Effects of Foliar Spraying of Dicarboxylicdimethylammonium Chloride on Cadmium and Arsenic Accumulation in Rice Grains.

A field experiment with double cropping rice was carried out to study the foliar application effects of dicarboxylicdimethylammonium chloride (DDAC) on cadmium (Cd) and arsenic (As) accumulation in rice grains. The results showed that the spraying of DDAC could significantly reduce the accumulation of Cd and As in rice grains. The highest reductions in Cd and As content were observed when 1.5 mmol L-1 DDAC was sprayed, with 49.1% and 27.4% reductions in Cd and As content in early rice grains and 56.5% and 28.1% reductions in Cd and As content in late rice grains, respectively. In addition, the content of calcium (Ca) in rice grains increased significantly after DDAC foliar application, which was also conducive to the synthesis of amino acids such as glutamate (Glu), glycine (Gly) and cysteine (Cys) in rice grains. The results indicated that the foliar spraying of DDAC can inhibit the absorption, transport, accumulation and toxicity of Cd and As in rice grains by increasing amino acid synthesis and regulating the absorption and transport of essential elements.

Efficient regulation of cadmium accumulation by carboxymethylammonium chloride in rice: Correlation analysis and expression of transporter gene OsGLR3.

The mechanism of carboxymethylammonium chloride (CC) regulating cadmium (Cd) accumulation in rice was studied in field and hydroponic experiments. Field experiments showed that 0.2-1.2 mmol L-1 CC spraying effectively reduced Cd accumulation by 44 %-77 % in early rice grains and 39 %-78 % in late rice grains, significantly increased calcium (Ca) content and amino acids content in grains, as well as alleviated Cd-induced oxidative damage in leaves. Hydroponic experiments further verified the inhibition effect of CC on Cd accumulation. 1.2 mmol L-1 CC made the highest decrease of Cd content in shoots and roots of hydroponic seedlings by 45 % and 53 %, respectively. Exogenous CC significantly increased glutamate (Glu), glycine (Gly) and glutathione (GSH) content, and improved the activities of catalase (CAT) and superoxide dismutase (SOD) by 41-131 % and 11-121 % in shoots of hydroponic seedlings, respectively. Exogenous CC also increased the relative expression of OsGLR3.1-3.5 in the shoots and roots of hydroponic seedlings. The quantum computational chemistry was used to clarify that the Gly radical provided by CC could form various complexes with Cd through carboxyl oxygen atoms. These results showed that exogenous application of CC improved the tolerance to Cd by enhancing the antioxidant capacity; inhibited the absorption, transport and accumulation of Cd in rice by (1) promoting chelation, (2) increasing the GLRs activity through upregulating the content of Glu, Gly, as well as the expression of OsGLR3.1-3.5.

Inhibitory effects of Pseudomonas sp. W112 on cadmium accumulation in wheat grains: Reduced the bioavailability in soil and enhanced the interception by plant organs.

Microorganisms play an important role in heavy metal bioremediation and soil fertility. The effects of soil inoculation with Pseudomonas sp. W112 on Cd accumulation in wheat were investigated by analyzing the transport, subcellular distribution and speciation of Cd in the soil and plants. Pseudomonas sp. W112 application significantly decreased Cd content in the roots, internode and grains by 10.2%, 29.5% and 33.0%, respectively, and decreased Cd transfer from the basal nodes to internodes by 63.5%. Treatment with strain W112 decreased the inorganic and water-soluble Cd content in the roots and increased the proportion of residual Cd in both the roots and basal nodes. At the subcellular level, the Cd content in the root cell wall and basal node cytosol increased by 19.6% and 61.8%, respectively, indicating that strain W112 improved the ability of the root cell wall and basal node cytosol to fix Cd. In the rhizosphere soil, strain W112 effectively colonized and significantly decreased the exchangeable Cd, carbonate-bound Cd and iron-manganese oxide-bound Cd content by 43.5%, 27.3% and 17.6%, respectively, while it increased the proportion of residual Cd by up to 65.2%. Moreover, a 3.1% and 23.5% increase in the pH and inorganic nitrogen content in the rhizosphere soil, respectively, was recorded. Similarly, soil bacterial community sequencing revealed that inoculating with strain W112 increased the abundance of Pseudomonas, Thauera and Azoarcus, which are associated with inorganic nitrogen metabolism, and decreased that of Acidobacteria, which is indicative of soil alkalinization. Hence, root application of Pseudomonas sp. W112 improved soil nitrogen availability and inhibited Cd accumulation in the wheat grains in a two-stage process: by reducing the Cd availability in the rhizosphere soil and by improving Cd interception and fixation in the wheat roots and basal nodes. Pseudomonas sp. W112 may be a suitable bioremediation agent for restoring Cd-contaminated wheat fields.

[Two-stage Inhibition Effects of Burkholderia sp. Y4 Application on Cadmium Uptake and Transport in Wheat].

In order to evaluate the feasibility of using Burkholderia sp. Y4 as a cadmium （Cd）-reducing bacterial agent in contaminated wheat fields， the changes in the rhizosphere soil microbial community and Cd available state， as well as the content and transport characteristics of Cd in the wheat root， basal node， internode， and grain under the treatment of strain Y4 were tested using microbial high-throughput sequencing， step-by-step extraction， subcellular distribution， and occurrence analyses. The results showed that root application of strain Y4 significantly reduced the root and grain Cd content of wheat by 7.7% and 30.3%， respectively， compared with that in the control treatment. The Cd content and Cd transfer factor results in wheat vegetative organs showed that strain Y4 reduced the Cd transfer factor from basal node to internode by 79.3%， and Cd content in the wheat internode stem also decreased by 50.9%. The study of Cd occurrence morphology showed that strain Y4 treatment increased the proportion of residual Cd in roots and basal ganglia， decreased the contents of inorganic and water-soluble Cd in roots， and increased the content of residual Cd in basal ganglia. Further examination of the subcellular distribution of Cd showed that the Cd content in root cell walls and basal ganglia cell fluid increased by 21.3% and 98.2%， respectively， indicating that the Cd fixation ability of root cell walls and basal ganglia cell fluid was improved by the strain Y4 treatment. In the rhizosphere soil， it was found that the microbial community structure was changed by strain Y4 application. Under the Y4 treatment， the relative abundance of Burkholderia increased from 9.6% to 11.5%， whereas that of Acidobacteriota decreased. Additionally， the relative abundance of Gemmatimonadales， Pseudomonadales， and Chitinophagales were also increased by strain Y4 treatment. At the same time， the application of strain Y4 increased the pH value of rhizosphere soil by 8.3%. The contents of exchangeable Cd， carbonate-bound Cd， and iron-manganese oxide-bound Cd in the soil decreased by 44.4%， 21.7%， and 15.9%， respectively， whereas the proportion of residual Cd reached 53.6%. Root application of strain Y4 increased the contents of nitrate nitrogen and ammonium nitrogen in the soil by 22.0% and 21.4%， respectively， and the contents of alkaline nitrogen also increased to a certain extent. In conclusion， the root application of strain Y4 not only improved soil nitrogen availability but also inhibited Cd transport and accumulation from contaminated soil to wheat grains in a "two-stage" manner by reducing Cd availability in rhizosphere soil and improving Cd interception and fixation capacity of wheat roots and basal nodes. Therefore， Burkholderia Y4 has application potential as a Cd-reducing and growth-promoting agent in wheat.

TGF-ß1 induces PD-1 expression in macrophages through SMAD3/STAT3 cooperative signaling in chronic inflammation.

Programmed cell death protein 1 (PD-1), a coinhibitory T cell checkpoint, is also expressed on macrophages in pathogen- or tumor-driven chronic inflammation. Increasing evidence underscores the importance of PD-1 on macrophages for dampening immune responses. However, the mechanism governing PD-1 expression in macrophages in chronic inflammation remains largely unknown. TGF-ß1 is abundant within chronic inflammatory microenvironments. Here, based on public databases, significantly positive correlations between PDCD1 and TGFB1 gene expression were observed in most human tumors. Of note, among immune infiltrates, macrophages as the predominant infiltrate expressed higher PDCD1 and TGFBR1/TGFBR2 genes. MC38 colon cancer and Schistosoma japonicum infection were used as experimental models for chronic inflammation. PD-1hi macrophages from chronic inflammatory tissues displayed an immunoregulatory pattern and expressed a higher level of TGF-ß receptors. Either TGF-ß1-neutralizing antibody administration or macrophage-specific Tgfbr1 knockdown largely reduced PD-1 expression on macrophages in animal models. We further demonstrated that TGF-ß1 directly induced PD-1 expression on macrophages. Mechanistically, TGF-ß1-induced PD-1 expression on macrophages was dependent on SMAD3 and STAT3, which formed a complex at the Pdcd1 promoter. Collectively, our study shows that macrophages adapt to chronic inflammation through TGF-ß1-triggered cooperative SMAD3/STAT3 signaling that induces PD-1 expression and modulates macrophage function.

Malic acid inhibits accumulation of cadmium, lead, nickel and chromium by down-regulation of OsCESA and up-regulation of OsGLR3 in rice plant.

Malic acid (MA) plays an important role in plant tolerance to toxic metals, but its effect in restricting the transport of harmful metals remains unclear. In this study, japonica rice NPB and its fragile-culm mutant fc8 with low cellulose and thin cell wall were used to investigate the influence of MA on the accumulation of 4 toxic elements (Cd, Pb, Ni, and Cr) and 8 essential elements (K, Mg, Ca, Fe, Mn, Zn, Cu and Mo) in rice. The results showed that fc8 accumulated less toxic elements but more Ca and glutamate in grains and vegetative organs than NPB. After foliar application with MA at rice anthesis stage, the content of Cd, Pb, Ni significantly decreased by 27.9-41.0%, while those of Ca and glutamate significantly increased in both NPB and fc8. Therefore, the ratios between Cd and Ca in grains of NPB (3.4‰) and fc8 (1.5‰) were greatly higher than that in grains of NPB + MA (1.1‰) and fc8+MA (0.8‰) treatments. Meanwhile, the expression of OsCEAS4,7,8,9 for the cellulose synthesis in secondary cell walls were down-regulated and cellulose content in vegetative organs of NPB and fc8 decreased by 16.7-21.1%. However, MA application significantly up-regulated the expression of GLR genes (OsGLR3.1-3.5) and raised the activity of glutamic-oxalacetic transaminease for glutamate synthesis in NPB and fc8. These results indicate that hazard risks of toxic elements in foods can be efficiently reduced through regulating cellulose biosynthesis and GLR channels in plant by combining genetic modification in vivo and malic acid application in vitro.

Effects of elevation and geomorphology on cadmium, lead and chromium enrichment in paddy soil and rice: A case study in the Xiangtan basin of China.

The distributions of heavy metals in paddy fields and rice along river valleys were studied to explore the key factors affecting the accumulation of heavy metals in the upstream terraces and downstream plains. Results from 975 sampling sites showed that elevation, growing season and soil organic matter (OM) had significant effects on the content of Cd and Pb in topsoil and rice. The content of Cd (0.47-0.66 mg kg-1) and Pb (49.9-68.6 mg kg-1) in paddy fields with low elevation (30-60 m) in the downstream plains was significantly higher than the content of Cd (0.29-0.38 mg kg-1) and Pb (43.9-56.3 mg kg-1) in the upstream terraces with high altitude (60-90 m). In the double-rice production area, late rice generally produced grains with higher Cd and Pb content than early rice. Soil Cd was positively increased with the content of OM, especially in the downstream plains. When elevation was used for principal component analysis, plains with low elevation were grouped together with high content of total and soluble Cd, OM and Pb in soil, as well as high content of Cd and Pb in late rice. Altitude is one of the key factors affecting Cd content in rice. Although content of Cr (93.7-138.0 mg kg-1) was significantly higher than that of Cd and Pb in soil, content of Cr was lower than that of Cd in rice. These results indicate that paddy fields with elevation of 30-60 m in the downstream plains had high risk to produce late rice with Cd and Pb content exceeding the food safety standard 0.2 mg kg-1, which may be resulted from the driving force of runoff on soil soluble Cd and Pb from terraces to alluvial plains in river valleys.

Disulfidptosis-associated long non-coding RNA signature predicts the prognosis, tumor microenvironment, and immunotherapy and chemotherapy options in colon adenocarcinoma.

BACKGROUND: Disulfidptosis is independent of apoptosis, ferroptosis, and cuproptosis and is associated with cancer progression, treatment response, and prognosis. However, the predictive potential of disulfidptosis-associated lncRNAs in colon adenocarcinoma (COAD) and their features in the tumor immune microenvironment (TIME) require further elucidation. METHODS: RNA transcriptome, clinical information, and mutation data of COAD samples were obtained from the TCGA database. The risk model was first constructed by co-expression analysis of disulfidptosis genes and lncRNAs, and prognostic lncRNAs were screened using Cox regression, followed by least absolute shrinkage and selection operator analysis. Enrichment analyses were performed to explore the underlying biological functions and signaling of model-associated differentially expressed genes (MADEGs). Moreover, TIME of MADEGs was analyzed to assess the immunotherapy. Finally, the expression levels of the lncRNAs were verified by taking specimens of patients with COAD from the Affiliated Hospital of Qingdao University. RESULTS: We constructed a prognosis-related risk model based on four disulfidptosis-associated lncRNAs (ZEB1-AS1, SNHG16, SATB2-AS1, and ALMS1-IT1). By analyzing the survival of patients in the whole, training, and test groups, we found that patients with COAD in the low-risk group had better overall survival than those in the high-risk group. Validation of the model via Cox analysis and clinical indicators demonstrated that the model had a decent potential for predicting the prognosis of patients with COAD. Enrichment analyses revealed that the MADEGs were related to disulfidptosis-associated biological functions and cancer pathways. Furthermore, patients with COAD in the high-risk group had more positive responses to immune checkpoint inhibitors (ICIs) than those in the low-risk group, as confirmed by TIME analysis. ZEB1-AS1, SNHG16, and ALMS1-IT1 were expressed at higher levels in tumor samples than those in the corresponding paracancerous samples (p < 0.05), whereas SATB2-AS1 was upregulated in the paracancerous samples (p < 0.05). CONCLUSIONS: This signature may guide prognosis, molecular mechanisms, and treatment strategies, including ICIs and chemotherapy, in patients with COAD.

Cadmium pollution leads to selectivity loss of glutamate receptor channels for permeation of Ca2+/Mn2+/Fe2+/Zn2+ over Cd2+ in rice plant.

The selective permeation of glutamate receptor channels (GLRs) for essential and toxic elements in plant cells is poorly understood. The present study found that the ratios between cadmium (Cd) and 7 essential elements (i.e., K, Mg, Ca, Mn, Fe, Zn and Cu) in grains and vegetative organs increased significantly with the increase of soil Cd levels. Accumulation of Cd resulted in the significant increase of Ca, Mn, Fe and Zn content and the expression levels of Ca channel genes (OsCNGC1,2 and OsOSCA1.1,2.4), while remarkable reduction of glutamate content and expression levels of GLR3.1-3.4 in rice. When planted in the same Cd-polluted soil, mutant fc8 displayed significantly higher content of Ca, Fe, Zn and expression levels of GLR3.1-3.4 than its wild type NPB. On the contrary, the ratios between Cd and essential elements in fc8 were significantly lower than that in NPB. These results indicate that Cd pollution may damage the structural integrity of GLRs by inhibiting glutamate synthesis and expression levels of GLR3.1-3.4, which leads to the increase of ion influx but the decrease of preferential selectivity for Ca2+/ Mn2+/ Fe2+/ Zn2+ over Cd2+ through GLRs in rice cells.

Mitigating the toxicity of reactive oxygen species induced by cadmium via restoring citrate valve and improving the stability of enzyme structure in rice.

The mechanism of reactive oxygen species (ROS) burst in rice cells induced by cadmium (Cd) stress remains poorly understood. The present study shows that the burst of superoxide anions (O2·-) and hydrogen peroxide (H2O2) in roots and shoots led by Cd stress was attributed to the disturbance of citrate (CA) valve and the damage of antioxidant enzyme structure in the rice seedlings. Cd accumulation in cells altered the molecular structure of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) through attacking glutamate (Glu) and other residues, leading to the significant reduction of their activities in clearing O2·- and decomposing H2O2. Citrate supplementation obviously increased the activity of antioxidant enzymes and decreased ∼20-30% of O2·- and H2O2 contents in roots and shoots. Meanwhile, the synthesis of metabolites/ligands such as CA, α-ketoglutarate (α-KG) and Glu as well as the activities of related enzymes in CA valve were remarkably improved. The activities of antioxidant enzymes were protected by CA through forming stable hydrogen-bonds between CA and antioxidant enzymes, and forming the stable chelates between ligands and Cd. These findings indicate that exogenous CA mitigated the toxicity of ROS under Cd stress by the ways of restoring CA valve function to reduce the production of ROS, and improving the stability of enzyme structure to enhance antioxidant enzymes activity.

Effects of Exogenous Chlorinated Amino Acetic Acid on Cadmium and Mineral Elements in Rice Seedlings.

To explore the effect of exogenous application of chlorinated amino acetic acid on cadmium (Cd) transport characteristics in rice seedlings, X24 and Z35 rice were taken as the research objects to carry out hydroponics experiments, and the changes of Cd content in rice seedlings, rice mineral elements and amino acid content in rice were analyzed. The results showed that exogenous application of 1.2 mmol·L-1 chlorinated amino acetic acid inhibited cadmium in shoots and roots of rice seedlings; Cd content in shoots and roots were reduced by up to 62.19% and 45.61%, respectively. The majority of cadmium was in the cell wall of shoots and roots; this decreased with the increase of the concentration of chlorinated acetic acid. In addition, the Mn content in shoots and Ca content in roots of rice seedlings increased significantly after the application of chlorinated amino acetic acid. The results of amino acid analysis showed that the contents of aspartic acid, glutamic acid and cystine in rice seedlings were increased. These results indicate that exogenous application of chlorinated amino acetic acid is beneficial to the synthesis of aspartic acid, glutamic acid and cysteine in rice seedlings, increases the content of Mn in shoots and Ca in roots of rice seedlings, and significantly alleviates cadmium stress in seedlings. This provides a theoretical basis for the development of an environmentally friendly Cd-lowering foliar fertilizer for rice.

A novel prognostic index of stomach adenocarcinoma based on immunogenomic landscape analysis and immunotherapy options.

Stomach adenocarcinoma (STAD) is one of the most common malignant tumors worldwide. In this study, we attempted to construct a valid immune-associated gene prognostic index risk model that can predict the survival of patients with STAD and the efficacy of immune checkpoint inhibitors (ICIs) treatment. Transcriptome, clinical, and gene mutational data were obtained from the TCGA database. Immune-related genes were downloaded from the ImmPort and InnateDB databases. A total of 493 immune-related genes were identified to be enriched in functions associated with immune response, as well as in immune and tumor-related pathways. Further, 36 candidate genes related to the overall survival (OS) of STAD were obtained by weighted gene co-expression network analysis (WGCNA). Next, based on a Cox regression analysis, we constructed an immune-associated gene prognostic index (IAGPI) risk model based on eight genes, which was verified using the GEO STAD cohort. The patients were divided into two subsets according to their risk score. Patients in the low-risk group had better OS than those in the high-risk group. In the low-risk group, there were more CD8, activated memory CD4, and follicular helper T cells, and M1 macrophages, whereas monocytes, M2 macrophages, eosinophils, and neutrophils were more abundant in the high-risk group. The patients in the low-risk group were more sensitive to ICIs therapy. The IAGPI risk model can precisely predict the prognosis, reflect the tumor immune microenvironment, and predict the efficacy of ICIs therapy in patients with STAD.

The TTYH3/MK5 Positive Feedback Loop regulates Tumor Progression via GSK3-ß/ß-catenin signaling in HCC.

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide, and identification of novel targets is necessary for its diagnosis and treatment. This study aimed to investigate the biological function and clinical significance of tweety homolog 3 (TTYH3) in HCC. TTYH3 overexpression promoted cell proliferation, migration, and invasion and inhibited HCCM3 and Hep3B cell apoptosis. TTYH3 promoted tumor formation and metastasis in vivo. TTYH3 upregulated calcium influx and intracellular chloride concentration, thereby promoting cellular migration and regulating epithelial-mesenchymal transition-related protein expression. The interaction between TTYH3 and MK5 was identified through co-immunoprecipitation assays and protein docking. TTYH3 promoted the expression of MK5, which then activated the GSK3ß/ß-catenin signaling pathway. MK5 knockdown attenuated the activation of GSK3ß/ß-catenin signaling by TTYH3. TTYH3 expression was regulated in a positive feedback manner. In clinical HCC samples, TTYH3 was upregulated in the HCC tissues compared to nontumor tissues. Furthermore, high TTYH3 expression was significantly correlated with poor patient survival. The CpG islands were hypomethylated in the promoter region of TTYH3 in HCC tissues. In conclusion, we identified TTYH3 regulates tumor development and progression via MK5/GSK3-ß/ß-catenin signaling in HCC and promotes itself expression in a positive feedback loop.

Rice organs concentrate cadmium by chelation of amino acids containing dicarboxyl groups and enhance risks to human and environmental health in Cd-contaminated areas.

When rice plants grown in paddy fields with Cd content of 0.3-1.5 mg kg-1, Cd quantities in roots and straws were 2-7 times higher than that in topsoil. Return of these vegetative organs to topsoil aggravated the ecological risk of Cd pollution. Cd content in rice grains was 0.1-1.3 mg kg-1, and hazard quotients for local consumers by intake of these rice were 0.7-8.8. Planting low-Cd-accumulating (LCA) cultivar reduced hazard quotients for consumers by intake of rice, but had similar ecological risks as high-accumulating (HCA) cultivars. LCA cultivar had lower Cd content in grains as well as higher efficiency of altering Cd into insoluble forms in flag leaves and upmost nodes than HCA cultivars. Insoluble Cd content in nodes was linearly increased with soil Cd content, companied by significant decline of 4 amino acids with dicarboxyl groups. Glu or Asp can form a cyclic complex with Cd by two O atoms from α-COO- and side chain-COO-. These results indicate that roots and straws have high potential to concentrate Cd by forming complexes between amino acids and Cd ions, and Cd-enriched straw return to topsoil may aggravate the ecological risk of Cd contamination.

Upregulation of TTYH3 promotes epithelial-to-mesenchymal transition through Wnt/ß-catenin signaling and inhibits apoptosis in cholangiocarcinoma.

PURPOSE: Cholangiocarcinoma (CCA) is a highly invasive malignant tumor originating from the bile duct epithelium. Tweety homolog 3 (TTYH3) is a member of the family of calcium-activated chloride channels, which have several biological functions. Here, we aimed to investigate the expression and biological function of TTYH3 in CCA. METHODS: The mRNA and protein expression levels of TTYH3 were investigated in primary human CCA tissues and normal tissues. The DNA methylation levels of three CpG sites in the TTYH3 promoter region were evaluated using pyrosequencing. The effect of TTYH3 expression on proliferation, apoptosis, migration and invasion were assessed in HUCCT1 and QBC939 cells. Xenograft models were developed to substantiate its role in the development of CCA. Western blot analysis was used to investigate the mechanistic role of TTYH3 in regulating CCA progression. RESULTS: We found that TTYH3 was highly expressed both at the mRNA and protein levels in CCA (p = 0.0001) and that the expression levels were significantly related to a poor overall survival of the patients (p = 0.0019). The DNA methylation levels of three CpG sites in the TTYH3 promoter region were significantly lower in CCA tissues compared to normal tissues (p < 0.05). In vitro studies indicated that TTYH3 can promote the proliferation, migration and invasion of the CCA cells. TTYH3 overexpression significantly promoted tumor progression and cellular proliferation in vivo as indicated by Ki-67 expression. In addition, we found that exogenous TTYH3 overexpression induced epithelial-mesenchymal transition (EMT) in CCA as indicated by expression changes in E-cadherin, N-cadherin and vimentin. The EMT process was found to occur through the Wnt/ß-catenin signaling pathway, with simultaneous changes in P-GSK3ß and ß-catenin levels. CONCLUSIONS: Our data indicate that DNA hypomethylation-induced overexpression of TTYH3 regulates CCA development and metastasis through the Wnt/ß-catenin pathway.

Inhibition effects of long-term calcium-magnesia phosphate fertilizer application on Cd uptake in rice: Regulation of the iron-nitrogen coupling cycle driven by the soil microbial community.

Cadmium (Cd) pollution in paddy soil seriously endangers food safety production. To investigate the effects and microbiological mechanisms of calcium-magnesium-phosphate (CMP) fertilizer application on Cd reduction in rice, field experiments were conducted in Cd-contaminated paddy soil. Compared with conventional compound fertilizer, CMP fertilizer treatments inhibited Cd uptake through plant roots, significantly decreasing Cd content in rice grains from 0.340 to 0.062 mg/kg. Soil pH and total Ca, Mg and P contents increased after CMP fertilizer application, resulting in a further decrease in soil available Cd content from 0.246 to 0.181 mg/kg. Specific extraction analysis recorded a decrease in both available Fe content and the ratio of nitrate to ammonium nitrogen, indicating that the soil Fe-N cycle was affected by the addition of CMP fertilizer. This finding was also recorded using soil bacterial community sequencing, with CMP fertilizer promoting the progress of nitrate-dependent Fe-oxidation driven by Thiobacillus (1.60-2.83%) and subsequent dissimilatory nitrate reduction to ammonium (DNRA) driven by Ignavibacteriae (1.01-1.92%); Fe-reduction driven by Anaeromyxobacter (3.09-2.23%) was also inhibited. Our results indicate that CMP fertilizer application regulates the Fe-N coupling cycle driven by the soil microbial community to benefit remediation of Cd contaminated paddy soil.

miRNA-Based Signature Associated With Tumor Mutational Burden in Colon Adenocarcinoma.

Colon adenocarcinoma (COAD) is one of the most common malignant tumors. Tumor mutation burden (TMB) has become an independent biomarker for predicting the response to immune checkpoint inhibitors (ICIs). miRNAs play an important role in cancer-related immune regulation. However, the relationship between miRNA expression and TMB in COAD remains unclear. Therefore, the transcriptome profiling data, clinical data, mutation annotation data, and miRNA expression profiles for cases of COAD were downloaded from the TCGA database. Subsequently, 323 COAD cases were randomly divided into training and test sets. The differential expression of miRNAs in the high and low TMB groups in the training set was obtained as a signature using the least absolute shrinkage and selection operator (LASSO) logistic regression and verified in the test set. Based on the LASSO method, principal component analysis (PCA), and ROC, we found that the signature was credible because it can discriminate between high and low TMB levels. In addition, the correlation between the 18-miRNA-based signature and immune checkpoints was performed, followed by qRT-PCR, to measure the relative expression of 18 miRNAs in COAD patients. The miRNA-based model had a strong positive correlation with TMB and a weak positive correlation with CTLA4 and CD274 (PD-L1). However, no correlation was observed between the model and SNCA (PD-1). Finally, enrichment analysis of the 18 miRNAs was performed to explore their biological functions. The results demonstrated that 18 miRNAs were involved in the process of immunity and cancer pathways. In conclusion, the 18-miRNA-based signature can effectively predict and discriminate between the different TMB levels of COAD and provide a guide for its treatment with ICIs.

Profiling and Integrated Analysis of Differentially Expressed MicroRNAs as Novel Biomarkers of Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) is a heterogeneous disease that has multiple etiologies. It is the most common primary liver cancer, the sixth highest cause of cancer incidences, and the fourth highest cause of cancer-related deaths. The discovery of new biomarkers for the early detection, treatment, and prognosis of HCC would therefore be extremely useful. This study investigated differentially expressed ribonucleic acid (RNA) profiles by constructing a genome-wide profile of clinical samples. Differential expression analysis identified 1,280 differentially expressed messenger RNAs (dif-mRNAs), 99 differentially expressed microRNAs (dif-miRNAs), 181 differentially expressed long non-coding RNAs (dif-lncRNAs), and 31 differentially expressed circular RNAs (dif-circRNAs). Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) path analysis were then conducted on these differentially expressed RNAs, revealing that they were clearly related to cell division, foreign body metabolism, and ribosome assembly. A competing endogenous RNA (ceRNA) network was then constructed based on the regulatory dif-miRNA-dif-mRNA and dif-miRNA-dif-lncRNA relationships. These results were also verified using HCC data from the Cancer Genome Atlas (TCGA); seven dif-miRNAs were verified in clinical samples by real-time quantitative polymerase chain reaction (RT-qPCR). Kaplan-Meier survival analysis revealed that the expression levels of Hsa-miR-1269a, Hsa-miR-421, and Hsa-miR-190b were correlated with overall survival. (P <0.05). Survival analysis of clinical samples showed that hsa-mir-1269a, hsa-mir-421 were associated with prognosis (p<0.05).This study revealed the general expression characteristics of specific differentially expressed miRNAs using a ceRNA network constructed from HCC samples. Hsa-mir-1269a, hsa-mir-421 may be promising candidates.

Competing Endogenous RNA (ceRNA) Network Analysis of Autophagy-Related Genes in Hepatocellular Carcinoma.

PURPOSE: Autophagy plays an important role in the occurrence and development of hepatocellular carcinoma (HCC). We aimed to develop an autophagy-related genes signature predicting the prognosis of HCC and to depict a competing endogenous RNA (ceRNA) network. METHODS: Differentially expressed autophagy-related genes (DE-ATGs), miRNAs and lncRNAs and clinical data of HCC patients were extracted from TCGA. The GO and KEGG analysis were performed to investigate the gene function. Univariate and multivariate Cox regression analysis were used to identify a prognostic signature with the DE-ATGs. And a nomogram, adapted to the clinical characteristics, was established. Then, we established a ceRNA network related to autophagy genes. RESULTS: We screened out 27 differentially expressed genes which were enriched in GO and KEGG pathways related to autophagy and cancers. In univariate and multivariate Cox regression analysis, BIRC5, HSPB8, and SQSTM1 were screened out to establish a prognostic risk score model (AUC=0.749, p<0.01). Kaplan-Meier survival analysis showed that the overall survival of high-risk patients was significantly worse. Furthermore, the signature was validated in the other two independent databases. The nomogram, including the autophagy-related risk signature, gender, stage and TNM, was constructed and validated (C-index=0.736). Finally, the ceRNA network was established based on DE-ATGs, differentially expressed miRNAs and lncRNAs. CONCLUSION: We constructed a reliable prognostic model of HCC with autophagy-related genes and depicted a ceRNA network of DE-ATGs in HCC which provides a basis for the study of post-transcriptional modification and regulation of autophagy-related genes in HCC.