Summary of Study ST002577

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 PR001662. The data can be accessed directly via it's Project DOI: 10.21228/M8VX33 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.

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Study IDST002577
Study TitleHydroxyproline Modulates Adaptive PD-L1 Expression and Autophagy
Study SummaryThe immune checkpoint protein PD-L1 plays critical roles in both immune system homeostasis and tumor progression. Impaired PD-1/PD-L1 function promotes autoimmunity and PD-L1 expression within tumors promotes immune evasion. If and how changes in metabolism or defined metabolites regulate PD-L1 expression is not fully understood. Here, using a metabolomics activity screening-based approach, we have determined that hydroxyproline (Hyp) significantly and directly enhances adaptive (i.e., IFN-γ induced) PD-L1 expression in multiple relevant myeloid and cancer cell types. Mechanistic studies reveal that Hyp acts as an inhibitor of IFN-γ-induced autophagic flux, which allows it to regulate this negative feedback mechanism, thereby contributing to its overall effect on PD-L1 expression. Due to its prevalence in fibrotic tumors, these findings suggest that hydroxyproline could contribute to the establishment of an immunosuppressive tumor microenvironment and that Hyp metabolism could be targeted to pharmacologically control PD-L1 expression for the treatment of cancer or autoimmune diseases.
Institute
Scripps Research Institute/University of California, Los Angeles
Last NamePalermo
First NameAmelia
AddressUniversity of California, Los Angeles, CA, USA
Emailapalermo@mednet.ucla.edu
Phone8582811389
Submit Date2023-04-10
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2023-05-17
Release Version1
Amelia Palermo Amelia Palermo
https://dx.doi.org/10.21228/M8VX33
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001662
Project DOI:doi: 10.21228/M8VX33
Project Title:Hydroxyproline Modulates Adaptive PD-L1 Expression and Autophagy
Project Summary:The immune checkpoint protein PD-L1 plays critical roles in both immune system homeostasis and tumor progression. Impaired PD-1/PD-L1 function promotes autoimmunity and PD-L1 expression within tumors promotes immune evasion. If and how changes in metabolism or defined metabolites regulate PD-L1 expression is not fully understood. Here, using a metabolomics activity screening-based approach, we have determined that hydroxyproline (Hyp) significantly and directly enhances adaptive (i.e., IFN-γ induced) PD-L1 expression in multiple relevant myeloid and cancer cell types. Mechanistic studies reveal that Hyp acts as an inhibitor of IFN-γ-induced autophagic flux, which allows it to regulate this negative feedback mechanism, thereby contributing to its overall effect on PD-L1 expression. Due to its prevalence in fibrotic tumors, these findings suggest that hydroxyproline could contribute to the establishment of an immunosuppressive tumor microenvironment and that Hyp metabolism could be targeted to pharmacologically control PD-L1 expression for the treatment of cancer or autoimmune diseases.
Institute:Scripps Research Institute/University of California, Los Angeles
Last Name:Palermo
First Name:Amelia
Address:Los Angeles, CA, USA 90095
Email:apalermo@mednet.ucla.edu
Phone:8582811389

Subject:

Subject ID:SU002679
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 Time
SA258753EXP1_S1_RPposT0
SA258754EXP1_S2_HILICnegT0
SA258755EXP1_S5_HILICposT0
SA258756EXP1_S4_HILICposT0
SA258757EXP1_S2_HILICposT0
SA258758EXP1_S1_HILICposT0
SA258759EXP1_S3_HILICposT0
SA258760EXP1_S1_HILICnegT0
SA258761EXP1_S5_HILICnegT0
SA258762EXP1_S2_RpposT0
SA258763EXP1_S4_HILICnegT0
SA258764EXP1_S3_HILICnegT0
SA258765EXP1_S5_RpposT0
SA258766EXP1_S4_RpposT0
SA258767EXP1_S3_RpposT0
SA258768EXP1_S7_HILICposT24
SA258769EXP1_S10_HILICposT24
SA258770EXP1_S9_HILICposT24
SA258771EXP1_S8_HILICposT24
SA258772EXP1_S6_RpposT24
SA258773EXP1_S6_HILICposT24
SA258774EXP1_S9_RpposT24
SA258775EXP1_S8_HILICnegT24
SA258776EXP1_S7_RpposT24
SA258777EXP1_S9_HILICnegT24
SA258778EXP1_S7_HILICnegT24
SA258779EXP1_S6_HILICnegT24
SA258780EXP1_S8_RpposT24
SA258781EXP1_S10_RpposT24
SA258782EXP1_S10_HILICnegT24
SA258783EXP1_S14_RpposT48
SA258784EXP1_S11_RpposT48
SA258785EXP1_S12_RpposT48
SA258786EXP1_S13_RpposT48
SA258787EXP1_S15_RpposT48
SA258788EXP1_S11_HILICposT48
SA258789EXP1_S12_HILICposT48
SA258790EXP1_S13_HILICposT48
SA258791EXP1_S12_HILICnegT48
SA258792EXP1_S13_HILICnegT48
SA258793EXP1_S14_HILICnegT48
SA258794EXP1_S15_HILICnegT48
SA258795EXP1_S14_HILICposT48
SA258796EXP1_S15_HILICposT48
SA258797EXP1_S11_HILICnegT48
SA258798EXP1_S19_RpposT72
SA258799EXP1_S20_RpposT72
SA258800EXP1_S16_RpposT72
SA258801EXP1_S18_RpposT72
SA258802EXP1_S17_RpposT72
SA258803EXP1_S18_HILICnegT72
SA258804EXP1_S17_HILICposT72
SA258805EXP1_S20_HILICposT72
SA258806EXP1_S19_HILICposT72
SA258807EXP1_S16_HILICposT72
SA258808EXP1_S20_HILICnegT72
SA258809EXP1_S17_HILICnegT72
SA258810EXP1_S18_HILICposT72
SA258811EXP1_S19_HILICnegT72
SA258812EXP1_S16_HILICnegT72
Showing results 1 to 60 of 60

Collection:

Collection ID:CO002672
Collection Summary:Cell pellets were washed with PBS and stored at -80 C until sample preparation
Sample Type:AML cells
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002691
Treatment Summary:THP-1 cells stimulated with IFN-gamma

Sample Preparation:

Sampleprep ID:SP002685
Sampleprep Summary:THP-1 cells were centrifuged and washed with PBS 3 times. The supernatant was discarded, and 1 mL cold MeOH/ACN/H2O (2:2:1) was added to the cell pellets, vortexed, and sonicated in an ice cold bath for 15 min, 3 times. Samples were kept at – 20 ˚C for 1h, centrifuged (13000 rpm for 15 min, 4˚C). The supernatant was evaporated and reconstituted in ACN/H2O (1:1) (volume normalized to viable cell count). Samples were transferred to glass vials and stored at - 80 ˚C until analysis.

Combined analysis:

Analysis ID AN004246 AN004247 AN004248
Analysis type MS MS MS
Chromatography type Reversed phase HILIC HILIC
Chromatography system Bruker Elute Bruker Elute Bruker Elute
Column ACQUITY BEH C18 (1.0 × 100 mm, 1.7-μm) ACQUITY BEH Amide (1.0 × 100 mm, 1.7 μm) ACQUITY BEH Amide (1.0 × 100 mm, 1.7 μm)
MS Type ESI ESI ESI
MS instrument type QTOF QTOF QTOF
MS instrument name Bruker Impact II Bruker Impact II Bruker Impact II
Ion Mode POSITIVE NEGATIVE POSITIVE
Units counts counts Counts

Chromatography:

Chromatography ID:CH003153
Chromatography Summary:For RP separation, an ACQUITY BEH C18 column (1.0 × 100 mm, 1.7-μm particle size; Waters Corporation, Milford, MA) was used. Flow was 150 μl/min, and a binary buffer system consisting of buffer A (0.1% FA) and buffer B (0.1% FA in acetonitrile) was used. The gradient for RP was: 99% A for 1 min, 1% A over 9 min, 35% A over 13 min, 60% A over 3 min, and held at 60% A for an additional 1 min. The sample injection volume was 2 μl.
Instrument Name:Bruker Elute
Column Name:ACQUITY BEH C18 (1.0 × 100 mm, 1.7-μm)
Column Temperature:27
Flow Gradient:99% A for 1 min, 1% A over 9 min, 35% A over 13 min, 60% A over 3 min, and held at 60% A for an additional 1 min
Flow Rate:150 μl/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% aetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH003154
Chromatography Summary:For HILIC separations, an ACQUITY BEH Amide (1.0 × 100 mm, 1.7 μm, Water Corporation, Milford, MA, USA) was used for the analysis. The gradient for HILIC consisted of 1% A for 1 min, 35% A over 13 min, 60% A over 3 min, and held at 60% A for 1 additional minute.
Instrument Name:Bruker Elute
Column Name:ACQUITY BEH Amide (1.0 × 100 mm, 1.7 μm)
Column Temperature:27
Flow Gradient:1% A for 1 min, 35% A over 13 min, 60% A over 3 min, and held at 60% A for 1 additional minute
Flow Rate:150 μl/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% aetonitrile; 0.1% formic acid
Chromatography Type:HILIC

MS:

MS ID:MS003993
Analysis ID:AN004246
Instrument Name:Bruker Impact II
Instrument Type:QTOF
MS Type:ESI
MS Comments:The mass spectrometer was calibrated using Sodium Formate peaks, before and post-run (internal calibration). Data were acquired over an m/z range of 50 to 1000 Da in positive and negative ionization mode. Electrospray source conditions were set as follows: end plate offset, 500 V; dry gas temperature, 200°C; drying gas, 6 liters/min; nebulizer, 1.6 bar; and capillary voltage, 3500 V.
Ion Mode:POSITIVE
  
MS ID:MS003994
Analysis ID:AN004247
Instrument Name:Bruker Impact II
Instrument Type:QTOF
MS Type:ESI
MS Comments:The mass spectrometer was calibrated using Sodium Formate peaks, before and post-run (internal calibration). Data were acquired over an m/z range of 50 to 1000 Da in positive and negative ionization mode. Electrospray source conditions were set as follows: end plate offset, 500 V; dry gas temperature, 200°C; drying gas, 6 liters/min; nebulizer, 1.6 bar; and capillary voltage, 3500 V.
Ion Mode:NEGATIVE
  
MS ID:MS003995
Analysis ID:AN004248
Instrument Name:Bruker Impact II
Instrument Type:QTOF
MS Type:ESI
MS Comments:The mass spectrometer was calibrated using Sodium Formate peaks, before and post-run (internal calibration). Data were acquired over an m/z range of 50 to 1000 Da in positive and negative ionization mode. Electrospray source conditions were set as follows: end plate offset, 500 V; dry gas temperature, 200°C; drying gas, 6 liters/min; nebulizer, 1.6 bar; and capillary voltage, 3500 V.
Ion Mode:POSITIVE
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