RNAscope™ Applications
HIV/SIV Research
Despite the success of anti-retroviral therapy (ART), the persistence of HIV reservoirs is a major barrier to overcome before finding a lasting cure. In order to completely eradicate HIV and advance therapeutic interventions, it is important to determine the biological nature of viral latency as well as productively infected cells in tissues including the gastrointestinal tract and those of the lymphatic system. RNAscope™, a highly specific and sensitive in situ hybridization technology, employs a powerful technique to study HIV and SIV in cellular and tissue environments.
Why use RNAscope™ Assay for HIV and SIV research?
Localize specific cell types and tissues infected with HIV/SIV – ideal for identifying and measuring persistent reservoirs with single-cell resolution in full morphological context.
Detect HIV/SIV RNA sequences despite low or undetectable plasma viral loads with specificity – with single RNA molecule detection technology, identify individual virus particles and infected cells.
Differential detection of viral RNA and proviral DNA – RNAscope™ probes can be designed to target the sense or antisense sequences to detect the three different configurations of HIV/SIV during the replication cycles:
viral RNA in a virus particle;
viral genomic RNA or mRNA in an infected cell;
proviral DNA integrated in the nucleus of an infected cell.
Read Science's news article 'Molecular microscope' finds hidden AIDS virus in the body" regarding Dr. Jake Estes of the Frederick National Laboratory of the National Cancer Institute and the application of RNAscope™ technology in HIV/SIV research. Dr. Estes and collaborators recently authored the publication Defining HIV and SIV Reservoirs in Lymphoid Tissues. The team of researchers outline methodology to visualize viral RNA and viral DNA simultaneously in HIV-1/SIV. Read more
"The identification and anatomic location of HIV-infected cells and the effects of tissue environment on virus replication and viral gene expression are all critical for evaluating the pathogenesis of HIV infection and for developing cure strategies to eliminate HIV reservoirs. RNAscope in situ hybridization (ISH) has enabled us to visualize and quantify HIV RNA with single-copy resolution. For work supported by a Federal Contract with NIAID, NIH, we are using this state-of-the-art ISH technology in combination with immunohistochemistry to characterize the tissue and cellular compartments where the virus resides in HIV-infected humanized mice."
UCSF School of Medicine. Recent publication citing RNAscope® assay:J Neurovirol. 2015 Nov 16. PMID: 26572785.
RNAscope® Catalog Probes Targeting HIV:
(Listed below are probes for manual RNAscope assay. Corresponding probes for automated assays are also available. )
Target species & region | Cat. No & Probe Description |
|---|---|
HIV1 Targeting Env, Gag, Pol genes | 450141 Probe-V-HIV1-env 450151 Probe-V-HIV1-env-sense 311921 Probe-V-HIV1 (Gag) 446211-C2 Probe-V-HIV1-Gag-C2 317691 Probe-V-HIV1-gagpol 317701 Probe-V-HIV1-gagpol-sense 317701-C2 Probe-V-HIV1-gagpol-sense-C2 445651 Probe-V-HIV1-gagpol-sense-scrambled 445651-C2 Probe-V-HIV1-gagpol-sense-scrambled-C2 |
HIV1, Excluding Gag and Pol genes | 317711 Probe-V-HIV1-nongagpol 317711-C2 Probe-V-HIV1-nongagpol-C2 453631 Probe-V-HIV1-nongagpol-scrambled 317721 Probe-V-HIV1-nongagpol-sense 317721-C3 Probe-V-HIV1-nongagpol-sense-C3 445661 Probe-V-HIV1-nongagpol-sense-scrambled |
HIV1, Subtype A | 416101 Probe-V-HIV1-CladeA 426341 Probe-V-HIV1-CladeA-sense |
HIV1, Subtype B | 416111 Probe-V-HIV1-CladeB 416111-C2 Probe-V-HIV1-CladeB-C2 444051 Probe-V-HIV1-CladeB-gag-pol-sense 447711 Probe-V-HIV1-CladeB-scrambled 425531 Probe-V-HIV1-CladeB-sense 425531-C2 Probe-V-HIV1-CladeB-sense-C2 425531-C3 Probe-V-HIV1-CladeB-sense-C3 444061-C2 Probe-V-HIV1-CladeB-vif-vpr-tat-rev-vpu-env-nef-tar-C2 |
HIV1, Subtype C | 429841 Probe-V-HIV1-CladeC 444021 Probe-V-HIV1-CladeC-gag-pol-sense 430171 Probe-V-HIV1-CladeC-sense 444041-C2 Probe-V-HIV1-CladeC-vif-vpr-rev-vpu-env-nef-tar-C2 |
HIV1, Subtype D | 416121 Probe-V-HIV1-CladeD 426351 Probe-V-HIV1-CladeD-sense |
HIV1, Subtype AE | 446551 Probe-V-HIV-CladeAE 444011 Probe-V-HIV1-CladeAE-gag-pol-sense 444031-C2 Probe-V-HIV1-CladeAE-vif-vpr-tat-rev-vpu-env-nef-tar-C2 |
HIV2 | 446221-C3 Probe-V-HIV2-gag-C3 |
RNAscope® Catalog Probes Targeting SIV:
(Listed below are probes for manual RNAscope assay. Corresponding probes for automated assays are also available. )
Target SIV strain | Cat. No & Probe Description |
|---|---|
SIV-Mac329 (rhesus monkey, Macaca mulatta) | 312811 Probe-SIVmac239 312811-C2 Probe-SIVmac239-C2 314071 Probe-SIVmac239-sense 314071-C2 Probe-SIVmac239-sense-C2 314451 Probe-SIVmac239-gag 445431 Probe-V-SIVmac239-rev-env 445441 Probe-V-SIVmac239-vif-vpr-tat 416131 Probe-V-SIVmac239-vif-env-nef-tar 416131-C2 Probe-V-SIVmac239-vif-env-nef-tar-C2 416141 Probe-V-SIVmac239-gag-pol-sense 416141-C2 Probe-V-SIVmac239-gag-pol-sense-C2 459071-C3 Probe-V-SIVmac239-vif-env-nef-tar-sense-C3 |
SIV-amg (african green monkey, Cercopithecus aethiops) | 431811 Probe-V-SIV-gag 431821 Probe-V-SIV-pol 431831 Probe-V-SIV-rev-env 431841 Probe-V-SIV-vif-vpr-tat 432081 Probe-V-SIV |
SIV-sm sooty mangabey (sooty mangabey, Cercocebus atys) | 415351 Probe-V-SIVsmm |
To target other HIV/SIV strains or regions, ACD can design and manufacture MADE-TO-ORDER Probes in just 2 weeks.
Related Publications
Recent publications where RNAscope™ assay was used to detect HIV or SIV.
| Title | Authors | Journal | PubMed ID | Year |
|---|---|---|---|---|
| The meningeal lymphatic system: a route for HIV brain migration? | Lamers SL, Rose R, Ndhlovu LC, Nolan DJ, Salemi M, Maidji E, Stoddart CA, McGrath MS. | J Neurovirol. 2015 Nov 16. | PMID: 26572785 | 2015 |
| CD4 depletion in SIV-infected macaques results in macrophage and microglia infection with rapid turnover of infected cells. | Micci L, Alvarez X, Iriele RI, Ortiz AM, Ryan ES, McGary CS, Deleage C, McAtee BB, He T, Apetrei C, Easley K, Pahwa S, Collman RG, Derdeyn CA, Davenport MP, Estes JD, Silvestri G, Lackner AA, Paiardini M. | PLoS Pathog. 2014 Oct 30;10(10):e1004467. | PMID: 25356757 | doi: 10.1371/journal.ppat.1004467. | 2014 |
| B cell follicle sanctuary permits persistent productive simian immunodeficiency virus infection in elite controllers. | Fukazawa Y, Lum R, Okoye AA, Park H, Matsuda K, Bae JY, Hagen SI, Shoemaker R, Deleage C, Lucero C, Morcock D, Swanson T, Legasse AW, Axthelm MK, Hesselgesser J, Geleziunas R, Hirsch VM, Edlefsen PT, Piatak M Jr, Estes JD, Lifson JD, Picker LJ. | Nat Med. 2015 Jan 19. | PMID: 25599132 | doi: 10.1038/nm.3781. | 2015 |
| Effect of Suberoylanilide Hydroxamic Acid (SAHA) Administration on the Residual Virus Pool in a Model of Combination Antiretroviral Therapy-Mediated Suppression in SIVmac239-Infected Indian Rhesus Macaques. | Del Prete GQ, Shoemaker R, Oswald K, Lara A, Trubey CM, Fast R, Schneider DK, Kiser R, Coalter V, Wiles A, Wiles R, Freemire B, Keele BF, Estes JD, Quiñones OA, Smedley J, Macallister R, Sanchez RI, Wai JS, Tan CM, Alvord WG, Hazuda DJ, Piatak M Jr, Lifson JD. | Antimicrob Agents Chemother. 2014 Nov;58(11):6790-806. | PMID: 25182644 |doi: 10.1128/AAC.03746-14. | 2014 |
| Tracking the Luminal Exposure and Lymphatic Drainage Pathways of Intravaginal and Intrarectal Inocula Used in Nonhuman Primate Models of HIV Transmission. | Smedley J, Turkbey B, Bernardo ML, Del Prete GQ, Estes JD, Griffiths GL, Kobayashi H, Choyke PL, Lifson JD, Keele BF. | PLoS One. 2014 Mar 25;9(3):e92830. | PMID: 24667371 | doi: 10.1371/journal.pone.0092830. | 2014 |
| Administration of Panobinostat Is Associated with Increased IL-17A mRNA in the Intestinal Epithelium of HIV-1 Patients | Christensen AB, Dige A, Vad-Nielsen J, Brinkmann CR, Bendix M, Østergaard L, Tolstrup M, Søgaard OS, Rasmussen TA, Nyengaard JR, Agnholt J, Denton PW. | Mediators of Inflammation (2015) | http://dx.doi.org/10.1155/2015/120605 | 2015 |
