Sensitized polygenic trait analysis

Development of a novel immune-related genes prognostic signature for osteosarcoma

Immune-related genes (IRGs) are responsible for osteosarcoma (OS) initiation and development. We aimed to develop an optimal IRGs-based signature to assess of OS prognosis. Sample gene expression profiles and clinical information were downloaded from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Genotype-Tissue Expression (GTEx) databases. IRGs were obtained from the ImmPort database. R software was used to screen differentially expressed IRGs (DEIRGs) and functional correlation analysis. DEIRGs were analyzed by univariate Cox regression and iterative LASSO Cox regression analysis to develop an optimal prognostic signature, and the signature was further verified by independent cohort (GSE39055) and clinical correlation analysis. The analyses yielded 604 DEIRGs and 10 hub IRGs. A prognostic signature consisting of 13 IRGs was constructed, which strikingly correlated with OS overall survival and distant metastasis (p < 0.05, p < 0.01), and clinical subgroup showed that the signature’s prognostic ability was independent of clinicopathological factors. Univariate and multivariate Cox regression analyses also supported its prognostic value. In conclusion, we developed an IRGs signature that is a prognostic indicator in OS patients, and the signature might serve as potential prognostic indicator to identify outcome of OS and facilitate personalized management of the high-risk patients.

A trans-acting Variant within the Transcription Factor RIM101 Interacts with Genetic Background to Determine its Regulatory Capacity

Most genetic variants associated with disease occur within regulatory regions of the genome, underscoring the importance of defining the mechanisms underlying differences in regulation of gene expression between individuals. We discovered a pair of co-regulated, divergently oriented transcripts, AQY2 and ncFRE6, that are expressed in one strain of Saccharomyces cerevisiae, ∑1278b, but not in another, S288c. By combining classical genetics techniques with high-throughput sequencing, we identified a trans-acting single nucleotide polymorphism within the transcription factor RIM101 that causes the background-dependent expression of both transcripts. Subsequent RNA-seq experiments revealed that RIM101 regulates many more targets in S288c than in ∑1278b and that deletion of RIM101 in both backgrounds abrogates the majority of differential expression between the strains. Strikingly, only three transcripts undergo a significant change in expression after swapping RIM101 alleles between backgrounds, implying that the differences in the RIM101 allele lead to a remarkably focused transcriptional response. However, hundreds of RIM101-dependent targets undergo a subtle but consistent shift in expression in the S288c RIM101-swapped strain, but not its ∑1278b counterpart. We conclude that ∑1278b may harbor a variant(s) that buffers against widespread transcriptional dysregulation upon introduction of a non-native RIM101 allele, emphasizing the importance of accounting for genetic background when assessing the impact of a regulatory variant.

Does your gene need a background check? How genetic background impacts the analysis of mutations, genes, and evolution

The premise of genetic analysis is that a causal link exists between phenotypic and allelic variation. However, it has long been documented that mutant phenotypes are not a simple result of a single DNA lesion, but are instead due to interactions of the focal allele with other genes and the environment. Although an experimentally rigorous approach focused on individual mutations and isogenic control strains has facilitated amazing progress within genetics and related fields, a glimpse back suggests that a vast complexity has been omitted from our current understanding of allelic effects. Armed with traditional genetic analyses and the foundational knowledge they have provided, we argue that the time and tools are ripe to return to the underexplored aspects of gene function and embrace the context-dependent nature of genetic effects. We assert that a broad understanding of genetic effects and the evolutionary dynamics of alleles requires identifying how mutational outcomes depend upon the 'wild type' genetic background. Furthermore, we discuss how best to exploit genetic background effects to broaden genetic research programs.

Quantitative trait loci for electrocardiographic parameters and arrhythmia in the mouse

Cardiac arrhythmias associated with sudden death are influenced by multiple biological pathways and are modulated by numerous genetic and environmental factors. Elevated heart rate and prolonged ECG indices of conduction and repolarization have been associated with risk of sudden death. Insight into the genetic underpinnings of these parameters thus provides an important means to the dissection of the genetic components modulating risk of sudden cardiac death. In this study we mapped quantitative trait loci (QTL) modulating heart rate, ECG indices of conduction and repolarization, and susceptibility to arrhythmia, in a conduction disease-sensitized F(2) mouse population. Heart rate, P-duration, PR-, QRS- and QT-interval were measured at baseline (n=502) and after flecainide administration (n=370) in mutant F(2) progeny (F(2)-MUT) resulting from the FVB/NJ-Scn5a1798(insD/+) X 129P2-Scn5a1798(insD/+) mouse cross. Episodes of sinus arrhythmia and ventricular tachyarrhythmia occurring post-flecainide were treated as binary traits. F(2)-MUT mice were genotyped using a genome-wide 768 single nucleotide polymorphism (SNP) panel. Interval mapping uncovered multiple QTL for ECG parameters and arrhythmia. A sex-interacting scan identified QTL displaying sex-dependency, and a two-dimensional QTL scan unmasked locus-locus (epistasis) interactions influencing ECG traits. A number of QTL coincided at specific chromosomal locations, suggesting pleiotropic effects at these loci. Through transcript profiling in myocardium from the parental mouse strains we identified genes co-localizing at the identified QTL that constitute highly relevant candidates for the observed effects. The detection of QTL influencing ECG indices and arrhythmia is an essential step towards identifying genetic networks for sudden, arrhythmic, cardiac death.

Genome-wide search for genes that modulate inflammatory arthritis caused by Ali18 mutation in mice

Many of inflammatory diseases, including inflammatory arthritis, are multifactorial bases. The Ali18 semidominant mutation induced by N-ethyl-N-nitrosourea in the C3HeB/FeJ (C3H) genome causes spontaneous inflammation of peripheral limbs and elevated immunoglobulin E (IgE) levels in mice. Although the Ali18 locus was mapped to a single locus on chromosome 4, the arthritic phenotype of Ali18/+ mice was completely suppressed in F1 hybrid genetic backgrounds. To determine the chromosomal locations of the modifier loci affecting the severity of arthritis, an autosomal genome scan of 22 affected Ali18/+ F2 mice was conducted using C57BL/6J as a partner strain. Interestingly, regions on chromosomes 1 and 3 in C3H showed significant genetic interactions. Moreover, 174 N2 (backcross to Ali18/Ali18) and 267 F2 animals were used for measurement of arthritis scores and plasma IgE levels, and also for genotyping with 153 genome-wide single nucleotide polymorphism (SNP) markers. In N2 populations, two significant trait loci for arthritis scores on chromosomes 1 and 15 were detected. Although no significant scores were detected in F2 mice besides chromosome 4, a suggestive score was detected on chromosome 3. In addition, a two-dimensional genome scan using F2 identified five suggestive scores of chromosomal combinations, chromosomes 1 x 10, 2 x 6, 3 x 4, 4 x 9, and 6 x 15. No significant trait loci affecting IgE levels were detected in both N2 and F2 populations. Identification of the Ali18 modifier genes by further detailed analyses such as congenic strains and expression profiling may dissect molecular complexity in inflammatory diseases.

Deletion of eIF2beta suppresses testicular cancer incidence and causes recessive lethality in agouti-yellow mice

The agouti-yellow (A(y)) deletion is the only genetic modifier known to suppress testicular germ cell tumor (TGCT) susceptibility in mice or humans. The A(y) mutation deletes Raly and Eif2s2, and induces the ectopic expression of agouti, all of which are potential TGCT-modifying mutations. Here we report that the reduced TGCT incidence of heterozygous A(y) males and the recessive embryonic lethality of A(y) are caused by the deletion of Eif2s2, the beta subunit of translation initiation factor eIF2. We found that the incidence of affected males was reduced 2-fold in mice that were partially deficient for Eif2s2 and that embryonic lethality occurred near the time of implantation in mice that were fully deficient for Eif2s2. In contrast, neither reduced expression of Raly in gene-trap mice nor ectopic expression of agouti in transgenic or viable-yellow (A(vy)) mutants affected TGCT incidence or embryonic viability. In addition, we provide evidence that partial deficiency of Eif2s2 attenuated germ cell proliferation and differentiation, both of which are important to TGCT formation. These results show that germ cell development and TGCT pathogenesis are sensitive to the availability of the eIF2 translation initiation complex and to changes in the rate of translation.

Loss of the transmembrane but not the soluble kit ligand isoform increases testicular germ cell tumor susceptibility in mice

Several genetic variants act as modifiers of testicular germ cell tumor (TGCT) susceptibility in the 129/Sv mouse model of human pediatric TGCTs. One such modifier, the Steel locus, encodes the transmembrane-bound and soluble ligand of the kit receptor. Some (Sl and SlJ) but not all (Sld) mutations of the Steel locus increase TGCT incidence in heterozygous mutant mice. Because Sl and SlJ are large deletions that affect multiple transcripts and Sld is an intragenic deletion of the kit ligand (Kitl) from which only the soluble protein is produced, it was uncertain whether Kitl or a neighboring gene is a modifier of TGCT susceptibility. We tested the effect of the small Steel grizzle-belly (Slgb) deletion on TGCT susceptibility to determine whether Kitl is a TGCT modifier gene. An increase in TGCT incidence was observed in Slgb/+ heterozygotes, and fine mapping of the deletion breakpoints revealed that Kitl is the only conventional gene deleted by the mutation, suggesting that Kitl is the TGCT modifier gene at the Steel locus. Additionally, we propose that soluble KITL in Sld/+ heterozygous mutant mice complements a dosage effect of transmembrane-associated kit ligand on TGCT susceptibility and that the kit receptor (Kit) is haplosufficient for primordial germ cell development.

Testicular germ cell tumors in mice: new ways to study a genetically complex trait

Testicular germ cell tumors (TGCTs) are the most common cancer affecting young men. Although TGCTs are common and the genetic component of susceptibility is unusually strong, discovery of TGCT susceptibility genes in humans has been challenging. The 129/Sv inbred mouse strain is an important experimental model for studying the genetic control of TGCT susceptibility. It is the only inbred mouse strain with an appreciable frequency of spontaneous TGCTs. TGCTs in 129/Sv males share various developmental and histological characteristics with human pediatric TGCTs. As in humans, susceptibility in 129/Sv is a genetically complex trait that is too complex for conventional genetic approaches. However, several genetic variants, when congenic or isogenic on the 129/Sv background, act as genetic modifiers of TGCT susceptibility. Alternative experimental approaches based on these modifier genes can be used to unravel the complex genetic control of TGCT susceptibility. We discuss the application of modifier genes in genetic interaction tests and sensitized polygenic trait analyses toward the understanding of the complex genetics and biology of TGCT susceptibility in mice.

Trans-generational epistasis between Dnd1Ter and other modifier genes controls susceptibility to testicular germ cell tumors

The genetic basis for susceptibility to testicular germ cell tumors (TGCTs) has been remarkably elusive. Although TGCTs are the most common cancer in young men and have an unusually strong familial risk, only one low-frequency susceptibility gene has been identified for this highly multigenic trait. In tests to determine whether pairs of genetic variants act epistatically to modulate susceptibility in the 129/Sv mouse model of spontaneous TGCTs, we discovered an unusual mode of inheritance that involved interactions between different genes in different generations. Any of six genetic variants, in either the female or male parent interacted with the Dnd1(Ter) mutation in male offspring to significantly increase both the frequency of affected Ter/+ males and the proportion of bilateral cases. Trans-generational epistasis is a novel mode of epigenetic inheritance that could account for the difficulty of finding TGCT susceptibility genes in humans and might represent a mechanism for transmitting information about genetic and environmental conditions from parents to offspring through the germline.

The genetics of health

Recent experience with several high-profile drugs demonstrates the great challenges in developing effective and safe therapeutics. A complementary approach to the popular paradigm of disease genetics is based on inherited factors that reduce the incidence and severity of disease among individuals who are genetically predisposed to disease. We propose testing specifically for modifier genes and protective alleles among at-risk individuals and studying the efficacy of therapeutics based on the genetics of health.

Genetic interactions between susceptibility loci reveal epistatic pathogenic networks in murine lupus

Interactions between Sle1 and other susceptibility loci were required for disease development in the NZM2410 model of lupus. Sle1 corresponds to at least three subloci, Sle1a, Sle1b, and Sle1c, each of which independently causes loss of tolerance to chromatin, but displays a distinctive immune profile. We have used congenic strains to analyze the interactions between the Sle1 subloci and other lupus susceptibility loci using Y autoimmunity accelerator (Yaa) and Faslpr as sensitizing mutations. Sle1 coexpressed with either one of these single susceptibility alleles resulted in a highly penetrant nephritis, splenomegaly, production of nephrophilic antibodies, and increased expression of B- and T-cell activation markers. Here, we show that only Sle1b interacted with Yaa to produce these phenotypes, suggesting that Sle1b and Yaa belong to the same functional pathway. Interactions between the three Sle1 loci and lpr resulted in lymphocyte activation and lupus nephritis, but a significant mortality was observed only for the Sle1a.lpr combination. This suggests a major role for the FAS pathway in keeping in check the loss of tolerance mediated by the Sle1 loci, especially for Sle1a. Our results illustrate the complexity of interactions between susceptibility loci in polygenic diseases such as lupus and may explain the clinical heterogeneity of the disease.

Quantitative trait loci analysis for plasma HDL-cholesterol concentrations and atherosclerosis susceptibility between inbred mouse strains C57BL/6J and 129S1/SvImJ

OBJECTIVE

The C57BL/6 (B6) and 129 mouse inbred strains differ markedly in plasma HDL-cholesterol concentrations and atherosclerosis susceptibility after a high-fat diet consumption. To identify loci controlling these traits, we performed quantitative trait loci (QTL) analysis.

METHODS AND RESULTS

We fed a high-fat diet to 294 (B6x129S1/SvImJ)F2 females for 14 weeks, measured plasma HDL concentrations and size of aortic fatty-streak lesions, genotyped F2 females, and performed QTL analysis. HDL concentrations were affected by six loci: Hdlq14 and Hdlq15 on chromosome 1 (peaks cM 80 and cM 104, logarithm of odds [LOD] 5.3 and 9.7, respectively); Hdlq16 on chromosome 8 (cM 44, LOD 2.6); Hdlq17 on chromosome 9 (cM 24, LOD 2.9); Hdlq18 on chromosome 12 (cM 20, LOD 5.9); and Hdlq19 on chromosome 2 (cM 90), which interacted with Hdlq15. Atherosclerosis susceptibility was affected by five loci: Ath17 on chromosome 10 (cM 34, LOD 6.6); Ath18 on chromosome 12 (cM 16, LOD 3.7); Ath19 (chromosome 11, cM 60), which interacted with Ath18; and Ath20 (chromosome 10, cM 10), which interacted with Ath21 (chromosome 12, cM 50).

CONCLUSIONS

We identified six loci for HDL and five loci for atherosclerosis susceptibility in a (B6x129S1/SvImJ)F2 intercross.

Mapping Modifiers Affecting Muscularity of the Myostatin Mutant (MstnCmpt-dl1Abc) Compact Mouse

The hypermuscular Compact phenotype was first noted in a line of mice selected for high body weight and protein content. A new line, based on mice showing the Compact phenotype, was formed and selected for maximum expression of the Compact phenotype. Previously we mapped and identified a 12-bp deletion in the myostatin gene, denoted MstnCmpt-dl1Abc, which can be considered as a major gene responsible for the hypermuscular phenotype. Genetic analysis revealed that full expression of the hypermuscular phenotype requires the action of modifier loci in addition to MstnCmpt-dl1Abc. To map these modifier loci, an interspecific F2 population was generated between Comp9, an inbred line homozygous for MstnCmpt-dl1Abc, and CAST/Ei, an inbred line generated from Mus musculus castaneus. Selective DNA pooling and genotyping, separately by gender, was carried out within a subpopulation of the F2 consisting of individuals homozygous for MstnCmpt-dl1Abc. Significant association with hypermuscularity at a false discovery rate (FDR) of 0.05 was found for markers on chromosomes 3, 5, 7, 11, 16, and X. In all cases, the marker allele derived from the Comp9 parent showed a higher frequency in the hypermuscular group and the CAST/Ei allele in the normal group. The modifier loci apparently exerted their effects on muscularity only in the presence of MstnCmpt-dl1Abc.

Primer on medical genomics. Part VIII: Essentials of medical genetics for the practicing physician

After the mapping and sequencing of the human genome, medical professionals from essentially all specialties turned their attention to investigating the role genes play in health and disease. Until recently, medical genetics was considered a specialty of minor practical relevance. This view has changed with the development of new diagnostic and therapeutic possibilities. It is now realized that genetic disease represents an important part of medical practice. Achievements in cancer genetics, in the field of prenatal diagnostics (including carrier testing for common recessive disorders), and in newborn screening for treatable metabolic disorders reinforce the rapidly expanding role of genetics in medicine. Diagnosing a genetic disorder not only allows for disease-specific management options but also has implications for the affected individual's entire family. A working understanding of the underlying concepts of genetic disease with regard to chromosome, single gene, mitochondrial, and multifactorial disorders is necessary for today's practicing physician. Routine clinical practice in virtually all medical specialties will soon require integration of these fundamental concepts for use in accurate diagnosis and ensuring appropriate referrals for patients with genetic disease and their families.

Genetic control of susceptibility to spontaneous testicular germ cell tumors in mice

Testicular germ cell tumors (TGCTs) are the most common cancer affecting young men. TGCT is a polygenic trait and genes that control susceptibility for TGCT development have not yet been identified. The 129/Sv inbred strain of mice is an important experimental model to study the genetics and development of TGCTs. We review several novel approaches that were developed to study the susceptibility of TGCTs in the 129/Sv mouse model and its application in humans. These approaches showed that several spontaneous and engineered mutations interact with 129/Sv-derived susceptibility genes to enhance or suppress susceptibility; two of these mutations (Ter and Trp53) revealed novel linkages for susceptibility genes in sensitized polygenic trait analysis. Linkage analysis with a chromosome substitution strains suggests that as many as 100 genes control susceptibility. Bilateral TGCTs result from the coincidental occurrence of unilateral tumors. These results highlight the important contributions that this mouse model can make to studies of TGCT susceptibility in humans.

Wild mice: an ever-increasing contribution to a popular mammalian model

Classical laboratory inbred strains of mice have been extremely helpful for research in immunology and oncology, and more generally, for the analysis of complex traits. Unfortunately, because they all derive from a relatively small pool of ancestors, their genetic polymorphism is rather limited. However, recently strains belonging to different species of Mus have been established from wild progenitors. These are an interesting addition to the arsenal of mouse geneticists, because they can be crossed with classical laboratory strains to produce viable and fertile offspring with a large number of polymorphisms of natural origin. These strains are helpful for making genome annotations because they permit highly refined genotype-phenotype correlations. They also allow the interpretation of molecular variation within a clear evolutionary framework. In this article, we provide examples with the aim of promoting the use of these new strains.

Finding genes that underlie complex traits

Phenotypic variation among organisms is central to evolutionary adaptations underlying natural and artificial selection, and also determines individual susceptibility to common diseases. These types of complex traits pose special challenges for genetic analysis because of gene-gene and gene-environment interactions, genetic heterogeneity, low penetrance, and limited statistical power. Emerging genome resources and technologies are enabling systematic identification of genes underlying these complex traits. We propose standards for proof of gene discovery in complex traits and evaluate the nature of the genes identified to date. These proof-of-concept studies demonstrate the insights that can be expected from the accelerating pace of gene discovery in this field.

Mouse models for neurological disease

The mouse has many advantages over human beings for the study of genetics, including the unique property that genetic manipulation can be routinely carried out in the mouse genome. Most importantly, mice and human beings share the same mammalian genes, have many similar biochemical pathways, and have the same diseases. In the minority of cases where these features do not apply, we can still often gain new insights into mouse and human biology. In addition to existing mouse models, several major programmes have been set up to generate new mouse models of disease. Alongside these efforts are new initiatives for the clinical, behavioural, and physiological testing of mice. Molecular genetics has had a major influence on our understanding of the causes of neurological disorders in human beings, and much of this has come from work in mice.