1
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Pfeifer M, Brammeld JS, Price S, Pilling J, Bhavsar D, Farcas A, Bateson J, Sundarrajan A, Miragaia RJ, Guan N, Arnold S, Tariq L, Grondine M, Talbot S, Guerriero ML, O'Neill DJ, Young J, Company C, Dunn S, Thorpe H, Martin MJ, Maratea K, Barrell D, Ahdesmaki M, Mettetal JT, Brownell J, McDermott U. Genome-wide CRISPR screens identify the YAP/TEAD axis as a driver of persister cells in EGFR mutant lung cancer. Commun Biol 2024; 7:497. [PMID: 38658677 PMCID: PMC11043391 DOI: 10.1038/s42003-024-06190-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/12/2024] [Indexed: 04/26/2024] Open
Abstract
Most lung cancer patients with metastatic cancer eventually relapse with drug-resistant disease following treatment and EGFR mutant lung cancer is no exception. Genome-wide CRISPR screens, to either knock out or overexpress all protein-coding genes in cancer cell lines, revealed the landscape of pathways that cause resistance to the EGFR inhibitors osimertinib or gefitinib in EGFR mutant lung cancer. Among the most recurrent resistance genes were those that regulate the Hippo pathway. Following osimertinib treatment a subpopulation of cancer cells are able to survive and over time develop stable resistance. These 'persister' cells can exploit non-genetic (transcriptional) programs that enable cancer cells to survive drug treatment. Using genetic and pharmacologic tools we identified Hippo signalling as an important non-genetic mechanism of cell survival following osimertinib treatment. Further, we show that combinatorial targeting of the Hippo pathway and EGFR is highly effective in EGFR mutant lung cancer cells and patient-derived organoids, suggesting a new therapeutic strategy for EGFR mutant lung cancer patients.
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Affiliation(s)
- Matthias Pfeifer
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
- Leibniz-Institute of Virology (LIV) and University hospital Hamburg-Eppendorf (UKE), Hamburg, Germany
| | | | - Stacey Price
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - James Pilling
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Deepa Bhavsar
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Anca Farcas
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | | | - Anjana Sundarrajan
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Ricardo J Miragaia
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Nin Guan
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Stephanie Arnold
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Laiba Tariq
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Michael Grondine
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Sarah Talbot
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Maria Lisa Guerriero
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Daniel J O'Neill
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Jamie Young
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Carlos Company
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Shanade Dunn
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Hannah Thorpe
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Matthew J Martin
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Kimberly Maratea
- Clinical Pharmacology & Safety, BioPharmaceuticals R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Daniel Barrell
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Miika Ahdesmaki
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Jerome T Mettetal
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - James Brownell
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
| | - Ultan McDermott
- Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK.
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2
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Lawson M, Cureton N, Ros S, Cheraghchi-Bashi A, Urosevic J, D'Arcy S, Delpuech O, DuPont M, Fisher DI, Gangl ET, Lewis H, Trueman D, Wali N, Williamson SC, Moss J, Montaudon E, Derrien H, Marangoni E, Miragaia RJ, Gagrica S, Morentin-Gutierrez P, Moss TA, Maglennon G, Sutton D, Polanski R, Rosen A, Cairns J, Zhang P, Sánchez-Guixé M, Serra V, Critchlow SE, Scott JS, Lindemann JP, Barry ST, Klinowska T, Morrow CJ, S Carnevalli L. The Next-Generation Oral Selective Estrogen Receptor Degrader Camizestrant (AZD9833) Suppresses ER+ Breast Cancer Growth and Overcomes Endocrine and CDK4/6 Inhibitor Resistance. Cancer Res 2023; 83:3989-4004. [PMID: 37725704 PMCID: PMC10690091 DOI: 10.1158/0008-5472.can-23-0694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/11/2023] [Accepted: 09/15/2023] [Indexed: 09/21/2023]
Abstract
Oral selective estrogen receptor degraders (SERD) could become the backbone of endocrine therapy (ET) for estrogen receptor-positive (ER+) breast cancer, as they achieve greater inhibition of ER-driven cancers than current ETs and overcome key resistance mechanisms. In this study, we evaluated the preclinical pharmacology and efficacy of the next-generation oral SERD camizestrant (AZD9833) and assessed ER-co-targeting strategies by combining camizestrant with CDK4/6 inhibitors (CDK4/6i) and PI3K/AKT/mTOR-targeted therapy in models of progression on CDK4/6i and/or ET. Camizestrant demonstrated robust and selective ER degradation, modulated ER-regulated gene expression, and induced complete ER antagonism and significant antiproliferation activity in ESR1 wild-type (ESR1wt) and mutant (ESR1m) breast cancer cell lines and patient-derived xenograft (PDX) models. Camizestrant also delivered strong antitumor activity in fulvestrant-resistant ESR1wt and ESR1m PDX models. Evaluation of camizestrant in combination with CDK4/6i (palbociclib or abemaciclib) in CDK4/6-naive and -resistant models, as well as in combination with PI3Kαi (alpelisib), mTORi (everolimus), or AKTi (capivasertib), indicated that camizestrant was active with CDK4/6i or PI3K/AKT/mTORi and that antitumor activity was further increased by the triple combination. The response was observed independently of PI3K pathway mutation status. Overall, camizestrant shows strong and broad antitumor activity in ER+ breast cancer as a monotherapy and when combined with CDK4/6i and PI3K/AKT/mTORi. SIGNIFICANCE Camizestrant, a next-generation oral SERD, shows promise in preclinical models of ER+ breast cancer alone and in combination with CDK4/6 and PI3K/AKT/mTOR inhibitors to address endocrine resistance, a current barrier to treatment.
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Affiliation(s)
- Mandy Lawson
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Natalie Cureton
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Susana Ros
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | | | - Jelena Urosevic
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Sophie D'Arcy
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Oona Delpuech
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Michelle DuPont
- Research and Early Development, Oncology R&D, AstraZeneca, Waltham, Massachusetts
| | - David I. Fisher
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Eric T. Gangl
- Research and Early Development, Oncology R&D, AstraZeneca, Waltham, Massachusetts
| | - Hilary Lewis
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Dawn Trueman
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Neha Wali
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | | | - Jennifer Moss
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | | | | | | | | | - Sladjana Gagrica
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | | | - Thomas A. Moss
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Gareth Maglennon
- Clinical Pharmacology and Safety Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Daniel Sutton
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Radoslaw Polanski
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Alan Rosen
- Research and Early Development, Oncology R&D, AstraZeneca, Waltham, Massachusetts
| | - Jonathan Cairns
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Pei Zhang
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Mònica Sánchez-Guixé
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Susan E. Critchlow
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - James S. Scott
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | | | - Simon T. Barry
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Teresa Klinowska
- Late Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
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3
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Criscione SW, Martin MJ, Oien DB, Gorthi A, Miragaia RJ, Zhang J, Chen H, Karl DL, Mendler K, Markovets A, Gagrica S, Delpuech O, Dry JR, Grondine M, Hattersley MM, Urosevic J, Floc’h N, Drew L, Yao Y, Smith PD. The landscape of therapeutic vulnerabilities in EGFR inhibitor osimertinib drug tolerant persister cells. NPJ Precis Oncol 2022; 6:95. [PMID: 36575215 PMCID: PMC9794691 DOI: 10.1038/s41698-022-00337-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 12/12/2022] [Indexed: 12/28/2022] Open
Abstract
Third-generation EGFR tyrosine kinase inhibitors (EGFR-TKIs), including osimertinib, an irreversible EGFR-TKI, are important treatments for non-small cell lung cancer with EGFR-TKI sensitizing or EGFR T790M resistance mutations. While patients treated with osimertinib show clinical benefit, disease progression and drug resistance are common. Emergence of de novo acquired resistance from a drug tolerant persister (DTP) cell population is one mechanism proposed to explain progression on osimertinib and other targeted cancer therapies. Here we profiled osimertinib DTPs using RNA-seq and ATAC-seq to characterize the features of these cells and performed drug screens to identify therapeutic vulnerabilities. We identified several vulnerabilities in osimertinib DTPs that were common across models, including sensitivity to MEK, AURKB, BRD4, and TEAD inhibition. We linked several of these vulnerabilities to gene regulatory changes, for example, TEAD vulnerability was consistent with evidence of Hippo pathway turning off in osimertinib DTPs. Last, we used genetic approaches using siRNA knockdown or CRISPR knockout to validate AURKB, BRD4, and TEAD as the direct targets responsible for the vulnerabilities observed in the drug screen.
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Affiliation(s)
- Steven W. Criscione
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Matthew J. Martin
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Derek B. Oien
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Aparna Gorthi
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA ,grid.267309.90000 0001 0629 5880Department of Cell Systems & Anatomy, Greehey Children’s Cancer Research Institute, University of Texas at Health San Antonio, San Antonio, TX USA
| | - Ricardo J. Miragaia
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Jingwen Zhang
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Huawei Chen
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Daniel L. Karl
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Kerrin Mendler
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Aleksandra Markovets
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Sladjana Gagrica
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Oona Delpuech
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Jonathan R. Dry
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Michael Grondine
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Maureen M. Hattersley
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Jelena Urosevic
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Nicolas Floc’h
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Lisa Drew
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Yi Yao
- grid.418152.b0000 0004 0543 9493Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA USA
| | - Paul D. Smith
- grid.417815.e0000 0004 5929 4381Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
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4
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Pore N, Wu S, Standifer N, Jure-Kunkel M, de Los Reyes M, Shrestha Y, Halpin R, Rothstein R, Mulgrew K, Blackmore S, Martin P, Meekin J, Griffin M, Bisha I, Proia TA, Miragaia RJ, Herbst R, Gupta A, Abdullah SE, Raja R, Frigault MM, Barrett JC, Dennis PA, Ascierto ML, Oberst MD. Resistance to durvalumab and durvalumab plus tremelimumab is associated with functional STK11 mutations in non-small-cell lung cancer patients and is reversed by STAT3 knockdown. Cancer Discov 2021; 11:2828-2845. [PMID: 34230008 DOI: 10.1158/2159-8290.cd-20-1543] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/30/2021] [Accepted: 07/02/2021] [Indexed: 11/16/2022]
Abstract
Mutations in the STK11 (LKB1) gene regulate resistance to PD-1/PD-L1 blockade. This study evaluated this association in patients with nonsquamous non-small-cell lung cancer enrolled in three Phase 1/2 trials. STK11 mutations were associated with resistance to the anti-PD-L1 antibody durvalumab (alone/with the anti-CTLA-4 antibody tremelimumab) independently of KRAS mutational status, highlighting STK11 as a potential driver of resistance to checkpoint blockade. Retrospective assessments of tumor tissue, whole blood and serum revealed a unique immune phenotype in patients with STK11 mutations, with increased expression of markers associated with neutrophils (i.e. CXCL2, IL6), Th17 contexture (i.e. IL17A) and immune checkpoints. Associated changes were observed in the periphery. Reduction of STAT3 in the tumor microenvironment using an antisense oligonucleotide reversed immunotherapy resistance in preclinical STK11 knockout models. These results suggest that STK11 mutations may hinder response to checkpoint blockade through mechanisms including suppressive myeloid cell biology, which could be reversed by STAT3-targeted therapy.
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Affiliation(s)
| | - Song Wu
- AstraZeneca, Gaithersburg, Maryland
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5
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Kumar S, Fonseca VR, Ribeiro F, Basto AP, Água-Doce A, Monteiro M, Elessa D, Miragaia RJ, Gomes T, Piaggio E, Segura E, Gama-Carvalho M, Teichmann SA, Graca L. Developmental bifurcation of human T follicular regulatory cells. Sci Immunol 2021; 6:6/59/eabd8411. [PMID: 34049865 DOI: 10.1126/sciimmunol.abd8411] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 02/22/2021] [Accepted: 04/29/2021] [Indexed: 12/20/2022]
Abstract
Germinal centers (GCs) are anatomic structures where B cells undergo affinity maturation, leading to production of high-affinity antibodies. The balance between T follicular helper (TFH) and regulatory (TFR) cells is critical for adequate control of GC responses. The study of human TFH and TFR cell development has been hampered because of the lack of in vitro assays reproducing in vivo biology, along with difficult access to healthy human lymphoid tissues. We used a single-cell transcriptomics approach to study the maturation of TFH and TFR cells isolated from human blood, iliac lymph nodes (LNs), and tonsils. As independent tissues have distinct proportions of follicular T cells in different maturation states, we leveraged the heterogeneity to reconstruct the maturation trajectory for human TFH and TFR cells. We found that the dominant maturation of TFR cells follows a bifurcated trajectory from precursor Treg cells, with one arm of the bifurcation leading to blood TFR cells and the other leading to the most mature GC TFR cells. Overall, our data provide a comprehensive resource for the transcriptomics of different follicular T cell populations and their dynamic relationship across different tissues.
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Affiliation(s)
- Saumya Kumar
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Válter R Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisboa, Portugal
| | - Filipa Ribeiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Afonso P Basto
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Ana Água-Doce
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Dikélélé Elessa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ricardo J Miragaia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Eliane Piaggio
- Institut Curie, PSL Research University, INSERM U932, Paris F-75005, France.,Centre d'Investigation Clinique Biotherapie CICBT 1428, Institut Curie, Paris F-75005, France
| | - Elodie Segura
- Institut Curie, PSL Research University, INSERM U932, Paris F-75005, France
| | - Margarida Gama-Carvalho
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisboa 1749-016, Portugal
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, JJ Thomson Ave., Cambridge CB3 0HE, UK
| | - Luis Graca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal. .,Instituto Gulbenkian de Ciência, Oeiras, Portugal
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6
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Miragaia RJ, Gomes T, Chomka A, Jardine L, Riedel A, Hegazy AN, Whibley N, Tucci A, Chen X, Lindeman I, Emerton G, Krausgruber T, Shields J, Haniffa M, Powrie F, Teichmann SA. Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation. Immunity 2019; 50:493-504.e7. [PMID: 30737144 PMCID: PMC6382439 DOI: 10.1016/j.immuni.2019.01.001] [Citation(s) in RCA: 283] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 09/28/2018] [Accepted: 12/31/2018] [Indexed: 02/07/2023]
Abstract
Non-lymphoid tissues (NLTs) harbor a pool of adaptive immune cells with largely unexplored phenotype and development. We used single-cell RNA-seq to characterize 35,000 CD4+ regulatory (Treg) and memory (Tmem) T cells in mouse skin and colon, their respective draining lymph nodes (LNs) and spleen. In these tissues, we identified Treg cell subpopulations with distinct degrees of NLT phenotype. Subpopulation pseudotime ordering and gene kinetics were consistent in recruitment to skin and colon, yet the initial NLT-priming in LNs and the final stages of NLT functional adaptation reflected tissue-specific differences. Predicted kinetics were recapitulated using an in vivo melanoma-induction model, validating key regulators and receptors. Finally, we profiled human blood and NLT Treg and Tmem cells, and identified cross-mammalian conserved tissue signatures. In summary, we describe the relationship between Treg cell heterogeneity and recruitment to NLTs through the combined use of computational prediction and in vivo validation.
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Affiliation(s)
- Ricardo J Miragaia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Agnieszka Chomka
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Experimental Medicine Division Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Laura Jardine
- Institute of Cellular Medicine, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Angela Riedel
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Ahmed N Hegazy
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Experimental Medicine Division Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Natasha Whibley
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Andrea Tucci
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Xi Chen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ida Lindeman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Guy Emerton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Thomas Krausgruber
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Experimental Medicine Division Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Experimental Medicine Division Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
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7
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Abstract
The starting material for all single-cell protocols is a cell suspension. The particular functions and spatial distribution of immune cells generally make them easy to isolate them from the tissues where they dwell. Here we describe tissue dissociation protocols that have been used to obtain human immune cells from lymphoid and nonlymphoid tissues to be then used as input to single-cell methods. We highlight the main factors that can influence the final quality of single-cell data, namely the stress signatures that can bias its interpretation.
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Affiliation(s)
| | - Ricardo J Miragaia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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8
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Chen X, Miragaia RJ, Natarajan KN, Teichmann SA. A rapid and robust method for single cell chromatin accessibility profiling. Nat Commun 2018; 9:5345. [PMID: 30559361 PMCID: PMC6297232 DOI: 10.1038/s41467-018-07771-0] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 11/13/2018] [Indexed: 11/30/2022] Open
Abstract
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) is widely used to identify regulatory regions throughout the genome. However, very few studies have been performed at the single cell level (scATAC-seq) due to technical challenges. Here we developed a simple and robust plate-based scATAC-seq method, combining upfront bulk Tn5 tagging with single-nuclei sorting. We demonstrate that our method works robustly across various systems, including fresh and cryopreserved cells from primary tissues. By profiling over 3000 splenocytes, we identify distinct immune cell types and reveal cell type-specific regulatory regions and related transcription factors.
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Affiliation(s)
- Xi Chen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ricardo J Miragaia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- MedImmune, Sir Aaron Klug Building, Granta Park, Cambridge, CB21 6GH, UK
| | - Kedar Nath Natarajan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Functional Biology and Metabolism Unit, Biochemistry and Molecular Biology, SDU, 5230, Odense, Denmark
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge, CB3 0HE, UK.
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Miragaia RJ, Zhang X, Gomes T, Svensson V, Ilicic T, Henriksson J, Kar G, Lönnberg T. Single-cell RNA-sequencing resolves self-antigen expression during mTEC development. Sci Rep 2018; 8:685. [PMID: 29330484 PMCID: PMC5766627 DOI: 10.1038/s41598-017-19100-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 12/14/2017] [Indexed: 01/03/2023] Open
Abstract
The crucial capability of T cells for discrimination between self and non-self peptides is based on negative selection of developing thymocytes by medullary thymic epithelial cells (mTECs). The mTECs purge autoreactive T cells by expression of cell-type specific genes referred to as tissue-restricted antigens (TRAs). Although the autoimmune regulator (AIRE) protein is known to promote the expression of a subset of TRAs, its mechanism of action is still not fully understood. The expression of TRAs that are not under the control of AIRE also needs further characterization. Furthermore, expression patterns of TRA genes have been suggested to change over the course of mTEC development. Herein we have used single-cell RNA-sequencing to resolve patterns of TRA expression during mTEC development. Our data indicated that mTEC development consists of three distinct stages, correlating with previously described jTEC, mTEChi and mTEClo phenotypes. For each subpopulation, we have identified marker genes useful in future studies. Aire-induced TRAs were switched on during jTEC-mTEC transition and were expressed in genomic clusters, while otherwise the subsets expressed largely overlapping sets of TRAs. Moreover, population-level analysis of TRA expression frequencies suggested that such differences might not be necessary to achieve efficient thymocyte selection.
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Affiliation(s)
- Ricardo J Miragaia
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Xiuwei Zhang
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- University of California, Berkeley, USA
| | - Tomás Gomes
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Valentine Svensson
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Tomislav Ilicic
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Johan Henriksson
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Gozde Kar
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Tapio Lönnberg
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom.
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
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Svensson V, Natarajan KN, Ly LH, Miragaia RJ, Labalette C, Macaulay IC, Cvejic A, Teichmann SA. Power analysis of single-cell RNA-sequencing experiments. Nat Methods 2017; 14:381-387. [PMID: 28263961 PMCID: PMC5376499 DOI: 10.1038/nmeth.4220] [Citation(s) in RCA: 358] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/07/2017] [Indexed: 12/19/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) has become an established and powerful method to investigate transcriptomic cell-to-cell variation, thereby revealing new cell types and providing insights into developmental processes and transcriptional stochasticity. A key question is how the variety of available protocols compare in terms of their ability to detect and accurately quantify gene expression. Here, we assessed the protocol sensitivity and accuracy of many published data sets, on the basis of spike-in standards and uniform data processing. For our workflow, we developed a flexible tool for counting the number of unique molecular identifiers (https://github.com/vals/umis/). We compared 15 protocols computationally and 4 protocols experimentally for batch-matched cell populations, in addition to investigating the effects of spike-in molecular degradation. Our analysis provides an integrated framework for comparing scRNA-seq protocols.
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Affiliation(s)
- Valentine Svensson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Kedar Nath Natarajan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Lam-Ha Ly
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ricardo J Miragaia
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Charlotte Labalette
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Iain C Macaulay
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ana Cvejic
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sarah A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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