scholarly journals Circular RNAs in osteoarthritis: indispensable regulators and novel strategies in clinical implications

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Wenchao Zhang ◽  
Lin Qi ◽  
Ruiqi Chen ◽  
Jieyu He ◽  
Zhongyue Liu ◽  
...  
Keyword(s):  
Hot Spot ◽  
Circular Rnas ◽  
Clinical Implications ◽  
Biological Processes ◽  
Future Directions ◽  
The Past ◽  
Prevalent Disease ◽  
Post Traumatic ◽  
Socioeconomic Burden ◽  
Insight Into

AbstractOver the past decades, circular RNAs (circRNAs) have emerged as a hot spot and sparked intensive interest. Initially considered as the transcriptional noises, further studies have indicated that circRNAs are crucial regulators in multiple cellular biological processes, and thus engage in the development and progression of many diseases including osteoarthritis (OA). OA is a prevalent disease that mainly affects those aging, obese and post-traumatic population, posing as a major source of socioeconomic burden. Recently, numerous circRNAs have been found aberrantly expressed in OA tissues compared with counterparts. More importantly, circRNAs have been demonstrated to interplay with components in OA microenvironments, such as chondrocytes, synoviocytes and macrophages, by regulation of their proliferation, apoptosis, autophagy, inflammation, or extracellular matrix reorganization. Herein, in this review, we extensively summarize the roles of circRNAs in OA microenvironment, progression, and putative treatment, as well as envision the future directions for circRNAs research in OA, with the aim to provide a novel insight into this field.

Comparison and Analysis of Computational Methods for Identifying N6 - methyladenosine Sites in Saccharomyces Cerevisiae

2020 ◽  
Vol 26 ◽  
Author(s):  
Pengmian Feng ◽  
Lijing Feng ◽  
Chaohui Tang
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Computational Methods ◽  
Computational Analysis ◽  
Computational Prediction ◽  
Experimental Methods ◽  
Biological Processes ◽  
Biological Functions ◽  
Precise Location ◽  
Future Directions ◽  
The Past

Background and Purpose: N 6 -methyladenosine (m6A) plays critical roles in a broad set of biological processes. Knowledge about the precise location of m6A site in the transcriptome is vital for deciphering its biological functions. Although experimental techniques have made substantial contributions to identify m6A, they are still labor intensive and time consuming. As good complements to experimental methods, in the past few years, a series of computational approaches have been proposed to identify m6A sites. Methods: In order to facilitate researchers to select appropriate methods for identifying m6A sites, it is necessary to give a comprehensive review and comparison on existing methods. Results: Since researches on m6A in Saccharomyces cerevisiae are relatively clear, in this review, we summarized recent progresses on computational prediction of m6A sites in S. cerevisiae and assessed the performance of existing computational methods. Finally, future directions of computationally identifying m6A sites were presented. Conclusion: Taken together, we anticipate that this review will provide important guides for computational analysis of m 6A modifications.

scholarly journals Chronic Myelomonocytic Leukemia—Hematopathology Perspective

2021 ◽  
Author(s):  
Siba El Hussein ◽  
Sa A. Wang ◽  
Naveen Pemmaraju ◽  
Joseph D. Khoury ◽  
Sanam Loghavi
Keyword(s):  
Risk Stratification ◽  
Large Scale ◽  
Chronic Myelomonocytic Leukemia ◽  
Clinical Implications ◽  
The Past ◽  
Genomic Landscape ◽  
Sequencing Studies ◽  
Myelomonocytic Leukemia ◽  
Insight Into

ABSTRACT Our understanding of chronic myelomonocytic leukemia (CMML) has evolved tremendously over the past decade. Large-scale sequencing studies have led to increased insight into the genomic landscape of CMML and clinical implications of these changes. This in turn has resulted in refined and improved risk stratification models, which to date remain versatile and subject to remodeling, as new and evolving studies continue to refine our understanding of this disease. In this article, we present an up-to-date review of CMML from a hematopathology perspective, while providing a clinically practical summary that sheds light on the constant evolution of our understanding of this disease.

scholarly journals Trends in the development of miRNA bioinformatics tools

2019 ◽  
Vol 20 (5) ◽  
pp. 1836-1852 ◽  
Author(s):  
Liang Chen ◽  
Liisa Heikkinen ◽  
Changliang Wang ◽  
Yang Yang ◽  
Huiyan Sun ◽  
...  
Keyword(s):  
Hot Spots ◽  
Target Prediction ◽  
Future Directions ◽  
Regulate Gene Expression ◽  
Small Noncoding Rnas ◽  
The Past ◽  
Manual Curation ◽  
Bioinformatics Tools ◽  
Insight Into ◽  
Epigenetic Processes

Abstract MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and ∼1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools.

scholarly journals A Guided Tour of the Structural Biology of Gaucher Disease: Acid-β-Glucosidase and Saposin C

2011 ◽  
Vol 2011 ◽  
pp. 1-15 ◽  
Author(s):  
Raquel L. Lieberman
Keyword(s):  
Crystal Structures ◽  
Structural Biology ◽  
Gaucher Disease ◽  
Lysosomal Storage ◽  
The Past ◽  
Current State ◽  
Saposin C ◽  
Prevalent Disease ◽  
Guided Tour ◽  
Insight Into

Mutations in both acid-β-glucosidase (GCase) and saposin C lead to Gaucher disease, the most common lysosomal storage disorder. The past several years have seen an explosion of structural and biochemical information for these proteins, which have provided new insight into the biology and pathogenesis of Gaucher disease, as well as opportunities for new therapeutic directions. Nearly 20 crystal structures of GCase are now available, from different heterologous sources, complexed with different ligands in the active site, in different glycosylation states, as well as one that harbors a prevalent disease-causing mutation, N370S. For saposin C, two NMR and 3 crystal structures have been solved, each with its unique snapshot. This review focuses on the details of these structures to highlight salient common and disparate features that contribute to our current state of knowledge of this complex orphan disease.

scholarly journals N6-Methyladenosine Modification Opens a New Chapter in Circular RNA Biology

2021 ◽  
Vol 9 ◽  
Author(s):  
Jun Wu ◽  
Xin Guo ◽  
Yi Wen ◽  
Shangqing Huang ◽  
Xiaohui Yuan ◽  
...  
Keyword(s):  
Cellular Localization ◽  
Circular Rna ◽  
Regulatory Mechanisms ◽  
Circular Rnas ◽  
Biological Functions ◽  
Future Directions ◽  
Rna Molecules ◽  
Physiological Processes ◽  
Rna Biology ◽  
Insight Into

As the most abundant internal modification in eukaryotic cells, N6-methyladenosine (m6A) in mRNA has shown widespread regulatory roles in a variety of physiological processes and disease progressions. Circular RNAs (circRNAs) are a class of covalently closed circular RNA molecules and play an essential role in the pathogenesis of various diseases. Recently, accumulating evidence has shown that m6A modification is widely existed in circRNAs and found its key biological functions in regulating circRNA metabolism, including biogenesis, translation, degradation and cellular localization. Through regulating circRNAs, studies have shown the important roles of m6A modification in circRNAs during immunity and multiple diseases, which represents a new layer of control in physiological processes and disease progressions. In this review, we focused on the roles played by m6A in circRNA metabolism, summarized the regulatory mechanisms of m6A-modified circRNAs in immunity and diseases, and discussed the current challenges to study m6A modification in circRNAs and the possible future directions, providing a comprehensive insight into understanding m6A modification of circRNAs in RNA epigenetics.

scholarly journals Metabolomic Interactions: An Insight into Health and Disease

2021 ◽  
pp. 61-67
Author(s):  
Maheswara Reddy Mallu ◽  
Shaik Mohammad Anjum ◽  
Sai Sri Samyutha Katravulapalli ◽  
Sri Sai Priya Avuthu ◽  
Koteswara Reddy Gujjula ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Human Body ◽  
Metabolic Pathways ◽  
Biological Processes ◽  
Therapeutic Treatment ◽  
The Past ◽  
Metabolic Functions ◽  
Health And Disease ◽  
Metabolic Reactions ◽  
Insight Into

Over the past decade, metabolic engineering has emerged as an active and distinct discipline characterized by its over-arching emphasis on integration. In practice, metabolic engineering is the directed improvement of cellular properties through the application of modern genetic methods. The concept of metabolic regulations deals with the varied and innumerable metabolic pathways that are present in the human body. A combination of such metabolic reactions paves the way to the proper functioning of different physiological and biological processes. Dealing with the adversities of a disease, engineering of novel metabolic pathways showcases the potential of metabolic engineering and its application in the therapeutic treatment of diseases. A proper and deeper understanding of the metabolic functions in the human body can be known from simulated yeast models. This review gives a brief understanding about the interactions between the molecular set of metabolome and its complexity.

scholarly journals The History of Gene Hunting in Hereditary Spinocerebellar Degeneration: Lessons From the Past and Future Perspectives

2021 ◽  
Vol 12 ◽  
Author(s):  
Ashraf Yahia ◽  
Giovanni Stevanin
Keyword(s):  
Precision Medicine ◽  
Correct Diagnosis ◽  
Biological Processes ◽  
Spinocerebellar Degeneration ◽  
Complex Disorders ◽  
The Past ◽  
History Of ◽  
Health And Disease ◽  
Gene Hunting ◽  
Insight Into

Hereditary spinocerebellar degeneration (SCD) encompasses an expanding list of rare diseases with a broad clinical and genetic heterogeneity, complicating their diagnosis and management in daily clinical practice. Correct diagnosis is a pillar for precision medicine, a branch of medicine that promises to flourish with the progressive improvements in studying the human genome. Discovering the genes causing novel Mendelian phenotypes contributes to precision medicine by diagnosing subsets of patients with previously undiagnosed conditions, guiding the management of these patients and their families, and enabling the discovery of more causes of Mendelian diseases. This new knowledge provides insight into the biological processes involved in health and disease, including the more common complex disorders. This review discusses the evolution of the clinical and genetic approaches used to diagnose hereditary SCD and the potential of new tools for future discoveries.

scholarly journals Circular RNAs in Hedgehog Signaling Activation and Hedgehog-Mediated Medulloblastoma Tumors

Cancers ◽  
2021 ◽  
Vol 13 (20) ◽  
pp. 5138
Author(s):  
Ani Azatyan ◽  
Shasha Zhang ◽  
Anna Darabi ◽  
Peter Siesjö ◽  
Ting Wang ◽  
...  
Keyword(s):  
Brain Function ◽  
Hedgehog Signaling ◽  
Low Frequency ◽  
Circular Rna ◽  
Circular Rnas ◽  
Cerebellar Tumor ◽  
Biological Processes ◽  
The Past ◽  
Signaling Activation ◽  
Normal Cerebellum

Within the past decade, circular RNAs have largely emerged as novel regulators of human biology, including brain function and cancer development. On the other hand, the Hedgehog pathway has established roles in regulating biological processes, including tumorigenesis. Here, the circular RNA transcriptome, in the context of Hedgehog signaling activation of medulloblastoma Daoy and human embryonic palatal mesenchyme HEPM cells, was determined. In total, 29 out of the 30 selected circular RNAs were validated by Sanger sequencing, with some regulated to a limited extent by Hedgehog signaling. Interestingly, back-spliced junctions, the marker of exonic RNA circles, were also identified at a low frequency within poly (A) mRNAs, reflecting exon repetition events. Thirteen circular RNAs had reduced expression in human medulloblastoma tumors in comparison to normal cerebellum. For seven out of these thirteen RNA circles, the linear mRNAs originating from the same genes did not exhibit a reduced expression. Depletion and/or overexpression of these seven circular RNAs minimally affected medulloblastoma cell proliferation. These findings highlight that differential expression of a gene product may not necessarily elicit an obvious phenotypic impact. Consequently, further analysis is required to determine the possible subtle contributions to the development of this cerebellar tumor.

scholarly journals Perspectives and future directions for epigenetics in hematology

Blood ◽  
2013 ◽  
Vol 121 (26) ◽  
pp. 5131-5137 ◽  
Author(s):  
Margaret A. Goodell ◽  
Lucy A. Godley
Keyword(s):  
Hematologic Malignancies ◽  
Mechanisms Of Action ◽  
Future Research ◽  
Clinical Implications ◽  
Future Directions ◽  
The Past ◽  
Pleiotropic Action ◽  
Epigenetic Regulators ◽  
Underlying Mechanisms

AbstractGenetic analysis of hematologic malignancies over the past 5 years has revealed abundant mutations in epigenetic regulators in all classes of disorders. Here, we summarize the observations made within our review series on the role of epigenetics in hematology. We highlight the clinical implications of mutations in epigenetic regulators and outline what we envision are some of the major areas that merit future research. Recent findings may have immediate prognostic value, but also offer new targets for drug development. However, the pleiotropic action of these regulators indicates caution is warranted and argues for investment in understanding of their underlying mechanisms of action as we proceed to exploit these findings for the benefit of patients.

Alcoholism: Development of the Diagnostic Concept

1994 ◽  
Vol 28 (2) ◽  
pp. 205-211 ◽  
Author(s):  
Doug Sellman
Keyword(s):  
Alcohol Dependence ◽  
Classification Systems ◽  
Withdrawal Symptoms ◽  
Clinical Implications ◽  
International Consensus ◽  
Future Directions ◽  
The Past ◽  
Icd 10 ◽  
Alcohol Dependence Syndrome ◽  
Key Aspects

This paper traces the diagnostic concepts of alcoholism featured in the major classification systems over the past 40 years. The description of alcoholism as a diagnostic concept has undergone considerable transformation over this time, but an international consensus now exists in the DSM-IIIR [2] criteria and ICD-10 [3]. Alcoholism is equated with alcohol dependence, and both definitions draw largely on the description of the alcohol dependence syndrome by Edwards and Gross [4]. Although the presence of withdrawal symptoms and relief use (key aspects of so-called physical addiction) is part of both systems, they are not necessary to make the diagnosis in either. Future directions and clinical implications of these developments are discussed.

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