Single-Cell RNA Sequencing Revealed the YY1/EZH2/MLH1 Axis As a Possible Therapeutic Target of Intractable Adult T-Cell Leukemia

Background: Due to clinical heterogeneity of adult T-cell leukemia/lymphoma (ATL) and its diverse genetic abnormality, common therapeutic targets of ATL remains unclear. Whereas the YY1/EZH2 axis regulates global epigenetic modification of genes in ATL, its downstream target genes have not been fully elucidated. Meanwhile, DNA mismatch repair proteins may be targeted in ATL. Here we explored underlying molecular axes for ATL progression through comprehensive single-cell RNA-sequencing (sc-RNA-seq).

Methods: Peripheral blood of 42 ATL patients and asymptomatic HTLV-1 carriers in addition to two cell lines of ATL43T and ED+ were subjected to the following analyses. Molecular markers associated with their clinical phenotypes were extracted through sc-RNA-seq analysis. Expression levels of DNA mismatch repair proteins (MLH1, MSH2) and target molecules were validated by flow cytometry. Finally, their function was verified through lentiviral shRNA-dependent knockdown and molecular-targeting reagents.

Results: While the frequencies of CADM1+ cells among CD4+ T cells were generally correlated with HTLV-1 proviral loads (R = 0.76, p < 0.001), substantial CADM1+ cells were detected but did not increase in some long-remitted cases; thus, CADM1+ cells are biologically heterogeneous. sc-RNA-seq of CADM1+ cells of four ATL cases identified a cluster of CD48-deficient cells. in silico promoter analysis of the cluster extracted a transcription factor YY1 as a candidate for common master regulators. EZH2 and the putative driver genes (CELF2, PTPRC, CBLB, ATXN1, IKZF2) were identified as differentially expressed genes (DEGs) in the cluster. The EZH2-overexpressed cluster was increased in acute-type ATL compared with remitted ATL and smoldering-type ATL. Interestingly, the cluster increased moderately in the other smoldering-type ATL, which required UVB irradiation due to intractable skin lesion. Given that YY1 and EZH2 were up-regulated in acute-type ATL, the cluster may represent tumor aggressiveness. Furthermore, biphasic expression of YY1/EZH2 was observed in 2 acute-type ATL, which indicates that the EZH2 ^high ATL cells confer malignant signature. In-house analysis on microarray dataset GSE55851 specified the MLH1 associated with YY1/EZH2. MLH1 within CADM1+ fraction was down-regulated in ATL patients with remission (n = 7) but maintained in progressive ATL (n = 6) (p < 0.05). Lentiviral shYY1 knockdown resulted in down-regulation of MLH1 in both ATL43T and ED+ (p < 0.01). The EZH1/2 inhibitor valemetostat down-regulated EZH2 (p = 0.018) and MLH1 (p = 0.014) in primary ATL cells. Finally, knockdown of either YY1 or MLH1 suppressed proliferation of ATL43T and ED+ (p < 0.0001).

Conclusions: Our findings indicate that down-regulation of MLH1 through YY1/EZH2 inhibition plays a key role in the treatment of aggressive ATL.