Abstract
Stimulator of interferon genes (STING) agonists and derivative molecules have 20
been extensively developed for tumor immunotherapy. However, systemic exposure toxicity 21
risks have constrained clinical trial progression and even threatened patient lives. Currently, 22
systematic toxicity assessments for STING agonists remain lacking, with the mode of action 23
for major organ injury yet to be elucidated. Here, we focused on STING agonist-induced lung 24
injury, revealing that systemic administration of STING agonists caused pulmonary 25
hemorrhage, inflammatory alterations, and respiratory dysfunction. Through single-cell RNA 26
sequencing and immune deletion studies, we found that lung endothelial cells could be 27
stimulated by STING agonists and then secreted chemokines and IL-15 to recruit and activate 28
NK cells. NK cells could induce endothelial cell apoptosis via IFN-γ. Tbx21+ NK 29
subpopulations, which activated by endothelial cells, could produce chemokines to recruit 30
neutrophils. Neutrophils secreted IL-1β through positive feedback pathways and form 31
neutrophil extracellular traps during lung injury. This study elucidates the critical role of the 32
endothelial cell-NK cell-neutrophil axis in mediating STING agonist-associated pneumonia, 33
offering insights for developing intervention strategies for STING agonist toxicity. 34
35
Keywords
STING agonist, pulmonary inflammation, immunotoxicology 36
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Introduction
37
The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway 38
detects pathogen DNA or damage-associated molecular patterns (DAMPs) DNA, serving a 39
vital function in the host's defense against infections and malignancies. cGAS, as a double-40
stranded DNA sensor, catalyzes the production of 2’3’ cyclic GMP-AMP (cGAMP)-the 41
endogenous ligand for STING-upon activation [1]. Subsequently, activated STING transfers 42
from the endoplasmic reticulum to the Golgi apparatus and promotes downstream effects 43
such as interferon (IFN) signaling, inflammasome activation, and light-chain 3B (LC3B) 44
lipidation through processes including TBK1-IRF3, NFκB, and proton leakage [2]. 45
Activation of the STING signaling promotes the antitumor effects of dendritic cells (DCs), 46
CD8+ T cells, natural killer (NK) cells, etc[3]. Besides, studies have further proposed that 47
STING activation in vascular endothelial cells can remodel the tumor vasculature [4] and 48
alter the structure of the tumor immune microenvironment in “cold” tumors [5]. 49
The anti-tumor effects of STING agonists were first observed in the cGAMP [6]. Studies 50
have demonstrated that injecting cGAMP into the glioma significantly reduces tumor volume 51
and improves survival rates of tumor-bearing mice in a STING-dependent manner [7]. 52
Meanwhile, amidobenzimidazole (ABZI)-based analogs were designed to improve systemic 53
delivery, which can bind to the C-terminal domain of STING and enhance the biding affinity. 54
The representative one is diABZI from linked ABZIs, which showed a potent effect in 55
ameliorating the affinity to STING and inducing the secretion of IFN-β in human peripheral 56
blood mononuclear cells (PBMCs). Administration of diABZI in mice bearing CT26 57
colorectal tumors resulted in significant tumor inhibition and enhanced survival, with 80% of 58
mice being tumor free [8]. Considering of the superior antitumor effects, numerous STING 59
agonists have now entered clinical development phases. For example, ADU-S100 [9] and 60
E7766 have been employed for treating advanced solid tumors or lymphoma [10]. Beyond 61
this, antibody-drug conjugates (ADCs) targeting STING agonists have also emerged as a 62
focal point in antitumor drug development. Examples include Takeda Pharmaceutical 63
Company's STING agonist-linked ADC, TAK-500, which targets CCR2 [11]. 64
However, multiple studies have raised concerns regarding the safety of STING agonists. 65
The injection of small-molecule STING agonists may lead to rapid systemic distribution, 66
thereby posing risks of uncontrolled inflammation and cytokine storms, tissue toxicity, and 67
autoimmune damage [12]. Chronic STING activation may also persistently stimulate 68
cytokine production, thereby fostering an inflammatory tumor microenvironment (TME) that 69
promotes tumor progression [13]. Meanwhile, Mersana's STING agonist-conjugated 70
antibody-drug conjugate XMT-2056, targeting HER2, has experienced a Grade 5 (fatal) 71
serious adverse event (SAE) in its Phase I clinical trial. The company then has announced a 72
voluntary suspension of the trial [14]. In non-human primates preclinical studies of E7766, 73
participating animals exhibited multiple respiratory adverse reactions including dyspnea, 74
hemoptysis, hypoxia, alveolar hemorrhage, pulmonary embolism, and pulmonary oedema 75
[10]. It is evident that the toxicity issues associated with STING agonists have resulted in a 76
narrow therapeutic window during clinical trials, thereby hindering dose escalation and 77
preventing trials from achieving efficacy endpoints. 78
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And recent studies increasingly indicate that activation of the cGAS-STING pathway 79
promotes or exacerbates the development of pneumonia. For instance, following DNA 80
recognition by macrophages, the STING pathway is activated, triggering IL-6 release which 81
subsequently activates fibroblasts and intensifies airway obstruction [15]. 82
Safety concerns regarding STING agonists, such as pulmonary toxicity, have severely 83
limited their clinical development. Therefore, in this study, we focused on systematically 84
evaluating the pulmonary toxicity risk of STING agonists, identifying the characteristics of 85
lung injury induced by STING agonists, and elucidating the underlying mechanisms. 86
87
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Results
88
Systemic administration of STING agonists causes lung injury in mice 89
Analysis of human single-cell databases revealed that STING is highly expressed in lung 90
tissues compared to other organs (Fig S1A). This led us to hypothesize that the lung is the 91
most likely target organ for STING agonist toxicity. Thus, we administered the human-mouse 92
cross-reactive STING-specific agonist diABZI [8] to mice and measured inflammatory 93
cytokine expression in lung, liver, kidney, and intestinal tissues. Lung tissues exhibited the 94
most significantly upregulated transcription levels of tumor necrosis factor-alpha (TNF-α), 95
interleukin-1 beta (IL-1β), and IFN-γ (Fig S1B). 96
To holistically evaluate the in vivo toxicity responses of diABZI, a concentration gradient 97
dosing regimen was established. Following intraperitoneal diABZI administration, mice 98
exhibited significant weight loss alongside elevated lung coefficients and wet-to-dry weight 99
ratios (Fig S1C, Fig 1A and B), preliminarily confirming STING agonist-induced pulmonary 100
injury. To confirm that diABZI-induced pneumonia is indeed caused by STING activation, 101
we administered natural ligand of STING, 2',3'-cGAMP to mice in vivo. The results mirrored 102
those observed with diABZI administration: the mice exhibited weight loss and elevated 103
expression of inflammatory cytokines in lung tissue (Fig S1D). Based on the the above 104
indicators, a 2 mg/kg dose was selected for subsequent in vivo assays. Further assessment of 105
pulmonary function during treatment revealed reduced peak expiratory flow rates and 106
increased respiratory rates (Fig 1B), indicating ventilatory dysfunction and respiratory 107
impairment. Histopathological examination revealed hemorrhage, congestion, disrupted 108
alveolar architecture, and increased immune cell infiltration in the lungs of diABZI-treated 109
mice (Fig 1C). Surfactant protein A (SP-A), which typically regulates alveolar gas exchange, 110
exhibits serum level elevation associated with pulmonary tissue injury [16, 17]. Western blot 111
analysis demonstrated a significant increase in serum SP-A levels 48 hours post diABZI 112
administration (Fig 1D). 113
Concurrently, the transcriptional levels of inflammatory cytokines IL-1β, IFN-γ, and IL-18 114
were substantially upregulated, rapidly peaking within 4 hours post-administration. 115
Following a decline at 6 hours, levels gradually rebounded to reach a plateau at 24 hours, 116
maintaining elevated expression thereafter (Fig 1E-G). Similarly, in vivo administration of 117
cGAMP also resulted in a significant increase in IFN-γ and IL-1β in lung tissues (Fig S2). 118
Flow cytometry analysis revealed a rapid and significant reduction in the proportion of T/B 119
lymphocytes within the pulmonary immune microenvironment following diABZI 120
administration. Regarding myeloid cells, the STING agonist induced increased neutrophil and 121
macrophage infiltration, reaching a plateau within 24 hours, concurrent with enhanced pro-122
inflammatory polarization of pulmonary macrophages (Fig 1H and I). 123
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In summary, STING agonists possessed significant pulmonary toxicity risks, potentially 124
leading to pathological lung injury, immune dysregulation, and impaired respiratory function. 125
Single-cell sequencing reveals alterations and interactions in pulmonary cell populations 126
post STING activation 127
To elucidate the alterations in cell population proportions, gene expression changes, and 128
cellular interactions induced by STING agonists, single-cell RNA sequencing (scRNA-seq) 129
was performed on mouse lung tissue collected at 0, 4, 6, 12, and 24 hours post intraperitoneal 130
administration of diABZI. Following t-SNE dimensionality reduction, the data were 131
identified as 12 distinct cell populations. T cells and B cells exhibited markedly reduced 132
proportions following administration, whereas neutrophil and macrophage proportions 133
significantly increased (Fig 2A), consistent with flow cytometry results (Fig 1H and I). 134
Notably, NK cells, macrophages, T cells, and B cells exhibited high STING expression at rest 135
(Fig 2B). Following STING agonist administration, the IFN-α response pathway was 136
substantially activated in endothelial cells, neutrophils, and monocytes, with increased gene 137
expression (Fig 2C). Previously, we demonstrated that diABZI induced elevated expression 138
of pulmonary inflammatory cytokines IL-1β and IFN-γ (Fig 1E). Further analysis of scRNA-139
seq data revealed that myeloid cells, particularly neutrophils, constitute the primary IL-1β-140
secreting population, peaking at 12 hours post treatment. Conversely, NK cells predominantly 141
secreted IFN-γ, peaking at 4 hours; in contrast, other cell populations exhibited negligible 142
IFN-γ secretion (Fig 2D). Combined with scRNA-seq data, flow cytometry results indicate 143
significant alterations in the proportion of pulmonary immune cell populations within 4 hours 144
post-administration. 145
To investigate the mechanisms underlying changes in the proportion of pulmonary 146
immune cell populations, we analyzed levels of CC and CXC subfamily chemokines. Within 147
4 hours post-administration, Cxcl1, Cxcl2, Cxcl9, Cxcl10, Ccl3, Ccl4, and Ccl5 were 148
significantly upregulated (Fig. S3A). Analysis of these chemokine expression levels at 0 and 149
4 hours by cell population revealed that multiple cell types upregulate chemokine expression 150
following administration. Specifically, DCs, endothelial cells, NK cells, neutrophils, and 151
monocyte-macrophages exhibited markedly elevated chemokine expression (Fig. 2E). This 152
suggests potential interactions and chemotaxis between these cell types following STING 153
agonist administration. 154
To validate this hypothesis, we employed CellChat for scRNA-seq data analysis and 155
visualization of cellular communications. Results demonstrated that both the number and 156
strength of cellular communication rapidly increased following drug administration, peaking 157
at 4 hours. Subsequently, communications gradually diminished at 4 hours yet remained 158
elevated compared to resting conditions (Fig. S3B). Scatter plots visualizing signal input and 159
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output probabilities across cell populations at different time points revealed that NK cell 160
communication probability substantially increased within 4 hours, while neutrophil and 161
endothelial cell output probabilities significantly rose. At 12 hours, neutrophil signal 162
exchange probability peaked, with intercellular communication probabilities subsequently 163
declining post-12 hours (Fig. 2F). Further analysis of specific interacting cell populations and 164
communication intensity revealed that between 0-4 hours, neutrophils and endothelial cells 165
transmitted signals to NK cells, with NK cells exhibiting the strongest signal reception 166
intensity; between 4 and 6 hours, the strength of signals transmitted by epithelial cells 167
increased, primarily received by NK cells, neutrophils, and macrophages; at 12 hours, 168
neutrophils replaced NK cells as the cell population receiving the strongest signals, primarily 169
from NK cells, macrophages, and self-activation; compared to 12 hours, at 24 hours, signal 170
exchange from non-immune cells, including endothelial and epithelial cells, was enhanced 171
(Fig. 2G). 172
Taken together, we hypothesized that after STING agonist administration, endothelial 173
cells may recruit and activate NK cells in the early phase, and then NK cells may secrete 174
IFN-γ and other chemokines, thereby acting upon neutrophils to enhance their infiltration and 175
IL-1β secretion. 176
Endothelial cells can be directly activated by SITNG agonists 177
Following systemic administration, pulmonary vascular endothelial cells constitute the 178
primary line of direct contact with STING agonists. Analysis of differentially expressed 179
genes and IFNα response pathway genes in pulmonary endothelial cells revealed substantial 180
pathway activation within 4 hours, concurrent with upregulation of chemokines Cxcl9, 181
Cxcl10, Ccl4, Ccl5, and classical NK cell activation factors Il15 (Fig. 3A-C) . 182
To determine whether endothelial cells could be directly activated by STING agonists, 183
we directly treated human pulmonary microvascular endothelial cell line (HPMEC) with 184
diABZI. Western Blot analysis confirmed that at working concentrations, diABZI 185
significantly increased the phosphorylation levels of STING and TBK1 (Fig. 3D). Validation 186
in mouse cell lines revealed that diABZI directly activated mouse pulmonary endothelial cells 187
(MPMVEC-SV40) and upregulated chemokines (Fig. S4A). 188
Next, to validate in vitro whether STING activation promotes endothelial cell chemotaxis 189
and inflammatory cytokine secretion, and to investigate the underlying mechanisms, we 190
analyzed pathways enriched in endothelial cell differentially expressed genes at 4 h post-191
treatment compared to 0 h in scRNA-seq data. Differentially expressed genes enriched in NF-192
κB, MAPK-CREB-TGF-β, and Wnt-related pathways (Fig. 3E). Targeting these enriched 193
pathways, TBK1-IRF3 pathway and LC3B lipidation, we assessed whether cytokine secretion 194
levels were affected by adding pathway-specific inhibitors to STING activation. Results 195
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indicated that the secretion of nearly all factors depended on IRF3 activation. Cxcl9 196
expression relied on CREB pathway activation. Cxcl10 expression was linked to LC3B 197
lipidation and other pathways but independent of NF-κB. Ccl5 expression mechanisms 198
resembled Cxcl9, largely dependent on CREB pathway activation. Whereas Il15, similar to 199
Cxcl10, was influenced by multiple pathways including LC3B lipidation (Fig. 3F). 200
Moreover, we were also investigating whether STING's newly discovered proton pump 201
function was involved in these processes [18]. Compound 53 is a STING agonist that inhibits 202
the function of the STING proton pump [2]. HPMECs activated by diABZI significantly 203
upregulated Ccl4, Ccl5, Cxcl9, Cxcl10, and Il15 expression, whereas Compound 53 204
administration markedly attenuated the upregulation of Cxcl10 and Il15 (Fig. 3G), suggesting 205
that this function depended on the STING proton pump. 206
In vivo, to confirm this process was indeed independent of other pulmonary immune 207
cells, we modelled NCG immunodeficient mice with equivalent diABZI doses and assessed 208
representative pulmonary chemokine levels. Results showed Cxcl10 and Ccl5 remained 209
significantly upregulated (Fig. 3H). To exclude interference from other non-immune cells, we 210
administered identical doses of diABZI to HPMEC, human lung epithelial cells (BEAS-2B), 211
and human lung fibroblasts (HLF-1) in vitro. Endothelial cells exhibited significantly higher 212
cytokine upregulation compared to epithelial and fibroblast cells (Fig. S3B). 213
Endothelial cells activated by STING agonists can recruit NK cells 214
Previously, we observed that within 4 hours of administration, the probability of endothelial 215
cell signal transmission increased substantially, with signals being communicated to NK cells 216
(Fig. 2, F and G). Given that STING agonists promoted endothelial cell expression of 217
chemokines, pulmonary endothelial cells we hypothesized that activated pulmonary 218
endothelial cells may recruit NK cells. Thus, we conducted transwell assays using both the 219
NK-92 cell line and primary NK cells isolated from human PBMCs. Results demonstrated 220
that, compared to the vehicle group, endothelial cells activated by diABZI attracted more NK 221
cells into the lower chamber (Fig. 3, I and J). 222
NK cells activated by endothelial cells produce IFN-γ to damage endothelial cells 223
Previously, we observed that activated endothelial cells could expression NK cell activator 224
IL-15. In subsequent experiments, we investigated the changes occurring in NK cells 225
following signal reception. Therefore, we continued to analyze whether the recruited NK 226
cells would be further activated. 227
scRNA-seq data revealed that STING expression in NK cells within the lungs rapidly 228
increased within 0–4 hours post-administration, with genes in the IFN-α response pathway 229
significantly upregulated (Fig. 4A) and signal reception intensity substantially elevated (Fig. 230
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2, F and G). To investigate the effects of factors secreted by endothelial cells on NK cells, 231
HPMECs were cultured in medium containing diABZI for 4 hours. NK-92 cells were 232
cultured in this medium for 4 hours, after which they were harvested for gene expression 233
analysis. Results revealed that upon receiving endothelial activation signals, NK-92 cells 234
exhibited markedly elevated expression of Ccl4, the classical receptor Ccr5 for CCL5, the 235
receptor Il15ra for IL-15, and Ifng. (Fig. 2E) Moreover, direct activation of NK-92 cells with 236
diABZI did not induce this upregulation (Fig. 4B), suggesting that the above changes 237
depended on endothelial cell-secreted factors. 238
Further analysis of NK cells in scRNA-seq data revealed four distinct subpopulations 239
after dimensionality reduction. Heatmaps indicated that clusters 0 and 1 predominantly 240
comprised Ifng-expression populations (Fig. 4C). Literature indicates that IFN-γ promotes 241
endothelial cell apoptosis, compromising the integrity of the endothelial barrier [19, 20]. We 242
hypothesized that activated NK cells could secrete elevated levels of IFN-γ, thereby 243
promoting endothelial cell apoptosis. scRNA-seq data revealed significantly increased 244
expression of endothelial apoptosis pathway genes within 0–4 hours post intraperitoneal 245
administration (Fig. 4D). Following 24-hour co-culture of NK-92 and HPMEC cells at 0:1, 246
3:1 and 5:1 ratio in vitro, NK-92 cells were removed, and then we add CCK-8 to detect the 247
viability of HPMECs. We observed a significant decrease in relative cell viability of 248
endothelial cells post-co-culture with NK-92 cells, indicating heightened endothelial cell 249
death (Fig. 4E). Then, in vivo, the neutralizing antibodies against CXCL10/CCL5/IL-15/IFN-250
γ/IL-1β were administered separately with diABZI. Through flow cytometry, results showed 251
that STING agonist reduced the proportion of pulmonary endothelial cells, indicating the 252
impairment of the endothelial barrier. Neutralizing IFN-γ mitigated this reduction, indicating 253
that NK cell activation and the IFN-γ they secrete exert damaging effects on the endothelium 254
(Fig. 4F), demonstrating the important role of IFN-γ, primarily expressed by NK cells, in this 255
process. 256
Taken together, we discovered that STING agonists could directly activate endothelial 257
cells, promoting their recruitment and activation of NK cells, and then the activated NK cells 258
could induce endothelial cell apoptosis via IFN-γ. 259
Tbx21+ NK cells activated by endothelial cells produce chemokines to recruit 260
neutrophils 261
Further analysis of NK cell alterations following administration of STING agonists, cell 262
interaction data indicated that, the strength of NK cell-to-neutrophil communication 263
progressively increased (Fig. 2G). Concurrently, neutrophil infiltration within lung tissue 264
substantially increased (Fig. 1I and 2A). Previous studies have demonstrated that during acute 265
lung injury, NK cells upregulate T-bet expression and secrete CXCL1/2 to chemotactically 266
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recruit CXCR2+ neutrophils, thereby exacerbating disease progression [21]. Therefore, we 267
subsequently analyzed the interactions between NK cells and neutrophils. 268
Analysis of NK cell T-bet (Tbx21) expression at different time points post administration, 269
we found that STING agonists significantly upregulated Tbx21 expression in cluster0/1 NK 270
cells (Fig. 5A). NicheNet analysis of the Tbx21+ NK population predicted downstream target 271
genes potentially upregulated following NK cell activation by endothelial cell-derived 272
ligands. Circos plot results indicated that cluster0/1 NK cells, upon receiving Ccl4, Ccl5 and 273
Il15 signals from endothelial cells, leading to increased expression of chemokines Ccl3, Ccl4, 274
Cxcl10, Ccr5, and Ifng (Fig. 5B). Moreover, within 0-4 hours, differentially expressed genes 275
in cluster 0 NK cells enriched for neutrophil chemotaxis related pathways (Fig. 5C). Thus, 276
single-cell data analysis preliminarily validated our hypothesis. 277
Subsequently, we assessed the secretion levels of various chemokines by NK-92 cells 278
activated by endothelial cells. Specifically, direct diABZI treatment of NK-92 cells markedly 279
increased Ccl3/Ccl4/Cxcl10 expression. In contrast, Cxcl1/Cxcl2/Cxcl10 expression was 280
significantly amplified by endothelial cell activation signals (Fig. 5D). 281
Neutrophils secrete IL-1β through positive feedback pathways and form NETs during 282
lung injury. 283
The aforementioned experiments have demonstrated that within a short period following 284
STING agonist administration, NK cells activated by endothelial cells recruit a substantial 285
infiltration of neutrophils into the pulmonary immune microenvironment. Furthermore, 286
neutrophil signaling activity peaks at 12 hours (Fig. 2F and G), with IL-1β secretion reaching 287
its highest level at this time point (Fig. 2D). To investigate how recruited neutrophils mediate 288
lung injury, differential gene analysis and pathway enrichment of 12-hour neutrophils from 289
scRNA-seq data were performed (Fig. 6A). Differentially expressed genes were enriched not 290
only in chemotaxis but also in neutrophil extracellular trap (NET) formation and related 291
pathways (Fig. 6B). Previous studies have demonstrated that in acute lung injury in mice, 292
NETs exacerbate disease progression by mediating parenchymal cell death [22, 23]. 293
Both multiplex immunofluorescence assays and western blot confirmed increased NETs 294
during STING agonist-mediated pulmonary injury (Fig. 6B and 6C). To validate the 295
contributions of potential immune cells and cytokines, we employed neutralizing antibodies 296
to eliminate NK cells, neutrophils, and interstitial macrophages, and neutralized IL-1β in the 297
diABZI treatment models. Pulmonary tissues expression of the NET marker MPO was 298
assessed by Western blot. Results demonstrated that STING agonists increased pulmonary 299
MPO expression, whilst depletion of NK cells, neutrophils, and interstitial macrophages, and 300
neutralization of IL-1β, all reduced pulmonary MPO levels (Fig. 6C). 301
Take together, recruited neutrophils may cause lung injury through NETs. 302
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Immune cells depletion and cytokine neutralization in vivo validates the mechanism of 303
lung injury caused by STING agonist. 304
To validate the contribution of the aforementioned immune cells and cytokines to the STING-305
mediated toxicity mechanism, we performed immune cell depletion and cytokine 306
neutralization in mice. For neutrophils, which exhibited the most pronounced infiltration 307
increase post-treatment, NK cell depletion reduced their proportion among total lung cells, 308
confirming the chemotactic effect of NK cells on neutrophils during lung injury. Neutralizing 309
IL-1β reduced the increased NK cell infiltration, whereas neutrophil depletion further 310
exacerbated NK cell infiltration. Regarding the markedly reduced pulmonary endothelial 311
cells post treatment, the proportion rebounded following depletion of NK cells, neutrophils, 312
or macrophages, suggesting the role of these three cell types in STING agonist induced 313
pulmonary injury. Neutrophil depletion or IL-1β neutralization partially mitigated the 314
increased interstitial macrophages infiltration, suggesting neutrophils and their secreted IL-1β 315
may exert chemotactic effects on interstitial macrophages (Fig. 7A). 316
RT-qPCR analysis of inflammatory cytokines and chemokines in lung tissues confirmed 317
that IL-1β was primarily secreted by neutrophils. Depletion of NK cells and macrophages, 318
alongside IL-1β neutralization, partially alleviated this upregulation. These findings indicated 319
that NK cell depletion indeed reduced neutrophil infiltration, thereby lowering IL-1β 320
secretion levels, with IL-1β secretion potentially exhibiting a positive feedback response. 321
Regarding IFN-γ, primarily secreted by NK cells, deletion of neutrophils reduced its secretion 322
levels, further validating the interaction between NK cells and neutrophils in the toxic 323
mechanism. Overall, deletion of macrophages, neutrophils, NK cells, or neutralization of IL-324
1β reduced chemokines production to varying degrees. However, STING agonist-induced 325
Ccl5 upregulation was largely unaffected by these immune cell deletions, suggesting that 326
Ccl5 elevation depends on other non-immune cells, including endothelial cells (Fig. 7B). 327
This directly demonstrated that these immune cells and inflammatory mediators 328
contribute to STING agonist-induced lung injury. 329
Discussion
330
In this study, we have demonstrated the crucial role of the “endothelial-NK-neutrophil” 331
axis in the pulmonary toxicity of STING agonists. 332
To investigate the effects of STING agonists on the pulmonary immune 333
microenvironment and gene expression, we performed dynamic monitoring of mouse lung 334
tissue at different time points post administration using single-cell RNA-seq and flow 335
cytometry. We observed that STING agonists induced dramatic alterations in the immune 336
microenvironment within a short timeframe. During the early phase, the proportion of T and 337
B lymphocytes plummeted. In fact, this phenomenon has been observed in multiple studies 338
involving gain-of-function STING mutation mice, as well as in experiments involving the 339
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administration of STING agonists such as cGAMP [24-26]. Mechanistically, existing studies 340
suggest this is unrelated to interferon signaling or the canonical IRF3 pathway, and may 341
instead be associated with endoplasmic reticulum stress [27-30]. Studies have also indicated 342
that high-dose intratumoral administration of STING agonists can inhibit the expansion of 343
anti-tumor CD8+ T cells [31]. This immunotoxicity effect of STING agonists may 344
compromise their sustained antitumor activity. 345
Cell communication analysis revealed that during the early phase, pulmonary vascular 346
endothelial cells served as the primary signal emitters, with NK cells acting as the core signal 347
recipients. This suggests that endothelial cells, being the first to encounter circulating STING 348
agonists, may be primed for activation and subsequently initiate immune cell recruitment. 349
The role of endothelial cells in lung injury is gradually being recognized. For example, 350
researchers found that overexpression of cGAS in pulmonary endothelial cells promotes its 351
expression of CCL5 to recruit T cells [32]. These T cells then secrete IFN-γ, causing 352
endothelial damage that mediates the development of pneumonia. Furthermore, multiple 353
studies using STING N153S gain-of-function mice have revealed that sustained STING 354
activation leads to severe pneumonia in these animals [26, 33]. Chimeric mouse experiments 355
indicate that STING activation in endothelial cells initiates pneumonia, but its progression 356
still requires STING activation in immune cells [34, 35]. 357
Both NicheNet predictions from scRNA-seq and in vitro transwell assays confirmed that 358
NK cells activated by endothelial cells exhibit a phenotype characterized by high expression 359
of the transcription factor T-bet (Tbx21), secreting factors such as CXCL1, CXCL2, and 360
CXCL10. These factors strongly recruit neutrophils to lung tissue by acting on receptors 361
including CXCR2 on neutrophil surfaces [21, 36, 37]. 362
Of course, our study has many limitations, and further research is needed. For instances, 363
we have identified the role of NK cells and neutrophils in the pulmonary toxicity of STING 364
agonists, but have not evaluated their function in the antitumor efficacy of STING agonists. 365
This limitation constrains research into the efficacy-toxicity balance of STING agonists. On 366
the other hand, this study did not propose specific STING toxicity intervention strategies. In 367
future studies, we plan to modify STING agonists to avoid their action on endothelial cells, or 368
to combine them with drugs that ameliorate endothelial injury. 369
In summary, this study systematically characterized the pulmonary toxicity phenotype of 370
STING agonists and elucidated the pathogenesis dependent on the endothelial cell-NK cell-371
neutrophil axis. Following administration of the STING agonists, pulmonary endothelial cells 372
were initially targeted. Upon activation, they recruited NK cells via CCL5 and further 373
activated NK cells through IL-15. Activated NK cells promoted endothelial cell apoptosis via 374
IFN-γ and recruited neutrophils via the CXCL2-CXCR2 axis. Neutrophils then caused lung 375
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injury through NETs, with IL-1β playing a pivotal role in this positive feedback loop. Our 376
research offers insights for developing safer STING agonists in the future, thereby enhancing 377
their potential for clinical application. 378
Methods
379
Mice. Male six- to eight-week-old C57BL/6 mice were purchased from Vital River. NCG 380
mice were purchased from GemPharmatech Co., Ltd. All mice were maintained under 381
specific pathogen-free (SPF) conditions in the animal facility of the Shanghai Institute of 382
Materia Medica, Chinese Academy of Sciences. Animal care and experiments were 383
performed in accordance with the Shanghai Institute of Materia Medica, Chinese Academy of 384
Sciences, using protocols approved by the Institutional Laboratory Animal Care and Use 385
Committee (IACUC). 386
387
Establishment of a STING agonist-mediated pulmonary inflammation model. diABZI 388
STING agonist-1 (TargetMol, T11035) was dissolved in DMSO to prepare a 40 mg/mL stock 389
solution. The administration concentration of diABZI is 2 mg/kg (200 μL, dissolved in 40% 390
PEG 300 + 8% Tween-80, then diluted to volume with saline). The pneumonia model was 391
established via intraperitoneal injection on consecutive 3 days (D0-D2). On day D3, blood 392
was collected from the posterior orbital sinus under anesthesia. Following blood collection, 393
mice were euthanized. Lung tissues were rapidly frozen in dry ice for RNA extraction or 394
fixed in formalin solution for paraffin sectioning. 395
396
Cells. NK-92 cell lines were purchased from SUNNCELL and HPMEC cell lines were 397
purchased from IMMOCELL. HPMEC and NK-92 cells were cultured in their respective 398
dedicated media. Human PBMCs were purchased from Milestone. All cells were cultured at 399
37° C in a 5% CO2 humidified atmosphere. 400
401
Immune deletion and cytokine neutralization. In the STING-associated pneumonia model, 402
anti-mouse immune cell deletion antibody (200 μg/animal; Starter) was administered 403
intraperitoneally on days D-1 and D1. On day -1, administer cytokine-neutralizing antibody 404
(200 μg/animal; BioXcell) via intraperitoneal injection. On days 0, 1, and 2, administer 405
cytokine-neutralizing antibody (100 μg/animal; BioXcell) via intraperitoneal injection to 406
maintain neutralizing effects. 407
408
Immunophenotype analysis. After obtaining the whole mouse lung, mince it and place it in 409
digestion buffer (3 mL phenol red-free RPMI 1640 + 2.1 mg collagenase I). Shake at 37° C 410
and 220 rpm for 30 minutes. Subsequently, filter the digested solution through a 70 μm filter 411
membrane. Centrifuge, then lyse with erythrocyte lysis buffer at room temperature for 8 412
minutes. Filter again after lysis, then centrifuged, washed, and resuspended to obtain a single-413
cell suspension. Then the cells were blocked with 4% FBS and anti-CD16/32 (BD 414
Biosciences), incubated with surface marker antibodies for 20 minutes at 4℃. Flow 415
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cytometry analysis was performed using ACEA NovoCyte and data processing was done 416
through NovoExpress software. Antibody staining was performed following the 417
manufacturer’s recommendations. 418
419
Immunofluorescence. NETs visualization was performed using immunofluorescence 420
confocal microscopy. Formalin-fixed and paraffin-embedded lung specimens from mice were 421
stained with anti-citrullinated histone-3 (citH3, 1:200; Abcam) and anti-myeloperoxidase 422
(diluted 1:200; Abcam 134132), a polyclonal goat anti-mouse Alexa Fluorite 647 antibody 423
(Thermo Fisher) and anti-rabbit Alexa Fluorite 488 antibody (Thermo Fisher) as secondary 424
Abs. The DNA was stained using DAPI (Sigma-Aldrich). All the samples were observed 425
under laser scanning confocal microscopy. 426
427
Cell preparation single cell for RNA-seq. After harvested, lung tissues were washed in ice-428
cold PBS (Hyclone SH30256.01) and dissociated using SeekMate Tissue Dissociation 429
Reagent Kit A Pro (SeekGene K01801-30) from SeekGene as instructions. DNase Ⅰ (Sigma 430
9003-98-9) treatment was optional according to the viscosity of the homogenate. Cell count 431
and viability was estimated using SeekMate Tinitan Fluorescence Cell Counter (SeekGene 432
M002C) with AO/PI reagent after removal erythrocytes (Solarbio R1010) and then debris and 433
dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). 434
Finally fresh cells were washed twice in the RPMI1640 (Gibco 11875119) and then 435
resuspended at 1×106 cells per ml in RPMI1640 and 2% FBS (Gibco 10100147C). 436
437
Single cell RNA-seq library construction and sequencing. Single-cell RNA-Seq libraries 438
were prepared using SeekOne® DD Single Cell 3’ library preparation kit (SeekGene Catalog 439
No.K00202). Briefly, appropriate number of cells were mixed with reverse transcription 440
reagent and then added to the sample well in SeekOne® chip S3. Subsequently Barcoded 441
Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells 442
separately in chip S3. After emulsion droplet generation reverse transcription were performed 443
at 42℃for 90 minutes and inactivated at 85℃ for 5 minutes. Next, cDNA was purified from 444
broken droplet and amplified in PCR reaction. The amplified cDNA product was then 445
cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the 446
indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing 447
genes which also contained Cell Barcode and Unique Molecular Index. The indexed 448
sequencing libraries were cleanup with V AHTS DNA Clean Beads (Vazyme N411-01), 449
analyzed by Qubit (Thermo Fisher Scientific Q33226) and Bio-Fragment Analyzer (Bioptic 450
Qsep400). The libraries were then sequenced on illumina NovaSeq X Plus with PE150 read 451
length. 452
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453
Statistical analysis. The in vivo experiments were randomized but the researchers were not 454
blinded to allocation during experiments and results analysis. Statistical analysis was 455
performed using GraphPad Prism 8 Software. A Student's t test was used for comparison 456
between the two groups. Multiple comparisons were performed using one-way ANOVA 457
followed by Tukey’s multiple comparisons test or two-way ANOVA followed by Tukey’s 458
multiple comparisons test. Detailed statistical methods and sample sizes in the experiments 459
are described in each figure legend. All statistical tests were two-sided and P-values < 0.05 460
were considered to be significant. ns not significant; *p < 0.05; **p < 0.01; ***p < 0.001. 461
462
Data availability 463
All data are available in the main text or the supplementary materials. Correspondence and 464
requests for materials should be addressed to Y.L. 465
466
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555
Acknowledgments 556
This work was supported by the Shanghai Rising-Star/Sailing Program (24YF2756000). All 557
the schematics are were created with BioRender.com. 558
559
Author contributions 560
Conceptualization, L.G. and Y.L.; Methodology, Y.L. and C.C.; Formal Analysis, Y.L.; 561
Investigation, C.C., Y.Z., F.D., R.L., X.Z., S.W., Y.W., F.Q., L.C., R.C., and F.L.; Resources, 562
L.G. and Y.L.; Writing – Original Draft, C.C. and Y.L.; Writing – Review & Editing, L.G. 563
and Y.L.; Supervision, L.G.; Funding Acquisition, L.G. and Y.L. 564
565
Competing interests 566
The authors declare that they have no competing interests. 567
568
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preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in
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Fig. 1 569
570
Fig. 1. Systemic administration of STING agonists causes lung injury in mice. Female 571
C57BL/6 mice received intraperitoneal injections of 2 mg/kg diABZI every day for three 572
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days. (A) Body weight change percent of mice was monitored after diABZI treatment from 573
day1 to day4 and lung coefficient was detected on day4 (n=6). (B) Lung wet/dry weight ratio 574
was detected on day4 and mice peak expiratory flow and respiratory rate was monitored 575
during day1 to day4 (n=6). (C) Representative H&E staining images of lung tissues from 576
mice. Scale bar, 200 μm. (D) Western blot analysis of surfactant protein A proteins in mouse 577
serum. (E-G) Transcription levels of multiple proinflammatory factor in mouse lung tissues 578
were detected (n=6). (H) Flow cytometric analysis of neutrophil macrophage M1-like and 579
M2-like macrophages in the lung tissues (n=6). (H) Flow cytometric analysis of lymphocytes 580
and myeloid cells in the lung tissues (n=6). The data are presented as the mean ± SEM. * p < 581
0.05; ** p < 0.01; *** p < 0.001; ns not significant by ns not significant by unpaired t test or 582
ANOVA followed by Tukey’s multiple comparisons test. 583
584
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Fig. 2 585
586
Fig. 2. Single-cell sequencing reveals alterations and interactions in pulmonary cell 587
populations during inflammation. (A) t-SNE plots and relative proportion of the indicated 588
cell types for scRNA-seq data of lung samples. (B) Tmem173 expression in t-SNE plots. (C) 589
Violin plot of gene expression scores for the HALLMARK INTERFERON ALPHA 590
RESPONSE pathway across cell populations. (D) Heatmap of IL-1β and IFN-γ expression 591
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levels in different cell populations at various time points (E) Heatmap of chemokine 592
expression levels in various cell populations at 0 and 4 hours. (F) Scatter plots visualized the 593
primary senders and receivers of cellular communication. The x-axis and y-axis respectively 594
represent the total outgoing or incoming communication probabilities associated with each 595
cell population. The size of each point indicates the number of relationships (both outgoing 596
and incoming) with each cell population. (G) Heatmap of relative signal strength at different 597
time points (red indicates an increase compared to the previous time point, blue indicates a 598
decrease). 599
600
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Fig. 3 601
602
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Fig. 3. Endothelial stimulated by STING agonist secret chemokines and cytokine to 603
recruit and activate NK cells. (A) Volcano plot of gene expression differences of 604
endothelial cells at different time points from scRNA-seq data of lung samples. (B) Heatmap 605
of chemokines expression level of endothelial cells. (C) Violin plot of gene expression scores 606
for the HALLMARK INTERFERON ALPHA RESPONSE pathway of endothelial cells. (D) 607
Western blot analysis of total and phosphorylated TBK1 and STING proteins in HPMEC cell 608
lines with or without diABZI treatment (n=3). (E) KEGG pathway enrichment analysis of 609
differentially expressed genes in NK cell at 4 h compared to 0 h. (F) Transcriptional levels of 610
Ccl5, Cxcl9/10 and Il15 of HPMEC with or without diABZI or inhibitor treatment (n=3). (G) 611
Transcriptional levels of Ccl4/5, Cxcl9/10 and Il15 of HPMEC with or without diABZI or 612
Compound 53 treatment (n=6). (H) Transcriptional levels of Ccl5 and Cxcl10 of NCG mice 613
with or without diABZI treatment (n=6). (I-J) Flow cytometry counting of NK-92 or 614
hPBMC-NK cells recruited to the basement membrane by HPMECs (n=3). The data are 615
presented as the mean ± SEM. * p < 0.05; ** p < 0.01; *** p < 0.001; ns not significant by ns 616
not significant by unpaired t test or ANOVA followed by Tukey’s multiple comparisons test. 617
618
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Fig. 4 619
620
Fig. 4. STING-activated endothelial cells release IL-15 to activate NK cells, which 621
produce IFN-γ to damage endothelial cells. (A) Heatmap of Tmem173 expression level and 622
violin plot of gene expression scores for the HALLMARK INTERFERON ALPHA 623
RESPONSE pathway of NK cells at different time points from scRNA-seq data of lung 624
samples. (B) Schematic diagram of HPMEC and NK-92 conditioned medium cultivation 625
workflow and transcriptional levels of Ccr5, Il15ra and Ifng of NK-92 (n=6). (C) UMAP 626
plots and heatmap of Ifng expression level of NK cell subsets for scRNA-seq data of lung 627
samples. (D) Violin plot of gene expression scores for the HALLMARK INTERFERON 628
ALPHA RESPONSE pathway of NK cell subsets. (E) Relative cell viability after co-629
culturing NK-92 cells with endothelial cells for 24 hours was determined by measuring the 630
absorbance at 450 nm following incubation with CCK-8 for 2 hours. (F) Flow cytometric 631
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analysis of endothelial in the lung tissues after neutralization of chemokines and cytokines 632
(n=4). The data are presented as the mean ± SEM. * p < 0.05; ** p < 0.01; *** p < 0.001; ns 633
not significant by ns not significant by unpaired t test or ANOVA followed by Tukey’s 634
multiple comparisons test. 635
636
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Fig. 5 637
638
Fig. 5. Tbx21+ NK cells activated by endothelial cells produce chemokines to recruit 639
neutrophils (A) Heatmap of Tbx21 expression level of NK cell subsets from scRNA-seq data 640
of lung samples. (B) Circos plot of NicheNet analysis of the Tbx21+ NK cell population 641
predicted downstream target genes potentially upregulated following NK cell activation by 642
endothelial cell-derived ligands. (C) GOBP and KEGG pathway enrichment analysis of 643
differentially expressed genes in cluster0 NK cell at 4 h compared to 0 h. (D) Transcriptional 644
levels of Ccl3/4 and Cxcl1/2/10 of NK-92 after conditioned medium cultivation with HPMEC 645
(n=6). The data are presented as the mean ± SEM. * p < 0.05; ** p < 0.01; *** p < 0.001; ns 646
not significant by ns not significant by unpaired t test or ANOVA followed by Tukey’s 647
multiple comparisons test. 648
649
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preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in
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Fig. 6 650
651
Fig. 6. Neutrophils secrete IL-1β through positive feedback pathways and form NETs 652
during lung injury. (A) Volcano plot of differentially expressed genes in Neutrophil at 12 h 653
compared to 6 h. (B) GOBP and KEGG pathway enrichment analysis of differentially 654
expressed genes in Neutrophil at 12 h compared to 6 h. (C) Representative images of IF 655
staining of citH3 and MPO in lung tissues. (D) Western blot analysis of MPO in mice lung 656
tissues after depletion of immune cells. The data are presented as the mean ± SEM. * p < 0.05 657
by unpaired t test or ANOVA followed by Tukey’s multiple comparisons test. 658
659
660
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Fig. 7 661
662
Fig. 7. Immune cells depletion and cytokine neutralization in vivo validates the 663
mechanism of lung injury caused by STING agonist. (A) Flow cytometric analysis of NK 664
cell, neutrophil, endothelial and IM in the lung tissues (n=4). (B) Transcriptional levels of 665
Il1b, Ifng, Ccl4/5 and Cxcl9/10 of the lung tissues after neutralization of chemokines and 666
cytokines (n=5). The data are presented as the mean ± SEM. * p < 0.05; ** p < 0.01; *** p < 667
0.001; ns not significant by ns not significant by unpaired t test or ANOVA followed by 668
Tukey’s multiple comparisons test. 669
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