Novel Cell Adhesion/Migration Pathways Are Predictive Markers of HDAC Inhibitor Resistance in Cutaneous T Cell Lymphoma

Background: Treatment for Cutaneous T Cell Lymphoma (CTCL) is generally not curative. Therefore, selecting a therapy that is both effective and tolerable is critical to clinical decision-making. Histone deacetylase inhibitors (HDACi), epigenetic modifier drugs, are commonly used but effective in only ~30% of patients. There are no predictive markers of HDACi response and the histone acetylation landscape in CTCL remains unmapped. We sought to identify pre-treatment molecular markers of resistance in CTCL that progressed on HDACi therapy. Methods: Purified T cells from 39 pre/post-treatment peripheral blood samples and skin biopsies from 20 patients were subjected to RNA-seq and ChIP-seq for histone acetylation marks (H3K14/9ac, H3K27ac). We correlated significant differences in histone acetylation with gene expression in HDACi-resistant/sensitive CTCL. We extended these findings in additional CTCL patient cohorts (RNA-seq, microarray), and using ELISA in matched CTCL patient plasma. Findings: Resistant CTCL exhibited high levels of histone acetylation, which correlated with increased expression of 338 genes (FC≥2, FDR<0.05), including some novel to CTCL: BIRC5 (anti-apoptotic); RRM2 (cell cycle); TXNDC5, GSTM1 (redox); and CXCR4, LAIR2 (cell adhesion/migration). Several of these, including LAIR2, were elevated pre-treatment in HDACiresistant CTCL. In CTCL patient plasma (n=6), LAIR2 protein was also elevated (p<0.01) compared to controls. Interpretation: This study is the first to connect genome-wide differences in chromatin acetylation and gene expression to HDACi-resistance in primary CTCL. Our results identify novel markers with high pre-treatment expression, such as LAIR2, as predictors of HDACi-resistance in CTCL. Funding Statement: This work was supported by NIH grants CA156690, CA188286 (J.E.P.), the Washington University Institute of Clinical and Translational Sciences grant UL1 TR000448 from the National Center for Advancing Translational Sciences (NCATS) (Pilot Award to J.E.P.), and Siteman Cancer Center (CA091842) (Pilot Award to J.E.P.) grants. Sequencing provided by the Genome Technology Access Center, which is partially supported by NCI Cancer Center Support Grant #P30 CA91842 to the Siteman Cancer Center and by ICTS/CTSA Grant# UL1 TR000448 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), and NIH Roadmap for Medical Research. The ICTS is funded by the NIH’s NCATS Clinical and Translational Science Award (CTSA) program grant #UL1 TR002345. Declaration of Interests: N. Mehta-Shah reports research funding from Celgene, Verastem Pharmaceuticals, Roche/Genentech, and Bristol Myers Squibb and is a consultant for Kiowa Hakka Kirin. K. R. Carson is also employed by Flatiron Health. A. C. Musiek reports research funding from Pfizer, Helsinn, miRagen, Solgenix, Kyowa, Elorac, and Actelion and is also on the advisory boards for Actelion and Kyowa. No potential conflicts of interest were disclosed by the other authors. Ethics Approval Statement: De-identified peripheral blood draws or skin punch biopsies were obtained from patients seen at the Washington University School of Medicine Cutaneous Lymphoma Clinic under IRB-approved protocols with patients providing informed consent. Peripheral blood was also drawn from healthy volunteers at WUSM with IRB approval.