Mutations in DNA repair genes are associated with increased neo-antigen load and activated T cell infiltration in lung adenocarcinoma.

Mutations in DNA repair genes lead to increased genomic instability and mutation frequency. These mutations represent potential biomarkers for cancer immunotherapy efficacy, as high tumor mutational burden has been associated with increased neo-antigens and tumor infiltrating lymphocytes. While mismatch repair mutations have successfully predicted response to anti-PD-1 therapy in colorectal and other cancers, they have not yet been tested for lung cancer, and few have investigated genes from other DNA repair pathways. We utilized TCGA samples to comprehensively immunophenotype lung tumors and analyze the links between DNA repair mutations, neo-antigen and total mutational burden, and tumor immune infiltration. Overall, 73% of lung tumors contained infiltration by at least one T cell subset, with high mutational burden tumors containing significantly increased infiltration by activated CD4 and CD8 T cells. Further, mutations in mismatch repair genes, homologous recombination genes, or POLE accurately predicted increased tumor mutational burden, neo-antigen load, and T cell infiltration. Finally, neo-antigen load correlated with expression of M1-polarized macrophage genes, PD-1, PD-L1, IFNγ, GZMB, and FASLG, among other immune-related genes. Overall, after defining the immune infiltrate in lung tumors, we demonstrate the potential value of utilizing gene mutations from multiple DNA repair pathways as biomarkers for lung cancer immunotherapy. Oncotarget 2018; 9(8):7949-796

Mutations in DNA repair genes are associated with increased neoantigen burden and a distinct immunophenotype in lung squamous cell carcinoma.

Deficiencies in DNA repair pathways, including mismatch repair (MMR), have been linked to higher tumor mutation burden and improved response to immune checkpoint inhibitors. However, the significance of MMR mutations in lung cancer has not been well characterized, and the relevance of other processes, including homologous recombination (HR) and polymerase epsilon (POLE) activity, remains unclear. Here, we analyzed a dataset of lung squamous cell carcinoma samples from The Cancer Genome Atlas. Variants in DNA repair genes were associated with increased tumor mutation and neoantigen burden, which in turn were linked with greater tumor infiltration by activated T cells. The subset of tumors with DNA repair gene variants but without T cell infiltration exhibited upregulation of TGF-β and Wnt pathway genes, and a combined score incorporating these genes and DNA repair status accurately predicted immune cell infiltration. Finally, high neoantigen burden was positively associated with genes related to cytolytic activity and immune checkpoints. These findings provide evidence that DNA repair pathway defects and immunomodulatory genes together lead to specific immunophenotypes in lung squamous cell carcinoma and could potentially serve as biomarkers for immunotherapy

Fast recovery of suppressed Norway spruce trees after selection harvesting on a drained peatland forest site

Continuous cover forestry (CCF) has been promoted as an environmentally sustainable option for drained peatlands. The CCF management has been challenged due to potentially lower tree growth compared to tradi-tional even-aged management, especially with suppressed trees that are released during a selection harvesting under CCF management. Our objective was to quantify the time lag of stem diameter growth response of suppressed Norway spruce trees (Picea abies Karst.) after a selection harvesting compared to that of dominant trees. We also tested if the carbon assimilation of the trees increased immediately after selection harvesting. We used radial increment cores from suppressed Norway spruce trees to estimate the impact of selection harvesting on the diameter growth and intrinsic water use efficiency (iWUE). We measured carbon isotope composition (delta 13C) of wood, to quantify how the reduced competition between trees altered iWUE and its components, the photosynthetic rate (A) and sto-matal conductance (g). The study was conducted in the Lettosuo experimental site on fertile forestry drained peatland area in southern Finland. Approximately 70 % of the initial stand area (18.5 ha) was harvested according to CCF principles by applying selection harvesting, and the rest of the area was divided to intact control area and to clear-cut area. In the study site, by selection harvest, trees were removed from multiple age classes, but especially mature trees individually or in a small groups were taken away to maintain uneven-aged structure of the forest. All the target trees grew in the similar competitive position before selection harvesting. Our results show that there was a delay with the diameter growth of the suppressed trees to selection har-vesting, whereas the most significant growth-enhancing effect occurred three-four years after selection har-vesting. In contrast to the delay in the increment, the photosynthetic rate relative to stomatal conductance increased immediately after selection harvesting, as shown by the instant 2.5 parts per thousand increase in delta 13C to a post-harvest level. Our results show that carbon uptake increased immediately for suppressed Norway spruce trees after selection harvesting, but the harvest did not induce a clear increase in stem diameter growth during the first years after the harvest.Peer reviewe

The writing on the wall: the concealed communities of the East Yorkshire horselads

This paper examines the graffiti found within late nineteenth and early-twentieth century farm buildings in the Wolds of East Yorkshire. It suggests that the graffiti were created by a group of young men at the bottom of the social hierarchy - the horselads – and was one of the ways in which they constructed a distinctive sense of communal identity, at a particular stage in their lives. Whilst it tells us much about changing agricultural regimes and social structures, it also informs us about experiences and attitudes often hidden from official histories and biographies. In this way, the graffiti are argued to inform our understanding, not only of a concealed community, but also about their hidden histor

Oxygen stable isotope ratios from British oak tree-rings provide a strong and consistent record of past changes in summer rainfall

United Kingdom (UK) summers dominated by anti-cyclonic circulation patterns are characterised by clear skies, warm temperatures, low precipitation totals, low air humidity and more enriched oxygen isotope ratios (δ18O) in precipitation. Such conditions usually result in relatively more positive (enriched) oxygen isotope ratios in tree leaf sugars and ultimately in the tree-ring cellulose formed in that year, the converse being true in cooler, wet summers dominated by westerly air flow and cyclonic conditions. There should therefore be a strong link between tree-ring δ18O and the amount of summer precipitation. Stable oxygen isotope ratios from the latewood cellulose of 40 oak trees sampled at eight locations across Great Britain produce a mean δ18O chronology that correlates strongly and significantly with summer indices of total shear vorticity, surface air pressure, and the amount of summer precipitation across the England and Wales region of the United Kingdom. The isotope-based rainfall signal is stronger and much more stable over time than reconstructions based upon oak ring widths. Using recently developed methods that are precise, efficient and highly cost-effective it is possible to measure both carbon (δ13C) and oxygen (δ18O) isotope ratios simultaneously from the same tree-ring cellulose. In our study region, these two measurements from multiple trees can be used to reconstruct summer temperature (δ13C) and summer precipitation (δ18O) with sufficient independence to allow the evolution of these climate parameters to be reconstructed with high levels of confidence. The existence of long, well-replicated oak tree-ring chronologies across the British Isles mean that it should now be possible to reconstruct both summer temperature and precipitation over many centuries and potentially millennia

The impact of financial incentives on the implementation of asthma or diabetes self-management: A systematic review

Introduction: Financial incentives are utilised in healthcare systems in a number of countries to improve quality of care delivered to patients by rewarding practices or practitioners for achieving set targets. Objectives: To systematically review the evidence investigating the impact of financial incentives for implementation of supported self-management on quality of care including: organisational process outcomes, individual behavioural outcomes, and health outcomes for individuals with asthma or diabetes; both conditions with an extensive evidence base for self-management. Methods: We followed Cochrane methodology, using a PICOS search strategy to search eight databases in November 2015 (updated May 2017) including a broad range of implementation methodologies. Studies were weighted by robustness of methodology, number of participants and the quality score. We used narrative synthesis due to heterogeneity of studies. Results: We identified 2,541 articles; 12 met our inclusion criteria. The articles were from the US (n = 7), UK (n = 4) and Canada (n = 1). Measured outcomes were HbA1c tests undertaken and/or the level achieved (n = 10), written action plans for asthma (n = 1) and hospital/emergency department visits (n = 1). Three of the studies were part of a larger incentive scheme including many conditions; one focused on asthma; eight focussed on diabetes. In asthma, the proportion receiving ‘perfect care’ (including providing a written action plan) increased from 4% to 88% in one study, and there were fewer hospitalisations/emergency department visits in another study. Across the diabetes studies, quality-of-care/GP performance scores improved in three, were unchanged in six and deteriorated in one. Conclusions: Results for the impact of financial incentives for the implementation of self-management were mixed. The evidence in diabetes suggests no consistent impact on diabetic control. There was evidence from a single study of improved process and health outcomes in asthma. Further research is needed to confirm these findings and understand the process by which financial incentives may impact (or not) on care

Health systems strengthening to arrest the global disability burden: Empirical development of prioritised components for a global strategy for improving musculoskeletal health

Introduction Despite the profound burden of disease, a strategic global response to optimise musculoskeletal (MSK) health and guide national-level health systems strengthening priorities remains absent. Auspiced by the Global Alliance for Musculoskeletal Health (G-MUSC), we aimed to empirically derive requisite priorities and components of a strategic response to guide global and national-level action on MSK health. Methods Design: mixed-methods, three-phase design. Phase 1: qualitative study with international key informants (KIs), including patient representatives and people with lived experience. KIs characterised the contemporary landscape for MSK health and priorities for a global strategic response. Phase 2: scoping review of national health policies to identify contemporary MSK policy trends and foci. Phase 3: informed by phases 1-2, was a global eDelphi where multisectoral panellists rated and iterated a framework of priorities and detailed components/actions. Results Phase 1: 31 KIs representing 25 organisations were sampled from 20 countries (40% low and middle income (LMIC)). Inductively derived themes were used to construct a logic model to underpin latter phases, consisting of five guiding principles, eight strategic priority areas and seven accelerators for action. Phase 2: of the 165 documents identified, 41 (24.8%) from 22 countries (88% high-income countries) and 2 regions met the inclusion criteria. Eight overarching policy themes, supported by 47 subthemes, were derived, aligning closely with the logic model. Phase 3: 674 panellists from 72 countries (46% LMICs) participated in round 1 and 439 (65%) in round 2 of the eDelphi. Fifty-nine components were retained with 10 (17%) identified as essential for health systems. 97.6% and 94.8% agreed or strongly agreed the framework was valuable and credible, respectively, for health systems strengthening. Conclusion An empirically derived framework, co-designed and strongly supported by multisectoral stakeholders, can now be used as a blueprint for global and country-level responses to improve MSK health and prioritise system strengthening initiatives

Nuggets, Pearls, and Vignettes of Master Heart Failure Clinicians

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73696/1/j.1527-5299.2001.00307.x.pd

Profiling CpG island field methylation in both morphologically normal and neoplastic human colonic mucosa

Aberrant CpG island (CGI) methylation occurs early in colorectal neoplasia. Quantitative methylation-specific PCR profiling applied to biopsies was used to quantify low levels of CGI methylation of 18 genes in the morphologically normal colonic mucosa of neoplasia-free subjects, adenomatous polyp patients, cancer patients and their tumours. Multivariate statistical analyses distinguished tumour from mucosa with a sensitivity of 78.9% and a specificity of 100% (P=3 × 10−7). In morphologically normal mucosa, age-dependent CGI methylation was observed for APC, AXIN2, DKK1, HPP1, N33, p16, SFRP1, SFRP2 and SFRP4 genes, and significant differences in CGI methylation levels were detected between groups. Multinomial logistic regression models based on the CGI methylation profiles from normal mucosa correctly identified 78.9% of cancer patients and 87.9% of non-cancer (neoplasia-free+polyp) patients (P=4.93 × 10−7) using APC, HPP1, p16, SFRP4, WIF1 and ESR1 methylation as the most informative variables. Similarly, CGI methylation of SFRP4, SFRP5 and WIF1 correctly identified 61.5% of polyp patients and 78.9% of neoplasia-free subjects (P=0.0167). The apparently normal mucosal field of patients presenting with neoplasia has evidently undergone significant epigenetic modification. Methylation of the genes selected by the models may play a role in the earliest stages of the development of colorectal neoplasia