Summary of Study ST002164
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 PR001377. The data can be accessed directly via it's Project DOI: 10.21228/M8QQ6X This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST002164 |
| Study Title | TMEM41B and VMP1 modulate cellular lipid and energy metabolism for facilitating Dengue virus infection |
| Study Type | untargeted analysis |
| Study Summary | Lipid metabolism is an intricate yet crucial cellular process co-opted by multiple viruses for replication and biogenesis. Transmembrane Protein 41B (TMEM41B) and Vacuole Membrane Protein 1 (VMP1) are two recently identified ER-resident lipid scramblases that play a role in autophagosome formation and cellular lipid metabolism. Importantly, TMEM41B is also a newly validated host dependency factor required for productive infection of several medically important enveloped RNA viruses, such as flaviviruses and human coronaviruses. However, the exact underlying mechanism of TMEM414B in modulating viral infections remains an open question. Here, we uncovered that TMEM41B and VMP1 deficiencies severely impaired replication of flavivirus and human coronavirus via multiple parallel cellular mechanisms. In accordance with previous reports, we validated that both TMEM41B and VMP1 are indispensable for all four serotypes of dengue virus (DENV) and human coronavirus OC43 (HCoV-OC43) to infect human cells, but not chikungunya virus, an alphavirus. Impaired dengue virus replication in TMEM41B and VMP1 deficient cells could induce a robust activation of innate immune RNA sensing as evidenced by hyperactivation of RIG-I and MDA5. However, this phenomenon was a consequence but not the root cause of the diminished viral replication. Notably, the impact of TMEM41B deficiency on DENV replication could be reversed by complementing the cells using exogenous unsaturated fatty acids, indicating a metabolic role for TMEM41B in flavivirus infection. Furthermore, we found that derailed cellular energy metabolism could be a contributing factor to block DENV infection as TMEM41B and VMP1 deficient cells harbored higher levels of compromised mitochondria that exhibited aberrant functions in facilitating beta-oxidation. Using lipidome and metabolome profiling of TMEM41B and VMP1 deficient cells, we further revealed that each of these genetic deficiencies result in distinctive cellular metabolic dysregulations, underlining their necessity for a balanced metabolic landscape, and strengthening the metabolic role of these ER membrane proteins in facilitating virus infection. Our results highlighted that TMEM41B and VMP1 are required for homeostasis of cellular metabolism, and this metabolic role contributes to their essentiality in facilitating DENV infection. |
| Institute | Singapore-MIT Alliance for Research and Technology (SMART Centre) |
| Last Name | Cui |
| First Name | Liang |
| Address | 1 CREATE Way, #03-12 Enterprise Wing, Singapore, Singapore, 138602, Singapore |
| liangcui@smart.mit.edu | |
| Phone | 65-84328978 |
| Submit Date | 2022-05-11 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-08-03 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001377 |
| Project DOI: | doi: 10.21228/M8QQ6X |
| Project Title: | TMEM41B and VMP1 modulate cellular lipid and energy metabolism for facilitating Dengue virus infection |
| Project Type: | untargeted metabolomics |
| Project Summary: | Lipid metabolism is an intricate yet crucial cellular process co-opted by multiple viruses for replication and biogenesis. Transmembrane Protein 41B (TMEM41B) and Vacuole Membrane Protein 1 (VMP1) are two recently identified ER-resident lipid scramblases that play a role in autophagosome formation and cellular lipid metabolism. Importantly, TMEM41B is also a newly validated host dependency factor required for productive infection of several medically important enveloped RNA viruses, such as flaviviruses and human coronaviruses. However, the exact underlying mechanism of TMEM414B in modulating viral infections remains an open question. Here, we uncovered that TMEM41B and VMP1 deficiencies severely impaired replication of flavivirus and human coronavirus via multiple parallel cellular mechanisms. In accordance with previous reports, we validated that both TMEM41B and VMP1 are indispensable for all four serotypes of dengue virus (DENV) and human coronavirus OC43 (HCoV-OC43) to infect human cells, but not chikungunya virus, an alphavirus. Impaired dengue virus replication in TMEM41B and VMP1 deficient cells could induce a robust activation of innate immune RNA sensing as evidenced by hyperactivation of RIG-I and MDA5. However, this phenomenon was a consequence but not the root cause of the diminished viral replication. Notably, the impact of TMEM41B deficiency on DENV replication could be reversed by complementing the cells using exogenous unsaturated fatty acids, indicating a metabolic role for TMEM41B in flavivirus infection. Furthermore, we found that derailed cellular energy metabolism could be a contributing factor to block DENV infection as TMEM41B and VMP1 deficient cells harbored higher levels of compromised mitochondria that exhibited aberrant functions in facilitating beta-oxidation. Using lipidome and metabolome profiling of TMEM41B and VMP1 deficient cells, we further revealed that each of these genetic deficiencies result in distinctive cellular metabolic dysregulations, underlining their necessity for a balanced metabolic landscape, and strengthening the metabolic role of these ER membrane proteins in facilitating virus infection. Our results highlighted that TMEM41B and VMP1 are required for homeostasis of cellular metabolism, and this metabolic role contributes to their essentiality in facilitating DENV infection |
| Institute: | Singapore-MIT Alliance for Research and Technology (SMART Centre) |
| Last Name: | Cui |
| First Name: | Liang |
| Address: | 1 CREATE Way, #03-12 Enterprise Wing, Singapore, Singapore, 138602, Singapore |
| Email: | liangcui@smart.mit.edu |
| Phone: | 65-84328978 |
Subject:
| Subject ID: | SU002250 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | genotype |
|---|---|---|
| SA207560 | DT3 | TMEM41B knockout |
| SA207561 | DT1 | TMEM41B knockout |
| SA207562 | DT2 | TMEM41B knockout |
| SA207563 | DV3 | VMP1 knockout |
| SA207564 | DV2 | VMP1 knockout |
| SA207565 | DV1 | VMP1 knockout |
| SA207566 | DH2 | wild type |
| SA207567 | DH3 | wild type |
| SA207568 | DH1 | wild type |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO002243 |
| Collection Summary: | 1x108 293FT, TMEM41B KO and VMP1 KO cells were washed with PBS thrice before adding 560 µl extraction solvent (methanol:water = 2:5), pre-cooled at −4°C. Cells were then scraped into the extraction solvent on ice and transferred into eppendorf tubes. |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR002262 |
| Treatment Summary: | NO TREATMENT |
Sample Preparation:
| Sampleprep ID: | SP002256 |
| Sampleprep Summary: | 1x108 293FT, TMEM41B KO and VMP1 KO cells were washed with PBS thrice before adding 560 µl extraction solvent (methanol:water = 2:5), pre-cooled at −4°C. Cells were then scraped into the extraction solvent on ice and transferred into eppendorf tubes. Then, 800 µL methyl tert-butyl ether (MTBE) was added and the samples were sonicated for 10 min. After centrifugation for 15 min at 3,000 rpm at 4°C to separate phases, the upper layer and lower layer were collected for lipidomics and metabolomics analysis, respectively. |
Combined analysis:
| Analysis ID | AN003546 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1290 ultrahigh pressure liquid chromatography system |
| Column | Agilent rapid resolution HT Zorbax SB-C18 |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6550 QTOF |
| Ion Mode | POSITIVE |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH002620 |
| Instrument Name: | Agilent 1290 ultrahigh pressure liquid chromatography system |
| Column Name: | Agilent rapid resolution HT Zorbax SB-C18 |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003304 |
| Analysis ID: | AN003546 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Mass data were collected between m/z 100 and 1000 at a rate of two scans per second. The ion spray voltage was set at 4,000 V, and the heated capillary temperature was maintained at 350°C. The drying gas and nebulizer nitrogen gas flow rates were 12.0 L/min and 50 psi, respectively. Two reference masses were continuously infused to the system to allow constant mass correction during the run: m/z 121.0509 (C5H4N4) and m/z 922.0098 (C18H18O6N3P3F24). Raw spectrometric data were analyzed by MassHunter Qualitative Analysis software (Agilent Technologies, US) and the molecular features characterized by retention time, chromatographic peak intensity and accurate mass, were obtained by using the Molecular Feature Extractor algorithm. The features were then analyzed by MassHunter Mass Profiler Professional software (Agilent Technologies, US). Only features with an intensity ≥ 20,000 counts (approximately three times the limit of detection of our LC-MS instrument), and found in at least 80% of the samples at the same sampling time point signal were kept for further processing. Next, a tolerance window of 0.15 min and 2 mDa was used for alignment of RT and m/z values. |
| Ion Mode: | POSITIVE |
