Abbreviations used in this manuscript
| Abbreviation | Definition | What is it? |
|---|---|---|
| 7SK snRNP | 7SK small nuclear ribonucleoprotein | Combine with other proteins (e.g. NF-kB) to form transcriptional complexes |
| AIDS | Acquired immune deficiency syndrome | The disease caused by HIV |
| AP-1 | Activator Protein 1 | Transcription factor, is part of the early response to cellular activation |
| APOBEC | Apolipoprotein B mRNA editing enzyme | Proteins with anti-HIV activity, induced by IFN stimulation |
| ART | Anti-retroviral therapy | Antiretroviral drugs, usually used in combination |
| cAMP | Cyclic adenosine monophosphate | Second-messenger in numerous signaling pathways |
| CCL | C-C Motif Chemokine Ligand (e.g.: CCL5) | Chemokine, some with pro-inflammatory effect |
| CCR | C-C type chemokine receptor (e.g.: CCR5, and HIV coreceptor) | Cellular receptor for CC chemokines, also co-receptor for HIV |
| CD | Cluster differentiation | Term used to indicate monoclonal antibodies that react with the same molecule/set of molecules |
| CNS | Central nervous system | Brain and spinal cord |
| CREB | cAMP response element-binding protein | Transcription factor activated by camp |
| CRP | C-reactive protein | An acute-phase reactant, marker of inflammation in the serum |
| CSF | Cerebrospinal fluid | Liquid present in the CNS cavities and meningeal spaces |
| CXCR | C-X-C type chemokine receptor (e.g.: CXCR4, an HIV co-receptor) | Cellular receptor for CXC chemokines |
| DOR | Delta opioid receptor | Enkefalins receptor |
| ENS | Enteric nervous system | Division of the peripheral nervous system (PNS) that can control gastrointestinal motility independently of central nervous system (CNS) input |
| GALT | Gut-associated immune tissue | Lymphoid tissue associated with the intestinal mucosa |
| GI | Gastrointestinal | Pertaining to the digestive tract |
| Glut1 | Glucose transporter 1 | Protein facilitating the transport of glucose across the cell membrane |
| HAND | HIV-associated neurocognitive disorders | Neurocognitive and neurological disorders associated with HIV infection |
| HDAC | Histone deacetylase | Chromatin modifier, involved in epigenetic regulation and silencing of genes |
| HIV | Human immunodeficiency virus | An RNA retrovirus that causes acquired immune deficiency syndrome (AIDS) in humans |
| HKMT | Histone lysine methyltransferase | Chromatin modifier, involved in epigenetic regulation and silencing of genes |
| IFN | Interferon | Group of secreted pro-inflammatory molecules with potent antiviral effects |
| IL- | Interleukin (e.g. IL-2, IL-6) | Small protein with biological/immunological effects |
| IP10 | Interferon (IFN)-γ inducible protein 10 (a.k.a. CXCL10) | Proinflammatory chemokine induced by interferons |
| IPDA | Intact proviral DNA assay | PCR-based method to assess intact cell-associated HIV |
| Ki67 | Kiel-67 antigen | A marker of cell proliferation |
| LBP | LPS-binding protein | Endogenous molecule that binds and inactivates bacterial LPS |
| LPS | Lipopolysaccaride | Lipopolysaccaride expressed on the cell wall of Gram-negative bacteria |
| LTR | Long-terminal repeat | Non-coding sequences in HIV RNA with regulatory function |
| MCP-1 | Monocyte chemoattractant protein 1 | Pro-inflammatory chemokine |
| miRNA | Micro-RNA | Small RNA molecules able to interfere with protein synthesis. Some have anti-HIV effects |
| MLCK | Myosin light chain kinase | Enzyme responsible for muscle contraction |
| MOR | Mu opiod receptor | One of the receptors for natural and synthetic opioids |
| MOUDs | Medications for opioid use disorder | Medications used to treat opioid use disorder, including methadone, naltrexone, and buprenorphine |
| NFAT | Nuclear factor of activated T cells | Transcription factor, is part of the early response to stimulation of T-cell receptor and other pathways |
| NF-kB | Nuclear factor kappa-light-chain-enhancer of activated B cells | Transcription factor, induces the transcription of various pro-inflammatory molecules |
| NK | Natural Killer | Innate immunity cells involved in first-line response to pathogens |
| OUD | Opioid use disorder | Problematic pattern of opioid use leading to clinically significant impairment or distress (DSM-5) |
| PBMC | Peripheral blood mononuclear cells | White blood cells including lymphocytes and monocytes, but not granulocytes or erythrocytes |
| PCR2 | Polycomb repressive complex 2 methyltransferase | Chromatin modifier, involved in epigenetic regulation and silencing of genes |
| PD1 | Programmed cell death protein 1 | A marker of cellular activation and exhaustion |
| PKC | Protein Kinase C | Signaling molecules, mediates cell activation |
| P-TEF B | Positive transcription elongation factor B | Combine with other proteins (e.g. Nf-kb) to form transcriptional complexes |
| PWID | Person who inject drugs | A person, often with OUD, who injects drugs, usually opioids |
| RANTES | Regulated upon Activation, Normal T Cell Expressed and Presumably Secreted | Pro-inflammatory chemokine with anti-HIV effects |
| sCD | Soluble CD (e.g., sCD14, sCD163) | Soluble variety of a molecule normally expressed on a cell membrane, originated by enzymatic cleavage or shedding |
| SIV | Simian immunodeficiency virus | Retrovirus similar to HIV, infecting non-human primates |
| T helper type 1 | Th-1 | Adaptive (memory) immune cells involved in long-term memory and cell-mediated responses to pathogens |
| TLR | TOLL-like receptor | Receptors sensing, among others, pathogen structures such as lipopolysacccarides or nucleic acids |
| TNF-α | Tumor necrosis factor-alpha | Pro-inflammatory molecule |
| Treg | Regulatory T cells | T cell subset responsible for the modulation/dampening of immune responses |
| TRIM | Tripartite motif-containing protein | Proteins with anti-HIV activity, induced by IFN stimulation |