| Literature DB >> 34893581 |
Rixing Lin1,2, Juan Pablo Lopez3, Cristiana Cruceanu4, Caroline Pierotti5, Laura M Fiori1, Alessio Squassina6, Caterina Chillotti7, Christoph Dieterich8,9,10, Nikolaos Mellios5,11, Gustavo Turecki12,13.
Abstract
Gene expression dysregulation in the brain has been associated with bipolar disorder, but little is known about the role of non-coding RNAs. Circular RNAs are a novel class of long noncoding RNAs that have recently been shown to be important in brain development and function. However, their potential role in psychiatric disorders, including bipolar disorder, has not been well investigated. In this study, we profiled circular RNAs in the brain tissue of individuals with bipolar disorder. Total RNA sequencing was initially performed in samples from the anterior cingulate cortex of a cohort comprised of individuals with bipolar disorder (N = 13) and neurotypical controls (N = 13) and circular RNAs were identified and analyzed using "circtools". Significant circular RNAs were validated by RT-qPCR and replicated in the anterior cingulate cortex in an independent cohort (24 bipolar disorder cases and 27 controls). In addition, we conducted in vitro studies using B-lymphoblastoid cells collected from bipolar cases (N = 19) and healthy controls (N = 12) to investigate how circular RNAs respond following lithium treatment. In the discovery RNA sequencing analysis, 26 circular RNAs were significantly differentially expressed between bipolar disorder cases and controls (FDR < 0.1). Of these, circCCNT2 was RT-qPCR validated showing significant upregulation in bipolar disorder (p = 0.03). This upregulation in bipolar disorder was replicated in an independent post-mortem human anterior cingulate cortex cohort and in B-lymphoblastoid cell culture. Furthermore, circCCNT2 expression was reduced in response to lithium treatment in vitro. Together, our study is the first to associate circCCNT2 to bipolar disorder and lithium treatment.Entities:
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Year: 2021 PMID: 34893581 PMCID: PMC8664854 DOI: 10.1038/s41398-021-01746-4
Source DB: PubMed Journal: Transl Psychiatry ISSN: 2158-3188 Impact factor: 6.222
Fig. 3Replication and effects of lithium treatment on circCCNT2 expression.
A Schematic diagram of the B-LCL cohort. B Expression of circCCNT2 in B-LCL cells collected from individuals with bipolar disorder (BD) and controls (CTL). Showing the main effect of the group from a two-way mixed ANOVA. C Expression of circCCNT2 in B-LCL cells that were treated and not treated with lithium. Showing the main effect of treatment from a two-way mixed ANOVA. D Expression of circCCNT2 showing the decomposition of the significant interaction of group by treatment from a two-way mixed ANOVA. Lithium treatment specifically reduces circCCNT2 expression in individuals with bipolar disorder with no effect in control subjects. All bar graphs represent the mean expression of circCCNT2; each dot represents a single data point; error bars represent SEM; *<0.05, **<0.01, ***<0.001, n.s. not significant.
Fig. 1circCCNT2 expression in ACC of individuals with bipolar disorder.
A Filtering of circRNA from sequence identified back splice junctions (BSJ), regulation in bipolar disorder, fold-change, and RT-qPCR validation. B circCCNT2 validation by RT-qPCR (left). circCCNT2 expression correlation between RNA sequencing and RT-qPCR (right). C Expression of circCCNT2 in an independent human postmortem ACC (BA24) replication cohort. Student’s two-tailed t tests were used to assess mean differences between individuals with bipolar disorder (BD) and controls (CTL). Pearson correlation coefficient (r) was used for correlation analysis. All bar plots represent the mean with individual data points as dots. Error bars represent S.E.M. (*<0.05).
Top ten differentially expressed circRNAs in BA24 of individuals with bipolar disordera.
| circRNA nameb | CircRNA IDc | Host gene description | Genomic locationd | Strand | BSJe | Sizef | Adjusted | Fold change (%) | |
|---|---|---|---|---|---|---|---|---|---|
| circCCNT2 | hsa_circ_0056537 | Cyclin T2 | chr2:134936841–134942674 | + | exon5–exon3 | 253nt | 0.00006 | 0.09035 | 83 |
| circCLOCK | hsa_circ_0126631 | Clock circadian regulator | chr4:55475963–55482828 | − | exon8–exon5 | 391nt | 0.00021 | 0.09362 | 82 |
| circRERE | hsa_circ_0002158 | Arginine–glutamic acid dipeptide repeats | chr1:8541214–8557523 | − | exon8–exon6 | 308nt | 0.00013 | 0.09035 | 66 |
| circSGMS1 | hsa_circ_0093713 | Sphingomyelin synthase 1 | chr10:50433476–50519921 | − | exon6–exon3 | 357nt | 0.0001 | 0.09035 | 43 |
| circPTPN4 | hsa_circ_0117151 | Protein tyrosine phosphatase non-receptor type 4 | chr2:119809837–119900806 | + | exon10–exon2 | 781nt | 0.00008 | 0.09035 | 36 |
| circUBR5 | N/A | Ubiquitin protein ligase E3 component N-recognin 5 | chr8:102271134–102272772 | − | exon49–exon48 | 356nt | 0.00009 | 0.09035 | −21 |
| circGLRB | hsa_circ_0125612 | Glycine receptor beta | chr4:157120556–157153010 | + | exon9–exon3 | 1075nt | 0.00003 | 0.09035 | −38 |
| circCYFIP2 | hsa_circ_0074763 | Cytoplasmic FMR1 interacting protein 2 | chr5:157294783–157304366 | + | exon7–exon4 | 588nt | 0.00023 | 0.09362 | −45 |
| circSHC3 | hsa_circ_0003708 | SHC adaptor protein 3 | chr9:89037993–89046994 | − | exon11–exon8 | 694nt | 0.00014 | 0.09035 | −51 |
| circLRBA | hsa_circ_0071174 | LPS responsive beige-like anchor protein | chr4:150735258–150808398 | − | exon36–exon32 | 449nt | 0.00013 | 0.09035 | −55 |
aCircRNA expression quantification followed by differential expression analysis and fold change filtering identified ten candidate circRNAs (BA: Brodmann’s Area).
bIn this study circRNAs were named as their host gene with “circ” prefix.
ccircRNA ID as listed in circBase. circUBR5 did not have a known circRNA ID and is believed to be a newly identified splice variant.
dGenomic location is outlined as follows: chromosome#:start-end for GRch38/hg38 build.
eBSJ: back splice junction. This column indicates between which two exons the back splice event occurred.
fSize of the mature circRNA splice variant in nucleotides (nt).
gNominal p-values were adjusted for false discovery rate (FDR) correction; significant at an FDR of <0.1.
Fig. 2circCCNT2 circularization confirmation.
A Schematic diagram of the predicted back splicing event that forms circCCNT2. Rectangles indicate exons (the number above indicates exon number), the solid line indicates introns, and the dotted line indicates a continuation of the CCNT2 gene up and downstream. Arrows below exon 3 and exon 5 indicate the location and direction of divergent and convergent primers as would appear on the linear CCNT2 gene. B Schematic diagram of the mature circCCNT2 transcript as a result of exon 5 to exon 3 back splice event. The red bar indicates the back splice junction. C Sanger sequencing confirming back splice junction sequence (BSJ back splice junction). D Divergent primer amplification showed enrichment of circCCNT2 in RNase R treated RNA compared to the non-treated control. Divergent primers failed to amplify circCCNT2 in oligonucleotide dT constructed cDNA since circRNAs do not contain a polyA tail. Convergent primer amplification of linear CCNT2 showed the opposite amplification profile as described for divergent primer amplification. Black arrows indicate divergent and convergent primers as described in (A) (Ran. Hex. random hexamer, Oligo. oligonucleotide, R RNase R treated RNA, C non-treated RNA).