Abstract

Applying spatial transcriptomics (ST) to explore a vast amount of formalin-fixed paraffin-embedded (FFPE) archival cancer tissues has been highly challenging due to several critical technical issues. In this work, we optimised ST protocols to generate unprecedented spatial gene expression data for FFPE skin cancer. Skin is among the most challenging tissue types for ST due to its fibrous structure and a high risk of RNAse contamination. We evaluated tissues collected from ten years to two years ago, spanning a range of tissue qualities and complexity. Technical replicates and multiple patient samples were assessed. Further, we integrated gene expression profiles with pathological information, revealing a new layer of molecular information. Such integration is powerful in cancer research and clinical applications. The data allowed us to detect the spatial expression of non-coding RNAs. Together, this work provides important technical perspectives to enable the applications of ST on archived cancer tissues.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

* https://stlearn.readthedocs.io/en/latest/

Details

Title
Benchmarking robust spatial transcriptomics approaches to capture the molecular landscape and pathological architecture of archived cancer tissues
Author
Vo, Tuan; Jones, Kahli; Yoon, Sohye; Lam, Pui Yeng; Yung-Ching Kao; Zhou, Chenhao; Prakrithi, P; Crawford, Joanna; Walters, Shaun; Gupta, Ishaa; Soyer, H Peter; Khosrotehrani, Kiarash; Stark, Mitchell S; Nguyen, Quan
University/institution
Cold Spring Harbor Laboratory Press
Section
New Results
Publication year
2023
Publication date
Feb 13, 2023
Publisher
Cold Spring Harbor Laboratory Press
ISSN
2692-8205
Source type
Working Paper
Language of publication
English
ProQuest document ID
2775839792
Copyright
© 2023. This article is published under http://creativecommons.org/licenses/by/4.0/ (“the License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.