4.7 Article

Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses

Kevin B. Einkauf et al.

Summary: By studying the evolution of transcriptionally active and silent proviral genomes and epigenomes in individuals receiving antiretroviral therapy, we have found that transcriptionally active HIV-1 proviruses are dynamically evolving under host factors' selection pressure.
Article Multidisciplinary Sciences

Longitudinal clonal dynamics of HIV-1 latent reservoirs measured by combination quadruplex polymerase chain reaction and sequencing

Alice Cho et al.

Summary: HIV-1 infection leads to the formation of a long-lasting reservoir of latently infected CD4(+) T cells, consisting of intact and defective proviruses. This study used Q4PCR to quantify the reservoir content and found that the defective reservoir remained stable while the intact proviral reservoir decayed over time. Both the intact and defective proviral reservoirs showed dynamic changes, with an enrichment of intact proviruses in expanded CD4(+) T cell clones and a decrease in overall reservoir complexity.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Multidisciplinary Sciences

TASOR epigenetic repressor cooperates with a CNOT1 RNA degradation pathway to repress HIV

Roy Matkovic et al.

Summary: The study reveals the mechanism of how the Human Silencing Hub (HUSH) complex, consisting of TASOR, MPP8, and Periphilin, recruits the histone methyl-transferase SETDB1 to spread repressive marks across genes and transgenes. It is found that TASOR interacts with RNA exosome and RNA Polymerase II, contributing to the repression of HIV expression at both transcriptional and post-transcriptional levels.

NATURE COMMUNICATIONS (2022)

Article Immunology

Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones

Jack A. Collora et al.

Summary: Understanding the driving factors and markers of clonally expanding HIV-1-infected CD4(+) T cells is crucial for the eradication of HIV-1. Utilizing single-cell ECCITE-seq technology, researchers tracked the dynamics of clonal expansion in longitudinally archived samples from HIV-1-infected individuals and uninfected individuals. The study revealed that persistent antigen and TNF responses shaped T cell clonal expansion, even in the presence of antiretroviral therapy. Additionally, HIV-1-infected cytotoxic CD4(+) T cell clones persisted and were enriched in cytotoxic effector memory Th1 cells.

IMMUNITY (2022)

Article Multidisciplinary Sciences

Prolonged viral suppression with anti-HIV-1 antibody therapy

Christian Gaebler et al.

Summary: Immunotherapy with anti-HIV-1 antibodies has the potential to suppress infection and increase the rate of clearance of infected cells. A clinical study showed that 76% of HIV-infected individuals who received a combination of antibodies maintained virologic suppression for at least 20 weeks without antiretroviral therapy. The administration of antibodies affected the HIV-1 reservoir, but further research is needed to define the precise effect of antibody immunotherapy.

NATURE (2022)

Article Multidisciplinary Sciences

Selective clonal persistence of human retroviruses in vivo: Radial chromatin organization, integration site, and host transcription

Anat Melamed et al.

Summary: Human retroviruses HTLV-1 and HIV-1 persist in the body as a reservoir of latently infected T cell clones. The study found that the position of the provirus in the nucleus, its distance from the centromere, and the intensity of local host genome transcription are important factors determining clonal survival. Similar factors were also found to explain clonal persistence of HIV-1. This research highlights the importance of the intranuclear and intrachromosomal location of the provirus and host transcription intensity in the persistence of human retroviruses.

SCIENCE ADVANCES (2022)

Article Cell Biology

Distinct gene expression by expanded clones of quiescent memory CD4+ T cells harboring intact latent HIV-1 proviruses

Georg H. J. Weymar et al.

Summary: The study discovered that clones of latent cells carrying dormant HIV-1 viruses mainly exist in a specific subgroup of CD4(+) T cells, which are predominantly T effector memory cells with distinctive gene expression. This finding opens up new possibilities for eradicating HIV-1.

CELL REPORTS (2022)

Article Immunology

Selective Decay of Intact HIV-1 Proviral DNA on Antiretroviral Therapy

Rajesh T. Gandhi et al.

Summary: Intact, replication-competent proviruses are selectively lost over time during suppressive ART, while defective provirus levels remain stable. The proportion of intact proviruses within the total HIV-1 DNA reservoir decreases over time on ART. Levels of intact proviruses on ART are correlated with total HIV-1 DNA and residual plasma viremia, but not with markers of inflammation or immune activation.

JOURNAL OF INFECTIOUS DISEASES (2021)

Article Immunology

Integration features of intact latent HIV-1 in CD4+ T cell clones contribute to viral persistence

Amy S. Huang et al.

Summary: Latent intact HIV-1 proviruses persist in long-lived CD4(+) T cells and can undergo clonal expansion. Expanded clones of CD4(+) T cells in the latent reservoir seem to preferentially integrate within ZNF genes, which may contribute to maintaining HIV-1 latency.

JOURNAL OF EXPERIMENTAL MEDICINE (2021)

Article Biochemistry & Molecular Biology

Distinct mechanisms of long-term virologic control in two HIV-infected individuals after treatment interruption of anti-retroviral therapy

Jana Blazkova et al.

Summary: The control of viral rebound after cessation of medication may be regulated by CD8 T cell activity or neutralizing antibodies, with different individuals exhibiting distinct mechanisms. Continuous monitoring of undisclosed use of medication and superinfection is crucial for controlling plasma viral rebound.

NATURE MEDICINE (2021)

Article Cell Biology

Signatures of immune selection in intact and defective proviruses distinguish HIV-1 elite controllers

Xiaodong Lian et al.

Summary: The study found that defective proviruses in elite controllers are more commonly located in permissive genic euchromatin positions, while intact proviruses are frequently found in heterochromatin regions, indicating differential immune selection pressure on intact and defective proviruses in ECs. The intact and defective proviruses from ECs also showed reduced frequencies of escape mutations in key immune response regions, possibly due to the small and poorly inducible reservoir in ECs. Additionally, a subset of ECs harbored nef deletions in intact proviruses, which may increase viral vulnerability to host immunity in these individuals.

SCIENCE TRANSLATIONAL MEDICINE (2021)

Article Immunology

HLA Alleles B*53:01 and C*06:02 Are Associated With Higher Risk of P. falciparum Parasitemia in a Cohort in Uganda

Jean C. Digitale et al.

Summary: The study found that HLA class I molecules play a role in restricting parasitemia caused by P. falciparum, but no HLA alleles were associated with protection from malaria. This suggests the essential role of the cellular immune response in P. falciparum immunity.

FRONTIERS IN IMMUNOLOGY (2021)

Article Multidisciplinary Sciences

In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia

Basiel Cole et al.

Summary: The authors developed a single-cell approach, STIP-Seq, to simultaneously sequence TCR, integration sites, and proviral genomes, revealing that the translation-competent reservoir mainly consists of proviruses with short deletions at the 5'-end of the genome. They also found that cell clones with predicted pathogen-specificity may harbor inducible proviruses.

NATURE COMMUNICATIONS (2021)

Article Immunology

Longitudinal Dynamics of Intact HIV Proviral DNA and Outgrowth Virus Frequencies in a Cohort of Individuals Receiving Antiretroviral Therapy

Shane D. Falcinelli et al.

Summary: This study demonstrates a close relationship between the frequencies of intact proviral DNA measured by IPDA and replication-competent HIV measured by QVOA. IPDA shows promise as a high-throughput approach to estimate changes in the frequency of the replication-competent reservoir.

JOURNAL OF INFECTIOUS DISEASES (2021)

Article Multidisciplinary Sciences

Robust and persistent reactivation of SIV and HIV by N-803 and depletion of CD8+ cells

Julia Bergild McBrien et al.

NATURE (2020)

Article Multidisciplinary Sciences

Defective HIV-1 proviruses produce viral proteins

Hiromi Imamichi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

Intact proviral DNA assay analysis of large cohorts of people with HIV provides a benchmark for the frequency and composition of persistent proviral DNA

Francesco R. Simonetti et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

Distinct viral reservoirs in individuals with spontaneous control of HIV-1

Chenyang Jiang et al.

NATURE (2020)

Article Multidisciplinary Sciences

TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control

Christopher H. Douse et al.

NATURE COMMUNICATIONS (2020)

Article Medicine, Research & Experimental

Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy

Kevin B. Einkauf et al.

JOURNAL OF CLINICAL INVESTIGATION (2019)

Article Multidisciplinary Sciences

Longitudinal HIV sequencing reveals reservoir expression leading to decay which is obscured by clonal expansion

Marilia Rita Pinzone et al.

NATURE COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

HIV-1 DNA sequence diversity and evolution during acute subtype C infection

Guinevere Q. Lee et al.

NATURE COMMUNICATIONS (2019)

Review Medicine, General & Internal

Deep latency: A new insight into a functional HIV cure

Maher M. Elsheikh et al.

EBIOMEDICINE (2019)

Editorial Material Microbiology

HIV Latency: Stochastic across Multiple Scales

Maike M. K. Hansen et al.

CELL HOST & MICROBE (2019)

Article Microbiology

Principles Governing Establishment versus Collapse of HIV-1 Cellular Spread

Jason M. Hataye et al.

CELL HOST & MICROBE (2019)

Article Immunology

Virological Blips and Predictors of Post Treatment Viral Control After Stopping ART Started in Primary HIV Infection

Sarah Fidler et al.

JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES (2017)

Article Medicine, Research & Experimental

Clonal expansion of genome-intact HIV-1 in functionally polarized Th1 CD4+ T cells

Guinevere Q. Lee et al.

JOURNAL OF CLINICAL INVESTIGATION (2017)

Article Multidisciplinary Sciences

Phase separation drives heterochromatin domain formation

Amy R. Strom et al.

NATURE (2017)

Article Biochemistry & Molecular Biology

Stimulating the RIG-I pathway to kill cells in the latent HIV reservoir following viral reactivation

Peilin Li et al.

NATURE MEDICINE (2016)

Article Biochemistry & Molecular Biology

HIV-1 Integration Landscape during Latent and Active Infection

Lillian B. Cohn et al.

Article Multidisciplinary Sciences

Integrative analysis of 111 reference human epigenomes

Anshul Kundaje et al.

NATURE (2015)

Article Multidisciplinary Sciences

Nuclear architecture dictates HIV-1 integration site selection

Bruna Marini et al.

NATURE (2015)

Article Multidisciplinary Sciences

Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells

Iva A. Tchasovnikarova et al.

SCIENCE (2015)

Article Biochemistry & Molecular Biology

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Suhas S. P. Rao et al.

Article Biochemistry & Molecular Biology

HIV-1 persistence in CD4+ T cells with stem cell like properties

Maria J. Buzon et al.

NATURE MEDICINE (2014)

Review Biochemistry & Molecular Biology

An Integrated Overview of HIV-1 Latency

Debbie S. Ruelas et al.

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Human heterochromatin proteins form large domains containing KRAB-ZNF genes

Maartje J. Vogel et al.

GENOME RESEARCH (2006)

Article Biochemistry & Molecular Biology

MUSCLE: multiple sequence alignment with high accuracy and high throughput

RC Edgar

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in resting CD4+ T cells

JD Siliciano et al.

NATURE MEDICINE (2003)

Article Biochemistry & Molecular Biology

HIV-1 integration in the human genome favors active genes and local hotspots

ARW Schröder et al.

Article Biochemical Research Methods

Detecting hypermutations in viral sequences with an emphasis on G→A hypermutation

PP Rose et al.

BIOINFORMATICS (2000)