Chronic Alcohol Exposure Alters Gene Expression and Neurodegeneration Pathways in the Brain of Adult Mice

Background: Chronic alcohol consumption can alter the structure of the central nervous system and disrupt cognitive function. Alcoholics are more likely to develop neurodegenerative disorders such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). However, the role of alcohol in promoting neurotoxicity and neurodegeneration remains unclear. Objective: In this study, we aimed at estimating the effects of chronic binge alcohol exposure on brain transcriptome and behavior changes in a chronic “Drinking in the Dark” (DID) mouse model. Methods: The adult C57BL/6J male mice were exposed to alcohol for 4 weeks. RNA-seq was applied to assess the effects of chronic alcohol exposure on transcriptome in brain. The open field test and novel object recognition test were used to assess the changes of anxiety level, locomotive function, and short-term memory induced by alcohol. RNA-seq analysis revealed that chronic alcohol exposure caused significant change in the brain transcriptome, especially in prefrontal cortex. Results: The gene dysregulation caused by chronic alcohol exposure includes pathways related to mitochondrial energy metabolism (such as oxidative phosphorylation) and multiple neurodegenerative diseases (such as AD and PD). Furthermore, the pathway and network analyses suggest that the genes involved in mitochondrial energy metabolism, ubiquitin-proteasome system, Wnt signaling pathway, and microtubules may attribute to the neurotoxicity and neurodegeneration caused by chronic alcohol consumption. Additionally, locomotive function was also significantly impaired. Conclusion: This work provides gene transcriptional profile data for future research on alcohol-induced neurodegenerative diseases, especially AD and PD.

Convergent Cerebrospinal Fluid Proteomes and Metabolic Ontologies in Humans and Animal Models of Rett Syndrome

MECP2 loss-of-function mutations cause Rett syndrome, a disorder that results from a disrupted brain transcriptome. How these transcriptional defects are decoded into a disease proteome remains unknown. We studied the proteome in Rett syndrome cerebrospinal fluid (CSF) across vertebrates. We identified a consensus proteome and ontological categories shared across Rett syndrome cerebrospinal fluid (CSF) from three species, including humans. Rett CSF proteomes enriched proteins annotated to HDL lipoproteins, complement, mitochondria, citrate/pyruvate metabolism, as well as synapse compartments. We used these prioritized and shared ontologies to select analytes for orthogonal quantification. These studies independently validated our proteome and ontologies. Ontologically selected CSF hits had genotypic discriminatory capacity as determined by Receiver Operating Characteristic (ROC) analysis and distinguished Rett from a related neurodevelopmental disorder, CDKL5 deficiency disorder. We propose that Mecp2 mutant CSF proteomes and ontologies inform novel putative mechanisms and biomarkers of disease. We suggest that Rett syndrome is a metabolic disorder impacting synapse function.

The Protective Effects of Apigenin on Cognitive Function and The Brain Transcriptome in Old Mice

Age-related declines in cognitive function increase the risk of developing mild cognitive impairment and dementia, but select nutraceuticals (bioactive plant compounds) may hold promise for protecting the brain and improving cognitive function with age. Apigenin is a flavonoid nutraceutical found in chamomile and reported to inhibit multiple hallmarks of aging; however, it has not been studied in the context of brain aging specifically. We treated young (6 mo) and old (27 mo) C57BL/6N mice with apigenin (0.5 mg/mL in 0.2% carboxymethylcellulose) or control (0.2% carboxymethylcellulose) drinking water for 6 weeks. Then, we assessed cognitive function and performed RNA-seq to characterize global transcriptomic changes and potential mechanisms of action in the brain. We observed impaired novel object recognition (NOR) test performance (an index of learning/memory) in old vs. young control mice (P<0.0001), but old apigenin mice had ~3-fold higher NOR performance relative to old control mice (P=0.02). Transcriptomic analyses also showed age-associated gene expression changes related to immune function and inflammation, consistent with the established role of inflammation in brain aging. However, some of these key changes were reversed by apigenin. In fact, >300 genes were differentially expressed in old apigenin-treated mice vs. old controls, and the biological processes linked with these differences were related to innate and adaptive immune function, and cytokine and chemokine regulation. We are performing protein/signaling pathway analyses to elucidate downstream cellular changes associated with apigenin treatment, but our current results suggest apigenin may be a promising nutraceutical candidate for preventing brain aging.

Brain Transcriptome of Autism Spectrum Disorders and Tourette Syndrome Defines Common Targetable Inflammatory Pathways Involving Cytokines, Complement, and Kinase Signalling

BackgroundNeurodevelopmental disorders (NDDs), including autism-spectrum disorders (ASD) and Tourette syndrome (TS) are common brain conditions which often co-exist, however current management focuses on symptom mitigation, with no approved treatments targeting disease mechanisms. There is accumulating literature implicating the immune system in NDDs, and transcriptomics of post-mortem brain tissue from individuals with NDDs has revealed an inflammatory signal. MethodsWe interrogated two RNA-sequencing datasets of ASD and TS (compared to age-matched controls) and identified the top 1000 differentially expressed genes, to explore commonly enriched pathways using an over-representation analysis through GO, KEGG and Reactome.ResultsIn the ASD analysis, the top 1000 DEGs enriched 754 GO terms (all upregulated), 55 KEGG pathways (54 upregulated), and 109 Reactome pathways (all upregulated), involving inflammation, cytokines, complement, cell signalling and epigenetic regulation. In the TS analysis, the top 1000 DEGs enriched 419 GO terms (416 upregulated), 56 KEGG pathways (all upregulated), and 28 Reactome (all upregulated) pathways, including inflammation, cytokines, signal transduction and immune response to stimuli. Of the top 1000 DEGs from the ASD and TS analyses, 133 DEGs were shared. Interaction networks of the common protein-coding DEGs using STRING revealed 5 central up-regulated hub genes: CSF2RB, HCK, HCLS1, LCP2 and PLEK, which are all kinases involved in cell signalling. Applying KEGG and Reactome analysis to these common DEGs identified pathways involving interleukins, complement activation, and cell signalling pathways. ConclusionsThese findings bring new evidence of shared inflammation in ASD and TS, and provide therapeutic opportunities targeting inflammation, epigenetic machinery, and cell signalling including kinases.

Do Fragile X Syndrome and Other Intellectual Disorders Converge at Aberrant Pre-mRNA Splicing?

Fragile X Syndrome is a neuro-developmental disorder caused by the silencing of the FMR1 gene, resulting in the loss of its protein product, FMRP. FMRP binds mRNA and represses general translation in the brain. Transcriptome analysis of the Fmr1-deficient mouse hippocampus reveals widespread dysregulation of alternative splicing of pre-mRNAs. Many of these aberrant splicing changes coincide with those found in post-mortem brain tissue from individuals with autism spectrum disorders (ASDs) as well as in mouse models of intellectual disability such as PTEN hamartoma syndrome (PHTS) and Rett Syndrome (RTT). These splicing changes could result from chromatin modifications (e.g., in FXS, RTT) and/or splicing factor alterations (e.g., PTEN, autism). Based on the identities of the RNAs that are mis-spliced in these disorders, it may be that they are at least partly responsible for some shared pathophysiological conditions. The convergence of splicing aberrations among these autism spectrum disorders might be crucial to understanding their underlying cognitive impairments.

Integrative brain transcriptome analysis links complement component 4 and HSPA2 to the APOE ε2 protective effect in Alzheimer disease

Mechanisms underlying the protective effect of apolipoprotein E (APOE) ε2 against Alzheimer disease (AD) are not well understood. We analyzed gene expression data derived from autopsied brains donated by 982 individuals including 135 APOE ɛ2/ɛ3 carriers. Complement pathway genes C4A and C4B were among the most significantly differentially expressed genes between ɛ2/ɛ3 AD cases and controls. We also identified an APOE ε2/ε3 AD-specific co-expression network enriched for astrocytes, oligodendrocytes and oligodendrocyte progenitor cells containing the genes C4A, C4B, and HSPA2. These genes were significantly associated with the ratio of phosphorylated tau at position 231 to total Tau but not with amyloid-β 42 level, suggesting this APOE ɛ2 related co-expression network may primarily be involved with tau pathology. HSPA2 expression was oligodendrocyte-specific and significantly associated with C4B protein. Our findings provide the first evidence of a crucial role of the complement pathway in the protective effect of APOE ε2 for AD.

Integrated Quantitative Neuro-transcriptome Analysis of Several Brain Areas in Human Trisomy 21

Background Although Down syndrome (DS) is a trisomy of chromosome 21 being the most frequent human chromosomal disorder mainly associated with variables dysfunctions. Objective In this context, we aimed to analyze and compare the disruption of transcriptome of several brain areas from individuals with DS and euploid controls as a new approach to consider a global systemic differential disruption of gene expression beyond of chromosome 21. Methods We used data from a DNA microarray experiment with ID GSE59630 previously deposited in the GEO DataSet of NCBI database. The array contained log2 values of 17,537 human genes expressed in several aeras of human brain. We calculated the differential gene expression (Z-ratio) of all genes. Results We found several differences in gene expression along the DS brain transcriptome, not only in the genes located at chromosome 21 but in other chromosomes. Moreover, we registered the lowest Z-ratio correlation between the age ranks of 16–22 weeks of gestation and 39–42 years (R 2 = 0.06) and the highest Z-ratio correlation between the age ranks of 30–39 years and 40–42 years (R 2 = 0.89). The analysis per brain areas showed that the hippocampus and the cerebellar cortex had the most different gene expression pattern when compared to the brain as a whole. Conclusions Our results support the hypothesis of a systemic imbalance of brain protein homeostasis, or proteostasis network of cognitive and neuroplasticity process as new model to explain the important effect on the neurophenotype of trisomy that occur not only in loci of chromosome 21 but also in genes located in other chromosomes.