Faten Zaibak’s research while affiliated with The Royal Children's Hospital and other places

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Publications (26)


QC and principal component analysis of gene expression data (detected probes only): Panel a: comparing components 1 (89.1% variance) and 2 (4.1% variance);
Mesodermal differentiation by MSCs from different sources. Left column: undifferentiated MSCs have a fibroblast-like phenotype, actin stained with phalloidin, and nuclei stained with DAPI. Middle column: calcium-rich matrix produced by osteoblasts is stained with Alizarin Red; right column: lipid droplets in adipocytes were stained with Oil Red O. Rows from top to bottom: MSCs sourced from term placenta (pMSCs), cord blood (USSCs) and bone marrow (bmMSCs). Magnification ×40.
Multipotent human stromal cells isolated from cord blood, term placenta and adult bone marrow show distinct differences in gene expression pattern
  • Article
  • Full-text available

March 2015

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85 Reads

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11 Citations

Genomics Data

Nicholas Matigian

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Faten Zaibak

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Kerry Atkinson

Multipotent mesenchymal stromal cells derived from human placenta (pMSCs), and unrestricted somatic stem cells (USSCs) derived from cord blood share many properties with human bone marrow-derived mesenchymal stromal cells (bmMSCs) and are currently in clinical trials for a wide range of clinical settings. Here we present gene expression profiles of human cord blood-derived unrestricted somatic stem cells (USSCs), human placental-derived mesenchymal stem cells (hpMSCs), and human bone marrow-derived mesenchymal stromal cells (bmMSCs), all derived from four different donors. The microarray data are available on the ArrayExpress database (www.ebi.ac.uk/arrayexpress) under accession number E-TABM-880. Additionally, the data has been integrated into a public portal, www.stemformatics.org. Our data provide a resource for understanding the differences in MSCs derived from different tissues.

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Additional file 3

April 2011

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12 Reads

Activin receptor (ACVR) protein levels in USSC grown in serum free conditions. Representative light micrographs depicting the localization of ACVR (brown staining) in USSC grown in serum free conditions (SCPM containing 0% FCS; 400×). Nuclei are counterstained blue with Haematoxylin. USSC 1 (left column) and USSC 2 (right column) expressed ACVR1b (A, B), ACVR2a (C, D) and ACVR2b (E, F). No staining was detected in the IgG controls (G, H).


Additional file 1

April 2011

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14 Reads

Activin A induction strategy. Cells were divided into one of three treatment groups; Normal serum control, Low serum control and Activin A. Normal serum control cells were seeded in SCPM containing 30% FCS and then cultured in SCPM containing 30% FCS for three days. For all treatment groups, the media was changed daily. Low serum control and Activin A cells were seeded in serum-free SCPM. Media was replaced with the following; serum-free SCPM on Day 1, SCPM containing 0.2% FCS on Day 2 and SCPM containing 2% FCS on Day 3; the media for Activin A cells on Days 1 to 3 was supplemented with 100 ng/ml Activin A.


Additional file 2

April 2011

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16 Reads

Cell proliferation index. The number of cells counted when USSC grown in SCPM containing 0%, 1%, 2% or 30% FCS for seven days are expressed as a percentage of the number of cells seeded. <100% initial seeding density indicates cell death has occurred, while >100% initial seeding density indicates cell proliferation has occurred. Different letters denote statistical significance (P < 0.05).


Stimulation of Activin A/Nodal signaling is insufficient to induce definitive endoderm formation of cord blood-derived unrestricted somatic stem cells

April 2011

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4,257 Reads

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11 Citations

Stem Cell Research & Therapy

Unrestricted somatic stem cells (USSC) derived from umbilical cord blood are an attractive alternative to human embryonic stem cells (hESC) for cellular therapy. USSC are capable of forming cells representative of all three germ line layers. The aim of this study was to determine the potential of USSC to form definitive endoderm following induction with Activin A, a protein known to specify definitive endoderm formation of hESC. USSC were cultured for (1) three days with or without 100 ng/ml Activin A in either serum-free, low-serum or serum-containing media, (2) three days with or without 100 ng/ml Activin A in combination with 10 ng/ml FGF4 in pre-induction medium, or (3) four days with or without small molecules Induce Definitive Endoderm (IDE1, 100 nM; IDE2, 200 nM) in serum-free media. Formation of definitive endoderm was assessed using RT-PCR for gene markers of endoderm (Sox17, FOXA2 and TTF1) and lung epithelium (surfactant protein C; SPC) and cystic fibrosis transmembrane conductance regulator; CFTR). The differentiation capacity of Activin A treated USSC was also assessed. Activin A or IDE1/2 induced formation of Sox17+ definitive endoderm from hESC but not from USSC. Activin A treated USSC retained their capacity to form cells of the ectoderm (nerve), mesoderm (bone) and endoderm (lung). Activin A in combination with FGF4 did not induce formation of Sox17+ definitive endoderm from USSC. USSC express both Activin A receptor subunits at the mRNA and protein level, indicating that these cells are capable of binding Activin A. Stimulation of the Nodal signaling pathway with Activin A or IDE1/2 is insufficient to induce definitive endoderm formation from USSC, indicating that USSC differ in their stem cell potential from hESC.





Unrestricted somatic stem cells from human umbilical cord blood grow in serum-free medium as spheres

December 2009

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163 Reads

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18 Citations

BMC Biotechnology

Human umbilical cord blood-derived unrestricted somatic stem cells (USSCs), which are capable of multilineage differentiation, are currently under investigation for a number of therapeutic applications. A major obstacle to their clinical use is the fact that in vitro expansion is still dependent upon fetal calf serum, which could be a source of pathogens. In this study, we investigate the capacity of three different stem cell culture media to support USSCs in serum-free conditions; HEScGRO, PSM and USSC growth medium ACF. Our findings demonstrate that USSCs do not grow in HEScGRO or PSM, but we were able to isolate, proliferate and maintain multipotency of three USSC lines in USSC growth medium ACF. For the first one to three passages, cells grown in USSC growth medium ACF proliferate and maintain their morphology, but with continued passaging the cells form spherical cell aggregates. Upon dissociation of spheres, cells continue to grow in suspension and form new spheres. Dissociated cells can also revert to monolayer growth when cultured on extracellular matrix support (fibronectin or gelatin), or in medium containing fetal calf serum. Analysis of markers associated with pluripotency (Oct4 and Sox2) and differentiation (FoxA2, Brachyury, Goosecoid, Nestin, Pax6, Gata6 and Cytokeratin 8) confirms that cells in the spheres maintain their gene expression profile. The cells in the spheres also retain the ability to differentiate in vitro to form cells representative of the three germline layers after five passages. These data suggest that USSC growth medium ACF maintains USSCs in an undifferentiated state and supports growth in suspension. This is the first demonstration that USSCs can grow in a serum- and animal component-free medium and that USSCs can form spheres.


Figure 1: Schematic representation of BAC265::FXN–EGFP. (a) The bacterial artificial chromosome (BAC) construct contains exons 1–5b of the FXN gene on a 188.2 kb genomic insert. It contains 110 kb of DNA upstream of exon 1 and 23 kb downstream of exon 5b of the FXN gene. BAC265::FXN has been shown to completely correct the embryonic lethality associated with knockout of the murine FXN gene, indicating that key regulatory elements controlling the expression of the FXN gene are present on this BAC insert.14 The genomic insert also contains sequences specific to the phosphatidylinositol-4-phosphate 5-kinase type 1 beta (PIPK51B) and Protein kinase cAMP-dependent catalytic gamma (PRKACG) genes located upstream of the FXN locus. The sacB and Chloramphenicol resistance (CmR) genes located on the backbone of the BAC vector are also indicated. The enhanced green fluorescent protein (EGFP) reporter gene is fused in frame with exon 5a of the FXN gene. The neomycin resistance (NeoR) gene, located downstream of EGFP, is driven from a SV40 promoter. The DNA construct was linearized with BsiWI before electroporation into unrestricted somatic stem cells (USSCs). The 26 kb DNA fragment obtained following BamHI digestion and detected with a NeoR-specific probe following Southern blot analysis is also shown. (b) Schematic representation of the BsiWI linearized BAC indicating the location of the PCR fragments. The shaded regions highlight the location of vector backbone sequences.
Table 1 Copy number determination
Figure 5: Directed differentiation of clones. (a) Microscopy images of undifferentiated and neuronally differentiated cells stained with neural specific -tubulin III antibody. (b) Microscopy images of undifferentiated cells and cells induced with osteogenic differentiation medium stained with Alizarin Red S to determine mineralization. (c) A representative reverse transcription (RT-PCR) for surfactant protein C (SPC) gene expression in undifferentiated cells and cells differentiated with small airway growth medium. RT-PCR analysis was performed on the total RNA extracted from undifferentiated (lanes 1 and 2) and differentiated (lanes 3 and 4) unrestricted somatic stem cells (USSCs), undifferentiated (lanes 5 and 6) and differentiated (lanes 7 and 8) clone 1 cells, undifferentiated (lanes 9 and 10) and differentiated (lanes 11 and 12) clone 2 cells. FXN-EGFP was also amplified to confirm the continued expression from the bacterial artificial chromosome (BAC) after differentiation. As a template control, GAPDH was amplified. Even numbers represent the respective reverse transcriptase negative samples, lane 13, is the epithelial cell line CFBE, which serves as a positive control for the SPC gene and Lane 14 is a PCR water control.
Integration of functional bacterial artificial chromosomes into human cord blood-derived multipotent stem cells

February 2009

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62 Reads

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11 Citations

Gene Therapy

Stem cells from a patient with a genetic disease could be used for cell therapy if it were possible to insert a functional copy of the defective gene. In this study, we investigate the transfection and subsequent integration of large genomic fragments into human cord blood-derived multipotent stem cells. We describe for the first time the creation of clonal stem cells carrying a human bacterial artificial chromosome (BAC) containing the Friedreich ataxia locus with an enhanced green fluorescent protein (EGFP) reporter gene fused to exon 5a of the frataxin (FXN) gene. Integration of the BAC into the host cell genome was confirmed by PCR, Southern blot and fluorescent in situ hybridization analysis. Reverse transcription-PCR and flow cytometry confirmed expression of FXN-EGFP. Correct mitochondrial localization of the protein was confirmed using fluorescent microscopy. The transfected stem cells also retained the ability to differentiate into cells from all three germline layers, as demonstrated by the capacity to form neuron-specific beta-tubulin-expressing cells, Alizarin Red S-positive bone-like cells, and epithelial-like cells expressing surfactant protein C. This is the first study to demonstrate that cord blood-derived multipotent stem cells may be useful targets for gene therapy applications using large genomic loci.


Citations (14)


... MSCs isolated from different tissue sources seem to have similar a secretome, with variations in the amount and proportions of the different components [137][138][139]. In addition to the inherent differences between the different sources of the cells, this parameter may also depend on culture and growth conditions of the cells [59,61,88,[140][141][142]. The main variations between the different types of MSCs may derive also from the sensitivity to stress signal receptors on the MSCs [143], although this point needs further investigation. ...

Reference:

Allogenic Use of Human Placenta-Derived Stromal Cells as a Highly Active Subtype of Mesenchymal Stromal Cells for Cell-Based Therapies
Multipotent human stromal cells isolated from cord blood, term placenta and adult bone marrow show distinct differences in gene expression pattern

Genomics Data

... ducing progeny cell lines that can be used to assign genes or cellular phenotypes to particular chromosomes (7). Hybrids can also be irradiated to fragment chromosomes and stimulate additional segregation of genetic information, an approach that has been used for fine mapping of genomic linkage relationships (8). ...

Stimulation of Activin A/Nodal signaling is insufficient to induce definitive endoderm formation of cord blood-derived unrestricted somatic stem cells

Stem Cell Research & Therapy

... Mutações CFTR podemser agrupadas emseis classesde acordo no seuefeitona produção da proteínaCFTR, tráfego para membrana, função ouestabilidade: I)provoca umaalteraçãona produção deRNAm,consequentemente,um defeitona transcriçãoda proteína; II) é caracterizada por modificações póstraducionais que não ocorremadequadamente, dessa forma, a proteínaé sintetizada, mas não há nenhumaglicosilação desta, que fica retidano retículoendoplasmáticoe é degradadaantes de alcançara membrana; III)está associadaa um defeitona regulaçãodaproteína, que écorretamente localizadanamembrana celular,masnão responde aestímulosagonistas do AMPc, que são essenciais para a aberturadocanal de cloreto;IV) há uma redução na condutânciade íons cloreto, onde estes não conseguemse moverde forma eficaz atravésdo canal, o que conduza um defeito na condutância; V)resulta emanormalidades no "splicing" do RNAm para a CFTR por um defeito na enzima que medeia este processo, levando a umaredução parcialdo número decanais de cloretofuncionais, assim como, umaquantidade reduzida dessas proteínas funcionais;VI)decorrentes de alterações deestabilidade da CFTR na superfície da membrana celular 11,14,15 . ...

Genetics and genomics: Providing new opportunities for the translation of basic research to clinical care for cystic fibrosis
  • Citing Article
  • February 2008

... Molecular analysis of the MSCs was performed according to the protocols described by Zaibak et al. and Demerdash et al. 12,13 Total RNA was extracted from trypsinized cells using an RNeasy Mini Kit (Qiagen, Hilden, Germany). Its concentration and purity were assessed by a Nano-Drop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, USA). ...

Unrestricted somatic stem cells from human umbilical cord blood grow in serum-free medium as spheres

BMC Biotechnology

... To be considered an appropriate source for autologous transplantation, the bone marrow-derived mesenchymal stem cells from FRDA patients, subjected to genetic correction, should display phenotypes of healthy neurons and cardiomyocytes and be free of FRDA-associated disease hallmarks. Successful transfection and integration of a human bacterial artificial chromosome containing the FRDA locus has been demonstrated in human umbilical cord blood-derived multipotent stem cells [21]. Furthermore, the transfected cells retained the ability to differentiate into cells from all three germ line layers. ...

Integration of functional bacterial artificial chromosomes into human cord blood-derived multipotent stem cells

Gene Therapy

Engineering EGFP reporter constructs into a 200 kb human β-globin BAC clone using GET Recombination

Nucleic Acids Research

... When lymphoblast and fibroblast cell lines were incubated with 55 Fe-Tf concentrations in the range of 0 -1600 nM iron, i.e. concentrations where saturation of TfR appeared, and the amount of intracellular radioactive iron was determined every 15 min, no significant alterations in the uptake of transferrinbound iron were detectable in the FRDA patient cell lines, thus indicating cellular TfR densities comparable to the controls (Fig. 5). This result is in line with a previous study, where the mean TfR concentrations of freshly isolated FRDA leukocytes and cultured lymphoblasts were found to be not significantly different from the control groups (46). However, alterations in the transferrin receptor density of blood cells from FRDA patients are discussed controversially (46 -48). ...

Normal levels of soluble transferrin receptor in Friedreich ataxia
  • Citing Article
  • October 2002

Clinical Genetics

... Therefore, investigators had to establish an EBNA1-expressing cell line before introducing a desired clone into human cells (Frengen et al., 2000). The shuttle vector pEBAC190G that was constructed later does contain the EBNA1 gene, but no human genomic libraries constructed in this vector have been reported (Al-Hasani et al., 2003). Additionally, none of these vector systems have the ability to activate a multi-copy origin of replication during propagation in Escherichia coli to increase the yield of individual library members to recover ample DNA for subsequent transfections into mammalian cells. ...

Development of a novel bacterial artificial chromosome cloning system for functional studies

Plasmid

... 74,76-81 These models do not fully replicate the genotypic characteristics and physiological changes of human βthalassaemia. 71,72 The first humanized mouse model, DH Δ4bp mice, carries a common β-thalassaemia splicing mutation, the codons 41-42 (-TTCT) deletion, 71 which can be used to investigate gene correction strategies in HSCs and to identify HbF inducers. The IVSI-110 mouse model carries the IVSI-110 splicing mutation and exhibits a 90% decrease in human β-globin chain synthesis, 73 which provides a valuable platform for testing strategies aimed at restoring normal splicing. ...

A humanized mouse model for a common β0-thalassemia mutation

Genomics

... Determination of transgene copy number. Expression of BAC transgenes typically correlates with transgene copy number [42][43][44] . Transgene copy number was determined by Taqman digital PCR using a human TNFAIP3-specific primer obtained from Thermo Fisher Scientific/Life Technologies. ...

Transgene copy number-dependent rescue of murine β-globin knockout mice carrying a 183 kb human β-globin BAC genomic fragment

Biochimica et Biophysica Acta