scholarly journals 4353 The Role of BCL2 Mediated Calcium Signaling on Leukemia Stem Cell Metabolism

2020 ◽  
Vol 4 (s1) ◽  
pp. 19-19
Author(s):  
Anagha Inguva ◽  
Shanshan Pei ◽  
Maria Amaya ◽  
Brett Stevens ◽  
Courtney Jones ◽  
...  
Keyword(s):  
Stem Cells ◽  
Calcium Signaling ◽  
Intracellular Calcium ◽  
Metal Ion ◽  
Molecular Mechanisms ◽  
Calcium Influx ◽  
Survival Rates ◽  
Rna Seq ◽  
Expression Of Genes ◽  
Er Membrane

OBJECTIVES/GOALS: The objective of this study is to define the molecular mechanisms that control survival of malignant stem cells in acute myeloid leukemia (AML). Leukemia stem cells (LSCs) are not effectively eradicated by standard treatment and lead to resistance and relapse, which contribute to poor survival rates. METHODS/STUDY POPULATION: The recently FDA approved venetoclax, a BCL2 inhibitor, with azacitidine, a hypomethylating agent leads to a 70% response rate in AML patients. Analysis of patients treated with this regimen showed direct targeting of LSCs. BCL2 has a non-canonical function in regulation of intracellular calcium. To determine how BCL2 mediated calcium signaling plays a role in LSC biology, we used LSCs isolated from venetoclax/azacitidine (ven/aza) sensitive and resistant patient samples to measure expression of calcium channels via RNA seq. BIO-ID, siRNA, flow cytometry, seahorse assays, calcium measurements and colony assays were used to determine the effects of calcium channel perturbation on LSC biology. RESULTS/ANTICIPATED RESULTS: BCL2 inhibition leads to decreased OXPHOS activity in primary AML specimens. BIO-ID studies revealed cation/metal ion transporters, ER membrane proteins and ER membrane organization as top enriched pathways interacting with BCL2. RNA-seq data showed increased expression of genes involved in calcium influx into the ER in ven/aza sensitive LSCs and increased expression of genes involved in calcium efflux from the ER in ven/aza resistant samples. Ven/Aza resistant LSCs have increased mitochondrial calcium content, consistent with their increased OXPHOS activity as calcium is required for OXPHOS. Perturbation of these channels leads to decreased OXPHOS activity and decreased viability in LSCs. DISCUSSION/SIGNIFICANCE OF IMPACT: We postulate that a deeper understanding of the mechanisms behind ven/aza targeting of LSCs will lead to the development of novel therapies for patients who do not respond to ven/aza. Our data show targeting intracellular calcium signaling could be a viable therapeutic strategy for AML patients.

scholarly journals Differential Expression of Genes Related to the Formation of Giant Leaves in Triploid Poplar

Forests ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 920 ◽  
Author(s):  
Kang Du ◽  
Qiang Han ◽  
Ying Zhang ◽  
Xiangyang Kang
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Leaf Growth ◽  
Growth Hormones ◽  
Endogenous Hormones ◽  
Rna Seq ◽  
Hormone Metabolism ◽  
Expression Of Genes ◽  
Genes Expression ◽  
Differential Expression Of Genes

Plant polyploids tend to have large leaves, but their formation mechanism has not yet been well explained. Therefore, daily transcriptomic differences between triploids and diploids from a synthetic Populus sect. Tacamahaca three times a day (i.e., 04:00, 09:00, and 21:00) were investigated using high-throughput RNA-seq analysis. In this study, we identified several transcription factors associated with giant leaves. The combined effects included the high expression of several transcription factors (WRKY, MYB, etc.) and hormone-related genes (e.g., activates auxin, cytokine, and brassinosteroid synthesis-related genes) that accelerate the synthesis and accumulation of endogenous hormones. High levels of growth hormones were maintained by reducing the genes’ expression of hormone metabolism and degradation. The coordination of hormones accumulated sufficient materials and energy for leaf growth and development. Thereby, cell division and growth were accelerated which enhanced the photosynthesis of leaves, and the increased accumulation of photosynthetic products led to giant triploid leaves. This study lays the foundation for revealing the molecular mechanisms in the formation of giant leaves in polyploids.

scholarly journals Transcriptome Analysis of Banana (Musa acuminate L.) in Response to Low-Potassium Stress

Agronomy ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 169
Author(s):  
Min Xu ◽  
Can-Bin Zeng ◽  
Rui He ◽  
Zhen Yan ◽  
Zhao Qi ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Dry Weight ◽  
Phenotypic Traits ◽  
Rna Seq ◽  
Expression Of Genes ◽  
K Deficiency ◽  
Banana Leaves ◽  
Gene Functional Classification ◽  
Low K

Potassium (K+) is an abundant and important macronutrient for plants. It plays crucial roles in many growth and developmental processes, and growth is inhibited under low −K+ conditions. The molecular mechanisms operating under K+ starvation have been little reported in banana, which is a non-model plant. We conducted a transcriptome analysis of banana (Musa acuminata L. AAA group, cv. Cavendish) in response to low −K+ stress. The phenotypic traits and transcriptomic profiles of banana leaves and roots were compared between low −K+ (LK) and normal −K+ (NK) groups. The phenotypic parameters for the LK group, including fresh and dry weight, were lower than those for the NK group, which suggested that low −K+ stress may inhibit some important metabolic and biosynthetic processes. K+ content and biomass were both decreased in the LK group compared to the NK group. Following ribonucleic acid sequencing (RNA-Seq), a total of 26,796 expressed genes were detected in normal −K+ leaves (NKL), 27,014 were detected in low −K+ leaves (LKL), 29,158 were detected in normal −K+ roots (NKR), and 28,748 were detected in low −K+ roots (LKR). There were 797 up-regulated differentially expressed genes (DEGs) and 386 down-regulated DEGs in NKL versus LKL, while there were 1917 up-regulated DEGs and 2830 down-regulated DEGs in NKR versus LKR. This suggested that the roots were more sensitive to low −K+ stress than the leaves. DEGs related to K+ transport and uptake were analyzed in detail. Gene functional classification showed that the expression of genes regarding ABC transporters, protein kinases, transcription factors, and ion transporters were also detected, and may play important roles during K+ deficiency.

scholarly journals Age effects aggressive behavior: RNA-seq analysis in cattle with implications for studying neoteny under domestication

2020 ◽  
Author(s):  
Paulina G. Eusebi ◽  
Natalia Sevane ◽  
Thomas O’Rourke ◽  
Manuel Pizarro ◽  
Cedric Boeckx ◽  
...  
Keyword(s):  
Prefrontal Cortex ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
Aggressive Behaviors ◽  
Intentional Actions ◽  
Expression Of Genes ◽  
Differential Gene ◽  
The Impact ◽  
The Brain ◽  
Novel Model

AbstractAggressiveness is one of the most basic behaviors, characterized by targeted intentional actions oriented to cause harm. The reactive type of aggression is regulated mostly by the brain’s prefrontal cortex; however, the molecular changes underlying aggressiveness in adults have not been fully characterized. Here we used an RNA-seq approach to investigate differential gene expression in the prefrontal cortex of bovines from the aggressive Lidia breed at different age stages: young three-year old and adult four-year-old bulls. A total of 50 up and 193 down-regulated genes in the adult group were identified. Furthermore, a cross-species comparative analysis retrieved 29 genes in common with previous studies on aggressive behaviors, representing an above-chance overlap with the differentially expressed genes in adult bulls.Particularly, we detected changes in the regulation of networks such as synaptogenesis, involved in maintenance and refinement of synapses, and the glutamate receptor pathway, which acts as excitatory driver in aggressive responses. Our results provide insights into candidate genes and networks involved in the molecular mechanisms leading to the maturation of the brain. The reduced reactive aggression typical of domestication has been proposed to form part of a retention of juvenile traits as adults (neoteny). The significant age-associated differential expression of genes implicated in aggressive behaviors and concomitant increase in Lidia cattle aggression validates this species as a novel model comparator to explore the impact of behavioral neoteny under domestication.

scholarly journals RNA-Seq analysis reveals pluripotency-associated genes and their interaction networks in human embryonic stem cells

2019 ◽  
Author(s):  
Arindam Ghosh ◽  
Anup Som
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Human Embryonic Stem Cells ◽  
Molecular Mechanisms ◽  
Gene List ◽  
Experimental Studies ◽  
Embryonic Stem ◽  
Pathway Enrichment Analysis ◽  
Rna Seq ◽  
Differentiation Markers

Insight into the key genes of pluripotency in human and their interrelationships is necessary for understanding the underlying mechanism of pluripotency and hence their successful application in regenerative medicine. The recent advances in transcriptomics technologies have created new opportunities to decipher the genes involved in pluripotency, genetic network that governs the unique properties of embryonic stem cells and lineage differentiation mechanisms in a deeper scale. There are a large number of experimental studies on human embryonic stem cells (hESCs) being routinely conducted for unfolding the underlying biology of embryogenesis and their clinical prospects. However, the outcome of these studies often lacks consensus due to differences in samples, experimental techniques and/or analysis protocols. A universal stemness gene list is still lacking. In this quest, we compared transcriptomic profiles of pluripotent and non-pluripotent samples from diverse cell lines/types generated through RNA-sequencing (RNA-seq). We used a uniform pipeline for the analysis of raw RNA-seq data in order to reduce the amount of variation. Our analysis revealed a consensus set of 498 pluripotency-associated genes and 432 genes as potential pluripotent cell differentiation markers. Furthermore, we predicted 32 genes as "pluripotency critical genes". Reconstruction and analysis of co-expression networks further highlighted the importance of these genes. Gene ontology (GO) and pathway enrichment analysis, StemChecker and literature survey confirmed the involvement of the genes in the induction and maintenance of pluripotency, though more experimental studies are required for understanding their molecular mechanisms in human.

scholarly journals UTX maintains functional integrity of murine hematopoietic system by globally regulating aging-associated genes

Blood ◽  
2020 ◽  
Author(s):  
Yasuyuki Sera ◽  
Yuichiro Nakata ◽  
Takeshi Ueda ◽  
Norimasa Yamasaki ◽  
Shuhei Koide ◽  
...  
Keyword(s):  
Stem Cells ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Extramedullary Hematopoiesis ◽  
Rna Seq ◽  
Dna Double Strand Breaks ◽  
Hematopoietic Stem ◽  
Hematopoietic System ◽  
Expression Of Genes ◽  
Hematopoietic Disorders

Epigenetic regulation is essential for the maintenance of the hematopoietic system, and its deregulation is implicated in hematopoietic disorders. Here, we show that UTX, a demethylase for lysine 27 on histone H3 (H3K27) and a component of Compass-like and SWI/SNF complexes, plays an essential role in the hematopoietic system by globally regulating aging-associated genes. Utx-deficient (UtxΔ/Δ) mice exhibited myeloid skewing with dysplasia, extramedullary hematopoiesis, impaired hematopoietic reconstituting ability, and increased susceptibility to leukemia, which are the hallmarks of hematopoietic aging. RNA-sequencing (RNA-seq) analysis revealed that Utx deficiency converted the gene expression profiles of young hematopoietic stem-progenitor cells (HSPCs) to those of aged HSPCs. Utx expression in HSCs declines with age and UtxΔ/Δ HSPCs exhibited increased expression of an aging-associated marker, accumulation of reactive oxygen species, and impaired repair of DNA double-strand breaks. Pathway and chromatin immunoprecipitation (ChIP) analyses coupled with RNA-seq data indicated that UTX contributes to hematopoietic homeostasis mainly by maintaining the expression of genes downregulated with aging, via both demethylase-dependent and -independent epigenetic programming. Of note, comparison of pathway changes in UtxΔ/Δ HSPCs, aged muscle stem cells, aged fibroblasts, and aged iPS-induced neuronal cells showed substantial overlap, strongly suggesting common aging mechanisms among different tissue stem cells.

Tracing the Formation of Haematopoietic Stem Cells in Mouse Embryos By Single-Cell Functional and RNA-Seq Analyses

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5046-5046
Author(s):  
Fuchou Tang
Keyword(s):  
Stem Cells ◽  
Endothelial Cells ◽  
Single Cell ◽  
Molecular Mechanisms ◽  
Conflicts Of Interest ◽  
Precursor Cells ◽  
Considerable Proportion ◽  
Rna Seq ◽  
Haematopoietic Stem Cells

Abstract Haematopoietic stem cells (HSCs) are derived early from embryonic precursor cells, such as haemogenic endothelial cells and pre-HSCs. However, the identity of precursor cells remains elusive due to their rareness, transience, and inability to be isolated efficiently. Here we employed potent surface markers to capture the nascent pre-HSCs at 30% purity, as rigorously validated by single-cell-initiated serial transplantation assay. Then we applied single-cell RNA-Seq technique to analyse five populations closely related to HSC formation: endothelial cells, CD45- and CD45+ pre-HSCs in E11 aorta-gonad-mesonephros (AGM) region, and mature HSCs in E12 and E14 foetal liver. In comparison, the pre-HSCs showed unique features in transcriptional machinery, arterial signature, apoptosis, metabolism state, signalling pathway, transcription factor network, and lncRNA expression pattern. Among signalling pathways enriched in pre-HSCs, the mTOR activation was uncovered indispensable for the emergence of HSCs but not haematopoietic progenitors from endothelial cells in vivo. Transcriptome data-based functional analysis revealed de novo the remarkable heterogeneity in cell cycle status of pre-HSCs, with considerable proportion being actively proliferative. By comparing with proximal populations without HSC potential, the core molecular signature of pre-HSCs was identified. Collectively, our work paves the way for dissection of complex molecular mechanisms regulating the step-wise generation of HSCs in vivo, informing future efforts to engineer HSCs for clinical application. Disclosures No relevant conflicts of interest to declare.

scholarly journals C28-induced autophagy of female germline stem cells in vitro and its potential mechanisms

2019 ◽  
Author(s):  
Rong Hu ◽  
Xiuying Pei ◽  
Huchen Zhou ◽  
Ji Wu ◽  
Ping Chen ◽  
...  
Keyword(s):  
Stem Cells ◽  
Er Stress ◽  
Cellular Response ◽  
Germline Stem Cells ◽  
Rna Seq ◽  
Sequestosome 1 ◽  
Expression Of Genes ◽  
Female Germline ◽  
Molecular Compounds

Abstract BackgroundThere are few studies indicating that small molecular compounds affect the proliferation, differentiation, apoptosis, and autophagy of female germline stem cells (FGSCs). However, the epigenetic regulatory mechanism of small molecular compounds that induce autophagy in FGSCs remains unknown.ResultsIn this study, we found that C28 reduced the viability and proliferation of FGSCs, respectively. Additionally, western blotting showed that the expression of autophagy marker light chain 3 beta II (LC3B-II) was significantly increased and expression of sequestosome-1 (SQSTM1) was significantly reduced in C28-treated groups. Immunofluorescence showed that, in C28-treated groups, the number of LC3B-II-positive puncta was increased significantly. These results indicated that C28 induced autophagy of FGSCs in vitro. ChIP-seq data showed that autophagy-related biological processes such as regulation of mitochondrial membrane potential, Golgi vesicle transport, and cellular response to reactive oxygen species were enriched. In addition, RNA-Seq showed that the expression of genes (Trib3, DDIT3, and ATF4) related to endoplasmic reticulum (ER) stress was enhanced by C28.ConclusionC28 could induce FGSC autophagy in vitro leading to a decrease in the number of FGSCs. H3K27ac and ER stress might play roles in C28-induced autophagy of FGSCs in vitro.

scholarly journals Investigations into the effects and related upstream/downstream regulatory mechanisms of long non-coding RNA WT1-AS in the maintenance and development of gastric cancer stem cells in vitro and in vivo

2021 ◽  
Author(s):  
Xiaobei Zhang ◽  
Meng Jin ◽  
Shiqi Liu ◽  
Mingde Zang ◽  
Lei Hu ◽  
...  
Keyword(s):  
Stem Cells ◽  
Cancer Stem Cells ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
Non Coding Rna ◽  
Gastric Cancer Stem Cells ◽  
Long Non Coding Rna ◽  
Development Of Gastric Cancer

Abstract Background Cancer stem cells (CSCs) are proposed to be responsible for almost all malignant phenotypes (e.g. heterogeneity, uncontrolled growth, metastasis, recurrence, chemoresistance) of tumors. Long non-coding RNA WT1 antisense RNA (WT1-AS) has been found to be involved in the regulation of lung cancer cell stemness. However, the roles and molecular mechanisms of WT1-AS in the maintenance and development of gastric cancer stem cells (GSCs) have not been investigated. Methods mRNA and protein expression was measured by RT-qPCR and western blot. CCK8 and Soft agar colony formation assays were performed to assess cell viability and colony clone formation ability. Cell cycle and apoptosis were determined by flow cytometry analysis. Cell transwell and wound healing analyses were carried out to assess cell migration ability. In vitro angiogenesis and 3D spheroid cultures assays were also performed. Moreover, in vitro experiments were carried out to explore the function of WT1-AS on tumor growth, metastasis and cell stemness. The upstream transcription factors or downstream genes of WT1-AS were screened through Bioinformatics, dual-luciferase assays and RNA-sequencing (RNA-seq) technology. Results Our present study demonstrated that WT1-AS knockdown or wilms tumor 1 (WT1) overexpression improved GSC proliferative and migratory capacities, promoted GSC EMT, enhanced GSC stemness, inhibited GSC apoptosis, potentiated the resistance of GSCs to 5-FU and induced HUVEC angiogenesis in vitro. WT1-AS loss or WT1 increase facilitated the formation of in-vitro 3D GSC aggregates. WT1-AS ameliorated the malignant phenotypes of GSCs by down-regulating WT in vitro. Additionally, WT1-AS inhibited tumor growth and metastasis, and reduced tumor stemness in GSCs-derived xenografts (s.c., i.p., and i.v.) in vivo. Furthermore, XBP1 was identified as an upstream regulator of WT1-AS in GSCs. RNA-seq and RT-qPCR data suggested that PSPH, GSTO2, FYN, and PHGDH might be the downstream targets of WT1-AS in GSCs. Conclusions Our data demonstrated that WT1-AS weakened the stem-cell like behaviors and characteristics of GSCs in vitro and in vivo by down-regulating WT1. Also, some upstream regulators and downstream targets of WT1-AS were identified in GSCs. Investigations on the molecular mechanisms underlying the complex phenotypes of GSCs might contribute to the better management of headaches in cancers.

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