SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression. Issue 3 (4th April 2022)

• Record Type: Journal Article
• Authors: Liu, Yusong; Wang, Tongxin; Duggan, Ben; Sharpnack, Michael; Huang, Kun; Zhang, Jie; Ye, Xiufen; Johnson, Travis S
• Is Part Of: Briefings in bioinformatics. Volume 23:Issue 3(2022)
• Publication Date: 2022-04-04
• Subjects: spatial transcriptomics -- imputation -- two-factor expression smoothing -- k-nearest neighbors -- tissue region partition -- pancreatic ductal adenocarcinoma -- dorsolateral prefrontal cortex -- high-grade serous ovarian cancer; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbac116
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: High-dimensional, localized ribonucleic acid (RNA) sequencing is now possible owing to recent developments in spatial transcriptomics (ST). ST is based on highly multiplexed sequence analysis and uses barcodes to match the sequenced reads to their respective tissue locations. ST expression data suffer from high noise and dropout events; however, smoothing techniques have the promise to improve the data interpretability prior to performing downstream analyses. Single-cell RNA sequencing (scRNA-seq) data similarly suffer from these limitations, and smoothing methods developed for scRNA-seq can only utilize associations in transcriptome space (also known as one-factor smoothing methods). Since they do not account for spatial relationships, these one-factor smoothing methods cannot take full advantage of ST data. In this study, we present a novel two-factor smoothing technique, spatial and pattern combined smoothing (SPCS), that employs the k -nearest neighbor (kNN) technique to utilize information from transcriptome and spatial relationships. By performing SPCS on multiple ST slides from pancreatic ductal adenocarcinoma (PDAC), dorsolateral prefrontal cortex (DLPFC) and simulated high-grade serous ovarian cancer (HGSOC) datasets, smoothed ST slides have better separability, partition accuracy and biological interpretability than the ones smoothed by preexisting one-factor methods. Source code of SPCS is provided in Github (https://github.com/Usos/SPCS ).