Journal: Oncotarget

Article Title: Connexin 32 dysfunction promotes ethanol-related hepatocarcinogenesis via activation of Dusp1-Erk axis

doi:

Figure Lengend Snippet: Up-regulated and down-regulated genes in the liver of EtOH-treated Tg rats

Article Snippet: Thereafter a polyclonal rabbit antibody against GST-P was used with biotin-conjugated anti-rabbit IgG and Cy5-labeled streptavidin (Thermo Fischer Scientific Inc.), and finally the section was incubated with an Alexa Fluor 350 conjugated rabbit anti-DUSP1 polyclonal antibody (Bioss Inc., Boston, MA).

Techniques:

Journal: Oncotarget

Article Title: Connexin 32 dysfunction promotes ethanol-related hepatocarcinogenesis via activation of Dusp1-Erk axis

doi:

Figure Lengend Snippet: Levels of Dusp1 mRNA A. and protein B. in whole liver tissues measured by quantitative RT-PCR and western blotting, respectively. Data of quantitative RT-PCR are presented as mean ± SD, n = 4 per groups. **, ***: P < 0.01 and 0.001 respectively. Representative image of laser microdissected tissue (upper) and Dusp1 mRNA level in GST-P positive foci as determined by quantitative RT-PCR (lower) C. Immunohistochemical staining for Dusp1 in GST-P positive foci of Tg and Wt rats that received 5%EtOH (upper) and the intensity score of Dusp1 in GST-P positive foci as compared to Wt-control rats (lower) D. Data are presented as mean ± SD, n = 5 per group, 10 foci/rat. *: P < 0.05.

Article Snippet: Thereafter a polyclonal rabbit antibody against GST-P was used with biotin-conjugated anti-rabbit IgG and Cy5-labeled streptavidin (Thermo Fischer Scientific Inc.), and finally the section was incubated with an Alexa Fluor 350 conjugated rabbit anti-DUSP1 polyclonal antibody (Bioss Inc., Boston, MA).

Techniques: Quantitative RT-PCR, Western Blot, Immunohistochemical staining, Staining

Journal: International Journal of Genomics

Article Title: Downregulation of the Coiled-Coil Domain Containing 80 and Its Perspective Mechanisms in Ovarian Carcinoma: A Comprehensive Study

doi: 10.1155/2021/3752871

Figure Lengend Snippet: The expression of CCDC80 protein in normal ovary (a) and (b) and ovarian carcinoma (c) and (d) tissues through immunohistochemical (IHC) staining.

Article Snippet: Afterward, immunohistochemical (IHC) staining conducted using CCDC80 polyclonal antibody (biorbyt, orb216089, rabbit-anti-human) with 150 OVCA tissues and 46 non-OVCA tissues from clinical samples and tissue microarrays.

Techniques: Expressing, Immunohistochemical staining, Immunohistochemistry

Journal: International Journal of Genomics

Article Title: Downregulation of the Coiled-Coil Domain Containing 80 and Its Perspective Mechanisms in Ovarian Carcinoma: A Comprehensive Study

doi: 10.1155/2021/3752871

Figure Lengend Snippet: Scatter plots of CCDC80 protein (a) and mRNA (b)–(i) expression of OVCA and the corresponding normal controls.

Article Snippet: Afterward, immunohistochemical (IHC) staining conducted using CCDC80 polyclonal antibody (biorbyt, orb216089, rabbit-anti-human) with 150 OVCA tissues and 46 non-OVCA tissues from clinical samples and tissue microarrays.

Techniques: Expressing

Journal: International Journal of Genomics

Article Title: Downregulation of the Coiled-Coil Domain Containing 80 and Its Perspective Mechanisms in Ovarian Carcinoma: A Comprehensive Study

doi: 10.1155/2021/3752871

Figure Lengend Snippet: The receiver operating characteristic (ROC, (a)–(i)) and sROC (j) curves of CCDC80 in OVCA and Deek's test for publication bias test (k).

Article Snippet: Afterward, immunohistochemical (IHC) staining conducted using CCDC80 polyclonal antibody (biorbyt, orb216089, rabbit-anti-human) with 150 OVCA tissues and 46 non-OVCA tissues from clinical samples and tissue microarrays.

Techniques:

Journal: International Journal of Genomics

Article Title: Downregulation of the Coiled-Coil Domain Containing 80 and Its Perspective Mechanisms in Ovarian Carcinoma: A Comprehensive Study

doi: 10.1155/2021/3752871

Figure Lengend Snippet: Combined standard mean difference (SMD, (a)) of CCDC80 expression between OVCA and non-OVCA group and Egger's test (b) for publication bias test (in mRNA group, TCGA_GTEx_ovary was a cohort of RNA-seq, and other cohorts began with “GSE” were gene chip cohorts).

Article Snippet: Afterward, immunohistochemical (IHC) staining conducted using CCDC80 polyclonal antibody (biorbyt, orb216089, rabbit-anti-human) with 150 OVCA tissues and 46 non-OVCA tissues from clinical samples and tissue microarrays.

Techniques: Expressing, RNA Sequencing

Journal: International Journal of Genomics

Article Title: Downregulation of the Coiled-Coil Domain Containing 80 and Its Perspective Mechanisms in Ovarian Carcinoma: A Comprehensive Study

doi: 10.1155/2021/3752871

Figure Lengend Snippet: The relationship between CCDC80 expression and the fraction of immune cell infiltration in OVCA based on CIBERSORT algorithms.

Article Snippet: Afterward, immunohistochemical (IHC) staining conducted using CCDC80 polyclonal antibody (biorbyt, orb216089, rabbit-anti-human) with 150 OVCA tissues and 46 non-OVCA tissues from clinical samples and tissue microarrays.

Techniques: Expressing

Journal: International Journal of Genomics

Article Title: Downregulation of the Coiled-Coil Domain Containing 80 and Its Perspective Mechanisms in Ovarian Carcinoma: A Comprehensive Study

doi: 10.1155/2021/3752871

Figure Lengend Snippet: The boxplots visualizing the single-sample gene set enrichment analysis (ssGSEA) in high- and low- CCDC80 expression group in OVCA based on immunocyte-related gene sets (a) and immune function-related gene sets (b) ( ∗∗∗ , P < 0.0001; ∗∗ , P < 0.001; ∗ , P < 0.05; ns, P ≥ 0.05).

Article Snippet: Afterward, immunohistochemical (IHC) staining conducted using CCDC80 polyclonal antibody (biorbyt, orb216089, rabbit-anti-human) with 150 OVCA tissues and 46 non-OVCA tissues from clinical samples and tissue microarrays.

Techniques: Expressing

Journal: International Journal of Genomics

Article Title: Downregulation of the Coiled-Coil Domain Containing 80 and Its Perspective Mechanisms in Ovarian Carcinoma: A Comprehensive Study

doi: 10.1155/2021/3752871

Figure Lengend Snippet: KEGG enrichment plots of the intersection genes from CCDC80 positively related coexpressed genes (CEGs) and downregulated differentially expressed genes (DEGs) (a), and CCDC80 negatively related CEGs and upregulated DEGs (b).

Article Snippet: Afterward, immunohistochemical (IHC) staining conducted using CCDC80 polyclonal antibody (biorbyt, orb216089, rabbit-anti-human) with 150 OVCA tissues and 46 non-OVCA tissues from clinical samples and tissue microarrays.

Techniques:

Journal: International Journal of Genomics

Article Title: Downregulation of the Coiled-Coil Domain Containing 80 and Its Perspective Mechanisms in Ovarian Carcinoma: A Comprehensive Study

doi: 10.1155/2021/3752871

Figure Lengend Snippet: A volcano plot shows the results of GSEA based on the OVCA cell lines and enrichment plots of immune-related gene sets in low- CCDC80 group (b) and (c) and high- CCDC80 group (d) and (e).

Article Snippet: Afterward, immunohistochemical (IHC) staining conducted using CCDC80 polyclonal antibody (biorbyt, orb216089, rabbit-anti-human) with 150 OVCA tissues and 46 non-OVCA tissues from clinical samples and tissue microarrays.

Techniques:

Journal: International Journal of Genomics

Article Title: Downregulation of the Coiled-Coil Domain Containing 80 and Its Perspective Mechanisms in Ovarian Carcinoma: A Comprehensive Study

doi: 10.1155/2021/3752871

Figure Lengend Snippet: Seqlogos of the motifs of transcription factor NR3C1 (a) and PBX3 (b); ChIP-seq peak (see red arrow) of NR3C1 in the upstream of the transcription start site of CCDC80 (c); and the yellow arrow indicates the transcription direction of CCDC80 ; no ChIP-seq peak of PBX3 in the upstream of the transcription start site of CCDC80 (d).

Article Snippet: Afterward, immunohistochemical (IHC) staining conducted using CCDC80 polyclonal antibody (biorbyt, orb216089, rabbit-anti-human) with 150 OVCA tissues and 46 non-OVCA tissues from clinical samples and tissue microarrays.

Techniques: ChIP-sequencing

Journal: International Journal of Genomics

Article Title: Downregulation of the Coiled-Coil Domain Containing 80 and Its Perspective Mechanisms in Ovarian Carcinoma: A Comprehensive Study

doi: 10.1155/2021/3752871

Figure Lengend Snippet: Violin plots visualizing the differences of estimated half maximal inhibitory concentration (IC50) of compounds between high- and low- CCDC80 expression group.

Article Snippet: Afterward, immunohistochemical (IHC) staining conducted using CCDC80 polyclonal antibody (biorbyt, orb216089, rabbit-anti-human) with 150 OVCA tissues and 46 non-OVCA tissues from clinical samples and tissue microarrays.

Techniques: Concentration Assay, Expressing

Journal: Life Sciences

Article Title: Vitamin D modulates systemic inflammation in patients with severe COVID-19

doi: 10.1016/j.lfs.2022.120909

Figure Lengend Snippet: VitD treatment decreased COVID-19 hyperinflammatory responses through attenuating STAT3 signaling, as well as JNK and AKT of the MAPK cascades in blood of severe COVID-19 patients. (A and B) mRNA and protein expression levels of VDR in whole blood of VitD treated compared to the VitD untreated COVID-19 patients. (C-E) Expression levels of pSTAT3, pJNK, and pAKT in whole blood of VitD treated compared to the VitD untreated COVID-19 patients. (F–I) mRNA and protein expression levels of DUSP1 and DUSP5 in whole blood of VitD treated compared to the VitD untreated COVID-19 patients. (J–M) The protein levels of IL-6, IL-17, IL-1β, and TNFα proinflammatory cytokines in plasma of VitD treated compared to VitD untreated patients. Correlation of IL-6, IL-17, IL-1β plasma levels with serum levels of D-dimer and CRP of these patients. Statistical tests; Comparison was done using unpaired t-test or Mann-Whitney U test, depending on the skewness of the data. Linear regression models adjusted for patient's age, male sex, BMI, and DM. P value of <0.05 was considered significant.

Article Snippet: The proteins were transferred onto a nitrocellulose membrane (Bio-Rad, Ca, USA), blocked in skimmed milk for 1 h at room temperature, incubated overnight at 4 °C with antibodies specific to (cat#12550, Cell Signaling Technology, Beverly, MA, USA), p-STAT3 (cat# 9145, Cell Signaling Technology, Beverly, MA, USA), STAT3 (cat# 9132, Cell Signaling Technology, Beverly, MA, USA), p-JNK (cat# 9251, Cell Signaling Technology, Beverly, MA, USA), (cat# 9252, Cell Signaling Technology, Beverly, MA, USA), p- (cat# 9271, Cell Signaling Technology, Beverly, MA, USA), AKT (cat# 9272, Cell Signaling Technology, Beverly, MA, USA), DUSP1 (cat# 35217, Cell Signaling Technology, Beverly, MA, USA), DUSP5 (cat# 3483, Cell Signaling Technology, Beverly, MA, USA), (cat#54376, Cell Signaling Technology, Beverly, MA, USA), and β-Actin (cat#8457, Cell Signaling Technology, Beverly, MA, USA) was used as loading controls.

Techniques: Expressing, Clinical Proteomics, Comparison, MANN-WHITNEY

Journal: mBio

Article Title: N 6 -Methyladenosine and Reader Protein YTHDF2 Enhance the Innate Immune Response by Mediating DUSP1 mRNA Degradation and Activating Mitogen-Activated Protein Kinases during Bacterial and Viral Infections

doi: 10.1128/mbio.03349-22

Figure Lengend Snippet: m 6 A mediates DUSP1 transcript stability during bacterial infection in RAW264.7 cells. (A) Tracks of m 6 A peaks on the DUSP1 transcript 0, 2, 4, and 6 h after infection with P. aeruginosa . (B) Expression levels of the DUSP1 transcript 0, 2, 4, and 6 h after infection with P. aeruginosa quantified by transcriptome sequencing (RNA-seq). (C) m 6 A levels on the DUSP1 transcript 0, 2, 4, and 6 h after infection with P. aeruginosa examined by MeRIP-qPCR. (D) Expression levels of the DUSP1 transcript 0, 2, 4, and 6 h after infection with P. aeruginosa quantified by RT-qPCR. (E) Examination of DUSP1 and ALKBH5 protein levels following ALKBH5 knockdown in RAW264.7 cells by Western blotting. (F) m 6 A levels on the DUSP1 transcript following ALKBH5 knockdown in RAW264.7 cells examined by MeRIP-qPCR. (G) Expression levels of the DUSP1 transcript following ALKBH5 knockdown examined by RT-qPCR. (H) Alterations in the half-lives (T1/2) of the DUSP1 transcript following ALKBH5 knockdown during P. aeruginosa infection examined by RT-qPCR at the indicated time points following the addition of 10 μg/mL actinomycin D. siALKBH5, siRNA targeting ALKBH5.

Article Snippet: The membrane was blocked with 5% milk and then incubated with primary antibody to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (catalog number 5174S; Cell Signaling Technology [CST]), p38 (catalog number 8690S; CST), p-p38 (catalog number 4511S; CST), ERK (catalog number 4695S; CST), p-ERK (catalog number 4370S; CST), JNK (catalog number 9252S; CST), p-JNK (catalog number 4668S; CST), DUSP1 (catalog number NBP2-67909; Novus), IL-1β (catalog number AB-401-NA; R&D Systems), or ALKBH5 (catalog number HPA007196; Sigma) overnight at 4°C.

Techniques: Infection, Expressing, Sequencing, RNA Sequencing Assay, Quantitative RT-PCR, Western Blot

Journal: mBio

Article Title: N 6 -Methyladenosine and Reader Protein YTHDF2 Enhance the Innate Immune Response by Mediating DUSP1 mRNA Degradation and Activating Mitogen-Activated Protein Kinases during Bacterial and Viral Infections

doi: 10.1128/mbio.03349-22

Figure Lengend Snippet: YTHDF2 mediates m 6 A-dependent DUSP1 transcript stability during bacterial and viral infections in RAW264.7 cells. (A) Protein levels of the m 6 A writers METTL3, METTL14, and WTAP; the erasers ALKBH5 and FTO; and the readers YTHDF1 and YTHDF2 with or without infection by C. diphtheriae , P. aeruginosa , or HSV-1 at the indicated time points examined by Western blotting. (B) Examination of DUSP1 and YTHDF2 protein levels following YTHDF2 knockdown by Western blotting. (C) Expression levels of the DUSP1 transcript following YTHDF2 knockdown examined by RT-qPCR. (D) Alterations of the half-lives of the DUSP1 transcript following YTHDF2 knockdown in RAW264.7 cells during P. aeruginosa infection examined by RT-qPCR at the indicated time points following the addition of 10 μg/mL actinomycin D. (E) Binding of YTHDF2 to the DUSP1 transcript at the indicated time points following P. aeruginosa infection examined by RIP-qPCR.

Article Snippet: The membrane was blocked with 5% milk and then incubated with primary antibody to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (catalog number 5174S; Cell Signaling Technology [CST]), p38 (catalog number 8690S; CST), p-p38 (catalog number 4511S; CST), ERK (catalog number 4695S; CST), p-ERK (catalog number 4370S; CST), JNK (catalog number 9252S; CST), p-JNK (catalog number 4668S; CST), DUSP1 (catalog number NBP2-67909; Novus), IL-1β (catalog number AB-401-NA; R&D Systems), or ALKBH5 (catalog number HPA007196; Sigma) overnight at 4°C.

Techniques: Infection, Western Blot, Expressing, Quantitative RT-PCR, Binding Assay

Journal: mBio

Article Title: N 6 -Methyladenosine and Reader Protein YTHDF2 Enhance the Innate Immune Response by Mediating DUSP1 mRNA Degradation and Activating Mitogen-Activated Protein Kinases during Bacterial and Viral Infections

doi: 10.1128/mbio.03349-22

Figure Lengend Snippet: DUSP1 regulates p38 and JNK phosphorylation and the expression of innate immune response genes during bacterial and viral infections in RAW264.7 cells. (A) DUSP1 knockdown enhanced p38 and JNK phosphorylation during infection by P. aeruginosa , C. diphtheriae , HSV-1, or the HSV-1 ICP34.5 mutant. (B) DUSP1 knockdown enhanced the expression of the IL-1β, CSF3, TGM2, and SRC genes during infection by P. aeruginosa , C. diphtheriae , HSV-1, or the HSV-1 ICP34.5 mutant. (C) DUSP1 knockdown enhanced the protein level of IL-1β during infection by P. aeruginosa , C. diphtheriae , or the HSV-1 ICP34.5 mutant.

Article Snippet: The membrane was blocked with 5% milk and then incubated with primary antibody to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (catalog number 5174S; Cell Signaling Technology [CST]), p38 (catalog number 8690S; CST), p-p38 (catalog number 4511S; CST), ERK (catalog number 4695S; CST), p-ERK (catalog number 4370S; CST), JNK (catalog number 9252S; CST), p-JNK (catalog number 4668S; CST), DUSP1 (catalog number NBP2-67909; Novus), IL-1β (catalog number AB-401-NA; R&D Systems), or ALKBH5 (catalog number HPA007196; Sigma) overnight at 4°C.

Techniques: Expressing, Infection, Mutagenesis

Journal: mBio

Article Title: N 6 -Methyladenosine and Reader Protein YTHDF2 Enhance the Innate Immune Response by Mediating DUSP1 mRNA Degradation and Activating Mitogen-Activated Protein Kinases during Bacterial and Viral Infections

doi: 10.1128/mbio.03349-22

Figure Lengend Snippet: Working model of the regulation of DUSP1, MAPKs, and innate immune response genes by m 6 A and the m 6 A-related proteins YTHDF2 and ALKBH5 during pathogenic infections.

Article Snippet: The membrane was blocked with 5% milk and then incubated with primary antibody to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (catalog number 5174S; Cell Signaling Technology [CST]), p38 (catalog number 8690S; CST), p-p38 (catalog number 4511S; CST), ERK (catalog number 4695S; CST), p-ERK (catalog number 4370S; CST), JNK (catalog number 9252S; CST), p-JNK (catalog number 4668S; CST), DUSP1 (catalog number NBP2-67909; Novus), IL-1β (catalog number AB-401-NA; R&D Systems), or ALKBH5 (catalog number HPA007196; Sigma) overnight at 4°C.

Techniques: