Journal: Cell reports

Article Title: Optic nerve regeneration screen identifies multiple genes restricting adult neural repair

doi: 10.1016/j.celrep.2021.108777

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: The following primary antibodies were incubated with tissue sections overnight at 4°C: anti-Iba1 (1:200, Abcam), anti-CD68 (1:250, Bio-Rad), anti-GFAP (1:500, Abcam), anti-DLK (1:100, Genetex), anti-Atf3 (1:200, Novus Biologicals), anti-GFP (1:500, Abcam), anti-Il22Ra1 (1:200, Bioss), anti-Rbpms (1:100; PhosphoSolutions), anti-βIII-tubulin antibody (1:500, Promega).

Techniques: Virus, Recombinant, SYBR Green Assay, DNA Extraction, Enzyme-linked Immunosorbent Assay, cDNA Synthesis, Gene Expression, shRNA, Expressing, Plasmid Preparation, Software

Journal: Cellular and Molecular Gastroenterology and Hepatology

Article Title: Interleukin 13 Promotes Maturation and Proliferation in Metaplastic Gastroids

doi: 10.1016/j.jcmgh.2024.101366

Figure Lengend Snippet: Antibodies Used

Article Snippet: ATF3 , Rabbit , Novus, NBP1-85816 , 1:500.

Techniques:

Journal: Journal of Neuroinflammation

Article Title: Tissue-resident M2 macrophages directly contact primary sensory neurons in the sensory ganglia after nerve injury

doi: 10.1186/s12974-021-02283-z

Figure Lengend Snippet: Antibodies used in the present study

Article Snippet: Anti-activating transcription factor 3 (ATF3) (a marker of damaged neuron) , HPA001562 , Rabbit , Polyclonal , 1:1000 , Atlas Antibodies, Stockholm, Sweden , AB_1078233.

Techniques: Concentration Assay, Marker, Binding Assay, Plasmid Preparation

Journal: Journal of Neuroinflammation

Article Title: Tissue-resident M2 macrophages directly contact primary sensory neurons in the sensory ganglia after nerve injury

doi: 10.1186/s12974-021-02283-z

Figure Lengend Snippet: Ganglionic macrophages proliferate after nerve injury. ATF3-positive cells (green) in the contralateral (contra) and ipsilateral (ipsi) sides of the maxillary nerve region of the trigeminal ganglion on day 1 after infraorbital nerve ligation ( a ) and the number of ATF3-positive cells ( n = 4–6/timepoints) ( b ). Iba1-positive cells (red) on day 7 after nerve ligation ( c ) and the number of Iba1-positive cells ( n = 4–6/timepoints) ( d ). BrdU (green)- and Iba1 (red)-positive cells ( e ), multiple staining showing co-localization (arrowhead) of BrdU signals (green) with nucleus (blue) of Iba1-positive cells (red) ( f ) on day 5 after a nerve ligation, and the number of BrdU- and Iba1-positive cells ( n = 4–6/timepoints) ( g ). See list of abbreviations. Scale bars are indicated. Data are represented as mean (S.D.), and differences were detected using two-way ANOVA with Tukey–Kramer test ( b , d , g )

Article Snippet: Anti-activating transcription factor 3 (ATF3) (a marker of damaged neuron) , HPA001562 , Rabbit , Polyclonal , 1:1000 , Atlas Antibodies, Stockholm, Sweden , AB_1078233.

Techniques: Ligation, Staining

Journal: Journal of Neuroinflammation

Article Title: Tissue-resident M2 macrophages directly contact primary sensory neurons in the sensory ganglia after nerve injury

doi: 10.1186/s12974-021-02283-z

Figure Lengend Snippet: Volume of ganglionic macrophages enlarges after nerve injury. Iba1-positive cells (red) in the contralateral (contra) and ipsilateral (ipsi) sides of the maxillary nerve region of the trigeminal ganglion on day 7 after infraorbital nerve ligation ( a ) and the cell areas of Iba1-positive cells ( n = 4–6/timepoints) ( b ). Z-stack images showing Iba1-positive cells (red) around ATF3-positive cells (green) ( c ), three-dimensional images showing Iba1-positive cells ( d ), and the cell volume of Iba1-positive cells ( n = 10 cells/group from 3 mice) ( e ) on day 7 after nerve ligation. See list of abbreviations. Scale bars are indicated. Data are represented as mean (S.D.), and differences were detected using two-way ANOVA with Tukey–Kramer test ( b ) and Student’s t test with Welch’s correction ( e )

Article Snippet: Anti-activating transcription factor 3 (ATF3) (a marker of damaged neuron) , HPA001562 , Rabbit , Polyclonal , 1:1000 , Atlas Antibodies, Stockholm, Sweden , AB_1078233.

Techniques: Ligation

Journal: Journal of Neuroinflammation

Article Title: Tissue-resident M2 macrophages directly contact primary sensory neurons in the sensory ganglia after nerve injury

doi: 10.1186/s12974-021-02283-z

Figure Lengend Snippet: Contact areas of ganglionic macrophages to primary sensory neurons are expanded after nerve injury. ATF3 (green)-, Iba1 (red)-, and PGP9.5 (blue)-positive cells in ipsilateral (ipsi) sides of the maxillary nerve region of the trigeminal ganglion on days 1 and 7 after infraorbital nerve ligation ( a ) and a percentage of contact-like structures (CLS) between ATF3-positive or negative neurons and Iba1-positive cells ( n = 4 or 5/group) ( b ). Multiple staining ( c ) and Z-stack images ( d ) showing Iba1-positive cells (green), Nissl-positive neurons (blue), and glutamine synthetase (GS)-positive satellite glial cells (red) in the contralateral (contra) and ipsilateral sides on day 7 after nerve ligation. White arrowhead indicates the contact sites between Iba1-positive cells and neurons. Three-dimensional images showing contact area of Iba1-positive cells and Nissl-positive neurons ( e ). Blue indicates the surface of Nissl-positive neurons, and yellow indicates the surface of Nissl-positive neurons with Iba1-positive cells in contact. Surface area of Iba1-positive or GS-positive satellite glial cells in contact with individual Nissl-positive neurons ( f ) and a percentage of these areas averaged together (averaging 10 cells/ipsi from 3 mice) ( g ) on day 7 after nerve ligation. Electron micrograph showing macrophages with electron-dense lipid bodies (asterisk) and lysosomes (arrow) in contact (black arrowhead) with neurons ( h ). “N” indicates the nucleus. See list of abbreviations. Scale bars are indicated

Article Snippet: Anti-activating transcription factor 3 (ATF3) (a marker of damaged neuron) , HPA001562 , Rabbit , Polyclonal , 1:1000 , Atlas Antibodies, Stockholm, Sweden , AB_1078233.

Techniques: Ligation, Staining

Journal: Biology Direct

Article Title: Platelet-activating factor induces ferroptosis by binding to ATF3 and inhibiting the SLC7A11/GPX4 axis to suppress the progression of endometrial carcinoma

doi: 10.1186/s13062-025-00713-z

Figure Lengend Snippet: PAF induces ferroptosis via the ATF3/GPX4 and ATF3/SLC7A11 axes. (A) Heat map representing the significantly regulated transcription factors detected via RNA-seq analysis of AN3CA and HEC1B cells. (B , C) The mRNA expression levels of ATF3 and DDIT3 were in AN3CA and HEC1B cells treated with PAF (60 µM) for 48 h. (D , E) Protein expression of ATF3 in AN3CA and HEC1B cells treated with PAF (0, 20, 40, and 60 µM) for 48 h (D), and the quantifiable data are shown (E). (F) Confocal microscopy of AN3CA and HEC1B cells in the presence of PAF (60 µM). Cells were stained for ATF3 (green) and phalloidin (red). DAPI was used to visualize the nucleus (blue). Scale bar, 50 μm (left) or 100 μm (right). (G) The potential binding sites between ATF3 and GPX4/SLC7A11 were predicted by JASPAR. (H) Schematic diagram of ATF3 binding site-mutated SLC7A11 reporter vector (pro-SLC7A11-mut) and GPX4 reporter vector (pro-GPX4-mut). (I , J) Dual luciferase assay of the luciferase activity of AN3CA (I) and HEC1B (J) cells. (K) Immunoblotting analysis of the expression of GPX4 and SLC7A11 following ATF3 overexpression in AN3CA and HEC1B cells. (L) Immunoblotting analysis of the protein expression of SLC7A11, GPX4, and ATF3 after ATF3 silencing with siRNA coupled with PAF treatment in AN3CA cells. * p < 0.05, ** p < 0.01 and *** p < 0.001, ns . not significant

Article Snippet: SPR assays were performed by TopScience Co., Ltd. (Shanghai, China) to detect the binding between the recombinant ATF3 protein (TMPH-01164, TargetMol) and C16-PAF (74389-68-7, TargetMol), with the ATF3 protein and anti-ATF3 antibody combination used as the positive control.

Techniques: RNA Sequencing, Expressing, Confocal Microscopy, Staining, Binding Assay, Plasmid Preparation, Luciferase, Activity Assay, Western Blot, Over Expression

Journal: Biology Direct

Article Title: Platelet-activating factor induces ferroptosis by binding to ATF3 and inhibiting the SLC7A11/GPX4 axis to suppress the progression of endometrial carcinoma

doi: 10.1186/s13062-025-00713-z

Figure Lengend Snippet: PAF binds to ATF3 and reduces its ubiquitination. (A , B) Molecular docking indicates the binding details between PAF and ATF3. The surface representation of the protein residues ( A ) and 2D representation of the binding interaction of PAF and ATF3 ( B ) are depicted. (C , D) Surface plasmon resonance of the affinity of anti-ATF3 antibody ( C ) and PAF ( D ) for ATF3 protein. K D , dissociation constant. (E) WB analysis shows that PAF stabilized ATF3 across different temperature gradients in the CETSA in 293T cells. (F) WB analysis indicates that PAF promoted the resistance of ATF3 to pronase digestion in the DARTS assay in 293T cells. (G) CHX chase analysis of ATF3 protein expression after treatment with PAF in AN3CA and HEC1B cells. (H) WB analysis of ATF3 in ATF3 -overexpressing AN3CA and HEC1B cells. The cells were pretreated with PAF (60 µM) for 24 h and then treated with CHX and MG132 for 24 h. (I) Representative WB images demonstrate the ubiquitination of ATF3 in 293T cells co-transfected with ATF3-Flag, HA-Ub, and plasmids for 24 h. Cellular lysates were collected after 3 h of treatment with PAF, purified with a Flag-tag protein purification kit, and then subjected to WB with anti-HA and anti-ATF3

Article Snippet: SPR assays were performed by TopScience Co., Ltd. (Shanghai, China) to detect the binding between the recombinant ATF3 protein (TMPH-01164, TargetMol) and C16-PAF (74389-68-7, TargetMol), with the ATF3 protein and anti-ATF3 antibody combination used as the positive control.

Techniques: Ubiquitin Proteomics, Binding Assay, SPR Assay, Expressing, Transfection, Purification, FLAG-tag, Protein Purification

Journal: Biology Direct

Article Title: Platelet-activating factor induces ferroptosis by binding to ATF3 and inhibiting the SLC7A11/GPX4 axis to suppress the progression of endometrial carcinoma

doi: 10.1186/s13062-025-00713-z

Figure Lengend Snippet: Schematic overview of the present study. Treatment with PAF attenuates EC cell proliferation by inducing ferroptosis. Mechanistically, PAF interacts with ATF3, enhancing its stability through deubiquitination and consequently suppressing the expression of the ferroptosis-related proteins SLC7A11 and GPX4

Article Snippet: SPR assays were performed by TopScience Co., Ltd. (Shanghai, China) to detect the binding between the recombinant ATF3 protein (TMPH-01164, TargetMol) and C16-PAF (74389-68-7, TargetMol), with the ATF3 protein and anti-ATF3 antibody combination used as the positive control.

Techniques: Expressing

Journal: Molecular Medicine Reports

Article Title: Role of indoleamine 2,3-dioxygenase in ischemia-reperfusion injury of renal tubular epithelial cells

doi: 10.3892/mmr.2021.12111

Figure Lengend Snippet: Effect of anoxia in the presence or absence of the IDO inhibitor 1-MT on ATF4, CHOP, ATF3, p-p53 and p53 levels. Representative western blots for the levels of (A) ATF4, (B) CHOP, (C) ATF3, (D) p-p53 and (E) p53. Semi-quantification of (F) ATF4, (G) CHOP, (H) ATF3, (I) p-p53 and (J) p53 protein levels. (K) p-p53/total p53 ratio. *P<0.05 vs. control; # P<0.05 vs. control with 1-MT; ^ P<0.05 vs. anoxia; & P<0.05 vs. anoxia with 1-MT. 1-MT, 1-DL-methyltryptophan; IDO, indoleamine 2,3-dioxygenase 1; ATF4, activating transcription factor 4; CHOP; C/EBP homologous protein; ATF4, activating transcription factor 3; p-, phosphorylated; OD, optical density.

Article Snippet: Primary antibodies were specific the following proteins: IDO (1:200; cat. no. sc-25809), GCN2K (1:100; cat. no. sc-374609) (both from Santa Cruz Biotechnology, Inc.), phosphorylated at Thr899 GCN2K (p-GCN2K; 1:1,000; cat. no. ab75836; Abcam), eukaryotic translation initiation factor-2α (eIF2α; 1:100; cat. no. sc-133132; Santa Cruz Biotechnology, Inc.), p at Ser51 eIF2α (p-eIF2α; 1:1,000; cat. no. 9721; Cell Signaling Technology, Inc.), activating transcription factor 4 (ATF4; 1:500; cat. no. CSB-PA002272KA01HU), ATF3 (1:500; cat. no. CSB-PA020022) (both Cusabio Technology LLC), C/EBP homologous protein (CHOP; 1:1,000; cat. no. 5554), p53 (1:1,000; cat. no. 2524), p at Ser15 p53 (p-p53; 1:1,000; cat. no. 9284), Bax (1:1,000; cat. no. 5023) (all Cell Signaling Technology, Inc.), death receptor 5 (DR5; 1:500; cat. no. CSB-PA018500; Cusabio Technology LLC), activated cleaved caspase-3 (CC3; 1:1,000; cat. no. ab13847; Abcam), AhR (1:200; cat. no. sc-133088), cytochrome P450 family 1 subfamily A polypeptide 1 (CYP1A1; 1:500; cat. no. sc-25304) (both Santa Cruz Biotechnology, Inc.) and β-actin (1:2,500; cat. no. 4967; Cell Signaling Technology, Inc.).

Techniques: Western Blot, Control

Journal: Molecular Medicine Reports

Article Title: Role of indoleamine 2,3-dioxygenase in ischemia-reperfusion injury of renal tubular epithelial cells

doi: 10.3892/mmr.2021.12111

Figure Lengend Snippet: IDO-mediated anoxia-induced apoptosis and reoxygenation-induced ferroptosis molecular pathways. IDO-mediated anoxia-induced apoptotic molecular pathway is depicted on the left. IDO-mediated reoxygenation-induced ferroptotic molecular pathway is depicted on the right. AIMP3/p18, aminoacyl-tRNA synthetase-interacting multifunctional protein-3/p18; AhR, aryl-hydrocarbon receptor; ATF3, activating transcription factor 3; ATF4, activating transcription factor 4; ATM/ATR, ataxia-telangiectasia mutated/ataxia-telangiectasia and Rad3 related protein complex; CHOP, C/EBP homologous protein; CC3, cleaved caspase-3; CYP1A1, cytochrome P450 family 1 subfamily A polypeptide 1; DR5, death receptor 5; IDO, indoleamine 2,3-dioxygenase 1; Kyn, kynurenine; p-, phosphorylated; eIF2a, eukaryotic translation initiation factor-2α; GCN2K, general control nonderepressible-2 kinase; MRS, methionyl-tRNA synthetase; p53, p53; ROS, reactive oxygen species; Trp, tryptophan.

Article Snippet: Primary antibodies were specific the following proteins: IDO (1:200; cat. no. sc-25809), GCN2K (1:100; cat. no. sc-374609) (both from Santa Cruz Biotechnology, Inc.), phosphorylated at Thr899 GCN2K (p-GCN2K; 1:1,000; cat. no. ab75836; Abcam), eukaryotic translation initiation factor-2α (eIF2α; 1:100; cat. no. sc-133132; Santa Cruz Biotechnology, Inc.), p at Ser51 eIF2α (p-eIF2α; 1:1,000; cat. no. 9721; Cell Signaling Technology, Inc.), activating transcription factor 4 (ATF4; 1:500; cat. no. CSB-PA002272KA01HU), ATF3 (1:500; cat. no. CSB-PA020022) (both Cusabio Technology LLC), C/EBP homologous protein (CHOP; 1:1,000; cat. no. 5554), p53 (1:1,000; cat. no. 2524), p at Ser15 p53 (p-p53; 1:1,000; cat. no. 9284), Bax (1:1,000; cat. no. 5023) (all Cell Signaling Technology, Inc.), death receptor 5 (DR5; 1:500; cat. no. CSB-PA018500; Cusabio Technology LLC), activated cleaved caspase-3 (CC3; 1:1,000; cat. no. ab13847; Abcam), AhR (1:200; cat. no. sc-133088), cytochrome P450 family 1 subfamily A polypeptide 1 (CYP1A1; 1:500; cat. no. sc-25304) (both Santa Cruz Biotechnology, Inc.) and β-actin (1:2,500; cat. no. 4967; Cell Signaling Technology, Inc.).

Techniques: Control

Journal: Brain structure & function

Article Title: Preservation of KCC2 expression in axotomized abducens motoneurons and its enhancement by VEGF

doi: 10.1007/s00429-023-02635-w

Figure Lengend Snippet: Antibodies used in this study

Article Snippet: ATF3 Used for injured motoneuron identification , Recombinant protein corresponding to aa 1-103 in human ATF3 , Mouse/monoclonal , Novus Clone 1685 NBP2-34489 , AB_2786997 Recognizes the epitope: ASAIVPCLSPPGSL (Manufacturer’s information) Not present in uninjured motoneurons , 1:200.

Techniques: Comparison, Expressing, Recombinant