Genetic Variation In Individuals Research Articles

Gene-Environment Correlation in Humans: Lessons from Psychology for Quantitative Genetics.

Evolutionary biologists have long been aware that the effects of genes can reach beyond the boundary of the individual, that is, the phenotypic effects of genes can alter the environment. Yet, we rarely apply a quantitative genetics approach to understand the causes and consequences of genetic variation in the ways that individuals choose and manipulate their environments, particularly in wild populations. Here, I aim to stimulate research in this area by reviewing empirical examples of such processes from the psychology literature. Indeed, psychology researchers have been actively investigating genetic variation in the environments that individuals experience-a phenomenon termed "gene-environment correlation" (rGE)-since the 1970s. rGE emerges from genetic variation in individuals' behavior and personality traits, which in turn affects the environments that they experience. I highlight concepts and examples from this literature, emphasizing the relevance to quantitative geneticists working on wild, nonhuman organisms. I point out fruitful areas of crossover between these disciplines, including how quantitative geneticists can test ideas about rGE in wild populations.

Genetic or Other Causation Should Not Change the Clinical Diagnosis of Cerebral Palsy.

High throughput sequencing is discovering many likely causative genetic variants in individuals with cerebral palsy. Some investigators have suggested that this changes the clinical diagnosis of cerebral palsy and that these individuals should be removed from this diagnostic category. Cerebral palsy is a neurodevelopmental disorder diagnosed on clinical signs, not etiology. All nonprogressive permanent disorders of movement and posture attributed to disturbances that occurred in the developing fetal and infant brain can be described as “cerebral palsy.” This definition of cerebral palsy should not be changed, whatever the cause. Reasons include stability, utility and accuracy of cerebral palsy registers, direct access to services, financial and social support specifically offered to families with cerebral palsy, and community understanding of the clinical diagnosis. Other neurodevelopmental disorders, for example, epilepsy, have not changed the diagnosis when genomic causes are found. The clinical diagnosis of cerebral palsy should remain, should prompt appropriate genetic studies and can subsequently be subclassified by etiology.

Effect of genetic polymorphisms on Alzheimer's disease treatment outcomes: an update.

Genetic variations in individuals may cause differences in the response to cholinesterase inhibitor drugs used in the treatment of Alzheimer’s disease (AD). Through this review, we aimed to understand the potential relationship between genetic polymorphisms and treatment response in AD. We conducted a systematic review of the studies published from 2006 to 2018 that assessed the relationship between genetic polymorphisms and the pharmacotherapeutic outcomes of patients with AD. Via several possible mechanisms, genetic polymorphisms of many genes, including ABCA1, ApoE3, CYP2D6, CHAT, CHRNA7, and ESR1, appear to have strong correlations with the treatment response of patients with AD. Indeed, these genetic polymorphisms, either in the form of single nucleotide polymorphisms or direct changes to one or more amino acids, have been shown to cause differences in the therapeutic response. In summary, our findings indicate that genetic polymorphisms should be considered in the management of AD to achieve both effective and efficient treatment outcomes in terms of cost and prognosis.

Study on the association SLC17A1 rs1165196 with gout in Vietnamese population

Gout is a common form of inflammatory arthritis caused by urate crystals in a joint from high levels of serum uric acid (SUA). The development of gout is not only triggered by environmental factors but also by genetic variants of individuals. Previous studies demonstrated that the genetic association with gout risk varies in different ethnic populations. The aim of this study was to assess the relationship between SLC17A1 rs1165196 and gout. A total of 169 patients with gout and 351 age-matched healthy controls were recruited at the Nguyen Trai hospital in Southern Vietnam for genomic DNA extraction. Genotypes of SLC17A1 rs1165196 were obtained using PCR-RFLP. Chi-Square test ( 16χ"> 2) was used to test whether allele distribution of rs1165196 follows Hardy-Weinberg Equilibrium (HWE). Associations of the clinical characteristics between gout patient and control groups were assessed using Mann-Whitney U. Chi-Square test or Fisher’s exact test was used to check four models (additive, recessive, dominant, co-dominant) for association of rs1165196 with gout. The results showed that SLC17A1 rs1165196 was in accordance with HWE (p>0.05) and the genotype frequencies of AA, AG and GG were 0.57, 0.38 and 0.05, respectively. The most differences between gout patient and control groups were uric acid and hyperuricemia (p=0.000). Other clinical characteristics such as BMI and CRP levels were also significantly different between gout patient and control groups (p<0.05). However, there was no association of SLC17A1 rs1165196 with the risk of gout in Vietnamese population (p>0.05). Further study with larger sample size should be implemented to confirm our results on the association of SLC17A1 rs1165196 and gout in the Vietnamese population.

Age-related clonal hematopoiesis: implications for hematopoietic stem cell transplantation.

Over the past decade, advances in hematopoietic stem cell transplantation (HSCT) have enabled older individuals to undergo the procedure as well as to serve as donors. Recently, aging has been linked with the development of age-related clonal hematopoiesis (ARCH), defined as the gradual clonal expansion of hematopoietic stem and progenitor cells (HSPC) carrying recurrent disruptive genetic variants in individuals without a diagnosis of hematologic malignancy. Here we will review the implications of ARCH in the context of HSCT. ARCH is highly prevalent in the general population and commonly involves genes that are recurrently mutated in hematologic malignancies. Nevertheless, the vast majority of individuals with ARCH will not develop overt hematologic disease in their lifetime. The presence of ARCH may increase the risk of therapy-related myeloid neoplasms (t-MN) in individuals undergoing autologous HSCT. In the setting of allogeneic HSCT, ARCH present in the donor may contribute to adverse outcomes such as unexplained cytopenias posttransplant and donor cell leukemia. A better understanding of the hematopoietic milieu of HSCT recipients and of the importance of ARCH in the context of the replicative pressures imposed on transplanted HSPCs is needed in order to optimize conditioning regimens, donor selection and clinical outcomes post-HSCT.

Genetic variation and structure of Juniperus chinensis L. (Cupressaceae) in Korea

BackgroundJuniperus chinensis L. populations are distributed locally on several areas including coastal cliffs which are difficult to access in the central eastern Korea. Wild populations inhabit relatively barren environments such as rocky areas and cliffs, which are very sensitive to even minor environmental disturbances including artificial interventions and natural disturbances, and thus demonstrate great fluctuations in the population size and density. This study aims to analyze the genetic diversity, differentiation, and genetic structure of each population in order to provide useful data required to establish a substantial conservation strategy of J. chinensis.ResultsThe genetic diversity of J. chinensis at the population level (P = 78.7%, h = 0.282, S.I. = 0.420) was somewhat higher compared with those measured in the same genus, Juniperus. The genetic differentiation degree among nine populations established naturally in central eastern Korea was 11.50% and that among sub-populations within the same area was 5.52%. On the other hand, genetic variation of individuals within the populations was 82.93%. But frequency of the main allele was different among loci. In particular, fixation of allele frequency and occurrence of rare allele in the highly isolated population suggest a likelihood that genetic drift would occur in populations of this plant. As the result of analysis on the genetic structure of nine populations, nearby populations and isolated populations tended to form separate clusters from each other as the hypothetical number of clusters (K) increase.ConclusionsThis result implies that if the population size of J. chinensis is reduced due to environmental change and artificial and/or natural disturbances in the future, it could affect negatively on the genetic diversity of the plant species. In order to maintain and conserve genetic diversity of J. chinensis, ecological network, which can help genetic exchange among the local populations, should be prepared, and conservation strategies in situ as well as ex situ are also required with continuous monitoring.

A Mini-Review: Leber Congenital Amaurosis: Identification of Disease-Causing Variants and Personalised Therapies.

Leber congenital amaurosis (LCA) encompasses a group of severe inherited retinal dystrophies (IRDs) responsible for early childhood blindness. There are currently 25 genes implicated in the pathogenesis of these diseases, and identification of disease-causing variants will be required for personalised therapies. Whole exome and whole genome sequencing is informative for detecting novel disease-causing genes, whilst next-generation sequencing has excelled at detecting novel variants in known disease-causing genes.A global effort will be required to identify patient populations for early intervention. At the Australian Inherited Retinal Disease Registry and DNA Bank, we seek to identify genetic variants in individuals with IRDs in the Australian population to identify potential candidates for clinical trials, to inform clinical management of patients including reproductive options and to expand existing knowledge of IRDs.Due to the diversity of genes implicated, personalised strategies are likely to be the benchmark for treating these diseases, and a combined approach of different therapies may be optimal in treating some of these diseases.

Variant genotyping with gap filling.

Although recent developments in DNA sequencing have allowed for great leaps in both the quality and quantity of genome assembly projects, de novo assemblies still lack the efficiency and accuracy required for studying genetic variation of individuals. Thus, efficient and accurate methods for calling and genotyping genetic variants are fundamental to studying the genomes of individuals. We study the problem of genotyping insertion variants. We assume that the location of the insertion is given, and the task is to find the insertion sequence. Insertions are the hardest structural variant to genotype, because the insertion sequence must be assembled from the reads, whereas genotyping other structural variants only requires transformations of the reference genome. The current methods for constructing insertion variants are mostly linked to variation calling methods and are only able to construct small insertions. A sub-problem in genome assembly, the gap filling problem, provides techniques that are readily applicable to insertion genotyping. Gap filling takes the context and length of a missing sequence in a genome assembly and attempts to assemble the intervening sequence. In this paper we show how tools and methods for gap filling can be used to assemble insertion variants by modeling the problem of insertion genotyping as filling gaps in the reference genome. We further give a general read filtering scheme to make the method scalable to large data sets. Our results show that gap filling methods are competitive against insertion genotyping tools. We further show that read filtering improves performance of insertion genotyping especially for long insertions. Our experiments show that on long insertions the new proposed method is the most accurate one, whereas on short insertions it has comparable performance as compared against existing tools.

DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification.

Mutations in somatic cells generate a heterogeneous genomic population and may result in serious medical conditions. Although cancer is typically associated with somatic variations, advances in DNA sequencing indicate that cell-specific variants affect a number of phenotypes and pathologies. Here, we show that mutagenic damage accounts for the majority of the erroneous identification of variants with low to moderate (1 to 5%) frequency. More important, we found signatures of damage in most sequencing data sets in widely used resources, including the 1000 Genomes Project and The Cancer Genome Atlas, establishing damage as a pervasive cause of sequencing errors. The extent of this damage directly confounds the determination of somatic variants in these data sets.

De Novo Mutations in SON Disrupt RNA Splicing of Genes Essential for Brain Development and Metabolism, Causing an Intellectual-Disability Syndrome

The overall understanding of the molecular etiologies of intellectual disability (ID) and developmental delay (DD) is increasing as next-generation sequencing technologies identify genetic variants in individuals with such disorders. However, detailed analyses conclusively confirming these variants, as well as the underlying molecular mechanisms explaining the diseases, are often lacking. Here, we report on an ID syndrome caused by de novo heterozygous loss-of-function (LoF) mutations in SON. The syndrome is characterized by ID and/or DD, malformations of the cerebral cortex, epilepsy, vision problems, musculoskeletal abnormalities, and congenital malformations. Knockdown of son in zebrafish resulted in severe malformation of the spine, brain, and eyes. Importantly, analyses of RNA from affected individuals revealed that genes critical for neuronal migration and cortex organization (TUBG1, FLNA, PNKP, WDR62, PSMD3, andHDAC6) and metabolism (PCK2, PFKL, IDH2, ACY1, and ADA) are significantly downregulated because of the accumulation of mis-spliced transcripts resulting from erroneous SON-mediated RNA splicing. Our data highlight SON as a master regulator governing neurodevelopment and demonstrate the importance of SON-mediated RNA splicing in human development.

Plasma Melatonin and Progesterone Profiles of Suffolk and Romney Marsh Ewes Implanted with Melatonin during Anoestrus Season at Lower Latitudes in Southern Hemisphere

Background: The subcutaneous implants of melatonin are stimulatory and mimic the positive effects of short photoperiod on reproduction in small ruminants. This study investigated the daily plasma melatonin profiles in ewes treated with melatonin implants and kept under natural photoperiod in Southeastern Brazil. The plasma progesterone concentrations were also investigated before and after melatonin implantation.Materials, Methods & Results: Romney Marsh (n = 11) and Suffolk (n = 10) ewes, which had been isolated from rams for at least 2 months prior to the beginning of the trial, were randomly allocated in two groups based on melatonin implant treatment (with or without melatonin implant). For plasma melatonin concentration, 43 days after melatonin implantation and 3 days before the ram introduction blood samples were collected every 2 hours during 24 hours. For plasma progesterone concentrations, blood samples were collected every once to twice a week for 2 different periods: prior to melatonin implantation and 46 days after the melatonin implantation and at the same day of the introduction of rams. The hormonal concentrations were determined by the radioimmunoassay method (RIA). The data were analyzed according to MIXED procedure (SAS) as repeated measurements for random animal effects. The effect of melatonin treatment on plasma melatonin 24-h period varied according to the breed. At the dark-phase, there were no plasma melatonin differences (P > 0.05) between implanted and no-implanted (228.02 ± 58.39 vs. 169.59 ± 48.39) Romney Marsh ewes whereas for Suffolk ewes the plasma melatonin levels were higher in implanted (305.61 ± 68.39 pg/mL) than no-implanted (151.26 ± 38.35 pg/mL) ones. At the light-phase, melatonin treatment effects could be evidenced and these differences (P < 0.01) consisted of higher melatonin values for implanted ewes and basal values for no-implanted ones in both breed groups. Before the melatonin implantation, the plasma progesterone levels were ˂ 1 ng/mL for Romney Marsh (0.41 ± 0.02 ng/mL) and Suffolk (0.47 ± 0.02 ng/mL) ewes. During the ram introduction period, no melatonin treatment effect was observed on plasma progesterone concentrations in both breed groups, but 2 days after ram introduction the plasma progesterone concentrations increased the mean values > than 1 ng/mL in implanted and no-implanted Suffolk ewes. In implanted Romney Marsh ewes the elevation of progesterone mean values was weak whereas in no-implanted Romney Marsh ewes the progesterone levels were maintained ˂ 1 ng/mL during all the blood sample collection times.Discussion: The melatonin treatment also produced a similar model of daily melatonin levels as reported previously by others, which is characterized by high plasma melatonin concentrations during the light phase of the day. The effect of melatonin implants on plasma melatonin profiles interacted with breed confirming an individual response to melatonin implantation which is proportional to genetic individual variation pattern of melatonin secretion. Before the melatonin implantation all Romney Marsh and Suffolk ewes were judged to be in non-ovulatory period (anoestrus) with plasma progesterone mean values lower than 1 ng/mL. The melatonin treatment helped to induce the ovulatory activity in most of the ewes that were in anestrous at the time of melatonin implantation and the efficacy of this treatment depends on the individual variation in ovulatory response to ram introduction. In Southeastern Brazil., melatonin implant altered the daily plasma melatonin profiles of Suffolk and Romney Marsh ewes by increasing the melatonin levels during the light-phase of the day. Melatonin implant also induced an ovulatory response in Suffolk and Romney Marsh after the introduction of the rams. For no-implanted Suffolk ewes, the male effect is sufficient to provoke an ovulatory response.

Whole-Exome Sequencing in Familial Parkinson Disease.

Parkinson disease (PD) is a progressive neurodegenerative disease for which susceptibility is linked to genetic and environmental risk factors. To identify genetic variants contributing to disease risk in familial PD. A 2-stage study design that included a discovery cohort of families with PD and a replication cohort of familial probands was used. In the discovery cohort, rare exonic variants that segregated in multiple affected individuals in a family and were predicted to be conserved or damaging were retained. Genes with retained variants were prioritized if expressed in the brain and located within PD-relevant pathways. Genes in which prioritized variants were observed in at least 4 families were selected as candidate genes for replication in the replication cohort. The setting was among individuals with familial PD enrolled from academic movement disorder specialty clinics across the United States. All participants had a family history of PD. Identification of genes containing rare, likely deleterious, genetic variants in individuals with familial PD using a 2-stage exome sequencing study design. The 93 individuals from 32 families in the discovery cohort (49.5% [46 of 93] female) had a mean (SD) age at onset of 61.8 (10.0) years. The 49 individuals with familial PD in the replication cohort (32.6% [16 of 49] female) had a mean (SD) age at onset of 50.1 (15.7) years. Discovery cohort recruitment dates were 1999 to 2009, and replication cohort recruitment dates were 2003 to 2014. Data analysis dates were 2011 to 2015. Three genes containing a total of 13 rare and potentially damaging variants were prioritized in the discovery cohort. Two of these genes (TNK2 and TNR) also had rare variants that were predicted to be damaging in the replication cohort. All 9 variants identified in the 2 replicated genes in 12 families across the discovery and replication cohorts were confirmed via Sanger sequencing. TNK2 and TNR harbored rare, likely deleterious, variants in individuals having familial PD, with similar findings in an independent cohort. To our knowledge, these genes have not been previously associated with PD, although they have been linked to critical neuronal functions. Further studies are required to confirm a potential role for these genes in the pathogenesis of PD.

Utilizing the Jaccard index to reveal population stratification in sequencing data: a simulation study and an application to the 1000 Genomes Project.

Population stratification is one of the major sources of confounding in genetic association studies, potentially causing false-positive and false-negative results. Here, we present a novel approach for the identification of population substructure in high-density genotyping data/next generation sequencing data. The approach exploits the co-appearances of rare genetic variants in individuals. The method can be applied to all available genetic loci and is computationally fast. Using sequencing data from the 1000 Genomes Project, the features of the approach are illustrated and compared to existing methodology (i.e. EIGENSTRAT). We examine the effects of different cutoffs for the minor allele frequency on the performance of the approach. We find that our approach works particularly well for genetic loci with very small minor allele frequencies. The results suggest that the inclusion of rare-variant data/sequencing data in our approach provides a much higher resolution picture of population substructure than it can be obtained with existing methodology. Furthermore, in simulation studies, we find scenarios where our method was able to control the type 1 error more precisely and showed higher power. dmitry.prokopenko@uni-bonn.de Supplementary data are available at Bioinformatics online.

Variation in size and condition of neonate pygmy bluetongue lizards, Tiliqua adelaidensis

Phenotypic variation among offspring of individual animals is an important life-history trait. In viviparous lizards, it could result from genetic variation of individuals and also differences in environments experienced by mothers during gestation. We investigated variation in phenotype and survival of neonate pygmy bluetongue lizards, Tiliqua adelaidensis, over three sampling years. We explored changes in body condition, using body size residuals as an index, and body size (snout-vent length (SVL) and mass) of neonates. For litters that were captured with their mothers, we hypothesised that body condition and size of offspring are influenced by the condition and size of their mothers, the presence of mothers in the burrow and litter size. We found that there were significant variations in body condition and mass of neonates among years. There was no significant relationship between neonate body condition, mass and SVL and post-partum body condition of their mothers. Results revealed that females with higher SVL produced larger litters. None of the analyses showed any effect of mother’s presence on neonate body condition, SVL or mass. Neither was there any effect of observed litter size on these parameters. Our findings have important conservation implications for this endangered species, given that the aim of conservation managers is to encourage conditions that promote optimum body condition and fitness in offspring in order to maximise their survival in fragmented habitats.

Identification of rod- and cone-specific expression signatures to identify candidate genes for retinal disease

Recent advances in technology have greatly increased our ability to identify genetic variants in individuals with retinal disease. However, determining which are likely to be pathogenic remains a challenging task. Using a transgenic coneless (cl) mouse model, together with rodless (rd/rd) and rodless/coneless (rd/rd cl) mice, we have characterised patterns of gene expression in the rod and cone photoreceptors at a genome-wide level. We examined the expression of >27,000 genes in the mice lacking rods, cones or both and compared them with wild type animals. We identified a list of 418 genes with highly significant changes in expression in one or more of the transgenic strains. Pathway analysis confirmed that expected Gene Ontology terms such as phototransduction were over-represented amongst these genes. However, many of these genes have no previously known function in the retina. Gene set enrichment analysis further demonstrated that the mouse orthologues of known human retinal disease genes were significantly enriched amongst those genes with decreased expression. Comparison of our data to human disease loci with no known causal genetic changes has highlighted genes with significant changes in expression making these strong candidates for further screening. These data add to the current literature through the utilisation of the specific cl and rd/rd cl models. Moreover, this study identifies genes that appear to be implicated in photoreceptor function thereby providing a valuable filter for variants identified by high-throughput sequencing in individuals with retinal disease.

Allele‐specific, Hybridization‐based, Washing‐free Fluorescence Signal Production Platforms for Quantitation of Single‐Base Change (C → U) in RNA

A single nucleotide polymorphism (SNP) is a single base‐pair substitution that commonly constitutes the genetic variation in individuals. Because of its association with disease susceptibility and drug resistance, SNP detection is of great value in studying the variation in drug responses. Here we report four types of washing‐free (i.e., separation‐free or sequential addition of reagents) and polymerase chain reaction (PCR)‐free fluorescence signal production platforms for quantitative detection of a single‐base mismatch in RNA and compare their analytical efficiency. The RNA‐templated SNP detection methods in this study are based on the allele‐specific hybridization approach and/or on the allele‐specific oligonucleotide ligation approach, and have been successfully applied to the quantitation of single‐base mutation (C → U) in RNA of the BCR–ABL fusion gene, by endpoint measurements of fluorescence intensity. These methods have several advantages for practical applications, such as direct discrimination of single‐base mismatch of the RNA extracted from cells, no requirement of PCR amplification, performance of homogeneous detection, easy design of detection probes, and suitability for large‐scale genotyping.

Identifying and predicting the impact of functional single nucleotide polymorphisms (SNPs) in human CAV-3 gene

Genetic mutations, such as Single nucleotide polymorphisms (SNPs) are known to be the most reported type of genetic variations in individuals and thought to have a crucial impact on the understanding of many genetic related diseases. One of the major challenges is to find the deleterious SNPs in disease-associated genes. In the current study, computational methods were used to analyze the SNPs which may effect the expression and function of CAV 3 gene. Of the total 377 SNPs, 288(76.8%) were found to be non-coding SNPs, while 53 (14.1%) were non synonymous (ns)SNPs and 4(1.1%) were in the mRNA UTRs. Forty nine nsSNPs encoding missense mutation were tested for the parable effect on protein structure and functions using SIFT, I-Mutant 2, PolyPhen 2 and PANTHER soft wares. Moreover, one nsSNP (R27Q) was further analyzed using HOPE project, and this mutation predicted to substantially affect the structure along with the function of caveolin 3 protein.

Effect of sampling on the extent and accuracy of the inferred genetic history of recombining genome

Accessible biotechnology is enabling the cataloging of genetic variants in individuals in populations at unprecedented scales. The use of phylogeny of the individuals within populations allows a model-based approach to studying these variations, which is important in understanding relationships between and across populations. For the somatic genome, however, the phylogeny must take recombinations (and other genetic mixing events) into account. Hence the resulting topology is more complex than a tree. Unlike a tree topology, it is not as apparent which events are visible from the extant samples. An earlier work presented a mathematical model (called the minimal descriptor) for teasing apart the inherent visible information from that which any specific algorithm might see. We use this framework to study the effect of sampling sizes on the overall inferred genetic history. In this paper, we seek to understand the extent, characteristics (in terms of recent versus ancient genetic events) and reliability of what was resolvable within field samples drawn from modern populations.We observed that most of the visible ancient events are recoverable from relatively small sample sizes. However, without identification of this relatively small minority of ancient genetic events, most of the signal will appear to reflect modern events and admixtures. We also found that the more ancient events are likely to be reproduced with higher fidelity between multiple samplings, and that the identified older events are less likely to yield false positive discrimination between populations.We conclude that a recombinant phylogenetic reconstruction is necessary to identify which markers are most likely to discriminate ancient events, and to discriminate between populations with lower risk of false positives. Secondly, on a broader note, this study also provides a general methodology for a critical assessment of the inferred common genetic history of populations (say, in plant cultivars or animal populations).

Association between host's genetic diversity and parasite burden in damselflies

Recent research indicates that low genetic variation in individuals can increase susceptibility to parasite infection, yet evidence from natural invertebrate populations remains scarce. Here, we studied the relationship between genetic heterozygosity, measured as AFLP-based inbreeding coefficient fAFLP , and gregarine parasite burden from eleven damselfly, Calopteryx splendens, populations. We found that in the studied populations, 5-92% of males were parasitized by endoparasitic gregarines (Apicomplexa: Actinocephalidae). Number of parasites ranged from none to 47 parasites per male, and parasites were highly aggregated in a few hosts. Mean individual fAFLP did not differ between populations. Moreover, we found a positive association between individual's inbreeding coefficient and parasite burden. In other words, the more homozygous the individual, the more parasites it harbours. Thus, parasites are likely to pose strong selection pressure against inbreeding and homozygosity. Our results support the heterozygosity-fitness correlation hypothesis, which suggests the importance of heterozygosity for an individual's pathogen resistance.

Cholesterol-Secreting and Statin-Responsive Hepatocytes from Human ES and iPS Cells to Model Hepatic Involvement in Cardiovascular Health

Hepatocytes play a central and crucial role in cholesterol and lipid homeostasis, and their proper function is of key importance for cardiovascular health. In particular, hepatocytes (especially periportal hepatocytes) endogenously synthesize large amounts of cholesterol and secrete it into circulating blood via apolipoprotein particles. Cholesterol-secreting hepatocytes are also the clinically-relevant cells targeted by statin treatment in vivo. The study of cholesterol homeostasis is largely restricted to the use of animal models and immortalized cell lines that do not recapitulate those key aspects of normal human hepatocyte function that result from genetic variation of individuals within a population. Hepatocyte-like cells (HLCs) derived from human embryonic and induced pluripotent stem cells can provide a cell culture model for the study of cholesterol homeostasis, dyslipidemias, the action of statins and other pharmaceuticals important for cardiovascular health. We have analyzed expression of core components for cholesterol homeostasis in untreated human iPS cells and in response to pravastatin. Here we show the production of differentiated cells resembling periportal hepatocytes from human pluripotent stem cells. These cells express a broad range of apolipoproteins required for secretion and elimination of serum cholesterol, actively secrete cholesterol into the medium, and respond functionally to statin treatment by reduced cholesterol secretion. Our research shows that HLCs derived from human pluripotent cells provide a robust cell culture system for the investigation of the hepatic contribution to human cholesterol homeostasis at both cellular and molecular levels. Importantly, it permits for the first time to also functionally assess the impact of genetic polymorphisms on cholesterol homeostasis. Finally, the system will also be useful for mechanistic studies of heritable dyslipidemias, drug discovery, and investigation of modes of action of cholesterol-modulatory drugs.