Biology subjects

Brosens, E.

Publications and source records attributed to Brosens, E..

5 recordsLinked to original sources

bioRxiv2025

Novel biomarkers in mutation-specific gene profiles highlight the involvement of COL9A3 in cancer cell plasticity in uveal melanoma

UM is a deadly ocular malignancy with well-described genetic alterations that predict disease outcome. However, our current understanding of the biological underpinnings of high-risk uveal melanoma progression remains relatively limited. On the basis of RNA expression profiles, we identified 12 novel biomarkers associated with high-risk UM, with protein expression validation of the 2 top markers RBFOX2 and COL9A3. Moreover, we investigated the functional contribution of COL9A3 via its overexpression in low-risk and high-risk UM cell lines. Our data suggest that COL9A3 enhances cell motility and cell proliferation and alters morphology specifically in high-risk UM cells. Furthermore, zebrafish xenograft studies revealed improved cell dissemination in a low-risk UM cell line upon overexpression of COL9A3, whereas a high-risk UM cell line remained under wild-type conditions. Interestingly, RNA sequencing revealed a high-stress profile in high-risk UM cell lines overexpressing COL9A3 and suggested the upregulation of plasticity markers, such as CD44, Nestin, EZH2, ABCB5, PAX3 and CD166, as a coping mechanism. These markers are known as differentiation markers during the development of melanocyte biogenesis and are implicated in plasticity in other high-risk cancers. The relationship between COL9A3 and plasticity was validated by multiplex immunohistochemistry of FFPE tissue, which demonstrated colocalization of COL9A3, CD44 and Nestin. BAP1mut-UM samples presented higher levels of COL9A3, CD44 and Nestin expression than EIF1AXmut- or SF3B1mut UM samples did. A positive correlation between COL9A3 and Nestin expression in triple-positive cells, regardless of the UM subtype, was observed. Together, our data suggest that COL9A3 is a novel high-risk biomarker that may be involved in UM cell plasticity and is most prevalent in BAP1mut UM.

cancer biology↗

bioRxiv2025

Transcriptional regulators FOXD1 and RBFOX2 contribute to metastatic capacity in BAP1mut uveal melanoma

Uveal melanoma is the most prevalent primary intraocular cancer, with a significant metastatic risk. This risk is dependent on the genetic drivers. Secondary mutations in EIF1AX, SF3B1 and BAP1 correlate with clinical outcomes and are recognized for their distinct transcriptomic and epigenetic profiles. Previously, we identified 480 genes involved in the development of ocular melanocytes. Top ranking genes RBFOX2 and FOXD1 were significantly associated with BAP1 UM and were independently correlated to poor progression. However, it is uncertain whether either RBFOX2 or FOXD1 have biological contribution to disease progression or are solely indicative. This study investigates if and how these high-risk associated transcription regulators FOXD1 and RBFOX2 could influence tumor progression through knock-out and overexpression models. Our results indicate that loss of RBFOX2 affects cell morphology, attachment and proliferation, particularly in BAP1neg cells. Additionally, both RBFOX2 and FOXD1 contribute to tumor growth and dissemination in zebrafish xenografts. Loss of either RBFOX2 or FOXD1 reduced tumor volume and cell dissemination, with the greatest effects seen in BAP1neg cells. Overexpression models demonstrated different morphological and invasive behavior depending on the genetic background, suggesting complex roles in a context dependent fashion. Overexpression of RBFOX2 did not alter BAP1pos cells yet made BAP1neg cells more aggressive in vitro and in vivo. This study underscores the influence of RBFOX2 and FOXD1 as important factors for UM progression.

cancer biology↗

bioRxiv2022

ChILL & DisCO to discover competitive, connective and allosteric Nanobodies that modulate the SOS1-RAS protein-protein interactions and tune the nucleotide exchange rate

Protein-protein interactions (PPIs) are central in cell metabolism but research tools for the structural and functional characterization of these PPIs are often missing. Here we introduce novel and broadly applicable immunization (Cross-link PPIs and immunize llamas, ChILL) and selection strategies (Display and co-selection, DisCO) for the discovery of diverse Nanobodies that either stabilize or disrupt PPIs in a single experiment. We applied ChILL and DisCO to identify competitive, connective or fully allosteric Nanobodies that inhibit or facilitate the formation of the SOS1*RAS complex and modulate the nucleotide exchange rate on this pivotal GTPase in vitro and RAS signalling in cellulo. One of these connective Nanobodies fills a cavity that was previously identified as the binding pocket for a series of therapeutic lead compounds. The long complementarity-determining region (CDR3) that penetrates this binding pocket serves as an innovative pharmacophore for extending the repertoire of potential leads.

bioengineering↗

bioRxiv2019

Abnormal vertebral patterns in genetically heterogeneous deceased fetuses and neonates: evidence of selection against variations

ObjectiveTo assess the vertebral pattern in a cohort of deceased fetuses and neonates, and to study the possible impact of DNA Copy Number Variations (CNVs) in coding regions and/or disturbing enhancers on the development of the vertebral pattern.\n\nMethodRadiographs of 445 fetuses and infants, deceased between 2009 and 2015, were assessed. Terminations of pregnancies, stillbirths and neonatal deaths were included. Patients were excluded if the vertebral pattern could not be determined. Copy number profiles of 265 patients were determined using single nucleotide polymorphism array.\n\nResults274/374 patients (73.3%) had an abnormal vertebral pattern. Cervical ribs were present in 188/374 (50.3%) and were significantly more common in stillbirths (69/128 (53.9%)) and terminations of pregnancies (101/188 (53.7%)), compared to live births (18/58, 31.0%, p = 0.006). None of the rare CNVs were recurrent or overlapped candidate genes for vertebral patterning.\n\nConclusionThe presence of an abnormal vertebral pattern, particularly in the cervical region, could be a sign of disruption at critical, highly interactive and conserved stages of embryogenesis. The vertebral pattern might provide valuable information regarding fetal and neonatal outcome. CNV analyses did not identify a mutual genetic cause for the occurrence of vertebral patterning abnormalities, indicating genetic heterogeneity.

evolutionary biology↗

bioRxiv2019

Models for infantile hypertrophic pyloric stenosis development in patients with esophageal atresia

Patients born with esophageal atresia (EA) have a 30 times higher prevalence of infantile hypertrophic pyloric stenosis (IHPS). This makes sense from a developmental perspective as both the esophagus and the pyloric sphincter are foregut derived structures. EA and IHPS are variable features in several (monogenetic) syndromes. This, and twin and familial studies, indicates a genetic component for both conditions as single entities. We hypothesized that genetic defects, disturbing foregut morphogenesis, are responsible for this combination of malformations. Non-genetic factors could also contribute, as mice exposed to Adriamycin develop EA and in utero diethylstilbestrol exposure is associated with EA.\n\nWe investigated the copy number profiles and protein coding variants of 15 patients with both EA and IHPS. As all parents were unaffected, we first considered dominant (de novo) or recessive inheritance models but could not identify putatively deleterious mutations or recessive variants. We did identify inherited variants in genes either known to be involved in EA or IHPS or important in foregut morphogenesis in all patients. Unfortunately, variant burden analysis did not show a significant difference with unaffected controls. However, the IHPS associated risk SNP rs1933683 had a significantly higher incidence (OR 3.29, p=0.009).\n\nAlthough the genetic variation in likely candidate genes as well as the predisposing locus near BARX1 (rs1933683) suggest a genetic component, it does not fully explain the abnormalities seen in these patients. Therefore, we hypothesize that a combination of high impact genetic, mechanical and environmental factors together can shift the balance to abnormal development.\n\nSummary statementInstead of one affected gene, the higher incidence of IHPS in EA patients is more likely the result of multiple (epi)genetic and environmental factors together shifting the balance to disease development.

genetics↗