Yan Xu Lab

Yan Xu Lab

Chen, K; Zhao, S; Guo, M; Reza, H; Wagner, A; Cakar, AC; Jiang, C; Zhang, E; Green, J; Martin, EP; Perl, AK; Sinner, D; Yu, JJ; Xu, Y. Decoding the Lymphangioleiomyomatosis (LAM) Niche Microenvironment via Integrative Analysis of Single Cell Multiomics and Spatial Transcriptomics. European Respiratory Journal. 2026.

Alharbi, S; Wagner, A; Merkle, S; Pastura, P; Mcdaniel, CG; Fox, D; Xu, Y; Le Cras, TD. MEK Inhibition Reduces Vascular Malformations and Gene Dysregulation in NRASQ61R Human Endothelial Cells. Pediatric Blood and Cancer. 2026; 73(3):e70002.

Xu, Y; Zhou, Z; Chen, W; Du, F; Huang, S; Qi, J; Zeng, Y; Su, H; Wang, J; Xiao, C; Fu, Y-X; Li, Z; Wang, D; Han, C. Tumors with microsatellite instability upregulate TREX1 to escape antitumor immunity. Journal of Experimental Medicine (JEM). 2025; 222(12).

Babaei-Jadidi, R; Clements, D; Wu, Y; Chen, K; Miller, S; Platé, M; Lim, K; Rue, R; Krymskaya, VP; Chambers, R; Rawlins, EL; Xu, Y; Johnson, SR. mTOR dysregulation induces IL-6 and paracrine AT2 cell senescence impeding lung repair in lymphangioleiomyomatosis. Nature Communications. 2025; 16(1):8996.

Kim, H; Yi, S; Roberts, M; Zhao, S; Wikenheiser-Brokamp, K; Xu, Y; Naren, A; Mun, K. 174 A 3D bioengineered human submucosal gland ductal model for studying mucociliary clearance in cystic fibrosis. Journal of Cystic Fibrosis. 2025; 24:s101.

Yu, JJ; Gupta, N; Guo, M; Olatoke, T; Xu, Y. Emerging Concepts in Pathogenesis, Multiomics Applications, and Clinical Research in Lymphangioleiomyomatosis. Seminars in Respiratory and Critical Care Medicine. 2025; 46(4):366-377.

Xu, Y; Mcmillan, A; Gupta, N; Lemke-Miltner, CD; Rataan, AO; Areecheewakul, S; Bhat, DS; Lanzel, EA; Geary, SM; Simons, AL; Weiner, GJ; Salem, AK. In situ treatment with a TLR9 agonist virus-like particle to promote immune responses against oral epithelial dysplasia progression. Cancer Immunology, Immunotherapy. 2025; 74(6):189.

Kim, H; Yi, S; Liyanage, P; Zhao, S; Wikenheiser-Brokamp, KA; Mcmillin, L; Xu, Y; Kitzmiller, JA; Whitsett, JA; Naren, AP; Mun, KS. Development of a 3D bioengineered human lung submucosal gland ductal airway model to study mucociliary clearance in vitro. Cell Biomater. 2025; 1(2).

Mcmillan, A; Hoffman, MR; Xu, Y; Wu, Z; Thayer, E; Peel, A; Guymon, A; Kanotra, S; Salem, AK. 3D bioprinted ferret mesenchymal stem cell-laden cartilage grafts for laryngotracheal reconstruction in a ferret surgical model. Biomaterials Science. 2025; 13(5):1304-1322.

Bottasso-Arias, N; Mohanakrishnan, M; Trovillion, S; Burra, K; Russell, NX; Wu, Y; Xu, Y; Sinner, D. Wnt5a and Notum influence the temporal dynamics of cartilaginous mesenchymal condensations in developing trachea. Frontiers in Cell and Developmental Biology. 2025; 13:1523833.

He, H; Bell, SM; Davis, AK; Zhao, S; Sridharan, A; Na, C-L; Guo, M; Xu, Y; Snowball, J; Swarr, DT; Zacharias, WJ; Whitsett, JA. PRDM3/16 regulate chromatin accessibility required for NKX2-1 mediated alveolar epithelial differentiation and function. Nature Communications. 2024; 15(1):8112.

Deng, R; Tian, R; Li, X; Xu, Y; Li, Y; Wang, X; Li, H; Wang, L; Xu, B; Yang, D; Tang, S; Xue, B; Zuo, C; Zhu, H. ISG12a promotes immunotherapy of HBV-associated hepatocellular carcinoma through blocking TRIM21/AKT/β-catenin/PD-L1 axis. iScience. 2024; 27(4):109533.

Bhattacharya, S; Myers, JA; Baker, C; Guo, M; Danopoulos, S; Myers, JR; Bandyopadhyay, G; Romas, ST; Huyck, HL; Misra, RS; Whitsett, JA; Xu, Y; Pryhuber, GS; Mariani, TJ. Single-Cell Transcriptomic Profiling Identifies Molecular Phenotypes of Newborn Human Lung Cells. Genes. 2024; 15(3).

Gaddis, N; Fortriede, J; Guo, M; Bardes, EE; Kouril, M; Tabar, S; Burns, K; Ardini-Poleske, ME; Loos, S; Schnell, D; Xu, Y; Tickle, T; Aronow, BJ; Salomonis, N. LungMAP Portal Ecosystem: Systems-level Exploration of the Lung. American Journal of Respiratory Cell and Molecular Biology. 2024; 70(2):129-139.

Deng, R; Zhang, L; Chen, S; Li, X; Xue, B; Li, H; Xu, Y; Tian, R; Liu, Q; Wang, L; Liu, S; Yang, D; Li, P; Tang, S; Zhu, H. PZR suppresses innate immune response to RNA viral infection by inhibiting MAVS activation in interferon signaling mediated by RIG-I and MDA5. Antiviral Research. 2024; 222:105797.

Hu, Q; Chen, S; Deng, R; Deng, H; Peng, M; Wang, X; Deng, S; Wang, J; Xu, B; Xu, Y; Zhu, H; Zheng, J; Xia, M; Zuo, C. Exosomal PDL1 Suppresses the Anticancer Activity of CD8+ T Cells in Hepatocellular Carcinoma. Cellular oncology (Dordrecht). 2024; 2024:1608582.

Rataan, AO; Xu, Y; Geary, SM; Zakharia, Y; Kamel, ES; Rustum, YM; Salem, AK. Targeting transforming growth factor-β1 by methylseleninic acid/seleno-L-methionine in clear cell renal cell carcinoma: Mechanisms and therapeutic potential. Cancer Treatment and Research Communications. 2024; 42:100864.

Guo, M; Wikenheiser-Brokamp, KA; Kitzmiller, JA; Jiang, C; Wang, G; Wang, A; Preissl, S; Hou, X; Buchanan, J; Karolak, JA; Stankiewicz, P; Kalinichenko, VV; Wambach, JA; Whitsett, JA. Single Cell Multiomics Identifies Cells and Genetic Networks Underlying Alveolar Capillary Dysplasia. American Journal of Respiratory and Critical Care Medicine. 2023; 208(6):709-725.

Guo, M; Morley, MP; Jiang, C; Wu, Y; Li, G; Du, Y; Zhao, S; Wagner, A; Cakar, AC; Kouril, M; Sun, X; Morrisey, EE; Whitsett, JA; Xu, Y. Guided construction of single cell reference for human and mouse lung. Nature Communications. 2023; 14(1):4566.

Lesnak, JB; Nakhla, DS; Plumb, AN; Mcmillan, A; Saha, S; Gupta, N; Xu, Y; Phruttiwanichakun, P; Rasmussen, L; Meyerholz, DK; Salem, AK; Sluka, KA. Selective androgen receptor modulator microparticle formulation reverses muscle hyperalgesia in a mouse model of widespread muscle pain. Pain. 2023; 164(7):1512-1523.

Sikkema, L; Ramírez-Suástegui, C; Strobl, DC; Gillett, TE; Zappia, L; Madissoon, E; Markov, NS; Zaragosi, L-E; Ji, Y; Ansari, M; Misharin, AV; Nawijn, MC; Luecken, MD; Theis, FJ. An integrated cell atlas of the lung in health and disease. Nature Medicine. 2023; 29(6):1563-1577.

Li, H; Liu, S; Feng, Q; Deng, R; Wang, J; Wang, X; Tian, R; Xu, Y; Chen, S; Liu, Q; Peng, Y; Tang, S; Xue, B; Zhu, H. Regulation of PKR-dependent RNA translation inhibition by TRIM21 upon virus infection or other stress. PLoS Pathogens. 2023; 19(6):e1011443.

Olatoke, T; Wagner, A; Astrinidis, A; Zhang, EY; Guo, M; Zhang, AG; Mattam, U; Kopras, EJ; Gupta, N; Smith, EP; Whitsett, JA; Mccormack, FX; Xu, Y; Yu, JJ. Single-cell multiomic analysis identifies a HOX-PBX gene network regulating the survival of lymphangioleiomyomatosis cells. Science Advances. 2023; 9(19):eadf8549.

Astrinidis, A; Li, C; Zhang, EY; Zhao, X; Zhao, S; Guo, M; Olatoke, T; Mattam, U; Huang, R; Zhang, AG; Setchell, KDR; Mccormack, FX; Xu, Y; Yu, JJ. Upregulation of acid ceramidase contributes to tumor progression in tuberous sclerosis complex. JCI Insight. 2023; 8(9).

Bian, F; Lan, Y-W; Zhao, S; Deng, Z; Shukla, S; Acharya, A; Donovan, J; Le, T; Milewski, D; Bacchetta, M; Xu, Y; Shi, D; Kalinichenko, VV; Kalin, TV. Lung endothelial cells regulate pulmonary fibrosis through FOXF1/R-Ras signaling. Nature Communications. 2023; 14(1):2560.

Minor, BMN; Lemoine, D; Seger, C; Gibbons, E; Koudouovoh, J; Taya, M; Kurtz, D; Xu, Y; Hammes, SR. Estradiol Augments Tumor-Induced Neutrophil Production to Promote Tumor Cell Actions in Lymphangioleiomyomatosis Models. Endocrinology. 2023; 164(6).

Zhang, Z; Zhou, J; Ni, P; Hu, B; Jolicoeur, N; Deng, S; Xiao, Q; He, Q; Li, G; Xia, Y; Zhang, B; Cai, K; Xu, Y; Liu, B. PF-D-Trimer, a protective SARS-CoV-2 subunit vaccine: immunogenicity and application. npj Vaccines. 2023; 8(1):38.

Uehara, Y; Tanaka, Y; Zhao, S; Nikolaidis, NM; Pitstick, LB; Wu, H; Yu, JJ; Zhang, E; Hasegawa, Y; Noel, JG; Inoue, Y; Altinişik, G; Xu, Y; Mccormack, FX. Insights into pulmonary phosphate homeostasis and osteoclastogenesis emerge from the study of pulmonary alveolar microlithiasis. Nature Communications. 2023; 14(1):1205.

Du, Y; Guo, M; Wu, Y; Wagner, A; Perl, AK; Wikenheiser-Brokamp, K; Yu, J; Gupta, N; Kopras, E; Krymskaya, V; Kwiatkowski, D; Henske, EP; Mccormack, F; Xu, Y. Lymphangioleiomyomatosis (LAM) Cell Atlas. Thorax. 2023; 78(1):85-87.

Xue, B; Li, H; Liu, S; Feng, Q; Xu, Y; Deng, R; Chen, S; Wang, J; Li, X; Wan, M; Tang, S; Zhu, H. The redox cycling of STAT2 maintains innate immune homeostasis. Cell reports. 2022; 40(7):111215.

Stevens, J; Steinmeyer, S; Bonfield, M; Peterson, L; Wang, T; Gray, J; Lewkowich, I; Xu, Y; Du, Y; Guo, M; Miller, L; Chougnet, C; O'connor, DH; Deshmukh, H. The balance between protective and pathogenic immune responses to pneumonia in the neonatal lung is enforced by gut microbiota. Science Translational Medicine. 2022; 14(649):eabl3981.

Xu, Y; Yang, Q; Xue, B; Wang, X; Tian, R; Deng, R; Chen, S; Wang, X; Wang, L; Wang, C; Liu, S; Yang, D; Tang, S; Zhu, H. Heat Shock-Binding Protein 21 Regulates the Innate Immune Response to Viral Infection. Journal of Virology. 2022; 96(7):e0000122.

Toth, A; Steinmeyer, S; Kannan, P; Gray, J; Jackson, CM; Mukherjee, S; Demmert, M; Sheak, JR; Benson, D; Kitzmiller, J; Chougnet, CA; Jobe, AH; Deshmukh, H; Zacharias, WJ. Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Science Translational Medicine. 2022; 14(638):eabl8574.

Chen, S; Liu, Q; Zhang, L; Ma, J; Xue, B; Li, H; Deng, R; Guo, M; Xu, Y; Tian, R; Li, X; Liu, S; Yang, D; Zhu, H. The Role of REC8 in the Innate Immune Response to Viral Infection. Journal of Virology. 2022; 96(6):e0217521.

Han, B; Li, X; Ai, R-S; Deng, S-Y; Ye, Z-Q; Deng, X; Ma, W; Xiao, S; Wang, J-Z; Wang, L-M; Xie, C; Zhang, Y; Xu, Y; Zhang, Y. Atmospheric particulate matter aggravates cns demyelination through involvement of TLR-4/NF-kB signaling and microglial activation. eLife. 2022; 11.

Bottasso-Arias, N; Leesman, L; Burra, K; Snowball, J; Shah, R; Mohanakrishnan, M; Xu, Y; Sinner, D. BMP4 and Wnt signaling interact to promote mouse tracheal mesenchyme morphogenesis. American Journal of Physiology - Lung Cellular and Molecular Physiology. 2022; 322(2):L224-L242.

Sun, X; Perl, A-K; Li, R; Bell, SM; Sajti, E; Kalinichenko, VV; Kalin, TV; Misra, RS; Deshmukh, H; Clair, G; Xu, Y; Pryhuber, G; Whitsett, J; Morrisey, EE. A census of the lung: CellCards from LungMAP. Developmental Cell. 2022; 57(1):112-145.e2.

Hudock, KM; Collins, MS; Imbrogno, MA; Kramer, EL; Brewington, JJ; Ziady, A; Zhang, N; Snowball, J; Xu, Y; Carey, BC; Gollomp, K; Mangalmurti, N; Trapnell, BC; Clancy, JP. Alpha-1 antitrypsin limits neutrophil extracellular trap disruption of airway epithelial barrier function. Frontiers in Immunology. 2022; 13:1023553.