A free radical is any atom or molecule containing one or more unpaired electrons, making it more reactive than the native species. They have been implicated in a large number of human diseases. The hydroxyl (OHO) radical is by far the most reactive species, but the others can generate more reactive species as breakdown products. When a free radical reacts with a nonradical, a chain reaction ensues resulting in direct tissue damage by lipid peroxidation of membranes. Hydroxyl radicals can cause mutations by attacking DNA. Interestingly ionising radiation used in cancer treatment can activate this mechanism by the interaction with water molecules.

Superoxide dismutases O2O (SOD) convert superoxide to hydrogen peroxide. Glutathione peroxidases are major enzymes that remove hydrogen peroxide generated by SOD in cytosol and mitochondria. Free radical scavengers bind reactive oxygen species (ROS). α-Tocopherol, urate, ascorbate, and glutathione remove free radicals by reacting in a direct and noncatalytic way. There is a growing evidence that cardiovascular diseases and cancer can be prevented by a diet rich in substances that diminish oxidative damage. Principal dietary antioxidants include vitamins C and E, β-carotene, and flavonoids.

Heat shock proteins (HSPs) are induced by heat shock and other chemical and physical stresses [20], and their functions include the export of proteins in and out of specific cell organelles, acting as molecular chaperones (the catalysis of protein folding and unfolding), and the degradation of proteins (often by ubiquitination pathways). The unifying feature, which leads to the activation of HSPs, is the accumulation of damaged intracellular protein. Tumors have an abnormal thermo-tolerance, which is the basis for the observation of enhanced cytotoxic effect of chemotherapeutic agents in hyperthermic subjects. The HSPs are expressed in a wide range of human cancers and are implicated in cell proliferation, differentiation, invasion, metastasis, cell death, and immune response [20]. Although HSP detection by immunocytochemistry has been an established practice, serum detection of HSP and its antibodies is still a new research area. Various types of HSP have been demonstrated in urogenital cancers including kidney, prostate, and bladder. For example, HSP27 expression in prostate cancer indicates poor clinical outcome [21, 22].

In necrotic cell death external factors damage the cell with influx of water and ions leading to the swelling and rupture of cellular organelles. Cell lysis induces acute inflammatory responses in vivo (Table 1.1). In apoptosis, cell death occurs through the deliberate activation of constituent genes whose function is to cause their own demise. Necrosis lacks the features of apoptosis and is an uncontrolled process. Another process is autophagy (self eating) which is lysosome mediated catabolic process. Apoptotic cell death has the following characteristic morphological features:

The nucleus of each diploid cell contains 3 × 10⁹ bp of DNA (Fig. 1.2). Chromosomes are massive structures containing one linear molecule of DNA that is wound around histone proteins, which are further wound to make up the structure of the chromosome itself. Diploid human cells have 46 chromosomes, 23 inherited from each parent; 22 pairs of autosomes, and two sex chromosomes (XX female and XY male). The chromosomes can be classified according to their size and shape, the largest being chromosome 1. The constriction in the chromosome is the centromere, which may be in the middle of the chromosome (metacentric) or at one extreme end (acrocentric). The centromere divides the chromosome into a short arm (p arm) and a long arm (q arm). In addition, chromosomes can be stained when they are in the metaphase stage of the cell cycle and are very condensed. The stain gives a different pattern of light and dark bands that is diagnostic for each chromosome. Each band is given a number, and gene mapping techniques allow genes to be positioned within a band within an arm of a chromosome. During cell division, mitosis, each chromosome divides into two so that each daughter nucleus has the same number of chromosomes as its parent cell. During gametogenesis, however, the number of chromosomes is halved by meiosis.

The ends of eukaryotic chromosomes, telomeres, do not contain genes but rather many repeats of a guanine-rich hexameric sequence TTAGGG. Telomeres are specialized DNA structures that protect the ends of chromosome from fusion and recombination events [27]. Telomerase is a ribonucleoprotein that is necessary to repair the telomeric losses. Replication of linear chromosomes starts at coding sites (origins of replication) within the main body of chromosomes and not at the two extreme ends. The extreme ends are therefore susceptible to single-stranded DNA degradation back to double-stranded DNA. As a consequence of multiple rounds of replication, the telomeres shorten, leading to chromosomal instability and ultimately cell death. Stem cells have longer telomeres than their terminally differentiated daughters. However, germ cells replicate without shortening of their telomeres because of telomerase. Most somatic cells (unlike germ and embryonic cells) switch off the activity of telomerase after birth and die as a result of apoptosis [28]. Many cancer cells, however, reactivate telomerase, contributing to their immortality. Conversely, cells from patients with progeria (premature ageing syndrome) have extremely short telomeres. Telomerase activity is detected in nearly all cancer cells [29]. Likewise, prostate cancer but not normal prostate or benign prostatic hyperplasia (BPH) tissue, expresses telomerase activity [30]. Inhibition of telomerase with DNA-damaging chemotherapy drugs seems a possibility in prostate cancer [31]. Telomerase from exfoliated transitional cell carcinoma cells has been used as a urinary marker in bladder cancer [32].

The mitochondrial chromosome is a circular DNA (mtDNA) molecule (16.5 kb), and every base pair makes up part of the coding sequence. These genes principally encode proteins or RNA molecules involved in mitochondrial function. These proteins are components of the mitochondrial respiratory chain involved in oxidative phosphorylation (OXPHOS) producing ATP. The mtDNA mutations are generated during OXPHOS through pathways involving reactive oxygen species (ROS), and unlike the nucleus these mutations may accumulate in mitochondria because they lack protective histones [33]. There are many reasons to believe that the biology of mitochondria could drive tumorigenesis: (1) mitochondria generate ROS, which in high concentrations are highly mitogenic to the nuclear and mitochondrial genomes; (2) mitochondria have a key role in effecting apoptosis; and (3) mitochondria accumulate in high density in some malignant tumors (renal cell carcinoma) as tumor cells have lesser dependence on mitochondria for their oxidative phosphorylation [34]. The mutations of mtDNA have been demonstrated in renal cell, prostate, and bladder cancers.

A gene is a portion of DNA that contains the codes for a polypeptide sequence. Three adjacent nucleotides (a codon) code for a particular amino acid, such as AGA for arginine, and TTC for phenylalanine. There are only 20 common amino acids, but 64 possible codon combinations that make up the genetic code. This means that more than one triplet encodes for some amino acids; other codons are used as signals for initiating or terminating polypeptide-chain synthesis. Genes consist of lengths of DNA that contain sufficient nucleotide triplets to code for the appropriate number of amino acids in the polypeptide chains of a particular protein. In bacteria the coding sequences are continuous, but in higher organisms these coding sequences (exons) are interrupted by intervening sequences that are noncoding (introns) at various positions. Some genes code for RNA molecules, which will not be further translated into proteins. These code for functional ribosomal RNA (rRNA) and transfer RNA (tRNA), which play vital roles in polypeptide synthesis.

The conversion of genetic information to polypeptides and proteins relies on the transcription of sequences of bases in DNA to mRNA molecules; mRNAs are found mainly in the nucleolus and the cytoplasm, and are polymers of nucleotides containing a ribose phosphate unit attached to a base (Fig. 1.3). RNA is a single-stranded molecule but it can hybridize with a complementary sequence of single-stranded DNA (ssDNA). Genetic information is carried from the nucleus to the cytoplasm by mRNA, which in turn acts as a template for protein synthesis. Each base in the mRNA molecule is lined up opposite to the corresponding base in the DNA: C to G, G to C, U to A, and A to T. A gene is always read in the 5′-3′orientation and at 5′ promoter sites, which specifically bind the enzyme.

RNA polymerase and so indicate where transcription is to commence. Eukaryotic genes have two AT-rich promoter sites. The first, the TATA box, is located about 25 bp upstream of (or before) the transcription start site, while the second, the CAAT box, is 75 bp upstream of the start site.

The initial or primary mRNA is a complete copy of one strand of DNA and therefore contains both introns and exons. While still in the nucleus, the mRNA undergoes posttranscriptional modification whereby the 5′and 3′ ends are protected by the addition of an inverted guanidine nucleotide (CAP) and a chain of adenine nucleotides (Poly A), respectively. In higher organisms, the primary transcript mRNA is further processed inside the nucleus, whereby the introns are spliced out. Splicing is achieved by small nuclear RNA in association with specific proteins. Furthermore, alternative splicing is possible whereby an entire exon can be omitted. Thus more than one protein can be coded from the same gene. The processed mRNA then migrates out of the nucleus into the cytoplasm. Polysomes (groups of ribosomes) become attached to the mRNA. Translation begins when the triplet AUG (methionine) is encountered. All proteins start with methionine, but this is often lost as the leading sequence of amino acids of the native peptides is removed during protein folding and posttranslational modification into a mature protein. Similarly the Poly A tail is not translated and is preceded by a stop codon, UAA, UAG, or UGA. The mRNA align on the endoplasmic reticulum and the ribosomal subunit synthesis the polypeptide chain in to the lumen of the ER.

Gene expression can be controlled at many points in the steps between the translation of DNA to proteins (Fig. 1.4). Proteins and RNA molecules are in a constant state of turnover; as soon as they are produced, processes for their destruction are at work. For many genes transcriptional control is the most important point of regulation. Deleterious, even oncogenic, changes to a cell’s biology may arise through no fault in the expression of a particular gene. Apparent overexpression may be due to non-breakdown of mRNA or protein product.

Aneuploidy refers to the state of an abnormal number of chromosomes (differing from the normal diploid number). Abnormalities may occur in either the number or the structure of the chromosomes.

The analysis of gross chromosomal disorders has traditionally involved the culture of isolated cells in the presence of toxins such as colchicine. It arrests the cell cycle in mitosis, and with appropriate staining, the chromosomes with their characteristic banding can be identified and any abnormalities detected. New molecular biology techniques, such as yeast artificial chromosome (YAC)-cloned probes, have made it simpler and cover large genetic regions of individual chromosomes. These probes can be labelled with fluorescently tagged nucleotides and used in in situ hybridization of the nucleus of isolated tissue from patients, as in fluorescent in-situ hybridization (FISH). These tagged probes allow rapid and relatively unskilled identification of metaphase chromosomes, and allow the identification of chromosomes dispersed within the nucleus. Furthermore, tagging two chromosome regions with different fluorescent tags allows easy identification of chromosomal translocations.

Characteristics resulting from a combination of genetic and environmental factors are said to be multifactorial; those involving multiple genes can also be said to be polygenic. Measurements of most biological traits (e.g., height) show a variation between individuals in a population. This variability is due to variation in genetic factors and environmental factors. Environmental factors may play a part in determining some characteristics, such as weight, while other characteristics such as height may be largely genetically determined. This genetic component is thought to be due to the additive effects of a number of alleles at a number of loci, many of which can be individually identified using molecular biological techniques [42].

Cancer cells are a clonal population of cells in which the accumulation of mutations in multiple genes has resulted in escape from the normally strictly regulated mechanisms that control growth and differentiation of somatic cells. The malignant phenotype acquired by cancer cells has the following properties [43]:

The process of oncogenesis can be thought of as a stepwise process, with mutations in particular genes being required for progression from one phase to another, that is, from transformed cell to metastatic cell; these gene mutations are rate-limiting. Rarely, if ever, is a single event responsible for conversion of a normal cell to a malignant cell. Mutations may be a combination of inherited, spontaneous, and environmentally induced factors. Oncogenes are mutated genes that cause normal cell to grow out of control and become cancer cells.

Tumor suppressor genes slow down cell division, repair DNA, and induce apoptosis. Often several oncogenes may be found within the same receptor-signalling pathway (Fig. 1.5).

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