Abnormalities in Prefrontal Cortical Gene Expression Profiles Relevant to Schizophrenia in MK-801-Exposed C57BL/6 Mice

Lactobacillus Johnsonii YH1136 alleviates schizophrenia-like behavior in mice: a gut-microbiota-brain axis hypothesis study

Based on the microbiota-gut-brain axis (MGBA) hypothesis, probiotics play an increasingly important role in treating various psychiatric disorders. Schizophrenia (SCZ) is a common mental disease with a complex pathogenesis and is challenging to treat. Although studies have elucidated the mechanisms associated with the interactions between the microbiota-gut-brain axis and SCZ, few have specifically used probiotics as a therapeutic intervention for SCZ. Accordingly, the current study determines whether L. johnsonii YH1136 effectively prevents SCZ-like behavior in mice and identifies the associated key microbes and metabolites. An SCZ mouse model was established by intraperitoneal injection of MK-801; L. johnsonii YH1136 was administered via oral gavage. L. johnsonii YH1136 significantly improves abnormal behaviors, including psychomotor hyperactivity and sociability and alleviates aberrant enzyme expression associated with tryptophan metabolism in SCZ mice. Additionally, L. johnsonii YH1136 upregulates hippocampal brain-derived neurotrophic factor (BDNF) levels while downregulating tryptophan 2,3-dioxygenase (TDO2), indoleamine-pyrrole 2,3-dioxygenase 1 (IDO1), kynurenine aminotransferase 1 (KAT1). Subsequent 16S rRNA sequencing of intestinal contents suggests that L. johnsonii YH1136 modulates the gut flora structure and composition by increasing the relative abundance of Lactobacillus and decreasing Dubosiella in SCZ mice. N-acetylneuraminic acid and hypoxanthine are the key serum metabolites mediating the interaction between the MGBA and SCZ. These results partially reveal the mechanism underlying the effects of L. johnsonii YH1136 on SCZ-like behavior in mice, supporting the development of therapeutic L. johnsonii probiotic formulations against SCZ.

Hippocampal reelin and GAD67 gene expression and methylation in the GFAP.HMOX1 mouse model of schizophrenia

Schizophrenia is a complex neuropsychiatric disorder featuring enhanced brain oxidative stress and deficient reelin protein. GFAP.HMOX10-12m mice that overexpress heme oxygenase-1 (HO-1) in astrocytes manifest a schizophrenia-like neurochemical, neuropathological and behavioral phenotype including brain oxidative stress and reelin downregulation. We used RT-PCR, targeted bisulfite next-generation sequencing, immunohistochemistry and in situ hybridization on hippocampal tissue of GFAP.HMOX10-12m mice to delineate a possible molecular mechanism for the downregulation of reelin and to identify the neuronal and non-neuronal (glial) cell types expressing reelin in our model. We found reduced reelin and increased DNMT1 and TET1 mRNA expression in the hippocampus of male GFAP.HMOX10-12m mice and reduced GAD67 mRNA expression in females. These mRNA changes were accompanied by sexually dimorphic alterations in DNA methylation levels of Reln and Gad1 genes. Reelin protein was expressed by oligodendrocytes and GABAergic interneurons, but not by astrocytes or microglia in GFAP.HMOX10-12m and wild-type brains of both sexes. Reelin mRNA was also observed in oligodendrocytes. Moreover, a significant downregulation of reelin-expressing oligodendrocytes was detected in the hippocampal dentate gyrus of male GFAP.HMOX10-12m mice. These results suggest a novel mechanism for brain reelin depletion in schizophrenia. Containment of the astrocytic HO-1 cascade by pharmacological or other means may protect against stress-induced brain reelin depletion in schizophrenia and other neurodevelopmental disorders.

MK-801-exposure induces increased translation efficiency and mRNA hyperacetylation of Grin2a in the mouse prefrontal cortex

Acute exposure to MK-801, the non-competitive N-methyl-D-aspartate (NMDA) receptor antagonist, induces schizophrenia-like behavioural changes in juvenile male mice. However, the effects of acute MK-801 exposure on brain gene expression at the translation level remain unclear. Here, we conducted ribosome profiling analysis on the prefrontal cortex (PFC) of acute MK-801-exposed juvenile male mice. We found 357 differentially translated genes, with the N4-acetylcytidine (ac4C) consensus motif enriched in the transcripts with increased translation efficiency. Acetylated RNA immunoprecipitation sequencing revealed 148 differentially acetylated peaks, of which 121 were hyperacetylated, and 27 were hypoacetylated. Genes harbouring these peaks were enriched in pathways related to axon guidance, Hedgehog signalling pathway, neuron differentiation, and memory. Grin2a encodes an NMDA receptor subunit NMDAR2A, and its human orthologue is a strong susceptibility gene for schizophrenia. Grin2a mRNA was hyperacetylated and exhibited significantly increased translation efficiency. NMDAR2A protein level was increased in MK-801-exposed PFC. Pretreatment of Remodelin, an inhibitor of N-acetyltransferase 10, returned the NMDAR2A protein levels to normal and partially reversed schizophrenia-like behaviours of MK-801-exposed mice, shedding light on the possible role of mRNA acetylation in the aetiology of schizophrenia.

Craniofacial anomalies in schizophrenia-relevant GFAP.HMOX10-12m mice

Subtle craniofacial dysmorphology has been reported in schizophrenia patients. This dysmorphology includes midline facial elongation, frontonasal anomalies and a sexually dimorphic deviation from normal directional asymmetry of the face, with male patients showing reduced and female patients showing enhanced facial asymmetry relative to healthy control subjects. GFAP.HMOX10-12m transgenic mice (Mus musculus) that overexpress heme oxygenase-1 in astrocytes recapitulate many schizophrenia-relevant neurochemical, neuropathological and behavioral features. As morphogenesis of the brain, skull and face are highly interrelated, we hypothesized that GFAP.HMOX10-12m mice may exhibit craniofacial anomalies similar to those reported in persons with schizophrenia. We examined craniofacial anatomy in male GFAP.HMOX10-12m mice and wild-type control mice at the early adulthood age of 6-8 months. We used computer vision techniques for the extraction and analysis of mouse head shape parameters from systematically acquired 2D digital images, and confirmed our results with landmark-based geometric morphometrics. We performed skull bone morphometry using digital calipers to take linear distance measurements between known landmarks. Relative to controls, adult male GFAP.HMOX10-12m mice manifested craniofacial dysmorphology including elongation of the nasal bones, alteration of head shape anisotropy and reduction of directional asymmetry in facial shape features. These findings demonstrate that GFAP.HMOX10-12m mice exhibit craniofacial anomalies resembling those described in schizophrenia patients, implicating heme oxygenase-1 in their development. As a preclinical mouse model, GFAP.HMOX10-12m mice provide a novel opportunity for the study of the etiopathogenesis of craniofacial and other anomalies in schizophrenia and related disorders.

Biclustering data analysis: a comprehensive survey

Biclustering, the simultaneous clustering of rows and columns of a data matrix, has proved its effectiveness in bioinformatics due to its capacity to produce local instead of global models, evolving from a key technique used in gene expression data analysis into one of the most used approaches for pattern discovery and identification of biological modules, used in both descriptive and predictive learning tasks. This survey presents a comprehensive overview of biclustering. It proposes an updated taxonomy for its fundamental components (bicluster, biclustering solution, biclustering algorithms, and evaluation measures) and applications. We unify scattered concepts in the literature with new definitions to accommodate the diversity of data types (such as tabular, network, and time series data) and the specificities of biological and biomedical data domains. We further propose a pipeline for biclustering data analysis and discuss practical aspects of incorporating biclustering in real-world applications. We highlight prominent application domains, particularly in bioinformatics, and identify typical biclusters to illustrate the analysis output. Moreover, we discuss important aspects to consider when choosing, applying, and evaluating a biclustering algorithm. We also relate biclustering with other data mining tasks (clustering, pattern mining, classification, triclustering, N-way clustering, and graph mining). Thus, it provides theoretical and practical guidance on biclustering data analysis, demonstrating its potential to uncover actionable insights from complex datasets.

Supplementation of PQQ from pregnancy prevents MK-801-induced schizophrenia-like behaviors in mice

RATIONALE

At present, the research on the prevention of schizophrenia is still in its infancy. Pyrroloquinoline quinone (PQQ) has potential to treat psychological and neurological diseases including schizophrenia. However, the preventive effect of PQQ on schizophrenia remains unclear.

OBJECTIVES

In this study, we aimed to examine the preventive effect of supplementation of dietary PQQ from pregnancy or after birth on dizocilpine (MK-801)-induced schizophrenia-like behaviors in mice.

RESULTS

Supplementation of dietary PQQ from pregnancy could effectively prevent MK-801-induced weight gain decrease, hyperlocomotion, stereotypical behavior, ataxia, exploratory activity decrease, social interaction disorder, memory deficit, and depression in mice. Supplementation of dietary PQQ after birth could effectively prevent MK-801-induced weight gain decrease, stereotypical behavior, ataxia, and memory deficit in mice. Female mice responded to a greater degree than males in preventing MK-801-induced weight gain decrease in both forms of PQQ supplementation. For mice that began PQQ supplementation after birth, females performed better than males in preventing MK-801-induced ataxia, memory deficit, and depression. For mice that began PQQ supplementation from pregnancy, males performed better than females in preventing MK-801-induced memory deficit. In vitro experiments indicated that PQQ supplementation in the earlier stage of life contributed to the growth of neurons and the development of neurites.

CONCLUSIONS

Our current study suggested that PQQ supplementation from pregnancy or postpartum could prevent some schizophrenia-like behaviors induced by MK-801 in mice. Our work supported the potential usage of dietary supplement of PQQ in preventing or alleviating symptoms associated with schizophrenia.

A comparison of transcriptome analysis methods with reference genome

Background

The application of RNA-seq technology has become more extensive and the number of analysis procedures available has increased over the past years. Selecting an appropriate workflow has become an important issue for researchers in the field.

Methods

In our study, six popular analytical procedures/pipeline were compared using four RNA-seq datasets from mouse, human, rat, and macaque, respectively. The gene expression value, fold change of gene expression, and statistical significance were evaluated to compare the similarities and differences among the six procedures. qRT-PCR was performed to validate the differentially expressed genes (DEGs) from all six procedures.

Results

Cufflinks-Cuffdiff demands the highest computing resources and Kallisto-Sleuth demands the least. Gene expression values, fold change, p and q values of differential expression (DE) analysis are highly correlated among procedures using HTseq for quantification. For genes with medium expression abundance, the expression values determined using the different procedures were similar. Major differences in expression values come from genes with particularly high or low expression levels. HISAT2-StringTie-Ballgown is more sensitive to genes with low expression levels, while Kallisto-Sleuth may only be useful to evaluate genes with medium to high abundance. When the same thresholds for fold change and p value are chosen in DE analysis, StringTie-Ballgown produce the least number of DEGs, while HTseq-DESeq2, -edgeR or -limma generally produces more DEGs. The performance of Cufflinks-Cuffdiff and Kallisto-Sleuth varies in different datasets. For DEGs with medium expression levels, the biological verification rates were similar among all procedures.

Conclusion

Results are highly correlated among RNA-seq analysis procedures using HTseq for quantification. Difference in gene expression values mainly come from genes with particularly high or low expression levels. Moreover, biological validation rates of DEGs from all six procedures were similar for genes with medium expression levels. Investigators can choose analytical procedures according to their available computer resources, or whether genes of high or low expression levels are of interest. If computer resources are abundant, one can utilize multiple procedures to obtain the intersection of results to get the most reliable DEGs, or to obtain a combination of results to get a more comprehensive DE profile for transcriptomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08465-0.

Double trouble: Prenatal immune activation in stress sensitive offspring

Viral infections during pregnancy are associated with increased incidence of psychiatric disorders in offspring. The pathological outcomes of viral infection appear to be caused by the deleterious effects of innate immune response-associated factors on development of the fetus, which predispose the offspring to pathological conditions in adulthood. The negative impact of viral infections varies substantially between pregnancies. Here, we explored whether differential stress sensitivity underlies the high heterogeneity of immune reactivity and whether this may influence the pathological consequences of maternal immune activation. Using mouse models of social dominance (Dom) and submissiveness (Sub), which possess innate features of stress resilience and vulnerability, respectively, we identified differential immune reactivity to the synthetic analogue of viral double-stranded RNA, Poly(I:C), in Sub and Dom nulliparous and pregnant females. More specifically, we found that Sub females showed an exacerbated pro- and anti-inflammatory cytokine response to Poly(I:C) as compared with Dom females. Sub offspring born to Sub mothers (stress sensitive offspring) showed enhanced locomotory response to the non-competitive NMDA antagonist, MK-801, which was potentiated by prenatal Poly(I:C) exposure. Our findings suggest that inherited stress sensitivity may lead to functional changes in glutamatergic signaling, which in turn is further exacerbated by prenatal exposure to viral-like infection. The maternal immunome seems to play a crucial role in these observed phenomena.

Decreased neuronal synaptosome associated protein 29 contributes to poststroke cognitive impairment by disrupting presynaptic maintenance

Background: Poststroke cognitive impairments are common in stroke survivors, and pose a high risk of incident dementia. However, the cause of these cognitive impairments is obscure and required an investigation.

Methods: Oxygen-glucose deprivation (OGD) model and middle cerebral artery occlusion (MCAO) model were used to imitate in vitro or in vivo acute cerebral ischemia, respectively. The differentially expressed synaptosome associated protein 29 (SNAP29)-interacting proteins upon ischemia and reperfusion were analyzed with bioinformatics analysis and the results indicated that the changes of SNAP29 after acute ischemia were mainly involved in the synaptic functions. The outcomes of SNAP29 reduction were assessed with SNAP29 knockdown, which mimicked the distribution of SNAP29 along neuronal processes after acute ischemia. Using the whole-cell patch clamp recording method and transmission electron microscope, the pre-synaptic function and readily releasable pool (RRP) were observed after SNAP29 knock down. Using photogenetic manipulations and behavioral tests, the neuronal projection and cognitive functions of mice with SNAP29 knock down in hippocampus CA1 region were evaluated.

Results: It was found that SNAP29 protein levels decreased in both in vitro and in vivo ischemic models. Further, the SNAP29 reduction wasn't associated with impaired autophagy flux and neuronal survival. When SNAP29 was knocked down in primary cortical neurons, the frequency of AMPARs-mediated mEPSCs, but not the amplitude, significantly decreased. Meanwhile, the mice with SNAP29 knockdown at CA1 region of hippocampus developed an impairment in hippocampus-mPFC (middle prefrontal cortex) circuit and behavioral dysfunctions. Moreover, the size of RRP at presynaptic sites was diminished.

Conclusion: Since SNAP29 protein levels didn't significantly influence the neuronal survival and its decrease was sufficient to disturb the neural circuit via a presynaptic manner, the SNAP29-associated strategies may be an efficient target against poststroke synaptic dysfunction and cognitive deficits.

Strategic Timing of Glial HMOX1 Expression Results in Either Schizophrenia-Like or Parkinsonian Behavior in Mice

Aims: In this original research communication, we assess the impact of shifting the window of glial HMOX1 overexpression in mice from early-to-midlife to mid-to-late life, resulting in two disparate conditions modeling schizophrenia (SCZ) and Parkinson's disease (PD). Mesolimbic hyperdopaminergia is a widely accepted feature of SCZ, while nigrostriatal hypodopaminergia is the sine qua non of idiopathic PD. Although the advent of parkinsonian features in SCZ patients after treatment with antidopaminergic agents is intuitive, subtle features of parkinsonism commonly observed in young, drug-naïve schizophrenics are not. Similarly, emergent psychosis in PD subjects receiving levodopa replacement is not unusual, whereas spontaneous hallucinosis in nonmedicated persons with idiopathic PD is enigmatic. Investigations using GFAP.HMOX1 mice may shed light on these clinical paradoxes. Results: Astroglial heme oxygenase-1 (HO-1) overexpression in mice throughout embryogenesis until 6 or 12 months of age resulted in hyperdopaminergia, hyperkinesia/stereotypy ameliorated with clozapine, deficient prepulse inhibition of the acoustic startle response, reduced preference for social novelty, impaired nest building, and cognitive dysfunction reminiscent of SCZ. On the contrary, astroglial HO-1 overexpression between 8.5 and 19 months of age yielded a PD-like behavioral phenotype with hypodopaminergia, altered gait, locomotor incoordination, and reduced olfaction. Innovation: We conjecture that region-specific disparities in the susceptibility of dopaminergic and other circuitry to the trophic and degenerative influences of glial HMOX1 induction may permit the concomitant expression of mixed SCZ and PD traits within affected individuals. Conclusion: Elucidation of these converging mechanisms may (i) help better understand disease pathogenesis and (ii) identify HO-1 as a potential therapeutic target in neurodevelopmental and neurodegenerative disorders.

Dentate Gyrus Immaturity in Schizophrenia

Hippocampal abnormalities have been heavily implicated in the pathophysiology of schizophrenia. The dentate gyrus of the hippocampus was shown to manifest an immature molecular profile in schizophrenia subjects, as well as in various animal models of the disorder. In this position paper, we advance a hypothesis that this immature molecular profile is accompanied by an identifiable immature morphology of the dentate gyrus granule cell layer. We adduce evidence for arrested maturation of the dentate gyrus in the human schizophrenia-affected brain, as well as multiple rodent models of the disease. Implications of this neurohistopathological signature for current theory regarding the development of schizophrenia are discussed.