Prevalence of programmed death ligand-1 (PD-L1) by demographic, disease and sample characteristics in unresectable, stage III NSCLC (PACIFIC)

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A long non-coding RNA that harbors a SNP associated with type 2 diabetes regulates the expression of TGM2 gene in pancreatic beta cells

IntroductionMost of the disease-associated single nucleotide polymorphisms (SNPs) lie in non- coding regions of the human genome. Many of these variants have been predicted to impact the expression and function of long non-coding RNAs (lncRNA), but the contribution of these molecules to the development of complex diseases remains to be clarified. MethodsHere, we performed a genetic association study between a SNP located in a lncRNA known as LncTGM2 and the risk of developing type 2 diabetes (T2D), and analyzed its implication in disease pathogenesis at pancreatic beta cell level. Genetic association study was performed on human samples linking the rs2076380 polymorphism with T2D and glycemic traits. The pancreatic beta cell line EndoC-bH1 was employed for functional studies based on LncTGM2 silencing and overexpression experiments. Human pancreatic islets were used for eQTL analysis. ResultsWe have identified a genetic association between LncTGM2 and T2D risk. Functional characterization of the LncTGM2 revealed its implication in the transcriptional regulation of TGM2, coding for a transglutaminase. The T2Dassociated risk allele in LncTGM2 disrupts the secondary structure of this lncRNA, affecting its stability and the expression of TGM2 in pancreatic beta cells. Diminished LncTGM2 in human beta cells impairs glucose-stimulated insulin release. ConclusionsThese findings provide novel information on the molecular mechanisms by which T2D-associated SNPs in lncRNAs may contribute to disease, paving the way for the development of new therapies based on the modulation of lncRNAs.This work was supported by grants from the Ministerio de Ciencia, Innovación y Universidades (PID2019-104475GA-I00 to I.S, and PGC2018-097573-A-I00 to AC-R) and the European Foundation for the Study of Diabetes (EFSD) - EFSD/JDRF/Lilly Programme on Type 1 Diabetes Research to IS. FO (MS19/00109) is recipient of the Miguel Servet scheme, and AL (FI19/00045) was supported by the Instituto de Salud Carlos III (ISCIII); Ministerio de Ciencia, Innovación y Universidades, Gobierno de España (ES). HR-M (PRE2019-089350) is supported by predoctoral grant from the Ministerio de Ciencia, Innovacion y Universidades, Gobierno de España (ES) IG-M, MS-C, JM-S and AO-G were supported by Predoctoral Fellowship Grants from the UPV/EHU (Universidad del Pais Vasco/EuskalHerrikoUnibertsitatea) and the Basque Department of Education. MC is supported by the Fonds National de la RechercheScientifique (FNRS), the Francophone Foundation for Diabetes Research (sponsored by the French Diabetes Federation, Abbott, Eli Lilly, Merck Sharp & Dohme, and Novo Nordisk) and FF and MC by the EFSD/BoehringerIngelheim European Research Programme on Multi-System Challenges in Diabetes. The funders were not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication

Craniopharyngioma in the elderly: a multicenter and nationwide study in Spain

[Abstract] Background: Craniopharyngioma (CP) is a rare tumor in the elderly whose clinical features and prognosis are not well known in this population. Aim: To evaluate the clinicopathological features and therapeutic outcomes of CP diagnosed in the elderly. Patients and Methods: This was a retrospective, multicenter, national study of CP patients diagnosed over the age of 65 years and surgically treated. Results: From a total of 384 adult CP patients, we selected 53 (13.8%) patients (27 women [50.9%], mean age 72.3 ± 5.1 years [range 65–83 years]) diagnosed after the age of 65 years. The most common clinical symptoms were visual field defects (71.2%) followed by headache (45.3%). The maximum tumor diameter was 2.9 ± 1.1 cm. In most patients, the tumor was suprasellar (96.2%) and mixed (solid-cystic) (58.5%). The surgical approach most commonly used was transcranial surgery (52.8%), and more than half of the patients (54.7%) underwent subtotal resection (STR). Adamantinomatous CP and papillary CP were present in 51 and 45.1%, respectively, with mixed forms in the remaining. Surgery was accompanied by an improvement in visual field defects and in headaches; however, pituitary hormonal hypofunction increased, mainly at the expense of an increase in the prevalence of diabetes insipidus (DI) (from 3.9 to 69.2%). Near-total resection (NTR) was associated with a higher prevalence of DI compared with subtotal resection (87.5 vs. 53.6%, p = 0.008). Patients were followed for 46.7 ± 40.8 months. The mortality rate was 39.6% with a median survival time of 88 (95% CI: 57–118) months. DI at last visit was associated with a lower survival. Conclusion: CP diagnosed in the elderly shows a similar distribution by sex and histologic forms than that diagnosed at younger ages. At presentation, visual field alterations and headaches are the main clinical symptoms which improve substantially with surgery. However, surgery, mainly NTR, is accompanied by worsening of pituitary function, especially DI, which seems to be a predictor of mortality in this population

Factors associated with therapeutic response in acromegaly diagnosed in the elderly in Spain

ContextSome reports suggest that acromegaly in elderly patients has a more benign clinical behavior and could have a better response to first-generation long-acting somatostatin receptor ligands (SRL). However, there is no specific therapeutic protocol for this special subgroup of patients. ObjectiveThis study aimed at identifying predictors of response to SRL in elderly patients. DesignMulticentric retrospective nationwide study of patients diagnosed with acromegaly at or over the age of 65 years. ResultsOne-hundred and eighteen patients (34 men, 84 women, mean age at diagnosis 71.7 +/- 5.4 years old) were included. Basal insulin-like growth factor type 1 (IGF-1) above the upper limit of normal (ULN) and growth hormone (GH) levels (mean +/- SD) were 2.7 +/- 1.4 and 11.0 +/- 11.9 ng/ml, respectively. The mean maximal tumor diameter was 12.3 +/- 6.4 mm, and up to 68.6% were macroadenoma. Seventy-two out of 118 patients (61.0%) underwent surgery as primary treatment. One-third of patients required first-line medical treatment due to a rejection of surgical treatment or non-suitability because of high surgical risk. After first-line surgery, 45/72 (63.9%) were in disease remission, and 16/34 (46.7%) of those treated with SRL had controlled disease. Patients with basal GH at diagnosis <= 6 ng/ml had lower IGF-1 levels and had smaller tumors, and more patients in this group reached control with SRL (72.7% vs. 33.3%; p < 0.04) [OR: 21.3, IC: 95% (2.4-91.1)], while male patients had a worse response [OR: 0.09, IC 95% (0.01-0.75)]. The predictive model curve obtained for SRL response showed an AUC of 0.82 CI (0.71-0.94). ConclusionsThe most frequent phenotype in newly diagnosed acromegaly in the elderly includes small adenomas and moderately high IGF-1 levels. GH at diagnosis <= 6 ng/ml and female gender, but not age per se, were associated with a greater chance of response to SRL

Evolutionary and functional history of the Escherichia coli K1 capsule

Escherichia coli is a leading cause of invasive bacterial infections in humans. Capsule polysaccharide has an important role in bacterial pathogenesis, and the K1 capsule has been firmly established as one of the most potent capsule types in E. coli through its association with severe infections. However, little is known about its distribution, evolution and functions across the E. coli phylogeny, which is fundamental to elucidating its role in the expansion of successful lineages. Using systematic surveys of invasive E. coli isolates, we show that the K1-cps locus is present in a quarter of bloodstream infection isolates and has emerged in at least four different extraintestinal pathogenic E. coli (ExPEC) phylogroups independently in the last 500 years. Phenotypic assessment demonstrates that K1 capsule synthesis enhances E. coli survival in human serum independent of genetic background, and that therapeutic targeting of the K1 capsule re-sensitizes E. coli from distinct genetic backgrounds to human serum. Our study highlights that assessing the evolutionary and functional properties of bacterial virulence factors at population levels is important to better monitor and predict the emergence of virulent clones, and to also inform therapies and preventive medicine to effectively control bacterial infections whilst significantly lowering antibiotic usage

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

p53 and ovarian carcinoma survival: an Ovarian Tumor Tissue Analysis consortium study

Our objective was to test whether p53 expression status is associated with survival for women diagnosed with the most common ovarian carcinoma histotypes (high-grade serous carcinoma [HGSC], endometrioid carcinoma [EC], and clear cell carcinoma [CCC]) using a large multi-institutional cohort from the Ovarian Tumor Tissue Analysis (OTTA) consortium. p53 expression was assessed on 6,678 cases represented on tissue microarrays from 25 participating OTTA study sites using a previously validated immunohistochemical (IHC) assay as a surrogate for the presence and functional effect of TP53 mutations. Three abnormal expression patterns (overexpression, complete absence, and cytoplasmic) and the normal (wild type) pattern were recorded. Survival analyses were performed by histotype. The frequency of abnormal p53 expression was 93.4% (4,630/4,957) in HGSC compared to 11.9% (116/973) in EC and 11.5% (86/748) in CCC. In HGSC, there were no differences in overall survival across the abnormal p53 expression patterns. However, in EC and CCC, abnormal p53 expression was associated with an increased risk of death for women diagnosed with EC in multivariate analysis compared to normal p53 as the reference (hazard ratio [HR] = 2.18, 95% confidence interval [CI] 1.36-3.47, p = 0.0011) and with CCC (HR = 1.57, 95% CI 1.11-2.22, p = 0.012). Abnormal p53 was also associated with shorter overall survival in The International Federation of Gynecology and Obstetrics stage I/II EC and CCC. Our study provides further evidence that functional groups of TP53 mutations assessed by abnormal surrogate p53 IHC patterns are not associated with survival in HGSC. In contrast, we validate that abnormal p53 IHC is a strong independent prognostic marker for EC and demonstrate for the first time an independent prognostic association of abnormal p53 IHC with overall survival in patients with CCC

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

SPAK-Independent NKCC2 Phosphorylation in Dahl SS Rats: A Role for TNIK in NKCC2 Hyperphosphorylation

Increased NaCl reabsorption in the Thick Ascending Limb (TAL) is implicated in salt sensitive hypertension. NaCl reabsorption by the TAL is mediated by the apical Na/K/2Cl cotransporter NKCC2. We reported that NKCC2 phosphorylation at Tre 96,101 and surface expression are enhanced in Dahl Salt sensitive rats (Dahl SS) on normal or high salt diets. The phosphorylation of SPS1-related proline/alanine-rich kinase (SPAK), an upstream kinase for Thre 96,101 in NKCC2, was found to be higher in Dahl SS TALs. Deletion of SPAK in Dahl SS, lowers NKCC2 phosphorylation and expression and blunts salt-sensitive hypertension, but does not completely prevent this. Other kinases may be involved in NKCC2 phosphorylation. Using a targeted proteomics approach, we identified TNIK (Traf2 and NCK interacting kinase) as a kinase that binds and phosphorylates Thre 96,101 in NKCC2. We hypothesize that TNIK is in part responsible for enhanced NKCC2 phosphorylation in Dahl SS rats. We first measured total expression of SPAK, OSR1 and TNIK by Western blot in TALs isolated form Dahl SS and control rats. SPAK and OSR1 expression (normalized to GAPDH) was similar between strains whereas TNIK expression was 3-fold higher in Dahl SS TALs (control: 100, Dahl SS: 396±80%, n =5, p\u3c.025). We then tested whether a novel TNIK inhibitor (KY-05009) decreased NKCC2 phosphorylation in Dahl SS rats. Treating TALs from Dahl SS with KY-05009 (1 µM) for 25 min decreased NKCC2 Thre 96,101 phosphorylation by 40±4% (p\u3c0.05, n=5). To study whether NKCC2 phosphorylation can be stimulated in the absence of SPAK, we used SPAK knockout Dahl SS rats. Baseline NKCC2 expression and phosphorylation in TALs was 50% lower in Dahl SS-SPAK KO TALs, however, stimulation of Beta-adrenergic receptors with Isoproterenol increased NKCC2 phosphorylation by 192±49% (p\u3c0.01, n =4) in SPAK-KO. Similarly, the cAMP analogue db-cAMP (500 µM) increased NKCC2 phosphorylation by 939±183% in SPAK KO (p\u3c0.01 n=4) and by 497±105% (p\u3c0.01 n=4) in control rat TALs, indicating that a kinase other than SPAK is essential for baseline and cAMP-stimulated NKCC2 phosphorylation in Dahl SS rats. We conclude that enhanced NKCC2 phosphorylation at baseline in Dahl SS TALs is in part caused by TNIK, which show 3-fold higher expression in this strain. SPAK also contributes to higher baseline NKCC2 phosphorylation, whereas a kinase other than SPAK (either TNIK or OSR1) is involved in cAMP-stimulated NKCC2 Thre 96,101 phosphorylation in Dahl SS TALs