publications

2024

1. Nargab

   SpikeFlow: automated and flexible analysis of ChIP-Seq data with spike-in control

   Davide Bressan, Daniel Fernández-Pérez, Alessandro Romanel, and 1 more author

   NAR Genomics and Bioinformatics, Aug 2024

   Abs DOI HTML PDF

   ChIP with reference exogenous genome (ChIP-Rx) is widely used to study histone modification changes across different biological conditions. A key step in the bioinformatics analysis of this data is calculating the normalization factors, which vary from the standard ChIP-seq pipelines. Choosing and applying the appropriate normalization method is crucial for interpreting the biological results. However, a comprehensive pipeline for complete ChIP-Rx data analysis is lacking. To address these challenges, we introduce SpikeFlow, an integrated Snakemake workflow that combines features from various existing tools to streamline ChIP-Rx data processing and enhance usability. SpikeFlow automates spike-in data scaling and provides multiple normalization options. It also performs peak calling and differential analysis with distinct modalities, enabling the detection of enrichment regions for histone modifications and transcription factor binding. Our workflow runs in-depth quality control at all the processing steps and generates an analysis report with tables and graphs to facilitate results interpretation. We validated the pipeline by performing a comparative analysis with DiffBind and SpikChIP, demonstrating robust performances in various biological models. By combining diverse functionalities into a single platform, SpikeFlow aims to simplify ChIP-Rx data analysis for the research community.

2. Sci. Adv.

   Increased genomic instability and reshaping of tissue microenvironment underlie oncogenic properties of Arid1a mutations

   A. D’Ambrosio, D. Bressan, and E. Ferracci

   Science Advances, Mar 2024

   Abs DOI Bib HTML PDF

   

   Oncogenic mutations accumulating in many chromatin-associated proteins have been identified in different tumor types. With a mutation rate from 10 to 57%, ARID1A has been widely considered a tumor suppressor gene. However, whether this role is mainly due to its transcriptional-related activities or its ability to preserve genome integrity is still a matter of intense debate. Here, we show that ARID1A is largely dispensable for preserving enhancer-dependent transcriptional regulation, being ARID1B sufficient and required to compensate for ARID1A loss. We provide in vivo evidence that ARID1A is mainly required to preserve genomic integrity in adult tissues. ARID1A loss primarily results in DNA damage accumulation, interferon type I response activation, and chronic inflammation leading to tumor formation. Our data suggest that in healthy tissues, the increased genomic instability that follows ARID1A mutations and the selective pressure imposed by the microenvironment might result in the emergence of aggressive, possibly immune-resistant, tumors.

   @article{paperArid1a,
     title = {Increased genomic instability and reshaping of tissue microenvironment underlie oncogenic properties of Arid1a mutations},
     author = {D'Ambrosio, A. and Bressan, D. and Ferracci, E.},
     journal = {Science Advances},
     volume = {10},
     issue = {11},
     pages = {eadh4435},
     numpages = {0},
     year = {2024},
     month = mar,
     publisher = {American Association for the Advancement of Science,},
     doi = {10.1126/sciadv.adh4435},
     url = {https://www.science.org/doi/10.1126/sciadv.adh4435},
     dimensions = {true},
   }

2023

1. Oral Talk

   Increased genomic instability and reshaping of tissue microenvironment drive ARID1A-dependent cancer formation

   D. Bressan

   SIBBM 2023. Frontiers in Molecular Biology - Bari, IT, Jun 2023

2022

1. Poster

   The role of mSWI/SNF complex in preserving liver tissue homeostasis and preventing hepatocellular carcinoma formation

   D. Bressan, A D’Ambrosio, and E. Ferracci

   PEZCOLLER SYMPOSIUM - Trento, IT, Jun 2022
2. Poster

   Role of the mSWI/SNF chromatin remodeling complex in preserving liver homeostasis

   D. Bressan, A D’Ambrosio, and E. Ferracci

   EACR - Seville, SP, Jun 2022