Great genotypic and phenotypic diversities associated with copy-number variations of complement C4 and RP-C4-CYP21-TNX (RCCX) modules: A comparison of Asian-Indian and European American populations

Abstract

Inter-individual gene copy-number variations (CNVs) probably afford human populations the flexibility to respond to a variety of environmental challenges, but also lead to differential disease predispositions. We investigated gene CNVs for complement component C4 and steroid 21-hydroxylase from the RP-C4-CYP21-TNX (RCCX) modules located in the major histocompatibility complex among healthy Asian-Indian Americans (AIA) and compared them to European Americans. A combination of definitive techniques that yielded cross-confirmatory results was used. The medium gene copy-numbers for C4 and its isotypes, acidic C4A and basic C4B, were 4, 2 and 2, respectively, but their frequencies were only 53-56%. The distribution patterns for total C4 and C4A are skewed towards the high copy-number side. For example, the frequency of AIA-subjects with three copies of C4A (30.7%) was 3.92-fold of those with a single copy (7.83%). The monomodular-short haplotype with a single C4B gene and the absence of C4A, which is in linkage-disequilibrium with HLA DRB1*0301 in Europeans and a strong risk factor for autoimmune diseases, has a frequency of 0.012 in AIA but 0.106 among healthy European Americans (p=6.6×10 −8 ). The copy-number and the size of C4 genes strongly determine the plasma C4 protein concentrations. Parallel variations in copy-numbers of CYP21A (CYP21A1P) and TNXA with total C4 were also observed. Notably, 13.1% of AIA-subjects had three copies of the functional CYP21B, which were likely generated by recombinations between monomodular and bimodular RCCX haplotypes. The high copy-numbers of C4 and the high frequency of RCCX recombinants offer important insights to the prevalence of autoimmune and genetic diseases.

Fine-tuned characterization of RCCX copy number variants and their relationship with extended MHC haplotypes

“…15 Former investigations have shed light on the existence of seven frequent and several rare RCCX variants with regard to the number and length of C4 genes involved. 2,10,15,19 Our results are consistent with previous data, but have also led to novel findings. We have proved the existence of both LLS and LSL (trimodule with two long (L) and one short (S) C4 gene in the designated order) structures, and also showed evidence that even those trimodular haplotypes can belong to a different structural variant that contains long and short RCCX segments in identical order and also carries the same number of both C4A and C4B genes.…”

“…21 Former RCCX-related studies sometimes also detected dosage ratios of TNX and CYP21 active genes and pseudogenes. 10,11 Our group did not examine the TNX genes, but CYP21A2 and CYP21A1P…”

“…9 Population studies regarding RCCX structural variations are traditionally carried out using Southern blot techniques, generally directed at the total number of long and short C4 genes in the haplotypes, length of the most telomeric RCCX module of each chromosome and total C4A and C4B copy numbers in the genome. 2,3,10,11 However, no systematic study describing precise localization of C4A and C4B genes has yet been published, nor has the exact order of long and short C4 genes in RCCX structures containing more than two modules ever been determined. Thus, detailed characterization of RCCX structural variants occurring in the healthy Caucasian population became our goal.…”

Genetics of Congenital Adrenal Hyperplasia

“…Monomodular and trimodular haplotypes are also found in most populations. [10][11][12] These modules are characterized by modular duplication or deletion events in which each duplicated or deleted module usually covers a CYP21A1P-TNXA-RP2-C4 unit. Copy number variation (CNV) of C4, CYP21, and TNX is widely found in humans; in patients with CAH, a greater C4 CNV with mutation-specific associations has been shown to possibly confer protection for autoimmune disease.…”

Genotypic Diversity of Complement Component C4 Does Not Predict Kidney Transplant Outcome

“…The C4 locus has a complex genetic organization caused by the combination of: (1) substantial copy number variation (CNV) of RCCX modules and hence interindividual differences in the number of C4 gene copies; (2) gene diversification resulting in two isotypes (C4A and C4B), either of which can be missing; and (3) dichotomous size variation leading to short (C4S) and long (C4L) genes. 12 Importantly, the number of copies inherited correlates closely with plasma C4 concentrations and functional complement activity 13,14 and may contribute to susceptibility to infection and autoimmune disease. [15][16][17][18] Consequently, genetic analysis in kidney transplant donor recipient pairs provides an unusual human model system to study the influence of C4 in immunemediated injury that uniquely is able to distinguish between local and systemic origin.…”