Identification, assembly and characterization of tumor immunoglobulin transcripts from RNA sequencing data using IgSeqR

Lam, K. P., Kuhn, R. & Rajewsky, K. In vivo ablation of surface immunoglobulin on mature B cells by inducible gene targeting results in rapid cell death. Cell 90, 1073–1083 (1997).

Article  CAS  PubMed  Google Scholar 

Stevenson, F. K. et al. The occurrence and significance of V gene mutations in B cell-derived human malignancy. Adv. Cancer Res. 83, 81–116 (2001).

Article  CAS  PubMed  Google Scholar 

Victora, G. D. & Nussenzweig, M. C. Germinal centers. Annu. Rev. Immunol. 40, 413–442 (2022).

Article  CAS  PubMed  Google Scholar 

Forconi, F., Lanham, S. A. & Chiodin, G. Biological and clinical insight from analysis of the tumor B-cell receptor structure and function in chronic lymphocytic leukemia. Cancers 14, 663 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stevenson, F. K., Forconi, F. & Kipps, T. J. Exploring the pathways to chronic lymphocytic leukemia. Blood 138, 827–835 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Efremov, D. G., Turkalj, S. & Laurenti, L. Mechanisms of B cell receptor activation and responses to B cell receptor inhibitors in B cell malignancies. Cancers 12, 1396 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Forconi, F. et al. The normal IGHV1-69-derived B-cell repertoire contains stereotypic patterns characteristic of unmutated CLL. Blood 115, 71–77 (2010).

Article  CAS  PubMed  Google Scholar 

Seifert, M. et al. Cellular origin and pathophysiology of chronic lymphocytic leukemia. J. Exp. Med. 209, 2183–2198 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Damle, R. N. et al. Ig V gene mutation status and CD38 expression as novel prognostic indicators in chronic lymphocytic leukemia. Blood 94, 1840–1847 (1999).

Article  CAS  PubMed  Google Scholar 

Hamblin, T. J., Davis, Z., Gardiner, A., Oscier, D. G. & Stevenson, F. K. Unmutated Ig VH genes are associated with a more aggressive form of chronic lymphocytic leukemia. Blood 94, 1848–1854 (1999).

Article  CAS  PubMed  Google Scholar 

Niemann, C. U. et al. Fixed-duration ibrutinib–venetoclax versus chlorambucil–obinutuzumab in previously untreated chronic lymphocytic leukaemia (GLOW): 4-year follow-up from a multicentre, open-label, randomised, phase 3 trial. Lancet Oncol. 24, 1423–1433 (2023).

Article  CAS  PubMed  Google Scholar 

Stevenson, F. K. & Forconi, F. The essential microenvironmental role of oligomannoses inserted into the antigen-binding sites of lymphoma cells. Blood 143, 1091–1100 (2023).

Article  Google Scholar 

Zhu, D. et al. Acquisition of potential N-glycosylation sites in the immunoglobulin variable region by somatic mutation is a distinctive feature of follicular lymphoma. Blood 99, 2562–2568 (2002).

Article  CAS  PubMed  Google Scholar 

Chiodin, G. et al. Insertion of atypical glycans into the tumor antigen-binding site identifies DLBCLs with distinct origin and behavior. Blood 138, 1570–1582 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Coelho, V. et al. Glycosylation of surface Ig creates a functional bridge between human follicular lymphoma and microenvironmental lectins. Proc. Natl Acad. Sci. USA 107, 18587–18592 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Linley, A. et al. Lectin binding to surface Ig variable regions provides a universal persistent activating signal for follicular lymphoma cells. Blood 126, 1902–1910 (2015).

Article  CAS  PubMed  Google Scholar 

Odabashian, M. et al. IGHV sequencing reveals acquired N-glycosylation sites as a clonal and stable event during follicular lymphoma evolution. Blood 135, 834–844 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sutton, L. A. et al. Immunoglobulin genes in chronic lymphocytic leukemia: key to understanding the disease and improving risk stratification. Haematologica 102, 968–971 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schmitz, R. et al. Genetics and pathogenesis of diffuse large B-cell lymphoma. N. Engl. J. Med. 378, 1396–1407 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wright, G. W. et al. A probabilistic classification tool for genetic subtypes of diffuse large B cell lymphoma with therapeutic implications. Cancer Cell 37, 551–568.e14 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bryant, D. et al. Network analysis reveals a major role for 14q32 cluster miRNAs in determining transcriptional differences between IGHV-mutated and unmutated CLL. Leukemia 37, 1454–1463 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Forconi, F. et al. Insight into the potential for DNA idiotypic fusion vaccines designed for patients by analysing xenogeneic anti-idiotypic antibody responses. Immunology 107, 39–45 (2002).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stevenson, G. T., Elliott, E. V. & Stevenson, F. K. Idiotypic determinants on the surface immunoglobulin of neoplastic lymphocytes: a therapeutic target. Fed. Proc. 36, 2268–2271 (1977).

CAS  PubMed  Google Scholar 

Hawkins, R. E. et al. Idiotypic vaccination against human B-cell lymphoma. Rescue of variable region gene sequences from biopsy material for assembly as single-chain Fv personal vaccines. Blood 83, 3279–3288 (1994).

Article  CAS  PubMed  Google Scholar 

Haas, B. J. et al. Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome Biol. 20, 213 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Forconi, F. et al. Tumor cells of hairy cell leukemia express multiple clonally related immunoglobulin isotypes via RNA splicing. Blood 98, 1174–1181 (2001).

Article  CAS  PubMed  Google Scholar 

D’Avola, A. et al. Surface IgM expression and function are associated with clinical behavior, genetic abnormalities, and DNA methylation in CLL. Blood 128, 816–826 (2016).

Article  PubMed  Google Scholar 

Wasim, L. et al. Mutations in the IgG B cell receptor associated with class-switched B cell lymphomas. Preprint at https://www.biorxiv.org/content/10.1101/2024.04.12.585865v2 (2024).

McCann, K., Sahota, S. S., Stevenson, F. K. & Ottensmeier, C. H. Idiotype gene rescue in follicular lymphoma. Methods Mol. Med. 115, 145–171 (2005).

CAS  PubMed  Google Scholar 

Ottensmeier, C. H. & Stevenson, F. K. Isotype switch variants reveal clonally related subpopulations in diffuse large B-cell lymphoma. Blood 96, 2550–2556 (2000).

Article  CAS  PubMed 

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