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Liu Y, Chen Y, Cai M, Hong Y, Wu X, Li S. m5C methylation modification guides the prognostic value and immune landscapes in acute myeloid leukemia. Aging (Albany NY) 2023; 15:9858-9876. [PMID: 37751592 PMCID: PMC10564437 DOI: 10.18632/aging.205059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/02/2023] [Indexed: 09/28/2023]
Abstract
The development, incidence, and metastasis of tumors are all intimately correlated with 5-methylcytosine (m5C). However, uncertainty surrounds the function of m5C in acute myeloid leukemia (AML). In this study, multicenter AML data were collected and analyzed comprehensively to grasp the gene expression level, clinicopathological characteristics, prognostic significance of m5C in AML and its relationship with the tumor microenvironment (TME). The m5C gene-mediated scoring system (m5CSS) was created using principal component analysis, and multiple cox regression analyses were utilized to determine the prognostic relevance of the m5C score. The investigation of the correlation among m5C, immune characteristics, clinical characteristics, immune infiltration level, as well as drug reaction at immune checkpoints, and immunotherapy efficacy confirmed that the change of the characteristics of immune cell infiltration and patient prognosis are linked with the m5C gene. Moreover, the m5CSS was employed to assess the pattern of m5C modification. Further analyses showed that the m5C score can served as a reliable indicator of AML prognosis. Crucially, the prognostic value of the m5C score was validated in terms of drug resistance and immunotherapy. This work reveals that AML diversity and the generation of complex TMEs are both impacted by m5C modifications. Therefore, understanding the m5C modification pattern will improve grasp of TME infiltration characteristics and assist exploring more efficient immunotherapeutic approaches.
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Affiliation(s)
- Ya Liu
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang 524045, China
| | - Yiying Chen
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Maoping Cai
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang 524045, China
| | - Yunguang Hong
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang 524045, China
| | - Xiang Wu
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang 524045, China
| | - Songyu Li
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang 524045, China
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2
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Duffy K, Arangundy-Franklin S, Holliger P. Modified nucleic acids: replication, evolution, and next-generation therapeutics. BMC Biol 2020; 18:112. [PMID: 32878624 PMCID: PMC7469316 DOI: 10.1186/s12915-020-00803-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are now increasingly amenable to in vitro evolution, accelerating lead discovery. Here, we review the most recent discoveries in this dynamic field with a focus on progress in the enzymatic replication and functional exploration of XNAs.
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Affiliation(s)
- Karen Duffy
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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3
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Zhou H, Rauch S, Dai Q, Cui X, Zhang Z, Nachtergaele S, Sepich C, He C, Dickinson BC. Evolution of a reverse transcriptase to map N 1-methyladenosine in human messenger RNA. Nat Methods 2019; 16:1281-1288. [PMID: 31548705 PMCID: PMC6884687 DOI: 10.1038/s41592-019-0550-4] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 08/05/2019] [Indexed: 11/09/2022]
Abstract
Chemical modifications to messenger RNA are increasingly recognized as a critical regulatory layer in the flow of genetic information, but quantitative tools to monitor RNA modifications in a whole-transcriptome and site-specific manner are lacking. Here we describe a versatile platform for directed evolution that rapidly selects for reverse transcriptases that install mutations at sites of a given type of RNA modification during reverse transcription, allowing for site-specific identification of the modification. To develop and validate the platform, we evolved the HIV-1 reverse transcriptase against N1-methyladenosine (m1A). Iterative rounds of selection yielded reverse transcriptases with both robust read-through and high mutation rates at m1A sites. The optimal evolved reverse transcriptase enabled detection of well-characterized m1A sites and revealed hundreds of m1A sites in human mRNA. This work develops and validates the reverse transcriptase evolution platform, and provides new tools, analysis methods and datasets to study m1A biology.
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Affiliation(s)
- Huiqing Zhou
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Simone Rauch
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Qing Dai
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Xiaolong Cui
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Zijie Zhang
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Sigrid Nachtergaele
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Caraline Sepich
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.,University of Chicago Medical Scientist Training Program, Chicago, USA
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, IL, USA. .,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA. .,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA. .,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA.
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4
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Engineering Polymerases for New Functions. Trends Biotechnol 2019; 37:1091-1103. [PMID: 31003719 DOI: 10.1016/j.tibtech.2019.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/08/2019] [Accepted: 03/19/2019] [Indexed: 01/04/2023]
Abstract
DNA polymerases are critical tools in biotechnology, enabling efficient and accurate amplification of DNA templates, yet many desired functions are not readily available in natural DNA polymerases. New or improved functions can be engineered in DNA polymerases by mutagenesis or through the creation of protein chimeras. Engineering often necessitates the development of new techniques, such as selections in water-in-oil emulsions that connect genotype to phenotype and allow more flexibility in engineering than phage display. Engineering efforts have led to DNA polymerases that can withstand extreme conditions or the presence of inhibitors, as well as polymerases with the ability to copy modified DNA templates. In this review we discuss polymerases for biotechnology that have been reported along with tools to enable further development.
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5
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Identification of Thermus aquaticus DNA polymerase variants with increased mismatch discrimination and reverse transcriptase activity from a smart enzyme mutant library. Sci Rep 2019; 9:590. [PMID: 30679705 PMCID: PMC6345897 DOI: 10.1038/s41598-018-37233-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/02/2018] [Indexed: 12/13/2022] Open
Abstract
DNA polymerases the key enzymes for several biotechnological applications. Obviously, nature has not evolved these enzymes to be compatible with applications in biotechnology. Thus, engineering of a natural scaffold of DNA polymerases may lead to enzymes improved for several applications. Here, we investigated a two-step approach for the design and construction of a combinatorial library of mutants of KlenTaq DNA polymerase. First, we selected amino acid sites for saturation mutagenesis that interact with the primer/template strands or are evolutionarily conserved. From this library, we identified mutations that little interfere with DNA polymerase activity. Next, these functionally active mutants were combined randomly to construct a second library with enriched sequence diversity. We reasoned that the combination of mutants that have minuscule effect on enzyme activity and thermostability, will result in entities that have an increased mutation load but still retain activity. Besides activity and thermostability, we screened the library for entities with two distinct properties. Indeed, we identified two different KlenTaq DNA polymerase variants that either exhibit increased mismatch extension discrimination or increased reverse transcription PCR activity, respectively.
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6
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Aschenbrenner J, Werner S, Marchand V, Adam M, Motorin Y, Helm M, Marx A. Engineering of a DNA Polymerase for Direct m 6 A Sequencing. Angew Chem Int Ed Engl 2018; 57:417-421. [PMID: 29115744 PMCID: PMC5768020 DOI: 10.1002/anie.201710209] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 12/16/2022]
Abstract
Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N6 -methyladenosine (m6 A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m6 A-containing RNA prior to sequencing, since m6 A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m6 A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for N6 -methylation. We identified a mutant that exhibits increased misincorporation opposite m6 A compared to unmodified A. Application of the generated DNA polymerase in next-generation sequencing allowed the identification of m6 A sites directly from the sequencing data of untreated RNA samples.
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Affiliation(s)
- Joos Aschenbrenner
- Department of Chemistry, Konstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Stephan Werner
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University MainzStaudingerweg 555128MainzGermany
| | - Virginie Marchand
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, IMoPA, UMR7365 CNRS-ULBiopôle de L'Université de Lorraine9, Avenue de la Forêt de Haye54505Vandoeuvre-les-NancyFrance
| | - Martina Adam
- Department of Chemistry, Konstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, IMoPA, UMR7365 CNRS-ULBiopôle de L'Université de Lorraine9, Avenue de la Forêt de Haye54505Vandoeuvre-les-NancyFrance
| | - Mark Helm
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University MainzStaudingerweg 555128MainzGermany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
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7
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Agudo R, Calvo PA, Martínez-Jiménez MI, Blanco L. Engineering human PrimPol into an efficient RNA-dependent-DNA primase/polymerase. Nucleic Acids Res 2017; 45:9046-9058. [PMID: 28911121 PMCID: PMC5587808 DOI: 10.1093/nar/gkx633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/12/2017] [Indexed: 02/01/2023] Open
Abstract
We have developed a straightforward fluorometric assay to measure primase-polymerase activity of human PrimPol (HsPrimPol). The sensitivity of this procedure uncovered a novel RNA-dependent DNA priming-polymerization activity (RdDP) of this enzyme. In an attempt to enhance HsPrimPol RdDP activity, we constructed a smart mutant library guided by prior sequence-function analysis, and tested this library in an adapted screening platform of our fluorometric assay. After screening less than 500 variants, we found a specific HsPrimPol mutant, Y89R, which displays 10-fold higher RdDP activity than the wild-type enzyme. The improvement of RdDP activity in the Y89R variant was due mainly to an increased in the stabilization of the preternary complex (protein:template:incoming nucleotide), a specific step preceding dimer formation. Finally, in support of the biotechnological potential of PrimPol as a DNA primer maker during reverse transcription, mutant Y89R HsPrimPol rendered up to 17-fold more DNA than with random hexamer primers.
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Affiliation(s)
- Rubén Agudo
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 91 196 46 85; Fax: +34 91 196 44 20; . Correspondence may also be addressed to Rubén Agudo. Tel: +34 91 196 46 86; Fax: +34 91 196 44 20;
| | - Patricia A. Calvo
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
| | | | - Luis Blanco
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 91 196 46 85; Fax: +34 91 196 44 20; . Correspondence may also be addressed to Rubén Agudo. Tel: +34 91 196 46 86; Fax: +34 91 196 44 20;
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8
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Variants of sequence family B Thermococcus kodakaraensis DNA polymerase with increased mismatch extension selectivity. PLoS One 2017; 12:e0183623. [PMID: 28832623 PMCID: PMC5568139 DOI: 10.1371/journal.pone.0183623] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/08/2017] [Indexed: 12/01/2022] Open
Abstract
Fidelity and selectivity of DNA polymerases are critical determinants for the biology of life, as well as important tools for biotechnological applications. DNA polymerases catalyze the formation of DNA strands by adding deoxynucleotides to a primer, which is complementarily bound to a template. To ensure the integrity of the genome, DNA polymerases select the correct nucleotide and further extend the nascent DNA strand. Thus, DNA polymerase fidelity is pivotal for ensuring that cells can replicate their genome with minimal error. DNA polymerases are, however, further optimized for more specific biotechnological or diagnostic applications. Here we report on the semi-rational design of mutant libraries derived by saturation mutagenesis at single sites of a 3’-5’-exonuclease deficient variant of Thermococcus kodakaraensis DNA polymerase (KOD pol) and the discovery for variants with enhanced mismatch extension selectivity by screening. Sites of potential interest for saturation mutagenesis were selected by their proximity to primer or template strands. The resulting libraries were screened via quantitative real-time PCR. We identified three variants with single amino acid exchanges—R501C, R606Q, and R606W—which exhibited increased mismatch extension selectivity. These variants were further characterized towards their potential in mismatch discrimination. Additionally, the identified enzymes were also able to differentiate between cytosine and 5-methylcytosine. Our results demonstrate the potential in characterizing and developing DNA polymerases for specific PCR based applications in DNA biotechnology and diagnostics.
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9
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Houlihan G, Arangundy-Franklin S, Holliger P. Exploring the Chemistry of Genetic Information Storage and Propagation through Polymerase Engineering. Acc Chem Res 2017; 50:1079-1087. [PMID: 28383245 PMCID: PMC5406124 DOI: 10.1021/acs.accounts.7b00056] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Nucleic
acids are a distinct form of sequence-defined biopolymer.
What sets them apart from other biopolymers such as polypeptides or
polysaccharides is their unique capacity to encode, store, and propagate
genetic information (molecular heredity). In nature, just two closely
related nucleic acids, DNA and RNA, function as repositories and carriers
of genetic information. They therefore are the molecular embodiment
of biological information. This naturally leads to questions regarding
the degree of variation from this seemingly ideal “Goldilocks”
chemistry that would still be compatible with the fundamental property
of molecular heredity. To address this question, chemists have
created a panoply of synthetic
nucleic acids comprising unnatural sugar ring congeners, backbone
linkages, and nucleobases in order to establish the molecular parameters
for encoding genetic information and its emergence at the origin of
life. A deeper analysis of the potential of these synthetic genetic
polymers for molecular heredity requires a means of replication and
a determination of the fidelity of information transfer. While non-enzymatic
synthesis is an increasingly powerful method, it currently remains
restricted to short polymers. Here we discuss efforts toward establishing
enzymatic synthesis, replication, and evolution of synthetic genetic
polymers through the engineering of polymerase enzymes found in nature. To endow natural polymerases with the ability to efficiently utilize
non-cognate nucleotide substrates, novel strategies for the screening
and directed evolution of polymerase function have been realized.
High throughput plate-based screens, phage display, and water-in-oil
emulsion technology based methods have yielded a number of engineered
polymerases, some of which can synthesize and reverse transcribe synthetic
genetic polymers with good efficiency and fidelity. The inception
of such polymerases demonstrates that, at a basic
level at least, molecular heredity is not restricted to the natural
nucleic acids DNA and RNA, but may be found in a large (if finite)
number of synthetic genetic polymers. And it has opened up these novel
sequence spaces for investigation. Although largely unexplored, first
tentative forays have yielded ligands (aptamers) against a range of
targets and several catalysts elaborated in a range of different chemistries.
Finally, taking the lead from established DNA designs, simple polyhedron
nanostructures have been described. We anticipate that further
progress in this area will expand the
range of synthetic genetic polymers that can be synthesized, replicated,
and evolved providing access to a rich sequence, structure, and phenotypic
space. “Synthetic genetics”, that is, the exploration
of these spaces, will illuminate the chemical parameter range for
en- and decoding information, 3D folding, and catalysis and yield
novel ligands, catalysts, and nanostructures and devices for applications
in biotechnology and medicine.
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Affiliation(s)
- Gillian Houlihan
- MRC Laboratory of Molecular Biology, Francis Crick
Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick
Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
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