Dataset Information

MS-based proteomic and phosphoproteomic characterization of the AML proteome

ABSTRACT: Acute myeloid leukemia (AML) is a hematological cancer that affects mainly the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly two-thirds relapse within a short interval. Therefore, understanding of the biological factors that determine relapse has become a major interest in clinical AML. In order to identify the proteins and their phosphorylated modifications involved in AML relapse, we performed a global proteome and phosphoproteome study by liquid chromatography tandem mass spectrometry (LC-MS/MS) with primary cells from 41 AML patients at time of diagnosis that were defined as RELAPSE or REL_FREE according to their relapse status after a 5-year clinical follow-up post diagnosis. Our findings showed that the diagnostic sample of patients relapsing had increased levels of RNA processing and decreased expression of V-ATPases proteins along with CDKs and CSK2 activities. LC-MS/MS-based results were further validated with cell proliferation assays using V-ATPase inhibitor bafilomycin A1, CSK2 inhibitor CX-4945, CDK4/6 inhibitor abemaciclib and CDK2/7/9 inhibitor SNS-032. Our study presents molecules that could predict AML relapse and direct new therapeutic strategies that might circumvent more aggressive AML episodes.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Cell, Primary Cell, Myeloblast, Blood

DISEASE(S): Acute Myeloid Leukemia

SUBMITTER: Elise Aasebo

LAB HEAD: Frode Steingrimsen Berven

PROVIDER: PXD014997 | Pride | 2020-04-14

REPOSITORIES: Pride

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Publications

Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia.

Aasebø Elise E Berven Frode S FS Bartaula-Brevik Sushma S Stokowy Tomasz T Hovland Randi R Vaudel Marc M Døskeland Stein Ove SO McCormack Emmet E Batth Tanveer S TS Olsen Jesper V JV Bruserud Øystein Ø Selheim Frode F Hernandez-Valladares Maria M

Cancers 20200317 3

Acute myeloid leukemia (AML) is a hematological cancer that mainly affects the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly two-thirds relapse within a short interval. Understanding biological factors that determine relapse has become of major clinical interest in AML. We utilized liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify the protein changes and protein phosphorylation events ...[more]

PMID: 32192169

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Project description:Background: A fundamental hallmark of cancer cells is their ability to sustain proliferative signaling and cell survival, reflected in a cellular chemotherapy response that is poorly understood. We questioned whether chemotherapy modulated phospho-signaling at 4 and 24 h in vivo could provide information about long-term survival in acute myeloid leukemia (AML), and if the signaling response to therapy was more informative than analysis at time of diagnosis. Methods: Peripheral blood was collected from 32 younger AML patients (age 16-74 years), before, 4- and 24 hours after start of induction chemotherapy. Samples were analyzed by 36-dimensional mass cytometry for assessment of alterations in immunophenotypes and intracellular signaling using unsupervised and supervised machine learning approaches. Results were validated by RNA sequencing and mass spectrometry proteomics (Super SILAC). Targeted sequencing was used to characterize patient samples for recurrent AML mutations. Drug sensitivity and resistance testing ex vivo was compared to activation of relevant signal transduction pathways and mutational profile. Findings: 5-year patient survival was accurately predicted in the leukemic cell population at 24 hours after therapy onset by phospho-proteins p-ERK1/2 (T202/Y204) and p-p38 (T180/Y182). RNA sequencing showed induction of MAPK target gene expression and the AP-1 transcription complex in patients with high p-ERK1/2. Super-SILAC proteomics confirmed an increase in the abundance of p38 prime target MAPKAPK2(MK2) 24 hours after start of induction therapy. Ex vivo drug sensitivity testing demonstrated high sensitivity to MEK inhibitors in the patient cells with high p-ERK1/2 measured at diagnosis or 24 hours after start of chemotherapy. Interpretation: Early single cell signaling response to chemotherapy provided precise prognostic information independent of stratification by genetics. We propose that early functional measurement of chemotherapy-potentiated MAPK pathway signaling could identify non-responders to intensive chemotherapy allowing precise treatment adjustment.

Project description:Extraintestinal pathogenic Escherichia coli (ExPEC) have a capacity to cause serious infections of blood, the central nervous system and particularly the urinary tract. Relatively little is known about how ExPEC adapt their cell-wide protein expression to environments with different carbon sources and other required nutrients. We used label-free quantitative (LFQ) proteomic analysis to determine proteomes of five ExPEC strains purified from clinical blood cultures, and compared them with proteomes of reference uropathogenic E. coli strain 536 derived from blood culture and two chemically different solid media. We identified 2,883 proteins in total, and for 90% of the detected proteins described their relative quantitative levels based on LFQ intensity scores. Comparison of anaerobic and aerobic blood cultures revealed significant differences in the levels of 32 proteins out of 1854 shared proteins. A majority of these proteins was associated with acquisition and utilization of metal ions, which are critical either for anaerobic (nickel) or aerobic (iron) respiration. ANOVA analysis of the relative quantitative levels of 1758 proteins shared between the strains identified 47 differentially expressed proteins, including proteins involved in vitamin B6 metabolism, cell motility and virulence. Comparison of strain 536 proteomes derived from blood cultures and solid media showed substantial variation in the relative quantitative levels of 200 proteins, which represented 11% of the common proteins between the conditions. Blood culture condition was characteristic by upregulation of anaerobic fermentative metabolism, cell motility and iron utilization. In a response to the growth on solid media increased levels of proteins functional in aerobic respiration, catabolism of various biochemicals obtained from the media and protection against environmental stresses. The study presents the largest coverage of ExPEC/UPEC proteome to date,with a detail account of ExPEC metabolism under three chemically different environments.

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Dataset Information

MS-based proteomic and phosphoproteomic characterization of the AML proteome

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Publications

Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia.

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