Nano Today, Journal Year: 2025, Volume and Issue: 62, P. 102700 - 102700
Published: Feb. 28, 2025
Language: Английский
Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(4), P. 272 - 285
Published: Jan. 9, 2024
Language: Английский
Citations
18
Nature Chemical Biology, Journal Year: 2024, Volume and Issue: 20(10), P. 1272 - 1281
Published: May 23, 2024
Language: Английский
Citations
18
Nature Biotechnology, Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 18, 2025
Abstract Understanding the diverse dynamic behaviors of individual RNA molecules in single cells requires visualizing them at high resolution real time. However, single-molecule live-cell imaging unmodified endogenous has not yet been achieved a generalizable manner. Here, we present fluorescence situ hybridization (smLiveFISH), robust approach that combines programmable RNA-guided, RNA-targeting CRISPR–Csm complex with multiplexed guide RNAs for direct and efficient visualization range cell types, including primary cells. Using smLiveFISH, track native NOTCH2 MAP1B transcripts living identify two distinct localization mechanisms cotranslational translocation mRNA endoplasmic reticulum directional transport toward periphery. This method potential to unlock principles governing spatiotemporal organization health disease.
Language: Английский
Citations
4
Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 11, 2025
MicroRNA (miRNA) is involved in the genesis viand development of colorectal cancer. The vivo imaging miRNA at tumor sites essential for understanding its role cancer pathology and therapeutic target identification. However, achieving accurate hindered by low abundance miRNAs cells nonspecific signal leakage normal tissues. Here, we report a multivariate-gated catalytic hairpin assembly (CHA) nanosensor specific amplified microRNA-21 (miR-21) human tissues to reveal underlying miR-21-associated molecular mechanism. endogenous glutathione exogenous near-infrared design combination with CHA probes improves strength miR-21 reduces background interference. enables vivo, signal-to-background ratios are 1.6-fold compared traditional methods. With assistance designed nanosensor, achieve preliminary identification from clinical surgical resection samples. overexpressed found suppress core mismatch repair recognition protein mutS homologue 2 DNA damage inhibit efficacy strategy probe design, which combines activation methods amplification system, applicable disease-relevant mechanism research.
Language: Английский
Citations
3
Nature Methods, Journal Year: 2025, Volume and Issue: unknown
Published: March 17, 2025
Advances in spatial profiling technologies are providing insights into how molecular programs influenced by local signaling and environmental cues. However, cell fate specification tissue patterning involve the interplay of biochemical mechanical feedback. Here we develop a computational framework that enables joint statistical analysis transcriptional signals context transcriptomics. To illustrate application utility approach, use transcriptomics data from developing mouse embryo to infer forces acting on individual cells, these results identify mechanical, morphometric gene expression signatures predictive compartment boundaries. In addition, geoadditive structural equation modeling modules predict behavior cells an unbiased manner. This is easily generalized other contexts, generic scheme for exploring biomolecular cues tissues. The authors present leverages force inference enable analyses between transcriptomic state.
Language: Английский
Citations
2
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: April 5, 2024
Abstract Background Spatial transcriptomics ( ST ) technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within their spatial tissue context. The rapid evolution methods, each with unique features, presents a challenge in selecting most appropriate technology for specific research objectives. Here, we compare four imaging-based methods – RNAscope HiPlex, Molecular Cartography, MERFISH/Merscope, Xenium together sequencing-based (Visium). These were used to study cryosections medulloblastoma extensive nodularity (MBEN), chosen its distinct microanatomical features. Results Our analysis reveals that automated well suited delineating intricate MBEN microanatomy, capturing cell-type-specific transcriptome profiles. We devise approaches sensitivity specificity different attributes guide method selection based on aim. Furthermore, demonstrate how reimaging slides after can markedly improve cell segmentation accuracy integrate additional transcript protein readouts expand analytical possibilities depth insights. Conclusions This highlights key distinctions between various provides set parameters evaluating performance. findings aid informed choice delineate enhancing resolution breadth transcriptomic analyses, thereby contributing advancing applications solid research.
Language: Английский
Citations
8
Nanoscale Horizons, Journal Year: 2024, Volume and Issue: 9(9), P. 1390 - 1416
Published: Jan. 1, 2024
Molecular disassembly is pioneering a new route to refined diagnostic and therapeutic solutions. This approach breaks down self-assembled molecules, offering enhanced precision efficiency in various bio-oriented applications.
Language: Английский
Citations
6
Transcription, Journal Year: 2023, Volume and Issue: 14(3-5), P. 127 - 145
Published: April 16, 2023
Single-cell sequencing of RNA (scRNA-seq) has advanced our understanding cellular heterogeneity and signaling in developmental biology disease. A large number complementary assays have been developed to profile transcriptomes individual cells, also combination with other readouts, such as chromatin accessibility or antibody-based analysis protein surface markers. As scRNA-seq technologies are advancing fast, it is challenging establish robust workflows up-to-date protocols that best suited address the range research questions. Here, we review techniques from mRNA end-counting total relation their specific features outline necessary sample preparation steps quality control measures. Based on experience dealing continuously growing portfolio perspective a central single-cell facility, aim provide guidance how can be automatized share coping continuous expansion techniques.
Language: Английский
Citations
16
Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(20), P. e101 - e101
Published: Oct. 9, 2023
N 6-methyladenosine (m6A) is an abundant RNA modification which plays critical roles in function and cellular physiology. However, our understanding of how m6A spatially regulated remains limited due to a lack methods for visualizing methylated transcripts interest cells. Here, we develop DART-FISH, method situ visualization specific sites target RNAs enables simultaneous detection both m6A-modified unmodified transcript copies. We demonstrate the ability DART-FISH visualize variety mRNAs across diverse cell types provide information on location stoichiometry at single-cell resolution. Finally, use reveal that not sufficient mRNA localization stress granules during oxidative stress. This technique provides powerful tool examining dynamics investigating individual
Language: Английский
Citations
14
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: April 14, 2024
Abstract When cells encounter environmental stress, they rapidly mount an adaptive response by switching from pro-growth to stress-responsive gene expression programs. It is poorly understood how selectively silence pre-existing, transcripts, yet efficiently translate transcriptionally-induced stress mRNA, and whether these transcriptional post-transcriptional responses are coordinated. Here, we show that following acute glucose withdrawal in S. cerevisiae, pre-existing mRNAs not first degraded halt protein synthesis, nor sequestered away P-bodies. Rather, their translation repressed through a sequence-independent mechanism differentiates between produced before after followed decay. Transcriptional induction of endogenous transcripts reporter during sufficient escape translational repression, while prior leads repression. Our results reveal timing-controlled coordination the nucleus cytoplasm ensuring rapid widescale reprogramming stress.
Language: Английский
Citations
6