Prospective Isolation of Poised iPSC Intermediates Reveals Principles of Cellular Reprogramming.

Cellular reprogramming converts differentiated cells into induced pluripotent stem cells (iPSCs). However, this process is typically very inefficient, complicating mechanistic studies. We identified and molecularly characterized rare, early intermediates poised to reprogram with up to 95% efficiency, without perturbing additional genes or pathways, during iPSC generation from mouse embryonic fibroblasts.

Increased jejunal permeability in human obesity is revealed by a lipid challenge and is linked to inflammation and type 2 diabetes.

Obesity and its metabolic complications are characterized by subclinical systemic and tissue inflammation. In rodent models of obesity, inflammation and metabolic impairments are linked with intestinal barrier damage. However, whether intestinal permeability is altered in human obesity remains to be investigated.

Mucosal-associated invariant T (MAIT) cells are depleted and prone to apoptosis in cardiometabolic disorders.

The disruption of systemic immune homeostasis is a key mediator in the progression of cardiometabolic diseases (CMDs). We aimed to extend knowledge regarding the clinical relevance of CMD-associated variation of circulating mucosal-associated invariant T (MAIT) cell abundance and to explore underlying cellular mechanisms. We analyzed cross-sectional data from 439 participants of the Metagenomics in Cardiometabolic Diseases (MetaCardis) study, stratified into 6 groups: healthy control subjects and patients with metabolic syndrome (MS), obesity, type 2 diabetes mellitus (T2DM), and coronary artery disease (CAD) without, or with congestive heart failure (CAD-CHF).

AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing.

Motivation: Unique molecular identifiers (UMIs) are added to DNA fragments before PCR amplification to discriminate between alleles arising from the same genomic locus and sequencing reads produced by PCR amplification. While computational methods have been developed to take into account UMI information in genome-wide and single-cell sequencing studies, they are not designed for modern amplicon-based sequencing experiments, especially in cases of high allelic diversity. Importantly, no guidelines are provided for the design of optimal UMI length for amplicon-based sequencing experiments.

[Adipose tissue fibrosis: an aggravating factor in obesity].

Obesity can be defined as the adaptive response of organism facing chronic nutrient overflow. In this context, the adipose tissue (AT) can expand, through increased adipocyte size and number, to function as the main energy-storing organ. However, over the course of obesity progression, the AT undergo continual remodeling, evolving into pathological alterations.

Major microbiota dysbiosis in severe obesity: fate after bariatric surgery.

Objectives: Decreased gut microbial gene richness (MGR) and compositional changes are associated with adverse metabolism in overweight or moderate obesity, but lack characterisation in severe obesity. Bariatric surgery (BS) improves metabolism and inflammation in severe obesity and is associated with gut microbiota modifications. Here, we characterised severe obesity-associated dysbiosis (ie, MGR, microbiota composition and functional characteristics) and assessed whether BS would rescue these changes.

Saturated Fat Is More Metabolically Harmful for the Human Liver Than Unsaturated Fat or Simple Sugars.

Objective: Nonalcoholic fatty liver disease (i.e., increased intrahepatic triglyceride [IHTG] content), predisposes to type 2 diabetes and cardiovascular disease.

An Intermediate Pluripotent State Controlled by MicroRNAs Is Required for the Naive-to-Primed Stem Cell Transition.

The embryonic stem cell (ESC) transition from naive to primed pluripotency is marked by major changes in cellular properties and developmental potential. ISY1 regulates microRNA (miRNA) biogenesis, yet its role and relevance to ESC biology remain unknown. Here, we find that highly dynamic ISY1 expression during the naive-to-primed ESC transition defines a specific phase of "poised" pluripotency characterized by distinct miRNA and mRNA transcriptomes and widespread poised cell contribution to mouse chimeras.

MC4R agonism promotes durable weight loss in patients with leptin receptor deficiency.

Genetic defects underlying the melanocortin-4 receptor (MC4R) signaling pathway lead to severe obesity. Three severely obese LEPR-deficient individuals were administered the MC4R agonist setmelanotide, resulting in substantial and durable reductions in hyperphagia and body weight over an observation period of 45-61 weeks. Compared to formerly developed and tested MC4R agonists, setmelanotide has the unique capability of activating nuclear factor of activated T cell (NFAT) signaling and restoring function of this signaling pathway for selected MC4R variants.

Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade.

CTLA-4 immune checkpoint blockade is clinically effective in a subset of patients with metastatic melanoma. We identify a subcluster of MAGE-A cancer-germline antigens, located within a narrow 75 kb region of chromosome Xq28, that predicts resistance uniquely to blockade of CTLA-4, but not PD-1. We validate this gene expression signature in an independent anti-CTLA-4-treated cohort and show its specificity to the CTLA-4 pathway with two independent anti-PD-1-treated cohorts.

A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.

While gene expression dynamics have been extensively cataloged during hematopoietic differentiation in the adult, less is known about transcriptome diversity of human hematopoietic stem cells (HSCs) during development. To characterize transcriptional and post-transcriptional changes in HSCs during development, we leveraged high-throughput genomic approaches to profile miRNAs, lincRNAs, and mRNAs. Our findings indicate that HSCs manifest distinct alternative splicing patterns in key hematopoietic regulators.

Author Correction: Global delay in nascent strand DNA methylation.

Following online publication of this article, the Gene Expression Omnibus records corresponding to accession codes GSM2406773, MN-d6, and GSM2406772, MN-d14, listed in the data availability statement were deleted. The data are now available under accession codes GSM3039355, WGBS_hESC_WT_D6_R4 (MN day 6), and GSM3039351, WGBS_hESC_WT_D14_R4 (MN day 14), and the data availability statement has been updated with the new accession codes in the HTML and PDF versions of the article.

Intergenerational response to the endocrine disruptor vinclozolin is influenced by maternal genotype and crossing scheme.

In utero exposure to vinclozolin (VIN), an antiandrogenic fungicide, is linked to multigenerational phenotypic and epigenetic effects. Mechanisms remain unclear. We assessed the role of antiandrogenic activity and DNA sequence context by comparing effects of VIN vs.

Global delay in nascent strand DNA methylation.

Cytosine methylation is widespread among organisms and essential for mammalian development. In line with early postulations of an epigenetic role in gene regulation, symmetric CpG methylation can be mitotically propagated over many generations with extraordinarily high fidelity. Here, we combine BrdU labeling and immunoprecipitation with genome-wide bisulfite sequencing to explore the inheritance of cytosine methylation onto newly replicated DNA in human cells.

Association of Resident Duty Hour Restrictions, Level of Trainee, and Number of Available Residents with Mortality in the Neonatal Intensive Care Unit.

Objective: This article assesses the effect of reducing consecutive hours worked by residents from 24 to 16 hours on yearly total hours worked per resident in the neonatal intensive care unit (NICU) and evaluates the association of resident duty hour reform, level of trainee, and the number of residents present at admission with mortality in the NICU.

Study Design: This is a 6-year retrospective cohort study including all pediatric residents working in a Level 3 NICU ( = 185) and infants admitted to the NICU ( = 8,159). Adjusted odds ratios (aOR) were estimated for mortality with respect to Epoch (2008-2011 [24-hour shifts] versus 2011-2014 [16-hour shifts]), level of trainee, and the number of residents present at admission.

Current standards for assessing pregnancy status before surgery are subjective and should be replaced with definitive, objective evidence.

We report a case of a young woman admitted electively for laparoscopic Nissen fundoplication, and again three days post-operatively as an emergency with profuse vomiting and abdominal pain. She underwent diagnostic laparoscopy, and a small gastric perforation was found at the site of the fundoplication and this was suture-repaired. On both admissions, she was "screened" for pregnancy as per current guidelines.

Visceral Adipose Tissue Drives Cardiac Aging Through Modulation of Fibroblast Senescence by Osteopontin Production.

Background: Aging induces cardiac structural and functional changes linked to the increased deposition of extracellular matrix proteins, including OPN (osteopontin), conducing to progressive interstitial fibrosis. Although OPN is involved in various pathological conditions, its role in myocardial aging remains unknown.

Methods: OPN deficient mice (OPN-/-) with their wild-type (WT) littermates were evaluated at 2 and 14 months of age in terms of cardiac structure, function, histology and key molecular markers.

Genome-wide tracking of dCas9-methyltransferase footprints.

In normal mammalian development cytosine methylation is essential and is directed to specific regions of the genome. Despite notable advances through mapping its genome-wide distribution, studying the direct contribution of DNA methylation to gene and genome regulation has been limited by the lack of tools for its precise manipulation. Thus, combining the targeting capability of the CRISPR-Cas9 system with an epigenetic modifier has attracted interest in the scientific community.

Variability in the prescribing of intravenous fluids: A cross sectional multicentre analysis of clinical practice.

Aims: Intravenous (IV) fluid administration continues to be a mainstay of care in General Surgery. Yet if they are prescribed incorrectly significant morbidity including electrolyte abnormalities, renal impairment and cardiac failure can develop. Despite this, it is frequently the responsibility of the most junior staff to prescribe IV fluids.

Genetic determinants and epigenetic effects of pioneer-factor occupancy.

Transcription factors (TFs) direct developmental transitions by binding to target DNA sequences, influencing gene expression and establishing complex gene-regultory networks. To systematically determine the molecular components that enable or constrain TF activity, we investigated the genomic occupancy of FOXA2, GATA4 and OCT4 in several cell types. Despite their classification as pioneer factors, all three TFs exhibit cell-type-specific binding, even when supraphysiologically and ectopically expressed.

Heminephrectomy in Adults: A Systematic Review with Cumulative Analysis.

Introduction: Duplex collecting system of the kidney is a relatively common abnormality, with the majority of symptomatic cases discovered in childhood. Treatment is commonly a heminephrectomy of the affected moiety. We aimed to conduct a systematic review of the literature to provide the best available evidence for heminephrectomy for duplex kidneys in the adult population.

A randomised trial comparing pain and ease of use of two different stabilising forceps for insertion of intrauterine contraception.

Background: Pain at intrauterine contraception (IUC) fitting may be a deterrent for women and any reduction in discomfort would be likely to be beneficial to both women and clinicians.

Aim: This study investigated the associated pain and the ease of use of two different stabilising forceps at the time of IUC placement.

Design: Single-blinded randomised controlled trial.

Gut microbiota and obesity: Concepts relevant to clinical care.

The composition and function of gut microbiota play a role in obesity and metabolic disease, yet the mechanisms have not been fully described. As new discoveries and advances in the field have occurred, the relevance of gut microbiota in clinical care has become more substantial. There is promising potential for manipulation of the gut microbiota as treatment of obesity and associated health complications, both as a standalone therapy and as part of interventions such as weight loss.