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

Journal: Communications Chemistry

Article Title: Comparative evaluation of Olink Explore 3072 and mass spectrometry with peptide fractionation for plasma proteomics

doi: 10.1038/s42004-025-01753-2

Figure Lengend Snippet: A Venn diagram of proteins detected in at least one sample with HiRIEF LC-MS/MS and/or Olink Explore 3072, based on unique UniProt IDs. B Number and percentage of Olink assays in each Olink Explore panel detected with both Olink and MS. C Detected proteins and missing values in the MS and Olink datasets. The y axis indicates the percentage of proteins in each dataset with a percentage of missing values within the intervals defined on the x axis. The dotted line shows the cumulative number of proteins with a proportion of missing values less than or equal to the upper bound of each interval. Percentages were calculated out of 88 samples analyzed with both methods. D Venn diagram comparing proteins detected by MS and Olink to proteins in the reference human plasma proteome, compiled from the Human Plasma Proteome Project (HPPP) database and the Human Protein Atlas (HPA). The bar plot shows the proportion of proteins in the reference plasma proteome detected with MS, Olink, or both methods. E Distribution of estimated concentrations, from the HPA, of all detected proteins (left) and proteins detected exclusively by MS or Olink (right). Medians and interquartile ranges are indicated with points and error bars. Differences in protein concentration between platforms were tested using a two-sided Wilcoxon rank-sum test. F Missing values per protein by estimated protein concentration. Differences in protein concentration between platforms were tested using a two-sided Wilcoxon rank-sum test, and p values were adjusted using the false discovery rate method. ns = not significant, * p < 0.05, *** p < 0.001, **** p < 0.0001. G Plasma proteome coverage by estimated protein concentration. Each bar shows the proportion of proteins in the reference plasma proteome, within a specific concentration interval, that were detected with either MS only, Olink only, both methods, or neither method (“Not detected”). The x axis intervals are right closed.

Article Snippet: F Human Protein Atlas (HPA) annotations enriched among MS-Olink correlations at 5% FDR.

Techniques: Liquid Chromatography with Mass Spectroscopy, Clinical Proteomics, Protein Concentration, Concentration Assay

Journal: Communications Chemistry

Article Title: Comparative evaluation of Olink Explore 3072 and mass spectrometry with peptide fractionation for plasma proteomics

doi: 10.1038/s42004-025-01753-2

Figure Lengend Snippet: A Comparison of the frequency of protein annotations from select Human Protein Atlas (HPA) categories among proteins detected with HiRIEF LC-MS/MS and Olink Explore 3072. The 15 most frequent annotations within each HPA category are shown for both platforms. Frequencies were calculated relative to the total number of proteins detected by each platform that were also found in the HPA. Asterisks indicate statistically significant differences in frequency between platforms (Fisher’s exact test, false discovery rate <0.05). B Overrepresentation analysis of Gene Ontology (GO) Biological Processes among proteins detected with each technology. All proteins detected by MS and/or Olink were used as the background protein list ( N = 4362). Points are colored by the proportion of input proteins (MS or Olink proteins) associated with each GO term.

Article Snippet: F Human Protein Atlas (HPA) annotations enriched among MS-Olink correlations at 5% FDR.

Techniques: Comparison, Liquid Chromatography with Mass Spectroscopy

Journal: Communications Chemistry

Article Title: Comparative evaluation of Olink Explore 3072 and mass spectrometry with peptide fractionation for plasma proteomics

doi: 10.1038/s42004-025-01753-2

Figure Lengend Snippet: A Technical factors influencing the agreement (Spearman correlation) between HiRIEF LC-MS/MS and Olink Explore 3072 protein measurements (linear regression, false discovery rate (FDR) < 0.05). Positive coefficients indicate associations with higher MS-Olink correlations. Error bars represent 95% confidence intervals. The percentage of variance explained by each factor is shown on the right, expressed as adjusted R 2 . B MS-Olink correlation by the proportion of missing values per protein in MS. Proteins with any missing values in the Olink data were excluded. P values were determined using a two-sided Wilcoxon rank-sum test and adjusted for multiple testing with the FDR method. ns = not significant, ** p < 0.01. C MS-Olink correlation by the proportion of missing values per protein in Olink. Proteins with any missing values in the MS data were excluded. P values were determined as in B . ns not significant, * p < 0.05. D MS-Olink correlation versus median number of unique peptides used for quantification across tandem mass tag (TMT) sets with MS. The x axis is on a log 10 scale. E Left: comparison of per-sample MS-Olink correlations of normalized protein expression (NPX) values with (“Warn”) versus without (“Pass”) a sample quality control (QC) warning in the Olink data. Right: comparison of the MS-Olink correlation of proteins with (“Warn”) and without (“Pass”) an assay QC warning in the Olink data. P values were determined as in B , C . ns not significant, **** p < 0.0001. F Human Protein Atlas (HPA) annotations enriched among MS-Olink correlations at 5% FDR. Each row shows the distribution of MS-Olink correlations for proteins associated with a specific HPA annotation.

Article Snippet: F Human Protein Atlas (HPA) annotations enriched among MS-Olink correlations at 5% FDR.

Techniques: Liquid Chromatography with Mass Spectroscopy, Comparison, Expressing, Control

Journal: bioRxiv

Article Title: Epidermal growth factor (EGF) receptor family signalling in cardiomyocyte hypertrophy and heart failure

doi: 10.64898/2026.05.16.724529

Figure Lengend Snippet: A , Schematic of the EGFR family and the ligands that bind to them (left). Illustration of receptor homodimerization and heterodimerization that allows all EGFR family members to activate intracellular signalling, responding to, for example, EGF or NRG1 (right). Overexpression of receptors can also result in oligomerization and activation in the absence of ligand. B , mRNA expression of receptors (upper panel) and ligands (centre and lower panels) in each of 17 cell types (c-0 to c-17) identified in human heart tissue. Expression of the EGFR family (EGFR, ERBB2, ERBB3, ERBB4) is compared with the two receptors for endothelin-1 (EDNRA, EDNRB). Expression of EGFR family ligands (EGF, AREG, EREG, HBEGF, NRG1) is compared with expression of endothelin-1 (EDN1), an established agonist involved in cardiac hypertrophy . Data are from the Human Protein Atlas version 25.0. C-D , mRNA expression of endothelin and the EGFR family ( C ) and EGFR family ligands ( D ) in human failing hearts (HF) compared with non-failing hearts (NF). Statistical analysis used Mann-Whitney tests. p values for significant (p<0.05) changes are shown in bold type with values of 0.05-0.1 in standard type.

Article Snippet: Single cell mRNA data for heart tissue were collected from the Human Protein Atlas (HPA) version 25.0 (release date: 11 November 2025) [ ].

Techniques: Over Expression, Activation Assay, Expressing, MANN-WHITNEY

Journal: Journal of proteins and proteomics

Article Title: The effects of retinal disease on intrinsic protein disorder and liquid–liquid‑phase separation

doi: 10.1007/s42485-025-00188-6

Figure Lengend Snippet: CH (charge hydropathy) and CDF (cumulative distribution function) plots for each of our six proteomes. A Human Protein Atlas (HPA) retinal transcriptome. B RetNet Protein Set. C Age-related macular degeneration (AMD) proteome. D Glaucoma proteome. E Diabetic retinopathy (DR) without glial activation proteome (DR(−) G). F DR with glial activation proteome (DR( +)G)

Article Snippet: We compared the features of proteins unique to each retinal disease proteome (AMD, DR with/without glial activation, Glaucoma) and the RetNet Protein Set with those overlapping with the Human Protein Atlas (HPA) control proteome ( ).

Techniques: Activation Assay

Journal: Journal of proteins and proteomics

Article Title: The effects of retinal disease on intrinsic protein disorder and liquid–liquid‑phase separation

doi: 10.1007/s42485-025-00188-6

Figure Lengend Snippet: ParSe V2 graphs indicating the likelihood of each subgroup to undergo phase separation. There were six proteomes that were analyzed. Length of identified phase separating intrinsically disordered regions (PS IDRs) were graphed by the percent of the inputted FASTA sequence that had PS IDRs of at least this specific length for the A human protein atlas (HPA) retinal proteome, RetNet protein set, age-related macular degeneration (AMD) proteome, diabetic retinopathy (DR) without glial activation proteome (DR(−)G), DR with glial activation proteome (DR( +)G), and ParSe V2 reference human proteome. B Recall plots were also generated for these six proteomes. Area under the curve (AUC) of > 0.5 indicated the presence of sequences with greater phase separation potential when compared to the reference human proteome

Article Snippet: We compared the features of proteins unique to each retinal disease proteome (AMD, DR with/without glial activation, Glaucoma) and the RetNet Protein Set with those overlapping with the Human Protein Atlas (HPA) control proteome ( ).

Techniques: Sequencing, Activation Assay, Generated

Journal: Non-coding RNA Research

Article Title: SNHG5 enhances colorectal cancer metastasis through RNA–protein interaction with GNB2 and activation of canonical Wnt signaling

doi: 10.1016/j.ncrna.2025.12.002

Figure Lengend Snippet: GNB2 is upregulated in colorectal cancer and predicts poor prognosis . (A) Violin plots from three independent GEO datasets consistently demonstrated elevated GNB2 mRNA levels in CRC tissues compared to adjacent normal mucosa ( GSE37182 and GSE35982 ), with further upregulation observed in liver metastases relative to primary CRC tumors ( GSE49355 ). (B) Expression distribution across TCGA-COAD patients showed substantial interpatient heterogeneity, with a subset exhibiting markedly high GNB2 expression. (C) Kaplan–Meier survival analysis based on TCGA-COAD data revealed that high GNB2 expression was significantly associated with shorter overall survival (median OS: 5.4 vs. 8.2 months; HR = 1.468; 95 % CI: 1.025–2.072; P = 0.0358). (D) Independent validation using the Kaplan–Meier Plotter for rectal adenocarcinoma confirmed the prognostic significance of GNB2, with high expression correlating with worse survival (HR = 3.01; 95 % CI: 1.31–6.91; P = 0.0067). (E) Representative IHC images from the Human Protein Atlas (HPA; antibody HPA040736) showed low cytoplasmic GNB2 staining in normal colonic epithelium and moderate staining in CRC tissues. Quantitative analysis revealed a significantly higher percentage of GNB2-positive cells in tumor tissues compared to normal controls. Data are presented as mean ± SEM. ∗ P < 0.05 (Student's t -test).

Article Snippet: To confirm GNB2 expression at the protein level, we examined immunohistochemical staining data from the Human Protein Atlas (HPA; antibody HPA040736).

Techniques: Expressing, Biomarker Discovery, Staining

Journal: Bioinformatics

Article Title: SPACE: STRING proteins as complementary embeddings

doi: 10.1093/bioinformatics/btaf496

Figure Lengend Snippet: Precision–recall curves of different embeddings and visualization of SPACE embeddings in protein subcellular localization prediction. (a) Precision–recall curves on SwissProt cross-validation set (24 816 proteins across 144 species) comparing SPACE (concatenation of aligned network and ProtT5 sequence embeddings, red), aligned network embeddings (black), and ProtT5 sequence embeddings (gray). (b) Precision–recall curves on Human Protein Atlas (HPA) test set (1646 human proteins), with DeepLoc2 predictions (blue star) included as an additional baseline. The curves demonstrate that SPACE embeddings consistently maintain higher precision across all recall values compared to individual embedding types. (c) UMAP visualization of aligned network embeddings based on their projections onto logistic regression weight vectors for subcellular localization prediction. The distinct clustering patterns demonstrate that the aligned embeddings successfully capture protein localization information across multiple species, with clear separation observed for major cellular compartments such as nucleus, mitochondrion, and cell membrane. Proteins with multiple localizations were excluded from this visualization to ensure clear compartment separation.

Article Snippet: We retained 24 816 out of 28 303 proteins, covering 144 species, from the Swiss-Prot cross-validation set, and 1646 out of 1717 proteins from the Human Protein Atlas (HPA) test set, which consists solely of human proteins.

Techniques: Biomarker Discovery, Sequencing, Membrane