Epigenome-wide Association Studies and the Interpretation of Disease -Omics

Epigenome-wide association studies represent one means of applying genome-wide assays to identify molecular events that could be associated with human phenotypes. The epigenome is especially intriguing as a target for study, as epigenetic regulatory processes are, by definition, heritable from parent to daughter cells and are found to have transcriptional regulatory properties. As such, the epigenome is an attractive candidate for mediating long-term responses to cellular stimuli, such as environmental effects modifying disease risk. Such epigenomic studies represent a broader category of disease -omics, which suffer from multiple problems in design and execution that severely limit their interpretability. Here we define many of the problems with current epigenomic studies and propose solutions that can be applied to allow this and other disease -omics studies to achieve their potential for generating valuable insights

Increased hyperpolarized [1-13 C] lactate production in a model of joint inflammation is not accompanied by tissue acidosis as assessed using hyperpolarized 13 C-labelled bicarbonate.

Arthritic conditions are a major source of chronic pain. Furthering our understanding of disease mechanisms creates the opportunity to develop more targeted therapeutics. In rheumatoid arthritis (RA), measurements of pH in human synovial fluid suggest that acidosis occurs, but that this is highly variable between individuals. Here we sought to determine if tissue acidosis occurs in a widely used rodent arthritis model: complete Freund's adjuvant (CFA)-induced inflammation. CFA robustly evoked paw and ankle swelling, concomitant with worsening clinical scores over time. We used magnetic resonance spectroscopic imaging of hyperpolarized [1-13 C]pyruvate metabolism to demonstrate that CFA induces an increase in the lactate-to-pyruvate ratio. This increase is indicative of enhanced glycolysis and an increased lactate concentration, as has been observed in the synovial fluid from RA patients, and which was correlated with acidosis. We also measured the 13 CO2 /H13 CO3- ratio, in animals injected with hyperpolarized H13 CO3- , to estimate extracellular tissue pH and showed that despite the apparent increase in glycolytic activity in CFA-induced inflammation there was no accompanying decrease in extracellular pH. The pH was 7.23 ± 0.06 in control paws and 7.32 ± 0.09 in inflamed paws. These results could explain why mice lacking acid-sensing ion channel subunits 1, 2 and 3 do not display any changes in mechanical or thermal hyperalgesia in CFA-induced inflammation

Probing the unfolded protein response in long-lived naked mole-rats.

The long-living naked mole-rat (NMR) shows negligible senescence and resistance to age-associated diseases. Recent evidence, based on protein-level assays, suggests that enhanced protein homeostasis machinery contributes to NMR stress-resistance and longevity. Here, we develop NMR-specific, transcriptional assays for measuring the unfolded protein response (UPR), a component of ER proteostasis. By varying doses and response times of pharmacological ER stressors applied to NMR kidney fibroblasts, we probe the NMR UPR in detail, demonstrating that NMR fibroblasts have a higher UPR activation threshold compared to mouse fibroblasts under mild ER-stress induction; whereas temporal analysis reveals that severe ER-stress induction results in no comparative differences. Probing NMR UPR activation with our robust assays may lead to insights into the proteostasis and ageing relationship.Herchel Smith PhD Research Scholarship Rosetrees Trust Gates Cambridge Trust scholarshi

Acid and inflammatory sensitisation of naked mole-rat colonic afferent nerves.

Acid sensing in the gastrointestinal tract is required for gut homeostasis and the detection of tissue acidosis caused by ischaemia, inflammation and infection. In the colorectum, activation of colonic afferents by low pH contributes to visceral hypersensitivity and abdominal pain in human disease including during inflammatory bowel disease. The naked mole-rat (Heterocephalus glaber) shows no pain-related behaviour to subcutaneous acid injection and cutaneous afferents are insensitive to acid, an adaptation thought to be a consequence of the subterranean, likely hypercapnic, environment in which it lives. As such we sought to investigate naked mole-rat interoception within the gastrointestinal tract and how this differed from the mouse (Mus Musculus). Here, we show the presence of calcitonin gene-related peptide expressing extrinsic nerve fibres innervating both mesenteric blood vessels and the myenteric plexi of the smooth muscle layers of the naked mole-rat colorectum. Using ex vivo colonic-nerve electrophysiological recordings, we show differential sensitivity of naked mole-rat, compared to mouse, colonic afferents to acid and the prototypic inflammatory mediator bradykinin, but not direct mechanical stimuli. In naked mole-rat, but not mouse, we observed mechanical hypersensitivity to acid, whilst both species sensitised to bradykinin. Collectively, these findings suggest that naked mole-rat colonic afferents are capable of detecting acidic stimuli; however, their intracellular coupling to downstream molecular effectors of neuronal excitability and mechanotransduction likely differs between species.The authors declare no competing financial interests. This work was supported by Rosetrees Postdoctoral Grant (A1296; JRFH and EStJS), BBSRC grant (BB/R006210/1; JRFH and EStJS), Versus Arthritis Pain Challenge Grant (RG21973; GC and EStJS), AstraZeneca PhD studentshipt (KHB), EMBO Long-Term Fellowship (ALTF1565-2015; ZH) and University of Cambridge Vice Chancellor’s Award (TST)

Warm H2_2 as a probe of massive accretion and feedback through shocks and turbulence across cosmic time

Galaxy formation depends on a complex interplay between gravitational collapse, gas accretion, merging, and feedback processes. Yet, after many decades of investigation, these concepts are poorly understood. This paper presents the argument that warm H$_2$ can be used as a tool to unlock some of these mysteries. Turbulence, shocks and outflows, driven by star formation, AGN activity or inflows, may prevent the rapid buildup of star formation in galaxies. Central to our understanding of how gas is converted into stars is the process by which gas can dissipate its mechanical energy through turbulence and shocks in order to cool. H$_2$ lines provide direct quantitative measurements of kinetic energy dissipation in molecular gas in galaxies throughout the Universe. Based on the detection of very powerful H$_2$ lines from z = 2 galaxies and proto-clusters at the detection limits of {\it Spitzer}, we are confident that future far-IR and UV H$_2$ observations will provide a wealth of new information and insight into galaxy evolution to high-z. Finally, at the very earliest epoch of star and galaxy formation, warm H$_2$ may also provide a unique glimpse of molecular gas collapse at 7 $<$ z $<$ 12 in massive dark matter (DM) halos on their way to forming the very first galaxies. Such measurements are beyond the reach of existing and planned observatories.Comment: Submitted as a science White Paper to the Astronomy and Astrophysics Astro 2020 Decadal Survey call issued by the National Academies of Sciences, Engineering and Medicine (March 11 2019

A deep Chandra observation of the poor cluster AWM 4 - I. Properties of the central radio galaxy and its effects on the intracluster medium

Using observations from the Chandra X-ray Observatory and Giant Metrewave Radio Telescope, we examine the interaction between the intracluster medium and central radio source in the poor cluster AWM 4. In the Chandra observation a small cool core or galactic corona is resolved coincident with the radio core. This corona is capable of fuelling the active nucleus, but must be inefficiently heated by jet interactions or conduction, possibly precluding a feedback relationship between the radio source and cluster. A lack of clearly detected X-ray cavities suggests that the radio lobes are only partially filled by relativistic plasma. We estimate a filling factor of phi=0.21 (3 sigma upper limit phi<0.42) for the better constrained east lobe. We consider the particle population in the jets and lobes, and find that the standard equipartition assumptions predict pressures and ages which agree poorly with X-ray estimates. Including an electron population extending to low Lorentz factors either reduces (gamma_min=100) or removes (gamma_min=10) the pressure imbalance between the lobes and their environment. Pressure balance can also be achieved by entrainment of thermal gas, probably in the first few kiloparsecs of the radio jets. We estimate the mechanical power output of the radio galaxy, and find it to be marginally capable of balancing radiative cooling.Comment: Accepted for publication in MNRAS, 18 pages, 9 postscript figures

MyD88 signaling inhibits protective immunity to the gastrointestinal helminth parasite heligmosomoides polygyrus

Helminth parasites remain one of the most common causes of infections worldwide, yet little is still known about the immune signaling pathways that control their expulsion. C57BL/6 mice are chronically susceptible to infection with the gastrointestinal helminth parasite Heligmosomoides polygyrus. In this article, we report that C57BL/6 mice lacking the adapter protein MyD88, which mediates signaling by TLRs and IL-1 family members, showed enhanced immunity to H. polygyrus infection. Alongside increased parasite expulsion, MyD88-deficient mice showed heightened IL-4 and IL-17A production from mesenteric lymph node CD4+ cells. In addition, MyD88-/- mice developed substantial numbers of intestinal granulomas around the site of infection, which were not seen in MyD88-sufficient C57BL/6 mice, nor when signaling through the adapter protein TRIF (TIR domain-containing adapter-inducing IFN-β adapter protein) was also ablated. Mice deficient solely in TLR2, TLR4, TLR5, or TLR9 did not show enhanced parasite expulsion, suggesting that these TLRs signal redundantly to maintain H. polygyrus susceptibility in wild-type mice. To further investigate signaling pathways that are MyD88 dependent, we infected IL-1R1-/- mice with H. polygyrus. This genotype displayed heightened granuloma numbers compared with wild-type mice, but without increased parasite expulsion. Thus, the IL-1R-MyD88 pathway is implicated in inhibiting granuloma formation; however, protective immunity in MyD88-deficient mice appears to be granuloma independent. Like IL-1R1-/- and MyD88-/- mice, animals lacking signaling through the type 1 IFN receptor (i.e., IFNAR1-/-) also developed intestinal granulomas. Hence, IL-1R1, MyD88, and type 1 IFN receptor signaling may provide pathways to impede granuloma formation in vivo, but additional MyD88-mediated signals are associated with inhibition of protective immunity in susceptible C57BL/6 mice

The angular distribution of the reaction νˉe+p→e++n\bar{\nu}_e + p \to e^+ + n

The reaction $\bar{\nu}_e + p \to e^+ + n$ is very important for low-energy ($E_\nu \lesssim 60$ MeV) antineutrino experiments. In this paper we calculate the positron angular distribution, which at low energies is slightly backward. We show that weak magnetism and recoil corrections have a large effect on the angular distribution, making it isotropic at about 15 MeV and slightly forward at higher energies. We also show that the behavior of the cross section and the angular distribution can be well-understood analytically for $E_\nu \lesssim 60$ MeV by calculating to ${\cal O}(1/M)$, where $M$ is the nucleon mass. The correct angular distribution is useful for separating $\bar{\nu}_e + p \to e^+ + n$ events from other reactions and detector backgrounds, as well as for possible localization of the source (e.g., a supernova) direction. We comment on how similar corrections appear for the lepton angular distributions in the deuteron breakup reactions $\bar{\nu}_e + d \to e^+ + n + n$ and $\nu_e + d \to e^- + p + p$. Finally, in the reaction $\bar{\nu}_e + p \to e^+ + n$, the angular distribution of the outgoing neutrons is strongly forward-peaked, leading to a measurable separation in positron and neutron detection points, also potentially useful for rejecting backgrounds or locating the source direction.Comment: 10 pages, including 5 figure

Clinical validation of a spectroscopic liquid biopsy for earlier detection of brain cancer

BackgroundDiagnostic delays impact the quality of life and survival of patients with brain tumors. Earlier and expeditious diagnoses in these patients are crucial to reduce the morbidities and mortalities associated with brain tumors. A simple, rapid blood test that can be administered easily in a primary care setting to efficiently identify symptomatic patients who are most likely to have a brain tumor would enable quicker referral to brain imaging for those who need it most.MethodsBlood serum samples from 603 patients were prospectively collected and analyzed. Patients either had non-specific symptoms that could be indicative of a brain tumor on presentation to the Emergency Department, or a new brain tumor diagnosis and referral to the neurosurgical unit, NHS Lothian, Scotland. Patient blood serum samples were analyzed using the Dxcover® Brain Cancer liquid biopsy. This technology utilizes infrared spectroscopy combined with a diagnostic algorithm to predict the presence of intracranial disease.ResultsOur liquid biopsy approach reported an area under the receiver operating characteristic curve of 0.8. The sensitivity-tuned model achieves a 96% sensitivity with 45% specificity (NPV 99.3%) and identified 100% of glioblastoma multiforme patients. When tuned for a higher specificity, the model yields a sensitivity of 47% with 90% specificity (PPV 28.4%).ConclusionsThis simple, non-invasive blood test facilitates the triage and radiographic diagnosis of brain tumor patients while providing reassurance to healthy patients. Minimizing time to diagnosis would facilitate the identification of brain tumor patients at an earlier stage, enabling more effective, less morbid surgical and adjuvant care