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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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Allogeneic immunity clears latent virus following allogeneic stem cell transplantation in SIV-infected ART-suppressed macaques

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.
CD4 T cells are rapidly depleted from tuberculosis granulomas following acute SIV co-infection

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.
Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments

Immunity

2022 Apr 12

Jiang, S;Chan, CN;Rovira-Clavé, X;Chen, H;Bai, Y;Zhu, B;McCaffrey, E;Greenwald, NF;Liu, C;Barlow, GL;Weirather, JL;Oliveria, JP;Nakayama, T;Lee, IT;Matter, MS;Carlisle, AE;Philips, D;Vazquez, G;Mukherjee, N;Busman-Sahay, K;Nekorchuk, M;Terry, M;Younger, S;Bosse, M;Demeter, J;Rodig, SJ;Tzankov, A;Goltsev, Y;McIlwain, DR;Angelo, M;Estes, JD;Nolan, GP;
PMID: 35447093 | DOI: 10.1016/j.immuni.2022.03.020

Understanding the mechanisms of HIV tissue persistence necessitates the ability to visualize tissue microenvironments where infected cells reside; however, technological barriers limit our ability to dissect the cellular components of these HIV reservoirs. Here, we developed protein and nucleic acid in situ imaging (PANINI) to simultaneously quantify DNA, RNA, and protein levels within these tissue compartments. By coupling PANINI with multiplexed ion beam imaging (MIBI), we measured over 30 parameters simultaneously across archival lymphoid tissues from healthy or simian immunodeficiency virus (SIV)-infected nonhuman primates. PANINI enabled the spatial dissection of cellular phenotypes, functional markers, and viral events resulting from infection. SIV infection induced IL-10 expression in lymphoid B cells, which correlated with local macrophage M2 polarization. This highlights a potential viral mechanism for conditioning an immunosuppressive tissue environment for virion production. The spatial multimodal framework here can be extended to decipher tissue responses in other infectious diseases and tumor biology.
Functional impairment of HIV-specific CD8+ T cells precedes aborted spontaneous control of viremia

Immunity

2021 Sep 02

Collins, DR;Urbach, JM;Racenet, ZJ;Arshad, U;Power, KA;Newman, RM;Mylvaganam, GH;Ly, NL;Lian, X;Rull, A;Rassadkina, Y;Yanez, AG;Peluso, MJ;Deeks, SG;Vidal, F;Lichterfeld, M;Yu, XG;Gaiha, GD;Allen, TM;Walker, BD;
PMID: 34496223 | DOI: 10.1016/j.immuni.2021.08.007

Spontaneous control of HIV infection has been repeatedly linked to antiviral CD8+ T cells but is not always permanent. To address mechanisms of durable and aborted control of viremia, we evaluated immunologic and virologic parameters longitudinally among 34 HIV-infected subjects with differential outcomes. Despite sustained recognition of autologous virus, HIV-specific proliferative and cytolytic T cell effector functions became selectively and intrinsically impaired prior to aborted control. Longitudinal transcriptomic profiling of functionally impaired HIV-specific CD8+ T cells revealed altered expression of genes related to activation, cytokine-mediated signaling, and cell cycle regulation, including increased expression of the antiproliferative transcription factor KLF2 but not of genes associated with canonical exhaustion. Lymphoid HIV-specific CD8+ T cells also exhibited poor functionality during aborted control relative to durable control. Our results identify selective functional impairment of HIV-specific CD8+ T cells as prognostic of impending aborted HIV control, with implications for clinical monitoring and immunotherapeutic strategies.
Lymphocyte-Dominant Encephalitis and Meningitis in Simian Immunodeficiency Virus–Infected Macaques Receiving Antiretroviral Therapy

Am J Pathol

2017 Dec 08

Mangus LM, Beck SE, Queen SE, Brill SA, Shirk EN, Metcalf Pate KA, Muth DC, Adams RJ, Gama L, Clements JE, Mankowski JL.
PMID: - | DOI: 10.1016/j.ajpath.2017.08.035

A retrospective neuropathologic review of 30 SIV-infected pigtailed macaques receiving combination antiretroviral therapy (cART) was conducted. Seventeen animals with lymphocyte-dominant inflammation in the brain and/or meninges that clearly was morphologically distinct from prototypic SIV encephalitis and human immunodeficiency virus encephalitis were identified. Central nervous system (CNS) infiltrates in cART-treated macaques primarily comprised CD20+ B cells and CD3+ T cells with fewer CD68+ macrophages. Inflammation was associated with low levels of SIV RNA in the brain as shown by in situ hybridization, and generally was observed in animals with episodes of cerebrospinal fluid (CSF) viral rebound or sustained plasma and CSF viremia during treatment. Although the lymphocytic CNS inflammation in these macaques shared morphologic characteristics with uncommon immune-mediated neurologic disorders reported in treated HIV patients, including CNS immune reconstitution inflammatory syndrome and neurosymptomatic CSF escape, the high prevalence of CNS lesions in macaques suggests that persistent adaptive immune responses in the CNS also may develop in neuroasymptomatic or mildly impaired HIV patients yet remain unrecognized given the lack of access to CNS tissue for histopathologic evaluation. Continued investigation into the mechanisms and outcomes of CNS inflammation in cART-treated, SIV-infected macaques will advance our understanding of the consequences of residual CNS HIV replication in patients on cART, including the possible contribution of adaptive immune responses to HIV-associated neurocognitive disorders.

Human immunodeficiency virus infection induces lymphoid fibrosis in the BM-liver-thymus-spleen humanized mouse model.

JCI Insight.

2018 Sep 20

Samal J, Kelly S, Na-Shatal A, Elhakiem A, Das A, Ding M, Sanyal A, Gupta P, Melody K, Roland B, Ahmed W, Zakir A, Bility M.
PMID: 30232273 | DOI: 10.1172/jci.insight.120430

A major pathogenic feature associated with HIV infection is lymphoid fibrosis, which persists during antiretroviral therapy (ART). Lymphoid tissues play critical roles in the generation of antigen-specific immune response, and fibrosis disrupts the stromal network of lymphoid tissues, resulting in impaired immune cell trafficking and function, as well as immunodeficiency. Developing an animal model for investigating the impact of HIV infection-induced lymphoid tissue fibrosis on immunodeficiency and immune cell impairment is critical for therapeutics development and clinical translation. Said model will enable in vivo mechanistic studies, thus complementing the well-established surrogate model of SIV infection-induced lymphoid tissue fibrosis in macaques. We developed a potentially novel human immune system-humanized mouse model by coengrafting autologous fetal thymus, spleen, and liver organoids under the kidney capsule, along with i.v. injection of autologous fetal liver-derived hematopoietic stem cells, thus termed the BM-liver-thymus-spleen (BLTS) humanized mouse model. BLTS humanized mouse model supports development of human immune cells and human lymphoid organoids (human thymus and spleen organoids). HIV infection in BLTS humanized mice results in progressive fibrosis in human lymphoid tissues, which was associated with immunodeficiency in the lymphoid tissues, and lymphoid tissue fibrosis persists during ART, thus recapitulating clinical outcomes.

Lymphatic Dissemination of SIV after Penile Inoculation

J Virol.

2016 Feb 10

Ma ZM, Dutra J, Fritts L, Miller CJ.
PMID: 26865706 | DOI: -

Abstract

The human immunodeficiency virus (HIV) is primarily transmitted by heterosexual contact and approximately equal numbers of men and women are infected with the virus worldwide. Understanding the biology of HIV acquisition and dissemination in men exposed to the virus by insertive penile intercourse is likely to help with the rational design of vaccines that can limit or prevent HIV transmission. To characterize the target cells and dissemination pathways involved in establishing systemic SIV infection, we necropsied male rhesus macaques at 1, 3, 7 and 14 days after penile SIV inoculation and quantified the levels unspliced SIV RNA and spliced SIV RNA in tissue lysates and the number of SIV RNA+ cells in tissues sections. We found that penile (glans, foreskin, coronal sulcus) T cells, and, to a lesser extent, macrophages and dendritic cells are primary targets of infection and that SIV rapidly reaches the regional lymph nodes. Seven days after inoculation SIV had disseminated to the blood, systemic lymph nodes and mucosal lymphoid tissues. Further, at 7 days post-inoculation (PI), spliced SIV RNA levels are highest in the genital lymph nodes indicating that this is the site where the infection is initially amplified. By 14 days PI spliced SIV RNA levels were high in all tissues, but they were highest in the gastrointestinal tract indicating that the primary site of virus replication had shifted from the genital lymph nodes to the gut. The stepwise pattern of virus replication and dissemination described here suggests that vaccine-elicited immune responses in the genital lymph nodes could help prevent the infection after penile SIV challenge.

IMPORTANCE:

To be most effective, vaccines should produce anti-viral immune responses in the anatomic sites of virus replication. Thus understanding the path taken by HIV from the mucosal surfaces, that are the site of virus exposure, to the deeper tissues where the virus replicates will provide insight into where AIDS vaccines should produce immunity to be most effective. In this study we determined that, by day 7 after penile inoculation, SIV has moved first to the inguinal lymph nodes and replicates to high levels. Although the virus is widely disseminated to other tissues by day 7, replication is largely limited to the inguinal lymph nodes. The step-by-step movement of SIV from penile mucosal surfaces to the draining lymph nodes may allow a HIV vaccine that produces immunity in these lymph nodes to block HIV from establishing an infection in an exposed person.

In Situ Characterization of Human Lymphoid Tissue Immune Cells by Multispectral Confocal Imaging and Quantitative Image Analysis; Implications for HIV Reservoir Characterization

Frontiers in immunology

2021 Jun 09

Moysi, E;Del Rio Estrada, PM;Torres-Ruiz, F;Reyes-Terán, G;Koup, RA;Petrovas, C;
PMID: 34177929 | DOI: 10.3389/fimmu.2021.683396

CD4 T cells are key mediators of adaptive immune responses during infection and vaccination. Within secondary lymphoid organs, helper CD4 T cells, particularly those residing in germinal centers known as follicular helper T cells (Tfh), provide critical help to B-cells to promote their survival, isotype switching and selection of high affinity memory B-cells. On the other hand, the important role of Tfh cells for the maintenance of HIV reservoir is well documented. Thus, interrogating and better understanding the tissue specific micro-environment and immune subsets that contribute to optimal Tfh cell differentiation and function is important for designing successful prevention and cure strategies. Here, we describe the development and optimization of eight multispectral confocal microscopy immunofluorescence panels designed for in depth characterization and immune-profiling of relevant immune cells in formalin-fixed paraffin-embedded human lymphoid tissue samples. We provide a comprehensive library of antibodies to use for the characterization of CD4+ T-cells -including Tfh and regulatory T-cells- as well as CD8 T-cells, B-cells, macrophages and dendritic cells and discuss how the resulting multispectral confocal datasets can be quantitatively dissected using the HistoCytometry pipeline to collect information about relative frequencies and immune cell spatial distributions. Cells harboring actively transcribed virus are analyzed using an in-situ hybridization assay for the characterization of HIV mRNA positive cells in combination with additional protein markers (multispectral RNAscope). The application of this methodology to lymphoid tissues offers a means to interrogate multiple relevant immune cell targets simultaneously at increased resolution in a reproducible manner to guide CD4 T-cell studies in infection and vaccination.
Quantitative Imaging Analysis of the Spatial Relationship between Antiretrovirals, RT-SHIV RNA, and Collagen in the Mesenteric Lymph Nodes of Nonhuman Primates

Antimicrobial agents and chemotherapy

2021 Mar 29

Scholz, EMB;Mwangi, JN;De la Cruz, G;Nekorchuk, M;Chan, CN;Busman-Sahay, K;Adamson, L;Luciw, P;Fedoriw, Y;Estes, JD;Rosen, EP;Kashuba, ADM;
PMID: 33782003 | DOI: 10.1128/AAC.00019-21

HIV persistence in tissue reservoirs is a major barrier to HIV cure. While antiretrovirals (ARVs) suppress viral replication, antiretroviral therapy (ART) interruption results in rapid rebound viremia that may originate from lymphoid tissues. To understand the relationship between anatomic distribution of ARV exposure and viral expression in lymph nodes, we performed mass spectrometry imaging (MSI) of 6 ARVs, RNAscope in situ hybridization for viral RNA, and immunohistochemistry of collagen in mesenteric lymph nodes from 8 uninfected and 10 reverse transcriptase-simian/human immunodeficiency virus (RT-SHIV) infected rhesus macaque nonhuman primates (NHPs) dosed to steady-state with combination ART. MATLAB-based quantitative imaging analysis was used to evaluate spatial and pharmacologic relationships between these ARVs, viral RNA (both vRNA+ cells and FDC-bound virions) and collagen deposition. Using MSI, 31% of mesenteric lymph node tissue area was not covered by any ARV. Additionally, 28% of FDC-trapped virions and 21% of infected cells were not exposed to any detected ARV. Of the 69% of tissue area that was covered by cumulative ART exposure, nearly 100% of concentrations were greater than in vitro IC50 values; however, 52% of total tissue coverage was from only one ARV, primarily maraviroc. Collagen covered ∼35% of tissue area, but did not influence ARV distribution heterogeneity. Our findings are consistent with our hypothesis that ARV distribution, in addition to total-tissue drug concentration, must be considered when evaluating viral persistence in lymph nodes and other reservoir tissues.
The human IL-15 superagonist N-803 promotes migration of virus-specific CD8+ T and NK cells to B cell follicles but does not reverse latency in ART-suppressed, SHIV-infected macaques

PLoS Pathog

2020 Mar 12

Webb GM, Molden J, Busman-Sahay K, Abdulhaqq S, Wu HL, Weber WC, Bateman KB, Reed JS, Northrup M, Maier N, Tanaka S, Gao L, Davey B, Carpenter BL, Axthelm MK, Stanton JJ, Smedley J, Greene JM, Safrit JT, Estes JD, Skinner PJ, Sacha JB
PMID: 32163523 | DOI: 10.1371/journal.ppat.1008339

Despite the success of antiretroviral therapy (ART) to halt viral replication and slow disease progression, this treatment is not curative and there remains an urgent need to develop approaches to clear the latent HIV reservoir. The human IL-15 superagonist N-803 (formerly ALT-803) is a promising anti-cancer biologic with potent immunostimulatory properties that has been extended into the field of HIV as a potential "shock and kill" therapeutic for HIV cure. However, the ability of N-803 to reactivate latent virus and modulate anti-viral immunity in vivo under the cover of ART remains undefined. Here, we show that in ART-suppressed, simian-human immunodeficiency virus (SHIV)SF162P3-infected rhesus macaques, subcutaneous administration of N-803 activates and mobilizes both NK cells and SHIV-specific CD8+ T cells from the peripheral blood to lymph node B cell follicles, a sanctuary site for latent virus that normally excludes such effector cells. We observed minimal activation of memory CD4+ T cells and no increase in viral RNA content in lymph node resident CD4+ T cells post N-803 administration. Accordingly, we found no difference in the number or magnitude of plasma viremia timepoints between treated and untreated animals during the N-803 administration period, and no difference in the size of the viral DNA cell-associated reservoir post N-803 treatment. These results substantiate N-803 as a potent immunotherapeutic candidate capable of activating and directing effector CD8+ T and NK cells to the B cell follicle during full ART suppression, and suggest N-803 must be paired with a bona fide latency reversing agent in vivo to facilitate immune-mediated modulation of the latent viral reservoir
ORAL SECONDARY SYPHILIS IN PEOPLE LIVING WITH HIV: A 16-YEAR EXPERIENCE IN MEXICO CITY

Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology

2021 Jul 01

Anaya-Saavedra, G;Castillejos-García, I;Maldonado-Mendoza, J;Ramírez-Amador, V;
| DOI: 10.1016/j.oooo.2021.03.041

Background The increase in syphilis rates worldwide, particularly in people living with HIV (PLWH), as well as the challenging diagnosis that secondary syphilis represents, make essential the accurate recognition of its manifestations, particularly in easy-access sites like the oral mucosa. Objective To describe the clinicopathologic spectrum of oral secondary syphilis (OSS) in PLWH. Methods A cross-sectional and descriptive study that included PLWH with OSS from 3 HIV referral centers in Mexico City (2004-2020). Demographic and clinical data were obtained. A comprehensive oral examination was done. OSS was diagnosed following established criteria. Histopathologic/cytological procedures were performed to rule out specific oral lesions. In all patients, Venereal Disease Research Laboratory tests were assessed and, if possible, a confirmatory fluorescent treponemal antibody test or biopsy was performed. Statistical analysis was performed using SPSS v25. Results Forty-seven PLWH with OSS (97.8% male, median age: 32 years, 63.8% with acquired immunodeficiency syndrome) were included. Thirty-five were receiving combination antiretroviral therapy (74.5%; median of 1146 [Q1-Q3: 337.5-1971] days) with a median CD4+ count of 385 (Q1-Q3: 223-664) cells/mm3 and a Log10 HIV viral load of 4.1 (Q1-Q3: 3.7-5.3) copies/mL. Forty had a complete clinical-serological diagnosis (85.1%; 17 had histopathologic confirmation) and 7 had a clinical-histopathologic diagnosis. Twenty-nine individuals presented 1 lesion (61.7%), and mucous patch was the most common type mainly on oropharyngeal mucosa, followed by ulcers and macular lesions. Ten patients presented maculopapular dermatosis (21.3%). Conclusions In PLWH, oral lesions, particularly mucous patch and/or ulcers on the oral and oropharyngeal mucosa, must alert specialists to consider a diagnosis of syphilis and perform a comprehensive panel of confirmatory tests.
CD4+ Cell infiltration into subcutaneous adipose tissue is not indicative of productively infected cells during acute SHIV infection.

J Med Primatol.

2017 Jul 27

Hsu DC, Wegner MD, Sunyakumthorn P, Silsorn D, Tayamun S, Inthawong D, Kuncharin Y, Im-Erbsin R, Ege C, O'Connell RJ, Michael NL, Ndhlovu LC, Vasan S.
PMID: 28748665 | DOI: 10.1111/jmp.12298

Limited longitudinal data exist on the effect of HIV on adipose tissue (AT). We found an increase in CD4+ cells and detectable SHIV-RNA in AT during acute SHIV infection. SHIV-RNA+ cells were rare, suggesting that AT is unlikely to be a major source of productively infected cells in SHIV 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
EnEmProbe targets exons n and m
En-EmProbe 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

Enabling research, drug development (CDx) and diagnostics

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