Journal: Nature Communications

Article Title: SPACEL: deep learning-based characterization of spatial transcriptome architectures

doi: 10.1038/s41467-023-43220-3

Figure Lengend Snippet: a Spatial domains identified by Splane in slice S2 and S5 from Wu et al. dataset, slice S10 from Zhao et al. dataset, and slice S11 released by 10X Genomics. b , c Spatial distribution of chromosome 1q&8q copy number gains ( b ) and 1p copy number losses ( c ) of ST spots in slices S11, calculated by inferCNV. Dashed lines represent the tumor domain. d , e CNVs of chromosome 1q & 8q ( d ) and chromosome 1p ( e ) in each spatial domain calculated by inferCNV. CNVs, copy number variations; center line, median value; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; n = 11 slices. f From left to right: Splane predicted spatial domains in slice S5, distribution of Splane predicted immune domains D7/D8/D9, distribution of Spoint predicted immune cells, and distribution of H&E staining marked immune spots. g Percentage of H&E staining marked immune spots in each domain of slice S1, S2, S5, and S6. The four slices were H&E stained in the original study. Bar height, mean value; whiskers, mean values ± 95% confidence intervals; n = 4 slices. h From left to right: Splane predicted spatial domains in slice S10, distribution of Splane predicted immune domains D7, D8, and D9, distribution of Spoint predicted immune cells, and distribution of CD3 + immunofluorescence (IF) staining marked immune spots. i Percentage of CD3 + IF staining marked immune spots in each domain of slice S10. Source data are provided as a Source Data file.

Article Snippet: The raw data of 11 ST datasets and five paired single-cell/nucleus RNA sequence datasets are available from the following studies: (1) 12 slices of human DLPFC 10X Visium data at http://research.libd.org/spatialLIBD/ ; (2) six slices of human breast cancer 10X Visium data at 10.5281/zenodo.4739739 ; (3) four slices of human breast cancer 10X Visium data: Parent_Visium_Human_BreastCancer, V1_Breast_Cancer_Block_A_Section_1, V1_Breast_Cancer_Block_A_Section_2 and Visium_FFPE_Human_Breast_Cancer at https://support.10xgenomics.com/spatial-gene-expression/datasets ; (4) one slice of human breast cancer 10X Visium data: Invasive Ductal Carcinoma Stained With Fluorescent CD3 Antibody at https://support.10xgenomics.com/spatial-gene-expression/datasets ; (5) Mouse brain STARmap data at https://www.starmapresources.org/data ; (6) 33 slices of Mouse MOp MERFISH data at https://doi.brainimagelibrary.org/doi/10.35077/g.21 ; (7) one slice of mouse E16.5 embryo brain Stereo-seq data, one slice of mouse brain Stereo-seq data, and 13 slices of mouse E16.5 whole embryo Stereo-seq data at https://db.cngb.org/stomics/mosta/download/ ; (8) ten slice of human brain MERFISH data at https://datadryad.org/stash/dataset/doi:10.5061/dryad.x3ffbg7mw ; (9) 75 slice of mouse whole brain Spatial Transcriptomics data are available in the GEO database under accession number GSE147747 ; (10) single-nucleus transcriptomics data across multiple human cortical areas at https://portal.brain-map.org/atlases-and-data/rnaseq/human-multiple-cortical-areas-smart-seq ; (11) single-cell transcriptomics data of human breast cancer data at https://singlecell.broadinstitute.org/single_cell/study/SCP1039 ; (12) single-cell transcriptomics data of mouse embryo brain at http://mousebrain.org/development/downloads.html ; (13) single-cell transcriptomics data of mouse whole cortex and hippocampus at https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x ; (14) single-cell transcriptomics data of mouse whole brain at mousebrain.org/adolescent/downloads.html .

Techniques: Staining, Immunofluorescence

Journal: BMC Immunology

Article Title: Establishment and validation of a recurrent prediction model for glioma: extrinsic apoptotic molecules FADD and CASP8 are closely associated with glioma recurrence

doi: 10.1186/s12865-025-00746-z

Figure Lengend Snippet: The association between recurrent score and classical apoptotic genes. (A) The relationship between the 6 genes and recurrent score in CGGA and TCGA database . (B) PPI network of CASP3, CASP9, FADD, CASP7, CASP8, BCL2，and the 9-gene signature from the STRING. (C-D) The expression levels of the 6 apoptotic genes in low- and high-risk levels . (E-J) Correlation between recurrent score and expression levels of apoptotic genes. *P<0.05; ***P<0.001; ns, not significant

Article Snippet: Characterizing the differential expression patterns of CASP8 and FADD in gliomas and normal tissues will play a crucial role in the further development of targeted therapeutic strategies for gliomas Fig. 9 RNA and protein levels of CASP8 and FADD in normal tissues and tumors. (A-B) RNA expression of CASP8 and FADD in normal tissues from the NCBI database (https://www.ncbi.nlm.nih.gov/). (C-D) RNA expression of CASP8 and FADD in normal tissues from the Human Protein Atlas database (https://www.proteinatlas.org/). (E) Protein levels of CASP8 and FADD in normal brain tissues from The Human Protein Atlas database. (F) Protein levels of CASP8 and FADD in normal tissues from The Human Protein Atlas database. (G) Protein levels of CASP8 and FADD in tumors from The Human Protein Atlas database

Techniques: Expressing

Journal: BMC Immunology

Article Title: Establishment and validation of a recurrent prediction model for glioma: extrinsic apoptotic molecules FADD and CASP8 are closely associated with glioma recurrence

doi: 10.1186/s12865-025-00746-z

Figure Lengend Snippet: RNA and protein levels of CASP8 and FADD in normal tissues and tumors. (A-B) RNA expression of CASP8 and FADD in normal tissues from the NCBI database (https://www.ncbi.nlm.nih.gov/). (C-D) RNA expression of CASP8 and FADD in normal tissues from the Human Protein Atlas database (https://www.proteinatlas.org/). (E) Protein levels of CASP8 and FADD in normal brain tissues from The Human Protein Atlas database. (F) Protein levels of CASP8 and FADD in normal tissues from The Human Protein Atlas database. (G) Protein levels of CASP8 and FADD in tumors from The Human Protein Atlas database

Article Snippet: Characterizing the differential expression patterns of CASP8 and FADD in gliomas and normal tissues will play a crucial role in the further development of targeted therapeutic strategies for gliomas Fig. 9 RNA and protein levels of CASP8 and FADD in normal tissues and tumors. (A-B) RNA expression of CASP8 and FADD in normal tissues from the NCBI database (https://www.ncbi.nlm.nih.gov/). (C-D) RNA expression of CASP8 and FADD in normal tissues from the Human Protein Atlas database (https://www.proteinatlas.org/). (E) Protein levels of CASP8 and FADD in normal brain tissues from The Human Protein Atlas database. (F) Protein levels of CASP8 and FADD in normal tissues from The Human Protein Atlas database. (G) Protein levels of CASP8 and FADD in tumors from The Human Protein Atlas database

Techniques: RNA Expression

Journal: Biochemistry and Biophysics Reports

Article Title: Transcriptome analysis of serum biomarker, shared gene signature and pharmacological targets between diabetic cardiomyopathy and nephropathy

doi: 10.1016/j.bbrep.2025.102194

Figure Lengend Snippet: PEA15 and TFPI2 expression in normal heart and kidney tissues is evidenced by the Human Protein Atlas. (A) Representative image: PEA15 and TFPI2 antibody staining in the kidney. (B) Representative image: PEA15 and TFPI2 expression in the kidney, measured using HPA RNA-seq. (C) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the kidney, as measured by HPA RNA-seq. (D) Percentage of cell types expressing PEA15 and TFPI2 in the kidney, determined through HPA RNA-seq. (E) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the kidney cortex and medulla, measured using GTEx RNA-seq. (F) Representative image: PEA15 and TFPI2 antibody staining in cardiomyocytes. (G) Representative image: PEA15 and TFPI2 expression in heart muscle, measured with HPA RNA-seq. (H) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in heart muscle, as measured by HPA RNA-seq. (I) Percentage of cell types expressing PEA15 and TFPI2 in heart muscle, determined through HPA RNA-seq. (J) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the atrial appendage and left ventricle, measured using GTEx RNA-seq.

Article Snippet: PEA15 and TFPI2 expression in normal heart and kidney tissues is evidenced by the Human Protein Atlas. (A) Representative image: PEA15 and TFPI2 antibody staining in the kidney. (B) Representative image: PEA15 and TFPI2 expression in the kidney, measured using HPA RNA-seq. (C) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the kidney, as measured by HPA RNA-seq. (D) Percentage of cell types expressing PEA15 and TFPI2 in the kidney, determined through HPA RNA-seq. (E) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the kidney cortex and medulla, measured using GTEx RNA-seq. (F) Representative image: PEA15 and TFPI2 antibody staining in cardiomyocytes. (G) Representative image: PEA15 and TFPI2 expression in heart muscle, measured with HPA RNA-seq. (H) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in heart muscle, as measured by HPA RNA-seq. (I) Percentage of cell types expressing PEA15 and TFPI2 in heart muscle, determined through HPA RNA-seq. (J) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the atrial appendage and left ventricle, measured using GTEx RNA-seq.

Techniques: Expressing, Staining, RNA Sequencing

Journal: Biochemistry and Biophysics Reports

Article Title: Transcriptome analysis of serum biomarker, shared gene signature and pharmacological targets between diabetic cardiomyopathy and nephropathy

doi: 10.1016/j.bbrep.2025.102194

Figure Lengend Snippet: Association of shared gene signatures and progressed cell death involving apoptosis and ferroptosis. (A) Expression levels of apoptosis-related genes in cardiomyocytes under a hyperglycemic environment (GSE 62203). (B) Expression levels of apoptosis-related genes in diabetic tubules (GSE 30122). (C) Correlation of the expression of two shared genes (PEA15 and TFPI2) and selected apoptosis-related genes in cardiomyocytes under a hyperglycemic environment (GSE 62203). (D) Correlation of the expression of two shared genes (PEA15 and TFPI2) and selected apoptosis-related genes in diabetic tubules (GSE 30122). (E) Expression levels of ferroptosis-related genes in diabetic cardiomyocytes (GSE 62203) and kidneys (GSE 30122). (F) Correlation of the expression of two shared genes (PEA15 and TFPI2) and selected ferroptosis-related genes in diabetic cardiomyocytes (GSE 62203) and kidneys (GSE 30122). (G) Expression levels of ferroptosis-related genes in the peripheral blood of patients with type II diabetes (GSE 23561) and glomeruli of diabetic nephropathy (GSE 96804). (H) Correlation of the expression of two shared genes (PEA15 and TFPI2) and selected ferroptosis-related genes in the peripheral blood of patients with type II diabetes (GSE 23561) and glomeruli of diabetic nephropathy (GSE 96804). The data has been normalized, and batch effects have been handled. A T-statistic test was employed to compare the expression levels of shared genes between the two groups. ∗ P < 0.05, ∗∗ P < 0.01 and ∗∗∗ P < 0.01 denotes statistical significance. DCM: diabetic cardiomyopathy; DT: diabetic tubuli; DNT: diabetic nephropathy tubuli; DNG: diabetic nephropathy glomeruli; DM: diabetes mellitus

Article Snippet: PEA15 and TFPI2 expression in normal heart and kidney tissues is evidenced by the Human Protein Atlas. (A) Representative image: PEA15 and TFPI2 antibody staining in the kidney. (B) Representative image: PEA15 and TFPI2 expression in the kidney, measured using HPA RNA-seq. (C) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the kidney, as measured by HPA RNA-seq. (D) Percentage of cell types expressing PEA15 and TFPI2 in the kidney, determined through HPA RNA-seq. (E) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the kidney cortex and medulla, measured using GTEx RNA-seq. (F) Representative image: PEA15 and TFPI2 antibody staining in cardiomyocytes. (G) Representative image: PEA15 and TFPI2 expression in heart muscle, measured with HPA RNA-seq. (H) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in heart muscle, as measured by HPA RNA-seq. (I) Percentage of cell types expressing PEA15 and TFPI2 in heart muscle, determined through HPA RNA-seq. (J) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the atrial appendage and left ventricle, measured using GTEx RNA-seq.

Techniques: Expressing

Journal: Biochemistry and Biophysics Reports

Article Title: Transcriptome analysis of serum biomarker, shared gene signature and pharmacological targets between diabetic cardiomyopathy and nephropathy

doi: 10.1016/j.bbrep.2025.102194

Figure Lengend Snippet: Clinical significance of shared genes in the Nephroseq database is illustrated through the following associations. (A) the relationship between PEA15 expression and glomerular filtration rate across all measured samples. (B) The correlation between PEA15 expression and serum creatinine levels in living donors. (C) The association of TFPI2 expression with glomerular filtration rate across all measured samples, and (D) The relationship between TFPI2 expression and serum creatinine levels in samples from patients with diabetic nephropathy.

Article Snippet: PEA15 and TFPI2 expression in normal heart and kidney tissues is evidenced by the Human Protein Atlas. (A) Representative image: PEA15 and TFPI2 antibody staining in the kidney. (B) Representative image: PEA15 and TFPI2 expression in the kidney, measured using HPA RNA-seq. (C) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the kidney, as measured by HPA RNA-seq. (D) Percentage of cell types expressing PEA15 and TFPI2 in the kidney, determined through HPA RNA-seq. (E) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the kidney cortex and medulla, measured using GTEx RNA-seq. (F) Representative image: PEA15 and TFPI2 antibody staining in cardiomyocytes. (G) Representative image: PEA15 and TFPI2 expression in heart muscle, measured with HPA RNA-seq. (H) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in heart muscle, as measured by HPA RNA-seq. (I) Percentage of cell types expressing PEA15 and TFPI2 in heart muscle, determined through HPA RNA-seq. (J) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the atrial appendage and left ventricle, measured using GTEx RNA-seq.

Techniques: Expressing, Filtration

Journal: Biochemistry and Biophysics Reports

Article Title: Transcriptome analysis of serum biomarker, shared gene signature and pharmacological targets between diabetic cardiomyopathy and nephropathy

doi: 10.1016/j.bbrep.2025.102194

Figure Lengend Snippet: Molecular docking of candidate compounds and shared genes, including transcription factor s. (A) Affinities of candidate compounds with RUNX2 (a transcription factor for PEA15), PEA15, and TFPI2. (B) Affinities of candidate compounds with transcription factors (HBA1, HBA2, and HBB) corresponding to the three hemoglobin subunits.

Article Snippet: PEA15 and TFPI2 expression in normal heart and kidney tissues is evidenced by the Human Protein Atlas. (A) Representative image: PEA15 and TFPI2 antibody staining in the kidney. (B) Representative image: PEA15 and TFPI2 expression in the kidney, measured using HPA RNA-seq. (C) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the kidney, as measured by HPA RNA-seq. (D) Percentage of cell types expressing PEA15 and TFPI2 in the kidney, determined through HPA RNA-seq. (E) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the kidney cortex and medulla, measured using GTEx RNA-seq. (F) Representative image: PEA15 and TFPI2 antibody staining in cardiomyocytes. (G) Representative image: PEA15 and TFPI2 expression in heart muscle, measured with HPA RNA-seq. (H) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in heart muscle, as measured by HPA RNA-seq. (I) Percentage of cell types expressing PEA15 and TFPI2 in heart muscle, determined through HPA RNA-seq. (J) Average normalized transcripts per million (nTPM) of PEA15 and TFPI2 in the atrial appendage and left ventricle, measured using GTEx RNA-seq.

Techniques:

Journal: BMC Immunology

Article Title: Establishment and validation of a recurrent prediction model for glioma: extrinsic apoptotic molecules FADD and CASP8 are closely associated with glioma recurrence

doi: 10.1186/s12865-025-00746-z

Figure Lengend Snippet: Biological functions associated with the recurrent scores. (A-B) The recurrent score related biological process revealed by Gene ontology analysis in the CGGA 693 and CGGA 325 database . (C-D) The heatmap showed the recurrent score and the enrichment scores of apoptosis-related functions of each patient in the CGGA 693 and CGGA 325 database. The samples were arranged in ascending order of the recurrent score. The column graph and line graph on the right showed the R -value and P -value of the correlation analysis. (E) Flow chart for recurrent score correlation analysis. (F-G) Using Pearson correlation analysis, the top 18 apoptosis-related genes mostly correlated with recurrent score were selected in CGGA 693 and CGGA 325 database. (H-I) The relationship between recurrent score and 6 apoptosis-related genes in glioma. The correlation coefficients were demonstrated as the proportion of the pie charts. The bottom right showed the correlation coefficient. The red parts represented a positive correlation. The correlation was tested by Pearson correlation analysis. (J) Correlation between the expression of the 6 genes in CGGA 693 and CGGA 325 database. ( K ) Expression levels of the 6 genes in primary glioma and recurrent glioma in CGGA 325 database and CGGA 693 database. (L) Survival analyses of the 6 genes by Kaplan-Meier curves and log-rank tests based on CCGA 693 database and CGGA 325 database. ( M ) Protein levels of SH3GLB1, NEK6, CASP8 and ITGB1 in normal tissues and GBM from The Human Protein Atlas database

Article Snippet: Characterizing the differential expression patterns of CASP8 and FADD in gliomas and normal tissues will play a crucial role in the further development of targeted therapeutic strategies for gliomas Fig. 9 RNA and protein levels of CASP8 and FADD in normal tissues and tumors. (A-B) RNA expression of CASP8 and FADD in normal tissues from the NCBI database (https://www.ncbi.nlm.nih.gov/). (C-D) RNA expression of CASP8 and FADD in normal tissues from the Human Protein Atlas database (https://www.proteinatlas.org/). (E) Protein levels of CASP8 and FADD in normal brain tissues from The Human Protein Atlas database. (F) Protein levels of CASP8 and FADD in normal tissues from The Human Protein Atlas database. (G) Protein levels of CASP8 and FADD in tumors from The Human Protein Atlas database

Techniques: Expressing

Journal: BMC Immunology

Article Title: Establishment and validation of a recurrent prediction model for glioma: extrinsic apoptotic molecules FADD and CASP8 are closely associated with glioma recurrence

doi: 10.1186/s12865-025-00746-z

Figure Lengend Snippet: The association between recurrent score and classical apoptotic genes. (A) The relationship between the 6 genes and recurrent score in CGGA and TCGA database . (B) PPI network of CASP3, CASP9, FADD, CASP7, CASP8, BCL2，and the 9-gene signature from the STRING. (C-D) The expression levels of the 6 apoptotic genes in low- and high-risk levels . (E-J) Correlation between recurrent score and expression levels of apoptotic genes. *P<0.05; ***P<0.001; ns, not significant

Article Snippet: Characterizing the differential expression patterns of CASP8 and FADD in gliomas and normal tissues will play a crucial role in the further development of targeted therapeutic strategies for gliomas Fig. 9 RNA and protein levels of CASP8 and FADD in normal tissues and tumors. (A-B) RNA expression of CASP8 and FADD in normal tissues from the NCBI database (https://www.ncbi.nlm.nih.gov/). (C-D) RNA expression of CASP8 and FADD in normal tissues from the Human Protein Atlas database (https://www.proteinatlas.org/). (E) Protein levels of CASP8 and FADD in normal brain tissues from The Human Protein Atlas database. (F) Protein levels of CASP8 and FADD in normal tissues from The Human Protein Atlas database. (G) Protein levels of CASP8 and FADD in tumors from The Human Protein Atlas database

Techniques: Expressing

Journal: BMC Immunology

Article Title: Establishment and validation of a recurrent prediction model for glioma: extrinsic apoptotic molecules FADD and CASP8 are closely associated with glioma recurrence

doi: 10.1186/s12865-025-00746-z

Figure Lengend Snippet: RNA and protein levels of CASP8 and FADD in normal tissues and tumors. (A-B) RNA expression of CASP8 and FADD in normal tissues from the NCBI database (https://www.ncbi.nlm.nih.gov/). (C-D) RNA expression of CASP8 and FADD in normal tissues from the Human Protein Atlas database (https://www.proteinatlas.org/). (E) Protein levels of CASP8 and FADD in normal brain tissues from The Human Protein Atlas database. (F) Protein levels of CASP8 and FADD in normal tissues from The Human Protein Atlas database. (G) Protein levels of CASP8 and FADD in tumors from The Human Protein Atlas database

Article Snippet: Characterizing the differential expression patterns of CASP8 and FADD in gliomas and normal tissues will play a crucial role in the further development of targeted therapeutic strategies for gliomas Fig. 9 RNA and protein levels of CASP8 and FADD in normal tissues and tumors. (A-B) RNA expression of CASP8 and FADD in normal tissues from the NCBI database (https://www.ncbi.nlm.nih.gov/). (C-D) RNA expression of CASP8 and FADD in normal tissues from the Human Protein Atlas database (https://www.proteinatlas.org/). (E) Protein levels of CASP8 and FADD in normal brain tissues from The Human Protein Atlas database. (F) Protein levels of CASP8 and FADD in normal tissues from The Human Protein Atlas database. (G) Protein levels of CASP8 and FADD in tumors from The Human Protein Atlas database

Techniques: RNA Expression