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Article ; Online: Advances in HIV Research Using Mass Cytometry.

George, Ashley F / Roan, Nadia R

2023 Volume 20, Issue 2, Page(s) 76–85

Abstract: Purpose of review: This review describes how advances in CyTOF and high-dimensional analysis methods have furthered our understanding of HIV transmission, pathogenesis, persistence, and immunity.: Recent findings: CyTOF has generated important ... ...

Abstract	Purpose of review: This review describes how advances in CyTOF and high-dimensional analysis methods have furthered our understanding of HIV transmission, pathogenesis, persistence, and immunity. Recent findings: CyTOF has generated important insight on several aspects of HIV biology: (1) the differences between cells permissive to productive vs. latent HIV infection, and the HIV-induced remodeling of infected cells; (2) factors that contribute to the persistence of the long-term HIV reservoir, in both blood and tissues; and (3) the impact of HIV on the immune system, in the context of both uncontrolled and controlled infection. CyTOF and high-dimensional analysis tools have enabled in-depth assessment of specific host antigens remodeled by HIV, and have revealed insights into the features of HIV-infected cells enabling them to survive and persist, and of the immune cells that can respond to and potentially control HIV replication. CyTOF and other related high-dimensional phenotyping approaches remain powerful tools for translational research, and applied HIV to cohort studies can inform on mechanisms of HIV pathogenesis and persistence, and potentially identify biomarkers for viral eradication or control.
MeSH term(s)	Humans ; HIV Infections ; CD4-Positive T-Lymphocytes ; Virus Latency ; Virus Replication
Language	English
Publishing date	2023-01-23
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ZDB-ID	2151206-1
ISSN	1548-3576 ; 1548-3568
ISSN (online)	1548-3576
ISSN	1548-3568
DOI	10.1007/s11904-023-00649-x
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Article ; Online: Resident T cells stand up to HIV.

Roan, Nadia R

Science immunology

2018 Volume 3, Issue 24

Abstract: HIV-specific resident memory T cells are abundant in lymphoid tissues of elite controllers and exhibit distinct functional properties. ...

Abstract	HIV-specific resident memory T cells are abundant in lymphoid tissues of elite controllers and exhibit distinct functional properties.
MeSH term(s)	CD8-Positive T-Lymphocytes ; HIV Infections ; HIV-1 ; Humans ; Lymphoid Tissue ; T-Lymphocytes
Language	English
Publishing date	2018-06-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review ; Comment
ISSN	2470-9468
ISSN (online)	2470-9468
DOI	10.1126/sciimmunol.aat6121
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Article ; Online: Systems analysis of innate and adaptive immunity in Long COVID.

Peluso, Michael J / Abdel-Mohsen, Mohamed / Henrich, Timothy J / Roan, Nadia R

Seminars in immunology

2024 Volume 72, Page(s) 101873

Abstract: Since the onset of the COVID-19 pandemic, significant progress has been made in developing effective preventive and therapeutic strategies against severe acute SARS-CoV-2 infection. However, the management of Long COVID (LC), an infection-associated ... ...

Abstract	Since the onset of the COVID-19 pandemic, significant progress has been made in developing effective preventive and therapeutic strategies against severe acute SARS-CoV-2 infection. However, the management of Long COVID (LC), an infection-associated chronic condition that has been estimated to affect 5-20% of individuals following SARS-CoV-2 infection, remains challenging due to our limited understanding of its mechanisms. Although LC is a heterogeneous disease that is likely to have several subtypes, immune system disturbances appear common across many cases. The extent to which these immune perturbations contribute to LC symptoms, however, is not entirely clear. Recent advancements in multi-omics technologies, capable of detailed, cell-level analysis, have provided valuable insights into the immune perturbations associated with LC. Although these studies are largely descriptive in nature, they are the crucial first step towards a deeper understanding of the condition and the immune system's role in its development, progression, and resolution. In this review, we summarize the current understanding of immune perturbations in LC, covering both innate and adaptive immune responses, and the cytokines and analytes involved. We explore whether these findings support or challenge the primary hypotheses about LC's underlying mechanisms. We also discuss the crosstalk between various immune system components and how it can be disrupted in LC. Finally, we emphasize the need for more tissue- and subtype-focused analyses of LC, and for enhanced collaborative efforts to analyze common specimens from large cohorts, including those undergoing therapeutic interventions. These collective efforts are vital to unravel the fundaments of this new disease, and could also shed light on the prevention and treatment of the larger family of chronic illnesses linked to other microbial infections.
MeSH term(s)	Humans ; Post-Acute COVID-19 Syndrome ; COVID-19 ; Pandemics ; SARS-CoV-2 ; Adaptive Immunity ; Systems Analysis ; Immunity, Innate
Language	English
Publishing date	2024-03-08
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1018141-6
ISSN	1096-3618 ; 1044-5323
ISSN (online)	1096-3618
ISSN	1044-5323
DOI	10.1016/j.smim.2024.101873
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Article: Isolation and Culture of Human Endometrial Epithelial Cells and Stromal Fibroblasts.

Chen, Joseph C / Roan, Nadia R

Bio-protocol

2016 Volume 5, Issue 20

Abstract: Purification and culture of endometrial epithelial cells (eEC) and stromal fibroblasts (eSF) from endometrial biopsies allows for downstream cell- ... ...

Abstract	Purification and culture of endometrial epithelial cells (eEC) and stromal fibroblasts (eSF) from endometrial biopsies allows for downstream cell-specific
Language	English
Publishing date	2016-06-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325
ISSN	2331-8325
DOI	10.21769/bioprotoc.1623
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Article ; Online: Friend or Foe: Innate Sensing of HIV in the Female Reproductive Tract.

Roan, Nadia R / Jakobsen, Martin R

Current HIV/AIDS reports

2016 Volume 13, Issue 1, Page(s) 53–63

Abstract: The female reproductive tract (FRT) is a major site for human immunodeficiency virus (HIV) infection. There currently exists a poor understanding of how the innate immune system is activated upon HIV transmission and how this activation may affect ... ...

Abstract	The female reproductive tract (FRT) is a major site for human immunodeficiency virus (HIV) infection. There currently exists a poor understanding of how the innate immune system is activated upon HIV transmission and how this activation may affect systemic spread of HIV from the FRT. However, multiple mechanisms for how HIV is sensed have been deciphered using model systems with cell lines and peripheral blood-derived cells. The aim of this review is to summarize recent progress in the field of HIV innate immune sensing and place this in the context of the FRT. Because HIV is somewhat unique as an STD that thrives under inflammatory conditions, the response of cells upon sensing HIV gene products can either promote or limit HIV infection depending on the context. Future studies should include investigations into how FRT-derived primary cells sense and respond to HIV to confirm conclusions drawn from non-mucosal cells. Understanding how cells of the FRT participate in and effect innate immune sensing of HIV will provide a clearer picture of what parameters during the early stages of HIV exposure determine transmission success. Such knowledge could pave the way for novel approaches for preventing HIV acquisition in women.
MeSH term(s)	Carrier Proteins/metabolism ; DNA-Binding Proteins ; Female ; Genitalia, Female/immunology ; Genitalia, Female/virology ; HIV Infections/immunology ; HIV Infections/prevention & control ; HIV Infections/transmission ; HIV Infections/virology ; HIV-1/immunology ; Humans ; Immunity, Innate/immunology ; Nuclear Proteins/immunology ; Nuclear Proteins/metabolism ; Nucleotidyltransferases/metabolism ; Phosphoproteins/immunology ; Toll-Like Receptors/immunology
Chemical Substances	Carrier Proteins ; DNA-Binding Proteins ; Nuclear Proteins ; PQBP1 protein, human ; Phosphoproteins ; Toll-Like Receptors ; IFI16 protein, human (148998-64-5) ; Nucleotidyltransferases (EC 2.7.7.-) ; cGAS protein, human (EC 2.7.7.-)
Language	English
Publishing date	2016-02-18
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2151206-1
ISSN	1548-3576 ; 1548-3568
ISSN (online)	1548-3576
ISSN	1548-3568
DOI	10.1007/s11904-016-0305-0
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Article ; Online: The hypoxia-regulated ectonucleotidase CD73 is a host determinant of HIV latency.

Sperber, Hannah S / Raymond, Kyle A / Bouzidi, Mohamed S / Ma, Tongcui / Valdebenito, Silvana / Eugenin, Eliseo A / Roan, Nadia R / Deeks, Steven G / Winning, Sandra / Fandrey, Joachim / Schwarzer, Roland / Pillai, Satish K

Cell reports

2023 Volume 42, Issue 11, Page(s) 113285

Abstract: Deciphering the mechanisms underlying viral persistence is critical to achieving a cure for human immunodeficiency virus (HIV) infection. Here, we implement a systems approach to discover molecular signatures of HIV latently infected ... ...

Abstract	Deciphering the mechanisms underlying viral persistence is critical to achieving a cure for human immunodeficiency virus (HIV) infection. Here, we implement a systems approach to discover molecular signatures of HIV latently infected CD4
MeSH term(s)	Humans ; Adenosine/metabolism ; CD4-Positive T-Lymphocytes ; HIV Infections ; HIV-1 ; Virus Activation ; Virus Latency/physiology ; Virus Replication/physiology
Chemical Substances	Adenosine (K72T3FS567) ; NT5E protein, human (EC 3.1.3.5)
Language	English
Publishing date	2023-10-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2023.113285
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Article ; Online: Corrigendum: Reliable estimation of CD8 T cell inhibition of

Xu, Yinyan / Weideman, Ann Marie / Abad-Fernandez, Maria / Mollan, Katie R / Kallon, Sallay / Samir, Shahryar / Warren, Joanna A / Clutton, Genevieve / Roan, Nadia R / Adimora, Adaora A / Archin, Nancie / Kuruc, JoAnn / Gay, Cynthia / Hudgens, Michael G / Goonetilleke, Nilu

Frontiers in immunology

2023 Volume 13, Page(s) 1104661

Abstract: This corrects the article DOI: 10.3389/fimmu.2021.666991.]. ...

Abstract	[This corrects the article DOI: 10.3389/fimmu.2021.666991.].
Language	English
Publishing date	2023-01-03
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.1104661
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Article ; Online: Subsets of Tissue CD4 T Cells Display Different Susceptibilities to HIV Infection and Death: Analysis by CyTOF and Single Cell RNA-seq.

Luo, Xiaoyu / Frouard, Julie / Zhang, Gang / Neidleman, Jason / Xie, Guorui / Sheedy, Emma / Roan, Nadia R / Greene, Warner C

Frontiers in immunology

2022 Volume 13, Page(s) 883420

Abstract: CD4 T lymphocytes belong to diverse cellular subsets whose sensitivity or resistance to HIV-associated killing remains to be defined. Working with lymphoid cells from human tonsils, we characterized the HIV-associated depletion of various CD4 T cell ... ...

Abstract	CD4 T lymphocytes belong to diverse cellular subsets whose sensitivity or resistance to HIV-associated killing remains to be defined. Working with lymphoid cells from human tonsils, we characterized the HIV-associated depletion of various CD4 T cell subsets using mass cytometry and single-cell RNA-seq. CD4 T cell subsets preferentially killed by HIV are phenotypically distinct from those resistant to HIV-associated cell death, in a manner not fully accounted for by their susceptibility to productive infection. Preferentially-killed subsets express CXCR5 and CXCR4 while preferentially-infected subsets exhibit an activated and exhausted effector memory cell phenotype. Single-cell RNA-seq analysis reveals that the subsets of preferentially-killed cells express genes favoring abortive infection and pyroptosis. These studies emphasize a complex interplay between HIV and distinct tissue-based CD4 T cell subsets, and the important contribution of abortive infection and inflammatory programmed cell death to the overall depletion of CD4 T cells that accompanies untreated HIV infection.
MeSH term(s)	CD4-Positive T-Lymphocytes ; HIV Infections ; HIV-1/physiology ; Humans ; RNA-Seq ; T-Lymphocyte Subsets
Language	English
Publishing date	2022-06-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.883420
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Article ; Online: Single-cell glycomics analysis by CyTOF-Lec reveals glycan features defining cells differentially susceptible to HIV.

Ma, Tongcui / McGregor, Matthew / Giron, Leila / Xie, Guorui / George, Ashley F / Abdel-Mohsen, Mohamed / Roan, Nadia R

eLife

2022 Volume 11

Abstract: High-parameter single-cell phenotyping has enabled in-depth classification and interrogation of immune cells, but to date has not allowed for glycan characterization. Here, we develop CyTOF-Lec as an approach to simultaneously characterize many protein ... ...

Abstract	High-parameter single-cell phenotyping has enabled in-depth classification and interrogation of immune cells, but to date has not allowed for glycan characterization. Here, we develop CyTOF-Lec as an approach to simultaneously characterize many protein and glycan features of human immune cells at the single-cell level. We implemented CyTOF-Lec to compare glycan features between different immune subsets from blood and multiple tissue compartments, and to characterize HIV-infected cell cultures. Using bioinformatics approaches to distinguish preferential infection of cellular subsets from viral-induced remodeling, we demonstrate that HIV upregulates the levels of cell-surface fucose and sialic acid in a cell-intrinsic manner, and that memory CD4+ T cells co-expressing high levels of fucose and sialic acid are highly susceptible to HIV infection. Sialic acid levels were found to distinguish memory CD4+ T cell subsets expressing different amounts of viral entry receptors, pro-survival factors, homing receptors, and activation markers, and to play a direct role in memory CD4+ T cells' susceptibility to HIV infection. The ability of sialic acid to distinguish memory CD4+ T cells with different susceptibilities to HIV infection was experimentally validated through sorting experiments. Together, these results suggest that HIV remodels not only cellular proteins but also glycans, and that glycan expression can differentiate memory CD4+ T cells with vastly different susceptibility to HIV infection.
MeSH term(s)	CD4-Positive T-Lymphocytes ; Disease Susceptibility ; Fucose ; Glycomics ; HIV Infections ; HIV-1/physiology ; Humans ; N-Acetylneuraminic Acid ; Polysaccharides
Chemical Substances	Polysaccharides ; Fucose (28RYY2IV3F) ; N-Acetylneuraminic Acid (GZP2782OP0)
Language	English
Publishing date	2022-07-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.78870
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Article ; Online: Improving preclinical models of HIV microbicide efficacy.

Roan, Nadia R / Münch, Jan

Trends in microbiology

2015 Volume 23, Issue 8, Page(s) 445–447

Abstract: Despite potent in vitro efficacy, most topical microbicides fail to effectively prevent HIV transmission. One reason for clinical failure may be that current microbicide testing does not reflect the environment encountered during sexual virus ... ...

Abstract	Despite potent in vitro efficacy, most topical microbicides fail to effectively prevent HIV transmission. One reason for clinical failure may be that current microbicide testing does not reflect the environment encountered during sexual virus transmission. We discuss how preclinical microbicide development could be improved by more closely mimicking real-life conditions.
MeSH term(s)	Animals ; Anti-Infective Agents/isolation & purification ; Anti-Infective Agents/pharmacology ; Disease Models, Animal ; Disease Transmission, Infectious/prevention & control ; Drug Evaluation, Preclinical/methods ; HIV Infections/prevention & control ; HIV Infections/transmission ; Humans ; Models, Theoretical
Chemical Substances	Anti-Infective Agents
Language	English
Publishing date	2015-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2015.05.001
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