View highlights of recent publications from the Gastrointestinal Epithelium Modeling Program at Children's Hospital of Philadelphia.  

2024  

Kennedy KV, Wang JX, McMillan E, Zhou Y, Teranishi R, Semeao A, Mirchandani L, Umeweni CN, Dhakal D, Baccarella A, Ishikawa S, Sasaki M, Itami T, Harman AC, Joannas L, Karakasheva TA, Nakagawa H, Muir AB. Lysyl Oxidase Mediates Proliferation and Differentiation in the Esophageal Epithelium. Biomolecules. 2024 Dec 7;14(12):1560. doi: 10.3390/biom14121560. PMID: 39766266; PMCID: PMC11674119. 

Karakasheva TA, Martinez CM, Zhou Y, Qui J, Chen XE, Soto GE, Nettleford SK, Hix OT, Roach DM, Laguerta AM, Thadi A, Edwards RM, Aleynick D, Weinbrom S, Borodyanskaya E, Pickering OH, Fulton MK, Chen CH, Peterson BV, Hagen EB, Yannuzzi IP, Haider Z, Cramer Z, Conrad M, Li N, Bewtra M, Uzun Y, Ta K, Kelsen JR, Minn AJ, Lengner CJ, Hamilton KE. An Epigenetic Basis for Sustained Inflammatory Epithelial Progenitor Cell States in Crohn’s Disease. bioRxiv [Preprint]. 2024.11.22.622113; doi: https://doi.org/10.1101/2024.11.22.622113. 

Ma X, Dawany N, Kondo A, Maurer K, Karakasheva T, Shraim R, Williams PA, Parham LR, Simon LA, Danan CH, Conrad MA, Piccoli DA, Devoto M, Sullivan KE, Kaestner KH, Kelsen JR, Hamilton KE. TNFSF13 insufficiency disrupts human colonic epithelial cell-mediated B cell differentiation. bioRxiv [Preprint]. 2024 Sep 23:2024.09.23.614260. doi: 10.1101/2024.09.23.614260. PMID: 39386555; PMCID: PMC11463615. 

Sasaki M, Hara T, Wang JX, Zhou Y, Kennedy KV, Umeweni CN, Alston MA, Spergel ZC, Ishikawa S, Teranishi R, Nakagawa R, McMillan EA, Whelan KA, Karakasheva TA, Hamilton KE, Ruffner MA, Muir AB. Lysyl Oxidase Regulates Epithelial Differentiation and Barrier Integrity in Eosinophilic Esophagitis. Cell Mol Gastroenterol Hepatol. 2024;17(6):923-937. doi: 10.1016/j.jcmgh.2024.01.025. Epub 2024 Feb 9. PMID: 38340809; PMCID: PMC11026689. 

Muir AB, Karakasheva TA, Whelan KA. Epithelial-Fibroblast Crosstalk in Eosinophilic Esophagitis. Cell Mol Gastroenterol Hepatol. 2024;17(5):713-718. doi: 10.1016/j.jcmgh.2024.01.020. Epub 2024 Feb 3. PMID: 38316214; PMCID: PMC10957450. 

2023  

Parham LR, Williams PA, Katada K, Nettleford SK, Chatterji P, Acheampong KK, Danan CH, Ma X, Simon LA, Naughton KE, Mizuno R, Karakasheva T, McMillan EA, Whelan KA, Brady DC, Shaffer SM, Hamilton KE. IGF2BP1/IMP1 Deletion Enhances a Facultative Stem Cell State via Regulation of MAP1LC3B. Cell Mol Gastroenterol Hepatol. 2024;17(3):439-451. doi: 10.1016/j.jcmgh.2023.12.001. Epub 2023 Dec 9. PMID: 38081361; PMCID: PMC10835461. 

Cruz-Acuña R, Kariuki SW, Sugiura K, Karaiskos S, Plaster EM, Loebel C, Efe G, Karakasheva T, Gabre JT, Hu J, Burdick JA, Rustgi AK. Engineered Hydrogel Reveals Contribution of Matrix Mechanics to Esophageal Adenocarcinoma and Identifies Matrix-activated Therapeutic Targets. J Clin Invest. 2023 Dec 1;133(23):e168146. doi: 10.1172/JCI168146. PMID: 37788109; PMCID: PMC10688988. 

Karakasheva TA, Zhou Y, Xie HM, Soto GE, Johnson TD, Stoltz MA, Roach DM, Nema N, Umeweni CN, Naughton K, Dolinsky L, Pippin JA, Wells AD, Grant SFA, Ghanem L, Terry N, Muir AB, Hamilton KE. Patient-derived Colonoids from Disease-spared Tissue Retain Inflammatory Bowel Disease-specific Transcriptomic Signatures. Gastro Hep Adv. 2023;2(6):830-842. doi: 10.1016/j.gastha.2023.05.003. Epub 2023 May 25. PMID: 37736163; PMCID: PMC10512767. 

Morral C, Ghinnagow R, Karakasheva T, Zhou Y, Thadi A, Li N, Yoshor B, Soto GE, Chen CH, Aleynick D, Weinbrom S, Fulton M, Uzun Y, Bewtra M, Kelsen JR, Lengner CJ, Tan K, Minn AJ, Hamilton KE. Isolation of Epithelial and Stromal Cells from Colon Tissues in Homeostasis and Under Inflammatory Conditions. Bio Protoc. 2023 Sep 20;13(18):e4825. doi: 10.21769/BioProtoc.4825. PMID: 37753470; PMCID: PMC10518784. 

Williams PA, Naughton KE, Simon LA, Soto GE, Parham LR, Ma X, Danan CH, Hu W, Friedman ES, McMillan EA, Mehta H, Stoltz MA, Ocaña JS, Zackular JP, Bittinger K, Whelan KA, Karakasheva TA, Hamilton KE. Intestinal epithelial autophagy is required for the regenerative benefit of calorie restriction. Am J Physiol Gastrointest Liver Physiol. 2023 May 1;324(5):G354-G368. doi: 10.1152/ajpgi.00248.2022. Epub 2023 Feb 28. PMID: 36852920; PMCID: PMC10069975. 

Gier RA, Hueros RAR, Rong J, DeMarshall M, Karakasheva TA, Muir AB, Falk GW, Zhang NR, Shaffer SM. Clonal cell states link Barrett's esophagus and esophageal adenocarcinoma. bioRxiv [Preprint]. 2023 Feb 6:2023.01.26.525564. doi: 10.1101/2023.01.26.525564. PMID: 36747708; PMCID: PMC9900873. 

2022  

Park SE, Kang S, Paek J, Georgescu A, Chang J, Yi AY, Wilkins BJ, Karakasheva TA, Hamilton KE, Huh DD. Geometric Engineering of Organoid Culture for Enhanced Organogenesis in a Dish. Nat Methods. 2022 Nov;19(11):1449-1460. doi: 10.1038/s41592-022-01643-8. Epub 2022 Oct 24. PMID: 36280722; PMCID: PMC10027401. 

Dmitrieva-Posocco O, Wong AC, Lundgren P, Golos AM, Descamps HC, Dohnalová L, Cramer Z, Tian Y, Yueh B, Eskiocak O, Egervari G, Lan Y, Liu J, Fan J, Kim J, Madhu B, Schneider KM, Khoziainova S, Andreeva N, Wang Q, Li N, Furth EE, Bailis W, Kelsen JR, Hamilton KE, Kaestner KH, Berger SL, Epstein JA, Jain R, Li M, Beyaz S, Lengner CJ, Katona BW, Grivennikov SI, Thaiss CA, Levy M. β-Hydroxybutyrate suppresses colorectal cancer. Nature. 2022 May;605(7908):160-165. doi: 10.1038/s41586-022-04649-6. Epub 2022 Apr 27. PMID: 35477756; PMCID: PMC9448510. 

Kabir MF, Karami AL, Cruz-Acuña R, Klochkova A, Saxena R, Mu A, Murray MG, Cruz J, Fuller AD, Clevenger MH, Chitrala KN, Tan Y, Keith K, Madzo J, Huang H, Jelinek J, Karakasheva T, Hamilton KE, Muir AB, Tétreault MP, Whelan KA. Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium. Nat Commun. 2022 Apr 20;13(1):2167. doi: 10.1038/s41467-022-29747-x. PMID: 35443762; PMCID: PMC9021266. 

Hara T, Kasagi Y, Wang J, Sasaki M, Aaron B, Karami A, Shimonosono M, Shimonosono R, Maekawa H, Dolinsky L, Wilkins B, Klein J, Wei J, Nunes K, Lynch K, Spergel JM, Hamilton KE, Ruffner MA, Karakasheva TA, Whelan KA, Nakagawa H, Muir AB. CD73⁺ Epithelial Progenitor Cells That Contribute to Homeostasis and Renewal Are Depleted in Eosinophilic Esophagitis. Cell Mol Gastroenterol Hepatol. 2022;13(5):1449-1467. doi: 10.1016/j.jcmgh.2022.01.018. Epub 2022 Jan 30. PMID: 35108658; PMCID: PMC8957025. 

2021  

Tang Q, Lento A, Suzuki K, Efe G, Karakasheva T, Long A, Giroux V, Islam M, Wileyto EP, Klein-Szanto AJ, Nakagawa H, Bass A, Rustgi AK. Rab11-FIP1 Mediates Epithelial-mesenchymal Transition and Invasion in Esophageal Cancer. EMBO Rep. 2021 Feb 3;22(2):e48351. doi: 10.15252/embr.201948351. Epub 2021 Jan 6. PMID: 33403789; PMCID: PMC7857540. 

Muir A, Falk GW. Eosinophilic Esophagitis: A Review. JAMA. 2021 Oct 5;326(13):1310-1318. doi: 10.1001/jama.2021.14920. PMID: 34609446; PMCID: PMC9045493. 

Karakasheva TA, Gabre JT, Sachdeva UM, Cruz-Acuña R, Lin EW, DeMarshall M, Falk GW, Ginsberg GG, Yang Z, Kim MM, Diffenderfer ES, Pitarresi JR, Li J, Muir AB, Hamilton KE, Nakagawa H, Bass AJ, Rustgi AK. Patient-derived organoids as a platform for modeling a patient's response to chemoradiotherapy in esophageal cancer. Sci Rep. 2021 Oct 29;11(1):21304. doi: 10.1038/s41598-021-00706-8. PMID: 34716381; PMCID: PMC8556341. 

Kelsen JR, Dawany N, Conrad MA, Karakasheva TA, Maurer K, Wei JM, Uman S, Dent MH, Behera R, Bryant LM, Ma X, Moreira L, Chatterji P, Shraim R, Merz A, Mizuno R, Simon LA, Muir AB, Giraudo C, Behrens EM, Whelan KA, Devoto M, Russo PA, Andres SF, Sullivan KE, Hamilton KE. Colonoids From Patients with Pediatric Inflammatory Bowel Disease Exhibit Decreased Growth Associated with Inflammation Severity and Durable Upregulation of Antigen Presentation Genes. Inflamm Bowel Dis. 2021 Jan 19;27(2):256-267. doi: 10.1093/ibd/izaa145. PMID: 32556182; PMCID: PMC7813751. 

2020  

Karakasheva TA, Kijima T, Shimonosono M, Maekawa H, Sahu V, Gabre JT, Cruz-Acuña R, Giroux V, Sangwan V, Whelan KA, Natsugoe S, Yoon AJ, Philipone E, Klein-Szanto AJ, Ginsberg GG, Falk GW, Abrams JA, Que J, Basu D, Ferri L, Diehl JA, Bass AJ, Wang TC, Rustgi AK, Nakagawa H. Generation and Characterization of Patient-Derived Head and Neck, Oral, and Esophageal Cancer Organoids. Curr Protoc Stem Cell Biol. 2020 Jun;53(1):e109. doi: 10.1002/cpsc.109. PMID: 32294323; PMCID: PMC7350550. 

Nakagawa H, Kasagi Y, Karakasheva TA, Hara T, Aaron B, Shimonosono M, Kijima T, Giroux V, Bailey D, Wilkins B, Abrams JA, Falk GW, Aceves SS, Spergel JM, Hamilton KE, Whelan KA, Muir AB. Modeling Epithelial Homeostasis and Reactive Epithelial Changes in Human and Murine Three-Dimensional Esophageal Organoids. Curr Protoc Stem Cell Biol. 2020 Mar;52(1):e106. doi: 10.1002/cpsc.106. PMID: 32105412; PMCID: PMC7288850. 

2019  

Chatterji P, Williams PA, Whelan KA, Samper FC, Andres SF, Simon LA, Parham LR, Mizuno R, Lundsmith ET, Lee DSM, Liang S, Wijeratne HRS, Marti S, Chau L, Giroux V, Wilkins BJ, Wu GD, Shah P, Targalia GG & Hamilton KE. Posttranscriptional Regulation of Colonic Epithelial Repair by RNA Binding Protein. IMP1/IGF2BP1. EMBO reports (Epub 2019 May 6) 20 (6):e47074.  

2018  

Kasagi Y, Chandramouleeswaran PM, Whelan KA, Tanaka K, Giroux V, Sharma M, Wang J, Benitez AJ, DeMarshall M, Tobias JW, Hamilton KE, Falk GW, Spergel JM, Klein-Sxanto AJ,  Rustgi AK, Muir AB, Nakagawa H. The Esophageal Organoid System Reveals Functional Interplay Between Notch and Cytokines in Reactive Epithelial Changes. Cell Mol Gastroenterol Hepatol. 2018 Jan 3; 5(3):333-352. Doi: 10.106/j.jcmgh.2017.12.013. PMID 29552622; PMCID: PMC5852293.