Our lab is interested in the function, regulation, and targeting of enzymes that control protein post-translational modifications (PTM). After the human genome is sequenced, a major challenge to understand biology and human diseases is to understand the function of all proteins. Proteins are not always expressed, and even if expressed, their activities are not always on. Their activities are often regulated by certain stresses and signals, which is crucial for all cell signaling events. Thus, to fully understand the function of a protein, it is also crucial to understand how it is regulated. We, therefore, focus on understanding the function and regulation of PTM enzymes and use the understanding to develop small molecule inhibitors for these enzymes as potential therapeutics for treating human diseases, including cancer, autoimmune diseases, and neurodegenerative diseases.
NAD-consuming enzymes: Sirtuins and PARPs
Among the PTM enzymes that we study, we are particularly interested in NAD-consuming enzymes. These enzymes stand out as they not only have diverse and important biological functions but also display very interesting chemistry.
Sirtuins and HDACs
The Sir2 (silencing information regulator 2) family of enzymes, or sirtuins, were originally known as NAD-dependent protein lysine deacetylases. They are present in all domains of life and have been shown to be important in regulating numerous biological pathways, including genome stability, metabolism, and longevity. Mammals have seven sirtuin enzymes, Sirt1-7. They are considered promising targets for treating several human diseases, including cancer and neurodegeneration. Among the seven mammalian sirtuins, only Sirt1-3 have efficient deacetylase activity. Sirt4-7 have very weak and sometimes undetectable deacetylase activity. We demonstrated that Sirt5 can remove succinyl and malonyl groups while Sirt6 can remove myristoyl and palmitoyl groups very efficiently. We demonstrated that protein lysine succinylation, malonylation, and long-chain fatty acylation are common protein posttranslational modifications (PTMs) that were previously unknown or under-recognized. We are continuing to understand the functions of sirtuins by discovering new substrates and their regulatory mechanisms. Furthermore, we are also utilizing information about the enzymatic activity of sirtuins to develop small molecule inhibitors for therapeutic applications.
PARPs
PARPs catalyze either poly-ADP-ribosylation or mono-ADP-ribosylation of various substrate proteins. There are 17 PARPs in humans,For most other PARPs, their biological functions are still unknown. Many PARP inhibitors are in clinical trial for treating cancers, especially triple-negative breast cancers. To better realize the potential of PARP inhibitors as therapeutics, it is important to understand the biological functions of various PARPs. Our earlier work focused on identifying the substrate proteins of PARPs. We developed clickable NAD analogs to identify PARP substrate proteins. The clickable NAD analog has an alkyne functional group, which allows the conjugation, via click chemistry, of different tags, such as fluorescent tags for in-gel visualization and affinity tags for purification. Furthermore, we demonstrate that by identifying the substrate proteins of PARP1, novel insights into its biological functions can be obtained.
Recently, we started to study the function of PARPs by understanding their regulation. Our work with TiPARP (PARP7) showed that it is transcriptionally up-regulated by HIF-1. The increased TiPARP expression serves to ADP-ribosylate HIF-1α and promote HIF-1α degradation, forming a negative feedback loop to turn off HIF-1 transcriptional activity. The most interesting part of this story is the mechanism via which TiPARP promotes the degradation of HIF-1α. We found that TiPARP, via its ADP-ribosylation activity, forms phase condensates (nuclear bodies) and recruits E3 ubiquitin ligases, thus leading to the ubiquitination and degradation of HIF-1α. We are currently investigating the detailed mechanism via which ADP-ribosylation promotes phase condensation.
ZDHHC and NMT long-chain acyltransferases
Our interest in sirtuins and HDACs led us to study the function of protein lysine long-chain acylation. In this process, we got interested in the long-chain acylation of other protein residues, such as cysteine and N-terminal glycine. Two families of enzymes are well-known to catalyze these long-chain acylations, ZDHHC family for cysteine palmitoylation and NMT for N-terminal glycine myristoylation. Our recent work surprisingly showed that NMT could also catalyze N-terminal lysine side chain myrisotylation on ARF6, This myristoylation can be removed by SIRT2 and this myristoylation-demyristoylation cycle is important for the activity of ARF6. We are currently working to discover other substrate proteins that are lysine myristoylated by NMT.
Similarly, we found another acylation-deacylation cycle for STAT3. STAT3 can be cysteine palmitoylated by ZDHHC7, which targets STAT3 to the plasma membrane, where it can be phosphorylated by JAK2. The phosphorylated STAT3 then is depalmitoylated by APT2, allowing phosphorylated STAT3 to go to the nucleus to turn on transcription of genes required for Th17 development. Thus, the palmitoylation-depalmitoylation cycle of STAT3 is crucial for its function and immune activation. We have shown that pharmacologically or genetically disrupting this cycle can effectively inhibit Th17 cell differentiation and suppress inflammatory bowel diseases. We are currently studying various ZDHHCs by discovering their substrate proteins and understand how cysteine palmitoylation regulates their functions.
Dipthamide: biosynthesis and biological function
Diphtheria was once a deadly disease causing many deaths before modern vaccination was available. The disease is caused by Corynebacterium diphtheriae, a bacterium that secrets diphtheria toxin. Diphtheria toxin catalyzes the ADP-ribosylation of a unique posttranslationally-modified His residue, termed diphthamide, in eukaryotic and archaeal translation elongation factor 2 (EF2). EF2 is a GTPase that catalyzes the translocation of the peptidyl-tRNA and mRNA from the ribosome A site to the P site, and therefore is essential for protein biosynthesis. The biological function of diphthamide is not understood yet, although it has been shown that knock out dph1 or dph2 is lethal in mouse, and dph1 heterozygote mouse are prone to tumor formation. The biosynthesis of the diphthamide residue has been a long time puzzle. There are at least seven genes (Dph1, Dph2, Dph3, Dph4, Dph5, Dph6, and Dph7) required for the biosynthesis. Our lab contributed to the discovery of Dph6 and Dph7.
Our goal is to use in vitro biochemistry to figure out the molecular functions of the proteins Dph1-7 in the biosynthesis of diphthamide, and study the effects of diphthamide formation on the function of EF2 in protein synthesis. The first step of the biosynthesis is of particular interest because of the uncommon C-C bond formation reaction, the uncommon use of SAM, and the requirement of multiple proteins (Dph1-4). Our evidences suggest that the enzyme catalyzing this step contains [4Fe-4S] cluster and uses an unusual radical reaction mechanism. Our work has led to a much better understanding of how this unusual [4Fe-4S] radical enzyme works. Our current focus is on understanding the biological function of this modification. Specifically, we are interested to find out the translation of what proteins are affected by diphthamide and what the cellular phenotypes are when diphthamide biosynthesis is disrupted.
Tsinghua University, Beijing, China
B.S., Chemistry
1998
Columbia University
Ph.D., Bioorganic Chemistry
2003
Harvard Medical School
Postdoctoral Fellow
2006
Cornell University
Assistant Professor, Department of Chemistry and Chemical Biology
2012
Cornell University
Associate Professor, Department of Chemistry and Chemical Biology
2013
Cornell University
Professor, Department of Chemistry and Chemical Biology
2024
Cornell University
Tri-Institutional Faculty Member
2024
Cornell University
- Howard Hughes Medical Institute Investigator
2024
The University of Chicago
Professor
Jin Y, Jana S, Abbasov ME, Lin H. Antibiotic target discovery by integrated phenotypic and activity-based profiling of electrophilic fragments. Cell Chem Biol. Published online February 26, 2025
Henze E, Burkhardt RN, Fox BW, et al. ATP-release pannexin channels are gated by lysophospholipids. Preprint. bioRxiv. 2025
Alimova I, Wang D, DeSisto J, et al. SIRT2 regulates the SMARCB1 loss-driven differentiation block in ATRT. Mol Cancer Res. Published online February 17, 2025
Liu R, Ren X, Park YE, et al. Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and gliomagenesis. Cell Metab. 2025
Hao J, Ahn B, Lin H. Loss of Diphthamide Increases DNA Replication Stress in Mammalian Cells by Modulating the Translation of RRM1. ACS Cent Sci. 2024;10(10):1835-1847. Published 2024
Jana S, Shang J, Hong JY, et al. A Mitochondria-Targeting SIRT3 Inhibitor with Activity against Diffuse Large B Cell Lymphoma. J Med Chem. 2024
Liu Y, Hou D, Chen W, et al. MAVS Cys508 palmitoylation promotes its aggregation on the mitochondrial outer membrane and antiviral innate immunity. Proc Natl Acad Sci U S A. 2024
Peng K, Wallace SD, Bagde SR, et al. GS-441524-Diphosphate-Ribose Derivatives as Nanomolar Binders and Fluorescence Polarization Tracers for SARS-CoV-2 and Other Viral Macrodomains. ACS Chem Biol. 2024
Yu T, Hou D, Zhao J, et al. NLRP3 Cys126 palmitoylation by ZDHHC7 promotes inflammasome activation. Cell Rep. 2024
Anmangandla A, Jana S, Peng K, et al. Correction to "A Fluorescence Polarization Assay for Macrodomains Facilitates the Identification of Potent Inhibitors of the SARS-CoV-2 Macrodomain". ACS Chem Biol. 2024
Tate EW, Soday L, de la Lastra AL, Wang M, Lin H. Protein lipidation in cancer: mechanisms, dysregulation and emerging drug targets. Nat Rev Cancer. 2024
Zhang B, Yu Y, Fox BW, et al. Amino acid and protein specificity of protein fatty acylation in C. elegans. Proc Natl Acad Sci U S A. 2024
Peng K, Anmangandla A, Jana S, Jin Y, Lin H. Iso-ADP-Ribose Fluorescence Polarization Probe for the Screening of RNF146 WWE Domain Inhibitors. ACS Chem Biol. 2024
Maio G, Smith M, Bhawal R, et al. Interactome Analysis Identifies the Role of BZW2 in Promoting Endoplasmic Reticulum-Mitochondria Contact and Mitochondrial Metabolism. Mol Cell Proteomics. 2024
Anmangandla A, Jana S, Peng K, et al. A Fluorescence Polarization Assay for Macrodomains Facilitates the Identification of Potent Inhibitors of the SARS-CoV-2 Macrodomain [published correction appears in ACS Chem Biol. 2024
Bai P, Liu Y, Yang L, et al. Development and Pharmacochemical Characterization Discover a Novel Brain-Permeable HDAC11-Selective Inhibitor with Therapeutic Potential by Regulating Neuroinflammation in Mice. J Med Chem. 2023
Jiang Y, Xu Y, Zhu C, et al. STAT3 palmitoylation initiates a positive feedback loop that promotes the malignancy of hepatocellular carcinoma cells in mice. Sci Signal. 2023
Smith MR, Zhang L, Jin Y, et al. A Turn-On Fluorescent Amino Acid Sensor Reveals Chloroquine's Effect on Cellular Amino Acids via Inhibiting Cathepsin L. ACS Cent Sci. 2023
Zhang Y, Zhao Q, Lin H. Identification of potential HDAC11 deacylase substrates by affinity pulldown MS. Methods Enzymol. 2023
Xu Y, Lin H. Use of alkyne-tagged myristic acid to detect N-terminal myristoylation. Methods Enzymol. 2023
O'Brien C, Ling T, Berman JM, et al. Simultaneous inhibition of Sirtuin 3 and cholesterol homeostasis targets acute myeloid leukemia stem cells by perturbing fatty acid β-oxidation and inducing lipotoxicity. Haematologica. 2023
Ho TT, Peng C, Seto E, Lin H. Trapoxin A Analogue as a Selective Nanomolar Inhibitor of HDAC11. ACS Chem Biol. 2023
Wang ZA, Markert JW, Whedon SD, et al. Structural Basis of Sirtuin 6-Catalyzed Nucleosome Deacetylation. J Am Chem Soc. 2023
Lin H. Christopher T. Walsh: A Prolific Scientist, Effective Academic Leader, and Responsive Mentor. ACS Chem Biol. 2023
Komaniecki G, Camarena MDC, Gelsleichter E, et al. Astrocyte Elevated Gene-1 Cys75 S-Palmitoylation by ZDHHC6 Regulates Its Biological Activity. Biochemistry. 2023
Lin H. Substrate-selective small-molecule modulators of enzymes: Mechanisms and opportunities. Curr Opin Chem Biol. 2023
Latifkar A, Wang F, Mullmann JJ, et al. IGF2BP2 promotes cancer progression by degrading the RNA transcript encoding a v-ATPase subunit. Proc Natl Acad Sci U S A. 2022
Anmangandla A, Ren Y, Fu Q, Zhang S, Lin H. The Acyl-CoA Specificity of Human Lysine Acetyltransferase KAT2A. Biochemistry. 2022
Su D, Kosciuk T, Lin H. Reply to Comment on "Binding Affinity Determines Substrate Specificity and Enables Discovery of substrates for N-Myristoyltransferases". ACS Catal. 2022
Wang M, Zhang Y, Komaniecki GP, et al. Golgi stress induces SIRT2 to counteract Shigella infection via defatty-acylation. Nat Commun. 2022
Miller SP, Maio G, Zhang X, et al. A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions. Mol Cell Proteomics. 2022
Zhang Y, Su D, Zhu J, et al. Oxygen level regulates N-terminal translation elongation of selected proteins through deoxyhypusine hydroxylation. Cell Rep. 2022
Zhang S, Nelson OD, Price IR, et al. Long-chain fatty acyl coenzyme A inhibits NME1/2 and regulates cancer metastasis. Proc Natl Acad Sci U S A. 2022
Wang ZA, Whedon SD, Wu M, et al. Histone H2B Deacylation Selectivity: Exploring Chromatin's Dark Matter with an Engineered Sortase. J Am Chem Soc. 2022
Bagchi RA, Robinson EL, Hu T, et al. Reversible lysine fatty acylation of an anchoring protein mediates adipocyte adrenergic signaling. Proc Natl Acad Sci U S A. 2022
Cheng WX, Ren Y, Lu MM, et al. Palmitoylation in Crohn's disease: Current status and future directions. World J Gastroenterol. 2021
Li M, Teater MR, Hong JY, et al. Translational Activation of ATF4 through Mitochondrial Anaplerotic Metabolic Pathways Is Required for DLBCL Growth and Survival. Blood Cancer Discov. 2022
Yang Y, Tapias V, Acosta D, et al. Altered succinylation of mitochondrial proteins, APP and tau in Alzheimer's disease. Nat Commun. 2022
Shang J, Smith MR, Anmangandla A, Lin H. NAD+-consuming enzymes in immune defense against viral infection [published correction appears in Biochem J. 2022
Cao Z, Gu Z, Lin S, et al. Attenuation of NLRP3 Inflammasome Activation by Indirubin-Derived PROTAC Targeting HDAC6. ACS Chem Biol. 2021
Su D, Kosciuk T, Yang M, Price IR, Lin H. Binding Affinity Determines Substrate Specificity and Enables Discovery of Substrates for N-Myristoyltransferases. ACS Catal. 2021
Hong JY, Lin H. Sirtuin Modulators in Cellular and Animal Models of Human Diseases. Front Pharmacol. 2021
Cao Z, Yang F, Wang J, et al. Indirubin Derivatives as Dual Inhibitors Targeting Cyclin-Dependent Kinase and Histone Deacetylase for Treating Cancer. J Med Chem. 2021
Taneja A, Ravi V, Hong JY, Lin H, Sundaresan NR. Emerging roles of Sirtuin 2 in cardiovascular diseases. FASEB J. 2021
Hong JY, Malgapo MIP, Liu Y, et al. Correction to "High-Throughput Enzyme Assay for Screening Inhibitors of the ZDHHC3/7/20 Acyltransferases". ACS Chem Biol. 2021
Zhang Y, Lin Z, Zhu J, Wang M, Lin H. Diphthamide promotes TOR signaling by increasing the translation of proteins in the TORC1 pathway. Proc Natl Acad Sci U S A. 2021
Wang J, Cao Z, Wang F, et al. Cysteine derivatives as acetyl lysine mimics to inhibit zinc-dependent histone deacetylases for treating cancer. Eur J Med Chem. 2021
Hong JY, Cassel J, Yang J, Lin H, Weiser BP. High-Throughput Screening Identifies Ascorbyl Palmitate as a SIRT2 Deacetylase and Defatty-Acylase Inhibitor. ChemMedChem. 2021
Hong JY, Malgapo MIP, Liu Y, et al. High-Throughput Enzyme Assay for Screening Inhibitors of the ZDHHC3/7/20 Acyltransferases [published correction appears in ACS Chem Biol. 2021
Komaniecki G, Lin H. Lysine Fatty Acylation: Regulatory Enzymes, Research Tools, and Biological Function. Front Cell Dev Biol. 2021;9:717503. Published 2021
Zhang Y, Su D, Dzikovski B, et al. Dph3 Enables Aerobic Diphthamide Biosynthesis by Donating One Iron Atom to Transform a [3Fe-4S] to a [4Fe-4S] Cluster in Dph1-Dph2. J Am Chem Soc. 2021
Hong JY, Fernandez I, Anmangandla A, Lu X, Bai JJ, Lin H. Pharmacological Advantage of SIRT2-Selective versus pan-SIRT1-3 Inhibitors. ACS Chem Biol. 2021
Wang M, Lin H. Understanding the Function of Mammalian Sirtuins and Protein Lysine Acylation. Annu Rev Biochem. 2021
Lin H. Protein cysteine palmitoylation in immunity and inflammation. FEBS J. 2021
Abril YLN, Fernandez IR, Hong JY, et al. Pharmacological and genetic perturbation establish SIRT5 as a promising target in breast cancer. Oncogene. 2021
Renowned Biochemist Hening Lin to join the University of Chicago Department of Chemistry