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Bryushkova EA, Mushenkova NV, Turchaninova MA, Lukyanov DK, Chudakov DM, Serebrovskaya EO. B cell clonality in cancer. Semin Immunol 2024; 72:101874. [PMID: 38508089 DOI: 10.1016/j.smim.2024.101874] [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: 05/24/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 03/22/2024]
Abstract
Carcinogenesis in the process of long-term co-evolution of tumor cells and immune environment essentially becomes possible due to incorrect decisions made, remembered, and reproduced by the immune system at the level of clonal populations of antigen-specific T- and B-lymphocytes. Tumor-immunity interaction determines the nature of such errors and, consequently, delineates the possible ways of successful immunotherapeutic intervention. It is generally recognized that tumor-infiltrating B cells (TIL-B) can play both pro-tumor and anti-tumor roles. However, the exact mechanisms that determine the contribution of clonal B cell lineages with different specificities and functions remain largely unclear. This is due to the variability of cancer types, the molecular heterogeneity of tumor cells, and, to a large extent, the individual pattern of each immune response. Further progress requires detailed investigation of the functional properties and phenotypes of clonally heterogeneous B cells in relation to their antigenic specificities, which determine the functionality of both effector B lymphocytes and immunoglobulins produced in the tumor environment. Based on a real understanding of the role of clonal antigen-specific populations of B lymphocytes in the tumor microenvironment, we need to learn how to develop new methods of targeted immunotherapy, as well as adapt existing treatment options to the specific needs of different patients and patient subgroups. In this review, we will cover B cells functional diversity and their multifaceted roles in the tumor environment.
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Affiliation(s)
- E A Bryushkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, Moscow, Russia
| | - N V Mushenkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Unicorn Capital Partners, Moscow, Russia
| | - M A Turchaninova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - D K Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - D M Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - E O Serebrovskaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Current position: Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
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2
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Serebrovskaya EO, Bryushkova EA, Lukyanov DK, Mushenkova NV, Chudakov DM, Turchaninova MA. Toolkit for mapping the clonal landscape of tumor-infiltrating B cells. Semin Immunol 2024; 72:101864. [PMID: 38301345 DOI: 10.1016/j.smim.2024.101864] [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: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Our current understanding of whether B cell involvement in the tumor microenvironment benefits the patient or the tumor - in distinct cancers, subcohorts and individual patients - is quite limited. Both statements are probably true in most cases: certain clonal B cell populations contribute to the antitumor response, while others steer the immune response away from the desired mechanics. To step up to a new level of understanding and managing B cell behaviors in the tumor microenvironment, we need to rationally discern these roles, which are cumulatively defined by B cell clonal functional programs, specificities of their B cell receptors, specificities and isotypes of the antibodies they produce, and their spatial interactions within the tumor environment. Comprehensive analysis of these characteristics of clonal B cell populations is now becoming feasible with the development of a whole arsenal of advanced technical approaches, which include (1) methods of single-cell and spatial transcriptomics, genomics, and proteomics; (2) methods of massive identification of B cell specificities; (3) methods of deep error-free profiling of B cell receptor repertoires. Here we overview existing techniques, summarize their current application for B cells studies and propose promising future directions in advancing B cells exploration.
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Affiliation(s)
- E O Serebrovskaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Current position: Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - E A Bryushkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, Moscow, Russia
| | - D K Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - N V Mushenkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Unicorn Capital Partners, 119049, Moscow, Russia
| | - D M Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - M A Turchaninova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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3
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Goncharov MM, Bryushkova EA, Sharaev NI, Skatova VD, Baryshnikova AM, Sharonov GV, Karnaukhov V, Vakhitova MT, Samoylenko IV, Demidov LV, Lukyanov S, Chudakov DM, Serebrovskaya EO. Pinpointing the tumor-specific T-cells via TCR clusters. eLife 2022; 11:77274. [PMID: 35377314 PMCID: PMC9023053 DOI: 10.7554/elife.77274] [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: 01/22/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Adoptive cell transfer (ACT) is a promising approach to cancer immunotherapy, but its efficiency fundamentally depends on the extent of tumor-specific T cell enrichment within the graft. This can be estimated via activation with identifiable neoantigens, tumor-associated antigens (TAAs), or living or lysed tumor cells, but these approaches remain laborious, time-consuming, and functionally limited, hampering clinical development of ACT. Here, we demonstrate that homology cluster analysis of T cell receptor (TCR) repertoires efficiently identifies tumor-reactive TCRs allowing to: (1) detect their presence within the pool of tumor-infiltrating lymphocytes (TILs); (2) optimize TIL culturing conditions, with IL-2low/IL-21/anti-PD-1 combination showing increased efficiency; (3) investigate surface marker-based enrichment for tumor-targeting T cells in freshly isolated TILs (enrichment confirmed for CD4+ and CD8+ PD-1+/CD39+ subsets), or re-stimulated TILs (informs on enrichment in 4-1BB-sorted cells). We believe that this approach to the rapid assessment of tumor-specific TCR enrichment should accelerate T cell therapy development.
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Affiliation(s)
- Mikhail M Goncharov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | | | - Nikita I Sharaev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Valeria D Skatova
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Anastasiya M Baryshnikova
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - George V Sharonov
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Vadim Karnaukhov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Maria T Vakhitova
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Igor V Samoylenko
- Oncodermatology Department, NN Blokhin Russian Cancer Research Center, Moscow, Russian Federation
| | - Lev V Demidov
- Oncodermatology Department, NN Blokhin Russian Cancer Research Center, Moscow, Russian Federation
| | - Sergey Lukyanov
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Dmitriy M Chudakov
- Department of genomics of adaptive immunity, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
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4
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Dyugay IA, Lukyanov DK, Turchaninova MA, Serebrovskaya EO, Bryushkova EA, Zaretsky AR, Khalmurzaev O, Matveev VB, Shugay M, Shelyakin PV, Chudakov DM. Accounting for B-cell Behavior and Sampling Bias Predicts Anti-PD-L1 Response in Bladder Cancer. Cancer Immunol Res 2022; 10:343-353. [PMID: 35013004 PMCID: PMC9381118 DOI: 10.1158/2326-6066.cir-21-0489] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/18/2021] [Accepted: 01/06/2022] [Indexed: 01/07/2023]
Abstract
Cancer immunotherapy is predominantly based on T cell-centric approaches. At the same time, the adaptive immune response in the tumor environment also includes clonally produced immunoglobulins and clonal effector/memory B cells that participate in antigen-specific decisions through their interactions with T cells. Here, we investigated the role of infiltrating B cells in bladder cancer via patient dataset analysis of intratumoral immunoglobulin repertoires. We showed that the IgG1/IgA ratio is a prognostic indicator for several subtypes of bladder cancer and for the whole IMVigor210 anti-PD-L1 immunotherapy study cohort. A high IgG1/IgA ratio associated with the prominence of a cytotoxic gene signature, T-cell receptor signaling, and IL21-mediated signaling. Immunoglobulin repertoire analysis indicated that effector B-cell function, rather than clonally produced antibodies, was involved in antitumor responses. From the T-cell side, we normalized a cytotoxic signature against the extent of immune cell infiltration to neutralize the artificial sampling-based variability in immune gene expression. Resulting metrics reflected proportion of cytotoxic cells among tumor-infiltrating immune cells and improved prediction of anti-PD-L1 responses. At the same time, the IgG1/IgA ratio remained an independent prognostic factor. Integration of the B-cell, natural killer cell, and T-cell signatures allowed for the most accurate prediction of anti-PD-L1 therapy responses. On the basis of these findings, we developed a predictor called PRedIctive MolecUlar Signature (PRIMUS), which outperformed PD-L1 expression scores and known gene signatures. Overall, PRIMUS allows for reliable identification of responders among patients with muscle-invasive urothelial carcinoma, including the subcohort with the low-infiltrated "desert" tumor phenotype.
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Affiliation(s)
- Ilya A. Dyugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Daniil K. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria A. Turchaninova
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina O. Serebrovskaya
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina A. Bryushkova
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Molecular Biology Department, Lomonosov Moscow State University, Moscow, Russia
| | - Andrew R. Zaretsky
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Oybek Khalmurzaev
- Department of Urology, Federal State Budgetary Institution “N.N. Blokhin National Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vsevolod B. Matveev
- Department of Urology, Federal State Budgetary Institution “N.N. Blokhin National Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Mikhail Shugay
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Pavel V. Shelyakin
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy M. Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Corresponding Author: Dmitriy M. Chudakov, Genomics of Adaptive Immunity, IBCH RAS, Miklukho-Maklaya, 16/10, Moscow 117997, Russia. Phone: 7 (495) 335-01-00; E-mail:
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5
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Serebrovskaya EO, Podvalnaya NM, Dudenkova VV, Efremova AS, Gurskaya NG, Gorbachev DA, Luzhin AV, Kantidze OL, Zagaynova EV, Shram SI, Lukyanov KA. Genetically Encoded Fluorescent Sensor for Poly-ADP-Ribose. Int J Mol Sci 2020; 21:ijms21145004. [PMID: 32679873 PMCID: PMC7404130 DOI: 10.3390/ijms21145004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/06/2020] [Accepted: 07/13/2020] [Indexed: 11/29/2022] Open
Abstract
Poly-(ADP-ribosyl)-ation (PARylation) is a reversible post-translational modification of proteins and DNA that plays an important role in various cellular processes such as DNA damage response, replication, transcription, and cell death. Here we designed a fully genetically encoded fluorescent sensor for poly-(ADP-ribose) (PAR) based on Förster resonance energy transfer (FRET). The WWE domain, which recognizes iso-ADP-ribose internal PAR-specific structural unit, was used as a PAR-targeting module. The sensor consisted of cyan Turquoise2 and yellow Venus fluorescent proteins, each in fusion with the WWE domain of RNF146 E3 ubiquitin ligase protein. This bipartite sensor named sPARroW (sensor for PARrelying on WWE) enabled monitoring of PAR accumulation and depletion in live mammalian cells in response to different stimuli, namely hydrogen peroxide treatment, UV irradiation and hyperthermia.
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Affiliation(s)
- Ekaterina O. Serebrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.O.S.); (N.M.P.); (N.G.G.); (D.A.G.)
| | - Nadezda M. Podvalnaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.O.S.); (N.M.P.); (N.G.G.); (D.A.G.)
- Institute of Molecular Genetics, Kurchatova Sq. 2, 123182 Moscow, Russia; (A.S.E.); (S.I.S.)
| | - Varvara V. Dudenkova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia; (V.V.D.); (E.V.Z.)
| | - Anna S. Efremova
- Institute of Molecular Genetics, Kurchatova Sq. 2, 123182 Moscow, Russia; (A.S.E.); (S.I.S.)
| | - Nadya G. Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.O.S.); (N.M.P.); (N.G.G.); (D.A.G.)
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Dmitry A. Gorbachev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.O.S.); (N.M.P.); (N.G.G.); (D.A.G.)
| | - Artem V. Luzhin
- Institute of Gene Biology, Vavilova 34/5, 119334 Moscow, Russia; (A.V.L.); (O.L.K.)
| | - Omar L. Kantidze
- Institute of Gene Biology, Vavilova 34/5, 119334 Moscow, Russia; (A.V.L.); (O.L.K.)
| | - Elena V. Zagaynova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia; (V.V.D.); (E.V.Z.)
- Lobachevsky State University of Nizhny Novgorod, Gagarin Ave. 23, 603950 Nizhny Novgorod, Russia
| | - Stanislav I. Shram
- Institute of Molecular Genetics, Kurchatova Sq. 2, 123182 Moscow, Russia; (A.S.E.); (S.I.S.)
| | - Konstantin A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.O.S.); (N.M.P.); (N.G.G.); (D.A.G.)
- Correspondence:
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6
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Yuzhakova DV, Volchkova LN, Pogorelyy MV, Serebrovskaya EO, Shagina IA, Bryushkova EA, Nakonechnaya TO, Izosimova AV, Zavyalova DS, Karabut MM, Izraelson M, Samoylenko IV, Zagainov VE, Chudakov DM, Zagaynova EV, Sharonov GV. Measuring Intratumoral Heterogeneity of Immune Repertoires. Front Oncol 2020; 10:512. [PMID: 32457825 PMCID: PMC7227437 DOI: 10.3389/fonc.2020.00512] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/23/2020] [Indexed: 12/22/2022] Open
Abstract
There is considerable clinical and fundamental value in measuring the clonal heterogeneity of T and B cell expansions in tumors and tumor-associated lymphoid structures—along with the associated heterogeneity of the tumor neoantigen landscape—but such analyses remain challenging to perform. Here, we propose a straightforward approach to analyze the heterogeneity of immune repertoires between different tissue sections in a quantitative and controlled way, based on a beta-binomial noise model trained on control replicates obtained at the level of single-cell suspensions. This approach allows to identify local clonal expansions with high accuracy. We reveal in situ proliferation of clonal T cells in a mouse model of melanoma, and analyze heterogeneity of immunoglobulin repertoires between sections of a metastatically-infiltrated lymph node in human melanoma and primary human colon tumor. On the latter example, we demonstrate the importance of training the noise model on datasets with depth and content that is comparable to the samples being studied. Altogether, we describe here the crucial basic instrumentarium needed to facilitate proper experimental setup planning in the rapidly evolving field of intratumoral immune repertoires, from the wet lab to bioinformatics analysis.
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Affiliation(s)
- Diana Vladimirovna Yuzhakova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Lilia N Volchkova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Mikhail Valerievich Pogorelyy
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina O Serebrovskaya
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Irina A Shagina
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina A Bryushkova
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Department of Molecular Biology, Moscow State University, Moscow, Russia
| | - Tatiana O Nakonechnaya
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anna V Izosimova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Daria S Zavyalova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Maria M Karabut
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Mark Izraelson
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Igor V Samoylenko
- Oncodermatology Department, N. N. Blokhin Russian Cancer Research Center, Moscow, Russia
| | - Vladimir E Zagainov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Volga District Medical Centre Under Federal Medical and Biological Agency, Nizhny Novgorod, Russia
| | - Dmitriy M Chudakov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Adaptive Immunity Group, Central European Institute of Technology, Masaryk University, Brno, Czechia.,MiLaboratory LLC, Skolkovo Innovation Centre, Moscow, Russia
| | - Elena V Zagaynova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - George Vladimirovich Sharonov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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7
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Zhigalova EA, Izosimova AI, Yuzhakova DV, Volchkova LN, Shagina IA, Turchaninova MA, Serebrovskaya EO, Zagaynova EV, Chudakov DM, Sharonov GV. RNA-Seq-Based TCR Profiling Reveals Persistently Increased Intratumoral Clonality in Responders to Anti-PD-1 Therapy. Front Oncol 2020; 10:385. [PMID: 32411589 PMCID: PMC7199218 DOI: 10.3389/fonc.2020.00385] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/04/2020] [Indexed: 12/30/2022] Open
Abstract
Substantial effort is being invested in the search for peripheral or intratumoral T cell receptor (TCR) repertoire features that could predict the response to immunotherapy. Here we demonstrate the utility of MiXCR software for TCR and immunoglobulin repertoire extraction from RNA-Seq data obtained from sorted tumor-infiltrating T and B cells. We use this approach to extract TCR repertoires from RNA-Seq data obtained from sorted tumor-infiltrating CD4+ and CD8+ T cells in an HKP1 (KrasG12Dp53-/-) syngeneic mouse model of lung cancer after anti-PD-1 treatment. For both subsets, we demonstrate decreased TCR diversity in response to therapy. At a later time point, repertoire diversity is restored in progressing disease but remains decreased in responders to therapy in both CD4+ and CD8+ subsets. These observations complement previous studies and suggest that stably increased intratumoral CD4+ and CD8+ T cell clonality after anti-PD-1/PD-L1 therapy could serve as a predictor of long-term response.
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Affiliation(s)
- Ekaterina A Zhigalova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anna I Izosimova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Diana V Yuzhakova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Lilia N Volchkova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Irina A Shagina
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Molecular Technologies Department, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maria A Turchaninova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Molecular Technologies Department, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina O Serebrovskaya
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Molecular Technologies Department, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Elena V Zagaynova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Molecular Technologies Department, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - George V Sharonov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Molecular Technologies Department, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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8
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Sharonov GV, Serebrovskaya EO, Yuzhakova DV, Britanova OV, Chudakov DM. B cells, plasma cells and antibody repertoires in the tumour microenvironment. Nat Rev Immunol 2020; 20:294-307. [DOI: 10.1038/s41577-019-0257-x] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2019] [Indexed: 02/07/2023]
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9
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Perfilov MM, Gurskaya NG, Serebrovskaya EO, Melnikov PA, Kharitonov SL, Lewis TR, Arshavsky VY, Baklaushev VP, Mishin AS, Lukyanov KA. Highly photostable fluorescent labeling of proteins in live cells using exchangeable coiled coils heterodimerization. Cell Mol Life Sci 2020; 77:4429-4440. [PMID: 31894363 DOI: 10.1007/s00018-019-03426-5] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/10/2019] [Accepted: 12/13/2019] [Indexed: 10/25/2022]
Abstract
Fluorescent proteins are commonly used to label target proteins in live cells. However, the conventional approach based on covalent fusion of targeted proteins with fluorescent protein probes is limited by the slow rate of fluorophore maturation and irretrievable loss of fluorescence due to photobleaching. Here, we report a genetically encoded protein labeling system utilizing transient interactions of small, 21-28 residues-long helical protein tags (K/E coils, KEC). In this system, a protein of interest, covalently tagged with a single coil, is visualized through binding to a cytoplasmic fluorescent protein carrying a complementary coil. The reversible heterodimerization of KECs, whose affinity can be tuned in a broad concentration range from nanomolar to micromolar, allows continuous exchange and replenishment of the tag bound to a targeted protein with the entire cytosolic pool of soluble fluorescent coils. We found that, under conditions of partial illumination of living cells, the photostability of labeling with KECs exceeds that of covalently fused fluorescent probes by approximately one order of magnitude. Similarly, single-molecule localization microscopy with KECs provided higher labeling density and allowed a much longer duration of imaging than with conventional fusion to fluorescent proteins. We also demonstrated that this method is well suited for imaging newly synthesized proteins, because the labeling efficiency by KECs is not dependent on the rate of fluorescent protein maturation. In conclusion, KECs can be used to visualize various target proteins which are directly exposed to the cytosol, thereby enabling their advanced characterization in time and space.
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Affiliation(s)
- Maxim M Perfilov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia
| | - Nadya G Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia.,Pirogov Russian National Research Medical University, Ostrovitianov St. 1, 117997, Moscow, Russia
| | - Ekaterina O Serebrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia.,Department of Ophthalmology, Duke University, Durham, NC, 27710, USA
| | - Pavel A Melnikov
- Serbsky National Medical Research Center for Psychiatry and Narcology, Kropotkinsky Lane 23, 119034, Moscow, Russia
| | - Sergey L Kharitonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia
| | - Tylor R Lewis
- Department of Ophthalmology, Duke University, Durham, NC, 27710, USA
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University, Durham, NC, 27710, USA.,Department of Pharmacology, Duke University, Durham, NC, 27710, USA
| | - Vladimir P Baklaushev
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, Orekhovy Blvd. 28, 115682, Moscow, Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia.
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia. .,Skolkovo Institute of Science and Technology, Bolshoy Blvd. 30, 121205, Moscow, Russia.
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10
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Isaeva OI, Sharonov GV, Serebrovskaya EO, Turchaninova MA, Zaretsky AR, Shugay M, Chudakov DM. Intratumoral immunoglobulin isotypes predict survival in lung adenocarcinoma subtypes. J Immunother Cancer 2019; 7:279. [PMID: 31665076 PMCID: PMC6819482 DOI: 10.1186/s40425-019-0747-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/20/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The role of tumor-infiltrating B-cells (TIBs) and intratumorally-produced antibodies in cancer-immunity interactions essentially remains terra incognita. In particular, it remains unexplored how driver mutations could be associated with distinct TIBs signatures and their role in tumor microenvironment. METHODS Here we analyzed associations of immunoglobulin isotypes and clonality with survival in TCGA RNA-Seq data for lung adenocarcinoma (LUAD), stratifying patients into 12 driver mutation and phenotypic tumor subgroups. RESULTS We revealed several unexpected associations between TIBs behavior and prognosis. Abundance and high proportion of IgG1 isotype, and low proportion of IgA among all intratumorally produced immunoglobulins were specifically associated with improved overall survival for KRASmut but not KRASwt LUAD, revealing the first link between a driver mutation and B-cell response. We found specific IgG1 signature associated with long survival, which suggests that particular specificities of IgG1+ TIBs could be beneficial in KRASmut LUAD. In contrast to our previous observations for melanoma, highly clonal IgG1 production by plasma cells had no meaningful effect on prognosis, suggesting that IgG1+ TIBs may exert a beneficial effect in KRASmut cases in an alternative way, such as efficient presentation of cognate antigens or direct B cell attack on tumor cells. Notably, a high proportion of the IgG1 isotype is positively correlated with the non-silent mutation burden both in the general LUAD cohort and in most patient subgroups, supporting a role for IgG1+ TIBs in antigen presentation. Complementing the recent finding that the presence of stromal IgG4-producing cells is associated with a favorable prognosis for patients with stage I squamous cell carcinoma, we show that the abundance of IgG4-producing TIBs likewise has a strong positive effect on overall survival in STK11mut and proximal proliferative subgroups of LUAD patients. We hypothesize that the positive role of IgG4 antibodies in some of the lung cancer subtypes could be associated with reported inability of IgG4 isotype to form immune complexes, thus preventing immunosuppression via activation of the myeloid-derived suppressor cell (MDSC) phenotype. CONCLUSIONS We discover prominent and distinct associations between TIBs antibody isotypes and survival in lung adenocarcinoma carrying specific driver mutations. These findings indicate that particular types of tumor-immunity relations could be beneficial in particular driver mutation context, which should be taken into account in developing strategies of cancer immunotherapy and combination therapies. Specificity of protective B cell populations in specific cancer subgroups could become a clue to efficient targeted immunotherapies for appropriate cohorts of patients.
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Affiliation(s)
- O I Isaeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,BostonGene LLC, Lincoln, MA, USA
| | - G V Sharonov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - E O Serebrovskaya
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - M A Turchaninova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - A R Zaretsky
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - M Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - D M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia. .,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia. .,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia. .,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.
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11
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Pennacchietti F, Serebrovskaya EO, Faro AR, Shemyakina II, Bozhanova NG, Kotlobay AA, Gurskaya NG, Bodén A, Dreier J, Chudakov DM, Lukyanov KA, Verkhusha VV, Mishin AS, Testa I. Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy. Nat Methods 2018; 15:601-604. [PMID: 29988095 DOI: 10.1038/s41592-018-0052-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/18/2018] [Indexed: 11/09/2022]
Abstract
Reversibly photoswitchable fluorescent proteins (rsFPs) are gaining popularity as tags for optical nanoscopy because they make it possible to image with lower light doses. However, green rsFPs need violet-blue light for photoswitching, which is potentially phototoxic and highly scattering. We developed new rsFPs based on FusionRed that are reversibly photoswitchable with green-orange light. The rsFusionReds are bright and exhibit rapid photoswitching, thereby enabling nanoscale imaging of living cells.
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Affiliation(s)
- Francesca Pennacchietti
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ekaterina O Serebrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Aline R Faro
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Irina I Shemyakina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Nina G Bozhanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey A Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Nadya G Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Andreas Bodén
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jes Dreier
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dmitry M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation.
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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12
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Kuzmin DV, Emelianova AA, Kalashnikova MB, Panteleev PV, Balandin SV, Serebrovskaya EO, Belogurova-Ovchinnikova OY, Ovchinnikova TV. Comparative in vitro study on cytotoxicity of recombinant β-hairpin peptides. Chem Biol Drug Des 2017; 91:294-303. [PMID: 28815904 DOI: 10.1111/cbdd.13081] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 07/19/2017] [Accepted: 07/27/2017] [Indexed: 02/06/2023]
Abstract
Natural antimicrobial peptides (AMPs) are important components of the innate immune system with a wide spectrum of biological activity. In this study, we investigated the cytotoxic effect of three recombinant β-hairpin cationic AMPs: arenicin-1 from the polychaeta Arenicola marina, tachyplesin I from the horseshoe crab Tachypleus tridentatus, and gomesin from the spider Acanthoscurria gomesiana. All the three β-hairpin AMPs were overexpressed in Escherichia coli. Different cell lines were incubated with various concentrations of the investigated AMPs in order to evaluate their cytotoxic activity. Double staining with subsequent flow cytometric analysis was used to determine the predominant way of cell death mediated by each AMP. Hemolytic activity of the peptides was tested against fresh human red blood cells. Our results indicated that all the three AMPs exhibited significant cytotoxic effect against cancer cells that varied depending on the cell line type and, in most cases, on the presence of serum components. Flow cytometric analysis implicitly indicated that tachyplesin I mostly promoted late apoptosis/necrosis, while arenicin-1 and gomesin induced early apoptosis under the same conditions. Tachyplesin I proved to be the most promising therapeutic candidate as it displayed the highest specific cytotoxicity against cancer cell lines, independent of the serum presence.
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Affiliation(s)
- Denis V Kuzmin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Anna A Emelianova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Mariana B Kalashnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Pavel V Panteleev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Sergey V Balandin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina O Serebrovskaya
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | | | - Tatiana V Ovchinnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
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13
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Kuzmin DV, Emelianova AA, Kalashnikova MB, Panteleev PV, Balandin SV, Serebrovskaya EO, Belogurova-Ovchinnikova OY, Ovchinnikova TV. Comparative in vitro study on cytotoxicity of recombinant β-hairpin peptides. Chem Biol Drug Des 2017. [PMID: 28815904 DOI: 10.1111/cbdd.13081.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural antimicrobial peptides (AMPs) are important components of the innate immune system with a wide spectrum of biological activity. In this study, we investigated the cytotoxic effect of three recombinant β-hairpin cationic AMPs: arenicin-1 from the polychaeta Arenicola marina, tachyplesin I from the horseshoe crab Tachypleus tridentatus, and gomesin from the spider Acanthoscurria gomesiana. All the three β-hairpin AMPs were overexpressed in Escherichia coli. Different cell lines were incubated with various concentrations of the investigated AMPs in order to evaluate their cytotoxic activity. Double staining with subsequent flow cytometric analysis was used to determine the predominant way of cell death mediated by each AMP. Hemolytic activity of the peptides was tested against fresh human red blood cells. Our results indicated that all the three AMPs exhibited significant cytotoxic effect against cancer cells that varied depending on the cell line type and, in most cases, on the presence of serum components. Flow cytometric analysis implicitly indicated that tachyplesin I mostly promoted late apoptosis/necrosis, while arenicin-1 and gomesin induced early apoptosis under the same conditions. Tachyplesin I proved to be the most promising therapeutic candidate as it displayed the highest specific cytotoxicity against cancer cell lines, independent of the serum presence.
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Affiliation(s)
- Denis V Kuzmin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Anna A Emelianova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Mariana B Kalashnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Pavel V Panteleev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Sergey V Balandin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina O Serebrovskaya
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | | | - Tatiana V Ovchinnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
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14
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Serebrovskaya EO, Yuzhakova DV, Ryumina AP, Druzhkova IN, Sharonov GV, Kotlobay AA, Zagaynova EV, Lukyanov SA, Shirmanova MV. Soluble OX40L favors tumor rejection in CT26 colon carcinoma model. Cytokine 2016; 84:10-6. [PMID: 27203665 DOI: 10.1016/j.cyto.2016.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 04/06/2016] [Accepted: 05/02/2016] [Indexed: 12/14/2022]
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15
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Ryumina AP, Serebrovskaya EO, Staroverov DB, Zlobovskaya OA, Shcheglov AS, Lukyanov SA, Lukyanov KA. Lysosome-associated miniSOG as a photosensitizer for mammalian cells. Biotechniques 2016; 61:92-4. [PMID: 27528074 DOI: 10.2144/000114445] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 01/29/2016] [Accepted: 05/16/2016] [Indexed: 11/23/2022] Open
Abstract
Genetically encoded photosensitizers represent a promising optogenetic tool for the induction of light-controlled oxidative stress strictly localized to a selected intracellular compartment. Here we tested the phototoxic effects of the flavin-containing phototoxic protein miniSOG targeted to the cytoplasmic surfaces of late endosomes and lysosomes by fusion with Rab7. In HeLa Kyoto cells stably expressing miniSOG-Rab7, we demonstrated a high level of cell death upon blue-light illumination. Pepstatin A completely abolished phototoxicity of miniSOG-Rab7, showing a key role for cathepsin D in this model. Using a far-red fluorescence sensor for caspase-3, we observed caspase-3 activation during miniSOG-Rab7-mediated cell death. We conclude that upon illumination, miniSOG-Rab7 induces lysosomal membrane permeabilization (LMP) and leakage of cathepsins into the cytosol, resulting in caspase-dependent apoptosis.
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Affiliation(s)
- Alina P Ryumina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - Ekaterina O Serebrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | | | | | | | - Sergey A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
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16
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Yuzhakova DV, Shirmanova MV, Serebrovskaya EO, Lukyanov KA, Druzhkova IN, Shakhov BE, Lukyanov SA, Zagaynova EV. CT26 murine colon carcinoma expressing the red fluorescent protein KillerRed as a highly immunogenic tumor model. J Biomed Opt 2015; 20:88002. [PMID: 26277828 DOI: 10.1117/1.jbo.20.8.088002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/20/2015] [Indexed: 06/04/2023]
Abstract
The development of tumor therapies based on the activation of antitumor immunity requires tumor models that are highly immunogenic. The immunologic response to fluorescent proteins, green fluorescent protein (GFP), or enhanced GFP (EGFP) was demonstrated in different cancer models. However, for live animal imaging, red and far-red fluorescent proteins are preferable, but their immunogenicity has not been studied. We assessed the immunogenicity of the red fluorescent protein, KillerRed (KR), in CT26 murine colon carcinoma. We showed a slower growth and a lower tumor incidence of KR-expressing tumors in comparison with nonexpressing ones. We found that KR-expressing lung metastases and rechallenged tumors were not formed in mice that had been surgically cured of KR-expressing primary tumors. The effect of low-dose cyclophosphamide (CY) treatment was also tested, as this is known to activate antitumor immune responses. The low-dose CY therapy of CT26-KR tumors resulted in inhibition of tumor growth and improved mouse survival. In summary, we have established a highly immunogenic tumor model that could be valuable for investigations of the mechanisms of antitumor immunity and the development of new therapeutic approaches.
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Affiliation(s)
- Diana V Yuzhakova
- Institute of Biomedical Technologies, Nizhny Novgorod State Medical Academy, Minin and Pozharsky Square, 10/1, Nizhny Novgorod 603005, RussiabLobachevsky State University of Nizhny Novgorod, Gagarina Avenue, 23, Nizhny Novgorod 603950, Russia
| | - Marina V Shirmanova
- Institute of Biomedical Technologies, Nizhny Novgorod State Medical Academy, Minin and Pozharsky Square, 10/1, Nizhny Novgorod 603005, Russia
| | - Ekaterina O Serebrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya Street, 16/10, Moscow 117997, Russia
| | - Konstantin A Lukyanov
- Institute of Biomedical Technologies, Nizhny Novgorod State Medical Academy, Minin and Pozharsky Square, 10/1, Nizhny Novgorod 603005, RussiacShemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya Street, 16/10, Moscow 117997, Russi
| | - Irina N Druzhkova
- Institute of Biomedical Technologies, Nizhny Novgorod State Medical Academy, Minin and Pozharsky Square, 10/1, Nizhny Novgorod 603005, Russia
| | - Boris E Shakhov
- Institute of Biomedical Technologies, Nizhny Novgorod State Medical Academy, Minin and Pozharsky Square, 10/1, Nizhny Novgorod 603005, Russia
| | - Sergey A Lukyanov
- Institute of Biomedical Technologies, Nizhny Novgorod State Medical Academy, Minin and Pozharsky Square, 10/1, Nizhny Novgorod 603005, RussiacShemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya Street, 16/10, Moscow 117997, Russi
| | - Elena V Zagaynova
- Institute of Biomedical Technologies, Nizhny Novgorod State Medical Academy, Minin and Pozharsky Square, 10/1, Nizhny Novgorod 603005, Russia
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17
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Serebrovskaya EO, Ryumina AP, Boulina ME, Shirmanova MV, Zagaynova EV, Bogdanova EA, Lukyanov SA, Lukyanov KA. Phototoxic effects of lysosome-associated genetically encoded photosensitizer KillerRed. J Biomed Opt 2014; 19:071403. [PMID: 24365992 DOI: 10.1117/1.jbo.19.7.071403] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 11/18/2013] [Indexed: 06/03/2023]
Abstract
KillerRed is a unique phototoxic red fluorescent protein that can be used to induce local oxidative stress by green-orange light illumination. Here we studied phototoxicity of KillerRed targeted to cytoplasmic surface of lysosomes via fusion with Rab7, a small GTPase that is known to be attached to membranes of late endosomes and lysosomes. It was found that lysosome-associated KillerRed ensures efficient light-induced cell death similar to previously reported mitochondria- and plasma membrane-localized KillerRed. Inhibitory analysis demonstrated that lysosomal cathepsins play an important role in the manifestation of KillerRed-Rab7 phototoxicity. Time-lapse monitoring of cell morphology, membrane integrity, and nuclei shape allowed us to conclude that KillerRed-Rab7-mediated cell death occurs via necrosis at high light intensity or via apoptosis at lower light intensity. Potentially, KillerRed-Rab7 can be used as an optogenetic tool to direct target cell populations to either apoptosis or necrosis.
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Affiliation(s)
- Ekaterina O Serebrovskaya
- Russian Academy of Sciences, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alina P Ryumina
- Russian Academy of Sciences, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Maria E Boulina
- Russian Academy of Sciences, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Marina V Shirmanova
- Nizhny Novgorod State Medical Academy, 603005 Minin Sq., 10/1, 603005, Nizhny Novgorod, Russia
| | - Elena V Zagaynova
- Nizhny Novgorod State Medical Academy, 603005 Minin Sq., 10/1, 603005, Nizhny Novgorod, Russia
| | - Ekaterina A Bogdanova
- Russian Academy of Sciences, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Sergey A Lukyanov
- Russian Academy of Sciences, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, RussiabNizhny Novgorod State Medical Academy, 603005 Minin Sq., 10/1, 603005, Nizhny Novgorod, Russia
| | - Konstantin A Lukyanov
- Russian Academy of Sciences, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
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Ryumina AP, Serebrovskaya EO, Shirmanova MV, Snopova LB, Kuznetsova MM, Turchin IV, Ignatova NI, Klementieva NV, Fradkov AF, Shakhov BE, Zagaynova EV, Lukyanov KA, Lukyanov SA. Flavoprotein miniSOG as a genetically encoded photosensitizer for cancer cells. Biochim Biophys Acta Gen Subj 2013; 1830:5059-67. [PMID: 23876295 DOI: 10.1016/j.bbagen.2013.07.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [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: 02/05/2013] [Revised: 06/20/2013] [Accepted: 07/15/2013] [Indexed: 11/28/2022]
Abstract
BACKGROUND Genetically encoded photosensitizers are a promising optogenetic instrument for light-induced production of reactive oxygen species in desired locations within cells in vitro or whole body in vivo. Only two such photosensitizers are currently known, GFP-like protein KillerRed and FMN-binding protein miniSOG. In this work we studied phototoxic effects of miniSOG in cancer cells. METHODS HeLa Kyoto cell lines stably expressing miniSOG in different localizations, namely, plasma membrane, mitochondria or chromatin (fused with histone H2B) were created. Phototoxicity of miniSOG was tested on the cells in vitro and tumor xenografts in vivo. RESULTS Blue light induced pronounced cell death in all three cell lines in a dose-dependent manner. Caspase 3 activation was characteristic of illuminated cells with mitochondria- and chromatin-localized miniSOG, but not with miniSOG in the plasma membrane. In addition, H2B-miniSOG-expressing cells demonstrated light-induced activation of DNA repair machinery, which indicates massive damage of genomic DNA. In contrast to these in vitro data, no detectable phototoxicity was observed on tumor xenografts with HeLa Kyoto cell lines expressing mitochondria- or chromatin-localized miniSOG. CONCLUSIONS miniSOG is an excellent genetically encoded photosensitizer for mammalian cells in vitro, but it is inferior to KillerRed in the HeLa tumor. GENERAL SIGNIFICANCE This is the first study to assess phototoxicity of miniSOG in cancer cells. The results suggest an effective ontogenetic tool and may be of interest for molecular and cell biology and biomedical applications.
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Affiliation(s)
- Alina P Ryumina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
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Shirmanova MV, Serebrovskaya EO, Lukyanov KA, Snopova LB, Sirotkina MA, Prodanetz NN, Bugrova ML, Minakova EA, Turchin IV, Kamensky VA, Lukyanov SA, Zagaynova EV. Phototoxic effects of fluorescent protein KillerRed on tumor cells in mice. J Biophotonics 2013; 6:283-90. [PMID: 22696211 DOI: 10.1002/jbio.201200056] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/12/2012] [Accepted: 05/21/2012] [Indexed: 06/01/2023]
Abstract
KillerRed is known to be a unique red fluorescent protein displaying strong phototoxic properties. Its effectiveness has been shown previously for killing bacterial and cancer cells in vitro. Here, we investigated the photototoxicity of the protein on tumor xenografts in mice. HeLa Kyoto cell line stably expressing KillerRed in mitochondria and in fusion with histone H2B was used. Irradiation of the tumors with 593 nm laser led to photobleaching of KillerRed indicating photosensitization reaction and caused significant destruction of the cells and activation of apoptosis. The portion of the dystrophically changed cells increased from 9.9% to 63.7%, and the cells with apoptosis hallmarks from 6.3% to 14%. The results of this study suggest KillerRed as a potential genetically encoded photosensitizer for photodynamic therapy of cancer.
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Affiliation(s)
- Marina V Shirmanova
- Nizhny Novgorod State Medical Academy, 603005 Minin Sq., 10/1, Nizhny Novgorod, Russia.
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Lukyanov KA, Serebrovskaya EO, Lukyanov S, Chudakov DM. Fluorescent proteins as light-inducible photochemical partners. Photochem Photobiol Sci 2010; 9:1301-6. [PMID: 20672171 DOI: 10.1039/c0pp00114g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 07/14/2010] [Indexed: 01/19/2023]
Abstract
Green Fluorescent Protein (GFP) and other related fluorescent proteins are generally used as genetically encoded, chemically inert labels in vivo. This review focuses on the emerging application of fluorescent proteins as light-inducible intracellular photochemical partners. The first example of a chemically active GFP-like protein was the phototoxic red fluorescent protein KillerRed, which can be used for precise light-induced killing of cells, protein inactivation, and studying reactive oxygen species signaling in different cellular compartments. Moreover, recent studies revealed that various GFPs can act as light-induced electron donors in photochemical reactions with biologically relevant electron acceptors. These findings have important implications for practical uses of fluorescent proteins as well as for our understanding of the evolution and biology of this protein family.
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