Selective loss of Y chromosomes in lung adenocarcinoma modulates the tumor immune environment through cancer/testis antigens

Abstract

There is increasing recognition that the sex chromosomes, X and Y, play an important role in health and disease that goes beyond the determination of biological sex. Loss of the Y chromosome (LOY) in blood, which occurs naturally in aging men, has been found to be a driver of cardiac fibrosis and heart failure mortality. LOY also occurs in most solid tumors in males and is often associated with worse survival, suggesting that LOY may give tumor cells a growth or survival advantage. We analyzed LOY in lung adenocarcinoma (LUAD) using both bulk and single-cell expression data and found evidence suggesting that LOY affects the tumor immune environment by altering cancer/testis antigen expression and consequently facilitating tumor immune evasion. Analyzing immunotherapy data, we show that LOY and changes in expression of particular cancer/testis antigens are associated with response to pembrolizumab treatment and outcome, providing a new and powerful biomarker for predicting immunotherapy response in LUAD tumors in males.

Keywords: cancer; immune evasion; loss of Y; lung adenocarcinoma.

Fig. 1. Measures of LOY and study overview.

a Measures of LOY including RNA-seq, copy number variant (CNV) estimates, and ratios of Y coverage to autosome coverage from whole genome sequence depicted as they would manifest with three different ratios of LOY to non-LOY cells (primary tumor). b Overview of this study. Using lung adenocarcinoma as a model, we identify measures of LOY, demonstrate that this is driven by tumor and not immune cells, identify an association between LOY and cancer testis antigens and use gene regulatory network inference to analyze their expression, and then explore how immunotherapy response changes with LOY.

Fig. 2. Proposed model of loss of Y in LUAD.

With increasing LOY we observed a change in tumor immune environment (TIME) associated with alterations in the expression of various cancer testis antigens (CTAs). The amount of NK, and CD4+ T-cells decreases with LOY, while M1 macrophage proportions consistently increase, steady proportions of immune cells are not shown. Created in BioRender. Lopes Ramos, C. (2024) BioRender.com/v90i141. Bottom right: a graphical mechanistic model of LOY.

Fig. 3. Loss of Y in LUAD.

a First two principal components of Y genes in TCGA primary tumor tissue of LUAD patients, providing evidence for LOY based on gene expression levels. b Visualization of the approach we used to estimate LOY in primary tumors, which uses the first three components of PCA applied to the expression of Y-chromosome genes, showing the first two principal components for patient i (only PC1 and PC2 are shown). c First two principal components of Y genes in TCGA adjacent normal tissue of LUAD patients. d First two principal components on Y genes of pseudobulked gene expression of annotated epithelial cells for all samples in HTAN LUAD data. e First two principal components on Y genes of pseudobulked gene expression of annotated immune cells for all samples in HTAN LUAD data. f Change of TF-regulated expression of CTAs along LOY as estimated by TIGER on TCGA LUAD. To account for individual-specific noise, we built seven equal-width bins across observed male pc-LOY, averaging networks across individuals within one bin. Visualized are CTAs that show a significant correlation with LOY after Benjamini-Hochberg correction.

Fig. 4. Immunotherapy response in context of LOY.

a Correlation of RPS4Y1 gene expression and pc-LOY (larger value means more LOY) in TCGA LUAD data. b Hazard ratio (y-axis) when comparing male LUAD patients treated with pembro split into two groups based on median expression value of CTA (x-axis, low expression group vs high expression group). HR values with confidence intervals and p-values in bold, all non-significant observed HRs are transparent for clarity of the results.