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HIV-1-induced cytokines deplete homeostatic ILCs and expand TCF7-dependent memory NK cells: Supplemental Figures and Tables

https://doi.org/10.1101/221010
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults
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HIV Infection and the Risk of Acute Myocardial Infarction
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ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide
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Molecular characterization of human CD94: A type II membrane glycoprotein related to the C‐type lectin superfamily
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Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells
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Systemic Human ILC Precursors Provide a Substrate for Tissue ILC Differentiation
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Homeostatic Control of Memory Cell Progenitors in the Natural Killer Cell Lineage
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Critical Role of CD2 Co-stimulation in Adaptive Natural Killer Cell Responses Revealed in NKG2C-Deficient Humans
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CD8+ T Lymphocyte Self-Renewal during Effector Cell Determination
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HIV-1 Control by NK Cells via Reduced Interaction between KIR2DL2 and HLA-C∗12:02/C∗14:03
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The Transcription Factor Tcf1 Contributes to Normal NK Cell Development and Function by Limiting the Expression of Granzymes
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CD44 Regulates Survival and Memory Development in Th1 Cells
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Epigenetic Modifications Induced by Blimp-1 Regulate CD8+ T Cell Memory Progression during Acute Virus Infection
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Systemic Effects of Inflammation on Health during Chronic HIV Infection
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Natural Killer Cell Memory
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Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression
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T Cell Factor 1-Expressing Memory-like CD8+ T Cells Sustain the Immune Response to Chronic Viral Infections
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Innate Lymphoid Cells: Diversity, Plasticity, and Unique Functions in Immunity
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Regulation of Interferon‐γ During Innate and Adaptive Immune Responses
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The end of AIDS: HIV infection as a chronic disease
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Independent component analysis: algorithms and applications
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Loss of mucosal CD103+ DCs and IL-17+ and IL-22+ lymphocytes is associated with mucosal damage in SIV infection
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A human natural killer cell subset provides an innate source of IL-22 for mucosal immunity
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TRIM5 is an innate immune sensor for the retrovirus capsid lattice
inferredcites →https://doi.org/10.1038/nature10237openalex-snapshot
HIV-1 adaptation to NK-cell-mediated immune pressure
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The biology of innate lymphoid cells
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Integrative genomics viewer
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The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
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Elimination of HIV-1-infected cells by broadly neutralizing antibodies
inferredcites →https://doi.org/10.1038/ng934openalex-snapshot
Epistatic interaction between KIR3DS1 and HLA-B delays the progression to AIDS
inferredcites →https://doi.org/10.1038/ni.1953openalex-snapshot
Critical role for the chemokine receptor CXCR6 in NK cell–mediated antigen-specific memory of haptens and viruses
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BACH2 regulates CD8+ T cell differentiation by controlling access of AP-1 factors to enhancers
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Tcf1 and Lef1 transcription factors establish CD8+ T cell identity through intrinsic HDAC activity
inferredcites →https://doi.org/10.1038/ni.3482openalex-snapshot
NK cells and type 1 innate lymphoid cells: partners in host defense
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Innate lymphoid cells as regulators of immunity, inflammation and tissue homeostasis
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Functions of natural killer cells
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Microbial translocation is a cause of systemic immune activation in chronic HIV infection
inferredcites →https://doi.org/10.1038/nm1720openalex-snapshot
Interleukin-22 mediates early host defense against attaching and effacing bacterial pathogens
inferredcites →https://doi.org/10.1038/nmeth.2688openalex-snapshot
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
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Targeted in situ genome-wide profiling with high efficiency for low cell numbers
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Natural killer cell memory in infection, inflammation and cancer
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Interleukin-7 receptor expression: intelligent design
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The molecular basis of the memory T cell response: differential gene expression and its epigenetic regulation
inferredcites →https://doi.org/10.1038/nri3349openalex-snapshot
Innate lymphoid cells — how did we miss them?
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Innate lymphoid cells — a proposal for uniform nomenclature
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Role of IL-15 in HIV-1-associated hypergammaglobulinaemia
inferredcites →https://doi.org/10.1056/nejmoa1113425openalex-snapshot
Immune-Correlates Analysis of an HIV-1 Vaccine Efficacy Trial
inferredcites →https://doi.org/10.1073/pnas.0813192106openalex-snapshot
Cytokine-induced memory-like natural killer cells
inferredcites →https://doi.org/10.1073/pnas.0914127107openalex-snapshot
Essential role of the Wnt pathway effector Tcf-1 for the establishment of functional CD8 T cell memory
inferredcites →https://doi.org/10.1084/jem.20161046openalex-snapshot
CD4+ T cell effector commitment coupled to self-renewal by asymmetric cell divisions
inferredcites →https://doi.org/10.1086/382090openalex-snapshot
Expression of Chemokine and Inhibitory Receptors on Natural Killer Cells: Effect of Immune Activation and HIV Viremia
inferredcites →https://doi.org/10.1089/aid.2011.0144openalex-snapshot
Increased Levels of Circulating Cytokines with HIV-Related Immunosuppression
inferredcites →https://doi.org/10.1089/aid.2011.0253openalex-snapshot
NKG2C Deletion Is a Risk Factor of HIV Infection
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1097/qad.0b013e3282ffde7eopenalex-snapshot
A combined genotype of KIR3DL1 high expressing alleles and HLA-B*57 is associated with a reduced risk of HIV infection
inferredcites →https://doi.org/10.1097/qad.0b013e3283367836openalex-snapshot
Plasma cytokine levels during acute HIV-1 infection predict HIV disease progression
inferredcites →https://doi.org/10.1101/286351openalex-snapshot
Profiling of pluripotency factors in individual stem cells and early embryos
inferredcites →https://doi.org/10.1101/gr.207902.116openalex-snapshot
End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data
inferredcites →https://doi.org/10.1111/j.1365-2567.2008.02887.xopenalex-snapshot
Increased proportion of CD56bright natural killer cells in active and inactive systemic lupus erythematosus
inferredcites →https://doi.org/10.1111/j.1365-2567.2008.03027.xopenalex-snapshot
CD56 bright natural killer (NK) cells: an important NK cell subset
inferredcites →https://doi.org/10.1111/j.1365-2796.2008.02045.xopenalex-snapshot
NK cells in HIV‐1 infection: evidence for their role in the control of HIV‐1 infection
inferredcites →https://doi.org/10.1126/science.aaf6517openalex-snapshot
Latency reversal and viral clearance to cure HIV-1
inferredcites →https://doi.org/10.1126/scitranslmed.3000632openalex-snapshot
Tryptophan Catabolism by Indoleamine 2,3-Dioxygenase 1 Alters the Balance of T H 17 to Regulatory T Cells in HIV Disease
inferredcites →https://doi.org/10.1126/scitranslmed.3005727openalex-snapshot
NCR3/NKp30 Contributes to Pathogenesis in Primary Sjögren’s Syndrome
inferredcites →https://doi.org/10.1128/cdli.8.6.1131-1135.2001openalex-snapshot
Calcein-Acetyoxymethyl Cytotoxicity Assay: Standardization of a Method Allowing Additional Analyses on Recovered Effector Cells and Supernatants
inferredcites →https://doi.org/10.1128/jvi.01844-08openalex-snapshot
Induction of a Striking Systemic Cytokine Cascade prior to Peak Viremia in Acute Human Immunodeficiency Virus Type 1 Infection, in Contrast to More Modest and Delayed Responses in Acute Hepatitis B and C Virus Infections
inferredcites →https://doi.org/10.1128/jvi.77.10.5632-5638.2003openalex-snapshot
Tmevpg1, a Candidate Gene for the Control of Theiler's Virus Persistence, Could Be Implicated in the Regulation of Gamma Interferon
inferredcites →https://doi.org/10.1146/annurev-immunol-020711-075053openalex-snapshot
Innate Lymphoid Cells: Emerging Insights in Development, Lineage Relationships, and Function
inferredcites →https://doi.org/10.1146/annurev.immunol.16.1.293openalex-snapshot
JAKS AND STATS: Biological Implications
inferredcites →https://doi.org/10.1158/0008-5472.can-08-1440openalex-snapshot
Natural Killer Cell Accumulation in Tumors Is Dependent on IFN-γ and CXCR3 Ligands
inferredcites →https://doi.org/10.1161/jaha.116.004243openalex-snapshot
Role of T‐Cell Dysfunction, Inflammation, and Coagulation in Microvascular Disease in HIV
inferredcites →https://doi.org/10.1182/blood-2002-07-2103openalex-snapshot
Expression of CD57 defines replicative senescence and antigen-induced apoptotic death of CD8+ T cells
inferredcites →https://doi.org/10.1182/blood-2007-09-077438openalex-snapshot
Human natural killer cells
inferredcites →https://doi.org/10.1182/blood-2009-11-253286openalex-snapshot
CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells
inferredcites →https://doi.org/10.1182/blood-2010-09-303057openalex-snapshot
Dissecting CD56dim human NK cells
inferredcites →https://doi.org/10.1182/blood-2012-04-419283openalex-snapshot
Cytokine activation induces human memory-like NK cells
inferredcites →https://doi.org/10.1182/blood-2013-11-427781openalex-snapshot
Human innate lymphoid cells
inferredcites →https://doi.org/10.1182/blood.v90.2.716openalex-snapshot
Signaling Pathways Regulating CD44-Dependent Cytolysis in Natural Killer Cells
inferredcites →https://doi.org/10.1186/1743-422x-10-33openalex-snapshot
High number of CD56bright NK-cells and persistently low CD4+ T-cells in a hemophiliac HIV/HCV co-infected patient without opportunistic infections
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
inferredcites →https://doi.org/10.1186/s12967-015-0601-2openalex-snapshot
Increased ex vivo cell death of central memory CD4 T cells in treated HIV infected individuals with unsatisfactory immune recovery
inferredcites →https://doi.org/10.1186/s13059-016-0938-8openalex-snapshot
CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq
inferredcites →https://doi.org/10.1198/106186005x59243openalex-snapshot
Cluster Validation by Prediction Strength
inferredcites →https://doi.org/10.1371/journal.pbio.1001208openalex-snapshot
Copy Number Variation of KIR Genes Influences HIV-1 Control
inferredcites →https://doi.org/10.1371/journal.pone.0167091openalex-snapshot
Interleukin-15 (IL-15) Strongly Correlates with Increasing HIV-1 Viremia and Markers of Inflammation
inferredcites →https://doi.org/10.1371/journal.ppat.1005421openalex-snapshot
A Conserved HIV-1-Derived Peptide Presented by HLA-E Renders Infected T-cells Highly Susceptible to Attack by NKG2A/CD94-Bearing Natural Killer Cells
inferredcites →https://doi.org/10.1371/journal.ppat.1006819openalex-snapshot
Infection and depletion of CD4+ group-1 innate lymphoid cells by HIV-1 via type-I interferon pathway
inferredcites →https://doi.org/10.1371/journal.ppat.1007104openalex-snapshot
Tracking KLRC2 (NKG2C)+ memory-like NK cells in SIV+ and rhCMV+ rhesus macaques
inferredcites →https://doi.org/10.1634/stemcells.2007-0066openalex-snapshot
Self-Renewal of Murine Embryonic Stem Cells Is Supported by the Serine/Threonine Kinases Pim-1 and Pim-3
inferredcites →https://doi.org/10.17615/k858-n421openalex-snapshot
Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults: 2016 Recommendations of the International Antiviral Society–USA Panel
inferredcites →https://doi.org/10.5282/ubm/epub.1769openalex-snapshot
Weighted k-Nearest-Neighbor Techniques and Ordinal Classification
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Accelerating t-SNE using tree-based algorithms
inferredcites →https://doi.org/10.7554/elife.21856openalex-snapshot
An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.immuni.2018.05.013openalex-snapshot
Innate Lymphoid Cells: Diversity, Plasticity, and Unique Functions in Immunity
inferred← citeshttps://doi.org/10.1186/s12865-021-00450-8openalex-snapshot
Innate lymphoid cell dysfunction during long-term suppressive antiretroviral therapy in an African cohort
inferred← citeshttps://doi.org/10.3389/fimmu.2021.668391openalex-snapshot
A Transcriptional Signature of PDGF-DD Activated Natural Killer Cells Predicts More Favorable Prognosis in Low-Grade Glioma
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