Name: Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations (Video) | JoVE Journal
Uploaded: 2016-08-04T13:00:00.000+00:00
Duration: 11 min 52 s
Description: Learn targeted RNA sequencing to enrich specific transcripts for next generation sequencing. This method enables analysis of gene expression, mutations, and gene fusions in molecular biology research.

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We give special thanks to Ezra Lyon, Eliot Zhu, Michele Wing, Esko Kautto and Eric Samorodnitsky for technical support. We would also like to thank Jenny Badillo for her administrative support for our team. We acknowledge the Ohio Supercomputer Center (OSC) for providing disk space, processing capacity, and support to run our analyses. We thank the Comprehensive Cancer Center (CCC) at The Ohio State University Wexner Medical Center for their administrative support of this work. S.R. and Team are supported by the American Cancer Society (MRSG-12-194-01-TBG), a Prostate Cancer Foundation Young Investigator Award, NHGRI (UM1HG006508-01A1), Fore Cancer Research Foundation, American Lung Association, and Pelotonia.

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S.R. receives funding from Novartis and Ariad Pharmaceuticals for conduct of clinical trials. S.R. immediate family members own stock in Johnson and Johnson.

RNAseq Capture is an intermediate strategy between RNAseq and microarray approaches for evaluating a selected part of the transcriptome. The advantages of Capture include reduced cost, rapid turnaround time on a desktop sequencer, high throughput, and detection of genomic alterations. The method can be adapted to characterize non-coding RNAs23, detect single nucleotide variants4-6, examine RNA splicing, and to identify gene fusions or structural rearrangements24. Further, this approach ca...

Whole transcriptome or RNA sequencing (RNAseq) is an unbiased sequencing method to assess all RNA products. The goal of targeted RNAseq (Capture) is a focused evaluation of selected transcripts with increased sensitivity, dynamic range, reduced cost or scale, and increased throughput compared to standard RNAseq. Similar to standard RNAseq, targeted enrichment approaches can be used to evaluate gene expression, multiple RNA species such as mRNA, microRNA (miRNA), lncRNA1, other noncoding RNAs2, gene fusions3, and mutations4-6.
Capture involves hybridization of complementary oligonucleotides to enrich cDNA libraries for sequencing. The rationale for RNAseq Capture is similar to microarray approaches where complementary oligonucleotides or probes are hybridized to samples and then measured for relative abundance. For microarray technologies, expression is based on relative signal measured for transcripts binding to these probes. Microarrays are thus limited by range, potential background noise from non-specific binding, and cross-hybridization of probes. Furthermore, arrays have limited dynamic range for low and highly expressed transcripts compared to RNAseq1. Microarrays are widely utilized due to their reduced cost and high throughput capacity compared to RNAseq. 
Here, we demonstrate a method for RNAseq Capture that offers a middle ground between RNAseq and microarray approaches for evaluating the transcriptome. RNAseq Capture has intermediate throughput, greater dynamic range and sensitivity, and is scaled for fast turnaround on desktop sequencers. RNAseq Capture also requires reduced computational resources in terms of storage space and data processing.

<table><tbody><tr><td>Thermomixer R</td><td>Eppendorf</td><td>21516-166</td><td></td></tr><tr><td>Centrifuge 5417R</td><td>Eppendorf</td><td>5417R</td><td></td></tr><tr><td>miRNeasy Mini Kit</td><td>Qiagen</td><td>217004</td><td></td></tr><tr><td>Molecular Biology Grade Ethanol</td><td>Sigma Aldrich</td><td>E7023-6X500ML</td><td></td></tr><tr><td>Thermoblock 24 x 1.5 ml</td><td>Eppendorf</td><td>21516-166</td><td></td></tr><tr><td>MiSeq Reagent Kit v2 (300-cycles)</td><td>Illumina</td><td>MS-102-2002</td><td></td></tr><tr><td>MiSeq Desktop Sequencer</td><td>Illumina</td><td></td><td></td></tr><tr><td>PhiX Control v3</td><td>Illumina</td><td>FC-110-3001</td><td></td></tr><tr><td>TruSeq Stranded Total RNA Kit with RiboZero Gold SetA</td><td>Illumina</td><td>RS-122-2301</td><td></td></tr><tr><td>25 rxn xGen&amp;reg; Universal Blocking Oligo - TS-p5</td><td>IDT</td><td>127040822</td><td></td></tr><tr><td>25 rxn xGen&amp;reg; Universal Blocking Oligo - TS-p7(6nt)</td><td>IDT</td><td>127040823</td><td></td></tr><tr><td>25 rxn xGen&amp;reg; Universal Blocking Oligo - TS-p7(8nt)</td><td>IDT</td><td>127040824</td><td></td></tr><tr><td>Agencourt&amp;reg; AMPure&amp;reg; XP - PCR Purification beads&amp;nbsp;</td><td>Beckman-Coulter</td><td>A63880</td><td></td></tr><tr><td>Dynabeads&amp;reg; M-270 Streptavidin</td><td>Life Technologies</td><td>65305</td><td></td></tr><tr><td>COT Human DNA, Fluorometric Grade, 1 mg</td><td>Roche Applied Science</td><td>05480647001</td><td></td></tr><tr><td>Qubit&amp;reg; Assay Tubes&amp;nbsp;</td><td>Life Technologies</td><td>Q32856</td><td></td></tr><tr><td>Qubit&amp;reg; dsDNA HS Assay Kit</td><td>Life Technologies</td><td>Q32851</td><td></td></tr><tr><td>SeqCap&amp;reg; EZ Hybridization and Wash Kits&amp;nbsp; (24 or 96 reactions)</td><td>Roche NimbleGen&amp;nbsp;</td><td>05634261001 or 05634253001&amp;nbsp;</td><td></td></tr><tr><td>Qubit&amp;reg; 2.0 Fluorometer&amp;nbsp;</td><td>Life Technologies</td><td>Q32866</td><td></td></tr><tr><td>10 x 2 ml IDTE pH 8.0 (1x TE Solution)</td><td>IDT</td><td></td><td></td></tr><tr><td>Tween20 BioXtra</td><td>Sigma</td><td>P7949-500ML</td><td></td></tr><tr><td>Nuclease Free Water</td><td>Life Technologies</td><td>AM9937</td><td></td></tr><tr><td>C1000 Touch&amp;trade; Thermal Cycler with 96&amp;ndash;Well Fast Rection Module</td><td>Biorad</td><td>185-1196</td><td></td></tr><tr><td>SeqCap EZ Hybridization and Wash Kits</td><td>Roche Applied Science</td><td>05634253001</td><td></td></tr><tr><td>SuperScript II Reverse Transcription 200 U/&amp;#956;l</td><td>Life Technologies</td><td>18064-014</td><td></td></tr><tr><td>D1000 ScreenTape</td><td>Agilent Technol. Inc.</td><td>5067-5582</td><td></td></tr><tr><td>Agencourt RNAClean XP - 40 ml</td><td>Beckman Coulter Inc</td><td>A63987</td><td></td></tr><tr><td>RNA ScreenTape</td><td>Agilent Technol. Inc.</td><td>5067-5576</td><td></td></tr><tr><td>RNA ScreenTape Ladder</td><td>Agilent Technol. Inc.</td><td>5067-5578</td><td></td></tr><tr><td>RNA ScreenTape Sample Buffer</td><td>Agilent Technol. Inc.</td><td>5067-5577</td><td></td></tr><tr><td>Sodium Hydroxide</td><td>Sigma</td><td>72068-100ML</td><td></td></tr><tr><td>DynaBeads MyOne Streptavidin T1</td><td>Life Technologies</td><td>65602</td><td></td></tr><tr><td>DYNAMAG -96 SIDE EACH</td><td>Life Technologies</td><td>12331D</td><td></td></tr><tr><td>Chloroform</td><td>Sigma</td><td>C2432-1L</td><td></td></tr><tr><td>KAPA HotStart ReadyMix</td><td>KAPA Biosystems</td><td>KK2602</td><td></td></tr><tr><td>NanoDrop 2000 Spectrophotometer</td><td>Thermo Scientific</td><td></td><td></td></tr><tr><td>My Block Mini Dry Bath</td><td>Benchmark</td><td>BSH200</td><td></td></tr><tr><td>D1000 Reagents</td><td>Agilent Technol. Inc.</td><td>5067- 5583</td><td></td></tr><tr><td>Vacufuge Plus</td><td>Eppendorf</td><td>022829861&amp;nbsp;</td><td></td></tr></tbody></table>

targeted rna sequencing assay to characterize gene expression and genomic alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding RNAs. Standard RNAseq requires 30 - 100 million sequencing reads and can include multiple RNA products such as mRNA and noncoding RNAs. We demonstrate how targeted RNAseq (capture) permits a focused study on selected RNA products using a desktop sequencer. RNAseq capture can characterize unannotated, low, or transiently expressed transcripts that may otherwise be missed using traditional RNAseq methods. Here we describe the extraction of RNA from cell lines, ribosomal RNA depletion, cDNA synthesis, preparation of barcoded libraries, hybridization and capture of targeted transcripts and multiplex sequencing on a desktop sequencer. We also outline the computational analysis pipeline, which includes quality control assessment, alignment, fusion detection, gene expression quantification and identification of single nucleotide variants. This assay allows for targeted transcript sequencing to characterize gene expression, gene fusions, and mutations.

A schematic highlighting key steps in RNAseq Capture is shown in Figure 1. Four cancer cell lines with known mutations were used to demonstrate the effectiveness of the RNAseq Capture technique (K562 with ABL1 fusion, LC2 with RET fusion, EOL1 with PDGFRalpha fusion and RT-4 with FGFR3 fusion). The four samples were pooled together and sequenced with 2x 100 bp reads on a desktop sequencer, which generates FASTQ files. FASTQ files were r...

We describe a targeted RNA sequencing-based method that includes preparation of indexed cDNA libraries, hybridization and capture with custom probes and data analysis to interrogate selected transcripts for gene expression, mutations, and gene fusions. Targeted RNAseq permits cost-effective, rapid evaluation of selected transcripts on a desktop sequencer.

RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding ...

The overall goal of this assay is to enrich target transcripts for next generation sequencing. This targeted RNA sequencing assay is a multi-step procedure that begins with the depletion of ribosomal RNA from total RNA, followed by chemical fragmentation and synthesis of complementary DNA, preparation of barcoded libraries, hybridization and capture of targeted transcripts, multiplexed sequencing, and ending with data analysis. This video will demonstrate the procedures for hybridization, target capture, and post capture PCR amplification for four samples.So this method can help answer key questions in molecular biology, such as identifying gene fusions, single nucleotide variations, relative gene expression, and alternative splicing involving targeted transcripts. The main advantage of this technique is that it is customizable for any genes of interest. To begin the procedure for hybridization, remove from the 20 degrees Celsius freezer and thaw on ice the following:custom hydrated probes, Cot-1 DNA, universal blocking oligos, and adapter specific blocking oligos.In a low binding 1.5 milliliter tube, combine 500 nanograms of DNA samples, 5 microliters of Cot-1 DNA, one microliter of universal blocking oligos, 0.5 microliters of six nucleotide adapter specific blocking oligos, and 0.5 microliters of eight nucleotide adapter specific blocking oligos. Place the sample tube in a vacuum concentrater with the cap open and facing the opposite direction of rotation. Dry the contents at 45 degrees Celsius for 20 minutes, or until complete evaporation of the liquid.Next, resuspend the dried content with 8.5 microliters of 2x hybridization buffer, 3.4 microliters of hybridization component A, and 1.1 microliter of nuclease-free water. Allow 10 minutes for resuspension, vortexing every 2.5 minutes. Transfer the resuspended material to a 0.2 milliliter PCR tube and incubate in a thermal cycler at 95 degrees Celsius for 10 minutes.Remove the hybridization sample tube from the thermal cycler and add two microliters of custom probes resuspended at a concentration of 1.5 picomoles per microliter. Incubate the hybridization reaction overnight at 65 degrees Celsius. The next step after multiplexeded hybridization is the capture of targeted RNA using streptavidin coupled paramagnetic beads.Remove a bottle of beads from four degrees Celsius and equilibrate it at room temperature for 30 minutes. Prepare 1x working solutions of all the required buffers. Aliquot 140 microliters of 1x wash buffer one into a fresh 1.5 milliliter tube.Heat this aliquotic buffer and the entire amount of 1x stringent buffer at 65 degrees Celsius in a heat block for at least two hours. Aliquot the appropriate amount of beads into a 1.5 milliliter tube. Place in the magnetic separation rack and discard the supernatant.Add bead wash buffer and vortex for 10 seconds. Place the tube in the magnetic separation rack for two to five minutes or until the supernatant is clear. Discard the supernatant.Repeat for a total of two washes. After removal of the bead wash buffer, add an equal volume of bead wash buffer as the initial starting volume. Resuspend and transfer to a 0.2 milliliter PCR tube.Place the tube in the magnetic rack for two to five minutes or until the supernatant is clear. Discard the supernatant. Place the tube with beads in a mini heat block at 65 degrees Celsius.Transfer the hybridization sample to the tube with beads, pipette up and down 10 times to mix, and incubate at 65 degrees Celsius for 45 minutes. Every 15 minutes, vortex the sample and spin down for four seconds using a fixed-speed tabletop mini centrifuge. When the 45 minute incubation is complete, remove the capture tube from the heat block.Add 100 microliters of preheated 1x wash buffer one to the tube, then vortex for 10 seconds to mix. Transfer the mixture to a fresh, low-binding 1.5 milliliter tube. Place the tube in the magnetic rack and allow two to five minutes for separation, or until the supernatant is clear.Discard the supernatant. Add 200 microliters of preheated 1x stringent wash buffer and pipette up and down 10 times to mix. Incubate at 65 degrees Celsius for five minutes.Place the tube in the magnetic rack and allow two to three minutes for separation. Discard the supernatant. Repeat the stringent wash once for a total of two washes.Add 200 microliters of room temperature 1x wash buffer one and vortex for two minutes to mix. Place the tube in the magnetic rack, allow two to five minutes for separation, and discard the supernatant. Add 200 microliters of room temperature 1x wash buffer two and vortex for one minute to mix.Place the tube in the magnetic separation rack for two to five minutes, and then discard the supernatant. Add 200 microliters of room temperature 1x wash buffer three and vortex for 30 seconds to mix. Place the tube in the magnetic separation rack for two to five minutes, and then discard the supernatant.Lastly, remove the tube from the magnetic separation rack and add 20 microliters of nuclease-free water to resuspend the beads. Mix thoroughly by pipetting up and down 10 times. Prior to setting up the post capture PCR amplification, remove paramagnetic beads from four degrees Celsius and equilibrate at room temperature for 30 minutes.Remove the 2x hot start PCR ready mix and PCR primer mix from the 20 degrees Celsius freezer, thaw at room temperature, and then place on ice. Prepare a library amplification master mix by combining 27.5 microliters of 2x hot start PCR ready mix, 2.75 microliters of PCR primer one, and 2.75 microliters of PCR primer two. Set up the reaction in a PCR tube by adding 20 microliters of beads plus captured DNA with 30 microliters of the library amplification master mix.Cap the tube properly and vortex to mix. Centrifuge the tube for four seconds using a fixed-speed mini tabletop centrifuge at six times G.Put the tube into the thermal cycler and initiate the PCR amplification using the following PCR program. An initial denaturation at 98 degrees Celsius for 45 seconds, 10 to 12 cycles of denaturation at 98 degrees Celsius for 15 seconds, annealing at 65 degrees Celsius for 30 seconds, and extension at 72 degrees Celsius for 60 seconds.One final extension cycle at 75 degrees Celsius for 60 seconds, and hold at four degrees Celsius. When the PCR is done, remove the sample from the thermal cycler. Add 75 microliters of paramagnetic beads, mix well, and incubate at room temperature for 15 minutes.Place the tube in the magnetic rack at room temperature for two to three minutes, and then remove the supernatant. Wash the beads on the magnet by adding 200 microliters of 80 percent ethanol, incubating for 30 seconds, and then removing the supernatant. Repeat for a total of two washes.After removing the supernatant from the second ethanol wash, incubate at room temperature for five to ten minutes to allow the beads to dry, but do not over-dry to cracking. Resuspend the beads in 22 microliters of Tris-EDTA pH 8.0 and allow three minutes for elution. Place the sample on the magnet for three to five minutes.Lastly, transfer 20 microliters of the eluted product to a fresh, low-binding 1.5 milliliter tube, ensuring no beads are carried over. A gene expression comparison between the capture method and non-targeted RNA sequencing in four cancer cell lines revealed that the capture method enriched targeted genes, shown in blue, by 10 to 1000 fold over non-targeted genes, shown in grey. Additionally, the percentage of reads mapping to targeted regions was increased in capture versus non-targeted RNA sequencing libraries.An assessment of quality control measures showed that capture and non-targeted RNA sequencing perform equally in terms of alignment to the transcriptome and main insert size. Using the capture method, a higher percentage of exonic regions and a lower percentage of intronic regions were sequenced. As expected, non-targeted RNA sequencing generated over 50 fold more total sequencing reads per sample than capture.Using the capture method, the percentage of ribosomal RNA sequences present in each sample was lower. Finally, comparisons of single nucleotide variants called in overlapping regions of capture and RNA sequencing for each of the four cell lines demonstrate a high concordance of variance between capture and RNA sequencing within the target region. Once mastered, this technique can be done in three to four days if it's performed properly.While attempting this procedure, it's important to remember to work quickly during the capture of hybridized targets and ensure the reaction stays at 65 degrees centigrade. After its development, this technique's paved the way for researchers in the field of molecular biology to study transcripts of interest in a high-throughput and cost-effective way.

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Research

JoVE Journal

Biology

We describe the preparation of barcoded DNA libraries and subsequent hybridization-based exon capture for detection of key cancer-associated mutations in clinical tumor specimens by massively parallel "next generation" sequencing. Targeted exon sequencing offers the benefits of high throughput, low cost, and deep sequence coverage, thus yielding high sensitivity for detecting low frequency mutations.

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

RNA-sequencing and bioinformatics analyses were used to identify significantly and differentially expressed transcription factors in Lin-CD34+ and Lin-CD34- subpopulations of mouse EMLcells. These transcription factors might play important roles in determining the switch between self-renewing Lin-CD34+ and partially differentiated Lin-CD34- cells.

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

An integrated system for targeted next-generation sequencing of oncology specimens is described. This cross-platform system is optimized for low-quality and low-quantity tumor biopsies, accommodates low DNA inputs, includes well-characterized multi-variant controls, and features a novel variant caller that is informed by quantitative pre-analytical quality control measures.

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Here we describe a protocol aimed at investigating the impact of aberrant splicing on drug resistance in solid tumors and hematological malignancies. To this goal, we analyzed the transcriptomic profiles of parental and resistant in vitro models through RNA-seq and established a qRT-PCR based method to validate candidate genes.

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Here, we describe an in situ hybridization assay which enables sensitive and specific detection of sequences as short as 50 nucleotides with single-nucleotide resolution at the single-cell level. The assay, which can be performed manually or automatically, can enable visualization of splice variants, short sequences, and mutations within the tissue context.

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay

miRNA therapeutics have significant potential in regulating cancer progression. Demonstrated here are analytical approaches used for identification of the activity of a combinatorial miRNA treatment in halting cell cycle and angiogenesis.

Analysis of Combinatorial miRNA Treatments to Regulate Cell Cycle and Angiogenesis

Here, the authors showcase the utility of MULTI-seq for phenotyping and subsequent paired scRNA-seq and scATAC-seq in characterizing the transcriptomic and chromatin accessibility profiles in retina.

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Here, we present a protocol for performing gene knockouts that are embryonic lethal in vivo in genetically engineered mouse model-derived tumors and then assessing the effect that the knockout has on tumor growth, proliferation, survival, migration, invasion, and the transcriptome in vitro and in vivo.

Defining Gene Functions in Tumorigenesis by Ex vivo Ablation of Floxed Alleles in Malignant Peripheral Nerve Sheath Tumor Cells

The protocol describes a tandem immunofluorescence hybridization assay with formalin-fixed paraffin-embedded tissue to detect and quantify microRNA and multiplexed proteins simultaneously.

MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as a Novel Detection and Quantification Method

This procedure describes how to establish primary hematopoietic cell cultures from murine bone marrow and is followed by transfection using the Gene Pulser MXCell electroporation system.

The Preparation of Primary Hematopoietic Cell Cultures From Murine Bone Marrow for Electroporation

Learn targeted RNA sequencing to enrich specific transcripts for next generation sequencing. This method enables analysis of gene expression, mutations, and gene fusions in molecular biology research.

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

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