scholarly journals Small RNA sequencing and differential expression of miRNAs in colorectal cancer

2017 ◽  
Vol 1 (2) ◽  
Author(s):  
Kwan-Liang Lye ◽  
Shiran Mohd Sidik ◽  
Sabariah Abdul Rahman ◽  
Yoke-Kqueen Cheah
Keyword(s):  
Colorectal Cancer ◽  
Rna Sequencing ◽  
Small Rna ◽  
Mirna Expression Profile ◽  
Small Rna Sequencing ◽  
Illumina Hiseq ◽  
Sequencing Platform ◽  
Normal Tissues ◽  
Cellular Processes ◽  
Generation Sequencing

MicroRNAs (miRNAs) are small, non-coding RNAs that are involved in various cellular processes. Many studies have shown that miRNAs are dysregulated in various types of cancer. In Malaysia, there are no published studies on miRNA expression profile for colorectal cancer, which is among the most common cancer here and other parts of the world. Next-generation sequencing platform was introduced in recent years and has revolutionized the biomedical research settings. In this study, we performed small RNA sequencing on Illumina HiSeq 2000 platform and found that 22 miRNAs were significantly differential expressed between cancer and normal tissues. Further validation on qRT-PCR on 5 of the miRNAs selected showed 3 of them were up-regulated (hsa-miR-106a, hsa-miR-135b, hsa-miR-21) while 2 were down-regulated (hsa-miR1, hsa-miR-504). These findings may lead to a simple profiling method to distinguish the risk of imdividuals in developing colorectal cancer.

scholarly journals Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis

2021 ◽  
Author(s):  
Jose Francisco Sanchez-Herrero ◽  
Raquel Pluvinet ◽  
Antonio Luna-de Haro ◽  
Lauro Sumoy
Keyword(s):  
Data Analysis ◽  
Rna Sequencing ◽  
Small Rna ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Technical Noise ◽  
Sequencing Errors ◽  
Abundance And Diversity ◽  
Template Dna ◽  
Generation Sequencing

Abstract Background Next generation sequencing has allowed the discovery of miRNA isoforms, termed isomirs. Some isomirs are derived from imprecise processing of pre-miRNA precursors, leading to length variants. Additional variability is introduced by non-templated addition of bases at the ends or editing of internal bases, resulting in base differences relative to the template DNA sequence. We hypothesized that some component of the isomir variation reported so far could be due to systematic technical noise and not real. Results We have developed the XICRA pipeline to analyze small RNA sequencing data at the isomir level. We exploited its ability to use single or merged reads to compare isomir results derived from paired-end (PE) reads with those from single reads (SR) to address whether detectable sequence differences relative to canonical miRNAs found in isomirs are true biological variations or the result of errors in sequencing. We have detected non-negligible systematic differences between SR and PE data which primarily affect putative internally edited isomirs, and at a much smaller frequency terminal length changing isomirs. This is relevant for the identification of true isomirs in small RNA sequencing datasets. Conclusions We conclude that potential artifacts derived from sequencing errors and/or data processing could result in an overestimation of abundance and diversity of miRNA isoforms. Efforts in annotating the isomirnome should take this into account.

scholarly journals A low-bias and sensitive small RNA library preparation method using randomized splint ligation

2020 ◽  
Vol 48 (14) ◽  
pp. e80-e80 ◽  
Author(s):  
Sean Maguire ◽  
Gregory J S Lohman ◽  
Shengxi Guan
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Small Rnas ◽  
Small Rna Sequencing ◽  
Preparation Process ◽  
Library Preparation ◽  
Normal Tissues ◽  
Levels Of Detail ◽  
Low Sensitivity ◽  
Next Generation Sequencing Ngs

Abstract Small RNAs are important regulators of gene expression and are involved in human development and disease. Next generation sequencing (NGS) allows for scalable, genome-wide studies of small RNA; however, current methods are challenged by low sensitivity and high bias, limiting their ability to capture an accurate representation of the cellular small RNA population. Several studies have shown that this bias primarily arises during the ligation of single-strand adapters during library preparation, and that this ligation bias is magnified by 2′-O-methyl modifications (2′OMe) on the 3′ terminal nucleotide. In this study, we developed a novel library preparation process using randomized splint ligation with a cleavable adapter, a design which resolves previous challenges associated with this ligation strategy. We show that a randomized splint ligation based workflow can reduce bias and increase the sensitivity of small RNA sequencing for a wide variety of small RNAs, including microRNA (miRNA) and tRNA fragments as well as 2′OMe modified RNA, including Piwi-interacting RNA and plant miRNA. Finally, we demonstrate that this workflow detects more differentially expressed miRNA between tumorous and matched normal tissues. Overall, this library preparation process allows for highly accurate small RNA sequencing and will enable studies of 2′OMe modified RNA with new levels of detail.

scholarly journals Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Sarah Tomkovich ◽  
Raad Z. Gharaibeh ◽  
Christine M. Dejea ◽  
Jillian L. Pope ◽  
Jinmai Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Microbial Communities ◽  
Rna Sequencing ◽  
Small Rna ◽  
Intestinal Bacteria ◽  
Distal Colon ◽  
Human Colon ◽  
Small Rna Sequencing ◽  
Microrna Sequencing

ABSTRACT Disrupted interactions between host and intestinal bacteria are implicated in colorectal cancer (CRC) development. However, activities derived from these bacteria and their interplay with the host are unclear. Here, we examine this interplay by performing mouse and microbiota RNA sequencing on colon tissues and 16S and small RNA sequencing on stools from germfree (GF) and gnotobiotic ApcMinΔ850/+;Il10−/− mice associated with microbes from biofilm-positive human CRC tumor (BF+T) and biofilm-negative healthy (BF-bx) tissues. The bacteria in BF+T mice differentially expressed (DE) >2,900 genes, including genes related to bacterial secretion, virulence, and biofilms but affected only 62 host genes. Small RNA sequencing of stools from these cohorts revealed eight significant DE host microRNAs (miRNAs) based on biofilm status and several miRNAs that correlated with bacterial taxon abundances. Additionally, computational predictions suggest that some miRNAs preferentially target bacterial genes while others primarily target mouse genes. 16S rRNA sequencing of mice that were reassociated with mucosa-associated communities from the initial association revealed a set of 13 bacterial genera associated with cancer that were maintained regardless of whether the reassociation inoculums were initially obtained from murine proximal or distal colon tissues. Our findings suggest that complex interactions within bacterial communities affect host-derived miRNA, bacterial composition, and CRC development. IMPORTANCE Bacteria and bacterial biofilms have been implicated in colorectal cancer (CRC), but it is still unclear what genes these microbial communities express and how they influence the host. MicroRNAs regulate host gene expression and have been explored as potential biomarkers for CRC. An emerging area of research is the ability of microRNAs to impact growth and gene expression of members of the intestinal microbiota. This study examined the bacteria and bacterial transcriptome associated with microbes derived from biofilm-positive human cancers that promoted tumorigenesis in a murine model of CRC. The murine response to different microbial communities (derived from CRC patients or healthy people) was evaluated through RNA and microRNA sequencing. We identified a complex interplay between biofilm-associated bacteria and the host during CRC in mice. These findings may lead to the development of new biomarkers and therapeutics for identifying and treating biofilm-associated CRCs.

scholarly journals Analysis of Small RNA Sequencing Data in Plants

2022 ◽  
pp. 497-509
Author(s):  
Vanika Garg ◽  
Rajeev K. Varshney
Keyword(s):  
Next Generation Sequencing ◽  
Rna Sequencing ◽  
Small Rna ◽  
Regulatory Mechanisms ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Meaningful Information ◽  
Expression Studies ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractOver the past decades, next-generation sequencing (NGS) has been employed extensively for investigating the regulatory mechanisms of small RNAs. Several bioinformatics tools are available for aiding biologists to extract meaningful information from enormous amounts of data generated by NGS platforms. This chapter describes a detailed methodology for analyzing small RNA sequencing data using different open source tools. We elaborate on various steps involved in analysis, from processing the raw sequencing reads to identifying miRNAs, their targets, and differential expression studies.

scholarly journals Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jose Francisco Sanchez Herrero ◽  
Raquel Pluvinet ◽  
Antonio Luna de Haro ◽  
Lauro Sumoy
Keyword(s):  
Data Analysis ◽  
Rna Sequencing ◽  
Small Rna ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Technical Noise ◽  
Sequencing Errors ◽  
Abundance And Diversity ◽  
Template Dna ◽  
Generation Sequencing

Abstract Background Next generation sequencing has allowed the discovery of miRNA isoforms, termed isomiRs. Some isomiRs are derived from imprecise processing of pre-miRNA precursors, leading to length variants. Additional variability is introduced by non-templated addition of bases at the ends or editing of internal bases, resulting in base differences relative to the template DNA sequence. We hypothesized that some component of the isomiR variation reported so far could be due to systematic technical noise and not real. Results We have developed the XICRA pipeline to analyze small RNA sequencing data at the isomiR level. We exploited its ability to use single or merged reads to compare isomiR results derived from paired-end (PE) reads with those from single reads (SR) to address whether detectable sequence differences relative to canonical miRNAs found in isomiRs are true biological variations or the result of errors in sequencing. We have detected non-negligible systematic differences between SR and PE data which primarily affect putative internally edited isomiRs, and at a much smaller frequency terminal length changing isomiRs. This is relevant for the identification of true isomiRs in small RNA sequencing datasets. Conclusions We conclude that potential artifacts derived from sequencing errors and/or data processing could result in an overestimation of abundance and diversity of miRNA isoforms. Efforts in annotating the isomiRnome should take this into account.

scholarly journals Small RNA sequencing revealed aberrant piRNA expression profiles in colorectal cancer

2019 ◽  
Author(s):  
Jie Yin ◽  
Wei Qi ◽  
Chen‑Guang Ji ◽  
Dong‑Xuan Zhang ◽  
Xiao‑Li Xie ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Rna Sequencing ◽  
Small Rna ◽  
Expression Profiles ◽  
Small Rna Sequencing

Small RNA Sequencing to Discover Circulating MicroRNA Biomarkers of Testicular Toxicity in Dogs

2020 ◽  
pp. 109158182096151
Author(s):  
Jennifer C. Shing ◽  
Kai Schaefer ◽  
Shaun E. Grosskurth ◽  
Andy H. Vo ◽  
Tatiana Sharapova ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Exploratory Study ◽  
Quantitative Polymerase Chain Reaction ◽  
Small Rna Sequencing ◽  
Circulating Microrna ◽  
Testicular Toxicity ◽  
Potential Candidate ◽  
Drug Induced ◽  
Organ Systems

Predictive indicators of testicular toxicity could improve drug development by allowing early in-life screening for this adverse effect before it becomes severe. We hypothesized that circulating microRNAs (miRNAs) could serve as testicular toxicity biomarkers in dogs. Herein, we describe the results of an exploratory study conducted to discover biomarkers of drug-induced testicular injury. Following a dose-selection study using the testicular toxicant ethylene glycol monomethyl ether (EGME), we chose a dose of 50 mg/kg/d EGME to avoid systemic toxicity and treated 2 groups of dogs (castrated, non-castrated) for 14 to 28 days. Castrated animals were used as negative controls to identify biomarkers specific for testicular toxicity because EGME can cause toxicity to organ systems in addition to the testis. Blood was collected daily during the dosing period, followed by recovery for 29 to 43 days with less frequent sampling. Dosing was well tolerated, resulting in mild-to-moderate degeneration in testes and epididymides. Global profiling of serum miRNAs at selected dosing and recovery time points was completed by small RNA sequencing. Bioinformatics data analysis using linear modeling demonstrated several circulating miRNAs that were differentially abundant during the dosing period compared with baseline and/or castrated control samples. Confirmatory reverse transcription quantitative polymerase chain reaction data in these animals was unable to detect sustained alterations of miRNAs in serum, except for 1 potential candidate cfa-miR-146b. Taken together, we report the results of a comprehensive exploratory study and suggest future directions for follow-up research to address the challenge of developing diagnostic biomarkers of testicular toxicity.

Sign in / Sign up

Export Citation Format

Share Document