KNeMAP: a network mapping approach for knowledge-driven comparison of transcriptomic profiles.

MOTIVATION: Transcriptomic data can be used to describe the mechanism of action (MOA) of a chemical compound. However, omics data tend to be complex and prone to noise, making the comparison of different datasets challenging. Often, transcriptomic profiles are compared at the level of individual gene expression values, or sets of differentially expressed genes. Such approaches can suffer from underlying technical and biological variance, such as the biological system exposed on or the machine/method used to measure gene expression data, technical errors and further neglect the relationships between the genes. We propose a network mapping approach for knowledge-driven comparison of transcriptomic profiles (KNeMAP), which combines genes into similarity groups based on multiple levels of prior information, hence adding a higher-level view onto the individual gene view. When comparing KNeMAP with fold change (expression) based and deregulated gene set-based methods, KNeMAP was able to group compounds with higher accuracy with respect to prior information as well as is less prone to noise corrupted data. RESULT: We applied KNeMAP to analyze the Connectivity Map dataset, where the gene expression changes of three cell lines were analyzed after treatment with 676 drugs as well as the Fortino et al. dataset where two cell lines with 31 nanomaterials were analyzed. Although the expression profiles across the biological systems are highly different, KNeMAP was able to identify sets of compounds that induce similar molecular responses when exposed on the same biological system. AVAILABILITY AND IMPLEMENTATION: Relevant data and the KNeMAP function is available at: https://github.com/fhaive/KNeMAP and 10.5281/zenodo.7334711.

Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment.

The COVID-19 disease led to an unprecedented health emergency, still ongoing worldwide. Given the lack of a vaccine or a clear therapeutic strategy to counteract the infection as well as its secondary effects, there is currently a pressing need to generate new insights into the SARS-CoV-2 induced host response. Biomedical data can help to investigate new aspects of the COVID-19 pathogenesis, but source heterogeneity represents a major drawback and limitation. In this work, we applied data integration methods to develop a Unified Knowledge Space (UKS) and used it to identify a new set of genes associated with SARS-CoV-2 host response, both in vitro and in vivo. Functional analysis of these genes reveals possible long-term systemic effects of the infection, such as vascular remodelling and fibrosis. Finally, we identified a set of potentially relevant drugs targeting proteins involved in multiple steps of the host response to the virus.

The responsiveness of TrkB to BDNF and antidepressant drugs is differentially regulated during mouse development.

BACKGROUND: Previous studies suggest that the responsiveness of TrkB receptor to BDNF is developmentally regulated in rats. Antidepressant drugs (AD) have been shown to increase TrkB signalling in the adult rodent brain, and recent findings implicate a BDNF-independent mechanism behind this phenomenon. When administered during early postnatal life, ADs produce long-lasting biochemical and behavioural alterations that are observed in adult animals. METHODOLOGY: We have here examined the responsiveness of brain TrkB receptors to BDNF and ADs during early postnatal life of mouse, measured as autophosphorylation of TrkB (pTrkB). PRINCIPAL FINDINGS: We found that ADs fail to induce TrkB signalling before postnatal day 12 (P12) after which an adult response of TrkB to ADs was observed. Interestingly, there was a temporally inverse correlation between the appearance of the responsiveness of TrkB to systemic ADs and the marked developmental reduction of BDNF-induced TrkB in brain microslices ex vivo. Basal p-TrkB status in the brain of BDNF deficient mice was significantly reduced only during early postnatal period. Enhancing cAMP (cyclic adenosine monophosphate) signalling failed to facilitate TrkB responsiveness to BDNF. Reduced responsiveness of TrkB to BDNF was not produced by the developmental increase in the expression of dominant-negative truncated TrkB.T1 because this reduction was similarly observed in the brain microslices of trkB.T1(-/-) mice. Moreover, postnatal AD administration produced long-lasting behavioural alterations observable in adult mice, but the responses were different when mice were treated during the time when ADs did not (P4-9) or did (P16-21) activate TrkB. CONCLUSIONS: We have found that ADs induce the activation of TrkB only in mice older than 2 weeks and that responsiveness of brain microslices to BDNF is reduced during the same time period. Exposure to ADs before and after the age when ADs activate TrkB produces differential long-term behavioural responses in adult mice.

The loop diuretic bumetanide blocks posttraumatic p75NTR upregulation and rescues injured neurons.

Injured neurons become dependent on trophic factors for survival. However, application of trophic factors to the site of injury is technically extremely challenging. Novel approaches are needed to circumvent this problem. Here, we unravel the mechanism of the emergence of dependency of injured neurons on brain-derived neurotrophic factor (BDNF) for survival. Based on this mechanism, we propose the use of the diuretic bumetanide to prevent the requirement for BDNF and consequent neuronal death in the injured areas. Responses to the neurotransmitter GABA change from hyperpolarizing in intact neurons to depolarizing in injured neurons. We show in vivo in rats and ex vivo in mouse organotypic slice cultures that posttraumatic GABA(A)-mediated depolarization is a cause for the well known phenomenon of pathological upregulation of pan-neurotrophin receptor p75(NTR). The increase in intracellular Ca(2+) triggered by GABA-mediated depolarization activates ROCK (Rho kinase), which in turn leads to the upregulation of p75(NTR). We further show that high levels of p75(NTR) and its interaction with sortilin and proNGF set the dependency on BDNF for survival. Thus, application of bumetanide prevents p75(NTR) upregulation and neuronal death in the injured areas with reduced levels of endogenous BDNF.

Re-analysis of bipolar disorder and schizophrenia gene expression complements the Kraepelinian dichotomy.

The differential diagnosis of schizophrenia (SZ) and bipolar disorder (BD) is based solely on clinical features and upon a subset of overlapping symptoms. Within the last years, an increasing amount of clinical, epidemiological and genetic data suggested inconsistent with the Kraepelinian dichotomy. We performed re-analysis of genome-wide gene expression data obtained from postmortem prefrontal cortex (PEC) of both BD and SZ patients with matched controls from four independent microarray experiments. We found 2,577 and 477 genes specifically altered in BD and SZ, respectively. Of these, 164 genes were shared between the syndromes. We identified genes of the transcriptional and post-transcriptional machineries altered in BD and genes of the development changed in SZ. Our results showed that the genomic expression profile of BD and SZ had some similarity but still could be well-distinguished by suitable statistical test.

Antidepressant drugs transactivate TrkB neurotrophin receptors in the adult rodent brain independently of BDNF and monoamine transporter blockade.

BACKGROUND: Antidepressant drugs (ADs) have been shown to activate BDNF (brain-derived neurotrophic factor) receptor TrkB in the rodent brain but the mechanism underlying this phenomenon remains unclear. ADs act as monoamine reuptake inhibitors and after prolonged treatments regulate brain bdnf mRNA levels indicating that monoamine-BDNF signaling regulate AD-induced TrkB activation in vivo. However, recent findings demonstrate that Trk receptors can be transactivated independently of their neurotrophin ligands. METHODOLOGY: In this study we examined the role of BDNF, TrkB kinase activity and monoamine reuptake in the AD-induced TrkB activation in vivo and in vitro by employing several transgenic mouse models, cultured neurons and TrkB-expressing cell lines. PRINCIPAL FINDINGS: Using a chemical-genetic TrkB(F616A) mutant and TrkB overexpressing mice, we demonstrate that ADs specifically activate both the maturely and immaturely glycosylated forms of TrkB receptors in the brain in a TrkB kinase dependent manner. However, the tricyclic AD imipramine readily induced the phosphorylation of TrkB receptors in conditional bdnf⁻/⁻ knock-out mice (132.4±8.5% of control; P = 0.01), indicating that BDNF is not required for the TrkB activation. Moreover, using serotonin transporter (SERT) deficient mice and chemical lesions of monoaminergic neurons we show that neither a functional SERT nor monoamines are required for the TrkB phosphorylation response induced by the serotonin selective reuptake inhibitors fluoxetine or citalopram, or norepinephrine selective reuptake inhibitor reboxetine. However, neither ADs nor monoamine transmitters activated TrkB in cultured neurons or cell lines expressing TrkB receptors, arguing that ADs do not directly bind to TrkB. CONCLUSIONS: The present findings suggest that ADs transactivate brain TrkB receptors independently of BDNF and monoamine reuptake blockade and emphasize the need of an intact tissue context for the ability of ADs to induce TrkB activity in brain.

Darkness reduces BDNF expression in the visual cortex and induces repressive chromatin remodeling at the BDNF gene in both hippocampus and visual cortex.

Neuronal activity regulates the expression of brain-derived neurotrophic factor (BDNF) in brain. In darkness, reduced neuronal activity in the visual cortex markedly decreases total BDNF transcription level in adult rats. Epigenetic mechanisms are crucially involved in the regulation of gene expression in response to environmental stimuli. In this study, we examined the effect of 1 week of light deprivation (LD) on the activity-dependent changes in BDNF expression from different promoters in the visual cortex and hippocampus. We analyzed the correlation between the chromatin state of Bdnf promoters, exon-specific transcripts levels, and total protein levels in light-deprived rats and in rats reared under normal light-dark cycle. We found that 1 week of LD significantly reduced Bdnf mRNA and protein in the visual cortex but not in the hippocampus. However, epigenetic analysis revealed that LD increased histone-3 methylation and DNA methylation at the Bdnf promoter IV in both the visual cortex and hippocampus. These data highlight the spatial differences in signaling pathways that lead to the BDNF expression in response to diminished ambient light.

Comparison of gene expression profile in embryonic mesencephalon and neuronal primary cultures.

In the mammalian central nervous system (CNS) an important contingent of dopaminergic neurons are localized in the substantia nigra and in the ventral tegmental area of the ventral midbrain. They constitute an anatomically and functionally heterogeneous group of cells involved in a variety of regulatory mechanisms, from locomotion to emotional/motivational behavior. Midbrain dopaminergic neuron (mDA) primary cultures represent a useful tool to study molecular mechanisms involved in their development and maintenance. Considerable information has been gathered on the mDA neurons development and maturation in vivo, as well as on the molecular features of mDA primary cultures. Here we investigated in detail the gene expression differences between the tissue of origin and ventral midbrain primary cultures enriched in mDA neurons, using microarray technique. We integrated the results based on different re-annotations of the microarray probes. By using knowledge-based gene network techniques and promoter sequence analysis, we also uncovered mechanisms that might regulate the expression of CNS genes involved in the definition of the identity of specific cell types in the ventral midbrain. We integrate bioinformatics and functional genomics, together with developmental neurobiology. Moreover, we propose guidelines for the computational analysis of microarray gene expression data. Our findings help to clarify some molecular aspects of the development and differentiation of DA neurons within the midbrain.

Physiology, pathology and relatedness of human tissues from gene expression meta-analysis.

BACKGROUND: Development and maintenance of the identity of tissues is of central importance for multicellular organisms. Based on gene expression profiles, it is possible to divide genes in housekeeping genes and those whose expression is preferential in one or a few tissues and which provide specialized functions that have a strong effect on the physiology of the whole organism. RESULTS: We have surveyed the gene expression in 78 normal human tissues integrating publicly available microarray gene expression data. A total amount of 1601 genes were identified as selectively expressed in one or more tissues. The tissue-selective genes covered a wide range of cellular and molecular functions, and could be linked to 361 human diseases with Mendelian inheritance. Based on the gene expression profiles, we were able to form a network of tissues reflecting their functional relatedness and, to certain extent, their development. Using co-citation driven gene network technique and promoter analysis, we predicted a transcriptional module where the co-operation of the transcription factors E2F and NF-kappaB can possibly regulate a number of genes involved in the neurogenesis that takes place in the adult hippocampus. CONCLUSIONS: Here we propose that integration of gene expression data from Affymetrix GeneChip experiments is possible through re-annotation and commonly used pre-processing methods. We suggest that some functional aspects of the tissues can be explained by the co-operation of multiple transcription factors that regulate the expression of selected groups of genes.

FLUOXETINE modifies the expression of serotonergic markers in a differentiation-dependent fashion in the mesencephalic neural cell line A1 mes c-myc.

Serotonin (5-HT) is a neurotransmitter involved in a variety of CNS functions during development and in adulthood. 5-HT neurons are also involved in the pathogenesis of a number of psychiatric disorders. FLUOXETINE (FLX), a prototypic antidepressant, is a selective 5-HT uptake inhibitor (SSRI) with a demonstrated clinical efficacy in these disorders. SSRI, in a short-term period, binds 5-HT transporter (SERT) raising 5-HT levels at the synapse. Nevertheless, clinical improvement is observed only after 3-4 weeks of treatment. Recently, it has been shown that antidepressants, besides interfering with neurotransmission, can also display an effect on neural cells' proliferation and differentiation. Therefore it has been proposed that antidepressant may exert their clinical effects also acting on cellular functions other then neurotransmission. Here we show that a mesencephalic neural cell line, mes-c-myc A1 (A1) produces 5-HT and expresses SERT and both peripheral (TPH1) and CNS-specific (TPH2) form of tryptophan hydroxylase, the limiting enzyme in 5-HT biosynthesis. Cyclic AMP-dependent neuronal differentiation of A1 cells modulates the expression of TPHs. FLX, as well as citalopram (CIT), another SSRI inhibitor, modulates expression of serotonergic markers depending on the differentiation status of the cells. Interestingly, long-term but not short-term FLX treatment selectively modulates mRNA levels of TPH2, only in differentiated A1 cells. Finally, FLX and citalopram selectively decrease the proliferation rate of undifferentiated A1 cells, whereas have no effects on NIH-3T3 fibroblasts proliferation. In conclusion, neuronal differentiation of A1 cells not only modulates the expression of serotonergic markers, but appears to affect the response to FLX.

Correlations between negative symptoms and peripheral G protein levels in mononuclear leukocytes of deficit and nondeficit schizophrenics. Preliminary results.

Receptor-coupled G proteins were measured in mononuclear leukocytes (MNL) of 17 drug-treated patients with deficit schizophrenia (DS) and 16 drug-treated patients with nondeficit schizophrenia (NDS). No significant difference was found in MNL levels of G(alphas), G(alphai), G(alphaq) and G(beta) proteins between the two groups; however, MNL levels of G(alphas) were inversely correlated to the severity of negative symptoms in DS patients, while MNL levels of G(alphaq) were positively correlated to negative symptoms in NDS patients. Since G(alphas) and G(alphaq) are coupled to D-1 and 5-HT(2) receptors, respectively, these findings may support the hypothesis that a prevalent dysfunction of D-1 receptors is involved in the pathophysiology of negative symptoms in DS, whereas a prevalent dysfunction of 5-HT(2) receptors underlies negative symptoms in NDS. These results must be regarded as preliminary because of the possible interference of antipsychotic drugs on the explored parameters.