Journal: Tumour Virus Research

Article Title: Association of PNPLA3 (rs738409) & TM6SF2 (rs58542926) and ATG16L1 (rs2241880) genetic variants with susceptibility to hepatocellular carcinoma in a group of Egyptian patients with HCV-induced liver cirrhosis

doi: 10.1016/j.tvr.2023.200256

Figure Lengend Snippet: Frequency of ATG16L1 (rs2241880) genetic variants & allelic distribution and odd's ratios among the studied groups.

Article Snippet: The TaqMan minor groove binder probes with non-fluorescent quenchers, they were ready to use supplied by ThermoFisher Scientific *3. PNPLA3, rs738409 (Assay ID: C_7241_10), TM6SF2, rs58542926 (Assay ID: C_89463510_10) and ATG16L1, rs2241880 (Assay ID: C_9095577_20 ).

Techniques: Control

Journal: Tumour Virus Research

Article Title: Association of PNPLA3 (rs738409) & TM6SF2 (rs58542926) and ATG16L1 (rs2241880) genetic variants with susceptibility to hepatocellular carcinoma in a group of Egyptian patients with HCV-induced liver cirrhosis

doi: 10.1016/j.tvr.2023.200256

Figure Lengend Snippet: Comparison between ATG16L1 (rs2241880) genotypic variants in HCC and cirrhosis groups regarding the laboratory data.

Article Snippet: The TaqMan minor groove binder probes with non-fluorescent quenchers, they were ready to use supplied by ThermoFisher Scientific *3. PNPLA3, rs738409 (Assay ID: C_7241_10), TM6SF2, rs58542926 (Assay ID: C_89463510_10) and ATG16L1, rs2241880 (Assay ID: C_9095577_20 ).

Techniques: Comparison

Journal: Aging cell

Article Title: Lysosomal storage and impaired autophagy lead to inflammasome activation in Gaucher macrophages.

doi: 10.1111/acel.12409

Figure Lengend Snippet: Fig. 4 Treatment of Gaucher macrophages (GMs) macrophages with the small-molecule NCGC758 results in reduced IL-1b secretion (A) Control (C) and GMs (P) were treated with NCGC758 (8 lM) in the presence and absence of Gaucher erythrocyte ghosts. Total lysates were immunoblotted and probed for LC3 and p62. (B) Gaucher cells were treated with NCGC758 or imiglucerase (20 lM) followed by LPS+ATP (5 mM). Total protein lysates were run on SDS-PAGE and were probed for LC3, P62, and Atg16L1. Blots represent two independent experiments. (C,D) Gaucher macrophages treated with NCGC758 in the presence of erythrocyte ghosts, or treated with LPS and ATP, were immunostained for (C) LC3 (green) and Lamp2 (red) and (D) LC3 (red) and p62 (green). Z-stack images were acquired using a Zeiss 510 confocal microscope (639 magnification). Insets corresponding to the regions marked show higher magnifications of the areas outlined with the position of the xy-, xz-, and yz-slices that are shown for each of the 3D stacks. Images are taken at the same laser settings and are representative of three independent experiments (scale bar; 5l). (E,F) Control (C) and GMs (P) were treated with NCGC758 (8 lM) or Imiglucerase in the presence and absence of LPS+ATP and the supernatants (E) or total protein lysates (F) were probed for IL-1b. Blots represent two independent experiments. n = number of patients.

Article Snippet: The blocked membrane was incubated in blocking buffer containing 0.1% Tween-20 and the respective primary antibodies LC3A/B (Cell signaling, Danvers, MA, USA, 1/1000), Atg7 (Cell signaling, 1:1000), histone H3 (Cell signaling, 4499, 1:2000), VPS34 (Sigma, V9764, 1:1000), SQSTM1/p62 (Abcam, Cambridge, MA, USA, 1:1000), b-actin (Abcam 1:1000), ASC (Enzo life science, Farmingdale, NY, USA 1:1000), caspase-1 (Enzo life science, 1/ 1000), NFKB (Origene, Rockville, MD, USA, 1:500), GAPDH (GeneTex, Irvine, CA, USA, 1:2000), Atg16L1 (Bethyl, Montgomery, TX, USA, 1:2000), cathepsin D (R&D systems, 1:1000), IL-1b/IL-1F2 (R&D systems, 1:1000)] overnight at 4 °C, followed by three 15-min washes, and then was incubated in blocking buffer containing 0.1% Tween-20 (Sigma), 0.01% SDS, and IRDye , 680RD secondary antibody 1:10 000 (Li-CORE Bioscience, Lincoln, NE, USA) for 1 h at RT.

Techniques: Control, SDS Page, Microscopy

Journal: Endocrinology

Article Title: The Autophagy Gene Atg16L1 is Necessary for Endometrial Decidualization

doi: 10.1210/endocr/bqz039

Figure Lengend Snippet: List of primers and probes

Article Snippet: Atg16L1 , Mouse , qPCR, Taqman , ABI , Mm00513084_m1.

Techniques: Sequencing

Journal: Endocrinology

Article Title: The Autophagy Gene Atg16L1 is Necessary for Endometrial Decidualization

doi: 10.1210/endocr/bqz039

Figure Lengend Snippet: Atg16L1 HM mice are fertile and maintain the ability to decidualize. A) Diagram of the Atg16L1 HM mutation. B) Live birth rate of Wildtype (Wt) and Atg16L1 HM mice reveals that Atg16L1 HM mice are fertile. C) In vitro hormonal decidualization of endometrial stromal cells from Wt and Atg16L1 HM mice and D) Expression of the decidualization marker Prp show proper decidualization in Atg16L1 mice (n = 3 Wt, 5 Atg16L1 HM). E) Diagram of in vivo artificial decidualization method. F) Uterine horns of Wt and Atg16L1 HM mice and G) Resulting wet weights demonstrate Atg16L1 HM mice maintain the ability to decidualize in vivo (n = 10 Wt, 12 Atg16L1 HM). E2-estrogen, P4-progesterone; **P < 0.01, ***P < 0.001. ****P < 0.0001.

Article Snippet: Atg16L1 , Mouse , qPCR, Taqman , ABI , Mm00513084_m1.

Techniques: Mutagenesis, In Vitro, Expressing, Marker, In Vivo

Journal: Endocrinology

Article Title: The Autophagy Gene Atg16L1 is Necessary for Endometrial Decidualization

doi: 10.1210/endocr/bqz039

Figure Lengend Snippet: Uterine specific knock out of Atg16L1 impairs fertility. A) Diagram of the Atg16L1 cKO mutation. B) Expression of Atg16L1 is decreased in the uterus of Atg16L1 cKO virgin mice (n = 6 Control, 7 Atg16L1 cKO). C) Live birth rate, D) Number of litters, E) Litter size, and F) Total number of pups produced by control and Atg16L1 cKO mice over a 6-month period reveals compromised fertility in Atg16L1 mice (n = 5 Controls, 6 Atg16L1 cKO). G) Time to first litter as measured by plug date to delivery date is extended in Atg16L1 cKO mice; *P < 0.05, **P < 0.01, ***P < 0.001. ****P < 0.0001.

Article Snippet: Atg16L1 , Mouse , qPCR, Taqman , ABI , Mm00513084_m1.

Techniques: Knock-Out, Mutagenesis, Expressing, Control, Produced

Journal: Endocrinology

Article Title: The Autophagy Gene Atg16L1 is Necessary for Endometrial Decidualization

doi: 10.1210/endocr/bqz039

Figure Lengend Snippet: Atg16L1 cKO mice have an implantation defect. A) Histological sections of 4 dpc ovaries from control and Atg16L1 cKO mice show normal morphology with the presence of corpora lutea (denoted CL) (n = 6 Control, 5 Atg16L1 cKO). B) Blastocysts flushed from the uterine horns of control and Atg16L1 cKO mice on 4 dpc show normal morphology (n = 7 Control, 5 Atg15L1 cKO pregnant dams). C) Implantation cites observed at 6 dpc in control and Atg16L1 cKO mice (n = 7 Control and 6 Atg16L1 cKO pregnant dams). D) Quantification of blastocysts at 4 dpc and implantation cites at 6 dpc reveal 2 fewer blastocysts implant in the Atg16L1 cKO uterus. Arrows indicate implantation sites; *P < 0.05

Article Snippet: Atg16L1 , Mouse , qPCR, Taqman , ABI , Mm00513084_m1.

Techniques: Control

Journal: Endocrinology

Article Title: The Autophagy Gene Atg16L1 is Necessary for Endometrial Decidualization

doi: 10.1210/endocr/bqz039

Figure Lengend Snippet: Atg16L1 mice have impaired decidualization. A) Dissected uteri, H&E histology, and B) Wet weights of control and Atg16L1 cKO mice that have been stimulated to decidualize (n = 13 Control and n = 11 Atg16L1 cKO). Expression of the decidualization markers C) Bmp2 and D) Wnt4 reveal impaired decidualization in Atg16L1 cKO mice. E) Expression of Atg16L1 in control and Atg16L1 cKO mice following artificial decidualization, (n = 6 Control, 5 Atg16L1 cKO). F) Immunoblotting of LC3B protein on the protein lysate collected from stimulated horn of Control and Atg16L1 cKO mice uteri (n = 3) mice. The GAPDH is used as an internal loading control; *P < 0.05, **P < 0.01, ***P < 0.001. ****P < 0.0001.

Article Snippet: Atg16L1 , Mouse , qPCR, Taqman , ABI , Mm00513084_m1.

Techniques: Control, Expressing, Western Blot

Journal: Endocrinology

Article Title: The Autophagy Gene Atg16L1 is Necessary for Endometrial Decidualization

doi: 10.1210/endocr/bqz039

Figure Lengend Snippet: Knock down of ATG16L1 in human endometrial stromal cells impairs decidualization. A) Cellular morphology and B) quantitative PCR analysis of the decidualization marker IGFBP1 and PRL following transfection with control or ATG16L1 siRNA and hormonal stimulation. Data is normalized to 18S and expressed as fold change over Day 0 controls. Results are shown as mean ± standard error (SE) from 3 replicates of 1 patient-derived primary endometrial cell line. The experiment carried out on hESCs derived from 4 different individuals. (n = 4). Black arrowhead indicates fibroblast morphology and red arrowhead indicates decidualizing morphology. C) Immunoblotting of ATG16L1 and LC3B on the protein lysate from the hESCs collected at day 0 and day 6 after transfected with control or ATG16L1 siRNA. The GAPDH is used as an internal loading control; ****P < 0.0001.

Article Snippet: Atg16L1 , Mouse , qPCR, Taqman , ABI , Mm00513084_m1.

Techniques: Knockdown, Real-time Polymerase Chain Reaction, Marker, Transfection, Control, Derivative Assay, Western Blot

Journal: Genes

Article Title: The Association of ATG16L1 Variations with Clinical Phenotypes of Adult-Onset Still’s Disease

doi: 10.3390/genes12060904

Figure Lengend Snippet: Single-nucleotide polymorphisms of six-candidate genes potentially involved in the autophagy signaling pathway.

Article Snippet: , rs10210302 , C_30179764_10 2:233250193 , transcript variant , T (C > T), 0.34 , 0.141.

Techniques: Variant Assay

Journal: Genes

Article Title: The Association of ATG16L1 Variations with Clinical Phenotypes of Adult-Onset Still’s Disease

doi: 10.3390/genes12060904

Figure Lengend Snippet: Direct sequencing demonstrated that the frequencies of ATG16L1 polymorphisms and haplotypes were associated with susceptibility to AOSD.

Article Snippet: , rs10210302 , C_30179764_10 2:233250193 , transcript variant , T (C > T), 0.34 , 0.141.

Techniques: Sequencing

Journal: Genes

Article Title: The Association of ATG16L1 Variations with Clinical Phenotypes of Adult-Onset Still’s Disease

doi: 10.3390/genes12060904

Figure Lengend Snippet: The linkage disequilibrium (LD) plot of the 3 SNPs of the ATG16L1 gene using Haploview with confidence bounds color scheme. All SNPs were in strong LD.

Article Snippet: , rs10210302 , C_30179764_10 2:233250193 , transcript variant , T (C > T), 0.34 , 0.141.

Techniques:

Journal: Genes

Article Title: The Association of ATG16L1 Variations with Clinical Phenotypes of Adult-Onset Still’s Disease

doi: 10.3390/genes12060904

Figure Lengend Snippet: Logistic regression analysis for the systemic pattern of adult-onset Still’s disease.

Article Snippet: , rs10210302 , C_30179764_10 2:233250193 , transcript variant , T (C > T), 0.34 , 0.141.

Techniques: Activity Assay

Journal: bioRxiv

Article Title: Macrophage scavenger receptor 1 controls Chikungunya virus infection through autophagy

doi: 10.1101/2020.02.28.969832

Figure Lengend Snippet: A, B ) Repression of CHIKV replication by MSR1 requires ATG5. Mouse primary embryonic fibroblasts were transfected with either 0.2 or 1.5 µg of empty vector (Vec) or FLAG-Msr1 (mouse) expression plasmid. 24hrs later the cells were then infected with CHIKV (multiplicity of infection MOI=0.5). A ) Immunoblots showing FLAG-Msr1 (mouse) and Atg5-Atg12 expression at 24hrs after plasmid DNA transfection. B ) Quantitative RT-PCR analyses of intracellular CHIKV RNA. C ) Repression of CHIKV replication by MSR1 requires ATG12. Human trophoblasts were transfected with either 0.2µg of empty vector or a FLAG-MSR1 (human) expression plasmid. Twenty four hours later, the cells were then infected with CHIKV MOI=0.5 for 12hrs. Intracellular CHIKV RNA was quantitated by RT-PCR. D ) Generation of human ATG16L1 -/- trophoblasts by CRISPR-Cas9. The immunoblot shows ATG16L1 knockout efficiency. E ) Repression of CHIKV replication by MSR1 requires the FBD domain of ATG16L1. ATG16L1 -/- trophoblasts were transfected with the indicated combinations of expression plasmids (human gene) and vector (Vec) (50ng each) respectively. After 24hrs, the cells were infected with CHIKV at a MOI of 0.5 for 16hrs. FL: full-length, ΔFBD: FBD domain deletion, ΔWD40: WD40 domain deletion of ATG16L1. The immunoblots show CHIKV Capsid and cellular protein expression. Bars: mean + s.e.m, *, P<0.05, **, P<0.01 (Student’s t-test), N=3.

Article Snippet: The Myc-DDK-tagged mouse Msr1 ORF clone (Cat# MR205384), Atg12 (Cat# MR200886), Atg5 (Cat# MR203691), Atg16l1 (Cat# MR209513), Atg9a (Cat# MR208753), Atg13 (Cat# MR207683) and, p62/Sqstm1 (Cat# MR226105), human MSR1 (Cat# RC209609) and Beclin 1 (Cat# MR207162) were obtained from Origene (Rockville, MD 20850, USA). pcDNA-FLAG-Ulk1 (Plasmid # 27636) and pcDNA4-VPS34-FLAG (Plasmid # 24398) were purchased from Addgene (Cambridge, MA 02139, USA).

Techniques: Transfection, Plasmid Preparation, Expressing, Infection, Western Blot, Quantitative RT-PCR, Reverse Transcription Polymerase Chain Reaction, CRISPR, Knock-Out

Journal: Frontiers in Pharmacology

Article Title: Exogenous Hydrogen Sulfide Ameliorates Diabetic Myocardial Fibrosis by Inhibiting Cell Aging Through SIRT6/AMPK Autophagy

doi: 10.3389/fphar.2020.01150

Figure Lengend Snippet: (A) Fluorescence microscope with Beclin1 Red Probe analysis and quantitative results of autophagy intensity in H9c2 cells treated with Control; HG; HG +H 2 S; H 2 S. (B) Quantitative results of BECLIN1 red fluorescence intensity in H9c2 treated with Control; HG; HG +H 2 S; H 2 S. Data were normalized to control. (C) Western blotting analysis the expression of Atg5, Atg12, Atg16L1 and Beclin1 in H9c2 cells treated with Control; HG; HG +H 2 S; H 2 S. n = 3; *p < 0.05 vs control, **p < 0.01 vs control, ***p < 0.001 vs control, # p < 0.05 vs HG, ## p < 0.01vs HG, $ p < 0.05 vs HG+H 2 S; $$ p < 0.01 vs HG+H2S; HG, high glucose; H 2 S, hydrogen sulfide; PAG, dl-propargylglycine.

Article Snippet: Dulbecco’s modified Eagle’s medium (DMEM 5.5 mM D-glucose), penicillin, streptomycin and fetal bovine serum (FBS) were from Hyclone (Grand Island, NY), antibodies against SIRT6, AMPK, p-AMPK, LC3A/B, BECLIN1, ATG5, ATG16L1, P53, P21, P16 were from Boster Biological Technology (Ltd. Wuhan, China.

Techniques: Fluorescence, Microscopy, Control, Western Blot, Expressing

Journal: Frontiers in Pharmacology

Article Title: Exogenous Hydrogen Sulfide Ameliorates Diabetic Myocardial Fibrosis by Inhibiting Cell Aging Through SIRT6/AMPK Autophagy

doi: 10.3389/fphar.2020.01150

Figure Lengend Snippet: H2S upregulates STZ-induced diabetic myocardial fibrosis mitophagy. (A) Representative images of transmission electron microscopy analysis the effect of STZ‐induced diabetic myocardial fibrosis in STZ-evoked mitophagy in the selected area. The insets in the above panels are magnified and are presented in the lower panel. Transmission electron micrographs at bars of 0.2 µm(Red arrow represents microscopy). (B) Western blotting analysis the expression of Atg5,Atg12,Atg16L1 in myocardial tissue treated with Control; STZ; STZ +H2S; H2S; n = 3, *p < 0.05 vs control. **p < 0.01 vs control. # p < 0.05 vs STZ. STZ, streptozotocin; H2S, hydrogen sulfide.

Article Snippet: Dulbecco’s modified Eagle’s medium (DMEM 5.5 mM D-glucose), penicillin, streptomycin and fetal bovine serum (FBS) were from Hyclone (Grand Island, NY), antibodies against SIRT6, AMPK, p-AMPK, LC3A/B, BECLIN1, ATG5, ATG16L1, P53, P21, P16 were from Boster Biological Technology (Ltd. Wuhan, China.

Techniques: Transmission Assay, Electron Microscopy, Microscopy, Western Blot, Expressing, Control