Systematic biases in reference-based plasma cell-free DNA fragmentomic profiling.

Plasma cell-free DNA (cfDNA) fragmentation patterns are emerging directions in cancer liquid biopsy with high translational significance. Conventionally, the cfDNA sequencing reads are aligned to a reference genome to extract their fragmentomic features. In this study, through cfDNA fragmentomics profiling using different reference genomes on the same datasets in parallel, we report systematic biases in such conventional reference-based approaches. The biases in cfDNA fragmentomic features vary among races in a sample-dependent manner and therefore might adversely affect the performances of cancer diagnosis assays across multiple clinical centers. In addition, to circumvent the analytical biases, we develop Freefly, a reference-free approach for cfDNA fragmentomics profiling. Freefly runs ∼60-fold faster than the conventional reference-based approach while generating highly consistent results. Moreover, cfDNA fragmentomic features reported by Freefly can be directly used for cancer diagnosis. Hence, Freefly possesses translational merit toward the rapid and unbiased measurement of cfDNA fragmentomics.

Generalizable transcriptome-based tumor malignant level evaluation and molecular subtyping towards precision oncology.

In cancer treatment, therapeutic strategies that integrate tumor-specific characteristics (i.e., precision oncology) are widely implemented to provide clinical benefits for cancer patients. Here, through in-depth integration of tumor transcriptome and patients' prognoses across cancers, we investigated dysregulated and prognosis-associated genes and catalogued such important genes in a cancer type-dependent manner. Utilizing the expression matrices of these genes, we built models to quantitatively evaluate the malignant levels of tumors across cancers, which could add value to the clinical staging system for improved prediction of patients' survival. Furthermore, we performed a transcriptome-based molecular subtyping on hepatocellular carcinoma, which revealed three subtypes with significantly diversified clinical outcomes, mutation landscapes, immune microenvironment, and dysregulated pathways. As tumor transcriptome was commonly profiled in clinical practice with low experimental complexity and cost, this work proposed easy-to-perform approaches for practical clinical promotion towards better healthcare and precision oncology of cancer patients.

Rhein ameliorates septic lung injury and intervenes in macrophage metabolic reprogramming in the inflammatory state by Sirtuin 1.

AIMS: Sepsis is an organ dysfunction syndrome caused by the maladjustment of response to infection. Acute lung injury (ALI) appears the earliest, with urgent onset and limited treatments. Previous pharmacological studies have found that rhein (RH), an active ingredient rich in rhubarb, has multiple pharmacological activities such as anti-inflammatory, anti-infection and metabolic regulation. This research aimed to explore whether RH alleviates septic acute lung injury and probe possible mechanisms. MAIN METHODS: In this study, the septic ALI mouse model was established by cecal ligation and perforation (CLP). LPS-induced RAW264.7 model was selected to further explore the protective mechanism of RH. H&E staining, Western blot, qRT-PCR, and 1H NMR analysis were used to verify the protective effect of RH on ALI in vivo and vitro. KEY FINDINGS: RH could relieve pathological lung injury and pulmonary edema, reduce the serum LPS and inhibit inflammatory response in CLP mice. Further studies displayed that RH affected the metabolism in vivo, with significant changes in serum and lung metabolomics. In vitro results demonstrated that RH inhibited the expression of inflammatory mediators and factors in macrophages by affecting metabolic reprogramming and upregulating the expression of Sirtuin 1. SIGNIFICANCE: RH improved the overall metabolic condition of sepsis mice by up-regulating and activating SIRT1, and inhibited the over activation of macrophages by regulating metabolism. These findings reveal the therapeutic mechanism of RH on sepsis ALI from the perspective of metabolism.

Identification of miRNA-mRNA-TF regulatory networks in peripheral blood mononuclear cells of type 1 diabetes.

BACKGROUND: Type 1 diabetes (T1D) is a T lymphocyte-mediated and B lymphocyte-assisted autoimmune disease. We aimed to identify abnormally expressed genes in peripheral blood mononuclear cells (PBMCs) of T1D and explore their possible molecular regulatory network. METHODS: Expression datasets were downloaded from the Gene Expression Omnibus (GEO) database. Then, the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) were identified, and functional enrichment and immune cell infiltration analysis were performed. The starBase, miRTarBase, TarBase, JASPAR, ENCODE, and TRRUST databases constructed the miRNA-mRNA-TF regulatory network. The ROC curves were plotted to evaluate the sensitivity and specificity of miRNAs and mRNAs. RESULT: A total of 216 DEGs directly or indirectly related to type I diabetes mellitus, natural killer cell-mediated cytotoxicity, Th1, and Th2 cell differentiation, and the IL-17 and TNF signaling pathways were obtained. The miRNA-mRNA-TF network indicates that miR-320a and SOX5 are the only miRNAs and TFs that both target ADM and RRAGD. The ROC curves showed that ADM (0.9375), RRAGD (0.8958), and hsa-mir-320a (0.9417) had high accuracy in T1D diagnosis. CONCLUSION: The constructed regulatory networks, including miR-320a/ADM/SOX5 and miR-320a/RRAGD/SOX5, may provide new insight into the mechanisms of development and progression in T1D.

Sinomenine ameliorates septic acute lung injury in mice by modulating gut homeostasis via aryl hydrocarbon receptor/Nrf2 pathway.

Sepsis is a systemic inflammatory response syndrome caused by a host's immune response to infection. Acute lung injury (ALI) is one of the most common complications of sepsis with high mortality and morbidity. Recent evidence demonstrated that the 'gut-lung axis' was related to the progression of septic acute lung injury, which regarded gut microbiota and intestinal barrier as two critical factors correlated with acute lung injury. Sinomenine is an isoquinoline alkaloid component extracted from Sinomenium acutum Rehd，et Wils, which has been already reported to have significant anti-inflammatory, immunosuppressive, and anti-arthritis properties. In this research, we observed that sinomenine could repair the lung injury and alleviate inflammatory response induced by cecum ligation and puncture (CLP). Illumine sequencing of 16S rDNA revealed that sinomenine could improve the richness of gut microbiota and modulate the composition of intestinal flora in cecum ligation and puncture mice. Meanwhile, sinomenine could reduce the colon pathological damage and improve the intestine barrier integrity in cecum ligation and puncture mice. We also found that the molecular mechanism of sinomenine's protective effect on intestinal tract was related to the activation of aryl hydrocarbon receptor/nuclear factor erythroid-2 related factor 2（Nrf2）pathway both in vivo and vitro experiments. Collectively, the prevention of septic acute lung injury by sinomenine might be mediated by modulating gut microbiota and restoring intestinal barrier via aryl hydrocarbon receptor/Nrf2-dependent pathway.

HOXC11 positively regulates the long non-coding RNA HOTAIR and is associated with poor prognosis in colon adenocarcinoma.

Colorectal cancer ranks third in terms of incidence and second in terms of mortality worldwide. The homeobox transcript antisense intergenic RNA (HOTAIR), which was found to be located on the antisense chain of the homeobox C (HOXC) gene cluster, is a long non-coding RNA involved in multiple types of tumors. The role of HOXC11 in tumors remains unclear. Reverse transcription-quantitative PCR was performed to detect the expression level of HOXC11 in colon adenocarcinoma. Cell proliferation and invasion were assessed. RNase protection assay was used to test the possibility of RNA duplex formation. The increased expression and co-expression trend of HOXC11 and HOTAIR were identified in multiple types of cancer from The Cancer Genome Atlas and the results were validated in 12 colon adenocarcinoma and paired non-tumor tissue samples. The expression of HOXC11 and HOTAIR was found to be associated with poor prognosis in colon adenocarcinoma and kidney renal clear cell carcinoma. Furthermore, HOXC11 was found to positively regulate HOTAIR by RNA duplex formation and promoted the proliferation and invasion of colon adenocarcinoma cells.

Characterization of a carboxyl methyltransferase in Fusarium graminearum provides insights into the biosynthesis of fusarin A.

Fusarium graminearum is a major fungal pathogen that causes a series of devastating crop diseases by producing a variety of mycotoxins. Fusarins are a class of polyketide-nonribosomal peptide hybrids. In Fusarium mycotoxins, a variable 2-pyrrolidone ring conjugates with a polyene chain substituted with a methyl ester moiety. The enzymatic route through which fusarin A, a major member of the fusarin family with a characteristic tetrohydrofuran-coupled pyrrolidone ring, is formed in F. graminearum has not been established. By targeting the final step in the biosynthesis of fusarin A, we report here an S-adenosyl methionine-dependent carboxyl methyltransferase responsible for the formation of the methyl ester moiety by in vivo gene inactivation, isolation and characterization of a key fusarin intermediate, and in vitro biochemical characterization. Related findings provide insights into the poorly understood biosynthetic pathway of fusarin A. Additionally, bioactivity assays demonstrate that the methyl ester is necessary for fusarin cytotoxicity.

Phenylboronic acid-functionalized F127-oligochitosan conjugate micelles for doxorubicin encapsulation.

Doxorubicin shows good anticancer activity, but poor pharmacokinetic property and high organ toxicity restrict its clinical application. The synthesized phenylboronic acid-modified F127-chitosan conjugate was used to prepare doxorubicin-loaded micelles through dialysis method. The physicochemical properties of the doxorubicin-loaded micelles were characterized. These micelles were further evaluated for in vitro release/cytotoxicity, in vivo activity/biosafety, and pharmacokinetic studies. in vitro release experiment demonstrated that the release of doxorubicin from drug-loaded micelles was pH-dependent. in vitro cytotoxic study showed that the introduction of phenylboronic acid resulted in lower IC50 against B16 cells than that in non-modified F127-chitosan micelles group, and the doxorubicin-loaded micelles displayed lower in vitro activity against B16, A549, and HT-29 cells than free doxorubicin did. However, in vivo experiments confirmed that the doxorubicin-loaded micelles were safe for mouse main organs, obviously improved pharmacokinetic parameters of doxorubicin in rat and achieved comparable inhibition of tumor growth with no animal death in B16-bearing mice models throughout the experiment when compared with free doxorubicin. The phenylboronic acid-sialic acid interaction and pH-sensitive drug release might play important roles in increased tumor targeting and therapeutic effect of the doxorubicin-loaded micelles.

Sini decoction ameliorates interrelated lung injury in septic mice by modulating the composition of gut microbiota.

Our work used cecal ligation and puncture (CLP) mice model and 16S rDNA sequencing to explore whether the therapeutic mechanism of Sini Decoction (SND) on sepsis was related to the intestinal flora currently of concern. Twenty-four hours after surgery, tissues and serum from three groups (Control, CLP and CLP + SND) were collected for further analysis and colon contents were isolated for 16S rDNA analysis. Mortality, histological examination and inflammatory cytokines levels confirmed that the sepsis model was induced successfully and resulted in serious pathological damage, while all of these could be reversed by SND. In intestinal flora analysis, the microbial richness and abundance were recovered after SND treatment. Furthermore, at the phylum level, the abundance of Proteobacteria showed drastic increase after CLP. Similarly, CLP surgery significantly disrupted the balance of intestinal flora, with a huge increase of Escherichia-Shigella, a Gram-negative genus that might release lipopolysaccharide (LPS) and other genera. And these shifts could be defused by SND, indicating its function of regulating gut microbiota. This study demonstrates that SND could ameliorate the symptoms and pathology associated with sepsis in CLP model via modulating the flora in intestinal tract, which enriches a possible mechanism of SND's therapeutic effect.

Hypoglycemic activity of CPU2206: A novel peptide from sika (Cervus nippon Temminck) antler.

Previous work had extracted and purified an antidiabetic peptide named CPU2206 with 7,127.6 Da. In this work, the toxicity of CPU2206 was first evaluated by daily administration to ICR mice, and after 28 days of administration, the body weight and lipid metabolism of the mice did not change significantly, which proved its safety and reliability. Second, further studies have focused on its hypoglycemic effects by daily intraperitoneal injection to alloxan-induced diabetic mice and KK-Ay mice, showing that CPU2206 effectively decreased the blood glucose and corresponding indicators of diabetic mice. Daily administration of CPU2206 nearly normalized the lipid metabolic parameters in diabetic mice. Histological examination also validated that CPU2206 ameliorated the pancreas injuries induced by alloxan or alleviated islet hypertrophy caused by insulin resistance in KK-Ay mice. To sum up, a totally new bioactive peptide CPU2206 obtained from sika antler showed significantly antidiabetic as well as lipid-lowering effects in diabetic mice. PRACTICAL APPLICATIONS: Antler has been used as a traditional Chinese medicine to invigorate primordial energy, enrich the blood, strengthen bones, and improve both male and female sexual functions for thousands of years. Traditionally, velvet antler can be grinded directly and taken orally, or used in porridge, wine and meat stew. Our experiment enriches the research on the function of edible antlers, provides the basis for developing it into functional health food, and on the other hand, provides an idea for finding new antidiabetic drugs.

Sini decoction ameliorates sepsis-induced acute lung injury via regulating ACE2-Ang (1-7)-Mas axis and inhibiting the MAPK signaling pathway.

Sepsis, as life-threatening organ dysfunction caused by a dysregulated host response to infection, is characterized by the extensive release of cytokines and other mediators. Sini decoction (SND), a traditional Chinese prescription medicine, has been used clinically for the treatment of sepsis. But its explicit mechanism of action is still unclear. The present study aims to evaluate the potential protective effects of SND on sepsis-induced acute lung injury (ALI). After SND intervention, the lung tissues of each experimental group were collected. H&E sections were used to observe the pathological changes of lung tissue, and alveolar lavage fluid was collected to detect the infiltration of inflammatory cells. Level of inflammatory factors in lung tissue were analyzed by qRT-PCR. The change of Renin angiotensin system (RAS), as well as downstream MAPK/NF-κB signaling pathways were measured by Western blot. For in vitro experiments, human umbilical vein endothelial cells (HUVECs) were pretreated with lipopolysaccharide (LPS) and treated with SND. Subsequently, the expression levels of RAS and MAPK/NF-κB signaling pathways were measured by Western blot. In vivo, we found that SND significantly attenuated sepsis-induced pathological injury in the lung. SND also inhibited LPS-mediated inflammatory cell infiltration, the expression of pro-apoptotic proteins and the production of IL-6, IL-1ß, TNF-α and MCP-1. In vitro, experiments using a co-culture of HUVECs with SND showed that there was a decrease in pro-apoptotic protein and pro-inflammatory mediator. In this research, we also found that SND protective action could be attributed to the regulation of renin-angiotensin system (RAS). MAPKs and NF-κB pathways. To conclude, our study demonstrated that SND ameliorates sepsis-induced-ALI via regulating ACE2-Ang (1-7)-Mas axis and inhibiting the MAPK signaling pathway.

2,4,5-Trichloro-6-((2,4,6-trichlorophenyl)amino)isophthalonitrile, Exerts Anti-bladder Activities through IGF-1R/STAT3 Signaling.

2,4,5-Trichloro-6-((2,4,6-trichlorophenyl)amino)isophthalonitrile (SYD007) is a small molecule compound that was synthesized according to the structure of diarylamine. In this study, we evaluated the anti-bladder activities of SYD007, and determined its cytotoxic mechanism. We found that SYD007 exerted cytotoxicity to bladder cancer cells. Furthermore, SYD007 induced bladder cancer cell early apoptosis and arrested cell cycle. Mechanistically, SYD007 suppressed phosphorylated signal transducer and activator of transcription 3 (p-STAT3) (Tyr705) level in parallel with increases of p-extracellular signal-regulated kinase (ERK) and p-AKT. SYD007 significantly inhibited insulin-like growth factor 1 (IGF-1)-induced STAT3 activation through down-regulation of total IGF-1R level. No dramatic changes in IGF-1R mRNA levels were observed in SYD007-treated cells, suggesting that SYD007 acted primarily at a posttranscriptional level. Using molecular docking analysis, SYD007 was identified as an IGF-1R inhibitor. In summary, we reported that SYD007 exerted anti-bladder activities, and these effects were partially due to inhibition of IGF-1R/STAT3 signaling.

Influence of Oxygen Vacancy Behaviors in Cooling Process on Semiconductor Gas Sensors: A Numerical Analysis.

The influence of oxygen vacancy behaviors during a cooling process in semiconductor gas sensors is discussed by the numerical analysis method based on the gradient-distributed oxygen vacancy model. A diffusion equation is established to describe the behaviors of oxygen vacancies, which follows the effects of diffusion and exclusion in the cooling process. Numerical analysis is introduced to find the accurate solutions of the diffusion equation. The solutions illustrate the oxygen vacancy distribution profiles, which are dependent on the cooling rate as well as the temperature interval of the cooling process. The gas-sensing characteristics of reduced resistance and response are calculated. Both of them, together with oxygen vacancy distribution, show the grain size effects and the re-annealing effect. It is found that the properties of gas sensors can be controlled or adjusted by the designed cooling process. The proposed model provides a possibility for sensor characteristics simulations, which may be beneficial for the design of gas sensors. A quantitative interpretation on the gas-sensing mechanism of semiconductors has been contributed.