Current Methods to Analyze DNA Damage in S-phase in Eukaryotic Cells

TOPICAL COLLECTIONS

Guest Editors

Alessandra Brambati

New York University School of Medicine

Dr. Alessandra Brambati is a post-doctoral fellow in the laboratory headed by Dr. Agnel Sfeir at the Skirball Institute at New York University. Her long-term research interest is a comprehensive understanding of the mechanisms that preserve genome integrity in human cells. Her project aims to elucidate the mechanistic basis of the error prone micro-homology end-joining pathway in the repair of DNA double-strand breaks. During the PhD training at the University of Pavia, Italy, Dr. Brambati studied how transcription induce replication stress leading to genome instability using budding yeast as a model system.

Antonio Maffia

University of California Berkeley

Dr. Antonio Maffia is a Postdoctoral Scholar in the Hockemeyer lab at the Molecular and Cell Biology Department at UC Berkeley. His scientific interest has always been at the intersection between DNA replication and cell cycle regulation in humans. The current purpose of his work is applying novel high throughput screening techniques to dissect the different mechanisms that allow telomeric DNA replication and maintenance.

Antonio Marzio

New York University School of Medicine

Dr. Antonio Marzio is a postdoctoral fellow in laboratory of Dr. Michele Pagano in the Biochemistry and Molecular Pharmacology Department at NYU School of Medicine. His longstanding interest is in the molecular mechanisms controlling the DNA damage response with a particular emphasis on homologous recombination repair (HRR). Dr. Marzio current post-doctoral research project revolves around the role of human E3 ubiquitin ligase in modulating PARP1 inhibitors (PARPis) sensitivity in triple negative breast cancer (TNBC). During his PhD studies, Dr. Marzio has been trained in the laboratory of Prof. Maurizio Gatti in the Biology and Biotechnology Department at University of Rome “SAPIENZA”. He made pioneering contributions to our understanding of high level of sugar and low level of Vitamin B6 induces genomic instability and cancer development.

Bárbara de la Peña Avalos

University of Texas Health San Antonio

Dr. Bárbara de la Peña Avalos is a Postdoctoral Research Fellow in the Biochemistry and Structural Biology Department at the University of Texas Health in San Antonio, Texas. She received her BS in Biochemistry and Microbiology from Universidad del Valle, Guatemala and a MSc in Molecular and Cell/Cellular Biology from Universidad Autónoma de Madrid, Spain where she worked on the characterization of ERAS, a putative novel human oncogene, in skin and breast. She then moved to Australia, as the recipient of a prestigious trainee award by the Princess Alexandra Research Foundation. There, she pursued a PhD in Biomedical Sciences with Dr Eloïse Dray, and became conversant with Molecular Biology, microscopy techniques and mice models. During her PhD, Bárbara studied a novel protein phosphatase and its role in preventing genomic instability and breast cancer development. She graduated in 2019 from Queensland University of Technology, Brisbane, Australia. In 2019, she joined the lab of Dr Patrick Sung, where she is currently focusing her research efforts in studying new breast cancer genes, to decipher their function in DNA damage repair, genomic stability maintenance and carcinogenesis.

Collection Overview

Errors during DNA replication are a major driver of tumorigenesis. Therefore, maintaining genomic integrity is crucial for faithful transmission of genetic information by preventing genome aberrations. Eukaryotic cells have evolved a sophisticated network of pathways called the DNA damage response (DDR), to preserve genomic stability. The DDR senses DNA lesions and activates cell cycle checkpoints that halt cell cycle progression, thereby preventing propagation of potentially deleterious mutations. During S-phase when active DNA replication is taking place, the genome is particularly vulnerable to exogenous insults such as mutagenic agents as well as endogenous sources of genomic instability such as common fragile sites, transcription-replication conflicts, and mis-incorporation of ribonucleotides.

It is well established that replication stress can be a driving force for cellular transformation and the DDR can be hijacked by cancer cells to develop chemotherapeutic resistance. However, the precise mechanisms by which eukaryotic cells cope with DNA damage during S-phase is not entirely understood. Expanding the methodology repertoire will help uncover novel mechanistic insights into the replication-coupled DDR.

This collection aims to provide a multidisciplinary selection of the current techniques that enable the analysis of the replication-coupled DDR at the biochemical, genetic, and cellular levels. Specifically, this collection will explore the analysis of cell cycle profiles, activation, and regulation of the S-phase checkpoint, physical visualization of damaged replication forks, and biochemical characterization of key regulating factors, among others.