Using a set of stringent and conserved host factors, it has been found that HIV does not always target ‘hubs’ or high-degree nodes in the human interactome. High-throughput screening of host-pathogen interactions may lead to interactions with already promiscuous proteins. Additionally, ‘hubs’ in a network are not necessarily involved in specific processes. Combining data from multiple sources reduced the number of false positives. Associations between a reliable ‘core set’ of HIV host factors and pathways or diseases may be more significant and specific, and reveal insights into the underlying molecular mechanisms of pathogenesis and comorbidities.
In conventional pathway enrichment methods (GSEA) all genes (host factors and genes in the human genome) must be ranked using a pre-specified criterion. Usually gene expression profiles of a certain phenotype (such as HIV infection) would be used. However, using this method, multiple factors or conditions cannot be considered together. Other than gene expression, the weight of evidence (number of independent studies reporting the gene being linked to the disease or condition) and degrees or centralities in protein-protein interaction networks could also be employed as ranking criteria. However, most of these criteria are unable to assign scores to all human genes, and would impact the calculations of enrichment scores and the ranking of pathways. Unlike the GSEA method, our method only requires a set of host factors. Associations between HIV and pathways are dependent on the set of HIV host factors. This is advantageous in terms of the computational complexity as the remaining genes in the human genome can be omitted from further study.
In this work, various cancer pathways were shown to be significantly associated with HIV. This observation is consistent with several studies investigating cancer risks in HIV/AIDS populations 
. Why does HIV associate with diverse types of cancers? HIV is known to integrate its genetic materials into the host genome, which could be a cause of HIV-defining carcinomas. The random sites of integration of HIV might corrupt the expression of tumor-suppresser genes and alter the behaviors of cells. For other non-HIV-defining cancers, it is recognized that apoptosis (the killing of damaged cells) 
and senescence (the inactivation of damaged cells) 
play critical roles in tumorigenesis.
One concern over the associations revealed in this work is whether highly ranked pathways were simply those with more genes, as larger pathways may include more host factors by chance. The KEGG database contains various types of pathways, including ‘Metabolism’, ‘Genetic Information Processing’, ‘Environmental Information Processing’, ‘Cellular Processes’, ‘Organismal Systems’, and ‘Human Diseases’ 
. Whether certain types of pathways would cluster at the top of the ranking may cause concern for the validity of the ranking results. To address these issues, the numbers of genes in pathways were plotted against the ranks of those pathways (). The resulting figure illustrates that ranks are not correlated with the numbers of genes in pathways. Other than ‘Metabolism’, which tends to rank low, most pathways do not exhibit obvious trends of clustering.
KEGG Pathway categories and ranks.
Many of the host factors studied were significantly involved in the apoptosis pathway, notably AKT1 and RELA (part of NF-κB). Apoptosis is a mechanism used by infected cells to control the spread of pathogens. Interactions between the HIV Tat protein and AKT1 and RELA inhibit apoptosis, and lead to the survival and proliferation of cells 
. Activation of NF-κB in turn activates a number of survival genes. This strategy might help HIV to spread to other cells. The activation of survival genes might also inadvertently promote the growth and proliferation of cancer cells. Several cancer pathways highlighted in this work shared similar molecular machinery.
The pancreatic cancer pathway was ranked first in the final ranking. There has been little data reported on the association between HIV and pancreatic cancer 
, which might be due to the low prevalence of pancreatic cancer in the general population and its resulting difficulty of study. HIV host factors involved in the pancreatic cancer pathway (hsa05212) are highlighted (). Many of these genes play important roles in a central pathway (the EGF/EGFR/JAK1/AKT/NF-κB axis) that might lead to the survival and proliferation of cancer cells, as noted above. Additionally, highly active anti-retroviral treatments (HAART) may also negatively affect the pancreas 
. The cause of the increased incidence of pancreatic cancers in HIV/AIDS populations 
is not clear; it is speculated that the introduction of HAART significantly prolonged the life-span of HIV/AIDS patients, which might contribute to increases in tumor-associated deaths 
HIV host factors in the pancreatic cancer pathway.
To further elucidate the interactions between host factors and pancreatic cancers, 80 mutated genes implicated in pancreatic cancers were retrieved from a systematic screening survey 
. A network of interactions among HIV proteins, host factors, and mutated genes in pancreatic cancers was constructed (). The resulting network illustrated the fact that HIV host factors do not interact with mutated pancreatic genes directly; instead, a set of ‘proxies’ or ‘hubs’ are connected with both sets of genes. Interactions from the HIV-human interaction database revealed that HIV proteins share more interactions with host factors and these ‘hubs’, and fewer interactions with genes mutated in pancreatic cancer. At first glance, these results might suggest that the association between HIV infection and pancreatic cancer arises from the ‘common interaction partner’ method used in this work. However, in the four approaches used to study these data, the pancreatic cancer pathway ranked 1st
, and 1st
, respectively, and these associations were all statistically significant (). Thus, the association was not solely determined by indirect human protein-protein interactions. The existence of ‘proxy’ genes in the interaction network suggests that HIV infections and pancreatic mutations might lead to common outcomes, notably the activation of anti-apoptotic and pro-survival signaling pathways.
PPI network of HIV proteins, host factors, and genes that are mutated in pancreatic cancer.
Chronic immune suppression was shown to increase the incidences of various cancers 
. HIV infection depletes CD4+ T-cells and macrophages, imposing a great impact on immune system functions. Recent studies revealed that CD4+ T-cells and macrophages are required in the clearance of senescent cells, which is critical to the prevention and regression of cancers 
. Without functioning immune systems and these immune cells, senescent cells promote tumor growth and metastasis, though the underlying mechanism for this promotion remains to be elucidated 
Notably, several anti-retroviral agents were shown to have anti-tumor activities, and were used to treat various types of cancers 
. Many HIV protease inhibitors also exhibited various degrees of kinase inhibition activity. For example, saquinavir, ritonavir, nelfinavir, and amprenavir were all able to inhibit phosphor-Akt (AKT1 was one of the host factors studied) and interfered with various signaling pathways. Among these protease inhibitors, nelfinavir has the most potent anti-cancer activity and was tested in clinical trials against pancreatic cancer 
. Computational modeling and screening of human kinases revealed that nelfinavir inhibited multiple kinases, and its potent anti-tumor activity might come from this combined effect 
. However, the tumor suppressor protein p21 (CDKN1A) was shown to confer HIV-1 resistance 
. This and other studies suggest that anti-tumor drugs, specifically cyclin-dependent kinase (CDK) inhibitors, might serve as novel HIV/AIDS treatments 
This work used a combined approach to identify associations between one specific pathogen (HIV) and human pathways. Various strategies are possible approaches to refining our method, such as comparisons of score combination and rank combination 
, and the use of a rank-score plot to identify the diversity of rankings and further improve combination results 
. The identification of several cancer pathways associated with HIV was consistent with epidemiological reports of comorbidities and increased cancer risks in the HIV/AIDS population. The involvements of host factors in various cancer-related pathways also suggested the existence of common drugs or treatment options, as exemplified by HIV protease inhibitors and other anti-retroviral agents 
, and CDK inhibitors 
. Further investigations into the targets of anti-tumor drugs and their relationships with HIV host factors might reveal insights into novel treatment strategies for both HIV infection and cancers.