Hypertrophic cardiomyopathy: from "heart tumour" to a complex molecular genetic disorder

Hypertrophic cardiomyopathy (HCM) is a disorder which has fascinated clinicians for many years. The remarkable diversity in clinical presentations, ranging from no symptoms to severe heart failure and sudden cardiac death, illustrates the complexity of this disorder. Over the last decade, major advances have been made in our understanding of the molecular basis of several cardiac conditions. HCM was the first cardiac disorder in which a genetic basis was identified and as such, has acted as a paradigm for the study of an inherited cardiac disorder. At least eleven genes have now been identified, defects in which cause HCM. Most of these genes encode proteins which comprise the basic contractile unit of the heart, i.e. the sarcomere. Genetic studies are now beginning to have a major impact on diagnosis in HCM, as well as in guiding treatment and preventative strategies. While much is known about which genes cause disease, relatively little is known about the molecular steps leading from the gene defect to the clinical phenotype, and what factors modify the expression of the mutant genes. Concurrent studies in cell culture and animal models of HCM are now beginning to shed light on the signalling pathways involved in HCM, and the role of both environmental and genetic modifying factors. Understanding these basic molecular mechanisms will ultimately improve our knowledge of the basic biology of heart muscle function, and will therefore provide new avenues for diagnosis and treatment not only for HCM, but for a range of cardiovascular diseases in man.     

Application of molecular biology to pulmonary disease

The techniques of molecular biology now make it possible to clone specific genes, determine the nature of their molecular message, produce their protein product, and study their function in health and disease. DNA probes, particularly those for ribosomal RNA, offer a new way for the diagnosis of infectious diseases affecting the lung, particularly TB. In addition, recombinant DNA libraries of mycobacteria can be used to isolate mycobacterial antigens recognized by patients with TB. This may allow development of better immunologic tests and vaccines. A specific chromosomal abnormality of human chromosome 3 has been found in small cell lung cancer. It is hypothesized that loss of genes from this region may play a role in the pathogenesis of lung cancer. Another important factor in development of the disease is the expression of cancer-associated oncogenes. In addition to insights into the biology of lung cancer, these oncogenes might provide a method to classify various types of lung cancer and predict response to therapy. Specialized DNA markers known as RFLPs have now been linked with CF. This has resulted in localization of the CF gene to human chromosome 7 and the detection of the gene in most of its carriers who have been studied. Knowing where the gene resides and use of techniques of genetic engineering will eventually allow isolation of the CF gene (or genes) on chromosome 11 and determination of the biochemical defect for which it codes. Similarly, the gene for human alpha 1-antitrypsin has also been cloned. A practical benefit is the production of normal and mutant enzyme for replacement therapy in patients.     

Use of gene transfer to study expression of steroid-responsive genes

The ability to introduce DNA into eucaryotic cells has provided a means to analyse the expression of cloned genes. By manipulating the genes in vitro using recombinant DNA techniques it is possible to identify regulatory DNA sequences which are important for individual steps in gene expression. This review will summarize how these techniques have been applied to study steroid-responsive genes and what we have learned about steroid hormone action.     

Genetic testing

The first genetic tests started to be developed about twenty years ago. Their initial applications were limited to genetic counselling and prenatal diagnosis of a few hereditary diseases. Technological progress and the identification of genes responsible for many hereditary diseases have led to their development and diffusion. They have become a nearly irreplaceable tool for the diagnosis of hereditary diseases. In the future, their indications should increase when genes implicated in multifactorial diseases are progressively identified. The impact will probably be particularly important in cardiology because most cardiovascular diseases are multifactorial. The first predisposing factors (factor V. prothrombin...) for a predisposition to thrombosis are now daily genetic investigations. In parallel, the progress in pharmacogenetics should enable everyone to have appropriate qualitative and quantitative treatment according to their genetic makeups, which should improve both efficacy and safety. In order to face up to the exponential increase in demand for the genetic tests which will result from these advances, the laboratories should have new high speed, powerful and economic equipment. DNA microchips, which are currently under development could, at least initially, provide a solution to this problem. It is now certain that genetic testing will become routine and, in time, it will be used massively in both hospital and community medicine.     

Genetics,genomics, and their relevance to pathology and therapy

Genetic and genomic investigations are a starting point for the study of human disease, seeking to discover causative variants relevant to disease pathophysiology. Over the past 5 years, massively parallel, high-throughput, next-generation sequencing techniques have revolutionized genetics and genomics, identifying the causes of many Mendelian diseases. The application of whole-genome sequencing and whole-exome sequencing to large populations has produced several publicly available sequence datasets that have revealed the scope of human genetic variation and have contributed to important methodological advances in the study of both common and rare genetic variants in genetically complex diseases. The importance of noncoding genetic variation has been highlighted by the Encyclopedia of DNA Elements (ENCODE) project and National Institutes of Health (NIH) Roadmap Epigenomics Program and integrated analyses of these datasets, together with disease-specific datasets, will provide an important and powerful tool for determining the mechanisms through which disease-associated, noncoding variation influences disease risk.     

Gene expression profiling in human asthma

Asthma is a chronic inflammatory disease of the lungs, characterized by airway hyperreactivity, mucus hypersecretion, and airflow obstruction. Despite recent advances, the genetic regulation of asthma pathogenesis is still largely unknown. Gene expression profiling techniques are well suited to study complex diseases and hold substantial promise for identifying novel genes and pathways in asthma; however, relatively few studies have been completed in human asthma. The few studies that have been done have identified many novel candidate genes and pathways in asthma pathogenesis, including ALOX15 and serine proteinase inhibitors cathepsin C and G. The interpretation of results of these studies should be cautious, as limitations include small sample sizes and heterogeneity of study populations and tissues sampled. In the future, the promise of gene expression studies would be enhanced by the use of larger sample sizes and attempts to standardize phenotype, sample collection techniques, and analysis. As the field of expression profiling in asthma advances, we hope it will improve our understanding of critical questions about mechanisms involved in susceptibility to the disease, as well as help to personalize care by improving appropriate selection of patients for prevention and treatment strategies.     

Genetics and osteoporosis

Over the past 10 years, many advances have been made in understanding the mechanisms by which genetic factors regulate susceptibility to osteoporosis. It has become clear from studies in man and experimental animals that different genes regulate BMD at different skeletal sites and in men and women. Linkage studies have identified several chromosomal regions that regulate BMD, but only a few causative genes have been discovered so far using this approach. In contrast, significant advances have been made in identifying the genes that cause monogenic bone diseases, and polymorphic variation is some of these genes has been found to contribute to the genetic regulation of BMD in the normal population. Other genes that have been investigated as possible candidates for susceptibility to osteoporosis because of their role in bone biology, such as vitamin D, have yielded mixed results. Many candidate gene association studies have been underpowered, and meta-analysis has been used to try to confirm or refute potential associations and gain a better estimate of their true effect size in the population. Most of the genetic variants that confer susceptibility to osteoporosis remain to be discovered. It is likely that new techniques such as whole-genome association will provide new insights into the genetic determinants of osteoporosis and will help to identify genes of modest effect size. From a clinical standpoint, genetic variants that are found to predispose to osteoporosis will advance our understanding of the pathophysiology of the disease. They could be developed as diagnostic genetic tests or form molecular targets for design of new drugs for the prevention and treatment of osteoporosis and other bone diseases.     

The use of genetic microarray analysis to classify and predict prognosis in haematological malignancies

The introduction of microarrays offers the opportunity to examine the expression of many thousands of genes in a single experiment. Investigations in leukaemia and lymphoma have led to the identification of a number of subgroups, with a defined gene expression pattern, not previously identified by morphology, cytogenetics or molecular techniques. In many cases these expression patterns can be linked to the tumour cells normal developmental counterpart, and represent distinct disease subgroups with different clinical presentations and outcomes. The technology has also identified genes that may be important in tumour cell biology including key genes in cell proliferation, adhesion, apoptosis, and the development of drug resistance. These early studies demonstrate that genetic microarrays will be useful in classifying haematological malignancies, predicting response to treatment, predicting prognosis, and identifying novel targets for therapy.     

Applications of molecular genetics to gastrointestinal and liver diseases. I. Technical approaches

Recent developments in recombinant DNA techniques have allowed an understanding of the molecular genetics of many diseases, some affecting the gastrointestinal tract and liver. DNA probes which detect sequences within or near disease genes can be selected by direct approaches, if the gene product or primary gene function is known, or by indirect methods when the chromosomal location is known. Such probes have resulted in extensive family studies which can now define risks to family members of developing a genetic disease. The development of the polymerase chain reaction will also be of considerable use in clinical genetics and in the diagnosis of some infectious diseases. The techniques are summarized and examples of their use are given. A glossary of terms is also provided.     

Mutational activation of the c-K-ras gene in human pancreatic carcinoma

We have reported the presence of c-K-ras oncogenes activated by single point mutations at codon 12 in a vast majority of human pancreatic carcinomas. Formalin-fixed, paraffin-embedded specimens from surgical resections, autopsies and biopsies were used as well as snap frozen surgical specimens. The high oncogene incidence has been confirmed in other studies and indicate that somatic mutational activation of the c-K-ras gene is an important event in the development, maintenance or progression of cancer of the exocrine pancreas. While the role that these point mutations play in any or all of these processes remains to be determined, their presence is useful clinically for the diagnosis of pancreatic carcinoma at the molecular genetic level. The detection of mutated c-K-ras oncogenes in fine needle aspirates of pancreatic masses, that by cytomorphology may be suspicious but not diagnostic of malignant disease, increases the sensitivity of the diagnosis for this cancer. The identification of codon 12 mutations in the c-K-ras gene in pancreatic adenocarcinomas has been possible by advances in recombinant DNA techniques, especially by the development of in vitro gene amplification by the polymerase chain reaction (PCR). The possibility of analysing formalin-fixed, paraffin-embedded tissue for the presence of genetic alterations as small as single point mutations by PCR in concert with other mutation detection techniques, should facilitate the molecular genetic analysis of pancreatic carcinoma. Retrospective studies using stored specimens are now feasible with the technology described and should yield important information on the molecular epidemiology and aetiology of this and other diseases.     

Molecular biology and gene therapy in gastroenterology and hepatology.

Molecular analyses have become an integral part of biomedical research as well as clinical medicine. The definition of the molecular and genetic basis of many human diseases has led to a better understanding of their pathogenesis and has in addition offered new perspectives for their diagnosis, therapy and prevention. Genetically, human diseases can be classified as monogenetic, complex genetic and acquired genetic diseases. Based on this classification, gene therapy is based on four concepts: gene substitution, gene augmentation, block of gene expression or function as well as DNA vaccination. While recent developments are promising, various delivery, targeting and safety issues need to be addressed before gene therapy will enter clinical practice. In the future, molecular diagnosis and gene therapy of gastrointestinal and liver diseases will be part of our patient management and complement existing diagnostic, therapeutic and preventive strategies.     

Molecular genetics of chronic liver diseases

The molecular genetics of five common single gene and one polygenic chronic liver disease is discussed. In two of the single gene disorders, alpha 1-antitrypsin deficiency and cystic fibrosis, the gene responsible is now known and the repertoire of different mutations underlying the disease is being defined. In the other three single gene defects (haemochromatosis, polycystic liver disease and Wilson's disease) the chromosomal location of the disease allele is known. It is anticipated that recombinant DNA techniques will enable the genes responsible for these diseases to be cloned in the near future, thus allowing the biochemical abnormalities to be defined through reverse genetics. In many chronic liver diseases the relative contribution of genetic and environmental factors remains unclear. Evidence suggests there is a definite genetic component in predisposition to alcoholic cirrhosis; the role of putative candidate genes is discussed. It is hoped that the definition of a genetic locus linked to alcoholic cirrhosis will ultimately teach us more about the basic pathogenesis of this disease.     

Complex diseases in gastroenterology and hepatology: GERD, Barrett's, and esophageal adenocarcinoma.

Gastroesophageal reflux disease, Barrett's esophagus, and esophageal adenocarcinoma are related diseases with environmental and genetic determinants. The genetic changes are relevant in 2 distinct ways. First, there are heritable variations in germline DNA that may influence the individual susceptibility to cancer. Second, there is an accumulation of somatic-cell genetic and epigenetic changes within the epithelium during the metaplasia-dysplasia-carcinoma sequence, which may be an important determinant for the likelihood for cancer progression. Esophageal cancer occurring in the context of a familial syndrome is rare and most cases are sporadic. The sporadic cases still may have heritable germline influences, but these are likely to involve multiple, low-penetrance susceptibility genes. To date, the relative contribution and identity of such genes are unknown. However, in the future the identification of susceptibility genes could have important public health implications for patient management. With regard to the epithelium, a map gradually is being created of the frequently occurring alterations. Some of these changes are critical whereas others are bystanders. As well as the identification of abnormalities in target genes, it also is possible to determine the global gene expression profile of these diseases and to correlate this profile with clinical outcome. It is hoped that these complementary approaches will enable patients to be stratified in terms of their cancer risk so that prevention, surveillance, and treatment strategies can be targeted appropriately. At the current time, genetics does not influence routine clinical management of patients with gastroesophageal reflux disease, Barrett's esophagus, or esophageal adenocarcinoma.     

Advances in the prenatal diagnosis of hematologic diseases

Prenatal diagnosis of hematologic diseases can now be performed with fetal blood, fetal amniotic fluid cell DNA, and fetal chorionic villi DNA. Some hemoglobinopathies can be detected by all three methods, and the choice will depend on the available obstetric and laboratory techniques, as well as the time of presentation of the pregnancy. Hopefully, further development of molecular probes and techniques will soon expand these options to all of the globin disorders. Detection of coagulation disorders in utero currently requires samples of pure fetal blood. Gene cloning is accomplished for some (factor IX and antithrombin III) and is underway for others (factor VIII), and further investigation is necessary to determine whether deficiencies in these gene products are due to gene deletion or to mutant genes linked to polymorphic restriction enzyme sites of diagnostic use. Thus, molecular biology may be applied to prenatal diagnosis of the clotting problems, but this has not yet been accomplished. Disorders affecting the number and/or function of erythrocytes, leukocytes, and platelets can be diagnosed by analysis of fetal blood. Blood samples will continue to be required until more is known about the molecular biology of hematopoiesis. Syndromes that can be diagnosed by chromosome studies should be revealed in cultures of amniotic fluid cells, fetal blood lymphocytes, and chorionic villi cells. Cultured cells can be examined for karyotypes, Y-chromatin, spontaneous or induced chromosome breakage, DNA repair, SCEs, and translocations. The techniques for culturing amniotic cells and fetal blood white cells are established, and those for growing cells from chorionic villi are improving rapidly. Direct preparations of cells from villi only may suffice for some of the above analyses. The study of hematologic disease in utero has thus come full circle, from the use of amniotic cells to determine the sex in X-linked disorders, to fetal blood sampling for the analysis of gene products, then back to amniocentesis for DNA, and now earlier in gestation to chorionic villi. All of this has occurred in less than ten years, and it is anticipated that developments in the next ten years will be equally dramatic. The future should bring all prenatal testing into the first trimester, use molecular probes, and provide for both early diagnosis and early treatment of genetic hematologic disease.     

Thalassaemia

Thalassaemia is one of the most common genetic diseases worldwide, with at least 60,000 severely affected individuals born every year. Individuals originating from tropical and subtropical regions are most at risk. Disorders of haemoglobin synthesis (thalassaemia) and structure (eg, sickle-cell disease) were among the first molecular diseases to be identified, and have been investigated and characterised in detail over the past 40 years. Nevertheless, treatment of thalassaemia is still largely dependent on supportive care with blood transfusion and iron chelation. Since 1978, scientists and clinicians in this specialty have met regularly in an international effort to improve the management of thalassaemia, with the aim of increasing the expression of unaffected fetal genes to improve the deficiency in adult β-globin synthesis. In this Seminar we discuss important advances in the understanding of the molecular and cellular basis of normal and abnormal expression of globin genes. We will summarise new approaches to the development of tailored pharmacological agents to alter regulation of globin genes, the first trial of gene therapy for thalassaemia, and future prospects of cell therapy.     

Genetic linkage analysis in hypertension: principles and practice.

BACKGROUND: Primary hypertension is a hereditary disorder characterized by a complex etiological interplay of multiple genetic and environmental factors, until now defying attempts at identifying pathogenetically important genes. The marriage of classical genetics and molecular techniques is now offering a powerful set of tools to uncover such disease-relevant genes. SUMMARY: Based upon the availability of methods to directly examine chromosomal and genomic DNA structures, molecular genetics has at its disposal today an array of markers far more numerous and specific than the phenotype parameters used in classical genetics. In addition, use of DNA polymorphisms takes the process of genetic analysis immediately to that level of investigation--the genome--from which relevant data will ultimately come forth. The deployment of these tools in the pursuit of elucidating the pathogenesis of hereditary hypertension, and their use for two commonly applied strategies, candidate gene analysis and reverse genetics, are discussed. SIGNIFICANCE: Whilst still in its early stages, the application of molecular genetic methods to the study of hereditary hypertension now holds the realistic promise of identifying disease-relevant genes. This will provide the basis for advanced diagnostic, preventive and therapeutic approaches.