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Single-cell landscape analysis reveals distinct regression trajectories and novel prognostic biomarkers in primary neuroblastoma

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Genes & Diseases 2022年第6期9卷 1624-1638页

作者： Qingqing Liu Zhenni Wang Yan Jiang Fengling Shao Yue Ma Mingzhao Zhu Qing Luo Yang Bi Lijian Cao Liang Peng Jianwu Zhou Zhenzhen Zhao Xiaobin Deng Tong-Chuan He Shan Wang Department of Pediatric Surgical Oncology Children’s Hospital of Chongqing Medical UniversityNational Clinical Research Center for Child Health and DisordersMinistry of Education Key Laboratory of Child Development and DisordersChongqing Key Laboratory of PediatricsChongqing 400014PR China Singleron Biotechnologies Co. LtdNanjingJiangsu 211800PR China Key Laboratory of Infection and Immunity Institute of BiophysicsChinese Academy of SciencesBeijing 100101PR China Molecular and Oncology Laboratory Department of Orthopaedic Surgery and Rehabilitation MedicineThe University of Chicago Medical CenterChicagoIL 60637USA

Neuroblastoma(NB),which is the most common pediatric extracranial solid tumor,varies widely in its clinical presentation and *** has a unique ability to spontaneously differentiate and regress,suggesting a potential direction for therapeutic ***,the underlying mechanisms of regression remain largely unknown,and more reliable prognostic biomarkers are needed for predicting trajectories for *** performed scRNAseq analysis on 17 NB clinical samples and three peritumoral adrenal *** NB displayed varied cell constitution,even among tumors of the same pathological *** number variation patterns suggested that neuroendocrine cells represent the malignant cell *** on the differential expression of sets of related marker genes,a subgroup of neuroendocrine cells was identified and projected to differentiate into a subcluster of benign fibroblasts with highly expressed CCL2 and ZFP36,supporting a progressive pathway of spontaneous NB *** also identified prognostic markers(STMN2,TUBA1A,PAGE5,and ETV1)by evaluating intra-tumoral ***,we determined that ITGB1 in M2-like macrophages was associated with favorable prognosis and may serve as a potential diagnostic marker and therapeutic *** conclusion,our findings reveal novel mechanisms underlying regression and potential prognostic markers and therapeutic targets of NB.

关键词： Neuroblastoma(NB) prognostic biomarkers Regression trajectory Single-cell RNA sequencing(scRNAseq) Tumor microenvironment

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Role of mi RNAs and their potential to be useful as diagnostic and prognostic biomarkers in gastric cancer

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World Journal of Gastroenterology 2016年第35期22卷 7951-7962页

作者： Kelly Cristina da Silva Oliveira Taíssa Maíra Thomaz Araújo Camila Inagaki Albuquerque Gabriela Alcantara Barata Carolina Oliveira Gigek Mariana Ferreira Leal Fernanda Wisnieski Fernando Augusto Rodrigues Mello Junior André Salim Khayat Paulo Pimentel de Assumpcao Rommel Mário Rodriguez Burbano Marília Cardoso Smith Danielle Queiroz Calcagno Núcleo de Pesquisas em Oncologia Universidade Federal do Pará Hospital Universitário Joao de Barros Barreto Disciplina de Genética Departamento de Morfologia e Genética Universidade Federal de Sao Paulo Laboratório de Citogenética Humana Instituto de Ciências Biológicas Universidade Federal do Pará

Alterations in epigenetic control of gene expression play an important role in many diseases, including gastric cancer. Many studies have identified a large number of upregulated oncogenic mi RNAs and downregulated tumour-suppressor mi RNAs in this type of cancer. In this review, we provide an overview of the role of mi RNAs, pointing to their potential to be useful as diagnostic and/or prognostic biomarkers in gastric cancer. Moreover, we discuss the influence of polymorphisms and epigenetic modifications on mi RNA activity.

关键词： Gastric cancer Epigenetic Diagnostic biomarkers miRNAs prognostic biomarkers

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Poly-hydroxylated bile acids and their prognostic roles in Alagille syndrome

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World Journal of Pediatrics 2023年第7期19卷 652-662页

作者： Meng-Xuan Wang Jun Han Teng Liu Ren-Xue Wang Li-Ting Li Zhong-Die Li Jun-Cong Yang Lang-Li Liu Yi Lu Xin-Bao XieJing-Yu Gong Shi-Yu Lei Zhang Victor Ling J Jian-She Wang Department of Pediatrics Jinshan Hospital of Fudan UniversityShanghai 201508China The Center for Pediatric Liver Diseases Children's Hospital of Fudan UniversityShanghai 201102China University of Victoria-Genome BC Proteomics Centre and Division of Medical Sciences VictoriaBritish ColumbiaCanada BC Cancer Research Centre VancouverBritish ColumbiaCanadaDepartment of PediatricsJinshan Hospital of Fudan UniversityShanghai 201508China Institutes of Biomedical Sciences Fudan UniversityShanghai 201199China Shanghai Key Laboratory of Birth Defect Shanghai 201102China

Background The liver manifestations of Alagille syndrome(ALGS)are highly variable,and factors affecting its prognosis are poorly *** asked whether the composition of bile acids in ALGS patients with good clinical outcomes differs from that in patients with poor outcomes and whether bile acids could be used as prognostic *** Blood for bile acid profiling was collected from genetically confirmed JAG1-associated ALGS patients before one year of age.A good prognosis was defined as survival with native liver and total bilirubin(TB)607.69 nmol/L was associated with native liver survival[hazard ratio:13.03,95%confidence interval(CI):(2.662-63.753),P=0.002].Conclusions We identified two poly-hydroxylated bile acids as liver prognostic biomarkers of ALGS *** hydroxylation of bile acids may result in better clinical outcomes.

关键词： Alagille syndrome Bile acid profile Poly-hydroxylated bile acids prognostic biomarkers

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Exploitation of Gene Expression and Cancer biomarkers in Paving the Path to Era of Personalized Medicine

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Genomics, Proteomics & Bioinformatics 2017年第4期15卷 220-235页

作者： Hala Fawzy Mohamed Kamel Hiba Saeed A.Bagader Al-Amodi Biochemistry Department Faculty of Medicine Umm AL-Qura University Medical Biochemistry Department Faculty of Medicine Ain Shams University

Cancer therapy agents have been used extensively as cytotoxic drugs against tissue or organ of a specific type of cancer. With the better understanding of molecular mcchanislns undcrlying carcinogenesis and cellular events during cancer progression and metastasis, it is now possible to use targeted therapy for these molecular events. Targeted therapy is able to identify cancer patients with dissimilar genetic defects at cellular level for the same cancer type and consequently requires individualized approach for treatment. Cancer therapy begins to shill steadily from the tra- ditional approach of ＂one regimen for all patients＂ to a more individualized approach, through which each patient will be treated specifically according to their specific genetic defects. Personalized medicine accordingly requires identification of indicators or markers that guide in the decision mak- ing of such therapy to the chosen patients for more effective therapy. Cancer biomarkcrs are fre- quently used in clinical practice for diagnosis and prognosis, as well as identification ol responsive patients and prediction of treatment response of cancer patient. The rapid breakthrough and development of microarray and sequencing technologies is probably the main tool for paving the way toward ＂individualized biomarker-driven cancer therapy＂ or ＂personalized medicine＂. In this review, we aim to provide an updated knowledge and overview of the currcnt landscape of cancer biomarkers and their role in personalized medicine, emphasizing the impact of gcnomics Oil the implementation of new potential targeted therapies and development of novel cancer biomarkers in improving the outcome of cancer therapy.

关键词： Personalized medicine Gene expression Targeted therapy Predictive biomarkers prognostic biomarkers

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Blood microRNAs as potential diagnostic and prognostic markers in cerebral ischemic injury

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Neural Regeneration Research 2016年第9期11卷 1375-1378页

作者： Bridget Martinez Philip V.Peplow Department of Molecular and Cellular Biology University of California Department of Anatomy University of Otago

MicroRNAs are a family of small, genome-encoded endogenous RNAs that are transcribed but are not translated into proteins. They serve essential roles in virtually every aspect of brain function, including neurogenesis, neural development, and cellular responses leading to changes in synaptic plasticity. They are also implicated in neurodegeneration and neurological disorders, in responses to hypoxia and ischemia, and in ischemic tolerance induced by ischemic preconditioning. In recent developments, miRNA expres- sion profiling has been examined in stroke, and these studies indicate that miRNAs have emerged as key mediators in ischemic stroke biology. Both increased and decreased miRNA levels may be needed either as prevention or treatment of stroke. Novel approaches are being developed to get miRNA related therapeu- tics into the brain across an intact blood-brain barrier, including chemical modification, use of targeting molecules and methods to disrupt the blood-brain barrier.

关键词： blood microRNAs diagnostic biomarkers prognostic biomarkers cerebral ischemic injury ischemicstroke human patients rat and mouse models

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N^(6)-methyladenosine Steers RNA Metabolism and Regulation in Cancer

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Cancer Communications 2021年第7期41卷 538-559页

作者： Shenghua Dong Yutong Wu Yadi Liu Hengyou Weng Huilin Huang Sun Yat-sen University Cancer Center State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangzhouGuangdong 510060P.R.China Bioland Laboratory Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangzhou 510005P.R.China

As one of the most studied ribonucleic acid(RNA)modifications in eukaryotes,N^(6)-methyladenosine(m^(6)A)has been shown to play a predominant role in controlling gene expression and influence physiological and pathological processes such as oncogenesis and tumor *** and eraser proteins,acting opposite to deposit and remove m^(6)A epigenetic marks,respectively,shape the cellular m^(6)A landscape,while reader proteins preferentially recognize m^(6)A modifications and mediate fate decision of the methylated RNAs,including RNA synthesis,splicing,exportation,translation,and ***,RNA metabolism in cells is greatly influenced by these three classes of m^(6)A *** expression of m^(6)A regulators has been widely reported in various types of cancer,leading to cancer initiation,progression,and drug *** close links between m^(6)A and cancer shed light on the potential use of m^(6)A methylation and its regulators as prognostic biomarkers and drug targets for cancer *** the notable effects of m^(6)A in reversing chemoresistance and enhancing immune therapy,it is a promising target for combined ***,we summarize the recent discoveries on m^(6)A and its regulators,emphasizing their influences on RNA metabolism,their dysregulation and impacts in diverse malignancies,and discuss the clinical implications of m^(6)A modification in cancer.

关键词： cancer therapy chemoresistance immunotherapy m^(6)A methylation oncogenesis prognostic biomarkers RNA epigenetics RNA metabolism

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Benzo[a]pyrene stimulates miR-650 expression to promote the pathogenesis of fatty liver disease and hepatocellular carcinoma via SOCS3/JAK/STAT3 cascades

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Journal of Molecular Cell Biology 2021年第8期13卷 556-564页

作者： Yang Ge Pengfei Gu Wenbo Wang Liyuan Cao Lulu Zhang Jingquan Li Wei Mu Hui Wang State Key Laboratory of Oncogenes and Related Genes Center for Single-cell OmicsSchool of Public HealthShanghai Jiao Tong University School of MedicineShanghai 200025China Department of Oncology Shanghai Tenth People’s HospitalSchool of MedicineTongji UniversityShanghai 200072China Institute of Military Health Management Second Military Medical UniversityShanghai 200433China CAS Key Laboratory of Nutrition Metabolism and Food SafetyShanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghai 200031China

Modern diets,which often feature high levels of fat and charcoal-grilled meat,contribute to the pathogenesis of obesity and non-alcoholic fatty liver disease(NAFLD),resulting in liver cancer ***(a)pyrene(B[a]P)is a common environ-mental and foodborne pollutant found in smoke and fire-grilled foods,which can have an adverse effect on human *** carcinoma(HCC)is the fifth leading cause of cancer and the second leading cause of cancer-related deaths *** epidemiological studies suggest that both environmental risk factors and chronic liver injury including NAFL are important for HCC development,but the precise mechanisms linking eating habits to hepato-carcinogenesis remain *** the present study,we demonstrated that various miRNAs in B[a]P-exposed tumor cells contribute to tumor metastasis,among which miR-650 could be the most potent ***,we found that the suppressor of cytokine signaling 3(SOCS3)is directly regulated by miR-650 and its suppression regulates the activation of the Janus kinase/signal transducer and activator of transcription 3 (JAK/STAT3)*** findings reveal a possible adverse outcome pathway of SOCS3/JAK/STAT3 regulation in B[a]P-induced HCC *** results provide a better understanding of the adverse effects of chronic exposure to B[a]P on human health.

关键词： hepatocellular carcinoma microRNAs tumor metastasis S0CS3 prognostic biomarkers

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Advancing prognostic precision in gastric cancer with an immunoinflammatory index

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World Journal of Gastroenterology 2024年第44期30卷 4754-4758页

作者： Hong-Mei Zhang Guo-Hua Wang Shan-Wen Sun Lei Yuan College of Life Science Northeast Forestry UniversityHarbin 150040Heilongjiang ProvinceChina College of Computer and Control Engineering Northeast Forestry UniversityHarbin 150040Heilongjiang ProvinceChina Department of Hepatobiliary Surgery Quzhou People’s HospitalQuzhou 324000Zhejiang ProvinceChina

Gastric cancer remains a major global health challenge with high morbidity and mortality *** advancements in immunology and inflammation research have highlighted the crucial roles that these biological processes play in tumor progression and patient *** has sparked new interest in developing prognostic biomarkers that integrate these two key biological *** this letter,we discuss the recent study by Ba et al,which proposed a novel prognostic immunoinflammatory index for patients with gastric *** underscore the importance of this research,its potential impact on medical practice,and the prospective avenues for further investigation in this rapidly emerging area of study.

关键词： Gastric cancer Immunoinflammatory index prognostic biomarkers Inflammation Immunology

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Gastrointestinal microbiota:A predictor of COVID-19 severity?

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World Journal of Gastroenterology 2022年第45期28卷 6328-6344页

作者： Maria Adriana Neag Damiana-Maria Vulturar Diana Gherman Codrin-Constantin Burlacu Doina Adina Todea Anca Dana Buzoianu Department of Pharmacology Toxicology and Clinical PharmacologyIuliu Hațieganu University of Medicine and PharmacyCluj-Napoca 400337Romania Department of Pneumology Iuliu Hatieganu University of Medicine and PharmacyCluj-Napoca 400332Romania Department of Radiology Iuliu Hațieganu University of Medicine and PharmacyCluj-Napoca 400347Romania Iuliu Haţieganu University of Medicine and Pharmacy Cluj-Napoca 400347Romania

Coronavirus disease 2019(COVID-19),caused by a severe acute respiratory syndrome coronavirus 2 infection,has raised serious concerns worldwide over the past 3 *** severity and clinical course of COVID-19 depends on many factors(e.g.,associated comorbidities,age,etc)and may have various clinical and imaging findings,which raises management *** microbiota composition is known to influence respiratory disease,and respiratory viral infection can also influence gut *** and lung microbiota and their relationship(gut-lung axis)can act as modulators of *** the intestinal microbiota,by improving its composition and diversity through nutraceutical agents,can have a positive impact in the prophylaxis/treatment of COVID-19.

关键词： Gut microbiota COVID-19 prognostic biomarkers Gut-lung axis Probiotics Nutraceuticals

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FDX1 as a novel biomarker and treatment target for stomach adenocarcinoma

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World Journal of Gastrointestinal Surgery 2024年第6期16卷 1803-1824页

作者： Xian-Ze Xie Lei Zuo Wei Huang Qiao-Mei Fan Ya-Yun Weng Wen-Dong Yao Jia-Li Jiang Jia-Qi Jin Department of Pharmacy The First Affiliated Hospital of Zhejiang Chinese Medical University(Zhejiang Provincial Hospital of Chinese Medicine)Hangzhou 310018Zhejiang ProvinceChina Anhui Province Huainan City Shou County Agricultural Machinery Affairs Management Center Huainan 232200Anhui ProvinceChina

BACKGROUND Stomach adenocarcinoma(STAD)is one of the main reasons for cancer-related deaths *** investigation aimed to define the connection between STAD and Cuproptosis-related genes(CRGs).Cuproptosis is a newly identified form of mitochondrial cell death triggered by *** To explore the identification of potential biomarkers for STAD disease based on *** A predictive model using Gene Ontology(GO),Least Absolute Shrinkage and Selection Operator(LASSO),Kyoto Encyclopedia of Genes and Genomes(KEGG),Gene Set Variation Analysis(GSVA),and Gene Set Enrichment Analysis analyzed gene interconnections,focusing on 3 copper-related genes and their expression in The Cancer Genome *** for mRNA-miRNA and mRNA-transcription factor interactions were *** prognostic significance of CRG scores was evaluated using time-receiver operating characteristic,Kaplan-Meier curves,and COX regression *** was conducted with datasets GSE26942,GSE54129,and *** of copper-related differ-entially expressed genes was also analyzed in various human tissues and gastric cancer subpopulations using the human protein *** Three significant genes(FDX1,LIAS,MTF1)were identified and selected via LASSO analysis to predict and classify individuals with STAD into high and low CRG score *** genes were down-regulated in both risk *** and KEGG analyses highlighted their involvement mainly in the electron transport *** validating their differential expression,FDX1 emerged as the most accurate diagnostic marker for gastric ***,the RCircos package localized FDX1 on chromosome *** Our study revealed that FDX1 could be a potential biomarker and treatment target for gastric malignancy,providing new ideas for further scientific research.

关键词： Stomach adenocarcinoma disease Copper death FDX1 prognostic biomarkers Cuproptosis-related genes

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