Jin Y, Yang H, Ji W, Wu W, Chen S, Zhang W, Duan G: Virology, Epidemiology, Pathogenesis, and Control of COVID-19. Viruses 2020, 12(4).
Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579(7798):270–3.
Article
CAS
Google Scholar
Guan WJ, Ni ZY, Hu Y, Liang WH, Ou CQ, He JX, Liu L, Shan H, Lei CL, Hui DSC et al: Clinical Characteristics of Coronavirus Disease 2019 in China. The New England journal of medicine 2020.
Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y, Qiu Y, Wang J, Liu Y, Wei Y, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020;395(10223):507–13.
Article
CAS
Google Scholar
Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Lancet. 2020;395(10223):497–506.
Article
CAS
Google Scholar
Zhang H, Kang Z, Gong H, Xu D, Wang J, Li Z, Li Z, Cui X, Xiao J, Zhan J, et al. Digestive system is a potential route of COVID-19: an analysis of single-cell coexpression pattern of key proteins in viral entry process. Gut. 2020;69(6):1010–8.
Article
CAS
Google Scholar
Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science (New York, NY). 2020;367(6483):1260–3.
Article
CAS
Google Scholar
Salvatore C, Roberta F, Angela L, Cesare P, Alfredo C, Giuliano G, Giulio L, Giuliana G, Maria RG, Paola BM et al: Clinical and laboratory data, radiological structured report findings and quantitative evaluation of lung involvement on baseline chest CT in COVID-19 patients to predict prognosis. La Radiologia medica 2020.
Xue G, Gan X, Wu Z, Xie D, Xiong Y, Hua L, Zhou B, Zhou N, Xiang J, Li J: Novel serological biomarkers for inflammation in predicting disease severity in patients with COVID-19. International immunopharmacology 2020, 89(Pt A):107065.
McElvaney OJ, Hobbs BD, Qiao D, McElvaney OF, Moll M, McEvoy NL, Clarke J, O'Connor E, Walsh S, Cho MH et al: A linear prognostic score based on the ratio of interleukin-6 to interleukin-10 predicts outcomes in COVID-19. EBioMedicine 2020, 61:103026.
Yang C, Wang J, Liu J, Huang S, Xiong B. Elevated carcinoembryonic antigen in patients with COVID-19 pneumonia. J Cancer Res Clin Oncol. 2020;146(12):3385–8.
Article
CAS
Google Scholar
Chen Q, Kong H, Qi X, Ding W, Ji N, Wu C, Huang C, Wu W, Huang M, Xie W et al: Carcinoembryonic Antigen: A Potential Biomarker to Evaluate the Severity and Prognosis of COVID-19. Frontiers in medicine 2020, 7:579543.
Lachat C, Hawwash D, Ocké MC, Berg C, Forsum E, Hörnell A, Larsson C, Sonestedt E, Wirfält E, Åkesson A et al: Strengthening the Reporting of Observational Studies in Epidemiology-Nutritional Epidemiology (STROBE-nut): An Extension of the STROBE Statement. PLoS medicine 2016, 13(6):e1002036.
Bossuyt PM, Reitsma JB, Bruns DE, Gatsonis CA, Glasziou PP, Irwig LM, Lijmer JG, Moher D, Rennie D, de Vet HC. Towards complete and accurate reporting of studies of diagnostic accuracy: the STARD initiative. Clin Chem Lab Med. 2003;41(1):68–73.
Article
CAS
Google Scholar
Liao M, Liu Y, Yuan J, Wen Y, Xu G, Zhao J, Cheng L, Li J, Wang X, Wang F, et al. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19. Nat Med. 2020;26(6):842–4.
Article
CAS
Google Scholar
Wilk AJ, Rustagi A, Zhao NQ, Roque J, Martínez-Colón GJ, McKechnie JL, Ivison GT, Ranganath T, Vergara R, Hollis T et al: A single-cell atlas of the peripheral immune response in patients with severe COVID-19. Nature medicine 2020.
Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018;36(5):411–20.
Article
CAS
Google Scholar
Chung NC, Storey JD. Statistical significance of variables driving systematic variation in high-dimensional data. Bioinformatics (Oxford, England). 2015;31(4):545–54.
Article
CAS
Google Scholar
Hou R, Denisenko E, Forrest ARR. scMatch: a single-cell gene expression profile annotation tool using reference datasets. Bioinformatics (Oxford, England). 2019;35(22):4688–95.
Article
CAS
Google Scholar
Aran D, Looney AP, Liu L, Wu E, Fong V, Hsu A, Chak S, Naikawadi RP, Wolters PJ, Abate AR, et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol. 2019;20(2):163–72.
Article
CAS
Google Scholar
Zhang X, Lan Y, Xu J, Quan F, Zhao E, Deng C, Luo T, Xu L, Liao G, Yan M, et al. Cell Marker: a manually curated resource of cell markers in human and mouse. Nucleic Acids Res. 2019;47(D1):D721-d728.
Article
CAS
Google Scholar
Qiu X, Mao Q, Tang Y, Wang L, Chawla R, Pliner HA, Trapnell C. Reversed graph embedding resolves complex single-cell trajectories. Nat Methods. 2017;14(10):979–82.
Article
CAS
Google Scholar
Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics. 2013;14:7.
Article
Google Scholar
Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1(6):417–25.
Article
CAS
Google Scholar
Efremova M, Vento-Tormo M, Teichmann SA, Vento-Tormo R. Cell PhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes. Nat Protoc. 2020;15(4):1484–506.
Article
CAS
Google Scholar
Peyser R, MacDonnell S, Gao Y, Cheng L, Kim Y, Kaplan T, Ruan Q, Wei Y, Ni M, Adler C, et al. Defining the Activated Fibroblast Population in Lung Fibrosis Using Single-Cell Sequencing. Am J Respir Cell Mol Biol. 2019;61(1):74–85.
Article
CAS
Google Scholar
Lin SE, Barrette AM, Chapin C, Gonzales LW, Gonzalez RF, Dobbs LG, Ballard PL: Expression of human carcinoembryonic antigen-related cell adhesion molecule 6 and alveolar progenitor cells in normal and injured lungs of transgenic mice. Physiological reports 2015, 3(12).
Fahim A, Crooks MG, Wilmot R, Campbell AP, Morice AH, Hart SP. Serum carcinoembryonic antigen correlates with severity of idiopathic pulmonary fibrosis. Respirology (Carlton, Vic). 2012;17(8):1247–52.
Article
Google Scholar
Ueno F, Kitaguchi Y, Shiina T, Asaka S, Miura K, Yasuo M, Wada Y, Yoshizawa A, Hanaoka M. The Preoperative Composite Physiologic Index May Predict Mortality in Lung Cancer Patients with Combined Pulmonary Fibrosis and Emphysema. Respiration; international review of thoracic diseases. 2017;94(2):198–206.
Article
CAS
Google Scholar
Yu WS, Lee JG, Paik HC, Kim SJ, Lee S, Kim SY, Park MS, Haam S. Carcinoembryonic antigen predicts waitlist mortality in lung transplant candidates with idiopathic pulmonary fibrosis. European journal of cardio-thoracic surgery : official journal of the European Association for Cardio-thoracic Surgery. 2018;54(5):847–52.
Article
Google Scholar
Riley RD, Ensor J, Snell KIE, Harrell FE, Jr., Martin GP, Reitsma JB, Moons KGM, Collins G, van Smeden M: Calculating the sample size required for developing a clinical prediction model. BMJ (Clinical research ed) 2020, 368:m441.
Harrell FE: Regression Modeling Strategies: With Applications to Linear Models, Logistic and Ordinal Regression, and Survival Analysis: Regression Modeling Strategies: With Applications to Linear Models, Logistic and Ordinal Regression, and Survival Analysis; 2015.
Snel B, Lehmann G, Bork P, Huynen MA. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 2000;28(18):3442–4.
Article
CAS
Google Scholar
Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A et al: Proteomics. Tissue-based map of the human proteome. Science (New York, NY) 2015, 347(6220):1260419.
Mafham MM, Spata E, Goldacre R, Gair D, Curnow P, Bray M, Hollings S, Roebuck C, Gale CP, Mamas MA, et al. COVID-19 pandemic and admission rates for and management of acute coronary syndromes in England. Lancet. 2020;396(10248):381–9.
Article
CAS
Google Scholar
Nagant C, Ponthieux F, Smet J, Dauby N, Doyen V, Besse-Hammer T, De Bels D, Maillart E, Corazza F: A score combining early detection of cytokines accurately predicts COVID-19 severity and intensive care unit transfer. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2020.
Pan P, Li Y, Xiao Y, Han B, Su M, Li Y, Zhang S, Jiang D, Chen X, Zhou F et al: Prognostic Assessment of COVID-19 in ICU by Machine Learning Methods: A Retrospective Study. Journal of medical Internet research 2020.
Duffy MJ. Carcinoembryonic antigen as a marker for colorectal cancer: is it clinically useful? Clin Chem. 2001;47(4):624–30.
Article
CAS
Google Scholar
Baranov V, Hammarström S. Carcinoembryonic antigen (CEA) and CEA-related cell adhesion molecule 1 (CEACAM1), apically expressed on human colonic M cells, are potential receptors for microbial adhesion. Histochem Cell Biol. 2004;121(2):83–9.
Article
CAS
Google Scholar
Klaile E, Klassert TE, Scheffrahn I, Müller MM, Heinrich A, Heyl KA, Dienemann H, Grünewald C, Bals R, Singer BB, et al. Carcinoembryonic antigen (CEA)-related cell adhesion molecules are co-expressed in the human lung and their expression can be modulated in bronchial epithelial cells by non-typable Haemophilus influenzae, Moraxella catarrhalis, TLR3, and type I and II interferons. Respir Res. 2013;14(1):85.
Article
Google Scholar
Li X, Ma X. Acute respiratory failure in COVID-19: is it “typical” ARDS? Critical care (London, England). 2020;24(1):198.
Article
Google Scholar
George PM, Wells AU, Jenkins RG. Pulmonary fibrosis and COVID-19: the potential role for antifibrotic therapy. Lancet Respir Med. 2020;8(8):807–15.
Article
CAS
Google Scholar
D’Alessio FR. Mouse Models of Acute Lung Injury and ARDS. Methods in molecular biology (Clifton, NJ). 2018;1809:341–50.
Article
CAS
Google Scholar
Liu T, De Los Santos FG, Phan SH. The Bleomycin Model of Pulmonary Fibrosis. Methods in molecular biology (Clifton, NJ). 2017;1627:27–42.
Article
CAS
Google Scholar
Chan CM, Chu H, Wang Y, Wong BH, Zhao X, Zhou J, Yang D, Leung SP, Chan JF, Yeung ML, et al. Carcinoembryonic Antigen-Related Cell Adhesion Molecule 5 Is an Important Surface Attachment Factor That Facilitates Entry of Middle East Respiratory Syndrome Coronavirus. J Virol. 2016;90(20):9114–27.
Article
CAS
Google Scholar
Kuespert K, Pils S, Hauck CR. CEACAMs: their role in physiology and pathophysiology. Curr Opin Cell Biol. 2006;18(5):565–71.
Article
CAS
Google Scholar
Gray-Owen SD, Blumberg RS. CEACAM1: contact-dependent control of immunity. Nat Rev Immunol. 2006;6(6):433–46.
Article
CAS
Google Scholar
Khairnar V, Duhan V, Maney SK, Honke N, Shaabani N, Pandyra AA, Seifert M, Pozdeev V, Xu HC, Sharma P, et al. CEACAM1 induces B-cell survival and is essential for protective antiviral antibody production. Nat Commun. 2015;6:6217.
Article
CAS
Google Scholar
Ziegler CGK, Allon SJ, Nyquist SK, Mbano IM, Miao VN, Tzouanas CN, Cao Y, Yousif AS, Bals J, Hauser BM, et al. 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.e1019.
Article
CAS
Google Scholar
Takahashi H, Nukiwa T, Matsuoka R, Danbara T, Natori H, Arai T, Kira S. Carcinoembryonic antigen in bronchoalveolar lavage fluid in patients with idiopathic pulmonary fibrosis. Jpn J Med. 1985;24(3):236–43.
Article
CAS
Google Scholar
Hadjiliadis D, Tapson VF, Davis RD, Palmer SM. Prognostic value of serum carcinoembryonic antigen levels in patients who undergo lung transplantation. J Heart Lung Transplant. 2001;20(12):1305–9.
Article
CAS
Google Scholar
Stevens DP, Mackay IR. Increased carcinoembryonic antigen in heavy cigarette smokers. Lancet. 1973;2(7840):1238–9.
Article
CAS
Google Scholar