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Okolo O, Honzel E, Britton WR, Yu VX, Flashner S, Martin C, Nakagawa H, Parikh AS. Experimental Modeling of Host-Bacterial Interactions in Head and Neck Squamous Cell Carcinoma. Cancers (Basel) 2023; 15:5810. [PMID: 38136355 PMCID: PMC10742111 DOI: 10.3390/cancers15245810] [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: 11/07/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The microscopic species colonizing the human body, collectively referred to as the microbiome, play a crucial role in the maintenance of tissue homeostasis, immunity, and the development of disease. There is evidence to suggest associations between alterations in the microbiome and the development of head and neck squamous cell carcinomas (HNSCC). The use of two-dimensional (2D) modeling systems has made significant strides in uncovering the role of microbes in carcinogenesis; however, direct mechanistic links remain in their infancy. Patient-derived three-dimensional (3D) HNSCC organoid and organotypic models have recently been described. Compared to 2D models, 3D organoid culture systems effectively capture the genetic and epigenetic features of parent tissue in a patient-specific manner and may offer a more nuanced understanding of the role of host-microbe responses in carcinogenesis. This review provides a topical literature review assessing the current state of the field investigating the role of the microbiome in HNSCC; including in vivo and in vitro modeling methods that may be used to characterize microbiome-epithelial interactions.
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Affiliation(s)
- Ogoegbunam Okolo
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10027, USA; (O.O.); (W.R.B.); (V.X.Y.); (S.F.); (C.M.); (H.N.)
- Columbia Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10027, USA;
| | - Emily Honzel
- Columbia Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10027, USA;
| | - William R. Britton
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10027, USA; (O.O.); (W.R.B.); (V.X.Y.); (S.F.); (C.M.); (H.N.)
- Columbia Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10027, USA;
| | - Victoria X. Yu
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10027, USA; (O.O.); (W.R.B.); (V.X.Y.); (S.F.); (C.M.); (H.N.)
- Department of Otolaryngology-Head and Neck Surgery, Columbia University, New York, NY 10027, USA
| | - Samuel Flashner
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10027, USA; (O.O.); (W.R.B.); (V.X.Y.); (S.F.); (C.M.); (H.N.)
| | - Cecilia Martin
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10027, USA; (O.O.); (W.R.B.); (V.X.Y.); (S.F.); (C.M.); (H.N.)
- Organoid and Cell Culture Core, Columbia University Digestive and Liver Diseases Research Center, Columbia University, New York, NY 10027, USA
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY 10027, USA
| | - Hiroshi Nakagawa
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10027, USA; (O.O.); (W.R.B.); (V.X.Y.); (S.F.); (C.M.); (H.N.)
- Organoid and Cell Culture Core, Columbia University Digestive and Liver Diseases Research Center, Columbia University, New York, NY 10027, USA
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY 10027, USA
| | - Anuraag S. Parikh
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10027, USA; (O.O.); (W.R.B.); (V.X.Y.); (S.F.); (C.M.); (H.N.)
- Department of Otolaryngology-Head and Neck Surgery, Columbia University, New York, NY 10027, USA
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Guan M, Wang X, Pan Y, Xu Y, Cao Y, Yan L, Ma L, Ma F, Zhang X. Delving into the molecular initiating event of cadmium toxification via the dose-dependent functional genomics approach in Saccharomyces cerevisiae. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121287. [PMID: 36791950 DOI: 10.1016/j.envpol.2023.121287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/03/2023] [Accepted: 02/12/2023] [Indexed: 06/18/2023]
Abstract
Determining dose-response relationship is essential for comprehensively revealing chemical-caused effects on organisms. However, uncertainty and complexity of gene/protein interactions cause the inability of traditional toxicogenomic methods (e.g., transcriptomics, proteomics and metabolomics) to effectively establish the direct relationship between chemical exposure and genes. In this work, we built an effective dose-dependent yeast functional genomics approach, which can clearly identify the direct gene-chemical link in the process of cadmium (Cd) toxification from a genome-wide scale with wide range concentrations (0.83, 2.49, 7.48, 22.45, 67.34, 202.03 and 606.1 μM). Firstly, we identified 220 responsive strains, and found that 142, 110, 91, 34, 8, 0 and 0 responsive strains can be respectively modulated by seven different Cd exposure concentrations ranging from high to low. Secondly, our results demonstrated that these genes induced by the high Cd exposure were mainly enriched in the process of cell autophagy, but ones caused by the low Cd exposure were primarily involved in oxidative stress. Thirdly, we found that the top-ranked GO biological processes with the lowest point of departure (POD) were transmembrane transporter complex and mitochondrial respiratory chain complex III, suggesting that mitochondrion might be the toxicity target of Cd. Similarly, nucleotide excision repair was ranked first in KEGG pathway with the least POD, indicating that this dose-dependent functional genomics approach can effectively detect the molecular initiating event (MIE) of cadmium toxification. Fourthly, we identified four key mutant strains (RIP1, QCR8, CYT1 and QCR2) as biomarkers for Cd exposure. Finally, the dose-dependent functional genomics approach also performed well in identifying MIE for additional genotoxicity chemical 4-nitroquinoline-1-oxide (4-NQO) data. Overall, our study developed a dose-dependent functional genomics approach, which is powerful to delve into the MIE of chemical toxification and is beneficial for guiding further chemical risk assessment.
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Affiliation(s)
- Miao Guan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China
| | - Xiaoyang Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China
| | - Yi Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China
| | - Yue Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China
| | - Yuqi Cao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China
| | - Lu Yan
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, China
| | - Lili Ma
- Jiangsu Engineering Lab of Water and Soil Eco-remediation, School of the Environment, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China.
| | - Fei Ma
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, China
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3
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Shore D, Griggs N, Graffeo V, Amin ARMR, Zha XM, Xu Y, McAleer JP. GPR68 limits the severity of chemical-induced oral epithelial dysplasia. Sci Rep 2023; 13:353. [PMID: 36611126 PMCID: PMC9825365 DOI: 10.1038/s41598-023-27546-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Head and neck cancer is the sixth most common malignancy, and there is an urgent need to identify physiological processes contributing to tumorigenesis. Extracellular acidification caused by aerobic glycolysis within tumor microenvironments can stimulate proton-sensing receptors. GPR68, or ovarian cancer G protein-coupled receptor 1, responds to extracellular acidity and is highly expressed in head and neck squamous cell carcinoma (HNSCC) as well as normal esophageal tissue. To study the role of GPR68 in oral dysplasia, wild-type and GPR68-/- mice were treated with 4-Nitroquinoline N-oxide (4NQO) in drinking water for 11-13 weeks, followed by normal water for 11-12 weeks. 4NQO treatment resulted in 45 percent of GPR68-/- mice developing severe dysplasia or squamous cell carcinoma compared to only 10.5 percent of GPR68+/+ mice. This correlated with increased frequencies of regulatory T cells in the spleens of male GPR68-/- mice. Dysplastic regions of the tongue had increased CD31 staining compared to normal regions in both GPR68-/- and GPR68+/+ mice, suggesting that angiogenesis was GPR68-independent. RNA knockdown studies using HNSCC cell lines demonstrated no direct effect of GPR68 on survival or growth. Overall, we demonstrate that GPR68-deficiency worsens the severity of chemical-induced oral dysplasia, suggesting a protective role for this gene in tumorigenesis.
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Affiliation(s)
- David Shore
- grid.259676.90000 0001 2214 9920Marshall University School of Pharmacy, Huntington, WV USA
| | - Nosakhere Griggs
- grid.259676.90000 0001 2214 9920Marshall University School of Pharmacy, Huntington, WV USA
| | - Vincent Graffeo
- grid.36425.360000 0001 2216 9681Marshall University Joan C. Edwards School of Medicine, Huntington, WV USA
| | - A. R. M. Ruhul Amin
- grid.259676.90000 0001 2214 9920Marshall University School of Pharmacy, Huntington, WV USA
| | - Xiang-ming Zha
- grid.266756.60000 0001 2179 926XUniversity of Missouri-Kansas City School of Pharmacy, Kansas City, MO USA
| | - Yan Xu
- grid.257413.60000 0001 2287 3919Indiana University School of Medicine, Indianapolis, IN USA
| | - Jeremy P. McAleer
- grid.259676.90000 0001 2214 9920Marshall University School of Pharmacy, Huntington, WV USA
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Amatatongchai M, Nontawong N, Ngaosri P, Chunta S, Wanram S, Jarujamrus P, Nacapricha D, Lieberzeit PA. Facile and Compact Electrochemical Paper-Based Analytical Device for Point-of-Care Diagnostic of Dual Carcinogen Oxidative Stress Biomarkers through a Molecularly Imprinted Polymer Coated on Graphene Quantum-Dot Capped Gold. Anal Chem 2022; 94:16692-16700. [DOI: 10.1021/acs.analchem.2c03120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Maliwan Amatatongchai
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Nongyao Nontawong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Pattanun Ngaosri
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | | | - Surasak Wanram
- Biomedical Science Research Unit, College of Medicine and Public Health, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Purim Jarujamrus
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Duangjai Nacapricha
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Peter A. Lieberzeit
- Faculty for Chemistry, Department of Physical Chemistry, University of Vienna, 1090 Vienna, Austria
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James SW, Palmer J, Keller NP, Brown ML, Dunworth MR, Francisco SG, Watson KG, Titchen B, Achimovich A, Mahoney A, Artemiou JP, Buettner KG, Class M, Sydenstricker AL, Anglin SL. A reciprocal translocation involving Aspergillus nidulans snxAHrb1/Gbp2 and gyfA uncovers a new regulator of the G2-M transition and reveals a role in transcriptional repression for the setBSet2 histone H3-lysine-36 methyltransferase. Genetics 2022; 222:iyac130. [PMID: 36005881 PMCID: PMC9526064 DOI: 10.1093/genetics/iyac130] [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: 06/27/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
Aspergillus nidulans snxA, an ortholog of Saccharomyces cerevisiae Hrb1/Gbp2 messenger RNA shuttle proteins, is-in contrast to budding yeast-involved in cell cycle regulation, in which snxA1 and snxA2 mutations as well as a snxA deletion specifically suppress the heat sensitivity of mutations in regulators of the CDK1 mitotic induction pathway. snxA mutations are strongly cold sensitive, and at permissive temperature snxA mRNA and protein expression are strongly repressed. Initial attempts to identify the causative snxA mutations revealed no defects in the SNXA protein. Here, we show that snxA1/A2 mutations resulted from an identical chromosome I-II reciprocal translocation with breakpoints in the snxA first intron and the fourth exon of a GYF-domain gene, gyfA. Surprisingly, a gyfA deletion and a reconstructed gyfA translocation allele suppressed the heat sensitivity of CDK1 pathway mutants in a snxA+ background, demonstrating that 2 unrelated genes, snxA and gyfA, act through the CDK1-CyclinB axis to restrain the G2-M transition, and for the first time identifying a role in G2-M regulation for a GYF-domain protein. To better understand snxA1/A2-reduced expression, we generated suppressors of snxA cold sensitivity in 2 genes: (1) loss of the abundant nucleolar protein Nsr1/nucleolin bypassed the requirement for snxA and (2) loss of the Set2 histone H3 lysine36 (H3K36) methyltransferase or a nonmethylatable histone H3K36L mutant rescued hypomorphic snxA mutants by restoring full transcriptional proficiency, indicating that methylation of H3K36 acts normally to repress snxA transcription. These observations are in line with known Set2 functions in preventing excessive and cryptic transcription of active genes.
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Affiliation(s)
- Steven W James
- Department of Biology, Gettysburg College, Gettysburg, PA 17325, USA
| | - Jonathan Palmer
- Data Analytics, Genencor Technology Center, IFF, Palo Alto, CA, 94306, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Morgan L Brown
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew R Dunworth
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
| | - Sarah G Francisco
- Department of Otolaryngology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Katherine G Watson
- School of Medicine, Noorda College of Osteopathic Medicine, Provo, UT 84606, USA
| | - Breanna Titchen
- Department of Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Alecia Achimovich
- Department of Chemistry, Gettysburg College, Gettysburg, PA 17325, USA
| | - Andrew Mahoney
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | | | - Kyra G Buettner
- School of Medicine, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Madelyn Class
- School of Medicine, Temple University, Philadelphia, PA 19140, USA
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A quantification method of somatic mutations in normal tissues and their accumulation in pediatric patients with chemotherapy. Proc Natl Acad Sci U S A 2022; 119:e2123241119. [PMID: 35895679 PMCID: PMC9351471 DOI: 10.1073/pnas.2123241119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Somatic mutations are accumulated in normal human tissues with aging and exposure to carcinogens. If we can accurately count any passenger mutations in any single DNA molecule, since their quantity is much larger than driver mutations, we can sensitively detect mutation accumulation in polyclonal normal tissues. Duplex sequencing, which tags both DNA strands in one DNA molecule, enables accurate count of such mutations, but requires a very large number of sequencing reads for each single sample of human-genome size. Here, we reduced the genome size to 1/90 using the BamHI restriction enzyme and established a cost-effective pipeline. The enzymatically cleaved and optimal sequencing (EcoSeq) method was able to count somatic mutations in a single DNA molecule with a sensitivity of as low as 3 × 10-8 per base pair (bp), as assessed by measuring artificially prepared mutations. Taking advantages of EcoSeq, we analyzed normal peripheral blood cells of pediatric sarcoma patients who received chemotherapy (n = 10) and those who did not (n = 10). The former had a mutation frequency of 31.2 ± 13.4 × 10-8 per base pair while the latter had 9.0 ± 4.5 × 10-8 per base pair (P < 0.001). The increase in mutation frequency was confirmed by analysis of the same patients before and after chemotherapy, and increased mutation frequencies persisted 46 to 64 mo after chemotherapy, indicating that the mutation accumulation constitutes a risk of secondary leukemia. EcoSeq has the potential to reveal accumulation of somatic mutations and exposure to environmental factors in any DNA samples and will contribute to cancer risk estimation.
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Bassler MC, Stefanakis M, Sequeira I, Ostertag E, Wagner A, Bartsch JW, Roeßler M, Mandic R, Reddmann EF, Lorenz A, Rebner K, Brecht M. Comparison of Whiskbroom and Pushbroom darkfield elastic light scattering spectroscopic imaging for head and neck cancer identification in a mouse model. Anal Bioanal Chem 2021; 413:7363-7383. [PMID: 34799750 PMCID: PMC8626402 DOI: 10.1007/s00216-021-03726-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/30/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022]
Abstract
The early detection of head and neck cancer is a prolonged challenging task. It requires a precise and accurate identification of tissue alterations as well as a distinct discrimination of cancerous from healthy tissue areas. A novel approach for this purpose uses microspectroscopic techniques with special focus on hyperspectral imaging (HSI) methods. Our proof-of-principle study presents the implementation and application of darkfield elastic light scattering spectroscopy (DF ELSS) as a non-destructive, high-resolution, and fast imaging modality to distinguish lingual healthy from altered tissue regions in a mouse model. The main aspect of our study deals with the comparison of two varying HSI detection principles, which are a point-by-point and line scanning imaging, and whether one might be more appropriate in differentiating several tissue types. Statistical models are formed by deploying a principal component analysis (PCA) with the Bayesian discriminant analysis (DA) on the elastic light scattering (ELS) spectra. Overall accuracy, sensitivity, and precision values of 98% are achieved for both models whereas the overall specificity results in 99%. An additional classification of model-unknown ELS spectra is performed. The predictions are verified with histopathological evaluations of identical HE-stained tissue areas to prove the model’s capability of tissue distinction. In the context of our proof-of-principle study, we assess the Pushbroom PCA-DA model to be more suitable for tissue type differentiations and thus tissue classification. In addition to the HE-examination in head and neck cancer diagnosis, the usage of HSI-based statistical models might be conceivable in a daily clinical routine.
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Affiliation(s)
- Miriam C Bassler
- Process Analysis and Technology (PA&T), Reutlingen University, Alteburgstr. 150, 72762, Reutlingen, Germany
- Institute of Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Mona Stefanakis
- Process Analysis and Technology (PA&T), Reutlingen University, Alteburgstr. 150, 72762, Reutlingen, Germany
- Institute of Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Inês Sequeira
- Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Edwin Ostertag
- Process Analysis and Technology (PA&T), Reutlingen University, Alteburgstr. 150, 72762, Reutlingen, Germany
| | - Alexandra Wagner
- Process Analysis and Technology (PA&T), Reutlingen University, Alteburgstr. 150, 72762, Reutlingen, Germany
- Institute of Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Jörg W Bartsch
- Department of Neurosurgery, Philipps University Marburg, Baldingerstraße, 35033, Marburg, Germany
| | - Marion Roeßler
- Department of Pathology, Philipps University Marburg, Baldingerstraße, 35033, Marburg, Germany
| | - Robert Mandic
- Department of Otorhinolaryngology, Philipps University Marburg, Baldingerstraße, 35033, Marburg, Germany
| | - Eike F Reddmann
- Process Analysis and Technology (PA&T), Reutlingen University, Alteburgstr. 150, 72762, Reutlingen, Germany
| | - Anita Lorenz
- Process Analysis and Technology (PA&T), Reutlingen University, Alteburgstr. 150, 72762, Reutlingen, Germany
| | - Karsten Rebner
- Process Analysis and Technology (PA&T), Reutlingen University, Alteburgstr. 150, 72762, Reutlingen, Germany
| | - Marc Brecht
- Process Analysis and Technology (PA&T), Reutlingen University, Alteburgstr. 150, 72762, Reutlingen, Germany.
- Institute of Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany.
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Dias LP, Souza RKF, Pupin B, Rangel DEN. Conidiation under illumination enhances conidial tolerance of insect-pathogenic fungi to environmental stresses. Fungal Biol 2021; 125:891-904. [PMID: 34649676 DOI: 10.1016/j.funbio.2021.06.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/17/2021] [Accepted: 06/07/2021] [Indexed: 11/25/2022]
Abstract
Light is an important signal for fungi in the environment and induces many genes with roles in stress and virulence responses. Conidia of the entomopathogenic fungi Aschersonia aleyrodis, Beauveria bassiana, Cordyceps fumosorosea, Lecanicillium aphanocladii, Metarhizium anisopliae, Metarhizium brunneum, Metarhizium robertsii, Simplicillium lanosoniveum, Tolypocladium cylindrosporum, and Tolypocladium inflatum were produced on potato dextrose agar (PDA) medium under continuous white light, on PDA medium in the dark, or under nutritional stress (= Czapek medium without sucrose = MM) in the dark. The conidial tolerance of these species produced under these different conditions were evaluated in relation to heat stress, oxidative stress (menadione), osmotic stress (KCl), UV radiation, and genotoxic stress caused by 4-nitroquinoline 1-oxide (4-NQO). Several fungal species demonstrated greater stress tolerance when conidia were produced under white light than in the dark; for instance white light induced higher tolerance of A. aleyrodis to KCl and 4-NQO; B. bassiana to KCl and 4-NQO; C. fumosorosea to UV radiation; M. anisopliae to heat and menadione; M. brunneum to menadione, KCl, UV radiation, and 4-NQO; M. robertsii to heat, menadione, KCl, and UV radiation; and T. cylindrosporum to menadione and KCl. However, conidia of L. aphanocladii, S. lanosoniveum, and T. inflatum produced under white light exhibited similar tolerance as conidia produced in the dark. When conidia were produced on MM, a much stronger stress tolerance was found for B. bassiana to menadione, KCl, UV radiation, and 4-NQO; C. fumosorosea to KCl and 4-NQO; Metarhizium species to heat, menadione, KCl, and UV radiation; T. cylindrosporum to menadione and UV radiation; and T. inflatum to heat and UV radiation. Again, conidia of L. aphanocladii and S. lanosoniveum produced on MM had similar tolerance to conidia produced on PDA medium in the dark. Therefore, white light is an important factor that induces higher stress tolerance in some insect-pathogenic fungi, but growth in nutritional stress always provides in conidia with stronger stress tolerance than conidia produced under white light.
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Affiliation(s)
- Luciana P Dias
- Escola de Engenharia de Lorena da Universidade de São Paulo (EEL/USP), Lorena, SP, 12602-810, Brazil
| | | | - Breno Pupin
- Centro de Ciência do Sistema Terrestre, Instituto Nacional de Pesquisas Espaciais - INPE, São José dos Campos, SP, 12227-010, Brazil
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BRCA1/Trp53 heterozygosity and replication stress drive esophageal cancer development in a mouse model. Proc Natl Acad Sci U S A 2021; 118:2108421118. [PMID: 34607954 PMCID: PMC8521688 DOI: 10.1073/pnas.2108421118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
BRCA1 germline mutations are associated with an increased risk of breast and ovarian cancer. Recent findings of others suggest that BRCA1 mutation carriers also bear an increased risk of esophageal and gastric cancer. Here, we employ a Brca1/Trp53 mouse model to show that unresolved replication stress (RS) in BRCA1 heterozygous cells drives esophageal tumorigenesis in a model of the human equivalent. This model employs 4-nitroquinoline-1-oxide (4NQO) as an RS-inducing agent. Upon drinking 4NQO-containing water, Brca1 heterozygous mice formed squamous cell carcinomas of the distal esophagus and forestomach at a much higher frequency and speed (∼90 to 120 d) than did wild-type (WT) mice, which remained largely tumor free. Their esophageal tissue, but not that of WT control mice, revealed evidence of overt RS as reflected by intracellular CHK1 phosphorylation and 53BP1 staining. These Brca1 mutant tumors also revealed higher genome mutation rates than those of control animals; the mutational signature SBS4, which is associated with tobacco-induced tumorigenesis; and a loss of Brca1 heterozygosity (LOH). This uniquely accelerated Brca1 tumor model is also relevant to human esophageal squamous cell carcinoma, an often lethal tumor.
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MEKK1-dependent activation of the CRL4 complex is important for DNA damage-induced degradation of p21 and DDB2 and cell survival. Mol Cell Biol 2021; 41:e0008121. [PMID: 34251884 PMCID: PMC8462458 DOI: 10.1128/mcb.00081-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cullin-4 ubiquitin ligase (CRL4) complexes are differentially composed and highly dynamic protein assemblies that control many biological processes including the global genome nucleotide excision repair (GG-NER) pathway. Here we identified the kinase mitogen-activated protein kinase kinase kinase 1 (MEKK1) as a novel constitutive interactor of a cytosolic CRL4 complex that disassembles after DNA damage due to the Caspase-mediated cleavage of MEKK1. The kinase activity of MEKK1 was important to trigger auto-ubiquitination of the CRL4 complex by K48- and K63-linked ubiquitin chains. MEKK1 knockdown prohibited DNA damage-induced degradation of the CRL4 component DNA-damage binding protein 2 (DDB2) and the CRL4 substrate p21 and also cell recovery and survival. A ubiquitin replacement strategy revealed a contribution of K63-branched ubiquitin chains for DNA damage-induced DDB2/p21 decay, cell cycle regulation and cell survival. These data might have also implications for cancer, as frequently occurring mutations of MEKK1 might have an impact on genome stability and the therapeutic efficacy of CRL4-dependent immunomodulatory drugs such as thalidomide-derivatives.
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11
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Pan B, Kaldhone PR, Alund AW, Du H, Guo X, Yan J, Chen Y, Zhou T, Robison TW, Chen T. Mutagenicity of silver nanoparticles evaluated using whole-genome sequencing in mouse lymphoma cells. Nanotoxicology 2021; 15:418-432. [PMID: 33710943 DOI: 10.1080/17435390.2021.1894614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The increasing medical and food applications of silver nanoparticles (AgNPs) raise concerns about their safety, including the potential health consequences of human exposure. Previous studies found that AgNPs were negative in the Ames test due to both their microbicidal activity and the inability of nanoparticles to penetrate bacterial cell walls. Thus, the mutagenicity of AgNPs is still not completely clear, though they do induce chromosome damage, as suggested by many previous genotoxicity studies. In this study, whole-genome sequencing (WGS) was used to analyze the mutagenicity of AgNPs in mouse lymphoma cells expanded from single-cell clones. The cells were treated with AgNPs, 4-nitroquinolone-1-oxide (4-NQO) as the positive control, and vehicle controls. Both AgNPs and 4-NQO significantly increased mutation frequencies over their concurrent controls by 1.12-fold and 4.89-fold with mutation rates at 4-fold and 130-fold, respectively. AgNP-induced mutations mainly occurred at G:C sites with G:C > T:A transversions, G:C > A:T transitions, and deletions as the most commonly observed mutations. AgNPs also induced higher fold changes in tandem mutations. The results suggest that the WGS mutation assay conducted here can detect the low-level mutagenicity of AgNPs, providing substantial support for the use of the WGS method as a possible alternative assay with respect to the mutagenic assessment of nanomaterials.
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Affiliation(s)
- Bohu Pan
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Pravin R Kaldhone
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Alexander W Alund
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Hua Du
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Xiaoqing Guo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Jian Yan
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Ying Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Tong Zhou
- Center for Veterinary Medicine, Food and Drug Administration, Rockville, MD, USA
| | - Timothy W Robison
- Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
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12
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Sagheer SH, Whitaker-Menezes D, Han JYS, Curry JM, Martinez-Outschoorn U, Philp NJ. 4NQO induced carcinogenesis: A mouse model for oral squamous cell carcinoma. Methods Cell Biol 2021; 163:93-111. [PMID: 33785171 DOI: 10.1016/bs.mcb.2021.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is the most common subsite of head and neck cancer, with a 5-year survival rate of only 50%. There is a pressing need for animal models that recapitulate the human disease to understand the factors driving OSCC carcinogenesis. Many laboratories have used the chemical carcinogen 4-nitroquinoline-1-oxide (4NQO) to investigate OSCC formation. The importance of the 4NQO mouse model is that it mimics the stepwise progression observed in OSCC patients. The 4NQO carcinogen model has the advantage that it can be used with transgenic mice with genetic modification in specific tissue types to investigate their role in driving cancer progression. Herein, we describe the basic approach for administering 4NQO to mice to induce OSCC and methods for assessing the tissue and disease progression.
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Affiliation(s)
- S Hamad Sagheer
- Department of Otolaryngology-Head and Neck Surgery, Thomas Jefferson University, Philadelphia, PA, United States
| | - Diana Whitaker-Menezes
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA, United States
| | - John Y S Han
- Department of Pathology, Anatomy & Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Joseph M Curry
- Department of Otolaryngology-Head and Neck Surgery, Thomas Jefferson University, Philadelphia, PA, United States.
| | | | - Nancy J Philp
- Department of Pathology, Anatomy & Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States.
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13
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Salogiannis J, Christensen JR, Songster LD, Aguilar-Maldonado A, Shukla N, Reck-Peterson SL. PxdA interacts with the DipA phosphatase to regulate peroxisome hitchhiking on early endosomes. Mol Biol Cell 2021; 32:492-503. [PMID: 33476181 PMCID: PMC8101442 DOI: 10.1091/mbc.e20-08-0559] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In canonical microtubule-based transport, adaptor proteins link cargoes to dynein and kinesin motors. Recently, an alternative mode of transport known as “hitchhiking” was discovered, where cargoes achieve motility by hitching a ride on already-motile cargoes, rather than attaching to a motor protein. Hitchhiking has been best studied in two filamentous fungi, Aspergillus nidulans and Ustilago maydis. In U. maydis, ribonucleoprotein complexes, peroxisomes, lipid droplets (LDs), and endoplasmic reticulum hitchhike on early endosomes (EEs). In A. nidulans, peroxisomes hitchhike using a putative molecular linker, peroxisome distribution mutant A (PxdA), which associates with EEs. However, whether other organelles use PxdA to hitchhike on EEs is unclear, as are the molecular mechanisms that regulate hitchhiking. Here we find that the proper distribution of LDs, mitochondria, and preautophagosomes do not require PxdA, suggesting that PxdA is a peroxisome-specific molecular linker. We identify two new pxdA alleles, including a point mutation (R2044P) that disrupts PxdA’s ability to associate with EEs and reduces peroxisome movement. We also identify a novel regulator of peroxisome hitchhiking, the phosphatase DipA. DipA colocalizes with EEs and its association with EEs relies on PxdA. Together, our data suggest that PxdA and the DipA phosphatase are specific regulators of peroxisome hitchhiking on EEs.
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Affiliation(s)
- John Salogiannis
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093.,Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Jenna R Christensen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Livia D Songster
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093.,Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, La Jolla, CA 92093
| | - Adriana Aguilar-Maldonado
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Nandini Shukla
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 043210.,Department of Molecular Genetics, The Ohio State University, Columbus, OH 043210
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093.,Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, La Jolla, CA 92093.,Howard Hughes Medical Institute, Chevy Chase, MD 20815
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14
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Melis M, Zhang T, Scognamiglio T, Gudas LJ. Mutations in long-lived epithelial stem cells and their clonal progeny in pre-malignant lesions and in oral squamous cell carcinoma. Carcinogenesis 2020; 41:1553-1564. [PMID: 32115621 PMCID: PMC7896111 DOI: 10.1093/carcin/bgaa019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/11/2020] [Accepted: 02/25/2020] [Indexed: 12/18/2022] Open
Abstract
Oral squamous cell carcinomas (OSCCs) are the most common cancers of the oral cavity, but the molecular mechanisms driving OSCC carcinogenesis remain unclear. Our group previously established a murine OSCC model based on a 10-week carcinogen [4-nitroquinoline 1-oxide (4-NQO)] treatment. Here we used K14CreERTAM;Rosa26LacZ mice to perform lineage tracing to delineate the mutational profiles in clonal cell populations resulting from single, long-lived epithelial stem cells, here called LacZ+ stem cell clones (LSCCs). Using laser-capture microdissection, we examined mutational changes in LSCCs immediately after the 10-week 4-NQO treatment and >17 weeks after 4-NQO treatment. We found a 1.8-fold ±0.4 (P = 0.009) increase in single-nucleotide variants and insertions/deletions (indels) in tumor compared with pre-neoplastic LSCCs. The percentages of indels and of loss of heterozygosity events were 1.3-fold±0.3 (P = 0.02) and 2.2-fold±0.7 (P = 0.08) higher in pre-neoplastic compared with tumor LSCCs. Mutations in cell adhesion- and development-associated genes occurred in 83% of the tumor LSCCs. Frequently mutated genes in tumor LSCCs were involved in planar cell polarity (Celsr1, Fat4) or development (Notch1). Chromosomal amplifications in 50% of the tumor LSCCs occurred in epidermal growth factor receptor, phosphoinositide 3-kinase and cell adhesion pathways. All pre-neoplastic and tumor LSCCs were characterized by key smoking-associated changes also observed in human OSCC, C>A and G>T. DeconstructSigs analysis identified smoking and head and neck cancer as the most frequent mutational signatures in pre-neoplastic and tumor LSCCs. Thus, this model recapitulates a smoking-associated mutational profile also observed in humans and illustrates the role of LSCCs in early carcinogenesis and OSCCs.
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Affiliation(s)
- Marta Melis
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Tuo Zhang
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Theresa Scognamiglio
- Pathology and Laboratory Medicine, Cornell University Joan and Sanford I Weill Medical College, New York, NY, USA
| | - Lorraine J Gudas
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Biomedical Sciences, New York, NY, USA
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15
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Sequeira I, Rashid M, Tomás IM, Williams MJ, Graham TA, Adams DJ, Vigilante A, Watt FM. Genomic landscape and clonal architecture of mouse oral squamous cell carcinomas dictate tumour ecology. Nat Commun 2020; 11:5671. [PMID: 33168804 PMCID: PMC7652942 DOI: 10.1038/s41467-020-19401-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 10/06/2020] [Indexed: 01/10/2023] Open
Abstract
To establish whether 4-nitroquinoline N-oxide-induced carcinogenesis mirrors the heterogeneity of human oral squamous cell carcinoma (OSCC), we have performed genomic analysis of mouse tongue lesions. The mutational signatures of human and mouse OSCC overlap extensively. Mutational burden is higher in moderate dysplasias and invasive SCCs than in hyperplasias and mild dysplasias, although mutations in p53, Notch1 and Fat1 occur in early lesions. Laminin-α3 mutations are associated with tumour invasiveness and Notch1 mutant tumours have an increased immune infiltrate. Computational modelling of clonal dynamics indicates that high genetic heterogeneity may be a feature of those mild dysplasias that are likely to progress to more aggressive tumours. These studies provide a foundation for exploring OSCC evolution, heterogeneity and progression.
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Affiliation(s)
- Inês Sequeira
- Centre for Stem Cells & Regenerative Medicine, King's College London, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK
- Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Mamunur Rashid
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Inês M Tomás
- Centre for Stem Cells & Regenerative Medicine, King's College London, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK
| | - Marc J Williams
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Trevor A Graham
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - David J Adams
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Alessandra Vigilante
- Centre for Stem Cells & Regenerative Medicine, King's College London, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK
| | - Fiona M Watt
- Centre for Stem Cells & Regenerative Medicine, King's College London, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK.
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16
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Ponnan A, Kulanthaiyesu A, Marudhamuthu M, Palanisamy K, Kadarkarai M. Protective effects of fucoidan against 4-nitroquinolin-1-oxide provoked genetic damage in mouse bone marrow cells. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:31760-31766. [PMID: 32504434 DOI: 10.1007/s11356-020-09472-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
Fucoidan is a unique bioactive and dietary polymer enriched mainly in the cell wall matrix of the brown seaweeds. This present study was intended to reveal the antigenotoxicity effect of fucoidan on 4-nitroquinolin-1-oxide (4-NQO) induced genetics damage and apoptosis in mice bone marrow cells. The 4-NQO caused genetic damages in the form of chromosome/chromatic breakage was estimated by micronuclei assay whereas apoptosis by annexin-V FITC kit and DNA damage by comet assay kit. In addition, oxidative damage in terms of plasma lipid peroxidation (LPO) and 8-OHdG was also estimated. In the experimental regime, six groups with each in five either sex of mice were used. Fucoidan constituted (50,100,200 mg/kg bwt) by orally for 5 days consequently and on 6th day, 4-NQO was administered (7.5 mg/kg bwt) by i.p. The results clearly show that negative control (H2O) and fucoidan alone constituted mice were not exhibited significant effect on LPO, genetic damages whereas positive control group (4-NQO 7.5 mg/kg bwt, i.p.) showed significant effect on genetic damage by showing increased level of LPO (6.25 vs 1.3 μM MDA), 8-OHdG (12 vs 4%), micronuclei about six-fold, 5-fold of comet, and 4-fold of apoptosis when compared with negative control, 11.6 ± 2.07, 5.00 ± 1.58, and 4.14 ± 0.65 respectively. Fucoidan pretreatment significantly protected the 4-NQO-induced genetic damage by 77% decreased level of micronuclei and 96% comet at dose of 200 mg/kg bwt over the positive control whereas LPO, 8-OHdG, and apoptosis were restored as equal to negative control. This study found as fucoidan possessing significant antigenotoxicity property by protecting 4-NQO-induced genetic damage in mice bone marrow cells as dose dependent manner suggest as valuable food supplements and medicine for mankind from environmental toxicants.
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Affiliation(s)
- Arumugam Ponnan
- Department of Zoology, School of Life Science, Bharathiar University, Coimbatore, Tamil Nadu, 641 046, India.
| | - Arunkumar Kulanthaiyesu
- Department of Plant Science, School of Biological Sciences, Central University of Kerala, Periye, Kasaragod, Kerala, 671 320, India
| | - Murugan Marudhamuthu
- Department of Microbial Technology, School of Biological Science, Madurai Kamaraj University, Madurai, Tamil Nadu, 625 021, India
| | - Kamalakkannan Palanisamy
- Department of Human Genetics and Molecular Biology, School of Life Science, Bharathiar University, Coimbatore, Tamil Nadu, 641 046, India
| | - Murugan Kadarkarai
- Department of Zoology, School of Life Science, Bharathiar University, Coimbatore, Tamil Nadu, 641 046, India
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17
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Wang Z, Xiao W. Distinct requirements for budding yeast Rev1 and Polη in translesion DNA synthesis across different types of DNA damage. Curr Genet 2020; 66:1019-1028. [PMID: 32623695 DOI: 10.1007/s00294-020-01092-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 02/04/2023]
Abstract
Certain replication-blocking lesions can escape DNA repair and must be bypassed to prevent fork collapse and cell death. Budding yeast DNA-damage tolerance consists of translesion DNA synthesis (TLS) and template switch. TLS utilizes specialized DNA polymerases to insert nucleotides opposite the damage site, followed by extension, allowing continual replication in the presence of lesions on the template DNA. Meanwhile, Rev1 is additionally required for the subsequent extension step of TLS regardless of the initial insertion polymerase utilized. Here we assess relative contributions of two Y-family TLS polymerases, Rev1 and Polη, in bypassing lesions induced by various types of DNA-damaging agents. Our experimental results collectively indicate that yeast cells preferentially utilize relatively error-free TLS polymerase(s) to bypass given lesions, and that the mutagenic TLS polymerase may serve as a backup. Interestingly, if Polη is unable to serve as a TLS polymerase under certain circumstances, it may be counter-active. The cooperation among TLS polymerases may strike a balance between survival and stress-induced mutagenesis. These observations indicate that specialized Y-family DNA polymerases have evolved to deal with different types of environmental genotoxic stresses.
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Affiliation(s)
- Zihao Wang
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Wei Xiao
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China. .,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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18
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Long LJ, Lee PH, Small EM, Hillyer C, Guo Y, Osley MA. Regulation of UV damage repair in quiescent yeast cells. DNA Repair (Amst) 2020; 90:102861. [PMID: 32403026 DOI: 10.1016/j.dnarep.2020.102861] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/10/2020] [Accepted: 04/15/2020] [Indexed: 12/27/2022]
Abstract
Non-growing quiescent cells face special challenges when repairing lesions produced by exogenous DNA damaging agents. These challenges include the global repression of transcription and translation and a compacted chromatin structure. We investigated how quiescent yeast cells regulated the repair of DNA lesions produced by UV irradiation. We found that UV lesions were excised and repaired in quiescent cells before their re-entry into S phase, and that lesion repair was correlated with high levels of Rad7, a recognition factor in the global genome repair sub-pathway of nucleotide excision repair (GGR-NER). UV exposure led to an increased frequency of mutations that included C->T transitions and T > A transversions. Mutagenesis was dependent on the error-prone translesion synthesis (TLS) DNA polymerase, Pol zeta, which was the only DNA polymerase present in detectable levels in quiescent cells. Across the genome of quiescent cells, UV-induced mutations showed an association with exons that contained H3K36 or H3K79 trimethylation but not with those bound by RNA polymerase II. Together, the data suggest that the distinct physiological state and chromatin structure of quiescent cells contribute to its regulation of UV damage repair.
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Affiliation(s)
- Lindsey J Long
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Po-Hsuen Lee
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Eric M Small
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Cory Hillyer
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Yan Guo
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Mary Ann Osley
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
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19
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Hautbergue T, Jamin EL, Debrauwer L, Puel O, Oswald IP. From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites. Nat Prod Rep 2019; 35:147-173. [PMID: 29384544 DOI: 10.1039/c7np00032d] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fungal secondary metabolites are defined by bioactive properties that ensure adaptation of the fungus to its environment. Although some of these natural products are promising sources of new lead compounds especially for the pharmaceutical industry, others pose risks to human and animal health. The identification of secondary metabolites is critical to assessing both the utility and risks of these compounds. Since fungi present biological specificities different from other microorganisms, this review covers the different strategies specifically used in fungal studies to perform this critical identification. Strategies focused on the direct detection of the secondary metabolites are firstly reported. Particularly, advances in high-throughput untargeted metabolomics have led to the generation of large datasets whose exploitation and interpretation generally require bioinformatics tools. Then, the genome-based methods used to study the entire fungal metabolic potential are reported. Transcriptomic and proteomic tools used in the discovery of fungal secondary metabolites are presented as links between genomic methods and metabolomic experiments. Finally, the influence of the culture environment on the synthesis of secondary metabolites by fungi is highlighted as a major factor to consider in research on fungal secondary metabolites. Through this review, we seek to emphasize that the discovery of natural products should integrate all of these valuable tools. Attention is also drawn to emerging technologies that will certainly revolutionize fungal research and to the use of computational tools that are necessary but whose results should be interpreted carefully.
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Affiliation(s)
- T Hautbergue
- Toxalim (Research Centre in Food Toxicology) Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, F-31027 Toulouse, France.
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20
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Jdey W, Kozlak M, Alekseev S, Thierry S, Lascaux P, Girard PM, Bono F, Dutreix M. AsiDNA Treatment Induces Cumulative Antitumor Efficacy with a Low Probability of Acquired Resistance. Neoplasia 2019; 21:863-871. [PMID: 31362243 PMCID: PMC6675950 DOI: 10.1016/j.neo.2019.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 11/01/2022] Open
Abstract
The Achilles heel of anticancer treatments is intrinsic or acquired resistance. Among many targeted therapies, the DNA repair inhibitors show limited efficacy due to rapid emergence of resistance. We examined evolution of cancer cells and tumors treated with AsiDNA, a new DNA repair inhibitor targeting all DNA break repair pathways. Effects of AsiDNA or Olaparib were analyzed in various cell lines. Frequency of AsiDNA- and olaparib-resistant clones was measured after 2 weeks of continuous treatment in KBM7 haploid cells. Cell survivals were also measured after one to six cycles of 1-week treatment and 1-week recovery in MDA-MB-231 and NCI-H446. Transcriptomes of cell populations recovering from cyclic treatments or mock treatment were compared. MDA-MB-231 xenografted models were treated with three cycles of AsiDNA to monitor the effects of treatment on tumor growth and transcriptional modifications. No resistant clones were selected after AsiDNA treatment (frequency < 3x10-8) in treatment conditions that generate resistance to olaparib at a frequency of 7.2x10-7 resistant clones per treated cell. Cyclic treatments promote cumulative sensitivity characterized by a higher mortality of cells having undergone previous treatment cycles. This sensitization was stable, and transcriptome analysis revealed a major gene downregulation with a specific overrepresentation of genes coding for targets of DNA-PK. Such changes were also detected in tumor models which showed impaired growth after cycles of AsiDNA treatment.
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Affiliation(s)
- Wael Jdey
- Institut Curie, PSL Research University, CNRS, INSERM, UMR 3347, F-91405, Orsay, France; Université Paris-Sud, Université Paris-Saclay, CNRS, INSERM, UMR 3347, F-91405 Orsay, France; Onxeo, F-75015, Paris, France
| | - Maria Kozlak
- Institut Curie, PSL Research University, CNRS, INSERM, UMR 3347, F-91405, Orsay, France; Université Paris-Sud, Université Paris-Saclay, CNRS, INSERM, UMR 3347, F-91405 Orsay, France
| | - Sergey Alekseev
- Institut Curie, PSL Research University, CNRS, INSERM, UMR 3347, F-91405, Orsay, France; Université Paris-Sud, Université Paris-Saclay, CNRS, INSERM, UMR 3347, F-91405 Orsay, France
| | - Sylvain Thierry
- Institut Curie, PSL Research University, CNRS, INSERM, UMR 3347, F-91405, Orsay, France; Université Paris-Sud, Université Paris-Saclay, CNRS, INSERM, UMR 3347, F-91405 Orsay, France
| | | | - Pierre-Marie Girard
- Institut Curie, PSL Research University, CNRS, INSERM, UMR 3347, F-91405, Orsay, France; Université Paris-Sud, Université Paris-Saclay, CNRS, INSERM, UMR 3347, F-91405 Orsay, France
| | | | - Marie Dutreix
- Institut Curie, PSL Research University, CNRS, INSERM, UMR 3347, F-91405, Orsay, France; Université Paris-Sud, Université Paris-Saclay, CNRS, INSERM, UMR 3347, F-91405 Orsay, France.
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21
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Chen YF, Liu CJ, Lin LH, Chou CH, Yeh LY, Lin SC, Chang KW. Establishing of mouse oral carcinoma cell lines derived from transgenic mice and their use as syngeneic tumorigenesis models. BMC Cancer 2019; 19:281. [PMID: 30922255 PMCID: PMC6440159 DOI: 10.1186/s12885-019-5486-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/18/2019] [Indexed: 12/31/2022] Open
Abstract
Background The survival of OSCC patient needs to be further improved. miR-211 is oncogenic in OSCC and its upregulation is associated with tumor progression and poor patient survival. K14-EGFP-miR-211 transgenic mice also exhibit augmented potential for OSCC induction. Methods Four murine OSCC cell lines, designated MOC-L1 to MOC-L4, are established from tongue tumors induced by 4-nitroquinoline 1-oxide using the K14-EGFP-miR-211 transgenic mouse model. The genetic disruption, in vitro oncogenicity, and the eligibilities of tumorigenesis and metastasis of the cell lines are analyzed. Results All cell lines show green fluorescence and express a range of epithelial markers. The MOC-L1, MOC-L2 and MOC-L3 cells carry missense mutations in the DNA binding domain of the p53 gene. MOC-L1 exhibits a high level of epithelial-mesenchymal transition and has the aggressive characteristics associated with this. MOC-L1 and MOC-L2 are clonogenic in vitro as well as being tumorigenic when implanted into the dermis or tongue of syngeneic recipients. Nonetheless, only MOC-L1 exhibits immense potential for local regional and distal metastasis. Since the expression of miR-196b in MOC-L1 xenografts is drastically decreased on cisplatin treatment, it would seem that targeting of miR-196b might facilitate tumor abrogation. Conclusions As cell lines established in this study originated from the C57BL/6 mouse, the strain most suitable for transgenic engineering, exploring the interplay of these OSCC cells with other genetically modified cells in immune-competent mice would provide important insights into OSCC pathogenesis. Electronic supplementary material The online version of this article (10.1186/s12885-019-5486-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yi-Fen Chen
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, No. 155, Li-Nong St., Section 2, Beitou District, Taipei, 112, Taiwan
| | - Chung-Ji Liu
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, No. 155, Li-Nong St., Section 2, Beitou District, Taipei, 112, Taiwan.,Department of Dentistry, MacKay Memorial Hospital, No. 45, Minsheng Rd., Tamsui District, New Taipei City, 251, Taiwan
| | - Li-Han Lin
- Department of Dentistry, MacKay Memorial Hospital, No. 45, Minsheng Rd., Tamsui District, New Taipei City, 251, Taiwan
| | - Chung-Hsien Chou
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, No. 155, Li-Nong St., Section 2, Beitou District, Taipei, 112, Taiwan
| | - Li-Yin Yeh
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, No. 155, Li-Nong St., Section 2, Beitou District, Taipei, 112, Taiwan
| | - Shu-Chun Lin
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, No. 155, Li-Nong St., Section 2, Beitou District, Taipei, 112, Taiwan. .,Department of Dentistry, School of Dentistry, National Yang-Ming University, No. 155, Li-Nong St., Section 2, Beitou District, Taipei, 112, Taiwan. .,Department of Stomatology, Taipei Veterans General Hospital, No.201, Sec. 2, Shipai Rd., Beitou District, Taipei, 112, Taiwan.
| | - Kuo-Wei Chang
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, No. 155, Li-Nong St., Section 2, Beitou District, Taipei, 112, Taiwan. .,Department of Dentistry, School of Dentistry, National Yang-Ming University, No. 155, Li-Nong St., Section 2, Beitou District, Taipei, 112, Taiwan. .,Department of Stomatology, Taipei Veterans General Hospital, No.201, Sec. 2, Shipai Rd., Beitou District, Taipei, 112, Taiwan.
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22
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Zhou YX, Fuentes-Creollo G, Ponce F, Langley SA, Jen KY, Celniker SE, Mao JH, Snijders AM. No difference in 4-nitroquinoline induced tumorigenesis between germ-free and colonized mice. Mol Carcinog 2019; 58:627-632. [PMID: 30632250 DOI: 10.1002/mc.22972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/14/2018] [Accepted: 01/03/2019] [Indexed: 12/24/2022]
Abstract
Variations in oral bacterial communities have been linked to oral cancer suggesting that the oral microbiome is an etiological factor that can influence oral cancer development. The 4-nitroquinoline 1-oxide (4-NQO)-induced murine oral and esophageal cancer model is frequently used to assess the effects of preventive and/or therapeutic agents. We used this model to assess the impact of the microbiome on tumorigenesis using axenic (germ-free) and conventionally housed mice. Increased toxicity was observed in germ-free mice, however, no difference in tumor incidence, multiplicity, and size was observed. Transcriptional profiling of liver tissue from germ-free and conventionally housed mice identified 254 differentially expressed genes including ten cytochrome p450 enzymes, the largest family of phase-1 drug metabolizing enzymes in the liver. Gene ontology revealed that differentially expressed genes were enriched for liver steatosis, inflammation, and oxidative stress in livers of germ-free mice. Our observations emphasize the importance of the microbiome in mediating chemical toxicity at least in part by altering host gene expression. Studies on the role of the microbiome in chemical-induced cancer using germ-free animal models should consider the potential difference in dose due to the microbiome-mediated changes in host metabolizing capacity, which might influence the ability to draw conclusions especially for tumor induction models that are dose dependent.
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Affiliation(s)
- Yan-Xia Zhou
- College of Marine Science, Shandong University at Weihai, Weihai, China.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Gabriela Fuentes-Creollo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Frank Ponce
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Sasha A Langley
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Kuang-Yu Jen
- Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, California
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, California.,School of BioEngineering and BioInformatics, Nanjing Medical University, Nanjing, China
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, California.,School of BioEngineering and BioInformatics, Nanjing Medical University, Nanjing, China
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23
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Araújo CA, Dias LP, Ferreira PC, Mittmann J, Pupin B, Brancini G, Braga GÚ, Rangel DE. Responses of entomopathogenic fungi to the mutagen 4-nitroquinoline 1-oxide. Fungal Biol 2018; 122:621-628. [DOI: 10.1016/j.funbio.2018.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/09/2018] [Accepted: 03/15/2018] [Indexed: 01/11/2023]
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24
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Genetic analyses of reddish-brown polyoxin-resistant mutants of Bipolaris maydis. MYCOSCIENCE 2018. [DOI: 10.1016/j.myc.2017.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Lan A, Li W, Liu Y, Xiong Z, Zhang X, Zhou S, Palko O, Chen H, Kapita M, Prigge JR, Schmidt EE, Chen X, Sun Z, Chen XL. Chemoprevention of oxidative stress-associated oral carcinogenesis by sulforaphane depends on NRF2 and the isothiocyanate moiety. Oncotarget 2018; 7:53502-53514. [PMID: 27447968 PMCID: PMC5288201 DOI: 10.18632/oncotarget.10609] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/03/2016] [Indexed: 12/20/2022] Open
Abstract
Oxidative stress is known to play an important role in oral cancer development. In this study we aimed to examine whether a chemical activator of NRF2, sulforaphane (SFN), may have chemopreventive effects on oxidative stress-associated oral carcinogenesis. We first showed that Nrf2 activation and oxidative damage were commonly seen in human samples of oral leukoplakia. With gene microarray and immunostaining, we found 4-nitroquinoline 1-oxide (4NQO) in drink activated the Nrf2 pathway and produced oxidative damage in mouse tongue. Meanwhile whole exome sequencing of mouse tongue identified mutations consistent with 4NQO's mutagenic profile. Using cultured human oral keratinocytes and 4NQO-treated mouse tongue, we found that SFN pre-treatment activated the NRF2 pathway and inhibited oxidative damage both in vitro and in vivo. On the contrary, a structural analogue of SFN without the isothiocyanate moiety did not have such effects. In a long-term chemoprevention study using wild-type and Nrf2-/- mice, we showed that topical application of SFN activated the NRF2 pathway, inhibited oxidative damage, and prevented 4NQO-induced oral carcinogenesis in an Nrf2-dependent manner. Our data clearly demonstrate that SFN has chemopreventive effects on oxidative stress-associated oral carcinogenesis, and such effects depend on Nrf2 and the isothiocyanate moiety.
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Affiliation(s)
- Aixian Lan
- Department of Oral Medicine, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, Beijing 100050, China
| | - Wenjun Li
- Department of Oral Medicine, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, Beijing 100050, China
| | - Yao Liu
- Department of Oral Medicine, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, Beijing 100050, China
| | - Zhaohui Xiong
- Cancer Research Program, JLC-BBRI, North Carolina Central University, Durham, NC 27707, USA
| | - Xinyan Zhang
- Department of Oral Medicine, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, Beijing 100050, China
| | - Shanshan Zhou
- Department of Pharmaceutical Engineering, School of Pharmaceutical & Life Sciences, Changzhou University, Jiangsu 213164, China
| | - Olesya Palko
- Cancer Research Program, JLC-BBRI, North Carolina Central University, Durham, NC 27707, USA
| | - Hao Chen
- Cancer Research Program, JLC-BBRI, North Carolina Central University, Durham, NC 27707, USA
| | - Mayanga Kapita
- Cancer Research Program, JLC-BBRI, North Carolina Central University, Durham, NC 27707, USA
| | - Justin R Prigge
- Department of Immunology and Infectious Diseases, Montana State University, Bozeman, MT 59717, USA
| | - Edward E Schmidt
- Department of Immunology and Infectious Diseases, Montana State University, Bozeman, MT 59717, USA
| | - Xin Chen
- Department of Pharmaceutical Engineering, School of Pharmaceutical & Life Sciences, Changzhou University, Jiangsu 213164, China
| | - Zheng Sun
- Department of Oral Medicine, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, Beijing 100050, China
| | - Xiaoxin Luke Chen
- Cancer Research Program, JLC-BBRI, North Carolina Central University, Durham, NC 27707, USA
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26
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Palmer JM, Drees KP, Foster JT, Lindner DL. Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Nat Commun 2018; 9:35. [PMID: 29295979 PMCID: PMC5750222 DOI: 10.1038/s41467-017-02441-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 11/30/2017] [Indexed: 02/08/2023] Open
Abstract
Bat white-nose syndrome (WNS), caused by the fungal pathogen Pseudogymnoascus destructans, has decimated North American hibernating bats since its emergence in 2006. Here, we utilize comparative genomics to examine the evolutionary history of this pathogen in comparison to six closely related nonpathogenic species. P. destructans displays a large reduction in carbohydrate-utilizing enzymes (CAZymes) and in the predicted secretome (~50%), and an increase in lineage-specific genes. The pathogen has lost a key enzyme, UVE1, in the alternate excision repair (AER) pathway, which is known to contribute to repair of DNA lesions induced by ultraviolet (UV) light. Consistent with a nonfunctional AER pathway, P. destructans is extremely sensitive to UV light, as well as the DNA alkylating agent methyl methanesulfonate (MMS). The differential susceptibility of P. destructans to UV light in comparison to other hibernacula-inhabiting fungi represents a potential “Achilles’ heel” of P. destructans that might be exploited for treatment of bats with WNS. White-nose syndrome, caused by the fungus Pseudogymnoascus destructans, is decimating North American bats. Here, Palmer et al. use comparative genomics to examine the evolutionary history of this pathogen, and show that it has lost a crucial DNA repair enzyme and is extremely sensitive to UV light.
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Affiliation(s)
- Jonathan M Palmer
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, WI, 53726, USA
| | - Kevin P Drees
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Jeffrey T Foster
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Daniel L Lindner
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, WI, 53726, USA.
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27
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Lovinskaya AV, Kolumbayeva SZ, Shalakhmetova TM, Marsova MV, Abilev SK. Antigenotoxic activity of biologically active substances from Inula britannica and Limonium gmelini. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417120080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Pfannenstiel BT, Zhao X, Wortman J, Wiemann P, Throckmorton K, Spraker JE, Soukup AA, Luo X, Lindner DL, Lim FY, Knox BP, Haas B, Fischer GJ, Choera T, Butchko RAE, Bok JW, Affeldt KJ, Keller NP, Palmer JM. Revitalization of a Forward Genetic Screen Identifies Three New Regulators of Fungal Secondary Metabolism in the Genus Aspergillus. mBio 2017; 8:e01246-17. [PMID: 28874473 PMCID: PMC5587912 DOI: 10.1128/mbio.01246-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/08/2017] [Indexed: 11/24/2022] Open
Abstract
The study of aflatoxin in Aspergillus spp. has garnered the attention of many researchers due to aflatoxin's carcinogenic properties and frequency as a food and feed contaminant. Significant progress has been made by utilizing the model organism Aspergillus nidulans to characterize the regulation of sterigmatocystin (ST), the penultimate precursor of aflatoxin. A previous forward genetic screen identified 23 A. nidulans mutants involved in regulating ST production. Six mutants were characterized from this screen using classical mapping (five mutations in mcsA) and complementation with a cosmid library (one mutation in laeA). The remaining mutants were backcrossed and sequenced using Illumina and Ion Torrent sequencing platforms. All but one mutant contained one or more sequence variants in predicted open reading frames. Deletion of these genes resulted in identification of mutant alleles responsible for the loss of ST production in 12 of the 17 remaining mutants. Eight of these mutations were in genes already known to affect ST synthesis (laeA, mcsA, fluG, and stcA), while the remaining four mutations (in laeB, sntB, and hamI) were in previously uncharacterized genes not known to be involved in ST production. Deletion of laeB, sntB, and hamI in A. flavus results in loss of aflatoxin production, confirming that these regulators are conserved in the aflatoxigenic aspergilli. This report highlights the multifaceted regulatory mechanisms governing secondary metabolism in Aspergillus Additionally, these data contribute to the increasing number of studies showing that forward genetic screens of fungi coupled with whole-genome resequencing is a robust and cost-effective technique.IMPORTANCE In a postgenomic world, reverse genetic approaches have displaced their forward genetic counterparts. The techniques used in forward genetics to identify loci of interest were typically very cumbersome and time-consuming, relying on Mendelian traits in model organisms. The current work was pursued not only to identify alleles involved in regulation of secondary metabolism but also to demonstrate a return to forward genetics to track phenotypes and to discover genetic pathways that could not be predicted through a reverse genetics approach. While identification of mutant alleles from whole-genome sequencing has been done before, here we illustrate the possibility of coupling this strategy with a genetic screen to identify multiple alleles of interest. Sequencing of classically derived mutants revealed several uncharacterized genes, which represent novel pathways to regulate and control the biosynthesis of sterigmatocystin and of aflatoxin, a societally and medically important mycotoxin.
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Affiliation(s)
| | - Xixi Zhao
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jennifer Wortman
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kurt Throckmorton
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joseph E Spraker
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alexandra A Soukup
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Xingyu Luo
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel L Lindner
- Center for Forest Mycology Research, Northern Research Station, U.S. Forest Service, Madison, Wisconsin, USA
| | - Fang Yun Lim
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin P Knox
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian Haas
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gregory J Fischer
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Tsokyi Choera
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Robert A E Butchko
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
| | - Jin-Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Katharyn J Affeldt
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jonathan M Palmer
- Center for Forest Mycology Research, Northern Research Station, U.S. Forest Service, Madison, Wisconsin, USA
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29
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Yamashita S, Iida N, Takeshima H, Hattori N, Maeda M, Kishino T, Nagano R, Shimazu T, Tsugane S, Ushijima T. A novel method to quantify base substitution mutations at the 10 -6 per bp level in DNA samples. Cancer Lett 2017. [PMID: 28642169 DOI: 10.1016/j.canlet.2017.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Somatic base substitution mutations of frequencies at the 10-6/bp level are expected to be present in many biomedical samples, such as tissues exposed to carcinogenic factors and exhausted stem cells. However, measurement of such rare mutations has been very difficult in human DNA samples. Here, we invented the use of 100 copies of genomic DNA as a template for amplicon deep sequencing so that a real mutation in a single DNA molecule would be detected at a variant allele frequency of 1% while sequencing errors have less frequency. In addition, we selected 15,552 error-resistant base positions whose mutation frequency was expected to reflect that of base positions that can drive carcinogenesis or potentially even of the entire genome. The validity of the method was first confirmed by the successful detection of mutations premixed at the frequency of 0.1%. Second, increasing mutation frequencies (4-60 × 10-6/bp) were successfully detected in cells treated with increasing doses of one of two mutagens, and their signature mutations were detected. The ratio of non-synonymous mutations to synonymous mutations time-dependently decreased after treatment with a mutagen, supporting the neutral theory of molecular evolution for somatic mutations. Importantly, gastric mucosae exposed to Helicobacter pylori infection was shown to have significantly higher mutation frequency than those without. These results demonstrated that our new method can be used to measure rare base substitution mutations at the 10-6/bp level, and is now ready for a wide range of applications.
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Affiliation(s)
- Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Iida
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahiro Maeda
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takayoshi Kishino
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Reiko Nagano
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Taichi Shimazu
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Shoichiro Tsugane
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.
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30
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Jeong Y, Jung M, Kim MJ, Hwang CH. A 4-Nitroquinoleneoxide-Induced Pleurotus eryngii Mutant Variety Increases Pin1 Expression in Rat Brain. J Med Food 2017; 20:65-70. [PMID: 28098518 DOI: 10.1089/jmf.2016.3809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
To develop Pleurotus eryngii varieties with improved medicinal qualities, protoplasts of P. eryngii were mutagenized using 4-nitroquinoleneoxide. The effects of the resulting variant mushrooms on a human cell were evaluated by applying their aqueous extracts to the human hepatoma cell line, HepG2, in vitro and examining any alteration in the proteomes of the treated HepG2. The P. eryngii mutant, NQ2A-12, was selected for its effects on increasing the expression level of Pin1 in HepG2. Pin1 is one of the peptidyl-prolyl cis-trans isomerases known to play an important role in repressing Alzheimer's disease pathogenesis. Validity of NQ2A-12 related to Alzheimer's disease was shown with an enhanced expression of Pin1 in a mouse brain tissue by injecting the NQ2A-12 extract. The mutant mushroom, NQ2A-12, could be developed as a new variety of P. eryngii with potential to protect against Alzheimer's disease.
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Affiliation(s)
- Yoonhwa Jeong
- 1 Department of Food Science and Nutrition, Dankook University , Cheonan, Korea.,2 Center for Industrialization of Natural Neutraceuticals, Dankook University , Cheonan, Korea
| | - Mina Jung
- 3 Department of Crop Science and Biotechnology, Dankook University , Cheonan, Korea
| | - Myeung Ju Kim
- 4 Department of Anatomy, Dankook University , Cheonan, Korea
| | - Cheol Ho Hwang
- 2 Center for Industrialization of Natural Neutraceuticals, Dankook University , Cheonan, Korea.,3 Department of Crop Science and Biotechnology, Dankook University , Cheonan, Korea
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31
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Oakley CE, Ahuja M, Sun WW, Entwistle R, Akashi T, Yaegashi J, Guo CJ, Cerqueira GC, Russo Wortman J, Wang CCC, Chiang YM, Oakley BR. Discovery of McrA, a master regulator of Aspergillus secondary metabolism. Mol Microbiol 2016; 103:347-365. [PMID: 27775185 DOI: 10.1111/mmi.13562] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2016] [Indexed: 01/17/2023]
Abstract
Fungal secondary metabolites (SMs) are extremely important in medicine and agriculture, but regulation of their biosynthesis is incompletely understood. We have developed a genetic screen in Aspergillus nidulans for negative regulators of fungal SM gene clusters and we have used this screen to isolate mutations that upregulate transcription of the non-ribosomal peptide synthetase gene required for nidulanin A biosynthesis. Several of these mutations are allelic and we have identified the mutant gene by genome sequencing. The gene, which we designate mcrA, is conserved but uncharacterized, and it encodes a putative transcription factor. Metabolite profiles of mcrA deletant, mcrA overexpressing, and parental strains reveal that mcrA regulates at least ten SM gene clusters. Deletion of mcrA stimulates SM production even in strains carrying a deletion of the SM regulator laeA, and deletion of mcrA homologs in Aspergillus terreus and Penicillum canescens alters the secondary metabolite profile of these organisms. Deleting mcrA in a genetic dereplication strain has allowed us to discover two novel compounds as well as an antibiotic not known to be produced by A. nidulans. Deletion of mcrA upregulates transcription of hundreds of genes including many that are involved in secondary metabolism, while downregulating a smaller number of genes.
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Affiliation(s)
- C Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
| | - Manmeet Ahuja
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
| | - Wei-Wen Sun
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA
| | - Ruth Entwistle
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
| | - Tomohiro Akashi
- Division of OMICS analysis, Nagoya University Graduate School of Medicine, 65 Tsurumai, Nagoya, Aichi, 466-8550, Japan
| | - Junko Yaegashi
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA
| | - Chun-Jun Guo
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA
| | - Gustavo C Cerqueira
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Jennifer Russo Wortman
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA.,Department of Chemistry, Dornsife Colleges of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA.,Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan City, Taiwan, 71710, Republic of China
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
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32
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Dissecting genetic and environmental mutation signatures with model organisms. Trends Genet 2015; 31:465-74. [PMID: 25940384 DOI: 10.1016/j.tig.2015.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 12/31/2022]
Abstract
Deep sequencing has impacted on cancer research by enabling routine sequencing of genomes and exomes to identify genetic changes associated with carcinogenesis. Researchers can now use the frequency, type, and context of all mutations in tumor genomes to extract mutation signatures that reflect the driving mutational processes. Identifying mutation signatures, however, may not immediately suggest a mechanism. Consequently, several recent studies have employed deep sequencing of model organisms exposed to discrete genetic or environmental perturbations. These studies exploit the simpler genomes and availability of powerful genetic tools in model organisms to analyze mutation signatures under controlled conditions, forging mechanistic links between mutational processes and signatures. We discuss the power of this approach and suggest that many such studies may be on the horizon.
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