Bottleneck genes

A recent study has identified another important property of biological networks, which is a bottleneck [61]. A bottleneck measures the amount of signaling

0 5 10 15

020406080

Betweenness (log2)

Degree

KLK3

MAPK3

AKT1

NFKB1 MAPK1

TP53

RB1 RAC1

PTEN S1PR1 Degree high, betweenness low

Degree low, betweenness high Degree high, betweenness high

Figure 4: Scatter plot of degree and betweenness.The network only contains gene activations and gene inhibitions from WikiPathways. The network consists of 1895 genes and 5859 regulations between them. In the scatter plot, the X and Y axes represent betweenness and degree, respectively. Betweenness is logarithmic based on two. Degree and betweenness were calculated using an R package igraph [60].

information that goes through a gene. Technically, a bottleneck is evaluated by betweenness centrality that counts the number of shortest paths passing through a gene from all genes to all other genes. The scale of bottlenecks is between zero to hundreds of thousands, while the median value is zero from the gene regulation network generated using WikiPathways database. It has been demonstrated that bottleneck genes play essential roles in controlling and mediating communication information flow from one cluster to another [61]. Bottleneck genes are analogous to bridges and tunnels on a highway map, while hub genes are analogous to roundabouts and highway crossings. Hence, both bottleneck and hub genes are crucial in biological networks.

The degree of bottleneck genes varies, ranging from 2 to 90, as measured from WikiPathways (Figure 4). Here we define a bottleneck as a gene whose betweenness is larger than 2¹⁰in the network generated from WikiPathways. Analysis of hub

G

Figure 5: Bottleneck role ofPTENandS1PR1.This small network is generated from WikiPathways wherePTEN,S1PR1, and their neighbors with distance smaller than two are involved. All signals from the genes in the cluster (red ellipse) must go through PTEN,AKT1, andS1PR1to the genes in another cluster (green ellipse).

and bottleneck genes shows high correlation between them in general (Pearson r=0.6; Figure 4). TP53is not only a hub gene but also a bottleneck gene with the largest betweenness and the highest degree. Interestingly, however, high bottleneck genes do not necessarily have high degree, and vice versa (Figure 4).PTENand S1PR1have high betweenness but low degree (Figure 4). A subnetwork of the biological network that is related to thePTENandS1PR1genes with their neighbors reveals thatPTENandS1PR1are the main signaling mediators and controllers from one module to another (Figure 5).S1PR1is directly regulated byATK1, which is activated byPTEN. Thus, all signaling from the module (red cluster in Figure 5) to another (blue cluster in Figure 5) must go throughPTEN, AKT1, andS1PR1.

Accordingly, any malfunction inPTEN, AKT1, orS1PR1completely destroys the signaling from one module to another.

4 Cancer

Cancer is a complex disease characterized by uncontrolled growth and spread of abnormal cells [62]. It is one of the most lethal diseases, and cancer deaths are predicted to rise from an estimated 8.2 million to 13 million per year worldwide by 2030. Cancer is well recognized as a disease of aging. Estimated tumorigenesis occurs at around the 20 years of age and cancer detection at around age 50 [63].

Cancer is partially caused by lifestyle and environmental factors. Unhealthy lifestyles, such as smoking and heavy alcohol consumption, increase the risk of developing cancer [64, 65]. For example, tobacco smokers have a 20 times greater risk of developing lung cancer than non-smokers and have an increased risk of developing many other tumor types as well [66]. Increased exposure to carcinogenic agents present in the occupational and general environment results in an elevated risk of developing cancer. Air pollution, mainly caused by smoke from coal consumption, contributes to a 36-40 times higher lung cancer risk than less-polluted air [67]. Accordingly, the World Health Organization now classifies smoke from coal consumption as a cancer-causing agent.

In this chapter, genomic alterations in cancer are introduced, followed by a discus-sion of dysregulation of biological networks and integrative approaches in cancer.

Finally, cancer heterogeneity is examined.

4.1 Genomic alterations

Cancer is a genomic disease. While an estimated 5% to 10% of all cancers are directly inherited from parents [68, 69], the majority of cancers happen sporadically.

Non-hereditary cancers are the focus of this thesis. Non-hereditary cancers arise from accumulated genome instability resulting from random genomic changes [70].

Genomic alterations consist of genetic changes, such as mutations, DNA copy-number alterations, gene expression changes, and epigenetic changes, including histone modifications and DNA methylation.

The hallmarks of cancer [71] are largely driven by genetic and epigenetic alterations [72, 73] through the central dogma of molecular biology. Genetic changes in cancer, such as aberrant expression of oncogenes or tumor-suppressor genes, disturb the protein expression leading to severe consequences. Since DNA copy-numbers are tightly linked to mRNA expression, alterations in DNA copy-numbers change gene expression located in the same DNA regions [74]. DNA point mutations also change mRNA expression by affecting the binding sites of transcription factors [75, 76] or miRNAs [77, 78]. Both DNA copy-number alterations and point mutations may

lead to expression changes of the corresponding proteins. However, genetic changes do not always alter gene expression but may modify protein functions via effects on protein folding and stability [79, 80].

In addition to genetic alterations, epigenetic changes also disturb protein expression in a similar manner by activating cancer genes or inactivating tumor-suppressor genes. Methylation, a type of epigenetic change, plays an important role in cancer through silencing transcription of critical growth regulators (such as tumor-suppressor genes [81]), which subsequently promotes carcinogenesis [82]. Addi-tionally, histone modifications (another type of epigenetic marker) are highly linked to DNA methylation changes and control of gene activity in cancer [83, 84, 85].

Changes in proteins and their expression through either genetic or epigenetic changes affect protein-protein interactions and gene regulation, which eventually impacts the dynamics of biological networks. Furthermore, dysregulation of biological networks results in disruption of fundamental biological processes such as cell death, proliferation, differentiation, and migration [86, 87]. Hence, cancer can be considered a disease of alterations on the biological network level, instead of a single-gene disease [4]. Genetic changes (especially transcriptome changes) and their effects on biological networks are the focus of this thesis.