Exploring tissue architecture using spatial transcriptomics

A Rao, D Barkley, GS França, I Yanai - Nature, 2021 - nature.com
Deciphering the principles and mechanisms by which gene activity orchestrates complex
cellular arrangements in multicellular organisms has far-reaching implications for research …

Clinical and translational values of spatial transcriptomics

L Zhang, D Chen, D Song, X Liu, Y Zhang… - … and Targeted Therapy, 2022 - nature.com
The combination of spatial transcriptomics (ST) and single cell RNA sequencing (scRNA-
seq) acts as a pivotal component to bridge the pathological phenomes of human tissues with …

Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions

A Andersson, L Larsson, L Stenbeck, F Salmén… - Nature …, 2021 - nature.com
In the past decades, transcriptomic studies have revolutionized cancer treatment and
diagnosis. However, tumor sequencing strategies typically result in loss of spatial …

Unraveling B cell trajectories at single cell resolution

D Morgan, V Tergaonkar - Trends in immunology, 2022 - cell.com
During adaptive immunity, B cells differentiate either into memory B cells or plasma cells and
produce antibodies against foreign antigens to fight infection. Additionally, they behave as …

Seamless integration of image and molecular analysis for spatial transcriptomics workflows

J Bergenstråhle, L Larsson, J Lundeberg - BMC genomics, 2020 - Springer
Background Recent advancements in in situ gene expression technologies constitute a new
and rapidly evolving field of transcriptomics. With the recent launch of the 10x Genomics …

Tumor cell invasion in glioblastoma

A Vollmann-Zwerenz, V Leidgens, G Feliciello… - International journal of …, 2020 - mdpi.com
Glioblastoma (GBM) is a particularly devastating tumor with a median survival of about 16
months. Recent research has revealed novel insights into the outstanding heterogeneity of …

Integrated spatial multiomics reveals fibroblast fate during tissue repair

DS Foster, M Januszyk, KE Yost… - Proceedings of the …, 2021 - National Acad Sciences
In the skin, tissue injury results in fibrosis in the form of scars composed of dense
extracellular matrix deposited by fibroblasts. The therapeutic goal of regenerative wound …

Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium

S Vickovic, D Schapiro, K Carlberg, B Lötstedt… - Communications …, 2022 - nature.com
The inflamed rheumatic joint is a highly heterogeneous and complex tissue with dynamic
recruitment and expansion of multiple cell types that interact in multifaceted ways within a …

CellDART: cell type inference by domain adaptation of single-cell and spatial transcriptomic data

S Bae, KJ Na, J Koh, DS Lee, H Choi… - Nucleic acids …, 2022 - academic.oup.com
Deciphering the cellular composition in genome-wide spatially resolved transcriptomic data
is a critical task to clarify the spatial context of cells in a tissue. In this study, we developed a …

Distinct disease-specific Tfh cell populations in 2 different fibrotic diseases: IgG4-related disease and Kimura disease

R Munemura, T Maehara, Y Murakami, R Koga… - Journal of Allergy and …, 2022 - Elsevier
Background How T follicular (Tfh) cells contribute to many different B-cell class-switching
events during T-cell–dependent immune responses has been unclear. Diseases with …