Genotypic hypervariability of melanoma: a therapeutic challenge

Cutaneous melanoma remains a management challenge. Melanoma is the leading cause of death from skin tumors worldwide. Melanoma progression is well defined in its clinical, histopathological and biological aspects, but the molecular mechanism involved and the genetic markers associated to metastatic dissemination are only beginning to be defined. The recent development of high-throughput technologies aimed at global molecular profiling of cancer is switching on the spotlight at previously unknown candidate genes involved in melanoma. Among those genes, BRAF is one of the most supposed to be of interest and targeted therapies are ongoing in clinical trials. In familial melanoma, germline mutations in two genes, CDKN2A and CDK4, that play a pivotal role in controlling cell cycle and division. It is hope that this better understanding of the biologic features of melanoma and the mechanisms underlying tumor-induced immunosuppression will lead to efficaceous targeted therapy.     

Evolutionary hypervariability in the hinge region of the immunoglobulin alpha gene

The hinge region of the immunoglobulin molecule is responsible for antigen-binding and cross-linking reactions, varying the distance between the two antigen-binding sites. As the amino acid sequence of the hinge region is identical among immunoglobulin molecules of the same (sub)class, it has been regarded as a constant region. By comparison of the nucleotide sequences among primate C alpha genes, it is clear that there is a wide variety of length among the hinge regions of hominoid C alpha genes, which basically consist of tandem repeats of a 15 base-pair sequence. This reiterated structure probably facilitates rapid evolutionary changes in the length of the hinge region. The hinge region of the Old World monkey C alpha gene has a non-reiterated structure whose nucleotide sequence is quite different from those of the hominoid C alpha genes, although its surrounding region is conserved during evolution. This unusual hypervariability reveals that the hinge region has evolved as a semi-variable region in contrast to its constant character from an ontogenic viewpoint.     

Mechanisms of idiosyncratic drug reactions: the case of felbamate

Idiosyncratic drug reactions (IDR) are a specific type of drug toxicity characterized by their delayed onset, low incidence and reactive metabolite formation with little, if any, correlation between pharmacokinetics or pharmacodynamics and the toxicological outcome. As the name implies, IDR are unpredictable and often result in the post marketing failure of otherwise useful therapies. Examples of drugs, which have failed as a result of IDR in recent years, include trovafloxacin, zileuton, troglitazone, tolcapone and felbamate. To date there exists no pre-clinical model to predict these adverse drug reactions and a mechanistic understanding of these toxicities remains limited. In an attempt to better understand this class of drug toxicities and gain mechanistic insight, we have studied the IDR associated with a model compound, felbamate. Our studies with felbamate are consistent with the theory that compounds which cause IDR undergo bioactivation to a highly reactive electrophilic metabolite that is capable of forming covalent protein adducts in vivo. In additon, our data suggest that under normal physiological conditions glutathione plays a protective role in preventing IDR during felbamate therapy, further emphasizing a correlation between reactive metabolite formation and a toxic outcome. Clinical studies with felbamate have been able to demonstrate an association between reactive metabolite formation and a clinically relevant toxicity; however, additional research is required to more fully understand the link between reactive metabolite formation and the events which elicit toxicity. Going forward, it seems reasonable that screening for reactive metabolite formation in early drug discovery may be an important tool in eliminating the post-marketing failure of otherwise useful therapies.     

A room temperature ionic liquid as convenient solvent for the oxidative folding of conopeptides

We report the first example of conopeptide oxidation performed in a biocompatible ionic liquid, 1‐ethyl‐3‐methylimidazolium acetate ([C₂mim][OAc]), which enables the efficient formation of both hydrophilic and poorly water‐soluble conotoxins compared with conventional methods. Moreover, the method features a high‐concentration approach ultimately leading to higher yields at reduced separation effort. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.     

Functional hypervariability and gene diversity of cardioactive neuropeptides

Crustacean cardioactive peptide (CCAP) and related peptides are multifunctional regulatory neurohormones found in invertebrates. We isolated a CCAP-related peptide (conoCAP-a, for cone snail CardioActive Peptide) and cloned the cDNA of its precursor from venom of Conus villepinii. The precursor of conoCAP-a encodes for two additional CCAP-like peptides: conoCAP-b and conoCAP-c. This multi-peptide precursor organization is analogous to recently predicted molluscan CCAP-like preprohormones, and suggests a mechanism for the generation of biological diversification without gene amplification. While arthropod CCAP is a cardio-accelerator, we found that conoCAP-a decreases the heart frequency in Drosophila larvae, demonstrating that conoCAP-a and CCAP have opposite effects. Intravenous injection of conoCAP-a in rats caused decreased heart frequency and blood pressure in contrast to the injection of CCAP, which did not elicit any cardiac effect. Perfusion of rat ventricular cardiac myocytes with conoCAP-a decreased systolic calcium, indicating that conoCAP-a cardiac negative inotropic effects might be mediated via impairment of intracellular calcium trafficking. The contrasting cardiac effects of conoCAP-a and CCAP indicate that molluscan CCAP-like peptides have functions that differ from those of their arthropod counterparts. Molluscan CCAP-like peptides sequences, while homologous, differ between taxa and have unique sequences within a species. This relates to the functional hypervariability of these peptides as structure activity relationship studies demonstrate that single amino acids variations strongly affect cardiac activity. The discovery of conoCAPs in cone snail venom emphasizes the significance of their gene plasticity to have mutations as an adaptive evolution in terms of structure, cellular site of expression, and physiological functions.     

Subtype-selective conopeptides targeted to nicotinic receptors:Concerted discovery and biomedical applications

Conus peptides that are selectively targeted to different molecular isoforms of nicotinic acetylcholine receptors (nAChRs) have been identified and characterized; several have recently been shown to have significant biomedical potential. An emerging strategy for the discovery from animal biodiversity of subtype-specific ligands for ion channel families is described in this review. Characterization of the gene family encoding a set of related ligands is required for discovery using a molecular genetics approach; when discovery is guided by a knowledge of the phylogeny of the biodiverse animal lineage being used as a source of ligands, a rational, efficient scan of the library of putative ligands becomes feasible. Together, these constitute an approach to uncover subtype-specific ligands, called “concerted discovery”; this was applied to the α-conotoxins, a family of Conus peptides generally targeted to nAChRs.     

Subtype-selective conopeptides targeted to nicotinic receptors: Concerted discovery and biomedical applications

Conus peptides that are selectively targeted to different molecular isoforms of nicotinic acetylcholine receptors (nAChRs) have been identified and characterized; several have recently been shown to have significant biomedical potential. An emerging strategy for the discovery from animal biodiversity of subtype-specific ligands for ion channel families is described in this review. Characterization of the gene family encoding a set of related ligands is required for discovery using a molecular genetics approach; when discovery is guided by a knowledge of the phylogeny of the biodiverse animal lineage being used as a source of ligands, a rational, efficient scan of the library of putative ligands becomes feasible. Together, these constitute an approach to uncover subtype-specific ligands, called "concerted discovery"; this was applied to the alpha-conotoxins, a family of Conus peptides generally targeted to nAChRs. Subtype-specific alpha-conotoxins were developed that target two groups of nAChRs, alpha(6)* and alpha(9)*. alpha-conotoxin MII has become the defining ligand for identifying the alpha(6)* nAChR subtype. A synthetic analog, MII [E11A], further subdivides alpha(6)* nAChRs into those that contain an alpha(4) subunit and those that do not. Importantly, these two subtypes are differentially affected by nigrostriatal damage, findings of likely relevance to the pathopysiology of Parkinson's disease. In contrast, alpha-conotoxins that target alpha(9) nAChR subtypes have potential as analgesics for the treatment of neuropathic pain that develops after nerve injury. The discovery of alpha-conotoxin RgIA enabled the identification of a novel role for alpha(9)* nAChRs. Use of alpha(9)* nAChR antagonists is associated with reversal of inflammation caused by the nerve injury. Thus, subtype-specific alpha-conotoxins targeted to particular nAChR isoforms are not only useful for understanding the physiological role of these receptors, but can have important diagnostic and therapeutic applications as well.     

A statistical examination of hypervariability in complementarity-determining regions of immunoglobulins

To determine the relative importance of gene conversion followed by natural selection and of natural selection for point mutation in generating variability in immunoglobulins, the numbers of synonymous and nonsynonymous substitutions in immunoglobulin sequences of various subgroups were estimated for complementarity-determining regions (CDRs) and for framework regions (FRs). Both the number of synonymous substitutions and the number of nonsynonymous substitutions in the CDR were found to exceed the corresponding numbers in the FR. Therefore, gene conversion is likely to be an important mechanism for providing variability in the CDR of immunoglobulins. The correlation coefficients between the number of synonymous substitutions and the number of nonsynonymous substitutions and between the substitution number in the CDR and that in the FR were found to be very low. Again, gene conversion is thought to be responsible for this finding.     

On hypervariability at the reactive center of proteolytic enzymes and their inhibitors

The pattern of synonymous and nonsynonymous substitutions at the reactive center of proteases (kallikrein) and their inhibitors (₁-antitrypsin and serpin) was examined. In the case of ₁-antitrypsin, the proportion of different nonsynonymous sites exceeds that of different synonymous sites at the reactive center for sequence pairs of recent duplication. The result indicates that the positive selection has operated after duplication to increase functional diversity. In the cases of kallikrein, serpin, and remote sequence pairs of ₁-antitrypsin, the proportion of different synonymous sites at the reactive center exceeds that of different synonymous sites at the remaining region. The result indicates that gene conversion followed by natural selection is working. On the whole, it is concluded that hypervariability of amino acids at the reactive center is generated by an interaction among natural selection, random genetic drift, point mutation, and gene conversion. Gene duplication may provide potential for them to interact.     

Spondyloarthritides: evolving therapies

TNF blockade therapy has substantially advanced the treatment of peripheral spondyloarthritides but revolutionised the treatment of severe ankylosing spondylitis. The capacity of biologic treatment to improve dramatically symptoms and quality of life in patients with spinal disease is undoubted, although important questions remain. Notable amongst these are concerns about skeletal disease modification and the true balance between costs and effectiveness. Guidelines for the biologic treatment of ankylosing spondylitis and psoriatic arthritis have been introduced in North America and Europe with considerable consensus. However, the absence of clear criteria for the diagnosis of early disease leaves the issue of biologic treatment of ankylosing spondylitis at the pre-radiographic stage unresolved. Newer biologic agents are entering the field, although superiority over TNF blockers will be difficult to demonstrate.     

Human cytomegalovirus UL144 open reading frame: sequence hypervariability in low-passage clinical isolates

Human cytomegalovirus (HCMV) infects a number of organs and cell types in vivo, leading to the hypothesis that HCMV disease and tissue tropism may be related to specific sequence variants. A potential component of HCMV variant strains is the UL144 open reading frame (ORF), which encodes a homologue of the herpesvirus entry mediator, HveA, a member of the tumor necrosis factor receptor superfamily. Sequence analysis of the UL144 ORF in 45 low-passage clinical isolates demonstrated significant strain-specific variability. In individual isolates, nucleotide substitutions occur at up to 21% of the 531 positions, resulting in approximately the same percentage of substitutions in the predicted 176-amino-acid sequence. Phylogenetic analysis indicated that the nucleotide and amino acid sequences diverge into three major groups. For genotypic comparison, the known hypervariable region encompassing the proteolytic cleavage site of the glycoprotein B (gB) gene was also sequenced. All of the isolates could be typed according to the four known gB groups; however, the gB and UL144 sequence groups appeared to be phylogenetically unlinked. The predicted UL144 product homology with tumor necrosis factor receptor family members, along with the unexpectedly high level of sequence variability of the UL144 ORF, suggests that the predicted product may play a role in HCMV infectivity and subsequent host disease.     

Systems biology: evolving into the mainstream

Systems approaches to biology are steadily widening their reach, but the road to integration and acceptance has been fraught with skepticism and technical hurdles. Interdisciplinary research teams at systems biology centers around the globe are working to win over the critics.     

Condition indices for conservation: new uses for evolving tools

Biologists have developed a wide range of morphological, biochemicaland physiological metrics to assess the health and, in particular,the energetic status of individual animals. These metrics originatedto quantify aspects of human health, but have also proven usefulto address questions in life history, ecology and resource managementof game and commercial animals. We review the application ofcondition indices (CI) for conservation studies and focus onmeasures that quantify fat reserves, known to be critical forenergetically challenging activities such as migration, reproductionand survival during periods of scarcity. Standard methods scorefat content, or rely on a ratio of body mass rationalized bysome measure of size, usually a linear dimension such as winglength or total body length. Higher numerical values of theseindices are interpreted to mean an animal has greater energyreserves. Such CIs can provide predictive information abouthabitat quality and reproductive output, which in turn can helpmanagers with conservation assessments and policies. We reviewthe issues about the methods and metrics of measurement anddescribe the linkage of CIs to measures of body shape. Debatesin the literature about the best statistical methods to usein computing and comparing CIs remain unresolved. Next, we commenton the diversity of methods used to measure body compositionand the diversity of physiological models that compute bodycomposition and CIs. The underlying physiological regulatorysystems that govern the allocation of energy and nutrients amongcompartments and processes within the body are poorly understood,especially for field situations, and await basic data from additionallaboratory studies and advanced measurement systems includingtelemetry. For now, standard physiological CIs can provide supportingevidence and mechanistic linkages for population studies thathave traditionally been the focus of conservation biology. Physiologistscan provide guidance for the field application of conditionsindices with validation studies and development of new instruments.