Investigating the role of the ATR-dependent DNA damage response in the aetiology of microcephalic primordial dwarfism disorders

Repair of damage to the DNA is essential for the maintenance of genomic stability, both during embryonic development and normal growth. The cell has therefore evolved a complex array of interconnected pathways to ensure the appropriate response to DNA damage is initiated, such as cell cycle checkpoint arrest, activation of DNA repair pathways or induction of apoptotic processes. These co-ordinated signal transduction pathways have been termed the DNA damage response (DDR). A previous study showed that ATR-dependent damage responses were frequently defective in cell lines from patients with Microcephalic Primordial Dwarfism (MPD) disorders. In this thesis I have further characterised ATR–dependent damage response signalling in several cell lines from patients with various MPD disorders. I have shown that novel mutations in PCNT, which encodes a structural centrosomal protein, result in an MPD disorder and have characterised the associated ATRdependent DNA damage responses. I also contributed to the identification of mutations in ORC1, encoding a component of the DNA replication Origin Recognition Complex, in further MPD patients and examined origin licensing and Sphase progression in the patient derived cell lines. As a novel finding, I observed defects in the ATR-dependent G2/M checkpoint response in these cells. Additionally, I have characterised novel mutations in ATRIP, a gene encoding the obligate partner of ATR, in Seckel Syndrome patients, denoting a novel genetic defect in this condition. Finally, I have explored the role of PLK1 and AurA kinase in ATRdependent G2/M checkpoint control and provided compelling evidence of misregulation of this pathway in various MPD-patient derived cell lines. Collectively these data provide important functional insights into the genetic defects that cause MPD disorders and further explore the link between defective ATR-dependent damage response signalling and microcephaly

Screening approaches to generating STAT inhibitors: Allowing the hits to identify the targets

STAT transcription factors are regulators of critical cellular processes such as proliferation, survival, and self-renewal. While the activity of these proteins is tightly regulated under physiological conditions, they can become constitutively activated in a broad range of human cancers. This inappropriate STAT activation leads to enhanced transcription of genes that can directly lead to the malignant phenotype. Since STATs are largely dispensable for normal cell function, this has raised the possibility that STATs might be key targets for cancer therapy. Although a number of structure-based strategies have been used to develop STAT inhibitors, an alternate approach is to use cell-based assays that make use of the transcriptional function of STATs. Employing these systems, one can screen large chemical libraries to identify compounds that specifically block the function of a given STAT. This approach can lead to the identification of compounds that inhibit STATs by a variety of mechanisms, and can suggest novel targets for therapy. This type of functional screening strategy has already identified a drug that potently inhibits STAT3, and which is now being evaluated in a clinical trial for patients with chronic lymphocytic leukemia

Identification of a novel motif in DNA ligases exemplified by DNA ligase IV

DNA ligase IV is an essential protein that functions in DNA non-homologous end-joining, the major mechanism that rejoins DNA double-strand breaks in mammalian cells. LIG4 syndrome represents a human disorder caused by mutations in DNA ligase IV that lead to impaired but not ablated activity. Thus far, five conserved motifs in DNA ligases have been identified. We previously reported G469E as a mutational change in a LIG4 syndrome patient. G469 does not lie in any of the previously reported motifs. A sequence comparison between DNA ligases led us to identify residues 468¿476 of DNA ligase IV as a further conserved motif, designated motif Va, present in eukaryotic DNA ligases. We carried out mutational analysis of residues within motif Va examining the impact on adenylation, double-stranded ligation, and DNA binding. We interpret our results using the DNA ligase I:DNA crystal structure. Substitution of the glycine at position 468 with an alanine or glutamic acid severely compromises protein activity and stability. Substitution of G469 with an alanine or glutamic acid is better tolerated but still impacts upon activity and protein stability. These finding suggest that G468 and G469 are important for protein stability and provide insight into the hypomorphic nature of the G469E mutation identified in a LIG4 syndrome patient. In contrast, residues 470, 473 and 476 within motif Va can be changed to alanine residues without any impact on DNA binding or adenylation activity. Importantly, however, such mutational changes do impact upon double-stranded ligation activity. Considered in light of the DNA ligase I:DNA crystal structure, our findings suggest that residues 470¿476 function as part of a molecular pincer that maintains the DNA in a conformation that is required for ligation

STAT3 Activity and Function in Cancer: Modulation by STAT5 and miR-146b

The transcription factor STAT3 regulates genes that control critical cellular processes such as proliferation, survival, pluripotency, and motility. Thus, under physiological conditions, the transcriptional function of STAT3 is tightly regulated as one part of a complex signaling matrix. When these processes are subverted through mutation or epigenetic events, STAT3 becomes highly active and drives elevated expression of genes underlying these phenotypes, leading to malignant cellular behavior. However, even in the presence of activated STAT3, other cellular modulators can have a major impact on the biological properties of a cancer cell, which is reflected in the clinical behavior of a tumor. Recent evidence has suggested that two such key modulators are the activation status of other STAT family members, particularly STAT5, and the expression of STAT3-regulated genes that are part of negative feedback circuits, including microRNAs such as miR-146b. With attention to these newly emerging areas, we will gain greater insight into the consequence of STAT3 activation in the biology of human cancers. In addition, understanding these subtleties of STAT3 signaling in cancer pathogenesis will allow the development of more rational molecular approaches to cancer therapy

Using metagenomics to investigate the impact of hospital stay and the ARK intervention on the human gut resistome

Antimicrobials are vital for modern medicine. Antimicrobial use selects for antimicrobial resistant bacteria, particularly among the gut microflora. Minimising antimicrobial resistance (AMR) selection by avoiding unnecessary antibiotic use helps combat AMR. Metagenomic analyses have the potential to provide accurate detection and quantification of AMR genes within an individual’s gut microbiome (gut ‘resistome’), allowing the impact of different types of antibiotic exposures to be evaluated and guide interventions to reduce AMR. We have developed a short-read sequencing approach to characterise the gut ‘resistome’ and piloted this in two clinical sample sets. The first consisted of paired stool samples from older hospitalised adults. 25 pairs of samples (1 to 50 days apart) showed a median AMR gene reads/kb/million total reads (RPKM) of 1841 (124 to 17,832), and a median AMR gene count of 55 (2 to 101). The second consisted of faecal discards from Clostridium difficile testing at a hospital eleven months apart. In these samples (n=21) the median AMR gene read was 923 RPKM (240 to 19,475), and the median AMR gene count was 36 (9 to 82). In both sample sets there was a trend towards an increase in AMR gene RPKM and number between the time points. dfrF, tetW and acrA were the commonest AMR genes in the first sample set, while ErmB, dfrF, CblA_1 and AHP_3 IIIa were the commonest in the second sample set. This approach is being applied to analyse the impact of an intervention (ARK-Hospital) designed to change antibiotic prescribing behaviour. The data will allow us to determine the patient-level impact of reduced antibiotic exposure on carried AMR

Extension rates across the northern Shanxi Grabens, China, from Quaternary geology, seismicity and geodesy

Discrepancies between geological, seismic and geodetic rates of strain can indicate that rates of crustal deformation, and hence seismic hazard, are varying through time. Previous studies in the northern Shanxi Grabens, at the northeastern corner of the Ordos Plateau in northern China, have found extension rates of anywhere between 0 and 6 mm a−1 at an azimuth of between 95° and 180°. In this paper we determine extension rates across the northern Shanxi Grabens from offset geomorphological features and a variety of Quaternary dating techniques (including new IRSL and Ar-Ar ages), a Kostrov summation using a 700 yr catalogue of historical earthquakes, and recent campaign GPS measurements. We observe good agreement between Quaternary, seismic and geodetic rates of strain, and we find that the northern Shanxi Grabens are extending at around 1–2 mm a−1 at an azimuth of ≈151°. The azimuth of extension is particularly well constrained and can be reliably inferred from catalogues of small earthquakes. We do not find evidence for any substantial variations in extension rate through time, though there is a notable seismic moment rate deficit since 1750. This deficit could indicate complex fault interactions across large regions, aseismic accommodation of deformation, or that we are quite late in the earthquake cycle with the potential for larger earthquakes in the relatively near future

Allogeneic Stem Cells Alter Gene Expression and Improve Healing of Distal Limb Wounds in Horses.

Distal extremity wounds are a significant clinical problem in horses and humans and may benefit from mesenchymal stem cell (MSC) therapy. This study evaluated the effects of direct wound treatment with allogeneic stem cells, in terms of gross, histologic, and transcriptional features of healing. Three full-thickness cutaneous wounds were created on each distal forelimb in six healthy horses, for a total of six wounds per horse. Umbilical cord-blood derived equine MSCs were applied to each wound 1 day after wound creation, in one of four forms: (a) normoxic- or (b) hypoxic-preconditioned cells injected into wound margins, or (c) normoxic- or (d) hypoxic-preconditioned cells embedded in an autologous fibrin gel and applied topically to the wound bed. Controls were one blank (saline) injected wound and one blank fibrin gel-treated wound per horse. Data were collected weekly for 6 weeks and included wound surface area, thermography, gene expression, and histologic scoring. Results indicated that MSC treatment by either delivery method was safe and improved histologic outcomes and wound area. Hypoxic-preconditioning did not offer an advantage. MSC treatment by injection resulted in statistically significant increases in transforming growth factor beta and cyclooxygenase-2 expression at week 1. Histologically, significantly more MSC-treated wounds were categorized as pro-healing than pro-inflammatory. Wound area was significantly affected by treatment: MSC-injected wounds were consistently smaller than gel-treated or control wounds. In conclusion, MSC therapy shows promise for distal extremity wounds in horses, particularly when applied by direct injection into the wound margin. Stem Cells Translational Medicine 2018;7:98-108

Health record hiccups—5,526 real-world time series with change points labelled by crowdsourced visual inspection

Background: Large routinely collected data such as electronic health records (EHRs) are increasingly used in research, but the statistical methods and processes used to check such data for temporal data quality issues have not moved beyond manual, ad hoc production and visual inspection of graphs. With the prospect of EHR data being used for disease surveillance via automated pipelines and public-facing dashboards, automation of data quality checks will become increasingly valuable. / Findings: We generated 5,526 time series from 8 different EHR datasets and engaged >2,000 citizen-science volunteers to label the locations of all suspicious-looking change points in the resulting graphs. Consensus labels were produced using density-based clustering with noise, with validation conducted using 956 images containing labels produced by an experienced data scientist. Parameter tuning was done against 670 images and performance calculated against 286 images, resulting in a final sensitivity of 80.4% (95% CI, 77.1%–83.3%), specificity of 99.8% (99.7%–99.8%), positive predictive value of 84.5% (81.4%–87.2%), and negative predictive value of 99.7% (99.6%–99.7%). In total, 12,745 change points were found within 3,687 of the time series. / Conclusions: This large collection of labelled EHR time series can be used to validate automated methods for change point detection in real-world settings, encouraging the development of methods that can successfully be applied in practice. It is particularly valuable since change point detection methods are typically validated using synthetic data, so their performance in real-world settings cannot be assumed to be comparable. While the dataset focusses on EHRs and data quality, it should also be applicable in other fields

Global Properties of Neutral Hydrogen in Compact Groups

Compact groups of galaxies provide a unique environment to study the evolution of galaxies amid frequent gravitational encounters. These nearby groups have conditions similar to those in the earlier universe when galaxies were assembled and give us the opportunity to witness hierarchical formation in progress. To understand how the compact group environment affects galaxy evolution, we examine the gas and dust in these groups. We present new single-dish GBT neutral hydrogen (HI) observations of 30 compact groups and define a new way to quantify the group HI content as the HI-to-stellar mass ratio of the group as a whole. We compare the HI content with mid-IR indicators of star formation and optical [g-r] color to search for correlations between group gas content and star formation activity of individual group members. Quiescent galaxies tend to live in HI-poor groups, and galaxies with active star formation are more commonly found in HI-rich groups. Intriguingly, we also find "rogue" galaxies whose star formation does not correlate with group HI content. In particular, we identify three galaxies (NGC 2968 in RSCG 34, KUG 1131+202A in RSCG 42, and NGC 4613 in RSCG 64) whose mid-IR activity is discrepant with the HI. We speculate that this mismatch between mid-IR activity and HI content is a consequence of strong interactions in this environment that can strip HI from galaxies and abruptly affect star-formation. Ultimately, characterizing how and on what timescales the gas is processed in compact groups will help us understand the interstellar medium in complex, dense environments similar to the earlier Universe.Comment: Accepted to A