Reducing Phenanthrene Contamination in Trifolium repens L. With Root-Associated Phenanthrene-Degrading Bacterium Diaphorobacter sp. Phe15.

Some root-associated bacteria could degrade polycyclic aromatic hydrocarbons (PAHs) in contaminated soil; however, their dynamic distribution and performance on root surface and in inner plant tissues are still unclear. In this study, greenhouse container experiments were conducted by inoculating the phenanthrene-degrading bacterium Diaphorobacter sp. Phe15, which was isolated from root surfaces of healthy plants contaminated with PAHs, with the white clover (Trifolium repens L.) via root irrigation or seed soaking. The dynamic colonization, distribution, and performance of Phe15 in white clover were investigated. Strain Phe15 could efficiently degrade phenanthrene in shaking flasks and produce IAA and siderophore. After cultivation for 30, 40, and 50 days, it could colonize the root surface of white clover by forming aggregates and enter its inner tissues via root irrigation or seed soaking. The number of strain Phe15 colonized on the white clover root surfaces was the highest, reaching 6.03 Log CFU⋅g-1 FW, followed by that in the roots and the least in the shoots. Colonization of Phe15 significantly reduced the contents of phenanthrene in white clover; the contents of phenanthrene in Phe15-inoculated plants roots and shoots were reduced by 29.92-43.16 and 41.36-51.29%, respectively, compared with the Phe15-free treatment. The Phe15 colonization also significantly enhanced the phenanthrene removal from rhizosphere soil. The colonization and performance of strain Phe15 in white clove inoculated via root inoculation were better than seed soaking. This study provides the technical support and the resource of strains for reducing the plant PAH pollution in PAH-contaminated areas.

The Added Value of Whole-Exome Sequencing for Anomalous Fetuses With Detailed Prenatal Ultrasound and Postnatal Phenotype.

OBJECTIVES: The objective of the study was to explore the added value of whole-exome sequencing (WES) in abnormal fetuses with detailed prenatal ultrasound and postnatal phenotype with normal karyotype and chromosomal microarray analysis (CMA). METHODS: Parents of fetuses with structural abnormalities by prenatal ultrasound who consented to provide fetal samples were prospectively recruited from January 2017 to December 2019. With aneuploidies or cases with copy number variations (CNVs) excluded, WES was performed for cases with normal karyotype and CMA results. Detailed prenatal ultrasound and postnatal imaging or pathology features were recommended for further interpretation of genetic variants. RESULTS: WES was performed for 94 eligible fetuses, DNA samples of which were extracted from 53 parent-fetus trios and 41 proband-only fetal tissues. A diagnostic genetic variant was identified in 37 (39.4%) of 94 fetuses, and 34 (64.2%) were detected in 53 trios, which was significantly greater than 3 (7.3%) in 41 proband-only cases (p < 0.001). In 34 trios with diagnostic genetic variants, 23 (67.6%) were de novo and 11 (32.4%) were inherited with two homozygous and nine heterozygous variants. Fourteen (14.9%) of 94 fetuses had a variant of uncertain significance (VUS). Among 94 cases, six affected pregnancies continued and 88 terminated, and 57 of 88 terminated cases underwent postmortem examinations. With accurate phenotypes demonstrated by prenatal ultrasound and postnatal autopsies, the clinical phenotypes were correlated in 33 (89.2%) of 37 cases with specific genotypes, with the highest matching ratio in skeletal diseases (20/33, 60.6%). CONCLUSION: WES has added value in the genetic diagnosis of abnormal fetuses with normal karyotypes and CMA, particularly in skeletal diseases. Using WES in various anomalous fetuses can broaden the understanding of prenatal phenotypes and genetic variants.

Integrative Characterization of Immune-relevant Genes in Hepatocellular Carcinoma.

BACKGROUND AND AIMS: Tumor microenvironment plays an essential role in cancer development and progression. Cancer immunotherapy has become a promising approach for the treatment of hepatocellular carcinoma (HCC). We aimed to analyze the HCC immune microenvironment characteristics to identify immune-related genetic changes. METHODS: Key immune-relevant genes (KIRGs) were obtained through integrating the differentially expressed genes of The Cancer Genome Atlas, immune genes from the Immunology Database and Analysis Portal, and immune differentially expressed genes determined by single-sample gene set enrichment analysis scores. Cox regression analysis was performed to mine therapeutic target genes. A regulatory network based on KIRGs, transcription factors, and immune-related long non-coding RNAs (IRLncRNAs) was also generated. The outcomes of risk score model were validated in a testing cohort and in clinical samples using tissue immunohistochemistry staining. Correlation analysis between risk score and immune checkpoint genes and immune cell infiltration were investigated. RESULTS: In total, we identified 21 KIRGs, including programmed cell death-1 (PD-1) and cytotoxic T-lymphocyte associated protein 4 (CTLA4), and found IKBKE, IL2RG, EDNRA, and IGHA1 may be equally important to PD-1 or CTLA4. Meanwhile, KIRGs, various transcription factors, and IRLncRNAs were integrated to reveal that the NRF1-AC127024.5-IKBKE axis might be involved in tumor immunity regulation. Furthermore, the immune-related risk score model was established according to KIRGs and key IRLncRNAs, and verified more obvious discriminating power in the testing cohort. Correlation analysis indicated TNFSF4 , LGALS9 , KIAA1429 , IDO2, and CD276 were closely related to the risk score, and CD4 T cells, macrophages, and neutrophils were the primary immune infiltration cell types. CONCLUSIONS: Our results highlight the importance of immune genes in the HCC microenvironment and further unravel the underlying molecular mechanisms in the development of HCC.

Colonization and performance of a pyrene-degrading bacterium Mycolicibacterium sp. Pyr9 on root surfaces of white clover.

Some rhizosphere bacteria could colonize on the root surface of plants, or even form biofilm to promote plant growth, enhance plant resistance to harsh external environments and block the soil contamination. In this study, to explore the effects of pyrene-degrading bacterium on root surface on plant uptake of pyrene, a pyrene-degrading bacterium Mycolicibacterium sp. Pyr9 was isolated from the root surface of Eleusine indica L. Gaertn. in PAH-contaminated fields; after antibiotic labeling, it was colonized onto the root surface of white clover (Trifolium repens L.), and its distribution and performance were monitored under different levels of pyrene contamination. Strain Pyr9 could degrade 98% of pyrene (with an initial concentration of 50 mg L-1) in culture solution within 8 d; it also owns a variety of plant growth promoting characteristics and appreciable tolerance to harsh environments. The transcription of pyrene catabolic genes in Pyr9 enhanced obviously when induced by pyrene. Pyr9 colonized and grew well on the root surface of white clover via root inoculation; some cells could even enter into the root tissues and move to the shoots. Compared with the Pyr9-free treatment, the pyrene contents in the roots and shoots of Pyr9-inoculated white clover decreased by 25%-30% and 33%-42%, respectively. Correspondingly, the pyrene accumulation and translocation factors in white clover decreased as well. These results indicate that Pyr9 would be a good potential to circumvent plant pyrene pollution. This research may provide a theoretical basis and technical support for the safety of agricultural products and human health in PAH-contaminated sites.

Clinical Effect of Driver Mutations of KRAS, CDKN2A/P16, TP53, and SMAD4 in Pancreatic Cancer: A Meta-Analysis.

Objective: To evaluate the prognostic value of driver mutations in the KRAS, CDKN2A/P16, TP53, and SMAD4 genes in pancreatic cancer to aid in the design of therapeutic strategies. Search Strategy: A systematic search was conducted using PubMed, MEDLINE, Springer, and Cochrane library to identify eligible studies published between January 1990 and June 2018 that reported an association between driver mutations in these genes and survival data. Inclusion Criteria: Articles which passed the primary screen were further scrutinized for the presence of all the following items: (1) cohort studies or case-control studies, evaluating the relationship between driver mutations and cancer; (2) cancer diagnoses clearly proved; and (3) hazard ratios (HR) and 95% confidence intervals (CIs) were characterized by sufficient information. Data Extraction and Analysis: Selection of included articles, data extraction, and methodological quality assessments were, respectively, conducted by two authors. Results: The meta-analysis was composed of 17 studies on the P53, 8 on SMAD4, 7 on CDKN2A/P16, and 2 on KRAS, containing 3373 samples. Our pooled results demonstrated that the patients with overexpression of the P53 (HR = 1.249, 95% CI = 1.003-1.554, p = 0.047), SMAD4 (HR = 1.397, 95% CI = 1.015-1.922, p = 0.040), CDKN2A/P16 (HR = 0.916, 95% CI = 0.583-1.439, p = 0.704), and KRAS (HR = 1.68, 95% CI = 1.27-2.22, p < 0.001) mutations all had poorer overall survival. Conclusion: This systematic review and meta-analysis supports the use of driver mutations in the P53, SMAD4, and KRAS genes as prognostic markers for pancreatic cancer.

Immune-Related lncRNA to Construct Novel Signature and Predict the Immune Landscape of Human Hepatocellular Carcinoma.

The signature composed of immune-related long noncoding ribonucleic acids (irlncRNAs) with no requirement of specific expression level seems to be valuable in predicting the survival of patients with hepatocellular carcinoma (HCC). Here, we retrieved raw transcriptome data from The Cancer Genome Atlas (TCGA), identified irlncRNAs by co-expression analysis, and recognized differently expressed irlncRNA (DEirlncRNA) pairs using univariate analysis. In addition, we modified Lasso penalized regression. Then, we compared the areas under curve, counted the Akaike information criterion (AIC) values of 5-year receiver operating characteristic curve, and identified the cut-off point to set up an optimal model for distinguishing the high- or low-disease-risk groups among patients with HCC. We then reevaluated them from the viewpoints of survival, clinic-pathological characteristics, tumor-infiltrating immune cells, chemotherapeutics efficacy, and immunosuppressed biomarkers. 36 DEirlncRNA pairs were identified, 12 of which were included in a Cox regression model. After regrouping the patients by the cut-off point, we could more effectively differentiate between them based on unfavorable survival outcome, aggressive clinic-pathological characteristics, specific tumor immune infiltration status, low chemotherapeutics sensitivity, and highly expressed immunosuppressed biomarkers. The signature established by paring irlncRNA regardless of expression levels showed a promising clinical prediction value.

Pan-cancer analysis of the CASP gene family in relation to survival, tumor-infiltrating immune cells and therapeutic targets.

The cysteinyl aspartate protease (caspase, or CASP) gene family plays a significant role in programmed cell death, inflammation and immunity. However, the correlation between CASP family members and prognosis and tumor-infiltrating lymphocytes in different tumors has not been determined. We investigated the role of CASP genes in cancer prognosis and their relationship with clinicopathological parameters. We also evaluated the correlation between the expression of CASP family members and cancer immune infiltration and evaluated whether these molecules can be used as targets for immunotherapy. The CASP1/2/4/5/7/9 genes may represent prognostic factors and therapeutic targets for breast cancer, hepatocellular carcinoma and pancreatic cancer. Another finding is that the CASP1/4/5 genes help to regulate innate immunity and T cell immunity and may also have an important effect on tumor checkpoint inhibition. These findings may elucidate the roles played by CASP family members in cancer progression and identify strategies to promote collaborative activities in the context of immunotherapy.

Immune-related prognosis biomarkers associated with osteosarcoma microenvironment.

BACKGROUND: Osteosarcoma is a highly aggressive bone tumor that most commonly affects children and adolescents. Treatment and outcomes for osteosarcoma have remained unchanged over the past 30 years. The relationship between osteosarcoma and the immune microenvironment may represent a key to its undoing. METHODS: We calculated the immune and stromal scores of osteosarcoma cases from the Target database using the ESTIMATE algorithm. Then we used the CIBERSORT algorithm to explore the tumor microenvironment and analyze immune infiltration of osteosarcoma. Differentially expressed genes (DEGs) were identified based on immune scores and stromal scores. Search Tool for the Retrieval of Interacting Genes Database (STRING) was utilized to assess protein-protein interaction (PPI) information, and Molecular Complex Detection (MCODE) plugin was used to screen hub modules of PPI network in Cytoscape. The prognostic value of the gene signature was validated in an independent GSE39058 cohort. Gene set enrichment analysis (GSEA) was performed to study the hub genes in signaling pathways. RESULTS: From 83 samples of osteosarcoma obtained from the Target dataset, 137 DEGs were identified, including 134 upregulated genes and three downregulated genes. Functional enrichment analysis and PPI networks demonstrated that these genes were mainly involved in neutrophil degranulation and neutrophil activation involved in immune response, and participated in neuroactive ligand-receptor interaction and staphylococcus aureus infection. CONCLUSIONS: Our study established an immune-related gene signature to predict outcomes of osteosarcoma, which may be important targets for individual treatment.

Evaluation of Cervical Elastography for Prediction of Spontaneous Preterm Birth in Low-Risk Women: A Prospective Study.

OBJECTIVES: The aim of this study was to determine whether cervical elastographic parameters in addition to cervical length (CL) during the 3 trimesters of pregnancy would be predictive of spontaneous preterm birth (sPTB) among low-risk women. METHODS: This work was a prospective nested case-control study evaluating cervical elastographic parameters and CL in low-risk women during the 3 trimesters of pregnancy. A binary logistic regression analysis was used to calculate significant covariates for prediction of sPTB. The area under the curve of the prediction model was calculated by using a receiver operating characteristic curve. RESULTS: There were 286 women (26 cases and 260 controls) included in the analysis. The parameters of cervical elasticity became softened and heterogeneous during the 3 trimesters of pregnancy in both women with and without sPTB. The differences in the mean strain value at the internal os of the cervix (IOS), ratio (strain ratio of the internal os to the external os) during the second trimester and the IOS during the third trimester between the groups had statistical significance (P < .01; P = .01; P < .01, respectively). The CL had no association with sPTB during the 3 trimesters. The IOS during the second trimester was a better predictor of sPTB, with an area under the curve of 0.730, and sensitivity was 72.73%. CONCLUSIONS: We observed multiple elastographic parameters and demonstrated the physiologic changes in the cervix during the 3 trimesters of pregnancy. Furthermore, we found that the IOS during the second trimester can be helpful in predicting sPTB. However, the CL had no association with sPTB during the 3 trimesters of pregnancy.

Quantitative elastography of cervical stiffness during the three trimesters of pregnancy with a semiautomatic measurement program: A longitudinal prospective pilot study.

AIM: To assess the reproducibility of a semiautomatic quantification tool for cervical stiffness and evaluate the normal changes in cervical elasticity during the three trimesters of pregnancy. METHODS: This longitudinal prospective pilot study evaluated cervical elasticity during the three trimesters of pregnancy (11-14, 20-24 and 28-32 weeks) in women with singleton pregnancies. Women with a history of conization, cerclage, cervical Naboth cysts (diameter > 10 mm), cervical tumors, or uterine malformation were excluded. A semiautomatic tool was used to evaluate the stiffness of the whole cervix and the internal and external cervical os with multiple quantitative elasticity parameters and the cervical length (CL) on the sagittal view via transvaginal elastography. Intraclass correlation coefficients (ICC) and Bland-Altman analysis were used to assess intra- and interobserver variability. E-Cervix parameters during the three trimesters were compared using the Friedman test. RESULTS: In total, 217 women with 651 strain examinations during the three trimesters were included. The intra- and interobserver ICC for the E-Cervix parameters ranged from 0.947 to 0.991 and 0.855 to 0.989, respectively. There were significant differences in all parameters among the three trimesters. Cervical elasticity showed significant softening and became heterogeneous during the three trimesters. The median CL was significantly shorter in the first trimester than in the second and third trimesters (P = 0.004, P < 0.001). CONCLUSION: E-Cervix provides a graphical tool for operators to easily define regions of interest and obtain multiple repeatable measures of elasticity. The normal references for E-Cervix parameters during the three trimesters reflect the physiological cervical changes during pregnancy.

Prognostic role of glycolysis for cancer outcome: evidence from 86 studies.

OBJECTIVE: The abnormal expression of the key enzymes in glycolytic pathways, including glucose transporter-1, glucose transporter-3, hexokinase-II, lactate dehydrogenase 5, pyruvate kinase M2, glucose-6-phosphate dehydrogenase, transketolase-like protein 1 and pyruvate dehydrogenase kinase-1 was reported to be associated with poor prognosis of various cancers. However, the association remains controversial. The objective of this study was to investigate the prognostic significance of glycolysis-related proteins. MATERIALS AND METHODS: We searched MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, using Pubmed and Ovid as search engines and Google Scholar from inception to April 2017. Eighty-six studies with 12,002 patients were included in the study. RESULTS: Our pooled results identified that glycolysis-related proteins in cancers were associated with shorter overall survival of colorectal cancer (HR 2.33, 95% CI 1.38-3.93, P = 0.002), gastric cancer (HR 1.55, 95% CI 1.31-1.82, P < 0.001), cancer of gallbladder or bile duct (HR 2.16, 95% CI 1.70-2.75, P < 0.001), oral cancer (HR 2.07, 95% CI 1.32-3.25, P < 0.001), esophageal cancer (HR 1.66, 95% CI 1.25-2.21, P = 0.01), hepatocellular carcinoma (HR 2.04, 95% CI 1.64-2.54, P < 0.001), pancreatic cancer (HR 1.72, 95% CI 1.39-2.13, P < 0.001), breast cancer(HR 1.67, 95% CI 1.34-2.08, P < 0.001), and nasopharyngeal carcinoma (HR 3.59, 95% CI 1.75-7.36, P < 0.001). No association was found for lung cancer, ovarian cancer or melanoma. The key glycolytic transcriptional regulators (HIF-1α, p53) were analyzed in parallel to the glycolysis-related proteins, and the pooled results identified that high-level expression of HIF-1α was significantly associated with shorter overall survival (HR 0.57, 95% CI 0.42-0.79, P < 0.001) Furthermore, glycolysis-related proteins linked with poor differentiated tumors (OR 1.81, 95% CI 1.46-2.25, P < 0.001), positive lymph node metastasis (OR 2.73, 95% CI 2.16-3.46, P < 0.001), positive vascular invasion (OR 2.05, 95% CI 1.37-3.07, P < 0.001), large tumor size (OR 2.06, 95% CI 1.80-2.37, P < 0.001), advanced tumor stage (OR 1.58, 95% CI 1.19-2.09, P < 0.001), and deeper invasion (OR 2.37, 95% CI 1.93-2.91, P < 0.001). CONCLUSION: Glycolytic transcriptional regulators and glycolysis-related proteins in cancers were significantly associated with poor prognosis, suggesting glycolytic status may be potentially valuable prognostic biomarkers for various cancers.

Colonization on root surface by a phenanthrene-degrading endophytic bacterium and its application for reducing plant phenanthrene contamination.

A phenanthrene-degrading endophytic bacterium, Pn2, was isolated from Alopecurus aequalis Sobol grown in soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Based on morphology, physiological characteristics and the 16S rRNA gene sequence, it was identified as Massilia sp. Strain Pn2 could degrade more than 95% of the phenanthrene (150 mg · L(-1)) in a minimal salts medium (MSM) within 48 hours at an initial pH of 7.0 and a temperature of 30 °C. Pn2 could grow well on the MSM plates with a series of other PAHs, including naphthalene, acenaphthene, anthracene and pyrene, and degrade them to different degrees. Pn2 could also colonize the root surface of ryegrass (Lolium multiflorum Lam), invade its internal root tissues and translocate into the plant shoot. When treated with the endophyte Pn2 under hydroponic growth conditions with 2 mg · L(-1) of phenanthrene in the Hoagland solution, the phenanthrene concentrations in ryegrass roots and shoots were reduced by 54% and 57%, respectively, compared with the endophyte-free treatment. Strain Pn2 could be a novel and useful bacterial resource for eliminating plant PAH contamination in polluted environments by degrading the PAHs inside plants. Furthermore, we provide new perspectives on the control of the plant uptake of PAHs via endophytic bacteria.

Isolation, plant colonization potential, and phenanthrene degradation performance of the endophytic bacterium Pseudomonas sp. Ph6-gfp.

This investigation provides a novel method of endophyte-aided removal of polycyclic aromatic hydrocarbons (PAHs) from plant bodies. A phenanthrene-degrading endophytic bacterium Pseudomonas sp. Ph6 was isolated from clover (Trifolium pratense L.) grown in a PAH-contaminated site. After being marked with the GFP gene, the colonization and distribution of strain Ph6-gfp was directly visualized in plant roots, stems, and leaves for the first time. After ryegrass (Lolium multiflorum Lam.) roots inoculation, strain Ph6-gfp actively and internally colonized plant roots and transferred vertically to the shoots. Ph6-gfp had a natural capacity to cope with phenanthrene in vitro and in planta. Ph6-gfp degraded 81.1% of phenanthrene (50 mg · L(-1)) in a culture solution within 15 days. The inoculation of plants with Ph6-gfp reduced the risks associated with plant phenanthrene contamination based on observations of decreased concentration, accumulation, and translocation factors of phenanthrene in ryegrass. Our results will have important ramifications in the assessment of the environmental risks of PAHs and in finding ways to circumvent plant PAH contamination.