Journal: Redox Biology

Article Title: SARS-CoV2 infection impairs the metabolism and redox function of cellular glutathione

doi: 10.1016/j.redox.2021.102041

Figure Lengend Snippet: Nrf2, Membrane transporters, and GCLC in SARS-CoV2 infected VERO-E6 cells treated with Nelfinavir (Nel) or Remdesivir (Rem). Immunoblot of Nrf2 protein expression ( A , left panels) was assessed 6 hpi and 24 hpi, and by semi-quantitative fluorescence analysis 48 hpi ( A , right panels). Fluorophores were FITC (green) for Nrf2 protein labelling, DAPI (blue) for nuclei and Phalloidin-Alexa Fluor595 (orange) for the cytosolic space. Immunoblot of xCT and MRP1 membrane transport proteins ( B ), and GCLC protein ( C ) were carried out as described in the section Methods 24 hpi. Infection conditions and treatments with antivirals were the same of . Control test with untreated cells (CTL -) vs infected cells or treatments: §p < 0.05, §§p < 0.01. Infected cells + DMSO vs antivirals *p < 0.05, **p < 0.001. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Article Snippet: The primary antibodies used were: Nrf2 Polyclonal Antibody, FITC Conjugated (bs-1074R-FITC, Bioss Antibodies, 1:50); NQO1 (A180, Mouse mAb #3187, CST, 1:50); GST-pi (610,718, mouse mAb, BD Biosciences, 1:500); PE anti-human IL-6 Antibody (BioLegend, 1:1000); PE anti-human IL-10 Antibody (BioLegend, 1:1000).

Techniques: Infection, Western Blot, Expressing, Fluorescence

Journal: Frontiers in Medicine

Article Title: Restored retinal physiology after administration of niacin with citicoline in a mouse model of hypertensive glaucoma

doi: 10.3389/fmed.2023.1230941

Figure Lengend Snippet: Western blot antibodies.

Article Snippet: Rabbit polyclonal anti-Nrf-2 , 1:1000 , Abcam (Cambridge, UK) , ab92946.

Techniques: Western Blot

Journal: Frontiers in Medicine

Article Title: Restored retinal physiology after administration of niacin with citicoline in a mouse model of hypertensive glaucoma

doi: 10.3389/fmed.2023.1230941

Figure Lengend Snippet: Effect of individual or combined administration of niacin and citicoline on MCE-induced oxidative stress. (A) Representative Western blots and densitometric analysis of nuclear factor erythroid 2-related factor-2 (Nrf-2) and (B) heme oxygenase-1 (HO-1) levels in control and MCE mice either untreated or treated with individual niacin and citicoline or their combination. Data are expressed as mean ± SEM ( n = 6 retinas for group). * p < 0.0001 vs. control; § p < 0.01, §§ p < 0.001, and §§§ p < 0.0001 vs. MCE (two-way ANOVA followed by Tukey’s multiple comparison post-hoc test).

Article Snippet: Rabbit polyclonal anti-Nrf-2 , 1:1000 , Abcam (Cambridge, UK) , ab92946.

Techniques: Western Blot, Comparison

Journal: bioRxiv

Article Title: Waves of transcription drive erythroid differentiation and launch the NRF2-activated antioxidant program

doi: 10.1101/2024.07.12.603281

Figure Lengend Snippet: A) Number of GATA-binding factor 1 (GATA1), GATA2, and nuclear factor erythroid 2-related factor 2 (NRF2) targets among induced and repressed genes, as detected with Enrichr. Significant p-values from Enrichr analysis are indicted. B) Time of NRF2 target gene induction upon erythroid differentiation. The colors indicate the three main pathways of antioxidant response: glutathione (GSH) production and metabolisms (light brown), thioredoxin (TXN)-based antioxidation (green) and NADPH production (blue). The bolded text indicates the earliest time point the gene’s nascent transcription is significantly induced. C) Schematic representation of the three main antioxidant pathways. Intermediates (bolded text) and hemin-induced NRF2 targets (rounded rectangles) are indicated. Dashed lines indicate intermediates not shown. D) Genome browser illustration of the induction of NRF2 target gene solute carrier family 7 member 11 ( SLC7A11 ) upon hemin-induced erythroid differentiation. RNA synthesis as PRO-seq reads per kilobase of gene body (gbRPK) are shown for each time point, indicating significant induction in red. E) Relative quantity of GSH and GSSG in K562 cells treated with 30 μM hemin for 60 min or 24 h. n=3. *p<0.05. F) Relative quantity of GSH and GSSG in K562 cells treated with the oxidative stress inducer menadione (MD) for 60 min. n=3. *p<0.05, **p<0.01. G) Schematic illustration comparing the ratio of protective GSH per oxidized GSSG (GSH/GSSG) in erythroid differentiation (left) versus oxidative stress (right). Related Supplementary Figures 5 and 6.

Article Snippet: The NRF2 antibody (D1Z9C, Cell Signaling Technology) was diluted in 5% milk-TBS-0.1% Tween20, applied to the membranes, and the membranes were incubated overnight at 4°C.

Techniques: Binding Assay

Journal: bioRxiv

Article Title: Waves of transcription drive erythroid differentiation and launch the NRF2-activated antioxidant program

doi: 10.1101/2024.07.12.603281

Figure Lengend Snippet: A-B) Hemin-induced RNA synthesis at NRF2 target genes A) glutamate-cysteine ligase modifier subunit ( GCLM ) and B) thioredoxin ( TXN ). C) Insets of e1 (left) and e4 (right) of the beta-globin LCR, shown in the main . The 5’-ends of nascent transcripts enrich at the precise transcription start nucleotide (+1 nt, TSN) and are indicated with asterisks. The 3’-ends of nascent transcripts (3’nt) show the active site of transcription. D) Inset of GCLM promoter region, showing the precise transcription start nucleotide (+1 nt, TSN), as identified from the 5’-ends of nascent RNAs (asterisk). NRF2 motif at the promoter of GCLM locates -26 nt from the +1 nt.

Article Snippet: The NRF2 antibody (D1Z9C, Cell Signaling Technology) was diluted in 5% milk-TBS-0.1% Tween20, applied to the membranes, and the membranes were incubated overnight at 4°C.

Techniques:

Journal: bioRxiv

Article Title: Waves of transcription drive erythroid differentiation and launch the NRF2-activated antioxidant program

doi: 10.1101/2024.07.12.603281

Figure Lengend Snippet: A) The NRF2-recognized DNA motif as identified by MEME-ChIP from the unison of all hemin-induced enhancers (n= 3,757). B) CentriMo analysis of the probability for NRF2 and GATA1 motifs with respect to the enhancer center. C) Fraction of hemin-induced and unchanged enhancers that contain at least one NRF2 motif. The statistical analyses were performed with chi-square. **p<0.01, ***p<0.001. D) DNase I-seq, GATA1 ChIP-seq, transcribed enhancers, NRF2 motifs, and nascent transcription (PRO-seq) at the β-globin locus. The hypersensitive sites 1-4 (HS1-4), here denoted e1-4, indicate the erythroid-specific enhancers in the β-globin locus control region (LCR). The transcriptional profile of e1-4 and the nearest globin gene ( HBE1 ) is shown upon 0 min, 60 min and 24 h hemin treatment, and after 48 h recovery from the 60-min hemin treatment. Quantification of HBE1 (gbRPK; in black), and e1-4 transcription (eRPK; gold, brown, light green, dark green) are shown. E) Quantification of HBE1 (black), HBG1/2 (dark red), and e1-4 transcription (gold, brown, light green, and dark green, respectively) during erythroid differentiation. e1+e2+e3+e4 indicates the total transcription (sum eRPK) across enhancers e1-4. F) Insets of e1 (left) and e4 (right) from panel D , zooming into the GATA1 ChIP-seq summit points. Underlying architecture of transcription initiation (arrows), initiator motif, 5’-ends of eRNAs, GATA motifs and NRF2 motifs are indicated. The precise transcription start nucleotides (+1 nt) are identified from the 5’-ends of nascent transcripts shown in . Related .

Article Snippet: The NRF2 antibody (D1Z9C, Cell Signaling Technology) was diluted in 5% milk-TBS-0.1% Tween20, applied to the membranes, and the membranes were incubated overnight at 4°C.

Techniques: ChIP-sequencing, Control

Journal: bioRxiv

Article Title: Waves of transcription drive erythroid differentiation and launch the NRF2-activated antioxidant program

doi: 10.1101/2024.07.12.603281

Figure Lengend Snippet: A) Significantly (p<0.05) induced (red) or repressed (blue) mRNAs upon hemin-induced erythroid differentiation, as compared to untreated K562 cells. B) Nascent RNA synthesis (left) and mRNA expression (right) of phosphoglycerate dehydrogenase ( PHGDH ). C) NRF2 and γ-globin protein levels in K562 cells transfected with NRF2 siRNA or control siRNA (scr). β-tubulin (TUBB) serves as a loading control. D) Clustering of SHARE-seq (combinatorial scATAC-seq and scRNA-seq) data in human bone marrow. The distinct cell populations are indicated, and the erythroid lineage framed. E) Transcription factor scores of GATA1 and NRF2 during erythroid specification, showing GATA1 activity from erythroid progenitors to late erythroid cells, and NRF2 activation to peak in the late erythroid cells. The SHARE-seq data (D-E) is from reference and visualized in ACAMShiny ( https://buenrostrolab.shinyapps.io/ACAMShiny/ ). F) Summary of transcription regulation in erythroid differentiation, and comparison of transcription mechanisms, kinetics, and regulators upon differentiation versus stress. Erythroid differentiation launches slow but persistent changes in transcription that proceed in waves and are coordinated at the rate-limiting step of initiation. On the contrary, acute stress triggers instant but transient transcriptional reprogramming, coordinated primarily at the Pol II pause-release. Differentiating cells utilize lineage-specific (blue) and stress-inducible (orange) trans -activators to prime and execute transcriptional reprogramming. Ordered activity of GABPA, GATA1, TAL1, HEMGN and NRF2, drive globin expression. Additionally, NRF2 activates the antioxidant program including the synthesis of glutathione (GSH), thioredoxin (TXN) and NADPH biogenesis to prepare differentiating erythroid cells to oxidative stress, encountered as the mature, enucleated oxygen-transporting erythrocytes. Related Supplementary Figures 6-8.

Article Snippet: The NRF2 antibody (D1Z9C, Cell Signaling Technology) was diluted in 5% milk-TBS-0.1% Tween20, applied to the membranes, and the membranes were incubated overnight at 4°C.

Techniques: Expressing, Transfection, Control, Activity Assay, Activation Assay, Comparison

Journal: bioRxiv

Article Title: Waves of transcription drive erythroid differentiation and launch the NRF2-activated antioxidant program

doi: 10.1101/2024.07.12.603281

Figure Lengend Snippet: A) Spearman’s rank correlation (rho) of each biological mRNA-seq replicate pair, measured as counts across exons of each gene. B) Genome browser showing mRNA levels of HSPA1A and HSPA1B genes in replicates 1, 2 and 3. C) mRNA expression of the NRF2 target gene solute carrier family 7 member 11 ( SLC7A11 ). Level of mRNA expression (FPM) is indicated in each condition, red denoting significant induction. D) Induced mRNA expression of NRF2 target genes in the glutathione (GSH) metabolism and synthesis (light brown), thioredoxin (TXN) based antioxidation (green) and NADPH regeneration (blue) pathways. The first time point an mRNA is detected induced is shown in bold. E) Number of genes associated with changed RNA synthesis within 24 h (PRO-seq), and mRNA expression at 48 h (RNA-seq) of erythroid differentiation. F) mRNA expression of the fetal hemoglobin genes HBG1 and HBG2 , and the embryonic hemoglobin gene HBE1 as measured with mRNA-seq upon hemin treatment, and after 4 h or 48 h recovery from a transient hemin exposure.

Article Snippet: The NRF2 antibody (D1Z9C, Cell Signaling Technology) was diluted in 5% milk-TBS-0.1% Tween20, applied to the membranes, and the membranes were incubated overnight at 4°C.

Techniques: Expressing, RNA Sequencing

Journal: bioRxiv

Article Title: Waves of transcription drive erythroid differentiation and launch the NRF2-activated antioxidant program

doi: 10.1101/2024.07.12.603281

Figure Lengend Snippet: A) mRNA expression of platelet-derived growth factor subunit B (PDGFB) upon hemin-induced erythroid differentiation. B) Immunoblot of γ-globin (γ-glob) and NRF2 protein levels in K562 cells treated with hemin for the indicated time point. For recovery, the hemin was removed, and the cells cultured in hemin-free media. β-tubulin (TUBB) was used as a loading control. C-D) Expression on C) GATA1 and D) NRF2 across human tissues, as identified by the Human Protein Atlas. E) GATA1 interactions reported by the Human Protein Atlas. GATA1 and NFE2L2/NRF2 are highlighted. Image credit for C-E: Modified from Human Protein Atlas .

Article Snippet: The NRF2 antibody (D1Z9C, Cell Signaling Technology) was diluted in 5% milk-TBS-0.1% Tween20, applied to the membranes, and the membranes were incubated overnight at 4°C.

Techniques: Expressing, Derivative Assay, Western Blot, Cell Culture, Control, Modification

Journal: bioRxiv

Article Title: Waves of transcription drive erythroid differentiation and launch the NRF2-activated antioxidant program

doi: 10.1101/2024.07.12.603281

Figure Lengend Snippet: A) Single cell mRNA expression of GABPA, GATA1 and HEMGN, and NRF2 target genes HBB, GCLC and GCLM in indicated human bone marrow cells. The mRNA expression is shown in distinct cell clusters that corresponds to the bone marrow populations shown in the main . B) DORC score for GATA1, TAL1, HEMGN and NRF2 in human bone marrow cells, showing their ordered activation during the erythroid lineage specification. The mRNA expression (scRNA-seq) in A , and the DORC score (scATAC-seq and scRNA-seq) in B originate from SHARE-seq data from the reference . The DORC score in erythroid lineage was visualized in ACAMShiny ( https://buenrostrolab.shinyapps.io/ACAMShiny/ ) and shows the same regions as the main . C) Protein expression in human erythrocytes as reported by quantitative mass spectrometry. The peptide counts are shown for all expressed proteins, NRF2 targets genes in the antioxidant pathways, and globins. The quantitative mass spectrometry in panel C originates from reference .

Article Snippet: The NRF2 antibody (D1Z9C, Cell Signaling Technology) was diluted in 5% milk-TBS-0.1% Tween20, applied to the membranes, and the membranes were incubated overnight at 4°C.

Techniques: Expressing, Activation Assay, Mass Spectrometry