Biology subjects

Merks, J. H. M.

Publications and source records attributed to Merks, J. H. M..

5 recordsLinked to original sources

bioRxiv2026

Domain-resolved epitope mapping of B7-H3-targeting VHH-Fcs defines isoform-selective binders for antibody-drug conjugate development

The immune checkpoint molecule B7-H3 has emerged as one of the most actively pursued therapeutic targets in solid tumors, and multiple B7-H3-targeting antibody-drug conjugates have entered clinical evaluation. B7-H3 occurs as a 2Ig isoform carrying a single IgV-IgC domain pair and a predominant 4Ig isoform carrying two tandem pairs of near-identical sequence in their extracellular domains. Resolving which pair an antibody engages, or how antibodies distinguish the two isoforms, requires epitope mapping at residue level. Here we generated a panel of six B7-H3-targeting VHH-Fcs and characterized them by surface plasmon resonance, epitope binning, domain-resolved deep mutational scanning and receptor internalization, benchmarked against the clinically advanced antibodies ifinatamab, mirzotamab and vobramitamab. Most VHH-Fcs bound the membrane-proximal pair more tightly than the distal pair, and 4Ig 10- to 100-fold more tightly than 2Ig, whereas the three clinical antibodies showed no such discrimination. Displaying each domain pair independently on yeast identified the residues that account for this selectivity. Internalization varied several-fold among binders, including between VHH-Fc 620 and 636, which have near-identical footprints and comparable affinities. VHH-Fc 620 internalized most efficiently, also compared to ifinatamab, and was conjugated to exatecan through a protease-cleavable linker. The conjugate showed B7-H3-dependent cytotoxicity that scaled with B7-H3 cell surface density, though it was less potent than ifinatamab-exatecan. Affinity, epitope and internalization therefore behaved as independent characteristics rather than integrating to predict antibody-drug conjugate potency. Together, these results define the molecular basis for isoform-selective recognition of B7-H3 and identify VHH-Fc 620 as a starting point for isoform-selective targeting.

cancer biology↗

bioRxiv2026

Oncogenic fusions induce an extensive cancer-restricted cryptic proteome in Ewing sarcoma

How tumors generate a cryptic "dark" proteome absent from healthy tissues, and whether it can be reversibly activated, remains unclear. In Ewing sarcoma, all tumors are driven by EWSR1::ETS fusions, making it a tractable model to study dark proteome activation. Integrating matched transcriptomes, translatomes and proteomes from 48 patient tumors with long-read RNA sequencing, single-cell Ribo-seq, proteomics and immunopeptidomics in cell line models, we show that EWSR1::FLI1 acts as a reversible switch recurrently inducing hundreds of cancer-specific neoproteins. Many arise from canonical coding regions via intragenic transcription start sites, generating truncated or out-of-frame neoproteins. We uncover a fusion-dependent increase in ribosomal readthrough into poly(A) tails, generating a stable 80-amino-acid TRPM4 neoprotein that, despite lacking a stop codon, is the most abundant tumor-specific microprotein across patients. Proteomic, immunopeptidomic, and immunofluorescence analyses validate neoproteins as tumor-restricted antigens, revealing a therapeutically actionable cancer dark proteome controlled by one oncogenic fusion.

cancer biology↗

bioRxiv2025

Mechanisms of dexamethasone-induced bone toxicity in developing bone: a single-cell perspective

AbstractGlucocorticoids, such as dexamethasone, are essential for treating severe childhood conditions, including cancer, organ transplantation, and inflammatory disorders. However, their long-term use can impair bone development, posing risks to pediatric bone health, which is vital for lifelong skeletal integrity. A mechanistic insight on how glucocorticoids negatively impact bone could improve decision-making in patient care to improve the quality of life for pediatric cancer patients and survivors. In this study, we aimed to elucidate the molecular mechanisms underlying dexamethasone-induced bone toxicity in developing bones using single-cell transcriptomics. We treated skeletally immature C57BL/6JRj mice with dexamethasone for 28 days, and assessed the bone architecture with micro-computed tomography, and characterized bone and bone marrow cells from the femurs using single-cell RNA sequencing. Our findings revealed a marked reduction in osteoblast and chondrocyte cell populations and impaired function of pre-osteoblasts. Additionally, dexamethasone adversely affected B cell subsets, significantly depleting early B cell progenitors while allowing some further developed immature B cells to persist. These cellular changes were accompanied by reduced longitudinal bone growth, compromised bone architecture, and increased bone fragility at the highest doses of dexamethasone. Interestingly, unlike observations in adults, dexamethasone did not enhance osteoclast activity in our model. Overall, our study suggests that the adverse effects of dexamethasone on bone development are primarily due to its impact on osteoblastic, chondroblastic and B cell lineages, disrupting the critical signaling crosstalk between the cells necessary for bone development and hematopoiesis. Layman summaryGlucocorticoids, like dexamethasone, are vital for treating severe childhood illnesses but can harm bone development when used long-term. This study investigated how dexamethasone affects bone health in young mice. Using advanced techniques, we found that dexamethasone reduced key bone-building cells (osteoblasts and chondrocytes) and weakened their function. It also disrupted immune cell development in the bone marrow, especially early B cells. These changes led to weaker, more fragile bones without increasing bone breakdown, unlike in adults. The findings highlight the need to carefully balance treatment benefits and risks for children to protect their bone health and overall well-being.

cancer biology↗

bioRxiv2023

Complex structural variation is prevalent and highly pathogenic in pediatric solid tumors

BackgroundIn pediatric cancer, structural variants (SVs) and copy number alterations can contribute to cancer initiation and progression, and hence aid diagnosis and treatment stratification. The few studies into complex rearrangements have found associations with tumor aggressiveness or poor outcome. Yet, their prevalence and biological relevance across pediatric solid tumors remains unknown. ResultsIn a cohort of 120 primary tumors, we systematically characterized patterns of extrachromosomal DNA, chromoplexy and chromothripsis across five pediatric solid cancer types: neuroblastoma, Ewing sarcoma, Wilms tumor, hepatoblastoma and rhabdomyosarcoma. Complex SVs were identified in 56 tumors (47%) and different classes occurred across multiple cancer types. Recurrently mutated regions tend to be cancer-type specific and overlap with cancer genes, suggesting that selection contributes to shaping the SV landscape. In total, we identified potentially pathogenic complex SVs in 42 tumors that affect cancer driver genes or result in unfavorable chromosomal alterations. Half of which were known drivers, e.g. MYCN amplifications due to ecDNA and EWSR1::FLI1 fusions due to chromoplexy. Recurrent novel candidate complex events include chromoplexy in WT1 in Wilms tumors, focal chromothripsis with 1p loss in hepatoblastomas and complex MDM2 amplifications in rhabdomyosarcomas. ConclusionsComplex SVs are prevalent and pathogenic in pediatric solid tumors. They represent a type of genomic variation which currently remains unexplored. Moreover, carrying complex SVs seems to be associated with adverse clinical events. Our study highlights the potential for complex SVs to be incorporated in risk stratification or exploited for targeted treatments.

cancer biology↗

bioRxiv2022

Mesenchymal tumor organoid models recapitulate rhabdomyosarcoma subtypes

Rhabdomyosarcomas (RMS) are mesenchyme-derived tumors and the most common childhood soft tissue sarcomas. Treatment is intense, with a nevertheless poor prognosis for high-risk patients. Discovery of new therapies would benefit from additional preclinical models. Here we describe the generation of a collection of pediatric RMS tumor organoid (tumoroid) models comprising all major subtypes. For aggressive tumors, tumoroid models can often be established within four to eight weeks, indicating the feasibility of personalized drug screening. Molecular, genetic and histological characterization show that the models closely resemble the original tumors, with genetic stability over extended culture periods of up to six months. Importantly, drug screening reflects established sensitivities and the models can be modified by CRISPR/Cas9 with TP53 knockout in an embryonal RMS model resulting in replicative stress drug sensitivity. Tumors of mesenchymal origin can therefore be used to generate organoid models, relevant for a variety of preclinical and clinical research questions.

cancer biology↗