Wong, L. S. | Search bioRxiv

bioRxiv2025

Binding of inhibitory checkpoints to CD18 in cis hinders anti-cancer immune responses

SIRP is an inhibitory receptor on macrophages that limits phagocytosis and anti-tumor activity of macrophages by "trans" interacting with CD47 on tumor cells. Herein, we found that a large component of SIRPs inhibitory function occurred independently of CD47-binding and phosphatase signaling. This function resulted from a direct interaction between SIRP and CD18 ({beta}2 integrin) in "cis" at the surface of macrophages, involving SIRP amino acids distinct from those implicated in the SIRP-CD47 interaction. The cis interaction prevented activation of CD18, which is necessary for phagocytosis. Combined blockade of SIRP-CD18 and SIRP-CD47 was essential for maximizing phagocytosis and suppression of tumor growth in vivo. Similar cis interactions between CD18 and other inhibitory checkpoints, including PD-1, were also observed. Thus, in addition to mediating effects when engaged by ligands in trans, inhibitory checkpoints suppress immune cell activation through a mechanism targeting CD18 in cis. This dual mode of action should be considered when developing blockers of inhibitory checkpoints for immunotherapy. One-Sentence SummaryIn addition to being engaged in "trans" by ligands on tumor cells, inhibitory receptors, such as SIRP and PD-1, hinder anti-cancer immune responses by "cis" interacting with {beta}2 integrin CD18.

immunology↗

bioRxiv2025

Comprehensive benchmarking of methods for mutation calling in circulating tumor DNA

Detection of somatic mutations in cell-free DNA (cfDNA) is challenging due to low variant allele frequencies and pronounced DNA degradation. Here, we present a novel approach and resource for benchmarking of somatic variant calling algorithms in cfDNA samples from cancer patients. Using longitudinally collected cfDNA samples from colorectal and breast cancer patients, we identify patient-matched samples with high and ultra-low circulating tumor DNA (ctDNA) levels. These sample pairs, preserving patient-specific germline and somatic haematopoiesis variant backgrounds, were used to generate dilution series capturing characteristics of bona-fide cfDNA samples. To benchmark the accuracy and limit of detection of 9 somatic variant calling algorithms, we used deep Whole Genome Sequencing (WGS, 150x) and ultra-deep Whole Exome Sequencing (WES, 2,000x) to construct a reference set of [~]37,000 Single Nucleotide Variants and [~]58,000 Insertions/Deletions. We tested methods under variable ctDNA levels and depth of sequencing, generating guidelines for method choice depending on use case. Using a machine learning approach, we further evaluated the potential of fine-tuning individual variant callers, revealing features that may improve accuracy in cfDNA samples. Overall, we present a new resource for benchmarking of somatic variant calling methods in cfDNA, providing insights on method choice to realize the potential of liquid biopsies in precision oncology.

bioinformatics↗