DOI: 10.5061/dryad.sqv9s4ngm
title: Data from: Single-cell perturbation atlas of PTB prevention candidate drugs

description: Preterm birth (PTB) is the leading cause of mortality in children under
 five, yet effective preventive therapies are lacking. PTB’s multifactorial
 nature, as well as the high cost and ethical challenges of pregnancy
 clinical trials, hinder drug development efforts. Meanwhile, targeting
 immune pathways that regulate labor timing is emerging as a promising
 preventive strategy. We present Simulated Immune Modeling of Clinical
 Outcomes (SIMCO), a prediction ensemble that integrates single-cell immune
 perturbation modeling with outcome prediction to rapidly evaluate PTB
 prevention candidate drugs. To train SIMCO, we generated a mass cytometry
 perturbation atlas of 218 million leukocytes, capturing drug effects on
 specific cell types and signaling pathways that differed between pregnant
 and non-pregnant individuals. SIMCO accurately recapitulated the
 single-cell modulation induced by nine repurposed candidate drugs. When
 applied to an independent longitudinal pregnancy cohort, SIMCO simulated
 each drug’s effect on gestational length, offering a scalable framework
 for drug prioritization. Tetrahydrofolate, maprotiline, and the
 combination of aspirin and lansoprazole emerged as top candidates for PTB
 prevention, delaying labor onset in preterm samples by 9.2 (± 2.1), 9.2 (±
 1.2), and 6.5 (± 1.8) days, respectively, primarily through enhanced mTOR
 signaling in innate immune cells and attenuated JAK/STAT signaling in
 naïve CD4⁺ T cells. This upload includes all raw .fcs files generated for
 the single-cell perturbation atlas pre-gated into 28 cell types via manual
 gating.
description: # Data from: Single-cell perturbation atlas of PTB prevention candidate
 drugs Dataset DOI: [10.5061/dryad.sqv9s4ngm](10.5061/dryad.sqv9s4ngm) ##
 Description of the data and file structure From 19 individuals (n = 11
 pregnant individuals, PV01-PV11, and n = 8 non-pregnant individuals,
 HV04-HV11), whole blood was exposed to nine candidate drugs for preterm
 birth. Candidate drugs are abbreviated as follows: chlorthalidone (CHT),
 maprotiline (MAP), metformin (MF), lansoprazole (LPZ), pravastatin (PRA),
 rifabutin (RIF), salicylic acid (SA), salicylic acid + lansoprazole
 (SALPZ), and 5-methyltetrahydrofolate (THF). Dimethyl sulfoxide (DMSO) was
 used in triplicate (DMSO1, DMSO2, DMSO3) as no-drug control. After 1 h of
 drug exposure, the in vitro cultured whole blood was stimulated with LPS
 (50 ng/ml), IFNα (50 ng/ml), IL-33 (50 ng/ml), GM-CSF (50 ng/ml), TNFα (50
 ng/ml), a cocktail of IL-2, IL-4, and IL-6 (each 50 ng/ml), PI (0.5×), or
 left unstimulated for 2 h at 37 °C and 5 % CO~2~ in a humidified
 incubator. Per individual, 96 conditions were tested (8 stimulation
 conditions × 12 treatment conditions). Mass cytometry was used to detect
 28 cell types and 20 functional markers per single-cell. ## Data structure
 Filenames (e.g., PTB_HV03_DMSO1_Unstim_Granulocytes.fcs) correspond to
 study abbreviation (PTB), individual (HV03), treatment (DMSO1),
 stimulation (Unstim), and cell population (Granulocytes). For each
 individual, there are 28 cell types × 96 conditions = 2688 files. The
 files are stored as .zip: PTB_HV_individuals.zip (all files for the eight
 non-pregnant individuals) and PTB_PV_individuals.zip (all files for the 11
 pregnant individuals). ## Code/software Cellengine.com was used for manual
 gating and export of the cell type specific .fcs files.