Single-Cell RNA Sequencing for the Detection of Clonotypic V(D)J Rearrangements in Multiple Myeloma
Multiple myeloma (MM) has a highly heterogeneous genetic background, which complicates its molecular tracking over time. Nevertheless, each MM patient’s malignant plasma cells (PCs) share unique V(D)J rearranged sequences at immunoglobulin loci, which represent ideal disease biomarkers. Because the...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-12-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/24/15691 |
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| author | Antonio Matera Alessio Marella Akihiro Maeda Matteo C. Da Vià Francesca Lazzaroni Sonia Fabris Stefania Pioggia Laura Porretti Federico Colombo Federica Torricelli Antonino Neri Elisa Taiana Giuseppina Fabbiano Valentina Traini Elisa Genuardi Daniela Drandi Niccolò Bolli Marta Lionetti |
| author_facet | Antonio Matera Alessio Marella Akihiro Maeda Matteo C. Da Vià Francesca Lazzaroni Sonia Fabris Stefania Pioggia Laura Porretti Federico Colombo Federica Torricelli Antonino Neri Elisa Taiana Giuseppina Fabbiano Valentina Traini Elisa Genuardi Daniela Drandi Niccolò Bolli Marta Lionetti |
| author_sort | Antonio Matera |
| collection | DOAJ |
| description | Multiple myeloma (MM) has a highly heterogeneous genetic background, which complicates its molecular tracking over time. Nevertheless, each MM patient’s malignant plasma cells (PCs) share unique V(D)J rearranged sequences at immunoglobulin loci, which represent ideal disease biomarkers. Because the tumor-specific V(D)J sequence is highly expressed in bulk RNA in MM patients, we wondered whether it can be identified by single-cell RNA sequencing (scRNA-seq). To this end we analyzed CD138<sup>+</sup> cells purified from bone marrow aspirates of 19 samples with PC dyscrasias by both a standard method based on bulk DNA and by an implementation of the standard 10x Genomics protocol to detect expressed V(D)J sequences. A dominant clonotype was easily identified in each sample, accounting on average for 83.65% of V(D)J-rearranged cells. Compared with standard methods, scRNA-seq analysis proved highly concordant and even more effective in identifying clonal productive rearrangements, by-passing limitations related to the misannealing of consensus primers in hypermutated regions. We next validated its accuracy to track 5 clonal cells with absolute sensitivity in a virtual sample containing 3180 polyclonal cells. This shows that single-cell V(D)J analysis may be used to find rare clonal cells, laying the foundations for functional single-cell dissection of minimal residual disease. |
| first_indexed | 2024-03-09T16:19:41Z |
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| id | doaj.art-67ca10ec1e1649838c79aab0e594f5dc |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T16:19:41Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-67ca10ec1e1649838c79aab0e594f5dc2023-11-24T15:26:06ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-12-0123241569110.3390/ijms232415691Single-Cell RNA Sequencing for the Detection of Clonotypic V(D)J Rearrangements in Multiple MyelomaAntonio Matera0Alessio Marella1Akihiro Maeda2Matteo C. Da Vià3Francesca Lazzaroni4Sonia Fabris5Stefania Pioggia6Laura Porretti7Federico Colombo8Federica Torricelli9Antonino Neri10Elisa Taiana11Giuseppina Fabbiano12Valentina Traini13Elisa Genuardi14Daniela Drandi15Niccolò Bolli16Marta Lionetti17Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, ItalyDepartment of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, ItalyDepartment of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, ItalyHematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, ItalyHematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, ItalyHematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, ItalyHematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, ItalyHematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, ItalyHematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, ItalyLaboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, ItalyScientific Directorate, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, ItalyHematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, ItalyHematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, ItalyDepartment of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, ItalyDepartment of Molecular Biotechnologies and Health Sciences, University of Torino, 10124 Torino, ItalyDepartment of Molecular Biotechnologies and Health Sciences, University of Torino, 10124 Torino, ItalyDepartment of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, ItalyDepartment of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, ItalyMultiple myeloma (MM) has a highly heterogeneous genetic background, which complicates its molecular tracking over time. Nevertheless, each MM patient’s malignant plasma cells (PCs) share unique V(D)J rearranged sequences at immunoglobulin loci, which represent ideal disease biomarkers. Because the tumor-specific V(D)J sequence is highly expressed in bulk RNA in MM patients, we wondered whether it can be identified by single-cell RNA sequencing (scRNA-seq). To this end we analyzed CD138<sup>+</sup> cells purified from bone marrow aspirates of 19 samples with PC dyscrasias by both a standard method based on bulk DNA and by an implementation of the standard 10x Genomics protocol to detect expressed V(D)J sequences. A dominant clonotype was easily identified in each sample, accounting on average for 83.65% of V(D)J-rearranged cells. Compared with standard methods, scRNA-seq analysis proved highly concordant and even more effective in identifying clonal productive rearrangements, by-passing limitations related to the misannealing of consensus primers in hypermutated regions. We next validated its accuracy to track 5 clonal cells with absolute sensitivity in a virtual sample containing 3180 polyclonal cells. This shows that single-cell V(D)J analysis may be used to find rare clonal cells, laying the foundations for functional single-cell dissection of minimal residual disease.https://www.mdpi.com/1422-0067/23/24/15691multiple myelomasingle-cell RNA sequencingclonal biomarkerV(D)J rearrangement |
| spellingShingle | Antonio Matera Alessio Marella Akihiro Maeda Matteo C. Da Vià Francesca Lazzaroni Sonia Fabris Stefania Pioggia Laura Porretti Federico Colombo Federica Torricelli Antonino Neri Elisa Taiana Giuseppina Fabbiano Valentina Traini Elisa Genuardi Daniela Drandi Niccolò Bolli Marta Lionetti Single-Cell RNA Sequencing for the Detection of Clonotypic V(D)J Rearrangements in Multiple Myeloma International Journal of Molecular Sciences multiple myeloma single-cell RNA sequencing clonal biomarker V(D)J rearrangement |
| title | Single-Cell RNA Sequencing for the Detection of Clonotypic V(D)J Rearrangements in Multiple Myeloma |
| title_full | Single-Cell RNA Sequencing for the Detection of Clonotypic V(D)J Rearrangements in Multiple Myeloma |
| title_fullStr | Single-Cell RNA Sequencing for the Detection of Clonotypic V(D)J Rearrangements in Multiple Myeloma |
| title_full_unstemmed | Single-Cell RNA Sequencing for the Detection of Clonotypic V(D)J Rearrangements in Multiple Myeloma |
| title_short | Single-Cell RNA Sequencing for the Detection of Clonotypic V(D)J Rearrangements in Multiple Myeloma |
| title_sort | single cell rna sequencing for the detection of clonotypic v d j rearrangements in multiple myeloma |
| topic | multiple myeloma single-cell RNA sequencing clonal biomarker V(D)J rearrangement |
| url | https://www.mdpi.com/1422-0067/23/24/15691 |
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