CDR3 sequencing of circulating memory B cells from metastatic melanoma patients for B cell receptor repertoire analysis

By examining the B-cell receptor (BCR) repertoire of metastatic melanoma (MM) patients with favorable treatment outcomes, it is now possible to identify unique patterns of immune responses, with the potential of discovering novel antitumor antibodies. As a result of our study (doi: 10.3389/fimmu.2025.1636722), upon immunotherapy stimulation in responder patients, we observed that some complementarity-determining region 3 (CDR3) clonotypes have emerged de novo. Among the nine candidate antibodies we assessed, two antibodies exhibited encouraging tumor-targeting properties, although they also showed a degree of cross-reactivity with normal skin and melanocytes.The Dataset includes sequencing of IgG-specific (folder: IgG CDR3 BCR sequencing) and isotype-unspecific IgH CDR3 regions (folder: IgH CDR3 BCR sequencing) was performed on an Illumina MiSeq platform using a 150 bp paired-end protocol. Immune repertoires were extracted using MiXCR (MiLaboratories Inc, USA), a software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling. Analysis and graphical processing of the data generated by MiXCR were then conducted with the VDJviz software, as previously described. The final output consists of a list of CDR3 sequences from all samples, including sample-specific information such as Reads, Diversity, Mean Clonotype Frequency and Mean CDR3 Length. It also provides sequence-specific details, including the nucleotide and amino acid sequences of the CDR3 region, Frequency (%), Counts, and the identified Variable, Diversity, and Joining segments.The file name consists of a number (1, 3, 4, 7, 8, or 9) representing the patient code, followed by "pre" or "post" indicating pre-therapy or post-therapy, then "rep1" or "rep2" indicating whether it is replicate 1 or 2, "IGG" or "IGH" indicating sequencing of either IGG-specific or IGH CDR3 regions, and a sequential number starting with "S." For example, "9-pre-rep2-IGG_S22" refers to patient 9, pre-therapy, replicate 2, IGG-specific CDR3 sequencing.