Genomic Consequences of Ovarian Cancer with Respect to DNA Damage and Repair Mechanism

Abstract

Ovarian cancer is not a single disorder having different histological types which are associated with germline or somatic mutations. Histological types include epithelial cancers that account for ~90% of ovarian cancers and include serous, endometrioid, clear-cell and mucinous carcinomas. There are several risk factors for developing ovarian cancer which includes a genetic factor, age, use of hormonal therapy after menopause, null parity, infertility and other factors including obesity, lifestyle, dietary habits. BRCA1 and BRCA2 are germ line mutations which are completely associated with epithelial ovarian cancer. Germ line mutations in DNA repair pathway which increase the risk of ovarian cancer such as RAD51C, RAD51D, BRIP1, BARD1, and PALB2. To understand the mechanism of progression of ovarian cancer it is very important to explore the mechanism behind the abruption of DNA repair genes that are associated with a high risk of ovarian cancer (such as BRCA1 and BRCA2). The study of these DNA repair genes holds a promise for identifying the women at high risk of developing the ovarian cancer in early stages. The main aim of this review is to investigate the development and progression of ovarian cancer and to explore the various genetic and non-genetic perspectives of cancer with special emphasis to personalized medicine.

1. Introduction

Ovarian cancer is a complex disease with the different biological mechanism at the clinical, cellular and molecular levels. It was clinically proved that ovarian cancer generally presents as a complicated cystic mass in the abdominal region of women. Due to this fact ovarian cancer has been termed the ‘mute murderer’; because majority of females have normal symptoms, even when the malignancy is still limited to the ovaries [1].

Majority of ovarian cancer symptoms are still very common where no one knows exactly why some women gets it and others does not. However, same symptoms are shared with many other common gastrointestinal, genitourinary and gynecological disorders and have not yet proved critical for early diagnosis. Ovarian cancer not only starts from ovaries but also originated from other nearby organs like HGSCs start from fallopian tube, peritoneum, endometrial tissue which located outside the uterus known as endometriosis [2]. WHO classifies the Ovarian cancer as tubal cancers [3]. Sometimes knowledge about the primary sites of ovarian cancer has facilitated the prevention strategies for the examination of an advanced stage of ovarian cancer, such as risk reducing and salpingectomy (Surgical removal of fallopian tube) [4]. The aim of this study is to gain a better knowledge of progression of ovarian cancer and how an abruption in DNA repair pathway could predispose one to ovarian cancer, this may help in modification and improvement of drug treatment for developing personalized medicine.

2. Histological types of ovarian carcinoma

The histological types of ovarian cancer can be distinguished into different types which based on risk factors, cells of origin, molecular compositions, clinical features and treatments. These histological types include epithelial cancers that account for ~90% of ovarian cancers and include serous, endometrioid, clear-cell and mucinous carcinomas.

1. High-grade serous carcinoma and high-grade endometrioid carcinoma can present with peritoneal carcinomatosis, ascites and/or pelvic mass or typically advanced stage at presentation in middle aged women (median reported age 50–65 years). These carcinomas are associated with BRCA and TP53 mutations.

2. Low-grade serous carcinoma presents in younger patients (median reported age: 43–55 years) and can be early or late stage at presentation. This type of carcinoma is associated with KRAS and BRAF mutations and tumors have genomic stability.

3. Low-grade endometrioid carcinoma (median average age of diagnosis-60 years) can be associated with endometriosis and associated with PTEN, ARID1A and PIK3CA mutations. These mutations have microsatellite instability.

4. Clear-cell carcinoma (median average age of diagnosis-55 years) can present with parenchymal metastases (in the liver and the lungs) and can be associated with hypercoagulability and hypercalcemia which is associated with ARID1A and PIK3CA mutations

5. Mucinous carcinoma is presents in younger patients (median average age of diagnosis-55 years) and is typically early stage at presentation which associated with KRAS mutations [5, 6, 7].

3. Incidence and mortality

Every year about, 225,500 new cases of ovarian cancer are diagnosed in all over the world having a death of about 140,200 ovarian cancer patients [8, 9]. Among all of the countries of the world, Russia and UK have the highest rate of ovarian cancer as compared to China is having the lowest rate of ovarian cancer [9]. Annually about 22,280 new cases of ovarian cancer were diagnosed in the US with projected number of deaths for 2016 is 14240 [10, 11]. However, the annual death rate due to ovarian cancer is decreased by 1.09% for women from 1998 to 2008 due to the adoption of new and changing method of hormonal therapy in females [12]. The overall survival rate of ovarian cancer totally depends on the stage of diagnosis; it was reported that the stage 1 patients 92.1% survive for 5 years but is 25% patients with stage III and stage IV cancer [10, 13]. As per 2006 assessment by Indian Council of Medical Research, females (0.428 million) are more susceptible to cancer than males (0.390 million) [14] and ovarian cancer ranks third among all types of cancer in females in India [14]. The rise in the prevalence of ovarian cancer makes it very important to understand the genetic status of cancer among different female population groups of India.

4. Risk factors

There are several risk factors for developing the ovarian cancer which includes genetic factor, age, use of hormonal therapy after menopause, null parity, infertility and other factors including obesity, lifestyle, dietary habits.

4.1 Reproductive factors

Previous studies have described various other factors that can induce the possibility of ovarian cancer, such as parity, prior tubal ligation, salpingectomy and unilateral or bilateral oophorectomy (surgical removal of the ovary) [15]. Even birth giving women have a reduced risk of all subtypes of ovarian cancer compared with women who have not given birth. There is a 30% risk reduction of ovarian cancer in women who undergo treatment of unilateral oophorectomy and bilateral oophorectomy, which is not specific to the particular histological subtype. It was found that women with BRCA mutations follow bilateral oophorectomy have 1.1% reduced the risk of ovarian cancer [13, 16]. Other preventive measures to avoid or to reduce the ovarian cancer is tubal ligation, hysterectomy [17]. Some studies have been identified that the breastfeeding and tubal ligation show decreased risk of ovarian cancer in women with germline (BRCA) mutation of ovarian cancer [15].

4.2 Hormone replacement therapy

Hormone replacement therapy (HRT) has been shown to elevate the possibility of developing ovarian cancer in postmenopausal women; only estrogen therapy promotes the risk by 22% and the both estrogen and progesterone therapy elevate the risk by 10% [18, 19]. Various meta-analysis studies also showed that regular use of hormone replacement therapy either combined progesterone and estrogen or single estrogen elevate the chance of ovarian cancer in menopausal women [20]. It was reported that women having menopausal symptoms and also diagnosed with ovarian cancer the use of hormone replacement therapy appear to be safe and overall has no effect on her survival. Thus it was proved that the hormone replacement therapy can be advised if women having serious menopausal symptoms [21].

5. Other factors

5.1 Obesity

Various previous studies have identified that the obesity is likely to risk factor for ovarian cancer in women. One Meta-analysis studies showed that there is 13% elevation in risk of ovarian cancer in postmenopausal women with weight gain who did not use any therapy of hormones [22].

5.2 Dietary habits

Several studies have investigated the association between the risk of ovarian cancer and dietary factors in the general population. Milk consumption does not advise any serious risk of ovarian cancer, but some limited studies have recognized a trend that showed a contrary association between the intake of skimmed milk and lactose in adulthood and risk of developing ovarian cancer [23]. Some studies reported that other dietary factors like including vitamins and flavonoids also associate with ovarian cancer [24, 25, 26] but it was proven that regular intake of vitamins A, C and E, flavonoids does not cause any ovarian cancer, whereas intake of flavonoids and black tea might be associated with decreased risk of ovarian cancer [27].

5.3 Lifestyle factors

Some other lifestyle factors include the use of talc powder, medications such as NSAIDS and smoking might be a cause of ovarian cancer [28]. Some studies prove that regular use of talcum powder is associated with ovarian cancer but others not [29, 30] Use of aspirin was also associated with decreased risk of developing ovarian cancer, especially among women who took daily, low-dose aspirin, regardless of their age [31]. Cigarette smoking was associated with a significantly lower risk of clear-cell carcinoma but an increased risk of mucinous carcinoma [26].

6. Genetics

The increased risk of ovarian cancer is associated with various genetic factors like BRCA1, BRCA2, BARD1,BRIPI, RAD51c, RAD51d, PALB2,MSH2,MSH6, MSH1,PMS2 [32, 33]. BRCA1 and BRCA2 mutations is one of the most predictable genes which are associated with the genetic risk factor of not only ovarian cancer but also with the other cancers in humans (breast, Prostate, melanoma) [34, 35]. Germ line mutations like BRCA1 and BRCA2 are completely associated with epithelial ovarian cancer but rarely with mucinous ovarian cancer [36]. It was proved that BRCA2 mutation carrier in ovarian cancer kill more cancer cells and survive more as compared to wild type because BRCA2 carrier is strongly associated with increased sensitivity to platinum [36, 37]. Both BRCA loci strongly associated with both breast and ovarian cancer. There are also genetic germ line mutations in DNA repair pathway which increase the risk of ovarian cancer such as RAD51C, RAD51D, BRIP1, BARD1 and PALB2 [33, 38, 39]. Other inherited mutations of DNA repair pathway which are strongly associated with ovarian cancer are CHEK2, MRE11A, RAD50, ATM and TP53 [33, 35, 38]. One major cause of ovarian cancer is Lynch syndrome as it is also associated with colorectal, endometrial urinary tract, stomach, small intestine and biliary tract cancers. Lynch syndrome is a mark of germ line mutation in genes MLH1, PMS2, MSH2 or MSH6, of DNA mismatch repair system [40, 41]. The specific reasons why these inherited mutated genes are involved in specific organs are not known yet.

The most commonly studied genetic alterations in ovarian cancer are those which involved in DNA repair. The mutations of both somatic or germline in homologous recombination genes have been recognized in nearly one- third one-third of ovarian carcinomas, comprising of both serous and non-serous histological types and subtypes that were not formerly admitted to having characteristics of homologous recombination deficiency (clear-cell and endometrioid carcinomas, as well as carcinosarcoma) [42]. As previously discussed, the frequently involved inherited genes are BRCA1, BRCA2, and BRIP1, genes that are part of the Fanconi anemia pathway (RAD51C, RAD51D, BRIP1, PALB2 and BARD1) and genes that are involved in DNA mismatch repair (MSH2, MSH6, MLH1 and PMS2) [43]. Although genomic data exhibit recurrent mutations in patients with ovarian cancer, some tumors, specifically the HGSC subtype, are genetically heterogeneous [43, 44] following the basic genomic complexity of this disease.

TP53 is driver mutation and ubiquitous in high-grade ovarian carcinoma. TP53 is the utmost mutated gene in HGSC [43]. TP53 commonly occur in the encoding region of the gene i.e., in DNA Binding domain and non-DNA binding domains. TP53 mutations can be missense or nonsense, frameshift insertions and deletions [45]. Lack of TP53 mutations in tumors have p53 Dys-functioning with a gain of copy number of MDM2 or MDM4, These MDM2 or MDM4 involved in regulation and degradation of P53 [45]. Some former studies of Genomic examination have disclosed the imperfections in homologous recombination in ~50% of analyzed HGSCs [34]. Imperfective homologous recombination is correlated with both germline and somatic BRCA mutations, as well as modifications in other DNA repair pathway genes [46]. The properties of BRCA1 is critical for DNA repair, cell cycle checkpoint control, mitosis, remodeling of chromatin and transcriptional regulation; whereas BRCA2 is important in homologous recombination and DNA repair [47].

Most common recurrent molecular modifications analyzed in ovarian carcinoma especially in high-grade serous carcinoma are defective Notch, phosphoinositide 3-kinases (PI3K), RAS–MEK and fork head box protein M1 (FOXM1) signaling pathways, there is a change in somatic copy number in the genes which encode proteins of these signaling pathways [46]. Some genes (AURKA, ERBB3, CDK2, mTOR, BRD4, and MYC) after mutation play an important role in the pathogenesis of ovarian carcinoma (High- grade serous carcinoma) and also act as therapeutic agents for ovarian cancer [48, 49].

Generally, ovarian cancer shares a common origin within ovarian surface epithelium (OSE). During the process of monthly ovulation in the female reproductive system, the OSE is degraded enzymatically in order to admit the follicular rupture and releasing of oocyte which creates a gap that must be repaired [50]. Throughout the period of a woman’s reproductive life, the process of damage and repair is continuously repeated many times will result in a bit by bit aggregation of genomic alterations, as hypothesized by the continuous ovulation hypothesis [51]. In inclusion of physical trauma, ovarian surface cells are subjected to ovulation-associated inflammatory cytokines, reactive oxygen species (ROS), and hormones (and its reactive metabolites) that are able to damage DNA and lead to an imbalance of hormonal metabolism [52]. In ovaries, cysts develop as an ovulation occur due to aging or becoming entrapped within the stroma. When cysts left with DNA damage, they may be the best spot for the progression of malignancy [53]. The association between DNA damage and ovarian cancer becomes stronger, so it will become important to thoroughly understand the role of DNA damage response (DDR) proteins in Ovarian cancer prevention. The identification of DNA damage and their resultant repair mechanism are critical in perspective of response or resistance of cancer cells to treatment. This means that cells with their particular DNA damage repair pathways are able to effectively repair the damage caused by chemo or radiotherapy, being responsible for the improvement of resistance in tumor cells [54, 55].

7. DNA damage and repair

In ovarian cancer, the process of DNA damage of double stranded DNA and homologous repair (shown in Figure 1) starts with identification of double-strand breaks (DSBs) by the process of meiotic recombination 11 homolog 1 (MRE11)–RAD50–Nijmegen breakage syndrome protein 1 (NBS1) (MRN) complex, both (MRE11)–RAD50 act as a stimulation site for the serine-protein kinase ATM. In DNA repair pathway, ATM plays an important role with a combination of homologous recombination. The phosphorylation of histone H2AX by ATM which ultimately attach with the mediator of DNA damage checkpoint protein 1 (MDC1) and NBS1 of the MRN complex for the enhancement of ATM binding. The phosphorylation of MDC1 helps in the formation of the binding site for the E3 ubiquitin-protein ligase RING finger protein 8 (RNF8), This admits ubiquitin-mediated enlistment of downstream DNA damage response proteins, such as receptor-associated protein 80 (RAP80; encoded by UIMC1), Whereas RAP80 is an important ubiquitin-interaction motif-containing protein that accomplice with the breast cancer type 1 susceptibility protein (BRCA1) complex over its communication with Abraxas (encoded by FAM175A); The main function of Abraxas is acting as middle adaptor protein and contains domains essential for BRCA1 interactions [46]. The RAP80–Abraxas compositely is critical for placing BRCA1 to the site of DNA repair. Both BRCA1 and BRCA2 act as scaffolds for other types of proteins involved in DNA repair. BRCA1-associated RING domain protein 1 (BARD1) and BRCA1-interacting protein 1 (BRIP1; also known as Fanconi anemia group J protein) attach precisely to BRCA1; whereas BARD1 in collaboration with BRCA1 forms a heterodimer which is most important for collective stability [42]. In addition, BRIP1 also attach to BRCA1 which is important and compulsory for activation of check-point of S phase. Companion and localizer of BRCA2 (PALB2) help BRCA1 and BRCA2 attach at sites of DNA damage and helps to lift the RAD51 proteins on to the BRCA proteins; the DNA repair protein XRCC2 is one of the five forewords of RAD51. When genes of homologous repair get mutated it will lead to accumulation of various double strands break So due to this way there is a formation of defective DNA repair pathway and in future, this will increase the chance of developing ovarian cancer [42].

Figure 1.

Double strand DNA damage and homologous repair: When DNA damage with any external agent takes place, ATM (ataxia telangiectasia mutated) act as main part of homologous recombination, it phosphorylates H2AX (histone family member X). ATM compliment and attach with mediator of DNA damage checkpoint protein 1 (MDC1) and NBS1 (Nijmegen breakage syndrome 1) of the MRN complex. The binding site for binding site for the E3 ubiquitin-protein ligase RING finger protein 8 (RNF8) is created after phosphorylation of MDC1. The phosphorylation leads to mediate the organization of downstream proteins involved with DNA damage response such as receptor-associated protein 80 (RAP80; encoded by UIMC1). For the interaction of BRCA1 breast cancer type 1 susceptibility protein (BRCA1) with RAP80 for the repair of DNA break, the abraxas (encoded by FAM175A) act as mediator adaptor protein. BRCA1‑associated RING domain protein 1 (BARD1) and BRCA1‑interacting protein 1 (BRIP1; also known as Fanconi anemia group J protein) forms heterodimer. BRCA lift other DNA repair protein like RAD51 (DNA repair homology), XRCC1 (X-ray repair cross complementing 1), BRIP1 proteins which helps in the repair of DNA break.

Mismatch repair: In the process of DNA mismatch the PMS2 (PMS1 homolog 2, mismatch repair system component) & MSH (MutS protein homolog 2) as a main initiator which helps in the proliferation of cell nuclear antigen. The abnormalities in any MUTl protein homolog led to mismatch in DNA repair. This mismatch is further harnessing the exonuclease 1 (EXO) for the removal of mismatch for the correction of double strand break with ligase and polymerase activity.

7.1 Mismatch repair

DNA Mismatch repair (MMR) corrects single base impairs as it identifies and repairs false insertion, deletion and mis-incorporation of nucleotides [56]. DNA mismatch repair pathway (Shown in is started by the MutS protein homolog 2 (MSH) proteins, as well as the endonuclease PMS2 which proliferate cell nuclear antigen (PCNA). In ovarian cancer, the mutation in genes encoding MutL protein homolog 1 (MLH1), MSH2, MSH6 and PMS2 there is an abnormality in DNA mismatch repair pathway [56]. Attachment of this complex to the mismatched bases facilitates the recruitment of MLH1 and PMS2. PCNA bind to the sites of base mismatch and assist to recruit and harness exonuclease 1 (EXO1; a member of the RAD2 exonuclease family) to the place of DNA damage. EXO1 excises the mismatched bases, which are then corrected by DNA polymerase and DNA ligase [42].

BRCA1 and BRCA2 are key genes which play important role DNA repair where BRCA1-associated RING domain protein 1 (BARD1) forms stable heterodimers with BRCA1 and this communication is important for the action of BRCA1 [57]. Therefore BARD1 improve efficient Homologous repair [58]. Collaborator and localizer of BRCA2 (PALB2) collaborate with both BRCA1 and BRCA2, and functions downstream of BRCA1, as the corporation with BRCA1 promote recruitment of PALB2 to damaged DNA [59]. PALB2 also combine directly with and maintain BRCA2 during the creation of the RAD51 nucleoprotein filament [60]. ATM then phosphorylates PALB2 to help RAD51 nucleoprotein filament maintenance [61]. Current data advise that the BRCA1– PALB2 interaction is regulated by the cell cycle to restrain homologous recombination repair in G1 phase, where the sister chromatid is not applicable for Homologous repair. This regulatory step regulates false by reducing the use of the homologous chromosome for homologous repair or the direct annealing of resected ends, which possibly could lead to loss of resected DNA pieces [62]. The RAD51 prefaces (RAD51B, RAD51C, RAD51D, XRCC2, and XRCC3) are also critical for RAD51 nucleoprotein filament formation, even though their exact mechanism is still unknown [63]. Some previous studies reported that the pathogenic mutations in BARD1 and PALB2 are significantly associated with an increased risk of breast cancer [64, 65, 66], when in fact the lifetime risk for ovarian cancer is suggested to be low [67]. It was reported in two studies that deleterious RAD51B mutations in patients with breast or ovarian cancer, but no risk estimates are currently available [68, 69]. In spite of recent report of pathogenic RAD51C mutations, truncating mutations in RAD51C and RAD51D are found mainly in families with ovarian cancer only or breast and ovarian cancer [70]. Rare mutations in XRCC2 have been advised to increase the risk of breast and ovarian cancer [71] but the data were not proved by another report [72]; therefore, large number studies are essential before XRCC2 can be regarded as an important Hereditary Breast and Ovarian Cancer gene. BRCA1-interacting protein carboxy-terminal helicase 1 (BRIP1; also known as Fanconi anemia group J protein (FANCJ)) and BRCA1-A complex subunit Abraxas (encoded by FAM175A) are also recommended to be involved in homologous repair by recruiting BRCA1 to DSBs [39]. The BRIP1 gene was basically advised to be a low-penetrant breast cancer susceptibility gene [73]. Easton et al., 2016 in their study proved that BRIP1 gene is not associated with an augmented risk of breast and ovarian cancer [74]. However, in some studies it was proved that carriers of BRIP1 mutation have a high risk for ovarian cancer [75]. There are various Pathogenic mutations have been identified in patients with ovarian cancer [76, 77], but the lifetime risk of ovarian cancer is still unknown.

8. Summary and future perspective of study

In ovarian cancer, the status of molecular alterations especially at the time of diagnosis is change over time due to the presence of some few driver mutations (XRCC1, RAD51) which is based on platinum-based drugs or due to the presence of large number of changes in copy number of genes of various signaling pathways which always characterize the complexity of genome of ovarian cancer.

Actually, this molecular complication support insight into perhaps why the advancement of effective therapies for ovarian carcinoma (especially high-grade serous carcinoma) has been problematic to attain. Various recent literature has shown the role of various DNA damage and repair signaling pathways in ovarian cancer in the world. However, such studies are lacking in Indian population. Studying the role of coding and noncoding genes in ovarian cancer pathogenesis will add to our understanding of the genetic landscape of ovarian cancer and our study may highlight the novel pathway associated with the disease other than the conventional pathways. Associated coding and noncoding genes can be targeted for development of new therapeutic strategies and a new step towards personalized medicine.