19
1
49
2
8
1b
1d
18
3a
73
1d
2 29
1d
25
Kathryn (Kate) Hamilton, PhD
78
73
Associate Professor of Pediatrics (Gastroenterology, Hepatology and Nutrition)
7
61
Department: Pediatrics
4
1
23
1f
Graduate Group Affiliations
8
a
b
1d
46
Contact information
51
4
3
3
3
2
29
51
Children's Hospital of Philadelphia
1e 3615 Civic Center Blvd
40 902F Abramson Research Center
Philadelphia, PA 19104
26
1e 3615 Civic Center Blvd
40 902F Abramson Research Center
Philadelphia, PA 19104
43
Lab: 267-426-5266
18
f
18
Links
b6 CHOP Press Release
c4 Penn Institute for Regenerative Medicine news
a9 CHOP Cornerstone Blog News
8a Penn Institute for Regenerative Medicine website
61 External lab website
d1 CHOP Cornerstone Blog Faculty Spotlight
79 PSOM lab website
d4 CHOP Cornerstone Blog News
b4 Penn Institute for Regenerative Medicine news
a0 Penn Engineering Today 2023
c
4
b
1f
b6 CHOP Press Release
c4 Penn Institute for Regenerative Medicine news
a9 CHOP Cornerstone Blog News
8a Penn Institute for Regenerative Medicine website
61 External lab website
d1 CHOP Cornerstone Blog Faculty Spotlight
79 PSOM lab website
d4 CHOP Cornerstone Blog News
b4 Penn Institute for Regenerative Medicine news
a0 Penn Engineering Today 2023
c
13
Education:
21 9 B.A. 14 (Biology) c
2b Assumption College, 2003.
21 a Ph.D. 2a (Cell and Molecular Physiology) c
41 University of North Carolina Chapel Hill, 2010.
c
3
3
3
3
92
Permanent link21 9 B.A. 14 (Biology) c
2b Assumption College, 2003.
21 a Ph.D. 2a (Cell and Molecular Physiology) c
41 University of North Carolina Chapel Hill, 2010.
c
2 29
21
1e
1d
24
5e
3a0 The gut epithelium acts as an arbiter between harmful substances in the external environment and the human body. The Hamilton laboratory specializes in understanding mechanisms regulating the gut epithelium in health and disease. We use in vivo models and patient-derived organoids to understand the molecular basis of intestinal regeneration including in inflammatory bowel disease (IBD). Our studies span three interrelated themes: 1) Defining how RNA binding proteins impart global, post-transcriptional regulation of key pathways in gut physiology and pathophysiology, 2) Evaluating how epithelial stem cell in patients with chronic gastrointestinal diseases behave differently than non-disease stem cells as a basis for stem cell targeted therapies to heal the gut epithelium, and 3) Exploring fundamental intestinal epithelial biology through the study of organoids from patients with rare, monogenic forms of IBD.
8
12 Keywords:
ca gastrointestinal biology, RNA binding proteins, epitranscriptomics, inflammatory bowel disease (IBD), organoids (enteroids/colonoids), post-transcriptional gene regulation, intestinal stem cells
8
19 Research Details:
4d3 Our laboratory incorporates molecular and cellular biology together with mammalian physiology/pathophysiology and human organoid biology. Techniques employed in the laboratory include tissue culture (2D and 3D, including human organoid models), live cell microscopy, molecular biology, histological analyses, flow cytometry, in vivo transgenic and disease models, single cell transcriptomics and chromatin accessibility analyses, and epitranscriptomics (m6A-seq and other RNA biochemical analyses). Dr. Hamilton is Co-founder and Co-Director of the CHOP Gastrointestinal Epithelium Modeling (GEM) Program (https://www.chop.edu/centers-programs/gastrointestinal-epithelium-modeling-gem-program#supportedresearch), which resides within the Hamilton lab suite in the CHOP Abramson Research Building. The GEM Program serves as a hub for patient-focused gastrointestinal organoid research and connects scientists across the Penn-CHOP campus and nationally to foster community and collaborations. The GEM Core was launched in 2024 at part of the CHOP Research Institute and the Penn P30 Center for Molecular Studies in Digestive and Liver Diseases (https://www.med.upenn.edu/CMSDLD/gastrointestinal-epithelium-modeling-gem-core.html)
8
1b Rotation Projects:
6e 1) Evaluate how intestinal epithelial mitophagy pathways prevents cell death in facultative stem cells
87 2) Define how inflammatory and other environmental factors alter functional outcomes in epithelial stem cells in celiac disease
76 3) Explore the epigenetic basis for altered progenitor cell states in chronic inflammatory diseases of the gut
8
16 Lab Personnel:
27 Emily McMillan, MS, Lab Manager
39 Shaneice Nettleford, PhD, Postdoctoral researcher
51 Kay Katada, BS, CAMB/Cell Biology, Physiology, and Metabolism PhD student
6d Daana Roach, BS, DVM-PhD student, CAMB/Developmental, Stem Cell, and Regenerative Biology PhD student
39 Ian Yannuzzi, BS, CAMB/Cancer Biology PhD student
29 Yusen Zhou, PhD, Bioinformatician
2e Heidi Winters, BS, Research specialist
82 Tatiana Karakesheva, PhD, Research Scientist, Associate Director, CHOP Gastrointestinal Epithelium Modeling (GEM) Program
5d Bella Peterson, BS, Lab Technician, Gastrointestinal Epithelium Modeling (GEM) Program
e 29
27
Description of Research Expertise
25 Research Interests:3a0 The gut epithelium acts as an arbiter between harmful substances in the external environment and the human body. The Hamilton laboratory specializes in understanding mechanisms regulating the gut epithelium in health and disease. We use in vivo models and patient-derived organoids to understand the molecular basis of intestinal regeneration including in inflammatory bowel disease (IBD). Our studies span three interrelated themes: 1) Defining how RNA binding proteins impart global, post-transcriptional regulation of key pathways in gut physiology and pathophysiology, 2) Evaluating how epithelial stem cell in patients with chronic gastrointestinal diseases behave differently than non-disease stem cells as a basis for stem cell targeted therapies to heal the gut epithelium, and 3) Exploring fundamental intestinal epithelial biology through the study of organoids from patients with rare, monogenic forms of IBD.
8
12 Keywords:
ca gastrointestinal biology, RNA binding proteins, epitranscriptomics, inflammatory bowel disease (IBD), organoids (enteroids/colonoids), post-transcriptional gene regulation, intestinal stem cells
8
19 Research Details:
4d3 Our laboratory incorporates molecular and cellular biology together with mammalian physiology/pathophysiology and human organoid biology. Techniques employed in the laboratory include tissue culture (2D and 3D, including human organoid models), live cell microscopy, molecular biology, histological analyses, flow cytometry, in vivo transgenic and disease models, single cell transcriptomics and chromatin accessibility analyses, and epitranscriptomics (m6A-seq and other RNA biochemical analyses). Dr. Hamilton is Co-founder and Co-Director of the CHOP Gastrointestinal Epithelium Modeling (GEM) Program (https://www.chop.edu/centers-programs/gastrointestinal-epithelium-modeling-gem-program#supportedresearch), which resides within the Hamilton lab suite in the CHOP Abramson Research Building. The GEM Program serves as a hub for patient-focused gastrointestinal organoid research and connects scientists across the Penn-CHOP campus and nationally to foster community and collaborations. The GEM Core was launched in 2024 at part of the CHOP Research Institute and the Penn P30 Center for Molecular Studies in Digestive and Liver Diseases (https://www.med.upenn.edu/CMSDLD/gastrointestinal-epithelium-modeling-gem-core.html)
8
1b Rotation Projects:
6e 1) Evaluate how intestinal epithelial mitophagy pathways prevents cell death in facultative stem cells
87 2) Define how inflammatory and other environmental factors alter functional outcomes in epithelial stem cells in celiac disease
76 3) Explore the epigenetic basis for altered progenitor cell states in chronic inflammatory diseases of the gut
8
16 Lab Personnel:
27 Emily McMillan, MS, Lab Manager
39 Shaneice Nettleford, PhD, Postdoctoral researcher
51 Kay Katada, BS, CAMB/Cell Biology, Physiology, and Metabolism PhD student
6d Daana Roach, BS, DVM-PhD student, CAMB/Developmental, Stem Cell, and Regenerative Biology PhD student
39 Ian Yannuzzi, BS, CAMB/Cancer Biology PhD student
29 Yusen Zhou, PhD, Bioinformatician
2e Heidi Winters, BS, Research specialist
82 Tatiana Karakesheva, PhD, Research Scientist, Associate Director, CHOP Gastrointestinal Epithelium Modeling (GEM) Program
5d Bella Peterson, BS, Lab Technician, Gastrointestinal Epithelium Modeling (GEM) Program
e 29
23
310 Tatiana A. Karakasheva, Clara Morral Martinez, Yusen Zhou, Jingya Qui, Xinyi E. Chen, Gloria E. Soto, Shaneice K. Nettleford, Olivia T. Hix, Daana M. Roach, Alyssa M. Laguerta, Anusha Thadi, Rachael M. Edwards, Daniel Aleynick, Sarah Weinbrom, Elizaveta Borodyanskaya, Oliver H. Pickering, MaryKate Fulton, Chia-Hui Chen, Bella V. Peterson, Erik B. Hagen, Ian P. Yannuzzi, Zainab Haider, Zvi Cramer, Maire Conrad, Ning Li, Meenakshi Bewtra, Yasin Uzun, Kai Tan, Judith R. Kelsen, Andy J. Minn, Christopher J. Lengner, Kathryn E. Hamilton: An epigenetic basis for sustained inflammatory epithelial progenitor cell states in Crohn’s disease. Cell and Molecular Gastroenterology and Hepatology November 2025.
1bf 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 17(6): 923-937, March 2024.
251 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 18(1): 15-40, March 2024.
15c 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 cf : 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.
1f0 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.
233 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 13(18): e4825, September 2023 Notes: Featured on issue cover.
2fb 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): G354-G368, 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).
15b 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 2 ea : Patient-derived colonoids from disease-spared tissue retain inflammatory bowel disease-specific transcriptomic signatures. Gastro Hep Advances 2(6): 830-842, April 2023 Notes: Featured on issue cover.
215 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 323(6): G571-G585, October 2022.
2c
7
1d
1f
Selected Publications
252 Xianghui Ma, Shaneice K. Nettleford, Yuhua Tian, Noor Dawany, Ayano Kondo, Yalan Li, Kelly Maurer, Tatiana Karakasheva, Rawan Shraim, Patrick A. Williams, Louis R. Parham, Lauren A. Simon, Charles H. Danan, Maire A. Conrad, David A. Piccoli, Marcella Devoto, Neil Romberg, Kathleen E. Sullivan, Klaus H. Kaestner, Judith R. Kelsen, Kathryn E. Hamilton: TNFSF13 insufficiency disrupts human colonic epithelial cell growth and associated B cell dynamics. The Journal of Clinical Investigation February 2026 Notes: In Press.310 Tatiana A. Karakasheva, Clara Morral Martinez, Yusen Zhou, Jingya Qui, Xinyi E. Chen, Gloria E. Soto, Shaneice K. Nettleford, Olivia T. Hix, Daana M. Roach, Alyssa M. Laguerta, Anusha Thadi, Rachael M. Edwards, Daniel Aleynick, Sarah Weinbrom, Elizaveta Borodyanskaya, Oliver H. Pickering, MaryKate Fulton, Chia-Hui Chen, Bella V. Peterson, Erik B. Hagen, Ian P. Yannuzzi, Zainab Haider, Zvi Cramer, Maire Conrad, Ning Li, Meenakshi Bewtra, Yasin Uzun, Kai Tan, Judith R. Kelsen, Andy J. Minn, Christopher J. Lengner, Kathryn E. Hamilton: An epigenetic basis for sustained inflammatory epithelial progenitor cell states in Crohn’s disease. Cell and Molecular Gastroenterology and Hepatology November 2025.
1bf 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 17(6): 923-937, March 2024.
251 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 18(1): 15-40, March 2024.
15c 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 cf : 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.
1f0 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.
233 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 13(18): e4825, September 2023 Notes: Featured on issue cover.
2fb 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): G354-G368, 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).
15b 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 2 ea : Patient-derived colonoids from disease-spared tissue retain inflammatory bowel disease-specific transcriptomic signatures. Gastro Hep Advances 2(6): 830-842, April 2023 Notes: Featured on issue cover.
215 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 323(6): G571-G585, October 2022.
2c