Bayesian Joint Modeling of Single-Cell Expression Data and Bulk Spatial Transcriptomic Data

Jinge Yu, Qiuyu Wu and Xiangyu Luo ()
Additional contact information
Jinge Yu: Renmin University of China
Qiuyu Wu: Renmin University of China
Xiangyu Luo: Renmin University of China

Statistics in Biosciences, 2023, vol. 15, issue 3, No 10, 719-733

Abstract: Abstract Single-cell RNA-sequencing (scRNA-seq) enables gene expression profiling at single-cell resolution, but it loses the spatial information of cells for solid tissues during the tissue dissociation step before sequencing. In contrast, bulk spatial transcriptomics (ST) methods can measure the expression of spatially organized spots in solid tissues, but as a spot comprises dozens of cells, ST expression levels are averaged signals and lack cellular resolution. Joint analysis of these two complementary data types provides the opportunity to recover the spatial patterns of cell types and obtain the cellular enrichment of spots. However, there is a lack of unified statistical methods to achieve this goal. This study develops a Bayesian statistical method named BEATS to jointly model scRNA-seq data and bulk ST data from a common sample in the presence of cellular and spatial heterogeneity. BEATS can simultaneously (a) discover cell types, where cells in a cell type share mean expression profiles; (b) identify spot regions, where a region is a set of spots with the same cellular compositions; and (c) estimate cell-type proportions for each spot region. The Bayesian posterior inference is performed through a hybrid Markov chain Monte Carlo sampling algorithm. Extensive simulation studies and application to datasets on pancreatic ductal adenocarcinoma tissues demonstrate the practical utility of BEATS.

Keywords: scRNA-seq; Spatial transcriptomics; Integrative analysis; Deconvolution; Heterogeneity (search for similar items in EconPapers)
Date: 2023
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
http://link.springer.com/10.1007/s12561-021-09308-4 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:spr:stabio:v:15:y:2023:i:3:d:10.1007_s12561-021-09308-4

Ordering information: This journal article can be ordered from
http://www.springer.com/journal/12561

DOI: 10.1007/s12561-021-09308-4

Access Statistics for this article

Statistics in Biosciences is currently edited by Hongyu Zhao and Xihong Lin

More articles in Statistics in Biosciences from Springer, International Chinese Statistical Association
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().