Publications by Daniele Tavernari

Decoding the Clinical and Molecular Signatures of EGFR Common, Compound, and Uncommon Mutations in NSCLC: A Brief Report

Introduction: EGFR mutations are key oncogenic drivers in lung adenocarcinoma (LUAD), predominantly affecting Asian, nonsmoking, and female populations. Although common mutations, such as exon 19 deletions and L858R, respond well to tyrosine kinase inhibit ...

ELSEVIER SCIENCE INC2025

Development of patient-derived lymphomoids with preserved tumor architecture for lymphoma therapy screening

Elisa Oricchio, Daniele Tavernari, Albert Santamaria Martinez

The efficacy of anti-cancer therapies depends on the genomic composition of the tumor, its microenvironment, spatial organization, and intra-tumor heterogeneity. B-cell lymphomas are a heterogeneous group of tumors emerging from B-cells at different stages ...

Nature Portfolio2024

CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity

Daniele Tavernari, Albert Santamaria Martinez, Giovanni Ciriello

Tissues are organized in cellular niches, the composition and interactions of which can be investigated using spatial omics technologies. However, systematic analyses of tissue composition are challenged by the scale and diversity of the data. Here we pres ...

Nature Portfolio2023

Whole-genome doubling drives oncogenic loss of chromatin segregation

Elisa Oricchio, Daniele Tavernari, Natalya Katanayeva, Ruxandra-Andreea Lambuta, Juan Diaz Miyar, Giovanni Ciriello

Whole-genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies(1-8). However, the three-dimensional organization of chromatin in WGD cells and its contribution to oncogenic phenotyp ...

NATURE PORTFOLIO2023

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Daniele Tavernari, Giovanni Ciriello

Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated ...

Wiley2023

Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci

Elisa Oricchio, Natalya Katanayeva, Daniele Tavernari, Stephanie Jocelyne Sungalee, Ruxandra-Andreea Lambuta, Giovanni Ciriello

In cancer cells, enhancer hijacking mediated by chromosomal alterations and/or increased deposition of acetylated histone H3 lysine 27 (H3K27ac) can support oncogene expression. However, how the chromatin conformation of enhancer-promoter interactions is a ...

2021

Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes

Elisa Oricchio, Stephanie Jocelyne Sungalee, Daniele Tavernari, Giovanni Ciriello, Marco Mina

Chromatin compartmentalization reflects biological activity. However, inference of chromatin sub-compartments and compartment domains from chromosome conformation capture (Hi-C) experiments is limited by data resolution. As a result, these have been charac ...

Nature Research2021

EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains

Suliana Manley, Elisa Oricchio, Kyle Michael Douglass, Natalya Katanayeva, Daniele Tavernari, Elena Battistello, Stephanie Jocelyne Sungalee, Maria Christine Donaldson, Timo Henry René Rey, Giovanni Ciriello

Chromatin is organized into topologically associating domains (TADs) enriched in distinct histone marks. In cancer, gain-of-function mutations in the gene encoding the enhancer of zeste homolog 2 protein (EZH2) lead to a genome-wide increase in histone-3 L ...

2019

Comparison of computational methods for the identification of topologically associating domains

Elisa Oricchio, Marie-Pierre Zufferey, Daniele Tavernari, Giovanni Ciriello

BackgroundChromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs). TADs have been characterized across multiple species, tissue types, and differentiati ...

2018

Pan-SRC kinase inhibition blocks B-cell receptor oncogenic signaling in non-Hodgkin lymphoma

Olivier Michielin, Elisa Oricchio, Daniele Tavernari, Natalya Katanayeva, Elena Battistello, Maria Christine Donaldson, Elie Charles Eugène Dheilly, Giovanni Ciriello

2018