{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,6]],"date-time":"2025-05-06T13:31:25Z","timestamp":1746538285476,"version":"3.37.3"},"reference-count":96,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T00:00:00Z","timestamp":1716336000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T00:00:00Z","timestamp":1716336000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100003339","name":"Consejo Superior de Investigaciones Cient\u00edficas","doi-asserted-by":"publisher","award":["PIE 202020E108 and SEV 2017-0712"],"award-info":[{"award-number":["PIE 202020E108 and SEV 2017-0712"]}],"id":[{"id":"10.13039\/501100003339","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministerio de Ciencia e Innovaci\u00f3n, Agencia Estatal de Investigaci\u00f3n","award":["PID2020-112758RB-I00 and PDC2021-121534-I00"],"award-info":[{"award-number":["PID2020-112758RB-I00 and PDC2021-121534-I00"]}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["AC17\/00019, PI18\/00154, COV20\/00349, ICI20\/00058, PI21\/00141"],"award-info":[{"award-number":["AC17\/00019, PI18\/00154, COV20\/00349, ICI20\/00058, PI21\/00141"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009947","name":"Merck Sharp and Dohme","doi-asserted-by":"publisher","award":["MISP# IIS 60257"],"award-info":[{"award-number":["MISP# IIS 60257"]}],"id":[{"id":"10.13039\/100009947","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100015756","name":"Spanish Society of Infectious Diseases and Clinical Microbiology","doi-asserted-by":"crossref","award":["Mobility grant"],"award-info":[{"award-number":["Mobility grant"]}],"id":[{"id":"10.13039\/501100015756","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Fundaci\u00f3n Agencia Espa\u00f1ola contra el C\u00e1ncer","award":["AC17\/00022"],"award-info":[{"award-number":["AC17\/00022"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Clin Proteom"],"published-print":{"date-parts":[[2024,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Information on the microbiome's human pathways and active members that can affect SARS-CoV-2 susceptibility and pathogenesis in the salivary proteome is very scarce. Here, we studied a unique collection of samples harvested from April to June 2020 from unvaccinated patients.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>We compared 10 infected and hospitalized patients with severe (<jats:italic>n<\/jats:italic>\u2009=\u20095) and moderate (<jats:italic>n<\/jats:italic>\u2009=\u20095) coronavirus disease (COVID-19) with 10 uninfected individuals, including non-COVID-19 but susceptible individuals (<jats:italic>n<\/jats:italic>\u2009=\u20095) and non-COVID-19 and nonsusceptible healthcare workers with repeated high-risk exposures (<jats:italic>n<\/jats:italic>\u2009=\u20095).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>By performing high-throughput proteomic profiling in saliva samples, we detected 226 unique differentially expressed (DE) human proteins between groups (q-value\u2009\u2264\u20090.05) out of 3376 unambiguously identified proteins (false discovery rate\u2009\u2264\u20091%). Major differences were observed between the non-COVID-19 and nonsusceptible groups. Bioinformatics analysis of DE proteins revealed human proteomic signatures related to inflammatory responses, central cellular processes, and antiviral activity associated with the saliva of SARS-CoV-2-infected patients (p-value\u2009\u2264\u20090.0004). Discriminatory biomarker signatures from human saliva include cystatins, protective molecules present in the oral cavity, calprotectins, involved in cell cycle progression, and histones, related to nucleosome functions. The expression levels of two human proteins related to protein transport in the cytoplasm, DYNC1 (p-value, 0.0021) and MAPRE1 (p-value, 0.047), correlated with angiotensin-converting enzyme 2 (ACE2) plasma activity. Finally, the proteomes of microorganisms present in the saliva samples showed 4 main microbial functional features related to ribosome functioning that were overrepresented in the infected group.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>Our study explores potential candidates involved in pathways implicated in SARS-CoV-2 susceptibility, although further studies in larger cohorts will be necessary.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Graphical Abstract<\/jats:title>\n                \n              <\/jats:sec>","DOI":"10.1186\/s12014-024-09482-9","type":"journal-article","created":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T14:02:13Z","timestamp":1716386533000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Proteomic snapshot of saliva samples predicts new pathways implicated in SARS-CoV-2 pathogenesis"],"prefix":"10.1186","volume":"21","author":[{"given":"Elena","family":"Moreno","sequence":"first","affiliation":[]},{"given":"Sergio","family":"Ciordia","sequence":"additional","affiliation":[]},{"given":"Santos Milhano","family":"F\u00e1tima","sequence":"additional","affiliation":[]},{"given":"Daniel","family":"Jim\u00e9nez","sequence":"additional","affiliation":[]},{"given":"Javier","family":"Mart\u00ednez-Sanz","sequence":"additional","affiliation":[]},{"given":"Pilar","family":"Vizcarra","sequence":"additional","affiliation":[]},{"given":"Raquel","family":"Ron","sequence":"additional","affiliation":[]},{"given":"Matilde","family":"S\u00e1nchez-Conde","sequence":"additional","affiliation":[]},{"given":"Rafael","family":"Bargiela","sequence":"additional","affiliation":[]},{"given":"Sergio","family":"Sanchez-Carrillo","sequence":"additional","affiliation":[]},{"given":"Santiago","family":"Moreno","sequence":"additional","affiliation":[]},{"given":"Fernando","family":"Corrales","sequence":"additional","affiliation":[]},{"given":"Manuel","family":"Ferrer","sequence":"additional","affiliation":[]},{"given":"Sergio","family":"Serrano-Villar","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2024,5,22]]},"reference":[{"key":"9482_CR1","doi-asserted-by":"publisher","first-page":"94","DOI":"10.14639\/0392-100X-1598","volume":"37","author":"M Castagnola","year":"2017","unstructured":"Castagnola M, Scarano E, Passali GCC, Messana I, et al. Salivary biomarkers and proteomics: future diagnostic and clinical utilities. Acta Otorhinolaryngol Ital. 2017;37:94\u2013101.","journal-title":"Acta Otorhinolaryngol Ital"},{"key":"9482_CR2","doi-asserted-by":"publisher","first-page":"1510","DOI":"10.1177\/00220345211014432","volume":"100","author":"WW Lau","year":"2021","unstructured":"Lau WW, Hardt M, Zhang YH, Freire M, Ruhl S. The human salivary proteome wiki: a community-driven research platform. J Dent Res. 2021;100:1510\u20139.","journal-title":"J Dent Res"},{"key":"9482_CR3","doi-asserted-by":"publisher","first-page":"1016","DOI":"10.1177\/154405910808701104","volume":"87","author":"BJF Keijser","year":"2008","unstructured":"Keijser BJF, Zaura E, Huse SM, van der Vossen JMBM, Schuren FHJ, Montijn RC, ten Cate JM, Crielaard W, et al. Pyrosequencing analysis of the Oral Microflora of healthy adults. J Dental Res. 2008;87:1016\u201320.","journal-title":"J Dental Res"},{"key":"9482_CR4","doi-asserted-by":"publisher","first-page":"636","DOI":"10.1101\/gr.084616.108","volume":"19","author":"I Nasidze","year":"2009","unstructured":"Nasidze I, Li J, Quinque D, Tang K, Stoneking M. Global diversity in the human salivary microbiome. Genome Res. 2009;19:636\u201343.","journal-title":"Genome Res"},{"key":"9482_CR5","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1038\/ismej.2010.30","volume":"4","author":"EM Bik","year":"2010","unstructured":"Bik EM, Long CD, Armitage GC, Loomer P, et al. Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J. 2010;4:962\u201374.","journal-title":"ISME J"},{"key":"9482_CR6","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1186\/1471-2180-9-259","volume":"9","author":"E Zaura","year":"2009","unstructured":"Zaura E, Keijser BJF, Huse SM, Crielaard W. Defining the healthy \u201ccore microbiome\u201d of oral microbial communities. BMC Microbiol. 2009;9:259.","journal-title":"BMC Microbiol"},{"key":"9482_CR7","doi-asserted-by":"publisher","first-page":"887907","DOI":"10.3389\/fcimb.2022.887907","volume":"12","author":"DG Moussa","year":"2022","unstructured":"Moussa DG, Ahmad P, Mansour TA, Siqueira WL. Current state and challenges of the global outcomes of dental caries research in the meta-omics era. Front Cell Infect Microbiol. 2022;12:887907.","journal-title":"Front Cell Infect Microbiol"},{"key":"9482_CR8","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1111\/j.2041-1014.2009.00558.x","volume":"25","author":"JDD Rudney","year":"2010","unstructured":"Rudney JDD, Xie H, Rhodus NLL, Ondrey FGG, Griffin TJJ. A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry. Mol Oral Microbiol. 2010;25:38\u201349.","journal-title":"Mol Oral Microbiol"},{"key":"9482_CR9","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.n436","author":"AH Attaway","year":"2021","unstructured":"Attaway AH, Scheraga RG, Bhimraj A, Biehl M, Hatipo\u011flu U. Severe covid-19 pneumonia: pathogenesis and clinical management. BMJ. 2021. https:\/\/doi.org\/10.1136\/bmj.n436.","journal-title":"BMJ"},{"key":"9482_CR10","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1186\/s12985-021-01578-0","volume":"18","author":"B Shakaib","year":"2021","unstructured":"Shakaib B, Zohra T, Ikram A, Shakaib MB, et al. A comprehensive review on clinical and mechanistic pathophysiological aspects of COVID-19 Malady: how far have we come? Virol J. 2021;18:120.","journal-title":"Virol J"},{"key":"9482_CR11","doi-asserted-by":"publisher","first-page":"4165","DOI":"10.1021\/acs.jproteome.1c00506","volume":"20","author":"D-G Mun","year":"2021","unstructured":"Mun D-G, Vanderboom PM, Madugundu AK, Garapati K, et al. DIA-based proteome profiling of nasopharyngeal swabs from COVID-19 patients. J Proteome Res. 2021;20:4165\u201375.","journal-title":"J Proteome Res"},{"key":"9482_CR12","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09234-6","author":"Y Zhou","year":"2019","unstructured":"Zhou Y, Zhou B, Pache L, Chang M, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019. https:\/\/doi.org\/10.1038\/s41467-019-09234-6.","journal-title":"Nat Commun"},{"key":"9482_CR13","doi-asserted-by":"publisher","first-page":"858","DOI":"10.1016\/j.chom.2019.05.002","volume":"25","author":"D Hotter","year":"2019","unstructured":"Hotter D, Bosso M, J\u00f8nsson KL, Krapp C, et al. IFI16 targets the transcription factor Sp1 to suppress HIV-1 transcription and latency reactivation. Cell Host Microbe. 2019;25:858-872.e13.","journal-title":"Cell Host Microbe"},{"key":"9482_CR14","doi-asserted-by":"publisher","first-page":"3007","DOI":"10.1042\/CS20200970","volume":"134","author":"F Ren","year":"2020","unstructured":"Ren F, Ren J-H, Song C-L, Tan M, et al. LncRNA HOTAIR modulates hepatitis B virus transcription and replication by enhancing SP1 transcription factor. Clin Sci. 2020;134:3007\u201322.","journal-title":"Clin Sci"},{"key":"9482_CR15","doi-asserted-by":"publisher","first-page":"11723","DOI":"10.1128\/JVI.01322-08","volume":"82","author":"MI Khalil","year":"2008","unstructured":"Khalil MI, Hay J, Ruyechan WT. Cellular transcription factors Sp1 and Sp3 suppress varicella-zoster virus origin-dependent DNA replication. J Virol. 2008;82:11723\u201333.","journal-title":"J Virol"},{"key":"9482_CR16","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00853-21","volume":"95","author":"J Xu","year":"2021","unstructured":"Xu J, Mao J, Han X, Shi F, et al. Porcine epidemic diarrhea virus inhibits HDAC1 expression to facilitate its replication via binding of its nucleocapsid protein to host transcription factor Sp1. J Virol. 2021;95: e0085321.","journal-title":"J Virol"},{"key":"9482_CR17","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/j.ymthe.2005.09.010","volume":"13","author":"C-H Nam","year":"2006","unstructured":"Nam C-H, Rabbitts TH. The role of LMO2 in development and in T cell leukemia after chromosomal translocation or retroviral insertion. Mol Ther. 2006;13:15\u201325.","journal-title":"Mol Ther"},{"key":"9482_CR18","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1038\/sj.leu.2404563","volume":"21","author":"K Pike-Overzet","year":"2007","unstructured":"Pike-Overzet K, de Ridder D, Weerkamp F, Baert MRM, et al. Ectopic retroviral expression of LMO2, but not IL2R\u03b3, blocks human T-cell development from CD34+ cells: implications for leukemogenesis in gene therapy. Leukemia. 2007;21:754\u201363.","journal-title":"Leukemia"},{"key":"9482_CR19","doi-asserted-by":"crossref","unstructured":"Hesari A, Ghasemi F, Salarinia R, Biglari H, Tabar Molla Hassan A, Abdoli V, Mirzaei H. Effects of curcumin on NF-\u03baB, AP- 2018, 119: 7898","DOI":"10.1002\/jcb.26829"},{"key":"9482_CR20","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1186\/s13567-019-0697-0","volume":"50","author":"C-Y Cheng","year":"2019","unstructured":"Cheng C-Y, Tseng H-H, Chiu H-C, Chang C-D, et al. Bovine ephemeral fever virus triggers autophagy enhancing virus replication via upregulation of the Src\/JNK\/AP1 and PI3K\/Akt\/NF-\u03baB pathways and suppression of the PI3K\/Akt\/mTOR pathway. Vet Res. 2019;50:79.","journal-title":"Vet Res"},{"key":"9482_CR21","doi-asserted-by":"publisher","first-page":"e00055","DOI":"10.1128\/Spectrum.00055-21","volume":"9","author":"EH Miller","year":"2021","unstructured":"Miller EH, Annavajhala MK, Chong AM, Park H, et al. Oral microbiome alterations and SARS-CoV-2 saliva viral load in patients with COVID-19. Microbiol Spectr. 2021;9:e00055-e121.","journal-title":"Microbiol Spectr"},{"key":"9482_CR22","doi-asserted-by":"publisher","first-page":"698","DOI":"10.1136\/gutjnl-2020-323020","volume":"70","author":"YK Yeoh","year":"2021","unstructured":"Yeoh YK, Zuo T, Lui GC-Y, Zhang F, et al. Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19. Gut. 2021;70:698\u2013706.","journal-title":"Gut"},{"key":"9482_CR23","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1038\/s41522-021-00254-z","volume":"7","author":"AJS Armstrong","year":"2021","unstructured":"Armstrong AJS, Parmar V, Blaser MJ. Assessing saliva microbiome collection and processing methods. npj Biofilms Microb. 2021;7:81.","journal-title":"npj Biofilms Microb"},{"key":"9482_CR24","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1053\/j.gastro.2020.05.048","volume":"159","author":"T Zuo","year":"2020","unstructured":"Zuo T, Zhang F, Lui GCY, Yeoh YK, et al. Alterations in gut microbiota of patients with COVID-19 during time of hospitalization. Gastroenterology. 2020;159:944-955.e8.","journal-title":"Gastroenterology"},{"key":"9482_CR25","doi-asserted-by":"publisher","first-page":"338881","DOI":"10.1016\/j.aca.2021.338881","volume":"1180","author":"F He","year":"2021","unstructured":"He F, Zhang T, Xue K, Fang Z, et al. Fecal multi-omics analysis reveals diverse molecular alterations of gut ecosystem in COVID-19 patients. Anal Chim Acta. 2021;1180:338881.","journal-title":"Anal Chim Acta"},{"key":"9482_CR26","doi-asserted-by":"publisher","first-page":"103723","DOI":"10.1016\/j.ebiom.2021.103723","volume":"74","author":"W Zhong","year":"2021","unstructured":"Zhong W, Altay O, Arif M, Edfors F, et al. Next generation plasma proteome profiling of COVID-19 patients with mild to moderate symptoms. EBioMedicine. 2021;74:103723.","journal-title":"EBioMedicine"},{"key":"9482_CR27","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0274228","volume":"17","author":"MA Ayass","year":"2022","unstructured":"Ayass MA, Cao W, Zhang J, Dai J, et al. Noninvasive nasopharyngeal proteomics of COVID-19 patient identify abnormalities related to complement and coagulation cascade and mucosal immune system. PLoS ONE. 2022;17: e0274228.","journal-title":"PLoS ONE"},{"key":"9482_CR28","doi-asserted-by":"publisher","first-page":"101177","DOI":"10.1016\/j.xpro.2022.101177","volume":"3","author":"A Banerjee","year":"2022","unstructured":"Banerjee A, Pai MGJ, Singh A, Nissa MU, Srivastava S. Mass spectrometry and proteome analysis to identify SARS-CoV-2 protein from COVID-19 patient swab samples. STAR Protoc. 2022;3:101177.","journal-title":"STAR Protoc"},{"key":"9482_CR29","doi-asserted-by":"publisher","first-page":"4407","DOI":"10.1021\/acs.jproteome.0c00535","volume":"19","author":"D Gouveia","year":"2020","unstructured":"Gouveia D, Miotello G, Gallais F, Gaillard J-C, et al. Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window. J Proteome Res. 2020;19:4407\u201316.","journal-title":"J Proteome Res"},{"key":"9482_CR30","doi-asserted-by":"publisher","first-page":"8601","DOI":"10.1021\/acsomega.1c06551","volume":"7","author":"S Ghosh","year":"2022","unstructured":"Ghosh S, Parikh S, Nissa MU, Acharjee A, et al. Semen proteomics of COVID-19 convalescent men reveals disruption of key biological pathways relevant to male reproductive function. ACS Omega. 2022;7:8601\u201312.","journal-title":"ACS Omega"},{"key":"9482_CR31","first-page":"326","volume":"5","author":"V Fanelli","year":"2013","unstructured":"Fanelli V, Vlachou A, Ghannadian S, Simonetti U, et al. Acute respiratory distress syndrome: new definition, current and future therapeutic options. J Thorac Dis. 2013;5:326\u201334.","journal-title":"J Thorac Dis"},{"key":"9482_CR32","doi-asserted-by":"publisher","first-page":"64","DOI":"10.3390\/biochem2010005","volume":"2","author":"L Pagani","year":"2022","unstructured":"Pagani L, Chinello C, Mahajneh A, Clerici F, et al. Untargeted mass spectrometry approach to study SARS-CoV-2 proteins in human plasma and saliva proteome. BioChem. 2022;2:64\u201383.","journal-title":"BioChem"},{"key":"9482_CR33","doi-asserted-by":"publisher","first-page":"444","DOI":"10.3389\/fphys.2018.00444","volume":"9","author":"E Pappa","year":"2018","unstructured":"Pappa E, Vastardis H, Mermelekas G, Gerasimidi-Vazeou A, et al. Saliva Proteomics analysis offers insights on type 1 diabetes pathology in a pediatric population. Front Physiol. 2018;9:444.","journal-title":"Front Physiol"},{"key":"9482_CR34","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1021\/pr8003776","volume":"8","author":"PV Rao","year":"2009","unstructured":"Rao PV, Reddy AP, Lu X, Dasari S, et al. Proteomic identification of salivary biomarkers of type-2 diabetes. J Proteome Res. 2009;8:239\u201345.","journal-title":"J Proteome Res"},{"key":"9482_CR35","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1023\/B:MCBI.0000028748.40917.6f","volume":"261","author":"AD Mata","year":"2004","unstructured":"Mata AD, Marques D, Rocha S, Francisco H, et al. Effects of diabetes mellitus on salivary secretion and its composition in the human. Mol Cell Biochem. 2004;261:137\u201342.","journal-title":"Mol Cell Biochem"},{"key":"9482_CR36","doi-asserted-by":"publisher","first-page":"4331","DOI":"10.1007\/s00394-021-02584-2","volume":"60","author":"C Chambon","year":"2021","unstructured":"Chambon C, Neyraud E, Sayd T, Bros P, et al. The salivary proteome reflects some traits of dietary habits in diabetic and non-diabetic older adults. Eur J Nutr. 2021;60:4331\u201344.","journal-title":"Eur J Nutr"},{"key":"9482_CR37","doi-asserted-by":"publisher","first-page":"605","DOI":"10.3233\/JAD-220246","volume":"89","author":"C Contini","year":"2022","unstructured":"Contini C, Serrao S, Manconi B, Olianas A, et al. Salivary proteomics reveals significant changes in relation to Alzheimer\u2019s disease and aging. JAD. 2022;89:605\u201322.","journal-title":"JAD"},{"key":"9482_CR38","doi-asserted-by":"publisher","first-page":"790091","DOI":"10.3389\/fmolb.2021.790091","volume":"8","author":"SY Jia","year":"2021","unstructured":"Jia SY, Zhang YL, Sun XY, Yuan C, Zheng SG. Impact of the glycemic level on the salivary proteome of middle-aged and elderly people with type 2 diabetes mellitus: an observational study. Front Mol Biosci. 2021;8:790091.","journal-title":"Front Mol Biosci"},{"key":"9482_CR39","doi-asserted-by":"publisher","first-page":"56","DOI":"10.2174\/1567205015666181022094924","volume":"16","author":"M Fran\u00e7ois","year":"2018","unstructured":"Fran\u00e7ois M, Bull CF, Fenech MF, Leifert WR. Current state of saliva biomarkers for aging and Alzheimer\u2019s disease. CAR. 2018;16:56\u201366.","journal-title":"CAR"},{"key":"9482_CR40","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1172\/JCI27883","volume":"116","author":"N Zelcer","year":"2006","unstructured":"Zelcer N, Tontonoz P. Liver X receptors as integrators of metabolic and inflammatory signaling. J Clin Invest. 2006;116:607\u201314.","journal-title":"J Clin Invest"},{"key":"9482_CR41","doi-asserted-by":"publisher","first-page":"895","DOI":"10.3892\/mmr.2012.758","volume":"5","author":"R Zhu","year":"2012","unstructured":"Zhu R, Ou Z, Ruan X, Gong J. Role of liver X receptors in cholesterol efflux and inflammatory signaling (review). Mol Med Rep. 2012;5:895\u2013900.","journal-title":"Mol Med Rep"},{"key":"9482_CR42","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1038\/s41421-022-00441-y","volume":"8","author":"X Tang","year":"2022","unstructured":"Tang X, Sun R, Ge W, Mao T, et al. Enhanced inflammation and suppressed adaptive immunity in COVID-19 with prolonged RNA shedding. Cell Discov. 2022;8:70.","journal-title":"Cell Discov"},{"key":"9482_CR43","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1016\/j.cell.2020.11.025","volume":"184","author":"R Karki","year":"2021","unstructured":"Karki R, Sharma BR, Tuladhar S, Williams EP, et al. Synergism of TNF-\u03b1 and IFN-\u03b3 triggers inflammatory cell death, tissue damage, and mortality in SARS-CoV-2 infection and cytokine shock syndromes. Cell. 2021;184:149-168.e17.","journal-title":"Cell"},{"key":"9482_CR44","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1016\/j.freeradbiomed.2021.06.018","volume":"172","author":"N Saheb Sharif-Askari","year":"2021","unstructured":"Saheb Sharif-Askari N, Saheb Sharif-Askari F, Mdkhana B, Hussain Alsayed HA, et al. Upregulation of oxidative stress gene markers during SARS-COV-2 viral infection. Free Radical Biol Med. 2021;172:688\u201398.","journal-title":"Free Radical Biol Med"},{"key":"9482_CR45","doi-asserted-by":"publisher","first-page":"1401","DOI":"10.1016\/j.cell.2020.08.002","volume":"182","author":"A Silvin","year":"2020","unstructured":"Silvin A, Chapuis N, Dunsmore G, Goubet A-G, et al. Elevated calprotectin and abnormal myeloid cell subsets discriminate severe from mild COVID-19. Cell. 2020;182:1401-1418.e18.","journal-title":"Cell"},{"key":"9482_CR46","doi-asserted-by":"publisher","first-page":"775","DOI":"10.3390\/jcm10040775","volume":"10","author":"R Udeh","year":"2021","unstructured":"Udeh R, Advani S, de Guadiana Romualdo LG, Dolja-Gore X. Calprotectin, an emerging biomarker of interest in COVID-19: a systematic review and meta-analysis. J Clin Med. 2021;10:775.","journal-title":"J Clin Med"},{"key":"9482_CR47","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1016\/j.cellimm.2010.03.012","volume":"263","author":"S Salmen","year":"2010","unstructured":"Salmen S, Colmenares M, Peterson DL, Reyes E, et al. HIV-1 Nef associates with p22-phox, a component of the NADPH oxidase protein complex. Cell Immunol. 2010;263:166\u201371.","journal-title":"Cell Immunol"},{"key":"9482_CR48","doi-asserted-by":"publisher","first-page":"1298","DOI":"10.3389\/fimmu.2018.01298","volume":"9","author":"S Wang","year":"2018","unstructured":"Wang S, Song R, Wang Z, Jing Z, et al. S100A8\/A9 in inflammation. Front Immunol. 2018;9:1298.","journal-title":"Front Immunol"},{"key":"9482_CR49","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1124\/jpet.107.120758","volume":"324","author":"AA Sauve","year":"2008","unstructured":"Sauve AA. NAD + and vitamin B 3: from metabolism to therapies. J Pharmacol Exp Ther. 2008;324:883\u201393.","journal-title":"J Pharmacol Exp Ther"},{"key":"9482_CR50","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1007\/s00109-021-02175-y","volume":"100","author":"IC Schultz","year":"2022","unstructured":"Schultz IC, Bertoni APS, Wink MR. Purinergic signaling elements are correlated with coagulation players in peripheral blood and leukocyte samples from COVID-19 patients. J Mol Med. 2022;100:569\u201384.","journal-title":"J Mol Med"},{"key":"9482_CR51","doi-asserted-by":"publisher","first-page":"4313","DOI":"10.2147\/JIR.S322430","volume":"14","author":"A Alaiya","year":"2021","unstructured":"Alaiya A, Alshukairi A, Shinwari Z, Al-Fares M, et al. Alterations in the plasma proteome induced by SARS-CoV-2 and MERS-CoV reveal biomarkers for disease outcomes for COVID-19 patients. J Inflamm Res. 2021;14:4313\u201328.","journal-title":"J Inflamm Res"},{"key":"9482_CR52","doi-asserted-by":"publisher","first-page":"1318","DOI":"10.1038\/nm.2053","volume":"15","author":"J Xu","year":"2009","unstructured":"Xu J, Zhang X, Pelayo R, Monestier M, et al. Extracellular histones are major mediators of death in sepsis. Nat Med. 2009;15:1318\u201321.","journal-title":"Nat Med"},{"key":"9482_CR53","doi-asserted-by":"publisher","first-page":"7044","DOI":"10.1128\/MCB.23.19.7044-7054.2003","volume":"23","author":"A Bedalov","year":"2003","unstructured":"Bedalov A, Hirao M, Posakony J, Nelson M, Simon JA. NAD+-dependent deacetylase Hst1p controls biosynthesis and cellular NAD+ levels in Saccharomyces cerevisiae. Mol Cell Biol. 2003;23:7044\u201354.","journal-title":"Mol Cell Biol"},{"key":"9482_CR54","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1021\/acs.jproteome.1c00786","volume":"21","author":"OE Alb\u00f3niga","year":"2022","unstructured":"Alb\u00f3niga OE, Jim\u00e9nez D, S\u00e1nchez-Conde M, Vizcarra P, et al. Metabolic snapshot of plasma samples reveals new pathways implicated in SARS-CoV-2 pathogenesis. J Proteom Res. 2022;21:623.","journal-title":"J Proteom Res"},{"key":"9482_CR55","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2013.00148","author":"M Kongsbak","year":"2013","unstructured":"Kongsbak M, Levring TB, Geisler C, von Essen MR. The vitamin D receptor and T cell function. Front Immunol. 2013. https:\/\/doi.org\/10.3389\/fimmu.2013.00148.","journal-title":"Front Immunol"},{"key":"9482_CR56","doi-asserted-by":"publisher","first-page":"5474","DOI":"10.4049\/jimmunol.159.11.5474","volume":"159","author":"Y Ohmori","year":"1997","unstructured":"Ohmori Y, Hamilton TA. IL-4-induced STAT6 suppresses IFN-gamma-stimulated STAT1-dependent transcription in mouse macrophages. J Immunol. 1997;159:5474\u201382.","journal-title":"J Immunol"},{"key":"9482_CR57","doi-asserted-by":"publisher","first-page":"41974","DOI":"10.18632\/oncotarget.9633","volume":"7","author":"S-F Hendrayani","year":"2016","unstructured":"Hendrayani S-F, Al-Harbi B, Al-Ansari MM, Silva G, Aboussekhra A. The inflammatory\/cancer-related IL-6\/STAT3\/NF-\u03baB positive feedback loop includes AUF1 and maintains the active state of breast myofibroblasts. Oncotarget. 2016;7:41974\u201385.","journal-title":"Oncotarget"},{"key":"9482_CR58","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1007\/s40620-021-01173-0","volume":"35","author":"F Salem","year":"2022","unstructured":"Salem F, Li XZ, Hindi J, Casablanca NM, et al. Activation of STAT3 signaling pathway in the kidney of COVID-19 patients. J Nephrol. 2022;35:735\u201343.","journal-title":"J Nephrol"},{"key":"9482_CR59","doi-asserted-by":"publisher","first-page":"12864","DOI":"10.1111\/jcmm.15838","volume":"24","author":"I Shamir","year":"2020","unstructured":"Shamir I, Abutbul-Amitai M, Abbas-Egbariya H, Pasmanik-Chor M, et al. STAT3 isoforms differentially affect ACE2 expression: a potential target for COVID-19 therapy. J Cell Mol Med. 2020;24:12864\u20138.","journal-title":"J Cell Mol Med"},{"key":"9482_CR60","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1038\/s41418-021-00866-0","volume":"29","author":"C Musiu","year":"2022","unstructured":"Musiu C, Caligola S, Fiore A, Lamolinara A, et al. Fatal cytokine release syndrome by an aberrant FLIP\/STAT3 axis. Cell Death Differ. 2022;29:420\u201338.","journal-title":"Cell Death Differ"},{"key":"9482_CR61","doi-asserted-by":"publisher","first-page":"104780","DOI":"10.1016\/j.compbiomed.2021.104780","volume":"137","author":"A Dhall","year":"2021","unstructured":"Dhall A, Patiyal S, Sharma N, Devi NL, Raghava GPS. Computer-aided prediction of inhibitors against STAT3 for managing COVID-19 associated cytokine storm. Comput Biol Med. 2021;137:104780.","journal-title":"Comput Biol Med"},{"key":"9482_CR62","doi-asserted-by":"publisher","first-page":"104836","DOI":"10.1016\/j.micpath.2021.104836","volume":"154","author":"A Jafarzadeh","year":"2021","unstructured":"Jafarzadeh A, Nemati M, Jafarzadeh S. Contribution of STAT3 to the pathogenesis of COVID-19. Microb Pathog. 2021;154:104836.","journal-title":"Microb Pathog"},{"key":"9482_CR63","doi-asserted-by":"publisher","first-page":"390","DOI":"10.1016\/j.drudis.2021.10.016","volume":"27","author":"BK Gajjela","year":"2022","unstructured":"Gajjela BK, Zhou M-M. Calming the cytokine storm of COVID-19 through inhibition of JAK2\/STAT3 signaling. Drug Discov Today. 2022;27:390\u2013400.","journal-title":"Drug Discov Today"},{"key":"9482_CR64","doi-asserted-by":"publisher","first-page":"3088","DOI":"10.1128\/JVI.05901-11","volume":"86","author":"H Yu","year":"2012","unstructured":"Yu H, Lu J, Zuo L, Yan Q, et al. Epstein-Barr virus downregulates microRNA 203 through the oncoprotein latent membrane protein 1: a contribution to increased tumor incidence in epithelial cells. J Virol. 2012;86:3088\u201399.","journal-title":"J Virol"},{"key":"9482_CR65","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1186\/1750-9378-8-24","volume":"8","author":"KZ Hemmaid","year":"2013","unstructured":"Hemmaid KZ, Awadalla A, Elsawy E, Hussein A-AM, et al. Impact of Hepatitis C Virus (HCV) infection on biomolecular markers influencing the pathogenesis of bladder cancer. Infect Agents Cancer. 2013;8:24.","journal-title":"Infect Agents Cancer"},{"key":"9482_CR66","doi-asserted-by":"publisher","first-page":"3618","DOI":"10.1074\/jbc.RA118.003744","volume":"294","author":"M Santerre","year":"2019","unstructured":"Santerre M, Bagashev A, Gorecki L, Lysek KZ, et al. HIV-1 Tat protein promotes neuronal dysregulation by inhibiting E2F transcription factor 3 (E2F3). J Biol Chem. 2019;294:3618\u201333.","journal-title":"J Biol Chem"},{"key":"9482_CR67","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1097\/IGC.0000000000000399","volume":"25","author":"D Geng","year":"2015","unstructured":"Geng D, Song X, Ning F, Song Q, Yin H. MiR-34a inhibits viability and invasion of human papillomavirus-positive cervical cancer cells by targeting E2F3 and regulating survivin. Int J Gynecol Cancer. 2015;25:707\u201313.","journal-title":"Int J Gynecol Cancer"},{"key":"9482_CR68","doi-asserted-by":"publisher","first-page":"10936","DOI":"10.3390\/ijms222010936","volume":"22","author":"MC Park","year":"2021","unstructured":"Park MC, Kim H, Choi H, Chang MS, Lee SK. Epstein-barr virus miR-BART1\u20133p regulates the miR-17\u201392 cluster by targeting E2F3. Int J Mol Sci. 2021;22:10936.","journal-title":"Int J Mol Sci"},{"key":"9482_CR69","first-page":"77","volume":"39","author":"WGW Pathirana","year":"2018","unstructured":"Pathirana WGW, Chubb SP, Gillett MJ, Vasikaran SD. Faecal Calprotectin. Clin Biochem Rev. 2018;39:77\u201390.","journal-title":"Clin Biochem Rev"},{"key":"9482_CR70","doi-asserted-by":"publisher","first-page":"1031","DOI":"10.1177\/0960327120909530","volume":"39","author":"F Shabani","year":"2020","unstructured":"Shabani F, Mahdavi M, Imani M, Hosseinpour-Feizi MAA, Gheibi N. Calprotectin (S100A8\/S100A9)-induced cytotoxicity and apoptosis in human gastric cancer AGS cells: alteration in expression levels of Bax, Bcl-2, and ERK2. Hum Exp Toxicol. 2020;39:1031\u201345.","journal-title":"Hum Exp Toxicol"},{"key":"9482_CR71","doi-asserted-by":"publisher","first-page":"2749","DOI":"10.1007\/s00018-017-2526-9","volume":"74","author":"R Donato","year":"2017","unstructured":"Donato R, Sorci G, Giambanco I. S100A6 protein: functional roles. Cell Mol Life Sci. 2017;74:2749\u201360.","journal-title":"Cell Mol Life Sci"},{"key":"9482_CR72","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/j.jconrel.2006.04.013","volume":"113","author":"M Kaouass","year":"2006","unstructured":"Kaouass M, Beaulieu R, Balicki D. Histonefection: novel and potent non-viral gene delivery. J Control Release. 2006;113:245\u201354.","journal-title":"J Control Release"},{"key":"9482_CR73","doi-asserted-by":"publisher","first-page":"23156","DOI":"10.1016\/S0021-9258(17)31633-2","volume":"269","author":"M Balb\u00edn","year":"1994","unstructured":"Balb\u00edn M, Hall A, Grubb A, Mason RW, et al. Structural and functional characterization of two allelic variants of human cystatin D sharing a characteristic inhibition spectrum against mammalian cysteine proteinases. J Biol Chem. 1994;269:23156\u201362.","journal-title":"J Biol Chem"},{"key":"9482_CR74","first-page":"189","volume":"42","author":"X Zhou","year":"2019","unstructured":"Zhou X, Wang X, Huang K, Liao X, et al. Investigation of the clinical significance and prospective molecular mechanisms of cystatin genes in patients with hepatitis B virus-related hepatocellular carcinoma. Oncol Rep. 2019;42:189\u2013201.","journal-title":"Oncol Rep"},{"key":"9482_CR75","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1007\/s40620-021-01139-2","volume":"35","author":"A Zinellu","year":"2022","unstructured":"Zinellu A, Mangoni AA. Cystatin C, COVID-19 severity and mortality: a systematic review and meta-analysis. J Nephrol. 2022;35:59\u201368.","journal-title":"J Nephrol"},{"key":"9482_CR76","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1038\/s41467-021-21414-x","volume":"12","author":"MR Neeland","year":"2021","unstructured":"Neeland MR, Bannister S, Clifford V, Dohle K, et al. Innate cell profiles during the acute and convalescent phase of SARS-CoV-2 infection in children. Nat Commun. 2021;12:1084.","journal-title":"Nat Commun"},{"key":"9482_CR77","doi-asserted-by":"publisher","first-page":"1808281","DOI":"10.1080\/20013078.2020.1808281","volume":"9","author":"C Conzelmann","year":"2020","unstructured":"Conzelmann C, Gro\u00df R, Zou M, Kr\u00fcger F, et al. Salivary extracellular vesicles inhibit Zika virus but not SARS-CoV-2 infection. J Extracell Vesicles. 2020;9:1808281.","journal-title":"J Extracell Vesicles"},{"key":"9482_CR78","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1136\/jmedgenet-2011-100542","volume":"49","author":"MH Willemsen","year":"2012","unstructured":"Willemsen MH, Vissers LEL, Willemsen MAAP, van Bon BWM, et al. Mutations in DYNC1H1 cause severe intellectual disability with neuronal migration defects. J Med Genet. 2012;49:179\u201383.","journal-title":"J Med Genet"},{"key":"9482_CR79","doi-asserted-by":"publisher","first-page":"995","DOI":"10.1021\/acschemneuro.0c00122","volume":"11","author":"AM Baig","year":"2020","unstructured":"Baig AM, Khaleeq A, Ali U, Syeda H. Evidence of the COVID-19 virus targeting the CNS: tissue distribution, host-virus interaction, and proposed neurotropic mechanisms. ACS Chem Neurosci. 2020;11:995\u20138.","journal-title":"ACS Chem Neurosci"},{"key":"9482_CR80","doi-asserted-by":"publisher","DOI":"10.1111\/ene.14227","volume":"27","author":"T Sun","year":"2020","unstructured":"Sun T, Guan J. Novel coronavirus and the central nervous system. Eur J Neurol. 2020;27: e52.","journal-title":"Eur J Neurol"},{"key":"9482_CR81","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.bbi.2020.03.031","volume":"87","author":"Y Wu","year":"2020","unstructured":"Wu Y, Xu X, Chen Z, Duan J, et al. Nervous system involvement after infection with COVID-19 and other coronaviruses. Brain Behav Immun. 2020;87:18\u201322.","journal-title":"Brain Behav Immun"},{"key":"9482_CR82","doi-asserted-by":"publisher","first-page":"2997","DOI":"10.1111\/j.1742-4658.2011.08252.x","volume":"278","author":"J Merino-Gracia","year":"2011","unstructured":"Merino-Gracia J, Garc\u00eda-Mayoral MF, Rodr\u00edguez-Crespo I. The association of viral proteins with host cell dynein components during virus infection. FEBS J. 2011;278:2997\u20133011.","journal-title":"FEBS J"},{"key":"9482_CR83","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/s12977-021-00563-3","volume":"18","author":"MH Naghavi","year":"2021","unstructured":"Naghavi MH. HIV-1 capsid exploitation of the host microtubule cytoskeleton during early infection. Retrovirology. 2021;18:19.","journal-title":"Retrovirology"},{"key":"9482_CR84","doi-asserted-by":"publisher","first-page":"2003730","DOI":"10.1183\/13993003.03730-2020","volume":"57","author":"SK Patel","year":"2021","unstructured":"Patel SK, Juno JA, Lee WS, Wragg KM, et al. Plasma ACE2 activity is persistently elevated following SARS-CoV-2 infection: implications for COVID-19 pathogenesis and consequences. Eur Respir J. 2021;57:2003730.","journal-title":"Eur Respir J"},{"key":"9482_CR85","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.152638","author":"E Dor\u00e9","year":"2022","unstructured":"Dor\u00e9 E, Joly-Beauparlant C, Morozumi S, Mathieu A, et al. The interaction of secreted phospholipase A2-IIA with the microbiota alters its lipidome and promotes inflammation. JCI Insight. 2022. https:\/\/doi.org\/10.1172\/jci.insight.152638.","journal-title":"JCI Insight"},{"key":"9482_CR86","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1038\/nri.2016.42","volume":"16","author":"MG Rooks","year":"2016","unstructured":"Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol. 2016;16:341\u201352.","journal-title":"Nat Rev Immunol"},{"key":"9482_CR87","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1097\/COH.0000000000000430","volume":"13","author":"S Serrano-Villar","year":"2018","unstructured":"Serrano-Villar S, Moreno S, Ferrer M. The functional consequences of the microbiome in HIV: insights from metabolomic studies. Curr Opin HIV AIDS. 2018;13:88\u201394.","journal-title":"Curr Opin HIV AIDS"},{"key":"9482_CR88","unstructured":"Centers for Disease Control (CDC) P for Disease Control C., (CDC), P. Interim Operational Considerations for Public Health Management of Healthcare Workers Exposed to or with Suspected or Confirmed COVID-19: non-US Healthcare Settings. Centers for disease control and prevention 2020, 2019, 1\u201311"},{"key":"9482_CR89","doi-asserted-by":"publisher","first-page":"103984","DOI":"10.1016\/j.jprot.2020.103984","volume":"230","author":"S Ciordia","year":"2021","unstructured":"Ciordia S, Alvarez-Sola G, Rull\u00e1n M, Urman JM, et al. Digging deeper into bile proteome. J Proteomics. 2021;230:103984.","journal-title":"J Proteomics"},{"key":"9482_CR90","doi-asserted-by":"publisher","first-page":"220149","DOI":"10.1098\/rsob.220149","volume":"12","author":"R Yang","year":"2022","unstructured":"Yang R, Meyer AS, Droujinine IA, Udeshi ND, et al. A genetic model for in vivo proximity labelling of the mammalian secretome. Open Biol. 2022;12:220149.","journal-title":"Open Biol"},{"key":"9482_CR91","doi-asserted-by":"publisher","first-page":"995","DOI":"10.1074\/mcp.RA118.001259","volume":"18","author":"SA Myers","year":"2019","unstructured":"Myers SA, Rhoads A, Cocco AR, Peckner R, et al. Streamlined protocol for deep proteomic profiling of FAC-sorted cells and its application to freshly isolated murine immune cells. Mol Cell Proteom. 2019;18:995\u20131009.","journal-title":"Mol Cell Proteom"},{"key":"9482_CR92","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-0716-1936-0_1","volume-title":"Clinical Proteomics","author":"S Ciordia","year":"2022","unstructured":"Ciordia S, Alvarez-Sola G, Rull\u00e1n M, Urman JM, et al. In: Corrales FJ, Paradela A, Marcilla M, editors., et al., Clinical Proteomics, vol. 2420. US, New York, NY: Springer; 2022. p. 1\u201310."},{"key":"9482_CR93","unstructured":"Qiagen, Qiagen IPA analysis features. Website 2022."},{"key":"9482_CR94","doi-asserted-by":"publisher","DOI":"10.1111\/acel.13063","volume":"19","author":"S Ruiz-Ruiz","year":"2020","unstructured":"Ruiz-Ruiz S, Sanchez-Carrillo S, Ciordia S, Mena MC, et al. Functional microbiome deficits associated with ageing: Chronological age threshold. Aging Cell. 2020;19: e13063.","journal-title":"Aging Cell"},{"key":"9482_CR95","volume-title":"R: A language and environment for statistical computing, Website","author":"Team,R C, R Core Team","year":"2022","unstructured":"Team,R C, R Core Team. R: A language and environment for statistical computing, Website. R Found Stat Comput: R Found Stat Comput; 2022."},{"key":"9482_CR96","doi-asserted-by":"publisher","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","volume":"50","author":"Y Perez-Riverol","year":"2022","unstructured":"Perez-Riverol Y, Bai J, Bandla C, Garc\u00eda-Seisdedos D, et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 2022;50:D543\u201352.","journal-title":"Nucleic Acids Res"}],"container-title":["Clinical Proteomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12014-024-09482-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12014-024-09482-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12014-024-09482-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T15:02:54Z","timestamp":1716390174000},"score":1,"resource":{"primary":{"URL":"https:\/\/clinicalproteomicsjournal.biomedcentral.com\/articles\/10.1186\/s12014-024-09482-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,22]]},"references-count":96,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,12]]}},"alternative-id":["9482"],"URL":"https:\/\/doi.org\/10.1186\/s12014-024-09482-9","relation":{},"ISSN":["1542-6416","1559-0275"],"issn-type":[{"type":"print","value":"1542-6416"},{"type":"electronic","value":"1559-0275"}],"subject":[],"published":{"date-parts":[[2024,5,22]]},"assertion":[{"value":"13 October 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 April 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 May 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The study was carried out at the Ram\u00f3n and Cajal University Hospital in Madrid (Spain) and was approved by the local research ethics committee (Comite etico de Investigacion clinica GAE Ramon y Cajal, ceic.hrc@salud.madrid.org, approval number 095\/20). Informed consent was obtained from all subjects and\/or their legal guardian(s). All methods were performed in accordance with the relevant guidelines and regulations.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"Outside the submitted work, S. S.-V. Reports personal fees from ViiV Healthcare, Janssen Cilag, Gilead Sciences, and MSD as well as nonfinancial support from ViiV Healthcare and Gilead Sciences and research grants from MSD and Gilead Sciences. J.M.-S. nonfinancial support from ViiV Healthcare, nonfinancial support from Jannsen Cilag, nonfinancial support from Gilead Sciences, outside the submitted work. E.M. has received mobility grants for conferences from Gilead and ViiV Healthcare; S.M. reports grants, personal fees and nonfinancial support from ViiV Healthcare, personal fees and nonfinancial support from Janssen, grants, personal fees and nonfinancial support from MSD, grants, personal fees and nonfinancial support from Gilead, outside the submitted work. There are no potential conflicts of interest.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"37"}}