A study of translation regulation in cancer by application of ribosome profiling

Cancer is the name given to diverse diseases, whose common characteristic is uncontrolled cell proliferation. In an effort to rationalise the complexity of cancer Hanahan and Weinberg (2000, 2011) proposed the hallmarks that comprise biological capabilities that enable tumour development. Dysregulation of molecular pathways underlie these hallmarks of tumour progression and their study has been central to cancer biology. The PI3K/AKT/mTOR pathway has a central role in translation, cell growth and proliferation and it is frequently dysregulated in various cancers. In this work we aimed to elucidate the role of the PI3K pathway and protein synthesis in cancer. Our work focused on various levels of the PI3K pathway and protein synthesis, with application of ribosome profiling; a powerful technique, which provides genome-wide information on protein synthesis, by capturing actively translating ribosomes and sequencing of their associated transcripts. Previous work on bioinformatics and ribosome profiling data suggested the presence of an N-terminal extension in the well-studied tumour suppressor PTEN. Mutational analysis and further investigation of the 5’ leader of this gene performed in this study led to the discovery of previously uncharacterized proteoforms with N-terminal extensions. Given the physiological importance of PTEN this discovery is expected to broaden our understanding of the translational regulation of this gene and elucidate its role in molecular pathology. Polyamines are ubiquitous small basic molecules with known but not well defined roles in a range of physiological processes, including translation. The enzymes involved in this pathway are themselves subject to extensive translational regulation. In an effort to further characterize regulation of polyamines and their effect on translation we applied ribosome profiling in a previously established system available in the lab. This work confirmed our previous knowledge on regulation of enzymes of the polyamine pathway and identified previously uncharacterized translational events. Translation has a central role in physiology and its aberrations can cause cancer. Merkel Cell Carcinoma is a rare but aggressive tumour with poor prognosis and increasing incident rates. Approximately 80% of these cancers are induced by the Merkel Cell Polyomavirus (MCV). The small T (sT) viral antigen had been proposed to have a causal role in tumour initiation by affecting cap dependent translation. To study this molecular interaction we aimed to develop a model system that inducibly expresses MCV sT to imitate the initial steps of tumourigenesis and applied ribosome profiling on metastatic cell lines

Systematic analysis of the PTEN 5 ' leader identifies a major AUU initiated proteoform

Abundant evidence for translation within the 5' leaders of many human genes is rapidly emerging, especially, because of the advent of ribosome profiling. In most cases, it is believed that the act of translation rather than the encoded peptide is important. However, the wealth of available sequencing data in recent years allows phylogenetic detection of sequences within 5' leaders that have emerged under coding constraint and therefore allow for the prediction of functional 5' leader translation. Using this approach, we previously predicted a CUG-initiated, 173 amino acid N-terminal extension to the human tumour suppressor PTEN. Here, a systematic experimental analysis of translation events in the PTEN 5' leader identifies at least two additional non-AUG-initiated PTEN proteoforms that are expressed in most human cell lines tested. The most abundant extended PTEN proteoform initiates at a conserved AUU codon and extends the canonical AUG-initiated PTEN by 146 amino acids. All N-terminally extended PTEN proteoforms tested retain the ability to downregulate the PI3K pathway. We also provide evidence for the translation of two conserved AUG-initiated upstream open reading frames within the PTEN 5' leader that control the ratio of PTEN proteoforms

Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response

Although stop codon readthrough is used extensively by viruses to expand their gene expression, verified instances of mammalian readthrough have only recently been uncovered by systems biology and comparative genomics approaches. Previously our analysis of conserved protein coding signatures that extend beyond annotated stop codons predicted stop codon readthrough of several mammalian genes, all of which have been validated experimentally. Four mRNAs display highly efficient stop codon readthrough, and these mRNAs have a UGA stop codon immediately followed by CUAG (UGA_CUAG) that is conserved throughout vertebrates. Extending on the identification of this readthrough motif, we here investigated stop codon readthrough, using tissue culture reporter assays, for all previously untested human genes containing UGA_CUAG. The readthrough efficiency of the annotated stop codon for the sequence encoding vitamin D receptor (VDR) was 6.7%. It was the highest of those tested but all showed notable levels of readthrough. The VDR is a member of the nuclear receptor superfamily of ligand-inducible transcription factors and binds its major ligand, calcitriol, via its C-terminal ligand-binding domain. Readthrough of the annotated VDR mRNA results in a 67 amino-acid-long C-terminal extension that generates a VDR proteoform named VDRx. VDRx may form homodimers and heterodimers with VDR but, compared to VDR, VDRx displayed a reduced transcriptional response to calcitriol even in the presence of its partner retinoid X receptor

Systematic analysis of the PTEN 5' leader identifies a major AUU initiated proteoform

Abundant evidence for translation within the 5′ leaders of many human genes is rapidly emerging, especially, because of the advent of ribosome profiling. In most cases, it is believed that the act of translation rather than the encoded peptide is important. However, the wealth of available sequencing data in recent years allows phylogenetic detection of sequences within 5′ leaders that have emerged under coding constraint and therefore allow for the prediction of functional 5′ leader translation. Using this approach, we previously predicted a CUG-initiated, 173 amino acid N-terminal extension to the human tumour suppressor PTEN. Here, a systematic experimental analysis of translation events in the PTEN 5′ leader identifies at least two additional non-AUG-initiated PTEN proteoforms that are expressed in most human cell lines tested. The most abundant extended PTEN proteoform initiates at a conserved AUU codon and extends the canonical AUG-initiated PTEN by 146 amino acids. All N-terminally extended PTEN proteoforms tested retain the ability to downregulate the PI3K pathway. We also provide evidence for the translation of two conserved AUG-initiated upstream open reading frames within the PTEN 5′ leader that control the ratio of PTEN proteoforms

AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation.

In addition to acting as template for protein synthesis, messenger RNA (mRNA) often contains sensory sequence elements that regulate this process1,2. Here we report a new mechanism that limits the number of complete protein molecules that can be synthesized from a single mRNA molecule of the human AMD1 gene encoding adenosylmethionine decarboxylase 1 (AdoMetDC). A small proportion of ribosomes translating AMD1 mRNA stochastically read through the stop codon of the main coding region. These readthrough ribosomes then stall close to the next in-frame stop codon, eventually forming a ribosome queue, the length of which is proportional to the number of AdoMetDC molecules that were synthesized from the same AMD1 mRNA. Once the entire spacer region between the two stop codons is filled with queueing ribosomes, the queue impinges upon the main AMD1 coding region halting its translation. Phylogenetic analysis suggests that this mechanism is highly conserved in vertebrates and existed in their common ancestor. We propose that this mechanism is used to count and limit the number of protein molecules that can be synthesized from a single mRNA template. It could serve to safeguard from dysregulated translation that may occur owing to errors in transcription or mRNA damage

L-Proline-Based Natural Deep Eutectic Solvents as Efficient Solvents and Catalysts for the Ultrasound-Assisted Synthesis of Aurones via Knoevenagel Condensation

Aurones are minor flavonoids that possess a wide variety of bioactivity, including antioxidant, anticancer, and enzyme inhibitory activity. L-proline-based natural deep eutectic solvents (NaDES) were synthesized and applied as solvents and catalysts for the Knoevenagel condensation reaction between benzofuranone and substituted benzaldehydes to produce aurones in high yields and purity. The reaction between benzofuranone and vanillin served as the model reaction. After screening three NaDESs, and testing microwave, as well as ultrasound as energy sources, we concluded that the optimum results are obtained using L-proline/glycerol 1:2 as catalyst and solvent and ultrasound irradiation. The scope of the reaction was evaluated using a variety of benzaldehydes, and the corresponding aurones were obtained in moderate to satisfactory yields (57–89%) and high purity. An important additional feature of the described methodology is the recyclability and reusability of the NaDES, which was recycled and effectively reused after 6 cycles

L-Proline-Based Natural Deep Eutectic Solvents as Efficient Solvents and Catalysts for the Ultrasound-Assisted Synthesis of Aurones via Knoevenagel Condensation

Aurones are minor flavonoids that possess a wide variety of bioactivity, including antioxidant, anticancer, and enzyme inhibitory activity. L-proline-based natural deep eutectic solvents (NaDES) were synthesized and applied as solvents and catalysts for the Knoevenagel condensation reaction between benzofuranone and substituted benzaldehydes to produce aurones in high yields and purity. The reaction between benzofuranone and vanillin served as the model reaction. After screening three NaDESs, and testing microwave, as well as ultrasound as energy sources, we concluded that the optimum results are obtained using L-proline/glycerol 1:2 as catalyst and solvent and ultrasound irradiation. The scope of the reaction was evaluated using a variety of benzaldehydes, and the corresponding aurones were obtained in moderate to satisfactory yields (57–89%) and high purity. An important additional feature of the described methodology is the recyclability and reusability of the NaDES, which was recycled and effectively reused after 6 cycles

“Novel chitosan/alginate hydrogels as carriers of phenolic-enriched extracts from saffron floral by-products using natural deep eutectic solvents as green extraction media”

The current saffron production system is generating several hundreds of tons of tepal waste, because only stigmas are used for food. Consequently, the valorization of saffron floral by-products by developing stable functional ingredients could lead to the environmental impact minimization. Thus, the main aim of this study was to develop innovative green extraction processes from saffron floral by-products by using Natural Deep Eutectic Solvents (NaDES) and ultrasound-assisted extraction (UAE) as ecological extraction method. Response surface methodology was used to optimize process parameters. To improve the stability of the optimal extracts, they were incorporated into chitosan/alginate hydrogels, studying their water-uptake and water retention capacity and the total phenolic content (TPC) during the in vitro digestion. The results indicated that the optimal extraction, regarding total phenolic and flavonoid content, was achieved in 20 min, using 180 W ultrasound power and 90% of NaDES. The results of the DPPH assay revealed the potent antioxidant activity of saffron floral by-products. The chitosan/alginate hydrogels incorporating the as-obtained NaDES extracts showed favorable properties whereas the TPC remained stable under intestinal conditions. Therefore, NaDES combined with UAE was an efficient technique to isolate high added-value compounds from saffron flowers, succeeding also the valorization of discarded waste by using green and low-cost strategies. Furthermore, these novel hydrogels could be used as promising candidates for food or cosmetic applications

Green Extraction of Greek Propolis Using Natural Deep Eutectic Solvents (NADES) and Incorporation of the NADES-Extracts in Cosmetic Formulation

In this work, a greener approach for the extraction of Greek propolis using ultrasound-assisted extraction method in combination with Natural Deep Eutectic Solvents (NADES) is presented. Propolis is a natural material of outmost interest as it possesses various biological and pharmacological activities and is therefore used for the manufacturing of extracts useful to various fields, such as pharmaceutics, cosmetics etc. Herein, five NADES were task-specifically selected as appropriate extraction solvents since they provide important assets to the final NADES-extracts, comparing to the conventionally used organic solvents. The screening study of the prepared solvents indicated the NADES L-proline/D,L-Lactic acid as the most effective medium for the raw propolis extraction due to the extract’s high total phenolic content as well as its’ significantly higher antioxidant activity. Then, the extraction using the selected NADES, was optimized by performing Experimental Design to study the effect of extraction time, propolis-to-solvent ratio and the %NADES content in the NADES-water system. All the extracts were characterized regarding their antioxidant activity and total phenolic content. The optimum NADES-extract as well as an extract derived by extraction using a conventional hydroethanolic solution were further characterized by performing LC/MS/MS analysis. The results showed that the NADES-extracts composition was similar or superior to the hydroethanolic extracts regarding the presence of valuable phytochemicals such as apigenin, naringenin etc. A disadvantage that is usually mentioned in the literature regarding the extractions using NADES is that the extracted bioactive compounds cannot be easily separated from the NADES in order to obtain dry extracts. However, this drawback can be converted to an asset as the task-specifically designed NADES that are used in this study add value to the end product and the optimum as-obtained NADES-extract has been successfully incorporated in a cosmetic cream formulation. In this work, The antioxidant activity and organoleptic characteristics of the cream formulation were also determined

Synthesis, Conformational Analysis and ctDNA Binding Studies of Flavonoid Analogues Possessing the 3,5-di-tert-butyl-4-hydroxyphenyl Moiety

Flavanones and their biochemical precursors, chalcones, are naturally occurring compounds and consist of privileged scaffolds used in drug discovery due to their wide range of biological activities. In this work, two novel flavanones (3 and 4), the arylidene flavanone 5, and the chalcone 6, displaying structural analogies with butylated hydroxytoluene (BHT), were synthesized via an aldol reaction. According to the antioxidant activity studies of the synthesized flavanones, the arylidene flavanone 5 was the most potent antioxidant (70.8% interaction with DPPH radical and 77.4% inhibition of lipid peroxidation). In addition, the ability of the synthesized compounds to bind with ctDNA was measured via UV-spectroscopy, revealing that chalcone 6 has the strongest interaction with DNA (Kb = 5.0 × 10−3 M−1), while molecular docking was exploited to simulate the compound-DNA complexes. In an effort to explore the conformational features of the novel synthetic flavanones (3 and 4), arylidene flavanone 5, and chalcone 6, theoretical calculations were applied and the calculation of their physicochemical properties was also performed