Genetica molecolare dell'autismo: studi di associazione ed analisi di geni candidati

Autism is a neurodevelpmental disorder characterized by impaired verbal communication, limited reciprocal social interaction, restricted interests and repetitive behaviours. Twin and family studies indicate a large genetic contribution to ASDs (Autism Spectrum Disorders). During my Ph.D. I have been involved in several projects in which I used different genetic approaches in order to identify susceptibility genes in autism on chromosomes 2, 7 and X: 1)High-density SNP association and CNV analysis of two Autism Susceptibility Loci. The International Molecular Genetic Study of Autism Consortium (IMGSAC) previously identified linkage loci on chromosomes 7 and 2, termed AUTS1 and AUTS5, respectively. In this study, we evaluated the patterns of linkage disequilibrium (LD) and the distribution of haplotype blocks, utilising data from the HapMap project, across the two strongest peaks of linkage on chromosome 2 and 7. More than 3000 SNPs have been selected in each locus in all known genes, as well as SNPs in non-genic highly conserved sequences. All markers have been genotyped to perform a high-density association analysis and to explore copy number variation within these regions. The study sample consisted of 127 and 126 multiplex families, showing linkage to the AUTS1 and AUTS5 regions, respectively, and 188 gender-matched controls. Association and CNV analysis implicated several new genes, including IMMP2L and DOCK4 on chromosome 7 and ZNF533 and NOSTRIN on the chromosome 2. Particularly, my contribution to this project focused on the characterization of the best candidate gene in each locus: On the AUTS5 locus I carried out a transcript study of ZNF533 in different human tissues to verify which isoforms and start exons were expressed. High transcript variability and a new exon, never described before, has been identified in this analysis. Furthermore, I selected 31 probands for the risk haplotype and performed a mutation screen of all known exons in order to identify novel coding variants associated to autism. On the AUTS1 locus a duplication was detected in one multiplex family that was transmitted from father to an affected son. This duplication interrupts two genes: IMMP2L and DOCK4 and warranted further analysis. Thus, I performed a screening of the cohort of IMGSAC collection (285 multiplex families), using a QMPSF assay (Quantitative Multiplex PCR of Short fluorescent Fragments) to analyse if CNVs in this genic region segregate with autism phenotype and compare their frequency with a sample of 475 UK controls. Evidence for a role of DOCK4 in autism susceptibility was supported by independent replication of association at rs2217262 and the finding of a deletion segregating in a sib-pair family. 2)Analysis of X chromosome inactivation. Skewed X chromosome inactivation (XCI) is observed in females carrying gene mutations involved in several X-linked syndromes. We aimed to estimate the role of X-linked genes in ASD susceptibility by ascertaining the XCI pattern in a sample of 543 informative mothers of children with ASD and in a sample of 164 affected girls. The study sample included families from different european consortia. I analysed the XCI inactivation pattern in a sample of italian mothers from singletons families with ASD and also a control groups (144 adult females and 40 young females). We observed no significant excess of skewed XCI in families with ASD. Interestingly, two mothers and one girl carrying known mutations in X-linked genes (NLGN3, ATRX, MECP2) showed highly skewed XCI, suggesting that ascertainment of XCI could reveal families with X-linked mutations. Linkage analysis was carried out in the subgroup of multiplex families with skewed XCI (≥80:20) and a modest increased allele sharing was obtained in the Xq27-Xq28 region, with a peak Z score of 1.75 close to rs719489. In this region FMR1 and MECP2 have been associated in some cases with austim and therefore represent candidates for the disorder. I performed a mutation screen of MECP2 in 33 unrelated probands from IMGSAC and italian families, showing XCI skewness. Recently, Xq28 duplications including MECP2, have been identified in families with MR, with asymptomatic carrier females showing extreme (>85%) skewing of XCI. For these reason I used the sample of probands from X-skewed families to perform CNV analysis by Real-time quantitative PCR. No duplications have been found in our sample. I have also confirmed all data using as alternative method the MLPA assay (Multiplex Ligation dependent Probe Amplification). 3)ASMT as functional candidate gene for autism. Recently, a possible involvement of the acetylserotonin O-methyltransferase (ASMT) gene in susceptibility to ASDs has been reported: mutation screening of the ASMT gene in 250 individuals from the PARIS collection revealed several rare variants with a likely functional role; Moreover, significant association was reported for two SNPs (rs4446909 and rs5989681) located in one of the two alternative promoters of the gene. To further investigate these findings, I carried out a replication study using a sample of 263 affected individuals from the IMGSAC collection and 390 control individuals. Several rare mutations were identified, including the splice site mutation IVS5+2T>C and the L326F substitution previously reported by Melke et al (2007), but the same rare variants have been found also in control individuals in our study. Interestingly, a new R319X stop mutation was found in a single autism proband of Italian origin and is absent from the entire control sample. Furthermore, no replication has been found in our case-control study typing the SNPs on the ASMT promoter B.

Studio di Mutazioni Geniche e Variazioni Copy-Number implicate nel deficit combinato degli Ormoni Ipofisari(CPHD)

La crescita normale di un individuo è il risultato dell’azione coordinata di molteplici ormoni e recettori codificati da geni e a tal proposito, discreto interesse è stato dato ai geni tipici dell’asse del GH. Tuttavia altri geni, più a monte di questi e responsabili dello sviluppo dell’ipofisi contribuiscono alla crescita normale o patologica. Alcuni geni studiati sono POU1F1, PROP1, LHX3, LHX4, HESX1, SOX3 e svariate loro mutazioni sono state identificate come causa di panipopituarismo (CPHD=Combined Pituitary Hormone Deficiency). In realtà la ricerca genetica non spiega ancora molte anomalie ipofisarie e molte mutazioni devono ancora essere identificate. Uno degli scopi del dottorato, svoltosi nel laboratorio di Genetica molecolare di Pediatria, è stata l’identificazione di mutazioni geniche da un gruppo di pazienti CPHD considerando in particolare i geni POU1F1, LHX3, SOX3, non ancora messi a punto presso il laboratorio. L’approccio sperimentale si è basato sulle seguenti fasi: prelievo delle informazioni di sequenza da GeneBank, progettazione di primers per amplificare le porzioni esoniche, messa a punto delle fasi della PCR e del sequenziamento, analisi della sequenza e confronto con le informazioni di sequenza depositate allo scopo di rintracciare eventuali mutazioni o varianti. La bassa percentuale di mutazioni in questi geni non ha permesso finora di rintracciare mutazioni nelle porzioni esoniche salvo che in un soggetto, nell’esone 6 di LHX3b (nuova mutazione, recessiva eterozigote, c.1248A>G implicata nella mutazione p.T377A della sequenza proteica). Un metodo di screening di questa mutazione impiegando l’enzima di restrizione SacII è stato usato, senza rilevare nessun altra occorrenza dell’allele mutato in 53 soggetti di controllo. Oltre alla messa a punto del sequenziamento e di alcune tecniche di analisi di singoli SNP o piccoli INDELs per i 3 geni, la ricerca svolta è stata orientata all’impiego di metodi di rilevamento di riarrangiamenti genetici comportanti ampie delezioni e/o variazioni del copy-number di esoni/interi geni detto MLPA (Multiplex Ligation-dependent Probe Amplification) e progettato da MRC-Holland. Il sequenziamento infatti non permette di rilevare tali alterazioni quando sono ampie ed in eterozigosi. Per esempio, in un’ampia delezione in eterozigosi, l’intervallo delimitato dai primers usati per la PCR può non includere totalmente la porzione interessata da delezione su un cromosoma cosicché la PCR ed il sequnziamento si basano solo sulle informazioni dell’altro cromosoma non deleto. Un vantaggio della tecnica MLPA, è l’analisi contemporanea di una quarantina di siti posti su svariati geni. Questa metodo tuttavia può essere affetto da un certo margine di errore spesso dipendente dalla qualità del DNA e dovrebbe essere affiancato e validato da altre tecniche più impegnativa dal punto di vista sperimentale ma più solide, per esempio la Real Time PCR detta anche PCR quantitativa (qPCR). In laboratorio, grazie all’MLPA si è verificata la condizione di delezione eterozigote di un paziente “storico” per il gene GH1 e la stessa mutazione è stata rilevata anche con la qPCR usando lo strumento Corbett Rotor Gene 6000 (Explera). Invece un’analisi solo con la qPCR di variazioni del copy-number (CNV) per SOX3 in pazienti maschili non ha ancora evidenziato anomalie. Entrambe le tecniche hanno aspetti interessanti, il miglior approccio al momento sembra un’analisi iniziale di pazienti con l’MLPA, seguita dalla verifica di un eventuale esito anomalo impiegando la real-time PCR.