A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes.

BACKGROUND: The rapid collection of diverse genome-scale data raises the urgent need to integrate and utilise these resources for biological discovery or biomedical applications. For example, diverse transcriptomic and gene copy number variation data are currently collected for various cancers, but relatively few current methods are capable to utilise the emerging information. METHODS: We developed and tested a data-integration method to identify gene networks that drive the biology of breast cancer clinical subtypes. The method simultaneously overlays gene expression and gene copy number data on protein-protein interaction, transcriptional-regulatory and signalling networks by identifying coincident genomic and transcriptional disturbances in local network neighborhoods. RESULTS: We identified distinct driver-networks for each of the three common clinical breast cancer subtypes: oestrogen receptor (ER)+, human epidermal growth factor receptor 2 (HER2)+, and triple receptor-negative breast cancers (TNBC) from patient and cell line data sets. Driver-networks inferred from independent datasets were significantly reproducible. We also confirmed the functional relevance of a subset of randomly selected driver-network members for TNBC in gene knockdown experiments in vitro. We found that TNBC driver-network members genes have increased functional specificity to TNBC cell lines and higher functional sensitivity compared with genes selected by differential expression alone. CONCLUSION: Clinical subtype-specific driver-networks identified through data integration are reproducible and functionally important.

Laser in situ keratomileusis with a scanning excimer laser for the correction of low to moderate myopia with and without astigmatism.

PURPOSE: To evaluate the safety and effectiveness of and patient satisfaction with laser in situ keratomileusis (LASIK) performed with a scanning excimer laser by experienced surgeons to correct low and moderate levels of myopia and astigmatism. SETTING: Clinique Laservue, Montreal, Quebec, Canada. METHODS: A consecutive series of 125 patients (236 eyes) with myopia of -0.5 to -7.0 diopters (D) and cylinder less than 2.5 D were enrolled in this single-center prospective clinical trial. The patients were treated with LASIK and followed for 6 months. The System-ALK Automated Corneal Shaper microkeratome (Bausch & Lomb Surgical) with a 180 microm thickness plate and the Technolas 217 excimer laser (Bausch & Lomb Surgical) with PlanoScan software for the stromal ablation were used in all procedures. Since this version of PlanoScan tended to undercorrect, a mean of 14.7% was added to the standard nomogram. Patient satisfaction was assessed by questionnaires administered preoperatively and 1 and 6 months postoperatively. Retreatments for enhancement were not performed during the 6-month follow-up. RESULTS: Six months after LASIK (86.4% follow-up), the mean postoperative manifest spherical equivalent was +0.02 D +/- 0.64 (SD) compared with a preoperative mean of -4.01 +/- 1.59 D. The uncorrected visual acuity was 20/40 or better in 94.6% of eyes and 20/20 or better in 81.9%. A total of 91.2% were within +/-1.0 D of emmetropia and 73.0% were within +/-0.5 D. Only 2 eyes were overcorrected by >1.0 D. Of the eyes with astigmatic myopia, 86.8% were within +/-1.0 D of the intended cylinder correction (by vector analysis) and 73.0% were within +/-0.5 D. The refractions were generally stable after 1 month, and the change in refraction between postoperative examinations was within +/-0.5 D in 88.0% of eyes. A 1-line decrease in best spectacle-corrected visual acuity was seen in 11.3% of eyes, and no eye lost more than 1 line. An increase of 1 or 2 lines was seen in 45.1%. No intraoperative problems occurred, and the interface was clear in all eyes. At 6 months, most symptoms present significantly more frequently than preoperatively were "mild"; none were "marked" or "severe." A total of 90.5% of eyes were reported with marked to extreme improvement in the overall quality of vision, and 99.0% of patients said they would choose LASIK surgery again. CONCLUSIONS: Mild to moderate myopia, with and without astigmatism, was corrected safely, effectively, and predictably with a high degree of patient satisfaction using LASIK with a scanning excimer laser and the System-ALK Automated Corneal Shaper.

Synchronization of hyperexcitable systems with phase-repulsive coupling.

We study two-dimensional arrays of FitzHugh-Nagumo elements with nearest-neighbor coupling from the viewpoint of synchronization. The elements are diffusively coupled. By varying the diffusion coefficient from positive to negative values, interesting synchronization patterns are observed. The results of the simulations resemble the intracellular oscillation patterns observed in cultured human epileptic astrocytes. Three measures are proposed to determine the degree of synchronization (or coupling) in both the simulated and the experimental system.

Relationship between baring of circumlinear vessels of the optic disc and glaucomatous visual field loss.

Stereo disc photographs of the eyes of 232 patients with normal or elevated intraocular pressure were reviewed to assess the value of baring of circumlinear vessels of the optic nerve head as a sign of glaucomatous damage. Baring and the presence of glaucomatous visual field defects were significantly correlated, as were this sign and consistent elevation of the intraocular pressure in patients without a visual field defect. Baring was absent in 35% of the eyes with circumlinear vessels and known glaucomatous visual field defects. However, it was present in only 6% of the eyes with normal pressure, a normal visual field and circumlinear vessels. Therefore, this sign should lead to further evaluation.

Treatment of encapsulated blebs with 30-gauge needling and injection of low-dose 5-fluorouracil.

We describe a simplified needling procedure, performed at the slit-lamp, with injection of low-dose 5-fluorouracil to treat encapsulated filtering blebs. Between August 1989 and December 1990 we treated 17 eyes of 14 patients with this procedure. At 2 months 13 of the eyes had needed only one needling procedure. Risk factors for reencapsulation of the bleb were a history of three or more previous surgical procedures (p less than 0.05) and prolonged preoperative use of topical adrenergic drugs (p less than 0.05). At 1 year all but one eye had an intraocular pressure below 21 mm Hg (median 15 mm Hg). Twelve of the eyes had needed more than one needling procedure. There were no serious complications of the 32 procedures performed. The incidence rate of minor complications (wound leaks, corneal erosion and small hyphemas) was 38%.

Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling.

To identify regulators of intracellular signaling, we targeted 541 kinases and kinase-related molecules with small interfering RNAs (siRNAs), and determined their effects on signaling with a functional proteomics reverse-phase protein array (RPPA) platform assessing 42 phospho and total proteins. The kinome-wide screen demonstrated a strong inverse correlation between phosphorylation of AKT and mitogen-activated protein kinase (MAPK) with 115 genes that, when targeted by siRNAs, demonstrated opposite effects on MAPK and AKT phosphorylation. Network-based analysis identified the MAPK subnetwork of genes along with p70S6K and FRAP1 as the most prominent targets that increased phosphorylation of AKT, a key regulator of cell survival. The regulatory loops induced by the MAPK pathway are dependent on tuberous sclerosis complex 2 but demonstrate a lesser dependence on p70S6K than the previously identified FRAP1 feedback loop. The siRNA screen also revealed novel bi-directionality in the AKT and GSK3 (Glycogen synthase kinase 3) interaction, whereby genetic ablation of GSK3 significantly blocks AKT phosphorylation, an unexpected observation as GSK3 has only been predicted to be downstream of AKT. This method uncovered novel modulators of AKT phosphorylation and facilitated the mapping of regulatory loops.

Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli.

Recent evidence indicates that potential interactions within metabolic, protein-protein interaction, and transcriptional regulatory networks are used differentially according to the environmental conditions in which a cell exists. However, the topological units underlying such differential utilization are not understood. Here we use the transcriptional regulatory network of Escherichia coli to identify such units, called origons, representing regulatory subnetworks that originate at a distinct class of sensor transcription factors. Using microarray data, we find that specific environmental signals affect mRNA expression levels significantly only within the origons responsible for their detection and processing. We also show that small regulatory interaction patterns, called subgraphs and motifs, occupy distinct positions in and between origons, offering insights into their dynamical role in information processing. The identified features are likely to represent a general framework for environmental signal processing in prokaryotes.

Noncontact thermal mode Nd:YAG laser transscleral cyclocoagulation in the treatment of glaucoma. Intermediate follow-up.

Noncontact transscleral Nd:YAG laser thermal mode cyclocoagulation is known to reduce intraocular pressure (IOP). Thirty-five eyes were treated at a mean of 2.5 Joules and followed for a mean of 28 months. The mean preoperative IOP of 39.8 mmHg (standard deviation, 11.7) was consistently decreased by 45% to 55% over the follow-up period (standard deviation, 19.9 to 30.8), along with a significant reduction of medical therapy. This effect is comparable with that obtained by investigators using much higher energy levels. Successful control was defined as IOP between 5 and 21 mmHg for eyes with visual acuity of counting fingers or better, between 5 and 25 mmHg for eyes with hand motions to light perception, and as control of ocular pain for eyes with no light perception; 71% to 75% of the eyes were successfully controlled for up to 3 years. The use of lower energy levels appears to be associated with a lower incidence of vision loss and, therefore, merits further controlled investigation.

[The neuro-retinal rim region in early glaucoma]. / Die neuroretinale Randzone beim frühen Glaukom.

The true neuro-retinal rim area of the optic disc was obtained by calculating the magnification using axial length, refraction and corneal curvature. Patients with very early chronic open angle glaucoma and normals were compared. The neuro-retinal rim area separated these two populations better than the standard cup/disc ratios. The size of the optic nerve did not appear to change with age. The implications for clinical practice are outlined.

Multi-flash campimetry as an indicator of visual field loss in glaucoma.

Multi-flash campimetry is a computer-implemented technique used for the rapid assessment of temporal resolving power across the visual field. On the basis of previous reports that glaucoma patients exhibit impaired temporal sensitivity earlier than conventional perimetric field loss, the question of whether multi-flash campimetry might also be sensitive to the visual consequences of glaucoma was explored. Of the 27 patients that were tested, only one had normal temporal resolving power in both eyes, suggesting that multi-flash campimetry might be a useful aid in determining whether a patient should be diagnosed and treated as a glaucoma suspect or as a confirmed glaucoma patient.

Experimental determination and system level analysis of essential genes in Escherichia coli MG1655.

Defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. We used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of Escherichia coli in rich media. We identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. Functional context analysis of these data allows individual functional assignments to be refined. Evolutionary context analysis demonstrates a significant tendency of essential E. coli genes to be preserved throughout the bacterial kingdom. Projection of these data over metabolic subsystems reveals topologic modules with essential and evolutionarily preserved enzymes with reduced capacity for error tolerance.