Rene' Massimiliano Marsano

Università degli Studi di Bari Aldo Moro | Università di Bari · Department of Biology

Small Cell Lung Cancer (SCLC) is treated as a homogeneous disease, although the expression of NEUROD1, ASCL1, POU2F3, and YAP1 identifies distinct molecular subtypes. The MYC oncogene, amplified in SCLC, was recently shown to act as a lineage-specific factor to associate subtypes with histological classes. Indeed, MYC-driven SCLCs show a distinct m...

Reporter genes inserted via P-element integration into different locations of the Drosophila melanogaster genome have been routinely used to monitor the functional state of chromatin domains. It is commonly thought that P-element-derived reporter genes are subjected to position effect variegation (PEV) when transposed into constitutive heterochroma...

Constitutive heterochromatin represents a significant fraction of eukaryotic genomes (10% in Arabidopsis, 20% in humans, 30% in D. melanogaster, and up to 85% in certain nematodes) and shares similar genetic and molecular properties in animal and plant species. Studies conducted over the last few years on D. melanogaster and other organisms led to...

Background: Neuroendocrine tumors (NETs) overexpress somatostatin receptors (SSTRs). Methods: We developed a second-generation, ligand-based, anti-SSTR chimeric antigen receptor (CAR) incorporating the somatostatin analog octreotide in its extracellular moiety. Results: Anti-SSTR CAR T cells exerted antitumor activity against SSTR+NET cell lin...

Transposable elements (TEs) are abundant components of constitutive heterochromatin of the most diverse evolutionarily distant organisms. TEs enrichment in constitutive heterochromatin was originally described in the model organism Drosophila melanogaster, but it is now considered as a general feature of this peculiar portion of the genomes. The ph...

Transposable elements (TEs) have been historically depicted as detrimental genetic entities that selfishly aim at perpetuating themselves, invading genomes, and destroying genes. Scientists often co-opt “special” TEs to develop new and powerful genetic tools, that will hopefully aid in changing the future of the human being. However, many TEs are g...

Mobility of eukaryotic transposable elements (TEs) are finely regulated to avoid an excessive mutational load caused by their movement. The transposition of retrotransposons is usually regulated through the interaction of host-and TE-encoded proteins, with non-coding regions (LTR and 5′-UTR) of the transposon. Examples of new potent cis-acting sequ...

Chromatin is a highly dynamic biological entity that allows for both the control of gene expression and the stabilization of chromosomal domains. Given the high degree of plasticity observed in model and non-model organisms, it is not surprising that new chromatin components are frequently described. In this work, we tested the hypothesis that the...

The role of extracellular vesicles (EVs) has been completely re-evaluated in the recent decades, and EVs are currently considered to be among the main players in intercellular communication. Beyond their functional aspects, there is strong interest in the development of faster and less expensive isolation protocols that are as reliable for post-iso...

Background: Brugada syndrome (BrS) is an autosomal dominantly inherited cardiac disease characterized by "coved type" ST-segment elevation in the right precordial leads, high susceptibility to ventricular arrhythmia and a family history of sudden cardiac death. The SCN5A gene, encoding for the cardiac voltage-gated sodium channel Nav1.5, accounts...

Expression vectors (EVs) are artificial nucleic acid molecules with a modular structure that allows for the transcription of DNA sequences of interest in either cellular or cell-free environments. These vectors have emerged as cross-disciplinary tools with multiple applications in an expanding Life Sciences market. The cis-regulatory sequences (CRS...

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 ec...

Background In man two mitochondrial aspartate/glutamate carrier (AGC) isoforms, known as aralar and citrin, are required to accomplish several metabolic pathways. In order to fill the existing gap of knowledge in Drosophila melanogaster, we have studied aralar1 gene, orthologue of human AGC-encoding genes in this organism. Methods The blastp algor...

Transposable elements (TEs) are constitutive components of both eukaryotic and prokaryotic genomes. The role of TEs in the evolution of genes and genomes has been widely assessed over the past years in a variety of model and non-model organisms. Drosophila is undoubtedly among the most powerful model organisms used for the purpose of studying the r...

Constitutive heterochromatin represents a significant portion of eukaryotic genomes, but its functions still need to be elucidated. Even in the most updated genetics and molecular biology textbooks, constitutive heterochromatin is portrayed mainly as the 'silent' component of eukaryotic genomes. However, there may be more complexity to the relation...

Background We have recently described a peculiar feature of the promoters in two Drosophila Tc1-like elements, Bari1 and Bari3. The AT-richness and the presence of weak core-promoter motifs make these promoters, that we have defined “blurry”, able to activate transcription of a reporter gene in cellular systems as diverse as fly, human, yeast and b...

Mitochondrial disorders associated with genetic defects of the ATP synthase are among the most deleterious diseases of the neuromuscular system that primarily manifest in newborns. Nevertheless, the number of established animal models for the elucidation of the molecular mechanisms behind such pathologies is limited. In this paper, we target the Dr...

Developmental expression of ATPsynC in Drosophila. (A) Expression pattern of ATPsynC during development, obtained from modENCODE data. (B) RT-qPCR analysis of ATPsynC expression in whole bodies of 5 days old adult males and females. (TIF)

Expression associated to ATPsynC transcriptional units. Uniquely mapping RNAseq data from the modENCODE project elucidate main expression at the ATPsynC locus: ATPsynC-RA being the predominant transcriptional unit and generating two polyadenylated mRNA forms. (TIF)

P-element insertions within ATPsynC. Annotated screenshot from the UCSC genome browser where the locations of the P-elements inserted in the 5’UTR of ATPsynC are highlighted in relation to the local sequence conservation. (TIF)

Sequence and secondary structure comparisons of principal 1rev alleles of ATPsynC. (A) Multiple alignment of alleles ATPsynC1rev18.3, ATPsynC1rev5.2, ATPsynC1rev24.2 and ATPsynC1rev16.2. (B) Secondary structure comparison of nascent ATPsynC RNAs from wild-type ATPsynC (i), ATPsynC1rev18.3 (ii), ATPsynC1rev5.2 (iii) ATPsynC1rev24.2 (iv) and ATPsynC1...

The contribution of the transposons’ promoter in the horizontal transfer process is quite overlooked in the scientific literature. To shed light on this aspect we have mimicked the horizontal transfer process in laboratory and assayed in a wide range of hosts (fly, human, yeast and bacteria) the promoter activity of the 5′ terminal sequences in Bar...

We here describe a leukemogenic role of the homeobox gene UNCX, activated by epigenetic modifications in acute myeloid leukemia. We found the ectopic activation of UNCX in a leukemia patient harboring a t(7;10)(p22;p14) translocation, in 22/61 of additional cases [a total of 23 positive patients out of 62 (37.1%)], and in 6/75 (8%) of acute myeloid...

The term heterochromatin has been long considered synonymous with gene silencing, but it is now clear that the presence of transcribed genes embedded in pericentromeric heterochromatin is a conserved feature in the evolution of eukaryotic genomes. Several studies have addressed the epigenetic changes that enable the expression of genes in pericentr...

Repeats content within syntenic blocks. The repeats found by RepBase analysis are highlighted in yellow. (A) The syntenic blocks Dpse_63A/Dvir_55D-53D. Percent repeats: Dpse_63A = 21,4; Dvir_55D = 0,2—Dvir_53D = 6,0.The large arrow in the lower diagram show the position of the breakpoint between Dvir_55D and Dvir_53D regions. (B) The syntenic block...

Gene structure of “wandered” genes. Exon-intron structure of genes present in non syntenic regions. (TIF)

Primers. List of the primer used for cloning species specific probes. (DOCX)

Intron size variations. This table lists the lenght of individual introns of orthologous genes within: A) The syntenic blocks Dpse_63A/Dvir_55D-53D; B) Dpse_83A/Dvir_47C/; C) The genes at the Dvir_42F-43A region compared to the unmapped genes in Dpse_82AB and to Dmel-HET genes; D) The control euchromatic blocks Dpse_78B/Dmel_47C1-3/Dvir_53-55D. (DO...

Revision annotations. Proposed revision of orthologous Het genes annotations. (DOCX)

Gene structure. Gene structure comparison among orthologous D. melanogaster heterochromatic genes retrieved by TBLASTN analysis over D. pseudoobscura, D. persimilis and D. virilis genomic sequences. The list of the variations supporting the alignments is reported in S3 Table. (TIF)

Myotonia congenita is an inherited disease that is characterized by impaired muscle relaxation after contraction caused by loss-of-function mutations in the skeletal muscle ClC-1 channel. We report a novel ClC-1 mutation, T335N, that is associated with a mild phenotype in 1 patient, located in the extracellular I-J loop. The purpose of this study w...

Bari elements are members of the Tc1-mariner superfamily of DNA transposons, originally discovered in Drosophila melanogaster, and subsequently identified in silico in 11 sequenced Drosophila genomes and as experimentally isolated in four non-sequenced Drosophila species. Bari-like elements have been also studied for their mobility both in vivo and...

Transposons co-occurrence near the insertion site of Bari elements in single species. The red-boxed area in each plot indicates area of significant (p<0,05) enrichment (positive values) or depletion (negative values) of the analyzed transposable elements’ super-families in the proximity of Bari elements in a sequence range of 2,5 kb. X axes report...

WebLogo analysis. Fifty bp upstream or downstream the Bari elements in 8 Drosophila species were analyzed. The number of sequences analyzed is reported (n). (TIF)

Complete dataset and features of Bari-related MITEs annotated in each species analyzed. (XLSX)

Tukey test and Kruskal-Wallis test results. (PDF)

P-distance analyses and deterioration profiles of Bari elements in all the analyzed species. (TIF)

Detection of a recombination site generating a deletion in the heterochromatic cluster. A. Possible molecular mechanism generating the observed adjacent heterochromatic copies carrying deletions of terminal sequences. (B) Global alignment (Needleman-Wunsch) of two adjacent canonical Bari1 heterochromatic copies and the detected copies carrying a de...

Multiple alignment of representative MITEs and reference Bari elements. (PDF)

Accession numbers and coordinates of 1000 randomly selected sequence used as control dataset in flanking sequences analysis. (XLSX)

Genome assemblies used for analyses. (PDF)

Complete dataset and features of Bari elements annotated in each species analyzed. (XLSX)

We describe a new AML entity, occurring in 30% of de novo acute myeloid leukemia, due to structural and epigenetic deregulation of the UNCX homeobox (HB) gene. By molecular approaches, we identified a M5 AML patient with a t(7;10)(p22;p14) translocation as the sole cytogenetic anomaly and showing ectopic expression of UNCX (7p22.3), which encode fo...

The invention refers to 5'TIR nucleotide sequences derived from the "Bari" family of transposable elements for the use as promoter in the expression of a transgene in a recombinant genetic construct adapted to be transfected in a host cell system.

Background Bari-like transposons belong to the Tc1-mariner superfamily, and they have been identified in several genomes of the Drosophila genus. This transposon’s family has been used as paradigm to investigate the complex dynamics underlying the persistence and structural evolution of transposable elements (TEs) within a genome. Three structural...

The transposons of the Bari family are mobile genetic elements widespread in the Drosophila genus. However, despite a broad diffusion, virtually no information is available on the mechanisms underlying their mobility. In this paper we report the functional characterization of the Bari elements transposition system. Using the Bari1 element as a mode...

The mitochondrial carriers are members of a family of transport proteins that mediate solute transport across the inner mitochondrial membrane. Two isoforms of the glutamate carriers, GC1 and GC2 (encoded by the SLC25A22 and SLC25A18 genes, respectively), have been identified in humans. Two independent mutations in SLC25A22 are associated with seve...

The exact mechanism by which ectonucleotide pyrophosphatase phosphodiesterase 1 (ENPP1) inhibits insulin signaling is not known. ENPP1 contains two somatomedin-B-like domains (i.e. SMB 1 and 2) involved in ENPP1 dimerization in animal cells. The aim of the present study was to investigate if these domains modulate ENPP1 inhibitory activity on insul...

A set of 67 novel LTR-retrotransposon has been identified by in silico analyses of the Culex quinquefasciatus genome using the LTR_STRUC program. The phylogenetic analysis shows that 29 novel and putatively functional LTR-retrotransposons detected belong to the Ty3/gypsy group. Our results demonstrate that, by considering only families containing p...

DNA sequences of the 67 LTR-retrotransposons identified in this paper. Each sequence contains 50 bases upstream and downstream allowing unique identification of a reference copy in the genome of C. quinquefasciatus. (TXT)

Multiple alignment file used to obtain the phylogenetic tree in figure 1 . (TXT)

Insulators or chromatin boundary are DNA elements that organize the genome into discrete regulatory domains by limiting the actions of enhancers and silencers through a "positional-blocking mechanism". The role of these sequences, both in modulation of the enhancers range of action (enhancer-promoter selectivity) and in the organization of the chro...

A peculiar form of hepatocerebral mtDNA depletion syndrome is caused by mutations in the MPV17 gene, which encodes a small hydrophobic protein of unknown function located in the mitochondrial inner membrane. In order to define the molecular basis of MPV17 variants associated with the human disorder, we have previously taken advantage of S. cerevisi...

Insulators or chromatin boundary are DNA elements that organize the genome into discrete regulatory domains by limiting the actions of enhancers and silencers through a " positional-blocking mechanism ". The role of these sequences, both in modulation of the enhancers range of action (enhancer–promoter selectivity) and in the organization of the ch...

We have detected seventy-six novel LTR retrotransposons in the genome of the mosquito Aedes aegypti by a genome wide analysis using the LTR_STRUC program. We have performed a phylogenetic classification of these novel elements and a distribution analysis in the genome of A. aegypti. These mobile elements belong either to the Ty3/gypsy or to the Bel...

To study the transcriptional analysis of glutamate dehydrogenase gene, involved in the amino acid conversion to aroma compound in Streptococcus thermophilus. Analysis of the gdhA gene nucleotide sequence of S. thermophilus CNRZ1066 revealed that the coding region is 1353 nucleotides long. The deduced amino acids sequence exhibits the putative GDH a...

In this work the structural variations of Terminal Inverted Repeats (TIR) of Bari like transposons in Drosophila species has been studied. The aim is to try and assess the relevance of different variants in the evolutionary distribution of Bari elements. Bari is a member of the widespread Tc1 superfamily of transposable elements that has colonized...

The realization of cross talks between transposable elements of class I and their host genome involves non-histonic chromatin proteins. These interactions have been widely analyzed through the characterization of the gypsy retrotransposon leader region, which holds a particularly strong insulator element, and the proteins required for its function,...