| Accession |
GSE110345
|
| Status |
2021/2/6 |
| Title |
Relative abundance of the integrant-derived viral RNAs in infected tissues harvested from chronic HBV carriers |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing |
| Summary |
Five matching sets of non-malignant liver tissues and HCCs from individuals chronically infected with hepatitis B virus (HBV) were examined. The HBV genomic sequences were determined using overlapping PCR amplicons covering the entire viral genome. Four pairs of tissues were infected with HBV of genotype C, while one pair - with genotype B. HBV replication markers were found in all tissues. In majority of HCC samples, the levels of pre-genomic/pre-core RNA (pgRNA) and covalently closed circular DNA (cccDNA) were lower than those of liver tissue counterparts. Regardless of the presence of HBV replication markers, (i) integrant-derived HBV RNAs (id-RNAs) were found using RT-PCR analysis in all tissues, and were considerably abundant or predominant in 6/10 tissue samples (2 livers and 4 HCCs); (ii) the RNAs that were polyadenylated using cryptic HBV polyadenylation signal and therefore could be produced by HBV replication or derived from integrated HBV DNA were found in 5/10 samples (3 livers and 2 HCCs), and were considerably abundant species in 3/10 tissues (2 livers and 1 HCC); and (iii) cccDNA-transcribed RNAs polyadenylated near position 1931 were not abundant in 7/10 tissues (2 livers and 5 HCCs), and were predominant only in two livers. Subsequent RNA sequencing analysis of selected liver/HCC samples also showed relative abundance of id-RNAs in most of examined tissues. Our findings suggesting that id-RNAs could represent a significant source of HBV envelope proteins, which is independent of viral replication, are discussed in the context of possible contribution of id-RNAs to the HBV life cycle. |
| Samples |
| GSM ID |
Sample info |
Characteristics |
Description |
|
GSM2987924
|
Liver3 |
tissue sample:# 3; tissue:liver (non-malignant); chronic infection:HBV |
Raw_Counts.txt |
|
GSM2987925
|
HCC4 |
tissue sample:# 4; tissue:liver (HCC); chronic infection:HBV |
Raw_Counts.txt |
|
GSM2987926
|
Liver7 |
tissue sample:# 7; tissue:liver (non-malignant); chronic infection:HBV |
Raw_Counts.txt |
|
GSM2987927
|
HCC8 |
tissue sample:# 8; tissue:liver (HCC); chronic infection:HBV |
Raw_Counts.txt |
|
| Platform |
GPL16791 : Illumina HiSeq 2500 (Homo sapiens) |
| Literature |
|
| Download |
Download xCell Data Download Expression Analysis Data
|
|
xCell Plot
|
|
* p<0.05 ** p<0.01
|
Virus Dataset Detail
