Cordeiro, P. | Search bioRxiv

bioRxiv2025

Therapeutic Inducers of NK cell Killing (ThINKK)-induced NK cell cytotoxicity against childhood acute lymphoblastic leukemia: unraveling the dual role of TRAIL leads to the establishment of an efficacy biomarker

BackgroundTherapeutic Inducers of Natural Killer cell Killing (ThINKK) represent a novel class of immunotherapy designed to enhance the graft-versus-leukemia effect of hematopoietic stem cell transplantation in pediatric patients with high-risk or relapse leukemia. Our previous work identified high expression of TRAIL as a key signature of Natural Killer (NK) cell stimulation by ThINKK. In this study, we aim to elucidate the mechanisms underlying acute lymphoblastic leukemia (ALL) killing by ThINNK-stimulated NK cells and to identify predictive sensitivity markers of this innovative approach. MethodsWe performed NK cell cytotoxic assays using a panel of genetically diverse ALL cell lines and patients samples. Gene deletion and gene enforced expression in sensitive or resistant cell lines were performed to demonstrate the role of TRAIL-receptors expression and death receptor signaling pathway in ALL cell death induced by ThINKK-stimulated NK cells. These findings were further validated through the analysis of primary patients samples and transcriptomic profiling of a cohort of 320 ALL patients from the CHU Sainte-Justine. ResultsWe found that ALL sensitivity to ThINKK-stimulated NK cell killing was independent of their genetic background or their HLA expression. In addition, our data revealed the dual role of TRAIL: first, a strong NK cell activating receptor that induced rapid killing of ALL expressing TRAIL-R2, and second, a death-receptor ligand inducing ALL apoptosis following sustained engagement with its receptors. The transcriptomic analysis of ALL patients samples indicated that TRAIL-R2 and TRAIL-R1 are widely expressed across ALL subtypes and are not downregulated at relapse. ConclusionThese findings support the use of TRAIL receptor expression as a biomarker of sensitivity to ThINKK immunotherapy and establish a mechanistic framework to guide patient stratification and therapeutic optimization.

immunology↗

bioRxiv2023

Epigenomic signatures as circulating and predictive biomarkers in sarcomatoid renal cell carcinoma

Renal cell carcinoma with sarcomatoid differentiation (sRCC) is associated with poor survival and heightened response to immune checkpoint inhibitors (ICIs). Two major barriers to improving outcomes for sRCC are (1) a limited understanding of its gene regulatory programs and (2) difficulty identifying sarcomatoid differentiation on tumor biopsies due to spatial heterogeneity. To address these challenges, we characterized the epigenomic landscape of sRCC by profiling 107 epigenomic libraries in tissue and plasma samples from 50 patients with RCC and healthy volunteers. We identified highly recurrent epigenomic reprogramming, as assessed by histone modifications and DNA methylation, that distinguishes sRCC from non-sarcomatoid RCC. Computational analysis of RCC epigenomic profiles and CRISPRa experiments implicated the transcription factor FOSL1 in activating sRCC-associated gene regulatory programs. Analysis of two randomized clinical trials identified FOSL1 expression as a predictive biomarker of response to ICIs in RCC. Finally, we demonstrate that epigenomic signatures of sRCC are detectable in patient plasma, establishing an approach for blood-based diagnosis of this clinically important phenotype. These findings provide a framework for the discovery and non-invasive detection of epigenomic correlates of tumor histology via liquid biopsy.

genomics↗