A5038408627- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Genomics and Rare Diseases
- Genomic variations and chromosomal abnormalities
- Chromosomal and Genetic Variations
- Renal Diseases and Glomerulopathies
- Genomics and Chromatin Dynamics
- Renal and related cancers
- Myeloproliferative Neoplasms: Diagnosis and Treatment
- Genetic factors in colorectal cancer
- Single-cell and spatial transcriptomics
- Chronic Kidney Disease and Diabetes
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Dialysis and Renal Disease Management
- Epigenetics and DNA Methylation
- Medical Imaging and Pathology Studies
- RNA and protein synthesis mechanisms
- Nanopore and Nanochannel Transport Studies
- Acute Myeloid Leukemia Research
- Chronic Myeloid Leukemia Treatments
- Viral-associated cancers and disorders
- Immunodeficiency and Autoimmune Disorders
- Adolescent and Pediatric Healthcare
University of Florence
2013-2025
University of Bari Aldo Moro
2022
University of Pisa
2021
Vanderbilt University
2017
Università Cattolica del Sacro Cuore
1996
The nanopore sequencing process is based on the transit of a DNA molecule through nanoscopic pore, and since 90s considered as one most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched beta-testing program that supplied scientific community with first prototype sequencer: MinION. Thanks this program, several research groups had opportunity evaluate performance novel instrument develop computational for analyzing new generation data....
Acute tissue injury causes DNA damage and repair processes involving increased cell mitosis polyploidization, leading to function alterations that may potentially drive cancer development. Here, we show acute kidney (AKI) the risk for papillary renal carcinoma (pRCC) development tumor relapse in humans as confirmed by data collected from several single-center multicentric studies. Lineage tracing of tubular epithelial cells (TECs) after AKI induction long-term follow-up mice showed...
Abstract Acute kidney injury (AKI) is frequent, often fatal and, for lack of specific therapies, can leave survivors with chronic disease (CKD). We characterize the distribution tubular cells (TC) undergoing polyploidy along AKI by DNA content analysis and single cell RNA-sequencing. Furthermore, we study functional roles polyploidization using transgenic models drug interventions. identify YAP1-driven TC outside site as a rapid way to sustain residual function early during AKI. This...
Crescentic glomerulonephritis is characterized by vascular necrosis and parietal epithelial cell hyperplasia in the space surrounding glomerulus, resulting formation of crescents. Little known about molecular mechanisms driving this process. Inducing crescentic two Pax2Cre reporter mouse models revealed that crescents derive from clonal expansion single immature cells. Preemptive delayed histone deacetylase inhibition with panobinostat, a drug used to treat hematopoietic stem disorders,...
The early phases of embryonic development and cancer share similar strategies to improve their survival in an inhospitable environment: both proliferate a hypoxic catecholamine‐rich context, increasing aerobic glycolysis. Recent studies show that β 3‐adrenergic receptor ( 3‐AR) is involved tumor progression, playing important role metastasis. Among ‐adrenergic receptors, 3‐AR the last identified member this family, it cell induction stromal reactivity microenvironment. well known as strong...
Although the adaptive immune response to SARS-CoV-2 has been characterised in acute and early convalescent phase of disease, few studies explore whether natural infection elicits long-lasting immunological memory recovered individuals. In this work, we aimed assess maintenance SARS-CoV-2.We evaluated long-term virus-specific cellular humoral members an Italian Serie A football team, who experienced a cluster COVID-19 March 2020, which was strictly following months.Our results highlight...
The NLRP3 inflammasome integrates several danger signals into the activation of innate immunity and inflammation by secreting IL-1β IL-18. Most published data relate to in immune cells, but some reports claim similar roles parenchymal, namely epithelial, cells. For example, podocytes, epithelial cells critical for maintenance kidney filtration, have been reported express release IL-β diabetic disease, contributing filtration barrier dysfunction injury. We questioned this hence performed...
Podocytes and podocyte progenitors are interdependent components of the kidney's glomerular structure, with podocytes forming filtration barrier being key players in regeneration during pathophysiological processes. Both cell types subjected to constant mechanical forces, whose alterations can initiate podocytopathy worsen injury. Despite this, specific mechanosensors mechanotransduction pathways involved their response cues remain only partially explored. We used transcriptomics,...
By examining the genotype calls generated by 1000 Genomes Project we discovered that human reference genome GRCh37 contains almost 20,000 loci in which allele has never been observed healthy individuals and around 70,000 it only heterozygous state. We show a large fraction of this rare (RRA) belongs to coding, functional regulatory elements could be linked Mendelian disorders as well cancer. also demonstrate classical germline somatic variant calling tools are not capable recognize when...
Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic condition in childhood. The disease etiology remains largely unknown; however, a key role JIA pathogenesis surely mediated by T cells. T-lymphocytes activity controlled via signals, known as immune checkpoints. Delivering an inhibitory signal or blocking stimulatory to achieve suppression critical autoimmune diseases. However, of checkpoints inflammation and autoimmunity must still be deciphered. In this study, we...
The past few years have seen the emergence of nanopore-based sequencing technologies which interrogate single molecule DNA and generate reads sequentially.In this paper, we demonstrate that, thanks to sequentiality nanopore process, data generated in first tens minutes a typical MinION/GridION run can be exploited resolve alterations human genome at karyotype level with resolution order Mb, while produced 6-12 h allow obtain comparable currently available array-based technologies, novel...
Abstract Aberrant DNA methylation at CpG dinucleotides is a cancer hallmark that associated with the emergence of resistance to anti treatment, though molecular mechanisms and biological significance remain elusive. Genome scale maps by currently used methods are based on chemical modification best suited for analyses rich regions (CpG islands). We report first high coverage whole-genome map in using long read nanopore technology, which allows simultaneous DNA-sequence -methylation native...
Polyploidization of tubular cells (TC) is triggered by acute kidney injury (AKI) to allow survival in the early phase after AKI, but long run promotes fibrosis and AKI-chronic disease (CKD) transition. The molecular mechanism governing link between polyploid TC remains be clarified. In this study, we demonstrate that immediately expression cell cycle markers mostly identifies a population DNA-damaged TC. Using transgenic mouse models single-cell RNA sequencing show that, unlike diploid TC,...
Background: detecting chronic kidney disease (CKD) may have important implications for the management of older and frail people. We aimed at investigating whether clinical setting (nursing home: NH versus hospital: H) affects agreement between glomerular filtration rate (GFR) values estimated by Chronic Kidney Disease-Epidemiology Collaboration (CKD-EPI), Cockcroft-Gault (CG) Modification Diet in Renal Disease (MDRD) equations.
The adoption of next generation sequencing based methods in cancer research allowed for the investigation complex genetic structure tumor samples. In last few years, considerable importance was given to somatic variants and several computational approaches were developed this purpose. Despite continuous improvements these programs, validation their results it's a hard challenge due multiple sources error. To overcome drawback different simulation are used generate synthetic samples but they...
The recent technological improvement of Oxford Nanopore sequencing pushed the throughput these devices to 10-20 Gb allowing generation millions reads. For reasons, availability fast software packages for evaluating experimental quality by generating highly informative and interactive summary plots is fundamental importance.We developed PyPore, a three module python toolbox designed handle raw FAST5 files from checking alignment reference genome explore their features through browsable HTML...
Abstract Copy Number Variants (CNVs) are structural rearrangements contributing to phenotypic variation but also associated with many disease states. In recent years, the identification of CNVs from high‐throughput sequencing experiments has become a common practice for both research and clinical purposes. Several computational methods have been developed so far. this unit, we describe give instructions on how run two read count–based tools, XCAVATOR EXCAVATOR2, which tailored detection...