Accumulating evidence has highlighted the effects of natural killer (NK) cells on shaping anti-tumor immunity. This study aimed to construct an NK cell marker gene signature (NKMS) to predict ...prognosis and therapeutic response of clear cell renal cell carcinoma (ccRCC) patients.
Publicly available single-cell and bulk RNA profiles with matched clinical information of ccRCC patients were collected from Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), ArrayExpress, and International Cancer Genome Consortium (ICGC) databases. A novel NKMS was constructed, and its prognostic value, associated immunogenomic features and predictive capability to immune checkpoint inhibitors (ICIs) and anti-angiogenic therapies were evaluated in ccRCC patients.
We identified 52 NK cell marker genes by single-cell RNA-sequencing (scRNA-seq) analysis in GSE152938 and GSE159115. After least absolute shrinkage and selection operator (LASSO) and Cox regression, the most prognostic 7 genes (
and
) composed NKMS using bulk transcriptome from TCGA. Survival and time-dependent receiver operating characteristic (ROC) analysis exhibited exceptional predictive capability of the signature in the training set and two independent validation cohorts (E-MTAB-1980 and RECA-EU cohorts). The seven-gene signature was able to identify patients within high Fuhrman grade (G3-G4) and American Joint Committee on Cancer (AJCC) stage (III-IV). Multivariate analysis confirmed the independent prognostic value of the signature, and a nomogram was built for clinical utility. The high-risk group was characterized by a higher tumor mutation burden (TMB) and greater infiltration of immunocytes, particularly CD8
T cells, regulatory T (Treg) cells and follicular helper T (Tfh) cells, in parallel with higher expression of genes negatively regulating anti-tumor immunity. Moreover, high-risk tumors exhibited higher richness and diversity of T-cell receptor (TCR) repertoire. In two therapy cohorts of ccRCC patients (PMID32472114 and E-MTAB-3267), we demonstrated that high-risk group showed greater sensitivity to ICIs, whereas the low-risk group was more likely to benefit from anti-angiogenic therapy.
We identified a novel signature that can be utilized as an independent predictive biomarker and a tool for selecting the individualized treatment for ccRCC patients.
On single-cell RNA-sequencing data, we consider the problem of assigning cells to known cell types, assuming that the identities of cell-type-specific marker genes are given but their exact ...expression levels are unavailable, that is, without using a reference dataset. Based on an observation that the expected over-expression of marker genes is often absent in a nonnegligible proportion of cells, we develop a method called scSorter. scSorter allows marker genes to express at a low level and borrows information from the expression of non-marker genes. On both simulated and real data, scSorter shows much higher power compared to existing methods.
Cancer immunotherapy is an increasingly successful strategy for treating patients with advanced or conventionally drug-resistant cancers. T cells have been proved to play important roles in ...anti-tumor and tumor microenvironment shaping, while these roles have not been explained in lung squamous cell carcinoma (LUSC). In this study, we first performed a comprehensive analysis of single-cell RNA sequencing (scRNA-seq) data from the gene expression omnibus (GEO) database to identify 72 T-cell marker genes. Subsequently, we constructed a 5-gene prognostic signature in the training cohort based on the T-cell marker genes from the cancer genome atlas (TCGA) database, which was further validated in the testing cohort and GEO cohort. The areas under the receiver operating characteristic curve at 1-, 3-, and 5-years were 0.614, 0.713 and 0.702 in the training cohort, 0.669, 0.603 and 0.645 in the testing cohort, 0.661, 0.628 and 0.590 in the GEO cohort, respectively. Furthermore, we created a highly reliable nomogram to facilitate clinical application. Gene set enrichment analysis showed that immune-related pathways were mainly enriched in the high-risk group. Tumor immune microenvironment indicated that high-risk group exhibited higher immune score, stromal score, and immune cell infiltration levels. Moreover, genes of the immune checkpoints and human leukocyte antigen family were all overexpressed in high-risk group. Drug sensitivity revealed that low-risk group was sensitive to 8 chemotherapeutic drugs and high-risk group to 4 chemotherapeutic drugs. In short, our study reveals a novel prognostic signature based on T-cell marker genes, which provides a new target and theoretical support for LUSC patients.
Numerous studies report different types of responses following exposure of plants to high frequency electromagnetic fields (HF-EMF). While this phenomenon is related to tissue heating in animals, the ...situation is much less straightforward in plants where metabolic changes seem to occur without tissue temperature increase. We have set up an exposure system allowing reliable measurements of tissue heating (using a reflectometric probe and thermal imaging) after a long exposure (30 min) to an electromagnetic field of 2.45 GHz transmitted through a horn antenna (about 100 V m−1 at the plant level). We did not observe any heating of the tissues, but we detected rapid increases (60 min) in the accumulation of transcripts of stress-related genes (TCH1 and ZAT12 transcription factor) or involved in ROS metabolism (RBOHF and APX1). At the same time, the amounts of hydrogen peroxide and dehydroascorbic acid increased while glutathione (reduced and oxidized forms), ascorbic acid, and lipid peroxidation remained stable. Therefore, our results unambiguously show that molecular and biochemical responses occur rapidly (within 60min) in plants after exposure to an electromagnetic field, in absence of tissue heating.
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•In our condition, 2.45 GHz HF-EMF exposure did not induce thermal effect in plants.•We observed rapid and transcient changes of gene expression and H2O2 metabolism.•Non-thermal biological responses to EMF exposure do exist in plants.
•The abundance of ureC gene was significantly correlated with NH4+-N concentration.•The abundance of AOA amoA gene was moderately correlated with NH4+-N concentration.•The abundance of AOB amoA gene ...was moderately correlated with NH4+-N concentration.•The abundance of nirK gene was moderately correlated with NO3−-N concentration.
In this article, the changes in the functional marker genes associated with nitrogen biological transformation during the organic-inorganic co-composting process with adding biochar or not were studied. Results showed that the addition of biochar increased the abundance of ureC, AOA amoA and AOB amoA gene while decreased the abundance of nirK gene. The addition of 10% biochar by weight ratio was better for the optimization of nitrogen biological transformation process. The correlation analysis showed that the ureC gene was highly correlated with NH4+-N concentration while the AOA amoA and AOB amoA genes were moderately correlated with NH4+-N concentration. Similarly, the nirK gene was moderately correlated with NO3−-N concentration. This work would contribute to understanding the mechanisms underlying in the nitrogen bio-transformation further at the molecular level during organic-inorganic co-composting.
As an essential component of the tumor microenvironment, B cells exist in all stages of tumor and exert important roles in anti-tumor immunity and shaping tumor development. We aimed to explore the ...expression profile of B cell marker genes and construct a prognostic signature based on these genes in Lung adenocarcinoma (LUAD). A total of 1268 LUAD patients from different cohorts were enrolled in this study. We performed an analysis of single-cell RNA-sequencing (scRNA-seq) data from Gene expression omnibus (GEO) database to identify B cell marker genes in LUAD. TCGA database was used to construct signature, and six cohorts from GEO database were used for validation. We also investigated the association between this signature and immunotherapy response. Based on 258 B cell marker genes identified by scRNA-seq analysis, a nine-gene signature was constructed for prognostic prediction in TCGA dataset, which classified patients into high-risk and low-risk groups according to overall survival. The multivariate analysis demonstrated that the signature was an independent prognostic factor. The signature's predictive power was verified in other six independent cohorts and different clinical subgroups. Analysis of immune profiles showed that high-risk groups presented discriminative immune-cell infiltrations and immune-suppressive states. More importantly, risk scores of the signature were closely correlated with PD-L1, tumor mutation burden, neoantigens, and tumor immune dysfunction and exclusion score. Our study proposed a novel prognostic signature based on B cell marker genes for LUAD patients. The signature could effectively indicate LUAD patients’ survival and serve as a predictor for immunotherapy.
Hepatic stellate cells (HSCs) are the major cellular source of extracellular matrix production in the liver. Therefore, this cell population has received considerable attention in studies ...investigating fundamental features of hepatic fibrosis. However, the limited supply and ever-increasing demand for these cells, combined with the additional tightening of formal standards in animal welfare policy, make working with these primary cells increasingly difficult. Moreover, researchers working in biomedical research are challenged to implement the 3R principle of "replacement," "reduction," and "refinement" in their work. This principle, originally proposed in 1959 by William M. S. Russell and Rex L. Burch, is now widely endorsed by legislators and regulatory bodies in many countries as a roadmap to tackle the ethical dilemma associated with animal experimentation. As such, working with immortalized HSC lines is a good alternative to limit the number of animals and their suffering in biomedical research. This article summarizes issues that need to be considered when working with established HSC cell lines and provides general guidelines for the maintenance and storage of HSC lines from mouse, rat, and humans.
Marker-gene sequencing is a cost-effective method of taxonomically profiling microbial communities. Unlike metagenomic approaches, marker-gene sequencing does not provide direct information about the ...functional genes that are present in the genomes of community members. However, by capitalizing on the rapid growth in the number of sequenced genomes, it is possible to infer which functions are likely associated with a marker gene based on its sequence similarity with a reference genome. The PICRUSt tool is based on this idea and can predict functional category abundances based on an input marker gene. In brief, this method requires a reference phylogeny with tips corresponding to taxa with reference genomes as well as taxa lacking sequenced genomes. A modified ancestral state reconstruction (ASR) method is then used to infer counts of functional categories for taxa without reference genomes. The predictions are written to pre-calculated files, which can be cross-referenced with other datasets to quickly generate predictions of functional potential for a community. This chapter will give an in-depth description of these methods and describe how PICRUSt should be used.
Purpose
Immune cells in the immune microenvironment of lung cancer have a great impact on the development of lung cancer. Our purpose was to analyze the immune cell infiltration features and related ...marker genes for lung cancer.
Methods
Single cell RNA sequencing data of 11,485 lung cancer cells were retrieved from the Gene Expression Omnibus. After quality control and data normalization, cell clustering was performed using the Seurat package. Based on the marker genes of each cell type from the CellMarker database, each cell was divided into G1, G2M, and S phases. Then, differential expression and functional enrichment analyses were performed. CIBERSORT was used to reconstruct immune cell types.
Results
Following cell filtering, highly variable genes were identified for all cells. 14 cell types were clustered. Among them, CD4 + T cell, B cell, plasma cell, natural killer cell and cancer stem cell were the top five cell types. Up-regulated genes were mainly enriched in immune-related biological processes and pathways. Using CIBERSORT, we identified the significantly higher fractions of naïve B cell, memory CD4 + T cell, T follicular helper cell, T regulatory helper cell and M1 macrophage in lung cancer tissues compared to normal tissues. Furthermore, the fractions of resting NK cell, monocyte, M0 macrophage, resting mast cell, eosinophil and neutrophil were significantly lower in tumor tissues than normal tissues.
Conclusion
Our findings dissected the immune cell infiltration features and related marker genes for lung cancer, which might provide novel insights for the immunotherapy of lung cancer.
Sugarcane straw has been considered a promising cost-effective feedstock for bioenergy production through pyrolysis. Straw-based biochar is a by-product from biomass pyrolysis that has the potential ...to mitigate nitrous oxide (N2O) emissions. However, the understanding of how biochar influences N2O emissions remains limited. This study assessed the effects of sugarcane straw-based biochar on soil N2O emissions and its interaction with functional genes associated with N2O production and consumption in tropical conditions. A greenhouse experiment was conducted for 60 days to evaluate the following treatments: control (CTR), N fertilizer (NF), NF + 15 Mg ha−1 straw (NF + S); NF + 5 Mg ha−1 biochar (NF + B5); and NF + 10 Mg ha−1 biochar (NF + B10). Results showed that N2O emissions were 73 % higher in the NF + S than in the biochar treatments. However, biochar treatments did not reduce N2O emissions compared to NF. Soil N–NH4+ availability was reduced under NF + S but was greater in biochar treatments at initial sampling time-points. High soil C content was observed in the NF + B10. Although NF + S increased sugarcane biomass, it registered the highest N2O-yield scaled emission. N2O-yield scaled emissions in NF + B5 and NF + B10 were 63 % and 62 % lower than in NF + S. The NF + S increased the abundance of AOB-amoA genes, suggesting that nitrification was the major N2O-producing pathway. Conversely, biochar effects on soil N2O emissions were not correlated with nitrification or denitrification genes. Thus, converting sugarcane straw into biochar is feasible strategy to reduce N2O emissions and increase soil C sequestration in tropical soil.
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•Straw coverage increased soil N2O emissions.•Soils under biochar application emitted 73 % less N2O than straw-covered soils.•High N2O emissions were driven by AOB-amoA genes.•Conversion of straw into biochar is a good strategy to mitigate soil GHG emissions.
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