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An online coronavirus analysis platform from the National genomics Data center

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Zoological Research 2020年第6期41卷 705-708页

作者： Zheng Gong Jun-Wei Zhu Cui-Ping Li Shuai Jiang Li-Na Ma Bi-Xia Tang Dong Zou Mei-Li Chen Yu-Bin Sun Shu-Hui Song Zhang Zhang Jing-Fa Xiao Yong-Biao Xue Yi-Ming Bao Zheng-Lin Du Wen-Ming Zhao China National center for Bioinformation&National genomics Data center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

DEAR EDITOR,Since the first reported severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection in December 2019,coronavirus disease 2019(COVID-19)has become a global pandemic,spreading to more than 200 countries and regions *** continued research progress and virus detection,SARS-CoV-2 genomes and sequencing data have been reported and accumulated at an unprecedented rate.

关键词： acute respiratory continued

In silico analysis of lncRNA-miRNA-mRNA signatures related to Sorafenib effectiveness in liver cancer cells

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World Journal of Gastroenterology 2025年第3期31卷 84-102页

作者： Patricia de la Cruz-Ojeda Ester Parras-Martínez Raquel Rey-Pérez Jordi Muntané Functional genomics of Solid Tumors Laboratory Centre de Recherche des CordeliersParis 75006France Department of Oncology Surgery Cell Therapy and Organ TransplantationInstitute of Biomedicine of SevilleVirgen del Rocio University HospitalSeville 41013Spain Biomedical Research center for Hepatic and Digestive Diseases CIBERehdMadrid 28029Spain Department of Medical Physiology and Biophysics University of SevilleSeville 41009Spain

BACKGROUND Hepatocellular carcinoma(HCC)is the most common subtype of primary liver cancer with varied incidence and epidemiology *** is still a recommended treatment for a large proportion of patients with advanced *** patterns of treatment responsiveness have been identified in differentiated hepatoblastoma HepG2 cells and metastatic HCC SNU449 *** To define the long non-codingRNA-microRNA-mRNA(lncRNA-miRNA-mRNA)predicted signatures related to selected hallmarks of cancer(apoptosis,autophagy,cell stress,cell dedifferentiation and invasiveness)in RNAseq studies using Sorafenib-treated HepG2 and SNU449 *** available software analyses allowed us to establish the lncRNA-miRNA-mRNA regulatory axes following treatment in HepG2 and SNU449 *** HepG2 and SNU449 cells were treated with Sorafenib(10μmol/L)for 24 *** RNA,including small and long RNA,was extracted with a commercial miRNeasy *** was carried out for the identification of changes in lncRNA-miRNA-mRNA regulatory *** MALAT,THAP9-AS1 and SNGH17 appeared to coordinately regulate miR-374b-3p and miR-769-5p that led to upregulation of SMAD7,TIRARP,TFAP4 and FAXDC2 in HepG2 ***12,EPB41 L4A-AS1,LINC01578,SNHG12 and GAS5 interacted with let-7b-3p,miR-195-5p and VEGFA in SNU449 *** axes MALAT1/hsamir-374b-3p/SMAD7 and MALAT1/hsa-mir-769-5p/TFAP4 were of high relevance for Sorafenib response in HepG2 cells,whereas PVT1/hsa-miR-195-5p/VEGFA was responsible for the differential response of SNU449 cells to Sorafenib *** Critical lncRNAs acting as sponges of miRNA were identified that regulated mRNA expression,whose proteins mainly increased the antitumor effectiveness of the treatment(SMAD7,TIRARP,TFAP4,FAXDC2 and ADRB2).However,the broad regulatory axis leading to increased VEGFA expression may be related to the side effect of Sorafenib in SNU449 cells.

关键词： Cell culture Hepatocellular carcinoma Non-coding RNA RNAseq Sorafenib

Unraveling brain aging through the lens of oral microbiota

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Neural Regeneration Research 2025年第7期20卷 1930-1943页

作者： Qinchao Hu Si Wang Weiqi Zhang Jing Qu Guang-Hui Liu State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijingChina Hospital of Stomatology Guanghua School of StomatologyGuangdong Provincial Key Laboratory of StomatologySun Yat-sen UniversityGuangzhouGuangdong ProvinceChina Advanced Innovation center for Human Brain Protection and National Clinical Research center for Geriatric Disorders Xuanwu HospitalCapital Medical UniversityBeijingChina Aging Translational Medicine center International Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuanwu HospitalCapital Medical UniversityBeijingChina CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina University of Chinese Academy of Sciences BeijingChina Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijingChina Aging Biomarker Consortium BeijingChina State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijingChina Beijing Institute for Stem Cell and Regenerative Medicine BeijingChina

The oral cavity is a complex physiological community encompassing a wide range of *** of oral microbiota can lead to various oral infectious diseases,such as periodontitis and tooth decay,and even affect systemic health,including brain aging and neurodegenerative *** studies have highlighted how oral microbes might be involved in brain aging and neurodegeneration,indicating potential avenues for intervention *** this review,we summarize clinical evidence demonstrating a link between oral microbes/oral infectious diseases and brain aging/neurodegenerative diseases,and dissect potential mechanisms by which oral microbes contribute to brain aging and *** also highlight advances in therapeutic development grounded in the realm of oral microbes,with the goal of advancing brain health and promoting healthy aging.

关键词： Alzheimer's disease brain aging multiple sclerosis neurodegeneration neurodegenerative diseases oral microbiota Parkinson's disease periodontitis bacteria Porphyromonas gingivalis

Small RNA in rice genome

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Science China(Life Sciences) 2002年第5期45卷 497-503页

作者：王凯朱小蓬钟兰陈润生 Beijing genomics Institute/center of genomics and Bioinformatics Chinese Academy of Sciences Beijing 101300 China Beijing Genomics Institute/Center of Genomics and Bioinformatics Chinese Academy of Sciences Beijing 101300 China College of Life Sciences Peking University Beijing 100871 China Beijing Genomics Institute/Center of Genomics and Bioinformatics Chinese Academy of Sciences Beijing 101300 China Laboratory of Bioinformatics Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China

Rice has many characteristics of a model plant. The recent completion of the draft of the rice genome represents an important advance in our knowledge of plant biology and also has an important contribution to the understanding of general genomic evolution. Besides the rice genome finishing map, the next urgent step for rice researchers is to annotate the genes and noncoding functional sequences. The recent work shows that noncoding RNAs (ncRNAs) play significant roles in biological systems. We have explored all the known small RNAs (a kind of ncRNA) within rice genome and other six species sequences, including Arabidopsis, maize, yeast, worm, mouse and pig. As a result we find 160 out of 552 small RNAs (sRNAs) in database have homologs in 108 rice scaffolds, and almost all of them (99.41%) locate in intron regions of rice by gene predication. 19 sRNAs only appear in rice. More importantly, we find two special U14 sRNAs: one is located in a set of sRNA ZMU14SNR9(s) which only appears in three plants, 86% sequences of them can be compared as the same sequence in rice, Arabidopsis and maize; the other conserved sRNA XLHS7CU14 has a segment which appears in almost all these species from plants to animals. All these results indicate that sRNA do not have evident borderline between plants and animals.

关键词： ncRNA, sRNA, conserved sequences, plant-specific sRNA gene.

OsSCE1 Encoding SUMO E2-Conjugating Enzyme Involves in Drought Stress Response of Oryza sativa

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Rice science 2018年第2期25卷 73-81页

作者： Dini NURDIANI Dwi WIDYAJAYANTIE Satya NUGROHO Laboratory of genomics and Crop Improvement Research Center for Biotechnology Indonesian Institute of Sciences

Small ubiquitin-like modifier(SUMO)-conjugating enzymes are involved in post-translational regulatory processes in eukaryotes, including the conjugation of SUMO peptides to protein substrate(SUMOylation). SUMOylation plays an important role in improving plant tolerance to abiotic stress such as salt, drought, heat and cold. Herein, we reported the isolation of OsSCE1(LOC_Os10 g39120) gene encoding a SUMO-conjugating enzyme from rice(Oryza sativa cv. Nipponbare) and its functional validation in response to drought stress. The E2 enzyme, Os SCE1, is one of three key enzymes involved in the conjugation of SUMO to its target proteins. Activated SUMO is transferred to the cysteine of an E2 enzyme and then to the target lysine residue of the substrate, with or without the help of an E3 SUMO ligase. Expression of OsSCE1 was strongly induced by polyethylene glycol 6000(PEG6000) treatment, which suggested OsSCE1 may be involved in the drought stress response. Overexpression of OsSCE1(OsSCE1-OX) in Nipponbare reduced the tolerance to drought stress. Conversely, the drought tolerance was slightly improved by the knockdown of OsSCE1(OsSCE1-KD). These results were further supported by measurement of proline content in OsSCE1-OX and OsSCE1-KD transgenic lines under induced drought stress, which showed OsSCE1-KD transgenic lines accumulated higher proline content than the wild type, whereas OsSCE1-OX line had lower proline content than the wild type. These findings suggested OsSCE1 may play a role as a negative regulator in response to drought stress in rice.

关键词： Oryza sativa drought stress small ubiquitin-like modifier SUMO-conjugating enzyme proline content gene expression

Genomic alterations in pancreatic cancer and their relevance to therapy

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World Journal of Gastrointestinal Oncology 2015年第10期7卷 250-258页

作者： Erina Takai Shinichi Yachida Division of Cancer genomics National Cancer Center Research Institute

Pancreatic cancer is a highly lethal cancer type, for which there are few viable therapeutic options. But, with the advance of sequencing technologies for global genomic analysis, the landscape of genomic alterations in pancreatic cancer is becoming increasingly well understood. In this review, we summarize current knowledge of genomic alterations in 12 core signaling pathways or cellular processes in pancreatic ductal adenocarcinoma, which is the most common type of malignancy in the pancreas, including four commonly mutated genes and many other genes that are mutated at low frequencies. We also describe the potential implications of these genomic alterations for development of novel therapeutic approaches in the context of personalized medicine.

关键词： Pancreatic cancer Genomic alterations Signaling pa

Investigating loss of heterozygosity in a SCRaMbLEd yeast genome

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Science China(Life Sciences) 2019年第6期62卷 868-869页

作者： Junbiao Dai Shenzhen Key Laboratory of Synthetic genomics and center for Synthetic genomics Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences

Loss of heterozygosity (LOH) is a phenomenon in which elimination of one parental genomic region occurs in interspecific hybrids. LOH is common in cancer (Deng et al., 1996;Koufos et al., 1985). However, genetic analy... 详细信息

关键词： Loss of heterozygosity elimination individual genomes

Inevitability or contingency: how many chromosomes do we really need?

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Science China(Life Sciences) 2019年第1期62卷 140-143页

作者： Shuangying Jiang Junbiao Dai Shenzhen Key Laboratory of Synthetic genomics and center for Synthetic genomics Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences

In an essay written by the evolutionary biologist Theodosius Dobzhansky in 1973,he pointed out that "Nothing in Biology Makes Sense Except in the Light of Evolution."An interesting phenomenon in biology is the presence of variable numbers of chromosomes in different *** several species,which possess multiple circular chromosomes or simply linear chromosomes (Baril et al. 1989;Suwanto and Kaplan,1989;Jumas-Bilak et al.,1998), most prokaryotes only possess one circular *** contrast,the genomes of eukaryotic species are usually packaged into linear chromosomes with numbers varying from one to hundreds (Crosland and Crozier,1986;Lukhtanov,2015).

关键词： Inevitability contingency evolutionary biologist

Circulating tumor DNA as a liquid biopsy target for detection of pancreatic cancer

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World Journal of Gastroenterology 2016年第38期22卷 8480-8488页

作者： Erina Takai Shinichi Yachida Division of Cancer genomics National Cancer Center Research InstituteTokyo

Most pancreatic cancer patients present with advanced metastatic disease, resulting in extremely poor 5-year survival, mainly because of the lack of a reliable modality for early detection and limited therapeutic options for advanced disease. Therefore, there is a need for minimally-invasive diagnostic tools for detecting pancreatic cancer at an early stage, when curative surgery and also novel therapeutic approaches including precision medicine may be feasible. The "liquid biopsy" addresses these unmet clinical needs based on the concept that simple peripheral blood sampling and detection of circulating tumor DNA(ct DNA) could provide diagnostic information. In this review, we provide an overview of the current status of bloodbased tests for diagnosis of pancreatic cancer and the potential utility of ct DNA for precision medicine. We also discuss challenges that remain to be addressed in developing practical ct DNA-based liquid biopsy approaches for early diagnosis of pancreatic cancer.

关键词： Circulating tumor DNA Pancreatic cancer Biomarker Precision medicine Liquid biopsy