Publications
2024
Endogenous Cellular Metabolite Methylgloxal Induces DNA-Protein Cross-Links in Living Cells
Hurben A, Zhang Q, Galligan J, Tretyakova N, Erber L. ACS Chemical Biology. 2024
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https://doi.org/10.1021/acschembio.4c00100
Summary: Methylglyoxal (MGO) has been hypothesized to form toxic DNA–protein cross-links (DPC), but the identities of proteins participating in such cross-linking in cells have not been determined. In the present work, we quantified DPC formation in human cells exposed to MGO and identified proteins trapped on DNA upon MGO exposure using mass spectrometry-based proteomics.
Improved detection of DNA replication fork-associated proteins
Rivard S, Chang Y, Ragland R, Thu Y, Kassab M, Mandal R, Van Riper S, Kulej K, Higgins L, Markowski T, Shang D, Hedberg J, Erber L, Garcia B, Chen Y, Bielinsky A, Brown E. Cell Reports. 2024
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Summary: We report on an innovation to the iPOND technique to purify, identify and quantify proteins participating in actively replicating DNA. We report that poly-K63-ubiquitination is associated with replisome stalling.
2023
Endogenous Metabolites and Genome Instability in Aging and Disease
Summary: Proper maintenance of genomic DNA is upheld by tight control of cellular metabolism and DNA processing. Herein, we review recent advances in examining the role of endogenous metabolites and genomic instability in aging and disease.
Defining the Commonalities between Post-Transcriptional and Post-Translational Modification Communities
Summary: Post-transcriptional modifications of RNA (PRMs) and post-translational modifications of proteins (PTMs) are important regulatory mechanisms in biological processes and have many commonalities. However, the integration of these research areas is lacking. A recent discussion identified the priorities, areas of emphasis, and necessary technologies to advance and integrate these areas of study.
2022
Developing Role for Artificial Intelligence in Drug Discovery in Drug Design, Development, and Safety Assessment.
Summary: Artificial intelligence (AI) is a rapidly growing discipline in the field of chemical toxicology. Herein, we provide a broad overview of research presented at the Fall 2022 American Chemical Society meeting, highlighting how AI is being applied across various facets of drug design, development, and safety assessment.
HypDB: A functionally annotated web-based database of the proline hydroxylation proteome.
Gong Y, Behera G, Erber L, Chen Y. PLOS Biology. 2022
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PMCID: PMC9455854
Summary: Proline hydroxylation (Hyp) regulates protein structure, stability, and protein–protein interaction. It is widely involved in diverse metabolic and physiological pathways in cells and diseases. To reveal functional features of the Hyp proteome, we integrated various data sources for deep proteome profiling of the Hyp proteome in humans and developed HypDB (https://www.HypDB.site), an annotated database and web server for Hyp proteome.
Quantitative Proteome and Transcriptome Dynamics Analysis Reveals Iron Deficiency Response Networks and Signature in Neuronal Cells
Erber L, Gong Y, Phu T, Chen Y. Molecules. 2022
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PMCID: PMC8779535
Summary: Iron and oxygen deficiencies are common features in pathophysiological conditions, such as ischemia, neurological diseases, and cancer. Cellular adaptive responses to such deficiencies include repression of mitochondrial respiration, promotion of angiogenesis, and cell cycle control. We applied a systematic proteomics analysis to determine the global proteomic changes caused by acute hypoxia and chronic and acute iron deficiency (ID) in hippocampal neuronal cells.
Publications Prior to 2022
17. Erber L, Goodman, S., Wright, F., Tretyakova, N., Rusyn, I. Intra- and inter-species variability in urinary N7-(1-hydroxy-3-buten-2-yl) guanine (EB-GII) adducts following inhalation exposure to 1,3-butadiene. Chemical Research in Toxicology 2021; PMDCID
16. Pujari, S., Wu, M., Thomforde, J., Wang, Z., Chao, C., Olson, N., Erber, L., Pomerantz, W., Cole, P., Tretyakova, N. Site-Specific 5-Formyl Cytosine Mediated DNA-Histone Cross-Links: Synthesis and Polymerase Bypass by Human DNA Polymerase η. Angewandte Chimie, 60(51):26489-26494 (2021).
15. Hurben, A., Erber, L., Tretyakova, N., Doran, T. Proteome-wide Profiling of Cellular Targets Modified by Dopamine Metabolites via a Bio-orthogonal Functionalized Probe. ACS Chemical Biology, 16 (11), 2581-2594 (2021).
14. Erber, L., Goodman, S., Jopikii Krueger, C., Rusyn, I., Tretyakova, N. Quantitative NanoLC/NSI+ -HRMS method for 1,3-butadiene induced bis-N7-guanine DNA-DNA crosslink adducts in urine. Toxics, 9 (10), 247 (2021).
13. Erber, L., Luo, A., Gong, Y., Beeson, M., Tu, M., Tran, P., Chen, Y. Iron Deficiency Reprograms Phosphorylation Signaling and Reduces O-GlcNAc Pathways in Neuronal Cells. Nutrients, 13 (1), 179 (2021).
12. Boysen, G., Degner, A., Arora, R., Vevang, K., Erber, L., Tretyakova, N., Peterson, L. Effect of GSTT1 Genotype on Detoxification of 1,3-Butadiene Derived Diepoxide and Formation of Promutagenic DNA Crosslinking in Human Hapmap Cell Lines. Chemical Research in Toxicology, 34 (1), 119-131 (2021).
11. Ndreu, L., Erber, L., Tornqvist, M., Tretyakova, N., Karlsson, I. Characterizing Adduct Formation of Electrophilic Skin Allergens with Human Serum Albumin and Hemoglobin. Chemical Research in Toxicology, 3 (10), 2623-2636 (2020).
10. Degner,A., Arora, R., Erber, L., Peterson, L., Tretyakova, N. Interindividual Differences in DNA Adduct Formation and Detoxification of 1,3-Butadiene Derived Epoxide in Human Hapmap Cell Lines. Chemical Research in Toxicology, 33 (7) 1698-1708 (2020).
9. Wang, X., Hennig, T., Whisnant, A., Erhard, F., Prusty, B., Friedel, C., Forouzmand, E., Hu, W., Erber, L., Chen, Y., Sandri-Goldin, R., Dölken, L., Shi, Y. Herpes simplex virus blots host transcription termination via the bimodal activities of ICP27, Nature Communications, 11 (1), 1-13 (2020).
8. Erber, L., Luo, A., Chen, Y. Targeted and interactome proteomics reveal the role of PHD2 in regulating BRD4 proline hydroxylation. Molecular and Cellular Proteomics, 18 (9), 1772-1781 (2019).
7. Yeh, H., Chang, JW., Park, M., Erber, L., Sun, J., Cheng, S., Bui, A., Fahmi, N., Nasti, R., Kuang, R., Chen, Y., Zhang, W., Yong, J., mTOR-coordinated U2AF1 isoform-specific transcriptions modulate translational control. Nucleic Acids Research, 47 (19), 10373-10387 (2019).
6. Li, Y., Evers, J., Luo, A., Erber, L., Postler, Z., Chen, Y. A Quantitative Chemical Proteomics Approach for Site-specific Stoichiomietry Analysis of Ubiquitination. Angewandte Chemie. 58, 537-541 (2019).
5. Smestad, J., Erber, L., Chen, Y., Maher, L. Chromatin succinylation correlates with active gene expression and is perturbed by defective TCA cycle metabolism. iScience, 2, 63-75 (2018).
4. Smestad, J., Hamidi, O., Wang, L., Holte, M., Al Khazal, F., Erber, L., Chen, Y., Maher, L. Characterization and metabolic synthetic lethal testing in a new model of SDH-loss familial pheochromocytoma and paraganglioma. Oncotarget, 9:6109-6127 (2018).
3. Chen, D., Tavana, O., Chu, B., Erber, L., Chen, Y., Baer, B., Gu, W. NRF2 is a major target of ARF in p53-independent tumor suppression. Molecular Cell, 68 (1), 224-232 (2017).
2. Zhou, T.*, Erber, L.*, Liu, B., Gao, Y., Ruan, H., & Chen, Y. Proteomic analysis reveals diverse proline hydroxylation-mediated oxygen-sensing cellular pathways in cancer cells. Oncotarget, 7, 48 (2016).
1. Zhao, F., Wang, X., Erber, L., Luo, M., Guo, A., Yang, S., Gu, J., Turman, R., Gao, Y., Li, D., Gui, Z., Zhang, Z., Bi, L., Baughn, A., Zhang, X., Deng, J. Binding pocket alterations in dihydrofolate synthase confer resistance to para-aminosalicylic acid in clinical isolates of Mycobacterium tuberculosis. Antimicrobial Agents and Chemotherapy, 2014