Bone marrow & lymphoid tissues

Bone marrow and lymphoid tissues are central components of the hematopoietic and immune systems, supporting blood cell production, immune cell development and the coordination of immune responses. Although these functions are conserved across mammals, differences in the anatomical organization, cellular composition and relative development of lymphoid organs may contribute to variation in gene expression profiles.

Bone marrow and the major lymphoid organs, including the thymus, lymph nodes and spleen, are represented across all four mammalian species, although their anatomical organization and cellular composition differ. For example, pig lymph nodes have a distinctive inverted organization, while rodents have particularly well-defined splenic marginal zones. Additional lymphoid structures, such as tonsils, are not present in rodent and only sampled in macaque and pig. The lymphoid tissues are combined into one main tissue type, for the tissue specificity analysis, while bone marrow is analysed separately. Expression patterns in individual organs can still be explored at the sample level, and corresponding human RNA data are available for bone marrow and lymphoid tissues.

Peripheral blood mononuclear cells (PBMCs) are additionally available for macaque, but not for pig, rat or mouse. Human PBMC expression data are available in the HPA, providing a complementary reference for comparisons of circulating immune cell populations.

Figure 1. Tissue sample overview and the hierarchy of grouped tissues representing Bone marrow & lymphoid tissues

Comparative transcriptomics of the bone marrow & lymphoid 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
Blood, PBMC	Macaque	0	n/a	n/a
Bone marrow	Macaque	63	3	2
	Mouse	581	122	172
	Rat	473	96	140
	Pig	96	22	22
Lymphoid tissue	Macaque	442	144	206
	Mouse	634	178	221
	Rat	588	157	204
	Pig	567	130	221

Bone marrow

Bone marrow is the primary site of blood cell production and contains hematopoietic stem cells, developing blood cells and specialized stromal populations. The distribution of active red marrow and fatty yellow marrow differs with age, species and skeletal location, potentially influencing the proportions of hematopoietic and adipose cells in tissue samples.

Species coverage

Lymphoid tissues

Thymus

The thymus supports T-cell development and selection through interactions between immature lymphocytes and specialized thymic epithelial cells. Its basic organization is conserved across mammals, but differences in lobulation, cellular composition and age-related involution may influence tissue-level gene expression profiles.

Lymph node

Lymph nodes filter lymph and provide specialized compartments for the activation and organization of immune responses. In humans, macaques, rats and mice, lymph nodes generally have an outer cortex containing B-cell follicles, deeper T-cell-rich regions and a central medulla. In contrast, pig lymph nodes have a distinctive inverted organization, with lymphoid follicles located more centrally and medullary structures towards the periphery. These differences may influence the distribution and relative abundance of immune cell populations in tissue samples.

Species coverage

Spleen

The spleen filters blood, removes ageing erythrocytes and supports immune responses through its red and white pulp compartments. The relative development of these compartments varies between species, with rodents having particularly well-defined marginal zones and specialized macrophage populations, while pigs have a more prominent blood-storage function and greater development of contractile structures. These differences may contribute to variation in the proportions of immune cells, erythrocytes and vascular components in bulk tissue expression profiles.

Tonsil

Tonsils are collections of lymphoid tissue associated with the upper respiratory and digestive tracts, contributing to immune surveillance at mucosal surfaces. Humans and macaques have well-developed tonsillar structures, while pigs possess a different arrangement of tonsillar tissues. Rats and mice lack conventional palatine tonsils but have other forms of mucosa-associated lymphoid tissue, including nasal-associated lymphoid tissue. These anatomical differences should be considered when comparing lymphoid tissue representation across species.

Peripheral blood mononuclear cells (PBMCs)

PBMCs comprise circulating lymphocytes and monocytes, providing a representation of immune cell populations in peripheral blood rather than solid lymphoid organs. Their relative cellular composition varies between species and with age, immune status and environmental exposure, potentially influencing bulk gene expression profiles. In the mammalian dataset, PBMCs are available only for macaque, with corresponding human data available in the HPA (Visit the immune cell resource).