Collection of Postmortem Brain Samples
This study has been reviewed and approved by an institutional review board of Marmara University Faculty of Medicine (IRB No: 09.2016.376). Postmortem human brain tissues consisting of the nucleus accumbens and ventral tegmental areas of 30 positive MDMA-users and 30 control samples were collected from the Morgue Department of the Council of Forensic Medicine in Istanbul, Turkey. Informed consent was obtained from family members of the postmortem individuals prior to autopsy, in accordance with the standards established by the Council of Forensic Medicine.
Blood tests were used to detect the presence of MDMA in those subjects included in this study. The drug-free control group was selected from postmortem individuals who had a negative result for all drugs, and no history of substance use prior to death. In both groups, the following cases were excluded: significant head injury, the presence of an infectious disease (e.g HIV/AIDS, hepatitis B or C), chronic disease, or a history of mental disorders. The brains were removed during autopsy, and tissue samples were immediately collected from the VTA and the NAc, then were flash-frozen in liquid nitrogen. The frozen tissues were individually kept in microcentrifuge tubes at -80 °C until RNA extraction.
Screening of Blood Samples in Postmortem Individuals
All blood samples were screened by general unknown screening. In this general method, the analysis of drugs was accomplished by liquid chromatography, coupled with tandem mass spectrometry (LC– MS/MS) and gas chromatography-mass spectrometry (GC–MS) techniques. GC– MS analyses were carried out using a Shimadzu 2010 QP GC–MS instrument and a Restek RTX-5-MS (30m 0.25mm 0.25mm; 5% phenylmethylsiloxane) column was used for chromatographic separations. The mass detector was operated in electronic impact mode at 70 eV and the mass spectra were scanned at m/z 60–550 amu. The injection volume was 1 µL in splitless mode. LC–MS/MS analyses were carried out using an Agilent 6460 triple quadruple tandem mass spectrometer instrument and Agilent Poroshell C18 (dimensions 150 mm 2.7 mm 4.6 mm) column for chromatographic separations. Tandem mass spectrometry (MS/MS) detection was performed using electrospray positive and negative ionization in MRM mode, with an injection volume of 10 µL. Many reports have shown that a toxic or even fatal dose entails blood levels ranging from 0.5 to 10 mg/L in most cases (
25).
Total RNA Extraction
NAc and VTA brain tissues were blended in 1 mL TRIzol reagent (Invitrogen, USA) per 50-100 mg of tissue. Total RNA was extracted as per the manufacturer’s instructions. Total RNA concentrations and purities of the samples were quantified by spectrophotometry using a NanoDrop ND-2000 system (Thermo Fisher Scientific, Inc., Wilmington, DE). The RNA Integrity Number (RIN) was measured by the Bioanalyzer 2100 (Agilent Technologies, USA).
miRNA Microarray and Data Analysis
miRNA expression profiling of the NAc and VTA regions of eight postmortem brain samples (four of them from MDMA users and four of them from the control group) were performed using Agilent 8X60K Human miRNA V21.0. An Agilent miRNA microarray slide contains 2,549 probes, including control probes, according to the latest version of Sanger miRBase (Release 21.0). All of the related reagents were purchased from Agilent Inc. 50 ng of total RNA from four MDMA users and four control brain tissues were labeled with Cy3, using the “Agilent miRNA Labeling and Hybridisation Kit”, following the protocol recommended by the manufacturers. Each labeled RNA sample was hybridized onto an Agilent 8X60K Human miRNA microarray V21 chip and incubated at 55 °C for 20 h. The chip was washed after hybridization and immediately scanned by an Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA). Feature Extraction v10.7.3.1 (Agilent Technologies) software was used to analyze the scanned images. Bioconductor software, a normalization tool for microarray data, was used on the raw data via R version 2.15 quantile normalization. Log transformed data was used to calculate fold change and P value for each sample. Potential candidate miRNAs with p < 0.01 and 1.4-fold change were selected for further validation by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The microarray data were then deposited into the NCBI Gene Expression Omnibus (GEO, Accession number GSE104315).
cDNA Synthesis and qRT-PCR
To validate the differential expression of miR-1202 and miR-7975, RNA extracted from the 30 MDMA users and 30 control samples (including the eight RNA samples used in the microarray) were studied using qRT-PCR. Complementary DNA (cDNA) synthesis was studied by using a “TaqMan MicroRNA Reverse Transcription Kit”, following the manufacturer’s protocol (Applied Biosystems, Foster City, CA). For each selected miRNA, TaqMan assays were purchased from Applied Biosystems, Foster City, CA. small-nucleolar RNA (snoRNA) RNU43 was used for normalization of miRNA expression analyses. (mir7975 5’ AUCCUAGUCACGGCACCA-3’, mir1202 5’- GUGCCAGCUGCAGUGGGGGAG-3).
Quantitative RT-PCR was performed using Universal Master Mix (Applied Biosystems) in a Roche LightCycler 480-II real-time thermal cycler (Roche, Switzerland, Basel). The reactions were applied in the following conditions: one cycle of 95 °C for 5 min followed by 40 cycles of 95 °C for 10 s, 60 °C for 20 s, and 72 °C for 25 s. Each was performed in triplicate. The relative quantification analysis was performed by the delta-delta-Ct method (2-ΔΔCT) as described previously (
26).
Statistical analysis
Data were plotted as mean ± standard error and two-sided Student’s tests were used for statistical analysis of the qRT-PCR. A two-sided p-value of 0.05 or below was considered statistically significant. Receiver operating characteristic (ROC) curves were plotted using SPSS (Statistical Package for the Social Sciences) to see the power of control and validated miRNAs to differentiate from the MDMA samples. For ROC analysis, logistic regression was conducted and the predicted probabilities were calculated for each miRNA for the VTA and NAc regions of brain. The area under the curve (AUC) was calculated with a 95% confidence interval and accepted as significantly different from 0.5 when the p-value was greater than 0.5, meaning that the logistic regression classifies the group significantly better than by chance.