Single-cell analysis reveals dynamics of human B cell differentiation and identifies novel B and antibody-secreting cell intermediates

Abstract
Data availability
Article and author information
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Abstract

Differentiation of B cells into antibody-secreting cells (ASCs) is a key process to generate protective humoral immunity. A detailed understanding of the cues controlling ASC differentiation is important to devise strategies to modulate antibody formation. Here, we dissected differentiation trajectories of human naive B cells into ASCs using single-cell RNA sequencing. By comparing transcriptomes of B cells at different stages of differentiation from an in vitro model with ex vivo B cells and ASCs, we uncovered a novel pre-ASC population present ex vivo in lymphoid tissues. For the first time, a germinal-center-like population is identified in vitro from human naive B cells and possibly progresses into a memory B cell population through an alternative route of differentiation, thus recapitulating in vivo human GC reactions. Our work allows further detailed characterization of human B cell differentiation into ASCs or memory B cells in both healthy and diseased conditions.

Data availability

All raw fastq files and digital gene expression matrixes (DGE) are available at the Gene Expression Omnibus (GEO) repository under accession no. GSE214265.

The following data sets were generated

1. Verstegen NJMC
2. Pollastro S
3. Unger PA
4. Marsman C
5. Elias G
6. Jorritsma T
7. Streutker M
8. Baβler K
9. Händler K
10. Rispens T
11. Schultze JL
12. ten Brinke A
13. Beyer M
14. van Ham SM
(2022) Single-cell analysis reveals dynamics of human B cell differentiation and identifies novel B and antibody-secreting cell intermediates
NCBI Gene Expression Omnibus, GSE214265.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE214265

The following previously published data sets were used

1. Longo NS
2. Lugar PL
3. Yavuz S
4. Zhang W
5. Krijger PHL
6. Russ DE
7. Jima DD
8. Dave SS
9. Grammer AC
10. Lipsky PE
(2009) Analysis of somatic hypermutation in X-linked hyper-IgM syndrome shows specific deficiencies in mutational targeting
NCBI Gene Expression Omnibus, GSE12366.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12366
1. Jardine L
2. Webb S
3. Goh I
4. Quiroga Londoño M
5. Reynolds G
6. Mather M
7. Olabi B
8. Stephenson E
9. Botting RA
10. Horsfall D
11. Engelbert J
12. Maunder D
13. Mende N
14. Murnane C
15. Dann E
16. McGrath J
17. King H
18. Kucinski I
19. Queen R
20. Carey CD
21. Shrubsole C
22. Poyner E
23. Acres M
24. Jones C
25. Ness T
26. Coulthard R
27. Elliott N
28. O'Byrne S
29. Haltalli MLR
30. Lawrence JE
31. Lisgo S
32. Balogh P
33. Meyer KB
34. Prigmore E
35. Ambridge K
36. Jain MS
37. Efremova M
38. Pickard K
39. Creasey T
40. Bacardit J
41. Henderson D
42. Coxhead J
43. Filby A
44. Hussain R
45. Dixon D
46. McDonald D
47. Popescu DM
48. Kowalczyk MS
49. Li B
50. Ashenberg O
51. Tabaka M
52. Dionne D
53. Tickle TL
54. Slyper M
55. Rozenblatt-Rosen O
56. Regev A
57. Behjati S
58. Laurenti E
59. Wilson NK
60. Roy A
61. Göttgens B
62. Roberts I
63. Teichmann SA
64. Haniffa M.
(2021) Blood and immune development in human fetal bone marrow and Down syndrome.
Metadata and matrices.

https://data.humancellatlas.org/explore/projects/cc95ff89-2e68-4a08-a234-480eca21ce79
1. Attaf N
2. Cervera-Marzal I
3. Dong C
4. Gil L
5. Renand A
6. Spinelli L
7. Milpied P
(2020) FB5P-seq: FACS-based 5-prime end single-cell RNAseq for integrative analysis of transcriptome and antigen receptor repertoire in B and T cells
NCBI Gene Expression Omnibus, GSE137275.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137275
1. Rizzetto S
2. Koppstein DNP
3. Samir J
4. Singh M
5. Reed JH
6. Cai CH
7. Lloyd AR
8. Eltahla AA
9. Goodnow CC
10. Luciani F.
(2018) B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle.
Metadata and matrices.

https://bitbucket.org/kirbyvisp/vdjpuzzle2

Article and author information

Author details

Niels JM Verstegen

Department of Immunopathology, Sanquin, Amsterdam, Netherlands

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-5732-4979
Sabrina Pollastro

Department of Immunopathology, Sanquin, Amsterdam, Netherlands

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-0950-7583
Peter-Paul A Unger

Department of Immunopathology, Sanquin, Amsterdam, Netherlands

Competing interests
The authors declare that no competing interests exist.
Casper Marsman

Department of Immunopathology, Sanquin, Amsterdam, Netherlands

Competing interests
The authors declare that no competing interests exist.
George Elias

Department of Immunopathology, Sanquin, Amsterdam, Netherlands

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-8419-9544
Tineke Jorritsma

Department of Immunopathology, Sanquin, Amsterdam, Netherlands

Competing interests
The authors declare that no competing interests exist.
Marij Streutker

Department of Immunopathology, Sanquin, Amsterdam, Netherlands

Competing interests
The authors declare that no competing interests exist.
kevin bassler

Genomics and Immunoregulation, University of Bonn, Bonn, Germany

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4780-372X
Kristian Haendler

Genomics and Immunoregulation, University of Bonn, Bonn, Germany

Competing interests
The authors declare that no competing interests exist.
Theo Rispens

Department of Immunopathology, Sanquin, Amsterdam, Netherlands

Competing interests
The authors declare that no competing interests exist.
Joachim L Schultze

Genomics and Immunoregulation, University of Bonn, Bonn, Germany

Competing interests
The authors declare that no competing interests exist.
Anja ten Brinke

Department of Immunopathology, Sanquin, Amsterdam, Netherlands

Competing interests
The authors declare that no competing interests exist.
Marc Beyer

Genomics and Immunoregulation, University of Bonn, Bonn, Germany

Competing interests
The authors declare that no competing interests exist.
Marieke SM van Ham

Department of Immunopathology, Sanquin, Amsterdam, Netherlands

For correspondence
m.vanham@sanquin.nl

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-1999-9494

Funding

LSBR (1609)

Marieke SM van Ham

PPOC (17-34/ L2263)

Marieke SM van Ham

German research foundation (272482170)

Marc Beyer

German research foundation (SFB1454-432325352)

Marc Beyer

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: All the healthy donors provided written informed consent following the protocol of the local institutional review board, the Medical Ethics Committee of Sanquin Blood Supply, and conforms to the principles of the Declaration of Helsinki.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.