Elia Lab

Research Summary

In response to DNA damage from environmental or endogenous sources, cells evoke an elaborate signaling network known as the DNA damage response (DDR). This response functions to preserve genomic integrity, which is necessary for normal development and the prevention of cancer. The Elia laboratory studies the DNA damage response, focusing on pathways regulated by ubiquitin-dependent signaling and pathways that promote the stabilization and repair of stalled replication forks. We utilize innovative proteomic and genetic approaches to investigate these processes. Our ultimate goal is to understand how DDR disruption influences cancer progression and can be exploited to target tumors with specific DNA repair defects.

Research Projects

Ubiquitin signaling in the DNA damage response

DNA within cells is under continual assault from metabolic and environmental sources. In response to the ensuing damage, cells activate a signaling network called the DNA damage response (DDR). Defects in this response can lead to hereditary cancer syndromes and can underlie the genomic instability which is a hallmark of sporadic cancers. The DDR promotes genomic integrity by targeting hundreds of factors in diverse pathways ranging from DNA replication and repair to cell-cycle arrest, senescence, and immune regulation. Execution of the DDR relies upon a dynamic array of protein modifications, with ubiquitination playing a central role. Our lab elucidates ubiquitindependent signaling pathways that regulate and integrate diverse DDR factors.

Replication-coupled repair and cancer

Replication fork collapse can induce chromosome instability and mutagenic events that cause cancer. Organisms have therefore evolved pathways to stabilize stalled replication forks and to repair collapsed forks through processes such as homologous recombination (HR). Multiple factors involved in HR and replication fork stabilization, such as BRCA1 and BRCA2, are mutated in hereditary cancer syndromes, highlighting the importance of these pathways. We have demonstrated that the ubiquitin ligase RFWD3, which is mutated in the cancer predisposition syndrome Fanconi anemia, ubiquitinates the singlestranded DNA binding factor RPA to promote homologous recombination at stalled replication forks and replication fork restart (Mol Cell 2015b).

Replication fork reversal is an important mechanism to protect the stability of stalled forks. While multiple enzymes have been identified that can remodel forks, their regulation remains poorly understood. We have recently discovered a new function for RFWD3 in the regulation of fork remodeling (J Cell Biol 2023). We have found that RFWD3 promotes PCNA polyubiquitination to recruit the DNA translocase ZRANB3 to stalled replication forks. Through the analysis of replication intermediates by electron microscopy, we found that RFWD3 promotes replication fork reversal in a ZRANB3-epistatic manner. We are continuing to elucidate novel mechanisms of replication-coupled repair and fork stabilization regulated by ubiquitin signaling.

Quantitative proteomics

Numerous ubiquitin ligases have been implicated in the DNA damage response, yet finding their substrates by simple binding techniques can be difficult due to weak substrate interactions. To circumvent this problem, we have pioneered a quantitative proteomic approach to globally profile ubiquitination. Initially, we used this approach to identify substrates of Cullin- RING ubiquitin ligases (Cell 2011), which are involved in numerous DNA repair processes. Subsequently, we used it to uncover novel ubiquitination events directly stimulated by DNA damage (Mol Cell 2015a), demonstrating the vast breadth of ubiquitin signaling in the DDR. We are continuing to use innovative proteomic approaches to characterize novel and poorly understood ubiquitin ligases in DNA damage signaling pathways.

Targeted cancer therapy

Defects in the DNA damage response can render tumors dependent upon specific DNA repair pathways for survival. Moreover, targeted modulation of the DDR can affect tumor sensitivity to genotoxic treatments and immunotherapy. Increased understanding of DNA repair pathways will lead to enhanced opportunities for developing therapies that target cancers with DNA repair defects, and for improving the efficacy of genotoxic and immunotherapy agents. We are employing methods to translate our work to the development of such therapies.

Research Positions

Postdoctoral Research Fellow

Postdoctoral fellow positions are available to study molecular mechanisms that maintain genomic stability after DNA damage, focusing on factors that regulate the repair of stalled replication forks. Among such factors is the ubiquitin ligase RFWD3, whose mutation causes the cancer predisposition syndrome Fanconi Anemia. Other projects include elucidation of pathways involved in DNA damage modulation of immune signaling. Studies will involve multi-disciplinary approaches including cell biology, biochemistry, proteomics, and functional genomics. The laboratory has strong ties throughout MGH and Harvard Medical School. It belongs to a vibrant DNA damage community at the MGH cancer center and interacts closely with the laboratory of Lee Zou.

Interested candidates with a PhD or MD are encouraged to apply. Strong applicants will be highly motivated and have first author publications. Please email your CV, contact information for three references, and a cover letter describing your research experience and interests to:

Andrew Elia, MD, PhD
Assistant Professor
Massachusetts General Hospital Cancer Center
Harvard Medical School
Associate Member, Broad Institute of MIT and Harvard
aelia@mgh.harvard.edu

Publications

Selected Publications

Moore CE, Yalcindag SE, Czeladko H, Ravindranathan R, Wijesekara Hanthi Y, Levy JC, Sannino V, Schindler D, Ciccia A, Costanzo V, Elia AE. RFWD3 Promotes ZRANB3 Recruitment to Regulate the Remodeling of Stalled Replication Forks. J Cell Biol, 2023; 222(5): e202106022

Duan H, Mansour S, Reed R, Gillis MK, Parent B, Liu B, Sztupinszki Z, Birkbak N, Szallasi Z, Elia AE, Garber JE, Pathania S. E3 ligase RFWD3 is a novel modulator of stalled fork stability in BRCA2-deficient cells. J Cell Biol. 2020; 219(6):e201908192.

Elia AE, Wang DC, Willis NA, Boardman AP, Hajdu I, Adeyemi RO, Lowry E, Gygi SP, Scully R, Elledge SJ. (2015) RFWD3-Dependent Ubiquitination of RPA Regulates Repair at Stalled Replication Forks. Molecular Cell. 60(2):280-93.

Elia AE, Boardman AP, Wang DC, Huttlin EL, Everley RA, Dephoure N, Zhou C, Koren I, Gygi SP, Elledge SJ. (2015) Quantitative Proteomic Atlas of Ubiquitination and Acetylation in the DNA Damage Response. Molecular Cell. 59(5):867-81.

Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ. (2011) Global identification of modular cullin-RING ligase substrates. Cell. 147(2):459-74.

Elia AE, Cantley LC, Yaffe MB. (2003) Proteomic screen finds pSer/pThr-binding domain localizing Plk1 to mitotic substrates. Science. 299:1228-31.

Elia AE, Rellos P, Haire LF, Chao JW, Ivins FJ, Hoepker K, Mohammad D, Cantley LC, Smerdon SJ, Yaffe MB. (2003) The molecular basis for phosphodependent substrate targeting and regulation of Plks by the Polo-box domain. Cell. 115:83-95.

*Co-first authors

Group Members

• Chandler Moore, MD
• Paola Lirofonis
• Dev Patel
• Edward Wang