Chronological Changes in MicroRNA Expression in the Developing Human Brain

<div><p>Objective</p><p>MicroRNAs (miRNAs) are endogenously expressed noncoding RNA molecules that are believed to regulate multiple neurobiological processes. Expression studies have revealed distinct temporal expression patterns in the developing rodent and porcine brain, but comprehensive profiling in the developing human brain has not been previously reported.</p><p>Methods</p><p>We performed microarray and TaqMan-based expression analysis of all annotated mature miRNAs (miRBase 10.0) as well as 373 novel, predicted miRNAs. Expression levels were measured in 48 post-mortem brain tissue samples, representing gestational ages 14–24 weeks, as well as early postnatal and adult time points.</p><p>Results</p><p>Expression levels of 312 miRNAs changed significantly between at least two of the broad age categories, defined as fetal, young, and adult.</p><p>Conclusions</p><p>We have constructed a miRNA expression atlas of the developing human brain, and we propose a classification scheme to guide future studies of neurobiological function.</p></div

Demographic information of brain tissue donors.

<p>samples excluded from expression analysis.</p><p>UMB# – Sample identifier, NICHD Brain and Tissues Bank for Developmental Disorders.</p><p>GA – gestational age.</p><p>Pool – indicates sample pooling for TaqMan arrays.</p><p>PMI – post-mortem interval (hours).</p

Temporal expression analysis using real-time quantitative PCR.

<p>The number of miRNAs that exceed the indicated fold difference are tabulated for each pair-wise sample type comparison.</p

Validation of a microRNA target site polymorphism in <i>H3F3B</i> that is potentially associated with a broad schizophrenia phenotype

<div><p>Despite much progress, few genetic findings for schizophrenia have been assessed by functional validation experiments at the molecular level. We previously reported evidence for genetic linkage of broadly defined schizophrenia to chromosome 17q25 in a sample of 24 multiplex families. 2,002 SNPs under this linkage peak were analyzed for evidence of linkage disequilibrium using the posterior probability of linkage (PPL) framework. SNP rs1060120 produced the strongest evidence for association, with a PPLD|L score of 0.21. This SNP is located within the 3'UTR of the histone gene <i>H3F3B</i> and colocalizes with potential gene target miR-616. A custom miRNA target prediction program predicted that the binding of miR-616 to <i>H3F3B</i> transcripts would be altered by the allelic variants of rs1060120. We used dual luciferase assays to experimentally validate this interaction. The rs1060120 A allele significantly reduced luciferase expression, indicating a stronger interaction with miR-616 than the G allele (p = 0.000412). These results provide functional validation that this SNP could alter schizophrenia epigenetic mechanisms thereby contributing to schizophrenia-related disease risk.</p></div

Linkage disequilibrium between 1,544 SNPs and broad schizophrenia spectrum phenotype.

<p>PPLD|L values for 1,544 SNPs, including five MirSNPs (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194233#pone.0194233.t001" target="_blank">Table 1</a>), from chr17: 74,684,647 to 83,257,441 (GRCh38), were calculated using KELVIN v2.4.0 and plotted vs physical distance. The MirSNP rs1060120 in <i>H3F3B</i> produced a PPLD|L of 0.21, notably higher than the remaining SNPs.</p

Predicted MirSNPs from the chromosome 17q25 region of association/linkage to broadly defined schizophrenia.

<p>Predicted MirSNPs from the chromosome 17q25 region of association/linkage to broadly defined schizophrenia.</p

Characteristics of participants in the Urban Health Study and the Women’s Interagency HIV Study.

<p>Characteristics of participants in the Urban Health Study and the Women’s Interagency HIV Study.</p

Manhattan plot showing the meta-analysis results of approximately 8 million SNPs and indels tested for association with HIV-1 acquisition in 2,004 African Americans and 1,132 European Americans from the Urban Health Study.

<p>The–log₁₀ (<i>P</i> value) is plotted by chromosomal position of SNPs (shown as circles) and indels (shown as triangles). The SNPs and indels selected for replication testing from 8 gene regions are highlighted in red. The gene region above the solid grey line (<i>P</i><5x10^-8) exceeded the threshold for genome-wide statistical significance. In addition, the 6 gene regions above the dashed black line (<i>P</i><1x10^-6) and the region around the top genotyped SNP (<i>P</i> = 1x10^-5 on chromosome 9) were selected for replication testing.</p

Overview of Study Design.

<p>AA represents African Americans, EA represents European Americans, and UofC represents University of Chicago.</p

Putative pathway between <i>FRMPD1</i> SNP rs4878712 and reduced risk of HIV acquisition through <i>FBXO10</i> and <i>BCL2</i>/Bcl-2.

<p>Putative pathway between <i>FRMPD1</i> SNP rs4878712 and reduced risk of HIV acquisition through <i>FBXO10</i> and <i>BCL2</i>/Bcl-2.</p