Academic literature on the topic 'Anemia di Fanconi'

Anemia Fanconi adalah kelainan autosom resesif dapat disebabkan karena kelainanbawaan atau faktor genetik, yang nantinya cenderung mengarah keganasan. Gen yangbermutasi pada penyakit ini di kenal sebagai FANC (Fanconi Anemia Complementation).Gambaran klinis muncul secara progresif akibat kegagalan sumsum tulang,mengakibatkan kelainan fisik yang paling sering berupa perawakan pendek,hiperpigmentasi kulit, abnormal pada kepala seperti mikrosefali ataupun hidrosefali.Temuan yang lain sangat mendasari ialah kelainan hematologi dimana jumlah eritrositmengalami penurunan.

Abstract Fanconi anemia (FA) is a rare inherited syndrome characterized by chromosomal instability, eventually resulting in a number of manifestations affecting the hematopoietic system and other organs. The phenotype of FA patients is largely heterogeneous, and encompasses different clinical manifestations that may be present at birth, or rather develop later during the disease course. Thus, even due to the rarity of the disease, the natural history of FA remains hard to be established in its details. To accomplish the need of a large disease registry, in 1994 we have established at the local health unit "ASL Napoli 1" a National Database named as "Registro Italiano Anemia di Fanconi " (RIAF): here we report on a 20-year experience of the Italian FA Registry. Patients were enrolled prospectively at diagnosis or later on, after signature of the informed consent form; epidemiological, genetic and clinical data were recorded at registration, with these latter information eventually collected periodically to assess the clinical course, possible complications and long-term survival. The main endpoint of the study was the description of the natural history, looking for the following variables: family history, disease presentation, development of hematological manifestations, development of malignancies, occurrence of hematopoietic stem cell transplantation (HSCT) and survival. Between 1994 and 2014 a total of 180 patients were included in the RIAF, belonging to 151 distinct families; all diagnoses were based on standard chromosome DEB (diepoxybutane) - or MMC (mytomicin C) - breakage test confirmed at specialized centers. The median age at diagnosis was 3170 days, and it was lower in patients born in the more recent periods; the median follow up of enrolled patient was 15.6 years. For the majority of patients the diagnosis was suspected based on the typical morphological abnormalities and/or growth retardation; congenital abnormalities (mostly skin pigmentation and skeletal abnormalities) were demonstrated in 90% of patients. The majority of patients (77%) exhibited some hematological abnormalities at diagnosis, which in most cases was a mild-to-moderate cytopenia. Looking at the subsequent disease course, a total of 172 (96%) FA patients developed some hematological manifestations, typically progressive cytopenia due to bone marrow failure. The cumulative incidences (CI) of any hematological disorder were 62%, 88% and 94% at 10, 20 and 30 years, respectively, whereas those of a hematological malignancy were 5%, 8% and 22% at 10, 20 and 30 years. Hematological manifestations led to an allogeneic hematopoietic stem cell transplantation (HSCT) in more than half of the patients (57%), with a CI of HSCT of 33%, 64% and 72%% at 10, 20 and 30 years, respectively; patients born in the most recent years were transplanted earlier. The presence at diagnosis of a solid tumor was quite rare; nevertheless, solid tumors were the most significant complication in the long-term period, with a CI of 1%, 15% and 32% at 10, 20 and 30 years respectively; head and neck were the most common cancer sites. Eighty-eight of the 180 FA patients enrolled in the RIAF died during their follow up; in non-transplanted patients, the main causes of death were related to the underlying disease (infections, bleeding, and solid tumors), whereas in transplanted patients graft versus host disease and other transplant-related complications played a major role. The median survival of this large cohort was 22.5 years; overall survival at 10, 20 and 30 years were 88%, 56% and 37%, respectively, with no improvement over the past decades. These data confirm the poor long-term prognosis of FA patients, irrespective of earlier diagnosis and improved treatment options achieved in the most recent years. Figure 1. Overall survival of the 180 patients enrolled in the RIAF Figure 1. Overall survival of the 180 patients enrolled in the RIAF Disclosures Risitano: Alexion Pharmaceuticals: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Alnylam: Consultancy, Research Funding; Rapharma: Consultancy, Research Funding; Novartis: Research Funding; Pfizer: Consultancy.

Abstract The Fanconi anemia (FA) pathway is a major player in the control of DNA replication integrity in response to replication stress. Germline defect in the pathway results in the FA syndrome characterized by developmental abnormalities, bone marrow (BM) failure, and genome instability which greatly elevates the incidence of cancers. A pivotal step in the activation of the FA DNA repair pathway is the monoubiquitination of the FANCD2 and FANCI proteins (ID2) by the FA core complex, a unique ubiquitin ligase complex which includes eight proteins (FANCA-FANCG, FANCL, and FAAP100) and UBE2T/FANCT. This monoubiquitination event enables the recruitment of the ID2 complex to chromatin and nuclear foci at sites of DNA damage. Cells with mutations in any of the FA core complex proteins lack the ability to monoubiquitinated ID2, making ID2 ubiquitination a convergence point in the pathway, with an estimation of>90% FA patients defective in this step. Additionally, somatic mutations In FA genes render tumor cells sensitive to DNA crosslinking agents, so identification of FA pathway defects provides an opportunity for therapeutic targeting. In search for additional potential target/substrate of this unique FA core ubiquitin ligase complex, we performed a high throughput genome-wide ubiquitin-specific proteomics (UbiScan) screen and found, in addition to the ID2 complex, many ubiquitinated proteins are dysregulated (mostly downregulated) in FA deficient cells compared with that of FA proficient cells. We used a Ubiquitin Remnant Motif (K- ∑-GG) Antibody Bead Conjugate (Cell Signaling Technology), a proprietary ubiquitin branch ("K- ∑-GG") antibody with specificity for a di-glycine tag that is the remnant of ubiquitin left on protein substrates after trypsin digestion, to enrich ubiquitinated peptides from trypsin digested cell samples (shNT vs shFANCA). This enrichment is followed by LC-MS/MS analysis for quantitative profiles of hundreds to over a thousand nonredundant ubiquitinated sequences. We were successful in demonstrating that under steady-state conditions (without proteasome inhibitor treatment), the ubiquitinated forms of both FANCD2 and FANCI proteins are much higher in control (shNT) HeLa cells compared with that of the cells depleted of FANCA (shFANCA). We then collaborated with the Cell signaling technology to perform a high throughput UbiScan® analysis of total ubiquitinated proteins both in total nuclei and chromatin fractions under replicative stress conditions. UbiScan® enables researchers to isolate, identify and quantitate large numbers of ubiquitin-modified cellular peptides with a high degree of specificity and sensitivity, providing a global overview of the ubiquitination sites in cellular proteins in cell and tissue samples without preconceived biases about where these modified sites occur. A total of 16,249 redundant modified peptide assignments to 7,856 modified sites for the Ubiquitin K-GG Remnant Motif Antibody were obtained. As expected, the amount of monoubiquitinated FANCD2 (at K651) and FANCI (at K523) were highly reduced in both the nuclear and chromatin fractions of Hela cells depleted of FANCA (shA). Consistent with the earlier findings, the amount of ubiquitinated ID2 proteins were extremely low in the chromatin fraction of the Hela cells depleted of FANCA. Since there are numerous ubiquitinated proteins found to be dysregulated in our UbiScan analyses, we used the following criteria to select the target proteins based on; a) -fold changes, and b) proteins that are known to participate in the DNA repair signaling pathways. We validated our UbiScan results by using an assay system to detect endogenous protein ubiquitination. We also found a significant reduction in the ubiquitination of several DNA repair-related proteins (found in our UbiScan analysis) in FANCA deficient cells. To assess FA pathway functions, we generated HAP1 and appropriate cells knock out of these select ubiquitinated target proteins by using CRISPR-Cas9 system. Then, the KO cells were examined for FA pathway functions. These results will be discussed. In conclusion, our findings reveal that the FA core ubiquitin ligase complex regulates (directly or indirectly) the ubiquitinated levels of many novel proteins outside of the ID2 complex, and these novel target proteins may provide important additional mechanistic insights into the FA DNA repair pathway. Disclosures No relevant conflicts of interest to declare.

Members of the ubiquitin-like protein family are known for their ability to modify substrates by covalent conjugation. The highly conserved ubiquitin relative UBL5/Hub1, however, is atypical because it lacks a carboxy-terminal di-glycine motif required for conjugation, and the whole E1-E2-E3 enzyme cascade is likely absent. Though the conjugation-mediated role of UBL5/Hub1 is controversial, it undoubtedly functions by interacting non-covalently with its partners. Several interactors of UBL5/Hub1 identified to date have suggested broad stress-responsive functions of the protein, for example, stress-induced control of pre-mRNA splicing, Fanconi anemia pathway of DNA damage repair, and mitochondrial unfolded protein response. While having an atypical mode of function, UBL5/Hub1 is still a stress protein that regulates feedback to various stimuli in a similar manner to other ubiquitin-like proteins. In this review, I discuss recent progress in understanding the functions of UBL5/Hub1 and the fundamental questions which remain to be answered.

Abstract The DNA damage response (DDR) pathway is frequently deregulated in cancer and it represent an attractive therapeutic opportunity. In acute myeloid leukemia (AML), different mechanisms of DDR deregulation have been identified, but a systematic investigation on DDR alterations is missing. To understand how the DDR pathways contribute to leukemogenesis, we studied the gene expression and mutational profiles of 274 DDR genes by analysing 539 AML cases profiled by whole genome (WGS) and RNA sequencing. WGS data were used to identify mutations in genes of the DDR and in a panel of genes known to be mutated in AML (n=73). Transcriptomic data were analysed through unsupervised clustering, differential expression and enrichment analysis. We detected 150 single nucleotide variants (SNVs) in 130 patients (24%, average 0.3 SNVs/case). Genes mutated in more than 1% of cases were ATM, BLM, BRCA2, POLG and POLQ. The most frequently altered pathway was the homologous recombination/Fanconi Anemia (HR) pathway (29%), followed by the genes that coordinates the DDR pathway (20%). We detected a trend toward mutual exclusivity between mutations in TP53 and mutations in genes of HR pathway or the genes that coordinates the DDR pathway (adj-p <0.02). To further investigate the interplay between TP53 mutations and the HR pathway, we analysed the expression profiles of HR genes in 539 patients. We identified two groups of patients having higher (HR-high) or lower (HR-low) expression levels of HR genes. A panel of 5 genes was able to discriminate patients between the two groups (BRCA1, RAD54B, RMI2, UBE2T and XRCC2; AUC=0.9). Enrichment analysis on differentially expressed genes and gene set enrichment analysis showed that the cell cycle pathway, together with the G2/M transition/mitotic phase, E2F targets and the fatty acid metabolism pathways were upregulated in HR-high patients, while the pRB, EZH2, RPS14 and HOXA9 pathways were downregulated. Moreover, we observed that AML expressing CBFB-MYH1, RUNX1-RUNXT1 or carrying RAD21 mutations had higher chances to express lower levels of HR genes (HR-low), while patients with STAG2, SRSF2, U2AF1, FLT3-ITD alterations had higher chances of having higher expression of HR genes (p<0.05). NPM1-mutated cases without FLT3-ITD clustered within the HR-low profile (adj-p<0.05), while TP53 mutated cases tended to cluster in the HR-high group, although statistical significance was not reached. In conclusion, our data showed the presence of alterations in the DDR pathway that might be the reflection of driver events in AML. Functional studies will elucidate the functional impact of these alterations. The results suggested the presence of a therapeutic window that might be exploited with DDR inhibitors in molecularly-defined subgroups of patients. Supported by the Torsten Haferlach-Leukämiediagnostik-Stiftung and AIRC IG 2019 (project 23810). Citation Format: Antonella Padella, Stephan Hutter, Wencke Walter, Constance Baer, Irene Azzali, Andrea Ghelli Luserna Di Rorà, Martina Ghetti, Lorenzo Ledda, Matteo Paganelli, Claudia Haferlach, Wolfgang Kern, Giorgia Simonetti, Giovanni Martinelli, Torsten Haferlach. Genomic and transcriptomic profiles of DNA damage response genes in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5788.

Abstract BRCA1 is one of the most important gene associated with familial breast and ovarian cancer susceptibility and is involved in the DNA damage repair and cell cycle arrest. Alterations in BRCA1 and their consequences are well characterized in breast and ovarian tumors, while little is known about its role in Acute Myeloid Leukemia (AML). We aimed to investigate the frequency and the interplay of BRCA1 alterations and patterns of somatic mutations (SNVs) and copy number variations (CNVs) of in AML patients. We genotyped 118 AML samples at either diagnosis or relapse by Single Nucleotide Polymorphism (SNP) array (SNP6.0 and Cytoscan HD, Affymetrix) to detect CNVs. In addition, we performed Whole-Exome Sequencing (WES, 100 bp paired-end, Illumina) of 56 genotyped AML patients to detect SNVs and small indels (MuTect and Varscan 2.0). Differences in survival were assessed using Kaplan-Meier survival analysis and Long-Rank test, or Breslow when indicated. We detected BRCA1 loss in 14 out of 118 patients (12%), ranging from 1,6 Kb to the loss of the entire chromosome 17, with none of the BRCA1 loss patients having a normal karyotype. Moreover, BRCA1 losses significantly co-occurred with PALB2 and RAD50 losses. Notably, the PALB2 loss (chromosome 16) mostly involved exon 12 and was detected also in patients without the BRCA1 loss, with a frequency of 11 out of 118 cases (9%), suggesting a pivotal and previously undescribed role in AML pathogenesis. BRCA1 loss patients were enriched for copy number alterations in genes involved in the regulation of mitotic recombination, DNA repair and positive regulation of kinase activity compared with BRCA1 wild-type cases (p <0.01). To investigate which genes and biological functions cooperates with the pathways affected by structural alterations, we integrated the analysis with WES data on 56 out of 118 AML patients. We focused on the genes involved in the DNA damage repair (DDR) and we identified somatic SNVs in BRCA1, TP53 and in the Fanconi Anemia genes BRCA2 and FANCE. Analysis of co-occurrence and mutual exclusivity revealed that BRCA1 loss and DDR-related alterations (BRCA1, PALB2, BRCA2, and FANCE) were significantly associated with TP53 alterations (p=0.0001 and p=0.0003, respectively). In addition, alterations in the DDR genes were mutually exclusive with mutations in KRAS, IDH1/2, BCOR, BCORL1, NPM1 and myeloid transcription factors as RUNX1 and CEBPA. Notably, patients without alteration in the DDR genes were enriched for mutations in DNMT3A and FLT3. Finally, BRCA1 and PALB2 alterations defined group of patients with poor overall survival (OS). In particular, patients with alterations of either BRCA1 or PALB2 had a worst prognosis compared to patients without alterations in the two genes (p=0.009 and p=0.001, respectively). Patients harboring PALB2 loss had a poorer prognosis compared with patients with complex karyotype (p=0.021, Breslow test). In addition, double BRCA1 and PALB2 loss, single BRAC1 or PALB2 hits and lack of alterations in BRCA1 and PALB2 defined three different classes of risks in our AML cohort (p<0.001). In summary, we define for the first time a novel subgroup of AML patients characterized by alterations targeting the DDR pathway, and in particular the BRCA1 and PALB2 genes. Our data suggest that a signature of genes involved in the DDR and cell cycle regulation synergize and led to the uncontrolled proliferation, independently of DNA damage accumulation. Our results may help improve patient stratification and define ad hoc therapeutic strategies for this aggressive leukemia type. Acknowledgments: ELN, AIL, AIRC, progetto Regione-Università 2010-12 (L. Bolondi), Fondazione del Monte di Bologna e Ravenna, FP7 NGS-PTL project. Disclosures Guadagnuolo: CellPly S.r.l.: Employment. Martinelli:Novartis: Speakers Bureau; Genentech: Consultancy; Roche: Consultancy, Speakers Bureau; BMS: Speakers Bureau; Celgene: Consultancy, Speakers Bureau; Amgen: Consultancy, Speakers Bureau; MSD: Consultancy; Pfizer: Consultancy, Speakers Bureau; Ariad: Consultancy, Speakers Bureau.

Abstract Abstract 885 Philadelphia-positive (Ph+) chronic myeloid leukemia (CML) has always been regarded as a genetically homogeneous disease. However, the fact that a proportion of patients (pts), especially in the high Sokal risk setting, fail tyrosine kinase inhibitor therapy and progress to blast crisis (BC) suggests that a certain degree of heterogeneity exists. It can be hypothesized that genetic factors additional to the Ph+ chromosome may be present in these pts. To address this issue, we are currently using massively parallel sequencing to perform a qualitative and quantitative survey of the whole transcriptome of Ph+ CML cells at diagnosis and at progression to BC. Results are being integrated with genome-wide search for copy number alterations by Affymetrix SNP 6.0 arrays. We used a Solexa Illumina Genome Analyzer to scan the transcriptome of a CML patient at the time of diagnosis, at the time of remission (major molecular response) and at the time of progression from chronic phase (CP) to lymphoid blast crisis (BC). Both custom scripts and published algorithms were used for read alignment against the human reference genome, for single nucleotide variant (SNV) calling, for identification of alternative splicings and fusion transcripts, and for digital gene expression profiling. Comparison of the SNVs identified in the diagnosis and relapse samples with the SNVs detected in the remission sample – representing inherited sequence variants not specific for the Ph+ clone – allowed the identification of eight missense mutations at diagnosis affecting the coding sequences of AMPD3 (encoding adenosine monophosphate deaminase 3), SUCNR1 (succinate receptor 1), FANCD2 (Fanconi anemia, complementation group D2), INCENP (inner centromere protein), BSPRY (B-box and SPRY domain containing), HEXDC (hexosaminidase containing), NUDT9 (ADP-ribose diphosphatase) and KIAA2018 (encoding a protein with predicted DNA binding and transcriptional regulation activity) genes. Six of these mutations (FANCD2, INCENP, BSPRY, HEXDC, NUDT9) were also detected in the Ph+ clone re-emerged at the time of disease progression, together with seven additional missense mutations affecting the coding sequences of IDH2 (isocitrate dehydrogenase isoform 2), DECR1 (2,4-dienoyl CoA reductase 1), C4Orf14 (mitochondrial nitric oxide synthase), MRM1 (mitochondrial rRNA methyltransferase 1), PRKD2 (protein kinase D2), TCHP (mitostatin) and ABL1 genes. Digital gene expression analysis showed downregulation of SUCNR1, that might be a consequence of the P292A mutation we detected. IDH2, MRM1, AMPD3, and KIAA2018 mutations were found in additional pts. The IDH2 R140Q mutation was detected in 3/75 (4%) myeloid BC, 1/31 (3.2%) lymphoid BC, 0/34 Ph+ ALL and 0/23 Philadelphia-negative (Ph-) ALL pts. The MRM1 C120S mutation was found in 6/70 (9%) additional BC pts (2 lymphoid and 4 myeloid). AMPD3 and KIAA2018 genes were found to harbour the same point mutations (N334S and S1818G, respectively) in 1 out of 20 additional CP patients analyzed. Massively parallel sequencing of the sample collected at diagnosis also revealed that the Bcr-Abl kinase domain was already harbouring point mutations at low levels (E308D, A344G, R386S) but not the T315I that was selected at the time of disease progression. Point mutations in untraslated regions where miRNAs are known to bind were also detected, and are currently under validation. Digital gene expression profiling comparing progression to diagnosis showed significant expression changes including upregulation of 134 genes and downregulation of 88 genes. In particular, we observed an upregulation of the B-cell developmental factor PAX5, its interactor Lef-1 and its targets IRF4, BLNK, Bik, EBF1, CD79A, CD79B, CD19, VpreB1, VpreB3, BOB1, RAG1 and RAG2; upregulation of PAX9; upregulation of WNT3A, WNT9A, GLI3 and downregulation of SFRP1, resulting in aberrant activation of the Wnt signalling pathway. In summary, our preliminary data highlighted putative key genes whose deregulation may be recurrent in a subset of CML patients and may be linked to disease pathogenesis or progression. Their actual role in CML is currently being exlored. Massively parallel sequencing of additional patients is ongoing. Supported by European LeukemiaNet, AIL, AIRC, Fondazione Del Monte di Bologna e Ravenna, FIRB 2006, PRIN 2008, Ateneo RFO grants. Disclosures: Baccarani: NOVARTIS: Honoraria; BRISTOL MYERS SQUIBB: Honoraria. Martinelli:Novartis: Consultancy, Honoraria; BMS: Consultancy, Honoraria; Pfizer: Consultancy.

2012/2013
L’anemia di Fanconi (FA) è una malattia genetica rara caratterizzata da malformazioni congenite, pancitopenia, predisposizione al cancro e aumentata sensibilità ad agenti, quali diepossibutano e mitomicina C, che formano legami tra i due filamenti di DNA. La FA è causata da almeno 16 geni che costituiscono, insieme ad altri componenti, un pathaway di riparazione del DNA. L’eterogeneità è uno dei principali motivi che complica la diagnosi molecolare della FA. E’ pertanto necessario un processo a più livelli che implica lo screening di molti esoni o, in alternativa, l’allestimento di linee cellulari e l’analisi di complementazione per la caratterizzazione del gene candidato. Gli scopi di questa tesi pertanto sono diretti a: • Ridurre i tempi per l’identificazione del gene mutato sostituendo l’analisi di complementazione con quella di espressione delle proteine FA basandosi sul presupposto che prodotti mutati siano rapidamente degradati; • Caratterizzare dal punto di vista molecolare gli effetti delle varianti identificate dall’analisi di sequenza. Per quanto riguarda il primo obiettivo, ci siamo focalizzati sullo studio della proteina FANCA in 44 linee cellulari linfoblastoidi appartenenti ai diversi gruppi di complementazione. E’ emerso che, fatta eccezione per FA-G, l’espressione di FANCA non è alterata da mutazioni nei geni FANCB, FANCC e FANCD2. Per quanto riguarda i pazienti con mutazioni in FANCA, invece, abbiamo osservato una correlazione tra il tipo di mutazione e il livello di espressione della proteina che può quelli essere paragonabile a quella dei controlli nel caso di mutazioni missenso o ampie delezioni in frame. In accordo con l’ipotesi invece, in presenza di mutazioni nonsenso e frameshift in entrambi gli alleli del gene, non si ha produzione di proteina. Sulla base di questi dati possiamo concludere che l’analisi di FANCA non è soddisfacente per assegnare ai pazienti il corrispondente gruppo di complementazione. Tuttavia, da questo studio è emersa l’ipotesi di un’associazione tra l’espressione stabile delle proteine FANCA mutate e un fenotipo meno grave nei pazienti. I dati preliminari dimostrano che queste proteine non sono traslocate nel nucleo e che quindi un’eventuale attività residua non sia da attribuire al processo di riparazione del DNA. Un potenziale ruolo andrebbe forse indagato a livello citoplasmatico dove, come sta emergendo dalla letteratura, almeno FANCG e FANCC, svolgono una funzione all’interno del mitocondrio tale da giustificare l’elevato grado di stress ossidativo delle cellule FA. Per il secondo obiettivo, lo studio dei casi arruolati nell'ambito dell'AIEOP (Associazione Italiana Ematologia Oncologia Pediatrica) ha consentito l'identificazione delle mutazioni in 100 famiglie. Dall’analisi dei dati emerge che la maggior parte delle mutazioni colpisce il gene FANCA (85%), seguito da FANCG (9%), FANCC (3%), FANCD2 (2%) e FANCB (1%). In assenza del dato di complementazione e/o in presenza di varianti alle quali non è sempre possibile attribuire un chiaro effetto patogenetico, sono state eseguite ulteriori indagini. Si citano a titolo di esempio la caratterizzazione delle ampie delezioni intrageniche mediante MLPA, l’analisi bioinformatica e a livello di RNA delle alterazioni di splicing che, qualora in frame, sono state ulteriormente confermate anche a livello proteico e, infine, lo studio bioinformatico di patogenicità delle sostituzioni aminoacidiche. La formulazione di un algoritmo efficace e rapido per la diagnosi molecolare della FA, nonché la chiara definizione del significato patogenetico delle varianti identificate, è molto importante per corretta presa in carico del paziente e della famiglia sia per l’identificazione dei portatori che per la diagnosi prenatale.
XXVI Ciclo
1984

2013/2014
Next Generation Sequencing (NGS) technologies, such the Ion Torrent platform, could allow to simplify the diagnostic process of diseases characterized by an high genetic and phenotypic heterogeneity, because of the possibility to sequence simultaneously more genes and more patients in a single sequencing run. In order to develop a new diagnostic algorithm for rapid molecular diagnosis of these disorders, we have applied the Ion Torrent technology on two different genetically heterogeneous diseases, Fanconi anemia (FA) and inherited thrombocytopenias (IT). Since FA is a disorder better characterized than ITs, we first validated the Ion torrent technology on 30 samples (2 wild type and 28 FA), 25 of which were already analyzed with Sanger sequencing. Because of their low sequencing quality, we have excluded from this type of analysis 2 of the 28 FA samples. Then, comparing Ion Torrent and Sanger sequencing data, we have evaluated the sensitivity (95%) and the specificity (100%) of Ion Torrent technology. Moreover, in order to detect copy number variations (CNVs) in FA genes, we have improved a statistical analysis based on coverage sequencing data, confirming the presence of large intragenic deletions on FANCA in 5 patients. In summary we have characterized 25 of the 26 FA patients analyzed, identifying also 4 mutant alleles in the rare complementation group FANCL and FANCF and 10 mutations in loci different from genes causing the disease. Since we cannot exclude that new genes are involved in FA, the only patient without any mutation identified is suitable for whole exome analysis. Taking advantage from these good sequencing data, we have developed a diagnostic algorithm that combines the identification of both point mutations and CNVs. In order to verify if this new diagnostic process could be applied also to other genetically heterogeneous diseases, we have analyzed 21 IT patients, already characterized by Sanger sequencing. Among the 2225 variants identified by Ion torrent technology, using this new approach, we have select those (N=75, 56 different) potentially pathogenetic because of their frequency (MAF<0.01), or of their presence in IT mutation database o because of bioinformatics analysis. Thirty of these variants were confirmed by Sanger sequencing, 14 (12 different) of which localized in loci different from the gene causing the disease. It would be interesting to carry out functional studies on these additional variants to unravel the molecular basis of ITs. In summary we were able to characterized 17 of the 21 IT patients, including 2 patients with deletions in RBM8A (Thrombocytopenia and Absent Radii syndrome, TAR). The remaining 4 mutant alleles were not detected because of a low sequencing coverage. In conclusion, according to our data, we can consider the Ion Torrent technology and in particular the diagnostic algorithm proposed in our study, as a feasible approaches for the study of diseases characterized by high genetic and phenotypic heterogeneity. RIASSUNTO Le tecnologie di Next Generation Sequencing (NGS) consentono di analizzare più geni e più campioni contemporaneamente. In questo modo potrebbe essere possibile ridurre i tempi e i costi di analisi di tutte quelle patologie caratterizzate da elevata eterogeneità genetica e fenotipica, la cui caratterizzazione risulta essere spesso complessa e dispendiosa. Al fine di elaborare un nuovo algoritmo diagnostico che consenta la rapida elaborazione di una diagnosi molecolare di tali patologie, abbiamo deciso di validare una tra le più innovative tecnologie NGS attualmente in commercio, la metodica Ion Torrent, su due differenti malattie, entrambe caratterizzate da eterogeneità genetica. l’anemia di Fanconi (FA) e le piastrinopenie ereditarie (IT). Siccome la FA è una patologia meglio caratterizzata rispetto alle IT, durante la prima fase di questo lavoro di tesi abbiamo analizzato 30 campioni (25 dei quali già precedentemente analizzati con sequenziamento Sanger), di cui 2 wild type e 28 affetti. In seguito all’esclusione dalla nostra analisi di 2 campioni FA a causa di una bassa qualità di sequenziamento, abbiamo determinato la sensibilità (95%) e la specificità (100%) della nuova metodica confronto i dati di sequenziamento Ion Torrent e quelli Sanger a nostra disposizione. Inoltre, utilizzando i dati di copertura della sequenza, abbiamo messo a punto un’analisi statistica volta all’identificazione delle Copy Number Variation (CNV), confermando le delezioni a carico del gene FANCA presenti in 5 pazienti. Abbiamo quindi caratterizzato 25 dei 26 pazienti analizzati, identificando inoltre 2 casi con mutazioni nei rari gruppi di complementazione FANCF e FANCL e 10 mutazioni in loci differenti dai geni causativi. Poiché non escludiamo la possibilità che un nuovo gene possa essere coinvolto nella patologia, riteniamo che l’unico paziente ancora privo di diagnosi molecolare possa essere un buon candidato per lo studio dell’esoma. Infine, avvalendoci dei buoni risultati ottenuti, abbiamo elaborato un nuovo processo diagnostico con il quale identificare in modo semplice e rapido sia le mutazioni sia le CNV a carico dei 16 geni coinvolti nella FA. Nella seconda parte del nostro studio, abbiamo verificato se l’applicazione di tale algoritmo possa essere estesa anche ad altre patologie ad elevata eterogeneità genetica. Per questo motivo abbiamo analizzato 21 campioni affetti da piastrinopenie ereditarie, già precedentemente analizzati mediante sequenziamento Sanger. Grazie all’algoritmo proposto abbiamo potuto selezionare tra le 2225 varianti identificate le 75 (56 differenti) che sono risultate essere potenzialmente patogenetiche in base alla loro frequenza nella popolazione (MAF<0.01), alla loro presenza nei database di mutazione e all’analisi bioinformatica di patogenicità. Trenta (27 differenti) di queste varianti sono state confermate mediante sequenziamento Sanger, di cui in particolare 14 (12 differenti) presenti in geni diversi da quelli causativi. Alla luce di questo dato si rendono necessari studi funzionali su tali varianti al fine di comprendere i meccanismi molecolari alla base delle piastrinopenie ereditarie. Infine, utilizzando l’algoritmo proposto, è stato possibile confermare la diagnosi molecolare in 17 dei 21 pazienti IT, compresi i 2 affetti da trombocitopenia con assenza del radio (TAR) e portatori di una delezione sul cromosoma 1q21.1. I restanti 4 alleli mutati non sono stati identificati a causa di una bassa copertura di sequenziamento. In conclusione, in base ai dati raccolti sui campioni affetti da FA e IT, possiamo affermare che la tecnologia di sequenziamento Ion Torrent e l’algoritmo diagnostico da noi proposto sono degli strumenti utili per ottenere una diagnosi molecolare completa, veloce ed economica.
XXVII Ciclo
1984