1
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Jusic A, Erpapazoglou Z, Dalgaard LT, Lakkisto P, de Gonzalo-Calvo D, Benczik B, Ágg B, Ferdinandy P, Fiedorowicz K, Schroen B, Lazou A, Devaux Y. Guidelines for mitochondrial RNA analysis. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102262. [PMID: 39091381 PMCID: PMC11292373 DOI: 10.1016/j.omtn.2024.102262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Mitochondria are the energy-producing organelles of mammalian cells with critical involvement in metabolism and signaling. Studying their regulation in pathological conditions may lead to the discovery of novel drugs to treat, for instance, cardiovascular or neurological diseases, which affect high-energy-consuming cells such as cardiomyocytes, hepatocytes, or neurons. Mitochondria possess both protein-coding and noncoding RNAs, such as microRNAs, long noncoding RNAs, circular RNAs, and piwi-interacting RNAs, encoded by the mitochondria or the nuclear genome. Mitochondrial RNAs are involved in anterograde-retrograde communication between the nucleus and mitochondria and play an important role in physiological and pathological conditions. Despite accumulating evidence on the presence and biogenesis of mitochondrial RNAs, their study continues to pose significant challenges. Currently, there are no standardized protocols and guidelines to conduct deep functional characterization and expression profiling of mitochondrial RNAs. To overcome major obstacles in this emerging field, the EU-CardioRNA and AtheroNET COST Action networks summarize currently available techniques and emphasize critical points that may constitute sources of variability and explain discrepancies between published results. Standardized methods and adherence to guidelines to quantify and study mitochondrial RNAs in normal and disease states will improve research outputs, their reproducibility, and translation potential to clinical application.
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Affiliation(s)
- Amela Jusic
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
| | - Zoi Erpapazoglou
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
| | - Louise Torp Dalgaard
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Päivi Lakkisto
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Bettina Benczik
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Bence Ágg
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Péter Ferdinandy
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | | | - Blanche Schroen
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
| | - Antigone Lazou
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
| | - on behalf of EU-CardioRNA COST Action CA17129
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
- NanoBioMedical Centre, Adam Mickiewicz University in Poznan, 61614 Poznan, Poland
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - AtheroNET COST Action CA21153
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
- NanoBioMedical Centre, Adam Mickiewicz University in Poznan, 61614 Poznan, Poland
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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2
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Rousseau M, Oulavallickal T, Williamson A, Arcus V, Patrick WM, Hicks J. Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus. Nucleic Acids Res 2024; 52:3924-3937. [PMID: 38421610 DOI: 10.1093/nar/gkae149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/23/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in next-generation sequencing of microRNAs. Thermophilic RNA ligases belonging to the RNA ligase 3 family are gaining attention for their use in molecular biology, for example a thermophilic RNA ligase from Methanobacterium thermoautotrophicum is commercially available for the adenylation of nucleic acids. Here we extensively characterise a newly identified RNA ligase from the thermophilic archaeon Palaeococcus pacificus (PpaRnl). PpaRnl exhibited significant substrate adenylation activity but low ligation activity across a range of oligonucleotide substrates. Mutation of Lys92 in motif I to alanine, resulted in an enzyme that lacked adenylation activity, but demonstrated improved ligation activity with pre-adenylated substrates (ATP-independent ligation). Subsequent structural characterisation revealed that in this mutant enzyme Lys238 was found in two alternate positions for coordination of the phosphate tail of ATP. In contrast mutation of Lys238 in motif V to glycine via structure-guided engineering enhanced ATP-dependent ligation activity via an arginine residue compensating for the absence of Lys238. Ligation activity for both mutations was higher than the wild-type, with activity observed across a range of oligonucleotide substrates with varying sequence and secondary structure.
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Affiliation(s)
- Meghan Rousseau
- School of Science, The University of Waikato, Hamilton 3216, New Zealand
| | - Tifany Oulavallickal
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Adele Williamson
- School of Science, The University of Waikato, Hamilton 3216, New Zealand
| | - Vic Arcus
- School of Science, The University of Waikato, Hamilton 3216, New Zealand
| | - Wayne M Patrick
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Joanna Hicks
- Te Huataki Waiora School of Health, The University of Waikato, Hamilton 3216, New Zealand
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3
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Tosar JP, Castellano M, Costa B, Cayota A. Small RNA structural biochemistry in a post-sequencing era. Nat Protoc 2024; 19:595-602. [PMID: 38057624 DOI: 10.1038/s41596-023-00936-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/25/2023] [Indexed: 12/08/2023]
Abstract
High-throughput sequencing has had an enormous impact on small RNA research during the past decade. However, sequencing only offers a one-dimensional view of the transcriptome and is often highly biased. Additionally, the 'sequence, map and annotate' approach, used widely in small RNA research, can lead to flawed interpretations of the data, lacking biological plausibility, due in part to database issues. Even in the absence of technical biases, the loss of three-dimensional information is a major limitation to understanding RNA stability, turnover and function. For example, noncoding RNA-derived fragments seem to exist mainly as dimers, tetramers or as nicked forms of their parental RNAs, contrary to widespread assumptions. In this perspective, we will discuss main sources of bias during small RNA-sequencing, present several useful bias-reducing strategies and provide guidance on the interpretation of small RNA-sequencing results, with emphasis on RNA fragmentomics. As sequencing offers a one-dimensional projection of a four-dimensional reality, prior structure-level knowledge is often needed to make sense of the data. Consequently, while less-biased sequencing methods are welcomed, integration of orthologous experimental techniques is also strongly recommended.
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Affiliation(s)
- Juan Pablo Tosar
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay.
- Analytical Biochemistry Unit, Center for Nuclear Research, School of Science, Universidad de la República, Montevideo, Uruguay.
| | - Mauricio Castellano
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Biochemistry Department, School of Science, Universidad de la República, Montevideo, Uruguay
| | - Bruno Costa
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Analytical Biochemistry Unit, Center for Nuclear Research, School of Science, Universidad de la República, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Hospital de Clínicas, Universidad de la República, Montevideo, Uruguay
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4
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Hiers NM, Li T, Traugot CM, Xie M. Target-directed microRNA degradation: Mechanisms, significance, and functional implications. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1832. [PMID: 38448799 PMCID: PMC11098282 DOI: 10.1002/wrna.1832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 03/08/2024]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play a fundamental role in enabling miRNA-mediated target repression, a post-transcriptional gene regulatory mechanism preserved across metazoans. Loss of certain animal miRNA genes can lead to developmental abnormalities, disease, and various degrees of embryonic lethality. These short RNAs normally guide Argonaute (AGO) proteins to target RNAs, which are in turn translationally repressed and destabilized, silencing the target to fine-tune gene expression and maintain cellular homeostasis. Delineating miRNA-mediated target decay has been thoroughly examined in thousands of studies, yet despite these exhaustive studies, comparatively less is known about how and why miRNAs are directed for decay. Several key observations over the years have noted instances of rapid miRNA turnover, suggesting endogenous means for animals to induce miRNA degradation. Recently, it was revealed that certain targets, so-called target-directed miRNA degradation (TDMD) triggers, can "trigger" miRNA decay through inducing proteolysis of AGO and thereby the bound miRNA. This process is mediated in animals via the ZSWIM8 ubiquitin ligase complex, which is recruited to AGO during engagement with triggers. Since its discovery, several studies have identified that ZSWIM8 and TDMD are indispensable for proper animal development. Given the rapid expansion of this field of study, here, we summarize the key findings that have led to and followed the discovery of ZSWIM8-dependent TDMD. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Nicholas M Hiers
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Conner M Traugot
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
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5
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Seki M, Kuze Y, Zhang X, Kurotani KI, Notaguchi M, Nishio H, Kudoh H, Suzaki T, Yoshida S, Sugano S, Matsushita T, Suzuki Y. An improved method for the highly specific detection of transcription start sites. Nucleic Acids Res 2024; 52:e7. [PMID: 37994784 PMCID: PMC10810191 DOI: 10.1093/nar/gkad1116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/17/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Precise detection of the transcriptional start site (TSS) is a key for characterizing transcriptional regulation of genes and for annotation of newly sequenced genomes. Here, we describe the development of an improved method, designated 'TSS-seq2.' This method is an iterative improvement of TSS-seq, a previously published enzymatic cap-structure conversion method to detect TSSs in base sequences. By modifying the original procedure, including by introducing split ligation at the key cap-selection step, the yield and the accuracy of the reaction has been substantially improved. For example, TSS-seq2 can be conducted using as little as 5 ng of total RNA with an overall accuracy of 96%; this yield a less-biased and more precise detection of TSS. We then applied TSS-seq2 for TSS analysis of four plant species that had not yet been analyzed by any previous TSS method.
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Affiliation(s)
- Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yuta Kuze
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Xiang Zhang
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Ken-ichi Kurotani
- Bioscience and Biotechnology Center, Nagoya University, Aichi, Japan
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center, Nagoya University, Aichi, Japan
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Nagoya, Japan
| | - Haruki Nishio
- Data Science and AI Innovation Research Promotion Center, Shiga University, Shiga, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Takuya Suzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Ibaraki, Japan
| | - Satoko Yoshida
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Sumio Sugano
- Institute of Kashiwa-no-ha Omics Gate, Chiba, Japan
- Future Medicine Education and Research Organization, Chiba University, Chiba, Japan
| | - Tomonao Matsushita
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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6
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Chen HC, Wang J, Shyr Y, Liu Q. FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing. PLoS Comput Biol 2024; 20:e1011786. [PMID: 38252662 PMCID: PMC10833567 DOI: 10.1371/journal.pcbi.1011786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 02/01/2024] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Adapter trimming is an essential step for analyzing small RNA sequencing data, where reads are generally longer than target RNAs ranging from 18 to 30 bp. Most adapter trimming tools require adapter information as input. However, adapter information is hard to access, specified incorrectly, or not provided with publicly available datasets, hampering their reproducibility and reusability. Manual identification of adapter patterns from raw reads is labor-intensive and error-prone. Moreover, the use of randomized adapters to reduce ligation biases during library preparation makes adapter detection even more challenging. Here, we present FindAdapt, a Python package for fast and accurate detection of adapter patterns without relying on prior information. We demonstrated that FindAdapt was far superior to existing approaches. It identified adapters successfully in 180 simulation datasets with diverse read structures and 3,184 real datasets covering a variety of commercial and customized small RNA library preparation kits. FindAdapt is stand-alone software that can be easily integrated into small RNA sequencing analysis pipelines.
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Affiliation(s)
- Hua-Chang Chen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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7
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Kelly SL, Strobel EJ. Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573115. [PMID: 38187752 PMCID: PMC10769408 DOI: 10.1101/2023.12.22.573115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
RNA can fold into structures that mediate diverse cellular functions. Understanding how RNA primary sequence directs the formation of functional structures requires methods that can comprehensively assess how changes in an RNA sequence affect its structure and function. Here we have developed a platform for performing high-throughput cotranscriptional RNA biochemical assays, called Transcription Elongation Complex display (TECdisplay). TECdisplay measures RNA function by fractionating a TEC library based on the activity of cotranscriptionally displayed nascent RNA. In this way, RNA function is measured as the distribution of template DNA molecules between fractions of the transcription reaction. This approach circumvents typical RNA sequencing library preparation steps that can cause technical bias. We used TECdisplay to characterize the transcription antitermination activity of 32,768 variants of the Clostridium beijerinckii pfl ZTP riboswitch designed to perturb steps within its cotranscriptional folding pathway. Our findings establish TECdisplay as an accessible platform for high-throughput RNA biochemical assays.
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Affiliation(s)
- Skyler L. Kelly
- Department of Biological Sciences, The University at Buffalo, Buffalo, NY 14260, USA
| | - Eric J. Strobel
- Department of Biological Sciences, The University at Buffalo, Buffalo, NY 14260, USA
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8
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Mimoso CA, Goldman SR. PRO-seq: Precise Mapping of Engaged RNA Pol II at Single-Nucleotide Resolution. Curr Protoc 2023; 3:e961. [PMID: 38149731 PMCID: PMC10836333 DOI: 10.1002/cpz1.961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Gene regulation is dependent on the production of mRNAs and a repertoire of non-coding RNAs by RNA polymerase II (RNAPII). Precision run-on sequencing (PRO-seq) maps the position of engaged RNAPII complexes at single-nucleotide resolution and can reveal direct targets of regulation, locations of enhancers, and transcription mechanisms that are difficult or impossible to measure by analysis of total cellular RNA. Briefly, this method first involves permeabilizing cells with mild detergents to remove intracellular NTPs and halt transcription. Transcription is then resumed in the presence of biotin-NTPs and sarkosyl to allow transcriptional incorporation of a single biotinylated NTP by RNAPII. The biotin moiety is then bound to streptavidin beads to stringently enrich for nascent RNAs. Sequencing libraries are then generated such that the first base read corresponds to the 3' end of the nascent transcript. Here, we describe our current protocol for generating PRO-seq libraries from metazoan cells, including adaptations of previously published protocols to incorporate unique molecular identifiers, reduce ligation bias, and improve library yields. Additional commentary describes quality control and processing of PRO-seq data and references for more advanced downstream analysis such as gene and enhancer identification. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Cell permeabilization for PRO-seq Basic Protocol 2: Construction of PRO-seq libraries Support Protocol: Adenylation of 3' adapter.
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Affiliation(s)
- Claudia A Mimoso
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Seth R Goldman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
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9
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Mao Y, Jia L, Dong L, Shu XE, Qian SB. Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation. Nat Struct Mol Biol 2023; 30:1816-1825. [PMID: 37957305 DOI: 10.1038/s41594-023-01119-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/07/2023] [Indexed: 11/15/2023]
Abstract
A translating ribosome is typically thought to follow the reading frame defined by the selected start codon. Using super-resolution ribosome profiling, here we report pervasive out-of-frame translation immediately from the start codon. Start codon-associated ribosomal frameshifting (SCARF) stems from the slippage of ribosomes during the transition from initiation to elongation. Using a massively paralleled reporter assay, we uncovered sequence elements acting as SCARF enhancers or repressors, implying that start codon recognition is coupled with reading frame fidelity. This finding explains thousands of mass spectrometry spectra that are unannotated in the human proteome. Mechanistically, we find that the eukaryotic initiation factor 5B (eIF5B) maintains the reading frame fidelity by stabilizing initiating ribosomes. Intriguingly, amino acid starvation induces SCARF by proteasomal degradation of eIF5B. The stress-induced SCARF protects cells from starvation by enabling amino acid recycling and selective mRNA translation. Our findings illustrate a beneficial effect of translational 'noise' in nutrient stress adaptation.
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Affiliation(s)
- Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Longfei Jia
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Leiming Dong
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Xin Erica Shu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA.
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10
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Anisimova AS, Karagöz GE. Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells. RNA (NEW YORK, N.Y.) 2023; 29:1818-1836. [PMID: 37582618 PMCID: PMC10578486 DOI: 10.1261/rna.079714.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
The conserved family of RNA-binding proteins (RBPs), IGF2BPs, plays an essential role in posttranscriptional regulation controlling mRNA stability, localization, and translation. Mammalian cells express three isoforms of IGF2BPs: IGF2BP1-3. IGF2BP3 is highly overexpressed in cancer cells, and its expression correlates with a poor prognosis in various tumors. Therefore, revealing its target RNAs with high specificity in healthy tissues and in cancer cells is of crucial importance. Photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) identifies the binding sites of RBPs on their target RNAs at nucleotide resolution in a transcriptome-wide manner. Here, we optimized the PAR-CLIP protocol to study RNA targets of endogenous IGF2BP3 in a human colorectal carcinoma cell line. To this end, we first established an immunoprecipitation protocol to obtain highly pure endogenous IGF2BP3-RNA complexes. Second, we modified the protocol to use highly sensitive infrared (IR) fluorescent dyes instead of radioactive probes to visualize IGF2BP3-crosslinked RNAs. We named the modified method "IR-PAR-CLIP." Third, we compared RNase cleavage conditions and found that sequence preferences of the RNases impact the number of the identified IGF2BP3 targets and introduce a systematic bias in the identified RNA motifs. Fourth, we adapted the single adapter circular ligation approach to increase the efficiency in library preparation. The optimized IR-PAR-CLIP protocol revealed novel RNA targets of IGF2BP3 in a human colorectal carcinoma cell line. We anticipate that our IR-PAR-CLIP approach provides a framework for studies of other RBPs.
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Affiliation(s)
- Aleksandra S Anisimova
- Max Perutz Labs, Vienna BioCenter Campus (VBC), 1030 Vienna, Austria
- Medical University of Vienna, Center for Medical Biochemistry, 1030 Vienna, Austria
- Vienna BioCenter PhD Program, a Doctoral School of the University of Vienna and the Medical University of Vienna, 1030 Vienna, Austria
| | - G Elif Karagöz
- Max Perutz Labs, Vienna BioCenter Campus (VBC), 1030 Vienna, Austria
- Medical University of Vienna, Center for Medical Biochemistry, 1030 Vienna, Austria
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11
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Morgunova A, Ibrahim P, Chen GG, Coury SM, Turecki G, Meaney MJ, Gifuni A, Gotlib IH, Nagy C, Ho TC, Flores C. Preparation and processing of dried blood spots for microRNA sequencing. Biol Methods Protoc 2023; 8:bpad020. [PMID: 37901452 PMCID: PMC10603595 DOI: 10.1093/biomethods/bpad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/07/2023] [Accepted: 09/19/2023] [Indexed: 10/31/2023] Open
Abstract
Dried blood spots (DBS) are biological samples commonly collected from newborns and in geographic areas distanced from laboratory settings for the purposes of disease testing and identification. MicroRNAs (miRNAs)-small non-coding RNAs that regulate gene activity at the post-transcriptional level-are emerging as critical markers and mediators of disease, including cancer, infectious diseases, and mental disorders. This protocol describes optimized procedural steps for utilizing DBS as a reliable source of biological material for obtaining peripheral miRNA expression profiles. We outline key practices, such as the method of DBS rehydration that maximizes RNA extraction yield, and the use of degenerate oligonucleotide adapters to mitigate ligase-dependent biases that are associated with small RNA sequencing. The standardization of miRNA readout from DBS offers numerous benefits: cost-effectiveness in sample collection and processing, enhanced reliability and consistency of miRNA profiling, and minimal invasiveness that facilitates repeated testing and retention of participants. The use of DBS-based miRNA sequencing is a promising method to investigate disease mechanisms and to advance personalized medicine.
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Affiliation(s)
- Alice Morgunova
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3A 1A1, Canada
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Pascal Ibrahim
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3A 1A1, Canada
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
| | - Gary Gang Chen
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
| | - Saché M Coury
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
- Department of Psychology, University of California, Los Angeles, CA 90095, United States
| | - Gustavo Turecki
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Michael J Meaney
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Quebec H3A 2B4, Canada
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Brenner Centre for Molecular Medicine, Singapore City 138632, Singapore
| | - Anthony Gifuni
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Ian H Gotlib
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
| | - Corina Nagy
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Tiffany C Ho
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
- Department of Psychology, University of California, Los Angeles, CA 90095, United States
| | - Cecilia Flores
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Quebec H3A 2B4, Canada
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12
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Mai HT, Vanness BC, Linz TH. Reverse transcription-free digital-quantitative-PCR for microRNA analysis. Analyst 2023; 148:3019-3027. [PMID: 37264955 PMCID: PMC10318481 DOI: 10.1039/d3an00351e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
MicroRNAs (miRNAs) are non-coding RNA sequences that regulate many biological processes and have become central targets of biomedical research. However, their naturally low abundances in biological samples necessitates the development of sensitive analytical techniques to conduct routine miRNA measurements in research laboratories. Digital PCR has the potential to meet this need because of its single-molecule detection capabilities, but PCR analyses of miRNAs are slowed by the ligation and reverse transcription steps first required to prepare samples. This report describes the development of a method to rapidly quantify miRNA in digital microwell arrays using base-stacking digital-quantitative-PCR (BS-dqPCR). BS-dqPCR expedites miRNA measurements by eliminating the need for ligation and reverse transcription steps, which reduces the time and cost compared to conventional miRNA PCR analyses. Under standard PCR thermocycling conditions, digital signals from miRNA samples were lower than expected, while signals from blanks were high. Therefore, a novel asymmetric thermocycling program was developed that maximized on-target signal from miRNA while minimizing non-specific amplification. The analytical response of BS-dqPCR was then evaluated over a range of miRNA concentrations. The digital PCR dimension increased in signal with increasing miRNA copy numbers. When the digital signal saturated, the quantitative PCR dimension readily discerned miRNA copy number differences. Overall, BS-dqPCR provides rapid, high-sensitivity measurements of miRNA over a wide dynamic range, which demonstrates its utility for routine miRNA analyses.
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Affiliation(s)
- Hao T Mai
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202, USA.
| | - Brice C Vanness
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202, USA.
| | - Thomas H Linz
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202, USA.
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13
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Green D, Singh A, Tippett VL, Tattersall L, Shah KM, Siachisumo C, Ward NJ, Thomas P, Carter S, Jeys L, Sumathi V, McNamara I, Elliott DJ, Gartland A, Dalmay T, Fraser WD. YBX1-interacting small RNAs and RUNX2 can be blocked in primary bone cancer using CADD522. J Bone Oncol 2023; 39:100474. [PMID: 36936386 PMCID: PMC10015236 DOI: 10.1016/j.jbo.2023.100474] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023] Open
Abstract
Primary bone cancer (PBC) comprises several subtypes each underpinned by distinctive genetic drivers. This driver diversity produces novel morphological features and clinical behaviour that serendipitously makes PBC an excellent metastasis model. Here, we report that some transfer RNA-derived small RNAs termed tRNA fragments (tRFs) perform as a constitutive tumour suppressor mechanism by blunting a potential pro-metastatic protein-RNA interaction. This mechanism is reduced in PBC progression with a gradual loss of tRNAGlyTCC cleavage into 5' end tRF-GlyTCC when comparing low-grade, intermediate-grade and high-grade patient tumours. We detected recurrent activation of miR-140 leading to upregulated RUNX2 expression in high-grade patient tumours. Both tRF-GlyTCC and RUNX2 share a sequence motif in their 3' ends that matches the YBX1 recognition site known to stabilise pro-metastatic mRNAs. Investigating some aspects of this interaction network, gain- and loss-of-function experiments using small RNA mimics and antisense LNAs, respectively, showed that ectopic tRF-GlyTCC reduced RUNX2 expression and dispersed 3D micromass architecture in vitro. iCLIP sequencing revealed YBX1 physical binding to the 3' UTR of RUNX2. The interaction between YBX1, tRF-GlyTCC and RUNX2 led to the development of the RUNX2 inhibitor CADD522 as a PBC treatment. CADD522 assessment in vitro revealed significant effects on PBC cell behaviour. In xenograft mouse models, CADD522 as a single agent without surgery significantly reduced tumour volume, increased overall and metastasis-free survival and reduced cancer-induced bone disease. Our results provide insight into PBC molecular abnormalities that have led to the identification of new targets and a new therapeutic.
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Key Words
- CADD522
- CADD522, computer aided drug design molecule 522
- CI, confidence interval
- CNV, copy number variant
- CS, chondrosarcoma
- CTC, circulating tumour cell
- DE, differentially expressed
- ES, Ewing sarcoma
- HD, high definition
- HR, hazard ratio
- OS, osteosarcoma
- RBP, RNA binding protein
- RNU6-1, U6 small nuclear 1
- ROI, region-of-interest
- Rnl, T4 RNA ligase
- SNV, single nucleotide variant
- SV, structural variant
- bone cancer
- iCLIP, individual nucleotide resolution cross-linking and immunoprecipitation
- mRNA, messenger RNA
- miRNA
- miRNA, microRNA
- piRNA, piwi interacting RNA
- sRNA, small RNA
- small RNA
- tRF
- tRF, transfer RNA fragment
- tRNA, transfer RNA
- ysRNA, Y RNA-derived sRNA
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Affiliation(s)
- Darrell Green
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, UK
- Corresponding author.
| | - Archana Singh
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Victoria L. Tippett
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, UK
| | - Luke Tattersall
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, UK
| | - Karan M. Shah
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, UK
| | | | - Nicole J. Ward
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Paul Thomas
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Henry Wellcome Laboratory for Cell Imaging, Faculty of Science, University of East Anglia, Norwich, UK
| | - Simon Carter
- Orthopaedic Oncology, Royal Orthopaedic Hospital, Birmingham, UK
| | - Lee Jeys
- Orthopaedic Oncology, Royal Orthopaedic Hospital, Birmingham, UK
| | - Vaiyapuri Sumathi
- Musculoskeletal Pathology, University Hospitals Birmingham, Royal Orthopaedic Hospital, Birmingham, UK
| | - Iain McNamara
- Orthopaedics & Trauma, Norfolk and Norwich University Hospital, Norwich, UK
| | | | - Alison Gartland
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - William D. Fraser
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, UK
- Clinical Biochemistry, Diabetes and Endocrinology, Norfolk and Norwich University Hospital, Norwich, UK
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14
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Mao Y, Jia L, Dong L, Shu XE, Qian SB. Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528768. [PMID: 36824937 PMCID: PMC9949036 DOI: 10.1101/2023.02.15.528768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
A translating ribosome is typically thought to follow the reading frame defined by the selected start codon. Using super-resolution ribosome profiling, here we report pervasive out-of-frame translation immediately from the start codon. The start codon-associated ribosome frameshifting (SCARF) stems from the slippage of ribosomes during the transition from initiation to elongation. Using a massively paralleled reporter assay, we uncovered sequence elements acting as SCARF enhancers or repressors, implying that start codon recognition is coupled with reading frame fidelity. This finding explains thousands of mass spectrometry spectra unannotated from human proteome. Mechanistically, we find that the eukaryotic initiation factor 5B (eIF5B) maintains the reading frame fidelity by stabilizing initiating ribosomes. Intriguingly, amino acid starvation induces SCARF by proteasomal degradation of eIF5B. The stress-induced SCARF protects cells from starvation by enabling amino acid recycling and selective mRNA translation. Our findings illustrate a beneficial effect of translational "noise" in nutrient stress adaptation.
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15
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Antoniali G, Dalla E, Mangiapane G, Zhao X, Jing X, Cheng Y, De Sanctis V, Ayyildiz D, Piazza S, Li M, Tell G. APE1 controls DICER1 expression in NSCLC through miR-33a and miR-130b. Cell Mol Life Sci 2022; 79:446. [PMID: 35876890 PMCID: PMC9314295 DOI: 10.1007/s00018-022-04443-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 12/04/2022]
Abstract
Increasing evidence suggests different, not completely understood roles of microRNA biogenesis in the development and progression of lung cancer. The overexpression of the DNA repair protein apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) is an important cause of poor chemotherapeutic response in lung cancer and its involvement in onco-miRNAs biogenesis has been recently described. Whether APE1 regulates miRNAs acting as prognostic biomarkers of lung cancer has not been investigated, yet. In this study, we analyzed miRNAs differential expression upon APE1 depletion in the A549 lung cancer cell line using high-throughput methods. We defined a signature of 13 miRNAs that strongly correlate with APE1 expression in human lung cancer: miR-1246, miR-4488, miR-24, miR-183, miR-660, miR-130b, miR-543, miR-200c, miR-376c, miR-218, miR-146a, miR-92b and miR-33a. Functional enrichment analysis of this signature revealed its biological relevance in cancer cell proliferation and survival. We validated DICER1 as a direct functional target of the APE1-regulated miRNA-33a-5p and miR-130b-3p. Importantly, IHC analyses of different human tumors confirmed a negative correlation existing between APE1 and Dicer1 protein levels. DICER1 downregulation represents a prognostic marker of cancer development but the mechanisms at the basis of this phenomenon are still completely unknown. Our findings, suggesting that APE1 modulates DICER1 expression via miR-33a and miR-130b, reveal new mechanistic insights on DICER1 regulation, which are of relevance in lung cancer chemoresistance and cancer invasiveness.
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Affiliation(s)
- Giulia Antoniali
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine, Italy
| | - Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine, Italy
| | - Xiaolong Zhao
- Cancer Center of Daping Hospital, Third Military Medical University, Chongqing, China
| | - Xinming Jing
- Cancer Center of Daping Hospital, Third Military Medical University, Chongqing, China
| | - Yi Cheng
- Cancer Center of Daping Hospital, Third Military Medical University, Chongqing, China
| | - Veronica De Sanctis
- Next Generation Sequence Facility, Department CIBIO, University of Trento, Trento, Italy
| | - Dilara Ayyildiz
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine, Italy
| | - Silvano Piazza
- Bioinformatics Core Facility, Department CIBIO, University of Trento, Trento, Italy.,Computational Biology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Mengxia Li
- Cancer Center of Daping Hospital, Third Military Medical University, Chongqing, China.
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine, Italy.
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16
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Small RNA-Sequencing for Analysis of Circulating miRNAs: Benchmark Study. J Mol Diagn 2022; 24:386-394. [PMID: 35081459 DOI: 10.1016/j.jmoldx.2021.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/15/2021] [Accepted: 12/20/2021] [Indexed: 11/22/2022] Open
Abstract
Small RNA-sequencing (RNA-Seq) is being increasingly used for profiling of circulating microRNAs (miRNAs), a new group of promising biomarkers. Unfortunately, small RNA-Seq protocols are prone to biases limiting quantification accuracy, which motivated development of several novel methods. Here, we present comparison of all small RNA-Seq library preparation approaches that are commercially available for quantification of miRNAs in biofluids. Using synthetic and human plasma samples, we compared performance of traditional two-adaptor ligation protocols (Lexogen, Norgen), as well as methods using randomized adaptors (NEXTflex), polyadenylation (SMARTer), circularization (RealSeq), capture probes (EdgeSeq), or unique molecular identifiers (QIAseq). There was no single protocol outperforming others across all metrics. Limited overlap of measured miRNA profiles was documented between methods largely owing to protocol-specific biases. Methods designed to minimize bias largely differ in their performance, and contributing factors were identified. Usage of unique molecular identifiers has rather negligible effect and, if designed incorrectly, can even introduce spurious results. Together, these results identify strengths and weaknesses of all current methods and provide guidelines for applications of small RNA-Seq in biomarker research.
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17
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Kaczmarek E, Nanayakkara J, Sedghi A, Pesteie M, Tuschl T, Renwick N, Mousavi P. Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures. BMC Bioinformatics 2022; 23:38. [PMID: 35026982 PMCID: PMC8756719 DOI: 10.1186/s12859-022-04559-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/30/2021] [Indexed: 11/14/2022] Open
Abstract
Background Accurate cancer classification is essential for correct treatment selection and better prognostication. microRNAs (miRNAs) are small RNA molecules that negatively regulate gene expression, and their dyresgulation is a common disease mechanism in many cancers. Through a clearer understanding of miRNA dysregulation in cancer, improved mechanistic knowledge and better treatments can be sought. Results We present a topology-preserving deep learning framework to study miRNA dysregulation in cancer. Our study comprises miRNA expression profiles from 3685 cancer and non-cancer tissue samples and hierarchical annotations on organ and neoplasticity status. Using unsupervised learning, a two-dimensional topological map is trained to cluster similar tissue samples. Labelled samples are used after training to identify clustering accuracy in terms of tissue-of-origin and neoplasticity status. In addition, an approach using activation gradients is developed to determine the attention of the networks to miRNAs that drive the clustering. Using this deep learning framework, we classify the neoplasticity status of held-out test samples with an accuracy of 91.07%, the tissue-of-origin with 86.36%, and combined neoplasticity status and tissue-of-origin with an accuracy of 84.28%. The topological maps display the ability of miRNAs to recognize tissue types and neoplasticity status. Importantly, when our approach identifies samples that do not cluster well with their respective classes, activation gradients provide further insight in cancer subtypes or grades. Conclusions An unsupervised deep learning approach is developed for cancer classification and interpretation. This work provides an intuitive approach for understanding molecular properties of cancer and has significant potential for cancer classification and treatment selection.
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18
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Maguire S, Guan S. Rolling circle reverse transcription enables high fidelity nanopore sequencing of small RNA. PLoS One 2022; 17:e0275471. [PMID: 36215256 PMCID: PMC9550094 DOI: 10.1371/journal.pone.0275471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/17/2022] [Indexed: 11/07/2022] Open
Abstract
Small RNAs (sRNAs) are an important group of non-coding RNAs that have great potential as diagnostic and prognostic biomarkers for treatment of a wide variety of diseases. The portability and affordability of nanopore sequencing technology makes it ideal for point of care and low resource settings. Currently sRNAs can't be reliably sequenced on the nanopore platform due to the short size of sRNAs and high error rate of the nanopore sequencer. Here, we developed a highly efficient nanopore-based sequencing strategy for sRNAs (SR-Cat-Seq) in which sRNAs are ligated to an adapter, circularized, and undergo rolling circle reverse transcription to generate concatemeric cDNA. After sequencing, the resulting tandem repeat sequences within the individual cDNA can be aligned to generate highly accurate consensus sequences. We compared our sequencing strategy with other sRNA sequencing methods on a short-read sequencing platform and demonstrated that SR-Cat-Seq can obtain low bias and highly accurate sRNA transcriptomes. Therefore, our method could enable nanopore sequencing for sRNA-based diagnostics and other applications.
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Affiliation(s)
- Sean Maguire
- New England Biolabs, Inc., Beverly, MA, United States of America
| | - Shengxi Guan
- New England Biolabs, Inc., Beverly, MA, United States of America
- * E-mail:
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19
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Xu H, Nottingham RM, Lambowitz AM. TGIRT-seq Protocol for the Comprehensive Profiling of Coding and Non-coding RNA Biotypes in Cellular, Extracellular Vesicle, and Plasma RNAs. Bio Protoc 2021; 11:e4239. [PMID: 35005084 PMCID: PMC8678547 DOI: 10.21769/bioprotoc.4239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/01/2021] [Accepted: 09/22/2021] [Indexed: 09/12/2023] Open
Abstract
High-throughput RNA sequencing (RNA-seq) has extraordinarily advanced our understanding of gene expression and disease etiology, and is a powerful tool for the identification of biomarkers in a wide range of organisms. However, most RNA-seq methods rely on retroviral reverse transcriptases (RTs), enzymes that have inherently low fidelity and processivity, to convert RNAs into cDNAs for sequencing. Here, we describe an RNA-seq protocol using Thermostable Group II Intron Reverse Transcriptases (TGIRTs), which have high fidelity, processivity, and strand-displacement activity, as well as a proficient template-switching activity that enables efficient and seamless RNA-seq adapter addition. By combining these activities, TGIRT-seq enables the simultaneous profiling of all RNA biotypes from small amounts of starting material, with superior RNA-seq metrics, and unprecedented ability to sequence structured RNAs. The TGIRT-seq protocol for Illumina sequencing consists of three steps: (i) addition of a 3' RNA-seq adapter, coupled to the initiation of cDNA synthesis at the 3' end of a target RNA, via template switching from a synthetic adapter RNA/DNA starter duplex; (ii) addition of a 5' RNA-seq adapter, by using thermostable 5' App DNA/RNA ligase to ligate an adapter oligonucleotide to the 3' end of the completed cDNA; (iii) minimal PCR amplification, to add capture sites and indices for Illumina sequencing. TGIRT-seq for the Illumina sequencing platform has been used for comprehensive profiling of coding and non-coding RNAs in ribodepleted, chemically fragmented cellular RNAs, and for the analysis of intact (non-chemically fragmented) cellular, extracellular vesicle (EV), and plasma RNAs, where it yields continuous full-length end-to-end sequences of structured small non-coding RNAs (sncRNAs), including tRNAs, snoRNAs, snRNAs, pre-miRNAs, and full-length excised linear intron (FLEXI) RNAs. Graphic abstract: Figure 1.Overview of the TGIRT-seq protocol for Illumina sequencing.Major steps are: (1) Template switching from a synthetic R2 RNA/R2R DNA starter duplex with a 1-nt 3' DNA overhang (a mixture of A, C, G, and T residues, denoted N) that base pairs to the 3' nucleotide of a target RNA, and upon initiating reverse transcription by adding dNTPs, seamlessly links an R2R adapter to the 5' end of the resulting cDNA; (2) Ligation of an R1R adapter to the 3' end of the completed cDNA; and (3) Minimal PCR amplification with primers that add Illumina capture sites (P5 and P7) and barcode sequences (indices 5 and 7). The index 7 barcode is required, while the index 5 barcode is optional, to provide unique dual indices (UDIs).
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Affiliation(s)
- Hengyi Xu
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas, 78712, USA
| | - Ryan M. Nottingham
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas, 78712, USA
| | - Alan M. Lambowitz
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas, 78712, USA
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20
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Genzor P, Konstantinidou P, Stoyko D, Manzourolajdad A, Marlin Andrews C, Elchert AR, Stathopoulos C, Haase AD. Cellular abundance shapes function in piRNA-guided genome defense. Genome Res 2021; 31:2058-2068. [PMID: 34667116 PMCID: PMC8559710 DOI: 10.1101/gr.275478.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 08/09/2021] [Indexed: 12/21/2022]
Abstract
Defense against genome invaders universally relies on RNA-guided immunity. Prokaryotic CRISPR-Cas and eukaryotic RNA interference pathways recognize targets by complementary base-pairing, which places the sequences of their guide RNAs at the center of self/nonself discrimination. Here, we explore the sequence space of PIWI-interacting RNAs (piRNAs), the genome defense of animals, and establish functional priority among individual sequences. Our results reveal that only the topmost abundant piRNAs are commonly present in every cell, whereas rare sequences generate cell-to-cell diversity in flies and mice. We identify a skewed distribution of sequence abundance as a hallmark of piRNA populations and show that quantitative differences of more than a 1000-fold are established by conserved mechanisms of biogenesis. Finally, our genomics analyses and direct reporter assays reveal that abundance determines function in piRNA-guided genome defense. Taken together, we identify an effective sequence space and untangle two classes of piRNAs that differ in complexity and function. The first class represents the topmost abundant sequences and drives silencing of genomic parasites. The second class sparsely covers an enormous sequence space. These rare piRNAs cannot function in every cell, every individual, or every generation but create diversity with potential for adaptation in the ongoing arms race with genome invaders.
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Affiliation(s)
- Pavol Genzor
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Parthena Konstantinidou
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Daniel Stoyko
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Amirhossein Manzourolajdad
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Celine Marlin Andrews
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Alexandra R Elchert
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | - Astrid D Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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21
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Kugelberg U, Nätt D, Skog S, Kutter C, Öst A. 5´XP sRNA-seq: efficient identification of transcripts with and without 5´ phosphorylation reveals evolutionary conserved small RNA. RNA Biol 2021; 18:1588-1599. [PMID: 33382953 PMCID: PMC8594926 DOI: 10.1080/15476286.2020.1861770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 12/21/2022] Open
Abstract
Small RNA (sRNA) sequencing has been critical for our understanding of many cellular processes, including gene regulation. Nonetheless, the varying biochemical properties of sRNA, such as 5´ nucleotide modifications, make many sRNA subspecies incompatible with common protocols for sRNA sequencing. Here we describe 5XP-seq that outlines a novel strategy that captures a more complete picture of sRNA. By tagging 5´P sRNA during library preparation, 5XP-seq combines an open approach that includes all types of 5'-terminal modifications (5´X), with a selective approach for 5-phosphorylated sRNA (5´P). We show that 5XP-seq not only enriches phosphorylated miRNA and piRNA but successfully discriminates these sRNA from all other sRNA species. We further demonstrate the importance of this strategy by successful inter-species validation of sRNAs that would have otherwise failed, including human to insect translation of several tRNA (tRFs) and rRNA (rRFs) fragments. By combining 5´ insensitive library strategies with 5´ sensitive tagging, we have successfully tackled an intrinsic bias in modern sRNA sequencing that will help us reveal the true complexity and the evolutionary significance of the sRNA world.
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Affiliation(s)
- Unn Kugelberg
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Daniel Nätt
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Signe Skog
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm
| | - Anita Öst
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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22
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Rohan TE, Ginsberg M, Wang Y, Couch FJ, Feigelson HS, Greenlee RT, Honda S, Stark A, Chitale D, Wang T, Xue X, Oktay MH, Sparano JA, Loudig O. Molecular markers of risk of subsequent invasive breast cancer in women with ductal carcinoma in situ: protocol for a population-based cohort study. BMJ Open 2021; 11:e053397. [PMID: 34702732 PMCID: PMC8549665 DOI: 10.1136/bmjopen-2021-053397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION Ductal carcinoma in situ (DCIS) of the breast is a non-obligate precursor of invasive breast cancer (IBC). Many DCIS patients are either undertreated or overtreated. The overarching goal of the study described here is to facilitate detection of patients with DCIS at risk of IBC development. Here, we propose to use risk factor data and formalin-fixed paraffin-embedded (FFPE) DCIS tissue from a large, ethnically diverse, population-based cohort of 8175 women with a first diagnosis of DCIS and followed for subsequent IBC to: identify/validate miRNA expression changes in DCIS tissue associated with risk of subsequent IBC; evaluate ipsilateral IBC risk in association with two previously identified marker sets (triple immunopositivity for p16, COX-2, Ki67; Oncotype DX Breast DCIS score); examine the association of risk factor data with IBC risk. METHODS AND ANALYSIS We are conducting a series of case-control studies nested within the cohort. Cases are women with DCIS who developed subsequent IBC; controls (2/case) are matched to cases on calendar year of and age at DCIS diagnosis. We project 485 cases/970 controls in the aim focused on risk factors. We estimate obtaining FFPE tissue for 320 cases/640 controls for the aim focused on miRNAs; of these, 173 cases/346 controls will be included in the aim focused on p16, COX-2 and Ki67 immunopositivity, and of the latter, 156 case-control pairs will be included in the aim focused on the Oncotype DX Breast DCIS score®. Multivariate conditional logistic regression will be used for statistical analyses. ETHICS AND DISSEMINATION Ethics approval was obtained from the Institutional Review Boards of Albert Einstein College of Medicine (IRB 2014-3611), Kaiser Permanente Colorado, Kaiser Permanente Hawaii, Henry Ford Health System, Mayo Clinic, Marshfield Clinic Research Institute and Hackensack Meridian Health, and from Lifespan Research Protection Office. The study results will be presented at meetings and published in peer-reviewed journals.
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Affiliation(s)
- Thomas E Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Mindy Ginsberg
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yihong Wang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Providence, Rhode Island, USA
- Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Robert T Greenlee
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Stacey Honda
- Center for Integrated Healthcare, Kaiser Permanente, Hawaii Permanente Medical Group, Honolulu, Hawaii, USA
| | - Azadeh Stark
- Department of Pathology and Laboratory Medicine, Henry Ford Health System, Detroit, Michigan, USA
- Breast Oncology Program and Department of Pathology, Henry Ford Health System, Detroit, Michigan, USA
| | - Dhananjay Chitale
- Department of Pathology and Laboratory Medicine, Henry Ford Health System, Detroit, Michigan, USA
- Breast Oncology Program and Department of Pathology, Henry Ford Health System, Detroit, Michigan, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Xiaonan Xue
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Maja H Oktay
- Department of Pathology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York, USA
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York, USA
| | - Joseph A Sparano
- Department of Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York, USA
| | - Olivier Loudig
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
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Wulf MG, Maguire S, Dai N, Blondel A, Posfai D, Krishnan K, Sun Z, Guan S, Corrêa IR. Chemical capping improves template switching and enhances sequencing of small RNAs. Nucleic Acids Res 2021; 50:e2. [PMID: 34581823 PMCID: PMC8754658 DOI: 10.1093/nar/gkab861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/26/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
Template-switching reverse transcription is widely used in RNA sequencing for low-input and low-quality samples, including RNA from single cells or formalin-fixed paraffin-embedded (FFPE) tissues. Previously, we identified the native eukaryotic mRNA 5′ cap as a key structural element for enhancing template switching efficiency. Here, we introduce CapTS-seq, a new strategy for sequencing small RNAs that combines chemical capping and template switching. We probed a variety of non-native synthetic cap structures and found that an unmethylated guanosine triphosphate cap led to the lowest bias and highest efficiency for template switching. Through cross-examination of different nucleotides at the cap position, our data provided unequivocal evidence that the 5′ cap acts as a template for the first nucleotide in reverse transcriptase-mediated post-templated addition to the emerging cDNA—a key feature to propel template switching. We deployed CapTS-seq for sequencing synthetic miRNAs, human total brain and liver FFPE RNA, and demonstrated that it consistently improves library quality for miRNAs in comparison with a gold standard template switching-based small RNA-seq kit.
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Affiliation(s)
- Madalee G Wulf
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Sean Maguire
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Nan Dai
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Alice Blondel
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Dora Posfai
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | | | - Zhiyi Sun
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Shengxi Guan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Ivan R Corrêa
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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24
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Abstract
Transcription start site (TSS) selection influences transcript stability and translation as well as protein sequence. Alternative TSS usage is pervasive in organismal development, is a major contributor to transcript isoform diversity in humans, and is frequently observed in human diseases including cancer. In this review, we discuss the breadth of techniques that have been used to globally profile TSSs and the resulting insights into gene regulation, as well as future prospects in this area of inquiry.
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Affiliation(s)
| | - Gabriel E. Zentner
- Department of Biology, Indiana University, Bloomington, IN 47401, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
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25
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Qin LX, Zou J, Shi J, Lee A, Mihailovic A, Farazi TA, Tuschl T, Singer S. Statistical Assessment of Depth Normalization for Small RNA Sequencing. JCO Clin Cancer Inform 2021; 4:567-582. [PMID: 32598180 PMCID: PMC7330947 DOI: 10.1200/cci.19.00118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Methods for depth normalization have been assessed primarily with simulated data or cell-line–mixture data. There is a pressing need for benchmark data enabling a more realistic and objective assessment, especially in the context of small RNA sequencing. METHODS We collected a unique pair of microRNA sequencing data sets for the same set of tumor samples; one data set was collected with and the other without uniform handling and balanced design. The former provided a benchmark for evaluating evidence of differential expression and the latter served as a test bed for normalization. Next, we developed a data perturbation algorithm to simulate additional data set pairs. Last, we assembled a set of computational tools to visualize and quantify the assessment. RESULTS We validated the quality of the benchmark data and showed the need for normalization of the test data. For illustration, we applied the data and tools to assess the performance of 9 existing normalization methods. Among them, trimmed mean of M-values was a better scaling method, whereas the median and the upper quartiles were consistently the worst performers; one variation of remove unwanted variation had the best chance of capturing true positives but at the cost of increased false positives. In general, these methods were, at best, moderately helpful when the level of differential expression was extensive and asymmetric. CONCLUSION Our study (1) provides the much-needed benchmark data and computational tools for assessing depth normalization, (2) shows the dependence of normalization performance on the underlying pattern of differential expression, and (3) calls for continued research efforts to develop more effective normalization methods.
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Affiliation(s)
- Li-Xuan Qin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jian Zou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jiejun Shi
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ann Lee
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Thalia A Farazi
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
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26
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La Rocca G, King B, Shui B, Li X, Zhang M, Akat KM, Ogrodowski P, Mastroleo C, Chen K, Cavalieri V, Ma Y, Anelli V, Betel D, Vidigal J, Tuschl T, Meister G, Thompson CB, Lindsten T, Haigis K, Ventura A. Inducible and reversible inhibition of miRNA-mediated gene repression in vivo. eLife 2021; 10:e70948. [PMID: 34463618 PMCID: PMC8476124 DOI: 10.7554/elife.70948] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/24/2021] [Indexed: 12/23/2022] Open
Abstract
Although virtually all gene networks are predicted to be controlled by miRNAs, the contribution of this important layer of gene regulation to tissue homeostasis in adult animals remains unclear. Gain and loss-of-function experiments have provided key insights into the specific function of individual miRNAs, but effective genetic tools to study the functional consequences of global inhibition of miRNA activity in vivo are lacking. Here we report the generation and characterization of a genetically engineered mouse strain in which miRNA-mediated gene repression can be reversibly inhibited without affecting miRNA biogenesis or abundance. We demonstrate the usefulness of this strategy by investigating the consequences of acute inhibition of miRNA function in adult animals. We find that different tissues and organs respond differently to global loss of miRNA function. While miRNA-mediated gene repression is essential for the homeostasis of the heart and the skeletal muscle, it is largely dispensable in the majority of other organs. Even in tissues where it is not required for homeostasis, such as the intestine and hematopoietic system, miRNA activity can become essential during regeneration following acute injury. These data support a model where many metazoan tissues primarily rely on miRNA function to respond to potentially pathogenic events.
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Affiliation(s)
- Gaspare La Rocca
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Bryan King
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Bing Shui
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, United States
| | - Xiaoyi Li
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Minsi Zhang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kemal M Akat
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, United States
| | - Paul Ogrodowski
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Chiara Mastroleo
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kevin Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Yilun Ma
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, United States
| | - Viviana Anelli
- Center of Integrative Biology, University of Trento, Trento, Italy
| | - Doron Betel
- Hem/Oncology, Medicine and Institution for Computational Biomedicine, Weill Cornell Medical College, New York, United States
| | - Joana Vidigal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, United States
| | - Gunter Meister
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Tullia Lindsten
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kevin Haigis
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, United States
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
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27
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Hu JF, Yim D, Ma D, Huber SM, Davis N, Bacusmo JM, Vermeulen S, Zhou J, Begley TJ, DeMott MS, Levine SS, de Crécy-Lagard V, Dedon PC, Cao B. Quantitative mapping of the cellular small RNA landscape with AQRNA-seq. Nat Biotechnol 2021; 39:978-988. [PMID: 33859402 PMCID: PMC8355021 DOI: 10.1038/s41587-021-00874-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 02/25/2021] [Indexed: 12/23/2022]
Abstract
Current next-generation RNA-sequencing (RNA-seq) methods do not provide accurate quantification of small RNAs within a sample, due to sequence-dependent biases in capture, ligation and amplification during library preparation. We present a method, absolute quantification RNA-sequencing (AQRNA-seq), that minimizes biases and provides a direct, linear correlation between sequencing read count and copy number for all small RNAs in a sample. Library preparation and data processing were optimized and validated using a 963-member microRNA reference library, oligonucleotide standards of varying length, and RNA blots. Application of AQRNA-seq to a panel of human cancer cells revealed >800 detectable miRNAs that varied during cancer progression, while application to bacterial transfer RNA pools, with the challenges of secondary structure and abundant modifications, revealed 80-fold variation in tRNA isoacceptor levels, stress-induced site-specific tRNA fragmentation, quantitative modification maps, and evidence for stress-induced, tRNA-driven, codon-biased translation. AQRNA-seq thus provides a versatile means to quantitatively map the small RNA landscape in cells.
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Affiliation(s)
- Jennifer F Hu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Bristol Myers Squibb, Seattle, WA, USA
| | - Daniel Yim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- A*STAR Genome Institute of Singapore, Singapore, Singapore
| | - Duanduan Ma
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sabrina M Huber
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Laboratory of Toxicology, ETH Zürich, Zürich, Switzerland
| | - Nick Davis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Theon Therapeutics, Cambridge, MA, USA
| | - Jo Marie Bacusmo
- Department of Microbiology & Cell Science, University of Florida, Gainesville, FL, USA
| | - Sidney Vermeulen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jieliang Zhou
- KK Research Center, KK Women's and ChildrenBristol Myers Squibb's Hospital, Singapore, Singapore
| | - Thomas J Begley
- The RNA Institute and Department of Biology, University at Albany, Albany, NY, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stuart S Levine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance IRG, Singapore, Singapore.
| | - Bo Cao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance IRG, Singapore, Singapore.
- College of Life Sciences, Qufu Normal University, Qufu, China.
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28
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Methyltransferase-directed orthogonal tagging and sequencing of miRNAs and bacterial small RNAs. BMC Biol 2021; 19:129. [PMID: 34158037 PMCID: PMC8220740 DOI: 10.1186/s12915-021-01053-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/24/2021] [Indexed: 12/13/2022] Open
Abstract
Background Targeted installation of designer chemical moieties on biopolymers provides an orthogonal means for their visualisation, manipulation and sequence analysis. Although high-throughput RNA sequencing is a widely used method for transcriptome analysis, certain steps, such as 3′ adapter ligation in strand-specific RNA sequencing, remain challenging due to structure- and sequence-related biases introduced by RNA ligases, leading to misrepresentation of particular RNA species. Here, we remedy this limitation by adapting two RNA 2′-O-methyltransferases from the Hen1 family for orthogonal chemo-enzymatic click tethering of a 3′ sequencing adapter that supports cDNA production by reverse transcription of the tagged RNA. Results We showed that the ssRNA-specific DmHen1 and dsRNA-specific AtHEN1 can be used to efficiently append an oligonucleotide adapter to the 3′ end of target RNA for sequencing library preparation. Using this new chemo-enzymatic approach, we identified miRNAs and prokaryotic small non-coding sRNAs in probiotic Lactobacillus casei BL23. We found that compared to a reference conventional RNA library preparation, methyltransferase-Directed Orthogonal Tagging and RNA sequencing, mDOT-seq, avoids misdetection of unspecific highly-structured RNA species, thus providing better accuracy in identifying the groups of transcripts analysed. Our results suggest that mDOT-seq has the potential to advance analysis of eukaryotic and prokaryotic ssRNAs. Conclusions Our findings provide a valuable resource for studies of the RNA-centred regulatory networks in Lactobacilli and pave the way to developing novel transcriptome and epitranscriptome profiling approaches in vitro and inside living cells. As RNA methyltransferases share the structure of the AdoMet-binding domain and several specific cofactor binding features, the basic principles of our approach could be easily translated to other AdoMet-dependent enzymes for the development of modification-specific RNA-seq techniques. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01053-w.
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29
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Anastasakis DG, Jacob A, Konstantinidou P, Meguro K, Claypool D, Cekan P, Haase AD, Hafner M. A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol. Nucleic Acids Res 2021; 49:e45. [PMID: 33503264 DOI: 10.1093/nar/gkab011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/28/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Crosslinking and immunoprecipitation (CLIP) methods are powerful techniques to interrogate direct protein-RNA interactions and dissect posttranscriptional gene regulatory networks. One widely used CLIP variant is photoactivatable ribonucleoside enhanced CLIP (PAR-CLIP) that involves in vivo labeling of nascent RNAs with the photoreactive nucleosides 4-thiouridine (4SU) or 6-thioguanosine (6SG), which can efficiently crosslink to interacting proteins using UVA and UVB light. Crosslinking of 4SU or 6SG to interacting amino acids changes their base-pairing properties and results in characteristic mutations in cDNA libraries prepared for high-throughput sequencing, which can be computationally exploited to remove abundant background from non-crosslinked sequences and help pinpoint RNA binding protein binding sites at nucleotide resolution on a transcriptome-wide scale. Here we present a streamlined protocol for fluorescence-based PAR-CLIP (fPAR-CLIP) that eliminates the need to use radioactivity. It is based on direct ligation of a fluorescently labeled adapter to the 3'end of crosslinked RNA on immobilized ribonucleoproteins, followed by isolation of the adapter-ligated RNA and efficient conversion into cDNA without the previously needed size fractionation on denaturing polyacrylamide gels. These improvements cut the experimentation by half to 2 days and increases sensitivity by 10-100-fold.
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Affiliation(s)
- Dimitrios G Anastasakis
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, 20892 MD, USA
| | - Alexis Jacob
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, 20892 MD, USA
| | - Parthena Konstantinidou
- Laboratory of Cellular and Molecular Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892 MD, USA
| | - Kazuyuki Meguro
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892 MD, USA
| | - Duncan Claypool
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, 20892 MD, USA
| | - Pavol Cekan
- MultiplexDX s.r.o., 841 04 Bratislava, Slovakia
| | - Astrid D Haase
- Laboratory of Cellular and Molecular Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892 MD, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, 20892 MD, USA
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30
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Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS. Multisite Evaluation of Next-Generation Methods for Small RNA Quantification. J Biomol Tech 2021; 31:47-56. [PMID: 31966025 DOI: 10.7171/jbt.20-3102-001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Small RNAs (smRNAs) are important regulators of many biologic processes and are now most frequently characterized using Illumina sequencing. However, although standard RNA sequencing library preparation has become routine in most sequencing facilities, smRNA sequencing library preparation has historically been challenging because of high input requirements, laborious protocols involving gel purifications, inability to automate, and a lack of benchmarking standards. Additionally, studies have suggested that many of these methods are nonlinear and do not accurately reflect the amounts of smRNAs in vivo. Recently, a number of new kits have become available that permit lower input amounts and less laborious, gel-free protocol options. Several of these new kits claim to reduce RNA ligase-dependent sequence bias through novel adapter modifications and to lessen adapter-dimer contamination in the resulting libraries. With the increasing number of smRNA kits available, understanding the relative strengths of each method is crucial for appropriate experimental design. In this study, we systematically compared 9 commercially available smRNA library preparation kits as well as NanoString probe hybridization across multiple study sites. Although several of the new methodologies do reduce the amount of artificially over- and underrepresented microRNAs (miRNAs), we observed that none of the methods was able to remove all of the bias in the library preparation. Identical samples prepared with different methods show highly varied levels of different miRNAs. Even so, many methods excelled in ease of use, lower input requirement, fraction of usable reads, and reproducibility across sites. These differences may help users select the most appropriate methods for their specific question of interest.
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Affiliation(s)
- Zachary T Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, Indiana, USA
| | | | - Fred W Kolling
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Carol S Ringelberg
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Ashley LeClerc
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA
| | - Yuriy O Alekseyev
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA.,Department of Pathology and Laboratory Medicine, Boston University, Boston, Massachusetts, USA
| | - Jun Fan
- Genomic Core Facility, Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, USA
| | - Jessica W Podnar
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Holly S Stevenson
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Gary Sommerville
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shipra Gupta
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Maura Berkeley
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Julie Koeman
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Allison R Scott
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - Jeffrey Malik
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - Kara L Pivarski
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Xinkun Wang
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Gina Kuffel
- Loyola Genomics Facility, Loyola University Chicago, Maywood, Illinois, USA
| | - Tania E Mesa
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Andrew T Smith
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Yoko Takata
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Thomas L Volkert
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jennifer A Love
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Yanping Zhang
- Interdisciplinary Center for Biotechnology Research Gene Expression and Genotyping, University of Florida, Gainsville, Florida, USA
| | - Jun Wang
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Xiaoling Xuei
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Stuart S Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Benesova S, Kubista M, Valihrach L. Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis. Diagnostics (Basel) 2021; 11:964. [PMID: 34071824 PMCID: PMC8229417 DOI: 10.3390/diagnostics11060964] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/15/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of small RNA molecules that have an important regulatory role in multiple physiological and pathological processes. Their disease-specific profiles and presence in biofluids are properties that enable miRNAs to be employed as non-invasive biomarkers. In the past decades, several methods have been developed for miRNA analysis, including small RNA sequencing (RNA-seq). Small RNA-seq enables genome-wide profiling and analysis of known, as well as novel, miRNA variants. Moreover, its high sensitivity allows for profiling of low input samples such as liquid biopsies, which have now found applications in diagnostics and prognostics. Still, due to technical bias and the limited ability to capture the true miRNA representation, its potential remains unfulfilled. The introduction of many new small RNA-seq approaches that tried to minimize this bias, has led to the existence of the many small RNA-seq protocols seen today. Here, we review all current approaches to cDNA library construction used during the small RNA-seq workflow, with particular focus on their implementation in commercially available protocols. We provide an overview of each protocol and discuss their applicability. We also review recent benchmarking studies comparing each protocol's performance and summarize the major conclusions that can be gathered from their usage. The result documents variable performance of the protocols and highlights their different applications in miRNA research. Taken together, our review provides a comprehensive overview of all the current small RNA-seq approaches, summarizes their strengths and weaknesses, and provides guidelines for their applications in miRNA research.
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Affiliation(s)
- Sarka Benesova
- Laboratory of Gene Expression, Institute of Biotechnology, CAS, BIOCEV, 252 50 Vestec, Czech Republic; (S.B.); (M.K.)
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology, CAS, BIOCEV, 252 50 Vestec, Czech Republic; (S.B.); (M.K.)
- TATAA Biocenter AB, 411 03 Gothenburg, Sweden
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology, CAS, BIOCEV, 252 50 Vestec, Czech Republic; (S.B.); (M.K.)
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32
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LaBelle J, Bowser M, Brown A, Farnam L, Kho A, Li J, McGeachie M, Chase R, Piehl S, Allen K, Hobbs BD, Weiss ST, Hersh C, Tantisira K, Amr SS. Commercially Available Blocking Oligonucleotides Effectively Suppress Unwanted Hemolysis-Related miRNAs in a Large Whole-Blood RNA Cohort. J Mol Diagn 2021; 23:671-682. [PMID: 33872788 DOI: 10.1016/j.jmoldx.2021.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 03/15/2021] [Accepted: 03/25/2021] [Indexed: 12/23/2022] Open
Abstract
When sequencing small RNA libraries derived from whole blood, the most abundant microRNAs (miRs) detected are often miR-486-5p, miR-451a, and miR-92a-3p. These highly expressed erythropoietic miRs are released into the sample from red blood cell hemolysis. Next-generation sequencing of these unwanted miRs leads to a waste in sequencing cost and diminished detection of lowly expressed miRNAs, including many potential miRNA biomarkers. Previous work has developed a method to reduce targeted miRNAs using oligonucleotides that bind their target miRNA and prevent its ligation during library construction, although the extent to which oligonucleotides can be multiplexed and their effect on larger cohorts has not been thoroughly explored. We present a method for suppressing detection of three highly abundant heme miRs in a single multiplexed blocking oligonucleotide reaction. In a small paired-sample pilot (n = 8) and a large cohort of samples (n = 901), multiplexed oligos reduced detection of their target miRNAs by approximately 70%, allowing for an approximately 10-fold increase in reads mapping to nonheme miRs and increased detection of very lowly expressed miRs, with minimal off-target effects. By removing all three highly expressed erythropoietic miRNAs from next-generational sequencing libraries, this commercially available multiplexed blocking oligonucleotide method allows for greater detection of lowly expressed biomarkers, improving the efficacy, cost-efficiency, and sensitivity of biomarker studies and diagnostic tests.
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Affiliation(s)
- Jenna LaBelle
- Mass General Brigham Personalized Medicine, Partners Healthcare, Cambridge, Massachusetts
| | - Mark Bowser
- Mass General Brigham Personalized Medicine, Partners Healthcare, Cambridge, Massachusetts
| | - Alison Brown
- Mass General Brigham Personalized Medicine, Partners Healthcare, Cambridge, Massachusetts
| | - Leanna Farnam
- School of Health Sciences, Lasell University, Auburndale, Massachusetts
| | - Alvin Kho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jiang Li
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Michael McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Robert Chase
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | | | - Brian D Hobbs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Scott T Weiss
- Mass General Brigham Personalized Medicine, Partners Healthcare, Cambridge, Massachusetts; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Craig Hersh
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kelan Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sami S Amr
- Mass General Brigham Personalized Medicine, Partners Healthcare, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
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Abstract
RNA silencing plays a critical role in diverse biological processes in plants including growth, development, and responses to abiotic and biotic stresses. RNA silencing is guided by small non-coding RNAs (sRNAs) with the length of 21-24 nucleotides (nt) that are loaded into Argonaute (AGO) to repress expression of target loci and transcripts through transcriptional or posttranscriptional gene silencing mechanisms. Identification and quantitative characterization of sRNAs are crucial steps toward appreciation of their functions in biology. Here, we developed a step-by-step protocol to precisely illustrate the process of cloning of sRNA libraries and correspondingly computational analysis of the recovered sRNAs. This protocol can be used in all kinds of organisms, including Arabidopsis, and is compatible with various high-throughput sequence technologies such as Illumina Hiseq. Thus, we wish that this protocol represents an accurate way to identify and quantify sRNAs in vivo.
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Affiliation(s)
- Di Sun
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
- Graduate Program for Molecular and Environmental Plant Science, Texas A&M University, College Station, TX, USA
| | - Zeyang Ma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Jiaying Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA.
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34
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Kupsco A, Prada D, Valvi D, Hu L, Petersen MS, Coull B, Grandjean P, Weihe P, Baccarelli AA. Human milk extracellular vesicle miRNA expression and associations with maternal characteristics in a population-based cohort from the Faroe Islands. Sci Rep 2021; 11:5840. [PMID: 33712635 PMCID: PMC7970999 DOI: 10.1038/s41598-021-84809-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 02/17/2021] [Indexed: 12/17/2022] Open
Abstract
Human milk plays a critical role in infant development and health, particularly in cognitive, immune, and cardiometabolic functions. Milk contains extracellular vesicles (EVs) that can transport biologically relevant cargo from mother to infant, including microRNAs (miRNAs). We aimed to characterize milk EV-miRNA profiles in a human population cohort, assess potential pathways and ontology, and investigate associations with maternal characteristics. We conducted the first study to describe the EV miRNA profile of human milk in 364 mothers from a population-based mother-infant cohort in the Faroe Islands using small RNA sequencing. We detected 1523 miRNAs with ≥ one read in 70% of samples. Using hierarchical clustering, we determined five EV-miRNA clusters, the top three consisting of 15, 27 and 67 miRNAs. Correlation coefficients indicated that the expression of many miRNAs within the top three clusters was highly correlated. Top-cluster human milk EV-miRNAs were involved in pathways enriched for the endocrine system, cellular community, neurodevelopment, and cancers. miRNA expression was associated with time to milk collection post-delivery, maternal body mass index, and maternal smoking, but not maternal parity. Future studies investigating determinants of human EV-miRNAs and associated health outcomes are needed to elucidate the role of human milk EV-miRNAs in health and disease.
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Affiliation(s)
- Allison Kupsco
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, 10023, USA.
| | - Diddier Prada
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, 10023, USA
- Unit for Biomedical Research in Cancer, Instituto Nacional de Cancerologia, Universidad Nacional Autonoma de Mexico, 14080, Mexico City, Mexico
| | - Damaskini Valvi
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lisa Hu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, 10023, USA
| | - Maria Skaalum Petersen
- Department of Occupational Medicine and Public Health, The Faroese Hospital System, Tórshavn, Faroe Islands
- Center of Health Science, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Brent Coull
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Philippe Grandjean
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Environmental Medicine, University of Southern Denmark, Odense C, Denmark
| | - Pal Weihe
- Department of Occupational Medicine and Public Health, The Faroese Hospital System, Tórshavn, Faroe Islands
- Center of Health Science, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, 10023, USA
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35
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Hafner M, Katsantoni M, Köster T, Marks J, Mukherjee J, Staiger D, Ule J, Zavolan M. CLIP and complementary methods. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00018-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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36
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van Dijk EL, Thermes C. A Small RNA-Seq Protocol with Less Bias and Improved Capture of 2'-O-Methyl RNAs. Methods Mol Biol 2021; 2298:153-167. [PMID: 34085244 DOI: 10.1007/978-1-0716-1374-0_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The study of small RNAs (sRNAs) by next-generation sequencing (NGS) is challenged by bias issues during library preparation. Several types of sRNAs such as plant microRNAs (miRNAs) carry a 2'-O-methyl (2'-OMe) modification at their 3' terminal nucleotide. This modification adds another level of difficulty as it inhibits 3' adapter ligation. We previously demonstrated that modified versions of the "TruSeq (TS)" protocol have less bias and an improved detection of 2'-OMe RNAs. Here we describe in detail protocol "TS5," which showed the best overall performance. We also provide guidelines for bioinformatics analysis of the sequencing data.
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Affiliation(s)
- Erwin L van Dijk
- Institute for Integrative Biology of the Cell, UMR9198, CNRS CEA Univ Paris-Sud, Université Paris-Saclay, Gif sur Yvette Cedex, France.
| | - Claude Thermes
- Institute for Integrative Biology of the Cell, UMR9198, CNRS CEA Univ Paris-Sud, Université Paris-Saclay, Gif sur Yvette Cedex, France
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37
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Charting Extracellular Transcriptomes in The Human Biofluid RNA Atlas. Cell Rep 2020; 33:108552. [PMID: 33378673 DOI: 10.1016/j.celrep.2020.108552] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/14/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023] Open
Abstract
Extracellular RNAs present in biofluids have emerged as potential biomarkers for disease. Where most studies focus on blood-derived fluids, other biofluids may be more informative. We present an atlas of messenger, circular, and small RNA transcriptomes of a comprehensive collection of 20 human biofluids. By means of synthetic spike-in controls, we compare RNA content across biofluids, revealing a 10,000-fold difference in concentration. The circular RNA fraction is increased in most biofluids compared to tissues. Each biofluid transcriptome is enriched for RNA molecules derived from specific tissues and cell types. Our atlas enables an informed selection of the most relevant biofluid to monitor particular diseases. To verify the biomarker potential in these biofluids, four validation cohorts representing a broad spectrum of diseases were profiled, revealing numerous differential RNAs between case and control subjects. Spike-normalized data are publicly available in the R2 web portal for further exploration.
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38
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Zhang W, Wu Q. Applications of phage-derived RNA-based technologies in synthetic biology. Synth Syst Biotechnol 2020; 5:343-360. [PMID: 33083579 PMCID: PMC7564126 DOI: 10.1016/j.synbio.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022] Open
Abstract
As the most abundant biological entities with incredible diversity, bacteriophages (also known as phages) have been recognized as an important source of molecular machines for the development of genetic-engineering tools. At the same time, phages are crucial for establishing and improving basic theories of molecular biology. Studies on phages provide rich sources of essential elements for synthetic circuit design as well as powerful support for the improvement of directed evolution platforms. Therefore, phages play a vital role in the development of new technologies and central scientific concepts. After the RNA world hypothesis was proposed and developed, novel biological functions of RNA continue to be discovered. RNA and its related elements are widely used in many fields such as metabolic engineering and medical diagnosis, and their versatility led to a major role of RNA in synthetic biology. Further development of RNA-based technologies will advance synthetic biological tools as well as provide verification of the RNA world hypothesis. Most synthetic biology efforts are based on reconstructing existing biological systems, understanding fundamental biological processes, and developing new technologies. RNA-based technologies derived from phages will offer abundant sources for synthetic biological components. Moreover, phages as well as RNA have high impact on biological evolution, which is pivotal for understanding the origin of life, building artificial life-forms, and precisely reprogramming biological systems. This review discusses phage-derived RNA-based technologies terms of phage components, the phage lifecycle, and interactions between phages and bacteria. The significance of RNA-based technology derived from phages for synthetic biology and for understanding the earliest stages of biological evolution will be highlighted.
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Affiliation(s)
- Wenhui Zhang
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
- Corresponding author. MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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39
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Maguire S, Lohman GJS, Guan S. A low-bias and sensitive small RNA library preparation method using randomized splint ligation. Nucleic Acids Res 2020; 48:e80. [PMID: 32496547 PMCID: PMC7641310 DOI: 10.1093/nar/gkaa480] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/22/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022] Open
Abstract
Small RNAs are important regulators of gene expression and are involved in human development and disease. Next generation sequencing (NGS) allows for scalable, genome-wide studies of small RNA; however, current methods are challenged by low sensitivity and high bias, limiting their ability to capture an accurate representation of the cellular small RNA population. Several studies have shown that this bias primarily arises during the ligation of single-strand adapters during library preparation, and that this ligation bias is magnified by 2′-O-methyl modifications (2′OMe) on the 3′ terminal nucleotide. In this study, we developed a novel library preparation process using randomized splint ligation with a cleavable adapter, a design which resolves previous challenges associated with this ligation strategy. We show that a randomized splint ligation based workflow can reduce bias and increase the sensitivity of small RNA sequencing for a wide variety of small RNAs, including microRNA (miRNA) and tRNA fragments as well as 2′OMe modified RNA, including Piwi-interacting RNA and plant miRNA. Finally, we demonstrate that this workflow detects more differentially expressed miRNA between tumorous and matched normal tissues. Overall, this library preparation process allows for highly accurate small RNA sequencing and will enable studies of 2′OMe modified RNA with new levels of detail.
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Affiliation(s)
- Sean Maguire
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | | | - Shengxi Guan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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40
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Comparison of Reproducibility, Accuracy, Sensitivity, and Specificity of miRNA Quantification Platforms. Cell Rep 2020; 29:4212-4222.e5. [PMID: 31851944 PMCID: PMC7499898 DOI: 10.1016/j.celrep.2019.11.078] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/17/2019] [Accepted: 11/19/2019] [Indexed: 01/08/2023] Open
Abstract
Given the increasing interest in their use as disease biomarkers, the establishment of reproducible, accurate, sensitive, and specific platforms for microRNA (miRNA) quantification in biofluids is of high priority. We compare four platforms for these characteristics: small RNA sequencing (RNA-seq), FirePlex, EdgeSeq, and nCounter. For a pool of synthetic miRNAs, coefficients of variation for technical replicates are lower for EdgeSeq (6.9%) and RNA-seq (8.2%) than for FirePlex (22.4%); nCounter replicates are not performed. Receiver operating characteristic analysis for distinguishing present versus absent miRNAs shows small RNA-seq (area under curve 0.99) is superior to EdgeSeq (0.97), nCounter (0.94), and FirePlex (0.81). Expected differences in expression of placenta-associated miRNAs in plasma from pregnant and non-pregnant women are observed with RNA-seq and EdgeSeq, but not FirePlex or nCounter. These results indicate that differences in performance among miRNA profiling platforms impact ability to detect biological differences among samples and thus their relative utility for research and clinical use. Using pools of synthetic RNA oligonucleotides and standardized extracellular RNA samples, Godoy et al. compare small RNA sequencing to three targeted miRNA quantification platforms to evaluate reproducibility, bias, specificity and sensitivity, and accuracy. Each platform has strengths and limitations important to consider for biomarker discovery, clinical validation, and broad clinical use.
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41
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Wong JJM, Ginter PS, Tyryshkin K, Yang X, Nanayakkara J, Zhou Z, Tuschl T, Chen YT, Renwick N. Classifying Lung Neuroendocrine Neoplasms through MicroRNA Sequence Data Mining. Cancers (Basel) 2020; 12:E2653. [PMID: 32957587 PMCID: PMC7564332 DOI: 10.3390/cancers12092653] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
Lung neuroendocrine neoplasms (NENs) can be challenging to classify due to subtle histologic differences between pathological types. MicroRNAs (miRNAs) are small RNA molecules that are valuable markers in many neoplastic diseases. To evaluate miRNAs as classificatory markers for lung NENs, we generated comprehensive miRNA expression profiles from 14 typical carcinoid (TC), 15 atypical carcinoid (AC), 11 small cell lung carcinoma (SCLC), and 15 large cell neuroendocrine carcinoma (LCNEC) samples, through barcoded small RNA sequencing. Following sequence annotation and data preprocessing, we randomly assigned these profiles to discovery and validation sets. Through high expression analyses, we found that miR-21 and -375 are abundant in all lung NENs, and that miR-21/miR-375 expression ratios are significantly lower in carcinoids (TC and AC) than in neuroendocrine carcinomas (NECs; SCLC and LCNEC). Subsequently, we ranked and selected miRNAs for use in miRNA-based classification, to discriminate carcinoids from NECs. Using miR-18a and -155 expression, our classifier discriminated these groups in discovery and validation sets, with 93% and 100% accuracy. We also identified miR-17, -103, and -127, and miR-301a, -106b, and -25, as candidate markers for discriminating TC from AC, and SCLC from LCNEC, respectively. However, these promising findings require external validation due to sample size.
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Affiliation(s)
- Justin J. M. Wong
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (J.J.M.W.); (K.T.); (X.Y.); (J.N.); (Z.Z.)
| | - Paula S. Ginter
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; (P.S.G.); (Y.-T.C.)
| | - Kathrin Tyryshkin
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (J.J.M.W.); (K.T.); (X.Y.); (J.N.); (Z.Z.)
| | - Xiaojing Yang
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (J.J.M.W.); (K.T.); (X.Y.); (J.N.); (Z.Z.)
| | - Jina Nanayakkara
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (J.J.M.W.); (K.T.); (X.Y.); (J.N.); (Z.Z.)
| | - Zier Zhou
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (J.J.M.W.); (K.T.); (X.Y.); (J.N.); (Z.Z.)
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA;
| | - Yao-Tseng Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; (P.S.G.); (Y.-T.C.)
| | - Neil Renwick
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (J.J.M.W.); (K.T.); (X.Y.); (J.N.); (Z.Z.)
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA;
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42
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Heinicke F, Zhong X, Zucknick M, Breidenbach J, Sundaram AY, T. Flåm S, Leithaug M, Dalland M, Rayner S, Lie BA, Gilfillan GD. An extension to: Systematic assessment of commercially available low-input miRNA library preparation kits. RNA Biol 2020; 17:1284-1292. [PMID: 32436772 PMCID: PMC7549702 DOI: 10.1080/15476286.2020.1761081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/18/2020] [Accepted: 04/22/2020] [Indexed: 11/12/2022] Open
Abstract
High-throughput sequencing has emerged as the favoured method to study microRNA (miRNA) expression, but biases introduced during library preparation have been reported. We recently compared the performance (sensitivity, reliability, titration response and differential expression) of six commercially-available kits on synthetic miRNAs and human RNA, where library preparation was performed by the vendors. We hereby supplement this study with data from two further commonly used kits (NEBNext, NEXTflex) whose manufacturers initially declined to participate. NEXTflex demonstrated the highest sensitivity, which may reflect its use of partially-randomized adapter sequences, but overall performance was lower than the QIAseq and TailorMix kits. NEBNext showed intermediate performance. We reaffirm that biases are kit specific, complicating the comparison of miRNA datasets generated using different kits.
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Affiliation(s)
- Fatima Heinicke
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Xiangfu Zhong
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Manuela Zucknick
- Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo, Norway
| | - Johannes Breidenbach
- National Forest Inventory, Norwegian Institute for Bioeconomy Research, Ås, Norway
| | - Arvind Y.M. Sundaram
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Siri T. Flåm
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Magnus Leithaug
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Marianne Dalland
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Simon Rayner
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Benedicte A. Lie
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Gregor D. Gilfillan
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
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43
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Kolenda T, Guglas K, Baranowski D, Sobocińska J, Kopczyńska M, Teresiak A, Bliźniak R, Lamperska K. cfRNAs as biomarkers in oncology - still experimental or applied tool for personalized medicine already? Rep Pract Oncol Radiother 2020; 25:783-792. [PMID: 32904167 PMCID: PMC7451588 DOI: 10.1016/j.rpor.2020.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/13/2020] [Accepted: 07/31/2020] [Indexed: 02/07/2023] Open
Abstract
Currently, the challenges of contemporary oncology are focused mainly on the development of personalized medicine and precise treatment, which could be achieved through the use of molecular biomarkers. One of the biological molecules with great potential are circulating free RNAs (cfRNAs) which are present in various types of body fluids, such as blood, serum, plasma, and saliva. Also, different types of cfRNA particles can be distinguished depending on their length and function: microRNA (miRNA), PIWI-interacting RNA (piRNA), tRNA-derived RNA fragments (tRFs), circular RNA (circRNA), long non-coding RNA (lncRNA), and messenger RNA (mRNA). Moreover, cfRNAs occur in various forms: as a free molecule alone, in membrane vesicles, such as exosomes, or in complexes with proteins and lipids. One of the modern approaches for monitoring patient's condition is a "liquid biopsy" that provides a non-invasive and easily available source of circulating RNAs. Both the presence of specific cfRNA types as well as their concentration are dependent on many factors including cancer type or even reaction to treatment. Despite the possibility of using circulating free RNAs as biomarkers, there is still a lack of validated diagnostic panels, defined protocols for sampling, storing as well as detection methods. In this work we examine different types of cfRNAs, evaluate them as possible biomarkers, and analyze methods of their detection. We believe that further research on cfRNA and defining diagnostic panels could lead to better and faster cancer identification and improve treatment monitoring.
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Dawid Baranowski
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Sobocińska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Magda Kopczyńska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
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44
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Linnstaedt SD, Zannas AS, McLean SA, Koenen KC, Ressler KJ. Literature review and methodological considerations for understanding circulating risk biomarkers following trauma exposure. Mol Psychiatry 2020; 25:1986-1999. [PMID: 31863020 PMCID: PMC7305050 DOI: 10.1038/s41380-019-0636-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 11/24/2019] [Accepted: 12/11/2019] [Indexed: 12/29/2022]
Abstract
Exposure to traumatic events is common. While many individuals recover following trauma exposure, a substantial subset develop adverse posttraumatic neuropsychiatric sequelae (APNS) such as posttraumatic stress, major depression, and regional or widespread chronic musculoskeletal pain. APNS cause substantial burden to the individual and to society, causing functional impairment and physical disability, risk for suicide, lost workdays, and increased health care costs. Contemporary treatment is limited by an inability to identify individuals at high risk of APNS in the immediate aftermath of trauma, and an inability to identify optimal treatments for individual patients. Our purpose is to provide a comprehensive review describing candidate blood-based biomarkers that may help to identify those at high risk of APNS and/or guide individual intervention decision-making. Such blood-based biomarkers include circulating biological factors such as hormones, proteins, immune molecules, neuropeptides, neurotransmitters, mRNA, and noncoding RNA expression signatures, while we do not review genetic and epigenetic biomarkers due to other recent reviews of this topic. The current state of the literature on circulating risk biomarkers of APNS is summarized, and key considerations and challenges for their discovery and translation are discussed. We also describe the AURORA study, a specific example of current scientific efforts to identify such circulating risk biomarkers and the largest study to date focused on identifying risk and prognostic factors in the aftermath of trauma exposure.
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Affiliation(s)
- Sarah D Linnstaedt
- Institute for Trauma Recovery, University of North Carolina, Chapel Hill, NC, USA
- Department of Anesthesiology, University of North Carolina, Chapel Hill, NC, USA
| | - Anthony S Zannas
- Institute for Trauma Recovery, University of North Carolina, Chapel Hill, NC, USA
- Departments of Psychiatry and Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, USA
| | - Samuel A McLean
- Institute for Trauma Recovery, University of North Carolina, Chapel Hill, NC, USA
- Department of Anesthesiology, University of North Carolina, Chapel Hill, NC, USA
- Department of Emergency Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Karestan C Koenen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kerry J Ressler
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA.
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45
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Duzdevich D, Carr CE, Szostak JW. Deep sequencing of non-enzymatic RNA primer extension. Nucleic Acids Res 2020; 48:e70. [PMID: 32427335 PMCID: PMC7337528 DOI: 10.1093/nar/gkaa400] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/02/2020] [Accepted: 05/05/2020] [Indexed: 12/02/2022] Open
Abstract
Life emerging in an RNA world is expected to propagate RNA as hereditary information, requiring some form of primitive replication without enzymes. Non-enzymatic template-directed RNA primer extension is a model of the copying step in this posited form of replication. The sequence space accessed by primer extension dictates potential pathways to self-replication and, eventually, ribozymes. Which sequences can be accessed? What is the fidelity of the reaction? Does the recently illuminated mechanism of primer extension affect the distribution of sequences that can be copied? How do sequence features respond to experimental conditions and prebiotically relevant contexts? To help answer these and related questions, we here introduce a deep-sequencing methodology for studying RNA primer extension. We have designed and vetted special RNA constructs for this purpose, honed a protocol for sample preparation and developed custom software that analyzes sequencing data. We apply this new methodology to proof-of-concept controls, and demonstrate that it works as expected and reports on key features of the sequences accessed by primer extension.
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Affiliation(s)
- Daniel Duzdevich
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christopher E Carr
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jack W Szostak
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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46
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Policastro RA, Raborn RT, Brendel VP, Zentner GE. Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq. Genome Res 2020; 30:910-923. [PMID: 32660958 PMCID: PMC7370879 DOI: 10.1101/gr.261545.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/18/2020] [Indexed: 01/07/2023]
Abstract
Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5' ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and reaction cleanups, a STRIPE-seq library can be constructed in about 5 h. We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for quantification of transcript levels and analysis of differential gene expression. In conjunction with our ready-to-use computational workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.
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Affiliation(s)
| | | | - Volker P Brendel
- Department of Biology
- Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
| | - Gabriel E Zentner
- Department of Biology
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana 46202, USA
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47
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Branco GP, Valieris R, Povoa LV, Araújo LFD, Fernandes GR, Souza JESD, Amorim MGD, Ferreira ENE, Silva ITD, Nunes DN, Dias-Neto E. A comparison between SOLiD 5500XLand Ion Torrent PGM-derived miRNA expression profiles in two breast cell lines. Genet Mol Biol 2020; 43:e20180351. [PMID: 32352476 PMCID: PMC7201575 DOI: 10.1590/1678-4685-gmb-2018-0351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 06/06/2019] [Indexed: 11/22/2022] Open
Abstract
Next-generation sequencing (NGS) platforms allow the analysis of hundreds of
millions of molecules in a single sequencing run, revolutionizing many research
areas. NGS-based microRNA studies enable expression quantification in
unprecedented scale without the limitations of closed-platforms. Yet, whereas a
massive amount of data produced by these platforms is available, comparisons of
quantification/discovery capabilities between platforms are still lacking. Here
we compare two NGS-platforms: SOLiD and PGM, by evaluating their microRNA
identification/quantification capabilities using two breast-derived cell-lines.
A high expression correlation (R2 > 0.9) was achieved, encompassing 97% of
the miRNAs, and the few discrepancies in miRNA counts were attributable to
molecules that have very low expression. Quantification divergences indicative
of artefactual representation were seen for 14 miRNAs (higher in SOLiD-reads)
and another 10 miRNAs more abundant in PGM-data. An inspection of these revealed
an increased and statistically significant count of uracyls and uracyl-stretches
for PGM-enriched miRNAs, compared to SOLiD and to the miRBase. In parallel,
adenines and adenine-stretches were enriched for SOLiDderived miRNA reads. We
conclude that, whereas both platforms are overall consistent and can be used
interchangeably for microRNA expression studies, particular sequence features
appear to be indicative of specific platform bias, and their presence in
microRNAs should be considered for database-analyses.
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Affiliation(s)
| | - Renan Valieris
- A.C.Camargo Cancer Center, Laboratório de Biologia Computacional, São Paulo, SP, Brazil
| | - Lucas Venezian Povoa
- A.C.Camargo Cancer Center, Laboratório de Biologia Computacional, São Paulo, SP, Brazil.,Instituto Tecnológico de Aeronáutica, Divisão de Ciências Computacionais, Grupo de Inteligência Artificial e Robótica, São José dos Campos, SP, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, Caraguatatuba, SP, Brazil
| | | | | | | | - Maria Galli de Amorim
- A.C.Camargo Cancer Center, Laboratório de Genômica Médica, CIPE, São Paulo, SP, Brazil
| | - Elisa Napolitano E Ferreira
- A.C.Camargo Cancer Center, Laboratório de Genômica e Biologia, CIPE, São Paulo, SP, Brazil.,Grupo Fleury Pesquisa e Desenvolvimento, São Paulo, SP, Brazil
| | - Israel Tojal da Silva
- A.C.Camargo Cancer Center, Laboratório de Biologia Computacional, São Paulo, SP, Brazil
| | - Diana Noronha Nunes
- A.C.Camargo Cancer Center, Laboratório de Genômica Médica, CIPE, São Paulo, SP, Brazil
| | - Emmanuel Dias-Neto
- A.C.Camargo Cancer Center, Laboratório de Genômica Médica, CIPE, São Paulo, SP, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Departamento & Instituto de Psiquiatria, Laboratório de Neurociências Alzira Denise Hertzog Silva (LIM-27), São Paulo, SP, Brazil
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48
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Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med 2020; 72:100825. [DOI: 10.1016/j.mam.2019.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
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49
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A whole-tissue RNA-seq toolkit for organism-wide studies of gene expression with PME-seq. Nat Protoc 2020; 15:1459-1483. [PMID: 32076350 DOI: 10.1038/s41596-019-0291-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 12/21/2019] [Indexed: 11/08/2022]
Abstract
The immune system operates at the scale of the whole organism in mammals. We currently lack experimental approaches to systematically track and study organism-wide molecular processes in mice. Here we describe an integrated toolkit for measuring gene expression in whole tissues, 3-prime mRNA extension sequencing, that is applicable to most mouse organs and any mouse model of interest. Further, the methods of RNA-seq described in this protocol are broadly applicable to other sample types beyond whole organs, such as tissue samples or isolated cell populations. We report procedures to collect, store and lyse a dozen organ types using conditions compatible with the extraction of high-quality RNA. In addition, we detail protocols to perform high-throughput and low-cost RNA extraction and sequencing, as well as downstream data analysis. The protocol takes 5 d to process 384 mouse organs from collecting tissues to obtaining raw sequencing data, with additional time required for data analysis and mining. The protocol is accessible to individuals with basic skills in (i) mouse perfusion and dissection for sample collection and (ii) computation using Unix and R for data analysis. Overall, the methods presented here fill a gap in our toolbox for studying organism-wide processes in immunology and physiology.
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50
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Juzenas S, Lindqvist CM, Ito G, Dolshanskaya Y, Halfvarson J, Franke A, Hemmrich-Stanisak G. Depletion of erythropoietic miR-486-5p and miR-451a improves detectability of rare microRNAs in peripheral blood-derived small RNA sequencing libraries. NAR Genom Bioinform 2020; 2:lqaa008. [PMID: 33575555 PMCID: PMC7671325 DOI: 10.1093/nargab/lqaa008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/07/2020] [Indexed: 12/31/2022] Open
Abstract
Erythroid-specific miR-451a and miR-486-5p are two of the most dominant microRNAs (miRNAs) in human peripheral blood. In small RNA sequencing libraries, their overabundance reduces diversity as well as complexity and consequently causes negative effects such as missing detectability and inaccurate quantification of low abundant miRNAs. Here we present a simple, cost-effective and easy to implement hybridization-based method to deplete these two erythropoietic miRNAs from blood-derived RNA samples. By utilization of blocking oligonucleotides, this method provides a highly efficient and specific depletion of miR-486-5p and miR-451a, which leads to a considerable increase of measured expression as well as detectability of low abundant miRNA species. The blocking oligos are compatible with common 5′ ligation-dependent small RNA library preparation protocols, including commercially available kits, such as Illumina TruSeq and Perkin Elmer NEXTflex. Furthermore, the here described method and oligo design principle can be easily adapted to target many other miRNA molecules, depending on context and research question.
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Affiliation(s)
- Simonas Juzenas
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, DE 24105 Kiel, Germany
| | - Carl M Lindqvist
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, DE 24105 Kiel, Germany.,School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE 70182 Örebro, Sweden
| | - Go Ito
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, DE 24105 Kiel, Germany
| | - Yewgenia Dolshanskaya
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, DE 24105 Kiel, Germany
| | - Jonas Halfvarson
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE 70182 Örebro, Sweden
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, DE 24105 Kiel, Germany
| | - Georg Hemmrich-Stanisak
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, DE 24105 Kiel, Germany
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