Transplant recipients exhibiting posttransplant antibodies are at a higher risk for acute and chronic antibody mediated rejection (AMR). The primary alloantigens recognized by antibodies in recipients with AMR are the highly polymorphic HLA class I and class II molecules expressed on the surface of the endothelial cells (ECs) of the graft. Traditionally, anti-HLA antibodies were thought to mediate graft injury through complement-dependent mechanisms. However, recent studies indicate that antibodies can also contribute to alterations in EC function through complement-independent mechanisms by transducing intracellular signals. Anti-HLA antibodies transduce signals that are both pro-inflammatory and pro-proliferative suggesting mechanistic roles in acute and chronic AMR.

The ligation of MHC class I molecules by class I antibodies on endothelial cells leads to both proliferation and survival signal transduction. This signaling pathway has been implicated in the development of acute and chronic antibody-mediated rejection. The ability of a graft to acquire resistance to immune-mediated graft injury is the basis of accommodation. The mechanisms of MHC class I-induced accommodation are unknown, but under certain circumstances following the ligation of MHC class I molecules by antibodies, the survival pathway is activated. This review explores what is currently known about accommodation and how MHC class I signaling may play a role in the process of enhancing graft survival.

Gene expression profiles of postmortem brain tissue represent important resources for understanding neuropsychiatric illnesses. The impact(s) of quality covariables on the analysis and results of gene expression studies are important questions. This paper addressed critical variables which might affect gene expression in two brain regions. Four broad groups of quality indicators in gene expression profiling studies (clinical, tissue, RNA, and microarray quality) were identified. These quality control indicators were significantly correlated, however one quality variable did not account for the total variance in microarray gene expression. The data showed that agonal factors and low pH correlated with decreased integrity of extracted RNA in two brain regions. These three parameters also modulated the significance of alterations in mitochondrial-related genes. The average F-ratio summaries across all transcripts showed that RNA degradation from the AffyRNAdeg program accounted for higher variation than all other quality factors. Taken together, these findings confirmed prior studies, which indicated that quality parameters including RNA integrity, agonal factors, and pH are related to differences in gene expression profiles in postmortem brain. Individual candidate genes can be evaluated with these quality parameters in post hoc analysis to help strengthen the relevance to psychiatric disorders. We find that clinical, tissue, RNA, and microarray quality are all useful variables for collection and consideration in study design, analysis, and interpretation of gene expression results in human postmortem studies.

Objective: The neural cell adhesion molecule (NCAM1) is a multifunction transmembrane protein involved in synaptic plasticity, neurodevelopment, and neurogenesis. Multiple NCAM1 proteins were differentially altered in bipolar disorder and schizophrenia. Single nucleotide polymorphisms (SNPs) in the NCAM1 gene were significantly associated with bipolar disorder in the Japanese population. Bipolar disorder and schizophrenia may share common vulnerability or susceptibility risk factors for shared features in each disorder.Methods: Both SNPs and splice variants in the NCAM1 gene were analysed in bipolar disorder and schizophrenia. A case-control study design for association of SNPs and differential exon expression in the NCAM1 gene was used.Results: A genotypic association between bipolar disorder and SNP b (rs2303377 near mini-exon b) and a suggestive association between schizophrenia and SNP 9 (rs646558) were found. Three of the two marker haplotypes for SNP 9 and SNP b showed varying frequencies between bipolar and controls (P < 0.0001) as well as between schizophrenia and controls (P < 0.0001). There were nine NCAM1 transcripts present in postmortem brain samples that involve alternative splicing of NCAM1 mini-exons (a, b, c) and the secreted (SEC) exon. Significant differences in the amounts of four alternatively spliced isoforms were found between NCAM1 SNP genotypes. In exploratory analysis, the c-SEC alternative spliced isoform was significantly decreased in bipolar disorder compared to controls for NCAM1 SNP b heterozygotes (P=0.013).Conclusions: Diverse NCAM1 transcripts were found with possibly different functions. The results suggest that SNPs within NCAM1 contribute differential risk for both bipolar disorder and schizophrenia possibly by alternative splicing of the gene.

Mitochondrial defects in gene expression have been implicated in the pathophysiology of bipolar disorder and schizophrenia. We have now contrasted control brains with low pH versus high pH and showed that 28% of genes in mitochondrial-related pathways meet criteria for differential expression. A majority of genes in the mitochondrial, chaperone and proteasome pathways of nuclear DNA-encoded gene expression were decreased with decreased brain pH, whereas a majority of genes in the apoptotic and reactive oxygen stress pathways showed an increased gene expression with a decreased brain pH. There was a significant increase in mitochondrial DNA copy number and mitochondrial DNA gene expression with increased agonal duration. To minimize effects of agonal-pH state on mood disorder comparisons, two classic approaches were used, removing all subjects with low pH and agonal factors from analysis, or grouping low and high pH as a separate variable. Three groups of potential candidate genes emerged that may be mood disorder related: (a) genes that showed no sensitivity to pH but were differentially expressed in bipolar disorder or major depressive disorder; (b) genes that were altered by agonal-pH in one direction but altered in mood disorder in the opposite direction to agonal-pH and (c) genes with agonal-pH sensitivity that displayed the same direction of changes in mood disorder. Genes from these categories such as NR4A1 and HSPA2 were confirmed with Q-PCR. The interpretation of postmortem brain studies involving broad mitochondrial gene expression and related pathway alterations must be monitored against the strong effect of agonal-pH state. Genes with the least sensitivity to agonal-pH could present a starting point for candidate gene search in neuropsychiatric disorders.

Multiple linkage regions have been reported in schizophrenia, and some appear to harbor susceptibility genes that are differentially expressed in postmortem brain tissue derived from unrelated individuals. We combined traditional genome-wide linkage analysis in a multiplex family with lymphocytic genome-wide expression analysis. A genome scan suggested linkage to a chromosome 4q marker (D4S1530, LOD 2.17, θ=0) using a dominant model. Haplotype analysis using flanking microsatellite markers delineated a 14 Mb region that cosegregated with all those affected. Subsequent genome-wide scan with SNP genotypes supported the evidence of linkage to 4q33–35.1 (LOD=2.39) using a dominant model. Genome-wide microarray analysis of five affected and five unaffected family members identified two differentially expressed genes within the haplotype AGA and GALNT7 (aspartylglucosaminidase and UDP- N -acetyl-alpha- D -galactosamine: polypeptide N -acetylgalactosaminyltransferase 7) with nominal significance; however, these genes did not remain significant following analysis of covariance. We carried out genome-wide linkage analyses between the quantitative expression phenotype and genetic markers. AGA expression levels showed suggestive linkage to multiple markers in the haplotype (maximum LOD=2.37) but to no other genomic region. GALNT7 expression levels showed linkage to regulatory loci at 4q28.1 (maximum LOD=3.15) and in the haplotype region at 4q33–35.1 (maximum LOD=2.37). ADH1B (alcohol dehydrogenase IB) was linked to loci at 4q21–q23 (maximum LOD=3.08) and haplotype region at 4q33–35.1 (maximum LOD=2.27). Seven differentially expressed genes were validated with RT-PCR. Three genes in the 4q33–35.1 haplotype region were also differentially expressed in schizophrenia in postmortem dorsolateral prefrontal cortex: AGA , HMGB2 , and SCRG1 . These results indicate that combining differential gene expression with linkage analysis may help in identifying candidate genes and potential regulatory sites. Moreover, they also replicate recent findings of complex trans - and cis - regulation of genes.

Cerebellum tissue was used to compare agonal-pH effects by copy number of mtDNA and by in situ hybridization (ISH) for a candidate gene, LRPPRC (leucine-rich PPR-motif containing). LRPPRC was chosen as it was dysregulated in the present study in bipolar disorder by microarray and the changes were validated by Q-PCR. A clear decrease in LRPPRC mRNA expression by 33% in cerebellum was seen in the agonal factors group (bottom panel) compared to the group with zero agonal factors (top panel, P=0.011). The LRPPRC ISH result also showed a 19% increase in BPD compared to controls (P=0.011). This result underscores the need to account for cases with agonal-pH factors in candidate mitochondrial gene searches in brain disorders. For more information on this topic, please refer to article by Vawter et al. on pages 663–679.

There are major concerns that specific agonal conditions, including coma and hypoxia, might affect ribonucleic acid (RNA) integrity in postmortem brain studies. We report that agonal factors significantly affect RNA integrity and have a major impact on gene expression profiles in microarrays. In contrast to agonal factors, gender, age, and postmortem factors have less effect on gene expression profiles. The Average Correlation Index is proposed as a method for evaluating RNA integrity on the basis of similarity of microarray profiles. Reducing the variance due to agonal factors is critical in investigating small but validated gene expression differences in messenger RNA levels between psychiatric patients and control subjects.

This project involves a multi-site collaborative effort to investigate gene expression in neuropsychiatric disorders in multiple brain regions. We have investigated schizophrenia (n = 9) and controls (n = 9) by microarray analysis using Affymetrix U133A and B chips. We report on the microarray comparison of three cortical regions: dorsolateral prefrontal cortex (DLPFC), anterior cingulate, and entorhinal cortex (ERC). We selected the top and bottom differentially expressed genes for schizophrenia from a robust probe level linear model analysis (http://stat- www.berkeley.edu/users/bolstad/AffyExtensions/AffyExtensions.html) for each brain region. The top 500 and bottom 500 changed genes were further classified using Gene Ontology and KEGG classifications. There was over-representation of ribosomal genes, heat shock related genes, chaperone genes, and immune genes in cortical regions. The preliminary gene classifications for the ERC, DLPFC and anterior cingulate will be compared to the results from the hippocampus. The preliminary microarray evidence suggests several cortical regions share overlapping expression patterns for genes dysregulated in schizophrenia.