Antoniolli, M. | bioRxiv Science

bioRxiv2026

Performance of the 10X Genomics Flex Single-Cell Sequencing Assay and its Application to Overcome Challenges in Clinical Trial Samples

BackgroundSingle-cell RNA sequencing (scRNA-seq) has become essential for understanding disease biology, yet its application in clinical trials is often limited by logistical challenges associated with the handling of biospecimens. Newly developed protocols aim to address these limitations by enabling profiling of fixed tissue. These new solutions need to be benchmarked against well-established protocols to assess their performance and suitability for clinical research. ResultsWe systematically compared different scRNA-seq protocols in a set of samples commonly analysed in clinical trials. The 10X Genomics GEM-X Flex Gene Expression assay (GEM-X Flex), in combination with the "chop-fix" preprocessing protocol, demonstrated superior performance to the standard GEM-X Universal Gene Expression solution when applied to both primary tumor tissue fragments and FFPE blocks. Moreover, the quality of the data obtained from GEM-X Flex applied to FFPE blocks outperformed that of single-nuclei RNA sequencing (snRNA-seq) from frozen biopsies, more robustly capturing the biological signals associated with the mechanism of action of a drug evaluated in an internal clinical trial. ConclusionsGEM-X Flex generates reliable, comprehensive transcriptomic data from both fixed tissue and clinical biopsies. By overcoming some of the limitations of fresh and frozen tissue analysis, this protocol offers a robust solution for the broad implementation of scRNA-seq in clinical trials.

genomics↗

bioRxiv2023

ARID1A Mutations Protect Follicular Lymphoma from FAS-dependent Immune Surveillance by Reducing RUNX3/ETS1-Driven FAS-Expression

The cell death receptor FAS and its ligand (FASLG) play crucial roles in the selection of B cells during the germinal center (GC) reaction. Failure to eliminate potentially harmful B cells via FAS can lead to lymphoproliferation and the development B cell malignancies. The classic form of follicular lymphoma (FL) is a prototypic GC-derived B cell malignancy, characterized by the t(14;18) (q32;q21)IGH::BCL2 translocation and overexpression of antiapoptotic BCL2. Additional alterations were shown to be clinically relevant, including mutations in ARID1A. ARID1A is part of the SWI/SNF nucleosome remodeling complex that regulates DNA accessibility ("openness"). However, the mechanism how ARID1A mutations contribute to FL pathogenesis remains unclear. We analyzed 151 FL biopsies of patients with advanced stage disease at initial diagnosis and found that ARID1A mutations were recurrent and mainly disruptive, with an overall frequency of 18%. Additionally, we observed that ARID1A mutant FL showed significantly lower FAS protein expression in the FL tumor cell population. Functional experiments in BCL2-translocated lymphoma cells demonstrated that ARID1A is directly involved in the regulation of FAS, and ARID1A loss leads to decreased FAS protein and gene expression. However, ARID1A loss did not affect FAS promotor openness. Instead, we identified and experimentally validated a previously unknown co-transcriptional complex consisting of RUNX3 and ETS1 that regulates FAS expression, and ARID1A loss leads to reduced RUNX3 promotor openness and gene expression. The reduced FAS levels induced by ARID1A loss rendered lymphoma cells resistant to both soluble and T cell membrane-anchored FASLG-induced apoptosis. In summary, we have identified a functionally and clinically relevant mechanism how FL cells can escape FAS-dependent immune surveillance, which may also impact the efficacy of T cell-based therapies, including bispecific antibodies and CAR T cells.

cancer biology↗