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Maerz MD, Cross DL, Seshadri C. Functional and biological implications of clonotypic diversity among human donor-unrestricted T cells. Immunol Cell Biol 2024. [PMID: 38659280 DOI: 10.1111/imcb.12751] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/04/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024]
Abstract
T cells express a T-cell receptor (TCR) heterodimer that is the product of germline rearrangement and junctional editing resulting in immense clonotypic diversity. The generation of diverse TCR repertoires enables the recognition of pathogen-derived peptide antigens presented by polymorphic major histocompatibility complex (MHC) molecules. However, T cells also recognize nonpeptide antigens through nearly monomorphic antigen-presenting systems, such as cluster of differentiation 1 (CD1), MHC-related protein 1 (MR1) and butyrophilins (BTNs). This potential for shared immune responses across genetically diverse populations led to their designation as donor-unrestricted T cells (DURTs). As might be expected, some CD1-, MR1- and BTN-restricted T cells express a TCR that is conserved across unrelated individuals. However, several recent studies have reported unexpected diversity among DURT TCRs, and increasing evidence suggests that this diversity has functional consequences. Recent reports also challenge the dogma that immune cells are either innate or adaptive and suggest that DURT TCRs may act in both capacities. Here, we review this evidence and propose an expanded view of the role for clonotypic diversity among DURTs in humans, including new perspectives on how DURT TCRs may integrate their adaptive and innate immune functions.
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Affiliation(s)
- Megan D Maerz
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Molecular Medicine and Mechanisms of Disease Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Deborah L Cross
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Chetan Seshadri
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
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2
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Merkenschlager J, Berz RM, Ramos V, Uhlig M, MacLean AJ, Nowosad CR, Oliveira TY, Nussenzweig MC. Continually recruited naïve T cells contribute to the follicular helper and regulatory T cell pools in germinal centers. Nat Commun 2023; 14:6944. [PMID: 37907454 PMCID: PMC10618265 DOI: 10.1038/s41467-023-41880-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/20/2023] [Indexed: 11/02/2023] Open
Abstract
Follicular helper T cells (TFH) mediate B cell selection and clonal expansion in germinal centers (GCs), and follicular regulatory T cells (TFR) prevent the emergence of self-reactive B cells and help to extinguish the reaction. Here we show that GC reactions continually recruit T cells from both the naïve conventional and naive thymic regulatory T cell (Treg) repertoires. In the early GC, newly recruited T cells develop into TFH, whereas cells entering during the contraction phase develop into TFR cells that contribute to GC dissolution. The TFR fate decision is associated with decreased antigen availability and is modulated by slow antigen delivery or mRNA vaccination. Thus, invasion of ongoing GCs by newly developing TFH and TFR helps remodel the GC based on antigen availability.
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Affiliation(s)
- Julia Merkenschlager
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA.
| | - Riza-Maria Berz
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Maximilian Uhlig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Andrew J MacLean
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Carla R Nowosad
- Translational Immunology Center, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, 10065, USA
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3
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Hodgkin PD. Kevin Lafferty and the lymphocyte costimulator: theory and practice in Canberra. Immunol Cell Biol 2023; 101:678-683. [PMID: 37610184 DOI: 10.1111/imcb.12683] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Between 1969 and 1983 the lab of Kevin Lafferty in Canberra developed the concept of the T-cell "costimulator," an essential second signal for activation. A great deal of the work appeared in this journal before it was known as Immunology & Cell Biology (ICB). As part of the 100-year anniversary of the journal, I offer a personal reflection on Kevin's legacy and impact.
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Affiliation(s)
- Philip D Hodgkin
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
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4
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Bourdeleau P, Couvelard A, Ronot M, Lebtahi R, Hentic O, Ruszniewski P, Cros J, de Mestier L. Spatial and temporal heterogeneity of digestive neuroendocrine neoplasms. Ther Adv Med Oncol 2023; 15:17588359231179310. [PMID: 37323185 PMCID: PMC10262621 DOI: 10.1177/17588359231179310] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/11/2023] [Indexed: 06/17/2023] Open
Abstract
Neuroendocrine neoplasms (NENs) are initially monoclonal neoplasms that progressively become polyclonal, with very different genotypic and phenotypic characteristics leading to biological differences, including the Ki-67 proliferation index, morphology, or sensitivity to treatments. Whereas inter-patient heterogeneity has been well described, intra-tumor heterogeneity has been little studied. However, NENs present a high degree of heterogeneity, both spatially within the same location or between different lesions, and through time. This can be explained by the emergence of tumor subclones with different behaviors. These subpopulations can be distinguished by the Ki-67 index, but also by the expression of hormonal markers or by differences in the intensity of uptake on metabolic imaging, such as 68Ga-somatostatin receptor and Fluorine-18 fluorodeoxyglucose positron emission tomography. As these features are directly related to prognosis, it seems mandatory to move toward a standardized, improved selection of the tumor areas to be studied to be as predictive as possible. The temporal evolution of NENs frequently leads to changes in tumor grade over time, with impact on prognosis and therapeutic decision-making. However, there is no recommendation regarding systematic biopsy of NEN recurrence or progression, and which lesion to sample. This review aims to summarize the current state of knowledge, the main hypotheses, and the main implications regarding intra-tumor spatial and temporal heterogeneity in digestive NENs.
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Affiliation(s)
- Pauline Bourdeleau
- Department of Pancreatology and Digestive Oncology, Beaujon Hospital (APHP.Nord), Université Paris-Cité, Clichy, France
| | - Anne Couvelard
- Department of Pathology, Beaujon/Bichat Hospitals (APHP.Nord), Université Paris-Cité, Clichy/Paris, France
- Centre de Recherche sur l’Inflammation, INSERM UMR1149, FHU MOSAIC, Paris, France
| | - Maxime Ronot
- Department of Radiology, Beaujon Hospital (APHP.Nord), Université Paris-Cité, Clichy, France, and Centre de Recherche sur l’Inflammation, INSERM UMR1149, FHU MOSAIC, Paris, France
| | - Rachida Lebtahi
- Department of Nuclear Medicine, Beaujon Hospital (APHP.Nord), Université Paris-Cité, Clichy, France Centre de Recherche sur l’Inflammation, INSERM UMR1149, FHU MOSAIC, Paris, France
| | - Olivia Hentic
- Department of Pancreatology and Digestive Oncology, Beaujon Hospital (APHP.Nord), Université Paris-Cité, Clichy, France
| | - Philippe Ruszniewski
- Department of Pancreatology and Digestive Oncology, Beaujon Hospital (APHP.Nord), Université Paris-Cité, Clichy, France
- Centre de Recherche sur l’Inflammation, INSERM UMR1149, FHU MOSAIC, Paris, France
| | - Jérôme Cros
- Department of Pathology, Beaujon/Bichat Hospitals (APHP.Nord), Université Paris-Cité, Clichy/Paris, France
- Centre de Recherche sur l’Inflammation, INSERM UMR1149, FHU MOSAIC, Paris, France
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Salavaty A, Azadian E, Naik SH, Currie PD. Clonal selection parallels between normal and cancer tissues. Trends Genet 2023; 39:358-380. [PMID: 36842901 DOI: 10.1016/j.tig.2023.01.007] [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: 07/27/2022] [Revised: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 02/28/2023]
Abstract
Clonal selection and drift drive both normal tissue and cancer development. However, the biological mechanisms and environmental conditions underpinning these processes remain to be elucidated. Clonal selection models are centered in Darwinian evolutionary theory, where some clones with the fittest features are selected and populate the tissue or tumor. We suggest that different subclasses of stem cells, each of which is responsible for a distinct feature of the selection process, share common features between normal and cancer conditions. While active stem cells populate the tissue, dormant cells account for tissue replenishment/regeneration in both normal and cancerous tissues. We also discuss potential mechanisms that drive clonal drift, their interactions with clonal selection, and their similarities during normal and cancer tissue development.
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Affiliation(s)
- Adrian Salavaty
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Systems Biology Institute Australia, Monash University, Clayton, VIC 3800, Australia.
| | - Esmaeel Azadian
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Shalin H Naik
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; EMBL Australia, Monash University, Clayton, VIC 3800, Australia.
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6
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Goel M, Eugster A, Schetelig J, Bonifacio E, Bornhäuser M, Link-Rachner CS. Potential of TCR sequencing in graft-versus-host disease. Bone Marrow Transplant 2023; 58:239-46. [PMID: 36477111 DOI: 10.1038/s41409-022-01885-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
Graft-versus-host disease (GvHD) remains one of the major complications following allogeneic haematopoietic stem cell transplantation (allo-HSCT). GvHD can occur in almost every tissue, with the skin, liver, and intestines being the mainly affected organs. T cells are implicated in initiating GvHD. T cells identify a broad range of antigens and mediate the immune response through receptors on their surfaces (T cell receptors, TCRs). The composition of TCRs within a T cell population defines the TCR repertoire of an individual, and this repertoire represents exposure to self and non-self proteins. Monitoring the changes in the TCR repertoire using TCR sequencing can provide an indication of the dynamics of a T cell population. Monitoring the frequency and specificities of specific TCR clonotypes longitudinally in different conditions and specimens (peripheral blood, GvHD-affected tissue samples) can provide insights into factors modulating immune reactions following allogeneic transplantation and will help to understand the underlying mechanisms mediating GvHD. This review provides insights into current studies of the TCR repertoire in GvHD and potential future clinical implications of TCR sequencing.
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Tomašević M, Lukić K, Ćurko N, Jagatić Korenika AM, Preiner D, Tuščić V, Jeromel A, Kovačević Ganić K. The Influence of Grape Clone and Yeast Strain on Varietal Thiol Concentrations and Sensory Properties of Graševina Wines. Foods 2023; 12. [PMID: 36900502 DOI: 10.3390/foods12050985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/16/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Varietal thiol concentration in wine is influenced by numerous factors, of which grape variety and winemaking practices are often highlighted as the most important. Therefore, the aim of this work was to study the effects of grape clone and yeast strain (Saccharomyces and non-Saccharomyces) on the varietal thiols concentrations and sensory characteristics of Graševina (Vitis vinifera L.) white wines. Two grape clones were evaluated (OB-412 and OB-445) along with three different commercial yeast strains (Saccharomyces cerevisiae Lalvin Sensy and Sauvy, and Metschnikowia pulcherrima Flavia). The results showed that the concentration of varietal thiols in Graševina wines amounted up to a total of 226 ng/L. The clone OB-412 was characterized by its significantly higher concentrations, especially of 3-sulfanylhexanol (3SH) and 3-sulfanylhexyl acetate (3SHA). Moreover, alcoholic fermentation with pure S. cerevisiae Sauvy yeasts generally resulted in higher thiol concentrations, while sequential fermentation involving M. pulcherrima positively affected only the 4-methyl-4-sulfanyl-pentan-2-one (4MSP) concentration. Finally, sensory analysis showed that fermentation with pure S. cerevisiae Sauvy yeast also produced more desirable wines. The results suggest that clonal, and especially yeast strain, selections are important modulators of the aroma and sensory properties of wine.
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8
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Snir T, Philip H, Gordin M, Zilberberg A, Efroni S. The temporal behavior of the murine T cell receptor repertoire following Immunotherapy. Sci Data 2023; 10:108. [PMID: 36823176 PMCID: PMC9950060 DOI: 10.1038/s41597-023-01982-x] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/24/2023] [Indexed: 02/25/2023] Open
Abstract
Immunotherapy is now an essential tool for cancer treatment, and the unique features of an individual's T cell receptor repertoire are known to play a key role in its effectiveness. The repertoire, famously vast due to a cascade of cellular mechanisms, can be quantified using repertoire sequencing. In this study, we sampled the repertoire over several time points following treatment with anti-CTLA-4, in a syngeniec mouse model for colorectal cancer, generating a longitudinal dataset of T cell clones and their abundance. The dynamics of the repertoire can be observed in response to treatment over a period of four weeks, as clonal expansion of specific clones ascends and descends. The data made available here can be used to determine treatment and predict its effect, while also providing a unique look at the behavior of the immune system over time.
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Affiliation(s)
- Tom Snir
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Hagit Philip
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Miri Gordin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alona Zilberberg
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sol Efroni
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
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9
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Madan E, Palma AM, Vudatha V, Trevino JG, Natarajan KN, Winn RA, Won KJ, Graham TA, Drapkin R, McDonald SAC, Fisher PB, Gogna R. Cell Competition in Carcinogenesis. Cancer Res 2022; 82:4487-4496. [PMID: 36214625 PMCID: PMC9976200 DOI: 10.1158/0008-5472.can-22-2217] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/04/2022] [Accepted: 09/29/2022] [Indexed: 01/30/2023]
Abstract
The majority of human cancers evolve over time through the stepwise accumulation of somatic mutations followed by clonal selection akin to Darwinian evolution. However, the in-depth mechanisms that govern clonal dynamics and selection remain elusive, particularly during the earliest stages of tissue transformation. Cell competition (CC), often referred to as 'survival of the fittest' at the cellular level, results in the elimination of less fit cells by their more fit neighbors supporting optimal organism health and function. Alternatively, CC may allow an uncontrolled expansion of super-fit cancer cells to outcompete their less fit neighbors thereby fueling tumorigenesis. Recent research discussed herein highlights the various non-cell-autonomous principles, including interclonal competition and cancer microenvironment competition supporting the ability of a tumor to progress from the initial stages to tissue colonization. In addition, we extend current insights from CC-mediated clonal interactions and selection in normal tissues to better comprehend those factors that contribute to cancer development.
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Affiliation(s)
- Esha Madan
- Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal
| | | | - Vignesh Vudatha
- Department of Surgery, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | - Jose G. Trevino
- Department of Surgery, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | | | - Robert A. Winn
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Kyoung Jae Won
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Trevor A. Graham
- Evolution and Cancer Laboratory, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, U.K
| | - Ronny Drapkin
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stuart AC. McDonald
- Clonal Dynamics in Epithelia Laboratory, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square. London, EC1M 6BQ UK
| | - Paul B. Fisher
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | - Rajan Gogna
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
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Zornikova KV, Khmelevskaya A, Sheetikov SA, Kiryukhin DO, Shcherbakova OV, Titov A, Zvyagin IV, Efimov GA. Clonal diversity predicts persistence of SARS-CoV-2 epitope-specific T-cell response. Commun Biol 2022; 5:1351. [PMID: 36494499 DOI: 10.1038/s42003-022-04250-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
T cells play a pivotal role in reducing disease severity during SARS-CoV-2 infection and formation of long-term immune memory. We studied 50 COVID-19 convalescent patients and found that T cell response was induced more frequently and persisted longer than circulating antibodies. We identified 756 clonotypes specific to nine CD8+ T cell epitopes. Some epitopes were recognized by highly similar public clonotypes. Receptors for other epitopes were extremely diverse, suggesting alternative modes of recognition. We tracked persistence of epitope-specific response and individual clonotypes for a median of eight months after infection. The number of recognized epitopes per patient and quantity of epitope-specific clonotypes decreased over time, but the studied epitopes were characterized by uneven decline in the number of specific T cells. Epitopes with more clonally diverse TCR repertoires induced more pronounced and durable responses. In contrast, the abundance of specific clonotypes in peripheral circulation had no influence on their persistence.
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11
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Singh NK, Alonso JA, Devlin JR, Keller GLJ, Gray GI, Chiranjivi AK, Foote SG, Landau LM, Arbuiso AG, Weiss LI, Rosenberg AM, Hellman LM, Nishimura MI, Baker BM. A class-mismatched TCR bypasses MHC restriction via an unorthodox but fully functional binding geometry. Nat Commun 2022; 13:7189. [PMID: 36424374 DOI: 10.1038/s41467-022-34896-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
MHC restriction, which describes the binding of TCRs from CD4+ T cells to class II MHC proteins and TCRs from CD8+ T cells to class I MHC proteins, is a hallmark of immunology. Seemingly rare TCRs that break this paradigm exist, but mechanistic insight into their behavior is lacking. TIL1383I is a prototypical class-mismatched TCR, cloned from a CD4+ T cell but recognizing the tyrosinase tumor antigen presented by the class I MHC HLA-A2 in a fully functional manner. Here we find that TIL1383I binds this class I target with a highly atypical geometry. Despite unorthodox binding, TCR signaling, antigen specificity, and the ability to use CD8 are maintained. Structurally, a key feature of TIL1383I is an exceptionally long CDR3β loop that mediates functions that are traditionally performed separately by hypervariable and germline loops in canonical TCR structures. Our findings thus expand the range of known TCR binding geometries compatible with normal function and specificity, provide insight into the determinants of MHC restriction, and may help guide TCR selection and engineering for immunotherapy.
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Jaffe DB, Shahi P, Adams BA, Chrisman AM, Finnegan PM, Raman N, Royall AE, Tsai F, Vollbrecht T, Reyes DS, Hepler NL, McDonnell WJ. Functional antibodies exhibit light chain coherence. Nature 2022; 611:352-357. [PMID: 36289331 PMCID: PMC9607724 DOI: 10.1038/s41586-022-05371-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 09/21/2022] [Indexed: 11/08/2022]
Abstract
The vertebrate adaptive immune system modifies the genome of individual B cells to encode antibodies that bind particular antigens1. In most mammals, antibodies are composed of heavy and light chains that are generated sequentially by recombination of V, D (for heavy chains), J and C gene segments. Each chain contains three complementarity-determining regions (CDR1-CDR3), which contribute to antigen specificity. Certain heavy and light chains are preferred for particular antigens2-22. Here we consider pairs of B cells that share the same heavy chain V gene and CDRH3 amino acid sequence and were isolated from different donors, also known as public clonotypes23,24. We show that for naive antibodies (those not yet adapted to antigens), the probability that they use the same light chain V gene is around 10%, whereas for memory (functional) antibodies, it is around 80%, even if only one cell per clonotype is used. This property of functional antibodies is a phenomenon that we call light chain coherence. We also observe this phenomenon when similar heavy chains recur within a donor. Thus, although naive antibodies seem to recur by chance, the recurrence of functional antibodies reveals surprising constraint and determinism in the processes of V(D)J recombination and immune selection. For most functional antibodies, the heavy chain determines the light chain.
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13
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Morganti S, Ivanova M, Ferraro E, Ascione L, Vivanet G, Bonizzi G, Curigliano G, Fusco N, Criscitiello C. Loss of HER2 in breast cancer: biological mechanisms and technical pitfalls. Cancer Drug Resist 2022; 5:971-980. [PMID: 36627895 PMCID: PMC9771738 DOI: 10.20517/cdr.2022.55] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/18/2022] [Accepted: 08/10/2022] [Indexed: 11/06/2022]
Abstract
Loss of HER2 in previously HER2-positive breast tumors is not rare, occurring in up to 50% of breast cancers; however, clinical research and practice underestimate this issue. Many studies have reported the loss of HER2 after neoadjuvant therapy and at metastatic relapse and identified clinicopathological variables more frequently associated with this event. Nevertheless, the biological mechanisms underlying HER2 loss are still poorly understood. HER2 downregulation, intratumoral heterogeneity, clonal selection, and true subtype switch have been suggested as potential causes of HER2 loss, but translational studies specifically investigating the biology behind HER2 loss are virtually absent. On the other side, technical pitfalls may justify HER2 loss in some of these samples. The best treatment strategy for patients with HER2 loss is currently unknown. Considering the prevalence of this phenomenon and its apparent correlation with worse outcomes, we believe that correlative studies specifically addressing HER2 loss are warranted.
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Affiliation(s)
- Stefania Morganti
- Division of Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, Milan 20144, Italy.,Department of Oncology and Haemato-Oncology, University of Milano, Milan 20122, Italy.,Breast Oncology Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA.,Correspondence to: Dr. Stefania Morganti, Department of Oncology and Haemato-Oncology, University of Milano, via Festa del Perdono 7, Milan 20122, Italy. E-mail:
| | - Mariia Ivanova
- Biobank for Translational and Digital Medicine Unit, IEO, European Institute of Oncology IRCCS, Milan 20144, Italy.,Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan 20144, Italy
| | - Emanuela Ferraro
- Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Liliana Ascione
- Division of Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, Milan 20144, Italy.,Department of Oncology and Haemato-Oncology, University of Milano, Milan 20122, Italy
| | - Grazia Vivanet
- Division of Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, Milan 20144, Italy.,Department of Oncology and Haemato-Oncology, University of Milano, Milan 20122, Italy
| | - Giuseppina Bonizzi
- Biobank for Translational and Digital Medicine Unit, IEO, European Institute of Oncology IRCCS, Milan 20144, Italy
| | - Giuseppe Curigliano
- Division of Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, Milan 20144, Italy.,Department of Oncology and Haemato-Oncology, University of Milano, Milan 20122, Italy
| | - Nicola Fusco
- Department of Oncology and Haemato-Oncology, University of Milano, Milan 20122, Italy.,Biobank for Translational and Digital Medicine Unit, IEO, European Institute of Oncology IRCCS, Milan 20144, Italy.,Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan 20144, Italy
| | - Carmen Criscitiello
- Division of Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, Milan 20144, Italy.,Department of Oncology and Haemato-Oncology, University of Milano, Milan 20122, Italy
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14
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van Rijswijck DMH, Bondt A, Hoek M, van der Straten K, Caniels TG, Poniman M, Eggink D, Reusken C, de Bree GJ, Sanders RW, van Gils MJ, Heck AJR. Discriminating cross-reactivity in polyclonal IgG1 responses against SARS-CoV-2 variants of concern. Nat Commun 2022; 13:6103. [PMID: 36243713 DOI: 10.1038/s41467-022-33899-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 10/07/2022] [Indexed: 12/24/2022] Open
Abstract
Existing assays to measure antibody cross-reactivity against different SARS-CoV-2 spike (S) protein variants lack the discriminatory power to provide insights at the level of individual clones. Using a mass spectrometry-based approach we are able to monitor individual donors' IgG1 clonal responses following a SARS-CoV-2 infection. We monitor the plasma clonal IgG1 profiles of 8 donors who had experienced an infection by either the wild type Wuhan Hu-1 virus or one of 3 VOCs (Alpha, Beta and Gamma). In these donors we chart the full plasma IgG1 repertoires as well as the IgG1 repertoires targeting the SARS-CoV-2 spike protein trimer VOC antigens. The plasma of each donor contains numerous anti-spike IgG1 antibodies, accounting for <0.1% up to almost 10% of all IgG1s. Some of these antibodies are VOC-specific whereas others do recognize multiple or even all VOCs. We show that in these polyclonal responses, each clone exhibits a distinct cross-reactivity and also distinct virus neutralization capacity. These observations support the need for a more personalized look at the antibody clonal responses to infectious diseases.
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15
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Ogasawara T, Fujii Y, Kakiuchi N, Shiozawa Y, Sakamoto R, Ogawa Y, Ootani K, Ito E, Tanaka T, Watanabe K, Yoshida Y, Kimura N, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Ogawa S. Genetic Analysis of Pheochromocytoma and Paraganglioma Complicating Cyanotic Congenital Heart Disease. J Clin Endocrinol Metab 2022; 107:2545-2555. [PMID: 35730597 DOI: 10.1210/clinem/dgac362] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Indexed: 11/19/2022]
Abstract
CONTEXT Pheochromocytoma and paraganglioma (PPGL) may appear as a complication of cyanotic congenital heart disease (CCHD-PPGL) with frequent EPAS1 mutations, suggesting a close link between EPAS1 mutations and tissue hypoxia in CCHD-PPGL pathogenesis. OBJECTIVE Our aim is to further investigate the role of EPAS1 mutations in the hypoxia-driven mechanism of CCHD-PPGL pathogenesis, particularly focusing on metachronous and/or multifocal CCHD-PPGL tumors. METHODS We performed whole-exome sequencing (WES) for somatic and germline mutations in 15 PPGL samples from 7 CCHD patients, including 3 patients with metachronous and/or multifocal tumors, together with an adrenal medullary hyperplasia (AMH) sample. RESULTS We detected EPAS1 mutations in 15 out of 16 PPGL/AMH samples from 7 cases. Conspicuously, all EPAS1 mutations in each of 3 cases with multifocal or metachronous tumors were mutually independent and typical examples of parallel evolution, which is suggestive of strong positive selection of EPAS1-mutated clones. Compared to 165 The Cancer Genome Atlas non-CCHD-PPGL samples, CCHD-PPGL/AMH samples were enriched for 11p deletions (13/16) and 2p amplifications (4/16). Of particular note, the multiple metachronous PPGL tumors with additional copy number abnormalities developed 18 to 23 years after the resolution of hypoxemia, suggesting that CCHD-induced hypoxic environments are critical for positive selection of EPAS1 mutants in early life, but may no longer be required for development of PPGL in later life. CONCLUSION Our results highlight a key role of activated hypoxia-inducible factor 2α due to mutated EPAS1 in positive selection under hypoxic environments, although hypoxemia itself may not necessarily be required for the EPAS1-mutated clones to progress to PPGL.
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Affiliation(s)
- Tatsuki Ogasawara
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8315, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Yoichi Fujii
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8315, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8315, Japan
- The Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8315, Japan
| | - Ryuichi Sakamoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Katsuki Ootani
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562,Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562,Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Kenichiro Watanabe
- Department of Hematology and Oncology, Shizuoka Children's Hospital, Shizuoka 420-8660, Japan
| | - Yusaku Yoshida
- Department of Endocrine Surgery, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Noriko Kimura
- Department of Clinical Research Pathology Division, National Hospital Organization Hakodate Hospital, Hakodate 041-8512, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Hiroko Tanaka
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8315, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm 14157, Sweden
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16
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Rückert T, Lareau CA, Mashreghi MF, Ludwig LS, Romagnani C. Clonal expansion and epigenetic inheritance of long-lasting NK cell memory. Nat Immunol 2022; 23:1551-63. [PMID: 36289449 DOI: 10.1038/s41590-022-01327-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/09/2022] [Indexed: 11/08/2022]
Abstract
Clonal expansion of cells with somatically diversified receptors and their long-term maintenance as memory cells is a hallmark of adaptive immunity. Here, we studied pathogen-specific adaptation within the innate immune system, tracking natural killer (NK) cell memory to human cytomegalovirus (HCMV) infection. Leveraging single-cell multiomic maps of ex vivo NK cells and somatic mitochondrial DNA mutations as endogenous barcodes, we reveal substantial clonal expansion of adaptive NK cells in HCMV+ individuals. NK cell clonotypes were characterized by a convergent inflammatory memory signature enriched for AP1 motifs superimposed on a private set of clone-specific accessible chromatin regions. NK cell clones were stably maintained in specific epigenetic states over time, revealing that clonal inheritance of chromatin accessibility shapes the epigenetic memory repertoire. Together, we identify clonal expansion and persistence within the human innate immune system, suggesting that these mechanisms have evolved independent of antigen-receptor diversification.
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17
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Meng Q, Xie S, Gray GK, Dezfulian MH, Li W, Huang L, Akshinthala D, Ferrer E, Conahan C, Perea Del Pino S, Grossman J, Elledge SJ, Hidalgo M, Muthuswamy SK. Empirical identification and validation of tumor-targeting T cell receptors from circulation using autologous pancreatic tumor organoids. J Immunother Cancer 2021; 9:jitc-2021-003213. [PMID: 34789550 PMCID: PMC8601084 DOI: 10.1136/jitc-2021-003213] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
Background Tumor-specific cytotoxic T cells and T cell receptors are effective tools for cancer immunotherapy. Most efforts to identify them rely on known antigens or lymphocytes that have infiltrated into the tumor bed. Approaches to empirically identify tumor-targeting T cells and T cell receptors by exploiting all antigens expressed on tumor cell surfaces are not well developed for most carcinomas, including pancreatic cancer. Methods Autologous tumor organoids were stimulated with T cells from the patients’ peripheral blood for 2 weeks to generate the organoid-primed T (opT) cells. opT cell phenotype was analyzed by monitoring changes in the expression levels of 28 cell surface and checkpoint proteins. Expression of ligands of the immune checkpoints was investigated by immunohistochemistry staining. T cells were labeled with carboxyfluorescein succinimidyl ester (CFSE) and assayed by flow cytometry to monitor tumor-induced T cell proliferation changes. opT cell-mediated killing of three-dimensional organoids was measured using an M30 ELISA kit. T cell receptors (TCRs) were identified by deep sequencing of gDNA isolated from T cells, and the TCR specificity was confirmed by transferring TCRs to the T cell line SKW-3 or donor T cells. Results The co-culture was effective in the generation of CD8 + or CD4+opT cells. The opT cells killed autologous tumors in a granzyme B or Fas-Fas ligand-dependent manner and expressed markers of tissue-resident memory phenotype. Each patient-derived opT cell culture displayed a unique complement of checkpoint proteins. Interestingly, only NKG2A blockade showed a potent increase in the interferon-γ production compared with blocking programmed cell death protein 1 (PD-1) or programmed cell death ligand 1 (PD-L1) or TIM3 or TIGIT or LAG3. Importantly, TCR sequencing demonstrated a dramatic clonal expansion of T cells with a restricted subset of TCRs. Cloning and transferring the TCRs to heterologous T cells was sufficient to confer tumor cell recognition and cytotoxic properties in a patient-specific manner. Conclusion We report a platform for expanding tumor-targeting T cells from the peripheral blood of patients with pancreatic cancer. We identify the NKG2A-HLA-E axis as a potentially important checkpoint for CD8 +T cells for pancreatic cancer. Lastly, we demonstrate empirical identification of tumor-targeting TCRs that can be used for TCR-therapeutics.
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Affiliation(s)
- Qingda Meng
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Shanshan Xie
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - G Kenneth Gray
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Weilin Li
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Ling Huang
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Dipikaa Akshinthala
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Elizabeth Ferrer
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Catherine Conahan
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Sofia Perea Del Pino
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph Grossman
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Manuel Hidalgo
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York, USA
| | - Senthil K Muthuswamy
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
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18
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Lo AA, Wallace A, Oreper D, Lounsbury N, Havnar C, Pechuan-Jorge X, Wu TD, Bourgon R, Jones R, Krogh K, Yang GY, Zill OA. Indication-specific tumor evolution and its impact on neoantigen targeting and biomarkers for individualized cancer immunotherapies. J Immunother Cancer 2021; 9:jitc-2021-003001. [PMID: 34599029 PMCID: PMC8488717 DOI: 10.1136/jitc-2021-003001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2021] [Indexed: 12/12/2022] Open
Abstract
Background Individualized neoantigen-specific immunotherapy (iNeST) requires robustly expressed clonal neoantigens for efficacy, but tumor mutational heterogeneity, loss of neoantigen expression, and variable tissue sampling present challenges. It is assumed that clonal neoantigens are preferred targets for immunotherapy, but the distributions of clonal neoantigens are not well characterized across cancer types. Methods We combined multiregion sequencing (MR-seq) analysis of five untreated, synchronously sampled metastatic solid tumors with re-analysis of published MR-seq data from 103 patients in order to characterize their globally clonal neoantigen content and factors that would impact neoantigen targeting. Results Branching evolution in colorectal cancer and renal cell carcinoma led to fewer clonal neoantigens and to clade-specific neoantigens (those shared across a subset of tumor regions but not fully clonal), with the latter not being readily distinguishable in single tumor samples. In colorectal, renal, and bladder cancer, most tumors had few globally clonal neoantigens. Prioritizing mutations with higher purity-adjusted and ploidy-adjusted variant allele frequency enriched for globally clonal neoantigens (those found in all tumor regions), whereas estimated cancer cell fraction derived from clustering-based tools, surprisingly, did not. Neoantigen quality was associated with loss of neoantigen expression in the bladder cancer case, and HLA-allele loss was observed in the renal and non-small cell lung cancer cases. Conclusions We show that tumor type, multilesion sampling, neoantigen expression, and HLA allele retention are important factors for iNeST targeting and patient selection, and may also be important factors to consider in the development of biomarker strategies.
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Affiliation(s)
- Amy A Lo
- Department of Research Pathology, Genentech Inc, South San Francisco, California, USA
| | - Andrew Wallace
- Department of Oncology Bioinformatics, Genentech Inc, South San Francisco, California, USA
| | - Daniel Oreper
- Department of Oncology Bioinformatics, Genentech Inc, South San Francisco, California, USA
| | - Nicolas Lounsbury
- Department of Oncology Bioinformatics, Genentech Inc, South San Francisco, California, USA
| | - Charles Havnar
- Department of Research Pathology, Genentech Inc, South San Francisco, California, USA
| | - Ximo Pechuan-Jorge
- Department of Cancer Immunology, Genentech Inc, South San Francisco, California, USA
| | - Thomas D Wu
- Department of Oncology Bioinformatics, Genentech Inc, South San Francisco, California, USA
| | - Richard Bourgon
- Department of Oncology Bioinformatics, Genentech Inc, South San Francisco, California, USA
| | - Ryan Jones
- Department of Pathology, Northwestern University, Chicago, Illinois, USA
| | - Katrina Krogh
- Department of Pathology, Northwestern University, Chicago, Illinois, USA
| | - Guang-Yu Yang
- Department of Pathology, Northwestern University, Chicago, Illinois, USA
| | - Oliver A Zill
- Department of Oncology Bioinformatics, Genentech Inc, South San Francisco, California, USA .,Current affiliation, init.bio, Inc, San Mateo, CA, USA
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19
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Niebuhr M, Belde J, Fähnrich A, Serge A, Irla M, Ellebrecht CT, Hammers CM, Bieber K, Westermann J, Kalies K. Receptor repertoires of murine follicular T helper cells reveal a high clonal overlap in separate lymph nodes in autoimmunity. eLife 2021; 10:70053. [PMID: 34402793 PMCID: PMC8370764 DOI: 10.7554/elife.70053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/02/2021] [Indexed: 12/21/2022] Open
Abstract
Follicular T helper cells (Tfh) are a specialized subset of CD4 effector T cells that are crucial for germinal center (GC) reactions and for selecting B cells to undergo affinity maturation. Despite this central role for humoral immunity, only few data exist about their clonal distribution when multiple lymphoid organs are exposed to the same antigen (Ag) as it is the case in autoimmunity. Here, we used an autoantibody-mediated disease model of the skin and injected one auto-Ag into the two footpads of the same mouse and analyzed the T cell receptor (TCR)β sequences of Tfh located in GCs of both contralateral draining lymph nodes. We found that over 90% of the dominant GC-Tfh clonotypes were shared in both lymph nodes but only transiently. The initially dominant Tfh clonotypes especially declined after establishment of chronic disease while GC reaction and autoimmune disease continued. Our data demonstrates a dynamic behavior of Tfh clonotypes under autoimmune conditions and emphasizes the importance of the time point for distinguishing auto-Ag-specific Tfh clonotypes from potential bystander activated ones.
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Affiliation(s)
- Markus Niebuhr
- Institute for Anatomy, University of Lübeck, Lübeck, Germany
| | - Julia Belde
- Institute for Anatomy, University of Lübeck, Lübeck, Germany
| | - Anke Fähnrich
- Institute for Anatomy, University of Lübeck, Lübeck, Germany.,Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Arnauld Serge
- Laboratoire Adhésion et Inflammation, Inserm U1067 CNRS, Aix-Marseille Université, Marseille, France
| | - Magali Irla
- Centre d'Immunologie de Marseille Luminy (CIML), INSERM U1104, Aix-Marseille Université UM2, Marseille, France
| | - Christoph T Ellebrecht
- Institute for Anatomy, University of Lübeck, Lübeck, Germany.,Department of Dermatology, University of Pennsylvania, Philadelphia, United States
| | - Christoph M Hammers
- Institute for Anatomy, University of Lübeck, Lübeck, Germany.,Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Katja Bieber
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | | | - Kathrin Kalies
- Institute for Anatomy, University of Lübeck, Lübeck, Germany
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20
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Parker TM, Gupta K, Palma AM, Yekelchyk M, Fisher PB, Grossman SR, Won KJ, Madan E, Moreno E, Gogna R. Cell competition in intratumoral and tumor microenvironment interactions. EMBO J 2021; 40:e107271. [PMID: 34368984 DOI: 10.15252/embj.2020107271] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
Tumors are complex cellular and acellular environments within which cancer clones are under continuous selection pressures. Cancer cells are in a permanent mode of interaction and competition with each other as well as with the immediate microenvironment. In the course of these competitive interactions, cells share information regarding their general state of fitness, with less-fit cells being typically eliminated via apoptosis at the hands of those cells with greater cellular fitness. Competitive interactions involving exchange of cell fitness information have implications for tumor growth, metastasis, and therapy outcomes. Recent research has highlighted sophisticated pathways such as Flower, Hippo, Myc, and p53 signaling, which are employed by cancer cells and the surrounding microenvironment cells to achieve their evolutionary goals by means of cell competition mechanisms. In this review, we discuss these recent findings and explain their importance and role in evolution, growth, and treatment of cancer. We further consider potential physiological conditions, such as hypoxia and chemotherapy, that can function as selective pressures under which cell competition mechanisms may evolve differently or synergistically to confer oncogenic advantages to cancer.
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Affiliation(s)
- Taylor M Parker
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Kartik Gupta
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | | | - Michail Yekelchyk
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Paul B Fisher
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,VCU Massey Cancer Center, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | - Steven R Grossman
- Department of Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kyoung Jae Won
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen North, Denmark.,Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen, Copenhagen North, Denmark
| | - Esha Madan
- Champalimaud Centre for the Unknown, Lisbon, Portugal
| | | | - Rajan Gogna
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen North, Denmark.,Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen, Copenhagen North, Denmark
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21
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Murray JS. TCR-pMHC: may the force be of you? Cell Mol Immunol 2021; 18:1622-1623. [PMID: 33479416 PMCID: PMC8245527 DOI: 10.1038/s41423-021-00635-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 12/31/2020] [Indexed: 11/09/2022] Open
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22
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Barthlott T, Handel AE, Teh HY, Wirasinha RC, Hafen K, Žuklys S, Roch B, Orkin SH, de Villartay JP, Daley SR, Holländer GA. Indispensable epigenetic control of thymic epithelial cell development and function by polycomb repressive complex 2. Nat Commun 2021; 12:3933. [PMID: 34168132 PMCID: PMC8225857 DOI: 10.1038/s41467-021-24158-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Thymic T cell development and T cell receptor repertoire selection are dependent on essential molecular cues provided by thymic epithelial cells (TEC). TEC development and function are regulated by their epigenetic landscape, in which the repressive H3K27me3 epigenetic marks are catalyzed by polycomb repressive complex 2 (PRC2). Here we show that a TEC-targeted deficiency of PRC2 function results in a hypoplastic thymus with reduced ability to express antigens and select a normal repertoire of T cells. The absence of PRC2 activity reveals a transcriptomically distinct medullary TEC lineage that incompletely off-sets the shortage of canonically-derived medullary TEC whereas cortical TEC numbers remain unchanged. This alternative TEC development is associated with the generation of reduced TCR diversity. Hence, normal PRC2 activity and placement of H3K27me3 marks are required for TEC lineage differentiation and function and, in their absence, the thymus is unable to compensate for the loss of a normal TEC scaffold.
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Affiliation(s)
- Thomas Barthlott
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland
| | - Adam E Handel
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Hong Ying Teh
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland
| | - Rushika C Wirasinha
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Katrin Hafen
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland
| | - Saulius Žuklys
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland
| | - Benoit Roch
- Genome Dynamics in the Immune System Laboratory, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Stuart H Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Jean-Pierre de Villartay
- Genome Dynamics in the Immune System Laboratory, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Stephen R Daley
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
- School of Health and Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Georg A Holländer
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland.
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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23
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Pan YG, Aiamkitsumrit B, Bartolo L, Wang Y, Lavery C, Marc A, Holec PV, Rappazzo CG, Eilola T, Gimotty PA, Hensley SE, Antia R, Zarnitsyna VI, Birnbaum ME, Su LF. Vaccination reshapes the virus-specific T cell repertoire in unexposed adults. Immunity 2021; 54:1245-1256.e5. [PMID: 34004140 PMCID: PMC8192456 DOI: 10.1016/j.immuni.2021.04.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/01/2021] [Accepted: 04/21/2021] [Indexed: 11/30/2022]
Abstract
We examined how baseline CD4+ T cell repertoire and precursor states impact responses to pathogen infection in humans using primary immunization with yellow fever virus (YFV) vaccine. YFV-specific T cells in unexposed individuals were identified by peptide-MHC tetramer staining and tracked pre- and post-vaccination by tetramers and TCR sequencing. A substantial number of YFV-reactive T cells expressed memory phenotype markers and contained expanded clones in the absence of exposure to YFV. After vaccination, pre-existing YFV-specific T cell populations with low clonal diversity underwent limited expansion, but rare populations with a reservoir of unexpanded TCRs generated robust responses. These altered dynamics reorganized the immunodominance hierarchy and resulted in an overall increase in higher avidity T cells. Thus, instead of further increasing the representation of dominant clones, YFV vaccination recruits rare and more responsive T cells. Our findings illustrate the impact of vaccines in prioritizing T cell responses and reveal repertoire reorganization as a key component of effective vaccination.
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Affiliation(s)
- Yi-Gen Pan
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamas Aiamkitsumrit
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laurent Bartolo
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yifeng Wang
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Criswell Lavery
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA 19104, USA
| | - Adam Marc
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA 19104, USA
| | - Patrick V Holec
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C Garrett Rappazzo
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Theresa Eilola
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Phyllis A Gimotty
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
| | | | - Michael E Birnbaum
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Laura F Su
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA 19104, USA.
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24
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Mansur MB, Furness CL, Nakjang S, Enshaei A, Alpar D, Colman SM, Minto L, Irving J, Poole BV, Noronha EP, Savola S, Iqbal S, Gribben J, Pombo-de-Oliveira MS, Ford TM, Greaves MF, van Delft FW. The genomic landscape of teenage and young adult T-cell acute lymphoblastic leukemia. Cancer Med 2021; 10:4864-4873. [PMID: 34080325 PMCID: PMC8290240 DOI: 10.1002/cam4.4024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/09/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Treatment on risk adapted intensive pediatric protocols has improved outcome for teenagers and young adults (TYA) with T-cell acute lymphoblastic leukemia (T-ALL). Understanding the biology of disease in this age group and the genetic basis of relapse is a key goal as patients with relapsed/refractory disease have poor outcomes with conventional chemotherapy and novel molecular targets are required. This study examines the question of whether TYA T-ALL has a specific biological-molecular profile distinct from pediatric or adult T-ALL. METHODS Genomic characterization was undertaken of a retrospective discovery cohort of 80 patients aged 15-26 years with primary or relapsed T-ALL, using a combination of Genome-Wide Human SNP Array 6.0, targeted gene mutation and promoter methylation analyses. Findings were confirmed by MLPA, real-time quantitative PCR, and FISH. Whole Exome Sequencing was performed in 4 patients with matched presentation and relapse to model clonal evolution. A prevalence analysis was performed on a final data set of 1,792 individual cases to identify genetic lesions with age specific frequency patterns, including 972 pediatric (1-14 years), 439 TYA (15-24 years) and 381 adult (≥25 years) cases. These cases were extracted from 19 publications with comparable genomic data identified through a PubMed search. RESULTS Genomic characterization of this large cohort of TYA T-ALL patients identified recurrent isochromosome 7q i(7q) in our discovery cohort (n = 3). Prevalence analysis did not identify any age specific genetic abnormalities. Genomic analysis of 6 pairs of matched presentation - relapsed T-ALL established that all relapses were clonally related to the initial leukemia. Whole exome sequencing analysis revealed recurrent, targetable, mutations disrupting NOTCH, PI3K/AKT/mTOR, FLT3, NRAS as well as drug metabolism pathways. CONCLUSIONS All genetic aberrations in TYA T-ALL occurred with an incidence similar or intermediate to that reported in the pediatric and adult literature, demonstrating that overall TYA T-ALL exhibits a transitional genomic profile. Analysis of matched presentation - relapse supported the hypothesis that relapse is driven by the Darwinian evolution of sub-clones associated with drug resistance (NT5C2 and TP53 mutations) and re-iterative mutation of known key T-ALL drivers, including NOTCH1.
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Affiliation(s)
- Marcela B Mansur
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.,Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.,Division of Clinical Research, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Caroline L Furness
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Sirintra Nakjang
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK.,Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Amir Enshaei
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Donat Alpar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.,HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Sue M Colman
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Lynne Minto
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Julie Irving
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Beth V Poole
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Elda P Noronha
- Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Suvi Savola
- Oncogenetics, MRC-Holland, Amsterdam, The Netherlands
| | - Sameena Iqbal
- Centre for Haemato-Oncology, Barts Cancer Institute, London, UK
| | - John Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, London, UK
| | - Maria S Pombo-de-Oliveira
- Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Tony M Ford
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Mel F Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Frederik W van Delft
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.,Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
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25
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Damaghi M, West J, Robertson-Tessi M, Xu L, Ferrall-Fairbanks MC, Stewart PA, Persi E, Fridley BL, Altrock PM, Gatenby RA, Sims PA, Anderson ARA, Gillies RJ. The harsh microenvironment in early breast cancer selects for a Warburg phenotype. Proc Natl Acad Sci U S A 2021; 118:e2011342118. [PMID: 33452133 DOI: 10.1073/pnas.2011342118] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Glucose is converted to energy through “fermentation” or “oxidation.” Generally, if oxygen is available, cells will oxidize glucose to CO2 because it is more efficient than fermentation, which produces lactic acid. But Warburg noted that cancers ferment glucose at a “remarkable” rate even if O2 is available! This “Warburg Effect” is still misunderstood because it doesn’t make sense that a cell would ferment glucose when it could get much more energy by oxidizing it. The current paper goes to the heart of this problem by defining the microenvironmental conditions that exist in early cancers that would select for a Warburg Effect. This is important because such cells are much more aggressive and like to lead to cancers that are lethal. The harsh microenvironment of ductal carcinoma in situ (DCIS) exerts strong evolutionary selection pressures on cancer cells. We hypothesize that the poor metabolic conditions near the ductal center foment the emergence of a Warburg Effect (WE) phenotype, wherein cells rapidly ferment glucose to lactic acid, even in normoxia. To test this hypothesis, we subjected low-glycolytic breast cancer cells to different microenvironmental selection pressures using combinations of hypoxia, acidosis, low glucose, and starvation for many months and isolated single clones for metabolic and transcriptomic profiling. The two harshest conditions selected for constitutively expressed WE phenotypes. RNA sequencing analysis of WE clones identified the transcription factor KLF4 as potential inducer of the WE phenotype. In stained DCIS samples, KLF4 expression was enriched in the area with the harshest microenvironmental conditions. We simulated in vivo DCIS phenotypic evolution using a mathematical model calibrated from the in vitro results. The WE phenotype emerged in the poor metabolic conditions near the necrotic core. We propose that harsh microenvironments within DCIS select for a WE phenotype through constitutive transcriptional reprogramming, thus conferring a survival advantage and facilitating further growth and invasion.
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26
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Russo G, Tramontano A, Iodice I, Chiariotti L, Pezone A. Epigenome Chaos: Stochastic and Deterministic DNA Methylation Events Drive Cancer Evolution. Cancers (Basel) 2021; 13:1800. [PMID: 33918773 DOI: 10.3390/cancers13081800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Cancer is a group of diseases characterized by abnormal cell growth with a high potential to invade other tissues. Genetic abnormalities and epigenetic alterations found in tumors can be due to high levels of DNA damage and repair. These can be transmitted to daughter cells, which assuming other alterations as well, will generate heterogeneous and complex populations. Deciphering this complexity represents a central point for understanding the molecular mechanisms of cancer and its therapy. Here, we summarize the genomic and epigenomic events that occur in cancer and discuss novel approaches to analyze the epigenetic complexity of cancer cell populations. Abstract Cancer evolution is associated with genomic instability and epigenetic alterations, which contribute to the inter and intra tumor heterogeneity, making genetic markers not accurate to monitor tumor evolution. Epigenetic changes, aberrant DNA methylation and modifications of chromatin proteins, determine the “epigenome chaos”, which means that the changes of epigenetic traits are randomly generated, but strongly selected by deterministic events. Disordered changes of DNA methylation profiles are the hallmarks of all cancer types, but it is not clear if aberrant methylation is the cause or the consequence of cancer evolution. Critical points to address are the profound epigenetic intra- and inter-tumor heterogeneity and the nature of the heterogeneity of the methylation patterns in each single cell in the tumor population. To analyze the methylation heterogeneity of tumors, new technological and informatic tools have been developed. This review discusses the state of the art of DNA methylation analysis and new approaches to reduce or solve the complexity of methylated alleles in DNA or cell populations.
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27
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Zattarin E, Leporati R, Ligorio F, Lobefaro R, Vingiani A, Pruneri G, Vernieri C. Hormone Receptor Loss in Breast Cancer: Molecular Mechanisms, Clinical Settings, and Therapeutic Implications. Cells 2020; 9:cells9122644. [PMID: 33316954 PMCID: PMC7764472 DOI: 10.3390/cells9122644] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/02/2020] [Accepted: 12/05/2020] [Indexed: 12/14/2022] Open
Abstract
Hormone receptor-positive breast cancer (HR+ BC) accounts for approximately 75% of new BC diagnoses. Despite the undisputable progresses obtained in the treatment of HR+ BC in recent years, primary or acquired resistance to endocrine therapies still represents a clinically relevant issue, and is largely responsible for disease recurrence after curative surgery, as well as for disease progression in the metastatic setting. Among the mechanisms causing primary or acquired resistance to endocrine therapies is the loss of estrogen/progesterone receptor expression, which could make BC cells independent of estrogen stimulation and, consequently, resistant to estrogen deprivation or the pharmacological inhibition of estrogen receptors. This review aims at discussing the molecular mechanisms and the clinical implications of HR loss as a result of the therapies used in the neoadjuvant setting or for the treatment of advanced disease in HR+ BC patients.
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Affiliation(s)
- Emma Zattarin
- Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. Venezian 1, 20133 Milan, Italy; (E.Z.); (R.L.); (F.L.); (R.L.); (A.V.); (G.P.)
| | - Rita Leporati
- Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. Venezian 1, 20133 Milan, Italy; (E.Z.); (R.L.); (F.L.); (R.L.); (A.V.); (G.P.)
| | - Francesca Ligorio
- Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. Venezian 1, 20133 Milan, Italy; (E.Z.); (R.L.); (F.L.); (R.L.); (A.V.); (G.P.)
| | - Riccardo Lobefaro
- Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. Venezian 1, 20133 Milan, Italy; (E.Z.); (R.L.); (F.L.); (R.L.); (A.V.); (G.P.)
| | - Andrea Vingiani
- Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. Venezian 1, 20133 Milan, Italy; (E.Z.); (R.L.); (F.L.); (R.L.); (A.V.); (G.P.)
| | - Giancarlo Pruneri
- Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. Venezian 1, 20133 Milan, Italy; (E.Z.); (R.L.); (F.L.); (R.L.); (A.V.); (G.P.)
- Department of Oncology and Haematology, University of Milan, Via Festa del Perdono 7, 20122 Milan, Italy
| | - Claudio Vernieri
- Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. Venezian 1, 20133 Milan, Italy; (E.Z.); (R.L.); (F.L.); (R.L.); (A.V.); (G.P.)
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
- Correspondence: ; Tel.: +39-02-2390-3650
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Danelli T, Laura M, Savona M, Landoni M, Adani F, Pilu R. Genetic Improvement of Arundo donax L.: Opportunities and Challenges. Plants (Basel) 2020; 9:E1584. [PMID: 33207586 PMCID: PMC7696946 DOI: 10.3390/plants9111584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/09/2020] [Accepted: 11/13/2020] [Indexed: 12/29/2022]
Abstract
Arundo donax L., the giant reed-being a long-duration, low-cost, non-food energy crop able to grow in marginal lands-has emerged as a potential alternative to produce biomass for both energy production, with low carbon emissions, and industrial bioproducts. In recent years, pioneering efforts have been made to genetically improve this very promising energy crop. This review analyses the recent advances and challenges encountered in using clonal selection, mutagenesis/somaclonal variation and transgenesis/genome editing. Attempts to improve crop yield, in vitro propagation efficiency, salt and heavy metal tolerance by clonal selection were carried out, although limited by the species' low genetic diversity and availability of mutants. Mutagenesis and somaclonal variation have also been attempted on this species; however, since Arundo donax is polyploid, it is very difficult to induce and select promising mutations. In more recent years, genomics and transcriptomics data are becoming available in Arundo, closing the gap to make possible the genetic manipulation of this energy crop in the near future. The challenge will regard the functional characterization of the genes/sequences generated by genomic sequencing and transcriptomic analysis in a complex polyploid genome.
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Affiliation(s)
- Tommaso Danelli
- Gruppo Ricicla Labs—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (T.D.); (F.A.)
- Agricultural Genetics Group—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
| | - Marina Laura
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso Degli Inglesi 508, 18038 Sanremo, Italy; (M.L.); (M.S.)
| | - Marco Savona
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso Degli Inglesi 508, 18038 Sanremo, Italy; (M.L.); (M.S.)
| | - Michela Landoni
- Department of Biosciences, Università’ Degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy;
| | - Fabrizio Adani
- Gruppo Ricicla Labs—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (T.D.); (F.A.)
- Agricultural Genetics Group—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
| | - Roberto Pilu
- Gruppo Ricicla Labs—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (T.D.); (F.A.)
- Agricultural Genetics Group—Department of Agricultural and Environmental Sciences—Production, Landscape and Agroenergy, Università’ Degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
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29
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van der Poel CE, Bajic G, Macaulay CW, van den Broek T, Ellson CD, Bouma G, Victora GD, Degn SE, Carroll MC. Follicular Dendritic Cells Modulate Germinal Center B Cell Diversity through FcγRIIB. Cell Rep 2020; 29:2745-2755.e4. [PMID: 31775042 PMCID: PMC7015177 DOI: 10.1016/j.celrep.2019.10.086] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/05/2019] [Accepted: 10/22/2019] [Indexed: 01/02/2023] Open
Abstract
Follicular dendritic cells (FDCs), a rare and enigmatic stromal cell type in the B cell follicles of secondary lymphoid organs, store and present antigen to B cells. While essential for germinal center (GC) responses, their exact role during GC B cell selection remains unknown. FDCs upregulate the inhibitory IgG Fc receptor FcγRIIB during GC formation. We show that the stromal deficiency of FcγRIIB does not affect GC B cell frequencies compared to wild-type mice. However, in the absence of FcγRIIB on FDCs, GCs show aberrant B cell selection during autoreactive and selective foreign antigen responses. These GCs are more diverse as measured by the AidCreERT2 -confetti system and show the persistence of IgM+ clones with decreased numbers of IgH mutations. Our results show that FDCs can modulate GC B cell diversity by the upregulation of FcγRIIB. Permissive clonal selection and subsequent increased GC diversity may affect epitope spreading during autoimmunity and foreign responses. van der Poel et al. show that follicular dendritic cells (FDCs) can regulate germinal center diversity through FcγRIIB. In the absence of this receptor, germinal centers appear more diverse. In addition, the loss of FcγRIIB on FDCs leads to the persistence of IgM clones with decreased levels of somatic hypermutation.
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Affiliation(s)
- Cees E van der Poel
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Goran Bajic
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Charles W Macaulay
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Boston University, Boston, MA 02215, USA
| | - Theo van den Broek
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Søren E Degn
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Michael C Carroll
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Burnett DL, Schofield P, Langley DB, Jackson J, Bourne K, Wilson E, Porebski BT, Buckle AM, Brink R, Goodnow CC, Christ D. Conformational diversity facilitates antibody mutation trajectories and discrimination between foreign and self-antigens. Proc Natl Acad Sci U S A 2020; 117:22341-50. [PMID: 32855302 DOI: 10.1073/pnas.2005102117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Conformational diversity and self-cross-reactivity of antigens have been correlated with evasion from neutralizing antibody responses. We utilized single cell B cell sequencing, biolayer interferometry and X-ray crystallography to trace mutation selection pathways where the antibody response must resolve cross-reactivity between foreign and self-proteins bearing near-identical contact surfaces, but differing in conformational flexibility. Recurring antibody mutation trajectories mediate long-range rearrangements of framework (FW) and complementarity determining regions (CDRs) that increase binding site conformational diversity. These antibody mutations decrease affinity for self-antigen 19-fold and increase foreign affinity 67-fold, to yield a more than 1,250-fold increase in binding discrimination. These results demonstrate how conformational diversity in antigen and antibody does not act as a barrier, as previously suggested, but rather facilitates high affinity and high discrimination between foreign and self.
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Klein-Scory S, Wahner I, Maslova M, Al-Sewaidi Y, Pohl M, Mika T, Ladigan S, Schroers R, Baraniskin A. Evolution of RAS Mutational Status in Liquid Biopsies During First-Line Chemotherapy for Metastatic Colorectal Cancer. Front Oncol 2020; 10:1115. [PMID: 32766143 PMCID: PMC7378792 DOI: 10.3389/fonc.2020.01115] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022] Open
Abstract
Treatment options for patients with metastatic colorectal cancer (mCRC) are limited. This particularly affects the largest group of patients with RAS mutations, who are considered ineligible for therapy with antiEGFR antibodies. In this liquid biopsy-based study, we performed the first in-depth analysis of the RAS mutational status in initially RAS-mutated patients during first-line therapy. RAS status of twelve patients with initially RAS-mutated mCRC was monitored longitudinally in 69 liquid biopsy samples. We focused on patients with stable disease (SD) or partial remission (PR) during first-line therapy (11 patients). Detection of fragmented RAS-mutated circulating cell-free tumor DNA (ctDNA) in plasma was performed by digital-droplet PCR (ddPCR) and BEAMing. Patients' total tumor masses were determined by measuring the tumor volumes using CT scan data. All patients with PR or SD at first follow-up showed a significant decrease of RAS mutational load. In ten patients (91%), the ctDNA-based RAS mutational status converted to wild-type in ddPCR and BEAMing. Remarkably, conversions were observed early after the first cycle of chemotherapy. Plasma concentration of ctDNA was controlled by determination of methylated WIF1-promotor ctDNA burden as a second tumor marker for mCRC. Persistent presence of methylated WIF1-promotor fragments confirmed the ongoing release of ctDNA during treatment. In patients with initially RAS-mutated mCRC, RAS mutations rapidly disappeared during first-line therapy in liquid biopsy, independent of type and intensity of chemotherapy and irrespective of anti-VEGF treatments. Following our results demonstrating conversion of RAS-mutational status, potential effectiveness of anti-EGFR antibodies in selected patients becomes an attractive hypothesis for future studies.
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Affiliation(s)
- Susanne Klein-Scory
- IMBL Medical Clinic, Ruhr University Bochum, University Hospital Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
| | - Ingo Wahner
- IMBL Medical Clinic, Ruhr University Bochum, University Hospital Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
| | - Marina Maslova
- Department of Radiology, University Hospital Knappschaftskrankenhaus Bochum GmbH, Ruhr University Bochum, Bochum, Germany
| | - Yosef Al-Sewaidi
- Department of Radiology, University Hospital Knappschaftskrankenhaus Bochum GmbH, Ruhr University Bochum, Bochum, Germany
| | - Michael Pohl
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum GmbH, Ruhr University Bochum, Bochum, Germany
| | - Thomas Mika
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum GmbH, Ruhr University Bochum, Bochum, Germany
| | - Swetlana Ladigan
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum GmbH, Ruhr University Bochum, Bochum, Germany
| | - Roland Schroers
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum GmbH, Ruhr University Bochum, Bochum, Germany
| | - Alexander Baraniskin
- IMBL Medical Clinic, Ruhr University Bochum, University Hospital Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum GmbH, Ruhr University Bochum, Bochum, Germany
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J. Heath J, D. Grant M. The Immune Response Against Human Cytomegalovirus Links Cellular to Systemic Senescence. Cells 2020; 9:cells9030766. [PMID: 32245117 PMCID: PMC7140628 DOI: 10.3390/cells9030766] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/11/2020] [Accepted: 03/17/2020] [Indexed: 12/12/2022] Open
Abstract
Aging reflects long-term decline in physiological function and integrity. Changes arise at a variable pace governed by time-dependent and -independent mechanisms that are themselves complex, interdependent and variable. Molecular decay produces inferior cells that eventually dominate over healthy counterparts in tissues they comprise. In a form of biological entropy, progression from molecular through cellular to tissue level degeneration culminates in organ disease or dysfunction, affecting systemic health. To better understand time-independent contributors and their potential modulation, common biophysical bases for key molecular and cellular changes underlying age-related physiological deterioration must be delineated. This review addresses the potential contribution of cytomegalovirus (CMV)-driven T cell proliferation to cellular senescence and immunosenescence. We first describe molecular processes imposing cell cycle arrest, the foundation of cellular senescence, then focus on the unique distribution, phenotype and function of CMV-specific CD8+ T cells in the context of cellular senescence and "inflammaging". Their features position CMV infection as a pathogenic accelerant of immune cell proliferation underlying immune senescence. In human immunodeficiency virus (HIV) infection, where increased inflammation and exaggerated anti-CMV immune responses accelerate immune senescence, CMV infection has emerged as a major factor in unhealthy aging. Thus, we speculate on mechanistic links between CMV-specific CD8+ T-cell expansion, immune senescence and prevalence of age-related disorders in HIV infection.
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Affiliation(s)
- John J. Heath
- Immunology and Infectious Diseases Program, Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, St. John’s, NL A1B 3V6, Canada;
- Lady Davis Institute for Medical Research, Jewish General Hospital, Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Michael D. Grant
- Immunology and Infectious Diseases Program, Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, St. John’s, NL A1B 3V6, Canada;
- Correspondence:
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Calleja A, Yun S, Moreilhon C, Karsenti JM, Gastaud L, Mannone L, Komrokji R, Al Ali N, Dadone-Montaudie B, Robert G, Auberger P, Raynaud S, Sallman DA, Cluzeau T. Clonal selection in therapy-related myelodysplastic syndromes and acute myeloid leukemia under azacitidine treatment. Eur J Haematol 2020; 104:488-498. [PMID: 31990086 DOI: 10.1111/ejh.13390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Therapy-related myelodysplastic syndrome and acute myeloid leukemia (t-MDS/AML) are defined as complications of previous cytotoxic therapy. Azacitidine (AZA), a hypomethylating agent, has showed activity in t-MDS/AML. OBJECTIVES We evaluated the clonal dynamics of AZA-treated t-MDS/AML. METHODS We collected bone marrow samples, at diagnosis and during treatment, from AZA-treated t-MDS/AML patients. NGS on 19 myeloid genes was performed, and candidate mutations with a variant allele frequency >5% were selected. RESULTS Seven t-AML and 12 t-MDS were included with median age of 71 (56-82) years old, median number of AZA cycles of 6 (1-15), and median overall survival (OS) of 14 (3-29) months. We observed correlation between AZA response and clonal selection. Decrease of TP53-mutated clone was correlated with response to AZA, confirming AZA efficacy in this subgroup. In some patients, emergence of mutations was correlated with progression or relapse without impact on OS. Clones with mutations in genes for DNA methylation regulation frequently occurred with other mutations and remained stable during AZA treatment, independent of AZA response. CONCLUSION We confirmed that the molecular complexity of t-MNs and that the follow-up of clonal selection during AZA treatment could be useful to define treatment combination.
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Affiliation(s)
- Anne Calleja
- Hematology Department, Cote D'Azur University, Nice Sophia Antipolis University, CHU of Nice, Nice, France.,Cote d'Azur University, INSERM U1065, Mediterranean Center of Molecular Medecine, Nice, France
| | - Seongseok Yun
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Chimène Moreilhon
- Cote D'Azur University, Nice Sophia Antipolis University, CHU of Nice, Onco-hematology Laboratory, Nice, France
| | - Jean Michel Karsenti
- Hematology Department, Cote D'Azur University, Nice Sophia Antipolis University, CHU of Nice, Nice, France
| | - Lauris Gastaud
- Oncology Department, Antoine Lacassagne Center, Nice, France
| | - Lionel Mannone
- Hematology Department, Cote D'Azur University, Nice Sophia Antipolis University, CHU of Nice, Nice, France
| | - Rami Komrokji
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Najla Al Ali
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Bérangère Dadone-Montaudie
- Anatomopathology Department, Cote d'Azur University, Nice Sophia Antipolis University, CHU of Nice, Nice, France
| | - Guillaume Robert
- Cote d'Azur University, INSERM U1065, Mediterranean Center of Molecular Medecine, Nice, France
| | - Patrick Auberger
- Cote d'Azur University, INSERM U1065, Mediterranean Center of Molecular Medecine, Nice, France
| | - Sophie Raynaud
- Cote D'Azur University, Nice Sophia Antipolis University, CHU of Nice, Onco-hematology Laboratory, Nice, France
| | - David A Sallman
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Thomas Cluzeau
- Hematology Department, Cote D'Azur University, Nice Sophia Antipolis University, CHU of Nice, Nice, France.,Cote d'Azur University, INSERM U1065, Mediterranean Center of Molecular Medecine, Nice, France
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Zhao Y, Maule J, McCracken J, Li Y, Rapisardo S, Yang LH, Wang E. Acute myeloid leukaemia with maturation demonstrates persistent disease with prominent megakaryoblastic differentiation 16 days following induction chemotherapy: an intra-myeloid lineage switch mediated by chemotherapy-induced clonal selection. Br J Haematol 2020; 189:e64-e67. [PMID: 32108332 DOI: 10.1111/bjh.16476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Yue Zhao
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China.,Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Jake Maule
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Jenna McCracken
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Yang Li
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA.,Division of Haematology/Oncology, Department of Medicine, Shengjing Hospital Affiliated to China Medical University, Shenyang, People's Republic of China
| | - Sarah Rapisardo
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Lian-He Yang
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China.,Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Endi Wang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
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Sheih A, Voillet V, Hanafi LA, DeBerg HA, Yajima M, Hawkins R, Gersuk V, Riddell SR, Maloney DG, Wohlfahrt ME, Pande D, Enstrom MR, Kiem HP, Adair JE, Gottardo R, Linsley PS, Turtle CJ. Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy. Nat Commun 2020; 11:219. [PMID: 31924795 PMCID: PMC6954177 DOI: 10.1038/s41467-019-13880-1] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 12/04/2019] [Indexed: 12/21/2022] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy has produced remarkable anti-tumor responses in patients with B-cell malignancies. However, clonal kinetics and transcriptional programs that regulate the fate of CAR-T cells after infusion remain poorly understood. Here we perform TCRB sequencing, integration site analysis, and single-cell RNA sequencing (scRNA-seq) to profile CD8+ CAR-T cells from infusion products (IPs) and blood of patients undergoing CD19 CAR-T immunotherapy. TCRB sequencing shows that clonal diversity of CAR-T cells is highest in the IPs and declines following infusion. We observe clones that display distinct patterns of clonal kinetics, making variable contributions to the CAR-T cell pool after infusion. Although integration site does not appear to be a key driver of clonal kinetics, scRNA-seq demonstrates that clones that expand after infusion mainly originate from infused clusters with higher expression of cytotoxicity and proliferation genes. Thus, we uncover transcriptional programs associated with CAR-T cell behavior after infusion.
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Affiliation(s)
- Alyssa Sheih
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Valentin Voillet
- Vaccine and Infectious Disease Division and Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Laïla-Aïcha Hanafi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Hannah A DeBerg
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, 98101, USA
| | - Masanao Yajima
- Department of Mathematics and Statistics, Boston University, Boston, Massachusetts, 02215, USA
| | - Reed Hawkins
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Vivian Gersuk
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, 98101, USA
| | - Stanley R Riddell
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Integrated Immunotherapy Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - David G Maloney
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Integrated Immunotherapy Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Martin E Wohlfahrt
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Dnyanada Pande
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Mark R Enstrom
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Hans-Peter Kiem
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Jennifer E Adair
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Integrated Immunotherapy Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Raphaël Gottardo
- Vaccine and Infectious Disease Division and Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Integrated Immunotherapy Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Peter S Linsley
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, 98101, USA
| | - Cameron J Turtle
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA.
- Department of Medicine, University of Washington, Seattle, Washington, USA.
- Integrated Immunotherapy Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA.
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Abstract
Neuroblastoma (NB) is the most common cancer of infancy and accounts for nearly one tenth of pediatric cancer deaths. This mortality rate has been attributed to the > 50% frequency of relapse despite intensive, multimodal clinical therapy in patients with progressive NB. Given the disease’s heterogeneity and developed resistance, attaining a cure after relapse of progressive NB is highly challenging. A rapid decrease in the timeline between successive recurrences is likely due to the ongoing acquisition of genetic rearrangements in undifferentiated NB-cancer stem cells (CSCs). In this review, we present the current understanding of NB-CSCs, their intrinsic role in tumorigenesis, their function in disease progression, and their influence on acquired therapy resistance and tumor evolution. In particular, this review focus on the intrinsic involvement of stem cells and signaling in the genesis of NB, the function of pre-existing CSCs in NB progression and therapy response, the formation and influence of induced CSCs (iCSCs) in drug resistance and tumor evolution, and the development of a CSC-targeted therapeutic approach.
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Affiliation(s)
- Natarajan Aravindan
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Department of Anesthesiology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Drishti Jain
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Dinesh Babu Somasundaram
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Terence S Herman
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Stephenson Cancer Center, Oklahoma City, OK 73104, USA
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Chakroborty D, Kurppa KJ, Paatero I, Ojala VK, Koivu M, Tamirat MZ, Koivunen JP, Jänne PA, Johnson MS, Elo LL, Elenius K. An unbiased in vitro screen for activating epidermal growth factor receptor mutations. J Biol Chem 2019; 294:9377-9389. [PMID: 30952700 DOI: 10.1074/jbc.ra118.006336] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 03/23/2019] [Indexed: 01/22/2023] Open
Abstract
Cancer tissues harbor thousands of mutations, and a given oncogene may be mutated at hundreds of sites, yet only a few of these mutations have been functionally tested. Here, we describe an unbiased platform for the functional characterization of thousands of variants of a single receptor tyrosine kinase (RTK) gene in a single assay. Our in vitro screen for activating mutations (iSCREAM) platform enabled rapid analysis of mutations conferring gain-of-function RTK activity promoting clonal growth. The screening strategy included a somatic model of cancer evolution and utilized a library of 7,216 randomly mutated epidermal growth factor receptor (EGFR) single-nucleotide variants that were tested in murine lymphoid Ba/F3 cells. These cells depend on exogenous interleukin-3 (IL-3) for growth, but this dependence can be compensated by ectopic EGFR overexpression, enabling selection for gain-of-function EGFR mutants. Analysis of the enriched mutants revealed EGFR A702V, a novel activating variant that structurally stabilized the EGFR kinase dimer interface and conferred sensitivity to kinase inhibition by afatinib. As proof of concept for our approach, we recapitulated clinical observations and identified the EGFR L858R as the major enriched EGFR variant. Altogether, iSCREAM enabled robust enrichment of 21 variants from a total of 7,216 EGFR mutations. These findings indicate the power of this screening platform for unbiased identification of activating RTK variants that are enriched under selection pressure in a model of cancer heterogeneity and evolution.
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Affiliation(s)
- Deepankar Chakroborty
- From the Institute of Biomedicine and Medicity Research Laboratories and.,the Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku 20520, Finland.,the Turku Center for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Kari J Kurppa
- From the Institute of Biomedicine and Medicity Research Laboratories and.,the Department of Medical Oncology and
| | - Ilkka Paatero
- the Turku Center for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Veera K Ojala
- From the Institute of Biomedicine and Medicity Research Laboratories and.,the Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku 20520, Finland.,the Turku Center for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Marika Koivu
- From the Institute of Biomedicine and Medicity Research Laboratories and.,the Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku 20520, Finland.,the Turku Center for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Mahlet Z Tamirat
- the Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
| | - Jussi P Koivunen
- the Department of Oncology and Radiotherapy, Oulu University Hospital and MRC Oulu, Oulu 90220, Finland, and
| | - Pasi A Jänne
- the Department of Medical Oncology and.,the Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Mark S Johnson
- the Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
| | - Laura L Elo
- the Turku Center for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Klaus Elenius
- From the Institute of Biomedicine and Medicity Research Laboratories and .,the Turku Center for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland.,the Department of Oncology, Turku University Hospital, Turku 20521, Finland
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Meyer-Hermann M, Binder SC, Mesin L, Victora GD. Computer Simulation of Multi-Color Brainbow Staining and Clonal Evolution of B Cells in Germinal Centers. Front Immunol 2018; 9:2020. [PMID: 30319600 PMCID: PMC6167470 DOI: 10.3389/fimmu.2018.02020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/16/2018] [Indexed: 01/18/2023] Open
Abstract
Clonal evolution of B cells in germinal centers (GCs) is central to affinity maturation of antibodies in response to pathogens. Permanent or tamoxifen-induced multi-color recombination of B cells based on the brainbow allele allows monitoring the degree of color dominance in the course of the GC reaction. Here, we use computer simulations of GC reactions in order to replicate the evolution of color dominance in silico and to define rules for the interpretation of these data in terms of clonal dominance. We find that a large diversity of clonal dominance is generated in simulated GCs in agreement with experimental results. In the extremes, a GC can be dominated by a single clone or can harbor many co-existing clones. These properties can be directly derived from the measurement of color dominance when all B cells are stained before the GC onset. Upon tamoxifen-induced staining, the correlation between clonal structure and color dominance depends on the timing and duration of the staining procedure as well as on the total number of stained B cells. B cells can be stained with 4 colors if a single brainbow allele is used, using both alleles leads to 10 different colors. The advantage of staining with 10 instead of 4 colors becomes relevant only when the 10 colors are attributed with rather similar probability. Otherwise, 4 colors exhibit a comparable predictive power. These results can serve as a guideline for future experiments based on multi-color staining of evolving systems.
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Affiliation(s)
- Michael Meyer-Hermann
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
- Centre for Individualised Infection Medicine, Hanover, Germany
| | - Sebastian C. Binder
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Luka Mesin
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, United States
| | - Gabriel D. Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, United States
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McCarthy KR, Watanabe A, Kuraoka M, Do KT, McGee CE, Sempowski GD, Kepler TB, Schmidt AG, Kelsoe G, Harrison SC. Memory B Cells that Cross-React with Group 1 and Group 2 Influenza A Viruses Are Abundant in Adult Human Repertoires. Immunity 2018; 48:174-184.e9. [PMID: 29343437 DOI: 10.1016/j.immuni.2017.12.009] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/12/2017] [Accepted: 12/08/2017] [Indexed: 01/08/2023]
Abstract
Human B cell antigen-receptor (BCR) repertoires reflect repeated exposures to evolving influenza viruses; new exposures update the previously generated B cell memory (Bmem) population. Despite structural similarity of hemagglutinins (HAs) from the two groups of influenza A viruses, cross-reacting antibodies (Abs) are uncommon. We analyzed Bmem compartments in three unrelated, adult donors and found frequent cross-group BCRs, both HA-head directed and non-head directed. Members of a clonal lineage from one donor had a BCR structure similar to that of a previously described Ab, encoded by different gene segments. Comparison showed that both Abs contacted the HA receptor-binding site through long heavy-chain third complementarity determining regions. Affinities of the clonal-lineage BCRs for historical influenza-virus HAs from both group 1 and group 2 viruses suggested that serial responses to seasonal influenza exposures had elicited the lineage and driven affinity maturation. We propose that appropriate immunization regimens might elicit a comparably broad response.
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40
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Stanimirovic B, Vujovic D, Pejin B, Popovic Djordjevic J, Maletic R, Raicevic P, Tesic Z. A contribution to the elemental profile of the leaf samples of newly developed Cabernet Franc varieties. Nat Prod Res 2018; 33:1209-1213. [PMID: 29600716 DOI: 10.1080/14786419.2018.1457671] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The elemental profile of the leaf samples of three Cabernet Franc clone candidates recently developed in Serbia (Nos. 02, 010 and 012) obtained in the last phase of clonal selection was examined within this study by ICP-OES. Optimal content of Al, Fe, Cu and Zn, the metals well known for their links with a number of neurodegenerative disorders including Alzheimer's disease, has actually highlighted the potential of the leaf sample No. 10 to afford a novel food supplement of natural origin possessing well balanced metal ingredients. Furthermore, lower content of some other elements (Cr, Mn, Ni and Pb) thoroughly supports such a claiming. Finally, the most favourable K/Na ratio observed for the aforementioned sample points out its likely cardioprotectivity. However, two other Cabernet Franc clone candidates might also be recommended for breeding in the same or similar viticultural conditions, since all obtained values were below toxic ones for human consumption.
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Affiliation(s)
- Bojana Stanimirovic
- a University of Belgrade , Faculty of Chemistry , Belgrade , Serbia.,b Institute MOL Ltd. , Stara Pazova , Serbia
| | - Dragan Vujovic
- c University of Belgrade , Faculty of Agriculture , Belgrade - Zemun , Serbia
| | - Boris Pejin
- d Department of Life Sciences , University of Belgrade, Institute for Multidisciplinary Research - IMSI , Belgrade , Serbia
| | | | - Radojka Maletic
- c University of Belgrade , Faculty of Agriculture , Belgrade - Zemun , Serbia
| | - Petar Raicevic
- c University of Belgrade , Faculty of Agriculture , Belgrade - Zemun , Serbia
| | - Zivoslav Tesic
- a University of Belgrade , Faculty of Chemistry , Belgrade , Serbia
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Wang T, Hoi KM, Stöckmann H, Wan C, Sim LC, Shi Jie Tay NHBK, Poo CH, Woen S, Yang Y, Zhang P, Rudd PM. LC/MS-based Intact IgG and Released Glycan Analysis for Bioprocessing Applications. Biotechnol J 2018; 13:e1700185. [PMID: 29341427 DOI: 10.1002/biot.201700185] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 01/06/2018] [Indexed: 01/27/2023]
Abstract
Robust plate based antibody glycan analysis platforms are urgently needed for biopharmaceutical development and manufacturing as well as for clinical biomarker research. A 96-well plate based workflow has been developed to analyze both intact IgG antibodies and released N-glycans using an Orbitrap Fusion Mass Spectrometer and an LC/MS method on the Waters UNIFI platform. Here, such a workflow including protein A purification, PNGaseF digestion, 2-AB labeling, and SPE clean-up is described. The measured IgG glycan profile is consistent with that obtained from non-plate based method and commercial kit and has the advantage of less hands-on time. Also the application of the workflow in cell culture monitoring and clonal selection work is demonstrated. Apart from checking the major glycan structure changes among clones, post translational modifications (PTMs) such as C-terminal lysine residue clipping and N-terminal pyroglutamic acid formation can also be deduced from the workflow.
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Affiliation(s)
- Tianhua Wang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Kong Meng Hoi
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Henning Stöckmann
- NIBRT GlycoScience Group, NIBRT - The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin 4, Ireland
| | - Corrine Wan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Lyn Chiin Sim
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | | | - Ce Huang Poo
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Susanto Woen
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Yuangsheng Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Peiqing Zhang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Pauline M Rudd
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore.,NIBRT GlycoScience Group, NIBRT - The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin 4, Ireland
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Poglio S, Lewandowski D, Calvo J, Caye A, Gros A, Laharanne E, Leblanc T, Landman-Parker J, Baruchel A, Soulier J, Ballerini P, Clappier E, Pflumio F. Speed of leukemia development and genetic diversity in xenograft models of T cell acute lymphoblastic leukemia. Oncotarget 2018; 7:41599-41611. [PMID: 27191650 PMCID: PMC5173081 DOI: 10.18632/oncotarget.9313] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 04/22/2016] [Indexed: 11/25/2022] Open
Abstract
T cell acute lymphoblastic leukemia (T-ALL) develops through accumulation of multiple genomic alterations within T-cell progenitors resulting in clonal heterogeneity among leukemic cells. Human T-ALL xeno-transplantation in immunodeficient mice is a gold standard approach to study leukemia biology and we recently uncovered that the leukemia development is more or less rapid depending on T-ALL sample. The resulting human leukemia may arise through genetic selection and we previously showed that human T-ALL development in immune-deficient mice is significantly enhanced upon CD7+/CD34+ leukemic cell transplantations. Here we investigated the genetic characteristics of CD7+/CD34+ and CD7+/CD34− cells from newly diagnosed human T-ALL and correlated it to the speed of leukemia development. We observed that CD7+/CD34+ or CD7+/CD34− T-ALL cells that promote leukemia within a short-time period are genetically similar, as well as xenograft-derived leukemia resulting from both cell fractions. In the case of delayed T-ALL growth CD7+/CD34+ or CD7+/CD34− cells were either genetically diverse, the resulting xenograft leukemia arising from different but branched subclones present in the original sample, or similar, indicating decreased fitness to mouse micro-environment. Altogether, our work provides new information relating the speed of leukemia development in xenografts to the genetic diversity of T-ALL cell compartments.
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Affiliation(s)
- Sandrine Poglio
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV-IRCM-SCSR-LSHL, UMR 967, Fontenay-aux-Roses, France.,INSERM, U967, Fontenay-aux-Roses, France.,Université Paris Diderot, Sorbonne Paris Cité, UMR 967, Fontenay-aux-Roses, France.,Université Paris-Sud, UMR 967, Fontenay-aux-Roses, France
| | - Daniel Lewandowski
- INSERM, U967, Fontenay-aux-Roses, France.,Université Paris Diderot, Sorbonne Paris Cité, UMR 967, Fontenay-aux-Roses, France.,Université Paris-Sud, UMR 967, Fontenay-aux-Roses, France.,CEA, DSV-IRCM-SCSR-LRTS, UMR 967, Fontenay-aux-Roses, France
| | - Julien Calvo
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV-IRCM-SCSR-LSHL, UMR 967, Fontenay-aux-Roses, France.,INSERM, U967, Fontenay-aux-Roses, France.,Université Paris Diderot, Sorbonne Paris Cité, UMR 967, Fontenay-aux-Roses, France.,Université Paris-Sud, UMR 967, Fontenay-aux-Roses, France
| | - Aurélie Caye
- Université Paris Diderot, Paris, France.,Assistance Publique-Hôpitaux de Paris (AP-HP), Département de Génétique, UF de Génétique Moléculaire, Hôpital Robert Debré Paris, France
| | - Audrey Gros
- INSERM, UMR1053 Bordeaux Research in Translational Oncology (BaRITOn), Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - Elodie Laharanne
- INSERM, UMR1053 Bordeaux Research in Translational Oncology (BaRITOn), Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - Thierry Leblanc
- AP-HP, Service d'hématologie Pédiatrique, Hôpital Robert Debré, Paris, France
| | | | - André Baruchel
- AP-HP, Service d'hématologie Pédiatrique, Hôpital Robert Debré, Paris, France
| | - Jean Soulier
- Université Paris Diderot, Paris, France.,AP-HP, Laboratoire d'Hématologie, Hôpital Saint-Louis, Paris, France.,Team Genome and Cancer, U944 INSERM, Paris, France
| | - Paola Ballerini
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV-IRCM-SCSR-LSHL, UMR 967, Fontenay-aux-Roses, France.,INSERM, U967, Fontenay-aux-Roses, France.,Université Paris Diderot, Sorbonne Paris Cité, UMR 967, Fontenay-aux-Roses, France.,Université Paris-Sud, UMR 967, Fontenay-aux-Roses, France.,AP-HP, Service d'hématologie Pédiatrique, Hôpital Armand Trousseau, Paris, France
| | - Emmanuelle Clappier
- Université Paris Diderot, Paris, France.,AP-HP, Laboratoire d'Hématologie, Hôpital Saint-Louis, Paris, France.,Team Genome and Cancer, U944 INSERM, Paris, France
| | - Françoise Pflumio
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV-IRCM-SCSR-LSHL, UMR 967, Fontenay-aux-Roses, France.,INSERM, U967, Fontenay-aux-Roses, France.,Université Paris Diderot, Sorbonne Paris Cité, UMR 967, Fontenay-aux-Roses, France.,Université Paris-Sud, UMR 967, Fontenay-aux-Roses, France
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43
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Parsons BL, McKim KL, Myers MB. Variation in organ-specific PIK3CA and KRAS mutant levels in normal human tissues correlates with mutation prevalence in corresponding carcinomas. Environ Mol Mutagen 2017; 58:466-476. [PMID: 28755461 PMCID: PMC5601221 DOI: 10.1002/em.22110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 05/27/2023]
Abstract
Large-scale sequencing efforts have described the mutational complexity of individual cancers and identified mutations prevalent in different cancers. As a complementary approach, allele-specific competitive blocker PCR (ACB-PCR) is being used to quantify levels of hotspot cancer driver mutations (CDMs) with high sensitivity, to elucidate the tissue-specific properties of CDMs, their occurrence as tumor cell subpopulations, and their occurrence in normal tissues. Here we report measurements of PIK3CA H1047R mutant fraction (MF) in normal colonic mucosa, normal lung, colonic adenomas, colonic adenocarcinomas, and lung adenocarcinomas. We report PIK3CA E545K MF measurements in those tissues, as well as in normal breast, normal thyroid, mammary ductal carcinomas, and papillary thyroid carcinomas. We report KRAS G12D and G12V MF measurements in normal colon. These MF measurements were integrated with previously published ACB-PCR data on KRAS G12D, KRAS G12V, and PIK3CA H1047R. Analysis of these data revealed a correlation between the degree of interindividual variability in these mutations (as log10 MF standard deviation) in normal tissues and the frequencies with which the mutations are detected in carcinomas of the corresponding organs in the COSMIC database. This novel observation has important implications. It suggests that interindividual variability in mutation levels of normal tissues may be used as a metric to identify mutations with critical early roles in tissue-specific carcinogenesis. Additionally, it raises the possibility that personalized cancer therapeutics, developed to target specifically activated oncogenic products, might be repurposed as prophylactic therapies to reduce the accumulation of cells carrying CDMs and, thereby, reduce future cancer risk. Environ. Mol. Mutagen. 58:466-476, 2017. © 2017 This article is a U.S. Government work and is in the public domain in the USA. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Barbara L. Parsons
- Division of Genetic and Molecular ToxicologyU.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansas
| | - Karen L. McKim
- Division of Genetic and Molecular ToxicologyU.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansas
| | - Meagan B. Myers
- Division of Genetic and Molecular ToxicologyU.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansas
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Abstract
The CRISPR/Cas9 genome engineering system has revolutionized biology by allowing for precise genome editing with little effort. Guided by a single guide RNA (sgRNA) that confers specificity, the Cas9 protein cleaves both DNA strands at the targeted locus. The DNA break can trigger either non-homologous end joining (NHEJ) or homology directed repair (HDR). NHEJ can introduce small deletions or insertions which lead to frame-shift mutations, while HDR allows for larger and more precise perturbations. Here, we present protocols for generating knockout cell lines by coupling established CRISPR/Cas9 methods with two options for downstream selection/screening. The NHEJ approach uses a single sgRNA cut site and selection-independent screening, where protein production is assessed by dot immunoblot in a high-throughput manner. The HDR approach uses two sgRNA cut sites that span the gene of interest. Together with a provided HDR template, this method can achieve deletion of tens of kb, aided by the inserted selectable resistance marker. The appropriate applications and advantages of each method are discussed.
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Affiliation(s)
- Erin L Sternburg
- Cell Biology and Neuroscience, University of California, Riverside
| | - Kristen C Dias
- Cell Biology and Neuroscience, University of California, Riverside
| | - Fedor V Karginov
- Cell Biology and Neuroscience, University of California, Riverside;
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Vujović D, Maletić R, Popović-Đorđević J, Pejin B, Ristić R. Viticultural and chemical characteristics of Muscat Hamburg preselected clones grown for table grapes. J Sci Food Agric 2017; 97:587-594. [PMID: 27098241 DOI: 10.1002/jsfa.7769] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 03/18/2016] [Accepted: 04/15/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND Clonal selection is one of the tools used for grapevine improvement and therefore is very important for obtaining clones with better characteristics than the variety population. The aim of this study was to select superior grapevines of Vitis vinifera L. cv. Muscat Hamburg grown for fresh consumption. RESULTS The viticultural parameters and fruit composition of 35 selected vines were determined during a 5-year period. The evaluated parameters showed high variability among selected vines. The significant effect of vintage was observed for all descriptors with the exception of the number of seeds per berry and sugar concentration. Additionally, all vines were examined for their tolerance to low temperatures and the results showed 73% and 90% of primary bud injury at -20 and -25 °C, respectively. In relation to berry classification, the percentage of first-class grapes ranged from 60% to 69% for all selected grapevines. Multivariate statistical analysis was performed to classify grapevines based on their performance. CONCLUSION Fourteen grapevines were identified as the most promising among the 35 vines initially planted, based on high yield, bunch and berry weight, sugar content and percentage of first-grade grapes. Those grapevines were selected for the next phase of the clonal selection. This study highlighted the importance of clonal selection for improvement of the variety population. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Dragan Vujović
- Faculty of Agriculture, University of Belgrade, 11080, Belgrade, Zemun, Serbia
| | - Radojka Maletić
- Faculty of Agriculture, University of Belgrade, 11080, Belgrade, Zemun, Serbia
| | | | - Boris Pejin
- Department of Life Sciences, Institute for Multidisciplinary Research - IMSI, University of Belgrade, 11030, Belgrade-, Serbia
| | - Renata Ristić
- School of Agriculture, Food and Wine, University of Adelaide, PMB 1, Glen Osmond, 5064, SA, Australia
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Kuraoka M, Schmidt AG, Nojima T, Feng F, Watanabe A, Kitamura D, Harrison SC, Kepler TB, Kelsoe G. Complex Antigens Drive Permissive Clonal Selection in Germinal Centers. Immunity 2016; 44:542-552. [PMID: 26948373 DOI: 10.1016/j.immuni.2016.02.010] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/06/2015] [Accepted: 12/07/2015] [Indexed: 12/26/2022]
Abstract
Germinal center (GC) B cells evolve toward increased affinity by a Darwinian process that has been studied primarily in genetically restricted, hapten-specific responses. We explored the population dynamics of genetically diverse GC responses to two complex antigens-Bacillus anthracis protective antigen and influenza hemagglutinin-in which B cells competed both intra- and interclonally for distinct epitopes. Preferred VH rearrangements among antigen-binding, naive B cells were similarly abundant in early GCs but, unlike responses to haptens, clonal diversity increased in GC B cells as early "winners" were replaced by rarer, high-affinity clones. Despite affinity maturation, inter- and intraclonal avidities varied greatly, and half of GC B cells did not bind the immunogen but nonetheless exhibited biased VH use, V(D)J mutation, and clonal expansion comparable to antigen-binding cells. GC reactions to complex antigens permit a range of specificities and affinities, with potential advantages for broad protection.
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Affiliation(s)
- Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Aaron G Schmidt
- Laboratory of Molecular Medicine, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Takuya Nojima
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Feng Feng
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Akiko Watanabe
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Daisuke Kitamura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
| | - Stephen C Harrison
- Laboratory of Molecular Medicine, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; Department of Mathematics and Statistics, Boston University, Boston, MA 02118, USA
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, NC 27710, USA; Human Vaccine Institute, Duke University, Durham, NC 27710, USA.
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Abstract
The proliferation of specific lymphocytes is the central tenet of the clonal selection paradigm. Antigen recognition by T cells triggers a series of events that produces expanded clones of differentiated effector cells. TCR signaling events are detectable within seconds and minutes and are likely to continue for hours and days in vivo. Here, I review the work done on the importance of TCR signals in the later part of the expansion phase of the primary T cell response, primarily regarding the regulation of the cell cycle in CD4(+) and CD8(+) cells. The results suggest a degree of programing by early signals for effector differentiation, particularly in the CD8(+) T cell compartment, with optimal expansion supported by persistent antigen presentation later on. Differences to CD4(+) T cell expansion and new avenues toward a molecular understanding of cell cycle regulation in lymphocytes are discussed.
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Affiliation(s)
- Reinhard Obst
- Institute for Immunology, Ludwig-Maximilians-University Munich, Munich, Germany
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48
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Affiliation(s)
- Georgios D Lianos
- Centre for Biosystems & Genomic Network Medicine, University of Ioannina, Ioannina, Greece
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Vandenbroucke H, Mournet P, Malapa R, Glaszmann JC, Chaïr H, Lebot V. Comparative analysis of genetic variation in kava (Piper methysticum) assessed by SSR and DArT reveals zygotic foundation and clonal diversification. Genome 2015; 58:1-11. [PMID: 25973616 DOI: 10.1139/gen-2014-0166] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Kava (Piper methysticum) is a major cash crop in the Pacific. The aim of this study was to assess genetic variation among 103 accessions of kava using SSRs and DArTs. Genetic structure was determined using clustering analyses (WPGMA) and principal coordinate analyses (PCA). Thirteen SSR primers and 75 DArT markers were found polymorphic, and the two types of markers generated similar clustering patterns. Genetic distances ranged from 0 to 0.65 with an average of 0.24 using SSRs and from 0 to 0.64 with an average of 0.24 using DArT. Eleven genotypes were identified with SSR while 28 genotypes were identified with DArT markers. By combining the two sets of markers, a total of only 30 distinct genotypes were observed. In the Vanuatu archipelago, noble cultivars originating from different islands clustered together within a very narrow genetic base despite their diversity of morphotypes. SSR and DArT fingerprints allowed the identification of kava cultivars unsuitable for consumption, so called two-days, and clearly differentiated the wild types classified as P. methysticum var. wichmannii from the cultivars as var. methysticum. Molecular data reveals that all noble cultivars evolved by the predominance of clonal selection. Although they are represented by clearly distinct morphotypes, these cultivars are genetically vulnerable and their potential to adapt to forthcoming changes is limited. These newly developed markers provide high resolution and will be useful for kava diversity analyses and quality assessment.
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Affiliation(s)
- Henri Vandenbroucke
- UMR AGAP, CIRAD, TA A108/03, Avenue Agropolis, 34398 Montpellier, Cédex 5, France
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50
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Dutton RW. In vitro Studies of the Antibody Response: Antibodies of Different Specificity are Made in Different Populations of Cells. Front Immunol 2014; 5:515. [PMID: 25389424 PMCID: PMC4211551 DOI: 10.3389/fimmu.2014.00515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 10/03/2014] [Indexed: 11/23/2022] Open
Affiliation(s)
- Richard W Dutton
- Pathology Department, University of Massachusetts Medical School , Worcester, MA , USA
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