Pan-cancer analysis of TCGA data reveals notable signaling pathways

Table 1 reveals that the notable pathways in the pan-cancer analysis are the focal adhesion pathway, P13k-Akt pathway, Rap1 pathway, and calcium signaling pathways. This result verifies previous research showing that three of these four pathways are major players in cancer. The focal adhesion pathway has been shown to be involved in invasion, metastasis, angiogenesis, epithelial-mesenchymal transition (EMT), maintenance of cancer stem cells, and globally promoting tumor cell survival [16]. Furthermore, the Focal Adhesion Kinase (FAK) gene is a non-receptor tyrosine kinase that controls cellular processes such as proliferation, adhesion, spreading, motility, and survival [17‐22]. FAK has been shown to be over-expressed in many types of tumors [23‐26]. Disruption of FAK and p53 interaction with small molecule compound R2 reactivated p53 and blocked tumor growth [27]. The PI3K-Akt signaling pathway has been shown to be the most frequently altered pathway in human tumors. It controls most hallmarks of cancer, including cell cycle, survival, metabolism, motility and genomic instability; angiogenesis and inflammatory cell recruitment [28]. The Calcium signaling pathway has diverse functions in cellular regulation, which was found previously (with cell adhesion) by pathway analysis in breast cancer [29]. Yang et al. [30] discuss regulation of calcium signaling in lung cancer. On the other hand, much less is known about the Rap1 signaling pathway and cancer. There are only 6 pubmed citations concerning Rap1 and cancer. In particular, Bailey et al. [31] provide evidence to support a role for aberrant Rap1 activation in prostate cancer progression. Our results indicate Rap1 might be as big of a player in all cancers as the other three pathways just discussed.

Next we discuss the individual cancer results. Each of these discussions refers to information provided in Table 1.

The only notable pathway in the breast cancer analysis is the ECM-receptor interaction pathway. This pathway was not found to be significant in the pan-cancer analysis, much less notable. However, previous research links changes in the extracellular matrix (ECM) to breast cancer. Lu et al. [32] recently discuss how the ECM’s biomechanical properties change under disease conditions. In particular, tumor stroma is typically stiffer than normal stroma; and in the case of breast cancer, diseased tissue can be 10 times stiffer than normal breast tissue.

There are 7 notable pathways in the case of colon adenocarcinoma, and all of them were found to be significant in the pan-cancer analysis. The PI3k-Akt signaling pathway and focal adhesion pathway were both found to be notable in the pan-cancer analysis and were discussed above. There are only 7 pubmed citations linking the highest ranking pathway, adrenergic signaling in cardiomyocytes, to cancer. The second pathway, namely the melanoma pathway, is of course linked to cancer. Furthermore, there is research substantiating that the BRAF mutation is prominent in melanoma and colorectal cancer [33]. BRAF is on the melanoma pathway. As to the cytokine-cytokine receptor interaction pathway, there has been research linking cytokine receptors to colorectal cancer [34]. The pathway in cancer pathway is of course linked to cancer. Our result substantiates its role in colon cancer in particular.

The top ranking pathway in the case of glioblastoma is the cytokine-cytokine receptor interaction pathway, whose relevance to cancer we just discussed. The second pathway is complement and coagulation cascades. Recent research has suggested an essential role of this pathway in multiple cancers [35], but not glioblastoma in particular. Our results support that it is also has a role in glioblastoma. The third pathway, namely system lupus erythematosus, has been linked to glioblastoma [36]. We have already discussed the PI3K-Akt signalling pathway, as it was one of the notable pathways in the pan-cancer analysis. Finally, chemokine signaling has been associated with a number of cancers including glioma [37].

The first and fourth pathways for kidney renal papillary cell carcinoma are two of the notable pathways in the pan-cancer analysis, and have already been discussed. The second pathway, namely the ECM-receptor interaction pathway was also discussed because it was the most significant pathway in breast cancer. Finally, the colorectal cancer pathway is of course linked to cancer, but we know of no specific study implicating it in kidney renal papillary cell carcinoma.

The chemokine signaling pathway and the cytokine-cytokine receptor interaction pathway are both notable in low grade glioma. These same two pathways were found to be significant in glioblastoma and were discussed above. The first pathway, namely focal adhesion, is one of the notable pathways in our pan-cancer analysis. The second pathway, ECM-receptor interaction, was previously discussed because it was the most notable pathway in breast cancer. Finally, the small cell lung cancer pathway is concerned with cancer, but a literature search did not reveal any study linking it specifically to glioma.

The two notable pathways in the case of lung adenocarcinoma are also notable in glioblastoma, and were discussed when we discussed that cancer. The cytokine-cytokine receptor interaction pathway has been implicated specifically with lung cancer [38], as has chemokine signaling [39].

The top two pathways in the case of lung squamous cell carcinoma are the same as the top two in the case of lung adenocarcinoma. Their relevance to lung cancer was just discussed. A pubmed search does not show any papers linking cancer with the third pathway, endocrine and other factor-regulated calcium absorption.

The notable pathways in ovarian cancer are all notable pathways in the pan-cancer analysis, and were previously discussed.

Three of the notable pathways in the rectum adenocarcinoma analysis, are notable pathways in the pan-cancer analysis. The third ranked pathway, RAS signaling, has been associated with renal carcinoma [40]. As to the prostate cancer pathway, prostate cancer and renal cell cancer have been shown to have some commonality [41].

Two of the three notable pathways for uterine corpus endometriod carcinoma are notable pathways in the pan-cancer analysis. As to the third pathway, the connection between maturity onset diabetes of the young and endometrial cancer has been well-established [42].

Out of 157 signaling pathways analyzed, only 18 were found to be notable in at least one cancer. Table 2 lists those pathways. Out of a total of 37 notable findings, 26 occurred for the top 7 pathways. So, our results indicate that relatively few pathways are responsible for much of the aberrant activity in cancer. Of those 7 pathways, 4 were found to be notable in the pan-cancer analysis, and 2 others were fairly significant (p-values of 0.006 and 0.007). So these pathways may play roles in many different cancers. However, the ECM-receptor interaction pathway was not significant in the pan-cancer analysis (p-value of 0.472), indicating that perhaps this pathway is relevant only to the 3 cancers in which it was found to be notable, namely breast cancer, kidney renal papillary cell carcinoma, and low grade glioma.

To gain insight as to how much each particular cancer has in common with all cancers, we computed the Jaccard Index comparing the notable pathways in the each cancer type to the notable pathways in the pan-cancer analysis. If A and B are the two sets, the Jaccard Index of A and B is given by

where A is the number of items in A. The value of J(A, B) is 0 if A and B have no items in common, and is 1 if A and B are the same set.

Table 3 shows the Jaccard Indices. Ovarian carcinoma is at the top with an index of 0.75. The index would have been even higher, namely 1.0, if we had included the fourth most significant pathway for Ovarian Cancer, which is Focal adhesion and has a p-value of 0.000366. At the bottom we have breast cancer and the two lung cancers with Jaccard Indices equal to 0.

If we look at the pathway diagrams for our seven most significant pathways appearing in Table 2, often different signaling molecules bind to different receptors (integrin, RTK, GPCR), but the responses converge on many of the same proteins. For example, PI3K-Akt, Focal Adhesion, and Rap1 all converge on protein PI3K. To gain insight as to how much overlap there is among the seven most significant pathways, we determined the number of proteins each pathway pair has in common. The results appear in Table 4. Two interesting relationships are discernable in that table, and they are depicted in Fig. 1.

The first relationship is that PI3K-Akt has substantial overlap will five of the other six pathways. This is shown in Fig. 1a. PI3K-Akt is “probably one of the most important pathways in cancer metabolism and growth” [43]. The fact that it overlaps substantially will five other significant pathways indicates that much of the aberrant signaling in many cancers might be located in regions where PI3K-Akt overlaps with other pathways.

The second interesting relationship is that the Calcium pathway hardly overlaps with the other six pathways. This is shown in Fig. 1b. The Calcium pathway was found to be notable in only ovarian and uterine cancer (Table 1). This result indicates that there might be a common region of aberrant signaling in these two cancers, which does not overlap with regions of aberrant signaling in other cancers.

To discover possible hotspots where other aberrant signaling might occur, we looked at higher order intersections. We discovered the intersections shown in Fig. 2. In each of the diagrams in that figure, the intersection of the pathways in the diagram includes essentially no proteins from the other significant pathways.

Perhaps the most interesting relationship appears in Fig. 2a, which shows that the majority of the proteins in the ECM-receptor interaction pathway are located in the intersection of the PI3K-Akt and Focal Adhesion pathways. The ECM-receptor interaction pathway was found to be notable in breast cancer, kidney cancer, and glioma. This result indicates that there may be a region of aberrant signaling, located in the intersection of PI3K-Akt and Focal Adhesion, in these cancers.

Figures 2b and c show other possible hot regions in PI3K-Akt, while Fig. 2d and e show possible hot regions not including PI3K-Akt. Of these figures, Fig. 2e is the most compelling. The Cytokine-cytokine receptor interaction and Chemokine signaling pathways have a large intersection that excludes other pathways. Both these pathways were found to be notable in glioblastoma, glioma, lung adenocarcinoma, and lung squamous cancer. Only the Cytokine-cytokine receptor interaction pathway was found to be notable in colon cancer. So there may be a region of aberrant signaling, located in the intersection of these pathways, in these cancers.

To investigate further how different cancers might share common causal mechanisms, we developed a heat map, based on hierarchical clustering, with cancer type on the horizontal, the 18 notable pathways on the vertical, and with the entry being p-value. Figure 3 shows the heat map. Ovarian cancer and uterine cancer constitute a primary group. This is consistent with our result mentioned about that the calcium pathway was found to be notable only in these two cancers. Furthermore, these cancers are in close proximity. Rectum cancer and colon cancer also constitute a primary group, which is consistent with their close proximity.