Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein

Identification of differentially expressed genes (DEGs) is well recognized to be variable across independent replications of genome-wide transcriptional studies. These are often employed to characterize disease state early in the process of discovery and prioritize novel targets aimed at addressing unmet medical need. Increasing reproducibility of biological findings from these studies could potentially positively impact the success rate of new clinical interventions. This work demonstrates that statistically sound combination of gene expression data with prior knowledge about biology in the form of large protein interaction networks can yield quantitatively more reproducible observations from studies characterizing human disease. The novel concept of Well-Associated Proteins (WAPs) introduced herein-gene products significantly associated on protein interaction networks with the differences in transcript levels between control and disease-does not require choosing a differential expression threshold and can be computed efficiently enough to enable false discovery rate estimation via permutation. Reproducibility of WAPs is shown to be on average superior to that of DEGs under easily-quantifiable conditions suggesting that they can yield a significantly more robust description of disease. Enhanced reproducibility of WAPs versus DEGs is first demonstrated with four independent data sets focused on systemic sclerosis. This finding is then validated over thousands of pairs of data sets obtained by random partitions of large studies in several other diseases. Conditions that individual data sets must satisfy to yield robust WAP scores are examined. Reproducible identification of WAPs can potentially benefit drug target selection and precision medicine studies.

Synthesis of nitrogen analogues of salacinol and their evaluation as glycosidase inhibitors

The syntheses of two nitrogen analogues (11 and 12) of the naturally occurring sulfonium ion, salacinol (7) are described. The latter compound is one of the active principles in the aqueous extracts of Salacia reticulata that are traditionally used in Sri Lanka and India for the treatment of diabetes. The synthetic strategy relies on the nucleophilic attack of a 1,4-dideoxy-1,4-imino-D- or L-arabinitol at the least hindered carbon of 2,4-O-benzylidene D- or L-erythritol-1,3-cyclic sulfate. The nitrogen analogues bear a permanent positive charge and serve as mimics of the sulfonium ion. We reasoned that these ammonium derivatives should function in a manner similar to that of known glycosidase inhibitors of the alkaloid class such as castanospermine (4) and deoxynojirimycin (5). Enzyme inhibition assays indicate that salacinol (7) is a weak (K(i) = 1.7 mM) inhibitor of glucoamylase, whereas compounds 11 and 12 inhibit glucoamylase with K(i) values in the range approximately 10-fold higher. The nitrogen analogues 11 and 12 showed no significant inhibitory effect of either barley alpha-amylase (AMY1) or porcine pancreatic alpha-amylase (PPA) at concentrations of 5 mM. In contrast, salacinol (7) inhibited AMY1 and PPA in the micromolar range, with K(i) values of 15 +/- 1 and 10 +/- 2 microM, respectively.

A new class of glycosidase inhibitor: synthesis of salacinol and its stereoisomers

Salacinol (4) is one of the active principles in the aqueous extracts of Salacia reticulata that are traditionally used in Sri Lanka and India for the treatment of diabetes. The syntheses of salacinol (4), the enantiomer of salacinol (5), and a diastereomer (7) are described. The synthetic strategy relies on the selective nucleophilic attack of 2,3,5-tri-O-benzyl-1,4-anhydro-4-thio-D- or L-arabinitol at C-1 of 2,4-O-benzylidene D- or L-erythritol-1,3-cyclic sulfate. The work serves to resolve the ambiguity about the exact structure of salacinol and establishes conclusively the structure of the natural product.

Limited use of cyclosporin A in skeletal muscle ischemia--reperfusion injury

Reperfusion injury is propagated by an inflammatory-mediated tissue edema and damage after reestablishment of vascular flow following an initial ischemic insult. In the field of transplantation, cyclosporin A(CsA) provides protection against chronic graft rejection through lymphocyte immunosuppression. Evidence for an independent protective effect of CsA against ischemia-reperfusion (IR) injury during organ transfer has prompted studies showing the benefit of CsA in various ischemia-exposed visceral organs. The authors hypothesized that CsA administration may similarly benefit IR injury after skeletal muscle amputations. To determine the effects of CsA on IR injury the authors induced 4 hours of ischemia on the gracilis muscle in a rat model. CsA (15 mg per kilogram orally) was administered in two experimental groups: (1) preischemic (N = 6): 48, 24, and 3 hours before ischemia; and (2) postischemic (N = 6): 30 minutes after induction of ischemia. The effects of CsA on IR muscle injury were observed in each of the experimental groups as well as a control group (N = 6) exposed to similar ischemia and administered a saline vehicle. Muscle viability (nitro blue tetrazolium staining) and muscle edema (wet-to-dry weight ratio) were assessed 24 hours after reperfusion. The preischemic CsA-treated gracilis muscle group demonstrated improved muscle viability (39.1 +/- 4.8%) when compared with the ischemic control muscle group (23.8 +/- 7.1%; p = 0.039). Furthermore, the preischemic CsA-treated muscle group demonstrated decreased edema (1.137 +/- 0.095 times the contralateral nonischemic muscle) when compared with the control ischemic muscle group (1.248 +/- 0.045 times the contralateral nonischemic muscle; p = 0.011). Although a trend toward improved muscle viability (32.1 +/- 4.2%) and decreased edema formation (1.200 +/- 0.062 times the contralateral nonischemic muscle) was observed in the peri-ischemic CsA-treated group when compared with the control ischemic muscle group, these differences were not significant. These observations confirm the beneficial effects of preischemic CsA therapy observed in organ transplantation research and suggest limited clinical use of peri-ischemic CsA therapy for patients with musculoskeletal amputations.

Stenting of the left main coronary artery. Local experience in Liège

We examined the immediate and long-term outcome after stenting of the left main coronary artery (LMCA) in 41 consecutive patients who had been considered unsuitable for coronary artery bypass graft surgery (CABG). The procedure was elective in thirty-two patients (78%) with a protected LMCA in 24 patients and non-protected LMCA in 8 patients; the procedure was acute in the setting of myocardial infarction or complication of a diagnostic angiography in 9 patients (22%). The mean follow-up duration was 19 +/- 13 months. There were 5 in-hospital and 3 late deaths; repeat angioplasty was performed in 5 cases, but only one for LMCA restenosis. Results varied considerably depending on the clinical presentation. For acute patients, technical success was achieved in 89%, survival at hospital discharge was 44% and there was no cardiac event at the late follow-up. For elective patients, technical success was achieved in 100%, survival at hospital discharge was 96% and 90% at follow-up. The results of our study suggest that when patients have surgical risks, elective LMCA stenting either protected or unprotected may be undertaken with a high procedural success rate and a favourable clinical late follow-up.

The youthful forehead: placement of skin incisions in hidden furrows

BACKGROUND

Attaining good aesthetic results remains a primary goal in removal of benign cutaneous facial lesions.

OBJECTIVE

Strategic planning of the incision is perhaps the most critical step in excision of such a lesion.

METHODS

A study of one case of epidermoid cyst excision from a youthful forehead was undertaken.

RESULTS

Poor surgical planning of a simple cyst excision from the forehead resulted in placement of the incision inferior to a natural furrow and within the basin defect, producing a noticeable scar. Facial animation accentuates the aesthetically poor placement of the surgical incision.

CONCLUSION

The detection of hidden furrows through facial animation during preoperative planning, especially in the youthful forehead, is imperative for achievement of an optimal aesthetic result. When possible, incisions should be concealed within natural furrows.

Differential addressing of 5-HT1A and 5-HT1B receptors in epithelial cells and neurons

The 5-HT1A and 5-HT1B serotonin receptors are expressed in a variety of neurons in the central nervous system. While the 5-HT1A receptor is found on somas and dendrites, the 5-HT1B receptor has been suggested to be localized predominantly on axon terminals. To study the intracellular addressing of these receptors, we have used in vitro systems including Madin-Darby canine kidney (MDCK II) epithelial cells and primary neuronal cultures. Furthermore, we have extended these studies to examine addressing in vivo in transgenic mice. In epithelial cells, 5-HT1A receptors are found on both apical and basolateral membranes while 5-HT1B receptors are found exclusively in intracellular vesicles. In hippocampal neuronal cultures, 5-HT1A receptors are expressed on somatodendritic membranes but are absent from axons. In contrast, 5-HT1B receptors are found on both dendritic and axonal membranes, including growth cones where they accumulate. Using 5-HT1A and 5-HT1B knockout mice and the binary tTA/tetO system, we generated mice expressing these receptors in striatal neurons. These in vivo experiments demonstrate that, in striatal medium spiny neurons, the 5-HT1A receptor is restricted to the somatodendritic level, while 5-HT1B receptors are shipped exclusively toward axon terminals. Therefore, in all systems we have examined, there is a differential sorting of the 5-HT1A and 5-HT1B receptors. Furthermore, we conclude that our in vivo transgenic system is the only model that reconstitutes proper sorting of these receptors.

Adenovirus-mediated expression of 5-HT1B receptors in cardiac ventricle myocytes; coupling to inwardly rectifying K+ channels

The 5-HT1B receptor is expressed on nerve terminals where it inhibits neurotransmitter release. When expressed ectopically in fibroblasts, the 5-HT1B receptor inhibits adenylyl cyclase. However, in the central nervous system, the effect of this receptor on neurotransmitter release appears to be cAMP-independent. We therefore investigated alternative effector systems that might be activated by the 5-HT1B receptor. We constructed a recombinant adenovirus that allows expression of high levels of the 5-HT1B receptor in a variety of cells. We chose cardiac ventricle myocytes because they express a muscarinic-gated, inwardly rectifying K+ channel (i[KACh]). In infected ventricle cells, both 5-HT and the muscarinic receptor agonist, carbachol, elicited a similar inwardly rectifying K+ current. The currents elicited by these agonists were pertussis-toxin sensitive and were not additive. These results suggest a common signal transduction pathway for 5-HT1B and muscarinic receptors in ventricle cells.