Yu Lab

Our understanding of how the biology of various diseases relates to the central dogma that DNA encodes RNA, which encodes protein has been buoyed by rapid technological advances in DNA and RNA sequencing and has led to some of the first advances in personalized medicine. However, characterization of the final and arguably most actionable element of the central dogma, protein, has lagged behind. Among the various proteomic parameters, a comprehensive description of the landscape of covalent protein modifications in any given cell is particularly challenging. Our research efforts are highly multidisciplinary, which have been largely focused on two programs, i.e., (1) novel protein posttranslational modifications (PTMs), and (2) novel covalent protein modifications by small molecule drugs. Regarding (1), the entire repertoire of protein posttranslational modifications (PTMs) is enormous, with ~400 different known types, and many more unknown ones (i.e., the “dark proteome”). PTMs are inaccessible by genomic sequencing tools. Instead, they are almost exclusively analyzed by proteomic technologies. The functional characterization of a PTM event ultimately depends on the unequivocal assignment of the modification site. However, the chemical natures of PTMs are diverse, and many types of PTMs are not amenable to traditional proteomic technologies for site-localization with single amino acid resolution because they are, for example, labile, heterogeneous or low-abundance. We have developed a multidisciplinary program (i.e., chemical biology, quantitative-/chemo-proteomics, computation biology, biochemistry, molecular biology and animal models) towards the functional analyses of a number of important PTMs, including protein tyrosine sulfation, phosphorylation and Poly-ADP-ribosylation. Regarding (2), besides these naturally occurring PTMs, covalent protein modification has been increasingly appreciated as a novel therapeutic modality. The current efforts on drug development have been mostly focused on targeting a small fraction of the human proteome with good pharmacological tractability (e.g., kinases). It has been estimated, however, that approximately 90% of human proteins (e.g., transcription factors, adaptors and intrinsically disordered proteins) have not been effectively targeted by small-molecule drugs, because, for example, they lack traditionally defined binding pockets. We have also been particularly active in the development of covalent protein modification and chemoproteomic technologies that potentially will revolutionize the principle of drug development by pushing the boundaries of the druggable proteome.

The Yu Lab's ongoing research program is currently focused in four core areas:

1. Quantitative Proteomics and Chemoproteomics

With the continuous development and optimization of the core modules, we have developed a highly sophisticated quantitative and chemoproteomic platform specifically for the global and site-specific analyses of protein covalent modifications. Some of the efforts in these areas include the development of novel sample preparation protocols, data acquisition methods, computational proteomics (e.g., protein sequence database search engines), and functional annotation tools. Through these studies, we have gained extensive experience in extracting meaningful information from large-scale proteomic data for follow-up mechanistic studies. These multidisciplinary approaches also put us in a unique position to identify aberrant protein modification patterns, decipher the mechanisms of their deregulation, establish the functional consequences of these molecular events, and facilitate the development of relevant therapeutic strategies (e.g., covalent inhibitors) for the relevant diseases (e.g., cancer, diabetes and neurodegeneration).

2. Poly-ADP-ribosylation, PARP, and Cell Stress Response

Poly-ADP-ribosylation (PARylation) is a reversible PTM that is catalyzed by a class of enzymes known as poly-ADP-ribose polymerases (PARPs). PARylation is critically involved in many biological processes linked to cell stress responses, particularly DNA damage response (DDR). Despite the tremendous success of PARP1 inhibitors in the clinic, the basic signaling mechanism of PARylation is poorly understood. We have taken a systematic approach to the unbiased discovery of novel PARylation events in the human proteome. Furthermore, we have elucidated the functional roles of PARylation on many important signaling proteins. These studies provided critical insights into the signaling output of PARP1 (and other PARP enzymes) in the context of cell stress responses. We have developed a series of PROTAC-based PARP1 degraders, and using these novel chemical probes, we were able to decouple PARP1 trapping from PARP1 inhibition. These studies have provided key insights into the MoA of PARP1 inhibitors, including their genotoxic, cytotoxic and immunomodulatory functions. We are also particularly interested in developing the next generation PARP1-targeting agents for the treatment of cancer, ischemia-reperfusion injury and neurodegeneration.

3. Phosphorylation, mTOR, and Cell Growth Control

We have been continuously involved in the development of novel mass spectrometric technologies in the field of phosphoproteomics. These unbiased approaches have been deployed to systematically interrogate the phosphoproteome regulated by key signaling proteins, including the insulin receptor, PI3K/Akt, mTORC1, mTORC2, ERK/MAPK, TBK1, SIK3 and chemokine receptors. We have also used these powerful technologies to probe the remodeling of the phosphoproteome during various biological states (e.g., during sleep-awake cycles). As an example, the evolutionarily conserved kinase complex, mTORC1, plays a critical role in regulating cell growth, proliferation, migration and survival. Although many upstream regulators of mTORC1 have been identified, the downstream targets of mTORC1 have been poorly defined. We have used quantitative proteomic approaches towards defining the signaling landscape downstream of both mTORC1 and mTORC2 (including the proteome, phosphoproteome and secretome). The identification and the subsequent functional characterization of these novel mTORC1 targets (e.g., Grb10, IGFBP5, LARP1, SRPK2, FOXK1 and STK11IP) led to transformative insights into how mTORC1 regulates many important biological processes, including the cross-talk with insulin/IGF signaling, protein translation, metabolism, autophagy, and lysosomal acidification.  

4. Targeting the Undruggable Proteome using Covalent Chemistry

The current efforts on drug development have been mostly focused on targeting a small fraction of the human proteome with good pharmacological tractability (e.g., kinases). It has been estimated, however, that approximately 90% of human proteins (e.g., transcription factors, adaptors and intrinsically disordered proteins) have not been effectively targeted by small-molecule drugs, because, for example, they lack traditionally defined binding pockets. The recent development of covalent small molecule inhibitors of EGFR, BTK and KRas^G12C has revolutionized the principle of drug development by pushing the boundaries of the druggable proteome. We have been developing novel chemoproteomic technologies that will allow the unbiased identification of novel hotspots on traditionally undruggable protein targets. In combination with novel covalent modifiers (from unexplored chemical space) and disease biology, these efforts point to the very exciting possibility of drugging many well-validated, yet previously inaccessible disease targets.

Selected Publications

1. Kim C, Wang XD, Liu Z, Hao J, Wang S, Li P, Zi Z, Ding Q, Jang S, Kim J, Luo Y, Huffman KE, Pal Choudhuri S, Del Rio S, Cai L, Liang H, Drapkin BJ, Minna JD, Yu Y. Induced degradation of lineage-specific oncoproteins drives the therapeutic vulnerability of small cell lung cancer to PARP inhibitors. Science Advances. 2024 Jan 19;10(3):eadh2579. 
2. Deng H, Deng H, Kim C, Li P, Wang X, Yu Y, Qin T. Synthesis of nimbolide and its analogues and their application as poly(ADP-ribose) polymerase-1 trapping inducers. Nature Synthesis. 2024 Mar;3(3):378-385. 
3. Li P, Zhen Y, Kim C, Liu Z, Hao J, Deng H, Deng H, Zhou M, Wang XD, Qin T, Yu Y. Nimbolide targets RNF114 to induce the trapping of PARP1 and synthetic lethality in BRCA-mutated cancer. Science Advances. 2023 Oct 27;9(43);eadg7752. 
4. Kim C, Wang XD, Liu Z, Zha S, Yu Y. Targeting Scaffolding Functions of Enzymes Using PROTAC Approaches. Biochemistry. 2022 Jul 14
5. Zi Z, Zhang Z, Feng Q, Kim C, Wang XD, Scherer PE, Gao J, Levine B, Yu Y. Quantitative phosphoproteomic analyses identify STK11IP as a lysosome-specific substrate of mTORC1 that regulates lysosomal acidification. Nature Communications. 2022 Apr 1;13(1):1760.
6. Kim C, Chen C, Yu Y. Avoid the trap: targeting PARP1 beyond human malignancy. Cell Chemical Biology., 2021 Apr 15;28(4):456-462.
7. Kim C, Wang X, Yu Y. PARP1 Inhibitors Trigger Innate Immunity via PARP1 Trapping-induced DNA Damage Response, eLife, 2020 Aug 26;9. doi: 10.7554/eLife.60637
8. Wang S, Han L, Han J, Li P, Ding Q, Zhang QJ, Liu ZP, Chen C, Yu Y. Uncoupling of PARP1 trapping and inhibition using selective PARP1 degradation. Nature Chemical Biology. 2019 Dec;15(12):1223-1231.
9. Wang XD, Hu R, Ding Q, Savage TK, Huffman KE, Williams N, Cobb MH, Minna JD, Johnson JE, Yu Y. Subtype-specific secretomic characterization of pulmonary neuroendocrine tumor cells. Nature Communications. 2019 Jul 19;10(1):3201.
10. Wang Z, Ma J, Miyoshi C, Li Y, Sato M, Ogawa Y, Lou T, Ma C, Gao X, Lee C, Fujiyama T, Yang X, Zhou S, Hotta-Hirashima N, Klewe-Nebenius D, Ikkyu A, Kakizaki M, Kanno S, Cao , Takahashi S, Peng J, Yu Y, Funato H, Yanagisawa M, Liu Q, “Quantitative phosphoproteomic analysis of the molecular substrates of sleep need”, Nature, (2018)
11. Zhen Y, Zhang Y, Yu Y., “A cell line-specific atlas of PARP-mediated protein Asp/Glu-ADP-ribosylation in breast cancer”, Cell Reports, 8, 2326, (2017).
12. Zhang Y, Zhang Y and Yu Y., “Global Phosphoproteomic analysis of Insulin/Akt/mTORC1/S6K signaling in Rat Hepatocytes”, Journal of Proteome Research, 16, 2825, (2017).
13. Gibson BA, Zhang Y, Jiang H, Hussey KM, Shrimp JH, Lin H, Schwede F, Yu Y, Kraus WL. “Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation”, Science, (research article), 353, 45-50, (2016).
14. Ding M, Bruick R, and Yu Y*. “Secreted IGFBP5 mediates mTORC1-dependent feedback inhibition of IGF-1 signaling”, Nature Cell Biology, 18, 319, (2016).
15. Xiang, S., Kato, M., Wu, L., Lin, Y., Ding, M., Zhang, Y., Yu, Y. and McKnight, S. L. “The LC Domain of hnRNPA2 adopts similar conformations in hydrogel polymers, liquid-like droplets and nuclei”, Cell, 163, 829-839 (2015).
16. Wang J, Zhang Y and Yu Y. “Crescendo: A Protein Sequence Database Search Engine for Tandem Mass Spectra”, J. Am. Soc. Mass. Spectrom., 26, 1077 (2015).
17. Zhang, Y., Wang, J., Ding, M. and Yu, Y. “Site-Specific Characterization of the Asp- and Glu-ADP-ribosylated Proteome”. Nature Methods, 10(10):981-4 (2013).
18. Yu, Y., Yoon, S., Poulogiannis, G., Yang, Q., Ma, M., Villen, J., Kubica, N., Hoffman, G., Cantley, L. C., Gygi, S. P. & Blenis, J. “Phosphoproteomic Analysis Identifies Grb10 as an mTORC1 Substrate That Negatively Regulates Insulin Signaling” Science, 332(6035), 1322-1326 (2011).

For a complete list of publications, please visit PubMed.gov