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Viral integration detection strategies and a technical update on Virus-Clip

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BIOCELL 2021年第6期45卷 1495-1500页

作者： DANIEL WAI-HUng HO XUEYIng LYU irene oi-lin ng Department of Pathology The University of Hong KongHong KongChina State Key Laboratory of Liver Research The University of Hong KongHong KongChina

Oncovirus infection is crucial in human *** oncoviruses can lead to structural variations in the human genome known as viral genomic integration,which can contribute to *** viral integration detection tools differ in their underlying algorithms pinpointing different aspects or features of viral integration *** discuss about major procedures in performing viral integration *** importantly,we provide a technical update on Virus-Clip to facilitate its usage on the latest human genome builds(hg19 and hg38)and the adoption of multi-thread mode for faster initial read *** comparing the execution of Virus-Clip using single-thread and multi-thread modes of read alignment on targeted-panel sequencing data of HBV-associated hepatocellular carcinoma patients,we demonstrate the marked improvement of multi-thread mode in terms of significantly reduced execution time,while there is negligible difference in memory *** together,with the current update of Virus-Clip,it will continue supporting the in silico detection of oncoviral integration for better understanding of various human malignancies.

关键词： Oncovirus Viral genomic integration In silico detection Tumorigenesis Human malignancies

The impact of hypoxia in hepatocellular carcinoma metastasis

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Frontiers of Medicine 2014年第1期8卷 33-41页

作者： Carmen Chak-Lui Wong Alan Ka-Lun Kai irene oi-lin ng The State Key Laboratory for Liver Research and Department of Pathology The Universi(v of Hong Kong Hong Kong China

Hypoxia is a common phenomenon in hepatocellular carcinoma （HCC）. Hypoxia stabilizes transcription factor, hypoxia-inducible factor （HIF）, to activate gene transcription. Expression of HIF is closely associated with metastasis and poor prognosis in HCC. HIF mediates expression of genes that are involved in every step of HCC metastasis including epithelial-mesenchymal transition, invasion of the extracellular matrix, intravasation, extravasation, and secondary growth of the metastases. Because HIF is the central regulator of HCC metastasis, HIF inhibitors are attractive tools when used alone or as combined treatment to curb HCC metastasis. This review will summarize the current findings on the impact of hypoxia/HIF in HCC, with a particular focus on cancer metastasis.

关键词： hypoxia hepatocellular carcinoma (HCC) metastasis hypoxia-inducible factor (HIF)

TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways in hepatocellular carcinoma

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Frontiers of Medicine 2015年第3期9卷 322-330页

作者： Daniel Wai-Hung Ho Alan Ka-Lun Kai irene oi-lin ng Department of Pathology and State Key Laboratory for Liver Research The University of Hong Kong ttong Kong SAR China

This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular carcinoma （HCC） by comparing the global gene expression profiles between tumors and their corresponding non- tumorous liver tissue. Based on the differential gene expression analysis, we identified a number of novel dysregulated genes, in addition to those previously reported. Top-listing upregulated （CENPF and FOXM1） and downregulated （CLEC4G, CRHBP, and CLEC1B） genes were successfully validated using qPCR on our cohort of 65 pairs of human HCCs. Further examination for the mechanistic overview by subjecting significantly upregulated and downregulated genes to gene set enrichment analysis showed that different cellular pathways were involved. This study provides useful information on the transcriptomic landscape and molecular mechanism of hepatocarcinogenesis for development of new biomarkers and further in-depth characterization.

关键词： TCGA whole-transcriptome sequencing HCC liver cancer

Single cell analysis informing therapy response in hepatocellular carcinoma and intrahepatic cholangiocarcinoma

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Hepatobiliary Surgery and Nutrition 2022年第1期11卷 126-128页

作者： Daniel Wai-Hung Ho irene oi-lin ng Department of Pathology The University of Hong KongHong KongChina State Key Laboratory of Liver Research The University of Hong KongHong KongChina

Liver cancer is known to have significant degree of intra-tumoral heterogeneity(ITH)(1).Hepatocellular carcinoma(HCC)and intrahepatic cholangiocarcinoma(ICC)are major forms of primary liver cancer,accounting for>95%of *** is linked,as least in part,to the aggressiveness and refractoriness of liver cancer,rendering its high lethality among human malignancies(2).The complex tumor microenvironment promotes tumor progression and contributes to poor treatment ***,it is vital to address the biological mechanisms underlying liver cancer progression and treatment response analyzing the cells in high resolution rather than the mixture of many cell *** advances in single-cell RNA sequencing(scRNA-seq)provide an avenue to dissect liver cancer in an unprecedented degree of high resolution to characterize the underlying pathogenesis and heterogeneity.

关键词： cancer intrahepatic Liver

MicroRNA-142-3p and microRNA-142-5p are downregulated in hepatocellular carcinoma and exhibit synergistic effects on cell motility

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Frontiers of Medicine 2015年第3期9卷 331-343页

作者： Felice Ho-Ching Tsang Sandy Leung-Kuen Au Lai Wei Dorothy ngo-Yin Fan Joyce Man-Fong Lee Carmen Chak-Lui Wong irene oi-lin ng Chun-Ming Wong State Key Laboratory for Liver Research and Department of Pathology Li Ka Shing Faculty of Medicine The University of Hong Kong HongKong SAR China

MicroRNAs （miRNAs）, an important class of small non-coding RNAs, regulate gene expression at the post-transcriptional level, miRNAs are involved in a wide range of biological processes and implicated in different diseases, including cancers. In this study, miRNA profiling and qRT-PCR validation revealed that miR-142-3p and miR-142-5p were significantly downregulated in hepatocellular carcinoma （HCC） and their expression levels decreased as the disease progressed. The ectopic expression of miR-142 significantly reduced HCC cell migration and invasion. Overexpression of either miR-142-3p or miR-142-5p suppressed HCC cell migration, and overexpression of both synergistically inhibited cell migration, which indicated that miR-142-3p and miR-142-5p may cooperatively regulate cell movement, miR-142-3p and miR-142-5p, which are mature miRNAs derived from the 3＇- and 5＇-strands of the precursor miR-142, target distinct pools of genes because of their different seed sequences. Pathway enrichment analysis showed a strong association of the putative gene targets of miR-142-3p and miR-142-5p with several cell motility-associated pathways, including those regulating actin cytoskeleton, adherens junctions, and focal adhesion. Importantly, a number of the putative gene targets were also significantly upregulated in human HCC cells. Moreover, overexpression of miR-142 significantly abrogated stress fiber formation in HCC cells and led to cell shrinkage. This study shows that mature miR-142 pairs collaboratively regulate different components of distinct signaling cascades and therefore affects the motility of HCC cells.

关键词： hepatocellular carcinoma microRNA metastasis cytoskeletal reorganization

Reassessing the AMPK-MTORC1 balance in autophagy in the central nervous system

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Neural Regeneration Research 2025年第11期20卷 3209-3210页

作者： Marta García-Juan Mario Villa irene Benito-Cuesta Lara Ordónez-Gutiérrez Francisco Wandosell Centro de Biología Molecular“Severo Ochoa”(CSIC-UAM) Nicolas Cabrera 1Universidad Autónoma de MadridMadridSpain Fisiología Animal Departamento de BiologíaFacultad de CienciasUniversidad Autónoma de MadridMadridSpain Department of Clinical Neuroscience CMM Karolinska Universitetssjukhuset SolnaStockholmSweden Departamento de Bioquímica y Biología Molecular Universidad Complutense de MadridMadridSpain Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas(CIBERNED) MadridSpain

Autophagy is a cellular degradation and recycling system,indispensable for cellular and organ development,homeostasis,and *** cellular process is evolutionarily highly conserved to quality control of many proteins and dysfunctional organelles,which finally recycle components as amino *** process is effective during normal physiology as part of anabolism and plays an additional important role during starvation(Dikic and Elazar,2018).Different types of autophagy have been chara cterized based on their dynamic,mechanism of action,target substrates,and protein *** of them are macroautophagy(hereafter called"autophagy"),microa utophagy,and chape rone-media ted autophagy(Fleming et al.,2022).

关键词： homeostasis system hereafter

Annealing cracking in Zr and a Zr-alloy with low hydrogen concentration

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Journal of Materials Science & Technology 2024年第15期182卷 165-175页

作者： Xi-Heng lin irene J.Beyerlein Wei-Zhong Han Center for Advancing Materials Performance from the Nanoscale State Key Laboratory for Mechanical Behavior of MaterialsXi’an Jiaotong UniversityXi’an 710049China Materials Department University of CaliforniaSanta BarbaraCA 93106-5070USA Department of Mechanical Engineering University of CaliforniaSanta BarbaraCA 93106-5070USA

Hydrogen embrittlement,also known as hydrogen-induced cracking,is a longstanding concern for zirco-nium(Zr)and its *** affinity for hydrogen in zirconium results in the formation of brittle *** are conventionally thought to facilitate crack propagation,and the prevailing recommendation to hinder hydride embrittlement involves reducing the hydrogen concentration in the material and ap-plying slow cooling to reduce thermal ***,in Zr with a maximum hydrogen concentration of 43 wppm,we show that cracks initiate unexpectedly after annealing,a step that involves slow cooling and no external *** a suite of high-resolution microscopy,we show that annealing cracks initiate at prismaticδ-hydrides,whose presence is *** microscopic annealing crack paths are conse-quently crystallographic,following the habit plane of these prismaticδ-*** commonly reportedγ-hydride andδ-hydrides that develop on the basal plane are found not to initiate *** rationalize that prismaticδhydrides result from the intergranular thermal residual stresses that develop during slow *** finding of uncommon annealing cracking further advances the mechanistic understanding of hydride embrittlement in zirconium and can lead to new strategies for design and fabrication of advanced zirconium alloys for harsh environments.

关键词： Zirconium Hydride Cracking Habit plane Reorientation

Helicobacter pylori associated gastric intestinal metaplasia:Treatment and surveillance

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World Journal of Gastroenterology 2016年第3期22卷 1311-1320页

作者： Kevin Sze-Hang Liu irene oi-ling Wong Wai K Leung Department of Medicine Li Ka Shing Faculty of MedicineUniversity of Hong KongHong KongChina School of Public Health Li Ka Shing Faculty of MedicineUniversity of Hong KongHong KongChina

Gastric cancer(GC) is one of the leading causes of cancer related death in the world, particularly in East Asia. According to the Correa's cancer cascade, noncardia GC is usually developed through a series of mucosal changes from non-atrophic gastritis to atrophic gastritis(AG), intestinal metaplasia(IM), dysplasia and adenocarcinoma. Atrophic gastritis and IM are therefore generally considered to be pre-neoplastic gastric lesions. Helicobacter pylori(H. pylori) infection is an important initiating and promoting step of this gastric carcinogenesis cascade. Emerging long-term data showed that eradication of H. pylori reduced the risk of subsequent cancer development. It however remains confusing whether eradication of the bacterium in individuals with pre-neoplastic gastric lesions could regress these changes as well as in preventing cancer. Whilst H. pylori eradication could likely regress AG, the presence of IM may be a point of no return in this cascade. Hence, surveillance by endoscopy may be indicated in those with extensive IM or those with incomplete IM, particularly in populations with high GC risk. The optimal interval and the best tool of surveillance endoscopy remains to be determined in future studies.

关键词： Helicobacter pylori Gastric cancer Intestinalmetaplasia Treatment Surveillance

Papillary thyroid cancer and inflammatory bowel disease:Is there a relationship?

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World Journal of Gastroenterology 2013年第7期19卷 1079-1084页

作者： irene S Sonu Wojciech Blonski Ming Valerie lin James Lewis Faten Aberra Gary R Lichtenstein Division of Internal Medicine Stanford University Hospital and ClinicsStanfordCA 94305United States Division of Internal Medicine UHS Wilson Medical CenterJohnson CityNY 13790United States Division of Digestive Diseases University of CincinnatiCincinnatiOH 45229United States Division of Gastroenterology Hospital of the University of PennsylvaniaUniversity of Pennsylvania School of MedicinePhiladelphiaPA 19103United States

AIM:To formally study age of diagnosis of papillary thyroid cancer(PTC) in inflammatory bowel disease(IBD) patients and evaluate the prevalence of PTC in IBD patients compared to a control *** that patients with IBD are more likely to be diagnosed with PTC than a control population.A retrospective cohort analysis was performed using the University of Pennsylvania Health System's electronic *** from 1998-2009 were included in the search,and patients in the cohort were selected based on ICD-9 *** criteria included the diagnosis of Crohn's disease(CD) or ulcerative colitis(UC) and the concurrent diagnosis of thyroid cancer in comparison to a control *** these methods 912 patients with CD and 1774 with UC were compared to 1638 diverticulitis and 19 447 asthma *** were performed using corrected chisquare *** primary outcome for this study was the diagnosis of *** to conduct this study was obtained by the Institutional Review Board at the University of ***:The mean age was 47.5 years(range:18-102 years) and 66% patients were *** analysis of variance model was used to compare the age of PTC diagnosis between the CD,UC,asthma and diverticulitis groups,and a statistically significant difference in age at PTC diagnosis was noted across all groups(F = 6.35,df = 3,P = 0.0006).The age of PTC diagnosis in CD patients was statistically significantly lower than UC,asthma,and diverticulitis patients(average PTC diagnosis age for CD 25,UC 49,asthma 45,diverticulitis 63).After covarying for sex and age in 2009,the difference in age at PTC diagnosis remained statistically significant(F = 4.13,df = 3,P = 0.0089).A total of 86 patients were diagnosed with *** patients(0.5%) with UC were diagnosed with *** with UC were not shown to be more likely to develop PTC [odds ratio(OR):1.544,95%CI 0.767-3.108] compared to asthma *** patients(0.4%) with CD were

关键词： Papillary thyroid cancer Inflammatory bowel disease Crohn disease Ulcerative colitis