Immune Repertoire after Immunization As Seen by Next-Generation Sequencing and Proteomics

Frontiers in Immunology
Martijn VanDuijnTheo Luider

Abstract

The immune system produces a diverse repertoire of immunoglobulins in response to foreign antigens. During B-cell development, VDJ recombination and somatic mutations generate diversity, whereas selection processes remove it. Using both proteomic and NGS approaches, we characterized the immune repertoires in groups of rats after immunization with purified antigens. Proteomics and NGS data on the repertoire are in qualitative agreement, but did show quantitative differences that may relate to differences between the biological niches that were sampled for these approaches. Both methods contributed complementary information in the characterization of the immune repertoire. It was found that the immune repertoires resulting from each antigen had many similarities that allowed samples to cluster together, and that mutated immunoglobulin peptides were shared among animals with a response to the same antigen significantly more than for different antigens. However, the number of shared sequences decreased in a log-linear fashion relative to the number of animals that share them, which may affect future applications. A phylogenetic analysis on the NGS reads showed that reads from different individuals immunized with the same antigen po...Continue Reading

References

Apr 14, 1983·Nature·S Tonegawa
Dec 26, 2001·Nucleic Acids Research·Ron EdgarAlex E Lash
Aug 10, 2002·Bioinformatics·Chaim Linhart, Ron Shamir
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Sep 6, 2007·The Journal of Immunology : Official Journal of the American Association of Immunologists·Tine Rugh PoulsenPeter S Andersen
May 9, 2009·Science·Joshua A WeinsteinStephen R Quake
Oct 29, 2009·BMC Bioinformatics·Mira V Han, Christian M Zmasek
Mar 13, 2010·PloS One·Morgan N PriceAdam P Arkin
Jul 10, 2010·The Journal of Biological Chemistry·Martijn M VanDuijnTheo M Luider
Aug 9, 2012·Journal of Autoimmunity·Georgia ArentzTom P Gordon
Nov 10, 2012·Nature Biotechnology·Shuji SatoRoberto D Polakiewicz
Jun 19, 2013·Cell Host & Microbe·Poornima ParameswaranAndrew Z Fire
Jul 31, 2013·Proceedings of the National Academy of Sciences of the United States of America·Christopher VollmersStephen R Quake
Aug 14, 2013·Clinical and Experimental Immunology·F Leypoldt, K-P Wandinger
Jan 21, 2014·Nature Biotechnology·George GeorgiouStephen R Quake
Jan 29, 2014·Proceedings of the National Academy of Sciences of the United States of America·Jason J LavinderGeorge Georgiou
Apr 2, 2014·Analytical Chemistry·Daniel R BoutzEdward M Marcotte
Apr 15, 2014·Nature Biotechnology·Juan A VizcaínoHenning Hermjakob
May 6, 2014·Nature Methods·Mikhail ShugayDmitriy M Chudakov
May 27, 2014·Trends in Immunology·Jacob D GalsonDominic F Kelly
Jun 12, 2014·Frontiers in Immunology·Lei Yu, Yongjun Guan
Nov 14, 2014·The Journal of Immunology : Official Journal of the American Association of Immunologists·Johannes TrückDominic F Kelly
Dec 24, 2014·Proceedings of the National Academy of Sciences of the United States of America·Chen WangScott D Boyd
May 16, 2015·Immunology and Cell Biology·Jacob D GalsonDominic F Kelly
May 29, 2015·BMC Bioinformatics·Vadim I NazarovIlgar Z Mamedov
Nov 26, 2015·PLoS Computational Biology·Mikhail ShugayDmitriy M Chudakov
Jan 24, 2016·Molecular Biology and Evolution·Kenneth B HoehnOliver G Pybus
Mar 28, 2017·Trends in Biotechnology·Simon FriedensohnSai T Reddy
Jun 22, 2017·Nature·Jacob GlanvilleMark M Davis

❮ Previous
Next ❯

Citations

Sep 16, 2018·The Journal of Immunology : Official Journal of the American Association of Immunologists·Aleksandr KovaltsukKonrad Krawczyk
Jul 25, 2019·Frontiers in Microbiology·Annalisa CiabattiniDonata Medaglini
Aug 15, 2018·Frontiers in Immunology·Oren AvramYariv Wine

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE98855

Methods Mentioned

BETA
PCR

Software Mentioned

VQuest
tcR
Bio
DomainGapAlign
MIGEC
ProgenesisQI
PEAKS
FastTree
Protease Perl package
R

Related Concepts

Related Feeds

Antibody Repertoire Diversity

Antibody repertoire diversity and its role during natural infection is a prerequisite for molecular and structural elucidation of functionally protective immunity. Discover the latest insights into antibody diversity here.

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.

B cell Differentiation

Depending on the signal received through the B cell receptor and other receptors, B cells differentiate into follicular or marginal zone B cells. Here is the latest research pertaining to this differentiation process.

Related Papers

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Uri Hershberg, Eline T Luning Prak
The New England Journal of Medicine
Howard J Jacob
Methods in Molecular Biology
Yu-Chang WuDeborah Dunn-Walters
© 2022 Meta ULC. All rights reserved