Circular RNAs (circRNAs) are a covalently closed subclass of non-coding RNA molecules formed by back splicing of linear precursor RNA. These molecules are relatively stable and particularly abundant ...in the mammalian brain and therefore may participate in neural development and function. With the emergence of circRNAs activity in gene regulation, these molecules have been implicated in several biological processes, including synaptic plasticity, and we therefore suspect they may have a role in neurobehavioral disorders. Here, we profile cortical circRNAs expression in 35 postmortem cortical gray matter (BA46) schizophrenia and a non-psychiatric comparison group, using circRNA enrichment sequencing. While more than 90,000 circRNAs species were identified in the dorsolateral prefrontal cortex (DLPFC), we observed lower complexity and substantial depletion in subjects with the disorder. Although circRNAs expression was independent of their host gene transcription, alternative splicing rates were lower in samples from cases compared to controls. Gene set analysis of differentially expressed circRNAs host genes revealed significant enrichment of neural functions and neurological disorders. Many of these depleted circRNAs are also predicted to sequester miRNAs that were shown previously to be increased in the disorder, potentially exacerbating the functional impact of their dysregulation through posttranscriptional gene silencing. While this is the first reported exploration of circRNAs in schizophrenia, there is significant potential for dysregulation more broadly in other major mental illnesses and behavioral disorders. Given their capacity for modulating miRNA function, circRNA may play a significant role in the pathophysiology of disease and even be targeted for therapeutic manipulation.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Population health research is increasingly focused on the genetic determinants of healthy ageing, but there is no public resource of whole genome sequences and phenotype data from healthy elderly ...individuals. Here we describe the first release of the Medical Genome Reference Bank (MGRB), comprising whole genome sequence and phenotype of 2570 elderly Australians depleted for cancer, cardiovascular disease, and dementia. We analyse the MGRB for single-nucleotide, indel and structural variation in the nuclear and mitochondrial genomes. MGRB individuals have fewer disease-associated common and rare germline variants, relative to both cancer cases and the gnomAD and UK Biobank cohorts, consistent with risk depletion. Age-related somatic changes are correlated with grip strength in men, suggesting blood-derived whole genomes may also provide a biologic measure of age-related functional deterioration. The MGRB provides a broadly applicable reference cohort for clinical genetics and genomic association studies, and for understanding the genetics of healthy ageing.
Bacterial lipopolysaccharides (LPS) are potent innate immunostimulants targeting the Toll-like receptor 4 (TLR4), an attractive and validated target for immunostimulation in cancer therapy. Although ...LPS possess anti-tumor activity, toxicity issues prevent their systemic administration at effective doses in humans. We first demonstrated that LPS formulated in liposomes preserved a potent antitumor activity
upon systemic administration in syngeneic models, and significantly enhance the antitumor activity of the anti-CD20 antibody rituximab in mice xenografted with the human RL lymphoma model. Liposomal encapsulation also allowed a 2-fold reduction in the induction of pro-inflammatory cytokines by LPS. Mice receiving an intravenous administration demonstrated a significant increase of neutrophils, monocytes and macrophages at the tumor site as well as an increase of macrophages in spleen. Further, we chemically detoxified LPS to obtain MP-LPS that was associated with a 200-fold decrease in the induction of proinflammatory cytokines. When encapsulated in a clinically approved liposomal formulation, toxicity, notably pyrogenicity (10-fold), was limited while the antitumor activity and immunoadjuvant effect were maintained. This improved tolerance profile of liposomal MP-LPS was associated with the preferential activation of the TLR4-TRIF pathway. Finally,
studies demonstrated that stimulation with encapsulated MP-LPS reversed the polarization of M2 macrophages towards an M1 phenotype, and a phase 1 trial in healthy dogs validated its tolerance upon systemic administration up to very high doses (10µg/kg). Altogether, our results demonstrate the strong therapeutic potential of MPLPS formulated in liposomes as a systemically active anticancer agent, supporting its evaluation in patients with cancer.
While the cytoplasmic function of microRNA (miRNA) as post-transcriptional regulators of mRNA has been the subject of significant research effort, their activity in the nucleus is less well ...characterized. Here we use a human neuronal cell model to show that some mature miRNA are preferentially enriched in the nucleus. These molecules were predominantly primate-specific and contained a sequence motif with homology to the consensus MAZ transcription factor binding element. Precursor miRNA containing this motif were shown to have affinity for MAZ protein in nuclear extract. We then used Ago1/2 RIP-Seq to explore nuclear miRNA-associated mRNA targets. Interestingly, the genes for Ago2-associated transcripts were also significantly enriched with MAZ binding sites and neural function, whereas Ago1-transcripts were associated with general metabolic processes and localized with SC35 spliceosomes. These findings suggest the MAZ transcription factor is associated with miRNA in the nucleus and may influence the regulation of neuronal development through Ago2-associated miRNA induced silencing complexes. The MAZ transcription factor may therefore be important for organizing higher order integration of transcriptional and post-transcriptional processes in primate neurons.
Abstract
Differentiation of neural progenitor cells into mature neuronal phenotypes relies on extensive temporospatial coordination of mRNA expression to support the development of functional brain ...circuitry. Cleavage and polyadenylation of mRNA has tremendous regulatory capacity through the alteration of mRNA stability and modulation of microRNA (miRNA) function, however the extent of utilization in neuronal development is currently unclear. Here, we employed poly(A) tail sequencing, mRNA sequencing, ribosome profiling and small RNA sequencing to explore the functional relationship between mRNA abundance, translation, poly(A) tail length, alternative polyadenylation (APA) and miRNA expression in an in vitro model of neuronal differentiation. Differential analysis revealed a strong bias towards poly(A) tail and 3′UTR lengthening during differentiation, both of which were positively correlated with changes in mRNA abundance, but not translation. Globally, changes in miRNA expression were predominantly associated with mRNA abundance and translation, however several miRNA–mRNA pairings with potential to regulate poly(A) tail length were identified. Furthermore, 3′UTR lengthening was observed to significantly increase the inclusion of non-conserved miRNA binding sites, potentially enhancing the regulatory capacity of these molecules in mature neuronal cells. Together, our findings suggest poly(A) tail length and APA function as part of a rich post-transcriptional regulatory matrix during neuronal differentiation.
Graphical Abstract
Graphical Abstract
Abstract
Background
The last few years has witnessed the emergence of a novel class of long non-coding RNA known as circular RNA (circRNA). These molecules are characterised by their circularity ...formed through the back splicing of 3’ and 5’ ends of transcript segments produced by one or more of its exons. CircRNAs function as transcriptional modulators, microRNA regulators, as well as template for translation. In our current study, we profiled circRNA expression in post-mortem brain samples from Schizophrenia (SZ) and control subjects using next-generation sequencing technology to discover the association of these novel RNA molecules with the pathogenesis of SZ.
Methods
Total RNA from cerebral cortex (BA46) of 17 SZ patients and 18 healthy controls were subjected to ribosomal RNA depletion and then RNase R treatment to further deplete linear RNA and enrich for exonuclease resistant circRNA transcripts. Sequencing libraries were constructed using Illumina TruSeq RNA Library Prep Kit (LT) (150 cycles) and sequenced by an Illumina NexSeq500. Sequencing data was analysed by the CIRCexplorer2 pipeline to identify circRNA transcripts. To validate the sequencing findings, real-time PCR was performed using outward primers sets designed to specifically amplify circular transcripts.
Results
We discovered a large number of distinct circRNAs (95,212), many of which were highly expressed throughout the cohort. Surprisingly, a large proportion (52%) of the identified circRNAs sequences were novel or not previously reported. Differential expression analysis suggested that there was substantial alteration in circRNA expression in SZ. More than two thirds of these molecules displayed decreased expression, whereas the remainder were upregulated. Functional annotation of the host genes was significantly enrichment for terms-related to neurobiology and neurocognitive impairment including clusters such as neurogenesis, differentiation and synapse. Many of these circRNAs were also predicted to interact with miRNAs, supporting a potential miRNA sponging function for these circRNA.
Discussion
RNA sequencing in the human postmortem DLPFC revealed dysregulation of circRNA expression in schizophrenia. This alteration was characterized by a substantial decrease in circRNA expression in the disorder. Bioinformatic predictions of circRNA interaction suggest they function as miRNA regulators and may have a broader role in etiology or pathophysiology of the disorder.
Circular RNAs (circRNAs) are a relatively new class of RNA transcript with high abundance in the mammalian brain. Here, we show that circRNAs expression in differentiated neuroblastoma cells were ...significantly altered after depolarization with 107 upregulated and 47 downregulated circRNAs. This coincided with a global alteration in the expression of microRNA (miRNA) (
= 269) and mRNA (
= 1511) in depolarized cells, suggesting a regulatory axis of circRNA-miRNA-mRNA is involved in the cellular response to neural activity. In support of this, our in silico analysis revealed that the circular transcripts had the capacity to influence mRNA expression through interaction with common miRNAs. Loss-of-function of a highly expressed circRNA, circ-EXOC6B, resulted in altered expression of numerous mRNAs enriched in processes related to the EXOC6B function, suggesting that circRNAs may specifically regulate the genes acting in relation to their host genes. We also found that a subset of circRNAs, particularly in depolarized cells, were associated with ribosomes, suggesting they may be translated into protein. Overall, these data support a role for circRNAs in the modification of gene regulation associated with neuronal activity.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Abstract
Background
Retinoic acid (RA) is intrinsically linked to neurodevelopment and has been implicated in schizophrenia (SZ). This is supported by preliminary trials of a retinoid receptor ...agonist, Bexarotene, as an adjuvant and the association of five common variants in proximity to members of this pathway at genome wide significance. In addition to these high frequency variants with small effect size, we suspect that this pathway is also affected by rare variants with much higher impact. We aimed to examine the burden of variants in retinoid loci in schizophrenia along with its potential consequences for clinical practice.
Methods
Whole genome sequencing was performed on SZ cases (N=331) and non-psychiatric controls (N=167). Cases were further clustered by cognitive measures to derive the cognitive deficit (CD; N=166) and cognitively spared (CS; N=165) subtypes. Disease and subtype associated genomic variation was then analysed in a panel of 129 genes selected for involvement in RA biology (Molecular Signatures Database). Rare variation was aggregated at the gene level using the optimal unified sequence kernel association test (SKAT-O). Clinical metadata was further examined for each case with a rare putative high impact loss of function variant in a RA panel gene predicted using SnpEff. The rare variant burden on target genes of RA receptor binding in SZ was investigated by logistic regression of variants mapped to consensus 5 base pair spaced direct repeat (DR5) retinoic acid response element (RARE) motifs.
Results
Gene level rare variant association uncovered suggestive associations with SZ (P < 0.01) for three retinoid genes – RBP3, ADH1C and RPE65. In addition, a stronger signal was detected overall for CD cases implicating four additional genes including the RA receptors RARB (P = 1.1 x 10–3) and RARG (P = 9.2 x 10–3). SZ patients with a rare high impact genotype predicted in a RA panel gene were more likely to have serious symptomology as defined by a global assessment of functioning (GAF) score below 50, P = 7.1 x 10–3 (Two-Tailed Fisher’s Exact Test). We also found evidence of an increased burden of rare variants within predicted DR5-RARE in SZ (P = 0.017, odds ratio OR = 1.094, 95% confidence interval CI = 1.023- 1.186), however, there was no significant difference between the cognitive subtypes (CD/CS, P = 0.8, OR = 1.002, 95% CI = 0.961–1.045).
Discussion
Our findings suggest that RA mediated control of gene expression is heterogeneously disrupted in SZ by rare variants in DR5-RARE motifs. Strong signals in the context of our sample size further support the possibility of enrichment of rare loci in genes involved with RA biology, particularly in CD cases with impaired cognition. Moreover, we identified a subset of patients with likely high effect size genotypes in the RA pathway. Future work will examine whether these high-risk patients would benefit from retinoid based pharmacological intervention.
Differentiation of neural progenitor cells into mature neuronal phenotypes relies on extensive temporospatial coordination of mRNA expression to support the development of functional brain circuitry. ...Cleavage and polyadenylation of mRNA has tremendous regulatory capacity through the alteration of mRNA stability and modulation of microRNA (miRNA) function, however the extent of utilization in neuronal development is currently unclear. Here, we employed poly(A) tail sequencing, mRNA sequencing, ribosome profiling and small RNA sequencing to explore the functional relationship between mRNA abundance, translation, poly(A) tail length, alternative polyadenylation (APA) and miRNA expression in an in vitro model of neuronal differentiation. Differential analysis revealed a strong bias towards poly(A) tail and 3'UTR lengthening during differentiation, both of which were positively correlated with changes in mRNA abundance, but not translation. Globally, changes in miRNA expression were predominantly associated with mRNA abundance and translation, however several miRNA-mRNA pairings with potential to regulate poly(A) tail length were identified. Furthermore, 3'UTR lengthening was observed to significantly increase the inclusion of non-conserved miRNA binding sites, potentially enhancing the regulatory capacity of these molecules in mature neuronal cells. Together, our findings suggest poly(A) tail length and APA function as part of a rich post-transcriptional regulatory matrix during neuronal differentiation.
Abstract
Genome-wide association studies (GWAS) of schizophrenia have strongly implicated a risk locus in close proximity to the gene for miR-137. While there are candidate single-nucleotide ...polymorphisms (SNPs) with functional implications for the microRNA’s expression encompassed by the common haplotype tagged by rs1625579, there are likely to be others, such as the variable number tandem repeat (VNTR) variant rs58335419, that have no proxy on the SNP genotyping platforms used in GWAS to date. Using whole-genome sequencing data from schizophrenia patients (n = 299) and healthy controls (n = 131), we observed that the MIR137 4-repeats VNTR (VNTR4) variant was enriched in a cognitive deficit subtype of schizophrenia and associated with altered brain morphology, including thicker left inferior temporal gyrus and deeper right postcentral sulcus. These findings suggest that the MIR137 VNTR4 may impact neuroanatomical development that may, in turn, influence the expression of more severe cognitive symptoms in patients with schizophrenia.
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