Thind AS, Monga I, Thakur PK, Kumari P, Dindhoria K, Krzak M, Ranson M, Ashford B (2021) Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology. Brief Bioinform 22(5):bbab259. https://doi.org/10.1093/bib/bbab259
Article CAS PubMed Google Scholar
Jovic D, Liang X, Zeng H, Lin L, Xu F, Luo Y (2022) Single-cell RNA sequencing technologies and applications: a brief overview. Clin Transl Med 12(3):e694. https://doi.org/10.1002/ctm2.694
Article CAS PubMed PubMed Central Google Scholar
Wang X, He Y, Zhang Q, Ren X, Zhang Z (2021) Direct comparative analyses of 10X genomics chromium and smart-seq2. Genom Proteo Bioinform 19(2):253–266. https://doi.org/10.1016/j.gpb.2020.02.005
Wang S, Sun ST, Zhang XY, Ding HR, Yuan Y, He JJ, Wang MS, Yang B, Li YB (2023) The evolution of single-cell RNA sequencing technology and application: progress and perspectives. Int J Mol Sci 24(3):2943. https://doi.org/10.3390/ijms24032943
Article CAS PubMed PubMed Central Google Scholar
Shi P, Nie Y, Yang J, Zhang W, Tang Z, Xu J (2022) Fundamental and practical approaches for single-cell ATAC-seq analysis. aBIOTECH 3(27):212–223. https://doi.org/10.1007/s42994-022-00082-5
Article CAS PubMed PubMed Central Google Scholar
Song HW, Martin J, Shi X, Tyznik AJ (2025) Key considerations on CITE-Seq for single-cell multiomics. Proteomics. https://doi.org/10.1002/pmic.202400011
Article PubMed PubMed Central Google Scholar
Huang Y, Wu Y, Han S, Wang Q, Cong G, Liu Z, Guan S, Huang X, Liu Y, Yin J, Xue J, Liu C (2024) Protocol for optimized nasal mucosa sample processing to obtain high-quality scrna-seq and scatac-seq data. STAR Protoc 5(3):103298. https://doi.org/10.1016/j.xpro.2024.103298
Article CAS PubMed PubMed Central Google Scholar
Geurkink N (1983) Nasal anatomy, physiology, and function. J Allergy Clin Immunol 72(2):123–128. https://doi.org/10.1016/0091-6749(83)90518-3
Article CAS PubMed Google Scholar
Salazar I, Sanchez-Quinteiro P, Barrios AW, López Amado M, Vega JA (2019) Anatomy of the olfactory mucosa. Handb Clin Neurol 164:47–65. https://doi.org/10.1016/B978-0-444-63855-7.00004-6
Lobo J, Zariwala MA, Noone PG (2015) Primary ciliary dyskinesia. Semin Respir Crit Care Med 36(2):169–179. https://doi.org/10.1055/s-0035-1546748
Article PubMed PubMed Central Google Scholar
Deprez M, Zaragosi LE, Truchi M, Becavin C, Ruiz García S, Arguel MJ, Plaisant M, Magnone V, Lebrigand K, Abelanet S, Brau F, Paquet A, Pe’er D, Marquette CH, Leroy S, Barbry P (2020) A single-cell atlas of the human healthy airways. Am J Respir Crit Care Med 202(12):1636–1645. https://doi.org/10.1164/rccm.201911-2199OC
Article CAS PubMed Google Scholar
Huang Y, Wu Y, Han S, Wang Q, Cong G, Liu Z, Guan S, Huang X, Liu Y, Yin J, Xue J, Liu C (2024) Protocol for optimized nasal mucosa sample processing to obtain high-quality scRNA-seq and scATAC-seq data. STAR Protoc 5(20):103298. https://doi.org/10.1016/j.xpro.2024.103298
Article CAS PubMed PubMed Central Google Scholar
Wu CT, Lidsky PV, Xiao Y, Cheng R, Lee IT, Nakayama T, Jiang S, He W, Demeter J, Knight MG, Turn RE, Rojas-Hernandez LS, Ye C, Chiem K, Shon J, Martinez-Sobrido L, Bertozzi CR, Nolan GP, Nayak JV, Milla C, Andino R, Jackson PK (2023) SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming. Cell 186(1):112-130.e20. https://doi.org/10.1016/j.cell.2022.11.030
Article CAS PubMed Google Scholar
Finlay JB, Brann DH, Abi Hachem R, Jang DW, Oliva AD, Ko T, Gupta R, Wellford SA, Moseman EA, Jang SS, Yan CH, Matsunami H, Tsukahara T, Datta SR, Goldstein BJ (2022) Persistent post-COVID-19 smell loss is associated with immune cell infiltration and altered gene expression in olfactory epithelium. Sci Transl Med 14(21):eadd0484. https://doi.org/10.1126/scitranslmed.add0484
Article CAS PubMed PubMed Central Google Scholar
Yeo NK, Jang YJ (2010) Rhinovirus infection-induced alteration of tight junction and adherens junction components in human nasal epithelial cells. Laryngoscope 120(2):346–352. https://doi.org/10.1002/lary.20764
De Boeck I, Wittouck S, Martens K, Claes J, Jorissen M, Steelant B, van den Broek MFL, Seys SF, Hellings PW, Vanderveken OM, Lebeer S (2019) Anterior nares diversity and pathobionts represent sinus microbiome in chronic rhinosinusitis. mSphere 4(27):e00532-19. https://doi.org/10.1128/mSphere.00532-19
Article PubMed PubMed Central Google Scholar
Li M, Bou-Dargham MJ, Yu J, Etwebi Z, Sun H, Chen YH (2021) TIPE polarity proteins are required for mucosal deployment of T lymphocytes and mucosal defense against bacterial infection. Mol Biomed. https://doi.org/10.1186/s43556-021-00059-8
Article PubMed PubMed Central Google Scholar
Ziegler CGK, Allon SJ, Nyquist SK, Mbano IM, Miao VN, Tzouanas CN, Cao Y, Yousif AS, Bals J, Hauser BM, Feldman J, Muus C, Wadsworth MH 2nd, Kazer SW, Hughes TK, Doran B, Gatter GJ, Vukovic M, Taliaferro F, Mead BE, Guo Z, Wang JP, Gras D, Plaisant M, Ansari M, Angelidis I, Adler H, Sucre JMS, Taylor CJ, Lin B, Waghray A, Mitsialis V, Dwyer DF, Buchheit KM, Boyce JA, Barrett NA, Laidlaw TM, Carroll SL, Colonna L, Tkachev V, Peterson CW, Yu A, Zheng HB, Gideon HP, Winchell CG, Lin PL, Bingle CD, Snapper SB, Kropski JA, Theis FJ, Schiller HB, Zaragosi LE, Barbry P, Leslie A, Kiem HP, Flynn JL, Fortune SM, Berger B, Finberg RW, Kean LS, Garber M, Schmidt AG, Lingwood D, Shalek AK, Ordovas-Montanes J; HCA Lung Biological Network. Electronic address: lung-network@humancellatlas.org; HCA Lung Biological Network. SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues. Cell. 2020;181(5):1016–1035.e19. https://doi.org/10.1016/j.cell.2020.04.035.
Wu CT, Lidsky PV, Xiao Y, Cheng R, Lee IT, Nakayama T, Jiang S, He W, Demeter J, Knight MG, Turn RE, Rojas-Hernandez LS, Ye C, Chiem K, Shon J, Martinez-Sobrido L, Bertozzi CR, Nolan GP, Nayak JV, Milla C, Andino R, Jackson PK (2023) SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming. Cell. https://doi.org/10.1016/j.cell.2022.11.030
Article PubMed PubMed Central Google Scholar
Sungnak W, Huang N, Bécavin C, Berg M, Queen R, Litvinukova M, Talavera-López C, Maatz H, Reichart D, Sampaziotis F, Worlock KB, Yoshida M, Barnes JL, HCA Lung Biological Network (2020) SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat Med 26(5):681–687. https://doi.org/10.1038/s41591-020-0868-6
Article CAS PubMed PubMed Central Google Scholar
Xu K, Shi X, Husted C, Hong R, Wang Y, Ning B, Sullivan TB, Rieger-Christ KM, Duan F, Marques H, Gower AC, Xiao X, Liu H, Liu G, Duclos G, Platt M, Spira AE, Mazzilli SA, Billatos E, Lenburg ME, Campbell JD, Beane JE (2022) Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways. Sci Rep. https://doi.org/10.1038/s41598-022-17832-6
Article PubMed PubMed Central Google Scholar
Mettelman RC, Allen EK, Thomas PG (2022) Mucosal immune responses to infection and vaccination in the respiratory tract. Immunity. https://doi.org/10.1016/j.immuni.2022.04.013
Article PubMed PubMed Central Google Scholar
Ziegler CGK, Miao VN, Owings AH, Navia AW, Tang Y, Bromley JD, Lotfy P, Sloan M, Laird H, Williams HB, George M, Drake RS, Christian T, Parker A, Sindel CB, Burger MW, Pride Y, Hasan M, Abraham GE 3rd, Senitko M, Robinson TO, Shalek AK, Glover SC, Horwitz BH, Ordovas-Montanes J (2021) Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19. Cell. https://doi.org/10.1016/j.cell.2021.07.023
Article PubMed PubMed Central Google Scholar
Ziegler CGK, Owings AH, Galeas-Pena M, Kazer SW, Miao VN, Navia AW, Tang Y, Bromley JD, Lotfy P, Sloan M, Laird H, Williams HB, George M, Drake RS, Pride Y, Abraham GE 3rd, Senitko M, Robinson TO, Diamond G, Lionakis MS, Shalek AK, Ordovas-Montanes J, Horwitz BH, Glover SC (2024) An enhanced IL17 and muted type I interferon nasal epithelial cell state characterizes severe COVID-19 with fungal coinfection. Microbiol Spectr. https://doi.org/10.1128/spectrum.03516-23
Article PubMed PubMed Central Google Scholar
Chua RL, Lukassen S, Trump S, Hennig BP, Wendisch D, Pott F, Debnath O, Thürmann L, Kurth F, Völker MT, Kazmierski J, Timmermann B, Twardziok S, Schneider S, Machleidt F, Müller-Redetzky H, Maier M, Krannich A, Schmidt S, Balzer F, Liebig J, Loske J, Suttorp N, Eils J, Ishaque N, Liebert UG, von Kalle C, Hocke A, Witzenrath M, Goffinet C, Drosten C, Laudi S, Lehmann I, Conrad C, Sander LE, Eils R (2020) COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis. Nat Biotechnol 38(8):970–979. https://doi.org/10.1038/s41587-020-0602-4
Article CAS PubMed Google Scholar
Viveiros A, Rasmuson J,
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