Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V’DJer

Abstract

Motivation: B-cell receptor (BCR) repertoire profiling is an important tool for understanding the biology of diverse immunologic processes. Current methods for analyzing adaptive immune receptor repertoires depend upon PCR amplification of VDJ rearrangements followed by long read amplicon sequencing spanning the VDJ junctions. While this approach has proven to be effective, it is frequently not feasible due to cost or limited sample material. Additionally, there are many existing datasets where short-read RNA sequencing data are available but PCR amplified BCR data are not.Results: We present here V’DJer, an assembly-based method that reconstructs adaptive immune receptor repertoires from short-read RNA sequencing data. This method captures expressed BCR loci from a standard RNA-seq assay. We applied this method to 473 Melanoma samples from The Cancer Genome Atlas and demonstrate V’DJer’s ability to accurately reconstruct BCR repertoires from short read mRNA-seq data.Availability and Implementation: V’DJer is implemented in C/C ++, freely available for academic use and can be downloaded from Github: https://github.com/mozack/vdjerContact: benjamin_vincent@med.unc.edu or parkerjs@email.unc.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Antigen receptor repertoire profiling from RNA-seq data

“…We also compared MiXCR with V’DJer software 16 for the extraction of Ig repertoires. For some samples (including large SPX6730 and SPX8151 RNA-seq datasets) V’DJer failed to extract Ig heavy chain (IGH) and light chains (IGL, IGK) repertoires within four days using 8 threads on a Xeon E5–2683 CPU with 50 GB of RAM.…”

A B cell-derived gene expression signature associates with an immunologically active tumor microenvironment and response to immune checkpoint blockade therapy

“…BCR abundance has previously been associated with melanoma patient survival in TCGA. 20 Thus, we tested this association, and how well BCR abundance associated with immune checkpoint inhibitor response, in the anti-PD-1 and anti-CTLA-4 datasets. While no significant associations were observed in the anti-PD-1 dataset (Supplementary Figure S7), BCR heavy chain abundance was associated with clinical benefit (P = 0.02; Figure 4B) and prolonged patient survival (P = 0.05; Figure 4C) in the anti-CTLA-4 dataset.

10.1080/2162402X.2018.1513440-F0004Figure 4.Relationship between B cell receptor expression, MBL score, and response and survival following anti-CTLA-4 therapy in melanoma.

…”

“…29 V’DJer with default settings was then run on the aligned files to infer each patient’s BCR heavy chain (IGH) repertoire. 20 V’DJer was initially unable to process some samples in the anti-PD-1 dataset as they contained reads of variable length. To address this, each sample in the anti-PD-1 dataset was filtered to only contain reads of 100 base pairs before being input into V’DJer.…”

Applications of Immunogenomics to Cancer

“…Computational methods have been developed to directly infer immune repertoires from unselected bulk tumor RNAseq data, such as TRUST for TCR (Li et al, 2016a) and V’DJer for BCR (Mose et al, 2016). The hypervariability of the CDR3 regions of TCR and BCR renders the RNAseq reads from these regions unmappable to the human reference genome sequence, and somatic hypermutation adds additional challenges to BCR mapping and alignment.…”

“…Although these approaches only recover the most abundant of the immune repertoires, they were used to analyze RNA-seq data across tumor samples profiled by The Cancer Genome Atlas (TCGA) and resulted in novel findings. For example, TRUST revealed increased T cell clonal diversity in tumor types with higher mutational loads and potential neoantigens based on their co-occurrence with CDR3-containing sequences in the tumors (Li et al, 2016a), while V’DJer reported higher somatic hypermutation in IgG and IgA than in IgM (Mose et al, 2016). …”