Journal: Cell Genomics

Article Title: Urine cf-nucleosomes: A non-invasive window into human physiology and disease

doi: 10.1016/j.xgen.2025.100974

Figure Lengend Snippet: cfChIP-seq of multiple histone modifications in human urine (A) Urine cfChIP-seq outline. Different cells release chromatin fragments into the urine. These fragments are immunoprecipitated using beads with covalently bound antibodies. DNA fragments are released, and sequencing libraries are generated. (B) Genome browser view of histone modification signals. Three sets of tracks are shown: two from cfChIP-seq of healthy donors and one from published epithelial tissue ChIP-seq data. (C) Metagene of normalized cfChIP-seq signal over promoters and enhancers. Line colors indicate activity levels of the genes based on >2,000 transcription start sites (TSSs) and enhancers from published ChIP-seq data. The y axis units denote coverage of fragments per million. (D) cfChIP-seq DNA fragment size distribution. Thin yellow lines show DNA fragments from 51 urine cfChIP-seq samples of various histone modifications (H3K27ac n = 6, H3K27me3 n = 5, H3K4me1 n = 13, H3K4me2 n = 13, and H3K4me3 n = 51), and the black line shows the median of all samples. (E) Fragmentation patterns of urine ChIP-seq cfnDNA and urine cfDNA. The lines show the median of n = 51 repeats in cfnDNA (black) and n = 10 repeats in cfDNA (blue). See also and .

Article Snippet: Native H3K4me3 ChIP-seq was performed in 500ul SDSless RIPA [10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100] or Bovine Serum Heat inactivated (Rockland D500-05-0500) using the same protocol as for urine cfChIP-seq.

Techniques: Immunoprecipitation, Sequencing, Generated, Modification, ChIP-sequencing, Activity Assay

Journal: Cell Genomics

Article Title: Urine cf-nucleosomes: A non-invasive window into human physiology and disease

doi: 10.1016/j.xgen.2025.100974

Figure Lengend Snippet: cfChIP-seq detects cfnDNA cell of origin (A) Schematic of genomic regions used as tissue-specific signatures based on reference ChIP-seq tissue atlas. For each tissue (rows in genome browser view), we identify genomic locations with high signals only in the target cell type (column with colored matching icons; colored squares represent tissue-specific windows; gray windows are non-specific or background windows) Given a urine cfChIP-seq sample (bottom row and right side of illustration), we sum the signal at signature locations and test against the null hypothesis of non-specific background coverage . (B) Heatmap of tissue signatures ( y axis) in H3K4me3 ChIP-seq signal of different tissues in the tissue atlas ( x axis). Color indicates the normalized read count of each genomic window in each tissue. (C) Top, tissue signatures in cfChIP-seq in 56 healthy samples from 21 donors. Each dot is a sample. Box limits: 25%–75% quantiles; the middle line indicates the median. The upper and lower whiskers extend to the largest and smallest values within 1.5× the interquartile range from the box edges. Dots in red indicate values significantly higher than background levels . Bottom, percentage of samples with significant signals for each signature. (D) Tissue signatures and Y chromosome coverage in female (27 samples from 9 donors) and male (29 samples from 12 donors) donors. Boxplots are as those described in (C). Wilcoxon test p values, adjusted for multiple comparisons, comparing the sexes are presented for each tissue signature: ∗adjusted p < 0.05, ∗∗adjusted p < 0.01, ∗∗∗adjusted p < 0.001, and ∗∗∗∗adjusted p < 0.0001. ns, not significantly different. See also .

Article Snippet: Native H3K4me3 ChIP-seq was performed in 500ul SDSless RIPA [10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100] or Bovine Serum Heat inactivated (Rockland D500-05-0500) using the same protocol as for urine cfChIP-seq.

Techniques: ChIP-sequencing

Journal: Cell Genomics

Article Title: Urine cf-nucleosomes: A non-invasive window into human physiology and disease

doi: 10.1016/j.xgen.2025.100974

Figure Lengend Snippet: Differences in promoter signals of three analytes (A) Comparison of urine cfChIP-seq ( x axis) vs. donor matching plasma cfChIP-seq ( y axis, left) and ChIP-seq of urine cells ( y axis, right). Dots represent signature scores of labeled tissues. (B) A genome browser view comparing the three analytes (urine cfChIP-seq, plasma cfChIP-seq, and urine-cell ChIP-seq) in two individuals. Each column features a promoter representative of a tissue type. Urine-exʹ cells denote urine-exfoliated cells. (C) Tissue signature distribution of multiple samples in the three analytes: urine cfChIP-seq (56 samples from 21 donors), urine cell ChIP-seq (5 samples from 4 donors), and plasma cfChIP-seq (35 samples from 35 donors). Each dot is a sample. Box limits: 25%–75% quantiles; the middle line indicates the median. The upper and lower whiskers extend to the largest and smallest values within 1.5× the interquartile range from the box edges. Wilcox-test adjusted p values for pairwise comparison between the three analytes are presented for each tissue signature: ∗adjusted p < 0.05, ∗∗adjusted p < 0.01, ∗∗∗adjusted p < 0.001, and ∗∗∗adjusted p < 0.0001. ns, not significantly different. Urine-exʹ cells is shorthand for urine-exfoliated cells. See also .

Article Snippet: Native H3K4me3 ChIP-seq was performed in 500ul SDSless RIPA [10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100] or Bovine Serum Heat inactivated (Rockland D500-05-0500) using the same protocol as for urine cfChIP-seq.

Techniques: Comparison, Clinical Proteomics, ChIP-sequencing, Labeling

Journal: Cell Genomics

Article Title: Urine cf-nucleosomes: A non-invasive window into human physiology and disease

doi: 10.1016/j.xgen.2025.100974

Figure Lengend Snippet: Y chromosome cfChIP-seq signal in urine and plasma and in healthy and pregnant individuals (A) Normalized promoter coverage in the Y chromosome in urine and plasma samples from healthy non-pregnant females, males, and pregnant females with male fetuses. (B) Normalized promoter coverage in the Y chromosome in urine and plasma samples from females pregnant with male fetuses across different gestational ages by week. Data point shapes represent sample type (dots are plasma cfChIP-seq samples, and triangles are urine cfChIP-seq samples), and colors indicate the pregnant donor. Plasma and urine samples from the same donor taken at the same gestational period are connected by dotted lines.

Article Snippet: Native H3K4me3 ChIP-seq was performed in 500ul SDSless RIPA [10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100] or Bovine Serum Heat inactivated (Rockland D500-05-0500) using the same protocol as for urine cfChIP-seq.

Techniques: Clinical Proteomics

Journal: Cell Genomics

Article Title: Urine cf-nucleosomes: A non-invasive window into human physiology and disease

doi: 10.1016/j.xgen.2025.100974

Figure Lengend Snippet: Pathology-driven changes in NMIBC cohort (A) Detection of genes with significantly high coverage in a sample from a healthy urine sample (left) and the urine of a patient with NMIBC (right). For each gene, we compared mean normalized coverage in a reference healthy cohort ( , x axis) against the normalized coverage in the cfChIP-seq sample ( y axis). Significance tests whether the observed number of reads is significantly higher than expected based on the distribution of values in healthy samples . (B) Cohort comparison across genes. Statistical significance ( y axis) and fold change of the NMIBC group over the healthy group ( x axis) of genes in both groups. Significance values represent the false discovery rate (FDR)-corrected q value of the likelihood ratio test between two groups . (C) Top, normalized count distribution of representative genes significantly different between the two cohorts. Red boxes represent NMIBC cohort samples, and gray boxes represent healthy samples. Box limits: 25%–75% quantiles; the middle line indicates the median. The upper and lower whiskers extend to the largest and smallest values within 1.5× the interquartile range from the box edges. Adjusted p values from the Wilcoxon test for pairwise comparisons between the two cohorts are shown for each tissue signature: ∗adjusted p < 0.05, ∗∗adjusted p < 0.01, ∗∗∗adjusted p < 0.001, and ∗∗∗∗adjusted p < 0.0001. ns, not significantly different. Bottom, a gene browser view of representative genes significantly different between the two cohorts (red tracks are NMIBC cohort samples, and gray tracks are healthy samples). (D) Heatmap representation of 177 genes significantly higher in the NMIBC cohort than in the healthy cohort. Rows (genes) are clustered by cell-type category. Heatmap values (colors) are log-transformed normalized values (log2 (1 + normalized gene reads)). (E) Comparison of cancer signature levels across the healthy and NMIBC discovery cohorts and the validation cohorts. Boxplot description and statistical test are as described in (C). (F) The receiver operating characteristic (ROC) curve illustrates the performance of a classifier using the cancer signature by plotting the true positive rate (sensitivity) on the y axis against the false positive rate (1-specificity) on the x axis. See also and .

Article Snippet: Native H3K4me3 ChIP-seq was performed in 500ul SDSless RIPA [10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100] or Bovine Serum Heat inactivated (Rockland D500-05-0500) using the same protocol as for urine cfChIP-seq.

Techniques: Comparison, Transformation Assay, Biomarker Discovery