Journal: bioRxiv

Article Title: Lipid Transfer Proteins and PI4KIIα Generate a Phosphoinositide-Linked Proteome

doi: 10.64898/2025.12.17.694959

Figure Lengend Snippet: a-c , MDA-MB-231 Cas cells harboring either a combined PITPα and PITPβ knockout or a control knockout were cultured under normal conditions. Cells were then lysed and proteins were precipitated using chloroform/methanol and resuspended before submitting for mass spectrometry proteomic analysis. All available abundance ratios and corresponding p-values were then graphed ( a ), categorized as either upregulated or downregulated, and submitted for pathway enrichment analysis using ShinyGO 0.85 ( b,c ). d-e , MDA-MB-231 cells were cultured under normal conditions and lysed. Then proteins were precipitated using chloroform/methanol, resuspended and incubated with anti-PI4,5P 2 antibody. The antibody and associated proteins were then recovered using Dynabeads and submitted for mass spectrometry proteomic analysis. Identified proteins were then graphed ( d ) and submitted for pathway enrichment analysis using ShinyGO 0.85 ( e ). T-tests were used to assess significance and fold change of 0.8-1.2 were used as cut offs. f-h , MDA-MB-231 cells were cultured and lysed under normal conditions and IQGAP1 ( f ), Talin-1 ( g ), and Ku80 ( h ) were immunoprecipitated and resolved via WB along with PI4,5P 2 . n=3 independent experiments. For all graphs, data are presented as the mean.

Article Snippet: For protein immunoprecipitation, antibody-conjugated agarose was purchased from Santa Cruz Biotechnology, including agarose-conjugated antibodies against IQGAP1 (#sc-374307AC), Talin-1 (#sc-365875AC), and Ku80 (#sc-5280AC).

Techniques: Knock-Out, Control, Cell Culture, Mass Spectrometry, Incubation, Immunoprecipitation

Journal: bioRxiv

Article Title: Lipid Transfer Proteins and PI4KIIα Generate a Phosphoinositide-Linked Proteome

doi: 10.64898/2025.12.17.694959

Figure Lengend Snippet: a-c , MDA-MB-231 Cas cells harboring either a combined PITPα and PITPβ knockout or a control knockout were cultured under normal conditions. Cells were then lysed and proteins were precipitated using chloroform/methanol and resuspended before submitting for mass spectrometry proteomic analysis. All available abundance ratios and corresponding p-values were then graphed ( a ), categorized as either upregulated or downregulated, and submitted for pathway enrichment analysis using ShinyGO 0.85 ( b,c ). d-e , MDA-MB-231 cells were cultured under normal conditions and lysed. Then proteins were precipitated using chloroform/methanol, resuspended and incubated with anti-PI4,5P 2 antibody. The antibody and associated proteins were then recovered using Dynabeads and submitted for mass spectrometry proteomic analysis. Identified proteins were then graphed ( d ) and submitted for pathway enrichment analysis using ShinyGO 0.85 ( e ). T-tests were used to assess significance and fold change of 0.8-1.2 were used as cut offs. f-h , MDA-MB-231 cells were cultured and lysed under normal conditions and IQGAP1 ( f ), Talin-1 ( g ), and Ku80 ( h ) were immunoprecipitated and resolved via WB along with PI4,5P 2 . n=3 independent experiments. For all graphs, data are presented as the mean.

Article Snippet: The monoclonal antibodies that were used are against p53 (clone DO-1, #SC-126, Santa Cruz Biotechnology), p53 (clone 7F5, #2527, Cell Signaling), pAkt S473 (clone 193H12, #4058, Cell Signaling), HA-tag (clone C29F4, #3724, Cell Signaling), GAPDH (clone 0411, #sc-47724, Santa Cruz Biotechnology), β-actin (clone 13E5, #4970, Cell Signaling), Lamin B2 (clone D8P3U, #12255, Cell Signaling), IQGAP1 (clone D-3, #sc-374307, Santa Cruz Biotechnology), Talin-1 (clone C-9, #sc-365875, Santa Cruz Biotechnology), Ku80 (clone C48E7, #2180, Cell Signaling), and polyclonal antibodies against PITPα (#16613-1-AP, ThermoFisher), PITPβ (#ab127563, abcam), PITPNC1 (IF, #ab222078, abcam), PITPNC1 (WB, #NBP2-19842, Novus), PI4KIIα (#NBP2-44158, Novus).

Techniques: Knock-Out, Control, Cell Culture, Mass Spectrometry, Incubation, Immunoprecipitation

Journal: Frontiers in Immunology

Article Title: Identification of genes associated with disulfidptosis in the subacute phase of spinal cord injury and analysis of potential therapeutic targets

doi: 10.3389/fimmu.2025.1642757

Figure Lengend Snippet: Identification and Expression Pattern Analysis of DE-DRGs in SCI. (A) PCA of the GSE151371 dataset, with different colors representing the SCI group (blue) and healthy control group (HC group, red). (B) Volcano plot showing the DEGs between the SCI and HC groups, with significantly upregulated and downregulated genes highlighted in orange and green, respectively. (C) Intersection analysis of 6948 SCI-related DEGs with 24 DRGs, identifying 8 DE-DRGs. (D) Heatmap displaying the expression levels of DE-DRGs in SCI samples, with colors ranging from red (high expression) to blue (low expression). (E–H) Box plots of representative DE-DRGs (ABI2, CD2AP, IQGAP1, and MYL6) showing significant expression differences between the SCI group (T) and HC group (N).

Article Snippet: In the first immunofluorescence staining, the sections were incubated overnight at 4 °C with the primary antibody against IQGAP1 (1:200; GB114934 , Servicebio, China).

Techniques: Expressing, Control

Journal: Frontiers in Immunology

Article Title: Identification of genes associated with disulfidptosis in the subacute phase of spinal cord injury and analysis of potential therapeutic targets

doi: 10.3389/fimmu.2025.1642757

Figure Lengend Snippet: Results of Mfuzz Analysis. (A) The Mfuzz clustering analysis shows the expression patterns of 9 representative gene clusters at different stages of SCI, with colors representing membership values (red indicating high membership). (B) Venn diagram displaying the intersection of the GSE45006 gene set and DE-DRGs, identifying 5 overlapping key genes. (C–G) Expression trend plots of the 5 key genes (ABI2, CYFIP1, IQGAP1, RPN1, TLN1) at different time points, highlighting the early activation and sustained high expression of IQGAP1.

Article Snippet: In the first immunofluorescence staining, the sections were incubated overnight at 4 °C with the primary antibody against IQGAP1 (1:200; GB114934 , Servicebio, China).

Techniques: Expressing, Activation Assay

Journal: Frontiers in Immunology

Article Title: Identification of genes associated with disulfidptosis in the subacute phase of spinal cord injury and analysis of potential therapeutic targets

doi: 10.3389/fimmu.2025.1642757

Figure Lengend Snippet: Identification of hub genes using machine learning and construction of PPI networks. (A) Error rate curve of the RF model. (B) Variable importance ranking based on the MeanDecreaseGini metric from the RF algorithm. (C, D) LASSO regression analysis: coefficient path plot and tenfold cross-validation to determine the optimal λ value. (E) STRING-based protein interaction network of the 8 DE-DRGs, with IQGAP1 located at the central position. (F) ROC curves evaluating the diagnostic performance of candidate genes in distinguishing SCI from healthy controls. (G) Extended PPI network comprising 38 nodes, showing IQGAP1 interacting with multiple signal regulation-related proteins.

Article Snippet: In the first immunofluorescence staining, the sections were incubated overnight at 4 °C with the primary antibody against IQGAP1 (1:200; GB114934 , Servicebio, China).

Techniques: Biomarker Discovery, Diagnostic Assay

Journal: Frontiers in Immunology

Article Title: Identification of genes associated with disulfidptosis in the subacute phase of spinal cord injury and analysis of potential therapeutic targets

doi: 10.3389/fimmu.2025.1642757

Figure Lengend Snippet: Molecular docking results of IQGAP1 with candidate small-molecule compounds. The left panels display the surface structures of IQGAP1, with hydrophobic regions highlighted in red. The right panels present enlarged 3D views of the binding pockets, illustrating the interaction patterns between the small-molecule ligands and IQGAP1 residues, including hydrogen bonds and hydrophobic contacts. Blue dashed lines represent hydrogen bonds, while gray lines indicate hydrophobic interactions. These results further confirm the favorable structural compatibility and binding affinity of the compounds with IQGAP1. (A) succinylsulfathiazole; (B) vitamin E; (C) cytochalasin D; (D) deptropine; (E) hexylcaine; (F) nocodazole.

Article Snippet: In the first immunofluorescence staining, the sections were incubated overnight at 4 °C with the primary antibody against IQGAP1 (1:200; GB114934 , Servicebio, China).

Techniques: Binding Assay

Journal: Frontiers in Immunology

Article Title: Identification of genes associated with disulfidptosis in the subacute phase of spinal cord injury and analysis of potential therapeutic targets

doi: 10.3389/fimmu.2025.1642757

Figure Lengend Snippet: Heatmap of GSVA enrichment analysis showing pathway activity differences between high and low IQGAP1 expression groups.

Article Snippet: In the first immunofluorescence staining, the sections were incubated overnight at 4 °C with the primary antibody against IQGAP1 (1:200; GB114934 , Servicebio, China).

Techniques: Activity Assay, Expressing

Journal: Frontiers in Immunology

Article Title: Identification of genes associated with disulfidptosis in the subacute phase of spinal cord injury and analysis of potential therapeutic targets

doi: 10.3389/fimmu.2025.1642757

Figure Lengend Snippet: GSEA enrichment analysis results. (A–D) Representative GSEA plots showing key functional pathways significantly enriched in the high IQGAP1 expression group.

Article Snippet: In the first immunofluorescence staining, the sections were incubated overnight at 4 °C with the primary antibody against IQGAP1 (1:200; GB114934 , Servicebio, China).

Techniques: Functional Assay, Expressing

Journal: Frontiers in Immunology

Article Title: Identification of genes associated with disulfidptosis in the subacute phase of spinal cord injury and analysis of potential therapeutic targets

doi: 10.3389/fimmu.2025.1642757

Figure Lengend Snippet: IQGAP1 expression in the lesion area at different time points following SCI. Representative immunofluorescence images showing IQGAP1 (red) and nuclei (DAPI, blue) staining in spinal cord sections from control rats (top), 1 week post-injury (middle), and 2 weeks post-injury (bottom). The right panels display magnified views of the boxed regions on the left. IQGAP1 expression was markedly increased in the injured area, peaking at 1 week post-injury and remaining elevated at 2 weeks, suggesting its potential involvement in SCI pathophysiology. Scale bars: left, 500 μm; right, 50 μm.

Article Snippet: In the first immunofluorescence staining, the sections were incubated overnight at 4 °C with the primary antibody against IQGAP1 (1:200; GB114934 , Servicebio, China).

Techniques: Expressing, Immunofluorescence, Staining, Control

Journal: Frontiers in Immunology

Article Title: Identification of genes associated with disulfidptosis in the subacute phase of spinal cord injury and analysis of potential therapeutic targets

doi: 10.3389/fimmu.2025.1642757

Figure Lengend Snippet: Colocalization of IQGAP1 with different cell-type markers after spinal cord injury. At 1 and 2 weeks post-SCI, spinal cord sections from control and injured rats were subjected to immunofluorescence staining. Sections were double-labeled with IQGAP1 (magenta) and cell-type markers (green), and nuclei were counterstained with DAPI (blue). Scale bar = 10 μm.

Article Snippet: In the first immunofluorescence staining, the sections were incubated overnight at 4 °C with the primary antibody against IQGAP1 (1:200; GB114934 , Servicebio, China).

Techniques: Control, Immunofluorescence, Staining, Labeling