Papers by Pietro D'Addabbo
Genome Research
Gibbons are the most speciose family of living apes, characterized by a diverse chromosome number... more Gibbons are the most speciose family of living apes, characterized by a diverse chromosome number and rapid rate of large-scale rearrangements. Here we performed single-cell template strand sequencing (Strand-seq), molecular cytogenetics, and deep in silico analysis of a southern white-cheeked gibbon genome, providing the first comprehensive map of 238 previously hidden small-scale inversions. We determined that more than half are gibbon specific, at least fivefold higher than shown for other primate lineage-specific inversions, with a significantly high number of small heterozygous inversions, suggesting that accelerated evolution of inversions may have played a role in the high sympatric diversity of gibbons. Although the precise mechanisms underlying these inversions are not yet understood, it is clear that segmental duplication–mediated NAHR only accounts for a small fraction of events. Several genomic features, including gene density and repeat (e.g., LINE-1) content, might ren...
Blood, Nov 16, 2008
Among all cytogenetic subtypes of ALL, the BCR-ABL1 fusion gene, which is causative of chronic my... more Among all cytogenetic subtypes of ALL, the BCR-ABL1 fusion gene, which is causative of chronic myeloid leukemia (CML), defines the subgroup of ALL with the worst prognosis. The reasons of the aggressive nature of BCR-ABL1-positive ALL have not yet been completely understood. To identify, at the submicroscopic level, oncogenic lesions that cooperate with BCR-ABL1 to induce ALL and blastic transformation of CML, we used an integrated molecular approach including high resolution genomic analysis of copy number alterations by single nucleotide polymorphism (SNP) arrays (500K, Affymetrix Inc., Santa Clara, CA, USA), genomic amplification, cloning, deep sequencing, gene expression profiling (GEP) and analysis of epigenetic changes to study 97 de novo BCR-ABL1- positive ALL adult patients (pts). High level amplification and homozygous deletions were identified in all pts, with deletions outnumbering amplification almost 3:1. The most frequent somatic copy number alteration was deletion on 7p12 of IKZF1, which encodes the transcription factor Ikaros identified in 59/97 pts (61%). Ikaros is required for the earliest stages of lymphoid lineage commitment and acts as tumor suppressor in mice. The IKZF1 deletions were predominantly mono-allelic (64% vs 36%) and were limited to the gene in all cases, identifying IKZF1 as the genetic target. Real-time quantitative PCR and FISH analysis confirmed SNP results. We characterized and mapped all breakpoints to recognize that two major deletions occur in BCR-ABL1-positive ALL: type A characterized by loss of exons 4–7 (37/97, 38%) and due to breakpoints occurring in the region spanning from 50380371 to 50380388 and from 50431123 to 50431167 in introns 3 and 7, respectively; type B characterized by removal of exons 2–7 (18/97, 19%) and due to a variable pattern of breakpoints in introns 1 (from 50317112 to 50317936) and 7. A variable number of nucleotides (patient-specific) were inserted at the conjunction and maintained with fidelity at the time of relapse. The extent of both deletions correlated with the expression of a dominant-negative isoform Ik6 with cytoplasmic localization and oncogenic activity, and of an aberrant transcript containing only exons 1 and 8, respectively. Interestingly, 2 pts with a homozygosis deletion showed simultaneously both type A and B deletions. In other 2 pts, the deletion involved the whole IKZF1 gene. The IKZF1 alteration was not a frequent event across different leukemias, since it was identified also at the progression of CML to lymphoid blast crisis (66%), but never in myeloid blast crisis CML (n=10), chronic phase CML (n=30) and acute myeloid leukemia (n=28). Known DNA sequences and structural features were mapped along the breakpoint cluster regions including heptamer recombination signal sequences recognized by the RAG enzymes during V(D)J recombination and activation-induced cytidine deaminase (AID) consensus motifs (DGYW/WRCH), suggesting that IKZF1 deletions could arise from aberrant RAG and/or AID-mediated recombination. GEP analysis of pts with IKZF1 deletion vs wild-type pts identified a unique signature characterized by a down-regulation of genes involved in pre-B-cell differentiation (e.g. VPREB1, VPREB3, IGLL3), demonstrating that genomic IKZF1 alterations have a strong impact on trascriptoma and contribute to a block of B-cell differentiation. For 83 out of 97 BCR-ABL1 ALL pts correlation between molecular data and clinical outcome was available. Univariate analysis showed that the IKZF1 deletion is a negative prognostic marker influencing the cumulative incidence of relapse (10.1 months for pts with deletion vs 56.1 months for wild-type pts, p=0.0103) and disease-free survival (DFS) (10.1 months vs 32.1 months, respectively, p=0.0229). The negative prognostic impact of the IKZF1 deletion on DFS was also confirmed by multivariate analysis (p=0.0445). In conclusion, deletion of IKZF1 resulting in either haploinsuffciency and in the expression of the dominant negative isoforms is an important event in the development of BCR-ABL1 B-progenitor ALL which significantly influences clinical outcome.
MicrobiologyOpen
The Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR‐associated proteins (CRI... more The Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR‐associated proteins (CRISPR–Cas) system of prokaryotes is an adaptative immune defense mechanism to protect themselves from invading genetic elements (e.g., phages and plasmids). Studies that describe the genetic organization of these prokaryotic systems have mainly reported on the Enterobacteriaceae family (now reorganized within the order of Enterobacterales). For some genera, data on CRISPR–Cas systems remain poor, as in the case of Serratia (now part of the Yersiniaceae family) where data are limited to a few genomes of the species marcescens. This study describes the detection, in silico, of CRISPR loci in 146 Serratia complete genomes and 336 high‐quality assemblies available for the species ficaria, fonticola, grimesii, inhibens, liquefaciens, marcescens, nematodiphila, odorifera, oryzae, plymuthica, proteomaculans, quinivorans, rubidaea, symbiotica, and ureilytica. Apart from subtypes I‐E and I‐F1 which...
Frontiers in Immunology
One gene, the immunoglobulin heavy chain (IgH) gene, is responsible for the expression of all the... more One gene, the immunoglobulin heavy chain (IgH) gene, is responsible for the expression of all the different antibody isotypes. Transcriptional regulation of the IgH gene is complex and involves several regulatory elements including a large element at the 3’ end of the IgH gene locus (3’RR). Animal models have demonstrated an essential role of the 3’RR in the ability of B cells to express high affinity antibodies and to express different antibody classes. Additionally, environmental chemicals such as aryl hydrocarbon receptor (AhR) ligands modulate mouse 3’RR activity that mirrors the effects of these chemicals on antibody production and immunocompetence in mouse models. Although first discovered as a mediator of the toxicity induced by the high affinity ligand 2,3,7,8-tetracholordibenzo-p-dioxin (dioxin), understanding of the AhR has expanded to a physiological role in preserving homeostasis and maintaining immunocompetence. We posit that the AhR also plays a role in human antibody ...
The Journal of Immunology
Aim. Incomplete maturation of immune system in the first years of life could affect different ind... more Aim. Incomplete maturation of immune system in the first years of life could affect different individual response to vaccination. To investigate the issue we studied a polymorphic genomic cis regulator of Ig heavy chain in response to vaccination with viral antigens. Method. Two cohorts of healthy subjects, one not yet 3 years and a second between 21 and 26 years old were vaccinated against H1N1, H2N3, B and HBV antigens respectively. From time zero the two cohorts were followed up for the total peripheral blood levels of Ig and for specific antibodies against the vaccine antigens. Subjects were genotyped for Ig heavy chain 3’ RR structural polymorphisms of enhancer hs1.2. Results. The serum specific antibodies in subjects Non responder, Responder and High responder to the vaccination is not associated with the levels of circulating IgM, IgG, IgA. However, the humoral concentration of Ig in the adult subjects correlates with hs1.2 allelic frequency as observed previously (p<0.001...
The CRISPR-Cas system of Prokaryotes is an adaptive immune defense mechanism to protect themselve... more The CRISPR-Cas system of Prokaryotes is an adaptive immune defense mechanism to protect themselves from invading genetic elements (e.g. phages and plasmids). Studies that describe the genetic organization of these prokaryotic systems have mainly reported on the Enterobacteriaceae family (now reorganized within the order Enterobacteriales). For some genera, data on CRISPR-Cas systems remain poor, as in the case of Serratia (now part of the Yersiniaceae family) where data are limited to a few genomes of the species marcescens. This study describes the detection, in silico, of CRISPR loci in 146 Serratia complete genomes and 336 high-quality assemblies available for the species ficaria, fonticola, grimesii, inhibens, liquefaciens, marcescens, nematodiphila, odorifera, oryzae, plymuthica, proteomaculans, quinivorans, rubidaea, symbiotic, and ureilytica. Apart from subtypes I-E and I-F1, which had previously been identified in marcescens, we report that of I-C and the variants I-ES1, I-E...
VII Congresso Associazione Italiana di Biologia e Genetica Generale e Molecolare (AIBG), 2004
Il gene DSCR1L2 (1p35.3-p33), identificato e clonato nel nostro laboratorio, appartiene alla fami... more Il gene DSCR1L2 (1p35.3-p33), identificato e clonato nel nostro laboratorio, appartiene alla famiglia genica umana DSCR1L (Down Sindrome critical region 1-like) di cui fanno parte anche i geni DSCR1 (21q22.12) e DSCR1L1 (6p12.3). Le sequenze del cDNA di questi geni non presentano alcuna somiglianza con quelle di membri di famiglie geniche note. L\u2019analisi genomica mostra che, mentre gli invertebrati contengono un solo gene di tipo DSCR1-like, nei vertebrati sono presenti tre membri della famiglia. Lo studio dei loci DSCR1, DSCR1L1 e DSCR1L2 mostra l\u2019esistenza nel genoma umano di una nuova regione di paralogia segmentale di circa 500 kb che comprende l\u20191,4% del cromosoma 21, nella quale si trovano nello stesso ordine tre membri delle tre famiglie geniche DSCR1L, Runt (AML, acute myeloid leukemia) e CLIC (chloride intracellular channel). L\u2019analisi filogenetica mostra una divergenza tardiva di DSCR1L1 e DSCR1L2 dal gene DSCR1 pi\uf9 ancestrale, e la conservazione della paralogia segmentale fin dai vertebrati inferiori. Lo studio dell\u2019mRNA di DSCR1L2 mostra una espressione ubiquitaria del gene, con un livello molto alto di espressione nel tessuto muscolare, in particolare in quello cardiaco. L\u2019analisi bioinformatica e mediante reazione a catena della polimerasi dopo retrotrascrizione (RT-PCR) ha permesso di identificare tre isoforme di mRNA generate da splicing alternativo. Una delle isoforme si ottiene per perdita degli esoni 2 e 3 del gene, con conseguente perdita della regione codificante per il dominio ricco in prolina caratteristico della famiglia, una seconda forma mostra la perdita dell\u2019esone 2, mentre la terza si caratterizza per la mancanza di 30 basi codificanti per 10 amminoacidi nella regione centrale della proteina. E\u2019 stato recentemente dimostrato da altri Autori che le proteine DSCR1 e DSCR1L1 si legano alla Calcineurina (CnA), una fosfatasi calcio-calmodulina dipendente che modula l\u2019espressione genica nel muscolo scheletrico e cardiaco durante lo sviluppo e in condizioni di ipertrofia provocata da stress ambientali o da patologie. Da parte di pi\uf9 Autori \ue8 stato supposto il legame anche di DSCR1L2 con la CnA stessa nonostante l\u2019assenza di prove sperimentali, solo sulla base dell\u2019omologia di sequenza. Il test dei due ibridi in lievito da noi eseguito per individuare l\u2019interazione proteina-proteina tra DSCR1L2 e una o pi\uf9 proteine tradotte a partire dai cDNA presenti in una genoteca di cuore umano non ha potuto tuttavia rilevare nessuna interazione con la CnA. E\u2019 stata invece dimostrata l\u2019interazione tra DSCR1L2 e la troponina I (TNNI3) cardiaca umana, la subunit\ue0 inibitoria del complesso delle troponine coinvolte nella contrazione muscolare. L\u2019interazione con TNNI3 della proteina DSCR1L2 mostra un caso interessante di divergenza funzionale nell\u2019ambito della famiglia genica DSCR1L, e contribuisce alla chiarificazione dei complessi proteici implicati nella contrazione muscolare. Inoltre, abbiamo identificato un secondo interattore proteico di DSCR1L2, corrispondente a un cDNA tradotto secondo un modulo di lettura non fisiologico; questo polipeptide non naturale di 48 amminoacidi potrebbe risultare di interesse farmacologico per il suo eventuale ruolo nella modulazione della funzione di DSCR1L2. L\u2019interazione tra DSCR1L2 e TNNI3 \ue8 stata confermata mediante cotrasformazione in lievito dei due plasmidi contenenti DSCR1L2 e TNNI3. Una ulteriore conferma di tale interazione viene da esperimenti di coimmunoprecipitazione in vitro. La zona di interazione \ue8 stata infine mappata mediante cotrasformazione del cDNA corrispondente alla isoforma di splicing di DSCR1L2 mancante degli esoni 2 e 3 e del cDNA di TNNI3. I risultati mostrano l\u2019assenza di interazione, individuando la zona di interazione nei domini codificati dagli esoni 2 e 3
FISH results for the PBR: under the chromosomes are reported the letter codes assigned to each BA... more FISH results for the PBR: under the chromosomes are reported the letter codes assigned to each BAC as reported in Additional data file 1 and Figure 1. BACs that yielded single signal both on MMU and HSA are listed in white, duplicated clones in MMU and HSA are listed in red, and duplicated BACs but with a different pattern of hybridization are listed in yellow. Results for the distal breakpoint region (DBR). Examples of hybridization on MMU and HSA with specific macaque BAC clones obtained by library screening or by analyses (for detail see the text) for both the PBR and DBR.<b>Copyright information:</b>Taken from "Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication"http://genomebiology.com/2008/9/2/R28Genome Biology 2008;9(2):R28-R28.Published online 7 Feb 2008PMCID:PMC2374708.
Pairwise sequence comparison between the ancestral loci and DUPA (a) and DUPB (b). We used ancest... more Pairwise sequence comparison between the ancestral loci and DUPA (a) and DUPB (b). We used ancestral state information provided by our previous study [56] and computed the pairwise alignment sequence identity (SeqID) between DUPA and DUPB and their putative ancestral loci. The alignment size is shown as the function of pairwise sequence identity between DUPA and DUPB versus their ancestral loci. The alignment size is illustrated as the function of pairwise sequence identity between DUPA and DUPB. The average pairwise alignment between DUPA and DUPB is 97.3% (highlighted by red vertical line).<b>Copyright information:</b>Taken from "Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication"http://genomebiology.com/2008/9/2/R28Genome Biology 2008;9(2):R28-R28.Published online 7 Feb 2008PMCID:PMC2374708.
Molecular Phylogenetics and Evolution, 2021
The number of reports concerning horizontal transposon transfers (HTT) in metazoan species is con... more The number of reports concerning horizontal transposon transfers (HTT) in metazoan species is considerably increased, alongside with the exponential growth of genomic sequence data However, our understanding of the mechanisms of such phenomenon is still at an early stage. Nematodes constitute an animal phylum successfully adapted to almost every ecosystem and for this reason could potentially contribute to spreading the genetic information through horizontal transfer. To date, few studies describe HTT of nematode retrotransposons. This is due to the lack of annotation of transposable elements in the sequenced nematode genomes, especially DNA transposons, which are acknowledged as the best horizontal travelers among mobile sequences. We have therefore started a survey of DNA transposons and their possible involvement in HTT in sequenced nematode genomes. Here, we describe 83 new Tc1/mariner elements distributed in 17 nematode species. Among them, nine families were possibly horizontally transferred between nematodes and the most diverse animal species, including ants as preferred partner of HTT. The results obtained suggest that HTT events involving nematodes Tc1/mariner elements are not uncommon, and that nematodes could have a possible role as transposon reservoir that, in turn, can be redistributed among animal genomes. Overall, this could be relevant to understand how the inter-species genetic flows shape the landscape of genetic variation of organisms inhabiting specific environmental communities.
The euonymus scale Unaspis euonymi (Comstock) (Hemiptera: Diaspididae) is a pest of spindle that ... more The euonymus scale Unaspis euonymi (Comstock) (Hemiptera: Diaspididae) is a pest of spindle that exhibits a strong preference for Euonymus, although it has been detected on at least 18 genera in 13 plant families (Buxus, Camellia, Celastrus, Daphne, Eugenia, Euonymus, Hibiscus, Ilex, Jasminum, Ligustrum, Lonicera, Olea, Pachistima, Pachysandra, Perychmenum, Prunus and Syringa) (Salisbury et al., 2013). Heavy infestation by this pest may lead to the death of the host plant and consequential loss of income from the cultivation of ornamental plants (Kaygin et al., 2008). U. euonymi is an armored scale insect originally from mild Eastern Asia and probably introduced into Europe in the 20th century (Pellizzari & Germain, 2010). Its lifecycle, depending on climate conditions, comprises two-three generations a year and the control measures to limit its diffusion mainly rely on the use of insecticides or the growing of resistant cultivars. The insects can engage mutualistic interactions or ...
Plasmid, 2020
In this study we describe the genetic elements and the antimicrobial resistance units (RUs) harbo... more In this study we describe the genetic elements and the antimicrobial resistance units (RUs) harboured by the Salmonella Typhimurium monophasic variant 1,4,[5],12:i:-strain ST1030. Of the three identified RUs two were chromosomal, RU1 (IS26-bla TEM-1-IS26-strAB-sul2-IS26) and RU2 (IS26-tetR(B)-tetA(B)-ΔIS26), and one, RU3 (a sul3-associated class 1 integron with cassette array dfrA12-orfF-aadA2-cmlA1-aadA1), was embedded in a Tn21derived element harboured by the conjugative I1 plasmid pST1030-1A. IS26 elements mediated the antimicrobial resistance gene (ARG) shuffling and this gave rise to pST1030-1A derivatives with different sets of ARGs. ST1030 also harboured two ColE1-like plasmids of which one, pST1030-2A, was mobilisable and the target of an intracellular translocation of the Tn21-derived element; the second (pST1030-3) was an orphan mob-associated oriT plasmid co-transferred with pST1030-1A and pST1030-2A. pST1030-2A and pST1030-3 also carried a parA gene and a type III restriction modification system, respectively. Overall analysis of our data reinforces the role played by IS26, Tn21-derived elements and non-conjugative plasmids in the spread of ARGs and supplies the first evidence, at least in Salmonella, for the identification of a natural isolate harbouring a three-element mobilisation system in the same cell.
Scientific Reports, 2020
The biodiversity and evolution of fungal communities were monitored over a period of 3 vintages i... more The biodiversity and evolution of fungal communities were monitored over a period of 3 vintages in a new winery. Samples were collected before grape receipt and 3 months after fermentation from 3 different wine related environments (WRE): floor, walls and equipment and analyzed using Illumina Mi-Seq. Genera of mold and filamentous fungi (294), non-enological (10) and wine-associated yeasts (25) were detected on all WREs before the arrival of the first harvest. Among them, genera likeAlternariaandAureobasidiumpersisted during two vintages. Therefore, these genera are not specific to winery environment and appear to be adapted to natural or anthropic environments due to their ubiquitous character. Some genera likeCandidawere also detected before the first harvest but only on one WREs, whereas, on the other WREs they were found after the harvest. The ubiquitous character and phenotypic traits of these fungal genera can explain their dynamics. After the first harvest and during 3 vintag...
Beverages, 2020
The aim of this work was to study the fungal colonization of a new winery over time, specifically... more The aim of this work was to study the fungal colonization of a new winery over time, specifically for Saccharomyces cerevisiae. Therefore, we analyzed the flora present before the arrival of the first harvest on the floor, the walls and the equipment of this new winery by Illumina MiSeq. The genus Saccharomyces (≤0.3%) was detected on floor and equipment but the presence of S. cerevisiae species was not reported. Wild S. cerevisiae strains were isolated from a ‘Pied de Cuve’ used during the first vintage to ensure the alcoholic fermentation (AF). Among 25 isolates belonging to this species, 17 different strains were identified highlighting a great intraspecific diversity. S. cerevisiae strains were also isolated from different vats throughout the spontaneous fermentations during the first vintage. The following year, some of these strains were isolated again during AF. Some of them (four) were found in the winery equipment before the arrival of the third harvest suggesting a potenti...
American Journal of Physical Anthropology, 2020
Blood, 2009
3261 Poster Board III-1 A crucial role of segmental duplications (SDs) of the human genome has be... more 3261 Poster Board III-1 A crucial role of segmental duplications (SDs) of the human genome has been demonstrated in chromosomal rearrangements associated with several genomic disorders. Limited knowledge is yet available on the molecular processes resulting in chromosomal rearrangements in tumors. The t(9;22)(q34;q11) causing the…
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Papers by Pietro D'Addabbo