Probes for HIV
ACD can configure probes for the various manual and automated assays for HIV for RNAscope Assay, or for Basescope Assay compatible for your species of interest.
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Emerging microbes & infections
2022 Dec 01
Gao, L;Jiao, YM;Ma, P;Sun, L;Zhao, H;Guo, AL;Fan, X;Zhang, C;Song, JW;Zhang, JY;Lu, F;Wang, FS;
PMID: 35253610 | DOI: 10.1080/22221751.2022.2049982
Semen is a known vector for both human immunodeficiency virus (HIV) infection and transmission. However, the distribution and characteristics of HIV-infected cells in semen remain unclear. Investigating the possibility of transmission through the spermatozoon in semen is of great clinical significance to improve the strategies for exposure prevention and assisted reproduction for HIV-infected partners. Twenty-six HIV-infected patients, including twelve treatment-naïve (TN) patients and fourteen antiretroviral treated (ART) patients, were enrolled in this study. HIV p24 protein in spermatozoa was detected using imaging flow cytometry and immunohistochemistry, and HIV RNA was identified using next-generation RNAscope in situ hybridization. Additionally, we described the rates of HIV-positive spermatozoon and CD4+ T lymphocytes in semen, and found that p24+ spermatozoon were mainly CD4 negative regardless of whether the patients received ART. Of note, p24-positive cells in semen are predominantly spermatozoa, and we confirmed that motile spermatozoa carried HIV into peripheral blood mononuclear cells of healthy men in vitro. Our findings provide evidence regarding the risk of HIV-infected spermatozoa.
AIDS (London, England)
2022 Jun 01
Fletcher, CV;Kroon, E;Schacker, T;Pinyakorn, S;Chomont, N;Chottanapund, S;Prueksakaew, P;Benjapornpong, K;Buranapraditkun, S;Phanuphak, N;Ananworanich, J;Vasan, S;Hsu, D;RV254/SEARCH 010 study Group, ;
PMID: 35184069 | DOI: 10.1097/QAD.0000000000003201
The ability of antiretroviral drugs to penetrate and suppress viral replication in tissue reservoir sites is critical for HIV remission. We evaluated antiretroviral concentrations in lymph nodes and their impact on HIV transcription.Participants of the RV254/SEARCH010 Acute HIV Infection Cohort in Thailand were enrolled. Group 1 (n = 6) initiated and continued antiretrovirals with two nucleoside reverse transcriptase inhibitors (NRTIs), dolutegravir (DTG) and mar- aviroc (MVC). Group 2 (n = 12) initiated antiretrovirals with two NRTIs as well as efavirenz and were switched to two NRTIs as well as DTG. Antiretroviral concentrations were measured by mass spectroscopy. HIV RNA+ and DNA+ cells were measured by in-situ hybridization.All participants were MSM. At lymph node biopsy, all had plasma HIV RNA less than 20 copies/ml. Group 2 had longer durations of antiretroviral and DTG use (medians of 135 and 63 weeks, respectively) compared with Group 1 (median 44 weeks for both). TFV-DP, 3TC-TP, DTG and MVC were quantifiable in all lymph node samples from participants receiving those drugs versus carbovir-triphosphate (CBV-TP) in four out of 14. Median ratios of lymph node to peripheral blood concentrations were DTG, 0.014; MVC, 6.9; CBV-TP, 0.38; 3TC-TP, 0.32; and TFV-DP, 3.78. Median inhibitory quotients [ratios of lymph node concentrations to in-vitro inhibitory levels (IC50-or-90)] were DTG, 0.8; MVC, 38.8; CBV-TP, 0.5; 3TC- TP, 4.1; and TFV-DP, 1.8. Ongoing viral transcription was detected in lymph node of all participants. Median lymph node RNA+ cells were 71 350 versus 99 750 cells/g for Groups 1 and 2, respectively (P = 0.111).MVC has enhanced lymph node penetration and thereby may contribute to more complete viral suppression in the lymph node.
Science immunology
2023 May 19
Collins, DR;Hitschfel, J;Urbach, JM;Mylvaganam, GH;Ly, NL;Arshad, U;Racenet, ZJ;Yanez, AG;Diefenbach, TJ;Walker, BD;
PMID: 37205767 | DOI: 10.1126/sciimmunol.ade5872
Follicular CD8+ T cells (fCD8) mediate surveillance in lymph node (LN) germinal centers against lymphotropic infections and cancers, but the precise mechanisms by which these cells mediate immune control remain incompletely resolved. To address this, we investigated functionality, clonotypic compartmentalization, spatial localization, phenotypic characteristics, and transcriptional profiles of LN-resident virus-specific CD8+ T cells in persons who control HIV without medications. Antigen-induced proliferative and cytolytic potential consistently distinguished spontaneous controllers from noncontrollers. T cell receptor analysis revealed complete clonotypic overlap between peripheral and LN-resident HIV-specific CD8+ T cells. Transcriptional analysis of LN CD8+ T cells revealed gene signatures of inflammatory chemotaxis and antigen-induced effector function. In HIV controllers, the cytotoxic effectors perforin and granzyme B were elevated among virus-specific CXCR5+ fCD8s proximate to foci of HIV RNA within germinal centers. These results provide evidence consistent with cytolytic control of lymphotropic infection supported by inflammatory recruitment, antigen-specific proliferation, and cytotoxicity of fCD8s.
Mucosal immunology
2022 Feb 16
Vine, EE;Rhodes, JW;Warner van Dijk, FA;Byrne, SN;Bertram, KM;Cunningham, AL;Harman, AN;
PMID: 35173293 | DOI: 10.1038/s41385-022-00492-0
In tissue, mononuclear phagocytes (MNP) are comprised of Langerhans cells, dendritic cells, macrophages and monocyte-derived cells. They are the first immune cells to encounter HIV during transmission and transmit the virus to CD4 T cells as a consequence of their antigen presenting cell function. To understand the role these cells play in transmission, their phenotypic and functional characterisation is important. With advancements in high parameter single cell technologies, new MNPs subsets are continuously being discovered and their definition and classification is in a state of flux. This has important implications for our knowledge of HIV transmission, which requires a deeper understanding to design effective vaccines and better blocking strategies. Here we review the historical research of the role MNPs play in HIV transmission up to the present day and revaluate these studies in the context of our most recent understandings of the MNP system.
The active human immunodeficiency virus reservoir during antiretroviral therapy: emerging players in viral persistence
Current opinion in HIV and AIDS
2021 Jul 01
Astorga-Gamaza, A;Buzon, MJ;
PMID: 33973900 | DOI: 10.1097/COH.0000000000000685
To discuss the role of CD4+ T cells with active Human immunodeficiency virus (HIV), meaning infected cells with transcriptional and/or translational viral activity during antiretroviral therapy (ART), focusing on new technologies for its detection, potential cell markers for its characterization, and evidences on the contribution of the active HIV reservoir to long-term viral persistence.HIV-infected cells expressing viral ribonucleic acid are systematically detected in subjects on long-term ART. In recent years, powerful new tools have provided significant insights into the nature, quantification, and identification of cells with active HIV, including the identification of new cell markers, and the presence of viral activity in specific cell populations located in different cellular and anatomical compartments. Moreover, studies on viral sequence integrity have identified cell clones with intact viral genomes and active viral transcription that could potentially persist for years. Together, new investigations support the notion that the active reservoir could represent a relevant fraction of long-term infected cells, and therefore, the study of its cell sources and mechanisms of maintenance could represent a significant advance in our understanding of viral persistence and the development of new curative strategies.The presence of HIV-infected cells with viral expression during ART has been traditionally overlooked for years. Based on recent investigations, this active viral reservoir could play an important role in HIV persistence.
The Journal of Pain
2022 May 01
Hobson, J;Gilstrap, S;Ho, M;Fehrmann, N;Gathright, J;White, D;Thomas, J;Goodin, B;Cody, S;
| DOI: 10.1016/j.jpain.2022.03.140
Emerging literature suggests that experiences of discrimination negatively influence health and well-being. It is unfortunately common for people living with HIV (PLWH) to be stigmatized and discriminated against because of their HIV status and other marginalized identities (e.g., ethnicity/race, sexual identity and orientation). To date, little research has specifically examined discrimination in PWLH and its associations with pain and other pain-relevant factors such as mood and sleep. The purpose of this ongoing study was to preliminarily analyze associations among daily experiences of discrimination, pain severity and interference, depressive symptoms, and sleep in PLWH. Participants included 24 PLWH recruited from a local HIV treatment center. Participants completed The Everyday Discrimination Scale (TEDS) followed by the Brief Pain Inventory - Short Form (BPI-SF), the Insomnia Severity Index (ISI), and the Center for Epidemiologic Studies - Depression Scale (CES-D). Initial findings tentatively suggest that more frequent daily experiences of discrimination may be significantly associated with greater pain interference on the BPI-SF (p = .030) and greater severity of insomnia symptoms on the ISI (p = .059). However, it appears that daily experiences of discrimination may not be meaningfully associated with pain severity on the BPI-SF (p = .401) or depressive symptoms on the CES-D (p = .235). Our findings highlight the potentially deleterious effects of daily discrimination experiences on pain and sleep in in PLWH. As this ongoing study recruits a larger sample of PLWH, data will need to be reanalyzed to better determine the durability of these preliminary findings. However, there is potential that findings from this study may assist in elucidating causal pathways linking discrimination to pain and pain relevant health behaviors like sleep in PLWH. Grant support from The Impact of Insomnia on Pain, Physical Function, and Inflammation in HIV (3R01HL147603-03S1).
Frontiers in Immunology
2023 Jan 01
Govindaraj, S;Babu, H;Sidharthan, SK;Vaccari, M;
| DOI: 10.3389/fimmu.2023.1203531
Currently, there are approximately 38.4 million individuals living with the Human Immunodeficiency Virus (HIV), of which 36.7 million adults, 1.7 million children (
PREPRINT
2023 May 04
Basova, L;Lindsey, A;McGovern, A;Gaskill, P;Rosander, A;Delorme-Walker, V;ElShamy, W;Pendyala, V;Ellis, R;Cherner, M;Iudicello, J;Marcondes, M;
| DOI: 10.20944/preprints202305.0132.v1
There is a significant overlap between HIV infection and substance use disorders. Dopamine (DA) is the most abundantly upregulated neurotransmitter in Methamphetamine abuse, with receptors (DRD1-5) that are expressed by neurons as well as by a large diversity of cell types, including innate immune cells that are targets of HIV infection, making them responsive to the hyperdopaminergic environment that is characteristic of stimulant drugs. Therefore, the presence of high levels of dopamine may affect the pathogenesis of HIV, particularly in the brain. The stimulation of HIV-latently infected U1 promonocytes with DA significantly increased viral p24 levels in the supernatant at 24 hrs, suggesting effects on activation and replication. Using selective agonists to different DRDs, we found that DRD1 played a major role in activating viral transcription, followed by DRD4, which increased p24 with a slower kinetic. Transcriptome and systems biology analyses led to the identification of a cluster of genes responsive to DA, where S100A8 and S100A9 were most significantly correlated with the early increase of p24 levels following DA stimulation. Conversely, DA increased the expression of these genes’ transcripts at the protein level, respectively MRP8 and MRP14, which form a complex also known as Calprotectin. Interestingly, MRP8/14 was able to stimulate HIV transcription in latent U1 cells, and this occurred via binding to the receptor for advanced glycosylation end-product (RAGE). Using selective agonists, both DRD1 and DRD4 increased MRP8/14 on the surface and in the cytoplasm, as well as secreted in the supernatants. On the other hand, while DRD1/5 did not affect the expression of RAGE, DRD4 stimulation caused its downregulation, offering a mechanistic for the delayed effect via DRD4 on p24 increase. To cross-validate MRP8/14 as a DA signature with biomarker value, we tested its expression in HIV+ Meth users’ brains and peripheral cells. MRP8/14+ cells were more frequently identified in mesolimbic areas such as basal ganglia of HIV+ Meth+ cases compared to HIV+ non-Meth users or to controls. Likewise, MRP8/14+ CD11b+ monocytes were more frequent in HIV+ Meth users, particularly in participants with detectable viral load in the CSF. Overall, our results suggest that the MRP8 and MRP14 complex may serve as a signature to distinguish subjects using addictive substances in the context of HIV, and that this may play a role in aggravating HIV pathology by promoting viral replication in people with HIV who use Meth.
Viruses
2022 Sep 09
Byrnes, SJ;Angelovich, TA;Busman-Sahay, K;Cochrane, CR;Roche, M;Estes, JD;Churchill, MJ;
PMID: 36146803 | DOI: 10.3390/v14091997
Human Immunodeficiency virus (HIV)-associated neurocognitive disorders are a major burden for people living with HIV whose viremia is stably suppressed with antiretroviral therapy. The pathogenesis of disease is likely multifaceted, with contributions from viral reservoirs including the brain, chronic and systemic inflammation, and traditional risk factors including drug use. Elucidating the effects of each element on disease pathogenesis is near impossible in human clinical or ex vivo studies, facilitating the need for robust and accurate non-human primate models. In this review, we describe the major non-human primate models of neuroHIV infection, their use to study the acute, chronic, and virally suppressed infection of the brain, and novel therapies targeting brain reservoirs and inflammation.
Nature communications
2022 Oct 11
Real, F;Zhu, A;Huang, B;Belmellat, A;Sennepin, A;Vogl, T;Ransy, C;Revol, M;Arrigucci, R;Lombès, A;Roth, J;Gennaro, ML;Bouillaud, F;Cristofari, S;Bomsel, M;
PMID: 36220814 | DOI: 10.1038/s41467-022-33401-x
HIV-1 eradication is hindered by viral persistence in cell reservoirs, established not only in circulatory CD4+T-cells but also in tissue-resident macrophages. The nature of macrophage reservoirs and mechanisms of persistence despite combined anti-retroviral therapy (cART) remain unclear. Using genital mucosa from cART-suppressed HIV-1-infected individuals, we evaluated the implication of macrophage immunometabolic pathways in HIV-1 persistence. We demonstrate that ex vivo, macrophage tissue reservoirs contain transcriptionally active HIV-1 and viral particles accumulated in virus-containing compartments, and harbor an inflammatory IL-1R+S100A8+MMP7+M4-phenotype prone to glycolysis. Reactivation of infectious virus production and release from these reservoirs in vitro are induced by the alarmin S100A8, an endogenous factor produced by M4-macrophages and implicated in "sterile" inflammation. This process metabolically depends on glycolysis. Altogether, inflammatory M4-macrophages form a major tissue reservoir of replication-competent HIV-1, which reactivate viral production upon autocrine/paracrine S100A8-mediated glycolytic stimulation. This HIV-1 persistence pathway needs to be targeted in future HIV eradication strategies.
Immunity
2023 May 13
Wu, HL;Busman-Sahay, K;Weber, WC;Waytashek, CM;Boyle, CD;Bateman, KB;Reed, JS;Hwang, JM;Shriver-Munsch, C;Swanson, T;Northrup, M;Armantrout, K;Price, H;Robertson-LeVay, M;Uttke, S;Kumar, MR;Fray, EJ;Taylor-Brill, S;Bondoc, S;Agnor, R;Junell, SL;Legasse, AW;Moats, C;Bochart, RM;Sciurba, J;Bimber, BN;Sullivan, MN;Dozier, B;MacAllister, RP;Hobbs, TR;Martin, LD;Panoskaltsis-Mortari, A;Colgin, LMA;Siliciano, RF;Siliciano, JD;Estes, JD;Smedley, JV;Axthelm, MK;Meyers, G;Maziarz, RT;Burwitz, BJ;Stanton, JJ;Sacha, JB;
PMID: 37236188 | DOI: 10.1016/j.immuni.2023.04.019
Allogeneic hematopoietic stem cell transplantation (alloHSCT) from donors lacking C-C chemokine receptor 5 (CCR5Δ32/Δ32) can cure HIV, yet mechanisms remain speculative. To define how alloHSCT mediates HIV cure, we performed MHC-matched alloHSCT in SIV+, anti-retroviral therapy (ART)-suppressed Mauritian cynomolgus macaques (MCMs) and demonstrated that allogeneic immunity was the major driver of reservoir clearance, occurring first in peripheral blood, then peripheral lymph nodes, and finally in mesenteric lymph nodes draining the gastrointestinal tract. While allogeneic immunity could extirpate the latent viral reservoir and did so in two alloHSCT-recipient MCMs that remained aviremic >2.5 years after stopping ART, in other cases, it was insufficient without protection of engrafting cells afforded by CCR5-deficiency, as CCR5-tropic virus spread to donor CD4+ T cells despite full ART suppression. These data demonstrate the individual contributions of allogeneic immunity and CCR5 deficiency to HIV cure and support defining targets of alloimmunity for curative strategies independent of HSCT.
Cell reports
2022 May 31
Foreman, TW;Nelson, CE;Kauffman, KD;Lora, NE;Vinhaes, CL;Dorosky, DE;Sakai, S;Gomez, F;Fleegle, JD;Parham, M;Perera, SR;Lindestam Arlehamn, CS;Sette, A;Tuberculosis Imaging Program, ;Brenchley, JM;Queiroz, ATL;Andrade, BB;Kabat, J;Via, LE;Barber, DL;
PMID: 35649361 | DOI: 10.1016/j.celrep.2022.110896
HIV/Mycobacterium tuberculosis (Mtb) co-infected individuals have an increased risk of tuberculosis prior to loss of peripheral CD4 T cells, raising the possibility that HIV co-infection leads to CD4 T cell depletion in lung tissue before it is evident in blood. Here, we use rhesus macaques to study the early effects of simian immunodeficiency virus (SIV) co-infection on pulmonary granulomas. Two weeks after SIV inoculation of Mtb-infected macaques, Mtb-specific CD4 T cells are dramatically depleted from granulomas, before CD4 T cell loss in blood, airways, and lymph nodes, or increases in bacterial loads or radiographic evidence of disease. Spatially, CD4 T cells are preferentially depleted from the granuloma core and cuff relative to B cell-rich regions. Moreover, live imaging of granuloma explants show that intralesional CD4 T cell motility is reduced after SIV co-infection. Thus, granuloma CD4 T cells may be decimated before many co-infected individuals experience the first symptoms of acute HIV infection.
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| Description | ||
|---|---|---|
| sense Example: Hs-LAG3-sense | Standard probes for RNA detection are in antisense. Sense probe is reverse complent to the corresponding antisense probe. | |
| Intron# Example: Mm-Htt-intron2 | Probe targets the indicated intron in the target gene, commonly used for pre-mRNA detection | |
| Pool/Pan Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G) | A mixture of multiple probe sets targeting multiple genes or transcripts | |
| No-XSp Example: Hs-PDGFB-No-XMm | Does not cross detect with the species (Sp) | |
| XSp Example: Rn-Pde9a-XMm | designed to cross detect with the species (Sp) | |
| O# Example: Mm-Islr-O1 | Alternative design targeting different regions of the same transcript or isoforms | |
| CDS Example: Hs-SLC31A-CDS | Probe targets the protein-coding sequence only | |
| EnEm | Probe targets exons n and m | |
| En-Em | Probe targets region from exon n to exon m | |
| Retired Nomenclature | ||
| tvn Example: Hs-LEPR-tv1 | Designed to target transcript variant n | |
| ORF Example: Hs-ACVRL1-ORF | Probe targets open reading frame | |
| UTR Example: Hs-HTT-UTR-C3 | Probe targets the untranslated region (non-protein-coding region) only | |
| 5UTR Example: Hs-GNRHR-5UTR | Probe targets the 5' untranslated region only | |
| 3UTR Example: Rn-Npy1r-3UTR | Probe targets the 3' untranslated region only | |
| Pan Example: Pool | A mixture of multiple probe sets targeting multiple genes or transcripts | |
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