Identification of Light Chain Amyloidosis-Associated Single Nucleotide Variants in Japanese People
Authors: Nakamura Shingen , Sato Youichi , Maeda Yusaku , Sumitani Ryohei , Oura Masahiro , Sogabe Kimiko , Yagi Hikaru , Fujii Shiro , Harada Takeshi , Abe Masahiro , Miki Hirokazu , Matsuoka Ken-ichi 
Published: December 2024

Background: Light chain (AL) amyloidosis is a plasma cell dyscrasia in which insoluble fibrils derived from misfolded paraprotein deposit in various organs, causing organ failures. AL amyloidosis develops due to an imbalance between the production and clearance of amyloidogenic proteins. The association of gene mutations in variable regions of immunoglobulin with misfolding of unstable proteins has been studied. However, the mechanisms underlying the degradation or clearance of amyloidogenic proteins and their related genetic factors remains largely unknown.
Aim: To identify single nucleotide variants (SNVs) common in patients with AL amyloidosis while rare in the general population.
Methods: Whole exome sequencing was performed using the illumina NovaSeq6000 platform for DNA isolated from peripheral blood mononuclear cells of patients with AL amyloidosis at Tokushima University Hospital. Genome mapping to the human reference genome (GRCh38) was performed using Burrows-Wheeler Alignment (ver. bwa-0.7.17) and duplicate reads were removed using Picard (ver. picard-tools-2.18.2-SNAPSHOT). The single nucleotide polymorphism database, dbSNP ver. 151, was used, variant calling was performed using the Genome Analysis Toolkit (ver. 4.0.5.1), and annotation was performed using SnpEff (ver. 4.3t2017-11-24). After excluding intron variants, SNVs common in amyloidosis with a frequency ≤ 1% in the 1,000-genome South Asian subset were extracted. Fisher's exact test was performed to compare the significance of allele frequencies in the Japanese Multi Omics Reference Panel, ToMMo 54KJPN-SNV/INDEL Allele Frequency Panel (v20230626r3). This study was approved by the review board of the Tokushima University Ethics Committee (approval No. 4301).
Results: Eleven patients with AL amyloidosis were examined and SNVs common in patients with amyloidosis and rare in the general population, such as MIR3675-LOC105376 (rs150815118, p=2.57 × 10−43; rs139655267, p=1.44 × 10-41), ANKRD36B (rs71427057, p=1.98 × 10-24), MIR4477A-FAM27E2 (rs62549177, p=1.09 × 10-27), AQP7P1-MIR4477A (rs80226612,p=8.45×10-33), and FAM104B (rs1047042, p=1.95×10-42) were identified. HLA-C (rs1050686, p=2.02×10-34; rs1050685, p=4.26 × 10-34) and POTED (rs2334600, p=9.23 × 10-22) were observed as common variants in 10 of 11 patients.
Discussion and conclusion: Patients with AL amyloidosis have SNVs in common. MicroRNAs are associated with the regulation of various genes. FAM104B protein is ubiquitously expressed in the nucleus and its mutation may affect protein transport. POTED protein is known as one of the cancer/testis antigens, and HLA-C is also an important factor for antigen recognition, therefore these factors may affect amyloid recognition by immune cells in cells with amyloid-deposits. These genetic bases may contribute to the development and pathophysiology of AL amyloidosis.