Hunting for disease genes in multi-functional diseases.

Disease genes may be identified through functional, positional, and candidate gene approaches. Although extensive and often labor-intensive studies such as family linkage analysis, functional investigation of gene products and genome database searches are usually involved, thousands of human disease genes, especially for monogenic diseases with Mendelian transmission, have been identified. However, in diseases caused by more than one gene, or by a combination of genetic and environmental factors, identification of the genes is even more difficult. Common examples include atherosclerosis, cancer, Alzheimer's disease, asthma, diabetes, glaucoma, and age-related macular degeneration. There have been conflicting reports on the roles of associated genes. Even with population-based case-control studies and new statistical methods such as the sib-ship disequilibrium test and the discordant alleles test, there is no agreement on whether alpha2-macroglobulin (A2M) is a gene for Alzheimer's disease. Another example is the inconsistent association between age-related macular degeneration and ATP-binding cassette transporter (ABCR). Ethnic variation causes further complications. In our investigation of LDL-receptor variants in familial hypercholesterolemia, and the trabecular meshwork inducible glucocorticoid response protein, or myocillin (TIGR-MYOC) mutation pattern in primary open angle glaucoma, we did find dissimilar results in Chinese compared to Caucasians. New information from the Human Genome Project and advancements in technologies will aid the search for and confirm identification of disease genes despite such challenges.     

Molecular diagnostics of genetic eye diseases

Eye diseases can be simple or complex, and mostly of heterogeneous molecular genetics. Some eye diseases are caused by mutations in a single gene, but some diseases, such as primary open angle glaucoma, can be due to sequence variations in multiple genes. In some diseases, both genetic and epigenetic mechanisms are involved, as was recently revealed in the mechanism of retinoblastoma. Disease causative mutations and phenotypes may vary by ethnicity and geography. To date, more than a hundred candidate genes for eye diseases are known, although less than 20 have definite disease-causing mutations. The three common genetic eye diseases, primary open angle glaucoma, age-related macular degeneration, and retinitis pigmentosa, all have known gene mutations, but these account for only a portion of the patients. While the search for eye disease genes and mutations still goes on, known mutations have been utilized for diagnosis. Genetic markers for pre-symptomatic and pre-natal diagnosis are available for specific diseases such as primary open angle glaucoma and retinoblastoma. This paper reviews the molecular basis of common genetic eye diseases and the available genetic markers for clinical diagnosis. Difficulties and challenges in molecular investigation of some eye diseases are discussed. Establishment of ethnic-specific disease databases that contain both clinical and genetic information for identification of genetic markers with diagnostic, prognostic, or pharmacological value is strongly advocated.     

Population and molecular genetics of susceptibility to tuberculosis.

Genetic influences on the course of mycobacterial infections during epidemics and in the endemic areas have always been suspected, but the precise nature of such genetic control and of the inherited mechanisms of susceptibility has been unknown. We have used the methods of population genetics in the mouse to discover a single dominant autosomal gene which controls the susceptibility to tuberculosis. The phenotypic expression of this gene has been defined as the nonspecific macrophage activation for bactericidal function. Using recombinant inbred strains we have mapped this gene to the centromeric part of Chromosome 1, and we have identified closely linked DNA polymorphisms (RFLP sites) which can be used as biochemical markers of innate susceptibility. It has recently become obvious that a homologous linkage group of RFLP sites is conserved in the bovine genome and also on the long arm (2q) of human Chromosome 2, suggesting the existence of a human homologue of the mouse host resistance gene. Experiments currently in progress test this hypothesis by linkage analysis of the trait of resistance and susceptibility to tuberculosis with the allelic forms of the 2q DNA markers. The identification of the human gene for susceptibility would be of major importance in the search for genetically susceptible individuals and in the development of novel strategies of specific prevention and treatment.     

Carrier detection of Hemophilia B by using a restriction site polymorphism associated with the coagulation Factor IX gene.

The cloned complementary DNA for coagulation Factor IX (FIX) detects a frequent restriction fragment length polymorphism (RFLP) in human genomic DNAs digested with the restriction endonuclease Taq I. This genetic marker was used, in parallel with coagulation and immunological assays, to follow the segregation of an abnormal FIX gene in a large Hemophilia B family. Among the six potential female carriers, functional assays showed that four had a high probability, and two a low probability of being carriers. Analysis at the DNA level with the cDNA probe was informative in five of the six cases, and in all these five the diagnosis of carrier state was definitively confirmed. This demonstrates the feasibility of using linkage analysis at the DNA level for the genetic screening of Hemophilia B. This method has the advantages over conventional assays of giving a diagnosis of certainty, and of being applicable to early prenatal diagnosis using biopsies of trophoblast villi. At present, the single known polymorphism associated with the FIX gene restricts the application of linkage analysis to informative cases (40%), but findings of additional RFLPs in this region should improve this figure.     

Microarray technology and applications in the arena of genome-wide association

BACKGROUND: there is a revolution occurring in single nucleotide polymorphism (SNP) genotyping technology, with high-throughput methods now allowing large numbers of SNPs (10(5)-10(6)) to be genotyped in large cohort studies. This has enabled large-scale genome-wide association (GWA) studies in complex diseases, such as diabetes, asthma, and inflammatory bowel disease, to be undertaken for the first time. CONTENT: the GWA approach serves the critical need for a comprehensive and unbiased strategy to identify causal genes related to complex disease, and is rapidly replacing the more traditional candidate gene studies and microsatellite-based linkage mapping approaches that have dominated gene discovery attempts for common diseases. As a consequence of employing array-based technologies, over the last 3 years dramatic discoveries of key variants involved in multiple complex diseases and related traits have been reported in the top scientific literature and, most importantly, have been largely replicated by independent investigator groups. As a consequence, several novel genes have been identified, most notably in the metabolic, cardiovascular, autoimmune, and oncology disease areas, that are clearly rooted in the biology of these disorders. These discoveries have opened up new avenues for investigators to address novel molecular pathways that were not previously linked to or thought of in relation with these diseases. SUMMARY: this review provides a synopsis of recent advances and what we may expect to still emerge from this field.     

Genetic organization of complement receptor-related genes in the mouse

Using an interspecific cross, gene linkage relationships among members of the murine complement receptor-related genes, C4bp, Cfh, Mcry, and Mcr2, were analyzed by segregation of RFLP in 200 mice. The human homologues of these genes are tightly linked, composing the RCA locus, which maps to human chromosome (Chr.)1q32, within a large linkage group conserved between human Chr.1q21-32 and mouse Chr.1. RFLP associated with C4bp and Cfh map within this conserved linkage group; Cfh is located 9 cM telomeric to C4bp, which is consistent with linkage data for their human homologues. Mcry and Mcr2, while tightly linked, are located outside the conserved group, 40 cM telomeric to C4bp. These data suggest that a translocation or inversion occurred within the RCA family during the evolution of the mouse, defining a breakpoint of this large conserved linkage group.     

Molecular genetics of human major histocompatibility complex: clinical applications

Techniques in molecular biology have proved to be very useful in the study of the biology and genetics of the MHC. In particular we have been able to study the Class II gene region in more detail. It is very important because most of the clinical interest of MHC has been focused on the Class II: Certain Class II alleles are strongly associated with autoimmune diseases, and Class II molecules play a crucial role in the interactions between the cells in immune response. DNA polymorphism studies (RFLP) have shown us that polymorphism of MHC genes seems to be considerable. Other close associations between diseases and Class II markers than using serological HLA typings have been found. Molecular cloning of the Class III genes has allowed us to analyse the molecular basis of the complement protein deficiencies, which are often associated with autoimmune diseases. Furthermore, cloning of the genes coding for steroid 21-hydroxylase has revealed the reason for the linkage between CAH and HLA, and has given a possibility for prenatal diagnosis of this disease at the DNA level.     

α-cardiac actin is a novel disease gene in familial hypertrophic cardiomyopathy

We identified the alpha-cardiac actin gene (ACTC) as a novel disease gene in a pedigree suffering from familial hypertrophic cardiomyopathy (FHC). Linkage analyses excluded all the previously reported FHC loci as possible disease loci in the family studied, with lod scores varying between -2.5 and -6.0. Further linkage analyses of plausible candidate genes highly expressed in the adult human heart identified ACTC as the most likely disease gene, showing a maximal lod score of 3.6. Mutation analysis of ACTC revealed an Ala295Ser mutation in exon 5 close to 2 missense mutations recently described to cause the inherited form of idiopathic dilated cardiomyopathy (IDC). ACTC is the first sarcomeric gene described in which mutations are responsible for 2 different cardiomyopathies. We hypothesize that ACTC mutations affecting sarcomere contraction lead to FHC and that mutations affecting force transmission from the sarcomere to the surrounding syncytium lead to IDC.     

Transgenic rabbits as therapeutic protein bioreactors and human disease models

Genetically modified laboratory animals provide a powerful approach for studying gene expression and regulation and allow one to directly examine structure-function and cause-and-effect relationships in pathophysiological processes. Today, transgenic mice are available as a research tool in almost every research institution. On the other hand, the development of a relatively large mammalian transgenic model, transgenic rabbits, has provided unprecedented opportunities for investigators to study the mechanisms of human diseases and has also provided an alternative way to produce therapeutic proteins to treat human diseases. Transgenic rabbits expressing human genes have been used as a model for cardiovascular disease, AIDS, and cancer research. The recombinant proteins can be produced from the milk of transgenic rabbits not only at lower cost but also on a relatively large scale. One of the most promising and attractive recombinant proteins derived from transgenic rabbit milk, human alpha-glucosidase, has been successfully used to treat the patients who are genetically deficient in this enzyme. Although the pronuclear microinjection is still the major and most popular method for the creation of transgenic rabbits, recent progress in gene targeting and animal cloning has opened new avenues that should make it possible to produce transgenic rabbits by somatic cell nuclear transfer in the future. Based on a computer-assisted search of the studies of transgenic rabbits published in the English literature here, we introduce to the reader the achievements made thus far with transgenic rabbits, with emphasis on the application of these rabbits as human disease models and live bioreactors for producing human therapeutic proteins and on the recent progress in cloned rabbits.     

Genetic analysis of autoimmune gld mice. I. Identification of a restriction fragment length polymorphism closely linked to the gld mutation within a conserved linkage group

A linkage map of distal mouse chromosome 1 was generated using restriction fragment length polymorphism (RFLP) analysis of DNA prepared from 95 [C3H-gld/gld X Mus spretus)F1 X C3H-gld/gld] backcross mice. The gene order was: (centromere) C4bp, Ren-1,2, Ly-5, [At-3/gld], Apoa-2/Ly-17, Spna-1 (telomere). All mice expressing the phenotype of gld homozygotes were homozygous for the At-3 RFLP characteristic of C3H mice and none of the mice heterozygous for At-3 RFLPs had characteristics of gld homozygotes, demonstrating close linkage between these genes. The identification of an RFLP closely linked to the gld gene provides a starting point for the identification of a genetic defect that results in abnormal T cells and autoimmune disease.     

Clinical applications of gene probes in human genetic disease, malignancy, and infectious disease

Recent developments in recombinant DNA technology have made possible the production of gene probes consisting of cloned gene segments, cloned segments of DNA linked to genes, and synthetic gene fragments. Several methods have been developed by which these probes may be used for the diagnosis of human disease. This technology has been outstandingly successful for prenatal diagnosis and carrier detection in many genetic diseases. These methods have also been successfully applied to the analysis of human malignancies, by providing for the determination of cell lineage and clonality in lymphoid neoplasms. Finally, these methods have shown potential for rapid and sensitive diagnosis of some infectious diseases.     

Molecular diversity of calcium channel activities by depolarization

Voltage-gated calcium channels are involved in a large variety of cellular functions such as excitation-contraction coupling, hormone secretion, firing and pacemaker activity, gene activation and proliferation. Cloning of complementary DNAs encoding for calcium channel subunits has challenged the study of the functional properties of calcium channels and has allowed analysis of the molecular basis of calcium channel diversity. Recently, pore-forming subunits of T-type calcium channels have been cloned. Recent data describing the genes encoding calcium channels, their molecular and pharmacological studies, as well as their linkage to human genetic diseases are reviewed in this article.     

Immunoregulatory genes in autoimmune thyroid disease]

Autoimmune thyroid diseases (AITD) has a strong genetic basis. Although several candidate genes have been studied, the AITD causing genes are still unknown. Major candidate immune regulatory genes include human leukocyte antigen (HLA) gene, Ig heavy chain genes, T cell receptor genes, IL-1 receptor antagonist gene, IL-1 alpha gene and cytotoxic T lymphocyte antigen-4 (CTLA-4) gene. The relation between HLA and AITD has extensively been studied. In addition, polymorphism of the 3'-untranslated region and codon 17 of the CTLA-4 gene has been reported to associate positively with AITD. However, no linkage analyses have showed positive relation between AITD and these candidate genes except for HLA.     

Gene mutations in retinitis pigmentosa and their clinical implications

Retinitis pigmentosa (RP) is a group of inherited progressive retinal diseases affecting about 1 in 3500 people worldwide. So far, there is no prevention or cure, with permanent visual loss or even blindness the ultimate consequence usually after midlife. The genetics of RP are complex. It can be sporadic, autosomal dominant, autosomal recessive, or X-linked. Thirty-two genes are known to be associated with RP, sometimes the same gene gets involved in different inheritance traits. Some RP cases have a digenic cause. About 60% RP cases still have no known genetic cause. A large number of mutations cause RP, and they can be deletions, insertions, or substitutions that cause missense mutations or truncations. The RHO, RP1, and RPGR genes contribute the greatest number of known mutations causative of RP. But there is no single mutation that alone accounts for more than 10% of unrelated patients. Genetic testing for RP therefore requires screening for a group of genes. High-throughput and automated sequence detection technologies are essential. Due to the complexity in phenotype and genetics, and the fact that RP is untreatable, genetic testing for presymptomatic diagnosis of RP is controversial. Meanwhile, new genes are still to be identified, mostly by family linkage and sib-pair analysis. Research on gene therapy for RP requires information on gene mutations causative of RP.     

Diabetes mellitus susceptibility with varied diseased phenotypes and its comparison with phenome interactome networks

An emerging area of interest in understanding disease phenotypes is systems genomics. Complex diseases such as diabetes have played an important role towards understanding the susceptible genes and mutations. A wide number of methods have been employed and strategies such as polygenic risk score and allele frequencies have been useful, but understanding the candidate genes harboring those mutations is an unmet goal. In this perspective, using systems genomic approaches, we highlight the application of phenome-interactome networks in diabetes and provide deep insights. LINC01128, which we previously described as candidate for diabetes, is shown as an example to discuss the approach.     

RNA Interference Improves Myopathic Phenotypes in Mice Over-expressing FSHD Region Gene 1 (FRG1)

Muscular dystrophies, and other diseases of muscle, arise from recessive and dominant gene mutations. Gene replacement strategies may be beneficial for the former, while gene silencing approaches may provide treatment for the latter. In the last two decades, muscle-directed gene therapies were primarily focused on treating recessive disorders. This disparity at least partly arose because feasible mechanisms to silence dominant disease genes lagged behind gene replacement strategies. With the discovery of RNA interference (RNAi) and its subsequent development as a promising new gene silencing tool, the landscape has changed. In this study, our objective was to demonstrate proof-of-principle for RNAi therapy of a dominant myopathy in vivo. We tested the potential of adeno-associated viral (AAV)-delivered therapeutic microRNAs, targeting the human Facioscapulohumeral muscular dystrophy (FSHD) region gene 1 (FRG1), to correct myopathic features in mice expressing toxic levels of human FRG1 (FRG1^−high mice). We found that FRG1 gene silencing improved muscle mass, strength, and histopathological abnormalities associated with muscular dystrophy in FRG1^−high mice, thereby demonstrating therapeutic promise for treatment of dominantly inherited myopathies using RNAi. This approach potentially applies to as many as 29 different gene mutations responsible for myopathies inherited as dominant disorders.     

The future of Duchenne muscular dystrophy gene therapy: shrinking the dystrophin gene

Duchenne muscular dystrophy is a debilitating muscle-wasting disease caused by mutations in the dystrophin gene - one of the largest genes identified thus far - and which ultimately results in premature death. With no current treatment available, the hopes of many sufferers lie in the establishment of an effective gene therapy. The adeno-associated virus is now emerging as a premium gene transfer vector eliciting minimal immune response from the host and allowing for long-term gene expression. It is the scope of this review to examine the recent efforts that have been made to develop ultra-truncated versions of the dystrophin gene that retain functionality, yet can still be cloned into recombinant adeno-associated viral vectors and other low-capacity vector systems.     

Use of nucleic acid probes in genetic tests

Advances in molecular genetics have led to the development of clinical assays for several genetic diseases. Two general testing approaches are available: direct detection of the genetic mutation or indirect detection using DNA markers close to, or within, the defective gene. Direct testing at the nucleic acid level is available for diseases in which the basic defect is well characterized, such as sickle cell anemia. Several methods are available for detection of the point mutation that causes sickle cell anemia including: routine Southern blot analysis, allele specific oligonucleotides, and polymerase chain reaction gene amplification. For diseases such as cystic fibrosis, in which the basic genetic defect has not yet been characterized, an indirect approach is used. This approach relies on linkage analysis using DNA markers close to the genetic defect. Inheritance of the DNA marker is followed through the family. Unlike direct testing, the DNA marker does not detect the actual genetic defect. Therefore, a prediction of inheritance of the linked disease is given based on the risk of recombination between the disease locus and the DNA marker. An appreciation of the differences between the direct and indirect approaches is necessary to understand their attributes and their limitations.