1
|
Nease LA, Church KP, Delclaux I, Murakami S, Astorkia M, Zerhouni M, Cascio G, Hughes RO, Aguirre KN, Zumbo P, Dow LE, Jaffrey S, Betel D, Piskounova E. Selenocysteine tRNA methylation promotes oxidative stress resistance in melanoma metastasis. NATURE CANCER 2024:10.1038/s43018-024-00844-8. [PMID: 39438623 DOI: 10.1038/s43018-024-00844-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 09/25/2024] [Indexed: 10/25/2024]
Abstract
Selenocysteine-containing proteins play a central role in redox homeostasis. Their translation is a highly regulated process and is dependent on two tRNASec isodecoders differing by a single 2'-O-ribose methylation called Um34. Here we characterized FTSJ1 as the Um34 methyltransferase and show that its activity is required for efficient selenocysteine insertion at the UGA stop codon during translation. Specifically, loss of Um34 leads to ribosomal stalling and decreased UGA recoding. FTSJ1-deficient cells are more sensitive to oxidative stress and show decreased metastatic colonization in xenograft models of melanoma metastasis. We found that FTSJ1 mediates efficient translation of selenoproteins essential for the cellular antioxidant response. Our findings uncover a role for tRNASec Um34 modification in oxidative stress resistance and highlight FTSJ1 as a potential therapeutic target specific for metastatic disease.
Collapse
Affiliation(s)
- Leona A Nease
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Kellsey P Church
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ines Delclaux
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Shino Murakami
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Maider Astorkia
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Marwa Zerhouni
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Graciela Cascio
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Riley O Hughes
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Kelsey N Aguirre
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Paul Zumbo
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Samie Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Elena Piskounova
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA.
- Department of Dermatology, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
2
|
Bessler L, Sirleaf J, Kampf CJ, Frankowska K, Leszczyńska G, Opatz T, Helm M. Esterification of Cyclic N 6-Threonylcarbamoyladenosine During RNA Sample Preparation. ChemMedChem 2024; 19:e202400115. [PMID: 38630955 DOI: 10.1002/cmdc.202400115] [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] [Received: 02/08/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
The continuous deciphering of crucial biological roles of RNA modifications and their involvement in various pathological conditions, together with their key roles in the use of RNA-based therapeutics, has reignited interest in studying the occurrence and identity of non-canonical ribonucleoside structures during the past years. Discovery and structural elucidation of new modified structures is usually achieved by combination of liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) at the nucleoside level and stable isotope labeling experiments. This approach, however, has its pitfalls as demonstrated in the course of the present study: we structurally elucidated a new nucleoside structure that showed significant similarities to the family of (c)t6A modifications and was initially considered a genuine modification, but subsequently turned out to be an in vitro formed glycerol ester of t6A. This artifact is generated from ct6A during RNA hydrolysis upon addition of enzymes stored in glycerol containing buffers in a mildly alkaline milieu, and was moreover shown to undergo an intramolecular transesterification reaction. Our results demand for extra caution, not only in the discovery of new RNA modifications, but also with regard to the quantification of known modified structures, in particular chemically labile modifications, such as ct6A, that might suffer from exposure to putatively harmless reagents during the diverse steps of sample preparation.
Collapse
Affiliation(s)
- Larissa Bessler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Jason Sirleaf
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Christopher J Kampf
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Katarzyna Frankowska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Grażyna Leszczyńska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| |
Collapse
|
3
|
Ubhi T, Zaslaver O, Quaile AT, Plenker D, Cao P, Pham NA, Békési A, Jang GH, O'Kane GM, Notta F, Moffat J, Wilson JM, Gallinger S, Vértessy BG, Tuveson DA, Röst HL, Brown GW. Cytidine deaminases APOBEC3C and APOBEC3D promote DNA replication stress resistance in pancreatic cancer cells. NATURE CANCER 2024; 5:895-915. [PMID: 38448522 DOI: 10.1038/s43018-024-00742-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/09/2024] [Indexed: 03/08/2024]
Abstract
Gemcitabine is a potent inhibitor of DNA replication and is a mainstay therapeutic for diverse cancers, particularly pancreatic ductal adenocarcinoma (PDAC). However, most tumors remain refractory to gemcitabine therapies. Here, to define the cancer cell response to gemcitabine, we performed genome-scale CRISPR-Cas9 chemical-genetic screens in PDAC cells and found selective loss of cell fitness upon disruption of the cytidine deaminases APOBEC3C and APOBEC3D. Following gemcitabine treatment, APOBEC3C and APOBEC3D promote DNA replication stress resistance and cell survival by deaminating cytidines in the nuclear genome to ensure DNA replication fork restart and repair in PDAC cells. We provide evidence that the chemical-genetic interaction between APOBEC3C or APOBEC3D and gemcitabine is absent in nontransformed cells but is recapitulated across different PDAC cell lines, in PDAC organoids and in PDAC xenografts. Thus, we uncover roles for APOBEC3C and APOBEC3D in DNA replication stress resistance and offer plausible targets for improving gemcitabine-based therapies for PDAC.
Collapse
Affiliation(s)
- Tajinder Ubhi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Olga Zaslaver
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Andrew T Quaile
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Dennis Plenker
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Xilis Inc., Durham, NC, USA
| | - Pinjiang Cao
- Living Biobank, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Living Biobank, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Angéla Békési
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Budapest, Hungary
- Genome Metabolism Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Research Network, Budapest, Hungary
| | - Gun-Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Grainne M O'Kane
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Division of Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Julie M Wilson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Beáta G Vértessy
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Budapest, Hungary
- Genome Metabolism Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Research Network, Budapest, Hungary
| | - David A Tuveson
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Hannes L Röst
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Grant W Brown
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
4
|
Bessler L, Groß J, Kampf CJ, Opatz T, Helm M. Reversible oxidative dimerization of 4-thiouridines in tRNA isolates. RSC Chem Biol 2024; 5:216-224. [PMID: 38456039 PMCID: PMC10915967 DOI: 10.1039/d3cb00221g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/31/2024] [Indexed: 03/09/2024] Open
Abstract
The occurrence of non-canonical nucleoside structures in RNA of biological or synthetic origin has encountered several recent boosts in attention, namely in the context of RNA modifications, and with an eye to RNA vaccines. New nucleoside structures introduce added functionality and function into biopolymers that are otherwise rather homogenous in their chemical structure. Here, we report the discovery of a presumed RNA modification that was identified by combination of liquid chromatography-tandem mass spectrometry (LC-MS/MS) with stable isotope labelling as a dimer of the known RNA modification 4-thiouridine (s4U). The disulfide-linked structure, which had previously been synthetically introduced into RNA, was here formed spontaneously in isolates of E. coli tRNA. Judicious application of stable isotope labelling suggested that this presumed new RNA modification was rather generated ex vivo by oxidation with ambient oxygen. These findings do not only underscore the need for caution in the discovery of new RNA modifications with respect to artifacts, but also raise awareness of an RNA vulnerability, especially to oxidative damage, during its transport or storage.
Collapse
Affiliation(s)
- Larissa Bessler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Jonathan Groß
- Department of Chemistry, Johannes Gutenberg University Mainz Duesbergweg 10-14 55128 Mainz Germany
| | - Christopher J Kampf
- Department of Chemistry, Johannes Gutenberg University Mainz Duesbergweg 10-14 55128 Mainz Germany
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg University Mainz Duesbergweg 10-14 55128 Mainz Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| |
Collapse
|
5
|
Deng L, Kumar J, Rose R, McIntyre W, Fabris D. Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code. MASS SPECTROMETRY REVIEWS 2024; 43:5-38. [PMID: 36052666 DOI: 10.1002/mas.21798] [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: 02/14/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
Collapse
Affiliation(s)
- L Deng
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - J Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - R Rose
- Department of Advanced Research Technologies, New York University Langone Health Center, New York, USA
| | - W McIntyre
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Daniele Fabris
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| |
Collapse
|
6
|
Ammann G, Berg M, Dalwigk JF, Kaiser SM. Pitfalls in RNA Modification Quantification Using Nucleoside Mass Spectrometry. Acc Chem Res 2023; 56:3121-3131. [PMID: 37944919 PMCID: PMC10666278 DOI: 10.1021/acs.accounts.3c00402] [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: 07/18/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023]
Abstract
In recent years, there has been a high interest in researching RNA modifications, as they are involved in many cellular processes and in human diseases. A substantial set of enzymes within the cell, called RNA writers, place RNA modifications selectively and site-specifically. Another set of enzymes, called readers, recognize these modifications which guide the fate of the modified RNA. Although RNA is a transient molecule and RNA modification could be removed by RNA degradation, a subclass of enzymes, called RNA erasers, remove RNA modifications selectively and site-specifically to alter the characteristics of the RNA. The detection of RNA modifications can be done by various methods including second and next generation sequencing but also mass spectrometry. An approach capable of both qualitative and quantitative RNA modification analysis is liquid chromatography coupled to mass spectrometry of enzymatic hydrolysates of RNA into nucleosides. However, for successful detection and quantification, various factors must be considered to avoid biased identification and inaccurate quantification. In this Account, we identify three classes of errors that may distort the analysis. These classes comprise (I) errors related to chemical instabilities, (II) errors revolving around enzymatic hydrolysis to nucleosides, and (III) errors arising from issues with chromatographic separation and/or subsequent mass spectrometric analysis.A prominent example for class 1 is Dimroth rearrangement of m1A to m6A, but class 1 also comprises hydrolytic reactions and reactions with buffer components. Here, we also present the conversion of m3C to m3U under mild alkaline conditions and propose a practical solution to overcome these instabilities. Class 2 errors-such as contaminations in hydrolysis reagents or nuclease specificities-have led to erroneous discoveries of nucleosides in the past and possess the potential for misquantification of nucleosides. Impurities in the samples may also lead to class 3 errors: For instance, issues with chromatographic separation may arise from residual organic solvents, and salt adducts may hamper mass spectrometric quantification. This Account aims to highlight various errors connected to mass spectrometry analysis of nucleosides and presents solutions for how to overcome or circumnavigate those issues. Therefore, the authors anticipate that many scientists, but especially those who plan on doing nucleoside mass spectrometry, will benefit from the collection of data presented in this Account as a raised awareness, toward the variety of potential pitfalls, may further enhance the quality of data.
Collapse
Affiliation(s)
- Gregor Ammann
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Maximilian Berg
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Jan Felix Dalwigk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Stefanie M. Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| |
Collapse
|
7
|
Obrador E, Salvador-Palmer R, Pellicer B, López-Blanch R, Sirerol JA, Villaescusa JI, Montoro A, Dellinger RW, Estrela JM. Combination of natural polyphenols with a precursor of NAD + and a TLR2/6 ligand lipopeptide protects mice against lethal γ radiation. J Adv Res 2023; 45:73-86. [PMID: 35599107 PMCID: PMC10006514 DOI: 10.1016/j.jare.2022.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Effective agents that could confer long-term protection against ionizing radiation in vivo would have applications in medicine, biotechnology, and in air and space travel. However, at present, drugs that can effectively protect against lethal ionizing radiations are still an unmet need. OBJECTIVE To investigate if combinations of natural polyphenols, known for their antioxidant potential, could protect against ionizing radiations. METHODS Plant-derived polyphenols were screened for their potential ability to confer radioprotection to mice given a lethal whole-body γ radiation (137Cs) dose expected to kill 50% of the animals in 30 days. Telomere and centromere staining, Q-FISH and comet assays were used to investigate chromosomal aberration, micronuclei formation and DNA breaks. Molecular oxidations were investigated by enzyme immunoassays and UPLC-MS/MS. RT-PCR, western blotting and siRNA-induced gene silencing were used to study signaling mechanisms and molecular interactions. RESULTS The combination of pterostilbene (PT) and silibinin (SIL) was the most effective against γ-irradiation, resulting in 100% of the mice surviving at 30 days and 20% survival at one year. Treatment post γ-irradiation with two potential radiomitigators nicotinamide riboside (NR, a vitamin B3 derivative), and/or fibroblast-stimulating lipoprotein 1 (FSL1, a toll-like receptor 2/6 agonist), did not extend survival. However, the combination of PT, SIL, NR and FSL1 achieved a 90% survival one year post γ-irradiation. The mechanism involves induction of the Nrf2-dependent cellular antioxidant defense, reduction of NF-kB signaling, upregulation of the PGC-1α/sirtuins 1 and 3 axis, PARP1-dependent DNA repair, and stimulation of hematopoietic cell recovery. The pathway linking Nrf2, sirtuin 3 and SOD2 is key to radioprotection. Importantly, this combination did not interfere with X-ray mediated killing of different tumor cells in vivo. CONCLUSION The combination of the radioprotectors PT and SIL with the radiomitigators NR and FSL1 confer effective, long-term protection against γ radiation in vivo. This strategy is potentially capable of protecting mammals against ionizing radiations.
Collapse
Affiliation(s)
- Elena Obrador
- Department of Physiology, Faculty of Medicine & Odontology, University of Valencia, 46010 Valencia, Spain.
| | - Rosario Salvador-Palmer
- Department of Physiology, Faculty of Medicine & Odontology, University of Valencia, 46010 Valencia, Spain
| | - Blanca Pellicer
- Service of Radiology, Sagunto Hospital, 46520 Sagunto, Valencia, Spain
| | - Rafael López-Blanch
- Department of Physiology, Faculty of Medicine & Odontology, University of Valencia, 46010 Valencia, Spain
| | - J Antoni Sirerol
- Department of Physiology, Faculty of Medicine & Odontology, University of Valencia, 46010 Valencia, Spain
| | - Juan I Villaescusa
- Service of Radiological Protection, Health Research Institute (IISLaFe), La Fe University Hospital, 46026 Valencia, Spain; Biomedical Imaging Research Group GIBI230, Health Research Institute (IISLaFe), La Fe University Hospital, 46026 Valencia, Spain
| | - Alegría Montoro
- Service of Radiological Protection, Health Research Institute (IISLaFe), La Fe University Hospital, 46026 Valencia, Spain; Biomedical Imaging Research Group GIBI230, Health Research Institute (IISLaFe), La Fe University Hospital, 46026 Valencia, Spain
| | | | - José M Estrela
- Department of Physiology, Faculty of Medicine & Odontology, University of Valencia, 46010 Valencia, Spain.
| |
Collapse
|
8
|
Jora M, Corcoran D, Parungao GG, Lobue PA, Oliveira LFL, Stan G, Addepalli B, Limbach PA. Higher-Energy Collisional Dissociation Mass Spectral Networks for the Rapid, Semi-automated Characterization of Known and Unknown Ribonucleoside Modifications. Anal Chem 2022; 94:13958-13967. [PMID: 36174068 DOI: 10.1021/acs.analchem.2c03172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Higher-energy collisional dissociation (HCD) of modified ribonucleosides generates characteristic and highly reproducible nucleoside-specific tandem mass spectra (MS/MS). Here, we demonstrate the capability of HCD spectra in combination with spectral matching for the semi-automated characterization of ribonucleosides. This process involved the generation of an HCD spectral library and the establishment of a mass spectral network for rapid detection with high sensitivity and specificity in a retention time-independent fashion. Systematic spectral matching analysis of the MS/MS spectra of tRNA hydrolysates from different organisms has helped us to uncover evidence for the existence of novel ribonucleoside modifications such as s2Cm and OHyW-14. Such an untargeted label-free approach has the potential to be integrated with other methods, including those that use isotope labeling, to simplify the characterization of unknown modified ribonucleosides. These findings suggest the compilation of a universal spectral network, for the characterization of known and unknown ribonucleosides, could accelerate discoveries in the epitranscriptome.
Collapse
Affiliation(s)
- Manasses Jora
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Daniel Corcoran
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Gwenn G Parungao
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Peter A Lobue
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Luiz F L Oliveira
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - George Stan
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Balasubrahmanyam Addepalli
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| |
Collapse
|
9
|
Gosset-Erard C, Lechner A, Wolff P, Aubriet F, Leize-Wagner E, Chaimbault P, François YN. Optimization of nucleotides dephosphorylation for RNA structural characterization by tandem mass spectrometry hyphenated with separation methods. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1208:123396. [PMID: 35917777 DOI: 10.1016/j.jchromb.2022.123396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 12/12/2022]
Abstract
As part of RNA characterization, the identification of post-transcriptional modifications can be performed using hyphenation of separation methods with mass spectrometry. To identify RNA modifications with those methods, a first total digestion followed by a dephosphorylation step are usually required to reduce RNA to nucleosides. Even though effective digestion and dephosphorylation are essential to avoid further complications in analysis and data interpretation, to our knowledge, no standard protocol is yet referenced in the literature. Therefore, the aim of this work is to optimize the dephosphorylation step using a total extract of transfer RNA (tRNA)1 from B. taurus as a model and to determine and fix two protocols, leading to complete dephosphorylation, based on time and bacterial alkaline phosphatase (BAP)2 consumptions. Capillary electrophoresis-tandem mass spectrometry (CE-MS/MS) was used to estimate the dephosphorylation efficiency of both protocols on many canonical and modified nucleotides. For a timesaving protocol, we established that full dephosphorylation was obtained after a 4-hour incubation at 37 °C with 7.5 U of BAP for 1 µg of tRNA. And for a BAP-saving protocol, we established that full dephosphorylation was obtained 3.0 U of BAP after an overnight incubation at 37 °C. Both protocols are suitable for quantitative analyses as no loss of analytes is expected. Moreover, they can be widely used for all other RNA classes, including messenger RNA or ribosomal RNA.
Collapse
Affiliation(s)
- Clarisse Gosset-Erard
- Université de Lorraine, LCP-A2MC, F-57000 Metz, France; Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France.
| | - Antony Lechner
- Architecture et Réactivité de l'ARN (ARN) UPR 9002, CNRS, Université de Strasbourg, Strasbourg, France; Plateforme Protéomique Strasbourg Esplanade FRC 1589, CNRS, Strasbourg, France.
| | - Philippe Wolff
- Architecture et Réactivité de l'ARN (ARN) UPR 9002, CNRS, Université de Strasbourg, Strasbourg, France; Plateforme Protéomique Strasbourg Esplanade FRC 1589, CNRS, Strasbourg, France.
| | | | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France.
| | | | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France.
| |
Collapse
|
10
|
Janssen KA, Xie Y, Kramer MC, Gregory BD, Garcia BA. Data-Independent Acquisition for the Detection of Mononucleoside RNA Modifications by Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:885-893. [PMID: 35357823 PMCID: PMC9425428 DOI: 10.1021/jasms.2c00065] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
RNA is dynamically modified in cells by a plethora of chemical moieties to modulate molecular functions and processes. Over 140 modifications have been identified across species and RNA types, with the highest density and diversity of modifications found in tRNA (tRNA). The methods used to identify and quantify these modifications have developed over recent years and continue to advance, primarily in the fields of next-generation sequencing (NGS) and mass spectrometry (MS). Most current NGS methods are limited to antibody-recognized or chemically derivatized modifications and have limitations in identifying multiple modifications simultaneously. Mass spectrometry can overcome both of these issues, accurately identifying a large number of modifications in a single run. Here, we present advances in MS data acquisition for the purpose of RNA modification identification and quantitation. Using this approach, we identified multiple tRNA wobble position modifications in Arabidopsis thaliana that are upregulated in salt-stressed growth conditions and may stabilize translation of salt stress induced proteins. This work presents improvements in methods for studying RNA modifications and introduces a possible regulatory role of wobble position modifications in A. thaliana translation.
Collapse
Affiliation(s)
- Kevin A. Janssen
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Corresponding Author: Correspondence to: Benjamin A. Garcia;
| |
Collapse
|
11
|
Lin W, Huang Z, Ping S, Zhang S, Wen X, He Y, Ren Y. Toxicological effects of atenolol and venlafaxine on zebrafish tissues: Bioaccumulation, DNA hypomethylation, and molecular mechanism. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 299:118898. [PMID: 35081461 DOI: 10.1016/j.envpol.2022.118898] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 01/02/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
The beta-blocker atenolol (ATE), and the selective serotonin and norepinephrine reuptake inhibitor, venlafaxine (VEN) are frequently detected in municipal wastewater effluents, but little is known about their ecotoxicological effect on aquatic animals. Herein, ATE and VEN were selected to explore their accumulation and global DNA methylation (GDM) in zebrafish tissues after a 30-day exposure. Molecular dynamics (MD) stimulation was used to investigate the toxic mechanism of ATE and VEN exposure. The results demonstrated that ATE and VEN could reduce the condition factor of zebrafish. The bioaccumulation capacity for ATE and VEN was in the order of liver > gut > gill > brain and liver > gut > brain > gill, respectively. After a 30-day recovery, ATE and VEN could still be detected in zebrafish tissues when exposure concentrations were ≥10 μg/L. Moreover, ATE and VEN induced global DNA hypomethylation in different tissues with a dose-dependent manner and their main target tissues were liver and brain. When the exposure concentrations of ATE and VEN were increased to 100 μg/L, the global DNA hypomethylation of liver and brain were reduced to 27% and 18%, respectively. In the same tissue exposed to the same concentration, DNA hypomethylation induced by VEN was more serious than that of ATE. After a 30-day recovery, the global DNA hypomethylations caused by the two drugs were still persistent, and the recovery of VEN was slower than that of ATE. The MD simulation results showed that both ATE and VEN could reduce the catalytic activity of DNA Methyltransferase 1 (DNMT1), while the effect of VEN on the 3D conformational changes of the DNMT1 domain was more significant, resulting in a lower DNA methylation rate. The current study shed new light on the toxic mechanism and potential adverse impacts of ATE and VEN on zebrafish, providing essential information to the further ecotoxicological risk assessment of these drugs in the aquatic environment.
Collapse
Affiliation(s)
- Wenting Lin
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Zhishan Huang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Senwen Ping
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Shuan Zhang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Xiufang Wen
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Yuhe He
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Yuan Ren
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China; The Key Laboratory of Environmental Protection and Eco-Remediation of Guangdong Regular Higher Education Institutions, China.
| |
Collapse
|
12
|
D’Esposito RJ, Myers CA, Chen AA, Vangaveti S. Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches. Genes (Basel) 2022; 13:540. [PMID: 35328093 PMCID: PMC8949676 DOI: 10.3390/genes13030540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/12/2023] Open
Abstract
RNA is critical to a broad spectrum of biological and viral processes. This functional diversity is a result of their dynamic nature; the variety of three-dimensional structures that they can fold into; and a host of post-transcriptional chemical modifications. While there are many experimental techniques to study the structural dynamics of biomolecules, molecular dynamics simulations (MDS) play a significant role in complementing experimental data and providing mechanistic insights. The accuracy of the results obtained from MDS is determined by the underlying physical models i.e., the force-fields, that steer the simulations. Though RNA force-fields have received a lot of attention in the last decade, they still lag compared to their protein counterparts. The chemical diversity imparted by the RNA modifications adds another layer of complexity to an already challenging problem. Insight into the effect of RNA modifications upon RNA folding and dynamics is lacking due to the insufficiency or absence of relevant experimental data. This review provides an overview of the state of MDS of modified RNA, focusing on the challenges in parameterization of RNA modifications as well as insights into relevant reference experiments necessary for their calibration.
Collapse
Affiliation(s)
- Rebecca J. D’Esposito
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (R.J.D.); (A.A.C.)
| | - Christopher A. Myers
- Department of Physics, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA;
| | - Alan A. Chen
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (R.J.D.); (A.A.C.)
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| |
Collapse
|
13
|
Frankowska K, Sochacka E. New efficient synthesis of tRNA related adenosines bearing the hydantoin ring (ct6A, ms2ct6A) by intramolecular cyclization of N6-(N-Boc-α-aminoacyl)-adenosine derivatives. Chembiochem 2022; 23:e202100655. [PMID: 34997683 DOI: 10.1002/cbic.202100655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/07/2022] [Indexed: 11/10/2022]
Abstract
A novel and efficient way for synthesis of N6-hydantoin modified adenosines, which utilizes readily available N6-(N-Boc-α-aminoacyl)-adenosine derivatives, was developed. The procedure is based on the epimerization free Tf2O-mediated conversion of the Boc group into an isocyanate moiety, followed by intramolecular cyclization. Using this method two recently discovered hydantoin modified tRNA adenosines, i.e. cyclic N6-threonylcarbamoyl-adenosine (ct6A) and 2-methylthio-N6-threonylcarbamoyladenosine (ms2ct6A) were prepared in good yields.
Collapse
Affiliation(s)
- Katarzyna Frankowska
- Lodz University of Technology: Politechnika Lodzka, Faculty of Chemistry, POLAND
| | - Elzbieta Sochacka
- Lodz University of Technology, Faculty of Chemistry, ul. Żeromskiego 116, 90-924, Łódź, POLAND
| |
Collapse
|
14
|
Clark KD, Rubakhin SS, Sweedler JV. Single-Neuron RNA Modification Analysis by Mass Spectrometry: Characterizing RNA Modification Patterns and Dynamics with Single-Cell Resolution. Anal Chem 2021; 93:14537-14544. [PMID: 34672536 PMCID: PMC8608286 DOI: 10.1021/acs.analchem.1c03507] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The entire collection of post-transcriptional modifications to RNA, known as the epitranscriptome, has been increasingly recognized as a critical regulatory layer in the cellular translation machinery. However, contemporary methods for the analysis of RNA modifications are limited to the detection of highly abundant modifications in bulk tissue samples, potentially obscuring unique epitranscriptomes of individual cells with population averages. We developed an approach, single-neuron RNA modification analysis by mass spectrometry (SNRMA-MS), that enables the detection and quantification of numerous post-transcriptionally modified nucleosides in single cells. When compared to a conventional RNA extraction approach that does not allow detection of RNA modifications in single cells, SNRMA-MS leverages an optimized sample preparation approach to detect up to 16 RNA modifications in individual neurons from the central nervous system of Aplysia californica. SNRMA-MS revealed that the RNA modification profiles of identified A. californica neurons with different physiological functions were mostly cell specific. However, functionally homologous neurons tended to demonstrate similar modification patterns. Stable isotope labeling with CD3-Met showed significant differences in RNA methylation rates that were dependent on the identity of the modification and the cell, with metacerebral cells (MCCs) displaying the fastest incorporation of CD3 groups into endogenous RNAs. Quantitative SNRMA-MS showed higher intracellular concentrations for 2'-O-methyladenosine and 2'-O-methylcytidine in homologous R2/LPl1 cell pairs than in MCCs. Overall, SNRMA-MS is the first analytical approach capable of simultaneously quantifying numerous RNA modifications in single neurons and revealing cell-specific modification profiles.
Collapse
Affiliation(s)
- Kevin D. Clark
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stanislav S. Rubakhin
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
15
|
Thomas NK, Poodari VC, Jain M, Olsen HE, Akeson M, Abu-Shumays RL. Direct Nanopore Sequencing of Individual Full Length tRNA Strands. ACS NANO 2021; 15:16642-16653. [PMID: 34618430 PMCID: PMC10189790 DOI: 10.1021/acsnano.1c06488] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We describe a method for direct tRNA sequencing using the Oxford Nanopore MinION. The principal technical advance is custom adapters that facilitate end-to-end sequencing of individual transfer RNA (tRNA) molecules at subnanometer precision. A second advance is a nanopore sequencing pipeline optimized for tRNA. We tested this method using purified E. coli tRNAfMet, tRNALys, and tRNAPhe samples. 76-92% of individual aligned tRNA sequence reads were full length. As a proof of concept, we showed that nanopore sequencing detected all 43 expected isoacceptors in total E. coli MRE600 tRNA as well as isodecoders that further define that tRNA population. Alignment-based comparisons between the three purified tRNAs and their synthetic controls revealed systematic nucleotide miscalls that were diagnostic of known modifications. Systematic miscalls were also observed proximal to known modifications in total E. coli tRNA alignments, including a highly conserved pseudouridine in the T loop. This work highlights the potential of nanopore direct tRNA sequencing as well as improvements needed to implement tRNA sequencing for human healthcare applications.
Collapse
|
16
|
Thomas NK, Poodari VC, Jain M, Olsen HE, Akeson M, Abu-Shumays RL. Direct Nanopore Sequencing of Individual Full Length tRNA Strands. ACS NANO 2021; 15:16642-16653. [PMID: 34618430 DOI: 10.1101/2021.1104.1126.441285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We describe a method for direct tRNA sequencing using the Oxford Nanopore MinION. The principal technical advance is custom adapters that facilitate end-to-end sequencing of individual transfer RNA (tRNA) molecules at subnanometer precision. A second advance is a nanopore sequencing pipeline optimized for tRNA. We tested this method using purified E. coli tRNAfMet, tRNALys, and tRNAPhe samples. 76-92% of individual aligned tRNA sequence reads were full length. As a proof of concept, we showed that nanopore sequencing detected all 43 expected isoacceptors in total E. coli MRE600 tRNA as well as isodecoders that further define that tRNA population. Alignment-based comparisons between the three purified tRNAs and their synthetic controls revealed systematic nucleotide miscalls that were diagnostic of known modifications. Systematic miscalls were also observed proximal to known modifications in total E. coli tRNA alignments, including a highly conserved pseudouridine in the T loop. This work highlights the potential of nanopore direct tRNA sequencing as well as improvements needed to implement tRNA sequencing for human healthcare applications.
Collapse
Affiliation(s)
- Niki K Thomas
- Biomolecular Engineering Department, Genomics Institute, and Center for Molecular Biology of RNA University of California, Santa Cruz, California 95064, United States
| | - Vinay C Poodari
- Biomolecular Engineering Department, Genomics Institute, and Center for Molecular Biology of RNA University of California, Santa Cruz, California 95064, United States
| | - Miten Jain
- Biomolecular Engineering Department, Genomics Institute, and Center for Molecular Biology of RNA University of California, Santa Cruz, California 95064, United States
| | - Hugh E Olsen
- Biomolecular Engineering Department, Genomics Institute, and Center for Molecular Biology of RNA University of California, Santa Cruz, California 95064, United States
| | - Mark Akeson
- Biomolecular Engineering Department, Genomics Institute, and Center for Molecular Biology of RNA University of California, Santa Cruz, California 95064, United States
| | - Robin L Abu-Shumays
- Biomolecular Engineering Department, Genomics Institute, and Center for Molecular Biology of RNA University of California, Santa Cruz, California 95064, United States
| |
Collapse
|
17
|
Kaiser S, Byrne SR, Ammann G, Asadi Atoi P, Borland K, Brecheisen R, DeMott MS, Gehrke T, Hagelskamp F, Heiss M, Yoluç Y, Liu L, Zhang Q, Dedon PC, Cao B, Kellner S. Strategien zur Vermeidung von Artefakten in der massenspektrometrischen Epitranskriptomanalytik. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Steffen Kaiser
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
- Institut für Pharmazeutische Chemie Goethe-Universität Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Deutschland
| | - Shane R. Byrne
- Department of Biological Engineering and Center for Environmental Health Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Gregor Ammann
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Paria Asadi Atoi
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Kayla Borland
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | | | - Michael S. DeMott
- Department of Biological Engineering and Center for Environmental Health Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Tim Gehrke
- Ella Biotech GmbH 82152 München Deutschland
| | - Felix Hagelskamp
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Matthias Heiss
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Yasemin Yoluç
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Lili Liu
- College of Life Sciences Qufu Normal University Qufu Shandong 273165 China
| | - Qinghua Zhang
- College of Life Sciences Qufu Normal University Qufu Shandong 273165 China
| | - Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA
- Antimicrobial Resistance Interdisciplinary Research Group Singapore-Massachusetts Institute of Technology Alliance for Research and Technology 138602 Singapore Singapur
| | - Bo Cao
- College of Life Sciences Qufu Normal University Qufu Shandong 273165 China
| | - Stefanie Kellner
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
- Institut für Pharmazeutische Chemie Goethe-Universität Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Deutschland
| |
Collapse
|
18
|
Kaiser S, Byrne SR, Ammann G, Asadi Atoi P, Borland K, Brecheisen R, DeMott MS, Gehrke T, Hagelskamp F, Heiss M, Yoluç Y, Liu L, Zhang Q, Dedon PC, Cao B, Kellner S. Strategies to Avoid Artifacts in Mass Spectrometry-Based Epitranscriptome Analyses. Angew Chem Int Ed Engl 2021; 60:23885-23893. [PMID: 34339593 PMCID: PMC8597057 DOI: 10.1002/anie.202106215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Indexed: 11/05/2022]
Abstract
In this report, we perform structure validation of recently reported RNA phosphorothioate (PT) modifications, a new set of epitranscriptome marks found in bacteria and eukaryotes including humans. By comparing synthetic PT-containing diribonucleotides with native species in RNA hydrolysates by high-resolution mass spectrometry (MS), metabolic stable isotope labeling, and PT-specific iodine-desulfurization, we disprove the existence of PTs in RNA from E. coli, S. cerevisiae, human cell lines, and mouse brain. Furthermore, we discuss how an MS artifact led to the initial misidentification of 2'-O-methylated diribonucleotides as RNA phosphorothioates. To aid structure validation of new nucleic acid modifications, we present a detailed guideline for MS analysis of RNA hydrolysates, emphasizing how the chosen RNA hydrolysis protocol can be a decisive factor in discovering and quantifying RNA modifications in biological samples.
Collapse
Affiliation(s)
- Steffen Kaiser
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
- Institute of Pharmaceutical ChemistryGoethe-University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Shane R. Byrne
- Department of Biological Engineering and Center for Environmental Health SciencesMassachusetts Institute of TechnologyCambridgeMA02139USA
| | - Gregor Ammann
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Paria Asadi Atoi
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Kayla Borland
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | | | - Michael S. DeMott
- Department of Biological Engineering and Center for Environmental Health SciencesMassachusetts Institute of TechnologyCambridgeMA02139USA
| | | | - Felix Hagelskamp
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Matthias Heiss
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Yasemin Yoluç
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Lili Liu
- College of Life SciencesQufu Normal UniversityQufuShandong273165China
| | - Qinghua Zhang
- College of Life SciencesQufu Normal UniversityQufuShandong273165China
| | - Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health SciencesMassachusetts Institute of TechnologyCambridgeMA02139USA
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore-Massachusetts Institute of Technology Alliance for Research and Technology138602SingaporeSingapore
| | - Bo Cao
- College of Life SciencesQufu Normal UniversityQufuShandong273165China
| | - Stefanie Kellner
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
- Institute of Pharmaceutical ChemistryGoethe-University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| |
Collapse
|
19
|
Guo J, Zhu P, Ye Z, Wang M, Yang H, Huang S, Shu Y, Zhang W, Zhou H, Li Q. YRDC Mediates the Resistance of Lenvatinib in Hepatocarcinoma Cells via Modulating the Translation of KRAS. Front Pharmacol 2021; 12:744578. [PMID: 34658879 PMCID: PMC8517968 DOI: 10.3389/fphar.2021.744578] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Lenvatinib is the latest and promising agent that has demonstrated a significant improvement of progression-free survival in advanced hepatocellular carcinoma (HCC). However, resistance emerges soon after initial treatment, limiting the clinical benefits of lenvatinib. Therefore, understanding the mechanism of resistance is necessary for improving lenvatinib efficacy. YRDC promotes the proliferation of hepatocarcinoma cells via regulating the activity of the RAS/RAF/MEK/ERK pathway, which was the primary pathway of the anticancer effect of lenvatinib. The purpose of this study is to investigate whether YRDC modulates the sensitivity of lenvatinib in hepatocarcinoma cells. Using the CCK-8 cell viability assay, wound-healing assay and clone formation assay in cell models, and xenograft assay in null mouse, we demonstrated that Huh7 cells with YRDC knockdown showed decreased susceptibility to lenvatinib than their control cells. Furthermore, we found that lenvatinib inhibited the expression of YRDC in a time-dependent manner. This effect may aggravate resistance to lenvatinib in hepatocarcinoma cells and may be an underlying cause of resistance, which emerges soon after lenvatinib initial treatment. To investigate how YRDC modulates the sensitivity of lenvatinib, we assessed the effect of tRNA with different t6A levels on the translation of the KRAS gene by in vitro rabbit reticulocyte translation system and measured the expression levels of the KRAS gene by western blot together with qPCR. We found that YRDC regulates the protein translation of KRAS in cell models, and the tRNA with low t6A modification level reduces the translation of the KRAS in the in vitro translation system. These results suggested that YRDC mediates the resistance of lenvatinib in hepatocarcinoma cells via modulating the translation of the KRAS. In this study, YRDC was confirmed to be a potential novel predictive biomarker of lenvatinib sensitivity in HCC.
Collapse
Affiliation(s)
- Jun Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Peng Zhu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Zhi Ye
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Mengke Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Haijun Yang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Shiqiong Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Yan Shu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China.,Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland at Baltimore, Baltimore, MD, United States
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Qing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| |
Collapse
|
20
|
Hagelskamp F, Kellner S. Analysis of the epitranscriptome with ion-pairing reagent free oligonucleotide mass spectrometry. Methods Enzymol 2021; 658:111-135. [PMID: 34517944 DOI: 10.1016/bs.mie.2021.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA modifications gain growing attention as a new frontier in the life sciences but with the rise of RNA vaccines also in biomedical drug development. Impeccable characterization of RNA modifications within their sequence context remains an analytical challenge. Oligonucleotide mass spectrometry (ON-MS), an approach similar to bottom-up proteome analysis, is capable of defining a short 5-15 nucleotide sequence context of an RNA modification while delivering information on the chemical character of the modified nucleotide. Commonly, ON-MS requires the use of ion pairing reagents for ON separation which is not compatible with most other MS-based applications and only few laboratories run dedicated MS instruments for the task. Here, we present an ON-MS technique which is independent of ion pairing reagents and can be used on any available mass spectrometer without risking its sensitivity for other analytes. In this chapter, we describe the experiments necessary for ON-MS method development, ON-MS application to native and synthetic RNAs and finally a guideline for data analysis.
Collapse
Affiliation(s)
- Felix Hagelskamp
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Frankfurt, Germany
| | - Stefanie Kellner
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Frankfurt, Germany.
| |
Collapse
|
21
|
Pezo V, Jaziri F, Bourguignon PY, Louis D, Jacobs-Sera D, Rozenski J, Pochet S, Herdewijn P, Hatfull GF, Kaminski PA, Marliere P. Noncanonical DNA polymerization by aminoadenine-based siphoviruses. Science 2021; 372:520-524. [PMID: 33926956 DOI: 10.1126/science.abe6542] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/25/2021] [Indexed: 01/05/2023]
Abstract
Bacteriophage genomes harbor the broadest chemical diversity of nucleobases across all life forms. Certain DNA viruses that infect hosts as diverse as cyanobacteria, proteobacteria, and actinobacteria exhibit wholesale substitution of aminoadenine for adenine, thereby forming three hydrogen bonds with thymine and violating Watson-Crick pairing rules. Aminoadenine-encoded DNA polymerases, homologous to the Klenow fragment of bacterial DNA polymerase I that includes 3'-exonuclease but lacks 5'-exonuclease, were found to preferentially select for aminoadenine instead of adenine in deoxynucleoside triphosphate incorporation templated by thymine. Polymerase genes occur in synteny with genes for a biosynthesis enzyme that produces aminoadenine deoxynucleotides in a wide array of Siphoviridae bacteriophages. Congruent phylogenetic clustering of the polymerases and biosynthesis enzymes suggests that aminoadenine has propagated in DNA alongside adenine since archaic stages of evolution.
Collapse
Affiliation(s)
- Valerie Pezo
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France
| | - Faten Jaziri
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France
| | - Pierre-Yves Bourguignon
- Werkstatt fuer Potenzielle Genetik, Naunynstrasse 30, 10997 Berlin, Germany.,TESSSI, 81 Rue Réaumur, 75002 Paris, France
| | | | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260 USA
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Sylvie Pochet
- Organic Chemistry, CNRS UMR3523, Department of Chemistry and Biocatalysis, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260 USA
| | - Pierre-Alexandre Kaminski
- Biology of Gram-Positive Pathogens, CNRS URL3526, Department of Microbiology, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Philippe Marliere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France. .,TESSSI, 81 Rue Réaumur, 75002 Paris, France
| |
Collapse
|
22
|
Waldern JM, Smith D, Piazza CL, Bailey EJ, Schiraldi NJ, Nemati R, Fabris D, Belfort M, Novikova O. Methylation of rRNA as a host defense against rampant group II intron retrotransposition. Mob DNA 2021; 12:9. [PMID: 33678171 PMCID: PMC7938551 DOI: 10.1186/s13100-021-00237-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/22/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Group II introns are mobile retroelements, capable of invading new sites in DNA. They are self-splicing ribozymes that complex with an intron-encoded protein to form a ribonucleoprotein that targets DNA after splicing. These molecules can invade DNA site-specifically, through a process known as retrohoming, or can invade ectopic sites through retrotransposition. Retrotransposition, in particular, can be strongly influenced by both environmental and cellular factors. RESULTS To investigate host factors that influence retrotransposition, we performed random insertional mutagenesis using the ISS1 transposon to generate a library of over 1000 mutants in Lactococcus lactis, the native host of the Ll.LtrB group II intron. By screening this library, we identified 92 mutants with increased retrotransposition frequencies (RTP-ups). We found that mutations in amino acid transport and metabolism tended to have increased retrotransposition frequencies. We further explored a subset of these RTP-up mutants, the most striking of which is a mutant in the ribosomal RNA methyltransferase rlmH, which exhibited a reproducible 20-fold increase in retrotransposition frequency. In vitro and in vivo experiments revealed that ribosomes in the rlmH mutant were defective in the m3Ψ modification and exhibited reduced binding to the intron RNA. CONCLUSIONS Taken together, our results reinforce the importance of the native host organism in regulating group II intron retrotransposition. In particular, the evidence from the rlmH mutant suggests a role for ribosome modification in limiting rampant retrotransposition.
Collapse
Affiliation(s)
- Justin M. Waldern
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Current address: Department of Biology, University of North Carolina, 270 Bell Tower Drive, Chapel Hill, NC 27599 USA
| | - Dorie Smith
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Carol Lyn Piazza
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - E. Jake Bailey
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Nicholas J. Schiraldi
- Academic and Research Computing Center, Information Technology Services, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Reza Nemati
- Department of Chemistry, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Current address: Biogen, 125 Broadway, Cambridge, MA 02142 USA
| | - Dan Fabris
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Department of Chemistry, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Current address: Department of Chemistry, University of Connecticut, 55 N. Eagleville Road, Storrs, CT 06268 USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Current address: Biology Department, SUNY Buffalo State College, 1300 Elmwood Avenue, Buffalo, NY 14222 USA
| |
Collapse
|
23
|
Yoluç Y, Ammann G, Barraud P, Jora M, Limbach PA, Motorin Y, Marchand V, Tisné C, Borland K, Kellner S. Instrumental analysis of RNA modifications. Crit Rev Biochem Mol Biol 2021; 56:178-204. [PMID: 33618598 DOI: 10.1080/10409238.2021.1887807] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Organisms from all domains of life invest a substantial amount of energy for the introduction of RNA modifications into nearly all transcripts studied to date. Instrumental analysis of RNA can focus on the modified residues and reveal the function of these epitranscriptomic marks. Here, we will review recent advances and breakthroughs achieved by NMR spectroscopy, sequencing, and mass spectrometry of the epitranscriptome.
Collapse
Affiliation(s)
- Yasemin Yoluç
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Gregor Ammann
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Pierre Barraud
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Manasses Jora
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA Sequencing Core facility, UM S2008, IBSLor, Nancy, France
| | - Carine Tisné
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Kayla Borland
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany.,Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, Germany
| |
Collapse
|
24
|
Jora M, Borland K, Abernathy S, Zhao R, Kelley M, Kellner S, Addepalli B, Limbach PA. Chemical Amination/Imination of Carbonothiolated Nucleosides During RNA Hydrolysis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Manasses Jora
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Kayla Borland
- Department of Chemistry Ludwig Maximilians University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Scott Abernathy
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Melissa Kelley
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Stefanie Kellner
- Department of Chemistry Ludwig Maximilians University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| |
Collapse
|
25
|
Wahba AE, Fedele D, Gebril H, AlHarfoush E, Toti KS, Jacobson KA, Boison D. Adenosine Kinase Expression Determines DNA Methylation in Cancer Cell Lines. ACS Pharmacol Transl Sci 2021; 4:680-686. [PMID: 33860193 DOI: 10.1021/acsptsci.1c00008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Indexed: 12/20/2022]
Abstract
DNA methylation has a major role in cancer, and its inhibitors are used therapeutically. DNA methylation depends on methyl group flux through the transmethylation pathway, which forms adenosine. We hypothesized that an adenosine kinase isoform with nuclear expression (ADK-L) determines global DNA methylation in cancer cells. We quantified ADK-L expression (Western Blot) and global DNA methylation as percent 5-methyldeoxycytidine (5mdC, LC-MS/MS) in three cancer lines (HeLa, HepG2, and U373). ADK-L expression and global DNA methylation correlated positively with the highest levels in HeLa cells compared to U373 and HepG2 cells. To determine whether ADK increases global DNA methylation and to validate its potential therapeutics, we treated HeLa cells with potent ADK inhibitors MRS4203 and MRS4380 (IC50 88 and 140 nM, respectively). Both nucleosides, but not a structurally related poor ADK inhibitor, significantly reduced global DNA methylation in HeLa cells in a concentration-dependent manner. Thus, ADK-L is a potential target for the therapeutic manipulation of DNA methylation levels in cancer.
Collapse
Affiliation(s)
- Amir E Wahba
- Department of Neurosurgery, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Denise Fedele
- Department of Neurosurgery, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Hoda Gebril
- Department of Neurosurgery, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Enmar AlHarfoush
- Department of Neurosurgery, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Kiran S Toti
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 8A, Room B1A-19, Bethesda, Maryland 20892-0810, United States
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 8A, Room B1A-19, Bethesda, Maryland 20892-0810, United States
| | - Detlev Boison
- Department of Neurosurgery, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, United States.,Rutgers Neurosurgery H.O.P.E. Center, Department of Neurosurgery, Rutgers University, New Brunswick, New Jersey 08901, United States
| |
Collapse
|
26
|
Kogaki T, Ohshio I, Ura H, Iyama S, Kitae K, Morie T, Fujii S, Sato S, Nagata T, Takeda AH, Aoki M, Ueda K, Minami K, Yamamoto M, Kawahara K, Furukawa T, Sato M, Ueda Y, Jingushi K, Tozuka Z, Saigusa D, Hase H, Tsujikawa K. Development of a highly sensitive method for the quantitative analysis of modified nucleosides using UHPLC-UniSpray-MS/MS. J Pharm Biomed Anal 2021; 197:113943. [PMID: 33601155 DOI: 10.1016/j.jpba.2021.113943] [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] [Received: 09/13/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 01/27/2023]
Abstract
There are more than 150 types of naturally occurring modified nucleosides, which are believed to be involved in various biological processes. Recently, an ultrahigh performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UHPLC-ESI-MS/MS) technique has been developed to measure low levels of modified nucleosides. A comprehensive analysis of modified nucleosides will lead to a better understanding of intracellular ribonucleic acid modification, but this analysis requires high-sensitivity measurements. In this perspective, we established a highly sensitive and quantitative method using the newly developed ion source, UniSpray. A mass spectrometer was used with a UniSpray source in positive ion mode. Our UHPLC-UniSpray-MS/MS methodology separated and detected the four major nucleosides, 42 modified nucleosides, and dG15N5 (internal standard) in 15 min. The UniSpray method provided good correlation coefficients (>0.99) for all analyzed nucleosides, and a wide range of linearity for 35 of the 46 nucleosides. Additionally, the accuracy and precision values satisfied the criteria of <15% for higher concentrations and <20% for the lowest concentrations of all nucleosides. We also investigated whether this method could measure nucleosides in biological samples using mouse tissues and non-small cell lung cancer clinical specimens. We were able to detect 43 and 31 different modified nucleosides from mouse and clinical tissues, respectively. We also found significant differences in the levels of N6-methyl-N6-threonylcarbamoyladenosine (m6t6A), 1-methylinosine (m1I), 2'-O-methylcytidine (Cm), 5-carbamoylmethyluridine (ncm5U), 5-methoxycarbonylmethyl-2-thiouridine (mcm5S2U), and 5-methoxycarbonylmethyl-2'-O-methyluridine (mcm5Um) between cancerous and noncancerous tissues. In conclusion, we developed a highly sensitive methodology using UHPLC-UniSpray-MS/MS to simultaneously detect and quantify modified nucleosides, which can be used for analysis of biological samples.
Collapse
Affiliation(s)
- Takahiro Kogaki
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ikumi Ohshio
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hasumi Ura
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Souta Iyama
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kaori Kitae
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshiya Morie
- Center for Supporting Drug Discovery and Life Science Research Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shintarou Fujii
- Center for Supporting Drug Discovery and Life Science Research Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shohei Sato
- Center for Supporting Drug Discovery and Life Science Research Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshiyuki Nagata
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Aya Harada Takeda
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Masaya Aoki
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Kazuhiro Ueda
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Kentaro Minami
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8544, Japan
| | - Masatatsu Yamamoto
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8544, Japan
| | - Kohichi Kawahara
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8544, Japan
| | - Tatsuhiko Furukawa
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8544, Japan
| | - Masami Sato
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Yuko Ueda
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kentaro Jingushi
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Zenzaburo Tozuka
- Center for Supporting Drug Discovery and Life Science Research Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 1-2 Seiryocho, Aobaku, Sendai, Miyagi 980-8573, Japan
| | - Hiroaki Hase
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Kazutake Tsujikawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
27
|
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used technique in the global analysis of epigenetic DNA modifications. The high-resolution chromatographic separation along with sensitive MS detection permits the identification and quantification of deoxyribonucleosides with precision and reliability. Although there have been tremendous advances in LC and MS instrumentation in recent years, sample preparation has not experienced a similar rate of development and is often a bottleneck to chemical analysis. Here we present a protocol for identification and quantification of cytosine modifications that combines a robust and efficient method to generate single nucleosides from genomic DNA samples followed by direct LC-MS/MS analysis.
Collapse
|
28
|
Jora M, Borland K, Abernathy S, Zhao R, Kelley M, Kellner S, Addepalli B, Limbach PA. Chemical Amination/Imination of Carbonothiolated Nucleosides During RNA Hydrolysis. Angew Chem Int Ed Engl 2020; 60:3961-3966. [DOI: 10.1002/anie.202010793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/17/2020] [Indexed: 01/10/2023]
Affiliation(s)
- Manasses Jora
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Kayla Borland
- Department of Chemistry Ludwig Maximilians University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Scott Abernathy
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Melissa Kelley
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Stefanie Kellner
- Department of Chemistry Ludwig Maximilians University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| |
Collapse
|
29
|
Funk HM, Zhao R, Thomas M, Spigelmyer SM, Sebree NJ, Bales RO, Burchett JB, Mamaril JB, Limbach PA, Guy MP. Identification of the enzymes responsible for m2,2G and acp3U formation on cytosolic tRNA from insects and plants. PLoS One 2020; 15:e0242737. [PMID: 33253256 PMCID: PMC7704012 DOI: 10.1371/journal.pone.0242737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/06/2020] [Indexed: 11/18/2022] Open
Abstract
Posttranscriptional modification of tRNA is critical for efficient protein translation and proper cell growth, and defects in tRNA modifications are often associated with human disease. Although most of the enzymes required for eukaryotic tRNA modifications are known, many of these enzymes have not been identified and characterized in several model multicellular eukaryotes. Here, we present two related approaches to identify the genes required for tRNA modifications in multicellular organisms using primer extension assays with fluorescent oligonucleotides. To demonstrate the utility of these approaches we first use expression of exogenous genes in yeast to experimentally identify two TRM1 orthologs capable of forming N2,N2-dimethylguanosine (m2,2G) on residue 26 of cytosolic tRNA in the model plant Arabidopsis thaliana. We also show that a predicted catalytic aspartate residue is required for function in each of the proteins. We next use RNA interference in cultured Drosophila melanogaster cells to identify the gene required for m2,2G26 formation on cytosolic tRNA. Additionally, using these approaches we experimentally identify D. melanogaster gene CG10050 as the corresponding ortholog of human DTWD2, which encodes the protein required for formation of 3-amino-3-propylcarboxyuridine (acp3U) on residue 20a of cytosolic tRNA. We further show that A. thaliana gene AT2G41750 can form acp3U20b on an A. thaliana tRNA expressed in yeast cells, and that the aspartate and tryptophan residues in the DXTW motif of this protein are required for modification activity. These results demonstrate that these approaches can be used to study tRNA modification enzymes.
Collapse
Affiliation(s)
- Holly M. Funk
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Maggie Thomas
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Sarah M. Spigelmyer
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Nichlas J. Sebree
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Regan O. Bales
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Jamison B. Burchett
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Justen B. Mamaril
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Michael P. Guy
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| |
Collapse
|
30
|
Lin CY, Lee HL, Hwang YT, Huang PC, Wang C, Sung FC, Wu C, Su TC. Urinary heavy metals, DNA methylation, and subclinical atherosclerosis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 204:111039. [PMID: 32738627 DOI: 10.1016/j.ecoenv.2020.111039] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/05/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
PURPOSE Lead (Pb) or cadmium (Cd) exposure has been linked to atherosclerosis. Co-exposure of these two heavy metals often occurs in humans. Recent evidence has indicated a crucial role of DNA methylation in atherosclerosis, while Pb or Cd exposure has also been shown to alter DNA methylation. However, it is still unknown whether DNA methylation plays a role in the pathological mechanism of these two heavy metals in atherosclerosis. APPROACH AND RESULTS We enrolled 738 participants (12-30 years) to investigate the association among concentrations of urine Pb or Cd, the 5mdC/dG value (a global DNA methylation marker) and the carotid intima-media thickness (CIMT). When each heavy metal was modeled separately, the results showed urine Pb and Cd concentrations were positively associated with the 5mdC/dG value and CIMT, respectively. When the two heavy metals were analyzed in the same model, urinary Pb concentrations were positively associated with the 5mdC/dG value and CIMT, while urinary Cd concentrations were only positively associated with the CIMT. When Pb and Cd are simultaneously considered in the same logistic regression model, the odds ratios (OR) of thicker CIMT (greater than 75th percentile) with one unit increase in ln-Pb level was 1.67 (95% C.I. = 1.17-2.46, P = 0.005) when levels of 5mdC/dG were above 50th percentile, which is higher than 5mdC/dG bellow the 50th percentile (OR = 1.50 (95% C.I. = 0.96-2.35), P = 0.076). In structural equation model (SEM), Pb or Cd levels are directly associated with CIMT. Moreover, Pb or Cd had an indirect association with CIMT through the 5mdC/dG. When we considered Pb and Cd together, Pb levels had a direct association with CIMT and an indirect association with CIMT through the 5mdC/dG value, while Cd only had a direct association with CIMT. CONCLUSIONS Our findings imply that Pb and Cd exposure might be associated with subclinical atherosclerosis, and global DNA methylation might mediate Pb-associated subclinical atherosclerosis in this young population. Future effort is necessary to elucidate the causal relationship.
Collapse
Affiliation(s)
- Chien-Yu Lin
- Department of Internal Medicine, En Chu Kong Hospital, New Taipei City, 237, Taiwan; School of Medicine, Fu Jen Catholic University, New Taipei City, 242, Taiwan; Department of Environmental Engineering and Health, Yuanpei University of Medical Technology, Hsinchu, 300, Taiwan.
| | - Hui-Ling Lee
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, 242, Taiwan
| | - Yi-Ting Hwang
- Department of Statistics, National Taipei University, New Taipei City, 237, Taiwan
| | - Po-Chin Huang
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli, 350, Taiwan; Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, 404, Taiwan
| | - Chikang Wang
- Department of Environmental Engineering and Health, Yuanpei University of Medical Technology, Hsinchu, 300, Taiwan
| | - Fung-Chang Sung
- Department of Health Services Administration, College of Public Health, China Medical University, Taichung, 404, Taiwan
| | - Charlene Wu
- Global Health Program, National Taiwan University, College of Public Health, 10055, Taiwan
| | - Ta-Chen Su
- Department of Environmental and Occupational Medicine, National Taiwan University Hospital, Taipei, 100, Taiwan; Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, 100, Taiwan; Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei, 100, Taiwan.
| |
Collapse
|
31
|
Fattorini P, Forzato C, Tierno D, De Martino E, Azzalini E, Canzonieri V, Stanta G, Bonin S. A Novel HPLC-Based Method to Investigate on RNA after Fixation. Int J Mol Sci 2020; 21:ijms21207540. [PMID: 33066070 PMCID: PMC7588918 DOI: 10.3390/ijms21207540] [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: 08/27/2020] [Revised: 09/24/2020] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
RNA isolated from fixed and paraffin-embedded tissues is widely used in biomedical research and molecular pathology for diagnosis. In the present study, we have set-up a method based on high performance liquid chromatography (HPLC) to investigate the effects of different fixatives on RNA. By the application of the presented method, which is based on the Nuclease S1 enzymatic digestion of RNA extracts followed by a HPLC analysis, it is possible to quantify the unmodified nucleotide monophosphates (NMPs) in the mixture and recognize their hydroxymethyl derivatives as well as other un-canonical RNA moieties. The results obtained from a set of mouse livers fixed/embedded with different protocols as well from a set of clinical samples aged 0 to 30 years-old show that alcohol-based fixatives do not induce chemical modification of the nucleic acid under ISO standard recommendations and confirm that pre-analytical conditions play a major role in RNA preservation.
Collapse
Affiliation(s)
- Paolo Fattorini
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Cristina Forzato
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy;
| | - Domenico Tierno
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
- Doctorate of Nanotechnology, University of Trieste, 34100 Trieste, Italy
| | - Eleonora De Martino
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Eros Azzalini
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Vincenzo Canzonieri
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Giorgio Stanta
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Serena Bonin
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
- Correspondence: ; Tel.: +39-040-399-3266
| |
Collapse
|
32
|
Lin CY, Lee HL, Hwang YT, Wang C, Hsieh CJ, Wu C, Sung FC, Su TC. The association between urine di-(2-ethylhexyl) phthalate metabolites, global DNA methylation, and subclinical atherosclerosis in a young Taiwanese population. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114912. [PMID: 32540595 DOI: 10.1016/j.envpol.2020.114912] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/04/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Di-(2-ethylhexyl) phthalate (DEHP) has been utilized in many products for years. DEHP exposure has been linked to cardiovascular diseases (CVD) and its risk factors. Recent evidence has found a crucial role for epigenetics, including DNA methylation, in CVD. Moreover, DEHP exposure has proved to alter DNA methylation in epidemiological studies. However, the interplay between DEHP exposure, global DNA methylation, and atherosclerosis has never been reported. In this current study, we enrolled 793 participants (12-30 years) from a Taiwanese population to investigate the association between concentrations of DEHP metabolites, 5mdC/dG (global DNA methylation marker) and the carotid intima-media thickness (CIMT). The results showed urine mono-2-ethylhexyl phthalate (MEHP) level was positively correlated with 5mdC/dG and CIMT, respectively. In logistic regression models, the odds ratios (OR) of thicker CIMT (greater than 75th percentile) with one unit increase in ln-MEHP level was higher when levels of 5mdC/dG were above 50%. In structural equation model, the result showed urine MEHP levels are directly associated with CIMT. Moreover, MEHP had an indirect association with CIMT through the 5mdC/dG after adjusting other confounding effects. In the current study, urine DEHP metabolite levels were positively correlated with 5mdC/dG, and CIMT. Our results showed DEHP had a direct and indirect association with CIMT through the 5mdC/dG. The finding implies that DNA methylation may mediate the association between DEHP exposures and subclinical atherosclerosis in this young population. Future effort is needed to elucidate the causal relationship between DEHP exposure, DNA methylation and CVD.
Collapse
Affiliation(s)
- Chien-Yu Lin
- Department of Internal Medicine, En Chu Kong Hospital, New Taipei City, 237, Taiwan; School of Medicine, Fu Jen Catholic University, New Taipei City, 242, Taiwan; Department of Environmental Engineering and Health, Yuanpei University of Medical Technology, Hsinchu, 300, Taiwan
| | - Hui-Ling Lee
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, 242, Taiwan
| | - Yi-Ting Hwang
- Department of Statistics, National Taipei University, New Taipei City, 237, Taiwan
| | - Chikang Wang
- Department of Environmental Engineering and Health, Yuanpei University of Medical Technology, Hsinchu, 300, Taiwan
| | - Chia-Jung Hsieh
- Department of Public Health, Tzu Chi University, Hualian County, 970, Taiwan
| | - Charlene Wu
- Global Health Program, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Fung-Chang Sung
- Department of Health Services Administration, College of Public Health, China Medical University, Taichung, 404, Taiwan
| | - Ta-Chen Su
- Department of Environmental and Occupational Medicine, National Taiwan University Hospital, Taipei, 100, Taiwan; Department of Internal Medicine and Cardiovascular Center, National Taiwan University Hospital, Taipei, 100, Taiwan; Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei, 100, Taiwan.
| |
Collapse
|
33
|
Clark KD, Philip MC, Tan Y, Sweedler JV. Biphasic Liquid Microjunction Extraction for Profiling Neuronal RNA Modifications by Liquid Chromatography-Tandem Mass Spectrometry. Anal Chem 2020; 92:12647-12655. [PMID: 32786436 PMCID: PMC7496823 DOI: 10.1021/acs.analchem.0c02830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
RNA modifications are emerging as critical players in the spatiotemporal regulation of gene expression. Although liquid chromatography-tandem mass spectrometry (LC-MS/MS) enables the simultaneous quantification of numerous enzymatically modified RNAs in a biological sample, conventional RNA extraction and enzymatic digestion protocols that are employed prior to analysis have precluded the application of this technique for small-volume samples. In this study, a biphasic liquid microjunction (LMJ) extraction system using coaxial capillaries that direct and aspirate extraction solvents onto a ∼350 μm diameter sample spot was developed and applied for the extraction of RNA from individual cell clusters in the central nervous system of the marine mollusk Aplysia californica. To maximize RNA recoveries, optimized extraction solvents consisting of 10% methanol and chloroform were evaluated under dynamic and static extraction conditions. An MS-compatible RNA digestion buffer was developed to minimize the number of sample-transfer steps and facilitate the direct enzymatic digestion of extracted RNA within the sample collection tube. Compared to RNA extraction using a conventional phenol-chloroform method, the LMJ-based method provided a 3-fold greater coverage of the neuronal epitranscriptome for similar amounts of tissues and also produced mRNA of sufficient purity for reverse transcription polymerase chain reaction amplification. Using this approach, the expression of RNA-modifying enzymes in a given neuronal cell cluster can be characterized and simultaneously correlated with the LC-MS/MS analysis of RNA modifications within the same subset of neurons.
Collapse
Affiliation(s)
- Kevin D. Clark
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Marina C. Philip
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yanqi Tan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
34
|
Lechner A, Wolff P, Leize-Wagner E, François YN. Characterization of Post-Transcriptional RNA Modifications by Sheathless Capillary Electrophoresis-High Resolution Mass Spectrometry. Anal Chem 2020; 92:7363-7370. [PMID: 32343557 DOI: 10.1021/acs.analchem.0c01345] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Over the past decade there has been a growing interest in RNA modification analysis. High performance liquid chromatography-tandem mass spectrometry coupling (HPLC-MS/MS) is classically used to characterize post-transcriptional modifications of ribonucleic acids (RNAs). Here we propose a novel and simple workflow based on capillary zone electrophoresis-tandem mass spectrometry (CE-MS/MS), in positive mode, to characterize RNA modifications at nucleoside and oligonucleotide levels. By first totally digesting the purified RNA, prior to CE-MS/MS analysis, we were able to identify the nucleoside modifications. Then, using a bottom-up approach, sequencing of the RNAs and mapping of the modifications were performed. Sequence coverages from 68% to 97% were obtained for four tRNAs. Furthermore, unambiguous identification and mapping of several modifications were achieved.
Collapse
Affiliation(s)
- Antony Lechner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg F-67081, France
| | - Philippe Wolff
- Architecture et Réactivité de l'ARN, UPR 9002-CNRS, Université de Strasbourg, F-67000 Strasbourg, France.,Plateforme Protéomique Strasbourg Esplanade, CNRS, FRC 1589, F-67000 Strasbourg, France
| | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg F-67081, France
| | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg F-67081, France
| |
Collapse
|
35
|
Boeckemeier L, Kraehenbuehl R, Keszthelyi A, Gasasira MU, Vernon EG, Beardmore R, Vågbø CB, Chaplin D, Gollins S, Krokan HE, Lambert SAE, Paizs B, Hartsuiker E. Mre11 exonuclease activity removes the chain-terminating nucleoside analog gemcitabine from the nascent strand during DNA replication. SCIENCE ADVANCES 2020; 6:eaaz4126. [PMID: 32523988 PMCID: PMC7259961 DOI: 10.1126/sciadv.aaz4126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
The Mre11 nuclease is involved in early responses to DNA damage, often mediated by its role in DNA end processing. MRE11 mutations and aberrant expression are associated with carcinogenesis and cancer treatment outcomes. While, in recent years, progress has been made in understanding the role of Mre11 nuclease activities in DNA double-strand break repair, their role during replication has remained elusive. The nucleoside analog gemcitabine, widely used in cancer therapy, acts as a replication chain terminator; for a cell to survive treatment, gemcitabine needs to be removed from replicating DNA. Activities responsible for this removal have, so far, not been identified. We show that Mre11 3' to 5' exonuclease activity removes gemcitabine from nascent DNA during replication. This contributes to replication progression and gemcitabine resistance. We thus uncovered a replication-supporting role for Mre11 exonuclease activity, which is distinct from its previously reported detrimental role in uncontrolled resection in recombination-deficient cells.
Collapse
Affiliation(s)
- L. Boeckemeier
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - R. Kraehenbuehl
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - A. Keszthelyi
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - M. U. Gasasira
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - E. G. Vernon
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - R. Beardmore
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - C. B. Vågbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - D. Chaplin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - S. Gollins
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - H. E. Krokan
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - S. A. E. Lambert
- Institut Curie, Paris-Saclay University, UMR3348, F-91450 Orsay, France
| | - B. Paizs
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - E. Hartsuiker
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| |
Collapse
|
36
|
Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation. Commun Biol 2020; 3:58. [PMID: 32029867 PMCID: PMC7005279 DOI: 10.1038/s42003-020-0780-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/17/2020] [Indexed: 01/09/2023] Open
Abstract
Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNAiMet. Here, we determine the cryo-EM structure of a 30S:mRNA:aIF1A:aIF2:GTP:Met-tRNAiMet complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N4-acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life.
Collapse
|
37
|
Kenderdine T, Nemati R, Baker A, Palmer M, Ujma J, FitzGibbon M, Deng L, Royzen M, Langridge J, Fabris D. High-resolution ion mobility spectrometry-mass spectrometry of isomeric/isobaric ribonucleotide variants. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4465. [PMID: 31697854 PMCID: PMC8363168 DOI: 10.1002/jms.4465] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/13/2019] [Accepted: 10/22/2019] [Indexed: 06/01/2023]
Abstract
In this report, we explored the benefits of cyclic ion mobility (cIM) mass spectrometry in the analysis of isomeric post-transcriptional modifications of RNA. Standard methyl-cytidine samples were initially utilized to test the ability to correctly distinguish different structures sharing the same elemental composition and thus molecular mass. Analyzed individually, the analytes displayed characteristic arrival times (tD ) determined by the different positions of the modifying methyl groups onto the common cytidine scaffold. Analyzed in mixture, the widths of the respective signals resulted in significant overlap that initially prevented their resolution on the tD scale. The separation of the four isomers was achieved by increasing the number of passes through the cIM device, which enabled to fully differentiate the characteristic ion mobility behaviors associated with very subtle structural variations. The placement of the cIM device between the mass-selective quadrupole and the time-of-flight analyzer allowed us to perform gas-phase activation of each of these ion populations, which had been first isolated according to a common mass-to-charge ratio and then separated on the basis of different ion mobility behaviors. The observed fragmentation patterns confirmed the structures of the various isomers thus substantiating the benefits of complementing unique tD information with specific fragmentation data to reach more stringent analyte identification. These capabilities were further tested by analyzing natural mono-nucleotide mixtures obtained by exonuclease digestion of total RNA extracts. In particular, the combination of cIM separation and post-mobility dissociation allowed us to establish the composition of methyl-cytidine and methyl-adenine components present in the entire transcriptome of HeLa cells. For this reason, we expect that this technique will benefit not only epitranscriptomic studies requiring the determination of identity and expression levels of RNA modifications, but also metabolomics investigations involving the analysis of natural extracts that may possibly contain subsets of isomeric/isobaric species.
Collapse
Affiliation(s)
| | | | - A. Baker
- Waters Corporation, Wilmslow SK9 4AX, UK
| | - M. Palmer
- Waters Corporation, Wilmslow SK9 4AX, UK
| | - J. Ujma
- Waters Corporation, Wilmslow SK9 4AX, UK
| | - M FitzGibbon
- University at Albany, Albany, NY 12222
- University of California San Diego, La Jolla, CA 92093
| | - L. Deng
- University at Albany, Albany, NY 12222
| | - M. Royzen
- University at Albany, Albany, NY 12222
| | | | - D. Fabris
- University at Albany, Albany, NY 12222
| |
Collapse
|
38
|
Debiec K, Matuszewski M, Podskoczyj K, Leszczynska G, Sochacka E. Chemical Synthesis of Oligoribonucleotide (ASL of tRNA Lys T. brucei) Containing a Recently Discovered Cyclic Form of 2-Methylthio-N 6 -threonylcarbamoyladenosine (ms 2 ct 6 A). Chemistry 2019; 25:13309-13317. [PMID: 31328310 DOI: 10.1002/chem.201902411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/16/2019] [Indexed: 01/25/2023]
Abstract
The synthesis of the protected form of 2-methylthio-N6 -threonylcarbamoyl adenosine (ms2 t6 A) was developed starting from adenosine or guanosine by using the optimized carbamate method and, for the first time, an isocyanate route. The hypermodified nucleoside was subsequently transformed into the protected ms2 t6 A-phosphoramidite monomer and used in a large-scale synthesis of the precursor 17nt ms2 t6 A-oligonucleotide (the anticodon stem and loop fragment of tRNALys from T. brucei). Finally, stereochemically secure ms2 t6 A→ms2 ct6 A cyclization at the oligonucleotide level efficiently afforded a tRNA fragment bearing the ms2 ct6 A unit. The applied post-synthetic approach provides two sequentially homologous ms2 t6 A- and ms2 ct6 A-oligonucleotides that are suitable for further comparative structure-activity relationship studies.
Collapse
Affiliation(s)
- Katarzyna Debiec
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Michal Matuszewski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Karolina Podskoczyj
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| |
Collapse
|
39
|
McIntyre W, Netzband R, Bonenfant G, Biegel JM, Miller C, Fuchs G, Henderson E, Arra M, Canki M, Fabris D, Pager CT. Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection. Nucleic Acids Res 2019; 46:5776-5791. [PMID: 29373715 PMCID: PMC6009648 DOI: 10.1093/nar/gky029] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/15/2018] [Indexed: 12/26/2022] Open
Abstract
More than 140 post-transcriptional modifications (PTMs) are known to decorate cellular RNAs, but their incidence, identity and significance in viral RNA are still largely unknown. We have developed an agnostic analytical approach to comprehensively survey PTMs on viral and cellular RNAs. Specifically, we used mass spectrometry to analyze PTMs on total RNA isolated from cells infected with Zika virus, Dengue virus, hepatitis C virus (HCV), poliovirus and human immunodeficiency virus type 1. All five RNA viruses significantly altered global PTM landscapes. Examination of PTM profiles of individual viral genomes isolated by affinity capture revealed a plethora of PTMs on viral RNAs, which far exceeds the handful of well-characterized modifications. Direct comparison of viral epitranscriptomes identified common and virus-specific PTMs. In particular, specific dimethylcytosine modifications were only present in total RNA from virus-infected cells, and in intracellular HCV RNA, and viral RNA from Zika and HCV virions. Moreover, dimethylcytosine abundance during viral infection was modulated by the cellular DEAD-box RNA helicase DDX6. By opening the Pandora's box on viral PTMs, this report presents numerous questions and hypotheses on PTM function and strongly supports PTMs as a new tier of regulation by which RNA viruses subvert the host and evade cellular surveillance systems.
Collapse
Affiliation(s)
- Will McIntyre
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Rachel Netzband
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Gaston Bonenfant
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Jason M Biegel
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Clare Miller
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Gabriele Fuchs
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Eric Henderson
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Manoj Arra
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208, USA
| | - Mario Canki
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208, USA
| | - Daniele Fabris
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Cara T Pager
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| |
Collapse
|
40
|
Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:280-290. [PMID: 30414470 DOI: 10.1016/j.bbagrm.2018.10.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/20/2018] [Accepted: 10/27/2018] [Indexed: 12/21/2022]
Abstract
A small set of ribonucleoside modifications have been found in different regions of mRNA including the open reading frame. Accurate detection of these specific modifications is critical to understanding their modulatory roles in facilitating mRNA maturation, translation and degradation. While transcriptome-wide next-generation sequencing (NGS) techniques could provide exhaustive information about the sites of one specific or class of modifications at a time, recent investigations strongly indicate cautionary interpretation due to the appearance of false positives. Therefore, it is suggested that NGS-based modification data can only be treated as predicted sites and their existence need to be validated by orthogonal methods. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an analytical technique that can yield accurate and reproducible information about the qualitative and quantitative characteristics of ribonucleoside modifications. Here, we review the recent advancements in LC-MS/MS technology that could help in securing accurate, gold-standard quality information about the resident post-transcriptional modifications of mRNA.
Collapse
|
41
|
Fouad MA, Salem SE, Hussein MM, Zekri ARN, Hafez HF, El Desouky ED, Shouman SA. Impact of Global DNA Methylation in Treatment Outcome of Colorectal Cancer Patients. Front Pharmacol 2018; 9:1173. [PMID: 30405408 PMCID: PMC6201055 DOI: 10.3389/fphar.2018.01173] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 09/28/2018] [Indexed: 12/16/2022] Open
Abstract
Background: Global DNA methylation has an impact in cancer pathogenesis and progression. This study aimed at investigating the impact of global DNA methylation in treatment outcome of Colorectal Cancer (CRC). Patients and Methods: Global DNA methylation was measured by LC/MS/MS in peripheral blood leucocytes of 102, 48, and 32 Egyptian CRC patients at baseline and after 3 and 6 months of Fluoropyrimidine (FP) therapy respectively, in addition to 32 normal healthy matched in age and sex. The genetic expressions of DNA methyl transferases (DNMTs) were determined and correlated with patients‘ survival using univariate and multivariate methods of analyses. Results: Egyptian CRC patients had significant global hypomethylation of 5mC level and 5mC % with overexpression of DNMT3A and DNMT3B. Significant higher 5mC levels were shown in patients > 45 years, male gender, T2 tumors, stage II, negative lymph nodes, and absence of metastasis. FP therapy significantly reduced DNA methylation particularly in the subgroups of patients with high DNA methylation level at baseline and good prognostic features. After 3 years of follow up, patients with 5mC % > 8.02% had significant poor overall survival (OS) while, significant better event-free survival (EFS) was found in patients with 5mC level > 0.55. High initial CEA level and presence of metastasis were significantly associated with hazards of disease progression and death. Conclusion: Global DNA methylation has a significant impact on the treatment outcome and survival of Egyptian CRC patients treated with FP- based therapy.
Collapse
Affiliation(s)
- Mariam A Fouad
- Pharmacology Unit, Department of Cancer Biology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Salem E Salem
- Department of Medical Oncology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Marwa M Hussein
- Department of Medical Oncology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Abdel Rahman N Zekri
- Virology and Immunology Unit, Department of Cancer Biology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Hafez F Hafez
- Pharmacology Unit, Department of Cancer Biology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Eman D El Desouky
- Department of Biostatistics and Epidemiology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Samia A Shouman
- Pharmacology Unit, Department of Cancer Biology, National Cancer Institute, Cairo University, Cairo, Egypt
| |
Collapse
|
42
|
Young AP, Bandarian V. TYW1: A Radical SAM Enzyme Involved in the Biosynthesis of Wybutosine Bases. Methods Enzymol 2018; 606:119-153. [PMID: 30097090 DOI: 10.1016/bs.mie.2018.04.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
Transfer RNA is extensively modified by the actions of a variety of enzymes. The radical S-adenosyl-l-methionine enzyme TYW1 modifies tRNAPhe forming the characteristic tricyclic ring via the condensation of carbons 2 and 3 of pyruvate. This chapter details methods that are required for studies of TYW1.
Collapse
Affiliation(s)
- Anthony P Young
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States.
| |
Collapse
|
43
|
Matuszewski M, Debiec K, Sochacka E. Efficient conversion of N 6-threonylcarbamoyladenosine (t 6A) into a tRNA native hydantoin cyclic form (ct 6A) performed at nucleoside and oligoribonucleotide levels. Chem Commun (Camb) 2018; 53:7945-7948. [PMID: 28657616 DOI: 10.1039/c7cc03560h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A t6A nucleoside was efficiently and stereospecifically transformed into a hydantoin cyclic form of N6-l-threonylcarbamoyladenosine (ct6A) by the use of polymer bounded carbodiimide (EDC-P) and HOBt. The procedure was successfully applied for a post-synthetic conversion of t6A-containing RNA 17-mers (of the sequences of anticodon stem and loop (ASL) fragments of S. pombe tRNAi and E. coli tRNALys) into the products bearing the ct6A unit.
Collapse
Affiliation(s)
- Michal Matuszewski
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | | | | |
Collapse
|
44
|
Microwave-assisted enzymatic hydrolysis of DNA for mass spectrometric analysis: A new strategy for accelerated hydrolysis. Anal Biochem 2018; 546:28-34. [PMID: 29408176 DOI: 10.1016/j.ab.2018.01.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 11/23/2022]
Abstract
Study of DNA base composition, DNA adducts and modification in its primary structure is a subject of interest in different fields of scientific research. Various methods like immunochemistry, capillary electrophoretic separation, chromatographic separation coupled with mass spectrometric (LC-MS/MS) detection have been developed for DNA analysis. During the past decade LC-MS/MS has emerged as a more sensitive and selective technique and now frequently used for the analysis of DNA. The workflow for the DNA analysis include DNA extraction, hydrolysis of DNA into mononucleosides and analysis. Though high-throughput methods are available for the analysis DNA hydrolysis oftentimes is a rate limiting step. Conventional enzymatic hydrolysis of DNA using a multienzyme mixture will take a minimum of 6-17 h to complete the hydrolysis. In this work, we developed an accelerated enzymatic hydrolysis of DNA using microwave-technology for the first time. 1.00 μg of calf thymus DNA was used to demonstrate the microwave assisted enzymatic hydrolysis of DNA. The resultant mononucleosides were separated on Atlantis T3 (50 × 2.1 mm i.d.; 3 μ particle size) C18 column and analyzed on ABSCIEX QTRAP 5500 LC/MS system. The sample through put and recovery of microwave-assisted digestion were compared with the conventional enzymatic hydrolysis. Efficient digestion of DNA with a performance similar to that obtained by the conventional overnight digestion procedure was attained in just 30 min with a hydrolysis yield of ≥90%. Furthermore, our method was found to be much more accurate and easier to perform. Thus, this new application of microwave technology to DNA enzymatic digestion will facilitate the application of DNA analysis in biological and clinical research.
Collapse
|
45
|
Matuszewski M, Wojciechowski J, Miyauchi K, Gdaniec Z, Wolf WM, Suzuki T, Sochacka E. A hydantoin isoform of cyclic N6-threonylcarbamoyladenosine (ct6A) is present in tRNAs. Nucleic Acids Res 2017; 45:2137-2149. [PMID: 27913732 PMCID: PMC5389693 DOI: 10.1093/nar/gkw1189] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/25/2016] [Indexed: 02/06/2023] Open
Abstract
N6-Threonylcarbamoyladenosine (t6A) and its derivatives are universally conserved modified nucleosides found at position 37, 3΄ adjacent to the anticodon in tRNAs responsible for ANN codons. These modifications have pleiotropic functions of tRNAs in decoding and protein synthesis. In certain species of bacteria, fungi, plants and protists, t6A is further modified to the cyclic t6A (ct6A) via dehydration catalyzed by TcdA. This additional modification is involved in efficient decoding of tRNALys. Previous work indicated that the chemical structure of ct6A is a cyclic active ester with an oxazolone ring. In this study, we solved the crystal structure of chemically synthesized ct6A nucleoside. Unexpectedly, we found that the ct6A adopted a hydantoin isoform rather than an oxazolone isoform, and further showed that the hydantoin isoform of ct6A was actually present in Escherichia coli tRNAs. In addition, we observed that hydantoin ct6A is susceptible to epimerization under mild alkaline conditions, warning us to avoid conventional deacylation of tRNAs. A hallmark structural feature of this isoform is the twisted arrangement of the hydantoin and adenine rings. Functional roles of ct6A37 in tRNAs should be reconsidered.
Collapse
Affiliation(s)
- Michal Matuszewski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Jakub Wojciechowski
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wojciech M Wolf
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| |
Collapse
|
46
|
Bouzon M, Perret A, Loreau O, Delmas V, Perchat N, Weissenbach J, Taran F, Marlière P. A Synthetic Alternative to Canonical One-Carbon Metabolism. ACS Synth Biol 2017; 6:1520-1533. [PMID: 28467058 DOI: 10.1021/acssynbio.7b00029] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
One-carbon metabolism is an ubiquitous metabolic pathway that encompasses the reactions transferring formyl-, hydroxymethyl- and methyl-groups bound to tetrahydrofolate for the synthesis of purine nucleotides, thymidylate, methionine and dehydropantoate, the precursor of coenzyme A. An alternative cyclic pathway was designed that substitutes 4-hydroxy-2-oxobutanoic acid (HOB), a compound absent from known metabolism, for the amino acids serine and glycine as one-carbon donors. It involves two novel reactions, the transamination of l-homoserine and the transfer of a one-carbon unit from HOB to tetrahydrofolate releasing pyruvate as coproduct. Since canonical reactions regenerate l-homoserine from pyruvate by carboxylation and subsequent reduction, every one-carbon moiety made available for anabolic reactions originates from CO2. The HOB-dependent pathway was established in an Escherichia coli auxotroph selected for prototrophy using long-term cultivation protocols. Genetic, metabolic and biochemical evidence support the emergence of a functional HOB-dependent one-carbon pathway achieved with the recruitment of the two enzymes l-homoserine transaminase and HOB-hydroxymethyltransferase and of HOB as an essential metabolic intermediate. Escherichia coli biochemical reprogramming was achieved by minimally altering canonical metabolism and leveraging on natural selection mechanisms, thereby launching the resulting strain on an evolutionary trajectory diverging from all known extant species.
Collapse
Affiliation(s)
- Madeleine Bouzon
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | - Alain Perret
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | | | - Valérie Delmas
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | - Nadia Perchat
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | - Jean Weissenbach
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | | | - Philippe Marlière
- Institute of Systems and Synthetic Biology, Génopole, 5 rue Desbruères, 91030 Evry Cedex, France
| |
Collapse
|
47
|
Torres-Cuevas I, Aupi M, Asensi MA, Vento M, Ortega Á, Escobar J. 7,8-hydroxy-2′-deoxyguanosine/2′-deoxiguanosine ratio determined in hydrolysates of brain DNA by ultrachromatrography coupled to tandem mass spectrometry. Talanta 2017; 170:97-102. [DOI: 10.1016/j.talanta.2017.03.072] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/20/2017] [Accepted: 03/23/2017] [Indexed: 02/05/2023]
|
48
|
Liou SH, Wu WT, Liao HY, Chen CY, Tsai CY, Jung WT, Lee HL. Global DNA methylation and oxidative stress biomarkers in workers exposed to metal oxide nanoparticles. JOURNAL OF HAZARDOUS MATERIALS 2017; 331:329-335. [PMID: 28273583 DOI: 10.1016/j.jhazmat.2017.02.042] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/11/2017] [Accepted: 02/22/2017] [Indexed: 06/06/2023]
Abstract
This is the first study to assess global methylation, oxidative DNA damage, and lipid peroxidation in workers with occupational exposure to metal oxide nanomaterials (NMs). Urinary and white blood cell (WBC) 8-hydroxydeoxyguanosine (8-OHdG), and exhaled breath condensate (EBC) 8-isoprostane were measured as oxidative stress biomarkers. WBC global methylation was measured as an epigenetic alteration. Exposure to TiO2, SiO2, and indium tin oxide (ITO) resulted in significantly higher oxidative biomarkers such as urinary 8-OHdG and EBC 8-isoprostane. However, significantly higher WBC 8-OHdG and lower global methylation were only observed in ITO handling workers. Significant positive correlations were noted between WBC and urinary 8-OHdG (Spearman correlation r=0.256, p=0.003). Furthermore, a significant negative correlation was found between WBC 8-OHdG and global methylation (r=-0.272, p=0.002). These results suggest that exposure to metal oxide NMs may lead to global methylation, DNA oxidative damage, and lipid peroxidation.
Collapse
Affiliation(s)
- Saou-Hsing Liou
- National Institute of Environmental Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Wei-Te Wu
- National Institute of Environmental Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Hui-Yi Liao
- National Institute of Environmental Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Chao-Yu Chen
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Cheng-Yen Tsai
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Wei-Ting Jung
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Hui-Ling Lee
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan.
| |
Collapse
|
49
|
Genome-wide profiling of DNA 5-hydroxymethylcytosine during rat Sertoli cell maturation. Cell Discov 2017; 3:17013. [PMID: 28529766 PMCID: PMC5423031 DOI: 10.1038/celldisc.2017.13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/24/2017] [Indexed: 01/04/2023] Open
Abstract
Sertoli cells have dual roles during the cells' lifetime. In the juvenile mammal, Sertoli cells proliferate and create the structure of the testis, and during puberty they cease to proliferate and take on the adult role of supporting germ cells through spermatogenesis. Accordingly, many genes expressed in Sertoli cells during testis formation are repressed during spermatogenesis. 5-Hydroxymethylcytosine (5hmC) is a DNA modification enzymatically generated from 5mC and present in all investigated mammalian tissues at varying levels. Using mass spectrometry and immunofluorescence staining we identified a substantial Sertoli cell-specific global 5hmC increase during rat puberty. Chemical labeling, pull-down and sequencing of 5hmC-containing genomic DNA from juvenile and adult rat Sertoli cells revealed that genes that lose or gain 5hmC belong to different functional pathways and mirror the functions of the cells in the two different states. Loss of 5hmC is associated with genes involved in development and cell structure, whereas gain of 5hmC is associated with genes involved in cellular pathways pertaining to the function of the adult Sertoli cells. This redistribution during maturation shows that 5hmC is a dynamic nucleotide modification, correlated to gene expression.
Collapse
|
50
|
Bon Ramos A, Bao L, Turner B, de Crécy-Lagard V, Iwata-Reuyl D. QueF-Like, a Non-Homologous Archaeosine Synthase from the Crenarchaeota. Biomolecules 2017; 7:biom7020036. [PMID: 28383498 PMCID: PMC5485725 DOI: 10.3390/biom7020036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 12/17/2022] Open
Abstract
Archaeosine (G+) is a structurally complex modified nucleoside ubiquitous to the Archaea, where it is found in the D-loop of virtually all archaeal transfer RNA (tRNA). Its unique structure, which includes a formamidine group that carries a formal positive charge, and location in the tRNA, led to the proposal that it serves a key role in stabilizing tRNA structure. Although G+ is limited to the Archaea, it is structurally related to the bacterial modified nucleoside queuosine, and the two share homologous enzymes for the early steps of their biosynthesis. In the Euryarchaeota, the last step of the archaeosine biosynthetic pathway involves the amidation of a nitrile group on an archaeosine precursor to give formamidine, a reaction catalyzed by the enzyme Archaeosine Synthase (ArcS). Most Crenarchaeota lack ArcS, but possess two proteins that inversely distribute with ArcS and each other, and are implicated in G+ biosynthesis. Here, we describe biochemical studies of one of these, the protein QueF-like (QueF-L) from Pyrobaculum calidifontis, that demonstrate the catalytic activity of QueF-L, establish where in the pathway QueF-L acts, and identify the source of ammonia in the reaction.
Collapse
Affiliation(s)
- Adriana Bon Ramos
- Department of Chemistry, Portland State University, Portland, OR 97207, USA.
| | - Lide Bao
- Department of Chemistry, Portland State University, Portland, OR 97207, USA.
| | - Ben Turner
- Department of Chemistry, Portland State University, Portland, OR 97207, USA.
| | - Valérie de Crécy-Lagard
- The Department of Microbiology and Cell Science Department, University of Florida, Gainesville, FL 32611, USA.
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, Portland, OR 97207, USA.
| |
Collapse
|