Auditing the Editor: A Review of Key Translational Issues in Epigenetic Editing

Currently, most advances in site-specific epigenetic editing for human use are concentrated in basic research, yet, there is considerable interest to translate this technology beyond the bench. This review highlights recent developments with epigenetic editing technology in comparison with the canonical CRISPR-Cas genome editing, as well as the epistemic and ethical considerations with preemptive translation of epigenetic editing into clinical or commercial use in humans. Key considerations in safety, equity, and access to epigenetic editing are highlighted, with a spotlight on the ethical, legal, and social issues of this technology in the context of global health equity

Enzyme‐free photothermally amplified fluorescent immunosorbent assay (PAFISA) for sensitive cytokine quantification

Abstract Cytokine monitoring has attracted great attention due to its significance in the diagnosis and treatment of many diseases, such as tumors, microbial infections, and immunological diseases. Enzyme‐linked immunosorbent assay (ELISA) is one of the most popular methods in cytokine detection, ascribing to the lavish signal amplification methods in the ELISA platform. In addition to classical enzymes, other signal amplifiers such as fluorescent probes, artificial nano‐enzymes, and photothermal reagents have been applied to reduce the detection limit and produce more sensitive ELISA kits. Due to the accumulative effect of heat, photothermal reagents are promising materials in the signal amplification of ELISA. However, the lack of efficient photothermal generation material at an aggregate scale may delay the further development of this area. In this contribution, based on an efficient organic photothermal aggregate material, an enzyme‐free photothermally amplified fluorescent immunosorbent assay system consisting of an assay microfluidic chip and detecting platform was developed. The photothermal nanoparticles with highly efficient photothermal conversion by harvesting energy via excited‐state intramolecular motions and enlarging molar absorptivity were successfully prepared. The detection concentration at 50 pg/mL of interleukin‐2 was achieved, realizing a signal improvement of detection limits by 20‐fold compared to that of previously reported photothermal ELISA. The microscopic imaging integrated with plane sweeping technology provided high spatial resolution and precision, indicating the potential of achieving high throughput profiling at the microscale. Moreover, as an alternative excitation source, light‐emitting diode not only provided a more affordable and miniaturized detection system but also revealed the great feasibility of intramolecular motion‐induced photothermy nanoparticles for biological analyses

Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope

Abstract The rapid emergence of spatial transcriptomics (ST) technologies is revolutionizing our understanding of tissue spatial architecture and biology. Although current ST methods, whether based on next-generation sequencing (seq-based approaches) or fluorescence in situ hybridization (image-based approaches), offer valuable insights, they face limitations either in cellular resolution or transcriptome-wide profiling. To address these limitations, we present SpatialScope, a unified approach integrating scRNA-seq reference data and ST data using deep generative models. With innovation in model and algorithm designs, SpatialScope not only enhances seq-based ST data to achieve single-cell resolution, but also accurately infers transcriptome-wide expression levels for image-based ST data. We demonstrate SpatialScope’s utility through simulation studies and real data analysis from both seq-based and image-based ST approaches. SpatialScope provides spatial characterization of tissue structures at transcriptome-wide single-cell resolution, facilitating downstream analysis, including detecting cellular communication through ligand-receptor interactions, localizing cellular subtypes, and identifying spatially differentially expressed genes

RNA splicing programs define tissue compartments and cell types at single-cell resolution

The extent splicing is regulated at single-cell resolution has remained controversial due to both available data and methods to interpret it. We apply the SpliZ, a new statistical approach, to detect cell-type-specific splicing in \u3e110K cells from 12 human tissues. Using 10x data for discovery, 9.1% of genes with computable SpliZ scores are cell-type-specifically spliced, including ubiquitously expressed genes MYL6 and RPS24. These results are validated with RNA FISH, single-cell PCR, and Smart-seq2. SpliZ analysis reveals 170 genes with regulated splicing during human spermatogenesis, including examples conserved in mouse and mouse lemur. The SpliZ allows model-based identification of subpopulations indistinguishable based on gene expression, illustrated by subpopulation-specific splicing of classical monocytes involving an ultraconserved exon in SAT1. Together, this analysis of differential splicing across multiple organs establishes that splicing is regulated cell-type-specifically

Designed Multifunctional Spider Silk Enabled by Genetically Encoded Click Chemistry

Spider silk is recognized for its exceptional mechanical properties and biocompatibility, making it a versatile platform for developing functional materials. In this study, a modular functionalization strategy for recombinant spider silk is presented using SpyTag/SpyCatcher chemistry, a prototype of genetically encoded click chemistry. The approach involves AlphaFold2-aided design of SpyTagged spider silk coupled with bacterial expression and biomimetic spinning, enabling the decoration of silk with various SpyCatcher-fusion motifs, such as fluorescent proteins, enzymes, and cell-binding ligands. The silk threads can be coated with a silica layer using silicatein, an enzyme for silicification, resulting in a hybrid inorganic–organic 1D material. The threads installed with RGD or laminin cell-binding ligands lead to enhanced endothelial cell attachment and proliferation. These findings demonstrate a straightforward yet powerful approach to 1D protein materials.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.ImPhys/Maresca grou