The published literature suggests a potential association between NINJ1 and glycine given that NINJ1 knockout and glycine treatment protect cells against a common set of lytic cell death pathways. Moreover, in pyroptosis, both allow for IL-1β secretion through the gasdermin D pore while preventing final membrane lysis (Kayagaki et al., 2021; Volchuk et al., 2020). We first sought to extend these associations by further characterizing functional and morphological similarities between NINJ1 knockout and glycine cytoprotection in pyroptosis, necrosis, and post-apoptosis lysis.

Using a CRISPR-Cas9 system, we generated a NINJ1 knockout cell line in mouse immortalized bone marrow-derived macrophages (iBMDMs; Figure 1A). Pyroptosis was induced in LPS(lipopolysaccharide)-primed wildtype and NINJ1 knockout iBMDM with nigericin (20 µM, 2 hr) in the absence or presence of 5 mM glycine. Glycine treatment at 5 mM was based on the reported literature (Loomis et al., 2019; Volchuk et al., 2020) and a dose-finding study (Figure 1—figure supplement 1). We performed a colorimetric assay to test for LDH release, a common marker of cell rupture. Both NINJ1 knockout and glycine treatment in wildtype iBMDM protected against cytotoxicity (Figure 1B). Similarly, cell membrane integrity was preserved following apoptosis (Figure 1C) and necrosis (Figure 1D) induced with venetoclax (25 µM, 16 hr) and pneumolysin (0.5 µg/mL, 15 min), respectively. Importantly, in NINJ1 knockout macrophages, treatment with glycine during lytic cell death did not confer any additional protection against cell lysis, suggesting that these distinct perturbations affect the same process (Figure 1B–D).

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When visualizing glycine-treated pyroptotic macrophages, we observed prominent plasma membrane ballooning (Figure 1E). This impressive morphology was comparable to that of LPS-primed NINJ1 knockout macrophages stimulated to undergo pyroptosis with nigericin, which we (Figure 1E) and others (Kayagaki et al., 2021) have observed. Together, these functional and morphologic similarities buttress the association between glycine cytoprotection and NINJ1-mediated plasma membrane rupture.

To further corroborate the above findings, we conducted pyroptosis assays in RAW mouse macrophages reconstituted with the inflammasome adaptor ASC (hereafter referred to as RAW-ASC). NINJ1 protein expression was ablated through CRISPR-Cas9 targeting as compared with the parental line (Figure 1—figure supplement 2A). Pyroptosis stimulation in this orthogonal murine macrophage model demonstrates NINJ1 deficiency functionally (Figure 1—figure supplement 2B) and morphologically (Figure 1—figure supplement 2C) phenocopies glycine treatment as was seen in the iBMDM system.

Human NINJ1 is 90% homologous to the mouse protein and was shown to be toxic when overexpressed in HEK293T cells (Kayagaki et al., 2021), but it is not known if endogenous NINJ1 is activated and mediates plasma membrane rupture in human cells undergoing programmed cell death. We knocked down NINJ1 in primary human monocyte-derived macrophages (hMDMs) using siRNA specific to NINJ1 (siNINJ1) and compared to non-targeting control siRNA (siCtrl) with an efficiency approaching 70% (Figure 4—figure supplement 2A). Both NINJ1 knockdown and glycine (50 mM; Figure 2—figure supplement 1) independently and completely prevented pyroptosis (LDH release) induced by nigericin (20 µM, 2 hr) in LPS-primed hMDMs. Notably, again there was no additional effect with combined NINJ1 deficiency and glycine treatment arguing that NINJ1 and glycine are involved in the same process in primary human cell death pathways (Figure 2A). In contrast, human macrophages induced to undergo necroptosis (zVAD 20 µM + SMAC mimetic BV6 10 µM followed by TNF 10 ng/mL) were unprotected by glycine treatment (Figure 2—figure supplement 2), consistent with the observation that Ninj1 knockout does not confer protection in necroptosis likely due to sufficient cytolytic activity of MLKL pores (Kayagaki et al., 2021). Like mouse macrophages, both siNINJ1 and glycine sustained the ballooned morphology of pyroptotic hMDMs (Figure 2B). While pyroptotic human macrophages maintained their plasma membrane integrity in the presence of glycine as demonstrated by suppressed LDH release, we next confirmed that they had nevertheless lost viability as measured by the loss of mitochondrial membrane potential and cellular ATP content (Figure 2—figure supplement 3).

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Together, these data using macrophage models from mouse and human demonstrate that genetic deletion or silencing of NINJ1 functionally and morphologically parallels glycine-mediated cytoprotection.

We therefore next posited that glycine targets NINJ1 as part of its cytoprotective effect. The working model of NINJ1-mediated membrane rupture involves its clustering within the plasma membrane (Kayagaki et al., 2021). Point mutants (e.g. K45Q and A59P) that prevent membrane rupture also fail to cluster upon induction of pyroptosis (Kayagaki et al., 2021), further reinforcing a connection between the clustering process and the capacity of NINJ1 to rupture membranes. To establish whether glycine directly interferes with NINJ1-mediated cell death, we next evaluated the effect of glycine treatment on NINJ1 clustering during cell lysis in pyroptosis, post-apoptosis lysis, and necrosis.

Using a biochemical native-PAGE approach that maintains native protein interactions, endogenous NINJ1 of otherwise untreated primary mouse bone marrow-derived macrophages (BMDM) migrates at approximately 40 kDa, potentially indicative of NINJ1 dimers or trimers in unstimulated cells (Figure 3A) and consistent with its known ability to form homotypic interactions (Bae et al., 2017). By native-PAGE, a band of approximately 160–200 kDa is also observed in the basal state, suggesting that higher-order multimers of NINJ1 consistent with decamers or higher-order multimers may also be present in the plasma membrane of unstimulated macrophages (Figure 3A). In response to pyroptosis (nigericin in LPS-primed BMDM), necrosis (pneumolysin), and apoptosis (venetoclax) induction in primary BMDM, the endogenous NINJ1 signal shifts to a high molecular weight aggregate, suggestive of a clustering process. Importantly, this shift is completely abrogated by glycine treatment (Figure 3A). Using this same native-PAGE approach, glycine treatment of primary hMDMs (Figure 4A) and mouse RAW-ASC cells (Figure 1—figure supplement 1D) undergoing pyroptosis prevented the shift of NINJ1 to a high molecular weight band. Finally, glycine inhibited NINJ1 oligomerization and pyroptotic lysis (as measured by LDH release) in LPS-primed and nigericin-treated human macrophages derived from induced pluripotent stem cells (iPSCs) derived macrophages (iPSDMs) without impairing secretion of IL-1β, confirming previous findings that glycine acts downstream of GSDMD pore formation (Figure 4—figure supplement 2B–D).

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To corroborate these biochemical findings, we proceeded to evaluate native NINJ1 oligomerization within the plasma membrane by total internal reflection fluorescence (TIRF) microscopy in primary BMDM and hMDMs induced to undergo pyroptosis. TIRF microscopy allows for the preferential excitation of a thin (~150 nm) layer that includes the ventral plasma membrane of adherent cells, thereby eliminating background fluorescence from structures outside this focal plane (e.g. endomembrane compartments). In LPS-primed BMDMs and hMDMs, NINJ1 appears in discrete, small puncta that are diffusely distributed across the plasma membrane in both cell types (Figure 3B, Figure 4B). Upon induction of pyroptosis, the density of these puncta decreases, and their intensity increases (Figure 3C–D, Figure 4C–D), consistent with the clustering or aggregation of the low-order multimers into high-order oligomers as seen on the native PAGE (Figure 3A, Figure 4A). Co-treatment with glycine abrogates the formation of these clusters (Figure 3B–D, Figure 4B–D).

While the use of TIRF microscopy allowed us to localize our evaluation of NINJ1 clustering to the plasma membrane, it inadequately resolved the spatial clustering due to its diffraction limitation. To partially overcome this limitation, we next probed NINJ1 membrane clustering using stimulated emission depletion (STED), a super-resolution fluorescence microscopy approach, in primary BMDM. With STED, we improved upon the resolution from a full-width half-maximum by confocal microscopy of 271±98 nm to 63±8 nm (Figure 3E). In the basal state, NINJ1 was observed in small discrete puncta, which decreased in density (Figure 3F) and increased in intensity (Figure 3G) upon pyroptosis induction with nigericin. Co-treatment with glycine (5 mM) limited clustering (Figure 3F–G). Together, our biochemical and microscopy-based data are consistent with the notion that during pyroptosis, low-order NINJ1 oligomers cluster within the plasma membrane, a phenomenon suppressed by glycine.

Thus far, our data do not rule out the possibility that glycine is able to target proteins upstream of NINJ1 in pyroptosis. To test whether this is indeed the case, we evaluated caspase-1 activation, GSDMD processing, and IL-1β processing and secretion in iBMDM induced with nigericin with and without 5 mM glycine. Co-treatment with glycine had no effect on these upstream processes (Figure 5A–B), supporting the hypothesis that the target of glycine is downstream and independent of GSDMD activation and oligomerization. To confirm that glycine interferes with NINJ1-mediated cellular rupture independent of upstream signaling pathways, we generated a doxycycline-inducible NINJ1 overexpression system in mouse macrophages (Figure 5—figure supplement 1) based on the rationale that sufficient overexpression of NINJ1 can drive spontaneous lysis as seen in 293T systems (Kayagaki et al., 2021). Using this cell-based system, we demonstrate that glycine dose-dependently suppresses NINJ1-mediated cell rupture independent of activation of upstream programmed cell death pathway activation (Figure 5C). Expression of N-terminal GSDMD using a similar inducible system was able to trigger a glycine-inhibitable cellular rupture (Figure 5D). To further address glycine’s mode of action, we evaluated glycine’s effect on NINJ1 clustering biochemically and found that glycine suppresses NINJ1 clustering when NINJ1 is overexpressed (Figure 5E).

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We next turned our attention to the purported amphipathic α-helix in the NINJ1 N-terminus (residues 40–69 of human NINJ1), which others have shown to be necessary for NINJ1-mediated plasma membrane rupture (Kayagaki et al., 2021). Circular dichroism (CD) of the α-helix at varying glycine concentrations between 0 and 20 mM did not affect the CD spectrum, indicating that at the trialed concentrations, glycine did not alter the stability of the helical secondary structure of this region of the NINJ1 N-terminus (Figure 5—figure supplement 2). We then functionally evaluated whether glycine interferes with the membrane lytic function of the helix using a reconstituted liposomal rupture assay. In this system, we demonstrate that while the α-helix was able to rupture liposomes, glycine did not interfere with this effect (Figure 5F). These data suggest that glycine can block full-length NINJ1 clustering and membrane rupture in cellulo but that additional unknown players may be affected within cells, or the mode of action is separate from the minimally sufficient lytic α-helix of the NINJ1 N-terminus as shown by intact liposome rupture.

Primary BMDMs were harvested from the femurs and tibia of wildtype mixed-sex cohorts of C57Bl/6 mice. The ends of cleaned bones were cut and centrifuged to collect bone marrow into sterile PBS. The cell suspension was washed with PBS and plated in DMEM with 10 ng/mL M-CSF (315-02; Peprotech Inc, Cranbury, NJ, USA). Following 5 days of culture, the BMDM were detached from the dishes with TBS with 5 mM EDTA, resuspended in fresh DMEM, and plated. ASC-expressing RAW264.7 mouse macrophages (RAW-ASC; raw-asc, InvivoGen, San Diego, CA, USA) are engineered to stably express murine ASC, which is absent in the parental RAW 264.7 macrophage cell line (Pelegrin et al., 2008) and therefore are able to undergo pyroptosis. iBMDM expressing Cas9 was obtained from Dr Jonathan Kagan (Boston Children’s Hospital, Boston) and described previously (Evavold et al., 2018). Cell lines were authenticated and negative for mycoplasma contamination.

RAW-ASC and iBMDM cells were transfected with custom CRISPR gRNA plasmid DNA (U6-gRNA:CMV-Cas-9–2 A-tGFP; Sigma-Aldrich, Oakville, Canada) using FuGENE HD transfection reagent (Promega, Madison, WI, USA). The Ninj1 target region sequence was GCCAACAAGAAGAGCGCTG. 24 hr later, the cells were FACS sorted for GFP into 96 well plates. Individual colonies were expanded and tested for NINJ1 expression by western blot. NINJ1 knockdown in hMDMs was performed by siRNA using Lipofectamine RNAiMAX (Invitrogen, Waltham, MA, USA) according to the manufacturer’s instructions. Cells were transfected with 20 nM pooled siRNA against NINJ1 (Thermo Scientific, HSS107188, HSS107190, HSS181529) or non-silencing control siRNA (Qiagen, Hilden, Germany, 1027310). hMDMs were siRNA-treated two times (day 3 and day 5) before medium was changed to RPMI with 1% serum (day 6), and cells were allowed to rest overnight prior to stimulation. Knockdown of NINJ1 was confirmed by western blotting.

PCR reactions were performed using ConeAmp HiFi master mix (Takara). Primers for mouse Ninj1 (insert) PCR reaction were: forward primer 5’gat tac gct gag tcg ggc act gag ga3’ and reverse primer 5’ctc ggt acc cta ctg ccg ggg cgc ca3’. Template DNA for the PCR reaction was mouse Ninj1 cDNA clone from Origene (Cat. No. MR225037). The template vector pcDNA3.1-HA was obtained from Addgene. Primers for pcDNA3.1-HA PCR (vector) reaction were: forward primer 5’cgg cag tag ggt acc gag ctc gga3’ and reverse primer 5’gcc cga ctc agc gta atc tgg aac atc3’. PCR reaction products were cleaned up using the NucleoSpin PCR Clean-up kit (Macherey-Nagel). The PCR products contained 18 bp overlapping regions between the pcDNA3.1-HA tag vector and the mouse NINJ1 insert. This allows for fusion of the insert and vector using the In-Fusion Snap Assembly EcoDry Cloning Kit (Takara, 638954) and transformation into Stellar competent bacterial cells (Takara). DNA sequencing with CMV-F primer confirmed Ninj1 insertion into the pcDNA3.1-HA vector and that NINJ1 was in-frame with the N-terminal HA-tag. HeLa cells (ATCC #CCL-2) were transfected with pcDNA 3.1HA-NINJ1 using Fugene HD transfection reagent (Promega) according to the manufacturer’s protocol.

iBMDMs with doxycycline-inducible expression of the N-terminal fragment of GSDMD fused to BFP are published (Evavold et al., 2021). We used the same stock of iBMDMs from Cas9-expressing mice in which the TET3G transactivator protein had introduced previously (Evavold et al., 2021) to generate cell lines with dox-inducible expression of NINJ1 carrying an N-terminal FLAG-tag. cDNA encoding full-length murine NINJ1 was ordered as a gBlock from Integrated DNA Techologies. This sequence was amplified by PCR to append an N-terminal FLAG-tag and cloned into pRETROX-TRE3G (TakaraBio) using BamHI and NotI restriction sites and into pMSCV IRES EGFP using NotI and SalI restriction sites. To introduce dox-inducible FLAG-NINJ1, 2.5×10⁶ Platinum-GP retrovirus packaging cells were seeded in a TC-treated 10 cm dish. On the next day, cells were transfected with 3 μg pCMV-VSV-G and 9 μg pRETROX-TRE3G encoding FLAG-NINJ1 using Lipofectamine 2000. After 18 hr, media was exchanged to 6 mL of fresh complete DMEM. The same day, 0.5×10⁶ Cas9- and TET3G-expressing iBMDMs were seeded per well of 6-well plate. The next day, retroviral supernatant was harvested and filtered through 0.45 μm syringe filter, supplemented with polybrene (1:2000; EMD Millipore), and spun onto cells (1250 g, 30°C, 1 hr). 6 mL of fresh cDMEM were added to retrovirus packaging cells, and spinfection was repeated the next day. 3 days after the second transduction, transduced cells were selected by growth in complete DMEM including 1.5 mg/mL G-418 and 10 μg/mL puromycin. To ensure maximal transgene expression, which correlates with the ability of FLAG-NINJ1 to induce cell death and lysis, FLAG-NINJ1 was also stably overexpressed in these cells using retroviral transduction with an MSCV(murine stem cell virus) retrovirus. Retrovirus production and spinfections were performed as described above, only using pMSCV IRES EGFP-FLAG-NINJ1 instead of pRETROX-TRE3G construct. Cells were then sorted on a BD Melody cell sorter for maximal EGFP expression (top 5–10%). Clonal cell lines were derived by limited serial dilution.

1×10⁵ cells per well in a black 96-well plate in DMEM (Gibco)/10% FBS(fetal bovine serum) (R&D, S11550) were induced with 2 µg/mL doxycycline (Sigma-Aldrich) in the presence or absence of increasing concentrations of glycine (Sigma-Aldrich 67126) in a total volume of 200 μL for 8 hr (iBMDM GSDMD-NT) or 12 hr (iBMDM FLAG-NINJ1) before supernatants were harvested for LDH-assay (Invitrogen) and cells detached (PBS/4 mM EDTA) for flow cytometry (Becton Dickinson Fortessa). iBMDM GSDMD-NT express BFP and were analyzed directly; iBMDM NINJ1 were stained with anti-FLAG APC antibody (1:100, Abcam Ab 72569; RRID: AB_1310127) in PBS/2% FBS, 2.5 mM EDTA on ice and washed once before analysis.

Pyroptosis was activated in BMDM primed with (0.5 µg/mL) LPS from Escherichia coli serotype 055:B5, which was first reconstituted at a stock concentration of 1 mg/mL. In primary BMDM, after 4.5 hr of LPS priming, pyroptosis was induced with 20 µM nigericin (Sigma N7143; stock 10 mM in ethanol) for 30 min. iBMDM were primed with LPS for 3 hr, followed by pyroptosis induction with 10 µM nigericin for 2 hr. Apoptosis was induced in non-primed macrophages using the Bcl-2 inhibitor venetoclax (ABT-199; Tocris, Bristol, United Kingdom; 6960) at 25 µM for 16 hr. Necrosis was induced by treating non-primed macrophages with pneumolysin (0.5 μg/mL) for 15 min in iBMDM or 45 min in primary BMDM. Pneumolysin was obtained from Dr John Brumell (Hospital for Sick Children, Toronto). In hMDMs, pyroptosis was induced by priming with 1 μg/mL LPS from E. coli serotype 0111:B4 for 2 hr, followed by stimulation with 20.7 μM nigericin (Invivogen tlrl-nig; stock 5 mg/mL in ethanol) for 2 hr and 15 min. Necroptosis was induced by treating cells with pan-caspase inhibitor zVAD (25 uM, Invivogen, tlrl-vad) and SMAC mimetic BV6 (10 uM, Invivogen, inh-bv6) for 30 min, before stimulation with recombinant human TNF-α (10 ng/mL, Peprotech, 300–01 A) for 4 hr. iPSDMs were stimulated with 200 ng/mL LPS for 3 hr and 20.7 μM nigericin for 1–1.5 hr.

Where indicated, mouse cells were treated with 5 mM glycine (Sigma, G7126) at the time of cell death induction. Human cells were pretreated with glycine (Millipore, Burlington, MA, USA; 104201) at a concentration of 50 mM for at least 10 min before stimuli was added.

BMDM were seeded at 200,000 cells per well in 12-well plates, treated as indicated, and cytotoxicity assayed by LDH release assay the following day. At the end of the incubations, cell culture supernatants were collected, cleared of debris by centrifugation for 5 min at 500× g. The cells were washed once with PBS then lysed in lysis buffer provided in the LDH assay kit (Invitrogen C20300). Supernatants and lysates were assayed for LDH using an LDH colorimetric assay kit as per the manufacturer’s instructions (Invitrogen C20300). hMDMs were seeded at 500,000 cells per well in 12-well plates and differentiated as described above. iPSDMs were seeded at 180,000–450,000 cells per well in 12-well plates and differentiated as described above. After cells were stimulated as described in figure legends, supernatants were harvested, and LDH release was assayed (Invitrogen C20301). Briefly, equal amounts of supernatant and reaction mixture were mixed and incubated for 30 min, followed by absorbance reads at 490 and 680 nm. To calculate the LDH release, the 680 nm background was subtracted from the 490 nm absorbance reads before further processing.

iBMDMs were seeded at 10⁶ cells per well in 12-well plates overnight, primed with 1 μg/mL E. coli LPS (Enzo; Serotype O111:B4) for 4 hr, or left unprimed before stimulation with 20 μM of nigericin (Invivogen) in 500 μL Opti-MEM (Gibco) with no serum. After 2 hr, 50 μL of supernatant was collected for analysis by ELISA. 125 μL of concentrated 5× SDS loading buffer with reducing agent TCEP(tris(2-carboxyethyl)phosphine) was added to each well to stop the reaction. This treatment ensured the capture of proteins in both the supernatant and the cell lysates for western blot analysis. Proteins were separated by SDS-PAGE and detected by western blot using primary antibodies against GSDMD (Abcam ab209845; RRID: #AB_2783550), Caspase-1 (Adipogen AG-20B-0042-C100; RRID: #AB_2755041), pro-IL-1β (Genetex GTX74034; RRID: #AB_378141), and actin (Sigma A5441; RRID: #AB_476744).

hMDMs were differentiated at 30,000 cells per well in glass-bottom 96-well plates (Cellvis, P96-1.5H-N). Parallel plates were prepared for live-cell imaging and LDH + CellTiter Glo analysis. hMDMs were either left untreated or pre-treated with glycine (50 mM) and primed with 1 μg/mL LPS (E. coli serotype 0111:B4) in RPMI complemented with 1% fetal calf serum for 3 hr before stimulation with 20.7 μM of nigericin (Invivogen). Tetramethylrhodamine ethyl ester perchlorate (TMRE, 200 or 10 nM, Sigma-Aldrich) was added to cells before the plates were placed in a heated incubator (37°C, 5% CO₂), and images were taken every 30 min over 18 or 22 hr (two independent experiments). In the second experiment, at the end of LPS priming, cells were labeled with CellTracker Deep Red (0.5 μM Invitrogen) for 15 min and washed before addition of fresh medium with TMRE (10 nM) with or without LPS, nigericin, and glycine. In parallel plates treated identically, supernatants were harvested and assayed for LDH, and cellular ATP was measured using CellTiterGlo (Promega) at 0, 2, 6, and 18/22 hr.

Mouse macrophages were cultured on 18 mm glass coverslips in 12-well plates at 150,000 cells per well. Cells were treated as indicated in the figure legends, washed with PBS, fixed in 4% paraformaldehyde (PFA) in PBS at room temperature for 15 min, and permeabilized with 0.1% Tween-20. Cells were then blocked in PBS supplemented with 10% donkey serum and 0.1% Tween-20 for 1 hr at room temperature prior to overnight incubation with primary antibody at 4°C. Rabbit monoclonal anti-mouse NINJ1 was used at 10 μg/mL. Next, cells were washed three times with PBS supplemented with 10% donkey serum prior to the addition of secondary antibody at room temperature for 1 hr. In validation studies of the rabbit anti-mouse NINJ1 monoclonal antibody, cells were stained with and without the primary antibody prior to application of the secondary antibody. Nuclei were labeled using DAPI containing mounting medium (ProLong Diamond Antifade Mountant, Invitrogen P36961). For total internal reflection microscopy, cells were co-stained with recombinant Cholera toxin subunit B conjugated to Fluor488 (Invitrogen C34775) at 1 μg/mL for less than 1 min prior to fixing and staining for NINJ1 as described above. The Cholera toxin subunit B served as a membrane marker to optimize plasma membrane visualization. TIRF imaging of mouse macrophages was conducted on a Zeiss Axio Observer Z1 microscope with a 100× objective and Andor iXon3 885 detector. For STED microscopy, primary mouse macrophages were cultured on 1.5 H 18 mm glass coverslips (Marienfeld) in 12-well plates at 150,000 cells per well. After treatments as indicated in the figure legend, cells were washed with PBS, then fixed in 4% PFA in PBS for 10–15 min at room temperature. Following fixation, cells were washed, then permeabilized in 0.1% Tween-20. Cells were blocked in in PBS supplemented with 10% donkey serum and 0.1% Tween-20 for 1 hr at room temperature, followed by primary antibody incubation in blocking solution overnight at 4°C. Rabbit monoclonal anti-mouse NINJ1 was used at 10 µg/mL. The next day, cells were incubated with Cy3-conjugated secondary antibody (diluted 1:100) in 1% serum in PBST for 1 hr at room temperature. After final washes, coverslips were mounted onto glass slides using ProLong Diamond Antifade Mountant (Invitrogen, P36965). STED microscopy was performed using a Leica TCS SP8 STED 3× microscope using HyD detectors and a 100×/1.4 oil objective. Samples labeled with Cy3-conjugated secondary antibody were excited using a white light laser at 554 nm. Emissions were time-gated 1.30–6.00 ns. A 1.5 W depletion laser at 660 nm was used at 70% maximal power. Images were acquired and deconvolved using Leica LAS X software with Lightning Deconvolution with an xy pixel size of 12.62 nm. For all fluorescence microscopy in mouse macrophages, rabbit monoclonal anti-mouse NINJ1 was obtained from Drs Nobuhiko Kayagaki and Vishva Dixit (Genentech Inc, San Francisco, CA, USA). Where indicated, images of live cell morphology were captured using the epifluorescence mode and with FM 4–64 (Invitrogen, T3166) added right before imaging.

Human primary macrophages were differentiated at 30,000 cells per well in glass-bottom 96-well plates (Cellvis, P96-1.5H-N). After stimuli, the cells were washed with PBS and thereafter stained with Cholera toxin subunit B Alexa Fluor 488 conjugate at 1 μg/mL in PBS for less than 1 min. Cells were then fixed in 4% PFA in PBS at room temperature for 15 min, followed by washing three times with PBS. We permeabilized the cells with PBS containing 0.01% saponin for 10 min at room temperature and thereafter blocked with PBS/0.01% saponin/20% pooled human serum for 3 hr. Cells were either left unstained or incubated with anti-human NINJ1 antibody (mouse IgG2b, R&D Systems, MAB5105, RRID: AB_11128852) or a control Ab (mouse IgG2a, Serotec, MCA929F; RRID: AB_322271) at 10 μg/mL in PBS/0,01% saponin/1% pooled human serum at 4°C for 41 hr and then washed three times with PBS/0.01% saponin/1% pooled human serum. Following this, we incubated the cells with far-red fluorescent rabbit anti-mouse antibody (Invitrogen, A27029, RRID: AB_2536092) at 2 μg/mL in PBS/0.01% saponin/1% pooled human serum at room temperature for 1 hr. Cells were washed three times with PBS/0.01% saponin/1% pooled human serum and thereafter three times with PBS before imaging. TIRF imaging of human macrophages was done on a Zeiss TIRF 3 microscope with a 63× objective and a Hamamatsu ORCA Fusion sCMOS detector. Images of morphology in live cells were captured using the epifluorescence mode and with FM 1–43 (Invitrogen, T3163) added at 5 μg/mL right before imaging.

For TMRE experiments, human macrophages were imaged using a Zeiss TIRF III (Carl Zeiss GmbH, Jena) equipped with an alpha Plan-Apochromat 100×/1.46 oil-immersion objective and a Hamamatsu ORCA-Fusion (C14440-20UP) CMOS camera. A Plan-Apochromat 10×/0.45 air objective was used for the time series experiments. TMRE was excited by a Colibri.2 470 nm LED, and the emission was detected between 510–542 nm. CellTracker Deep Red was excited by a 638 nm diode laser, and the emission was detected between 665 and 711 nm. Image processing was done in FIJI (Schindelin et al., 2012). Automatic counting of TMRE-positive cells was done in CellProfiler v.4.2.4 (Stirling et al., 2021) by using the IdentifyPrimaryObjects module with either Maximum Cross-Entropy adaptive thresholding or Otsu thresholding, and settings were optimized for each dataset to enhance accuracy.

Mouse macrophages were lysed with native-PAGE lysis buffer (150 mM NaCl, 1% Digitonin, 50 mM Tris pH7.5, and 1× Complete Protease Inhibitor). Following centrifugation at 20,800× g for 30 min, lysates were mixed with 4× NativePAGE sample buffer and Coomassie G-250 (ThermoFisher) and resolved using NativePAGE 3–12% gels. For SDS-PAGE, cells were washed with 1× PBS and lysed in RIPA lysis buffer containing protease inhibitors (Protease inhibitor tablet, Pierce A32955). Proteins were resolved using NuPAGE 4–12% Bis-Tris gels (Invitrogen), transferred to PVDF(polyvinylidene difluoride) membranes, and immunoblotted. For HA-NINJ1 overexpression experiments, rabbit monoclonal anti-HA (Cell Signaling Technology, Inc, Danvers, MA, USA; #3724; RRID: AB_1549585) was used. GAPDH (Santa Cruz Biotechnology, Dallas, TX, USA; sc-25778; RRID: AB_10167668 1:1000) was used for a loading control.

hMDMs and iPSDMs were lysed with 1× NativePAGE Sample Buffer containing 1% Digitonin. After centrifugation at 21,000× g for 30 min, protein concentration of lysates was measured using Pierce BCA Protein Assay Kit (ThermoFisher) to ensure equal loading of proteins. For Native-PAGE on hMDMs, lysates were mixed with Novex Tris-Glycine Native Sample Buffer (Invitrogen) and resolved using Novex 4–12% Tris-Glycine gels (Invitrogen). For Native-PAGE on human iPSDMs, lysates were mixed with Coomassie G-250 (ThermoFisher) and resolved using NativePAGE 3–12% Bis-Tris gels (Invitrogen). For SDS-PAGE, lysates were mixed with DTT(dithiothreitol) and NuPAGE LDS sample buffer (Invitrogen), denatured for 5 min at 95 °C, and resolved using NuPAGE 4–12% Bis-Tris gels (Invitrogen). Proteins were transferred to PVDF membranes and immunoblotted. NINJ1 (R&D Systems, MAB5105, RRID: AB_11128852) was used to determine NINJ1 expression, while β-actin (Cell Signaling Technology, Danvers, MA, USA; Cat# 8457, RRID: AB_10950489) was used as loading control.

Supernatants from human iPSDMs and mouse iBMDM were assessed for IL-1β (R&D Systems, DY201 or Invitrogen 88–7013, respectively) by ELISA according to the protocol of the manufacturer.

To generate large unilamellar vesicles (LUVs), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC, Avanti Polar Lipids) and 1,2-dioleoyl-sn-glycero-3-phospho-l-serine (sodium salt) (DOPS, Avanti Polar Lipids) were first prepared at 80% DOPC and 20% DOPS, freeze dried, and hydrated with a solution containing 25 mM 6-carboxyfluorescein. The suspension was bath sonicated, freeze-thawed, and extruded (Avanti Mini Extruder) using a Nucleopore 0.1 μm membrane (Whatman) to yield LUVs, which were washed three times in PBS to remove excess 6-carboxyfluorescein. At this concentration, the fluorescence of 6-carboxyflurescein self-quenches. With liposomal rupture, the 6-carboxyfluorescein is released into the bathing solution, thereby releasing the self-quenching with fluorescence monitored in a spectrofluorometer. The liposomal rupture assay was setup by mixing equal amounts of the prepared LUVs with 0.4 mg/mL human NINJ1 α-helix region peptide (HYASKKSAAESMLDIALLMANASQLKAVVE; GenScript Biotech Corporation) with either vehicle or glycine (50 mM) in PBS buffer. Where indicated, a sequence-scrambled analog peptide (IAAAAMKMYLANSLEHAKSLKVVLASQDS; GenScript Biotech Corporation) was used as a negative control for the human NINJ1 α-helix region peptide. Following 45 min, all liposomes were then ruptured by adding Triton X-100 and the maximum fluorescence (cargo release) recorded. The results were converted to percentage cargo release and background control subtracted. The lytic yeast peptide candidalysin (SIIGIIMGILGNIPQVIQIIMSIVKAFKGNK; Peptide Protein Research) was used as an additional positive control.

The secondary structure of the human NINJ1 α-helix region (amino acids 40–69; HYASKKSAAESMLDIALLMANASQLKAVVE; GenScript Biotech Corporation) was measured using a Jasco J-1500 spectropolarimeter. For this assay, peptide solutions from a 10 mg/mL stock in 5% DMSO in ddH₂O were diluted to 0.2 mg/mL in buffer (20 mM sodium phosphate, pH 7.4, 10 mM NaCl, and 1% sodium dodecyl sulfate) with the final peptide concentration determined using a bicinchoninic acid (BCA) protein assay. NINJ1 helix peptide was titrated with glycine between 0 and 20 mM. 250 µL of the glycine titrated human NINJ1 helix peptide solutions were pipetted into 1 mm path length quartz CD cuvettes, capped, and placed in the Peltier temperature-controlled CD sample holder for analysis. A corresponding buffer blank spectrum was subtracted out from the sample datasets. In all conditions, spectra were recorded between 260 and 190 nm using 50 nm/min scanning speed, 0.5 nm data pitch, 1 s DIT, and 1 nm bandwidth. Between 3 and 20 accumulations were averaged. The CD studies were performed at the Structural and Biophysical Core Facility, The Hospital for Sick Children, Toronto, Canada.

TIRF and STED microscopy images of mouse macrophages were analyzed in Imaris (Oxford Instruments, Abingdon, United Kingdom) software. The Spot tool was used to identify NINJ1 puncta with parameters (estimated puncta XY diameter, region type, and quality filter) set using images from the LPS-primed group and applied to all samples across all experiments. Cells were contoured using the surfaces tool to measure cell area. The density of NINJ1 puncta was calculated on a per-cell basis by dividing the total number of puncta within the contoured plasma membrane area. TIRF microscopy images of human primary macrophages were analyzed in FIJI, applying thresholds (triangle algorithm) and using the analyze particles tool to segment cells in the Cholera toxin subunit B channel. The find maxima command was used to identify NINJ1 puncta within these cell outlines, and the measurement tool was used to measure the area of the cell outlines. The density of NINJ1 puncta was calculated on a per-cell basis by dividing the number of puncta within a cell outline with its area.

Statistical testing was calculated using Prism 8.3.1 or 9.0 (GraphPad Software Inc, La Jolla, CA, USA). Experiments with more than two groups were tested using ANOVA with Tukey’s multiple comparison test. Unless otherwise indicated, presented data are representative of at least three independent experiments or donors and are provided as mean ± SEM. All collected data was analyzed. Unless otherwise specified, for non-quantitative data, such as western blots, experiments were replicated three times with representative images shown in the figures.

All animal studies were approved by the Hospital for Sick Children Animal Care Committee (AUP #47781). All human studies were conducted according to the principles expressed in the Helsinki Declaration and approved by the Regional Committee for Medical and Health Research Ethics (No. 2009/2245). Informed consent was obtained from all subjects prior to sample collection.

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

We thank Dr Nobuhiko Kayagaki and Dr Vishva Dixit for providing the rabbit monoclonal anti-mouse NINJ1 antibody, Dr John Brumell for providing pneumolysin, and Anne Marstad for technical assistance. We thank Dr Greg Wasney at the Structural and Biophysical Core Facility, The Hospital for Sick Children, for his technical assistance with the circular dichroism studies. All imaging of the mouse and human cells was performed at the SickKids Imaging Facility at The Hospital for Sick Children and the Cellular and Molecular Imaging Core Facility at NTNU, respectively. Graphical abstract created with BioRender.com. The authors declare no competing financial interests.

This work was supported by a Mentored Research Award from the International Anesthesia Research Society and an Early Investigator Award from the Department of Anesthesiology and Pain Medicine, University of Toronto to BES; by grants (287696, 223255) from the Research Council of Norway to THF; a Ragon Early Independence Fellowship to CLE; NIH grants AI133524, AI093589, AI116550, and P30DK34854 to JCK; and a fellowship to PD by the Boehringer Ingelheim Fonds.

Human subjects: All human studies were conducted according to the principles expressed in the Helsinki Declaration and approved by the Regional Committee for Medical and Health Research Ethics (No. 2009/2245). Informed consent was obtained from all subjects prior to sample collection.

All animal studies were approved by the Hospital for Sick Children Animal Care Committee (AUP #47781).

1. Preprint posted: December 12, 2021 (view preprint)
2. Received: March 14, 2022
3. Accepted: December 5, 2022
4. Accepted Manuscript published: December 5, 2022 (version 1)
5. Accepted Manuscript updated: December 8, 2022 (version 2)
6. Version of Record published: December 15, 2022 (version 3)

© 2022, Borges, Sætra et al.

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