MicroRNAs of rat articular cartilage at different developmental stages identified by Solexa sequencing

BACKGROUND

Expression profiles of microRNAs (miRNAs) can shape the repertoire of proteins expressed in development, differentiation and diseases. This study aimed to identify miRNA profile of articular cartilage at different developmental stages in rats.

METHODS

Three small RNA libraries were constructed from the femoral head cartilage of Sprague-Dawley (SD) rats at postnatal day 0, day 21 and day 42 and sequenced by a deep sequencing approach. Then a bioinformatics approach was employed to distinguish genuine miRNAs from small RNAs represented in the mass sequencing data. The expression of indicated miRNAs was determined by stem-loop RT-qPCR to valuate the consistency with Solexa sequencing.

RESULTS

Two hundred and fifty-eight of 310 known miRNA and miRNA* genes were organized into 91 compact clusters. Two hundred and forty-six miRNAs were detected in all three small RNA libraries of rat articular cartilage. Forty-six, fifty-two and fifty-six miRNA* genes were identified from three small RNA libraries, respectively, and 86 novel miRNA candidate genes were found simultaneously. In addition, 23 known miRNAs were up-regulated (fold change ≥ 4); six were down-regulated (fold change ≤ -4) during articular cartilage development. The predicted targets of differentially expressed miRNAs were locally secreted factors and transcription factors that regulate proliferation and differentiation of chondrocytes. The same expression tendency of indicated miRNAs during articular cartilage development stages was observed by using Solexa sequencing and stem-loop RT-qPCR.

CONCLUSION

Our study provided a unique opportunity to decipher how the elaboration of the miRNA repertoire contributes to the development process of articular cartilage.

AUC-based biomarker ensemble with an application on gene scores predicting low bone mineral density

MOTIVATION

The area under the receiver operating characteristic (ROC) curve (AUC), long regarded as a 'golden' measure for the predictiveness of a continuous score, has propelled the need to develop AUC-based predictors. However, the AUC-based ensemble methods are rather scant, largely due to the fact that the associated objective function is neither continuous nor concave. Indeed, there is no reliable numerical algorithm identifying optimal combination of a set of biomarkers to maximize the AUC, especially when the number of biomarkers is large.

RESULTS

We have proposed a novel AUC-based statistical ensemble methods for combining multiple biomarkers to differentiate a binary response of interest. Specifically, we propose to replace the non-continuous and non-convex AUC objective function by a convex surrogate loss function, whose minimizer can be efficiently identified. With the established framework, the lasso and other regularization techniques enable feature selections. Extensive simulations have demonstrated the superiority of the new methods to the existing methods. The proposal has been applied to a gene expression dataset to construct gene expression scores to differentiate elderly women with low bone mineral density (BMD) and those with normal BMD. The AUCs of the resulting scores in the independent test dataset has been satisfactory.

CONCLUSION

Aiming for directly maximizing AUC, the proposed AUC-based ensemble method provides an efficient means of generating a stable combination of multiple biomarkers, which is especially useful under the high-dimensional settings.

CONTACT

lutian@stanford.edu.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

From two-dimensional colloidal self-assembly to three-dimensional nanolithography

A number of "top-down" lithographic and "bottom-up" self-assembly methods have been developed to fabricate three-dimensional (3D) nanostructures to support the recent advances in nanotechnology. But they are limited by a number of factors such as fabrication cost, pattern resolution, and/or flexibility of geometry. Here we present a 3D nanolithography process that utilizes self-assembled nanospheres to create a periodic array of focal spots, which are then replicated across multiple depth in a transparent medium according to the Talbot effect. The Talbot field then exposes a pattern onto the underlying photoresist, recording the 3D intensity distribution. We have demonstrated designable complex 3D periodic structures with 80 nm minimum feature size, roughly one-fourth of the operating wavelength. This approach combines 2D colloidal self-assembly and 3D phase lithography, is robust, cost-effective, and widely applicable to nanoscale research and manufacturing.

The relationship between high density lipoprotein subclass profile and apolipoprotein concentrations

The HDL fraction in human plasma is heterogeneous in terms of size, shape, composition, and surface charge. The HDL subclasses contents were quantified by 2-dimensional non-denaturing gel electrophoresis, immunoblotting, and image analysis. This research review systematically analyzed the relationship between the contents of HDL subclasses and the concentrations and ratios of the 5 major plasma apolipoproteins (apo). As the concentration of apoA-I increases, the contents of all HDL subclasses increase significantly. The most significant association was observed between large-sized HDL2b contents and apoA-I. ApoA-II played a dual function in the contents of HDL subclasses, and both small-sized HDL3b and HDL3a and large-sized HDL2b tended to increase with apoA-II concentration. An increase in the concentrations of apoC-II, C-III, and B-100 resulted in higher levels of small-sized HDL particles and lower levels of large-sized HDL particles. Plasma apoB- 100, apoC-II, and apoC-III appear to play a coordinated role in assembly of HDL particles and the determination of their contents. Higher concentrations of apoA-I could inhibit the reduction in content of large-sized HDL2b effected by apoB-100, C-II, and C-III. The preβ1-HDL contents increased significantly and those of HDL2b declined progressively with an increased apoB-100/apoA-I or a decreased apoC-III/apoC-II ratio. In summary, each apo has distinct but interrelated roles in HDL particle generation and metabolism. ApoA-I and apoC-II concentrations are independent determinants of HDL subtypes in circulation and apoA-I levels might be a more powerful factor to influence HDL subclasses distribution. Moreover, apoB- 100/apoA-I ratio could reliably and sensitively reflect the HDL subclass profile.

The CKLF1-C19 peptide attenuates allergic lung inflammation by inhibiting CCR3- and CCR4-mediated chemotaxis in a mouse model of asthma

BACKGROUND

  Human chemokine-like factor 1 (CKLF1) is a functional ligand for human CCR4, which is highly expressed on Th2 lymphocytes and plays an important role in the pathogenesis of asthma. The expression and function of CKLF1 are associated with asthma. The CKLF1 C-terminal peptides C19 and C27 also interact with human CCR4. Albeit with weaker chemotactic activity, C19 can inhibit chemotaxis induced by both CKLF1 and CCL17. Here, we explore whether C19 can act as an antagonist in the development of asthma.

METHODS

  A mouse model of asthma and in vitro and in vivo chemotaxis assays were used.

RESULTS

  Using a mouse model of asthma, we demonstrate here that C19 reduces airway eosinophilia, lung inflammation and airway hyperresponsiveness; in contrast, C27 has little effect on these parameters. The inhibitory effects of C19 on CCR4-mediated chemotaxis could be observed in human Th2 lymphocytes and in the splenocytes from ovalbumin-sensitized mice. Furthermore, we show that C19 can inhibit CCL11-induced chemotaxis of mouse eosinophils and human CCR3-transfected or mouse Ccr3-transfected HEK293 cells. In vivo chemotaxis assays revealed that C19 and C27 can reduce CCL11-mediated recruitment of eosinophils into the peritoneal cavity and that this inhibitory effect is stronger for C19 than for C27.

CONCLUSIONS

  Thus, C19 can attenuate airway eosinophilia and lung inflammation by inhibiting CCR3- and CCR4-mediated chemotaxis in a mouse model of asthma. Given its ability to inhibit human CCR3- and CCR4-meditated chemotaxis, C19 has great therapeutic potential for use in the treatment and control of allergic asthma.

Abstract P4-09-16: WAVE3 Over-Expression Is Associated with Adverse Tumor Characteristics and Mortality in Breast Cancer

Background: WAVE3 regulates actin polymerization and subsequent cell migration leading to enhanced metastatic potential. Based on pilot data that suggested WAVE3 expression was associated with high histologic grade and absence of estrogen receptor (ER) expression we hypothesized that WAVE3 expression would correlate with ER status and tumor grade in a matched group of breast cancer (BC) patients. WAVE3 expression was alsoanalyzed in relation to adverse tumor characteristics, distant recurrence (DR) and BC specific mortality. Methods: Our institutional BC database was reviewed for patients who presented with, invasive BC from 1999-2009. Matching by stage and treatment was achieved for 61 patients with Scarff-Bloom-Richardson (SBR) grade 1 and ER+ tumors (SBR1/ER+) to 61 patients with SBR grade 3 and ER-tumors (SBR3/ER-). Cytosolic WAVE3 tumor expression was determined by immunohistochemistry. The product of stain intensity (0-3) and percentage of cells staining (0-100) was used to derive a WAVE3 score (0-300). The log rank test was utilized to compare BC specific mortality or distant recurrence free survival at various WAVE3 scores. A score of ≥212 was found to have the strongest association with poor outcome. The association between WAVE3 score and clinicopatholigic features, DR and BC specific mortality was assessed. Results: Increased frequency of Her2-neu (+) status, DR and BC specific mortality was noted in the SBR3/ER-group but WAVE3 score was no different between the two groups(Table1). In all 122 patients median WAVE3 score increased with tumor size (0.234, p=0.009), (+) lymph node status 200 vs. (-), 145, p =0.03, and stage (I, 160 vs. II,180 vs III, 240, p=0.012). There was no association between WAVE3 score and Her2-neu status(+200 vs. -180, p=0.51). In the SBR1/ER+ group only (+) lymph node status remained associated with WAVE3 score(+) 200 vs. (-) 130 (p=0.02). In the SBR3/ER-group only lymph node status lost association with WAVE3 score (+)180 vs.(-)170, (p=0.50). DR and BC specific survival could only be assessed in the SBR3/ER-group. Median WAVE3 score was elevated with DR (240 vs. none, 160, p=0.03) and BC specific mortality (270 vs. none 170, p=0.004). A WAVE3 score ≥212 was associated with distant recurrence and BC specific mortality on Kaplan Meier analysis (p=0.01) and P<0.001). On multivariate analysis a WAVE3 score ≥212 was associated with an increased risk for BC specific mortality (p=0.009). The association of DR and WAVE3 score ≥212 approached significance (p=0.068).

Table 1

Conclusion: WAVE3 expression is not associated with tumor grade, and ER or Her2 neu status. WAVE3 is associated with tumor size, stage, DR and BC specific mortality in the high risk SBR3/ER-group. A WAVE3 score of ≥212 is associated with distant recurrence and breast cancer specific mortality on univariate analysis and BC specific mortality on uni-and multivariate analysis. WAVE3 expression may contribute to adverse outcome in high risk breast cancer patients.

Epigenetic inactivation of T-box transcription factor 5, a novel tumor suppressor gene, is associated with colon cancer

T-box transcription factor 5 (TBX5) is a member of a phylogenetically conserved family of genes involved in the regulation of developmental processes. The function of TBX5 in cancer development is largely unclear. We identified that TBX5 was preferentially methylated in cancer using methylation-sensitive arbitrarily primed PCR. We aim to clarify the epigenetic inactivation, biological function and clinical significance of TBX5 in colon cancer. Promoter methylation was evaluated by combined bisulfite restriction analysis and bisulfite genomic sequencing. Cell proliferation was examined by cell viability assay and colony formation assay, apoptosis by flow cytometry and cell migration by wound-healing assay. TBX5 target genes were identified by cDNA microarray analysis. Cox regression model and log-rank test were used to identify independent predictors of prognosis. TBX5 was silenced or downregulated in 88% (7/8) colon cancer cell lines, but was expressed in normal colon tissues. Loss of gene expression was associated with promoter methylation. The biological function of TBX5 in human colon cancer cells was examined. Re-expression of TBX5 in silenced colon cancer cell lines suppressed colony formation (P<0.001), proliferation (P<0.001), migration and induced apoptosis (P<0.01). Induction of apoptosis was mediated through cross-talk of extrinsic apoptosis pathway, apoptotic BCL2-associated X protein and Granzyme A signaling cascades. TBX5 suppressed tumor cell proliferation and metastasis through the upregulation of cyclin-dependent kinase inhibitor 2A, metastasis suppressor 1 and downregulation of synuclein gamma and metastasis-associated protein 1 family member 2. TBX5 methylation was detected in 68% (71/105) of primary colon tumors. Multivariate analysis showed that patients with TBX5 methylation had a significantly poor overall survival (P=0.0007). In conclusion, we identified a novel functional tumor suppressor gene TBX5 inactivated by promoter methylation in colon cancer. Detection of methylated TBX5 may serve as a potential biomarker for the prognosis of this malignancy.

Genome-wide association identifies SKIV2L and MYRIP as protective factors for age-related macular degeneration

Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly in the developed world. We conducted a genome-wide association study in a series of families enriched for AMD and completed a meta-analysis of this new data with results from reanalysis of an existing study of a late-stage case-control cohort. We tested the top findings for replication in 1896 cases and 1866 controls and identified two novel genetic protective factors for AMD. In addition to the complement factor H (CFH) (P=2.3 × 10⁻⁶⁴) and age-related maculopathy susceptibility 2 (ARMS2) (P=1.2 × 10⁻⁶⁰) loci, we observed a protective effect at rs429608, an intronic SNP in SKIV2L (P=5.3 × 10⁻¹⁵), a gene near the complement component 2 (C2)/complement factor B (BF) locus, that indicates the protective effect may be mediated by variants other than the C2/BF variants previously studied. Haplotype analysis at this locus identified three protective haplotypes defined by the rs429608 protective allele. We also identified a new potentially protective effect at rs2679798 in MYRIP (P=2.9 × 10⁻⁴), a gene involved in retinal pigment epithelium melanosome trafficking. Interestingly, MYRIP was initially identified in the family-based scan and was confirmed in the case-control set. From these efforts, we report the identification of two novel protective factors for AMD and confirm the previously known associations at CFH, ARMS2 and C3.

Circuit QED and sudden phase switching in a superconducting qubit array

Superconducting qubits connected in an array can form quantum many-body systems such as the quantum Ising model. By coupling the qubits to a superconducting resonator, the combined system forms a circuit QED system. Here, we study the nonlinear behavior in the many-body state of the qubit array using a semiclassical approach. We show that sudden switchings as well as a bistable regime between the ferromagnetic phase and the paramagnetic phase can be observed in the qubit array. A superconducting circuit to implement this system is presented with realistic parameters.

Association of the CD226 single nucleotide polymorphism with systemic lupus erythematosus in the Chinese Han population

A novel non-synonymous (Gly307Ser) variant, rs763361, of the CD226 gene on chromosome 18q22 was recently shown to be associated with multiple autoimmune diseases. Taking into consideration that different autoimmune diseases may share some common pathogenic pathways, in this study we performed case-control studies to assess any genetic linkage with systemic lupus erythemtosus (SLE). An association between the Gly307Ser single nucleotide polymorphism (SNP) and susceptibility to SLE was identified. The TT genotype [odds ratio (OR) = 1.79, 95% confidence interval (CI) = 1.07-3.01, P = 0.025] and the T allele (OR = 1.34, 95% CI = 1.05-1.74, P = 0.018) of the rs763361 SNP were associated with the risk of SLE. This finding indicates that polymorphism of Gly307Ser (rs763361) in exon 7 of the CD226 gene may be associated with the development of SLE.

Growth suppression of human laryngeal squamous cell carcinoma by adenoviral-mediated interleukin-12

This study explored the inhibitory role of the adenoviral-mediated-interleukin (IL)-12 (Ad.mIL-12) gene in the growth of laryngeal squamous cell carcinoma (LSCC). Human epithelial type 2 (Hep-2) cells were transfected with Ad.mIL-12, and IL-12 gene expression of the cells was evaluated. The proliferation and apoptosis of Hep-2 cells in vitro were detected by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay and flow cytometry. Experimental tumours in mice were injected intratumourally with the same recombinant adenoviruses and inhibition of tumour growth observed. Apoptosis in Hep-2 xenotransplants was detected using TUNEL (terminal deoxynucleotidyl transferase dUTP nick-end labelling) assay and transmission electron microscopy. The expression of IL-12 in Ad.mIL-12 transfected Hep-2 cells was significantly increased. In vitro, Ad.mIL-12 decreased the viability of and increased apoptosis in Hep-2 cells. Increased apoptosis was also seen in vivo. The mean weight and volume of tumours in Ad.mIL-12 treated mice were significantly lower than in the control group. It is concluded that Ad.mIL-12 can suppress LSCC growth and induce apoptosis.

Epigenetic inactivation of T-box transcription factor 5, a novel tumor suppressor gene, is associated with colon cancer

T-box transcription factor 5 (TBX5) is a member of a phylogenetically conserved family of genes involved in the regulation of developmental processes. The function of TBX5 in cancer development is largely unclear. We identified that TBX5 was preferentially methylated in cancer using methylation-sensitive arbitrarily primed PCR. We aim to clarify the epigenetic inactivation, biological function and clinical significance of TBX5 in colon cancer. Promoter methylation was evaluated by combined bisulfite restriction analysis and bisulfite genomic sequencing. Cell proliferation was examined by cell viability assay and colony formation assay, apoptosis by flow cytometry and cell migration by wound-healing assay. TBX5 target genes were identified by cDNA microarray analysis. Cox regression model and log-rank test were used to identify independent predictors of prognosis. TBX5 was silenced or downregulated in 88% (7/8) colon cancer cell lines, but was expressed in normal colon tissues. Loss of gene expression was associated with promoter methylation. The biological function of TBX5 in human colon cancer cells was examined. Re-expression of TBX5 in silenced colon cancer cell lines suppressed colony formation (P<0.001), proliferation (P<0.001), migration and induced apoptosis (P<0.01). Induction of apoptosis was mediated through cross-talk of extrinsic apoptosis pathway, apoptotic BCL2-associated X protein and Granzyme A signaling cascades. TBX5 suppressed tumor cell proliferation and metastasis through the upregulation of cyclin-dependent kinase inhibitor 2A, metastasis suppressor 1 and downregulation of synuclein gamma and metastasis-associated protein 1 family member 2. TBX5 methylation was detected in 68% (71/105) of primary colon tumors. Multivariate analysis showed that patients with TBX5 methylation had a significantly poor overall survival (P=0.0007). In conclusion, we identified a novel functional tumor suppressor gene TBX5 inactivated by promoter methylation in colon cancer. Detection of methylated TBX5 may serve as a potential biomarker for the prognosis of this malignancy.

Essential roles of Jab1 in cell survival, spontaneous DNA damage and DNA repair

Jun activation domain-binding protein 1 (JAB1) is a multifunctional protein that participates in the control of cell proliferation and the stability of multiple proteins. JAB1 overexpression has been implicated in the pathogenesis of human cancer. JAB1 regulates several key proteins and thereby produces varied effects on cell cycle progression, genome stability and cell survival. However, the biological significance of JAB1 activity in these cellular signaling pathways is unclear. Therefore, we developed mice that were deficient in Jab1 and analyzed the null embryos and heterozygous cells. This disruption of Jab1 in mice resulted in early embryonic lethality due to accelerated apoptosis. Loss of Jab1 expression sensitized both mouse primary embryonic fibroblasts and osteosarcoma cells to γ-radiation-induced apoptosis, with an increase in spontaneous DNA damage and homologous recombination (HR) defects, both of which correlated with reduced levels of the DNA repair protein Rad51 and elevated levels of p53. Furthermore, the accumulated p53 directly binds to Rad51 promoter, inhibits its activity and represents a major mechanism underlying the HR repair defect in Jab1-deficient cells. These results indicate that Jab1 is essential for efficient DNA repair and mechanistically link Jab1 to the maintenance of genome integrity and to cell survival.

A systematic comparison between collagen-induced arthritis and pristane-induced arthritis in Dark Agouti rats

OBJECTIVES

Both collagen-induced arthritis (CIA) and pristane-induced arthritis (PIA) are commonly used rat models of rheumatoid arthritis (RA). The aim of this study was systematically to compare the differences between CIA and PIA in Dark Agouti (DA) rats.

METHODS

The CIA was induced by immunising DA rats intradermally with collagen type (C) and PIA was induced by injecting subcutaneously with pristane. The arthritis was evaluated macroscopically and microscopically. Nitric oxide (NO) level of plasma was determined by Griess reaction method. Plasma autoimmune antibodies, including C specific IgG antibody (anti-C IgG), cyclic citrullinated peptide specific IgG antibody (anti-CCP IgG), IgM and IgG rheumatoid factors (IgM RF and IgG RF), were detected by the enzyme-linked immunosorbent assay.

RESULTS

The onset of PIA rats was earlier than that of CIA rats. The involved sites of PIA rats were mostly wrist/ankle and metacarpophalangeal/metatarsophalangeal (MCP/MTP) joints while those of CIA rats were primarily distal interphalangeal (DIP) joints. NO level of plasma was increased in PIA rats, as anti-C IgG, anti-CCP IgG, IgM RF and IgG RF levels of plasma were increased in CIA rats. The kidney hyaline casts were more frequent in CIA rats than in control rats, with 9/12 in PIA group, 8/8 in CIA, and 4/8 in control, respectively.

CONCLUSIONS

PIA mainly affected wrist/ankle joints and MCP/MTP joints, had more severe inflammation and hardly involved other organs; while CIA mostly influenced DIP joints, had more autoimmune antibodies in plasma, and always showed hyaline casts in kidney. These findings will be useful to select the animal model of RA.

Calibrating parametric subject-specific risk estimation

For modern evidence-based medicine, decisions on disease prevention or management strategies are often guided by a risk index system. For each individual, the system uses his/her baseline information to estimate the risk of experiencing a future disease-related clinical event. Such a risk scoring scheme is usually derived from an overly simplified parametric model. To validate a model-based procedure, one may perform a standard global evaluation via, for instance, a receiver operating characteristic analysis. In this article, we propose a method to calibrate the risk index system at a subject level. Specifically, we developed point and interval estimation procedures for t-year mortality rates conditional on the estimated parametric risk score. The proposals are illustrated with a dataset from a large clinical trial with post-myocardial infarction patients.