IntLIM: integration using linear models of metabolomics and gene expression data

Abstract

Background: Integration of transcriptomic and metabolomic data improves functional interpretation of disease-related metabolomic phenotypes, and facilitates discovery of putative metabolite biomarkers and gene targets. For this reason, these data are increasingly collected in large (> 100 participants) cohorts, thereby driving a need for the development of user-friendly and open-source methods/tools for their integration. Of note, clinical/translational studies typically provide snapshot (e.g. one time point) gene and metabolite profiles and, oftentimes, most metabolites measured are not identified. Thus, in these types of studies, pathway/network approaches that take into account the complexity of transcript-metabolite relationships may neither be applicable nor readily uncover novel relationships. With this in mind, we propose a simple linear modeling approach to capture disease-(or other phenotype) specific gene-metabolite associations, with the assumption that co-regulation patterns reflect functionally related genes and metabolites.

Results: The proposed linear model, metabolite ~ gene + phenotype + gene:phenotype, specifically evaluates whether gene-metabolite relationships differ by phenotype, by testing whether the relationship in one phenotype is significantly different from the relationship in another phenotype (via a statistical interaction gene:phenotype p-value). Statistical interaction p-values for all possible gene-metabolite pairs are computed and significant pairs are then clustered by the directionality of associations (e.g. strong positive association in one phenotype, strong negative association in another phenotype). We implemented our approach as an R package, IntLIM, which includes a user-friendly R Shiny web interface, thereby making the integrative analyses accessible to non-computational experts. We applied IntLIM to two previously published datasets, collected in the NCI-60 cancer cell lines and in human breast tumor and non-tumor tissue, for which transcriptomic and metabolomic data are available. We demonstrate that IntLIM captures relevant tumor-specific gene-metabolite associations involved in known cancer-related pathways, including glutamine metabolism. Using IntLIM, we also uncover biologically relevant novel relationships that could be further tested experimentally.

Conclusions: IntLIM provides a user-friendly, reproducible framework to integrate transcriptomic and metabolomic data and help interpret metabolomic data and uncover novel gene-metabolite relationships. The IntLIM R package is publicly available in GitHub ( https://github.com/mathelab/IntLIM ) and includes a user-friendly web application, vignettes, sample data and data/code to reproduce results.

Keywords: Integration; Linear Modeling; Metabolomics; Transcriptomics.

Fig. 1

IntLIM defines phenotype-specific gene-metabolite pairs by uncovering gene-metabolite pairs that show an association in one phenotype (e.g. tumors) and another or no association in another phenotype (e.g. non-tumors)

Fig. 2

Results of IntLIM applied to NCI-60 data. a Clustering of Spearman correlations of 1009 identified gene-metabolite pairs (16,188 genes and 220 metabolites, 57 cell lines) (FDR adjusted p-value of interaction coefficient < 0.10 with Spearman correlation difference of > 0.5) in “BPO” and leukemia NCI-60 cell lines. Examples of two gene-metabolite associations with significant differences: (b) FSCN1 and malic acid (FDR adj. p-value = 0.082, BPO Spearman Correlation = − 0.75, Leukemia Spearman Correlation = 0.94), (c) DLG4 and leucine (FDR adj. p-value = 0.0399, BPO Spearman Correlation = 0.78, Leukemia Spearman Correlation = − 0.93)

Fig. 3

Results of IntLIM applied to a breast cancer datase. a Clustering of Spearman correlations of 2842 identified gene-metabolite pairs(18,228 genes and 379 metabolites, with 61 tumor and 47 non-tumor samples) (FDR-adjusted p-value of interaction coefficient < 0.05 with Spearman correlation difference of > 0.5) in tumor and non-tumor tissue from breast cancer tissue. b GPT2 association with 2-hydroxyglutarate (FDR-adjusted p-value = 0.046, Normal Spearman Correlation = − 0.11, Tumor Spearman Correlation = 0.40). c Lack of association between 2-hydroxygutarate with MYC (FDR adj. p-value = 0.90, Normal Spearman Correlation = − 0.20, Tumor Spearman Correlation = 0.04)