Peer-reviewed papers (chronological)
1. Nancy A. Louis, Kathryn E. Hamilton, Tianqing Kong, Sean P. Colgan. HIF-dependent induction of apical CD55 coordinates epithelial clearance of neutrophils. FASEB Journal 2005 June; 19(8): 950-9. PMID:15923405.
2. Holger K. Eltzschig, Parween Abdulla, Edgar Hoffman, Kathryn E. Hamilton, Dionne Daniels, Caroline Schönfeld, Michaela Löffler, German Reyes, Michael Duszenko, Jorn Karhausen, Andreas Robinson, Karen A. Westerman, Imogen R. Coe, and Sean P. Colgan: HIF-1-dependent repression of equilibrative nucleoside transporter (ENT) in hypoxia. Journal of Experimental Medicine 2015 Dec;202(11): 1493-505. PMCID: PMC2213326.
3. Nancy A. Louis, Kathryn E. Hamilton, Geraldine Canny, Laurie L. Shekels, Samuel B. Ho, Sean P. Colgan. Selective induction of mucin-3 by hypoxia in intestinal epithelia. Journal of Cellular Biochemistry 2006 Dec;99(6): 1616-27. PMID: 16823775.
4. Kathryn E. Hamilton, P. Kay Lund, Joseph A. Galanko, Robert S. Sandler, Temitope O. Keku: Suppressor of cytokine signaling 3 (SOCS3) is not an independent biomarker of colorectal adenoma risk. Biomed Central Research Notes 2010 May;3(144). PMCID: PMC2883989.
5. Kathryn E. Hamilton, James G. Simmons, Shengli Ding, Laurianne Van Landeghem, P. Kay Lund . Cytokine induction of tumor necrosis factor receptor 2 is mediated by STAT3 in colon cancer cells. Molecular Cancer Research 2011 Dec;9(12): 1718-31. PMCID: PMC3243771.
6. Kathryn E. Hamilton Felicite K. Noubissi Prateek S. Katti Christopher M. Hahn Sonya R. Davey Emma T. Lundsmith Andres J. Klein-Szanto Andrew D. Rhim Vladimir S. Spiegelman Anil K. Rustgi. IMP1 promotes tumor growth, dissemination and a tumor-initiating cell phenotype in colorectal cancer cell xenografts. Carcinogenesis 2013 Nov; 34(11): 2647-54. PMCID: PMC3810836.
7. Long Apple, Giroux Véronique, Whelan Kelly A, Hamilton Kathryn E, Tétreault Marie-Pier, Tanaka Koji, Lee Ju-Seog, Klein-Szanto Andres J, Nakagawa Hiroshi, Rustgi Anil K. WNT10A promotes an invasive and self-renewing phenotype in esophageal squamous cell carcinoma. Carcinogenesis 2015 May;36(5): 598-606. PMCID: PMC4498148.
8. Kathryn E. Hamilton, Priya Chatterji, Emma T. Lundsmith, Sarah F. Andres, Veronique Giroux, Philip D. Hicks, Felicite K. Noubissi, Vladimir S. Spiegelman, Anil K. Rustgi: Loss of stromal IMP1 promotes a tumorigenic microenvironment in the colon. Molecular Cancer Research 2015 Nov;13(11): 1478-86. PMCID: PMC4644674.
9. Ravi K. Amaravadi, Kathryn E. Hamilton, Xiaohong Ma, Shengfu Piao, Armando Del Portillo, Katherine L. Nathanson, Matteo S. Carlino, Georgina V. Long, Igor Puzanov, Xiaowei Xu, Jennifer J.D. Morrissette, Kenneth Y. Tsai, Keith T. Flaherty, Jeffrey A. Sosman, Grant R. Goodman, Grant A. McArthur, Anil K. Rustgi, David C. Metz, Lynn M. Schuchter, Paul B. Chapman, and Antonia R. Sepulveda. Multiple gastrointestinal polyps in patients treated with BRAF inhibitors. Clinical Cancer Research. 2015 Dec 1;21(23):5215-21. PMCID:PMC4668213.
10. Kelly A Whelan, Jamie F Merves, Veronique Giroux, Koji Tanaka, Andy Guo,Prasanna M Chandramouleeswaran, Alain J Benitez, Kara Dods, Jianwen Que, Joanne C Masterson, Shahan D Fernando, Bridget C Godwin, Andres J Klein-Szanto, Kudakwashe Chikwava, Eduardo D Ruchelli, Kathryn E Hamilton, Amanda B Muir, Mei-Lun Wang, Glenn T Furuta, Gary W Falk, Jonathan M Spergel, Hiroshi Nakagawa. Autophagy mediates epithelial cytoprotection in eosinophilic oesophagitis. Gut 2017 Jul;66(7):1197-1207. PMCID: PMC4987278.
11. Dana Almohazey, Yuan-Hung Lo, Claire Vossler, Alan Simmons, Jonathan Hsieh, Edie Bucar, Michael Schumacher, Kathryn Hamilton, Ken Lau, Noah Shroyer, Mark Frey. The ErbB3 receptor tyrosine kinase negatively regulates Paneth cells by PI3K-dependent suppression of Atoh1. Cell Death and Differentiation. 2017 May;24(5):855-865. PMCID: PMC5423110.
12. Véronique Giroux, Ashley A. Lento, Mirazul Islam, Jason R. Pitarresi, Akriti Kharbanda, Kathryn E. Hamilton, Kelly A. Whelan, Apple Long, Ben Rhoades, Qiaosi Tang, Hiroshi Nakagawa, Christopher J. Lengner, Adam J. Bass, E. Paul Wileyto, Andres J. Klein-Szanto, Timothy C. Wang, and Anil K. Rustgi. Long-lived keratin 15+ esophageal progenitor cells contribute to homeostasis and regeneration. Journal of Clinical Investigation. 2017 June;27(6):2378-2391. PMCID: PMC5451220.
13. Rei Mizuno, Priya Chatterji, Sarah F. Andres, Kathryn E. Hamilton, Lauren A. Simon, Shawn Foley, Arjun Jeganathan, Brian Gregory, Blair B. Madison, and Anil K. Rustgi. Differential regulation of LET-7 by LIN28B isoform-specific functions. Molecular Cancer Research. 2018 Mar;16(3):403-416. PMCID: PMC5835183.
14. Yuta Kasagi, Prasanna M. Chandramouleeswarana, Kelly A. Whelan, Koji Tanaka, Veronique Giroux, Medha Sharma, Joshua Wang, Alain J. Benitez, Maureen DeMarshall, John W. Tobias, Kathryn E. Hamilton, Gary W. Falk, Jonathan M. Spergel, Andres J. Klein-Szanto, Anil K. Rustgi, Amanda B. Muirb, Hiroshi Nakagawa. The esophageal organoid system reveals functional interplay between Notch and cytokines in reactive epithelial changes. Cell and Molecular Gastroenterology 2018 Jan;5(3):333-352. PMCID: PMC5852293.
15. Véronique Giroux, Julien Stephan, Priya Chatterji, Ben Rhoades, Andres J. Klein-Szanto, Christopher J. Lengner, Kathryn E. Hamilton, Anil K. Rustgi: Mouse intestinal krt15+ crypt cells are radio-resistant and tumor-initiating. Stem Cell Reports 2018 Jun;10(6):1947-1958. PMCID: PMC5993649.
16. Priya Chatterji*, Kathryn E. Hamilton*, Shun Liang, Sarah F. Andres, H. R. Sagara Wijeratne, Rei Mizuno, Lauren A. Simon, Philip D. Hicks, Shawn W. Foley, Jason R. Pitarresi, Andres J. Klein-Szanto,Amanda T. Mah, Laurianne Van Landeghem, Brian D. Gregory, Christopher J. Lengner, Blair B.Madison, Premal Shah, and Anil K. Rustgi. The LIN28B-IMP1 post-transcriptional regulon has opposing effects on oncogenic signaling in the intestine. Genes and Development 2018 June. *co-first author
17. Priya Chatterji, Patrick A. Williams, Kelly A. Whalen, Fernando C. Samper, Sarah F. Andres, Lauren A. Simon, Louis R. Parham, Rei Mizuno, Emma T. Lundsmith, Shun Liang, Sagara HR Wijeratne, Stefani Marti, Lillian Chua, Veronique Giroux, Benjamin J. Wilkins, Gary D. Wu, Premal Shah, Gian G. Tartaglia, Kathryn E. Hamilton. Posttranscriptional regulation of colonic epithelial repair by RNA binding protein IGF2BP1/IMP1. EMBO Reports 2019, April.
18. Sarah F. Andres, Kathy N. Williams, Rei Mizuno, Jeff Headd, Priya Chatterji, Kathryn E. Hamilton, Anil K. Rustgi: IMP1 3' UTR shortening enhances metastatic burden in colorectal cancer. Carcinogenesis 40(4): 569-579, June 2019.
19. Hiroshi Nakagawa, Yuta Kasagi, Tatiana A. Karakasheva, Takeo Hara, Bailey Aaron, Takashi Kijima, Veronique Giroux, Dominique Bailey, Benjamin Wilkins, Julian A. Abrams, Gary W. Falk, Seema Aceves, Jonathan M. Spergel, Kathryn E. Hamilton, Kelly A. Whelan, Amanda Muir: Modeling epithelial homeostasis and reactive epithelial changes in human and murine three-dimensional esophageal organoids. Current Protocols in Stem Cell Biology February 2020.
20. Judith R. Kelsen, Noor Dawany, Maire A. Conrad, Tatiana Karakasheva, Kelly Maurer, Jane M. Wei, Selen Uman, Maiah H. Dent, Rithika Behera, Laura M. Bryant, Xianghui Ma, Leticia Moreira, Priya Chatterji, Rawan Shraim, Audrey Merz, Rei Mizuno, Lauren A. Simon, Amanda B. Muir, Claudio Giraudo, Edward M. Behrens, Kelly A. Whelan, Marcella Devoto, Pierre A. Russo, Sarah F. Andres, Kathleen E. Sullivan, Kathryn E. Hamilton: Colonoids from patients with pediatric inflammatory bowel disease exhibit decreased growth associated with inflammation severity and durable upregulation of antigen presentation genes. Inflammatory Bowel Diseases January 2021.
21. Sarah A. Smith, Sayaka A. Ogawa, Lillian Chau, Kelly A. Whelan, Kathryn E. Hamilton, Jie Chen, Lu Tan, Eric Z. Chen, Sue Keilbaugh, Franz Fogt, Meenakshi Bewtra, Jonathan Braun, Ramnik J. Xavier, Clary B. Clish, Barry Slaff, Aalim M. Weljie, Frederic D. Bushman, James D. Lewis, Hongzhe Li, Stephen R. Master, Michael J. Bennett, Hiroshi Nakagawa, and Gary D. Wu. Mitochondrial dysfunction in inflammatory bowel disease alters intestinal epithelial metabolism of hepatic acylcarnitines. Journal of Clinical Investigation. January 2021.
22. Jodie Ouahed, Judith R. Kelsen, Waldo A. Spessott, Kameron Kooshesh, Maria L. Sanmillan, Noor Dawany, Kathleen E. Sullivan, Kathryn Hamilton, Voytek Slowik, Sergey Nejentsev, João Farela Neves, Helena Flores, Wendy K. Chung, Ashley Wilson, Kwame Anyane Yeboa, Karen Wou, Preti Jain, Michael Field, Sophia Tollefson, Dalin Li1, Dermot P.B. McGovern, Daniel Kotlarz, Christoph Klein, Jonathan Evans, Neil Warner, Abdul Elkadri, Aleixo M. Muise, Jeffrey Goldsmith, Agnes Toth-Petroczy, Dana Vuzman, Nikkola Carmichae, Corneliu Bodea, Christopher A. Cassa, Marcella Devoto, Richard L. Maas, Edward M. Behrens, Claudio G. Giraudo, and Scott B. Snapper: Variants in STXBP3 Result in Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Deficiency Journal of Crohn's and Colitis February 2021.
23. Tatiana A Karakasheva, Joel T Gabre, Uma M Sachdeva, Ricardo Cruz-Acuña, Eric W Lin, Maureen DeMarshall, Gary W Falk, Gregory G Ginsberg, Zhaohai Yang, Michele M Kim, Eric S Diffenderfer, Jason R Pitarresi, Jinyang Li, Amanda B Muir, Kathryn E Hamilton, Hiroshi Nakagawa, Adam J Bass, Anil K Rustgi: Patient-derived organoids as a platform for modeling a patient's response to chemoradiotherapy in esophageal cancer. Scientific Reports October 2021.
24. Takeo Hara, PhD, Yuta Kasagi, Joshua Wang, Masaru Sasaki1, Bailey Aaron1, Adam Karami, Masataka Shimonosono, Rieko Shimonosono, Hisatsugu Maekawa, Lauren Dolinsky, Benjamin Wilkins, Jeremy Klein, Jane Wei, Kathryn Nunes, Kristle Lynch, Jonathan M. Spergel, Kathryn E. Hamilton PhD, Melanie A. Ruffner, Tatiana A. Karakasheva PhD, Kelly A. Whelan, Hiroshi Nakagawa, Amanda B. Muir: CD73+ epithelial progenitor cells which contribute to homeostasis and renewal are depleted in eosinophilic esophagitis. Cellular and Molecular Gastroenterology and Hepatology December 2021 Notes: In Press.
25. Mohammad Faujul Kabir1, Adam Karami1, Ricardo Cruz-Acuna, Alena Klochkova, Reshu Saxena, Anbin Mu, Mary Grace Murray, Jasmine Cruz, Annie E. Fuller, Margarette Clevenger, Kumaraswamy Naidu Chitrala, Yin Fei Tan, Kelsey Keith, Jozef Madzo, Hugh Huang, Jaroslav Jelinek, Tatiana Karakasheva, Kathryn E. Hamilton, Amanda B. Muir, Marie-Pier Tetreault, Kelly A. Whelan: Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium and age-associated mitochondrial dysfunction. Nature Communications April 2022 Notes: Accepted March 2022.
26. Oxana Dmitrieva-Posocco, Andrea C. Wong, Patrick Lundgren, Aleksandra M. Golos, Hélène C. Descamps, Lenka Dohnalová, Zvi Cramer, Yuhua Tian, Brian Yueh, Onur Eskiocak, Gabor Egervari, Yemin Lan, Jinping Liu, Jiaxin Fan, Jihee Kim, Bhoomi Madhu, Kai Markus Schneider, Svetlana Khoziainova, Natalia Andreeva, Qiaohong Wang, Ning Li, Emma E. Furth, Will Bailis, Judith R. Kelsen, Kathryn E. Hamilton, Klaus H. Kaestner, Shelley L. Berger, Jonathan A. Epstein, Rajan Jain, Mingyao Li, Semir Beyaz, Christopher J. Lengner, Bryson W. Katona, Sergei I. Grivennikov, Christoph A. Thaiss, Maayan Levy: Beta-hydroxybutyrate suppresses colorectal cancer. Nature May 2022.
27. Cynthia López-Haber, Zachary Hutchins, Xianghui Ma, Kathryn E. Hamilton and Adriana R. Mantegazza: SLC15A4 favors inflammasome function via mTORC1 signaling and autophagy restraint in dendritic cells. EMBO September 2022.
28. Nicolette M. Johnson*, Louis R. Parham*, Jeeyoon Na, Kaitlyn E. Monaghan, Hannah M. Kolev, Alena Klochkova, Melissa S. Kim, Charles H. Danan, Zvi Cramer, Lauren A. Simon, Kaitlyn E. Naughton, Stephanie Adams-Tzivelekidis, Youjen Tian, Patrick A. Williams, Simone Sidoli, Kelly A. Whelan, Ning Li, Christopher J. Lengner**, Kathryn E. Hamilton**: Autophagic state prospectively identifies facultative stem cells in the intestinal epithelium. EMBO Reports September 2022.
29. Sunghee Estelle Park, Shawn Kang, Jungwook Paek, Andrei Georgescu, Jeehan Chang, Alex Yoon, Benjamin J. Wilkins, Tatiana Karakasheva, Kathryn E. Hamilton, Dan Dongeun Huh: Geometric engineering of organoid culture for enhanced organogenesis in a dish. Nature Methods October 2022 Notes: Accompanying News and Views: https://www.nature.com/articles/s41592-022-01656-3.
30. Madeline Kuhn, Yang Zhang, John Favate, Mayu Morita, Aurora Blucher, Sukanya Das, Shun Liang, Ranjan Preet, Louis R. Parham, Kathy Williams, Sudheer Molugu, Randall Armstrong, Wei Zhang, Jiegang Yang, Kathryn E. Hamilton, Dan Dixon, Gordon Mills, Terry Morgan, Premal Shah, and Sarah F. Andres: IMP1/IGF2BP1 in human colorectal cancer extracellular vesicles. American Journal of Physiology-Gastrointestinal and Liver Physiology October 2022.
31. Tatiana A. Karakasheva, Yusen Zhou, Hongbo M. Xie, Gloria E. Soto, Tiana D. Johnson, Madison A. Stoltz, Daana M. Roach, Noor Nema, Chizoba N. Umeweni, Kaitlyn Naughton, Lauren Dolinsky, James A. Pippin, Andrew D. Wells, Struan F.A. Grant, Louis Ghanem, Natalie Terry, Amanda B. Muir, Kathryn E. Hamilton : Patient-derived colonoids from disease-spared tissue retain inflammatory bowel disease-specific transcriptomic signatures. Gastro Hep Advances April 2023.
32. Patrick A. Williams, Kaitlyn E. Naughton, Lauren A. Simon, Gloria E. Soto, Louis R. Parham, Xianghui Ma, Charles H. Danan, Weiming Hu, Elliot S. Friedman, Emily A. McMillan; Hritik Mehta, Madison A. Stoltz, Joshua Soto Ocaña, Joseph Zackular, Kyle Bittinger, Kelly A. Whelan, Tatiana A. Karakasheva, Kathryn E. Hamilton: Intestinal epithelial autophagy is required for the regenerative benefit of calorie restriction. American Journal of Physiology-Gastrointestinal and Liver Physiology 324(5), May 2023 Notes: Article was selected for APSselect, a monthly collection from the APS that showcases some of the best recently published articles in physiological research (May 2023). PMCID: PMC10069975
33. Clara Morral, Reem Ghinnagow, Tatiana A. Karakasheva, Yusen Zhou, Anusha E Thadi, Ning Li, Benjamin Yoshor, Gloria E. Soto, Chia-Hui Chen, Daniel Aleynick, Sarah Weinbrom, MaryKate Fulton, Yasin Uzun, Meenakshi Bewtra, Judith R. Kelsen, Christopher J. Lengner, Kai Tan, Andy J. Minn, Kathryn E. Hamilton: Isolation of epithelial and stromal cells from colon tissues in homeostasis and under inflammatory conditions. BioProtocols 2023 Notes: Peer-reviewed protocol. Accepted July 7, 2023.
34. Charles H. Danan, Kaitlyn E. Naughton, Katharina E. Hayer, Sangeevan Vellappan, Emily A. McMillan, Yusen Zhou, Rina Matsuda, Shaneice K. Nettleford, Kay Katada, Louis R. Parham, Xianghui Ma, Afrah Chowdhury, Benjamin J. Wilkins, Premal Shah, Matthew D. Weitzman, Kathryn E. Hamilton: Intestinal transit amplifying cells require METTL3 for growth factor signaling and cell survival. JCI Insight 8(23): e171657, October 2023. PMCID: PMC10104132
35. Louis R. Parham, Patrick A. Williams, Kay Katada, Shaneice K. Nettleford, Priya Chatterji, Kofi K. Acheampong, Charles H. Danan, Xianghui Ma, Lauren A. Simon, Kaitlyn E. Naughton, Rei Mizuno, Tatiana Karakasheva, Emily A. McMillan, Kelly A. Whelan, Donita C. Brady, Sydney M. Shaffer, Kathryn E. Hamilton: IGF2BP1/IMP1 deletion enhances a facultative stem cell state via regulation of MAP1LC3B. Cellular and Molecular Gastroenterology and Hepatology 17(3): 439-451, December 2023.
36. Alena Klochkova, Adam L. Karami, Annie D. Fuller, Louis R. Parham, Surali R. Panchani, Shruthi Natarajan, Jazmyne L. Jackson, Anbin Mu, Yinfei Tan, Kathy Q. Cai, Andres J. Klein-Szanto, Amanda B. Muir, Marie-Pier Tétreault, Kathryn E. Hamilton, Kelly A. Whelan: Autophagy contributes to homeostasis in esophageal epithelium where high autophagic vesicle level marks basal cells with limited proliferation and enhanced self-renewal potential. Cell and Molecular Gastroenterology and Hepatology Page: In press, March 2024.
37. Sasaki M, Hara T, Wang JX, Zhou Y, Kennedy KV, Umeweni N, Alston M, Spergel ZC, Ishikawa S, Teranishi R, Nakagawa R, Mcmillan E, Whelan KA, Karakasheva TA, Hamilton KE, Ruffner MA, Muir AB: Lysyl oxidase regulates epithelial differentiation and barrier integrity in eosinophilic esophagitis. Cellular and Molecular Gastroenterology and Hepatology Page: In press, March 2024.
Current Preprints
Editorials, Reviews, Chapters, Commentaries
1. Louis NA, Hamilton KE, Colgan SP. Lipid mediator networks and leukocyte transmigration. Prostaglandins, leukotrienes, and essential fatty acids 73(3-4): 197-202, September 2005.
2. Hamilton KE, Tétreault MP, Kay PK. Opportunities and challenges for women PhD investigators in gastrointestinal research. Gastroenterology 145(2): 266-71, August 2013. PMCID: PMC3744331.
3. Hamilton KE, Crissey MS, Lynch JP, Rustgi AK. Culturing adult stem cells from mouse small intestinal crypts. Cold Spring Harbor protocols 2015(4): 354-8, April 2015.
4. Long AG, Lundsmith ET, Hamilton KE. Inflammation and Colorectal Cancer. Current Colorectal Cancer Reports 4, August 2017. PMCID: PMC5678998.
5. Hamilton KE: Microfabricated Crypt Scaffolds. A New Foundation for Evaluating Human Colon Stem Cells. Cell and Molecular Gastroenterology 5(5), December 2017.
6. Hall TM, Tetreault MP, Hamilton KE, Whelan KA. Autophagy as a cytoprotective mechanism in esophageal squamous cell carcinoma. Current Opinion in Pharmacology Elizabeth Yeh (eds.). 2018.
7. Parham LR, Williams PA, Chatterji P, Whelan KA, Hamilton KE. RNA regulons are essential in intestinal homeostasis.Peer-reviewed review. American Journal of Physiology Gastrointestinal and Liver Physiology. 2018, Dec; Epub.
8. Taylor DM, Tan K, Aronow B, White PS, Bernt K, Salomonis N, Frolova A, Henrickson SE, Wells A, Greene CS, Whitsett J, Hamilton KE, Kelsen JR, Heuckeroth RO, Vella LA, Terry NA, Pei L, Ghanem LR, Kennedy BC, Helbig I, Sullivan KS, Castelo-Soccio L, S. Potter S, Vento-Tormo R, MacParland S, Barrett DM , Haendel M, Harris N, Alimohamed S, Harenza-Rokita JL, GarmireL, Zhang Y, Singh LN, Wallace D, Nazarian J, Peng T, Ding Y, Kim MS, Xing Y, Kong SW, Mandl KD (abbreviated author list). The Pediatric Cell Atlas: defining the growth phase of human development at single-cell resolution. Perspective. Developmental Cell. 2019. In Press
9. Reshu Saxena, Alena Klochkova, Mary Grace Murray, Mohammad Faujul Kabir,Safiyah Samad, Tyler Beccari, Julie Gang, Kishan Patel, Kathryn E. Hamiltonand Kelly A. Whelan: Roles for Autophagy in Esophageal Carcinogenesis: Implications for Improving Patient Outcomes. Cancers October 2019 Notes: In Press.
10. Charles H. Danan, Kay Katada, Louis R. Parham, Kathryn E. Hamilton: Spatial transcriptomics add a new dimension to our understanding of the gut. American Journal of Physiology-Gastrointestinal and Liver Physiology 324(2): G91-G98, December 2022. PMCID: PMC9870576
11. Louis R. Parham, Nicolette M. Johnson, Christopher J. Lengner, Kathryn E. Hamilton: High autophagic vesicle content marks facultative stem cells of the gut. Autophagy 19(9): 2611-2612, December 2022. PMCID: PMC10392747
1. Nancy A. Louis, Kathryn E. Hamilton, Tianqing Kong, Sean P. Colgan. HIF-dependent induction of apical CD55 coordinates epithelial clearance of neutrophils. FASEB Journal 2005 June; 19(8): 950-9. PMID:15923405.
2. Holger K. Eltzschig, Parween Abdulla, Edgar Hoffman, Kathryn E. Hamilton, Dionne Daniels, Caroline Schönfeld, Michaela Löffler, German Reyes, Michael Duszenko, Jorn Karhausen, Andreas Robinson, Karen A. Westerman, Imogen R. Coe, and Sean P. Colgan: HIF-1-dependent repression of equilibrative nucleoside transporter (ENT) in hypoxia. Journal of Experimental Medicine 2015 Dec;202(11): 1493-505. PMCID: PMC2213326.
3. Nancy A. Louis, Kathryn E. Hamilton, Geraldine Canny, Laurie L. Shekels, Samuel B. Ho, Sean P. Colgan. Selective induction of mucin-3 by hypoxia in intestinal epithelia. Journal of Cellular Biochemistry 2006 Dec;99(6): 1616-27. PMID: 16823775.
4. Kathryn E. Hamilton, P. Kay Lund, Joseph A. Galanko, Robert S. Sandler, Temitope O. Keku: Suppressor of cytokine signaling 3 (SOCS3) is not an independent biomarker of colorectal adenoma risk. Biomed Central Research Notes 2010 May;3(144). PMCID: PMC2883989.
5. Kathryn E. Hamilton, James G. Simmons, Shengli Ding, Laurianne Van Landeghem, P. Kay Lund . Cytokine induction of tumor necrosis factor receptor 2 is mediated by STAT3 in colon cancer cells. Molecular Cancer Research 2011 Dec;9(12): 1718-31. PMCID: PMC3243771.
6. Kathryn E. Hamilton Felicite K. Noubissi Prateek S. Katti Christopher M. Hahn Sonya R. Davey Emma T. Lundsmith Andres J. Klein-Szanto Andrew D. Rhim Vladimir S. Spiegelman Anil K. Rustgi. IMP1 promotes tumor growth, dissemination and a tumor-initiating cell phenotype in colorectal cancer cell xenografts. Carcinogenesis 2013 Nov; 34(11): 2647-54. PMCID: PMC3810836.
7. Long Apple, Giroux Véronique, Whelan Kelly A, Hamilton Kathryn E, Tétreault Marie-Pier, Tanaka Koji, Lee Ju-Seog, Klein-Szanto Andres J, Nakagawa Hiroshi, Rustgi Anil K. WNT10A promotes an invasive and self-renewing phenotype in esophageal squamous cell carcinoma. Carcinogenesis 2015 May;36(5): 598-606. PMCID: PMC4498148.
8. Kathryn E. Hamilton, Priya Chatterji, Emma T. Lundsmith, Sarah F. Andres, Veronique Giroux, Philip D. Hicks, Felicite K. Noubissi, Vladimir S. Spiegelman, Anil K. Rustgi: Loss of stromal IMP1 promotes a tumorigenic microenvironment in the colon. Molecular Cancer Research 2015 Nov;13(11): 1478-86. PMCID: PMC4644674.
9. Ravi K. Amaravadi, Kathryn E. Hamilton, Xiaohong Ma, Shengfu Piao, Armando Del Portillo, Katherine L. Nathanson, Matteo S. Carlino, Georgina V. Long, Igor Puzanov, Xiaowei Xu, Jennifer J.D. Morrissette, Kenneth Y. Tsai, Keith T. Flaherty, Jeffrey A. Sosman, Grant R. Goodman, Grant A. McArthur, Anil K. Rustgi, David C. Metz, Lynn M. Schuchter, Paul B. Chapman, and Antonia R. Sepulveda. Multiple gastrointestinal polyps in patients treated with BRAF inhibitors. Clinical Cancer Research. 2015 Dec 1;21(23):5215-21. PMCID:PMC4668213.
10. Kelly A Whelan, Jamie F Merves, Veronique Giroux, Koji Tanaka, Andy Guo,Prasanna M Chandramouleeswaran, Alain J Benitez, Kara Dods, Jianwen Que, Joanne C Masterson, Shahan D Fernando, Bridget C Godwin, Andres J Klein-Szanto, Kudakwashe Chikwava, Eduardo D Ruchelli, Kathryn E Hamilton, Amanda B Muir, Mei-Lun Wang, Glenn T Furuta, Gary W Falk, Jonathan M Spergel, Hiroshi Nakagawa. Autophagy mediates epithelial cytoprotection in eosinophilic oesophagitis. Gut 2017 Jul;66(7):1197-1207. PMCID: PMC4987278.
11. Dana Almohazey, Yuan-Hung Lo, Claire Vossler, Alan Simmons, Jonathan Hsieh, Edie Bucar, Michael Schumacher, Kathryn Hamilton, Ken Lau, Noah Shroyer, Mark Frey. The ErbB3 receptor tyrosine kinase negatively regulates Paneth cells by PI3K-dependent suppression of Atoh1. Cell Death and Differentiation. 2017 May;24(5):855-865. PMCID: PMC5423110.
12. Véronique Giroux, Ashley A. Lento, Mirazul Islam, Jason R. Pitarresi, Akriti Kharbanda, Kathryn E. Hamilton, Kelly A. Whelan, Apple Long, Ben Rhoades, Qiaosi Tang, Hiroshi Nakagawa, Christopher J. Lengner, Adam J. Bass, E. Paul Wileyto, Andres J. Klein-Szanto, Timothy C. Wang, and Anil K. Rustgi. Long-lived keratin 15+ esophageal progenitor cells contribute to homeostasis and regeneration. Journal of Clinical Investigation. 2017 June;27(6):2378-2391. PMCID: PMC5451220.
13. Rei Mizuno, Priya Chatterji, Sarah F. Andres, Kathryn E. Hamilton, Lauren A. Simon, Shawn Foley, Arjun Jeganathan, Brian Gregory, Blair B. Madison, and Anil K. Rustgi. Differential regulation of LET-7 by LIN28B isoform-specific functions. Molecular Cancer Research. 2018 Mar;16(3):403-416. PMCID: PMC5835183.
14. Yuta Kasagi, Prasanna M. Chandramouleeswarana, Kelly A. Whelan, Koji Tanaka, Veronique Giroux, Medha Sharma, Joshua Wang, Alain J. Benitez, Maureen DeMarshall, John W. Tobias, Kathryn E. Hamilton, Gary W. Falk, Jonathan M. Spergel, Andres J. Klein-Szanto, Anil K. Rustgi, Amanda B. Muirb, Hiroshi Nakagawa. The esophageal organoid system reveals functional interplay between Notch and cytokines in reactive epithelial changes. Cell and Molecular Gastroenterology 2018 Jan;5(3):333-352. PMCID: PMC5852293.
15. Véronique Giroux, Julien Stephan, Priya Chatterji, Ben Rhoades, Andres J. Klein-Szanto, Christopher J. Lengner, Kathryn E. Hamilton, Anil K. Rustgi: Mouse intestinal krt15+ crypt cells are radio-resistant and tumor-initiating. Stem Cell Reports 2018 Jun;10(6):1947-1958. PMCID: PMC5993649.
16. Priya Chatterji*, Kathryn E. Hamilton*, Shun Liang, Sarah F. Andres, H. R. Sagara Wijeratne, Rei Mizuno, Lauren A. Simon, Philip D. Hicks, Shawn W. Foley, Jason R. Pitarresi, Andres J. Klein-Szanto,Amanda T. Mah, Laurianne Van Landeghem, Brian D. Gregory, Christopher J. Lengner, Blair B.Madison, Premal Shah, and Anil K. Rustgi. The LIN28B-IMP1 post-transcriptional regulon has opposing effects on oncogenic signaling in the intestine. Genes and Development 2018 June. *co-first author
17. Priya Chatterji, Patrick A. Williams, Kelly A. Whalen, Fernando C. Samper, Sarah F. Andres, Lauren A. Simon, Louis R. Parham, Rei Mizuno, Emma T. Lundsmith, Shun Liang, Sagara HR Wijeratne, Stefani Marti, Lillian Chua, Veronique Giroux, Benjamin J. Wilkins, Gary D. Wu, Premal Shah, Gian G. Tartaglia, Kathryn E. Hamilton. Posttranscriptional regulation of colonic epithelial repair by RNA binding protein IGF2BP1/IMP1. EMBO Reports 2019, April.
18. Sarah F. Andres, Kathy N. Williams, Rei Mizuno, Jeff Headd, Priya Chatterji, Kathryn E. Hamilton, Anil K. Rustgi: IMP1 3' UTR shortening enhances metastatic burden in colorectal cancer. Carcinogenesis 40(4): 569-579, June 2019.
19. Hiroshi Nakagawa, Yuta Kasagi, Tatiana A. Karakasheva, Takeo Hara, Bailey Aaron, Takashi Kijima, Veronique Giroux, Dominique Bailey, Benjamin Wilkins, Julian A. Abrams, Gary W. Falk, Seema Aceves, Jonathan M. Spergel, Kathryn E. Hamilton, Kelly A. Whelan, Amanda Muir: Modeling epithelial homeostasis and reactive epithelial changes in human and murine three-dimensional esophageal organoids. Current Protocols in Stem Cell Biology February 2020.
20. Judith R. Kelsen, Noor Dawany, Maire A. Conrad, Tatiana Karakasheva, Kelly Maurer, Jane M. Wei, Selen Uman, Maiah H. Dent, Rithika Behera, Laura M. Bryant, Xianghui Ma, Leticia Moreira, Priya Chatterji, Rawan Shraim, Audrey Merz, Rei Mizuno, Lauren A. Simon, Amanda B. Muir, Claudio Giraudo, Edward M. Behrens, Kelly A. Whelan, Marcella Devoto, Pierre A. Russo, Sarah F. Andres, Kathleen E. Sullivan, Kathryn E. Hamilton: Colonoids from patients with pediatric inflammatory bowel disease exhibit decreased growth associated with inflammation severity and durable upregulation of antigen presentation genes. Inflammatory Bowel Diseases January 2021.
21. Sarah A. Smith, Sayaka A. Ogawa, Lillian Chau, Kelly A. Whelan, Kathryn E. Hamilton, Jie Chen, Lu Tan, Eric Z. Chen, Sue Keilbaugh, Franz Fogt, Meenakshi Bewtra, Jonathan Braun, Ramnik J. Xavier, Clary B. Clish, Barry Slaff, Aalim M. Weljie, Frederic D. Bushman, James D. Lewis, Hongzhe Li, Stephen R. Master, Michael J. Bennett, Hiroshi Nakagawa, and Gary D. Wu. Mitochondrial dysfunction in inflammatory bowel disease alters intestinal epithelial metabolism of hepatic acylcarnitines. Journal of Clinical Investigation. January 2021.
22. Jodie Ouahed, Judith R. Kelsen, Waldo A. Spessott, Kameron Kooshesh, Maria L. Sanmillan, Noor Dawany, Kathleen E. Sullivan, Kathryn Hamilton, Voytek Slowik, Sergey Nejentsev, João Farela Neves, Helena Flores, Wendy K. Chung, Ashley Wilson, Kwame Anyane Yeboa, Karen Wou, Preti Jain, Michael Field, Sophia Tollefson, Dalin Li1, Dermot P.B. McGovern, Daniel Kotlarz, Christoph Klein, Jonathan Evans, Neil Warner, Abdul Elkadri, Aleixo M. Muise, Jeffrey Goldsmith, Agnes Toth-Petroczy, Dana Vuzman, Nikkola Carmichae, Corneliu Bodea, Christopher A. Cassa, Marcella Devoto, Richard L. Maas, Edward M. Behrens, Claudio G. Giraudo, and Scott B. Snapper: Variants in STXBP3 Result in Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Deficiency Journal of Crohn's and Colitis February 2021.
23. Tatiana A Karakasheva, Joel T Gabre, Uma M Sachdeva, Ricardo Cruz-Acuña, Eric W Lin, Maureen DeMarshall, Gary W Falk, Gregory G Ginsberg, Zhaohai Yang, Michele M Kim, Eric S Diffenderfer, Jason R Pitarresi, Jinyang Li, Amanda B Muir, Kathryn E Hamilton, Hiroshi Nakagawa, Adam J Bass, Anil K Rustgi: Patient-derived organoids as a platform for modeling a patient's response to chemoradiotherapy in esophageal cancer. Scientific Reports October 2021.
24. Takeo Hara, PhD, Yuta Kasagi, Joshua Wang, Masaru Sasaki1, Bailey Aaron1, Adam Karami, Masataka Shimonosono, Rieko Shimonosono, Hisatsugu Maekawa, Lauren Dolinsky, Benjamin Wilkins, Jeremy Klein, Jane Wei, Kathryn Nunes, Kristle Lynch, Jonathan M. Spergel, Kathryn E. Hamilton PhD, Melanie A. Ruffner, Tatiana A. Karakasheva PhD, Kelly A. Whelan, Hiroshi Nakagawa, Amanda B. Muir: CD73+ epithelial progenitor cells which contribute to homeostasis and renewal are depleted in eosinophilic esophagitis. Cellular and Molecular Gastroenterology and Hepatology December 2021 Notes: In Press.
25. Mohammad Faujul Kabir1, Adam Karami1, Ricardo Cruz-Acuna, Alena Klochkova, Reshu Saxena, Anbin Mu, Mary Grace Murray, Jasmine Cruz, Annie E. Fuller, Margarette Clevenger, Kumaraswamy Naidu Chitrala, Yin Fei Tan, Kelsey Keith, Jozef Madzo, Hugh Huang, Jaroslav Jelinek, Tatiana Karakasheva, Kathryn E. Hamilton, Amanda B. Muir, Marie-Pier Tetreault, Kelly A. Whelan: Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium and age-associated mitochondrial dysfunction. Nature Communications April 2022 Notes: Accepted March 2022.
26. Oxana Dmitrieva-Posocco, Andrea C. Wong, Patrick Lundgren, Aleksandra M. Golos, Hélène C. Descamps, Lenka Dohnalová, Zvi Cramer, Yuhua Tian, Brian Yueh, Onur Eskiocak, Gabor Egervari, Yemin Lan, Jinping Liu, Jiaxin Fan, Jihee Kim, Bhoomi Madhu, Kai Markus Schneider, Svetlana Khoziainova, Natalia Andreeva, Qiaohong Wang, Ning Li, Emma E. Furth, Will Bailis, Judith R. Kelsen, Kathryn E. Hamilton, Klaus H. Kaestner, Shelley L. Berger, Jonathan A. Epstein, Rajan Jain, Mingyao Li, Semir Beyaz, Christopher J. Lengner, Bryson W. Katona, Sergei I. Grivennikov, Christoph A. Thaiss, Maayan Levy: Beta-hydroxybutyrate suppresses colorectal cancer. Nature May 2022.
27. Cynthia López-Haber, Zachary Hutchins, Xianghui Ma, Kathryn E. Hamilton and Adriana R. Mantegazza: SLC15A4 favors inflammasome function via mTORC1 signaling and autophagy restraint in dendritic cells. EMBO September 2022.
28. Nicolette M. Johnson*, Louis R. Parham*, Jeeyoon Na, Kaitlyn E. Monaghan, Hannah M. Kolev, Alena Klochkova, Melissa S. Kim, Charles H. Danan, Zvi Cramer, Lauren A. Simon, Kaitlyn E. Naughton, Stephanie Adams-Tzivelekidis, Youjen Tian, Patrick A. Williams, Simone Sidoli, Kelly A. Whelan, Ning Li, Christopher J. Lengner**, Kathryn E. Hamilton**: Autophagic state prospectively identifies facultative stem cells in the intestinal epithelium. EMBO Reports September 2022.
29. Sunghee Estelle Park, Shawn Kang, Jungwook Paek, Andrei Georgescu, Jeehan Chang, Alex Yoon, Benjamin J. Wilkins, Tatiana Karakasheva, Kathryn E. Hamilton, Dan Dongeun Huh: Geometric engineering of organoid culture for enhanced organogenesis in a dish. Nature Methods October 2022 Notes: Accompanying News and Views: https://www.nature.com/articles/s41592-022-01656-3.
30. Madeline Kuhn, Yang Zhang, John Favate, Mayu Morita, Aurora Blucher, Sukanya Das, Shun Liang, Ranjan Preet, Louis R. Parham, Kathy Williams, Sudheer Molugu, Randall Armstrong, Wei Zhang, Jiegang Yang, Kathryn E. Hamilton, Dan Dixon, Gordon Mills, Terry Morgan, Premal Shah, and Sarah F. Andres: IMP1/IGF2BP1 in human colorectal cancer extracellular vesicles. American Journal of Physiology-Gastrointestinal and Liver Physiology October 2022.
31. Tatiana A. Karakasheva, Yusen Zhou, Hongbo M. Xie, Gloria E. Soto, Tiana D. Johnson, Madison A. Stoltz, Daana M. Roach, Noor Nema, Chizoba N. Umeweni, Kaitlyn Naughton, Lauren Dolinsky, James A. Pippin, Andrew D. Wells, Struan F.A. Grant, Louis Ghanem, Natalie Terry, Amanda B. Muir, Kathryn E. Hamilton : Patient-derived colonoids from disease-spared tissue retain inflammatory bowel disease-specific transcriptomic signatures. Gastro Hep Advances April 2023.
32. Patrick A. Williams, Kaitlyn E. Naughton, Lauren A. Simon, Gloria E. Soto, Louis R. Parham, Xianghui Ma, Charles H. Danan, Weiming Hu, Elliot S. Friedman, Emily A. McMillan; Hritik Mehta, Madison A. Stoltz, Joshua Soto Ocaña, Joseph Zackular, Kyle Bittinger, Kelly A. Whelan, Tatiana A. Karakasheva, Kathryn E. Hamilton: Intestinal epithelial autophagy is required for the regenerative benefit of calorie restriction. American Journal of Physiology-Gastrointestinal and Liver Physiology 324(5), May 2023 Notes: Article was selected for APSselect, a monthly collection from the APS that showcases some of the best recently published articles in physiological research (May 2023). PMCID: PMC10069975
33. Clara Morral, Reem Ghinnagow, Tatiana A. Karakasheva, Yusen Zhou, Anusha E Thadi, Ning Li, Benjamin Yoshor, Gloria E. Soto, Chia-Hui Chen, Daniel Aleynick, Sarah Weinbrom, MaryKate Fulton, Yasin Uzun, Meenakshi Bewtra, Judith R. Kelsen, Christopher J. Lengner, Kai Tan, Andy J. Minn, Kathryn E. Hamilton: Isolation of epithelial and stromal cells from colon tissues in homeostasis and under inflammatory conditions. BioProtocols 2023 Notes: Peer-reviewed protocol. Accepted July 7, 2023.
34. Charles H. Danan, Kaitlyn E. Naughton, Katharina E. Hayer, Sangeevan Vellappan, Emily A. McMillan, Yusen Zhou, Rina Matsuda, Shaneice K. Nettleford, Kay Katada, Louis R. Parham, Xianghui Ma, Afrah Chowdhury, Benjamin J. Wilkins, Premal Shah, Matthew D. Weitzman, Kathryn E. Hamilton: Intestinal transit amplifying cells require METTL3 for growth factor signaling and cell survival. JCI Insight 8(23): e171657, October 2023. PMCID: PMC10104132
35. Louis R. Parham, Patrick A. Williams, Kay Katada, Shaneice K. Nettleford, Priya Chatterji, Kofi K. Acheampong, Charles H. Danan, Xianghui Ma, Lauren A. Simon, Kaitlyn E. Naughton, Rei Mizuno, Tatiana Karakasheva, Emily A. McMillan, Kelly A. Whelan, Donita C. Brady, Sydney M. Shaffer, Kathryn E. Hamilton: IGF2BP1/IMP1 deletion enhances a facultative stem cell state via regulation of MAP1LC3B. Cellular and Molecular Gastroenterology and Hepatology 17(3): 439-451, December 2023.
36. Alena Klochkova, Adam L. Karami, Annie D. Fuller, Louis R. Parham, Surali R. Panchani, Shruthi Natarajan, Jazmyne L. Jackson, Anbin Mu, Yinfei Tan, Kathy Q. Cai, Andres J. Klein-Szanto, Amanda B. Muir, Marie-Pier Tétreault, Kathryn E. Hamilton, Kelly A. Whelan: Autophagy contributes to homeostasis in esophageal epithelium where high autophagic vesicle level marks basal cells with limited proliferation and enhanced self-renewal potential. Cell and Molecular Gastroenterology and Hepatology Page: In press, March 2024.
37. Sasaki M, Hara T, Wang JX, Zhou Y, Kennedy KV, Umeweni N, Alston M, Spergel ZC, Ishikawa S, Teranishi R, Nakagawa R, Mcmillan E, Whelan KA, Karakasheva TA, Hamilton KE, Ruffner MA, Muir AB: Lysyl oxidase regulates epithelial differentiation and barrier integrity in eosinophilic esophagitis. Cellular and Molecular Gastroenterology and Hepatology Page: In press, March 2024.
Current Preprints
Editorials, Reviews, Chapters, Commentaries
1. Louis NA, Hamilton KE, Colgan SP. Lipid mediator networks and leukocyte transmigration. Prostaglandins, leukotrienes, and essential fatty acids 73(3-4): 197-202, September 2005.
2. Hamilton KE, Tétreault MP, Kay PK. Opportunities and challenges for women PhD investigators in gastrointestinal research. Gastroenterology 145(2): 266-71, August 2013. PMCID: PMC3744331.
3. Hamilton KE, Crissey MS, Lynch JP, Rustgi AK. Culturing adult stem cells from mouse small intestinal crypts. Cold Spring Harbor protocols 2015(4): 354-8, April 2015.
4. Long AG, Lundsmith ET, Hamilton KE. Inflammation and Colorectal Cancer. Current Colorectal Cancer Reports 4, August 2017. PMCID: PMC5678998.
5. Hamilton KE: Microfabricated Crypt Scaffolds. A New Foundation for Evaluating Human Colon Stem Cells. Cell and Molecular Gastroenterology 5(5), December 2017.
6. Hall TM, Tetreault MP, Hamilton KE, Whelan KA. Autophagy as a cytoprotective mechanism in esophageal squamous cell carcinoma. Current Opinion in Pharmacology Elizabeth Yeh (eds.). 2018.
7. Parham LR, Williams PA, Chatterji P, Whelan KA, Hamilton KE. RNA regulons are essential in intestinal homeostasis.Peer-reviewed review. American Journal of Physiology Gastrointestinal and Liver Physiology. 2018, Dec; Epub.
8. Taylor DM, Tan K, Aronow B, White PS, Bernt K, Salomonis N, Frolova A, Henrickson SE, Wells A, Greene CS, Whitsett J, Hamilton KE, Kelsen JR, Heuckeroth RO, Vella LA, Terry NA, Pei L, Ghanem LR, Kennedy BC, Helbig I, Sullivan KS, Castelo-Soccio L, S. Potter S, Vento-Tormo R, MacParland S, Barrett DM , Haendel M, Harris N, Alimohamed S, Harenza-Rokita JL, GarmireL, Zhang Y, Singh LN, Wallace D, Nazarian J, Peng T, Ding Y, Kim MS, Xing Y, Kong SW, Mandl KD (abbreviated author list). The Pediatric Cell Atlas: defining the growth phase of human development at single-cell resolution. Perspective. Developmental Cell. 2019. In Press
9. Reshu Saxena, Alena Klochkova, Mary Grace Murray, Mohammad Faujul Kabir,Safiyah Samad, Tyler Beccari, Julie Gang, Kishan Patel, Kathryn E. Hamiltonand Kelly A. Whelan: Roles for Autophagy in Esophageal Carcinogenesis: Implications for Improving Patient Outcomes. Cancers October 2019 Notes: In Press.
10. Charles H. Danan, Kay Katada, Louis R. Parham, Kathryn E. Hamilton: Spatial transcriptomics add a new dimension to our understanding of the gut. American Journal of Physiology-Gastrointestinal and Liver Physiology 324(2): G91-G98, December 2022. PMCID: PMC9870576
11. Louis R. Parham, Nicolette M. Johnson, Christopher J. Lengner, Kathryn E. Hamilton: High autophagic vesicle content marks facultative stem cells of the gut. Autophagy 19(9): 2611-2612, December 2022. PMCID: PMC10392747