30 results on '"Huang, Peide"'
Search Results
2. The ChinaMAP reference panel for the accurate genotype imputation in Chinese populations
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Li, Lin, Huang, Peide, Sun, Xiaohui, Wang, Siyu, Xu, Min, Liu, Sha, Feng, Zhimin, Zhang, Qing, Wang, Xiaoji, Zheng, Xiaole, Dai, Mengyao, Bi, Yufang, Ning, Guang, Cao, Yanan, and Wang, Weiqing
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- 2021
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3. Multi-omics analyses of G6PD deficiency variants in Chinese population
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Ji, He, Chen, Jiahuan, Huang, Peide, Feng, Zhimin, Hu, Weining, Dai, Mengyao, Sun, Xiaohui, Jin, Xiao, Chen, Guangquan, Ning, Guang, Li, Lin, Wang, Weiqing, and Cao, Yanan
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- 2024
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4. Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations
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Cao, Yanan, Li, Lin, Feng, Zhimin, Wan, Shengqing, Huang, Peide, Sun, Xiaohui, Wen, Fang, Huang, Xuanlin, Ning, Guang, and Wang, Weiqing
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- 2020
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5. What Went Wrong? Closing the Sim-to-Real Gap via Differentiable Causal Discovery
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Huang, Peide, Zhang, Xilun, Cao, Ziang, Liu, Shiqi, Xu, Mengdi, Ding, Wenhao, Francis, Jonathan, Chen, Bingqing, and Zhao, Ding
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FOS: Computer and information sciences ,Computer Science - Robotics ,Robotics (cs.RO) - Abstract
Training control policies in simulation is more appealing than on real robots directly, as it allows for exploring diverse states in a safe and efficient manner. Yet, robot simulators inevitably exhibit disparities from the real world, yielding inaccuracies that manifest as the simulation-to-real gap. Existing literature has proposed to close this gap by actively modifying specific simulator parameters to align the simulated data with real-world observations. However, the set of tunable parameters is usually manually selected to reduce the search space in a case-by-case manner, which is hard to scale up for complex systems and requires extensive domain knowledge. To address the scalability issue and automate the parameter-tuning process, we introduce an approach that aligns the simulator with the real world by discovering the causal relationship between the environment parameters and the sim-to-real gap. Concretely, our method learns a differentiable mapping from the environment parameters to the differences between simulated and real-world robot-object trajectories. This mapping is governed by a simultaneously-learned causal graph to help prune the search space of parameters, provide better interpretability, and improve generalization. We perform experiments to achieve both sim-to-sim and sim-to-real transfer, and show that our method has significant improvements in trajectory alignment and task success rate over strong baselines in a challenging manipulation task.
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- 2023
6. Multimodal Representation Learning of Cardiovascular Magnetic Resonance Imaging
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Qiu, Jielin, Huang, Peide, Nakashima, Makiya, Lee, Jaehyun, Zhu, Jiacheng, Tang, Wilson, Chen, Pohao, Nguyen, Christopher, Kim, Byung-Hak, Kwon, Debbie, Weber, Douglas, Zhao, Ding, and Chen, David
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FOS: Computer and information sciences ,Computer Vision and Pattern Recognition (cs.CV) ,Computer Science - Computer Vision and Pattern Recognition - Abstract
Self-supervised learning is crucial for clinical imaging applications, given the lack of explicit labels in healthcare. However, conventional approaches that rely on precise vision-language alignment are not always feasible in complex clinical imaging modalities, such as cardiac magnetic resonance (CMR). CMR provides a comprehensive visualization of cardiac anatomy, physiology, and microstructure, making it challenging to interpret. Additionally, CMR reports require synthesizing information from sequences of images and different views, resulting in potentially weak alignment between the study and diagnosis report pair. To overcome these challenges, we propose \textbf{CMRformer}, a multimodal learning framework to jointly learn sequences of CMR images and associated cardiologist's reports. Moreover, one of the major obstacles to improving CMR study is the lack of large, publicly available datasets. To bridge this gap, we collected a large \textbf{CMR dataset}, which consists of 13,787 studies from clinical cases. By utilizing our proposed CMRformer and our collected dataset, we achieved remarkable performance in real-world clinical tasks, such as CMR image retrieval and diagnosis report retrieval. Furthermore, the learned representations are evaluated to be practically helpful for downstream applications, such as disease classification. Our work could potentially expedite progress in the CMR study and lead to more accurate and effective diagnosis and treatment., 24 pages
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- 2023
7. lncRNA profile study reveals the mRNAs and lncRNAs associated with docetaxel resistance in breast cancer cells
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Huang, Peide, Li, Fengyu, Li, Lin, You, Yuling, Luo, Shizhi, Dong, Zhensheng, Gao, Qiang, Wu, Song, Brünner, Nils, and Stenvang, Jan
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- 2018
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8. Group Distributionally Robust Reinforcement Learning with Hierarchical Latent Variables
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Xu, Mengdi, Huang, Peide, Niu, Yaru, Kumar, Visak, Qiu, Jielin, Fang, Chao, Lee, Kuan-Hui, Qi, Xuewei, Lam, Henry, Li, Bo, and Zhao, Ding
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FOS: Computer and information sciences ,Computer Science - Machine Learning ,Machine Learning (cs.LG) - Abstract
One key challenge for multi-task Reinforcement learning (RL) in practice is the absence of task indicators. Robust RL has been applied to deal with task ambiguity, but may result in over-conservative policies. To balance the worst-case (robustness) and average performance, we propose Group Distributionally Robust Markov Decision Process (GDR-MDP), a flexible hierarchical MDP formulation that encodes task groups via a latent mixture model. GDR-MDP identifies the optimal policy that maximizes the expected return under the worst-possible qualified belief over task groups within an ambiguity set. We rigorously show that GDR-MDP's hierarchical structure improves distributional robustness by adding regularization to the worst possible outcomes. We then develop deep RL algorithms for GDR-MDP for both value-based and policy-based RL methods. Extensive experiments on Box2D control tasks, MuJoCo benchmarks, and Google football platforms show that our algorithms outperform classic robust training algorithms across diverse environments in terms of robustness under belief uncertainties. Demos are available on our project page (\url{https://sites.google.com/view/gdr-rl/home})., 27 pages, 10 figures
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- 2022
9. Trustworthy Reinforcement Learning Against Intrinsic Vulnerabilities: Robustness, Safety, and Generalizability
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Xu, Mengdi, Liu, Zuxin, Huang, Peide, Ding, Wenhao, Cen, Zhepeng, Li, Bo, and Zhao, Ding
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FOS: Computer and information sciences ,Computer Science - Machine Learning ,Machine Learning (cs.LG) - Abstract
A trustworthy reinforcement learning algorithm should be competent in solving challenging real-world problems, including {robustly} handling uncertainties, satisfying {safety} constraints to avoid catastrophic failures, and {generalizing} to unseen scenarios during deployments. This study aims to overview these main perspectives of trustworthy reinforcement learning considering its intrinsic vulnerabilities on robustness, safety, and generalizability. In particular, we give rigorous formulations, categorize corresponding methodologies, and discuss benchmarks for each perspective. Moreover, we provide an outlook section to spur promising future directions with a brief discussion on extrinsic vulnerabilities considering human feedback. We hope this survey could bring together separate threads of studies together in a unified framework and promote the trustworthiness of reinforcement learning., 36 pages, 5 figures
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- 2022
10. How BMP-2 induces EMT and breast cancer stemness through Rb and CD44?
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Zhang, Guanglin, Huang, Peide, Chen, Anan, He, Weiyi, Li, Zhen, Liu, Ge, and Wang, Ju
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- 2018
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11. A Comprehensive RNA Study to Identify circRNA and miRNA Biomarkers for Docetaxel Resistance in Breast Cancer.
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Huang, Peide, Li, Fengyu, Mo, Zongchao, Geng, Chunyu, Wen, Fang, Zhang, Chunyan, Guo, Jia, Wu, Song, Li, Lin, Brünner, Nils, and Stenvang, Jan
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CIRCULAR RNA ,LINCRNA ,RNA ,DOCETAXEL ,NON-coding RNA - Abstract
To investigate the relationship between non-coding RNAs [especially circular RNAs (circRNAs)] and docetaxel resistance in breast cancer, and to find potential predictive biomarkers for taxane-containing therapies, we have performed transcriptome and microRNA (miRNA) sequencing for two established docetaxel-resistant breast cancer (DRBC) cell lines and their docetaxel-sensitive parental cell lines. Our analyses revealed differences between circRNA signatures in the docetaxel-resistant and -sensitive breast cancer cells, and discovered circRNAs generated by multidrug-resistance genes in taxane-resistant cancer cells. In DRBC cells, circABCB1 was identified and validated as a circRNA that is strongly up-regulated, whereas circEPHA3.1 and circEPHA3.2 are strongly down-regulated. Furthermore, we investigated the potential functions of these circRNAs by bioinformatics analysis, and miRNA analysis was performed to uncover potential interactions between circRNAs and miRNAs. Our data showed that circABCB1, circEPHA3.1 and circEPHA3.2 may sponge up eight significantly differentially expressed miRNAs that are associated with chemotherapy and contribute to docetaxel resistance via the PI3K-Akt and AGE-RAGE signaling pathways. We also integrated differential expression data of mRNA, long non-coding RNA, circRNA, and miRNA to gain a global profile of multi-level RNA changes in DRBC cells, and compared them with changes in DNA copy numbers in the same cell lines. We found that Chromosome 7 q21.12-q21.2 was a common region dominated by multi-level RNA overexpression and DNA amplification, indicating that overexpression of the RNA molecules transcribed from this region may result from DNA amplification during stepwise exposure to docetaxel. These findings may help to further our understanding of the mechanisms underlying docetaxel resistance in breast cancer. [ABSTRACT FROM AUTHOR]
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- 2021
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12. Comprehensive Study of Germline Mutations and Double-Hit Events in Esophageal Squamous Cell Cancer.
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Zeng, Bing, Huang, Peide, Du, Peina, Sun, Xiaohui, Huang, Xuanlin, Fang, Xiaodong, and Li, Lin
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SQUAMOUS cell carcinoma ,ESOPHAGEAL cancer ,TUMOR suppressor genes ,GERM cells ,CANCER genes ,FANCONI'S anemia - Abstract
Esophageal squamous cell cancer (ESCC) is the eighth most common cancer around the world. Several reports have focused on somatic mutations and common germline mutations in ESCC. However, the contributions of pathogenic germline alterations in cancer susceptibility genes (CSGs), highly frequently mutated CSGs, and pathogenically mutated CSG-related pathways in ESCC remain unclear. We obtained data on 571 ESCC cases from public databases and East Asian from the 1000 Genomes Project database and the China Metabolic Analytics Project database to characterize pathogenic mutations. We detected 157 mutations in 75 CSGs, accounting for 25.0% (143/571) of ESCC cases. Six genes had more than five mutations: TP53 (n = 15 mutations), GJB2 (n = 8), BRCA2 (n = 6), RECQL4 (n = 6), MUTYH (n = 6), and PMS2 (n = 5). Our results identified significant differences in pathogenic germline mutations of TP53, BRCA2 , and RECQL4 between the ESCC and control cohorts. Moreover, we identified 84 double-hit events (16 germline/somatic double-hit events and 68 somatic/somatic double-hit events) occurring in 18 tumor suppressor genes from 83 patients. Patients who had ESCC with germline/somatic double-hit events were diagnosed at younger ages than patients with the somatic/somatic double-hit events, though the correlation was not significant. Fanconi anemia was the most enriched pathway of pathogenically mutated CSGs, and it appeared to be a primary pathway for ESCC predisposition. The results of this study identified the underlying roles that pathogenic germline mutations in CSGs play in ESCC pathogenesis, increased our awareness about the genetic basis of ESCC, and provided suggestions for using highly mutated CSGs and double-hit features in the early discovery, prevention, and genetic counseling of ESCC. [ABSTRACT FROM AUTHOR]
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- 2021
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13. A Lightweight Surface Reconstruction Method for Online 3D Scanning Point Cloud Data Oriented toward 3D Printing
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Buyun Sheng, Xiyan Yin, Chenglei Zhang, Huang Peide, Hui Wang, and Feiyu Zhao
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0209 industrial biotechnology ,Article Subject ,business.industry ,Computer science ,General Mathematics ,lcsh:Mathematics ,General Engineering ,Point cloud ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,3D printing ,Iterative closest point ,3d scanning ,02 engineering and technology ,lcsh:QA1-939 ,Computational science ,020901 industrial engineering & automation ,lcsh:TA1-2040 ,0202 electrical engineering, electronic engineering, information engineering ,020201 artificial intelligence & image processing ,business ,lcsh:Engineering (General). Civil engineering (General) ,Surface reconstruction ,ComputingMethodologies_COMPUTERGRAPHICS - Abstract
The existing surface reconstruction algorithms currently reconstruct large amounts of mesh data. Consequently, many of these algorithms cannot meet the efficiency requirements of real-time data transmission in a web environment. This paper proposes a lightweight surface reconstruction method for online 3D scanned point cloud data oriented toward 3D printing. The proposed online lightweight surface reconstruction algorithm is composed of a point cloud update algorithm (PCU), a rapid iterative closest point algorithm (RICP), and an improved Poisson surface reconstruction algorithm (IPSR). The generated lightweight point cloud data are pretreated using an updating and rapid registration method. The Poisson surface reconstruction is also accomplished by a pretreatment to recompute the point cloud normal vectors; this approach is based on a least squares method, and the postprocessing of the PDE patch generation was based on biharmonic-like fourth-order PDEs, which effectively reduces the amount of reconstructed mesh data and improves the efficiency of the algorithm. This method was verified using an online personalized customization system that was developed with WebGL and oriented toward 3D printing. The experimental results indicate that this method can generate a lightweight 3D scanning mesh rapidly and efficiently in a web environment.
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- 2018
14. SET domain containing 1B gene is mutated in primary hepatic neuroendocrine tumors.
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Yang, Penghui, Huang, Xuanlin, Lai, Chengcai, Li, Lin, Li, Tieling, Huang, Peide, Ouyang, Songying, Yan, Jin, Cheng, Sijie, Lei, Guanglin, Wang, Zhaohai, Yu, Linxiang, Hong, Zhixian, Li, Ruisheng, Dong, Hui, Wang, Cheng, Yu, Yinghao, Wang, Xuan, Li, Xianghong, and Wang, Liming
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NEUROENDOCRINE tumors ,NEURAL development ,GENES ,SOMATIC mutation ,CELL cycle - Abstract
Primary hepatic neuroendocrine tumors (PHNETs) are extremely rare NETs originating from the liver. These tumors are associated with heterogeneous prognosis, and few treatment targets for PHNETs have been identified. Because the major genetic alterations in PHNET are still largely unknown, we performed whole‐exome sequencing of 22 paired tissues from PHNET patients and identified 22 recurring mutations of somatic genes involved in the following activities: epigenetic modification (BPTF, MECP2 and WDR5), cell cycle (TP53, ATM, MED12, DIDO1 and ATAD5) and neural development (UBR4, MEN1, GLUL and GIGYF2). Here, we show that TP53 and the SET domain containing the 1B gene (SETD1B) are the most frequently mutated genes in this set of samples (3/22 subjects, 13.6%). A biological analysis suggests that one of the three SETD1B mutants, A1054del, promotes cell proliferation, migration and invasion compared to wild‐type SETD1B. Our work unveils that SETD1B A1054del mutant is functional in PHNET and implicates genes including TP53 in the disease. Our findings thus characterize the mutational landscapes of PHNET and implicate novel gene mutations linked to PHNET pathogenesis and potential therapeutic targets. What's new? Neuroendocrine tumors often metastasize to the liver but primary hepatic neuroendocrine tumors are extremely rare. Here the authors sequenced tumors from 22 patients in China and provide a first look at the mutational landscape of primary hepatic neuroendocrine tumors. The study points to a possible etiological role of the SET domain containing 1B gene (SETD1B) as it was among the most frequently mutated genes, a role that needs to be further explored. [ABSTRACT FROM AUTHOR]
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- 2019
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15. AB203. The mutational landscapes of adrenal cortex aldosterone-producing adenoma (APA) diversified between different populations
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Wu, Song, Huang, Peide, and Zhang, Meng
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education ,mental disorders ,Accepted Abstracts ,Adrenal adenoma ,whole-exome sequencing ,genetic ,psychological phenomena and processes ,East Asian - Abstract
Objective The genetic determinants of aldosterone-producing adrenal adenoma (APA), one of the most common causes of secondary hypertension, had been studied intensively in European patients but its mutational landscapes in Asian populations remained unclear. We aim to further understand the genetic determinants of APA in East Asian patients. Methods We perform Whole-exome sequencing and comprehensive data analyses in tumors and matched normal tissues from 22 Chinese APA patients. Results Notably, we identified KCNJ5 as an ultra-high frequency mutation gene (72.7%) in our cohort compared with previous studies, which highlights the importance of KCNJ5 mutations in the diagnosis and targeted therapy for East Asian APA patients. We also identified somatic mutations in another potassium channel gene and other four cancer relative genes in our APA cohort. Conclusions These findings extend our knowledge about the genetic mechanism of APA development and would contribute to the diagnosis and targeted therapy for East Asian APA patients.
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- 2015
16. A Lightweight Surface Reconstruction Method for Online 3D Scanning Point Cloud Data Oriented toward 3D Printing.
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Sheng, Buyun, Zhao, Feiyu, Yin, Xiyan, Zhang, Chenglei, Wang, Hui, and Huang, Peide
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SURFACE reconstruction ,DATA transmission systems ,CLOUD computing ,CLOUD storage ,WEBSITES - Abstract
The existing surface reconstruction algorithms currently reconstruct large amounts of mesh data. Consequently, many of these algorithms cannot meet the efficiency requirements of real-time data transmission in a web environment. This paper proposes a lightweight surface reconstruction method for online 3D scanned point cloud data oriented toward 3D printing. The proposed online lightweight surface reconstruction algorithm is composed of a point cloud update algorithm (PCU), a rapid iterative closest point algorithm (RICP), and an improved Poisson surface reconstruction algorithm (IPSR). The generated lightweight point cloud data are pretreated using an updating and rapid registration method. The Poisson surface reconstruction is also accomplished by a pretreatment to recompute the point cloud normal vectors; this approach is based on a least squares method, and the postprocessing of the PDE patch generation was based on biharmonic-like fourth-order PDEs, which effectively reduces the amount of reconstructed mesh data and improves the efficiency of the algorithm. This method was verified using an online personalized customization system that was developed with WebGL and oriented toward 3D printing. The experimental results indicate that this method can generate a lightweight 3D scanning mesh rapidly and efficiently in a web environment. [ABSTRACT FROM AUTHOR]
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- 2018
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17. Telomerase Reverse Transcriptase Gene Promoter Mutations Help Discern the Origin of Urogenital Tumors: A Genomic and Molecular Study.
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Wu, Song, Huang, Peide, Li, Chong, Huang, Yi, Li, Xianxin, Wang, Yongqiang, Chen, Chao, Lv, Zhaojie, Tang, Aifa, Sun, Xiaojuan, Lu, Jingxiao, Li, Weiping, Zhou, Jie, Gui, Yaoting, Zhou, Fangjian, Wang, Daping, and Cai, Zhiming
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TELOMERASE reverse transcriptase , *GENETIC mutation , *PROMOTERS (Genetics) , *MOLECULAR biology , *BLADDER cancer , *CELLULAR signal transduction , *GENETICS ,GENITOURINARY organ tumors - Abstract
Abstract: Activation of telomerase can be observed in almost all human tumor histotypes and detection of the urinary telomerase activities is useful for the diagnosis and surveillance of bladder cancer. In this study, we screened, by Sanger sequencing, 302 patients with various urogenital cancers for somatic mutations in the promoter of the telomerase reverse transcriptase (TERT) gene and determined the clinical relevance of TERT promoter mutations in urogenital cancer. In vitro assays were also performed to evaluate the functional influence of the discovered mutations. We found that the frequencies of somatic mutations in the TERT promoter varied substantially between different types of urogenital tumors (range: 0–63.7%), with urothelial carcinomas showing the highest mutation frequency and prostate cancer showing no mutation. The mutations upregulated the expression of TERT and enhanced the invasiveness of the tumor cells. The mutations were more prevalent in older patients with invasive diseases and advanced tumor stages, and were associated with significantly shorter survival time. Moreover, we also observed a significant co-occurrence of mutations between the TERT promoter and the tumor protein 51/retinoblastoma1 (TP53/RB1) signaling pathway. Hence, TERT promoter mutations may serve as important markers for the differential diagnosis and surveillance of urogenital tumors. [Copyright &y& Elsevier]
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- 2014
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18. Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation.
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Guo, Guangwu, Sun, Xiaojuan, Chen, Chao, Wu, Song, Huang, Peide, Li, Zesong, Dean, Michael, Huang, Yi, Jia, Wenlong, Zhou, Quan, Tang, Aifa, Yang, Zuoquan, Li, Xianxin, Song, Pengfei, Zhao, Xiaokun, Ye, Rui, Zhang, Shiqiang, Lin, Zhao, Qi, Mingfu, and Wan, Shengqing
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BLADDER cancer treatment ,BLADDER cancer genetics ,EXONS (Genetics) ,CHROMOSOME segregation ,TRANSITIONAL cell carcinoma ,GENETIC mutation ,GENETIC transcription ,NUCLEOTIDE sequence - Abstract
Bladder cancer is one of the most common cancers worldwide, with transitional cell carcinoma (TCC) being the predominant form. Here we report a genomic analysis of TCC by both whole-genome and whole-exome sequencing of 99 individuals with TCC. Beyond confirming recurrent mutations in genes previously identified as being mutated in TCC, we identified additional altered genes and pathways that were implicated in TCC. Notably, we discovered frequent alterations in STAG2 and ESPL1, two genes involved in the sister chromatid cohesion and segregation (SCCS) process. Furthermore, we also detected a recurrent fusion involving FGFR3 and TACC3, another component of SCCS, by transcriptome sequencing of 42 DNA-sequenced tumors. Overall, 32 of the 99 tumors (32%) harbored genetic alterations in the SCCS process. Our analysis provides evidence that genetic alterations affecting the SCCS process may be involved in bladder tumorigenesis and identifies a new therapeutic possibility for bladder cancer. [ABSTRACT FROM AUTHOR]
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- 2013
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19. New drug for wide-ranging tumor inhibition: The human recombinant soluble ectodomain of FGFR2IIIc
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He, Ying, Wang, Ju, Hong, An, Liu, Xueting, Huang, Peide, and Peng, Dan
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- 2008
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20. In-home Gait Abnormality Detection through Footstep-Induced Floor Vibration Sensing and Person-Invariant Contrastive Learning.
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Dong Y, Kim SE, Schadl K, Huang P, Ding W, Rose J, and Noh HY
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Detecting gait abnormalities is crucial for assessing fall risks and early identification of neuromusculoskeletal disorders such as Parkinson's and stroke. Traditional assessments in gait clinics are infrequent and pose barriers, particularly for disadvantaged populations. Previous efforts have explored sensor-based approaches for in-home gait assessments, yet they face limitations such as visual obstructions (cameras), limited coverage (pressure mats), and the need for device carrying (wearables and insoles). To overcome these limitations, we introduce an in-home gait abnormality detection system using footstep-induced floor vibrations, enabling low-cost, non-intrusive, device-free gait health monitoring. The main research challenge is the high uncertainty in floor vibrations due to gait variations among people, making it challenging to develop a generalizable model for new patients. To address this, we analyze time-frequency-domain features of floor vibration data during specific gait phases and develop a feature transformation method through contrastive learning to address the between-people gait variation challenge. Our method transforms the features from vibrations to an embedding space where samples from different people stay close to each other (robust to people variation) while normal and abnormal gait samples are far apart (sensitive to gait abnormality). After that, gait abnormalities are detected by a downstream classifier after feature transformation. We evaluated our approach through a real-world walking experiment with 21 participants and achieved an 85% to 95% mean accuracy in detecting various gait abnormalities. This novel method overcomes prior limitations in in-home gait assessments, offering accessible gait abnormality detection without the need for intrusive devices or labels for new patients.
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- 2024
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21. Progresses in epigenetic studies of asthma from the perspective of high-throughput analysis technologies: a narrative review.
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Zhang T, Huang P, and Qiu C
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Background and Objective: Asthma is the most common chronic respiratory disease in the world with an estimated heritability between 50% and 60%, and recent studies have shown that epigenetic mechanisms play an important role in its development. Many cutting-edge epigenetic research techniques have been applied to the study of the pathogenesis of asthma, which has promoted the development of asthma etiology and brought new possibilities for treatment. We summarized recent advances in epigenetic research of the pathogenesis of asthma, especially from the perspective of high-throughput analysis techniques, to find potential epigenetic biomarkers and possible molecular targets for the future intervention and treatment of the disease., Methods: We reviewed and summarized recent progress in epigenomic studies of asthma on a "pre-transcriptional level", including DNA methylation, histone modification, and chromatin remodeling, and on a "post-transcriptional level" with a focus on non-coding RNA, from the perspective of high-throughput analysis technologies., Key Content and Findings: We have summarized the progress of different kinds of recent epigenetic studies in asthma, including DNA methylation studies [candidate genes methylation studies and epigenome-wide association study (EWAS)], histone modification studies (histone acetylation/deacetylation studies and histone methylation studies), non-coding RNA studies [microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs)], to help the readers to gain a comprehensive insight into the epigenetic research fields for asthma. The application of high-throughput analysis techniques in asthma research, including EWAS (DNA methylation chips), chromatin immunoprecipitation sequencing (CHIP-seq), microRNA sequencing, whole transcriptome sequencing, co-expression network and competing endogenous RNA (ceRNA) analyses, were introduced accompany with the main findings. And the potential epigenetic biomarkers and possible molecular targets identified via high-throughput analyses were also discussed., Conclusions: Epigenetic research has become a hotspot in research on the pathogenesis of asthma. The combination of high-throughput epigenetic analysis technologies and traditional biological function and clinical studies will bring new breakthrough in the pathogenesis study of asthma, which will improve the genetic interpretation of the disease and bring more possibilities for the development of precision medicine to treat it., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://atm.amegroups.com/article/view/10.21037/atm-22-929/coif). DH reports that he is from BGIShenzhen. The other authors have no conflicts of interest to declare., (2022 Annals of Translational Medicine. All rights reserved.)
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- 2022
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22. Identification of second primary tumors from lung metastases in patients with esophageal squamous cell carcinoma using whole-exome sequencing.
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Xue L, Li W, Fan X, Zhao Z, Zhou W, Feng Z, Liu L, Lin H, Li L, Xue X, Huang X, Huang P, Guo J, Du P, Lu N, Li L, Zhan Q, and Song Y
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- Adult, Aged, Aged, 80 and over, Diagnosis, Differential, Esophageal Neoplasms genetics, Esophageal Neoplasms surgery, Esophageal Squamous Cell Carcinoma genetics, Esophageal Squamous Cell Carcinoma secondary, Esophageal Squamous Cell Carcinoma surgery, Esophagectomy, Esophagus pathology, Female, Humans, Lung pathology, Lung Neoplasms genetics, Lung Neoplasms secondary, Lung Neoplasms surgery, Male, Middle Aged, Neoplasms, Second Primary genetics, Neoplasms, Second Primary pathology, Neoplasms, Second Primary surgery, Pneumonectomy, Exome Sequencing, Biomarkers, Tumor genetics, Esophageal Neoplasms pathology, Esophageal Squamous Cell Carcinoma diagnosis, Lung Neoplasms diagnosis, Neoplasms, Second Primary diagnosis
- Abstract
Esophageal squamous cell carcinoma (ESCC) patients with a synchronous or metachronous lung tumor can be diagnosed with lung metastasis (LM) or a second primary tumor (SPT), but the accurate discrimination between LM and SPT remains a clinical dilemma. This study aimed to investigate the feasibility of using the whole-exome sequencing (WES) technique to distinguish SPT from LM. Methods: We performed WES on 40 tumors from 14 patients, including 12 patients with double squamous cell carcinomas (SCCs) of the esophagus and lung (lymph node metastases were sequenced as internal controls) diagnosed as LM according to pathological information and 2 patients with paired primary ESCC and non-lung metastases examined as external controls. Results: Shared genomic profiles between esophageal (T) and lung (D) tumors were observed in 7 patients, suggesting their clonal relatedness, thus indicating that the lung tumors of these patients should be LM. However, distinct genomic profiles between T and D tumors were observed in the other 5 patients, suggesting the possibility of SPTs that were likely formed through independent multifocal oncogenesis. Conclusions: Our data demonstrate the limitations and insufficiency of clinicopathological criteria and that WES could be useful in understanding the clonal relationships of multiple SCCs., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)
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- 2020
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23. Meta-analysis of 16S rRNA Microbial Data Identified Distinctive and Predictive Microbiota Dysbiosis in Colorectal Carcinoma Adjacent Tissue.
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Mo Z, Huang P, Yang C, Xiao S, Zhang G, Ling F, and Li L
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As research focusing on the colorectal cancer fecal microbiome using shotgun sequencing continues, increasing evidence has supported correlations between colorectal carcinomas (CRCs) and fecal microbiome dysbiosis. However, large-scale on-site and off-site (surrounding adjacent) tissue microbiome characterization of CRC was underrepresented. Here, considering each taxon as a feature, we demonstrate a machine learning-based method to investigate tissue microbial differences among CRC, colorectal adenoma (CRA), and healthy control groups using 16S rRNA data sets retrieved from 15 studies. A total of 2,099 samples were included and analyzed in case-control comparisons. Multiple methods, including differential abundance analysis, random forest classification, cooccurrence network analysis, and Dirichlet multinomial mixture analysis, were conducted to investigate the microbial signatures. We showed that the dysbiosis of the off-site tissue of colonic cancer was distinctive and predictive. The AUCs (areas under the curve) were 80.7%, 96.0%, and 95.8% for CRC versus healthy control random forest models using stool, tissue, and adjacent tissue samples and 69.9%, 91.5%, and 89.5% for the corresponding CRA models, respectively. We also found that the microbiota ecologies of the surrounding adjacent tissues of CRC and CRA were similar to their on-site counterparts according to network analysis. Furthermore, based on the enterotyping of tissue samples, the cohort-specific microbial signature might be the crux in addressing classification generalization problems. Despite cohort heterogeneity, the dysbiosis of lesion-adjacent tissues might provide us with further perspectives in demonstrating the role of the microbiota in colorectal cancer tumorigenesis. IMPORTANCE Turbulent fecal and tissue microbiome dysbiosis of colorectal carcinoma and adenoma has been identified, and some taxa have been proven to be carcinogenic. However, the microbiomes of surrounding adjacent tissues of colonic cancerous tissues were seldom investigated uniformly on a large scale. Here, we characterize the microbiome signatures and dysbiosis of various colonic cancer sample groups. We found a high correlation between colorectal carcinoma adjacent tissue microbiomes and their on-site counterparts. We also discovered that the microbiome dysbiosis in adjacent tissues could discriminate colorectal carcinomas from healthy controls effectively. These results extend our knowledge on the microbial profile of colorectal cancer tissues and highlight microbiota dysbiosis in the surrounding tissues. They also suggest that microbial feature variations of cancerous lesion-adjacent tissues might help to reveal the microbial etiology of colonic cancer and could ultimately be applied for diagnostic and screening purposes., (Copyright © 2020 Mo et al.)
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- 2020
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24. The molecular landscape of synchronous colorectal cancer reveals genetic heterogeneity.
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Wang X, Fang H, Cheng Y, Li L, Sun X, Fu T, Huang P, Zhang A, Feng Z, Li C, Huang X, Li G, Du P, Yang H, Fang X, Li F, Gao Q, and Liu B
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- Apoptosis genetics, DNA Copy Number Variations genetics, Epithelial-Mesenchymal Transition genetics, Exome genetics, Genetic Heterogeneity, Genetic Predisposition to Disease genetics, High-Throughput Nucleotide Sequencing methods, Humans, Mutation genetics, Signal Transduction genetics, Colorectal Neoplasms genetics
- Abstract
Synchronous colorectal cancers (syCRCs), which present two or more lesions at diagnosis, are rare and pose a great challenge for clinical management. Although some predisposing factors associated with syCRCs have been studied with limited accession, the full repertoire of genomic events among the lesions within an individual and the causes of syCRCs remain unclear. We performed whole-exome sequencing of 40 surgical tumour samples of paired lesions from 20 patients to characterize the genetic alterations. Lesions from same patient showed distinct landscapes of somatic aberrations and shared few mutations, which suggests that they originate and develop independently, although they shared the similar genetic background. Canonical genes, such as APC, KRAS, TP53 and PIK3CA, were frequently mutated in the syCRCs, and most of them show different mutation profile compared with solitary colorectal cancer. We identified a recurrent somatic alteration (K15fs) in RPL22 in 25% of the syCRCs. Functional analysis indicated that mutated RPL22 may suppress cell apoptosis and promote the epithelial-mesenchymal transition (EMT). Potential drug targets were identified in several signalling pathways, and they present great discrepancy between lesions from the same patient. Our data show that the syCRCs within the same patient present great genetic heterogeneity, and they may be driven by distinct molecular events and develop independently. The discrepancy of potential drug targets and mutation burden in lesions from one patient provides valuable information in clinical management for patients with syCRCs.
- Published
- 2018
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25. Comprehensive genomic analysis of Oesophageal Squamous Cell Carcinoma reveals clinical relevance.
- Author
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Du P, Huang P, Huang X, Li X, Feng Z, Li F, Liang S, Song Y, Stenvang J, Brünner N, Yang H, Ou Y, Gao Q, and Li L
- Subjects
- Carcinoma, Squamous Cell diagnosis, Esophageal Neoplasms diagnosis, Female, Humans, Male, Prognosis, Carcinoma, Squamous Cell genetics, Databases, Nucleic Acid, Esophageal Neoplasms genetics, Mutation, Neoplasm Proteins genetics
- Abstract
Oesophageal carcinoma is the fourth leading cause of cancer-related death in China, and more than 90% of these tumours are oesophageal squamous cell carcinoma (ESCC). Although several ESCC genomic sequencing studies have identified mutated somatic genes, the number of samples in each study was relatively small, and the molecular basis of ESCC has not been fully elucidated. Here, we performed an integrated analysis of 490 tumours by combining the genomic data from 7 previous ESCC projects. We identified 18 significantly mutated genes (SMGs). PTEN, DCDC1 and CUL3 were first reported as SMGs in ESCC. Notably, the AJUBA mutations and mutational signature4 were significantly correlated with a poorer survival in patients with ESCC. Hierarchical clustering analysis of the copy number alteration (CNA) of cancer gene census (CGC) genes in ESCC patients revealed three subtypes, and subtype3 exhibited more CNAs and marked for worse prognosis compared with subtype2. Moreover, database annotation suggested that two significantly differential CNA genes (PIK3CA and FBXW7) between subtype3 and subtype2 may serve as therapeutic drug targets. This study has extended our knowledge of the genetic basis of ESCC and shed some light into the clinical relevance, which would help improve the therapy and prognosis of ESCC patients.
- Published
- 2017
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26. BMP-2 induces EMT and breast cancer stemness through Rb and CD44.
- Author
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Huang P, Chen A, He W, Li Z, Zhang G, Liu Z, Liu G, Liu X, He S, Xiao G, Huang F, Stenvang J, Brünner N, Hong A, and Wang J
- Abstract
Bone morphogenetic protein 2 (BMP-2) has been reported to facilitate epithelial-to-mesenchymal transition (EMT) and bone metastasis in breast cancer xenograft models. To investigate the role of BMP-2 in the development of breast cancer stem cells (BCSCs), and to further elucidate the mechanisms underlying its influence on breast cancer metastasis, we conducted a comprehensive molecular study using breast cancer cell lines and clinical samples. Our results showed that downregulation of Rb by BMP-2 was associated with ubiquitin-mediated degradation activated by phosphorylation of Rb via the PI3K/AKT signal pathway. In addition, the Smad signaling pathways are implicated in upregulation of CD44 protein expression by BMP-2. It was suggested that cross-talk exists between Rb and CD44 signaling pathways, as recombinant human BMP-2 (rhBMP-2) was found to regulate CD44 expression partly through Rb signals. In clinical tissues, BMP-2 was positively and negatively correlated with CD44 and Rb expression, respectively. Based on the in vitro and in vivo results, we have established an integrated mechanism by which rhBMP-2 induces EMT and stemness of breast cancer cells via the Rb and CD44 signaling pathways, which then contribute to breast cancer metastasis. These findings may be helpful for developing new strategies for the treatment and prognosis of advanced breast cancer., Competing Interests: The authors declare no conflict of interest.
- Published
- 2017
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27. Novel variants in MLL confer to bladder cancer recurrence identified by whole-exome sequencing.
- Author
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Wu S, Yang Z, Ye R, An D, Li C, Wang Y, Wang Y, Huang Y, Liu H, Li F, He L, Sun D, Yu Y, Li Q, Huang P, Zhang M, Zhao X, Bi T, Zhuang X, Zhang L, Lu J, Sun X, Zhou F, Liu C, Yang G, Hou Y, Fan Z, and Cai Z
- Subjects
- Animals, Apoptosis, Blotting, Western, Case-Control Studies, Cell Proliferation, Chromatin Immunoprecipitation, Female, GATA4 Transcription Factor genetics, Humans, Immunoenzyme Techniques, Mice, Mice, Inbred NOD, Mice, SCID, Neoplasm Recurrence, Local pathology, Prognosis, Proto-Oncogene Protein c-ets-1 genetics, RNA, Messenger genetics, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, Survival Rate, Tumor Cells, Cultured, Urinary Bladder Neoplasms pathology, Xenograft Model Antitumor Assays, Biomarkers, Tumor genetics, Exome genetics, High-Throughput Nucleotide Sequencing methods, Histone-Lysine N-Methyltransferase genetics, Mutation genetics, Myeloid-Lymphoid Leukemia Protein genetics, Neoplasm Recurrence, Local genetics, Urinary Bladder Neoplasms genetics
- Abstract
Bladder cancer (BC) is distinguished by high rate of recurrence after surgery, but the underlying mechanisms remain poorly understood. Here we performed the whole-exome sequencing of 37 BC individuals including 20 primary and 17 recurrent samples in which the primary and recurrent samples were not from the same patient. We uncovered that MLL, EP400, PRDM2, ANK3 and CHD5 exclusively altered in recurrent BCs. Specifically, the recurrent BCs and bladder cancer cells with MLL mutation displayed increased histone H3 tri-methyl K4 (H3K4me3) modification in tissue and cell levels and showed enhanced expression of GATA4 and ETS1 downstream. What's more, MLL mutated bladder cancer cells obtained with CRISPR/Cas9 showed increased ability of drug-resistance to epirubicin (a chemotherapy drug for bladder cancer) than wild type cells. Additionally, the BC patients with high expression of GATA4 and ETS1 significantly displayed shorter lifespan than patients with low expression. Our study provided an overview of the genetic basis of recrudescent bladder cancer and discovered that genetic alterations of MLL were involved in BC relapse. The increased modification of H3K4me3 and expression of GATA4 and ETS1 would be the promising targets for the diagnosis and therapy of relapsed bladder cancer.
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- 2016
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28. Induction of estrogen receptor α-36 expression by bone morphogenetic protein 2 in breast cancer cell lines.
- Author
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Wang D, Huang P, Zhu B, Sun L, Huang Q, and Wang J
- Subjects
- Antineoplastic Agents, Hormonal pharmacology, Bone Morphogenetic Protein 2 genetics, Bone Morphogenetic Protein Receptors, Type I antagonists & inhibitors, Bone Morphogenetic Protein Receptors, Type I genetics, Bone Morphogenetic Protein Receptors, Type I metabolism, Breast Neoplasms, Cell Line, Tumor, Cell Proliferation drug effects, Estradiol pharmacology, Estrogen Receptor alpha genetics, Estrogens pharmacology, Female, Humans, RNA Interference, RNA, Small Interfering metabolism, Recombinant Proteins genetics, Recombinant Proteins metabolism, Recombinant Proteins pharmacology, Signal Transduction drug effects, Tamoxifen pharmacology, Up-Regulation drug effects, Bone Morphogenetic Protein 2 metabolism, Estrogen Receptor alpha metabolism
- Abstract
The expression of estrogen receptor-α (ERα) is one of the most important diagnostic and prognostic factors of breast cancer. Recently, ERα-36 has been identified as a novel variant of ER-α. ERα-36 lacks intrinsic transcription activity and mainly mediates non-genomic estrogen signaling. Bone morphogenetic proteins (BMPs) are recognized as key factors during the control of cell fate and cancer development. However, the correlation between BMP and the ER signaling pathway remains unclear. In this study, we show that BMP2, a member of the BMP family, is a novel inducer of ERα-36 expression in breast cancer cells. As shown by western blot assays, the upregulation of ERα-36 by BMP2 was significant. In MDA-MB-231 cells which are ERα-66-negative, BMP2 was able to induce the expression of ERα-36 in a dose-dependent manner, and the RNA interference assay indicated a correlation between BMP2 and ERα-36 expression. BMP2 inhibited the growth of MCF-7 and MDA-MB-231 cells; however, the inhibitory effect was antagonized by tamoxifen, suggesting that the ER signal was involved. The growth of MDA-MB‑231 cells was stimulated by 17-β-estradiol (E2) after BMP2 induction, even though the cells were previously insensitive to E2. These results suggest that BMP2 induces ERα-36 expression and alters tumor resistance to endocrine therapy by changing the expression profile of ERs.
- Published
- 2012
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29. Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma.
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Guo G, Gui Y, Gao S, Tang A, Hu X, Huang Y, Jia W, Li Z, He M, Sun L, Song P, Sun X, Zhao X, Yang S, Liang C, Wan S, Zhou F, Chen C, Zhu J, Li X, Jian M, Zhou L, Ye R, Huang P, Chen J, Jiang T, Liu X, Wang Y, Zou J, Jiang Z, Wu R, Wu S, Fan F, Zhang Z, Liu L, Yang R, Liu X, Wu H, Yin W, Zhao X, Liu Y, Peng H, Jiang B, Feng Q, Li C, Xie J, Lu J, Kristiansen K, Li Y, Zhang X, Li S, Wang J, Yang H, Cai Z, and Wang J
- Subjects
- Humans, Mutation Rate, Proteolysis, Signal Transduction, Ubiquitination, Basic Helix-Loop-Helix Transcription Factors genetics, Carcinoma, Renal Cell genetics, Hypoxia-Inducible Factor 1, alpha Subunit genetics, Kidney Neoplasms genetics, Mutation
- Abstract
We sequenced whole exomes of ten clear cell renal cell carcinomas (ccRCCs) and performed a screen of ∼1,100 genes in 88 additional ccRCCs, from which we discovered 12 previously unidentified genes mutated at elevated frequencies in ccRCC. Notably, we detected frequent mutations in the ubiquitin-mediated proteolysis pathway (UMPP), and alterations in the UMPP were significantly associated with overexpression of HIF1α and HIF2α in the tumors (P = 0.01 and 0.04, respectively). Our findings highlight the potential contribution of UMPP to ccRCC tumorigenesis through the activation of the hypoxia regulatory network.
- Published
- 2011
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30. Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder.
- Author
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Gui Y, Guo G, Huang Y, Hu X, Tang A, Gao S, Wu R, Chen C, Li X, Zhou L, He M, Li Z, Sun X, Jia W, Chen J, Yang S, Zhou F, Zhao X, Wan S, Ye R, Liang C, Liu Z, Huang P, Liu C, Jiang H, Wang Y, Zheng H, Sun L, Liu X, Jiang Z, Feng D, Chen J, Wu S, Zou J, Zhang Z, Yang R, Zhao J, Xu C, Yin W, Guan Z, Ye J, Zhang H, Li J, Kristiansen K, Nickerson ML, Theodorescu D, Li Y, Zhang X, Li S, Wang J, Yang H, Wang J, and Cai Z
- Subjects
- Chromosome Aberrations, Humans, Carcinoma, Transitional Cell genetics, Chromatin Assembly and Disassembly genetics, Gene Expression Regulation, Neoplastic, Mutation, Urinary Bladder Neoplasms genetics
- Abstract
Transitional cell carcinoma (TCC) is the most common type of bladder cancer. Here we sequenced the exomes of nine individuals with TCC and screened all the somatically mutated genes in a prevalence set of 88 additional individuals with TCC with different tumor stages and grades. In our study, we discovered a variety of genes previously unknown to be mutated in TCC. Notably, we identified genetic aberrations of the chromatin remodeling genes (UTX, MLL-MLL3, CREBBP-EP300, NCOR1, ARID1A and CHD6) in 59% of our 97 subjects with TCC. Of these genes, we showed UTX to be altered substantially more frequently in tumors of low stages and grades, highlighting its potential role in the classification and diagnosis of bladder cancer. Our results provide an overview of the genetic basis of TCC and suggest that aberration of chromatin regulation might be a hallmark of bladder cancer.
- Published
- 2011
- Full Text
- View/download PDF
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