Person:

Sekar, Aswin

The human genome's strongest influences on two common diseases, systemic lupus erythematosus (SLE) and schizophrenia, arise from genetic variation in the Human Leukocyte Antigen (HLA) locus. However, the genes and functional alleles driving these genetic relationships have remained unknown. We hypothesized that a complex, multi-allelic form of structural variation in the Complement component 4 (C4) gene, within the HLA locus, underlies these relationships. Loci that exist in many structural forms and vary widely in copy number have been difficult to analyze molecularly. As a result, we know little about their population genetic properties or their influence on phenotypes. In this work, we developed molecular and statistical methods to characterize such loci and to evaluate their contribution to phenotypes. Applying these methods to the C4 locus, we found that C4 segregates in four common and at least eleven low-frequency structural forms in human populations. Although there was only partial correlation between C4 structural variation and individual single nucleotide polymorphisms (SNPs), we developed an imputation approach to enable statistical prediction of C4 structural states from flanking SNP haplotypes. C4 structural variation associated to gene expression in lymphoblastoid cell lines and human brain tissue. Applying our imputation strategy to SLE and schizophrenia case-control cohorts totaling > 75,000 individuals, we found that structural variation in C4 contributes to risk of both phenotypes in a manner predicted by its effect on gene expression in relevant tissues, and with largely opposite directions of effect - alleles that were protective for schizophrenia increased risk for SLE, and vice versa. Leveraging a natural allelic series of C4 structural forms, we developed a novel form of association testing and showed that the association to C4 is unlikely to be caused by correlation with HLA SNPs. C4 was expressed in human neurons, whereas other upstream complement pathway genes were expressed primarily by microglia. Mice lacking C4 showed a deficit in synaptic pruning that was rescued by human C4. The methods developed in this thesis enable analysis of complex structural variation, and our results identify a novel form of genome variation as making a strong contribution to phenotypes.

Schizophrenia is a heritable brain illness with unknown pathogenic mechanisms. Schizophrenia’s strongest genetic association at a population level involves variation in the Major Histocompatibility Complex (MHC) locus, but the genes and molecular mechanisms accounting for this have been challenging to recognize. We show here that schizophrenia’s association with the MHC locus arises in substantial part from many structurally diverse alleles of the complement component 4 (C4) genes. We found that these alleles promoted widely varying levels of C4A and C4B expression and associated with schizophrenia in proportion to their tendency to promote greater expression of C4A in the brain. Human C4 protein localized at neuronal synapses, dendrites, axons, and cell bodies. In mice, C4 mediated synapse elimination during postnatal development. These results implicate excessive complement activity in the development of schizophrenia and may help explain the reduced numbers of synapses in the brains of individuals affected with schizophrenia.

Many common illnesses differentially affect men and women for unknown reasons. The autoimmune diseases lupus and Sjögren’s syndrome affect nine times more women than men, whereas schizophrenia affects men more frequently and severely. All three illnesses have their strongest common genetic associations in the Major Histocompatibility Complex (MHC) locus, an association that in lupus and Sjögren’s syndrome has long been thought to arise from alleles of the human leukocyte antigen (HLA) genes at that locus. Here we show that the complement component 4 (C4) genes, which are also in the MHC locus and were recently found to increase risk for schizophrenia, generate 7-fold variation in risk for lupus (95% CI: 5.88-8.61; p < 10-117 in total) and 16-fold variation in risk for Sjögren’s syndrome (95% CI: 8.59-30.89; p < 10-23 in total) among individuals with common C4 genotypes, with C4A protecting more strongly than C4B in both illnesses. The same alleles that increase risk for schizophrenia greatly reduced risk for lupus and Sjögren’s syndrome. In all three illnesses, C4 alleles acted more strongly in men than in women: common combinations of C4A and C4B generated 14-fold variation in risk for lupus, 31-fold variation in risk for Sjögren’s syndrome, and 1.7-fold variation in schizophrenia risk among men (vs. 6-fold, 15-fold, and 1.26-fold among women respectively). At a protein level, both C4 and its effector C3 were present at greater levels in men than women in cerebrospinal fluid (p < 10-5 for both C4 and C3) and plasma among adults ages 20-50, corresponding to the ages of differential disease vulnerability. Sex differences in complement protein levels may help explain the larger effects of C4 alleles in men, women’s greater risk of SLE and Sjögren’s, and men’s greater vulnerability in schizophrenia. These results implicate the complement system as a source of sexual dimorphism in vulnerability to diverse illnesses.