Biology subjects

Zuin, J.

Publications and source records attributed to Zuin, J..

3 recordsLinked to original sources

bioRxiv2023

Epitope Engineered Human Haematopoietic Stem Cells are Shielded from CD123-targeted Immunotherapy

Targeted eradication of transformed or otherwise dysregulated cells using monoclonal antibodies (mAb), antibody-drug conjugates (ADC), T cell engagers (TCE) or chimeric antigen receptor (CAR) cells is very effective for haematologic diseases. Unlike the breakthrough progress achieved for B cell malignancies, there is a pressing need to find suitable antigens for immunotherapy of myeloid malignancies. CD123, the interleukin-3 (IL-3) receptor alpha-chain, is highly expressed in various haematological malignancies, including acute myeloid leukaemia (AML) and blastic plasmacytoid dendritic cell neoplasm (BPDCN). However, shared expression of CD123 on healthy haematopoietic stem and progenitor cells (HSPCs) bears the risk for extensive myelotoxicity upon targeted depletion. Here, we demonstrate that rationally designed, epitope-engineered HSPCs were completely shielded from CD123-targeted immunotherapy but remained fully functional while CD123-deficient HSPCs displayed a competitive disadvantage. Thus, molecularly shielded HSPCs could allow tumor-selective targeted immunotherapy and in parallel enable rebuilding a fully functional haematopoietic system. We envision that this approach is broadly applicable to many targets and cells, could render hitherto undruggable targets accessible to immunotherapy and will allow continued posttransplant immunotherapy, for instance to treat minimal residual disease (MRD) or be used as a salvage therapy. Since the function of the engineered targets is preserved, multiplexed molecular shielding could also enable targeted combination immunotherapies to address tumor heterogeneity. More generally, epitope shielding will be applicable for replacement of other cell types including the many immune cells which are currently being considered for engineered cellular therapies.

bioengineering↗

bioRxiv2022

Live-cell imaging and physical modeling reveal control of chromosome folding dynamics by cohesin and CTCF

Physical proximity between genomic sequences in mammalian chromosomes controls key biological processes such as transcriptional regulation and DNA repair. Yet it is currently unknown if chromosomal contacts are rare and stable or instead frequent and dynamic, and how they depend on the loop extrusion activity of cohesin or barriers such as CTCF. By imaging chromosomal locations at high spatial and temporal resolution over several hours in living cells, we show that sequences within topological associating domains (TADs) frequently come into physical proximity during the course of a cell cycle and remain close to each other only for a few minutes. Such contacts become nonetheless substantially longer and more frequent in the presence of convergent CTCF sites, resulting in a suppression of variability in chromosome folding in single cells across time. Supported by physical models of chromosome dynamics, our data additionally suggests that individual CTCF-anchored loops last around 10 minutes. The estimates of chromosomal contact dynamics in our study provide a novel quantitative framework to link chromosome structure to function and show that cohesin and CTCF stabilize otherwise highly dynamic chromosome structures to facilitate selected subsets of chromosomal interactions.

molecular biology↗

bioRxiv2021

Nonlinear control of transcription through enhancer-promoter interactions

Chromosome structure in mammals is thought to regulate transcription by modulating the three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated interactions and topologically associating domains (TADs)1-4. However, how chromosome interactions are actually translated into transcriptional outputs remains unclear. To address this question we use a novel assay to position an enhancer at a large number of densely spaced chromosomal locations relative to a fixed promoter, and measure promoter output and interactions within a genomic region with minimal regulatory and structural complexity. Quantitative analysis of hundreds of cell lines reveal that the transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a non-linear relationship. Mathematical modeling and validation against experimental data further provide evidence that nonlinearity arises from transient enhancer-promoter interactions being memorized into longer-lived promoter states in individual cells, thus uncoupling the temporal dynamics of interactions from those of transcription. This uncovers a potential mechanism for how enhancers control transcription across large genomic distances despite rarely meeting their target promoters, and for how TAD boundaries can block distal enhancers. We finally show that enhancer strength additionally determines not only absolute transcription levels, but also the sensitivity of a promoter to CTCF-mediated functional insulation. Our unbiased, systematic and quantitative measurements establish general principles for the context-dependent role of chromosome structure in long-range transcriptional regulation.

molecular biology↗