scholarly journals Quantitative proteomic alterations of human iPSC-based neuronal development indicate early onset of Rett syndrome

2019 ◽  
Author(s):  
Suzy Varderidou-Minasian ◽  
Lisa Hinz ◽  
Dominique Hagemans ◽  
Danielle Posthuma ◽  
Maarten Altelaar ◽  
...  
Keyword(s):  
Stem Cell ◽  
Rett Syndrome ◽  
Molecular Mechanisms ◽  
Neuronal Development ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Induced Pluripotent Stem Cell ◽  
Gene Encoding ◽  
Neurodevelopmental Disease ◽  
New Biomarkers

AbstractRett syndrome (RTT) is a progressive neurodevelopmental disease often caused by mutations in the X-linked gene encoding methyl-CpG binding protein 2 (MeCP2). The mechanisms by which impaired MeCP2 induces the pathological abnormalities in the brain are not understood. To understand the molecular mechanisms involved in disease, we used an RTT patient induced pluripotent stem cell (iPSC)-based model and applied an in-depth high-resolution quantitative mass spectrometry-based analysis during early stages of neuronal development. Our data provide evidence of proteomic alteration at developmental stages long before the phase that symptoms of RTT syndrome become apparent. Differences in expression profiles became more pronounced from early to late neural stem cell phases, although proteins involved in immunity, metabolic processes and calcium signaling were already affected at initial stages. These results can help development of new biomarkers and therapeutic approaches by selectively target the affected proteins in RTT syndrome.

scholarly journals Quantitative proteomic analysis shows alterations in patient Rett syndrome iPSC cultures at early neuronal progenitor stages

2020 ◽  
Author(s):  
Suzy Varderidou-Minasian ◽  
Lisa Hinz ◽  
Dominique Hagemans ◽  
Danielle Posthuma ◽  
Maarten Altelaar ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Stem Cell ◽  
Rett Syndrome ◽  
Proteomic Analysis ◽  
Molecular Mechanisms ◽  
Disease Onset ◽  
Data Depth ◽  
Dendrite Morphology ◽  
Neurodevelopmental Disease ◽  
Neuronal Progenitor

Abstract BackgroundRett syndrome (RTT) is a progressive neurodevelopmental disease that is characterized by abnormalities in cognitive, social and motor skills. RTT is often caused by mutations in the X-linked gene encoding methyl-CpG binding protein 2 (MeCP2). The mechanism by which impaired MeCP2 induces the pathological abnormalities in the brain is not understood. Both patients and mouse models have shown abnormalities at molecular and cellular level before typical RTT-associated symptoms appear. This implies that underlying mechanisms are already affected during neurodevelopmental stages.MethodsTo understand the molecular mechanisms involved in disease onset, we used an RTT patient induced pluripotent stem cell (iPSC)-based model with isogenic controls and performed time-series of proteomic analysis using in-depth high-resolution quantitative mass spectrometry during early stages of neuronal development. ResultsWe provide mass spectrometry-based quantitative proteomic data, depth of about 7000 proteins, at neuronal progenitor developmental stages of RTT patient cells and isogenic controls. Our data gives evidence of proteomic alteration at early neurodevelopmental stages, suggesting alterations long before the phase that symptoms of RTT syndrome become apparent. We found changes in proteins involved in pathway associated with RTT phenotypes, including dendrite morphology and synaptogenesis. Differential expression increased from early to late neural stem cell phases, although proteins involved in immunity, metabolic processes and calcium signaling were affected throughout all stages analyzed. LimitationsThe limitation of our study is the number of biological replicates. As the aim of our study was to investigate a large number of proteins, only a limited amount of biological replicates were suitable for inclusions without reducing the number of target proteins. Therefore, larger sample sizes derived from RTT patients will be needed to validate results. ConclusionsOur results provide a valuable resource of proteins to study potential targets for early treatment of RTT symptoms. We found consistent and time-point specific alterations during early neuronal differentiation in RTT cultures. Insight into altered protein levels can help development of new biomarkers and therapeutic approaches in RTT syndrome. Therefore, we hope that our results give awareness of the early pre-natal onset of RTT, providing new insights to explore early diagnosis and treatment.

scholarly journals Comparative Transcriptomic Analysis of Riptortus pedestris (Hemiptera: Alydidae) to Characterize Wing Formation across All Developmental Stages

Insects ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 226
Author(s):  
Siying Fu ◽  
Yujie Duan ◽  
Siqi Wang ◽  
Yipeng Ren ◽  
Wenjun Bu
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Economic Losses ◽  
Future Research ◽  
Economic Damage ◽  
Wing Formation ◽  
Riptortus Pedestris

Riptortus pedestris (Hemiptera: Alydidae) is a major agricultural pest in East Asia that causes considerable economic losses to the soybean crop each year. However, the molecular mechanisms governing the growth and development of R. pedestris have not been fully elucidated. In this study, the Illumina HiSeq6000 platform was employed to perform de novo transcriptome assembly and determine the gene expression profiles of this species across all developmental stages, including eggs, first-, second-, third-, fourth-, and fifth-instar nymphs, and adults. In this study, a total of 60,058 unigenes were assembled from numerous raw reads, exhibiting an N50 length of 2126 bp and an average length of 1199 bp, and the unigenes were annotated and classified with various databases, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Furthermore, various numbers of differentially expressed genes (DEGs) were calculated through pairwise comparisons of all life stages, and some of these DEGs were associated with immunity, metabolism, and development by GO and KEGG enrichment. In addition, 35,158 simple sequence repeats (SSRs) and 715,604 potential single nucleotide polymorphisms (SNPs) were identified from the seven transcriptome libraries of R. pedestris. Finally, we identified and summarized ten wing formation-related signaling pathways, and the molecular properties and expression levels of five wing development-related genes were analyzed using quantitative real-time PCR for all developmental stages of R. pedestris. Taken together, the results of this study may establish a foundation for future research investigating developmental processes and wing formation in hemimetabolous insects and may provide valuable data for pest control efforts attempting to reduce the economic damage caused by this pest.

scholarly journals A Novel Regulatory Axis, CHD1L-MicroRNA 486-Matrix Metalloproteinase 2, Controls Spermatogonial Stem Cell Properties

2018 ◽  
Vol 39 (4) ◽  
Author(s):  
Shan-Shan Liu ◽  
Eithne Margaret Maguire ◽  
Yin-Shan Bai ◽  
Li Huang ◽  
Yurong Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Matrix Metalloproteinase ◽  
Molecular Mechanisms ◽  
Nuclear Translocation ◽  
Expression Profiles ◽  
Matrix Metalloproteinase 2 ◽  
Small Rna Sequencing ◽  
Growth Properties ◽  
The Matrix

ABSTRACT Spermatogonial stem cells (SSCs) are unipotent germ cells that are at the foundation of spermatogenesis and male fertility. However, the underlying molecular mechanisms governing SSC stemness and growth properties remain elusive. We have recently identified chromodomain helicase/ATPase DNA binding protein 1-like (Chd1l) as a novel regulator for SSC survival and self-renewal, but how these functions are controlled by Chd1l remains to be resolved. Here, we applied high-throughput small RNA sequencing to uncover the microRNA (miRNA) expression profiles controlled by Chd1l and showed that the expression levels of 124 miRNA transcripts were differentially regulated by Chd1l in SSCs. KEGG pathway analysis shows that the miRNAs that are differentially expressed upon Chd1l repression are significantly enriched in the pathways associated with stem cell pluripotency and proliferation. As a proof of concept, we demonstrate that one of the most highly upregulated miRNAs, miR-486, controls SSC stemness gene expression and growth properties. The matrix metalloproteinase 2 (MMP2) gene has been identified as a novel miR-486 target gene in the context of SSC stemness gene regulation and growth properties. Data from cotransfection experiments showed that Chd1l, miR-486, and MMP2 work in concert in regulating SSC stemness gene expression and growth properties. Finally, our data also revealed that MMP2 regulates SSC stemness gene expression and growth properties through activating β-catenin signaling by cleaving N-cadherin and increasing β-catenin nuclear translocation. Our data demonstrate that Chd1l–miR-486–MMP2 is a novel regulatory axis governing SSC stemness gene expression and growth properties, offering a novel therapeutic opportunity for treating male infertility.

Abstract 14908: Anatomic Validation of Induced Pluripotent Stem Cell-derived Aortic Smooth Muscle Cell Model of Loeys Dietz Syndrome

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Albert J Pedroza ◽  
Samantha Churovich ◽  
Nobu Yokoyama ◽  
Ken Nakamura ◽  
Cristiana Iosef Husted ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Stem Cell ◽  
Aortic Root ◽  
Pluripotent Stem Cell ◽  
Cell Model ◽  
Expression Profiles ◽  
Induced Pluripotent Stem Cell ◽  
Aortic Root Aneurysm ◽  
Ligand Expression ◽  
Induced Pluripotent

Introduction: Mutations in TGF-beta (TGF-ß) signaling genes lead to aortic root aneurysm in Loeys Dietz syndrome (LDS). Smooth muscle cells (SMCs) in the proximal aorta develop from two embryologic origins: second heart field (SHF) and neural crest (NC). Induced pluripotent stem cell (iPSC) models simulate these lineages, but direct correlation to clinical disease is lacking. Hypothesis: iPSC-derived SMCs accurately model lineage-specific aortopathy in LDS. Methods: We generated SMC lines from root and ascending aortic surgical tissue and iPSC-derived SMCs through SHF and NC-specific pathways from an LDS patient ( TGFBR1 mutation). Lineage-specific TGF-ß responses were determined by western blot/ELISA. RNA sequencing and RT-PCR identified SMC transcriptomes. Results: Aortic root SMCs showed greater canonical TGF-ß activation (p-SMAD2/3) versus ascending at baseline and with TGF-ß stimulation ( Figure ). Synonymous results were seen in SHF versus NC SMCs from the iPSC pathway. RNAseq identified 1,600 differentially expressed genes between iPSC lineages, including altered TGF-ß receptor and ligand expression profiles. Primary aortic lines validated iPSC data: root SMCs showed enriched TGF-ß receptor 1/2/3 expression (1.7-, 3.9- and 5.9-fold) while ascending SMCs overexpressed TGFB1 and TGFB2 ligands (1.8- and 3.5-fold). Despite discordant TGF-ß activation, SMC contractile gene expression was similar between lineages in aortic and iPSC-SMCs, suggesting alternative downstream effects in LDS aneurysm. Conclusion: iPSC-derived SMCs effectively model lineage-specific aortic root aneurysm pathology, validating this model as a tool for mechanistic testing and therapy discovery.

scholarly journals Potential Pathways and Genes Involved in Lac Synthesis and Secretion in Kerria chinensis (Hemiptera: Kerriidae) Based on Transcriptomic Analyses

Insects ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 430
Author(s):  
Weiwei Wang ◽  
Pengfei Liu ◽  
Qin Lu ◽  
Xiaofei Ling ◽  
Jinwen Zhang ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Future Studies ◽  
Natural Resin ◽  
Beneficial Insect ◽  
Excellent Adhesion ◽  
The Military ◽  
Secretion Rates

Lac is a type of natural resin secreted by lac insects and is widely used in the military and other industries because of its excellent adhesion and insulation properties. The main ingredients of lac are lactones and lactides, which are formed from hydroxy fatty acids and sesquiterpene esters. In this study, we measured lac secretion rates by the insect Kerria chinensis at different developmental stages and identified lac secretion-minimum and lac secretion-active stages of the insect. We then analyzed transcriptomes of lac secretion-minimum and lac secretion-active stages of the insect. Based on expression profiles of genes in different stages of the insect, we identified pathways and genes that are potentially involved in lac synthesis and secretion in K. chinensis. Our study lays a foundation for future studies to reveal the molecular mechanisms and pathways of lac synthesis and secretion in this beneficial insect.

scholarly journals Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages

2016 ◽  
Vol 16 (1) ◽  
Author(s):  
Juan Ma ◽  
Rongyan Wang ◽  
Xiuhua Li ◽  
Bo Gao ◽  
Shulong Chen
Keyword(s):  
Sweet Potato ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Average Length ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Cylas Formicarius ◽  
Important Pest

Abstract The sweet potato weevil, Cylas formicarius (F.) (Coleoptera: Brentidae), is an important pest of sweet potato worldwide. However, there is limited knowledge on the molecular mechanisms underlying growth and differentiation of C. formicarius. The transcriptomes of the eggs, second instar larvae, third instar larvae (L3), pupae, females, and males of C. formicarius were sequenced using Illumina sequencing technology for obtaining global insights into developing transcriptome characteristics and elucidating the relative functional genes. A total of 54,255,544 high-quality reads were produced, trimmed, and de novo assembled into 115,281 contigs. 61,686 unigenes were obtained, with an average length of 1,009 nt. Among these unigenes, 17,348 were annotated into 59 Gene Ontology (GO) terms and 12,660 were assigned to 25 Cluster of Orthologous Groups classes, whereas 24,796 unigenes were mapped to 258 pathways. Differentially expressed unigenes between various developmental stages of C. formicarius were detected. Higher numbers of differentially expressed genes (DEGs) were recorded in the eggs versus L3 and eggs versus male samples (2,141 and 2,058 unigenes, respectively) than the others. Genes preferentially expressed in each stage were also identified. GO and pathway-based enrichment analysis were used to further investigate the functions of the DEGs. In addition, the expression profiles of ten DEGs were validated by quantitative real-time PCR. The transcriptome profiles presented in this study and these DEGs detected by comparative analysis of different developed stages of C. formicarius will facilitate the understanding of the molecular mechanism of various living process and will contribute to further genome-wide research.

scholarly journals Characterization of the molecular mechanisms underlying increased ischemic damage in the aldehyde dehydrogenase 2 genetic polymorphism using a human induced pluripotent stem cell model system

2014 ◽  
Vol 6 (255) ◽  
pp. 255ra130-255ra130 ◽  
Author(s):  
Antje D. Ebert ◽  
Kazuki Kodo ◽  
Ping Liang ◽  
Haodi Wu ◽  
Bruno C. Huber ◽  
...  
Keyword(s):  
Stem Cell ◽  
Genetic Polymorphism ◽  
Cell Survival ◽  
Pluripotent Stem Cell ◽  
Molecular Mechanisms ◽  
Induced Pluripotent Stem Cell ◽  
Model System ◽  
Ischemic Damage ◽  
Aldehyde Dehydrogenase 2 ◽  
Induced Pluripotent

Nearly 8% of the human population carries an inactivating point mutation in the gene that encodes the cardioprotective enzyme aldehyde dehydrogenase 2 (ALDH2). This genetic polymorphism (ALDH2*2) is linked to more severe outcomes from ischemic heart damage and an increased risk of coronary artery disease (CAD), but the underlying molecular bases are unknown. We investigated the ALDH2*2 mechanisms in a human model system of induced pluripotent stem cell–derived cardiomyocytes (iPSC-CMs) generated from individuals carrying the most common heterozygous form of the ALDH2*2 genotype. We showed that the ALDH2*2 mutation gave rise to elevated amounts of reactive oxygen species and toxic aldehydes, thereby inducing cell cycle arrest and activation of apoptotic signaling pathways, especially during ischemic injury. We established that ALDH2 controls cell survival decisions by modulating oxidative stress levels and that this regulatory circuitry was dysfunctional in the loss-of-function ALDH2*2 genotype, causing up-regulation of apoptosis in cardiomyocytes after ischemic insult. These results reveal a new function for the metabolic enzyme ALDH2 in modulation of cell survival decisions. Insight into the molecular mechanisms that mediate ALDH2*2-related increased ischemic damage is important for the development of specific diagnostic methods and improved risk management of CAD and may lead to patient-specific cardiac therapies.

scholarly journals Transcriptional and Functional Description of Stem Cell Heterogeneity in Native and Transplantation Hematopoiesis

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 3844-3844
Author(s):  
Alejo E Rodriguez-Fraticelli ◽  
Caleb Weinreb ◽  
Allon Moshe Klein ◽  
Fernando Camargo
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Steady State ◽  
Hematopoietic Stem Cells ◽  
Single Cell ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Significant Proportion ◽  
Cell Heterogeneity ◽  
Hematopoietic Stem

Abstract The hematopoietic system follows a hierarchical organization, with multipotent long-term repopulating hematopoietic stem cells (LT-HSCs) occupying the top tier. This paradigm, developed mostly through cell transplantation assays, has recently been contested by a series of studies performed under native conditions, without transplantation. Application of systems-level single cell methods in this setting has revealed a heterogeneity of cell states within progenitors and stem cells, prompting a reevaluation of the theories of hematopoietic lineage fate decisions. We have previously described that hematopoietic stem cell fates are clonally heterogeneous under steady state and uncovered that a fraction of LT-HSCs contributes to a significant proportion of the megakaryocytic cell lineage under steady state, while rarely generating other types of progeny in unperturbed conditions. To elucidate the molecular underpinnings of this functional lineage-output heterogeneity, we developed a technique to barcode hematopoietic cells at the RNA level in order to simultaneously capture the lineage relationships and transcriptional states of HSCs. Using a droplet-based massive single cell RNAseq platform, we analyzed thousands of engrafted hematopoietic stem cells together with a sufficiently significant representation of downstream progenitor cells to measure HSC output. Inspection of the resulting "stem cell state-fate maps" revealed a variety of stem cell behaviors, including single cell quiescence, asymmetric and symmetric divisions, and clonal expansion. We also connected these behaviors with some of the previously observed heterogeneity in stem cell outcomes, including lineage bias, lineage output and clonal competition. Importantly, clustering of expression profiles revealed significant differences in the transcriptional programs related with some of these behaviors, which illuminate the molecular machineries that operate at the stem cell level to define this heterogeneity. Thus, our work has identified potential novel mediators for stem cell heterogeneity, which we are functionally analyzing in further detail to understand their molecular mechanisms. Disclosures No relevant conflicts of interest to declare.

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