Contact:
Nadia Roan, PhD
Gladstone Institutes
University of California, San Francisco
Nadia.roan@gladstone.ucsf.edu
Nadia.roan@ucsf.edu

Dates of collection:
3/23/19 – 1/16/23

Information about geographic location of data collection:
Original specimens were from individuals in Denmark enrolled in three trials (CLEAR, PMID 26423811; REACH PMID 30932955; and REDUC PMID 27658863) and individuals in USA enrolled in ACTG A5345 (PMID 38329130). CyTOF datasets were generated in San Francisco, California, USA.

Data and File Overview

Included are standard flow cytometry (FCS) files generated from clinical trial specimens of people with HIV (PWH) suppressed on antiretroviral therapy (ART) who underwent analytical treatment interruption (ATI). All specimens were obtained before analytical treatment interruption, and the primary association of the study was the time it took for HIV to rebound to 1,000 copies/ml during the ATI. Specimens from four trials are included. Three trials were interventional trials performed in Denmark: CLEAR wherein participants orally received the latency reversal agent (LRA) panobinostat for 8 weeks (n=9 participants), REDUC wherein participants received therapeutic vaccination followed by intravenous administration of romidepsin as an LRA (n=16 participants), and TEACH wherein participants received the TLR9 agonist lefitolimod as both an LRA and an immune-boosting agent (n=9 participants). The fourth trial was the AIDS Clinical Trials Group (ACTG) trial A5345, a prospective study wherein individuals underwent ATI in the absence of any therapeutic intervention (n=41 participants). All specimens were analyzed by CyTOF using separate phenotyping panels dedicated for T cell or NK cell analysis.

The data files are made available as FCS files, within eight zip files:
A5345_NK_cells.zip
A5345_T_cells.zip
CLEAR_NK_cells.zip
CLEAR_T_cells.zip
REDUC_NK_cells.zip
REDUC_T_cells.zip
TEACH_NK_cells.zip
TEACH_T_cells.zip

The first part of the zip file name refers to the cohort (A5345, CLEAR, REDUC, or TEACH), while the second part refers to the type of cell analyzed (T cells or NK cells). The FCS files within each of these zipped folders includes the cohort identifier (“A5345”, “TEACH”, “CLEAR”, or “REDUC”), a de-identified participant ID (the PID, a 5-6 digit number), and an indication of whether the data were generated using the T cell or NK cell panel (“NKcells” or “Tcells”). T cell datasets were pre-gated on live, singlet CD3+CD19- cells. NK cell datasets were pre-gated on live, singlet CD3-CD19-CD14-CD33- cells for TEACH, CLEAR, and REDUC, and CD3-CD19-CD14-CD33-CD4-CD7- cells for ACTG A5345.

As standard FCS files, the data can be analyzed using conventional flow cytometry software such as FlowJo. Free software to analyze FCS files include https://floreada.io/analysis.

Data-specific information

Please see information under “data and file overview” and “methodological information”. The associated FCS files were generated from PBMCs from ART-suppressed PWH prior to ATI. One primary goal of generating these datasets was to identify immune features associated with time-to-rebound of HIV after ATI. Hence, we have included two tables (uploaded as CSV files, entitled “Table 1” and Table 2” within the “data” section) listing the time-to-rebound of HIV viremia to 1,000 copies/ml (a primary outcome in the study) for each of the analyzed specimen. Table 1 provides the rebound time for the CLEAR, TEACH, and REDUC trials (in days to viral rebound to >1,000 copies/ml HIV RNA), while Table 2 provides the rebound time for the ACTG A5345 trial (in weeks to viral rebound to >1,000 copies/ml HIV RNA). For both Tables 1 and 2, we provide in the first column the cohort name followed by the PID, and in the second column we provide the days or weeks to viral rebound, as appropriate.

In addition, we have included three tables (Tables 1-3) depicting the panels used to generate the CyTOF data. For each table, we depict the antigen specificity of the antibody (first column), the metal label used (second column), and the antibody clone name (third column). Note that antigens labeled with an asterisk were detected at the intracellular level. Table 3 lists the antibody panel for T cell analysis of CLEAR, TEACH, REDUC, and ACTG A5345. Table 4 lists the antibody panel for NK cell analysis of CLEAR, TEACH, and REDUC. Table 5 lists the antibody panel for NK cell analysis of ACTG A5345.

The included tables:
Table1_CLEAR_TEACH_REDUC_DaysRebound.csv
Table2_ACTGA5345_WeeksRebound.csv
Table3_Tcells_CLEAR_TEACH_REDUC_ACTGA5345.csv
Table4_NKcells_CLEAR_TEACH_REDUC.csv
Table5_NKcells_ACTGA5345.xlsx

Sharing and access information

No licenses or restrictions are placed on the data.

Methodological Information

Methods used for generating and analyzing the CyTOF datasets generated from clinical specimens have been previously described:

https://pubmed.ncbi.nlm.nih.gov/35154118/
https://pubmed.ncbi.nlm.nih.gov/39798087/

Human subjects data

We have received consent from participants to published the de-identified CyTOF data in the public domain. Each participant specimen was given an ID number that cannot be traced back to the individual.