Comprendere come lo stato genetico di TP53 influenza la risposta al deficit indotto sul Complesso I mitocondriale come terapia anticancro

Il Complesso I (CI) mitocondriale è uno dei target metabolici più promettenti nelle terapie anti- cancro. In particolare, la metformina è un inibitore noto del CI, capace di inibire la crescita delle cellule tumorali, ma non di eradicare la patologia. Recentemente, l’associazione metformina ed ipoglicemia si è rivelata letale per i tumori, sebbene l’efficacia terapeutica del trattamento sinergico possa essere influenzata dall’accumulo di alterazioni genetiche nei più noti drivers della tumorigenesi. Abbiamo così investigato l’effetto dello stress metabolico indotto dalla restrizione di glucosio in un pannello di linee cellulari tumorali con un severo deficit sul CI e con un diverso stato genetico di TP53. Il deficit del CI associato alla carenza di glucosio inducono un abbattimento dei livelli di espressione della proteina p53 mutata, ma non della controparte wild-type. Il fenomeno biologico osservato non dipende né da un blocco trascrizionale, né dall’innesco di vie di degradazione intracellulare, come proteasoma ed autofagia. La scomparsa di p53 mutata, invece, sembra dipendere da un blocco generale della sintesi proteica, verosimilmente indotto dallo stress energetico e nutrizionale. Nella controparte p53 wild-type, invece, si osserva solo una parziale riduzione della sintesi proteica, suggerendo l’innesco di possibili vie di adattamento per compensare il danno sul CI. La carenza di amminoacidi è una caratteristica dei tumori solidi che potrebbe essere esacerbata in condizioni di deficit generali della catena respiratoria mitocondriale. In particolare, l’inibizione del CI causa auxotrofia da aspartato, metabolita limitante per la proliferazione, condizione che potrebbe generare il blocco della sintesi proteica osservato. L’incremento di espressione dei livelli del trasportatore aspartato/glutatammato mediata da p53 mutata compensa l’auxotrofia da aspartato, identificando un meccanismo di adattamento al deficit del CI. Dunque, i risultati ottenuti sottolineano l’importanza di implementare la terapia anti-complesso I nel cancro, poiché il diverso stato di p53 può alterare l’efficacia del trattamento.

Harnessing the cellular and molecular complexity of high-risk neuroblastoma to investigate novel potential treatment approaches

Neuroblastoma (NB) is the most common type of tumor in infants and the third most common cancer in children. Current clinical practices employ a variety of strategies for NB treatment, ranging from standard chemotherapy to immunotherapy. Due to a lack of knowledge about the molecular mechanisms underlying the disease's onset, aggressive phenotype, and therapeutic resistance, these approaches are ineffective in the majority of instances. MYCN amplification is one of the most well-known genetic alterations associated with high risk in NB. The following work is divided into three sections and aims to provide new insights into the biology of NB and hypothetical new treatment strategies. First, we identified RUNX1T1 as a key gene involved in MYCN-driven NB onset in a transgenic mouse model. Our results suggested that that RUNX1T1 may recruit the Co-REST complex on target genes that regulate the differentiation of NB cells and that the interaction with RCOR3 is essential. Second, we provided insights into the role of MYCN in dysregulating the CDK/RB/E2F pathway controlling the G1/S transition of the cell cycle. We found that RB is dispensable in regulating MYCN amplified NB's cell cycle, providing the rationale for using cyclin/CDK complexes inhibitors in NBs carrying MYCN amplification and relatively high levels of RB1 expression. Third, we generated an M13 bacteriophage platform to target GD2-expressing cells in NB. Here, we generated a recombinant M13 phage capable of binding GD2-expressing cells selectively (M13GD2). Our results showed that M13GD2 chemically conjugated with the photosensitizer ECB04 preserves the retargeting capability, inducing cell death even at picomolar concentrations upon light irradiation. These results provided proof of concept for M13 phage employment in targeted photodynamic therapy for NB, an exciting strategy to overcome resistance to classical immunotherapy.

QTL mapping identifies novel major loci for ear fasciation, ear prolificacy and tillering in maize (ZEA MAYS L.)

Maize ear fasciation originates from excessive or abnormal proliferation of the ear meristem and usually manifests as multiple-tipped ear, ear flatness and/or disordered kernel arrangement. Ear prolificacy expresses as multiple ears per node. Both traits can affect grain yield. In this study, the genetic control of the two traits was analyzed using two recombinant inbred lines (RIL) populations (B73 × Lo1016 and Lo964 × Lo1016) with Lo1016 and Lo964 as donors of ear fasciation and prolificacy, respectively. Four ear fasciation-related traits (ear fasciation, kernel distribution and ear ovality indexes and ratio of ear diameters), number of kernel rows, ear prolificacy and number of tillers were phenotyped in multi-year field experiments. Ear fasciation traits and number of kernel rows showed relatively high heritability (h2 > 0.5) except ratio of ear diameters, and showed correlation. Prolificacy and tillering h2 ranged 0.41 - 0.78 and did not correlate. QTL mapping identified four QTL for ear fasciation, on chr. 1 (two QTLs), 5 and 7, the latter two overlapping with QTLs for number of kernel rows. However, the strongest effect QTL for number of kernel rows mapped on chr. 2 independently from ear fasciation. Four and five non-overlapping QTLs were mapped for ear prolificacy and tillering, respectively. Two ear fasciation QTLs from this study, qFas1.2 and qFas7, overlapped with formerly known fasciation QTLs and spanned candidate genes expressed in ear meristems namely compact plant2 and ramosa1. Our study identified novel ear fasciation, ear prolificacy and tillering loci which are unexpectedly still segregating in elite maize materials, and provides foundation for genomics-assisted breeding for yield components

Characterization and cloning of chemically-induced mutants in barley (Hordeum vulgare L.)

Induced mutagenesis has been exploited for crop improvement and for investigating gene function and regulation. To unravel molecular mechanisms of stress resilience, we applied state-of-the-art genomics-based gene cloning methods to barley mutant lines showing altered root and shoot architecture and disease lesion mimic phenotypes. With a novel method that we named complementation by sequencing, we cloned NEC3, the causal gene for an orange-spotted disease lesion mimic phenotype. NEC3 belongs to the CYP71P1 gene family and it is involved in serotonin biosynthesis. By comparative phylogenetic analysis we showed that CYP71P1 emerged early in angiosperm evolution but was lost in some lineages including Arabidopsis thaliana. By BSA-Seq, we cloned the gene whose mutation increased leaf width, and we showed that the gene corresponded to the previously cloned BROADLEAF1. By BSA coupled to WGS sequencing, we cloned EGT1 and EGT2, two genes that regulate root gravitropic set point angle. EGT1 encodes a Tubby-like F-box protein and EGT2 encodes a Sterile Alpha Motive protein; EGT2 is phylogenetically related to AtSAM5 in Arabidopsis and to WEEP in peach where it regulates branch angle. Both EGT1 and EGT2 are conserved in wheat. We hypothesized that both participate to an anti-gravitropic offset mechanism since their disruption causes mutant roots to grow along the gravity vector. By the MutMap+ method, we cloned the causal gene of a short and semi-rigid root mutant and found that it encodes for an endoglucanase and is the ortholog of OsGLU3 in rice whose mutant has the same phenotype, suggesting that the gene is conserved in barley and rice. The mutants and the corresponding genes which were cloned in this work are involved in the response to stress and can potentially contribute to crop adaptation.

Specificità, efficacia e risposte adattative mediate da mutazioni dell'oncosoppressore TP53 degli inibitori del Complesso I mitocondriale nella terapia oncologica personalizzata: dai meccanismi molecolari allo sviluppo di modelli preclinici avanzati

L'inibizione del complesso respiratorio I (CI) è una strategia antitumorale emergente, sebbene la specificità e l’efficacia di nuovi farmaci restino poco investigate. La generazione di modelli cellulari tumorali nulli per il CI rivela la specificità di EVP 4593 e BAY 872243 nell’indurre gli effetti antiproliferativi non associati all’apoptosi, selettivamente via CI, riducendo eventuali effetti collaterali. Studi preliminari in vivo evidenziano un rallentamento della crescita tumorale negli animali trattati con EVP 4593, il quale emerge come l’inibitore più potente. Per il suo ruolo nella riprogrammazione metabolica, e la sua elevata frequenza di mutazioni nelle neoplasie umane, sono stati investigati i potenziali meccanismi di adattamento alla terapia anti-CI sulla base dello stato mutazionale di TP53. L’auxotrofia da aspartato, un hallmark metabolico delle cellule tumorali con un danno al CI, causa un blocco della sintesi proteica mTORC1-dipendente nelle linee cellulari con una p53 mutata o nulla, inducendo un collasso metabolico. Viceversa, l'attivazione del sensore energetico AMPK promuove un recupero parziale della sintesi di aspartato in linee cellulari con la forma wild type di P53, che è in grado di sostenere una migliore anaplerosi attraverso SCO2, fattore di assemblaggio del complesso respiratorio IV. Al fine di traslare questi risultati in un modello preclinico, si è ottimizzato l’ottenimento di colture di tumori umani espiantati tramite il bioreattore U-CUP. Il modello scelto è stato quello di carcinoma sieroso ad alto grado dell’ovaio (HGSOC), a partire da tessuto congelato, per l’elevata frequenza di mutazioni driver in TP53. I tessuti congelati preservano l'eterogeneità delle componenti cellulari del tessuto di origine e sono caratterizzati da cellule in attiva proliferazione senza attivazione di apoptosi. Dati preliminari mostrano un trend di riduzione dell’area tumorale nei tessuti trattati con EVP 4593 e supportano l’utilizzo del modello preclinico nello studio di nuovi inibitori del CI sfruttando materiale primario di pazienti oncologici.

Identification of resistance factors to the main wheat diseases in the Mediterranean area

Several diseases challenge bread and durum wheat productions worldwide. The importance of these cereals requires adequate protection to pathogens that can cause strong yield and grain quality losses. The main work of this thesis was related to phenotype GDP (Global Durum Panel) in the Mediterranean region (Italy, Egypt, Lebanon, Morocco and Turkey) and Argentina across three years (2019-2021) for yellow rust resistance (infection type and severity). GWAS shows in particular, loci in chromosome 1B, 2B, 4B, 5A, 6A, 7B showed high significance across nurseries/years, with various patterns of GxE. The second chapter is about Zymoseptoria tritici, agent of STB (Septoria Tritici Blotch), a foliar pathogen that yearly causes high damages if not controlled. In recent years research in durum wheat breeding is focused on the identification of novel, underexploited resistance genes to be subsequently and conveniently moved into the pre-breeding and breeding stream. The plants were phenotyped for disease height characters, infection type at the flag leaf and infection type at the level of the canopy below the flag leaf. This experiment opens up a rich scenario of analysis and opportunities to investigate and discover new loci of resistance to STB. Third chapter is about Fusarium head blight (FHB) is a fungal disease caused by pathogens belonging to the genus Fusarium. In particular, Fusarium culmorum and Fusarium graminearum species cause severe grain yield losses and accumulation of mycotoxins in wheat that compromise food safety. Over 250 QTL/genes for FHB resistance have been identified in bread wheat, such as Fhb 1 and Fhb 5 but only a small number of FHB resistance loci have been mapped in durum wheat. The aim of this work is to find loci of partial resistance to FHB already present in durum and bread wheat germplasm and therefore easily cumulative.

Gwas analysis for the identification of molecular basis responsible for yield related traits and disease resistance in durum wheat

The PhD thesis was developed in the framework of Innovar H2020 project. This project aimed at using genomics, transcriptomics and phenotyping techniques to update varietal registration procedure used in Europe for Value of Cultivation and Use (VCU) and Distinctiness Uniformity and Stability (DUS) protocols. The phenotypic and genotypic diversity of a durum wheat panel were assessed for different agronomic traits, connected with wheat development, disease resistance and spike fertility. A panel of 253 durum wheat varieties was characterized for VCU and DUS traits and genotyped with Illumina 90K SNP Chip array (Wang et al., 2014). GWAS analysis was performed, detecting strong QTLs confirmed also by literature review. Candidate genes were identified for each trait and molecular markers will be developed to be used for marker assisted selection in breeding programs. As for disease resistance, the panel was evaluated for resistance to Soil-Borne-Cereal-Mosaic-Virus (SBCMV). A major QTL, sbm2, was detected on chromosome 2B responsible for durum wheat resistance (Maccaferri et al., 2011). The sbm2 interval was explored by fine mapping on segregant population using KASP markers and by RNASeq analysis, detecting candidate genes involved in plant-pathogen reaction. As regards yield related traits, detailed analysis was performed on the GNI-2A QTL (Milner et al., 2016), responsible for increased number spike fertility. Fine mapping analysis was performed on durum panel identifying hox2 a strong candidate gene, codifying for transcription factor protein. The gene is paralogue of GNI-1 (Sakuma et al., 2019), and it has a 4 kbp deletion responsible for increased number of florets per spikelet. To conclude, the herein reported thesis shows a complete characterization of agronomic and disease resistance traits in modern durum wheat varieties. The results obtained will augment available information for each variety, identifying informative molecular markers for breeding purposes and QTLs/candidate genes responsible for different agronomic traits.

Ruolo di Glutaredossina-2 nella trasformazione tumorale oncocitaria

Gli oncocitomi sono tumori epiteliali caratterizzati da un accumulo di mitocondri strutturalmente e funzionalmente compromessi, a prognosi generalmente benigna. Le cause genetiche della trasformazione oncocitaria sono tuttora sconosciute; pertanto, lo studio di oncocitomi in contesti familiari sindromici è utile nella ricerca dei determinanti genetici predisponenti il fenotipo. Diversi membri di una famiglia affetta da sindrome dell’iperparatiroidismo con tumore della mandibola (HPT-JT), dovuta ad un'ampia delezione in CDC73, hanno mostrato recidiva di tumori paratiroidei oncocitari. Il sequenziamento dell’esoma ha escluso mutazioni private della famiglia; all'interno della delezione ereditata, tuttavia, sono stati individuati elementi regolatori del gene glutaredossina 2 (GLRX2), codificante un'isoforma mitocondriale deputata alla deglutationilazione proteica reversibile -modificazione modulante l’attività di numerosi target- il cui ruolo nel cancro non è noto. La proteina è risultata assente in tutti i tumori e dimezzata nei tessuti sani dei soggetti. Per indagare se la sua assenza alteri la deglutationilazione proteica predisponendo al fenotipo oncocitario, sono stati generati modelli cellulari TPC1 e HCT116 GLRX2 KO in cui sono stati riscontrati un ridotto tasso proliferativo ed un'alterata glutationilazione proteica, particolarmente in seguito a stress ossidativo. Un esperimento pilota in vivo ha mostrato cellule KO oncocitoidi, con mitocondri morfologicamente alterati, suggerendo che l’alterazione redox innescata dall’assenza di GLRX2 possa indurre una disfunzione metabolica mitocondriale tale da mimare quelle osservate negli oncocitomi. L’analisi proteomica ha individuato diversi target di glutationilazione nei campioni KO identificando proteine del ciclo di Krebs e della catena respiratoria mitocondriale. In particolare, una marcata glutationilazione del complesso della piruvato deidrogenasi (PDHc) è stata correlata ad una ridotta sintesi di ATP dipendente da piruvato. Considerando l'importanza dello stress ossidativo nella fisiopatologia del cancro ed il ruolo del glutatione nella risposta antiossidante, GLRX2 rappresenta un potenziale candidato nella regolazione del metabolismo ossidativo nelle cellule tumorali esposte allo stress e nella modulazione del fenotipo tumorale.

Characterization of an international tetraploid wheat germplasm including landraces and primitive wheat towards improved resilience to abiotic and biotic stresses and quality

This thesis aimed to characterise two large tetraploid germplasm collections. The Global Durum Panel, involving modern cultivars and landrances and the Tetraploid Global Collection which comprises all the tetraploid wheat subgroups. Two distinct parallel studies were carried out. The first is focused on the characterisation of both collection for yield and quality related traits. The panel were phenotyped for two consecutive years each. In this phase the following traits were collected: the number of fertile spikelets per spike, the number of fertile florets of central spikelet for the spike-related traits. The following grain related traits were also phenotyped: the thousand kernel weight, the average grain area, average grain length, average grain width, grain brightness, grain redness, grain yellowness. GWAS analysis were performed for each collected trait and major QTLs were subjected to candidate gene analysis. Major QTLs emerging from GWA study were located on chromosome 2A with a strong bibliographic evidence for grain number-related traits such as the fertile spikelet number, the number of fertile florets per central spikelet. On the other hand two evident peaks were detected on chromosomes 6A and 7B for grain size and weight related traits. The second work was focused on the characterisation of the Global Durum Panel for root system architecture components, namely the root growth angle. GWAS analysis was perfomed and three major QTLs were detected on chromosome 2A, 6A and 7A. These three QTLs all have a bibliographic evidence.

Integrating structural variant calling, annotation and prioritization into whole genome analysis workflows: a practical application in the molecular diagnosis of neurodevelopmental disorders

Background: WGS is increasingly used as a first-line diagnostic test for patients with rare genetic diseases such as neurodevelopmental disorders (NDD). Clinical applications require a robust infrastructure to support processing, storage and analysis of WGS data. The identification and interpretation of SVs from WGS data also needs to be improved. Finally, there is a need for a prioritization system that enables downstream clinical analysis and facilitates data interpretation. Here, we present the results of a clinical application of WGS in a cohort of patients with NDD. Methods: We developed highly portable workflows for processing WGS data, including alignment, quality control, and variant calling of SNVs and SVs. A benchmark analysis of state-of-the-art SV detection tools was performed to select the most accurate combination for SV calling. A gene-based prioritization system was also implemented to support variant interpretation. Results: Using a benchmark analysis, we selected the most accurate combination of tools to improve SV detection from WGS data and build a dedicated pipeline. Our workflows were used to process WGS data from 77 NDD patient-parent families. The prioritization system supported downstream analysis and enabled molecular diagnosis in 32% of patients, 25% of which were SVs and suggested a potential diagnosis in 20% of patients, requiring further investigation to achieve diagnostic certainty. Conclusion: Our data suggest that the integration of SNVs and SVs is a main factor that increases diagnostic yield by WGS and show that the adoption of a dedicated pipeline improves the process of variant detection and interpretation.

Morte cardiaca improvvisa in Emilia-Romagna: caratteristiche della rete multidisciplinare e risultati dei primi quattro anni

Introduzione: dal 2018 è attiva in Emilia-Romagna una rete multidisciplinare per i casi di morte cardiaca improvvisa (MCI). In questo studio sono riportate le caratteristiche della rete e i risultati dei primi quattro anni di attività. Materiali e metodi: sono inclusi i casi di MCI avvenuti in Emilia-Romagna dal 2018 in soggetti con età > 1 anno e ≤55 anni. L’autopsia è stata eseguita secondo le raccomandazioni internazionali ed il cuore inviato all’Unità di Patologia Cardiovascolare del Policlinico di Sant’Orsola. A seconda degli scenari sono state eseguite analisi genetiche, tossicologiche e microbiologiche. In caso di patologie geneticamente determinate o nelle morti sine materia è stato avviato lo screening familiare. Risultati: nei primi quattro anni di attività sono pervenuti 83 casi (età media 37 anni). In tutti i casi è stato eseguito un esame cardio-patologico completo e in 55 soggetti (66%) l’analisi genetica. Tra i 75 casi completati, è stata identificata una causa certa/altamente probabile di decesso in 66 (88%). Le patologie coronariche sono la patologia più frequentemente diagnostica (20 casi, 27%) seguita dalle cardiomiopatie (21%), mentre in 9 soggetti è stata riscontrata una malattia infiammatoria. L’indagine genetica è stata completata in 42 casi, identificando in 8 una mutazione causativa o una variante verosimilmente patogena (materiale inidoneo in 9). Successivamente, è stato eseguito lo screening in 14 famiglie di probandi deceduti per patologie non acquisite identificando sei soggetti di altrettante famiglie con un fenotipo positivo o dubbio. L’analisi genetica ha permesso di individuare quattro parenti con la stessa mutazione/variante verosimilmente patogena del probando. Complessivamente, in quattro soggetti è stato impiantato un defibrillatore per la prevenzione primaria della MCI. Conclusioni: la rete multidisciplinare della MCI in Emilia-Romagna ha permesso di identificare una causa di decesso in quasi nove casi su dieci, diagnosticare diversi parenti affetti e approntare strategie preventive per la MCI.

Investigation of plant genetic-microbiome interactions in different plant species

The rhizosphere, i.e. the soil surrounding the plant roots, and endosphere, i.e. the microbial communities within the plant organs harbors microbes known to influence root and plant physiological processes. An important question is to what extent plant species, genotypes and environmental conditions affect bacterial and fungal communities. The objectives of the first research study were to unravel and compare the rhizospheric microbiota of grape in two independent vineyards using 16S and ITS amplicon sequencing, evaluate location and varietal effects, and test the correlation between bioavailable copper levels and other soil parameters with microbiota composition and diversity. Our results showed that the microbial alpha diversity based on Shannon index differed significantly between vineyards while it did not differ between two grape cultivars. In the second study, we were focusing on different wheat species and genotypes such as Bread Wheat, Wild Emmer Wheat, Domesticated Emmer Wheat, Durum Wheat Landraces, Durum Wheat cultivars, T. monococcum and triticale in two fields located in Bologna and Foggia. The objectives of this research experiment were to elucidate and compare the rhizospheric and endophytic microbiota of 30 diverse wheat genotypes in two different fields using 16S amplicon sequencing. Our results showed that the microbial alpha diversity based on Shannon index differed significantly between fields of Bologna and Foggia, in which Bologna had a higher diversity in respect to Foggia for both rhizospheric and endophytic communities. Using Shannon index there was significant differences, for instance, between Durum Emmer Wheat and Wild Emmer Wheat in Bologna, and between Bread Wheat and Durum Wheat Landraces in Foggia. Our results contribute to understand the role of wheat species and genotype and the filed management on the root-microbe-soil interactions in the perspective of understanding their impact on crop systems sustainability.

Exploring mediterranean durum wheat wild relatives and elite diversity panel for future breeding

Durum wheat (Triticum durum) is an important crop that has been used for millennia for human consumption, and modern breeding can take advantage of the wide variability useful for the adaptation to new challenges. Novel beneficial alleles can be found in wild relatives and landraces thus enhancing crop adaptation to many biotic and abiotic stresses. This dissertation considers the source of variability from both before and after wheat domestication, that caused a loss of potentially useful alleles. Chapter 1. is the thesis introduction, which outlines the importance of wheat in the world, providing an historical overview of the domestication, the evolution mechanisms that led to the current forms of durum wheat and the use of wild relatives as a source of germplasm for future breeding programs is crucial. Moreover, the emergence of Z. tritici has been considered as the main pathogen of wheat since it contains extremely high levels of genetic variability and is thus difficult to control. Chapter 2. Considers the contribution of the phenotypic diversity of 242 accessions of Aegilops tauschii from the Open Wild Wheat Consortium, involved in wheat domestication, provided with whole-genome resequencing. The accessions were phenotyped both in the field and in controlled conditions and A k-mer-based GWAS was performed to identify genomic regions involved in useful traits. Chapter 3. Describes the genetic basis of resistance to Z. tritici in a durum wheat elite diversity panel representative of the germplasm bred in Mediterranean. Quantitative trait loci (QTL) analysis results revealed several loci involved in the STB response that were found in several chromosome regions with a high infection rate. The genomic regions associated with STB resistance identified in this study could be of interest for marker assisted selection (MAS) in durum wheat breeding programs.

Role of CARM1 (PRMT4) in high grade serous ovarian cancer metabolism and function of PRMT5 in ARID1A- deficient endometrial cancer invasion

The arginine methyltransferase CARM1 (PRMT4) is amplified and overexpressed in ~20% of high-grade serous ovarian cancer (HGSOC) and correlates with a poor survival. Therapeutic approaches based on CARM1 expression remain to be an unmet need. Here we show that fatty acid metabolism represents a metabolic vulnerability for HGSOC in a CARM1 expression status dependent manner. CARM1 promotes the de novo synthesis of fatty acids and monounsaturated fatty acids (MUFAs). The disruption of MUFAs synthesis by inhibition of SCD1 results in excessive accumulation of cytotoxic saturated fatty acids and it is synthetic lethal with CARM1 expression. Collectively, our data show that the pharmacological inhibition of MUFAs synthesis via SCD1 inhibition represents a therapeutic strategy for CARM1-high HGSOC. Another arginine methyltransferase, PRMT5, has been identified by our CRISPR screening analysis as a promising candidate for invasive ARID1A-deficient endometrial cancer. Endometrial Cancer frequently harbor somatic inactivating mutation of ARID1A that can promote an invasive phenotype. Our in vitro approach validated the CRISPR screening showing that both PRTM5 knock down and its pharmaceutical inhibition specifically hamper the invasion of ARID1A inactivated cells. Mechanistically, PRMT5 directly regulates the epithelia to mesenchymal transition pathway genes interacting with the SWI/SNF complexes. Moreover, in vivo experiments showed that PRMT5 inhibition contrasted the myometrium invasion highlighting PRMT5 inhibition as promising therapeutic strategy for ARID1A- inactivated aggressive endometrial cancer.

Decoding Agc1 deficiency: bioinformatics approaches to unveil the functional implications of Slc25a12 on the transcriptome and epigenome

In the brain, mutations in SLC25A12 gene encoding AGC1 cause an ultra-rare genetic disease reported as a developmental and epileptic encephalopathy associated with global cerebral hypomyelination. Symptoms of the disease include diffused hypomyelination, arrested psychomotor development, severe hypotonia, seizures and are common to other neurological and developmental disorders. Amongst the biological components believed to be most affected by AGC1 deficiency are oligodendrocytes, glial cells responsible for myelination. Recent studies (Poeta et al, 2022) have also shown how altered levels of transcription factors and epigenetic modifications greatly affect proliferation and differentiation in oligodendrocyte precursor cells (OPCs). In this study we explore the transcriptomic landscape of Agc1 in two different system models: OPCs silenced for Agc1 and iPSCs from human patients differentiated to neural progenitors. Analyses range from differential expression analysis, alternative splicing, master regulator analysis. ATAC-seq results on OPCs were integrated with results from RNA-Seq to assess the activity of a TF based on the accessibility data from its putative targets, which allows to integrate RNA-Seq data to infer their role as either activators or repressors. All the findings for this model were also integrated with early data from iPSCs RNA-seq results, looking for possible commonalities between the two different system models, among which we find a downregulation in genes encoding for SREBP, a transcription factor regulating fatty acids biosynthesis, a key process for myelination which could explain the hypomyelinated state of patients. We also find that in both systems cells tend to form more neurites, likely losing their ability to differentiate, considering their progenitor state. We also report several alterations in the chromatin state of cells lacking Agc1, which confirms the hypothesis for which Agc1 is not a disease restricted only to metabolic alterations in the cells, but there is a profound shift of the regulatory state of these cells.