Zorn Lab

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.

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.

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.

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.

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.

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.

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.

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. 2022; 3.

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.

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.

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.

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

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.

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.

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.

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.

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.

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. 2019; 57.

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.

Steimle, JD; Rankin, SA; Slagle, CE; Bekeny, J; Rydeen, AB; Chan, SS-K; Kweon, J; Yang, XH; Ikegami, K; Nadadur, RD; et al. Evolutionarily conserved Tbx5-Wnt2/2b pathway orchestrates cardiopulmonary development. Proceedings of the National Academy of Sciences of the United States of America. 2018; 115:E10615-E10624.

Ustiyan, V; Bolte, C; Zhang, Y; Han, L; Xu, Y; Yutzey, KE; Zorn, AM; Kalin, TV; Shannon, JM; Kalinichenko, VV. FOXF1 transcription factor promotes lung morphogenesis by inducing cellular proliferation in fetal lung mesenchyme. Developmental Biology. 2018; 443:50-63.

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.

Takebe, T; Wells, JM; Helmrath, MA; Zorn, AM. Organoid Center Strategies for Accelerating Clinical Translation. Cell Stem Cell. 2018; 22:806-809.

James-Zorn, C; Ponferrada, V; Fisher, ME; Burns, K; Fortriede, J; Segerdell, E; Karimi, K; Lotay, V; Wang, DZ; Chu, S; et al. Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database. Methods in Molecular Biology. 2018; 1757:251-305.

Rankin, SA; McCracken, KW; Luedeke, DM; Han, L; Wells, JM; Shannon, JM; Zorn, AM. Timing is everything: Reiterative Wnt, BMP and RA signaling regulate developmental competence during endoderm organogenesis. Developmental Biology. 2018; 434:121-132.

Karimi, K; Fortriede, JD; Lotay, VS; Burns, KA; Wang, DZ; Fisher, ME; Pells, TJ; James-Zorn, C; Wang, Y; Ponferrada, VG; et al. Xenbase: a genomic, epigenomic and transcriptomic model organism database. Nucleic Acids Research. 2018; 46:D861-D868.

Pells, T; Fisher, ME; Segerdell, E; Fortnede, JD; James-Zorn, C; Burns, KA; Ponferrada, V; Chaturvedi, P; Lotay, V; Nenni, M; et al. (2018) Visualization of gene expression and expression as a phenotype with the XPO, XAO and DO using a combination of experimental data sources. 2285.

Trisno, SL; Philo, KE D; McCracken, KW; Cata, EM; Rankin, SA; Han, L; Nasr, T; Chatuvedi, P; Mandegar, MA; Zorn, AM; et al. Generation of Esophageal Organoids from Human Pluripotent Stem Cells and Their Use to Study Human Development. 2018.