Bringing Down Cancer Aircraft: Searching for Essential Hypomutated Proteins in Skin Melanoma

We propose an approach to detection of essential genes/proteins required for cancer cell survival. A gene is considered essential if a mutation with high impact upon the function of encoded protein causes death of the cancer cell. We draw an analogy between essential cancer proteins and well-known Abraham Wald’s work on estimating the plane critical areas using data on survivability of aircraft encountering enemy fire. Wald reasoned that parts with no bullet holes on the airplanes returned to the airbase from a combat flight are the most crucial ones for the airplane functioning: a hit in one of these parts downs an airplane, so it does not return back for the survey. We have envisaged that the airplane surface is a cancer genome and the bullets are somatic mutations with high impact upon protein function. Similarly we propose that genes specifically essential for tumor cell survival should carry less high-impact mutations in cancer cells compared to polymorphisms found in normal cells. We used data on mutations from the Cancer Genome Atlas and polymorphisms found in healthy humans (from 1000 Genomes Project) to predict 91 protein-coding genes essential for melanoma. These genes were selected according to several criteria, including negative selection, expression in melanocytes and decrease in the proportion of high-impact mutations in cancer compared with normal cells. The Gene Ontology analysis revealed enrichment of essential proteins related to membrane and cell periphery. We speculate that this could be a sign of immune system-driven negative selection of cancer neo-antigens. Another finding is the overrepresentation of semaphorin receptors, which can mediate distinctive signaling cascades and are involved in various aspects of tumor development. Cytokine receptors CCR5 and CXCR1 were also identified as cancer essential proteins and this is confirmed by other studies. Overall, our goal was to illustrate the idea of detecting proteins whose sequence integrity and functioning is important for cancer cell survival. Hopefully, this prediction of essential cancer proteins may point to new targets for anti-tumor therapies.     

Fungal incompatibility: Evolutionary origin in pathogen defense?

In fungi, cell fusion between genetically unlike individuals triggers a cell death reaction known as the incompatibility reaction. In Podospora anserina, the genes controlling this process belong to a gene family encoding STAND proteins with an N‐terminal cell death effector domain, a central NACHT domain and a C‐terminal WD‐repeat domain. These incompatibility genes are extremely polymorphic, subject to positive Darwinian selection and display a remarkable genetic plasticity allowing for constant diversification of the WD‐repeat domain responsible for recognition of non‐self. Remarkably, the architecture of these proteins is related to pathogen‐recognition receptors ensuring innate immunity in plants and animals. Here, we hypothesize that these P. anserina incompatibility genes could be components of a yet‐unidentified innate immune system of fungi. As already proposed in the case of plant hybrid necrosis or graft rejection in mammals, incompatibility could be a by‐product of pathogen‐driven divergence in host defense genes.     

趋化因子及其受体家族分子适应性进化分析

Branch-Site模型是检测基因序列中单个密码子位点是否具有选择作用的统计学方法。该模型能有效地检测基因在进化历程中是否受到选择作用, 并预测出那些在进化过程中对功能分化有重要贡献的、受正选择作用的密码子位点。趋化因子是一类控制免疫细胞定向迁移的细胞因子, 其功能行使由趋化因子受体介导。该文用Branch-Site模型分析趋化因子及其受体基因家族的分子适应性, 发现只有少数种类基因受到正选择作用, 如RANTES、CCR5等。并预测出一些可能受到正选择作用的位点, 蛋白3D分析显示, 它们均位于趋化因子和相应受体相互作用的结构区域。     

Development and validation of stable ferroptosis- and pyroptosis-related signatures in predicting prognosis and immune status in breast cancer

To develop and validate the predictive effects of stable ferroptosis- and pyroptosis-related features on the prognosis and immune status of breast cancer (BC). We retrieved as well as downloaded ferroptosis- and pyroptosis-related genes from the FerrDb and GeneCards databases. The minimum absolute contraction and selection operator (LASSO) algorithm in The Cancer Genome Atlas (TCGA) was used to construct a prognostic classifier combining the above two types of prognostic genes with differential expression, and the Integrated Gene Expression (GEO) dataset was used for validation. Seventeen genes presented a close association with BC prognosis. Thirteen key prognostic genes with prognostic value were considered to construct a new expression signature for classifying patients with BC into high- and low-risk groups. Kaplan–Meier analysis revealed a worse prognosis in the high-risk group. The receiver operating characteristic (ROC) curve and multivariate Cox regression analysis identified its predictive and independent features. Immune profile analysis showed that immunosuppressive cells were upregulated in the high-risk group, and this risk model was related to immunosuppressive molecules. We successfully constructed combined features of ferroptosis and pyroptosis in BC that are closely related to prognosis, clinicopathological and immune features, chemotherapy efficacy and immunosuppressive molecules. However, further experimental studies are required to verify these findings.     

Interleukin‐27 expression modifies prostate cancer cell crosstalk with bone and immune cells in vitro

Prostate cancer is frequently associated with bone metastases, where the crosstalk between tumor cells and key cells of the bone microenvironment (osteoblasts, osteoclasts, immune cells) amplifies tumor growth. We have explored the potential of a novel cytokine, interleukin‐27 (IL‐27), for inhibiting this malignant crosstalk, and have examined the effect of autocrine IL‐27 on prostate cancer cell gene expression, as well as the effect of paracrine IL‐27 on gene expression in bone and T cells. In prostate tumor cells, IL‐27 upregulated genes related to its signaling pathway while downregulating malignancy‐related receptors and cytokine genes involved in gp130 signaling, as well as several protease genes. In both undifferentiated and differentiated osteoblasts, IL‐27 modulated upregulation of genes related to its own signaling pathway as well as pro‐osteogenic genes. In osteoclasts, IL‐27 downregulated several genes typically involved in malignancy and also downregulated osteoclastogenesis‐related genes. Furthermore, an osteogenesis‐focused real‐time PCR array revealed a more extensive profile of pro‐osteogenic gene changes in both osteoblasts and osteoclasts. In T‐lymphocyte cells, IL‐27 upregulated several activation‐related genes and also genes related to the IL‐27 signaling pathway and downregulated several genes that could modulate osteoclastogenesis. Overall, our results suggest that IL‐27 may be able to modify interactions between prostate tumor and bone microenvironment cells and thus could be used as a multifunctional therapeutic for restoring bone homeostasis while treating metastatic prostate tumors. J. Cell. Physiol. © 2012 Wiley Periodicals, Inc.     

Microevolutionary selection dynamics acting on immune genes of the green‐veined white butterfly,Pieris napi

Insects rely on their innate immune system to successfully mediate complex interactions with their microbiota, as well as the microbes present in the environment. Previous work has shown that components of the canonical immune gene repertoire evolve rapidly and have evolutionary characteristics originating from interactions with fast‐evolving microorganisms. Although these interactions are likely to vary among populations, there is a poor understanding of the microevolutionary dynamics of immune genes, especially in non‐Dipteran insects. Here, we use the full set of canonical insect immune genes to investigate microevolutionary dynamics acting on these genes between and among populations by comparing three allopatric populations of the green‐veined white butterfly, Pieris napi (Linné; Lepidoptera, Pieridae). Immune genes showed increased genetic diversity compared to genes from the rest of the genome and various functional categories exhibited different types of signatures of selection, at different evolutionary scales, presenting a complex pattern of selection dynamics. Signatures of balancing selection were identified in 10 genes, and 17 genes appear to be under positive selection. Genes involved with the cellular arm of the immune response as well as the Toll pathway appear to be enriched among our outlier loci, regardless of functional category. This suggests that the targets of selection might focus upon an entire pathway, rather than functional subsets across pathways. Our microevolutionary results are similar to previously observed macroevolutionary patterns from diverse taxa, suggesting that either the immune system is robust to dramatic differences in life history and microbial communities, or that diverse microbes exert similar selection pressures.     

Immunoepigenetics: the unseen side of cancer immunoediting

Cancer immunosurveillance representing, till recently, the explanatory framework relating cancer and the immune system, does not convincingly explain tumor escape. At the beginning of the decade, a new theory emerged, namely the immunoediting theory, and it comprehensively defines the role of the immune system in carcinogenesis. The core of this theory embraces the concept that the immune system on the one hand protects the body from cancer and on the other it shapes the immunogenicity of these cancers, thus presents a persuasive rationalization of the resistance of tumors against the immune response. With the immune system playing, in this context, such a pivotal role in shaping the tumor immune profile and in subsequent oncogenesis, it seems rather paradoxical to accept the immunocompetent host's immune system as a constant moiety. While DNA mutations of immune genes create a rather polymorphic condition, their frequency is much lower than that of other genetic events. Of these, epigenetic alterations give rise to new epialleles, which can reach up to 100% per locus. Bearing in mind that cancer is characterized by a tremendous amount of epigenetic aberrations, in both gene and global level, it is reasonable to postulate that, for the same unknown causes, analogous aberrations could affect the immune genes. Should this be the case, the relation between oncogenesis and the immune system appears much more dynamic and complex. Such an immunoepigenetic approach to carcinogenesis could improve our understanding of a series of common cancer-related aspects, such as environmental risk factors, effectiveness of demethylating agents, failure of current immunotherapies, etc. Moreover, this immunoepigenetic paradigm will take the current perception of the immune system and cancer interrelation further and beyond, constituting that the immunoresistant cancer cell phenotype is not shaped by the immune system acting as a steady and rigid evolutionary pressure, but rather as an extremely dynamic variable.     

Evidence for selection at cytokine loci in a natural population of field voles (Microtus agrestis)

Individuals in natural populations are frequently exposed to a wide range of pathogens. Given the diverse profile of gene products involved in responses to different types of pathogen, this potentially results in complex pathogen-specific selection pressures acting on a broad spectrum of immune system genes in wild animals. Thus far, studies into the evolution of immune genes in natural populations have focused almost exclusively on the Major Histocompatibility Complex (MHC). However, the MHC represents only a fraction of the immune system and there is a need to broaden research in wild species to include other immune genes. Here, we examine the evidence for natural selection in a range of non-MHC genes in a natural population of field voles (Microtus agrestis). We concentrate primarily on genes encoding cytokines, signalling molecules critical in eliciting and mediating immune responses and identify signatures of natural selection acting on several of these genes. In particular, genetic diversity within Interleukin 1 beta and Interleukin 2 appears to have been maintained through balancing selection. Taken together with previous findings that polymorphism within these genes is associated with variation in resistance to multiple pathogens, this suggests that pathogen-mediated selection may be an important force driving genetic diversity at cytokine loci in voles and other natural populations. These results also suggest that, along with the MHC, preservation of genetic variation within cytokine genes should be a priority for the conservation genetics of threatened wildlife populations.     

Rapid evolution of immunoglobulin superfamily C2 domains expressed in immune system cells

To test the hypothesis that proteins expressed in cells of the vertebrate immune system evolve unusually rapidly, 107 orthologous immunoglobulin C2 domains were compared between human and murine rodent. The analysis showed that the rate of nonsynonymous (amino-acid- altering) nucleotide substitution in these domains was correlated with factors associated with protein structure and with breadth of tissue expression, as well as with the rate of synonymous substitution. However, when such factors were controlled for statistically, there remained a strong positive association between expression in the immune system and nonsynonymous rate, with the highest rates being seen in genes expressed in the immune system only. Certain immune system genes are known to be subject to positive selection favoring diversity at the amino acid level; most of these genes encode receptors that interact directly with foreign antigens. The observed acceleration of the rate of nonsynonymous evolution in C2 domains of immune system proteins may be explained by either (1) reduced constraint at the amino acid level on molecules interacting with immune system receptors that are themselves evolving rapidly due to positive diversifying selection or (2) positive selection favoring amino acid changes correlated with changes in the immune system receptors.      

Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions

ABSTRACT: BACKGROUND: Cancer, much like most human disease, is routinely studied by utilizing model organisms. Of these model organisms, mice are often dominant. However, our assumptions of functional equivalence fail to consider the opportunity for divergence conferred by ~180 Million Years (MY) of independent evolution between these species. For a given set of human disease related genes, it is therefore important to determine if functional equivalency has been retained between species. In this study we test the hypothesis that cancer associated genes have different patterns of substitution akin to adaptive evolution in different mammal lineages. RESULTS: Our analysis of the current literature and colon cancer databases identified 22 genes exhibiting colon cancer associated germline mutations. We identified orthologs for these 22 genes across a set of high coverage (>6X) vertebrate genomes. Analysis of these orthologous datasets revealed significant levels of positive selection. Evidence of lineage-specific positive selection was identified in 14 genes in both ancestral and extant lineages. Lineage-specific positive selection was detected in the ancestral Euarchontoglires and Hominidae lineages for STK11, in the ancestral primate lineage for CDH1, in the ancestral Murinae lineage for both SDHC and MSH6 genes and the ancestral Muridae lineage for TSC1. CONCLUSION: Identifying positive selection in the primate, Hominidae, Muridae and Murinae lineages suggest an ancestral functional shift in these genes between the rodent and primate lineages. Analyses such as this, combining evolutionary theory and predictions - along with medically relevant data, can thus provide us with important clues for modeling human diseases.     

Natural selection on quantitative immune defence traits: a comparison between theory and data

Parasites present a threat for free‐living species and affect several ecological and evolutionary processes. Immune defence is the main physiological barrier against infections, and understanding its evolution is central for predicting disease dynamics. I review theoretical predictions and empirical data on natural selection on quantitative immune defence traits in the wild. Evolutionary theory predicts immune traits to be under stabilizing selection owing to trade‐offs between immune function and life‐history traits. Empirical data, however, support mainly positive directional selection, but also show variation in the form of selection among study systems, immune traits and fitness components. I argue that the differences between theory and empirical data may at least partly arise from methodological difficulties in testing stabilizing selection as well as measuring fitness. I also argue that the commonness of positive directional selection and the variation in selection may be caused by several biological factors. First, selection on immune function may show spatial and temporal variation as epidemics are often local/seasonal. Second, factors affecting the range of phenotypic variation in immune traits could alter potential for selection. Third, different parasites may impose different selective pressures depending on their characteristics. Fourth, condition dependence of immune defence can obscure trade‐offs related to it, thus possibly modifying observed selection gradients. Fifth, nonimmunological defences could affect the form of selection by reducing the benefits of strong immune function. To comprehensively understand the evolution of immune defence, the role of above factors should be considered in future studies.     

Evolution of Functional Genes in Cetaceans Driven by Natural Selection on a Phylogenetic and Population Level

Cetaceans represent an evolutionary lineage marked by drastic morphological and physiological changes during their adaptation to an exclusively marine existence. In addition, several cetacean species exhibit geographical ranges that encompass different marine environments, with genetic breaks being sometimes consistent with environmental breaks. As such, genes that underwent adaptation during the land-sea transition can also be potential candidates for adaptation to different oceanic environments. In this study, we analysed 3 milk protein genes (β-casein, κ-casein, and α-lactalbumin) and 2 immunity related genes (MHC DQβ1 and γ-fibrinogen) for selection based on available phylogenetic datasets of both mammals and cetaceans, and used the results from this analysis to assess adaptation to different environments on a population level in the European common dolphin (Delphinus delphis). We found that evidence for positive selection could be detected in all genes in the phylogenetic analyses, with β-casein showing a further increase in selective pressure in the cetacean lineage. At the population level, both the immune system locus DQβ1 and β-casein genes showed patterns of variation consistent with divergent selection, and in each case the same populations showed differentiation. One of these populations was also differentiated at neutral markers, while the other was not. We discuss possible inference, and the potential for the further development of these ideas using genomic technologies.     

DNA shuffling: induced molecular breeding to produce new generation long-lasting vaccines

The paradigm for classic vaccines has been to mimic natural infection, and their success relies mostly on the induction of neutralizing antibodies followed by long-lasting immunity. The outcome of aggressive chronic infections such as HIV and HCV, the reappearance of fastidious diseases such as tuberculosis and the progression of cancer growth suggest that natural immune responses are definitely insufficient in many cases. A new paradigm is needed to design and develop a new high-efficiency generation of vaccines ideally able to surpass the capabilities of natural immune responses. In vitro evolution is a new, important laboratory method to evolve molecules with desired properties, which appears as an appealing alternative to achieve this goal. In its battle against disease, the vertebrate immune system triggers a series of well-known molecular events in order to produce protective neutralizing antibodies. This natural in vivo response shares remarkable similarities with the in vitro technique known as molecular breeding or "DNA shuffling." This method exploits the recombination between genes to dramatically accelerate the rate at which genes can be evolved under selection pressure in the laboratory, producing optimized high-efficiency mutant proteins. Since new generation vaccines are aimed to overcome natural selection and environmental pressures to fully inactivate rapidly developing pathogen variants, they could be engineered, developed and selected through the application of directed DNA shuffling procedures. This review highlights the potential of the procedure in the complex context of natural immune responses and the equilibrium and interaction existing in nature between hosts and pathogens.     

利用高密度SNP检测不同猪品种间X染色体选择信号

在家猪的培育过程中,许多重要的经济性状受到过高强度的人工选择,高密度SNP标记为通过选择信号检测追踪这些性状经历的选择提供了可能,并能根据选择信号利用生物信息学寻找到与选择相关的基因。X染色体由于其特殊性,在传统的遗传分析中许多针对常染色体的方法往往不适用,需要采取特殊的方法,选择信号检测可以作为一种行之有效的方法对X染色体进行分析。文章利用长白、松辽黑猪和大白3个猪品种,通过品种间选择信号检测方法 XP-EHH,利用高密度SNP标记对X染色体进行选择信号检测,并通过生物信息学分析寻找选择信号区域内重要基因。在长白、松辽黑猪和大白3个品种中分别检测出29、13和15个选择信号区域,每个选择信号区域平均包含3.59、4.92、4.07个SNPs,长白和松辽黑猪、长白和大白有部分重叠选择信号区域,大白和松辽黑猪没有发现重叠选择信号区域。生物信息学分析发现各品种选择信号区域内有与繁殖、免疫等性状相关基因,其中部分在猪中尚未见报道,可作为研究猪相关性状的重要候选基因。     

Molecular Profiling of Tumor Tissue in Mexican Patients with Colorectal Cancer

Colorectal cancer is a heterogeneous disease with multiple genomic changes that influence the clinical management of patients; thus, the search for new molecular targets remains necessary. The aim of this study was to identify genetic variants in tumor tissues from Mexican patients with colorectal cancer, using massive parallel sequencing. A total of 4813 genes were analyzed in tumoral DNA from colorectal cancer patients, using the TruSight One Sequencing panel. From these, 192 variants with clinical associations were found distributed in 168 different genes, of which 46 variants had not been previous reported in the literature or databases, although genes harboring those variants had already been described in colorectal cancer. Enrichment analysis of the affected genes was performed using Reactome software; pathway over-representation showed significance for disease, signal transduction, and immune system subsets in all patients, while exclusive subsets such as DNA repair, autophagy, and RNA metabolism were also found. Those characteristics, whether individual or shared, could give tumors specific capabilities for survival, aggressiveness, or response to treatment. Our results can be useful for future investigations targeting specific characteristics of tumors in colorectal cancer patients. The identification of exclusive or common pathways in colorectal cancer patients could be important for better diagnosis and personalized cancer treatment.     

A Meta Analysis of Pancreatic Microarray Datasets Yields New Targets as Cancer Genes and Biomarkers

The lack of specific symptoms at early tumor stages, together with a high biological aggressiveness of the tumor contribute to the high mortality rate for pancreatic cancer (PC), which has a five year survival rate of less than 5%. Improved screening for earlier diagnosis, through the detection of diagnostic and prognostic biomarkers provides the best hope of increasing the rate of curatively resectable carcinomas. Though many serum markers have been reported to be elevated in patients with PC, so far, most of these markers have not been implemented into clinical routine due to low sensitivity or specificity. In this study, we have identified genes that are significantly upregulated in PC, through a meta-analysis of large number of microarray datasets. We demonstrate that the biological functions ascribed to these genes are clearly associated with PC and metastasis, and that that these genes exhibit a strong link to pathways involved with inflammation and the immune response. This investigation has yielded new targets for cancer genes, and potential biomarkers for pancreatic cancer. The candidate list of cancer genes includes protein kinase genes, new members of gene families currently associated with PC, as well as genes not previously linked to PC. In this study, we are also able to move towards developing a signature for hypomethylated genes, which could be useful for early detection of PC. We also show that the significantly upregulated 800+ genes in our analysis can serve as an enriched pool for tissue and serum protein biomarkers in pancreatic cancer.     

Genomic signatures of local adaptation in the Drosophila immune response

As environments and pathogen landscapes shift, host defenses must evolve to remain effective. Due to this selection pressure, among-species comparisons of genetic sequence data often find immune genes to be among the fastest evolving genes across the genome. The full extent and nature of these immune adaptations, however, remain largely unexplored. In a recent study, we analyzed patterns of selection within distinct components of the Drosophila melanogaster immune pathway. While we found evidence of positive selection within some immune processes, immune genes were not universally characterized by signatures of strong selection. On the contrary, we even found that some immune functions show greater than expected constraint. Overall these results highlight 2 major factors that appear to play an outsize role in determining a gene's evolutionary rate: the type of pathogen the gene targets and the gene's position within the immune network. These results join a growing body of literature that highlight the complexity of immune adaptation. Rather than there being uniformly strong selection across all immune genes, a combination of pathogen-specificity and host genetic constraints appear to play key roles in determining each immune gene's individual evolutionary trajectory.