Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Y chromosome loss in cancer drives growth by evasion of adaptive immunity

An Author Correction to this article was published on 29 January 2024

This article has been updated

Abstract

Loss of the Y chromosome (LOY) is observed in multiple cancer types, including 10–40% of bladder cancers1,2,3,4,5,6, but its clinical and biological significance is unknown. Here, using genomic and transcriptomic studies, we report that LOY correlates with poor prognoses in patients with bladder cancer. We performed in-depth studies of naturally occurring LOY mutant bladder cancer cells as well as those with targeted deletion of Y chromosome by CRISPR–Cas9. Y-positive (Y+) and Y-negative (Y) tumours grew similarly in vitro, whereas Y tumours were more aggressive than Y+ tumours in immune-competent hosts in a T cell-dependent manner. High-dimensional flow cytometric analyses demonstrated that Y tumours promote striking dysfunction or exhaustion of CD8+ T cells in the tumour microenvironment. These findings were validated using single-nuclei RNA sequencing and spatial proteomic evaluation of human bladder cancers. Of note, compared with Y+ tumours, Y tumours exhibited an increased response to anti-PD-1 immune checkpoint blockade therapy in both mice and patients with cancer. Together, these results demonstrate that cancer cells with LOY mutations alter T cell function, promoting T cell exhaustion and sensitizing them to PD-1-targeted immunotherapy. This work provides insights into the basic biology of LOY mutation and potential biomarkers for improving cancer immunotherapy.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: LOY is associated with a worse prognosis for men with MIBC.
Fig. 2: LOY and deletion of the Y chromosome genes Kdm5d and Uty promotes bladder tumour growth in an immune-competent host.
Fig. 3: Ylow bladder cancer overcomes T cell immunity and endows an immune-suppressive TME.
Fig. 4: Human Ylow bladder cancers are enriched with CD8+ T cells with evidence of exhaustion.
Fig. 5: Improved response of Ylow bladder cancer to anti-PD-1 ICB therapy.
Fig. 6: Increased genomic instability in Ylow bladder cancer.

Similar content being viewed by others

Data availability

The data supporting the findings of this study are available within the article, extended data and supplementary information files. RNA-seq and WES data are available at the Gene Expression Omnibus with accession reference GSE229233 and GSE230820Source data are provided with this paper.

Change history

References

  1. Caceres, A., Jene, A., Esko, T., Perez-Jurado, L. A. & Gonzalez, J. R. Extreme downregulation of chromosome Y and cancer risk in men. J. Natl Cancer Inst. 112, 913–920 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  2. Kido, T. & Lau, Y. F. Roles of the Y chromosome genes in human cancers. Asian J. Androl. 17, 373–380 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Brown, D. W. & Machiela, M. J. Why Y? Downregulation of chromosome Y genes potentially contributes to elevated cancer risk. J. Natl Cancer Inst. 112, 871–872 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  4. Panani, A. D. & Roussos, C. Sex chromosome abnormalities in bladder cancer: Y polysomies are linked to PT1-grade III transitional cell carcinoma. Anticancer Res. 26, 319–323 (2006).

    PubMed  Google Scholar 

  5. Sauter, G. et al. Y chromosome loss detected by FISH in bladder cancer. Cancer Genet. Cytogenet. 82, 163–169 (1995).

    Article  CAS  PubMed  Google Scholar 

  6. Powell, I., Tyrkus, M. & Kleer, E. Apparent correlation of sex chromosome loss and disease course in urothelial cancer. Cancer Genet. Cytogenet. 50, 97–101 (1990).

    Article  CAS  PubMed  Google Scholar 

  7. Maan, A. A. et al. The Y chromosome: a blueprint for men’s health? Eur. J. Hum. Genet. 25, 1181–1188 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Adikusuma, F., Williams, N., Grutzner, F., Hughes, J. & Thomas, P. Targeted deletion of an entire chromosome using CRISPR/Cas9. Mol. Ther. 25, 1736–1738 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Sano, S. et al. Hematopoietic loss of Y chromosome leads to cardiac fibrosis and heart failure mortality. Science 377, 292–297 (2022).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  10. Forsberg, L. A. et al. Mosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer. Nat. Genet. 46, 624–628 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Fadl-Elmula, I. et al. Karyotypic characterization of urinary bladder transitional cell carcinomas. Genes Chromosomes Cancer 29, 256–265 (2000).

    Article  CAS  PubMed  Google Scholar 

  12. Sauter, G., Moch, H., Mihatsch, M. J. & Gasser, T. C. Molecular cytogenetics of bladder cancer progression. Eur. Urol. 33, 9–10 (1998).

    Article  PubMed  Google Scholar 

  13. Smeets, W., Pauwels, R., Laarakkers, L., Debruyne, F. & Geraedts, J. Chromosomal analysis of bladder cancer. III. Nonrandom alterations. Cancer Genet. Cytogenet. 29, 29–41 (1987).

    Article  CAS  PubMed  Google Scholar 

  14. Sauter, G. et al. DNA aberrations in urinary bladder cancer detected by flow cytometry and FISH. Urol. Res. 25, S37–S43 (1997).

    Article  ADS  CAS  PubMed  Google Scholar 

  15. Neuhaus, M. et al. Polysomies but not Y chromosome losses have prognostic significance in pTa/pT1 urinary bladder cancer. Hum. Pathol. 30, 81–86 (1999).

    Article  CAS  PubMed  Google Scholar 

  16. Siegel, R. L., Miller, K. D., Fuchs, H. E. & Jemal, A. Cancer statistics, 2021. CA Cancer J. Clin. 71, 7–33 (2021).

    Article  PubMed  Google Scholar 

  17. Johansson, S. L. & Cohen, S. M. Epidemiology and etiology of bladder cancer. Semin. Surg. Oncol. 13, 291–298 (1997).

    Article  CAS  PubMed  Google Scholar 

  18. Dumanski, J. P. et al. Smoking is associated with mosaic loss of chromosome Y. Science 347, 81–83 (2015).

    Article  ADS  CAS  PubMed  Google Scholar 

  19. Tabayoyong, W. & Gao, J. The emerging role of immunotherapy in advanced urothelial cancers. Curr. Opin. Oncol. 30, 172–180 (2018).

    Article  CAS  PubMed  Google Scholar 

  20. Rouanne, M. et al. Development of immunotherapy in bladder cancer: present and future on targeting PD(L)1 and CTLA-4 pathways. World J. Urol. 36, 1727–1740 (2018).

    Article  CAS  PubMed  Google Scholar 

  21. Prokop, J. W. & Deschepper, C. F. Chromosome Y genetic variants: impact in animal models and on human disease. Physiol. Genomics 47, 525–537 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Robertson, A. G. et al. Comprehensive molecular characterization of muscle-invasive bladder cancer. Cell 171, 540–556.e525 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lindskrog, S. V. et al. An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer. Nat. Commun. 12, 2301 (2021).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  24. Gonzalez, J. R. et al. MADloy: robust detection of mosaic loss of chromosome Y from genotype-array-intensity data. BMC Bioinformatics 21, 533 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Summerhayes, I. C. & Franks, L. M. Effects of donor age on neoplastic transformation of adult mouse bladder epithelium in vitro. J. Natl Cancer Inst. 62, 1017–1023 (1979).

    CAS  PubMed  Google Scholar 

  26. Chan, E., Patel, A., Heston, W. & Larchian, W. Mouse orthotopic models for bladder cancer research. BJU Int. 104, 1286–1291 (2009).

    Article  PubMed  Google Scholar 

  27. White-Gilbertson, S., Davis, M., Voelkel-Johnson, C. & Kasman, L. M. Sex differences in the MB49 syngeneic, murine model of bladder cancer. Bladder 3, e22 (2016).

    Article  PubMed  Google Scholar 

  28. Tu, M. M. et al. Targeting DDR2 enhances tumor response to anti-PD-1 immunotherapy. Sci. Adv. 5, eaav2437 (2019).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  29. Sugiura, K. & Stock, C. C. The effect of 2,4,6-triethylenimino-s-triazine on the growth of a variety of mouse and rat tumors. Cancer 5, 979–991 (1952).

    Article  CAS  PubMed  Google Scholar 

  30. Gouin, K. H. 3rd et al. An N-cadherin 2 expressing epithelial cell subpopulation predicts response to surgery, chemotherapy and immunotherapy in bladder cancer. Nat. Commun. 12, 4906 (2021).

    Article  ADS  PubMed  PubMed Central  Google Scholar 

  31. Becht, E. et al. Dimensionality reduction for visualizing single-cell data using UMAP. Nat. Biotechnol. 37, 38–44 (2019).

    Article  CAS  Google Scholar 

  32. Hashimoto, M. et al. CD8 T cell exhaustion in chronic infection and cancer: opportunities for interventions. Annu. Rev. Med. 69, 301–318 (2018).

    Article  CAS  PubMed  Google Scholar 

  33. Kwon, H. et al. Androgen conspires with the CD8+ T cell exhaustion program and contributes to sex bias in cancer. Sci. Immunol. 7, eabq2630 (2022).

    Article  MathSciNet  CAS  PubMed  PubMed Central  Google Scholar 

  34. Mariathasan, S. et al. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature 554, 544–548 (2018).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  35. Zhang, Q. et al. Mosaic loss of chromosome Y promotes leukemogenesis and clonal hematopoiesis. JCI Insight 7, e153768 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  36. Minner, S. et al. Y chromosome loss is a frequent early event in urothelial bladder cancer. Pathology 42, 356–359 (2010).

    Article  PubMed  Google Scholar 

  37. Fabris, V. T. et al. Cytogenetic characterization of the murine bladder cancer model MB49 and the derived invasive line MB49-I. Cancer Genet. 205, 168–176 (2012).

    Article  CAS  PubMed  Google Scholar 

  38. Ler, L. D. et al. Loss of tumor suppressor KDM6A amplifies PRC2-regulated transcriptional repression in bladder cancer and can be targeted through inhibition of EZH2. Sci. Transl. Med. 9, eaai8312 (2017).

    Article  PubMed  Google Scholar 

  39. Walport, L. J. et al. Human UTY(KDM6C) is a male-specific N-methyl lysyl demethylase. J. Biol. Chem. 289, 18302–18313 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Li, N. et al. JARID1D is a suppressor and prognostic marker of prostate cancer invasion and metastasis. Cancer Res. 76, 831–843 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Seo, H. et al. TOX and TOX2 transcription factors cooperate with NR4A transcription factors to impose CD8+ T cell exhaustion. Proc. Natl Acad. Sci. USA 116, 12410–12415 (2019).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  42. Khan, O. et al. TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion. Nature 571, 211–218 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Thompson, D. J. et al. Genetic predisposition to mosaic Y chromosome loss in blood. Nature 575, 652–657 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Lattime, E. C., Gomella, L. G. & McCue, P. A. Murine bladder carcinoma cells present antigen to BCG-specific CD4+ T-cells. Cancer Res. 52, 4286–4290 (1992).

    CAS  PubMed  Google Scholar 

  45. Tu, M. M. et al. Inhibition of the CCL2 receptor, CCR2, enhances tumor response to immune checkpoint therapy. Commun. Biol. 3, 720 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Song, N. J. et al. Treatment with soluble CD24 attenuates COVID-19-associated systemic immunopathology. J. Hematol. Oncol. 15, 5 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Richmond, C. S. et al. Glycogen debranching enzyme (AGL) is a novel regulator of non-small cell lung cancer growth. Oncotarget 9, 16718–16730 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).

    Article  Google Scholar 

  49. Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    Article  CAS  PubMed  Google Scholar 

  50. Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Ewels, P., Magnusson, M., Lundin, S. & Kaller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047–3048 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  53. DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Hernandez, S. et al. Challenges and opportunities for immunoprofiling using a spatial high-plex technology: the NanoString GeoMx((R)) digital spatial profiler. Front. Oncol. 12, 890410 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Hänzelmann, S., Castelo, R. & Guinney, J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics 14, 7 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  56. Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  57. Rosenberg, J. E. et al. Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial. Lancet 387, 1909–1920 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Hedegaard, J. et al. Comprehensive transcriptional analysis of early-stage urothelial carcinoma. Cancer Cell 30, 27–42 (2016).

    Article  CAS  PubMed  Google Scholar 

  59. Becht, E. et al. Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol. 17, 218 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  60. Andreatta, M. et al. Interpretation of T cell states from single-cell transcriptomics data using reference atlases. Nat. Commun. 12, 2965 (2021).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  61. Bassez, A. et al. A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer. Nat. Med. 27, 820–832 (2021).

    Article  CAS  PubMed  Google Scholar 

  62. Daud, A. I. et al. Tumor immune profiling predicts response to anti-PD-1 therapy in human melanoma. J. Clin. Invest. 126, 3447–3452 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  63. Gros, A. et al. PD-1 identifies the patient-specific CD8+ tumor-reactive repertoire infiltrating human tumors. J. Clin. Invest. 124, 2246–2259 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Miller, B. C. et al. Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade. Nat. Immunol. 20, 326–336 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Siddiqui, I. et al. Intratumoral Tcf1+PD-1+CD8+ T cells with stem-like properties promote tumor control in response to vaccination and checkpoint blockade immunotherapy. Immunity 50, 195–211.e110 (2019).

    Article  CAS  PubMed  Google Scholar 

  66. Thommen, D. S. et al. A transcriptionally and functionally distinct PD-1+CD8+ T cell pool with predictive potential in non-small-cell lung cancer treated with PD-1 blockade. Nat. Med. 24, 994–1004 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Kumagai, S. et al. The PD-1 expression balance between effector and regulatory T cells predicts the clinical efficacy of PD-1 blockade therapies. Nat. Immunol. 21, 1346–1358 (2020).

    Article  CAS  PubMed  Google Scholar 

  68. Nielsen, M. & Andreatta, M. NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. Genome Med. 8, 33 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported in part by NIH P01CA278732 and R01CA143971 to D.T. and NIH R01CA262069, R01CA262388 and R01AI077283 to Z.L. J.M.S. and T.D.G. were supported by the Ohio State University Comprehensive Cancer Center’s Tumor Immunology T32 (2T32CA09223-16A1) post-doctoral fellowship award. We thank K. Walsh for providing the LOY gRNA plasmids, and N.-J. Song and B. Riesenberg for development of the ‘all immune phenotyping’ flow antibody panel. We acknowledge resources from the Immune Monitoring and Discovery Platform and the Pelotonia Institute for Immuno-Oncology at OSU Comprehensive Cancer Center (P30CA016058).

Author information

Authors and Affiliations

Authors

Contributions

The study was initiated by H.A.A.-H. and D.T. H.A.A.-H., J.M.S., X.C., T.X. and T.D.G. developed methodology. H.A.A.-H., J.M.S., X.C., T.X. and T.D.G. acquired data. H.A.A.-H. generated the MB49 cell line models and conducted the wild-type versus immune-compromised mouse model experiments. J.M.S. conducted the Y+ versus Y mouse experiments and associated flow cytometry studies. T.X. and T.D.G. conducted the CRISPR Y-Scr and CRISPR Y-KO mouse experiments and associated flow cytometry studies. X.C. performed the human sample biostatistical analyses and associated graph generations. H.A.A.-H., J.M.S., X.C., T.X., T.D.G., Z.L. and D.T. analysed and interpreted data. H.A.A.-H., J.M.S., Z.L. and D.T. wrote the manuscript. D.T. and Z.L. supervised the study. All authors reviewed and approved the final manuscript.

Corresponding author

Correspondence to Dan Theodorescu.

Ethics declarations

Competing interests

Z.L. reports personal consultation fees from Alphamab, HanchorBio, Henlius, Heat Biologic and Ikonisys outside the submitted work. All other authors declare no competing interests.

Peer review

Peer review information

Nature thanks Mitchell Machiela, Soichi Sano and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 LOY is associated with a worse clinical outcome for patients with MIBC and NMIBC.

a, Y chromosome genes expressed in normal bladder urothelium that were used to create a Y chromosome gene expression signature. b, Logrank p-values based on stratification by Y chromosome gene expression (normalized FPKM) on TCGA MIBC patient overall survival (OS). Genes resulting in statistically significant OS are plotted in panel c. NE, not expressed. c, Kaplan-Meier plots of OS from TCGA data for males with MIBC and either high or low KDM5D, TBL1Y, UTY (KDM6C), or ZFY expression. d, Kaplan-Meier survival curves stratified by the Y signature score or expression levels for UTY and KDM5D in NMIBC from the E-MTAB-4321 cohort. Survival differences are based on Logrank statistics. e, ChrY gene expression signature scores of TCGA data plotted with respect to extreme downregulation of chromosome Y (EDY, left panel) and Mosaic Alteration Detection for LOY (mLOY, right panel) levels. Statistical significance was determined by Wilcoxon rank-sum test (NoLOY n = 151, LOY n = 90, NoEDY n = 165, EDY n = 76). Boxplots represent the mean with first and third quartile data. Minimum and maximum datapoints are included.

Extended Data Fig. 2 Generation of Y+ and Y- BC models.

a, Histogram representation of deferentially regulated genes (DEG) from Y+ vs. Y- MB49 RNAseq data per mouse chromosome. b, qRT-PCR analysis of Uty, Kdm5d, Eifs3y, and Ddx3y expression in MB49 clones isolated from the parental MB49 compared to female murine breast cancer (E0771) and bladder cancer cells (NA13), and testis tissue. Curly brackets indicate the clonal lines used to generate the pooled Y+ and Y- MB49 sublines. c, qRT-PCR analysis of Uty and Kdm5d expression in the pooled Y+ and Y- sublines described in a. n = 3 biological replicates. Data are mean ± s.e.m. d, Bar graph of sequencing depth for each chromosome after performing whole exome sequencing (WES) on DNA from the Parental, Y-, and Y+ MB49 cell lines.

Extended Data Fig. 3 LOY has no effect on colony forming ability of BC in vitro.

a, MB49 Y+ and Y- cells were grown in 0.4% agar for two weeks. Colonies were stained with Nitro-BT and quantified using ImageJ. Average colony number and area were determined from those with a diameter that exceeded 100 µm (n = 4 biological replicates). Data representative of three independent experiments. Statistical significance was determined by two-sided unpaired t-test, P-value = 0.722. Data are mean ± s.e.m. b, In vitro cell proliferation (MTT cell viability) over a 6–8-day time course using three sets of genetically engineered MB49 cells: Y+, Y+ Kdm5d KO, Y+ Uty KO (left panel), Y-, Y- Kdm5d OE, Y- Uty OE (middle panel), and CRISPR-Y-Scr vs. CRISPR-Y-KO (right panel). n = 3 biological replicates. Data are mean ± s.e.m. c, qRT-PCR analysis of Uty expression in MB49 clones isolated from the CRISPR-generated Y-KO and Y-Scr MB49 cell lines. Curly brackets indicate the clonal lines used to generate the pooled Y+ Control and Y- KO MB49 sublines. Representative immunofluorescence images of the CRISPR-generated Y-KO and Y-Scr MB49 cell lines. Scale bar, 150 µM.

Extended Data Fig. 4 Increased lymphocyte activation in Y+ tumors.

a, Volcano plot of DEGs from bulk RNA isolated from Y+ and Y- MB49 tumors grown in male WT mice. Blue (Y+ tumors) and red (Y- tumors) genes correspond to statistically significant (Benjamini-Hochberg method, P < 0.05) genes that have a | >1 log2 | fold-change in expression. b, PCA of DEGs described in a. c, Gene ontology (GO) pathway enrichment score plots of statistically significant gene set enrichment analyses (GSEA) using DEGs from a. NES, normalized enrichment score.

Extended Data Fig. 5 Comprehensive immune phenotyping of tumor-infiltrating leukocytes (TILs) in Y+ and Y- MB49 tumors.

a, UMAPs demonstrating individual spectral flow cytometry analysis of protein marker expression in CD45+ immune cells isolated from Y+ and Y- MB49 tumors grown in WT male mice. b, Heatmap of relative protein expression from immune cells described in a. c, Violin plots of each tumor sample across each cluster from the CD45+ immune cell UMAP (see Fig. 3b). d, Violin plot of PD-1 and PD-L1 mean fluorescence intensity in CD45+ immune cells from Y+ and Y- MB49 tumors. e, Representative dot plots and percentages of CD8+ and CD4+ T cells gated on total CD3+ T cells from CRISPR-Y-Scr (n = 8) and CRISPR-Y-KO (n = 9), MB49 tumors grown for 22 or 17 days, respectively, in male WT mice (left panels). Percentage of CD8+ T cells of total CD3+ T cells per tumor sample (right panel). f, Percentage of CD206+PDL1+ macrophages among total CD11b+F4/80+ macrophages from Control and Y KO MB49 tumors described in e. Statistics were determined using two-sided unpaired t-tests.

Extended Data Fig. 6 GeoMX histological evaluation of infiltrating immune cells in Y- and Y+ MB49 tumors.

a, Table of markers that are functionally categorized for GeoMX evaluation of Y+ and Y- MB49 tumors. b, Representative H&E image (left), immunofluorescence detection of nuclei (blue), cytokeratin (green), CD45+ immune cells (red) (middle), and associated computational digital profiling (right) to quantify markers shown in a. Scale bar, 125 µM. c, Quantification (log2 fold change and P-value) of the markers listed in Y+ versus Y- MB49 tumors (n = 10 tumors per group and three TMA cores per tumor). Data representative of two independent experiments. Statistical significance was determined by two-sided unpaired t-test.

Extended Data Fig. 7 Characterization of tumor-infiltrating CD8+ T cells after PD-1 pathway blockade.

ac, Relative spectral flow protein expression (a), sample-level violin plots per cluster (b), and heatmap of individual targets per cluster (c) after 200 μg anti-PD-1 or isotype control IgG treatments for 7 days using CD8+ T cells from Y+ and Y- MB49 tumors. d, Representative dot plots and percentages of TOX and/or GZMB-expressing CD8+ T cells from CRISPR-Y-Scr and CRISPR-Y-KO MB49 tumors grown in male WT mice after 200 μg anti-PD-1 or isotype control IgG treatments for 7 days. ef, Percentage of PD1+TOX+ CD8+ T cells (e) and TOXCD44+ (top panel) or TOXICOS+ (bottom panel) CD8+ T cells (f) from tumor samples described in d. See Fig. 5 for additional method details. Statistical significance was determined by two-sided unpaired t-test. Tests were conducted between isotype controls or between isotype controls and anti-PD1 treatment groups.

Extended Data Fig. 8 DDR-related pathways in TCGA Ylow vs. Yhigh BC.

a, Heatmap of the indicated pathways and metadata from BC TCGA data. bc, box plot of tumor neoantigen burden (TNB) per megabase (P = 0.700) (b), and associated pathway enrichment levels (c) from Yhigh and Ylow tumors described in Fig. 1a. Statistical significance was determined by Wilcoxon test (Ylow n = 118 and Yhigh n = 182). Boxplots represent the mean with first and third quartile data. Minimum and maximum datapoints are included.

Extended Data Fig. 9 Defective DDR pathway activation in Y- MB49 cells.

Normalized enrichment scores of statistically significant GSEA GO pathways using DEGs from Y- vs. Y+ MB49 cell cultures. Purple color denotes DNA repair-related pathways enriched in Y- cells.

Extended Data Fig. 10 Elevated genomic instability in LOY, Uty KO, and Kdm5d KO MB49 lines.

Genome instability pathway enrichment scores using RNA-seq data from control and genetically modified MB49 cell lines (Y+ and Y- cells, n = 5 technical replicates. n = 3 for all other cell lines). Two-sided unpaired t-test. Boxplots represent the mean with first and third quartile data. Minimum and maximum datapoints are included.

Supplementary information

Supplementary Fig. 1

Spectral flow gating strategies.

Reporting Summary

Supplementary Table 1

Y chromosome gene expression in MB49 clones.

Supplementary Table 2

Immune Phenotyping spectral flow cytometry antibody panel.

Source data

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Abdel-Hafiz, H.A., Schafer, J.M., Chen, X. et al. Y chromosome loss in cancer drives growth by evasion of adaptive immunity. Nature 619, 624–631 (2023). https://doi.org/10.1038/s41586-023-06234-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41586-023-06234-x

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing: Cancer

Sign up for the Nature Briefing: Cancer newsletter — what matters in cancer research, free to your inbox weekly.

Get what matters in cancer research, free to your inbox weekly. Sign up for Nature Briefing: Cancer