Epigenetic control and genomic imprinting dynamics of the Dlk1-Dio3 domain.

Genomic imprinting is an epigenetic process whereby genes are monoallelically expressed in a parent-of-origin-specific manner. Imprinted genes are frequently found clustered in the genome, likely illustrating their need for both shared regulatory control and functional inter-dependence. The Dlk1-Dio3 domain is one of the largest imprinted clusters. Genes in this region are involved in development, behavior, and postnatal metabolism: failure to correctly regulate the domain leads to Kagami-Ogata or Temple syndromes in humans. The region contains many of the hallmarks of other imprinted domains, such as long non-coding RNAs and parental origin-specific CTCF binding. Recent studies have shown that the Dlk1-Dio3 domain is exquisitely regulated via a bipartite imprinting control region (ICR) which functions differently on the two parental chromosomes to establish monoallelic expression. Furthermore, the Dlk1 gene displays a selective absence of imprinting in the neurogenic niche, illustrating the need for precise dosage modulation of this domain in different tissues. Here, we discuss the following: how differential epigenetic marks laid down in the gametes cause a cascade of events that leads to imprinting in the region, how this mechanism is selectively switched off in the neurogenic niche, and why studying this imprinted region has added a layer of sophistication to how we think about the hierarchical epigenetic control of genome function.

Lessons Learned From a COVID-19 Dog Screening Pilot in California K-12 Schools.

This diagnostic study describes a dog screening program used to identify COVID-19 infections among schoolchildren.

Reassessment of weak parent-of-origin expression bias shows it rarely exists outside of known imprinted regions.

In mouse and human, genes subjected to genomic imprinting have been shown to function in development, behavior, and post-natal adaptations. Failure to correctly imprint genes in human is associated with developmental syndromes, adaptive, and metabolic disorders during life as well as numerous forms of cancer. In recent years researchers have turned to RNA-seq technologies applied to reciprocal hybrid strains of mice to identify novel imprinted genes, causing a threefold increase in genes reported as having a parental origin-specific expression bias. The functional relevance of parental origin-specific expression bias is not fully appreciated especially since many are reported with only minimal parental bias (e.g. 51:49). Here, we present an in-depth meta-analysis of previously generated RNA-seq data and show that the methods used to generate and analyze libraries greatly influence the calling of allele-specific expression. Validation experiments show that most novel genes called with parental-origin-specific allelic bias are artefactual, with the mouse strain contributing a larger effect on expression biases than parental origin. Of the weak novel genes that do validate, most are located at the periphery of known imprinted domains, suggesting they may be affected by local allele- and tissue-specific conformation. Together these findings highlight the need for robust tools, definitions, and validation of putative imprinted genes to provide meaningful information within imprinting databases and to understand the functional and mechanistic implications of the process.

Balanced gene dosage control rather than parental origin underpins genomic imprinting.

Mammalian parental imprinting represents an exquisite form of epigenetic control regulating the parent-specific monoallelic expression of genes in clusters. While imprinting perturbations are widely associated with developmental abnormalities, the intricate regional interplay between imprinted genes makes interpreting the contribution of gene dosage effects to phenotypes a challenging task. Using mouse models with distinct deletions in an intergenic region controlling imprinting across the Dlk1-Dio3 domain, we link changes in genetic and epigenetic states to allelic-expression and phenotypic outcome in vivo. This determined how hierarchical interactions between regulatory elements orchestrate robust parent-specific expression, with implications for non-imprinted gene regulation. Strikingly, flipping imprinting on the parental chromosomes by crossing genotypes of complete and partial intergenic element deletions rescues the lethality of each deletion on its own. Our work indicates that parental origin of an epigenetic state is irrelevant as long as appropriate balanced gene expression is established and maintained at imprinted loci.

Patient-Reported Care Coordination is Associated with Better Performance on Clinical Care Measures.

BACKGROUND: Prior studies using aggregated data suggest that better care coordination is associated with higher performance on measures of clinical care process; it is unclear whether this relationship reflects care coordination activities of health plans or physician practices. OBJECTIVE: Estimate within-plan relationships between beneficiary-reported care coordination measures and HEDIS measures of clinical process for the same individuals. DESIGN: Mixed-effect regression models in cross-sectional data. PARTICIPANTS: 2013 Medicare Advantage CAHPS respondents (n=152,069) with care coordination items linked to independently collected HEDIS data on clinical processes. MAIN MEASURES: Care coordination measures assessed follow-up, whether doctors had medical records during visits, whether doctors discussed medicines being taken, how informed doctors seemed about specialist care, and help received with managing care among different providers. HEDIS measures included mammography, colorectal cancer screening, cardiovascular LDL-C screening, controlling blood pressure, 5 diabetes care measures (LDL-C screening, retinal eye exam, nephropathy, blood sugar/HbA1c <9%, LCL-C<100 mg/dL), glaucoma screening in older adults, BMI assessment, osteoporosis management for women with a fracture, and rheumatoid arthritis therapy. KEY RESULTS: For 9 of the 13 HEDIS measures, within health plans, beneficiaries who reported better care coordination also received better clinical care (p<0.05) and none of the associations went in the opposite direction; HEDIS differences between those with excellent and poor coordination exceeded 5 percentage points for 7 measures. Nine measures had positive associations (breast cancer screening, colorectal cancer screening, cardiovascular care LDL-C screening, 4 of 5 diabetes care measures, osteoporosis management, and rheumatoid arthritis therapy). CONCLUSIONS: Within health plans, beneficiaries who report better care coordination also received higher-quality clinical care, particularly for care processes that entail organizing patient care activities and sharing information among different healthcare providers. These results extend prior research showing that health plans with better beneficiary-reported care coordination achieved higher HEDIS performance scores.

Gender Differences in Patient Experience Across Medicare Advantage Plans.

BACKGROUND: Medicare beneficiaries annually select fee-for-service Medicare or a private Medicare insurance (managed care) plan; information about plan performance on quality measures can inform their decisions. Although there is drill-down information available regarding quality variation by race and ethnicity, there remains a dearth of evidence regarding the extent to which care varies by other key beneficiary characteristics, such as gender. We measured gender differences for six patient experience measures and how gender gaps differ across Medicare plans. METHODS: We used data from 300,979 respondents to the 2015-2016 Medicare Advantage Consumer Assessment of Healthcare Providers and Systems surveys. We fit case mix-adjusted linear mixed-effects models to estimate gender differences and evaluate heterogeneity in differences across health plans. RESULTS: Nationally, women's experiences were better than men's (p < .05) by 1 percentage point on measures involving interactions with administrative staff (+1.6 percentage point for customer service) and timely access to care (+1.1 percentage point for getting care quickly), but worse on a measure that may involve negotiation with physicians (getting needed care). Gender gaps varied across plans, particularly for getting care quickly and getting needed care, where plan-level differences of up to 5 to 6 percentage points were observed. CONCLUSIONS: Although the average national differences in patient experience by gender were generally small, gender gaps were larger in some health plans and for specific measures. This finding indicates opportunities for health plans with larger gender gaps to implement quality improvement efforts.

The origins of genomic imprinting in mammals.

Genomic imprinting is a process that causes genes to be expressed according to their parental origin. Imprinting appears to have evolved gradually in two of the three mammalian subclasses, with no imprinted genes yet identified in prototheria and only six found to be imprinted in marsupials to date. By interrogating the genomes of eutherian suborders, we determine that imprinting evolved at the majority of eutherian specific genes before the eutherian radiation. Theories considering the evolution of imprinting often relate to resource allocation and recently consider maternal-offspring interactions more generally, which, in marsupials, places a greater emphasis on lactation. In eutherians, the imprint memory is retained at least in part by zinc finger protein 57 (ZFP57), a Kruppel associated box (KRAB) zinc finger protein that binds specifically to methylated imprinting control regions. Some imprints are less dependent on ZFP57invivo and it may be no coincidence that these are the imprints that are found in marsupials. Because marsupials lack ZFP57, this suggests another more ancestral protein evolved to regulate imprints in non-eutherian subclasses, and contributes to imprinting control in eutherians. Hence, understanding the mechanisms acting at imprinting control regions across mammals has the potential to provide valuable insights into our understanding of the origins and evolution of genomic imprinting.

Using predicted Spanish preference to target bilingual mailings in a mail survey with telephone follow-up.

OBJECTIVE: Spanish-preferring Medicare beneficiaries are underrepresented in national patient experience surveys. We test a method for improving their representation via higher response rates. DATA SOURCES/STUDY SETTING: 2009-2010 Medicare CAHPS surveys; Medicare population. STUDY DESIGN: We used surname and address to predict Spanish-language preference for a national sample of 177 139 beneficiaries. We randomized half of the 10 000 non-Puerto Rico beneficiaries with the highest predicted probabilities of Spanish preference (>10 percent) to bilingual mailings (intervention) and half to standard English-only mailings (control). DATA COLLECTION: Medicare CAHPS Survey data were collected through mail surveys with telephone follow-up of nonrespondents. PRINCIPAL FINDINGS: Mail response rate was higher for intervention (28.7 percent) than control (23.9 percent) (P < 0.0001); phone response rates among mail nonrespondents were similar in intervention and control arms (15.8 percent vs 15.7 percent, P = 0.90). Targeted bilingual mailings induced 6.5 percent of those who would not have responded to respond by mail and 54.0 percent of those who would have responded in English to respond in Spanish. Beneficiaries with greater Spanish probabilities showed greater increases in response rates, a higher proportion of responses in Spanish, and lower control response rates among. CONCLUSIONS: Targeted bilingual mailing of mixed-mode surveys using commonly available surname and address information can efficiently increase representation of this underrepresented group.

Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control.

Approximately half the mammalian genome is composed of repetitive sequences, and accumulating evidence suggests that some may have an impact on genome function. Here, we characterized a large array class of repeats of long-interspersed elements (LINE-1). Although widely distributed in mammals, locations of such arrays are species specific. Using targeted deletion, we asked whether a 170-kb LINE-1 array located at a mouse imprinted domain might function as a modulator of local transcriptional control. The LINE-1 array is lamina associated in differentiated ES cells consistent with its AT-richness, and although imprinting occurs both proximally and distally to the array, active LINE-1 transcripts within the tract are biallelically expressed. Upon deletion of the array, no perturbation of imprinting was observed, and abnormal phenotypes were not detected in maternal or paternal heterozygous or homozygous mutant mice. The array does not shield nonimprinted genes in the vicinity from local imprinting control. Reduced neural expression of protein-coding genes observed upon paternal transmission of the deletion is likely due to the removal of a brain-specific enhancer embedded within the LINE array. Our findings suggest that presence of a 170-kb LINE-1 array reflects the tolerance of the site for repeat insertion rather than an important genomic function in normal development.

A trans-homologue interaction between reciprocally imprinted miR-127 and Rtl1 regulates placenta development.

The paternally expressed imprinted retrotransposon-like 1 (Rtl1) is a retrotransposon-derived gene that has evolved a function in eutherian placentation. Seven miRNAs, including miR-127, are processed from a maternally expressed antisense Rtl1 transcript (Rtl1as) and regulate Rtl1 levels through RNAi-mediated post-transcriptional degradation. To determine the relative functional role of Rtl1as miRNAs in Rtl1 dosage, we generated a mouse specifically deleted for miR-127. The miR-127 knockout mice exhibit placentomegaly with specific defects within the labyrinthine zone involved in maternal-fetal nutrient transfer. Although fetal weight is unaltered, specific Rtl1 transcripts and protein levels are increased in both the fetus and placenta. Phenotypic analysis of single (ΔmiR-127/Rtl1 or miR-127/ΔRtl1) and double (ΔmiR-127/ΔRtl1) heterozygous miR-127- and Rtl1-deficient mice indicate that Rtl1 is the main target gene of miR-127 in placental development. Our results demonstrate that miR-127 is an essential regulator of Rtl1, mediated by a trans-homologue interaction between reciprocally imprinted genes on the maternally and paternally inherited chromosomes.

Phenotypic outcomes of imprinted gene models in mice: elucidation of pre- and postnatal functions of imprinted genes.

Genomic imprinting is an epigenetic process causing expression of a subset of genes in a parent-of-origin-specific manner. Among vertebrates, only therian mammals have been demonstrated to imprint, indicating that placentation and imprinting arose at similar time points in evolution and that imprinting may be involved in key mammal-specific processes. However, although several theories have been posited to explain the evolution of imprinting, each has shortcomings and none fully explains the wide variety of genes regulated by imprinting. In this review, we catalog the phenotypes associated with genetic mutation and overexpression at particular imprinted loci in order to consider the wide impact of imprinted genes on development. In addition to the well-described roles of imprinted genes in prenatal growth and placentation, more recent data emphasize that imprinted genes are critical for specific aspects of postnatal mammalian development involving adaptive processes, metabolism, and behavior.

Care experiences of managed care Medicare enrollees near the end of life.

OBJECTIVES: To compare reports about care experiences of individuals who died within 1 year of survey with reports of those who did not. DESIGN: Medicare Advantage (MA) Consumer Assessment of Healthcare Providers and Systems (CAHPS) surveys asked about care experiences. Survey completion dates were linked to Social Security Administration death records to identify enrollees dying within 1 year of survey completion. Propensity-score weighting combined with regression-based case-mix adjustment was used to compare these individuals' experiences with experiences of those who were alive 1 year later. SETTING: Nationally representative sample of MA enrollees. PARTICIPANTS: Four hundred two thousand five hundred ninety-three MA enrollees responding to 2008 and 2009 CAHPS Surveys. MEASUREMENTS: Outcomes were five care ratings (plan, prescription drug coverage, doctor, specialists, care) and five composite measures of care (getting needed care, getting care quickly, doctor communication, getting drugs, getting drug information). Analyses were adjusted for age, sex, race and ethnicity, education, Medicaid status, geographic region, and several health status measures. RESULTS: Twelve thousand one hundred two enrollees (3%) died within 1 year of survey completion (near-end-of-life group). Those enrollees reported slightly better experiences than other enrollees with respect to getting care quickly (+2%, P < .001) and gave slightly higher ratings for their plans (+1%, P = .02) and prescription drug coverage (+1%, P < .001). There were no measures of participant experience for which the near-end-of-life group reported worse experiences than other enrollees. CONCLUSION: Contrary to analyses based on retrospective reports from surviving relatives after an individual's death, MA enrollees' reports about care within 1 year of death were as good as or better than reports of other MA enrollees. Future research might investigate whether results are similar in other Medicare populations.

Components of care vary in importance for overall patient-reported experience by type of hospitalization.

BACKGROUND: Patients are hospitalized for disparate conditions and procedures. Patient experiences with care may depend on hospitalization type (HT). OBJECTIVES: Determine whether the contributions of patient experience composite measures to overall hospital ratings on the Hospital Consumer Assessment of Healthcare Providers and Systems Survey vary by HT. RESEARCH DESIGN: In cross-sectional observational data, we defined 24 HTs using major diagnostic category and service line (medical, surgical, or obstetrical). To assess the importance of each composite for each HT, we calculated the simultaneous partial correlations of 7 composite scores with an overall hospital rating, controlling for patient demographics. SUBJECTS: Nineteen thousand seven hundred twenty English- or Spanish-speaking adults with nonpsychiatric primary diagnoses discharged home 12/02-1/03 after an overnight inpatient stay in any of 132 general acute care hospitals in 3 states. MEASURES: Patient-reported doctor communication, nurse communication, staff responsiveness, physical environment, new medicines explained, pain control, and postdischarge information; overall 0 to 10 rating of care. RESULTS: Nurse communication was most important overall, with a 0.34 average partial correlation (range: 0.17-0.49; P < 0.05 and among the 3 most important composites for all HTs). Discharge information was least important (0.05 average partial correlation; P < 0.05 for 10 of 24 HTs). Interactions demonstrated significant (P < 0.05) variation in partial correlations by HT for 5 of 7 composites (all but responsiveness and environment), with nurse communication, doctor communication, and pain control showing the most variation (F > 2, P < 0.05). CONCLUSIONS: The importance of patient experience dimensions differs substantially and varies by HT. Quality improvement efforts should target those aspects of patient experience that matter most for each HT.

The evolution of the DLK1-DIO3 imprinted domain in mammals.

A comprehensive, domain-wide comparative analysis of genomic imprinting between mammals that imprint and those that do not can provide valuable information about how and why imprinting evolved. The imprinting status, DNA methylation, and genomic landscape of the Dlk1-Dio3 cluster were determined in eutherian, metatherian, and prototherian mammals including tammar wallaby and platypus. Imprinting across the whole domain evolved after the divergence of eutherian from marsupial mammals and in eutherians is under strong purifying selection. The marsupial locus at 1.6 megabases, is double that of eutherians due to the accumulation of LINE repeats. Comparative sequence analysis of the domain in seven vertebrates determined evolutionary conserved regions common to particular sub-groups and to all vertebrates. The emergence of Dlk1-Dio3 imprinting in eutherians has occurred on the maternally inherited chromosome and is associated with region-specific resistance to expansion by repetitive elements and the local introduction of noncoding transcripts including microRNAs and C/D small nucleolar RNAs. A recent mammal-specific retrotransposition event led to the formation of a completely new gene only in the eutherian domain, which may have driven imprinting at the cluster.

Genomic imprinting at the mammalian Dlk1-Dio3 domain.

Genomic imprinting causes genes to be expressed or repressed depending on their parental origin. The majority of imprinted genes identified to date map in clusters and much of our knowledge of the mechanisms, function and evolution of imprinting have emerged from their analysis. The cluster of imprinted genes delineated by the delta-like homolog 1 gene and the type III iodothyronine deiodinase gene (Dlk1-Dio3) is located on distal mouse chromosome 12 and human chromosome 14. Its developmental importance is exemplified by severe phenotypes associated with altered dosage of these genes in mice and humans. The domain contains three imprinted protein-coding genes, Dlk1, Rtl1 and Dio3, expressed from the paternally inherited chromosome and several imprinted large and small noncoding RNA genes expressed from the maternally inherited homolog. Here, we discuss the function and regulation of imprinting at this domain.

The evolution of imprinting: chromosomal mapping of orthologues of mammalian imprinted domains in monotreme and marsupial mammals.

BACKGROUND: The evolution of genomic imprinting, the parental-origin specific expression of genes, is the subject of much debate. There are several theories to account for how the mechanism evolved including the hypothesis that it was driven by the evolution of X-inactivation, or that it arose from an ancestrally imprinted chromosome. RESULTS: Here we demonstrate that mammalian orthologues of imprinted genes are dispersed amongst autosomes in both monotreme and marsupial karyotypes. CONCLUSION: These data, along with the similar distribution seen in birds, suggest that imprinted genes were not located on an ancestrally imprinted chromosome or associated with a sex chromosome. Our results suggest imprinting evolution was a stepwise, adaptive process, with each gene/cluster independently becoming imprinted as the need arose.

Mechanisms regulating imprinted genes in clusters.

Clustered imprinted genes are regulated by differentially methylated imprinting control regions (ICRs) that affect gene activity and repression in cis over a large region. Although a primary imprint signal for each of these clusters is DNA methylation, different mechanisms are used to establish and maintain these marks. The majority of ICRs are methylated in the maternal germline and are usually promoters for antisense transcripts whose elongation is associated with imprinting control in the domain. In contrast, ICRs methylated in the paternal germline do not appear to act as promoters and are located between genes. At least one, at the Igf2/H19 locus, is known to function as an insulator. Analysis of ICRs suggests that maternal and paternal methylation imprints function in distinct ways.

A genome annotation-driven approach to cloning the human ORFeome.

We have developed a systematic approach to generating cDNA clones containing full-length open reading frames (ORFs), exploiting knowledge of gene structure from genomic sequence. Each ORF was amplified by PCR from a pool of primary cDNAs, cloned and confirmed by sequencing. We obtained clones representing 70% of genes on human chromosome 22, whereas searching available cDNA clone collections found at best 48% from a single collection and 60% for all collections combined.