Xinning Shan

Cell-cell communication is fundamental to tissue organization, homeostasis, and disease progression. Recent advances in spatial transcriptomics provide unprecedented opportunities to systematically characterize ligand-receptor interactions directly within intact tissues. However, robust inference of spatial ligand-receptor interactions remains challenging because intrinsic features of spatial transcriptomics data, including spatial autocorrelation, variation in total molecular counts, and measurement errors, can induce spurious spatial co-expression and lead to inflated false-positive results. Most existing methods do not adequately account for these confounding factors, limiting the reliability of inferred cellular communication. Here, we present CONCISE, a statistical method for spatially constrained co-expression and ligand-receptor interaction inference that jointly models spatial autocorrelation, variation in total molecular counts, measurement errors, and spatial proximity constraints. CONCISE combines efficient moment-based parameter estimation with analytical hypothesis testing, enabling fast and statistically rigorous inference without restrictive distributional assumptions. Through extensive simulations, real-data permutation experiments, and biologically motivated negative-control analyses across different spatial transcriptomics platforms, we show that most existing methods presented inflated false-positive rates, whereas CONCISE achieved well-calibrated inference, robust false-positive control, and improved detection power. Application of CONCISE to high-resolution MERFISH and CosMx datasets from intestinal inflammation and non-small cell lung cancer further highlights its biological utility in disease contexts. CONCISE uncovered inflammation-associated fibroblast-specific interactions during intestinal inflammation and delineated complex tumor-immune and tumor-stromal signaling networks within the tumor microenvironment.

Cell-type-specific gene co-expression networks are widely used to characterize gene relationships. Although many methods have been developed to infer such co-expression networks from single-cell data, the lack of consideration of false positive control in many evaluations and downstream analyses may lead to incorrect conclusions because higher reproducibility, higher functional coherence, and a larger overlap with known biological networks may not imply better performance if the false positives are not well controlled. In this study, we systematically compared two distinct criteria for selecting correlated gene pairs from single-cell data, p-value versus correlation strength. We found that the use of p-values instead of correlation strength is more robust for both selecting meaningful gene pairs and for the fair benchmarking of co-expression estimation methods. To make this approach universally applicable, we extended and validated a simulation method that can efficiently and reliably generate empirical p-values for co-expression estimation methods that do not have corresponding or well-controlled p-values. Furthermore, we demonstrated that a fair comparison of the estimation methods requires adjusting for the varying number of gene pairs they identified and accounting for the inherent expression-level biases within ground truth biological networks. Our study provides a practical guide for researchers to select reliable correlated gene pairs for downstream study and establishes a more rigorous standard for the evaluation and comparison of gene co-expression network estimation methods.

Cell-type-specific gene co-expression networks are widely used to characterize gene relationships. Although many methods have been developed to infer such co-expression networks from single-cell data, the lack of consideration of false positive control in many evaluations and downstream analyses may lead to incorrect conclusions because higher reproducibility, higher functional coherence, and a larger overlap with known biological networks may not imply better performance if the false positives are not well controlled. In this study, we systematically compared two distinct criteria for selecting correlated gene pairs from single-cell data, p-value versus correlation strength. We found that the use of p-values instead of correlation strength is more robust for both selecting meaningful gene pairs and for the fair benchmarking of co-expression estimation methods. To make this approach universally applicable, we extended and validated a simulation method that can efficiently and reliably generate empirical p-values for co-expression estimation methods that do not have corresponding or well-controlled p-values. Furthermore, we demonstrated that a fair comparison of the estimation methods requires adjusting for the varying number of gene pairs they identified and accounting for the inherent expression-level biases within ground truth biological networks. Our study provides a practical guide for researchers to select reliable correlated gene pairs for downstream study and establishes a more rigorous standard for the evaluation and comparison of gene co-expression network estimation methods.

The inference of gene co-expressions from microarray and RNA-sequencing data has led to rich insights on biological processes and disease mechanisms. However, the bulk samples analyzed in most studies are a mixture of different cell types. As a result, the inferred co-expressions are confounded by varying cell type compositions across samples and only offer an aggregated view of gene regulations that may be distinct across different cell types. The advancement of single cell RNA-sequencing (scRNA-seq) technology has enabled the direct inference of co-expressions in specific cell types, facilitating our understanding of cell-type-specific biological functions. However, the high sequencing depth variations and measurement errors in scRNA-seq data present significant challenges in inferring cell-type-specific gene co-expressions, and these issues have not been adequately addressed in the existing methods. We propose a statistical approach, CS-CORE, for estimating and testing cell-type-specific co-expressions, built on a general expression-measurement model that explicitly accounts for sequencing depth variations and measurement errors in the observed single cell data. Systematic evaluations show that most existing methods suffer from inflated false positives and biased co-expression estimates and clustering analysis, whereas CS-CORE has appropriate false positive control, unbiased co-expression estimates, good statistical power and satisfactory performance in downstream co-expression analysis. When applied to analyze scRNA-seq data from postmortem brain samples from Alzheimer’s disease patients and controls and blood samples from COVID-19 patients and controls, CS-CORE identified cell-type-specific co-expressions and differential co-expressions that were more reproducible and/or more enriched for relevant biological pathways than those inferred from other methods.