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Erratum to: Targeting the PELP1-KDM1 axis as a potential therapeutic strategy for breast cancer

Breast Cancer Research 2012年第6期14卷 1-2页

作者： Valerie Cortez Monica Mann Seshidhar Tekmal Ratna K Vadlamudi Takayoshi Suzuki Naoki Miyata Cristian Rodriguez-Aguayo Gabriel Lopez-Berestein Anil K Sood Department of Obstetrics and Gynecology University of Texas Health Science Center San Antonio TX 78229 USA Department of Cell and Structural Biology University of Texas Health Science Center San Antonio TX 78229 USA Cancer Therapy and Research Center University of Texas Health Science Center San Antonio TX 78229 USA Graduate School of Medical Science Kyoto Prefectural University of Medicine 13 Taishogun Nishitakatsukasa-Cho Kita-ku Kyoto 403-8334 Japan PRESTO Japan Science and Technology Agency 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan Graduate School of Pharmaceutical Sciences Nagoya City University 3-1 Tanabe-dori Mizuho-ku Nagoya Aichi 467-8673 Japan Department of Gynecologic Oncology University of Texas MD Anderson Cancer Center Houston TX 78030 USA Center for RNA Interference and Non-coding RNA University of Texas MD Anderson Cancer Center Houston TX 78030 USA Department of Cancer Biology University of Texas MD Anderson Cancer Center Houston TX 78030 USA

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HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts

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CELL DEATH AND DIFFERENTIATION 2013年第12期20卷 1675-1687页

作者： Ferdin, J. Nishida, N. Wu, X. Nicoloso, M. S. Shah, M. Y. Devlin, C. Ling, H. Shimizu, M. Kumar, K. Cortez, M. A. Ferracin, M. Bi, Y. Yang, D. Czerniak, B. Zhang, W. Schmittgen, T. D. Voorhoeve, M. P. Reginato, M. J. Negrini, M. Davuluri, R. V. Kunej, T. Ivan, M. Calin, G. A. Univ Texas MD Anderson Canc Ctr Dept Expt Therapeut Ctr RNA Interference & Non Coding RNAs Houston TX 77030 USA Univ Ljubljana Biotech Fac Dept Anim Sci Chair Genet Anim Biotechnol & Immunol Domzale 1230 Slovenia Osaka Univ Dept Surg Gastroenterol Grad Sch Med Suita Osaka Japan Indiana Univ Sch Med Dept Med Indianapolis IN 46202 USA Univ Ferrara Dept Morphol Surg & Expt Med LTTA I-44100 Ferrara Italy Wistar Inst Anat & Biol Mol & Cellular Oncogenesis Program Ctr Syst & Computat Biol Philadelphia PA 19104 USA Univ Texas MD Anderson Canc Ctr Dept Pathol Houston TX USA Ohio State Univ Coll Pharm Columbus OH 43210 USA Duke NUS Grad Med Sch Canc & Stem Cell Biol Program Singapore Singapore Natl Univ Singapore Yong Loo Lin Sch Med Dept Biochem Singapore 117595 Singapore Drexel Univ Coll Med Dept Biochem & Mol Biol Philadelphia PA 19104 USA

Recent data have linked hypoxia, a classic feature of the tumor microenvironment, to the function of specific micrornas (mirnas);however, whether hypoxia affects other types of noncoding transcripts is currently unknown. Starting from a genome-wide expression profiling, we demonstrate for the first time a functional link between oxygen deprivation and the modulation of long noncoding transcripts from ultraconserved regions, termed transcribed-ultraconserved regions (T-UCRs). Interestingly, several hypoxia-upregulated T-UCRs, henceforth named 'hypoxia-induced noncoding ultraconserved transcripts' (HINCUTs), are also overexpressed in clinical samples from colon cancer patients. We show that these T-UCRs are predominantly nuclear and that the hypoxia-inducible factor (HIF) is at least partly responsible for the induction of several members of this group. One specific HINCUT, uc.475 (or HINCUT-1) is part of a retained intron of the host protein-coding gene, O-linked N-acetylglucosamine transferase, which is overexpressed in epithelial cancer types. Consistent with the hypothesis that T-UCRs have important function in tumor formation, HINCUT-1 supports cell proliferation specifically under hypoxic conditions and may be critical for optimal O-GlcNAcylation of proteins when oxygen tension is limiting. Our data gives a first glimpse of a novel functional hypoxic network comprising protein-coding transcripts and noncoding rnas (ncrnas) from the T-UCRs category.

关键词： ultraconserved genes colorectal cancer glioblastoma hypoxia OGT

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CORRIGENDUM: GATA3 as a master regulator for interactions of tumor-associated macrophages with high-grade serous ovarian carcinoma

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Cellular signalling 2022年 89卷 110147页

作者： Amr Ahmed El-Arabey Merve Denizli Pinar Kanlikilicer Recep Bayraktar Cristina Ivan Mohammed Rashed Nashwa Kabil Bulent Ozpolat George A Calin Salama Abdou Salama Adel Rashad Abd-Allah Anil K Sood Gabriel Lopez-Berestein Department of Experimental Therapeutics The University of Texas MD Anderson Cancer Center Houston TX USA Department of Pharmacology and Toxicology Al-Azhar University Faculty of Pharmacy Cairo Egypt. Department of Experimental Therapeutics The University of Texas MD Anderson Cancer Center Houston TX USA. Center for RNA Interference and Non-Coding RNA The University of Texas MD Anderson Cancer Center Houston TX USA. Center for RNA Interference and Non-Coding RNA The University of Texas MD Anderson Cancer Center Houston TX USA Department of Gynecologic Oncology and Reproductive Medicine The University of Texas MD Anderson Cancer Center Houston TX USA. Department of Gynecologic Oncology and Reproductive Medicine The University of Texas MD Anderson Cancer Center Houston TX USA Department of Cancer Biology The University of Texas MD Anderson Cancer Center Houston TX USA.

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Microrna or not microrna?

MicroRNA or not microRNA?

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Lecture Notes in Computer Science

作者： Langenberger, David Bartschat, Sebastian Hertel, Jana Hoffmann, Steve Tafer, Hakim Stadler, Peter F. Bioinformatics Group Department of Computer Science University of Leipzig D-04107 Leipzig United Kingdom Interdisciplinary Center for Bioinformatics University of Leipzig Härtelstraße 16-18 D-04107 Leipzig Germany LIFE - Leipzig Research Center for Civilization Diseases University of Leipzig Germany Max Planck Institute for Mathematics in the Sciences Inselstraße 22 D-04103 Leipzig Germany Fraunhofer Institut für Zelltherapie und Immunologie Perlickstraße 1 D-04103 Leipzig Germany Department of Theoretical Chemistry University of Vienna Währingerstraße 17 A-1090 Wien Austria Center for Non-coding RNA in Technology and Health University of Copenhagen Grønnegårdsvej 3 DK-1870 Frederiksberg C Denmark Santa Fe Institute 1399 Hyde Park Rd. Santa Fe NM 87501 United States

ISBN: (纸本)9783642228247

The avalanche of next generation sequencing data has led to a rapid increase of annotated micrornas in the last few years. Many of them are specific to individual species or rather narrow clades. A closer inspection of the current version of miRBase shows that dozens of entries conflict with other ncrnas, in particular snornas. With few exceptions, these cases show little similarities to canonical micrornas, however, and thus they should be considered as mis-annotations. © 2011 Springer-Verlag.

关键词： rna

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A novel tissue engineered nerve graft constructed with autologous vein and nerve microtissue repairs a longsegment sciatic nerve defect

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Neural Regeneration Research 2021年第1期16卷 143-149页

作者： Jing Wang Ya-Qiong Zhu Yu Wang Hong-Guang Xu Wen-Jing Xu Yue-Xiang Wang Xiao-Qing Cheng Qi Quan Yong-Qiang Hu Chang-Feng Lu Yan-Xu Zhao Wen Jiang Chen Liu Liang Xiao Wei Lu Chen Zhu Ai-Yuan Wang Spine Research Center of Wannan Medical College Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution(Wannan Medical College)Department of Spine SurgeryYijishan HospitalThe First Affiliated Hospital of Wannan Medical CollegeWuhuAnhui ProvinceChina Department of Ultrasound Chinese PLA General HospitalBeijingChina Department of Orthopedic Surgery Key Laboratory of Musculoskeletal Trauma&War Injuries PLABeijing Key Lab of Regenerative Medicine in OrthopedicsChinese PLA General HospitalBeijingChina Medical College of Nankai University TianjinChina The Neural Regeneration Co-Innovation Center of Jiangsu Province NantongJiangsu ProvinceChina Department of Anesthesiology the Second Affiliated Hospital of Inner Mongolia Medical UniversityHuhhotInner Mongolia Autonomous RegionChina Department of Orthopedic Surgery Yan’an University Affiliated HospitalYan’anShaanxi ProvinceChina Department of Orthopedic Surgery the First Affiliated Hospital of Medical CollegeShihezi UniversityShiheziXinjiang Uygur Autonomous RegionChina Department of Orthopedic Surgery The First Peoples’Hospital of Yunnan ProvinceKunmingYunnan ProvinceChina Department of Orthopedic Surgery Anhui Provincial HospitalThe First Affiliated Hospital of University of Science and Technology of ChinaHeifeiAnhui ProvinceChina

Veins are easy to obtain,have low immunogenicity,and induce a relatively weak inflammatory ***,veins have the potential to be used as conduits for nerve ***,because of the presence of venous valves and the great elasticity of the venous wall,the vein is not conducive to nerve *** this study,a novel tissue engineered nerve graft was constructed by combining normal dissected nerve microtissue with an autologous vein graft for repairing 10-mm peripheral nerve defects in *** with rats given the vein graft alone,rats given the tissue engineered nerve graft had an improved sciatic static index,and a higher amplitude and shorter latency of compound muscle action ***,rats implanted with the microtissue graft had a higher density and thickness of myelinated nerve fibers and reduced gastrocnemius muscle atrophy compared with rats implanted with the vein ***,the tissue engineered nerve graft had a lower ability to repair the defect than autogenous nerve *** summary,although the tissue engineered nerve graft constructed with autologous vein and nerve microtissue is not as effective as autologous nerve transplantation for repairing long-segment sciatic nerve defects,it may nonetheless have therapeutic potential for the clinical repair of long sciatic nerve *** study was approved by the Experimental Animal Ethics Committee of Chinese PLA General Hospital(approval No.2016-x9-07)on September 7,2016.

关键词： in vivo injury motor neurological function peripheral nerve injury rat recovery regeneration repair

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Key nodes of a microrna network associated with the integrated mesenchymal subtype of high-grade serous ovarian cancer

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Chinese Journal of Cancer 2015年第1期34卷 28-40页

作者： Sun, Yan Guo, Fei Bagnoli, Marina Xue, Feng-Xia Sun, Bao-Cun Shmulevich, Ilya Mezzanzanica, Delia Chen, Ke-Xin Sood, Anil K. Yang, Da Zhang, Wei Departments of Pathology Tianjin Medical University Cancer Institute and Hospital Tianjin 300060 China Departments of Epidemiology and Biostatistics Tianjin Medical University Cancer Institute and Hospital Tianjin 300060 China The Key Laboratory of Tianjin Cancer Prevention and Treatment Tianjin Medical University Cancer Institute and Hospital Tianjin 300060 China Department of Gynecology and Obstetrics Tianjin Medical University General Hospital Tianjin China Department of Experimental Oncology and Molecular Medicine Fondazione IRCCS Istituto Nazionale dei Tumori Milano 20133 Italy Institute for Systems Biology Seattle 98109 WA United States Departments of Gynecologic Oncology and Reproductive Medicine The University of Texas MD Anderson Cancer Center Houston 77030 TX United States Departments of Pathology The University of Texas MD Anderson Cancer Center Houston 77030 TX United States Center for RNAi and Non-Coding RNA The University of Texas MD Anderson Cancer Center Houston 77030 TX United States Department of Pharmaceutical Sciences Center for Pharmacogenetics University of Pittsburgh School of Pharmacy Pittsburgh 15261 PA United States

Metastasis is the main cause of cancer mortality. One of the initiating events of cancer metastasis of epithelial tumors is epithelial-to-mesenchymal transition (EMT), during which cells dedifferentiate from a relatively rigid cell structure/morphology to a flexible and changeable structure/morphology often associated with mesenchymal cells. The presence of EMT in human epithelial tumors is reflected by the increased expression of genes and levels of proteins that are preferentially present in mesenchymal cells. The combined presence of these genes forms the basis of mesenchymal gene signatures, which are the foundation for classifying a mesenchymal subtype of tumors. Indeed, tumor classification schemes that use clustering analysis of large genomic characterizations, like The Cancer Genome Atlas (TCGA), have defined mesenchymal subtype in a number of cancer types, such as high-grade serous ovarian cancer and glioblastoma. However, recent analyses have shown that gene expression-based classifications of mesenchymal subtypes often do not associate with poor survival. This “paradox” can be ameliorated using integrated analysis that combines multiple data types. We recently found that integrating mrna and microrna (mirna) data revealed an integrated mesenchymal subtype that is consistently associated with poor survival in multiple cohorts of patients with serous ovarian cancer. This network consists of 8 major mirnas and 214 mrnas. Among the 8 mirnas, 4 are known to be regulators of EMT. This review provides a summary of these 8 mirnas, which were associated with the integrated mesenchymal subtype of serous ovarian cancer. © 2015 Landes Bioscience. All Rights reserved.

关键词： Cancer Epithelial-to-mesenchymal transition (EMT) Microrna (mirna) miR-101 miR-506 Ovary

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The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experiments

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BMC Research Notes 2018年第1期11卷 1-5页

作者： Wiegreffe, Daniel Müller, Lydia Steuck, Jens Zeckzer, Dirk Stadler, Peter F. Image and Signal Processing Group Department of Computer Science University of Leipzig Augustusplatz 10 Leipzig 04109 Germany Natural Language Processing Department Department of Computer Science University of Leipzig Augustusplatz 10 Leipzig 04109 Germany Bioinformatics Group Department of Computer Science University of Leipzig Härtelstraße 16-18 Leipzig 04107 Germany Interdisciplinary Center for Bioinformatics University of Leipzig Härtelstraße 16-18 Leipzig 04107 Germany Max Planck Institute MIS Inselstraße 22 Leipzig 04103 Germany Fraunhofer Institute for Cell Therapy and Immunology IZI Perlickstraße 1 Leipzig 04103 Germany Institute for Theoretical Chemistry University of Vienna Währinger Straße 17 Vienna 1090 Austria Center for Non-coding RNA in Technology and Health University of Copenhagen Grønnegårdsvej 3 Copenhagen 1870 Denmark Santa Fe Institute 1399 Hyde Park Road Santa Fe 87501 NM United States

Objective: Sierra Platinum is a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering. The required computing resources are optimized but still may exceed the resources available to researchers at biological research institutes. Results: Sierra Platinum Service provides the full functionality of Sierra Platinum: using a web interface, a new instance of the service can be generated. Then experimental data is uploaded and the computation of the peaks is started. Upon completion, the results can be inspected interactively and then downloaded for further analysis, at which point the service terminates. © 2018 The Author(s).

关键词： ChIP-seq Histone modifications Peak-caller Replicate analysis

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Association between nonalcoholic Fatty Liver Disease and Carotid Artery Disease in a Community-Based Chinese Population： A Cross-Sectional Study

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Chinese Medical Journal 2018年第19期131卷 2269-2276页

作者： Yu-Chen Guo Yong Zhou Xing Gao Yan Yao Bin Geng Qing-Hua Cui Ji-Chun Yang Hong-Pu Hu Department of Health Information Management Institute of Medical Information Peking Union Medical College & Chinese Academy of Medical Sciences Beijing 100020 China Beijing Institute of Heart Lung and Blood Vessel Diseases Beijing Anzhen Hospital Capital Medical University Beijing 100029 China Department of Cardiology Beijing Anzhen Hospital Capital Medical University Beijing 100029 China Hypertension Center Fuwai Hospital Chinese Academy of Medical Sciences and Peking Union Medical College State Key Laboratory of Cardiovascular Disease Beijing 100037 China Department of Biomedical Informatics School of Basic Medical Sciences Key Laboratory of Molecular Cardiovascular Science of the Ministry of Education Center for Non-coding RNA Medicine Peking University Health Science Center Beijing 100191 China Department of Physiology and Pathophysiology School of Basic Medical Sciences Peking University Health Science Center Beijing 100191 China

Background： nonalcoholic fatty liver disease （NAFLD） is one of the most common chronic liver diseases with a high prevalence in the general population. The association between NAFLD and cardiovascular disease has been well addressed in previous studies. However, whether NAFLD is associated with carotid artery disease in a community-based Chinese population remained unclear. The aim of this study was to investigate the association between NAFLD and carotid artery disease. Methods： A total of 2612 participants （1091 men and 1521 women） aged 40 years and older from Jidong of Tangshan city （China） were selected for this study. NAFLD was diagnosed by abdominal ultrasonography. The presence of carotid stenosis or plaque was evaluated by carotid artery ultrasonography. Logistic regression was used to analyze the association between NAFLD and carotid artery disease. Results： Participants with NAFLD have a higher prevalence of carotid stenosis （12.9% vs. 4.6%） and carotid plaque （21.9% vs. 15.0%） than those without NAFLD. After adjusting for age, gender, smoking status, income, physical activity, diabetes, hypertension, triglyceride, waist-hip ratio, and high-density lipoprotein, NAFLD is significantly associated with carotid stenosis （odds ratio [OR]： 2.06, 95% confidence interval [CI]： 1.45-2.91）, but the association between NAFLD and carotid plaque is not statistically significant （OR： 1. 10, 95% CI： 0.86-1.40）. Conclusion： A significant association between NAFLD and carotid stenosis is found in a Chinese population.

关键词： Association Carotid Artery Disease Carotid Stenosis nonalcoholic Fatty Liver Disease

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TH-302-loaded nanodrug reshapes the hypoxic tumour microenvironment and enhances PD-1 blockade efficacy in gastric cancer

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Journal of Nanobiotechnology 2023年第1期21卷 440-440页

作者： Wang, Zhixiong Zhu, Menglin Dong, Runyu Cao, Danping Li, Yanna Chen, Zhiqiang Cai, Juan Zuo, Xueliang Department of Gastrointestinal Surgery The First Affiliated Hospital Yijishan Hospital of Wannan Medical College Wuhu241001 China Hepatobiliary Center The First Affiliated Hospital of Nanjing Medical University Key Laboratory of Liver Transplantation Chinese Academy of Medical Sciences NHC Key Laboratory of Living Donor Liver Transplantation Nanjing China Anhui Province Key Laboratory of Non-coding RNA Basic and Clinical Transformation Wannan Medical College Wuhu241001 China Department of Oncology The First Affiliated Hospital Yijishan Hospital of Wannan Medical College Wuhu241001 China

Background: Hypoxia, a common characteristic of the tumour microenvironment, is involved in tumour progression and immune evasion. Targeting the hypoxic microenvironment has been implicated as a promising antitumour therapeutic strategy. TH-302 can be selectively activated under hypoxic conditions. However, the effectiveness of TH-302 in gastric cancer combined immunotherapy remains unclear. Methods: We designed mPEG-PLGA-encapsulated TH-302 (TH-302 NPs) to target the hypoxic area of tumour tissues. A particle size analyzer was used to measure the average size and zeta potential of TH-302 NPs. The morphology was observed by transmission electron microscopy and scanning electron microscopy. The hypoxic area of tumour tissues was examined by immunofluorescence assays using pimonidazole. Flow cytometry analysis was performed to measure the levels of TNF-α, IFN-γ, and granzyme B. The synergistic antitumour activity of the combination of TH-302 NPs with anti-PD-1 (α-PD-1) therapy was assessed in vitro and in vivo. Haematoxylin and eosin staining of major organs and biochemical indicator detection were performed to investigate the biological safety of TH-302 NPs in vivo. Results: TH-302 NPs inhibited the proliferation and promoted the apoptosis of gastric cancer cells under hypoxic conditions. In vitro and in vivo experiments confirmed that TH-302 NPs could effectively alleviate tumour hypoxia. TH-302 NPs exhibited high bioavailability, effective tumour-targeting ability and satisfactory biosafety. Moreover, the combination of TH-302 NPs with α-PD-1 significantly improved immunotherapeutic efficacy in vivo. Mechanistically, TH-302 NPs reduced the expression of HIF-1α and PD-L1, facilitated the infiltration of CD8+ T cells and increased the levels of TNF-α, IFN-γ, and granzyme B in tumours, thereby enhancing the efficacy of α-PD-1 therapy. Conclusion: TH-302 NPs alleviated the hypoxic tumour microenvironment and enhanced the efficacy of PD-1 blockade. Our results provide e

关键词： Cell death

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TP53 loss creates therapeutic vulnerability in colorectal cancer (vol 30, pg 697, 2015)

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NATURE 2021年第7875期597卷 E6-E6页

作者： Liu, Yunhua Zhang, Xinna Han, Cecil Wan, Guohui Huang, Xingxu Ivan, Cristina Jiang, Dahai Rodriguez-Aguayo, Cristian Lopez-Berestein, Gabriel Rao, Pulivarthi H. Maru, Dipen M. Pahl, Andreas He, Xiaoming Sood, Anil K. Ellis, Lee M. Anderl, Jan Lu, Xiongbin Department of Cancer Biology The University of Texas MD Anderson Cancer Center Houston TX USA Department of Gynaecologic Oncology and Reproductive Medicine The University of Texas MD Anderson Cancer Center Houston USA Center for RNA Interference and Non-coding RNAs The University of Texas MD Anderson Cancer Center Houston TX USA Department of Experimental Therapeutics The University of Texas MD Anderson Cancer Center Houston TX USA School of Life Science and Technology ShanghaiTech University Shanghai China Department of Paediatrics Baylor College of Medicine Houston TX USA Department of Pathology The University of Texas MD Anderson Cancer Center Houston TX USA Heidelberg Pharma GmbH Ladenburg Germany Department of Biomedical Engineering The Ohio State University Columbus OH USA Department of Surgical Oncology The University of Texas MD Anderson Cancer Center Houston TX USA

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