Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
PreprintCited by 5

The DOI matches its Crossref record; the references it cites are not checked yet.

Establishment and characterization of a new Pseudomonas aeruginosa infection model using 2D airway organoids and dual RNA sequencing

Pleguezuelos-Manzano, Cayetano, Beenker, Wouter A. G., van Son, Gijs J.F., Begthel, Harry, Amatngalim, Gimano D., Beekman, Jeffrey M., Clevers, Hans, den Hertog, Jeroen·2023
DOI 10.1101/2023.03.11.532178
Open this paper in CoChat — free account

Abstract

Pseudomonas aeruginosa is a Gram-negative bacterium that is notorious for infections in the airway of cystic fibrosis (CF) subjects. Often, these infections become chronic, leading to higher morbidity and mortality rates. Bacterial quorum sensing (QS) coordinates the expression of virulence factors and the formation of biofilms at a population level. QS has become the focus of attention for development of alternatives to antimicrobials targeting P. aeruginosa infections. However, a better understanding of the bacteria-host interaction, and the role of QS in infection, is required. In this study, we set up a new P. aeruginosa infection model, using 2D airway organoids derived from healthy and CF individuals. Using dual RNA-sequencing, we dissected their interaction, focusing on the role of QS. As expected, P. aeruginosa induced epithelial inflammation. However, QS signaling did not affect the epithelial airway cells. The epithelium influenced several infection-related processes of P. aeruginosa , including metabolic changes, induction of type 3 and type 6 secretion systems (T3SS and T6SS), and increased expression of antibiotic resistance genes, including mexXY efflux pump and several porins. Interestingly, the epithelium influenced the regulation by QS of the type 2 (T2SS) and T6SS. Finally, we compared our model with in vivo P. aeruginosa transcriptomic datasets, from samples directly isolated from the airways of CF subjects. This shows that our model recapitulates important aspects of in vivo infection, like enhanced denitrification, betaine/choline metabolism, increased antibiotic resistance, as well as an overall decrease of motility-related genes. This relevant infection model is interesting for future investigations, helping to reduce the burden of P. aeruginosa infections in CF.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2023.03.11.532178

Cites

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

The citation lists haven’t been fetched yet

Cited by 5

Research works printed but not linked: 86

  1. 10.1128/CMR.00031-19 · DOI · Paper page
  2. 10.1016/S0140-6736(08)61162-9 · DOI · Paper page
  3. 2017, Bicarbonate in cystic fibrosis, J. Cyst. Fibros, 16, 653, 10.1016/j.jcf.2017.06.005 · doi:10.1016/j.jcf.2017.06.005
  4. 10.1038/nrdp.2015.49 · doi:10.1038/nrdp.2015.49
  5. 2020, Cystic fibrosis in the year 2020: A disease with a new face, Acta Paediatr. Int. J. Paediatr, 109, 893, 10.1111/apa.15155 · DOI · Paper page
  6. Rossi, E. et al. Pseudomonas aeruginosa adaptation and evolution in patients with cystic fibrosis. Nat. Rev. Microbiol. 19, (2021). · DOI · Paper page
  7. 10.1128/CMR.00068-09 · DOI · Paper page
  8. 10.1164/rccm.202004-1322OC · DOI
  9. Parkins, M. D. , Somayaji, R. & Waters, V. J. Epidemiology, biology, and impact of clonal pseudomonas aeruginosa infections in cystic fibrosis. Clin. Microbiol. Rev. 31, (2018). · DOI · Paper page
  10. 10.1016/j.drup.2019.07.002 · DOI · Paper page
  11. 10.1016/j.cell.2006.04.001 · DOI · Paper page
  12. 2001, Quorum-sensing in Gram-negative bacteria, FEMS Microbiol. Lett, 25, 365, 10.1111/j.1574-6976.2001.tb00583.x · doi:10.1111/j.1574-6976.2001.tb00583.x · Paper page
  13. 2014, The hierarchy quorum sensing network in Pseudomonas aeruginosa, Protein Cell, 6, 26
  14. 10.1093/emboj/cdg366 · DOI · Paper page
  15. Singh, V. K. et al. Tackling Recalcitrant Pseudomonas aeruginosa Infections In Critical Illness via Anti-virulence Monotherapy. Nat. Commun. 13, (2022). · DOI
  16. Tang, H. et al. Epigallocatechin-3-Gallate Ameliorates Acute Lung Damage by Inhibiting Quorum-Sensing-Related Virulence Factors of Pseudomonas aeruginosa. Front. Microbiol. 13, (2022). · DOI
  17. Azimi, S. , Klementiev, A. D. , Whiteley, M. & Diggle, S. P. Bacterial Quorum Sensing During Infection. 201–219 (2020). · DOI · Paper page
  18. Cornforth, D. M. et al. Pseudomonas aeruginosa transcriptome during human infection. Proc. Natl. Acad. Sci. U. S. A. 115, (2018). · DOI · Paper page
  19. 10.1038/ng.3148 · DOI · Paper page
  20. 10.1073/pnas.0602138103 · DOI · Paper page
  21. 10.1073/pnas.1419677112 · DOI · Paper page
  22. 10.3791/62420 · DOI
  23. 10.1371/journal.pone.0162755 · DOI · Paper page
  24. 10.1128/JB.01138-07 · DOI · Paper page
  25. 10.1099/jmm.0.019984-0 · DOI
  26. 2018, Animal and Model Systems for Studying Cystic Fibrosis, J. Cyst. Fibros, 17, S28, 10.1016/j.jcf.2017.09.001 · DOI
  27. 10.1128/mBio.02205-20 · DOI
  28. 2018, Airway disease phenotypes in animal models of cystic fibrosis, Respir. Res, 19, 1
  29. 10.3791/62761 · DOI
  30. Harrington, N. E. , Littler, J. L. & Harrison, F. Transcriptome Analysis of Pseudomonas aeruginosa Biofilm Infection in an Ex Vivo Pig Model of the Cystic Fibrosis Lung. Appl. Environ. Microbiol. 88, (2022). · doi:10.1128/aem.01789-21
  31. 2005, NF-κB activation and sustained IL-8 gene expression in primary cultures of cystic fibrosis airway epithelial cells stimulated with Pseudomonas aeruginosa, Am. J. Physiol. - Lung Cell. Mol. Physiol, 288, 471, 10.1152/ajplung.00066.2004 · DOI
  32. 2017, Bronchial epithelial cells from cystic fibrosis patients express a specific long non-coding RNA signature upon Pseudomonas aeruginosa infection, Front. Cell. Infect. Microbiol, 7, 1
  33. Tang, M. et al. Evaluating Bacterial Pathogenesis Using a Model of Human Airway Organoids Infected with Pseudomonas aeruginosa Biofilms. Microbiol. Spectr. (2022). · DOI
  34. 10.1128/IAI.72.9.5433-5438.2004 · DOI
  35. 10.1128/IAI.01772-05 · DOI · Paper page
  36. 2006, Innate immune responses of human tracheal epithelium to Pseudomonas aeruginosa flagellin, TNF-α, and IL-1ß, Am. J. Physiol.-Cell Physiol, 290, 678, 10.1152/ajpcell.00166.2005 · DOI
  37. 10.3389/fimmu.2020.01022 · DOI · Paper page
  38. 10.15252/embj.201899894 · DOI
  39. 10.1038/nm.3201 · DOI · Paper page
  40. Pleguezuelos-Manzano, C. et al. Establishment and Culture of Human Intestinal Organoids Derived from Adult Stem Cells. Curr. Protoc. Immunol. 130, (2020). · DOI · Paper page
  41. 2021, Intestinal organoid cocultures with microbes, Nat. Protoc, 16, 4633, 10.1038/s41596-021-00589-z · DOI · Paper page
  42. 10.1007/978-1-4939-7634-8_4 · DOI
  43. Beenker, W. A. G. , Hoeksma, J. , Bannier-Hélaouët, M. , Clevers, H. & den Hertog, J. Paecilomycone inhibits quorum sensing in Gram-negative bacteria. BioRxiv (2022). · doi:10.1101/2022.09.12.507720
  44. 10.1038/nprot.2015.115 · DOI · Paper page
  45. 10.26508/lsa.202101228 · DOI
  46. 10.1186/s13059-015-0866-z · DOI · Paper page
  47. 10.1093/bioinformatics/bts635 · DOI · Paper page
  48. 10.1093/bioinformatics/btt656 · DOI · Paper page
  49. 10.1038/35023079 · DOI · Paper page
  50. 10.1093/database/baz149 · DOI
  51. 10.1186/gb-2014-15-1-r1 · DOI · Paper page
  52. 2012, ClusterProfiler: An R package for comparing biological themes among gene clusters, Omi. A J. Integr. Biol, 16, 284, 10.1089/omi.2011.0118 · DOI · Paper page
  53. 10.1093/nar/gkv1227 · DOI · Paper page
  54. 10.1093/nar/gky1131 · DOI · Paper page
  55. Moura-Alves, P. et al. Host monitoring of quorum sensing during Pseudomonas aeruginosa infection. Science (80-.). 366, (2019). · DOI · Paper page
  56. 10.1038/nrmicro1836 · DOI · Paper page
  57. 10.3391/mbi.2016.7.1.01 · DOI · Paper page
  58. 10.1046/j.1365-2958.1999.01586.x · DOI · Paper page
  59. 10.1007/s11274-019-2732-8 · DOI
  60. 10.1111/j.1574-6976.2010.00218.x · DOI · Paper page
  61. 10.3389/fmicb.2014.00153 · DOI · Paper page
  62. 10.1128/JB.00162-07 · DOI
  63. 10.1038/s41467-018-02974-x · DOI · Paper page
  64. 10.1038/nrmicro2199 · DOI · Paper page
  65. 10.1111/cmi.13170 · DOI
  66. 10.1016/j.micres.2015.01.004 · DOI
  67. Sana, T. G. , Berni, B. & Bleves, S. The T6SSs of Pseudomonas aeruginosa strain pao1 and their effectors: Beyond bacterial-cell targeting. Front. Cell. Infect. Microbiol. 6, (2016). · DOI · Paper page
  68. 10.1074/jbc.M112.376368 · DOI · Paper page
  69. 10.1128/IAI.00437-16 · DOI
  70. 10.1128/JB.180.17.4466-4474.1998 · doi:10.1128/jb.180.17.4466-4474.1998
  71. 10.1136/thorax.55.9.795 · DOI
  72. Huang, H. et al. An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa. Nat. Commun. 10, (2019). · DOI · Paper page
  73. 10.1128/IAI.00943-17 · DOI
  74. Kordes, A. et al. Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung. Nat. Commun. 10, (2019). · DOI
  75. 10.1371/journal.pone.0054583 · DOI · Paper page
  76. 10.1007/978-1-61779-120-8_18 · DOI
  77. Liu, Y. C. et al. Contribution of the Alkylquinolone Quorum-Sensing System to the Interaction of Pseudomonas aeruginosa With Bronchial Epithelial Cells. Front. Microbiol. 9, (2018). · DOI
  78. 2023, CRISPR engineering in organoids for gene repair and disease modelling, Nat. Rev. Bioeng, 1, 32, 10.1038/s44222-022-00013-5 · DOI · Paper page
  79. Moura-Alves, P. et al. Host monitoring of quorum sensing during Pseudomonas aeruginosa infection. Science (80-.). 366, (2019). · DOI · Paper page
  80. 10.1038/nature13684 · DOI · Paper page
  81. 10.1016/j.immuni.2018.06.016 · DOI · Paper page
  82. 10.1073/pnas.0911934107 · DOI · Paper page
  83. Rossy, T. et al. Pseudomonas aeruginosa contracts mucus to rapidly form biofilms in tissue-engineered human airways. bioRxiv 2, 2022.05.26.493615 (2022). · DOI
  84. Dar, D. , Dar, N. , Cai, L. & Newman, D. K. Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution. Science (80-.). 373, (2021). · DOI · Paper page
  85. 10.1038/s41586-020-2983-4 · DOI · Paper page
  86. 10.1002/pmic.200800918 · DOI

Metadata

Authors
Pleguezuelos-Manzano, C., Beenker, W. A. G., van Son, G. J. F., Begthel, H., Amatngalim, G. D., Beekman, J. M., Clevers, H., & den Hertog, J.
Publisher
openRxiv
Published
2023-03-11
DOI
10.1101/2023.03.11.532178
Cited by
5
Type
Preprint

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Establishment and characterization of a new Pseudomonas aeruginosa infection model using 2D airway organoids and dual RNA sequencing. https://app.cochat.ai/papers/10.1101/2023.03.11.532178
The paper
Pleguezuelos-Manzano, C., Beenker, W. A. G., van Son, G. J. F., Begthel, H., Amatngalim, G. D., Beekman, J. M., Clevers, H., & den Hertog, J. (2023). Establishment and characterization of a new Pseudomonas aeruginosa infection model using 2D airway organoids and dual RNA sequencing. https://doi.org/10.1101/2023.03.11.532178

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.