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Lin CP, Levy PL, Alflen A, Apriamashvili G, Ligtenberg MA, Vredevoogd DW, Bleijerveld OB, Alkan F, Malka Y, Hoekman L, Markovits E, George A, Traets JJH, Krijgsman O, van Vliet A, Poźniak J, Pulido-Vicuña CA, de Bruijn B, van Hal-van Veen SE, Boshuizen J, van der Helm PW, Díaz-Gómez J, Warda H, Behrens LM, Mardesic P, Dehni B, Visser NL, Marine JC, Markel G, Faller WJ, Altelaar M, Agami R, Besser MJ, Peeper DS. Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness. Cancer Cell 2024; 42:623-645.e10. [PMID: 38490212 PMCID: PMC11003465 DOI: 10.1016/j.ccell.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/03/2024] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
Genes limiting T cell antitumor activity may serve as therapeutic targets. It has not been systematically studied whether there are regulators that uniquely or broadly contribute to T cell fitness. We perform genome-scale CRISPR-Cas9 knockout screens in primary CD8 T cells to uncover genes negatively impacting fitness upon three modes of stimulation: (1) intense, triggering activation-induced cell death (AICD); (2) acute, triggering expansion; (3) chronic, causing dysfunction. Besides established regulators, we uncover genes controlling T cell fitness either specifically or commonly upon differential stimulation. Dap5 ablation, ranking highly in all three screens, increases translation while enhancing tumor killing. Loss of Icam1-mediated homotypic T cell clustering amplifies cell expansion and effector functions after both acute and intense stimulation. Lastly, Ctbp1 inactivation induces functional T cell persistence exclusively upon chronic stimulation. Our results functionally annotate fitness regulators based on their unique or shared contribution to traits limiting T cell antitumor activity.
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Affiliation(s)
- Chun-Pu Lin
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pierre L Levy
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Tumor Immunology and Immunotherapy Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Astrid Alflen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Hematology and Medical Oncology, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany; Research Center for Immunotherapy (FZI), University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany
| | - Georgi Apriamashvili
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten A Ligtenberg
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - David W Vredevoogd
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ferhat Alkan
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Yuval Malka
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ettai Markovits
- Ella Lemelbaum Institute for Immuno-oncology and Melanoma, Sheba Medical Center, Ramat Gan 52612, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel
| | - Austin George
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joleen J H Traets
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alex van Vliet
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joanna Poźniak
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Carlos Ariel Pulido-Vicuña
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Beaunelle de Bruijn
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Susan E van Hal-van Veen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Julia Boshuizen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pim W van der Helm
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Judit Díaz-Gómez
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Hamdy Warda
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Leonie M Behrens
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Paula Mardesic
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Bilal Dehni
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Nils L Visser
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Gal Markel
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel; Davidoff Cancer Center and Samueli Integrative Cancer Pioneering Institute, Rabin Medical Center, Petach Tikva 4941492, Israel
| | - William J Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Michal J Besser
- Ella Lemelbaum Institute for Immuno-oncology and Melanoma, Sheba Medical Center, Ramat Gan 52612, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel; Davidoff Cancer Center and Samueli Integrative Cancer Pioneering Institute, Rabin Medical Center, Petach Tikva 4941492, Israel; Felsenstein Medical Research Center, Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Pathology, VU University Amsterdam, 1081 HV Amsterdam, the Netherlands.
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Horiuchi Y, Nakamura A, Imai T, Murakami T. Infection of tumor cells with Salmonella typhimurium mimics immunogenic cell death and elicits tumor-specific immune responses. PNAS NEXUS 2024; 3:pgad484. [PMID: 38213616 PMCID: PMC10783808 DOI: 10.1093/pnasnexus/pgad484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/21/2023] [Indexed: 01/13/2024]
Abstract
Some properties of Salmonella-infected cells overlap with immunogenic cell death. In this study, we demonstrated that intracellular infection of melanoma with Salmonella typhimurium induced high immunogenicity in melanoma cells, leading to antitumor effects with melanoma-antigen-specific T-cell responses. Murine B16F10 melanoma cells were infected with tdTomato-expressing attenuated S. typhimurium (VNP20009; VNP-tdT), triggering massive cell vacuolization. VNP-tdT-infected B16F10 cells were phagocytosed efficiently, which induced the activation of antigen-presenting cells with CD86 expression in vitro. Subcutaneous coimplantation of uninfected and VNP-tdT-infected B16F10 cells into C57BL/6 mice significantly suppressed tumor growth compared with the implantation of uninfected B16F10 cells alone. Inoculation of mice with VNP-tdT-infected B16F10 cells elicited the proliferation of melanoma-antigen (gp100)-specific T cells, and it protected the mice from the second tumor challenge of uninfected B16F10 cells. These results suggest that Salmonella-infected tumor cells acquire effective adjuvanticity, leading to ideal antitumor immune responses.
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Affiliation(s)
- Yutaka Horiuchi
- Department of Microbiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Akihiro Nakamura
- Department of Microbiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Takashi Imai
- Department of Microbiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Takashi Murakami
- Department of Microbiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
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Adu-Berchie K, Liu Y, Zhang DKY, Freedman BR, Brockman JM, Vining KH, Nerger BA, Garmilla A, Mooney DJ. Generation of functionally distinct T-cell populations by altering the viscoelasticity of their extracellular matrix. Nat Biomed Eng 2023; 7:1374-1391. [PMID: 37365267 PMCID: PMC10749992 DOI: 10.1038/s41551-023-01052-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/05/2023] [Indexed: 06/28/2023]
Abstract
The efficacy of adoptive T-cell therapies largely depends on the generation of T-cell populations that provide rapid effector function and long-term protective immunity. Yet it is becoming clearer that the phenotypes and functions of T cells are inherently linked to their localization in tissues. Here we show that functionally distinct T-cell populations can be generated from T cells that received the same stimulation by altering the viscoelasticity of their surrounding extracellular matrix (ECM). By using a model ECM based on a norbornene-modified collagen type I whose viscoelasticity can be adjusted independently from its bulk stiffness by varying the degree of covalent crosslinking via a bioorthogonal click reaction with tetrazine moieties, we show that ECM viscoelasticity regulates T-cell phenotype and function via the activator-protein-1 signalling pathway, a critical regulator of T-cell activation and fate. Our observations are consistent with the tissue-dependent gene-expression profiles of T cells isolated from mechanically distinct tissues from patients with cancer or fibrosis, and suggest that matrix viscoelasticity could be leveraged when generating T-cell products for therapeutic applications.
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Affiliation(s)
- Kwasi Adu-Berchie
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Yutong Liu
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - David K Y Zhang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Benjamin R Freedman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Joshua M Brockman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Kyle H Vining
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Preventative and Restorative Sciences, School of Dental Medicine, and Department of Materials Science and Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Bryan A Nerger
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | | | - David J Mooney
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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Adu-Berchie K, Brockman JM, Liu Y, To TW, Zhang DKY, Najibi AJ, Binenbaum Y, Stafford A, Dimitrakakis N, Sobral MC, Dellacherie MO, Mooney DJ. Adoptive T cell transfer and host antigen-presenting cell recruitment with cryogel scaffolds promotes long-term protection against solid tumors. Nat Commun 2023; 14:3546. [PMID: 37322053 PMCID: PMC10272124 DOI: 10.1038/s41467-023-39330-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
Although adoptive T cell therapy provides the T cell pool needed for immediate tumor debulking, the infused T cells generally have a narrow repertoire for antigen recognition and limited ability for long-term protection. Here, we present a hydrogel that locally delivers adoptively transferred T cells to the tumor site while recruiting and activating host antigen-presenting cells with GMCSF or FLT3L and CpG, respectively. T cells alone loaded into these localized cell depots provided significantly better control of subcutaneous B16-F10 tumors than T cells delivered through direct peritumoral injection or intravenous infusion. T cell delivery combined with biomaterial-driven accumulation and activation of host immune cells prolonged the activation of the delivered T cells, minimized host T cell exhaustion, and enabled long-term tumor control. These findings highlight how this integrated approach provide both immediate tumor debulking and long-term protection against solid tumors, including against tumor antigen escape.
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Affiliation(s)
- Kwasi Adu-Berchie
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Boston, MA, USA
| | - Joshua M Brockman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Boston, MA, USA
| | - Yutong Liu
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Boston, MA, USA
| | - Tania W To
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Boston, MA, USA
| | - David K Y Zhang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Boston, MA, USA
| | - Alexander J Najibi
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Boston, MA, USA
| | - Yoav Binenbaum
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Boston, MA, USA
| | - Alexander Stafford
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Boston, MA, USA
| | - Nikolaos Dimitrakakis
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Boston, MA, USA
| | - Miguel C Sobral
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Boston, MA, USA
| | - Maxence O Dellacherie
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Boston, MA, USA
| | - David J Mooney
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Boston, MA, USA.
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Yu C, Caothien R, Pham A, Tam L, Alcantar T, Bacarro N, Reyes J, Jackson M, Nakao B, Roose-Girma M. ASIS-Seq: Transgene Insertion Site Mapping by Nanopore Adaptive Sampling. Methods Mol Biol 2023; 2631:135-153. [PMID: 36995666 DOI: 10.1007/978-1-0716-2990-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Generation of transgenic mice by direct microinjection of foreign DNA into fertilized ova has become a routine technique in biomedical research. It remains an essential tool for studying gene expression, developmental biology, genetic disease models, and their therapies. However, the random integration of foreign DNA into the host genome that is inherent to this technology can lead to confounding effects associated with insertional mutagenesis and transgene silencing. Locations of most transgenic lines remain unknown because the methods are often burdensome (Nicholls et al., G3: Genes Genomes Genetics 9:1481-1486, 2019) or have limitations (Goodwin et al., Genome Research 29:494-505, 2019). Here, we present a method that we call Adaptive Sampling Insertion Site Sequencing (ASIS-Seq) to locate transgene integration sites using targeted sequencing on Oxford Nanopore Technologies' (ONT) sequencers. ASIS-Seq requires only about 3 ug of genomic DNA, 3 hours of hands-on sample preparation time, and 3 days of sequencing time to locate transgenes in a host genome.
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Affiliation(s)
- Charles Yu
- Genentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA
| | - Roger Caothien
- Genentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA
| | - Anna Pham
- Genentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA
| | - Lucinda Tam
- Genentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA
| | - Tuija Alcantar
- Genentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA
| | - Natasha Bacarro
- Genentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA
| | - Juan Reyes
- Genentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA
| | - Marques Jackson
- Genentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA
| | - Brian Nakao
- Genentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA
| | - Merone Roose-Girma
- Genentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA.
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Stirling ER, Terabe M, Wilson AS, Kooshki M, Yamaleyeva LM, Alexander-Miller MA, Zhang W, Miller LD, Triozzi PL, Soto-Pantoja DR. Targeting the CD47/thrombospondin-1 signaling axis regulates immune cell bioenergetics in the tumor microenvironment to potentiate antitumor immune response. J Immunother Cancer 2022; 10:e004712. [PMID: 36418073 PMCID: PMC9685258 DOI: 10.1136/jitc-2022-004712] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND CD47 is an integral membrane protein that alters adaptive immunosurveillance when bound to the matricellular glycoprotein thrombospondin-1 (TSP1). We examined the impact of the CD47/TSP1 signaling axis on melanoma patient response to anti-PD-1 therapy due to alterations in T cell activation, proliferation, effector function, and bioenergetics. METHODS A syngeneic B16 mouse melanoma model was performed to determine if targeting CD47 as monotherapy or in combination with anti-PD-1 impacted tumor burden. Cytotoxic (CD8+) T cells from Pmel-1 transgenic mice were used for T cell activation, cytotoxic T lymphocyte, and cellular bioenergetic assays. Single-cell RNA-sequencing, ELISA, and flow cytometry was performed on peripheral blood mononuclear cells and plasma of melanoma patients receiving anti-PD-1 therapy to examine CD47/TSP1 expression. RESULTS Human malignant melanoma tissue had increased CD47 and TSP1 expression within the tumor microenvironment compared with benign tissue. Due to the negative implications CD47/TSP1 can have on antitumor immune responses, we targeted CD47 in a melanoma model and observed a decrease in tumor burden due to increased tumor oxygen saturation and granzyme B secreting CD8+ T cells compared with wild-type tumors. Additionally, Pmel-1 CD8+ T cells exposed to TSP1 had reduced activation, proliferation, and effector function against B16 melanoma cells. Targeting CD47 allowed CD8+ T cells to overcome this TSP1 interaction to sustain these functions. TSP1 exposed CD8+ T cells have a decreased rate of glycolysis; however, targeting CD47 restored glycolysis when CD8+ T cells were exposed to TSP1, suggesting CD47 mediated metabolic reprogramming of T cells. Additionally, non-responding patients to anti-PD-1 therapy had increased T cells expressing CD47 and circulating levels of TSP1 compared with responding patients. Since CD47/TSP1 signaling axis negatively impacts CD8+ T cells and non-responding patients to anti-PD-1 therapy have increased CD47/TSP1 expression, we targeted CD47 in combination with anti-PD-1 in a melanoma model. Targeting CD47 in combination with anti-PD-1 treatment further decreased tumor burden compared with monotherapy and control. CONCLUSION CD47/TSP1 expression could serve as a marker to predict patient response to immune checkpoint blockade treatment, and targeting this pathway may preserve T cell activation, proliferation, effector function, and bioenergetics to reduce tumor burden as a monotherapy or in combination with anti-PD-1.
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Affiliation(s)
- Elizabeth R Stirling
- Department of Cancer Biology, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
| | - Masaki Terabe
- Neuro-Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Adam S Wilson
- Department of Surgery, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
| | - Mitra Kooshki
- Department of Hematology & Oncology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
- Department of Radiation Oncology, Wake Forest University School of Medicine, WInston-Salem, North Carolina, USA
| | - Liliya M Yamaleyeva
- Department of Surgery, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
| | - Martha A Alexander-Miller
- Department of Microbiology & Immunology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Wei Zhang
- Department of Cancer Biology, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
- Atrium Health Wake Forest Baptist Medical Center, Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
- Atrium Health Wake Forest Baptist Medical Center, Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
| | - Pierre L Triozzi
- Department of Cancer Biology, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
- Department of Hematology & Oncology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
- Atrium Health Wake Forest Baptist Medical Center, Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
| | - David R Soto-Pantoja
- Department of Cancer Biology, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
- Department of Surgery, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
- Department of Radiation Oncology, Wake Forest University School of Medicine, WInston-Salem, North Carolina, USA
- Atrium Health Wake Forest Baptist Medical Center, Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
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7
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Börjesson V, Martinez-Monleon A, Fransson S, Kogner P, Johnsen JI, Milosevic J, López MD. TC-hunter: identification of the insertion site of a transgenic gene within the host genome. BMC Genomics 2022; 23:149. [PMID: 35184734 PMCID: PMC8859905 DOI: 10.1186/s12864-022-08376-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Transgenic animal models are crucial for the study of gene function and disease, and are widely utilized in basic biological research, agriculture and pharma industries. Since the current methods for generating transgenic animals result in the random integration of the transgene under study, the phenotype may be compromised due to disruption of known genes or regulatory regions. Unfortunately, most of the tools that predict transgene insertion sites from high-throughput data are not publicly available or not properly maintained. Results We implemented TC-hunter, Transgene-Construct hunter, an open tool that identifies transgene insertion sites and provides simple reports and visualization aids. It relies on common tools used in the analysis of high-throughput data and makes use of chimeric reads and discordant read pairs to identify and support the transgenic insertion site. To demonstrate its applicability, we applied TC-hunter to four transgenic mice samples harboring the human PPM1D gene, a model used in the study of malignant tumor development. We identified the transgenic insertion site in each sample and experimentally validated them with Touchdown-polymerase chain reaction followed by Sanger sequencing. Conclusions TC-hunter is an accessible bioinformatics tool that can automatically identify transgene insertion sites from DNA sequencing data with high sensitivity (98%) and precision (92.45%). TC-hunter is a valuable tool that can aid in evaluating any potential phenotypic complications due to the random integration of the transgene and can be accessed at https://github.com/bcfgothenburg/SSF. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08376-0.
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Verma V, Jafarzadeh N, Boi S, Kundu S, Jiang Z, Fan Y, Lopez J, Nandre R, Zeng P, Alolaqi F, Ahmad S, Gaur P, Barry ST, Valge-Archer VE, Smith PD, Banchereau J, Mkrtichyan M, Youngblood B, Rodriguez PC, Gupta S, Khleif SN. MEK inhibition reprograms CD8 + T lymphocytes into memory stem cells with potent antitumor effects. Nat Immunol 2021; 22:53-66. [PMID: 33230330 PMCID: PMC10081014 DOI: 10.1038/s41590-020-00818-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022]
Abstract
Regenerative stem cell-like memory (TSCM) CD8+ T cells persist longer and produce stronger effector functions. We found that MEK1/2 inhibition (MEKi) induces TSCM that have naive phenotype with self-renewability, enhanced multipotency and proliferative capacity. This is achieved by delaying cell division and enhancing mitochondrial biogenesis and fatty acid oxidation, without affecting T cell receptor-mediated activation. DNA methylation profiling revealed that MEKi-induced TSCM cells exhibited plasticity and loci-specific profiles similar to bona fide TSCM isolated from healthy donors, with intermediate characteristics compared to naive and central memory T cells. Ex vivo, antigenic rechallenge of MEKi-treated CD8+ T cells showed stronger recall responses. This strategy generated T cells with higher efficacy for adoptive cell therapy. Moreover, MEKi treatment of tumor-bearing mice also showed strong immune-mediated antitumor effects. In conclusion, we show that MEKi leads to CD8+ T cell reprogramming into TSCM that acts as a reservoir for effector T cells with potent therapeutic characteristics.
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Affiliation(s)
- Vivek Verma
- The Loop Immuno-Oncology Laboratory, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
- Georgia Cancer Center, Augusta University, Augusta, GA, USA
| | - Nazli Jafarzadeh
- The Loop Immuno-Oncology Laboratory, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Shannon Boi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Subhadip Kundu
- The Loop Immuno-Oncology Laboratory, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Zhinuo Jiang
- The Loop Immuno-Oncology Laboratory, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jose Lopez
- The Loop Immuno-Oncology Laboratory, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Rahul Nandre
- The Loop Immuno-Oncology Laboratory, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD, USA
| | - Peng Zeng
- Georgia Cancer Center, Augusta University, Augusta, GA, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Fatmah Alolaqi
- The Loop Immuno-Oncology Laboratory, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Shamim Ahmad
- Georgia Cancer Center, Augusta University, Augusta, GA, USA
- Kite Pharma/A GILEAD Company, Emeryville, CA, USA
| | - Pankaj Gaur
- The Loop Immuno-Oncology Laboratory, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Simon T Barry
- Bioscience, Early Oncology, AstraZeneca, Cambridge, UK
| | | | - Paul D Smith
- Bioscience, Early Oncology, AstraZeneca, Cambridge, UK
| | | | - Mikayel Mkrtichyan
- The Loop Immuno-Oncology Laboratory, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Benjamin Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paulo C Rodriguez
- Georgia Cancer Center, Augusta University, Augusta, GA, USA
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Seema Gupta
- The Loop Immuno-Oncology Laboratory, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
- Georgia Cancer Center, Augusta University, Augusta, GA, USA
| | - Samir N Khleif
- The Loop Immuno-Oncology Laboratory, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA.
- Georgia Cancer Center, Augusta University, Augusta, GA, USA.
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9
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Mohammad S, Page SJ, Sasaki T, Ayvazian N, Rakic P, Kawasawa YI, Hashimoto-Torii K, Torii M. Long-term spatial tracking of cells affected by environmental insults. J Neurodev Disord 2020; 12:38. [PMID: 33327938 PMCID: PMC7745478 DOI: 10.1186/s11689-020-09339-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 11/13/2020] [Indexed: 11/15/2022] Open
Abstract
Background Harsh environments surrounding fetuses and children can induce cellular damage in the developing brain, increasing the risk of intellectual disability and other neurodevelopmental disorders such as schizophrenia. However, the mechanisms by which early damage leads to disease manifestation in later life remain largely unknown. Previously, we demonstrated that the activation of heat shock (HS) signaling can be utilized as a unique reporter to label the cells that undergo specific molecular/cellular changes upon exposure to environmental insults throughout the body. Since the activation of HS signaling is an acute and transient event, this approach was not intended for long-term tracing of affected cells after the activation has diminished. In the present study, we generated new reporter transgenic mouse lines as a novel tool to achieve systemic and long-term tracking of affected cells and their progeny. Methods The reporter transgenic mouse system was designed so that the activation of HS signaling through HS response element (HSE) drives flippase (FLPo)-flippase recognition target (FRT) recombination-mediated permanent expression of the red fluorescent protein (RFP), tdTomato. With a priority on consistent and efficient assessment of the reporter system, we focused on intraperitoneal (i.p.) injection models of high-dose, short prenatal exposure to alcohol (ethanol) and sodium arsenite (ethanol at 4.0 g/kg/day and sodium arsenite at 5.0 mg/kg/day, at embryonic day (E) 12 and 13). Long-term reporter expression was examined in the brain of reporter mice that were prenatally exposed to these insults. Electrophysiological properties were compared between RFP+ and RFP− cortical neurons in animals prenatally exposed to arsenite. Results We detected RFP+ neurons and glia in the brains of postnatal mice that had been prenatally exposed to alcohol or sodium arsenite. In animals prenatally exposed to sodium arsenite, we also detected reduced excitability in RFP+ cortical neurons. Conclusion The reporter transgenic mice allowed us to trace the cells that once responded to prenatal environmental stress and the progeny derived from these cells long after the exposure in postnatal animals. Tracing of these cells indicates that the impact of prenatal exposure on neural progenitor cells can lead to functional abnormalities in their progeny cells in the postnatal brain. Further studies using more clinically relevant exposure models are warranted to explore this mechanism. Supplementary Information The online version contains supplementary material available at 10.1186/s11689-020-09339-w.
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Affiliation(s)
- Shahid Mohammad
- Center for Neuroscience Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
| | - Stephen J Page
- Center for Neuroscience Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
| | - Toru Sasaki
- Center for Neuroscience Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.,Department of Obstetrics and Gynecology, Tokyo Medical University, Tokyo, Japan
| | - Nicholas Ayvazian
- Center for Neuroscience Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.,Institute of Biomedical Sciences, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Pasko Rakic
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University, New Haven, CT, USA
| | - Yuka Imamura Kawasawa
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA, USA.,Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Kazue Hashimoto-Torii
- Center for Neuroscience Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA. .,Department of Pediatrics, Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA.
| | - Masaaki Torii
- Center for Neuroscience Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA. .,Department of Pediatrics, Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA.
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10
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Hajaj E, Eisenberg G, Klein S, Frankenburg S, Merims S, Ben David I, Eisenhaure T, Henrickson SE, Villani AC, Hacohen N, Abudi N, Abramovich R, Cohen JE, Peretz T, Veillette A, Lotem M. SLAMF6 deficiency augments tumor killing and skews toward an effector phenotype revealing it as a novel T cell checkpoint. eLife 2020; 9:e52539. [PMID: 32122464 PMCID: PMC7075692 DOI: 10.7554/elife.52539] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/11/2020] [Indexed: 12/29/2022] Open
Abstract
SLAMF6 is a homotypic receptor of the Ig-superfamily whose exact role in immune modulation has remained elusive. Its constitutive expression on resting and activated T cells precludes it from being a bona fide exhaustion marker. By breeding Pmel-1 mice with SLAMF6 -/- mice, we generated donors for T cells lacking SLAMF6 and expressing a transgenic TCR for gp100-melanoma antigen. Activated Pmel-1xSLAMF6 -/- CD8+ T cells displayed improved polyfunctionality and strong tumor cytolysis. T-bet was the dominant transcription factor in Pmel-1 x SLAMF6 -/- cells, and upon activation, they acquired an effector-memory phenotype. Adoptive transfer of Pmel-1 x SLAMF6 -/- T cells to melanoma-bearing mice resulted in lasting tumor regression in contrast to temporary responses achieved with Pmel-1 T cells. LAG-3 expression was elevated in the SLAMF6 -/- cells, and the addition of the LAG-3-blocking antibody to the adoptive transfer protocol improved the SLAMF6 -/- T cells and expedited the antitumor response even further. The results from this study support the notion that SLAMF6 is an inhibitory immune receptor whose absence enables powerful CD8+ T cells to eradicate tumors.
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Affiliation(s)
- Emma Hajaj
- Sharett Institute of Oncology, Hadassah Hebrew University HospitalJerusalemIsrael
- Wohl Institute for Translational Medicine, Hadassah Medical OrganizationJerusalemIsrael
- Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, Hebrew UniversityJerusalemIsrael
| | - Galit Eisenberg
- Sharett Institute of Oncology, Hadassah Hebrew University HospitalJerusalemIsrael
- Wohl Institute for Translational Medicine, Hadassah Medical OrganizationJerusalemIsrael
| | - Shiri Klein
- Sharett Institute of Oncology, Hadassah Hebrew University HospitalJerusalemIsrael
- Wohl Institute for Translational Medicine, Hadassah Medical OrganizationJerusalemIsrael
| | - Shoshana Frankenburg
- Sharett Institute of Oncology, Hadassah Hebrew University HospitalJerusalemIsrael
- Wohl Institute for Translational Medicine, Hadassah Medical OrganizationJerusalemIsrael
| | - Sharon Merims
- Sharett Institute of Oncology, Hadassah Hebrew University HospitalJerusalemIsrael
- Wohl Institute for Translational Medicine, Hadassah Medical OrganizationJerusalemIsrael
| | - Inna Ben David
- Sharett Institute of Oncology, Hadassah Hebrew University HospitalJerusalemIsrael
- Wohl Institute for Translational Medicine, Hadassah Medical OrganizationJerusalemIsrael
| | | | - Sarah E Henrickson
- Broad Institute of MIT and HarvardCambridgeUnited States
- Boston Children's Hospital, Department of PediatricsBostonUnited States
| | - Alexandra Chloé Villani
- Broad Institute of MIT and HarvardCambridgeUnited States
- Center for Cancer Research, Massachusetts General HospitalCharlestownUnited States
- Department of Medicine, Harvard Medical SchoolBostonUnited States
- Center for Immunology and Inflammatory Diseases, Massachusetts General HospitalCharlestownUnited States
| | - Nir Hacohen
- Broad Institute of MIT and HarvardCambridgeUnited States
- Center for Cancer Research, Massachusetts General HospitalCharlestownUnited States
- Department of Medicine, Harvard Medical SchoolBostonUnited States
| | - Nathalie Abudi
- Wohl Institute for Translational Medicine, Hadassah Medical OrganizationJerusalemIsrael
- Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University HospitalJerusalemIsrael
| | - Rinat Abramovich
- Wohl Institute for Translational Medicine, Hadassah Medical OrganizationJerusalemIsrael
- Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University HospitalJerusalemIsrael
| | - Jonathan E Cohen
- Sharett Institute of Oncology, Hadassah Hebrew University HospitalJerusalemIsrael
- Wohl Institute for Translational Medicine, Hadassah Medical OrganizationJerusalemIsrael
| | - Tamar Peretz
- Sharett Institute of Oncology, Hadassah Hebrew University HospitalJerusalemIsrael
| | | | - Michal Lotem
- Sharett Institute of Oncology, Hadassah Hebrew University HospitalJerusalemIsrael
- Wohl Institute for Translational Medicine, Hadassah Medical OrganizationJerusalemIsrael
- Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, Hebrew UniversityJerusalemIsrael
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11
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Verma V, Shrimali RK, Ahmad S, Dai W, Wang H, Lu S, Nandre R, Gaur P, Lopez J, Sade-Feldman M, Yizhak K, Bjorgaard SL, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hammond SA, Tan M, Qi J, Wong P, Merghoub T, Wolchok J, Hacohen N, Janik JE, Mkrtichyan M, Gupta S, Khleif SN. PD-1 blockade in subprimed CD8 cells induces dysfunctional PD-1 +CD38 hi cells and anti-PD-1 resistance. Nat Immunol 2019; 20:1231-1243. [PMID: 31358999 PMCID: PMC7472661 DOI: 10.1038/s41590-019-0441-y] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/06/2019] [Indexed: 01/25/2023]
Abstract
Understanding resistance to antibody to programmed cell death protein 1 (PD-1; anti-PD-1) is crucial for the development of reversal strategies. In anti-PD-1-resistant models, simultaneous anti-PD-1 and vaccine therapy reversed resistance, while PD-1 blockade before antigen priming abolished therapeutic outcomes. This was due to induction of dysfunctional PD-1+CD38hi CD8+ cells by PD-1 blockade in suboptimally primed CD8 cell conditions induced by tumors. This results in erroneous T cell receptor signaling and unresponsiveness to antigenic restimulation. On the other hand, PD-1 blockade of optimally primed CD8 cells prevented the induction of dysfunctional CD8 cells, reversing resistance. Depleting PD-1+CD38hi CD8+ cells enhanced therapeutic outcomes. Furthermore, non-responding patients showed more PD-1+CD38+CD8+ cells in tumor and blood than responders. In conclusion, the status of CD8+ T cell priming is a major contributor to anti-PD-1 therapeutic resistance. PD-1 blockade in unprimed or suboptimally primed CD8 cells induces resistance through the induction of PD-1+CD38hi CD8+ cells that is reversed by optimal priming. PD-1+CD38hi CD8+ cells serve as a predictive and therapeutic biomarker for anti-PD-1 treatment. Sequencing of anti-PD-1 and vaccine is crucial for successful therapy.
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Affiliation(s)
- Vivek Verma
- Georgia Cancer Center, Augusta University, Augusta, GA, USA.,Present address: Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Rajeev K Shrimali
- Georgia Cancer Center, Augusta University, Augusta, GA, USA.,Present address: Therapeutic Discovery, MD Anderson Cancer Center, Houston, TX, USA
| | - Shamim Ahmad
- Georgia Cancer Center, Augusta University, Augusta, GA, USA.,Present address: Five Prime Therapeutics Inc., South San Francisco, CA, USA
| | - Winjie Dai
- Georgia Cancer Center, Augusta University, Augusta, GA, USA
| | - Hua Wang
- Georgia Cancer Center, Augusta University, Augusta, GA, USA
| | - Sumin Lu
- Georgia Cancer Center, Augusta University, Augusta, GA, USA
| | - Rahul Nandre
- Georgia Cancer Center, Augusta University, Augusta, GA, USA.,Present address: Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Pankaj Gaur
- Georgia Cancer Center, Augusta University, Augusta, GA, USA.,Present address: Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Jose Lopez
- Present address: Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Moshe Sade-Feldman
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Keren Yizhak
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Stacey L. Bjorgaard
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Keith T. Flaherty
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Jennifer A. Wargo
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Ryan J. Sullivan
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Gad Getz
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Ming Tan
- Department of Biostatistics, Bioinformatics & Biomathematics, Georgetown University, Washington, DC, USA
| | - Jingjing Qi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Phillip Wong
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Taha Merghoub
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical and Graduate Schools, New York, NY, USA
| | - Jedd Wolchok
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical and Graduate Schools, New York, NY, USA
| | - Nir Hacohen
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - John E. Janik
- Georgia Cancer Center, Augusta University, Augusta, GA, USA.,Present address: Incyte Inc., Wilmington, DE, USA
| | - Mikayel Mkrtichyan
- Georgia Cancer Center, Augusta University, Augusta, GA, USA.,Present address: Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA.,Present address: A2 Biotherapeutics, Agoura Hills, CA, USA
| | - Seema Gupta
- Georgia Cancer Center, Augusta University, Augusta, GA, USA.,Present address: Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Samir N. Khleif
- Georgia Cancer Center, Augusta University, Augusta, GA, USA.,Present address: Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA.,Correspondence and requests for materials should be addressed to S.N.K.
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12
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Fcmr regulates mononuclear phagocyte control of anti-tumor immunity. Nat Commun 2019; 10:2678. [PMID: 31213601 PMCID: PMC6581943 DOI: 10.1038/s41467-019-10619-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/09/2019] [Indexed: 12/13/2022] Open
Abstract
Myeloid cells contribute to tumor progression, but how the constellation of receptors they express regulates their functions within the tumor microenvironment (TME) is unclear. We demonstrate that Fcmr (Toso), the putative receptor for soluble IgM, modulates myeloid cell responses to cancer. In a syngeneic melanoma model, Fcmr ablation in myeloid cells suppressed tumor growth and extended mouse survival. Fcmr deficiency increased myeloid cell population density in this malignancy and enhanced anti-tumor immunity. Single-cell RNA sequencing of Fcmr-deficient tumor-associated mononuclear phagocytes revealed a unique subset with enhanced antigen processing/presenting properties. Conversely, Fcmr activity negatively regulated the activation and migratory capacity of myeloid cells in vivo, and T cell activation by bone marrow-derived dendritic cells in vitro. Therapeutic targeting of Fcmr during oncogenesis decreased tumor growth when used as a single agent or in combination with anti-PD-1. Thus, Fcmr regulates myeloid cell activation within the TME and may be a potential therapeutic target. Myeloid cells modulate the immune response within the tumour microenvironment, but the underlying mechanisms remain largely unknown. Here, the authors show that Fcmr – the putative receptor for soluble IgM – is a potent negative regulator of anti-tumour immunity.
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13
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Gautam S, Fioravanti J, Zhu W, Le Gall JB, Brohawn P, Lacey NE, Hu J, Hocker JD, Hawk NV, Kapoor V, Telford WG, Gurusamy D, Yu Z, Bhandoola A, Xue HH, Roychoudhuri R, Higgs BW, Restifo NP, Bender TP, Ji Y, Gattinoni L. The transcription factor c-Myb regulates CD8 + T cell stemness and antitumor immunity. Nat Immunol 2019; 20:337-349. [PMID: 30778251 PMCID: PMC6489499 DOI: 10.1038/s41590-018-0311-z] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 12/19/2018] [Indexed: 12/13/2022]
Abstract
Stem cells are maintained by transcriptional programs that promote self-renewal and repress differentiation. Here, we found that the transcription factor c-Myb was essential for generating and maintaining stem cells in the CD8+ T cell memory compartment. Following viral infection, CD8+ T cells lacking Myb underwent terminal differentiation and generated fewer stem cell-like central memory cells than did Myb-sufficient T cells. c-Myb acted both as a transcriptional activator of Tcf7 (which encodes the transcription factor Tcf1) to enhance memory development and as a repressor of Zeb2 (which encodes the transcription factor Zeb2) to hinder effector differentiation. Domain-mutagenesis experiments revealed that the transactivation domain of c-Myb was necessary for restraining differentiation, whereas its negative regulatory domain was critical for cell survival. Myb overexpression enhanced CD8+ T cell memory formation, polyfunctionality and recall responses that promoted curative antitumor immunity after adoptive transfer. These findings identify c-Myb as a pivotal regulator of CD8+ T cell stemness and highlight its therapeutic potential.
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Affiliation(s)
- Sanjivan Gautam
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jessica Fioravanti
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Wei Zhu
- Department of Bioinformatics, Inova Translational Medicine Institute, Fairfax, VA, USA
| | - John B Le Gall
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Neal E Lacey
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jinhui Hu
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - James D Hocker
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Nga Voong Hawk
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Veena Kapoor
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - William G Telford
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Devikala Gurusamy
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zhiya Yu
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Hai-Hui Xue
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Rahul Roychoudhuri
- Laboratory of Lymphocyte Signaling and Development, Babraham Institute, Cambridge, UK
| | | | - Nicholas P Restifo
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Timothy P Bender
- Department of Microbiology, University of Virginia, Charlottesville, VA, USA
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, USA
| | - Yun Ji
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Cellular Biomedicine Group, Gaithersburg, MD, USA
| | - Luca Gattinoni
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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14
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Cain-Hom C, Splinter E, van Min M, Simonis M, van de Heijning M, Martinez M, Asghari V, Cox JC, Warming S. Efficient mapping of transgene integration sites and local structural changes in Cre transgenic mice using targeted locus amplification. Nucleic Acids Res 2017; 45:e62. [PMID: 28053125 PMCID: PMC5416772 DOI: 10.1093/nar/gkw1329] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/20/2016] [Indexed: 12/23/2022] Open
Abstract
Cre/LoxP technology is widely used in the field of mouse genetics for spatial and/or temporal regulation of gene function. For Cre lines generated via pronuclear microinjection of a Cre transgene construct, the integration site is random and in most cases not known. Integration of a transgene can disrupt an endogenous gene, potentially interfering with interpretation of the phenotype. In addition, knowledge of where the transgene is integrated is important for planning of crosses between animals carrying a conditional allele and a given Cre allele in case the alleles are on the same chromosome. We have used targeted locus amplification (TLA) to efficiently map the transgene location in seven previously published Cre and CreERT2 transgenic lines. In all lines, transgene insertion was associated with structural changes of variable complexity, illustrating the importance of testing for rearrangements around the integration site. In all seven lines the exact integration site and breakpoint sequences were identified. Our methods, data and genotyping assays can be used as a resource for the mouse community and our results illustrate the power of the TLA method to not only efficiently map the integration site of any transgene, but also provide additional information regarding the transgene integration events.
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Affiliation(s)
- Carol Cain-Hom
- Department of Transgenic Technology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Erik Splinter
- Cergentis BV, Yalelaan 62, 3584 CM Utrecht, the Netherlands
| | - Max van Min
- Cergentis BV, Yalelaan 62, 3584 CM Utrecht, the Netherlands
| | | | | | - Maria Martinez
- Department of Transgenic Technology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Vida Asghari
- Department of Transgenic Technology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - J Colin Cox
- Department of Transgenic Technology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Søren Warming
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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15
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Jiang K, Xu P, Li W, Yang Q, Li L, Qiao C, Gong H, Zheng H, Zhou Z, Fu H, Li Q, Xing Y, Ren J. The increased expression of follicle-stimulating hormone leads to a decrease of fecundity in transgenic Large White female pigs. Transgenic Res 2017. [PMID: 28631185 DOI: 10.1007/s11248-017-0026-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Follicle-stimulating hormone (FSH) is a pituitary gonadotropin regulating reproduction in mammals. Overexpression of the exogenous FSHα/β genes from Chinese Erhualian pigs improved female fecundity of transgenic (TG) mice and male spermatogenesis ability of Large White TG boars. Here, we investigated the impact of the exogenous FSHα/β genes on female reproductive performance of Large White TG pigs. First, we identified the integration site of the exogenous FSHα/β genes at 140,646,456 bp on chromosome 9 in these TG pigs using whole-genome sequencing. Then, we showed that TG gilts had higher levels of serum FSH and FSHβ protein in pituitary while had a potentially lower number of born piglets than their wild-type half sibs. TG gilts grew healthily and normally without significant difference in growth and health parameters as compared to WT gilts. The expression levels of FSHR, LHR, ESR1 and ESR2 were significantly lower in TG gilts than in WT gilts at the age of 300 days. Taken together, we proposed that the overexpressed FSHα/β transgenes could cause deteriorate fecundity via disturbing the normal expression of the endogenous reproduction-related genes in female pigs. Our findings provide insight into the effect of overexpression of FSHα/β on female reproduction performance in pigs.
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Affiliation(s)
- Kai Jiang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Pan Xu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.,Jiangsu Agri-animal Husbandry Vocational College, Taizhou, 225300, People's Republic of China
| | - Wanbo Li
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Qiang Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Longyun Li
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Chuanmin Qiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Huanfa Gong
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Hao Zheng
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Zhimin Zhou
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Hao Fu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Qiuyan Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yuyun Xing
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
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16
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Ishii S, Torii M, Son AI, Rajendraprasad M, Morozov YM, Kawasawa YI, Salzberg AC, Fujimoto M, Brennand K, Nakai A, Mezger V, Gage FH, Rakic P, Hashimoto-Torii K. Variations in brain defects result from cellular mosaicism in the activation of heat shock signalling. Nat Commun 2017; 8:15157. [PMID: 28462912 PMCID: PMC5418582 DOI: 10.1038/ncomms15157] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 03/03/2017] [Indexed: 11/18/2022] Open
Abstract
Repetitive prenatal exposure to identical or similar doses of harmful agents results in highly variable and unpredictable negative effects on fetal brain development ranging in severity from high to little or none. However, the molecular and cellular basis of this variability is not well understood. This study reports that exposure of mouse and human embryonic brain tissues to equal doses of harmful chemicals, such as ethanol, activates the primary stress response transcription factor heat shock factor 1 (Hsf1) in a highly variable and stochastic manner. While Hsf1 is essential for protecting the embryonic brain from environmental stress, excessive activation impairs critical developmental events such as neuronal migration. Our results suggest that mosaic activation of Hsf1 within the embryonic brain in response to prenatal environmental stress exposure may contribute to the resulting generation of phenotypic variations observed in complex congenital brain disorders. Prenatal exposure to environmental stressors is known to impair cortical development. Here the authors show that upon exposure to stressors, the activation of Hsf1-Hsp signalling is highly variable among cells in the embryonic cortex of mice, and either too much or too little activation can result in defects in cortical development.
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Affiliation(s)
- Seiji Ishii
- Center for Neuroscience Research, Children's National Medical Center, Washington, District of Columbia 20010, USA
| | - Masaaki Torii
- Center for Neuroscience Research, Children's National Medical Center, Washington, District of Columbia 20010, USA.,Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Department of Pediatrics, Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, Washington, District of Columbia 20052, USA
| | - Alexander I Son
- Center for Neuroscience Research, Children's National Medical Center, Washington, District of Columbia 20010, USA
| | - Meenu Rajendraprasad
- Center for Neuroscience Research, Children's National Medical Center, Washington, District of Columbia 20010, USA.,Department of Biomedical Engineering, School of Engineering and Applied Science, George Washington University, Washington, District of Columbia 20052, USA
| | - Yury M Morozov
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Yuka Imamura Kawasawa
- Department of Pharmacology, Pennsylvania State University College of Medicine, 500 University Dr., Hershey, Pennsylvania 17033, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, 500 University Dr., Hershey, Pennsylvania 17033, USA.,Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Dr., Hershey, Pennsylvania 17033, USA
| | - Anna C Salzberg
- Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Dr., Hershey, Pennsylvania 17033, USA
| | - Mitsuaki Fujimoto
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube 755-8505, Japan
| | - Kristen Brennand
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York 10029, USA.,Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, California 92037, USA
| | - Akira Nakai
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube 755-8505, Japan
| | - Valerie Mezger
- CNRS, UMR7216 Epigenetics and Cell Fate, Paris 75205, France.,University Paris Diderot, 75205 Paris, France.,Département Hospitalo-Universitaire DHU PROTECT, Paris 75019, France
| | - Fred H Gage
- Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, California 92037, USA
| | - Pasko Rakic
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Kazue Hashimoto-Torii
- Center for Neuroscience Research, Children's National Medical Center, Washington, District of Columbia 20010, USA.,Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Department of Pediatrics, Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, Washington, District of Columbia 20052, USA
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17
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Holst-Jensen A, Spilsberg B, Arulandhu AJ, Kok E, Shi J, Zel J. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products. Anal Bioanal Chem 2016; 408:4595-614. [PMID: 27100228 PMCID: PMC4909802 DOI: 10.1007/s00216-016-9549-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 12/13/2022]
Abstract
The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.
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Affiliation(s)
- Arne Holst-Jensen
- Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750, Sentrum, 0106, Oslo, Norway.
| | - Bjørn Spilsberg
- Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750, Sentrum, 0106, Oslo, Norway
| | - Alfred J Arulandhu
- RIKILT, Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Esther Kok
- RIKILT, Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Jana Zel
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
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18
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Glioma Stemlike Cells Enhance the Killing of Glioma Differentiated Cells by Cytotoxic Lymphocytes. PLoS One 2016; 11:e0153433. [PMID: 27073883 PMCID: PMC4830556 DOI: 10.1371/journal.pone.0153433] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/29/2016] [Indexed: 01/16/2023] Open
Abstract
Glioblastoma multiforme, the most aggressive primary brain tumor, is maintained by a subpopulation of glioma cells with self-renewal properties that are able to recapitulate the entire tumor even after surgical resection or chemo-radiotherapy. This typifies the vast heterogeneity of this tumor with the two extremes represented on one end by the glioma stemlike cells (GSC) and on the other by the glioma differentiated cells (GDC). Interestingly, GSC are more sensitive to immune effector cells than the GDC counterpart. However, how GSC impact on the killing on the GDC and vice versa is not clear. Using a newly developed cytotoxicity assay allowing to simultaneously monitor cytotoxic lymphocytes-mediated killing of GSC and GDC, we found that although GSC were always better killed and that their presence enhanced the killing of GDC. In contrast, an excess of GDC had a mild protective effect on the killing of GSC, depending on the CTL type. Overall, our results suggest that during combination therapy, immunotherapy would be the most effective after prior treatment with conventional therapies.
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19
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Guttikonda SK, Marri P, Mammadov J, Ye L, Soe K, Richey K, Cruse J, Zhuang M, Gao Z, Evans C, Rounsley S, Kumpatla SP. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach. PLoS One 2016; 11:e0149515. [PMID: 26908260 PMCID: PMC4764375 DOI: 10.1371/journal.pone.0149515] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/01/2016] [Indexed: 11/18/2022] Open
Abstract
Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.
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Affiliation(s)
- Satish K. Guttikonda
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Pradeep Marri
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Jafar Mammadov
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Liang Ye
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Khaing Soe
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Kimberly Richey
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - James Cruse
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Meibao Zhuang
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Zhifang Gao
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Clive Evans
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Steve Rounsley
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Siva P. Kumpatla
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
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20
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Guttikonda SK, Marri P, Mammadov J, Ye L, Soe K, Richey K, Cruse J, Zhuang M, Gao Z, Evans C, Rounsley S, Kumpatla SP. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach. PLoS One 2016. [PMID: 26908260 DOI: 10.1016/j.futures.2016.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.
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Affiliation(s)
- Satish K Guttikonda
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Pradeep Marri
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Jafar Mammadov
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Liang Ye
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Khaing Soe
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Kimberly Richey
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - James Cruse
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Meibao Zhuang
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Zhifang Gao
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Clive Evans
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Steve Rounsley
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
| | - Siva P Kumpatla
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana, 46268, United States of America
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21
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Raman P, Grachtchouk V, Lyons RH, Koenig RJ. Identification of the Genomic Insertion Site of the Thyroid Peroxidase Promoter-Cre Recombinase Transgene Using a Novel, Efficient, Next-Generation DNA Sequencing Method. Thyroid 2015; 25:1162-6. [PMID: 26179797 PMCID: PMC4589305 DOI: 10.1089/thy.2015.0215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND It can be useful to know the transgene insertion site in transgenic mice for a variety of reasons, but determining the insertion site generally is a time consuming, expensive, and laborious task. METHODS A simple method is presented to determine transgene insertion sites that combines the enrichment of a sequencing library by polymerase chain reaction (PCR) for sequences containing the transgene, followed by next-generation sequencing of the enriched library. This method was applied to determine the site of integration of the thyroid peroxidase promoter-Cre recombinase mouse transgene that is commonly used to create thyroid-specific gene deletions. RESULTS The insertion site was found to be between bp 12,372,316 and 12,372,324 on mouse chromosome 9, with the nearest characterized genes being Cntn5 and Jrkl, ∼1.5 and 0.9 Mbp from the transgene, respectively. One advantage of knowing a transgene insertion site is that it facilitates distinguishing hemizygous from homozygous transgenic mice. Although this can be accomplished by real-time quantitative PCR, the expected Ct difference is only one cycle, which is challenging to assess accurately. Therefore, the transgene insertion site information was used to develop a 3-primer qualitative PCR assay that readily distinguishes wild type, hemizygous, and homozygous TPO-Cre mice based upon size differences of the wild type and transgenic allele PCR products. CONCLUSIONS Identification of the genomic insertion site of the thyroid peroxidase promoter-Cre mouse transgene should facilitate the use of these mice in studies of thyroid biology.
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Affiliation(s)
- Priyadarshini Raman
- 1 Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan , Ann Arbor, Michigan
| | - Vladimir Grachtchouk
- 1 Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan , Ann Arbor, Michigan
| | - Robert H Lyons
- 2 Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan
| | - Ronald J Koenig
- 1 Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan , Ann Arbor, Michigan
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22
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CONTRAILS: A tool for rapid identification of transgene integration sites in complex, repetitive genomes using low-coverage paired-end sequencing. GENOMICS DATA 2015; 6:175-81. [PMID: 26697366 PMCID: PMC4664744 DOI: 10.1016/j.gdata.2015.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 09/02/2015] [Indexed: 11/22/2022]
Abstract
Transgenic crops have become a staple in modern agriculture, and are typically characterized using a variety of molecular techniques involving proteomics and metabolomics. Characterization of the transgene insertion site is of great interest, as disruptions, deletions, and genomic location can affect product selection and fitness, and identification of these regions and their integrity is required for regulatory agencies. Here, we present CONTRAILS (Characterization of Transgene Insertion Locations with Sequencing), a straightforward, rapid and reproducible method for the identification of transgene insertion sites in highly complex and repetitive genomes using low coverage paired-end Illumina sequencing and traditional PCR. This pipeline requires little to no troubleshooting and is not restricted to any genome type, allowing use for many molecular applications. Using whole genome sequencing of in-house transgenic Glycine max, a legume with a highly repetitive and complex genome, we used CONTRAILS to successfully identify the location of a single T-DNA insertion to single base resolution. We developed a pipeline for transgene identification using paired-end sequencing. This method requires little troubleshooting and is applicable to any genome. Identification of insertion sites is required for deregulation of modified food crops. This assists in identifying potential genomic disruptions in transgenic events.
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23
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Ma J, Chai J, Shang Y, Li Y, Chen R, Jia J, Jiang S, Peng J. Swine PPAR-γ2 expression upregulated in skeletal muscle of transgenic mice via the swine Myozenin-1 gene promoter. Transgenic Res 2014; 24:409-20. [PMID: 25421932 DOI: 10.1007/s11248-014-9849-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/05/2014] [Indexed: 10/24/2022]
Abstract
Myozenin-1 (Myoz1) gene-encoded calsarcin-2 protein was expressed exclusively in fast-twitch muscles. Peroxisome proliferator-activated receptor γ2 (PPAR-γ2) is a key regulator of adipocyte differentiation, fatty acid uptake and storage in mammals. In this study, transgenic (TG) mice were generated by injecting linearized DNA that contained mouse creatine kinase M-type enhancer, Myoz1 core promoter, swine PPAR-γ2 (sPPAR-γ2) and SV40 polyadenylation sequences into pronuclei of fertilized FVB/NJ mouse embryos using microinjection technology. Then, the TG mice were used to identify whether swine Myoz1 (sMyoz1) promoter could upregulate sPPAR-γ2 expression in skeletal muscle in a TG mouse model. The results showed that the sMyoz1 promoter indeed upregulated sPPAR-γ2 expression on both the RNA and protein levels. The target genes of PPAR-γ in fat formation pathways, such as fatty acid-binding protein 4 (FABP4) and lipoprotein lipase (LPL), were also overexpressed on the RNA level. Meanwhile, the level of skeletal muscle triacylglycerol in TG mice was increased (P < 0.05), and the result of Oil Red-O staining in the skeletal muscle sections also showed that the number of lipid droplets was significantly increased in TG mice compared to wild-type mice, which might improve the intramuscular fat (IMF) content. For pork, the quality was mostly influenced by the IMF; the identification of swine muscle-specific promoter, sMyoz1, could further serve to develop transgenic pigs with higher intramuscular fat contents and improve pork quality.
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Affiliation(s)
- Juanjuan Ma
- Agricultural Ministry Key Laboratory of Swine Breeding and Genetics and Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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