scholarly journals A novel machine learning based approach for iPS progenitor cell identification

2019 ◽  
Author(s):  
Haishan Zhang ◽  
Ximing Shao ◽  
Yin Peng ◽  
Yanning Teng ◽  
Konda Mani Saravanan ◽  
...  
Keyword(s):  
Machine Learning ◽  
Image Analysis ◽  
Progenitor Cells ◽  
Progenitor Cell ◽  
Early Stage ◽  
Time Windows ◽  
Underlying Mechanism ◽  
Ips Cells ◽  
Microscopic Image ◽  
Induced Pluripotent

AbstractIdentification of induced pluripotent stem (iPS) progenitor cells, the iPS forming cells in early stage of reprogramming, could provide valuable information for studying the origin and underlying mechanism of iPS cells. However, it is very difficult to identify experimentally since there are no biomarkers known for early progenitor cells, and only about 6 days after reprogramming initiation, iPS cells can be experimentally determined via fluorescent probes. What is more, the ratio of progenitor cells during early reprograming period is below 5%, which is too low to capture experimentally in the early stage.In this paper, we propose a novel computational approach for the identification of iPS progenitor cells based on machine learning and microscopic image analysis. Firstly, we record the reprogramming process using a live cell imaging system after 48 hours of infection with retroviruses expressing Oct4, Sox2 and Klf4, later iPS progenitor cells and normal murine embryonic fibroblasts (MEFs) within 3 to 5 days after infection are labeled by retrospectively tracing the time-lapse microscopic image. We then calculate 11 types of cell morphological and motion features such as area, speed, etc., and select best time windows for modeling and perform feature selection. Finally, a prediction model using XGBoost is built based on the selected six types of features and best time windows. Our model allows several missing values/frames in the sample datasets, thus it is applicable to a wide range of scenarios.Cross-validation, holdout validation and independent test experiments showed that the minimum precision is above 52%, that is, the ratio of predicted progenitor cells within 3 to 5 days after viral infection is above 52%. The results also confirmed that the morphology and motion pattern of iPS progenitor cells is different from that of normal MEFs, which helps with the machine learning methods for iPS progenitor cell identification.Author SummaryIdentification of induced pluripotent stem (iPS) progenitor cells could provide valuable information for studying the origin and underlying mechanism of iPS cells. However, it is very difficult to identify experimentally since there are no biomarkers known for early progenitor cells, and only after about 6 days of induction, iPS cells can be experimentally determined via fluorescent probes. What is more, the percentage of the progenitor cells during the early induction period is below 5%, too low to capture experimentally in early stage. In this work, we proposed an approach for the identification of iPS progenitor cells, the iPS forming cells, based on machine learning and microscopic image analysis. The aim is to help biologists to enrich iPS progenitor cells during the early stage of induction, which allows experimentalists to select iPS progenitor cells with much higher probability, and furthermore to study the biomarkers which trigger the reprogramming process.

scholarly journals Bone Morphogenetic Protein 4 (BMP4) Enhances the Differentiation of Human Induced Pluripotent Stem Cells into Limbal Progenitor Cells

2021 ◽  
Vol 43 (3) ◽  
pp. 2124-2134
Author(s):  
Hyun Soo Lee ◽  
Jeewon Mok ◽  
Choun-Ki Joo
Keyword(s):  
Progenitor Cells ◽  
Dermal Fibroblast ◽  
Ips Cells ◽  
Human Dermal Fibroblast ◽  
Corneal Epithelial ◽  
Specific Medium ◽  
Morphogenetic Protein ◽  
Human Ips Cells ◽  
Limbal Stem Cell ◽  
Induced Pluripotent

Corneal epithelium maintains visual acuity and is regenerated by the proliferation and differentiation of limbal progenitor cells. Transplantation of human limbal progenitor cells could restore the integrity and functionality of the corneal surface in patients with limbal stem cell deficiency. However, multiple protocols are employed to differentiate human induced pluripotent stem (iPS) cells into corneal epithelium or limbal progenitor cells. The aim of this study was to optimize a protocol that uses bone morphogenetic protein 4 (BMP4) and limbal cell-specific medium. Human dermal fibroblast-derived iPS cells were differentiated into limbal progenitor cells using limbal cell-specific (PI) medium and varying doses (1, 10, and 50 ng/mL) and durations (1, 3, and 10 days) of BMP4 treatment. Differentiated human iPS cells were analyzed by real-time polymerase chain reaction (RT-PCR), Western blotting, and immunocytochemical studies at 2 or 4 weeks after BMP4 treatment. Culturing human dermal fibroblast-derived iPS cells in limbal cell-specific medium and BMP4 gave rise to limbal progenitor and corneal epithelial-like cells. The optimal protocol of 10 ng/mL and three days of BMP4 treatment elicited significantly higher limbal progenitor marker (ABCG2, ∆Np63α) expression and less corneal epithelial cell marker (CK3, CK12) expression than the other combinations of BMP4 dose and duration. In conclusion, this study identified a successful reprogramming strategy to induce limbal progenitor cells from human iPS cells using limbal cell-specific medium and BMP4. Additionally, our experiments indicate that the optimal BMP4 dose and duration favor limbal progenitor cell differentiation over corneal epithelial cells and maintain the phenotype of limbal stem cells. These findings contribute to the development of therapies for limbal stem cell deficiency disorders.

scholarly journals Reprogramming of Mouse Calvarial Osteoblasts into Induced Pluripotent Stem Cells

2018 ◽  
Vol 2018 ◽  
pp. 1-11
Author(s):  
Yinxiang Wang ◽  
Jessica Aijia Liu ◽  
Keith K. H. Leung ◽  
Mai Har Sham ◽  
Danny Chan ◽  
...  
Keyword(s):  
Stem Cells ◽  
Early Stage ◽  
Expression Profiles ◽  
Embryonic Stem ◽  
Gene Expression Profiles ◽  
Ips Cells ◽  
Egfp Expression ◽  
Retroviral Transduction ◽  
Intramembranous Bone ◽  
Induced Pluripotent

Previous studies have demonstrated the ability of reprogramming endochondral bone into induced pluripotent stem (iPS) cells, but whether similar phenomenon occurs in intramembranous bone remains to be determined. Here we adopted fluorescence-activated cell sorting-based strategy to isolate homogenous population of intramembranous calvarial osteoblasts from newborn transgenic mice carrying both Osx1-GFP::Cre and Oct4-EGFP transgenes. Following retroviral transduction of Yamanaka factors (Oct4, Sox2, Klf4, and c-Myc), enriched population of osteoblasts underwent silencing of Osx1-GFP::Cre expression at early stage of reprogramming followed by late activation of Oct4-EGFP expression in the resulting iPS cells. These osteoblast-derived iPS cells exhibited gene expression profiles akin to embryonic stem cells and were pluripotent as demonstrated by their ability to form teratomas comprising tissues from all germ layers and also contribute to tail tissue in chimera embryos. These data demonstrate that iPS cells can be generated from intramembranous osteoblasts.

scholarly journals Novel Technique for Retinal Nerve Cell Regeneration with Electrophysiological Functions Using Human Iris-Derived iPS Cells

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 743
Author(s):  
Naoki Yamamoto ◽  
Noriko Hiramatsu ◽  
Mahito Ohkuma ◽  
Natsuko Hatsusaka ◽  
Shun Takeda ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Nerve Cell ◽  
Ips Cells ◽  
Ips Cell ◽  
Cell Markers ◽  
Retinal Tissue ◽  
Human Iris ◽  
Stem And Progenitor Cells ◽  
Neural Stem Progenitor Cells ◽  
Induced Pluripotent

Regenerative medicine in ophthalmology that uses induced pluripotent stem cells (iPS) cells has been described, but those studies used iPS cells derived from fibroblasts. Here, we generated iPS cells derived from iris cells that develop from the same inner layer of the optic cup as the retina, to regenerate retinal nerves. We first identified cells positive for p75NTR, a marker of retinal tissue stem and progenitor cells, in human iris tissue. We then reprogrammed the cultured p75NTR-positive iris tissue stem/progenitor (H-iris stem/progenitor) cells to create iris-derived iPS (H-iris iPS) cells for the first time. These cells were positive for iPS cell markers and showed pluripotency to differentiate into three germ layers. When H-iris iPS cells were pre-differentiated into neural stem/progenitor cells, not all cells became positive for neural stem/progenitor and nerve cell markers. When these cells were pre-differentiated into neural stem/progenitor cells, sorted with p75NTR, and used as a medium for differentiating into retinal nerve cells, the cells differentiated into Recoverin-positive cells with electrophysiological functions. In a different medium, H-iris iPS cells differentiated into retinal ganglion cell marker-positive cells with electrophysiological functions. This is the first demonstration of H-iris iPS cells differentiating into retinal neurons that function physiologically as neurons.

Enhanced Generation of Human Hematopoietic Stem/Progenitor Cells From ES and Patient Derived IPS Cells Using a Novel Compound Screen

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1294-1294
Author(s):  
Roger Emanuel Rönn ◽  
Roksana Moraghebi ◽  
Carolina Guibentif ◽  
Niels-Bjarne Woods
Keyword(s):  
Progenitor Cells ◽  
Progenitor Cell ◽  
Molecular Mechanisms ◽  
Conflicts Of Interest ◽  
Hematopoietic Cells ◽  
Ips Cells ◽  
Cell Generation ◽  
P Value ◽  
Hematopoietic Stem ◽  
Compound A

Abstract Abstract 1294 The ability to generate hematopoietic stem and progenitor cells from patient derived induced pluripotent stem (iPS) cells, would enable the generation of an unlimited supply of HLA matched transplantable cells for the treatment of both hematological disorders and malignancies. The goal of this project is to identify novel pathways involved in hematopoietic stem and progenitor cell generation and expansion from human ES and iPS cells. By using a small molecule compound library with our optimized iPS-2-blood lineage differentiation protocol, we have identified two novel chemical compounds that specifically enhance the generation of phenotypic adult hematopoietic stem cells. Compound A and compound B both enable increases of CD45/43+CD34+CD38-CD90+CD45RA- cells by 183+/−53%, n=5 and 275%, n=1, respectively. This is in comparison to DMSO carrier control wells, where the percentage of blood cells (CD45/43+) produced per total cells for these experiments was 73+/−2.9%, n=5. The increase in hematopoietic cell output using compound A was highly significant for the adult phenotypical hematopoietic stem cell fraction with a P-value of 0.03, n=5 (see Figure). Hematopoietic progenitor, CD45/43+ CD34+, counts were also slightly increased for compound A and B at 129+/−32%, n=5 and at 211%, n=1, respectively. Interestingly, no statistically significant increase in the number of total blood CD45/43+ cells was detected at the time of harvest, with either compound; at 108% +/− 8.4%, n=5, for compound A, and 164%, n=1, for compound B. In addition to the improvements, as measured by FACS, compounds A and B both increased the numbers of clonogenic progenitors as measured by CFU-assay, allowing for a 241+/−67%, n=4, and 443%, n=1, increase in total hematopoietic colony counts, respectively. These results identify 2 novel compounds with the ability to expand the more primitive fractions of hematopoietic cells with preferential expansion of the most primitive fraction of hematopoietic cells derived from human ES and iPS lines. We are currently performing transplantation experiments with cells generated using these compounds to assess their repopulating potential. Further studies are being performed to investigate the molecular mechanisms of these compounds for hematopoietic stem and progenitor cell generation from ES and iPS cells. Disclosures: No relevant conflicts of interest to declare.

β-Globin-Expressing Definitive Erythroid Progenitor Cells Generated from Embryonic and Induced Pluripotent Stem Cell-Derived Sacs

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 2674-2674
Author(s):  
Naoya Uchida ◽  
Atsushi Fujita ◽  
Thomas Winkler ◽  
John F. Tisdale
Keyword(s):  
Progenitor Cells ◽  
Erythroid Differentiation ◽  
Ips Cells ◽  
Cell Fraction ◽  
Erythroid Cells ◽  
Erythroid Progenitor ◽  
Ips Cell ◽  
Erythroid Progenitor Cells ◽  
Spherical Cells ◽  
Induced Pluripotent

Abstract Human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells represent a potential alternative source for red blood cell (RBC) transfusion. When ES cell-derived erythroid cells are generated using embryoid bodies, these cells predominantly express embryonic type ε-globin, with lesser fetal type γ-globin and small amounts of adult type β-globin; however, no β-globin expression is detected in iPS cell-derived erythroid cells. Recently, the ES cell-derived sac (ES sac) was reported to express hemangioblast markers and could generate functional platelets (Takayama, Blood. 2008). We previously demonstrated that erythroid cells were also efficiently generated via the ES sac (2013 ASH). We extend this work to evaluate globin expression in ES sac-derived erythroid cells. We generated ES sacs from human H1 ES or iPS cells using VEGF for 15 days, as previously described. The spherical cells within ES sacs were harvested and cultured on OP9 feeder cells for 2 days, and the suspension cells were differentiated into erythroid cells using human erythroid massive amplification culture for 13 days (Blood cells Mol Dis. 2002). The globin types expressed in erythroid cells were evaluated by RT-qPCR and hemoglobin electrophoresis. When hematopoietic cell-stimulating cytokines (SCF, FLT3L, TPO, IL3, EPO, and BMP4) were added in ES sac cultures on day 9-15, we observed 1.4-fold greater amounts of GPA+ erythroid cells (p<0.05) and 1.3-fold lower ε-globin expression in ES sac-derived erythroid cells (p<0.05), suggesting that cytokine stimulation might induce more hematopoietic/stem progenitor cells (HSPC) which can be differentiated to γ- or β-globin-expressing erythroid cells. Thus, we hypothesized that the ES sac contains both primitive and definitive erythroid progenitor cells capable of ε-globin-expression or γ- or β-globin-expression upon differentiation; respectively, and that these progenitors are selectable based upon surface markers of erythroid progenitor cells or HSPCs. To investigate whether primitive erythropoiesis is switched to definitive erythropoiesis during ES sac maturation, we evaluated spherical cells within the ES sac on day 9, 12, 15, and 18 after ES sac culture. A high percentage of GPA+ erythroid cells (29.2±3.7%) were observed on as early as day9. At that time point, almost no CD34+CD45+ HSPCs were present; however, the number increased upon further ES sac maturation until day 15 (6.8±1.6%). Cells further differentiated in erythroid culture had lower ε-globin expression and higher β-globin expression (up to 13.8±1.5%) when harvested from the ES sac at later time points. These data suggest that more matured ES sacs favor less primitive erythropoiesis and more definitive erythropoiesis. On day 15, the ES sacs contained a high percentage of GPA+(CD34-) erythroid cells (68.7±4.0%) and relatively lower amounts of CD34+(GPA-) HSPCs (16.7±2.1%). Therefore, we separated GPA+ and GPA- spherical cells from ES sac by magnetic selection before further erythroid differentiation, which resulted in higher ε-globin expression (43.0±16.6% vs 4.4±1.2%, p<0.01) and lower β-globin expression (7.6±5.3x10e-7% vs 19.8±2.7%, p<0.01) from the GPA+ cell fraction. In contrast, after erythroid differentiation from CD34+ or CD34- sorted spherical cells, lower ε-globin expression (3.7±0.3% vs 17.1±0.9%, p<0.01) and higher β-globin expression (17.4±0.7 % vs 0.9±0.4 %, p<0.01) were observed from the CD34+ cell fraction. These data suggest that the ES sac contains both primitive erythroid progenitor cells in the CD34- or GPA+ cell fraction and definitive erythroid progenitor cells in the CD34+ or GPA- cell fraction. In addition, iPS sac-derived erythroid cells were generated from 2 clones of fibroblast-derived iPS cells, which demonstrated 9.0±2.6% (clone #1) and 7.3±3.7% (clone #2) of β-globin expression. These data demonstrate that similar to ES sac-derived erythroid cells, iPS cell-derived erythroid cells can produce β-globin when differentiated from iPS sacs. In conclusion, we demonstrate that human ES and iPS cells can generate both primitive and definitive erythroid progenitor cells when differentiated in ES/iPS sac. CD34 or GPA discriminates between primitive and definitive erythroid progenitor cells in ES sac. The presented differentiation and selection strategy represent an important step to develop in vitro RBC production system from pluripotent stem cells. Disclosures No relevant conflicts of interest to declare.

Establishment of retinal progenitor cell clones by transfection with Pax6 gene of mouse induced pluripotent stem (iPS) cells

2012 ◽  
Vol 509 (2) ◽  
pp. 116-120 ◽  
Author(s):  
Noboru Suzuki ◽  
Jun Shimizu ◽  
Kenji Takai ◽  
Nagisa Arimitsu ◽  
Yuji Ueda ◽  
...  
Keyword(s):  
Progenitor Cell ◽  
Ips Cells ◽  
Pax6 Gene ◽  
Retinal Progenitor Cell ◽  
Retinal Progenitor ◽  
Cell Clones ◽  
Induced Pluripotent

scholarly journals Induced Pluripotent Stem (IPS) Cells to Assess the Cardioprotective and Proangiogenic Activities of Exosomes Secreted by Human Cardiac Progenitor Cells

2016 ◽  
Vol 110 (3) ◽  
pp. 595a-596a ◽  
Author(s):  
Claudia Altomare ◽  
Elisabetta Cervio ◽  
Ciullo Alessandra ◽  
Giuseppina Milano ◽  
Tiziano Torre ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Ips Cells ◽  
Cardiac Progenitor Cells ◽  
Induced Pluripotent

scholarly journals Spatial Transcriptomics for the Analysis of Human Pituitary Development

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. A554-A554
Author(s):  
Ryusaku Matsumoto ◽  
Mio Kabata ◽  
Hidetaka Suga ◽  
Takuya Yamamoto
Keyword(s):  
Cell Differentiation ◽  
Progenitor Cells ◽  
Progenitor Cell ◽  
Cell Populations ◽  
Pituitary Cells ◽  
Human Pituitary ◽  
Pituitary Development ◽  
Spatially Resolved ◽  
Oral Ectoderm ◽  
Induced Pluripotent

Abstract The pituitary develops from oral ectoderm in contact with the adjacent hypothalamus. However, the precise mechanisms underlying pituitary development in concert with plural tissues are not fully understood, especially in human. A protocol to induce pituitary cells from human induced pluripotent stem cells (hiPSCs) has been established and applied to study pituitary development and disorders. In the method, oral ectoderm and hypothalamus are induced in one organoid, which enables recapitulation of the interactions between these tissues during embryonic development. It leads to self-organization of pituitary cells. Recently, spatial transcriptome technology has been developed and is suitable for the analysis of tissue interactions. Here, we utilized spatial transcriptomics to analyze pituitary organoids, especially focusing on the mechanisms regulating pituitary progenitor cell differentiation. Spatial transcriptomics revealed that the organoids consisted of several cell populations including hypothalamus, oral ectoderm, neural retina, and cortex neuron cells. Pituitary progenitor cells, characterized by the upregulation of LHX3, were included as part of the oral ectoderm population. Further analysis of the population identified human pituitary progenitor-specific genes including many causal genes for congenital hypopituitarism (CPH). Finally, using spatially resolved gene expression data, we examined the hypothalamic population that was in contact with pituitary progenitor cells and identified hypothalamic factors that might regulate progenitor cell differentiation in a paracrine manner. The genes upregulated in the pituitary progenitor and neighboring hypothalamus cell populations are potential causal gene candidates for CPH. In conclusion, spatial transcriptomics provides a novel platform to analyze tissue interaction networks during human pituitary development.

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