (RTA). Additionally, the expression profiles of 16 genes involved in the LOX and green leaves volatiles (GLV) pathway were studied and the lipoxygenase activity was investigated in the same lines as well. Furthermore, the genome editing technology of Clustered Regularly Interspaced Short Palindromic Repeat/associated Cas9 (CRISPR/Cas9) was applied in order to investigate the possible implication of the lipoxygenase gene ZmLOX6 and the transcription factor ZmWRKY125 in the resistance mechanisms against Fv. The enhanced expression of these genes was previously observed by RNA - Seq experiments in maize resistant genotypes and Genome Wide Association Studies (GWAS) resulted in one SNP significantly associated with ZmWRKY125. Moreover, the gene ZmLOX4 was over-expressed in the line A188 for evaluating a possible improvement of the disease resistance towards Fv. The CRISPR cloning was based on a double cloning using two different guides (sgRNA) for one gene target. The constructs under the maize promoter ZmpUBI in the binary vector p1609 were transformed into the maize A188 line using Agrobacterium tumefaciens mediated transformation. Maize plants edited in the genes ZmLOX6 and ZmWRKY125, and over-expressing ZmLOX4 will be characterized for Fv resistance using rolled towel assay, field assay and for their fumonisin content. Furthermore, the content of jasmonic acid, its derivative metabolites, and oxylipins will be tested, as well as the expression analysis of the main genes involved in the jasmonic acid pathway will be performed.

La diversité morphologique des muscles squelettiques permet la précision et la coordination des mouvements propres à chaque espèce animale. L'établissement du patron musculaire a lieu au cours du développement embryonnaire durant le processus de myogenèse. Il a été décomposé en quatre étapes chez la drosophile : la spécification de groupes de myoblastes équivalents (groupes promusculaires) à des positions précises du mésoderme, la sélection d'une ou plusieurs cellules progéniteurs à partir de chaque groupe, la division asymétrique des progéniteurs en cellules fondatrices des muscles, et enfin, la fusion d'une cellule fondatrice avec un nombre défini de myoblastes compétents pour la fusion qui forme une myofibre syncytiale. Ce processus aboutit à la mise en place d'un patron stéréotypé de muscles morphologiquement distincts par leur taille, orientation, forme, et sites d'attachement au squelette ; ces caractères définissant l'identité du muscle. Chez la drosophile, chacun des 30 muscles par hémisegment de la larve est constitué d'une seule myofibre. Il a été proposé que l'identité morphologique de cette fibre soit contrôlée par une combinatoire de facteurs de transcription identitaires (FTi) exprimés par la cellule fondatrice. Mon projet de thèse a porté sur le contrôle transcriptionnel de l'identité musculaire, avec comme modèle d'étude, un muscle dorso-latéral de la larve de drosophile, le muscle DA3 dont un FTi est Collier/EBF (Col). La transcription de col est activée dans un groupe promusculaire, puis transitoirement dans les quatre progéniteurs issus de ce groupe, avant d'être maintenue spécifiquement dans la myofibre DA3. Dans des embryons mutants pour col, le DA3 est transformé en muscle plus dorsal, DA2. Les travaux précédents de l'équipe ont montré que la transcription de col dans le lignage DA3 est contrôlée par deux modules cis-régulateurs, EarlyCRM et LateCRM, séparés physiquement sur le chromosome et agissant séquentiellement. Leur chevauchement temporel d'activité restreint au progéniteur DA3 et l'autorégulation directe du LateCRM ont mené à l'hypothèse d'un mécanisme de " passage de témoin " entre ces deux CRM, spécifique au progéniteur DA3. L'objectif de ma thèse était de tester cette hypothèse et de comprendre comment une information temporelle et spatiale intégrée par un CRM est transmise à un autre CRM, pour définir une identité cellulaire, une question fondamentale au-delà du cas d'espèce que constitue le muscle DA3.[...] / The morphological diversity of skeletal muscles allows the precision and coordination of movements specific to each animal species. Establishment of a stereotypic pattern of muscles takes places during the process of myogenesis. Studies in Drosophila, an insect model, have identified four steps in this process: the specification of equivalence groups of myoblasts (promuscular clusters) at defined positions within the somatic mesoderm, the selection of progenitor(s) from each group, asymmetric division of each progenitor into post-mitotic muscle founder cells, and finally the fusion of each founder cell with a given number of fusion competent cells to form a syncytial myofiber. This dynamic, integrated process leads to establishing a stereotyped pattern of morphologically distinct muscles which can each be distinguished, based on size, orientation, shape, sites of attachment to the skeleton, all properties defining muscle identity. In the Drosophila larva, each of the about 30 different muscles per hemisegment is made of a single myofiber. It has been proposed that final morphology of a myofiber reflects the combinatorial code of identity Transcription Factors (iTF) expressed by its founder cell, although many questions remain unanswered. My thesis project aimed at better understanding the mechanism of specification of muscle identity, using as model a dorso-lateral muscle of the Drosophila larva, the DA3 muscle whose identity is controlled by the Collier/EBF (Col) iTF. col transcription is activated in one promuscular cluster, transient in the 4 progenitors issued from this cluster and stably maintained in the DA3 myofiber. In col mutant embryos, the DA3 muscle is transformed into a more dorsal, DA2-like muscle. Previous work has shown that col transcription in the DA3 lineage is controlled by two cis-regulatory modules (EarlyCRM and LateCRM), physically distant on the chromosome and acting sequentially. The temporal overlap of EarlyCRM and LateCRM in the DA3 progenitor and direct col autoregulation via the LateCRM led to hypothesize a handover between the two CRM in the DA3 progenitor. One goal of my thesis project was to challenge this hypothesis and understand how positional and temporal information integrated by EarlyCRM could be memorized via LateCRM, in order to specify cell identity, a fundamental question of developmental biology beyond the specific case of the Drosophila DA3 muscle. [...]