Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

SK Longo, MG Guo, AL Ji, PA Khavari - Nature Reviews Genetics, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but
does not capture their spatial distribution nor reveal local networks of intercellular …

Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

ZA Clarke, TS Andrews, J Atif, D Pouyabahar… - Nature protocols, 2021 - nature.com
Single-cell transcriptomics can profile thousands of cells in a single experiment and identify
novel cell types, states and dynamics in a wide variety of tissues and organisms. Standard …

[HTML][HTML] clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng… - The innovation, 2021 - cell.com
Functional enrichment analysis is pivotal for interpreting high-throughput omics data in life
science. It is crucial for this type of tool to use the latest annotation databases for as many …

Human microglial state dynamics in Alzheimer's disease progression

N Sun, MB Victor, YP Park, X Xiong, AN Scannail… - Cell, 2023 - cell.com
Altered microglial states affect neuroinflammation, neurodegeneration, and disease but
remain poorly understood. Here, we report 194,000 single-nucleus microglial transcriptomes …

Spatially resolved multi-omics highlights cell-specific metabolic remodeling and interactions in gastric cancer

C Sun, A Wang, Y Zhou, P Chen, X Wang… - Nature …, 2023 - nature.com
Mapping tumor metabolic remodeling and their spatial crosstalk with surrounding non-tumor
cells can fundamentally improve our understanding of tumor biology, facilitates the …

scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data

F Yang, W Wang, F Wang, Y Fang, D Tang… - Nature Machine …, 2022 - nature.com
Annotating cell types on the basis of single-cell RNA-seq data is a prerequisite for research
on disease progress and tumour microenvironments. Here we show that existing annotation …

[HTML][HTML] Single-cell RNA sequencing reveals a pro-invasive cancer-associated fibroblast subgroup associated with poor clinical outcomes in patients with gastric …

X Li, Z Sun, G Peng, Y Xiao, J Guo, B Wu, X Li… - Theranostics, 2022 - ncbi.nlm.nih.gov
Background: The protumor activities of cancer-associated fibroblasts (CAFs) suggest that
they are potential therapeutic targets for the treatment of cancer. The mechanism of CAF …

[HTML][HTML] ACE2 expression in pancreas may cause pancreatic damage after SARS-CoV-2 infection

F Liu, X Long, B Zhang, W Zhang, X Chen… - Clinical …, 2020 - ncbi.nlm.nih.gov
Methods A public database was used to explore the expression and distribution of ACE2 in
normal pancreases. We also retrospectively analyzed patients diagnosed with COVID-19 …

Single-cell analysis reveals transcriptomic remodellings in distinct cell types that contribute to human prostate cancer progression

S Chen, G Zhu, Y Yang, F Wang, YT Xiao, N Zhang… - Nature cell …, 2021 - nature.com
Prostate cancer shows remarkable clinical heterogeneity, which manifests in spatial and
clonal genomic diversity. By contrast, the transcriptomic heterogeneity of prostate tumours is …

The allergy mediator histamine confers resistance to immunotherapy in cancer patients via activation of the macrophage histamine receptor H1

H Li, Y Xiao, Q Li, J Yao, X Yuan, Y Zhang, X Yin… - Cancer cell, 2022 - cell.com
Reinvigoration of antitumor immunity remains an unmet challenge. Our retrospective
analyses revealed that cancer patients who took antihistamines during immunotherapy …