Journal Article

Leveraging inter-individual transcriptional correlation structure to infer discrete signaling mechanisms across metabolic tissues

Molendijk, Jeffrey, Tamburini, Ian, Cheon, Youngseo, Larson, Natalie, Parker, Benjamin L, Johnson, Casey, Nicholas, Dequina, Le, Johnny, Seldin, Marcus M, Zhou, Mingqi, Kershaw, Erin E, Pulido, Ron, Bae, Hosung, Pannunzio, Nicholas, Velez, Leandro M, Marazzi, Ivan, Sparks, Lauren, Jang, Cholsoon, Nascimento-Filho, Carlos HV, Masri, Selma, Hevener, Andrea L, Chang, Ivan Yao-Yi, Justice, Jamie, Van, Cassandra, Nguyen, Christy M, Yeo, Reichelle

2024

Overview

Inter-organ communication is a vital process to maintain physiologic homeostasis, and its dysregulation contributes to many human diseases. Given that circulating bioactive factors are stable in serum, occur naturally, and are easily assayed from blood, they present obvious focal molecules for therapeutic intervention and biomarker development. Recently, studies have shown that secreted proteins mediating inter-tissue signaling could be identified by ‘brute force’ surveys of all genes within RNA-sequencing measures across tissues within a population. Expanding on this intuition, we reasoned that parallel strategies could be used to understand how individual genes mediate signaling across metabolic tissues through correlative analyses of gene variation between individuals. Thus, comparison of quantitative levels of gene expression relationships between organs in a population could aid in understanding cross-organ signaling. Here, we surveyed gene-gene correlation structure across 18 metabolic tissues in 310 human individuals and 7 tissues in 103 diverse strains of mice fed a normal chow or high-fat/high-sucrose (HFHS) diet. Variation of genes such as FGF21, ADIPOQ, GCG, and IL6 showed enrichments which recapitulate experimental observations. Further, similar analyses were applied to explore both within-tissue signaling mechanisms (liver PCSK9 ) and genes encoding enzymes producing metabolites (adipose PNPLA2 ), where inter-individual correlation structure aligned with known roles for these critical metabolic pathways. Examination of sex hormone receptor correlations in mice highlighted the difference of tissue-specific variation in relationships with metabolic traits. We refer to this resource as g ene-derived correlations across tissues (GD-CAT) where all tools and data are built into a web portal enabling users to perform these analyses without a single line of code ( gdcat.org ). This resource enables querying of any gene in any tissue to find correlated patterns of genes, cell types, pathways, and network architectures across metabolic organs.