PUBLICATIONS

Liu, Y., Carbonetto, P., Willwerscheid, J., Oakes, S.A., Macleod, K., Stephens, M. 2025.Dissecting tumor transcriptional heterogeneity from single-cell RNA-Seq data by generalized binary covariance decomposition. Nature Genetics. https://doi.org/10.1038/s41588-024-01997-z.

Qiao, Z., Nguyen, L., Dann, C., Yang, D., Dann, C., Thomas, D.M., Henn, M., Valdespino, A., Swenson, C. Oakes, S.A., Rosner, M.R., Moellering, R.E. 2024. Direct inhibition of tumor hypoxia response with synthetic transcriptional repressors. Nat Chem Biol. doi: 10.1038/s41589-024-01716-z.

Muralidharan, C., Huang, F., Enriquez, J.R., Wang, J.E., Nelson, J.B., Nargis, T., May, S.C., Chakraborty, A., Figatner, K.T., Navitskaya, S., Anderson, C.M., Calvo, V., Surguladze, D., Mulvihill, M.J., Yi, X., Sarkar, S., Oakes, S.A., Webb-Robertson, B-J.M., Sims, E.K., Staschke, K.A.,  Eizirik, D.L., Nakayasu, E.S., Stokes, M.E., Tersey, S.A., Mirmira,  R.G. 2024. Inhibition of the eukaryotic initiation factor-2-a kinase PERK decreases risk of autoimmune diabetes in mice. J. Clin Invest. Jun 18:e176136. doi: 10.1172/JCI176136. Online ahead of print.

Pincus, D., Oakes, S.A. 2024. Unfolding emergency calls stress granules to the ER. Nat Cell Biol. doi. 10.1038/s41556-024-01434-7.

Malnassy, G., Ziolkowski, L., Macleod, K.F., Oakes, S.A. 2024. Role of the integrated stress response in pancreatic development, tissue homeostasis, and cancer. Gastroenterology. 167(7):1292-1306. doi: 10.1053/j.gastro.2024.05.009.

Tuchman, A.M., Kulkarni, R.N., Oakes, S.A., Drossos, T., Varady, K., Xu, P., Thomas, C.C., Sargis, R.M., Mirmira, R.G., Wallia, W., Weissberg-Benchell, J., Layden, B.T., Knutson, K.L., Reutrakul, S., Martyn-Nemeth, P., Danielson, K.K., Hoffman, M.B., Gatta, E., Solway, J., Philipson, L.H. 2023. Stress and human health in diabetes: A report from the 19^th Chicago Biomedical Consortium. J Clin Transl Sci. 7(1):e263. doi: 10.1017/cts.2023.646.

Kesaraju, S., Li, Y., Tracy, M., Wannemo, K., Kainov, J., Rana, N., Sidahmed, M., Hyoju.,S., Smith, L., Matthews, J., Tay, S., Khalili-Araghi, G., Rana, M., Oakes, S.A.*, Shen, L.*, Weber, C.R*. 2023. Claudin-2 limits pancreatitis development through regulating tight junction-controlled pancreatic ductal transport. (manuscript submitted and available at https://www.biorxiv.org/content/10.1101/2023.09.01.555960v1) *Co-corresponding authors

Mastracci, T.L., Apte, M., Amundadottir, L.T., Alvarsson, A., Artandi, S., Bellin, M.D.,Bernal-Mizrachi, E., Caicedo, A., Campbell-Thompson, M., Cruz-Monserrate, Z., El Quaamari, A., Gaulton, K.J., Geisz, A., Goodarzi, M.O., Hara, M., Hull-Miechle, R.L., Kleger, A., Klein, A.P., Kopp, J.L., Kulkarni, R.N., Muzumdar, M.D., Naren, A.P., Oakes, S.A., Olesen, S.S., Phelps, E.A., Powers, A.C., Stabler, C.L., Tirkes, T., Whitcomb, D.C., Yadav, D., Yong, J., Zaghloul, N.A., Pandol, S.J., Sander, M. 2023. Integrated physiology of the exocrine and endocrine compartments in pancreatic diseases: workshop proceedings. Diabetes. 72:433-448. https://doi.org/10.2337/db22-0942

Massaoudi, D., Gorman, S., Kuo, Y-M., Iwawaki, T., Oakes, S.A., Papa, F.R., Gould, D.B. 2023. Deletion of the unfolded protein response transducer IRE1α is detrimental to aging photoreceptors and to ER stress-mediated retinal degeneration. Invest Opththalmol Vis Sci. 64(4):30. doi: 10.1167/iovs.64.4.30.

Nguyen, L.C., Renner, D.M., Silva, D., Yang, P., Medina, K.M., Nicolaescu, V., Gula, H., Drayman, N., Valdespino, A., Mohamed, A., Dann, C., Wannemo, K., Robinson-Mailman, L., Gonzalez, A., Stock, L., Cao, M., Qiao, Z., Moellering, R.E., Tay, S., Randall, G, Beers, M.F., Rosner, M.R.*, Oakes, S.A.*, Weiss, S.R.* 2022. SARS-CoV-2 diverges from other betacoronaviruses in only partially activating the IRE1α/XBP1 ER stress pathway in human lung-derived cells. mBio. 13(5): e02415-11. https://doi.org/10.1128/mbio.02415-22 *co-corresponding authors.

Son, R.G., Kandasamy, B., Bowden, T., Azzam, R.K., Oakes, S.A., Philipson, L.H., Greeley, S.A.W. 2022. Acute recurrent pancreatitis in a child with INS-related monogenic diabetes and a heterozygous pathogenic CFTR mutation. J Endocr Soc. 7(3):bvac182. doi:10.1210/jendso/bvac182.

Ibarra, J., Elbanna, Y., Kurylowicz, K., Ciboddo, M., Greenbaum, H.S., Arellano, N., Rodriguez, D., Evers, M., Bock-Hughes, A., Liu, C., Smith, Q., Lutze, J., Baumeister, J., Kalmer, M., Olschok, K., Nicolson, Silva, D., Maxwell, L., Dowgielewicz, J., Rumi, E., Pietra, D., Casetti, I.C., Catricala, S., Koschmieder, S., Gurbuxani, S., Schneider, R.K., Oakes, S.A., Elf, S.E. 2022. Type 1 but not type 2 calreticulin mutations activate the IRE1α-XBP1 pathway of the unfolded protein response to drive myeloproliferative neoplasms. Blood Cancer Discovery. Doi: 10.1158/2643-3230.BCD-21-0144. Online ahead of print.

Stormo, A.E.D., Shavarebi, F., Fitzgibbon, M., Earley, E.M., Ahrendt, H., Lum, L.S., Verscheuren, E., Swaney, D.L., Skibinski, G., Ravisankar, A., von Haren, J., Davis, E.J., Johnson, J.R., Von Dollen, J., Balen, C., Porath, J., Crosio, C., Mirescu, C., Iaccarino, C., Dauer, W.T., Nichols, R.J., Wittman, T., Cox, T.C., Finkbeiner, S., Krogan, N.J., Oakes, S.A.* , and A. Hiniker*. 2022. The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity. J Cell Biol. 221(4): e202010065 *co-corresponding authors.

Nguyen, L.C., Yang, D., Nicolaescu, V., Best, T., Gula, H., Ohtsuki, T., Chen, S., Friesen, J.B., Drayman, N., Mohamed, A., Silva, D., Robinson-Mailman, L., Valdespino, A., Dann, C., Stock, L., Suarez, E., Jones, K.A., Millis, M.J., Dickinson, B.C., Tay, S., Oakes, S.A., Missiakas, D., Pauli, G.F., The National COVID Cohort Collaborative Consortium, Meltzer D.O., Randall, G., and M.R. Rosner. 2022. Cannabidiol inhibits SARS-CoV-2 replication through induction of the host ER stress and innate immune responses. Science Advances (PMID: 35050692; eabi6110. Online ahead of print).

Oakes, S.A. Endoplasmic reticulum stress signaling in cancer cells. Am J Path. 2020 May;190(5):934-946.

Moore PC, Qi JY, Thamsen M, Ghosh R, Peng J, Gliedt MJ, Meza-Acevedo R, Warren RE, Hiniker A, Kim GE, Maly DJ, Backes BJ, Papa FR, Oakes S.A. Parallel signaling through IRE1 and PERK regulates pancreatic neuroendocrine tumor growth and survival. Cancer Research. 2019 Dec 15;79(24):6190-6203.

Moore PC, Cortez JT, Chamberlain CE, Alba D, Berger AC, Quandt Z, Chan A, Cheng MH, Bautista JL, Peng J, German MS, Anderson MS, Oakes S.A. Elastase 3B mutation links to familial pancreatitis with diabetes and pancreatic adenocarcinoma. J Clin Invest. 2019 Aug 1;130:4676-4681.

Brondfield, S., Boscardin, C., Strewler, G., Hyland, K., Oakes, S.A., Nishimura, H., Crawford, J., Hauer, K.E. A medical student inquiry behavior assessment tool: development and validity evidence. Acad Med. 2019 Apr;94(4):586-594. doi: 10.1097/ACM.0000000000002520.

Hiniker, A., Oakes, S.A., Rao, R.C. Bilateral choroidal metastases from pancreatic adenocarcinoma. Ophthalmology. 2017;124(12):1825. doi: 10.1016/j.ophtha.2017.08.020.

Oakes, S.A. Endoplasmic reticulum proteostasis: a key checkpoint in cancer. Am J Physiol Cell Physiol. 2017 Feb 1;312(2):C93-C102. doi: 10.1152/ajpcell.00266.2016. Epub 2016 Nov 16.

Moore, P.C., Oakes, S.A. CPEB4 links the clock and the UPR to protect the liver. Nat Cell Biol. 2017 Jan 31;19(2):79-81. doi: 10.1038/ncb3460.

Wang, E.S., Reyes, N.A., Melton, C., Huskey, N.E., Momcilovic, O., Goga, A., Blelloch, R., Oakes, S.A. Fas-activated mitochondrial apoptosis culls stalled embryonic stem cells to promote differentiation. Curr Biol. 2015 Dec 7;25(23):3110-8. doi: 10.1016/j.cub.2015.10.020. Epub 2015 Nov 12.

Hetz, C., Chevet, E., Oakes, S.A. Erratum: Proteostasis control by the unfolded protein response. Nat Cell Biol. 2015 Aug;17(8):1088. doi: 10.1038/ncb3221. No abstract available.

Hetz, C., Chevet, E., Oakes, S.A. Proteostasis control by the unfolded protein response. Nat Cell Biol. 2015 17(7):829-38.

Crane, C.A., Austgen, K., Haberthur, K., Hofmann, C., Moyes, K.W., Avaneysan, L., Fong, L., Campbell, M.J., Cooper, S., Oakes, S.A., Parsa, A.T., Lanier, L.L.. Immune evasion mediated by tumor-derived lactate dehydrogenase induction of NKG2D ligands on myeloid cells in glioblastoma patients. Proc Natl Acad Sci USA, 2014; 0.1073/pnas.1413933111.

Wang, Y., Guo, W.T., Yan, Y.L., Wang, X.W., Melton, C., Shenoy, A., Reyes, N.A., Oakes, S.A., Blelloch, R. Suppression of epithelial-mesenchymal transition and apoptotic pathways by miR-294/302 family synergistically blocks let-7 induced silencing of self-renewal in embryonic stem cells. Cell Death Differ, 2014 Dec 12. doi: 10.1038/cdd.2014.205. [Epub ahead of print].

Oakes, S.A., Papa, F.R. The role of endoplasmic reticulum stress in human pathology. Annu Rev Pathol Mech. 2015;10:173-94.

Huskey, N.E., Guo, T., Evanson, K.J., Momcilovic, O., Pardo, D., Creaseman, K.J., Judson, R.L., Blelloch, R., Oakes, S.A., Hebrok, M., Goga, A. Cdk1 inhibition targets the p53-Noxa-Mcl1 axis, selectively kills embryonic stem cells, and prevents teratoma formation. Stem Cell Reports, 2015 Mar 10;4(3):374-89

Ghosh, R., Wang, L., Wang, E.S., Perera, B.G.K., Igbaria, A., Morita, S., Prado, K., Thamsen, M., Caswell, D., Macias, H., Weiberth, K.F., Gliedt, M.J., Alavi, M.V., Hari, S.B., Mitra, A.K., Bhhatarai, B., Schurer, S.C., Snapp, E.L., Gould, D.B., German, M.S., Backes, B.J., Maly, D.J., Oakes, S.A.*, Papa, F.R.*. 2014. Allosteric inhibition of the IRE1alpha RNase preserves cell viability and function during endoplasmic reticulum stress. Cell.158:1-15. *Co-corresponding authors.

Van Dis, V., Kuijpers, M., Haasdijk, E.D., Teuling, E., Oakes, S.A., Hoogenraad, C.C., Jaarsma, D. 2014. Golgi fragmentation precedes neuromuscular denervation and is associated with endosome abnormalities in SOD1-ALS mouse motor neurons. Acta Neuropathol Commun. 2:38.

Wang, L., Perera, B.G., Hari, S.B., Bhhatarai, B., Backes, B.J., Seelinger, M.A., Schurer, S.C., Oakes, S.A., Papa, F.R., Maly, D.J. 2012. Divergent allosteric control of the IRE1alpha endoribonuclease using kinase inhibitors. Nat Chem Biol. 8(12):982-9.

Upton, J.P., Wang, L., Han, D., Wang, E.S., Huskey, N.E., Lim, L., Truit, M., McManus, M.T., Ruggero, D., Goga, A., Papa, F.R., Oakes, S.A., 2012. IRE1alpha cleaves select microRNAs during ER stress to derepress translation of proapoptotic caspase-2. Science. 338(6108):818-22. [Abstract] [Reprint]

Lerner, A.G., Upton, J.P., Tayakuniyal, P.P., Ghosh, R., Shen, S., Nakagawa, Y., Nguyen, V., Truisina, A., Heiman, M., Heintz, N., Greengard, P., Backes, B.J., Hui, S., Tang, Q., Oakes, S.A.*, Papa, F.R.* 2012. IRE1alpha induces thioredoxin-interacting protein (TXNIP) to activate the NLRP3 inflammasome and promote cell death. Cell Metab. 16:250-64. *Co-corresponding authors.

Cheng, C.K., Gustafson, W.C., Charron, E., Houseman, B.T., Zunder, E., Goga, A., Gray, N.S., Pollok, B., Oakes, S.A., James, C.D., Shokat, K.M., Weiss, W.A., Fan, Q.W. Dual blockade of lipid and cyclin-dependent kinases induces synthetic lethality in malignant gliioma. 2012. Proc Natl Acad Sci USA. 109(31):12722-12727.

Austgen, K., Oakes, S.A., Ganem, D. 2012. Multiple defects, including premature apoptosis, prevent Kaposi’s sarcoma-associated herpesvirus replication in murine cells. J Virol. 86(3):1877-82.

Shore, G.C., Papa, F.R., Oakes, S.A. 2011. Signaling cell death from the endoplasmic reticulum stress response. Curr Opin Cell Biol. 23(2):143-9.

Austgen, K., Johnson, E.T., Park, T.J., Curran, T., Oakes, S.A. 2011. The adaptor protein CRK is a pro-apoptotic transducer of endoplasmic reticulum stress. Nat Cell Biol. 14(1):87-92.

Fan, Q.W., Cheng, C., Hackett, C., Feldman, M., Houseman, B.T., Nicolaides, T., Hass-Kogan, D., James, C.D., Oakes, S.A., Debnath, J., Shokat, K.M., Weiss, W.A. 2010. Akt and autophagy cooperate to promote survival of drug-resistant glioma. Sci Signal. 3(147):ra81.

Reyes, N.A., Fisher, J.K., Austgen, K., VandenBerg, S., Huang, E.J., and Oakes, S.A. Blocking the mitochondrial apoptotic pathway preserves motor neuron viability and function in a mouse model of amyotrophic lateral sclerosis. 2010. J. Clin. Invest. 120(10):3673-3679.

Han, D., Lerner, A.G., Vande Walle, L., Upton, J.P., Xu, W., Hagen, A., Backes, B.J., Oakes, S.A., and Papa, F.R. 2009. IRE1alpha kinase activation modes control alternate endoribonuclease outputs to determine divergent cell fates. Cell 138, 562-575.

Upton, J.P., Austgen, K., Nishino, M., Coakley, K.M., Hagen, A., Han, D., Papa, F.R., and Oakes, S.A. 2008. Caspase-2 cleavage of BID is a critical apoptotic signal downstream of endoplasmic reticulum stress. Mol. Cell. Biol. 28, 3943-3951.

Han, D., Upton, J.P., Hagen, A., Callahan, J., Oakes, S.A., and Papa F.R. 2008. A kinase inhibitor activates the IRE1alpha RNase to confer cytoprotection against ER stress. Biochem. Biophys. Res. Commun. 365, 777-783.

Oakes S.A. 2007. Mitochondria control calcium entry at the immunological synapse. Proc. Natl. Acad. Sci. USA 104, 15171-15172.

Oakes, S.A. and Lin, S.S., Bassik, M.C. 2006. The control of endoplasmic reticulum-initiated apoptosis by the BCL-2 family of proteins. Curr. Mol. Med. 6, 99-109.

Oakes, S.A ., Scorrano, L., Opferman, J.T., Bassik, M.C., Nishino, M., Pozzan, T., and Korsmeyer, S.J. 2005. Proapoptotic BAX and BAK regulated IP3R-1 and calcium leak from the endoplasmic reticulum. Proc. Natl. Acad. Sci. USA 102, 105-110.

Oakes, S.A., and Korsmeyer, S.J. 2004. Untangling the web: mitochondrial fission and apoptosis. Dev Cell. 7:460-462.

Bassik, M.C., Scorrano, L., Oakes, S.A., Pozzan, T., and Korsmeyer, S.J. 2004. Phosphorylation of BCL-2 regulates ER Ca 2+ homeostasis and apoptosis. EMBO J . 23, 1207-1216.

Oakes S.A ., Opferman J.T., Pozzan T., Korsmeyer, S.J., and Scorrano, L. 2003. Regulation of endoplasmic reticulum Ca 2+ dynamics by proapoptotic BCL-2 family members. Biochem Pharmacol. 66, 1335-1340.

Scorrano, L.*, Oakes, S.A *, Opferman, J.T., Cheng E.H., Sorcinelli, M.D., Pozzan, T., and Korsmeyer, S.J. 2003. BAX and BAK regulation of endoplasmic reticulum Ca 2+ : a control point for apoptosis. Science 300, 135-139. *These authors contributed equally.

Scorrano, L., Ashiya, M., Buttle, K., Weiler, S., Oakes, S.A., Mannella, C.A., and Korsmeyer, S.J. 2002. Distinct pathways remodel mitochondrial cristae or release cytochrome c during apoptosis. Dev. Cell 2, 55-67.

Candotti, F., Oakes, S.A., Johnston, J.A., Giliani, S., Schumacher, R.F., Mella, P., Fiorini, M., Ugazio, A.G., Badolato, R., Notarangelo, L.D., Bozzi, F., Macchi, P., Strina, D., Vezzoni, P., Blaese, R.M., O’Shea, J.J., and Villa, A. 1997. Structural and functional basis for JAK3-deficient severe combined immunodeficiency. Blood 90, 3996-4003.

Taylor, N., Candott, F., Smith, S., Oakes, S.A., Jahn, T., Isakov, J., Puck, J.M., O’Shea, J.J., Weinberg, K., and Johnston, J.A. 1997. Interluekin-4 signaling in B lymphocytes from patients with X-linked severe combined immunodeficiency. J. Biol. Chem. 272, 7314-7319.

Oakes, S.A., Candotti, F., Johnston, J.A., Chen, Y.Q., Ryan, J.J., Taylor, N., Lui, X., Hennighauser, L., Notarangelo, L.D., Paul, W.E., Blaese, R.M., and O’Shea, J.J. 1996. Signaling via IL-2 and IL-4 in JAK3-deficient severe combined immunodeficiency lymphocytes: JAK3-dependent and -independent pathways. Immunity 5, 605-615.

Candotti, F., Oakes, S.A., Johnston, J.A., Notarangelo, L.D., O’Shea, J.J., and Blaese, R.M. 1996. In vitro correction of JAK3-deficient severe combined immunodeficiency by retroviral-mediated gene transduction. J. Exp. Med. 183, 2687-2692.

Johnston, J.A., Wang, L.M., Hanson, E.P., Sun, X.J., White, M.F., Oakes, S.A., Pierce, J.H., and O’Shea, J.J. 1995. Interleukins 2, 4, 7, and 15 stimulate tyrosine phosphorylation of insulin receptor substrates 1 and 2 in T cells. Potential role of JAK kinases. J. Biol. Chem. 270, 28527-28530.