Judith R Kelsen ¹, Noor Dawany ², Maire A Conrad ¹, Tatiana A Karakasheva ¹, Kelly Maurer ³, Jane M Wei ¹, Selen Uman ⁴, Maiah H Dent ¹, Rithika Behera ¹, Laura M Bryant ¹, Xianghui Ma ¹, Leticia Moreira ⁵, Priya Chatterji ⁶, Rawan Shraim ¹, Audrey Merz ¹, Rei Mizuno ⁷, Lauren A Simon ¹, Amanda B Muir ¹, Claudio Giraudo ⁸, Edward M Behrens ⁹, Kelly A Whelan ¹⁰, Marcella Devoto ^11 12, Pierre A Russo ¹³, Sarah F Andres ¹⁴, Kathleen E Sullivan ³, Kathryn E Hamilton ¹

Author information

• ¹Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, United States.
• ²Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, United States.
• ³Division of Allergy Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, United States.
• ⁴Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States.
• ⁵Department of Gastroenterology, Hospital Clinic, Centro de Investigacion Biomedica en Red en Enfermedades Hepaticas y Digestivas (CIBERehd), IDIBAPS, University of Barcelona, Catalonia, Spain.
• ⁶Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States.
• ⁷Department of Medicine, Gastroenterology Division, University of Pennsylvania, Philadelphia, PA, United States.
• ⁸Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States.
• ⁹Division of Rheumatology, Children's Hospital of Philadelphia, Philadelphia, PA, United States.
• ¹⁰Fels Institute for Cancer Research & Molecular Biology, Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States.
• ¹¹Division of Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
• ¹²Division of Anatomic Pathology, Children's Hospital of Philadelphia, Philadelphia, PA, United States.
• ¹³Department of Pediatrics, Oregon Health & Science University, Portland, OR, United States.
• ¹⁴Department of Translational and Precision Medicine, University of Rome Sapienza, Rome, Italy.

Abstract

Background: Defining epithelial cell contributions to inflammatory bowel disease (IBD) is essential for the development of much needed therapies for barrier repair. Children with very early onset (VEO)-IBD have more extensive, severe, and refractory disease than older children and adults with IBD and, in some cases, have defective barrier function. We therefore evaluated functional and transcriptomic differences between pediatric IBD (VEO and older onset) and non-IBD epithelium using 3-dimensional, biopsy-derived organoids.

Methods: We measured growth efficiency relative to histopathological and clinical parameters in patient enteroid (ileum) and colonoid (colon) lines. We performed RNA-sequencing on patient colonoids and subsequent flow cytometry after multiple passages to evaluate changes that persisted in culture.

Results: Enteroids and colonoids from pediatric patients with IBD exhibited decreased growth associated with histological inflammation compared with non-IBD controls. We observed increased LYZ expression in colonoids from pediatric IBD patients, which has been reported previously in adult patients with IBD. We also observed upregulation of antigen presentation genes HLA-DRB1 and HLA-DRA, which persisted after prolonged passaging in patients with pediatric IBD.

Conclusions: We present the first functional evaluation of enteroids and colonoids from patients with VEO-IBD and older onset pediatric IBD, a subset of which exhibits poor growth. Enhanced, persistent epithelial antigen presentation gene expression in patient colonoids supports the notion that epithelial cell-intrinsic differences may contribute to IBD pathogenesis.