scholarly journals The Emerging Roles of RNA Modifications in Glioblastoma

Cancers ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 736 ◽  
Author(s):  
Zhen Dong ◽  
Hongjuan Cui
Keyword(s):  
Tumor Type ◽  
Messenger Rnas ◽  
Rna Modifications ◽  
Transfer Rnas ◽  
Pathological Mechanism ◽  
Fast Development ◽  
Living Organisms ◽  
Almost All ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Glioblastoma (GBM) is a grade IV glioma that is the most malignant brain tumor type. Currently, there are no effective and sufficient therapeutic strategies for its treatment because its pathological mechanism is not fully characterized. With the fast development of the Next Generation Sequencing (NGS) technology, more than 170 kinds of covalent ribonucleic acid (RNA) modifications are found to be extensively present in almost all living organisms and all kinds of RNAs, including ribosomal RNAs (rRNAs), transfer RNAs (tRNAs) and messenger RNAs (mRNAs). RNA modifications are also emerging as important modulators in the regulation of biological processes and pathological progression, and study of the epi-transcriptome has been a new area for researchers to explore their connections with the initiation and progression of cancers. Recently, RNA modifications, especially m6A, and their RNA-modifying proteins (RMPs) such as methyltransferase like 3 (METTL3) and α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5), have also emerged as important epigenetic mechanisms for the aggressiveness and malignancy of GBM, especially the pluripotency of glioma stem-like cells (GSCs). Although the current study is just the tip of an iceberg, these new evidences will provide new insights for possible GBM treatments. In this review, we summarize the recent studies about RNA modifications, such as N6-methyladenosine (m6A), N6,2′O-dimethyladenosine (m6Am), 5-methylcytosine (m5C), N1-methyladenosine (m1A), inosine (I) and pseudouridine (ψ) as well as the corresponding RMPs including the writers, erasers and readers that participate in the tumorigenesis and development of GBM, so as to provide some clues for GBM treatment.

scholarly journals Human Papillomavirus and the Development of Different Cancers

2016 ◽  
Vol 150 (3-4) ◽  
pp. 185-193 ◽  
Author(s):  
Ge Gao ◽  
David I. Smith
Keyword(s):  
Cervical Cancer ◽  
Squamous Cell Carcinomas ◽  
Human Papillomaviruses ◽  
Whole Genome ◽  
Physical Status ◽  
Cervical Cancers ◽  
Mate Pair ◽  
Almost All ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Human papillomaviruses (HPV) are responsible for the development of almost all cervical cancers. HPV is also found in 85% of anal cancer and in 50% of penile, vulvar, and vaginal cancers, and they are increasingly found in a subset of head and neck cancers, i.e., oropharyngeal squamous cell carcinomas (OPSCC). The model for how HPV causes cancer is derived from several decades of study on cervical cancer, and it is just presumed that this model is not only completely valid for cervical cancer but for all other HPV-driven cancers as well. Next-generation sequencing (NGS) has now provided the necessary tools to characterize genomic alterations in cancer cells and can precisely determine the physical status of HPV in those cells as well. We discuss recent discoveries from different applications of NGS in both cervical cancer and OPSCCs, including whole-genome sequencing and mate-pair NGS. We also discuss what NGS studies have revealed about the different ways that HPV can be involved in cancer formation, specifically comparing cervical cancer and OPSCC.

scholarly journals Comparison of Next-Generation Sequencing Systems

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Lin Liu ◽  
Yinhu Li ◽  
Siliang Li ◽  
Ni Hu ◽  
Yimin He ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genomic Sequence ◽  
Sequence Information ◽  
Ion Torrent ◽  
Next Generation ◽  
Extensive Experience ◽  
Ion Torrent Pgm ◽  
Fast Development ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world’s biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.

CLO19-034: The Clinical Outcomes of Next-Generation Sequencing Testing at a Community Oncology Practice

2019 ◽  
Vol 17 (3.5) ◽  
pp. CLO19-034
Author(s):  
Christie Hancock ◽  
Jacob Bitran
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Management ◽  
Tumor Biology ◽  
Therapeutic Interventions ◽  
Tumor Type ◽  
Next Generation ◽  
Hormone Receptor Positive ◽  
Oncology Practice ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Background: The value of next-generation sequencing (NGS) tests is dependent on how it changes clinical management, if at all. There are not any guidelines on when a physician should obtain testing; what certain genetic variations can be clinically, meaningfully intervened on; and if this active drug is financially practical. A NGS test ideally should identify a targetable mutational profile that leads to a treatment that can be obtained and produces lasting responses. We reviewed the NGS testing practices at our community hospital. Methods: Patients in our oncology clinic that underwent NGS testing of their tumor were reviewed. Specifically, the patient’s age, gender, diagnosis, date of diagnosis, previous lines of treatment, date of NGS testing, and reported molecular targets were recorded. Details of the changes in clinical management based on the NGS and survival time after the NGS test was ordered were also analyzed. Results: Forty-three patient cases were reviewed that had NGS testing obtained between the years 2014–2015 and 2017. Eighteen patients were males and 25 were females. Median age was 60 years. Most common tumor type was breast; 3 were triple-negative and 6 were only hormone-receptor positive. Second most common type was colorectal. NGS changed management in 12 cases. Two patients were able to enter a clinical trial and the other 10 had therapeutic changes based on protein or mRNA overexpression. Median time of change in management to survival in these patients was 7 months. Thirty-seven patients died; overall time from ordering of test to death was 7 months. Overall time of ordering test to survival for all patients was 8 months. Conclusions: NGS gathers a significant amount of information of a patient’s cancer, but this information is difficult to interpret in the clinical setting. Twenty-eight percent of our patients had a change in treatment, but this did not translate into lasting responses compared to other patients. Furthermore, the responses that were seen may have not been related to the therapeutic interventions, but intrinsic tumor biology. It is important to be aware of the clinical utility in ordering these tests for both the physician and patient.

RNA Sequencing of Formalin-Fixed and Paraffin-Embedded Tissue as a Complementary Method in Ophthalmopathology

2020 ◽  
Vol 237 (07) ◽  
pp. 860-866
Author(s):  
Günther Schlunck ◽  
Stefaniya Boneva ◽  
Julian Wolf ◽  
Anja Schlecht ◽  
Thomas Reinhard ◽  
...  
Keyword(s):  
Cost Effective ◽  
Messenger Rnas ◽  
Rna Molecules ◽  
Complementary Method ◽  
High Throughput Method ◽  
Next Generation Sequencing Ngs ◽  
Insight Into ◽  
Generation Sequencing ◽  
Formalin Fixed ◽  
Methodological Strategy

AbstractThe high-throughput method of “Next Generation Sequencing” (NGS) allows cost-effective decoding of the nucleotide sequences of millions of RNA molecules in a sample. This makes it possible to determine the number of distinct RNA molecules in tissues or cells and to use these data to draw conclusions. The entirety of RNAs, in particular mRNAs (messenger RNAs) as potential precursors of proteins, provides a comprehensive insight into the functional state of the cells and tissues under investigation. In addition to cell cultures or unfixed tissue, formalin-fixed and paraffin-embedded (FFPE) tissue can also be analysed for this purpose using specific methods. In this overview, the methodological strategy and its application to the field of ophthalmic histopathology are presented.

scholarly journals Molecular and Genetic Mechanism of Non-Syndromic Congenital Cataracts. Mutation Screening in Spanish Families

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 580
Author(s):  
Celia Fernández-Alcalde ◽  
María Nieves-Moreno ◽  
Susana Noval ◽  
Jesús M. Peralta ◽  
Victoria E. F. Montaño ◽  
...  
Keyword(s):  
De Novo ◽  
Mutation Screening ◽  
Disease Genes ◽  
De Novo Mutations ◽  
Congenital Cataracts ◽  
Pathogenic Variants ◽  
Unknown Significance ◽  
Almost All ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Our purpose was to identify mutations responsible for non-syndromic congenital cataracts through the implementation of next-generation sequencing (NGS) in our center. A sample of peripheral blood was obtained from probands and willing family members and genomic DNA was extracted from leukocytes. DNA was analyzed implementing a panel (OFTv2.1) including 39 known congenital cataracts disease genes. 62 probands from 51 families were recruited. Pathogenic or likely pathogenic variants were identified in 32 patients and 25 families; in 16 families (64%) these were de novo mutations. The mutation detection rate was 49%. Almost all reported mutations were autosomal dominant. Mutations in crystallin genes were found in 30% of the probands. Mutations in membrane proteins were detected in seven families (two in GJA3 and five in GJA8). Mutations in LIM2 and MIP were each found in three families. Other mutations detected affected EPHA2, PAX6, HSF4 and PITX3. Variants classified as of unknown significance were found in 5 families (9.8%), affecting CRYBB3, LIM2, EPHA2, ABCB6 and TDRD7. Mutations lead to different cataract phenotypes within the same family.

scholarly journals Is Next-Generation Sequencing Alone Sufficient to Reliably Diagnose Gliomas?

2020 ◽  
Vol 79 (7) ◽  
pp. 763-766 ◽  
Author(s):  
Kwok Ling Kam ◽  
Christina L Appin ◽  
Qinwen Mao ◽  
Sachie Ikegami ◽  
Rimas V Lukas ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Tumor Location ◽  
Study Cohort ◽  
Tumor Type ◽  
Next Generation ◽  
Optimal Patient Care ◽  
Histologic Evaluation ◽  
Grade Ii ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract The power and widespread use of next-generation sequencing (NGS) in surgical neuropathology has raised questions as to whether NGS might someday fully supplant histologic-based examination. We therefore sought to determine the feasibility of relying on NGS alone for diagnosing infiltrating gliomas. A total of 171 brain lesions in adults, all of which had been analyzed by GlioSeq NGS, comprised the study cohort. Each case was separately diagnosed by 6 reviewers, based solely on age, sex, tumor location, and NGS results. Results were compared with the final integrated diagnoses and scored on the following scale: 0 = either wrong tumor type or correct tumor type but off by 2+ grades; 1 = off by 1 grade; 2 = exactly correct. Histology alone was treated as a seventh reviewer. Overall reviewer accuracy ranged from 81.6% to 94.2%, while histology alone scored 87.1%. For glioblastomas, NGS was more accurate than histology alone (93.8%–97.9% vs 87.5%). The NGS accuracy for grade II and III astrocytoma and oligodendroglioma was only 54.3%–84.8% and 34.4%–87.5%, respectively. Most uncommon gliomas, including BRAF-driven tumors, could not be accurately classified just by NGS. These data indicate that, even in this era of advanced molecular diagnostics, histologic evaluation is still an essential part of optimal patient care.

scholarly journals Novel NGS Pipeline for Virus Discovery from a Wide Spectrum of Hosts and Sample Types

2020 ◽  
Author(s):  
Ilya Plyusnin ◽  
Ravi Kant ◽  
Anne J. Jääskeläinen ◽  
Tarja Sironen ◽  
Liisa Holm ◽  
...  
Keyword(s):  
Wide Spectrum ◽  
Domestic Animals ◽  
Metagenomic Data ◽  
Virus Discovery ◽  
Taxonomic Profiling ◽  
Sequencing Technologies ◽  
Living Organisms ◽  
Next Generation Sequencing Ngs ◽  
Microbiome Data ◽  
Generation Sequencing

ABSTRACTThe study of the microbiome data holds great potential for elucidating the biological and metabolic functioning of living organisms and their role in the environment. Metagenomic analyses have shown that humans, along with e.g. domestic animals, wildlife and arthropods, are colonized by an immense community of viruses. The current Coronavirus pandemic (COVID-19) heightens the need to rapidly detect previously unknown viruses in an unbiased way. The increasing availability of metagenomic data in this era of next-generation sequencing (NGS), along with increasingly affordable sequencing technologies, highlight the need for reliable and comprehensive methods to manage such data. In this article, we present a novel stand-alone pipeline called LAZYPIPE for identifying both previously known and novel viruses in host-associated or environmental samples and give examples of virus discovery based on it. LAZYPIPE is a Unix-based pipeline for automated assembling and taxonomic profiling of NGS libraries implemented as a collection of C++, Perl, and R scripts.

scholarly journals DNA metabarcoding allows non-invasive identification of arthropod prey provisioned to nestling Rufous hummingbirds (Selasphorus rufus)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6596 ◽  
Author(s):  
Alison J. Moran ◽  
Sean W.J. Prosser ◽  
Jonathan A. Moran
Keyword(s):  
Alimentary Tract ◽  
Selasphorus Rufus ◽  
Non Invasive ◽  
Single Pellet ◽  
Wide Range ◽  
Dna Metabarcoding ◽  
Rufous Hummingbird ◽  
Almost All ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Hummingbirds consume sugars from nectar, sap and honeydew, and obtain protein, fat and minerals from arthropods. To date, the identity of arthropod taxa in hummingbird diets has been investigated by observation of foraging or examination of alimentary tract contents. Direct examination of nestling provisioning adds the extra complication of disturbance to the young and mother. Here, we show that arthropod food items provisioned to Rufous hummingbird (Selasphorus rufus) nestlings can be identified by a safe and non-invasive protocol using next-generation sequencing (NGS) of DNA from nestling fecal pellets collected post-fledging. We found that females on southern Vancouver Island (British Columbia, Canada) provisioned nestlings with a wide range of arthropod taxa. The samples examined contained three Classes, eight Orders, 48 Families, and 87 Genera, with from one to 15 Families being identified in a single pellet. Soft-bodied Dipterans were found most frequently and had the highest relative abundance; hard-bodied prey items were absent from almost all samples. Substantial differences in taxa were found within season and between years, indicating the importance of multi-year sampling when defining a prey spectrum.

scholarly journals Detection and Analysis of RNA Ribose 2′-O-Methylations: Challenges and Solutions

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 642 ◽  
Author(s):  
Yuri Motorin ◽  
Virginie Marchand
Keyword(s):  
Messenger Rnas ◽  
Small Nucleolar Rnas ◽  
Rna Modifications ◽  
Site Specific ◽  
Transfer Rnas ◽  
Small Nuclear Rnas ◽  
Regulatory Rnas ◽  
Traditional Approaches ◽  
Nucleolar Rnas ◽  
Made In

Ribose 2′-O-methylation is certainly one of the most common RNA modifications found in almost any type of cellular RNA. It decorates transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), small nuclear RNAs (snRNAs) (and most probably small nucleolar RNAs, snoRNAs), as well as regulatory RNAs like microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), and finally, eukaryotic messenger RNAs (mRNAs). Due to this exceptional widespread of RNA 2′-O-methylation, considerable efforts were made in order to precisely map these numerous modifications. Extensive studies of RNA 2′-O-methylation were also stimulated by the discovery of C/D-box snoRNA-guided machinery, which insures site-specific modification of hundreds 2′-O-methylated residues in archaeal and eukaryotic rRNAs and some other RNAs. In this brief review we discussed both traditional approaches of RNA biochemistry and also modern deep sequencing-based methods, used for detection/mapping and quantification of RNA 2′-O-methylations.

INSIDE INDUSTRY

2015 ◽  
Vol 19 (03) ◽  
pp. 61-66
Keyword(s):  
Multiple Sclerosis ◽  
Next Generation Sequencing ◽  
Drug Abuse ◽  
Oral Treatment ◽  
Rna Modifications ◽  
First Line ◽  
Young Investigator ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Collaboration Agreement

Helsinn Group signs exclusive agreement with Mundipharma for distribution and licensing of netupitant/palonosetron (NEPA) in Brazil. CrystalGenomics partners with Daewoong Pharmaceutical for Acelex commercialization in Korea. Roche acquires Signature Diagnostics to advance translational research for next generation sequencing (NGS) diagnostics. Boehringer Ingelheim renews global technology collaboration agreement with VTU Technology. Maverix wins $150,000 STTR Award by the National Institute on Drug Abuse for detection of RNA modifications. Rosetta Genomics receives first patent allowance in Japan. First-line oral treatment for multiple sclerosis approved in India. LKCMedicine scientist wins Young Investigator Award at 40th Lorne Conference.

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