Research

We are broadly interested in cellular mechanisms maintaining genome stability and their implications in human diseases, including cancer and neurodegenerative disorders.

    Mechanistic studies of DNA mismatch repair

    DNA mismatch repair (MMR) maintains genome stability by primarily correcting DNA replication errors in the newly synthesized strand. Defects in MMR leads to cancer and other human diseases. The MMR reaction has been reconstituted, which involves mismatch recognition by MutS family proteins (MutS in prokaryotes and MSH2•MSH6-formed MutSα or MSH2•MSH3-formed MutSβ in eukaryotes), removal of the mispaired base by nucleases in a manner dependent on MutS- and MutL-family proteins, and repair DNA synthesis by a replicative DNA polymerase in concert with DNA replication factors. Despite extensive studies, many fundamental questions in MMR are still unknown.

    1. How is MMR specifically targeted to the newly-synthesized strand?

    Unlike the obvious DNA lesions for other DNA repair pathways, both bases in a mismatch (e.g., mispaired G•T or C•A) are normal DNA components. Thus, to remove the incorrect base, the MMR system has to know the wrong information-containing daughter strand. Previous studies have revealed that DNA strand breaks in the newly synthesized daughter strand serve as a strand discrimination signal, ensuring the repair specifically targeted to the daughter strand. However, a strand break is usually several hundred base pairs away from a mismatch, how these two distal sites communicate with each other during MMR has been a standing puzzle in the field. Our lab has reconstituted the human MMR reaction in a defined system. Using this reconstituted system, we aim to resolve this fundamental but important problem in MMR.

    dna mismatch

    2. How does MMR occur in vivo?

    Our knowledge about the mechanism of MMR essentially came from the in vitro studies using naked DNA heteroduplexes. However, DNA is packed into nucleosome-consisting chromatin in vivo. How MMR occur in vivo is largely unknown. Recently, we have shown that MutSα is recruited to replicating chromatin through its physical interaction with H3K36me3 (histone H3 lysine 36 trimethylation). Consistent with this observation, disrupting the MutS-H3K36me3 interaction leads to a mutator phenotype similar to that of cells defective in MMR genes. How are other MMR proteins recruited to chromatin? How do they interact with each other in vivo? Understanding these questions will provide critical information for clinical practice, including cancer diagnosis and therapy. Using cutting-edge technologies, we are studying the in vivo MMR reaction.

    recruitment mutsa to chromatin

    Representative Publications

    Ortega J, Lee GS, Gu L, Yang W, Li GM (2021). Mispair-bound human MutS-MutL complex triggers DNA incisions and activates mismatch repairCell Res 2021 Jan 28. doi: 10.1038/s41422-021-00468-y.

    Fang J, Huang Y, Mao G, Yang S, Rennert G, Gu L, Li H, Li GM (2018). Cancer-driving H3G34V/R/D mutations block H3K36 methylation and H3K36me3–MutSα interactionProc Natl Acad Sci USA. 115: 9598-9603.

    Huang Y, Gu L, Li GM (2018). H3K36me3-mediated mismatch repair preferentially protects actively transcribed genes from mutationJ Biol Chem 293, 7811-7823.

    Li F, Mao G, Tong D, Huang J, Gu L, Yang W, Li GM (2013). The histone mark H3K36me3 regulates human DNA mismatch repair through its interaction with MutSαCell 153, 590-600.

    Ortega J, Li JY, Lee S, Tong D, Gu L, Li GM (2015). Phosphorylation of PCNA by EGFR inhibits mismatch repair and promotes misincorporation during DNA synthesisProc Natl Acad Sci USA 112, 5667-5672.

    Zhang M, Xiang S, Joo HY, Wang L, Williams KA, Liu W, Hu C, Tong D, Haakenson J, Wang Cet al. (2014). HDAC6 deacetylates and ubiquitinates MSH2 to maintain proper levels of MutSαMol Cell 55, 31-46.

    Li GM (2008). Mechanisms and functions of DNA mismatch repairCell Res 18, 85-98.

    Zhang Y, Yuan F, Presnell SR, Tian K, Gao Y, Tomkinson AE, Gu L, Li GM (2005). Reconstitution of 5'-directed human mismatch repair in a purified systemCell 122, 693-705.

    Mismatch Repair in Cancer Therapy

    Despite decades of extensive studies, cancer is still the number 2 leading cause of death in the United States, with a total of 1.7 million new cancer cases and ~600,000 cancer deaths each year. The major problem is that none of the existing therapies can fully eradicate the malignant clone and avoid drug resistance and side effects. Cancer cells defective in MMR are highly resistant to many chemo- and radiation-therapeutic drugs. However, recent studies have shown that tumors defective in MMR respond very well to immunotherapy, but the molecular mechanism is not fully understood.

    Our lab is studying the mechanism by which MMR deficiency triggers immunotherapy and identifying/developing molecules specifically targeting to the MMR reaction for cancer cell killing. The latter project includes small molecules and altered MMR proteins capable of triggering cell death during MMR.

    Representative Publications

    Guan J, Lu C, Jin Q, Lu H, Chen X, Tian L, Zhang Y, Ortega J, Zhang J, Siteni S, Chen M, Gu L, Shay J, Davis A, Chen ZJ, Fu YX, Li GM (2021). MLH1 deficiency-triggered DNA hyper-excision by exonuclease 1 activates the cGAS-STING pathwayCancer Cell, 39, 109–121.

    Lu C, Guan J, Lu S, Jin Q, Rousseau B, Lu T, Stephens D, Zhang H, Zhu J, Yang M, Ren Z, Liang Y, Liu Z, Han C, Liu L, Cao X, Zhang A, Qiao J, Batten K, Chen M, Castrillon DH, Li B, Li GM, Fu YX (2021). DNA sensing in mismatch repair-deficient tumor cells is essential for anti-tumor immunityCancer Cell, 39, 96-108.

    Ortega J, Lee GS, Gu L, Yang W, Li GM (2021) Mispair-bound human MutS-MutL complex triggers DNA incisions and activates mismatch repairCell Res 2021 Jan 28. doi: 10.1038/s41422-021-00468-y.

    Li GM (2008). Mechanisms and functions of DNA mismatch repairCell Res 18, 85-98.

    Wu J, Gu L, Wang H, Geacintov NE, Li GM (1999). Mismatch repair processing of carcinogen-DNA adducts triggers apoptosisMol Cell Biol 19, 8292-8301.

    Mismatch Repair in Neurodegenerative Diseases

    Trinucleotide repeat expansions cause more than 30 severe neuromuscular and neurodegenerative disorders, including Huntington’s disease, myotonic dystrophy type 1, and fragile X syndrome. Although the MMR system is well known for its role in maintaining replication fidelity, key MMR proteins, especially MutSβ, have been implicated in promoting trinucleotide repeat instability. However, the molecular basis by which the MMR system causes trinucleotide repeat expansions is not known.

    Representative Publications

    Williams G, Paschalis V, Ortega J, Li GM, Schwabe J, Lahue R (2020). HDAC3 deacetylates the DNA mismatch repair protein MutSβ to stimulate triplet repeat expansionsProc Natl Acad Sci USA, 117 (38) 23597-23605 https://doi.org/10.1073/pnas.2013223117

    Chan, NL, Guo J, Zhang T, Mao G, Hou C, Yuan F, Huang J, Zhang Y, Wu J, Gu L, et al. (2013). Coordinated processing of 3' slipped (CAG)n/(CTG)n hairpins by DNA polymerases beta and delta preferentially induces repeat expansionsJ Biol Chem 288, 15015-15022.

    Guo J, Gu L, Leffak M, Li GM (2016). MutSbeta promotes trinucleotide repeat expansion by recruiting DNA polymerase beta to nascent (CAG)n or (CTG)n hairpins for error-prone DNA synthesisCell Res 26, 775-786.

    Hou C, Chan NL, Gu L, Li GM (2009). Incision-dependent and error-free repair of (CAG)(n)/(CTG)(n) hairpins in human cell extractsNat Struct Mol Biol 16, 869-875.

    Zhang T, Huang J, Gu L, Li GM (2012). In vitro repair of DNA hairpins containing various numbers of CAG/CTG trinucleotide repeatsDNA Repair 11, 201-209.