Decoding the tumor microenvironment with spatial technologies

LA Walsh, DF Quail - Nature Immunology, 2023 - nature.com
Visualization of the cellular heterogeneity and spatial architecture of the tumor
microenvironment (TME) is becoming increasingly important to understand mechanisms of …

IL-1β+ macrophages fuel pathogenic inflammation in pancreatic cancer

N Caronni, F La Terza, FM Vittoria, G Barbiera… - Nature, 2023 - nature.com
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with high resistance to
therapies. Inflammatory and immunomodulatory signals co-exist in the pancreatic tumour …

De novo detection of somatic mutations in high-throughput single-cell profiling data sets

F Muyas, CM Sauer, JE Valle-Inclán, R Li… - Nature …, 2024 - nature.com
Abstract Characterization of somatic mutations at single-cell resolution is essential to study
cancer evolution, clonal mosaicism and cell plasticity. Here, we describe SComatic, an …

Spatial transcriptomics in development and disease

R Zhou, G Yang, Y Zhang, Y Wang - Molecular Biomedicine, 2023 - Springer
The proper functioning of diverse biological systems depends on the spatial organization of
their cells, a critical factor for biological processes like shaping intricate tissue functions and …

Multi-omic profiling of clear cell renal cell carcinoma identifies metabolic reprogramming associated with disease progression

J Hu, SG Wang, Y Hou, Z Chen, L Liu, R Li, N Li… - Nature Genetics, 2024 - nature.com
Clear cell renal cell carcinoma (ccRCC) is a complex disease with remarkable immune and
metabolic heterogeneity. Here we perform genomic, transcriptomic, proteomic, metabolomic …

Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing

J Cao, Z Zheng, D Sun, X Chen, R Cheng, T Lv… - Nature …, 2024 - nature.com
Spatial transcriptomics technologies with high resolution often lack high sensitivity in mRNA
detection. Here we report a dendrimeric DNA coordinate barcoding design for spatial RNA …

Domain generalization enables general cancer cell annotation in single-cell and spatial transcriptomics

Z Zhong, J Hou, Z Yao, L Dong, F Liu, J Yue… - Nature …, 2024 - nature.com
Single-cell and spatial transcriptome sequencing, two recently optimized transcriptome
sequencing methods, are increasingly used to study cancer and related diseases. Cell …

Single‐cell profiling identifies distinct hormonal, immunologic, and inflammatory signatures of endometriosis‐constituting cells

S Shin, YJ Chung, SW Moon, EJ Choi… - The Journal of …, 2023 - Wiley Online Library
Endometriosis consists of ectopic endometrial epithelial cells (EEECs) and ectopic
endometrial stromal cells (EESCs) mixed with heterogeneous stromal cells. To address how …

Mesenchymal-like tumor cells and myofibroblastic cancer-associated fibroblasts are associated with progression and immunotherapy response of clear cell renal cell …

G Davidson, A Helleux, YA Vano, V Lindner, A Fattori… - Cancer Research, 2023 - AACR
Immune checkpoint inhibitors (ICI) represent the cornerstone for the treatment of patients
with metastatic clear cell renal cell carcinoma (ccRCC). Despite a favorable response for a …

Single-cell RNA sequencing in cancer research: discovering novel biomarkers and therapeutic targets for immune checkpoint blockade

B Sun, Z Xun, N Zhang, K Liu, X Chen, H Zhao - Cancer Cell International, 2023 - Springer
Immune checkpoint blockade (ICB) has become a promising strategy in treating advanced
cancers, providing significant survival benefits for patients with various cancer types …