Supplementary Materials and Methods
Comprehensive quantitative proteomic profiling of the pharmacodynamic
changes induced by MLN4924 in acute myeloid leukemia cells establishes
rationale for its combination with azacitidine
*
*
Valeria Visconte1 , Steffan T. Nawrocki2 , Claudia M. Espitia2, Kevin R. Kelly3, Anthony Possemato4,
Sean A. Beausoleil4, Yingchun Han1, Hetty E. Carraway5, Aziz Nazha5, Anjali S. Advani5, Jaroslaw P.
Maciejewski1, Mikkael A. Sekeres1,5, and Jennifer S. Carew1
1
Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland
Clinic, Cleveland, OH, USA; 2Division of Hematology/Oncology, Cancer Therapy and Research Center
at The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA; 3USC
Norris Comprehensive Cancer Center, Los Angeles, CA, USA; 4Cell Signaling Technology, Danvers,
MA, USA;
5
Leukemia Program, Department of Hematology/Oncology, Taussig Cancer Institute,
Cleveland Clinic, Cleveland, OH, *These two authors contributed equally to this work
Proteome profiling
MV4-11 cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum, 5,000
I.U/mL penicillin and 5,000 g/mL streptomycin. Cells were treated if cell viability was
estimated more than 95%. Cells (5 x 106) were treated with MLN4924 (1 μM) or vehicle control
(dimethyl sulfoxide) for 24 hours. Samples were collected in a urea lysis buffer, reduced, and
alkylated before being digested with Lys-C (Wako). After digestion, samples were purified over
SepPak C18 columns and eluted peptides were lyophilized. After lyophilization, 100 μg of each
sample was labeled using tandem mass tag (TMT) reagents (Thermo Fisher Pierce). Labeled
samples
were
then
combined
and
subjected
to
strong
cation
exchange
(SCX)
chromatography. The 6-plexes were run on the Accela high speed LC system (Thermo Fisher)
over a 4.6 mm × 200 mm SCX column packed with polysulfoethyl aspartamide material (5 μm
particle size, 200-Å pore). A 50-minute gradient was used to elute peptides from the column
and fractions were collected at every minute for the entire gradient. The first 40 fractions were
combined into 20 fractions before being purified again over a C18 SepPak column. All fractions
were then run individually on the Orbi-Velos using a 140-minute gradient. Peptide identification
was carried out in MS2 scans, whereas quantification of reporter ions was carried out using
MS3 scans1. In total, the 20 fractions were run consecutively for each 6-plex, occupying
approximately 47 hours of instrument time. Data generated from the mass spectrometry (MS)
analysis were processed using in-house software (Cell Signaling Technology) resulting in an
average of 3,900 quantified proteins per 6-plex.
Legends to the Supplemental Tables
Supplemental Table S1. Pathway analysis of up-regulated proteins in MV4-11 cells
treated with MLN4924. The list of 47 top ranked proteins with fold change 2 or greater in
MV4-11 treated with MLN4924 was analyzed using
Reactome network database
(http://www.reactome.org/) to specifically cluster the proteins.
Supplemental Table S2. List of the differentially expressed proteins between MV4-11
AML cells and A375 melanoma cells following treatment with MLN4924. Comparison of
the changes in proteomic profiling between MV4-11 AML cells and A375 melanoma cells (Liao
H, et al., Mol Cell Proteomics 2011).
Supplemental Table S3. Potential pathogenic and therapeutic implications of the
proteins significantly affected by MLN4924 treatment in AML. A literature search was
conducted for the proteins listed in Table 1 in order to find previously reported genetic and/or
protein interactions and available compounds targeting the specific proteins or pathways.
Supplemental Table S4. RNA helicase family members altered by treatment with
MLN4924 in MV4-11 cells. A complete list of RNA helicase family members was generated
by comparison of the proteomic profiling of MV4-11 MLN4924- treated vs. vehicle treated.
References
1. Ting L, Rad R, Gygi SP, Haas W. MS3 eliminates ratio distortion in isobaric multiplexed
quantitative proteomics. Nat Methods 2011; 8:937-940.