Chapter 3 Genetic, environmental and infectious causes of disease
CAUSES OF DISEASE
In terms of causation, diseases may be:
Features pointing to a significant genetic contribution to the cause of a disease include a high incidence in particular families or races, or an association with a known inherited feature (e.g. gender, blood groups, histocompatibility haplotypes). Environmental factors are suggested by disease associations with occupations or geography. Ultimately, however, only laboratory investigation can provide irrefutable identification of the cause of a disease. The extent to which a disease is due to genetic or environmental causes can often be deduced from some of its main features (Table 3.1).
Table 3.1 Clues to a disease being caused by either genetic or environmental factors
| Disease characteristic | Genetic cause | Environmental cause |
|---|---|---|
| Age of onset | Usually early (often in childhood) | Any age |
| Familial incidence | Common | Unusual (unless family exposed to same environmental agent) |
| Remission | No (except by gene therapy) | Often (when environmental cause can be eliminated) |
| Incidence | Relatively uncommon | Common |
| Clustering | In families | Temporal or spatial or both |
| Linkage to inherited factors | Common | Relatively rare |
Infectious agents (e.g. viruses, bacteria) are the most common and important environmental agents of disease.
Predisposing factors and precursors of disease
Many diseases are the predictable consequence of exposure to the initiating cause; host (i.e. genetic) factors make relatively little contribution to the outcome. This is particularly true of physical injury: the results of mechanical trauma and radiation injury are largely dose-related; the effect is directly proportional to the physical force.
Other diseases are the probable consequence of exposure to causative factors, but they are not absolutely inevitable. For example, infectious diseases result from exposure to potentially harmful environmental agents (e.g. bacteria, viruses), but the outcome is often influenced by various host factors such as age, nutritional status and genetic variables.
Some diseases predispose to others; for example, ulcerative colitis predisposes to carcinoma of the colon, and hepatic cirrhosis predisposes to hepatocellular carcinoma. Diseases predisposing to tumours are called pre-neoplastic conditions; lesions from which tumours can develop are called pre-neoplastic lesions. Some diseases occur most commonly in those individuals with a congenital predisposition. For example, ankylosing spondylitis, a disabling inflammatory disease of the spinal joints of unknown aetiology, is much more common in people with the HLA-B27 haplotype (Ch. 25).
Some diseases predispose to others because they have a permissive effect allowing environmental agents that are not normally pathogenic to cause disease. For example, opportunistic infections occur in those patients with impaired defence mechanisms, allowing infection by normally non-pathogenic organisms (Ch. 9).
Prenatal factors
Prenatal factors, other than genetic abnormalities, contributing to disease risk are:
Diseases due to transplacental transfer of environmental agents from the mother to the fetus include fetal alcohol syndrome, congenital malformations due to maternal rubella infection, and vaginal adenocarcinoma due to administration of diethylstilbestrol (DES). Fetal alcohol syndrome is still a serious problem, but malformations due to rubella are much less common now that immunisation is widespread. DES is no longer used during pregnancy.
The notion that disease risk in adult life could be due to fetal nutritional deprivation has gained support from the work of David Barker. The Barker hypothesis is that an adult’s risk of, for example, ischaemic heart disease and hypertension is programmed partly by nutritional deprivation in utero. This is plausible; nutritional deprivation could have profound effects during critical periods of fetal morphogenesis.
Aetiology and age of disease onset
Do not assume that all diseases manifest at birth have an inherited or genetic basis; as noted previously (Ch. 2), diseases present at birth are classified into those with a genetic basis (further subdivided into those in which the genetic abnormality is inherited and those in which the genetic abnormality is acquired during gestation) and those without a genetic basis. Conversely, although most adult diseases have an entirely environmental cause, genetic influences to disease susceptibility and vulnerability to environmental agents are being increasingly discovered.
Multifactorial aetiology of disease
Many diseases with no previously known cause are being shown to be due to an interplay of environmental factors and genetic susceptibility (Fig. 3.1). These discoveries are the rewards of detailed family studies and, in particular, application of the new techniques of molecular genetics. Diseases of adults in which there appears to be a significant genetic component include:
Fig. 3.1 Proportionate risk of disease due to genetic or environmental factors. Some conditions are due solely to genetic (e.g. cystic fibrosis) or environmental (e.g. traumatic head injury) factors. An increasing number of other diseases (e.g. diabetes, breast cancer) are being shown to have a genetic component to their risk, particularly in cases diagnosed at a relatively young age.
One of the reasons why there may be only slow progress in characterising the genetic component of the diseases listed above and others is that two or more genes, as well as environmental factors, may be involved. Pursuing the genetic basis of these polygenic disorders requires complex analyses.
Evidence for genetic and environmental factors
Genetic contributions to disease incidence are exposed when any putative environmental factors are either widely prevalent (most individuals are exposed) or non-existent (no known environmental agents). The epidemiologist Geoffrey Rose exemplified this by suggesting that, if every individual smoked 40 cigarettes a day, we would never discover that smoking was responsible for the high incidence of lung cancer; however, any individual (especially familial) variation in susceptibility to lung cancer would have to be attributed to genetic differences. An environmental cause, such as smoking, is easier to identify when there are significant individual variations in exposure which can be correlated with disease incidence; indeed, this enabled Doll and Hill in the 1950s to demonstrate a strong aetiological link to lung cancer risk.
Family studies
Strong evidence for the genetic cause of a disease, with little or no environmental contribution, comes from observations of its higher than expected incidence in families, particularly if they are affected by a disease that is otherwise very rare in the general population. Such diseases are said to ‘run in families’.
Having identified the abnormality in a family, it is then important to provide genetic counselling so that parents can make informed decisions about future pregnancies. The precise mode of inheritance (p. 36) will determine the proportion of family members (i.e. children) likely to be affected. Because inherited genetic disorders are either sex-linked or autosomally dominant or recessive, not all individuals in one family may be affected even if the disease has no environmental component.
Studies on twins
Observations on the incidence of disease in monozygotic (identical) twins are particularly useful in disentangling the relative influences of ‘nature and nurture’; of greatest value in this respect are identical twins who, through unfortunate family circumstances, are reared in separate environments. Uncommon diseases occurring in both twins are more likely to have a genetic component to their aetiology, especially if the twins have been brought up and lived in different environments.
Studies on migrants
The unusually high incidence of a particular disease in a country or region could be due either to the higher prevalence of a genetic predisposition in the racial or ethnic group(s) in that country or to some environmental factor such as diet or climatic conditions. Compelling evidence of the relative contributions of genetic and environmental factors in the aetiology and pathogenesis of a disease can be yielded by observations on disease incidence in migrant populations (Fig. 3.2). For example, if a racial group with a low incidence of a particular disease migrates to another country in which the disease is significantly more common, there are two possible outcomes leading to different conclusions:
Fig. 3.2 Clues to genetic and environmental causes from disease incidence in migrants. When people with a low incidence of a disease migrate to a country in which the indigenous population has a high incidence, any change in the incidence of the disease in the migrants provides important clues to the role of genetic and environmental factors in causing the disease. A rapid rise in incidence would attribute the disease to unavoidable environmental factors such as climate or widely prevalent micro-organisms. A more gradual rise would be due to factors such as diet, over which there may be some initial cultural resistance to change. No change in disease incidence attributes the high incidence to genetic factors in the indigenous population. The distinctions are rarely as clear-cut as in this graphic example.
Most observations on disease incidence in migrant populations have been made on neoplastic disorders (cancer). This is because cancer is a major illness, likely to be reliably diagnosed by biopsy, and, in many countries, documented in cancer registries.
Association with gene polymorphisms
Within the population there are many normal genetic variations or polymorphisms. The effect of some of these polymorphisms is obvious: examples are skin, hair and eye colour, body habitus, etc. When possessed by large groups of people of common ancestry, a cluster of polymorphic variants constitutes racial characteristics. In other instances the polymorphism has no visible effects: examples are blood groups and HLA types (see below); these are evident only by laboratory testing.
The polymorphisms of greatest relevance to disease susceptibility are:
HLA types
Clinical and experimental observations on the fate of organ transplants led to the discovery of genes known as the major histocompatibility complex (MHC). In humans, the MHC genes reside on chromosome 6 and are designated HLA genes (human leukocyte antigen genes). HLA genes are expressed on cell surfaces as substances referred to as ‘antigens’, not because they normally behave as antigens in the host that bears them, but because of their involvement in graft rejection (Ch. 9). The body does not normally react to these substances, because it is immunologically tolerant of them and they are recognised as ‘self’ antigens.
HLA types are grouped into classes, principally:
Diseases may be associated with HLA types because:
Diseases associated with HLA types are listed in Table 3.2. They are all chronic inflammatory or immunological disorders. In some instances the association is so strong that HLA testing is important diagnostically: the best example is the association of HLA-B27 with ankylosing spondylitis (Ch. 25).
Table 3.2 Examples of disease associated with HLA types
| Disease | HLA type(s) | Comments |
|---|---|---|
| Allergic disorders (e.g. eczema, asthma) | A23 | Requires environmental allergen |
| Ankylosing spondylitis | B27 | Associated in c. 90% of cases |
| Coeliac disease | DR3, B8 | Gluten sensitivity |
| Graves’ disease (primary thyrotoxicosis) | DR3, B8 | Due to thyroid-stimulating immunoglobulin |
| Hashimoto’s thyroiditis | DR5 | Aberrant HLA class II expression on thyroid epithelium |
| Insulin-dependent (juvenile onset) diabetes mellitus | DR3, DR4, B8 | Immune injury to beta-cells in pancreatic islets |
| Rheumatoid disease | DR4 | Autoimmune disease |
Autoimmune diseases (diseases in which the body’s immunity destroys its own cells) are most frequently associated with specific HLA types. The combination of HLA-DR3 and HLA-B8 is particularly strong in this regard, but it must be emphasised that it is present in only a minority of patients with autoimmune disease. Autoimmune diseases also illustrate a separate feature of the association between HLA types and disease. Normally, class II types are not expressed on epithelial cells. However, in organs affected by autoimmune disease, the target cells for immune destruction are often found to express class II types. This expression enables their immune recognition and facilitates their destruction.
Blood groups
Blood group expression is directly involved in the pathogenesis of a disease only rarely; the best example is haemolytic disease of the newborn due to rhesus antibodies (Ch. 23). A few diseases show a weaker and indirect association with blood groups. This association may be due to genetic linkage; the blood group determinant gene may lie close to the gene directly involved in the pathogenesis of the disease.
Cytokine genes
There is evidence linking the incidence or severity of chronic inflammatory diseases to polymorphisms within or adjacent to cytokine genes. Cytokines are important mediators and regulators of inflammatory and immunological reactions. It is logical, therefore, to explore the possibility that enhanced or abnormal expression of cytokine genes may be relevant.
Associations have been found between a tumour necrosis factor (TNF) gene polymorphism and Graves’ disease of the thyroid (Ch. 17) and systemic lupus erythematosus (Ch. 25). The TNF gene resides on chromosome 6 between the HLA classes I and II loci, linkage with which may explain an indirect association between TNF gene polymorphism and disease. There are also associations between interleukin-1 gene cluster (chromosome 2) polymorphisms and chronic inflammatory diseases. The associations seem to be stronger with disease severity than with susceptibility.
Gender and disease
Gender, like any other genetic feature of an individual, may be directly or indirectly associated with disease. An example of a direct association, other than the absurdly simple (e.g. carcinoma of the uterus and being female), is haemophilia. Haemophilia is an inherited X-linked recessive disorder of blood coagulation. It is transmitted by females to their male children. Haemophilia is rare in females because they have two X chromosomes, only one of which is likely to be defective. Males always inherit their single X chromosome from their mother; if the mother is a haemophilia carrier, half of her male children are likely to have inherited the disease.
Some diseases show a predilection for one of the sexes. For example, autoimmune diseases (e.g. rheumatoid disease, systemic lupus erythematosus) are generally more common in females than in males; the reason for this is unclear. Atheroma and its consequences (e.g. ischaemic heart disease) tend to affect males earlier than females, but after the menopause the female incidence approaches that in males. Females are more prone to osteoporosis, a common cause of bone weakening, particularly after the menopause.
In some instances the sex differences in disease incidence are due to social or behavioural factors. The higher incidence of carcinoma of the lung in males is due to the fact that they smoke more cigarettes than do women.
Racial differences
Racial differences in disease incidence may be genetically determined or attributable to behavioural or environmental factors. Racial differences may also reflect adaptational responses to the threat of disease. A good example is provided by malignant melanoma (Ch. 24). Very strong evidence implicates ultraviolet light in the causation of malignant melanoma of the skin; the highest incidence is in Caucasians living in parts of the world with high ambient levels of sunlight, such as Australia. The tumour is, however, relatively uncommon in Africa, despite its high sunlight levels, because the indigenous population has evolved with an abundance of melanin in the skin; they are classified racially as blacks and benefit from the protective effect of the melanin in the skin.
Some abnormal genes are more prevalent in certain races. For example, the cystic fibrosis gene is carried by 1 in 20 Caucasians, whereas this gene is rare in blacks and Asians. Conversely, the gene causing sickle cell anaemia is more common in blacks than in any other race. These associations may be explained by a heterozygote advantage conferring protection against an environmental pathogen (Table 3.3).
Table 3.3 Associations between disease and race
| Disease | Racial association | Explanation |
|---|---|---|
| Cystic fibrosis | Caucasians | Hypothesised that defective gene increases resistance to intestinal infection by Salmonella bacteria |
| Sickle cell anaemia (HbS gene) | Blacks | Sickle cells resist malarial parasitisation |
| HbS gene more common in blacks in areas of endemic malaria | ||
| Haemochromatosis | Caucasians | Mutant HFE protein may have conferred protection against European plagues caused by Yersinia bacteria |
Other diseases in different races may be due to socio-economic factors. Perinatal mortality rates are often used as an indicator of the socio-economic welfare of a population. Regrettably, the perinatal mortality rate is much higher in certain racial groups, but this outcome is due almost entirely to their social circumstances and is, therefore, theoretically capable of improvement.
Parasitic infestations are more common in tropical climates, not because the races predominantly dwelling there are more susceptible, but often because the parasites cannot complete their life-cycles without other hosts that live only in the prevailing environmental conditions.
GENETIC ABNORMALITIES IN DISEASE
Genetic abnormalities may be inherited, acquired during conception or embryogenesis, or acquired during post-natal life
Advances in genetics and molecular biology have revolutionised our understanding of the aetiology and pathogenesis of many diseases and, with the advent of gene therapy, may lead to their amelioration in affected individuals (Table 3.4).
Table 3.4 Landmarks in genetics and molecular biology
| Date | Discovery |
|---|---|
| 1940s | Genes encoded by combinations of only four nucleotides in nuclear DNA |
| 1950s |
1960s
1970s
1980s
1990sGene therapyEarly 21st century
Defective genes in the germline (affecting all cells) and present at birth, because of either inherited or acquired abnormalities, cause a wide variety of conditions, such as:
Most well-characterised inherited abnormalities are attributable to a single defective gene (i.e. they are monogenic). However, some inherited abnormalities or disease predispositions are determined by multiple genes at different loci; such conditions are said to be polygenic.
Genetic damage after birth, for example due to ionising radiation, is not present in the germline and causes neither obvious metabolic defects affecting the entire individual, because the defect is concealed by the invariably larger number of cells with normal metabolism, nor structural abnormalities, because morphogenesis has ceased. The main consequence of genetic damage after birth is, therefore, tumour formation (Ch. 11). There is, however, increasing evidence to suggest that cumulative damage to mitochondrial genes contributes to ageing (Ch. 12).
Gene structure and function
Nuclear DNA
Each of the 23 paired human chromosomes contains, on average, approximately 107 base (nucleotide) pairs arranged on the double helix of DNA; genes are encoded in a relatively small proportion of this DNA. To accommodate this length of DNA within the relatively small nucleus, the DNA is tightly folded. The first level of compaction involves wrapping the double helix around a series of histone proteins; the bead-like structures thus formed are nucleosomes. At the second level of compaction, the DNA strands are coiled to form a chromatin fibre and then tightly looped. During metaphase, when the duplicated chromosomes separate before forming the nuclei of two daughter cells, the DNA is even more tightly compacted.
During DNA synthesis (S phase) the bases are copied by complementary nucleotide pairing. Any copying errors are at risk of being inherited by the daughter cells and may result in disease. Copying during DNA synthesis starts in a co-ordinated way at approximately 1000 places along an average chromosome.
Nuclear genes
Genes are encoded by combinations of four nucleotides (adenine, cytosine, guanine, thymine) within DNA. Nuclear DNA is double-stranded with complementary specific bonding between nucleotides on the sense and anti-sense strands—adenine to thymine, guanine to cytosine—the anti-sense strand thereby serving as a template for synthesis of the sense strand. Most of the DNA in eukaryotic (nucleated, e.g. mammalian) cells is within nuclei; a relatively smaller amount resides in mitochondria.
The nuclear DNA in human cells is distributed between 23 pairs of chromosomes: 22 are called autosomes; 1 pair are sex chromosomes (XX in females, XY in males). Only approximately 10% of nuclear DNA encodes functional genes; the remainder comprises a large quantity of anonymous variable and repetitive sequences distributed between genes and between segments of genes. These non-coding sequences include satellite DNA which is highly repetitive, located at specific sites along the chromosomes and probably important for maintaining chromosome structure. A crucial site of repetitive non-coding DNA is the telomere at the ends of each chromosome. Its integrity is essential for chromosomal replication. In cells lacking telomerase (i.e. most somatic cells) the telomeres shorten with each mitotic division, until eventually the cells are incapable of further replication.
The segments of genes encoding for the final product are known as exons; the segments of anonymous DNA between exons are called introns (Fig. 3.3). The exons comprise sequences of codons, triplets of nucleotides each encoding for an amino acid via messenger RNA (mRNA). In addition, there are start and stop codons defining the limits of each gene. Some genes are regulated by upstream promoters. During mRNA synthesis from the DNA template, the introns are spliced out and the exons may be rearranged.
Fig. 3.3 Simplified structure of a gene and its mRNA product. Upstream of the gene is a promoter DNA sequence through which, by specific binding with regulating proteins, the translation of the gene is controlled. Start and termination codons mark the limits of the gene, bounded by untranslated sequences. The encoding portion of the gene is divided into exons, four in this example, interspersed with introns which do not appear in the mRNA product.
Gene linkage and recombination
Linkage and recombination are important processes enabling tracing of genes associated with disease. During meiosis there is exchange of chromosomal material between maternally and paternally derived chromosomes. Adjacent genes on the same chromosome are unlikely to be separated by this process and are said to show a high degree of linkage. When exchange of chromosomal material does occur, the result is called recombination. The distance between genes can be expressed in centimorgans (after a geneticist called T H Morgan); one centimorgan is the distance between two gene loci showing recombination in 1 in 100 gametes.
These processes of linkage and recombination are not only responsible for the balance between familial characteristics and individual diversity but are also important phenomena enabling defective genes to be identified, even when their precise function or sequence is unknown, by tracking the inheritance of neighbouring DNA in affected individuals and families.
Gene transcription and translation
The normal flow of biochemically encoded information is that a messenger RNA transcript is made corresponding to the nucleotide sequence of the gene encoded in the DNA (in RNA, uracil replaces thymine). The RNA transcript comprises nucleotide sequences encoding only the exons of the gene. The RNA is then translated into a sequence of amino acids specified by the code and the protein is assembled.
Under some circumstances, however, the flow of genetic information is reversed. In the presence of reverse transcriptase, an enzyme present in some RNA viruses, a DNA copy can be made from the RNA (Fig. 3.4).
Fig. 3.4 Reverse transcription of DNA from RNA. Normally, the genetic information encoded in DNA is transcribed to RNA and translated into amino acids from which the protein is synthesised. However, some RNA viruses contain reverse transcriptase, an enzyme that produces a DNA transcript of the RNA; this may then be incorporated into the genome of the cell, possibly altering permanently its behaviour and potentially leading to tumour formation (Ch. 11).
Recently, RNA-mediated interference (RNAi) has been discovered as a potentially important mechanism of target gene inhibition. This may have novel therapeutic uses.
Homeobox genes
Homeobox (HOX) genes contain a highly conserved 183 base-pair sequence. They are clustered on chromosomes as a homeotic sequence. Their expression during embryogenesis follows the order in which they are arranged, thereby sequentially directing body axis formation.
HOX genes can be subject to endocrine regulation, for example in the endometrium through the menstrual cycle and pregnancy. They can also be modulated by vitamin A (or its analogues such as retinoic acid), thus accounting for the malformations induced by excess or deficiency.
Mitochondrial genes
Most inherited disorders are carried on abnormal genes within nuclear DNA. There are, however, a small but significant number of genetic abnormalities inherited through mitochondrial DNA. Mitochondrial DNA differs from nuclear DNA in several important respects; it is characterised by:
The structure of mitochondrial DNA resembles that of bacterial DNA. Consequently, it is postulated that eukaryotic cells acquired mitochondria as a result of an evolutionary advantageous symbiotic relationship with bacteria.
Because the head of the fertilising spermatozoon consists almost entirely of its nucleus, the mitochondria of an individual are derived from the cytoplasm of the mother’s ovum. Thus, mitochondrial disorders are transmitted by females, but may be expressed in males and females.
The genes in mitochondrial DNA encode mainly for enzymes involved in oxidative phosphorylation. Therefore, defects of these enzymes resulting from abnormal mitochondrial genes tend to be associated with clinicopathological effects in tissues with high energy requirements, notably neurones and muscle cells. Examples of disorders due to inheritance of defective mitochondrial genes include familial mitochondrial encephalopathy and Kearns–Sayre syndrome.
Mitochondria and ageing
Because mitochondria play a key role in intracellular oxygen metabolism, it is hypothesised that defects of mitochondrial genes and the enzymes encoded by them could lead to the accumulation of free oxygen radical-mediated injury. Such injury could include damage to nuclear DNA, thus explaining not only the phenomenon of ageing (Ch. 12) but also the higher incidence of neoplasia in the elderly (Ch. 11).
Gene therapy
Currently, significant advances are anticipated in the specific treatment of genetic disorders (such as inherited metabolic disorders and cancer). This is the relatively new clinical science of gene therapy.
There are two approaches. First, it may be possible to replace a defective gene with a normal version in the affected tissues. This would be an ideal solution to the problem of inherited disorders such as cystic fibrosis and Duchenne muscular dystrophy. Indeed, attempts are being made to correct the respiratory tract problems in cystic fibrosis by local gene therapy applied by inhalation to the airways. Second, the function of an abnormal gene may be abrogated by administering anti-sense RNA or by RNA-mediated interference, as is being explored for Huntington’s disease.
Techniques for studying genetic disorders
Genetic disorders can be studied at various complementary levels:
