LGEA News
Our recent research activities related to SARS-CoV-2
- Sungnak W, et al, and Network HCALB. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat Med 26: 681-687, 2020. Drs. Jeffrey Whitsett, Xin Sun, Yan Xu and Minzhe Guo from LungMAP are involved in this study, investigated SARS-CoV-2 potential tropism by surveying expression of viral entry-associated genes in single-cell RNAseq data from healthy human donors. Access these data at www.covid19cellatlas.org
- Muus C, et al. Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells. bioRxiv 2020.
- Wang A, et al. Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection. Elife. 2020 Nov 9;9:e62522. Elife, PubMed
- The project page for our new paper with samples from ACDMPV and control patients is available online.
- New data is available in LAM Cell Atlas Web-Portal (LCA) including integrative scRNA kidney samples.
- Check out LAM Cell Atlas Web-Portal (LCA) for LAM projects and datasets with lung, kidney and uterus cells from LAM patients.
- Check out LGEA (LungMAP phase 3) for more datasets from normal and disease lungs.
- LGEA provides query links to access DESCARTES (Human Gene Expression During Development) website in LungDTC panel.
- Minzhe Guo, Michael P. Morley, Cheng Jiang, Yixin Wu, Guangyuan Li, Yina Du, Shuyang Zhao, Andrew Wagner, Adnan Cihan Cakar, Michal Kouril, Kang Jin, Nathan Gaddis, Joseph A. Kitzmiller, Kathleen Stewart, Maria C. Basil, Susan M. Lin, Yun Ying, Apoorva Babu, Kathryn A. Wikenheiser-Brokamp, Kyu Shik Mun, Anjaparavanda P. Naren, Geremy Clair, Joshua N. Adkins, Gloria S. Pryhuber, Ravi S. Misra, Bruce J. Aronow, Timothy L. Tickle, Nathan Salomonis, Xin Sun, Edward E. Morrisey, Jeffrey A. Whitsett, NHLBI LungMAP Consortium, Yan Xu Guided construction of single cell reference for human and mouse lung. Nature Communications 14, 1-20, 2023. Nature Communications
- Minzhe Guo, Kathryn A. Wikenheiser-Brokamp, Joseph A. Kitzmiller, Cheng Jiang, Guolun Wang, Allen Wang, Sebastian Preissl, Xiaomeng Hou, Justin Buchanan, Justyna A. Karolak, Yifei Miao, David B. Frank, William J. Zacharias, Xin Sun, Yan Xu, Mingxia Gu, Pawel Stankiewicz, Vladimir V. Kalinichenko, Jennifer A. Wambach, Jeffery A. Whitsett Single cell multiomics identifies cells and genetic networks underlying alveolar capillary dysplasia. Am J Respir Crit Care Med 2023. AJRCMB
- Stevens J, Steinmeyer S, Bonfield M, Peterson L, Wang T, Gray J, Lewkowich I, Xu Y, Du Y, Guo M, Wynn JL, Zacharias W, Salomonis N, 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. Sci Transl Med 2022; 14: eabl3981. PubMed bioRxiv
- Du Y, Guo M, Wu Y, Wagner A, Perl AK, Wikenheiser-Brokamp K, Yu J, Gupta N, Kopras E, Krymskaya V, Obraztsova K, Tang Y, Kwiatkowski D, Henske EP, McCormack F, Xu Y. Lymphangioleiomyomatosis (LAM) Cell Atlas. Thorax 2022: thoraxjnl-2022-218772
- Guo M, Morley MP, Wu Y, Du Y, Zhao S, Wagner A, Kouril M, Jin K, Gaddis N, Kitzmiller JA, Stewart K, Basil MC, Lin SM, Ying Y, Babu A, Wikenheiser-Brokamp KA, Mun KS, Naren AP, Lin S, Clair G, Adkins JN, Pryhuber GS, Misra RS, Aronow BJ, Tickle TL, Salomonis N, Sun X, Morrisey EE, Whitsett JA, Xu Y, Consortium NL. Guided construction of single cell reference for human and mouse lung. bioRxiv 2022: 2022.2005.2018.491687
- Toth A, Steinmeyer S, Kannan P, Gray J, Jackson CM, Mukherjee S, Demmert M, Sheak JR, Benson D, Kitzmiller J, Wayman JA, Presicce P, Cates C, Rubin R, Chetal K, Du Y, Miao Y, Gu M, Guo M, Kalinichenko VV, Kallapur SG, Miraldi ER, Xu Y, Swarr D, Lewkowich I, Salomonis N, Miller L, Sucre JS, Whitsett JA, Chougnet CA, Jobe AH, Deshmukh H, Zacharias WJ. Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Sci Transl Med 2022; 14: eabl8574. PubMed bioRxiv
- Gokey JJ, Snowball J, Green J, Waltamath M, Spinney JJ, Black KE, Hariri LP, Xu Y, Perl AK. Pretreatment of aged mice with retinoic acid supports alveolar regeneration via upregulation of reciprocal PDGFA signaling.. Thorax 2021; 76: 456-467. thoraxjnl PubMed
- Du Y, Ouyang W, Kitzmiller JA, Guo M, Zhao S, Jeffrey A Whitsett JA, Xu Y. Lung Gene Expression Analysis (LGEA) Web Portal v3: Lung at a Glance. AJRCMB. 2021. AJRCMB PubMed bioRxiv
- Wen B, Li E, Ustiyan V, Wang G, Guo M, Na CL, Kalin GT, Galvan V, Xu Y, Weaver TE, Kalin TV, Whitsett JA, Kalinichenko VV. In Vivo Generation of Lung and Thyroid Tissues from Embryonic Stem Cells Using Blastocyst Complementation. Am J Respir Crit Care Med 2021; 203: 471-483. AJRCMB PubMed
- Wang G, Wen B, Ren X, Li E, Zhang Y, Guo M, Xu Y, Whitsett JA, Kalin TV, Kalinichenko VV. Generation of Pulmonary Endothelial Progenitor Cells for Cell-based Therapy Using Interspecies Mouse-Rat Chimeras. Am J Respir Crit Care Med 2021; 204: 326-338. PubMed
- Sitaraman S, Martin EP, Na CL, Zhao S, Green J, Deshmukh H, Perl AT, Bridges JP, Xu Y, Weaver TE. Surfactant protein C mutation links postnatal type 2 cell dysfunction to adult disease. . JCI Insight 2021; 6. JCI PubMed
- Milewski D, Shukla S, Gryder BE, Pradhan A, Donovan J, Sudha P, Vallabh S, Pyros A, Xu Y, Barski A, Szabo S, Turpin B, Pressey JG, Millay DP, Khan J, Kalinichenko VV, Kalin TV. FOXF1 is required for the oncogenic properties of PAX3-FOXO1 in rhabdomyosarcoma. Oncogene 2021; 40: 2182-2199. Nature PubMed
- Gokey JJ, Snowball J, Sridharan A, Sudha P, Kitzmiller JA, Xu Y, Whitsett JA. YAP regulates alveolar epithelial cell differentiation and AGER via NFIB/KLF5/NKX2-1. iScience 2021; 24: 102967. PubMed
- Sun X, Perl AK, Li R, Bell SM, Sajti E, Kalinichenko VV, Kalin TV, Misra RS, Deshmukh H, Clair G, Kyle J, Crotty Alexander LE, Masso-Silva JA, Kitzmiller JA, Wikenheiser-Brokamp KA, Deutsch G, Guo M, Du Y, Morley MP, Valdez MJ, Yu HV, Jin K, Bardes EE, Zepp JA, Neithamer T, Basil MC, Zacharias WJ, Verheyden J, Young R, Bandyopadhyay G, Lin S, Ansong C, Adkins J, Salomonis N, Aronow BJ, Xu Y, Pryhuber G, Whitsett J, Morrisey EE, Consortium NL. A census of the lung: CellCards from LungMAP. Dev Cell 2022; 57: 112-145 e112. PubMed
- 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. Am J Physiol Lung Cell Mol Physiol 2022; 322: L224-L242. AJPLCMP PubMed
Cite LungGENS, LGEA web portal and Lung at a glance
2. Du Y, Kitzmiller JA, Sridharan A, Perl AK, Bridges JP, Misra RS, Pryhuber GS, Mariani TJ, Bhattacharya S, Guo M, Potter SS, Dexheimer P, Aronow B, Jobe AH, Whitsett JA, Xu Y. Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development. Thorax 2017;72(5):481-84.
3. Du Y, Ouyang W, Kitzmiller JA, Guo M, Zhao S, Whitsett JA, Xu Y. Lung Gene Expression Analysis Web Portal Version 3: Lung-at-a-Glance. Am J Respir Cell Mol Biol. 2021 Jan;64(1):146-149.
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