Subjects
Postmortem samples from Brodmann’s area 46 in the DLPFC were obtained from the University of Maryland Brain and Tissue Bank in conjunction with the National Institute of Child Health and Development (N=65). The individuals in this cohort ranged from 6 weeks old to 25 years old. Subjects (neonates, infants, toddlers, school-age children, teenagers, and young adults) were assigned to one of six age groups based on cognitive development stages in consultation with a pediatrician. These developmental groups roughly correspond with stages of sensory and cognitive development, i.e., visual acuity and grasping (Neonates: birth-3 months old); sitting upright and environmental engagement (Infants: 4 months-1 year old); preoperational, pre-conceptual rapid language development (Toddlers: 1.5-4 years old); concrete operations (School-age children: 5-12 years old); formal operations, reproductive competence and heightened peer interactions (Teenagers: 14-18 years old); social independence and early maturity (Young Adults: around 22 years old). Eight to thirteen samples were selected per developmental group as described: groups were established with care to balance male and female samples as best as possible, and groups were matched for RNA integrity number (RIN), pH, and postmortem interval (PMI) for most groups. However, PMI was significantly longer in neonates and infants than in older ages (ANOVA, F(5,51)=2.881, p=0.023). Age groups analyzed, and their respective demographic and tissue quality information, are reported in Table 1. We have also included several Sudden Infant Death Syndrome (SIDS) samples in our age groups under two years old. A role for inflammation in SIDS has been proposed (91). However, the syndrome remains poorly understood, with much potential for heterogeneous causes of death. We studied ages 25 and under to focus on developmental processes, rather than aging (92) – however, the time at which “aging” begins remains an area of debate (93-96). All subjects were free of neurological and psychiatric symptoms at the time of death. Individual sample information, including age, sex, RIN, pH, PMI, and cause of death, are in Supplementary Table 1.
Table 1. Summary of patient demographics. RIN, pH, and PMI are presented as mean ± standard deviation.
Age Group
|
Age Range (years)
|
# Male/Female
|
RIN
|
pH
|
PMI
|
n
|
Neonate
|
0.11-0.24
|
5/5
|
7.48±1.36
|
6.52±0.20
|
22.3±5.36
|
10
|
Infant
|
0.25-0.91
|
8/5
|
7.58±0.59
|
6.61±0.16
|
17.46±6.36
|
13
|
Toddler
|
1.58-4.86
|
5/4
|
7.02±1.02
|
6.66±0.26
|
22.33±9.26
|
9
|
School-age
|
5.39-12.97
|
4/4
|
7.33±0.63
|
6.70±0.17
|
14.75±4.86
|
8
|
Teenager
|
15-17.82
|
6/2
|
7.45±0.71
|
6.75±0.09
|
15.5±5.26
|
8
|
Young Adult
|
20.14-25.38
|
6/3
|
7.53±0.79
|
6.67±0.23
|
13.67±8.26
|
9
|
Total
|
0.11-25.38
|
34/23
|
7.41±0.87
|
6.64±0.20
|
17.82±7.31
|
57
|
RNA extraction and cDNA synthesis
Total RNA was extracted from 30-100 mg of frozen DLPFC tissue using the Trizol (Cat# 15596026, Invitrogen, Thermo Scientific, Waltham, MA, USA) reagent method. A tissue homogenizer (Model PT10/35, Brinkmann Instruments) was used to homogenize frozen tissues on wet ice. Chloroform was used to dissociate nucleoprotein complexes; then, soluble RNA was removed from each sample. RNA was precipitated using isopropyl alcohol and re-suspended in diethyl-pyrocarbonate-treated water (97). The yield and purity of the extracted RNA were determined via spectrophotometer analysis. Following extraction, the RIN was determined for each sample using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). All samples had 260/280 ratios >1.70 and RIN values >6. RNA (1.5 μg)/sample was converted into cDNA using Superscript IV First Strand Synthesis Kit (Cat # 18091200, Thermo Scientific, Waltham, MA, USA) as described (98).
High-throughput quantitative PCR
High-throughput quantitative PCR was run on a Biomark HD (Fluidigm, South San Francisco, CA, USA) using a 96.96 Dynamic IFC high-throughput qPCR chip (Cat# 100-6123, Fluidigm, South San Francisco, CA, USA), enabling simultaneous Taqman gene expression assays on all samples. All probes are included in Supplementary Table 2. The following transcripts passed quality control analysis: IL6, IL1B, IL18, TNF, IL1R1, IL18R1, IL6R, IL6ST, TNFRSF1A, TNFRSF1B. No signal in either the no-template control or the no-RT control exceeded cycle threshold levels. Therefore, no transcripts were excluded from further analysis based on a low expression. ‘Low expression’ here is categorized as having a detectable signal in less than five samples of any given age group or a detectable signal in less than three points of the standard curve.
Single target quantitative RT-PCR
Quantitative PCR was run on an Applied Biosystems 7900HT Fast Real-Time PCR System (Thermo Fisher, Waltham, MA, USA). Taqman gene expression assays were used (Supplementary Table 3). A 1:6 plate cDNA dilution was used for transcripts IL10, IL13, IL1RN, and IL1RAP, which were added for analysis following the high-throughput quantitative PCR. In addition, serial dilutions of pooled cDNA from these samples were used to establish a standard curve, with dilutions 1:1, 1:3, 1:9, 1:27, 1:81, 1:243, and 1:729. No signal in the no-template control or the no-RT control exceeded cycle threshold levels for any qPCR run.
Protein extraction
Total protein was extracted from 30-60 mg of fresh frozen human DLPFC tissue. We used neuronal protein extraction reagent (N-PER) (Fisher Scientific, Hampton, NH, USA, Cat# PI87792) and Halt protease and phosphatase inhibitor cocktail plus 0.5 mM ethylenediaminetetraacetic acid (0.5mM EDTA) (Fisher Scientific, Hampton, NH, USA, Cat# PI78440) at 10 µL N-PER per 1 mg tissue in 1.5mL Axygen centrifuge tubes (Cat# MCT-175-C, Axygen). Tissues were homogenized on wet ice with hand-held Axygen tissue grinders (Fisher Scientific, Hampton, NH, Cat# 14 222 358) for 10 min using continual manual agitation. The homogenate was then incubated on wet ice for an additional ten minutes. Microcentrifuge tubes of homogenate were then centrifuged for 10 min at 10,000g at 4°C to pellet tissue debris and insoluble material. The supernatant was removed and stored in 1.5 ml low-protein binding centrifuge tubes (Fisher Scientific, Hampton, NH, USA, Cat# E925000090) at -80°C. Before use, the protein was quantified by bicinchoninic acid (BCA) assay. All samples were then diluted in N-PER with Halt protease and phosphatase inhibitor cocktail to a concentration of 2 mg/mL.
Multiplex immunoassay
For cytokine protein expression, multiplex immunoassays were performed. Multiplex immunoassays were run on a BioRad BioPlex 200 System (Bio-Rad, Hercules, CA, USA, Cat# 171000201). A custom 4-Plex Human Cytokine Assay Kit, including two 96-well plates, was used. The custom-designed assay targeted human cytokines IL6, IL1B, IL18, and TNF used existing probe antibodies from a 48-plex kit (Bio-Plex Pro Human Cytokine Screening Panel, Bio-Rad, Hercules, CA, USA, Cat #12007283). The assay used the 100-region bead map with a bead count of 50 beads per region. The sample timeout was set to 60 seconds. Multiplex immunoassays were run in the Molecular Core of SUNY Upstate Medical University, following the manufacturer’s protocol. Before running experimental samples, the measurement error (variation in values for repeated measurement of the same sample for each of the cytokines) was estimated. Samples (100 µg) were run in triplicate, and pooled internal controls were included in triplicate on each plate to monitor plate-to-plate variability. The samples used are reported in Supplementary Table 1. The kit provided lyophilized standards that were reconstituted in 250 µL in Standard Diluent HB (Bio-Rad, Hercules, CA, USA). Standards were diluted to ratios of 1:4, 1:16, 1:64, 1:256, 1:1,024, 1:4,096, 1:16,384, 1:65,536, and 1:262,144. The coefficient of variation (% CV) was calculated for triplicate readings of each sample. Samples that exceeded ± 15% CV (30% CV total) had one “outlier replicate” removed, which resulted in <± 15% CV from replicate measures for each sample.
Statistical analysis
Statistical tests of qPCR and multiplex immunoassay results were performed using SPSS statistics (Version 25, OSX, IBM, Armonk, NY, USA). Outliers by age group were identified using the ROUT test for outliers using GraphPad Prism (GraphPad Prism version 9.3.1 for Windows, GraphPad Software, San Diego, CA, USA) and then removed (~ 2 outliers per transcript). For TNF mRNA, 5 out of 11 samples in the neonate and infant groups were below the level of detection. Since the visual inspection of the data suggested the neonates and infants had similar levels of TNF mRNA (when detectable), the neonate and infant groups were combined for this analysis. Outliers were then removed using ROUT analysis. Data were tested for normality using Kolmogorov-Smirnoff testing and for homogeneity of variance using Levene’s test. If the data were non-normally distributed, data were logged, and Cox Box transformed (Real Statistics Excel plug-in, Release 5.4. Copyright 2013 – 2018 Charles Zaiontz. www.real-statistics.com). Data were tested for correlation with pH, RIN, and PMI.
Data without covariates that were normally distributed were analyzed using ANOVA, and non-normally distributed data were analyzed using the Kruskal-Wallis test. Normally distributed data with covariates were analyzed by ANCOVA. Non-normally distributed data with covariates were analyzed using Quade’s ranked test. A significant ANOVA, ANCOVA, Kruskal-Wallis, or Quade’s ranked test was followed by a Fisher’s Least Significant Difference (LSD) posthoc test. Welch’s ANOVA was used for normally distributed data exhibiting non-homogenous variance between groups (99, 100), followed by the Games-Howell posthoc test. Sex differences were analyzed by independent sample 2-tailed t-tests for each transcript but could not be compared between age groups due to sample size limitations. All transcripts were tested for correlation with age under the age of 5 years old using Spearman’s ρ. Statistical significance was set at p≤0.05.