4.5 Article

Identification of key genes and pathways in Ewing's sarcoma patients associated with metastasis and poor prognosis

Journal

ONCOTARGETS AND THERAPY
Volume 12, Issue -, Pages 4153-4165

Publisher

DOVE MEDICAL PRESS LTD
DOI: 10.2147/OTT.S195675

Keywords

genes; miRNAs; Ewing's sarcoma; metastasis; bioinformatic analysis

Funding

  1. National Natural Science Foundation of China [G3FW155310]

Ask authors/readers for more resources

Background: Ewing sarcoma (ES) is the second commonest primary malignant bone neoplasm. Metastatic status at diagnosis strongly predicted poor prognosis of Ewing sarcoma patients. Yet little was known about the underlying mechanism of ES metastasis. Purpose: This study intended to identify the relationship between key genes/pathways and metastasis/poor prognosis in Ewing's sarcoma patients by using bioinformatic method. Methods: In this study, multi-center sequencing data were obtained from the GEO database, including gene and miRNA expression profile and prognosis information of ES patients. Differentially expressed genes (DEGs) were identified between primary and metastasis ES samples by the GEO2R online tool. Gene ontology (Go) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses of DEGs were performed. And PPI network analyses were conducted. The ES patient's prognostic information was employed for survival analysis, and the potential relationship between miRNAs and key genes was analyzed. Results: The results showed that a total of 298 and 428 DEGs were screened out in metastasis samples based on GSE17618 and GSE12102 dataset compared to primary samples respectively. The most significantly enriched KEGG pathway was the mismatch repair (MMR) pathway. MSH2, MSH6, RPA2, and RFC2 that belong to the MMR pathway were identified as key genes. Moreover, the expression of key genes was increased in metastasis samples compared with primary ones and was associated with poor event-free and overall survival of ES patients. The negative correlation of the expression level of the key genes with patients prognosis also supported by TCGA sarcoma database. Furthermore, knockdown of EWSR/FLI1 fusion in ES cell line A673 down-regulates the expression of the 4 key genes was revealed by GDS4962. Conclusion: In conclusion, the present study indicated that the key genes promote our understanding of the molecular mechanisms underlying the development of ES metastasis, and might be used as molecular targets and diagnostic biomarkers for the treatment of ES.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.5
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Article Computer Science, Artificial Intelligence

Modeling learnable electrical synapse for high precision spatio-temporal recognition

Zhenzhi Wu, Zhihong Zhang, Huanhuan Gao, Jun Qin, Rongzhen Zhao, Guangshe Zhao, Guoqi Li

Summary: Bio-inspired methods are being introduced into artificial neural networks for efficient processing of spatio-temporal tasks, with the Leaky Integrate and Fire (LIF) model being the most prominent. The introduction of electrical synapses is shown to be an important factor in achieving high accuracy on realistic spatio-temporal tasks, with the proposed network showing significant improvement over traditional LIF models on five datasets. Through modeling electrical synapses in artificial LIF neurons and training deep networks using the ECLIF model, high accuracy has been achieved.

NEURAL NETWORKS (2022)

Article Multidisciplinary Sciences

Brain-inspired global-local learning incorporated with neuromorphic computing

Yujie Wu, Rong Zhao, Jun Zhu, Feng Chen, Mingkun Xu, Guoqi Li, Sen Song, Lei Deng, Guanrui Wang, Hao Zheng, Songchen Ma, Jing Pei, Youhui Zhang, Mingguo Zhao, Luping Shi

Summary: This article introduces a neuromorphic global-local synergic learning model that combines brain-inspired metalearning and differentiable spiking models, allowing for multiscale learning and achieving significant advantages in various tasks.

NATURE COMMUNICATIONS (2022)

Article Automation & Control Systems

Adaptive Control of Second-Order Nonlinear Systems With Injection and Deception Attacks

Yue Yang, Jiangshuai Huang, Xiaojie Su, Kai Wang, Guoqi Li

Summary: This article discusses the adaptive control for a class of strict-feedback nonlinear systems with uncertainties under injection and deception attacks. It proposes an adaptive control scheme to deal with the attacks while ensuring that regulation errors can be made arbitrarily small by adjusting control parameters.

IEEE TRANSACTIONS ON SYSTEMS MAN CYBERNETICS-SYSTEMS (2022)

Article Radiology, Nuclear Medicine & Medical Imaging

Quantification of Early Diffuse Myocardial Fibrosis Through 7.0 T Cardiac Magnetic Resonance T1 Mapping in a Type 1 Diabetic Mellitus Mouse Model

Hongkai Zhang, Chunyan Shi, Lin Yang, Nan Zhang, Guoqi Li, Zhen Zhou, Yifeng Gao, Dongting Liu, Lei Xu, Zhanming Fan

Summary: In this study, early DMIF changes in a T1DM mouse model were evaluated using MRI T1 mapping, with ECV identified as an accurate imaging marker for quantitatively assessing DMIF changes over time. The findings suggest that ECV has the potential to accurately detect DMIF in the early stage, making it a useful imaging tool for assessing the need for early intervention in T1DM mice.

JOURNAL OF MAGNETIC RESONANCE IMAGING (2023)

Article Chemistry, Physical

Boosting the Electrocatalytic Activity of Nickel-Iron Layered Double Hydroxide for the Oxygen Evolution Reaction byTerephthalic Acid

Guoqi Li, Jihao Zhang, Lin Li, Chunze Yuan, Tsu-Chien Weng

Summary: In this study, a new type of NiFe double-layer hydroxide (NiFe-LDH) catalyst was synthesized using the hydrothermal method, mixed with different equivalent terephthalic acid (TPA). The catalyst with one equivalent of TPA showed the best performance in terms of oxygen evolution reaction (OER), with low overpotential and high current density, as well as excellent stability.

CATALYSTS (2022)

Article Automation & Control Systems

Spatiotemporal Input Control: Leveraging Temporal Variation in Network Dynamics

Yihan Lin, Jiawei Sun, Guoqi Li, Gaoxi Xiao, Changyun Wen, Lei Deng, H. Eugene Stanley

Summary: The number of control sources is a limiting factor in many network control tasks, but exploiting the temporal variation of network topology can overcome this limitation. The proposed spatiotemporal input control strategy reduces the required number of sources to 2, which is significant for complex network control problems.

IEEE-CAA JOURNAL OF AUTOMATICA SINICA (2022)

Article Computer Science, Artificial Intelligence

Semi-supervised partial label learning algorithm via reliable label propagation

Ying Ma, Dayuan Chen, Tian Wang, Guoqi Li, Ming Yan

Summary: Partial label learning is a weakly supervised learning method that predicts one label from a candidate label set. However, there may be noisy labels in the training data due to the assignment of candidate labels. It is also challenging to improve accuracy due to the combination of partial label learning and semi-supervised learning. Existing methods in semi-supervised partial label learning neglect the noisy labels, leading to contaminated data. We propose a method called SeePLL that addresses the label contamination issue through reliable label propagation.

APPLIED INTELLIGENCE (2023)

Article Computer Science, Artificial Intelligence

A Tandem Learning Rule for Effective Training and Rapid Inference of Deep Spiking Neural Networks

Jibin Wu, Yansong Chua, Malu Zhang, Guoqi Li, Haizhou Li, Kay Chen Tan

Summary: Spiking neural networks (SNNs) are a prominent biologically inspired computing model but are not directly applicable to standard error backpropagation algorithm due to the nondifferentiable nature of spiking neuronal functions. In this work, a tandem learning framework consisting of an SNN and an artificial neural network (ANN) is proposed to train the SNN at the spike-train level. The proposed tandem learning rule demonstrates competitive pattern recognition and regression capabilities with reduced inference time and total synaptic operations.

IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS (2023)

Article Computer Science, Artificial Intelligence

Exploring Adversarial Attack in Spiking Neural Networks With Spike-Compatible Gradient

Ling Liang, Xing Hu, Lei Deng, Yujie Wu, Guoqi Li, Yufei Ding, Peng Li, Yuan Xie

Summary: This study investigates the adversarial attack against spiking neural networks (SNNs) and identifies challenges distinct from artificial neural networks (ANNs) attack. Two approaches are proposed to address the gradient-input incompatibility and gradient vanishing issues, contributing to the development of an adversarial attack methodology for SNNs. Experimental results validate the effectiveness of the proposed methods and provide comparisons with ANN under different attack methods.

IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS (2023)

Article Computer Science, Artificial Intelligence

Kronecker CP Decomposition With Fast Multiplication for Compressing RNNs

Dingheng Wang, Bijiao Wu, Guangshe Zhao, Man Yao, Hengnu Chen, Lei Deng, Tianyi Yan, Guoqi Li

Summary: This article introduces a method for compressing recurrent neural networks (RNNs) based on Kronecker CANDECOMP/PARAFAC (KCP) decomposition. Experimental results demonstrate that KCP-RNNs achieve comparable accuracy, high compression ratios, and efficiency in both space and computation complexity compared to other tensor decomposition methods.

IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS (2023)

Article Computer Science, Artificial Intelligence

Comprehensive SNN Compression Using ADMM Optimization and Activity Regularization

Lei Deng, Yujie Wu, Yifan Hu, Ling Liang, Guoqi Li, Xing Hu, Yufei Ding, Peng Li, Yuan Xie

Summary: This paper investigates the compression of spiking neural networks (SNNs) and presents a comprehensive approach to achieve SNN compression. The study shows that the running efficiency of SNNs can be improved through methods such as connection pruning, weight quantization, and activity regularization, while accuracy loss can be minimized through spatiotemporal backpropagation and alternating direction method of multipliers.

IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS (2023)

Proceedings Paper Computer Science, Artificial Intelligence

Self-Knowledge Distillation from Target-Embedding AutoEncoder for Multi-Label Classification

Qizheng Pan, Ming Yan, Guoqi Li, Jianmin Li, Ying Ma

Summary: This paper introduces a new method called SKDTEA, which improves the performance of multi-label classification through self-knowledge distillation. The method addresses the issue of output bias induced by overfitting by removing the latent space alignment in TEA-based solutions. Experimental results demonstrate significant superiority of the proposed method in multi-label classification.

2022 IEEE INTERNATIONAL CONFERENCE ON KNOWLEDGE GRAPH (ICKG) (2022)

Article Engineering, Electrical & Electronic

General spiking neural network framework for the learning trajectory from a noisy mmWave radar

Xin Liu, Mingyu Yan, Lei Deng, Yujie Wu, De Han, Guoqi Li, Xiaochun Ye, Dongrui Fan

Summary: This paper proposes a general neuromorphic framework called mm-SNN, which utilizes spiking neural networks to process mmWave radar data, overcoming noise and sparsity issues, and achieving considerable performance in trajectory estimation task.

NEUROMORPHIC COMPUTING AND ENGINEERING (2022)

Article Automation & Control Systems

Efficient Visual Recognition: A Survey on Recent Advances and Brain-inspired Methodologies

Yang Wu, Ding-Heng Wang, Xiao-Tong Lu, Fan Yang, Man Yao, Wei-Sheng Dong, Jian-Bo Shi, Guo-Qi Li

Summary: Visual recognition is a key research area in computer vision, pattern recognition, and artificial intelligence. While accuracy is important, efficiency is also crucial for both academic research and industrial applications. This survey reviews recent advances and proposes new directions for improving the efficiency of visual recognition approaches.

MACHINE INTELLIGENCE RESEARCH (2022)

Proceedings Paper Automation & Control Systems

Accelerating Spatiotemporal Supervised Training of Large-Scale Spiking Neural Networks on GPU

Ling Liang, Zhaodong Chen, Lei Deng, Fengbin Tu, Guoqi Li, Yuan Xie

Summary: Spiking neural networks have the potential to achieve brain-like intelligence, but suffer from low accuracy and training efficiency on GPUs. This work presents a framework to solve the inefficiency of training SNNs on GPUs, which achieves significant speedup and reduced memory consumption compared to vanilla Pytorch implementation.

PROCEEDINGS OF THE 2022 DESIGN, AUTOMATION & TEST IN EUROPE CONFERENCE & EXHIBITION (DATE 2022) (2022)

No Data Available