Chapter 3 Genetic, environmental and infectious causes of disease

CAUSES OF DISEASE

• entirely genetic—either inherited or prenatally acquired defects of genes

• multifactorial—interaction of genetic and environmental factors

• entirely environmental—no genetic component to risk of disease.

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:

• transplacental transmission of environmental agents

• nutritional deprivation.

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.

The incidence of many diseases rises with age because:

• Probability of contact with an environmental cause increases with duration of exposure risk.

• The disease may depend on the cumulative effects of one or more environmental agents.

• Impaired immunity with ageing increases susceptibility to some infections.

• The latent interval between the exposure to cause and the appearance of symptoms may be decades long.

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:

• breast cancer

• Alzheimer’s disease

• diabetes mellitus

• osteoporosis

• coronary atherosclerosis.

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.

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.

Examples of blood group-associated diseases include:

• duodenal ulceration and group O

• gastric carcinoma and group A.

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

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	Complementary double-stranded helical structure of DNA 46 chromosomes in humans DNA polymerase enzyme
1960s	Plasmids—providing a mechanism for transfer of genes to bacteria Lyon hypothesis Restriction endonucleases
1970s	Recombinant DNA technology Chromosome banding Hybridisation techniques Southern blotting
1980s	Gene polymorphisms Polymerase chain reaction Transgenic mice
1990s	Gene therapy
Early 21st century	Human genome project completed RNA-mediated interference (RNAi)

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:

• metabolic defects (e.g. cystic fibrosis, phenylketonuria)

• structural abnormalities (e.g. Down’s syndrome)

• predisposition to tumours (e.g. familial adenomatous polyposis, retinoblastoma, multiple endocrine neoplasia syndromes).

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.