Beyond modules and hubs: the potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders.

In a research environment dominated by reductionist approaches to brain disease mechanisms, gene network analysis provides a complementary framework in which to tackle the complex dysregulations that occur in neuropsychiatric and other neurological disorders. Gene-gene expression correlations are a common source of molecular networks because they can be extracted from high-dimensional disease data and encapsulate the activity of multiple regulatory systems. However, the analysis of gene coexpression patterns is often treated as a mechanistic black box, in which looming 'hub genes' direct cellular networks, and where other features are obscured. By examining the biophysical bases of coexpression and gene regulatory changes that occur in disease, recent studies suggest it is possible to use coexpression networks as a multi-omic screening procedure to generate novel hypotheses for disease mechanisms. Because technical processing steps can affect the outcome and interpretation of coexpression networks, we examine the assumptions and alternatives to common patterns of coexpression analysis and discuss additional topics such as acceptable datasets for coexpression analysis, the robust identification of modules, disease-related prioritization of genes and molecular systems and network meta-analysis. To accelerate coexpression research beyond modules and hubs, we highlight some emerging directions for coexpression network research that are especially relevant to complex brain disease, including the centrality-lethality relationship, integration with machine learning approaches and network pharmacology.

Molecular evidence for BDNF- and GABA-related dysfunctions in the amygdala of female subjects with major depression.

Women are twice as likely as men to develop major depressive disorder (MDD) and are more prone to recurring episodes. Hence, we tested the hypothesis that the illness may associate with robust molecular changes in female subjects, and investigated large-scale gene expression in the post-mortem brain of MDD subjects paired with matched controls (n=21 pairs). We focused on the lateral/basolateral/basomedian complex of the amygdala as a neural hub of mood regulation affected in MDD. Among the most robust findings were downregulated transcripts for genes coding for γ-aminobutyric acid (GABA) interneuron-related peptides, including somatostatin (SST), tachykinin, neuropeptide Y (NPY) and cortistatin, in a pattern reminiscent to that previously reported in mice with low brain-derived neurotrophic factor (BDNF). Changes were confirmed by quantitative PCR and not explained by demographic, technical or known clinical parameters. BDNF itself was significantly downregulated at the RNA and protein levels in MDD subjects. Investigating putative mechanisms, we show that this core MDD-related gene profile (including SST, NPY, TAC1, RGS4 and CORT) is recapitulated by complementary patterns in mice with constitutive (BDNF-heterozygous) or activity-dependent (exon IV knockout) decreases in BDNF function, with a common effect on SST and NPY. Together, these results provide both direct (low RNA/protein) and indirect (low BDNF-dependent gene pattern) evidence for reduced BDNF function in the amygdala of female subjects with MDD. Supporting studies in mutant mice models suggest a complex mechanism of low constitutive and activity-dependent BDNF function in MDD, particularly affecting SST/NPY-related GABA neurons, thus linking the neurotrophic and GABA hypotheses of depression.

Inhibition of prostate cancer growth and metastasis using small interference RNA specific for minichromosome complex maintenance component 7.

Minichromosome complex maintenance component 7 (MCM7) is a critical component of DNA replication licensing. Amplification and overexpression of MCM7 leads to high rate of prostate cancer metastasis. Recent studies indicate that MCM7 genome encodes a putative 'super-oncogene' cluster including MCM7 oncogene and a miRNA cluster that knocks down the expression of several critical tumor-suppressor genes. In this study, we constructed a vector that constitutively expresses small interference RNA (siRNA) specific for MCM7. Introduction of this vector into prostate cancer cell lines PC3 or Du145 decreases the expression of MCM7 by 80%. The vector inhibits DNA synthesis and generates growth arrest of these cancer cells. Severe combined immunodeficient mice were xenografted PC3 or Du145 tumors, and subsequently treated with this vector through tail vein injection with polyethylenimine. The animals had dramatically smaller tumor volume, less metastasis and better survival rate in comparison with the controls. As a result, intervention of MCM7 expression using siRNA approach may hold the promise for treating androgen refractory prostate cancer.

Efficacy of an intravenous proton pump inhibitor after endoscopic therapy with epinephrine injection for peptic ulcer bleeding in patients with uraemia: a case-control study.

BACKGROUND: Patients with peptic ulcer bleeding and uraemia are prone to re-bleeding. AIM: To compare the efficacy of an intravenous proton pump inhibitor in treating peptic ulcer bleeding in patients with uraemia and those without uraemia. METHODS: High-risk peptic ulcer bleeding patients received endoscopic therapy with epinephrine (adrenaline) injection plus intravenous omeprazole (40 mg bolus followed by 40 mg infusion every 12 h) for 3 days. Re-bleeding, volume of blood transfusion, hospital stay, need for surgery, and mortality were analysed. RESULTS: The uraemic group had similar 7-day re-bleeding rate (6/42, 14.29% vs. 6/46, 13.04%, P = 0.865) to that of non-uraemic patients, but more re-bleeding episodes beyond 7 days (4/42, 9.52% vs. 0/46, 0%, P = 0.032, OR [95% CI] = 1.105 [1.002-1.219]) and all-cause mortality (4/42 vs. 0/46 P = 0.032, OR [95% CI] = 1.105 [1.002-1.219]). The uraemic group also had more units of blood transfusion after endoscopic therapy (mean +/- s.d. 4.33 +/- 3.35 units vs. 2.15 +/- 1.65 units, P < 0.001), longer hospital stay (mean +/- s.d. 8.55 +/- 8.12 days vs. 4.11 +/- 1.60 days, P < 0.001) and complications during hospitalization (9/42 vs. 0/46, P = 0.001, OR [95% CI] = 1.273 [1.087-1.490]). CONCLUSION: Endoscopic therapy with epinephrine injection plus an intravenous proton pump inhibitor can offer protection against early re-bleeding in uraemic patients with peptic ulcer bleeding, but has a limited role beyond 7 days.

Comparison of two-phase (201)Tl SPECT with chest CT to differentiate thoracic malignancies from benign lesions.

AIM: This study was conducted to compare the performance of (201)Tl single photon emission computed tomography ((201)Tl SPECT) with chest computed tomography (CT) in differentiating thoracic malignancies from benign lesions. METHODS: One hundred and seventy patients with confirmed diagnostic thoracic lesions found in chest radiographs were prospectively examined by (201)Tl SPECT. The performance of (201)Tl SPECT in differentiating thoracic malignancies from benign lesions was evaluated in 161 patients with a measurable retention index (RI), using the region-of-interest method. Chest CT scans were retrospectively collected from 165 patients and were interpreted by two independent observers. RESULTS: The areas under the receiver operating characteristics curves were 0.85 using the RI value to differentiate thoracic malignancies from benign lesions. The sensitivity, specificity, and accuracy were 71.9%, 83.1%, and 76.4%, respectively, with a cutoff level for the RI set at 20%. Similarly, the sensitivity, specificity and accuracy of chest CT scans to differentiate malignancies from benign lesions were 78.2%, 69.7% and 74.9%, respectively. Focusing on patients with concordant results in both (201)Tl SPECT and chest CT scans, we can differentiate thoracic malignancies from benign lesions with a sensitivity of 89.1%, a specificity of 90%, and an accuracy of 89.4%. CONCLUSION: Both (201)Tl SPECT and chest CT scans are useful imaging tools in differentiating thoracic malignancies from benign lesions, with an accuracy of around 75%. By combining these two image modalities, the accuracy improves to 89.4%, which may circumvent the need for invasive procedures for certain equivocal cases, using either single image alone.

Recurrence of peptic ulcer in uraemic and non-uraemic patients after Helicobacter pylori eradication: a 2-year study.

BACKGROUND: The role of Helicobacter pylori in the pathogenesis of peptic ulcer disease in patients with uraemia remains unclear. AIM: To evaluate the long-term effect of H. pylori eradication in these patients. METHODS: Uraemic and non-uraemic patients with peptic ulcer were enrolled in this study. Patients having history of non-steroidal anti-inflammatory drugs use or cardiovascular disease that need aspirin use were excluded. After confirmation of H. pylori infection, they received a triple therapy and were followed up for 2 years. RESULTS: Between September 1999 and December 2005, 34 patients (41%) of the end-stage renal disease [H. pylori (+) group] and 67 (84%) of the non-uraemic patients with peptic ulcer disease (PU group) received anti-H. pylori therapy. After triple therapy, 32 (94%) from the end-stage renal disease group and 64 (96%) from the peptic ulcer group obtained successful eradication. During the 2-year follow-up, three patients in the end-stage renal disease group were excluded because of the presence of cardiovascular disease and aspirin use in two cases and died of heart failure in one case; two patients in peptic ulcer group refused follow-up. Finally, 29 uraemic and 62 non-uraemic patients had achieved the follow-up. Recurrence of peptic ulcer was more in the end-stage renal disease group than in the peptic ulcer group with intention-to-treat analysis (eight of 32, 25% vs. two of 64, 3%, P = 0.001, OR: 10.0, 95% CI: 1.979-50.540) or per-protocol analysis (eight of 29, 28% vs. two of 62, 3%, P < 0.001, OR: 11.4, 95% CI: 2.245-58.168). CONCLUSIONS: Peptic ulcer recurrence after H. pylori eradication is higher in end-stage renal disease patients with peptic ulcer than in peptic ulcer patients without renal disease. Factors aside from H. pylori play an important role in peptic ulcer recurrence in end-stage renal disease patients.

Lack of serotonin1B receptor expression leads to age-related motor dysfunction, early onset of brain molecular aging and reduced longevity.

Normal aging of the brain differs from pathological conditions and is associated with increased risk for psychiatric and neurological disorders. In addition to its role in the etiology and treatment of mood disorders, altered serotonin (5-HT) signaling is considered a contributing factor to aging; however, no causative role has been identified in aging. We hypothesized that a deregulation of the 5-HT system would reveal its contribution to age-related processes and investigated behavioral and molecular changes throughout adult life in mice lacking the regulatory presynaptic 5-HT(1B) receptor (5-HT(1B)R), a candidate gene for 5-HT-mediated age-related functions. We show that the lack of 5-HT(1B)R (Htr1b(KO) mice) induced an early age-related motor decline and resulted in decreased longevity. Analysis of life-long transcriptome changes revealed an early and global shift of the gene expression signature of aging in the brain of Htr1b(KO) mice. Moreover, molecular changes reached an apparent maximum effect at 18-months in Htr1b(KO) mice, corresponding to the onset of early death in that group. A comparative analysis with our previous characterization of aging in the human brain revealed a phylogenetic conservation of age-effect from mice to humans, and confirmed the early onset of molecular aging in Htr1b(KO) mice. Potential mechanisms appear independent of known central mechanisms (Bdnf, inflammation), but may include interactions with previously identified age-related systems (IGF-1, sirtuins). In summary, our findings suggest that the onset of age-related events can be influenced by altered 5-HT function, thus identifying 5-HT as a modulator of brain aging, and suggesting age-related consequences to chronic manipulation of 5-HT.

Oxidative stress in nonallergic nasal polyps associated with bronchial hyperresponsiveness.

BACKGROUND: Nasal polyposis (NP) is a chronic inflammatory disease of upper airway with unknown etiology. NP is frequently associated with asthma; the interaction between these comorbidities remains interesting. Oxidative stress has been implicated in the pathophysiology of NP and asthma. The aim of this study is to investigate the significance of oxidative stress in sinonasal microenvironments by evaluating its association with clinopathological parameters and its impacts on the pathogenesis of bronchial hyperresponsiveness (BHR) in NP. METHODS: Polyp biopsy specimens were obtained from 20 nonallergic patients; control mucosas were obtained from 20 volunteers. The levels of free radicals in the tissues and in blood were determined by a sensitive chemiluminescence (CL) method. NP patients were substratified into three subgroups, NP without BHR, NP with asymptomatic BHR, and NP with BHR and asthma by the results of provocative testing. Four histological characteristics of NP, inflammatory cells, eosinophil infiltration, edema and fibrosis were estimated and applied to correlate with the tissue-CL. RESULTS: The mean CL level in polyp-tissues, but not in blood, was higher than in the control specimens. In NP patients, tissue-CL was associated with endoscopy score; high tissue-CL levels were positively correlated with the abundance of inflammatory cells and eosinophils. Tissue-CL and endoscopy score were associated with BHR/asthma phenotype. CONCLUSION: These results suggest an important role for oxidative stress in the pathophysiology of NP and a causal relation between oxidative stress and inflammatory cells, especially the eosinophils. Free radical levels in polyp-tissues associated with NP severity and with BHR/asthma phenotype in nonallergic NP patients.

MCM7 amplification and overexpression are associated with prostate cancer progression.

The genomic DNA profiles of prostate cancers with aggressive features were compared to the profiles of matched normal DNA to identify genes that are selectively amplified in the cancer cells. One of the identified genes, MCM7, which is a component of the DNA replication licensing complex, has been studied extensively both at the DNA and protein levels in human prostate tissues. Approximately half of the prostate cancer specimens studied showed MCM7 gene amplification, and 60% of the aggressive prostate cancer specimens had increased MCM7 protein expression. Amplification or overexpression of MCM7 was significantly associated with relapse, local invasion and a worse tumor grade. Constitutive expression of MCM7 in a human prostate cancer cell line, DU145, resulted in markedly increased DNA synthesis and cell proliferation compared to vector-only controls, and an increased cell invasion in vitro. Indeed, MCM7 overexpression produced primary tumors 12 times larger than vector-only controls and resulted in a rapid demise of mice bearing those tumors. These studies implicate MCM7, and the DNA replication licensing gene family, in prostate cancer progression, growth and invasion.

Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects.

We consider the problem of comparing the gene expression levels of cells grown under two different conditions using cDNA microarray data. We use a quality index, computed from duplicate spots on the same slide, to filter out outlying spots, poor quality genes and problematical slides. We also perform calibration experiments to show that normalization between fluorescent labels is needed and that the normalization is slide dependent and non-linear. A rank invariant method is suggested to select non-differentially expressed genes and to construct normalization curves in comparative experiments. After normalization the residuals from the calibration data are used to provide prior information on variance components in the analysis of comparative experiments. Based on a hierarchical model that incorporates several levels of variations, a method for assessing the significance of gene effects in comparative experiments is presented. The analysis is demonstrated via two groups of experiments with 125 and 4129 genes, respectively, in Escherichia coli grown in glucose and acetate.

Endometrial stromal sarcoma of twenty cases.

BACKGROUND: Endometrial stromal sarcoma is a rare neoplasm. We reviewed twenty cases to study the characteristics of this disease. METHODS: Twenty cases of endometrial stromal sarcoma were treated at our hospital. The clinical stage, treatment and outcome were retrospectively analyzed. RESULTS: Endometrial stromal sarcoma comprised 4.3% of corpus cancers and 46.4% of uterine sarcomas at our hospital. Seven cases were stage I, one was stage II, ten were stage III, and two were stage IV at the time of diagnosis. Histopathologically, seventeen cases were classified as low-grade sarcoma and three were high-grade sarcoma. Seven patients had recurrence and five of them had already died of disease. Among these recurrent patients, one was stage II and six were stage III. All three patients with high-grade sarcoma and four with low-grade sarcoma had recurrence. CONCLUSIONS: We think mitotic count is an important prognostic factor in low-grade endometrial stromal sarcoma and high-grade endometrial stromal sarcoma has a poor prognosis even with post-operative adjuvant treatment.

Scalene lymph node metastases with the negative pelvic nodes in invasive cervical carcinoma.

Cervical carcinoma spreads predominantly by lymphatic routes and lymph node metastases may occur even in early stages of disease. Metastases usually first appear in pelvic lymph nodes, then disseminate along the efferent lymphatic chain to the extrapelvic lymph nodes. Cases of positive lymph node metastases with negative pelvic nodes in invasive cervical carcinoma are extremely rare. We report a 50-year-old woman with bulky stage IIA cervical carcinoma who had scalene lymph node metastases in the absence of pelvic lymph node metastases after radical hysterectomy and postoperative pelvic irradiation. This rare "skipping" nodal metastasis was probably via posterior trunk lymphatic drainage of the bulky cervical carcinoma which mainly invaded the posterior vaginal cuff. Neoadjuvant or adjuvant chemotherapy is recommended to prolong survival of patients in such cases.

Congenital nephrotic syndrome with microcephaly: report of a case.

Congenital nephrotic syndrome is an uncommon disease with variable etiology, course and prognosis; its association with microcephaly is even more unusual. A case is reported here of congenital nephrotic syndrome because of focal glomerulosclerosis in a three-month-old female infant with microcephaly since birth. There were no known renal diseases nor hereditary disorders in her family. The serologic tests for syphilis, toxoplasmosis, rubella, and cytomegalovirus infections were negative. Magnetic resonance imaging of the brain showed diffuse atrophic change of the cerebral hemispheres and brain stem with a remarkable increase of extracerebral space. The infant died at the age of four months without any clinical cause other than congenital nephrotic syndrome. These findings, including congenital nephrotic syndrome and microcephaly accompanied by various other clinical symptoms, have been described as a clinical entity with an autosomal recessive mode of inheritance.