The bone marrow-specific proteome

Bone marrow is the tissue in the interior cavities of bones, constituting approximately 4% of the total body mass of humans. The red marrow, which constitutes the hematopoietic component of bone marrow, is responsible for producing hematopoietic cells of all lineages, which subsequently use the bone marrow vasculature as a conduit to the body's systemic circulation. Transcriptome analysis shows that 62% (n=12358) of all human proteins (n=20090) are expressed in the bone marrow and 908 of these genes show an elevated expression in the bone marrow compared to other tissue types.

  • 908 elevated genes
  • 106 enriched genes
  • 165 group enriched genes
  • Bone marrow has most group enriched gene expression in common with lymphoid tissue


The bone marrow transcriptome

Transcriptome analysis of the bone marrow can be visualized with regard to the specificity and distribution of transcribed mRNA molecules (Figure 1). Specificity illustrates the number of genes with elevated or non-elevated expression in the bone marrow compared to other tissues. Elevated expression includes three subcategory types of elevated expression:

  • Tissue enriched: At least four-fold higher mRNA level in bone marrow compared to any other tissues.
  • Group enriched: At least four-fold higher average mRNA level in a group of 2-5 tissues compared to any other tissue.
  • Tissue enhanced: At least four-fold higher mRNA level in bone marrow compared to the average level in all other tissues.

Distribution, on the other hand, visualizes how many genes have, or do not have, detectable levels (nTPM≥1) of transcribed mRNA molecules in the bone marrow compared to other tissues. As evident in Table 1, all genes elevated in bone marrow are categorized as:

  • Detected in single: Detected in a single tissue
  • Detected in some: Detected in more than one but less than one-third of tissues
  • Detected in many: Detected in at least a third but not all tissues
  • Detected in all: Detected in all tissues

A. Specificity

B. Distribution

Figure 1. (A) The distribution of all genes across the five categories based on transcript specificity in bone marrow as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (nTPM≥1) in bone marrow as well as in all other tissues.

As shown in Figure 1, 908 genes show some level of elevated expression in the bone marrow compared to other tissues. The three categories of genes with elevated expression in bone marrow compared to other organs are shown in Table 1. In Table 2, the 12 genes with the highest enrichment in bone marrow are defined.

Table 1. The number of genes in the subdivided categories of elevated expression in bone marrow.

Distribution in the 36 tissues
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Tissue enriched 8403820 106
Group enriched 0588522 165
Tissue enhanced 3107300227 637
Total 11205423269 908


Table 2. The 12 genes with the highest level of enriched expression in bone marrow. "Tissue distribution" describes the transcript detection (nTPM≥1) in bone marrow as well as in all other tissues. "mRNA (tissue)" shows the transcript level in bone marrow as nTPM values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in bone marrow and the tissue with the second-highest expression level.

Gene Description Tissue distribution mRNA (tissue) Tissue specificity score
CTSG cathepsin G Detected in many 5399.9 153
PRSS57 serine protease 57 Detected in some 166.6 102
RNASE3 ribonuclease A family member 3 Detected in some 942.7 95
MS4A3 membrane spanning 4-domains A3 Detected in some 424.0 93
ELANE elastase, neutrophil expressed Detected in many 3927.4 91
BPI bactericidal permeability increasing protein Detected in some 1516.9 88
DEFA3 defensin alpha 3 Detected in many 37966.0 64
RAB44 RAB44, member RAS oncogene family Detected in single 59.4 63
AHSP alpha hemoglobin stabilizing protein Detected in many 1683.5 62
MPO myeloperoxidase Detected in some 4058.2 61
SERPINB10 serpin family B member 10 Detected in some 75.4 60
DEFA4 defensin alpha 4 Detected in some 2725.9 58


Protein expression of genes elevated in bone marrow

In-depth analysis of the elevated genes in bone marrow using antibody-based protein profiling allowed us to visualize the expression patterns of these proteins. The analysis showed expression in various hematopoietic cells, for example granulocytes and mast cells.

Proteins with enriched expression in granulocytes

Besides erythropoietic cells and thrombocytes, polymorphonuclear leukocytes cells, and in particular cells of the granulocyte lineage, make up the majority of hematopoietic cells in bone marrow. CTSG (Cathepsin G) and DEFA4 (Defensin alpha 4) are two of the elevated genes within bone marrow. They are known to be expressed in neutrophils and involved in the defense against bacteria. PRTN3 (Proteinase-3), a neutrophil serine protease (NSPs) differs from the other two NSPs (CTSG and ELANE) in terms of function. An example being that proteinase-3 also acts as a feedback regulator in myeloid differentiation. Protein profiles for CTSG, PRTN3 and DEFA4 show strong staining of granulocytes.


CTSG

PRTN3

DEFA4

Proteins with enriched expression in mast cells

Mast cells are present in lower numbers than granulocytes in bone marrow. MCEMP1, a fairly uncharacterized gene found to encode a single-pass transmembrane protein expressed in human mast cell, displays a group enriched expression in bone marrow, along with lung and appendix. The RNA-seq data is supported by immunohistochemistry, with positivity in subsets of cells in bone marrow and appendix, as well as in alveolar macrophages in the lung.


MCEMP1 - bone marrow

MCEMP1 - lung

MCEMP1 - appendix


Gene expression shared between bone marrow and other tissues

There are 165 group enriched genes expressed in bone marrow. Group enriched genes are defined as genes showing a 4-fold higher average level of mRNA expression in a group of 2-5 tissues, including bone marrow, compared to all other tissues.

To illustrate the relation of bone marrow tissue to other tissue types, a network plot was generated, displaying the number of genes with a shared expression between different tissue types.

Figure 2. An interactive network plot of the bone marrow enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of bone marrow enriched genes and orange nodes represent the number of genes that are group enriched. The sizes of the red and orange nodes are related to the number of genes displayed within the node. Each node is clickable and results in a list of all enriched genes connected to the highlighted edges. The network is limited to group enriched genes in combinations of up to 3 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.


Bone marrow shares most group enriched gene expression with lymphoid tissue. The reason for this is that lymphoid tissues consist mostly of immune cells, many of which originate from bone marrow. Among the group enriched genes in bone marrow, we found Immunoglobulin lambda like polypeptide 1 (IGLL1), which encodes a receptor expressed on the surface of pre-B-cells and pro-B-cells and is involved in cell proliferation and differentiation. Immunohistochemistry displays cytoplasmic staining in bone marrow and testis, which is supported by RNA-seq data.


IGLL1 - bone marrow

IGLL1 - testis


Bone marrow function

The main functions of the bone marrow are to maintain constant levels of the different blood cell types in the peripheral blood, i.e. producing erythrocytes, leukocytes and thrombocytes. Bone marrow also contributes to the degradation of aged erythrocytes, along with the liver and spleen.


Bone marrow histology

Bone marrow is divided into red and yellow regions, caused by a predominance of either hematopoietic-rich (red) or adipose-rich (yellow) tissue. Red marrow consists of a highly vascularized stromal network containing pluripotent and committed stem cells of all hematopoietic lineages, i.e. erythrocytes, leukocytes, thrombocytes. While erythrocytes and leukocytes develop from stages of precursors, thrombocytes, small blood cell fragments involved in clotting, originate from giant marrow cells called megakaryocytes. In contrast, yellow marrow contains mesenchymal stem cells which differentiate into several stromal lineages, such as chondrocytes, osteoblasts, fibroblasts and adipocytes.

At birth and until around the age of seven, all human marrow is red, as the need for new blood formation is high. Adipose tissue gradually replaces the red marrow, which in adults is mainly found in flat bones, such as the vertebrae, ilium, sternum and cranium as well as at the epiphyseal ends of the long bones of the arm and leg.



Figure 3. Schematic view of bone marrow tissue. Attribution: By Mysid [Public domain], via Wikimedia Commons. Source

The histology of human bone marrow including detailed images and information can be viewed in the Protein Atlas Histology Dictionary.


Background

Here, the protein-coding genes expressed in bone marrow are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in bone marrow.

Transcript profiling was based on a combination of two transcriptomics datasets (HPA and GTEx), corresponding to a total of 14590 samples from 55 different human normal tissue types. The final consensus normalized expression (nTPM) value for each tissue type was used for the classification of all genes according to the tissue-specific expression into two different categories, based on specificity or distribution.


Relevant links and publications

Uhlén M et al., Tissue-based map of the human proteome. Science (2015)
PubMed: 25613900 DOI: 10.1126/science.1260419

Yu NY et al., Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res. (2015)
PubMed: 26117540 DOI: 10.1093/nar/gkv608

Fagerberg L et al., Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics. (2014)
PubMed: 24309898 DOI: 10.1074/mcp.M113.035600

Andersson S et al., The transcriptomic and proteomic landscapes of bone marrow and secondary lymphoid tissues. PLoS One. (2014)
PubMed: 25541736 DOI: 10.1371/journal.pone.0115911

Histology dictionary - bone marrow