Immunoglobulin repertoire sequencing and de novo sequencing – Powerful tools for identifying free light chains from patients with light chain cast nephropathy
peer-reviewed · International Immunopharmacology · 2024
| Date | 2024-06-01 |
| Type | peer-reviewed |
| Venue | International Immunopharmacology |
| Publisher | Elsevier BV |
| Contribution | downstream-application |
| DOI | 10.1016/j.intimp.2024.112302 |
| Citations (OpenAlex) | 1 |
Abstract
In patients with light chain cast nephropathy (LCCN), abundantly produced monoclonal immunoglobulin free light chains (FLCs) play a vital role in pathogenesis. Determining the precise sequences of patient-derived FLCs is therefore highly desirable. Although immunoglobulin repertoire sequencing (5’ RACE-seq) has been proven to be sensitive enough to provide full-length V(D)J region (variable, diversity and joining genes) of FLCs using bone marrow samples, an invasive and bone marrow independent method is still in demand. Here a de novo sequencing workflow based on the bottom-up proteomics for patient-derived FLCs was established. PEAKS software was used for the de novo sequencing of peptides that were further assembled into full-length FLC sequences. This de novo protein sequencing method can obtain the full-length amino acid sequences of FLCs, and had been shown to be as reliable as 5’ RACE-seq. The two LCCN sequences derived from above the two methods were identical, and they possessed more hydrophobic or nonpolar amino acids compared with the corresponding germline, which may be associated with the pathogenesis.
Methods and tools
- Light chain cast nephropathy FLC sequencing: Bottom-up de novo workflow with PEAKS and assembly that recovers full-length monoclonal free light chain sequences from patients with light chain cast nephropathy, identical to repertoire sequencing.
Methods it uses
- PEAKS: Commercial DP-based de novo