The Human PPI Network

Experimental data on protein interactions are spread among multiple databases. Even if the data in these databases partially overlap, the reliability of data differs because of the variations in the experimental techniques and the organisms used. In addition, information of the same protein can be stored with different designations in different databases. Therefore, all the available data should be queried properly and matches should be combined to form a comprehensive human PPI network. We made use of BIANA [31] (Biological Integration And Network Analysis) bioinformatics tool in order to form human PPI network. BIANA gathered PPI data from various databases and dealt with mapping between the different identifiers. We combined DIP[32], MIPS[33], HPRD[34], BIND[35], IntAct[36], MINT[37] and BioGRID [38] databases (all downloaded on May, 2011). Interactions and protein information were integrated with BIANA assuming that two proteins from different databases were the same if they had the same UNIPROT Accession, amino acid sequence, or Entrez Gene Identifier.

The Sub-Networks Implicated in Lung and Brain Metastatic Breast Cancer

We used GUILD, a network-based disease-gene prioritization tool [39] to identify the sub-networks implicated in the two phenotypes of our interest: 1) breast cancer metastasis in lung, and 2) breast cancer metastasis in brain. GUILD package includes several methods of “guilt-by-asssociation” to prioritize a list of candidate genes associated with a phenotype. Guilt-by-association approaches are based on a set of genes associated with a phenotype, named seeds, and the tendency that other genes associated with the same phenotype will interact with the seeds. We took 18 genes that mediate breast cancer to lung metastasis [4], 17 genes mediating breast cancer to brain metastasis [13] identified by Massagué and his co-workers and used them as seeds for each phenotype (Table 1).

We employed the NetCombo algorithm in GUILD using the default parameters as in [39] to rank all the proteins of the major component of the human PPI network. This algorithm combines the algorithms of NetScore, NetZcore and NetShort. The scores were different for proteins produced by genes associated with brain metastasis than those associated with lung metastasis. Therefore, two different sub-networks were considered with the proteins associated with lung or brain metastasis and their interactions.

GUILD scored only the nodes (proteins/genes) but not the edges (PPIs) and gene-gene associations), therefore we needed to transfer the score of the nodes into the edges. Thus, we defined the score of the edge as the average of the scores of its nodes (the values of these scores lie between 0 and 1). We selected a common threshold cut-off on the score of the edges to set up the sub-networks of brain and lung metastasis with similar size.

Gene Expression in the Related Tissues

We used HPRD [34], UNIPROT [40,41] and TIGER[42] databases for checking the expression of genes in breast tissue.

Functional Analysis of Brain and Lung Metastatic Networks

We used the ClueGo [43], a Cytoscape [44] plugin, designed for biological interpretation of gene sets. The significance (enrichment) analysis was performed with right-sided hyper-geometric testing with a Bonferroni step down P-value correction factor. KEGG pathways used for the calculations are downloaded in 24.05.2012. P-values smaller than 0.05 were considered significant.

Introducing Structural Information to Metastasis Sub-Networks

We used PRISM [45–47] server, for predicting the interface structures of interacting protein-protein couples. An interface is the contact region between two interacting proteins. In our study interfaces consist of PDB chains. Interface templates are the available structures of protein complexes. They are the PDB structures of interacting proteins. PRISM bioinformatics tool predicts possible interactions, and how the interaction partners connect structurally, based on geometrical comparisons of the template structures and the target structures. The details of this method can be found in a previous publication [47].

An interface template consists of two chains of a PDB structures. The template is named with the combination of PDB ID and chain names. For example, in Figure S1 in File S1 FN 1 and LTBP1 are predicted to be interacting via 1ywkAC template. This template is originating from A and C chains of structure with the 1ywk PDB ID.

In recent years, we applied PRISM algorithm on various signaling pathways and obtained reasonable structural models of the unknown interactions [29,48,49]. The performance of the PRISM algorithm was recently investigated on standard docking benchmarks and was established to be comparable to other rigid docking approaches, though, noticeably more efficient [50].

PRISM uses template based prediction approach, and needs the 3D structure of the queried proteins. It cannot make estimation for a protein, which does not have a 3D structure deposited to PDB. Accordingly if an edge is not connecting two proteins whose 3D structures are available, PRISM will not be able to find results for that edge. Thus, via the PDB we searched for the 3D structural information of the proteins of lung metastasis sub-networks (LMSN) and brain metastasis sub-networks (BMSN). Brain metastasis network has 255 proteins and for 117 of them we found 1612 PDB structures. On the other hand, LMSN has 322 proteins and for 182 proteins we found 2712 PDB structures. In BMSN there are 58 interactions connecting proteins with known structure stored in the PDB (these interactions can be modeled with PRISM) and in LMSN there are 102 such interactions. This means that, we could only make models for these edges.

We eliminated redundancy of similar structures corresponding to the same interface using TM-align[51]. Accordingly, we grouped PDBs that have a TM-score greater than 0.5 and an RMSD score smaller than 2.5A. We chose one representative for each group of PDBs that describe the same region. We ended up with 255 PDB structures for 117 proteins of the BMSN, and with 414 PDB structures for 182 proteins of the LMSN.

In this experiment we have used 7922 interface templates (mined in 2006 from PDB) [47]. We filtered the PRISM results by considering only the interaction predictions with an energy value lower than 0. For each interface model PRISM structurally compares 2 PDB chains (target chains) to all 7922 interface templates. PRISM made multiple predictions for some of the interactions; we used the models with the lowest free binding energies.

Source Organisms of the Templates

We have used “uniprot_sprot.dat” (downloaded in November of 2012, from UNIPROT’s ftp server) for detecting the source organisms of the PDB chains used for modeling the protein complexes in both metastasis networks.

For significance testing, we have calculated the p-value of a hyper-geometric distribution using the R package[52]. P-values smaller than 0.05 were considered significant. Please refer to Table 2 for the numbers we have used for calculations.

Every protein-protein interface consists of two chains. The 7922 template interfaces used in the experiments, consist of 15844 template chains. Among them the source organism of 11255 were available in “uniprot_sprot.dat” and 4918 were coming from microorganisms (bacteria/virus).

Interface Clusters

The protein interfaces that are available in PDB are clustered according to their structural similarity. These clusters are provided in PRINT database which can be accessed from the http://prism.ccbb.ku.edu.tr/interface/ address. We mentioned these structurally similar protein clusters as PRINT clusters all through the text.

While detecting the source organisms of the template interfaces, we have taken into account all the interfaces, not only the representative interfaces (in each PRINT cluster). Besides, we have used the biological process and the molecular functions listed in UNIPROT database for our analyses.

Host-Pathogen Relationships

We have made use of UNIPROT and HPIDB[53] databases to mine the knowledge on the host-pathogen relationships of the related proteins. We have checked whether the proteins are known to be interacting with pathogens or not Table S1 in File S1 and Table S2 in File S1).

Determining Hub Proteins

The average node degree is 2.6 for BMSN and 2 for LMSN. Nodes with 12 or more edges are considered to be hubs.

Genetic Variations on Interface Surfaces

We obtained the available point mutations related with cancer from COSMIC [54] database and humsavar.txt of UNIPROT database. UNIPROT [40,41] provides the variants of a protein’s amino-acid sequence. These variations can be polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations or RNA editing events. Both databases provide detailed information about the mutations, as well as the mutated residue numbers. Then, we mapped these point mutations to the interface regions of interacting proteins in the metastasis sub-networks (BMSN and LMSN). We used the PDBSWS database [55] for the PDB and Uniprot residue-level alignment.

We used Naccess [56] for determining the surface and core residues. Naccess computes the atomic accessible area by rolling a probe (typically with the same radius as water (1.4 Angstroms)) around the Van der Waal’s surface of macromolecule. It employs the Lee & Richards method [57], whereby a probe of given radius is rolled around the surface of the molecule, and the path traced out by its centre is the accessible surface.

For the statistical calculations of location preferences of genetic variations we used fisher’s (exact) test and two-tailed P-value for statistical significance (P-value smaller than 0.05 was considered statistically significant) as described in David et al.’s [23] article. We used the R package[52] for the statistical calculations.

Hot Spot Prediction

Hot spots are the residues that contribute more to the binding free energy with respect to other residues in the protein-protein interface. We have used HotPoint [58] for hot spot predictions. This webserver calculates the hot spots in protein interfaces using an empirical model with 70% accuracy.

Visualization Tools Used For Figures

We have used VMD [59] for visualizing protein structures and for network visualizations we have used Cytoscape [44].

Identifying Brain & Lung Metastatic Breast Cancer Sub-networks and Their Functional Annotations

We have built a comprehensive human PPI network that consisted of 11,123 proteins and 149,931 interactions. We ranked each PPI in the network, according to its relevance to the seed nodes causing breast cancer metastasis, using GUILD (Genes Underlying Inheritance Linked Disorders) network-based prioritization tool [39].

We defined a score threshold and discarded interactions below the threshold based on the following reasoning: 1) we need two comparable sets of nodes and edges for brain and lung metastasis, where the topology may be different but not the size; 2) predicting the interface structures of interacting proteins is a highly time-consuming step, therefore we needed to reduce the network to a limited sub-network of small but highly relevant edges (i.e. less than 500) for each metastasis under study.

We plotted the number of edges versus their scores to select the best cut-off (see Figure S2 in File S1). We observed a dramatic rise in the number of interactions (and also nodes), between scores 0.15 and 0.18 for the punctuation of brain and lung metastasis (Figure S3 in File S1 and Table 3). Accordingly, we selected 0.178 as the common GUILD cut-off score to generate both sub-networks. This cutoff yielded a BMSN with 255 nodes and 335 edges (Figure 1a), and a LMSN with 322 nodes and 327 edges (Figure 1b).

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Figure 1. The BMSN and the LMSN networks.

We obtained a) the BMSN and b) the LMSN by choosing the edges of human PPI network with GUILD Score higher than 0.178. The proteins that have PDB structures are highlighted in pink, plus the edges that have complexes modeled by PRISM are also in pink color. c) PLOD2 cluster (the first-degree neighbors of PLOD2) from the BMSN d) BMSN and LMSN merged as a one big network. There are 84 common proteins and 71 common PPIs (blue edges). The edges that are only present in LMSN are shown with green and the edges that are only present in BMSN are shown with pink.

https://doi.org/10.1371/journal.pone.0081035.g001

Although we used all proteins of both sub-networks (BMSN and LMSN) in our analyses, we tracked down the evidence for the expressions of the genes that coded the proteins in both sub-networks in breast tissue. We found that 87% of the genes in the LMSN (280 out of 322, see Table S3 in File S1) and 93% in the BMSN (238 out of 255, see Table S4 in File S1) are expressed in breast tissue.

We used ClueGo [43] to find significant KEGG pathways in BMSN (Table S5 in File S1) and LMSN (Table S6 in File S1). Each pathway in KEGG belongs to a class according to KEGG Orthology (KO) [60]. Then we mapped each KEGG pathway to its KEGG class. Subsequently, we calculated the percentages of observed KEGG classes (Figure 2). We found out that “Transport and Catabolism Cellular Processes” and “Replication and Repair Genetic Information Processing” classes contain the most abundant significant pathways in BMSN “Infectious Diseases”, “Cancer” and “Immune System” were the classes of most abundant pathways in the LMSN.

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Figure 2. The percentages of KEGG classes observed in LMSN and BMSN.

https://doi.org/10.1371/journal.pone.0081035.g002

According to the functional analysis we have observed a functional link between lung metastasis of breast cancer, infectious diseases and immune system. Although, BMSN was also significantly enriched in some pathways that are governed by “Immune system” and “Infectious Diseases”, these two classes were not covering the most abundant pathways. It is interesting that immune system and infectious diseases seem to play an important role in lung metastasis, while transport and catabolism seem to play a major role for brain metastasis. Indeed, lung tissue is in contact with the environment, being likely prepared for infection, while brain is separated of circulating blood by the blood-brain barrier and it requires metabolic processes to transport and catabolize glucose. Still, these results are obtained for networks which expression is produced mostly in breast.

Structural Analysis of the Metastasis Sub-Networks

The network representation of PPIs provides information about the sets of interacting proteins (i.e. whether two proteins bind or do not bind and the number of interactions a protein can have). Introducing structural knowledge to PPI networks adds an extra dimension of data to the representation. When we know how proteins are interacting structurally, we can detect multiple proteins trying to bind the same region on a protein surface. This extra knowledge may help us realize which interactions cannot happen concurrently. Besides, there may be protein pairs interacting via similar interface architectures. A drug targeting on any of these PPIs will have a high probability of targeting the others as well [29,30], since ligands have tendency to bind to similar binding sites [26–28]. Moreover, knowing the interface region of two proteins helps us to check whether mutations of these proteins occur in the interface or not.

Among the PPIs of the BMSN, only 4 of them had 3D structural data of the binary complex in PDB. Similarly, for LMSN, only 2 PPIs were found with the structure of the binary complex in PDB (see Table 4). In order to increase the structural coverage of interactions of our sub-networks, it is necessary to use modeling. We used PRISM [45–47] in order to predict, assign and model the structure of the interface of protein-pairs in the BMSN and LMSN (see Methods for the details).

PRISM produces template-based predictions and it models the structure of an interaction based on the known 3D structure of two interacting proteins. The BMSN has 58 interactions with known 3D structures for both partners. LMSN has 102 such interactions. PRISM modeled 18 out of 58 interactions as a binary complex in the BMSN (see Figure 1a). For the LMSN, 50 out of 102 interactions were modeled (see Figure 1b and Table 5).

We should note that PRISM can model an interaction using structurally different interface templates or can use the same template interface to model different interacting protein pairs. Besides, a protein may be embodied with different chains (as identified in the PDB) or domains describing different portions or protein-states (i.e. due to post-transcriptional modifications). Therefore, the interaction between two proteins can imply more than one interface region (i.e. produced by two or more pairs of domains) that may or may not occur at the same time. This would explain the causes for multiple interface predictions. On the other hand, template interfaces can be assigned to several interactions, some of them being common for different sub-networks or highly frequent in some sub-network. This arises a particular interest because it can explain a phenotype but also has implications on the putative use of drugs disrupting a particular set of interactions. As a consequence, for BMSN we obtained 32 predictions for 18 PPIs coming from 28 interface templates. Therefore, the average template interface frequency in BMSN is 1.14 (32/28). For LMSN, we obtained 99 predictions for 50 interactions and 75 out of 99 corresponded to different template interfaces. Thus, the average template interface frequency for LMSN is 1.32 (99/75). The numbers of occurrences of interfaces in both metastasis networks are shown in Table S7 in File S1.

We studied the common template interfaces in the BMSN and LMSN. We observed top 3 high frequency template interfaces in the LMSN: 1) 2b8nAB 8 times, the interface extracted from the homodimer Glycerate kinase, putative. 2) 1jogCD 5 times, the interface extracted from the homodimer Uncharacterized protein HI_0074. 3) 2a6aAB 4 times, the interface extracted from the homodimer Peptidase M22 glycoprotease. We observed 4 template interfaces with less frequency (only in 2 PPIs) in the BMSN: 1) 2b8nAB (as for LMSN), 2) 1nqlAB, taken from the interface between EGFR-EGF, 3) 1qjcAB the interface extracted from the homodimer phosphopantetheine adenylyltransferase and 1moxAC (the interface between EGFR-TGFA). Interestingly, the 2b8nAB template interface is the most frequent interface in both sub-networks (see Figure 3 and Figure 4). Details of the most frequent interface templates can be found in Table 6 and Table 7. We observed that the three most common interface templates in LMSN are all coming from bacterial proteins.

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Figure 3. Commonly observed interfaces of lung metastasis network.

In this figure structural sub-networks are also included. In these sub-networks only the interactions that have PRISM modeled complex structures are present. Each node represents a protein that has 3D structure and each edge stands for a distinct model between two proteins. The relevant template interfaces are represented with pink edges in these structural sub-networks.

https://doi.org/10.1371/journal.pone.0081035.g003

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Figure 4. Commonly observed interfaces of brain metastasis network.

Legend for the sub-networks is the same as in Figure 3.

https://doi.org/10.1371/journal.pone.0081035.g004

Then we studied the source organisms of all the template interfaces used in our sub-networks. We used 28 different template interfaces (Table S7 in File S1) for modeling the complexes in BMSN. Each template interface consists of 2 chains, thus there are 56 template interface chains utilized for the predictions. Among them, 30 template interface chains are originating from microbes (bacteria/virus). The probability of observing 30 or more microbial chains in a randomly selected set of 56 template interface chains is not significant (p-value = 0.09). Likewise, there were 150 template interface chains (75 template interfaces see Table S7 in File S1) used for the modeling of LMSN’s complexes. 78 out of 150 template interface chains are coming from microbes. Observing 78 or more template interface chains found in microbes in a randomly selected set of 150 is significant (p-value=0.024). Thus, metastasis protein complexes may be mimicking microbial interface architectures to form complexes, although only for LMSN this feature is significant.

Then we investigated the interactions modeled with templates of protein interactions found in microbes. 53% of the models are coming from microbial origin in BMSN (Figure 5, left) and 59% of the models are coming from microbes in LMSN (Figure 5, right). Again, the protein complexes in LMSN, utilize more interface templates with microbial origin than the ones in brain network.

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Figure 5. Percentages of source organisms.

We considered the interfaces’ number of observations in the networks. 53% of the modeled complexes use microbial template interfaces in BMSN and this percentage is 59% in LMSN.

https://doi.org/10.1371/journal.pone.0081035.g005

There are 14 proteins in BMSN whose interactions are modeled via templates originating from microbes. Seven out of these 14 proteins (Table S1 in File S1) are actually known to be involved in host-pathogen interactions. For LMSN this ratio is 14/40 (Table S2 in File S1). These proteins have binding sites similar to microbial interfaces and some of them are observed to be involved in the host-pathogen protein-protein interactions This finding suggests that these metastasis related proteins might be involved in mechanisms shared by metastasis and infectious diseases.

Likewise, except 1nqlAB and 1moxAC templates, all the common interfaces observed in both metastasis sub-networks are coming from bacteria. The human proteins in our networks, which are using these frequent templates, have mostly cell adhesion biological process. Moreover, 50 % of all the proteins modeled with microbial templates in our sub-networks are related with cell adhesion (Table S8 in File S1 – Table S9 in File S1). Besides, in BMSN, 25% of the proteins modeled with non-microbial interface predictions are related with cell adhesion. Finally, 21% of the proteins in the LMSN use non-microbial interface architecture (an interface other than microbial interfaces) to interact. Cell adhesion molecules play a significant role in cancer metastasis [61,62]. Those molecules use mechanisms of cell adhesion for creating metastasis in another organ [63]. Proteins using bacterial interface architectures for interacting with other proteins may be reproducing the adhesion ability of the bacterial proteins.

Moreover, both functional analysis discussed above and the structural analysis suggest a relationship between pathogens, immune system and metastasis. Pathogens may be triggering some mechanisms that lead to metastasis of a primary breast cancer tumor or vice-versa, metastasis may create the proper environment for bacteria invasion.

Actually, previous studies highlighted the resemblances in cellular and molecular mechanisms of invasion between metastasis and infectious diseases [64–67]. Besides, in a recent study, Haile et al. hypothesized that metastasis process and pathogens should be utilizing the same pathways [68]. Liu et al. also mentioned that certain pathogens, activated immune cells and tumor cells may be sharing same tactics to spread in the body [69]. These findings reinforce our functional and structural analyses results.

Overview of the Lung/Brain Metastasis Sub-networks

Network representation of the proteins and their interactions provides a systems level abstraction. Via network representation we may identify the proteins that are central and important. Hubs, proteins with a high number of interactions, are the vulnerable points of scale-free networks and are very important. As expected the hub proteins in the LMSB and BMSN are actually the protein products of the seed genes mentioned earlier. However, not all of the seed genes’ products are hubs in these two networks (Table 1). In BMSN PLOD2, HBEGF, MMP1, LAMA4, FSCN1, TNFSF10 and SCNN1A are the hubs (Figure 1a), whereas in LMSN KRT81 (KRTHB1), FSCN1, ID1, NEDD9, CXCR4, VCAM1 and MMP1 are the hubs (Figure 1b). Consequently, these seed genes are more critical from a systems point of view.

Furthermore, there are 2 hub nodes, LAMC1 and ITGA3, in BMSN that are not seed genes. They became hub nodes in the network because of the their interactions with PLOD2’s interaction partners (shown with green edges in Figure 1c). PLOD2 cluster (the first degree neighbors of PLOD2) is shown in Figure 1c. They have a very high potential of being major players in brain metastasis formation. In fact, ITGA3 is down regulated in metastatic medulloblastoma tumors and claimed to be allowing metastatic tumors to spread more eagerly [70].

There are 84 common proteins and 71 common PPIs (blue edges in Figure 1d) in both metastasis networks. There are PPIS present only in LMSN (green edges in Figure 1d) and only in BMSN (pink edges in Figure 1d). As one can see from Figure 1d, FSCN1 and MMP1 are two hubs that are common to both metastasis sub-networks, thus they are not very helpful in differentiating two metastasis types. On the other hand, the interactions of PLOD2, the highest ranked protein in BMSN, are only present in BMSN. Similarly, KRT81 is the highest ranked protein in LMSN and its interactions are only present in LMSN. These two proteins may be playing key roles in the related metastasis types.

In Figure 1a and Figure 1b the proteins that have PDB structures are shown with pink nodes, while the proteins that don’t have PDB structures are shown with blue nodes. Most of the hub nodes do not have PDB structures, thus we couldn’t make further structural analyses for them. The edges that are modeled with PRISM are shown in pink in Figure 1a and Figure 1b.

In Figure 3 and Figure 4 the most frequently observed template interfaces in LMSN and BMSN are depicted. In these figures structural sub-networks are also included. In these sub-networks only the interactions that have PRISM modeled complex structures are present. Each node represents a protein that has 3D structure and each edge stands for a distinct model between two proteins. The relevant template interfaces are represented with pink edges in these structural sub-networks. According to structural sub-network of lung metastasis NEDD9 is a hub protein with multiple interface architectures on different regions of its surface.

Genetic Variations on Interface Surfaces

There are 6 proteins that are present in both metastasis sub-networks and have at least one different interaction partner in each network. We wanted to find out whether the reason why these proteins are changing partners is related with genetic variations. By mapping the mutations on the proteins’ 3D structure we may see if the mutation is on the interface region and if the mutated residue is a hotspot, which may intensely affect the interaction strength.

We have PRISM models for 12 interactions that these 6 proteins are involved in (Table 8). These 12 interactions are happening between 13 proteins. By using the genetic variation data in UNIPROT and COSMIC we made further investigations for them. There are 386 genetic variations taking place on the mentioned 13 proteins; 251 variations on the surface, 135 variations in the core. Among these 386 genetic variations, only 28 of them are happening on the interface regions. Even in recent publications it is mentioned that in-frame mutations [21] and disease causing SNPs [23] have a tendency to occur on protein-protein interfaces we have not encountered this phenomenon (Table S10 in File S1 and Table S11 in File S1). However, if we had a larger protein set, this result might have been different. Plus the structural information we have on interfaces is very limited, most probably we are missing some additional interfaces. Thus the genetic variations mapped on the surface region may be coinciding with interfaces as well.

Two of the interactions that have genetic variations on their interface regions are discussed further as case studies below.

EGFR and ERBB4

The EGFR and ERBB4 proteins interact with HBEGF in BMSN, whereas they interact with EREG in LMSN. In fact HBEGF is a gene known to have a role in brain metastasis of breast cancer [13], while EREG is a gene known to be mediating lung metastasis of breast cancer [4]. The structural models of these interactions are not available in PDB, but we have PRISM predictions for these complexes. HBEGF is predicted to interact with EGFR and ERBB4 via the same binding site on its surface, and this is also the case for EREG (Figure 6).

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Figure 6. The PRISM predictions for a) EREG (blue) – EGFR (pink), b) EREG (blue) – ERBB4 (green) interaction, c) HBEGF (purple) - EGFR (pink) interacrion and d) HBEGF (purple) – ERBB4 (green) interaction.

We have discovered multiple genetic variations happening on these interfaces.

https://doi.org/10.1371/journal.pone.0081035.g006

Both EREG and HBEGF are growth factors that may be integrated to the membrane and can also be present in the extracellular space. EGFR binds EGF family members via its L1 (between residues 1-151) and L2 (between residues 312-481) domains [71]. The interface residues modeled with PRISM on EGFR (interfaces with HBEGF and EREG) are lying in these domains. Similar to EGFR; ERBB4 binds to EGF family members via its L1 and L2 domains (between residues 27-198 and 324-517 [72]). Most of the interface residues of ERBB4 modeled by PRISM are coinciding with these domains as well. Plus, the EGF-like domain (between residues 20-208) of HBEGF is known to have an important role in binding to EGFR [73]. The predicted interface residues for HBEGF are taking place in its EGF-like domain. EREG’s C-terminal (between residues 96-106) is suggested to be involved with its binding to ErbB receptors[74]. The C-terminus of EREG is in the interface model produced by PRISM.

There are a number of EGFR complexes, one ERBB4 complex and one HBEGF complex available in PDB, while there are no EREG complexes. When we compare our model’s interface residues with the binding sites of the available PDB complexes, we see that they are all overlapping (see Table S12 in File S1, Table S13 in File S1, Table S14 in File S1 and Table S15 in File S1).

Position 102 in the amino-acid sequence of EREG acquires a SNP (p.R102L) in some cancer patients (derived from COSMIC database). This amino acid is on the interface region of EREG-ERBB4 interaction. Plus, this residue lies in the C-terminal of EREG that is known to be essential for its interactions with ErbB receptors. Moreover, ERBB4 acquires 5 different mutations that coincide with its interfaces. These mutations are observed in cancer patients (derived from COSMIC). Genetic variations p. L39F, p.A90T, p. 409L and p.V468F mutations are coinciding with ERBB4-EREG interactions. Furthermore p. L39F and p.N352S mutations are coinciding with ERBB4-HBEGF interaction. Additionally, 4 mutations of EGFR derived from COSMIC database are coinciding with its interactions. While p. D46N, p.Q432H and p.V441I are affecting EGFR-EREG interaction, p. R377S mutation is affecting both EGFR-EREG and EGFR-HBEGF interactions.

These mutations may be making the mentioned interactions stronger or weaker but they are most probably changing the functions of the EREG, HBEGF, EGFR and ERBB4 proteins (Figure 6). Besides, there may be a relationship between the metastasis progression and these mutations.

ELANE (ELA2)

ELANE interacts with CSF3 in BMSN, while it is switching its interaction partner to VCAM1 in LMSN. CSF3 is a seed gene in BMSN [13], while VCAM1 is a seed gene in LMSN [4]. The structural models of these interactions are not available in PDB, but we have PRISM predictions for these complexes.

ELANE has a variants that coincides with its interfaces (p. V98L, p.V101L, p.V101M and p. S126L (derived from UNIPROT)). The variances in the amino acid 101, which are polymorphisms, coincides with one of the hotspots of the interface region between ELANE and CSF3 and the variances in the amino acids 98 (polymorphism) and 126 (unclassified variation) are inside the interface region of VCAM1 on ELANE (Figure 7). These amino-acid variances may be affecting the interactions of ELANE with CSF3 and VCAM1. As a result, these amino acid variations may be related with metastasis progression in breast cancer patients.

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Figure 7. The PRISM predictions for ELANE (orange) - VCAM1 (green) and ELANE - CSF3 (blue) interaction.

The amino acids 98, 101, 126 (red amino acids) on ELANE have genetic variations. Amino acid 101 is a hotspot in the CSF3 – ELANE interface, moreover amino acids 98 and 126 are part of the ELANE – VCAM1 interface.

https://doi.org/10.1371/journal.pone.0081035.g007