cytoHubba: identifying hub objects and sub-networks from complex interactome

Background

Network is a useful way for presenting many types of biological data including protein-protein interactions, gene regulations, cellular pathways, and signal transductions. We can measure nodes by their network features to infer their importance in the network, and it can help us identify central elements of biological networks.

Results

We introduce a novel Cytoscape plugin cytoHubba for ranking nodes in a network by their network features. CytoHubba provides 11 topological analysis methods including Degree, Edge Percolated Component, Maximum Neighborhood Component, Density of Maximum Neighborhood Component, Maximal Clique Centrality and six centralities (Bottleneck, EcCentricity, Closeness, Radiality, Betweenness, and Stress) based on shortest paths. Among the eleven methods, the new proposed method, MCC, has a better performance on the precision of predicting essential proteins from the yeast PPI network.

Conclusions

CytoHubba provide a user-friendly interface to explore important nodes in biological networks. It computes all eleven methods in one stop shopping way. Besides, researchers are able to combine cytoHubba with and other plugins into a novel analysis scheme. The network and sub-networks caught by this topological analysis strategy will lead to new insights on essential regulatory networks and protein drug targets for experimental biologists. According to cytoscape plugin download statistics, the accumulated number of cytoHubba is around 6,700 times since 2010.

Comparison of various formulae for estimating low-density lipoprotein cholesterol by a combination of ages and genders in Taiwanese adults

Background

The accuracy and precision of the Friedewald formula for estimating low-density lipoprotein cholesterol (LDL-C) is questionable. Although other formulae have been developed, only a few studies compare them. Thus, we compared the efficiencies of various formulae, based on the age and gender of adults, to determine which ones yield more accurate estimations in terms of mean squared error, and which formulae underestimated and overestimated LDL-C performance.

Methods

This study compares various formulae in terms of mean squared error (MSE), as well as underestimation and overestimation of LDL-C concentrations, using subjects of various ages and both genders. Six groups were examined in this study based on age and gender: males 20–44 years old, 45–64, and 65 and above, and females in the same three age ranges.

Results

The results show that the Friedewald formula has relatively low accuracy, and while its performance among older (aged 45 and above) women with triglyceride concentrations ≤ 400 mg/dL is better than that with other groups, it is still more inaccurate than the other formulae. In terms of prediction errors and mean squared errors, Tsai’s formula (TF) and a calibrated TF provide the most accurate results with regard to the LDL-C concentration. Moreover, based on a cross-validation of age and gender, these two formulae provide highly accurate results for the LDL-C concentrations of all the studied groups, except for women aged 20–44 years.

Conclusions

Based on the experimental results, this study provides a set of benchmarks for the formulae used in LDL-C tests when considering the factors of age and gender. Therefore, it is a valuable method for providing formula benchmarking.

EUS-guided FNA cytology of pancreatic neuroendocrine tumour (PanNET): a retrospective study of 132 cases over an 18-year period in a single institution

OBJECTIVE

To determine the diagnostic accuracy and pitfalls of endoscopic ultrasound (EUS)-guided fine needle aspiration (FNA) cytology of pancreatic neuroendocrine tumour (PanNET).

METHODS

A search of our laboratory information system was performed from July 1992 to June 2010 to identify all FNA cytology and corresponding surgical specimens in which the diagnosis of PanNET was rendered or considered.

RESULTS

One hundred and thirty-two cases diagnosed by EUS-guided FNA were collected. Histological correlation was available for 77 (58%) of FNAs; 55 patients may have been treated elsewhere or had no surgery because of advanced disease or co-morbidity. Among 56 cases diagnosed as PanNET on FNA, 54 (96%) were confirmed histologically; the remaining two were poorly differentiated adenocarcinoma with focal neuroendocrine features in one case and no tumour was found in the other. Follow-up histology of nine patients diagnosed as suspicious for PanNET on FNA showed four PanNETs, two pancreatic ductal adenocarcinomas (PDA), one solid pseudopapillary tumour (SPT) and two cases of chronic pancreatitis. Nine cases rendered by FNA as atypical (n = 3), no atypical cells identified (n = 4) or unsatisfactory (n = 2) were PanNETs on histology. Lastly, three cases of oncocytic variant of PanNET were misdiagnosed on FNA as either adenocarcinoma (n = 2) or as suspicious for carcinoma (n = 1).

CONCLUSIONS

Overall, 54 of the 70 histologically confirmed PanNET cases (77%) were correctly diagnosed by preoperative FNA as PanNET. FNA cases designated as no atypical cells identified and unsatisfactory (7/132, 5%) were attributable to sampling error. Diagnostic pitfalls in our study mainly included PDA, SPT and chronic pancreatitis.

Effect of dietary cadmium on the activity of glutathione S-transferase and carboxylesterase in different developmental stages of the Oxya chinensis (Orthoptera: Acridoidea)

Glutathione S-transferases (GSTs) and carboxylesterases (CarEs) play important roles in the detoxification of endogenous and exogenous compounds. In this study, the biochemical effects of dietary cadmium (Cd) on the activities of GST and CarE in different developmental stages of the rice grasshopper Oxya chinensis Thunberg were studied. The results showed that the effects of the Cd concentration and developmental stage on GST activity were statistically significant. GST activity in O. chinensis increased at the highest Cd concentration in most nymphs, suggesting that GST is typically inducible by Cd. However, GST activity was inhibited in adults under Cd stress owing to life-stage-specific physiological characteristics. The results showed that the substrates, developmental stage, and Cd concentration had statistically significant effects on CarE activity. In most studies of CarE activity, the interaction between any two studied factors was statistically significant, although the interaction effects of the substrates, developmental stages, and Cd concentrations were not significant, which implied that the insect physiological condition and the external environmental may affect CarE activity. The results suggest that the insect's life stage and enzyme substrates should be considered when enzyme activity under Cd stress is studied.

Relationships of single nucleotide polymorphisms of monocyte chemoattractant protein 1 and chemokine receptor 2 with susceptibility and clinicopathologic characteristics of neoplasia of uterine cervix in Taiwan women

Few studies reported the implication of single nucleotide polymorphisms (SNPs) of monocyte chemoattractant protein 1 (MCP-1) and its receptor chemokine receptor 2 (CCR-2) in clinical significance of cancer of uterine cervix. We hypothesized that SNPs of MCP-1 and CCR-2 may affect the expression of these genes and then proteins. Therefore, we investigated the influence of the gene polymorphisms of MCP-1 and CCR-2 on the susceptibility and clinicopathologic characteristics of cervical neoplasia in Taiwan women. We recruited 86 patients with invasive cancer and 61 with high-grade dysplasia and 253 control women and selected 1 MCP-1 SNP rs1024611 (-2518G/A) and 1 CCR-2 SNP rs1799864 (190G/A; V64I) to determine their genotypes distribution using polymerase chain reaction-restriction fragment length polymorphism. In comparison to normal individuals with homozygotes GG in MCP-2 SNP, women with GA or AA carried a 2.01 odds ratio of developing cervical cancer. Nevertheless, it was not demonstrated in CCR-2 SNP. Furthermore, women with mutant homozygote (AA) of MCP-1 SNP increased the risk of deep stromal invasion, large tumor diameter, and parametrium invasion of cervical cancer, when compared to those with wild homozygote GG or heterozygote GA. However, women with mutant homozygotes (AA) of CCR-2 SNP did not increase the risk of poor clinicopathologic characteristics. In conclusion, MCP-1 SNP may be correlated with the development, deep stromal invasion, large tumor diameter, and parametrium invasion of cervical cancer but not with cancer recurrence or survival of Taiwan women patients with cancer. However, the SNP of its receptor, CCR-2, is not implicated in cervical cancer.

Preimplantation and prenatal genetic diagnosis of aromatic L-amino acid decarboxylase deficiency with an amplification refractory mutation system-quantitative polymerase chain reaction

OBJECTIVES

To develop a diagnostic platform for preimplantation genetic diagnosis (PGD) and prenatal genetic diagnosis (PND) to prevent births of aromatic L-amino acid decarboxylase deficiency (AADC) patients.

MATERIALS AND METHODS

Five Taiwanese families carrying AADC were enrolled. A novel technique, amplification refractory mutation system-quantitative polymerase chain reaction (ARMS-qPCR), was developed for both of PGD and PND. For PGD, blastomere biopsies of day-3 cleavage-stage embryos were subjected to ARMS-qPCR. Villi, cultured amniocytes, or both were used to confirm the PGD result; this approach could also be used as the sole method for PND after in vivo conception).

RESULTS

Unaffected live births were achieved in four of the five families, except one with ongoing PGD. The ARMS-qPCR correctly classified blastomeres (from day-3 cleavage-stage embryos) as affected (homozygous mutant), carrier (heterozygous for mutant and wild-type alleles), or normal (homozygous wild-type) within 1 working day.

CONCLUSIONS

To our knowledge, this is the first report of successful PGD of AADC. The molecular technique we devised (ARMS-qPCR) was applicable for PGD as well as PND of AADC. Furthermore, it has great potential for similar applications in other monogenic disorders.

Cyclophilin A and nuclear factor of activated T cells are essential in cyclosporine-mediated suppression of polyomavirus BK replication

Immunosuppressants have impacts on the development of polyomavirus-associated nephropathy. We previously demonstrated that cyclosporin A (CsA) suppressed polyomavirus BK (BKV) replication. The role of cyclophilin A (CypA) and nuclear factor of activated T cells (NFAT) in CsA-imposed suppression of BKV replication was determined in this study. Results demonstrated that knockdown of CypA but not CypB significantly reduced BKV large T antigen (TAg) expression and BKV titer. Overexpression of CypA reversed CypA siRNA-induced inhibition in BKV TAg expression. In addition, CypA overexpression attenuated the suppressive effect of CsA on TAg expression, suggesting CypA implicated in CsA-mediated anti-BKV effect. Knockdown of NFATc3 abrogated TAg expression, while overexpression of NFATc3 promoted TAg expression and augmented BKV promoter activity. NFATc3 binding to the BKV promoter was verified by chromatin immunoprecipitation assay and electrophoretic mobility shift assay. Renal histology also displayed an increase in NFATc3 expression in tubulointerstitium of BKV-associated nephropathy. Furthermore, overexpression of NFATc3 rescued CsA-mediated inhibition of BKV load and TAg expression. A CsA analog, NIM811, which cannot block NFAT functionality, failed to suppress TAg expression. In conclusion, CypA and NFAT are indispensable in BKV replication. CsA inhibits BKV replication through CypA and NFAT, which may be potential targets of anti-BKV treatment.

Association of interleukin-1beta (IL1B) polymorphisms with Graves' ophthalmopathy in Taiwan Chinese patients

PURPOSE

To evaluate whether variations in the IL1B gene could be associated with Graves' ophthalmopathy (GO) in patients with Graves' disease (GD).

METHOD

This case-control study included 471 Taiwan Chinese patients with GD (200 with GO and 271 without GO) and 160 healthy volunteers. Eight single-nucleotide polymorphisms (SNPs) in IL1B were genotyped with an allele-specific extension and ligation assay.

RESULTS

In the IL1B SNPs examined, the C allele of rs1143634 was associated with GD, whereas the T/T genotype of the SNPs rs1143634 and rs16944 were less associated with the disease. The A/A genotype of the SNPs rs3917368 and rs1143643, which had the strongest interaction, may increase the risk of GO (P = 0.024 and P = 0.017, respectively). Several GD susceptibility and insusceptibility IL1B haplotypes have been identified, and the Ht4-GCGCCTCC haplotype, composed of eight SNPs and associated with low circulating IL1β levels, may be protective against the development of GO (P = 0.025). Moreover, that the GO-susceptible genotype was associated with lower plasma IL1β concentrations implies that the origin of GO may go beyond the IL1B polymorphism-associated elevation of circulating IL1β.

CONCLUSIONS

The data for IL1B polymorphisms and the association of GD and GO with plasma IL1β levels show that IL1B polymorphisms may be associated with the development of GD and GO.

Serum anti-Müllerian hormone predicts ovarian response and cycle outcome in IVF patients

PURPOSE

This prospective study was designed to investigate whether anti-Müllerian hormone (AMH) levels at basal and ovulation triggering day are associated with ovarian response and pregnancy outcome for in vitro fertilization (IVF).

METHOD

60 infertility women undergoing IVF were prospectively studied. On day 3 of the menstrual cycle (D3), measurements of AMH, inhibin B, FSH, LH, and E2 and ultrasound evaluation of antral follicle count (AFC) were performed. Serum AMH and inhibin B levels were remeasured on the day of hCG administration (DhCG). The outcome measures were the number of retrieved oocytes and clinical pregnancy.

RESULTS

Number of retrieved oocytes was statistically significant and correlated with D3 AMH, AFC, DhCG AMH, DhCG inhibin B, FSH, and age (r=0.885, 0.874, 0.742, 0.732, -0.521, -0.385, respectively). Statistically significant differences were found between pregnant and non-pregnant women regarding D3 AMH and AFC. Multiple regression analysis for prediction of pregnancy showed D3 AMH to be a good predictor of clinical pregnancy.

CONCLUSION

AMH correlates better than age, FSH, and inhibin B with the number of retrieved oocytes. Serum basal AMH may offer a better prognostic value for clinical pregnancy than other currently available markers of IVF outcome in our preliminary study.

Ruptured corpus luteum with hemoperitoneum: case characteristics and demographic changes over time

OBJECTIVE

Women of reproductive age are at risk of ruptured corpus luteum with hemoperitoneum. We identified the clinical and demographic features of patients recently treated in our institution and compared the findings with those from an earlier series, to detect any changes in disease identity that have occurred over the past 20 years.

MATERIALS AND METHODS

Charts of patients treated between January 2001 and December 2003 at Changhua Christian Hospital were reviewed. Clinical parameters were compared with those from our previous study in the 1980s.

RESULTS

A total of 91 women were diagnosed with ruptured corpus luteum and hemoperitoneum (mean age, 26 years; range, 15-42 years). Most ruptures (60.4%) occurred during the secretory phase and most women (57.1%) reported recent sexual intercourse prior to the onset of pain. Most patients (81.3%) required laparoscopic intervention to achieve hemostasis. No obvious differences were found between the results of this study and those from the 1985 series, except that our patients were younger, were more often unmarried, chose laparoscopic interventions rather than laparotomy, and that there was an emerging trend towards conservative treatment.

CONCLUSION

The manifestations of corpus luteum hemorrhage in this study were similar to those observed in the 1980s at the same medical center. However, the demographic parameters (age, marital status) and the modalities of treatment (conservative treatment, mode of surgical interventions) had changed in line with the evolution of society, culture, and the progress of medical science over the past 20 years.