Methionine oxidation selectively enhances T cell reactivity against a melanoma antigen

. 2023 Jun 25;26(7):107205. doi: 10.1016/j.isci.2023.107205

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

Tyrosinase T311	Santa Cruz Biotechnology	Cat#sc-20035; R RID:AB_628420
Calnexin	Abcam	Cat#ab-22595; R RID:AB_2069006
FITC Mouse Anti-Human HLA-A2 Clone BB7.2	BD Pharmingen™	Cat# 551285; R RID:AB_394130
FITC Mouse Anti-Human CD8 Clone RPA-T8	BD Pharmingen™	Cat#561948; R RID: AB_11154582
anti-human MHC Class I (HLA-A, HLA-B, HLA-C) W6/32	Department of Oncology, UNIL-CHUV, University of Lausanne, Epalinges, Switzerland	N/A
Donkey anti-mouse	JacksonImmunoResearch	Cat#715-035-150; RRID: AB_2340770
Donkey anti-rabbit	JacksonImmunoResearch	Cat# 711-035-152; RRID: AB_10015282

Chemicals, peptides, and recombinant proteins

Hydrogen peroxide	Sigma-Aldrich	16911
Methanol	Sigma-Aldrich	34966
LC-MS water	Sigma-Aldrich	39253
Formic acid – FA	Sigma-Aldrich	56302
Acetonitrile – ACN	Sigma-Aldrich	34967
MgCl₂	Sigma Aldrich	M4880
NaCl	Santa Cruz Biotechnology	sc-203274
EDTA	Santa Cruz Biotechnology	sc-29092
Citric acid	Merck Millipore	100241
Na₂HPO₄	Santa Cruz Biotechnology	sc-203277
Tris	Santa Cruz Biotechnology	sc-3715
Triton X-100	Sigma Aldrich	T-9284
Peptide: YM2_SODGTM6_SOSQV (>98 % purity),	Gene Script	N/A
Peptides: YMDGTMSQV (Tyr_369-377) light, heavy, YM2_SODGTM6_SOSQV (>98 % purity),	Gene Script	N/A
Peptide: GLYDGMEHL (MAGE-A10_254-262)	Peptide and Tetramer Core Facility, UNIL-CHUV, Epalinges, Switzerland	N/A
Peptides: GILGFVFTL (Influenza matrix58-66) labelled or unlabelled with biotin,	Peptide and Tetramer Core Facility, UNIL-CHUV, Epalinges, Switzerland	N/A
Peptide: ELAGIGILTV (Melan-A_26-35)	Peptide and Tetramer Core Facility, UNIL-CHUV, Epalinges, Switzerland	N/A
Peptide: EAAGIGILTI	Peptide and Tetramer Core Facility, UNIL-CHUV, Epalinges, Switzerland	N/A
Peptide: Cy5-labeled HBVc	Peptide and Tetramer Core Facility, UNIL-CHUV, Epalinges, Switzerland	N/A
Tetramer: APC-labeled HLA-A2/YMDGTMSQV	Peptide and Tetramer Core Facility, UNIL-CHUV, Epalinges, Switzerland	N/A
Tetramer: APC-labeled HLA-A2/GLYDGMEHL	Peptide and Tetramer Core Facility, UNIL-CHUV, Epalinges, Switzerland	N/A
E coli purified HLA-A∗02:01	Peptide and Tetramer Core Facility, UNIL-CHUV, Epalinges, Switzerland	N/A
Human β2-microglobulin	Proteintech	Ag27803
IL-2	PeproTech	200-02

Critical commercial assays

IFNγ -ELISA kit	MyBiosource	MBS161542
Pierce™ BCA Protein Assay Kit	Thermo Fisher Scientific	23225
Immobilon Crescendo Western HRP substrate	Merck Millipore	WBLUR0500

Deposited data

Raw and analyzed data	This paper	PXD039318

Experimental models: Cell lines

Tyrosinase_369-377(YMD) and MAGE-A10 specific CD8⁺ T cells	Ludwig Institute for Cancer Research, Lausanne Branch; Lausanne; Switzerland.	N/A
Human T2 cells, CEMx721.174.T2	Ludwig Institute for Cancer Research, Lausanne Branch; Lausanne; Switzerland.	RRID: CVCL_2211
A375	European Collection of Animal Cell Cultures	RRID: CVCL_0132
A375-Tyr	Chiritoiu G. N. et al. (2016)³²	10.1002/elps.201500449
Me 290	Ludwig Institute for Cancer Research, Lausanne Branch; Lausanne; Switzerland.	RRID: CVCL_S598
Me 275	Ludwig Institute for Cancer Research, Lausanne Branch; Lausanne; Switzerland.	RRID: CVCL_S597
Me 319	Ludwig Institute for Cancer Research, Lausanne Branch; Lausanne; Switzerland.	N/A

Software and algorithms

XCalibur v2.2/3.0	Thermo Fisher Scientific	https://thermo.flexnetoperations.com
LTQ Tune v2.70.112SP2	Thermo Fisher Scientific	https://thermo.flexnetoperations.com
Skyline software v2.6.0	MacCoss Lab Software	https://skyline.ms/project/home/software/Skyline/begin.view
CellQuest	BD Bioscience	https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/14_cellquest_prosoft_acquisit.pdf
FlowJo	Beckman Coulter	https://www.flowjo.com/solutions/flowjo/downloads
Cytobank	Beckman Coulter	https://community.cytobank.org
Generalized Amber Force Field - GAFF2	Wang, J. et al. (2004).⁴²	https://ambermd.org/AmberModels_organic.php
Antechamber from the AmberTools suite	Case, D.A. et al. (2020).⁴³	http://ambermd.org/antechamber/ac.html
OpenMM v.7.4.1	Eastman, P. et al. (2017).⁴⁴	https://github.com/openmm/openmm/releases
Modeller v.9.21	Webb, B. et al. (2016).⁴⁵	https://salilab.org/modeller/9.21/manual/
YANK v.0.25.2	Wang, K. et al. (2013).⁴⁶	N/A
PyMBAR package	Shirts, M.R. et al. (2008).⁴⁷	https://pypi.org/project/pymbar/
MDTraj 1.9.3	McGibbon, R. T. et al. (2015).⁴⁸	https://mdtraj.org/1.9.3/index.html
FreeSASA 2.0.3	Mitternacht, S. (2016).⁴⁹	https://pypi.org/project/freesasa/2.0.3/
Scipy v. 1.3.2	Virtanen, P. et al. (2020).⁵⁰	https://pypi.org/project/scipy/1.3.2/
PyMOL v.2.2.3	Schrödinger, L. (2018).⁵¹	https://pymol.org/2/
Molprobity server	Davis, I.W. et al. (2007).⁵²	http://molprobity.biochem.duke.edu
R v3.6.3	R Core Team	https://www.r-project.org
Prism software (GraphPad v.6.0).	GraphPad	https://www.graphpad.com
Prism software (GraphPad v.9.4.1)	GraphPad	https://www.graphpad.com
Image J	Image J	https://imagej.nih.gov/ij/download.html

Other

DMEM	Gibco	31966047
RPMI	Gibco	61870044
FBS	Gibco	10270106
Glutamine	Gibco	25030081
HEPES	Gibco	15630056
Sodium pyruvate	Gibco	11360039
Penicillin/Streptomycin	Gibco	15140122
Geneticin	Invivogen	ant-gn-5
Na₂⁵¹CrO₄ (⁵¹Cr)	PerkinElmer	NEZ030S
EndoH	Neb	P0702
Protease inhibitors	Roche	11697498001
LumaPlate	PerkinElmer	6005630
Terasaki multiwell plates	Greiner Bio-One	654180
v-bottom 96-well plate	Greiner Bio-One	651101
Analytical column (100 mm or 150 mm x 75 μm ID) packed with 3 μm ReproSil-Pur C18-AQ resin	Dr. Maisch GmbH	https://www.thermofisher.com/
Reversed-phase (RP) C18, 1.9 μm, Hypersil GOLD column (50 mm x 2.1 ID)	Thermo Fisher Scientific (Cat. No.: 25002-052130	https://www.thermofisher.com/
Preparative RP column C18 (100 x 10 mm, 5 μm)	Thermo Fischer Scientific (Cat. No.: 25005-109070)	https://www.thermofisher.com/
Dionex AFC 3000 fraction collector	Thermo Fisher Scientific	https://www.thermofisher.com/
Easy nanoLC II	Proxeon Biosystems	https://www.thermofisher.com/
LTQ-Orbitrap Velos Pro	Thermo Fisher Scientific	https://www.thermofisher.com/
Nanospray Flex Ion Source	Thermo Fisher Scientific	https://www.thermofisher.com/
HPLC Accela 600	Thermo Fisher Scientific	https://www.thermofisher.com/
FACS Calibur	BD Bioscience	https://www.bdbiosciences.com/en-eu/products/instruments/flow-cytometers/clinical-cell-analyzers/calibur-discontinuation
Gallios	Beckman Coulter	https://www.beckman.com/resources/videos/products/gallios-overview
FACS Verse	BD Bioscience	https://www.bdbiosciences.com/en-eu/products/instruments/flow-cytometers/research-cell-analyzers/bd-facsverse
TopCount NXT Microplate Scintillation	PerkinElmer	https://resources.perkinelmer.com/corporate/cmsresources/images/44-73884spc_topcountnxtmicropltscint.pdf