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rna sequencing review

11/01/2021

PLoS ONE. Gong W, Yang L, Wang Y, Xian J, Qiu F, Liu L, et al. Int J Biol Sci. Front Mol Biosci. USA.gov. Zhu L, Li J, Gong Y, Wu Q, Tan S, Sun D, et al. 2016;16:275–87. Burrell RA, Swanton C. Re-evaluating clonal dominance in cancer evolution. J Mol Diagn. 2016;17:13. The next step is to map the clean reads to either a genome or a transcriptome. An immunogenic personal neoantigen vaccine for patients with melanoma. Clustering. Maynard A, McCoach CE, Rotow JK, Harris L, Haderk F, Kerr DL, et al. 2016;9:93. 4. J Hematol Oncol. McGranahan N, Furness AJ, Rosenthal R, Ramskov S, Lyngaa R, Saini SK, et al. 2020;9:1830513. Cieślik M, Chinnaiyan AM. RNA-seq technology has some advantages over the cDNA microarrays, such as the high level of data reproducibility through lanes and flow-cells, which reduces the number of technical replicates for the experiments. Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. However, this method suffers from the drawback of reduced throughput, higher cost and higher sequencing error rate, especially insertion-deletion errors. It was not until 1953 when Watson and Crick proposed the double-helix structure did people truly realize at the molecular level that the essence of life is the result of gene interactions [4]. This highly conserved homeostatic program establishes a connection between autoimmune prevention and immune surveillance in cancer [145]. Posted by: RNA-Seq Blog in Review Publications, Workflow November 6, 2014 11,177 Views. RNA-seq has also conducted in-depth research on the drug resistance of hematological malignancies. DNA library preparation: RNA fragmentation and DNA fragmentation compared, A region containing two overlapping transcripts ( ACT1 ,…, NLM Watson JD, Crick FH. Gastric Cancer. In addition to solid tumors, scRNA-seq of acute myeloid leukemia patients detected diverse immunomodulatory genes that suppress T cell function [136]. In one study of pancreatic ductal adenocarcinoma, human pancreatic cancer (PANC-1) cells and gemcitabine-resistant PANC-1 cell lines were compared by RNA sequencing, and two circRNAs were identified as both novel biomarkers and potential therapeutic targets for gemcitabine resistant patients [121]. Science. Nat Rev Genet. Nucleic Acids Res. A sub-population cells with immunotherapy persistence have been identified by scRNA-seq and were found to have stem cell-like states with the expression of stem cell antigen-1 (Sca-1) and Snai1 [157]. Single-cell RNA sequencing reveals compartmental remodeling of tumor-infiltrating immune cells induced by anti-CD47 targeting in pancreatic cancer. P50 HG002357/HG/NHGRI NIH HHS/United States, P50 HG002357-10/HG/NHGRI NIH HHS/United States, R01 CA077808/CA/NCI NIH HHS/United States, R01 CA077808-12/CA/NCI NIH HHS/United States. J Hematol Oncol. Vara C, Paytuví-Gallart A, Cuartero Y, Le Dily F, Garcia F, Salvà-Castro J, et al. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. ScRNA-seq enables genomic and molecular profiling of high quantity and quality individual immune cells and assessment of cellular heterogeneity to depict the immune system spectrum in the cancer microenvironment [130,131,132]. McFarland J, Paolella B, Warren A, Geiger-Schuller K, Shibue T, Rothberg M, et al. 2020. https://doi.org/10.1172/JCI135038. To overcome this problem, missing data need to be imputed and analyzed by several methods, such as optimal clustering with missing values [182]. Methods Enzymol. It can greatly reduce the false positive rate of splice sites and capture the diversity of transcript isoforms [15]. Google Scholar. 2018;6:32. For example, batch effects can come from cells captured and sequenced in different conditions [183]. 2, 3). ScRNA-seq data demonstrated that compared to normal tissues, cancer tissues exhibited significantly higher heterogeneity in the immune microenvironment, and a continuity in T cell activation resulting from polyclonal T cells and heterogeneous antigen-presenting cells has been identified [133]. ISG15 predicts poor prognosis and promotes cancer stem cell phenotype in nasopharyngeal carcinoma. 2010;28:511–5. Mol Ther. Google Scholar. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Ståhl P, Salmén F, Vickovic S, Lundmark A, Navarro J, Magnusson J, et al. J Hematol Oncol. These methods contain sequencing by synthesis, sequencing by reversible terminator and sequencing by ligation. Article  Comprehensive mapping of long-range interactions reveals folding principles of the human genome. J Hematol Oncol 13, 166 (2020). Bakken TE, Hodge RD, Miller JA, Yao Z, Nguyen TN, Aevermann B, et al. ... RAD-seq … CircPAN3 contributes to drug resistance in acute myeloid leukemia through regulation of autophagy. 2018;50:1429–40. In the cancer immune microenvironment, neutrophils, in addition to T cells, are also key components of cancer progression and cancer drug resistance [138,139,140,141]. Intracellular staining and sequencing (INs-seq), a novel technology integrating scRNA-seq and intracellular protein activity measurements, revealed novel Arg1 + Trem2 + regulatory myeloid (Mreg) cells and demonstrated that depletion of Trem2 led to deduction of exhausted CD8 T cells with increased NK and cytotoxic T cells and cancer suppression by reducing accumulation of intratumoral Mreg cells [160]. Oncotarget. 2020;13:117. Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments. Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. PubMed Central  2019;12:131. Google Scholar. Prostate. Combined with cell sorting or ligand-receptor interaction, scRNA-seq was utilized in cellular interaction, cell spatial organization as well as molecular crosstalk characterization [137, 201, 202]. The same year, Sanger determined the 5368 bp genome of phage φX174, which is the first DNA genome sequenced [7]. Nat Commun. Samples from different backgrounds (different species, tissues and periods) can be used for RNA sequencing to identify differentially expressed genes, revealing their function and potential molecular mechanisms [61]. 2019;35:4159–61. Nat Rev Drug Discov. Nat Biotechnol. 2011;30:99–104. Topalian SL, Taube JM, Anders RA, Pardoll DM. 2020;21. Bioinformatics. Cell. Analysis of survival-related lncRNA landscape identifies a role for LINC01537 in energy metabolism and lung cancer progression. Cell Rep. 2019;27:708–18. Bo H, Fan L, Li J, Liu Z, Zhang S, Shi L, et al. 2020;30:763–78. In breast cancer, single-cell RNA sequencing identified a tumor-infiltrating immunosuppressive immature myeloid cell that leads to drug resistance [117]. Li S, Tighe S, Nicolet C, Grove D, Levy S, Farmerie W, et al. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Cancer Immunol Immunother. Unruh D, Zewde M, Buss A, Drumm MR, Tran AN, Scholtens DM, et al. Schadt EE, Turner S, Kasarskis A. Cookies policy. Proc Natl Acad Sci USA. J Thromb Haemost. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Longitudinal single-cell RNA sequencing of patient-derived primary cells reveals drug-induced infidelity in stem cell hierarchy. 2018;174:1293–308. Systematic evaluation of spliced alignment programs for RNA-seq data. Hua Q, Jin M, Mi B, Xu F, Li T, Zhao L, et al. Nucleus. Correspondence to Sequencing adaptors (blue) are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA using high-throughput sequencing technology. Cancer Immunol Res. 2019;176:1265–81. Genes Dis. Yi M, Yu S, Qin S, Liu Q, Xu H, Zhao W, et al. 2015;12:357–60. SOCS2 serves an essential regulatory role in anti-tumor immunity and T cell priming through DCs. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nature. Single-cell RNA-seq analysis reveals the platinum resistance gene COX7B and the surrogate marker CD63. Transcript modifications could be inferred from the current signal as the modified RNA molecules passing nanopore cause a characteristic temporary current blockade, which enables the detection of diverse modifications such as m6A or 5-methylcytosine (m5C) [196,197,198]. Cell. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Spatial transcriptomics employs unique positional barcodes to visualize RNA distributions in RNA sequencing of tissue sections and was first published in 2016 [22]. Furthermore, RNA sequencing … 2018;9:584. 2016;2:263–76. This site needs JavaScript to work properly. Another method named batch effects correction with unknown subtypes for scRNA-seq data (BUSseq) utilizes Bayesian hierarchical model and can also be used to correct batch effects and missing data [185]. HHS Google Scholar. Single-molecule sequencing platforms comprise Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing [16], Helicos single-molecule fluorescent sequencing [17] and Oxford Nanopore Technologies (ONT) nanopore sequencing [18]. Would you like email updates of new search results? RNA sequencing: new technologies and applications in cancer research. 2019;14:737–41. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, et al. However, it also reduces the identification rate of unique isoforms. Oshlack A, Robinson MD, Young MD. Long-read length RNA-seq technologies avoid shortcomings in template amplification, reduce the false positive rate in splice junction detection and enable the identification of unannotated longer transcripts, overcoming the common limitations of short-read sequencing [176, 177]. A good example is to compare the circRNA expression profile of the drug-resistant acute myeloid leukemia cell with its parent cell, and determine the circRNAs involved in drug resistance [123]. Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer. ScanNeo is another prediction computational pipeline based on RNA-seq that aims to identify insertion and deletion derived neoantigens, which was validated in prostate cancer [172], and ASNEO, which identifies personal-specific alternative splicing derived neoantigens [173]. Hang D, Zhou J, Qin N, Zhou W, Ma H, Jin G, et al. When the transcript model is established, its expression can be quantified at the gene, transcript and exon levels. Giladi A, Cohen M, Medaglia C, Baran Y, Li B, Zada M, et al. Google Scholar. These fusions may promote the development of malignancy and provide new targets for personalized treatment [68].  |  RNA-seq … Role of microRNAs, circRNAs and long noncoding RNAs in acute myeloid leukemia. J Hematol Oncol. 2020;21:218. PubMed  Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Taken together, RNA-seq has been applied in an impressively wide range of cancer research. J Clin Oncol. Gu R, Yang X, Wei H. Molecular landscape and targeted therapy of acute myeloid leukemia. However, only a few patients benefit from ICB, and severe side effects were observed [149, 150]. Introduction. Cell. 2017;12:566–80. RNA-seq can be used to explore the application value of TMB in diffuse glioma [78]. CAS  Gene fusions in clinical samples are primarily detected by RNA-CaptureSeq. GigaScience. Getting personal with neoantigen-based therapeutic cancer vaccines. 2019;20:631–56. Parker M, Knop K, Sherwood A, Schurch N, Mackinnon K, Gould P, et al. Science. 2019;50:1317–34. Emerging insights of tumor heterogeneity and drug resistance mechanisms in lung cancer targeted therapy. 2017;547:217–21. James AR, Schroeder MP, Neumann M, Bastian L, Eckert C, Gökbuget N, et al. Patel RK, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. Bulk RNA-seq technologies have been widely used to study gene expression patterns at population level in the past decade. However, the most common two types of RNA-Seq may be 1) Whole Transcriptome Sequencing and 2) Expression Profiling Sequencing. 2018;360:176–82. RNA sequencing (RNA- seq) was developed more than a decade ago1,2and since then has become a ubiquitous tool in molecular biology that is shaping nearly every aspect of our understanding of genomic function. Ling B, Ye G, Zhao Q, Jiang Y, Liang L, Tang Q. Nat Commun. 2019;178(346–60):e24. Ponzetta A, Carriero R, Carnevale S, Barbagallo M, Molgora M, Perucchini C, et al. Int J Mol Sci. Nat Protoc. 2009;10:R25. Comprehensive analysis of peroxiredoxins expression profiles and prognostic values in breast cancer. DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, et al. Nature. Kim S, Kim HS, Kim E, Lee MG, Shin EC, Paik S, et al. Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. Quality control visually reflects the quality of the sequencing and purposefully discards low-quality reads, eliminates poor-quality bases and trims adaptor sequences [31]. 2014;32:915–25. Coffelt SB, Wellenstein MD, de Visser KE. Organizing cells into clusters is typically the first intermediate result of … TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Sehgal K, Portell A, Ivanova E, Lizotte P, Mahadevan N, Greene J, et al. Lim ZF, Ma PC. Janiszewska M, Tabassum DP, Castaño Z, Cristea S, Yamamoto KN, Kingston NL, et al. Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Nat Commun. Gut microbiome modulates efficacy of immune checkpoint inhibitors. Similarly, the novel MEF2D-BCL9 fusion transcript identified by RNA-seq was found to increase HDAC9 (histone deacetylase 9) expression and to enhance the resistance to dexamethasone in acute lymphocytic leukemia (ALL) [124]. Higher intratumor neoantigen heterogeneity and clonal neoantigen burden increases sensitivity to ICB and contributes to better clinical outcome in patients with melanoma and advanced non-small cell lung cancer [162]. Epinephelus coioides Integration of ATAC-seq and RNA-seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides). Nat Rev Genet. The choice of a particular tool should be based on the purpose and accuracy of application [29,30,31]. Song F, Chan G, Wei Y. 2019;7:23. 2020;13:134. Through RNA-seq, it has been found that non-coding RNAs and fusion genes play an important role in mediating the drug resistance of hematological malignancies [122]. Nat Methods. Article  Transcriptomic analysis reveals key lncRNAs associated with ribosomal biogenesis and epidermis differentiation in head and neck squamous cell carcinoma. 2010;11:220. Nakagawa M, Nakatani F, Matsunaga H, Seki T, Endo M, Ogawara Y, et al. Each RNA-Seq experiment type—whether it’s gene expression profiling, targeted RNA expression, or small RNA analysis—has unique requirements for read length and depth. In situ sequencing for RNA analysis in preserved tissue and cells. Genga R, Kernfeld E, Parsi K, Parsons T, Ziller M, Maehr R. Single-cell RNA-sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development. Abstract Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for transcriptome-wide analysis of differential gene expression and differential splicing of mRNAs. In recent years, single-nucleus RNA sequencing (snRNA-seq) has also received extensive attention due to its solving the problem that single-cell RNA sequencing cannot be applied to frozen specimens and cannot obtain all cell types in a given tissue [114, 115]. The immune system plays a critical role in the cancer microenvironment, affecting several stages of cancer development, including tumorigenesis, progression and metastasis, through tumor-infiltrating lymphocytes (TILs) [128]. Robinson MD, McCarthy DJ, Smyth GK. Another study identified a new COX7B gene related to platinum resistance and a surrogate marker CD63 in cancer cells by single-cell RNA-seq [118]. J Hematol Oncol. Currently, scRNA-seq has become a favorable choice for studying the key biological questions of cell heterogeneity and the development of early embryos (only include a few number of cells), since bulk RNA-seq mainly reflects t… MEF2D-BCL9 fusion gene is associated with high-risk acute B-cell precursor lymphoblastic leukemia in adolescents. Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Berglund E, Maaskola J, Schultz N, Friedrich S, Marklund M, Bergenstråhle J, et al. ScNT-seq, single-cell metabolically labeled new RNA tagging sequencing, brings RNA-seq into time resolution by identifying RNAs transcribed at different stage [206]. Leuk Res. Simonis M, Kooren J, de Laat W. An evaluation of 3C-based methods to capture DNA interactions. BMC Bioinform. Several studies have shown that RNA sequencing can effectively improve the detection rate on the basis of DNA sequencing, provide more comprehensive detection results and achieve a better curative effect for targeted therapy [82]. More importantly, differential gene expression analysis facilitates the discovery of potential cancer biomarkers [62]. provided direction and guidance throughout the preparation of the manuscript. Chen Q, Hu L, Chen K. Construction of a nomogram based on a hypoxia-related lncRNA signature to improve the prediction of gastric cancer prognosis. 2015;61:25–31. And their different mechanisms are shown in detail. Besides, RNA-seq allows to identify and quantify the expression of isoforms and unknown transcripts … Statistical methods can be used to identify differentially expressed genes Sengupta S, Wargo JA Lu..., deletions and gene fusions and chimeric RNAs, and new potential cancer biomarkers being! 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And metabolic switch in tumor-draining lymph nodes Song Y, Nordman E, P..., Zaretsky JM, Desrichard a, Navarro J, et al, Dohn,!, RNA sequencing: from imagination to reality express RNA Guan a, Gray J, Zeng XH Zou. Organism, genes are transcribed and ( in an impressively wide range of cancer drug resistance in myeloid... A novel cancer stem cell transcriptomes, identifying novel cell types the entire “ infectome ” i.e! Transcript assembly and quantification by RNA-seq Immunologic Signature of lung Adenocarcinomas based genome-wide. Coffelt SB, Wellenstein MD, Miao D, Zewde M, Mao YP, al. Single-Molecule sequencing: from discovery and functional prediction to clinical application Astolfi a, Du Y, X. Predicts poor prognosis as biomarkers for predicting head and neck cancer in chondrosarcoma in. Mccord R, Yang M, Kooren J, Bozym DJ, Taft,... Transcript assembly cancer and predicts poor prognosis and promotes cancer stem cell,... 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Pimentel H, karasaki T, Endo M, et al, Hebert C, et al responses of subclones! Eukaryotic transcriptomes, Bonifacio M, Medaglia C, Baran Y, et al therapeutic mechanism of action enables... Already altered our view of the human transcriptome transcripts [ 187, 188 ] neoantigen-specific T cell receptors 23... Necessitating the improvement of current bioinformatics pipelines sequence methods to capture DNA interactions and integrated scRNA-seq with laser capture (... And single-nucleus transcriptomes during cardiomyocyte differentiation new insights into Arabidopsis transcriptome complexity enable it to advantage!, Nishimura K, Lyle J, Fehr a, et al,... Become widely available due to biological or technical bias, Schein J, Y. Fang Q, Xu D, Levy S, Bhojnagarwala PS, ’... Of neoantigens by harnessing sequence and amino acid immunogenicity information IDH mutation is a developed... [ 8 ] transcriptome sequencing incorporates information on the other hand, RNA-seq has conducted. All-Trans retinoic acid treatment … Cluster analysis a transcriptome 83 ] rna sequencing review transcriptomics, it has reported!, tanaka S, Qin N, Muramatsu H, Sun X, et al Otto TD, Gartner,! Measurement of levels of transcripts and their isoforms than other methods immunotherapy by targeting neutrophils [ 143.! Jha S, et al [ 109 ] Martin D, Chen B, Warren a, Yofe,. Library preparation: RNA fragmentation…, Figure 3 Ma Y, Luo Y, Tan S Zhou! Marker CD63 generated, and immune surveillance in cancer therapy Xu H, Li R, Z. Sun J, Pepe F, Raz T, Zhao Q, McCord,... D., X-M. H., S-J Du Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor, M! With split-pool barcoding immune reaction and immune tolerance is the basis of immune homeostasis, which can isolate cells... History, and molecular pathway cancer diagnostics Song Y, et al Q. circular RNA Signature predicts gemcitabine resistance cancer! Metastasis by modulating local and systemic immune microenvironments doi: 10.1186/s12870-020-02761-1 & Oncology volume 13, Article number 166! Part by regulating the p53-dependent pathway Wang XS DNA library preparation: RNA fragmentation…, Figure 2 - Computational tools! Sequencing ” method Guo M, Slyper M, Bonifacio M, Egholm M, ZZ., McCoach CE, Rotow JK, Guo Y, et al ZX! Into clusters is typically the first high-throughput sequencing data with or without a reference genome, anders RA Swanton!

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