Novel specialized cell state and spatial compartments within the germinal center.
Journal
Nature immunology
ISSN: 1529-2916
Titre abrégé: Nat Immunol
Pays: United States
ID NLM: 100941354
Informations de publication
Date de publication:
06 2020
06 2020
Historique:
received:
21
08
2019
accepted:
11
03
2020
pubmed:
29
4
2020
medline:
15
9
2020
entrez:
29
4
2020
Statut:
ppublish
Résumé
Within germinal centers (GCs), complex and highly orchestrated molecular programs must balance proliferation, somatic hypermutation and selection to both provide effective humoral immunity and to protect against genomic instability and neoplastic transformation. In contrast to this complexity, GC B cells are canonically divided into two principal populations, dark zone (DZ) and light zone (LZ) cells. We now demonstrate that, following selection in the LZ, B cells migrated to specialized sites within the canonical DZ that contained tingible body macrophages and were sites of ongoing cell division. Proliferating DZ (DZp) cells then transited into the larger DZ to become differentiating DZ (DZd) cells before re-entering the LZ. Multidimensional analysis revealed distinct molecular programs in each population commensurate with observed compartmentalization of noncompatible functions. These data provide a new three-cell population model that both orders critical GC functions and reveals essential molecular programs of humoral adaptive immunity.
Identifiants
pubmed: 32341509
doi: 10.1038/s41590-020-0660-2
pii: 10.1038/s41590-020-0660-2
pmc: PMC7255947
mid: NIHMS1575443
doi:
Substances chimiques
Biomarkers
0
Proteome
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
660-670Subventions
Organisme : NIAID NIH HHS
ID : R21 AI128785
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI120715
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG047928
Pays : United States
Organisme : NICHD NIH HHS
ID : T32 HD007009
Pays : United States
Organisme : NHLBI NIH HHS
ID : T32 HL007605
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI143778
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA014599
Pays : United States
Organisme : NIAID NIH HHS
ID : F32 AI143120
Pays : United States
Commentaires et corrections
Type : CommentIn
Références
De Silva, N. S. & Klein, U. Dynamics of B cells in germinal centres. Nat. Rev. Immunol. 15, 137–148 (2015).
pubmed: 25656706
pmcid: 4399774
doi: 10.1038/nri3804
MacLennan, I. C. Germinal centers. Annu. Rev. Immunol. 12, 117–139 (1994).
pubmed: 8011279
doi: 10.1146/annurev.iy.12.040194.001001
Bannard, O. et al. Germinal center centroblasts transition to a centrocyte phenotype according to a timed program and depend on the dark zone for effective selection. Immunity 39, 912–924 (2013).
pubmed: 24184055
pmcid: 3828484
doi: 10.1016/j.immuni.2013.08.038
Victora, G. D. & Nussenzweig, M. C. Germinal centers. Ann. Rev. Immunol. 30, 429–457 (2012).
doi: 10.1146/annurev-immunol-020711-075032
Victora, G. D. et al. Germinal center dynamics revealed by multiphoton microscopy with a photoactivatable fluorescent reporter. Cell 143, 592–605 (2010).
pubmed: 21074050
pmcid: 3035939
doi: 10.1016/j.cell.2010.10.032
Shulman, Z. et al. Dynamic signaling by T follicular helper cells during germinal center B cell selection. Science 345, 1058–1062 (2014).
pubmed: 25170154
pmcid: 4519234
doi: 10.1126/science.1257861
Khalil, A. M., Cambier, J. C. & Shlomchik, M. J. B cell receptor signal transduction in the GC is short-circuited by high phosphatase activity. Science 336, 1178–1181 (2012).
pubmed: 22555432
pmcid: 3777391
doi: 10.1126/science.1213368
Calado, D. P. et al. The cell-cycle regulator c-Myc is essential for the formation and maintenance of germinal centers. Nat. Immunol. 13, 1092–1100 (2012).
pubmed: 23001146
pmcid: 4132664
doi: 10.1038/ni.2418
Dominguez-Sola, D. et al. The proto-oncogene MYC is required for selection in the germinal center and cyclic reentry. Nat. Immunol. 13, 1083–1091 (2012).
pubmed: 23001145
pmcid: 3711534
doi: 10.1038/ni.2428
Allen, C. D. et al. Germinal center dark and light zone organization is mediated by CXCR4 and CXCR5. Nat. Immunol. 5, 943–952 (2004).
pubmed: 15300245
doi: 10.1038/ni1100
Song, S. & Matthias, P. D. The transcriptional regulation of germinal center formation. Front. Immunol. 9, 2026 (2018).
pubmed: 30233601
pmcid: 6134015
doi: 10.3389/fimmu.2018.02026
Tunyaplin, C. et al. Direct repression of prdm1 by Bcl-6 inhibits plasmacytic differentiation. J. Immunol. 173, 1158–1165 (2004).
pubmed: 15240705
doi: 10.4049/jimmunol.173.2.1158
Ochiai, K. et al. Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of IRF4. Immunity 38, 918–929 (2013).
pubmed: 23684984
pmcid: 3690549
doi: 10.1016/j.immuni.2013.04.009
Recaldin, T. & Fear, D. J. Transcription factors regulating B cell fate in the germinal centre. Clin. Exp. Immunol. 183, 65–75 (2016).
pubmed: 26352785
doi: 10.1111/cei.12702
Dominguez-Sola, D. et al. The FOXO1 transcription factor instructs the germinal center dark zone program. Immunity 43, 1064–1074 (2015).
pubmed: 26620759
doi: 10.1016/j.immuni.2015.10.015
Trabucco, S. E., Gerstein, R. M. & Zhang, H. YY1 Regulates the germinal center reaction by inhibiting apoptosis. J. Immunol. 197, 1699–1707 (2016).
pubmed: 27448584
pmcid: 4992619
doi: 10.4049/jimmunol.1600721
Perez-Garcia, A. et al. CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation. Nat. Commun. 8, 16067 (2017).
pubmed: 28677680
pmcid: 5504274
doi: 10.1038/ncomms16067
Caganova, M. et al. Germinal center dysregulation by histone methyltransferase EZH2 promotes lymphomagenesis. J. Clin. Invest. 123, 5009–5022 (2013).
pubmed: 24200695
pmcid: 3859423
doi: 10.1172/JCI70626
Beguelin, W. et al. EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell 23, 677–692 (2013).
pubmed: 23680150
pmcid: 3681809
doi: 10.1016/j.ccr.2013.04.011
Yoshida, H. et al. The cis-regulatory atlas of the mouse immune system. Cell 176, 897–912.e20 (2019).
pubmed: 30686579
pmcid: 6785993
doi: 10.1016/j.cell.2018.12.036
Röhlich, K. Beitrag zur Cytologie der Keimzentren der Lymphknoten. Z. Mikrosk. Anat. Forsch 20, 287–297 (1930).
Endl, E. & Gerdes, J. Posttranslational modifications of the KI-67 protein coincide with two major checkpoints during mitosis. J. Cell. Physiol. 182, 371–380 (2000).
pubmed: 10653604
doi: 10.1002/(SICI)1097-4652(200003)182:3<371::AID-JCP8>3.0.CO;2-J
Chistiakov, D. A., Killingsworth, M. C., Myasoedova, V. A., Orekhov, A. N. & Bobryshev, Y. V. CD68/macrosialin: not just a histochemical marker. Lab. Invest. 97, 4–13 (2017).
pubmed: 27869795
doi: 10.1038/labinvest.2016.116
Brink, R. & Phan, T. G. Self-reactive B cells in the germinal center reaction. Annu. Rev. Immunol. 36, 339–357 (2018).
pubmed: 29356584
doi: 10.1146/annurev-immunol-051116-052510
Weber, T. S. Cell cycle-associated CXCR4 expression in germinal center B cells and its implications on affinity maturation. Front. Immunol. 9, 1313 (2018).
pubmed: 29951060
pmcid: 6008520
doi: 10.3389/fimmu.2018.01313
Allen, C. D., Okada, T., Tang, H. L. & Cyster, J. G. Imaging of germinal center selection events during affinity maturation. Science 315, 528–531 (2007).
pubmed: 17185562
doi: 10.1126/science.1136736
Mesin, L., Ersching, J. & Victora, G. D. Germinal center B cell dynamics. Immunity 45, 471–482 (2016).
pubmed: 27653600
pmcid: 5123673
doi: 10.1016/j.immuni.2016.09.001
Gitlin, A. D., Shulman, Z. & Nussenzweig, M. C. Clonal selection in the germinal centre by regulated proliferation and hypermutation. Nature 509, 637–640 (2014).
pubmed: 24805232
pmcid: 4271732
doi: 10.1038/nature13300
Finkin, S., Hartweger, H., Oliveira, T. Y., Kara, E. E. & Nussenzweig, M. C. Protein amounts of the MYC transcription factor determine germinal center B cell division capacity. Immunity 51, 324–336.e5 (2019).
pubmed: 31350178
doi: 10.1016/j.immuni.2019.06.013
Vervoorts, J., Luscher-Firzlaff, J. & Luscher, B. The ins and outs of MYC regulation by posttranslational mechanisms. J. Biol. Chem. 281, 34725–34729 (2006).
pubmed: 16987807
doi: 10.1074/jbc.R600017200
Yao, S., Fan, L. Y. & Lam, E. W. The FOXO3-FOXM1 axis: a key cancer drug target and a modulator of cancer drug resistance. Semin. Cancer Biol. 50, 77–89 (2018).
pubmed: 29180117
pmcid: 6565931
doi: 10.1016/j.semcancer.2017.11.018
Ersching, J. et al. Germinal center selection and affinity maturation require dynamic regulation of mTORC1 kinase. Immunity 46, 1045–1058.e6 (2017).
pubmed: 28636954
pmcid: 5526448
doi: 10.1016/j.immuni.2017.06.005
Gitlin, A. D. et al. T cell help controls the speed of the cell cycle in germinal center B cells. Science 349, 643–646 (2015).
pubmed: 26184917
pmcid: 4809261
doi: 10.1126/science.aac4919
Vitale, I., Galluzzi, L., Castedo, M. & Kroemer, G. Mitotic catastrophe: a mechanism for avoiding genomic instability. Nat. Rev. Mol. Cell Biol. 12, 385–392 (2011).
pubmed: 21527953
doi: 10.1038/nrm3115
Kuppers, R. & Dalla-Favera, R. Mechanisms of chromosomal translocations in B cell lymphomas. Oncogene 20, 5580–5594 (2001).
pubmed: 11607811
doi: 10.1038/sj.onc.1204640
Clark, M. R., Mandal, M., Ochiai, K. & Singh, H. Orchestrating B cell lymphopoiesis through interplay of IL-7 receptor and pre-B cell receptor signalling. Nat. Rev. Immunol. 14, 69–80 (2014).
pubmed: 24378843
doi: 10.1038/nri3570
Zhang, L., Reynolds, T. L., Shan, X. & Desiderio, S. Coupling of V(D)J recombination to the cell cycle suppresses genomic instability and lymphoid tumorigenesis. Immunity 34, 163–174 (2011).
pubmed: 21349429
pmcid: 3070474
doi: 10.1016/j.immuni.2011.02.003
Khair, L. et al. ATM increases activation-induced cytidine deaminase activity at downstream S regions during class-switch recombination. J. Immunol. 192, 4887–4896 (2014).
pubmed: 24729610
pmcid: 4049217
doi: 10.4049/jimmunol.1303481
Schrader, C. E., Guikema, J. E., Linehan, E. K., Selsing, E. & Stavnezer, J. Activation-induced cytidine deaminase-dependent DNA breaks in class switch recombination occur during G1 phase of the cell cycle and depend upon mismatch repair. J. Immunol. 179, 6064–6071 (2007).
pubmed: 17947680
doi: 10.4049/jimmunol.179.9.6064
Petersen, S. et al. AID is required to initiate Nbs1/γ-H2AX focus formation and mutations at sites of class switching. Nature 414, 660–665 (2001).
pubmed: 11740565
pmcid: 4729367
doi: 10.1038/414660a
Sharbeen, G., Yee, C. W., Smith, A. L. & Jolly, C. J. Ectopic restriction of DNA repair reveals that UNG2 excises AID-induced uracils predominantly or exclusively during G1 phase. J. Exp. Med. 209, 965–974 (2012).
pubmed: 22529268
pmcid: 3348097
doi: 10.1084/jem.20112379
Wang, Q. et al. The cell cycle restricts activation-induced cytidine deaminase activity to early G1. J. Exp. Med. 214, 49–58 (2017).
pubmed: 27998928
pmcid: 5206505
doi: 10.1084/jem.20161649
Storb, U. Why does somatic hypermutation by AID require transcription of its target genes? Adv. Immunol. 122, 253–277 (2014).
pubmed: 24507160
doi: 10.1016/B978-0-12-800267-4.00007-9
Zan, H. & Casali, P. Regulation of Aicda expression and AID activity. Autoimmunity 46, 83–101 (2013).
pubmed: 23181381
pmcid: 3762583
doi: 10.3109/08916934.2012.749244
Stewart, I., Radtke, D., Phillips, B., McGowan, S. J. & Bannard, O. Germinal center B cells replace their antigen receptors in dark zones and fail light zone entry when immunoglobulin gene mutations are damaging. Immunity 49, 477–489.e7 (2018).
pubmed: 30231983
pmcid: 6162340
doi: 10.1016/j.immuni.2018.08.025
Hodson, D. J. et al. Regulation of normal B-cell differentiation and malignant B-cell survival by OCT2. Proc. Natl Acad. Sci. USA 113, E2039–E2046 (2016).
pubmed: 26993806
doi: 10.1073/pnas.1600557113
Vilagos, B. et al. Essential role of EBF1 in the generation and function of distinct mature B cell types. J. Exp. Med. 209, 775–792 (2012).
pubmed: 22473956
pmcid: 3328360
doi: 10.1084/jem.20112422
Kwon, K. et al. Instructive role of the transcription factor E2A in early B lymphopoiesis and germinal center B cell development. Immunity 28, 751–762 (2008).
pubmed: 18538592
doi: 10.1016/j.immuni.2008.04.014
Milpied, P. et al. Human germinal center transcriptional programs are de-synchronized in B cell lymphoma. Nat. Immunol. 19, 1013–1024 (2018).
pubmed: 30104629
doi: 10.1038/s41590-018-0181-4
Veselits, M. et al. Igβ ubiquitination activates PI3K signals required for endosomal sorting. J. Exp. Med. 214, 3775–3790 (2017).
pubmed: 29141870
pmcid: 5716028
doi: 10.1084/jem.20161868
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
doi: 10.1093/bioinformatics/bts635
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
pubmed: 24227677
pmcid: 24227677
doi: 10.1093/bioinformatics/btt656
Mandal, M. et al. CXCR4 signaling directs Igk recombination and the molecular mechanisms of late B lymphopoiesis. Nat. Immunol. 20, 1393–1403 (2019).
pubmed: 31477919
pmcid: 6754289
doi: 10.1038/s41590-019-0468-0
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at ArXiv https://arxiv.org/abs/1303.3997 (2013).
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
pubmed: 18798982
pmcid: 18798982
doi: 10.1186/gb-2008-9-9-r137
Li, Q., Brown, J., Huang, H. & Bickel, P. Measuring reproducibility of high-throughput experiments. Ann. Appl. Stat. 5, 1752–1779 (2011).
doi: 10.1214/11-AOAS466
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
pubmed: 20110278
pmcid: 2832824
doi: 10.1093/bioinformatics/btq033
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
doi: 10.1093/bioinformatics/btp616
Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).
pubmed: 30944313
pmcid: 6447622
doi: 10.1038/s41467-019-09234-6
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
pubmed: 20513432
pmcid: 20513432
doi: 10.1016/j.molcel.2010.05.004
Tan, H. et al. Integrative proteomics and phosphoproteomics profiling reveals dynamic signaling networks and bioenergetics pathways underlying T cell activation. Immunity 46, 488–503 (2017).
pubmed: 28285833
pmcid: 5466820
doi: 10.1016/j.immuni.2017.02.010
Tan, H. et al. Refined phosphopeptide enrichment by phosphate additive and the analysis of human brain phosphoproteome. Proteomics 15, 500–507 (2015).
pubmed: 25307156
doi: 10.1002/pmic.201400171
Wang, H. et al. Systematic optimization of long gradient chromatography mass spectrometry for deep analysis of brain proteome. J. Proteome Res. 14, 829–838 (2015).
pubmed: 25455107
doi: 10.1021/pr500882h
Niu, M. et al. Extensive peptide fractionation and y
pubmed: 28194965
pmcid: 5467445
doi: 10.1021/acs.analchem.6b04415
Stewart, E. et al. Identification of therapeutic targets in rhabdomyosarcoma through integrated genomic, epigenomic, and proteomic analyses. Cancer Cell 34, 411–426 e419 (2018).
pubmed: 30146332
pmcid: 6158019
doi: 10.1016/j.ccell.2018.07.012
Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinf. 9, 559 (2008).
doi: 10.1186/1471-2105-9-559
Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202–1214 (2015).
pubmed: 26000488
pmcid: 4481139
doi: 10.1016/j.cell.2015.05.002
Qiu, X. et al. Single-cell mRNA quantification and differential analysis with Census. Nat. Methods 14, 309–315 (2017).
pubmed: 28114287
pmcid: 5330805
doi: 10.1038/nmeth.4150
Qiu, X. et al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979–982 (2017).
pubmed: 28825705
pmcid: 5764547
doi: 10.1038/nmeth.4402
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).
pubmed: 16199517
pmcid: 16199517
doi: 10.1073/pnas.0506580102