Biology subjects

Segers, H.

Publications and source records attributed to Segers, H..

3 recordsLinked to original sources

bioRxiv2025

Long-read single-cell genome, transcriptome and open chromatin profiling links genotype to phenotypes.

Current single-cell multiomics methods typically provide limited genomic information, constraining genotype-phenotype studies. To address this gap, we developed SPLONGGET (Single-cell Profiling of LONG-read Genome, Epigenome, and Transcriptome), which integrates 10X Genomics barcoding with Oxford Nanopore sequencing to simultaneously profile genome, chromatin accessibility, and full-length transcriptomes in thousands of single cells. By retaining all tagmentation fragments during library preparation, SPLONGGET delivers whole-genome coverage, supports target enrichment for effective single-cell genotyping, and remains backwards compatible with existing short-read workflows. SPLONGGET enables comprehensive calling of small variants, structural variants, and copy number alterations. Applying SPLONGGET to paediatric B-cell acute lymphoblastic leukaemia revealed clonal dynamics and the phenotypic effects of somatic variants. Notably, we evidence parallel evolution of immune escape variants with four distinct splice site mutations and loss of heterozygosity in the CAR T-cell therapy CD19 target. In conclusion, SPLONGGET enables integrated high-throughput analysis of genetic variation and molecular phenotypes using off-the-shelf kits, offering a timely and powerful tool to study genetically heterogeneous samples, such as tumours but also ageing normal tissues.

genomics↗

bioRxiv2024

Dual targeting of EZH2 and Histone Deacetylases in hematological malignancies promotes transcriptional and metabolic deregulation leading to ferroptosis

The methyltransferase EZH2 functions as the enzymatic component of the PRC2 complex, which deposits methyl groups on H3K27, leading to chromatin condensation and gene repression. Recent studies have shown that EZH2 can also act as a transcriptional modulator outside of the PRC2 complex and thus, independent of its methyltransferase activity. In this study, we first aimed to investigate the effects of EZH2 enzymatic inhibition versus protein degradation in hematological malignancies. We demonstrate that EZH2 degradation is more effective in blocking cellular proliferation compared to EZH2 enzymatic inhibition, and that EZH2 targeting upregulates the cholesterol biosynthesis pathway. Secondly, combined targeting of EZH2 and HDACs showed synergistic effects in a broader spectrum of hematological malignancies. Mechanistically, combined targeting of EZH2 and HDACs induced increased levels of H3K27 acetylation and strong upregulation of cholesterol biosynthesis. This leads to metabolic stress due to acetyl-CoA depletion, ultimately inducing ferroptotic cell death. Statement of significanceWe show that combined EZH2 and HDAC targeting is a promising therapeutic strategy for a broad spectrum of hematological malignancies. We uncover that EZH2 targeting induces upregulation of cholesterol biosynthesis, which is crucial for the synergistic effect with HDAC inhibition, ultimately leading to ferroptosis induction.

cancer biology↗

bioRxiv2024

Resistance to PSEN1-selective γ-secretase inhibitors in T-cell acute lymphoblastic leukemia

PSEN1-selective gamma-secretase inhibitors (GSI), such as MRK-560, are a potential option for the treatment of T-cell acute lymphoblastic leukemia (T-ALL) with NOTCH1 activating mutations, as these show less toxicity compared to broad-spectrum GSIs. However, an important challenge with targeted therapies for cancer treatment is the rapid development of drug resistance. We therefore investigated if PSEN1 mutations could confer resistance to MRK-560 in T-ALL. We performed a CRISPR-mediated mutagenesis screen in a T-ALL cell line to identify mutations leading to MRK-560 resistance and confirmed these findings in additional cell lines. We identified 3 types of resistance mutations. Mutations at the enzyme-drug interface directly disrupt the interaction of MRK-560 with PSEN1. Mutations at the enzyme-substrate interface cause a shift in relative binding affinities towards drug and/or substrate. The third resistance mechanism involves a mutation at the enzyme-substrate interface that hinders the entrance of MRK-560 to the binding pocket. These findings contribute to the understanding of the PSEN1-selectivity of MRK-560 and can help to design other PSEN1-selective GSIs to overcome resistance in cancer therapy.

cancer biology↗