Integrative analysis of GWAS, eQTLs and meQTLs data suggests that multiple gene sets are associated with bone mineral density

Objectives

Several genome-wide association studies (GWAS) of bone mineral density (BMD) have successfully identified multiple susceptibility genes, yet isolated susceptibility genes are often difficult to interpret biologically. The aim of this study was to unravel the genetic background of BMD at pathway level, by integrating BMD GWAS data with genome-wide expression quantitative trait loci (eQTLs) and methylation quantitative trait loci (meQTLs) data

Method

We employed the GWAS datasets of BMD from the Genetic Factors for Osteoporosis Consortium (GEFOS), analysing patients’ BMD. The areas studied included 32 735 femoral necks, 28 498 lumbar spines, and 8143 forearms. Genome-wide eQTLs (containing 923 021 eQTLs) and meQTLs (containing 683 152 unique methylation sites with local meQTLs) data sets were collected from recently published studies. Gene scores were first calculated by summary data-based Mendelian randomisation (SMR) software and meQTL-aligned GWAS results. Gene set enrichment analysis (GSEA) was then applied to identify BMD-associated gene sets with a predefined significance level of 0.05.

Results

We identified multiple gene sets associated with BMD in one or more regions, including relevant known biological gene sets such as the Reactome Circadian Clock (GSEA p-value = 1.0 × 10^-4 for LS and 2.7 × 10^-2 for femoral necks BMD in eQTLs-based GSEA) and insulin-like growth factor receptor binding (GSEA p-value = 5.0 × 10^-4 for femoral necks and 2.6 × 10^-2 for lumbar spines BMD in meQTLs-based GSEA).

Conclusion

Our results provided novel clues for subsequent functional analysis of bone metabolism, and illustrated the benefit of integrating eQTLs and meQTLs data into pathway association analysis for genetic studies of complex human diseases.

Cite this article: W. Wang, S. Huang, W. Hou, Y. Liu, Q. Fan, A. He, Y. Wen, J. Hao, X. Guo, F. Zhang. Integrative analysis of GWAS, eQTLs and meQTLs data suggests that multiple gene sets are associated with bone mineral density. Bone Joint Res 2017;6:572–576.

White matter integrity correlates with choline level in dorsal anterior cingulate cortex of obsessive compulsive disorder patients: A combined DTI-MRS study

Structural and functional neuroimaging studies have indicated that the cortico-striato -thalamo-cortical (CSTC) circuit contributes to the pathophysiology of obsessive compulsive disorder (OCD). As an essential component of CSTC circuit, the dorsal anterior cingulate cortex (dACC) plays an important role for its advanced function in cognition and emotion control. A comprehensive understanding of the dACC disruption in OCD pathological mechanism is desired. In this study, we performed a combined diffusion tensor imaging (DTI) and magnetic resonance spectroscopy (MRS) study in 15 OCD patients and 15 healthy controls to investigate the association between structural abnormality and metabolic alterations within the dACC area. We found a positive correlation between the dACC fractional anisotropy (FA) value and choline concentration in patients. Moreover, the FA was positively associated with OCD clinical symptom, especially the compulsive behavior, which showed the clinical relevance of dACC white matter integrity in OCD. To our knowledge, the present work is the first combined DTI-MRS study of OCD. Our findings demonstrated the co-occurrence of structural and metabolic changes within dACC in OCD patients. It was suggested that the disrupted white matter integrity might be accompanied with degraded cellular membrane turnover.

Transgenic overexpression of NanogP8 in the mouse prostate is insufficient to initiate tumorigenesis but weakly promotes tumor development in the Hi-Myc mouse model

This project was undertaken to address a critical cancer biology question: Is overexpression of the pluripotency molecule Nanog sufficient to initiate tumor development in a somatic tissue? Nanog1 is critical for the self-renewal and pluripotency of ES cells, and its retrotransposed homolog, NanogP8 is preferentially expressed in somatic cancer cells. Our work has shown that shRNA-mediated knockdown of NanogP8 in prostate, breast, and colon cancer cells inhibits tumor regeneration whereas inducible overexpression of NanogP8 promotes cancer stem cell phenotypes and properties. To address the key unanswered question whether tissue-specific overexpression of NanogP8 is sufficient to promote tumor development in vivo, we generated a NanogP8 transgenic mouse model, in which the ARR₂PB promoter was used to drive NanogP8 cDNA. Surprisingly, the ARR₂PB-NanogP8 transgenic mice were viable, developed normally, and did not form spontaneous tumors in >2 years. Also, both wild type and ARR₂PB-NanogP8 transgenic mice responded similarly to castration and regeneration and castrated ARR₂PB-NanogP8 transgenic mice also did not develop tumors. By crossing the ARR₂PB-NanogP8 transgenic mice with ARR₂PB-Myc (i.e., Hi-Myc) mice, we found that the double transgenic (i.e., ARR₂PB-NanogP8; Hi-Myc) mice showed similar tumor incidence and histology to the Hi-Myc mice. Interestingly, however, we observed white dots in the ventral lobes of the double transgenic prostates, which were characterized as overgrown ductules/buds featured by crowded atypical Nanog-expressing luminal cells. Taken together, our present work demonstrates that transgenic overexpression of NanogP8 in the mouse prostate is insufficient to initiate tumorigenesis but weakly promotes tumor development in the Hi-Myc mouse model.

Metformin inhibited esophageal squamous cell carcinoma proliferation in vitro and in vivo and enhanced the anti-cancer effect of cisplatin

Esophageal squamous cell carcinoma (ESCC) is an aggressive malignancy with poor prognosis in China. Chemotherapy now is one of the most frequently used treatments for patients with ESCC in middle or late stage, however the effects were often limited by increased chemoresistance or treatment toxicity. So it is urgent to find new drugs to treat ESCC patients. Metformin with low cost and toxicity has proved to have anti-cancer effects in a numerous cancers, while its role and mechanism in ESCC has seldom been studied. In the present study, we found that metformin exhibited not only an anti-proliferation ability in a dose and time dependent manner but also a proapoptosis effect in a dose dependent manner in ESCC cell line KYSE450. Our in vivo experiment also showed that metformin markedly inhibited KYSE450 xenograft tumors growth compared to those treated with normal saline. What’s more, no obvious toxic reactions were observed. To further explore the underlying mechanism, we found that metformin treatment could significantly damp the expression of 4EBP1 and S6K1 in KYSE 450 cells in vitro and in vivo, furthermore, the p-4EBP1 and p-S6K1 expression in KYSE 450 cells were also inhibited greatly in vitro and in vivo. During the therapy of cancer, in order to overcome side effects, combination therapy was often used. In this paper, we demonstrated that metformin potentiated the effects of cisplatin via inhibiting cell proliferation and promoting cell apoptosis. Taken together, metformin owned the potential anti-cancer effect on ESCC in monotherapy or was combined with cisplatin and these results laid solid basis for the use of metformin in ESCC.

miR-4417 Targets Tripartite Motif-Containing 35 (TRIM35) and Regulates Pyruvate Kinase Muscle 2 (PKM2) Phosphorylation to Promote Proliferation and Suppress Apoptosis in Hepatocellular Carcinoma Cells

BACKGROUND MicroRNAs (miRNAs) are a class of small non-coding RNAs that are strongly involved in various types of carcinogenesis, including hepatocellular carcinoma (HCC). This study aimed to clarify whether miR-4417 promotes HCC growth by targeting TRIM35 and regulating PKM2 phosphorylation. MATERIAL AND METHODS Online software, including TargetScan and miRanda, was used to predict the potential target of miR-4417. Real-Time PCR (qRT-PCR) and Western blot assays were performed to detect the expression levels of mRNA and protein, respectively. Cell proliferation was measured by MTT assay and apoptosis in A549 cells was examined by flow cytometry. RESULTS Bioinformatics reveal that TRIM35 mRNA contains 1 conserved target site of miR-4417. High level of miR-4417 and low levels of TRIM35 mRNA and protein were observed in HCC cells compared with a normal liver cell line. Biological function analysis showed that miR-4417 inhibitor inhibits cell proliferation and promotes apoptosis in HCC cells. Furthermore, we verified that TRIM35 is a functional target of miR-4417 by use of luciferase reporter assay, and TRIM35 overexpressing showed an elevation of proliferation and a reduction of apoptosis in HCC cells. We subsequently investigated whether miR-4417 and TRIM35 regulate HCC cell proliferation and apoptosis through PKM2 Y105 phosphorylation, and the results supported our speculation that miR-4417 targets TRIM35 and regulates the Y105 phosphorylation of PKM2 to promote hepatocarcinogenesis. CONCLUSIONS Our findings indicate that miR-4417 may function as an oncogene in HCC and is a potential alternative therapeutic target for this deadly disease.

Clinical significance of serum cathepsin B and cystatin C levels and their ratio in the prognosis of patients with esophageal cancer

OBJECTIVE

The main purpose of this study was to analyze the serum cathepsin B (CTSB) and cystatin C (CysC) levels in patients with esophageal carcinoma and their correlation with the clinical indices and prognosis.

METHODS

The serum levels of CTSB and CysC from 56 patients with esophageal carcinoma and 30 healthy donors were determined preoperatively by using enzyme-linked immunosor-bent assay. The correlation between CTSB and CysC was evaluated by Spearman correlation coefficient test. Kaplan-Meier survival curves were plotted, while the survival rates were compared using the log-rank test. Univariate and multivariate analyses of prognostic factors for survival were performed using the Cox proportional hazard regression model with a 95% confidence interval.

RESULTS

CTSB (38.35±4.3 ng/mL) and CysC (703.96±23.6 ng/mL) levels were significantly higher in the sera of the patients than in controls. A significant correlation was observed between CTSB and CysC (r=0.754, P<0.001). The levels of CTSB and CysC/CTSB in the patient serum significantly correlated with the T status. CysC/CTSB ratio was also found to be significantly correlated with lymph node metastasis. None of the parameters were observed to be related to CysC, including age, gender, pathologic type, tumor differentiation and tumor invasion depth. Kaplan-Meier analysis showed that patients with higher levels of CysC/CTSB and negative lymph node metastasis experienced significantly longer overall survival time, whereas patients with higher CSTB levels tended to live shorter, although the difference was not statistically significant (P=0.081).

CONCLUSION

Serum CTSB and CysC levels are of diagnostic significance in esophageal cancer. The ratio of serum CysC/CTSB is prognostic for the survival of esophageal carcinoma patients.

High-performance and compact-designed flexible thermoelectric modules enabled by a reticulate carbon nanotube architecture

It is a great challenge to substantially improve the practical performance of flexible thermoelectric modules due to the absence of air-stable n-type thermoelectric materials with high-power factor. Here an excellent flexible n-type thermoelectric film is developed, which can be conveniently and rapidly prepared based on the as-grown carbon nanotube continuous networks with high conductivity. The optimum n-type film exhibits ultrahigh power factor of ∼1,500 μW m⁻¹ K⁻² and outstanding stability in air without encapsulation. Inspired by the findings, we design and successfully fabricate the compact-configuration flexible TE modules, which own great advantages compared with the conventional π-type configuration modules and well integrate the superior thermoelectric properties of p-type and n-type carbon nanotube films resulting in a markedly high performance. Moreover, the research results are highly scalable and also open opportunities for the large-scale production of flexible thermoelectric modules.

Thermoelectric modules can generate electricity directly from heat and have applications to waste heat-energy conversion. Here Zhou et al. have fabricated a thermoelectric module based on an air-stable n-type single-walled carbon nanotube sheet which can reach a high power factor of 1500 μWm⁻¹K⁻².

miR-202 Promotes Cell Apoptosis in Esophageal Squamous Cell Carcinoma by Targeting HSF2

Esophageal squamous cell carcinoma (ESCC) is one of the most common malignant cancers with high mortality around the world. However, the regulatory mechanism of ESCC carcinogenesis is not completely known. Here we demonstrate the novel role of miR-202 in regulating ESCC cell apoptosis. The analysis of data obtained from the GEO database showed that the expression of miR-202 is aberrantly decreased in tumor tissue from ESCC patients and cultured ESCC cell lines. After transfection with miR-202 mimic or inhibitor, the apoptotic capacity of ESCC cells was significantly increased by miR-202 overexpression but reduced by miR-202 repression. We then identified HSF2 as a direct target of miR-202 with the binding site on the 3′-UTR of HSF2 mRNA in ESCC cells. The apoptosis of ESCC cells induced by the miR-202 mimic could be repressed by HSF2 overexpression. Further studies indicated that HSF2 overexpression strongly upregulated the expression of Hsp70 at both the mRNA and protein levels. In addition, HSF2/Hsp70 suppressed ESCC cell apoptosis by preventing caspase 3 activation. In conclusion, miR-202 is a potential tumor suppressor in human ESCC and acts by regulating the apoptosis of ESCC cells by targeting HSF2, in which caspase 3 activation is involved. This might provide a novel therapeutic target for human ESCC.

Hydro-actuation of hybrid carbon nanotube yarn muscles

Hybrid hydro-responsive actuators are developed by infiltrating carbon nanotube yarns using poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate). These actuators demonstrate impressive rotation and contraction in response to water due to volumetric expansion of the helical arrangement of carbon nanotubes. The total torsional stroke is 3720 revolutions per m and the simultaneously generated contractive strain reaches 24% at a paddle-to-yarn mass ratio of 350. The contraction output can furthermore be significantly enhanced by constraining the rotational motion and it reaches 68% with an applied stress of 1 MPa. Additionally, hybrid yarns exhibit an approximately linear response to humidity changes and show extra capability of electrical actuation, which, combined with the excellent hydro-actuation performance, endow them with great potential for a variety of applications including artificial muscles, hydro-driven generators, moisture switches and microfluidic mixers.

Spontaneous neuronal activity in insula predicts symptom severity of unmedicated obsessive compulsive disorder adults

Emerging evidence has suggested that the pathophysiology of obsessive compulsive disorder (OCD) might involve widely distributed large-scale brain systems. The dysfunction within salience network, which is comprised of dorsal anterior cingulated cortex (dACC) and bilateral insular areas, has been proposed to contribute to OCD onset. The mechanism underlying salience network abnormality remains unclear and it is worthwhile to investigate its clinical relevance using functional neuroimaging approaches. In this study, we performed the spontaneous brain activity measurement using resting-state functional magnetic resonance imaging (fMRI) on unmedicated OCD patients (n=23). Specifically, the amplitude of low frequency (0.01-0.08 Hz) fluctuations (ALFF) was calculated for regions in salience network. The voxel-based Pearson's correlative analysis was conducted to explore the relationship beween ALFF measures and symptom severity for OCD patients. The results showed that the spontaneous neuronal activity in insula was significantly correlated to OCD clinical symptoms, especially compulsive behaviors. Our findings consolidated that the salience network played an important role in the pathogenesis of OCD and the intensity of intrinsic brain activity in insula provided a predictive biomarker for OCD symptom severity.

Ultrahigh-Power-Factor Carbon Nanotubes and an Ingenious Strategy for Thermoelectric Performance Evaluation

An ingenious strategy is put forward to evaluate accurately the thermoelectric performance of carbon nanotube (CNT) thin films, including thermal conductivity, electrical conductivity, and Seebeck coefficient in the same direction. The results reveal that the as-prepared CNT interconnected films and CNT fibers possess enormous potential of thermoelectric applications because of their ultrahigh power factors.

Icotinib in Patients with Pretreated Advanced Esophageal Squamous Cell Carcinoma with EGFR Overexpression or EGFR Gene Amplification: A Single-Arm, Multicenter Phase 2 Study

INTRODUCTION

Epidermal growth factor receptor (EGFR) has been reported to be overexpressed and amplified in a high percentage of patients with esophageal squamous cell carcinoma (ESCC). The activity of icotinib, an EGFR tyrosine kinase inhibitor, was assessed in previously treated ESCC with EGFR overexpression or amplification.

METHODS

For this phase 2, single-arm, multicenter trial undertaken at six hospitals in China, we included Chinese patients with previously treated, histologically confirmed advanced ESCC and EGFR overexpression (immunohistochemical staining sore of 3+) or amplification (positive fluorescence in situ hybridization result). These patients received oral icotinib (250 mg, three times daily).The primary end point was the proportion of patients with objective responses as assessed by an independent radiology review committee.

RESULTS

Between December 5, 2013, and May 28, 2015, a total of 281 patients were screened. Fifty-four eligible patients were enrolled. Nine responses were observed, including one complete response and eight partial responses, and 16 patients had stable disease, resulting in a 16.7% objective response rate (95% confidence interval [CI]: 6.7-26.6) and 46.3% disease control rate (95% CI: 33.0-59.6). The median progression-free survival and overall survival times were 52 (95% CI: 40-95) days and 153 (95% CI: 139-218) days, respectively. A total of 43 patients experienced at least one adverse event, but most were only grade 1 to 2 in severity. The most frequent was rash (48.1%), followed by diarrhea (22.2%).

CONCLUSIONS

Icotinib showed favorable activity in patients with advanced, previously treated ESCC with EGFR overexpression or amplification. These findings suggest further research into EGFR overexpression or amplification for selecting responsive patients.

Optimal regimen of trastuzumab in combination with oxaliplatin/ capecitabine in first-line treatment of HER2-positive advanced gastric cancer (CGOG1001): a multicenter, phase II trial

Background

The ToGA study showed that trastuzumab plus chemotherapy prolonged median survival in patients with human epidermal growth factor receptor 2 (HER2)-positive advanced gastric cancer. Among chemotherapy options, oxaliplatin might be as effective as cisplatin but has shown to be more tolerable. To further improve treatment options for patients with advanced gastric cancer, we initiated a study to evaluate the efficacy and safety of trastuzumab plus oxaliplatin/capecitabine in patients with HER2-positive advanced gastric cancer.

Methods

CGOG1001 was an open-label, multicenter, prospective phase II study. Patients with chemotherapy-naive HER2-positive advanced gastric cancer were eligible. Trastuzumab was administered at a loading dose of 8 mg/kg followed by 6 mg/kg infusion every 3 weeks (q3w). Oxaliplatin was administrated as a 130 mg/m² infusion, q3w, for up to 6 cycles. Capecitabine 1000 mg/m² was given orally twice daily on days 1–14 followed by a 7-day rest interval. Trastuzumab and capecitabine were continued until disease progression or intolerable toxicity. The primary endpoint was objective response rate. Simon two-stage design (H₀ = 40 %, H₁ = 60 %, α = 0.05, β = 0.2) by Response Evaluation Criteria In Solid Tumors 1.0 was applied.

Results

Fifty-one patients were enrolled. Confirmed response was recorded in 46 patients. One patient achieved complete response and 33 patients achieved partial response (response rate 34/51 [66.7 %] in the intent-to-treat population). Median follow-up time was 28.6 months, with a median progression-free survival of 9.2 months (95 % confidence interval [CI]: 6.5–11.6) and a median overall survival (OS) of 19.5 months (95 % CI: 15.5–26.0). Patients with a HER2/CEP17 ratio of greater than five achieved improved OS (20.9 vs 19.5 months, p = 0.001). The most common adverse events of grade 3 or above were thrombocytopenia (21.6 %), neutropenia (13.7 %), anemia (5.9 %) and leucopenia (3.9 %).

Conclusion

The addition of trastuzumab to oxaliplatin/capecitabine was well tolerated and the results demonstrated encouraging efficacy.

Trial registration

ClinicalTrials.gov NCT01364493.

miR-367 promotes proliferation and invasion of hepatocellular carcinoma cells by negatively regulating PTEN

MicroRNAs play important roles in the carcinogenesis of many types of cancers by inhibiting gene expression at posttranscriptional level. However, the roles of microRNAs in hepatocellular carcinoma, are still unclear. Here, we identified that miR-367 promotes hepatocellular carcinoma (HCC) cell proliferation by negatively regulates its target gene PTEN. The expression of miR-367 and PTEN are significantly inverse correlated in 35 HCC patients. In HCC cell line, CCK-8 proliferation assay indicated that the cell proliferation was promoted by miR-367, while miR-367 inhibitor significantly inhibited the cell proliferation. Transwell assay showed that miR-367 mimics significantly promoted the migration and invasion of HCC cells, whereas miR-367 inhibitors significantly reduced cell migration and invasion. Luciferase assays confirmed that miR-367 directly bound to the 3'untranslated region of PTEN, and western blotting showed that miR-367 suppressed the expression of PTEN at the protein levels. This study indicated that miR-367 negatively regulates PTEN and promotes proliferation and invasion of HCC cells. Thus, miR-367 may represent a potential therapeutic target for HCC intervention.

RKIP suppresses the proliferation and invasion ofchoriocarcinoma cells through inhibiting the MAPK signaling pathway

Raf kinase inhibitor protein (RKIP), an inhibitor of Raf-mediated activation of mitogen-activated protein/extracellular signal-regulated kinase kinase (MEK), has been identified as a metastasis suppressor gene. However, the role of RKIP in human choriocarcinoma remains undetermined. Therefore, in the present study, we investigated the expression of RKIP in human choriocarcinoma cells and evaluated the effects of RKIP on choriocarcinoma cell proliferation and invasion. Our results indicated that RKIP was lowly expressed in human choriocarcinoma cells. Overexpression of RKIP inhibits choriocarcinoma cell proliferation, migration and invasion, promotes the apoptosis of choriocarcinoma cells. Furthermore, overexpression of RKIP significantly inhibited the expression of MEK and ERK phosphorylation in choriocarcinoma cells. Taken together, these data suggest that RKIP suppresses cell proliferation and invasion in choriocarcinoma cells through inhibiting the MAPK signaling pathway, implying that RKIP may serve as a potential molecular target for the treatment of human choriocarcinoma.

Scanning tunneling microscopy study of the possible topological surface states in BiTeCl

Recently, the non-centrosymmetric bismuth tellurohalides such as BiTeCl are being studied as possible candidates for topological insulators. While some photoemission studies showed that BiTeCl is an inversion asymmetric topological insulator, others showed that it is a normal semiconductor with Rashba splitting. Meanwhile, first-principle calculations have failed to confirm the existence of topological surface states in BiTeCl so far. Therefore, the topological nature of BiTeCl requires further investigation. Here we report a low-temperature scanning tunneling microscopy study on the surface states of BiTeCl single crystals. On the tellurium (Te) -terminated surfaces with relatively low defect density, evidence for topological surface states is observed in the quasi-particle interference patterns, both in the anisotropy of the scattering vectors and the fast decay of the interference near the step edges. Meanwhile, on the samples with much higher defect densities, we observed surface states that behave differently. Our results may help to resolve the current controversy on the topological nature of BiTeCl.