THE HUMAN TISSUE PROTEOMES

The duodenum-specific proteome


The duodenum is the most proximal section of the small intestine and represents a major site of food breakdown. It receives chyme from the stomach and bile and pancreatic fluids from the pancreaticobiliary duct. After entering the duodenum the acidic contents from the stomach are neutralized by secretions from the intestine and pancreas. Enzymes secreted from the pancreas start the degradation of lipids, carbohydrates and proteins to enable absorption. The transcriptome analysis shows that 69% of all human proteins (n=19628) are expressed in the duodenum and 331 of these genes show an elevated expression in duodenum compared to other tissue types. An analysis of the genes with elevated expression in the duodenum with regards to subcellular localization reveals that the corresponding proteins are most often located in the brush border, secreted mucus, cellular membrane, or cytoplasm.

  • 5 duodenum enriched genes
  • 331 genes defined as elevated in the duodenum
  • Most group enriched genes shared expression with the small intestine

Figure 1. The distribution of all genes across the five categories based on transcript abundance in duodenum as well as in all other tissues.


331 genes show some level of elevated expression in the duodenum compared to other tissues. The three categories of genes with elevated expression in duodenum compared to other organs are shown in Table 1.

Table 1. The genes with elevated expression in duodenum

Category

Number of genes

Description

Tissue enriched 5 At least five-fold higher mRNA levels in a particular tissue as compared to all other tissues
Group enriched 156 At least five-fold higher mRNA levels in a group of 2-7 tissues
Tissue enhanced 170 At least five-fold higher mRNA levels in a particular tissue as compared to average levels in all tissues
Total 331 Total number of elevated genes in duodenum


Table 2. The 5 genes with the highest level of enriched expression in duodenum. "Predicted localization" shows the classification of each gene into three main classes: Secreted, Membrane, and Intracellular, where the latter consists of genes without any predicted membrane and secreted features. "mRNA (tissue)" shows the transcript level asáTPM values,áTS-score (Tissue Specificity score) corresponds to the score calculated as the fold change to the second highest tissue.

Gene

Description

Predicted localization

mRNA (tissue)

TS-score

TMPRSS15 transmembrane protease, serine 15 Intracellular 1039.0 44
ADA adenosine deaminase Intracellular 501.3 14
S100G S100 calcium binding protein G Intracellular 247.6 11
PDX1 pancreatic and duodenal homeobox 1 Intracellular 44.8 7
MLN motilin Secreted 260.7 6

Some of the proteins predicted to be membrane-spanning are intracellular, e.g. in the Golgi or mitochondrial membranes, and some of the proteins predicted to be secreted can potentially be retained in a compartment belonging to the secretory pathway, such as the ER, or remain attached to the outer face of the cell membrane by a GPI anchor.

The duodenum transcriptome


An analysis of the expression levels of each gene makes it possible to calculate the relative mRNA pool for each of the categories. The analysis shows that 78% of the mRNA molecules derived from duodenum corresponds to housekeeping genes and that 12% of the mRNA pool correspond to genes categorized as duodenum enriched, group enriched or, duodenum enhanced. Thus, most of the transcriptional activity in the duodenum relates to proteins with presumed housekeeping functions as they are found in all tissues and cells analyzed.



Protein expression of genes elevated in duodenum


In-depth analysis of the elevated genes in duodenum using antibody-based protein profiling allowed us to visualize the protein expression patterns in the duodenum with respect to cellular compartments. A variability in subcellular location was observed; PDX1 is located to the nucleus, ACE in luminal membrane, CDH17 in cellular membrane, CLCA1 secreted mucus and RBP2 cytoplasm.

PDX1 - nucleus
ACE - luminal membrane
CDH17 - cellular membrane


CLCA1 - secreted mucus
RBP2 - cytoplasm


Genes shared between duodenum and other tissues


There are 156 group enriched genes expressed in the duodenum. Group enriched genes are defined as genes showing a 5-fold higher average level of mRNA expression in a group of 2-7 tissues, including duodenum, compared to all other tissues.

In order to illustrate the relation of duodenum tissue to other tissue types, a network plot was generated, displaying the number of commonly expressed genes between different tissue types.

Figure 2. An interactive network plot of theáduodenumáenriched and group enriched genes connected to their respective enriched tissues (grey circles).áRedánodes represent the number ofáduodenum enriched genes andáorangeánodes 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 toá3átissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.



Duodenum histology


The most proximal and widest part of the small intestine is the duodenum. It starts at the pylorus of the stomach, ends at the duodenojejunal junction and measures about 25 cm long. It receives partly digested food (chyme) from the stomach and bile and pancreatic fluids from the pancreaticobiliary duct. After entering the duodenum the acidic contents from the stomach is neutralized by secretion from the intestine and pancreas. Enzymes secreted from the pancreas starts the degradation of lipids, carbohydrates and proteins to enable absorption.

As in all of the small intestine, the mucosa forms finger-like projections called villi that extend into the intestinal lumen. These are epithelial folds lined by two types of cells, enterocytes and goblet cells. Enterocytes are simple columnar cells with basal elongated nuclei and an apical brush border. The brush border is the microscopic representation of small protrusions of the cell membrane, microvilli, which greatly increase the surface area of the cell enhancing absorptive capacity. The other cell type is mucus secreting goblet cells that can be recognized by the presence of an apical mucous cup. The core of the villus is part of the lamina propria. The most numerous cells in the lamina propria are immune cells, most of which are lymphocytes. Because villi are the site of absorption of nutrition they have a rich blood supply, each villus is supplied by central arterioles and drained by central venules and a central lymph vessel.

Underlying the villi are the intestinal glands, also called the crypts of Lieberkuhn. These glands are lined with numerous relatively undifferentiated columnar cells that usually undergo two rounds of mitosis before differentiating into either absorptive cells or goblet cells. Enterocytes, goblet cells, paneth cells that secrete antibacterial enzymes (recognized by eosinophilic granules in their apical cytoplasm) and enteroendocrine cells also line the crypt. A thin layer of smooth muscle marks the end of the mucosa, the muscularis mucosae. In the submucosa there are numerous pale stained glands present, namely the Brunner's glands. These are branched tubular or alveotubular glands lined with columnar secretory epithelium. They secrete large amounts of alkaline mucous that neutralize the acidic contents from the stomach.

The histology of human duodenum including detailed images and information about the different cell types can be viewed in the Protein Atlas Histology Dictionary.

Background


Here, the protein-coding genes expressed in the duodenum are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize protein expression patterns of proteins that correspond to genes with elevated expression in the duodenum.

Transcript profiling and RNA-data analyses based on normal human tissues have been described previously (Fagerberg et al., 2013). Analyses of mRNA expression including over 99% of all human protein-coding genes was performed using deep RNA sequencing of 172 individual samples corresponding to 37 different human normal tissue types. RNA sequencing results of 2 fresh frozen tissues representing normal duodenum was compared to 170 other tissue samples corresponding to 36 tissue types, in order to determine genes with elevated expression in duodenum. A tissue-specific score, defined as the ratio between mRNA levels in duodenum compared to the mRNA levels in all other tissues, was used to divide the genes into different categories of expression. These categories include: genes with elevated expression in duodenum, genes expressed in all tissues, genes with a mixed expression pattern, genes not expressed in duodenum, and genes not expressed in any tissue. Genes with elevated expression in duodenum were further sub-categorized as i) genes with enriched expression in duodenum, ii) genes with group enriched expression including duodenum and iii) genes with enhanced expression in duodenum.

Human tissue samples used for protein and mRNA expression analyses were collected and handled in accordance with Swedish laws and regulation and obtained from the Department of Pathology, Uppsala University Hospital, Uppsala, Sweden as part of the sample collection governed by the Uppsala Biobank. All human tissue samples used in the present study were anonymized in accordance with approval and advisory report from the Uppsala Ethical Review Board.


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

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

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

Gremel G et al, 2014. The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling. J Gastroenterol.
PubMed: 24789573 DOI: 10.1007/s00535-014-0958-7

Histology dictionary - the duodenum