Identification of key lncRNAs contributing to diabetic nephropathy by gene co-expression network analysis

LncRNA is reported to have important role in diabetic nephropathy (DN). Here, we aim to identify key lncRNAs of DN using bioinformatics and systems biological methods. Method: Five microarray data sets from Gene Expression Omnibus (GEO) database were included. Probe sets were re-annotated. In the training set, differential expressed genes (DEGs) were identified. Weighted gene co-expression network analysis (WGCNA) was constructed to screen diabetic-related hub genes and reveal their potential biological function. Two more human data sets and mouse data sets were used as validation sets. Results: A total of 424 DEGs, including 10 lncRNAs, were filtered in the training data set. WGCNA and enrichment analysis of hub genes showed that inflammation and metabolic disorders are prominent in DN. Three key lncRNAs (NR_130134.1, NR_029395.1 and NR_038335.1) were identified. These lncRNAs are also differently expressed in another two human data sets. Functional enrichment of the mouse data sets showed consistent changes with that in human, indicating similar changes in gene expression pattern of DN and confirmed confidence of our analysis. Human podocytes and mesangial cells were culture in vitro. QPCR and fluorescence in situ hybridization were taken out to validate the expression and relationship of key lncRNAs and their related mRNAs. Results were also consistent with our analysis. Conclusions: Inflammation and metabolic disorders are prominent in DN. We identify three lncRNAs that are involved in these processes possibly by interacting with co-expressed mRNAs.

Chemerin/ChemR23 axis promotes inflammation of glomerular endothelial cells in diabetic nephropathy

Diabetic nephropathy (DN) is characterized by inflammation of renal tissue. Glomerular endothelial cells (GEnCs) play an important role in inflammation and protein leakage in urine in DN patients. Chemerin and its receptor ChemR23 are inducers of inflammation. The aim of this study was to investigate the function of chemerin/ChemR23 in GEnCs of DN patients. Immunohistochemical staining and qRT‐PCR were used to measure the expression of chemerin, ChemR23 and inflammatory factors in renal tissues of DN patients. Db/db mice were used as animal model. ChemR23 of DN mice was knocked down by injecting LV3‐shRNA into tail vein. Inflammation, physiological and pathological changes in each group was measured. GEnCs were cultured as an in vitro model to study potential signalling pathways. Results showed that expression of chemerin, ChemR23 and inflammatory factors increased in DN patients and mice. LV3‐shRNA alleviated renal damage and inflammation in DN mice. GEnCs stimulated by glucose showed increased chemerin, ChemR23 and inflammatory factors and decreased endothelial marker CD31. Both LV3‐shRNA and SB203580 (p38 MAPK inhibitor) attenuated chemerin‐induced inflammation and injury in GEnCs. Taken together, chemerin/ChemR23 axis played an important role in endothelial injury and inflammation in DN via the p38 MAPK signalling pathway. Suppression of ChemR23 alleviated DN damage.

Development of an interactive tumor vascular suppression strategy to inhibit multidrug resistance and metastasis with pH/H2O2 responsive and oxygen-producing nanohybrids

An ideal cancer therapeutic strategy should not only reverse multidrug resistance (MDR), but also prevent cancer metastasis. In this study, we address these cancer treatment challenges through an interactive vascular suppression strategy.

Significant Excess of Electronlike Events in the MiniBooNE Short-Baseline Neutrino Experiment

The MiniBooNE experiment at Fermilab reports results from an analysis of ν_{e} appearance data from 12.84×10^{20} protons on target in neutrino mode, an increase of approximately a factor of 2 over previously reported results. A ν_{e} charged-current quasielastic event excess of 381.2±85.2 events (4.5σ) is observed in the energy range 200<E_{ν}^{QE}<1250  MeV. Combining these data with the ν[over ¯]_{e} appearance data from 11.27×10^{20} protons on target in antineutrino mode, a total ν_{e} plus ν[over ¯]_{e} charged-current quasielastic event excess of 460.5±99.0 events (4.7σ) is observed. If interpreted in a two-neutrino oscillation model, ν_{μ}→ν_{e}, the best oscillation fit to the excess has a probability of 21.1%, while the background-only fit has a χ^{2} probability of 6×10^{-7} relative to the best fit. The MiniBooNE data are consistent in energy and magnitude with the excess of events reported by the Liquid Scintillator Neutrino Detector (LSND), and the significance of the combined LSND and MiniBooNE excesses is 6.0σ. A two-neutrino oscillation interpretation of the data would require at least four neutrino types and indicate physics beyond the three neutrino paradigm. Although the data are fit with a two-neutrino oscillation model, other models may provide better fits to the data.

The regulation of CIRBP by transforming growth factor beta during heat shock-induced testicular injury

BACKGROUND

Cold-inducible RNA-binding protein (CIRBP) is associated with cell stress. However, its upstream regulatory factors are still largely unknown.

OBJECTIVES

This study investigated whether CIRBP expression was regulated by transforming growth factor beta (TGF-β) during the process of heat-induced testicular damage.

MATERIALS AND METHODS

Ten male adult ICR mice were allocated to heat treatment (scrotal hyperthermia at 43 °C for 30 min, n = 5) and control group (n = 5); CIRBP and TGF-β1, TGF-β2, and TGF-β3 expression levels in the testis in mRNA and protein were analyzed. Then, we conducted in vivo and in vitro studies to investigate the regulatory effects of TGF-β on CIRBP. In the in vivo study, male adult ICR mice were subjected to testicular hyperthermia followed by a local testicular injection of TGF-β antagonist (non-selective TGF-β I/II receptor inhibitor, 5 μg or 10 μg). In the in vitro study, GC2-spd cells were cultured under 43 °C for 30 min or with different TGF-β isoforms (10 ng/mL), and CIRBP expression levels in the testis and GC2-spd cells were analyzed 24 and 48 h, respectively, after treatment.

RESULTS

As a result, heat treatment significantly downregulated the relative CIRBP mRNA and protein expression (p = 0.006 and 0.011), and significantly upregulated TGF-β2 and TGF-β3 expression levels (p = 0.022 and 0.04, for mRNA, and p = 0.001 for both protein levels). Local testicular injection of 10 μg TGF-β antagonist significantly attenuated heat-induced histological damage to the testes and CIRBP downregulation (p = 0.038). Furthermore, TGF-β2 and TGF-β3 significantly downregulated CIRBP mRNA and protein expression in GC2-spd cells (all p < 0.01), exerting a similar effect to heat treatment.

DISCUSSION AND CONCLUSION

Our in vivo and in vitro experiments demonstrated that heat-induced CIRBP downregulation in the testes was mediated by the upregulation of TGF-β. Further studies are needed to clarify the molecular mechanisms underlying these processes.

Transcriptomic analysis of hepatocellular carcinoma reveals molecular features of disease progression and tumor immune biology

Hepatocellular carcinoma (HCC) develops in the context of chronic inflammatory liver disease and has an extremely poor prognosis. An immunosuppressive tumor microenvironment may contribute to therapeutic failure in metastatic HCC. Here, we identified unique molecular signatures pertaining to HCC disease progression and tumor immunity by analyzing genome-wide RNA-Seq data derived from HCC patient tumors and non-tumor cirrhotic tissues. Unsupervised clustering of gene expression data revealed a gradual suppression of local tumor immunity that coincided with disease progression, indicating an increasingly immunosuppressive tumor environment during HCC disease advancement. IHC examination of the spatial distribution of CD8+ T cells in tumors revealed distinct intra- and peri-tumoral subsets. Differential gene expression analysis revealed an 85-gene signature that was significantly upregulated in the peri-tumoral CD8+ T cell-excluded tumors. Notably, this signature was highly enriched with components of underlying extracellular matrix, fibrosis, and epithelial-mesenchymal transition (EMT). Further analysis condensed this signature to a core set of 23 genes that are associated with CD8+ T cell localization, and were prospectively validated in an independent cohort of HCC specimens. These findings suggest a potential association between elevated fibrosis, possibly modulated by TGF-β, PDGFR, SHH or Notch pathway, and the T cell-excluded immune phenotype. Indeed, targeting fibrosis using a TGF-β neutralizing antibody in the STAM™ model of murine HCC, we found that ameliorating the fibrotic environment could facilitate redistribution of CD8+ lymphocytes into tumors. Our results provide a strong rationale for utilizing immunotherapies in HCC earlier during treatment, potentially in combination with anti-fibrotic therapies.

miR-15a-5p suppresses inflammation and fibrosis of peritoneal mesothelial cells induced by peritoneal dialysis via targeting VEGFA

Long-term peritoneal dialysis (PD) often ends up with ultrafiltration failure (UFF) which is partially caused by persistent inflammation and fibrosis of peritoneal tissues. However, the mechanism is still unclear. In the current study, the peritoneum from UFF patients demonstrated inflammation and fibrosis which were positively related to the expression of vascular endothelial growth factor A (VEGFA). The in vitro model using human peritoneal mesothelial cells (HPMCs) stimulated by high glucose or advanced glycation end (AGE) product showed consistent changes of inflammation, fibrosis, and VEGFA. What's more, we showed that VEGFA was an instigator of inflammation and fibrosis. Several microRNAs (miRNAs) have been reported to regulate expression of VEGFA elsewhere. Five of them were selected to test the expression in the peritoneum of patients with PD. Results suggested that miR-15a-5p was the most significantly downregulated one. Also, in high glucose or AGE product-stimulated HPMCs, miR-15a-5p decreased. When miRNA mimic was used to restore the expression of miR-15a-5p, high glucose-induced VEGFA was repressed. The predicted binding site between these two molecules was confirmed by the dual-luciferase assay. Restoration of miR-15a-5p restrained inflammation and fibrosis of HPMCs. TGF-β1/Smad2 was shown to be the downstream signaling pathway and their activity was regulated by miR-15a-5p/VEGFA. In conclusion, our current study demonstrates that miR-15a-5p acts as a regulator of VEGFA mRNA and the following inflammation and fibrosis in peritoneal mesothelial cells. The miR-15a-5p/VEGFA pathway may be a potential target for preventing ultrafiltration failure in patients with PD.

Microarray analysis reveals long non‑coding RNA SOX2OT as a novel candidate regulator in diabetic nephropathy

Diabetic nephropathy (DN) is a highly complex syndrome involving multiple dysregulated biological processes. Long non-coding RNAs (lncRNAs) are now believed to have an important function in various diseases. However, their roles in DN remain largely unknown. Therefore, the present study was performed in order to investigate the lncRNAs that have a crucial role in DN. db/db mice were used as a DN model while db/m mice served as a control to search for lncRNAs which may have important roles in DN. Microarray and bioinformatics analysis gave an overview of the features of differentially expressed genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis demonstrated the typical biological alterations in DN. A co-expression network of lncRNAs and mRNAs revealed the complex interaction pattern in DN conditions. Further data investigation indicated that SOX2-overlapping transcript (SOX2OT), which was significantly downregulated in DN mice, may be the potentially functional lncRNA contributing to the onset of DN. The UCSC database demonstrated that SOX2OT was highly conserved in mice and humans. Additionally further study using cultured human podocytes and mesangial cells confirmed the downregulation of SOX2OT using reverse transcription-quantitative polymerase chain reaction and fluorescence in situ hybridization. However, the cellular location of SOX2OT depended on certain cell types. Taken together, the results of the present study indicated that SOX2OT may act as an important regulator in the pathogenesis of DN by interacting with various mRNAs with critical roles in DN.

[Clinicopathologic and molecular genetic analysis of secretory carcinoma of salivary gland]

Objective: To investigate the clinicopathologic and molecular genetic features of secretory carcinoma of salivary gland (SCSG). Methods: Six cases of SCSG were collected from Zhejiang Provincial People's Hospital from January 2011 to March 2018. The clinical, histopathological and immunohistochemical features were analyzed and fluorescence in situ hybridization (FISH) was used to detect ETV6 gene rearrangement. Results: Four out of 6 tumors originated in the parotid gland and one of each in the minor salivary glands of soft palate and the buccal mucosa. Grossly, 4 cases were solid and 2 were partially cystic with maximum diameter ranging from 1.0 to 4.0 cm. Microscopically, 5 tumors showed typical features of low grade SCSG with tumor divided by thin fibrous septa into lobules composed of solid acinar, microcystic, follicular and papillary structures with abundant extracellular mucinous secretions. The tumor cells had cuolated or hobnail cytoplasm with low-grade nuclei and scarce mitoses. Perineural invasion was present in 1 case. The remaining tumor showed about 30% of the tumor areas with high-grade transformation characterized by proliferation of a distinct population of anaplastic cells arranged in irregular glandular, small nested and single cell patterns that were surrounded by desmoplastic stroma and invaded into surface mucosa with ulceration. Immunohistochemistry showed that all 6 tumors had diffuse and strong reactivities to S100 protein and cytokeratin 7, and 4 cases showed focal reactivity to gross cystic disease fluid protein 15 (GCDFP15), all were negative for discovered on gist 1 (DOG1), cytokeratin 20, p63 and calponin. High grade transformation cases were analysed, the high grade SCSG components showed a significantly increased Ki-67 index and cyclin D1 positive tumor cells compared to the conventional SCSG components. FISH analyses showed that 4 cases had ETV6 gene rearrangement. Eleven to seventy one months' follow-up showed no evidence of tumor recurrence nor metastasis. Conclusions: SCSG harbors characteristic genetic abnormalities with ETV6 gene rearrangement and typically shows a low grade morphology with occasionally, high grade transformation can be present.

WNT signaling is required for peritoneal membrane angiogenesis

The wingless-type mouse mammary tumor virus integration site family (WNT) signaling pathway is involved in wound healing and fibrosis. We evaluated the WNT signaling pathway in peritoneal membrane injury. We assessed WNT1 protein expression in the peritoneal effluents of 54 stable peritoneal dialysis (PD) patients and WNT-related gene expression in ex vivo mesothelial cell cultures from 21 PD patients. In a transforming growth factor-β (TGF-β)-mediated animal model of peritoneal fibrosis, we evaluated regulation of the WNT pathway and the effect of WNT inhibition on peritoneal fibrosis and angiogenesis. WNT1 and WNT2 gene expression were positively correlated with peritoneal membrane solute transport in PD patients. In the mouse peritoneum, TGF-β-induced peritoneal fibrosis was associated with increased expression of WNT2 and WNT4. Peritoneal β-catenin protein was significantly upregulated after infection with adenovirus expressing TGF-β (AdTGF-β) along with elements of the WNT signaling pathway. Treatment with a β-catenin inhibitor (ICG-001) in mice with AdTGF-β-induced peritoneal fibrosis resulted in attenuation of peritoneal angiogenesis and reduced vascular endothelial growth factor. Similar results were also observed with the WNT antagonist Dickkopf-related protein (DKK)-1. In addition to this, DKK-1 blocked epithelial-mesenchymal transition and increased levels of the cell adhesion protein E-cadherin. We provide evidence that WNT signaling is active in the setting of experimental peritoneal fibrosis and WNT1 correlates with patient peritoneal membrane solute transport in PD patients. Intervention in this pathway is a possible therapy for peritoneal membrane injury.

Efficient point-by-point Bragg gratings fabricated in embedded laser-written silica waveguides using ultrafast Bessel beams

We demonstrate highly efficient Bragg gratings written point-by-point by sequential single-pulse ultrashort Bessel laser beams in laser photoinscribed single-mode waveguides in bulk fused silica. The use of chirped non-diffractive Bessel beams determines a strong Bragg resonance in a weak-to-strong transitional regime, augmenting to a record value of 40  dB/cm at 1550 nm in the third order. The Bessel-induced refractive index modulation is negative and localized to sub-micrometer (200 nm) transverse scales. The strong light confinement in Bessel beams ensuring uniform one-dimensional void conditions thus allows for enhanced precision in the Bragg grating waveguide design. We demonstrate flexible fabrication of multiplexed waveguide gratings for multiple and tunable spectral resonances.

First Measurement of Monoenergetic Muon Neutrino Charged Current Interactions

We report the first measurement of monoenergetic muon neutrino charged current interactions. MiniBooNE has isolated 236 MeV muon neutrino events originating from charged kaon decay at rest (K^{+}→μ^{+}ν_{μ}) at the NuMI beamline absorber. These signal ν_{μ}-carbon events are distinguished from primarily pion decay in flight ν_{μ} and ν[over ¯]_{μ} backgrounds produced at the target station and decay pipe using their arrival time and reconstructed muon energy. The significance of the signal observation is at the 3.9σ level. The muon kinetic energy, neutrino-nucleus energy transfer (ω=E_{ν}-E_{μ}), and total cross section for these events are extracted. This result is the first known-energy, weak-interaction-only probe of the nucleus to yield a measurement of ω using neutrinos, a quantity thus far only accessible through electron scattering.