Skunk River Review September 1989, vol 1 no 1

https://openspace.dmacc.edu/skunkriver/1004/thumbnail.jp

Transcriptome Analysis of Mouse Stem Cells and Early Embryos

Understanding and harnessing cellular potency are fundamental in biology and are also critical to the future therapeutic use of stem cells. Transcriptome analysis of these pluripotent cells is a first step towards such goals. Starting with sources that include oocytes, blastocysts, and embryonic and adult stem cells, we obtained 249,200 high-quality EST sequences and clustered them with public sequences to produce an index of approximately 30,000 total mouse genes that includes 977 previously unidentified genes. Analysis of gene expression levels by EST frequency identifies genes that characterize preimplantation embryos, embryonic stem cells, and adult stem cells, thus providing potential markers as well as clues to the functional features of these cells. Principal component analysis identified a set of 88 genes whose average expression levels decrease from oocytes to blastocysts, stem cells, postimplantation embryos, and finally to newborn tissues. This can be a first step towards a possible definition of a molecular scale of cellular potency. The sequences and cDNA clones recovered in this work provide a comprehensive resource for genes functioning in early mouse embryos and stem cells. The nonrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Gene Expression Profiling of Embryo-Derived Stem Cells Reveals Candidate Genes Associated With Pluripotency and Lineage Specificity

Large-scale gene expression profiling was performed on embryo-derived stem cell lines to identify molecular signatures of pluripotency and lineage specificity. Analysis of pluripotent embryonic stem (ES) cells, extraembryonic-restricted trophoblast stem (TS) cells, and terminally-differentiated mouse embryo fibroblast (MEF) cells identified expression profiles unique to each cell type, as well as genes common only to ES and TS cells. Whereas most of the MEF-specific genes had been characterized previously, the majority (67%) of the ES-specific genes were novel and did not include known differentiated cell markers. Comparison with microarray data from embryonic material demonstrated that ES-specific genes were underrepresented in all stages sampled, whereas TS-specific genes included known placental markers. Investigation of four novel TS-specific genes showed trophoblast-restricted expression in cell lines and in vivo, whereas one uncharacterized ES-specific gene, Esg-1, was found to be exclusively associated with pluripotency. We suggest that pluripotency requires a set of genes not expressed in other cell types, whereas lineage-restricted stem cells, like TS cells, express genes predictive of their differentiated lineage. [Supplemental material is available online at www.genome.org and http://lgsun.grc.nia.nih.gov/microarray/data.html

Public Bariatric Surgery: A National Framework

Obesity is a chronic progressive disease that leads to physical, psychological, and metabolic health problems. The prevalence of obesity is increasing across the globe and in 2017-18 Australia ranked fifth among OECD countries with over one third (31%) of Australian adults living with obesity (1 p. 1). Despite this increasing prevalence, access to the full suite of effective treatments is limited in Australia, including access to bariatric-metabolic surgery Bariatric-metabolic surgery (also referred to as bariatric surgery) is a well-established, safe and effective form of obesity treatment with demonstrable meaningful and sustained weight loss over the medium to long term. Bariatric surgery has also been shown to be highly effective in reversing or improving obesity-related risks and complications in patients, especially for type 2 diabetes (2). Research evidence is consistent in supporting the cost-effectiveness of surgery in the treatment of obesity and its complication (3). Although bariatric-metabolic surgery (bariatric surgery) is one of the most effective methods for treatment of obesity, there remain barriers to access especially in the public hospital setting and access remain inadequate. Over 90% of all bariatric surgery is currently performed in the private system as access to the public hospital system remains poor, even for those with the greatest need (4 p. 5). In 2015-16 only 950 of approximately 24,000 bariatric surgeries performed in Australia occurred in public hospitals (5). A recent (2017) study suggested only 15 public hospitals from a potential 700 institutions nation-wide formally offered a bariatric-metabolic surgical programme (6). In 2019 the National Bariatric Registry recorded 22 public hospitals with bariatric cases but only 10 of these with significant (>75 per year) case load (7). This inequity of access to care is concerning. With appropriate considerations, making bariatric surgery available within the public hospital setting can provide life-changing health and wellbeing benefits to those who need it most. Further, there is increasing recognition of bariatric surgery as an early treatment option in the care of diabetes (and other chronic diseases) in both international and emerging Australian-developed guidelines (8). This is becoming the new “standard of care” for such diseases. Australian public hospitals have the opportunity to meet this standard of care through increased provision of bariatric surgery. The 2017 Public Bariatric Surgery ANZMOSS1 Summit identified that a National Framework was required to provide clear guidelines to health policy makers, clinical governance boards and health practitioners to enable: facilitation of successful implementation of bariatric surgery more widely in Australia’s public hospital system; standardisation of key care elements such as patient eligibility and prioritisation; a reduction in variations in preoperative and postoperative care pathways; development of a sustainable model of care integrated with multimodal treatment of obesity. This National Framework is the result of expert consensus from the ANZMOSS and Collective Public Bariatric Surgery Taskforce (the Taskforce), involving and endorsed by key stakeholder organisations in the treatment of obesity and bariatric surgery (see Taskforce members and participating organisations in Appendix A). The National Framework has been designed to deliver: efficient patient centred care; sustainable use of resources to cater to the disease burden of obesity in the community; deliver surgical care to the most appropriate patient populations. This Framework is complementary to the first National Framework for Clinical Obesity Services in Australia (9), developed by NACOS – a collaborative group of concerned health care professionals, which offers practical guidance on best design, delivery, and access to clinical obesity (or ‘weight management’) services in our health system. It is intended that as these frameworks go forward, surgical pathways of care as outlined in this framework and nationwide obesity services pathways and standards, as developed in the NACOS Framework, will be integrated further. Currently, this National Framework does not include considerations for children and adolescents who may need bariatric services. Additional considerations and guidelines will be developed for paediatric and adolescent bariatric surgery at a later stage

Evidence That Glucose Metabolism Regulates Leptin Secretion from Cultured Rat Adipocytes*

Circulating leptin secreted from adipocytes is correlated with fat mass and plasma insulin concentrations in humans and rodents. Plasma leptin, insulin, and glucose decrease during fasting and increase after refeeding; however, the underlying mechanisms regulating the changes of leptin secretion are not known. To investigate the role of insulin-stimulated glucose metabolism in the regulation of leptin secretion, we examined the effects of insulin and inhibitors of glucose transport and metabolism on leptin secretion from rat adipocytes in primary culture. Insulin (0.16-16 nM) increased leptin secretion over 96 h; however, the increase in leptin was more closely related to the amount of glucose taken up by the adipocytes (r = 0.64; P < 0.0001) than to the insulin concentration per se (r = 0.20; P < 0.28), suggesting a role for glucose transport and/or metabolism in regulating leptin secretion. 2-Deoxy-D-glucose (2-DG), a competitive inhibitor of glucose transport and phosphorylation, caused a concentration-dependent (2-50 mg/dl) inhibition of leptin release in the presence of 1.6 nM insulin. The inhibitory effect of 2-DG was reversed by high concentrations of glucose. Two other inhibitors of glucose transport, phloretin (0.05-0.25 mM) and cytochalasin-B (0.5-50 microM), also inhibited leptin secretion. Inhibition of leptin secretion by these agents was proportional to the inhibition of glucose uptake (r = 0.60 to 0.86; all P < 0.01). Two inhibitors of glycolysis, iodoacetate (0.005-1.0 mM) and sodium fluoride (0.1-5 mM), produced concentration-dependent inhibition of leptin secretion in the presence of 1.6 nM insulin. In addition, both 2-DG and sodium fluoride markedly decreased the leptin (ob) messenger RNA content of cultured adipocytes, but did not affect 18S ribosomal RNA content. We conclude that glucose transport and metabolism are important factors in the regulation of leptin expression and secretion and that the effect of insulin to increase adipocyte glucose utilization is likely to contribute to insulin-stimulated leptin secretion. Thus, in vivo, decreased adipose glucose metabolism may be one mechanism by which fasting decreases circulating leptin, whereas increased adipose glucose metabolism would increase leptin after refeeding

PCA Analysis of EST Frequency

<p>The results were obtained by analyzing 2,812 genes that exceeded 0.1% in at least one library. (A) 3D biplot that shows both cell types (red spheres) and genes (yellow boxes). (B) 2D PCA of cell types. EST frequencies were log-transformed before the analysis. Names of some cells and tissues are abbreviated as follows: 6.5 EP, E6.5 whole embryo (embryo plus placenta); 7.5 EP, E7.5 whole embryo (embryo plus placenta); 8.5 EP, E8.5 whole embryo (embryo plus placenta); 9.5 EP, E9.5 whole embryo (embryo plus placenta); 7.5 E, E7.5 embryonic part only; 7.5 P, E7.5 extraembryonic part only; NbOvary, newborn ovary; NbBrain, newborn brain; NbHeart, newborn heart; NbKidney, newborn kidney; 13.5 VMB, E13.5 ventral midbrain dopamine cells; 12.5 Gonad (F), E12.5 female gonad/mesonephros; 12.5 Gonad (M), E12.5 male gonad/mesonephros; HS (Kit⁻, Sca1⁻), hematopoietic stem/progenitor cells (Lin⁻, Kit⁻, Sca1⁻); HS (Kit⁻, Sca1⁺), hematopoietic stem/progenitor cells (Lin⁻, Kit⁻, Sca1⁺); HS (Kit⁺, Sca1⁻), hematopoietic stem/progenitor cells (Lin⁻, Kit⁺, Sca1⁻); HS (Kit⁺, Sca1⁺), hematopoietic stem/progenitor cells (Lin⁻, Kit⁺, Sca1⁺); and NS-D, differentiated NS cells.</p