iScience
Volume 26, Issue 3, 17 March 2023, 106260
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Article
Demultiplexing Ig repertoires by parallel mRNA/DNA sequencing shows major differential alterations in severe COVID-19

https://doi.org/10.1016/j.isci.2023.106260Get rights and content
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open access

Highlights

  • Severe COVID-19 expands double-negative B cells, plasma cells, and B10 cells

  • Parallel DNA and RNA repertoires dissociate high Ig expression from cell expansion

  • COVID-19 memory repertoire reveals short CDR-H3 and progressive affinity maturation

  • Early increase of IgG1 clonotypes with long uncharged CDR3 correlates with ARDS

Summary

To understand the fine differential elements that can lead to or prevent acute respiratory distress syndrome (ARDS) in COVID-19 patients, it is crucial to investigate the immune response architecture. We herein dissected the multiple layers of B cell responses by flow cytometry and Ig repertoire analysis from acute phase to recovery. Flow cytometry with FlowSOM analysis showed major changes associated with COVID-19 inflammation such as an increase of double-negative B-cells and ongoing plasma cell differentiation. This paralleled COVID-19-driven expansion of two disconnected B-cell repertoires. Demultiplexing successive DNA and RNA Ig repertoire patterns characterized an early expansion of IgG1 clonotypes with atypically long and uncharged CDR3, the abundance of this inflammatory repertoire being correlated with ARDS and likely pejorative. A superimposed convergent response included convergent anti-SARS-CoV-2 clonotypes. It featured progressively increasing somatic hypermutation together with normal-length or short CDR3 and it persisted until a quiescent memory B-cell stage after recovery.

Subject areas

Immunology
Respiratory medicine

Data and code availability

  • RACE-RepSeq data have been deposited at GEO and are publicly available as of the date of publication. Accession numbers are listed in the key resources table. DNA repertoire and FCM data reported in this paper will be shared by the lead contact upon request.

  • All original code is available in this paper’s supplemental information.

  • Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Cited by (0)

9

Senior authors

10

These authors contributed equally

11

Lead contact