antionecut2  (Bioss)

Journal: bioRxiv

Article Title: Lineage plasticity of the integrated stress response is a hallmark of cancer evolution

doi: 10.1101/2025.02.10.637516

Figure Lengend Snippet: ( a ) CellRank analysis for the identification of the entropy of fate probability as a measure of the uncertainty in cell fate decisions. Entropy is maximal when there is no fate bias and decreases as cells move toward terminal states. This analysis highlights the dynamics of cell fate decisions and their contributions to tumor evolution and heterogeneity. The accompanying violin plot illustrates the distribution of entropy across different cell clusters. ( b ) The total Bhattacharyya distance quantifies the overall similarity between a selected cluster and all other inferred cell lineages. ( c ) The UMAP plot visualizes the lung transition cluster derived from eIF2α S/S and eIF2α A/A tumors, encompassing a total of 3,909 cells. ( d ) The dot plot of top DEGs in eIF2α S/S and eIF2α A/A tumors from panel C. ( e ) The smoothed gene expression trends of Tomm20, Eif5a, Onecut2 and Hmga2 along pseudotime are visualized, with each trend weighted by CellRank fate probabilities. The data shows the dynamic changes in gene expression over time, highlighting the correlation of these genes with predicted cell fate trajectories. Tomm20, Eif5a are key driver genes for Mito-Dysf cluster, while Onecut2 and Hmga2 are the key driver genes for pre-EMT cluster. ( f ) The scatter plot illustrates the correlation of each gene with different fates, plotted along the x-axis and y-axis. Each point represents a gene, colored according to its average expression across all cells. (g) Correlation analyses between Cytotrace stemness scores, ISR activity, and MYC activity. Spearman’s correlation test was used to calculate p-values.

Article Snippet: Briefly, rabbit polyclonal anti-ONECUT2 (Proteintech, cat# 21916-1-AP), anti-EIF4EBP1 (Cell Signaling Technology, cat#9452), anti-CHCHD10 (Proteintech, cat#25671-1-AP), and anti-NKX2-1 (Abcam, cat# EP1584Y) diluted at in the antibody diluent (Roche Tissue Diagnostics, 06440002001) were manually applied for 32min at 37°C then followed by the appropriate detection kit (OmniMap anti-Rabbit-HRP, Roche Tissue Diagnostics, 05269679001, for 8min, followed by ChromoMap-DAB, Roche Tissue Diagnostics, 05266645001).

Techniques: Derivative Assay, Expressing, Activity Assay

Journal: bioRxiv

Article Title: Lineage plasticity of the integrated stress response is a hallmark of cancer evolution

doi: 10.1101/2025.02.10.637516

Figure Lengend Snippet: ( a ) The Venn diagram illustrates the percentages of unique and overlapping gene sets between the top pre-EMT fate driver genes identified by CellRank and the ISR gene set. ( b ) The pathway enrichment analysis of the 50 common genes identified in panel A highlights key biological pathways and processes enriched in this gene set. The analysis provides insights into the shared mechanisms linking ISR signaling and pre-EMT fate-driving genes. ( c ) The Protein-Protein Interaction (PPI) plot illustrates the network of the 50 common genes identified in panel A, with interaction strength represented by color intensity and circle size. Nodes with higher interaction degrees are highlighted with larger circles and more intense colors, indicating their central roles in the network. Atf4 and Eif2s1 nodes are manually integrated into the plot, emphasizing their critical regulatory roles and connections within the network. ( d ) The IHC staining analysis of the high-stemness/pre-EMT marker 4EBP1 ( n = 4 mice) and the pre-EMT marker ONECUT2 ( n = 3 mice) was conducted in in eIF2α S/S and eIF2α A/A mouse tumors; scalebars, 50 μm. Statistical comparisons between the groups were performed using a two-tailed unpaired t-test, with results presented as mean ± SD. ( e ) UMAP analysis merging cells from eIF2α S/S and eIF2α S/A genotypes, with each dot representing a single cell. Cells are colored by Rbm3 expression levels, ranging from low (blue) to high (red).

Article Snippet: Briefly, rabbit polyclonal anti-ONECUT2 (Proteintech, cat# 21916-1-AP), anti-EIF4EBP1 (Cell Signaling Technology, cat#9452), anti-CHCHD10 (Proteintech, cat#25671-1-AP), and anti-NKX2-1 (Abcam, cat# EP1584Y) diluted at in the antibody diluent (Roche Tissue Diagnostics, 06440002001) were manually applied for 32min at 37°C then followed by the appropriate detection kit (OmniMap anti-Rabbit-HRP, Roche Tissue Diagnostics, 05269679001, for 8min, followed by ChromoMap-DAB, Roche Tissue Diagnostics, 05266645001).

Techniques: Immunohistochemistry, Marker, Two Tailed Test, Expressing

Journal: bioRxiv

Article Title: Lineage plasticity of the integrated stress response is a hallmark of cancer evolution

doi: 10.1101/2025.02.10.637516

Figure Lengend Snippet: ( a ) Representative histograms depicting the distribution of ITGA2 expression in vehicle-treated and ISRIB-treated eIF2α S/S tumors. Statistical analysis was conducted using a two-tailed unpaired t-test (n = 3 mice per group) ( b ) Detection of ITGA2 expression by flow cytometry in primary tumor populations of the indicated genotypes. ( c ) Violin plots illustrating the expression of Atp5k , Lcn2 , Hmga2 , Hnf4a marker genes in tumors treated with either ISRIB or vehicle control. ( d ) Heatmap showing the mean expression levels of Onecut2 and Eif4ebp1 across clusters in tumors treated with either vehicle or ISRIB. ( e ) Cluster cell proportions in LUAD tumors of the indicated genotypes visualized after integrating all ISR sequencing datasets.

Article Snippet: Briefly, rabbit polyclonal anti-ONECUT2 (Proteintech, cat# 21916-1-AP), anti-EIF4EBP1 (Cell Signaling Technology, cat#9452), anti-CHCHD10 (Proteintech, cat#25671-1-AP), and anti-NKX2-1 (Abcam, cat# EP1584Y) diluted at in the antibody diluent (Roche Tissue Diagnostics, 06440002001) were manually applied for 32min at 37°C then followed by the appropriate detection kit (OmniMap anti-Rabbit-HRP, Roche Tissue Diagnostics, 05269679001, for 8min, followed by ChromoMap-DAB, Roche Tissue Diagnostics, 05266645001).

Techniques: Expressing, Two Tailed Test, Flow Cytometry, Marker, Control, Sequencing

Journal: Cell reports

Article Title: Embryonic temporal–spatial delineation of excitatory spinal V3 interneuron diversity

doi: 10.1016/j.celrep.2023.113635

Figure Lengend Snippet: Key resources table

Article Snippet: Human ONECUT2/OC-2 Affinity Purified Polyclonal Ab , R and D Systems , RRID:AB_10640365.

Techniques: Recombinant, Affinity Purification, Produced, Virus, Plasmid Preparation, Labeling, Software

Journal: Aging (Albany NY)

Article Title: The tumor microenvironment in gastrointestinal adenocarcinomas revealed a prognostic and immunotherapeutic biomarker

doi: 10.18632/aging.204463

Figure Lengend Snippet: TMEscore was an independent factor for predicting patient survival . ( A ) The identification flowchart of six prognostic genes (C6orf223, EPHX4, HES6, NKD2 OLR1 and ONECUT2). ( B ) The expression of the six genes in GIAC tumor and normal samples from TCGA cohort. ( C ) The RNA expression of the six genes in 55 pairs of CRC tumor and normal samples from our center (GAD and ESAD see in , ). ( D ) The expression of the five proteins in 10 pairs of CRC tumor and normal samples from our center (GAD and ESAD see in , ). ( E ) The WB image of protein expression for CRC (GAD and ESAD see in , ). ( F – K ) The survival time (OS and PFS) of patients with high/low TMEscore in TCGA cohort ( F , G ), GSE17536 ( H , I ) and GSE39582 ( J , K ).

Article Snippet: Primary antibodies used in this study include rabbit anti-β-tubulin (Abcam, ab6046, 1:1000 dilution for WB), rabbit anti-EPHX4 (Abcam, ab183739, 1:1000 dilution for WB), mouse anti-HES6 (Abcam, ab172800, 1:1000 dilution for WB), rabbit anti-NKD2 (CST, 2073T, 1:1000 dilution for WB), rabbit anti-OLR1 (Bioss, bs-2044R, 1:1000 dilution for WB) and anti-ONECUT2 (Bioss, bs-19643R, 1:1000 dilution for WB).

Techniques: Expressing, RNA Expression