A5046625423- RNA Research and Splicing
- RNA modifications and cancer
- Neuroblastoma Research and Treatments
- Cancer, Hypoxia, and Metabolism
- Cancer Cells and Metastasis
- Cancer-related molecular mechanisms research
- Single-cell and spatial transcriptomics
- Cancer-related Molecular Pathways
- Molecular Biology Techniques and Applications
- Virus-based gene therapy research
- Genomics and Chromatin Dynamics
- Advanced biosensing and bioanalysis techniques
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Epigenetics and DNA Methylation
- Peroxisome Proliferator-Activated Receptors
- Bipolar Disorder and Treatment
- Chromatin Remodeling and Cancer
- Click Chemistry and Applications
- Plant and Fungal Interactions Research
- Insect Resistance and Genetics
- Wind Energy Research and Development
- Histone Deacetylase Inhibitors Research
- Brain Tumor Detection and Classification
- Otitis Media and Relapsing Polychondritis
New York Genome Center
2021-2025
Cornell University
2024-2025
Universidad de Navarra
2016-2024
Weill Cornell Medicine
2024
Navarre Institute of Health Research
2016-2020
Mario Negri Institute for Pharmacological Research
2019
University of Trento
2014-2016
University of Insubria
2011-2014
It is now obvious that the majority of cellular transcripts do not code for proteins, and a significant subset them are long non-coding RNAs (lncRNAs). Many lncRNAs show aberrant expression in cancer, some have been linked to cell transformation. However, underlying mechanisms remain poorly understood it unknown how sequences lncRNA dictate their function. Here we characterize function p53-regulated human LINC-PINT cancer. We find downregulated multiple types cancer acts as tumor suppressor...
Epithelial-to-mesenchymal transition (EMT) is a core process underlying cell movement during embryonic development and morphogenesis. Cancer cells hijack this developmental program to execute multi-step cascade, leading tumorigenesis metastasis. CD133 (PROM1), marker of cancer stem cells, has been shown facilitate EMT in various cancers, but the regulatory networks controlling gene expression function remain incompletely delineated. In study, we show that ribonucleoprotein complex including...
LncRNAs have been shown to be direct players in chromatin regulation, but little is known about their role at active genomic loci. We investigate the of lncRNAs gene activation by profiling RNA interactome SMARCB1-containing SWI/SNF complexes proliferating and senescent conditions. The isolation SMARCB1-associated transcripts, together with profiling, shows prevalent association regions where SMARCB1 differentially binds locally transcribed RNAs. identify SWINGN, a lncRNA interacting...
The therapeutic use of adeno-associated viral vector (AAV)-mediated gene disruption using CRISPR-Cas9 is limited by potential off-target modifications and the risk uncontrolled integration genomes into CRISPR-mediated double-strand breaks. To address these concerns, we explored AAV-delivered paired Staphylococcus aureus nickases (D10ASaCas9) to target Hao1 for treatment primary hyperoxaluria type 1 (PH1). Our study demonstrated effective disruption, a significant decrease in glycolate...
Cancer is characterized by genomic instability leading to deletion or amplification of oncogenes tumor suppressors. However, most the altered regions are devoid known cancer drivers. Here, we identify lncRNAs frequently lost amplified in cancer. Among them, found lncRNA associated with lung cancer-1 (ALAL-1) as adenocarcinomas. ALAL-1 also overexpressed additional types, such squamous carcinoma. The RNA product able promote proliferation and tumorigenicity cells. a TNFα- NF-κB-induced...
SUMMARY Gene expression is coordinated by a multitude of transcription factors (TFs), whose binding to the genome directed through multiple interconnected epigenetic signals, including chromatin accessibility and histone modifications. These complex networks have been shown be disrupted during aging, disease, cancer. However, profiling these across diverse cell types states has limited due technical constraints existing methods for mapping DNA:Protein interactions in single cells. As result,...
Abstract Neuroblastoma has a low mutation rate for the p53 gene. Alternative ways of inactivation have been proposed in neuroblastoma, such as abnormal cytoplasmic accumulation wild-type p53. However, mechanisms leading to via are not well investigated. Here we show that neuroblastoma risk-associated locus 6p22.3-derived tumor suppressor NBAT1 is p53-responsive lncRNA regulates subcellular levels. Low expression provided resistance genotoxic drugs by promoting cytoplasm and loss from...
Abstract Somatic evolution leads to the emergence of clonal diversity across tissues with broad implications for human health. A striking example somatic is VEXAS (Vacuoles E1 enzyme X-linked Autoinflammatory Somatic) syndrome, caused by UBA1 mutations in hematopoietic stem cells (HSCs), inducing treatment-refractory, systemic inflammation. However, mechanisms that lead survival and expansion mutant HSCs are unknown, limiting development effective therapies. The lack animal or cellular...
The tumor suppressor p53 was previously shown to markedly up-regulate the expression of PRODH gene, encoding proline dehydrogenase (PRODH) enzyme, which catalyzes first step in degradation. Also PRODH2, degrades 4-hydroxy-L-proline, a product protein (e.g. collagen) catabolism, recently described as target. Here, we confirmed p53-dependent induction endogenous response genotoxic damage cell lines different histological origin. We established that over-expression TAp73β or TAp63β is...
// Alessandra Bisio 1 , Judit Zámborszky 1, 3 Sara Zaccara Mattia Lion 4 Toma Tebaldi 2 Vasundhara Sharma Ivan Raimondi Federica Alessandrini Yari Ciribilli Alberto Inga Laboratory of Transcriptional Networks, Centre for Integrative Biology, CIBIO, University Trento, 38123, Italy Translational Genomics, Institute Enzymology, Research Natural Sciences, Budapest, Hungary Department Genetics, Massachusetts General Hospital, Boston, MA, USA Correspondence to: Ciribilli, e-mail:...
// Paola Monti 1,* , Yari Ciribilli 2,* Alessandra Bisio *2 Giorgia Foggetti 1 Ivan Raimondi 2,3 Campomenosi 3,4 Menichini Gilberto Fronza 1,** Alberto Inga 2,** Mutagenesis Unit, Istituto di Ricerca e Cura a Carattere Scientifico Azienda Ospedaliera Universitaria San Martino-IST-Istituto Nazionale per la sul Cancro, Genoa, Italy; 2 Laboratory of Transcriptional Networks, Centre for Integrative Biology, CIBIO, University Trento, 3 Department Biotechnology and Life Sciences, DBSV, Insubria,...
Abstract Cells have evolved a robust and highly regulated DNA damage response to preserve their genomic integrity. Although increasing evidence highlights the relevance of RNA regulation, our understanding its impact on fully efficient remains limited. Here, through targeted CRISPR-knockout screen, we identify RNA-binding proteins modifiers that participate in p53 response. Among top hits, find m 6 A reader YTHDC1 as master regulator expression. binds transcription start sites TP53 other...
Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility, and other factors. However, most current single-cell-resolution methods unable to measure more than one aspect chromatin state in single experiment, limiting our ability accurately states. Here, we introduce nanobody-tethered transposition followed sequencing (NTT-seq), new assay capable measuring the genome-wide presence multiple modifications...
Co-evolution of transcription factors (TFs) with their respective cis-regulatory network enhances functional diversity in the course evolution. We present a new approach to investigate transactivation capacity sequence-specific TFs evolutionary studies. Saccharomyces cerevisiae was used as an vivo test tube and p53 proteins derived from human five commonly animal models were chosen proof concept. is highly conserved master regulator environmental stress responses. Previous reports indicated...
Abstract We report the expression of recombinant RNASET2, only human member Rh/T2/S family acid ribonucleases, in yeast Pichia pastoris and baculovirus‐insect cell heterologous systems. In both models, yield protein was comparable ranged between 5 mg/L (for a catalytically impaired mutant version RNASET2) 30 for wild‐type protein. Thus, produced rather than system used appears to influence after optimization culture conditions. The found undergo heterogeneous glycosylation systems,...
Abstract New technologies that profile chromatin modifications at single-cell resolution offer enormous promise for functional genomic characterization. However, the sparsity of these measurements and challenge integrating multiple binding maps represent significant challenges. Here we introduce scCUT&Tag-pro, a multimodal assay profiling protein-DNA interactions coupled with abundance surface proteins in single cells. In addition, scChromHMM, which integrates data from experiments to...
Cells have evolved a robust and highly regulated DNA damage response to preserve their genomic integrity. Although increasing evidence highlights the relevance of RNA regulation, our understanding its impact on fully efficient remains limited. Here, through targeted CRISPR-knockout screen, we identified binding proteins modifiers that participate in mediating p53 response. Among top hits, m6A reader YTHDC1 was as master regulator expression. binds transcription start sites TP53 other genes...
Somatic mutations are crucial for cancer initiation and evolution, have been identified across a number of healthy tissues in the human body. These can disrupt normal cellular functions, leading to aberrant clonal expansions via acquired fitness advantages or skewed differentiation topologies. GoT-ChA similar methods (e.g. GoT, TARGET-seq) aim pair targeted genotyping with single-cell sequencing approaches order understand impact somatic directly patient samples, both malignant non-malignant...