See the Unseen: Red-Emissive Carbon Dots for Visualizing the Nucleolar Structures in Two Model Animals and In Vivo Drug Toxicity.

Nucleolus, which participates in many crucial cellular activities, is an ideal target for evaluating the state of a cell or an organism. Here, bright red-emissive carbon dots (termed CPCDs) with excitation-independent/polarity-dependent fluorescence emission are synthesized by a one-step hydrothermal reaction between congo red and p-phenylenediamine. The CPCDs can achieve wash-free, real-time, long-term, and high-quality nucleolus imaging in live cells, as well as in vivo imaging of two common model animals-zebrafish and Caenorhabditis elegans (C. elegans). Strikingly, CPCDs realize the nucleolus imaging of organs/flowing blood cells in zebrafish at a cellular level for the first time, and the superb nucleolus imaging of C. elegans suggests that the germ cells in the spermatheca probably have no intact nuclei. These previously unachieved imaging results of the cells/tissues/organs may guide the zebrafish-related studies and benefit the research of C. elegans development. More importantly, a novel strategy based on CPCDs for in vivo toxicity evaluation of materials/drugs (e.g., Ag+ ), which can visualize the otherwise unseen injuries in zebrafish, is developed. In conclusion, the CPCDs represent a robust tool for visualizing the structures and dynamic behaviors of live zebrafish and C. elegans, and may find important applications in cell biology and toxicology.

NDUFAB1 protects against obesity and insulin resistance by enhancing mitochondrial metabolism.

Mitochondria are fundamental organelles for cellular and systemic metabolism, and their dysfunction has been implicated in the development of diverse metabolic diseases. Boosted mitochondrial metabolism might be able to protect against metabolic stress and prevent metabolic disorders. Here we show that NADH:ubiquinone oxidoreductase (NDU)-FAB1, also known as mitochondrial acyl carrier protein, acts as a novel enhancer of mitochondrial metabolism and protects against obesity and insulin resistance. Mechanistically, NDUFAB1 coordinately enhances lipoylation and activation of pyruvate dehydrogenase mediated by the mitochondrial fatty acid synthesis pathway and increases the assembly of respiratory complexes and supercomplexes. Skeletal muscle-specific ablation of NDUFAB1 causes systemic disruption of glucose homeostasis and defective insulin signaling, leading to growth arrest and early death within 5 postnatal days. In contrast, NDUFAB1 overexpression effectively protects mice against obesity and insulin resistance when the animals are challenged with a high-fat diet. Our findings indicate that NDUFAB1 could be a novel mitochondrial target to prevent obesity and insulin resistance by enhancing mitochondrial metabolism.-Zhang, R., Hou, T., Cheng, H., Wang, X. NDUFAB1 protects against obesity and insulin resistance by enhancing mitochondrial metabolism.

Efficient strand displacement amplification via stepwise movement of a bipedal DNA walker on an electrode surface for ultrasensitive detection of antibiotics.

DNA walkers, one of the artificial molecular machines which are constructed via smart synthetic DNA, have attracted rapidly growing attention from researchers in the biosensing field. In this work, we design an Exonuclease III (Exo III)-aided target-aptamer binding recycling (ETBR) activated bipedal DNA machine for highly sensitive electrochemical detection of antibiotics. To the best of our knowledge, this is the first time that a bipedal DNA machine has been applied in electrochemical sensing for antibiotics. On the one hand, the bipedal DNA walker exceeds the conventional single swing arm DNA walker in terms of walking efficiency and stability. On the other hand, the ETBR strategy, along with efficient strand displacement amplification via stepwise movement of a bipedal DNA walker significantly promotes the signal amplification efficiency. Under optimal conditions, this bipedal DNA machine possesses a detection limit of 7.1 fM within a linear detection range from 10 fM to 100 pM. Moreover, this electrochemical biosensor is expected to detect a wide variety of analytes using the corresponding target recognition probes. Thus, our proposed strategy offers a highly efficient, stable and practical platform for small molecule analysis.

Highly efficient fluorescence sensing of kanamycin using Endo IV-powered DNA walker and hybridization chain reaction amplification.

An ultrasensitive fluorescence sensing strategy for kanamycin (KANA) determination using endonuclease IV (Endo IV)-powered DNA walker, and hybridization chain reaction (HCR) amplification was reported. The sensing system consists of Endo IV-powered 3D DNA walker using for the specific recognition of KANA and the formation of the initiators, two metastable hairpin probes as the substrates of HCR and a tetrahydrofuran abasic site (AP site)-embeded fluorescence-quenched probe for fluorescence signal output. On account of this skilled design of sensing system, the specific binding between KANA and its aptamer activates DNA walker, in which the swing arm can move autonomously along the 3D track via Endo IV-mediated hydrolysis of the anchorages, inducing the formation of initiators that initiates HCR and the following Endo IV-assisted cyclic cleavage of fluorescence reporter probes. The use of Endo IV offers the advantages of simplified and accessible design without the need of specific sequence in DNA substrates. Under the optimal experimental conditions, the fluorescence biosensor shows excellent sensitivity toward KANA detection with a detection limit as low as 1.01 pM (the excitation wavelength is 486 nm). The practical applicability of this strategy is demonstrated by detecting KANA in spiked milk samples with recovery in the range of 98 to 102%. Therefore, this reported strategy might create an accurate and robust fluorescence sensing platform for trace amounts of antibiotic residues determination and related safety analysis. Graphical abstract Highly efficient fluorescence sensing of kanamycin using Endo IV-powered DNA Walker and hybridization chain, reaction amplification, Xiaonan Qu, Jingfeng Wang, Rufeng Zhang, Yihan Zhao, Shasha Li, Yu Wang, Su Liu*, Jiadong Huang, and Jinghua Yu, an ultrasensitive fluorescence sensing strategy for kanamycin determination using endonuclease IV-powered DNA walker, and hybridization chain reaction amplification is reported.

Robust and highly specific fluorescence sensing of Salmonella typhimurium based on dual-functional phi29 DNA polymerase-mediated isothermal circular strand displacement polymerization.

A simple and robust fluorescence sensing strategy has been developed for the detection of pathogenic bacteria by the combination of the dual functionality of phi29 DNA polymerase with isothermal circular strand displacement polymerization (ICSDP). The strategy relies on target-triggered formation of a mature primer that initiates the cyclic strand displacement polymerization reaction with the aid of dual functional phi29; thus, amplified detection of the target can be achieved. To our knowledge, this work is the first report where dual functional phi29-assisted ICSDP has been employed for fluorescence sensing of pathogenic bacteria. It is worth noting that a hairpin pre-primer is introduced that can be trimmed into a mature primer for initiating ICSDP via the 3' → 5' proofreading exonuclease activity of phi29, which contributes to the ultrahigh specificity of the strategy owing to the elimination of the unwished nonspecific extension. On the basis of the present amplification strategy, our biosensor exhibits excellent specificity and sensitivity toward S. typhimurium with an excellent detection limit as low as 1.5 cfu mL-1. In addition, the strategy offers the advantages of a simplified operation, shortened analysis time, and highly sensitive detection of pathogens with only a one-step reaction. Furthermore, by redesigning the corresponding binding molecules, the proposed strategy can be easily extended for the detection of a wide spectrum of analytes. Hence, the dual functional phi29-assisted ICSDP strategy indeed creates a robust and convenient fluorescence sensing platform for the identification of pathogenic bacteria and related food safety analysis.

Triple-helix molecular-switch-actuated exponential rolling circular amplification for ultrasensitive fluorescence detection of miRNAs.

We have formulated a rapid and high-efficiency fluorescent biosensing platform based on a target-activated triple-helix molecular switch (THMS)-conformation-change-induced exponential rolling circular amplification (RCA) strategy for the ultrasensitive detection of miR-21. In this strategy, there are several aspects that are worthwhile. First, the functionalized THMS, comprising a typical triplex structure (T-A·T), specific recognition sequence for nicking endonuclease, complementary sequence for miR-21, and RCA product-annealing sequence, was concurrently used to perform signal transduction with one fluorophore and one quencher. As compared to the traditional double-helix molecular switches or molecular beacons, one of the biggest differentiating factors is that the properties of THMSs are independent of any specific binding sequence that they may contain. As far as we know, this is the first time that an ingeniously designed THMS not only contains the primer for exponential RCA, but also functions as the tracer for fluorescence assay. In the presence of miR-21, targets can induce conformation changes in THMS with the release of the trapped DNA segment (P), which, in turn, can activate the first run of the RCA process. Meanwhile, the RCA reaction is also initiated by the formation of a similar primer (SP) as the trapped DNA through a continuous "extension-nicking" reaction. Secondly, the resultant first-generation RCA product consists of numerous tandem repeated regions that can attach to countless THMSs, resulting in the release of the trapped DNA segment (P) for initiating the second run of the RCA reaction. Significantly, a large amount of THMSs were continuously consumed to yield a remarkably strong fluorescent signal. In addition, this biosensor was demonstrated to exhibit improved sensitivity owing to the high efficiency and rapid amplification kinetics of the exponential RCA and high selectivity toward miR-21 with a limit of detection as low as 1.1 aM. Hence, the target-mediated THMS-conformation-change-initiated exponential RCA strategy presents an optimal detection performance toward analytes for potential applications in related fundamental research and clinical diagnosis.

A label-free electrochemical platform for the detection of antibiotics based on cascade enzymatic amplification coupled with a split G-quadruplex DNAzyme.

Herein, a split G-quadruplex DNAzyme as a signal reporter was integrated into an electrochemical sensing platform for the detection of antibiotics with specificity and sensitivity. To improve the signal-to-noise ratio, two G-rich oligonucleotide sequences (G1 and G2) were blocked into two different hairpin probes, preventing the two segments from assembling into a spilt G-quadruplex structure. Moreover, we designed a double-arch probe, consisting of an aptamer as the recognition element and two-step enzymatic signal amplification. Concretely, the first is the Nt.BbvCI-assisted nicking cyclic reaction activated by target-aptamer binding, and the second is exonuclease III-aided cyclic amplification for generating abundant G1 and G2. The modified capture probe on the electrode was used to combine G1 and G2 to form the spilt G-quadruplex/hemin when K+ and hemin were present. This complex plays the role of DNAzyme with superior horseradish peroxidase activity in catalyzing the decomposition of H2O2. Under optimal conditions, this biosensor showed an excellent performance for sensing kanamycin with a detection limit of 83 fM for kanamycin concentrations ranging from 100 fM to 1 nM. Hence, the proposed strategy has potential as an efficient and actual platform for small molecule analysis.

Protons Trigger Mitochondrial Flashes.

Emerging evidence indicates that mitochondrial flashes (mitoflashes) are highly conserved elemental mitochondrial signaling events. However, which signal controls their ignition and how they are integrated with other mitochondrial signals and functions remain elusive. In this study, we aimed to further delineate the signal components of the mitoflash and determine the mitoflash trigger mechanism. Using multiple biosensors and chemical probes as well as label-free autofluorescence, we found that the mitoflash reflects chemical and electrical excitation at the single-organelle level, comprising bursting superoxide production, oxidative redox shift, and matrix alkalinization as well as transient membrane depolarization. Both electroneutral H(+)/K(+) or H(+)/Na(+) antiport and matrix proton uncaging elicited immediate and robust mitoflash responses over a broad dynamic range in cardiomyocytes and HeLa cells. However, charge-uncompensated proton transport, which depolarizes mitochondria, caused the opposite effect, and steady matrix acidification mildly inhibited mitoflashes. Based on a numerical simulation, we estimated a mean proton lifetime of 1.42 ns and diffusion distance of 2.06 nm in the matrix. We conclude that nanodomain protons act as a novel, to our knowledge, trigger of mitoflashes in energized mitochondria. This finding suggests that mitoflash genesis is functionally and mechanistically integrated with mitochondrial energy metabolism.

Photosynthetic responses of Oryza sativa L. seedlings to cadmium stress: physiological, biochemical and ultrastructural analyses.

In the present study, photosynthetic responses induced by cadmium stress in chlorophyll biosynthesis, photochemical activities, the stability of thylakoid membranes chlorophyll-protein complexes and the chloroplast ultrastructure of the cereal crop Oryza sativa L. were characterized. Cadmium inhibited the biosynthesis of chlorophyll by interfering with activity of δ-aminolevulinic acid dehydratase in the rice seedlings. For the photochemical activities analyses, the extent of the decrease in photosystem II activity was much greater than that in the PS I activity. The variations in the chlorophyll a fluorescence parameters also indicated that cadmium toxicity drastically affected the photochemistry of PS II. Biochemical analyses by BN-PAGE and protein immunoblot showed that cadmium toxicity considerably affected the stability of PS II-core, cytb 6 /f, RuBisCO, PSI + LHCI and LHCII (Trimeric). We observed the rate of the thylakoid membranes protein degradation, was mainly at the level of RbcL, PsaA, Lhca1 and D1. In addition, the damages to chloroplast structure and thylakoid stacking analyzed by transmission electron microscopy were indicative of general disarray in the photosynthetic functions exerted by cadmium toxicity. These results are valuable for understanding the biological consequences of heavy metals contamination particularly in soils devoted to organic agriculture.

Russell Mechanism-Mediated Cancer Therapy: A Minireview.

The Russell mechanism, proposed by Russell, is a cyclic mechanism for the formation of linear tetroxide intermediates, which can spontaneously produce cytotoxic singlet oxygen (1O2) independent of oxygen, suggesting its anticancer potential. Compared with other mainstream anticancer strategies, the Russell mechanism employed for killing cancer cells does not require external energy input, harsh pH condition, and sufficient oxygen. However, up till now, the applications of Russell mechanism in antitumor therapy have been relatively rare, and there is almost no summary of the Russell mechanism in the cancer therapy field. This minireview introduces the different metal elements-based Russell mechanisms and the relevant research progress in Russell mechanism-based cancer therapy in recent years. At the same time, we briefly discussed the current challenges and future development regarding the applications of Russell mechanism. It is hoped that this review can further expand the research of Russell Mechanism in the biomedical field, and inspire researchers to extend its application fields to antibacterial, antiinflammatory, and wound healing uses.

Unveiling the bidirectional role of MMP9: A key player in kidney injury.

Matrix metalloproteinases (MMPs) are a group of zinc-dependent proteolytic metalloenzymes that are involved in numerous pathological conditions, including nephropathy. MMP9, a member of the MMPs family, is categorized as a constituent of the gelatinase B subgroup, and its involvement in extracellular matrix (ECM) remodeling and renal fibrosis highlights its importance in the development and progression of renal diseases. The exact role of MMP9 in the development of kidney diseases is still controversial. This study investigated the dual role of MMP9 in kidney injury, discussing its implications in the pathogenesis of kidney diseases and investigating the design and mechanism of MMP9 inhibitors based on previous studies. This study provides an effective basis for the development of novel and selective MMP9 inhibitors for treating renal diseases.

Celastrol attenuates HFD-induced obesity and improves metabolic function independent of adiponectin signaling.

Backgound: Celastrol, a leptin sensitiser, has been shown to inhibit food intake and reduce body weight in diet-induced obese mice, making it a potential treatment for obesity and metabolic diseases. Adiponectin signalling has been reported to play an important role in the treatment of obesity, inflammation, and non-alcoholic fatty liver disease.Materials and methods: Wild-type (WT) and AdipoR1 knockout (AdipoR1-/-) mice were placed on a chow diet or a high-fat diet (HFD) and several metabolic parameters were measured. Celastrol was then administered to the HFD-induced mice and the response of WT and AdipoR1-/- mice to celastrol in terms of body weight, blood glucose, and food intake was also recorded.Results: AdipoR1 knockout caused elevated blood glucose and lipids, impaired glucose tolerance and insulin resistance in mice, as well as increased susceptibility to HFD-induced obesity. After 14 days of treatment, WT and AdipoR1-/- mice showed significant reductions in body weight and blood glucose and improvements in glucose tolerance.Conclusion: The present study demonstrated that AdipoR1 plays a critical role in metabolic regulation and that the improvement of weight and metabolic function by celastrol is independent of the AdipoR1-mediated signalling pathway.

Self-Supervised Learning by Estimating Twin Class Distribution.

We present Twist, a simple and theoretically explainable self-supervised representation learning method by classifying large-scale unlabeled datasets in an end-to-end way. We employ a siamese network terminated by a softmax operation to produce twin class distributions of two augmented images. Without supervision, we enforce the class distributions of different augmentations to be consistent. However, simply minimizing the divergence between augmentations will generate collapsed solutions, i.e., outputting the same class distribution for all images. In this case, little information about the input images is preserved. To solve this problem, we propose to maximize the mutual information between the input image and the output class predictions. Specifically, we minimize the entropy of the distribution for each sample to make the class prediction assertive, and maximize the entropy of the mean distribution to make the predictions of different samples diverse. In this way, Twist can naturally avoid the collapsed solutions without specific designs such as asymmetric network, stop-gradient operation, or momentum encoder. As a result, Twist outperforms previous state-of-the-art methods on a wide range of tasks. Specifically on the semi-supervised classification task, Twist achieves 61.2% top-1 accuracy with 1% ImageNet labels using a ResNet-50 as backbone, surpassing previous best results by an improvement of 6.2%. Codes and pre-trained models are available at https://github.com/bytedance/TWIST.

Sparse R-CNN: An End-to-End Framework for Object Detection.

Object detection serves as one of most fundamental computer vision tasks. Existing works on object detection heavily rely on dense object candidates, such as k anchor boxes pre-defined on all grids of an image feature map of size H×W. In this paper, we present Sparse R-CNN, a very simple and sparse method for object detection in images. In our method, a fixed sparse set of learned object proposals ( N in total) are provided to the object recognition head to perform classification and localization. By replacing HWk (up to hundreds of thousands) hand-designed object candidates with N (e.g., 100) learnable proposals, Sparse R-CNN makes all efforts related to object candidates design and one-to-many label assignment completely obsolete. More importantly, Sparse R-CNN directly outputs predictions without the non-maximum suppression (NMS) post-processing procedure. Thus, it establishes an end-to-end object detection framework. Sparse R-CNN demonstrates highly competitive accuracy, run-time and training convergence performance with the well-established detector baselines on the challenging COCO dataset and CrowdHuman dataset. We hope that our work can inspire re-thinking the convention of dense prior in object detectors and designing new high-performance detectors.

Quantitative Assessment of Water Quality Improvement by Reducing External Loadings at Lake Erhai, Southwest China.

To quantitatively evaluate the effects on water quality improvement caused by reducing external loadings entering Lake Erhai through inflow rivers, a one-dimensional hydrodynamic and ecological model (DYRESM-CAEDYM) was set up to simulate the water quality and water level variations. The calibrated and validated model was used to conduct six scenarios for evaluating the water quality responses to different amounts of external loading reduction at Lake Erhai. The results show (1) the total nitrogen (TN) concentration of Lake Erhai will be higher than 0.5 mg/L without any watershed pollution control during April-November 2025, which cannot meet Grade II standard of the China Surface Water Environmental Quality Standards (GB3838-2002). (2) External loading reductions can significantly reduce the concentrations of nutrients and Chla at Lake Erhai. The effects of water quality improvement will be proportional to the reduction rate of external loading reductions. (3) Internal release might be an important source of pollution It needs to be seriously considered as well as external loading for mitigating the eutrophication at Lake Erhai in the future.

A new NASH model in aged mice with rapid progression of steatohepatitis and fibrosis.

Non-alcoholic fatty liver disease (NAFLD) has a high prevalence worldwide, with a significant proportion of patients progressing into non-alcoholic steatohepatitis (NASH) and further into cirrhosis and hepatocellular carcinoma (HCC). Most of the current animal models of NASH have limitations, such as incompatibility with human pathogenesis characteristics or long induction periods, which severely limit the development of new drugs and preclinical studies for NASH. We investigated the progression of NASH and fibrosis, as well as metabolic indicators, at different time points in aged mice induced by the Gubra Amylin NASH (GAN) diet, a high-fat, high-sugar, high-cholesterol diet, and attempted to establish a rapid and useful mouse model of NASH. Young and aged C57BL/6 mice were induced on a normal chow or GAN diet for 12 and 21 weeks, respectively. After 12 weeks of induction, aged mice developed NASH, including hepatic steatosis, lobular inflammation and hepatic ballooning, and the phenotype was more severe compared with young mice. After 21 weeks of induction, aged mice developed hepatic fibrosis, which greatly shortened the induction time compared with young mice. Furthermore, analysis of immune cell infiltration in the liver by flow cytometry elucidated the changes of multiple immune cells during the pathogenesis of NASH. These findings suggest that aged mice may develop NASH and fibrosis more rapidly under GAN diet induction, which may significantly shorten the period for preclinical studies of NASH.

The establishment and application of CD3E humanized mice in immunotherapy.

In the field of cancer immunotherapy, monoclonal antibody drugs, bispecific antibodies, and antibody-conjugated drugs have become the focus of current research, and gene-edited animal models play an essential role in the entire drug development process. In this study, CD3E humanized mice were established by replacing the second to the seventh exon of the Cd3e mouse gene with the same exon of the human gene. The expression of human CD3E in CD3E humanized mice was detected by RT-PCR as well as flow cytometry, also a tumor model was established based on CD3E humanized mice, and the pharmacodynamic effects of CD3E monoclonal antibodies were evaluated. The results showed that CD3E humanized mice expressed only human CD3E, and the proportion of each lymphocyte in the thymus and spleen was not significantly changed compared with wild-type mice. CD3E monoclonal antibody could promote tumor growth after treatment, which may be related to the activation-induced cell death effect caused by this CD3E antibody. In contrast, Bispecific antibody blinatumomab inhibited tumor growth significantly. Thus, the CD3E humanized mice provided an adequate animal model for evaluating the efficacy and safety of CD3E antibody drugs.

SOLO: A Simple Framework for Instance Segmentation.

Compared to many other dense prediction tasks, e.g., semantic segmentation, it is the arbitrary number of instances that has made instance segmentation much more challenging. In order to predict a mask for each instance, mainstream approaches either follow the "detect-then-segment" strategy (e.g., Mask R-CNN), or predict embedding vectors first then cluster pixels into individual instances. In this paper, we view the task of instance segmentation from a completely new perspective by introducing the notion of "instance categories", which assigns categories to each pixel within an instance according to the instance's location. With this notion, we propose segmenting objects by locations (SOLO), a simple, direct, and fast framework for instance segmentation with strong performance. We derive a few SOLO variants (e.g., Vanilla SOLO, Decoupled SOLO, Dynamic SOLO) following the basic principle. Our method directly maps a raw input image to the desired object categories and instance masks, eliminating the need for the grouping post-processing or the bounding box detection. Our approach achieves state-of-the-art results for instance segmentation in terms of both speed and accuracy, while being considerably simpler than the existing methods. Besides instance segmentation, our method yields state-of-the-art results in object detection (from our mask byproduct) and panoptic segmentation. We further demonstrate the flexibility and high-quality segmentation of SOLO by extending it to perform one-stage instance-level image matting. Code is available at: https://git.io/AdelaiDet.

Fluorescent dendrimer-based probes for cell membrane imaging: Zebrafish epidermal labeling-based toxicity evaluation.

Visualizing the plasma membrane of living mammalian cells both in vitro and in vivo is crucial for tracking their cellular activities. However, due to the complex and dynamic nature of the plasma membrane, most commercial dyes for membrane staining can only realize very limited imaging performance. Thus, precise and stable plasma membrane imaging remains technically challenging. Here, by taking advantage of the small, well-defined, and amine-rich dendrimers, we prepared poly(ethylene glycol)-cholesterol (PEG-Chol)-conjugated and cyanine dye (e.g., cyanine2, cyanine3, and cyanine5)-labeled dendrimer nanoprobes (termed DPC-Cy2, DPC-Cy3, and DPC-Cy5 NPs). It was revealed that these probes enabled universal, wash-free, long-term (at least 8 h), and multicolor (green, yellow, and red) plasma membrane labeling of a variety of live mammalian cells. Further, we confirmed that the nanoprobes (using DPC-Cy5 as a representative) could achieve high-quality, wash-free, and stable cell surface labeling of live zebrafish embryos. More importantly, we demonstrated that our probes could act as biosensors to visualize the toxicity of metal-organic frameworks (MOFs) toward the epidermal cells of zebrafish embryos, and thus they hold great potential for identifying the toxic effect of drugs/materials at the single-cell scale or in live animals. The present work highlights the advantages of utilizing dendrimers for constructing functional imaging materials, and it is also believed that the fluorescent dendrimer nanoprobes developed in this work may find wide applications like cell imaging, drug toxicity evaluation, and cellular state monitoring.

Bioinformatics analysis reveals biomarkers with cancer stem cell characteristics in kidney renal clear cell carcinoma.

BACKGROUND: Kidney renal clear cell carcinoma (KIRC) is a renal cortical tumor. KIRC is the most common subtype of kidney cancer, accounting for 70%-80% of kidney cancer. Early identification of the risk of KIRC patients can facilitate more accurate clinical treatment, but there is a lack of effective prognostic markers. We aimed to identify new prognostic biomarkers for KIRC on the basis of the cancer stem cell (CSC) theory. METHODS: RNA-sequencing (RNA-seq) data and related clinical information were downloaded from The Cancer Genome Atlas (TCGA) database. Weighted gene co-expression network analysis (WGCNA) was used to identify significant modules and hub genes, and predictive hub genes were used to construct prognostic characteristics. RESULTS: The messenger RNA expression-based stemness index (mRNAsi) in tumor tissues of patients in the TCGA database is higher than that of the corresponding normal tissues. In addition, some clinical features and results are highly correlated with mRNAsi. WGCNA found that the green module is the most prominent module associated with mRNAsi; the genes in the green module are mainly concentration in Notch binding, endothelial cell development, Notch signaling pathway, and Rap 1 signaling pathway. A protein-protein interaction (PPI) network showed that the top 10 central genes were significantly associated with the transcriptional level. Moreover, the 10 hub genes were up-regulated in KIRC. Regarding survival analysis, the nomogram of the prognostic markers of the seven pivotal genes showed a higher predictive value. The classical receiver operating characteristic (ROC) curve analysis showed that risk score biomarkers had the highest accuracy and specificity with an area under the curve (AUC) value of 0.701. CONCLUSIONS: mRNAsi-related genes may be good prognostic biomarkers for KIRC.