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Unraveling the Rat Intestine, Spleen and Liver Genome-Wide Transcriptome after the Oral Administration of Lavender Oil by a Two-Color Dye-Swap DNA Microarray Approach.

Kubo H, Shibato J, Saito T, Ogawa T, Rakwal R, Shioda S - PLoS ONE (2015)

Bottom Line: Fourteen days after LO treatment and compared with a control group (sham), a total of 156 and 154 up (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes, 174 and 66 up- (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes, and 222 and 322 up- (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes showed differential expression at the mRNA level in the small intestine, spleen and liver, respectively.Using bioinformatics, including Ingenuity Pathway Analysis (IPA), differentially expressed genes were functionally categorized by their Gene Ontology (GO) and biological function and network analysis, revealing their diverse functions and potential roles in LO-mediated effects in rat.These results are the first such inventory of genes that are affected by lavender essential oil (LO) in an animal model, forming the basis for further in-depth bioinformatics and functional analyses and investigation.

View Article: PubMed Central - PubMed

Affiliation: Department of Anatomy I, Showa University School of Medicine, Shinagawa, Tokyo, Japan; Oriental Aromatherapy College, Katsushika, Tokyo, Japan.

ABSTRACT
The use of lavender oil (LO)--a commonly, used oil in aromatherapy, with well-defined volatile components linalool and linalyl acetate--in non-traditional medicine is increasing globally. To understand and demonstrate the potential positive effects of LO on the body, we have established an animal model in this current study, investigating the orally administered LO effects genome wide in the rat small intestine, spleen, and liver. The rats were administered LO at 5 mg/kg (usual therapeutic dose in humans) followed by the screening of differentially expressed genes in the tissues, using a 4×44-K whole-genome rat chip (Agilent microarray platform; Agilent Technologies, Palo Alto, CA, USA) in conjunction with a dye-swap approach, a novelty of this study. Fourteen days after LO treatment and compared with a control group (sham), a total of 156 and 154 up (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes, 174 and 66 up- (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes, and 222 and 322 up- (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes showed differential expression at the mRNA level in the small intestine, spleen and liver, respectively. The reverse transcription-polymerase chain reaction (RT-PCR) validation of highly up- and down-regulated genes confirmed the regulation of the Papd4, Lrp1b, Alb, Cyr61, Cyp2c, and Cxcl1 genes by LO as examples in these tissues. Using bioinformatics, including Ingenuity Pathway Analysis (IPA), differentially expressed genes were functionally categorized by their Gene Ontology (GO) and biological function and network analysis, revealing their diverse functions and potential roles in LO-mediated effects in rat. Further IPA analysis in particular unraveled the presence of novel genes, such as Papd4, Or8k5, Gprc5b, Taar5, Trpc6, Pld2 and Onecut3 (up-regulated top molecules) and Tnf, Slc45a4, Slc25a23 and Samt4 (down-regulated top molecules), to be influenced by LO treatment in the small intestine, spleen and liver, respectively. These results are the first such inventory of genes that are affected by lavender essential oil (LO) in an animal model, forming the basis for further in-depth bioinformatics and functional analyses and investigation.

No MeSH data available.


Pathway- and disease states-focused gene classification of genes in the liver of LO-treated rats.The genes (up-regulated–A; down-regulated–B) were classified based on the available categories of more than 100 biological pathways or specific disease states in the SABiosciences PCR array list (QIAGEN; www.sabiosciences.com) for Rattus norvegicus. The numbers in the Y-axis represent the number of genes in each category as indicated on the X-axis.
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pone.0129951.g007: Pathway- and disease states-focused gene classification of genes in the liver of LO-treated rats.The genes (up-regulated–A; down-regulated–B) were classified based on the available categories of more than 100 biological pathways or specific disease states in the SABiosciences PCR array list (QIAGEN; www.sabiosciences.com) for Rattus norvegicus. The numbers in the Y-axis represent the number of genes in each category as indicated on the X-axis.

Mentions: The functionally categorized genes post-analysis using the SABiosciences PCR array list (Qiagen) are presented graphically in Fig 5 (small intestine), Fig 6 (spleen) and Fig 7 (liver). In Figs 5 and 6 and 7 the numbers on the y-axis represent the number of genes in each category, which are indicated on the x-axis. The gene function and the genes description contained within each functional category are shown for small intestine (up-regulated, S4 Table; down-regulated, S5 Table), spleen (up-regulated, S6 Table; down-regulated, S7 Table), and liver (up-regulated, S8 Table; down-regulated, S9 Table). Some interesting facts could be ascertained using the known gene classifications. First, in the case of the small intestine, although up-regulated genes were more abundant (even by two genes), the functions were mainly down-regulated (Fig 5). In the case of the spleen, additional functions were correlated with additional up-regulated genes, as seen in Fig 6. In the liver, more down-regulated genes numbers also correlated with more functions (Fig 7). These functions were characterized by the presence of genes on both sides, up- and down-regulated. Interestingly and common to all the three tissues, among the up-regulated genes, there were pockets of functions that were specific to the induced genes only; these pockets are marked by boxed areas with broken lines (Figs 5 and 6 and 7), indicating that the LO specifically influenced some known genes and functions as up-regulation rather than down-regulation under the present analysis conditions of utilizing the well-annotated genes and functional categories as referenced from Qiagen (see Materials and Methods section above). In the small intestine, the G protein-coupled receptors gene function was the most highly up-regulated; in the spleen, the molecular toxicology pathway finder and G protein coupled receptors were the top-two highly up-regulated gene functions; and in the liver, the cell cycle was the highest up-regulated function. This regulation indicates diverse gene functions being influenced by LO ingestion in these three different tissues. Therefore, the first objective of identifying genes and their functions by DNA microarray in conjunction using an annotated gene function list was achieved.


Unraveling the Rat Intestine, Spleen and Liver Genome-Wide Transcriptome after the Oral Administration of Lavender Oil by a Two-Color Dye-Swap DNA Microarray Approach.

Kubo H, Shibato J, Saito T, Ogawa T, Rakwal R, Shioda S - PLoS ONE (2015)

Pathway- and disease states-focused gene classification of genes in the liver of LO-treated rats.The genes (up-regulated–A; down-regulated–B) were classified based on the available categories of more than 100 biological pathways or specific disease states in the SABiosciences PCR array list (QIAGEN; www.sabiosciences.com) for Rattus norvegicus. The numbers in the Y-axis represent the number of genes in each category as indicated on the X-axis.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4498626&req=5

pone.0129951.g007: Pathway- and disease states-focused gene classification of genes in the liver of LO-treated rats.The genes (up-regulated–A; down-regulated–B) were classified based on the available categories of more than 100 biological pathways or specific disease states in the SABiosciences PCR array list (QIAGEN; www.sabiosciences.com) for Rattus norvegicus. The numbers in the Y-axis represent the number of genes in each category as indicated on the X-axis.
Mentions: The functionally categorized genes post-analysis using the SABiosciences PCR array list (Qiagen) are presented graphically in Fig 5 (small intestine), Fig 6 (spleen) and Fig 7 (liver). In Figs 5 and 6 and 7 the numbers on the y-axis represent the number of genes in each category, which are indicated on the x-axis. The gene function and the genes description contained within each functional category are shown for small intestine (up-regulated, S4 Table; down-regulated, S5 Table), spleen (up-regulated, S6 Table; down-regulated, S7 Table), and liver (up-regulated, S8 Table; down-regulated, S9 Table). Some interesting facts could be ascertained using the known gene classifications. First, in the case of the small intestine, although up-regulated genes were more abundant (even by two genes), the functions were mainly down-regulated (Fig 5). In the case of the spleen, additional functions were correlated with additional up-regulated genes, as seen in Fig 6. In the liver, more down-regulated genes numbers also correlated with more functions (Fig 7). These functions were characterized by the presence of genes on both sides, up- and down-regulated. Interestingly and common to all the three tissues, among the up-regulated genes, there were pockets of functions that were specific to the induced genes only; these pockets are marked by boxed areas with broken lines (Figs 5 and 6 and 7), indicating that the LO specifically influenced some known genes and functions as up-regulation rather than down-regulation under the present analysis conditions of utilizing the well-annotated genes and functional categories as referenced from Qiagen (see Materials and Methods section above). In the small intestine, the G protein-coupled receptors gene function was the most highly up-regulated; in the spleen, the molecular toxicology pathway finder and G protein coupled receptors were the top-two highly up-regulated gene functions; and in the liver, the cell cycle was the highest up-regulated function. This regulation indicates diverse gene functions being influenced by LO ingestion in these three different tissues. Therefore, the first objective of identifying genes and their functions by DNA microarray in conjunction using an annotated gene function list was achieved.

Bottom Line: Fourteen days after LO treatment and compared with a control group (sham), a total of 156 and 154 up (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes, 174 and 66 up- (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes, and 222 and 322 up- (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes showed differential expression at the mRNA level in the small intestine, spleen and liver, respectively.Using bioinformatics, including Ingenuity Pathway Analysis (IPA), differentially expressed genes were functionally categorized by their Gene Ontology (GO) and biological function and network analysis, revealing their diverse functions and potential roles in LO-mediated effects in rat.These results are the first such inventory of genes that are affected by lavender essential oil (LO) in an animal model, forming the basis for further in-depth bioinformatics and functional analyses and investigation.

View Article: PubMed Central - PubMed

Affiliation: Department of Anatomy I, Showa University School of Medicine, Shinagawa, Tokyo, Japan; Oriental Aromatherapy College, Katsushika, Tokyo, Japan.

ABSTRACT
The use of lavender oil (LO)--a commonly, used oil in aromatherapy, with well-defined volatile components linalool and linalyl acetate--in non-traditional medicine is increasing globally. To understand and demonstrate the potential positive effects of LO on the body, we have established an animal model in this current study, investigating the orally administered LO effects genome wide in the rat small intestine, spleen, and liver. The rats were administered LO at 5 mg/kg (usual therapeutic dose in humans) followed by the screening of differentially expressed genes in the tissues, using a 4×44-K whole-genome rat chip (Agilent microarray platform; Agilent Technologies, Palo Alto, CA, USA) in conjunction with a dye-swap approach, a novelty of this study. Fourteen days after LO treatment and compared with a control group (sham), a total of 156 and 154 up (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes, 174 and 66 up- (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes, and 222 and 322 up- (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes showed differential expression at the mRNA level in the small intestine, spleen and liver, respectively. The reverse transcription-polymerase chain reaction (RT-PCR) validation of highly up- and down-regulated genes confirmed the regulation of the Papd4, Lrp1b, Alb, Cyr61, Cyp2c, and Cxcl1 genes by LO as examples in these tissues. Using bioinformatics, including Ingenuity Pathway Analysis (IPA), differentially expressed genes were functionally categorized by their Gene Ontology (GO) and biological function and network analysis, revealing their diverse functions and potential roles in LO-mediated effects in rat. Further IPA analysis in particular unraveled the presence of novel genes, such as Papd4, Or8k5, Gprc5b, Taar5, Trpc6, Pld2 and Onecut3 (up-regulated top molecules) and Tnf, Slc45a4, Slc25a23 and Samt4 (down-regulated top molecules), to be influenced by LO treatment in the small intestine, spleen and liver, respectively. These results are the first such inventory of genes that are affected by lavender essential oil (LO) in an animal model, forming the basis for further in-depth bioinformatics and functional analyses and investigation.

No MeSH data available.