Human papillomavirus(HPV) genital infection is a very common sexual transmitted disease.Mostly,the infection is transient and asymptomatic.The induction of effective immune responses usually allows the infection to be...Human papillomavirus(HPV) genital infection is a very common sexual transmitted disease.Mostly,the infection is transient and asymptomatic.The induction of effective immune responses usually allows the infection to be spontaneously cured.However,the infection sometimes can be responsible for an intraepithelial lesion,which may progress to be cervical cancer.Cervical cancer is one of the most common neoplastic diseases affecting women.It is clear that carcinogenic HPV infection is the necessary process for the development of cervical cancer.HPV infection is very frequent in young women aged less than 25 years and viral clearance lasts for 8 months in average.This clearance is the consequence of host immunity intervention,which leads to spontaneous regression of infection and the overwhelming majority of low-grade squamous intraepithelial lesions(more than 80% within a period of 2 years).The major factor,which permits the progression to high grade squamous intraepithelial lesions and invasive cervical cancer,is the persistent feature of HPV infection.HPV infection is usually transient,but several factors were identified as host factors(genetic,immunodepression,oral contraception and smoking) and viral factors(genotype,variants,viral load and integration) to increase the persistence.Cervical cancer is clearly the first virus-induced solid tumor discovered in human.Furthermore,it represents a woman death cause that can be avoided.展开更多
INTRODUCTIONHepatitis B virus (HBV) belongs to the group ofhepatovirus, a major pathogen of human acute andchronic hepatitis B[1 4], which has a very closeassociation with human hepatocellular carcinoma(HCC)[5-8], For...INTRODUCTIONHepatitis B virus (HBV) belongs to the group ofhepatovirus, a major pathogen of human acute andchronic hepatitis B[1 4], which has a very closeassociation with human hepatocellular carcinoma(HCC)[5-8], For example, a statistical data from ahospital in Shanghai showed that 80% of HCCpatients were positive for HBsAg ( personalcommunication).展开更多
Hepatitis B virus(HBV) is still a worldwide health concern. While divergent factors are involved in its pathogenesis, it is now clear that HBV RNAs, principally templates for viral proteins and viral DNAs, have divers...Hepatitis B virus(HBV) is still a worldwide health concern. While divergent factors are involved in its pathogenesis, it is now clear that HBV RNAs, principally templates for viral proteins and viral DNAs, have diverse biological functions involved in HBV pathogenesis. These functions include viral replication, hepatic fibrosis and hepatocarcinogenesis. Depending on the sequence similarities, HBV RNAs may act as sponges for host mi RNAs and may deregulate mi RNA functions, possibly leading to pathological consequences. Some parts of the HBV RNA molecule may function as viralderived mi RNA, which regulates viral replication. HBV DNA can integrate into the host genomic DNA and produce novel viral-host fusion RNA, which may have pathological functions. To date, elimination of HBVderived covalently closed circular DNA has not been achieved. However, RNA transcription silencing may be an alternative practical approach to treat HBVinduced pathogenesis. A full understanding of HBV RNA transcription and the biological functions of HBV RNA may open a new avenue for the development of novel HBV therapeutics.展开更多
Oncovirus infection is crucial in human malignancies.Certain oncoviruses can lead to structural variations in the human genome known as viral genomic integration,which can contribute to tumorigenesis.Existing viral in...Oncovirus infection is crucial in human malignancies.Certain oncoviruses can lead to structural variations in the human genome known as viral genomic integration,which can contribute to tumorigenesis.Existing viral integration detection tools differ in their underlying algorithms pinpointing different aspects or features of viral integration phenomenon.We discuss about major procedures in performing viral integration detection.More 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 alignment.By 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 usage.Taken 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.展开更多
文摘Human papillomavirus(HPV) genital infection is a very common sexual transmitted disease.Mostly,the infection is transient and asymptomatic.The induction of effective immune responses usually allows the infection to be spontaneously cured.However,the infection sometimes can be responsible for an intraepithelial lesion,which may progress to be cervical cancer.Cervical cancer is one of the most common neoplastic diseases affecting women.It is clear that carcinogenic HPV infection is the necessary process for the development of cervical cancer.HPV infection is very frequent in young women aged less than 25 years and viral clearance lasts for 8 months in average.This clearance is the consequence of host immunity intervention,which leads to spontaneous regression of infection and the overwhelming majority of low-grade squamous intraepithelial lesions(more than 80% within a period of 2 years).The major factor,which permits the progression to high grade squamous intraepithelial lesions and invasive cervical cancer,is the persistent feature of HPV infection.HPV infection is usually transient,but several factors were identified as host factors(genetic,immunodepression,oral contraception and smoking) and viral factors(genotype,variants,viral load and integration) to increase the persistence.Cervical cancer is clearly the first virus-induced solid tumor discovered in human.Furthermore,it represents a woman death cause that can be avoided.
基金This work was supported by Projects of Tackling Key Problems in ScienceTechnology from the State Science+2 种基金Technology Ministry (TJ99-LA01) Shanghai ScienceTechnology Commission (994919033 )
文摘INTRODUCTIONHepatitis B virus (HBV) belongs to the group ofhepatovirus, a major pathogen of human acute andchronic hepatitis B[1 4], which has a very closeassociation with human hepatocellular carcinoma(HCC)[5-8], For example, a statistical data from ahospital in Shanghai showed that 80% of HCCpatients were positive for HBsAg ( personalcommunication).
基金Supported by the Research Program on Hepatitis from Japan Agency for Medical Research and Development,AMED to Otsuka M,No.JP18fk0210214the Project for Cancer Research and Therapeutic Evolution(P-CREATE)from AMED to Otsuka M,No.JP19cm0106602
文摘Hepatitis B virus(HBV) is still a worldwide health concern. While divergent factors are involved in its pathogenesis, it is now clear that HBV RNAs, principally templates for viral proteins and viral DNAs, have diverse biological functions involved in HBV pathogenesis. These functions include viral replication, hepatic fibrosis and hepatocarcinogenesis. Depending on the sequence similarities, HBV RNAs may act as sponges for host mi RNAs and may deregulate mi RNA functions, possibly leading to pathological consequences. Some parts of the HBV RNA molecule may function as viralderived mi RNA, which regulates viral replication. HBV DNA can integrate into the host genomic DNA and produce novel viral-host fusion RNA, which may have pathological functions. To date, elimination of HBVderived covalently closed circular DNA has not been achieved. However, RNA transcription silencing may be an alternative practical approach to treat HBVinduced pathogenesis. A full understanding of HBV RNA transcription and the biological functions of HBV RNA may open a new avenue for the development of novel HBV therapeutics.
基金the National Natural Science Foundation of China(81872222)Hong Kong Research Grants Council Theme-based Research Scheme(T12-704/16-R)。
文摘Oncovirus infection is crucial in human malignancies.Certain oncoviruses can lead to structural variations in the human genome known as viral genomic integration,which can contribute to tumorigenesis.Existing viral integration detection tools differ in their underlying algorithms pinpointing different aspects or features of viral integration phenomenon.We discuss about major procedures in performing viral integration detection.More 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 alignment.By 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 usage.Taken 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.
