Zorn Lab

Publications

Han, L; Chaturvedi, P; Kishimoto, K; Koike, H; Nasr, T; Iwasawa, K; Giesbrecht, K; Witcher, PC; Eicher, A; Haines, L; et al. Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis. Nature Communications. 2020; 11:4158.

Mukherjee, S; Chaturvedi, P; Rankin, SA; Fish, MB; Wlizla, M; Paraiso, KD; MacDonald, M; Chen, X; Weirauch, MT; Blitz, IL; et al. Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endoderm gene regulatory network. eLife. 2020; 9:e58029.

Nasr, T; Mancini, P; Rankin, SA; Edwards, NA; Agricola, ZN; Kenny, AP; Kinney, JL; Daniels, K; Vardanyan, J; Han, L; et al. Endosome-Mediated Epithelial Remodeling Downstream of Hedgehog-Gli Is Required for Tracheoesophageal Separation. Developmental Cell. 2019; 51:665-674.e6.

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

Trisno, SL; Philo, KE D; McCracken, KW; Cata, EM; Ruiz-Torres, S; Rankin, SA; Han, L; Nasr, T; Chaturvedi, P; Rothenberg, ME; et al. Esophageal Organoids from Human Pluripotent Stem Cells Delineate Sox2 Functions during Esophageal Specification. Cell Stem Cell. 2018; 23:501-515.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 (Cambridge). 2017; 144:1283-1295.

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; 16:66-78.

Rankin, SA; Gallas, AL; Neto, A; Luis Gomez-Skarmeta, J; 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 (Cambridge). 2012; 139:3010-3020.

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; 23:292-304.

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

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

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 and Development. 2008; 22:3050-3063.

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

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 (Cambridge). 2006; 133:1955-1966.

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

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; 4:487-498.

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; 43:1478-1493.

Bouffi, C; Wikenheiser-Brokamp, KA; Chaturvedi, P; Sundaram, N; Goddard, GR; Wunderlich, M; Brown, NE; Staab, JF; Latanich, R; Zachos, NC; et al. In vivo development of immune tissue in human intestinal organoids transplanted into humanized mice. Nature Biotechnology. 2023; 41:824-831.

Fisher, M; James-Zorn, C; Ponferrada, V; Bell, AJ; Sundararaj, N; Segerdell, E; Chaturvedi, P; Bayyari, N; Chu, S; Pells, T; et al. Xenbase: key features and resources of the Xenopus model organism knowledgebase. Editor, Wood V. Genetics: a periodical record of investigations bearing on heredity and variation. 2023; 224:iyad018.

Gene Ontology Consortium, ; Aleksander, SA; Balhoff, J; Carbon, S; Cherry, JM; Drabkin, HJ; Ebert, D; Feuermann, M; Gaudet, P; Harris, NL; et al. The Gene Ontology knowledgebase in 2023. Editor, Baryshnikova A. Genetics: a periodical record of investigations bearing on heredity and variation. 2023; 224:iyad031.

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; 65:4-5.

Fisher, ME; Segerdell, E; Matentzoglu, N; Nenni, MJ; Fortriede, JD; Chu, S; Pells, TJ; Osumi-Sutherland, D; Chaturvedi, P; James-Zorn, C; et al. The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development. BMC Bioinformatics. 2022; 23:99.

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; 64:472-473.

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:e77055.

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; 17:2699-2719.

Kimura, M; Iguchi, T; Iwasawa, K; Dunn, A; Thompson, WL; Yoneyama, Y; Chaturvedi, P; Zorn, AM; Wintzinger, M; Quattrocelli, M; et al. En masse organoid phenotyping informs metabolic-associated genetic susceptibility to NASH. Cell. 2022; 185:4216-4232.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; 64:347-361.

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

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; 40:111247.

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

Zahn, N; James-Zorn, C; Ponferrada, VG; Adams, DS; Grzymkowski, J; Buchholz, DR; Nascone-Yoder, NM; Horb, M; Moody, SA; Vize, PD; et al. Normal Table of Xenopus development: a new graphical resource. Development (Cambridge). 2022; 149:dev200356.

Zhong, G; Ahimaz, P; Edwards, NA; Hagen, JJ; Faure, C; Lu, Q; Kingma, P; Middlesworth, W; Khlevner, J; El Fiky, M; et al. Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas. HGG Advances. 2022; 3:100107.

Jansen, C; Paraiso, KD; Zhou, JJ; Blitz, IL; Fish, MB; Charney, RM; Cho, JS; Yasuoka, Y; Sudou, N; Bright, AR; et al. Uncovering the mesendoderm gene regulatory network through multi-omic data integration. Cell Reports. 2022; 38:110364.

Eicher, AK; Kechele, DO; Sundaram, N; Berns, HM; Poling, HM; Haines, LE; Sanchez, JG; Kishimoto, K; Krishnamurthy, M; Han, L; et al. Functional human gastrointestinal organoids can be engineered from three primary germ layers derived separately from pluripotent stem cells. Cell Stem Cell. 2022; 29:36-51.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; 28:2037-2038.

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:e69288.

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.

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.

Azizgolshani, H; Coppeta, JR; Vedula, EM; Marr, EE; Cain, BP; Luu, RJ; Lech, MP; Kann, SH; Mulhern, TJ; Tandon, V; et al. 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: miniaturisation for chemistry, physics, biology, materials science and bioengineering. 2021; 21:1454-1474.

Nasr, T; Holderbaum, AM; Chaturvedi, P; Agarwal, K; Kinney, JL; Daniels, K; Trisno, SL; Ustiyan, V; Shannon, JM; Wells, JM; et al. Disruption of a hedgehog-foxf1-rspo2 signaling axis leads to tracheomalacia and a loss of sox9+ tracheal chondrocytes. DMM Disease Models and Mechanisms. 2021; 14:dmm046573.

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

Han, L; Chaturvedi, P; Kishimoto, K; Koike, H; Nasr, T; Iwasawa, K; Giesbrecht, K; Witcher, PC; Eicher, A; Haines, L; et al. Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis. Nature Communications. 2020; 11:4158.

Naert, T; Tulkens, D; Edwards, NA; Carron, M; Shaidani, NI; Wlizla, M; Boel, A; Demuynck, S; Horb, ME; Coucke, P; et al. Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafish embryos. Scientific Reports. 2020; 10:14662.

Kishimoto, K; Furukawa, KT; Luz-Madrigal, A; Yamaoka, A; Matsuoka, C; Habu, M; Alev, C; Zorn, AM; Morimoto, M. Bidirectional Wnt signaling between endoderm and mesoderm confers tracheal identity in mouse and human cells. Nature Communications. 2020; 11:4159.

Mukherjee, S; Chaturvedi, P; Rankin, SA; Fish, MB; Wlizla, M; Paraiso, KD; MacDonald, M; Chen, X; Weirauch, MT; Blitz, IL; et al. Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endoderm gene regulatory network. eLife. 2020; 9:e58029.

Fortriede, JD; Pells, TJ; Chu, S; Chaturvedi, P; Wang, D; Fisher, ME; James-Zorn, C; Wang, Y; Nenni, MJ; Burns, KA; et al. Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database. Nucleic Acids Research. 2020; 48:D776-D782.

Nasr, T; Mancini, P; Rankin, SA; Edwards, NA; Agricola, ZN; Kenny, AP; Kinney, JL; Daniels, K; Vardanyan, J; Han, L; et al. Endosome-Mediated Epithelial Remodeling Downstream of Hedgehog-Gli Is Required for Tracheoesophageal Separation. Developmental Cell. 2019; 51:665-674.e6.

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

Sterner, ZR; Rankin, SA; Wlizla, M; Choi, JA; Luedeke, DM; Zorn, AM; Buchholz, DR. Novel vectors for functional interrogation of Xenopus ORFeome coding sequences. Genesis: the Journal of Genetics and Development. 2019; 57:e23329.

Nenni, MJ; Fisher, ME; James-Zorn, C; Pells, TJ; Ponferrada, V; Chu, S; Fortriede, JD; Burns, KA; Wang, Y; Lotay, VS; et al. Xenbase: Facilitating the Use of Xenopus to Model Human Disease. Frontiers in Physiology. 2019; 10:154.