Whole Exome Sequencing of Plasma Cells Precancerosis MGUS and Malignant AL Amyloidosis Reveals Small Number of Shared Mutated Genes

Background: Immunoglobulin light chain amyloidosis (ALA) is a plasma cell dyscrasia that develops, similarly as multiple myeloma (MM), from clinically indistinguishable precancerous stage, monoclonal gammopathy of undetermined significance (MGUS). The specific mutations causing malignant transformation from MGUS to amyloidogenic immunoglobulin producing ALA are still unknown. The next generation sequencing (NGS) technology is a powerful tool that allows comprehensive description of the whole genome sequence. Previous studies have already shown highly overlapping phenotypic profile between ALA and both MGUS and MM and lack of unifying mutations in ALA patients (Paiva, 2016). Here we present whole exome NGS data of aberrant plasma cells (aPCs) obtained from patients with MGUS (n=10) and ALA (n=9). Further comparison of the exome sequences of the precancerosis and malignant stage will help to identify recurrently occurring mutations, novel oncogenic drivers and tumor suppressor genes. This will offer new prognostic markers to distinguish potential malignant plasma cell clones in MGUS that will ultimately lead to the development of fatal ALA.

Aims: Revealing the mutational status of aPCs in MGUS and ALA using the whole exome NGS.

Material and methods: aPCs and peripheral blood (to exclude germinal mutations) were collected from 9 ALA and 10 MGUS samples. aPCs were separated using fluorescence activated cell sorting and genomic DNA was isolated using AllPrep DNA/RNA Micro Kit (Qiagen) and amplified with REPLI-g Mini (Qiagen). DNA library was prepared using SureSelect Human All Exon V5 Kit and sequenced on Illumina HiSeq 4000 platform with average coverage 50x. Somatic variants were called against human genome version 38 using VarScan v2.0. Only non-synonymous mutations, indels and splice site alterations were considered for further investigation.

Results: Using NGS we describe whole exome profile for 9 ALA and 10 MGUS patients. Total number of mutated genes for ALA was 554 (average 69 SNVs per patient) and for MGUS 558 (average 73 SNVs per patient). The number of shared mutated genes between both groups was only 26. Among these genes, we identified 4 functional groups: A) Killer-Cell Immunoglobulin Like Receptors (KIR2DL1, KIR3DL2), B) Mucins (MUC16, MUC3A, MUC6), C) Poly(A) Binding Cytoplasmic Proteins (PABPC1, PABPC3) and D) Serine Proteases (PRSS1, PRSS2, PRSS3). Genetic profiles in ALA and MGUS did not reveal any already known MM driver mutations (KRAS, NRAS, BRAF, FAM46C, TP53 and DIS3), with the exception of one ALA patient possessing mutated DIS3 gene. Importantly, we have observed a significant heterogeneity between the samples, as the number of mutated genes shared by all MGUS or ALA patients was only 7 and 3 genes, respectively.

Conclusions: ALA develops from a precancerous stage MGUS. Whole exome sequencing of the aPCs showed comparable number of mutated genes between both disease stages (554 vs. 558). Nevertheless, the mutated genes in both groups were very distinct. We identified only 26 mutated genes shared in both ALA and MGUS. Interestingly, none of these genes was previously linked to tumorigenesis. Moreover, genetic profiles were very heterogeneous among individual patients. Future analysis of the presented data will include comparison with genomic profiles obtained from MM plasma cells to reveal additional insights into the mechanisms of clonal plasma cells development in monoclonal gammopathies.

Acknowledgment: This work was supported by the Ministry of Health (15-29667A; DRO - FNOs/2014, DRO - FNOs/2016) and the Ministry of Education, Youth and Sports (Institutional Development Plan of University of Ostrava-IRP201550).