Leveraging inter-individual transcriptional correlation structure to infer discrete signaling mechanisms across metabolic tissues
Authors: Zhou Mingqi , Tamburini Ian J. , Van Cassandra , Molendijk Jeffrey , Nguyen Christy M , Chang Ivan Yao-Yi , Johnson Casey , Velez Leandro M. , Cheon Youngseo , Yeo Reichelle X. , Bae Hosung , Le Johnny , Larson Natalie , Pulido Ron , Filho Carlos , Jang Cholsoon , Marazzi Ivan , Justice Jamie N. , Pannunzio Nicholas , Hevener Andrea , Sparks Lauren M. , Kershaw Erin E. , Nicholas Dequina , Parker Benjamin , Masri Selma , Seldin Marcus 
Published: December 2023

Inter-organ communication is a vital process to maintain physiologic homeostasis, and its dysregulation contributes to many human diseases. Beginning with the discovery of insulin over a century ago, characterization of molecules responsible for signal between tissues has required careful and elegant experimentation where these observations have been integral to deciphering physiology and disease. 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. For example, physiologic dissection of the actions of soluble proteins such as proprotein convertase subtilisin/kexin type 9 (
PCSK9
) and glucagon-like peptide 1 (
GLP1
) have yielded among the most promising therapeutics to treat cardiovascular disease and obesity, respectively
1–4
. A major obstacle in the characterization of such soluble factors is that defining their tissues and pathways of action requires extensive experimental testing in cells and animal models. 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
5–9
. 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 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
) as well as 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-

D

erived

C

orrelations

A

cross
T
issues (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.