Biomarker-Based Targeted Therapeutics

Cancer biomarkers are emerging as important tools for disease diagnosis, prediction and prognosis. A significant number of studies have been reported in the field of biomarker discovery due to their potential as personalized targeted therapy. With the converging gap about their utilization as specific targets, studies have focused on identifying disease-specific biomarkers in different cancer types. This chapter provides a comprehensive overview about different cancer-associated biomarkers, their prevalence in different cancer types and their use as targeted therapy. Additionally, we provide an in-sight on the therapeutic and diagnostic potential of different noncoding RNAs as cancer biomarkers

Differential microRNA expression signatures and cell type-specific association with Taxol resistance in ovarian cancer cells

Paclitaxel (Taxol) resistance remains a major obstacle for the successful treatment of ovarian cancer. MicroRNAs (miRNAs) have oncogenic and tumor suppressor activity and are associated with poor prognosis phenotypes. miRNA screenings for this drug resistance are needed to estimate the prognosis of the disease and find better drug targets. miRNAs that were differentially expressed in Taxol-resistant ovarian cancer cells, compared with Taxol-sensitive cells, were screened by Illumina Human MicroRNA Expression BeadChips. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used to identify target genes of selected miRNAs. Kaplan–Meier survival analysis was applied to identify dysregulated miRNAs in ovarian cancer patients using data from The Cancer Genome Atlas. A total of 82 miRNAs were identified in ovarian carcinoma cells compared to normal ovarian cells. miR-141, miR-106a, miR-200c, miR-96, and miR-378 were overexpressed, and miR-411, miR-432, miR-494, miR-409-3p, and miR-655 were underexpressed in ovarian cancer cells. Seventeen miRNAs were overexpressed in Taxol-resistant cells, including miR-663, miR-622, and HS_188. Underexpressed miRNAs in Taxol-sensitive cells included miR-497, miR-187, miR-195, and miR-107. We further showed miR-663 and miR-622 as significant prognosis markers of the chemo-resistant patient group. In particular, the downregulation of the two miRNAs was associated with better survival, perhaps increasing the sensitivity of cancer cells to Taxol. In the chemo-sensitive patient group, only miR-647 could be a prognosis marker. These miRNAs inhibit several interacting genes of p53 networks, especially in TUOS-3 and TUOS-4, and showed cell line-specific inhibition effects. Taken together, the data indicate that the three miRNAs are closely associated with Taxol resistance and potentially better prognosis factors. Our results suggest that these miRNAs were successfully and reliably identified and would be used in the development of miRNA therapies in treating ovarian cancer

MicroRNAs in melanoma development and resistance to target therapy

microRNAs constitute a complex class of pleiotropic post-transcriptional regulators of gene expression involved in the control of several physiologic and pathologic processes. Their mechanism of action is primarily based on the imperfect matching of a seed region located at the 5' end of a 21-23 nt sequence with a partially complementary sequence located in the 3' untranslated region of target mRNAs. This leads to inhibition of mRNA translation and eventually to its degradation. Individual miRNAs are capable of binding to several mRNAs and several miRNAs are capable of influencing the function of the same mRNAs. In recent years networks of miRNAs are emerging as capable of controlling key signaling pathways responsible for the growth and propagation of cancer cells. Furthermore several examples have been provided which highlight the involvement of miRNAs in the development of resistance to targeted drug therapies. In this review we provide an updated overview of the role of miRNAs in the development of melanoma and the identification of the main downstream pathways controlled by these miRNAs. Furthermore we discuss a group of miRNAs capable to influence through their respective up- or down-modulation the development of resistance to BRAF and MEK inhibitors

Diagnostic, Prognostic and Therapeutic Value of Gene Signatures

Gene expression studies have revealed diagnostic profiles and upregulation of specific pathways in many solid tumors. Some gene-expression signatures are already used as predictors of relapse in early breast cancer patients. The explosion of new information in gene expression profiling could potentially lead to the development of tailored treatments in many solid tumors. In addition, many studies are ongoing to validate these signatures also in predicting response to hormonal, chemotherapeutic, and targeted agents in breast cancer as well as in other tumors. This book has been carried out with the aim of providing readers a useful and comprehensive resource about the range of applications of microarray technology on oncological diseases. The book is principally addressed to resident and fellow physicians, medical oncologists, molecular biologists, biotechnologists, and those who study oncological diseases. The chapters have been written by leading international researchers on these topics who have prepared their manuscripts according to current literature and field experience with microarray technology

MicroRNA applications for prostate, ovarian and breast cancer in the era of precision medicine.

The high degree of conservation in microRNA from Caenorhabditiselegans to humans has enabled relatively rapid implementation of findings in model systems to the clinic. The convergence of the capacity for genomic screening being implemented in the prevailing precision medicine initiative and the capabilities of microRNA to address these changes holds significant promise. However, prostate, ovarian and breast cancers are heterogeneous and face issues of evolving therapeutic resistance. The transforming growth factor-beta (TGFβ) signaling axis plays an important role in the progression of these cancers by regulating microRNAs. Reciprocally, microRNAs regulate TGFβ actions during cancer progression. One must consider the expression of miRNA in the tumor microenvironment a source of biomarkers of disease progression and a viable target for therapeutic targeting. The differential expression pattern of microRNAs in health and disease, therapeutic response and resistance has resulted in its application as robust biomarkers. With two microRNA mimetics in ongoing restorative clinical trials, the paradigm for future clinical studies rests on the current observational trials to validate microRNA markers of disease progression. Some of today's biomarkers can be translated to the next generation of microRNA-based therapies

Systems biology-based investigation of cooperating microRNAs as monotherapy or adjuvant therapy in cancer

MicroRNAs (miRNAs) are short, noncoding RNAs that regulate gene expression by suppressing mRNA translation and reducing mRNA stability. A miRNA can potentially bind many mRNAs, thereby affecting the expression of oncogenes and tumor suppressor genes as well as the activity of whole pathways. The promise of miRNA therapeutics in cancer is to harness this evolutionarily conserved mechanism for the coordinated regulation of gene expression, and thus restoring a normal cell phenotype. However, the promiscuous binding of miRNAs can provoke unwanted off-target effects, which are usually caused by high-dose single-miRNA treatments. Thus, it is desirable to develop miRNA therapeutics with increased specificity and efficacy. To achieve that, we propose the concept of miRNA cooperativity in order to exert synergistic repression on target genes, thus lowering the required total amount of miRNAs. We first review miRNA therapies in clinical application. Next, we summarize the knowledge on the molecular mechanism and biological function of miRNA cooperativity and discuss its application in cancer therapies. We then propose and discuss a systems biology approach to investigate miRNA cooperativity for the clinical setting. Altogether, we point out the potential of miRNA cooperativity to reduce off-target effects and to complement conventional, targeted, or immune-based therapies for cancer

Non-Coding RNAs in Ovarian Cancer

Ovarian cancer (OC) is the most lethal form of gynaecological cancer, with high- grade serous ovarian carcinoma (HGSOC) being the most common and the deadliest subtype. Non-coding RNAs are a recently discovered species of RNAs that do not code for proteins, yet play a crucial role in both normal physiology and disease. The overall goal of this thesis was to apply the power of non-coding RNAs to OC with the following aims: (1) to identify novel small non-coding RNAs present in serum that could separate patients with HGSOC from healthy women as well as predict their surgical outcome, (2) to assess the role of long non-coding RNAs (lncRNAs) in promoting cisplatin resistance in cell line models of OC, and (3) to study the effects of mutant-p53 on mRNAs and lncRNAs using a small compound known as APR-246 as well as investigating the drug’s mechanisms of action. Firstly, the lethality of OC could partially be attributed to the lack of specific symptoms, leading this disease to be termed the ‘silent killer’, as well as low inci- dence rate of 9.4 cases per 100,000 individuals, both requiring a highly accurate test for population screening that remains an ongoing challenge. Measuring the levels of small non-coding RNAs, known as microRNAs, in serum, experiments described in this thesis aimed to identify novel microRNAs that could separate pa- tients with HGSOC from healthy women as well as predict their surgical outcome, one of the most important factors influencing overall patient survival. Because serum microRNAs can be affected by pre-analytical factors such as haemolysis, the sensitivity of four methodologies to detect low levels of haemolysis was first determined. This work is published in Plos One. The work described in this thesis identified a novel serum microRNA, miR-375, that could improve the accuracy of CA-125, a routinely used biomarker in diagnosing OC, in separating patients with HGSOC from healthy women. Next, serum microRNA miR-34a-5p was found to predict the surgical outcome of patients with HGSOC. In fact, miR-34a-5p was found to be superior to CA-125 for this purpose. Although the standard therapy for treating OC consists of surgical removal of the tumour followed by chemotherapy containing platinum/taxane agents, this regimen may be too aggressive for a sub- set of patients who might benefit from neoadjuvant chemotherapy, i.e. chemother- apy followed by the surgery. A pre-operative expectation of the the surgical out- come could help surgeons decide on optimal timing for surgery. Both miR-375 and miR-34a-5p were also unaffected by haemolysis. Secondly, although OC is initially sensitive to chemotherapy, most patients develop resistance within two years, resulting in recurrent disease that is difficult to treat. To identify novel lncRNAs that could promote drug resistance, expression of ninety lncRNAs was profiled in cell line models of cisplatin resistance. Five lncRNAs were found to have the potential to promote cisplatin resistance in vitro, and lncRNA Urothelial Cancer Associated 1 (UCA1) was selected for further investigations. Despite its role in promoting cisplatin resistance in bladder cancer, UCA1 was not found to promote cisplatin resistance in cell line models of OC. Lastly, the tumour suppressor TP53 plays a central role in the biology of cancer and it is almost universally mutated in HGSOC. Recent evidence suggests that p53, the protein encoded by TP53, can significantly influence the expression of both small and long non-coding RNAs. Experiments described in this thesis aimed to investigate the effect of mutant-p53 on protein-coding and non-coding RNAs by using a small compound known as APR-246 which has been reported to restore wild-type p53 activities in multiple cancers by stabilising the structure of mutant- p53. Despite currently undergoing a phase Ib/II clinical trial for potential treatment of recurrent HGSOC, the ability of APR-246 to restore wild-type p53 activities in HGSOC has not been tested. A global transcriptomic analysis conducted in this thesis discovered that p53-responsive mRNAs and lncRNAs were not robustly induced following APR-246 treatment in two cell line models of HGSOC, but indicated that APR-246 could function by inducing high levels of reactive oxidative species (ROS). Overall, data presented in this thesis demonstrated the utility of small non- coding RNAs in identifying patients with HGSOC from healthy women as well as predicting their surgical outcome. This thesis also implicated that lncRNAs, in general, could have a role in promoting cisplatin resistance in OC as well as suggested that APR-246 could, based on evidence obtained from the expression of p53-responsive mRNAs and lncRNAs, act independently of mutant-p53. Together, this research raises novel ways for clinical management of patients with HGSOC and addresses the challenge of drug resistance using non-coding RNAs, as well as questions the assumed mechanisms of action of the ‘p53-activating’ drug APR- 246