Search

Supplementary Figure 1

Supplementary Table 2

In biofluid, long RNAs are more informative than microRNAs in terms of gene number and variation type. Therefore, cell-free long RNAs have shown promising potential as biomarkers in liquid biopsy, while they are mostly fragmented. In order to investigate these fragmented cell-free RNAs (cfRNAs), we developed a cost-effective cfRNA sequencing method, DETECTOR-seq (depletion-assisted multiplexing cell-free total RNA sequencing). It utilized a set of customized guide RNAs to remove large amounts of unwanted RNAs (i.e., fragmented ribosomal and mitochondrial RNAs) in human plasma. Early barcoding was also incorporated to save cost and plasma volume. After demonstrating its superior performance to other methods, we used DETECTOR-seq to investigate cell-free transcriptomes in whole human plasma and extracellular vesicles (EVs) it contains. We first observed different type distributions: structured circular RNAs, tRNAs, Y RNAs, and virus RNAs were enriched in plasma, while mRNAs and srpRNAs were enriched in EVs. We also uncovered distinct functional pathways: RNA splicing-related ribonucleoproteins (RNPs) and antimicrobial humoral response genes were enriched in plasma, while transcriptional activity, cell migration, and antigen receptor-mediated immune signals were enriched in EVs. Subsequently, we compared the performances of these distinct cfRNAs in whole plasma versus EVs on classifying cancer patients. The accuracies were comparable when discriminating cancer patients from healthy donors (AUCs: 0.936 versus 0.953). Meanwhile, cancer types (i.e., colorectal versus lung cancer) were better classified with microbial cfRNAs in plasma than in EV (AUCs: 0.898 versus 0.772). Overall, by investigating total and EV cfRNAs in the pairwise plasma samples, our work provides practical guidance for the proper decision of EV purification when launching a cfRNA-based study. Furthermore, as a cost-effective method, DETECTOR-seq would facilitate transcriptome-wide studies in the fields of extracellular RNA biology and clinical liquid biopsy.Key PointsDETECTOR-seq enables efficient and specific depletion of sequences derived from fragmented ribosomal and mitochondrial RNAs in plasma.Distinct cfRNA signatures in whole plasma versus EVs were revealed.Both Plasma and EV cfRNAs were capable of distinguishing cancer patients from normal individuals.Microbial RNAs in Plasma cfRNAs enabled better classification of cancer types than EV cfRNAs.

During cancer development, host’s tumorigenesis and immune signals are released to and informed by circulating molecules, like cell-free DNA (cfDNA) and RNA (cfRNA) in blood. However, these two kinds of molecules are still not systematically compared in gastrointestinal cancer. Here, we profiled 4 types of cell-free omics data from colorectal and stomach cancer patients, and assayed 15 types of genomic, epi-genomic, and transcriptomic variations. First, we demonstrated that the multi-omics data were more capable of detecting cancer genes than the single-omics data, where cfRNAs were more sensitive and informative than cfDNAs in terms of detection ratio, variation type, altered number, and enriched functional pathway. Moreover, we revealed several peripheral immune signatures that were suppressed in cancer patients and originated from specific circulating and tumor-microenvironment cells. Particularly, we defined a γδ-T-cell score and a cancer-associated-fibroblast (CAF) score using the cfRNA-seq data of 143 cancer patients. They were informative of clinical status like cancer stage, tumor size, and survival. In summary, our work reveals the cell-free multi-molecular landscape of colorectal and stomach cancer, and provides a potential monitoring utility in blood for the personalized cancer treatment.

Background: Extramammary Paget’s disease (EMPD) is a rare malignant cutaneous tumour that is commonly located in anogenital regions. The diagnosis of the disease is always delayed, and treatment is usually troublesome. This study aims to summarise the clinicopathological characteristics and the risk factors of prognosis for EMPD in anogenital regions, potentially providing evidence for the diagnosis and treatment of anogenital EMPD. Methods: 688 patients were sourced from the Surveillance, Epidemiology and End Results (SEER) program between 1992 and 2021. In total, 176 participants from our centre from between 2011 and 2021 were included to investigate the characteristics and prognosis for EMPD in anogenital regions. Results: From the SEER program data, patient age of 65 years or older, metastasis of lymph nodes, Spanish-Hispanic-Latino race, diameter exceeding 10cm and lesions located anally were revealed as independent risk factors for shorter cancer-specific survival (CSS). However, the data from our centre highlighted that metastasis of lymph nodes and tumours extending through the epidermis are independent risk factors of shortened progression-free survival (PFS) and CSS of anogenital EMPD. Conclusion: This synthesised study revealed that some characteristics are regarded as risk factors for poor clinical prognosis, which have potential value in formulating more normative and effective strategies for patients with EMPD in anogenital regions.

Immunotherapy can elicit robust anticancer responses in the clinic. However, a large proportion of patients with colorectal cancer do not benefit from treatment. Although previous studies have shown that hydrogen sulfide (H2S) is involved in colorectal cancer development and immune escape, further insights into the mechanisms and related molecules are needed to identify approaches to reverse the tumor-supportive functions of H2S. Here, we observed significantly increased H2S levels in colorectal cancer tissues. Decreasing H2S levels by using CBS+/− mice or feeding mice a sulfur amino acid-restricted diet (SARD) led to a marked decrease in differentiated CD4+CD25+Foxp3+ Tregs and an increase in the CD8+ T-cell/Treg ratio. Endogenous or exogenous H2S depletion enhanced the efficacy of anti–PD-L1 and anti–CTLA4 treatment. H2S promoted Treg activation through the persulfidation of ENO1 at cysteine 119. Furthermore, H2S inhibited the migration of CD8+ T cells by increasing the expression of AAK-1 via ELK4 persulfidation at cysteine 25. Overall, reducing H2S levels engenders a favorable immune microenvironment in colorectal cancer by decreasing the persulfidation of ENO1 in Tregs and ELK4 in CD8+ T cells. SARD represents a potential dietary approach to promote responses to immunotherapies in colorectal cancer.Significance:H2S depletion increases the CD8+ T-cell/Treg ratio and enhances the efficacy of anti–PD-L1 and anti–CTLA4 treatment in colon cancer, identifying H2S as an anticancer immunotherapy target.

The immobilization of microorganisms on high-quality and inexpensive carriers to remediate oil-contaminated soil is an effective strategy for contaminated soil remediation. Due to the abundance in nutrients, large specific surface area, and fewer pathogens, the composting sludge is considered a high-quality immobilized material. Herein, two non-ionic surfactants, TW-80 and sophorolipid, were used to modify composted sludge. High-efficiency petroleum hydrocarbon-degrading bacteria groups selected in the laboratory were fixed on the modified composting sludge under optimal conditions. The immobilized material was placed in the soil contaminated by petroleum hydrocarbons at an additive amount of 2wt/%, and a simulated remediation experiment was performed for 90 days. Both soil properties and microbial structure were characterized. Surfactant-modified compost sludge enhances the adsorption capacity to petroleum hydrocarbon. The immobilized microorganisms in the modified compost sludge showed a good effect on the remediation of soil contaminated by petroleum hydrocarbons. In addition, immobilized materials also increase the diversity of the microbial community structure in the soil. High-efficiency petroleum hydrocarbon-degrading bacteria immobilized on surfactant-modified compost can effectively promote the degradation of petroleum hydrocarbons in the soil and increase the abundance of microorganisms in the soil. It shows the feasibility of eco-friendly remediation of hydrocarbon-contaminated soil.

Background Colorectal cancer (CRC) is the third most common cancer worldwide. The opening of the TCGA and GEO databases has promoted the progress of CRC prognostic assessment, while the aging-related risk signature has never been mentioned. Methods R software packages, GSEA software, Venn diagram, Metascape, STRING, Cytoscape, cBioPortal, TIMER and GeneMANIA website were used in this study. Results Aging-related gene sets, GO_AGING, GO_CELL_AGING and GO_CELLULAR_SENESCENCE, were activated significantly in CRC tissues. We constructed an aging-related risk signature using LASSO COX regression in training group TCGA and validated in testing group GSE39582. The risk score was significantly associated with the overall survival of CRC patients, whose stability was clarified by stratified survival analysis and accuracy was demonstrated using the ROC curve. The risk score was significantly increased in the advanced stage, T3-4, N1-3 and M1 and positively correlated with the richness of immune cell infiltration in the tumor microenvironment. We further investigated the molecular characteristics of 15 hub genes at the DNA and protein levels and performed GSEA between high- and low-risk groups. Conclusions The aging-related signature is a reliable prognostic analysis model and can predict the severity and immune cell infiltration of CRC patients.

Background: As the third confirmed gaseous transmitter, the role of hydrogen sulfide (H2S) in the pathogenesis of multiple types of cancer has been attracting increasing attention. Increased expression of cystathionine β-synthase (CBS) and H2S in colon cancer tissue samples has been validated and tumor-derived H2S, mainly produced by CBS, stimulates bioenergetics, cell proliferation, and angiogenesis in colon cancer. Recently, the therapeutic manipulation of H2S has been proposed as a promising anticancer approach. However, the effect of aminooxyacetic acid (AOAA), which has been widely used as an inhibitor of CBS dependent synthesis of H2S, on the chemotherapeutic effect of oxaliplatin (OXA) and the underlying mechanisms remain to be illustrated. Methods: We examined the expression of CBS in human colorectal cancer specimens and matched normal mucosa by immunohistochemistry. The effect of AOAA on the sensitivity of colon cancer cells to OXA and the level of apoptosis induced by caspase cascade was investigated in both HCT116 and HT29 cell lines utilizing CCK-8 assays, flow cytometry analysis and western blot analysis. The endogenous levels of reactive oxygen species (ROS) were detected fluorescently by DCF-DA, and glutathione (GSH) levels were measured by a Total GSH Detection Kit. Tumor bearing xenograft mouse models and in vivo imaging systems were further used to investigate the effect of AOAA in vivo and immunohistochemistry (IHC) and TUNEL analysis were performed. Results: In the current study, we confirmed CBS, the main target of AOAA, is overexpressed in human colorectal cancer by immunohistochemistry. The inhibitory effect of AOAA on the synthesis of H2S was validated utilizing fluorescent probe and specific electrode. AOAA significantly reduced the IC50 values of OXA in both colon cancer cell lines. Co-incubation with AOAA elicited increased apoptosis induced by OXA, featured by increased activation of caspase cascade. Besides, AOAA further increased the levels of ROS induced by OXA and attenuated the synthesis of glutathione (GSH), which is a vital antioxidant. Besides, the results of in vivo imaging and following IHC and TUNEL analysis were in accordance with cellular experiments, indicating that AOAA sensitizes colon cancer cells to OXA via exaggerating intrinsic apoptosis. Conclusion: The results suggested that CBS is overexpressed in colorectal cancer tissues and AOAA sensitizes colon cancer cells to OXA via exaggerating apoptosis both in vitro and in vivo. Decreasing the endogenous level of GSH and consequently impaired detoxification of ROS might be one of the mechanisms underlying the effect of AOAA.

The utility of cell-free nucleic acids in monitoring cancer has been recognized by both scientists and clinicians. In addition to human transcripts, a fraction of cell-free nucleic acids in human plasma were proven to be derived from microbes and reported to have relevance to cancer. To obtain a better understanding of plasma cell-free RNAs (cfRNAs) in cancer patients, we profiled cfRNAs in ~300 plasma samples of 5 cancer types (colorectal cancer, stomach cancer, liver cancer, lung cancer, and esophageal cancer) and healthy donors (HDs) with RNA-seq. Microbe-derived cfRNAs were consistently detected by different computational methods when potential contaminations were carefully filtered. Clinically relevant signals were identified from human and microbial reads, and enriched Kyoto Encyclopedia of Genes and Genomes pathways of downregulated human genes and higher prevalence torque teno viruses both suggest that a fraction of cancer patients were immunosuppressed. Our data support the diagnostic value of human and microbe-derived plasma cfRNAs for cancer detection, as an area under the ROC curve of approximately 0.9 for distinguishing cancer patients from HDs was achieved. Moreover, human and microbial cfRNAs both have cancer type specificity, and combining two types of features could distinguish tumors of five different primary locations with an average recall of 60.4%. Compared to using human features alone, adding microbial features improved the average recall by approximately 8%. In summary, this work provides evidence for the clinical relevance of human and microbe-derived plasma cfRNAs and their potential utilities in cancer detection as well as the determination of tumor sites.

Background: The utilities of cell free nucleic acids in monitoring cancer have been recognized by both scientists and clinicians. In addition to human transcripts, a fraction of cell free nucleic acids in human plasma were proved to derived from microbes, and reported to have some relevance to cancer. Methods: To get a better understanding of plasma cell free RNAs (cfRNAs) in cancer patients, we profiled cfRNAs in ~300 plasma samples of five cancer types (colorectal cancer, stomach cancer, liver cancer, lung cancer, esophageal cancer) and healthy donors with RNA-seq. Results: Microbe derived cfRNAs were consistently detected by different computational methods when potential contaminations were carefully filtered. Clinically relevant signals can be identified from human and microbial reads, and alteration in human cfRNA expression and virus abundance both suggests some cancer patients were immunosuppressed, as indicated by enriched KEGG pathways of downregulated human genes and higher prevalence torque teno virus. Our data supports the diagnostic value of human and microbe derived plasma cfRNAs for cancer detection, as an area under receiver operating characteristic (ROC) curve of 0.931 for distinguishing cancer patients from healthy donors was achieved on validation set, using both human and microbial features. Moreover, these cfRNAs both have some cancer type specificity, and could distinguish tumors of different primary locations. Compared to using human feature alone, combining human and microbial features improves the average validation accuracy of between cancer type classification by 11.5%. Conclusions: In summary, this work provides evidence for the clinical relevance of human and microbe derived plasma cfRNAs, and their potential utilities in cancer detection, and determination of tumor sites.

The activated form of vitamin D3, 1,25-dihydroxyvitamin D3 [1,25(OH)2D3], regulates numerous cellular processes, including inhibition of cancer progression. IL-1β has been reported to facilitate cancer development, especially by inducing an epithelial-to-mesenchymal transition (EMT) in several malignant tumors. However, the underlying mechanism of 1,25(OH)2D3 and IL-1β in colorectal cancer (CRC) still remains largely unknown. To fill in this knowledge gap, we measured cell proliferation and invasion by CCK-8 and Transwell assays after stimulation with 1,25(OH)2D3 and IL-1β. E-cadherin and vimentin were chosen as markers of EMT measured by immunofluorescence, quantitative real-time PCR (qRT-PCR), and Western blot. The expression and function of the vitamin D receptor (VDR) was evaluated by Western blot and luciferase reporter assay. qRT-PCR and RNA-FISH were performed to detect the expression and location of lncTCF7 in vitro. The binding sites of VDR in the lncTCF7 promoter were confirmed by a chromatin immunoprecipitation assay. Based on the above experiments, we found that 1,25(OH)2D3 attenuates IL-1β-induced increased proliferation and invasion in colorectal cancer through enhancing VDR, which inhibits the expression of lncTCF7 by directly binding to its promoter region.

Long non-coding RNA (Lnc)TCF7 is a novel lncRNA that is involved in tumorigenesis. Previous studies have revealed that lncTCF7 serves an essential role in maintaining cancer stem cell self-renewal; however, the functions of lncTCF7 in colorectal cancer (CRC) remain unknown. Therefore, the present study aimed to investigate the role of lncTCF7 in CRC. LncTCF7 was upregulated in 52/58 CRC tissues, and its expression correlated with tumor size, lymph metastasis and tumor-node-metastasis stage in CRC. Knocking down lncTCF7 in colon cancer cell lines decreased cell proliferation, migration and invasion, while lncTCF7 overexpression showed opposite changes. In addition, lncTCF7 promoted cell proliferation in vivo. LncTCF7 activated the Wnt/β-catenin signaling pathway, which is essential for cancer development. Survival analysis revealed that patients with higher expression of lncTCF7 had significantly worse prognosis compared with patients with low expression. These findings indicate that lncTCF7 regulates CRC progression and support the notion of lncTCF7 as a CRC prognostic marker.

Long non-coding RNA-imprinted maternally expressed transcript (non-protein coding) (H19) has been previously identified to be involved in the development of a number of types of cancer. However, the function of H19 in the pathogenesis of colorectal cancer remains unclear. The expression level of H19 in colorectal tumor tissues, and the association between H19 expression and clinicopathological variables and prognosis was investigated in the present study. In addition, the effect of H19 overexpression on viability, migration and epithelial-mesenchymal transition (EMT) of colon cancer cells was investigated in HCT-116 and SW-480 cells. The results of the present study suggest that overexpression of H19 is associated with decreased recurrence-free survival and overall survival rates in patients with colorectal cancer, and increased viability and migration in colon cancer cells. The induction of the EMT process may be an underlying molecular mechanism associated with the H19-induced increased metastasis potential of colon cancer cells.

The long noncoding (lnc) RNA H19 was involved in the tumorigenesis of many types of cancer. However, the role of H19 in the tumorigenesis of colon cancer has not been fully illustrated. Recent studies suggested a potential relationship between H19 and vitamin D receptor (VDR) signaling. Considering the pivotal role of VDR signaling in the colon epithelium both physiologically and pathologically, the correlation between H19 and VDR signaling may have an important role in the development of colon cancer. In this study, the correlation between H19 and vitamin D receptor (VDR) signaling and the underlying mechanisms in colon cancer were investigated both in vitro and in vivo. The results suggested that VDR signaling was able to inhibit the expression of H19 through regulating C-Myc/Mad-1 network. H19, on the other hand, was able to inhibit the expression of VDR through micro RNA 675-5p (miR-675-5p). Furthermore, H19 overexpression induced resistance to the treatment with 1,25(OH)2D3 both in vitro and in vivo. Together, these results suggested that H19 overexpression might be one of the mechanisms underlying the development of resistance to the treatment with 1,25(OH)2D3 in the advanced stage of colon cancer.

This paper studies the problem of using minimum power to provide satisfactory performance for real-time applications over unreliable and fading wireless channels. We demonstrate that this problem can be formulated as a linear programming problem. However, this formulation involves exponentially many constraints, and many parameters are either unavailable or difficult to compute, which makes it infeasible to employ standard techniques to solve the linear programming problem. Instead, we propose a simple online algorithm for this problem. We prove that our algorithm provides satisfactory performance to all real-time applications, and the total power consumption can be made arbitrarily close to the theoretical lower bound. Furthermore, our algorithm has very low complexity and does not require knowledge of many parameters in the linear programming problem, including the distributions of channel qualities. We further extend our algorithm to address systems where real-time applications and non-real-time ones coexist. We demonstrate that our algorithm achieves both low total power consumption and high utility for each non-real-time client while satisfying the performance requirements of real-time clients. Simulation results further provide some insights in setting important parameters of our algorithms, and demonstrate that our algorithm indeed achieves a significant reduction in power consumption.

Intestinal barrier injury has been reported to play a vital role in the pathogenesis of endotoxemia. This study aimed to investigate the protective effect of GYY4137, a newly synthesized H2S donor, on the intestinal barrier function in the context of endotoxemia both in vitro and in vivo. Caco-2 (a widely used human colon cancer cell line in the study of intestinal epithelial barrier function) monolayers incubated with lipopolysaccharide (LPS) or TNF-α/IFN-γ and a mouse model of endotoxemia were used in this study. The results suggested that GYY4137 significantly attenuated LPS or TNF-α/IFN-γ induced increased Caco-2 monolayer permeability. The decreased expression of TJ (tight junction) proteins induced by LPS and the altered localization of TJs induced by TNF-α/IFN-γ was significantly inhibited by GYY4137; similar results were obtained in vivo. Besides, GYY4137 promoted the clinical score and histological score of mice with endotoxemia. Increased level of TNF-α/IFN-γ in the plasma and increased apoptosis in colon epithelial cells was also attenuated by GYY4137 in mice with endotoxemia. This study indicates that GYY4137 preserves the intestinal barrier function in the context of endotoxemia via multipathways and throws light on the development of potential therapeutic approaches for endotoxemia.

Background: Tyrosine kinase inhibitors (TKIs) are widely used for patients with cancer, although liver injury has been observed in a small proportion of these patients. The aim of this study was to investigate the mechanisms underlying TKI-induced liver injury according to HLA polymorphisms. Methods: We systematically searched three electronic databases (PubMed, PMC, EmBase, and the Cochrane library) to identify studies that evaluated the impact of HLA polymorphisms on the incidence of TKI-induced liver injury in cancer patients as of November 2018. The summary odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using a random-effects model. Further, sensitivity analysis and publication bias assessments were also performed. Results: In the final analysis, four studies that involved a total of 12,181 patients were included. Three of the studies included patients who received lapatinib, and the other study included patients who received pazopanib. Overall, carriers of HLA-DQA1*02:01 were associated with an increased risk of liver injury (OR: 6.85; 95%CI: 2.34-20.02; P

Smart nanocarriers attract considerable interest in the filed of precision nanomedicine. Dynamic control of the interaction between nanocarriers and cells offers the feasibility that in situ activates cellular internalization at the targeting sites. Herein, we demonstrate a novel class of enzyme-responsive asymmetric polymeric vesicles self-assembled from matrix metalloproteinase (MMP)-cleavable peptide-linked triblock copolymer, poly(ethylene glycol)-GPLGVRG-b-poly(ε-caprolactone)-b-poly(3-guanidinopropyl methacrylamide) (PEG-GPLGVRG-PCL-PGPMA), in which the cell-penetrating PGPMA segments asymmetrically distribute in the outer and inner shells with fractions of 9% and 91%, respectively. Upon treatment with MMP-2 to cleave the stealthy PEG shell, the vesicles undergo morphological transformation into fused multicavity vesicles and small nanoparticles, accompanied by redistribution of PGPMA segments with 76% exposed to the outside. The vesicles after dePEGylation show significantly increased cellular internalization efficiency (∼10 times) as compared to the original ones due to the triggered availability of cell-penetrating shells. The vesicles loading hydrophobic anticancer drug paclitaxel (PTX) in the membrane exhibit significantly enhanced cytotoxicity against MMP-overexpressing HT1080 cells and multicellular spheroids. The proposed vesicular system can serve as a smart nanoplatform for in situ activating intracellular drug delivery in MMP-enriched tumors.

Adsorption of plasma proteins to nanomaterial surfaces has a great influence on their bio-functionality. However, there is limited understanding of the relationship between the functional proteins in the protein corona and the biological identity of the materials. Here we show that the in situ generated thrombin in the protein corona of a Ca-zeolite surface displays a calcium-dependent, unusually high (∼3,000 NIH U/mg) procoagulant activity, which is even stable against antithrombin deactivation. Removing the encapsulated Ca2+ in the zeolites leads to deactivation by antithrombin. Our observations suggest that the thrombin activity can be regulated by the inorganic surface and cations. Most importantly, our discovery indicates the link between the biomolecules in the protein corona and the procoagulant activity of the materials, providing a new molecular basis for the procoagulant mechanism for zeolite hemostatics.

The combination of 5-FU and Oxaliplatin has been widely adopted as one of the first line chemotherapeutic regimens for colon cancer patients. However, the development of chemoresistance can lead to early recurrence and metastasis to distant organs, thus remaining a leading cause of death from colon cancer. In the present study, the increased production of hydrogen sulfide (H2S) in colon cancer tissues was validated and the effect of inhibition of production of endogenous H2S on the responses of colon cancer cells to 5-FU and Oxaliplatin was further analyzed. The results suggested that inhibition of the enzymatic activity of cystathionine-β-synthase (CBS), a major producer of H2S in colon cancer cells, significantly decreased the IC50s of both 5-FU and Oxaliplatin. Inhibition of CBS leads to decreased PI3K-Akt signaling and consequently decreased expression of thymidylate synthetase (TYMS), which is the target of 5-FU. Inhibition of CBS utilizing aminooxyacetic acid (AOAA) leads to increased production of reactive oxygen species (ROS) and exaggerated mitochondrial damages in colon cancer cells. Analysis performed on CompuSyn confirmed the synergetic effect of AOAA with both 5-FU and Oxaliplatin. In vivo imaging of tumorigenesis in nude mice further confirmed the effect of inhibition of CBS on the therapeutic effect of both 5-FU and Oxaliplatin. Together, these results suggested that inhibition of production of endogenous H2S might be a promising target for chemoresistance in colon cancer. Citation Format: Shanwen Chen, Shuai Zuo. Increased production of endogenous hydrogen sulfide (H2S) induced resistance to 5-FU and Oxaliplatin in colon cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3824.

BACKGROUND Recently, long noncoding RNA (lncRNA) H19 has been reported to be related with VDR signaling and the development of inflammatory diseases including osteoarthritis. The aim of this study was to investigate the correlation between the expression level of H19 and VDR in ulcerative colitis (UC) tissues and to investigate the effect of H19 overexpression on intestinal epithelial barrier function. METHODS The expression level of H19, miR-675-5p, and VDR in UC tissues and paired normal tissues collected from 12 patients with UC was investigated by quantitative real-time polymerase chain reaction. Caco-2 monolayers were used to test the effect of H19 and miR-675-5p overexpression on the intestinal epithelial barrier function and the status of tight junction proteins and VDR. Luciferase assay was used to validate the target site of miR-675-5p in the 3'UTR of VDR mRNA. RESULTS The expression of H19 was found to be negatively correlated with the expression of VDR in UC tissues (r = 0.5369, P < 0.05). The expression of miR-675-5p was also found to be negatively correlated with the expression of VDR in UC tissues (r = 0.5233, P < 0.01). H19 overexpression increased Caco-2 monolayer permeability and decreased the expression of tight junction proteins and VDR, which was significantly attenuated by cotransfection with miR-675-5p inhibitors. The 3'UTR of VDR mRNA was validated to be one of the direct targets of miR-675-5p. CONCLUSIONS This study reveals the destructive effect of H19 overexpression on intestinal epithelial barrier function and suggests a potential role of H19 in the development of UC. In addition, H19 overexpression may be one of the mechanisms underlying the decreased expression of VDR in UC tissues and the interaction between H19 and VDR signaling may provide potential therapeutic targets for UC.

Inflammation is tightly regulated by nuclear factor-kappa B (NF-kappaB), and if left unchecked excessive NF-kappaB activation for cytokine overproduction can lead to various pathogenic consequences including carcinogenesis. A proinflammatory cytokine, tumor necrosis factor-alpha (TNF-alpha), can be used to explore possible mechanisms whereby unknown functional pathways modulate the NF-kappaB activity for regulating TNF-alpha-induced inflammation. Given the multifunctional nature of 14-3-3 family proteins and the recent finding of their presence in the TNF-alpha/NF-kappaB pathway network, we used a dual-tagging quantitative proteomic method to first profile the TNF-alpha-inducible interacting partners of 14-3-3 epsilon, the least characterized 14-3-3 isomer in the family. For the first time, we found that TNF-alpha stimulation enhances the interactions between 14-3-3 epsilon and some key components in the mitogen-activated protein kinase (MAPK) signal module which is located at the immediate upstream of NF-kappaB, including transforming growth factor-beta activated kinase-1 (TAK1) and its interacting protein, protein phosphatase 2C beta (PPM1B). By using confocal laser scanning, we observed the TNF-alpha-induced colocalizations among 14-3-3 epsilon, TAK1, and protein phosphatase 2C beta (PPM1B), and these interactions were also TNF-alpha-inducible in different cell types. Further, we found that during the full course of the cellular response to TNF-alpha, the interactions between 14-3-3 epsilon and these two proteins were dynamic and were closely correlated with the time course-dependent changes in NF-kappaB activity, suggesting that these 14-3-3 epsilon interactions are the critical points of convergence for TNF-alpha signaling for modulating NF-kappaB activity. We then postulated a mechanistic view describing how 14-3-3 epsilon coordinates its dynamic interactions with TAK1 and PPM1B for differentially modulating TNF-alpha-induced changes in NF-kappaB activity. By using bioinformatics tools, we constructed the network involving most of the 14-3-3 epsilon interacting proteins identified in our proteomic study. We revealed that 14-3-3 epsilon coordinates the cross talks between the MAPK signal module and other molecular pathways/biological processes primarily including protein metabolism and synthesis, DNA repair, and cell cycle regulation where pharmacological targets for therapeutic intervention could be systematically located.

In mammalian cells, when tandem affinity purification approach is employed, the existence of untagged endogenous target protein and repetitive washing steps together result in overall low yield of purified/stable complexes and the loss of weakly and transiently interacting partners of biological significance. To avoid the trade-offs involving in methodological sensitivity, precision, and throughput, here we introduce an integrated method, biotin tagging coupled with amino acid-coded mass tagging, for highly sensitive and accurate screening of mammalian protein-protein interactions. Without the need of establishing a stable cell line, using a short peptide tag which could be specifically biotinylated in vivo, the biotin-tagged target/bait protein was then isolated along with its associates efficiently by streptavidin magnetic microbeads in a single step. In a pulled-down complex amino acid-coded mass tagging serves as "in-spectra" quantitative markers to distinguish those bait-specific interactors from non-specific background proteins under stringent criteria. Applying this biotin tagging coupled with amino acid-coded mass tagging approach, we first biotin-tagged in vivo a multi-functional protein family member, 14-3-3epsilon, which was expressed at close to endogenous level. Starting with approximately 20 millions of 293T cells which were significantly less than what needed for a tandem affinity purification run, 266 specific interactors of 14-3-3epsilon were identified in high confidence.

Upon stimulation by distinct bacterial/viral products/agonists, APCs including macrophages tend to express particular TLR molecules to coordinate the signaling that ultimately target at chromatin and mediate the activity of downstream transcriptional factors in regulating characteristic sets of gene expression for innate immune response. To investigate largely unknown regulatory mechanism underlying agonist-specific TLR-mediated innate immune responses, at subcellular resolution, we first analyzed Pam3CSK4-induced proteome changes in living macrophages and identified the differentially expressed proteins in the cytosol and chromatin-associated fractions, respectively, by using AACT/SILAC-based quantitative proteomic approach. In the cytosol fraction, we found that the proteins with notable Pam3CSK4-induced expression changes were primarily involved in post-translational events, energy metabolism, protein transporting, and apoptosis. Among them, a ubiquitous and highly conserved iron-binding protein, Ferritin, was further characterized as a modulator for the expression of a TLR2-specific cytokine IL-10 in murine macrophage cells by using small-interfering RNA (siRNA). Interestingly, we simultaneously identified multiple apoptosis-related proteins showing opposite trend in their regulated expressions, which clearly indicated the existence of systems regulation in differentially modulating the signal for the cross-road balance between protecting cell from apoptosis and the apoptosis of infected cells. For those regulated proteins identified in the nuclear fraction, we integrated bioinformatics to find the interactions of certain chromatin-associated proteins, which suggested their interconnected involvements in proteasome-ubiquitin pathway, DNA replication, and post-translational activity upon Pam3CSK4 stimulation. Certain regulated proteins in our quantitative proteomic data set showed the similar trend of up-regulation in both Pam3CSK4- and LPS-stimulated macrophages (Nature 2007, 447, 972), suggesting their belonging to the recently identified class of pro-inflammatory genes. The regulatory discrepancy between both data sets for other set of genes indicated their agonist-specific nature in innate immune responses.

Studies have verified the protective effect of Hydrogen Sulfide (H2S) on gastric ulcer and ulcerative colitis, but the mechanisms are not fully illustrated. In this study, the possible protective effect of H2S on TNF-α/IFN-γ induced barrier dysfunction was investigated in Caco-2 cell monolayers. The barrier function of Caco-2 monolayers was evaluated by measuring trans-epithelial electrical resistance (TEER) and FITC-Dextran 4 kDa (FD-4) trans-membrane flux. ZO-1 and Occludin were chosen as markers of the localization of tight junction (TJ) proteins for immunofluorescence. The expression of MLCK and phosphorylation level of myosin light chain (MLC) were measured by immunoblotting. The activation of NF-kB p65 was analyzed by EMSA and immunofluorescence. NaHS at 500uM significantly attenuated TNF-α/IFN-γ-indueced Caco-2 monolayer barrier injury. The increased expression of MLCK and increased phosphorylation level of MLC induced by TNF-α/IFN-γ was also inhibited significantly by NaHS. Additionally, NaHS inhibited TNF-α/IFN-γ induced activation and nuclear translocation of NF-kB p65. The present study reveals the protective effect of H2S on TNF-α and IFN-γ-induced injury of intestinal epithelial barrier function in Caco-2 monolayers and suggests that the suppression of MLCK-P-MLC signaling mediated by NF-kB P65 might be one of the mechanisms underlying the protective effect of H2S.

Studies have suggested the role of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) in protecting intestinal barrier function from injuries induced by multiple reagents. Vitamin D deficiency was reported to be associated with poor prognosis in patients with alcoholic liver disease (ALD). This study is designed to investigate the effect of 1,25(OH)2D3 on ethanol-induced intestinal barrier dysfunction and the underlying mechanisms utilizing Caco-2 cell monolayers and a mouse model with acute ethanol injury. In Caco-2 monolayers, ethanol significantly increased monolayer permeability, disrupted TJ distribution, increased phosphorylation level of MLC, and induced generation of ROS compared with controls. However, pre-treatment with 1,25(OH)2D3 greatly ameliorated the ethanol-induced barrier dysfunction, TJ disruption, phosphorylation level of MLC, and generation of ROS compared with ethanol-exposed monolayers. Mice fed with vitamin d-sufficient diet had a higher plasma level of 25(OH)D3 and were more resistant to ethanol-induced acute intestinal barrier injury compared with the vitamin d-deficient group. These results suggest that the suppression of generation of ROS and increased phosphorylation level of MLC might be one of the mechanisms underlying the protective effect of 1,25(OH)2D3 on ethanol-induced intestinal barrier injury and provide evidence for the application of vitamin D as therapeutic factors against ethanol-induced gut leakiness.

Smart nanocarriers are of particular interest for highly effective photodynamic therapy (PDT) in the field of precision nanomedicine. Nevertheless, a critical challenge still remains in the exploration of potent PDT treatment against hypoxic tumor. Herein, light-triggered clustered polymeric vesicles for photoinduced hypoxic tumor ablation are demonstrated, which are able to deeply penetrate into the tumor and simultaneously afford oxygen supply upon light irradiation. Hydrogen peroxide (H2O2) and poly(amidoamine) dendrimer conjugating chlorin e6/cypate (CC-PAMAM) are coassembled with reactive-oxygen-species-responsive triblock copolymer into the polymeric vesicles. Upon 805 nm irradiation, the vesicles exhibit the light-triggered thermal effect that is able to decompose H2O2 into O2, which distinctly ensures the alleviation of tumor hypoxia at tumor. Followed by 660 nm irradiation, the vesicles are rapidly destabilized through singlet oxygen-mediated cleavage of copolymer under light irradiation and thus allow the release of photoactive CC-PAMAM from the vesicular chambers, followed by their deep penetration in the poorly permeable tumor. Consequently, the light-triggered vesicles with both self-supplied oxygen and deep tissue penetrability achieve the total ablation of hypoxic hypopermeable pancreatic tumor through photodynamic damage. These findings represent a general and smart nanoplatform for effective photoinduced treatment against hypoxic tumor.

Lipopolysaccharide was found to be elevated in the plasma of necrotizing enterocolitis (NEC) and inflammatory bowel disease (IBD) patients and may play an important role in the pathogenesis and propagation of these intestinal diseases. To illustrate the destructive effect of lipopolysaccharide (LPS) and to test the protective effect of 1,25-Dihydroxyvitamin D3 (1,25(OH)2D3) on LPS-induced barrier injury, an in vitro intestinal epithelia barrier model was established with Caco-2 monolayers and treated with clinically relevant concentrations (1-10 ng/ml) of LPS with or without 1,25(OH)2D3. Transepithelial electrical resistance (TEER) and FITC-Dextran 40kda (FD-40) flux were measured to reflect monolayer permeability. We found that LPS at clinically relevant concentrations increased intestinal permeability by downregulating and redistributing tight junction (TJ) proteins. 1,25(OH)2D3 added at baseline or at day 4 abrogated the destructive effect of LPS on monolayer permeability by restoring the expression and localization of TJ proteins. LPS, at clinically relevant concentrations, also downregulated the expression of vitamin D receptor (VDR); 1,25 (OH)2D3, however, could restore the expression of VDR. Our findings illustrate the mechanism underlying the destructive effect of clinically relevant concentrations of LPS on intestinal TJ barrier and provide evidence for the clinical application of vitamin D in LPS-related intestinal barrier dysfunction.

This paper studies the problem of using minimum power to provide satisfactory performance for realtime applications over unreliable and fading wireless channels. We demonstrate that this problem can be formulated as a linear programming problem. However, this formulation involves exponentially many constraints, and many parameters are either unavailable or difficult to compute, which makes it infeasible to employ standard techniques to solve the linear programming problem. Instead, we propose a simple online scheduling algorithm for this problem. This algorithm has very low complexity and makes scheduling decisions solely based on system history and current channel conditions. It is also compatible with any power control algorithms. We prove that our algorithm provides satisfactory performance to all realtime applications, and the total power consumption can be made arbitrarily close to the theoretical lower bound. Simulation results show that our scheduling algorithm indeed achieves small power consumption with fast convergence.

The inflammatory bowel diseases (IBDs), consisting of ulcerative colitis (UC) and Crohn's disease (CD), are characterized by idiopathic, chronic inflammation of the gastrointestinal tract. The overall incidence of IBDs is constantly increasing in eastern countries. In comparison with the data from western nations, in China, the incidence of male IBDs is relatively higher, the onset age is older. The severity of most cases is mild to moderate. The occurrence of fistula and peri-anal involvement are rare. Although significant improvements of IBDs therapy have been achieved in recent years, there are still over 30% UC and 70% CD cases need at least one surgery throughout their life span. Here we review the literatures published in recent years about the surgical management of IBDs.