Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers

Asher MI, Rutter CE, Bissell K, Chiang C-Y, El Sony A, Ellwood E, et al. Worldwide trends in the burden of asthma symptoms in school-aged children: Global Asthma Network Phase I cross-sectional study. Lancet. 2021;398:1569–80.

Article  PubMed  PubMed Central  Google Scholar 

Asher MI, Garcia-Marcos L, Pearce NE, Strachan DP. Trends in worldwide asthma prevalence. Eur Respir J. 2020;56:2002094.

Porsbjerg C, Melen E, Lehtimaki L, Shaw D. Asthma. Lancet. 2023;401:858–73.

Edwards MR, Saglani S, Schwarze J, Skevaki C, Smith JA, Ainsworth B, et al. Addressing unmet needs in understanding asthma mechanisms: From the European Asthma Research and Innovation Partnership (EARIP) Work Package (WP)2 collaborators. Eur Respir J. 2017;49:1602448.

Gauvreau GM, El-Gammal AI, O’Byrne PM. Allergen-induced airway responses. Eur Respir J. 2015;46:819–31.

Article  CAS  PubMed  Google Scholar 

Sajuthi SP, Everman JL, Jackson ND, Saef B, Rios CL, Moore CM, et al. Nasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology. Nat Commun. 2022;13:1632.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhu Z, Camargo CA Jr, Raita Y, Freishtat RJ, Fujiogi M, Hahn A, et al. Nasopharyngeal airway dual-transcriptome of infants with severe bronchiolitis and risk of childhood asthma: a multicenter prospective study. J Allergy Clin Immunol. 2022;150:806–16.

Article  CAS  PubMed  Google Scholar 

Do AN, Chun Y, Grishina G, Grishin A, Rogers AJ, Raby BA, et al. Network study of nasal transcriptome profiles reveals master regulator genes of asthma. J Allergy Clin Immunol. 2021;147:879–93.

Article  CAS  PubMed  Google Scholar 

Chun Y, Do A, Grishina G, Grishin A, Fang G, Rose S, et al. Integrative study of the upper and lower airway microbiome and transcriptome in asthma. JCI Insight. 2020;5:e133707.

Forno E, Zhang R, Jiang Y, Kim S, Yan Q, Ren Z, et al. Transcriptome-wide and differential expression network analyses of childhood asthma in nasal epithelium. J Allergy Clin Immunol. 2020;146:671–5.

Article  PubMed  PubMed Central  Google Scholar 

Hekking PP, Loza MJ, Pavlidis S, de Meulder B, Lefaudeux D, Baribaud F, et al. Pathway discovery using transcriptomic profiles in adult-onset severe asthma. J Allergy Clin Immunol. 2018;141:1280–90.

Article  CAS  PubMed  Google Scholar 

Park HW, Weiss ST. Understanding the molecular mechanisms of asthma through transcriptomics. Allergy Asthma Immunol Res. 2020;12:399–411.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Crisford H, Sapey E, Rogers GB, Taylor S, Nagakumar P, Lokwani R, et al. Neutrophils in asthma: the good, the bad and the bacteria. Thorax. 2021;76:835–44.

Carr TF, Zeki AA, Kraft M. Eosinophilic and noneosinophilic asthma. Am J Respir Crit Care Med. 2018;197:22–37.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jackson DJ, Akuthota P, Roufosse F. Eosinophils and eosinophilic immune dysfunction in health and disease. Eur Respir Rev. 2022;31:210150.

Chavakis T, Mitroulis I, Hajishengallis G. Hematopoietic progenitor cells as integrative hubs for adaptation to and fine-tuning of inflammation. Nat Immunol. 2019;20:802–11.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bigler J, Boedigheimer MJ, Schofield JPR, Skipp PJ, Corfield J, Rowe A, et al. A severe asthma disease signature from gene expression profiling of peripheral blood from U-BIOPRED cohorts. Am J Respir Crit Care Med. 2017;195:1311–20.

Article  CAS  PubMed  Google Scholar 

Lemonnier N, Melen E, Jiang Y, Joly S, Menard C, Aguilar D, et al. A novel whole blood gene expression signature for asthma, dermatitis, and rhinitis multimorbidity in children and adolescents. Allergy. 2020;75:3248–60.

Article  CAS  PubMed  Google Scholar 

Jiang Y, Gruzieva O, Wang T, Forno E, Boutaoui N, Sun T, et al. Transcriptomics of atopy and atopic asthma in white blood cells from children and adolescents. Eur Respir J. 2019;53:1900102.

Hoda U, Pavlidis S, Bansal AT, Takahashi K, Hu S, Ng Kee Kwong F, et al. Clinical and transcriptomic features of persistent exacerbation-prone severe asthma in U-BIOPRED cohort. Clin Transl Med. 2022;12:e816.

Altman MC, Gill MA, Whalen E, Babineau DC, Shao B, Liu AH, et al. Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children. Nat Immunol. 2019;20:637–51.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schatz M, Kosinski M, Yarlas AS, Hanlon J, Watson ME, Jhingran P. The minimally important difference of the Asthma Control Test. J Allergy Clin Immunol. 2009;124(719–23): e1.

Article  Google Scholar 

Graham BL, Steenbruggen I, Miller MR, Barjaktarevic IZ, Cooper BG, Hall GL, et al. Standardization of Spirometry 2019 Update. An Official American Thoracic Society and European Respiratory Society Technical Statement. Am J Respir Crit Care Med. 2019;200:e70-e88.

Anders S, Pyl PT, Huber W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.

Article  CAS  PubMed  Google Scholar 

Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.

Article  CAS  PubMed  Google Scholar 

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.

Article  PubMed  PubMed Central  Google Scholar 

Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.

Article  PubMed  PubMed Central  Google Scholar 

Sherman BT, Hao M, Qiu J, Jiao X, Baseler MW, Lane HC, et al. DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res. 2022;50:W216–W221.

Newman AM, Steen CB, Liu CL, Gentles AJ, Chaudhuri AA, Scherer F, et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat Biotechnol. 2019;37:773–82.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ordovas-Montanes J, Dwyer DF, Nyquist SK, Buchheit KM, Vukovic M, Deb C, et al. Allergic inflammatory memory in human respiratory epithelial progenitor cells. Nature. 2018;560:649–54.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhu J, Sova P, Xu Q, Dombek KM, Xu EY, Vu H, et al. Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation. PLoS Biol. 2012;10: e1001301.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, et al. Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet. 2008;40:854–61.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Irizar H, Chun Y, Arditi Z, Do A, Grishina G, Grishin A, et al. Examination of host genetic effects on nasal microbiome composition. J Allergy Clin Immunol. 2022;150:1232–6.

Article  CAS  PubMed  Google Scholar 

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.

Article  CAS  PubMed  Google Scholar 

van der Auwera GA, O’Connor BD. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. 1st ed. O’Reilly Media; 2020.

Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007;81:1084–97.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Browning BL, Zhou Y, Browning SR. A one-penny imputed genome from next-generation reference panels. Am J Hum Genet. 2018;103:338–48.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience. 2015;4:7.

Hart T, Moffat J. BAGEL: a computational framework for identifying essential genes from pooled library screens. BMC Bioinformatics. 2016;17:164.

Article  PubMed  PubMed Central  Google Scholar 

Shabalin AA. Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics. 2012;28:1353–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhu J, Wiener MC, Zhang C, Fridman A, Minch E, Lum PY, et al. Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations. PLoS Comput Biol. 2007;3: e69.

Article  PubMed  PubMed Central  Google Scholar 

Zhang B, Zhu J. Identification of key causal regulators in gene networks. Proceedings of the World Congress on Engineering. London, UK. 2013;II:5–8.

Rosseel Y. lavaan: An R Package for Structural Equation Modeling. J Stat Softw. 2012;48:1–36.

Zhang L, Chun Y, Irizar H, Arditi Z, Grishina G, Grishin A, et al. Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers. Synapse. 2023. https://doi.org/10.7303/syn51061925.

Article  PubMed  Google Scholar 

Watson CT, Cohain AT, Griffin RS, Chun Y, Grishin A, Hacyznska H, et al. Integrative transcriptomic analysis reveals key drivers of acute peanut allergic reactions. Nat Commun. 2017;8:1943.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ogawa K, Tanaka K, Ishii A, Nakamura Y, Kondo S, Sugamura K, et al. A novel serum protein that is selectively produced by cytotoxic lymphocytes. J Immunol. 2001;166:6404–12.

Article  CAS  PubMed 

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