Muscle and vascular tissue

Muscle and vascular tissues support circulation, movement and the mechanical functions of internal organs. These tissues include cardiac, skeletal and smooth muscle, as well as blood vessels, each with specialized structural and contractile properties. Although their fundamental functions are conserved across mammals, differences in anatomy, muscle fibre composition and physiological demands may contribute to variation in gene expression.

For the tissue specificity analysis, samples are grouped into four main tissue types: heart muscle, blood vessels, skeletal muscle and smooth muscle. The sampled anatomical structures vary between species, partly due to technical challenges in obtaining sufficient material. For example, heart valve sampling was unsuccessful in rat.

Skeletal muscle is represented by samples from the thigh in macaque, pig and rat, while diaphragm samples are additionally available for rat and mouse. In mouse, the thigh muscle sample did not pass sequencing quality control, but the diaphragm provides an alternative representation of skeletal muscle, as it consists primarily of striated muscle fibres. However, differences in muscle fibre composition and physiological function between the diaphragm and limb muscles should be considered when interpreting cross-species expression patterns. Smooth muscle is represented by intestinal and uterine samples in all four species.

Figure 1. Tissue sample overview and the hierarchy of grouped tissues representing muscle and vascular tissues.

Comparative transcriptomics of the muscle and vascular tissue

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
Blood vessel	Macaque	148	0	65
	Mouse	169	0	16
	Rat	70	0	4
	Pig	126	0	25
Heart muscle	Macaque	286	44	114
	Mouse	454	30	134
	Rat	305	42	101
	Pig	266	47	89
Skeletal muscle	Macaque	427	68	244
	Mouse	331	24	224
	Rat	452	51	269
	Pig	343	54	229
Smooth muscle	Macaque	98	2	4
	Mouse	174	1	3
	Rat	122	1	3
	Pig	95	1	6

Heart

Heart wall

The heart wall contains cardiac muscle cells that generate the contractions required to circulate blood throughout the body. Cardiomyocyte size, nucleation and the relative proportions of muscle, connective tissue and vascular cells differ between mammals, with adult rodent cardiomyocytes more commonly binucleated than human cardiomyocytes.

Heart atrium

The atria receive blood returning to the heart and pass it to the ventricles. Their muscle contractions contribute to ventricular filling, and atrial cells also release hormones involved in fluid balance.

Heart valve

Heart valves ensure that blood flows in the correct direction through the heart. Their flexible connective-tissue leaflets open and close in response to pressure changes during each heartbeat

Species coverage

Blood vessels

Aorta

The aorta is the largest artery and contains elastic fibres and smooth muscle cells that allow it to withstand and distribute the pressure generated by the heart. Its wall thickness, elastic lamellar organization and relative proportions of extracellular matrix components vary with species and body size.

Peripheral vasculature

Peripheral blood vessels regulate blood distribution, vascular resistance and exchange between the circulation and surrounding tissues. Although arteries and veins differ in their structure and cellular composition, they were not always possible to distinguish during dissection, and histological examination revealed that some samples contained both vessel types. Arterial and venous samples were therefore combined into a single tissue category, peripheral blood vessels, for the tissue specificity analysis.

Species coverage

Skeletal muscle

Skeletal muscle consists of multinucleated muscle fibres responsible for voluntary movement and contains different fibre types specialized for endurance or rapid contraction. The proportions of slow oxidative and fast glycolytic fibres vary between species and anatomical locations, reflecting differences in locomotion, posture and metabolic demands. Skeletal muscle samples were collected from the thigh in macaque, pig and rat, while diaphragm samples were additionally collected in rat and mouse. In mouse, the thigh muscle sample did not pass sequencing quality control, leaving the diaphragm as the only representation of skeletal muscle. Although the diaphragm also consists of striated skeletal muscle, differences in fibre composition and physiological function compared with limb muscles may influence cross-species gene expression comparisons.

Species coverage

Smooth muscle

Smooth muscle controls involuntary contractions in organs such as the intestine, uterus and blood vessels. The sampled smooth muscle tissues originate from the intestine and uterus, where the muscle layers were manually separated from the surrounding tissue. However, complete separation is challenging, and samples may contain residual cells from the tissue of origin, resulting in some overlap in gene expression profiles between smooth muscle and the corresponding intestinal or uterine tissues.