scholarly journals Non-Coding RNAs in Cartilage Development: An Updated Review

2019 ◽  
Vol 20 (18) ◽  
pp. 4475 ◽  
Author(s):  
Ehsan Razmara ◽  
Amirreza Bitaraf ◽  
Hassan Yousefi ◽  
Tina H. Nguyen ◽  
Masoud Garshasbi ◽  
...  
Keyword(s):  
Cell Biology ◽  
Endochondral Ossification ◽  
Association Studies ◽  
Post Translational Modifications ◽  
Cartilage Development ◽  
Complex Process ◽  
Cartilage Cells ◽  
Non Coding Rnas ◽  
Skeletal Disorders

In the development of the skeleton, the long bones are arising from the process of endochondral ossification (EO) in which cartilage is replaced by bone. This complex process is regulated by various factors including genetic, epigenetic, and environmental elements. It is recognized that DNA methylation, higher-order chromatin structure, and post-translational modifications of histones regulate the EO. With emerging understanding, non-coding RNAs (ncRNAs) have been identified as another mode of EO regulation, which is consist of microRNAs (miRNAs or miRs) and long non-coding RNAs (lncRNAs). There is expanding experimental evidence to unlock the role of ncRNAs in the differentiation of cartilage cells, as well as the pathogenesis of several skeletal disorders including osteoarthritis. Cutting-edge technologies such as epigenome-wide association studies have been employed to reveal disease-specific patterns regarding ncRNAs. This opens a new avenue of our understanding of skeletal cell biology, and may also identify potential epigenetic-based biomarkers. In this review, we provide an updated overview of recent advances in the role of ncRNAs especially focus on miRNA and lncRNA in the development of bone from cartilage, as well as their roles in skeletal pathophysiology.

MicroRNAs as Biomarker for Breast Cancer

2020 ◽  
Vol 20 (10) ◽  
pp. 1597-1610 ◽  
Author(s):  
Taru Aggarwal ◽  
Ridhima Wadhwa ◽  
Riya Gupta ◽  
Keshav Raj Paudel ◽  
Trudi Collet ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Association Studies ◽  
Large Family ◽  
Breast Cancer Diagnosis ◽  
Cell Multiplication ◽  
Cell Physiology ◽  
Gene Transcript ◽  
Genome Wide Association Studies ◽  
Non Coding Rnas

Regardless of advances in detection and treatment, breast cancer affects about 1.5 million women all over the world. Since the last decade, genome-wide association studies (GWAS) have been extensively conducted for breast cancer to define the role of miRNA as a tool for diagnosis, prognosis and therapeutics. MicroRNAs are small, non-coding RNAs that are associated with the regulation of key cellular processes such as cell multiplication, differentiation, and death. They cause a disturbance in the cell physiology by interfering directly with the translation and stability of a targeted gene transcript. MicroRNAs (miRNAs) constitute a large family of non-coding RNAs, which regulate target gene expression and protein levels that affect several human diseases and are suggested as the novel markers or therapeutic targets, including breast cancer. MicroRNA (miRNA) alterations are not only associated with metastasis, tumor genesis but also used as biomarkers for breast cancer diagnosis or prognosis. These are explained in detail in the following review. This review will also provide an impetus to study the role of microRNAs in breast cancer.

scholarly journals Discovery of pluripotency-associated microRNAs in rabbit preimplantation embryos and embryonic stem-like cells

Reproduction ◽  
2013 ◽  
Vol 145 (4) ◽  
pp. 421-437 ◽  
Author(s):  
Pouneh Maraghechi ◽  
László Hiripi ◽  
Gábor Tóth ◽  
Babett Bontovics ◽  
Zsuzsanna Bősze ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Cell Biology ◽  
Embryonic Stem ◽  
Blastocyst Stage ◽  
Expression Level ◽  
Preimplantation Embryos ◽  
Regulatory Function ◽  
Low Level ◽  
Non Coding Rnas

MicroRNAs (miRNAs) are small non-coding RNAs that regulate multiple biological processes. Increasing experimental evidence implies an important regulatory role of miRNAs during embryonic development and in embryonic stem (ES) cell biology. In the current study, we have described and analyzed the expression profile of pluripotency-associated miRNAs in rabbit embryos and ES-like cells. The rabbit specific ocu-miR-302 and ocu-miR-290 clusters, and three homologs of the human C19MC cluster (ocu-miR-512, ocu-miR-520e, and ocu-miR-498) were identified in rabbit preimplantation embryos and ES-like cells. The ocu-miR-302 cluster was highly similar to its human homolog, while ocu-miR-290 revealed a low level of evolutionary conservation with its mouse homologous cluster. The expression of the ocu-miR-302 cluster began at the 3.5 days post-coitum early blastocyst stage and they stayed highly expressed in rabbit ES-like cells. In contrast, a high expression level of the ocu-miR-290 cluster was detected during preimplantation embryonic development, but a low level of expression was found in rabbit ES-like cells. Differential expression of the ocu-miR-302 cluster and ocu-miR-512 miRNA was detected in rabbit trophoblast and embryoblast. We also found that Lefty has two potential target sites in its 3′UTR for ocu-miR-302a and its expression level increased upon ocu-miR-302a inhibition. We suggest that the expression of the ocu-miR-302 cluster is characteristic of the rabbit ES-like cell, while the ocu-miR-290 cluster may play a crucial role during early embryonic development. This study presents the first identification, to our knowledge, of pluripotency-associated miRNAs in rabbit preimplantation embryos and ES-like cells, which can open up new avenues to investigate the regulatory function of ocu-miRNAs in embryonic development and stem cell biology.

scholarly journals Autophagy and Tumor Database: ATdb, a novel database connecting autophagy and tumor

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Kelie Chen ◽  
Dexin Yang ◽  
Fan Zhao ◽  
Shengchao Wang ◽  
Yao Ye ◽  
...  
Keyword(s):  
Dependent Manner ◽  
Post Translational Modifications ◽  
Tumor Subtypes ◽  
Autophagy Gene ◽  
Anti Cancer ◽  
Functional Implications ◽  
Tumor Research ◽  
Non Coding Rnas ◽  
Context Dependent

Abstract Autophagy is an essential cellular process that is closely implicated in diverse pathophysiological processes and a variety of human diseases, especially tumors. Autophagy is regarded as not only an anti-cancer process in tumorigenesis but also a pro-tumor process in progression and metastasis according to current research. It means the role of autophagy in tumor is considered to be complex, controversial and context dependent. Hence, a comprehensive database is of great significance to obtain an in-depth understanding of such complex correlations between autophagy and tumor. To achieve this objective, here we developed the Autophagy and Tumor Database (named as ATdb, http://www.bigzju.com/ATdb/#/) to compile the published information concerning autophagy and tumor research. ATdb connected 25 types of tumors with 137 genes required for autophagy-related pathways, containing 219 population filters, 2650 hazard ratio trend plots, 658 interacting microRNAs, 266 interacting long non-coding RNAs, 155 post-translational modifications, 298 DNA methylation records, 331 animal models and 70 clinical trials. ATdb could enable users to search, browse, download and carry out efficient online analysis. For instance, users can make prediction of autophagy gene regulators in a context-dependent manner and in a precise subpopulation and tumor subtypes. Also, it is feasible in ATdb to cluster tumors into distinguished groups based on the gene-related long non-coding RNAs to gain novel insights into their potential functional implications. Thus, ATdb offers a powerful online database for the autophagy community to explore the complex world of autophagy and tumor. Database URL: http://www.bigzju.com/ATdb/#/

scholarly journals Circular RNA-Centered Regulatory Networks in the Physiopathology of Cardiovascular Diseases

2020 ◽  
Vol 21 (2) ◽  
pp. 456 ◽  
Author(s):  
André F. Gabriel ◽  
Marina C. Costa ◽  
Francisco J. Enguita
Keyword(s):  
Cardiovascular Diseases ◽  
Cell Biology ◽  
Regulatory Networks ◽  
Current Knowledge ◽  
Circular Rna ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Regulatory Rnas ◽  
Eukaryotic Genomes

Non-coding regulatory RNAs are generated as a core output of the eukaryotic genomes, being essential players in cell biology. At the organism level, they are key functional actors in those tissues and organs with limited proliferation capabilities such as the heart. The role of regulatory networks mediated by non-coding RNAs in the pathophysiology of cardiovascular conditions is starting to be unveiled. However, a deeper knowledge of the functional interactions among the diverse non-coding RNA families and their phenotypic consequences is required. This review presents the current knowledge about the functional crosstalk between circRNAs and other biomolecules in the framework of the cardiovascular diseases.

scholarly journals The role of ubiquitination and deubiquitination in cancer metabolism

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Tianshui Sun ◽  
Zhuonan Liu ◽  
Qing Yang
Keyword(s):  
Cancer Metabolism ◽  
Biological Activities ◽  
Redox Homeostasis ◽  
Metabolic Reprogramming ◽  
Post Translational Modification ◽  
Cancer Cell Growth ◽  
Post Translational Modifications ◽  
New Therapeutic Approaches ◽  
Complex Process

Abstract Metabolic reprogramming, including enhanced biosynthesis of macromolecules, altered energy metabolism, and maintenance of redox homeostasis, is considered a hallmark of cancer, sustaining cancer cell growth. Multiple signaling pathways, transcription factors and metabolic enzymes participate in the modulation of cancer metabolism and thus, metabolic reprogramming is a highly complex process. Recent studies have observed that ubiquitination and deubiquitination are involved in the regulation of metabolic reprogramming in cancer cells. As one of the most important type of post-translational modifications, ubiquitination is a multistep enzymatic process, involved in diverse cellular biological activities. Dysregulation of ubiquitination and deubiquitination contributes to various disease, including cancer. Here, we discuss the role of ubiquitination and deubiquitination in the regulation of cancer metabolism, which is aimed at highlighting the importance of this post-translational modification in metabolic reprogramming and supporting the development of new therapeutic approaches for cancer treatment.

Insights into multiple sclerosis provided by non-coding RNAs: meeting summary from the symposium ‘Non-coding RNAs in autoimmune disorders of the central nervous system’ on 5 April 2013 in Warsaw, Poland

2014 ◽  
Vol 20 (11) ◽  
pp. 1439-1442 ◽  
Author(s):  
Marcin P Mycko ◽  
Howard L Weiner ◽  
Krzysztof W Selmaj
Keyword(s):  
Multiple Sclerosis ◽  
Central Nervous System ◽  
Cell Biology ◽  
Potential Role ◽  
Mechanisms Of Action ◽  
Ribonucleic Acids ◽  
The Central Nervous System ◽  
Non Coding Rnas ◽  
Autoimmune Demyelination

More than 80% of the human genome is biochemically active, whereas less than 3% of the genome encodes proteins. The emerging field of non-coding ribonucleic acids (RNAs) that are products of the genome, but do not program proteins, has revolutionized our understanding of cell biology. This was followed by a growing interest in the role of non-coding RNAs in the pathogenesis of human diseases, including multiple sclerosis (MS). In April 2013, a symposium in Warsaw, Poland, was the first meeting entirely dedicated to advances in the understanding of the roles of various subclasses of non-coding RNAs and showcased their involvement in autoimmune demyelination and MS. New mechanisms of action of small non-coding RNAs, as well as the advent of long non-coding RNAs were discussed, including the potential role of non-coding RNAs as MS biomarkers and their use for therapeutic intervention in MS.

scholarly journals Deletion at an 1q24 locus reveals a critical role of long noncoding RNA DNM3OS in skeletal development

2020 ◽  
Author(s):  
Ting-ting Yu ◽  
Qiu-fan Xu ◽  
Hui-jie Huang ◽  
Sarah Dugan ◽  
Lei Shao ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Endochondral Ossification ◽  
Bone Growth ◽  
Skeletal Development ◽  
Critical Role ◽  
Chondrocyte Proliferation ◽  
Complex Processes ◽  
Opposite Strand ◽  
Non Coding Rnas

Abstract Background: Skeletal development and maintenance are complex processes known to be coordinated by multiple genetic and epigenetic signaling pathways. However, the role of long non-coding RNAs (lncRNAs), a class of crucial epigenetic regulatory molecules, has been under explored in skeletal biology. Results: Here we report a young patient with short stature, hypothalamic dysfunction and mild macrocephaly, who carries a maternally inherited 690kb deletion at Chr.1q24.2 encompassing a noncoding RNA gene, DNM3OS, embedded on the opposite strand in an intron of the DYNAMIN 3 (DNM3)gene. We show that lncRNA DNM3OS sustains the proliferation of chondrocytes independent of two co-cistronic microRNAs miR-199a and miR-214. We further show that nerve growth factor (NGF), a known factor of chondrocyte growth, is a key target of DNM3OS-mediated control of chondrocyte proliferation.Conclusion: This work demonstrates that DNM3OS is essential for preventing premature differentiation of chondrocytes required for bone growth through endochondral ossification.

scholarly journals Regulation of Hippo, TGFβ/SMAD, Wnt/β-Catenin, JAK/STAT, and NOTCH by Long Non-Coding RNAs in Pancreatic Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Ammad Ahmad Farooqi ◽  
Sawera Nayyab ◽  
Chiara Martinelli ◽  
Rossana Berardi ◽  
Hector Katifelis ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Genetic Material ◽  
Post Translational Modifications ◽  
Non Coding Rna ◽  
Competitive Endogenous Rnas ◽  
Non Coding Rnas ◽  
Underlying Mechanisms ◽  
Molecular Pathophysiology ◽  
Modern Era

Rapidly evolving and ever-increasing knowledge of the molecular pathophysiology of pancreatic cancer has leveraged our understanding altogether to a next level. Compared to the exciting ground-breaking discoveries related to underlying mechanisms of pancreatic cancer onset and progression, however, there had been relatively few advances in the therapeutic options available for the treatment. Since the discovery of the DNA structure as a helix which replicates semi-conservatively to pass the genetic material to the progeny, there has been conceptual refinement and continuous addition of missing pieces to complete the landscape of central dogma. Starting from transcription to translation, modern era has witnessed non-coding RNA discovery and central role of these versatile regulators in onset and progression of pancreatic cancer. Long non-coding RNAs (lncRNAs) have been shown to act as competitive endogenous RNAs through sequestration and competitive binding to myriad of microRNAs in different cancers. In this article, we set spotlight on emerging evidence of regulation of different signaling pathways (Hippo, TGFβ/SMAD, Wnt/β-Catenin, JAK/STAT and NOTCH) by lncRNAs. Conceptual refinements have enabled us to understand how lncRNAs play central role in post-translational modifications of various proteins and how lncRNAs work with epigenetic-associated machinery to transcriptionally regulate gene network in pancreatic cancer.

scholarly journals Neural Precursor Cells Expanded Inside the 3D Micro-Scaffold Nichoid Present Different Non-Coding RNAs Profiles and Transcript Isoforms Expression: Possible Epigenetic Modulation by 3D Growth

Biomedicines ◽  
2021 ◽  
Vol 9 (9) ◽  
pp. 1120
Author(s):  
Letizia Messa ◽  
Bianca Barzaghini ◽  
Federica Rey ◽  
Cecilia Pandini ◽  
Gian Vincenzo Zuccotti ◽  
...  
Keyword(s):  
Cell Biology ◽  
Cellular Response ◽  
Precursor Cells ◽  
Neural Precursor Cells ◽  
Functional Enrichment ◽  
Neural Precursor ◽  
Mechanical Stimuli ◽  
3D Scaffold ◽  
Non Coding Rnas

Non-coding RNAs show relevant implications in various biological and pathological processes. Thus, understanding the biological implications of these molecules in stem cell biology still represents a major challenge. The aim of this work is to study the transcriptional dysregulation of 357 non-coding genes, found through RNA-Seq approach, in murine neural precursor cells expanded inside the 3D micro-scaffold Nichoid versus standard culture conditions. Through weighted co-expression network analysis and functional enrichment, we highlight the role of non-coding RNAs in altering the expression of coding genes involved in mechanotransduction, stemness, and neural differentiation. Moreover, as non-coding RNAs are poorly conserved between species, we focus on those with human homologue sequences, performing further computational characterization. Lastly, we looked for isoform switching as possible mechanism in altering coding and non-coding gene expression. Our results provide a comprehensive dissection of the 3D scaffold Nichoid’s influence on the biological and genetic response of neural precursor cells. These findings shed light on the possible role of non-coding RNAs in 3D cell growth, indicating that also non-coding RNAs are implicated in cellular response to mechanical stimuli.

scholarly journals An atlas of genetic variation for linking pathogen-induced cellular traits to human disease

2017 ◽  
Author(s):  
Liuyang Wang ◽  
Kelly J. Pittman ◽  
Jeffrey R. Barker ◽  
Raul E. Salinas ◽  
Ian B. Stanaway ◽  
...  
Keyword(s):  
Cell Biology ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Disease Mechanisms ◽  
Genome Wide ◽  
Emerge Network ◽  
Inflammatory Bowel ◽  
Association Data ◽  
Genome Wide Significance

SummaryGenome-wide association studies (GWAS) have identified thousands of genetic variants associated with disease. To facilitate moving from associations to disease mechanisms, we leveraged the role of pathogens in shaping human evolution with the Hi-HOST Phenome Project (H2P2): a catalog of cellular GWAS comprised of 79 phenotypes in response to 8 pathogens in 528 lymphoblastoid cell lines. Seventeen loci surpass genome-wide significance (p<5×10−8) for phenotypes ranging from pathogen replication to cytokine production. Combining H2P2 with clinical association data from the eMERGE Network and experimental validation revealed evidence for mechanisms of action and connections with diseases. We identified a SNP near CXCL10 as a cis-cytokine-QTL and a new risk factor for inflammatory bowel disease. A SNP in ZBTB20 demonstrated pleiotropy, partially mediated through NFκB signaling, and was associated with viral hepatitis. Data are available in an H2P2 web portal to facilitate further interpreting human genome variation through the lens of cell biology.

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