Fig. 3: LOY in malignant and benign cells shows concurrent enrichment in tumours.
From: Concurrent loss of the Y chromosome in cancer and T cells impacts outcome
a, LOYSCR and WTYSCR cell proportions across principal cell populations in human tumours (top) and mouse bladder tumours induced by BBN (bottom). b, Correlation of cell group proportions across human tumours, defined by cell type and LOYSCR status. Cell type proportions across samples are shown in yellow (x axis, left; y axis, top), while LOYSCR cell proportions are in blue (x axis, right; y axis, bottom). Within groups, cell types are ordered alphabetically. c, Proportion of Y chromosome signal-positive nuclei per tissue core (FISH experiment), categorized by CD45 status. Data are presented as mean ± s.e.m., normalized to the normal male Y chromosome signal. Values <0 or >1 arise from normalization and do not reflect absolute signal levels. d, Y chromosome gene (Kdm5d, Uty, Eif2s3y, Ddx3y) DNA levels in each cell line before injection, confirming LOY status. Data are mean ± s.e.m.; dots, biological and technical replicates. e, DNA qPCR analysis of Y chromosome genes in immune cells (CD45+) across MB49 WTY (Y+), MB49 LOY (Y−) and MB49 clone 5 (C.5) groups. Y+, n = 8; Y−, n = 15 for Kdm5d and n = 12 for other genes; MB49 C.5, n = 10. Data are mean ± s.e.m. Two-sided Wilcoxon rank sum tests. n = total number of all the technical duplicates obtained from all the samples used for the assay. f, DNA qPCR analysis of Y chromosome genes in epithelial (CD45−, TdTomato+, left) and immune cells (CD45+, right) from CRISPR Y-Scr and CRISPR Y-KO groups. For CD45− Y‐Scr, n = 3; Y‐KO, n = 6. For CD45+ Y‐Scr, n = 7; Y‐KO, n = 27 (Kdm5d) and n = 24 (other genes). Data are mean ± s.e.m. Two-sided Wilcoxon rank sum tests. n = total number of all the technical triplicates obtained from all the samples used for the assay. g, Genomic DNA qPCR was performed to assess Y chromosome genes (Kdm5d, Uty, Ssty1, Ssty2) in CD3+ T cells from PBMCs of mice bearing CRISPR Y-Scr or CRISPR Y-KO tumours. Fold change (FC) was calculated relative to the average in vivo values and normalized to both endogenous controls separately. Purple dots, normalization to Gapdh; yellow dots, normalization to Actb. Each dot denotes pooled samples from six independent tumours. Data are mean ± s.e.m. Two-sided Wilcoxon rank sum tests.
