Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1087553 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR28349073.fastq.gz | Fastqsanger.gz | |||
| SRR28349074.fastq.gz | Fastqsanger.gz | |||
| SRR28349075_1.fastq.gz | Fastqsanger.gz | |||
| SRR28349076_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 7 |
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Project description:BCR repertoire sequencing in humans following Hepatitis B booster vaccination
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Project description:BCR repertoire sequencing in humans following Hepatitis B primary vaccination
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Project description:Seasonal influenza contributes to a substantial disease burden annually, resulting in approximately 10 million hospital visits and 50 thousand deaths in a typical year in the US. 90% of the annual mortality from influenza occurs in people over the age of 65. While influenza vaccination is the best protection against the virus, it is less effective for the elderly. This may be due to differences in the quantity or type of B cells induced by vaccination in older individuals. To investigate this possibility, we leveraged recent development in single-cell technology that allows for simultaneous measurement of both gene expression profile and the B cell receptor (BCR) at single-cell resolution. Pre- and post-vaccination peripheral blood B cells were sorted from three young and three older adults who responded to the inactivated influenza vaccine and were profiled using single-cell RNAseq with paired BCR sequencing. At pre-vaccination, we observed a higher somatic hypermutation frequency and a higher abundance of activated B cells in older adults than in young adults. Following vaccination, young adults mounted a more clonal response than older adults. The response involved a mix of plasmablasts, activated B cells, and resting memory B cells in both age groups. The response in young adults was dominated by expansion in plasmablasts, while the response in older adults also involved activated B cells. We observed a consistent change in gene expression in plasmablasts after vaccination between age groups but not in the activated B cells. These quantitative and qualitative differences in the B cell response may provide insights into the age-related change of influenza vaccination response.
2023-08-20 | GSE175523 | GEO
Project description:Seasonal influenza contributes to a substantial disease burden annually, resulting in approximately 10 million hospital visits and 50 thousand deaths in a typical year in the US. 90% of the annual mortality from influenza occurs in people over the age of 65. While influenza vaccination is the best protection against the virus, it is less effective for the elderly. This may be due to differences in the quantity or type of B cells induced by vaccination in older individuals. To investigate this possibility, we leveraged recent development in single-cell technology that allows for simultaneous measurement of both gene expression profile and the B cell receptor (BCR) at single-cell resolution. Pre- and post-vaccination peripheral blood B cells were sorted from three young and three older adults who responded to the inactivated influenza vaccine and were profiled using single-cell RNAseq with paired BCR sequencing. At pre-vaccination, we observed a higher somatic hypermutation frequency and a higher abundance of activated B cells in older adults than in young adults. Following vaccination, young adults mounted a more clonal response than older adults. The response involved a mix of plasmablasts, activated B cells, and resting memory B cells in both age groups. The response in young adults was dominated by expansion in plasmablasts, while the response in older adults also involved activated B cells. We observed a consistent change in gene expression in plasmablasts after vaccination between age groups but not in the activated B cells. These quantitative and qualitative differences in the B cell response may provide insights into the age-related change of influenza vaccination response.
2023-08-20 | GSE175522 | GEO
Project description:Proteomic identification and characterization of antibodies comprising the serological response to antigen can provide unique insight into the functional dynamics of adaptive immunity. We have developed a novel method to overcome the technical challenges which previously limited the direct analysis of immunoglobulin proteins in serum, as demonstrated by the identification of human anti-tetanus toxoid (TT) immunoglobulin G (IgG) proteins following booster vaccination. We analyzed the serum IgG repertoire across four time-points corresponding to pre-vaccination, 7 days, 3 months, and 9 months post vaccination. Antigen-specific antibodies were affinity purified against immobilized TT protein and sequenced by bottom-up nanoLC-MS/MS. Interpretation of mass spectra required a custom reference database of IgG heavy and light chain variable sequences determined by NextGen RNA sequencing of the donor's circulating plasmablasts and memory B cells following booster vaccination.
2014-04-24 | PXD000917 | Pride
Project description:An enduring issue in evolutionary and cancer biology is how replication infidelity influences genome composition and vice versa. Here we examine this issue by sequencing the genomes of diploid budding yeast strains that are either mismatch repair (MMR) proficient or deficient and encode wild type or mutator variants of the three major nuclear DNA replicases. Analysis of over 43,000 mutations that accumulated in the absence of selective pressure demonstrates that the nuclear DNA replication machinery generates less than one mismatch per genome and in combination with MMR, achieves a genome-wide per base error rate of 1.7 x 10-10. Absent both MMR and purifying selection, replication error patterns strongly depend on replication origin proximity, replication fork direction, and the local DNA sequence. Preferred sequences were observed for base substitutions and deletions. Error rates also vary with replication time, in linker versus nucleosome-bound DNA, in 5'- and 3'-untranslated regions, in coding regions and in intergenic DNA. This genome-wide view shows that replication fidelity is amazingly high but heterogeneous, in patterns that suggest the underlying mechanisms by which replication modulates genome stability and composition and vice versa. Six to ten isolates were sequenced for each combination of DNA polymerase (WT, pol1-L868M, pol2-M644G, pol3-L612M) and mismatch repair (proficient, deficient) genotypes. A single WT isolate was sequenced following micrococcal nuclease digestion.
2014-08-25 | E-GEOD-56939 | biostudies-arrayexpress
Project description:Background & Aims: The precise mechanism underlying the attenuation of the antigen-specific B cell response induced by therapeutic vaccination during chronic HBV infection remains unclear. The development of vaccines or strategies targeting this impediment through rational design could potentially result in significant advancements in the treatment of chronic hepatitis B. Methods: A mouse model with a knock-in of a B cell receptor specific to the hepatitis B virus surface antigen was generated under the name E6F6-B. This model was utilized to investigate the temporal and spatial patterns of humoral responses induced by therapeutic vaccination in the presence of persistent antigen stimulation. Through the use of multiple transcriptome sequencing techniques, the differentiation trajectory of HBsAg-specific B cells post therapeutic vaccination during chronic hepatitis B infection was elucidated. Results: In light of the E6F6-B transfer model, a significant reduction in antibody secreting cells were observed two weeks after vaccination. Additionally, an atypical pre-plasma cell population (BLIMP-1+ IRF4+ CD40- CD138-) was identified as a consequence of persistent BCR signaling in the absence of CD40 co-stimulation. A therapeutic antibody-induced suppression of BCR signaling revitalized the HBsAg-specific B cell response.
2024-04-28 | GSE230861 | GEO
Project description:Background & Aims: The precise mechanism underlying the attenuation of the antigen-specific B cell response induced by therapeutic vaccination during chronic HBV infection remains unclear. The development of vaccines or strategies targeting this impediment through rational design could potentially result in significant advancements in the treatment of chronic hepatitis B. Methods: A mouse model with a knock-in of a B cell receptor specific to the hepatitis B virus surface antigen was generated under the name E6F6-B. This model was utilized to investigate the temporal and spatial patterns of humoral responses induced by therapeutic vaccination in the presence of persistent antigen stimulation. Through the use of multiple transcriptome sequencing techniques, the differentiation trajectory of HBsAg-specific B cells post therapeutic vaccination during chronic hepatitis B infection was elucidated. Results: In light of the E6F6-B transfer model, a significant reduction in antibody secreting cells were observed two weeks after vaccination. Additionally, an atypical pre-plasma cell population (BLIMP-1+ IRF4+ CD40- CD138-) was identified as a consequence of persistent BCR signaling in the absence of CD40 co-stimulation. A therapeutic antibody-induced suppression of BCR signaling revitalized the HBsAg-specific B cell response.
2024-04-28 | GSE230862 | GEO
Project description:Single-cell RNA sequencing can to resolve transcriptional features from large numbers of individual immune cells, but techniques capable of resolving the variable regions of B cell receptors (BCR) – defining features that confer antigen specificity to B cells – remain limited, especially from widely-used 3`-barcoded libraries. Here, we report a method that for recovering paired, full-length variable region sequences of the BCRs from 3`-barcoded single-cell whole transcriptome libraries. We first verified this method could produce accurate, full-length BCR sequences. We then applied this method to profile antigen-specific B cell responses elicited against the capsular polysaccharide of Streptococcus pneumoniae serotype 3 (ST3) by glycoconjugate vaccines in infant rhesus macaques. Using our method, we defined features of the BCR associated with specificity for the ST3 antigen and showed that these sequence characteristics are present in multiple vaccinated monkeys, indicating a convergent response to vaccination. These results demonstrate the utility of our method to resolve key features of the B cell repertoire and for profiling antigen-specific responses elicited by vaccination.
2023-05-19 | GSE232873 | GEO