Characterization of Sole Loss of the Y Chromosome and Associated Effects on Adaptive Immunity in Adult Male Patients with Acute Myeloid Leukemia (AML)

Loss of the Y chromosome (LOY) is frequently found in healthy aging men, which challenged evaluation of its clinical relevance for decades. Recently, however, LOY was identified as causative event for tumorigenesis via evasion of adaptive immunity in solid tumors. In AML, sole LOY is found in about 6% of newly diagnosed AML, comprising approximately 15% of the cytogenetic abnormalities frequently detected. Thus, we set out to characterize the possible role of LOY in AML pathogenesis and clonal evolution to delineate the clinical and translational relevance of this recurrent, yet least appreciated cytogenetic abnormality in adult patients with AML.

Using an integrative bioinformatics methodology, we explored the transcriptomic profile of 23 bone marrow (BM) samples from male AML patients with LOY as the sole cytogenetic abnormality and a comparison group of 218 cytogenetically normal (CN) male patients with AML. As an additional control group, we also included 203 CN BM samples from female AML patients, all of which were derived from newly diagnosed, adult AML patients who were similarly treated on Cancer and Leukemia Group B/Alliance for Clinical Trials in Oncology frontline protocols. Using DESeq2, we first identified differential gene expression patterns, including 364 genes (2.3%) that were upregulated and 74 genes (0.46%) that were downregulated in the LOY compared with the CN male samples (adj p-value<0.05). Among the downregulated genes were genes known to be located on the Y chromosome, including KDM5D (adj p-value=0.0036), ZFY (adj p-value=0.0123) and DDX3Y (adj p-value=0.0480). Gene Ontology (GO) Biological Process (BP) enrichment analysis showed significant enrichment in, among others, pathways related to angiogenesis, cell-cell interaction, Wnt signaling, and regulation of ion transmembrane transport in the sole LOY male samples. Conversely, the downregulated genes showed significant enrichment in pathways related to innate immune regulation, such as inflammatory response (GO:0006954) and Toll-Like Receptor (TLR) Signaling pathways (GO:0002224, 0034135, 0034163). In line with these findings, Gene Set Enrichment Analysis showed that terms related to T cell activation, TLR signaling and NFkB activity were significantly underrepresented in the LOY male samples compared with their CN counterparts. To better understand the immune cell composition between groups, we performed deconvolution to estimate cell-type fractions within mixed cell populations, using CIBERSORTx. We found that LOY samples had higher proportions of Cytotoxic T cells (p=0.048) compared with CN male samples, while there was no difference between the LOY male and CN female group. Consistently, LOY patients had lower proportions of naïve T cells compared with CN male patients (p=0.00007).

Lastly, we used high dimensional spectral flow cytometry to characterize the immune profile in 8 BM mononuclear (BMMC) samples from male AML patients with LOY as a sole cytogenetic abnormality, and 8 male CN-AML patients. The analysis was performed within the live CD34^-CD45^high single cells. While there was no difference in the proportion of CD8⁺ or CD4⁺ cells within the CD3⁺ T cell compartment, we found a significant increase of the CD45RA^-CD45RO⁺ cells in the CD8⁺ T cell fraction in the LOY samples (p=0.0158) that was accompanied by a decrease in the CD45RA⁺CD45RO^- CD8⁺ T cells (p=0.0131). Specifically, CD45RA^-CD45RO⁺CD28⁺ memory-like CD8⁺ T cells (Tm) were significantly increased in the BM of the LOY patients (p=0.02), coupled by a sharp reduction of CD45RA⁺CD45RO^-CD27^-CD28^- effector CD8⁺ T cells (Teff) (p=0.0001), which was validated in a second cohort of 6 LOY and 6 CN-AML BM samples. This finding suggested a potential block of Tm to Teff transition in AML with LOY.

In summary, our results strongly suggest an immunomodulatory capacity of LOY in AML patients, thereby challenging the paradigm of LOY merely being an age-associated phenomenon without functional consequences. These results warrant additional follow-up studies to better understand the possible pathogenetic and clinical significance of LOY in AML, including amenability to immunotherapy approaches.

Byrd:Abbvie, AstraZeneca, and Syndax: Consultancy; Vincerx Pharma, Eilean Therapeutics, and Kurome Therapeutics: Current equity holder in private company. Stone:AbbVie: Consultancy, Other: Research funding to my institution; AMGEN: Consultancy; Aptevo: Consultancy; AvenCell: Consultancy; BerGenBio: Consultancy; Bristol Meyers Squibb: Consultancy; Cellarity: Consultancy; CTI Biopharma: Consultancy; Curis Oncology: Consultancy; Daiichi Sankyo: Consultancy; ENSEM: Consultancy; Epizyme: Consultancy, Other: DSMB; Glycomimetrics: Consultancy; Glaxosmithkline: Consultancy; Hermavant: Consultancy; Janssen: Other: Research funding to my institution; Jazz: Consultancy; Kura Oncology: Consultancy; Lava Therapeutics: Consultancy; Ligand Pharma: Consultancy; Novartis: Other: Research funding to my institution; Redona therapeutics: Consultancy; Rigel: Consultancy; Syndax: Other: Research funding to my institution; Syntrix: Other: DSMB; Takeda: Other: DSMB. Eisfeld:Karyopharm Therapeutics: Other: Spouse employment; AstraZeneca US: Membership on an entity's Board of Directors or advisory committees; OncLive: Honoraria; Dava Oncology: Honoraria; VJ HemeOnc: Honoraria; GTC: Honoraria.