Genes Oct4 Research Articles

The response of PIK3CA/KRAS-mutant colorectal cancer stem-like cells to RGD-peptide FraC produced by the strawberry anemone: A promising water-soluble peptide-based inhibitor of metastasis-driver gene CXCR4, stem cell regulatory genes and self-renewal

Colorectal cancer (CRC) is a stem cell-based disease. PIK3CA/KRAS-mutant CRC stem cells (CRCSCs) display high self-renewal, metastatic properties, high activity of PI3K and KRAS signaling pathways with chemoresistant phenotypes. Recently, RGD peptide (containing Arg-Gly-Asp motif)-based therapy of solid tumor cells has attracted much attention. However, little is known whether this method can target self-renewal capacity, key effectors of PI3K and KRAS signaling pathways such as metastasis-driver gene CXCR4 and stem cell regulatory genes with caspase-3 reactivation in CRCSCs overexpressing RGD-dependent integrins.The sea anemone Actinia fragacea produces a water-soluble RGD-peptide fragacea toxin C (FraC) suggesting the possible activity of FraC against PIK3CA/KRAS-mutant CRCSCs.Recombinant FraC was expressed via pET-28a(+)-FraC in E. coli and purified through affinity chromatography followed by performing SDS-PAGE and hemolytic activity assay. Next, PIK3CA/KRAS-mutant HCT-116 cells that serve as an attractive model for CRCSCs were treated with FraC. Thereafter, cell numbers, viability, proliferation, LDH activity, cytotoxicity index, CXCR4 and pluripotency network genes expression, self-renewal capacity, caspase-3 activity with apoptosis were evaluated. Caspase-1, -2, -3,…, -9 sequences were analyzed for RGD-binding motifs. FraC sequence and structure were also evaluated by bioinformatics software.FraC altered cellular morphology to round shapes and disrupted cell connections. 48 h post-treatment with 0.056˗ to 7.2 μM FraC resulted in 12 %–99 % and 8 %–97.6 % decreases in cell numbers and viabilities respectively and increased LDH activity by 0.2 %–66.7 % in a dose-dependent manner. The results of the cytotoxicity index showed that FraC induces significant toxicity on HCT-116 cells compared to PBMCs and Huvec cells. FraC dramatically decreased the expression of CXCR4 and pluripotency network genes Bmi-1, Sox-2, Oct-4 and Nanog followed by remarkable decreases in self-renewal capacity ranged from 91- to 0 colonies per well for 0.056˗ to 3.6 μM FraC after 2 weeks. Caspase-3 was found to contain an RGD-binding motif and its activity increased with increasing FraC concentrations followed by apoptosis induction. Potential RGD-binding motifs for FraC were also found in caspase-1, -7, -8 and -9.Unique advantages of FraC peptide, such as low molecular weight, water solubility, high sensitivity of CRC stem-like cells with more selective toxicity to this compound, targeting tumor cell membrane and self-renewal capacity along with the modulation of CXCR4 and stem cell regulatory genes as upstream and downstream effectors of undruggable PI3K and KRAS signaling pathways may open up avenues for FraC peptide-based therapy of PIK3CA/KRAS-mutant CRCSCs with lower toxicity on healthy cells.

Breast tumour cell subpopulations with expression of the MYC and OCT4 proteins.

The MYC and OCT4 genes are known factors associated with maintaining pluripotency and are linked with a more aggressive course, progression, and resistance to therapy in cancer. Determining the subpopulations of tumour cells expressing the Myc and Oct4 proteins will provide an opportunity to understand which tumour cell subpopulations expressing MYC and OCT4 are associated with metastasis and resistance and which subpopulations can be targeted by anti-MYC and anti-OCT4 therapy. The study included paraffin-embedded tissue from tumours from 27 patients with luminal B breast cancer obtained after neoadjuvant chemotherapy (NACT). Immunofluorescence staining was used to identify subpopulations of tumour cells expressing Myc, Oct4 and Snai2 (Opal™ 7-Color Kit (PerkinElmer, Hopkinton, MA). The following tumour cell subpopulations were identified with the Myc and Oct4 proteins and the Snai2 EMT marker: stem/progenitor tumour cells with/without Myc, Oct4 or Snai2 expression; differentiated tumour cells with/without Myc, Oct4 or Snai2 expression; and other nontumour cells (CK7-EpCAM-CD44+/-Myc+/-(Oct4, Snai2)+/-) within the inflammatory infiltrate in the tumour parenchyma and stroma. The circulating tumour cell subpopulations with Oct4 protein expression in the bloodstream were studied by flow cytometry. It was found that in patients with partial regression (PR) in response to NACT, the frequency of tumour stem cells was 3.6-fold increased (p = 0.038) in the non-EMT state (CK7+EpCam+CD44+Snai2-). In patients with metastases, there was a statistically significant 2.5-fold increase in the frequency of differentiated tumour cells with Myc expression (CK7+EpCam+CD44-Myc+) and a 2.7-fold increase in the frequency of cells with Oct4 expression (CK7+EpCam+CD44-OCT4+). In the next stage, the frequencies of subpopulations with expression of the Oct4 protein and signs of EMT among circulating tumour cells (CTCs) were determined. In patients with metastases, the frequency of tumour stem cells in the EMT state (CD326+CD44+CD24-CD325+) (p = 0.015) was more than fourfold increased, and the frequency of progenitor tumour cells with expression of the Oct4 stem protein (CD326+CD44+CD24+Oct4+) (p = 0.016) was almost sixfold higher than that in patients without metastases. Nonstem (differentiated) tumour cells with expression of the stemness proteins Myc and Oct4 were present in the breast tumour. Their content was significantly higher in residual tumours after NACT in patients who subsequently developed metastases compared with that in patients without metastases. Such cells are a new in situ marker of metastasis.

Fluorescence cross-correlation spectroscopy as a valuable tool to characterize cationic liposome-DNA nanoparticle assembly.

The development of nonviral gene delivery vehicles for therapeutic applications requires methods capable of quantifying the association between the genes and their carrier counterparts. Here we investigate the potential of fluorescence cross-correlation spectroscopy (FCCS) to characterize and optimize the assembly of nonviral cationic liposome (CL)-DNA complexes based on a CL formulation consisting of the cationic lipid DOTAP and zwitterionic lipid DOPC. We use a DNA plasmid for lipoplex loading encoding the Oct4 gene, critically involved in reprogramming somatic cells into induced pluripotent stem cells. We demonstrate that FCCS is able to quantitatively determine the extent of the association between DNA and the liposomes and assess its loading capacity. We also establish that the cationic lipid fraction, being proportional to the liposome membrane charge density, as well as charge ratio between the CLs and anionic DNA play an important role in the degree of interaction between the liposomes and DNA.

SIX1 ve Kanser Kök Hücre Belirteçlerinin Hepatoselluler Karsinomada Kapsamlı Analizi

Objective: Transcription factor SIX1 aberrant expression has been shown in various mammalian tumors, and also recent studies indicated that SIX1 has a role in cancer stem cell properties. However, its roles in HCC cancer stem cell characteristics remain unclear. The aim of the study, to evaluate the EMT-inducer SIX1 and cancer stem cell markers expression profile in-vitro and in-vivo analyses.
 Material and Methods: SIX1 expression was suppressed by short hairpin RNA transduction in the SNU398 HCC cell line. Tumorsphere formation assay is a golden useful assay for cancer stem cell analysis. SIX1-dependent cancer stem cell markers PROM1, EPCAM, and OCT4 differential gene expression profiles were assessed in tumorsphere formation assay by RT-qPCR. Differential expression and correlation analyses were performed in transcriptome data in cirrhosis and HCC tissue samples.
 Results: Assessment of SIX1-knockdown expression of target genes in tumorsphere formation assay revealed PROM1, EPCAM expressions were significantly up-regulated but OCT4 gene expression was significantly down-regulated. Conformably, PROM1 and EPCAM expressions were inversely but OCT4 expression was positively correlated in transcriptome arrays in HCC tissues. Interestingly, to the evaluation of the same gene expressions were shown different patterns except, OCT4 in cirrhosis samples. The mRNA expression profiles did not change between cirrhosis and HCC samples in the SIX1, EPCAM, PROM1, and OCT4 gene expression profiles.
 Conclusion: Cancer stem cells are self‐renewable cell types and are responsible for cancer progression. Findings from this study highlight the SIX1 and cancer stemness-related genes expression correlations to improve our knowledge for HCC molecular signatures.

Improvement of in vitro proliferation of cockerel spermatogonial stem cells using different combinations of growth factors

ABSTRACT 1. This study examined whether in vitro proliferation and maintenance of cockerel spermatogonial stem cells (SSCs) could be improved by adding different combinations of growth factors (GFs), including glial cell line-derived neurotrophic factor (GDNF), basic fibroblast growth factor (bFGF) or leukaemia inhibitory factor (LIF) into the culture medium. 2. The SSCs were isolated from the testes of immature cockerels. For short-term cultures, a medium supplemented with different combinations of GFs for 7 d in 5 replicates was used. The groups were classified as follows: without GF (control group); with GDNF (G group); with GDNF and bFGF (GF group); and with GDNF, bFGF and LIF (GFL group). The number of colonies and cells per colony, as well as the transcript abundance of STRA8 and OCT4 genes, was determined 7 d after the initial culturing. Immunofluorescence staining of SSEA-1, SSEA-3 and VASA protein markers, besides periodic acid-Schiff (PAS) staining, was carried out. 3. The number of colonies and cells per colony increased in the G, GF and GFL groups, compared to the control group (P < 0.01); however, the highest proliferation and colony formation were observed in the GFL group. The positive immunofluorescence staining of SSEA-1, SSEA-3 and VASA protein markers, as well as PAS staining, confirmed the self-renewal and colonisation of cockerel SSCs. The proliferation results were supported by the increased STRA8 and OCT4 transcript abundance in the treated groups (G, GF and GLF), compared to the control group. The SSC proliferation was associated with the higher transcript abundance of STAR8 and OCT4 genes in the GFL group, compared to the G and GF groups (P < 0.01). 4. The results showed that proliferation and colony-forming capacity of cockerel SSCs were positively improved by GDNF, bFGF and LIF. However, the most significant effect was observed when the medium was supplemented with LIF in combination with GDNF and bFGF.

Perinatal exposure to Bisphenol A disturbs the early differentiation of male germ cells

Understanding the effects of Bisphenol A (BPA) on early germ cell differentiation and their consequences in adult life is an area of growing interest in the field of endocrine disruption. Herein, we investigate whether perinatal exposure to BPA affects the differentiation of male germ cells in early life using a transgenic mouse expressing the GFP reporter protein under the Oct4 promoter. In this model, the expression of GFP reflects the expression of the Oct4 gene. This pluripotency gene is required to maintain the spermatogonial stem cells in an undifferentiated stage. Thus, GFP expression was used as a parameter to evaluate the effect of BPA on early germ cell development. Female pregnant transgenic mice were exposed to BPA by oral gavage, from embryonic day 5.5 to postnatal day 7 (PND7). The effects of BPA on male germ cell differentiation were evaluated at PND7, while sperm quality, testicular morphology, and protein expression of androgen receptor and proliferating cell nuclear antigen were studied at PND130.We found that perinatal/lactational exposure to BPA up-regulates the expression of Oct4-driven GFP in testicular cells at PND7. This finding suggests a higher proportion of undifferentiated spermatogonia in BPA-treated animals compared with non-exposed mice. Moreover, in adulthood, the number of spermatozoa per epididymis was reduced in those animals perinatally exposed to BPA.This work shows that developmental exposure to BPA disturbed the normal differentiation of male germ cells early in life, mainly by altering the expression of Oct4 and exerted long-lasting sequelae at the adult stage, affecting sperm count and testis.

Human Mesenchymal Stromal Cells Unveil an Unexpected Differentiation Potential toward the Dopaminergic Neuronal Lineage.

Degeneration of dopaminergic neurons represents the cause of many neurodegenerative diseases, with increasing incidence worldwide. The replacement of dead cells with new healthy ones may represent an appealing therapeutic approach to these pathologies, but currently, only pluripotent stem cells can generate dopaminergic neurons with high efficiency. However, with the use of these cells arises safety and/or ethical issues. Human mesenchymal stromal cells (hFM-MSCs) are perinatal stem cells that can be easily isolated from the amniochorionic membrane after delivery. Generally considered multipotent, their real differentiative potential is not completely elucidated. The aim of this study was to analyze their stemness characteristics and to evaluate whether they may overcome their mesenchymal fate, generating dopaminergic neurons. We demonstrated that hFM-MSCs expressed embryonal genes OCT4, NANOG, SOX2, KLF4, OVOL1, and ESG1, suggesting they have some features of pluripotency. Moreover, hFM-MSCs that underwent a dopaminergic differentiation protocol gradually increased the transcription of dopaminergic markers LMX1b, NURR1, PITX3, and DAT. We finally obtained a homogeneous population of cells resembling the morphology of primary midbrain dopaminergic neurons that expressed the functional dopaminergic markers TH, DAT, and Nurr1. In conclusion, our results suggested that hFM-MSCs retain the expression of pluripotency genes and are able to differentiate not only into mesodermal cells, but also into neuroectodermal dopaminergic neuron-like cells.

XIST lost induces ovarian cancer stem cells to acquire taxol resistance via a KMT2C-dependent way

Background/aimsThe expression levels of long non-coding RNA XIST are significantly associated with paclitaxel (Pac) sensitivity in ovarian cancer, but the mechanism of action remains unclear. Therefore, this experimental design was based on lncRNA XIST analysis to regulate the effect of XIST on the tumor stem cell and paclitaxel sensitivity in ovarian cancer.MethodsSphere assay and fluorescence activated cell sorting (FACS) were used to determine the expression levels of XIST and sensitivity to paclitaxel treatment. The effect of the proliferation was detected by MTT assay. Target gene prediction and screening, luciferase reporter assays were used to validate downstream target genes for lncRNA XIS and KMT2C. The expression of KMT2C was detected by RT-qPCR and Western blotting. RT-qPCR was used to detect the expression of cancer stem cell-associated genes SOX2, OCT4 and Nanog. The tumor changes in mice were detected by in vivo experiments in nude mice.ResultsThere was an inverse correlation between the expression of XIST and cancer stem cell (CD44 + /CD24−) population. XIST promoted methylation of histone H3 methylation at lysine 4 by enhancing the stability of lysine (K)-specific methyltransferase 2C (KMT2C) mRNA. XIST acted on the stability of KMT2C mRNA by directly targeting miR-93-5p. Overexpression of miR-93-5p can reverse the XIST overexpression-induced KMT2C decrease and sphere number increase. Overexpression of KMT2C inhibited XIST silencing-induced proliferation of cancer stem cells, and KMT2C was able to mediate paclitaxel resistance induced by XIST in ovarian cancer. The study found that XIST can affect the expression of KMT2C in the ovarian cancer via targeting miR-93-5p.ConclusionXIST promoted the sensitivity of ovarian cancer stem cells to paclitaxel in a KMT2C-dependent manner.

TET3 overexpression facilitates DNA reprogramming and early development of bovine SCNT embryos.

Somatic cell nuclear transfer (SCNT) has been successfully used for cloning in a variety of mammalian species. However, SCNT reprogramming efficiency is relatively low, in part, due to incomplete DNA methylation reprogramming of donor cell nuclei. We previously showed that ten-eleven translocation 3 (TET3) is responsible for active DNA demethylation during preimplantation embryonic development in bovines. In this study, we constructed TET3-overexpressing cell lines in vitro and observed that the use of these fibroblasts as donor cells increased the blastocyst rate by approximately 18 percentage points compared to SCNT. The overexpression of TET3 in bovine SCNT embryos caused a decrease in the global DNA methylation level of the pluripotency genes Nanog and Oct-4, ultimately resulting in an increase in the transcriptional activity of these pluripotency genes. Moreover, the quality of bovine TET3-NT embryos at the blastocyst stage was significantly improved, and bovine TET3-NT blastocysts possessed more total number of cells and fewer apoptotic cells than the SCNT blastocysts, similar to in vitro fertilization (IVF) embryos. Nevertheless, DNA methylation of the imprinting control region (ICR) for the imprinted genes H19-IGF2 in SCNT embryos remained unaffected by TET3 overexpression, maintaining parent-specific activity for further development. Thus, the results of our study provide a promising approach to rectify incomplete epigenetic reprogramming and achieve higher cloning efficiency.

Establishment of drug screening in human embryonic stem cells based on a high-content screening system

High-content screening (HCS) systems can be used for high-throughput screening of drugs in human embryonic stem cells (hESCs). However, hESCs require immunofluorescence staining with stemness markers (e.g., Oct-4) prior to HCS, which can be time consuming and labor intensive. In this study, we employed transgenic hESCs with enhanced green fluorescent protein driven by stemness gene Oct-4 promoter (Oct-4-EGFP-H9), in which the colony area and relative green fluorescence area inferred a state of hESC proliferation and stemness, respectively. The Oct-4-EGFP-H9 transgenic hESCs were cultured in mTeSR medium with different concentrations of 5-Fluorouracil (5-FU), vitamin C (VC), or retinoic acid (RA) for 5–7 days, followed by repeated imaging using the HCS system. Finally, the hESC colony area and green fluorescence area were calculated. Results showed that 5-FU treatment markedly reduced colony area in a dose-dependent manner, whereas VC and RA treatments did not. MTT assay and flow cytometry indicated that 5-FU inhibited the proliferation of hESCs significantly, verifying reliability of the data from the HCS system based on colony area analysis. The green fluorescence to total colony area ratio decreased with RA treatment, suggesting that RA significantly promoted differentiation, whereas 5-FU and VC had almost no effect, as verified by quantitative real-time polymerase chain reaction and western blot analysis. In conclusion, our study established a rapid and efficient drug screening system without the requirement of staining based on HCS.

Regulation of β-catenin by IGFBP2 and its cytoplasmic actions in glioma

IGFBP2 is one of the highly expressed genes in glioblastoma (GBM). It has both IGF dependent and independent activities. IGF independent actions are mediated by the activation of integrin signalling through its RGD motif present at C-terminal domain. One of the actions of IGFBP2 is to regulate β-catenin by the inactivation of GSK3β, which preferentially accumulates in the cytoplasm. The mechanism of nuclear β-catenin regulation by IGFBP2 and role of cytoplasmic β-catenin is not clear. We aimed to understand the mechanism in GBM cell lines. The gene expression studies were performed by RT-PCR, western blot analysis; the knockdown of genes was performed by shRNA transfection; RNAIP and luciferase reporter assays were utilized to study the cytoplasmic regulation of genes by β-catenin; neurosphere assays were performed to study the stemness of cells. IGFBP2 overexpression or treatment in GBM cells regulates β-catenin, TRIM33 (E3 ubiquitin ligase) and Oct4 genes. TRIM33 was induced by IGFBP2. β-catenin was found to accumulate predominantly in the cytoplasm and nuclear β-catenin was depleted by IGFBP2 induced TRIM33. IGFBP2 regulated cytoplasmic β-catenin binds to 3' UTR of Oct4 RNA. IGFBP2 was also able to induce stemness of glioma cells. IGFBP2 induces TRIM33 which regulates the nuclear β-catenin protein. In addition, IGFBP2 stabilizes the cytoplasmic β-catenin which is involved in the regulation of Oct4 transcript and consequently induction of stemness of glioma cells.

3134 – CHARACTERIZATION OF THE HEMATOPOIETIC STEM CELLS AND BONE MARROW MICROENVIRONMENT IN SICKLE CELL DISEASE PATIENTS

Little is known about the status of the bone marrow (BM) in Sickle Cell Disease (SCD) patients. In this study, we characterized the hematopoietic stem and progenitors (HSPC) and the stromal cells from BM aspirates of eight SCD patients before transplant in comparison with age-matched BM aspirates from healthy individuals. By using multiparametric flow analysis, we observed a group of SCD patients (n=4) with characteristics similar to controls, and a distinct group of SCD patients (n=4) that exhibited lower average frequency of CD34+ cells, HSCs, multipotent and lymphoid progenitors. Methylcellulose colony assays showed a decreased ability of the BM cells of these patients to form colonies compared to control BM. scRNA-seq analysis of sorted BM CD34+ cells from SCD patients indicated changes in the DNA damage and cell cycle regulatory pathways compared to controls. Interestingly, all SCD patients displayed an increase in the BM non-hematopoietic cells including CD45-/CD31+ and CD45-/CD105+ subsets compared to controls, suggesting a change in their BM stromal niche. In vitro, SCD BM-derived stromal cells revealed distinct gene expression patterns including an increase in inflammatory cytokine (IL-6) & cell death-related genes (p16 and Bax) but decrease expression of a pluripotent gene (Oct4). We also detected an increase of inflammatory regulators, miR-155, and miR-146 in all BM-derived stromal cells from SCD patients, which correlates with increased inflammatory gene expression in these cells. Finally, analysis of the BM biopsies revealed alterations in the stromal components as evidenced by an overall decrease in cellularity in some patients, and increased iron deposits and activated macrophages. Taken together, these preliminary data suggest that the BM cells and BM microenvironment of SCD patients are phenotypically & molecularly different from control BM. Further studies will clarify whether there are correlations between the severity of the disease and BM alterations and whether the BM status at pre-transplant may help in predicting engraftment and outcomes of BM transplants in SCD patients.

Effect of OCT4 Gene Expression Upregulation on the Expression of iPSC-related Transcription Factors in Human Bone Marrow Derived Mesenchymal Stem Cells

To explore the effect of OCT4 over-expression on the expression of induced pluripotent stem cell (iPSC)-related transcription factors (cMYC，KLF4，LIN28，NANOG and SOX2) in human bone marrow derived mesenchymal stem cells (hBMMSCs), so as to provide fundamental basis for exploring the pathogenesis of hematological diseases (leukemia, aplastic anemia, etc.) from the perspective of hemopoietic microenvironment in the future. Recombinant plasmid pcDNA3.1-OCT4 was constructed and transferred into the optimal generation P3-4 hBMMSCs by liposome transfection. The cells with stable and high expression of OCT4（hBMMSCs-OCT4）were screened by G418 resistance screening (limited dilution) and subcloning, the expression of OCT4 mRNA and OCT4 protein was verified by RT-PCR and FCM, respectively. The expression of iPSC-related transcription factors (cMYC, KLF4, LIN28, NANOG and SOX2) were also determined by FCM and RT-PCR, so as to evaluate the effect of ectopic high expression of OCT4 on the expression of iPSC related transcription factors in hBMMSCs. Recombinant plasmid pcDNA3.1-OCT4 was successfully constructed and cells with stable and high expression of OCT4 were successfully screened from hBMMSCs by limited dilution and subcloning. The result of flow cytometry showed that the mean expression level of OCT4 protein increased from (3.03±1.49)% to (95.46±1.40)% compared with the untransfected parental MSCs, which was also confirmed by RT-PCR analysis. At the same time, the expression levels of OCT4 protein and mRNA were compared between transient transfection (day 4) and stable expression cells (day 96), respectively, it was showed that the OCT4 protein level increased from (36.36±0.28)% at day 4 to (96.25±1.38)% at day 96, and the OCT4 mRNA level increased from 2.75-folds to 6.23-folds, respectively. Compared with the untransfected parental MSCs, the average expression levels of stemness transcription factors increased from (1.12±0.47)% (cMYC), (0.84±0.30)% (KLF4), (2.14±0.79)% (LIN28), (0.63±0.37)% (NANOG) and (14.34±2.44)% (SOX2) to (80.65±4.75)%, (73.03±4.70)%, (68.08±3.05)%, (39.39±1.85)%and (91.45±4.56)% in hBMMSCs-OCT4, respectively, which were consistent with results of RT-PCR analysis. Moreover, the expression levels of NANOG and SOX2 positively correlated with the mean expression of OCT4 (OCT4 vs NANOG: r=0.7802，OCT4 vs SOX2: r=0.4981；NANOG vs SOX2: r=0.7426). Cells with stable and high expression of OCT4 have been successfully established from hBMMSCs. Ectopic high expression of transcription factor OCT4 in hBMMSCs can up-regulate the expression of other iPSC-related transcription factors such as cMYC, KLF4, LIN28, NANOG and SOX2.

Model-based analysis of chromatin interactions from dCas9-Based CAPTURE-3C-seq.

Deciphering long-range chromatin interactions is critical for understanding temporal and tissue-specific gene expression regulated by cis- and trans-acting factors. By combining the chromosome conformation capture (3C) and biotinylated dCas9 system, we previously established a method CAPTURE-3C-seq to unbiasedly identify high-resolution and locus-specific long-range DNA interactions. Here we present the statistical model and a flexible pipeline, C3S, for analysing CAPTURE-3C-seq or similar experimental data from raw sequencing reads to significantly interacting chromatin loci. C3S provides all steps for data processing, quality control and result illustration. It can automatically define the bin size based on the binding peak of the dCas9-targeted regions. Furthermore, it supports the analysis of intra- and inter-chromosomal interactions for different mammalian cell types. We successfully applied C3S across multiple datasets in human K562 cells and mouse embryonic stem cells (mESC) for detecting known and new chromatin interactions at multiple scales. Integrative and topological analysis of the interacted loci at the human β-globin gene cluster provides new insights into mechanisms in developmental gene regulation and network structure in local chromosomal architecture. Furthermore, computational results in mESCs reveal a role for chromatin interacting loops between enhancers and promoters in regulating alternative transcripts of the pluripotency gene OCT4.

Pluripotency transcription factor Nanog and its association with overall oral squamous cell carcinoma progression, cisplatin-resistance, invasion and stemness acquisition.

Cisplatin-resistant oral squamous cell carcinoma (OSCC) cells acquire stem-like characteristics and are difficult to treat. Nanog is a transcription factor and needed for maintenance of pluripotency, but its transcription-promoting role in OSCC progression and cisplatin resistance is poorly understood. Here, 110 fresh human tissue specimens of various stages, including invasive (N1-3 )/chemoradiation-resistant OSCC samples, cisplatin-resistant (CisR-SCC-4/-9) OSCC cells/parental cells, photochemical ECGC, and siRNA (Nanog) were used. Nanog overexpression was associated with overall progression, chemoresistance, and invasion of OSCC. Nanog recruitment to c-Myc, Slug, E-cadherin, and Oct-4 gene promoter was observed. Positive correlation of Nanog protein expression with c-Myc, Slug, cyclin D1, MMP-2/-9, and Oct-4 and negative correlation with E-cadherin gene expression were found. Knockdown of Nanog and treatment of epicatechin-3-gallate reversed cisplatin resistance and diminished invasion/migration potential. Nanog directly participated in the regulation of Slug, E-cadherin, Oct-4, and c-Myc genes, causing cisplatin resistance/recurrence of OSCC.

Nanosecond pulsed electric fields enhance mesenchymal stem cells differentiation via DNMT1-regulated OCT4/NANOG gene expression

BackgroundMultiple strategies have been proposed to promote the differentiation potential of mesenchymal stem cells (MSCs), which is the fundamental property in tissue formation and regeneration. However, these strategies are relatively inefficient that limit the application. In this study, we reported a novel and efficient strategy, nanosecond pulsed electric fields (nsPEFs) stimulation, which can enhance the trilineage differentiation potential of MSCs, and further explained the mechanism behind.MethodsWe used histological staining to screen out the nsPEFs parameters that promoted the trilineage differentiation potential of MSCs, and further proved the effect of nsPEFs by detecting the functional genes. In order to explore the corresponding mechanism, we examined the expression of pluripotency genes and the methylation status of their promoters. Finally, we targeted the DNA methyltransferase which was affected by nsPEFs.ResultsThe trilineage differentiation of bone marrow-derived MSCs was significantly enhanced in vitro by simply pre-treating with 5 pulses of nsPEFs stimulation (energy levels as 10 ns, 20 kV/cm; 100 ns, 10 kV/cm), due to that the nsPEFs demethylated the promoters of stem cell pluripotency genes OCT4 and NANOG through instantaneous downregulation of DNA methylation transferase 1 (DNMT1), thereby increasing the expression of OCT4 and NANOG for up to 3 days, and created a treatment window period of stem cells.ConclusionsIn summary, nsPEFs can enhance MSCs differentiation via the epigenetic regulation and could be a safe and effective strategy for future stem cell application.

Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis.

Rupture and erosion of advanced atherosclerotic lesions with a resultant myocardial infarction or stroke are the leading worldwide cause of death. However, we have a limited understanding of the identity, origin, and function of many cells that make up late-stage atherosclerotic lesions, as well as the mechanisms by which they control plaque stability. We conducted a comprehensive single-cell RNA sequencing of advanced human carotid endarterectomy samples and compared these with single-cell RNA sequencing from murine microdissected advanced atherosclerotic lesions with smooth muscle cell (SMC) and endothelial lineage tracing to survey all plaque cell types and rigorously determine their origin. We further used chromatin immunoprecipitation sequencing (ChIP-seq), bulk RNA sequencing, and an innovative dual lineage tracing mouse to understand the mechanism by which SMC phenotypic transitions affect lesion pathogenesis. We provide evidence that SMC-specific Klf4- versus Oct4-knockout showed virtually opposite genomic signatures, and their putative target genes play an important role regulating SMC phenotypic changes. Single-cell RNA sequencing revealed remarkable similarity of transcriptomic clusters between mouse and human lesions and extensive plasticity of SMC- and endothelial cell-derived cells including 7 distinct clusters, most negative for traditional markers. In particular, SMC contributed to a Myh11-, Lgals3+ population with a chondrocyte-like gene signature that was markedly reduced with SMC-Klf4 knockout. We observed that SMCs that activate Lgals3 compose up to two thirds of all SMC in lesions. However, initial activation of Lgals3 in these cells does not represent conversion to a terminally differentiated state, but rather represents transition of these cells to a unique stem cell marker gene-positive, extracellular matrix-remodeling, "pioneer" cell phenotype that is the first to invest within lesions and subsequently gives rise to at least 3 other SMC phenotypes within advanced lesions, including Klf4-dependent osteogenic phenotypes likely to contribute to plaque calcification and plaque destabilization. Taken together, these results provide evidence that SMC-derived cells within advanced mouse and human atherosclerotic lesions exhibit far greater phenotypic plasticity than generally believed, with Klf4 regulating transition to multiple phenotypes including Lgals3+ osteogenic cells likely to be detrimental for late-stage atherosclerosis plaque pathogenesis.

The Use of Stem Cell Differentiation Stage Factors (SCDSFs) Taken from Zebrafish Embryos during Organogenesis and Their Role in Regulating the Gene Expression of Normal and Pathological (Stem) Cells.

Studies conducted on Zebrafish embryos in our laboratory have allowed for the identification of precise moments of organogenesis in which a lot of genes are switched on and off, a sign that the genome is undergoing substantial changes in gene expression. Stem cell growth and differentiation stage-factors present in different moments of organogenesis have proven to have different specific functions in gene regulation. The substances present in the first stages of cell differentiation in Zebrafish embryos have demonstrated an ability to counteract the senescence of stem cells, reducing the expression of the beta-galactosidase marker, enhancing the genes Oct-4, Sox-2, c-Myc, TERT, and the transcription of Bmi-1, which act as key telomerase-independent repressors of cell aging. The molecules present in the intermediate to late stages of cell differentiation have proven to be able to reprogram pathological human cells, such as cancer cells and those of the basal layer of the epidermis in psoriasis, which present a higher multiplication rate than normal cells. The factors present in all the stages of cell differentiation are able to counteract neurodegeneration, and to regenerate tissues: It has been possible to regenerate hair follicles in many patients with androgenetic alopecia through transdermal administration of stem cell differentiation stage factors (SCDSFs) by means of cryopass-laser.

Effect of Conditioned Medium from Human Umbilical Cord-Derived Mesenchymal Stromal Cells on Rejuvenation of Nucleus Pulposus Derived Stem/Progenitor Cells from Degenerated Intervertebral Disc.

Background and ObjectivesMesenchymal stromal cells (MSCs)-based treatment for degeneration of intervertebral disc (IVD) has been proposed recently. We here addressed whether MSC secreted factors can rejuvenate nucleus pulposus-derived stem/progenitor cells from degenerated disc (D-NPSCs) in vitro.Methods and ResultsWe analyzed the expression of MSCs and NP cell specific surface markers, pluripotency related genes, multilineage potential and cell proliferative capacity of D-NPSCs upon incubation with the conditioned medium which was collected from the umbilical cord derived MSCs (UCMSCs). Our results indicated that the conditioned medium restore the stemness of D-NPSCs by up-regulating the expression level of CD29 and CD105, pluripotency related genes OCT4 and Nanog, and NP progenitor marker Tie2. The increased stemness was accompanied by promoted cell proliferative capacity and improved osteogenic and chondrogenic differentiation potential.ConclusionsOur findings suggested that the UCMSCs derived conditioned medium might be used to rejuvenate the degenerated NP stem/progenitor cells.

Optimizing 5-aza-2′-deoxycytidine treatment to enhance the development of porcine cloned embryos by inhibiting apoptosis and improving DNA methylation reprogramming

Apoptosis and incomplete DNA methylation reprogramming in cloned embryos reduce cloning efficiency. 5-aza-2′-deoxycytidine (5-aza-dC) is proven to regulate apoptosis and DNA methylation reprogramming, however, the treatment method and potential role of 5-aza-dC during cloned embryo development are still not well studied. This study displayed that treating donor cells with 5-aza-dC (AN group) significantly reduced the blastocyst rate, while treating cloned embryos (NA group) or both donor cells and cloned embryos (ANA group) significantly promoted the blastocyst formation, and the ANA group was the best treatment of 5-aza-dC to enhance the development of cloned embryos. Then, compared with the NT group, the ANA group showed the significantly enhanced nuclear remodeling. The apoptotic cell numbers and rates of blastocysts were significantly reduced, and the expression levels of significantly upregulated anti-apoptosis gene Bcl2l1 and downregulated pro-apoptosis genes Bax, P53 and Caspase3 were observed in the ANA group. Further study demonstrated that the transcription levels of DNA methylation reprogramming genes Dnmt1, Dnmt3a, Tet1 and Tet3 were significantly upregulated, and, significant genomic DNA remethylation, DNA demethylation of pluripotency gene Oct4, and DNA remethylation of tissue specific gene Thy1 were observed at the blastocyst stage in the ANA group. Embryo development related genes including Igf2, H19, Oct4, Nanog, Sox2, Eif1a, Cdx2 and ATP1b1 were significantly upregulated, and Thy1 and Col5a2 were remarkably silenced at the 4-cell and blastocyst stages in the ANA group. In conclusion, the best 5-aza-dC treatment enhanced the development of cloned embryos by inhibiting apoptosis and improving DNA methylation reprogramming.