Prospects Of Non-Coding Elements In Genomic Dna Based Gene Therapy

Potential Use ◽

: Gene therapy has made significant development since the commencement of the first clinical trials a few decades ago and has remained a dynamic area of research regardless of obstacles such as immune response and insertional mutagenesis. Progression in various technologies like next-generation sequencing (NGS) and nanotechnology has established the importance of non-coding segments of a genome, thereby taking gene therapy to the next level. In this review, we have summarized the importance of non-coding elements, highlighting the advantages of using full-length genomic DNA loci (gDNA) compared to complementary DNA (cDNA) or minigene, currently used in gene therapy. The focus of this review is to provide an overview of the advances and the future of potential use of gDNA loci in gene therapy, expanding the therapeutic repertoire in molecular medicine.

The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers

Life ◽

10.3390/life10100228 ◽

2020 ◽

Vol 10 (10) ◽

pp. 228

Author(s):

Soyeon Kim ◽

Joo Won Lee ◽

Young-Seok Park

Keyword(s):

Next Generation Sequencing ◽

Oral Cancer ◽

Genetic Alterations ◽

Eligibility Criterion ◽

Next Generation ◽

Novel Biomarkers ◽

Targeted Gene Therapy ◽

Potential Use ◽

Despite the introduction of next-generation sequencing in the realm of DNA sequencing technology, it is not often used in the investigation of oral squamous cell carcinoma (OSCC). Oral cancer is one of the most frequently occurring malignancies in some parts of the world and has a high mortality rate. Patients with this malignancy are likely to have a poor prognosis and may suffer from severe facial deformity or mastication problems even after successful treatment. Therefore, a thorough understanding of this malignancy is essential to prevent and treat it. This review sought to highlight the contributions of next-generation sequencing (NGS) in unveiling the genetic alterations and differential expressions of miRNAs involved in OSCC progression. By applying an appropriate eligibility criterion, we selected relevant studies for review. Frequently identified mutations in genes such as TP53, NOTCH1, and PIK3CA are discussed. The findings of existing miRNAs (e.g., miR-21) as well as novel discoveries pertaining to OSCC are also covered. Lastly, we briefly mention the latest findings in targeted gene therapy and the potential use of miRNAs as biomarkers. Our goal is to encourage researchers to further adopt NGS in their studies and give an overview of the latest findings of OSCC treatment.

Genomic constitution of diploid species of the genus Avena L. with A-genome according to the data of the next-generation sequencing (NGS)

Проблемы ботаники Южной Сибири и Монголии ◽

10.14258/pbssm.2021066 ◽

2021 ◽

Vol 20 (1) ◽

pp. 333-335

Author(s):

N. N. Nosov ◽

A. A. Gnutikov ◽

I. G. Loskutov ◽

E. V. Blinova ◽

A. V. Rodionov

Keyword(s):

Next Generation Sequencing ◽

Diploid Species ◽

Rrna Gene ◽

Next Generation ◽

Illumina Platform ◽

5.8S Rrna Gene ◽

A Genome ◽

5.8S Rrna ◽

For diploid (2x) species with the A-genome, as well as for hexaploid (6x) from the genus Avena, a locus-specific next-generation sequencing (NGS) of the sequence of the region of the internal transcribed spacer ITS1 and the beginning of the 5.8S rRNA gene was carried out on the Illumina platform. The high diversity and heterogeneity of the genomes of diploid species are shown. It was revealed that the genomes of modern diploid oat species are relatively far removed from the hexaploid species. It was found that A. canariensis occupies an isolated position among other diploid species, and also takes only an insignificant role in the formation of hexaploid genomes.

MicroRNA Profile of Patients with Chronic Limb-Threatening Ischemia

Diagnostics ◽

10.3390/diagnostics10040230 ◽

2020 ◽

Vol 10 (4) ◽

pp. 230 ◽

Cited By ~ 2

Author(s):

Muzammil H. Syed ◽

Abdelrahman Zamzam ◽

Jason Valencia ◽

Hamzah Khan ◽

Shubha Jain ◽

...

Keyword(s):

Early Stage ◽

P Value ◽

Discovery Phase ◽

Genome Wide ◽

A Genome ◽

Microrna Profile ◽

Mirna Sequencing ◽

Confirmatory Phase ◽

Chronic limb-threatening ischemia (CLTI) results in devastating complications such as lower-limb amputations. In this study, a genome-wide plasma microRNAs (miRNA) sequencing was performed to identify miRNA(s) associated with CLTI. Blood samples were collected from early stage CLTI patients (ABI < 0.9) and non-PAD controls (ABI ≥ 0.9) for 3 experiments: discovery phase (n = 23), confirmatory phase (n = 52) and validation phase (n = 20). In the discovery phase, next generation sequencing (NGS) was used to identify miRNA circulating in the plasma CLTI (n = 13) patients, compared to non-PAD controls (n = 10). Two down-regulated miRNAs (miRNA-6843-3p and miRNA-6766-5p) and three upregulated miRNAs (miRNA-1827, miRNA-320 and miRNA-98-3p) were identified (≥2-fold change). In the confirmatory phase, these 5 deregulated miRNAs were further investigated in non-PAD (n = 21) and CTLI (n = 31) patients using qRT-PCR. Only miRNA-1827 was found to be significantly upregulated (≥3-fold, p-value < 0. 001) in the CLTI group. Lastly, to minimize the influence of confounding factors, miRNA-1827 plasma levels were validated in a third cohort of CLTI patients (n = 10) matched to non-PAD controls (n = 10). Our analysis demonstrated that miRNA-1827 expression was increased in the CLTI cohort (≥2-folds, p-value < 0.001). In summary, circulating miRNA-1827 is significantly elevated in patients with CLTI.

CRISPR/Cas9 System and its Research Progress in Gene Therapy

Anti-Cancer Agents in Medicinal Chemistry ◽

10.2174/1871520619666191014103711 ◽

2020 ◽

Vol 19 (16) ◽

pp. 1912-1919

Author(s):

Wenlou Liu ◽

Chunsheng Yang ◽

Yanqun Liu ◽

Guan Jiang

Keyword(s):

Gene Therapy ◽

Genome Editing ◽

Dna Sequences ◽

Genetic Information ◽

Genomic Dna ◽

Cancer Gene Therapy ◽

Research Progress ◽

Genome Sequences ◽

Site Mutation ◽

A Genome

Genome editing refers to changing the genome sequence of an organism by knockout, insertion, and site mutation, resulting in changes in the genetic information of the organism. The clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein-9 nuclease (Cas9) system is a genome editing technique developed by the acquired immune system in the microbes, such as bacteria and archaebacteria, which targets and edits genome sequences according to the principle of complementary base pairing. This technique can be used to edit endogenous genomic DNA sequences in organisms accurately and has been widely used in fields, such as biotechnology, cancer gene therapy, and dermatology. In this review, we summarize the history, structure, mechanism, and application of CRISPR/Cas9 in gene therapy and dermatological diseases.

Enhanced characterization of 109 genomic dna reference material for 6 HLA loci by next-generation sequencing (NGS)

Human Immunology ◽

10.1016/j.humimm.2015.07.099 ◽

2015 ◽

Vol 76 ◽

pp. 70

Author(s):

Deborah Ferriola ◽

Jamie Duke ◽

Anh Huynh ◽

Alison Gasiewski ◽

Marianne Rogers ◽

...

Keyword(s):

Next Generation Sequencing ◽

Reference Material ◽

Genomic Dna ◽

Next Generation ◽

SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis

10.1101/269365 ◽

2018 ◽

Author(s):

Dejian Zhao ◽

Deyou Zheng

Keyword(s):

Chromatin Immunoprecipitation ◽

Preparation Method ◽

Pcr Primers ◽

Library Preparation ◽

Peak Calling ◽

Dna Templates ◽

A Genome ◽

Generation Sequencing ◽

Library Preparation Method

AbstractBackgroundNoises and artifacts may arise in several steps of the next-generation sequencing (NGS) process. Recently, a NGS library preparation method called SMART, orSwitchingMechanismAt the 5’ end of theRNATranscript, is introduced to prepare ChIP-seq (chromatin immunoprecipitation and deep sequencing) libraries from small amount of DNA material. The protocol adds Ts to the 3’ end of DNA templates, which is subsequently recognized and used by SMART poly(dA) primers for reverse transcription and then addition of PCR primers and sequencing adapters. The poly(dA) primers, however, can anneal to poly(T) sequences in a genome and amplify DNA fragments that are not enriched in the immunoprecipitated DNA templates. This off-target amplification results in false signals in the ChIP-seq data.ResultsHere, we show that the off-target ChIP-seq reads derived from false amplification of poly(T/A) genomic sequences have unique and strand-specific features. Accordingly, we develop a tool (called “SMARTcleaner”) that can exploit the features to remove SMART ChIP-seq artifacts. Application of SMARTcleaner to several SMART ChIP-seq datasets demonstrates that it can remove reads from off-target amplification effectively, leading to improved ChIP-seq peaks and results.ConclusionsSMARTcleaner could identify and clean the false signals in SMART-based ChIP-seq libraries, leading to improvement in peak calling, and downstream data analysis and interpretation.

piRNA-IPdb: a PIWI-bound piRNAs database to mining NGS sncRNA data and beyond

BMC Genomics ◽

10.1186/s12864-021-08071-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Odei Barreñada ◽

Eduardo Larriba ◽

Miguel A. Brieño-Enriquez ◽

Jesús del Mazo

Keyword(s):

Cell Types ◽

High Plasticity ◽

Rna Seq ◽

Bona Fide ◽

Argonaute Family ◽

The Stability ◽

Different Cell Types ◽

Potential Use ◽

Abstract Background PIWI-interacting RNAs (piRNAs) are an abundant single-stranded type of small non-coding RNAs (sncRNAs), which initially were discovered in gonadal cells, with a role as defenders of genomic integrity in the germline, acting against the transposable elements. With a regular size range of 21-35 nt, piRNAs are associated with a PIWI-clade of Argonaute family proteins. The most widely accepted mechanisms of biogenesis for piRNAs involve the transcription of longer precursors of RNAs to be processed, by complexes of proteins, to functional size, preferentially accommodating uridine residues at the 5’ end and 3’ methylation to increase the stability of these molecules. piRNAs have also been detected in somatic cells, with diverse potential functions, indicating their high plasticity and pleiotropic activity. Discovered about two decades ago, piRNAs are a large and versatile type of sncRNA and that remain insufficiently identified and analyzed, through next-generation sequencing (NGS), to evaluate their processing, functions, and biogenesis in different cell types and during development. piRNAs’ distinction from other sncRNAs has led to controversial results and interpretation difficulties when using existing databases because of the heterogeneity of the criteria used in making the distinction. Description We present “piRNA-IPdb”, a database based uniquely on datasets obtaining after the defining characteristic of piRNAs: those small RNAs bound to PIWI proteins. We selected and analyzed sequences from piRBase that exclusively cover the binding to PIWI. We pooled a total of 18,821,815 sequences from RNA-seq after immunoprecipitation that included the binding to any of the mouse PIWI proteins (MILI, MIWI, or MIWI2). Conclusions In summary, we present the characteristics and potential use of piRNA-IPdb database for the analysis of bona fide piRNAs.

The Potential use of Bacterial Diversity Analysis of Soft Rotted Potato Tubers and Their Geocaulospheres

10.21203/rs.3.rs-185928/v1 ◽

2021 ◽

Author(s):

Sanja Marković ◽

Tatjana Popović ◽

Tanja Berić ◽

Ivica Dimkić ◽

Aleksandra Jelušić ◽

...

Keyword(s):

Bacterial Communities ◽

Soft Rot ◽

Diversity Analysis ◽

Potato Tubers ◽

Soft Or ◽

New Approach ◽

Potential Use ◽

Generation Sequencing ◽

Potential Antimicrobial Activity

Abstract The soft rot caused by Pectobacterium and Dickeya spp. is among the most important potato disease, responsible for outbreaks worldwide. In 2018, potato tubers (cultivar Lady Claire) with and without visible soft rot symptom, together with their geocaulospheres were sampled from the field in Bačka region (Serbia). The 16S rRNA Next Generation Sequencing (NGS) of tubers with and without soft rot symptom and their corresponding soils was performed to detect differences in microbial diversity and, using this data to predict causal agent(s) of disease and which samples are potentially best for isolating biocontrol strains. The ubiquitous soil bacteria from the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were dominant in all samples. The sequences identified as Pectobacterium aroidearum, P. carotovorum, and P. polaris were present in all tested samples and it can be hypothesized that they caused soft rot. The K3 sample showed the presence of genera with potential antimicrobial activity (Pseudomonas, Arthrobacter, Chryseobacterium, Bacillus, and Exiguobacterium). This result shows that diversity analysis could be used for checking for the presence of potential antagonistic bacteria at infected sites. Also, following the presence or absence of particular taxa could point out a capacity of soil to endure a growth season without an outbreak of soft or to maintain it without significant losses. This is a new approach to interpreting the results of the diversity of bacterial communities of tubers and can be useful for screening the health status of the soil.

Assessing Host-Pathogen Interaction Networks via RNA-Seq Profiling: A Systems Biology Approach

10.5772/intechopen.96706 ◽

2021 ◽

Author(s):

Sudhesh Dev Sareshma ◽

Bhassu Subha

Keyword(s):

Rna Sequencing ◽

High Throughput Sequencing ◽

Ribosome Profiling ◽

Host Pathogen Interaction ◽

Host Pathogen ◽

Experimental Approaches ◽

The Common ◽

Potential Use ◽

RNA sequencing is a valuable tool brought about by advances in next generation sequencing (NGS) technology. Initially used for transcriptome mapping, it has grown to become one of the ‘gold standards’ for studying molecular changes that occur in niche environments or within and across infections. It employs high-throughput sequencing with many advantages over previous methods. In this chapter, we review the experimental approaches of RNA sequencing from isolating samples all the way to data analysis methods. We focus on a number of NGS platforms that offer RNA sequencing with each having their own strengths and drawbacks. The focus will also be on how RNA sequencing has led to developments in the field of host-pathogen interactions using the dual RNA sequencing technique. Besides dual RNA sequencing, this review also explores the application of other RNA sequencing techniques such as single cell RNA sequencing as well as the potential use of newer techniques like ‘spatialomics’ and ribosome-profiling in host-pathogen interaction studies. Finally, we examine the common challenges faced when using RNA sequencing and possible ways to overcome these challenges.

Integrate Heterogeneous NGS and TGS Data to Boost Genome-free Transcriptome Research

10.1101/2020.05.27.117796 ◽

2020 ◽

Author(s):

Yangmei Qin ◽

Zhe Lin ◽

Dan Shi ◽

Mindong Zhong ◽

Te An ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Computational Method ◽

Protein Coding ◽

Third Generation Sequencing ◽

A Genome ◽

Amphioxus Genome ◽

AbstractIt is a long-term challenge to undertake reliable transcriptomic research under different circumstances of genome availability. Here, we newly developed a genome-free computational method to aid accurate transcriptome assembly, using the amphioxus as the example. Via integrating ten next generation sequencing (NGS) transcriptome datasets and one third-generation sequencing (TGS) dataset, we built a sequence library of non-redundant expressed transcripts for the amphioxus. The library consisted of overall 91,915 distinct transcripts, 51,549 protein-coding transcripts, and 16,923 novel extragenic transcripts. This substantially improved current amphioxus genome annotation by expanding the distinct gene number from 21,954 to 38,777. We consolidated the library significantly outperformed the genome, as well as de novo method, in transcriptome assembly from multiple aspects. For convenience, we curated the Integrative Transcript Library database of the amphioxus (http://www.bio-add.org/InTrans/). In summary, this work provides a practical solution for most organisms to alleviate the heavy dependence on good quality genome in transcriptome research. It also ensures the amphioxus transcriptome research grounding on reliable data.