Developmental Biology

Publications

Alavattam, KG; Esparza, JM; Hu, M; Shimada, R; Kohrs, AR; Abe, H; Munakata, Y; Otsuka, K; Yoshimura, S; Kitamura, Y; Kim, J; Andreassen, PR; Ishiguro, KI; Namekawa, SH. ATF7IP2/MCAF2 directs H3K9 methylation and meiotic gene regulation in the male germline. Genes and Development. 2024; 38:115-130.

Aleksander, SA; Anagnostopoulos, AV; Antonazzo, G; Arnaboldi, V; Attrill, H; Becerra, A; Bello, SM; Blodgett, O; Bradford, YM; Bult, CJ; Wright, A; Yook, K; Zhou, P; Zorn, A. Updates to the Alliance of Genome Resources central infrastructure. Editor, Wood V. Genetics: a periodical record of investigations bearing on heredity and variation. 2024; 227:iyae049.

Barnada, SM; Giner de Gracia, A; Morenilla-Palao, C; López-Cascales, MT; Scopa, C; Waltrich, FJ; Mikkers, HM M; Cicardi, ME; Karlin, J; Trotti, D; Santen, GW E; McMahon, SB; Herrera, E; Trizzino, M. ARID1A-BAF coordinates ZIC2 genomic occupancy for epithelial-to-mesenchymal transition in cranial neural crest specification. The American Journal of Human Genetics. 2024; 111:2232-2252.

Brooks, EC; Han, SJ Y; Bonatto Paese, CL; Lewis, AA; Aarnio-Peterson, M; Brugmann, SA. The ciliary protein C2cd3 is required for mandibular musculoskeletal tissue patterning. Differentiation; Research in Biological Diversity. 2024; 138:100782.

Brugmann, SA; Clouthier, DE; Fantauzzo, KA; Harris, MP; Jeong, J; Saint-Jeannet, JP; Stottmann, RW; Merrill, AE. The society for craniofacial genetics and developmental biology 46th annual meeting. American Journal of Medical Genetics, Part A. 2024; 194:e63615.

Chandel, S; Kumaragurubaran, R; Giri, H; Dixit, M. Isolation and Culture of Human Umbilical Vein Endothelial Cells (HUVECs). Methods in molecular biology (Clifton, N.J.). 2024; 2711:147-162.

Dao, L; You, Z; Lu, L; Xu, T; Sarkar, AK; Zhu, H; Liu, M; Calandrelli, R; Yoshida, G; Lin, P; Vadivelu, S; Zhong, S; Huang, LF; Guo, Z. Modeling blood-brain barrier formation and cerebral cavernous malformations in human PSC-derived organoids. Cell Stem Cell. 2024; 31:818-833.e11.

D'Souza, SP; Upton, BA; Eldred, KC; Glass, I; Nayak, G; Grover, K; Ahmed, A; Nguyen, MT; Hu, YC; Gamlin, P; Lang, RA. Developmental control of rod number via a light-dependent retrograde pathway from intrinsically photosensitive retinal ganglion cells. Developmental Cell. 2024; 59:2897-2911.e6.

Ducey, J; Lansdale, N; Gorst, S; Bray, L; Teunissen, N; Cullis, P; Faulkner, J; Gray, V; Gammino, LG; 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:e002262.

Esfahani, SN; Zheng, Y; Arabpour, A; Irizarry, AM R; Kobayashi, N; Xue, X; Shao, Y; Zhao, C; Agranonik, NL; Sparrow, M; Yang, R; Chien, KR; Clark, AT; Fu, J. Derivation of human primordial germ cell-like cells in an embryonic-like culture. Nature Communications. 2024; 15:167.

Gilbert, PM; Hofmann, S; Ng, HH; Vankelecom, H; Wells, JM. Organoids in endocrine and metabolic research: current and emerging applications. Nature Reviews Endocrinology. 2024; 20:195-201.

Gu, L; Cai, H; Chen, L; Gu, M; Tchieu, J; Guo, F. Functional Neural Networks in Human Brain Organoids. BME Frontiers. 2024; 5:0065.

Heekin, S; Lopez-Nunez, O; Smith, J; Denson, N; Denson, L; Miethke, A; Dillman, J; Miraldi, E; Kofron, JM; Dhaliwal, J; Erdman, L. (2024) Trade-Offs in Deep Learning Model Loss and Configuration for Sparse Histological Segmentation: A Case Study in Pediatric Ileal Histology. Institute of Electrical and Electronics Engineers (IEEE). 00:1-8.

Huang, HZ; Ai, WQ; Wei, N; Zhu, LS; Liu, ZQ; Zhou, CW; Deng, MF; Zhang, WT; Zhang, JC; Yang, CQ; Lu, Y; Shu, K; Zhu, LQ; Liu, D. Senktide blocks aberrant RTN3 interactome to retard memory decline and tau pathology in social isolated Alzheimer's disease mice. Protein and Cell. 2024; 15:261-284.

Kang, SY; Kimura, M; Shrestha, S; Lewis, P; Lee, S; Cai, Y; Joshi, P; Acharya, P; Liu, J; Yang, Y; Alsberg, E; Wells, JM; Takebe, T; Lee, MY. A Pillar and Perfusion Plate Platform for Robust Human Organoid Culture and Analysis. Advanced healthcare materials. 2024; 13:e2302502.

Koparir, A; Lekszas, C; Keseroglu, K; Rose, T; Rappl, L; Rad, A; Maroofian, R; Narendran, N; Hasanzadeh, A; Karimiani, EG; Özbudak, EM; Vona, B; Haaf, T; Liedtke, D. Zebrafish as a model to investigate a biallelic gain-of-function variant in MSGN1, associated with a novel skeletal dysplasia syndrome. Human Genomics. 2024; 18:23.

Lan, Y; Wu, Z; Liu, H; Jiang, R. Lineage-specific requirements of Alx4 function in craniofacial and hair development. Developmental Dynamics. 2024; 253:940-948.

Li, W; Guo, J; Hobson, EC; Xue, X; Li, Q; Fu, J; Deng, CX; Guo, Z. Metabolic‐Glycoengineering‐Enabled Molecularly Specific Acoustic Tweezing Cytometry for Targeted Mechanical Stimulation of Cell Surface Sialoglycans. Angewandte Chemie International Edition. 2024; 136.

Liu, X; Xin, DE; Zhong, X; Zhao, C; Li, Z; Zhang, L; Dourson, AJ; Lee, L; Mishra, S; Bayat, AE; Jankowski, MP; Barton, SK; He, X; Lu, QR. Small-molecule-induced epigenetic rejuvenation promotes SREBP condensation and overcomes barriers to CNS myelin regeneration. Cell. 2024; 187:2465-2484.e22.

Liu, Y; Kim, YS; Xue, X; Miao, Y; Kobayashi, N; Sun, S; Yan, RZ; Yang, Q; Pourquié, O; Fu, J. A human pluripotent stem cell-based somitogenesis model using microfluidics. Cell Stem Cell. 2024; 31:1113-1126.e6.

Liu, Y; Xue, X; Sun, S; Kobayashi, N; Kim, YS; Fu, J. Morphogenesis beyond in vivo. Nature Reviews Physics. 2024; 6:28-44.

Matsui, S; Granitto, M; Buckley, M; Ludwig, K; Koigi, S; Shiley, J; Zacharias, WJ; Mayhew, CN; Lim, HW; Iwafuchi, M. Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Molecular Cell. 2024; 84:476-489.e10.

Matsui, S; Shiley, JR; Buckley, M; Lim, HW; Hu, YC; Mayhew, CN; Iwafuchi, M. Protocol for establishing inducible CRISPRd system for blocking transcription factor-binding sites in human pluripotent stem cells. Star Protocols. 2024; 5:103233.

Matsui, S; Shiley, JR; Granitto, M; Ludwig, K; Buckley, M; Koigi, S; Mirizio, G; Hu, YC; Mayhew, CN; Iwafuchi, M. Protocol for establishing inducible CRISPR interference system for multiple-gene silencing in human pluripotent stem cells. Star Protocols. 2024; 5:103221.

Pavličev, M; McDonough-Goldstein, CE; Zupan, AM; Muglia, L; Hu, YC; Kong, F; Monangi, N; Dagdas, G; Zupančič, N; Maziarz, J; Sinner, D; Zhang, G; Wagner, G; Muglia, L. A common allele increases endometrial Wnt4 expression, with antagonistic implications for pregnancy, reproductive cancers, and endometriosis. Nature Communications. 2024; 15:1152.

Perl, AJ; Liu, H; Hass, M; Adhikari, N; Chaturvedi, P; Hu, YC; Jiang, R; Liu, Y; Kopan, R. Reduced Nephron Endowment in Six2-TGCtg Mice Is Due to Six3 Misexpression by Aberrant Enhancer-Promoter Interactions in the Transgene. Journal of the American Society of Nephrology : JASN. 2024; 35:566-577.

Poling, HM; Sundaram, N; Fisher, GW; Singh, A; Shiley, JR; Nattamai, K; Govindarajah, V; Cortez, AR; Krutko, MO; Ménoret, S; Mayhew, CN; Takebe, T; Mahe, MM; Helmrath, MA. Human pluripotent stem cell-derived organoids repair damaged bowel in vivo. Cell Stem Cell. 2024; 31:1513-1523.e7.

Rudman-Melnick, V; Adam, M; Stowers, K; Potter, A; Ma, Q; Chokshi, SM; Vanhoutte, D; Valiente-Alandi, I; Lindquist, DM; Nieman, ML; Kofron, JM; Chung, E; Park, JS; Potter, SS; Devarajan, P. Single-cell sequencing dissects the transcriptional identity of activated fibroblasts and identifies novel persistent distal tubular injury patterns in kidney fibrosis. Scientific Reports. 2024; 14:439.

Rudman-Melnick, V; Vanhoutte, D; Stowers, K; Sargent, M; Adam, M; Ma, Q; Perl, AK T; Miethke, AG; Burg, A; Shi, T; Hildeman, DA; Woodle, ES S; Kofron, JM; Devarajan, P. Gucy1α1 specifically marks kidney, heart, lung and liver fibroblasts. Scientific Reports. 2024; 14:29307.

Salomone, J; Farrow, E; Gebelein, B. Homeodomain complex formation and biomolecular condensates in Hox gene regulation. Seminars in Cell and Developmental Biology. 2024; 152-153:93-100.

Sanchez, JG; Rankin, S; Paul, E; McCauley, HA; Kechele, DO; Enriquez, JR; Jones, NH; Greeley, SA W; Letourneau-Friedberg, L; Zorn, AM; Krishnamurthy, M; Wells, JM. RFX6 regulates human intestinal patterning and function upstream of PDX1. Development (Cambridge). 2024; 151:dev202529.

Shen, XY; Zhang, J; Huang, HZ; Li, SD; Zhou, L; Wu, SP; Tang, C; Huang, X; Liu, ZQ; Guo, ZY; Li, X; Man, HY; Lu, YM; Zhu, LQ; Liu, D. The interaction of Synapsin 2a and Synaptogyrin-3 regulates fear extinction in mice. The Journal of Clinical Investigation. 2024; 134:e172802.

Skurat, AV; Segvich, DM; Contreras, CJ; Hu, YC; Hurley, TD; DePaoli-Roach, AA; Roach, PJ. Impaired malin expression and interaction with partner proteins in Lafora disease. The Journal of biological chemistry. 2024; 300:107271.

Sturchio, A; Rocha, EM; Kauffman, MA; Marsili, L; Mahajan, A; Saraf, AA; Vizcarra, JA; Guo, Z; Espay, AJ. Recalibrating the Why and Whom of Animal Models in Parkinson Disease: A Clinician's Perspective. Brain Sciences. 2024; 14:151.

Taranov, A; Bedolla, A; Iwasawa, E; Brown, FN; Baumgartner, S; Fugate, EM; Levoy, J; Crone, SA; Goto, J; Luo, Y. The choroid plexus maintains adult brain ventricles and subventricular zone neuroblast pool, which facilitates poststroke neurogenesis. Proceedings of the National Academy of Sciences of USA. 2024; 121:e2400213121.

Tornabene, P; Wells, JM. Exploring optimal protocols for generating and preserving glucose-responsive insulin-secreting progenitor cells derived from human pluripotent stem cells. European Journal of Cell Biology. 2024; 103:151464.

Tschuck, J; Padmanabhan Nair, V; Galhoz, A; Zaratiegui, C; Tai, HM; Ciceri, G; Rothenaigner, I; Tchieu, J; Stockwell, BR; Studer, L; Cabianca, DS; Menden, MP; Vincendeau, M; Hadian, K. Suppression of ferroptosis by vitamin A or radical-trapping antioxidants is essential for neuronal development. Nature Communications. 2024; 15:7611.

Venkatakrishnan, J; Yuan, Y; Zhang, J; Yu, Y; Hu, YC; Kao, WW Y. Self-complementary AAV vector therapy for treating corneal cloudiness of mucopolysaccharidosis type VII (MPS VII). The Ocular Surface. 2024; 32:39-47.

Wang, C; Nagayach, A; Patel, H; Dao, L; Zhu, H; Wasylishen, AR; Fan, Y; Kendler, A; Guo, Z. Utilizing human cerebral organoids to model breast cancer brain metastasis in culture. BREAST CANCER RESEARCH. 2024; 26:108.

Wang, X; Du, W; Li, Y; Yang, HH; Zhang, Y; Akbar, R; Morgan, H; Peng, T; Chen, J; Sadayappan, S; Hu, YC; Fan, Y; Huang, W; Fan, GC. Macrophage-enriched Sectm1a promotes efficient efferocytosis to attenuate ischemia/reperfusion-induced cardiac injury. JCI insight. 2024; 9:e173832.

Webb, JA; Farrow, E; Cain, B; Yuan, Z; Yarawsky, AE; Schoch, E; Gagliani, EK; Herr, AB; Gebelein, B; Kovall, RA. Cooperative Gsx2-DNA binding requires DNA bending and a novel Gsx2 homeodomain interface. Nucleic Acids Research (NAR). 2024; 52:7987-8002.

Wilderman, A; D’haene, E; Baetens, M; Yankee, TN; Winchester, EW; Glidden, N; Roets, E; Van Dorpe, J; Janssens, S; Miller, DE; Weaver, KN; Brugmann, SA; Cox, TC; Cotney, J. A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development. Nature Communications. 2024; 15:136.

Wu, Q; Zhang, J; Kumar, S; Shen, S; Kincaid, M; Johnson, CB; Zhang, YS; Turcotte, R; Alt, C; Ito, K; Ito, K; Way, SS; Kofron, JM; Lucas, D. Resilient anatomy and local plasticity of naive and stress haematopoiesis. Nature. 2024; 627:839-846.

Xue, X; Kim, YS; Ponce-Arias, AI; O’Laughlin, R; Yan, RZ; Kobayashi, N; Tshuva, RY; Tsai, YH; Sun, S; Zheng, Y; Song, H; Ming, GL; Reiner, O; Fu, J. A patterned human neural tube model using microfluidic gradients. Nature. 2024; 628:391-399.

Zhu, LS; Lai, C; Zhou, CW; Chen, HY; Liu, ZQ; Guo, Z; Man, H; Du, HY; Lu, Y; Hu, F; Chen, Z; Shu, K; Zhu, LQ; Liu, D. Postsynaptic lncRNA Sera/Pkm2 pathway orchestrates the transition from social competition to rank by remodeling the neural ensemble in mPFC. Cell Discovery. 2024; 10:87.