New insights into repeat instability McIvor, Elizabeth I.; Polak, Urszula; Napierala, Marek
RNA biology,
20/9/1/, Letnik:
7, Številka:
5
Journal Article
Recenzirano
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Expansion of tandem repeat sequences is responsible for more than 20 human diseases. Several cis elements and trans factors involved in repeat instability (expansion and contraction) have been ...identified. However no comprehensive model explaining large intergenerational or somatic changes of the length of the repeating sequences exists. Several lines of evidence, accumulated from different model studies, indicate that transcription through repeat sequences is an important factor promoting their instability. The persistent interaction between transcription template DNA and nascent RNA (RNA*DNA hybrids, R loops) was shown to stimulate genomic instability. Recently, we demonstrated that cotranscriptional RNA*DNA hybrids are preferentially formed at GC-rich trinucleotide and tetranucleotide repeat sequences in vitro as well as in human genomic DNA. Additionally, we showed that cotranscriptional formation of RNA*DNA hybrids at CTG*CAG and GAA*TTC repeats stimulate instability of these sequences in both E. coli and human cells. Our results suggest that persistent RNA*DNA hybrids may also be responsible for other downstream effects of expanded trinucleotide repeats, including gene silencing. Considering the extent of transcription through the human genome as well as the abundance of GC-rich and/or non-canonical DNA structure forming tandem repeats, RNA*DNA hybrids may represent a common mutagenic conformation. Hence, R loops are potentially attractive therapeutic target in diseases associated with genomic instability.
We present three fold symmetric microstructured fibers and their application potential for customized single mode supercontinuum generation. In our microstructured fibers we simultaneously achieve ...high nonlinearity and single mode operation by increasing three cladding air holes, which are next to the core. Selectively modified microstructures allow a large degree of freedom in the dispersion profile design. With the use of sub nanosecond pump source at the wavelength of 1064nm we show, that the designed microstructure provides various ways of generating a unique flat and broadband spectrum.
•Experimental results for customized supercontinuum generation in visible and/or infrared spectra ranges.•Single mode operation, nonlinearity and dispersion control by three fold symmetry fibers.•Increased degree of freedom in supercontinuum design by loss dispersion and nonlinearity control.
We demonstrate an experimental study of the chromatic dispersion properties for a series of microstructured fibers (MSFs) dedicated for a supercontinuum generation. With white-light interferometry ...application we analyze experimentally how the small variations of structural parameters, i.e. an air-hole diameter and a lattice constant, influence dispersion characteristics in different groups of MSFs. Our study provides useful information on how to design the fiber which is less sensitive to the fabrication imperfections. Moreover those investigations are the initial step to the development of the customized or tunable supercontinuum light sources based on MSFs with slightly changed structural parameters which can generate light with a different spectrum range, adapted to a proper application.
Tumor heterogeneity has hampered the development of novel effective therapeutic options for aggressive cancers, including the deadly primary adult brain tumor glioblastoma (GBM). Intratumoral ...heterogeneity is partially attributed to the tumor initiating cell (TIC) subset that contains highly tumorigenic, stem-like cells. TICs display metabolic plasticity but can have a reliance on aerobic glycolysis. Elevated expression of GLUT1 and GLUT3 is present in many cancer types, with GLUT3 being preferentially expressed in brain TICs (BTICs) to increase survival in low nutrient tumor microenvironments, leading to tumor maintenance. Through structure-based virtual screening (SBVS), we identified potential novel GLUT inhibitors. The screening of 13 compounds identified two that preferentially inhibit the growth of GBM cells with minimal toxicity to non-neoplastic astrocytes and neurons. These compounds, SRI-37683 and SRI-37684, also inhibit glucose uptake and decrease the glycolytic capacity and glycolytic reserve capacity of GBM patient-derived xenograft (PDX) cells in glycolytic stress test assays. Our results suggest a potential new therapeutic avenue to target metabolic reprogramming for the treatment of GBM, as well as other tumor types, and the identified novel inhibitors provide an excellent starting point for further lead development.
Substantial progress has been realized in the past several years in our understanding of the molecular mechanisms responsible for the expansions and deletions (genetic instabilities) of repeating ...tri-, tetra- and pentanucleotide repeating sequences associated with a number of hereditary neurological diseases. These instabilities occur by replication, recombination and repair processes, probably acting in concert, due to slippage of the DNA complementary strands relative to each other. The biophysical properties of the folded-back repeating sequence strands play a critical role in these instabilities. Non-B DNA structural elements (hairpins and slipped structures, DNA unwinding elements, tetraplexes, triplexes and sticky DNA) are described. The replication mechanisms are influenced by pausing of the replication fork, orientation of the repeat strands, location of the repeat sequences relative to replication origins and the flap endonuclease. Methyl-directed mismatch repair, nucleotide excision repair, and repair of damage caused by mutagens are discussed. Genetic recombination and double-strand break repair advances in Escherichia coli, yeast and mammalian models are reviewed. Furthermore, the newly discovered capacities of certain triplet repeat sequences to cause gross chromosomal rearrangements are discussed.
Abstract
Despite available treatments including surgical resection, radiation and chemotherapy, glioblastoma (GBM) is incurable with rapid recurrence and low median survival rate of just fourteen ...months. Development of more effective treatments is difficult due to the highly heterogeneous nature of GBM. One aspect of that heterogeneity involves brain tumor initiating cells (BTICs) that have a stem cell-like ability to self-renew. BTICs can readily alter their metabolism and survive in low nutrient environments due in part to increased GLUT3 expression. We believe that the higher expression of GLUT3 in cancer cells compared to non-tumor cells makes it a therapeutic target, although the potential for toxicity must be considered. In recently accepted studies by Libby et al., we reported on two novel GLUT inhibitors identified by structure based virtual screening (SBVS) using a GLUT3 homology model. We are creating a structure-activity relationship profile and seek to increase the potency, selectivity and stability of the GLUT inhibitors. In this study we have tested a number of novel analogs and identified three that have maintained efficacy against BTICs in vitro. Importantly, these compounds display minimal toxicity against human astrocytes. The novel derivatives have increased stability compared to the lead compounds and are efficacious in the nanomolar range. In the future, we intend to utilize our anti-GLUT compounds alone and in combination with radio- and chemotherapy with the hope of clinical translation.
We report on a photonic crystal fiber with a large mode area designed for compact high power fiber lasers and amplifiers. The fiber suppresses higher order modes when bent around a 10-cm radius and ...enables single mode operation in small footprint laser and amplifier architectures. We experimentally confirm the peculiar bending properties of this fiber in its passive version, by reporting on the measurement results of fundamental mode loss in bent and straight fibers, and of the influence of the bending plane orientation on this fiber loss.
The 2018 FARA Biomarker Meeting highlighted the current state of development of biomarkers for Friedreich’s ataxia. A mass spectroscopy assay to sensitively measure mature frataxin (reduction of ...which is the root cause of disease) is being developed. Biomarkers to monitor neurological disease progression include imaging, electrophysiological measures and measures of nerve function, which may be measured either in serum and/or through imaging-based technologies. Potential pharmacodynamic biomarkers include metabolic and protein biomarkers and markers of nerve damage. Cardiac imaging and serum biomarkers may reflect cardiac disease progression. Considerable progress has been made in the development of biomarkers for various contexts of use, but further work is needed in terms of larger longitudinal multisite studies, and identification of novel biomarkers for additional use cases
Biomarkers are characteristics that can be objectively measured, evaluated and used as indicators of disease progression or the effect of a therapy. Friedreich’s ataxia is a progressive multisystem neuromuscular disease with no treatment. Current clinical measures cannot robustly detect disease progression in less than a year, meaning that clinical trials are long and drug development is slow. The Friedreich’s Ataxia Research Alliance and the scientific community are looking for biomarkers that show change in shorter time frames that can accelerate drug development. The 2018 FARA Biomarker Meeting summarized the exciting findings that represent the current state of the field.
Abstract
Patient prognosis for individuals diagnosed with GBM remains incredibly poor with a median survival of only 15 months despite aggressive treatment with surgical tumor resection, ...chemotherapy, and radiation therapy. Therapeutic development to prolong survival has been hampered by a high degree of inter- and intra-tumoral heterogeneity. Contributing to tumor heterogeneity is a subset of highly tumorigenic cells, termed brain tumor initiating cells (BTICs), that can self-renew and have been shown to be highly invasive and resistant to therapy. BTICs can survive under nutrient poor conditions due to their increased expression of glucose transporter 3 (GLUT3). In a recently accepted study, we utilized structure based virtual screening (SBVS) using a GLUT3 homology model to identify two novel GLUT inhibitors. We are now generating a structure-activity relationship profile based on a highly efficacious compound (IC50= ~300 nM) with the same backbone structure identified in the initial screen and seek to improve the potency, selectivity and drug-like properties of the GLUT inhibitors. We have tested several novel analogs and identified four that have maintained efficacy against BTICs in vitro (IC50= 300–600 nM). Importantly, these analogs have displayed less toxicity to astrocytes than lead compounds in addition to improved stability in mouse liver microsomes. As proof of concept, we have begun to test the GLUT inhibitors alone and in combination with chemotherapy in vivo. Thus far, our work has demonstrated that targeting glucose transport is a promising therapeutic avenue to explore.
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