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

Targeting the Ubiquitin Proteasome System in Cancer

The ubiquitin proteasome system is involved in a myriad of biological functions including cell cycle progression, intracellular signaling and protein degradation. As such, it is not surprising to find many components of the system misregulated in cancer. The clinical success of Bortezomib for treatment of multiple myeloma proves that targeting the ubiquitin proteasome system is valid and feasible. Here, a detailed examination of the strategies used to target the ubiquitin proteasome system in cancer is discussed. The inhibitors available, its targets, the cancer type and the developmental stage it is in are discussed

Learning cross-lingual phonological and orthagraphic adaptations: a case study in improving neural machine translation between low-resource languages

Out-of-vocabulary (OOV) words can pose serious challenges for machine translation (MT) tasks, and in particular, for low-resource language (LRL) pairs, i.e., language pairs for which few or no parallel corpora exist. Our work adapts variants of seq2seq models to perform transduction of such words from Hindi to Bhojpuri (an LRL instance), learning from a set of cognate pairs built from a bilingual dictionary of Hindi--Bhojpuri words. We demonstrate that our models can be effectively used for language pairs that have limited parallel corpora; our models work at the character level to grasp phonetic and orthographic similarities across multiple types of word adaptations, whether synchronic or diachronic, loan words or cognates. We describe the training aspects of several character level NMT systems that we adapted to this task and characterize their typical errors. Our method improves BLEU score by 6.3 on the Hindi-to-Bhojpuri translation task. Further, we show that such transductions can generalize well to other languages by applying it successfully to Hindi -- Bangla cognate pairs. Our work can be seen as an important step in the process of: (i) resolving the OOV words problem arising in MT tasks, (ii) creating effective parallel corpora for resource-constrained languages, and (iii) leveraging the enhanced semantic knowledge captured by word-level embeddings to perform character-level tasks.Comment: 47 pages, 4 figures, 21 tables (including Appendices

Prognostic Biomarkers for Breast Cancer Metastasis

Breast cancer treatment has improved rapidly through the years, starting from surgery, to hormonal therapy, to targeted therapy. Despite this, tumor metastasis remains the highest cause of breast cancer–related death. The current regime to deter metastasis is through adjuvant therapy, but such therapy frequently yields undesirable side effects. As such, prognostic markers for metastasis are important to stratify patients for adjuvant therapy so as to ameliorate the standard of living of patients with low metastatic potential. So far, only a few well-characterized prognostic biomarkers for metastasis are used in clinics. This chapter will cover both established and novel prognostic biomarkers for breast cancer metastasis and metastatic breast cancer prognosis. The potential of using these biomarkers as predictive biomarkers or new targeted therapy will also be discussed

Breast Cancer: From Transcriptional Control to Clinical Outcome

Breast cancer is the most common malignancy in women worldwide. The risk of breast cancer in women increases with age, and this is partly attributable to the accumulation of genetic lesions. Growing evidence demonstrates the role played by epigenetic modifiers and the tumor microenvironment in contributing to the increased risk of breast cancer. This chapter provides a comprehensive overview of the epigenetic regulatory signatures that impact the well-studied signaling pathways in breast tissues. Additionally, we will also delve into the therapeutic and diagnostic potential of noncoding RNAs in breast cancer

Epigenetic Factors: Key Regulators Targeted in Cancers

Gene expression is tightly regulated via a myriad of mechanisms in the cell to allow canonical processes to occur. However, in the context of cancer, some of these mechanisms are dysregulated, and aberrant gene expression ensues. Some of the dysregulated mechanisms include changes to transcription factor activity, epigenetic marks (such as DNA methylation, histone modifications and chromatin state), or the stability of mRNA and protein. Disruption of these regulators would result changes in transcriptional landscape, affecting multiple pathways and eventually lead to continual cell proliferation and the formation of the tumor. Here, we discuss epigenetic factors that affect gene expression which are dysregulated in cancer, and summarize the therapeutic options available to target these factors

ABC multidrug transporter Cdr1p of Candida albicans has divergent nucleotide-binding domains which display functional asymmetry

In order to ascertain the molecular basis of ATP-mediated drug extrusion by Cdr1p, a multidrug transporter of Candida albicans, we recently have reported that the Walker A motif of the N-terminal nucleotide biding domain (NBD) of this protein contains an uncommon cysteine residue (C193; GXXGXGC̲S/T) which is indispensable for ATP hydrolysis. This residue is exceptionally conserved in N-terminal NBDs of fungal ABC transporters and hence makes these transporters an evolutionarily divergent group. However, the presence of a conventional lysine residue at a similar position in the Walker A motif of the C-terminal NBD warrants the individual contribution of both the NBDs in the ATP-driven efflux function of such transporters. In this study we have investigated the contribution of this divergent Walker A motif in the context of the full Cdr1p protein under in vivo conditions by swapping these two crucial amino acids (C193K in Walker A motif of N-terminal NBD and K901C in Walker A motif of C-terminal NBD) between the two NBDs. Both the native and the mutant variants of Cdr1p were integrated at the PDR5 locus as GFP-tagged fusion proteins and were hyper-expressed. Our study shows that both C193K- and K901C-expressing cells elicit a severe impairment of Cdr1p's ATPase function. However, both these mutations have distinct phenotypes with respect to other functional parameters such as substrate efflux and drug resistance profiles. In contrast to C193K, K901C mutant cells were substantially hypersensitive to the tested drugs (fluconazole, ansiomycin, miconazole and cycloheximide) and were unable to expel rhodamine 6G. Our results for the first time show that both NBDs influence the Cdr1p function asymmetrically, and that the positioning of the cysteine and lysine residues within the respective Walker A motifs is functionally not interchangeable

Functional characterization of Candida albicans ABC transporter Cdr1p

In view of the importance of Candida drug resistance protein (Cdr1p) in azole resistance, we have characterized it by overexpressing it as a green fluorescent protein (GFP)-tagged fusion protein (Cdr1p-GFP). The overexpressed Cdr1p-GFP in Saccharomyces cerevisiae is shown to be specifically labeled with the photoaffinity analogs iodoarylazidoprazosin (IAAP) and azidopine, which have been used to characterize the drug-binding sites on mammalian drug-transporting P-glycoproteins. While nystatin could compete for the binding of IAAP, miconazole specifically competed for azidopine binding, suggesting that IAAP and azidopine bind to separate sites on Cdr1p. Cdr1p was subjected to site-directed mutational analysis. Among many mutant variants of Cdr1p, the phenotypes of F774A and ΔF774 were particularly interesting. The analysis of GFP-tagged mutant variants of Cdr1p revealed that a conserved F774, in predicted transmembrane segment 6, when changed to alanine showed increased binding of both photoaffinity analogues, while its deletion (ΔF774), as revealed by confocal microscopic analyses, led to mislocalization of the protein. The mislocalized ΔF774 mutant Cdr1p could be rescued to the plasma membrane as a functional transporter by growth in the presence of a Cdr1p substrate, cycloheximide. Our data for the first time show that the drug substrate-binding sites of Cdr1p exhibit striking similarities with those of mammalian drug-transporting P-glycoproteins and despite differences in topological organization, the transmembrane segment 6 in Cdr1p is also a major contributor to drug substrate-binding site(s)

Alanine scanning of transmembrane helix 11 of Cdr1p ABC antifungal efflux pump of Candida albicans: identification of amino acid residues critical for drug efflux

Objectives: To investigate the role of transmembrane segment 11 (TMS11) of Candida albicans drug resistance protein (Cdr1p) in drug extrusion. Methods: We replaced each of the 21 putative residues of TMS11 with alanine by site-directed mutagenesis. The Saccharomyces cerevisiae AD1-8u− strain was used to overexpress the green fluorescent protein tagged wild-type and mutant variants of TMS11 of Cdr1p. The cells expressing mutant variants were functionally characterized. Results: Out of 21 residues of TMS11, substitution of seven residues, i.e. A1346G, A1347G, T1351A, T1355A, L1358A, F1360A and G1362A, affected differentially the substrate specificity of Cdr1p, while 14 mutants had no significant effect on Cdr1p function. TMS11 projection in an α-helical configuration revealed with few exceptions (A1346 and F1360), a distinct segregation of mutation-sensitive residues (A1347, T1351, T1355, L1358 and G1362) towards the more hydrophilic face. Interestingly, mutation-insensitive residues seem to cluster towards the hydrophobic side of the helix. Competition of rhodamine 6G efflux, in the presence of excess of various substrates in the cells expressing native Cdr1p, revealed for the first time the overlapping binding site between azoles (such as ketoconazole, miconazole and itraconazole) and rhodamine 6G. The ability of these azoles to compete with rhodamine 6G was completely lost in mutants F1360A and G1362A, while it was selectively lost in other variants of Cdr1p. We further confirmed that fungicidal synergism of calcineurin inhibitor FK520 with azoles is mediated by Cdr1p; wherein in addition to conserved T1351, substitution of T1355, L1358 and G1362 of TMS11 also resulted in abrogation of synergism. Conclusions: Our study for the first time provides an insight into the possible role of TMS11 of Cdr1p in drug efflux