Genome-wide DNA methylation analysis of human brain tissue from schizophrenia patients

Recent studies suggest that genetic and environmental factors do not account for all the schizophrenia risk, and epigenetics also has a role in disease susceptibility. DNA methylation is a heritable epigenetic modification that can regulate gene expression. Genome-wide DNA methylation analysis was performed on post-mortem human brain tissue from 24 patients with schizophrenia and 24 unaffected controls. DNA methylation was assessed at over 485 000 CpG sites using the Illumina Infinium HumanMethylation450 Bead Chip. After adjusting for age and post-mortem interval, 4641 probes corresponding to 2929 unique genes were found to be differentially methylated. Of those genes, 1291 were located in a CpG island and 817 were in a promoter region. These include NOS1, AKT1, DTNBP1, DNMT1, PPP3CC and SOX10, which have previously been associated with schizophrenia. More than 100 of these genes overlap with a previous DNA methylation study of peripheral blood from schizophrenia patients in which 27 000 CpG sites were analysed. Unsupervised clustering analysis of the top 3000 most variable probes revealed two distinct groups with significantly more people with schizophrenia in cluster one compared with controls (P=1.74 × 10⁻⁴). The first cluster composed of 88% of patients with schizophrenia and only 12% controls, whereas the second cluster composed of 27% of patients with schizophrenia and 73% controls. These results strongly suggest that differential DNA methylation is important in schizophrenia etiology and add support for the use of DNA methylation profiles as a future prognostic indicator of schizophrenia.     

A method for the extraction of genomic DNA from human brain tissue fixed and stored in formalin for many years

We report a method providing access to high molecular weight, polymerase chain reaction (PCR)-amplifiable genomic DNA from brains stored in formalin for many years. It consists mainly of an intensive proteinase K treatment of ground tissue previously embedded in agarose plugs, followed by a washing and an elution step. The method was tested on brains fixed and stored in formalin for up to 46 years. All extracted DNA show an identical pattern of degradation ranging from well-preserved (more than 20 kb) to 400-bp-long fragments. This was demonstrated for DNA extracted from the cerebellums of elderly psychiatric and geriatric patients (of more than 60 years of age), male and female, demented or not, with postmortem delays longer than 1 h and shorter than 1 day. In all these cases PCR amplification of a 838-bp-long β-actin product was successfully performed when proteinase K treatment was sufficiently effective to generate pure DNA. Thus, high molecular weight, PCR-amplifiable genomic DNA can be extracted from brains stored in formalin for almost half a century. Received: 20 June 1996 / Revised: 28 August 1996 / Accepted: 9 October 1996     

Retrieval of mRNA from paraffin-embedded human infant brain tissue for non-radioactive in situ hybridization using oligonucleotides

In situ hybridization (ISH) is used to examine the spatiotemporal distribution of gene expression in a range of tissues. Neuroscience research in human brain tissue requires techniques that can be used in formalin fixed and paraffin-embedded tissue rather than frozen tissue which is recommended, but difficult to obtain. This study presents a method for non-radioactive (DIG) ISH for detecting NR1 gene expression, in human infant brain tissue. We compared three pre-treatment effects, protease digestion, autoclaving (in citrate and Tris/EDTA buffer) and microwaving (in citrate and Tris/EDTA buffer). Tissue had been fixed in formalin for 2-12 weeks. Results were compared for the hybridization and background signal intensities, and tissue morphology. We found that optimum results were obtained using 12-min microwave pre-treatment in Tris/EDTA buffer. This method produced optimum signal to background ratio in infant and adult tissue, preserved tissue morphology, and was suitable for use across a broad range of fixation times.     

Assembly of the prothrombinase complex on the surface of human foreskin fibroblasts: Implications for connective tissue growth factor

Activated factor X (FXa) and thrombin can up-regulate gene expression of connective tissue growth factor (CTGF/CCN2) on fibroblasts. Since tissue factor (TF) is expressed on these cells, we hypothesized that they may assemble the prothrombinase complex leading to CTGF/CCN2 upregulation. In addition, the effect of thrombospondin-1 (TSP1) on this reaction was evaluated. Human foreskin fibroblasts were incubated with purified factor VII (FVII), factor X (FX), factor V (FV), prothrombin and calcium in the presence and absence of TSP1. Generation of FXa and of thrombin were assessed using chromogenic substrates. SMAD pathway phosphorylation was detected via Western-blot analysis. Pre-incubation of fibroblasts with FVII led to its auto-activation by cell-surface expressed TF, which in turn in the presence of FX, FVa, prothrombin and calcium led to FXa (9.7 ± 0.8 nM) and thrombin (7.9 ± 0.04 U/mL × 10-3) generation. Addition of TSP1 significantly enhanced thrombin (23.3 ± 0.7 U/mL × 10-3) but not FXa (8.5 ± 0.6 nM) generation. FXa and thrombin generation leads to upregulation of CTGF/CCN2. TSP1 alone upregulated CTGF/CCN2, an effect mediated via activation of transforming growth factor beta (TGFβ) as shown by phosphorylation of the SMAD pathway, an event blunted by using a TGFβ receptor I inhibitor (TGFβRI). FXa- and thrombin-induced upregulation of CTGF/CCN2 was not blocked by TGFβRI. In summary, assembly of the prothrombinase complex occurs on fibroblast's surface leading to serine proteases generation, an event enhanced by TSP1 and associated with CTGF/CCN2 upregulation. These mechanisms may play an important role in human diseases associated with fibrosis.