Dynamic Perturbations of the T-Cell Receptor Repertoire in Chronic HIV Infection and following Antiretroviral Therapy

Frontiers in Immunology
James M HeatherBenjamin Chain

Abstract

HIV infection profoundly affects many parameters of the immune system and ultimately leads to AIDS, yet which factors are most important for determining resistance, pathology, and response to antiretroviral treatment - and how best to monitor them - remain unclear. We develop a quantitative high-throughput sequencing pipeline to characterize the TCR repertoires of HIV-infected individuals before and after antiretroviral therapy, working from small, unfractionated samples of peripheral blood. This reveals the TCR repertoires of HIV(+) individuals to be highly perturbed, with considerably reduced diversity as a small proportion of sequences are highly overrepresented. HIV also causes specific qualitative changes to the repertoire including an altered distribution of V gene usage, depletion of public TCR sequences, and disruption of TCR networks. Short-term antiretroviral therapy has little impact on most of the global damage to repertoire structure, but is accompanied by rapid changes in the abundance of many individual TCR sequences, decreases in abundance of the most common sequences, and decreases in the majority of HIV-associated CDR3 sequences. Thus, high-throughput repertoire sequencing of small blood samples that are easy ...Continue Reading

References

Aug 26, 1998·The Journal of Experimental Medicine·J D WilsonA J McMichael
Aug 8, 2002·The Journal of Immunology : Official Journal of the American Association of Immunologists·Naeem KhanPaul A H Moss
Oct 23, 2002·The Journal of Immunology : Official Journal of the American Association of Immunologists·Takamasa UenoMasafumi Takiguchi
Dec 13, 2002·Developmental and Comparative Immunology·Marie-Paule LefrancGérard Lefranc
Jan 11, 2003·Clinical and Diagnostic Laboratory Immunology·Monica KharbandaSavita Pahwa
Jun 18, 2003·The Journal of General Virology·Judie B AlimontiKeith R Fowke
Mar 26, 2004·Nature Reviews. Immunology·Janko Nikolich-ZugichIlhem Messaoudi
Jul 14, 2004·The Journal of Experimental Medicine·Derek C MacallanDavid F Tough
Dec 15, 2004·The Journal of Experimental Medicine·Tao DongSarah L Rowland-Jones
Mar 23, 2006·Annual Review of Immunology·Markus G RudolphIan A Wilson
Sep 5, 2006·The Journal of Immunology : Official Journal of the American Association of Immunologists·Geraldine M A GillespieSarah L Rowland-Jones
Nov 23, 2006·Nature Medicine·Jason M BrenchleyDaniel C Douek
Nov 30, 2006·Proceedings of the National Academy of Sciences of the United States of America·Vanessa VenturiMiles P Davenport
Sep 12, 2008·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Nina KhannaUNKNOWN Swiss HIV Cohort Study
Sep 20, 2008·The Journal of Immunology : Official Journal of the American Association of Immunologists·Brenna C SimonsSpyros A Kalams
Nov 20, 2008·The Journal of Immunology : Official Journal of the American Association of Immunologists·Vanessa VenturiMiles P Davenport
Jun 23, 2009·Genome Research·J Douglas FreemanRobert A Holt
Feb 9, 2011·Immunology and Cell Biology·John J MilesDavid A Price
May 13, 2011·The Journal of Immunology : Official Journal of the American Association of Immunologists·Joseph A ConradSpyros A Kalams
Jul 8, 2011·Blood·Maria Candela IglesiasVictor Appay
Jan 4, 2012·Cell Research·Hanjie LiJiahuai Han

❮ Previous
Next ❯

Citations

Sep 16, 2016·Frontiers in Immunology·Dongni HouYuanlin Song
Oct 11, 2017·The Journal of Immunology : Official Journal of the American Association of Immunologists·Madhura MukhopadhyayLisa A Chakrabarti
Nov 8, 2017·Nature Reviews. Microbiology·Lucy C K Bell, Mahdad Noursadeghi
Jun 4, 2019·JAMA Oncology·Thomas S UldrickUNKNOWN Cancer Immunotherapy Trials Network (CITN)-12 Study Team
Oct 19, 2019·Briefings in Bioinformatics·Yanfang ZhangZhenhai Zhang
Jun 6, 2018·Frontiers in Immunology·Wahiba ChaaraAdrien Six
Jan 30, 2020·Frontiers in Immunology·Timothy John LooneyLi Zhang
Sep 27, 2019·Frontiers in Immunology·Camille E PuronenThomas S Uldrick
Jan 13, 2017·Briefings in Bioinformatics·James M HeatherBenny Chain
Aug 3, 2016·The Journal of Immunology : Official Journal of the American Association of Immunologists·Gabriel K WongMark Cobbold
Nov 23, 2017·Frontiers in Immunology·Felix BredenThomas B Kepler
Mar 14, 2019·Frontiers in Immunology·Joanna A WarrenNilu Goonetilleke
Oct 27, 2020·Frontiers in Oncology·Polina ShindiapinaRobert A Baiocchi
Mar 19, 2021·Frontiers in Immunology·Carolin T TurnerMahdad Noursadeghi
Jul 16, 2020·Cell Reports·Cinque SotoJames E Crowe
Aug 11, 2021·Viruses·Yessica Sánchez-Ponce, Ezequiel M Fuentes-Pananá
Sep 9, 2020·Nature Biotechnology·Pierre BarennesEncarnita Mariotti-Ferrandiz

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRP045430

Methods Mentioned

BETA
PCR

Key Resources (RRID) Mentioned

OMICS_00001

Software Mentioned

igraph
ineq
RCytoscape
R
Decombinator
vegan

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.