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Cited by 273Gut microbiota and healthCircadian rhythm and melatoninAnimal Nutrition and Physiology

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The Mouse Microbiome Is Required for Sex-Specific Diurnal Rhythms of Gene Expression and Metabolism

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Weger, Benjamin D., Gobet, Cédric, Yeung, Jake, Martin, Eva, Jimenez, Sonia, Betrisey, Bertrand, Foata, Francis, Berger, Bernard, Balvay, Aurélie, Foussier, Anne, Charpagne, Aline, Boizet-Bonhoure, Brigitte, Chou, Chieh Jason, Naef, Felix, Gachon, Frédéric·2019·Cell Metabolism
DOI 10.1016/j.cmet.2018.09.023PMC PMC6370974
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Abstract

The circadian clock and associated feeding rhythms have a profound impact on metabolism and the gut microbiome. To what extent microbiota reciprocally affect daily rhythms of physiology in the host remains elusive. Here, we analyzed transcriptome and metabolome profiles of male and female germ-free mice. While mRNA expression of circadian clock genes revealed subtle changes in liver, intestine, and white adipose tissue, germ-free mice showed considerably altered expression of genes associated with rhythmic physiology. Strikingly, the absence of the microbiome attenuated liver sexual dimorphism and sex-specific rhythmicity. The resulting feminization of male and masculinization of female germ-free animals is likely caused by altered sexual development and growth hormone secretion, associated with differential activation of xenobiotic receptors. This defines a novel mechanism by which the microbiome regulates host metabolism.

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Figure 1 Gut Microbiota Alters Rhythmic Gene Expression in Peripheral Organs but Mildly Affects Clock Gene Expression (A) Alteration of rhythmic gene expression in male GF (GF♂) mice is assessed by model selection (model 1–5): black line, stable transcription; black wave, rhythmic transcription; red wave, rhythmic profiles with different rhythmic parameters (i.e., phase and/or amplitude). (B) Model distribution of all expressed genes in the examined organs. Coloring indicates the corresponding models as shown in (A); gray, genes not assigned to any specific model. (C) Heatmaps of normalized mRNA levels in male ConvR (ConvR♂) and GF♂ mice (red, high expression; green, low expression). Colored bars indicate the corresponding models. Black and white bars represent light conditions. (D) The assignment of circadian clock genes to their corresponding models shows that their temporal profiles are only mildly affected. (E) Liver genes with altered rhythmicity (models 2, 3, and 5) in GF mice are associated with metabolic and steroidogenic pathways and neurological disorders.
Figure 1 Gut Microbiota Alters Rhythmic Gene Expression in Peripheral Organs but Mildly Affects Clock Gene Expression (A) Alteration of rhythmic gene expression in male GF (GF♂) mice is assessed by model selection (model 1–5): black line, stable transcription; black wave, rhythmic transcription; red wave, rhythmic profiles with different rhythmic parameters (i.e., phase and/or amplitude). (B) Model distribution of all expressed genes in the examined organs. Coloring indicates the corresponding models as shown in (A); gray, genes not assigned to any specific model. (C) Heatmaps of normalized mRNA levels in male ConvR (ConvR♂) and GF♂ mice (red, high expression; green, low expression). Colored bars indicate the corresponding models. Black and white bars represent light conditions. (D) The assignment of circadian clock genes to their corresponding models shows that their temporal profiles are only mildly affected. (E) Liver genes with altered rhythmicity (models 2, 3, and 5) in GF mice are associated with metabolic and steroidogenic pathways and neurological disorders.CC BY-NC-ND · PubMed Central
Figure 2 A Lack of Gut Microbiota Decreases Sex-Specific Gene Expression by Feminizing Male and Masculinizing Female Hepatic Gene Expression (A) Experimental design to detect sex-specific changes. (B) Volcano plot of differences in mRNA expression between ConvR♂ and GF♂ categorized by sex-biased expression in ConvR mice (ConvR♂ versus ConvR female [ConvR♀]). Colors indicate male-biased (blue), female-biased (red), and unbiased (gray) expressed genes. (C) Volcano plot of expression difference in mRNA expression between female GF (GF♀) and ConvR♀ mice. Color code is identical to (B). (D) Statistical analysis of male- and female-biased genes showing a significant inversion of sex-biased genes toward the opposite sex in GF mice. (E) Number of the shared differentially expressed genes (intersections size) between the four indicated contrasts. Lower heatmap indicates the enrichment for chromosomal location (Chr) for the corresponding intersection. (F) Expression changes of differentially expressed Mup genes in GF♂ mice as assessed by RNA-seq. Most Mup genes are downregulated in GF♂ mice. The highest expressed Mup in female liver (Mup3) is downregulated in GF♀ mice. Colored gene name indicates unbiased (black) and male-biased (blue) expression. Triangle indicates the direction of significant change in GF♂ (blue) and GF♀ (red) mice in comparison with ConvR. (G) Protein levels of MUP in the urine of GF♂ and GF♀ mice are significantly downregulated in male and female mice compared with their ConvR counterparts (each Tukey boxplot represents four independent biological replicates per condition). ∗p ≤ 0.05, ∗∗∗p ≤ 0.001.
Figure 2 A Lack of Gut Microbiota Decreases Sex-Specific Gene Expression by Feminizing Male and Masculinizing Female Hepatic Gene Expression (A) Experimental design to detect sex-specific changes. (B) Volcano plot of differences in mRNA expression between ConvR♂ and GF♂ categorized by sex-biased expression in ConvR mice (ConvR♂ versus ConvR female [ConvR♀]). Colors indicate male-biased (blue), female-biased (red), and unbiased (gray) expressed genes. (C) Volcano plot of expression difference in mRNA expression between female GF (GF♀) and ConvR♀ mice. Color code is identical to (B). (D) Statistical analysis of male- and female-biased genes showing a significant inversion of sex-biased genes toward the opposite sex in GF mice. (E) Number of the shared differentially expressed genes (intersections size) between the four indicated contrasts. Lower heatmap indicates the enrichment for chromosomal location (Chr) for the corresponding intersection. (F) Expression changes of differentially expressed Mup genes in GF♂ mice as assessed by RNA-seq. Most Mup genes are downregulated in GF♂ mice. The highest expressed Mup in female liver (Mup3) is downregulated in GF♀ mice. Colored gene name indicates unbiased (black) and male-biased (blue) expression. Triangle indicates the direction of significant change in GF♂ (blue) and GF♀ (red) mice in comparison with ConvR. (G) Protein levels of MUP in the urine of GF♂ and GF♀ mice are significantly downregulated in male and female mice compared with their ConvR counterparts (each Tukey boxplot represents four independent biological replicates per condition). ∗p ≤ 0.05, ∗∗∗p ≤ 0.001.CC BY-NC-ND · PubMed Central
Figure 3 Sex Hormones and the GH Signaling Network Are Perturbed in GF Mice (A and B) Serum levels of testosterone (A) and E2 (B) in male and female ConvR and GF mice. (C) Circulating GH total secretion, peak number, and levels in male and female ConvR and GF mice. (D) Representative examples of temporal profiles of GH secretion in ConvR♂, GF♂, ConvR♀, and GF♀ animals. (E) Enrichment analysis of FOXA1, FOXA2, BCL6, CUX2, and STAT5 (male and female specific) target genes for differentially expressed genes of indicated contrasts (♂ = GF♂ versus ConvR♂; ♀ = GF♀ versus ConvR♀; ConvR = ConvR♂ versus ConvR♀; GF = GF♂ versus GF♀). Target genes have been identified by published chromatin immunoprecipitation sequencing (ChIP-seq) data. (F) Phosphorylation of STAT5 (Tyr694) in male and female ConvR and GF mice. (G) Hepatic mRNA and protein levels of the other GH-dependent TFs BCL6 and CUX2 that are involved in sex-dimorphic gene expression for the indicated conditions. (H) Experimental design to mimic male-specific GH pulses in GF mice. (I) Volcano plot of expression difference in mRNA expression between GH-injected and vehicle-injected GF male mice show a rescue in sex-biased gene expression. (J) Enrichment analysis of male- and female-specific genes (♂ biased, ♀ biased) or repressed or induced genes in GF mice (down or up in GF♂) for differentially expressed genes of the contrast GH- versus vehicle-injected GF♂ mice. (K) Experimental design of an in vitro system of primary hepatocytes treated with sera of different sources (ConvR♂, ConvR♀, and GF♀). (L) Volcano plot of expression difference in mRNA expression of female hepatocytes treated with GF♀ serum versus ConvR♀ serum. Color code corresponds to (B). (M) Enrichment analysis of male- and female-specific genes (♂ biased, ♀ biased) for differentially expressed genes of the indicated contrasts (serum treatment: ConvR♂ versus ConvR♀ or GF♀ versus ConvR♀) in female hepatocytes. (N) Cartoon depicting the experimental design to evaluate the effect of a tonic GH treatment. (O) Number of differentially expressed genes in function of an adjusted p value threshold for the indicated contrast. GH treatment diminished the number of differentially expressed genes between female hepatocytes treated with GF♀ serum and ConvR♀ serum. (P) Enrichment analysis of male- and female-specific genes (♂ biased, ♀ biased) for differentially expressed genes between GH-treated versus untreated female hepatocytes. All boxplots represent at least 12 independent biological replicates per condition, except for (G), for which at least six biological replicates were used. ∗p ≤ 0.05, ∗∗p ≤ 0.01, ∗∗∗p ≤ 0.001. All boxplots are Tukey boxplots.
Figure 3 Sex Hormones and the GH Signaling Network Are Perturbed in GF Mice (A and B) Serum levels of testosterone (A) and E2 (B) in male and female ConvR and GF mice. (C) Circulating GH total secretion, peak number, and levels in male and female ConvR and GF mice. (D) Representative examples of temporal profiles of GH secretion in ConvR♂, GF♂, ConvR♀, and GF♀ animals. (E) Enrichment analysis of FOXA1, FOXA2, BCL6, CUX2, and STAT5 (male and female specific) target genes for differentially expressed genes of indicated contrasts (♂ = GF♂ versus ConvR♂; ♀ = GF♀ versus ConvR♀; ConvR = ConvR♂ versus ConvR♀; GF = GF♂ versus GF♀). Target genes have been identified by published chromatin immunoprecipitation sequencing (ChIP-seq) data. (F) Phosphorylation of STAT5 (Tyr694) in male and female ConvR and GF mice. (G) Hepatic mRNA and protein levels of the other GH-dependent TFs BCL6 and CUX2 that are involved in sex-dimorphic gene expression for the indicated conditions. (H) Experimental design to mimic male-specific GH pulses in GF mice. (I) Volcano plot of expression difference in mRNA expression between GH-injected and vehicle-injected GF male mice show a rescue in sex-biased gene expression. (J) Enrichment analysis of male- and female-specific genes (♂ biased, ♀ biased) or repressed or induced genes in GF mice (down or up in GF♂) for differentially expressed genes of the contrast GH- versus vehicle-injected GF♂ mice. (K) Experimental design of an in vitro system of primary hepatocytes treated with sera of different sources (ConvR♂, ConvR♀, and GF♀). (L) Volcano plot of expression difference in mRNA expression of female hepatocytes treated with GF♀ serum versus ConvR♀ serum. Color code corresponds to (B). (M) Enrichment analysis of male- and female-specific genes (♂ biased, ♀ biased) for differentially expressed genes of the indicated contrasts (serum treatment: ConvR♂ versus ConvR♀ or GF♀ versus ConvR♀) in female hepatocytes. (N) Cartoon depicting the experimental design to evaluate the effect of a tonic GH treatment. (O) Number of differentially expressed genes in function of an adjusted p value threshold for the indicated contrast. GH treatment diminished the number of differentially expressed genes between female hepatocytes treated with GF♀ serum and ConvR♀ serum. (P) Enrichment analysis of male- and female-specific genes (♂ biased, ♀ biased) for differentially expressed genes between GH-treated versus untreated female hepatocytes. All boxplots represent at least 12 independent biological replicates per condition, except for (G), for which at least six biological replicates were used. ∗p ≤ 0.05, ∗∗p ≤ 0.01, ∗∗∗p ≤ 0.001. All boxplots are Tukey boxplots.CC BY-NC-ND · PubMed Central
Figure 4 Expression of the Male-Specific Repressor Bcl6 Anti-correlates with a GH-Responsive AS Transcript (A) RNA-seq read mapping to the Bcl6 gene locus. The tracks are color coded for the indicated conditions. The log2 normalized read count versus chromosomal position is plotted across the y axis for sense (upper part) and AS (lower part) transcription. The schematic represents exons and introns of Bcl6 (ss) and the two AS transcripts (as-1, as-2). (B) Correlation matrix based on Pearson's rank correlation coefficient test between the expression levels of the indicated exon, intron, and AS transcript. Colors indicate positive (blue) and negative (red) correlation. Size of the circles correspond to more significant p values, only correlation with an adjusted p value lower than 0.05 are depicted with a circle. (C) Normalized read counts per exon (upper graph), intron, and AS transcript (lower graph) of the Bcl6 gene locus in liver of ConvR♂ (dark blue), ConvR♀ (dark red), GF♂ (light blue), and GF♀ mice (light red). (D) Normalized read counts of GH-treated and vehicle-injected GF♂ mice for sense (left) and AS-1 transcript (right). (E) Experimental design. (F) Normalized read counts of GH- and vehicle-treated female hepatocytes under GF♀ serum incubation for sense (left) and antisense-1 transcript (right). (G) Changes in sense and AS transcript levels between ConvR♂ versus ConvR (left), GF♂ versus ConvR♂ (middle), and GF♀ versus ConvR♀ (right). Significantly upregulated and downregulated genes on the level of Δsense–Δanti-sense are shown in red (false discovery rate<0.01 and logFCinteraction > 1). Gene names are depicted for genes with opposite behavior in the x and y axis (logFCx > 0.5 and logFCy < −0.5) or (logFCx < −0.5 and logFCy > 0.5). Globally, only Bcl6 showed robust differences between sense and AS transcript levels across all conditions indicating that a sex-specific AS transcript that potentially regulates sex-biased expression of a gene is unique. All boxplots represent at least 12 independent biological replicates per condition, except for (F) for which three biological replicates were used. ∗p ≤ 0.05, ∗∗p ≤ 0.01, ∗∗∗p ≤ 0.001. All boxplots are Tukey boxplots.
Figure 4 Expression of the Male-Specific Repressor Bcl6 Anti-correlates with a GH-Responsive AS Transcript (A) RNA-seq read mapping to the Bcl6 gene locus. The tracks are color coded for the indicated conditions. The log2 normalized read count versus chromosomal position is plotted across the y axis for sense (upper part) and AS (lower part) transcription. The schematic represents exons and introns of Bcl6 (ss) and the two AS transcripts (as-1, as-2). (B) Correlation matrix based on Pearson's rank correlation coefficient test between the expression levels of the indicated exon, intron, and AS transcript. Colors indicate positive (blue) and negative (red) correlation. Size of the circles correspond to more significant p values, only correlation with an adjusted p value lower than 0.05 are depicted with a circle. (C) Normalized read counts per exon (upper graph), intron, and AS transcript (lower graph) of the Bcl6 gene locus in liver of ConvR♂ (dark blue), ConvR♀ (dark red), GF♂ (light blue), and GF♀ mice (light red). (D) Normalized read counts of GH-treated and vehicle-injected GF♂ mice for sense (left) and AS-1 transcript (right). (E) Experimental design. (F) Normalized read counts of GH- and vehicle-treated female hepatocytes under GF♀ serum incubation for sense (left) and antisense-1 transcript (right). (G) Changes in sense and AS transcript levels between ConvR♂ versus ConvR (left), GF♂ versus ConvR♂ (middle), and GF♀ versus ConvR♀ (right). Significantly upregulated and downregulated genes on the level of Δsense–Δanti-sense are shown in red (false discovery rate<0.01 and logFCinteraction > 1). Gene names are depicted for genes with opposite behavior in the x and y axis (logFCx > 0.5 and logFCy < −0.5) or (logFCx < −0.5 and logFCy > 0.5). Globally, only Bcl6 showed robust differences between sense and AS transcript levels across all conditions indicating that a sex-specific AS transcript that potentially regulates sex-biased expression of a gene is unique. All boxplots represent at least 12 independent biological replicates per condition, except for (F) for which three biological replicates were used. ∗p ≤ 0.05, ∗∗p ≤ 0.01, ∗∗∗p ≤ 0.001. All boxplots are Tukey boxplots.CC BY-NC-ND · PubMed Central
Figure 5 Gut Microbiota Modulates the Sex-Dimorphic Metabolome (A and B) Principal-component analysis score plots of mass spectroscopy-based metabolic profiling of male (♂) and female (♀) ConvR and GF mice in liver (A) and serum (B). (C) Enrichment analysis of sex-biased metabolites in the upregulated (dark blue and red) and downregulated (light blue and red) fractions of metabolites in GF animals (GF versus ConvR) in the indicated tissue (liver or serum). (D–F) Schematic depicting regulation by sex and microbiota for folate, purine, and pyrimidine metabolism (D), glycolysis and FA oxidation (E), and the metabolic network of glutathione (GSH, methionine, PL, and BA) (F). Metabolites and genes involved in the steps where genes or metabolites showing sex-biased or microbiota-dependent changes. All gene names and metabolites are color coded for male-biased (blue), female-biased (red), and sex-unbiased (black) levels in the liver. The triangles that follow a gene or metabolite name indicate the direction of change in GF versus ConvR male (blue) and female (red) mice. (G) Sex-biased rhythmicity in gene expression was assessed by model selection (models 1–5) in both ConvR and GF mice: black line, stable transcription; black wave, rhythmic transcription; red wave, rhythmic profiles with different rhythmic parameters. (H) Heatmap of normalized mRNA levels in ConvR♂ and GF♂, and ConvR♀ and GF♀, across a day. Colored bars indicate the corresponding sex-specific models (2–5) in ConvR mice. Black and white bars on the bottom represent light conditions. (I and J) Heatmaps of relative metabolite levels in liver (I) and serum (J) sorted by the sex-specific models 2–5. (K) Fraction of genes corresponding to models 1–5 in ConvR and their assigned model in GF mice. The blue color in each box represents the fraction size of genes between ConvR and GF mice, with darkest blue corresponding to highest fraction. (L and M) Fraction of metabolites that are assigned to specific models for ConvR and GF mice in liver (E) and serum (F). (N–P) Feeding (N) and drinking (O) rhythms are not different between ConvR and GF mice (p > 0.05). Locomotor activity is higher activity in ConvR♀ mice (p < 0.001) but not different from males under GF conditions (P). Error bars represent SEM.
Figure 5 Gut Microbiota Modulates the Sex-Dimorphic Metabolome (A and B) Principal-component analysis score plots of mass spectroscopy-based metabolic profiling of male (♂) and female (♀) ConvR and GF mice in liver (A) and serum (B). (C) Enrichment analysis of sex-biased metabolites in the upregulated (dark blue and red) and downregulated (light blue and red) fractions of metabolites in GF animals (GF versus ConvR) in the indicated tissue (liver or serum). (D–F) Schematic depicting regulation by sex and microbiota for folate, purine, and pyrimidine metabolism (D), glycolysis and FA oxidation (E), and the metabolic network of glutathione (GSH, methionine, PL, and BA) (F). Metabolites and genes involved in the steps where genes or metabolites showing sex-biased or microbiota-dependent changes. All gene names and metabolites are color coded for male-biased (blue), female-biased (red), and sex-unbiased (black) levels in the liver. The triangles that follow a gene or metabolite name indicate the direction of change in GF versus ConvR male (blue) and female (red) mice. (G) Sex-biased rhythmicity in gene expression was assessed by model selection (models 1–5) in both ConvR and GF mice: black line, stable transcription; black wave, rhythmic transcription; red wave, rhythmic profiles with different rhythmic parameters. (H) Heatmap of normalized mRNA levels in ConvR♂ and GF♂, and ConvR♀ and GF♀, across a day. Colored bars indicate the corresponding sex-specific models (2–5) in ConvR mice. Black and white bars on the bottom represent light conditions. (I and J) Heatmaps of relative metabolite levels in liver (I) and serum (J) sorted by the sex-specific models 2–5. (K) Fraction of genes corresponding to models 1–5 in ConvR and their assigned model in GF mice. The blue color in each box represents the fraction size of genes between ConvR and GF mice, with darkest blue corresponding to highest fraction. (L and M) Fraction of metabolites that are assigned to specific models for ConvR and GF mice in liver (E) and serum (F). (N–P) Feeding (N) and drinking (O) rhythms are not different between ConvR and GF mice (p > 0.05). Locomotor activity is higher activity in ConvR♀ mice (p < 0.001) but not different from males under GF conditions (P). Error bars represent SEM.CC BY-NC-ND · PubMed Central
Figure 6 Microbiota-Depleted Mice Show Differential Activation of Xenobiotic Receptors and Alteration in Sexual Development (A–C) Changes in hepatic gene expression (log2FC) and adjusted p values of Ahr KO (A), Fxr KO (B), and Pxr KO (C) mouse models presented as a volcano plot. (D) Adjusted p value for the enrichment of male- and female-biased genes in the indicated receptor KO model. (E) Heatmap illustrating the statistical overrepresentation of target genes from different xenobiotic sensing nuclear receptors in differentially expressed genes of GF♂ mice liver (GF♂ versus ConvR♂). Target genes have been defined as significantly up- or downregulated in the respective KO model. (F–H) Volcano plots depicting sex-biased hepatic gene expression across different conditions; for plot details see (A)–(C). (F and G) LDP-treated male (F) and female (G) animals versus their untreated counterparts. (H) Comparison between transfaunation of cecal microbiota into GF♀ mice from LDP-treated and -untreated animals. (I) Adjusted p value for the enrichment of male- and female-biased genes under the indicated antibiotics treatment. (J–L) GF mice show an alteration in spermatid differentiation. (J) Periodic acid–Schiff (PAS)-stained sections of testis from ConvR (left) and GF mice (middle and right) show that more seminiferous tubules of GF animals lack spermatids (white arrows) (right) than in their ConvR counterparts (left). (K) Tukey boxplots of at least five animals per group quantifying this difference (p < 0.05, Mann-Whitney U test). (L) Heatmap illustrating the statistical overrepresentation of marker genes of different stages of spermatogenesis in differentially up- or downregulated genes of testis in GF animals. (M and N) GF mice present defects in follicle organization. (M) PAS-stained sections of follicles from ConvR (left) and GF mice (middle and right) show severe effects on the theca (Th) organization (left and right) and disorganization of some follicles in their granulosa (Gr) in GF animals. (N) Statistical overrepresentation of gene markers for fetal germ cells to oocyte development indicate defects in oocytes of GF mice. Scale bars, 100 μm (lower magnification) and 320 μm (higher magnification).
Figure 6 Microbiota-Depleted Mice Show Differential Activation of Xenobiotic Receptors and Alteration in Sexual Development (A–C) Changes in hepatic gene expression (log2FC) and adjusted p values of Ahr KO (A), Fxr KO (B), and Pxr KO (C) mouse models presented as a volcano plot. (D) Adjusted p value for the enrichment of male- and female-biased genes in the indicated receptor KO model. (E) Heatmap illustrating the statistical overrepresentation of target genes from different xenobiotic sensing nuclear receptors in differentially expressed genes of GF♂ mice liver (GF♂ versus ConvR♂). Target genes have been defined as significantly up- or downregulated in the respective KO model. (F–H) Volcano plots depicting sex-biased hepatic gene expression across different conditions; for plot details see (A)–(C). (F and G) LDP-treated male (F) and female (G) animals versus their untreated counterparts. (H) Comparison between transfaunation of cecal microbiota into GF♀ mice from LDP-treated and -untreated animals. (I) Adjusted p value for the enrichment of male- and female-biased genes under the indicated antibiotics treatment. (J–L) GF mice show an alteration in spermatid differentiation. (J) Periodic acid–Schiff (PAS)-stained sections of testis from ConvR (left) and GF mice (middle and right) show that more seminiferous tubules of GF animals lack spermatids (white arrows) (right) than in their ConvR counterparts (left). (K) Tukey boxplots of at least five animals per group quantifying this difference (p < 0.05, Mann-Whitney U test). (L) Heatmap illustrating the statistical overrepresentation of marker genes of different stages of spermatogenesis in differentially up- or downregulated genes of testis in GF animals. (M and N) GF mice present defects in follicle organization. (M) PAS-stained sections of follicles from ConvR (left) and GF mice (middle and right) show severe effects on the theca (Th) organization (left and right) and disorganization of some follicles in their granulosa (Gr) in GF animals. (N) Statistical overrepresentation of gene markers for fetal germ cells to oocyte development indicate defects in oocytes of GF mice. Scale bars, 100 μm (lower magnification) and 320 μm (higher magnification).CC BY-NC-ND · PubMed Central
Figure 7 Sexual Dimorphism Is Attenuated in Clock-Deprived Mice, and Ghrelin Plays an Important Role in Sustaining Sexually Dimorphic Gene Expression (A–C) Changes in hepatic gene expression (log2FC) and adjusted p values of the clock-deprived models Cry1/Cry2 KO (A) and Bmal1 KO (B) compared with wild-type and chronically jet-lagged versus non-jet-lagged male animals (C) presented as a volcano plot. WT, wild-type. (D) Graph depicting the adjusted p value of the analysis assessing the enrichment of male- and female-biased genes in the different conditions shown in (A)–(C). (E–H) Ghrelin blunts the feminized expression signature of GF♂ mice. (E) Experimental design to evaluate the effect of ghrelin on hepatic sexually dimorphic gene expression. (F) Changes in hepatic gene expression (log2FC) and adjusted p values of ghrelin-injected GF♂ mice presented as a volcano plot. (G) Enrichment analysis of male- and female-specific genes (♂ biased, ♀ biased) or repressed or induced genes in GF mice (down or up in GF♂) for differentially expressed genes of the contrast ghrelin- versus vehicle-injected males. (H) The differences of differentially expressed sex-biased genes between GF and ConvR male mice are strongly attenuated by ghrelin injections (∗∗∗p < 0.001, paired t test). (I) Working model for the control of sex-specific rhythmic gene expression and metabolism by microbiota.
Figure 7 Sexual Dimorphism Is Attenuated in Clock-Deprived Mice, and Ghrelin Plays an Important Role in Sustaining Sexually Dimorphic Gene Expression (A–C) Changes in hepatic gene expression (log2FC) and adjusted p values of the clock-deprived models Cry1/Cry2 KO (A) and Bmal1 KO (B) compared with wild-type and chronically jet-lagged versus non-jet-lagged male animals (C) presented as a volcano plot. WT, wild-type. (D) Graph depicting the adjusted p value of the analysis assessing the enrichment of male- and female-biased genes in the different conditions shown in (A)–(C). (E–H) Ghrelin blunts the feminized expression signature of GF♂ mice. (E) Experimental design to evaluate the effect of ghrelin on hepatic sexually dimorphic gene expression. (F) Changes in hepatic gene expression (log2FC) and adjusted p values of ghrelin-injected GF♂ mice presented as a volcano plot. (G) Enrichment analysis of male- and female-specific genes (♂ biased, ♀ biased) or repressed or induced genes in GF mice (down or up in GF♂) for differentially expressed genes of the contrast ghrelin- versus vehicle-injected males. (H) The differences of differentially expressed sex-biased genes between GF and ConvR male mice are strongly attenuated by ghrelin injections (∗∗∗p < 0.001, paired t test). (I) Working model for the control of sex-specific rhythmic gene expression and metabolism by microbiota.CC BY-NC-ND · PubMed Central

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Authors
Weger, B. D., Gobet, C., Yeung, J., Martin, E., Jimenez, S., Betrisey, B., Foata, F., Berger, B., Balvay, A., Foussier, A., Charpagne, A., Boizet-Bonhoure, B., Chou, C. J., Naef, F., & Gachon, F.
Affiliations
  • Centre Hospitalier Universitaire Vaudois (CH)
  • École Polytechnique Fédérale de Lausanne (CH)
  • Nestlé (Switzerland) (CH)
  • AgroParisTech (FR)
Corresponding author
Gachon, Frédéric
ORCID
Venue
Cell Metabolism
Publisher
Elsevier BV
Published
2019-02
Volume
29
Issue
2
Pages
362-382.e8
ISSN
1550-4131 (ISSN-L)
DOI
10.1016/j.cmet.2018.09.023
PMC
PMC6370974
OpenAlex
W2897926834
Cited by
269
References
193
Citations by year
2026: 23 · 2025: 32 · 2024: 33 · 2023: 37 · 2022: 31 · 2021: 44 · 2020: 39 · 2019: 26
FWCI
10.14
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell Metabolism (publishedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
  • HAL (submittedVersion, cc-by-nc-nd)
Funders
  • European Research Council (ERC-2010-StG-260988)
  • Swiss National Science Foundation (310030_173079)
  • Natural Sciences and Engineering Research Council of Canada
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Life Sciences › Neuroscience › Endocrine and Autonomic Systems › Circadian rhythm and melatonin
  • Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Nutrition and Physiology
Keywords
gut microbiota, circadian clock, sex differences, germ-free mice, growth hormone secretion, xenobiotic receptors, sexual development, metabolism, transcriptome, metabolome
MeSH terms
Gastrointestinal Microbiome, Animals, Circadian Rhythm, Female, Intestines, Liver, Male, Mice, Inbred C57BL, Sex Characteristics, Mice, Adipose Tissue, White, Ghrelin, Circadian Clocks, Transcriptome

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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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