CDK7 ENABLES THE FUNCTIONAL CROSSTALK BETWEEN LYMPHOMA AND MICROENVIRONMENT (TME) CELLS IN PERIPHERAL T-CELL LYMPHOMA (PTCL)

Introduction: PTCL cell survival and proliferation depend on crosstalk with TME cells. The acquisition of pro-tumoral phenotypes in TME cells requires transcriptional changes, creating a therapeutic vulnerability. This is critical for improving treatment of PTCL-NOS lacking actionable alterations.

Methods: RNA-seq and multiparametric imaging of PTCL patient samples. Drug screening in stromal-lymphoma cocultures. In vivo efficacy, RNA-seq and proteomics of PTCL-NOS PDX.

Results: To identify pro-tumoral TME pathways, we analyzed the cellular constitution and activity of PTCL TME using functional signature deconvolution (n = 845). Among four biologically and clinically relevant TME categories, we identified one with high pro-tumoral-polarized macrophages and cancer-associated fibroblasts (CAF). We established a co-culture of PDX-derived PTCL-NOS lymphoma cells (PDX-IL2) with matched CAF (PDX-IL2-CAF). PDX-IL2-CAF improved PDX-IL2 cell survival specifically, while mismatched PDX-CAF from four other PTCL PDX did not. RNA-seq of matched PDX-IL2-CAF showed upregulation of "transcription", "DNA replication", "RNA POL2” and the "CDK7 complex". This suggests that CDK7, by enabling transcription initiation, is required to maintain the educated phenotype. We showed that CDK7 inhibition decreases oncogene-induced transcription, causing cytotoxicity in PTCL cells. To determine if CDK7 is required for establishing cell state-induced transcription in CAF, enabling crosstalk with lymphoma cells (LyC), we administered low-dose (10 mg/kg per day) of the covalently selective CDK7 inhibitor YKL5124 to PDX-IL2 bearing mice and conducted RNA-seq and proteomics of isolated LyC and CAF at two time points. Ligand-receptor analysis identified CXCL12 in CAF and CXCR4 in LyC as the main CDK7-dependent crosstalk interaction. In CAF, the acquisition of "cytokine signaling" and "immune cell modulation" phenotypes was CDK7 dependent. Functional validation using cytokine profiling of YKL5124-treated PDX-IL2-CAF showed decreased secretion of pro-inflammatory cytokines IL6, CCL2, ICAM1, and CXCL1. Meanwhile, LyCs showed activation of pathways likely to compensate for decreased CDK7-dependent transcription including "stress response," "RNA processing" and "protein synthesis" with upregulation of ALYREF and EIF4E, previously identified as XPO1 targets. Because this may represent new therapeutic vulnerabilities, we conducted a viability screening of PDX-IL2 CAF and LyC co-cultures with a library of 40 clinical-phase compounds targeting these compensatory mechanisms. Two drugs, targeting XPO1 (Selinexor) and translation (Omacetaxine), were the most potent combination with YKL5124. These are being tested in PTCL-NOS PDX mice.

Conclusion: CDK7 activity in both lymphoma and CAF is required to establish functional pro-tumoral crosstalk that can be exploited therapeutically.

Research funding declaration: Funding for this work was provided by the Leukemia and Lymphoma Society and the U.S. NIH–NCI.

Keywords: microenvironment; aggressive T-cell non-Hodgkin lymphoma; targeting the tumor microenvironment

No potential sources of conflict of interest.