Journal: Nature Neuroscience

Article Title: Hypoxia ameliorates neurodegeneration and movement disorder in a mouse model of Parkinson’s disease

doi: 10.1038/s41593-025-02010-4

Figure Lengend Snippet: a , Volcano plot showing the log 2 fold change of transcripts in the SN 12 weeks after striatal injection of PFF versus α-syn monomer in mice breathing 21% O 2 , plotted against the −log 10 ( P adj ). Significantly changing genes (log 2 fold change > 0.25, P adj < 0.05 from a DESeq2 Wald test with multiple testing using the Benjamini–Hochberg procedure) are denoted in black. b , Volcano plot showing the log 2 fold change of transcripts in the SN 12 weeks after striatal injection of PFF versus α-syn monomer in mice breathing 11% O 2 , plotted against the −log 10 ( P adj ). Significantly changing genes (log 2 fold change > 0.25, P adj < 0.05) are denoted in black. c , d , Box plot showing Tfrc ( c ) and Slc40a1 ( Fpn ) ( d ) expression. Significance is indicated using P adj calculated in the DESeq2 analysis of all genes (that is, DESeq2 Wald test with multiple testing correction using the Benjamini–Hochberg procedure). e , Box plot showing HIF targets upregulated in the SN of mice breathing 11% O 2 . The y axes in the box plots represent the transcripts per million (TPM) normalized for each gene to the mean TPM of α-syn-monomer-treated mice breathing 21% O 2 . The box plots are annotated with the adjusted P values calculated in the DESeq2 analysis of all genes (that is, DESeq2 Wald test with multiple testing correction using the Benjamini–Hochberg procedure). a – e , The number of mice in each group was 21% O 2 , monomer ( n = 11); 21% O 2 , PFF ( n = 12); 11% O 2 , monomer ( n = 9); and 11% O 2 , PFF ( n = 10). f , Box plot showing HIF target proteins upregulated in the SN of mice breathing 11% O 2 . The y axes in the box plots represent the TMT intensity normalized for each gene to the mean intensity of α-syn-monomer-treated mice breathing 21% O 2 . The number of mice in each group was 21% O 2 , monomer ( n = 3); 21% O 2 , PFF ( n = 4); 11% O 2 , monomer ( n = 3); and 11% O 2 , PFF ( n = 3). Box plots are annotated with the adjusted P values calculated in the differential expression analysis of all proteins using limma (that is, a two-tailed moderated t -test with multiple testing correction using the Benjamini–Hochberg procedure). For all box plots, the center line shows the median, the box shows the IQR and the whiskers show the extent of the data distribution up to 1.5 times the IQR.

Article Snippet: TaqMan probes for 18S (Mm03928990_g1), Gapdh (Mm99999915_g1) , Vegfa (Mm01281449_m1), Kdr (Mm01222421_m1), Adm (Mm00437438_g1), Iba1 (Mm00479862_g1), Tfrc (Mm01344477_g1), Slc16a3 (Mm00446102_m1) and Slc40a1 (Mm01254822_m1) were used for the qPCR reactions.

Techniques: Injection, Expressing, Quantitative Proteomics, Two Tailed Test

Journal: Nature Neuroscience

Article Title: Hypoxia ameliorates neurodegeneration and movement disorder in a mouse model of Parkinson’s disease

doi: 10.1038/s41593-025-02010-4

Figure Lengend Snippet: ( a ) and ( b ): Venn diagrams show the numbers of shared and distinct downregulated ( a ) and upregulated ( b ) genes when comparing the transcriptomic effects of hypoxia treatment (11% O 2 , monomer vs 21% O 2 , monomer) to the effects of PFF treatment (21% O 2 , PFF vs 21% O 2 , monomer). ( c ) and ( d ): Heatmaps show the z-score scaled expression across condition for all 186 downregulated genes ( c ) and all 271 upregulated genes ( d ) in the 21% O 2 , PFF versus 21% O 2 , monomer comparison. Columns (genes) were hierarchically clustered using fastcluster.linkage (v1.2.6), with metric=euclidean and method=single. N = 12 in each group. Results of RT-qPCR for Iba1 ( e ), Vegfa ( f ), Tfrc ( g ), Slc16a3 ( h ) and Slc40a1 ( i ). N = 3-8. Two-way ANOVA followed by Dunnett’s correction for post-hoc comparisons was conducted for panel ( e – i ).

Article Snippet: TaqMan probes for 18S (Mm03928990_g1), Gapdh (Mm99999915_g1) , Vegfa (Mm01281449_m1), Kdr (Mm01222421_m1), Adm (Mm00437438_g1), Iba1 (Mm00479862_g1), Tfrc (Mm01344477_g1), Slc16a3 (Mm00446102_m1) and Slc40a1 (Mm01254822_m1) were used for the qPCR reactions.

Techniques: Expressing, Comparison, Quantitative RT-PCR

Journal: Antioxidants (Basel, Switzerland)

Article Title: OTUB1-SLC7A11 Axis Mediates 4-Octyl Itaconate Protection Against Acetaminophen-Induced Ferroptotic Liver Injury.

doi: 10.3390/antiox14060698

Figure Lengend Snippet: Figure 3. 4-OI mitigates APAP-induced dysregulation of iron metabolism. (A) Pathways associated with genes/proteins interacting with differential metabolites were analyzed using the R package CePa. logP (x-axis): negative log of the enrichment p-value for drug bias-related metabolites. foldP (y-axis): ratio of enrichment p-values for efficacy-related vs. bias-related metabolites. The red circle highlights the ferroptosis pathway, which is identified as the most prominent among all analyzed pathways. (B) Hepatic iron content (n = 3). (C–I) Representative Western blot images and quantification of transferrin, TFR1, FTH1, FTL1, FPN1, and hepcidin protein levels in mouse liver tissues (n = 3). (J–L) A RT-qPCR assay determined the mRNA expression of FTH1, FTL1, and FPN1 (n = 6). (M) Representative immunohistochemical staining images showing FTH1, FTL1, and FPN1 expression. Scale bar: 100 µm, n = 3. GAPDH was used as internal loading control. * p < 0.05, ** p < 0.01, *** p < 0.001; ns: not significant.

Article Snippet: Primary antibodies for SLC7A11, OTUB1, CD44, ubiquitin, GPX4, Nrf2, transferrin, TFR1, FTH1, FTL1, FPN1, hepcidin, and GAPDH were obtained from the following sources: SLC7A11 and OTUB1 antibodies from Abcam (Cambridge, UK); hepcidin antibody from Affinity (Changzhou, China); CD44, ubiquitin, GPX4, Nrf2, transferrin, TFR1, FTH1, FTL1, FPN1, and GAPDH antibodies from Proteintech (Wuhan, China).

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

Journal: Scientific Reports

Article Title: Tissue-targeted R-spondin mimetics for liver regeneration

doi: 10.1038/s41598-020-70912-3

Figure Lengend Snippet: Design and characterization of cell type specific Wnt signaling enhancing mimetic molecules. ( A ) Scheme of designed molecules. Fragments of RSPO2 spanning the Fu1 and Fu2 domains (action module) were fused the C-terminus of cell type specific or control scFv (targeting module). Specific mutations used are indicated. ( B ) In vitro STF activity of four RSPO proteins. Furin domains of human RSPO1-4 were tested as fusions to an anti-GFP scFv. RSPO2 furin domain alone (N37-E143) was used as a control. Luciferase activity unit is arbitrary (RLU). ( C ) STF activity of RSPO mimetics on HEK293 ( top ) or HuH-7 ( bottom ) in the presence ( left ) or absence ( right ) of an exogenous Wnt source (30% Wnt3a conditioned media). ( D ) Quantitative PCR analysis of ASGR1 , ASGR2 and TFRC gene expression in HEK293, HuH-7 and A431 cells. The signals were relative to ACTB . ( E ) Western Blot analysis on LRP6 receptor and DVL2 phosphorylation in HuH-7 cells. Asterisk indicates a non-specific band that is detected in HuH-7 by the antibody used. The lower bands indicated by the arrow correspond to DVL2 with and without phosphorylation. Tubulin (TUB) is used as the loading control. 10% Wnt3a conditioned media was used as the exogenous Wnt source. Images were cropped for clarity. The uncropped images are presented in Fig. .

Article Snippet: For overexpression of exogenous receptors, cells were transiently transfected with plasmids containing receptors of interest under eukaryotic expression promoters ( ASGR1 was clone OHU03658D from GenScript, ASGR2 was in-house cloned isoform d/NP_001188281.1, and TFRC was clone HG11020-UT from SinoBiologicals), then split into 96-well plates (20,000 cells per well) for STF assay 24 h post transfection.

Techniques: In Vitro, Activity Assay, Luciferase, Real-time Polymerase Chain Reaction, Expressing, Western Blot

Journal: Scientific Reports

Article Title: Tissue-targeted R-spondin mimetics for liver regeneration

doi: 10.1038/s41598-020-70912-3

Figure Lengend Snippet: Confirmation of receptor-specific activation of Wnt signaling. ( A ) STF activity in HEK293 cells transiently transfected with TFR1 (control, top ), ASGR1 ( middle ), and ASGR1 together with ASGR 2 cDNAs ( bottom ), either in the presence ( left ) or absence ( right ) of exogenous Wnt source (30% Wnt3a conditioned media). ( B ) STF activity in A431 cells with TFR1 or ASGR1 overexpression as specified. ( C ) Flow cytometry analysis of cell surface level of FZD proteins. HEK293 cells were transiently transfected with either ZNRF3 alone ( top ) or ASGR1 and ZNRF3 cDNAs ( bottom ), treated with RSPO mimetics as specified at 10 nM, then stained by the pan-FZD antibody 18R5.

Article Snippet: For overexpression of exogenous receptors, cells were transiently transfected with plasmids containing receptors of interest under eukaryotic expression promoters ( ASGR1 was clone OHU03658D from GenScript, ASGR2 was in-house cloned isoform d/NP_001188281.1, and TFRC was clone HG11020-UT from SinoBiologicals), then split into 96-well plates (20,000 cells per well) for STF assay 24 h post transfection.

Techniques: Activation Assay, Activity Assay, Transfection, Over Expression, Flow Cytometry, Staining

Journal: Scientific Reports

Article Title: Tissue-targeted R-spondin mimetics for liver regeneration

doi: 10.1038/s41598-020-70912-3

Figure Lengend Snippet: In vivo tissue-specific enhancement of Wnt signaling. ( A ) STF activity of the RSPO mimetic molecules in the appended-IgG format. ( B ) BLI analysis of the ASGR1 antibody (expressed as a Fab) on human and mouse ASGR1. The affinity (Kd) determined by steady-state fitting is indicated. ( C ) Axin2 and ( D ) Ki67 expression in liver ( upper panel ) and small intestine ( lower panel ) were analyzed by quantitative PCR, 48 h after i.p. injection of proteins as specified (n = 8 mice per group). Statistical analysis was performed using 1-way ANOVA: (ns) not significant, ** p < 0.01, **** p < 0.0001. ( E ) Immunofluorescence staining of liver samples for Ki67 and HNF4α from 10 mg/kg treatment groups. White arrows denote some double-positive cells as examples. DAPI was used to stain nuclei.

Article Snippet: For overexpression of exogenous receptors, cells were transiently transfected with plasmids containing receptors of interest under eukaryotic expression promoters ( ASGR1 was clone OHU03658D from GenScript, ASGR2 was in-house cloned isoform d/NP_001188281.1, and TFRC was clone HG11020-UT from SinoBiologicals), then split into 96-well plates (20,000 cells per well) for STF assay 24 h post transfection.

Techniques: In Vivo, Activity Assay, Expressing, Real-time Polymerase Chain Reaction, Injection, Immunofluorescence, Staining