Loss of chromosome Y in regulatory T cells

Abstract

Background: Mosaic loss of chromosome Y (LOY) in leukocytes is the most prevalent somatic aneuploidy in aging humans. Men with LOY have increased risks of all-cause mortality and the major causes of death, including many forms of cancer. It has been suggested that the association between LOY and disease risk depends on what type of leukocyte is affected with Y loss, with prostate cancer patients showing higher levels of LOY in CD4 + T lymphocytes. In previous studies, Y loss has however been observed at relatively low levels in this cell type. This motivated us to investigate whether specific subsets of CD4 + T lymphocytes are particularly affected by LOY. Publicly available, T lymphocyte enriched, single-cell RNA sequencing datasets from patients with liver, lung or colorectal cancer were used to study how LOY affects different subtypes of T lymphocyte. To validate the observations from the public data, we also generated a single-cell RNA sequencing dataset comprised of 23 PBMC samples and 32 CD4 + T lymphocytes enriched samples.

Results: Regulatory T cells had significantly more LOY than any other studied T lymphocytes subtype. Furthermore, LOY in regulatory T cells increased the ratio of regulatory T cells compared with other T lymphocyte subtypes, indicating an effect of Y loss on lymphocyte differentiation. This was supported by developmental trajectory analysis of CD4 + T lymphocytes culminating in the regulatory T cells cluster most heavily affected by LOY. Finally, we identify dysregulation of 465 genes in regulatory T cells with Y loss, many involved in the immunosuppressive functions and development of regulatory T cells.

Conclusions: Here, we show that regulatory T cells are particularly affected by Y loss, resulting in an increased fraction of regulatory T cells and dysregulated immune functions. Considering that regulatory T cells plays a critical role in the process of immunosuppression; this enrichment for regulatory T cells with LOY might contribute to the increased risk for cancer observed among men with Y loss in leukocytes.

Keywords: GSEA; Gene set enrichment analysis; LOY; Mosaic loss of chromosome Y; Regulatory T cells; Single-cell RNA sequencing; Tregs; scRNA-seq; scRNAseq.

Fig. 1

(A) Boxplot showing the overall percentage of LOY in different T lymphocyte subsets, in each studied subject of the public datasets. Each dot corresponds to the LOY frequency of one patient, color-coded for each cell type. (B) Similar boxplot as in A, stratified by tissue of origin for T lymphocytes as indicated. Peripheral, Normal and Tumour indicates peripheral blood, normal tissue adjacent to tumour and tumour tissue, respectively. Note that the dots here marks outliers, and has therefore been coloured red to differentiate them from the dots in A

Fig. 2

(A) Boxplot showing the percentage of LOY in the studied leukocytes of the validation dataset. Each dot represents the value of one sample. Median values are marked with black lines, where Tregs have the highest median of any studied cell type. (B) Subset of A; specifically the T lymphocytes

Fig. 3

Illustration of the distribution of LOY in different types of CD4 + T lymphocytes, as well as their developmental trajectories. The full UMAP can be seen in Supplementary Fig. 10B. (A) The distribution of the identified cell types. (B) The LOY status of the cells in A, with LOY-cells being marked red. (C) Developmental trajectory of CD4 + T lymphocytes. Colour denotes pseudotime, with more developed cells being brighter. The lines indicate the suggested trajectories from naive to more differentiated CD4 + cells.

Fig. 4

The top 20 categories from the gene set enrichment analysis. Categories within the left and right frames were upregulated and downregulated, respectively. The coloured clusters to the left indicate the same branch of the gene ontology (GO) tree. Dot size and colour indicates gene count and P-value, respectively