Cellular response of inorganic nanoparticles
(NPs) is strongly
dependent on their surface chemistry. By taking advantage of robust
single-particle fluorescence and giant Raman enhancements of unique
polycrystalline silver NPs (AgNPs), we quantitatively investigated
effects of two well-known surface chemistries, passive PEGylation
and active c-RGD peptide conjugation, on in vitro behaviors of AgNPs at high temporal and spatial resolution as well
as chemical level using fluorescence and Raman microscopy. The results
show that specific c-RGD peptide−αvβ3 integrin interactions not only induced endosome formation
more rapidly, enhanced constrained diffusion, but also minimized nonspecific
chemical interactions between the NPs and intracellular biomolecules
than passive PEGylation chemistry; as a result, surface enhanced Raman
scattering (SERS) signals of c-RGD peptides were well resolved inside
endosomes in the live cells, while Raman signals of PEGylated AgNPs
remained unresolvable due to interference of surrounding biomolecules,
opening up an opportunity to investigate specific ligand–receptor
interactions in real time at the chemical level.
Fundamental understanding of ion channel formation by amyloid peptides, which is strongly linked to cell toxicity, is very critical for (pre)clinical treatment of neurodegenerative diseases. Here, we combine atomistic simulations and experiments to demonstrate a broad range of conformational states of hIAPP double channels in lipid membranes. All individual channels display high selectivity of Cl− ions over cations, but the co-existence of polymorphic double channels of different conformations and orientations with different populations determines the non-ionic selectivity nature of the channels, which is different from the typical amyloid-β channels that exhibit Ca2+ selective ion-permeable characteristics. This work provides a more complete physicochemical mechanism of amyloid-channel-induced toxicity.
Amylin; Amyloid channels; Ion selectivity; Ion permeability; Amyloid diseases; Molecular dynamics
Evidence has shown that psoriasis is closely associated with infection; however, the mechanism of this association remains unclear. In mammalian cells, viral or bacterial infection is accompanied by the release of cytosolic DNA, which in turn triggers the production of type-I interferons (IFNs). Type I IFNs and their associated genes are significantly upregulated in psoriatic lesions. RIG-I is also highly upregulated in psoriatic lesions and is responsible for IFN production. However, RIG-I mediated regulatory signaling in psoriasis is poorly understood.
We screened a cDNA library and identified potential RIG-I interacting partners that may play a role in psoriasis.
We found that serine/arginine-rich splicing factor 1 (SRSF1) could specifically interact with RIG-I to facilitate RIG-I mediated production of type-I IFN that is triggered by cytosolic DNA. We found SRSF1 associates with RNA polymerase III and RIG-I in a DNA-dependent manner. In addition, treatment with a TNFα inhibitor downregulated SRSF1 expression in peripheral blood mononuclear cells (PBMCs) from psoriasis vulgaris patients.
Based on the abundance of pathogenic cytosolic DNA that is detected in psoriatic lesions, our finding that RIG-I interacts with SRSF1 to regulate type-I IFN production reveals a critical link regarding how cytosolic DNA specifically activates aberrant IFN expression. These data may provide new therapeutic targets for the treatment of psoriasis.
Mechanical forces play an important role in the rupture of vulnerable plaques. This process is often associated with cardiovascular syndromes, such as heart attack and stroke. In this study, magnetic resonance imaging (MRI)-based models were used to investigate the association between plaque wall stress (PWS) and coronary artery disease (CAD).
Ex vivo MRI data of coronary plaques from 12 patients were used to construct 12 three-dimensional (3D) fluid-structure interaction (FSI) computational models. Six of the patients had died from CAD and six had died from non-CAD causes. PWS was assessed using all nodal points on the lumen surface of each plaque. The maximum PWS from all possible vulnerable sites of each plaque was defined as the 3D critical plaque wall stress (CPWS).
Mean 3D CPWS in the CAD group was 94.3% higher than that in the non-CAD group (265.6 vs. 136.7 kPa, P=0.0029). There was no statistically significant difference in global maximum plaque wall stress (GMPWS) between the two groups (P=0.347). There was also no statistically significant difference in plaque burden between the CAD group (84.4 ± 5%) and the non-CAD group (82.0 ± 8%, P=0.552). The results indicate that plaques from patients who died from CAD were associated with higher CPWS compared with those from patients who died from non-CAD causes. With further validation, analysis of CPWS may prove to be an important component in assessment of plaque vulnerability.
coronary artery disease; fluid structure interactions; magnetic resonance imaging; vulnerable plaque; stress
In literature, the effect of the inflow boundary condition was investigated by examining the impact of the waveform and the shape of the spatial profile of the inlet velocity on the cardiac hemodynamics. However, not much work has been reported on comparing the effect of the different combinations of the inlet/outlet boundary conditions on the quantification of the pressure field and flow distribution patterns in stenotic right coronary arteries.
Non-Newtonian models were used to simulate blood flow in a patient-specific stenotic right coronary artery and investigate the influence of different boundary conditions on the phasic variation and the spatial distribution patterns of blood flow. The 3D geometry of a diseased artery segment was reconstructed from a series of IVUS slices. Five different combinations of the inlet and the outlet boundary conditions were tested and compared.
The temporal distribution patterns and the magnitudes of the velocity, the wall shear stress (WSS), the pressure, the pressure drop (PD), and the spatial gradient of wall pressure (WPG) were different when boundary conditions were imposed using different pressure/velocity combinations at inlet/outlet. The maximum velocity magnitude in a cardiac cycle at the center of the inlet from models with imposed inlet pressure conditions was about 29% lower than that from models using fully developed inlet velocity data. Due to the fact that models with imposed pressure conditions led to blunt velocity profile, the maximum wall shear stress at inlet in a cardiac cycle from models with imposed inlet pressure conditions was about 29% higher than that from models with imposed inlet velocity boundary conditions. When the inlet boundary was imposed by a velocity waveform, the models with different outlet boundary conditions resulted in different temporal distribution patterns and magnitudes of the phasic variation of pressure. On the other hand, the type of different boundary conditions imposed at the inlet and the outlet did not have significant effect on the spatial distribution patterns of the PD, the WPG and the WSS on the lumen surface, regarding the locations of the maximum and the minimum of each quantity.
The observations from this study indicated that the ways how pressure and velocity boundary conditions are imposed in computational models have considerable impact on flow velocity and shear stress predictions. Accuracy of in vivo measurements of blood pressure and velocity is of great importance for reliable model predictions.
Recently, tomatoes have been implicated as a primary vehicle in food-borne outbreaks of Salmonella enterica serovar Newport and other Salmonella serovars. Long-term intervention measures to reduce Salmonella prevalence on tomatoes remain elusive for growing and postharvest environments. A naturally occurring bacterium identified by 16S rRNA gene sequencing as Paenibacillus alvei was isolated epiphytically from plants native to the Virginia Eastern Shore tomato-growing region. After initial antimicrobial activity screening against Salmonella and 10 other bacterial pathogens associated with the human food supply, strain TS-15 was further used to challenge an attenuated strain of S. Newport on inoculated fruits, leaves, and blossoms of tomato plants in an insect-screened high tunnel with a split-plot design. Survival of Salmonella after inoculation was measured for groups with and those without the antagonist at days 0, 1, 2, and 3 and either day 5 for blossoms or day 6 for fruits and leaves. Strain TS-15 exhibited broad-range antimicrobial activity against both major food-borne pathogens and major bacterial phytopathogens of tomato. After P. alvei strain TS-15 was applied onto the fruits, leaves, and blossoms of tomato plants, the concentration of S. Newport declined significantly (P ≤ 0.05) compared with controls. Astonishingly, >90% of the plants had no detectable levels of Salmonella by day 5 for blossoms. The naturally occurring antagonist strain TS-15 is highly effective in reducing the carriage of Salmonella Newport on whole tomato plants. The application of P. alvei strain TS-15 is a promising approach for reducing the risk of Salmonella contamination during tomato production.
β-catenin plays essential roles in cell adhesion and Wnt signaling, while deregulation of β-catenin is associated with multiple diseases including cancers. Here, we report the crystal structures of full-length zebrafish β-catenin and a human β-catenin fragment that contains both the armadillo repeat and the C-terminal domains. Our structures reveal that the N-terminal region of the C-terminal domain, a key component of the C-terminal transactivation domain, forms a long α helix that packs on the C-terminal end of the armadillo repeat domain, and thus forms part of the β-catenin superhelical core. The existence of this helix redefines our view of interactions of β-catenin with some of its critical partners, including ICAT and Chibby, which may form extensive interactions with this C-terminal domain α helix. Our crystallographic and NMR studies also suggest that the unstructured N-terminal and C-terminal tails interact with the ordered armadillo repeat domain in a dynamic and variable manner.
Dermal IL-17-producing γδT cells play a critical role in skin inflammation. However, their development and peripheral regulation have not been fully elucidated. Here we demonstrate that dermal γδT cells develop from the embryonic thymus and undergo homeostatic proliferation after birth with diversified TCR repertoire. Vγ6T cells are bona fide resident but precursors of dermal Vγ4T cells may require extrathymic environment for imprinting skin homing properties. Thymic Vγ6T cells are more competitive than Vγ4 for dermal γδT cell reconstitution and TCRδ−/− mice reconstituted with Vγ6 develop psoriasis-like inflammation after IMQ-application. Although both IL-23 and IL-1β promote Vγ4 and Vγ6 proliferation, Vγ4 are the main source of IL-17 production, which requires IL-1 signaling. Mice with deficiency of IL-1RI signaling have significantly decreased skin inflammation. These studies reveal a differential developmental requirement and peripheral regulation for dermal Vγ6 and Vγ4 γδT cells, implying a new mechanism that may be involved in skin inflammation.
Non-B cell immunoglobulins (Igs) are widely expressed in epithelial cancer cells. The past 20 years of research have demonstrated that non-B cell Igs are associated with cancer cell proliferation, the cellular cytoskeleton and cancer stem cells. In this study we explored the transcriptional mechanism of IgM production in non-B cells.
The promoter region of a V-segment of the heavy mu chain gene (VH6-1) was cloned from a colon cancer cell line HT-29. Next, the promoter activities in non-B cells and B-cells were detected using the dual-luciferase reporter assay. Then the transcription factor binding to the promoter regions was evaluated by electrophoretic mobility shift assays (EMSAs) and gel supershift experiments.
Our data showed that the sequence 1200 bp upstream of VH6-1 exhibited promoter activity in both B and non-B cells. No new regulatory elements were identified within the region 1200 bp to 300 bp upstream of VH6-1. In addition, Oct-1 was found to bind to the octamer element of the Ig gene promoter in cancer cells, in contrast to B cells, which utilize the transcriptional factor Oct-2.
The regulatory mechanisms among different cell types controlling the production of IgM heavy chains are worth discussing.
VH6-1; Promoter activity; Oct-1; Transcriptional regulation; Non-B cells
Tumor targeting; Renal clearance; Luminescent gold nanoparticle; PEGylation; Zwitterionization
Breast cancer is the most common type of malignancy among females. Previous studies examining breast cancer tissue have demonstrated the presence of stem cells, and have detected octamer-binding protein 4 (Oct4) and Nanog transcription factor expression. In the present study, breast cancer stem cells (CSCs) were isolated and enriched from MDA-MB-231 breast cancer cell lines, and were defined as MDA-MB-231 stem cells using flow cytometry. The expression of Oct4 and Nanog in breast CSCs were detected by quantitative polymerase chain reaction and western blotting. RNA interference (RNAi) was used in order to downregulate the expression of Oct4 and Nanog. Drug resistance and tumor-initiating capability following in vivo injection of MDA-MB-231 stem cells transduced with negative RNAi, Oct4 RNAi and Nanog RNAi were compared with that of MDA-MB-231 stem cells without siRNA transfection as a control group. In addition the capability of MDA-MB-231 breast cancer cells to initiate tumor formation in mice was compared with that of MDA-MB-231 stem cells. A paclitaxel inhibition test was also conducted in order to detect resistance of MDA-MB-231 breast cancer stem cells to this treatment. The MDA-MB-231 stem cells were revealed to exhibit elevated percentages of the cluster of differentiation (CD)44+CD24−/low subset, high tumorigenicity and resistance to chemotherapy, all of which are characteristic stem cell properties. In addition, the MDA-MB-231 stem cells were more tumorigenic in vivo. Furthermore, the breast CSCs also expressed high levels of the Oct4 and Nanog transcription factors. Therefore, downregulation of Oct4 or Nanog expression may reduce chemotherapeutic drug resistance and tumorigenicity in breast CSCs. In conclusion, Oct4 and Nanog expression may be a key factor in the development of resistance to chemotherapy and tumor growth of breast CSCs. This finding indicates that Oct4 or Nanog-targeted therapy may be a promising means of overcoming resistance to chemotherapy and inhibiting tumor growth in breast cancer treatment.
breast cancer stem cells; isolation and identification; octamer-binding protein 4; Nanog; tumorigenicity; drug resistance
Objective: To investigate the causes and managements of early postoperative complications of degenerative scoliosis (DS) treated with internal pedicle screw fixation. Methods: From Jan 2000 to Apr 2013, 325 DS patients treated with internal pedicle screw fixation in our hospital were retrospectively involved. The categories, causes, managements and outcomes of early postoperative complications were statistically analyzed. Results: Early postoperative complications occurred in 10.76% of the patients including 16 cases of lower limb numb or pain, 6 cases of decreased lower limb sensitivity and motor functions, which accounted for 62.86% of all complications, followed by incision infections (4/35, 11.43%) and rare cases of cerebrospinal fluid leakage, cardiac and renal inadequacy, urinary system and pulmonary infections. The incidence of overall complications (19.79%, p = 0.001) and nerve injuries (11.46%, p = 0.000) were significantly higher in long-segment than in short-segment fixations. Improper screw implanting, over correction of scoliosis and insufficient blood supply of the spinal cord during operation were risk factors for early postoperative complications and most of them were cured by anti-infection medication, incision dressing change, nerve nourishment, adjusting the screws and anti-osteoporosis treatments within 6 months after surgery. Only three cases with severe nerve injury did not improve until the 6 months postoperative follow-up. Conclusions: Most of the postoperative complications in our DS patients disappeared within 6 months after surgery and more than half of complications were nerve injuries.
Degenerative scoliosis; internal fixation; postoperative complications
Over the course of its intraerythrocytic developmental cycle (IDC), the malaria parasite Plasmodium falciparum tightly orchestrates the rise and fall of transcript levels for hundreds of genes. Considerable debate has focused on the relative importance of transcriptional versus post-transcriptional processes in the regulation of transcript levels. Enzymatically active forms of RNAPII in other organisms have been associated with phosphorylation on the serines at positions 2 and 5 of the heptad repeats within the C-terminal domain (CTD) of RNAPII. We reasoned that insight into the contribution of transcriptional mechanisms to gene expression in P. falciparum could be obtained by comparing the presence of enzymatically active forms of RNAPII at multiple genes with the abundance of their associated transcripts.
We exploited the phosphorylation state of the CTD to detect enzymatically active forms of RNAPII at most P. falciparum genes across the IDC. We raised highly specific monoclonal antibodies against three forms of the parasite CTD, namely unphosphorylated, Ser5-P and Ser2/5-P, and used these in ChIP-on-chip type experiments to map the genome-wide occupancy of RNAPII. Our data reveal that the IDC is divided into early and late phases of RNAPII occupancy evident from simple bi-phasic RNAPII binding profiles. By comparison to mRNA abundance, we identified sub-sets of genes with high occupancy by enzymatically active forms of RNAPII and relatively low transcript levels and vice versa. We further show that the presence of active and repressive histone modifications correlates with RNAPII occupancy over the IDC.
The simple early/late occupancy by RNAPII cannot account for the complex dynamics of mRNA accumulation over the IDC, suggesting a major role for mechanisms acting downstream of RNAPII occupancy in the control of gene expression in this parasite.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-959) contains supplementary material, which is available to authorized users.
A major goal in cancer medicine is to find selective drugs with reduced side effect. A pair of genes is called synthetic lethality (SL) if mutations of both genes will kill a cell while mutation of either gene alone will not. Hence, a gene in SL interactions with a cancer-specific mutated gene will be a promising drug target with anti-cancer selectivity. Wet-lab screening approach is still so costly that even for yeast only a small fraction of gene pairs has been covered. Computational methods are therefore important for large-scale discovery of SL interactions. Most existing approaches focus on individual features or machine-learning methods, which are prone to noise or overfitting. In this paper, we propose an approach named MetaSL for predicting yeast SL, which integrates 17 genomic and proteomic features and the outputs of 10 classification methods. MetaSL thus combines the strengths of existing methods and achieves the highest area under the Receiver Operating Characteristics (ROC) curve (AUC) of 87.1% among all competitors on yeast data. Moreover, through orthologous mapping from yeast to human genes, we then predicted several lists of candidate SL pairs in human cancer. Our method and predictions would thus shed light on mechanisms of SL and lead to discovery of novel anti-cancer drugs. In addition, all the experimental results can be downloaded from http://www.ntu.edu.sg/home/zhengjie/data/MetaSL.
synthetic lethality; cancer; classification; meta-analysis; comparative genomics; functional ortholog
Phage typing has been used for the epidemiological surveillance of Salmonella enterica serovar Enteritidis for over 2 decades. However, knowledge of the genetic and evolutionary relationships between phage types is very limited, making differences difficult to interpret. Here, single nucleotide polymorphisms (SNPs) identified from whole-genome comparisons were used to determine the relationships between some S. Enteritidis phage types (PTs) commonly associated with food-borne outbreaks in the United States. Emphasis was placed on the predominant phage types PT8, PT13a, and PT13 in North America. With >89,400 bp surveyed across 98 S. Enteritidis isolates representing 14 distinct phage types, 55 informative SNPs were discovered within 23 chromosomally anchored loci. To maximize the discriminatory and evolutionary partitioning of these highly homogeneous strains, sequences comprising informative SNPs were concatenated into a single combined data matrix and subjected to phylogenetic analysis. The resultant phylogeny allocated most S. Enteritidis isolates into two distinct clades (clades I and II) and four subclades. Synapomorphic (shared and derived) sets of SNPs capable of distinguishing individual clades/subclades were identified. However, individual phage types appeared to be evolutionarily disjunct when mapped to this phylogeny, suggesting that phage typing may not be valid for making phylogenetic inferences. Furthermore, the set of SNPs identified here represents useful genetic markers for strain differentiation of more clonal S. Enteritidis strains and provides core genotypic markers for future development of a SNP typing scheme with S. Enteritidis.
Twenty-four prostate cancer (PCa) risk-associated single nucleotide polymorphisms (SNPs) in Chinese men have been cataloged. We evaluated whether these SNPs can independently predict outcomes of prostate biopsy, and improve the predictive performance of existing clinical variables.
Three hundred eight consecutive patients that underwent prostate biopsy for detection of PCa at Huashan Hospital, Shanghai, China between April 2011 and August 2012 were recruited. Clinical variables such as serum prostate-specific antigen (PSA) levels and peripheral blood samples were collected prior to a 10-core biopsy. A genetic score based on these 24 PCa associated SNPs was calculated for each individual.
Among 308 patients underwent prostate biopsy, 141 (45.8%) were diagnosed with PCa. Genetic score was significantly higher in patients with PCa (median = 1.30) than without (median = 0.89), P = 3.81 × 10−6. The difference remained significant after adjusting for age and total PSA, P = 0.007. The PCa detection rate increased with increasing genetic score; 26.3%, 43.2%, and 60.0% for men with lower (<0.5), average (0.5–1.5), and higher (>1.5) genetic score, respectively, P−trend = 0.0003. For patients with moderately elevated PSA levels (1.6–20 ng/ml), the PCa detection rate was 31.2% overall and was 16.7%, 31.2%, and 40.9% for men with lower (<0.5), average (0.5–1.5), and higher (>1.5) genetic score, respectively, P−trend = 0.03. For patients with PSA 2: 20 ng/ml, however, the PCa detection rates were high (>69%) regardless of genetic score.
A genetic score based on PCa risk-associated SNPs is an independent predictor of prostate biopsy outcomes in Chinese men and may be helpful to determine the need for prostate biopsy among patients within a ‘‘gray zone’’ of PCa risk.
ChinaPCa; SNPs; risk assessment; PSA
The Notch pathway is a cell signaling pathway determining initial specification and subsequent cell fate in the inner ear. Previous studies have suggested that new hair cells (HCs) can be regenerated in the inner ear by manipulating the Notch pathway. In the present study, delivery of siRNA to Hes1 and Hes5 using a transfection reagent or siRNA to Hes1 encapsulated within poly(lactide-co-glycolide acid) (PLGA) nanoparticles increased HC numbers in non-toxin treated organotypic cultures of cochleae and maculae of postnatal day 3 mouse pups. An increase in HCs was also observed in cultured cochleae and maculae of mouse pups pre-conditioned with a HC toxin (4-hydroxy-2-nonenal or neomycin) and then treated with the various siRNA formulations. Treating cochleae with siRNA to Hes1 associated with a transfection reagent or siRNA to Hes1 delivered by PLGA nanoparticles decreased Hes1 mRNA and up-regulated Atoh1 mRNA expression allowing supporting cells (SCs) to acquire a HC fate. Experiments using cochleae and maculae of p27kip1/-GFP transgenic mouse pups demonstrated that newly generated HCs trans-differentiated from SCs. Furthermore, PLGA nanoparticles are non-toxic to inner ear tissue, readily taken up by cells within the tissue of interest, and present a synthetic delivery system that is a safe alternative to viral vectors. These results indicate that when delivered using a suitable vehicle, Hes siRNAs are potential therapeutic molecules that may have the capacity to regenerate new HCs in the inner ear and possibly restore human hearing and balance function.
hair cell regeneration; inner ear; Notch pathway; siRNA; nanoparticle; mouse
Hemangiopericytoma is a rare perivascular tumor that often involves the extremities, pelvis, head and neck, and meninges, but rarely occurs in the kidney. The differentiation from renal cancer prior to surgery is extremely challenging; therefore, almost all cases of renal hemangiopericytoma are diagnosed by pathological examination. The majority of cases are identified in patients between the ages of 20 and 50 years of age, and a considerable proportion of patients exhibit hypertension, hypoglycaemia or additional paraneoplastic syndromes. The current study reports a rare case of renal hemangiopericytoma with drug refractory hypertension in a 14-year-old female. Following the complete resection of the tumor, the patient’s blood pressure returned to normal. No evidence of recurrence or metastasis was observed during a follow-up of 12 months following surgery. The present case indicated that surgery provides satisfactory outcomes and appears to be the most effective modality of treatment for renal hemangiopericytoma. Furthermore, this case also demonstrated that secondary hypertension may also recover following tumor excision.
hemangiopericytoma; kidney neoplasm; hypertension; nephrectomy
AIM: To evaluate the effect of β-catenin immunohistochemical expression on the prognosis of gastric cancer (GC).
METHODS: We searched Pubmed and Embase to identify eligible studies. The search ended on November 10, 2013, with no lower date limit. The citation lists associated with the studies were used to identify additional eligible studies. We included studies reporting sufficient information to estimate the HR and 95%CI, and information to estimate the OR in the analysis of clinicopathological features. The qualities of these studies were assessed using the Newcastle-Ottawa Quality Assessment Scale. HRs and ORs and their variance were calculated and pooled using Review Manager Version 5.2.
RESULTS: A total of 24 studies were identified and comprised 3404 cases. β-catenin expression was significantly correlated with poor overall survival (OS) in GC patients (HR = 1.85, 95%CI: 1.39-2.46), but showed a significant degree of heterogeneity (I2 = 71%, P < 0.0001). Subgroup analysis indicated that an abnormal pattern of β-catenin expression had an unfavorable effect on OS (HR = 1.79, 95%CI: 1.39-2.32). However, accumulation in the nucleus or loss of membrane did not influence the survival of GC patients independently. Moreover, the combined OR of β-catenin indicated that β-catenin expression was associated with Lauren classification (OR = 1.98, 95%CI: 1.19-3.29), lymph node metastasis (OR = 2.00, 95%CI: 1.44-2.77), distant metastasis (OR = 2.69, 95%CI: 1.35-5.38) and grade of differentiation (OR = 2.68, 95%CI: 1.66-4.34). β-catenin expression did not correlate with TNM stage (OR = 1.34 95%CI: 0.96-1.86), the depth of invasion (OR = 1.48, 95%CI: 0.94-2.33) or vascular invasion (OR = 1.11, 95%CI: 0.70-1.76).
CONCLUSION: Abnormal β-catenin immunohistochemical expression may be associated with tumor progression and could be a predictive factor of poor prognosis in patients with GC.
β-catenin; Immunohistochemistry; Gastric cancer; Prognosis; Meta-analysis
The regulatory mechanism of recombination is one of the most fundamental problems in genomics, with wide applications in genome wide association studies (GWAS), birth-defect diseases, molecular evolution, cancer research, etc. Recombination events cluster into short genomic regions called “recombination hotspots”. Recently, a zinc finger protein PRDM9 was reported to regulate recombination hotspots in human and mouse genomes. In addition, a 13-mer motif contained in the binding sites of PRDM9 is found to be enriched in human hotspots. However, this 13-mer motif only covers a fraction of hotspots, indicating that PRDM9 is not the only regulator of recombination hotspots. Therefore, the challenge of discovering other regulators of recombination hotspots becomes significant. Furthermore, recombination is a complex process. Hence, multiple proteins acting as machinery, rather than individual proteins, are more likely to carry out this process in a precise and stable manner. Therefore, the extension of the prediction of individual trans-regulators to protein complexes is also highly desired.
In this paper, we introduce a pipeline to identify genes and protein complexes associated with recombination hotspots. First, we prioritize proteins associated with hotspots based on their preference of binding to hotspots and coldspots. Second, using the above identified genes as seeds, we apply the Random Walk with Restart algorithm (RWR) to propagate their influences to other proteins in protein-protein interaction (PPI) networks. Hence, many proteins without DNA-binding information will also be assigned a score to implicate their roles in recombination hotspots. Third, we construct sub-PPI networks induced by top genes ranked by RWR for various species (e.g., yeast, human and mouse) and detect protein complexes in those sub-PPI networks.
The GO term analysis show that our prioritizing methods and the RWR algorithm are capable of identifying novel genes associated with recombination hotspots. The trans-regulators predicted by our pipeline are enriched with epigenetic functions (e.g., histone modifications), demonstrating the epigenetic regulatory mechanisms of recombination hotspots. The identified protein complexes also provide us with candidates to further investigate the molecular machineries for recombination hotspots. Moreover, the experimental data and results are available on our web site http://www.ntu.edu.sg/home/zhengjie/data/RecombinationHotspot/NetPipe/.
Meiotic recombination hotspots; Trans-regulators; Protein-protein interactions (PPI); Random walk; Protein complexes; Gene Ontology (GO) term analysis; Epigenetic functions
Hedgehog (Hh) signaling is activated in numerous malignant tumors, but its role in human colorectal cancer remains uncertain. Celecoxib, a selective cyclooxygenase-2 inhibitor, has been shown to exhibit chemoprevention in colorectal cancer, however, the effects of celecoxib on Hh signaling remain unknown. The current study presents an evaluation of Hh signaling in colon cancer cell lines and the effects of celecoxib in vitro. Active Hh signaling was observed in LoVo and HT-29 cells, with particularly high levels in the LoVo cells. However, Hh signaling activity was absent in HCT-116 cells. Quantitative polymerase chain reaction indicated that the expression of Hh receptor patched homolog 1 (PTCH1) was absent in the LoVo cells, but that they exhibited high levels of glioma-associated oncogene homolog-1 (GLI1) expression, while high expression levels of PTCH1 and low expression levels of smoothened (SMO) and GLI1 were observed in the HCT-116 cells. The HCT-116 cells were extremely sensitive to celecoxib, whereas the LoVo cells were resistant to the anticancer effect of the drug. Celecoxib downregulated the expression of GLI1 in the HCT-116 and HT-29 cells, but did not change the expression of GLI1 in the LoVo cells. The results presented in this study indicated that the anticancer effect of celecoxib is selective in colon cancer cells; celecoxib may target cancer cells via the SMO-independent modulation of GLI1 activity, and Hh signaling may be significant in maintaining the malignant state of LoVo cells. These findings may aid in improving our understanding of the carcinogenesis of colon cancer and the development of novel approaches for the targeted therapy of this disease.
colon cancer cells; hedgehog signaling; celecoxib; cyclopamine; glioma-associated oncogene homolog-1
Glutathione-coated luminescent gold nanoparticles (GS-AuNPs) of ~ 2.5 nm behave like small dye molecules (IRdye 800CW) in physiological stability and renal clearance, but exhibit much longer tumor retention time and faster normal tissue clearance than the dye molecules, indicating that well-known enhanced permeability and retention (EPR) effect, a unique strength of conventional nanoparticles (NPs) in tumor targeting, still exists in such small NPs. These merits enable the AuNPs to more rapidly detect tumor than the dye molecules without severe accumulation in reticuloendothelial system (RES) organs, holding great promise in cancer diagnosis and therapy.