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41 results on '"Fedorenko, Denis A."'

1. Targeted depletion of TRBV9+ T cells as immunotherapy in a patient with ankylosing spondylitis

Author

Britanova, Olga V., Lupyr, Kseniia R., Staroverov, Dmitry B., Shagina, Irina A., Aleksandrov, Alexey A., Ustyugov, Yakov Y., Somov, Dmitry V., Klimenko, Alesia, Shostak, Nadejda A., Zvyagin, Ivan V., Stepanov, Alexey V., Merzlyak, Ekaterina M., Davydov, Alexey N., Izraelson, Mark, Egorov, Evgeniy S., Bogdanova, Ekaterina A., Vladimirova, Anna K., Iakovlev, Pavel A., Fedorenko, Denis A., Ivanov, Roman A., Skvortsova, Veronika I., Lukyanov, Sergey, and Chudakov, Dmitry M.

Published
2023
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3. Avoiding Echo-Responses in a Retrieval-Based Conversation System

Author

Fedorenko, Denis, Smetanin, Nikita, and Rodichev, Artem

Subjects
Computer Science - Computation and Language
Abstract

Retrieval-based conversation systems generally tend to highly rank responses that are semantically similar or even identical to the given conversation context. While the system's goal is to find the most appropriate response, rather than the most semantically similar one, this tendency results in low-quality responses. We refer to this challenge as the echoing problem. To mitigate this problem, we utilize a hard negative mining approach at the training stage. The evaluation shows that the resulting model reduces echoing and achieves better results in terms of Average Precision and Recall@N metrics, compared to the models trained without the proposed approach.

Published
2017
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5. Bulk TCR repertoires, Anti-TRBV9 therapy, Case report

Author

Britanova, Olga V., Lupyr, Kseniia R., Staroverov, Dmitry B., A. Shagina, Irina, Aleksandrov, Alexey A., Ustyugov, Yakov Y., Somov, Dmitry V., Klimenko, Alesia, Shostak, Nadejda A., Zvyagin, Ivan V., V. Stepanov, Alexey, Merzlyak, Ekaterina M., Davydov, Alexey N., Izraelson, Mark, Egorov, Evgeniy S., Bogdanova, Ekaterina A., Vladimirova, Anna K., Iakovlev, Pavel A., Fedorenko, Denis A., Ivanov, Roman A., Skvortsova, Veronika I., Lukyanov, Sergey A., and Chudakov, Dmitry M.

Abstract

Cytotoxic humanized anti-TRBV9 monoclonal antibody. We performed first-in-human targeted depletion of TRBV-restricted T cells in an HLA–B*27-positive patient with AS. TCR repertoires Preparation of unique molecular identifier (UMI)-labeled TCRβ cDNA libraries was performed using HUMAN TCR RNA MULTIPLEX kit (MiLaboratories) according to the manufacturer's manuals. Sequencing was performed on Illumina MiSeq and NextSeq 550, using 150+150 nt paired-end mode. MIGEC v1.2.9 was used for UMI-based read grouping and error correction. MiXCR v3.0.13 was used for extraction of TCRβ CDR3 repertoires. VDJtools v1.2.1 was used for downstream post-analysis. The repertoires include only productive sequences with more than one read per UMI.

Published
2023
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6. Macaca mulatta, Anti-TRBV9 therapy

Author

Britanova, Olga V., Lupyr, Kseniia R., Staroverov, Dmitry B., A. Shagina, Irina, Aleksandrov, Alexey A., Ustyugov, Yakov Y., Somov, Dmitry V., Klimenko, Alesia, Shostak, Nadejda A., Zvyagin, Ivan V., V. Stepanov, Alexey, Merzlyak, Ekaterina M., Davydov, Alexey N., Izraelson, Mark, Egorov, Evgeniy S., Bogdanova, Ekaterina A., Vladimirova, Anna K., Iakovlev, Pavel A., Fedorenko, Denis A., Ivanov, Roman A., Skvortsova, Veronika I., Lukyanov, Sergey A., and Chudakov, Dmitry M.

Abstract

Cytotoxic humanized anti-TRBV9 monoclonal antibody. A single intravenous (i.v.) dose of the antibody administered to rhesus macaques (Macaca mulatta), resulted in prominent depletion of peripheral blood TRBV9+ T cells in a dose-dependent manner. Animals After quarantine, 12 Macaca mulatta males aged 5–8 years were selected for this experiment. For TCR repertoire profiling peripheral blood samples were collected before and 3, 40, 150, and 300 days after a single administration of BCD-180. We divided the animals into two groups (n = 4 for each group) that received 1 mg or 10 mg BCD-180 i.v. per animal, along with a control group that included four animals and received human intravenous IgG immunoglobulins (Microgen). Animals were kept in accordance with the guidelines for accommodation and care of laboratory animals, with species-specific provisions for nonhuman primates. The local ethics committee approved experiments for these studies. TCR repertoires Sequencing was performed on Illumina HiSeq1500. MIGEC v1.2.9 was used for UMI-based read grouping and error correction. MiXCR v3.0.13 was used for extraction of TCRβ CDR3 repertoires. VDJtools v1.2.1 was used for downstream post-analysis. The repertoires include only productive sequences with more than one read per UMI.

Published
2023
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7. TRBV9 TCR repertoires, Anti-TRBV9 therapy, Case report

Author

Britanova, Olga V., Lupyr, Kseniia R., Staroverov, Dmitry B., Shagina, Irina A., Aleksandrov, Alexey A., Ustyugov, Yakov Y., Somov, Dmitry V., Klimenko, Alesia, Shostak, Nadejda A., Zvyagin, Ivan V., V. Stepanov, Alexey, Merzlyak, Ekaterina M., Davydov, Alexey N., Izraelson, Mark, Egorov, Evgeniy S., Bogdanova, Ekaterina A., Vladimirova, Anna K., Iakovlev, Pavel A., Fedorenko, Denis A., Ivanov, Roman A., Skvortsova, Veronika I., Lukyanov, Sergey A., and Chudakov, Dmitry M.

Abstract

Cytotoxic humanized anti-TRBV9 monoclonal antibody. We performed first-in-human targeted depletion of TRBV-restricted T cells in an HLA–B*27-positive patient with AS. TCR repertoires Preparation of unique molecular identifier (UMI)-labeled TCRβ cDNA libraries was performed using HUMAN TCR RNA MULTIPLEX kit (MiLaboratories) according to the manufacturer's manuals. TRBV9-focused TCRβ cDNA libraries were prepared using an adapted version of the HUMAN TCR RNA MULTIPLEX kit (MiLaboratories). Sequencing was performed on Illumina MiSeq and NextSeq 550, using 150+150 nt paired-end mode. MIGEC v1.2.9 was used for UMI-based read grouping and error correction. MiXCR v3.0.13 was used for extraction of TCRβ CDR3 repertoires. VDJtools v1.2.1 was used for downstream post-analysis. The repertoires include only productive sequences with more than one read per UMI.

Published
2023
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11. Targeted depletion of TRBV9+T cells as immunotherapy in a patient with ankylosing spondylitis

Author

Britanova, Olga V., Lupyr, Kseniia R., Staroverov, Dmitry B., Shagina, Irina A., Aleksandrov, Alexey A., Ustyugov, Yakov Y., Somov, Dmitry V., Klimenko, Alesia, Shostak, Nadejda A., Zvyagin, Ivan V., Stepanov, Alexey V., Merzlyak, Ekaterina M., Davydov, Alexey N., Izraelson, Mark, Egorov, Evgeniy S., Bogdanova, Ekaterina A., Vladimirova, Anna K., Iakovlev, Pavel A., Fedorenko, Denis A., Ivanov, Roman A., Skvortsova, Veronika I., Lukyanov, Sergey, and Chudakov, Dmitry M.

Abstract

Autoimmunity is intrinsically driven by memory T and B cell clones inappropriately targeted at self-antigens. Selective depletion or suppression of self-reactive T cells remains a holy grail of autoimmune therapy, but disease-associated T cell receptors (TCRs) and cognate antigenic epitopes remained elusive. A TRBV9-containing CD8+TCR motif was recently associated with the pathogenesis of ankylosing spondylitis, psoriatic arthritis and acute anterior uveitis, and cognate HLA-B*27-presented epitopes were identified. Following successful testing in nonhuman primate models, here we report human TRBV9+T cell elimination in ankylosing spondylitis. The patient achieved remission within 3 months and ceased anti-TNF therapy after 5 years of continuous use. Complete remission has now persisted for 4 years, with three doses of anti-TRBV9 administered per year. We also observed a profound improvement in spinal mobility metrics and the Bath Ankylosing Spondylitis Metrology Index (BASMI). This represents a possibly curative therapy of an autoimmune disease via selective depletion of a TRBV-defined group of T cells. The anti-TRBV9 therapy could potentially be applicable to other HLA-B*27-associated spondyloarthropathies. Such targeted elimination of the underlying cause of the disease without systemic immunosuppression could offer a new generation of safe and efficient therapies for autoimmunity.

Published
2023
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13. Treatment and in-Hospital Overall Survival in Hematological Patients with Grade 4 Neutropenia and Coronavirus Infection

Author

Kaluzhskaya, Ksenia V., primary, Polyakov, Yuri Yu., additional, Baryakh, Elena A., additional, Gemdzhian, Eduard G., additional, Misyurina, Elena N., additional, Zhelnova, Evgenia I., additional, Yatskov, Konstantin V., additional, Kochneva, Olga L., additional, Samsonova, Inna V., additional, Lysenko, Mariana A., additional, Ivanova, Diana D., additional, Chudnova, Tatyana S., additional, and Fedorenko, Denis A., additional

Published
2021
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16. High-dose chemotherapy following autologous hematopoietic stem cell transplantation for multiple myeloma in the real world setting. Single-center experience

Author

Mochkin, Nikita E., primary, Sarzhevskiy, Vladislav O., additional, Dubinina, Julia N., additional, Smirnova, Elena G., additional, Fedorenko, Denis A., additional, Bannikova, Anna E., additional, Kolesnikova, Dina S., additional, Bogatyrev, Vladimir S., additional, Samoylova, Anastasia A., additional, Faddeev, Nikolay M., additional, and Melnichenko, Vladimir Ya., additional

Published
2020
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17. Hematopoietic Stem Cell Transplantation for CNS Autoimmune Disorders for Adults and Children: Long-Term Outcomes - Experience of the Russian Federation

Author

Kirgizov, Kirill, primary, Skorobogatova, Elena, additional, Fedorenko, Denis, additional, Volkova, Elvira, additional, Polushin, Alexey, additional, Pristanskova, Ekaterina, additional, Blagonravova, Oksana, additional, Piliya, Sergey, additional, Bembeeva, Raisa, additional, Zubarovskaya, Ludmila, additional, Zander, Axel, additional, Afanasyev, Boris, additional, and Rumyantsev, Alexander, additional

Published
2018
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19. Long-Term Outcomes of Dasatinib Therapy in Patients with Imatinib-Resistant or -Intolerant Chronic Myeloid Leukemia from Physician’s and Patient’s Perspective

Author

Ionova, Tatyana I, primary, Nikitina, Tatyana P, additional, Fedorenko, Denis A, additional, Gritsenko, Taras A, additional, Ivanova, Valentina L, additional, Kuchma, Galina B, additional, Shnaider, Tatyana V, additional, Sannikova, Inga V, additional, Usacheva, Elena I, additional, and Kurbatova, Kira A, additional

Published
2014
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20. Texterra: A Framework for Text Analysis

Author

Turdakov, Denis, primary, Astrakhantsev, Nikita, additional, Nedumov, Yaroslav, additional, Sysoev, Andrey, additional, Andrianov, Ivan, additional, Mayorov, Vladimir, additional, Fedorenko, Denis, additional, Korshunov, Anton, additional, and Kuznetsov, Sergey, additional

Published
2014
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21. Efficacy Of Dasatinib Therapy In Patients With Imatinib-Resistant Or -Intolerant Chronic Myeloid Leukemia From Physician’s and Patient’s Perspective: “Real World” Data

Author

Ionova, Tatyana I, primary, Nikitina, Tatyana P, additional, Gritsenko, Taras A, additional, Ivanova, Valentina L, additional, Kuchma, Galina B, additional, Shnaider, Tatyana V, additional, Sannikova, Inga V, additional, Fedorenko, Denis A, additional, and Kurbatova, Kira A, additional

Published
2013
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27. Four Strategies of Autologous Hematopoietic Stem Cell Transplantation for Multiple Sclerosis Treatment

Author

Novik, Andrei A., primary, Afanasyev, Boris V, primary, Lisukov, Igor A, primary, Rykavicin, Oleg A, primary, Myasnikov, Alexandr A, primary, Ionova, Tatiana I, primary, Melnichenko, Vladimir Y, primary, Fedorenko, Denis A, primary, Osipova, Nina E, primary, Zdorov, Artur E, primary, Kruglina, Ruslana V, primary, Kishtovich, Anton V, primary, Ivanov, Roman I, primary, and Gorodokin, Gary J, primary

Published
2008
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30. Which Strategy of Immunoablative Therapy with Autologous Stem Cell Transplantation (ASCT) Is Preferable in Multiple Sclerosis (MS) Patients?.

Author

Shevchenko, Yury L., primary, Novik, Andrei A., additional, Kuznetcov, Alexey N., additional, Afanasiev, Boris A., additional, Lisukov, Igor A., additional, Rykavicin, Oleg A., additional, Myasnikov, Alexandr A., additional, Ionova, Tatyana I., additional, Melnichenko, Vladimir J., additional, Fedorenko, Denis A., additional, Kishtovich, Anton V., additional, Ivanov, Roman A., additional, and Gorodokin, Gary J., additional

Published
2007
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31. Multicenter Experience of High Dose Chemotherapy (HDCT)+Autologous Stem Cell Transplantation (ASCT) in Multiple Sclerosis (MS) Patients.

Author

Shevchenko, Yury L., primary, Novik, Andrei A., additional, Kuznetcov, Alexey N., additional, Afanasiev, Boris V., additional, Lisukov, Igor A., additional, Rykavicin, Oleg A., additional, Myasnikov, Alexandr A., additional, Ionova, Tatiana I., additional, Shamanski, Sergey V., additional, Kulagin, Andrey D., additional, Malysheva, Olga A., additional, Baziy, Nikolay I., additional, Melnichenko, Vladimir Y., additional, Fedorenko, Denis A., additional, Vereschagina, Inna V., additional, Zdorov, Andrey E., additional, Kishtovich, Anton V., additional, Ivanov, Roman A., additional, Fedotov, Yury N., additional, and Gorodokin, Gary I., additional

Published
2006
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33. Quality of Life (QoL) Impairment and International Prognostic Index (IPI) in New Aggressive Non-Hodgkin’s Lymphoma (ANHL) Patients.

Author

Novik, Andrei A., primary, Ionova, Tatiana I., additional, Kishtovich, Anton V., additional, Myasnikov, Alexander A., additional, Chagorova, Tatiana V., additional, Kopp, Mikhail V., additional, Osipova, Nina E., additional, Lebedeva, Julia K., additional, Malakchova, Natalia N., additional, Pankova, Anastasia V., additional, Fedorenko, Denis A., additional, and Gorodokin, Gary I., additional

Published
2005
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34. Treatment Outcomes in Multiple Sclerosis (MS) Patients after Early, Conventional and Salvage High Dose Chemotherapy (HDCT)+Autologous Stem Cell Transplantation (ASCT).

Author

Shevchenko, Yury L., primary, Novik, Andrei A., primary, Afanasiev, Boris V., primary, Lisukov, Igor A., primary, Ionova, Tatiana I., primary, Kulagin, Andrei D., primary, Malysheva, Olga A., primary, Bisaga, Gennady N., primary, Melnichenko, Vladimir J., primary, Voloshin, Sergei V., primary, Fedorenko, Denis A., primary, Vereschagina, Inna V., primary, Kishtovich, Anton V., primary, Fedotov, Yury N., primary, and Gorodokin, Gary I., primary

Published
2005
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35. Clinical and Quality of Life Outcomes in Patients with Multiple Sclerosis (MS) after High Dose Chemotherapy(HDCT)+Autologous Stem Cell Transplantation (ASCT).

Author

Shevchenko, Yury L., primary, Novik, Andri A., additional, Afanasiev, Boris V., additional, Lisukov, Igor A., additional, Fedotov, Yury N., additional, Ionova, Tatiana I., additional, Kulagin, Alexandr D., additional, Malysheva, Olga A., additional, Bisaga, Gennadi N., additional, Melnichenko, Vladimir Y., additional, Chelombit, Lubov V., additional, Voloshin, Sergei V., additional, Fedorenko, Denis A., additional, Vereschagina, Inna V., additional, and Kishtovich, Anton V., additional

Published
2004
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