Journal: Food & Nutrition Research

Article Title: Inositol hexaphosphate promotes intestinal adaptation in short bowel syndrome via an HDAC3-mediated epigenetic pathway

doi: 10.29219/fnr.v67.8694

Figure Lengend Snippet: IP6 regulates the FOXO3/CCND1 signaling pathway in rats. (a) The relative mRNA expression levels of Hdac3 in the distal small intestine ( n = 6 per group). Values were normalized to Actb expression. (b) The relative mRNA expression levels of Foxo3 in the distal small intestine ( n = 6 per group). Values were normalized to Actb expression. (c) The relative mRNA expression levels of Ccnd1 in the distal small intestine ( n = 6 per group). Values were normalized to Actb expression. (d) Western blotting analysis of the mucosa of the distal small intestine was performed to detect the protein expression levels of HDAC3, H3K9AC, FOXO3, and CCND1. Histone H3 was used as an internal control. (e) Relative protein expression of HDAC3, H3K9AC, FOXO3, and CCND1 of the mucosa in the distal small intestine. Values are mean ± SEM; ns, not significant; ** P < 0.01, SBS group versus Sham group; # P < 0.05, ### P < 0.001, SBS + IP6 group versus SBS group.

Article Snippet: The primary antibodies used in this study included anti-histone H3 antibody (1:1000, Cat# ab1791, Abcam, UK), anti-cyclin D1 (1:200, Cat# ab16663, Abcam, UK), HDAC3 antibody (1:1000, Cat# AF5349-50 μL, Affinity, China), anti-histone H3 (acetyl K9) antibody (1:500, Cat# ab32129, Abcam, UK), and FoxO3a (75D8) rabbit mAb (1:1000, Cat# 2497S, Cell Signaling Technology, USA).

Techniques: Expressing, Western Blot, Control

Journal: Food & Nutrition Research

Article Title: Inositol hexaphosphate promotes intestinal adaptation in short bowel syndrome via an HDAC3-mediated epigenetic pathway

doi: 10.29219/fnr.v67.8694

Figure Lengend Snippet: IP3 regulates the FOXO3/CCND1 signaling pathway in IEC-6 cells. (a) Western blotting analysis of IEC-6 cells was performed to detect the protein expression levels of HDAC3, H3K9AC, FOXO3, and CCND1. Histone H3 was used as an internal control. (b) Relative protein expression of HDAC3, H3K9AC, FOXO3, and CCND1 of the mucosa in the distal small intestine. Values are mean ± SEM; ns, not significant; * P < 0.05, ** P < 0.01, **** P < 0.0001, SBS group versus Sham group; # P < 0.05, ## P < 0.01, SBS + IP6 group versus SBS group.

Article Snippet: The primary antibodies used in this study included anti-histone H3 antibody (1:1000, Cat# ab1791, Abcam, UK), anti-cyclin D1 (1:200, Cat# ab16663, Abcam, UK), HDAC3 antibody (1:1000, Cat# AF5349-50 μL, Affinity, China), anti-histone H3 (acetyl K9) antibody (1:500, Cat# ab32129, Abcam, UK), and FoxO3a (75D8) rabbit mAb (1:1000, Cat# 2497S, Cell Signaling Technology, USA).

Techniques: Western Blot, Expressing, Control

Journal: Developmental cell

Article Title: Autophagy inhibition mediates apoptosis sensitization in cancer therapy by relieving FOXO3a turnover

doi: 10.1016/j.devcel.2018.02.014

Figure Lengend Snippet: (A) (left) HCT116 p53 −/− cells were transduced with two different lentiviral shRNAs targeting FOXO3a transcripts. After 24hrs of vehicle or bafilomycin A1 10nM treatment, PUMA mRNA levels were measured relative to 18s rRNA control. (right) western blot showing FOXO3a protein levels after treatment with two independent shRNAs targeting FOXO3a or shCtrl.

Article Snippet: Primers are listed in the . table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal FOXO3a Cell Signaling Technology Cat# 3938, RRID:AB_2106669 Rabbit monoclonal ATG7 Cell Signaling Technology Cat# 8558, RRID:AB_10831194 Rabbit monoclonal ATG5 Cell Signaling Technology Cat# 9980S, RRID:AB_10829153 Rabbit polyclonal PUMA/BBC3 Cell Signaling Technology Cat# 4976, RRID:AB_2064551) Rabbit polyclonal ULK1 Cell Signaling Technology Cat# 4773S, RRID:AB_2288252 Rabbit polyclonal PI3 Kinase Class III Cell Signaling Technology Cat# 3811S, RRID:AB_2062856 Rabbit polyclonal LC3 Novus Cat# NB100-2220, RRID:AB_10003146 Mouse monoclonal beta-Actin Sigma-Aldrich Cat# A5441, RRID:AB_476744 Mouse monoclonal p62/SQSTM1 Novus Cat# H00008878-M01, RRID:AB_548364 Mouse monoclonal Purified anti-RNA Polymerase II RPB1 antibody Clone H5 Biolegend Cat# 920204, RRID:AB_2616695 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Bafilomycin A1 Sigma-Aldrich B1792; CAS RN: 88899-55-2 Chloroquine MP Biomedicals 93919; CAS RN: 50-63-5 Nutlin-3a Cayman Chemicals 10004372; CAS RN: 548472-68-0 Protease inhibitor cocktail Roche 11836153001 Phosphatase inhibitor Sigma-Aldrich P5726 Protein A/G Plus beads Santa Cruz SC-2003 Critical Commercial Assays Qiagen RNeasy RNA isolation kit Qiagen Cat# 74104 QuantiTect Reverse Transcription Kit Qiagen Cat# 205311 Deposited Data Experimental Models: Cell Lines HCT116 Authenticated N/A MCF7 Authenticated N/A MCF10a Authenticated N/A HeLa N/A Experimental Models: Organisms/Strains Oligonucleotides See Table S1 for ChIP primers This paper N/A See Table S1 for QPCR primers This paper N/A See Table S1 for gRNAs This paper N/A Recombinant DNA pBABE puro mCherry-GFP-HA-FOXO3a This paper and Addgene x 2 #1787 and #1764 Software and Algorithms Other SYBR Green CFX for QPCR Applied Biosystems 4472942 Mirus Transit LT1 transfection reagent Mirus MIR2304 CRISPR Max ThermoFisher CMAX00001 Cell Event Caspase 3/7 Invitrogen C10423 MatTek 35mm dishes for living imaging MatTek P35GC-1.5-14-C LysoTracker Blue DND-22 ThermoFisher Cat# L7525 Incucyte ZOOM imaging system Essen BioScience N/A Open in a separate window KEY RESOURCES TABLE Expression constructs, shRNAs, and transduction Protein depletion by shRNA was achieved by using the pLKO.1 system.

Techniques: Transduction, Western Blot

Journal: Developmental cell

Article Title: Autophagy inhibition mediates apoptosis sensitization in cancer therapy by relieving FOXO3a turnover

doi: 10.1016/j.devcel.2018.02.014

Figure Lengend Snippet: (A) HCT116 cells treated with bafilomycin A1 10nM, an autophagy inhibitor, for indicated duration. Whole-cell lysates were probed for FOXO3a protein levels. See also Figure S3.

Article Snippet: Primers are listed in the . table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal FOXO3a Cell Signaling Technology Cat# 3938, RRID:AB_2106669 Rabbit monoclonal ATG7 Cell Signaling Technology Cat# 8558, RRID:AB_10831194 Rabbit monoclonal ATG5 Cell Signaling Technology Cat# 9980S, RRID:AB_10829153 Rabbit polyclonal PUMA/BBC3 Cell Signaling Technology Cat# 4976, RRID:AB_2064551) Rabbit polyclonal ULK1 Cell Signaling Technology Cat# 4773S, RRID:AB_2288252 Rabbit polyclonal PI3 Kinase Class III Cell Signaling Technology Cat# 3811S, RRID:AB_2062856 Rabbit polyclonal LC3 Novus Cat# NB100-2220, RRID:AB_10003146 Mouse monoclonal beta-Actin Sigma-Aldrich Cat# A5441, RRID:AB_476744 Mouse monoclonal p62/SQSTM1 Novus Cat# H00008878-M01, RRID:AB_548364 Mouse monoclonal Purified anti-RNA Polymerase II RPB1 antibody Clone H5 Biolegend Cat# 920204, RRID:AB_2616695 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Bafilomycin A1 Sigma-Aldrich B1792; CAS RN: 88899-55-2 Chloroquine MP Biomedicals 93919; CAS RN: 50-63-5 Nutlin-3a Cayman Chemicals 10004372; CAS RN: 548472-68-0 Protease inhibitor cocktail Roche 11836153001 Phosphatase inhibitor Sigma-Aldrich P5726 Protein A/G Plus beads Santa Cruz SC-2003 Critical Commercial Assays Qiagen RNeasy RNA isolation kit Qiagen Cat# 74104 QuantiTect Reverse Transcription Kit Qiagen Cat# 205311 Deposited Data Experimental Models: Cell Lines HCT116 Authenticated N/A MCF7 Authenticated N/A MCF10a Authenticated N/A HeLa N/A Experimental Models: Organisms/Strains Oligonucleotides See Table S1 for ChIP primers This paper N/A See Table S1 for QPCR primers This paper N/A See Table S1 for gRNAs This paper N/A Recombinant DNA pBABE puro mCherry-GFP-HA-FOXO3a This paper and Addgene x 2 #1787 and #1764 Software and Algorithms Other SYBR Green CFX for QPCR Applied Biosystems 4472942 Mirus Transit LT1 transfection reagent Mirus MIR2304 CRISPR Max ThermoFisher CMAX00001 Cell Event Caspase 3/7 Invitrogen C10423 MatTek 35mm dishes for living imaging MatTek P35GC-1.5-14-C LysoTracker Blue DND-22 ThermoFisher Cat# L7525 Incucyte ZOOM imaging system Essen BioScience N/A Open in a separate window KEY RESOURCES TABLE Expression constructs, shRNAs, and transduction Protein depletion by shRNA was achieved by using the pLKO.1 system.

Techniques:

Journal: Developmental cell

Article Title: Autophagy inhibition mediates apoptosis sensitization in cancer therapy by relieving FOXO3a turnover

doi: 10.1016/j.devcel.2018.02.014

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Primers are listed in the . table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal FOXO3a Cell Signaling Technology Cat# 3938, RRID:AB_2106669 Rabbit monoclonal ATG7 Cell Signaling Technology Cat# 8558, RRID:AB_10831194 Rabbit monoclonal ATG5 Cell Signaling Technology Cat# 9980S, RRID:AB_10829153 Rabbit polyclonal PUMA/BBC3 Cell Signaling Technology Cat# 4976, RRID:AB_2064551) Rabbit polyclonal ULK1 Cell Signaling Technology Cat# 4773S, RRID:AB_2288252 Rabbit polyclonal PI3 Kinase Class III Cell Signaling Technology Cat# 3811S, RRID:AB_2062856 Rabbit polyclonal LC3 Novus Cat# NB100-2220, RRID:AB_10003146 Mouse monoclonal beta-Actin Sigma-Aldrich Cat# A5441, RRID:AB_476744 Mouse monoclonal p62/SQSTM1 Novus Cat# H00008878-M01, RRID:AB_548364 Mouse monoclonal Purified anti-RNA Polymerase II RPB1 antibody Clone H5 Biolegend Cat# 920204, RRID:AB_2616695 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Bafilomycin A1 Sigma-Aldrich B1792; CAS RN: 88899-55-2 Chloroquine MP Biomedicals 93919; CAS RN: 50-63-5 Nutlin-3a Cayman Chemicals 10004372; CAS RN: 548472-68-0 Protease inhibitor cocktail Roche 11836153001 Phosphatase inhibitor Sigma-Aldrich P5726 Protein A/G Plus beads Santa Cruz SC-2003 Critical Commercial Assays Qiagen RNeasy RNA isolation kit Qiagen Cat# 74104 QuantiTect Reverse Transcription Kit Qiagen Cat# 205311 Deposited Data Experimental Models: Cell Lines HCT116 Authenticated N/A MCF7 Authenticated N/A MCF10a Authenticated N/A HeLa N/A Experimental Models: Organisms/Strains Oligonucleotides See Table S1 for ChIP primers This paper N/A See Table S1 for QPCR primers This paper N/A See Table S1 for gRNAs This paper N/A Recombinant DNA pBABE puro mCherry-GFP-HA-FOXO3a This paper and Addgene x 2 #1787 and #1764 Software and Algorithms Other SYBR Green CFX for QPCR Applied Biosystems 4472942 Mirus Transit LT1 transfection reagent Mirus MIR2304 CRISPR Max ThermoFisher CMAX00001 Cell Event Caspase 3/7 Invitrogen C10423 MatTek 35mm dishes for living imaging MatTek P35GC-1.5-14-C LysoTracker Blue DND-22 ThermoFisher Cat# L7525 Incucyte ZOOM imaging system Essen BioScience N/A Open in a separate window KEY RESOURCES TABLE Expression constructs, shRNAs, and transduction Protein depletion by shRNA was achieved by using the pLKO.1 system.

Techniques: Purification, Recombinant, Protease Inhibitor, Isolation, Software, SYBR Green Assay, Transfection, CRISPR, Imaging

Journal: bioRxiv

Article Title: Specific telomere protection ensured by FOXO3a upon genotoxic stress and during aging

doi: 10.1101/2021.08.04.454762

Figure Lengend Snippet: (A) FOXO3a full-length structure (top) showing relevant domains and truncated mutant forms (ΔCR1, ΔFH, ΔCR2C and ΔCR3). FOXO3a is composed by three conserved regions: CR1, CR2 and CR3 known to interact with several proteins. CR2 is divided in three subregions: CR2A, CR2B and CR2C. FOXO3a contains a Forkhead (FH) or DNA binding domain, that recognizes a TGTTTAC consensus DNA sequence, followed by a nuclear localization sequence (NLS). (B) Western blotting showing endogen FOXO3a downregulation, FOXO3a fulllength rescue and expression of FOXO3a truncated proteins. FOXO3a-Cell Signaling Technologies #2497 monoclonal antibody does not recognize ΔCR1 form because its epitope surrounds Glu50 (N-terminal). Cells were transduced 5 days with lentiviruses and the last 3 days transfected with siRNA. GAPDH was used as loading control. (C) sTIF quantification in siFOXO3a + truncated FOXO3a overexpression in BJ-HELT treated with bleomycin (50 μg/mL, 24hr), n=3. Conditions were compared to siFOXO3a-FOXO3a+Bleo using a Kruskal-Wallis’ multiple comparisons test. siFOXO3a-FOXO3a+Bleo vs siFOXO3a-△CR2C+Bleo , p-value =0,0345. (D) PLA showing TRF2-FOXO3a association in siFOXO3a + truncated FOXO3a overexpression in BJ-HELT treated with bleomycin (50 μg/mL, 24hr), n=3. (E) TRF2-FOXO3a PLA in transfected BJ-HELT cells treated with bleomycin, n=2. Statistical analyses were performed using Kruskal-Wallis’ multiple comparisons test (* p < 0.05, ** p < 0.001, *** p < 0.001, **** p < 0.0001). (F) Telomere specific damage upon p300 inhibition. siCtrl and sip300 transfected BJ-HELT cells were treated with bleomycin. Means ± SEM of two replicated are shown, Man-Whitney U test ( p-value= 0,0346).

Article Snippet: The following primary antibodies were used: TRF2, mouse monoclonal, (NB100-56506, 1:1000, Novus Biologicals); TRF2, rabbit monoclonal, (NB110-57130, 1:5000, Novus Biologicals); FOXO3a, rabbit monoclonal (clone 75D8, 1:1500, Cell Signaling Technology); GAPDH, rabbit polyclonal (1:2000, NB100-56875, Novus Biologicals).

Techniques: Mutagenesis, Binding Assay, Sequencing, Western Blot, Expressing, Transfection, Control, Over Expression, Inhibition

Journal: Cell reports

Article Title: Mitohormesis Primes Tumor Invasion and Metastasis

doi: 10.1016/j.celrep.2019.04.095

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Rabbit monoclonal anti-FOXO3a (75D8) , Cell Signaling Technology , Cat#2497; RRID:AB_836876.

Techniques: Virus, Recombinant, Plasmid Preparation, Transfection, Membrane, Cell Culture, Pore Size, Staining, Gene Expression, shRNA, Software

Journal: BMC Cancer

Article Title: Exosomal miR-99a-5p is elevated in sera of ovarian cancer patients and promotes cancer cell invasion by increasing fibronectin and vitronectin expression in neighboring peritoneal mesothelial cells

doi: 10.1186/s12885-018-4974-5

Figure Lengend Snippet: Quantitative proteomics by the Tandem Mass Tag (TMT) method

Article Snippet: Antibodies against vitronectin 65/75 (D-8; #sc-74,484) and fibronectin (EP5; #sc-8422) were purchased from Santa Cruz Biotechnology (Dallas, TX).

Techniques: Quantitative Proteomics, Activity Assay, Coagulation

Journal: BMC Cancer

Article Title: Exosomal miR-99a-5p is elevated in sera of ovarian cancer patients and promotes cancer cell invasion by increasing fibronectin and vitronectin expression in neighboring peritoneal mesothelial cells

doi: 10.1186/s12885-018-4974-5

Figure Lengend Snippet: EOC-derived exosomes enhanced fibronectin and vitronectin expression in HPMCs through the transfer of miR-99a-5p. a Western blotting. HPMCs were transfected with miR-99a-5p or negative control miRNA. Thereafter, cell lysates were collected, and immunoblotting was performed with antibodies against fibronectin, vitronectin, or β-actin as a loading control. Representative blots from three independent experiments are shown. b After HPMCs were treated with IOSE- and EOC-derived exosomes at 100 μg/mL for 24 h, cell lysates were collected, and western blotting was performed as described above. c HPMCs transfected with negative control miRNA and anti-miR-99a-5p were treated with exosomes at 100 μg/mL for 24 h. Thereafter, cell lysates were collected, and western blotting was performed as described above. d Densitometric ratios of fibronectin, vitronectin, and β-actin expression. e Model. EOC-derived exosomes affect HPMCs through the transfer of miR-99a-5p. See text for details

Article Snippet: Antibodies against vitronectin 65/75 (D-8; #sc-74,484) and fibronectin (EP5; #sc-8422) were purchased from Santa Cruz Biotechnology (Dallas, TX).

Techniques: Derivative Assay, Expressing, Western Blot, Transfection, Negative Control, Control