Biology subjects

Scaffidi, P.

Publications and source records attributed to Scaffidi, P..

4 recordsLinked to original sources

bioRxiv2022

H4K16ac activates transcription of transposable elements and contribute to their cis regulatory function

Mammalian genomes harbour a large number of transposable elements (TEs) and their remnants. Many epigenetic repression mechanisms are known to silence TE transcription. However, TEs are upregulated during early development, neuronal lineage, and cancers, although the epigenetic factors contributing to the transcription of TEs have yet to be fully elucidated. Here we demonstrated that the male-specific lethal (MSL) complex mediated acetylation of histone H4 lysine 16 (H4K16ac) activates transcription of long interspersed nuclear elements (LINE1, L1) and long terminal repeats (LTRs). Furthermore, we show that the H4K16ac marked L1 and LTR subfamilies function as enhancers and are enriched with chromatin features associated with active enhancers and looping factors. L1 and LTRs enriched with histone acetylations are bound by chromatin looping factors and these regions loop with genes. CRISPR-based epigenetic perturbation and genetic deletion of L1s reveal that H4K16ac marked L1s and LTRs regulate the expression of genes in cis. Overall, TEs enriched with H4K16ac contribute to the cis-regulatory landscape of a significant portion of the mammalian genome by maintaining an active chromatin landscape at TEs. One Sentence SummaryH4K16ac activates LINE1 and ERV/LTR transcription and rewires the cis-regulatory landscape of a significant portion of the mammalian genome by increasing the transcriptional activity at TEs.

genomics↗

bioRxiv2020

ARID2 deficiency promotes tumor progression and is associated with higher sensitivity to PARP inhibition in lung cancer

The survival rate in lung cancer remains stubbornly low and there is an urgent need for the identification of new therapeutic targets. Last decades research has evidenced a clear role of chromatin structure in cancer development and several members of the SWI/SNF chromatin remodeling complexes have been described altered in different tumor types. Nevertheless, the precise mechanisms of their impact on cancer progression, as well as the application of this knowledge to cancer patient management are largely unknown. In this study, we have performed targeted sequencing of a cohort of lung cancer patients on genes involved in chromatin structure, as well as functional experiments to identify the molecular mechanisms linking alterations of chromatin remodeling genes and tumor development. We have identified ARID2 production loss in 20% of lung cancer patients. Additionally, we have shown that ARID2-deficiency provokes profound chromatin structural changes, alters the transcriptional programme and impairs DNA repair which bolster the proliferative and metastatic potential of the cells both in vitro and in vivo. Moreover, we have demonstrated that ARID2 deficiency significantly affects the sensitivity of the cells to PARP inhibition. All these results support that ARID2 is a bona-fide tumor suppressor gene in lung cancer that might be exploited therapeutically.

cancer biology↗

bioRxiv2018

Target-specific precision of CRISPR-mediated genome editing

The CRISPR-Cas9 system has successfully been adapted to edit the genome of various organisms. However, our ability to predict editing accuracy, efficacy and outcome at specific sites is limited by an incomplete understanding of how the bacterial system interacts with eukaryotic genomes and DNA repair machineries. Here, we performed the largest comparison of indel profiles to date, examining over one thousand sites in the genome of human cells, and uncovered general principles guiding CRISPR-mediated DNA editing. We find that precision of DNA editing varies considerably among sites, with some targets showing one highly-preferred indel and others displaying a wide range of infrequent indels. Editing precision correlates with editing efficiency, homology-associated end-joining for both insertions and deletions, and a preference for single-nucleotide insertions. Precise targets and the identity of their preferred indel can be predicted based on simple rules that mainly depend on the fourth nucleotide upstream of the PAM sequence. Regardless of precision, site-specific indel profiles are highly robust and depend on both DNA sequence and chromatin features. Our findings have important implications for clinical applications of CRISPR technology and reveal general patterns of broken end-joining that can inform us on DNA repair mechanisms in human cells.

molecular biology↗

bioRxiv2018

Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma

The identification of somatic alterations with a cancer promoting role is challenging in highly unstable and heterogeneous cancers, such as esophageal adenocarcinoma (EAC). Here we developed a machine learning algorithm to identify cancer genes in individual patients considering all types of damaging alterations simultaneously (mutations, copy number alterations and structural rearrangements). Analysing 261 EACs from the OCCAMS Consortium, we discovered a large number of novel cancer genes that, together with well-known drivers, help promote cancer. Validation using 107 additional EACs confirmed the robustness of the approach. Unlike known drivers whose alterations recur across patients, the large majority of the newly discovered cancer genes are rare or patient-specific. Despite this, they converge towards perturbing cancer-related processes, including intracellular signalling, cell cycle regulation, proteasome activity and Toll-like receptor signalling. Recurrence of process perturbation, rather than individual genes, divides EACs into six clusters that differ in their molecular and clinical features and suggest patient stratifications for personalised treatments. By experimentally mimicking or reverting alterations of predicted cancer genes, we validated their contribution to cancer progression and revealed EAC acquired dependencies, thus demonstrating their potential as therapeutic targets.

cancer biology↗