Mechanism of action of Rhodiola, salidroside, tyrosol and triandrin in isolated neuroglial cells: an interactive pathway analysis of the downstream effects using RNA microarray data.
Aim: The aim of this study was to identify the targets (genes, interactive signaling pathways, and molecular networks) of Rhodiola rosea extract in isolated neuroglia cells and to predict the effects of Rhodiola extract on cellular functions and diseases. In addition, the potential mechanism of action of Rhodiola rosea extract was elucidated, and the "active principle" among the three isolated constituents (salidroside, triandrin, and tyrosol) was identified.
Methods: Gene expression profiling was performed using the T98G human neuroglia cell line after treatment with the Rhodiola rosea SHR-5 extract and several of its individual constituents (salidroside, triandrin and tyrosol). An interactive pathway analysis of the downstream effects was performed using datasets containing significantly up- and down-regulated genes, and the effects on cellular functions and diseases were predicted.
Results: In total, the expression of 1062 genes was deregulated by the Rhodiola extract (631 analyzed, 336 --up-regulated, 295--down-regulated), and 1052,1062, and 1057 genes were deregulated by salidroside, triandrin, and tyrosol, respectively. The analysis of the downstream effects shows that the most significant effects of Rhodiola are associated with cardiovascular (72 deregulated genes), metabolic (63 genes), gastrointestinal (163 genes), neurological (95 genes), endocrine (60 genes), behavioral (50 genes), and psychological disorders (62 genes).
The most significantly affected canonical pathways across the entire dataset, which contains the 1062 genes deregulated by Rhodiola, were the following: (a) communication between innate and adaptive immune cells, (b) eNOS signaling, (c) altered T and B cell signaling in rheumatoid arthritis, (d) axonal guidance signaling, (e) G-protein coupled receptor signaling, (f) glutamate receptor signaling, (g) ephrin receptor signaling, (h) cAMP-mediated, and (i) atherosclerosis signaling pathways.
Genes associated with behavior and behavioral diseases were identified within intracellular signaling pathways (d) through (h). The analysis of the downstream effects predicted decreases in emotional and aggressive behavior, which corroborates the results from preclinical and clinical studies of the use of Rhodiola for the treatment of depression and anxiety. Of the 17 genes that regulate emotional behavior, nine exhibit expression patterns that are consistent with decreases in emotional behavior (z-score -2.529), and all five relevant genes are expressed in a manner consistent with decreases in aggressive behavior (z-score -2.197). A decrease in seizures and infarct sizes and an increase in the chemotaxis of cells were predicted to accompany the decrease in emotional and aggressive behaviors.
Conclusions: Rhodiola exhibits a multi-targeted effect on transcription to regulate the cellular response, affecting the various signaling pathways and molecular networks associated with beneficial effects on emotional behavior, particularly aggressive behavior, and with psychological, neurological, cardiovascular, metabolic, endocrine, and gastrointestinal disorders. Each of the purified compounds has its own pharmacological profile, which is both similar to and different from that of the total Rhodiola extract. In general, several compounds contribute to the specific cellular or/and physiological function of the extract in various diseases.
Rhodiola rosea is an 'adaptogen' indicated 'for temporary relief from symptoms of stress such as fatigue and the sensation of weakness' [EMEA, 2102]. Numerous clinical trials have demonstrated that repeated administrations of Rhodiola rosea extract SHR-5 exert anti-fatigue effects that increase mental performance, particularly the ability to concentrate [Darbinyan et al., 1999; Spasov et al., 2000a; Shevtsov et al., 2003], and reduce burnout in patients with fatigue syndrome [Olsson et al., 2009]. Encouraging results have been found for the use of Rhodiola against mild to moderate depression [Darbinyan et al., 2007] and generalized anxiety [Spasov et al., 2000b; Bystritsky et al., 2008]. These data agree with the results of in vitro studies using isolated cells [Asea et al., 2013; Panossian et al., 2012, 2013], nematodes [Wiegant et al., 2008, 2009], and animal models [Panossian et al., 2007, 2008a,b, 2009]. Collectively, the evidence supports the use of Rhodiola for the treatment of mental and behavioral disorders [Panossian and Wikman, 2009, 2010], which are usually treated with synthetic drugs targeting serotonergic, noradrenergic, glutamatergic, and GABA-ergic transmission (Nutt et al., 2002); these synthetic drugs, which have many adverse effects, include selective serotonin reuptake inhibitors (SSRIs), selective serotonin and noradrenalin reuptake inhibitors (SNRIs), and benzodiazepines (Tyrer and Baldwin, 2006).
The pathophysiology of mental and behavioral disorders is a multistaged and complex process that is not limited to the canonical pathways mentioned above. The beneficial stress-protective activity of Rhodiola is associated with several levels of regulation for homeostasis, the hypothalamic-pituitary-adrenal axis [Panossian, 2013], and the key mediators of intracellular communications. These key mediators include molecular chaperons, particularly Hsp70 [Prodius et al., 1997; Panossian et al., 2009; Lishmanov et al., 1996; Wiegant et al., 2008], stress-activated c-Jun N-terminal protein kinase 1 (JNK) [Panossian et al., 2007], forkhead box O (FOX-O) transcription factor DAF-16 [Wiegant et al., 2009], cortisol [Lishmanov et al., 1987; Panossian et al., 2007; Olsson et al., 2009], nitric oxide (NO) [Panossian et al., 2007], and [beta]-endorphin [Lishmanov et al., 1987; Maslov et al., 1997; Maimeskulova et al., 1997] and the biosynthesis of ATP, which changes the energy source [Abidov et al., 2003]. Studies on the anti-depressive and anxiolytic activity of Rhodiola rosea suggest that several of its mechanisms of action may contribute to (i) monoamine-oxidase A inhibition [van Diermen et al., 2009], (ii) monoamine modulation [Stancheva and Mosharrof, 1987], (iii) normalization of 5-HT (7), (iv) HPA-axis modulation (inhibition of cortisol, stress-induced protein kinases, and nitric oxide) (1, 6), and (v) anti-stress effects in animal depression models [Panossian et al., 2008a,b; Perfumi and Mattioli, 2007; Mattioli et al., 2009].
Initially, rhodioloside (syn. salidroside) was discovered to be an active principle in Rhodiola rosea root extract [Aksenova et al., 1968], Further pharmacological studies identified many other active constituents [Panossian et al., 2008a; van Diermen et al., 2009]. Consequently, the total extract is considered an active pharmaceutical ingredient in various Rhodiola rosea extracts, such as SHR-5 and FB300A, which may differ based on their phytochemical and pharmacological profiles. In this study, we tested the effects of the Rhodiola SHR-5 extract and three isolated compounds, specifically salidroside, triandrin, and tyrosol, on the gene expression profiles of isolated human neuroglia cells, which were measured using m-RNA arrays.
This study aimed to identify all of the molecular pathways and networks affected by Rhodiola at the transcriptional level for the regulation of cell responses. Therefore, we analyzed the microarray-based transcriptome-wide mRNA expression profiles of the T98G neuroglial cell line after exposure to Rhodiola rosea SHR-5 extract and three individual active compounds isolated from this plant: salidroside, tyrosol, and triandrin. The T98G neuroblastoma cell line was chosen based on a previous publication [Panossian et al., 2013], An interactive pathway downstream analysis was performed using datasets containing significantly up- or down-regulated genes, and the effects on relevant cellular functions and diseases were predicted and identified.
Materials and methods
Drugs and chemicals
Salidroside and tyrosol were purchased from Chromadex (Irvine, CA). Triandrin was isolated by the Swedish Herbal Institute (SHI) Research and Development (Goteborg, Sweden) and identified through comparison (HPLC, TLC, and UV) with an authentic reference sample that was kindly provided by Prof. Zapesoznaya (Institute of Officinal and Aromatic plants VILAR, Moscow, Russia). Pharmaceutical-grade standardized extracts of R. rosea L. roots were manufactured in accordance with the ICH Q7A and EMEA guidelines for Good Agricultural and Collecting Practice (GACP) and Good Manufacturing Practice (GMP) of active pharmaceutical ingredients (API). The working samples used during the experiments were prepared using diluted stock solutions (5mg/ml) of genuine Radix Rhodiola extract or 10mM solutions of purified analytical markers, specifically salidroside (3 mg/ml), triandrin (3.1 mg/ml), or tyrosol (1.4 mg/ml), in the appropriate volumes of phosphate buffered saline solution (PBS). Aliquots of the working solutions (200 [micro]L) were added to 3 ml of the cell culture to obtain final concentrations of the active markers and genuine extract equal to those obtained in the incubation media containing Rhodiola SHR-5 (Table 1 and Fig. 1).
The 40 [micro]g/ml dose (final concentration of Rhodiola SHR-5 in the incubation media) was chosen based on a recent pharmacokinetic study of Rhodiola rosea-derived salidroside in human blood plasma; we measured concentrations of approximately 1 [micro]g/ml, which equals 3 [micro]M (Panossian et al., 2010).
The concentrations of the total extracts of the three herbal ingredients and their active constituents are compatible in all of the test samples: the final concentration of salidroside was maintained at 3 [micro]M (900 [micro]g/l) across all of the test samples containing salidroside, including the Rhodiola extract. Similarly, the triandrin and tyrosol concentrations were calculated based on an HPLC analysis of their contents in genuine extracts and combinations thereof. The concentration of the genuine Rhodiola extract was calculated using specification to ensure that it corresponds to the therapeutically effective doses.
The T98G human neuroglial cell line was purchased from the American Type Culture Collection (ATCC, CRL-1690). The cells were grown in DMEM + GlutaMAX-1 (Gibco, Darmstadt, Germany) with 10% fetal bovine serum (Gibco, Darmstadt) and 1% penicillin/streptomycin (Gibco, Darmstadt). The cells were passaged twice a week and maintained in a 37[degrees]C incubator under a humidified atmosphere containing 5% C[O.sub.2]. All of the experiments were conducted using cells in the logarithmic growth phase.
The T98G cells were seeded 24 h before treatment on six-well plates at a density of 150,000 cells per well. The next day, the medium was removed, and the cells were treated in a final volume of 3 ml (Table 1).
The ethanol content of the media of the cells treated with the isolated compounds and the vehicle (control cells) was 0.8%. Two technical replicates were performed for each sample. The cells were incubated with the test substances for 24 h at 37[degrees]C prior to RNA isolation.
mRNA isolation and quality control
The cells were harvested after 24 h of treatment. The total RNA was isolated using the InviTrap Spin Universal RNA Mini kit (Stratec Molecular, Berlin, Germany) and dissolved in RNAse-free water. The RNA from the two technical replicates was combined (1:1) to generate one treatment sample and one control sample. The quality of the total RNA was assessed via gel analysis using the Total RNA Nano chip assay on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany). All of the samples were of the highest quality and had RIN values of 10.
Gene expression profiling
The microarray hybridizations were performed at the Institute of Molecular Biology (Mainz, Germany). Whole Human Genome RNA chips (8 x 60K Agilent) were used to profile the gene expression. The probe labeling and hybridization procedures were carried out according to the one-color microarray-based gene expression analysis protocol (http://www.chem.agilent.com/Library/ usermanuals/Public/G414090040_GeneExpression.One-color.v6. 5.pdf). Briefly, the total RNA was labeled and converted to cDNA, and fluorescent cRNA (cyanine 3-CTP) was then synthesized. The resulting material was purified using a QIAgen RNeasy Kit. After the cRNA was fragmented, the samples were hybridized for 17 h at 65[degrees]C. The microarray slides were washed and scanned with an Agilent Microarray Scanning system. The images were analyzed, and the data were extracted. The background was subtracted, and the data were normalized using the standard procedures included in the Agilent Feature Extraction Software.
Microarray data analysis
The expression data were analyzed further using the Chipster software (http://chipster.csc.fi/) to filter genes based on their expression and significance. These steps include the filtering of genes to isolate those that were up- or down-regulated between one- and three folds of the standard deviation (depending on the total number of extremely up- or down-regulated genes). A subsequent assessment of the significance of the genes using an empirical Bayes t-test narrowed the pool of genes further. All of the genes that were considered in the subsequent analysis were significantly different (p-value<0.05) compared with the control unless noted otherwise. The filtered data were then subjected to an Ingenuity pathway (Core) analysis to reveal the networks and pathways influenced by the treatments (http://www.ingenuity.com/).
The microarray data were validated using real-time RT-PCR as previously described [Panossian et al., 2013].
Interactive pathway analysis (IPA) of complex omics data
The signaling pathways related to the deregulated genes identified via the microarray analyses were determined as previously described (http://www.ingenuity.com/).
A microarray-based transcriptome-wide mRNA expression analysis was performed to identify the possible targets of the tested substances in T98G cells. The T98G cells were treated with the test substances for 24 h in two technical replicates, and the total RNA was then isolated and pooled for microarray hybridization. The significantly deregulated genes were identified relative to the untreated controls (p < 0.05) through an analysis using the Chipster software.
Ingenuity pathway analyses were performed using datasets containing the significantly up- or down-regulated genes: 1062 genes were deregulated by treatment with the Rhodiola extract (631 analyzed, 336 up-regulated, 295 down-regulated), and 1052, 1062, and 1057 genes were deregulated by treatment with salidroside, triandrin, and tyrosol, respectively.
Supplementary Table 1 lists the genes deregulated by more than twofold, as well as their magnitude of change, type, and location within the cell. Table 2 and Fig. 2 show the canonical pathways that were most strongly affected and their associated genes. The most significantly affected canonical pathways across the entire dataset containing the 1062 genes deregulated by Rhodiola were the following: (a) communication between the innate and adaptive immune cells, (b) eNOS signaling, (c) altered T and B cell signaling in rheumatoid arthritis, (d) axonal guidance signaling, (e) G-protein coupled receptor signaling, (f) glutamate receptor signaling, (g) ephrin receptor signaling, (h) cAMP-mediated signaling, and (i) atherosclerosis signaling pathways. Of these pathways, pathways (d) through (h) are associated with behavior and behavioral diseases.
The analysis of the downstream effects shows that the most significant effects of Rhodiola are associated with cardiovascular (72 genes), metabolic (63 genes), gastrointestinal (163 genes), neurological diseases (95 genes), endocrine (60 genes), behavioral (50 genes), and psychological disorders (62 genes). Fig. 3 displays the cellular functions and diseases associated with the genes and genetic networks that showed significant differences in expression after treatment with the test sample.
The analysis of the downstream effects predicted decreases in emotional and aggressive behavior and in neurological and cardiovascular diseases, as shown in Table 3.
The downstream effect analysis of the behavioral cluster showed that 50 genes involved in the regulation of behavior were affected by Rhodiola, as shown in Table 4. Among these, the effects on emotional and aggressive behaviors were predictable. This conclusion agrees with the results of preclinical and clinical studies on the use of Rhodiola for the treatment of depression and anxiety.
Of the 17 genes that regulate emotional behavior, nine exhibited expression levels consistent with decreases in emotional behavior. Therefore, decreases in emotional (z-score -2.529, overlap p-value 4.57E-06) and aggressive behavior were predicted (Tables 3 and 4), and all five relevant genes presented expression levels consistent with decreases in aggressive behavior (z-score -2.197, overlap p-value 5.74E-03), as shown in Table 5.
Fig. 4 shows the molecular network associated with emotional function and the effects of Rhodiola on the related gene expression.
Fig. 5 displays the most significantly affected canonical pathways associated with behavior and behavioral diseases, specifically behavioral disorders. The affected pathways include neuronal signaling pathways, intracellular pathways, and second messenger signaling pathways (Figs. 6-8).
The most significantly influenced pathways are the axonal guidance (Fig. 6 and Table 6), G-protein coupled receptor (Fig. 7 and Table 7), glutamate receptor (Fig. 8 and Table 8), ephrin receptor, and cAMP-mediated pathways.
Table 9 shows the effects of Rhodiola on the genes involved in psychological disorders, and Table 10 shows the effects of this extract on the genes involved in depression.
Of the 14 deregulated genes associated with depressive disorders, 11 encode various proteins located on the cell membrane, particularly receptor proteins (Fig. 9)
ADRAB (associated with alpha2-adrenergic Gi protein-coupled receptor) is one of the up-regulated genes. These sites play an essential role during numerous diseases, including attention deficit hyperactivity disorder, hypertension, cardiovascular disorder, multiple sclerosis, heart disease, post-traumatic stress disorder, stroke, major depression, bipolar disorder, Parkinson's disease, attention deficit disorder, psychomotor agitation, insomnia, mood disorder, anxiety disorder, social anxiety disorder, Alzheimer's disease, panic disorder, depressive disorder, and psychosis.
In addition to decreases in emotional and aggressive behaviors, decreases in seizures (8 of 17 affected genes exhibit a change in expression direction consistent with decreases in seizures, as shown in Table 11, overlap p-value 6.66E-03, activation z-score -2.2) and infarct sizes (7 of 9 affected genes exhibit a change in expression direction consistent with decreases in size of infarct sizes, as shown in Tables 12 and 13, overlap p-value 1.72E-03, activation z-score -2.157) were predicted.
An increase in cell chemotaxis (p-value 8.05E-04, activation z-score -2.206) was also predicted because 16 of 23 affected genes exhibited a change in expression direction consistent with an increase in chemotaxis.
Among affected genes in total of 256 genes are involved in cancer; however only for 27 genes, (Table 14) relationship between increased expression and tumor growth is known (Table 14). Based on gene expression direction of 14 genes, namely CCR2, CXCL6, DACT2, ELF5, ENAH, ESR1, FLT1, LIN28B, NCAM1, NOX4, SERPINA1, TLE1, TLR7, XRCC5, it can be concluded that Rhodiola may have beneficial effect in cancer, that is in line with growing body of evidence about antitumor activity of Rhodiola and salidroside [Cai et al., 2012; Zhang et al., 2013; Liu et al., 2012; Bocharova et al., 1995; Dement'eva and laremenko, 1987]. However effects on expression of 5 other genes, CDKN2C, FHL1, HGF, IL1RL1, CD53, are associated with tumor growth and carcinogenesis. Therefore, at this stage of knowledge it is not possible to predict overall effect of Rhodiola in cancer, based on the data available from this study and indirect literature data.
Tables 15-19 demonstrate the similarities and differences between the effects of the Rhodiola extract and those of the purified compounds isolated from the extract (salidroside, triandrin, and tyrolsol) on the following:
--gene expression profiles (Table 15) of isolated neuroglia cells,
--canonical pathways (Table 19),
--molecular and cellular functions (Table 17),
--physiological system functions (Table 18), and
--diseases and disorders (Table 16) associated with these effects.
The mechanisms utilized by the Rhodiola extract have been studied extensively. The mechanisms through which SHR-5 and its active constituents act on human emotion and behavior have been studied using isolated cells and through analyses of hormones and stress markers in animals. These studies have shown that the anti-depressive effects of SHR-5 and salidroside presumably operate in tandem with their effects on the following:
--the NPY-Hsp70-mediated effects on glucocorticoid receptors, including the expression and release of neuropeptide Y (NPY) and stress-activated proteins (Hsp70 and JNK); the activation of neuropeptide Y expression (Panossian et al., 2012), which is low during depression: and the activation of Hsp72 expression (Panossian et al., 2012), which inhibits stress-activated protein kinase JNK, a protein that plays an important role during the suppression of glucocorticoid receptors and consequently induces increases in cortisol expression during stress and depression (Panossian et al., 2007), the down-regulation of some G-protein coupled receptors, particularly the serotonin receptors in isolated neuroglia cells (Panossian et al., 2013), and
--the down-regulation of the estrogen alpha receptors in isolated neuroglia cells (Panossian et al., 2013).
The proposed mechanisms underlying the effect of Rhodiola on cognitive function, memory, learning, and attention are the following;
* the partial deregulation of GPCR, including the down-regulation of serotonin 5-HT3 GPCR,
* the deregulation of cAMP followed by the closure of hyperpolarization-activated channels,
* the up-regulation of P13K, which is required for the long-term potentiation of neurons,
* the up-regulation of IP3, which is important for inducing plasticity in cerebellar Purkinje cells,
* the up-regulation of the SERPINIi gene (serpin peptidase inhibitor, neuroserpin), which plays an important role in synapse development and regulates synaptic plasticity, and
* the normalization of cortisol homeostasis (Panossian et al., 2013).
In this study, we found many other intracellular targets for Rhodiola and its active constituents. Fig. 10 shows the scope and limitations of the conclusions based on this study.
During our study, we assessed gene expression in isolated neuroglia cells exposed to Rhodiola extract or one of its active constituents (salidroside, triandrin, and tyrosol) by analyzing mRNA arrays. An additional interactive pathway downstream analysis of the mRNA microarray data predicted the effects of Rhodiola on cellular functions, biological processes, and pharmacological activity. These effects exclude any possible interactions between Rhodiola at the metabolomics level of cellular response regulation and posttranslational steps, including agonistic or antagonistic effects on the receptors and effects on the allosteric regulation of enzymes that bind with cofactors.
The mechanisms of action (MOA) discussed above are related to a substance that consists of many compounds; this substance is extracted from dry roots and is called the "total extract". Total extracts are usually characterized using content marker compounds; these compounds, including salidroside, are found to be active toward some isolated cells, animals, and humans through some/various bioassays.
Initially, rhodioloside (syn. salidroside) was discovered to be an active principle of Rhodiola rosea root extract [Aksenova et al., 1968]. Further pharmacological studies identified many other active constituents; however, there is limited information regarding their activity and clinical importance [Panossian et al., 2008a,b; van Diermen et al., 2009] because these compounds lack sufficient scientific scrutiny. Consequently, the total extract is as an active pharmaceutical ingredient in various Rhodiola Rosea extracts, such as SHR-5 and FB300A; this substance may vary depending on its phytochemical and pharmacological profiles. In this study, we tested the effects of Rhodiola SHR-5 extract and three isolated compounds (salidroside, triandrin, and tyrosol) on the gene expression profile of isolated human neuroglia cells using an n-RNA array.
Furthermore, we analyzed the similarities and differences between the effects of the Rhodiola extract and those of the compounds isolated from the extract (salidroside, triandrin, and tyrosol):
--gene expression profiles (Table 15) in isolated neuroglia cells,
--canonical pathways (Table 19),
--molecular and cellular functions (Table 17),
--physiological system functions (Table 18), and
--diseases and disorders (Table 16) associated with these effects.
Fig. 11 shows Venn diagrams depicting the deregulated genes, and these reveal the common and unique aspects of each individual compound relative to the genes. Therefore, 265 (!) target genes are shared by the three compounds (Fig. 11a). Notably, only 153 of these 265 genes are targeted by the Rhodiola total extract, whereas 112 remain unaffected due to the antagonistic interactions of molecular networks, as discussed in a previous publication [Panossian et al., 2013], Therefore, the biological activity of the Rhodiola total extract differs from the activity of the purified compounds; however, some pharmacological features associated with these 112 inactive genes that are associated with the pure substances cannot be observed with the extract.
Consequently, each purified compound exhibited its own pharmacological profile, which presents with similarities to and differences from the profile obtained after treatment with the total Rhodiola extract. In general, several compounds contribute to the specific cellular or/and physiological functions associated with various diseases. The results of this study support both the principles of pharmacognosy based on the "magic bullet" model and the concept of multi-targeted therapy. Both of these concepts are relevant depending on the application, which is to develop a new specific drug from a complex or to develop a drug with a novel MOA.
Based on the results obtained during this study, we can draw some additional conclusions. Rhodiola has a multi-targeted effect at the transcriptional level on cell response regulation, affecting various signaling pathways and molecular networks associated with beneficial effects on emotional behavior, particularly aggressive behavior, as well as psychological, neurological, cardiovascular, metabolic, endocrine, and gastrointestinal disorders.
Appendix A. Supplementary data
Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.phymed. 2014.07.008.
Conflict of interest
R.H., T.E., and A.P. declare no competing financial interests. G.W. is a stockholder in the Swedish Herbal Institute (SHI).
Received 6 May 2014
Accepted 10 July 2014
This work was supported in part by the Swedish Herbal Institute (A.P., G.W.). We are indebted to Dr. Tolga Eichhorn (Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, University of Mainz, Mainz Germany) for his scientific discussions.
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Alexander Panossian (a), *, Rebecca Hamm (b), Georg Wikman (a), Thomas Efferth (b)
(a) Swedish Herbal Institute Research and Development, Goteborg, Sweden
(b) Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
* Corresponding author at: Swedish Herbal Institute Research and Development, Grondalsgatan 11 A, SE-412 62 Goteborg, Sweden. Tel.: +46 702818171.
E-mail addresses: email@example.com, firstname.lastname@example.org, email@example.com (A. Panossian).
Table 1 Concentrations used to treat T98G neuroglial cells during the microarray experiments. Drug Concentration Designation Rhodiola extract 40 [micro]g/ml Test sample F Salidroside (I) 3 [micro]M Test sample I Triandrin (II) 1.5 [micro]M Test sample J Tyrosol (III) 3 [micro]M Test sample K Table 2 Most significantly affected canonical pathways across the dataset containing the 1094 genes deregulated by Rhodiola. Ingenuity canonical pathways -log (p-value) (a) Ratio (b) Communication between innate and 3.6E00 7.14E-02 adaptive immune cells eNOS signaling 3.18E00 5.81E-02 Altered T cell and B cell 3.01E00 7E-02 signaling in rheumatoid arthritis Dendritic cell maturation 2.8E00 4.74E-02 Axonal guidance signaling 2.64E00 3.52E-02 G-protein coupled receptor 2.55E00 4.35E-02 signaling Stearate biosynthesis 1 (animals) 2.44E00 8.16E-02 Glutamate receptor signaling 2.36E00 6.94E-02 Ephrin receptor signaling 2.32E00 4.29E-02 Atherosclerosis signaling 2.18E00 5.07E-02 cAMP-mediated signaling 2.14E00 4.42E-02 Maturity onset diabetes of young 2.09E00 9.09E-02 (MODY) signaling NF-[kappa]B signaling 1.95E00 4.6E-02 Ephrin A signaling 1.95E00 7.41E-02 1L-12 signaling and production in 1.94E00 4.46E-02 macrophages Leptin signaling in obesity 1.93E00 5.88E-02 Intrinsic prothrombin activation 1.86E00 8.11E-02 pathway Primary immunodeficiency 1.83E00 6.25E-02 signaling Cytokines in communication 1.75E00 7.27E-02 between immune cells Thiamin salvage 111 1.74E00 2E-01 TR/RXR activation 1.71E00 4.59E-02 LXR/RXR activation 1.63E00 4.32E-02 Coagulation system 1.59E00 7.89E-02 tRNA splicing 1.59E00 6.52E-02 Cellular effects of viagra 1.51E00 3.87E-02 Estrogen biosynthesis 1.5E00 6.12E-02 Ingenuity canonical pathways Molecules/genes Communication between innate and TLR10,CD40LG,IL12B,HLA-B,TLR8, adaptive immune cells TLR7,IGHA1,TNFRSF17 eNOS signaling ADCY2,PRKGI,FLTI,PIK3C2G,CHRNB4, CNGB3,AQP4,ESR1,AQP2 Altered T cell and B cell IL21,TLR10,CD40LG,IL12B,TLR8, signaling in rheumatoid TLR7,TNFRSF17 arthritis Dendritic cell maturation CD1D,CD40LC,IL12B,LEPR,ZBTB12, HLAB,COL2A1,PIK3C2G,CD1C ,PLCD4 Axonal guidance signaling EPHA7,RGS3,PIK3C2G,WNT16,EPHA3, NTNG1,EPHA6,EPHB1, ADAM30, SEMA6D,SEMA3D,GNAT1,MMP8,UNC5D, PAK7,ADAM29,PLCD4 G-protein coupled receptor ADRA2B,ADCY2,RGS18,PDE3A,CNR1, signaling TAAR1,CALCR,PIK3C2G,PDE11A, PDE4D,AVPR1A,MC4R Stearate biosynthesis 1 (animals) SLC27A2,CYP2E1,ELOVL2,ACOT4 Glutamate receptor signaling SLC17A8,GRIN1,SLC17A6,GRIK2,GRIA3 Ephrin receptor signaling EPHA7,EPHA6,GRIN1,EPHB1,RGS3, GNAT1,PIK3C2G,PAK7,EPHA3 Atherosclerosis signaling CD40LG,APOA2,LPL,COL2A1,ALOX12, SERPINA1,CCR2 cAMP-mediated signaling ADRA2B,ADCY2,RGS18,PDE3A,CNR1, TAAR1,CNGB3,PDE11A,PDE4D,MC4R Maturity onset diabetes of young SLC2A2,FABP1,HNF1A (MODY) signaling NF-[kappa]B signaling TLR10,CD40LC,FLT1,TLR8,TLR7, PIK3C2G,BMPR1B,TNFRSF17 Ephrin A signaling EPHA7,EPHA6,PIK3C2G,EPHA3 1L-12 signaling and production in CD40LG,IL12B,APOA2,IFNA7,PIK3C2G, macrophages ALOX12,SERPINA1 Leptin signaling in obesity ADCY2,LEPR,PDE3A,PIK3C2G,PLCD4 Intrinsic prothrombin activation F10,CO2A1,FGB pathway Primary immunodeficiency CD40LG,IGHM,IGHA1,AICDA signaling Cytokines in communication IL21,IL20,IL12B,IFNA7 between immune cells Thiamin salvage 111 TPK1 TR/RXR activation F10,RXRG,DIO1,UCP1,PIK3C2C LXR/RXR activation RXRG,IL1RL1,APOA2,LPL,SERPINA1, CETP Coagulation system F10,SERPINA1,FGB tRNA splicing PDE3A,PDE11A,PDE4D Cellular effects of viagra ADCY2,PRKG1,GPR37,PDE3A,PDE4D, PLCD4 Estrogen biosynthesis HSD17B13,CYP2E1,CYP4X1 (a) Fisher's exact test. (b) The ratio was calculated as follows: # of genes in a given pathway that meet the cutoff criteria divided by total # of genes that make up that pathway. Table 3 Predicted effects of Rhodiola on behavioral disorders and neurological and cardiovascular diseases. The effects were determined using data of the deregulated genes and downstream effects. Category Disease or function p-Value Predicted annotation activation state Behavior Emotional behavior 4.57E-06 Decreased Behavior Aggressive behavior 5.74E-03 Decreased Neurological Seizures 6.66E-03 Decreased disease Cardiovascular Size of infarct 1.72E-03 Decreased disease Category Activation Molecules # z-score (a) molecules Behavior -2.529 AVPRIA,CCR2,CNR1,ESR1,GCN 17 T4,GRIK2,GRIN1,IRS4,LEPR,NP S,PAK7,RIMSI,SLCI7A6,SLC17 A8,SLC9A1,TACR3,XRCC5 Behavior -2.197 CNR1,ESR1,GCNT4,LEPR,PAK7 5 Neurological -2.203 CA9,CHRNB4,CNR1,GRIK2,GRI 17 disease N1,KAL1,KCNK2,NCAM1,NR4A 3,PIK3C2G,RIMS1,SCN10A,SCN 11A,SCN2B,SLC17A8,SLC9A1,T IPARP Cardiovascular -2.157 CCR2,CD40LG,CNR1,FGB,GP6,H 9 disease GF,HLA-B,NOX4,PPP1R1A (a) The z-score measures how much a particular value, such as x, differs from the mean value, denoted m. This difference (x-m) is then divided by the standard deviation (SD) to provide the z-score; z=(x-m)/SD; z<-2 or z> 2 implies significance. The z-score (normal scores, standardized variable) is the number of standard deviations that an observation is above the mean; z = (x-m)/SD, where: x--is the raw score, m--is the mean, and SD--is the standard deviation. The absolute value of z represents the distance between the raw score and the mean in units of the standard deviation. Table 4 Predicted effects of Rhodiola on behavioral disorders. The effects were determined based on the deregulated genes and data from the downstream effect analysis. Disease or function p-Value Predicted Activation annotation activation state z-score Behavior 7.69E-07 -0.240 Emotional behavior 4.57E-06 Decreased -2.529 Locomotion 3.08E-04 0.820 Licking behavior 3.12E-04 Nurture 6.69E-04 Active avoidance 1.49E-03 response Social behavior 1.71E-03 Self-administration 3.18E-03 of cocaine Conditioning 4.12E-03 0.728 Sexual receptivity 4.72E-03 of female organism Maternal nurturing 4.87E-03 Aggressive 5.74E-03 Decreased -2.197 behavior Ingestion of 5.87E-03 0.415 ethanol Aggressive 6.22E-03 behavior toward males Abnormal circadian 7.11E-03 phase Appetite 1.02E-02 Maternal behavior 1.02E-02 Disease or function Molecules # Molecules annotation Behavior AQP4,AVPR1A,BMPR1B,CCKBR,CCR2, 45 CHRNG,CNR1,CYP2E1,CYP46AI,DDC, EPHA,ESR1,FABP1,GCNT4,GNAT3, GRIK2,GRIN1,HNF4G,IRS4,LEPR, MC4R,MTM1,MTNR1A,NCAM1,NPS, NR4A3,PAK7,PDE11A,PRKG1,RIMSI, RXRG,SCN11A,SCN2B,SLC17A6, SLC17A8,SLC9A1,SMTNL1,SNRPN, TAAR1,TACR3,TAS1R2,TAS1R3, TAS2R4,TBX1,XRC5 Emotional behavior AVPR1A,CCR2,CNR1,ESR1,GCNT4,GRl 17 K2,GRIN1,IRS4,LEPR,NPS,PAK7, RIMS1,SLCl76,SLC17A8,SLC9A1, TACR3,XRCC5 Locomotion ALK,CCKBR,CHRNB4,CNR1,DAB1, 17 ESR1,GPR7,GRlA3,GRIN1,HNF4G, MC4R,NCAM1,NPS,PDE11A,RIMS1, RXRG,SLC17A6 Licking behavior ESRI,TAS1R2,TAS1R3 3 Nurture ESRI,GRIN1,IRS4,RIMS1,XRCC5 5 Active avoidance CNR1,PAK7,TACR3 3 response Social behavior AVPR1A,CNR1,GRIN1,PDE11A,RIMS1, 6 TBX1 Self-administration NPS,SLC17A6 2 of cocaine Conditioning ALK,BMPR1B,CCR2,CNR1,EPHA6, 10 ESR1,GR,GRIN1,NCAM1,SLC17A6 Sexual receptivity AVPR1A,ESR1 2 of female organism Maternal nurturing ESR1,IRS4,RIMS1,XRCC5 4 Aggressive CNR1,ESR1,GCNT4,LEPR,PAK7 5 behavior Ingestion of CCR2,CNR1,GRIA3,NPS 4 ethanol Aggressive ESR1,GCNT4,PAK7 3 behavior toward males Abnormal circadian MC4R,MTNR1A,NCAM1 3 phase Appetite LEPR,MC4R,SLC17A6 3 Maternal behavior AVPR1A,ESR1,IRS4 3 Table 5 Effect of Rhodiola on genes associated with emotional and aggressive behavior. Gene ID Entrez Gene Name and summary-target protein; http://www.ncbi.nlm.nih.gov/gene/ ESR1 Estrogen receptor 1 This gene encodes an estrogen receptor, specifically a ligand-activated transcription factor composed of several domains that are important for hormone binding, DNA binding, and transcription activation. The protein localizes at the nucleus. Estrogen and its receptors are essential for sexual development, reproductive function, and the development of other tissues, such as bone. Estrogen receptors are also involved in pathological processes, including breast cancer, endometrial cancer, and osteoporosis. CNR1 This gene encodes one of two guanine-nucleotide-binding GPCR proteins, which inhibit adenylate cyclase activity and are involved in the cannabinoid-induced CNS effects (including alterations in mood and cognition) experienced by users of marijuana. LEPR Leptin receptor. This protein is a receptor for leptin (an adipocyte-specific hormone that regulates body weight) and is involved in the regulation of fat metabolism and of a novel hematopoietic pathway required for normal lymphopoiesis. GRIK2 Glutamate receptor--the predominant excitatory neurotransmitter receptor inthe brain activated during various normal neurophysiologic processes. It is involved in the following: the negative regulation of synaptic transmission and glutamatergic and neuron apoptotic processes; the positive regulation of neuron apoptotic process and synaptic transmission; and the regulation of action potentials in a neuron, the JNK cascade, and the long-and short-term neuronal synaptic plasticity and transmission. Mutations in this gene have been associated with autosomal recessive mental retardation. PAK7 The protein encoded by this gene is a member of the PAK family of Ser/Thr protein kinases that regulate cytoskeletal dynamics, proliferation, and cell survival signaling. This kinase is predominantly expressed in the brain; it can promote neurite outgrowth and thus might affect neurite development, learning, locomotor behavior, and memory; AVPR1A The protein encoded by this gene acts as a GPC receptor for arginine vasopressin. Its activity is mediated by G-proteins that stimulate a phosphatidylinositol-calcium second messenger system. The receptor mediates cell contraction and proliferation, platelet aggregation, release of coagulation factor, and glycogenolysis. It is involved in social behavior, maternal aggressive behavior, negative regulation of transmission of nerve impulse, regulation of corticotropin secretion, penile erection, sperm ejaculation, etc. SLC17AS This gene encodes a vesicular glutamate transporter. The encoded protein transports glutamate into the synaptic vesicles before it is released into the synaptic cleft. GCNT4 This gene encodes an enzyme called N-acetyl lactosaminide beta-1,6-N-acetylglucosaminyl-transferase, which is involved in the regulation of carbohydrates, proteins, and thyroid hormone metabolism, post-translational protein modification, protein 0-linked glycosylation, inter-male aggressive behavior, etc. NPS This gene encodes a neuropeptide that is involved in the regulation of the action potential, the positive regulation of GABAergic synaptic transmission, the positive regulation of synaptic transmission, and visual learning. GRIN1 Glutamate receptor, ionotropic, N-methyl D-aspartate 1. The protein encoded by this gene is a critical subunit of the N-methyl-D-aspartate receptors, which are members of the glutamate receptor channel superfamily. These heteromeric protein complexes have multiple subunits arranged to form a ligand-gated ion channel. These subunits are critical for the plasticity of synapses, which supports memory and learning. CCR2 The receptors encoded by this gene mediate the agonist-dependent calcium mobilization and the inhibition of adenylyl cyclase. SLC17A6 This gene encodes a glutamate transporter that is involved in the regulation of neurotransmitter transport and uptake. IRS4 IRS4 encodes the insulin receptor substrate 4, which is a cytoplasmic protein that contains many potential tyrosine and serine/threonine phosphorylation sites. The tyrosine-phosphorylated IRS4 protein associates with cytoplasmic signaling molecules that contain SH2 domains. The IRS4 protein is involved in insulin-like growth factor receptor and insulin receptor-mediated signal transduction. RIMS1 The protein encoded by this gene is a RAS gene superfamily member that regulates synaptic vesicle exocytosis. This gene regulates the voltage-gated calcium channels during neurotransmitter and insulin release, glutamate secretion, long-term synaptic potentiation, neuronal synaptic plasticity, neurotransmitter secretion and transport, the positive regulation of synaptic vesicle fusion to the presynaptic membrane, and visual perception. XRCC5 The protein encoded by this gene is the 80-kilodalton subunit of the ATP-dependent DNA helicase II or DNA repair protein XRCC5 and is involved in the repair of double-stranded DNA breakage. It is involved in brain development, DNA recombination, DNA repair, the positive regulation of neurogenesis, etc. SLC9A1 The encoded protein is a plasma membrane transporter that plays a central role in regulating pH homeostasis. It is involved in neuronal death, the positive regulation of the action potential, apoptotic processes, the positive regulation of cell growth, mitochondrial membrane permeability, protein oligomerization, proton transport, transmembrane transport, etc. TACR3 This gene belongs to a family of genes that function as GPCR receptors for tachykinins. These genes regulate aging, the neuropeptide signaling pathway, dopamine metabolic processes, feeding behavior, the response to morphine, signal transduction, synaptic transmission, etc. Gene ID Prediction (based on change in Fold change expression direction) ESR1 Decreased -7.516 ESR1 is known to increase emotional behavior and is down-regulated by Rhodiola; therefore, it is predicted to decrease emotional behavior. CNR1 Decreased 3.182 CNRI is known to decrease emotional behavior and is up-regulated by Rhodiola; therefore, it is predicted to decrease emotional behavior. LEPR Decreased 2.676 LEPR is known to decrease emotional behavior and is up-regulated by Rhodiola; therefore, it is predicted to decrease emotional behavior. GRIK2 Decreased -3.182 GRIK2 is known to increase emotional behavior and is down-regulated by Rhodiola; therefore, it is predicted to decrease emotional behavior. PAK7 Decreased -3.095 PAK7 is known to increase emotional behavior and is down-regulated by Rhodiola; therefore, it is predicted to decrease emotional behavior. AVPR1A Decreased -3.482 AVPR1A is known to increase emotional behavior and is down-regulated by Rhodiola; therefore, it is predicted to decrease emotional behavior. SLC17AS Decreased 4.317 SLC17A8 is known to decrease emotional behavior and is up-regulated by Rhodiola; therefore, it is predicted to decrease emotional behavior. GCNT4 Decreased 2.809 GCNT4 is known to decrease emotional behavior and is up-regulated by Rhodiola; therefore, it is predicted to decrease emotional behavior. NPS Decreased 2.848 NPS is known to decrease emotional behavior and is up-regulated by Rhodiola; therefore, it is predicted to decrease emotional behavior. GRIN1 Increased 3.864 GRIN1 is known to increase emotional behavior and is up-regulated by Rhodiola; therefore, it is predicted to increase emotional behavior. CCR2 Affected -3.010 The literature indicates that this gene is involved in emotional behavior but does not indicate whether it increases or decreases the function. SLC17A6 Affected -2.751 IRS4 Affected -3.555 RIMS1 Affected 4.532 XRCC5 Affected 4.627 SLC9A1 Affected 3.340 TACR3 Affected -2.676 Gene ID Findings and references ESR1 Increases (Ogawa et al., 1997) CNR1 Decreases (Martin et al., 2002) LEPR Decreases (O'Rahilly et al., 2003) GRIK2 Increases (Ko et al., 2005) PAK7 Increases (Nekrasova et al., 2008) AVPR1A Increases (Bielsky et al., 2004) SLC17AS Decreases (Stone et al., 2009) GCNT4 Decreases (Amilhon et al., 2010) NPS Decreases (Rizzi et al., 2008) GRIN1 Increases CCR2 Affects SLC17A6 Affects IRS4 Affects RIMS1 Affects XRCC5 Affects SLC9A1 Affects TACR3 Affects Table 6 Genes involved in axonal guidance pathway that are deregulated by Rhodiola. Symbol Entrez gene name WNT16 Wingless-type MMTV integration site family, member 16 PLCD4 Phospholipase C, delta 4 ADAM29 ADAM metallopeptidase domain 29 MMP8 Matrix metallopeptidase 8 (neutrophil collagenase) EPHA6 EPH receptor A6 PAK7 p21 protein (Cdc42/Rac)-activated kinase 7 EPHA7 EPH receptor A7 EPHA3 EPH receptor A3 SEMA6D Serna domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D ADAM30 ADAM metallopeptidase domain 30 UNC5D Unc-5 homolog D (C. elegans) SEMA3D Serna domain, immunoglobulin domain (Ig), short basic domain, secreted. (semaphorin) 3D GNAT1 Guanine nucleotide binding protein (G-protein), alpha transducing activity polypeptide 1 NTNG1 Netrin G1 RGS3 Regulator of G-protein signaling 3 PIK3C2G Phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma EPHB1 EPH receptor B1 Symbol Fold change Location Type(s) WNT16 -7.781 Extracellular space Other PLCD4 -5.098 Cytoplasm Enzyme ADAM29 -4.993 Plasma membrane Peptidase MMP8 -3.227 Extracellular space Peptidase EPHA6 -3.095 Plasma membrane Kinase PAK7 -3.095 Nucleus Kinase EPHA7 -2.888 Plasma membrane Kinase EPHA3 -2.868 Plasma membrane Kinase SEMA6D -2.751 Plasma membrane Other ADAM30 2.848 Plasma membrane Peptidase UNC5D 3.272 Plasma membrane Other SEMA3D 3.605 Extracellular space Other GNAT1 3.681 Plasma membrane Enzyme NTNG1 4.056 Extracellular space Other RGS3 5.134 Nucleus Other PIK3C2G 6.589 Cytoplasm Kinase EPHB1 6.821 Plasma membrane Kinase Table 7 Genes involved in GPCR signaling pathways that are deregulated by Rhodiola. Symbol Entrez gene name PDE3A Phosphodiesterase 3A, cGMP-inhibited PIK3C2G Phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma PDE11A Phosphodiesterase 11A MC4R Melanocortin 4 receptor PDE4D Phosphodiesterase 4D, cAMP-specific TAAR1 Trace amine associated receptor 1 CNR1 Cannabinoid receptor 1 (brain) RGS18 Regulator of G-protein signaling 18 ADRA2B Adrenoceptor alpha 2B CALCR Calcitonin receptor AVPR1A Arginine vasopressin receptor 1A ADCY2 Adenylate cyclase 2 (brain) Symbol Fold change Location Type(s) PDE3A 9.000 Cytoplasm Enzyme PIK3C2G 6.589 Cytoplasm Kinase PDE11A 5.776 Cytoplasm Enzyme MC4R 4.659 Plasma membrane G-protein Coupled Receptor PDE4D 4.028 Cytoplasm Enzyme TAAR1 3.945 Plasma membrane G-protein Coupled Receptor CNR1 3.182 Plasma membrane G-protein Coupled Receptor RGS18 3.053 Cytoplasm Other ADRA2B 2.928 Plasma membrane G-protein Coupled Receptor CALCR 2.713 Plasma membrane G-protein Coupled Receptor AVPR1A -3.482 Plasma membrane G-protein Coupled Receptor ADCY2 -3.681 Plasma membrane Enzyme Table 8 Genes associated with the glutamate receptor signaling pathway that are deregulated by Rhodiola. Symbol Entrez gene name SLC17A8 Solute carrier family 17 (vesicular glutamate transporter), member 8 GRIN1 Glutamate receptor, ionotropic, N-methyl-D-aspartate 1 GRIA3 Glutamate receptor, ionotropic, AMPA 3 SLC17A6 Solute carrier family 17 (vesicular glutamate transporter), member 6 GRIK2 Glutamate receptor, ionotropic, kainate 2 Symbol Fold change Networks Location Type(s) SLC17A8 4.317 17 Plasma membrane Transporter GRIN1 3.864 7 Plasma membrane Ion channel GRIA3 3.031 7 Plasma membrane Ion channel SLC17A6 -2.751 12,14 Plasma membrane Transporter GRIK2 -3.182 7 Plasma membrane Ion channel Table 9 Effect of Rhodiola on genes involved in psychological diseases. Disease or p-Value Molecules # Molecules function annotation Substance-related 6.98E-06 ADRA2B,APOA2,AVPR1A,CA9, 13 disorders CHRNA1,CHRNB4,CHRNG, CNR1,DDC,GRIN1,PDE4D, SCN11A,SCN2B Addiction 1.62E-04 ADRA2B,APOA2,CA9,CHRNA1, 10 CHRNB4,CHRNG,CNR1,DDC, SCN11A,SCN2B Mood disorders 3.73E-04 ADRA2B,ALOX12,AQP4,CA9, 22 CACNB2,CCKBR,CHRNA1,CHR NB4,CHRNG,DDC,ESR1,GRIA3, GRIK2,GRIN1,KCNK2,MTNR1A, MYOM1,NCAM1,NDUFS7, PDE11A,SCN11A,SCN2B Depressive 7.90E-04 ADRA2B,AQP4,CACNB2, 14 disorder CCKBR,CHRNA1,CHRNB4, CHRNG,ESR1,CRIA3,GRIN1, KCNK2,MYOM1,NCAM1,PDE11A Tauopathy 8.33E-04 ADRA2B,APOA2,CETP,CNR1, 24 CYP46A1,DCX,DDC,ESR1,GNR HR,GRIA3,GRIN1,IGHM,LPL, MRC1,MTNR1A,PARP15,PDE3A, RAB6A,REG1A,SCN10A, SCN11A,SCN2B,SERPINA1, SLC2A2 Tobacco-related 1.36E-03 CHRNA1,CHRNB4,CHRNG,DDC 4 disorder Alcoholism 1.95E-03 ADRA2B,APOA2,CA9,CHRNA1, 8 CHRNB4,CHRNG,SCN11A,SCN2B Alzheimer's 4.51E-03 ADRA2B,APOA2,CETP,CNR1, 21 disease CYP46A1,DCX,DDC,ESR1,GNR HR,GRIA3,GRIN1,IGHM,LPL, MRC1,MTNR1A,PARP15, PDE3A,RAB6A,REG1A, SERPINA1,SLC2A2 Bipolar disorder 6.13E-03 ADRA2B,ALOX12,CA9,CACNB2, 14 DDC,ESR1,CRIA3,CR1K2, GRIN1,MTNR1A,NCAM1, NDUFS7,SCNUA,SCN2B Schizoaffective 6.32E-03 ADRA2B,CHRNA1,CHRNB4, 6 disorder CHRNG,ESR1,MTNR1A Pervasive 6.55E-03 ADRA2B,DCX,GRIN1,SNRPN, 5 developmental TCF7L2 disorder Delirium 7.91E-03 ADRA2B,CHRNA1,CHRNB4, 5 CHRNG,GRIN1 Disorder of the 9.49E-03 ADCY2,ADRA2B,AP1S2,AQP4, 28 basal ganglia BBOX1,CCKBR,CNR1,DDC, GPR88,GRIK2,GRIN1,HLA-B, KCNJ4,KCNK2,LPL,MTNR1A, PDE4D,PFKFB1,PPP1R1A, RAB6A,RXRG,SCN10A,SCN11A, SCN2B,SERPINA1,SLC17A4, SLC19A3,TMED10 Schizophrenia 1.07E-02 ADRA2B,ALK,CHRNA1,CHRNB4, 20 CHRNG,CNR1,CYP2E1,DAB1, ESR1,GPR37,GRIK2,GRIN1, MTNR1A,NCAM1,NTNG1, PIK3C2G,RXRG,SLC15A1, TCF7L2,TNXB Table 10 Effect of Rhodiolo on genes involved in depression. Symbol Entrees gene name and summary-target protein; Fold http://www.ncbi.nim.nih.gov/gene/ change ADRA2B Adrenoceptor alpha 2B. 2.928 Alpha-2-adrenergic receptors are members of the G-protein-coupled receptor superfamily. These receptors are critical for regulating the neurotransmitter release from sympathetic nerves and adrenergic neurons in the central nervous system AQP4 Aquaporin 4 3.01 This gene encodes a member of the aquaporin family of intrinsic membrane proteins that function as water-selective channels in the plasma membranes of many cells. The encoded protein is the predominant aquaporin found in the brain CACNB2 Calcium channel, voltage-dependent, beta 2 subunit. -3.387 This gene encodes a subunit of a voltage-dependent calcium channel protein that is a member of the voltage-gated calcium channel superfamily CCKBR Cholecystokinin B receptor. -2.621 This gene encodes a G-protein coupled receptor for gastrin and cholecystokinin (CCK), regulatory peptides of the brain and gastrointestinal tract CHRNA1 Cholinergic receptor, nicotinic, alpha I (muscle) -2.77 The muscle acetylcholine receptor consists of five subunits of four different types: two alpha subunits and one beta, gamma, and delta subunit. This gene encodes an alpha subunit that participates in acetylcholine binding/channel gating CHRNB4 Cholinergic receptor, nicotinic, beta 4 (neuronal) 5.464 CHRNG Cholinergic receptor, nicotinic, gamma (muscle) -5.028 The mammalian acetylcholine receptor is a transmembrane glycoprotein with several subunits. This gene encodes the gamma subunit, which participates in neuromuscular organogenesis and ligand binding. ESR1 Estrogen receptor 1 -7.516 This gene encodes an estrogen receptor, which is a ligand-activated transcription factor composed of several domains that are important for hormone binding, DNA binding, and transcription activation. The protein localizes to the nucleus, and estrogen and its receptors are essential for sexual development and reproductive function, as well as the development of other tissues, such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis GRIA3 Glutamate receptor, ionotropic, AMPA 3 3.031 Glutamate receptors are the predominant excitatory neurotransmitter receptors in the mammalian brain and are activated during various normal neurophysiologic processes. These receptors are heteromeric protein complexes composed of multiple subunits that are arranged to form ligand-gated ion channels GRIN1 Glutamate receptor, ionotropic, N-methyl-D- 3.864 aspartate 1 The protein encoded by this gene is a critical subunit of the N-methyl-D-aspartate receptors. These members of the glutamate receptor channel superfamily are heteromeric protein complexes with multiple subunits arranged to form a ligand-gated ion channel. These subunits are critical for the plasticity of synapses, which is believed to support memory and learning KCNK2 Potassium channel, subfamily K, member 2 3.411 This gene encodes one of the members of the two-pore-domain background potassium channel protein family. This type of potassium channel is formed by two homodimers that create a channel that releases potassium from the cell to control the resting membrane potential. MYOM1 Myomesin 1 2.732 NCAM1 Neural cell adhesion molecule 1 2.657 This gene encodes a cell adhesion protein that is involved in cell-to-cell interactions and cell-matrix interactions during development and differentiation. The encoded protein is involved in the development of the nervous system and cells involved in the expansion ofT cells and dendritic cells, which are critical for immune surveillance PDE11A 3',5'-cyclic-nucleotide phosphodiesterase (PDE) 5.776 The 3',5'-cyclic nucleotides CAMP and cGMP are the second messengers among numerous signal transduction pathways. The 3',5'-cyclic nucleotide phosphodiesterases (PDEs) catalyze the hydrolysis of CAMP and cGMP to form the corresponding 5'-monophosphates and provide a mechanism for dawn-regulating CAMP and cGMP signaling. This gene encodes a member of the PDE protein superfamily Symbol Depression-related biological process and role in cell ADRA2B Activation of MAPK cascade; activation of protein kinase B activity; adrenergic receptor signaling pathway; cell-cell signaling; GPCR-signaling pathway; negative regulation of epinephrine and norepinephrine secretion; positive regulation of neuron differentiation; signal transduction AQP4 Nervous system development; protein homooligomerization; renal water absorption; response to glucocorticoid stimulus; response to radiation; sensory perception of sound; transmembrane transport; regulation of dopamine and t-glutamic acid CACNB2 Axon guidance; calcium ion import; calcium ion transport; neuromuscular junction development; synaptic transmission; visual perception CCKBR Behavioral defense response; feeding behavior; phospholipase C-activating G-protein coupled receptor signaling pathway; GABAergic; positive regulation of synaptic transmission, glutamatergic; sensory perception; signal transduction; regulation of alpha catenin CHRNA1 Ion transmembrane transport; musculoskeletal movement; neuromuscular synaptic transmission; neuron homeostasis; signal transduction; synaptic transmission CHRNB4 Behavioral response to nicotine; ion transport; locomotor behavior; regulation of membrane potential; regulation of neurotransmitter secretion; smooth muscle contraction; synaptic transmission; synaptic transmission CHRNG Acetylcholine-activated cation-selective channel activity; acetylcholine receptor activity; cation transport; ion transmembrane transport; muscle contraction; regulation of membrane potential; signal transduction; synaptic transmission ESR1 Cellular response to estradiol stimulus; elevation of cytosolic calcium ion concentration; gene expression; intracellular steroid hormone receptor signaling pathway; male gonad development; negative regulation of the 1-kappaB kinase/NF-kappaB cascade; phospholipase C-activating G-protein coupled receptor signaling pathway; positive regulation of the nitric oxide biosynthetic process; signal transduction; transcription GRIA3 Glutamate receptor signaling pathway; ion transmembrane transport; ion transport; regulation of receptor recycling; synaptic transmission; long-term potentiation, long-term depression, plasticity, excitatory postsynaptic potential, depolarization, depotentiation, depression, GRIN1 Apoptosis, plasticity, synaptic transmission, long-term potentiation, cell death, transmembrane potential, excitotoxicity, cytotoxicity, communication, homeostasis KCNK2 G-protein coupled receptor signaling pathway; ion transport; potassium ion transmembrane transport; potassium ion transport; regulation of ion transmembrane transport; stabilization of membrane potential; synaptic transmission MYOM1 Muscle contraction NCAM1 Aging; axon guidance; cell surface receptor signaling pathway; learning or memory; multicellular organismal response to stress; negative regulation of cell death; neuron development; neuron projection development; organ regeneration; peripheral nervous system axon regeneration; positive regulation of calcium-mediated signaling; regulation of the sensory perception of pain; thalamus development PDE11A CAMP catabolic process; cGMP catabolic process; metabolic process; signal transduction Symbol Related disease ADRA2B Attention deficit hyperactivity disorder, hypertension, cardiovascular disorder, multiple sclerosis, heart disease, post-traumatic stress disorder, stroke, major depression, bipolar disorder, Parkinson's disease, attention deficit disorder, psychomotor agitation, insomnia, mood disorder, anxiety disorder, social anxiety disorder, Alzheimer's disease, panic disorder, depressive disorder, psychosis AQP4 Major depression, Huntington's disease, Parkinson's disease CACNB2 Hypertension, hype rcholesterolemia, hyperlipidemia, mania, depressive disorder, migraines, short-QT syndrome 4, Brugada syndrome, bipolar disorder, Alzheimer's disease CCKBR Withdrawal syndrome, hypergastrinemia, Huntington's disease, major depression, hyperphagia CHRNA1 Depressive disorder, seizures, psychomotor agitation, schizophrenia, stroke, coronary disease, etc. CHRNB4 Seizures, psychomotor agitation, schizophrenia, schizoaffective disorder, depressive disorder CHRNG Psychomotor agitation, schizophrenia, depressive disorder, Escobar syndrome, lethal multiple pterygium syndrome ESR1 Breast cancer, weight gain, atherosclerosis, obesity, depressive disorder, Alzheimer's disease, etc. GRIA3 Tremor, X-linked mental retardation, major depression, Alzheimer's disease, bipolar disorder GRIN1 Schizophrenia, Alzheimer's disease, Parkinson's disease, bipolar disorder, major depression, obsessive-compulsive disorder, multiple sclerosis, frontal lobe dementia, Lewy body disease, bipolar depression, binge eating disorder, opioid dependence, morbid obesity, autosomal dominant mental retardation type 8, attention deficit hyperactivity disorder, drug abuse, Down's syndrome, ataxia, frontotemporal dementia, anxiety disorder, autism, open-angle glaucoma, cognition disorder, postoperative pain, delirium, Huntington's disease, depressive disorder, dementia, breast cancer, partial seizure, tuberculosis, urinary tract infection, Lennox-Gastaut syndrome, epileptic seizure, hypophagia, starvation, neurodegeneration, bipolar I disorder KCNK2 Seizures, major depression, prostatic carcinoma, Huntington's disease MYOM1 Major depression NCAM1 Major depression, bipolar disorder PDE11A Physical disability, cardiovascular disorder, diabetes mellitus, major depression Table 11 Predicted effects of Rhodiola on seizures. The effects were determined based on the deregulated genes and the downstream effect analysis data. Genes in Prediction (based on Fold change Findings (number dataset change in expression of supporting direction) publications) CNR1 Decreased 3.182 Decreases (4) GRIN1 Decreased 3.864 Decreases (3) NCAMI Decreased 2.657 Decreases (2) SLC9A1 Decreased 3.340 Decreases (2) RIMS1 Decreased 4.532 Decreases (1) SCN2B Decreased 3.605 Decreases (4) SLC17A8 Decreased 4.317 Decreases (1) KCNK2 Decreased 3.411 Decreases (1) CHRNB4 Increased 5.464 Increases (2) NR4A3 Affected -3.272 Affects (1) GRIK2 Affected -3.182 Affects (2) KAL1 Affected 2.657 Affects (1) CA9 Affected 4.959 Affects (16) SCN10A Affected 5.856 Affects (6) TIPARP Affected -3.411 Affects (1) PIK3C2G Affected 6.589 Affects (1) SCN11A Affected 3.411 Affects (3) Table 12 Predicted effect of Rhodiola on genes involved in cardiovascular diseases and disorders. Disease or function p-Value Activation z-score annotation Size of Infarct 1.72E-03 -2.157 (a) Infarction 1.28E-03 -1.961 Vascular Disease 3.37E-09 -1.342 Cardiomyopathy 6.95E-03 -1.128 Heart Disease 6.05E-08 -0.994 Vascular Lesion 4.72E-04 -0.988 Atherosclerotic Lesion 7.43E-04 -0.843 Disorder of Artery 2.67E-08 -0.821 Ischemic Injury of the 9.29E-06 -0.816 Brain Cerebrovascular 1.24E-05 -0.816 Dysfunction Ischemia of the Brain 6.30E-04 -0.816 Arteriosclerosis 3.21E-08 -0.552 Atherosclerosis 7.19E-08 -0.293 Heart Dysfunction 6.98E-03 -0.228 Heart Failure 2.31E-03 0.246 Coronary Disease 2.20E-07 Hypertension 1.69E-06 Coronary Artery 7.85E-06 Disease Ischemic 2.11E-04 Cardiomyopathy Hyper-triglyceridemia 6.93E-04 Pulmonary Hypertension 9.83E-04 Intermittent 2.31E-03 Claudication Peripheral Vascular 2.59E-03 Disease Atherogenesis 2.78E-03 Venoocclusion 2.80E-03 Congestive Heart 2.91E-03 Failure Preeclampsia 3.19E-03 Stroke 4.13E-03 Pulmonary Hypertensive 4.42E-03 Arterial Disease Formation of Vascular 4.84E-03 Lesion Arrhythmia of Heart 5.36E-03 Ventricle Malignant Hypertension 5.41E-03 Growth of 6.52E-03 Atherosclerotic Lesion Angina Pectoris 6.55E-03 Heart Septa1 Defect 6.98E-03 Arrhythmia 7.37E-03 Hypotension 8.40E-03 Familial Combined 8.59E-03 Hyperlipidemia Hypercholesterol emia 9.62E-03 Cardiac Fibrillation 9.88E-03 Disease or function Molecules # Molecules annotation Size of Infarct CCR2,CD40LG,CNR1,FGB,GP6,HGF, 9 HLA-B,NOX4,PPPR1A Infarction ADRA2B,CCR2,CD40LG,CNR1,ESR1, 15 F10,FGB,GP6,GRIN1,HGF,HLA-B, NOX4,PDE3A,PPP1R1A,REG1A Vascular Disease ADRA2B,ALOX12,APOA2,AQP4, 49 BMPR1B,CACNB2,CCR2,CD1D,CD40LG, CL-FP,CHRNA1,CHRNB4,CHRNG, CNGB3,CNR1,CNTN5,COL2A1,DDC, EPHA3,ESR1,F10,FHL1,FLT1,GP6, GRIK2,GRIN1,IL1RL1,IL20,KCNK2, KL,KLF6,LPL,MCF2L,MGAM,MMP8, MTNR1A,MYO3B,NKX26,NOX4,PDE11A, PDE3A,PDE4D,PRKG,RASGRF2, SCN10A,SLC9A1,TBX1,TLR7,VWA3B Cardiomyopathy CACNB2,CCR2,CHRNA1,CHRNB4, 13 CHRNG,FHL1,LDB3,LEPR,PDE11A, PDE3A,PDE4D,PPP1R1A,TBX20 Heart Disease ADRA2B,AQP2,BMPR1B,CA9,CACNB2, 49 CCR2,CD40LG,CHRNA1,CHRNB4, CHRNG,CNGB3,CNR1,CNTN5,DDC, DPP6,EN04,EPHA3,ESR1,F10,FHL1, FLT1,GP6,HGF,HHEX,IGHM,IL1RL1, KCN2,KL,LDB3,LEFTY2,LEPR,LPL, MCF2L,MGAM,MY03B,NHLH1,NKX26, NOX4,PDE11A,PDE3A,PDE4D,PFKFB1, PPP1R1A,SCN10A,SLC9A1,TBX, TBX20,UBE4B,VWA3B Vascular Lesion APOA2,CCR2,CD1D,CD40LG,CETP, 13 ESR1,FLT1,IL1RL1,LPL,MMP8, MTNR1A,PCSK5,PRKG1 Atherosclerotic Lesion APOA2,CCR2,CD1D,CD40LG,CETP, 10 ESR1,FLT1,IL1RL1,LPL,PRKG1 Disorder of Artery ADRA2B,APOA2,BMPR1B,CACNB2, 35 CCR2,CD1D,CD40LG,CETP,CNGB3, CNR1,CNTN5,COL2A1,ESR1,F10, FLT1,GRIN1,IL1RL1,IL20,KL, KLF6,LPL,MCF2L,MGAM,MMP8, MTNR1A,MYO3B,NKX26,PDE11A, PDE3A,PDE4D,PRKG1,SLC9A1,TBX1, TLR7,VWA3B Ischemic Injury of the AQP4,CD1D,CNR1,KCNK2,NOX4, 6 Brain RASGRF2 Cerebrovascular ADRA2B,AQP4,CD1D,CHRNA1,CHRNB4, 14 Dysfunction CHRNG,CNR1,DDC,F10,KCNK2,NOX4, PDE3A,PDE4D,RASGRF2 Ischemia of the Brain AQP4,CD1D,CNR1,F10,KCNK2,NOX4, 7 RASGRF2 Arteriosclerosis ADRA2B,APOA2,BMPR1B,CACNB2, 31 CCR2,CD1D,CD40LG,CETP,CNGB3, CNR1,CNTN5,COL2A1,ESR1,F10, FLT1,GRIN1,IL1RL1,IL20,KL, KLF6,LPL,MCF2L,MGAM,MMP8, MY03B,PDE11A,PDE3A,PDE4D, PRKG1,SLC9A1,VWA3B Atherosclerosis ADRA2B,APOA2,BMPR1B,CACNB2, 30 CCR2,CD1D,CD40LG,CETP,CNGB3, CNR1,CNTN5,ESR1,F10,FLT1, GRIN1,IL1RL1,IL20,KL,KLF6,LPL, MCF2L,MGAM,MMP8,MYO3B,PDE11A, PDE3A,PDE4D,PRKG1,SLC9A1,VWA3B Heart Dysfunction CACNB2,FLT1,LPL,NOX4 4 Heart Failure ADRA2B,AQP2,CA9,CACNB2,ENO4, 12 EPHA3,IL1RL1,PDE11A,PDE3A, PDE4D,SLC9A1,UBE4B Coronary Disease ADRA2B,BMPR1B,CACNB2,CHRNA1, 22 CHRNB4,CHRNG,CNGB3,CNR1,CNTNS, ESR1,F10,FLT1,KL,LPL,MCF2L, MGAM,MYO3B,PDE11A,PDE3A,PDE4D, SLC9A1,VWA3B Hypertension ADRA2B,ALOX12,BMPR1B,CA9, 22 CACNB2,CHRNA1,CHRNB4,CHRNG, ESR1,F10,FHL1,FLT1,LPL,MYO3B, NOX4,PDE11A,PDE3A,PDE4D,PRKG1, SCN10A,SLC9A1,VWA3B Coronary Artery ADRA2B,BMPR1B,CACNB2,CNGB3, 18 Disease CNR1,CNTN5,F10,FLT1,KL,LPL, MCF2L,MGAM,MY03B,PDE11A,PDE3A, PDE4D,SLC9A1,VWA3B Ischemic CHRNA1,CHRNB4,CHRNG,PDE11A, 7 Cardiomyopathy PDE3A,PDE4D,PPP1R1A Hyper-triglyceridemia APOA2,CA9,CETP,LEPR,LPL,RP1 6 Pulmonary Hypertension ADRA2B,BMPR1B,FHL1,PDE11A, 6 SCN10A,SLC9A1 Intermittent PDE11A,PDE3A,PDE4D 3 Claudication Peripheral Vascular F10,LPL,PDE3A,SLC9A1 4 Disease Atherogenesis APOA2,CD1D,CD40LG,CETPESR1,LPL 6 Venoocclusion EPHA3,F10,LPL 3 Congestive Heart ADRA2B,AQP2,CACNB2,EPHA3, 7 Failure PDE3A,PDE4D,UBE4B Preeclampsia ADRA2B,ESR1,F10,FLT1,SCN10A 5 Stroke ADRA2B,CHRNA1,CHRNB4,CHRNG, 8 DDC,F10,PDE3A,PDE4D Pulmonary Hypertensive BMPR1B,FHL1,PDE11A,SCN10A 4 Arterial Disease Formation of Vascular APOA2,CD1D,CD40LG,CETP,ESR1, 7 Lesion LPL,PCSK5 Arrhythmia of Heart ADRA2B,CACNB2,DPP6,NHLH1, 5 Ventricle SCN10A Malignant Hypertension CHRNA1,CHRNB4,CHRNG 3 Growth of CCR2,FLT1 2 Atherosclerotic Lesion Angina Pectoris CACNB2,GP6,PDE11A,PDE3A,PDE4D 5 Heart Septa1 Defect ADRA2B,LEFTY2,TBXl,TBX20 4 Arrhythmia ADRA2B,CACNB2,CNTN5,DPP6,F10, 9 KCNK2,NHLH1,PDE4D,SCN10A Hypotension ADRA2B,AVPR1A,CNR1,DDC,F10 5 Familial Combined LPL,RXRG 2 Hyperlipidemia Hypercholesterol emia APOA2,CD40LG,FABP1,LPL 4 Cardiac Fibrillation ADRA2B,CNTN5,DPP6,F10,KCNK2, 6 NHLH1 (a) Predicted activation state. Table 13 Effects of Rhodiola on infarct size. Genes in Prediction (based Fold change Findings (number dataset on change in of supporting expression publications) direction) NOX4 Decreased -4.000 Increases (1) CP6 Decreased -3.227 Increases (1) HCF Decreased 3.580 Decreases (2) CNR1 Decreased 3.182 Decreases (2) FGB Decreased 2.908 Decreases (1) CD40LC Decreased -3.053 Increases (1) CCR2 Decreased -3.010 Increases (1) HLA-B Increased 3.182 Increases (1) PPP1R1A Affected 3.531 Affects (1) Table 14 Predicted effect of Rhodiola in cancer, deregulated genes and downstream effect analysis data. Genes in Prediction (based Fold change Findings (number dataset on expression of supporting direction) publications) CCR2 Decreased -3.010 Increases (12) CXCL6 Decreased 3.117 Decreases (3) DACT2 Decreased 2.504 Decreases (2) ELF5 Decreased 4.757 Decreases (2) ENAH Decreased -8.877 Increases (9) ESRl Decreased -7.516 Increases (206) FLT1 Decreased -2.657 Increases (224) LIN28B Decreased -3.010 Increases (6) NCAM1 Decreased 2.657 Decreases (30) NOX4 Decreased -4.000 Increases (7) SERPINA1 Decreased 12.729 Decreases (6) TLE1 Decreased -4.469 Increases (3) TLR7 Decreased 2.676 Decreases (46) XRCC5 Decreased 4.627 Decreases (9) AICDA Increased 10.126 Increases (3) CD53 Increased 3.732 Increases (1) CDKN2C Increased -2.990 Decreases (27) FHL1 Increased -8.398 Decreases (8) HCF Increased 3.580 Increases (42) IL1RL1 Increased 3.891 Increases (16) Table 15 Top up-and down-regulated genes by Rhodiola, salidroside, triandrin and tyrosol in T98C cells. The values show the fold changes compared with the control. Rhodiola rosea Slaidroside Gene Fold Gene Fold Symbol Change Symbol Change SERPINA1 12.729 KCNK10 13.086 AICDA 10.126 CHIT1 9.918 PDE3A 9.000 FETUB 9.918 GJB5 8.877 NMNAT3 9.646 K1R2DS3 8.574 OR51L1 9.646 OR51L1 7.516 EOMES 8.754 TNXB 7.013 AKR1D1 8.225 APOBEC2 6.821 PLA2G4D 8.225 EPHB1 6.821 DNAJC16 7.413 PPIP5K1 6.727 SLC15A1 6.916 SLC17A4 6.727 SMTNL1 6.916 UBXN10 6.727 BAI3 6.364 GALNT14 6.681 VN1R4 6.021 GCNT3 6.589 KCNK10 13.086 PIK3C2G 6.589 EPHB1 5.979 SF3B2 6.453 CHN2 5.938 SLC6A15 -5.938 CTNNA2 -6.589 HHEX -5.979 HTR3D -6.589 PDLIM2 -6.681 MCF2L -6.589 APLF -6.727 P2RY13 -6.589 DNAH7 -6.821 MTNR1A -6.916 PARP15 -7.210 GPR83 -7.210 ESB1 -7.516 POLN -7.210 TBX20 -7.674 TRDN -7.210 WNT16 -7.781 LRRC25 -7.464 GSTA3 -8.168 LILRB5 -7.890 FHL1 -8.398 NTN3 -8.574 ENAH -8.877 AGXT2 -8.754 UGT2A3 -9.254 PLCD4 -10.126 CETP -9.781 SLC6A15 -10.483 HNF4G -11.551 AKAP14 -11.236 Triandrin Tyrosol Gene Fold Gene Fold Symbol Change Symbol Change KCNH7 36.002 OR51L1 13.086 FETUB 10.853 PCDH8 10.483 DNAJC16 10.703 HS3ST5 9.918 SUCNR1 10.126 APOBEC2 9.849 TKTL2 9.781 CHIT1 9.514 CHIT1 9.318 K1R2DS3 8.515 ACTG2 8.815 SMTNL1 8.515 KIR2DS3 8.168 KLF6 8.056 OR51L1 7.89 FETUB 7.413 TLR8 7.413 DNAH2 6.774 PDE3A 7.062 XRCC5 6.727 SMTNL1 7.013 PHACTR3 6.364 APOBEC2 6.589 SGPP2 6.364 COL21A1 6.589 SLC15A1 6.364 KLF6 6.589 TCF7L2 6.364 SGPP2 6.589 AKR1D1 6.32 HFE -5.736 USP45 -22.785 EPHA6 -6.148 E2F2 -23.264 NPBWR2 -7.311 EFEMP2 -26.355 NTRK2 -7.362 NFIL3 -28.641 THNSL2 -9.254 DARS2 -29.857 CETP -9.514 KHDRBS1 -32.672 RAD9B -9.849 RB1CC1 -33.825 LPAR5 -9.918 LAP3 -35.753 ANP32A -11.236 HERC3 -41.355 UNC13A -16.45 TYMP -47.177 HFE -5.736 ETNK1 -57.282 EPHA6 -6.148 ZNF516 -245.572 NPBWR2 -7.311 NDUFAF1 -380.038 NTRK2 -7.362 CD151 -630.346 THNSL2 -9.254 ICTI -680.287 The gene symbols are color coded to indicate up-regulation (red) or down-regulation (green). Table 16 Top five diseases and disorders affected by Rhodiola, salidroside, triandrin, and tyrosol in T98G cells. Rhodiola extract p-Value # Genes Cardiovascular disease 3.37E-11-9.88E-03 72 Endocrine system disorders 3.35E-10-3.02E-03 60 Gastrointestinal disease 3.35E-10-8.69E-03 163 Metabolic disease 3.35E-10-9.62E-03 63 Organismal injury and abnormalities 1.24E-08-1.09E-02 62 Salidroside p-Value # Genes Cardiovascular disease 6.97E-05-1.91E-02 50 Neurological disease 9.37E-05-1.91E-02 83 Endocrine system disorders 9.57E-05-7.25E-04 40 Gastrointestinal disease 9.57E-05-1.91E-02 151 Metabolic disease 9.57E-05-1.91E-02 46 Tyrosol p-Value # Genes Neurological disease 2.93E-04-3.73E-02 33 Ophthalmic disease 2.93E-04-3.73E-02 15 Endocrine system disorders 3.35E-04-3.73E-02 34 Metabolic disease 3.35E-04-3.73E-02 41 Gastrointestinal disease 8.67E-04-4.19E-02 32 Triandrin p-Value # Genes Metabolic disease 2.46E-03-4.98E-02 37 Developmental disorder 4.09E-03-4.22E-02 18 Hereditary disorder 4.09E-03-4.22E-02 27 Neurological disease 4.09E-03-4.73E-02 20 Psychological disorders 4.09E-03-3.74E-02 3 Table 17 Top five molecular and cellular functions affected by Rhodiola, salidroside, triandrin and tyrosol in T98G cells. Rhodiola extract p-Value # Genes Cell-to-cell signaling and interaction 3.76E-07-1.06E-02 78 Cellular movement 4.24E-06-1.04E-02 74 Molecular transport 9.21E-06-1.04E-02 89 Cell morphology 2.39E-05-1.09E-02 63 Cellular assembly and organization 2.39E-05-6.52E-03 14 Salidroside p-Value # Genes Cell-To-Cell Signaling and Interaction 8.36E-06-1.91E-02 70 Nucleic Acid Metabolism 3.40E-05-1.91E-02 36 Small Molecule Biochemistry 3.40E-05-1.91E-02 60 Cellular Compromise 6.96E-05-1.91E-02 23 Cell Death and Survival 1.14E-04-1.91E-02 102 Tyrosol p-Value # Genes Lipid metabolism 1.39E-03-5.00E-02 19 Molecular transport 1.39E-03-5.00E-02 14 Small molecule biochemistry 1.39E-03-5.00E-02 30 Nucleic acid metabolism 2.50E-03-3.73E-02 4 Cellular assembly and organization 4.06E-03-4.19E-02 13 Triandrin p-Value # Genes Lipid Metabolism 1.40E-03-4.22E-02 14 Molecular Transport 1.40E-03-3.74E-02 8 Small Molecule Biochemistry 1.40E-03-4.22E-02 19 Cell-To-Cell Signaling and Interaction 2.53E-03-3.74E-02 16 Carbohydrate Metabolism 7.97E-03-3.74E-02 4 Table 18 Top five physiological system functions affected by Rhodiola, salidroside, triandrin, and tyrosol in T98G cells. Rhodiola extract p-Value # Genes Behavior 7.69E-07-1.02E-02 50 Nervous system function 3.60E-06-1.00E-02 65 Humoral immune response 2.39E-05-6.52E-03 28 Hematological system function 8.50E-05-1.06E-02 64 Organ morphology 9.59E-05-1.09E-02 61 Salidroside p-Value # Genes Behavior 2.14E-06-1.83E-02 40 Nervous system function 6.77E-05-1.91E-02 60 Cardiovascular system function 1.13E-04-1.91E-02 24 Hematological system function 2.16E-04-1.91E-02 68 Tissue morphology 2.92E-04-1.91E-02 71 Tyrosol p-Value # Genes Hair and skin development and function 1.29E-02-3.73E-02 6 Hematological system function 1.29E-02-3.73E-02 10 Hematopoiesis 1.29E-02-3.73E-02 4 Lymphoid tissue structure and development 1.29E-02-3.73E-02 3 Nervous system function 1.88E-02-1.88E-02 2 Triandrin p-Value # Genes Tissue development 2.53E-03-3.74E-02 14 Cardiovascular system function 6.86E-03-3.74E-02 4 Organismal development 6.86E-03-3.74E-02 8 Cell-mediated immune response 7.97E-03-3.74E-02 2 Hematological system function 7.97E-03-3.74E-02 8 Table 19 Top Canonical Pathways affected by Rhodiola, salidroside, triandrin, and tyrosol in T98G cells. Rhodiola extract Ingenuity canonical pathways Ratio Communication between 7.14E-02 innate and adaptive immune cells eNOS signaling 5.81E-02 Altered Tcell and B ceil 7E-02 signaling in rheumatoid arthritis Dendritic cell maturation 4.74E-02 Axonal guidance signaling 3.52E-02 G-protein coupled receptor 4.35E-02 signaling Stearate biosynthesis I 8.16E-02 Glutamate receptor signaling 6.94E-02 Ephrin receptor signaling 4.29E-02 Atherosclerosis signaling 5.07E-02 Salidroside Ingenuity canonical pathways Ratio cAMP-mediated signaling 14/226 (0.062) B cell development 5/36 (0.139) Phototransduction pathway 5/67 (0.075) eNOS signaling 8/155 (0.052) Protein ubiquitination pathway 12/270 (0.044) G-protein coupled receptor 4.35E-02 signaling tRNA splicing 8.7E-02 Cardiac [beta]-adrenergic signaling 5.06E-02 Altered T cell and B cell signaling in 6E-02 rheumatoid arthritis Protein kinase A signaling 3.69E-02 Tyrosol Ingenuity canonical pathways Ratio G-protein coupled receptor signaling 32/515 (0.062) cAMP-mediated signaling 15/213 (0.07) Hematopoiesis from pluripotent stem 5/55 (0.091) cells Primary immunodeficiency signaling 5/55 (0.091) PPARa/RXRa activation 11/169 (0.065) Phototransduction pathway 9.09E-02 Aminosugars metabolism 8.45E-02 Estrogen-mediated S-phase entry 1.11E-01 LPS/IL-1 mediated inhibition of RXR 5.5E-02 function Starch and sucrose metabolism 7.94E-02 Triandrin Ingenuity canonical pathways Ratio B cell development 5/29 (0.172) G-protein coupled receptor signaling 30/515 (0.058) Dopamine-DARPP32 feedback in cAMP 11/164 (0.067) signaling Netrin signaling 4/45 (0.089) Communication between innate and 6/93 (0.065) adaptive immune cells Neuropathic pain signaling in dorsal 6.6E-02 horn neurons nNOS signaling in neurons 8.7E-02 Phenylalanine, tyrosine and 1.33E-01 tryptophan biosynthesis Chondroitin sulfate biosynthesis 8E-02 Parkinson's signaling 1.25E-01
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|Author:||Panossian, Alexander; Hamm, Rebecca; Wikman, Georg; Efferth, Thomas|
|Publication:||Phytomedicine: International Journal of Phytotherapy & Phytopharmacology|
|Date:||Sep 25, 2014|
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