Connective & soft tissue

Connective and soft tissues provide structural support, protection, cushioning and specialized interfaces between organs. This diverse group includes cartilage, adipose tissue, connective tissue coverings, peripheral nerves, and mesothelial and synovial tissues. Although their basic functions are conserved across mammals, species differ in tissue organization, extracellular matrix composition and relative proportions of specialized cell types. These differences, together with variation in anatomical sampling, may contribute to differences in tissue-level gene expression profiles.

The sampled tissues vary considerably between species, partly reflecting differences in anatomical accessibility and technical challenges in obtaining sufficient material of suitable quality for RNA sequencing. Adipose tissue is represented in all four mammalian species and in human, although samples originate from different anatomical depots. Brown adipose tissue is additionally sampled in macaque, rat and mouse, but not pig. Cartilage and synovial tissue are represented in all four mammalian species, whereas mesothelial tissue is available in macaque, pig and rat, with sampling in mouse limited by the small amount of accessible tissue. Meningeal tissues are represented by meninges in rat and dura mater in macaque and pig, while peripheral nerve samples are included in macaque, rat and pig.

For tissue specificity analysis, adipose tissue provides the main opportunity for direct comparisons with human RNA data, although differences between anatomical depots should be considered. The other tissue types are not represented in the human RNA dataset but provide valuable information about specialized connective and soft tissues across mammals. Human protein expression data for cartilage are additionally available through immunohistochemistry (IHC) in the HPA Tissue Resource. Importantly, the absence of a tissue from an individual species dataset often reflects difficulties in sampling or RNA quality control rather than the anatomical absence of that tissue.

Figure 1. Tissue sample overview and the hierarchy of grouped tissues representing connective & soft tissues

Comparative transcriptomics of the mammalian connective and soft tissues

The transcriptomic data is used to identify genes with elevated expression in individual tissues or groups of tissues, classified into three categories:

Tissue enriched: Genes with elevated expression in a single tissue compared with all other tissues.
Group enriched: Genes with elevated expression in a limited group of tissues compared with the remaining tissues.
Tissue enhanced: Genes with elevated expression in one or more tissues compared with the average expression across tissues (gap ratio ≥2)

Tissue specificity is evaluated at two levels: first, within each species using all available tissue types, and second, using only tissues that can be directly compared between the species and human. This distinction makes it possible to explore both tissue-specific expression within each species and the conservation of expression patterns across evolution.

The results can be explored for individual genes on the gene summary pages or searched to identify genes with specific expression patterns. To assess evolutionary conservation, pairwise overlap analysis compares each species individually with human, identifying genes that share the same tissue specificity classification in corresponding tissues and quantifying the extent of overlap between species.

Tissue	Species	Elevated	Human elevated overlap
Tissue	Species	Elevated	Complete overlap	Partial overlap
Adipose tissue	Macaque	287	5	43
	Mouse	314	1	30
	Rat	204	4	29
	Pig	117	5	24
Cartilage	Macaque	246	n/a	n/a
	Mouse	99	n/a	n/a
	Rat	173	n/a	n/a
	Pig	375	n/a	n/a
Dura mater	Macaque	43	n/a	n/a
Dura mater	Pig	78	n/a	n/a
Meninges	Rat	79	n/a	n/a
Mesothelial tissue	Macaque	161	n/a	n/a
	Rat	37	n/a	n/a
	Pig	86	n/a	n/a
Synovial tissue	Macaque	30	n/a	n/a
	Mouse	69	n/a	n/a
	Rat	40	n/a	n/a
	Pig	79	n/a	n/a
Vagus nerve	Macaque	74	n/a	n/a
	Rat	161	n/a	n/a
	Pig	150	n/a	n/a

Adipose tissue

Adipose tissue stores energy, provides insulation and cushioning, and produces signaling molecules involved in metabolism, inflammation and endocrine regulation. Samples from subcutaneous, visceral, orbital and brown adipose tissue represent different anatomical and functional subsets, with variation in adipocyte composition, metabolic activity and the proportions of immune and stromal cells. Although these differences may influence gene expression profiles, all adipose samples are grouped into a single main tissue type, adipose tissue, for the tissue specificity analysis.

Species coverage

Cartilage

Cartilage provides structural support and resistance to mechanical stress through a specialized extracellular matrix produced by chondrocytes. Its cellular density, matrix composition and thickness vary with anatomical location, species and mechanical loading, particularly between articular cartilage and elastic cartilage such as that found in the ear.

Species coverage

Mesothelial tissue

Mesothelial tissue forms a thin cellular lining covering internal organs and body cavities, providing a protective, low-friction surface that facilitates organ movement. The sampled tissues include the pleura, covering the lungs and thoracic cavity; pericardium, surrounding the heart; and peritoneum, lining the abdominal cavity and covering abdominal organs. The representation of these structures varies between species, partly due to challenges in dissecting these thin membranes and obtaining sufficient material for RNA sequencing. For the tissue specificity analysis, the different samples are combined into one main tissue type, mesothelial tissue, although differences in anatomical origin and the proportions of mesothelial cells and underlying connective tissue may influence gene expression profiles.

Species coverage

Meninges

The meninges form protective connective tissue coverings around the brain and spinal cord and contribute to vascular support, immune surveillance and cerebrospinal fluid-associated functions. They consist of three layers, the dura mater, arachnoid mater and pia mater, which differ in their structural organization and cellular composition. The relative representation of these layers may vary between samples, influencing gene expression profiles.

Species coverage

Dura mater

The dura mater is the outermost and most fibrous layer of the meninges, providing mechanical protection and structural support for the central nervous system. It contains dense collagen-rich connective tissue, blood vessels, fibroblasts and immune cells, with differences in thickness and vascular organization between species potentially contributing to variation in tissue-level gene expression.

Species coverage

Vagus nerve

The vagus nerve contains sensory and autonomic nerve fibres connecting the brainstem with internal organs, including the heart, lungs and digestive tract. Its overall functions are conserved across mammals, although differences in fibre composition, branching patterns and organ innervation may influence the relative abundance of neuronal and supporting cell populations.

Species coverage

Synovial tissue

Synovial tissue lines the inner surfaces of joint capsules and contributes to the production of synovial fluid, which lubricates joints and supports cartilage function. The collected samples represent a mixture of soft tissues from the joint region between adjacent bones, potentially including synovial membrane, tendons, ligaments and other connective tissue components. This heterogeneous composition should be considered when interpreting gene expression profiles, which may reflect a combination of joint-associated tissues rather than synovial cells alone.