Tom Rutkowski, PhD
Introduction
Our laboratory seeks to understand a fundamental but very poorly understood question in biology: When a cell encounters stress (i.e., anything that perturbs normal cellular function), how does it decide whether to adapt to the stress or die? We use diverse experimental approaches to address this question, encompassing systems biology, molecular and cell biology, and vertebrate genetics and physiology. By tackling this question, we hope to better understand diseases of stress, including neurodegeneration, cancer, metabolic syndrome, and others, and even normal cellular development and function. There are many ways in which stress can be manifested to a cell, including pathogenic infection, chemical insult, genetic mutation, nutrient deprivation, and the course of normal cellular function. The endoplasmic reticulum (ER) is the site of synthesis and folding of secretory and cell-surface proteins. The cellular response to ER stress (also known as the Unfolded Protein Response, or UPR) serves as a model for understanding not only the mechanisms by which stress is sensed, but also the ways in which the consequences of alterations of homeostasis in one location (i.e., the ER) impact diverse areas of cell function, including gene expression, metabolism, cancer, cell signaling, and apoptosis.
I was born and raised in St. Louis, Missouri, then went to college in Delaware and grad school in San Francisco before finding myself by happenstance again in the Midwest. In my spare time I’m a triathlete/runner, crossworder, and some-time cartoonist, and of late am spending time in the kitchen making bread, ice cream, tortillas, and other goodies. Scientifically, I translocated into the endoplasmic reticulum in graduate school and have never left it, so I apparently have a KDEL tag.
Current Positions
- Associate Professor of Anatomy and Cell Biology
- Associate Professor of Internal Medicine
Education
- BS in Biotechnology, University of Delaware, Newark, Delaware, United States
- PhD in Cell Biology, University of California San Francisco, San Francisco, California, United States
- Postdoctoral Fellow, Howard Hughes Medical Institute, University of Michigan Medical Center, Ann Arbor, Michigan, United States
Graduate Program Affiliations
Center, Program and Institute Affiliations
Research Interests
- Endoplasmic reticulum stress
- Steatotic liver disease and liver injury
- Gene regulation
- Cell fate decisions
Selected Publications
- Liu K, Zhao C, Adajar RC, DeZwaan-McCabe D, Rutkowski DT.EMBO Rep. 2024 Jan;25(1):228-253. doi: 10.1038/s44319-023-00026-0. Epub 2024 Jan 2.PMID: 38177915. A beneficial adaptive role for CHOP in driving cell fate selection during ER stress.
- Shah A, Huck I, Duncan K, Gansemer ER, Liu K, Adajar RC, Apte U, Stamnes MA, Rutkowski DT.Hepatol Commun. 2023 Oct 12;7(11):e0278. doi: 10.1097/HC9.0000000000000278. eCollection 2023 Nov 1.PMID: 37820274 Free PMC article. Interference with the HNF4-dependent gene regulatory network diminishes endoplasmic reticulum stress in hepatocytes.
- Gansemer, E. R., McCommis, K. S., Martino, M., King-McAlpin, A. Q., Potthoff, M. J., Finck, B. N., Taylor, E. B. & Rutkowski, D. T. (2020). NADPH and Glutathione Redox Link TCA Cycle Activity to Endoplasmic Reticulum Homeostasis. iScience 23 (5) 101116. DOI: 10.1016/j.isci.2020.101116. PMID: 32417402.
- Diedrichs, D. R., Gomez, J. A., Huang, C. S., Rutkowski, D. T. & Curtu, R. (2018). A data-entrained computational model for testing the regulatory logic of the vertebrate unfolded protein response. Molecular biology of the cell 29 (12) 1502-1517. DOI: 10.1091/mbc.E17-09-0565. PMID: 29668363. PMCID: PMC6014097.
- Rutkowski, D. T. (2019). Liver function and dysfunction - a unique window into the physiological reach of ER stress and the unfolded protein response. FEBS J. 286 (2) 356-378. DOI: http://dx.doi.org/10.1111/febs.14389. PMID: 29360258. PMCID: PMC6056347.
- DeZwaan-McCabe, D., Sheldon, R. D., Gorecki, M. C., Guo, D. F., Gansemer, E. R., Kaufman, R. J., Rahmouni, K., Gillum, M. P., Taylor, E. B., Teesch, L. M. & Rutkowski, D. T. (2017). ER Stress Inhibits Liver Fatty Acid Oxidation while Unmitigated Stress Leads to Anorexia-Induced Lipolysis and Both Liver and Kidney Steatosis. Cell Reports 19 (9) 1794-1806. DOI: 10.1016/j.celrep.2017.05.020. PMID: 28564599. PMCID: PMC5520660.
- Gomez, J. A. & Rutkowski, D. T. (2016). Experimental reconstitution of chronic ER stress in the liver reveals feedback suppression of BiP mRNA expression. eLife 5 e20390. DOI: 10.7554/eLife.20390. PMID: 27938665. PMCID: PMC5179193.
- DeZwaan-McCabe, D., Riordan, J. D., Arensdorf, A. M., Icardi, M. S., Dupuy, A. J. & Rutkowski, D. T. (2013). The stress-regulated transcription factor CHOP promotes hepatic inflammatory gene expression, fibrosis, and oncogenesis. PLoS Genetics 9 (12) e1003937. DOI: 10.1371/journal.pgen.1003937. PMID: 24367269. PMCID: PMC3868529.
- Arensdorf, A. M., Dezwaan McCabe, D., Kaufman, R. J. & Rutkowski, D. T. (2013). Temporal clustering of gene expression links the metabolic transcription factor HNF4α to the ER stress-dependent gene regulatory network. Frontiers in genetics 4 188. DOI: 10.3389/fgene.2013.00188. PMID: 24069029. PMCID: PMC3781334.
- Arensdorf, A. M. & Rutkowski, D. T. (2013). Endoplasmic reticulum stress impairs IL-4/IL-13 signaling through C/EBPβ-mediated transcriptional suppression. Journal of cell science 126 (Pt 17) 4026-36. DOI: 10.1242/jcs.130757. PMID: 23813955. PMCID: PMC3757336.