SMaRT M-Seq: an optimized step-by-step protocol for M protein sequencing in monoclonal gammopathies

In patients with monoclonal gammopathies, tumor B cells or plasma cells secrete a monoclonal antibody (M protein) that not only serves as a biomarker for tumor tracking but can also cause potentially life-threatening organ damage. This damage is driven by the patient-specific sequence of the M protein. Methods for sequencing M proteins have been limited by their high cost and time-consuming nature, and while recent approaches using next-generation sequencing or mass spectrometry offer advancements, they may require tumor cell sorting, are limited to subsets of immunoglobulin genes or patients, and/or lack extensive validation. To address these limitations, we have recently developed a novel method, termed Single Molecule Real-Time Sequencing of the M protein (SMaRT M-Seq), which combines the unbiased amplification of expressed immunoglobulin genes via inverse PCR from circularized cDNA with long-read DNA sequencing, followed by bioinformatic and immunogenetic analyses. This approach enables the unambiguous identification of full-length variable sequences of M protein genes across diverse patient cohorts, including those with low tumor burden. Our protocol has undergone technical validation and has been successfully applied to large patient cohorts with monoclonal gammopathies. Here we present the step-by-step protocol for SMaRT M-Seq. By enabling the parallel sequencing of M proteins from a large number of samples in a cost-effective and time-efficient manner, SMaRT M-Seq facilitates access to patient-specific M protein sequences, advancing personalized medicine approaches and enabling deeper mechanistic studies in monoclonal gammopathies.