Journal: Nature Communications

Article Title: Bile salt hydrolase in non-enterotoxigenic Bacteroides potentiates colorectal cancer

doi: 10.1038/s41467-023-36089-9

Figure Lengend Snippet: a – g Apc f/w and Cdx 2 Apc f/w mice were fed a HFD for 12 weeks ( n = 8 mice for Apc f/w ; n = 5 mice for Cdx 2 Apc f/w ). a Representative pictures of ileum and colon, revealing the tumor occurrence (in red circle). b Tumor numbers in different segments of intestine from 5 Cdx 2 Apc f/w mice, Duo: duodenum; Jeju: jejunum; Ile: Ileum. c Length of small intestine and colon. d Top 15 species of gut microbiota that led to the differences between two groups. e Relative abundance of variable gut microbiota species levels. Kruskal–Wallis test with Dunn’s post hoc test. f bsh hits in the variable gut microbiota species. g Unconjugated bile acid profiles in the colon contents. Mann–Whitney U test with two-sided. ωMCA: ω-muricholic acid. Data are presented as mean values +/– SEM in ( b , c , e , g ). Source data are provided as a Source Data File for Fig. 2.

Article Snippet: For short-term C7 treatment, 6- to 8-week-old male Cdx 2 Apc f/w mice were pretreated with 60% HFD for 10 weeks, and then colonized with BF BSH high and fed a 60% HFD or 60% HFD containing 1 mg/g C7 (TargetMol), which equates to 10 mg/kg/d consumption.

Techniques: MANN-WHITNEY

Journal: Nature Communications

Article Title: Bile salt hydrolase in non-enterotoxigenic Bacteroides potentiates colorectal cancer

doi: 10.1038/s41467-023-36089-9

Figure Lengend Snippet: a – h HFD-fed Cdx 2 Apc f/w mice were colonized with heat-killed B. fragilis 9343 (HBF) or B. fragilis 9343 (BF) for 12 weeks ( n = 7 mice for HBF; n = 9 mice for BF). a Length of colon. The ileum ( b ) and colon ( c ) tumor incidence, and tumor numbers with different sizes (<4 mm 2 , >4 mm 2 and the sum of both). Mann–Whitney U test with two-sided. d Total tumor number in the intestine. Two-tailed Student’s t test. e , f Representative pictures of colon (left), gross images of tumor (top right) in the colon and H&E staining (bottom right) of colon tumor sections. Scale bars: 1.5 mm (top right) and 100 μm (bottom right). g Unconjugated bile acid profiles in the colon contents. Mann–Whitney U test with two sided. h Total unconjugated bile acid levels in the colon contents. Two-tailed Student’s t test. i Relative mRNA levels of WNT target genes in non-tumor (NT) and tumor (T) colon tissues ( n = 7 for HBF-NT; n = 9 for BF-NT; n = 5 for HBF-T; n = 9 for BF-T;). Kruskal–Wallis test with Dunn’s post hoc test. j WB data of proteins encoded by WNT target genes, n = 3 independent samples/group. k Representative IHC staining of Ki-67, a proliferation marker ( n = 5 independent slides for HBF; n = 7 independent slides for BF). Scale bars: 100 μm. Data are presented as mean values +/− SEM in ( a – d , g – i ). Source data are provided as a Source Data file for Fig. 3.

Article Snippet: For short-term C7 treatment, 6- to 8-week-old male Cdx 2 Apc f/w mice were pretreated with 60% HFD for 10 weeks, and then colonized with BF BSH high and fed a 60% HFD or 60% HFD containing 1 mg/g C7 (TargetMol), which equates to 10 mg/kg/d consumption.

Techniques: MANN-WHITNEY, Two Tailed Test, Staining, Immunohistochemistry, Marker

Journal: Nature Communications

Article Title: Bile salt hydrolase in non-enterotoxigenic Bacteroides potentiates colorectal cancer

doi: 10.1038/s41467-023-36089-9

Figure Lengend Snippet: a – f HFD-fed Cdx 2 Apc f/w mice were colonized with B. fragilis 638R with low BSH activity (BF BSH low ) or B. fragilis 638R with high BSH activity (BF BSH high ) for 2 weeks ( n = 7 mice for BF BSH low ; n = 8 mice for BF BSH high ). Bile acid profiles ( a ) and total bile acid levels ( b ) in the ileum contents. Mann–Whitney U test with two-sided ( a ); two-tailed Student’s t test ( b ). Bile acid profiles ( c ) and total bile acid levels ( d ) in the cecum contents. Mann–Whitney U test with two-sided ( c ). Bile acid profiles ( e ) and total bile acid levels ( f ) in the colon contents. Mann–Whitney U test with two-sided ( e ); two-tailed Student’s t test ( f ). g Schematic diagram showing that conjugated bile acids are deconjugated by BSH-expressing bacteria and escape into colon in the form of unconjugated bile acids. Created with BioRender.com. Data are presented as mean values +/− SEM in a-f. Source data are provided as a Source Data File for Fig. 4.

Article Snippet: For short-term C7 treatment, 6- to 8-week-old male Cdx 2 Apc f/w mice were pretreated with 60% HFD for 10 weeks, and then colonized with BF BSH high and fed a 60% HFD or 60% HFD containing 1 mg/g C7 (TargetMol), which equates to 10 mg/kg/d consumption.

Techniques: Activity Assay, MANN-WHITNEY, Two Tailed Test, Expressing, Bacteria

Journal: Nature Communications

Article Title: Bile salt hydrolase in non-enterotoxigenic Bacteroides potentiates colorectal cancer

doi: 10.1038/s41467-023-36089-9

Figure Lengend Snippet: a – h HFD-fed Cdx 2 Apc f/w mice were colonized with BF BSH low or BF BSH high for 12 weeks ( n = 11 mice for BF BSH low ; n = 12 mice for BF BSH high ). Unconjugated bile acid profiles ( a ) and total unconjugated bile acid levels ( b ) in the colon contents. Mann–Whitney U test with two-sided ( a ). Two-tailed Student’s t test ( b ). The ileum ( c ) and colon ( d ) tumor incidence, and tumor numbers with different sizes (<4 mm 2 , >4 mm 2 and the sum of both. Mann–Whitney U test with two-sided. e Total tumor numbers in the intestine. Two-tailed Student’s t test. f , g Representative pictures of colon (left), gross images of tumors (top right) in the colon and H&E staining (bottom right) of colon tumor sections. Scale bars: 1.5 mm (top right) and 100 μm (bottom right). h Relative mRNA levels of WNT target genes in colon non-tumor (NT) and tumor (T) tissues ( n = 10 for BF BSH low -NT; n = 12 for BF BSH high -NT; n = 8 for BF BSH low -T; n = 10 for BF BSH high -T). Kruskal–Wallis test with Dunn’s post hoc test. i WB data of proteins involved in WNT signaling ( n = 3 independent samples/group). j Representative IHC staining of Ki-67 ( n = 8 independent slides for BF BSH low ; n = 9 independent slides for BF BSH high ). Scale bars: 100 μm. Data are presented as mean values +/− SEM in ( a – e , h ). Source data are provided as a Source Data File for Fig. 5.

Article Snippet: For short-term C7 treatment, 6- to 8-week-old male Cdx 2 Apc f/w mice were pretreated with 60% HFD for 10 weeks, and then colonized with BF BSH high and fed a 60% HFD or 60% HFD containing 1 mg/g C7 (TargetMol), which equates to 10 mg/kg/d consumption.

Techniques: MANN-WHITNEY, Two Tailed Test, Staining, Immunohistochemistry

Journal: Nature Communications

Article Title: Bile salt hydrolase in non-enterotoxigenic Bacteroides potentiates colorectal cancer

doi: 10.1038/s41467-023-36089-9

Figure Lengend Snippet: a – c HFD-fed Cdx 2 Apc f/w mice were colonized with BF BSH low or BF BSH high for 12 weeks, from which the colon non-tumor (NT) and tumor (T) tissues were applied for mRNA sequencing (pooled sample sizes: n = 4 independent samples for BF BSH low _NT; n = 4 independent samples for BF BSH high _NT; n = 4 independent samples for BF BSH low _T; n = 3 independent samples for BF BSH high _T). a Volcano plot showing the upregulated and downregulated genes in colon tumor tissues. Red dots (upregulated) and blue dots (downregulated) were identified as significantly changed mRNAs with multiple comparisons adjusted P value < 0.05 and |logFC| > 1. Two-tailed Student’s t test. b Significantly (multiple comparisons adjusted P value < 0.05) enriched pathway terms of upregulated genes in colon tumor tissues under microbial BSH overexpression (BSH high vs BSH low ) indicated by KEGG pathway analysis. Two-tailed Student’s t test. c Heatmap showing all the upregulated genes that involved in cytokine–cytokine receptor interaction and cell adhesion molecules (CAM) under microbial BSH overexpression (BSH high vs BSH low ). The genes in red were identified as markers of T reg cells as reported. d – g HFD-fed Cdx 2 Apc f/w mice were colonized with BF BSH low or BF BSH high for 12 weeks, from which the colon tumor tissues were applied for flow cytometry analysis ( n = 4 independent samples/group). Flow cytometry analysis determined the FOXP3 + CD25 + T reg cells ( d ) and CD8 + T cells ( e ) in colon tumor tissues. The portion of FOXP3 + CD25 + T re g cells in CD4 + T cells ( f ) and CD8 + T cells in total T cells ( g ). Two-tailed Student’s t test. h HFD-fed Cdx 2 Apc f/w mice were colonized with BF BSH low or BF BSH high for 12 weeks ( n = 11 mice for BF BSH low ; n = 12 mice for BF BSH high ). Representative IHC staining of TUNEL, an apoptosis marker ( n = 8 independent slides for BF BSH low ; n = 9 independent slides for BF BSH high ). Scale bars: 100 μm. Data are presented as mean values +/− SEM in ( f , g ). Source data are provided as a Source Data File for Fig. 6.

Article Snippet: For short-term C7 treatment, 6- to 8-week-old male Cdx 2 Apc f/w mice were pretreated with 60% HFD for 10 weeks, and then colonized with BF BSH high and fed a 60% HFD or 60% HFD containing 1 mg/g C7 (TargetMol), which equates to 10 mg/kg/d consumption.

Techniques: Sequencing, Two Tailed Test, Over Expression, Flow Cytometry, Immunohistochemistry, TUNEL Assay, Marker

Journal: Nature Communications

Article Title: Bile salt hydrolase in non-enterotoxigenic Bacteroides potentiates colorectal cancer

doi: 10.1038/s41467-023-36089-9

Figure Lengend Snippet: a HFD-fed Cdx 2 Apc f/w mice that were colonized with BF BSH low or BF BSH high for 12 weeks ( n = 8 mice for BF BSH low ; n = 10 mice for BF BSH high ). Ccl28 relative expression in colon tumor tissues. Two-tailed Student’s t test. b CCL28 protein levels ( n = 3 independent samples/group). c – f Cdx 2 Apc f/w mice were fed with HFD for 10 weeks, and then the mice were colonized with BF BSH high and injected (i.p.) with IgG or mCCL28 neutralizing antibody for another 2 weeks. The colon tumor tissues were used for flow cytometry analysis ( n = 4 independent samples/group). Flow cytometry analysis determined the FOXP + CD25 + T reg cells ( c ) and CD8 + T cells ( d ) in colon tumor tissues. The portion of FOXP + CD25 + T reg cells in CD4 + T cells ( e ) and CD8 + T cells in total T cells ( f ). Two-tailed Student’s t test. g – n HFD-fed Cdx 2 Apc f/w mice were fed with HFD for 6 weeks, and then colonized with BF BSH high and injected (i.p.) with IgG, mCCL28 Ab or mCD25 Ab neutralizing antibody for another 6 weeks ( n = 13 mice for IgG Ab; n = 8 mice for mCCL28 Ab; n = 9 mice for mCD25 Ab). The ileum ( g ) and colon ( h ) tumor incidence, and tumor numbers with different sizes (<4 mm 2 , >4 mm 2 and the sum of both). Mann–Whitney U test with two-sided. i Total tumor number i n the intestine. Two-tailed Student’s t test. j – l Representa t ive pictures of colon (left), gross images of tumors (top right) in the colon and H&E staining (bottom right) of colon tumor sections. Scale bars: 1.5 mm (top right) and 100 μm (bottom right). Representative IHC staining ( m ) and quantification ( n ) of TUNEL ( n = 10 in dependent slides for IgG Ab; n = 7 independent slides for mCCL28 Ab; n = 7 independent slides for mCD25 Ab). Scale bars: 100 μm. Two-tailed Student’s t test. Data are presen t ed as mean values +/− SEM in ( a , e – i , n ). Source data are provided as a Source Data File for Fig. 7.

Article Snippet: For short-term C7 treatment, 6- to 8-week-old male Cdx 2 Apc f/w mice were pretreated with 60% HFD for 10 weeks, and then colonized with BF BSH high and fed a 60% HFD or 60% HFD containing 1 mg/g C7 (TargetMol), which equates to 10 mg/kg/d consumption.

Techniques: Expressing, Two Tailed Test, Injection, Flow Cytometry, MANN-WHITNEY, Staining, Immunohistochemistry, TUNEL Assay

Journal: Nature Communications

Article Title: Bile salt hydrolase in non-enterotoxigenic Bacteroides potentiates colorectal cancer

doi: 10.1038/s41467-023-36089-9

Figure Lengend Snippet: a HFD-fed Cdx 2 Apc f/w mice were colonized with BF BSH low or BF BSH high for 12 weeks ( n = 8 mice for BF BSH low ; n = 10 mice for BF BSH high ). Relative expression of Fxr , Tgr5 and Vdr , as well as their target genes, in colon tumor tissues. Mann–Whitney U test with two-sided. b Relative expression of Fxr , Tgr5 and Vdr in colon non-tumor (NT) and tumor (T) tissues ( n = 11 independent samples for NT; n = 8 independent samples for T). Mann–Whitney U test with two-sided. c – e Cdx 2 Apc f/w and Cdx 2 Tgr5 −/− Apc f/w mice were fed with HFD for over 10 weeks, and then the colon tumors were used for colon organoid isolation and further culturing ( n = 3 independent samples /group). c Relative expression of Tgr5 . d Representative images of colon tumor-derived organoids at day 3 after passage. Scale bars: 200 μm. e Relative expression of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${{{{{\rm{\beta }}}}}}$$\end{document} β -catenin target genes. Mann–Whitney U test with two-sided. f Isolated colon tumor organoids were treated with DMSO or MSAB (10 μM, a β -catenin protein degrader) overnight ( n = 3 technical replicates/group). Relative expression of Ccl28 . Two-tailed Student’s t test. g , h Cdx 2 Apc f/w and Cdx 2 Tgr5 −/− Apc f/w mice were fed with a HFD for over 10 weeks, and then the colon tumors were used for colon organoid isolation and further culturing ( n = 3 tech n ical replicates/group). g Relative expression of Ccl28 . Two-tailed Student’s t test. h Relative expression of Ccl28 under DMSO, DCA (100 μM), LCA (100 μM), MSAB treatment overnight. Kruskal–Wallis test with Dunn’s post hoc test. i Diagram that uncovers that DCA/LCA-TGR5 signaling regulates Ccl28 expression in the presence of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${{{{{\rm{\beta }}}}}}$$\end{document} β -catenin in colon cancer cell. Created with BioRender.com. Data are presented as mean values +/− SEM in ( a – c , e – h ). Source data are provided as a Source Data File for Fig. 8.

Article Snippet: For short-term C7 treatment, 6- to 8-week-old male Cdx 2 Apc f/w mice were pretreated with 60% HFD for 10 weeks, and then colonized with BF BSH high and fed a 60% HFD or 60% HFD containing 1 mg/g C7 (TargetMol), which equates to 10 mg/kg/d consumption.

Techniques: Expressing, MANN-WHITNEY, Isolation, Derivative Assay, Two Tailed Test

Journal: Nature Communications

Article Title: Bile salt hydrolase in non-enterotoxigenic Bacteroides potentiates colorectal cancer

doi: 10.1038/s41467-023-36089-9

Figure Lengend Snippet: a – d Cdx 2 Apc f/w mice were fed with HFD for 10 weeks, and then the mice were colonized with BF BSH high and fed with HFD or HFD with compound 7 for another 2 weeks. The colon tumor tissues were used for flow cytometry analysis ( n = 4 independent samples/group). Flow cytometry analysis determined the FOXP + CD25 + T reg cells ( a ) and CD8 + T cells ( b ) in colon tumor tissues. The portion of FOXP + CD25 + T reg cells in CD4 + T cells ( c ) and CD8 + T cells in total T cells ( d ). Two-tailed Student’s t test. e – k Under BF BSH high colonization, Cdx 2 Apc f/w mice were fed with HFD or HFD with compound 7 for 12 weeks ( n = 13 mice for Vehicle; n = 11 mice for C7). e Unconjugated bile acid profiles in colon contents. Mann–Whitney U test with two-sided. The ileum ( f ) and colon ( g ) tumor incidence, and tumor numbers with different sizes (<4 mm 2 , >4 mm 2 and the sum of both). Mann–Whitney U test with two-sided. h Relative mRNA levels of WNT target genes and Ccl28 in colon tumor tissues. Mann–Whitney U test with two-sided. i WB data of CCL28 and proteins involved in WNT signaling ( n = 3 independent samples/group). j , k Representative pictures of colon (left), gross images of tumor (top right) in the colon and H&E staining (bottom right) of colon tumor sections. Scale bars: 1.5 mm (top right) and 100 μm (bottom right). Representative IHC staining of Ki-67 ( l ) and TUNEL ( m ). n = 9 independent slides for Vehicle; n = 9 independent slides for C7. Scale bars: 100 μm. Data are presented as mean values +/− SEM in ( c – h ). Source data are provided as a Source Data File for Fig. 9.

Article Snippet: For short-term C7 treatment, 6- to 8-week-old male Cdx 2 Apc f/w mice were pretreated with 60% HFD for 10 weeks, and then colonized with BF BSH high and fed a 60% HFD or 60% HFD containing 1 mg/g C7 (TargetMol), which equates to 10 mg/kg/d consumption.

Techniques: Flow Cytometry, Two Tailed Test, MANN-WHITNEY, Staining, Immunohistochemistry, TUNEL Assay

Journal: Scientific Reports

Article Title: Porcine milk-derived exosomes promote proliferation of intestinal epithelial cells

doi: 10.1038/srep33862

Figure Lengend Snippet: ( a–d ) Expression of CDX2 , PCNA , p53 and IGF-1R mRNAs, respectively. CDX2 , PCNA and IGF-1R levels were significantly improved, while p53 was inhibited in the 0.27 ± 0.03 μg total RNA treatment group ( P < 0.01 , n = 6). ( e–h ) Expression of CDX2, IGF-1R, p53 and PCNA proteins, respectively. CDX2, IGF-1R and PCNA were increased significantly, while p53 was inhibited significantly ( P < 0.01 ) (n = 6).

Article Snippet: Anti-p53 (D120082), anti-CDX2 (D162691) and anti-PCNA (D120014) antibodies were purchased from BBI Antibody (Sangon Biotech, Shanghai, China).

Techniques: Expressing

Journal: Scientific Reports

Article Title: Porcine milk-derived exosomes promote proliferation of intestinal epithelial cells

doi: 10.1038/srep33862

Figure Lengend Snippet: ( a–d ) Expression of CDX2 , PCNA , IGF-1R and p53 mRNAs, respectively. Expression of CDX2 , PCNA and IGF-1R genes significantly increased at different treatment concentrations (0.125 μg and 0.25 μg treatment groups), except for the expression of IGF-1R in the 0.125 μg treatment group ( P = 0.055 ). Meanwhile, p53 significantly decreased (n = 6). ( e–h ) Expression of CDX2, p53, IGF-1R and PCNA proteins, respectively. Except for the IGF-1R protein expression in the 0.25 μg treatment group which did not change significantly, expression levels of other proteins were consistent with those of their corresponding mRNAs (n = 6).

Article Snippet: Anti-p53 (D120082), anti-CDX2 (D162691) and anti-PCNA (D120014) antibodies were purchased from BBI Antibody (Sangon Biotech, Shanghai, China).

Techniques: Expressing

Journal: Scientific Reports

Article Title: Porcine milk-derived exosomes promote proliferation of intestinal epithelial cells

doi: 10.1038/srep33862

Figure Lengend Snippet: Primers for qRT-PCR.

Article Snippet: Anti-p53 (D120082), anti-CDX2 (D162691) and anti-PCNA (D120014) antibodies were purchased from BBI Antibody (Sangon Biotech, Shanghai, China).

Techniques: Sequencing

Journal: Frontiers in Oncology

Article Title: Large-Section Histopathology Can Better Indicate the Immune Microenvironment and Predict the Prognosis of Pancreatic Ductal Adenocarcinoma Than Small-Section Histopathology

doi: 10.3389/fonc.2021.694933

Figure Lengend Snippet: Main reagents and instruments.

Article Snippet: IHC: rabbit anti-CDX2 (monoclonal, EP25) , ZSGB-BIO , ZA-0520.

Techniques: Polymer, Imaging