Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis

Gene expression is the fundamental level at which the results of various genetic and regulatory programs are observable. The measurement of transcriptome-wide gene expression has convincingly switched from microarrays to sequencing in a matter of years. RNA sequencing (RNA-seq) provides a quantitative and open system for profiling transcriptional outcomes on a large scale and therefore facilitates a large diversity of applications, including basic science studies, but also agricultural or clinical situations. In the past 10 years or so, much has been learned about the characteristics of the RNA-seq data sets, as well as the performance of the myriad of methods developed. In this review, we give an overview of the developments in RNA-seq data analysis, including experimental design, with an explicit focus on the quantification of gene expression and statistical approachesfor differential expression. We also highlight emerging data types, such as single-cell RNA-seq and gene expression profiling using long-read technologies.

Spermatozoal mRNAs expression implicated in embryonic development were influenced by dietary folate supplementation of breeder roosters by altering spermatozoal piRNA expression profiles

Dietary folate intake, together with changes in its metabolism process, have effects on male reproduction, sperm epigenetic patterning and offspring outcome. Previous studies have proven that PIWI-interacting RNAs (piRNAs) play important roles in successful spermatogenesis and regulating genes expression of sperm and offspring embryo. Herein, we fed breeder roosters with five different levels (0, 0.25, 1.25, 2.50, and 5.00 mg/kg) of folate throughout life and found that paternal folate supplementation was beneficial to the growth and organ development of offspring broilers. Further spermatozoal mRNAs sequencing analyses implied that the dietary folate supplementation could regulate the spermatozoal mRNA abundance of genes related to the fetal development. Furthermore, global piRNAs analyses of breeder roosters' sperm revealed that differential concentration of dietary folate supplementation could change piRNAs profiles. Combined mRNAs sequencing and target gene prediction of differentially expressed gene-derived piRNAs, embryonic development and metabolism related pathways and biological processes, which were consisted to the regulatory roles of paternal folate supplementations, were significantly affected by the differentially expressed gene-derived piRNAs based on the GO and KEGG analyses. Overall, our results provided a novel insight into the role of piRNAs in response to folate intake, which will broaden the understanding about the relationship between folate and sperm epigenetic patterning of breeder roosters.

Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq

Background

Limited accessibility to intestinal epithelial tissue in wild animals and humans makes it challenging to study patterns of intestinal gene regulation, and hence to monitor physiological status and health in field conditions. To explore solutions to this limitation, we have used a noninvasive approach via fecal RNA-seq, for the quantification of gene expression markers in gastrointestinal cells of free-range primates and a forager human population. Thus, a combination of poly(A) mRNA enrichment and rRNA depletion methods was used in tandem with RNA-seq to quantify and compare gastrointestinal gene expression patterns in fecal samples of wild Gorilla gorilla gorilla (n = 9) and BaAka hunter-gatherers (n = 10) from The Dzanga Sangha Protected Areas, Central African Republic.

Results

Although only a small fraction (< 4.9%) of intestinal mRNA signals was recovered, the data was sufficient to detect significant functional differences between gorillas and humans, at the gene and pathway levels. These intestinal gene expression differences were specifically associated with metabolic and immune functions. Additionally, non-host RNA-seq reads were used to gain preliminary insights on the subjects’ dietary habits, intestinal microbiomes, and infection prevalence, via identification of fungi, nematode, arthropod and plant RNA.

Conclusions

Overall, the results suggest that fecal RNA-seq, targeting gastrointestinal epithelial cells can be used to evaluate primate intestinal physiology and gut gene regulation, in samples obtained in challenging conditions in situ. The approach used herein may be useful to obtain information on primate intestinal health, while revealing preliminary insights into foraging ecology, microbiome, and diet.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5813-z) contains supplementary material, which is available to authorized users.

Prognostic modeling of the immune-centric transcriptome reveals interleukin signaling candidates contributing to differential patient outcomes

Immunotherapy is a promising advancement in the treatment of non-small-cell lung carcinoma (NSCLC), although much of how lung tumors interact with the immune system in the natural course of disease remains unknown. We investigated the impact of the expression of immune-centric genes and pathways in tumors on patient survival to reveal novel candidates for immunotherapeutic research. Tumor transcriptomes and detailed clinical characteristics were obtained from patients with NSCLC who were participants of either the Inflammation, Health and Lung Epidemiology (INHALE) (discovery, N = 280) or The Cancer Genome Atlas (TCGA) Lung (replication, N = 1026) studies. Expressions of 2253 genes derived from 48 major immune pathways were assessed for association with patient prognosis using a multivariable Cox model and pathway effects were assessed with an in-house implementation of the Gene Set Enrichment Analysis (GSEA) algorithm. Prognosis-guided gene and pathway analysis of immune-centric expression in tumors revealed significant survival enrichments across both cohorts. The 'Interleukin Signaling' pathway, containing 430 genes, was found to be statistically and significantly enriched with prognostic signal in both the INHALE (P = 0.008) and TCGA (P = 0.039) datasets. Subsequent leading-edge analysis identified a subset of genes (N = 23) shared between both cohorts, driving the pathway enrichment. Cumulative expression of this leading-edge gene signature was a strong predictor of patient survival [discovery: hazard ratio (HR) = 1.59, P = 3.0 × 10-8; replication: HR = 1.29, P = 7.4 × 10-7]. These data demonstrate the impact of immune-centric expression on patient outcomes in NSCLC. Furthermore, prognostic gene effects were localized to discrete immune pathways, of which Interleukin Signaling had the greatest impact on overall survival and the subset of genes driving these effects have promise for future therapeutic intervention.

Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

BACKGROUND

Full RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification agreement between RNA-Seq and a digital multiplexed gene expression platform, and the subtype call after running the PAM50 assay in a series of breast cancer patients classified as triple negative by IHC/FISH. The goal of this study is to analyze the concordance between both expression platforms overall, and for calling PAM50 triple negative breast cancer intrinsic subtypes in particular.

RESULTS

The analyses were performed in paraffin-embedded tissues from 96 patients recruited in a multicenter, prospective, non-randomized neoadjuvant triple negative breast cancer trial (NCT01560663). Pre-treatment core biopsies were obtained following clinical practice guidelines and conserved as FFPE for further RNA extraction. PAM50 was performed on both digital multiplexed gene expression and RNA-Seq platforms. Subtype assignment was based on the nearest centroid classification following this procedure for both platforms and it was concordant on 96% of the cases (N = 96). In four cases, digital multiplexed gene expression analysis and RNA-Seq were discordant. The Spearman correlation to each of the centroids and the risk of recurrence were above 0.89 in both platforms while the agreement on Proliferation Score reached up to 0.97. In addition, 82% of the individual PAM50 genes showed a correlation coefficient > 0.80.

CONCLUSIONS

In our analysis, the subtype calling in most of the samples was concordant in both platforms and the potential discordances had reduced clinical implications in terms of prognosis. If speed and cost are the main driving forces then the preferred technique is the digital multiplexed platform, while if whole genome patterns and subtype are the driving forces, then RNA-Seq is the preferred method.

Discovering and Mapping the Modified Nucleotides That Comprise the Epitranscriptome of mRNA

An important mechanism of gene expression regulation is the regulated modification of nucleotides in messenger RNA (mRNA). These modified nucleotides affect mRNA translation, stability, splicing, and other processes. A cluster of nucleotide modifications is found adjacent to the mRNA cap structure and another set can be found internally within transcripts. The most prominent modifications are methylations of adenosine to form either N ⁶-methyladenosine (m⁶A), an internal modified nucleotide, or N ⁶,2'-O-dimethyladenosine (m⁶Am), which is found exclusively at the first templated nucleotide of certain mRNAs. In addition, other rare modified nucleotides have been identified and together these form the epitranscriptomic code of mRNA. In the case of some modified nucleotides, the presence, location, or abundance is a subject of debate. Here, we review the methods that enable the discovery of modified nucleotides and how these approaches can be used to map epitranscriptomic modifications in mRNA.

HPV transcription in skin tumors

BACKGROUND

Although more than 95% of viral sequences found in skin tumors typically belong to human papillomaviruses (HPVs), HPV transcription has so far not been detected. As current technology allows very deep transcriptome sequencing, we examined skin tumors and precursor lesions for HPV transcription.

METHOD

Fresh frozen biopsies from 12 skin specimens (11/12 were positive for HPV DNA) were subjected to total RNA sequencing. The cervical cancer cell line CaSki was included as a positive control for HPV transcription.

RESULTS

HPV RNA was detected and confirmed in 1/12 skin lesions at a median depth of 66 million reads per sample. One specimen was positive for HPV 110 transcripts mapping to E6, E7, E2/E4 and L2 open reading frames, as well as to a spliced E1^E4 transcript.

CONCLUSION

In conclusion, the study revealed that a minority of skin lesions contains HPV transcripts and that HPV DNA detection does not predict HPV transcriptional activity.

Systematic analysis of TruSeq, SMARTer and SMARTer Ultra-Low RNA-seq kits for standard, low and ultra-low quantity samples

High-throughput RNA-sequencing has become the gold standard method for whole-transcriptome gene expression analysis, and is widely used in numerous applications to study cell and tissue transcriptomes. It is also being increasingly used in a number of clinical applications, including expression profiling for diagnostics and alternative transcript detection. However, despite its many advantages, RNA sequencing can be challenging in some situations, for instance in cases of low input amounts or degraded RNA samples. Several protocols have been proposed to overcome these challenges, and many are available as commercial kits. In this study, we systematically test three recent commercial technologies for RNA-seq library preparation (TruSeq, SMARTer and SMARTer Ultra-Low) on human biological reference materials, using standard (1 mg), low (100 ng and 10 ng) and ultra-low (<1 ng) input amounts, and for mRNA and total RNA, stranded and unstranded. The results are analyzed using read quality and alignment metrics, gene detection and differential gene expression metrics. Overall, we show that the TruSeq kit performs well with an input amount of 100 ng, while the SMARTer kit shows decreased performance for inputs of 100 and 10 ng, and the SMARTer Ultra-Low kit performs relatively well for input amounts <1 ng. All the results are discussed in detail, and we provide guidelines for biologists for the selection of an RNA-seq library preparation kit.

Apoptotic endothelial cells release small extracellular vesicles loaded with immunostimulatory viral-like RNAs

Endothelial cells have multifaceted interactions with the immune system, both as initiators and targets of immune responses. In vivo, apoptotic endothelial cells release two types of extracellular vesicles upon caspase-3 activation: apoptotic bodies and exosome-like nanovesicles (ApoExos). Only ApoExos are immunogenic: their injection causes inflammation and autoimmunity in mice. Based on deep sequencing of total RNA, we report that apoptotic bodies and ApoExos are loaded with divergent RNA cargos that are not released by healthy endothelial cells. Apoptotic bodies, like endothelial cells, contain mainly ribosomal RNA whereas ApoExos essentially contain non-ribosomal non-coding RNAs. Endogenous retroelements, bearing viral-like features, represented half of total ApoExos RNA content. ApoExos also contained several copies of unedited Alu repeats and large amounts of non-coding RNAs with a demonstrated role in autoimmunity such as U1 RNA and Y RNA. Moreover, ApoExos RNAs had a unique nucleotide composition and secondary structure characterized by strong enrichment in U-rich motifs and unstably folded RNAs. Globally, ApoExos were therefore loaded with RNAs that can stimulate a variety of RIG-I-like receptors and endosomal TLRs. Hence, apoptotic endothelial cells selectively sort in ApoExos a diversified repertoire of immunostimulatory "self RNAs" that are tailor-made for initiation of innate immune responses and autoimmunity.

Robustness of RNA sequencing on older formalin-fixed paraffin-embedded tissue from high-grade ovarian serous adenocarcinomas

Formalin-fixed paraffin-embedded (FFPE) tissues are among the most widely available clinical specimens. Their potential utility as a source of RNA for transcriptome studies would greatly enhance population-based cancer studies. Although preliminary studies suggest FFPE tissue may be used for RNA sequencing, the effect of storage time on these specimens needs to be determined. We conducted this study to determine whether RNA in archived FFPE high-grade ovarian serous adenocarcinomas from Surveillance, Epidemiology and End Results (SEER) registries was present in sufficient quantity and quality for RNA-Seq analysis. FFPE tissues, stored from 7 to 32 years, were obtained from three SEER sites. RNA was extracted, quantified, quality assessed, and subjected to RNA-Seq (a whole transcriptome sequencing technology). FFPE specimens stored for longer periods of time had poorer RNA sample quality as indicated by negative correlations between specimen storage time and fragment distribution values (DV). In addition, sample contamination was a common issue among the RNA, with 41 of 67 samples having 5% to 48% bacterial contamination. However, regardless of specimen storage time and bacterial contamination, 60% of the samples yielded data that enabled gene expression quantification, identifying more than 10,000 genes, with the correlations among most biological replicates above 0.7. This study demonstrates that FFPE high-grade ovarian serous adenocarcinomas specimens stored in repositories for up to 32 years and under varying storage conditions are a promising source of RNA for RNA-Seq. We also describe certain caveats to be considered when designing RNA-Seq studies using archived FFPE tissues.

FastqPuri: high-performance preprocessing of RNA-seq data

Background

RNA sequencing (RNA-seq) has become the standard means of analyzing gene and transcript expression in high-throughput. While previously sequence alignment was a time demanding step, fast alignment methods and even more so transcript counting methods which avoid mapping and quantify gene and transcript expression by evaluating whether a read is compatible with a transcript, have led to significant speed-ups in data analysis. Now, the most time demanding step in the analysis of RNA-seq data is preprocessing the raw sequence data, such as running quality control and adapter, contamination and quality filtering before transcript or gene quantification. To do so, many researchers chain different tools, but a comprehensive, flexible and fast software that covers all preprocessing steps is currently missing.

Results

We here present FastqPuri, a light-weight and highly efficient preprocessing tool for fastq data. FastqPuri provides sequence quality reports on the sample and dataset level with new plots which facilitate decision making for subsequent quality filtering. Moreover, FastqPuri efficiently removes adapter sequences and sequences from biological contamination from the data. It accepts both single- and paired-end data in uncompressed or compressed fastq files. FastqPuri can be run stand-alone and is suitable to be run within pipelines. We benchmarked FastqPuri against existing tools and found that FastqPuri is superior in terms of speed, memory usage, versatility and comprehensiveness.

Conclusions

FastqPuri is a new tool which covers all aspects of short read sequence data preprocessing. It was designed for RNA-seq data to meet the needs for fast preprocessing of fastq data to allow transcript and gene counting, but it is suitable to process any short read sequencing data of which high sequence quality is needed, such as for genome assembly or SNV (single nucleotide variant) detection. FastqPuri is most flexible in filtering undesired biological sequences by offering two approaches to optimize speed and memory usage dependent on the total size of the potential contaminating sequences. FastqPuri is available at https://github.com/jengelmann/FastqPuri. It is implemented in C and R and licensed under GPL v3.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2799-0) contains supplementary material, which is available to authorized users.

Distinguishing RNA modifications from noise in epitranscriptome maps

Messenger RNA (mRNA) and long noncoding RNA (lncRNA) can be subjected to a variety of post-transcriptional modifications that markedly influence their fate and function. This concept of 'epitranscriptomic' modifications and the understanding of their function has been driven by new technologies for transcriptome-wide mapping of modified nucleotides using next-generation sequencing. Mapping technologies have successfully documented the location and prevalence of several modified nucleotides in the transcriptome. However, some mapping methods have led to proposals of pervasive novel RNA modifications that have subsequently been shown to be exceptionally rare. These controversies have resulted in confusion about the identity of the modified nucleotides comprising the epitranscriptome in mRNA and lncRNA. Here we discuss the different transcriptome-wide technologies for mapping modified nucleotides. We describe why these methods can have poor accuracy and specificity. Finally, we describe emerging strategies that minimize false positives and other pitfalls associated with mapping and measuring epitranscriptomic modifications.

RNA-sequencing in ophthalmology research: considerations for experimental design and analysis

High-throughput, massively parallel sequence analysis has revolutionized the way that researchers design and execute scientific investigations. Vast amounts of sequence data can be generated in short periods of time. Regarding ophthalmology and vision research, extensive interrogation of patient samples for underlying causative DNA mutations has resulted in the discovery of many new genes relevant to eye disease. However, such analysis remains functionally limited. RNA-sequencing accurately snapshots thousands of genes, capturing many subtypes of RNA molecules, and has become the gold standard for transcriptome gene expression quantification. RNA-sequencing has the potential to advance our understanding of eye development and disease; it can reveal new candidates to improve our molecular diagnosis rates and highlight therapeutic targets for intervention. But with a wide range of applications, the design of such experiments can be problematic, no single optimal pipeline exists, and therefore, several considerations must be undertaken for optimal study design. We review the key steps involved in RNA-sequencing experimental design and the downstream bioinformatic pipelines used for differential gene expression. We provide guidance on the application of RNA-sequencing to ophthalmology and sources of open-access eye-related data sets.

Mapping the dsRNA World

Long double-stranded RNAs (dsRNAs) are abundantly expressed in animals, in which they frequently occur in introns and 3' untranslated regions of mRNAs. Functions of long, cellular dsRNAs are poorly understood, although deficiencies in adenosine deaminases that act on RNA, or ADARs, promote their recognition as viral dsRNA and an aberrant immune response. Diverse dsRNA-binding proteins bind cellular dsRNAs, hinting at additional roles. Understanding these roles is facilitated by mapping the genomic locations that express dsRNA in various tissues and organisms. ADAR editing provides a signature of dsRNA structure in cellular transcripts. In this review, we detail approaches to map ADAR editing sites and dsRNAs genome-wide, with particular focus on high-throughput sequencing methods and considerations for their successful application to the detection of editing sites and dsRNAs.

Demodifying RNA for Transcriptomic Analyses of Archival Formalin-Fixed Paraffin-Embedded Samples

Archival formalin-fixed paraffin-embedded (FFPE) tissue samples offer a vast but largely untapped resource for genomic research. The primary technical issues limiting use of FFPE samples are RNA yield and quality. In this study, we evaluated methods to demodify RNA highly fragmented and crosslinked by formalin fixation. Primary endpoints were RNA recovery, RNA-sequencing quality metrics, and transcriptional responses to a reference chemical (phenobarbital, PB). Frozen mouse liver samples from control and PB groups (n = 6/group) were divided and preserved for 3 months as follows: frozen (FR); 70% ethanol (OH); 10% buffered formalin for 18 h followed by ethanol (18F); or 10% buffered formalin (3F). Samples from OH, 18F, and 3F groups were processed to FFPE blocks and sectioned for RNA isolation. Additional sections from 3F received the following demodification protocols to mitigate RNA damage: short heated incubation with Tris-Acetate-EDTA buffer; overnight heated incubation with an organocatalyst using 2 different isolation kits; or overnight heated incubation without organocatalyst. Ribo-depleted, stranded, total RNA libraries were built and sequenced using the Illumina HiSeq 2500 platform. Overnight incubation (± organocatalyst) increased RNA yield >3-fold and RNA integrity numbers and fragment analysis values by > 1.5- and >3.0-fold, respectively, versus 3F. Postsequencing metrics also showed reduced bias in gene coverage and deletion rates for overnight incubation groups. All demodification groups had increased overlap for differentially expressed genes (77%-84%) and enriched pathways (91%-97%) with FR, with the highest overlap in the organocatalyst groups. These results demonstrate simple changes in RNA isolation methods that can enhance genomic analyses of FFPE samples.

Long noncoding RNA expression profiling in cancer: Challenges and opportunities

In recent years, technological advances in transcriptome profiling revealed that the repertoire of human RNA molecules is more diverse and extended than originally thought. This diversity and complexity mainly derive from a large ensemble of noncoding RNAs. Because of their key roles in cellular processes important for normal development and physiology, disruption of noncoding RNA expression is intrinsically linked to human disease, including cancer. Therefore, studying the noncoding portion of the transcriptome offers the prospect of identifying novel therapeutic and diagnostic targets. Although evidence of the relevance of noncoding RNAs in cancer is accumulating, we still face many challenges when it comes to accurately profiling their expression levels. Some of these challenges are inherent to the technologies employed, whereas others are associated with characteristics of the noncoding RNAs themselves. In this review, we discuss the challenges related to long noncoding RNA expression profiling, highlight how cancer long noncoding RNAs provide new opportunities for cancer diagnosis and treatment, and reflect on future developments.

Transcriptome Sequencing Approaches to Elucidate Host-Microbe Interactions in Opportunistic Human Fungal Pathogens

Infections caused by opportunistic human fungal pathogens are a source of increasing medical concern, due to their growing incidence, the emergence of novel pathogenic species, and the lack of effective diagnostics tools. Fungal pathogens are phylogenetically diverse, and their virulence mechanisms can differ widely across species. Despite extensive efforts, the molecular bases of virulence in pathogenic fungi and their interactions with the human host remain poorly understood for most species. In this context, next-generation sequencing approaches hold the promise of helping to close this knowledge gap. In particular, high-throughput transcriptome sequencing (RNA-Seq) enables monitoring the transcriptional profile of both host and microbes to elucidate their interactions and discover molecular mechanisms of virulence and host defense. Here, we provide an overview of transcriptome sequencing techniques and approaches, and survey their application in studying the interplay between humans and fungal pathogens. Finally, we discuss novel RNA-Seq approaches in studying host-pathogen interactions and their potential role in advancing the clinical diagnostics of fungal infections.

Genome-wide isoform-level analysis reveals tumor-specific isoforms for lung adenocarcinoma diagnosis and prognosis

Last decades have witnessed the great progress in exploration of tumor transcriptome. However, most researches were restricted in gene-level expression. mRNA isoforms, especially tumor-specific isoforms have not been fully explored in tumor. Here, by analyzing RNA-seq data derived from hundreds of samples in TCGA projects, we comprehensively characterized the expression variations of mRNA isoforms in adenocarcinoma of lung (LUAD), which is one of leading causes of cancer-related death. Our analysis found that a variety of mRNA isoforms showed differential expression in LUAD tumor samples. Some of them even showed distinct variations compared to their host genes. Further analysis of functional enrichment revealed that up- and down-regulated mRNA isoforms took part in different types of biological process. In addition, we also identified hundreds of isoforms that expressed exclusively in LUAD tumor samples. Furthermore, the expression level of several isoforms, such as uc001kuk.3 and uc003yls.2, could separate tumor patients by overall survival periods. Our study provided new candidates for the diagnosis and prognosis of lung cancer.

Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

Guanine-rich RNA sequences can fold into four-stranded structures, termed G-quadruplexes (G4-RNAs), whose biological roles are poorly understood, and in vivo existence is debated. To profile biologically relevant G4-RNA in the human transcriptome, we report here on G4RP-seq, which combines G4-RNA-specific precipitation (G4RP) with sequencing. This protocol comprises a chemical crosslinking step, followed by affinity capture with the G4-specific small-molecule ligand/probe BioTASQ, and target identification by sequencing, allowing for capturing global snapshots of transiently folded G4-RNAs. We detect widespread G4-RNA targets within the transcriptome, indicative of transient G4 formation in living human cells. Using G4RP-seq, we also demonstrate that G4-stabilizing ligands (BRACO-19 and RHPS4) can change the G4 transcriptomic landscape, most notably in long non-coding RNAs. G4RP-seq thus provides a method for studying the G4-RNA landscape, as well as ways of considering the mechanisms underlying G4-RNA formation, and the activity of G4-stabilizing ligands.

Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection

Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive approach for pathogen detection. The cost of high-throughput or next-generation sequencing has been reduced by several orders of magnitude since its advent in 2004, and it has emerged as an enabling technological platform for the detection and taxonomic characterization of microorganisms in clinical samples from patients. This review focuses on the application of untargeted metagenomic next-generation sequencing to the clinical diagnosis of infectious diseases, particularly in areas in which conventional diagnostic approaches have limitations. The review covers ( a) next-generation sequencing technologies and common platforms, ( b) next-generation sequencing assay workflows in the clinical microbiology laboratory, ( c) bioinformatics analysis of metagenomic next-generation sequencing data, ( d) validation and use of metagenomic next-generation sequencing for diagnosing infectious diseases, and ( e) significant case reports and studies in this area. Next-generation sequencing is a new technology that has the promise to enhance our ability to diagnose, interrogate, and track infectious diseases.

The Development and Use of Scalable Systems for Studying Aberrant Splicing in SF3B1-Mutant CLL

Mutational landscape of CLL is now known to include recurrent non-synonymous mutations in SF3B1, a core splicing factor. About 5-10% of newly diagnosed CLL harbor these mutations which are typically limited to HEAT domains in the carboxyl-terminus of the protein. Importantly, the mutations are not specific to CLL but also present in several unrelated clonal disorders. Analysis of patient samples and cell lines has shown the primary splicing aberration in SF3B1-mutant cells to the use of novel or "cryptic" 3' splice sites (3SS). Advances in genome-editing and next-generation sequencing (NGS) have allowed development of isogenic models and detailed analysis of changes to the transcriptome with relative ease. In this manuscript, we focus on two relevant methods to study splicing factor mutations in CLL: development of isogenic scalable cell lines and informatics analysis of RNA-Seq datasets.

Global Transcriptome Analysis During Adipogenic Differentiation and Involvement of Transthyretin Gene in Adipogenesis in Cattle

Adipose tissue plays central role in determining the gustatory quality of beef, but traditional Chinese beef cattle have low levels of fat content. We applied RNA-seq to study the molecular mechanisms underlying adipocyte differentiation in Qinchuan cattle. A total of 18,283 genes were found to be expressed in preadipocytes and mature adipocytes, respectively. 470 of which were significantly differentially expressed genes (DEGs) [false discovery rate (FDR) values < 0.05 and fold change ≥ 2]. In addition, 4534 alternative splicing (AS) events and 5153 AS events were detected in preadipocytes and adipocytes, respectively. We constructed a protein interaction network, which suggested that collagen plays an important role during bovine adipogenic differentiation. We characterized the function of the most down-regulated DEG (P < 0.001) among genes we have detected by qPCR, namely, the transthyretin (TTR) gene. Overexpression of TTR appears to promote the expression of the peroxisome proliferator activated receptor γ (PPARγ) (P < 0.05) and fatty acid binding Protein 4 (FABP4) (P < 0.05). Hence, TTR appears to be involved in the regulation of bovine adipogenic differentiation. Our study represents the comprehensive approach to explore bovine adipocyte differentiation using transcriptomic data and reports an involvement of TTR during bovine adipogenic differentiation. Our results provide novel insights into the molecular mechanisms underlying bovine adipogenic differentiation.

RNA sequencing (RNA-Seq) and its application in ovarian cancer

Despite the surgical and chemotherapeutic advances over the past few decades, ovarian cancer remains the leading cause of gynecological cancer-related mortality. The absence of biomarkers in early detection and the development of drug resistance are principal causes of treatment failure in ovarian cancer. Recent progress in RNA sequencing (RNA-Seq) with Next Generation Sequencing technology has expanded the understanding of the molecular pathogenesis of ovarian cancer. As compared to previous hybridization-based microarray and Sanger sequence-based methods, RNA-Seq provides multiple layers of resolutions and transcriptome complexity, with less background noise and a broader dynamic range of RNA expression. Beyond quantifying gene expression, the data generated by RNA-Seq accelerates the identification of alternatively spliced genes, fusion genes, mutations/SNPs, allele-specific expression, novel transcripts and non-coding RNAs. RNA-Seq has been successfully applied in ovarian cancer research for earlier detection, ascertaining pathological origin, and defining the aberrant genes and dysregulated molecular pathways across patient groups. This review outlines the distinct advantages of RNA-Seq compared to other transcriptomics methods and its recent applications in ovarian cancer.

Alternative Splicing Plays a Critical Role in Maintaining Mineral Nutrient Homeostasis in Rice (Oryza sativa)

Alternative splicing (AS) of pre-mRNAs promotes transcriptome and proteome diversity and plays important roles in a wide range of biological processes. However, the role of AS in maintaining mineral nutrient homeostasis in plants is largely unknown. To clarify this role, we obtained whole transcriptome RNA sequencing data from rice (Oryza sativa) roots grown in the presence or absence of several mineral nutrients (Fe, Zn, Cu, Mn, and P). Our systematic analysis revealed 13,291 alternatively spliced genes, representing ∼53.3% of the multiexon genes in the rice genome. As the overlap between differentially expressed genes and differentially alternatively spliced genes is small, a molecular understanding of the plant's response to mineral deficiency is limited by analyzing differentially expressed genes alone. We found that the targets of AS are highly nutrient-specific. To verify the role of AS in mineral nutrition, we characterized mutants in genes encoding Ser/Arg (SR) proteins that function in AS. We identified several SR proteins as critical regulators of Zn, Mn, and P nutrition and showed that three SR protein-encoding genes regulate P uptake and remobilization between leaves and shoots of rice, demonstrating that AS has a key role in regulating mineral nutrient homeostasis in rice.

Single sample sequencing (S3EQ) of epigenome and transcriptome in nucleus accumbens

BACKGROUND

High-throughput sequencing has been widely applied to uncover the molecular mechanisms underlying neurological and psychiatric disorders. The large body of data support the role of epigenetic mechanisms in neurological function of both human and animals. Yet, the existing data is limited by the fact that epigenetic and transcriptomic changes have only been measured in separate cohorts. This has limited precise correlation of epigenetic changes in gene expression.

NEW METHOD

Single Sample Sequencing (S3EQ) is an innovative approach to analyze both epigenetic and transcriptomic regulation within a single neuronal sample. Using this method, we analyzed chromatin immunoprecipitation (ChIP)- and RNA-sequencing data from the nucleus accumbens (NAc) of the same animal.

RESULTS

ChIP-S3EQ of neuronal nuclei reliably identified hPTM enrichment in the adult mouse NAc with high precision. Comparing cellular compartments, we found that the spliceosome of whole cell RNA-seq was more closely recapitulated by cytosolic RNA-S3EQ than nuclear RNA-seq. Finally, S3EQ showed increased sensitivity for correlating chromatin modifications with gene expression, especially for lowly expressed transcripts.

COMPARISON WITH EXISTING METHODS

S3EQ accurately generates both RNA- and ChIP-seq from a single sample, providing a clear advantage over existing methods which require two samples. ChIP-S3EQ performance was comparable to ChIP-seq, while RNA-S3EQ generated an almost identical expression profile to nuclear-enriched and whole cell RNA-seq. Finally, we directly compared RNA-seq by cellular compartments, addressing a limitation of RNA-seq studies limited to neuronal nuclei.

CONCLUSION

The S3EQ method can be applied to improve the correlative power of transcriptomic and epigenomic studies in neuronal tissue.

Abnormal Small Intestinal Epithelial Microvilli in Patients With Crohn's Disease

BACKGROUND & AIMS

Crohn disease (CD) presents as chronic and often progressive intestinal inflammation, but the contributing pathogenic mechanisms are unclear. We aimed to identify alterations in intestinal cells that could contribute to the chronic and progressive course of CD.

METHODS

We took an unbiased system-wide approach by performing sequence analysis of RNA extracted from formalin-fixed paraffin-embedded ileal tissue sections from patients with CD (n = 36) and without CD (controls; n = 32). We selected relatively uninflamed samples, based on histology, before gene expression profiling; validation studies were performed using adjacent serial tissue sections. A separate set of samples (3 control and 4 CD samples) was analyzed by transmission electron microscopy. We developed methods to visualize an overlapping modular network of genes dysregulated in the CD samples. We validated our findings using biopsy samples (110 CD samples for gene expression analysis and 54 for histologic analysis) from the UNITI-2 phase 3 trial of ustekinumab for patients with CD and healthy individuals (26 samples used in gene expression analysis).

RESULTS

We identified gene clusters that were altered in nearly all CD samples. One cluster encoded genes associated with the enterocyte brush border, leading us to investigate microvilli. In ileal tissues from patients with CD, the microvilli were of decreased length and had ultrastructural defects compared with tissues from controls. Microvilli length correlated with expression of genes that regulate microvilli structure and function. Network analysis linked the microvilli cluster to several other down-regulated clusters associated with altered intracellular trafficking and cellular metabolism. Enrichment of a core microvilli gene set also was lower in the UNITI-2 trial CD samples compared with controls; expression of microvilli genes was correlated with microvilli length and endoscopy score and was associated with response to treatment.

CONCLUSIONS

In a transcriptome analysis of formalin-fixed and paraffin-embedded ileal tissues from patients with CD and controls, we associated transcriptional alterations with histologic alterations, such as differences in microvilli length. Decreased microvilli length and decreased expression of the microvilli gene set might contribute to epithelial malfunction and the chronic and progressive disease course in patients with CD.

Identification of microR-106b as a prognostic biomarker of p53-like bladder cancers by ActMiR

Bladder cancers can be categorized into subtypes according to gene expression patterns. P53-like muscle-invasive bladder cancers are generally resistant to cisplatin-based chemotherapy, but exhibit heterogeneous clinical outcomes with a prognosis intermediate to that of the luminal and basal subtypes. The optimal approach to p53-like tumors remains poorly defined and better means to risk-stratify such tumors and identification of novel therapeutic targets is urgently needed. MicroRNAs (miRNAs) play a key role in cancer, both in tumorigenesis and tumor progression. In the past few years, miRNA expression signatures have been reported as prognostic biomarkers in different tumor types including bladder cancer. However, miRNA’s expression does not always correlate well with its activity. We previously developed ActMiR, a computational method for explicitly inferring miRNA activities. We applied ActMiR to The Cancer Genome Atlas (TCGA) bladder cancer data set and identified the activities of miR-106b-5p and miR-532-3p as potential prognostic markers of the p53-like subtype, and validated them in three independent bladder cancer data sets. Especially, higher miR-106b-5p activity was consistently associated with better survival in these data sets. Furthermore, we experimentally validated causal relationships between miR-106-5p and its predicted target genes in p53-like cell line HT1197. HT1197 cells treated with the miR-106b-5p-specific inhibitor were more invasive while cells treated with the miR-106b-5p-specific mimic were less invasive than corresponding controls. Altogether, our results suggest that miR-106b-5p activity can categorize p53-like bladder tumors into more and less-favorable prognostic groups, which provides critical information for personalizing treatment option for p53-like bladder cancers.

RNA sequencing confirms similarities between PPI-responsive oesophageal eosinophilia and eosinophilic oesophagitis

BACKGROUND

Although current American guidelines distinguish proton pump inhibitor-responsive oesophageal eosinophilia (PPI-REE) from eosinophilic oesophagitis (EoE), these entities are broadly similar. While two microarray studies showed that they have similar transcriptomes, more extensive RNA sequencing studies have not been done previously.

AIM

To determine whether RNA sequencing identifies genetic markers distinguishing PPI-REE from EoE.

METHODS

We retrospectively examined 13 PPI-REE and 14 EoE biopsies, matched for tissue eosinophil content, and 14 normal controls. Patients and controls were not PPI-treated at the time of biopsy. We did RNA sequencing on formalin-fixed, paraffin-embedded tissue, with differential expression confirmation by quantitative polymerase chain reaction (PCR). We validated the use of formalin-fixed, paraffin-embedded vs RNAlater-preserved tissue, and compared our formalin-fixed, paraffin-embedded EoE results to a prior EoE study.

RESULTS

By RNA sequencing, no genes were differentially expressed between the EoE and PPI-REE groups at the false discovery rate (FDR) ≤0.01 level. Compared to normal controls, 1996 genes were differentially expressed in the PPI-REE group and 1306 genes in the EoE group. By less stringent criteria, only MAPK8IP2 was differentially expressed between PPI-REE and EoE (FDR = 0.029, 2.2-fold less in EoE than in PPI-REE), with similar results by PCR. KCNJ2, which was differentially expressed in a prior study, was similar in the EoE and PPI-REE groups by both RNA sequencing and real-time PCR.

CONCLUSION

Eosinophilic oesophagitis and PPI-REE have comparable transcriptomes, confirming that they are part of the same disease continuum.

Identification and characterization of long noncoding RNAs and mRNAs expression profiles related to postnatal liver maturation of breeder roosters using Ribo-zero RNA sequencing

BACKGROUND

The liver is mainly hematopoietic in the embryo, and converts into a major metabolic organ in the adult. Therefore, it is intensively remodeled after birth to adapt and perform adult functions. Long non-coding RNAs (lncRNAs) are involved in organ development and cell differentiation, likely they have potential roles in regulating postnatal liver development. Herein, in order to understand the roles of lncRNAs in postnatal liver maturation, we analyzed the lncRNAs and mRNAs expression profiles in immature and mature livers from one-day-old and adult (40 weeks of age) breeder roosters by Ribo-Zero RNA-Sequencing.

RESULTS

Around 21,939 protein-coding genes and 2220 predicted lncRNAs were expressed in livers of breeder roosters. Compared to protein-coding genes, the identified chicken lncRNAs shared fewer exons, shorter transcript length, and significantly lower expression levels. Notably, in comparison between the livers of newborn and adult breeder roosters, a total of 1570 mRNAs and 214 lncRNAs were differentially expressed with the criteria of log2fold change > 1 or < - 1 and P values < 0.05, which were validated by qPCR using randomly selected five mRNAs and five lncRNAs. Further GO and KEGG analyses have revealed that the differentially expressed mRNAs were involved in the hepatic metabolic and immune functional changes, as well as some biological processes and pathways including cell proliferation, apoptotic and cell cycle that are implicated in the development of liver. We also investigated the cis- and trans- regulatory effects of differentially expressed lncRNAs on its target genes. GO and KEGG analyses indicated that these lncRNAs had their neighbor protein coding genes and trans-regulated genes associated with adapting of adult hepatic functions, as well as some pathways involved in liver development, such as cell cycle pathway, Notch signaling pathway, Hedgehog signaling pathway, and Wnt signaling pathway.

CONCLUSIONS

This study provides a catalog of mRNAs and lncRNAs related to postnatal liver maturation of chicken, and will contribute to a fuller understanding of biological processes or signaling pathways involved in significant functional transition during postnatal liver development that differentially expressed genes and lncRNAs could take part in.

Identification of Pasteurella multocida transcribed genes in porcine lungs through RNAseq

Pasteurella multocida is one of the most important pathogen that causes pneumonia in swine. Although several virulence factors are known, the pathogenesis of this bacterium is not well-studied. Therefore, to study the pathogenesis of P. multocida infection in porcine lung, next-generation RNA sequencing was used to compare the transcriptomes of P. multocida grown in vivo and in vitro, respectively. After P. multocida infection a total of 704 genes were expressed in vitro, 1422 genes were expressed in vivo, and 237 genes were differentially expressed based on statistical analyses, padj of ≤0.1. Genes encoding ribosomal proteins or other products that function in the regulation of transcription and translation were downregulated, whereas genes whose products affected cellular processes (protein transport and RNA degradation) and metabolic pathways, such as those of amino acid metabolism and nucleotide metabolism, were upregulated in vitro compared with in vivo. This study shows that differentially expressed genes in P. multocida regulate pathways that operate during stress, iron capture, heat shock, and nitrogen regulation. However, extensive investigation of the pathogenic mechanism of P. multocida is still required.

mRNA-seq whole transcriptome profiling of fresh frozen versus archived fixed tissues

Background

The main bottleneck for genomic studies of tumors is the limited availability of fresh frozen (FF) samples collected from patients, coupled with comprehensive long-term clinical follow-up. This shortage could be alleviated by using existing large archives of routinely obtained and stored Formalin-Fixed Paraffin-Embedded (FFPE) tissues. However, since these samples are partially degraded, their RNA sequencing is technically challenging.

Results

In an effort to establish a reliable and practical procedure, we compared three protocols for RNA sequencing using pairs of FF and FFPE samples, both taken from the same breast tumor. In contrast to previous studies, we compared the expression profiles obtained from the two matched sample types, using the same protocol for both. Three protocols were tested on low initial amounts of RNA, as little as 100 ng, to represent the possibly limited availability of clinical samples. For two of the three protocols tested, poly(A) selection (mRNA-seq) and ribosomal-depletion, the total gene expression profiles of matched FF and FFPE pairs were highly correlated. For both protocols, differential gene expression between two FFPE samples was in agreement with their matched FF samples. Notably, although expression levels of FFPE samples by mRNA-seq were mainly represented by the 3′-end of the transcript, they yielded very similar results to those obtained by ribosomal-depletion protocol, which produces uniform coverage across the transcript. Further, focusing on clinically relevant genes, we showed that the high correlation between expression levels persists at higher resolutions.

Conclusions

Using the poly(A) protocol for FFPE exhibited, unexpectedly, similar efficiency to the ribosomal-depletion protocol, with the latter requiring much higher (2–3 fold) sequencing depth to compensate for the relative low fraction of reads mapped to the transcriptome. The results indicate that standard poly(A)-based RNA sequencing of archived FFPE samples is a reliable and cost-effective alternative for measuring mRNA-seq on FF samples. Expression profiling of FFPE samples by mRNA-seq can facilitate much needed extensive retrospective clinical genomic studies.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4761-3) contains supplementary material, which is available to authorized users.

Credentialing Individual Samples for Proteogenomic Analysis

An integrated analysis of DNA, RNA and protein, so called proteogenomic studies, has the potential to greatly increase our understanding of both normal physiology and disease development. However, such studies are challenged by a lack of a systematic approach to credential individual samples resulting in the introduction of noise into the system that limits the ability to identify important biological signals. Indeed, a recent proteogenomic CPTAC study identified 26% of samples as unsatisfactory, resulting in a marked increase in cost and loss of information content. Based on a large-scale analysis of RNA-seq and proteomic data generated by reverse phase protein arrays (RPPA) and by mass spectrometry, we propose a protein-mRNA correlation-based (PMC) score as a robust metric to credential single samples for integrated proteogenomic studies. Samples with high PMC scores have significantly higher protein-mRNA correlation, total protein content and tumor purity. Our results highlight the importance of credentialing individual samples prior to proteogenomic analysis.

Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction

All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.

Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer

Breast cancer metastasis remains a clinical challenge, even within a single patient across multiple sites of the disease. Genome-wide comparisons of both the DNA and gene expression of primary tumors and metastases in multiple patients could help elucidate the underlying mechanisms that cause breast cancer metastasis. To address this issue, we performed DNA exome and RNA sequencing of matched primary tumors and multiple metastases from 16 patients, totaling 83 distinct specimens. We identified tumor-specific drivers by integrating known protein-protein network information with RNA expression and somatic DNA alterations and found that genetic drivers were predominantly established in the primary tumor and maintained through metastatic spreading. In addition, our analyses revealed that most genetic drivers were DNA copy number changes, the TP53 mutation was a recurrent founding mutation regardless of subtype, and that multiclonal seeding of metastases was frequent and occurred in multiple subtypes. Genetic drivers unique to metastasis were identified as somatic mutations in the estrogen and androgen receptor genes. These results highlight the complexity of metastatic spreading, be it monoclonal or multiclonal, and suggest that most metastatic drivers are established in the primary tumor, despite the substantial heterogeneity seen in the metastases.

Integrity, standards, and QC-related issues with big data in pre-clinical drug discovery

The tremendous expansion of data analytics and public and private big datasets presents an important opportunity for pre-clinical drug discovery and development. In the field of life sciences, the growth of genetic, genomic, transcriptomic and proteomic data is partly driven by a rapid decline in experimental costs as biotechnology improves throughput, scalability, and speed. Yet far too many researchers tend to underestimate the challenges and consequences involving data integrity and quality standards. Given the effect of data integrity on scientific interpretation, these issues have significant implications during preclinical drug development. We describe standardized approaches for maximizing the utility of publicly available or privately generated biological data and address some of the common pitfalls. We also discuss the increasing interest to integrate and interpret cross-platform data. Principles outlined here should serve as a useful broad guide for existing analytical practices and pipelines and as a tool for developing additional insights into therapeutics using big data.

Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction

Background

Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. The latter method is of particular interest because it is compatible with degraded samples such as those extracted from FFPE and also captures transcripts that are not poly-adenylated such as some non-coding RNAs. Here we provide a cross-site study that evaluates the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples.

Results

We find that all of the kits are capable of performing significant ribosomal depletion, though there are differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ~ 14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes between kits suggests that transcript length may be a key factor in library production efficiency.

Conclusions

These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4585-1) contains supplementary material, which is available to authorized users.

Developmental transcriptome profiling of bovine muscle tissue reveals an abundant GosB that regulates myoblast proliferation and apoptosis

The formation of bovine skeletal muscle involves complex developmental and physiological processes that play a vital role in determining the quality of beef; however, the regulatory mechanisms underlying differences in meat quality are largely unknown. We conducted transcriptome analysis of bovine muscle tissues to compare gene expression profiles between embryonic and adult stages. Total RNAs from skeletal muscle of Qinchuan cattle at fetal and adult stages were used to construct libraries for Illumina next-generation sequencing using the Ribo-Zero RNA sequencing (RNA-Seq) method. We found a total of 19,695 genes to be expressed in fetal and adult stages, whereby 3,299 were expressed only in fetal, and 433 only in adult tissues. We characterized the role of a candidate gene (GosB), which was highly (but differentially) expressed in embryonic and adult skeletal muscle tissue. GosB increased the number of myoblasts in the S-phase of the cell cycle, and decreased the proportion of cells in the G0/G1 phase. GosB promoted the proliferation of myoblasts and protected them from apoptosis via regulating Bcl-2 expression and controlling the intracellular calcium concentration. Modulation of GosB expression in muscle tissue may emerge as a potential target in breeding strategies attempting to alter myoblast numbers in cattle.

P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

BACKGROUND

Obtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene regions. Genomes are widely transcribed, generating messenger and non-coding RNAs. These widespread transcripts can be used to scaffold genomes and complete transcribed regions.

RESULTS

We present P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs. Tested in various species, P_RNA_scaffolder exhibited higher speed and efficiency than the existing state-of-the-art scaffolders. This tool also improved the contiguity of genome assemblies generated by current mate-pair scaffolding and third-generation single-molecule sequencing assembly.

CONCLUSIONS

The P_RNA_scaffolder can improve the contiguity of genome assembly and benefit gene prediction. This tool is available at http://www.fishbrowser.org/software/P_RNA_scaffolder .

RNA-QC-chain: comprehensive and fast quality control for RNA-Seq data

BACKGROUND

RNA-Seq has become one of the most widely used applications based on next-generation sequencing technology. However, raw RNA-Seq data may have quality issues, which can significantly distort analytical results and lead to erroneous conclusions. Therefore, the raw data must be subjected to vigorous quality control (QC) procedures before downstream analysis. Currently, an accurate and complete QC of RNA-Seq data requires of a suite of different QC tools used consecutively, which is inefficient in terms of usability, running time, file usage, and interpretability of the results.

RESULTS

We developed a comprehensive, fast and easy-to-use QC pipeline for RNA-Seq data, RNA-QC-Chain, which involves three steps: (1) sequencing-quality assessment and trimming; (2) internal (ribosomal RNAs) and external (reads from foreign species) contamination filtering; (3) alignment statistics reporting (such as read number, alignment coverage, sequencing depth and pair-end read mapping information). This package was developed based on our previously reported tool for general QC of next-generation sequencing (NGS) data called QC-Chain, with extensions specifically designed for RNA-Seq data. It has several features that are not available yet in other QC tools for RNA-Seq data, such as RNA sequence trimming, automatic rRNA detection and automatic contaminating species identification. The three QC steps can run either sequentially or independently, enabling RNA-QC-Chain as a comprehensive package with high flexibility and usability. Moreover, parallel computing and optimizations are embedded in most of the QC procedures, providing a superior efficiency. The performance of RNA-QC-Chain has been evaluated with different types of datasets, including an in-house sequencing data, a semi-simulated data, and two real datasets downloaded from public database. Comparisons of RNA-QC-Chain with other QC tools have manifested its superiorities in both function versatility and processing speed.

CONCLUSIONS

We present here a tool, RNA-QC-Chain, which can be used to comprehensively resolve the quality control processes of RNA-Seq data effectively and efficiently.

Accurate RNA Sequencing From Formalin-Fixed Cancer Tissue To Represent High-Quality Transcriptome From Frozen Tissue

PURPOSE

Accurate transcriptional sequencing (RNA-seq) from formalin-fixation and paraffin-embedding (FFPE) tumor samples presents an important challenge for translational research and diagnostic development. In addition, there are now several different protocols to prepare a sequencing library from total RNA. We evaluated the accuracy of RNA-seq data generated from FFPE samples in terms of expression profiling.

METHODS

We designed a biospecimen study to directly compare gene expression results from different protocols to prepare libraries for RNA-seq from human breast cancer tissues, with randomization to fresh-frozen (FF) or FFPE conditions. The protocols were compared using multiple computational methods to assess alignment of reads to reference genome, and the uniformity and continuity of coverage; as well as the variance and correlation, of overall gene expression and patterns of measuring coding sequence, phenotypic patterns of gene expression, and measurements from representative multigene signatures.

RESULTS

The principal determinant of variance in gene expression was use of exon capture probes, followed by the conditions of preservation (FF versus FFPE), and phenotypic differences between breast cancers. One protocol, with RNase H-based rRNA depletion, exhibited least variability of gene expression measurements, strongest correlation between FF and FFPE samples, and was generally representative of the transcriptome from standard FF RNA-seq protocols.

CONCLUSION

Method of RNA-seq library preparation from FFPE samples had marked effect on the accuracy of gene expression measurement compared to matched FF samples. Nevertheless, some protocols produced highly concordant expression data from FFPE RNA-seq data, compared to RNA-seq results from matched frozen samples.

Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial

This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA. The personalized genomic vaccine (PGV) pipeline is modular and consists of independently usable tools and software libraries. We hope that the functionality of these tools may extend beyond the specifics of the PGV-001 trial and enable other research groups in their own neoantigen investigations.

Systematic analysis of the regulatory roles of microRNAs in postnatal maturation and metergasis of liver of breeder cocks

The liver function of chickens is intensively remodeled from birth to adult, which was validated by metabolomics research in the present study. In order to understand the roles of microRNAs (miRNA) in liver maturation and metergasis, miRNA expression profiles in livers of 20 male chicks aged one day and five adult cocks aged 35 weeks were determined. A total of 191 differentially expressed miRNAs with the criteria of P < 0.05 and fold changes either >1.5 or <0.67 and 32 differentially expressed miRNAs with the criteria of false discovery value (FDR) < 0.05 and fold changes either >1.5 or <0.67 were detected. Subsequently, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of the targets revealed that candidate miRNAs may involve in the regulation of hepatic metabolism and immune functions, and some pathways including cell cycle which were implicated in postnatal liver development. Furthermore, 1211 differentially expressed mRNAs (messenger RNA) in livers between the postnatal and matured chickens were used to define the roles of differentially expressed miRNAs in regulating the expression of target genes. Our results revealed the first miRNA profile related to the adaption of mature liver functions after birth in breeder cock.

Dexamethasone downregulates SIRT1 and IL6 and upregulates EDN1 genes in stem cells derived from gingivae via the AGE/RAGE pathway

OBJECTIVES

To evaluate the effects of dexamethasone on the aging of mesenchymal stem cells from human gingiva using next-generation sequencing.

RESULTS

Four mRNAs were upregulated and 12 were downregulated when the results of dexamethasone at 24 h were compared with the control at 24 h. Expressions of SIRT1 and IL6 were decreased in dexamethasone at 24 h but expression of EDN1 was increased.

CONCLUSIONS

Application of dexamethasone reduced the expression of SIRT1 and IL6 but enhanced the expression of EDN1 of stem cells.

Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation

As part of normal development most eukaryotic organisms, ranging from insects and mammals to plants, display variations in nuclear ploidy levels resulting from somatic endopolyploidy. Endoreduplication is the major source of endopolyploidy in higher plants. Endoreduplication is a remarkable characteristic of the fleshy pericarp tissue of developing tomato fruits, where it establishes a highly integrated cellular system that acts as a morphogenetic factor supporting cell growth. However, the functional significance of endoreduplication is not fully understood. Although endoreduplication is thought to increase metabolic activity due to a global increase in transcription, the issue of gene-specific ploidy-regulated transcription remains open. To investigate the influence of endoreduplication on transcription in tomato fruit, we tested the feasibility of a RNA sequencing (RNA-Seq) approach using total nuclear RNA extracted from purified populations of flow cytometry-sorted nuclei based on their DNA content. Here we show that cell-based approaches to the study of RNA-Seq profiles need to take into account the putative global shift in expression between samples for correct analysis and interpretation of the data. From ploidy-specific expression profiles we found that the activity of cells inside the pericarp is related both to the ploidy level and their tissue location.

A Guide to the Chloroplast Transcriptome Analysis Using RNA-Seq

Since its first use in plants in 2007, high-throughput RNA sequencing (RNA-Seq) has generated a vast amount of data for both model and nonmodel species. Organellar transcriptomes, however, are virtually always overlooked at the data analysis step. We therefore developed ChloroSeq, a bioinformatic pipeline aimed at facilitating the systematic analysis of chloroplast RNA metabolism, and we provide here a step-by-step user's manual. Following the alignment of quality-controlled data to the genome of interest, ChloroSeq measures genome expression level along with splicing and RNA editing efficiencies. When used in combination with the Tuxedo suite (TopHat and Cufflinks), ChloroSeq allows the simultaneous analysis of organellar and nuclear transcriptomes, opening the way to a better understanding of nucleus-organelle cross talk. We also describe the use of R commands to produce publication-quality figures based on ChloroSeq outputs. The effectiveness of the pipeline is illustrated through analysis of an RNA-Seq dataset covering the transition from growth to maturation to senescence of Arabidopsis thaliana leaves.

A pilot systematic genomic comparison of recurrence risks of hepatitis B virus-associated hepatocellular carcinoma with low- and high-degree liver fibrosis

BACKGROUND

Chronic hepatitis B virus (HBV) infection leads to liver fibrosis, which is a major risk factor in hepatocellular carcinoma (HCC) and an independent risk factor of recurrence after HCC tumor resection. The HBV genome can be inserted into the human genome, and chronic inflammation may trigger somatic mutations. However, how HBV integration and other genomic changes contribute to the risk of tumor recurrence with regards to the different degree of liver fibrosis is not clearly understood.

METHODS

We sequenced mRNAs of 21 pairs of tumor and distant non-neoplastic liver tissues of HBV-HCC patients and performed comprehensive genomic analyses of our RNAseq data and public available HBV-HCC sequencing data.

RESULTS

We developed a robust pipeline for sensitively identifying HBV integration sites based on sequencing data. Simulations showed that our method outperformed existing methods. Applying it to our data, 374 and 106 HBV host genes were identified in non-neoplastic liver and tumor tissues, respectively. When applying it to other RNA sequencing datasets, consistently more HBV integrations were identified in non-neoplastic liver than in tumor tissues. HBV host genes identified in non-neoplastic liver samples significantly overlapped with known tumor suppressor genes. More significant enrichment of tumor suppressor genes was observed among HBV host genes identified from patients with tumor recurrence, indicating the potential risk of tumor recurrence driven by HBV integration in non-neoplastic liver tissues. We also compared SNPs of each sample with SNPs in a cancer census database and inferred samples' pathogenic SNP loads. Pathogenic SNP loads in non-neoplastic liver tissues were consistently higher than those in normal liver tissues. Additionally, HBV host genes identified in non-neoplastic liver tissues significantly overlapped with pathogenic somatic mutations, suggesting that HBV integration and somatic mutations targeting the same set of genes are important to tumorigenesis. HBV integrations and pathogenic mutations showed distinct patterns between low and high liver fibrosis patients with regards to tumor recurrence.

CONCLUSIONS

The results suggest that HBV integrations and pathogenic SNPs in non-neoplastic tissues are important for tumorigenesis and different recurrence risk models are needed for patients with low and high degrees of liver fibrosis.