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Unraveling brain aging through the lens of oral microbiota

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

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Genome-Wide Analysis of Epigenetic Modifications

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Journal of Computer Science & Technology 2010年第1期25卷 35-41页

作者：梁守丹 Department of Bioinformatics and computational biology The University of Texas M.D. Anderson Cancer Center Houston

In plants and animals, gene expression can be altered by changes that do not alter the sequence of nucleotides in DNA but rather modify the chemical structure of either the DNA or the histones that interact with the DNA. These so-called epigenetic modifications are not transient, but persist through cell divisions. Rapidly advancing technologies, such as next-generation DNA sequencing, have dramatically increased our ability to survey epigenetic markers throughout an entire genome. These techniques are revealing in great detail that the many forms and stages of cancer are characterized by a massive number of epigenetic changes. Interpreting such epigenetic marks in cell differentiation and in carcinogenesis is computationally challenging. We review several examples of epigenetic data analysis and discuss the need for computational methods that will enable us to learn from the data the relationships between different kinds of histone modifications and DNA methylation.

关键词： epigenetics non-coding DNA DNA methylations histone modifications

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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

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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

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Applications of probability and statistics in cancer genomics

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Quantitative biology 2020年第2期8卷 95-108页

作者： Xiaotu Ma Sasi Arunachalam Yanling Liu Department of computational biology and Cancer Biology ProgramComprehensive Cancer CenterSt Jude Children's Research HospitalMemphisTN 38105USA

Background:The past decade has witnessed a rapid progress in our understanding of the genetics of cancer and its *** and statistical modeling played a pivotal role in the discovery of general patterns from cancer genomics datasets and continue to be of central importance for personalized ***:In this review we introduce cancer genomics from a probabilistic and statistical *** start from(1)functional classification of genes into oncogenes and tumor suppressor genes,then(2)demonstrate the importance of comprehensive analysis of different mutation types for individual cancer genomes,followed by(3)tumor purity analysis,which in turn leads to(4)the concept of ploidy and clonality,that is next connected to(5)tumor evolution under treatment pressure,which yields insights into cancer drug *** also discuss future challenges including the non-coding genomic regions,integrative analysis of genomics and epigenomics,as well as early cancer ***:We believe probabilistic and statistical modeling will continue to play important roles for novel discoveries in the field o f cancer genomics and personalized medicine.

关键词： cancer genomics sequence analysis probability and statistics

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Convergent Usage of Amino Acids in Human cancers as A Reversed Process of Tissue Development

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genomics, Proteomics & Bioinformatics 2022年第1期20卷 147-162页

作者： Yikai Luo Han Liang Graduate Program in Quantitative and computational Biosciences Baylor College of MedicineHoustonTX 77030USA Department of Bioinformatics and computational biology The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA Department of Systems biology The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA

Genome-and transcriptome-wide amino acid usage preference across different species is a well-studied phenomenon in molecular evolution,but its characteristics and implication in cancer evolution and therapy remain largely ***,we analyzed large-scale transcriptome/proteome profiles,such as The cancer Genome Atlas(TCGA),the Genotype-Tissue Expression(GTEx),and the Clinical Proteomic Tumor Analysis Consortium(CPTAC),and found that compared to normal tissues,different cancer types showed a convergent pattern toward using biosynthetically low-cost amino *** a pattern can be accurately captured by a single index based on the average biosynthetic energy cost of amino acids,termed energy cost per amino acid(ECPA).With this index,we further compared the trends of amino acid usage and the contributing genes in cancer and tissue development,and revealed their reversed ***,focusing on the liver,a tissue with a dramatic increase in ECPA during development,we found that ECPA represents a powerful biomarker that could distinguish liver tumors from normal liver samples consistently across 11 independent patient cohorts and outperforms any index based on single *** study reveals an important principle underlying cancer evolution and suggests the global amino acid usage as a system-level biomarker for cancer diagnosis.

关键词： Amino acid usage Tissue development Biosynthetic energy Diagnostic biomarker

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Single-cell technologies: current and near future

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Science China Life Sciences 2025年第01期 1-4页

作者： Chenfei Wang Qi Liu Xiaohui Fan Tieliu Shi Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration Ministry of EducationOrthopedics DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University center for Bioinformatics and computational biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Key Laboratory of Advanced Theory and Application in Statistics and Data Science (MOE) School of StatisticsEast China Normal University

Single-cell technologies enable the indepth exploration of multiple biological hierarchies at the scale of individual cells,which have deepened our knowledge of cellular diversity, tissue organization, and overall organism function(Sun et al.,2024). In 2009, single-cell RNA sequencing(sc RNA-seq) was first developed as a powerful tool to dissect gene expression and uncover transcriptional *** the rapid advancement of technology, single-cell approaches have expanded to encompass other omics, such as genomics, epigenomics, proteomics,and metabolomics.

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De novo transcriptome assembly of RNA-Seq reads with different strategies

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Science China(Life Sciences) 2011年第12期54卷 1129-1133页

作者： CHEN Geng YIN KangPing WANG Charles SHI TieLiu center for Bioinformatics and computational biology Institute of Biomedical Sciences School of Life Science East China Normal University Shanghai 200241 China Functional genomics Core Beckman Research Institute City of Hope Comprehensive Cancer Center Duarte CA 91010 USA

De novo transcriptome assembly is an important approach in RNA-Seq data analysis and it can help us to reconstruct the transcriptome and investigate gene expression profiles without reference genome *** carried out transcriptome assemblies with two RNA-Seq datasets generated from human brain and cell line,*** then determined an efficient way to yield an optimal overall assembly using three different *** first assembled brain and cell line transcriptome using a single k-mer *** we tested a range of values of k-mer length and coverage cutoff in ***,we combined the assembled contigs from a range of k values to generate a final *** comparing these assembly results,we found that using only one k-mer value for assembly is not enough to generate good assembly results,but combining the contigs from different k-mer values could yield longer contigs and greatly improve the overall assembly.

关键词： RNA-Seq de novo transcriptome assembly next generation sequencing

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eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses

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National Science Review 2019年第5期6卷 867-869页

作者： Dalang Yu Lili Dong Fangqi Yan Hailong Mu Bixia Tang Xiao Yang Tao Zeng Qing Zhou Feng Gao Zhonghuang Wang Ziqian Hao Hongen Kang Yi Zheng Hongwei Huang Yuzhang Wei Wei Pan Yaochen Xu Junwei Zhu Shilei Zhao Ciran Wang Pengyu Wang Long Dai Mushan Li Li Lan Yiwei Wang Hua Chen Yi-Xue Li Yun-Xin Fu Zhen Shao Yiming Bao Fangqing Zhao Luo-Nan Chen Guo-Qing Zhang Wenming Zhao Haipeng Li CAS Key Laboratory of computational biology CAS-MPG Partner Institute for Computational Biology Shanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of Sciences Chinese Academy of Sciences University of Chinese Academy of Sciences BIG Data center Beijing Institute of GenomicsChinese Academy of Sciences Shanghai center for Bioinformation Technology Key Laboratory of Systems biology Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai Institute of Biochemistry and Cell biology Chinese Academy of Sciences CAS Laboratory of Genomic and Precision Medicine Beijing Institute of Genomics Chinese Academy of Sciences center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Department of Biostatistics and Data Science School of Public Health University of Texas Health Science Center at Houston computational genomics Lab Beijing Institutes of Life Science Chinese Academy of Sciences Shanghai Research center for Brain Science and Brain-Inspired Intelligence

It has become increasingly challenging for researchers to analyze the exponentially expanding amount of multi-omic ***, we describe multi-functional software named evolutionary GenotypePhenotype Systems (eGPS) that en... 详细信息

关键词： GPS eGPS 1.0 comprehensive software for multi-omic and evolutionary analyses

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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

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