Abstract
Human embryonic stem cells (hESCs) derived from the pluripotent Inner cell mass (ICM) of the blastocyst are fundamental tools for understanding human development, yet are not identical to their tissue of origin. To investigate this divergence we compared the transcriptomes of genetically paired ICM and trophectoderm (TE) samples with three hESC lines: MAN1, HUES3 and HUES7 at similar passage. We generated inferred interactome networks unique to the ICM or TE using transcriptomic data, and defined a hierarchy of modules (highly connected regions with shared function). We compared network properties and the modular hierarchy and show that the three hESC lines had limited overlap with the ICM specific transcriptome (6%-12%). However, this overlap was enriched for network properties related to transcriptional activity in ICM (p=0.016); greatest in MAN1 compared to HUES3 (p=0.048) or HUES7 (p=0.012). The hierarchy of modules in the ICM interactome contained a greater proportion of MAN1 specific gene expression (46%) compared to HUES3 (28%) and HUES7 (25%) (p=9.0×10−4).
These findings show that traditional methods based on transcriptome overlap are not sufficient to identify divergence of hESCs from ICM. Our approach also provides a valuable approach to the quantification of differences between hESC lines.
Footnotes
Updated manuscript with further work supporting the original findings.
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121982
Glossary of Network Concepts
- Modular Hierarchy
- Biological networks form regions of higher connectivity than would be expected by chance, known as modules. Modules represent functionally related elements of a network and their relative influence in a system can be estimated by their centrality.
- Metanode
- The most central ten connected genes within a module.
- Connectivity
- The number of links existing between a given node and its neighbours. An increased connectivity is indicative of a gene which is involved in numerous processes.
- Community Centrality
- A measure of the relative ‘importance’ of a node, characterised by high connectivity or connections between areas of high connectivity.
- Bridgeness
- A property of a node in a network which sits between two areas of high connectivity, such that if removed, it would cause the separation of a single module into two. These nodes act as ‘bridges’ between modules and an increased bridgeness identifies a node which connects multiple modules.
- Party hub
- A node with multiple connections which, in a biological system, is thought to represent a gene with many active simultaneous interactions, such as protein complexes. It is characterised by a node which has a reduced bridgeness at a given centrality when compared to a date-hub.
- Date hub
- A node with multiple connections which, in a biological system, has non-concurrent interactions with other nodes. These are thought to represent transcription factors. It is characterised by a node which has an increased bridgeness at a given centrality when compared to a party-hub.
- Similarity Network Fusion
- A network approach which uses nearest neighbour relationships to combine datasets and identify regions of similarity within and between them. In the context of this manuscript, coherency between datasets represents genes whose expression patterns are conserved between cells derived from embryonic tissue and human embryonic stem cell lines.