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1. Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome

Author

Parry, Erin M, Leshchiner, Ignaty, Guièze, Romain, Johnson, Connor, Tausch, Eugen, Parikh, Sameer A, Lemvigh, Camilla, Broséus, Julien, Hergalant, Sébastien, Messer, Conor, Utro, Filippo, Levovitz, Chaya, Rhrissorrakrai, Kahn, Li, Liang, Rosebrock, Daniel, Yin, Shanye, Deng, Stephanie, Slowik, Kara, Jacobs, Raquel, Huang, Teddy, Li, Shuqiang, Fell, Geoff, Redd, Robert, Lin, Ziao, Knisbacher, Binyamin A, Livitz, Dimitri, Schneider, Christof, Ruthen, Neil, Elagina, Liudmila, Taylor-Weiner, Amaro, Persaud, Bria, Martinez, Aina, Fernandes, Stacey M, Purroy, Noelia, Anandappa, Annabelle J, Ma, Jialin, Hess, Julian, Rassenti, Laura Z, Kipps, Thomas J, Jain, Nitin, Wierda, William, Cymbalista, Florence, Feugier, Pierre, Kay, Neil E, Livak, Kenneth J, Danysh, Brian P, Stewart, Chip, Neuberg, Donna, Davids, Matthew S, Brown, Jennifer R, Parida, Laxmi, Stilgenbauer, Stephan, Getz, Gad, and Wu, Catherine J

Subjects
Cancer, Rare Diseases, Lymphoma, Genetics, Hematology, Human Genome, Humans, Leukemia, Lymphocytic, Chronic, B-Cell, Lymphoma, Large B-Cell, Diffuse, Serine-Arginine Splicing Factors, Medical and Health Sciences, Immunology
Abstract

Richter syndrome (RS) arising from chronic lymphocytic leukemia (CLL) exemplifies an aggressive malignancy that develops from an indolent neoplasm. To decipher the genetics underlying this transformation, we computationally deconvoluted admixtures of CLL and RS cells from 52 patients with RS, evaluating paired CLL-RS whole-exome sequencing data. We discovered RS-specific somatic driver mutations (including IRF2BP2, SRSF1, B2M, DNMT3A and CCND3), recurrent copy-number alterations beyond del(9p21)(CDKN2A/B), whole-genome duplication and chromothripsis, which were confirmed in 45 independent RS cases and in an external set of RS whole genomes. Through unsupervised clustering, clonally related RS was largely distinct from diffuse large B cell lymphoma. We distinguished pathways that were dysregulated in RS versus CLL, and detected clonal evolution of transformation at single-cell resolution, identifying intermediate cell states. Our study defines distinct molecular subtypes of RS and highlights cell-free DNA analysis as a potential tool for early diagnosis and monitoring.

Published
2023

2. Molecular map of chronic lymphocytic leukemia and its impact on outcome

Author

Knisbacher, Binyamin A, Lin, Ziao, Hahn, Cynthia K, Nadeu, Ferran, Duran-Ferrer, Martí, Stevenson, Kristen E, Tausch, Eugen, Delgado, Julio, Barbera-Mourelle, Alex, Taylor-Weiner, Amaro, Bousquets-Muñoz, Pablo, Diaz-Navarro, Ander, Dunford, Andrew, Anand, Shankara, Kretzmer, Helene, Gutierrez-Abril, Jesus, López-Tamargo, Sara, Fernandes, Stacey M, Sun, Clare, Sivina, Mariela, Rassenti, Laura Z, Schneider, Christof, Li, Shuqiang, Parida, Laxmi, Meissner, Alexander, Aguet, François, Burger, Jan A, Wiestner, Adrian, Kipps, Thomas J, Brown, Jennifer R, Hallek, Michael, Stewart, Chip, Neuberg, Donna S, Martín-Subero, José I, Puente, Xose S, Stilgenbauer, Stephan, Wu, Catherine J, Campo, Elias, and Getz, Gad

Subjects
Hematology, Clinical Research, Cancer, Human Genome, Rare Diseases, Biotechnology, Genetics, Lymphoma, Humans, Leukemia, Lymphocytic, Chronic, B-Cell, Immunoglobulin Variable Region, Mutation, Prognosis, Genomics, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Recent advances in cancer characterization have consistently revealed marked heterogeneity, impeding the completion of integrated molecular and clinical maps for each malignancy. Here, we focus on chronic lymphocytic leukemia (CLL), a B cell neoplasm with variable natural history that is conventionally categorized into two subtypes distinguished by extent of somatic mutations in the heavy-chain variable region of immunoglobulin genes (IGHV). To build the 'CLL map,' we integrated genomic, transcriptomic and epigenomic data from 1,148 patients. We identified 202 candidate genetic drivers of CLL (109 new) and refined the characterization of IGHV subtypes, which revealed distinct genomic landscapes and leukemogenic trajectories. Discovery of new gene expression subtypes further subcategorized this neoplasm and proved to be independent prognostic factors. Clinical outcomes were associated with a combination of genetic, epigenetic and gene expression features, further advancing our prognostic paradigm. Overall, this work reveals fresh insights into CLL oncogenesis and prognostication.

Published
2022

4. Multifunctional barcoding with ClonMapper enables high-resolution study of clonal dynamics during tumor evolution and treatment

Author

Gutierrez, Catherine, Al’Khafaji, Aziz M, Brenner, Eric, Johnson, Kaitlyn E, Gohil, Satyen H, Lin, Ziao, Knisbacher, Binyamin A, Durrett, Russell E, Li, Shuqiang, Parvin, Salma, Biran, Anat, Zhang, Wandi, Rassenti, Laura, Kipps, Thomas J, Livak, Kenneth J, Neuberg, Donna, Letai, Anthony, Getz, Gad, Wu, Catherine J, and Brock, Amy

Subjects
Cancer, Biotechnology, Hematology, Human Genome, Emerging Infectious Diseases, Genetics, Cell Line, Clone Cells, Genomics, Humans, Leukemia, Lymphocytic, Chronic, B-Cell, Transcriptome
Abstract

Lineage-tracing methods have enabled characterization of clonal dynamics in complex populations, but generally lack the ability to integrate genomic, epigenomic and transcriptomic measurements with live-cell manipulation of specific clones of interest. We developed a functionalized lineage-tracing system, ClonMapper, which integrates DNA barcoding with single-cell RNA sequencing and clonal isolation to comprehensively characterize thousands of clones within heterogeneous populations. Using ClonMapper, we identified subpopulations of a chronic lymphocytic leukemia cell line with distinct clonal compositions, transcriptional signatures and chemotherapy survivorship trajectories; patterns that were also observed in primary human chronic lymphocytic leukemia. The ability to retrieve specific clones before, during and after treatment enabled direct measurements of clonal diversification and durable subpopulation transcriptional signatures. ClonMapper is a powerful multifunctional approach to dissect the complex clonal dynamics of tumor progression and therapeutic response.

Published
2021

5. ZNF683 marks a CD8+ T cell population associated with anti-tumor immunity following anti-PD-1 therapy for Richter syndrome

Author

Parry, Erin M., Lemvigh, Camilla K., Deng, Stephanie, Dangle, Nathan, Ruthen, Neil, Knisbacher, Binyamin A., Broséus, Julien, Hergalant, Sébastien, Guièze, Romain, Li, Shuqiang, Zhang, Wandi, Johnson, Connor, Long, Jaclyn M., Yin, Shanye, Werner, Lillian, Anandappa, Annabelle, Purroy, Noelia, Gohil, Satyen, Oliveira, Giacomo, Bachireddy, Pavan, Shukla, Sachet A., Huang, Teddy, Khoury, Joseph D., Thakral, Beenu, Dickinson, Michael, Tam, Constantine, Livak, Kenneth J., Getz, Gad, Neuberg, Donna, Feugier, Pierre, Kharchenko, Peter, Wierda, William, Olsen, Lars Rønn, Jain, Nitin, and Wu, Catherine J.

Published
2023
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6. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

Author

Ouspenskaia, Tamara, Law, Travis, Clauser, Karl R., Klaeger, Susan, Sarkizova, Siranush, Aguet, François, Li, Bo, Christian, Elena, Knisbacher, Binyamin A., Le, Phuong M., Hartigan, Christina R., Keshishian, Hasmik, Apffel, Annie, Oliveira, Giacomo, Zhang, Wandi, Chen, Sarah, Chow, Yuen Ting, Ji, Zhe, Jungreis, Irwin, Shukla, Sachet A., Justesen, Sune, Bachireddy, Pavan, Kellis, Manolis, Getz, Gad, Hacohen, Nir, Keskin, Derin B., Carr, Steven A., Wu, Catherine J., and Regev, Aviv

Published
2022
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7. IGLV3-21R110 mutation has prognostic value in patients with treatment-naive chronic lymphocytic leukemia

Author

Syrykh, Charlotte, primary, Pons-Brun, Berta, additional, Russiñol, Núria, additional, Playa-Albinyana, Heribert, additional, Baumann, Tycho, additional, Duran-Ferrer, Martí, additional, Kulis, Marta, additional, Carbó-Meix, Anna, additional, Mozas, Pablo, additional, Alcoceba, Miguel, additional, González, Marcos, additional, Navarro-Bailón, Almudena, additional, Colado, Enrique, additional, Payer, Ángel R., additional, Aymerich, Marta, additional, Terol, María J., additional, Lu, Junyan, additional, Knisbacher, Binyamin A., additional, Hahn, Cynthia K., additional, Ruiz-Gaspà, Sílvia, additional, Enjuanes, Anna, additional, Wu, Catherine J., additional, Getz, Gad, additional, Zenz, Thorsten, additional, López-Guillermo, Armando, additional, Martín-Subero, José I., additional, Colomer, Dolors, additional, Delgado, Julio, additional, Campo, Elías, additional, and Nadeu, Ferran, additional

Published
2023
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11. IGLV3-21R110 mutation has prognostic value in patients with treatment-naive chronic lymphocytic leukemia

Author

Fundación la Caixa, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Instituto de Salud Carlos III, European Commission, Generalitat de Catalunya, National Institutes of Health (US), National Cancer Institute (US), Centro de Investigación Biomédica en Red Cáncer (España), Ministerio de Universidades (España), Fundación Científica Asociación Española Contra el Cáncer, National Heart, Lung, and Blood Institute (US), American Association for Cancer Research, Lady Tata Memorial Trust, Institución Catalana de Investigación y Estudios Avanzados, Centro Esther Koplowitz, Syrykh, Charlotte, Pons-Brun, Berta, Russiñol, Núria, Playa-Albinyana, Heribert, Baumann, Tycho, Duran-Ferrer, Martí, Kulis, Marta, Carbó-Meix, Anna, Mozas, Pablo, Alcoceba, Miguel, González, Marcos, Navarro-Bailón, Almudena, Colado, Enrique, Payer, Ángel R., Aymerich, Marta, Terol, María J., Lu, Junyan, Knisbacher, Binyamin A., Hahn, Cynthia K., Ruiz-Gaspà, Sílvia, Enjuanes, Anna, Wu, Catherine J., Getz, Gad, Zenz, Thorsten, López-Guillermo, Armando, Martín-Subero, José I., Colomer, Dolors, Delgado, Julio, Campo, Elías, Nadeu, Ferran, Fundación la Caixa, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Instituto de Salud Carlos III, European Commission, Generalitat de Catalunya, National Institutes of Health (US), National Cancer Institute (US), Centro de Investigación Biomédica en Red Cáncer (España), Ministerio de Universidades (España), Fundación Científica Asociación Española Contra el Cáncer, National Heart, Lung, and Blood Institute (US), American Association for Cancer Research, Lady Tata Memorial Trust, Institución Catalana de Investigación y Estudios Avanzados, Centro Esther Koplowitz, Syrykh, Charlotte, Pons-Brun, Berta, Russiñol, Núria, Playa-Albinyana, Heribert, Baumann, Tycho, Duran-Ferrer, Martí, Kulis, Marta, Carbó-Meix, Anna, Mozas, Pablo, Alcoceba, Miguel, González, Marcos, Navarro-Bailón, Almudena, Colado, Enrique, Payer, Ángel R., Aymerich, Marta, Terol, María J., Lu, Junyan, Knisbacher, Binyamin A., Hahn, Cynthia K., Ruiz-Gaspà, Sílvia, Enjuanes, Anna, Wu, Catherine J., Getz, Gad, Zenz, Thorsten, López-Guillermo, Armando, Martín-Subero, José I., Colomer, Dolors, Delgado, Julio, Campo, Elías, and Nadeu, Ferran

Abstract

Chronic lymphocytic leukemia (CLL) has high biological and clinical heterogeneity.1,2 A few prognostic factors are used in clinical practice, including immunoglobulin heavy-chain variable (IGHV) gene somatic hypermutation (SHM) status, chromosome aberrations, and gene mutations, which remain insufficient for personalized patient management.3,4 Recent studies have shown that expression of the immunoglobulin lambda light chain IGLV3-21 gene carrying an SHM-derived G>C mutation changing the glycine at position 110 to an arginine (IGLV3-21R110) defines a subset of CLL with an intermediate epigenetic profile and an aggressive clinical course.5,6 When occurring on the IGLV3-21∗01 or ∗04 alleles, the R110 mutation allows homotypic B-cell receptor (BCR) interactions, triggering cell-autonomous BCR signaling5,7 and/or facilitating T-cell–independent engagement with superantigen.8 IGLV3-21R110 has been detected in up to 6.5% of patients with CLL at diagnosis and in up to 25% of patients enrolled in clinical trials.5,6,9 We6 and others5 have shown that all CLL cases belonging to aggressive stereotyped subset #2 carried the IGLV3-21R110. Nonetheless, approximately half of IGLV3-21R110 CLL are not classified as stereotyped subset #2 but seem to have a similar clinical outcome,5,6 suggesting that the conventional stereotyped subset #2 classification might not completely recognize this clinically aggressive subgroup of CLL. In addition, IGLV3-21R110 seems to have a prognostic value independent of the IGHV gene SHM status and methylation–based epigenetic subtypes.5,6 However, further studies in independent cohorts are needed to support its application in clinical practice.1,2,10-12 The aim of this study was to assess the prognostic value of IGLV3-21R110 in large and independent population-based cohorts of patients with CLL.

Published
2023

12. IGLV3-21$^{R110}$ mutation has prognostic value in patients with treatment-naive chronic lymphocytic leukemia

Author

Nadeu, Ferran; https://orcid.org/0000-0003-2910-9440, Syrykh, Charlotte, Pons-Brun, Berta, Russiñol, Núria, Playa-Albinyana, Heribert; https://orcid.org/0000-0002-3447-3848, Baumann, Tycho Stephan, Duran-Ferrer, Martí; https://orcid.org/0000-0003-1666-5819, Kulis, Marta; https://orcid.org/0000-0001-8104-9620, Carbó-Meix, Anna, Mozas, Pablo; https://orcid.org/0000-0001-9528-4971, Alcoceba, Miguel, González, Marcos; https://orcid.org/0000-0001-6637-1072, Navarro-Bailón, Almudena; https://orcid.org/0000-0002-7972-5666, Colado, Enrique, Payer, Ángel, Aymerich, Marta, Terol, María José, Lu, Junyan; https://orcid.org/0000-0002-9211-0746, Knisbacher, Binyamin Asher; https://orcid.org/0000-0002-4962-9956, Hahn, Cynthia K; https://orcid.org/0000-0001-8284-7261, Ruiz-Gaspà, Sílvia, Enjuanes, Anna, Wu, Catherine J; https://orcid.org/0000-0002-3348-5054, Getz, Gad, Zenz, Thorsten; https://orcid.org/0000-0001-7890-9845, López-Guillermo, Armando, Martin-Subero, Jose I; https://orcid.org/0000-0001-8809-5195, Colomer, Dolors, Delgado, Julio; https://orcid.org/0000-0002-5157-4376, Campo, Elías; https://orcid.org/0000-0001-9850-9793, Nadeu, Ferran; https://orcid.org/0000-0003-2910-9440, Syrykh, Charlotte, Pons-Brun, Berta, Russiñol, Núria, Playa-Albinyana, Heribert; https://orcid.org/0000-0002-3447-3848, Baumann, Tycho Stephan, Duran-Ferrer, Martí; https://orcid.org/0000-0003-1666-5819, Kulis, Marta; https://orcid.org/0000-0001-8104-9620, Carbó-Meix, Anna, Mozas, Pablo; https://orcid.org/0000-0001-9528-4971, Alcoceba, Miguel, González, Marcos; https://orcid.org/0000-0001-6637-1072, Navarro-Bailón, Almudena; https://orcid.org/0000-0002-7972-5666, Colado, Enrique, Payer, Ángel, Aymerich, Marta, Terol, María José, Lu, Junyan; https://orcid.org/0000-0002-9211-0746, Knisbacher, Binyamin Asher; https://orcid.org/0000-0002-4962-9956, Hahn, Cynthia K; https://orcid.org/0000-0001-8284-7261, Ruiz-Gaspà, Sílvia, Enjuanes, Anna, Wu, Catherine J; https://orcid.org/0000-0002-3348-5054, Getz, Gad, Zenz, Thorsten; https://orcid.org/0000-0001-7890-9845, López-Guillermo, Armando, Martin-Subero, Jose I; https://orcid.org/0000-0001-8809-5195, Colomer, Dolors, Delgado, Julio; https://orcid.org/0000-0002-5157-4376, and Campo, Elías; https://orcid.org/0000-0001-9850-9793

Published
2023

13. Data from In Vivo Modeling of CLL Transformation to Richter Syndrome Reveals Convergent Evolutionary Paths and Therapeutic Vulnerabilities

Author

ten Hacken, Elisa, primary, Sewastianik, Tomasz, primary, Yin, Shanye, primary, Hoffmann, Gabriela Brunsting, primary, Gruber, Michaela, primary, Clement, Kendell, primary, Penter, Livius, primary, Redd, Robert A., primary, Ruthen, Neil, primary, Hergalant, Sébastien, primary, Sholokhova, Alanna, primary, Fell, Geoffrey, primary, Parry, Erin M., primary, Broséus, Julien, primary, Guieze, Romain, primary, Lucas, Fabienne, primary, Hernández-Sánchez, María, primary, Baranowski, Kaitlyn, primary, Southard, Jackson, primary, Joyal, Heather, primary, Billington, Leah, primary, Regis, Fara Faye D., primary, Witten, Elizabeth, primary, Uduman, Mohamed, primary, Knisbacher, Binyamin A., primary, Li, Shuqiang, primary, Lyu, Haoxiang, primary, Vaisitti, Tiziana, primary, Deaglio, Silvia, primary, Inghirami, Giorgio, primary, Feugier, Pierre, primary, Stilgenbauer, Stephan, primary, Tausch, Eugen, primary, Davids, Matthew S., primary, Getz, Gad, primary, Livak, Kenneth J., primary, Bozic, Ivana, primary, Neuberg, Donna S., primary, Carrasco, Ruben D., primary, and Wu, Catherine J., primary

Published
2023
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14. Supplementary Figures from In Vivo Modeling of CLL Transformation to Richter Syndrome Reveals Convergent Evolutionary Paths and Therapeutic Vulnerabilities

Author

ten Hacken, Elisa, primary, Sewastianik, Tomasz, primary, Yin, Shanye, primary, Hoffmann, Gabriela Brunsting, primary, Gruber, Michaela, primary, Clement, Kendell, primary, Penter, Livius, primary, Redd, Robert A., primary, Ruthen, Neil, primary, Hergalant, Sébastien, primary, Sholokhova, Alanna, primary, Fell, Geoffrey, primary, Parry, Erin M., primary, Broséus, Julien, primary, Guieze, Romain, primary, Lucas, Fabienne, primary, Hernández-Sánchez, María, primary, Baranowski, Kaitlyn, primary, Southard, Jackson, primary, Joyal, Heather, primary, Billington, Leah, primary, Regis, Fara Faye D., primary, Witten, Elizabeth, primary, Uduman, Mohamed, primary, Knisbacher, Binyamin A., primary, Li, Shuqiang, primary, Lyu, Haoxiang, primary, Vaisitti, Tiziana, primary, Deaglio, Silvia, primary, Inghirami, Giorgio, primary, Feugier, Pierre, primary, Stilgenbauer, Stephan, primary, Tausch, Eugen, primary, Davids, Matthew S., primary, Getz, Gad, primary, Livak, Kenneth J., primary, Bozic, Ivana, primary, Neuberg, Donna S., primary, Carrasco, Ruben D., primary, and Wu, Catherine J., primary

Published
2023
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15. Supplementary Tables from In Vivo Modeling of CLL Transformation to Richter Syndrome Reveals Convergent Evolutionary Paths and Therapeutic Vulnerabilities

Author

ten Hacken, Elisa, primary, Sewastianik, Tomasz, primary, Yin, Shanye, primary, Hoffmann, Gabriela Brunsting, primary, Gruber, Michaela, primary, Clement, Kendell, primary, Penter, Livius, primary, Redd, Robert A., primary, Ruthen, Neil, primary, Hergalant, Sébastien, primary, Sholokhova, Alanna, primary, Fell, Geoffrey, primary, Parry, Erin M., primary, Broséus, Julien, primary, Guieze, Romain, primary, Lucas, Fabienne, primary, Hernández-Sánchez, María, primary, Baranowski, Kaitlyn, primary, Southard, Jackson, primary, Joyal, Heather, primary, Billington, Leah, primary, Regis, Fara Faye D., primary, Witten, Elizabeth, primary, Uduman, Mohamed, primary, Knisbacher, Binyamin A., primary, Li, Shuqiang, primary, Lyu, Haoxiang, primary, Vaisitti, Tiziana, primary, Deaglio, Silvia, primary, Inghirami, Giorgio, primary, Feugier, Pierre, primary, Stilgenbauer, Stephan, primary, Tausch, Eugen, primary, Davids, Matthew S., primary, Getz, Gad, primary, Livak, Kenneth J., primary, Bozic, Ivana, primary, Neuberg, Donna S., primary, Carrasco, Ruben D., primary, and Wu, Catherine J., primary

Published
2023
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16. In VivoModeling of CLL Transformation to Richter Syndrome Reveals Convergent Evolutionary Paths and Therapeutic Vulnerabilities

Author

ten Hacken, Elisa, primary, Sewastianik, Tomasz, additional, Yin, Shanye, additional, Hoffmann, Gabriela Brunsting, additional, Gruber, Michaela, additional, Clement, Kendell, additional, Penter, Livius, additional, Redd, Robert A., additional, Ruthen, Neil, additional, Hergalant, Sébastien, additional, Sholokhova, Alanna, additional, Fell, Geoffrey, additional, Parry, Erin M., additional, Broséus, Julien, additional, Guieze, Romain, additional, Lucas, Fabienne, additional, Hernández-Sánchez, María, additional, Baranowski, Kaitlyn, additional, Southard, Jackson, additional, Joyal, Heather, additional, Billington, Leah, additional, Regis, Fara Faye D., additional, Witten, Elizabeth, additional, Uduman, Mohamed, additional, Knisbacher, Binyamin A., additional, Li, Shuqiang, additional, Lyu, Haoxiang, additional, Vaisitti, Tiziana, additional, Deaglio, Silvia, additional, Inghirami, Giorgio, additional, Feugier, Pierre, additional, Stilgenbauer, Stephan, additional, Tausch, Eugen, additional, Davids, Matthew S., additional, Getz, Gad, additional, Livak, Kenneth J., additional, Bozic, Ivana, additional, Neuberg, Donna S., additional, Carrasco, Ruben D., additional, and Wu, Catherine J., additional

Published
2022
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17. Proteogenomic Analysis of SF3B1 mut CLL Reveals Altered Protein Signaling Cascades and Metabolomic Pathways

Author

Klaeger, Susan, primary, Tausch, Eugen, additional, Knisbacher, Binyamin A., additional, Apffel, Annie, additional, Clauser, Karl R, additional, Williams, Corinne, additional, Clish, Clary, additional, Rassenti, Laura Z., additional, Kipps, Thomas J., additional, Fischer, Kirsten, additional, Hallek, Michael, additional, Gillette, Michael A, additional, Neuberg, Donna S., additional, Getz, Gad, additional, Mani, DR, additional, Stilgenbauer, Stephan, additional, Wu, Catherine J., additional, and Carr, Steven A, additional

Published
2022
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18. Association of Clonal Hematopoiesis of Indeterminate Potential with Time to First Treatment, Incidence of Richter's Syndrome, and Overall Survival in Patients with Chronic Lymphocytic Leukemia

Author

Vijenthira, Abi, primary, Sekar, Aswin, additional, Gibson, Christopher J., additional, Martindale, Stephen P., additional, Fardoun, Rayan, additional, Tyekucheva, Svitlana, additional, Ren, Yue, additional, Fernandes, Stacey M., additional, Knisbacher, Binyamin A., additional, Hahn, Cynthia K., additional, Getz, Gad, additional, Wu, Catherine J., additional, Davids, Matthew S., additional, and Brown, Jennifer R., additional

Published
2022
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20. Prevalence of Clonal Hematopoiesis of Indeterminate Potential in Patients with Monoclonal B-Cell Lymphocytosis Compared to Untreated Chronic Lymphocytic Leukemia

Author

Patel, Anisha V., primary, Vijenthira, Abirami, additional, Sekar, Aswin, additional, Gibson, Christopher J., additional, Martindale, Stephen P., additional, Fardoun, Rayan, additional, Tyekucheva, Svitlana, additional, Fernandes, Stacey M., additional, Knisbacher, Binyamin A., additional, Hahn, Cynthia K., additional, Getz, Gad, additional, Wu, Catherine J., additional, Davids, Matthew S., additional, and Brown, Jennifer R., additional

Published
2022
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21. Evolutionary History of Transformation from Chronic Lymphocytic Leukemia to Richter Syndrome

Author

Parry, Erin Michelle, primary, Guieze, Romain, additional, Leshchiner, Ignaty, additional, Johnson, Connor, additional, Tausch, Eugen, additional, Parikh, Sameer A., additional, Lemvigh, Camilla K, additional, Broséus, Julien, additional, Hergalant, Sébastien, additional, Messer, Connor, additional, Utro, Filippo, additional, Levovitz, Chaya, additional, Rhrissorrakrai, Kahn, additional, Li, Liang, additional, Li, Shuqiang, additional, Fell, Geoffrey G, additional, Redd, Robert A., additional, Lin, Ziao, additional, Knisbacher, Binyamin A., additional, Schneider, Christof, additional, Fernandes, Stacey M., additional, Hess, Julian M., additional, Rassenti, Laura Z., additional, Kipps, Thomas J., additional, Jain, Nitin, additional, Wierda, William G., additional, Cymbalista, Florence, additional, Feugier, Pierre, additional, Kay, Neil E., additional, Livak, Kenneth J, additional, Danysh, Brian P, additional, Stewart, Chip, additional, Neuberg, Donna S., additional, Davids, Matthew S., additional, Brown, Jennifer R., additional, Parida, Laxmi, additional, Stilgenbauer, Stephan, additional, Getz, Gad, additional, and Wu, Catherine J., additional

Published
2022
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22. ZNF683 (Hobit) Marks a CD8+ T Cell Population Associated with Anti-Tumor Immunity Following Anti-PD-1 Therapy for Richter Syndrome

Author

Lemvigh, Camilla K, primary, Parry, Erin Michelle, additional, Deng, Stephanie L, additional, Dangle, Nathan J, additional, Ruthen, Neil, additional, Knisbacher, Binyamin A., additional, Broséus, Julien, additional, Hergalant, Sébastien, additional, Guieze, Romain, additional, Li, Shuqiang, additional, Yin, Shanye, additional, Huang, Teddy, additional, Livak, Kenneth J, additional, Getz, Gad, additional, Neuberg, Donna S., additional, Feugier, Pierre, additional, Kharchenko, Peter, additional, Wierda, William G., additional, Olsen, Lars Rønn, additional, Jain, Nitin, additional, and Wu, Catherine J., additional

Published
2022
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23. Abstract A13: Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome

Author

Parry, Erin M, primary, Leshchiner, Ignaty, additional, Guieze, Romain, additional, Johnson, Connor, additional, Tausch, Eugen, additional, Parikh, Sameer A, additional, Lemvigh, Camilla K, additional, Messer, Conor, additional, Utro, Filippo, additional, Levovitz, Chaya, additional, Rhrissorrakrai, Kahn, additional, Davids, Matthew S, additional, Broseus, Julien, additional, Li, Shuqiang, additional, Lin, Ziao, additional, Knisbacher, Binyamin A, additional, Schneider, Christof, additional, Rassenti, Laura Z, additional, Kipps, Thomas J, additional, Jain, Nitin, additional, Wierda, William, additional, Cymbalista, Florence, additional, Kay, Neil E, additional, Livak, Kenneth J, additional, Danysh, Brian P, additional, Stewart, Chip, additional, Neuberg, Donna, additional, Brown, Jennifer R, additional, Paridi, Laxmi, additional, Stilgenbauer, Stephan, additional, Getz, Gaddy, additional, and Wu, Catherine, additional

Published
2022
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25. Abstract 4007: Evolutionary history of transformation from chronic lymphocytic leukemia to Richter’s syndrome

Author

Parry, Erin M., primary, Leshchiner, Ignaty, additional, Guièze, Romain, additional, Johnson, Connor, additional, Tausch, Eugen, additional, Parikh, Sameer, additional, Lemvigh, Camilla, additional, Messer, Conor, additional, Rosebrock, Daniel, additional, Utro, Filippo, additional, Levovitz, Chaya, additional, Rhrissorrakrai, Kahn, additional, Davids, Matthew, additional, Jacobs, Raquel A., additional, Slowik, Kara, additional, Broseus, Julien, additional, Yin, Shanye, additional, Li, Shuqiang, additional, Fell, Geoff, additional, Lin, Ziao, additional, Knisbacher, Binyamin A., additional, Ruthen, Neil, additional, Livitz, Dimitri, additional, Schneider, Christof, additional, Ma, Jialin, additional, Hess, Julian, additional, Rassenti, Laura Z., additional, Kipps, Thomas J., additional, Jain, Nitin, additional, Wierda, William, additional, Cymbalista, Florence, additional, Kay, Neil E., additional, Livak, Kenneth J., additional, Danysh, Brian P., additional, Stewart, Chip, additional, Neuberg, Donna, additional, Brown, Jennifer R., additional, Parida, Laxmi, additional, Stilgenbauer, Stephan, additional, Getz, Gad, additional, and Wu, Catherine J., additional

Published
2022
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26. Molecular map of chronic lymphocytic leukemia and its impact on outcome

Author

Knisbacher, Binyamin A., Lin, Ziao, Hahn, Cynthia K., Nadeu, Ferran, Duran-Ferrer, Marti, Stevenson, Kristen E., Tausch, Eugen, Delgado, Julio, Barbera-Mourelle, Alex, Taylor-Weiner, Amaro, Bousquets-Munoz, Pablo, Diaz-Navarro, Ander, Dunford, Andrew, Anand, Shankara, Kretzmer, Helene, Gutierrez-Abril, Jesus, Lopez-Tamargo, Sara, Fernandes, Stacey M., Sun, Clare, Sivina, Mariela, Rassenti, Laura Z., Schneider, Christof, Li, Shuqiang, Parida, Laxmi, Meissner, Alexander, Aguet, Francois, Burger, Jan A., Wiestner, Adrian, Kipps, Thomas J., Brown, Jennifer R., Hallek, Michael, Stewart, Chip, Neuberg, Donna S., Martin-Subero, Jose, I, Puente, Xose S., Stilgenbauer, Stephan, Wu, Catherine J., Campo, Elias, Getz, Gad, Knisbacher, Binyamin A., Lin, Ziao, Hahn, Cynthia K., Nadeu, Ferran, Duran-Ferrer, Marti, Stevenson, Kristen E., Tausch, Eugen, Delgado, Julio, Barbera-Mourelle, Alex, Taylor-Weiner, Amaro, Bousquets-Munoz, Pablo, Diaz-Navarro, Ander, Dunford, Andrew, Anand, Shankara, Kretzmer, Helene, Gutierrez-Abril, Jesus, Lopez-Tamargo, Sara, Fernandes, Stacey M., Sun, Clare, Sivina, Mariela, Rassenti, Laura Z., Schneider, Christof, Li, Shuqiang, Parida, Laxmi, Meissner, Alexander, Aguet, Francois, Burger, Jan A., Wiestner, Adrian, Kipps, Thomas J., Brown, Jennifer R., Hallek, Michael, Stewart, Chip, Neuberg, Donna S., Martin-Subero, Jose, I, Puente, Xose S., Stilgenbauer, Stephan, Wu, Catherine J., Campo, Elias, and Getz, Gad

Abstract

A genomic, transcriptomic and epigenomic analysis of chronic lymphocytic leukemia identifies genetic drivers and molecular subtypes associated with clinical outcomes. Recent advances in cancer characterization have consistently revealed marked heterogeneity, impeding the completion of integrated molecular and clinical maps for each malignancy. Here, we focus on chronic lymphocytic leukemia (CLL), a B cell neoplasm with variable natural history that is conventionally categorized into two subtypes distinguished by extent of somatic mutations in the heavy-chain variable region of immunoglobulin genes (IGHV). To build the 'CLL map,' we integrated genomic, transcriptomic and epigenomic data from 1,148 patients. We identified 202 candidate genetic drivers of CLL (109 new) and refined the characterization of IGHV subtypes, which revealed distinct genomic landscapes and leukemogenic trajectories. Discovery of new gene expression subtypes further subcategorized this neoplasm and proved to be independent prognostic factors. Clinical outcomes were associated with a combination of genetic, epigenetic and gene expression features, further advancing our prognostic paradigm. Overall, this work reveals fresh insights into CLL oncogenesis and prognostication.

Published
2022

27. Proteogenomic Analysis of SF3B1mut CLL Reveals Altered Protein Signaling Cascades and Metabolomic Pathways

Author

Klaeger, Susan, Tausch, Eugen, Knisbacher, Binyamin A., Apffel, Annie, Clauser, Karl R., Williams, Corinne, Clish, Clary, Rassenti, Laura Z., Kipps, Thomas J., Fischer, Kirsten, Hallek, Michael, Gillette, Michael A., Neuberg, Donna S., Getz, Gad, Mani, Dr, Stilgenbauer, Stephan, Wu, Catherine J., Carr, Steven A., Klaeger, Susan, Tausch, Eugen, Knisbacher, Binyamin A., Apffel, Annie, Clauser, Karl R., Williams, Corinne, Clish, Clary, Rassenti, Laura Z., Kipps, Thomas J., Fischer, Kirsten, Hallek, Michael, Gillette, Michael A., Neuberg, Donna S., Getz, Gad, Mani, Dr, Stilgenbauer, Stephan, Wu, Catherine J., and Carr, Steven A.

Published
2022

29. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

Author

Ouspenskaia, Tamara, primary, Law, Travis, additional, Clauser, Karl R., additional, Klaeger, Susan, additional, Sarkizova, Siranush, additional, Aguet, François, additional, Li, Bo, additional, Christian, Elena, additional, Knisbacher, Binyamin A., additional, Le, Phuong M., additional, Hartigan, Christina R., additional, Keshishian, Hasmik, additional, Apffel, Annie, additional, Oliveira, Giacomo, additional, Zhang, Wandi, additional, Chen, Sarah, additional, Chow, Yuen Ting, additional, Ji, Zhe, additional, Jungreis, Irwin, additional, Shukla, Sachet A., additional, Justesen, Sune, additional, Bachireddy, Pavan, additional, Kellis, Manolis, additional, Getz, Gad, additional, Hacohen, Nir, additional, Keskin, Derin B., additional, Carr, Steven A., additional, Wu, Catherine J., additional, and Regev, Aviv, additional

Published
2021
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30. The CLL-1100 Project: Towards Complete Genomic Characterization and Improved Prognostics for CLL

Author

Knisbacher, Binyamin A., primary, Lin, Ziao, additional, Hahn, Cynthia K., additional, Nadeu, Ferran, additional, Duran-Ferrer, Martí, additional, Stevenson, Kristen E., additional, Tausch, Eugen, additional, Barbera-Mourelle, Alex, additional, Dunford, Andrew, additional, Anand, Shankara, additional, Delgado, Julio, additional, Hess, Julian M., additional, Taylor-Weiner, Amaro, additional, Kretzmer, Helene, additional, Bousquets Muñoz, Pablo, additional, Shaughnessy, Conner J., additional, Fernandes, Stacey M., additional, Sivina, Mariela, additional, Rassenti, Laura Z., additional, Meissner, Alexander, additional, Wiestner, Adrian, additional, Burger, Jan A., additional, Kipps, Thomas J., additional, Brown, Jennifer R, additional, Hallek, Michael, additional, Aguet, François, additional, Neuberg, Donna S., additional, Puente, Xose S, additional, Stewart, Chip, additional, Martín-Subero, José I., additional, Stilgenbauer, Stephan, additional, Wu, Catherine J., additional, Campo, Elías, additional, and Getz, Gad, additional

Published
2020
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31. RPS15 and TP53 Co-Mutation Drives B Cell Malignancy through Altered Translation and MYC Activation in a Murine Model

Author

Gutierrez, Catherine, primary, Ouspenskaia, Tamara, additional, Fu, Doris, additional, Waddicor, Peyton, additional, Biran, Anat, additional, Liani, Aviv, additional, Lazarian, Gregory, additional, Ten Hacken, Elisa, additional, Witten, Elizabeth, additional, Regis, Fara Faye, additional, Joyal, Heather, additional, Billington, Leah, additional, Lucas, Fabienne, additional, Zheng, Mei, additional, Tye, Blake, additional, Hernandez-Sanchez, Maria, additional, Quijada Álamo, Miguel, additional, Li, Shuqiang, additional, Knisbacher, Binyamin A., additional, Lin, Ziao, additional, Al'Khafaji, Aziz, additional, Wang, Lili, additional, Livak, Kenneth J., additional, Neuberg, Donna S., additional, Cymbalista, Florence, additional, Getz, Gad, additional, Churchman, Stirling, additional, Carrasco, Ruben D., additional, Shao, Sichen, additional, Regev, Aviv, additional, and Wu, Catherine J., additional

Published
2020
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32. Abstract 169: Discovery of clinically distinct CLL subgroups by integrative mapping of large-scale genetic, epigenetic, expression and clinical data

Author

Knisbacher, Binyamin A., primary, Lin, Ziao, additional, Stewart, Chip, additional, Hahn, Cynthia K., additional, Stevenson, Kristen E., additional, Neuberg, Donna S., additional, Martín-Subero, José I., additional, Puente, Xose S., additional, Campo, Elias, additional, Wu, Catherine J., additional, and Getz, Gad, additional

Published
2020
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33. Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

Author

Ouspenskaia, Tamara, primary, Law, Travis, additional, Clauser, Karl R., additional, Klaeger, Susan, additional, Sarkizova, Siranush, additional, Aguet, François, additional, Li, Bo, additional, Christian, Elena, additional, Knisbacher, Binyamin A., additional, Le, Phuong M., additional, Hartigan, Christina R., additional, Keshishian, Hasmik, additional, Apffel, Annie, additional, Oliveira, Giacomo, additional, Zhang, Wandi, additional, Chow, Yuen Ting, additional, Ji, Zhe, additional, Jungreis, Irwin, additional, Shukla, Sachet A., additional, Bachireddy, Pavan, additional, Kellis, Manolis, additional, Getz, Gad, additional, Hacohen, Nir, additional, Keskin, Derin B., additional, Carr, Steven A., additional, Wu, Catherine J., additional, and Regev, Aviv, additional

Published
2020
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36. Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-Based Genome Diversification and Multiple SINE Births and Deaths

Author

Ray, David A, primary, Grimshaw, Jenna R, additional, Halsey, Michaela K, additional, Korstian, Jennifer M, additional, Osmanski, Austin B, additional, Sullivan, Kevin A M, additional, Wolf, Kristen A, additional, Reddy, Harsith, additional, Foley, Nicole, additional, Stevens, Richard D, additional, Knisbacher, Binyamin A, additional, Levy, Orr, additional, Counterman, Brian, additional, Edelman, Nathaniel B, additional, and Mallet, James, additional

Published
2019
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37. Analysis of 19 Heliconiine Butterflies Shows Rapid TE-based Diversification and Multiple SINE Births and Deaths

Author

Ray, David A, primary, Grimshaw, Jenna R, additional, Halsey, Michaela K, additional, Korstian, Jennifer M, additional, Osmanski, Austin B, additional, Sullivan, Kevin AM, additional, Wolf, Kristen A, additional, Reddy, Harsith, additional, Foley, Nicole, additional, Stevens, Richard D, additional, Knisbacher, Binyamin, additional, Levy, Orr, additional, Counterman, Brian, additional, Edelman, Nathan B, additional, and Mallet, James, additional

Published
2019
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38. Integrating networks and comparative genomics reveals retroelement proliferation dynamics in hominid genomes

Author

Levy, Orr, Knisbacher, Binyamin A., Levanon, Erez Y., and Havlin, Shlomo

Subjects
0301 basic medicine, Retroelements, Alu element, Genomics, Minisatellite Repeats, Computational biology, Biology, Genome, Evolution, Molecular, 03 medical and health sciences, Alu Elements, Animals, Cluster Analysis, Humans, Gene, Research Articles, Comparative genomics, Genetics, Multidisciplinary, Genome, Human, Mechanism (biology), SciAdv r-articles, Life Sciences, Hominidae, 030104 developmental biology, Human genome, Haystack, Research Article
Abstract

Integrating comparative genomics and network science delineates the dynamics of retroelement activity in the genome, Retroelements (REs) are mobile DNA sequences that multiply and spread throughout genomes by a copy-and-paste mechanism. These parasitic elements are active in diverse genomes, from yeast to humans, where they promote diversity, cause disease, and accelerate evolution. Because of their high copy number and sequence similarity, studying their activity and tracking their proliferation dynamics is a challenge. It is particularly difficult to pinpoint the few REs in a genome that are still active in the haystack of degenerate and suppressed elements. We develop a computational framework based on network theory that tracks the path of RE proliferation throughout evolution. We analyze SVA (SINE-VNTR-Alu), the youngest RE family in human genomes, to understand RE dynamics across hominids. Integrating comparative genomics and network tools enables us to track the course of SVA proliferation, identify yet unknown active communities, and detect tentative “master REs” that played key roles in SVA propagation, providing strong support for the fundamental “master gene” model of RE proliferation. The method is generic and thus can be applied to REs of any of the thousands of available genomes to identify active RE communities and master REs that were pivotal in the evolution of their host genomes.

Published
2017
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41. Whole-genome sequencing reveals principles of brain retrotransposition in neurodevelopmental disorders

Author

Jacob-Hirsch, Jasmine, primary, Eyal, Eran, additional, Knisbacher, Binyamin A, additional, Roth, Jonathan, additional, Cesarkas, Karen, additional, Dor, Chen, additional, Farage-Barhom, Sarit, additional, Kunik, Vered, additional, Simon, Amos J, additional, Gal, Moran, additional, Yalon, Michal, additional, Moshitch-Moshkovitz, Sharon, additional, Tearle, Rick, additional, Constantini, Shlomi, additional, Levanon, Erez Y, additional, Amariglio, Ninette, additional, and Rechavi, Gideon, additional

Published
2018
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43. Control and automation of multilayered integrated microfluidic device fabrication

Author

Kipper, Sarit, primary, Frolov, Ludmila, additional, Guy, Ortal, additional, Pellach, Michal, additional, Glick, Yair, additional, Malichi, Asaf, additional, Knisbacher, Binyamin A., additional, Barbiro-Michaely, Efrat, additional, Avrahami, Dorit, additional, Yavets-Chen, Yehuda, additional, Levanon, Erez Y., additional, and Gerber, Doron, additional

Published
2017
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45. Correction: Corrigendum: Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax

Author

Fang, Xiaodong, primary, Nevo, Eviatar, additional, Han, Lijuan, additional, Levanon, Erez Y., additional, Zhao, Jing, additional, Avivi, Aaron, additional, Larkin, Denis, additional, Jiang, Xuanting, additional, Feranchuk, Sergey, additional, Zhu, Yabing, additional, Fishman, Alla, additional, Feng, Yue, additional, Sher, Noa, additional, Xiong, Zhiqiang, additional, Hankeln, Thomas, additional, Huang, Zhiyong, additional, Gorbunova, Vera, additional, Zhang, Lu, additional, Zhao, Wei, additional, Wildman, Derek E., additional, Xiong, Yingqi, additional, Gudkov, Andrei, additional, Zheng, Qiumei, additional, Rechavi, Gideon, additional, Liu, Sanyang, additional, Bazak, Lily, additional, Chen, Jie, additional, Knisbacher, Binyamin A., additional, Lu, Yao, additional, Shams, Imad, additional, Gajda, Krzysztof, additional, Farré, Marta, additional, Kim, Jaebum, additional, Lewin, Harris A., additional, Ma, Jian, additional, Band, Mark, additional, Bicker, Anne, additional, Kranz, Angela, additional, Mattheus, Tobias, additional, Schmidt, Hanno, additional, Seluanov, Andrei, additional, Azpurua, Jorge, additional, McGowen, Michael R., additional, Ben Jacob, Eshel, additional, Li, Kexin, additional, Peng, Shaoliang, additional, Zhu, Xiaoqian, additional, Liao, Xiangke, additional, Li, Shuaicheng, additional, Krogh, Anders, additional, Zhou, Xin, additional, Brodsky, Leonid, additional, and Wang, Jun, additional

Published
2015
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47. ZNF683(Hobit) Marks a CD8+ T Cell Population Associated with Anti-Tumor Immunity Following Anti-PD-1 Therapy for Richter Syndrome

Author

Lemvigh, Camilla K, Parry, Erin Michelle, Deng, Stephanie L, Dangle, Nathan J, Ruthen, Neil, Knisbacher, Binyamin A., Broséus, Julien, Hergalant, Sébastien, Guieze, Romain, Li, Shuqiang, Yin, Shanye, Huang, Teddy, Livak, Kenneth J, Getz, Gad, Neuberg, Donna S., Feugier, Pierre, Kharchenko, Peter, Wierda, William G., Olsen, Lars Rønn, Jain, Nitin, and Wu, Catherine J.

Published
2022
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48. Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax.

Author

Kexin Li, Liuyang Wang, Knisbacher, Binyamin A., Qinqin Xu, Levanon, Erez Y., Huihua Wang, Frenkel-Morgenstern, Milana, Tagore, Satabdi, Xiaodong Fang, Bazak, Lily, Buchumenski, Ilana, Yang Zhao, Lövyh, Matĕej, Xiangfeng Li, Lijuan Han, Frenkel, Zeev, Beiles, Avigdor, Yi Bin Cao, Zhen Long Wang, and Nevo, Eviatar

Subjects
NATURAL selection, SYMPATRIC speciation, MICRORNA, DNA, BLIND mole rats, BIOLOGICAL divergence, GENE expression
Abstract

Incipient sympatric speciation in blind mole rat, Spalax galili, in Israel, caused by sharp ecological divergence of abutting chalk- basalt ecologies, has been proposed previously based on mitochondrial and whole-genome nuclear DNA. Here, we present new evidence, including transcriptome, DNA editing, microRNA, and codon usage, substantiating earlier evidence for adaptive divergence in the abutting chalk and basalt populations. Genetic divergence, based on the previous and new evidence, is ongoing despite restricted gene flow between the two populations. The principal component analysis, neighbor-joining tree, and genetic structure analysis of the transcriptome clearly show the clustered divergent two mole rat populations. Gene-expression level analysis indicates that the population transcriptome divergence is displayed not only by soil divergence but also by sex. Gene ontology enrichment of the differentially expressed genes from the two abutting soil populations highlights reproductive isolation. Alternative splicing variation of the two abutting soil populations displays two distinct splicing patterns. L-shaped FST distribution indicates that the two populations have undergone divergence with gene flow. Transcriptome divergent genes highlight neurogenetics and nutrition characterizing the chalk population, and energetics, metabolism, musculature, and sensory perception characterizing the abutting basalt population. Remarkably, microRNAs also display divergence between the two populations. The GC content is significantly higher in chalk than in basalt, and stress-response genes mostly prefer nonoptimal codons. The multiple lines of evidence of ecological- genomic and genetic divergence highlight that natural selection overrules the gene flow between the two abutting populations, substantiating the sharp ecological chalk-basalt divergence driving sympatric speciation. [ABSTRACT FROM AUTHOR]

Published
2016
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49. DNA Editing of LTR Retrotransposons Reveals the Impact of APOBECs on Vertebrate Genomes.

Author

Knisbacher, Binyamin A. and Levanon, Erez Y.

Abstract

Long terminal repeat retrotransposons (LTR) are widespread in vertebrates and their dynamism facilitates genome evolution. However, these endogenous retroviruses (ERVs) must be restricted to maintain genomic stability. The APOBECs, a protein family that can edit C-to-U in DNA, do so by interfering with reverse transcription and hypermutating retrotransposon DNA. In some cases, a retrotransposon may integrate into the genome despite being hypermutated. Such an event introduces a unique sequence into the genome, increasing retrotransposon diversity and the probability of developing new function at the locus of insertion. The prevalence of this phenomenon and its effects on vertebrate genomes are still unclear. In this study, we screened ERV sequences in the genomes of 123 diverse species and identified hundreds of thousands of edited sites in multiple vertebrate lineages, including placental mammals, marsupials, and birds. Numerous edited ERVs carry high mutation loads, some with greater than 350 edited sites, profoundly damaging their open-reading frames. For many of the species studied, this is the first evidence that APOBECs are active players in their innate immune system. Unexpectedly, some birds and especially zebra finch and medium ground-finch (one of Darwin's finches) are exceptionally enriched in DNA editing. We demonstrate that edited retrotransposons may be preferentially retained in active genomic regions, as reflected from their enrichment in genes, exons, promoters, and transcription start sites, thereby raising the probability of their exaptation for novel function. In conclusion, DNA editing of retrotransposons by APOBECs has a substantial role in vertebrate innate immunity and may boost genome evolution. [ABSTRACT FROM AUTHOR]

Published
2016
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50. IGLV3-21R110mutation has prognostic value in patients with treatment-naive chronic lymphocytic leukemia

Author

Syrykh, Charlotte, Pons-Brun, Berta, Russiñol, Núria, Playa-Albinyana, Heribert, Baumann, Tycho, Duran-Ferrer, Martí, Kulis, Marta, Carbó-Meix, Anna, Mozas, Pablo, Alcoceba, Miguel, González, Marcos, Navarro-Bailón, Almudena, Colado, Enrique, Payer, Ángel R., Aymerich, Marta, Terol, María J., Lu, Junyan, Knisbacher, Binyamin A., Hahn, Cynthia K., Ruiz-Gaspà, Sílvia, Enjuanes, Anna, Wu, Catherine J., Getz, Gad, Zenz, Thorsten, López-Guillermo, Armando, Martín-Subero, José I., Colomer, Dolors, Delgado, Julio, Campo, Elías, and Nadeu, Ferran

Published
2023
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