Summary of Study ST002738

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001703. The data can be accessed directly via it's Project DOI: 10.21228/M8K99P This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study ID	ST002738
Study Title	Innate immune and metabolic signaling retain damaged mitochondria at cell membranes for mitoxyperilysis
Study Summary	Innate immune activation coupled with metabolic disruptions play critical roles in many diseases, often leading to mitochondrial dysfunction and oxidative stress that drive pathogenesis. However, mechanistic regulation under these conditions remains poorly defined. Here, we report a distinct lytic cell death mechanism induced by innate immune signaling and metabolic disruption, independent of caspase activity and previously described pyroptosis, PANoptosis, necroptosis, ferroptosis, and oxeiptosis. Instead, mitochondria undergoing BAX/BAK1/BID-dependent oxidative stress maintained prolonged plasma membrane contact, leading to local oxidative damage, a process we termed mitoxyperiosis. This process then caused membrane lysis and cell death, mitoxyperilysis. mTORC2 regulated the cell death, and mTOR inhibition restored cytoskeletal activity for lamellipodia retractions to mobilize mitochondria away from the membrane, preserving integrity. Activating this pathway in vivo regressed tumors in an mTORC2-dependent manner. Overall, our results identify a lytic cell death modality in response to the synergism of innate immune signaling and metabolic disruption.
Institute	St Jude Children's Research Hospital
Last Name	Wang
First Name	Yaqiu
Address	262 Danny Thomas Pl
Email	yaqiu.wang@stjude.org
Phone	901-595--3477
Submit Date	2023-06-16
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2025-11-28
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001703
Project DOI:	doi: 10.21228/M8K99P
Project Title:	Innate immune and metabolic signaling retain damaged mitochondria at cell membranes for mitoxyperilysis
Project Summary:	Innate immune activation coupled with metabolic disruptions play critical roles in many diseases, often leading to mitochondrial dysfunction and oxidative stress that drive pathogenesis. However, mechanistic regulation under these conditions remains poorly defined. Here, we report a distinct lytic cell death mechanism induced by innate immune signaling and metabolic disruption, independent of caspase activity and previously described pyroptosis, PANoptosis, necroptosis, ferroptosis, and oxeiptosis. Instead, mitochondria undergoing BAX/BAK1/BID-dependent oxidative stress maintained prolonged plasma membrane contact, leading to local oxidative damage, a process we termed mitoxyperiosis. This process then caused membrane lysis and cell death, mitoxyperilysis. mTORC2 regulated the cell death, and mTOR inhibition restored cytoskeletal activity for lamellipodia retractions to mobilize mitochondria away from the membrane, preserving integrity. Activating this pathway in vivo regressed tumors in an mTORC2-dependent manner. Overall, our results identify a lytic cell death modality in response to the synergism of innate immune signaling and metabolic disruption.
Institute:	St Jude Children's Research Hospital
Last Name:	Wang
First Name:	Yaqiu
Address:	262 Danny Thomas Pl, Memphis, Tennessee, 38105, USA
Email:	yaqiu.wang@stjude.org
Phone:	+1-901-595-3477

Subject:

Subject ID:	SU002845
Subject Type:	Cultured cells
Subject Species:	Mus musculus
Taxonomy ID:	10090
Species Group:	Mammals

Factors:

Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment
SA288762	YW_01272023_Metabo_00_Neg	BLANK
SA288763	YW_01272023_Metabo_00_Pos	BLANK
SA288764	YW_01272023_Metabo_10_Neg	CS+LPS_WT
SA288765	YW_01272023_Metabo_11_Neg	CS+LPS_WT
SA288766	YW_01272023_Metabo_10_Pos	CS+LPS_WT
SA288767	YW_01272023_Metabo_11_Pos	CS+LPS_WT
SA288768	YW_01272023_Metabo_12_Pos	CS+LPS_WT
SA288769	YW_01272023_Metabo_12_Neg	CS+LPS_WT
SA288770	YW_01272023_Metabo_07_Neg	CS_WT
SA288771	YW_01272023_Metabo_08_Neg	CS_WT
SA288772	YW_01272023_Metabo_09_Neg	CS_WT
SA288773	YW_01272023_Metabo_07_Pos	CS_WT
SA288774	YW_01272023_Metabo_09_Pos	CS_WT
SA288775	YW_01272023_Metabo_08_Pos	CS_WT
SA288776	YW_01272023_Metabo_06_Pos	LPS_WT
SA288777	YW_01272023_Metabo_06_Neg	LPS_WT
SA288778	YW_01272023_Metabo_04_Neg	LPS_WT
SA288779	YW_01272023_Metabo_04_Pos	LPS_WT
SA288780	YW_01272023_Metabo_05_Neg	LPS_WT
SA288781	YW_01272023_Metabo_05_Pos	LPS_WT
SA288782	YW_01272023_Metabo_01_Pos	Media_WT
SA288783	YW_01272023_Metabo_01_Neg	Media_WT
SA288784	YW_01272023_Metabo_02_Neg	Media_WT
SA288785	YW_01272023_Metabo_03_Pos	Media_WT
SA288786	YW_01272023_Metabo_03_Neg	Media_WT
SA288787	YW_01272023_Metabo_02_Pos	Media_WT

Showing results 1 to 26 of 26

Showing results 1 to 26 of 26

Collection:

Collection ID:	CO002838
Collection Summary:	Ten million BMDMs were stimulated as indicated in 100 mm plates for 9 h. The medium was removed by aspiration, and the cells were washed once with ice-cold saline. Next, the cells were carefully harvested using a plastic scraper in 1.5 ml ice-cold saline. The cells were centrifuged at 150 × g for 2 min at room temperature, and the cell pellets were flash-frozen in liquid nitrogen and then stored at −80°C for a later extraction of metabolites.
Sample Type:	Cultured cells
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR002854
Treatment Summary:	Treatment of cells were done as indicated in the study design table. Four types of treatment were used in WT cells. "Media_WT", "LPS_WT", "CS_WT", "CS+LPS_WT" denote the WT cells receiving Media, LPS(lipopolysaccharide), CS(starvation) and CS+LPS treatment, respectively.

Sample Preparation:

Sampleprep ID:	SP002851
Sampleprep Summary:	Extraction of hydrophilic metabolites To extract the molecules with different polarity, an adapted three-phase solvent system was utilized to obtain total hydrophilic metabolites and lipids78. Briefly, the cell pellets were resuspended with 150 µL of saline, then 1.2 mL of chloroform/methanol/water (3:4:1, v/v/v) was added and homogenized using a Bead Ruptor Elite (OMNI international) for 30 s at 8 m/s. The homogenate was allowed to rest at 4ºC for 30 s and then centrifuged for 10 min at 21,000 g at 4ºC. After centrifugation, the upper aqueous phase was transferred into a new tube, frozen on dry ice, and then lyophilized. The dried extracts containing hydrophilic metabolites were dissolved using 40 µL of water: acetonitrile (95:5, v/v) supplemented with 10 mM ammonium acetate, then transferred into autosampler vials, and 4 µL per injection was analyzed by LC-MS.

Sampleprep ID:

SP002851

Sampleprep Summary:

Extraction of hydrophilic metabolites To extract the molecules with different polarity, an adapted three-phase solvent system was utilized to obtain total hydrophilic metabolites and lipids78. Briefly, the cell pellets were resuspended with 150 µL of saline, then 1.2 mL of chloroform/methanol/water (3:4:1, v/v/v) was added and homogenized using a Bead Ruptor Elite (OMNI international) for 30 s at 8 m/s. The homogenate was allowed to rest at 4ºC for 30 s and then centrifuged for 10 min at 21,000 g at 4ºC. After centrifugation, the upper aqueous phase was transferred into a new tube, frozen on dry ice, and then lyophilized. The dried extracts containing hydrophilic metabolites were dissolved using 40 µL of water: acetonitrile (95:5, v/v) supplemented with 10 mM ammonium acetate, then transferred into autosampler vials, and 4 µL per injection was analyzed by LC-MS.

Combined analysis:

Analysis ID	AN004440	AN004441
Chromatography ID	CH003336	CH003336
MS ID	MS004187	MS004188
Analysis type	MS	MS
Chromatography type	HILIC	HILIC
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	Waters XBridge BEH Amide (150 x 2.1mm, 2.5um)	Waters XBridge BEH Amide (150 x 2.1mm, 2.5um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Exactive Plus Orbitrap	Thermo Exactive Plus Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	area	area

Chromatography:

Chromatography ID:	CH003336
Chromatography Summary:	A Vanquish Horizon UHPLC (Thermo Fisher Scientific) was used for the LC separations, using stepped gradient conditions as follows: 0–16.5 min, 1 to 50% B; 16.5–18 min, 50 to 99% B; 18–36 min, 99% B; 36–39 min, 99 to 1% B; 39–45 min, 1% B. Mobile phase A was water supplemented with 10 mM ammonium acetate. Mobile phase B was acetonitrile. The column used was an xBride BEH Amide Column (2.1 mm x 150 mm, 2.5 μm) (Waters Corp.), operated at 40°C. The flow rate was 100 μL/min, and the injection volume was 4 μL. The collected positive and negative mode data were analyzed separately.
Instrument Name:	Thermo Vanquish
Column Name:	Waters XBridge BEH Amide (150 x 2.1mm, 2.5um)
Column Temperature:	40
Flow Gradient:	0–16.5 min, 1 to 50% B; 16.5–18 min, 50 to 99% B; 18–36 min, 99% B; 36–39 min, 99 to 1% B; 39–45 min, 1% B.
Flow Rate:	100 μL/min
Solvent A:	water supplemented with 10 mM ammonium acetate
Solvent B:	acetonitrile
Chromatography Type:	HILIC

MS:

MS ID:	MS004187
Analysis ID:	AN004440
Instrument Name:	Thermo Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	A Thermo Fisher Scientific Q Exactive hybrid quadrupole-Orbitrap mass spectrometer (QE-MS) (Thermo Fisher Scientific) equipped with a HESI-II probe was employed as the detector. For each sample, two chromatographic runs were carried out subsequently, acquiring separately data for negative and positive ions. The QE-MS was operated using a data-dependent LC-MS/MS method (Top10 dd-MS2) for both, positive and negative ion modes. The mass spec was operated at a resolution of 140,000 (FWHM, at m/z 200), AGC targeted of 3 × 106, Max injection time 100 msec. The instrument’s operating conditions were: scan range 60–900 m/z, sheath gas flow 20, aux gas flow 5, sweep gas 1, spray voltage 3.6 kV for positive mode and 2.5 kV for negative mode, capillary temperature 320ºC, S-lenses RF level 55, aux gas heater 320ºC. For the Top10 dd-MS2 conditions a resolution of 35,000 was used, AGC targeted of 1 × 105, max injection time 100 msec, MS2 isolation width 1.0 m/z, NCE 35. The collected data from negative and positive mode were analyzed separately in Compound Discoverer 3.3 (CD3.3) (Thermo Fisher Scientific). A pre-defined workflow from the software was employed: Untargeted Metabolomics with statistics, Detect Unknowns with ID using online databases and mzLogic. The spectra alignment node used the first sample as the reference file. The compound detection option was set for a signal-to-noise ratio ≥ 1.5, min peak intensity 1 × 106, parent ion mass tolerance of ±5 ppm, RT tolerance of 0.25 min, and preferred fragments data selection M+H, M-H. The data was normalized by the constant mean algorithm. The metabolites identifications and pathway analysis nodes used the default features in this metabolomics workflow.
Ion Mode:	POSITIVE

MS ID:	MS004188
Analysis ID:	AN004441
Instrument Name:	Thermo Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	A Thermo Fisher Scientific Q Exactive hybrid quadrupole-Orbitrap mass spectrometer (QE-MS) (Thermo Fisher Scientific) equipped with a HESI-II probe was employed as the detector. For each sample, two chromatographic runs were carried out subsequently, acquiring separately data for negative and positive ions. The QE-MS was operated using a data-dependent LC-MS/MS method (Top10 dd-MS2) for both, positive and negative ion modes. The mass spec was operated at a resolution of 140,000 (FWHM, at m/z 200), AGC targeted of 3 × 106, Max injection time 100 msec. The instrument’s operating conditions were: scan range 60–900 m/z, sheath gas flow 20, aux gas flow 5, sweep gas 1, spray voltage 3.6 kV for positive mode and 2.5 kV for negative mode, capillary temperature 320ºC, S-lenses RF level 55, aux gas heater 320ºC. For the Top10 dd-MS2 conditions a resolution of 35,000 was used, AGC targeted of 1 × 105, max injection time 100 msec, MS2 isolation width 1.0 m/z, NCE 35. The collected data from negative and positive mode were analyzed separately in Compound Discoverer 3.3 (CD3.3) (Thermo Fisher Scientific). A pre-defined workflow from the software was employed: Untargeted Metabolomics with statistics, Detect Unknowns with ID using online databases and mzLogic. The spectra alignment node used the first sample as the reference file. The compound detection option was set for a signal-to-noise ratio ≥ 1.5, min peak intensity 1 × 106, parent ion mass tolerance of ±5 ppm, RT tolerance of 0.25 min, and preferred fragments data selection M+H, M-H. The data was normalized by the constant mean algorithm. The metabolites identifications and pathway analysis nodes used the default features in this metabolomics workflow.
Ion Mode:	NEGATIVE