Topologically associating domains are stable units of replication-timing regulation.

Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains'), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.

A comparative encyclopedia of DNA elements in the mouse genome.

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.

Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation.

The expansion of repressive epigenetic marks has been implicated in heterochromatin formation during embryonic development, but the general applicability of this mechanism is unclear. Here we show that nuclear rearrangement of repressive histone marks H3K9me3 and H3K27me3 into nonoverlapping structural layers characterizes senescence-associated heterochromatic foci (SAHF) formation in human fibroblasts. However, the global landscape of these repressive marks remains unchanged upon SAHF formation, suggesting that in somatic cells, heterochromatin can be formed through the spatial repositioning of pre-existing repressively marked histones. This model is reinforced by the correlation of presenescent replication timing with both the subsequent layered structure of SAHFs and the global landscape of the repressive marks, allowing us to integrate microscopic and genomic information. Furthermore, modulation of SAHF structure does not affect the occupancy of these repressive marks, nor vice versa. These experiments reveal that high-order heterochromatin formation and epigenetic remodeling of the genome can be discrete events.

Many paths lead chromatin to the nuclear periphery.

It is now well accepted that defined architectural compartments within the cell nucleus can regulate the transcriptional activity of chromosomal domains within their vicinity. However, it is generally unclear how these compartments are formed. The nuclear periphery has received a great deal of attention as a repressive compartment that is implicated in many cellular functions during development and disease. The inner nuclear membrane, the nuclear lamina, and associated proteins compose the nuclear periphery and together they interact with proximal chromatin creating a repressive environment. A new study by Harr et al. identifies specific protein-DNA interactions and epigenetic states necessary to re-position chromatin to the nuclear periphery in a cell-type specific manner. Here, we review concepts in gene positioning within the nucleus and current accepted models of dynamic gene repositioning within the nucleus during differentiation. This study highlights that myriad pathways lead to nuclear organization.

Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia.

Abnormal replication timing has been observed in cancer but no study has comprehensively evaluated this misregulation. We generated genome-wide replication-timing profiles for pediatric leukemias from 17 patients and three cell lines, as well as normal B and T cells. Nonleukemic EBV-transformed lymphoblastoid cell lines displayed highly stable replication-timing profiles that were more similar to normal T cells than to leukemias. Leukemias were more similar to each other than to B and T cells but were considerably more heterogeneous than nonleukemic controls. Some differences were patient specific, while others were found in all leukemic samples, potentially representing early epigenetic events. Differences encompassed large segments of chromosomes and included genes implicated in other types of cancer. Remarkably, differences that distinguished leukemias aligned in register to the boundaries of developmentally regulated replication-timing domains that distinguish normal cell types. Most changes did not coincide with copy-number variation or translocations. However, many of the changes that were associated with translocations in some leukemias were also shared between all leukemic samples independent of the genetic lesion, suggesting that they precede and possibly predispose chromosomes to the translocation. Altogether, our results identify sites of abnormal developmental control of DNA replication in cancer that reveal the significance of replication-timing boundaries to chromosome structure and function and support the replication domain model of replication-timing regulation. They also open new avenues of investigation into the chromosomal basis of cancer and provide a potential novel source of epigenetic cancer biomarkers.

Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse.

In multicellular organisms, developmental changes to replication timing occur in 400-800 kb domains across half the genome. While examples of epigenetic control of replication timing have been described, a role for DNA sequence in mammalian replication-timing regulation has not been substantiated. To assess the role of DNA sequences in directing developmental changes to replication timing, we profiled replication timing in mice carrying a genetically rearranged Human Chromosome 21 (Hsa21). In two distinct mouse cell types, Hsa21 sequences maintained human-specific replication timing, except at points of Hsa21 rearrangement. Changes in replication timing at rearrangements extended up to 900 kb and consistently reconciled with the wild-type replication pattern at developmental boundaries of replication-timing domains. Our results are consistent with DNA sequence-driven regulation of Hsa21 replication timing during development and provide evidence that mammalian chromosomes consist of multiple independent units of replication-timing regulation.

Pigmented rice bran and plant sterol combination reduces serum lipids in overweight and obese adults.

OBJECTIVE: This study investigated the dietary effect of including pigmented rice bran with or without plant sterols on lipid profiles during energy restriction-induced weight loss in overweight and obese adults not taking cholesterol-lowering medication. In addition, the study examined the effect of intervention on biomarkers of oxidative stress and inflammation. METHODS: A group of 24 overweight and obese adults (age: 43 ± 6 years, body mass index 32 ± 1 kg/m(2), 18 females) were randomized to a 25% calorie-restricted diet containing either pigmented rice bran (RB) or the RB with addition of plant sterols (RB+PS) snack bars for 8 weeks. The individualized nutrient-balanced diet contained ∼70% of daily energy needs assessed from indirect calorimetry measured resting energy expenditure (EE) and physical activity-related EE assessed using accelerometry. Anthropometrics, blood pressure, blood lipids, glucose, urinary F2-isoprostanes, C-reactive protein, insulin, and leptin were measured at baseline and after 8 weeks of intervention. RESULTS: Participants lost approximately 4.7 ± 2.2 kg (p < 0.001). Weight loss was not significant between the RB+PS and RB group (p = 0.056). Changes in body fat corresponded to changes in body weight. Average decrease in total cholesterol was significantly higher in the RB+PS group than in the RB group (difference 36 ± 25 g/dL vs 7 ± 16 g/dL; p = 0.044). A similar pattern was observed for the decrease in low-density lipoprotein (LDL) cholesterol (difference 22.3 ± 25.2 g/dL vs 4.4 ± 18.9 g/dL; p = 0.062). Changes in systolic blood pressure, serum levels of leptin, and F2-isoprostanes were significant between baseline values and after 8 weeks on the diet in both groups (p < 0.05) but did not differ between the 2 groups. CONCLUSIONS: A nutrient-balanced and energy-restricted diet supplemented with rice bran and plant sterols resulted in a significant decrease in total and LDL cholesterol in overweight and obese adults.

Prevalence and correlates of metabolic syndrome among women living in urban slums, Mysore, India.

Metabolic Syndrome (MetSyn) is a predictor of cardiovascular disease (CVD). About a third of urban Indians suffer from MetSyn. This study examined the prevalence of MetSyn among women living in urban slums. A cross-sectional survey was carried out between October 2017 and May 2018 among a non-probability sample of slum-dwelling women, 40-64 years of age, in six government-designated slums in Mysore, India. Data were collected on demographics, diet, behavioral risks, anthropometry, blood pressure, serum glucose, hemoglobin A1c, and serum lipids. The study used a definition of MetSyn from the International Diabetes Federation Task Force on Epidemiology and Prevention with an HbA1c measure for average blood glucose. About two-fifths of the 607 participants had MetSyn (41.5%; 95% CI: 37.7-45.5). Of those, 40.9% met three criteria, 38.1% four, and 25.0%, all five criteria. Elevated BP was the most prevalent MetSyn factor (79.6%), followed by increased waist circumference (54.5%), low HDL (50.1%), elevated Hb A1c (37.1%), and elevated triglycerides (36.1%). Odds for MetSyn were 1.52 times greater for those who were 50-59 years of age compared with those 40-49 years of age (adjusted odds ratio[AOR]:1.52; 95% CI:0.96-2.40). Women with mobility issues had 1.29 times higher odds of MetSyn than those without it (AOR: 0.76, 95% CI: 0.96, 1.75). Housewives had 1.29 times greater odds of MetSyn (AOR: 1.29, 95% CI: 1.00, 1.67). There is a high prevalence of MetSyn among urban slum-dwelling women in Mysore. There is a need for interventions aimed at reducing CVD risk factors in this population.

Oral Human Papillomavirus Infection among Smokeless Tobacco-using Tribal Women in Mysuru, India.

Smokeless tobacco (SLT) is consumed by more than 300 million people worldwide. Studies show high use among Indian indigenous women who are also at high risk for oral cancers. Both human papillomavirus infection (HPV) and SLT have been associated with oral cancer, this study examined the presence of high-risk HPV in oral samples collected from tribal smokeless tobacco users in Mysuru, India. Between June and August 2019, 100 tribal females (50 SLT-users and 50 non-users) from rural Mysuru District, Karnataka, were enrolled in a cross-sectional study. Following informed consent, demographic data and oral samples were collected and processed using a digene HC2 High-Risk HPV DNA test (Qiagen, USA). On average participants were 45.5 (SD: ±6.6) years. Chronic SLT users were mostly married (73%), Hindu (100%), illiterate (62%), and employed (90%). One woman was positive for high-risk HPV infection. Oral HPV infection was low in this sample and this is consistent with the literature from other low and middle-income countries. SLT use is high in this group so interventions to reduce tobacco use are warranted.

Spatial dispersion in three-dimensional drawn magnetic metamaterials.

We characterize spatial dispersion in longitudinally invariant drawn metamaterials with a magnetic response at terahertz frequencies, whereby a change in the angle of the incident field produces a shift in the resonant frequency. We present a simple analytical model to predict this shift. We also demonstrate that the spatial dispersion is eliminated by breaking the longitudinal invariance using laser ablation. The experimental results are in agreement with numerical simulations.

Domain-wide regulation of DNA replication timing during mammalian development.

Studies of replication timing provide a handle into previously impenetrable higher-order levels of chromosome organization and their plasticity during development. Although mechanisms regulating replication timing are not clear, novel genome-wide studies provide a thorough survey of the extent to which replication timing is regulated during most of the early cell fate transitions in mammals, revealing coordinated changes of a defined set of 400-800 kb chromosomal segments that involve at least half the genome. Furthermore, changes in replication time are linked to changes in sub-nuclear organization and domain-wide transcriptional potential, and tissue-specific replication timing profiles are conserved from mouse to human, suggesting that the program has developmental significance. Hence, these studies have provided a solid foundation for linking megabase level chromosome structure to function, and suggest a central role for replication in domain-level genome organization.

Building Biomimetic Potency Tests for Islet Transplantation.

Diabetes is a disease of insulin insufficiency, requiring many to rely on exogenous insulin with constant monitoring to avoid a fatal outcome. Islet transplantation is a recent therapy that can provide insulin independence, but the procedure is still limited by both the availability of human islets and reliable tests to assess their function. While stem cell technologies are poised to fill the shortage of transplantable cells, better methods are still needed for predicting transplantation outcome. To ensure islet quality, we propose that the next generation of islet potency tests should be biomimetic systems that match glucose stimulation dynamics and cell microenvironmental preferences and rapidly assess conditional and continuous insulin secretion with minimal manual handing. Here, we review the current approaches for islet potency testing and outline technologies and methods that can be used to arrive at a more predictive potency test that tracks islet secretory capacity in a relevant context. With the development of potency tests that can report on islet secretion dynamics in a context relevant to their intended function, islet transplantation can expand into a more widely accessible and reliable treatment option for individuals with diabetes.

Acceptability and Concordance of Self- Versus Clinician- Sampling for HPV Testing among Rural South Indian Women.

BACKGROUND: Despite being largely preventable, HPV-related cervical cancers continues to be the second highest cause of cancer deaths among Indian women. HPV testing using self-sampled samples may offer an opportunity to expand cervical cancer screening in India where there is currently a shortage of providers and facilities for cervical cancer screening. The study examines acceptability and concordance of self vs. clinician collected samples for HPV-relted cervical cancer screening among rural South Indian women. METHODS: Between May and August 2017, eight mobile screening clinics were conducted among 120 eligible women in rural villages in Mysore District, India. Women over the age of 30 underwent informed consent process and then self-sampled a sample for cervicovaginal HPV DNA testing. Next, the women underwent clinical exam where the clinician collected a cervicovaginal HPV DNA sample. Following the clinical exam, all participants answered an interviewer-administered questionnaire to assess their history of cervical cancer screening and acceptability of self- and clinician-sampling methods. To assess diagnostic accuracy, concordance of self- and clinician-sampled HPV DNA specimens was calculated in addition to five measures of acceptability (feeling of caring, privacy, embarrassment, genital discomfort, and genital pain). RESULTS: Study participants had a median age 39 years, about four-in-ten (41.7%) had a secondary education or above, the vast majority (87.5%) were married and only 3.4% reported having screened for cervical cancer. For all measures of participant acceptability, self-sampling was rated significantly higher than clinician-sampling. Cohen's kappa was 0.73 (95% CI: 0.34, 1.00), indicating substantial agreement between self- and clinician-sampling. CONCLUSION: This study demonstrates that HPV self-sampling for cervical cancer screening is feasible and acceptable in a community setting among South Indian rural women. Concordance between self-sampling and clinician-sampling was adequate for screening in community settings.  
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Parity and later life risk for coronary heart disease among slum-dwelling women in Mysore, India.

BACKGROUND: To examine the role of parity in coronary heart disease (CHD) among middle-aged Indian women living in government-designated slums in Mysore, India. METHODS: Between October 2017 and May 2018, a cross-sectional study was carried out among women, 40-64 years of age, residing in government-designated slums in Mysore, India. In addition to socio-demographics, data were collected on CVD risk factors including use of tobacco and alcohol, diet, physical activity, sleep, quality of life, and personal and family history of chronic disease. Patients underwent a medical examination and a venous blood sample was taken for fasting lipid measurement. Resting electrocardiography was carried out by a trained medical technician. Multivariable logistic regression with associated 95% confidence intervals was used to examine the relationship between parity and coronary heart disease. RESULTS: The prevalence of CHD in this sample of middle-aged women was 6.4%. Nulliparous women were at heightened risk for CHD compared to parous women with up to five live births. In the adjusted model, women who had 1-2 and 3-5 live births had 0.24 times lower odds (95% Confidence Interval [CI]: 0.05-1.29) and 0.38 times lower odds (95%CI: 0.178-0.87) of CHD, respectively, as compared to nulliparous women. CONCLUSION: Among a fairly homogenous population of slum-dwelling women reporting almost universal breastfeeding for three or more months following birth, parity up to five births appeared protective against CHD. Further studies are needed to evaluate whether near universal breastfeeding rates in this population mediated the relationship of parity and CHD.

Cardiac Syncope with Anoxic Seizure Activity.

This is a case report, which explores the presentation to the emergency department of a fit and well female with a known ventricular bigeminy. She presented with convulsive episodes. The working differential diagnosis was of possible cardiac syncope with anoxic seizure activity or neurogenically mediated arrhythmia secondary to subarachnoid haemorrhage. On further collateral history, the patient was on citalopram. The ECGs demonstrated PVCs of multiple morphologies that were transiently bidirectional, raising the possibility of catecholaminergic polymorphic ventricular tachycardia. The presentation of a young fit patient with syncope and seizure-like episodes should always raise concern for the admitting emergency medicine clinician of an underlying cardiac pathology.

The role of extracellular matrix in normal and pathological pregnancy: Future applications of microphysiological systems in reproductive medicine.

IMPACT STATEMENT: Extracellular matrix in the womb regulates the initiation, progression, and completion of a healthy pregnancy. The composition and physical properties of extracellular matrix in the uterus and at the maternal-fetal interface are remodeled at each gestational stage, while maladaptive matrix remodeling results in obstetric disease. As in vitro models of uterine and placental tissues, including micro-and milli-scale versions of these organs on chips, are developed to overcome the inherent limitations of studying human development in vivo, we can isolate the influence of cellular and extracellular components in healthy and pathological pregnancies. By understanding and recreating key aspects of the extracellular microenvironment at the maternal-fetal interface, we can engineer microphysiological systems to improve assisted reproduction, obstetric disease treatment, and prenatal drug safety.

Mitoregulin Controls ß-Oxidation in Human and Mouse Adipocytes.

We previously discovered in mouse adipocytes an lncRNA (the homolog of human LINC00116) regulating adipogenesis that contains a highly conserved coding region. Here, we show human protein expression of a peptide within LINC00116, and demonstrate that this peptide modulates triglyceride clearance in human adipocytes by regulating lipolysis and mitochondrial ß-oxidation. This gene has previously been identified as mitoregulin (MTLN). We conclude that MTLN has a regulatory role in adipocyte metabolism as demonstrated by systemic lipid phenotypes in knockout mice. We also assert its adipocyte-autonomous phenotypes in both isolated murine adipocytes as well as human stem cell-derived adipocytes. MTLN directly interacts with the ß subunit of the mitochondrial trifunctional protein, an enzyme critical in the ß-oxidation of long-chain fatty acids. Our human and murine models contend that MTLN could be an avenue for further therapeutic research, albeit not without caveats, for example, by promoting white adipocyte triglyceride clearance in obese subjects.

Endothelial extracellular vesicles contain protective proteins and rescue ischemia-reperfusion injury in a human heart-on-chip.

Extracellular vesicles (EVs) derived from various stem cell sources induce cardioprotective effects during ischemia-reperfusion injury (IRI). These have been attributed mainly to the antiapoptotic, proangiogenic, microRNA (miRNA) cargo within the stem cell-derived EVs. However, the mechanisms of EV-mediated endothelial signaling to cardiomyocytes, as well as their therapeutic potential toward ischemic myocardial injury, are not clear. EV content beyond miRNA that may contribute to cardioprotection has not been fully illuminated. This study characterized the protein cargo of human vascular endothelial EVs (EEVs) to identify lead cardioactive proteins and assessed the effect of EEVs on human laminar cardiac tissues (hlCTs) exposed to IRI. We mapped the protein content of human vascular EEVs and identified proteins that were previously associated with cellular metabolism, redox state, and calcium handling, among other processes. Analysis of the protein landscape of human cardiomyocytes revealed corresponding modifications induced by EEV treatment. To assess their human-specific cardioprotection in vitro, we developed a human heart-on-a-chip IRI assay using human stem cell-derived, engineered cardiac tissues. We found that EEVs alleviated cardiac cell death as well as the loss in contractile capacity during and after simulated IRI in an uptake- and dose-dependent manner. Moreover, we found that EEVs increased the respiratory capacity of normoxic cardiomyocytes. These results suggest that vascular EEVs rescue hlCTs exposed to IRI possibly by supplementing injured myocytes with cargo that supports multiple metabolic and salvage pathways and therefore may serve as a multitargeted therapy for IRI.