Zorn Lab
Publications

Publications

Mukherjee, S; Chaturvedi, P; Rankin, SA; Fish, MB; Wlizla, M; Paraiso, KD; Macdonald, M; Chen, X; Weirauch, MT; Blitz, IL; Cho, KW; Zorn, AM. Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endoderm gene regulatory network. eLife. 2020; 9.

Han, L; Chaturvedi, P; Kishimoto, K; Koike, H; Nasr, T; Iwasawa, K; Giesbrecht, K; Witcher, PC; Eicher, A; Haines, L; Morimoto, M; Wells, JM; Takebe, T; Zorn, AM. Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis. Nature Communications. 2020; 11(1):4158.

Nasr, T; Mancini, P; Rankin, SA; Edwards, NA; Agricola, ZN; Kenny, AP; Kinney, JL; Daniels, K; Vardanyan, J; Han, L; Trisno, SL; Cha, S-W; Wells, JM; Kofron, MJ; Zorn, AM. Endosome-Mediated Epithelial Remodeling Downstream of Hedgehog-Gli Is Required for Tracheoesophageal Separation. Developmental Cell. 2019; 51(6):665-674.e6.

Koike, H; Iwasawa, K; Ouchi, R; Maezawa, M; Giesbrecht, K; Saiki, N; Ferguson, A; Kimura, M; Thompson, WL; Wells, JM; Zorn, AM; Takebe, T. Modelling human hepato-biliary-pancreatic organogenesis from the foregut-midgut boundary. Nature. 2019; 574(7776):112-116.

Trisno, SL; Philo, KED; Mccracken, KW; Catá, EM; Ruiz-Torres, S; Rankin, SA; Han, L; Nasr, T; Chaturvedi, P; Rothenberg, ME; Mandegar, MA; Wells, SI; Zorn, AM; Wells, JM. Esophageal Organoids from Human Pluripotent Stem Cells Delineate Sox2 Functions during Esophageal Specification. Cell Stem Cell. 2018; 23(4):501-515.e7.

Stevens, ML; Chaturvedi, P; Rankin, SA; Macdonald, M; Jagannathan, S; Yukawa, M; Barski, A; Zorn, AM. Genomic integration of Wnt/β-catenin and BMP/Smad1 signaling coordinates foregut and hindgut transcriptional programs. Development. 2017; 144(7):1283-1295.

Rankin, SA; Han, L; Mccracken, KW; Kenny, AP; Anglin, CT; Grigg, EA; Crawford, CM; Wells, JM; Shannon, JM; Zorn, AM. A Retinoic Acid-Hedgehog Cascade Coordinates Mesoderm-Inducing Signals and Endoderm Competence during Lung Specification. Cell reports. 2016; 16(1):66-78.

Kenny, AP; Rankin, SA; Allbee, AW; Prewitt, AR; Zhang, Z; Tabangin, ME; Shifley, ET; Louza, MP; Zorn, AM. Sizzled-tolloid interactions maintain foregut progenitors by regulating fibronectin-dependent BMP signaling. Developmental Cell. 2012; 23(2):292-304.

Rankin, SA; Gallas, AL; Neto, A; Gómez-Skarmeta, JL; Zorn, AM. Suppression of Bmp4 signaling by the zinc-finger repressors Osr1 and Osr2 is required for Wnt/β-catenin-mediated lung specification in Xenopus. Development. 2012; 139(16):3010-3020.

Spence, JR; Mayhew, CN; Rankin, SA; Kuhar, MF; Vallance, JE; Tolle, K; Hoskins, EE; Kalinichenko, VV; Wells, SI; Zorn, AM; Shroyer, NF; Wells, JM. Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro. Nature. 2011; 470(7332):105-109.

Kormish, JD; Sinner, D; Zorn, AM. Interactions between SOX factors and Wnt/beta-catenin signaling in development and disease. Developmental Dynamics. 2010; 239(1):56-68.

Zorn, AM; Wells, JM. Vertebrate endoderm development and organ formation. Annual Review of Cell and Developmental Biology. 2009; 25:221-251.

Li, Y; Rankin, SA; Sinner, D; Kenny, AP; Krieg, PA; Zorn, AM. Sfrp5 coordinates foregut specification and morphogenesis by antagonizing both canonical and noncanonical Wnt11 signaling. Genes & Development. 2008; 22(21):3050-3063.

Mclin, VA; Rankin, SA; Zorn, AM. Repression of Wnt/beta-catenin signaling in the anterior endoderm is essential for liver and pancreas development. Development. 2007; 134(12):2207-2217.

Sinner, D; Kirilenko, P; Rankin, S; Wei, E; Howard, L; Kofron, M; Heasman, J; Woodland, HR; Zorn, AM. Global analysis of the transcriptional network controlling Xenopus endoderm formation. Development. 2006; 133(10):1955-1966.

Sinner, D; Rankin, S; Lee, M; Zorn, AM. Sox17 and beta-catenin cooperate to regulate the transcription of endodermal genes. Development. 2004; 131(13):3069-3080.

Zorn, AM; Barish, GD; Williams, BO; Lavender, P; Klymkowsky, MW; Varmus, HE. Regulation of Wnt signaling by Sox proteins: XSox17 alpha/beta and XSox3 physically interact with beta-catenin. Molecular Cell. 1999; 4(4):487-498.

Rezvani, M; Quach, S; Lewis, K; Saiki, N; Xue, C; Kimura, M; Iwasawa, K; Weihs, J; Elzobair, T; Al Reza, H; Zorn, A; Wells, JM; Yoshimoto, M; Takebe, T. Modeling Immune Lineage Co-Development in Human Pluripotent Stem Cell-derived Liver Organoids. Journal of Hepatology. 2025.

Chu, S; Bell, AJ; Lotay, V; Ly, N; Pells, TJ; Kwon, T; Agalakov, S; Ponferrada, V; Lenz, C; James-Zorn, C; Fisher, M; Karimi, K; Zorn, AM; Vize, PD. Xenbase: 25 years of integrating molecular and biomedical data from Xenopus. Genetics. 2025.

Edwards, NA; Rankin, SA; Kashyap, A; Warren, A; Agricola, ZN; Kenny, AP; Kofron, M; Shen, Y; Chung, WK; Zorn, AM. Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in Xenopus trachea-esophageal morphogenesis. Developmental Cell. 2025; 60(18):2487-2502.e4.

Miao, Y; Pek, NM; Tan, C; Jiang, C; Yu, Z; Iwasawa, K; Shi, M; Kechele, DO; Sundaram, N; Pastrana-Gomez, V; Zorn, AM; Chen, Y-W; Guo, M; Gu, M. Co-development of mesoderm and endoderm enables organotypic vascularization in lung and gut organoids. Cell. 2025; 188(16):4295-4313.e27.

Feuermann, M; Mi, H; Gaudet, P; Muruganujan, A; Lewis, SE; Ebert, D; Mushayahama, T; Thomas, PD. A compendium of human gene functions derived from evolutionary modelling. Nature. 2025; 640(8057):146-154.

Tominaga, K; Kechele, DO; Sanchez, JG; Vales, S; Jurickova, I; Roman, L; Asai, A; Enriquez, JR; Mccauley, HA; Kishimoto, K; Zorn, AM; Helmrath, MA; Denson, LA; Wells, JM. Deriving Human Intestinal Organoids with Functional Tissue-Resident Macrophages All From Pluripotent Stem Cells. Cellular and Molecular Gastroenterology and Hepatology (CMGH). 2025; 19(4):101444.

Hyatt, BA; Lundberg, E; Eye, R; Rankin, SA; Zorn, AM. Temporal induction of the homeodomain transcription factor Nkx2-1 is sufficient to respecify foregut and hindgut endoderm to a pulmonary fate in Xenopus laevis. microPublication Biology. 2025; 2025.

Sanchez, JG; Rankin, S; Paul, E; Mccauley, HA; Kechele, DO; Enriquez, JR; Jones, N-H; Greeley, SAW; Letourneau-Frieberg, L; Zorn, AM; Krishnamurthy, M; Wells, JM. RFX6 regulates human intestinal patterning and function upstream of PDX1. Development. 2024; 151(9).

Ducey, J; Lansdale, N; Gorst, S; Bray, L; Teunissen, N; Cullis, P; Faulkner, J; Gray, V; Gutierrez Gammino, L; Slater, G; Teague, WJ; Zorn, AM; Hall, NJ; Thursfield, R. Developing a core outcome set for the health outcomes for children and adults with congenital oesophageal atresia and/or tracheo-oesophageal fistula: OCELOT task group study protocol. BMJ Paediatrics Open. 2024; 8(1).

Ochi, H; Kato, T; Zorn, A; Hayashi, T; Inoue, T; Kondo, M; Taira, M; Michiue, T. Versatile utilities of amphibians (part 5). Development Growth and Differentiation. 2023; 65(8):459-460.

O'donnell, A; Gonzalez, BA; Mukherjee, S; Wilson, R; Alfieri, CM; Swoboda, CO; Millay, DP; Zorn, AM; Yutzey, KE. Localized Prox1 Regulates Aortic Valve Endothelial Cell Diversity and Extracellular Matrix Stratification in Mice. Arteriosclerosis, Thrombosis, and Vascular Biology. 2023; 43(8):1478-1493.

Bouffi, C; Wikenheiser-Brokamp, KA; Chaturvedi, P; Sundaram, N; Goddard, GR; Wunderlich, M; Brown, NE; Staab, JF; Latanich, R; Zachos, NC; Mulloy, JC; Zorn, AM; Wells, JM; Helmrath, MA. In vivo development of immune tissue in human intestinal organoids transplanted into humanized mice. Nature Biotechnology. 2023; 41(6):824-831.

Fisher, M; James-Zorn, C; Ponferrada, V; Bell, AJ; Sundararaj, N; Segerdell, E; Chaturvedi, P; Bayyari, N; Chu, S; Pells, T; Foley, S; Karimi, K; Vize, PD; Zorn, AM. Xenbase: key features and resources of the Xenopus model organism knowledgebase. Genetics. 2023; 224(1).

Aleksander, SA; Balhoff, J; Carbon, S; Cherry, JM; Drabkin, HJ; Ebert, D; Feuermann, M; Gaudet, P; Harris, NL; Hill, DP; Zorn, A; Ramachandran, S; Ruzicka, L; Westerfield, M. The Gene Ontology knowledgebase in 2023. Genetics. 2023; 224(1).

Gipson, GR; Nolan, K; Kattamuri, C; Kenny, AP; Agricola, Z; Edwards, NA; Zinski, J; Czepnik, M; Mullins, MC; Zorn, AM; Thompson, TB. Formation and characterization of BMP2/GDF5 and BMP4/GDF5 heterodimers. BMC Biology. 2023; 21(1):16.

Ochi, H; Michiue, T; Kato, T; Zorn, A; Hayashi, T; Inoue, T; Kondo, M; Taira, M. Versatile utilities of amphibians (part 4). Development Growth and Differentiation. 2023; 65(1):4-5.

Michiue, T; Kato, T; Ochi, H; Zorn, A; Hayashi, T; Inoue, T; Kondo, M; Taira, M. Versatile utilities of amphibians (Part 3). Development Growth and Differentiation. 2022; 64(9):472-473.

Ramachandran, J; Zhou, W; Bardenhagen, AE; Nasr, T; Yates, ER; Zorn, AM; Ji, H; Vokes, SA. Hedgehog regulation of epithelial cell state and morphogenesis in the larynx. eLife. 2022; 11.

Kishimoto, K; Iwasawa, K; Sorel, A; Ferran-Heredia, C; Han, L; Morimoto, M; Wells, JM; Takebe, T; Zorn, AM. Directed differentiation of human pluripotent stem cells into diverse organ-specific mesenchyme of the digestive and respiratory systems. Nature Protocols. 2022; 17(11):2699-2719.

Kimura, M; Iguchi, T; Iwasawa, K; Dunn, A; Thompson, WL; Yoneyama, Y; Chaturvedi, P; Zorn, AM; Wintzinger, M; Quattrocelli, M; Myers, RP; Subramanian, GM; Hwa, V; Takebe, T. En masse organoid phenotyping informs metabolic-associated genetic susceptibility to NASH. Cell. 2022; 185(22):4216-4232.e16.

Rankin, SA; Zorn, AM. The homeodomain transcription factor Ventx2 regulates respiratory progenitor cell number and differentiation timing during Xenopus lung development. Development Growth and Differentiation. 2022; 64(7):347-361.

Michiue, T; Zorn, AM; Kato, T; Ochi, H; Hayashi, T; Inoue, T. Versatile utilities of amphibians (part 2). Development Growth and Differentiation. 2022; 64(7):346.

Mukherjee, S; Luedeke, DM; Mccoy, L; Iwafuchi, M; Zorn, AM. SOX transcription factors direct TCF-independent WNT/β-catenin responsive transcription to govern cell fate in human pluripotent stem cells. Cell reports. 2022; 40(8):111247.

Michiue, T; Zorn, AM; Kato, T; Ochi, H; Hayashi, T; Inoue, T. Versatile Utilities of Amphibians (part 1). Development Growth and Differentiation. 2022; 64(6):264-265.

Zahn, N; James-Zorn, C; Ponferrada, VG; Adams, DS; Grzymkowski, J; Buchholz, DR; Nascone-Yoder, NM; Horb, M; Moody, SA; Vize, PD; Zorn, AM. Normal Table of Xenopus development: a new graphical resource. Development. 2022; 149(14).

Zhong, G; Ahimaz, P; Edwards, NA; Hagen, JJ; Faure, C; Lu, Q; Kingma, P; Middlesworth, W; Khlevner, J; El Fiky, M; Kenny, AP; Zorn, AM; Shen, Y; Chung, WK. Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas. HGG Advances. 2022; 3(3):100107.

Fisher, ME; Segerdell, E; Matentzoglu, N; Nenni, MJ; Fortriede, JD; Chu, S; Pells, TJ; Osumi-Sutherland, D; Chaturvedi, P; James-Zorn, C; Arshinoff, BI; Karimi, K; Vize, PD; Zorn, AM. The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development. BMC Bioinformatics. 2022; 23(1):99.

Jansen, C; Paraiso, KD; Zhou, JJ; Blitz, IL; Fish, MB; Charney, RM; Cho, JS; Yasuoka, Y; Sudou, N; Bright, AR; Taira, M; Zorn, AM; Mortazavi, A; Cho, KWY. Uncovering the mesendoderm gene regulatory network through multi-omic data integration. Cell reports. 2022; 38(7):110364.

Eicher, AK; Kechele, DO; Sundaram, N; Berns, HM; Poling, HM; Haines, LE; Sanchez, JG; Kishimoto, K; Krishnamurthy, M; Han, L; Zorn, AM; Helmrath, MA; Wells, JM. Functional human gastrointestinal organoids can be engineered from three primary germ layers derived separately from pluripotent stem cells. Cell Stem Cell. 2022; 29(1):36-51.e6.

Gu, M; Zorn, AM. Follow your heart and trust your gut: Co-development of heart and gut tissue in organoids. Cell Stem Cell. 2021; 28(12):2037-2038.

Rankin, SA; Steimle, JD; Yang, XH; Rydeen, AB; Agarwal, K; Chaturvedi, P; Ikegami, K; Herriges, MJ; Moskowitz, IP; Zorn, AM. Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development. eLife. 2021; 10.

Edwards, NA; Shacham-Silverberg, V; Weitz, L; Kingma, PS; Shen, Y; Wells, JM; Chung, WK; Zorn, AM. Developmental basis of trachea-esophageal birth defects. Developmental Biology. 2021; 477:85-97.

Azizgolshani, H; Coppeta, JR; Vedula, EM; Marr, EE; Cain, BP; Luu, RJ; Lech, MP; Kann, SH; Mulhern, TJ; Tandon, V; Wiellette, EL; Williams, C; Isenberg, BC; Charest, JL. High-throughput organ-on-chip platform with integrated programmable fluid flow and real-time sensing for complex tissue models in drug development workflows. Lab on a Chip. 2021; 21(8):1454-1474.

Edwards, NA; Zorn, AM. Modeling endoderm development and disease in Xenopus. Current Topics in Developmental Biology. 2021; 145:61-90.

Trisno, SL; Higano, NS; Kechele, D; Nasr, T; Chung, W; Zorn, AM; Woods, JC; Wells, JM; Kingma, PS. Case Report: Esophageal Bronchus in a Neonate, With Image, Histological, and Molecular Analysis. Frontiers in Pediatrics. 2021; 9:707822.

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