scholarly journals Analysis of Dual Class I Histone Deacetylase and Lysine Demethylase Inhibitor Domatinostat (4SC-202) on Growth and Cellular and Genomic Landscape of Atypical Teratoid/Rhabdoid

Cancers ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 756 ◽  
Author(s):  
Mariah M. Hoffman ◽  
Jessica S. Zylla ◽  
Somshuvra Bhattacharya ◽  
Kristin Calar ◽  
Timothy W. Hartman ◽  
...  
Keyword(s):  
Stem Cell ◽  
Single Cell ◽  
Class I ◽  
Specific Cell ◽  
Normal Brain ◽  
Stem Cell Markers ◽  
Sequencing Data ◽  
Aberrant Expression ◽  
Atypical Teratoid ◽  
Lysine Demethylase

Central nervous system atypical teratoid/rhabdoid tumors (ATRTs) are rare and aggressive tumors with a very poor prognosis. Current treatments for ATRT include resection of the tumor, followed by systemic chemotherapy and radiation therapy, which have toxic side effects for young children. Gene expression analyses of human ATRTs and normal brain samples indicate that ATRTs have aberrant expression of epigenetic markers including class I histone deacetylases (HDAC’s) and lysine demethylase (LSD1). Here, we investigate the effect of a small molecule epigenetic modulator known as Domatinostat (4SC-202), which inhibits both class I HDAC’s and Lysine Demethylase (LSD1), on ATRT cell survival and single cell heterogeneity. Our findings suggest that 4SC-202 is both cytotoxic and cytostatic to ATRT in 2D and 3D scaffold cell culture models and may target cancer stem cells. Single-cell RNA sequencing data from ATRT-06 spheroids treated with 4SC-202 have a reduced population of cells overexpressing stem cell-related genes, including SOX2. Flow cytometry and immunofluorescence on 3D ATRT-06 scaffold models support these results suggesting that 4SC-202 reduces expression of cancer stem cell markers SOX2, CD133, and FOXM1. Drug-induced changes to the systems biology landscape are also explored by multi-omics enrichment analyses. In summary, our data indicate that 4SC-202 has both cytotoxic and cytostatic effects on ATRT, targets specific cell sub-populations, including those with cancer stem-like features, and is an important potential cancer therapeutic to be investigated in vivo.

EXTH-24. TUMOR PHARMACOKINETICS, PHARMACODYNAMICS AND RADIATION SENSITIZATION IN PATIENT-DERIVED XENOGRAFT MODELS OF GLIOBLASTOMA TREATED WITH THE SECOND-GENERATION HDAC INHIBITOR, QUISINOSTAT

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi168-vi168
Author(s):  
Costanza Lo Cascio ◽  
Tigran Margaryan ◽  
Ernesto Luna Melendez ◽  
James McNamara ◽  
William Knight ◽  
...  
Keyword(s):  
Stem Cell ◽  
Hdac Inhibitor ◽  
Equilibrium Dialysis ◽  
Drug Uptake ◽  
Class I ◽  
Normal Brain ◽  
Treatment Schedule ◽  
Stem Cell Markers ◽  
Post Dose ◽  
Radiation Sensitization

Abstract BACKGROUND Class I Histone deacetylases (HDACs) are highly expressed in glioblastoma (GBM) and are considered promising therapeutic targets for cancer treatment. Quisinostat is a class I HDAC inhibitor with high specificity for HDAC1 and 2. In this study, we evaluated the pharmacokinetics (PK), pharmacodynamics (PD), and radiation sensitization properties of quisinostat in orthotopic and flank human glioma models of GBM. METHODS In vitro drug-uptake and PK-PD correlation experiments were conducted in patient-derived glioma stem cell (GSC) lines. Pilot PK studies were performed in mice to optimize the dosing regimen and administration route (subcutaneous (s.q.), intraperitoneal (i.p.) and oral gavage). Athymic mice with intracranial or flank tumors were treated with the most optimized treatment schedule to evaluate plasma PK profile and brain/tumor distribution of quisinostat. The drug levels in plasma, normal brain, and tumor-tissue were measured by liquid chromatography tandem mass spectrometry (LC-MS/MS). Unbound fractions were determined by equilibrium dialysis. Western blot analysis and immunocytochemistry were performed to assess changes in acetylated histone, Ki67 (proliferation) and cleaved caspase 3 (cell death) levels. Tumor-bearing mice were randomized to four cohorts – vehicle, radiotherapy, quisinostat monotherapy, and quisinostat plus radiotherapy. RESULTS Quisinostat exhibited potent growth inhibition in multiple GSC lines (IC50 ~60 nM), radiosensitization, increased histone acetylation, and decreased expression of key stem cell markers. Significant toxicity was observed at 10 mg/kg s.q. dosing while the same dosing via i.p. route was tolerated relatively well. The unbound concentration of quisinostat was 19 nmol/L, 0.03 nmol/kg and 0.03 nmol/kg in plasma, tumor, and brain tissue, respectively, at 2 hours post-dose. Pharmacodynamic changes were observed in flank but not in intracranial tumors. CONCLUSION Our data indicate low free quisinostat levels in the brain primarily due to drug instability.

scholarly journals Single-cell transcriptome provides novel insights into antler stem cells, a cell type capable of mammalian organ regeneration

2018 ◽  
Author(s):  
Hengxing Ba ◽  
Datao Wang ◽  
Weiyao Wu ◽  
Hongmei Sun ◽  
Chunyi Li
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Single Cell ◽  
Large Cell ◽  
Stem Cell Markers ◽  
Single Cell Level ◽  
Cell Type ◽  
Cell Level ◽  
Homogeneous Population ◽  
Organ Regeneration

AbstractAntler regeneration, a stem cell-based epimorphic process, has potential as a valuable model for regenerative medicine. A pool of antler stem cells (ASCs) for antler development is located in the antlerogenic periosteum (AP). However, whether this ASC pool is homogenous or heterogeneous has not been fully evaluated. In this study, we produced a comprehensive transcriptome dataset at the single-cell level for the ASCs based on the 10x Genomics platform (scRNA-seq). A total of 4,565 ASCs were sequenced and classified into a large cell cluster, indicating that the ASCs resident in the AP are likely to be a homogeneous population. The scRNA-seq data revealed that tumor-related genes were highly expressed in these homogeneous ASCs: i.e. TIMP1, TMSB10, LGALS1, FTH1, VIM, LOC110126017 and S100A4. Results of screening for stem cell markers suggest that the ASCs may be considered as a special type of stem cell between embryonic (CD9) and adult (CD29, CD90, NPM1 and VIM) stem cells. Our results provide the first comprehensive transcriptome analysis at the single-cell level for the ASCs, and identified only one major cell type resident in the AP and some key stem cell genes, which may hold the key to why antlers, the unique mammalian organ, can fully regenerate once lost.

scholarly journals scRNA-seq in medulloblastoma shows cellular heterogeneity and lineage expansion support resistance to SHH inhibitor therapy

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jennifer Ocasio ◽  
Benjamin Babcock ◽  
Daniel Malawsky ◽  
Seth J. Weir ◽  
Lipin Loo ◽  
...  
Keyword(s):  
Stem Cell ◽  
Cell Types ◽  
Lineage Tracing ◽  
Inhibitor Therapy ◽  
Cellular Heterogeneity ◽  
Specific Cell ◽  
Stem Cell Markers ◽  
Shh Pathway ◽  
Oncogenic Pathways ◽  
Support Resistance

AbstractTargeting oncogenic pathways holds promise for brain tumor treatment, but inhibition of Sonic Hedgehog (SHH) signaling has failed in SHH-driven medulloblastoma. Cellular diversity within tumors and reduced lineage commitment can undermine targeted therapy by increasing the probability of treatment-resistant populations. Using single-cell RNA-seq and lineage tracing, we analyzed cellular diversity in medulloblastomas in transgenic, medulloblastoma-prone mice, and responses to the SHH-pathway inhibitor vismodegib. In untreated tumors, we find expected stromal cells and tumor-derived cells showing either a spectrum of neural progenitor-differentiation states or glial and stem cell markers. Vismodegib reduces the proliferative population and increases differentiation. However, specific cell types in vismodegib-treated tumors remain proliferative, showing either persistent SHH-pathway activation or stem cell characteristics. Our data show that even in tumors with a single pathway-activating mutation, diverse mechanisms drive tumor growth. This diversity confers early resistance to targeted inhibitor therapy, demonstrating the need to target multiple pathways simultaneously.

scholarly journals Optimizing Silanization to Functionalize Stainless Steel Wire: Towards Breast Cancer Stem Cell Isolation

Materials ◽  
2020 ◽  
Vol 13 (17) ◽  
pp. 3693
Author(s):  
Aliya Bekmurzayeva ◽  
Kanat Dukenbayev ◽  
Helena S. Azevedo ◽  
Enrico Marsili ◽  
Daniele Tosi ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Stainless Steel ◽  
Stem Cell ◽  
Cancer Stem Cell ◽  
Breast Cancer Stem Cell ◽  
Target Cells ◽  
Specific Cell ◽  
Stem Cell Markers ◽  
In Vitro Test ◽  
Steel Wires

Chemically modified metal surfaces have been used to recognize and capture specific cell types and biomolecules. In this work, stainless steel wires were functionalized with aptamers against breast cancer stem cell markers. Stainless steel wires were first electropolished and silanized via electrodeposition. Aptamers were then attached to the silanized surface through a cross-linker. The functionalized wires were able to capture the target cells in an in vitro test. During surface modification steps, wires were analyzed by atomic force microscopy, cyclic voltammetry, scanning electron and fluorescence microscopy to determine their surface composition and morphology. Optimized conditions of silanization (applied potential, solution pH, heat treatment temperature) for obtaining an aptamer-functionalized wire were determined in this work together with the use of several surface characterization techniques suitable for small-sized and circular wires. These modified wires have potential applications for the in vivo capture of target cells in blood flow, since their small size allows their insertion as standard guidewires in biomedical devices.

Aberrant expression of cancer stem cell markers (CD44, CD90, and CD133) contributes to disease progression and reduced survival in hepatoblastoma patients: 4-year survival data

2015 ◽  
Vol 165 (3) ◽  
pp. 396-406 ◽  
Author(s):  
Abeer A. Bahnassy ◽  
Mohamed Fawzy ◽  
Mohamed El-Wakil ◽  
Abdel-Rahman N. Zekri ◽  
Ahmed Abdel-Sayed ◽  
...  
Keyword(s):  
Stem Cell ◽  
Cancer Stem Cell ◽  
Disease Progression ◽  
Survival Data ◽  
Stem Cell Markers ◽  
Aberrant Expression ◽  
Cell Markers ◽  
Cancer Stem Cell Markers

scholarly journals Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets

2019 ◽  
Author(s):  
Haruka Ozaki ◽  
Tetsutaro Hayashi ◽  
Mana Umeda ◽  
Itoshi Nikaido
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cellular Heterogeneity ◽  
Specific Cell ◽  
Read Coverage ◽  
Cell Heterogeneity ◽  
Sequencing Data ◽  
Rna Transcription ◽  
Link Type ◽  
Single Cell Rna Sequencing

AbstractBackgroundRead coverage of RNA sequencing data reflects gene expression and RNA processing events. Single-cell RNA sequencing (scRNA-seq) methods, particularly “full-length” ones, provide read coverage of many individual cells and have the potential to reveal cellular heterogeneity in RNA transcription and processing. However, visualization tools suited to highlighting cell-to-cell heterogeneity in read coverage are still lacking.ResultsHere, we have developed Millefy, a tool for visualizing read coverage of scRNA-seq data in genomic contexts. Millefy is designed to show read coverage of all individual cells at once in genomic contexts and to highlight cell-to-cell heterogeneity in read coverage. By visualizing read coverage of all cells as a heat map and dynamically reordering cells based on diffusion maps, Millefy facilitates discovery of “local” region-specific, cell-to-cell heterogeneity in read coverage, including variability of transcribed regions.ConclusionsMillefy simplifies the examination of cellular heterogeneity in RNA transcription and processing events using scRNA-seq data. Millefy is available as an R package (https://github.com/yuifu/millefy) and a Docker image to help use Millefy on the Jupyter notebook (https://hub.docker.com/r/yuifu/datascience-notebook-millefy).

scholarly journals Delayed Cutaneous Wound Healing and Aberrant Expression of Hair Follicle Stem Cell Markers in Mice Selectively Lacking Ctip2 in Epidermis

PLoS ONE ◽  
2012 ◽  
Vol 7 (2) ◽  
pp. e29999 ◽  
Author(s):  
Xiaobo Liang ◽  
Shreya Bhattacharya ◽  
Gaurav Bajaj ◽  
Gunjan Guha ◽  
Zhixing Wang ◽  
...  
Keyword(s):  
Wound Healing ◽  
Stem Cell ◽  
Hair Follicle ◽  
Stem Cell Markers ◽  
Cutaneous Wound Healing ◽  
Aberrant Expression ◽  
Cutaneous Wound ◽  
Cell Markers ◽  
Hair Follicle Stem Cell

scholarly journals Endogenous Retroviral Elements in Human Development and Central Nervous System Embryonal Tumors

2021 ◽  
Vol 11 (12) ◽  
pp. 1332
Author(s):  
Tara T. Doucet-O’Hare ◽  
Jared S. Rosenblum ◽  
Ashish H. Shah ◽  
Mark R. Gilbert ◽  
Zhengping Zhuang
Keyword(s):  
Stem Cell ◽  
Human Development ◽  
Chromatin Remodeling ◽  
Tumor Development ◽  
Endogenous Retroviruses ◽  
Stem Cell Markers ◽  
Embryonal Tumors ◽  
Herv Element ◽  
Atypical Teratoid ◽  
And Migration

Human endogenous retroviruses (HERVs), which are critical to normal embryologic development and downregulated during normal maturation, have been implicated in a variety of cancers. Abnormal persistent production of HERVs has been suggested to play a role in oncogenesis and to confer stem cell properties to cells. We recently demonstrated that the most recently incorporated HERV element (HERV-K HML-2) has been associated with the pathogenesis of the embryonal atypical teratoid rhabdoid tumor (AT/RT), shifting our understanding of embryonal tumor development. HML-2 expression is vital for proper human development and its expression is suppressed via methylation or chromatin remodeling as cells differentiate. We previously found that dysfunctional chromatin remodeling due to loss of SMARCB1 expression induces HML-2 envelope (env) expression, impairing cellular differentiation and migration, and facilitating tumor growth in AT/RT. Epigenetic dysregulation in other embryonal tumors with concomitant expression of stem-cell markers may facilitate HML-2 expression. Future studies could utilize HML-2 as potential diagnostic criteria, use its expression as a treatment biomarker, and investigate the efficacy of therapies targeting cells with high HML-2 expression.

Allelic expression analysis of Imprinted and X-linked genes from bulk and single-cell transcriptomes

2020 ◽  
Author(s):  
Paolo Martini ◽  
Gabriele Sales ◽  
Valentina Perrera ◽  
Linda Diamante ◽  
Chiara Romualdi ◽  
...  
Keyword(s):  
Single Cell ◽  
Genomic Imprinting ◽  
Early Embryo ◽  
Ease Of Use ◽  
Allelic Expression ◽  
Sequencing Data ◽  
Aberrant Expression ◽  
New Genes ◽  
Wide Range ◽  
Induced Pluripotent

AbstractGenomic imprinting and X chromosome inactivation (XCI) are two prototypical epigenetic mechanisms whereby a set of genes is expressed monoallelically in order to fine tune their expression levels. Defects in genomic imprinting have been observed in several neurodevelopmental disorders, in a wide range of tumors and in induced pluripotent stem cells (iPSCs). Single Nucleotide Variations (SNVs) are readily detectable by RNA-sequencing allowing determination of whether imprinted or X-linked genes are aberrantly expressed from both alleles, although standardised analysis methods are still missing. We have developed a tool, named BrewerIX, that provides comprehensive information about allelic expression of a large, manually-curated set of imprinted and X-linked genes. BrewerIX does not require programming skills, runs on a standard personal computer, and can analyse both bulk and single-cell transcriptomes of human and mouse cells directly from raw sequencing data. BrewerIX confirmed and extended previous observations regarding the aberrant expression of imprinted genes in pluripotent cells, in the early embryo and in breast cancer cells and identified new genes escaping XCI in human somatic cells. We believe BrewerIX will be useful for the study of genomic imprinting and XCI during development and reprogramming, and for detecting aberrations in cancer and iPSCs. Due to its ease of use to non-computational biologists, its implementation could become standard practice during sample assessment, thus raising robustness and reproducibility of future studies.

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