DNA damage can occur as a result of many different factors and the damage itself can take various forms. Some are known to occur more frequently than others. For instance, oxidative damage to DNA bases occurs (and is repaired) as often as 10$^5$ times per day in every cell, whereas more excessive types of damage, like double-strand breaks, happen much more infrequently. Despite this disproportion in prevalence, such breaks are one of the most cytotoxic forms of lesions, as they can severely destabilize the genome (through the breaking of chromosomes and the loss of genes). The severe consequences of such lesions make the homologous recombination repair, which deals with such damages, a highly critical mechanism for every proliferating cell.
The key feature of the homologous recombination is the exchange of DNA strands between a pair of homologous DNA sequences. The mechanism allows one stretch of DNA duplex to act as a template in the process of restoring lost or damaged information on the second stretch. The lack of any loss or alteration of nucleotides gives the homologous repair an advantage over other processes of being more accurate.
In this sense, homologous recombination resembles other DNA processes, where a template is utilized to restore the damaged DNA. However, instead of using the partner complementary strand as a template, as occurs in most DNA repair pathways, homologous recombination exploits a complementary strand from a separate DNA duplex. Sister chromatids, two separate but homologous duplexes, are available in close proximity only during and shortly after DNA replication. The replication process (the occurrence of replication forks to be more precise) is, as a matter of fact, one of the major sources of the double-strand breaks. Since the forks occur during nearly every round of the DNA replication, it again emphasizes the importance of the homologous end-joining.
The mechanisms of the homologous recombination, although simple in its idea, is highly regulated. The protein of interest, the Brca1 protein, is involved in the very first step of the homologous recombination – the processing of broken ends of the DNA double strand. Activated only by the beginning of a replication cycle, it interacts with the Rad51 and Rad52 proteins responsible for carrying out the next phases of the repair: DNA strand exchange, searching for the homologous sequences through base-pairing and finally working with the polymerases to extend the strands, and synthesize the ends. As Brca1 regulates such an early stage of the DNA repair, its proper functioning is of particular importance. The reduction or silencing of the protein inevitably increases the mutation rates and chromosomal rearrangements, and accumulation of such DNA damage could result in cancer.
The vitality of the DNA repair system justifies its complexity- the alternative signaling pathways exist and can potentially act as a backup to the homologous recombination, albeit more error-prone due to the lack of a template. The striking statistics of the likelihood of developing a tumor resulting from a Brca1 mutation, therefore, seems not fully justified by the only one protein function, which is, to some extent, replaceable. In fact, Brca1 has been linked to mediating multiple phases in the cell cycle. Apart from the postreplication DNA damage response pathway, Brca1 is also involved in the transcription regulation, where it associates with components of RNA polymerase apparatus. The activity in the transcription process is regarded as consistent with the suggested role as a DNA repair protein, as various DNA repair elements are often seen with association with RNAp complexes. Additionally, Brca1 is believed to induce apoptosis through the activation of the stress-activated protein kinases. The apoptotic potential, the ability to control the rate at which cells proliferate and the DNA repair function are the reasons why emph{Brca1} has been classified as a tumor suppressor gene. A loss of any of the above functions could contribute to the tumor development, especially if a cell happens to have an undetected DNA damage and is about to enter the mitosis stage of the cell cycle.
Suppose a mutation in the Brca1 protein has led to an ineffective DNA repair and, as a result, the cell contains some amount of damaged DNA. Because double-strand breaks, dealt with by the Brca1, are particularly dangerous for the cell's genome, the cell may die before even dividing. If the damage does not impact the cell as drastically, the cell will enter the mitosis preparation stage. During early stages of the mitosis process, eukaryotic cells build a scaffold, a cytoskeletal component called the spindle apparatus. The spindle fibers, with the help of motor proteins, are responsible for moving chromosomes during cell division ensuring that each daughter cell gets the correct number of chromosomes. The fibers move the chromosomes by attaching to the chromosomes' arms and centromeres, a region where duplicated chromosomes are joined. In the case of a damaged DNA, the spindles may happen to attach to the wrong part of the DNA. The cell has the ability to check if spindles are attached correctly, and usually, a cell with a defective spindle will die. However, if the warning is ignored, the cell will continue to divide and the mitosis could lead to unequal chromosome segregation, abnormal nuclear division, and aneuploidy.
Cells which do not have the right number of chromosomes pose a particular risk. Much so that mutations in the components carrying out and regulating DNA repair processes are responsible for several inherited forms of cancer. The reason being is that the vast majority of the DNA is noncoding, meaning it does not contain a peptide-encoding open reading frame and is therefore not translated into proteins cite{noncoding}. The non-coding regions include regulatory and functional structures, equally important for correctly functioning cells. Cells with a disturbed chromosome segregation process become capable of cancerous growth. They may disregard signals regulating cell proliferation, for instance by resisting apoptosis or escaping cell division checkpoints. The genetic instability could result in a cell which does not differentiate correctly and undergoes an uncontrolled growth. In extreme cases, the cell escapes the tissue it originated from (i.e. becomes invasive) and survives in foreign sites (i.e. metastasizes).
The cancer cells are thus defective in repairing their local DNA damage or any replication errors, and as mentioned above struggle to maintain the integrity of their chromosomes. The cells allowed uncontrolled division, start displaying distinct abnormalities and form a tumor. Tumors in breasts may arise from connective tissue or, more commonly, from epithelial structures and usually form palpable, sometimes painful masses.
In the late 90s certain variations in the emph{Brca1} gene, chromosome 17 (Fig. ref{fig:chromosome}), were found to lead to increased risks for both breast and ovarian cancer cite{candidate}. The specificity of the emph{Brca1}-linked cancers remains a conundrum. The DNA repair process addresses a very general problem relevant to every cell, yet, the cancers associated with mutations of the genes encoding products participating in DNA damage response pathways are seen in some tissues more frequently than others. So far the only remotely connected observation has been that emph{Brca1} is mainly expressed in cells present in breasts cite{candidate}. It has been speculated that potential carcinogens give rise to tissue-specific diseases because they concentrate in certain cell types. The breast ductal epithelium is thought to accumulate these carcinogens and consequently to suffer a significantly increased level of DNA mutations. The unusual amount of DNA fragments requiring repair, in turn, stresses the homologous repair (and/or other) pathways, the activity and effectiveness of which depends upon the Brca1 protein. cite{pathway}
Another, perhaps more obvious, connection made has suggested a hormonal imbalance and the effect of estrogen in particular. Estrogens stimulate the production of growth factors, which may promote tumor development through paracrine and autocrine mechanisms. Certain laboratories have also shown that various estrogen derivatives generated by the action of enzymes acquire alkylating activity, effectively becoming carcinogenic (at least in rats). The observation gives a basis for speculation that estrogen becomes a carcinogen in cells in which it concentrates in.
Genetically, the emph{Brca1} mutations can be inherited or sporadic. If the mutation is inherited it is associated with a hereditary breast-ovarian cancer syndrome. Considering the mutations in the Mendelian terms may cause some confusion, as they are neither strictly dominant nor strictly recessive A strictly dominant genetic trait is understood to mean that it is expressed in a person who has only one copy of that allele. It is strictly recessive if it is expressed only when two copies of alleles are present. Inheriting a single copy of mutated emph{Brca1}increases the susceptibility of breast cancer drastically (the lifetime risk up to 82% depending on the mutation and the family history) and in such sense it is dominant. However, as emph{Brca1} is a tumor suppressor gene, it is by definition functionally recessive and both copies of the gene must be mutated (for the protein encoded to be nonfunctional). It is worth noting that inheriting two mutated copies of emph{Brca1} is essentially lethal for a developing embryo. The literature, therefore, classifies it as emph{autosomal dominant}, as one mutated allele is inherited and the other undergoes mutation later in life.
Inherited mutations are a cause of roughly 10% of all the breast cancers, out of which roughly one-sixth are the mutations of emph{Brca1}. What differentiates the emph{Brca1}-related cancers is a strikingly higher proliferation rate compared to other hereditary cancers. Other properties of the emph{Brca1}-related tumors vary significantly depending on the specificity of mutations. Due to the wider availability of genetic testing, more than 350 mutations have been identified in the emph{Brca1} but only some have been linked to the cancer susceptibility.
The variation in the risk depending on the position and type of the mutation has been of particular interest. There is a significant dependence of the risk of the breast cancer on the location of the mutation. Mutations in the central region have been associated with a lower risk, which increases with mutation position from the 5' to the 3' end. The 3' end of the DNA sequence corresponds to a big terminal domain present in the protein in two tandems (Fig.). Analyses of the disease-predisposing mutations have revealed that truncations in this region are the major means of inactivating Brca1 and the terminal domain has been implicated to be involved in the tumor suppressor function.
As the Brca1 is a relatively big protein composed of 1863 amino acids, it is reasonable to expect several potential functions for a polypeptide this size. The ability of the mutation to be tumorigenic is believed to depend on which functions and to what extent the mutation affects. However, analyzing the functional effects of mutations in proteins, not only the Brca1 but all proteins in general, is altogether an immensely complicated task. Even though crystallography-based and computational models prove to be useful in studying wild-type compounds, they are of very little use when it comes to their mutant counterparts.
The wide variety of identified and possible mutations is yet another obstacle in the already difficult treatment of breast cancer. In recent years, personalized medicine has evolved substantially and it has been proving more effective. The broad spectrum of possible treatment strategies, ranging from prevention, early detection, diagnosis, to a treatment of an already progressing disease, is an opportunity for scientists with non-medical backgrounds to contribute to the field. This is especially important because of the genomic variations between the tumors and even between populations. Constructing statistical databases might prove useful to identify high-risk mutations and attempt modeling the tumor growth and its response to common treatment options such as chemotherapy. Studying protein structures (from atomic to molecular level), how they are expressed and how they function within the signal transduction pathways is absolutely necessary for designing a patient-specific treatment. The treatment could be further advanced by developing drugs with desired profiles or more precise imaging techniques.
Regardless of the time scale required to make certain advances, all the pieces of the collaborations need to eventually come together. Since the War on Cancer was announced by Richard Nixon, some battles might have been won, but the war was definitely not- the death rate from breast cancer decreased by only 2% from 1990 to 2006 cite{war}. Interdisciplinary research is essential to study cancer at various time and length scales, because “once we know what all the moving parts are and how they interact, cancer research goes from a black art to an engineering technologyâ€.