Publications by authors named "Angelique Schnerch"

15 Publications

  • Page 1 of 1

Author Correction: Direct conversion of human fibroblasts to multilineage blood progenitors.

Nature 2018 08;560(7719):E32

Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5.

In this Article, there were duplicated empty lanes in Supplementary Figs. 2e and 3b. The corrected figures are presented in the Supplementary Information to the accompanying Amendment. The original Article has not been corrected.
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http://dx.doi.org/10.1038/s41586-018-0402-xDOI Listing
August 2018

Histone modification profiling in normal and transformed human embryonic stem cells using micro chromatin immunoprecipitation, scalable to genome-wide microarray analyses.

Methods Mol Biol 2013 ;1029:149-61

Stem Cell and Cancer Research Institute, McMaster University, Hamilton, ON, Canada.

Comparing normal human embryonic stem cells (hESCs) to those that have acquired cellular properties of neoplasm provides a unique opportunity to study the distinguishing molecular features of human cellular transformation. As global alterations in the epigenetic landscape are a common feature of cancer, we sought to investigate the loci-specific and global differences between normal and transformed hESCs using ChIP-PCR and ChIP-microarray (also known as ChIP-chip). Here, specific emphasis was placed on optimizing ChIP for low cell numbers (termed micro-ChIP; μChIP) towards applications where the target population is rare, such as the case for somatic human tumors containing a low frequency of cancer stem cell populations and for single-colony analysis of embryonic and induced pluripotent stem cells emerging from initial derivation. Using these methods, we suggest that μChIP-PCR and microarray analysis is thus a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer, and regenerative medicine where target populations regulating the biological process can only be isolated in small numbers.
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http://dx.doi.org/10.1007/978-1-62703-478-4_11DOI Listing
March 2014

Notch-HES1 signaling axis controls hemato-endothelial fate decisions of human embryonic and induced pluripotent stem cells.

Blood 2013 Aug 3;122(7):1162-73. Epub 2013 Jun 3.

McMaster Stem Cell and Cancer Research Institute, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada.

Notch signaling regulates several cellular processes including cell fate decisions and proliferation in both invertebrates and mice. However, comparatively less is known about the role of Notch during early human development. Here, we examined the function of Notch signaling during hematopoietic lineage specification from human pluripotent stem cells of both embryonic and adult fibroblast origin. Using immobilized Notch ligands and small interfering RNA to Notch receptors we have demonstrated that Notch1, but not Notch2, activation induced hairy and enhancer of split 1 (HES1) expression and generation of committed hematopoietic progenitors. Using gain- and loss-of-function approaches, this was shown to be attributed to Notch-signaling regulation through HES1, which dictated cell fate decisions from bipotent precursors either to the endothelial or hematopoietic lineages at the clonal level. Our study reveals a previously unappreciated role for the Notch pathway during early human hematopoiesis, whereby Notch signaling via HES1 represents a toggle switch of hematopoietic vs endothelial fate specification.
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http://dx.doi.org/10.1182/blood-2012-12-471649DOI Listing
August 2013

Human embryonic stem cell-derived hematopoietic cells maintain core epigenetic machinery of the polycomb group/Trithorax Group complexes distinctly from functional adult hematopoietic stem cells.

Stem Cells Dev 2013 Jan 4;22(1):73-89. Epub 2012 Sep 4.

Faculty of Health Sciences, Stem Cell and Cancer Research Institute (SCC-RI), McMaster University, Hamilton, Canada.

Hematopoietic cells derived from human embryonic stem cells (hESCs) have a number of potential utilities, including the modeling of hematological disorders in vitro, whereas the use for cell replacement therapies has proved to be a loftier goal. This is due to the failure of differentiated hematopoietic cells, derived from human pluripotent stem cells (hPSCs), to functionally recapitulate the in vivo properties of bona fide adult hematopoietic stem/progenitor cells (HSPCs). To better understand the limitations of differentiation programming at the molecular level, we have utilized differential gene expression analysis of highly purified cells that are enriched for hematopoietic repopulating activity across embryonic, fetal, and adult human samples, including in vivo explants of human HSPCs 8-weeks post-transplantation. We reveal that hESC-derived hematopoietic progenitor cells (eHPCs) fail to express critical transcription factors which are known to govern self-renewal and myeloid/lymphoid development and instead retain the expression of Polycomb Group (PcG) and Trithorax Group (TrxG) factors which are more prevalent in embryonic cell types that include EZH1 and ASH1L, respectively. These molecular profiles indicate that the differential expression of the core epigenetic machinery comprising PcGs/TrxGs in eHPCs may serve as previously unexplored molecular targets that direct hematopoietic differentiation of PSCs toward functional HSPCs in humans.
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http://dx.doi.org/10.1089/scd.2012.0204DOI Listing
January 2013

Direct conversion of human fibroblasts to multilineage blood progenitors.

Nature 2010 Nov 7;468(7323):521-6. Epub 2010 Nov 7.

Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada L8N 3Z5.

As is the case for embryo-derived stem cells, application of reprogrammed human induced pluripotent stem cells is limited by our understanding of lineage specification. Here we demonstrate the ability to generate progenitors and mature cells of the haematopoietic fate directly from human dermal fibroblasts without establishing pluripotency. Ectopic expression of OCT4 (also called POU5F1)-activated haematopoietic transcription factors, together with specific cytokine treatment, allowed generation of cells expressing the pan-leukocyte marker CD45. These unique fibroblast-derived cells gave rise to granulocytic, monocytic, megakaryocytic and erythroid lineages, and demonstrated in vivo engraftment capacity. We note that adult haematopoietic programs are activated, consistent with bypassing the pluripotent state to generate blood fate: this is distinct from haematopoiesis involving pluripotent stem cells, where embryonic programs are activated. These findings demonstrate restoration of multipotency from human fibroblasts, and suggest an alternative approach to cellular reprogramming for autologous cell-replacement therapies that avoids complications associated with the use of human pluripotent stem cells.
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http://dx.doi.org/10.1038/nature09591DOI Listing
November 2010

Distinguishing between mouse and human pluripotent stem cell regulation: the best laid plans of mice and men.

Stem Cells 2010 Mar;28(3):419-30

Stem Cell and Cancer Research Institute, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada.

Pluripotent stem cells (PSCs) have been derived from the embryos of mice and humans, representing the two major sources of PSCs. These cells are universally defined by their developmental properties, specifically their self-renewal capacity and differentiation potential which are regulated in mice and humans by complex transcriptional networks orchestrated by conserved transcription factors. However, significant differences exist in the transcriptional networks and signaling pathways that control mouse and human PSC self-renewal and lineage development. To distinguish between universally applicable and species-specific features, we collated and compared the molecular and cellular descriptions of mouse and human PSCs. Here we compare and contrast the response to signals dictated by the transcriptome and epigenome of mouse and human PSCs that will hopefully act as a critical resource to the field. These analyses underscore the importance of accounting for species differences when designing strategies to capitalize on the clinical potential of human PSCs.
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http://dx.doi.org/10.1002/stem.298DOI Listing
March 2010

Characterization of human embryonic stem cells with features of neoplastic progression.

Nat Biotechnol 2009 Jan 4;27(1):91-7. Epub 2009 Jan 4.

Stem Cell and Cancer Research Institute, Michael G. DeGroote School of Medicine, MDCL 5029, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada.

Cultured human embryonic stem (hES) cells can acquire genetic and epigenetic changes that make them vulnerable to transformation. As hES cells with cancer-cell characteristics share properties with normal hES cells, such as self-renewal, teratoma formation and the expression of pluripotency markers, they may be misconstrued as superior hES cells with enhanced 'stemness'. We characterize two variant hES cell lines (v-hESC-1 and v-hESC-2) that express pluripotency markers at high levels and do not harbor chromosomal abnormalities by standard cytogenetic measures. We show that the two lines possess some features of neoplastic progression, including a high proliferative capacity, growth-factor independence, a 9- to 20-fold increase in frequency of tumor-initiating cells, niche independence and aberrant lineage specification, although they are not malignant. Array comparative genomic hybridization reveals an amplification at 20q11.1-11.2 in v-hESC-1 and a deletion at 5q34a-5q34b;5q3 and a mosaic gain of chromosome 12 in v-hESC-2. These results emphasize the need for functional characterization to distinguish partially transformed and normal hES cells.
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http://dx.doi.org/10.1038/nbt.1516DOI Listing
January 2009

The histone demethylase KDM5b/JARID1b plays a role in cell fate decisions by blocking terminal differentiation.

Mol Cell Biol 2008 Sep 30;28(17):5312-27. Epub 2008 Jun 30.

Stem Cell and Cancer Institute, MDCL Rm. 5030, Faculty of Health Sciences, McMaster University, 1200 Main St. W, Hamilton, ON, Canada.

The histone demethylase lysine demethylase 5b (KDM5b) specifically demethylates lysine 4 of histone H3 (meH3K4), thereby repressing gene transcription. KDM5b regulates cell cycle control genes in cancer and is expressed in the early epiblast. This suggests that KDM5b plays a developmental role by maintaining uncommitted progenitors. Here we show that transient overexpression of KDM5b in embryonic stem cells decreases the expression of at least three different modulators of cell fate decisions, Egr1, p27(KIP1), and BMI1, by demethylation of their promoters. Constitutively increased KDM5b expression results in an increased mitotic rate and a decreased global 3meH3K4 but no change in cell identity. Results of two separate differentiation assays, neural differentiation and embryoid body EB (EB) formation, showed that KDM5b reduced the terminally differentiated cells and increased proliferating progenitors. These were achieved by two mechanisms, blocking of the upregulation of cell lineage markers and maintenance of cyclins, that allowed cells to escape differentiation and remain uncommitted. Additionally, EBs maintain high levels of Oct4 and Nanog and can be dissociated to reestablish highly proliferative cultures. The persistence of uncommitted progenitors may be due to the direct regulation of the Tcf/Lef family member mTcf3/hTcf7L1, an upstream regulator of Nanog expression. These findings demonstrate a role for KDM5b in the choice between proliferation and differentiation during development.
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http://dx.doi.org/10.1128/MCB.00128-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519745PMC
September 2008

LongSAGE profiling of nine human embryonic stem cell lines.

Genome Biol 2007 ;8(6):R113

Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3.

To facilitate discovery of novel human embryonic stem cell (ESC) transcripts, we generated 2.5 million LongSAGE tags from 9 human ESC lines. Analysis of this data revealed that ESCs express proportionately more RNA binding proteins compared with terminally differentiated cells, and identified novel ESC transcripts, at least one of which may represent a marker of the pluripotent state.
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http://dx.doi.org/10.1186/gb-2007-8-6-r113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394759PMC
February 2008

A modified polymerase chain reaction-long serial analysis of gene expression protocol identifies novel transcripts in human CD34+ bone marrow cells.

Stem Cells 2007 Jul 5;25(7):1681-9. Epub 2007 Apr 5.

Terry Fox Laboratory, Vancouver, BC, Canada V5Z 1L3.

Transcriptome profiling offers a powerful approach to investigating developmental processes. Long serial analysis of gene expression (LongSAGE) is particularly attractive for this purpose because of its inherent quantitative features and independence of both hybridization variables and prior knowledge of transcript identity. Here, we describe the validation and initial application of a modified protocol for amplifying cDNA preparations from <10 ng of RNA (<10(3) cells) to allow representative LongSAGE libraries to be constructed from rare stem cell-enriched populations. Quantitative real-time polymerase chain reaction (Q-RT-PCR) analyses and comparison of tag frequencies in replicate LongSAGE libraries produced from amplified and nonamplified cDNA preparations demonstrated preservation of the relative levels of different transcripts originally present at widely varying levels. This PCR-LongSAGE protocol was then used to obtain a 200,000-tag library from the CD34+ subset of normal adult human bone marrow cells. Analysis of this library revealed many anticipated transcripts, as well as transcripts not previously known to be present in CD34+ hematopoietic cells. The latter included numerous novel tags that mapped to unique and conserved sites in the human genome but not previously identified as transcribed elements in human cells. Q-RT-PCR was used to demonstrate that 10 of these novel tags were expressed in cDNA pools and present in extracts of other sources of normal human CD34+ hematopoietic cells. These findings illustrate the power of LongSAGE to identify new transcripts in stem cell-enriched populations and indicate the potential of this approach to be extended to other sources of rare cells. Disclosure of potential conflicts of interest is found at the end of this article.
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http://dx.doi.org/10.1634/stemcells.2006-0794DOI Listing
July 2007

Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation.

Am J Hum Genet 2006 Sep 25;79(3):500-13. Epub 2006 Jul 25.

Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.

The cause of mental retardation in one-third to one-half of all affected individuals is unknown. Microscopically detectable chromosomal abnormalities are the most frequently recognized cause, but gain or loss of chromosomal segments that are too small to be seen by conventional cytogenetic analysis has been found to be another important cause. Array-based methods offer a practical means of performing a high-resolution survey of the entire genome for submicroscopic copy-number variants. We studied 100 children with idiopathic mental retardation and normal results of standard chromosomal analysis, by use of whole-genome sampling analysis with Affymetrix GeneChip Human Mapping 100K arrays. We found de novo deletions as small as 178 kb in eight cases, de novo duplications as small as 1.1 Mb in two cases, and unsuspected mosaic trisomy 9 in another case. This technology can detect at least twice as many potentially pathogenic de novo copy-number variants as conventional cytogenetic analysis can in people with mental retardation.
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http://dx.doi.org/10.1086/507471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1559542PMC
September 2006

Sequence biases in large scale gene expression profiling data.

Nucleic Acids Res 2006 Jul 13;34(12):e83. Epub 2006 Jul 13.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.

We present the results of a simple, statistical assay that measures the G+C content sensitivity bias of gene expression experiments without the requirement of a duplicate experiment. We analyse five gene expression profiling methods: Affymetrix GeneChip, Long Serial Analysis of Gene Expression (LongSAGE), LongSAGELite, 'Classic' Massively Parallel Signature Sequencing (MPSS) and 'Signature' MPSS. We demonstrate the methods have systematic and random errors leading to a different G+C content sensitivity. The relationship between this experimental error and the G+C content of the probe set or tag that identifies each gene influences whether the gene is detected and, if detected, the level of gene expression measured. LongSAGE has the least bias, while Signature MPSS shows a strong bias to G+C rich tags and Affymetrix data show different bias depending on the data processing method (MAS 5.0, RMA or GC-RMA). The bias in the Affymetrix data primarily impacts genes expressed at lower levels. Despite the larger sampling of the MPSS library, SAGE identifies significantly more genes (60% more RefSeq genes in a single comparison).
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http://dx.doi.org/10.1093/nar/gkl404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524917PMC
July 2006

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

Genome Res 2004 Oct;14(10B):2121-7

The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.
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http://dx.doi.org/10.1101/gr.2596504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528928PMC
October 2004

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.

Proc Natl Acad Sci U S A 2002 Dec 11;99(26):16899-903. Epub 2002 Dec 11.

National Cancer Institute, Bethessda, MD 20892-2580, USA.

The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene. ESTs were generated from libraries enriched for full-length cDNAs and analyzed to identify candidate full-ORF clones, which then were sequenced to high accuracy. The MGC has currently sequenced and verified the full ORF for a nonredundant set of >9,000 human and >6,000 mouse genes. Candidate full-ORF clones for an additional 7,800 human and 3,500 mouse genes also have been identified. All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http:mgc.nci.nih.gov).
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http://dx.doi.org/10.1073/pnas.242603899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC139241PMC
December 2002

An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones.

Nucleic Acids Res 2002 Jun;30(11):2460-8

Genome Sciences Centre, BC Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada.

We describe an efficient high-throughput method for accurate DNA sequencing of entire cDNA clones. Developed as part of our involvement in the Mammalian Gene Collection full-length cDNA sequencing initiative, the method has been used and refined in our laboratory since September 2000. Amenable to large scale projects, we have used the method to generate >7 Mb of accurate sequence from 3695 candidate full-length cDNAs. Sequencing is accomplished through the insertion of Mu transposon into cDNAs, followed by sequencing reactions primed with Mu-specific sequencing primers. Transposon insertion reactions are not performed with individual cDNAs but rather on pools of up to 96 clones. This pooling strategy reduces the number of transposon insertion sequencing libraries that would otherwise be required, reducing the costs and enhancing the efficiency of the transposon library construction procedure. Sequences generated using transposon-specific sequencing primers are assembled to yield the full-length cDNA sequence, with sequence editing and other sequence finishing activities performed as required to resolve sequence ambiguities. Although analysis of the many thousands (22 785) of sequenced Mu transposon insertion events revealed a weak sequence preference for Mu insertion, we observed insertion of the Mu transposon into 1015 of the possible 1024 5mer candidate insertion sites.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC117194PMC
http://dx.doi.org/10.1093/nar/30.11.2460DOI Listing
June 2002