Research Papers:

A systematic approach for peptide characterization of B-cell receptor in chronic lymphocytic leukemia cells

Paula Díez, Nieves Ibarrola, Rosa M. Dégano, Quentin Lécrevisse, Arancha Rodriguez-Caballero, Ignacio Criado, Wendy G. Nieto, Rafael Góngora, Marcos González, Julia Almeida, Alberto Orfao and Manuel Fuentes _

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Oncotarget. 2017; 8:42836-42846. https://doi.org/10.18632/oncotarget.17076

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Paula Díez1,2, Nieves Ibarrola2, Rosa M. Dégano2, Quentin Lécrevisse1, Arancha Rodriguez-Caballero1, Ignacio Criado1, Wendy G. Nieto1, Rafael Góngora1, Marcos González3, Julia Almeida1, Alberto Orfao1 and Manuel Fuentes1,2

1Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain

2Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain

3Hematology Service, Institute of Biomedical Research of Salamanca, University Hospital of Salamanca, Cancer Research and Institute of Molecular Biology and Cellular Oncology, 37007 Salamanca, Spain

Correspondence to:

Manuel Fuentes, email: [email protected]

Keywords: B-cell receptor, chronic lymphocytic leukemia, immunoglobulin, mass spectrometry, peptide sequencing

Received: December 22, 2016     Accepted: March 22, 2017     Published: April 13, 2017


A wide variety of immunoglobulins (Ig) is produced by the immune system thanks to different mechanisms (V(D)J recombination, somatic hypermutation, and antigen selection). The profiling of Ig sequences (at both DNA and peptide levels) are of great relevance to developing targeted vaccines or treatments for specific diseases or infections. Thus, genomics and proteomics techniques (such as Next-Generation Sequencing (NGS) and mass spectrometry (MS)) have notably increased the knowledge in Ig sequencing and serum Ig peptide profiling in a high-throughput manner. However, the peptide characterization of membrane-bound Ig (e.g., B-cell receptors, BCR) is still a challenge mainly due to the poor recovery of mentioned Ig.

Herein, we have evaluated three different sample processing methods for peptide sequencing of BCR belonging to chronic lymphocytic leukemia (CLL) B cells identifying up to 426 different peptide sequences (MS/MS data are available via ProteomeXchange with identifier PXD004466). Moreover, as a consequence of the results here obtained, recommended guidelines have been described for BCR-sequencing of B-CLL samples by MS approaches.

For this purpose, an in–house algorithm has been designed and developed to compare the MS/MS results with those obtained by molecular biology in order to integrate both proteomics and genomics results and establish the steps to follow when sequencing membrane-bound Ig by MS/MS.

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