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A proteomic approach to understand the clinical significance of acute myeloid leukemia-derived extracellular vesicles reflecting essential characteristics of leukemia

ABSTRACT: Acute myeloid leukemia (AML) is the most common form of acute leukemia in adults and its overall incidence has been increasing gradually over the years. Extracellular vesicles (EVs) are known to express the properties of their parental cells, including proteins, RNAs, and DNAs. As EVs are representative of their parental tissues, they are excellent tools for understanding how cancer cells adapt to their environment. Proteomic analysis is a useful technique in cancer research that can be both quantitative and qualitative when determining the interrelationships between proteins in cells. It is clinically important to identify novel differentially expressed proteins (DEPs) from EVs in AML that could be used as biomarkers

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Cell, Stem Cell, Fibroblast

DISEASE(S): Acute Leukemia

SUBMITTER: Hyoseon Kim

LAB HEAD: Kwang Pyo Kim

PROVIDER: PXD022758 | Pride | 2020-12-03

REPOSITORIES: Pride

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			Action	DRS
	20170824_leukemia_F1-1.raw	Raw
	20170824_leukemia_F1-2.raw	Raw
	20170824_leukemia_F1-3.msf	Msf
	20170824_leukemia_F1-3.mzML	Mzml
	20170824_leukemia_F1-3.mzid.gz	Mzid

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Project description:Macrophages play a critical role in innate immunity, and the expression of early response genes orchestrate much of the initial response of the immune system. Macrophages undergo extensive transcriptional reprogramming in response to inflammatory stimuli such as Lipopolysaccharide (LPS). To identify gene transcription regulation patterns involved in early innate immune responses, we used two genome-wide approaches - gene expression profiling and chromatin immunoprecipitation-sequencing (ChIP-seq) analysis. We examined the effect of 2 hrs LPS stimulation on early gene expression and its relation to chromatin remodeling (H3 acetylation; H3Ac) and promoter binding of Sp1 and RNA polymerase II phosphorylated at serine 5 (S5P RNAPII), which is a marker for transcriptional initiation. Our results indicate novel and alternative gene regulatory mechanisms for certain proinflammatory genes. We identified two groups of up-regulated inflammatory genes with respect to chromatin modification and promoter features. One group, including highly up-regulated genes such as tumor necrosis factor (TNF), was characterized by H3Ac, high CpG content and lack of TATA boxes. The second group, containing inflammatory mediators (interleukins and CCL chemokines), was up-regulated upon LPS stimulation despite lacking H3Ac in their annotated promoters, which were low in CpG content but did contain TATA boxes. Genome-wide analysis showed that few H3Ac peaks were unique to either +/-LPS condition. However, within these, an unpacking/expansion of already existing H3Ac peaks was observed upon LPS stimulation. In contrast, a significant proportion of S5P RNAPII peaks (approx 40%) was unique to either condition. Furthermore, data indicated a large portion of previously unannotated TSSs, particularly in LPS-stimulated macrophages, where only 28% of unique S5P RNAPII peaks overlap annotated promoters. The regulation of the inflammatory response appears to occur in a very specific manner at the chromatin level for specific genes and this study highlights the level of fine-tuning that occurs in the immune response. 2 pairs of THP-1 cells either stimulated with LPS or not. ChIP using either H3K9/K14Ac, RNA Pol II (phospho S5) or SP1 antibody. This submission represents chip-seq component of study.

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A proteomic approach to understand the clinical significance of acute myeloid leukemia-derived extracellular vesicles reflecting essential characteristics of leukemia

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