Two lessons from the interface of genetics and medicine

Fisher's historic 1922 paper On the dominance ratio

R.A. Fisher's 1922 paper On the dominance ratio has a strong claim to be the foundation paper for modern population genetics. It greatly influenced subsequent work by Haldane and Wright, and contributed 3 major innovations to the study of evolution at the genetic level. First, the introduction of a general model of selection at a single locus, which showed how variability could be maintained by heterozygote advantage. Second, the use of the branching process approach to show that a beneficial mutation has a substantial chance of loss from the population, even when the population size is extremely large. Third, the invention of the concept of a probability distribution of allele frequency, caused by random sampling of allele frequencies due to finite population size, and the first use of a diffusion equation to investigate the properties of such a distribution. Although Fisher was motivated by an inference that later turned out to lack strong empirical support (a substantial contribution of dominance to quantitative trait variability), and his use of a diffusion equation was marred by a technical mistake, the paper introduced concepts and methods that pervade much subsequent work in population genetics.

Mechanisms of action of mycophenolate mofetil

Mycophenolate mofetil (MMF, CellCept®) is a prodrug of mycophenolic acid (MPA), an inhibitor of inosine-5′‘monophosphate dehydrogenase. MPA depletes guanosine nucleotides preferentially in T and B lymphocytes and inhibits their proliferation, thereby suppressing cell-mediated immune responses and antibody formation. MPA also inhibits the glycosylation and expression of adhesion molecules, and the recruitment of lymphocytes and monocytes into sites of inflammation. MPA depletes tetrahydrobiopterin and decreases the production of nitric oxide by inducible NO synthase without affecting the activity of constitutive NO synthases. Activated macrophages produce NO and superoxide, which combine to generate tissue-damaging peroxynitrite. By these two mechanisms MMF exerts anti-inflammatory activity. Unlike calcineurin inhibitors, MMF is not nephrotoxic and does not induce the production of TGF β, which is fibrogenic. MMF does not increase blood pressure, cholesterol levels or triglyceride levels in recipients. MMF reduces acute and chronic rejection in allograft recipients and is efficacious in some nephropathies. Evidence is accumulating that MMF may have clinical utility in some autoimmune disorders.

Environment-dependent variation in selection on life history across small spatial scales

Variation in life-history traits is ubiquitous, even though genetic variation is thought to be depleted by selection. One potential mechanism for the maintenance of trait variation is spatially variable selection. We explored spatial variation in selection in the field for a colonial marine invertebrate that shows phenotypic differences across a depth gradient of only 3 m. Our analysis included life-history traits relating to module size, colony growth, and phenology. Directional selection on colony growth varied in strength across depths, while module size was under directional selection at one depth but not the other. Differences in selection may explain some of the observed phenotypic differentiation among depths for one trait but not another: instead, selection should actually erode the differences observed for this trait. Our results suggest selection is not acting alone to maintain trait variation within and across environments in this system.

Differential impact of sickle cell trait on symptomatic and asymptomatic malaria

Individuals who carry the sickle cell trait (S-gene) have a greatly reduced risk of experiencing symptomatic malaria infections. However, previous studies suggest that the sickle cell trait does not protect against acquiring asymptomatic malaria infections, although the proportion of symptomatic infections is up to 50% in areas where malaria is endemic. To examine the differential impact of the sickle cell trait on symptomatic and asymptomatic malaria, we developed a mathematical model of malaria transmission that incorporates the evolutionary dynamics of S-gene frequency. Our model indicates that the fitness of sickle cell trait is likely to increase with the proportion of symptomatic malaria infections. Our model also shows that control efforts aimed at diminishing the burden of symptomatic malaria are not likely to eradicate malaria in endemic areas, due to the increase in the relative prevalence of asymptomatic infection, the reservoir of malaria. Furthermore, when the prevalence of symptomatic malaria is reduced, both the fitness and frequency of the S-gene may decrease. In turn, a decreased frequency of the S-gene may eventually increase the overall prevalence of both symptomatic and asymptomatic malaria. Therefore, the control of symptomatic malaria might result in evolutionary repercussions, despite short-term epidemiological benefits.

Population genetics of malaria resistance in humans

The high mortality and widespread impact of malaria have resulted in this disease being the strongest evolutionary selective force in recent human history, and genes that confer resistance to malaria provide some of the best-known case studies of strong positive selection in modern humans. I begin by reviewing JBS Haldane's initial contribution to the potential of malaria genetic resistance in humans. Further, I discuss the population genetics aspects of many of the variants, including globin, G6PD deficiency, Duffy, ovalocytosis, ABO and human leukocyte antigen variants. Many of the variants conferring resistance to malaria are 'loss-of-function' mutants and appear to be recent polymorphisms from the last 5000-10 000 years or less. I discuss estimation of selection coefficients from case-control data and make predictions about the change for S, C and G6PD-deficiency variants. In addition, I consider the predicted joint changes when the two β-globin alleles S and C are both variable in the same population and when there is a variation for α-thalassemia and S, two unlinked, but epistatic variants. As more becomes known about genes conferring genetic resistance to malaria in humans, population genetics approaches can contribute both to investigating past selection and predicting the consequences in future generations for these variants.

The role played by natural selection on Mendelian traits in humans

Detecting whether and how natural selection has targeted regions of the human genome represents a complementary strategy for identifying functionally important loci and variants involved in disease resistance and adaptation to the environment. In contrast with most complex diseases or traits, the genetic architecture of most Mendelian traits is relatively well established. Most mutations associated with Mendelian disease-related traits are highly penetrant and kept at low population frequencies because of the effects of purifying selection. However, this is not always the case. Here, we review several examples of Mendelian mutations-associated with various disease conditions or other traits of anthropological interest-that have increased in frequency in the human population as a result of past positive selection. These examples clearly illustrate the value of a population genetics approach to unravel the biological mechanisms that have been central to our past and present survival against the selective pressures imposed by diseases and other environmental factors.

Uncertainty in mapping malaria epidemiology: implications for control

Malaria is a location-specific, dynamic infectious disease transmitted by mosquitoes to humans and is influenced by environmental, vector, parasite, and host factors. The principal purposes of malarial epidemiology are 1) to describe the malarial distribution in space and time along with the physical, biologic, and social etiologic factors and 2) to guide control objectives for either modeling impact or measuring progress of control tactics. Mapping malaria and many of its causative factors has been achieved on many different levels from global distribution to biologic quantitative trait localization in humans, parasites, and mosquitoes. Despite these important achievements, a large degree of uncertainty still exists on the annual burden of malarial cases. Accurate, sensitive detection and treatment of asymptomatic reservoirs important to infectious transmission are additional components necessary for future control measures. Presently spurred by the leadership and funding of Bill and Melinda Gates, the malarial community is developing and implementing plans for elimination of malaria. The challenge for malariologists is to digitally integrate and map epidemiologic factors and intervention measures in space and time to target effective, sustainable control alongside research efforts.

Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense

Infectious diseases have been paramount among the threats to health and survival throughout human evolutionary history. Natural selection is therefore expected to act strongly on host defense genes, particularly on innate immunity genes whose products mediate the direct interaction between the host and the microbial environment. In insects and mammals, the Toll-like receptors (TLRs) appear to play a major role in initiating innate immune responses against microbes. In humans, however, it has been speculated that the set of TLRs could be redundant for protective immunity. We investigated how natural selection has acted upon human TLRs, as an approach to assess their level of biological redundancy. We sequenced the ten human TLRs in a panel of 158 individuals from various populations worldwide and found that the intracellular TLRs—activated by nucleic acids and particularly specialized in viral recognition—have evolved under strong purifying selection, indicating their essential non-redundant role in host survival. Conversely, the selective constraints on the TLRs expressed on the cell surface—activated by compounds other than nucleic acids—have been much more relaxed, with higher rates of damaging nonsynonymous and stop mutations tolerated, suggesting their higher redundancy. Finally, we tested whether TLRs have experienced spatially-varying selection in human populations and found that the region encompassing TLR10-TLR1-TLR6 has been the target of recent positive selection among non-Africans. Our findings indicate that the different TLRs differ in their immunological redundancy, reflecting their distinct contributions to host defense. The insights gained in this study foster new hypotheses to be tested in clinical and epidemiological genetics of infectious disease.

The detrimental effects of microbial infections have led to the evolution of a variety of host defense mechanisms. A vast array of host innate immunity receptors, critical sensors of viruses, bacteria, and fungi, exist to achieve permanent surveillance of intruding pathogens. The best characterized class of microbial sensors is the Toll-like receptor (TLR) family, which elicits inflammatory and antimicrobial responses after activation by microbial products. Here we investigated how microbes have exerted selective pressure on the human TLR family to gain insights on the extent to which they are functionally important in the immune system. By resequencing the ten TLRs in different worldwide populations, we show that intracellular TLRs—principally specialized in viral recognition—evolve under strong purifying selection, indicating their essential role in host survival, while the remaining TLRs display higher levels of immunological redundancy. However, for this latter group of genes, we also show that mutations altering immune responses have been in some cases beneficial for host survival, as attested by the signature of positive selection favoring a reduced TLR1-mediated response in Europeans. Our findings taken together indicate that the different human TLRs differ in their biological relevance and provide clues to be experimentally tested in clinical, immunological, and epidemiological studies.

Immunology in natura: clinical, epidemiological and evolutionary genetics of infectious diseases

The field of human genetics of infectious diseases defines the genes and alleles rendering individuals (clinical genetics) and populations (epidemiological genetics) vulnerable to infection, and studies those selected by previous infections (evolutionary genetics). These disciplines--clinical, epidemiological and evolutionary genetics-delineate the redundant and nonredundant functions of host defense genes for past and present survival in natura--in natural ecosystems governed by natural selection. These disciplines, in other words, assess the ecologically relevant and evolutionarily selected roles of human genes and alleles in protective immunity to diverse and evolving microorganisms. The genetic dissection of human immunity to infection in natura provides unique immunological insight, making it an indispensable complement to experimental immunology in vitro and in vivo in plants and animals.

Normophosphatemic familial tumoral calcinosis is caused by deleterious mutations in SAMD9, encoding a TNF-alpha responsive protein

Normophosphatemic familial tumoral calcinosis (NFTC) is an autosomal recessive disorder characterized by calcium deposition in skin and mucosae and associated with unremitting pain and life-threatening skin infections. A homozygous missense mutation (p.K1495E), resulting in SAMD9 protein degradation, was recently shown to cause NFTC in five families of Jewish-Yemenite origin. In this study, we evaluated another Jewish-Yemenite NFTC kindred. All patients were compound heterozygous for two mutations in SAMD9: K1495E and a previously unreported nonsense mutation, R344X, predicted to result in a markedly truncated molecule. Screening of unaffected population-matched controls revealed heterozygosity for K1495E and R344X only in individuals of Jewish-Yemenite ancestry, but not in more than 700 control samples of other origins, including 93 non-Jewish Yemenite. These data may be suggestive of positive selection, considering the rarity of NFTC and the small size of the Jewish-Yemenite population; alternatively, they may reflect genetic drift or the effect of a population-specific modifier trait. Calcifications in NFTC generally develop over areas subjected to repeated trauma and are associated with marked inflammatory manifestations, indicating that SAMD9 may play a role in the inflammatory response to tissue injury. We therefore assessed the effect of cellular stress and tumor necrosis factor-alpha (TNF-alpha), a potent pro-inflammatory cytokine, on SAMD9 gene expression. Whereas exogenous hydrogen peroxide and heat shock did not affect SAMD9 transcription, osmotic shock was found to markedly upregulate SAMD9 expression. In addition, incubation of endothelial cells with TNF-alpha caused a dose-related, p38-dependant increase in SAMD9 expression. These data link NFTC and SAMD9 to the TNF-alpha signaling pathway, suggesting a role for this system in the regulation of extra-osseous calcification.

Elevated basal hepcidin levels in the liver may inhibit the development of malaria infection: another piece towards solving the malaria puzzle?

BACKGROUND

Inflammatory cytokines play a crucial role in the human immune response to infection by malaria. During the initial sporozoite infection of the liver the presence of Interleukin-6 (IL-6) can be determinant. IL-6 controls systemic iron homeostasis through hepcidin, which is produced mainly by hepatocytes. An elevated basal hepcidin level in the liver can be induced by chronic inflammatory disease. Hepcidin is also a peptide with antimicrobial properties.

PRESENTATION OF THE HYPOTHESIS

We hypothesize that elevated basal hepcidin levels in the liver inhibit the development of malaria infection. When hepcidin is abundant, hepatocytes sequester iron, and this inhibits sporozoite development in liver-stage malaria infection.

TESTING THE HYPOTHESIS

The validity of our hypothesis can be proven by observing sporozoite growth in hepcidin-treated hepatocytes, or in hepatocytes, stimulated with IL-6 to increase hepcidin levels before incubation with malaria sporozoites and observing the effect the hepcidin knockout function has on the infection.

IMPLICATIONS OF THE HYPOTHESIS

Confirmation of our hypothesis could help to understand the complexity of the malaria infection.

Mycophenolate Mofetil and Atherosclerosis: Results of Animal and Human Studies

The immunosuppressive agent mycophenolate mofetil (MMF) has beneficial effects in cardiac transplant patients beyond the suppression of tissue rejection. Patients with regimens containing MMF experience diminished intimal thickening and cardiac allograft vasculopathy compared to patients treated with azathioprine. Studies have shown that diet-induced atherosclerosis (a related vasculopathy) is a chronic inflammatory process, and so MMF has also been used to reduce atherosclerosis in a rabbit model of hyperlipidemia. These data hold out the intriguing possibility that MMF might be a viable primary or secondary preventive agent in people at significant risk for atherosclerosis.

Primary immunodeficiencies: a field in its infancy

A paradigm shift is occurring in the field of primary immunodeficiencies, with revision of the definition of these conditions and a considerable expansion of their limits. Inborn errors of immunity were initially thought to be confined to a few rare, familial, monogenic, recessive traits impairing the development or function of one or several leukocyte subsets and resulting in multiple, recurrent, opportunistic, and fatal infections in infancy. A growing number of exceptions to each of these conventional qualifications have gradually accumulated. It now appears that most individuals suffer from at least one of a multitude of primary immunodeficiencies, the dissection of which is helping to improve human medicine while describing immunity in natura.

Of PCSK9, cholesterol homeostasis and parasitic infections: Possible survival benefits of loss-of-function PCSK9 genetic polymorphisms

Cholesterol is important for cell membrane structure and functions as well as for production of steroid hormones and bile acids. It is transported through the body as lipoprotein particles of varying density and composition. Cholesterol homeostasis is maintained through finely tuned mechanisms regulating dietary uptake, hepatic biosynthesis and secretion as well as plasma clearance. Proprotein convertase subtilisin/kexin type 9 (PCSK9) reduces cellular uptake of plasma low-density lipoprotein-cholesterol (LDL-C) by promoting LDL receptor (LDLR) degradation. Two nonsense single-nucleotide polymorphisms (SNPs) at the PCSK9 locus have been associated with life-long hypocholesterolemia and a remarkable reduction of the risk for coronary heart disease (CHD) in African-Americans. These loss-of-function SNPs presumably render PCSK9 less capable of inducing LDLR catabolism, effectively increasing LDLR availability and allowing efficient removal of plasma LDL-C. The combined frequency of heterozygosity for these nonsense SNPs is approximately 3-4% in populations of African descent. Homozygosity for either SNP, which would aggravate hypocholesterolemia, is reportedly rare. Whether such an aggravation would represent a health risk is still a matter of debate. From an evolutionary point of view, the cardioprotective effect of these nonsense SNPs may be a secondary phenotype made evident by the dyslipidemia-inducing lifestyle of today's North America. Their relatively high frequency in African-Americans must be interpreted in the context of the ancestral environment of these subjects in Africa, where diet and lifestyle were presumably less predisposing to atherosclerosis and where parasitic infections were major causes of morbidity and mortality before reproductive age. Parasites feed on host cholesterol for successful infection. The nonsense PCSK9 SNPs may have been positively selected because they reduced susceptibility to severe parasitic infections through cholesterol restriction. If so, these SNPs should be significantly more frequent in Sub-Saharan Africa where parasitic diseases, malaria in particular, have been and still are major selective forces.

Mechanisms of action of mycophenolate mofetil in preventing acute and chronic allograft rejection

Mycophenolate mofetil (MMF), a prodrug of mycophenolic acid (MPA), an inhibitor of inosine-5'-monophosphate dehydrogenase, has several immunosuppressant actions. MPA depletes guanosine and deoxyguanosine nucleotides preferentially in T and B lymphocytes, inhibiting proliferation and suppressing cell-mediated immune responses and antibody formation, major factors in acute and chronic rejection. MPA also can induce T-lymphocyte apoptosis. MPA suppresses dendritic cell maturation and can induce human monocyte-macrophage cell line differentiation, decreasing the expression of interleukin (IL)-1 and enhancing expression of the IL-1 receptor antagonist. In addition, MPA inhibits adhesion molecule glycosylation and expression and lymphocyte and monocyte recruitment. Activated macrophages produce nitric oxide (NO) and superoxide, which combine to generate tissue-damaging peroxynitrite. MPA depletes tetrahydrobiopterin and decreases NO production by inducible NO synthase without affecting constitutive NO synthase activity. By these mechanisms, MMF exerts anti-inflammatory activity, which could attenuate both acute and chronic rejection. Unlike calcineurin inhibitors, MMF is nonnephrotoxic and does not induce transforming growth factor-beta production, which is fibrogenic. MMF inhibits arterial smooth muscle cell proliferation, a contributor to graft proliferative arteriopathy, and does not increase blood pressure, cholesterol, or triglyceride levels. By decreasing high-density lipoprotein oxidation and macrophage recruitment, MMF also may delay onset/progression of graft atherosclerosis. Thus, MMF may prevent chronic rejection by several mechanisms. MMF activity is synergistic with that of other agents such as valganciclovir for treating cytomegalovirus infection. MMF also has synergistic activity with angiotensin-converting enzyme inhibitors or angiotensin II receptor antagonists in the treatment of some nephropathies in experimental animals. This combination may prevent progression toward end-stage renal disease in humans with chronic allograft, lupus, and diabetic nephropathies.

Mechanisms of action of mycophenolate mofetil

Mycophenolate mofetil (MMF, CellCept) is a prodrug of mycophenolic acid (MPA), an inhibitor of inosine-5'-monophosphate dehydrogenase. MPA depletes guanosine nucleotides preferentially in T and B lymphocytes and inhibits their proliferation, thereby suppressing cell-mediated immune responses and antibody formation. MPA also inhibits the glycosylation and expression of adhesion molecules, and the recruitment of lymphocytes and monocytes into sites of inflammation. MPA depletes tetrahydrobiopterin and decreases the production of nitric oxide by inducible NO synthase without affecting the activity of constitutive NO synthases. Activated macrophages produce NO and superoxide, which combine to generate tissue-damaging peroxynitrite. By these two mechanisms MMF exerts anti-inflammatory activity. Unlike calcineurin inhibitors, MMF is not nephrotoxic and does not induce the production of TGFbeta, which is fibrogenic. MMF does not increase blood pressure, cholesterol levels or triglyceride levels in recipients. MMF reduces acute and chronic rejection in allograft recipients and is efficacious in some nephropathies. Evidence is accumulating that MMF may have clinical utility in some autoimmune disorders.

Evolutionary explanations in medical and health profession courses: are you answering your students' "why" questions?

BACKGROUND

Medical and pre-professional health students ask questions about human health that can be answered in two ways, by giving proximate and evolutionary explanations. Proximate explanations, most common in textbooks and classes, describe the immediate scientifically known biological mechanisms of anatomical characteristics or physiological processes. These explanations are necessary but insufficient. They can be complemented with evolutionary explanations that describe the evolutionary processes and principles that have resulted in human biology we study today. The main goal of the science of Darwinian Medicine is to investigate human disease, disorders, and medical complications from an evolutionary perspective.

DISCUSSION

This paper contrasts the differences between these two types of explanations by describing principles of natural selection that underlie medical questions. Thus, why is human birth complicated? Why does sickle cell anemia exist? Why do we show symptoms like fever, diarrhea, and coughing when we have infection? Why do we suffer from ubiquitous age-related diseases like arteriosclerosis, Alzheimer's and others? Why are chronic diseases like type II diabetes and obesity so prevalent in modern society? Why hasn't natural selection eliminated the genes that cause common genetic diseases like hemochromatosis, cystic fibrosis, Tay sachs, PKU and others?

SUMMARY

In giving students evolutionary explanations professors should underscore principles of natural selection, since these can be generalized for the analysis of many medical questions. From a research perspective, natural selection seems central to leading hypotheses of obesity and type II diabetes and might very well explain the occurrence of certain common genetic diseases like cystic fibrosis, hemochromatosis, Tay sachs, Fragile X syndrome, G6PD and others because of their compensating advantages. Furthermore, armed with evolutionary explanations, health care professionals can bring practical benefits to patients by treating their symptoms of infection more specifically and judiciously. They might also help curtail the evolutionary arms race between pathogens and antibiotic defenses.