1
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Baker AM, Nageswaran G, Nenclares P, Ronel T, Smith K, Kimberley C, Laclé MM, Bhide S, Harrington KJ, Melcher A, Rodriguez-Justo M, Chain B, Graham TA. FUME-TCRseq Enables Sensitive and Accurate Sequencing of the T-cell Receptor from Limited Input of Degraded RNA. Cancer Res 2024; 84:1560-1569. [PMID: 38479434 PMCID: PMC11094417 DOI: 10.1158/0008-5472.can-23-3340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/19/2024] [Accepted: 02/27/2024] [Indexed: 05/16/2024]
Abstract
Genomic analysis of the T-cell receptor (TCR) reveals the strength, breadth, and clonal dynamics of the adaptive immune response to pathogens or cancer. The diversity of the TCR repertoire, however, means that sequencing is technically challenging, particularly for samples with low-quality, degraded nucleic acids. Here, we developed and validated FUME-TCRseq, a robust and sensitive RNA-based TCR sequencing methodology that is suitable for formalin-fixed paraffin-embedded samples and low amounts of input material. FUME-TCRseq incorporates unique molecular identifiers into each molecule of cDNA, allowing correction for sequencing errors and PCR bias. Using RNA extracted from colorectal and head and neck cancers to benchmark the accuracy and sensitivity of FUME-TCRseq against existing methods demonstrated excellent concordance between the datasets. Furthermore, FUME-TCRseq detected more clonotypes than a commercial RNA-based alternative, with shorter library preparation time and significantly lower cost. The high sensitivity and the ability to sequence RNA of poor quality and limited amount enabled quantitative analysis of small numbers of cells from archival tissue sections, which is not possible with other methods. Spatially resolved FUME-TCRseq analysis of colorectal cancers using macrodissected archival samples revealed the shifting T-cell landscapes at the transition to an invasive phenotype and between tumor subclones containing distinct driver alterations. In summary, FUME-TCRseq represents an accurate, sensitive, and low-cost tool for the characterization of T-cell repertoires, particularly in samples with low-quality RNA that have not been accessible using existing methodology. SIGNIFICANCE FUME-TCRseq is a TCR sequencing methodology that supports sensitive and spatially resolved detection of TCR clones in archival clinical specimens, which can facilitate longitudinal tracking of immune responses through disease course and treatment.
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Affiliation(s)
- Ann-Marie Baker
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Gayathri Nageswaran
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Pablo Nenclares
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, United Kingdom
| | - Tahel Ronel
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Kane Smith
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Christopher Kimberley
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Miangela M. Laclé
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Shreerang Bhide
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, United Kingdom
- Head and Neck Unit, The Royal Marsden Hospital NHS Trust, London, United Kingdom
| | - Kevin J. Harrington
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, United Kingdom
| | - Alan Melcher
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, United Kingdom
- Division of Breast Cancer Research, Institute of Cancer Research, London, United Kingdom
| | | | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Trevor A. Graham
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
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2
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Menchits Y, Salimova T, Komkov A, Abramov D, Konyukhova T, Abasov R, Raykina E, Itov A, Gaskova M, Borkovskaia A, Kazakova A, Soldatkina O, Kashpor S, Semchenkova A, Popov A, Novichkova G, Olshanskaya Y, Maschan A, Zerkalenkova E. Unusual Presentation of SET::NUP214-Associated Concomitant Hematological Neoplasm in a Child-Diagnostic and Treatment Struggle. Int J Mol Sci 2023; 24:14451. [PMID: 37833906 PMCID: PMC10572181 DOI: 10.3390/ijms241914451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 10/15/2023] Open
Abstract
Simultaneous multilineage hematologic malignancies are uncommon and associated with poorer prognosis than single-lineage leukemia or lymphoma. Here, we describe a concomitant malignant neoplasm in a 4-year-old boy. The child presented with massive lymphoproliferative syndrome, nasal breathing difficulties, and snoring. Morphological, immunocytochemical, and flow cytometry diagnostics showed coexistence of acute myeloid leukemia (AML) and peripheral T-cell lymphoma (PTCL). Molecular examination revealed a rare t(9;9)(q34;q34)/SET::NUP214 translocation as well as common TCR clonal rearrangements in both the bone marrow and lymph nodes. The disease showed primary refractoriness to both lymphoid and myeloid high-dose chemotherapy as well as combined targeted therapy (trametinib + ruxolitinib). Hence, HSCT was performed, and the patient has since been in complete remission for over a year. This observation highlights the importance of molecular techniques for determining the united nature of complex SET::NUP214-positive malignant neoplasms arising from precursor cells with high lineage plasticity.
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Affiliation(s)
- Yaroslav Menchits
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Tatiana Salimova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Alexander Komkov
- Abu Dhabi Stem Cells Center, Mahdar Qutouf Str., 25, Abu Dhabi 22404, United Arab Emirates;
| | - Dmitry Abramov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Tatiana Konyukhova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Ruslan Abasov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Elena Raykina
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Albert Itov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Marina Gaskova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Aleksandra Borkovskaia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Anna Kazakova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Olga Soldatkina
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Svetlana Kashpor
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Alexandra Semchenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Alexander Popov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Galina Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Yulia Olshanskaya
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Alexey Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
| | - Elena Zerkalenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samora Maschela Str., 1, 117998 Moscow, Russia (T.K.); (R.A.)
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3
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Smirnova AO, Miroshnichenkova AM, Belyaeva LD, Kelmanson IV, Lebedev YB, Mamedov IZ, Chudakov DM, Komkov AY. Novel bimodal TRBD1-TRBD2 rearrangements with dual or absent D-region contribute to TRB V-(D)-J combinatorial diversity. Front Immunol 2023; 14:1245175. [PMID: 37744336 PMCID: PMC10513440 DOI: 10.3389/fimmu.2023.1245175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
T-cell receptor (TR) diversity of the variable domains is generated by recombination of both the alpha (TRA) and beta (TRB) chains. The textbook process of TRB chain production starts with TRBD and TRBJ gene rearrangement, followed by the rearrangement of a TRBV gene to the partially rearranged D-J gene. Unsuccessful V-D-J TRB rearrangements lead to apoptosis of the cell. Here, we performed deep sequencing of the poorly explored pool of partial TRBD1-TRBD2 rearrangements in T-cell genomic DNA. We reconstructed full repertoires of human partial TRBD1-TRBD2 rearrangements using novel sequencing and validated them by detecting V-D-J recombination-specific byproducts: excision circles containing the recombination signal (RS) joint 5'D2-RS - 3'D1-RS. Identified rearrangements were in compliance with the classical 12/23 rule, common for humans, rats, and mice and contained typical V-D-J recombination footprints. Interestingly, we detected a bimodal distribution of D-D junctions indicating two active recombination sites producing long and short D-D rearrangements. Long TRB D-D rearrangements with two D-regions are coding joints D1-D2 remaining classically on the chromosome. The short TRB D-D rearrangements with no D-region are signal joints, the coding joint D1-D2 being excised from the chromosome. They both contribute to the TRB V-(D)-J combinatorial diversity. Indeed, short D-D rearrangements may be followed by direct V-J2 recombination. Long D-D rearrangements may recombine further with J2 and V genes forming partial D1-D2-J2 and then complete V-D1-D2-J2 rearrangement. Productive TRB V-D1-D2-J2 chains are present and expressed in thousands of clones of human antigen-experienced memory T cells proving their capacity for antigen recognition and actual participation in the immune response.
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Affiliation(s)
- Anastasia O. Smirnova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Laima D. Belyaeva
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ilya V. Kelmanson
- Department of Biomolecular Sciences and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Yuri B. Lebedev
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ilgar Z. Mamedov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Dmitriy M. Chudakov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Abu Dhabi Stem Cells Center (ADSCC), Abu Dhabi, United Arab Emirates
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Alexander Y. Komkov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Abu Dhabi Stem Cells Center (ADSCC), Abu Dhabi, United Arab Emirates
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
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4
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Semchenkova A, Zerkalenkova E, Demina I, Kashpor S, Volchkov E, Zakharova E, Larin S, Olshanskaya Y, Novichkova G, Maschan A, Maschan M, Popov A. Recognizing Minor Leukemic Populations with Monocytic Features in Mixed-Phenotype Acute Leukemia by Flow Cell Sorting Followed by Cytogenetic and Molecular Studies: Report of Five Exemplary Cases. Int J Mol Sci 2023; 24:ijms24065260. [PMID: 36982331 PMCID: PMC10049081 DOI: 10.3390/ijms24065260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Mixed-phenotype acute leukemia (MPAL), a rare and heterogeneous category of acute leukemia, is characterized by cross-lineage antigen expression. Leukemic blasts in MPAL can be represented either by one population with multiple markers of different lineages or by several single-lineage populations. In some cases, a major blast population may coexist with a smaller population that has minor immunophenotypic abnormalities and may be missed even by an experienced pathologist. To avoid misdiagnosis, we suggest sorting doubtful populations and leukemic blasts and searching for similar genetic aberrations. Using this approach, we examined questionable monocytic populations in five patients with dominant leukemic populations of B-lymphoblastic origin. Cell populations were isolated either for fluorescence in situ hybridization or for clonality assessment by multiplex PCR or next-generation sequencing. In all cases, monocytic cells shared the same gene rearrangements with dominant leukemic populations, unequivocally confirming the same leukemic origin. This approach is able to identify implicit cases of MPAL and therefore leads to the necessary clinical management for patients.
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Affiliation(s)
- Alexandra Semchenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia
- Correspondence:
| | - Elena Zerkalenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia
| | - Irina Demina
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia
| | - Svetlana Kashpor
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia
| | - Egor Volchkov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Elena Zakharova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia
| | - Sergey Larin
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia
| | - Yulia Olshanskaya
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia
| | - Galina Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia
| | - Alexey Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia
| | - Michael Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia
| | - Alexander Popov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia
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5
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Demina I, Zerkalenkova E, Semchenkova A, Volchkov E, Boychenko E, Prudnikova M, Novichkova G, Maschan M, Maschan A, Olshanskaya Y, Popov A. Rare case of pediatric trilineal mixed-phenotype acute leukemia with t(11;19)(q23.3;p13)/KMT2A::ELL. Leuk Res 2023; 125:107018. [PMID: 36640593 DOI: 10.1016/j.leukres.2023.107018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023]
Affiliation(s)
- Irina Demina
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Elena Zerkalenkova
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Alexandra Semchenkova
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Egor Volchkov
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Elmira Boychenko
- City Children's Hospital № 1, Saint Petersburg, Russian Federation
| | - Maria Prudnikova
- City Children's Hospital № 1, Saint Petersburg, Russian Federation
| | - Galina Novichkova
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Michael Maschan
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Alexey Maschan
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Yulia Olshanskaya
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Alexander Popov
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation.
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6
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Smirnova AO, Miroshnichenkova AM, Olshanskaya YV, Maschan MA, Lebedev YB, Chudakov DM, Mamedov IZ, Komkov A. The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling. eLife 2023; 12:69157. [PMID: 36692004 PMCID: PMC9901932 DOI: 10.7554/elife.69157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 01/22/2023] [Indexed: 01/25/2023] Open
Abstract
High-throughput sequencing of adaptive immune receptor repertoires is a valuable tool for receiving insights in adaptive immunity studies. Several powerful TCR/BCR repertoire reconstruction and analysis methods have been developed in the past decade. However, detecting and correcting the discrepancy between real and experimentally observed lymphocyte clone frequencies are still challenging. Here, we discovered a hallmark anomaly in the ratio between read count and clone count-based frequencies of non-functional clonotypes in multiplex PCR-based immune repertoires. Calculating this anomaly, we formulated a quantitative measure of V- and J-genes frequency bias driven by multiplex PCR during library preparation called Over Amplification Rate (OAR). Based on the OAR concept, we developed an original software for multiplex PCR-specific bias evaluation and correction named iROAR: immune Repertoire Over Amplification Removal (https://github.com/smiranast/iROAR). The iROAR algorithm was successfully tested on previously published TCR repertoires obtained using both 5' RACE (Rapid Amplification of cDNA Ends)-based and multiplex PCR-based approaches and compared with a biological spike-in-based method for PCR bias evaluation. The developed approach can increase the accuracy and consistency of repertoires reconstructed by different methods making them more applicable for comparative analysis.
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Affiliation(s)
- Anastasia O Smirnova
- Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
| | - Anna M Miroshnichenkova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Yulia V Olshanskaya
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Michael A Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Yuri B Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Dmitriy M Chudakov
- Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Abu Dhabi Stem Cells CenterAbu DhabiUnited Arab Emirates
| | - Ilgar Z Mamedov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Alexander Komkov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
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7
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Mikhailova E, Illarionova O, Komkov A, Zerkalenkova E, Mamedov I, Shelikhova L, Olshanskaya Y, Miakova N, Novichkova G, Karachunskiy A, Maschan M, Popov A. Reliable Flow-Cytometric Approach for Minimal Residual Disease Monitoring in Patients with B-Cell Precursor Acute Lymphoblastic Leukemia after CD19-Targeted Therapy. Cancers (Basel) 2022; 14:5445. [PMID: 36358863 PMCID: PMC9658935 DOI: 10.3390/cancers14215445] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 09/10/2023] Open
Abstract
We aimed to develop an antibody panel and data analysis algorithm for multicolor flow cytometry (MFC), which is a reliable method for minimal residual disease (MRD) detection in patients with B-cell precursor acute lymphoblastic leukemia (BCP-ALL) treated with CD19-directed therapy. The development of the approach, which was adapted for the case of possible CD19 loss, was based on the additional B-lineage marker expression data obtained from a study of primary BCP-ALL patients, an analysis of the immunophenotypic changes that occur during blinatumomab or CAR-T therapy, and an analysis of very early CD19-negative normal BCPs. We have developed a single-tube 11-color panel for MFC-MRD detection. CD22- and iCD79a-based primary B-lineage gating (preferably consecutive) was recommended. Based on patterns of antigen expression changes and the relative expansion of normal CD19-negative BCPs, guidelines for MFC data analysis and interpretation were established. The suggested approach was tested in comparison with the molecular techniques: IG/TR gene rearrangement detection by next-generation sequencing (NGS) and RQ-PCR for fusion-gene transcripts (FGTs). Qualitative concordance rates of 82.8% and 89.8% were obtained for NGS-MRD and FGT-MRD results, respectively. We have developed a sensitive and reliable approach that allows MFC-MRD monitoring after CD19-directed treatment, even in the case of possible CD19 loss.
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Affiliation(s)
- Ekaterina Mikhailova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia
| | - Olga Illarionova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia
| | - Alexander Komkov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117998 Moscow, Russia
| | - Elena Zerkalenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia
| | - Ilgar Mamedov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117998 Moscow, Russia
| | - Larisa Shelikhova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia
| | - Yulia Olshanskaya
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia
| | - Natalia Miakova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia
| | - Galina Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia
| | - Alexander Karachunskiy
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia
| | - Michael Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia
| | - Alexander Popov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia
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8
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Sycheva AL, Komech EA, Pogorelyy MV, Minervina AA, Urazbakhtin SZ, Salnikova MA, Vorovitch MF, Kopantzev EP, Zvyagin IV, Komkov AY, Mamedov IZ, Lebedev YB. Inactivated tick-borne encephalitis vaccine elicits several overlapping waves of T cell response. Front Immunol 2022; 13:970285. [PMID: 36091004 PMCID: PMC9449805 DOI: 10.3389/fimmu.2022.970285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/05/2022] [Indexed: 12/02/2022] Open
Abstract
The development and implementation of vaccines have been growing exponentially, remaining one of the major successes of healthcare over the last century. Nowadays, active regular immunizations prevent epidemics of many viral diseases, including tick-borne encephalitis (TBE). Along with the generation of virus-specific antibodies, a highly effective vaccine should induce T cell responses providing long-term immune defense. In this study, we performed longitudinal high-throughput T cell receptor (TCR) sequencing to characterize changes in individual T cell repertoires of 11 donors immunized with an inactivated TBE vaccine. After two-step immunization, we found significant clonal expansion of both CD4+ and CD8+ T cells, ranging from 302 to 1706 vaccine-associated TCRβ clonotypes in different donors. We detected several waves of T cell clonal expansion generated by distinct groups of vaccine-responding clones. Both CD4+ and CD8+ vaccine-responding T cell clones formed 17 motifs in TCRβ sequences shared by donors with identical HLA alleles. Our results indicate that TBE vaccination leads to a robust T cell response due to the production of a variety of T cell clones with a memory phenotype, which recognize a large set of epitopes.
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Affiliation(s)
- Anastasiia L. Sycheva
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- *Correspondence: Anastasiia L. Sycheva, ; Yuri B. Lebedev,
| | - Ekaterina A. Komech
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Mikhail V. Pogorelyy
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Anastasia A. Minervina
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Shamil Z. Urazbakhtin
- Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maria A. Salnikova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail F. Vorovitch
- Laboratory of Tick-Borne Encephalitis and Other Encephalitis, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS (FSASI “Chumakov FSC R&D IBP RAS”), Moscow, Russia
- Department of Organization and Technology of Production of Immune-and-Biological Products, Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Eugene P. Kopantzev
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Ivan V. Zvyagin
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexander Y. Komkov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Laboratory of Cytogenetics and Molecular Genetics, Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology, Moscow, Russia
| | - Ilgar Z. Mamedov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Yuri B. Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- *Correspondence: Anastasiia L. Sycheva, ; Yuri B. Lebedev,
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9
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Semchenkova A, Mikhailova E, Komkov A, Gaskova M, Abasov R, Matveev E, Kazanov M, Mamedov I, Shmitko A, Belova V, Miroshnichenkova A, Illarionova O, Olshanskaya Y, Tsaur G, Verzhbitskaya T, Ponomareva N, Bronin G, Kondratchik K, Fechina L, Diakonova Y, Vavilova L, Myakova N, Novichkova G, Maschan A, Maschan M, Zerkalenkova E, Popov A. Lineage Conversion in Pediatric B-Cell Precursor Acute Leukemia under Blinatumomab Therapy. Int J Mol Sci 2022; 23:4019. [PMID: 35409391 PMCID: PMC8999738 DOI: 10.3390/ijms23074019] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/24/2022] [Accepted: 04/02/2022] [Indexed: 12/28/2022] Open
Abstract
We report incidence and deep molecular characteristics of lineage switch in 182 pediatric patients affected by B-cell precursor acute lymphoblastic leukemia (BCP-ALL), who were treated with blinatumomab. We documented six cases of lineage switch that occurred after or during blinatumomab exposure. Therefore, lineage conversion was found in 17.4% of all resistance cases (4/27) and 3.2% of relapses (2/63). Half of patients switched completely from BCP-ALL to CD19-negative acute myeloid leukemia, others retained CD19-positive B-blasts and acquired an additional CD19-negative blast population: myeloid or unclassifiable. Five patients had KMT2A gene rearrangements; one had TCF3::ZNF384 translocation. The presented cases showed consistency of gene rearrangements and fusion transcripts across initially diagnosed leukemia and lineage switch. In two of six patients, the clonal architecture assessed by IG/TR gene rearrangements was stable, while in others, loss of clones or gain of new clones was noted. KMT2A-r patients demonstrated very few additional mutations, while in the TCF3::ZNF384 case, lineage switch was accompanied by a large set of additional mutations. The immunophenotype of an existing leukemia sometimes changes via different mechanisms and with different additional molecular changes. Careful investigation of all BM compartments together with all molecular -minimal residual disease studies can lead to reliable identification of lineage switch.
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Affiliation(s)
- Alexandra Semchenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Ekaterina Mikhailova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Alexander Komkov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117998 Moscow, Russia
| | - Marina Gaskova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Ruslan Abasov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Evgenii Matveev
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
- Institute for Information Transmission Problems (the Kharkevich Institute, RAS), 127051 Moscow, Russia
| | - Marat Kazanov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
- Institute for Information Transmission Problems (the Kharkevich Institute, RAS), 127051 Moscow, Russia
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Ilgar Mamedov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117998 Moscow, Russia
| | - Anna Shmitko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 119334 Moscow, Russia; (A.S.); (V.B.)
| | - Vera Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 119334 Moscow, Russia; (A.S.); (V.B.)
| | - Anna Miroshnichenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Olga Illarionova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Yulia Olshanskaya
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Grigory Tsaur
- Regional Clinical Children Hospital, 620149 Ekaterinburg, Russia; (G.T.); (T.V.); (L.F.)
- Research Institute of Medical Cell Technologies, 620026 Ekaterinburg, Russia
| | - Tatiana Verzhbitskaya
- Regional Clinical Children Hospital, 620149 Ekaterinburg, Russia; (G.T.); (T.V.); (L.F.)
- Research Institute of Medical Cell Technologies, 620026 Ekaterinburg, Russia
| | | | - Gleb Bronin
- Morozov City Children Clinical Hospital, 119049 Moscow, Russia; (G.B.); (K.K.)
| | | | - Larisa Fechina
- Regional Clinical Children Hospital, 620149 Ekaterinburg, Russia; (G.T.); (T.V.); (L.F.)
- Research Institute of Medical Cell Technologies, 620026 Ekaterinburg, Russia
| | - Yulia Diakonova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Liudmila Vavilova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Natalia Myakova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Galina Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Alexey Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Michael Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Elena Zerkalenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Alexander Popov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
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10
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The use of additional immunophenotypic criteria for the differential diagnosis of Burkitt lymphoma/leukemia: An exemplary case report. Leuk Res 2021; 110:106662. [PMID: 34242914 DOI: 10.1016/j.leukres.2021.106662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/11/2021] [Accepted: 06/30/2021] [Indexed: 11/22/2022]
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11
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Navrkalova V, Plevova K, Hynst J, Pal K, Mareckova A, Reigl T, Jelinkova H, Vrzalova Z, Stranska K, Pavlova S, Panovska A, Janikova A, Doubek M, Kotaskova J, Pospisilova S. LYmphoid NeXt-Generation Sequencing (LYNX) Panel: A Comprehensive Capture-Based Sequencing Tool for the Analysis of Prognostic and Predictive Markers in Lymphoid Malignancies. J Mol Diagn 2021; 23:959-974. [PMID: 34082072 DOI: 10.1016/j.jmoldx.2021.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 04/21/2021] [Accepted: 05/03/2021] [Indexed: 02/07/2023] Open
Abstract
B-cell neoplasms represent a clinically heterogeneous group of hematologic malignancies with considerably diverse genomic architecture recently endorsed by next-generation sequencing (NGS) studies. Because multiple genetic defects have a potential or confirmed clinical impact, a tendency toward more comprehensive testing of diagnostic, prognostic, and predictive markers is desired. This study introduces the design, validation, and implementation of an integrative, custom-designed, capture-based NGS panel titled LYmphoid NeXt-generation sequencing (LYNX) for the analysis of standard and novel molecular markers in the most common lymphoid neoplasms (chronic lymphocytic leukemia, acute lymphoblastic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma). A single LYNX test provides the following: i) accurate detection of mutations in all coding exons and splice sites of 70 lymphoma-related genes with a sensitivity of 5% variant allele frequency, ii) reliable identification of large genome-wide (≥6 Mb) and recurrent chromosomal aberrations (≥300 kb) in at least 20% of the clonal cell fraction, iii) the assessment of immunoglobulin and T-cell receptor gene rearrangements, and iv) lymphoma-specific translocation detection. Dedicated bioinformatic pipelines were designed to detect all markers mentioned above. The LYNX panel represents a comprehensive, up-to-date tool suitable for routine testing of lymphoid neoplasms with research and clinical applicability. It allows a wide adoption of capture-based targeted NGS in clinical practice and personalized management of patients with lymphoproliferative diseases.
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Affiliation(s)
- Veronika Navrkalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jakub Hynst
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karol Pal
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Department of Internal Medicine II - Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andrea Mareckova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Tomas Reigl
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Hana Jelinkova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Zuzana Vrzalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kamila Stranska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Andrea Janikova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jana Kotaskova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic.
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