Lnc-ing Trained Immunity to Chromatin Architecture

Human innate immune cells exposed to certain infections or stimuli develop enhanced immune responses upon re-infection with a different second stimulus, a process termed trained immunity. Recent studies have revealed that hematopoietic stem cells (HSCs) are integral to trained immune responses as they are able to “remember” transcriptional responses and transmit this state to their progeny to educate them how to respond to future infections. The macrophages that arise from trained HSCs are epigenetically reprogrammed and as a result robustly express immune genes, enhancing their capability to resolve infection. Accumulation of H3K4me3 epigenetic marks on multiple immune gene promoters underlie robust transcriptional responses during trained immune responses. However, the mechanism underpinning how these epigenetic marks accumulate at discrete immune gene loci has been poorly understood. In this review, we discuss the previously unexplored contributions of nuclear architecture and long non-coding RNAs on H3K4me3 promoter priming in trained immunity. Altering the activity of these lncRNAs presents a promising therapeutic approach to achieve immunomodulation in inflammatory disease states

The lncRNA Connection Between Cellular Metabolism and Epigenetics in Trained Immunity

Trained immunity describes the ability of innate immune cells to form immunological memories of prior encounters with pathogens. Recollection of these memories during a secondary encounter manifests a broadly enhanced inflammatory response characterized by the increased transcription of innate immune genes. Despite this phenomenon having been described over a decade ago, our understanding of the molecular mechanisms responsible for this phenotype is still incomplete. Here we present an overview of the molecular events that lead to training. For the first time, we highlight the mechanistic role of a novel class of long non-coding RNAs (lncRNAs) in the establishment and maintenance of discrete, long lasting epigenetic modifications that are causal to the trained immune response. This recent insight fills in significant gaps in our understanding of trained immunity and reveals novel ways to exploit trained immunity for therapeutic purposes

Mathematical Modeling and Optimal Blank Generation in Glass Manufacturing

This paper discusses the stock size selection problem (Chambers and Dyson, 1976), which is of relevance in the float glass industry. Given a fixed integer N, generally between 2 and 6 (but potentially larger), we find the N best sizes for intermediate stock from which to cut a roster of orders. An objective function is formulated with the purpose of minimizing wastage, and the problem is phrased as a combinatorial optimization problem involving the selection of columns of a cost matrix. Some bounds and heuristics are developed, and two exact algorithms (depth-first search and branch-and-bound) are applied to the problem, as well as one approximate algorithm (NOMAD). It is found that wastage reduces dramatically as N increases, but this trend becomes less pronounced for larger values of N (beyond 6 or 7). For typical values of N, branch-and-bound is able to find the exact solution within a reasonable amount of time

The influence of various regions of the FOXP2 sequence on its structure and DNA binding function

Funding: University of the Witwatersrand, South African National Research Foundation Grant 80681 to S.F., Grant 68898 to H.W.D., the South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation Grant 64788 to H.W.D., the Medical Research Council of South Africa and the Royal Society Grant NAF/R2/180787 to SF.FOX proteins are a superfamily of transcription factors which share a DNA-binding domain referred to as the forkhead domain. Our focus is on the FOXP subfamily members, which are involved in language and cognition amongst other things. The FOXP proteins contain a conserved zinc finger and a leucine zipper motif in addition to the forkhead domain. The remainder of the sequence is predicted to be unstructured and includes an acidic C-terminal tail. In the present study, we aim to investigate how both the structured and unstructured regions of the sequence cooperate so as to enable FOXP proteins to perform their function. We do this by studying the effect of these regions on both oligomerisation and DNA binding. Structurally, the FOXP proteins appear to be comparatively globular with a high proportion of helical structure. The proteins multimerise via the leucine zipper, and the stability of the multimers is controlled by the unstructured interlinking sequence including the acid rich tail. FOXP2 is more compact than FOXP1, has a greater propensity to form higher order oligomers, and binds DNA with stronger affinity. We conclude that while the forkhead domain is necessary for DNA binding, the affinity of the binding event is attributable to the leucine zipper, and the unstructured regions play a significant role in the specificity of binding. The acid rich tail forms specific contacts with the forkhead domain which may influence oligomerisation and DNA binding, and therefore the acid rich tail may play an important regulatory role in FOXP transcription.Publisher PDFPeer reviewe

Incidence and Cost of Acute Kidney Injury in Hospitalized Patients with Infective Endocarditis

Acute kidney injury (AKI) is a frequent complication of hospitalized patients with infective endocarditis (IE). Further, AKI in the setting of IE is associated with high morbidity and mortality. We aimed to examine the incidence, clinical parameters, and hospital costs associated with AKI in hospitalized patients with IE in an endemic area with an increasing prevalence of opioid use. This retrospective cohort study included 269 patients admitted to a major referral center in Kentucky with a primary diagnosis of IE from January 2013 to December 2015. Of these, 178 (66.2%) patients had AKI by Kidney Disease Improving Global Outcomes (KDIGO) serum creatinine criteria: 74 (41.6%) had AKI stage 1 and 104 (58.4%) had AKI stage ≥ 2. In multivariable analysis, higher comorbidity scores and the need for diuretics were independently associated with AKI, while the involvement of the tricuspid valve and the need for vasopressor/inotrope support were independently associated with severe AKI (stage ≥ 2). The median total direct cost of hospitalization was progressively higher according to each stage of AKI ($17,069 for no AKI;$37,111 for AKI stage 1; and $61,357 for AKI stage ≥ 2; p \u3c 0.001). In conclusion, two-thirds of patients admitted to the hospital due to IE had incident AKI. The occurrence of AKI significantly increased healthcare costs. The higher level of comorbidity, the affection of the tricuspid valve, and the need for diuretics and/or vasoactive drugs were associated with severe AKI in this susceptible population

Rapid generation of endogenously driven transcriptional reporters in cells through CRISPR/Cas9

CRISPR/Cas9 technologies have been employed for genome editing to achieve gene knockouts and knock-ins in somatic cells. Similarly, certain endogenous genes have been tagged with fluorescent proteins. Often, the detection of tagged proteins requires high expression and sophisticated tools such as confocal microscopy and flow cytometry. Therefore, a simple, sensitive and robust transcriptional reporter system driven by endogenous promoter for studies into transcriptional regulation is desirable. We report a CRISPR/Cas9-based methodology for rapidly integrating a firefly luciferase gene in somatic cells under the control of endogenous promoter, using the TGFβ-responsive gene PAI-1. Our strategy employed a polycistronic cassette containing a non-fused GFP protein to ensure the detection of transgene delivery and rapid isolation of positive clones. We demonstrate that firefly luciferase cDNA can be efficiently delivered downstream of the promoter of the TGFβ-responsive gene PAI-1. Using chemical and genetic regulators of TGFβ signalling, we show that it mimics the transcriptional regulation of endogenous PAI-1 expression. Our unique approach has the potential to expedite studies on transcription of any gene in the context of its native chromatin landscape in somatic cells, allowing for robust high-throughput chemical and genetic screens

Asthma: a comparison of animal models using stereological methods

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Characterization of Defects in Ion Transport and Tissue Development in Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)-Knockout Rats

Animal models for cystic fibrosis (CF) have contributed significantly to our understanding of disease pathogenesis. Here we describe development and characterization of the first cystic fibrosis rat, in which the cystic fibrosis transmembrane conductance regulator gene (CFTR) was knocked out using a pair of zinc finger endonucleases (ZFN). The disrupted Cftr gene carries a 16 base pair deletion in exon 3, resulting in loss of CFTR protein expression. Breeding of heterozygous (CFTR+/−) rats resulted in Mendelian distribution of wild-type, heterozygous, and homozygous (CFTR−/−) pups. Nasal potential difference and transepithelial short circuit current measurements established a robust CF bioelectric phenotype, similar in many respects to that seen in CF patients. Young CFTR−/− rats exhibited histological abnormalities in the ileum and increased intracellular mucus in the proximal nasal septa. By six weeks of age, CFTR−/− males lacked the vas deferens bilaterally. Airway surface liquid and periciliary liquid depth were reduced, and submucosal gland size was abnormal in CFTR−/− animals. Use of ZFN based gene disruption successfully generated a CF animal model that recapitulates many aspects of human disease, and may be useful for modeling other CF genotypes, including CFTR processing defects, premature truncation alleles, and channel gating abnormalities