Journal: Scientific Reports

Article Title: The role and robustness of the Gini coefficient as an unbiased tool for the selection of Gini genes for normalising expression profiling data

doi: 10.1038/s41598-019-54288-7

Figure Lengend Snippet: Robustness of the Gini coefficient. ( A) IQR of different genes in Klijn/Genentech vs HPA cell-line dataset. Left panel shows all genes considered in this study, with right panel showing genes with IQR < 2 in both datasets. Line of best linear fit (in log space) shown is y = 0.01 + 1.11 × (r = 0.937). ( B) IQR of different genes in CCLE vs HPA cell-line dataset. Left panel shows all genes considered in this study, with right panel showing genes with IQR < 2 in both datasets. Line of best linear fit (in log space) shown is y = 0.04 + 0.99 × (r = 0.930). ( C) Min vs Max: Median expression levels in HPA data set. Colour code as in Fig. .

Article Snippet: Figure 4 Robustness of the Gini coefficient. ( A) IQR of different genes in Klijn/Genentech vs HPA cell-line dataset.

Techniques: Expressing

Journal: Scientific Reports

Article Title: The role and robustness of the Gini coefficient as an unbiased tool for the selection of Gini genes for normalising expression profiling data

doi: 10.1038/s41598-019-54288-7

Figure Lengend Snippet: Robustness of GC for finding stably expressed genes using shared genes between HPA, CCLE and Klijn/Genentech cell-line data sets with GC < 0.2. Shown are the results for the Klijn/Genentech dataset. ( A) IQR vs GC, ( B ). Max:Mean vs Min. Colour coding: Blue, Caracausi; Green, GeneGini reference genes; Grey, neither. Shape coding: Circle, other; Triangle, SLC coding gene.

Article Snippet: Figure 4 Robustness of the Gini coefficient. ( A) IQR of different genes in Klijn/Genentech vs HPA cell-line dataset.

Techniques: Stable Transfection

Journal: Scientific Reports

Article Title: The role and robustness of the Gini coefficient as an unbiased tool for the selection of Gini genes for normalising expression profiling data

doi: 10.1038/s41598-019-54288-7

Figure Lengend Snippet: Robustness of the Gini coefficient in the HPA tissue data set. ( A) RSD versus Gini coefficient of candidate reference genes. Line of best linear fit (in log space) shown is y = 2.45 + 1.24 × (r 2 = 0.938) ( B ). IQR versus Gini coefficient of candidate reference genes. Line of best linear fit (in log space) shown is y = 0.87 + 0.96 × (r 2 = 0.566). Colour code as in Fig. .

Article Snippet: Figure 4 Robustness of the Gini coefficient. ( A) IQR of different genes in Klijn/Genentech vs HPA cell-line dataset.

Techniques:

Journal: Experimental Hematology & Oncology

Article Title: Extracellular matrix stiffness reduces DNA 6 ma level to facilitate colorectal cancer progression via disrupting P53 binding to CDKN1A promoter

doi: 10.1186/s40164-025-00704-w

Figure Lengend Snippet: DNA 6 mA levels gradually decreased as CRC development. ( A ) Schematic diagram of DSS/AOM induced CRC model in C57BL/6J mice. ( B-C ) DNA 6 mA levels in DSS/AOM CRC model were determined by dot blot ( B ) and ELISA assays ( C ). ( D ) Schematic diagram of transgenic APC min/+ mice induced CRC. ( E-F ) Dot blot (E) and ELISA assays ( F ) detected DNA 6 mA levels in transgenic APC min/+ CRC model. ( G ) Schematic diagram of DNA 6 mA levels in orthotopic xenograft CRC model. ( H-I ) Dot blot ( H ) and ELISA assays ( I ) of DNA 6 mA levels derived from orthotopic xenograft CRC model. ( J ) The DNA 6 mA levels in the NCM460 cell line and CRC cell lines (HT29, HCT116, SW480, HCT15, and RKO) were determined by dot blot (up panel) followed by relative quantitative analysis (down panel). ( K ) ELISA assays indicated DNA 6 mA levels in NCM460 cell line and CRC cell lines (HT29, HCT116, SW480, HCT15, and RKO). ( L ) Representative IHC of 6 mA modification levels in human adjacent tissue and CRC tissues at different stages. ( M-P ) The histograms of 6 mA IHC scores at different AJCC stages ( M ), T stages(N), N stages ( O ), and M stages ( P ) Data are represented as mean ± SEM. * P < 0.05

Article Snippet: Consistently, the Human Protein Atlas (HPA) public immunostaining dataset demonstrated elevated ALKBH1 protein expression in primary CRC tissues (Fig. E).

Techniques: Dot Blot, Enzyme-linked Immunosorbent Assay, Transgenic Assay, Derivative Assay, Modification

Journal: Experimental Hematology & Oncology

Article Title: Extracellular matrix stiffness reduces DNA 6 ma level to facilitate colorectal cancer progression via disrupting P53 binding to CDKN1A promoter

doi: 10.1186/s40164-025-00704-w

Figure Lengend Snippet: Extracellular matrix stiffness was associated with a reduction of 6 mA level. ( A ) Dot blot (left panel) and relative quantitative statistics (right panel) showed DNA 6 mA level of HCT116 cells (up panel) and RKO cells (down panel) stimulated by soft and stiff substrate. ( B-C ) ELISA assay ( B ) and IF staining ( C ) indicated DNA 6 mA levels of HCT116 cells (up panel) and RKO cells (down panel) stimulated by soft and stiff substrate. ( D-E ) Representative IHC ( D ) and Spearman’s correlation analysis ( E ) of collagen I and 6 mA in human CRC tissues. ( F-G ) Histogram ( F ) and heat map ( G ) of elastic modulus among normal colorectal tissues, AOM-induced neoplasia tissues, and AOM-induced CRC tissues. ( H ) Spearman’s correlation analysis of 6 mA IHC scores and elastic modulus in neoplasia tissues and CRC tissues of DSS/AOM-induced mice. ( I ) The BAPN treatment process for orthotopic xenograft mice model. ( J ) Histogram of elastic modulus in PBS-treated xenografts and BAPN-treated xenografts. ( K ) Western blot of vimentin, E-cadherin, CDKN1A in PBS-treated xenografts and BAPN-treated xenografts, using GAPDH as a control. ( L ) Representative IHC (left panel) and relative quantitative statistics (right panel) of 6 mA modification levels in PBS-treated xenografts and BAPN-treated xenografts Data are represented as mean ± SEM. * P < 0.05

Article Snippet: Consistently, the Human Protein Atlas (HPA) public immunostaining dataset demonstrated elevated ALKBH1 protein expression in primary CRC tissues (Fig. E).

Techniques: Dot Blot, Enzyme-linked Immunosorbent Assay, Staining, Western Blot, Control, Modification

Journal: Experimental Hematology & Oncology

Article Title: Extracellular matrix stiffness reduces DNA 6 ma level to facilitate colorectal cancer progression via disrupting P53 binding to CDKN1A promoter

doi: 10.1186/s40164-025-00704-w

Figure Lengend Snippet: Substrate stiffness upregulates ALKBH1. ( A ) Histograms of mRNA expression of ALKBH1, METTL4 and N6AMT1 in HCT116 (left panel) and RKO cells (right panel) stimulated by soft and stiff substrate. ( B ) Western blot of ALKBH1, METTL4 and N6AMT1 in HCT116 (left panel) and RKO cells (right panel) stimulated by soft and stiff substrate, using GAPDH as a control. ( C-D ) IF staining indicated ALKBH1 levels of HCT116 cells ( C ) and RKO cells ( D ) stimulated by soft and stiff substrate. ( E-F ) Western blot ( E ) and qRT-PCR (F) of ALKBH1, METTL4 and N6AMT1 in orthotopic xenograft model treated by PBS and BAPN, using GAPDH as a control. ( G-H ) Western blot ( G ) and qRT-PCR (H) of ALKBH1, METTL4 and N6AMT1 in DSS/AOM-induced CRC model treated by PBS and BAPN, using GAPDH as a control. ( I-J ) Representative IHC (left panel) and relative quantitative statistics (right panel) of ALKBH1 in orthotopic xenograft model ( I ) and DSS/AOM-induced CRC model ( J ) treated by PBS and BAPN. ( K ) Representative IHC of ALKBH1 in low collagen I group and high collagen I group of human CRC tissues. ( L ) Spearman’s correlation analysis of ALKBH1 IHC scores and collagen I IHC scores in human CRC tissues. ( M ) Representative IHC of ALKBH1 in low stiffness group and high stiffness group of DSS/AOM induced CRC mice. ( N ) Spearman’s correlation analysis of ALKBH1 IHC scores and elastic modulus in AOM/DSS-induced CRC tissues Data are represented as mean ± SEM. * P < 0.05; ns, not significant

Article Snippet: Consistently, the Human Protein Atlas (HPA) public immunostaining dataset demonstrated elevated ALKBH1 protein expression in primary CRC tissues (Fig. E).

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

Journal: Experimental Hematology & Oncology

Article Title: Extracellular matrix stiffness reduces DNA 6 ma level to facilitate colorectal cancer progression via disrupting P53 binding to CDKN1A promoter

doi: 10.1186/s40164-025-00704-w

Figure Lengend Snippet: Demethylase ALKBH1 was responsible for 6 mA downregulation stimulated by stiffness. ( A ) Western blot of ALKBH1 distribution in HCT116 and RKO cells, using GAPDH as a cytoplasmic control and Lamin B1 as a nuclear control. ( B ) Representative confocal microscopy images of ALKBH1 and 6 mA in HCT116 and RKO cells. ( C-D ) Spearman’s correlation analysis of 6 mA and ALKBH1 IHC scores in human CRC ( C ) and AOM/DSS-induced neoplasia and CRC tissues ( D ). ( E-F ) Elisa assays of 6 mA levels in HCT116 (up panel) and RKO cells (down panel) transfecting ALKBH1 plasmids ( E ) or shALKBH1 plasmids ( F ). ( G-H ) Dot blot of 6 mA levels in HCT116 ( G ) and RKO cells ( H ) transfecting shALKBH1 plasmids (up panel) or ALKBH1 plasmids (down panel). ( I ) Diagram of 6 mA PGL4 luciferase reporter containing 3 X GGAGG motif. ( J-K ) Histograms of luciferase activity of 6 mA in HCT116 (up panel) and RKO (down panel) with ALKBH1 downregulation ( J ) and ALKBH1 overexpression ( K ). ( L ) Diagram of mutant 6 mA PGL4 luciferase reporter containing 3 X GGTGG motif. ( M ) Histograms of luciferase activity of 6 mA and mutant 6 mA in HCT116 (up panel) and RKO (down panel) transfecting ALKBH1 plasmid and plasmid vector. ( N ) Histograms of 6 mA luciferase activity of HCT116 (left panel) and RKO cells (right panel) stimulated by soft and stiff substrate. ( O-P ) Dot blot ( O ) and ELISA ( P ) showed DNA 6 mA levels of HCT116 cells with knockdown ALKBH1 and control after soft and stiff substrate stimulation. Data are represented as mean ± SEM. * P < 0.05; ns, not significant; Nuc: nucleus; Cyto: cytoplasm

Article Snippet: Consistently, the Human Protein Atlas (HPA) public immunostaining dataset demonstrated elevated ALKBH1 protein expression in primary CRC tissues (Fig. E).

Techniques: Western Blot, Control, Confocal Microscopy, Enzyme-linked Immunosorbent Assay, Dot Blot, Luciferase, Activity Assay, Over Expression, Mutagenesis, Plasmid Preparation, Knockdown

Journal: Experimental Hematology & Oncology

Article Title: Extracellular matrix stiffness reduces DNA 6 ma level to facilitate colorectal cancer progression via disrupting P53 binding to CDKN1A promoter

doi: 10.1186/s40164-025-00704-w

Figure Lengend Snippet: Demethylase ALKBH1 was associated with poor prognosis in CRC. ( A ) Boxplot presented ALKBH1 expression in CRC and adjacent normal tissues using the TCGA combined with GTEx datasets. ( B ) Scatter plot of ALKBH1 expression using TCGA paired datasets. ( C-D ) Boxplot presented ALKBH1 expression in CRC and adjacent normal tissues from GSE25071 ( C ) and GSE18105 datasets ( D ). ( E ) Representative IHC (left panel) and IHC (right panel) analysis of ALKBH1 protein expression in normal tissues and CRC tissues from HPA immunostaining dataset. ( F-G ) The protein ( F ) and mRNA levels ( G ) of ALKBH1 in CRC cells lines (HT29, HCT116, SW480, RKO and HCT15) and normal colon endothelial cell line (NCM460), using GAPDH as a control. ( H ) Representative IHC of ALKBH1 in human adjacent normal tissues and CRC tissues under different stages. ( I-L ) The histograms of ALKBH1 scores at different AJCC stages ( I ), T stages( J ), N stages ( K ), and M stages ( L ). ( M ) Boxplot presented ALKBH1 expression in primary CRC tissues and metastasis tissues from GSE77953 dataset. ( N ) Heat map of ALKBH1 expression in CRC tissues of different stages from TCGA, GSE20970 , GSE77955 , GSE103512 , GSE128449 , GSE156451 , and GSE211831 datasets. ( O-P ) Kaplan-Meier plots of overall survival of CRC patients from TCGA ( O ) and Kaplan-Meier Plotter datasets ( P ), stratified according to mean ALKBH1 expression. Data are represented as mean ± SEM. * P < 0.05; ns, not significant

Article Snippet: Consistently, the Human Protein Atlas (HPA) public immunostaining dataset demonstrated elevated ALKBH1 protein expression in primary CRC tissues (Fig. E).

Techniques: Expressing, Immunostaining, Control