The Number of Overlapping AID Hotspots in Germline IGHV Genes Is Inversely Correlated with Mutation Frequency in Chronic Lymphocytic Leukemia

Abstract

The targeting of mutations by Activation-Induced Deaminase (AID) is a key step in generating antibody diversity at the Immunoglobulin (Ig) loci but is also implicated in B-cell malignancies such as chronic lymphocytic leukemia (CLL). AID has previously been shown to preferentially deaminate WRC (W = A/T, R = A/G) hotspots. WGCW sites, which contain an overlapping WRC hotspot on both DNA strands, mutate at much higher frequency than single hotspots. Human Ig heavy chain (IGHV) genes differ in terms of WGCW numbers, ranging from 4 for IGHV3-48*03 to as many as 12 in IGHV1-69*01. An absence of V-region mutations in CLL patients (“IGHV unmutated”, or U-CLL) is associated with a poorer prognosis compared to “IGHV mutated” (M-CLL) patients. The reasons for this difference are still unclear, but it has been noted that particular IGHV genes associate with U-CLL vs M-CLL. For example, patients with IGHV1-69 clones tend to be U-CLL with a poor prognosis, whereas patients with IGHV3-30 tend to be M-CLL and have a better prognosis. Another distinctive feature of CLL is that ~30% of (mostly poor prognosis) patients can be classified into “stereotyped” subsets, each defined by HCDR3 similarity, suggesting selection, possibly for a self-antigen. We analyzed >1000 IGHV genes from CLL patients and found a highly significant statistical relationship between the number of WGCW hotspots in the germline V-region and the observed mutation frequency in patients. However, paradoxically, this correlation was inverse, with V-regions with more WGCW hotspots being less likely to be mutated, i.e., more likely to be U-CLL. The number of WGCW hotspots in particular, are more strongly correlated with mutation frequency than either non-overlapping (WRC) hotspots or more general models of mutability derived from somatic hypermutation data. Furthermore, this correlation is not observed in sequences from the B cell repertoires of normal individuals and those with autoimmune diseases.

An MPER antibody neutralizes HIV-1 using germline features shared among donors

“…Fortunately, the SHM-reverted PGZL1 gVmDmJ antibody neutralized up to 28% of viruses tested, albeit mostly with limited potency; many somatic mutations in 4E10 and 10E8 are also non-essential 18,19 . V H 1-69 is also highly mutable due to several SHM hotspots 36 . V H 1-69 has been associated with autoantibodies of leukemia 36 , HCV-associated mixed cryoglobulinemia 37 , as well as bnAbs highly specific to the influenza hemagglutinin stem 38 and HCV E2 39 .…”

“…V H 1-69 is also highly mutable due to several SHM hotspots 36 . V H 1-69 has been associated with autoantibodies of leukemia 36 , HCV-associated mixed cryoglobulinemia 37 , as well as bnAbs highly specific to the influenza hemagglutinin stem 38 and HCV E2 39 . Thus, any vaccine strategy to elicit V H 1-69 MPER bnAbs must be MPER specific and avoid or limit activation of off-target B cells.…”

AID in Chronic Lymphocytic Leukemia: Induction and Action During Disease Progression

“…Because overlapping AID hotspots are critical sites for V region diversification ( 61 ) and key evolutionary components of human IgHV genes ( 62 ), Yuan et al analyzed those IgHVs most used in CLL patients and in the clinically relevant U-CLL and M-CLL subgroups for such hotspots ( 180 ). This revealed a highly significant, but surprisingly inverse relationship between the number of WGCW hotspots in the germline IgHV and the observed mutation frequency in patients.…”

Evidence of somatic hypermutation in the antigen binding sites of patients with CLL harboring IGHV genes with 100% germline identity

“…Similar to normal B cells ( 37 ), SHM in CLL preferentially clusters within certain hotspot motifs which represent targets of the AID enzyme ( 38 ). Of note, all VH CDR3 nucleotide changes identified in subset #1 as well as the respective changes in the subclonal variants of subset #6 patients were located at a/t sites adjacently to AID hotspots, consistent with a non-canonical SHM mechanism ( 39 ).…”