Liver-Specific Gene Expression in Cultured Human Hematopoietic Stem Cells

Abstract Abstract SCI-33 Epigenetic deregulation of gene expression through aberrant DNA methylation or histone modification plays an important role in the malignant transformation of hematopoietic cells. In particular, acute myeloid leukemias (AMLs) can be classified according to epigenetic signatures affecting DNA methylation or histone modifications affecting specific gene sets. Heterozygous somatic mutations in the loci encoding isocitrate dehydrogenase 1 and 2 (IDH1/2) occur in ∼20% of AMLs and are accompanied by global DNA hypermethylation and hypermethylation and silencing of a number of specific gene promoters. IDH1/2 mutations are almost completely mutually exclusive with somatic loss-of-function mutations in TET2, which hydroxylates methylcytosine (mCpG). DNA hydroxymethylation can function as an intermediate step in mCpG demethylation. TET2 mutant de novo AMLs also display global and promoter specific hypermethylation partially overlapping with IDH1/2 mutant cases. Mutations in the IDH1/2 loci result in a neomorphic enzyme that generates the aberrant oncometabolite 2-hydroxyglutarate (2HG) using α-ketoglutarate (αKG) as a substrate. 2HG can disrupt the activity of enzymes that use αKG as a cofactor, including TET2 and the jumonji family of histone demethylases. Expression of mutant IDH isoforms inhibits TET2 hydroxymethylation and jumonji histone demethylase functions. IDH and TET2 mutant AMLs accordingly exhibit reduced levels of hydroxymethylcytosine and a trend towards increased histone methylation. Mutant IDH or TET2 loss of function causes differentiation blockade and expansion of hematopoietic stem cells and TET2 knockout results in a myeloproliferative phenotype in mice. Hydroxymethylcytosine is in abundance in hematopoietic stem cells and displays specific distribution patterns, yet the function of this covalent modification is not fully understood. Recent data link TET2 with the function of cytosine deaminases as a pathway towards DNA demethylation, which has implications as well for B cell lymphomas and CML lymphoid blast crisis, which are linked with the actions of activation induced cytosine deaminase. Altogether, the available data implicate mutations in IDH1/2 and TET2 in promoting malignant transformation in several tissues, by disrupting epigenomics programming and altering gene expression patterning. Disclosures: Thompson: Agios Pharmaceuticals: Consultancy.

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Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics

Nature Communications ◽

10.1038/s41467-021-21650-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Lars Velten ◽

Benjamin A. Story ◽

Pablo Hernández-Malmierca ◽

Simon Raffel ◽

Daniel R. Leonce ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Cancer Stem Cells ◽

Single Cell ◽

Lineage Tracing ◽

Specific Gene ◽

Leukemic Stem Cells ◽

Hematopoietic Stem ◽

Mutational Status

AbstractCancer stem cells drive disease progression and relapse in many types of cancer. Despite this, a thorough characterization of these cells remains elusive and with it the ability to eradicate cancer at its source. In acute myeloid leukemia (AML), leukemic stem cells (LSCs) underlie mortality but are difficult to isolate due to their low abundance and high similarity to healthy hematopoietic stem cells (HSCs). Here, we demonstrate that LSCs, HSCs, and pre-leukemic stem cells can be identified and molecularly profiled by combining single-cell transcriptomics with lineage tracing using both nuclear and mitochondrial somatic variants. While mutational status discriminates between healthy and cancerous cells, gene expression distinguishes stem cells and progenitor cell populations. Our approach enables the identification of LSC-specific gene expression programs and the characterization of differentiation blocks induced by leukemic mutations. Taken together, we demonstrate the power of single-cell multi-omic approaches in characterizing cancer stem cells.

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A highly efficient reporter system for identifying and characterizing in vitro expanded hematopoietic stem cells

10.1101/2021.06.18.448972 ◽

2021 ◽

Author(s):

James Lok Chi Che ◽

Daniel Bode ◽

Iwo Kucinski ◽

Alyssa H Cull ◽

Fiona Bain ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Hematopoietic Stem Cells ◽

Gene Expression Signature ◽

The Body ◽

Molecular Profile ◽

Functional Screening ◽

Hematopoietic Stem ◽

Wide Range ◽

Single Clone

Hematopoietic stem cells (HSCs) cultured outside the body are the fundamental component of a wide range of cellular and gene therapies. Recent efforts have achieved more than 200-fold expansion of functional HSCs, but their molecular characterization has not been possible due to the substantial majority of cells being non-HSCs and single cell-initiated cultures displaying substantial clone-to-clone variability. Using the Fgd5 reporter mouse in combination with the EPCR surface marker, we report exclusive identification of HSCs from non-HSCs in expansion cultures. Linking single clone functional transplantation data with single clone gene expression profiling, we show that the molecular profile of expanded HSCs is similar to actively cycling fetal liver HSCs and shares a gene expression signature with functional HSCs from all sources, including Prdm16, Fstl1 and Palld. This new tool can now be applied to a wide-range of functional screening and molecular experiments previously not possible due to limited HSC numbers.

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Hematopoietic stem cells exhibit a specific ABC transporter gene expression profile clearly distinct from other stem cells

BMC Pharmacology ◽

10.1186/1471-2210-10-12 ◽

2010 ◽

Vol 10 (1) ◽

pp. 12 ◽

Cited By ~ 36

Author(s):

Leilei Tang ◽

Saskia M Bergevoet ◽

Christian Gilissen ◽

Theo de Witte ◽

Joop H Jansen ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Hematopoietic Stem Cells ◽

Gene Expression Profile ◽

Abc Transporter ◽

Expression Profile ◽

Transporter Gene ◽

Hematopoietic Stem

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Specific Gene Expression in Lgr5+ Stem Cells by Using Cre-Lox Recombination

Methods in Molecular Biology - Intestinal Stem Cells ◽

10.1007/978-1-0716-0747-3_16 ◽

2020 ◽

pp. 249-255

Author(s):

Pierre Dessen ◽

Joerg Huelsken ◽

Paloma Ordóñez-Morán

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Specific Gene ◽

Specific Gene Expression

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Comparative gene expression analysis of zebrafish and mammals identifies common regulators in hematopoietic stem cells

Blood ◽

10.1182/blood-2009-07-232322 ◽

2010 ◽

Vol 115 (2) ◽

pp. e1-e9 ◽

Cited By ~ 25

Author(s):

Isao Kobayashi ◽

Hiromasa Ono ◽

Tadaaki Moritomo ◽

Koichiro Kano ◽

Teruyuki Nakanishi ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Hematopoietic Stem Cells ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Side Population ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Cell Junction ◽

Hematopoietic Stem

Abstract Hematopoiesis in teleost fish is maintained in the kidney. We previously reported that Hoechst dye efflux activity of hematopoietic stem cells (HSCs) is highly conserved in vertebrates, and that Hoechst can be used to purify HSCs from teleost kidneys. Regulatory molecules that are strongly associated with HSC activity may also be conserved in vertebrates. In this study, we identified evolutionarily conserved molecular components in HSCs by comparing the gene expression profiles of zebrafish, murine, and human HSCs. Microarray data of zebrafish kidney side population cells (zSPs) showed that genes involved in cell junction and signal transduction tended to be up-regulated in zSPs, whereas genes involved in DNA replication tended to be down-regulated. These properties of zSPs were similar to those of mammalian HSCs. Overlapping gene expression analysis showed that 40 genes were commonly up-regulated in these 3 HSCs. Some of these genes, such as egr1, gata2, and id1, have been previously implicated in the regulation of HSCs. In situ hybridization in zebrafish kidney revealed that expression domains of egr1, gata2, and id1 overlapped with that of abcg2a, a marker for zSPs. These results suggest that the overlapping genes identified in this study are regulated in HSCs and play important roles in their functions.

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