DOI: 10.5061/dryad.vhhmgqp2q
title: Anatomical, subset, and HIV-dependent expression of viral sensors and restriction factors

description: The fate of a cell exposed to HIV is affected by its ability to sense the
 virus and restrict its replication. To explore this, we developed VIral
 SensOr Restriction factor-CyTOF (VISOR-CyTOF), which profiles 19 viral
 sensors and restriction factors (VISORs) simultaneously in single cells,
 and applied it to 41 post-mortem tissues from people with HIV. We found
 that myeloid cells, particularly those in mucosa, are well-equipped with
 SAMHD1 and sensors of viral capsid and DNA, while CD4+ T cells –
 particularly the highly-susceptible Tem subset – are not. In lymph node
 CD4+ Tfh, VISOR expression patterns favor HIV integration while blocking
 HIV gene expression, thus favoring viral latency. HIV preferentially fuses
 to CD4+ T cells with a permissive VISOR profile, but early induction of
 select VISORs by type I interferon prevents productive HIV infection. Our
 findings document the diverse patterns of VISOR profiles across tissues
 and cell subsets, and define their association with susceptibility to HIV.
description: # Anatomical, subset, and HIV-dependent expression of viral sensors and
 restriction factors Nadia Roan, PhD Gladstone Institutes University of
 California, San Francisco
 [nadia.roan@gladstone.ucsf.edu](mailto:nadia.roan@gladstone.ucsf.edu)
 [nadia.roan@ucsf.edu](mailto:nadia.roan@ucsf.edu) Dates of collection:
 November 2019 to May 2023 Information about geographic location of data
 collection: San Diego Area (for Last Gift tissue donors) and San Francisco
 Bay Area (for PBMC donors) HIV preferentially fuses with CD4+ T cells
 exhibiting a permissive VISOR profile, but early induction of specific
 VISORs by type I interferon inhibits productive infection. Our findings
 highlight the diverse VISOR patterns across tissues and cell subsets and
 their link to HIV susceptibility. Included are 220 flow cytometry standard
 (FCS) files from 64 different CyTOF specimens. FCS files can be viewed
 using software used for analyzing flow cytometry or CyTOF data (e.g.,
 FlowJo, Cytobank). The Descriptions of each file are detailed in the table
 below. Each file name begins with the Group category. The groups are Last
 Gift (from *ex vivo* experiments), and from the *in vitro* experiments, 1)
 baseline (D0), 2) HIV-unfused (Unfused) or HIV-fused (Fused), 3) HIV+
 (HIVpos) or HIV- (HIVneg), or 4) cGAMP VLP treated (cGAMP) or mock VLP
 treated (Mock). This is followed by a study participant identifier (PID).
 Next, the Organ category indicates whether the specimen was from a tissue
 (bone marrow [BM], gut, kidney, liver, spleen, lymph node [LN], male
 reproductive tract [Repro], heart, or lung) or PBMCs. Finally, the Cell
 Type category indicates whether data exported correspond to: CD4+ T
 (CD4T), CD8+ T (CD8T), myeloid (myeloid), or B cells (Bcell). For CD4+ and
 CD8+ T cells, some files are further gated on memory (Tm) or naïve (Tn)
 subsets. No licenses or restrictions are placed on the data. References
 for methodological information: Methods used for generating and analyzing
 the CyTOF datasets are similar to those described before:
 [https://elifesciences.org/articles/72619](https://elifesciences.org/articles/72619) [https://journals.aai.org/jimmunol/article/207/5/1344/234507/Protracted-yet-Coordinated-Differentiation-of-Long](https://journals.aai.org/jimmunol/article/207/5/1344/234507/Protracted-yet-Coordinated-Differentiation-of-Long) [https://doi.org/10.1016/j.celrep.2021.109414](https://doi.org/10.1016/j.celrep.2021.109414) [https://doi.org/10.1016/j.xcrm.2020.100081](https://doi.org/10.1016/j.xcrm.2020.100081) [https://www.nature.com/articles/s41590-023-01724-6](https://www.nature.com/articles/s41590-023-01724-6) | **Group** | **PID** | **Organ** | **Cell Type** | | :-------- | :------- | :-------- | :------------ | | Last Gift | PID022 | BM | CD4T | | Last Gift | PID022 | BM | CD8T | | Last Gift | PID022 | BM | Myeloid | | Last Gift | PID022 | BM | Bcell | | Last Gift | PID022 | Gut | CD4T | | Last Gift | PID022 | Gut | CD8T | | Last Gift | PID022 | Gut | Myeloid | | Last Gift | PID022 | Gut | Bcell | | Last Gift | PID022 | Kidney | CD4T | | Last Gift | PID022 | Kidney | CD8T | | Last Gift | PID022 | Kidney | Myeloid | | Last Gift | PID022 | Kidney | Bcell | | Last Gift | PID022 | Liver | CD4T | | Last Gift | PID022 | Liver | CD8T | | Last Gift | PID022 | Liver | Myeloid | | Last Gift | PID022 | Liver | Bcell | | Last Gift | PID022 | LN | CD4T | | Last Gift | PID022 | LN | CD8T | | Last Gift | PID022 | LN | Myeloid | | Last Gift | PID022 | LN | Bcell | | Last Gift | PID022 | Repro | CD4T | | Last Gift | PID022 | Repro | CD8T | | Last Gift | PID022 | Repro | Myeloid | | Last Gift | PID022 | Repro | Bcell | | Last Gift | PID022 | Spleen | CD4T | | Last Gift | PID022 | Spleen | CD8T | | Last Gift | PID022 | Spleen | Myeloid | | Last Gift | PID022 | Spleen | Bcell | | Last Gift | PID028 | BM | CD4T | | Last Gift | PID028 | BM | CD8T | | Last Gift | PID028 | BM | Myeloid | | Last Gift | PID028 | BM | Bcell | | Last Gift | PID028 | LN | CD4T | | Last Gift | PID028 | LN | CD8T | | Last Gift | PID028 | LN | Myeloid | | Last Gift | PID028 | LN | Bcell | | Last Gift | PID028 | Spleen | CD4T | | Last Gift | PID028 | Spleen | CD8T | | Last Gift | PID028 | Spleen | Myeloid | | Last Gift | PID028 | Spleen | Bcell | | Last Gift | PID029 | Gut | CD8T | | Last Gift | PID029 | Gut | Bcell | | Last Gift | PID029 | Liver | CD4T | | Last Gift | PID029 | Liver | CD8T | | Last Gift | PID029 | Liver | Myeloid | | Last Gift | PID029 | Liver | Bcell | | Last Gift | PID029 | Repro | CD4T | | Last Gift | PID029 | Repro | CD8T | | Last Gift | PID029 | Repro | Myeloid | | Last Gift | PID029 | Repro | Bcell | | Last Gift | PID029 | Spleen | CD4T | | Last Gift | PID029 | Spleen | CD8T | | Last Gift | PID029 | Spleen | Myeloid | | Last Gift | PID029 | Spleen | Bcell | | Last Gift | PID030 | BM | CD4T | | Last Gift | PID030 | BM | CD8T | | Last Gift | PID030 | BM | Myeloid | | Last Gift | PID030 | BM | Bcell | | Last Gift | PID030 | Gut | CD4T | | Last Gift | PID030 | Gut | CD8T | | Last Gift | PID030 | Gut | Myeloid | | Last Gift | PID030 | Gut | Bcell | | Last Gift | PID030 | Heart | CD4T | | Last Gift | PID030 | Heart | CD8T | | Last Gift | PID030 | Heart | Myeloid | | Last Gift | PID030 | Heart | Bcell | | Last Gift | PID030 | Kidney | CD4T | | Last Gift | PID030 | Kidney | CD8T | | Last Gift | PID030 | Kidney | Myeloid | | Last Gift | PID030 | Kidney | Bcell | | Last Gift | PID030 | Liver | CD4T | | Last Gift | PID030 | Liver | CD8T | | Last Gift | PID030 | Liver | Myeloid | | Last Gift | PID030 | Liver | Bcell | | Last Gift | PID030 | Spleen | CD4T | | Last Gift | PID030 | Spleen | CD8T | | Last Gift | PID030 | Spleen | Myeloid | | Last Gift | PID030 | Spleen | Bcell | | Last Gift | PID031 | Gut | CD4T | | Last Gift | PID031 | Gut | CD8T | | Last Gift | PID031 | Gut | Myeloid | | Last Gift | PID031 | Gut | Bcell | | Last Gift | PID031 | Kidney | CD4T | | Last Gift | PID031 | Kidney | CD8T | | Last Gift | PID031 | Kidney | Myeloid | | Last Gift | PID031 | Liver | CD4T | | Last Gift | PID031 | Liver | CD8T | | Last Gift | PID031 | Liver | Myeloid | | Last Gift | PID031 | LN | CD4T | | Last Gift | PID031 | LN | CD8T | | Last Gift | PID031 | LN | Myeloid | | Last Gift | PID031 | Lung | CD4T | | Last Gift | PID031 | Lung | CD8T | | Last Gift | PID031 | Lung | Myeloid | | Last Gift | PID031 | Lung | Bcell | | Last Gift | PID031 | Spleen | CD4T | | Last Gift | PID031 | Spleen | CD8T | | Last Gift | PID031 | Spleen | Myeloid | | Last Gift | PID033 | Gut | CD4T | | Last Gift | PID033 | Gut | CD8T | | Last Gift | PID033 | Gut | Myeloid | | Last Gift | PID033 | Gut | Bcell | | Last Gift | PID033 | Heart | CD4T | | Last Gift | PID033 | Heart | CD8T | | Last Gift | PID033 | Heart | Myeloid | | Last Gift | PID033 | Kidney | CD4T | | Last Gift | PID033 | Kidney | CD8T | | Last Gift | PID033 | Kidney | Myeloid | | Last Gift | PID033 | Kidney | Bcell | | Last Gift | PID033 | Liver | CD4T | | Last Gift | PID033 | Liver | CD8T | | Last Gift | PID033 | Liver | Myeloid | | Last Gift | PID033 | Lung | CD4T | | Last Gift | PID033 | Lung | CD8T | | Last Gift | PID033 | Lung | Myeloid | | Last Gift | PID033 | Lung | Bcell | | Last Gift | PID033 | Repro | CD4T | | Last Gift | PID033 | Repro | CD8T | | Last Gift | PID033 | Repro | Myeloid | | Last Gift | PID033 | Repro | Bcell | | Last Gift | PID033 | Spleen | CD4T | | Last Gift | PID033 | Spleen | CD8T | | Last Gift | PID033 | Spleen | Myeloid | | Last Gift | PID033 | Spleen | Bcell | | Last Gift | PID034 | Gut | CD4T | | Last Gift | PID034 | Gut | CD8T | | Last Gift | PID034 | Gut | Myeloid | | Last Gift | PID034 | Gut | Bcell | | Last Gift | PID034 | Heart | CD4T | | Last Gift | PID034 | Heart | CD8T | | Last Gift | PID034 | Heart | Myeloid | | Last Gift | PID034 | Heart | Bcell | | Last Gift | PID034 | Kidney | CD4T | | Last Gift | PID034 | Kidney | CD8T | | Last Gift | PID034 | Kidney | Myeloid | | Last Gift | PID034 | Kidney | Bcell | | Last Gift | PID034 | Liver | CD4T | | Last Gift | PID034 | Liver | CD8T | | Last Gift | PID034 | Liver | Myeloid | | Last Gift | PID034 | Liver | Bcell | | Last Gift | PID034 | LN | CD4T | | Last Gift | PID034 | LN | CD8T | | Last Gift | PID034 | LN | Myeloid | | Last Gift | PID034 | LN | Bcell | | Last Gift | PID034 | Repro | CD4T | | Last Gift | PID034 | Repro | CD8T | | Last Gift | PID034 | Repro | Myeloid | | Last Gift | PID034 | Repro | Bcell | | Last Gift | PID034 | Spleen | CD4T | | Last Gift | PID034 | Spleen | CD8T | | Last Gift | PID034 | Spleen | Myeloid | | Last Gift | PID034 | Spleen | Bcell | | D0 | PID91 | PBMCs | CD4Tm | | D0 | PID91 | PBMCs | CD4Tn | | D0 | PID91 | PBMCs | CD8Tm | | D0 | PID91 | PBMCs | CD8Tn | | D0 | PID91 | PBMCs | Myeloid | | D0 | PID91 | PBMCs | Bcell | | D0 | PID92 | PBMCs | CD4Tm | | D0 | PID92 | PBMCs | CD4Tn | | D0 | PID92 | PBMCs | CD8Tm | | D0 | PID92 | PBMCs | CD8Tn | | D0 | PID92 | PBMCs | Myeloid | | D0 | PID92 | PBMCs | Bcell | | D0 | PID93 | PBMCs | CD4Tm | | D0 | PID93 | PBMCs | CD4Tn | | D0 | PID93 | PBMCs | CD8Tm | | D0 | PID93 | PBMCs | CD8Tn | | D0 | PID93 | PBMCs | Myeloid | | D0 | PID93 | PBMCs | Bcell | | D0 | PID94 | PBMCs | CD4Tm | | D0 | PID94 | PBMCs | CD4Tn | | D0 | PID94 | PBMCs | CD8Tm | | D0 | PID94 | PBMCs | CD8Tn | | D0 | PID94 | PBMCs | Myeloid | | D0 | PID94 | PBMCs | Bcell | | HIVneg | PID91 | PBMCs | CD4T | | HIVpos | PID91 | PBMCs | CD4T | | HIVneg | PID91 | PBMCs | Myeloid | | HIVpos | PID91 | PBMCs | Myeloid | | HIVneg | PID92 | PBMCs | CD4T | | HIVpos | PID92 | PBMCs | CD4T | | HIVneg | PID92 | PBMCs | Myeloid | | HIVpos | PID92 | PBMCs | Myeloid | | HIVneg | PID93 | PBMCs | CD4T | | HIVpos | PID93 | PBMCs | CD4T | | HIVneg | PID93 | PBMCs | Myeloid | | HIVpos | PID93 | PBMCs | Myeloid | | HIVneg | PID94 | PBMCs | CD4T | | HIVpos | PID94 | PBMCs | CD4T | | HIVneg | PID94 | PBMCs | Myeloid | | HIVpos | PID94 | PBMCs | Myeloid | | Unfused | PID43482 | PBMCs | CD4Tm | | Fused | PID43482 | PBMCs | CD4Tm | | Unfused | PID43482 | PBMCs | Myeloid | | Fused | PID43482 | PBMCs | Myeloid | | Unfused | PID44750 | PBMCs | CD4Tm | | Fused | PID44750 | PBMCs | CD4Tm | | Unfused | PID44750 | PBMCs | Myeloid | | Fused | PID44750 | PBMCs | Myeloid | | Unfused | PID44890 | PBMCs | CD4Tm | | Fused | PID44890 | PBMCs | CD4Tm | | Unfused | PID44890 | PBMCs | Myeloid | | Fused | PID44890 | PBMCs | Myeloid | | Unfused | PID47000 | PBMCs | CD4Tm | | Fused | PID47000 | PBMCs | CD4Tm | | Unfused | PID47000 | PBMCs | Myeloid | | Fused | PID47000 | PBMCs | Myeloid | | cGAMP | PID24 | PBMCs | CD4Tm | | Mock | PID24 | PBMCs | CD4Tm | | cGAMP | PID24 | PBMCs | Myeloid | | Mock | PID24 | PBMCs | Myeloid | | cGAMP | PID25 | PBMCs | CD4Tm | | Mock | PID25 | PBMCs | CD4Tm | | cGAMP | PID25 | PBMCs | Myeloid | | Mock | PID25 | PBMCs | Myeloid | | cGAMP | PID27 | PBMCs | CD4Tm | | Mock | PID27 | PBMCs | CD4Tm | | cGAMP | PID27 | PBMCs | Myeloid | | Mock | PID27 | PBMCs | Myeloid |