Spatial multi-omics analysis of the microenvironment in traumatic spinal cord injury: a narrative review DOI Creative Commons

Run Peng,

Liang Zhang, Yongqi Xie

et al.

Frontiers in Immunology, Journal Year: 2024, Volume and Issue: 15

Published: Aug. 29, 2024

Traumatic spinal cord injury (tSCI) is a severe to the central nervous system that categorized into primary and secondary injuries. Among them, local microenvironmental imbalance in caused by includes accumulation of cytokines chemokines, reduced angiogenesis, dysregulation cellular energy metabolism, dysfunction immune cells at site injury, which severely impedes neurological recovery from (SCI). In recent years, single-cell techniques have revealed heterogeneity multiple genomic, transcriptomic, proteomic, metabolomic levels after tSCI, further deepening our understanding mechanisms underlying tSCI. However, spatial information about tSCI microenvironment, such as cell location cell-cell interactions, lost these approaches. The application multi-omics technology can solve this problem combining data obtained immunohistochemistry multiparametric analysis reveal changes microenvironment different times SCI. review, we systematically review progress study SCI, including discuss potential future therapeutic strategies.

Language: Английский

Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics DOI
Adam Dorey, Stefan Howorka

Nature Chemistry, Journal Year: 2024, Volume and Issue: 16(3), P. 314 - 334

Published: March 1, 2024

Language: Английский

Citations

44
Multiscale biochemical mapping of the brain through deep-learning-enhanced high-throughput mass spectrometry DOI Creative Commons
Yuxuan Richard Xie, Daniel C. Castro, Stanislav S. Rubakhin

et al.

Nature Methods, Journal Year: 2024, Volume and Issue: 21(3), P. 521 - 530

Published: Feb. 16, 2024

Abstract Spatial omics technologies can reveal the molecular intricacy of brain. While mass spectrometry imaging (MSI) provides spatial localization compounds, comprehensive biochemical profiling at a brain-wide scale in three dimensions by MSI with single-cell resolution has not been achieved. We demonstrate complementary and mapping using MEISTER, an integrative experimental computational (MS) framework. Our framework integrates deep-learning-based reconstruction that accelerates high-mass-resolving MS 15-fold, multimodal registration creating three-dimensional (3D) distributions data integration method fitting cell-specific spectra to 3D datasets. imaged detailed lipid profiles tissues millions pixels large populations acquired from rat identified region-specific contents localizations lipids depending on both cell subpopulations anatomical origins cells. workflow establishes blueprint for future development multiscale characterization

Language: Английский

Citations

28
Enhancing aortic valve drug delivery with PAR2-targeting magnetic nano-cargoes for calcification alleviation DOI Creative Commons
Jinyong Chen, Tanchen Ren, Lan Xie

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 16, 2024

Abstract Calcific aortic valve disease is a prevalent cardiovascular with no available drugs capable of effectively preventing its progression. Hence, an efficient drug delivery system could serve as valuable tool in screening and potentially enhance therapeutic efficacy. However, due to the rapid blood flow rate associated stenosis lack specific markers, achieving targeted for calcific has proved be challenging. Here we find that protease-activated-receptor 2 (PAR2) expression up-regulated on plasma membrane osteogenically differentiated valvular interstitial cells. Accordingly, develop magnetic nanocarrier functionalized PAR2-targeting hexapeptide dual-active targeting delivery. We show nanocarriers deliver XCT790—an anti-calcification drug—to calcified under extra field navigation. demonstrate nano-cargoes consequently inhibit osteogenic differentiation cells, alleviate calcification high-fat diet-fed low-density lipoprotein receptor-deficient ( Ldlr −/− ) mouse model. This work combining PAR2- magnetic-targeting presents effective treating murine model, promising future clinical translation.

Language: Английский

Citations

18
Single-cell metabolic fingerprints discover a cluster of circulating tumor cells with distinct metastatic potential DOI Creative Commons
Wenjun Zhang, Feifei Xu, Yao Jiang

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: April 29, 2023

Abstract Circulating tumor cells (CTCs) are recognized as direct seeds of metastasis. However, CTC count may not be the “best” indicator metastatic risk because their heterogeneity is generally neglected. In this study, we develop a molecular typing system to predict colorectal cancer metastasis potential based on metabolic fingerprints single CTCs. After identification metabolites potentially related using mass spectrometry-based untargeted metabolomics, setup home-built single-cell quantitative spectrometric platform for target metabolite analysis in individual CTCs and use machine learning method composed non-negative matrix factorization logistic regression, divided into two subgroups, C1 C2, 4-metabolite fingerprint. Both vitro vivo experiments demonstrate that C2 subgroup closely associated with incidence. This an interesting report presence specific population distinct at level.

Language: Английский

Citations

30
Global Literature Analysis of Organoid and Organ‐on‐Chip Research DOI Creative Commons
Jun‐ya Shoji, Richard P. Davis, Christine L. Mummery

et al.

Advanced Healthcare Materials, Journal Year: 2023, Volume and Issue: 13(21)

Published: July 22, 2023

Organoids and cells in organ-on-chip platforms replicate higher-level anatomical, physiological, or pathological states of tissues organs. These technologies are widely regarded by academia, the pharmacological industry regulators as key biomedical developments. To map advances this emerging field, a literature analysis 16,000 article metadata based on quality-controlled text-mining algorithm is performed. The covers titles, keywords, abstracts categorized academic publications preprint databases published after 2010. identifies tracks 149 107 organs organ substructures modeled organoids organ-on-chip, respectively, stem cell sources, well 130 diseases, 16 groups organisms other than human mouse which organoid/organ-on-chip technology applied. illustrates changing diversity focus research captures its geographical distribution. downloadable dataset provided robust framework for researchers to interrogate with their own questions.

Language: Английский

Citations

29
The application and development of electron microscopy for three-dimensional reconstruction in life science: a review DOI
Jingjing Zhao, Xiaoping Yu,

Xuping Shentu

et al.

Cell and Tissue Research, Journal Year: 2024, Volume and Issue: 396(1), P. 1 - 18

Published: Feb. 28, 2024

Language: Английский

Citations

11
Nanopore: Emerging for detecting protein post-translational modifications DOI
Xinjia Zhao, Haijuan Qin, Mingliang Tang

et al.

TrAC Trends in Analytical Chemistry, Journal Year: 2024, Volume and Issue: 173, P. 117658 - 117658

Published: March 19, 2024

Language: Английский

Citations

10
In situ architecture of the intercellular organelle reservoir between epididymal epithelial cells by volume electron microscopy DOI Creative Commons

Xia Li,

Feng Qiao, Jiansheng Guo

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 15, 2025

Mammalian epididymal epithelial cells are crucial for sperm maturation. Historically, vacuole-like ultrastructures in were observed via transmission electron microscopy but undefined. Here, we utilize volume (vEM) to generate 3D reconstructions of and identify these vacuoles as intercellular organelle reservoirs (IORs) the lateral space (LIS), which contains protein aggregates, autophagosomes, lysosome-related organelles mitochondrial residues. Immunolabelling markers such P62, LC3, LAMP1 TOMM20 confirm findings. The IOR size or number varies across four regions decreases with age. Rab27a mutant mice exhibit reduced IORs caput epididymis a subfertility phenotype, suggesting involvement formation IORs. Furthermore, observe presence between intestinal besides epididymis. Amino acid transporters at edges suggest dynamic recycling. Our findings reveal that is an important structure critical turnover recycling outside limited self-degradation capabilities. Undefined have been observed. authors structures contain residues aggregates reservoir

Language: Английский

Citations

1
Activation of the Wnt/β-catenin signalling pathway enhances exosome production by hucMSCs and improves their capability to promote diabetic wound healing DOI Creative Commons
Liming Wang, Jun Chen, Jia Song

et al.

Journal of Nanobiotechnology, Journal Year: 2024, Volume and Issue: 22(1)

Published: June 26, 2024

Abstract Background The use of stem cell-derived exosomes (Exos) as therapeutic vehicles is receiving increasing attention. Exosome administration has several advantages over cell transplantation, thus making promising candidates for large-scale clinical implementation and commercialization. However, exosome extraction purification efficiencies are relatively low, heterogeneity high due to differences in culture conditions viability. Therefore, this study, we investigated a priming procedure enhance the production effects from human umbilical cord mesenchymal cells (hucMSCs). After preconditioning hucMSCs with agonists/inhibitors that target Wnt/β-catenin pathway, assessed both efficacy optimized context diabetic wound healing, hoping provide safer, more stable effective option application. Results Wnt signalling pathway agonist CHIR99021 increased by 1.5-fold without causing obvious changes characteristics or size particles. Further studies showed promoted facilitating exocytosis. This process was partly mediated SNAP25. To further explore whether changed cargo loaded into its effects, performed proteomic transcriptomic analyses primed control hucMSCs. results significantly upregulated expression proteins associated migration healing. Animal experiments confirmed that, compared hucMSC-derived exosomes, CHIR99021-pretreated (CHIR-Exos) accelerated healing mice, enhanced local collagen deposition, angiogenesis, reduced chronic inflammation. Subsequent vitro CHIR-Exos migration, inhibiting oxidative stress-induced apoptosis, preventing cycle arrest. Conclusions secretion hucMSCs, which Notably, treatment also exosomal levels resulting acceleration All these suggested pretreatment not only but improved efficacy, providing Graphical

Language: Английский

Citations

7
Full‐Length Single Protein Molecules Tracking and Counting in Thin Silicon Channels DOI Creative Commons

Shilo Ohayon,

Liran Taib,

Navneet C. Verma

et al.

Advanced Materials, Journal Year: 2024, Volume and Issue: 36(25)

Published: March 9, 2024

Emerging single-molecule protein sensing techniques are ushering in a transformative era biomedical research. Nevertheless, challenges persist realizing ultra-fast full-length sensing, including loss of molecular integrity due to fragmentation, biases introduced by antibodies affinity, identification proteoforms, and low throughputs. Here, method for parallel separation tracking is introduced, yielding multi-dimensional properties used their identification. Proteins tagged chemo-selective dual amino-acid specific labels electrophoretically separated mass/charge custom-designed thin silicon channel with subwavelength height. This approach allows analysis thousands individual proteins within few minutes motion during the migration. The power demonstrated quantifying cytokine panel host-response discrimination between viral bacterial infections. Moreover, it shown that two clinically-relevant splice isoforms Vascular endothelial growth factor (VEGF) can be accurately quantified from human serum samples. Being non-destructive compatible intact proteins, this opens up ways antibody-free single-protein molecule quantification.

Language: Английский

Citations

5