دورية أكاديمية
أعرض في EDS

Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens.

التفاصيل البيبلوغرافية
العنوان: Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens.
المؤلفون: Papalexi E; Center for Genomics and Systems Biology, New York University, New York, NY, USA.; New York Genome Center, New York, NY, USA., Mimitou EP; Technology Innovation Lab, New York Genome Center, New York, NY, USA., Butler AW; Center for Genomics and Systems Biology, New York University, New York, NY, USA.; New York Genome Center, New York, NY, USA., Foster S; New York Genome Center, New York, NY, USA., Bracken B; Center for Genomics and Systems Biology, New York University, New York, NY, USA.; New York Genome Center, New York, NY, USA., Mauck WM 3rd; New York Genome Center, New York, NY, USA., Wessels HH; New York Genome Center, New York, NY, USA., Hao Y; Center for Genomics and Systems Biology, New York University, New York, NY, USA.; New York Genome Center, New York, NY, USA., Yeung BZ; BioLegend Inc., San Diego, CA, USA., Smibert P; Technology Innovation Lab, New York Genome Center, New York, NY, USA., Satija R; Center for Genomics and Systems Biology, New York University, New York, NY, USA. rsatija@nygenome.org.; New York Genome Center, New York, NY, USA. rsatija@nygenome.org.
المصدر: Nature genetics [Nat Genet] 2021 Mar; Vol. 53 (3), pp. 322-331. Date of Electronic Publication: 2021 Mar 01.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Co Country of Publication: United States NLM ID: 9216904 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1546-1718 (Electronic) Linking ISSN: 10614036 NLM ISO Abbreviation: Nat Genet Subsets: MEDLINE
أسماء مطبوعة: Original Publication: New York, NY : Nature Pub. Co., c1992-
مواضيع طبية MeSH: B7-H1 Antigen/*genetics , Immune Checkpoint Proteins/*physiology , Single-Cell Analysis/*methods, B7-2 Antigen/metabolism ; B7-H1 Antigen/metabolism ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Clustered Regularly Interspaced Short Palindromic Repeats ; Cullin Proteins/genetics ; Cullin Proteins/metabolism ; Humans ; Kelch-Like ECH-Associated Protein 1/genetics ; NF-E2-Related Factor 2/genetics ; NF-E2-Related Factor 2/metabolism ; Programmed Cell Death 1 Ligand 2 Protein/metabolism ; Receptors, Interferon/genetics ; Reproducibility of Results ; Signal-To-Noise Ratio ; THP-1 Cells ; Transcription Factors/genetics ; Transcription Factors/metabolism
مستخلص: The expression of inhibitory immune checkpoint molecules, such as programmed death-ligand (PD-L)1, is frequently observed in human cancers and can lead to the suppression of T cell-mediated immune responses. Here, we apply expanded CRISPR-compatible (EC)CITE-seq, a technology that combines pooled CRISPR screens with single-cell mRNA and surface protein measurements, to explore the molecular networks that regulate PD-L1 expression. We also develop a computational framework, mixscape, that substantially improves the signal-to-noise ratio in single-cell perturbation screens by identifying and removing confounding sources of variation. Applying these tools, we identify and validate regulators of PD-L1 and leverage our multimodal data to identify both transcriptional and post-transcriptional modes of regulation. Specifically, we discover that the Kelch-like protein KEAP1 and the transcriptional activator NRF2 mediate the upregulation of PD-L1 after interferon (IFN)-γ stimulation. Our results identify a new mechanism for the regulation of immune checkpoints and present a powerful analytical framework for the analysis of multimodal single-cell perturbation screens.
References: Greenwald, R. J., Freeman, G. J. & Sharpe, A. H. The B7 family revisited. Annu. Rev. Immunol. 23, 515–548 (2005). (PMID: 10.1146/annurev.immunol.23.021704.115611)
Pardoll, D. M. The blockade of immune checkpoints in cancer immunotherapy. Nat. Rev. Cancer 12, 252–264 (2012). (PMID: 10.1038/nrc3239)
Dong, H. et al. Tumor-associated B7-H1 promotes T-cell apoptosis: a potential mechanism of immune evasion. Nat. Med. 8, 793–800 (2002).
Zou, W. & Chen, L. Inhibitory B7-family molecules in the tumour microenvironment. Nat. Rev. Immunol. 8, 467–477 (2008). (PMID: 10.1038/nri2326)
Freeman, G. J. et al. Engagement of the PD-1 immunoinhibitory receptor by a novel B7 family member leads to negative regulation of lymphocyte activation. J. Exp. Med. 192, 1027–1034 (2000). (PMID: 10.1084/jem.192.7.1027)
Wang, X., Teng, F., Kong, L. & Yu, J. PD-L1 expression in human cancers and its association with clinical outcomes. Onco. Targets Ther. 9, 5023–5039 (2016). (PMID: 10.2147/OTT.S105862)
Chen, J. et al. Interferon-γ induced PD-L1 surface expression on human oral squamous carcinoma via PKD2 signal pathway. Immunobiology 217, 385–393 (2012). (PMID: 10.1016/j.imbio.2011.10.016)
Abiko, K. et al. IFN-γ from lymphocytes induces PD-L1 expression and promotes progression of ovarian cancer. Br. J. Cancer 112, 1501–1509 (2015). (PMID: 10.1038/bjc.2015.101)
Moon, J. W. et al. IFNγ induces PD-L1 overexpression by JAK2/STAT1/IRF-1 signaling in EBV-positive gastric carcinoma. Sci. Rep. 7, 17810 (2017).
Bellucci, R. et al. Interferon-γ-induced activation of JAK1 and JAK2 suppresses tumor cell susceptibility to NK cells through upregulation of PD-L1 expression. Oncoimmunology 4, e1008824 (2015). (PMID: 10.1080/2162402X.2015.1008824)
Garcia-Diaz, A. et al. Interferon receptor signaling pathways regulating PD-L1 and PD-L2 expression. Cell Rep. 19, 1189–1201 (2017). (PMID: 10.1016/j.celrep.2017.04.031)
Zou, J. et al. MYC inhibition increases PD-L1 expression induced by IFN-γ in hepatocellular carcinoma cells. Mol. Immunol. 101, 203–209 (2018). (PMID: 10.1016/j.molimm.2018.07.006)
Hogg, S. J. et al. BET-bromodomain inhibitors engage the host immune system and regulate expression of the immune checkpoint ligand PD-L1. Cell Rep. 18, 2162–2174 (2017). (PMID: 10.1016/j.celrep.2017.02.011)
Zhu, B. et al. Targeting the upstream transcriptional activator of PD-L1 as an alternative strategy in melanoma therapy. Oncogene 37, 4941–4954 (2018). (PMID: 10.1038/s41388-018-0314-0)
Zhang, J. et al. Cyclin D–CDK4 kinase destabilizes PD-L1 via cullin 3–SPOP to control cancer immune surveillance. Nature 553, 91–95 (2018). (PMID: 10.1038/nature25015)
Burr, M. L. et al. CMTM6 maintains the expression of PD-L1 and regulates anti-tumour immunity. Nature 549, 101–105 (2017).
Mezzadra, R. et al. Identification of CMTM6 and CMTM4 as PD-L1 protein regulators. Nature 549, 106–110 (2017).
Mimitou, E. P. et al. Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells. Nat. Methods 16, 409–412 (2019). (PMID: 10.1038/s41592-019-0392-0)
Dixit, A. et al. Perturb-seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell 167, 1853–1866 (2016). (PMID: 10.1016/j.cell.2016.11.038)
Datlinger, P. et al. Pooled CRISPR screening with single-cell transcriptome readout. Nat. Methods 14, 297–301 (2017). (PMID: 10.1038/nmeth.4177)
Jaitin, D. A. et al. Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-seq. Cell 167, 1883–1896 (2016).
Stoeckius, M. et al. Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 14, 865–868 (2017).
Hast, B. E. et al. Cancer-derived mutations in KEAP1 impair NRF2 degradation but not ubiquitination. Cancer Res. 74, 808–817 (2014). (PMID: 10.1158/0008-5472.CAN-13-1655)
Postow, M. A., Callahan, M. K. & Wolchok, J. D. Immune checkpoint blockade in cancer therapy. J. Clin. Oncol. 33, 1974–1982 (2015). (PMID: 10.1200/JCO.2014.59.4358)
Duan, B. et al. Model-based understanding of single-cell CRISPR screening. Nat. Commun. 10, 2233 (2019). (PMID: 10.1038/s41467-019-10216-x)
Hastie, T. & Tibshirani, R. Discriminant analysis by Gaussian mixtures. J. R. Stat. Soc. Ser. B 58, 155–176 (1996).
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019). (PMID: 10.1016/j.cell.2019.05.031)
Zhu, H. et al. BET bromodomain inhibition promotes anti-tumor immunity by suppressing PD-L1 expression. Cell Rep. 16, 2829–2837 (2016). (PMID: 10.1016/j.celrep.2016.08.032)
Nguyen, T., Nioi, P. & Pickett, C. B. The Nrf2-antioxidant response element signaling pathway and its activation by oxidative stress. J. Biol. Chem. 284, 13291–13295 (2009).
Cullinan, S. B., Gordan, J. D., Jin, J., Harper, J. W. & Diehl, J. A. The Keap1-BTB protein is an adaptor that bridges Nrf2 to a Cul3-based E3 ligase: oxidative stress sensing by a Cul3–Keap1 ligase. Mol. Cell. Biol. 24, 8477–8486 (2004). (PMID: 10.1128/MCB.24.19.8477-8486.2004)
Taguchi, K. & Yamamoto, M. The KEAP1–NRF2 system in cancer. Front. Oncol. 7, 85 (2017). (PMID: 10.3389/fonc.2017.00085)
Argelaguet, R. et al. MOFA: a statistical framework for comprehensive integration of multi-modal single-cell data. Genome Biol. 21, 111 (2020).
Cao, J. et al. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science 361, 1380–1385 (2018). (PMID: 10.1126/science.aau0730)
Clark, S. J. et al. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nat. Commun. 9, 781 (2018). (PMID: 10.1038/s41467-018-03149-4)
Rubin, A. J. et al. Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks. Cell 176, 361–376 (2019). (PMID: 10.1016/j.cell.2018.11.022)
Chen, S., Lake, B. B. & Zhang, K. High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. Nat. Biotechnol. 37, 1452–1457 (2019). (PMID: 10.1038/s41587-019-0290-0)
Ashland, O. R. FlowJo Software, version 10.6.2 (Becton, Dickinson and Company, 2020).
Stoeckius, M. et al. Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. Genome Biol. 19, 224 (2018).
Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36, 411–420 (2018). (PMID: 10.1038/nbt.4096)
Dang, Y. et al. Optimizing sgRNA structure to improve CRISPR-Cas9 knockout efficiency. Genome Biol. 16, 280 (2015). (PMID: 10.1186/s13059-015-0846-3)
Meier, J. A., Zhang, F. & Sanjana, N. E. GUIDES: sgRNA design for loss-of-function screens. Nat. Methods 14, 831–832 (2017).
Ran, F. A. et al. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 8, 2281–2308 (2013). (PMID: 10.1038/nprot.2013.143)
Brinkman, E. K. & van Steensel, B. Rapid quantitative evaluation of CRISPR genome editing by TIDE and TIDER. Methods Mol. Biol. 1961, 29–44 (2019). (PMID: 10.1007/978-1-4939-9170-9_3)
McGinnis, C. S. et al. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nat. Methods 16, 619–626 (2019). (PMID: 10.1038/s41592-019-0433-8)
McInnes, L., Healy, J. & Melville, J. UMAP: Uniform Manifold Approximation and Projection for dimension reduction. Preprint at https://arxiv.org/abs/1802.03426 (2018).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009). (PMID: 10.1093/bioinformatics/btp352)
Robinson, J. T. et al. Integrative Genomics Viewer. Nat. Biotechnol. 29, 24–26 (2011). (PMID: 10.1038/nbt.1754)
Chen, E. Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013). (PMID: 10.1186/1471-2105-14-128)
Kuleshov, M. V. et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 44, W90–W97 (2016). (PMID: 10.1093/nar/gkw377)
Yau, E. H. & Rana, T. M. Next-generation sequencing of genome-wide CRISPR screens. Methods Mol. Biol. 1712, 203–216 (2018). (PMID: 10.1007/978-1-4939-7514-3_13)
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012). (PMID: 10.1038/nmeth.1923)
de Boer, C. G., Ray, J. P., Hacohen, N. & Regev, A. MAUDE: inferring expression changes in sorting-based CRISPR screens. Genome Biol. 21, 134 (2020).
Satija, R. Barcoded plate-based single cell RNA-seq version 1. protocols.io https://doi.org/10.17504/protocols.io.nkgdctw (2018).
معلومات مُعتمدة: DP2 HG009623 United States HG NHGRI NIH HHS; R21 HG009748 United States HG NHGRI NIH HHS; RM1 HG011014 United States HG NHGRI NIH HHS
المشرفين على المادة: 0 (B7-2 Antigen)
0 (B7-H1 Antigen)
0 (BRD4 protein, human)
0 (CD274 protein, human)
0 (CUL3 protein, human)
0 (Cell Cycle Proteins)
0 (Cullin Proteins)
0 (IFNGR2 protein, human)
0 (Immune Checkpoint Proteins)
0 (KEAP1 protein, human)
0 (Kelch-Like ECH-Associated Protein 1)
0 (NF-E2-Related Factor 2)
0 (NFE2L2 protein, human)
0 (PDCD1LG2 protein, human)
0 (Programmed Cell Death 1 Ligand 2 Protein)
0 (Receptors, Interferon)
0 (Transcription Factors)
تواريخ الأحداث: Date Created: 20210302 Date Completed: 20210408 Latest Revision: 20210903
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC8011839
DOI: 10.1038/s41588-021-00778-2
PMID: 33649593
قاعدة البيانات: MEDLINE
الوصف
تدمد:1546-1718
DOI:10.1038/s41588-021-00778-2