Identification, sorting and profiling of functional killer cells via the capture of fluorescent target-cell lysate.
Journal
Nature biomedical engineering
ISSN: 2157-846X
Titre abrégé: Nat Biomed Eng
Pays: England
ID NLM: 101696896
Informations de publication
Date de publication:
31 Aug 2023
31 Aug 2023
Historique:
received:
15
07
2022
accepted:
04
08
2023
medline:
1
9
2023
pubmed:
1
9
2023
entrez:
31
8
2023
Statut:
aheadofprint
Résumé
Assays for assessing cell-mediated cytotoxicity are largely target-cell-centric and cannot identify and isolate subpopulations of cytotoxic effector cells. Here we describe an assay compatible with flow cytometry for the accurate identification and sorting of functional killer-cell subpopulations in co-cultures. The assay, which we named PAINTKiller (for 'proximity affinity intracellular transfer identification of killer cells'), relies on the detection of an intracellular fluorescent protein 'painted' by a lysed cell on the surface of the lysing cytotoxic cell (specifically, on cell lysis the intracellular fluorescein derivative carboxyfluorescein succinimidyl ester is captured on the surface of the natural killer cell by an antibody for anti-fluorescein isothiocyanate linked to an antibody for the pan-leucocyte surface receptor CD45). The assay can be integrated with single-cell RNA sequencing for the analysis of molecular pathways associated with cell cytotoxicity and may be used to uncover correlates of functional immune responses.
Identifiants
pubmed: 37652987
doi: 10.1038/s41551-023-01089-z
pii: 10.1038/s41551-023-01089-z
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : MOH | National Medical Research Council (NMRC)
ID : MOH-OFIRG18nov-003
Organisme : Ministry of Education - Singapore (MOE)
ID : MOE-T2EP30120-0008
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature Limited.
Références
Kagi, D., Ledermann, B., Burki, K., Zinkernagel, R. M. & Hengartner, H. Molecular mechanisms of lymphocyte-mediated cytotoxicity and their role in immunological protection and pathogenesis in vivo. Annu. Rev. Immunol. 14, 207–232 (1996).
pubmed: 8717513
doi: 10.1146/annurev.immunol.14.1.207
Prager, I. & Watzl, C. Mechanisms of natural killer cell-mediated cellular cytotoxicity. J. Leukoc. Biol. 105, 1319–1329 (2019).
pubmed: 31107565
doi: 10.1002/JLB.MR0718-269R
Brunner, K. T., Mauel, J., Cerottini, J. C. & Chapuis, B. Quantitative assay of the lytic action of immune lymphoid cells on
pubmed: 4966657
pmcid: 1409286
Sepp, A., Binns, R. M. & Lechler, R. I. Improved protocol for colorimetric detection of complement-mediated cytotoxicity based on the measurement of cytoplasmic lactate dehydrogenase activity. J. Immunol. Methods 196, 175–180 (1996).
pubmed: 8841455
doi: 10.1016/0022-1759(96)00112-3
Wong, P., Wagner, J. A., Berrien-Elliott, M. M., Schappe, T. & Fehniger, T. A. Flow cytometry-based ex vivo murine NK cell cytotoxicity assay. STAR Protoc. 2, 100262 (2021).
pubmed: 33490978
pmcid: 7806516
doi: 10.1016/j.xpro.2020.100262
Kandarian, F., Sunga, G. M., Arango-Saenz, D. & Rossetti, M. A flow cytometry-based cytotoxicity assay for the assessment of human NK cell activity. J. Vis. Exp. (126), e56191 (2017).
Wu, X., Zhang, Y., Li, Y. & Schmidt-Wolf, I. G. H. Improvements in flow cytometry-based cytotoxicity assay. Cytometry A 99, 680–688 (2021).
pubmed: 33068327
doi: 10.1002/cyto.a.24242
Peper, J. K. et al. An impedance-based cytotoxicity assay for real-time and label-free assessment of T-cell-mediated killing of adherent cells. J. Immunol. Methods 405, 192–198 (2014).
pubmed: 24486140
doi: 10.1016/j.jim.2014.01.012
Vembadi, A., Menachery, A. & Qasaimeh, M. A. Cell cytometry: review and perspective on biotechnological advances. Front. Bioeng. Biotechnol. 7, 147 (2019).
pubmed: 31275933
pmcid: 6591278
doi: 10.3389/fbioe.2019.00147
Slota, M., Lim, J. B., Dang, Y. & Disis, M. L. ELISpot for measuring human immune responses to vaccines. Expert Rev. Vaccines 10, 299–306 (2011).
pubmed: 21434798
pmcid: 3360522
doi: 10.1586/erv.10.169
Alter, G., Malenfant, J. M. & Altfeld, M. CD107a as a functional marker for the identification of natural killer cell activity. J. Immunol. Methods 294, 15–22 (2004).
pubmed: 15604012
doi: 10.1016/j.jim.2004.08.008
Bryceson, Y. T., March, M. E., Barber, D. F., Ljunggren, H. G. & Long, E. O. Cytolytic granule polarization and degranulation controlled by different receptors in resting NK cells. J. Exp. Med. 202, 1001–1012 (2005).
pubmed: 16203869
pmcid: 2213171
doi: 10.1084/jem.20051143
Wolint, P., Betts, M. R., Koup, R. A. & Oxenius, A. Immediate cytotoxicity but not degranulation distinguishes effector and memory subsets of CD8+ T cells. J. Exp. Med. 199, 925–936 (2004).
pubmed: 15051762
pmcid: 2211884
doi: 10.1084/jem.20031799
Skelley, A. M., Kirak, O., Suh, H., Jaenisch, R. & Voldman, J. Microfluidic control of cell pairing and fusion. Nat. Methods 6, 147–152 (2009).
pubmed: 19122668
pmcid: 3251011
doi: 10.1038/nmeth.1290
Dura, B. et al. Profiling lymphocyte interactions at the single-cell level by microfluidic cell pairing. Nat. Commun. 6, 5940 (2015).
pubmed: 25585172
doi: 10.1038/ncomms6940
Dura, B. et al. Longitudinal multiparameter assay of lymphocyte interactions from onset by microfluidic cell pairing and culture. Proc. Natl Acad. Sci. USA 113, E3599–E3608 (2016).
pubmed: 27303033
pmcid: 4932925
doi: 10.1073/pnas.1515364113
Assenmacher, M., Lohning, M. & Radbruch, A. Detection and isolation of cytokine secreting cells using the cytometric cytokine secretion assay. Curr. Protoc. Immunol. https://doi.org/10.1002/0471142735.im0627s46 (2002).
McKinnon, K. M. Flow cytometry: an overview. Curr. Protoc. Immunol. https://doi.org/10.1002/cpim.40 (2018).
Deng, N. & Mosmann, T. R. Optimization of the cytokine secretion assay for human IL-2 in single and combination assays. Cytometry A 87, 777–783 (2015).
pubmed: 25919308
pmcid: 4759652
doi: 10.1002/cyto.a.22668
Trinklein, N. D. et al. Efficient tumor killing and minimal cytokine release with novel T-cell agonist bispecific antibodies. MAbs 11, 639–652 (2019).
pubmed: 30698484
pmcid: 6601548
doi: 10.1080/19420862.2019.1574521
Good, Z. et al. Proliferation tracing with single-cell mass cytometry optimizes generation of stem cell memory-like T cells. Nat. Biotechnol. 37, 259–266 (2019).
pubmed: 30742126
pmcid: 6521980
doi: 10.1038/s41587-019-0033-2
Matera, G., Lupi, M. & Ubezio, P. Heterogeneous cell response to topotecan in a CFSE-based proliferation test. Cytometry A 62, 118–128 (2004).
pubmed: 15536634
doi: 10.1002/cyto.a.20097
Ponchio, L. et al. Mitomycin C as an alternative to irradiation to inhibit the feeder layer growth in long-term culture assays. Cytotherapy 2, 281–286 (2000).
pubmed: 12042037
doi: 10.1080/146532400539215
Llames, S., Garcia-Perez, E., Meana, A., Larcher, F. & del Rio, M. Feeder layer cell actions and applications. Tissue Eng. B Rev. 21, 345–353 (2015).
doi: 10.1089/ten.teb.2014.0547
Krzewski, K., Gil-Krzewska, A., Nguyen, V., Peruzzi, G. & Coligan, J. E. LAMP1/CD107a is required for efficient perforin delivery to lytic granules and NK-cell cytotoxicity. Blood 121, 4672–4683 (2013).
pubmed: 23632890
pmcid: 3674668
doi: 10.1182/blood-2012-08-453738
Liu, D. et al. Integrin-dependent organization and bidirectional vesicular traffic at cytotoxic immune synapses. Immunity 31, 99–109 (2009).
pubmed: 19592272
pmcid: 2740634
doi: 10.1016/j.immuni.2009.05.009
Suen, W. C., Lee, W. Y., Leung, K. T., Pan, X. H. & Li, G. Natural killer cell-based cancer immunotherapy: a review on 10 years completed clinical trials. Cancer Invest. 36, 431–457 (2018).
pubmed: 30325244
doi: 10.1080/07357907.2018.1515315
Surman, D. R., Dudley, M. E., Overwijk, W. W. & Restifo, N. P. Cutting edge: CD4+ T cell control of CD8+ T cell reactivity to a model tumor antigen. J. Immunol. 164, 562–565 (2000).
pubmed: 10623795
doi: 10.4049/jimmunol.164.2.562
Rosenberg, S. A. & Dudley, M. E. Cancer regression in patients with metastatic melanoma after the transfer of autologous antitumor lymphocytes. Proc. Natl Acad. Sci. USA 101, 14639–14645 (2004).
pubmed: 15381769
pmcid: 521998
doi: 10.1073/pnas.0405730101
Caligiuri, M. A. Human natural killer cells. Blood 112, 461–469 (2008).
pubmed: 18650461
pmcid: 2481557
doi: 10.1182/blood-2007-09-077438
Spiegel, J. Y. et al. CAR T cells with dual targeting of CD19 and CD22 in adult patients with recurrent or refractory B cell malignancies: a phase 1 trial. Nat. Med. 27, 1419–1431 (2021).
pubmed: 34312556
pmcid: 8363505
doi: 10.1038/s41591-021-01436-0
Prager, I. et al. NK cells switch from granzyme B to death receptor-mediated cytotoxicity during serial killing. J. Exp. Med. 216, 2113–2127 (2019).
pubmed: 31270246
pmcid: 6719417
doi: 10.1084/jem.20181454
Park, J. et al. Multifunctional microparticles with stimulation and sensing capabilities for facile NK cell activity assay. ACS Sens. 6, 693–697 (2021).
pubmed: 33606518
doi: 10.1021/acssensors.0c02138
Dybkaer, K. et al. Genome wide transcriptional analysis of resting and IL2 activated human natural killer cells: gene expression signatures indicative of novel molecular signaling pathways. BMC Genomics 8, 230 (2007).
pubmed: 17623099
pmcid: 1959522
doi: 10.1186/1471-2164-8-230
Zhang, J. et al. Sequential actions of EOMES and T-BET promote stepwise maturation of natural killer cells. Nat. Commun. 12, 5446 (2021).
pubmed: 34521844
pmcid: 8440589
doi: 10.1038/s41467-021-25758-2
van Helden, M. J. et al. Terminal NK cell maturation is controlled by concerted actions of T-bet and Zeb2 and is essential for melanoma rejection. J. Exp. Med. 212, 2015–2025 (2015).
pubmed: 26503444
pmcid: 4647267
doi: 10.1084/jem.20150809
Chester, C., Fritsch, K. & Kohrt, H. E. Natural killer cell immunomodulation: targeting activating, inhibitory, and co-stimulatory receptor signaling for cancer immunotherapy. Front. Immunol. 6, 601 (2015).
pubmed: 26697006
pmcid: 4667030
doi: 10.3389/fimmu.2015.00601
Connor, J. H., Weiser, D. C., Li, S., Hallenbeck, J. M. & Shenolikar, S. Growth arrest and DNA damage-inducible protein GADD34 assembles a novel signaling complex containing protein phosphatase 1 and inhibitor 1. Mol. Cell. Biol. 21, 6841–6850 (2001).
pubmed: 11564868
pmcid: 99861
doi: 10.1128/MCB.21.20.6841-6850.2001
Wang, X. W. et al. GADD45 induction of a G2/M cell cycle checkpoint. Proc. Natl Acad. Sci. USA 96, 3706–3711 (1999).
pubmed: 10097101
pmcid: 22358
doi: 10.1073/pnas.96.7.3706
Li, Y., Yu, M., Yin, J., Yan, H. & Wang, X. Enhanced calcium signal induces NK cell degranulation but inhibits its cytotoxic activity. J. Immunol. 208, 347–357 (2022).
pubmed: 34911773
doi: 10.4049/jimmunol.2001141
Jacobi, C. et al. Exposure of NK cells to intravenous immunoglobulin induces IFN gamma release and degranulation but inhibits their cytotoxic activity. Clin. Immunol. 133, 393–401 (2009).
pubmed: 19828380
doi: 10.1016/j.clim.2009.09.006
Stoeckius, M. et al. Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 14, 865–868 (2017).
pubmed: 28759029
pmcid: 5669064
doi: 10.1038/nmeth.4380
Parish, C. R. Fluorescent dyes for lymphocyte migration and proliferation studies. Immunol. Cell Biol. 77, 499–508 (1999).
pubmed: 10571670
doi: 10.1046/j.1440-1711.1999.00877.x
Zheng, Y., Tang, L., Mabardi, L., Kumari, S. & Irvine, D. J. Enhancing adoptive cell therapy of cancer through targeted delivery of small-molecule immunomodulators to internalizing or noninternalizing receptors. ACS Nano 11, 3089–3100 (2017).
pubmed: 28231431
pmcid: 5647839
doi: 10.1021/acsnano.7b00078
Wu, T., Womersley, H. J., Wang, J. R., Scolnick, J. & Cheow, L. F. Time-resolved assessment of single-cell protein secretion by sequencing. Nat. Methods 20, 723–734 (2023).
pubmed: 37037998
doi: 10.1038/s41592-023-01841-y
Roelli, P., bbimber, Flynn, B., santiagorevale & Gui, G. Hoohm/CITE-seq-Count: 1.4.2 (1.4.2). Zenodo https://doi.org/10.5281/zenodo.2585469 (2019).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).
pubmed: 34062119
pmcid: 8238499
doi: 10.1016/j.cell.2021.04.048
Pont, F., Tosolini, M. & Fournie, J. J. Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets. Nucleic Acids Res. 47, e133 (2019).
pubmed: 31294801
pmcid: 6868346
doi: 10.1093/nar/gkz601
Yu, G., Wang, L. G., Han, Y. & He, Q. Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284–287 (2012).
pubmed: 22455463
pmcid: 3339379
doi: 10.1089/omi.2011.0118
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: 1239896
doi: 10.1073/pnas.0506580102