Assessing the effectiveness of "BETTER Women", a community-based, primary care-linked peer health coaching programme for chronic disease prevention: protocol for a pragmatic, wait-list controlled, type 1 hybrid effectiveness-implementation trial.

INTRODUCTION: The Building on Existing Tools to Improve Cancer and Chronic Disease Prevention and Screening in Primary Care (BETTER) programme trains allied health professionals working in primary care settings to develop personalised chronic disease 'prevention prescriptions' with patients. However, maintenance of health behaviour changes is difficult without ongoing support. Sustainable options to enhance the BETTER programme and ensure accessibility to underserved populations are needed. We designed the BETTER Women programme, which uses a digital app to match patients with a trained peer health coach (PHC) who provides ongoing support for health behaviour change after receipt of a BETTER prevention prescription in primary care. METHODS AND ANALYSIS: We will conduct a type 1 hybrid implementation-effectiveness patient-randomised trial. Interested women aged 40-68 years will be recruited from three large, sociodemographically distinct primary care clinics (urban, suburban and rural). Patients will be randomised 1:1 to intervention or wait-list control after receipt of their BETTER prevention prescription. We will aim to recruit 204 patients per group (408 total). Effectiveness will be assessed by the primary outcome of targeted behaviours achieved for each participant at 6 months, consisting of three cancer screening tests (cervical, breast and colorectal) and four behavioural determinants of cancer and chronic disease (diet, smoking, alcohol use and physical activity). Data will be collected through patient survey and clinical chart review, measured at 3, 6 and 12 months. Implementation outcomes will be assessed through patient surveys and interviews with patients, peer health coaches and healthcare providers. An embedded economic evaluation will examine cost per quality-adjusted life-year and per additional health behavioural targets achieved. ETHICS AND DISSEMINATION: This study has been approved by Women's College Hospital Research Ethics Board (REB), the Royal Victoria Regional Health Centre REB and the University of Toronto REB. All participants will provide informed consent prior to enrolment. Participation is voluntary and withdrawal will have no impact on the usual care received from their primary care provider. The results of this trial will be published in peer-reviewed journals and shared via conference presentations. Deidentified datasets will be shared on request, after publication of results. TRIAL REGISTRATION NUMBER: NCT04746859.

Predicting gene expression state and prioritizing putative enhancers using 5hmC signal.

BACKGROUND: Like its parent base 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) is a direct epigenetic modification of cytosines in the context of CpG dinucleotides. 5hmC is the most abundant oxidized form of 5mC, generated through the action of TET dioxygenases at gene bodies of actively-transcribed genes and at active or lineage-specific enhancers. Although such enrichments are reported for 5hmC, to date, predictive models of gene expression state or putative regulatory regions for genes using 5hmC have not been developed. RESULTS: Here, by using only 5hmC enrichment in genic regions and their vicinity, we develop neural network models that predict gene expression state across 49 cell types. We show that our deep neural network models distinguish high vs low expression state utilizing only 5hmC levels and these predictive models generalize to unseen cell types. Further, in order to leverage 5hmC signal in distal enhancers for expression prediction, we employ an Activity-by-Contact model and also develop a graph convolutional neural network model with both utilizing Hi-C data and 5hmC enrichment to prioritize enhancer-promoter links. These approaches identify known and novel putative enhancers for key genes in multiple immune cell subsets. CONCLUSIONS: Our work highlights the importance of 5hmC in gene regulation through proximal and distal mechanisms and provides a framework to link it to genome function. With the recent advances in 6-letter DNA sequencing by short and long-read techniques, profiling of 5mC and 5hmC may be done routinely in the near future, hence, providing a broad range of applications for the methods developed here.

TET Enzymes in the Immune System: From DNA Demethylation to Immunotherapy, Inflammation, and Cancer.

Ten-eleven translocation (TET) proteins are iron-dependent and α-ketoglutarate-dependent dioxygenases that sequentially oxidize the methyl group of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). All three epigenetic modifications are intermediates in DNA demethylation. TET proteins are recruited by transcription factors and by RNA polymerase II to modify 5mC at enhancers and gene bodies, thereby regulating gene expression during development, cell lineage specification, and cell activation. It is not yet clear, however, how the established biochemical activities of TET enzymes in oxidizing 5mC and mediating DNA demethylation relate to the known association of TET deficiency with inflammation, clonal hematopoiesis, and cancer. There are hints that the ability of TET deficiency to promote cell proliferation in a signal-dependent manner may be harnessed for cancer immunotherapy. In this review, we draw upon recent findings in cells of the immune system to illustrate established as well as emerging ideas of how TET proteins influence cellular function.

OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide.

The O- GlcNAc transferase OGT interacts robustly with all three mammalian TET methylcytosine dioxygenases. We show here that deletion of the Ogt gene in mouse embryonic stem cells (mESC) results in a widespread increase in the TET product 5-hydroxymethylcytosine (5hmC) in both euchromatic and heterochromatic compartments, with concomitant reduction of the TET substrate 5-methylcytosine (5mC) at the same genomic regions. mESC engineered to abolish the TET1-OGT interaction likewise displayed a genome-wide decrease of 5mC. DNA hypomethylation in OGT-deficient cells was accompanied by de-repression of transposable elements (TEs) predominantly located in heterochromatin, and this increase in TE expression was sometimes accompanied by increased cis -expression of genes and exons located 3' of the expressed TE. Thus, the TET-OGT interaction prevents DNA demethylation and TE expression in heterochromatin by restraining TET activity genome-wide. We suggest that OGT protects the genome against DNA hypomethylation and impaired heterochromatin integrity, preventing the aberrant increase in TE expression observed in cancer, autoimmune-inflammatory diseases, cellular senescence and ageing.

Cellular reprogramming by protein degradation: The next frontier in cancer immunotherapy.

In this issue of Cell Chemical Biology, Lane et al.1 introduce a transgene-based system to express fusion proteins that recruit transcription factors to E3 ligases. This approach expands the target repertoire for engineered cell therapies as exemplified by the targeting of SMAD proteins to overcome a TGFß-mediated suppressive mechanism that weakens anti-tumor responses.

Role of the cyclosporin-sensitive transcription factor NFAT1 in the allergic response

Proteins belonging to the NFAT (nuclear factor of activated T cells) family of transcription factors are expressed in most immune cell types, and play a central role in the transcription of cytokine genes, such as IL-2, IL-4, IL-5, IL-13, IFN-gamma, TNF-alpha, and GM-CSF. The activity of NFAT proteins is regulated by the calcium/calmodulin-dependent phosphotase calcinerium, a target for inhibition by CsA and FK506. Recently, two different groups have described that mice lacking the NFAT1 transcription factor show an enhanced immune reponse, with tendency towards the development of a late Th-like response. This review evaluates the possible role of NFAT proteins in the Th immune response and in the eosinophil-mediated allergic response.