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Proteomic profiling reveals complexity of AML MSC
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PPARG PRKAA1.2 p172 PSMD9 p10 PSMD9
PTGS2
PTK2 RPS6KB1 p389 RPS6KB1
SFN
SMAD1
SRC
SRC p416
SRC p527 STAT1
STAT3 p727 STAT3 p727 STAT5A.B STK11
STMN1
TCF4
TGM2
TP53
TP53 p15
XIAP
YWHAE YWHAZ
CTNNB1 BECN1, HDAC3
LEF1 CTNNB1
AKT3, ATF3, CTNNB1
ELK1 p383
CTNNB1
AKT3, BIRC5, CTNNB1, XIAP
MAPK14, STAT5A.B AKT1S1
ARC, JMJD6 STAT1
GSK3A.B ERBB2 p1248
ATF3
SRC p416 BECN1, CDK4
SMAD1 SRC p527
CTNNB1 CAV1
BIRC5
CREB1, STMN1 NPM1, PPARG,
EGLN1
PRKAA1.2 p172, MAPK1.3 p202.p204
HNRNPK
BCL2L11, SFN EGLN1 EIF2S1 p51 CREB2 p133
MAP2K1 EGLN1 CTNNB1
Clinical correlation
Among the AML cases, there were very few clinical or laboratory features that showed a statistically significant correlation with the four MSC PCs. Specifically there was no association for continuous variables: age, percent BM or blood blasts, hemoglobin, platelet count, serum lactate dehydrogenase, albumin, creatinine, bilirubin fibrinogen, CD7, CD10, CD13, CD14, CD20, CD33 or CD34, or dis- crete variables disease status (new vs. salvage), race, French-American-British (FAB) Classification, perform- ance status, history of an antecedent hematologic disor- der, presence of an FLT3-ITD or presence of an NPM1 mutation (Table 1). However, a few notable associations between MSC protein signature and clinical features were observed. There was a statistical difference in presence of FLT3 D835 mutation (P=0.05). While no Class 1 or Class 2 samples contained FLT3 D835 mutation, 9.4% of Class 4 MSC and 5.6% of Class 3 MSC had the mutation (Table 1). Interestingly, there was a statistical difference in MSC population types between men and women (P=0.03) (Table 1). Men had a higher percentage of Class 4 and Class 3 MSC while women had a higher percentage of Class 1 and Class 2 MSC. At present it is unclear if sex influences MSC biology in the leukemic niche. Sex-specif- ic effects in the microenvironment in leukemia is not unprecedented as integrin-mediated adhesion-triggered activation of GSK3B occurs exclusively in leukemia pro- genitor cells derived from female AML patients.35 Total GSK3 and ITGA2 are present in protein constellation 1
Based on various combinations of proteins expressed within these three groups, we observed that normal or leukemic MSC samples clustered into four distinct PCs. The first (aqua in Figure 1A; top row of annotations above the heat map in Figure 1B), was comprised predominantly of NL-MSC (42 of 46 members), characterized by lower expression of proteins in constellations 1 and 2, and higher expression of constellation 3 proteins. This was consid- ered to represent the protein expression pattern of NL- MSC. AML cases in this signature are hereafter called Class 2.
A second signature (blue in Figure 1A and B) was com- prised predominantly of AML-MSC (62 of 72 members), and was characterized by the opposite protein expres- sion of the NL-MSC signature, with high expression of PC1 and 2 proteins and lower expression of PC3 pro- teins. This signature is called Class 4. Two groups with expression signatures between that of the Class 2 MSC and Class 4 MSC were also recognized. One signature (yellow in Figure 1A and top row of Figure 1B), com- prised of 12 AML-MSC and 11 NL-MSC, mirrored the expression of Class 2 for protein constellation 1, but that of Class 4 for PC2 and 3. AML cases in this group are hereafter referred to as Class 1. The final signature (orange in Figure 1A and top row of Figure 1B), consist- ing of 16 AML-MSC and 8 NL-MSC, mirrored the expression of Class 4 for PC1 and 3 but had low expres- sion of PC2, similar to Class 2. AML cases from this sig- nature are referred to as Class 3.
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