3-Research and Funding

Research Interests: Molecular Mechanisms of Genome Integrity

Research Projects:

1. Dissecting DNA single-strand break repair and signaling pathways. As the most common type of DNA damage, DNA single-strand breaks (SSBs) are generated approximately 10,000 times each day per mammalian cell. Unrepaired SSBs impair DNA replication and transcription machineries, leading to genome instability and associated diseases such as cancer and neurodegenerative disorders. We have developed defined plasmid-based site-specific SSB structures that can trigger ATR-Chk1 DDR pathway activation in a eukaryotic cell-free system (1A-1B). We demonstrate that APE2 interacts with PCNA through two distinct modes for DDR pathway activation 1A. We recently demonstrated that APE1 and its exonuclease are required for the recruitment of APE2 to SSB sites and SSB repair and signaling (1C). We proposed a two-step APE1/APE2-mediated mechanism in SSB end resection (1C). The impact of this innovative work is partially reflected by the News and Views in NSMB (1D). In addition, we found that APE1 endonuclease-mediated ssDNA damage is regulated by the DNA glycosylase NEIL3 via a non-canonical role (1E).

Publications:
(1A) Lin Y, Bai L, Cupello S, Hossain MA, Deem B, McLeod M, Raj J, Yan S*. APE2 promotes DNA damage response pathway from a single-strand break. Nucleic Acids Res. 2018 Mar 16; 46(5):2479-2494.
(1B) Lin Y, Ha A, Yan S*. Methods for studying DNA single-strand break repair and signaling in Xenopus laevis egg extracts. Methods Mol Biol. 2019; 1999:161-172.
(1C) Lin Y, Raj J, Li J, Ha A, Hossain MA, Richardson C, Mukherjee P, Yan S*. APE1 senses DNA single-strand breaks for repair and signaling. Nucleic Acids Res. 2020 Feb 28; 48(4):1925-1940.
(1D) Yan S*. Resolution of a complex crisis at DNA 3′ termini. Nat Struct Mol Biol. 2019 May; 26(5):335-336.
(1E) Ha A, Lin Y, Yan S*. A non-canonical role for the DNA glycosylase NEIL3 in suppressing APE1 endonuclease-mediated ssDNA damage. J Biol Chem. 2020 Oct 9; 295(41):14222-14235.

2. Elucidating the molecular mechanisms of DNA damage response pathway in oxidative stress. Oxidative stress has been associated with several human diseases such as cancer and neurodegenerative disorders (2A). My lab is the first to demonstrate that the ATR-Chk1 DDR pathway is activated in response to hydrogen peroxide-induced oxidative stress in Xenopus egg extracts (2B). Notably, APE2 plays a previously uncharacterized, but pivotal, role in the DDR pathway in oxidative stress. Mechanistically, APE2 resects the oxidative DNA damage in the 3′ to 5′ direction and recruits Chk1 to activated ATR for activation, providing novel insights into how ATR DDR pathway is activated by oxidative stress (2B). We further demonstrated that APE2 Zf-GRF binds with ssDNA, but not dsDNA, and regulates APE2’s exonuclease activity in oxidative stress response (2C). We recently revealed that XRCC1 is required for repairing oxidative DNA damage but not defined SSB and gapped structures (2D). This body of work has revealed the novel mechanisms of DDR in oxidative stress and has opened up a new significant direction of research in oxidative stress response.

Publications:
(2A) Yan S*, Sorrell M, Berman Z. Functional interplay between ATM/ATR-mediated DNA damage response and DNA repair pathways in oxidative stress. Cell Mol Life Sci. 2014 Oct; 71(20):3951-3967.
(2B) Willis J, Patel Y, Lentz BL, Yan S*. APE2 is required for ATR-Chk1 checkpoint activation in response to oxidative stress. Proc Natl Acad Sci USA. 2013 Jun 25; 110(26):10592-10597.
(2C) Wallace BD, Berman Z, Mueller GA, Lin Y, Chang T, Andres SN, Wojtaszek JL, DeRose EF, Appel CD, London RE, Yan S*, Williams RS*. APE2 Zf-GRF facilitates 3′-5′ resection of DNA damage following oxidative stress. Proc Natl Acad Sci USA. 2017 Jan 10; 114(2):304-309.
(2D) Cupello S, Lin Y, Yan S*. Distinct roles of XRCC1 in genome integrity in Xenopus egg extracts. Biochem J. 2019 Dec 23; 476(24):3791-3804.

3. Revealing the molecular mechanisms of DNA replication/damage stress response and genome stability. Stressful conditions during DNA replication are detrimental to genomic stability. However, it is not fully understood how DNA replication stress is sensed by checkpoint signaling to coordinate cell cycle progress with DNA repair. I was the first to demonstrate that TopBP1 is a bona fide checkpoint protein in DNA replication stress response (3A). My further mechanistic studies have demonstrated that TopBP1 recruits checkpoint clamp Rad9-Rad1-Hus1 complex and DNA polymerase alpha onto stalled replication forks (3B-3C). We further demonstrated that continued primer synthesis via replicative DNA polymerases plays an essential role in checkpoint activation (3D). We have shown how TopBP1 is imported into nucleus and recruited to sites of DNA damage (3E-3F). These studies have determined the mechanisms of how TopBP1 plays essential roles in ATR-mediated DNA replication stress response.

Publications:
(3A) Yan S, Lindsay HD, Michael WM*. Direct requirement for Xmus101 in ATR-mediated phosphorylation of Claspin bound Chk1 during checkpoint signaling. J Cell Biol. 2006 Apr 24;173(2):181-6.
(3B) Yan S, Michael WM*. TopBP1 and DNA polymerase-alpha directly recruit the 9-1-1 complex to stalled DNA replication forks. J Cell Biol. 2009 Mar 23;184(6):793-804.
(3C) Yan S, Michael WM*. TopBP1 and DNA polymerase alpha-mediated recruitment of the 9-1-1 complex to stalled replication forks: implications for a replication restart-based mechanism for ATR checkpoint activation. Cell Cycle. 2009 Sep 15;8(18):2877-84.
(3D) Van C, Yan S, Michael WM, Waga S, Cimprich KA*. Continued primer synthesis at stalled replication forks contributes to checkpoint activation. J Cell Biol. 2010 Apr 19;189(2):233-46.
(3E) Bai L, Michael WM, Yan S*. Importin β-dependent nuclear import of TopBP1 in ATR-Chk1 checkpoint in Xenopus egg extracts. Cell Signal. 2014 May; 26 (5):857-867.
(3F) Acevedo J, Yan S, Michael WM*. Direct binding of RPA-coated ssDNA allows recruitment of the ATR activator TopBP1 to sites of DNA damage. J Biol Chem. 2016 June 17; 291 (25):13124-13131.

4. Characterizing novel basic mechanisms of cancer etiology and therapeutics. Working with our collaborators in the field of cancer biology, we have started to investigate novel basic mechanisms of cancer development and therapeutics. First, working with Dr. Xiaoqi Liu from University of Kentucky, we have demonstrated that Mre11 phosphorylation by Plk1 results in premature termination of DDR and reduced DNA repair capacity, contributing to prostate cancer progression (4A). Second, we are the first showing genomic alterations and abnormal expression of APE2 in multiple cancers (4B). In addition, we found that APE2 over-expression is implicated in cisplatin-induced acute kidney injury via its novel function in mitochondria (4C).

Publications:
(4A) Li Z, Li J, Kong Y, Yan S, Ahmad N, Liu X*. Plk1 phosphorylation of Mre11 antagonizes the DNA damage response. Cancer Res. 2017 Jun 15;77(12):3169-3180.

(4B) Jensen KA, Shi X, Yan S*. Genomic alterations and abnormal expression of APE2 in multiple cancers. Sci Rep. 2020 Feb 28;10(1):3758.

(4C) Hu Y, Yang C, Amorim T, Maqbool M, Lin J, Li C, Fang C, Xue L, Kwart A, Fang H, Yin M, Janocha AJ, Tsuchimoto D, Nakabeppu Y, Jiang X, Mejia-Garcia A, Anwer F, Khouri J, Qi X, Zheng QY, Yu JS, Yan S, LaFramboise T, Anderson KC, Herlitz LC, Munshi NC, Lin J, Zhao J. Cisplatin-mediated upregulation of APE2 binding to MYH9 provokes mitochondrial fragmentation and acute kidney injury. Cancer Res. 2021 Feb 1; 81 (3): 713-723.