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Biomedical subjects

Bing Lim

Publications and source records attributed to Bing Lim.

At least 19 recordsLinked to original sources
PubMed2006

The molecular basis of ageing in stem cells.

Ageing is often defined in the context of telomerase activity and telomere length regulation. Most somatic cells have limited replication ability and undergo senescence eventually. Stem cells are unique as they possess more abundant telomerase activity and are able to maintain telomere lengths for a longer period. Embryonic stem cells are particularly resistant to ageing and can be propagated indefinitely. Remarkably, adult somatic cells can be reprogrammed to an ESC-like state by various means including cell fusion, exposure to ESC cell-free extracts, enforced expression of specific molecules, and somatic cell nuclear transfer. Thus, the rejuvenation of an 'aged' state can be effected by the activation of specific key molecules in the cell. Here, we argue that cellular ageing is a reversible process, and this is determined by the balance of biological molecules which directly or indirectly control telomere length and telomerase activity, either through altering gene expression and/or modulating the epigenetic state of the chromatin.

Animals↗
PubMed2006

Identification of common pathways mediating differentiation of bone marrow- and adipose tissue-derived human mesenchymal stem cells into three mesenchymal lineages.

Mesenchymal stem cells derived from human bone marrow (hBMSCs) and human adipose tissue (hAMSCs) represent a useful source of progenitor cells for cell therapy and tissue engineering. However, it is not clear what the similarities and differences between them are. Like hBMSCs, hAMSCs can differentiate into osteogenic, adipogenic, and chondrogenic cells. Whether MSCs derived from different tissue sources represent fundamentally similar or different cell types is not clear. Given the possible different sources of MSCs for cell therapy, a comprehensive comparison of the different MSCs would be very useful. Here, we compared the transcriptome profile of hAMCS and hBMSCs during directed differentiation into bone, cartilage, and fat. Our data revealed considerable similarities between bone marrow-derived MSCs (BMSCs) and adipose tissue-derived MSCs (AMSCs). We uncovered an interesting bifurcation of pathways in both BMSCs and AMSCs, in which osteogenesis and adipogenesis appear to be linked in a differentiation branch separate from chondrogenesis. Our data suggest that although a set of common genes may be needed for early differentiation into all three lineages, a different set of signature genes is associated with maturation into fully differentiated cells. The recruitment of different late differentiation factors explains and supports our conclusion that BMSCs differentiate more efficiently into bone and cartilage, whereas AMSCs differentiate better into adipocytes. This study not only generated a rich database for continuing molecular characterization of various MSCs but also provided a rational basis for assessing qualities of MSCs from different sources for the purpose of cell-based therapy and tissue engineering.

Adipose Tissue↗
PubMed2006

Derivation of clinically compliant MSCs from CD105+, CD24- differentiated human ESCs.

Adult tissue-derived mesenchymal stem cells (MSCs) have demonstrated therapeutic efficacy in treating diseases or repairing damaged tissues through mechanisms thought to be mediated by either cell replacement or secretion of paracrine factors. Characterized, self-renewing human ESCs could potentially be an invariable source of consistently uniform MSCs for therapeutic applications. Here we describe a clinically relevant and reproducible manner of generating identical batches of hESC-derived MSC (hESC-MSC) cultures that circumvents exposure to virus, mouse cells, or serum. Trypsinization and propagation of HuES9 or H1 hESCs in feeder- and serum-free selection media generated three polyclonal, karyotypically stable, and phenotypically MSC-like cultures that do not express pluripotency-associated markers but displayed MSC-like surface antigens and gene expression profile. They differentiate into adipocytes, osteocytes, and chondrocytes in vitro. Gene expression and fluorescence-activated cell sorter analysis identified CD105 and CD24 as highly expressed antigens on hESC-MSCs and hESCs, respectively. CD105+, CD24- monoclonal isolates have a typical MSC gene expression profiles and were identical to each other with a highly correlated gene expression profile (r(2) > .90). We have developed a protocol to reproducibly generate clinically compliant and identical hESC-MSC cultures.

Adipogenesis↗
PubMed2006

A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes.

We present rna22, a method for identifying microRNA binding sites and their corresponding heteroduplexes. Rna22 does not rely upon cross-species conservation, is resilient to noise, and, unlike previous methods, it first finds putative microRNA binding sites in the sequence of interest, then identifies the targeting microRNA. Computationally, we show that rna22 identifies most of the currently known heteroduplexes. Experimentally, with luciferase assays, we demonstrate average repressions of 30% or more for 168 of 226 tested targets. The analysis suggests that some microRNAs may have as many as a few thousand targets, and that between 74% and 92% of the gene transcripts in four model genomes are likely under microRNA control through their untranslated and amino acid coding regions. We also extended the method's key idea to a low-error microRNA-precursor-discovery scheme; our studies suggest that the number of microRNA precursors in mammalian genomes likely ranges in the tens of thousands.

Algorithms↗
PubMed2006

Sall4 modulates embryonic stem cell pluripotency and early embryonic development by the transcriptional regulation of Pou5f1.

Embryonic stem (ES) cells are pluripotent cells that can self-renew or differentiate into many cell types. A unique network of transcription factors and signalling molecules are essential for maintaining this capability. Here, we report that a spalt family member, Sall4, is required for the pluripotency of ES cells. Similarly to Oct4, a reduction in Sall4 levels in mouse ES cells results in respecification, under the appropriate culture conditions, of ES cells to the trophoblast lineage. Sall4 regulates transcription of Pou5f1 which encodes Oct4. Sall4 binds to the highly conserved regulatory region of the Pou5f1 distal enhancer and activates Pou5f1 expression in vivo and in vitro. Microinjection of Sall4 small interfering (si) RNA into mouse zygotes resulted in reduction of Sall4 and Oct4 mRNAs in preimplantation embryos and significant expansion of Cdx2 expression into the inner cell mass. These results demonstrate that Sall4 is a transcriptional activator of Pou5f1 and has a critical role in the maintenance of ES cell pluripotency by modulating Oct4 expression. The data also indicates that Sall4 is important for early embryonic cell-fate decisions.

Animals↗
PubMed2006

The transcriptome of human oocytes.

The identification of genes and deduced pathways from the mature human oocyte can help us better understand oogenesis, folliculogenesis, fertilization, and embryonic development. Human metaphase II oocytes were used within minutes after removal from the ovary, and its transcriptome was compared with a reference sample consisting of a mixture of total RNA from 10 different normal human tissues not including the ovary. RNA amplification was performed by using a unique protocol. Affymetrix Human Genome U133 Plus 2.0 GeneChip arrays were used for hybridizations. Compared with reference samples, there were 5,331 transcripts significantly up-regulated and 7,074 transcripts significantly down-regulated in the oocyte. Of the oocyte up-regulated probe sets, 1,430 have unknown function. A core group of 66 transcripts was identified by intersecting significantly up-regulated genes of the human oocyte with those from the mouse oocyte and from human and mouse embryonic stem cells. GeneChip array results were validated using RT-PCR in a selected set of oocyte-specific genes. Within the up-regulated probe sets, the top overrepresented categories were related to RNA and protein metabolism, followed by DNA metabolism and chromatin modification. This report provides a comprehensive expression baseline of genes expressed in in vivo matured human oocytes. Further understanding of the biological role of these genes may expand our knowledge on meiotic cell cycle, fertilization, chromatin remodeling, lineage commitment, pluripotency, tissue regeneration, and morphogenesis.

Animals↗
PubMed2006

Sall4 interacts with Nanog and co-occupies Nanog genomic sites in embryonic stem cells.

Embryonic stem (ES) cells are pluripotent cells with self-renewing property. Nanog is a homeobox transcription factor required to maintain ES cells in a non-differentiated state. Using affinity purification coupled to liquid chromatography-tandem mass spectrometry analysis, we identified Sall4 as a Nanog co-purified protein. Co-immunoprecipitation and glutathione S-transferase pulldown experiments confirmed the interaction between Nanog and Sall4. We showed that Nanog and Sall4 co-occupied Nanog and Sall4 enhancer regions in living ES cells. Knockdown of Nanog or Sall4 by RNA interference led to a reduction in Nanog and Sall4 enhancer activities, providing evidence that these factors are positively regulating these enhancers. Importantly, co-transfection of Sall4 with these ES cell-specific enhancers led to transactivation in heterologous somatic cells. Chromatin immunoprecipitation experiments also showed that Sall4 co-occupied many Nanog binding sites in ES cells. Our data implicate Sall4 as an important component of the transcription regulatory networks in ES cells by cooperating with Nanog. We suggest that Sall4 and Nanog form a regulatory circuit similar to that of Oct4 and Sox2. This study highlights the extensive regulatory loops connecting genes, which encode for key transcription factors in ES cells.

Animals↗
PubMed2006

The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells.

Oct4 and Nanog are transcription factors required to maintain the pluripotency and self-renewal of embryonic stem (ES) cells. Using the chromatin immunoprecipitation paired-end ditags method, we mapped the binding sites of these factors in the mouse ES cell genome. We identified 1,083 and 3,006 high-confidence binding sites for Oct4 and Nanog, respectively. Comparative location analyses indicated that Oct4 and Nanog overlap substantially in their targets, and they are bound to genes in different configurations. Using de novo motif discovery algorithms, we defined the cis-acting elements mediating their respective binding to genomic sites. By integrating RNA interference-mediated depletion of Oct4 and Nanog with microarray expression profiling, we demonstrated that these factors can activate or suppress transcription. We further showed that common core downstream targets are important to keep ES cells from differentiating. The emerging picture is one in which Oct4 and Nanog control a cascade of pathways that are intricately connected to govern pluripotency, self-renewal, genome surveillance and cell fate determination.

Animals↗
PubMed2006

A global map of p53 transcription-factor binding sites in the human genome.

The ability to derive a whole-genome map of transcription-factor binding sites (TFBS) is crucial for elucidating gene regulatory networks. Herein, we describe a robust approach that couples chromatin immunoprecipitation (ChIP) with the paired-end ditag (PET) sequencing strategy for unbiased and precise global localization of TFBS. We have applied this strategy to map p53 targets in the human genome. From a saturated sampling of over half a million PET sequences, we characterized 65,572 unique p53 ChIP DNA fragments and established overlapping PET clusters as a readout to define p53 binding loci with remarkable specificity. Based on this information, we refined the consensus p53 binding motif, identified at least 542 binding loci with high confidence, discovered 98 previously unidentified p53 target genes that were implicated in novel aspects of p53 functions, and showed their clinical relevance to p53-dependent tumorigenesis in primary cancer samples.

Binding Sites↗
PubMed2006

CD14 promoter polymorphisms have no functional significance and are not associated with atopic phenotypes.

OBJECTIVES: A polymorphism at CD14/-159 has been reported to be associated with atopic phenotypes in several studies. However, conflicting results from association studies in different populations have been reported. This study aimed to investigate the relationship between CD14 promoter polymorphisms and atopic phenotypes in Singaporean Chinese and the biological characterization of these polymorphisms. METHODS: A total of 171 atopic and 160 non-atopic adult subjects were included and their serum soluble CD14 (sCD14) and total immunoglobulin E (tIgE) levels were measured. Screening of single nucleotide polymorphisms (SNPs) in the CD14 promoter was performed using direct PCR-sequencing and restriction fragment length polymorphism methods. The functional significance of SNPs was investigated using reporter assay system. RESULTS: Three previous reported SNPs (CD14/-159, -1145 and -1359) and a novel SNP (CD14/-550) were detected. Significant linkage disequilibrium was found among these four loci of CD14 gene. However, no significant difference was found in the genotype frequencies of these SNPs between non-atopy and atopy groups. Furthermore, no transcriptional activities of these SNPs were detected using reporter gene assay in three cell-lines (HepG-2, THP-1 and U937). CONCLUSIONS: This study confirms three reported SNPs and one novel SNP in the CD14 promoter in our local population. However, these SNPs do not play a decisive role in the development of atopic phenotypes.

Adult↗
PubMed2005

Characterization of Rho-GDIgamma and Rho-GDIalpha mRNA in the developing and mature brain with an analysis of mice with targeted deletions of Rho-GDIgamma.

Rho-GDIs are a family of Rho GDP-dissociation inhibitors that are critical in modulating the activity of the small GTPases, Cdc42 and RhoA. Two Rho-GDI isoforms are expressed in the brain, Rho-GDIgamma and Rho-GDIalpha. Here, we describe the expression of both of these isoforms in the developing and mature brain. The mRNA expression patterns of Rho-GDIgamma and Rho-GDIalpha were almost identical in the brain with expression in the developing and mature cerebral cortex, striatum, and hippocampus. In addition, we generated mice with targeted deletions of Rho-GDIgamma that are viable and fertile and have no obvious phenotypic abnormalities. Mutant brains looked histologically normal and demonstrated normal patterns of dendritogenesis and neuronal layering as determined by Golgi staining. Mutant mice had normal sleep/wake patterns and sleep EEGs and showed normal hippocampal-dependent learning as assayed by the Morris water maze task. Based on the co-expression of Rho-GDIalpha and Rho-GDIgamma in identical populations of cells in the brain, the lack of phenotype caused by targeted deletion of Rho-GDIgamma may not be surprising given that Rho-GDIalpha may compensate for the loss of Rho-GDIgamma. Whether deletion of both Rho-GDIalpha and Rho-GDIgamma, thereby eliminating all GDI activity in the brain, would produce an observable phenotype remains to be determined.

Analysis of Variance↗
PubMed2005

hZimp7, a novel PIAS-like protein, enhances androgen receptor-mediated transcription and interacts with SWI/SNF-like BAF complexes.

Members of the PIAS (protein inhibitor of activated signal transducer and activator of transcription) family are negative regulators of the Janus family of tyrosine kinase (JAK)-signal transducer and activator of transcription pathway. Recently, PIAS proteins have been shown to interact with multiple signaling pathways in various cellular processes, and it has been demonstrated that PIAS and PIAS-like proteins interact with nuclear hormone receptors. In this study, we have identified a novel human PIAS-like protein, provisionally termed hZimp7, which shares a high degree of sequence similarity with hZimp10 (human zinc finger-containing, Miz1, PIAS-like protein on chromosome 10). hZimp7 (human zinc finger-containing, Miz1, PIAS-like protein on chromosome 7) possesses a molecular mass of approximately 100 kDa and contains a conserved Miz (msx-interacting zinc finger) domain, a nuclear translocation signal sequence, and a C-terminal transactivation domain. Northern blot analysis revealed that hZimp7 is predominantly expressed in testis, heart, brain, prostate, and ovary. Moreover, immunohistochemical staining of prostate tissues revealed that endogenous hZimp7 protein localizes to the nuclei of prostate epithelial cells and costains with the androgen receptor (AR). Further analysis of hZimp7 subcellular localization revealed that hZimp7 and the AR colocalize within the nucleus and form a protein complex at replication foci. Transient transfection experiments showed that hZimp7 augments the transcriptional activity of the AR and other nuclear hormone receptors. In contrast, reduction of endogenous hZimp7 protein expression by RNA interference decreased AR-mediated transcription. Finally, we determined that hZimp7 physically associates with Brg1 and BAF57, components of the ATP-dependent mammalian SWI/SNF-like BAF chromatin-remodeling complexes. The above data illustrate a potential role for hZimp7 in modulation of AR and/or other nuclear receptor-mediated transcription, possibly through alteration of chromatin structure by SWI/SNF-like BAF complexes.

Animals↗
PubMed2005

Mayven induces c-Jun expression and cyclin D1 activation in breast cancer cells.

Mayven is a member of the kelch-related superfamily of proteins, characterized by a series of 'kelch' repeats at their carboxyl terminus and a BTB/POZ domain at their NH2-terminus. Little is known about the role of Mayven in cancer. Here, we report that Mayven expression was abundant and diffuse in primary human epithelial breast tumor cells as compared to normal breast epithelial cells, where Mayven was detected in the normal breast layer of the mammary ducts. Overexpression of Mayven resulted in an induction of c-Jun protein levels, as well as increased AP-1 (activating protein 1) transcriptional activity in MCF-7 and T47D breast cancer cells through its BTB/POZ domain. Furthermore, Mayven activated c-Jun N-terminal kinase in breast cancer cells. Mayven, through its BTB/POZ domain, induced cyclin D1 expression and cyclin D1 promoter activity and promoted cell cycle progression from the G1 to S phase. MCF-7 cells transduced with the recombinant retroviral sense Mayven (pMIG-W-Mayven) showed significant induction of c-Jun and cyclin D1 mRNA expression and activities as compared to the retroviral vector alone, while MCF-7 cells transduced by the recombinant retroviral antisense Mayven (pMIG-W-Mayven-AS) demonstrated a significant decrease in c-Jun and cyclin D1 expression and activities. Given the crucial functions of cyclin D1 and AP-1 signaling in oncogenesis, our results strongly suggest that overexpression of Mayven may promote tumor growth through c-Jun and cyclin D1.

Breast Neoplasms↗
PubMed2005

Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells.

Embryonic stem cells (ESCs) are pluripotent cells that can either self-renew or differentiate into many cell types. Oct4 and Sox2 are transcription factors essential to the pluripotent and self-renewing phenotypes of ESCs. Both factors are upstream in the hierarchy of the transcription regulatory network and are partners in regulating several ESC-specific genes. In ESCs, Sox2 is transcriptionally regulated by an enhancer containing a composite sox-oct element that Oct4 and Sox2 bind in a combinatorial interaction. It has previously been shown that Pou5f1, the Oct4 gene, contains a distal enhancer imparting specific expression in both ESCs and preimplantation embryos. Here, we identify a composite sox-oct element within this enhancer and show that it is involved in Pou5f1 transcriptional activity in ESCs. In vitro experiments with ESC nuclear extracts demonstrate that Oct4 and Sox2 interact specifically with this regulatory element. More importantly, by chromatin immunoprecipitation assay, we establish that both Oct4 and Sox2 bind directly to the composite sox-oct elements in both Pou5f1 and Sox2 in living mouse and human ESCs. Specific knockdown of either Oct4 or Sox2 by RNA interference leads to the reduction of both genes' enhancer activities and endogenous expression levels in addition to ESC differentiation. Our data uncover a positive and potentially self-reinforcing regulatory loop that maintains Pou5f1 and Sox2 expression via the Oct4/Sox2 complex in pluripotent cells.

Animals↗
PubMed2005

Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state.

Human embryonic stem cells (hESCs) are an important source of stem cells in regenerative medicine, and much remains unknown about their molecular characteristics. To develop a detailed genomic profile of ESC lines in two different species, we compared transcriptomes of one murine and two different hESC lines by massively parallel signature sequencing (MPSS). Over 2 million signature tags from each line and their differentiating embryoid bodies were sequenced. Major differences and conserved similarities between species identified by MPSS were validated by reverse transcription polymerase chain reaction (RT-PCR) and microarray. The two hESC lines were similar overall, with differences that are attributable to alleles and propagation. Human-mouse comparisons, however, identified only a small (core) set of conserved genes that included genes known to be important in ESC biology, as well as additional novel genes. Identified were major differences in leukemia inhibitory factor, transforming growth factor-beta, and Wnt and fibroblast growth factor signaling pathways, as well as the expression of genes encoding metabolic, cytoskeletal, and matrix proteins, many of which were verified by RT-PCR or by comparing them with published databases. The study reported here underscores the importance of cross-species comparisons and the versatility and sensitivity of MPSS as a powerful complement to current array technology.

Animals↗
PubMed2004

RhoH is required to maintain the integrin LFA-1 in a nonadhesive state on lymphocytes.

Lymphocyte function-associated antigen 1 (LFA-1) is relatively nonadhesive on resting lymphocytes; however, the mechanisms underlying changes in its adhesiveness are poorly understood. In this study, we generated a Jurkat T cell clone, J+hi1.14, that contained low amounts of mRNA for RhoH, a leukocyte-specific inhibitory Rho family member. J+hi1.14 cells expressed constitutively adhesive LFA-1 and the cells bound spontaneously to intracellular adhesion molecules 1, 2 and 3. Reconstitution of RhoH mRNA expression in J+hi1.14 cells reverted the adhesion phenotype to that of wild-type. We obtained similar results using RNA interference in peripheral blood lymphocytes. These data demonstrate that RhoH is required for maintenance of lymphocyte LFA-1 in a nonadhesive state.

Blotting, Southern↗
PubMed2004

Inhibition of SARS coronavirus infection in vitro with clinically approved antiviral drugs.

Severe acute respiratory syndrome (SARS) is an infectious disease caused by a newly identified human coronavirus (SARS-CoV). Currently, no effective drug exists to treat SARS-CoV infection. In this study, we investigated whether a panel of commercially available antiviral drugs exhibit in vitro anti-SARS-CoV activity. A drug-screening assay that scores for virus-induced cytopathic effects on cultured cells was used. Tested were 19 clinically approved compounds from several major antiviral pharmacologic classes: nucleoside analogs, interferons, protease inhibitors, reverse transcriptase inhibitors, and neuraminidase inhibitors. Complete inhibition of cytopathic effects of SARS-CoV in culture was observed for interferon subtypes, b-1b, a-n1, a-n3, and human leukocyte interferon a. These findings support clinical testing of approved interferons for the treatment of SARS.

Antiviral Agents↗