Gastrointestinal tract

650 genes are classified as stomach elevated out of which 31 genes are highlighted as stomach enriched. Based on the expression in small intestine 545 genes are classified as elevated compared to other tissue types, out of which 43 genes are highlighted as tissue enriched. 445 genes are classified as large intestine elevated out of which 17 genes are highlighted as large intestine enriched.

Besides the spiral organization of colon, a large cecum and no appendix, the pig and human GI looks similar from a histological perspective, which can be observed in the pig tissue dictionary.

Stomach

The stomach is the first storage chamber for food intake. Certain cells of the stomach wall release hydrochloric acid and enzymes, which are responsible in breaking down food into small particles, such as carbohydrates, protein and fats. Some of these particles can be taken in from the stomach into the blood, other substances that can’ t be absorbed pass to the small intestine for further digestion and nutrient uptake. Besides, the acidic environment in stomach can also offer a barrier against ingested microorganisms.

Gene expression in stomach is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 2 summarizes the number of genes in respective category. In total, 15861 genes are detected above cut of (1NX) in pig stomach. The tissue distribution category highlights 16 genes only detected in stomach while 650 genes are classified as stomach elevated compared to other tissues. Table 1 shows the overlap for the stomach elevated genes and tissue distribution category.

Figure 2, (A) The distribution of all genes across the five categories based on transcript specificity in stomach as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in stomach as well as in all other tissues. The combination of the two categories is shown in table 1.

Table 1, Number of genes in the subdivided categories of elevated expression and tissue distribution in stomach

Stomach enriched expression

Gene with stomach-elevated expression in previous human analysis was also found in the characterization of pig stomach. Examples are GKN1, GKN2 and GAST. Previous study has shown that GNK1 has mitotic activity and may play an important role in maintaining the integrity of gastric mucosal epithelium. GAST encodes a hormone, called gastrin, whose function is to stimulate the gastric mucosa to secrete hydrochloric acid. Another example is the PGC gene, which encodes a digestive enzyme that constitutes a major component of the gastric mucosa.

Table 2, The 10 genes with the highest level of enriched expression in stomach. "mRNA (tissue)" shows the transcript level in stomach as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in stomach and the tissue with second highest expression level.

Small intestine

The small intestine is a hollow and spiral tube, which lies between stomach and large intestine. Most of final digestion of food and assimilation of nutrients take place here. The small intestine can be divided into three distinct regions: the duodenum, ileum and jejunum. The duodenum starts at the pylorus of the stomach, ends at the junction of duodenum and jejunum. Secretions from liver, gall bladder and pancreas are added to the duodenum that helps start degradation of lipid and carbohydrates to facilitate uptake in the jejunum and ileum. The highest expression observed among duodenum, jejunum and ileum is used as representation when comparing small intestine with other tissue types of the pig body.

Gene expression in small intestine is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 3 summarizes the number of genes in respective category. In total, 16194 genes are detected above cut of (1NX) in pig small intestine. The tissue distribution category highlights 16 genes only detected in small intestine while 545 genes are classified as small intestine elevated compared to other tissues. Table 3 shows the overlap for the small intestine elevated genes and tissue distribution category.

Figure 3, (A) The distribution of all genes across the five categories based on transcript specificity in small intestine as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in small intestine as well as in all other tissues. The combination of the two categories is shown in table 1.

Table 3, Number of genes in the subdivided categories of elevated expression and tissue distribution in small intestine

Small intestine enriched expression

The small intestine is the main site for nutrients absorption. To meet this need, some proteins related to small nutritional molecules transport are abundantly expressed in the small intestinal epithelium, such as RBP2 and FABP6. The former is thought to participate in the uptake of intracellular metabolism of vitamin A, while the latter is involved in fatty acid uptake, transport, and metabolism.

Table 4, The 10 genes with the highest level of enriched expression in small intestine. "mRNA (tissue)" shows the transcript level in small intestine as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in small intestine and the tissue with second highest expression level.

Expression comparison between duodenum, ilium and jejunum

The expression variation category enables further details related to expression heterogeneity within the tissues that include grouped samples. In this case, expression profiles from the different parts of the small intestine (the duodenum, jejunum and ileum) are compared to each other, resulting in 117 genes highlighted as variable.

Large intestine

The last part of gastrointestinal tract, the large intestine, includes cecum, colon and rectum. It is shorter but larger in diameter than small intestine. Most of water and some nutrients are absorbed, and the food residue is stored here before being removed by final defecation. In the large intestine we can also observed species differences between pig and human, pig lack appendix, has a large cecum and a spiral colon.

Gene expression in large intestine is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 4 summarizes the number of genes in respective category. In total, 15591 genes are detected above cut of (1NX) in pig large intestine. The tissue distribution category highlights 1 genes only detected in large intestine while 445 genes are classified as large intestine elevated compared to other tissues. Table 5 shows the overlap for the large intestine elevated genes and tissue distribution category.

Figure 4, (A) The distribution of all genes across the five categories based on transcript specificity in large intestine as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in large intestine as well as in all other tissues. The combination of the two categories is shown in table 1.

Table 5, Number of genes in the subdivided categories of elevated expression and tissue distribution in large intestine

Large intestine enriched expression

CA1 show elevated expression in cecum and colon, it is thought to be responsible for the reversible hydration of carbon dioxide. Additionally, proteins like INSL5, related to gut contractility also show enriched expression level in the large intestine

Table 6, The 10 genes with the highest level of enriched expression in large intestine. "mRNA (tissue)" shows the transcript level in large intestine as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in large intestine and the tissue with second highest expression level.

Expression comparison between cecum, colon and rectum

The expression variation category enables further details related to expression heterogeneity within the tissues that include grouped samples. In this case, expression profile from cecum, colon and rectum are compared, resulting in 113 genes highlighted as variable.

Gene expression in the GI tract compared to other tissues

The different tissues of GI tract share several proteins, such as SPINK4, MYO1A and PTPRH. However there is also a clear differences between stomach and the intestine, since small and large intestine share many more group enriched genes with each other than with stomach, which is the case with PARP15, SPAI-2 and CDX1.

In order to illustrate the relation of gastrointestinal tissue to other tissue types, a network plot was generated, displaying the number of genes shared between different tissue types. Group enriched genes are defined as genes showing a 4-fold higher average level of mRNA expression in a group of 2-5 tissues, compared to all other tissues.

Figure 5. An interactive network plot of gastrointestinal tract enriched and group enriched genes connected to their respective enriched tissues (grey circles). Black circles shows gastrointestinal tract tissues..Red nodes represent the number of tissue 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.