3.1 Variants likely associated with CVID
Firstly, subtractive analysis of the variant call files between the affected and unaffected family members was carried out using recessive and dominant models according to the law of Mendelian inheritance. The two models respectively revealed 41 and 9 variants but none were predicted to have a deleterious effect on protein function according to SIFT, PolyPhen-2, Mutation-Taster, or CADD.
Then we filtered out 1845 nonsynonymous SNVs from 3401 variants shared by the twins. Among them, 675 rare variants (MAF < 0.01) were screened out in 1000 Genomes database. 398 candidate variants (heterozygous) were predicted to be deleterious based on criteria with CADD score over than 10. But no previously published monogenic CVID variants were identified. Systematic assessment of bioinformatical predictions, published literature, gene annotation and the clinical and immunological phenotype of CVID, reduced the list to seven candidate variants have been reported to confer susceptibility to the disease or to originate similar phenotypes to CVID. The bioinformatics analysis process is shown in Fig. 1c. Among them, VDR (Vitamin D receptor, c.71C > A), NHEJ1 (DNA non-homologous end-joining factor 1, c.475A > G), DOCK5 (dedicator of cytokinesis-5, c.824A > G) and NOD2 (nucleotide-binding oligomerization domain 2, c.1330C > T and c.1411C > T) were inherited from mother. C3 (complement 3, c.2851C > T and c.1940C > T) were inherited from father (detailed in Table 2).
Table 2
Candidate genes associated with CVID pathogenesis
Gene | Chr | mRNA.refGene | Coding change | Protein change | SIFT/PolyPhen-2/Mutation-Taster/CADD∗ | From | ACMG |
VDR | chr12 | NM_001017536: exon2 | c.71C > A | p.A24D | D/B/N/10.85 | mother | U(PM1 + PM2 + PP2) |
NHEJ1 | chr2 | NM_024782: exon4 | c.475A > G | p.M159V | T/B/N/12.56 | mother | U(PM2) |
DOCK5 | chr8 | NM_024940: exon9 | c.824A > G | p.N275S | T/P/D/16.13 | mother | U |
NOD2 | chr16 | NM_001293557: exon3 | c.1330C > T | p.R444C | T/B/N/11.12 | mother | B(PM1 + BS1 + BS2 + BP4) |
NOD2 | chr16 | NM_022162: exon4 | c.1411C > T | p.R471C | T/B/N/11.12 | mother | B(PM1 + BS1 + BS2 + BP4) |
C3 | chr19 | NM_000064: exon22 | c.2851C > T | p.R951C | D/D/N/20.8 | father | U(PP2) |
C3 | chr19 | NM_000064: exon15 | c.1940C > T | p.T647M | D/P/N/15.23 | father | U(PM2 + PP2) |
∗ Using SIFT, PolyPhen-2, MutationTaster, and CADD to predict deleterious SNVs. SIFT (T, tolerated; D, deleterious); PolyPhen-2 (D, probably damaging; P, possibly damaging; B, benign); Mutation-Taster (D, disease-causing; N, polymorphism); CADD (score > 10 implied deleterious variations); ACMG (U, uncertain significance; B, benign; PM1-6, pathogenic moderate; PP1-5, pathogenic supporting; BS1-4, benign strong; BP1-6, benign supporting.) |
3.2 VDR deficiency
Results of Sanger sequencing identified the heterozygous VDR mutation (chr12-48276554: G/T, NM_001017536: exon2: c.71C > A: p.A24D) in the twins and their mother (Fig. 2a). The expression of VDR gene after mutation was significantly lower than that of father’s wild type (Fig. 2b). The p.24 mutation was located at the DNA-binding domain (DBD) (Fig. 2c). The DBD is organized into two zinc-nucleated modules, which called as vitamin D-responsive elements (VDREs). Mutations in DBD would result in defective DNA binding and the most severe clinical phenotypes of vitamin D resistance. Through online prediction, we found that the mutant amino introduces a charge, which can cause repulsion of ligands or other residues with the same charge. The mutant residue is bigger than the wild-type and might lead to bumps. The hydrophobicity of the mutant residue will be lost, either in the core of the protein or on the surface (Fig. 2d).
VDR and Vitamin D play an important role in the innate immune system and modulate Toll-like receptor-related responses [11]. VDR can affect immune information transmission and B cell activation by affecting calcium ions [12]. Ardeniz [13] found that VDR expression in patients with CVID were lower in the peripheral blood mononuclear cells and hair follicles when compared to the healthy group. Apparently, VDR also affects bone metabolism. We speculate that osteoporosis symptoms in the twins are associated with VDR mutations. Their increased serum ALP may confirm the association.
3.3 NHEJ1 deficiency
Heterozygous mutation of NHEJ1 (chr2-220012433: T/C, NM_024782: exon4: c.475A > G, p.M159V) occurred in the twins and their mother (Fig. 2e). The expression of mutant NHEJ1 was significantly lower than that of the father’s wild type (Fig. 2f). Analysis by the HOPE software suggested that the mutant residue is smaller than the wild-type (Fig. 2g). This will cause a possible loss of external interactions. The mild mutation should not cause misfolding of the protein, but the extra acquired Valine may lead to greater hydrophobicity and may change the interaction between the protein and the corresponding protein (Fig. 2h).
CVID associated with defective DNA double-strand breaks (DNA-DSBs) repair [14]. NHEJ1 mediates the predominant pathway in DSB repair in mammalians, especially during V(D)J recombination. V(D)J recombination defects will block differentiation of T and B cells, then lead to immune deficiency in patients [15]. So, we speculate that the NHEJ1 mutation may be involved in the pathogenesis of the twins.
3.4 NOD2 deficiency
NOD2 has been reported to be a possible disease modifying polymorphism in CVID [16]. NOD2 was initially observed for its role in the inflammatory bowel condition Crohn’s disease and NOD2-RIP2/NF-κB signaling activation [17]. Watery diarrhea is one of the classic hallmarks of Crohn’s disease. NF-κB signaling has a vital role in B and T cell activation and development. Thus, we supposed that NOD2 variant may be related to the CVID twins and the clinical manifestation of diarrhea.
3.5 DOCK5 deficiency
As an atypical guanine nucleotide exchange factor, DOCK5 has been extensively studied in cellular functions. Chen [18] has shown that DOCK5 regulates the peripheral B cell differentiation via controlling the CD19-BTK signaling axis as well as actin reorganization through a DOCK5 knockout mouse model. The variant of c.824A > G is novel and has not been reported before. It may be a harmful change through the prediction of PolyPhen-2, Mutation-Taster and CADD.
3.6 C3 deficiency
The complement system and Toll-like receptors (TLRs) are key elements of innate defense mechanisms [19]. B lymphocytes express both TLRs and complement receptors (CRs) [20]. Simultaneous or sequential engagement of these structures expressed either on the cell membrane or intracellularly, may fundamentally alter and fine tune activation, antibody and cytokine production of B cells. Activation products of the complement system, particularly C3-derived fragments, play an important role in the regulation of B cell responses by binding to their corresponding receptors [21–23]. In our case, C3 variants (c.2851C > T and c.1940C > T) may be harmful changes through the prediction of SIFT, PolyPhen-2 and CADD.
3.7 Acquired pure red cell aplasia
CVID is prone to autoimmune thrombocytopenia, hemolytic anemia and other hematological disorders [24]. As for immunosuppressive agent, cyclosporine shows effective to granulomatous diseases [25] and non-infection diarrhea in CVID patients by suppressing abnormal activation of B cells and T cells [26]. Cyclosporine also has a rapid control effect on our proband regarded as PRCA associated CVID. After 5-month’s treatment with cyclosporine, the patient was relieved. This is different from the case Sklarz T. [27] reported that a female was diagnosed with CVID at her 12 years’ old. When she was 48 years’ old, she was notable for a low reticulocyte count and a hypocellular marrow with an absence of erythroid precursors, consistent with acquired red cell aplasia. However, she was treated with cyclosporine without response and eventually progressed to aplastic anemia at her 50’s. The pathogenesis of PRCA happened in CVID is unrevealed, but the phenomenon implies that lack of antibody responses may lead to aberrant cytotoxic T lymphocyte (CTL) responses with cross-reactivity directed to red cell precursors [28].