Different roles for Tet1 and Tet2 proteins in reprogramming-mediated erasure of imprints induced by EGC fusion.

Genomic imprinting directs the allele-specific marking and expression of loci according to their parental origin. Differential DNA methylation at imprinted control regions (ICRs) is established in gametes and, although largely preserved through development, can be experimentally reset by fusing somatic cells with embryonic germ cell (EGC) lines. Here, we show that the Ten-Eleven Translocation proteins Tet1 and Tet2 participate in the efficient erasure of imprints in this model system. The fusion of B cells with EGCs initiates pluripotent reprogramming, in which rapid re-expression of Oct4 is accompanied by an accumulation of 5-hydroxymethylcytosine (5hmC) at several ICRs. Tet2 was required for the efficient reprogramming capacity of EGCs, whereas Tet1 was necessary to induce 5-methylcytosine oxidation specifically at ICRs. These data show that the Tet1 and Tet2 proteins have discrete roles in cell-fusion-mediated pluripotent reprogramming and imprint erasure in somatic cells.

Chronic kidney disease in type 2 diabetes: Implications for managing glycaemic control, cardiovascular and renal risk.

This review examines the current literature relating to diabetes related kidney disease (DKD) and the optimal management of cardio-renal risk. DKD develops in approximately 40% of patients with type 2 diabetes mellitus. The mainstay of therapy is to reduce the progression of DKD by optimising hyperglycaemia, blood pressure, lipids and lifestyle. Evidence supports the role for renin-angiotensin system blockade in limiting the progression of DKD. Recent data from diabetes related cardiovascular outcome trials and renal specific trials have provided a novel insight on the additional benefits of sodium-glucose cotransporter-2 inhibitors (SGLT2i) in reducing the progression of DKD as well as cardiovascular risk. Lessons have been learnt from CREDENCE and there are expectations that DAPA-CKD and EMPA-KIDNEY will further support the benefits of SGLT2 inhibition in relation to DKD. As a consequence, international guidelines have been updated to reflect the positive benefits. In addition, novel steroidal mineralocorticoid receptor antagonists offer a potential role in future years. The review examines the current evidence and future approach to optimising outcomes for renal protection in patients with diabetes.

A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation.

Cohesin enables post-replicative DNA repair and chromosome segregation by holding sister chromatids together from the time of DNA replication in S phase until mitosis. There is growing evidence that cohesin also forms long-range chromosomal cis-interactions and may regulate gene expression in association with CTCF, mediator or tissue-specific transcription factors. Human cohesinopathies such as Cornelia de Lange syndrome are thought to result from impaired non-canonical cohesin functions, but a clear distinction between the cell-division-related and cell-division-independent functions of cohesion--as exemplified in Drosophila--has not been demonstrated in vertebrate systems. To address this, here we deleted the cohesin locus Rad21 in mouse thymocytes at a time in development when these cells stop cycling and rearrange their T-cell receptor (TCR) α locus (Tcra). Rad21-deficient thymocytes had a normal lifespan and retained the ability to differentiate, albeit with reduced efficiency. Loss of Rad21 led to defective chromatin architecture at the Tcra locus, where cohesion-binding sites flank the TEA promoter and the Eα enhancer, and demarcate Tcra from interspersed Tcrd elements and neighbouring housekeeping genes. Cohesin was required for long-range promoter-enhancer interactions, Tcra transcription, H3K4me3 histone modifications that recruit the recombination machinery and Tcra rearrangement. Provision of pre-rearranged TCR transgenes largely rescued thymocyte differentiation, demonstrating that among thousands of potential target genes across the genome, defective Tcra rearrangement was limiting for the differentiation of cohesin-deficient thymocytes. These findings firmly establish a cell-division-independent role for cohesin in Tcra locus rearrangement and provide a comprehensive account of the mechanisms by which cohesin enables cellular differentiation in a well-characterized mammalian system.

Barriers and facilitators of the use of clinical informatics resources to facilitate pharmacogenomic implementation in resource-limited settings.

Objective: Understand perceived barriers to and facilitators of using clinical informatics applications for pharmacogenomic (PGx) implementation in resource-limited settings. Materials and Methods: We conducted a qualitative research study using a semi-structured interview guide informed by the Consolidated Framework for Implementation Research (CFIR). Interview questions assessed CFIR contextual determinants related to: electronic health record (EHR) infrastructure; clinical informatics personnel and resources; EHR integration of PGx test results; PGx clinical decision support (CDS) tools; institutional resources; and partner receptivity. Transcripts were coded and analyzed to identify themes. Results: We interviewed 24 clinical informaticists and executive leaders working in rural or underserved health care settings in Montana (n = 15) and Colorado (n = 9) and identified three major themes: (1) EHR infrastructure limitations, (2) insufficient supporting resources, and (3) unique contextual considerations for resource-limited settings. EHR infrastructure limitations included limited agency related to EHR build and interoperability concerns. Theme 1 highlighted challenges associated with integrating structured data into the EHR and inadequate vendor support. Theme 2 included limited familiarity with PGx across the care team, cost concerns, and allocation of non-financial resources. Theme 3 highlighted perceptions about the clinical utility of PGx within rural and underrepresented populations. Potential facilitators, such as being able to act nimbly, were found to coexist among the reported barriers. Discussion and Conclusion: Our results provide insight into the clinical informatics infrastructure in resource-limited settings and identify unique considerations for clinical informatics-facilitated PGx implementation. Future efforts in these settings should consider innovative partnerships and strategies to leverage facilitators and minimize barriers associated with integrating PGx CDS applications.

Bioluminescence imaging of Cyp1a1-luciferase reporter mice demonstrates prolonged activation of the aryl hydrocarbon receptor in the lung.

Aryl hydrocarbon receptor (AHR) signalling integrates biological processes that sense and respond to environmental, dietary, and metabolic challenges to ensure tissue homeostasis. AHR is a transcription factor that is inactive in the cytosol but upon encounter with ligand translocates to the nucleus and drives the expression of AHR targets, including genes of the cytochrome P4501 family of enzymes such as Cyp1a1. To dynamically visualise AHR activity in vivo, we generated reporter mice in which firefly luciferase (Fluc) was non-disruptively targeted into the endogenous Cyp1a1 locus. Exposure of these animals to FICZ, 3-MC or to dietary I3C induced strong bioluminescence signal and Cyp1a1 expression in many organs including liver, lung and intestine. Longitudinal studies revealed that AHR activity was surprisingly long-lived in the lung, with sustained Cyp1a1 expression evident in discrete populations of cells including columnar epithelia around bronchioles. Our data link diet to lung physiology and also reveal the power of bespoke Cyp1a1-Fluc reporters to longitudinally monitor AHR activity in vivo.

Dynamic assembly of silent chromatin during thymocyte maturation.

Considerable knowledge has been gained from temporal analyses of molecular events culminating in gene activation, but technical hurdles have hindered comparable studies of gene silencing. Here we describe the temporal assembly of silent chromatin at the mouse terminal transferase gene (Dntt), which is silenced and repositioned to pericentromeric heterochromatin during thymocyte maturation. Silencing was nucleated at the Dntt promoter by the ordered deacetylation of histone H3 at Lys9 (H3-Lys9), loss of methylation at H3-Lys4 and acquisition of methylation at H3-Lys9, followed by bidirectional spreading of each event. Deacetylation at H3-Lys9 coincided with pericentromeric repositioning, and neither of these early events required de novo protein synthesis. CpG methylation increased primarily in mature T cells that had left the thymus. A transformed thymocyte line supported reversible inactivation of Dntt without repositioning. In these cells, histone modification changes were nucleated at the promoter but did not spread. These results provide a foundation for elucidating the mechanisms of silent chromatin assembly during development.

Active genes dynamically colocalize to shared sites of ongoing transcription.

The intranuclear position of many genes has been correlated with their activity state, suggesting that migration to functional subcompartments may influence gene expression. Indeed, nascent RNA production and RNA polymerase II seem to be localized into discrete foci or 'transcription factories'. Current estimates from cultured cells indicate that multiple genes could occupy the same factory, although this has not yet been observed. Here we show that, during transcription in vivo, distal genes colocalize to the same transcription factory at high frequencies. Active genes are dynamically organized into shared nuclear subcompartments, and movement into or out of these factories results in activation or abatement of transcription. Thus, rather than recruiting and assembling transcription complexes, active genes migrate to preassembled transcription sites.

Beyond the Individual: Community-Centric Approaches to Increase Diversity in Biomedical Research.

Community-centric approaches to engage underrepresented populations-including community engagement, community-level consent practices, and capacity development for research-are means to enhance diversity in biomedical research populations in a more ethical way. Low diversity is a known problem in biomedical research that presents challenges in translating the benefits of research to the global population. Through long-term partnerships built on trust and collaboration, communities who would otherwise avoid research may be more willing to participate. When communities are engaged in research as partners and research questions are motivated by community health priorities, research is more meaningful and research methods are more respectful. Conversely, a lack of consultation throughout the research process can further alienate the very communities that these efforts are designed to engage. A number of underserved populations-for example American Indian and Alaska Native peoples-may value the benefits of research to a community equally or more than individual benefits. A community's autonomy must be considered, particularly when that community is not adequately protected by traditional informed consent processes. Opportunities for capacity development to support collaborative partnerships between communities and researchers are required to support engagement and understanding of the research process. Changes to research processes and infrastructure that encourage a higher level of research oversight within the community should be supported. In this paper, we present approaches that may improve diversity and equitable access to research and the delivery of health innovations for people that have historically been left out of biomedical research.

Keeping pace with CYP2D6 haplotype discovery: innovative methods to assign function.

The discovery of haplotypes with unknown or uncertain function in the CYP2D6 pharmacogene is outpacing the capabilities of traditional in vitro and in vivo approaches to characterize their function. This challenge will undoubtedly grow as pharmacogenomic research becomes more inclusive of globally diverse populations. As accurate phenotypic assignment is paramount to the utility of pharmacogenomics, high-throughput technologies are needed for this complex pharmacogene. We describe the evolving landscape of innovative approaches to assign function to CYP2D6 haplotypes and possibilities for adopting these technologies into cohesive processes. Promising approaches include ADME-optimized prediction frameworks, machine learning algorithms, deep mutational scanning and phenoconversion predictions. Implementing these approaches will lead to improved personalization of treatment for patients.

Ensuring equity: Pharmacogenetic implementation in rural and tribal communities.

Implementation strategies for pharmacogenetic testing have been largely limited to major academic medical centers and large health systems, threatening to exacerbate healthcare disparities for rural and tribal populations. There exists a need in Montana (United States)-a state where two-thirds of the population live in rural areas and with a large proportion of tribal residents-to develop novel strategies to make pharmacogenetic testing more broadly available. We established partnerships between University of Montana (UM) and three early adopter sites providing patient-centered care to historically neglected populations. We conducted 45 semi-structured interviews with key stakeholders at each site and solicited participant feedback on the utility of a centralized pharmacogenetic service at UM offering consultations to patients and providers statewide via telehealth. For settings serving rural patients-tribal and non-tribal-participants described healthcare facilities without adequate infrastructure, personnel, and funding to implement pharmacogenetic services. Participants serving tribal communities stressed the need for ethical practices for collecting biospecimens and returning genetic results to patients, largely due to historical and contemporary traumas experienced by tribal populations with regard to genetic research. Participants expressed that pharmacogenetic testing could benefit patients by achieving therapeutic benefit sooner, reducing the risk of side effects, and improving adherence outcomes for patients with limited access to follow-up services in remote areas. Others expressed concern that financial barriers to pharmacogenetic testing for patients of lower socioeconomic status would further exacerbate inequities in care. Participants valued the role of telehealth to deliver pharmacogenetic consults from a centralized service at UM, describing the ability to connect providers and patients to resources and expertise as imperative to driving successful pharmacogenetic implementation. Our results support strategies to improve access to pharmacogenetic testing for neglected patient populations and create opportunities to reduce existing healthcare inequities. By exploring critical challenges for pharmacogenetic implementation focused on serving underserved communities, this work can help guide equitable frameworks to serve as a model for other resource-limited settings looking to initiate pharmacogenetic testing.

Heritable gene silencing in lymphocytes delays chromatid resolution without affecting the timing of DNA replication.

Temporal control of DNA replication has been implicated in epigenetic regulation of gene expression on the basis of observations that certain tissue-specific genes replicate earlier in expressing than non-expressing cells. Here, we show evidence that several leukocyte-specific genes replicate early in lymphocytes regardless of their transcription and also in fibroblasts, where these genes are never normally expressed. Instead, the heritable silencing of some genes (Rag-1, TdT, CD8alpha and lambda5) and their spatial recruitment to heterochromatin domains within the nucleus of lymphocytes resulted in a markedly delayed resolution of sister chromatids into doublet signals discernable by 3D fluorescence in situ hybridization (FISH). Integration of transgenes within heterochromatin (in cis) did, however, confer late replication and this was reversed after variegated transgene expression. These findings emphasise that chromosomal location is important for defining the replication timing of genes and show that retarded sister-chromatid resolution is a novel feature of inactive chromatin.

Reprogramming lineage identity through cell-cell fusion.

The conversion of differentiated cells to a pluripotent state through somatic cell nuclear transfer provided the first unequivocal evidence that differentiation was reversible. In more recent times, introducing a combination of key transcription factors into terminally differentiated mammalian cells was shown to drive their conversion to induced pluripotent stem cells (iPSCs). These discoveries were transformative, but the relatively slow speed (2-3 weeks) and low efficiency of reprogramming (0.1-1%) made deciphering the underlying molecular mechanisms difficult and complex. Cell fusion provides an alternative reprogramming approach that is both efficient and tractable, particularly when combined with modern multi-omics analysis of individual cells. Here we review the history and the recent advances in cell-cell fusion that are enabling a better understanding cell fate conversion, and we discuss how this knowledge could be used to shape improved strategies for regenerative medicine.

Centromeric repositioning of coreceptor loci predicts their stable silencing and the CD4/CD8 lineage choice.

The differentiation of CD4(+) CD8(+) double positive (DP) thymocytes requires the irreversible choice between two alternative lineages, distinguished by the mutually exclusive expression of either CD4 or CD8. Differentiating DP cells transiently down-regulate both CD4 and CD8, and this has complicated the debate whether the mechanism of CD4/CD8 lineage choice is instructive, stochastic/selective, or more complex in nature. Using fluorescence in situ hybridization, we show that the stable silencing of coreceptor loci, and ultimately lineage choice, is predicted by the spatial repositioning of coreceptor alleles to centromeric heterochromatin domains. These data provide evidence that lineage-specific developmental programs are established early during the transition from the DP to the single positive stage.

A high-resolution map of transcriptional repression.

Turning genes on and off is essential for development and homeostasis, yet little is known about the sequence and causal role of chromatin state changes during the repression of active genes. This is surprising, as defective gene silencing underlies developmental abnormalities and disease. Here we delineate the sequence and functional contribution of transcriptional repression mechanisms at high temporal resolution. Inducible entry of the NuRD-interacting transcriptional regulator Ikaros into mouse pre-B cell nuclei triggered immediate binding to target gene promoters. Rapid RNAP2 eviction, transcriptional shutdown, nucleosome invasion, and reduced transcriptional activator binding required chromatin remodeling by NuRD-associated Mi2beta/CHD4, but were independent of HDAC activity. Histone deacetylation occurred after transcriptional repression. Nevertheless, HDAC activity contributed to stable gene silencing. Hence, high resolution mapping of transcriptional repression reveals complex and interdependent mechanisms that underpin rapid transitions between transcriptional states, and elucidates the temporal order, functional role and mechanistic separation of NuRD-associated enzymatic activities.

A randomized trial of primary intensive care to reduce hospital admissions in patients with high utilization of inpatient services.

Randomized controlled trials of case management in primary care have been infrequent and contradictory. The aim of this study was to determine if a clinic-based ambulatory case management intervention, Primary Intensive Care (PIC), would reduce hospital utilization and total cost and/or improve health outcomes among primary care patients with a recent history of high use of inpatient services. Current patients with > or =2 hospital admissions per year in the 12-18 months prior to recruitment in an urban primary care clinic were enrolled in a randomized clinical trial. Patients were randomized to the PIC intervention or usual care. PIC patients underwent a comprehensive multidisciplinary assessment with the result being a team-generated plan. The PIC team nurse practitioner served as case manager for the 12 months of follow-up and provided services designed to implement the care plan for those in the experimental group. Health care use, function, and a medication adherence scale were measured at baseline and at 12 months. There were no significant differences when either comparing the number of admissions pre and post enrollment within groups or the followup results post intervention between groups. A similar result was noted for the number of emergency department visits. The number of clinic visits increased in the intervention group by 1.5 visits per year which was statistically significant when compared to the control group. Overall functional status, health outcomes, and the Mental Health Functional Status subscore did not change significantly in either group during the study. We were unable to detect a difference in hospital use or functional status, mental health function, or medication adherence among patients who require frequent hospital admissions using our intervention.

Preventing communication errors in telephone medicine.

Errors in telephone communication can result in outcomes ranging from inconvenience and anxiety to serious compromises in patient safety. Although 25% of interactions between physicians and patients take place on the telephone, little has been written about telephone communication and medical mishaps. Similarly, training in telephone medicine skills is limited; only 6% of residency programs teach any aspect of telephone medicine. Increasing familiarity with common telephone challenges with patients may help physicians decrease the likelihood of negative outcomes. We use case vignettes to highlight communication errors in common telephone scenarios. These scenarios include giving sensitive test results, requests for narcotics, managing ill patients who are not sick enough for the emergency room, dealing with late-night calls, communicating with unintelligible patients, and handling calls from family members. We provide management strategies to minimize the occurrence of these errors.

Primary intensive care: pilot study of a primary care-based intervention for high-utilizing patients.

This pilot study was conducted to determine whether primary care patients with perceived inappropriate high healthcare utilization would require fewer emergency or inpatient services while enrolled in a weekly multidisciplinary clinic. Seventeen high-utilizing or difficult management patients of a primary care center were referred for the special intervention, Primary Intensive Care (PIC). Although not selected for the presence of psychopathology, 16 patients had comorbid psychiatric diagnoses. Patients followed in the PIC Clinic had significantly lower inpatient and emergency department use during their enrollment in the intervention when compared to the matched pre-enrollment time period, although the total hospital cost differences did not reach statistical significance. Patient and staff satisfaction was high, although the intervention was very difficult for the providers.

Jarid2 Coordinates Nanog Expression and PCP/Wnt Signaling Required for Efficient ESC Differentiation and Early Embryo Development.

Jarid2 is part of the Polycomb Repressor complex 2 (PRC2) responsible for genome-wide H3K27me3 deposition. Unlike other PRC2-deficient embryonic stem cells (ESCs), however, Jarid2-deficient ESCs show a severe differentiation block, altered colony morphology, and distinctive patterns of deregulated gene expression. Here, we show that Jarid2(-/-) ESCs express constitutively high levels of Nanog but reduced PCP signaling components Wnt9a, Prickle1, and Fzd2 and lowered ß-catenin activity. Depletion of Wnt9a/Prickle1/Fzd2 from wild-type ESCs or overexpression of Nanog largely phenocopies these cellular defects. Co-culture of Jarid2(-/-) with wild-type ESCs restores variable Nanog expression and ß-catenin activity and can partially rescue the differentiation block of mutant cells. In addition, we show that ESCs lacking Jarid2 or Wnt9a/Prickle1/Fzd2 or overexpressing Nanog induce multiple ICM formation when injected into normal E3.5 blastocysts. These data describe a previously unrecognized role for Jarid2 in regulating a core pluripotency and Wnt/PCP signaling circuit that is important for ESC differentiation and for pre-implantation development.

Mutations in CDK5RAP2 cause Seckel syndrome.

Seckel syndrome is a heterogeneous, autosomal recessive disorder marked by prenatal proportionate short stature, severe microcephaly, intellectual disability, and characteristic facial features. Here, we describe the novel homozygous splice-site mutations c.383+1G>C and c.4005-9A>G in CDK5RAP2 in two consanguineous families with Seckel syndrome. CDK5RAP2 (CEP215) encodes a centrosomal protein which is known to be essential for centrosomal cohesion and proper spindle formation and has been shown to be causally involved in autosomal recessive primary microcephaly. We establish CDK5RAP2 as a disease-causing gene for Seckel syndrome and show that loss of functional CDK5RAP2 leads to severe defects in mitosis and spindle organization, resulting in cells with abnormal nuclei and centrosomal pattern, which underlines the important role of centrosomal and mitotic proteins in the pathogenesis of the disease. Additionally, we present an intriguing case of possible digenic inheritance in Seckel syndrome: A severely affected child of nonconsanguineous German parents was found to carry heterozygous mutations in CDK5RAP2 and CEP152. This finding points toward a potential additive genetic effect of mutations in CDK5RAP2 and CEP152.