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He D, Zhang M, Li Y, Liu F, Ban B. Insights into the ANKRD11 variants and short-stature phenotype through literature review and ClinVar database search. Orphanet J Rare Dis 2024; 19:292. [PMID: 39135054 PMCID: PMC11318275 DOI: 10.1186/s13023-024-03301-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/05/2024] [Indexed: 08/16/2024] Open
Abstract
Ankyrin repeat domain containing-protein 11 (ANKRD11), a transcriptional factor predominantly localized in the cell nucleus, plays a crucial role in the expression regulation of key genes by recruiting chromatin remodelers and interacting with specific transcriptional repressors or activators during numerous biological processes. Its pathogenic variants are strongly linked to the pathogenesis and progression of multisystem disorder known as KBG syndrome. With the widespread application of high-throughput DNA sequencing technologies in clinical medicine, numerous pathogenic variants in the ANKRD11 gene have been reported. Patients with KBG syndrome usually exhibit a broad phenotypic spectrum with a variable degree of severity, even if having identical variants. In addition to distinctive dental, craniofacial and neurodevelopmental abnormalities, patients often present with skeletal anomalies, particularly postnatal short stature. The relationship between ANKRD11 variants and short stature is not well-understood, with limited knowledge regarding its occurrence rate or underlying biological mechanism involved. This review aims to provide an updated analysis of the molecular spectrum associated with ANKRD11 variants, investigate the prevalence of the short stature among patients harboring these variants, evaluate the efficacy of recombinant human growth hormone in treating children with short stature and ANKRD11 variants, and explore the biological mechanisms underlying short stature from both scientific and clinical perspectives. Our investigation indicated that frameshift and nonsense were the most frequent types in 583 pathogenic or likely pathogenic variants identified in the ANKRD11 gene. Among the 245 KBGS patients with height data, approximately 50% displayed short stature. Most patients showed a positive response to rhGH therapy, although the number of patients receiving treatment was limited. ANKRD11 deficiency potentially disrupts longitudinal bone growth by affecting the orderly differentiation of growth plate chondrocytes. Our review offers crucial insights into the association between ANKRD11 variants and short stature and provides valuable guidance for precise clinical diagnosis and treatment of patients with KBG syndrome.
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Affiliation(s)
- Dongye He
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, China.
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, China.
| | - Mei Zhang
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, China
- Chinese Research Center for Behavior Medicine in Growth and Development, Jining, China
| | - Yanying Li
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, China
- Chinese Research Center for Behavior Medicine in Growth and Development, Jining, China
| | - Fupeng Liu
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, China
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, China
| | - Bo Ban
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, China.
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, China.
- Chinese Research Center for Behavior Medicine in Growth and Development, Jining, China.
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2
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Li Y, Zhu R, Jin J, Guo H, Zhang J, He Z, Liang T, Guo L. Exploring the Role of Clustered Mutations in Carcinogenesis and Their Potential Clinical Implications in Cancer. Int J Mol Sci 2024; 25:6744. [PMID: 38928450 PMCID: PMC11203652 DOI: 10.3390/ijms25126744] [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: 04/23/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Abnormal cell proliferation and growth leading to cancer primarily result from cumulative genome mutations. Single gene mutations alone do not fully explain cancer onset and progression; instead, clustered mutations-simultaneous occurrences of multiple mutations-are considered to be pivotal in cancer development and advancement. These mutations can affect different genes and pathways, resulting in cells undergoing malignant transformation with multiple functional abnormalities. Clustered mutations influence cancer growth rates, metastatic potential, and drug treatment sensitivity. This summary highlights the various types and characteristics of clustered mutations to understand their associations with carcinogenesis and discusses their potential clinical significance in cancer. As a unique mutation type, clustered mutations may involve genomic instability, DNA repair mechanism defects, and environmental exposures, potentially correlating with responsiveness to immunotherapy. Understanding the characteristics and underlying processes of clustered mutations enhances our comprehension of carcinogenesis and cancer progression, providing new diagnostic and therapeutic approaches for cancer.
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Affiliation(s)
- Yi Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Rui Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaming Jin
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Haochuan Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaxi Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Zhiheng He
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Li Guo
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
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Rogozin IB, Saura A, Poliakov E, Bykova A, Roche-Lima A, Pavlov YI, Yurchenko V. Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2. Int J Mol Sci 2024; 25:3696. [PMID: 38612505 PMCID: PMC11011937 DOI: 10.3390/ijms25073696] [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: 02/25/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
SARS-CoV-2 has accumulated many mutations since its emergence in late 2019. Nucleotide substitutions leading to amino acid replacements constitute the primary material for natural selection. Insertions, deletions, and substitutions appear to be critical for coronavirus's macro- and microevolution. Understanding the molecular mechanisms of mutations in the mutational hotspots (positions, loci with recurrent mutations, and nucleotide context) is important for disentangling roles of mutagenesis and selection. In the SARS-CoV-2 genome, deletions and insertions are frequently associated with repetitive sequences, whereas C>U substitutions are often surrounded by nucleotides resembling the APOBEC mutable motifs. We describe various approaches to mutation spectra analyses, including the context features of RNAs that are likely to be involved in the generation of recurrent mutations. We also discuss the interplay between mutations and natural selection as a complex evolutionary trend. The substantial variability and complexity of pipelines for the reconstruction of mutations and the huge number of genomic sequences are major problems for the analyses of mutations in the SARS-CoV-2 genome. As a solution, we advocate for the development of a centralized database of predicted mutations, which needs to be updated on a regular basis.
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Affiliation(s)
- Igor B. Rogozin
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Eugenia Poliakov
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities—RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan 00936, Puerto Rico
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
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4
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Pi Y, Huang Z, Xu X, Zhang H, Jin M, Zhang S, Lin G, Hu L. Increases in computationally predicted deleterious variants of unknown significance and sperm mtDNA copy numbers may be associated with semen quality. Andrology 2024; 12:585-598. [PMID: 37622679 DOI: 10.1111/andr.13521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/24/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Mitochondria are essential for sperm motility because they provide the energy required for the movement. Changes in sperm mtDNA, such as point mutations, large-scale deletions, or copy number variations, may interfere with ATP production and reduce sperm motility. However, it is not clear if changes in mtDNA are linked to semen quality. OBJECTIVES To explore the association between sperm mitochondrial DNA (mtDNA) changes and semen quality. MATERIALS AND METHODS Sixty-five oligo and/or astheno and/or terato patients (O/A/T) patients and 41 controls were recruited from couples undergoing assisted reproduction. Semen and blood samples were collected from the same individual on the day of oocyte retrieval to extract, isolate and purify mtDNA for next-generation sequencing. mtDNA copy numbers were assessed in 64 patient and 39 control sperm DNA samples using quantitative real-time PCR. The 4977 bp deletion was assessed in 20 patient and 20 control sperm DNA samples using polymerase chain reaction. RESULTS The mtDNA of patients was more likely to carry pathogenic variants or variants of unknown significance (VUSs) (P = 0.091) with higher heteroplasmy levels (P < 0.05) than that of controls. Interestingly, 33.85% of O/A/T patients (22 out of 65) lacked unique variants in their spermatozoa. but presented an exceptionally high mtDNA copy number (P < 0.0001). Moreover, we observed a decrease in the heteroplasmy level of common mtDNA variants shared by somatic and gamete cells (P < 0.0001) and the emergence of a very large number of de novo mtDNA variants with low-level heteroplasmy in spermatozoa. DISCUSSION AND CONCLUSION The increases in the number of computationally predicted deleterious VUS and mtDNA copies in spermatozoa may be associated with semen quality. Exposure to environmental mutation pressure that causes novel mtDNA variants with low-level heteroplasmy may occur during spermatogenesis. Furthermore, when a certain harmful threshold is reached, male germ cells may degrade mtDNA with mutations and replicate the correct mtDNA sequence to maintain the mitochondrial function in spermatozoa.
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Affiliation(s)
- Yuze Pi
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Zhuo Huang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Xilin Xu
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Huan Zhang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
| | - Miao Jin
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
| | - Shuoping Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
- National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China
| | - Liang Hu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
- National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation base of Development and Carcinogenesis, Changsha, Hunan, China
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5
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de Groen PC. A new, all-encompassing aetiology of type 1 diabetes. Immunology 2024; 171:77-91. [PMID: 37772700 DOI: 10.1111/imm.13700] [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: 04/26/2023] [Accepted: 09/10/2023] [Indexed: 09/30/2023] Open
Abstract
The aetiology of type 1 diabetes (T1D) is considered multifactorial with the contribution of the MHC on chromosome 6 being most important. Multiple factors also contribute to the aetiology of colorectal neoplasia, but the final event causing the change from normal mucosa to polyp and from polyp to cancer is due to a single somatic mutation event. Repeated formation of colorectal neoplasia within an at-risk population results in a predictable, tapering, exponential neoplasia distribution. Critical mutations driving colorectal neoplasia formation occur in mutation-prone DNA. These observations led to three hypotheses related to T1D. First, a single somatic mutation within the MHC of antigen presenting cells results in a change in phenotype from normal to T1D. Second, the distribution of additional autoimmune diseases (AAIDs) among persons with T1D adheres to a predictable, tapering, exponential distribution. And third, critical mutations driving development of T1D occur in mutation-prone DNA. To address the hypotheses in an orderly fashion, a new analytical method called genome-wide aetiology analysis (GWEA) consisting of nine steps is presented. All data required for GWEA of T1D are obtained from peer-reviewed publications or publicly available genome and proteome databases. Critical GWEA steps include AAID distribution among persons with T1D, analysis of at-risk HLA loci for mutation-prone DNA, determination of the role of non-MHC genes on GWAS, and verification of human data by cell culture or animal experiments. GWEA results show that distribution of AAID among persons with T1D adheres to a predictable, tapering, exponential distribution. A single, critical, somatic mutation within the epitope-binding groove of at-risk HLA loci alters HLA-insulin-peptide-T-cell-receptor (TCR) complex binding affinity and creates a new pathway that leads to loss of self-tolerance. The at-risk HLA loci, in particular binding pockets P1, P4 and P9, are encoded by mutation-prone DNA: GC-rich DNA sequence and somatic hypermutation hotspots. All other genes on GWAS can but do not have to amplify the new autoimmune pathway by facilitating DNA mutations, changing peptide binding affinity, reducing signal inhibition or augmenting signal intensity. Animal experiments agree with human studies. In conclusion, T1D is caused by a somatic mutation within the epitope-binding groove of an at-risk HLA gene that affects HLA-insulin-peptide-TCR complex binding affinity and initiates an autoimmune pathway. The nature of the peptide that binds to a mutated epitope-binding groove of an at-risk HLA gene determines the type of autoimmune disease that develops, that is, one at-risk HLA locus, multiple autoimmune diseases. Thus, T1D and AAIDs, and therefore common autoimmune diseases, share a similar somatic mutation-based aetiology.
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Affiliation(s)
- Piet C de Groen
- Division of Gastroenterology, Hepatology & Nutrition, University of Minnesota, Minneapolis, Minnesota, USA
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6
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Arbel-Groissman M, Menuhin-Gruman I, Yehezkeli H, Naki D, Bergman S, Udi Y, Tuller T. The Causes for Genomic Instability and How to Try and Reduce Them Through Rational Design of Synthetic DNA. Methods Mol Biol 2024; 2760:371-392. [PMID: 38468099 DOI: 10.1007/978-1-0716-3658-9_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Genetic engineering has revolutionized our ability to manipulate DNA and engineer organisms for various applications. However, this approach can lead to genomic instability, which can result in unwanted effects such as toxicity, mutagenesis, and reduced productivity. To overcome these challenges, smart design of synthetic DNA has emerged as a promising solution. By taking into consideration the intricate relationships between gene expression and cellular metabolism, researchers can design synthetic constructs that minimize metabolic stress on the host cell, reduce mutagenesis, and increase protein yield. In this chapter, we summarize the main challenges of genomic instability in genetic engineering and address the dangers of unknowingly incorporating genomically unstable sequences in synthetic DNA. We also demonstrate the instability of those sequences by the fact that they are selected against conserved sequences in nature. We highlight the benefits of using ESO, a tool for the rational design of DNA for avoiding genetically unstable sequences, and also summarize the main principles and working parameters of the software that allow maximizing its benefits and impact.
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Affiliation(s)
- Matan Arbel-Groissman
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hader Yehezkeli
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Yarin Udi
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.
- The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel.
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7
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Beal MA, Meier MJ, Dykes A, Yauk CL, Lambert IB, Marchetti F. The functional mutational landscape of the lacZ gene. iScience 2023; 26:108407. [PMID: 38058303 PMCID: PMC10696112 DOI: 10.1016/j.isci.2023.108407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/23/2023] [Accepted: 11/03/2023] [Indexed: 12/08/2023] Open
Abstract
The lacZ gene of Escherichia coli encodes β-galactosidase (β-gal), a lactose metabolism enzyme of the lactose operon. Previous chemical modification or site-directed mutagenesis experiments have identified 21 amino acids that are essential for β-gal catalytic activity. We have assembled over 10,000 lacZ mutations from published studies that were collected using a positive selection assay to identify mutations in lacZ that disrupted β-gal function. We analyzed 6,465 independent lacZ mutations that resulted in 2,732 missense mutations that impaired β-gal function. Those mutations affected 492 of the 1,023 lacZ codons, including most of the 21 previously known residues critical for catalytic activity. Most missense mutations occurred near the catalytic site and in regions important for subunit tetramerization. Overall, our work provides a comprehensive and detailed map of the amino acid residues affecting the structure and catalytic activity of the β-gal enzyme.
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Affiliation(s)
- Marc A. Beal
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Matthew J. Meier
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Angela Dykes
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Iain B. Lambert
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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8
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Arbel-Groissman M, Menuhin-Gruman I, Naki D, Bergman S, Tuller T. Fighting the battle against evolution: designing genetically modified organisms for evolutionary stability. Trends Biotechnol 2023; 41:1518-1531. [PMID: 37442714 DOI: 10.1016/j.tibtech.2023.06.008] [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: 03/07/2023] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
Abstract
Synthetic biology has made significant progress in many areas, but a major challenge that has received limited attention is the evolutionary stability of synthetic constructs made of heterologous genes. The expression of these constructs in microorganisms, that is, production of proteins that are not necessary for the organism, is a metabolic burden, leading to a decrease in relative fitness and make the synthetic constructs unstable over time. This is a significant concern for the synthetic biology community, particularly when it comes to bringing this technology out of the laboratory. In this review, we discuss the issue of evolutionary stability in synthetic biology and review the available tools to address this challenge.
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Affiliation(s)
- Matan Arbel-Groissman
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
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9
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Hudson KM, Klimczak LJ, Sterling JF, Burkholder AB, Kazanov M, Saini N, Mieczkowski PA, Gordenin DA. Glycidamide-induced hypermutation in yeast single-stranded DNA reveals a ubiquitous clock-like mutational motif in humans. Nucleic Acids Res 2023; 51:9075-9100. [PMID: 37471042 PMCID: PMC10516655 DOI: 10.1093/nar/gkad611] [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: 03/19/2023] [Revised: 06/28/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
Mutagens often prefer specific nucleotides or oligonucleotide motifs that can be revealed by studying the hypermutation spectra in single-stranded (ss) DNA. We utilized a yeast model to explore mutagenesis by glycidamide, a simple epoxide formed endogenously in humans from the environmental toxicant acrylamide. Glycidamide caused ssDNA hypermutation in yeast predominantly in cytosines and adenines. The most frequent mutations in adenines occurred in the nAt→nGt trinucleotide motif. Base substitutions A→G in this motif relied on Rev1 translesion polymerase activity. Inactivating Rev1 did not alter the nAt trinucleotide preference, suggesting it may be an intrinsic specificity of the chemical reaction between glycidamide and adenine in the ssDNA. We found this mutational motif enriched in published sequencing data from glycidamide-treated mouse cells and ubiquitous in human cancers. In cancers, this motif was positively correlated with the single base substitution (SBS) smoking-associated SBS4 signature, with the clock-like signatures SBS1, SBS5, and was strongly correlated with smoking history and with age of tumor donors. Clock-like feature of the motif was also revealed in cells of human skin and brain. Given its pervasiveness, we propose that this mutational motif reflects mutagenic lesions to adenines in ssDNA from a potentially broad range of endogenous and exogenous agents.
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Affiliation(s)
- Kathleen M Hudson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Joan F Sterling
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Adam B Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Marat D Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, 34956, Turkey
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Natalie Saini
- Department of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Piotr A Mieczkowski
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
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10
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Tosto NM, Beasley ER, Wong BBM, Mank JE, Flanagan SP. The roles of sexual selection and sexual conflict in shaping patterns of genome and transcriptome variation. Nat Ecol Evol 2023; 7:981-993. [PMID: 36959239 DOI: 10.1038/s41559-023-02019-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 02/21/2023] [Indexed: 03/25/2023]
Abstract
Sexual dimorphism is one of the most prevalent, and often the most extreme, examples of phenotypic variation within species, and arises primarily from genomic variation that is shared between females and males. Many sexual dimorphisms arise through sex differences in gene expression, and sex-biased expression is one way that a single, shared genome can generate multiple, distinct phenotypes. Although many sexual dimorphisms are expected to result from sexual selection, and many studies have invoked the possible role of sexual selection to explain sex-specific traits, the role of sexual selection in the evolution of sexually dimorphic gene expression remains difficult to differentiate from other forms of sex-specific selection. In this Review, we propose a holistic framework for the study of sex-specific selection and transcriptome evolution. We advocate for a comparative approach, across tissues, developmental stages and species, which incorporates an understanding of the molecular mechanisms, including genomic variation and structure, governing gene expression. Such an approach is expected to yield substantial insights into the evolution of genetic variation and have important applications in a variety of fields, including ecology, evolution and behaviour.
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Affiliation(s)
- Nicole M Tosto
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Emily R Beasley
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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11
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Cano AV, Gitschlag BL, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. Mutation bias and the predictability of evolution. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220055. [PMID: 37004719 PMCID: PMC10067271 DOI: 10.1098/rstb.2022.0055] [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: 11/01/2022] [Accepted: 02/16/2023] [Indexed: 04/04/2023] Open
Abstract
Predicting evolutionary outcomes is an important research goal in a diversity of contexts. The focus of evolutionary forecasting is usually on adaptive processes, and efforts to improve prediction typically focus on selection. However, adaptive processes often rely on new mutations, which can be strongly influenced by predictable biases in mutation. Here, we provide an overview of existing theory and evidence for such mutation-biased adaptation and consider the implications of these results for the problem of prediction, in regard to topics such as the evolution of infectious diseases, resistance to biochemical agents, as well as cancer and other kinds of somatic evolution. We argue that empirical knowledge of mutational biases is likely to improve in the near future, and that this knowledge is readily applicable to the challenges of short-term prediction. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Alejandro V. Cano
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bryan L. Gitschlag
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Hana Rozhoňová
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Arlin Stoltzfus
- Office of Data and Informatics, Material Measurement Laboratory, National Institute of Standards and Technology, Rockville, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - David M. McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joshua L. Payne
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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12
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Goyal S, Singh K, Uppal A, Vanita V. A nonsense mutation in C8orf37 linked with retinitis pigmentosa, early macular degeneration, cataract, and myopia in an arRP family from North India. BMC Ophthalmol 2023; 23:210. [PMID: 37170250 PMCID: PMC10173570 DOI: 10.1186/s12886-023-02936-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
OBJECTIVE This study aimed at identifying the underlying genetic defect in a consanguineous autosomal recessive retinitis pigmentosa (arRP) (RP-1175) family having RP with early macular degeneration, cataract, and myopia. METHODS Whole-exome sequencing (WES) was performed on the DNA of the proband, and variants observed were validated in the rest of the affected and unaffected family members by Sanger sequencing. Different bioinformatics tools were applied to access the pathogenicity of the observed variant. RESULTS A nonsense mutation i.e., c.555G > A (p.Trp185Ter) in C8orf37 in homozygous form, has been identified that segregated with the disease in the affected members. c.555G > A was absent in unaffected family members and in 107 ethnically matched controls, therefore ruling out its possibility of being a polymorphism. CONCLUSIONS Present study identifies a nonsense mutation (c.555G > A) at codon 185 in C8orf37 linked with arRP, early macular degeneration, posterior subcapsular cataract, and myopia. The identical mutation has previously been reported in a Pakistani family with isolated RP and in a Chinese family with RP and macular degeneration. This variable expressivity of the identified mutation c.555G > A in C8orf37 in the analyzed Indian family may be attributed to the presence of the modifier alleles. Also, Trp185 might be a mutation hotspot in Asian arRP patients and in the future, p.Trp185Ter in C8orf37 may be tested during initial screening in arRP cases especially belonging to a similar population.
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Affiliation(s)
- Shiwali Goyal
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Kabir Singh
- Dr. Daljit Singh Eye Hospital, Amritsar, Punjab, India
| | - Aashna Uppal
- Dr. Daljit Singh Eye Hospital, Amritsar, Punjab, India
| | - Vanita Vanita
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India.
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13
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Ostroverkhova D, Przytycka TM, Panchenko AR. Cancer driver mutations: predictions and reality. Trends Mol Med 2023:S1471-4914(23)00067-9. [PMID: 37076339 DOI: 10.1016/j.molmed.2023.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Cancer cells accumulate many genetic alterations throughout their lifetime, but only a few of them drive cancer progression, termed driver mutations. Driver mutations may vary between cancer types and patients, can remain latent for a long time and become drivers at particular cancer stages, or may drive oncogenesis only in conjunction with other mutations. The high mutational, biochemical, and histological tumor heterogeneity makes driver mutation identification very challenging. In this review we summarize recent efforts to identify driver mutations in cancer and annotate their effects. We underline the success of computational methods to predict driver mutations in finding novel cancer biomarkers, including in circulating tumor DNA (ctDNA). We also report on the boundaries of their applicability in clinical research.
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Affiliation(s)
- Daria Ostroverkhova
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Teresa M Przytycka
- National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada; Department of Biology and Molecular Sciences, Queen's University, Kingston, ON, Canada; School of Computing, Queen's University, Kingston, ON, Canada; Ontario Institute of Cancer Research, Toronto, ON, Canada.
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14
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Marques AC, Ferraro-Peyret C, Michaud F, Song L, Smith E, Fabre G, Willig A, Wong MML, Xing X, Chong C, Brayer M, Fenouil T, Hervieu V, Bancel B, Devouassoux M, Balme B, Meyronet D, Menu P, Lopez J, Xu Z. Improved NGS-based detection of microsatellite instability using tumor-only data. Front Oncol 2022; 12:969238. [PMID: 36465367 PMCID: PMC9714634 DOI: 10.3389/fonc.2022.969238] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/18/2022] [Indexed: 01/09/2024] Open
Abstract
Microsatellite instability (MSI) is a molecular signature of mismatch repair deficiency (dMMR), a predictive marker of immune checkpoint inhibitor therapy response. Despite its recognized pan-cancer value, most methods only support detection of this signature in colorectal cancer. In addition to the tissue-specific differences that impact the sensitivity of MSI detection in other tissues, the performance of most methods is also affected by patient ethnicity, tumor content, and other sample-specific properties. These limitations are particularly important when only tumor samples are available and restrict the performance and adoption of MSI testing. Here we introduce MSIdetect, a novel solution for NGS-based MSI detection. MSIdetect models the impact of indel burden and tumor content on read coverage at a set of homopolymer regions that we found are minimally impacted by sample-specific factors. We validated MSIdetect in 139 Formalin-Fixed Paraffin-Embedded (FFPE) clinical samples from colorectal and endometrial cancer as well as other more challenging tumor types, such as glioma or sebaceous adenoma or carcinoma. Based on analysis of these samples, MSIdetect displays 100% specificity and 96.3% sensitivity. Limit of detection analysis supports that MSIdetect is sensitive even in samples with relatively low tumor content and limited microsatellite instability. Finally, the results obtained using MSIdetect in tumor-only data correlate well (R=0.988) with what is obtained using tumor-normal matched pairs, demonstrating that the solution addresses the challenges posed by MSI detection from tumor-only data. The accuracy of MSI detection by MSIdetect in different cancer types coupled with the flexibility afforded by NGS-based testing will support the adoption of MSI testing in the clinical setting and increase the number of patients identified that are likely to benefit from immune checkpoint inhibitor therapy.
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Affiliation(s)
| | - Carole Ferraro-Peyret
- Cancer Research Centre of Lyon, INSERM 1052, Centre National de la Recherche Scientifique (CNRS) 5286, University of Lyon, Lyon, France
- Hospices Civils de Lyon, Biopathology of Tumours, GH Est (GHE) Hospital, Bron, France
| | | | - Lin Song
- SOPHiA GENETICS, Saint-Sulpice, Switzerland
| | - Ewan Smith
- SOPHiA GENETICS, Saint-Sulpice, Switzerland
| | | | | | | | | | | | | | - Tanguy Fenouil
- Hospices Civils de Lyon, Biopathology of Tumours, GH Est (GHE) Hospital, Bron, France
| | - Valérie Hervieu
- Hospices Civils de Lyon, Biopathology of Tumours, GH Est (GHE) Hospital, Bron, France
| | - Brigitte Bancel
- Hospices Civils de Lyon, Biopathology of Tumours, GH Est (GHE) Hospital, Bron, France
| | - Mojgan Devouassoux
- Hospices Civils de Lyon, Department of Anatomopathology, Lyon-Sud Hospital, Lyon, France
| | - Brigitte Balme
- Hospices Civils de Lyon, Department of Anatomopathology, Lyon-Sud Hospital, Lyon, France
| | - David Meyronet
- Hospices Civils de Lyon, Biopathology of Tumours, GH Est (GHE) Hospital, Bron, France
| | | | - Jonathan Lopez
- Cancer Research Centre of Lyon, INSERM 1052, Centre National de la Recherche Scientifique (CNRS) 5286, University of Lyon, Lyon, France
- Hospices Civils de Lyon, Biochemistry and Molecular Biology Department, Lyon-Sud Hospital, Lyon, France
| | - Zhenyu Xu
- SOPHiA GENETICS, Saint-Sulpice, Switzerland
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15
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Naumenko NV, Petruseva IO, Lavrik OI. Bulky Adducts in Clustered DNA Lesions: Causes of Resistance to the NER System. Acta Naturae 2022; 14:38-49. [PMID: 36694906 PMCID: PMC9844087 DOI: 10.32607/actanaturae.11741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/18/2022] [Indexed: 01/22/2023] Open
Abstract
The nucleotide excision repair (NER) system removes a wide range of bulky DNA lesions that cause significant distortions of the regular double helix structure. These lesions, mainly bulky covalent DNA adducts, are induced by ultraviolet and ionizing radiation or the interaction between exogenous/endogenous chemically active substances and nitrogenous DNA bases. As the number of DNA lesions increases, e.g., due to intensive chemotherapy and combination therapy of various diseases or DNA repair impairment, clustered lesions containing bulky adducts may occur. Clustered lesions are two or more lesions located within one or two turns of the DNA helix. Despite the fact that repair of single DNA lesions by the NER system in eukaryotic cells has been studied quite thoroughly, the repair mechanism of these lesions in clusters remains obscure. Identification of the structural features of the DNA regions containing irreparable clustered lesions is of considerable interest, in particular due to a relationship between the efficiency of some antitumor drugs and the activity of cellular repair systems. In this review, we analyzed data on the induction of clustered lesions containing bulky adducts, the potential biological significance of these lesions, and methods for quantification of DNA lesions and considered the causes for the inhibition of NER-catalyzed excision of clustered bulky lesions.
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Affiliation(s)
- N. V. Naumenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - I. O. Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - O. I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
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16
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Thapa MJ, Fabros RM, Alasmar S, Chan K. Analyses of mutational patterns induced by formaldehyde and acetaldehyde reveal similarity to a common mutational signature. G3 GENES|GENOMES|GENETICS 2022; 12:6694047. [PMID: 36073936 PMCID: PMC9635668 DOI: 10.1093/g3journal/jkac238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/22/2022] [Indexed: 12/23/2022]
Abstract
Formaldehyde and acetaldehyde are reactive small molecules produced endogenously in cells as well as being environmental contaminants. Both of these small aldehydes are classified as human carcinogens, since they are known to damage DNA and exposure is linked to cancer incidence. However, the mutagenic properties of formaldehyde and acetaldehyde remain incompletely understood, at least in part because they are relatively weak mutagens. Here, we use a highly sensitive yeast genetic reporter system featuring controlled generation of long single-stranded DNA regions to show that both small aldehydes induced mutational patterns characterized by predominantly C/G → A/T, C/G → T/A, and T/A → C/G substitutions, each in similar proportions. We observed an excess of C/G → A/T transversions when compared to mock-treated controls. Many of these C/G → A/T transversions occurred at TC/GA motifs. Interestingly, the formaldehyde mutational pattern resembles single base substitution signature 40 from the Catalog of Somatic Mutations in Cancer. Single base substitution signature 40 is a mutational signature of unknown etiology. We also noted that acetaldehyde treatment caused an excess of deletion events longer than 4 bases while formaldehyde did not. This latter result could be another distinguishing feature between the mutational patterns of these simple aldehydes. These findings shed new light on the characteristics of 2 important, commonly occurring mutagens.
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Affiliation(s)
- Mahanish J Thapa
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa , Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa , Ottawa, ON K1H 8M5, Canada
| | - Reena M Fabros
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa , Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa , Ottawa, ON K1H 8M5, Canada
| | - Salma Alasmar
- Biopharmaceutical Sciences Undergraduate Program, University of Ottawa , Ottawa, ON K1N 6N5, Canada
| | - Kin Chan
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa , Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa , Ottawa, ON K1H 8M5, Canada
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17
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Effect of Silver Nanoparticles on the In Vitro Regeneration, Biochemical, Genetic, and Phenotype Variation in Adventitious Shoots Produced from Leaf Explants in Chrysanthemum. Int J Mol Sci 2022; 23:ijms23137406. [PMID: 35806413 PMCID: PMC9266331 DOI: 10.3390/ijms23137406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
Novel and unique properties of nanomaterials, which are not apparent in larger-size forms of the same material, encourage the undertaking of studies exploring the multifaced effects of nanomaterials on plants. The results of such studies are not only scientifically relevant but, additionally, can be implemented to plant production and/or breeding. This study aimed to verify the applicability of silver nanoparticles (AgNPs) as a mutagen in chrysanthemum breeding. Chrysanthemum × grandiflorum (Ramat.) Kitam. ‘Lilac Wonder’ and ‘Richmond’ leaf explants were cultured on the modified MS medium supplemented with 0.6 mg·L−1 6-benzylaminopurine (BAP) and 2 mg·L−1 indole-3-acetic acid (IAA) and treated with AgNPs (spherical; 20 nm in diameter size; 0, 50, and 100 mg·L−1). AgNPs strongly suppressed the capability of leaf explants to form adventitious shoots and the efficiency of shoot regeneration. The content of primary and secondary metabolites (chlorophyll a, chlorophyll b, total chlorophylls, carotenoids, anthocyanins, phenolic compounds) and the activity of enzymatic antioxidants (superoxide dismutase and guaiacol peroxide) in leaf explants varied depending on the AgNPs treatment and age of culture. Phenotype variations of ex vitro cultivated chrysanthemums, covering the color and pigment content in the inflorescence, were detected in one 50 mg·L−1 AgNPs-derived and five 100 mg·L−1 AgNPs-derived ‘Lilac Wonder’ plants and were manifested as the color change from pink to burgundy-gold. However, no changes in inflorescence color/shape were found among AgNPs-treated ‘Richmond’ chrysanthemums. On the other hand, the stem height, number of leaves, and chlorophyll content in leaves varied depending on the AgNPs treatment and the cultivar analyzed. A significant effect of AgNPs on the genetic variation occurrence was found. A nearly two-fold higher share of polymorphic products, in both cultivars studied, was generated by RAPD markers than by SCoTs. To conclude, protocols using leaf explant treatment with AgNPs can be used as a novel breeding technique in chrysanthemum. However, the individual cultivars may differ in biochemical response, the efficiency of in vitro regeneration, genetic variation, and frequency of induced mutations in flowering plants.
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18
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Sebesta J, Xiong W, Guarnieri MT, Yu J. Biocontainment of Genetically Engineered Algae. FRONTIERS IN PLANT SCIENCE 2022; 13:839446. [PMID: 35310623 PMCID: PMC8924478 DOI: 10.3389/fpls.2022.839446] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Algae (including eukaryotic microalgae and cyanobacteria) have been genetically engineered to convert light and carbon dioxide to many industrially and commercially relevant chemicals including biofuels, materials, and nutritional products. At industrial scale, genetically engineered algae may be cultivated outdoors in open ponds or in closed photobioreactors. In either case, industry would need to address a potential risk of the release of the engineered algae into the natural environment, resulting in potential negative impacts to the environment. Genetic biocontainment strategies are therefore under development to reduce the probability that these engineered bacteria can survive outside of the laboratory or industrial setting. These include active strategies that aim to kill the escaped cells by expression of toxic proteins, and passive strategies that use knockouts of native genes to reduce fitness outside of the controlled environment of labs and industrial cultivation systems. Several biocontainment strategies have demonstrated escape frequencies below detection limits. However, they have typically done so in carefully controlled experiments which may fail to capture mechanisms of escape that may arise in the more complex natural environment. The selection of biocontainment strategies that can effectively kill cells outside the lab, while maintaining maximum productivity inside the lab and without the need for relatively expensive chemicals will benefit from further attention.
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19
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Raven SA, Payne B, Bruce M, Filipovska A, Rackham O. In silico evolution of nucleic acid-binding proteins from a nonfunctional scaffold. Nat Chem Biol 2022; 18:403-411. [PMID: 35210620 DOI: 10.1038/s41589-022-00967-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 01/04/2022] [Indexed: 11/09/2022]
Abstract
Directed evolution emulates the process of natural selection to produce proteins with improved or altered functions. These approaches have proven to be very powerful but are technically challenging and particularly time and resource intensive. To bypass these limitations, we constructed a system to perform the entire process of directed evolution in silico. We employed iterative computational cycles of mutation and evaluation to predict mutations that confer high-affinity binding activities for DNA and RNA to an initial de novo designed protein with no inherent function. Beneficial mutations revealed modes of nucleic acid recognition not previously observed in natural proteins, highlighting the ability of computational directed evolution to access new molecular functions. Furthermore, the process by which new functions were obtained closely resembles natural evolution and can provide insights into the contributions of mutation rate, population size and selective pressure on functionalization of macromolecules in nature.
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Affiliation(s)
- Samuel A Raven
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia.,University of Western Australia Centre for Medical Research, Nedlands, Western Australia, Australia
| | - Blake Payne
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia.,University of Western Australia Centre for Medical Research, Nedlands, Western Australia, Australia
| | - Mitchell Bruce
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia.,University of Western Australia Centre for Medical Research, Nedlands, Western Australia, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia.,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia. .,Curtin Medical School, Curtin University, Bentley, Western Australia, Australia. .,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, Western Australia, Australia. .,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, Australia.
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20
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Abstract
Data from a long time evolution experiment with Escherichia Coli and from a large study on copy number variations in subjects with European ancestry are analyzed in order to argue that mutations can be described as Levy flights in the mutation space. These Levy flights have at least two components: random single-base substitutions and large DNA rearrangements. From the data, we get estimations for the time rates of both events and the size distribution function of large rearrangements.
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Affiliation(s)
- Dario A Leon
- University of Modena & Reggio Emilia, 41125, Modena, Italy.
- Institute of Cybernetics, Mathematics and Physics, 10400, Havana, Cuba.
| | - Augusto Gonzalez
- Institute of Cybernetics, Mathematics and Physics, 10400, Havana, Cuba
- University of Electronic Science and Technology, Chengdu, 610051, People's Republic of China
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21
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Chung SS, Ng JCF, Laddach A, Thomas NSB, Fraternali F. Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks. NAR Genom Bioinform 2021; 3:lqab010. [PMID: 33709075 PMCID: PMC7936661 DOI: 10.1093/nargab/lqab010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/19/2020] [Accepted: 01/26/2021] [Indexed: 11/13/2022] Open
Abstract
Direct drug targeting of mutated proteins in cancer is not always possible and efficacy can be nullified by compensating protein-protein interactions (PPIs). Here, we establish an in silico pipeline to identify specific PPI sub-networks containing mutated proteins as potential targets, which we apply to mutation data of four different leukaemias. Our method is based on extracting cyclic interactions of a small number of proteins topologically and functionally linked in the Protein-Protein Interaction Network (PPIN), which we call short loop network motifs (SLM). We uncover a new property of PPINs named 'short loop commonality' to measure indirect PPIs occurring via common SLM interactions. This detects 'modules' of PPI networks enriched with annotated biological functions of proteins containing mutation hotspots, exemplified by FLT3 and other receptor tyrosine kinase proteins. We further identify functional dependency or mutual exclusivity of short loop commonality pairs in large-scale cellular CRISPR-Cas9 knockout screening data. Our pipeline provides a new strategy for identifying new therapeutic targets for drug discovery.
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Affiliation(s)
- Sun Sook Chung
- Department of Haematological Medicine, King's College London, London, SE5 9NU, UK
| | - Joseph C F Ng
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
| | - Anna Laddach
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
| | - N Shaun B Thomas
- Department of Haematological Medicine, King's College London, London, SE5 9NU, UK
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
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22
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Bányai L, Trexler M, Kerekes K, Csuka O, Patthy L. Use of signals of positive and negative selection to distinguish cancer genes and passenger genes. eLife 2021; 10:e59629. [PMID: 33427197 PMCID: PMC7877913 DOI: 10.7554/elife.59629] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/10/2021] [Indexed: 12/14/2022] Open
Abstract
A major goal of cancer genomics is to identify all genes that play critical roles in carcinogenesis. Most approaches focused on genes positively selected for mutations that drive carcinogenesis and neglected the role of negative selection. Some studies have actually concluded that negative selection has no role in cancer evolution. We have re-examined the role of negative selection in tumor evolution through the analysis of the patterns of somatic mutations affecting the coding sequences of human genes. Our analyses have confirmed that tumor suppressor genes are positively selected for inactivating mutations, oncogenes, however, were found to display signals of both negative selection for inactivating mutations and positive selection for activating mutations. Significantly, we have identified numerous human genes that show signs of strong negative selection during tumor evolution, suggesting that their functional integrity is essential for the growth and survival of tumor cells.
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Affiliation(s)
- László Bányai
- Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Maria Trexler
- Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Krisztina Kerekes
- Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Orsolya Csuka
- Department of Pathogenetics, National Institute of OncologyBudapestHungary
| | - László Patthy
- Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
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23
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Unravelling roles of error-prone DNA polymerases in shaping cancer genomes. Oncogene 2021; 40:6549-6565. [PMID: 34663880 PMCID: PMC8639439 DOI: 10.1038/s41388-021-02032-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/01/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
Mutagenesis is a key hallmark and enabling characteristic of cancer cells, yet the diverse underlying mutagenic mechanisms that shape cancer genomes are not understood. This review will consider the emerging challenge of determining how DNA damage response pathways-both tolerance and repair-act upon specific forms of DNA damage to generate mutations characteristic of tumors. DNA polymerases are typically the ultimate mutagenic effectors of DNA repair pathways. Therefore, understanding the contributions of DNA polymerases is critical to develop a more comprehensive picture of mutagenic mechanisms in tumors. Selection of an appropriate DNA polymerase-whether error-free or error-prone-for a particular DNA template is critical to the maintenance of genome stability. We review different modes of DNA polymerase dysregulation including mutation, polymorphism, and over-expression of the polymerases themselves or their associated activators. Based upon recent findings connecting DNA polymerases with specific mechanisms of mutagenesis, we propose that compensation for DNA repair defects by error-prone polymerases may be a general paradigm molding the mutational landscape of cancer cells. Notably, we demonstrate that correlation of error-prone polymerase expression with mutation burden in a subset of patient tumors from The Cancer Genome Atlas can identify mechanistic hypotheses for further testing. We contrast experimental approaches from broad, genome-wide strategies to approaches with a narrower focus on a few hundred base pairs of DNA. In addition, we consider recent developments in computational annotation of patient tumor data to identify patterns of mutagenesis. Finally, we discuss the innovations and future experiments that will develop a more comprehensive portrait of mutagenic mechanisms in human tumors.
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24
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Chen S, He X, Li R, Duan X, Niu B. HotSpot3D web server: an integrated resource for mutation analysis in protein 3D structures. Bioinformatics 2020; 36:3944-3946. [PMID: 32315389 DOI: 10.1093/bioinformatics/btaa258] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/25/2020] [Accepted: 04/15/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION HotSpot3D is a widely used software for identifying mutation hotspots on the 3D structures of proteins. To further assist users, we developed a new HotSpot3D web server to make this software more versatile, convenient and interactive. RESULTS The HotSpot3D web server performs data pre-processing, clustering, visualization and log-viewing on one stop. Users can interactively explore each cluster and easily re-visualize the mutational clusters within browsers. We also provide a database that allows users to search and visualize proximal mutations from 33 cancers in the Cancer Genome Atlas. AVAILABILITY AND IMPLEMENTATION http://niulab.scgrid.cn/HotSpot3D/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Shanyu Chen
- Computer Network Information Center, Chinese Academy of Sciences.,University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyu He
- Computer Network Information Center, Chinese Academy of Sciences.,University of Chinese Academy of Sciences, Beijing 100190, China
| | - Ruilin Li
- Computer Network Information Center, Chinese Academy of Sciences
| | - Xiaohong Duan
- ChosenMed Technology (Beijing) Co. Ltd, Beijing 100176, China
| | - Beifang Niu
- Computer Network Information Center, Chinese Academy of Sciences.,University of Chinese Academy of Sciences, Beijing 100190, China.,ChosenMed Technology (Beijing) Co. Ltd, Beijing 100176, China
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25
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Ghorbani A, Samarfard S, Ramezani A, Izadpanah K, Afsharifar A, Eskandari MH, Karbanowicz TP, Peters JR. Quasi-species nature and differential gene expression of severe acute respiratory syndrome coronavirus 2 and phylogenetic analysis of a novel Iranian strain. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104556. [PMID: 32937193 PMCID: PMC7487081 DOI: 10.1016/j.meegid.2020.104556] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/30/2020] [Accepted: 09/09/2020] [Indexed: 01/06/2023]
Abstract
A novel coronavirus related to severe acute respiratory syndrome virus, (SARS-CoV-2) is the causal agent of the COVID-19 pandemic. Despite the genetic mutations across the SARS-CoV-2 genome being recently investigated, its transcriptomic genetic polymorphisms at inter-host level and the viral gene expression level based on each Open Reading Frame (ORF) remains unclear. Using available High Throughput Sequencing (HTS) data and based on SARS-CoV-2 infected human transcriptomic data, this study presents a high-resolution map of SARS-CoV-2 single nucleotide polymorphism (SNP) hotspots in a viral population at inter-host level. Four throat swab samples from COVID-19 infected patients were pooled, with RNA-Seq read retrieved from SRA NCBI to detect 21 SNPs and a replacement across the SARS-CoV-2 genomic population. Twenty-two RNA modification sites on viral transcripts were identified that may cause inter-host genetic diversity of this virus. In addition, the canonical genomic RNAs of N ORF showed higher expression in transcriptomic data and reverse transcriptase quantitative PCR compared to other SARS-CoV-2 ORFs, indicating the importance of this ORF in virus replication or other major functions in virus cycle. Phylogenetic and ancestral sequence analyses based on the entire genome revealed that SARS-CoV-2 is possibly derived from a recombination event between SARS-CoV and Bat SARS-like CoV. Ancestor analysis of the isolates from different locations including Iran suggest shared Chinese ancestry. These results propose the importance of potential inter-host level genetic variations to the evolution of SARS-COV-2, and the formation of viral quasi-species. The RNA modifications discovered in this study may cause amino acid sequence changes in polyprotein, spike protein, product of ORF8 and nucleocapsid (N) protein, suggesting further insights to understanding the functional impacts of mutations in the life cycle and pathogenicity of SARS-CoV-2.
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Affiliation(s)
- Abozar Ghorbani
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Samira Samarfard
- Queensland Biosciences Precinct, The University of Queensland, St Lucia 4072, Queensland, Australia.
| | - Amin Ramezani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Alireza Afsharifar
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Mohammad Hadi Eskandari
- Department of Food Science and Technology, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Thomas P. Karbanowicz
- Queensland Biosciences Precinct, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Jonathan R. Peters
- Queensland Biosciences Precinct, The University of Queensland, St Lucia 4072, Queensland, Australia
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26
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Ding Y, Xue H, Ding X, Zhao Y, Zhao Z, Wang D, Wu J. On the complexity measures of mutation hotspots in human TP53 protein. CHAOS (WOODBURY, N.Y.) 2020; 30:073118. [PMID: 32752620 DOI: 10.1063/1.5143584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
The role of sequence complexity in 23 051 somatic missense mutations including 73 well-known mutation hotspots across 22 major cancers was studied in human TP53 proteins. A role for sequence complexity in TP53 protein mutations is suggested since (i) the mutation rate significantly increases in low amino acid pair bias complexity; (ii) probability distribution complexity increases following single point substitution mutations and strikingly increases after mutation at the mutation hotspots including six detectable hotspot mutations (R175, G245, R248, R249, R273, and R282); and (iii) the degree of increase in distribution complexity is significantly correlated with the frequency of missense mutations (r = -0.5758, P < 0.0001) across 20 major types of solid tumors. These results are consistent with the hypothesis that amino acid pair bias and distribution probability may be used as novel measures for protein sequence complexity, and the degree of complexity is related to its susceptibility to mutation, as such, it may be used as a predictor for modeling protein mutations in human cancers.
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Affiliation(s)
- Yan Ding
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hongsheng Xue
- Institute for Translational Medicine, The Affiliated Zhongshan Hospital of Dalian University, Dalian 116001, China
| | - Xinjia Ding
- Department of Urology, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China
| | - Yuqing Zhao
- Department of Urology, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China
| | - Zhilong Zhao
- Institute for Translational Medicine, The Affiliated Zhongshan Hospital of Dalian University, Dalian 116001, China
| | - Dazhi Wang
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jianlin Wu
- Institute for Translational Medicine, The Affiliated Zhongshan Hospital of Dalian University, Dalian 116001, China
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27
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Kim P, Li H, Wang J, Zhao Z. Landscape of drug-resistance mutations in kinase regulatory hotspots. Brief Bioinform 2020; 22:5854404. [PMID: 32510566 DOI: 10.1093/bib/bbaa108] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/23/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
More than 48 kinase inhibitors (KIs) have been approved by Food and Drug Administration. However, drug-resistance (DR) eventually occurs, and secondary mutations have been found in the previously targeted primary-mutated cancer cells. Cancer and drug research communities recognize the importance of the kinase domain (KD) mutations for kinasopathies. So far, a systematic investigation of kinase mutations on DR hotspots has not been done yet. In this study, we systematically investigated four types of representative mutation hotspots (gatekeeper, G-loop, αC-helix and A-loop) associated with DR in 538 human protein kinases using large-scale cancer data sets (TCGA, ICGC, COSMIC and GDSC). Our results revealed 358 kinases harboring 3318 mutations that covered 702 drug resistance hotspot residues. Among them, 197 kinases had multiple genetic variants on each residue. We further computationally assessed and validated the epidermal growth factor receptor mutations on protein structure and drug-binding efficacy. This is the first study to provide a landscape view of DR-associated mutation hotspots in kinase's secondary structures, and its knowledge will help the development of effective next-generation KIs for better precision medicine.
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28
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Kulus D. Shoot Tip Cryopreservation of Lamprocapnos spectabilis (L.) Fukuhara Using Different Approaches and Evaluation of Stability on the Molecular, Biochemical, and Plant Architecture Levels. Int J Mol Sci 2020; 21:E3901. [PMID: 32486149 PMCID: PMC7311993 DOI: 10.3390/ijms21113901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/22/2020] [Accepted: 05/29/2020] [Indexed: 01/22/2023] Open
Abstract
The aim of this study is to optimize and evaluate the effectiveness of vitrification, droplet-vitrification, and encapsulation-vitrification techniques in the cryopreservation of Lamprocapnos spectabilis (L.) Fukuhara 'Gold Heart', a popular medicinal and ornamental plant species. In vitro-derived shoot tips were used in the experiments. All three techniques were based on explant dehydration with plant vitrification solution 3 (PVS3; 50% glycerol and 50% sucrose) for 0, 30, 60, 90, 120, 150, or 180 min. The recovered microshoots were subjected to morphometric, biochemical, and molecular analyses (RAPD, ISSR, SCoT). The highest recovery level was reported with the encapsulation-vitrification protocol based on 150 min dehydration (73.1%), while the vitrification technique was the least effective (maximum 25.8% recovery). Explants cryopreserved with the encapsulation-vitrification technique produced the highest mean number of shoots (4.9); moreover, this technique was optimal in terms of rooting efficiency. The highest fresh weight of shoots, on the other hand, was found with the vitrification protocol based on a 30-min PVS3 treatment. The concentrations of chlorophyll a and b were lower in all cryopreservation-derived plants, compared to the untreated control. On the other hand, short dehydration and cryopreservation of non-encapsulated explants stimulated the synthesis of anthocyanins. A small genetic variation in 5% of all samples analyzed was detected by RAPD and ISSR marker systems. Only plants recovered from the encapsulation-vitrification protocol had no DNA sequence alternations.
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Affiliation(s)
- Dariusz Kulus
- Laboratory of Ornamental Plants and Vegetable Crops, Faculty of Agriculture and Biotechnology, UTP University of Science and Technology in Bydgoszcz, Bernardyńska 6, 85-029 Bydgoszcz, Poland
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29
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Kader F, Ghai M, Olaniran AO. Characterization of DNA methylation-based markers for human body fluid identification in forensics: a critical review. Int J Legal Med 2019; 134:1-20. [PMID: 31713682 DOI: 10.1007/s00414-019-02181-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023]
Abstract
Body fluid identification in crime scene investigations aids in reconstruction of crime scenes. Several studies have identified and reported differentially methylated sites (DMSs) and regions (DMRs) which differ between forensically relevant tissues (tDMRs) and body fluids. Diverse factors affect methylation patterns such as the environment, diets, lifestyle, disease, ethnicity, genetic variation, amongst others. Thus, it is important to analyse the stability of markers employed for forensic identification. Furthermore, even though epigenetic modifications are described as stable and heritable, epigenetic inheritance of potential markers for body fluid identification needs to be assessed in the long term. Here, we discuss the current status of reported DNA methylation-based markers and their verification studies. Such thorough investigation is crucial to develop a stable panel of DNA methylation-based markers for accurate body fluid identification.
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Affiliation(s)
- Farzeen Kader
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, Republic of South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, Republic of South Africa.
| | - Ademola O Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, Republic of South Africa
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30
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Basak M, Uzun B, Yol E. Genetic diversity and population structure of the Mediterranean sesame core collection with use of genome-wide SNPs developed by double digest RAD-Seq. PLoS One 2019; 14:e0223757. [PMID: 31600316 PMCID: PMC6786593 DOI: 10.1371/journal.pone.0223757] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/27/2019] [Indexed: 12/15/2022] Open
Abstract
The Mediterranean sesame core collection contains agro-morphologically superior sesame accessions from geographically diverse regions in four continents. In the present investigation, the genetic diversity and population structure of this collection was analyzed with 5292 high-quality SNPs discovered by double-digest restriction site associated DNA (ddRAD) sequencing, a cost-effective and flexible next-generation sequencing method. The genetic distance between pairs of accessions varied from 0.023 to 0.524. The gene diversity was higher in accessions from Asia than from America, Africa, and Europe. The highest genetic differentiation was observed between accessions collected from America and Europe. Structure analysis showed the presence of three subpopulations among the sesame accessions, and only six accessions were placed in an admixture group. Phylogenetic tree and principal coordinate analysis clustered the accessions based on their countries of origin. However, no clear division was evident among the sesame accessions with regard to their continental locations. This result was supported by an AMOVA analysis, which revealed a genetic variation among continental groups of 5.53% of the total variation. The large number of SNPs clearly indicated that the Mediterranean sesame core collection is a highly diverse genetic resource. The collection can be exploited by breeders to select appropriate accessions that will provide high genetic gain in sesame improvement programs. The high-quality SNP data generated here should also be used in genome-wide association studies to explore qualitative trait loci and SNPs related to economically and agronomically important traits in sesame.
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Affiliation(s)
- Merve Basak
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Bulent Uzun
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Engin Yol
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
- * E-mail:
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31
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de Paz AM, Cybulski TR, Marblestone AH, Zamft BM, Church GM, Boyden ES, Kording KP, Tyo KEJ. High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing. Nucleic Acids Res 2019; 46:e78. [PMID: 29718339 PMCID: PMC6061839 DOI: 10.1093/nar/gky296] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 04/12/2018] [Indexed: 02/06/2023] Open
Abstract
DNA polymerase fidelity is affected by both intrinsic properties and environmental conditions. Current strategies for measuring DNA polymerase error rate in vitro are constrained by low error subtype sensitivity, poor scalability, and lack of flexibility in types of sequence contexts that can be tested. We have developed the Magnification via Nucleotide Imbalance Fidelity (MagNIFi) assay, a scalable next-generation sequencing assay that uses a biased deoxynucleotide pool to quantitatively shift error rates into a range where errors are frequent and hence measurement is robust, while still allowing for accurate mapping to error rates under typical conditions. This assay is compatible with a wide range of fidelity-modulating conditions, and enables high-throughput analysis of sequence context effects on base substitution and single nucleotide deletion fidelity using a built-in template library. We validate this assay by comparing to previously established fidelity metrics, and use it to investigate neighboring sequence-mediated effects on fidelity for several DNA polymerases. Through these demonstrations, we establish the MagNIFi assay for robust, high-throughput analysis of DNA polymerase fidelity.
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Affiliation(s)
- Alexandra M de Paz
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
| | - Thaddeus R Cybulski
- Interdepartmental Neuroscience Program, Northwestern University, Chicago, IL 60611, USA
| | - Adam H Marblestone
- Biophysics Program, Harvard University, Boston, MA 02115, USA.,Wyss Institute, Harvard University, Boston, MA 02115, USA
| | - Bradley M Zamft
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - George M Church
- Biophysics Program, Harvard University, Boston, MA 02115, USA.,Wyss Institute, Harvard University, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Konrad P Kording
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
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32
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Růžička M, Souček P, Kulhánek P, Radová L, Fajkusová L, Réblová K. Bending of DNA duplexes with mutation motifs. DNA Res 2019; 26:341-352. [PMID: 31230075 PMCID: PMC6704406 DOI: 10.1093/dnares/dsz013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/27/2019] [Indexed: 01/30/2023] Open
Abstract
Mutations can be induced by environmental factors but also arise spontaneously during DNA replication or due to deamination of methylated cytosines at CpG dinucleotides. Sites where mutations occur with higher frequency than would be expected by chance are termed hotspots while sites that contain mutations rarely are termed coldspots. Mutations are permanently scanned and repaired by repair systems. Among them, the mismatch repair targets base pair mismatches, which are discriminated from canonical base pairs by probing altered elasticity of DNA. Using biased molecular dynamics simulations, we investigated the elasticity of coldspots and hotspots motifs detected in human genes associated with inherited disorders, and also of motifs with Czech population hotspots and de novo mutations. Main attention was paid to mutations leading to G/T and A+/C pairs. We observed that hotspots without CpG/CpHpG sequences are less flexible than coldspots, which indicates that flexible sequences are more effectively repaired. In contrary, hotspots with CpG/CpHpG sequences exhibited increased flexibility as coldspots. Their mutability is more likely related to spontaneous deamination of methylated cytosines leading to C > T mutations, which are primarily targeted by base excision repair. We corroborated conclusions based on computer simulations by measuring melting curves of hotspots and coldspots containing G/T mismatch.
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Affiliation(s)
- Michal Růžička
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Přemysl Souček
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Petr Kulhánek
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Radová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lenka Fajkusová
- Centre of Molecular Biology and Gene Therapy, University Hospital Brno, Brno, Czech Republic
| | - Kamila Réblová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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33
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Rogozin IB, Pavlov YI, Goncearenco A, De S, Lada AG, Poliakov E, Panchenko AR, Cooper DN. Mutational signatures and mutable motifs in cancer genomes. Brief Bioinform 2019; 19:1085-1101. [PMID: 28498882 DOI: 10.1093/bib/bbx049] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Indexed: 12/22/2022] Open
Abstract
Cancer is a genetic disorder, meaning that a plethora of different mutations, whether somatic or germ line, underlie the etiology of the 'Emperor of Maladies'. Point mutations, chromosomal rearrangements and copy number changes, whether they have occurred spontaneously in predisposed individuals or have been induced by intrinsic or extrinsic (environmental) mutagens, lead to the activation of oncogenes and inactivation of tumor suppressor genes, thereby promoting malignancy. This scenario has now been recognized and experimentally confirmed in a wide range of different contexts. Over the past decade, a surge in available sequencing technologies has allowed the sequencing of whole genomes from liquid malignancies and solid tumors belonging to different types and stages of cancer, giving birth to the new field of cancer genomics. One of the most striking discoveries has been that cancer genomes are highly enriched with mutations of specific kinds. It has been suggested that these mutations can be classified into 'families' based on their mutational signatures. A mutational signature may be regarded as a type of base substitution (e.g. C:G to T:A) within a particular context of neighboring nucleotide sequence (the bases upstream and/or downstream of the mutation). These mutational signatures, supplemented by mutable motifs (a wider mutational context), promise to help us to understand the nature of the mutational processes that operate during tumor evolution because they represent the footprints of interactions between DNA, mutagens and the enzymes of the repair/replication/modification pathways.
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Affiliation(s)
- Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - Youri I Pavlov
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, USA
| | | | | | - Artem G Lada
- Department Microbiology and Molecular Genetics, University of California, Davis, USA
| | - Eugenia Poliakov
- Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Institutes of Health, USA
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34
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Goncearenco A, Rager SL, Li M, Sang QX, Rogozin IB, Panchenko AR. Exploring background mutational processes to decipher cancer genetic heterogeneity. Nucleic Acids Res 2019; 45:W514-W522. [PMID: 28472504 PMCID: PMC5793731 DOI: 10.1093/nar/gkx367] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/21/2017] [Indexed: 01/08/2023] Open
Abstract
Much remains unknown about the progression and heterogeneity of mutational processes in different cancers and their diagnostic and clinical potential. A growing body of evidence supports mutation rate dependence on the local DNA sequence context for various types of mutations. We propose several tools for the analysis of cancer context-dependent mutations, which are implemented in an online computational framework MutaGene. The framework explores DNA context-dependent mutational patterns and underlying somatic cancer mutagenesis, analyzes mutational profiles of cancer samples, identifies the combinations of underlying mutagenic processes including those related to infidelity of DNA replication and repair machinery, and various other endogenous and exogenous mutagenic factors. As a result, the combination of mutagenic processes can be identified in any query sample with subsequent comparison to mutational profiles derived from malignant and benign samples. In addition, mutagen or cancer-specific mutational background models are applied to calculate expected DNA and protein site mutability to decouple relative contributions of mutagenesis and selection in carcinogenesis, thus elucidating the site-specific driving events in cancer. MutaGene is freely available at https://www.ncbi.nlm.nih.gov/projects/mutagene/.
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Affiliation(s)
| | - Stephanie L Rager
- National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA.,Columbia University, School of Engineering and Applied Science, New York, NY 10027, USA
| | - Minghui Li
- National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA
| | - Qing-Xiang Sang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA
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35
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Tajik S, Badalzadeh M, Fazlollahi MR, Houshmand M, Bazargan N, Movahedi M, Mahlouji Rad M, Mahdaviani SA, Mamishi S, Khotaei GT, Mansouri D, Zandieh F, Pourpak Z. Genetic and molecular findings of 38 Iranian patients with chronic granulomatous disease caused by p47-phox defect. Scand J Immunol 2019; 90:e12767. [PMID: 30963593 DOI: 10.1111/sji.12767] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 03/25/2019] [Accepted: 03/31/2019] [Indexed: 01/16/2023]
Abstract
One of the components of NADPH oxidase is p47-phox, encoded by NCF1 gene. This study aims to find new genetic changes and clinical features in 38 Iranian patients with autosomal recessive chronic granulomatous disease (AR-CGD) caused by NCF1 gene defect. Patients who had abnormal NBT and DHR-1,2,3 assay with loss of p47-phox in Western blotting were included in this study. After recording demographic and clinical data, PCR amplification was performed followed by direct sequencing for all exons and exon-intron boundaries. The most common form of CGD in Iran was AR-CGD due to consanguinity marriages. Among patients with AR-CGD, NCF1 deficiency was found to be more common than other forms. Cutaneous involvements (53%), pulmonary infections (50%) and lymphadenopathy (29%) were more prevalent than other clinical manifestations of CGD. Mutation analysis of NCF1 gene identified five different mutations. Homozygous delta GT deletion (c.75_76delGT) was the most frequent mutation and was detected in more than 63% of families. Six families had a nonsense mutation in exon 7 (c.579G > A). Two novel mutations were found in exon 4 in two families, including a missense mutation (c.328C > T) and a nine-nucleotide deletion (c.331_339delTGTCCCCAC). Genetic detection of these mutations may result in early diagnosis and prevention of possible complications of the disease. This could be useful for timely decision-making for haematopoietic stem cell transplantation and for carrier detection as well as prenatal diagnosis of next children in the affected families. Our findings might help to predict outcomes, raise awareness and help effective treatment in these patients.
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Affiliation(s)
- Shaghayegh Tajik
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohsen Badalzadeh
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran.,Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Mohammad Reza Fazlollahi
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Massoud Houshmand
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Nasrin Bazargan
- Department of Pediatrics, Kerman University of Medical Sciences, Kerman, Iran
| | - Masoud Movahedi
- Department of Immunology and Allergy, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Mahlouji Rad
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Alireza Mahdaviani
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Setareh Mamishi
- Department of Infectious Diseases, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghamar Taj Khotaei
- Department of Infectious Diseases, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Davood Mansouri
- National Research Institute of Tuberculosis and Lung Disease, Masih Daneshvari University Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fariborz Zandieh
- Department of Asthma, Allergy and Immunology, Bahrami Children Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Pourpak
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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36
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Hashiya F, Ito S, Sugiyama H. Electron injection from mitochondrial transcription factor A to DNA associated with thymine dimer photo repair. Bioorg Med Chem 2018; 27:278-284. [PMID: 30552005 DOI: 10.1016/j.bmc.2018.11.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 01/11/2023]
Abstract
Electron transfer through π-stacked arrays of double-stranded DNA contributes to the redox chemistry of bases, including guanine oxidation and thymine-thymine dimer repair by photolyase. 5-Bromouracil is an attractive photoreactive thymine analogue that can be used to investigate electron transfer in DNA, and is a useful probe for protein-DNA interaction analysis. In the present study using BrU we found that UV irradiation facilitated electron injection from mitochondrial transcription factor A into DNA. We also observed that this electron injection could lead to repair of a thymine-thymine dimer.
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Affiliation(s)
- Fumitaka Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Shinji Ito
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
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37
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Spatial Vulnerabilities of the Escherichia coli Genome to Spontaneous Mutations Revealed with Improved Duplex Sequencing. Genetics 2018; 210:547-558. [PMID: 30076202 DOI: 10.1534/genetics.118.301345] [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: 07/10/2018] [Accepted: 07/31/2018] [Indexed: 12/20/2022] Open
Abstract
Investigation of spontaneous mutations by next-generation sequencing technology has attracted extensive attention lately due to the fundamental roles of spontaneous mutations in evolution and pathological processes. However, these studies only focused on the mutations accumulated through many generations during long-term (possibly be years of) culturing, but not the freshly generated mutations that occur at very low frequencies. In this study, we established a molecularly barcoded deep sequencing strategy to detect low abundant spontaneous mutations in genomes of bacteria cell cultures. Genome-wide spontaneous mutations in 15 Escherichia coli cell culture samples were defined with a high confidence (P < 0.01). We also developed a hotspot-calling approach based on the run-length encoding algorithm to find the genomic regions that are vulnerable to the spontaneous mutations. The hotspots for the mutations appeared to be highly conserved across the bacteria samples. Further biological annotation of these regions indicated that most of the spontaneous mutations were located at the repeat domains or nonfunctional domains of the genomes, suggesting the existence of mechanisms that could somehow prevent the occurrence of mutations in crucial genic areas. This study provides a more faithful picture of mutation occurrence and spectra in a single expansion process without long-term culturing.
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38
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Poletto E, Pasqualim G, Giugliani R, Matte U, Baldo G. Worldwide distribution of common IDUA
pathogenic variants. Clin Genet 2018; 94:95-102. [DOI: 10.1111/cge.13224] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 01/09/2018] [Accepted: 01/23/2018] [Indexed: 12/13/2022]
Affiliation(s)
- E. Poletto
- Gene Therapy Center; Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
- Postgraduate Program in Genetics and Molecular Biology; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
| | - G. Pasqualim
- Gene Therapy Center; Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
- Postgraduate Program in Genetics and Molecular Biology; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
| | - R. Giugliani
- Gene Therapy Center; Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
- Postgraduate Program in Genetics and Molecular Biology; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
- Medical Genetics Service; Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
- Department of Genetics; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
- INAGEMP; National Institute of Population Medical Genetics; Porto Alegre Brazil
| | - U. Matte
- Gene Therapy Center; Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
- Postgraduate Program in Genetics and Molecular Biology; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
- Department of Genetics; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
| | - G. Baldo
- Gene Therapy Center; Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
- Postgraduate Program in Genetics and Molecular Biology; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
- Department of Physiology; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
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39
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Roche-Lima A, Carrasquillo-Carrión K, Gómez-Moreno R, Cruz JM, Velázquez-Morales DM, Rogozin IB, Baerga-Ortiz A. The Presence of Genotoxic and/or Pro-inflammatory Bacterial Genes in Gut Metagenomic Databases and Their Possible Link With Inflammatory Bowel Diseases. Front Genet 2018; 9:116. [PMID: 29692798 PMCID: PMC5902703 DOI: 10.3389/fgene.2018.00116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/22/2018] [Indexed: 01/19/2023] Open
Abstract
Background: The human gut microbiota is a dynamic community of microorganisms that mediate important biochemical processes. Differences in the gut microbial composition have been associated with inflammatory bowel diseases (IBD) and other intestinal disorders. In this study, we quantified and compared the frequencies of eight genotoxic and/or pro-inflammatory bacterial genes found in metagenomic Whole Genome Sequences (mWGSs) of samples from individuals with IBD vs. a cohort of healthy human subjects. Methods: The eight selected gene sequences were clbN, clbB, cif, cnf-1, usp, tcpC from Escherichia coli, gelE from Enterococcus faecalis and murB from Akkermansia muciniphila. We also included the sequences for the conserved murB genes from E. coli and E. faecalis as markers for the presence of Enterobacteriaceae or Enterococci in the samples. The gene sequences were chosen based on their previously reported ability to disrupt normal cellular processes to either promote inflammation or to cause DNA damage in cultured cells or animal models, which could be linked to a role in IBD. The selected sequences were searched in three different mWGS datasets accessed through the Human Microbiome Project (HMP): a healthy cohort (N = 251), a Crohn's disease cohort (N = 60) and an ulcerative colitis cohort (N = 17). Results: Firstly, the sequences for the murB housekeeping genes from Enterobacteriaceae and Enterococci were more frequently found in the IBD cohorts (32% E. coli in IBD vs. 12% in healthy; 13% E. faecalis in IBD vs. 3% in healthy) than in the healthy cohort, confirming earlier reports of a higher presence of both of these taxa in IBD. For some of the sequences in our study, especially usp and gelE, their frequency was even more sharply increased in the IBD cohorts than in the healthy cohort, suggesting an association with IBD that is not easily explained by the increased presence of E. coli or E. faecalis in those samples. Conclusion: Our results suggest a significant association between the presence of some of these genotoxic or pro-inflammatory gene sequences and IBDs. In addition, these results illustrate the power and limitations of the HMP database in the detection of possible clinical correlations for individual bacterial genes.
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Affiliation(s)
- Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities - RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Kelvin Carrasquillo-Carrión
- Center for Collaborative Research in Health Disparities - RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Ramón Gómez-Moreno
- Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico.,Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Juan M Cruz
- Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Dayanara M Velázquez-Morales
- Center for Collaborative Research in Health Disparities - RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Igor B Rogozin
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD, United States
| | - Abel Baerga-Ortiz
- Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico.,Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
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40
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Chan K. Molecular Genetic Characterization of Mutagenesis Using a Highly Sensitive Single-Stranded DNA Reporter System in Budding Yeast. Methods Mol Biol 2018; 1672:33-42. [PMID: 29043615 DOI: 10.1007/978-1-4939-7306-4_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mutations are permanent alterations to the coding content of DNA. They are starting material for the Darwinian evolution of species by natural selection, which has yielded an amazing diversity of life on Earth. Mutations can also be the fundamental basis of serious human maladies, most notably cancers. In this chapter, I describe a highly sensitive reporter system for the molecular genetic analysis of mutagenesis, featuring controlled generation of long stretches of single-stranded DNA in budding yeast cells. This system is ~100- to ~1000-fold more susceptible to mutation than conventional double-stranded DNA reporters, and is well suited for generating large mutational datasets to investigate the properties of mutagens.
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Affiliation(s)
- Kin Chan
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8 M5, Canada.
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41
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42
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Růžička M, Kulhánek P, Radová L, Čechová A, Špačková N, Fajkusová L, Réblová K. DNA mutation motifs in the genes associated with inherited diseases. PLoS One 2017; 12:e0182377. [PMID: 28767725 PMCID: PMC5540541 DOI: 10.1371/journal.pone.0182377] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/17/2017] [Indexed: 11/18/2022] Open
Abstract
Mutations in human genes can be responsible for inherited genetic disorders and cancer. Mutations can arise due to environmental factors or spontaneously. It has been shown that certain DNA sequences are more prone to mutate. These sites are termed hotspots and exhibit a higher mutation frequency than expected by chance. In contrast, DNA sequences with lower mutation frequencies than expected by chance are termed coldspots. Mutation hotspots are usually derived from a mutation spectrum, which reflects particular population where an effect of a common ancestor plays a role. To detect coldspots/hotspots unaffected by population bias, we analysed the presence of germline mutations obtained from HGMD database in the 5-nucleotide segments repeatedly occurring in genes associated with common inherited disorders, in particular, the PAH, LDLR, CFTR, F8, and F9 genes. Statistically significant sequences (mutational motifs) rarely associated with mutations (coldspots) and frequently associated with mutations (hotspots) exhibited characteristic sequence patterns, e.g. coldspots contained purine tract while hotspots showed alternating purine-pyrimidine bases, often with the presence of CpG dinucleotide. Using molecular dynamics simulations and free energy calculations, we analysed the global bending properties of two selected coldspots and two hotspots with a G/T mismatch. We observed that the coldspots were inherently more flexible than the hotspots. We assume that this property might be critical for effective mismatch repair as DNA with a mutation recognized by MutSα protein is noticeably bent.
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Affiliation(s)
- Michal Růžička
- CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, Czech Republic
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic
| | - Petr Kulhánek
- CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno, Czech Republic
| | - Lenka Radová
- CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, Czech Republic
| | - Andrea Čechová
- CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, Czech Republic
| | - Naďa Špačková
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic
| | - Lenka Fajkusová
- Centre of Molecular Biology and Gene Therapy, University Hospital Brno and Masaryk University, Jihlavská 20, Brno, Czech Republic
| | - Kamila Réblová
- CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, Czech Republic
- * E-mail:
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43
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Hu D, Li Y, Zhang J, Pfeiffer R, Gollob MH, Healey J, Harrell DT, Makita N, Abe H, Sun Y, Guo J, Zhang L, Yan G, Mah D, Walsh EP, Leopold HB, Giustetto C, Gaita F, Zienciuk-Krajka A, Mazzanti A, Priori SG, Antzelevitch C, Barajas-Martinez H. The Phenotypic Spectrum of a Mutation Hotspot Responsible for the Short QT Syndrome. JACC Clin Electrophysiol 2017; 3:727-743. [DOI: 10.1016/j.jacep.2016.11.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 11/18/2016] [Accepted: 11/22/2016] [Indexed: 10/20/2022]
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44
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Standley M, Allen J, Cervantes L, Lilly J, Camps M. Fluorescence-Based Reporters for Detection of Mutagenesis in E. coli. Methods Enzymol 2017. [PMID: 28645368 DOI: 10.1016/bs.mie.2017.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Mutagenesis in model organisms following exposure to chemicals is used as an indicator of genotoxicity. Mutagenesis assays are also used to study mechanisms of DNA homeostasis. This chapter focuses on detection of mutagenesis in prokaryotes, which boils down to two approaches: reporter inactivation (forward mutation assay) and reversion of an inactivating mutation (reversion mutation assay). Both methods are labor intensive, involving visual screening, quantification of colonies on solid media, or determining a Poisson distribution in liquid culture. Here, we present two reversion reporters for in vivo mutagenesis that produce a quantitative output, and thus have the potential to greatly reduce the amount of test chemical and labor involved in these assays. This output is obtained by coupling a TEM β lactamase-based reversion assay with GFP fluorescence, either by placing the two genes on the same plasmid or by fusing them translationally and interrupting the N-terminus of the chimeric ORF with a stop codon. We also describe a reporter aimed at facilitating the monitoring of continuous mutagenesis in mutator strains. This reporter couples two reversion markers, allowing the temporal separation of mutation events in time, thus providing information about the dynamics of mutagenesis in mutator strains. Here, we describe these reporter systems, provide protocols for use, and demonstrate their key functional features using error-prone Pol I mutagenesis as a source of mutations.
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Affiliation(s)
- Melissa Standley
- University of California-Santa Cruz, Santa Cruz, CA, United States
| | - Jennifer Allen
- University of California-Santa Cruz, Santa Cruz, CA, United States
| | - Layla Cervantes
- University of California-Santa Cruz, Santa Cruz, CA, United States
| | - Joshua Lilly
- University of California-Santa Cruz, Santa Cruz, CA, United States
| | - Manel Camps
- University of California-Santa Cruz, Santa Cruz, CA, United States.
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45
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Shagin DA, Shagina IA, Zaretsky AR, Barsova EV, Kelmanson IV, Lukyanov S, Chudakov DM, Shugay M. A high-throughput assay for quantitative measurement of PCR errors. Sci Rep 2017; 7:2718. [PMID: 28578414 PMCID: PMC5457411 DOI: 10.1038/s41598-017-02727-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/18/2017] [Indexed: 01/01/2023] Open
Abstract
The accuracy with which DNA polymerase can replicate a template DNA sequence is an extremely important property that can vary by an order of magnitude from one enzyme to another. The rate of nucleotide misincorporation is shaped by multiple factors, including PCR conditions and proofreading capabilities, and proper assessment of polymerase error rate is essential for a wide range of sensitive PCR-based assays. In this paper, we describe a method for studying polymerase errors with exceptional resolution, which combines unique molecular identifier tagging and high-throughput sequencing. Our protocol is less laborious than commonly-used methods, and is also scalable, robust and accurate. In a series of nine PCR assays, we have measured a range of polymerase accuracies that is in line with previous observations. However, we were also able to comprehensively describe individual errors introduced by each polymerase after either 20 PCR cycles or a linear amplification, revealing specific substitution preferences and the diversity of PCR error frequency profiles. We also demonstrate that the detected high-frequency PCR errors are highly recurrent and that the position in the template sequence and polymerase-specific substitution preferences are among the major factors influencing the observed PCR error rate.
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Affiliation(s)
- Dmitriy A Shagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Irina A Shagina
- Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Andrew R Zaretsky
- Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Ekaterina V Barsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Ilya V Kelmanson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Sergey Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia. .,Pirogov Russian National Research Medical University, Moscow, Russia. .,Skolkovo Institute of Science and Technology, Moscow, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia. .,Pirogov Russian National Research Medical University, Moscow, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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46
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Carotenoid production and phenotypic variation in Azospirillum brasilense. Res Microbiol 2017; 168:493-501. [DOI: 10.1016/j.resmic.2017.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/17/2017] [Accepted: 02/21/2017] [Indexed: 11/22/2022]
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47
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Yang J, Ruff AJ, Arlt M, Schwaneberg U. Casting epPCR (cepPCR): A simple random mutagenesis method to generate high quality mutant libraries. Biotechnol Bioeng 2017; 114:1921-1927. [DOI: 10.1002/bit.26327] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/03/2017] [Accepted: 04/23/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Jianhua Yang
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 Aachen 52074 Germany
| | - Anna J. Ruff
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 Aachen 52074 Germany
| | - Marcus Arlt
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 Aachen 52074 Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 Aachen 52074 Germany
- DWI-Leibniz Institut für Interaktive Materialien; Aachen Germany
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48
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Xochelli A, Baliakas P, Kavakiotis I, Agathangelidis A, Sutton LA, Minga E, Ntoufa S, Tausch E, Yan XJ, Shanafelt T, Plevova K, Boudjogra M, Rossi D, Davis Z, Navarro A, Sandberg Y, Vojdeman FJ, Scarfo L, Stavroyianni N, Sudarikov A, Veronese S, Tzenou T, Karan-Djurasevic T, Catherwood M, Kienle D, Chatzouli M, Facco M, Bahlo J, Pott C, Pedersen LB, Mansouri L, Smedby KE, Chu CC, Giudicelli V, Lefranc MP, Panagiotidis P, Juliusson G, Anagnostopoulos A, Vlahavas I, Antic D, Trentin L, Montillo M, Niemann C, Döhner H, Langerak AW, Pospisilova S, Hallek M, Campo E, Chiorazzi N, Maglaveras N, Oscier D, Gaidano G, Jelinek DF, Stilgenbauer S, Chouvarda I, Darzentas N, Belessi C, Davi F, Hadzidimitriou A, Rosenquist R, Ghia P, Stamatopoulos K. Chronic Lymphocytic Leukemia with Mutated IGHV4-34 Receptors: Shared and Distinct Immunogenetic Features and Clinical Outcomes. Clin Cancer Res 2017; 23:5292-5301. [PMID: 28536306 DOI: 10.1158/1078-0432.ccr-16-3100] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/11/2017] [Accepted: 05/18/2017] [Indexed: 11/16/2022]
Abstract
Purpose: We sought to investigate whether B cell receptor immunoglobulin (BcR IG) stereotypy is associated with particular clinicobiological features among chronic lymphocytic leukemia (CLL) patients expressing mutated BcR IG (M-CLL) encoded by the IGHV4-34 gene, and also ascertain whether these associations could refine prognostication.Experimental Design: In a series of 19,907 CLL cases with available immunogenetic information, we identified 339 IGHV4-34-expressing cases assigned to one of the four largest stereotyped M-CLL subsets, namely subsets #4, #16, #29 and #201, and investigated in detail their clinicobiological characteristics and disease outcomes.Results: We identified shared and subset-specific patterns of somatic hypermutation (SHM) among patients assigned to these subsets. The greatest similarity was observed between subsets #4 and #16, both including IgG-switched cases (IgG-CLL). In contrast, the least similarity was detected between subsets #16 and #201, the latter concerning IgM/D-expressing CLL. Significant differences between subsets also involved disease stage at diagnosis and the presence of specific genomic aberrations. IgG subsets #4 and #16 emerged as particularly indolent with a significantly (P < 0.05) longer time-to-first-treatment (TTFT; median TTFT: not yet reached) compared with the IgM/D subsets #29 and #201 (median TTFT: 11 and 12 years, respectively).Conclusions: Our findings support the notion that BcR IG stereotypy further refines prognostication in CLL, superseding the immunogenetic distinction based solely on SHM load. In addition, the observed distinct genetic aberration landscapes and clinical heterogeneity suggest that not all M-CLL cases are equal, prompting further research into the underlying biological background with the ultimate aim of tailored patient management. Clin Cancer Res; 23(17); 5292-301. ©2017 AACR.
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Affiliation(s)
- Aliki Xochelli
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ioannis Kavakiotis
- Department of informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Eva Minga
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | | | - Eugen Tausch
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Xiao-Jie Yan
- Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York
| | - Tait Shanafelt
- Department of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Myriam Boudjogra
- Department of Hematology, Hopital Pitie-Salpetriere and University Pierre et Marie Curie, Paris, France
| | - Davide Rossi
- Division of Haematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Zadie Davis
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - Alba Navarro
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Yorick Sandberg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | - Lydia Scarfo
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | | | - Silvio Veronese
- Molecular Pathology Unit and Haematology Department, Niguarda Cancer Center, Niguarda Ca' Granda Hospital, Milan, Italy
| | - Tatiana Tzenou
- First Department of Propaedeutic Medicine, University of Athens, Athens, Greece
| | - Teodora Karan-Djurasevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Mark Catherwood
- Department of Haemato-Oncology, Belfast City Hospital, Belfast, United Kingdom
| | - Dirk Kienle
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Maria Chatzouli
- Hematology Department, Nikea General Hospital, Piraeus, Greece
| | - Monica Facco
- Department of Medicine, Hematology and Clinical Immunology Branch, Padua University School of Medicine, Padova, Italy
| | - Jasmin Bahlo
- Department I of Internal Medicine and Center of Integrated Oncology, University Hospital Cologne, Cologne, Germany
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Karin E Smedby
- Department of Medicine Solna, Clinical Epidemiology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Charles C Chu
- Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York
| | - Véronique Giudicelli
- IMGT®, the international ImMunoGeneTics information system®, Université de Montpellier, LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier, France
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Université de Montpellier, LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier, France
| | | | - Gunnar Juliusson
- Lund University and Hospital Department of Hematology, Lund Stem Cell Center, Lund, Sweden
| | | | - Ioannis Vlahavas
- Department of informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Darko Antic
- Clinic for Hematology, Clinical Center, Belgrade, Serbia.,Medical faculty, University of Belgrade, Belgrade, Serbia
| | - Livio Trentin
- Department of Medicine, Hematology and Clinical Immunology Branch, Padua University School of Medicine, Padova, Italy
| | - Marco Montillo
- Molecular Pathology Unit and Haematology Department, Niguarda Cancer Center, Niguarda Ca' Granda Hospital, Milan, Italy
| | - Carsten Niemann
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Anton W Langerak
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michael Hallek
- Department I of Internal Medicine and Center of Integrated Oncology, University Hospital Cologne, Cologne, Germany
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Nicholas Chiorazzi
- Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York
| | - Nikos Maglaveras
- Laboratory of Medical Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - Gianluca Gaidano
- Division of Haematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Diane F Jelinek
- Department of Immunology, Mayo Clinic, Rochester, Minnesota, United States
| | | | - Ioanna Chouvarda
- Laboratory of Medical Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikos Darzentas
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Frederic Davi
- Department of Hematology, Hopital Pitie-Salpetriere and University Pierre et Marie Curie, Paris, France
| | - Anastasia Hadzidimitriou
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece. .,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Paolo Ghia
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Università Vita-Salute San Raffaele and IRCCS Istituto Scientifico San Raffaele, Milan, Italy
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
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49
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Chen W, Hou L, Zhang Z, Pang X, Li Y. Genetic Diversity, Population Structure, and Linkage Disequilibrium of a Core Collection of Ziziphus jujuba Assessed with Genome-wide SNPs Developed by Genotyping-by-sequencing and SSR Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:575. [PMID: 28458680 PMCID: PMC5394126 DOI: 10.3389/fpls.2017.00575] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 03/30/2017] [Indexed: 05/24/2023]
Abstract
Chinese jujube (Ziziphus jujuba Mill) is an economically important fruit species native to China with high nutritious and medicinal value. Genotyping-by-sequencing was used to detect and genotype single nucleotide polymorphisms (SNPs) in a core collection of 150 Chinese jujube accessions and further to characterize their genetic diversity, population structure, and linkage disequilibrium (LD). A total of 4,680 high-quality SNPs were identified, of which 38 sets of tri-allelic SNPs were detected. The average polymorphism information content (PIC) values based on bi-allelic SNPs and tri-allelic SNPs were 0.27 and 0.38, respectively. STRUCTURE and principal coordinate analyses based on SNPs revealed that the 150 accessions could be clustered into two groups. However, neighbor-joining trees indicated the accessions should be grouped into three major clusters. Our data confirm that the resolving power for genetic diversity was similar for the SSRs and SNPs. In contrast, regarding population structure, the resolving power was higher for SSRs than for SNPs. The LD pattern in Chinese jujube was investigated for the first time. We observed a relatively rapid LD decay with a short range (∼10 kb) for all pseudo-chromosomes and for individual pseudo-chromosomes. Our findings provide important information for future genome-wide association analyses and marker-assisted selective breeding of Chinese jujube.
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Affiliation(s)
- Wu Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China
| | - Lu Hou
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China
| | - Zhiyong Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Xiaoming Pang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China
| | - Yingyue Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China
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50
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Alexander HK, Mayer SI, Bonhoeffer S. Population Heterogeneity in Mutation Rate Increases the Frequency of Higher-Order Mutants and Reduces Long-Term Mutational Load. Mol Biol Evol 2017; 34:419-436. [PMID: 27836985 PMCID: PMC5850754 DOI: 10.1093/molbev/msw244] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Mutation rate is a crucial evolutionary parameter that has typically been treated as a constant in population genetic analyses. However, the propensity to mutate is likely to vary among co-existing individuals within a population, due to genetic polymorphisms, heterogeneous environmental influences, and random physiological fluctuations. We review the evidence for mutation rate heterogeneity and explore its consequences by extending classic population genetic models to allow an arbitrary distribution of mutation rate among individuals, either with or without inheritance. With this general new framework, we rigorously establish the effects of heterogeneity at various evolutionary timescales. In a single generation, variation of mutation rate about the mean increases the probability of producing zero or many simultaneous mutations on a genome. Over multiple generations of mutation and selection, heterogeneity accelerates the appearance of both deleterious and beneficial multi-point mutants. At mutation-selection balance, higher-order mutant frequencies are likewise boosted, while lower-order mutants exhibit subtler effects; nonetheless, population mean fitness is always enhanced. We quantify the dependencies on moments of the mutation rate distribution and selection coefficients, and clarify the role of mutation rate inheritance. While typical methods of estimating mutation rate will recover only the population mean, analyses assuming mutation rate is fixed to this mean could underestimate the potential for multi-locus adaptation, including medically relevant evolution in pathogenic and cancerous populations. We discuss the potential to empirically parameterize mutation rate distributions, which have to date hardly been quantified.
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Affiliation(s)
- Helen K. Alexander
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Switzerland
| | - Stephanie I. Mayer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Switzerland
| | - Sebastian Bonhoeffer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Switzerland
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