Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis

Abstract

Monozygotic or 'identical' twins have been widely studied to dissect the relative contributions of genetics and environment in human diseases. In multiple sclerosis (MS), an autoimmune demyelinating disease and common cause of neurodegeneration and disability in young adults, disease discordance in monozygotic twins has been interpreted to indicate environmental importance in its pathogenesis. However, genetic and epigenetic differences between monozygotic twins have been described, challenging the accepted experimental model in disambiguating the effects of nature and nurture. Here we report the genome sequences of one MS-discordant monozygotic twin pair, and messenger RNA transcriptome and epigenome sequences of CD4(+) lymphocytes from three MS-discordant, monozygotic twin pairs. No reproducible differences were detected between co-twins among approximately 3.6 million single nucleotide polymorphisms (SNPs) or approximately 0.2 million insertion-deletion polymorphisms. Nor were any reproducible differences observed between siblings of the three twin pairs in HLA haplotypes, confirmed MS-susceptibility SNPs, copy number variations, mRNA and genomic SNP and insertion-deletion genotypes, or the expression of approximately 19,000 genes in CD4(+) T cells. Only 2 to 176 differences in the methylation of approximately 2 million CpG dinucleotides were detected between siblings of the three twin pairs, in contrast to approximately 800 methylation differences between T cells of unrelated individuals and several thousand differences between tissues or between normal and cancerous tissues. In the first systematic effort to estimate sequence variation among monozygotic co-twins, we did not find evidence for genetic, epigenetic or transcriptome differences that explained disease discordance. These are the first, to our knowledge, female, twin and autoimmune disease individual genome sequences reported.

Figure 1. Comparison of the genomic locations of heterozygous cSNPs exhibiting imbalanced allelic expression in mRNA of twins 041896-001 and -101.

a, b, Allelic imbalance for 041896-001 (a) and 041896-101 (b) was detected in cSNPs called by ≥10 gDNA reads with Q ≥ 20 and where 20–80% of uniquely aligning gDNA reads called the SNP, together with detection in ≥10 mRNA reads with Q ≥ 20. Out of 14,461 heterozygous cSNPs, 268 (1.9%) showed significant allelic imbalance in expression (P < 10^-7), of which 153 (57%) were of the same magnitude and direction in both subjects. TCRVB is the T cell receptor beta locus, V (variable) segment, locus symbol TRB@. WDR40B is also known as DCAF12L1. PowerPoint slide

Figure 2. Comparisons of methylation of genomic CpG sites in CD4⁺ lymphocytes and breast and lung tissue samples.

a, Frequency distribution of CpG site methylation in 041896-001 (blue) and -101 (red) using ELAND-extended. b–j, Pairwise comparisons of CpG site methylation using ELAND-extended in CD4⁺ lymphocytes from monozygotic twin siblings 041896-001 and -101 (b), 230178-001 and -101 (c) and 041907-001 and -101 (d); inter-individual differences between CD4⁺ lymphocytes from 041896-001 and 041907-001 (e) and 041896-001 and 230178-101 (f); neoplastic differences between breast tissue and breast cancer (g) and between normal lung tissue and lung cancer (h); and between-tissue differences between CD4⁺ lymphocytes and breast tissue (i) and lung tissue (j). PowerPoint slide