scholarly journals Fetal Membrane Epigenetics

2020 ◽  
Vol 11 ◽  
Author(s):  
Tamas Zakar ◽  
Jonathan W. Paul
Keyword(s):  
Gene Expression ◽  
Early Stage ◽  
Expression Patterns ◽  
Normal Pregnancy ◽  
Clinical Samples ◽  
Fetal Membrane ◽  
Stage Of Development ◽  
Micro Rnas ◽  
Non Coding Rnas ◽  
Adverse Pregnancy

The characteristics of fetal membrane cells and their phenotypic adaptations to support pregnancy or promote parturition are defined by global patterns of gene expression controlled by chromatin structure. Heritable epigenetic chromatin modifications that include DNA methylation and covalent histone modifications establish chromatin regions permissive or exclusive of regulatory interactions defining the cell-specific scope and potential of gene activity. Non-coding RNAs acting at the transcriptional and post-transcriptional levels complement the system by robustly stabilizing gene expression patterns and contributing to ordered phenotype transitions. Here we review currently available information about epigenetic gene regulation in the amnion and the chorion laeve. In addition, we provide an overview of epigenetic phenomena in the decidua, which is the maternal tissue fused to the chorion membrane forming the anatomical and functional unit called choriodecidua. The relationship of gene expression with DNA (CpG) methylation, histone acetylation and methylation, micro RNAs, long non-coding RNAs and chromatin accessibility is discussed in the context of normal pregnancy, parturition and pregnancy complications. Data generated using clinical samples and cell culture models strongly suggests that epigenetic events are associated with the phenotypic transitions of fetal membrane cells during the establishment, maintenance and termination of pregnancy potentially driving and consolidating the changes as pregnancy progresses. Disease conditions and environmental factors may produce epigenetic footprints that indicate exposures and mediate adverse pregnancy outcomes. Although knowledge is expanding rapidly, fetal membrane epigenetics is still in an early stage of development necessitating further research to realize its remarkable basic and translational potential.

Circulating melanoma cells isolated from clinical blood samples and characterized by full-length mRNA sequencing at single-cell level.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 10539-10539 ◽  
Author(s):  
Yu-Chieh Wang ◽  
Daniel Ramskold ◽  
Shujun Luo ◽  
Robin Li ◽  
Qiaolin Deng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Melanoma Cells ◽  
Clinical Samples ◽  
Single Cell Level ◽  
Cell Level ◽  
Blood Samples

10539 Background: Melanoma is the most aggressive type of skin cancer. Late-stage melanoma is highly metastatic and currently lacks effective treatment. This discouraging clinical observation highlights the need for a better understanding of the molecular mechanisms underlying melanoma initiation and progression and for developing new therapeutic approaches based on novel targets. Although genome-wide transcriptome analyses have been frequently used to study molecular alterations in clinical samples, it has been technically challenging to obtain the transcriptomic profiles at single-cell level. Methods: Using antibody-mediated magnetic activated cell separation (MACS), we isolated and individualized putative circulating melanoma cells (CMCs) from the blood samples of the melanoma patients at advance stages. The transcriptomic analysis based on a novel and robust mRNA-Seq protocol (Smart-Seq) was established and applied to the putative CMCs for single-cell profiling. Results: We have discovered distinct gene expression patterns, including new putative markers for CMCs. Meanwhile, the gene expression profiles derived of the CMC candidates isolated from the patient’s blood samples are closely-related to the expression profiles of other cells originated from human melanocytes, including normal melanocytes in primary culture and melanoma cell lines. Compared with existing methods, Smart-Seq has improved read coverage across transcripts, which provides advantage for better analyzing transcript isoforms and SNPs. Conclusions: Our results suggest that the techniques developed in this research for cell isolation and transcriptomic analyses can potentially be used for addressing many biological and clinical questions requiring genomewide transcriptome profiling in rare cells.

Gene expression patterns in melanocytic cells: candidate markers for early stage and malignant transformation

2001 ◽  
Vol 196 (1) ◽  
pp. 51-58 ◽  
Author(s):  
Clifton B. Meije ◽  
Theodorus B. M. Hakvoort ◽  
Guido W. M. Swart ◽  
Wiete Westerhof ◽  
Wouter H. Lamers ◽  
...  
Keyword(s):  
Gene Expression ◽  
Malignant Transformation ◽  
Early Stage ◽  
Expression Patterns ◽  
Gene Expression Patterns

scholarly journals Gene expression patterns in bone following lipopolysaccharide stimulation

2014 ◽  
Vol 19 (4) ◽  
Author(s):  
Jing Yang ◽  
Nan Su ◽  
Xiaolan Du ◽  
Lin Chen
Keyword(s):  
Gene Expression ◽  
Bone Formation ◽  
Real Time ◽  
Real Time Pcr ◽  
Early Stage ◽  
System Development ◽  
Expression Patterns ◽  
Osteoclast Differentiation ◽  
Gene Expression Patterns ◽  
Expression Levels

AbstractBone displays suppressed osteogenesis in inflammatory diseases such as sepsis and rheumatoid arthritis. However, the underlying mechanisms have not yet been clearly explained. To identify the gene expression patterns in the bone, we performed Affymetrix Mouse Genome 430 2.0 Array with RNA isolated from mouse femurs 4 h after lipopolysaccharide (LPS) administration. The gene expressions were confirmed with real-time PCR. The serum concentration of the N-terminal propeptide of type I collagen (PINP), a bone-formation marker, was determined using ELISA. A total of 1003 transcripts were upregulated and 159 transcripts were downregulated (more than twofold upregulation or downregulation). Increased expression levels of the inflammation-related genes interleukin-6 (IL-6), interleukin-1β (IL-1β) and tumor necrosis factor α (TNF-α) were confirmed from in the period 4 h to 72 h after LPS administration using real-time PCR. Gene ontogene analysis found four bone-related categories involved in four biological processes: system development, osteoclast differentiation, ossification and bone development. These processes involved 25 upregulated genes. In the KEGG database, we further analyzed the transforming growth factor β (TGF-β) pathway, which is strongly related to osteogenesis. The upregulated bone morphogenetic protein 2 (BMP2) and downregulated inhibitor of DNA binding 4 (Id4) expressions were further confirmed by real-time PCR after LPS stimulation. The osteoblast function was determined through examination of the expression levels of core binding factor 1 (Cbfa1) and osteocalcin (OC) in bone tissues and serum PINP from 4 h to 72 h after LPS administration. The expressions of OC and Cbfa1 decreased 6 h after administration (p < 0.05). Significantly suppressed PINP levels were observed in the later stage (from 8 h to 72 h, p < 0.05) but not in the early stage (4 h or 6 h, p > 0.05) of LPS stimulation. The results of this study suggest that LPS induces elevated expressions of skeletal system development- and osteoclast differentiation-related genes and inflammation genes at an early stage in the bone. The perturbed functions of these two groups of genes may lead to a faint change in osteogenesis at an early stage of LPS stimulation. Suppressed bone formation was found at later stages in response to LPS stimulation.

scholarly journals Comparative analysis of differential gene expression indicates divergence in ontogenetic strategies of leaves in two conifer genera

2021 ◽  
Author(s):  
Cynthia Webster ◽  
Laura Figueroa-Corona ◽  
Iván Méndez-González ◽  
Lluvia Soto-Álvarez ◽  
David Neale ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Life Stage ◽  
Expression Patterns ◽  
Adult Life ◽  
Gene Interaction ◽  
Gene Families ◽  
Interaction Patterns ◽  
Gene Interaction Network ◽  
Stage Of Development

In land plants, heteroblasty broadly refers to a drastic change in morphology during growth through ontogeny. Juniperus flaccida and Pinus cembroides are conifers of independent lineages known to exhibit leaf heteroblasty between the juvenile and adult life stage of development. Juvenile leaves of P. cembroides develop spirally on the main stem and appear decurrent, flattened and needle-like; whereas, adult photosynthetic leaves are triangular or semi-circular needle-like, and grow in whorls on secondary or tertiary compact dwarf shoots. By comparison, J. flaccida juvenile leaves are decurrent and needle-like, and adult leaves are compact, short and scale-like. Comparative analyses were performed to evaluate differences in anatomy and gene expression patterns between developmental phases in both species. RNA from twelve samples was sequenced and analyzed with available software. They were assembled de novo from the RNA-Seq reads. Following assembly, 63,741 high quality transcripts were functionally annotated in P. cembroides and 69,448 in J. flaccida. Evaluation of the orthologous groups yielded 4,140 shared gene families among the four references (adult and juvenile from each species). Activities related to cell division and development were more abundant in juveniles than adults in P. cembroides, and more abundant in adults than juveniles in J. flaccida. Overall, there were 509 up-regulated and 81 down-regulated genes in the juvenile condition of P. cembroides and 18 up-regulated and 20 down-regulated in J. flaccida. Gene interaction network analysis showed evidence of co-expression and co-localization of up-regulated genes involved in cell wall and cuticle formation, development, and phenylpropanoid pathway, in juvenile P. cembroides leaves. Whereas in J. flaccida, differential expression and gene interaction patterns were detected in genes involved in photosynthesis and chloroplast biogenesis. Although J. flaccida and P. cembroides both exhibit leaf heteroblastic development, little overlap was detected and unique genes and pathways were highlighted in this study.

scholarly journals A Model for Initiation of Mosaic HOX Gene Expression Patterns by Non-Coding RNAs in Early Embryos

RNA Biology ◽  
2007 ◽  
Vol 4 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Svetlana Petruk ◽  
Yurii Sedkov ◽  
Hugh W. Brock ◽  
Alexander Mazo
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Hox Gene ◽  
Early Embryos ◽  
Non Coding Rnas

scholarly journals BEST: A Novel Computational Approach for Comparing Gene Expression Patterns From Early Stages of Drosophila melanogaster Development

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 2037-2047
Author(s):  
Sudhir Kumar ◽  
Karthik Jayaraman ◽  
Sethuraman Panchanathan ◽  
Rajalakshmi Gurunathan ◽  
Ana Marti-Subirana ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Biology ◽  
Drosophila Melanogaster ◽  
Expression Pattern ◽  
Early Stage ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Computational Approach ◽  
Gene Expression Patterns ◽  
Early Stages

Abstract Embryonic gene expression patterns are an indispensable part of modern developmental biology. Currently, investigators must visually inspect numerous images containing embryonic expression patterns to identify spatially similar patterns for inferring potential genetic interactions. The lack of a computational approach to identify pattern similarities is an impediment to advancement in developmental biology research because of the rapidly increasing amount of available embryonic gene expression data. Therefore, we have developed computational approaches to automate the comparison of gene expression patterns contained in images of early stage Drosophila melanogaster embryos (prior to the beginning of germ-band elongation); similarities and differences in gene expression patterns in these early stages have extensive developmental effects. Here we describe a basic expression search tool (BEST) to retrieve best matching expression patterns for a given query expression pattern and a computational device for gene interaction inference using gene expression pattern images and information on the associated genotypes and probes. Analysis of a prototype collection of Drosophila gene expression pattern images is presented to demonstrate the utility of these methods in identifying biologically meaningful matches and inferring gene interactions by direct image content analysis. In particular, the use of BEST searches for gene expression patterns is akin to that of BLAST searches for finding similar sequences. These computational developmental biology methodologies are likely to make the great wealth of embryonic gene expression pattern data easily accessible and to accelerate the discovery of developmental networks.

scholarly journals Relationship Between Pregnancy and Acute Disseminated Encephalomyelitis: A Single-Case Study

2021 ◽  
Vol 11 ◽  
Author(s):  
Shuwen Deng ◽  
Ke Qiu ◽  
Ranran Tu ◽  
Haiping Zheng ◽  
Wei Lu
Keyword(s):  
Real Time ◽  
Early Stage ◽  
Single Case ◽  
Normal Pregnancy ◽  
Acute Disseminated Encephalomyelitis ◽  
Fetal Membrane ◽  
Disturbance Of Consciousness ◽  
Immune Changes ◽  
Real Time Qpcr ◽  
Maternal Fetal Interface

The relationship between pregnancy and autoimmune diseases is unclear. This study investigated the possible role of local immune changes and the activation state of the HMGB1/TLR4/Nf-κB/IL-6 pathway at the maternal–fetal interface during pregnancy in the pathogenesis of acute disseminated encephalomyelitis (ADEM). Clinical data and blood samples of a patient with ADEM were collected to observe the dynamic changes in lymphocyte populations after an abortion. The expression of HMGB1, TLR4, Nf-κB, AQP4, IL-2, IL-4, IL-6, and TNF-α in the fetal membrane and placenta was compared between the patient with pregnancy-related ADEM and a woman with a normal pregnancy using Real-time qPCR and western blotting (WB). The patient was diagnosed with ADEM in the early stage of pregnancy after showing limb weakness symptoms. In the third month of gestation, the symptoms worsened, with a disturbance of consciousness and breathing. After the abortion, the patient relapsed with vertigo and visual rotation. Analysis of lymphocyte subsets by flow cytometry showed that B lymphocytes increased, while natural killer T lymphocytes decreased. WB and Real-time qPCR showed that the expression levels of HMGB1, TLR4, Nf-κB, AQP4, and IL-6 in the fetal membrane and placenta were higher in the patient with pregnancy-related ADEM than in the woman with a normal pregnancy, while those of IL-2 were lower in the patient than in the woman with a normal pregnancy. The local immune changes and the activation of the HMGB1/TLR4/Nf-κB/IL-6 pathway at the maternal–fetal interface may be related to the pathogenesis of ADEM.

scholarly journals Non-coding RNAs and chromatin: key epigenetic factors from spermatogenesis to transgenerational inheritance

2021 ◽  
Vol 54 (1) ◽  
Author(s):  
Carolina Cheuquemán ◽  
Rodrigo Maldonado
Keyword(s):  
Gene Expression ◽  
Germ Line ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Chromatin Organization ◽  
Sperm Maturation ◽  
Transgenerational Inheritance ◽  
Epigenetic Factors ◽  
Germ Cell Differentiation ◽  
Non Coding Rnas

AbstractCellular fate and gene expression patterns are modulated by different epigenetic factors including non-coding RNAs (ncRNAs) and chromatin organization. Both factors are dynamic throughout male germ cell differentiation on the seminiferous tubule, despite the transcriptional inactivation in the last stages of spermatogenesis. Sperm maturation during the caput-to-cauda transit on the epididymis involves changes in chromatin organization and the soma-to-germ line transference of ncRNAs that are essential to obtain a functional sperm for fertilization and embryo development. Here, the male environment (diseases, drugs, mental stress) is crucial to modulate these epigenetic factors throughout sperm maturation, affecting the corresponding offspring. Paternal transgenerational inheritance has been directly related to sperm epigenetic changes, most of them associated with variations in the ncRNA content and chromatin marks. Our aim is to give an overview about how epigenetics, focused on ncRNAs and chromatin, is pivotal to understand spermatogenesis and sperm maturation, and how the male environment impacts the sperm epigenome modulating the offspring gene expression pattern.

scholarly journals Segmenting Gene Expression Patterns of Early-stage Drosophila Embryos

2008 ◽  
pp. 313-327 ◽  
Author(s):  
Min-Yu Huang ◽  
Oliver Rübel ◽  
Gunther H. Weber ◽  
Cris L. Luengo Hendriks ◽  
Mark D. Biggin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Early Stage ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Drosophila Embryos

scholarly journals Optimizing the Use of Gene Expression Profiling in Early-Stage Breast Cancer

2016 ◽  
Vol 34 (36) ◽  
pp. 4390-4397 ◽  
Author(s):  
Hyun-seok Kim ◽  
Christopher B. Umbricht ◽  
Peter B. Illei ◽  
Ashley Cimino-Mathews ◽  
Soonweng Cho ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Decision Making ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Early Stage ◽  
Recurrence Score ◽  
Clinical Samples ◽  
Risk Category ◽  
Clinical Risk

Purpose Gene expression profiling assays are frequently used to guide adjuvant chemotherapy decisions in hormone receptor–positive, lymph node–negative breast cancer. We hypothesized that the clinical value of these new tools would be more fully realized when appropriately integrated with high-quality clinicopathologic data. Hence, we developed a model that uses routine pathologic parameters to estimate Oncotype DX recurrence score (ODX RS) and independently tested its ability to predict ODX RS in clinical samples. Patients and Methods We retrospectively reviewed ordered ODX RS and pathology reports from five institutions (n = 1,113) between 2006 and 2013. We used locally performed histopathologic markers (estrogen receptor, progesterone receptor, Ki-67, human epidermal growth factor receptor 2, and Elston grade) to develop models that predict RS-based risk categories. Ordering patterns at one site were evaluated under an integrated decision-making model incorporating clinical treatment guidelines, immunohistochemistry markers, and ODX. Final locked models were independently tested (n = 472). Results Distribution of RS was similar across sites and to reported clinical practice experience and stable over time. Histopathologic markers alone determined risk category with > 95% confidence in > 55% (616 of 1,113) of cases. Application of the integrated decision model to one site indicated that the frequency of testing would not have changed overall, although ordering patterns would have changed substantially with less testing of estimated clinical risk–high or clinical risk–low cases and more testing of clinical risk–intermediate cases. In the validation set, the model correctly predicted risk category in 52.5% (248 of 472). Conclusion The proposed model accurately predicts high- and low-risk RS categories (> 25 or ≤ 25) in a majority of cases. Integrating histopathologic and molecular information into the decision-making process allows refocusing the use of new molecular tools to cases with uncertain risk.

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