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Allen AG, Khan SQ, Margulies CM, Viswanathan R, Lele S, Blaha L, Scott SN, Izzo KM, Gerew A, Pattali R, Cochran NR, Holland CS, Zhao AH, Sherman SE, Jaskolka MC, Wu M, Wilson AC, Sun X, Ciulla DM, Zhang D, Nelson JD, Zhang P, Mazzucato P, Huang Y, Giannoukos G, Marco E, Nehil M, Follit JA, Chang KH, Shearman MS, Wilson CJ, Zuris JA. A highly efficient transgene knock-in technology in clinically relevant cell types. Nat Biotechnol 2024; 42:458-469. [PMID: 37127662 DOI: 10.1038/s41587-023-01779-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/04/2023] [Indexed: 05/03/2023]
Abstract
Inefficient knock-in of transgene cargos limits the potential of cell-based medicines. In this study, we used a CRISPR nuclease that targets a site within an exon of an essential gene and designed a cargo template so that correct knock-in would retain essential gene function while also integrating the transgene(s) of interest. Cells with non-productive insertions and deletions would undergo negative selection. This technology, called SLEEK (SeLection by Essential-gene Exon Knock-in), achieved knock-in efficiencies of more than 90% in clinically relevant cell types without impacting long-term viability or expansion. SLEEK knock-in rates in T cells are more efficient than state-of-the-art TRAC knock-in with AAV6 and surpass more than 90% efficiency even with non-viral DNA cargos. As a clinical application, natural killer cells generated from induced pluripotent stem cells containing SLEEK knock-in of CD16 and mbIL-15 show substantially improved tumor killing and persistence in vivo.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Meng Wu
- Editas Medicine, Cambridge, MA, USA
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Viswanathan R, Cheruba E, Wong PM, Yi Y, Ngang S, Chong DQ, Loh YH, Tan IB, Cheow LF. DARESOME enables concurrent profiling of multiple DNA modifications with restriction enzymes in single cells and cell-free DNA. Sci Adv 2023; 9:eadi0197. [PMID: 37713482 PMCID: PMC10881072 DOI: 10.1126/sciadv.adi0197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/15/2023] [Indexed: 09/17/2023]
Abstract
5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are the most abundant DNA modifications that have important roles in gene regulation. Detailed studies of these different epigenetic marks aimed at understanding their combined effects and dynamic interconversion are, however, hampered by the inability of current methods to simultaneously measure both modifications, particularly in samples with limited quantities. We present DNA analysis by restriction enzyme for simultaneous detection of multiple epigenomic states (DARESOME), an assay based on modification-sensitive restriction digest and sequential tag ligation that can concurrently perform quantitative profiling of unmodified cytosine, 5mC, and 5hmC in CCGG sites genome-wide. DARESOME reveals the opposing roles of 5mC and 5hmC in gene expression regulation as well as their interconversion during aging in mouse brain. Implementation of DARESOME in single cells demonstrates pronounced 5hmC strand bias that reflects the semiconservative replication of DNA. Last, we showed that DARESOME enables integrative genomic, 5mC, and 5hmC profiling of cell-free DNA that uncovered multiomics cancer signatures in liquid biopsy.
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Affiliation(s)
- Ramya Viswanathan
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Elsie Cheruba
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Pui-Mun Wong
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Yao Yi
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Shaun Ngang
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Dawn Qingqing Chong
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Yuin-Han Loh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Iain Beehuat Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
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Liu DD, Muliaditan D, Viswanathan R, Cui X, Cheow LF. Melt-Encoded-Tags for Expanded Optical Readout in Digital PCR (METEOR-dPCR) Enables Highly Multiplexed Quantitative Gene Panel Profiling. Adv Sci (Weinh) 2023; 10:e2301630. [PMID: 37485651 PMCID: PMC10520687 DOI: 10.1002/advs.202301630] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/27/2023] [Indexed: 07/25/2023]
Abstract
Digital PCR (dPCR) is an important tool for precise nucleic acid quantification in clinical setting, but the limited multiplexing capability restricts its applications for quantitative gene panel profiling. Here, this work describes melt-encoded-tags for expanded optical readout in digital PCR (METEOR-dPCR), a simple two-step assay that enables simultaneous quantification of a large panel of arbitrary genes in a dPCR platform. Target genes are quantitatively converted into DNA tags with unique melting temperatures through a ligation approach. These tags are then counted and distinguished by their melt-curve profiles on a dPCR platform. A multiplexing capacity of M^N, where M is the number of resolvable melting temperature and N is the number of fluorescence channel, can be achieved. This work validates METEOR-dPCR with simultaneous DNA copy number profiling of 60 targets using dPCR in cancer cells, and demonstrates its sensitivity for estimating tumor fraction in mixed tumor and normal DNA samples. The rapid, quantitative, and highly multiplexed METEOR-dPCR assay will have wide appeal for many clinical applications.
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Affiliation(s)
- Dong Dong Liu
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
| | - Daniel Muliaditan
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
- Genome institute of SingaporeAgency for ScienceTechnology and ResearchSingapore138672Singapore
| | - Ramya Viswanathan
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
| | - Xu Cui
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
| | - Lih Feng Cheow
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
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Nithya K, Parameswari B, Kumar S, Annadurai A, Nithyanantham R, Mahadevaswamy HK, Viswanathan R. Prospecting true ScYLV resistance in Saccharum hybrid parental population in India by symptom phenotyping and viral titre quantification. 3 Biotech 2023; 13:125. [PMID: 37041801 PMCID: PMC10082694 DOI: 10.1007/s13205-023-03541-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 03/28/2023] [Indexed: 04/13/2023] Open
Abstract
In sugarcane (Saccharum spp. hybrids) cultivation, viral diseases pose a great challenge across the globe. Yellow leaf (YL) disease is one of the important viral diseases caused by Sugarcane yellow leaf virus (ScYLV), a positive-sense ssRNA virus, genus Polerovirus, family Solemoviridae. The disease symptoms appear in later stages of crop growth during grand growth to maturity phase with intense midrib yellowing in the abaxial leaf surface. At present, this disease is managed through tissue (meristem) culture and healthy seed nurseries in India. However, the virus-free plants are infected quickly by secondary inoculum from aphid vectors in the field, which necessitates the importance of developing YL-resistant varieties. We screened about 600-625 sugarcane parental clones to identify true YL resistance based on 0-5 disease rating scale since 2015 and categorised them as resistant, moderately resistant, moderately susceptible, susceptible and highly susceptible. Leaf samples were collected from all these categories of plants during 2018-20 for the viral titre estimation through absolute quantification method (qRT-PCR assay). The viral load was invariably high in all categories of susceptible samples that ranged from 4.40 × 102 to 8.429 × 106, whereas in YL-free asymptomatic clones, the viral load ranged from 82.35 ± 5.90 to 5.121 × 104. The results clearly indicated that highest viral titre of 105-107 copies was present in all the susceptible clones irrespective of their disease severity grades. Our results clearly established that about 22.85% of apparently resistant sugarcane clones remained free from YL symptoms with significantly low ScYLV titre although we could not find a significant correlation between virus titre and symptom expression. The identified resistant parents will serve as sources of YL resistance to develop virus resistant sugarcane varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03541-y.
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Affiliation(s)
- K. Nithya
- ICAR-Sugarcane Breeding Institute, Coimbatore, 641007 India
| | - B. Parameswari
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Hyderabad, 500030 India
- ICAR-Sugarcane Breeding Institute, Research Centre, Karnal, Haryana 132001 India
| | - Subham Kumar
- ICAR-Sugarcane Breeding Institute, Research Centre, Karnal, Haryana 132001 India
| | - A. Annadurai
- ICAR-Sugarcane Breeding Institute, Coimbatore, 641007 India
| | | | | | - R. Viswanathan
- ICAR-Sugarcane Breeding Institute, Coimbatore, 641007 India
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Morgan EL, Toni T, Viswanathan R, Robbins Y, Yang X, Cheng H, Gunti S, Huynh A, Sowers AL, Mitchell JB, Allen CT, Chen Z, Van Waes C. Inhibition of USP14 promotes TNFα-induced cell death in head and neck squamous cell carcinoma (HNSCC). Cell Death Differ 2023; 30:1382-1396. [PMID: 37055579 PMCID: PMC10154301 DOI: 10.1038/s41418-023-01144-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 04/15/2023] Open
Abstract
TNFα is a key mediator of immune, chemotherapy and radiotherapy-induced cytotoxicity, but several cancers, including head and neck squamous cell carcinomas (HNSCC), display resistance to TNFα due to activation of the canonical NFκB pro-survival pathway. However, direct targeting of this pathway is associated with significant toxicity; thus, it is vital to identify novel mechanism(s) contributing to NFκB activation and TNFα resistance in cancer cells. Here, we demonstrate that the expression of proteasome-associated deubiquitinase USP14 is significantly increased in HNSCC and correlates with worse progression free survival in Human Papillomavirus (HPV)- HNSCC. Inhibition or depletion of USP14 inhibited the proliferation and survival of HNSCC cells. Further, USP14 inhibition reduced both basal and TNFα-inducible NFκB activity, NFκB-dependent gene expression and the nuclear translocation of the NFκB subunit RELA. Mechanistically, USP14 bound to both RELA and IκBα and reduced IκBα K48-ubiquitination leading to the degradation of IκBα, a critical inhibitor of the canonical NFκB pathway. Furthermore, we demonstrated that b-AP15, an inhibitor of USP14 and UCHL5, sensitized HNSCC cells to TNFα-mediated cell death, as well as radiation-induced cell death in vitro. Finally, b-AP15 delayed tumor growth and enhanced survival, both as a monotherapy and in combination with radiation, in HNSCC tumor xenograft models in vivo, which could be significantly attenuated by TNFα depletion. These data offer new insights into the activation of NFκB signaling in HNSCC and demonstrate that small molecule inhibitors targeting the ubiquitin pathway warrant further investigation as a novel therapeutic avenue to sensitize these cancers to TNFα- and radiation-induced cytotoxicity.
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Affiliation(s)
- Ethan L Morgan
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA.
- School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK.
| | - Tiffany Toni
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
- NIH Medical Research Scholars Program, Bethesda, MD, USA
| | - Ramya Viswanathan
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Yvette Robbins
- Translational Tumor Immunology Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Xinping Yang
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Hui Cheng
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Sreenivasulu Gunti
- Sinonasal and Skull Base Tumor Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Angel Huynh
- Translational Tumor Immunology Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Anastasia L Sowers
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James B Mitchell
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clint T Allen
- Translational Tumor Immunology Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Zhong Chen
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Carter Van Waes
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
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Toni T, Viswanathan R, Robbins Y, Gunti S, Yang X, Huynh A, Cheng H, Sowers AL, Mitchell JB, Allen CT, Morgan EL, Van Waes C. Combined Inhibition of IAPs and WEE1 Enhances TNFα- and Radiation-Induced Cell Death in Head and Neck Squamous Carcinoma. Cancers (Basel) 2023; 15:1029. [PMID: 36831373 PMCID: PMC9954698 DOI: 10.3390/cancers15041029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) remains a prevalent diagnosis with current treatment options that include radiotherapy and immune-mediated therapies, in which tumor necrosis factor-α (TNFα) is a key mediator of cytotoxicity. However, HNSCC and other cancers often display TNFα resistance due to activation of the canonical IKK-NFκB/RELA pathway, which is activated by, and induces expression of, cellular inhibitors of apoptosis proteins (cIAPs). Our previous studies have demonstrated that the IAP inhibitor birinapant sensitized HNSCC to TNFα-dependent cell death in vitro and radiotherapy in vivo. Furthermore, we recently demonstrated that the inhibition of the G2/M checkpoint kinase WEE1 also sensitized HNSCC cells to TNFα-dependent cell death, due to the inhibition of the pro-survival IKK-NFκB/RELA complex. Given these observations, we hypothesized that dual-antagonist therapy targeting both IAP and WEE1 proteins may have the potential to synergistically sensitize HNSCC to TNFα-dependent cell death. Using the IAP inhibitor birinapant and the WEE1 inhibitor AZD1775, we show that combination treatment reduced cell viability, proliferation and survival when compared with individual treatment. Furthermore, combination treatment enhanced the sensitivity of HNSCC cells to TNFα-induced cytotoxicity via the induction of apoptosis and DNA damage. Additionally, birinapant and AZD1775 combination treatment decreased cell proliferation and survival in combination with radiotherapy, a critical source of TNFα. These results support further investigation of IAP and WEE1 inhibitor combinations in preclinical and clinical studies in HNSCC.
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Affiliation(s)
- Tiffany Toni
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
- Pritzker School of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Ramya Viswanathan
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yvette Robbins
- Section on Translational Tumor Immunology, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Building 10, Room 7N240C, Bethesda, MD 20892, USA
| | - Sreenivasulu Gunti
- Sinonasal and Skull Base Tumor Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xinping Yang
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Angel Huynh
- Section on Translational Tumor Immunology, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Building 10, Room 7N240C, Bethesda, MD 20892, USA
| | - Hui Cheng
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anastasia L. Sowers
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James B. Mitchell
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Clint T. Allen
- Section on Translational Tumor Immunology, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Building 10, Room 7N240C, Bethesda, MD 20892, USA
| | - Ethan L. Morgan
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Carter Van Waes
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
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Nithya K, Vardhan JV, Balasaravanan S, Kaverinathan K, Viswanathan R. Natural infection of Ca. Phytoplasma sacchari causing sugarcane grassy shoot disease in Sorghum bicolor. Vegetos 2023. [DOI: 10.1007/s42535-022-00560-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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8
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Janiga PK, Nithya K, Viswanathan R. Dynamics of Genetic Diversity Among Indian Sugarcane Bacilliform Virus Species and Implications of Associated Recombination Events in the Virus. Sugar Tech 2022. [DOI: 10.1007/s12355-022-01224-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Geetha N, Viswanathan R, Ramasubramanian T, Salin KP, Yogambal C, Devi PN, Karthigeyan S, Chitra N. Phenacoccus saccharifolii (Green) (Pseudococcidae: Hemiptera) on sugarcane in Tamil Nadu, India. CURR SCI INDIA 2022. [DOI: 10.18520/cs/v123/i9/1142-1151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Cheruba E, Viswanathan R, Wong PM, Womersley HJ, Han S, Tay B, Lau Y, Gan A, Poon PSY, Skanderup A, Ng SB, Chok AY, Chong DQ, Tan IB, Cheow LF. Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients. Sci Adv 2022; 8:eabn4030. [PMID: 36083902 PMCID: PMC9462700 DOI: 10.1126/sciadv.abn4030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 07/22/2022] [Indexed: 06/01/2023]
Abstract
Genome-wide analysis of cell-free DNA methylation profile is a promising approach for sensitive and specific detection of many cancers. However, scaling such assays for clinical translation is impractical because of the high cost of whole-genome bisulfite sequencing. We show that the small fraction of GC-rich genome is highly enriched in CpG sites and disproportionately harbors most of the cancer-specific methylation signature. Here, we report on the simple and effective heat enrichment of CpG-rich regions for bisulfite sequencing (Heatrich-BS) platform that allows for focused methylation profiling in these highly informative regions. Our novel method and bioinformatics algorithm enable accurate tumor burden estimation and quantitative tracking of colorectal cancer patient's response to treatment at much reduced sequencing cost suitable for frequent monitoring. We also show tumor epigenetic subtyping using Heatrich-BS, which could enable patient stratification. Heatrich-BS holds great potential for highly scalable screening and monitoring of cancer using liquid biopsy.
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Affiliation(s)
- Elsie Cheruba
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Ramya Viswanathan
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Pui-Mun Wong
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Howard John Womersley
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Shuting Han
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Brenda Tay
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Yiting Lau
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Anna Gan
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Polly S. Y. Poon
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Anders Skanderup
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Sarah B. Ng
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Aik Yong Chok
- Department of Colorectal Surgery, Singapore General Hospital, Singapore 169608, Singapore
| | - Dawn Qingqing Chong
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Iain Beehuat Tan
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
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11
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Walder M, Edelstein E, Carroll M, Lazarev S, Fajardo JE, Fiser A, Viswanathan R. Integrated structure-based protein interface prediction. BMC Bioinformatics 2022; 23:301. [PMID: 35879651 PMCID: PMC9316365 DOI: 10.1186/s12859-022-04852-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
Background Identifying protein interfaces can inform how proteins interact with their binding partners, uncover the regulatory mechanisms that control biological functions and guide the development of novel therapeutic agents. A variety of computational approaches have been developed for predicting a protein’s interfacial residues from its known sequence and structure. Methods using the known three-dimensional structures of proteins can be template-based or template-free. Template-based methods have limited success in predicting interfaces when homologues with known complex structures are not available to use as templates. The prediction performance of template-free methods that only rely only upon proteins’ intrinsic properties is limited by the amount of biologically relevant features that can be included in an interface prediction model. Results We describe the development of an integrated method for protein interface prediction (ISPIP) to explore the hypothesis that the efficacy of a computational prediction method of protein binding sites can be enhanced by using a combination of methods that rely on orthogonal structure-based properties of a query protein, combining and balancing both template-free and template-based features. ISPIP is a method that integrates these approaches through simple linear or logistic regression models and more complex decision tree models. On a diverse test set of 156 query proteins, ISPIP outperforms each of its individual classifiers in identifying protein binding interfaces. Conclusions The integrated method captures the best performance of individual classifiers and delivers an improved interface prediction. The method is robust and performs well even when one of the individual classifiers performs poorly on a particular query protein. This work demonstrates that integrating orthogonal methods that depend on different structural properties of proteins performs better at interface prediction than any individual classifier alone. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04852-2.
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Affiliation(s)
- M Walder
- Department of Chemistry, Yeshiva College, Yeshiva University, New York, NY, 10033, USA
| | - E Edelstein
- Department of Chemistry, Yeshiva College, Yeshiva University, New York, NY, 10033, USA
| | - M Carroll
- Department of Chemistry, Yeshiva College, Yeshiva University, New York, NY, 10033, USA
| | - S Lazarev
- Department of Chemistry, Yeshiva College, Yeshiva University, New York, NY, 10033, USA
| | - J E Fajardo
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - A Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - R Viswanathan
- Department of Chemistry, Yeshiva College, Yeshiva University, New York, NY, 10033, USA.
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12
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Toni T, Morgan E, Viswanathan R, Yang X, Cheng H, Van Waes C. Abstract 2997: Combination treatment with cIAP and WEE1 inhibitors exhibits synergism in HPV-positive and HPV-negative head and neck squamous carcinoma cells. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Head and neck squamous cell carcinoma (HNSCC) remains a lethal and prevalent diagnosis with limited treatment options for recurrent metastatic cases, particularly in patients with sporadic, human papillomavirus (HPV) negative disease. Recently, the Human Cancer Genome Project identified cell death and NF-κB signaling alterations in a subset of HPV- and HPV+ HNSCC. Co-amplification of Fas-associated death domain (FADD) and cellular inhibitor of apoptosis protein 1 (cIAP1) was identified in HPV- HNSCC, whereas Tumor Necrosis Factor receptor-associated factor 3 (TRAF3) deletion was linked with HPV+ HNSCC. Birinapant, a cIAP inhibitor with primary affinity for cIAP1, functions as a SMAC mimetic to modulate downstream TNF death signaling and promote apoptosis. Clinical trials with Birinapant have demonstrated tolerability and favorable pharmacokinetics but limited activity as a single agent. Our lab recently demonstrated a key interaction between TNF-NF-κB signaling and the G2/M checkpoint kinase WEE1, providing a possible rationale for combination treatment targeting these pathways. We hypothesize that dual-antagonist therapy has the potential to synergistically inhibit TNF-induced canonical NF- κB pro-survival signaling, while enhancing sensitization to TNF-caspase and G2/M mitotic cell death. To investigate this, in vitro studies of Birinapant in combination with Adavosertib, a potent WEE1 inhibitor, were performed. Birinapant and Adavosertib demonstrated drug synergism to varying degrees in all HPV- and HPV+ cell lines tested, both in the presence and absence of tumor necrosis factor alpha (TNF-α), according to the Chou-Talalay method. In the majority of cell lines, synergistic drug activity, as indicated by a low combination index, was positively correlated with percent inhibition. These results were confirmed by increased levels of apoptosis as demonstrated by flow cytometry and both early and sustained cell growth inhibition over time in impedance assays. Ongoing studies include additional characterization of the downstream effects of these agents on NF-κB pro-survival signaling and the cell cycle, along with evaluation in a preclinical murine xenograft model with combined radiotherapy.
Citation Format: Tiffany Toni, Ethan Morgan, Ramya Viswanathan, Xinping Yang, Hui Cheng, Carter Van Waes. Combination treatment with cIAP and WEE1 inhibitors exhibits synergism in HPV-positive and HPV-negative head and neck squamous carcinoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2997.
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Affiliation(s)
| | | | | | | | - Hui Cheng
- 1National Institutes of Health, Bethesda, MD
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Morgan EL, Toni T, Yang X, Cheng H, Viswanathan R, Chen Z, Van Waes C. Abstract 2988: Proteasomal deubiquitinases represent an attractive therapeutic target in head and neck squamous cell carcinomas (HNSCC). Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite recent advances in treatment options for Human Papillomavirus (HPV)- head and neck squamous cell carcinoma (HNSCC), the overall survival (OS) rate for HNSCC is low, demonstrating the need for novel therapies for these cancers. Targeting the ubiquitin-proteasome system (UPS) has emerged as a potential target for the development of novel anti-cancer therapies. Bortezomib, a first generation proteasome inhibitor clinically approved for the treatment of Multiple Myeloma, has previously been demonstrated to induce tumor regression in a subset of HNSCC patients through the inhibition of canonical NFκB activity; however, the failure of Bortezomib to inhibit other pro-survival pathways such as MAPK and STAT3 signalling resulted in heterologous responses. A recently developed alternative to proteasome inhibitors is the small molecule b-AP15, which inhibits the proteasomal deubiquitinases USP14 and UCHL5, thus allowing more specificity and less toxicity than proteasome inhibitors.
Here, we show b-AP15 inhibits proliferation and colony formation in multiple HPV- and HPV+ HNSCC cell lines, with minimal effects in normal oral keratinocytes. Furthermore, b-AP15 induces significant caspase-dependent apoptosis. Using siRNA targetting USP14 and UCHL5, only USP14 depletion significantly reduced cell proliferation and colony formation. Mechanistically, b-AP15 treatment reduces TNFα-induced NFκB activity and the expression of pro-survival proteins such as cIAP2 and TRAF2, promoting the formation of the TNFR complex II and sensitizing cells to TNFα-induced cell death. Finally, TCGA data demonstrates that USP14 is highly expressed in HNSCC when compared with normal tissue and is significantly correlated with worse overall survival. Together, we have identified that inhibition of proteasomal deubiquitinases inhibits the proliferation and survival of HNSCC cells and enhanced TNFα-induced cell death via the inhibition of NFκB activity. Our data suggest that combination therapies with b-AP15 could potentially offer a clinical benefit in HNSCC patients by promoting TNFα-induced cytotoxicity. Further studies will focus on the mechanism by which USP14 regulates NFκB signalling in HNSCC cells and the effect of b-AP15 activity in combination with radiation treatment in in vivo mouse xenograft models.
Citation Format: Ethan L. Morgan, Tiffany Toni, Xinping Yang, Hui Cheng, Ramya Viswanathan, Zhong Chen, Carter Van Waes. Proteasomal deubiquitinases represent an attractive therapeutic target in head and neck squamous cell carcinomas (HNSCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2988.
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Affiliation(s)
- Ethan L. Morgan
- 1Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Tiffany Toni
- 2Tumor Biology Section and Clinical Genomics Unit, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Xinping Yang
- 1Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Hui Cheng
- 2Tumor Biology Section and Clinical Genomics Unit, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Ramya Viswanathan
- 1Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Zhong Chen
- 3Oral & Salivary Cancer Biology Program, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD
| | - Carter Van Waes
- 1Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
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Hu Z, Viswanathan R, Cheng H, Chen J, Yang X, Huynh A, Clavijo P, An Y, Robbins Y, Silvin C, Allen C, Ormanoglu P, Martin S, Cornelius S, Saleh A, Chen Z, Van Waes C, Morgan EL. Inhibiting WEE1 and IKK-RELA Crosstalk Overcomes TNFα Resistance in Head and Neck Cancers. Mol Cancer Res 2022; 20:867-882. [PMID: 35176168 DOI: 10.1158/1541-7786.mcr-21-0624] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/20/2021] [Accepted: 02/10/2022] [Indexed: 12/27/2022]
Abstract
TNFα is a key mediator of immune and radiotherapy-induced cytotoxicity, but many cancers, including head and neck squamous cell carcinomas (HNSCC), display TNF resistance due to activation of the canonical IKK-NF-κB/RELA pro-survival pathway. However, toxicities associated with direct targeting of the canonical pathway point to the need to identify mechanism(s) contributing to TNFα resistance and synthetic lethal targets to overcome such resistance in cancer cells. Here, RNAi screening for modulators of TNFα-NF-κB reporter activity and cell survival unexpectedly implicated the WEE1 and CDC2 G2-M checkpoint kinases. The IKKα/β-RELA and WEE1-CDC2 signaling pathways are activated by TNFα and form a complex in cell lines derived from both human papillomavirus (-) and (+) subtypes of HNSCC. WEE1 inhibitor AZD1775 reduced IKK/RELA phosphorylation and the expression of NF-κB-dependent pro-survival proteins Cyclin D1 and BCL2. Combination of TNFα and AZD1775 enhanced caspase-mediated apoptosis in vitro, and combination treatment with radiotherapy and AZD1775 potentiated inhibition of HNSCC tumor xenograft growth in vivo, which could be significantly attenuated by TNFα depletion. These data offer new insight into the interplay between NF-κB signaling and WEE1-mediated regulation of the G2-M cell-cycle checkpoint in HNSCC. IMPLICATIONS Inhibiting WEE1 and IKK-RELA crosstalk could potentially enhance the effects of therapies mediated by TNFα with less systemic immune suppression and toxicity than observed with direct interruption of IKK-NF-κB/RELA signaling.
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Affiliation(s)
- Zhengbo Hu
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland.,Shaoguan First People's Hospital, Affiliated Hospital of Southern Medical University, Shaoguan, Guangdong, China
| | - Ramya Viswanathan
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Hui Cheng
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Jianghong Chen
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Xinping Yang
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Angel Huynh
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Paul Clavijo
- Translational Tumor Immunology Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Yi An
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Yvette Robbins
- Translational Tumor Immunology Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Christopher Silvin
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Clint Allen
- Translational Tumor Immunology Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Pinar Ormanoglu
- RNAi Screening Facility, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Scott Martin
- RNAi Screening Facility, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Shaleeka Cornelius
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Anthony Saleh
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Zhong Chen
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Carter Van Waes
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Ethan L Morgan
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
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Sathyabhama M, Viswanathan R, Prasanth CN, Malathi P, Sundar AR. Differential host responses of sugarcane to Colletotrichum falcatum reveal activation of probable effector triggered immunity (ETI) in defence responses. Plant Cell Rep 2022; 41:1461-1476. [PMID: 35415786 DOI: 10.1007/s00299-022-02870-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/22/2022] [Indexed: 02/05/2023]
Abstract
KEY MESSAGE The differential compatibility responses of sugarcane to Colletotrichum falcatum pathotypes depend on the nature of both host primary defence signalling cascades and pathogen virulence. The complex polyploidy of sugarcane genome and genetic variations in different cultivars of sugarcane remain a challenge to identify and characterise specific genes controlling the compatible and incompatible interactions between sugarcane and the red rot pathogen, Colletotrichum falcatum. To avoid host background variation in the interaction study, suppression subtractive hybridization (SSH)-based next-generation sequencing (NGS) technology was used in a sugarcane cultivar Co 7805 which is compatible with one C. falcatum pathotype but incompatible with another one. In the incompatible interaction (ICI-less virulent) 10,038 contigs were assembled from ~ 54,699,263 raw reads, while 4022 contigs were assembled from ~ 52,509,239 in the compatible interaction (CI-virulent). The transcripts homologous to CEBiP receptor and those involved in the signalling pathways of ROS, Ca2+, BR, and ABA were expressed in both interaction responses. In contrast, MAPK, ET, PI signalling pathways and JA amino conjugation related transcripts were found only in ICI. In temporal gene expression assays, 16 transcripts showed their highest induction in ICI than CI. Further, more than 17 transcripts specific to the pathogen were found only in CI, indicating that the pathogen colonizes the host tissue whereas it failed to do so in ICI. Overall, this study has identified for the first time that a probable PAMP triggered immunity (PTI) in both responses, while a more efficient effector triggered immunity (ETI) was found only in ICI. Moreover, pathogen proliferation could be predicted in CI based on transcript expression, which were homologous to Glomerella graminicola, the nearest clade to the perfect stage of C. falcatum (G. tucumanensis).
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Affiliation(s)
- M Sathyabhama
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
- Department of Biotechnology, PSG College of Arts and Science, Coimbatore, 641014, India
| | - R Viswanathan
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India.
| | - C N Prasanth
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - P Malathi
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - A Ramesh Sundar
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
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Prasanth CN, Viswanathan R, Malathi P, Sundar AR. Carbohydrate active enzymes (CAZy) regulate cellulolytic and pectinolytic enzymes in Colletotrichum falcatum causing red rot in sugarcane. 3 Biotech 2022; 12:48. [PMID: 35127303 PMCID: PMC8787009 DOI: 10.1007/s13205-022-03113-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/08/2022] [Indexed: 02/05/2023] Open
Abstract
Colletotrichum falcatum, an ascomycete pathogen causes red rot of sugarcane which is specialized to infect cane stalks. Cellulolytic and pectinolytic enzymes are necessary for degradation of plant cell wall which stands as barrier for successful fungal pathogenesis. In the study, we have confined to the CAZy genes that regulate cellulolytic and pectinolytic enzymes in two distinctive pathotypes of C. falcatum. Comparative transcriptome analysis revealed that a number of CAZy genes producing cellulolytic and pectinolytic enzyme were present in the virulent (Cf671) and least virulent (RoC) pathotypes. Two consecutive transcriptome analyses (in vitro) were performed using Illumina Hi Seq 2500, further analysis was done with various bioinformatic tools. In vitro expression analysis of cutinase, glycoside hydrolyase and pectin-related genes revealed number of genes that attributes virulence. Numerous pectin-related genes involved in degradation of plant cell wall, pectinase and pectin lyase are considered to be key precursor in degradation of pectin in sugarcane. These results suggest that cellulolytic enzymes, cutinase and pectin-related genes are essential for degradation of sugarcane cell wall and considered to be an important pathogenic factor in C. falcatum. This is the first detailed report on sugarcane cell wall-degrading enzymes during its interaction with C. falcatum and also this comparative transcriptome analysis provided more insights into pathogen mechanism on C. falcatum. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-022-03113-6.
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Affiliation(s)
- C. Naveen Prasanth
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - R. Viswanathan
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - P. Malathi
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - A. Ramesh Sundar
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
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Viswanathan R, Singh SP, Selvakumar R, Singh D, Bharti YP, Chhabra ML, Parameswari B, Sharma A, Minnatullah M. Varietal Break Down to Red Rot in the Sugarcane Variety Co 0238 Mimics Vertifolia Effect: Characterizing New Colletotrichum falcatum Pathotype CF13. Sugar Tech 2022. [DOI: 10.1007/s12355-021-01070-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Viswanathan R, Ramasubramanian T, Chinnaraja C, Selvakumar R, Pathy TL, Manivannan K, Nithyanantham R. Population dynamics of Melanaphis sacchari (Zehntner), the aphid vector of sugarcane yellow leaf virus under tropical conditions in India. Trop plant pathol 2022. [DOI: 10.1007/s40858-021-00483-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Balan S, Nithya K, Cherian KA, Viswanathan R. True Seed Transmission of Sugarcane bacilliform virus (SCBV) in Sugarcane. Sugar Tech 2021. [DOI: 10.1007/s12355-021-01031-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Viswanathan R, Selvakumar R, Geetha N, Balaji CG, Annadurai A, Pazhani AS, Malathi P, Sundar AR, Nithiyanantham R, Manivannan K. Epidemiology of sugarcane wilt: predisposition by root borer Polyocha depresella a myth or reality. Indian Phytopathology 2021. [DOI: 10.1007/s42360-021-00398-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Viswanathan R, Rao GP, Solomon S. Measures to Minimize the Growing Menace of Red Rot of Sugarcane in Subtropical India. Sugar Tech 2021. [DOI: 10.1007/s12355-021-01013-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Viswanathan R. Impact of yellow leaf disease in sugarcane and its successful disease management to sustain crop production. Indian Phytopathology 2021. [DOI: 10.1007/s42360-021-00391-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Parameswari B, Nithya K, Kumar S, Holkar SK, Chabbra ML, Kumar P, Viswanathan R. Genome wide association studies in sugarcane host pathogen system for disease resistance: an update on the current status of research. Indian Phytopathology 2021. [DOI: 10.1007/s42360-021-00323-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Nandakumar M, Malathi P, Sundar AR, Viswanathan R. Expression Analyses of Resistance-Associated Candidate Genes During Sugarcane-Colletotrichum falcatum Went Interaction. Sugar Tech 2021. [DOI: 10.1007/s12355-021-00976-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Nandakumar M, Malathi P, Sundar AR, Rajadurai CP, Philip M, Viswanathan R. Role of miRNAs in the host-pathogen interaction between sugarcane and Colletotrichum falcatum, the red rot pathogen. Plant Cell Rep 2021; 40:851-870. [PMID: 33818644 DOI: 10.1007/s00299-021-02682-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023]
Abstract
KEY MESSAGE Sugarcane microRNAs specifically involved during compatible and incompatible interactions with red rot pathogen Colletotrichum falcatum were identified. We have identified how the miRNAs regulate their gene targets and elaborated evidently on the underlying molecular mechanism of sugarcane defense response to C. falcatum for the first time. Resistance against the fungal pathogen Colletotrichum falcatum causing red rot is one of the most desirable traits for sustainable crop cultivation in sugarcane. To gain new insight into the host defense mechanism against C. falcatum, we studied the role of sugarcane microRNAs during compatible and incompatible interactions by adopting the NGS platform. We have sequenced a total of 80 miRNA families that comprised 980 miRNAs, and the putative targets of the miRNAs include transcription factors, membrane-bound proteins, glutamate receptor proteins, lignin biosynthesis proteins, signaling cascade proteins, transporter proteins, mitochondrial proteins, ER proteins, defense-related, stress response proteins, translational regulation proteins, cell proliferation, and ubiquitination proteins. Further, qRT-PCR analyses of 8 differentially regulated miRNAs and 26 gene transcript targets expression indicated that these miRNAs have a regulatory effect on the expression of respective target genes in most of the cases. Also, the results suggest that certain miRNA regulates many target genes that are involved in inciting early responses to the pathogen infection, signaling pathways, endoplasmic reticulum stress, and resistance gene activation through feedback response from various cellular processes during the compatible and incompatible interaction with the red rot pathogen C. falcatum. The present study revealed the role of sugarcane miRNAs and their target genes during sugarcane-C. falcatum interaction and provided new insight into the miRNA-mediated defense mechanism in sugarcane for the first time.
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Affiliation(s)
- M Nandakumar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - P Malathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - A R Sundar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - C P Rajadurai
- AgriGenome Labs, Infopark-Smart City Short Rd, Kochi, Kerala, 682030, India
| | - Manuel Philip
- AgriGenome Labs, Infopark-Smart City Short Rd, Kochi, Kerala, 682030, India
| | - R Viswanathan
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India.
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Nandakumar M, Viswanathan R, Malathi P, Ramesh Sundar A. Selection of reference genes for normalization of microRNA expression in sugarcane stalks during its interaction with Colletotrichum falcatum. 3 Biotech 2021; 11:72. [PMID: 33489689 DOI: 10.1007/s13205-020-02632-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/28/2020] [Indexed: 02/05/2023] Open
Abstract
The microRNAs role in various cellular and metabolic functions is gaining more limelight in line with second-generation NGS technology. For the validation of candidate miRNA genes, the quantitative real-time PCR is the widely trusted and efficient method to follow. Sugarcane miRNAs are less explored in sugarcane defense response during their interaction with Colletotrichum falcatum inciting red rot. Further, for RT-qPCR experiments involving sugarcane miRNA expression studies, a stable internal reference gene is required. Hence, we have taken a study involving 20 candidate genes to identify stable expressing reference genes using NormFinder, geNorm, BestKeeper, and deltaCt statistical algorithms. The candidate reference genes included miRNAs and protein-coding genes. The results indicated that there is a variation in ranking among the algorithms. We found miR1862c as the stably expressed miRNA reference gene among the candidates and miR444b.2 along miR1862c formed the best reference gene pair combination, which can be used in the experiments aiming to explore sugarcane miRNAs in the defense mechanism against C. falcatum. The stable miRNA reference gene was further validated with other lesser stable reference gene candidates to assess the effect of stable reference genes during normalization. The present study evaluating the sugarcane miRNAs as reference genes for normalizing RT-qPCR expression data involving miRNAs during sugarcane × C. falcatum interaction is the first of its kind. Further, this systematic approach can be followed to assess the reference gene in various experimental conditions involving sugarcane miRNAs.
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Affiliation(s)
- M Nandakumar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - R Viswanathan
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - P Malathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - A Ramesh Sundar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
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Patel V, Viswanathan R, Ruffner R, Peris-Celda M, Pinheiro-Neto CD. Comparing nasal physiology after superior ethmoidal and traditional endoscopic anterior cranial base approaches. Rhinology 2021; 58:629-631. [PMID: 32926008 DOI: 10.4193/rhin20.325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- V Patel
- Division of Otolaryngology / Head and Neck Surgery, Department of Surgery, Albany Medical Center, Albany, NY, USA
| | | | - R Ruffner
- Division of Otolaryngology / Head and Neck Surgery, Department of Surgery, Albany Medical Center, Albany, NY, USA
| | - M Peris-Celda
- Department of Neurosurgery, Albany Medical Center, Albany, NY, USA;Adjunct Assistant Professor, Department of Neurosurgery, Mayo Clinic, Rochester, MN, USA
| | - C D Pinheiro-Neto
- Division of Otolaryngology / Head and Neck Surgery, Department of Surgery, Albany Medical Center, Albany, NY, USA; Department of Neurosurgery, Albany Medical Center, Albany, NY, USA
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Gopi R, Mahendran B, Chandran K, Nisha M, Viswanathan R. Plant and Weather Factors on Resistance of Saccharum officinarum Germplasm Against Ring Spot Disease. Sugar Tech 2021. [DOI: 10.1007/s12355-020-00943-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Prasanth CN, Viswanathan R, Malathi P, Sundar AR. Development and characterization of genomic SSR marker for virulent strain-specific Colletotrichum falcatum infecting sugarcane. 3 Biotech 2021; 11:20. [PMID: 33442518 DOI: 10.1007/s13205-020-02572-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/28/2020] [Indexed: 02/05/2023] Open
Abstract
Colle totrichum falcatum, an intriguing pathogen causing red rot in sugarcane, exhibits enormous variation for pathogenicity under field conditions. A species-specific marker is very much needed to classify the virulence among the varying population and to identify the potential of a pathotype by mining the microsatellites, which are considered to be the largest genetic source to develop molecular markers for an organism. In this study, we have mined the C. falcatum genome using MISA database which yielded 12,121 SSRs from 48.1 Mb and 2745 SSRs containing sequences. The most frequent SSR types from the genome of C. falcatum was di-nucleotide which constitutes 50.89% followed by tri-nucleotide 39.60%, hepta-nucleotide 6.7%, hexa-nucleotide 1.38% and penta-nucleotide 1.3%. Over 90 SSR containing sequences from the genome were predicted using BlastX which are found to be non-homologs. Most of the annotated SSR containing sequences fell in CAZy superfamilies, proteases, peptidases, plant cell wall degrading enzymes (PCDWE) and membrane transporters which are considered to be pathogenicity gene clusters. Among them, glycosyl hydrolases (GH) were found to be abundant in SSR containing sequences which again proved our previous transcriptome results. Our in-silico results suggested that the mined microsatellites from C. falcatum genome show absence of homolog sequences which suggests that these markers could be used as an ideal species-specific molecular marker. Two virulence specific markers were characterized using conventional PCR assays from C. falcatum along with virulent species-specific (VSS) marker developed for C. gloeosporioides. The study lays the foundation for the development of C. falcatum specific molecular marker to phenotype the pathotypes based on virulence.
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Affiliation(s)
- C Naveen Prasanth
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, Coimbatore, 641007 India
| | - R Viswanathan
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, Coimbatore, 641007 India
| | - P Malathi
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, Coimbatore, 641007 India
| | - A Ramesh Sundar
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, Coimbatore, 641007 India
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Jayakumar V, Ramesh Sundar A, Viswanathan R. Biocontrol of Colletotrichum falcatum with volatile metabolites produced by endophytic bacteria and profiling VOCs by headspace SPME coupled with GC–MS. Sugar Tech 2020. [DOI: 10.1007/s12355-020-00891-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Viswanathan R, Hu Z, Chen J, Yang X, Huynh A, Clavijo P, An Y, Robbins Y, Silvin C, Allen C, Saleh A, Chen Z, Van Waes C. Abstract 6042: TNFa co-activates IKK/NF-kB/RELA prosurvival and WEE1-CDC2 G2/M checkpoint signaling and is targetable by WEE1 antagonist AZD1775 in head and neck cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-6042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cytotoxic and genotoxic therapies are known to induce the prosurvival Inhibitor-kappaB kinase (IKK)-NF-κB/RELA pathway and DNA repair at the G2/M checkpoint, thereby promoting therapeutic resistance, but the coordination of these mechanisms is unclear. Our recent RNAi screen unexpectedly uncovered possible crosstalk between WEE1, a G2/M checkpoint kinase and the TNFα-IKK-NF-κB prosurvival pathway components. siRNAs targeting WEE1 and IKKs both inhibited TNFα-inducible NF-κB activity in a HNSCC reporter line, suggesting a mechanistic linkage. We investigated this potential connection further and studied the effect of WEE1 inhibition using AZD1775 in head and neck squamous cell carcinoma (HNSCC) cells and mouse xenograft models. Increased expression, phosphorylation and cellular localization of IKK-NF-κB and WEE1-CDC2 axis proteins co-occurred in a subset of HNSCC lines, and were inversely co-modulated by TNFα and WEE1 kinase inhibitor AZD1775. WEE1 co-immunoprecipitated with the IKKα/β and RELA protein complex, and AZD1775 or an IKK inhibitor, IKK16, inhibited phosphorylation and kinase activities, further suggesting that these two axes interact with each other. AZD1775 sensitized HNSCC cells to TNFα-induced cytotoxicity, in part by inhibiting IKK-dependent phosphorylation and nuclear localization of NF-κB activation, and expression of target prosurvival protein BCL-2. Combination of AZD1775 with radiation, a known inducer of TNFα- and DNA-mediated cytotoxicity, potently inhibited HPV+/- HNSCC tumor xenografts. Depleting TNFα abolished the anti-tumor activity of combined therapy with AZD1775 and radiation. The findings of our study reveal that TNFα co-modulates a novel interaction between the prosurvival IKK/NF-κB/RELA and WEE1-CDC2 G2/M checkpoint pathway and that components of both the pathways are inhibited by AZD1775. Our mouse xenograft experiments suggest that AZD1775, when combined with radiation, significantly delays the growth of xenograft HNSCC tumors differing in HPV status in a TNFα-dependent manner. The current findings reveal a novel mechanism whereby crosstalk and co-activation of WEE1- and NF-κB-signaling promotes resistance to TNFα-mediated cytotoxicity, which may be targeted using WEE1 inhibitors.
Supported by NIDCD projects ZIA-DC-000016, -73 and 74.
Citation Format: Ramya Viswanathan, Zhengbo Hu, Jianghong Chen, Xinping Yang, Angel Huynh, Paul Clavijo, Yi An, Yvette Robbins, Christopher Silvin, Clint Allen, Anthony Saleh, Zhong Chen, Carter Van Waes. TNFa co-activates IKK/NF-kB/RELA prosurvival and WEE1-CDC2 G2/M checkpoint signaling and is targetable by WEE1 antagonist AZD1775 in head and neck cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6042.
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Affiliation(s)
- Ramya Viswanathan
- 1Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Zhengbo Hu
- 2The First People's Hospital of Shaoguan, Affiliated Hospital of Southern Medical University, Shaoguan, Guangdong, China, China
| | - Jianghong Chen
- 1Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Xinping Yang
- 1Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Angel Huynh
- 1Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Paul Clavijo
- 3Translational Tumor Immunology Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Yi An
- 1Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Yvette Robbins
- 3Translational Tumor Immunology Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Christopher Silvin
- 1Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Clint Allen
- 3Translational Tumor Immunology Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Anthony Saleh
- 1Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Zhong Chen
- 1Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Carter Van Waes
- 1Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
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Luo Y, Viswanathan R, Hande MP, Loh AHP, Cheow LF. Massively parallel single-molecule telomere length measurement with digital real-time PCR. Sci Adv 2020; 6:eabb7944. [PMID: 32937369 PMCID: PMC7442360 DOI: 10.1126/sciadv.abb7944] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/09/2020] [Indexed: 05/02/2023]
Abstract
Telomere length is a promising biomarker for age-associated diseases and cancer, but there are still substantial challenges to routine telomere analysis in clinics because of the lack of a simple and rapid yet scalable method for measurement. We developed the single telomere absolute-length rapid (STAR) assay, a novel high-throughput digital real-time PCR approach for rapidly measuring the absolute lengths and quantities of individual telomere molecules. We show that this technique provides the accuracy and sensitivity to uncover associations between telomere length distribution and telomere maintenance mechanisms in cancer cell lines and primary tumors. The results indicate that the STAR assay is a powerful tool to enable the use of telomere length distribution as a biomarker in disease and population-wide studies.
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Affiliation(s)
- Yongqiang Luo
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Ramya Viswanathan
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Manoor Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Amos Hong Pheng Loh
- Department of Paediatric Surgery, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore.
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
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Bothmer A, Gareau KW, Abdulkerim HS, Buquicchio F, Cohen L, Viswanathan R, Zuris JA, Marco E, Fernandez CA, Myer VE, Cotta-Ramusino C. Detection and Modulation of DNA Translocations During Multi-Gene Genome Editing in T Cells. CRISPR J 2020; 3:177-187. [PMID: 32584143 DOI: 10.1089/crispr.2019.0074] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Multiplexed genome editing with DNA endonucleases has broad application, including for cellular therapies, but chromosomal translocations, natural byproducts of inducing simultaneous genomic breaks, have not been explored in detail. Here we apply various CRISPR-Cas nucleases to edit the T cell receptor alpha and beta 2 microglobulin genes in human primary T cells and comprehensively evaluate the frequency and stability of the resulting translocations. A thorough translocation frequency analysis using three orthogonal methods (droplet digital PCR, unidirectional sequencing, and metaphase fluorescence in situ hybridization) yielded comparable results and an overall translocation rate of ∼7% between two simultaneous CRISPR-Cas9 induced edits. In addition, we show that chromosomal translocations can be reduced when using different nuclease combinations, or by the presence of a homologous single stranded oligo donor for multiplexed genome editing. Importantly, the two different approaches for translocation reduction are compatible with cell therapy applications.
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Affiliation(s)
- Anne Bothmer
- Editas Medicine, Cambridge, Massachusetts, USA
- Tessera Therapeutic, Cambridge, Massachusetts, USA
| | | | - Hayat S Abdulkerim
- Editas Medicine, Cambridge, Massachusetts, USA
- Third Rock NewCo, Cambridge, Massachusetts, USA
| | - Frank Buquicchio
- Editas Medicine, Cambridge, Massachusetts, USA
- Program in Immunology, Stanford University, Stanford, California, USA
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Lucas Cohen
- Editas Medicine, Cambridge, Massachusetts, USA
- University of California San Diego, La Jolla, California, USA
| | | | | | | | - Cecilia A Fernandez
- Editas Medicine, Cambridge, Massachusetts, USA
- Diagon Therapeutic, Boston Massachusetts, USA
| | - Vic E Myer
- Editas Medicine, Cambridge, Massachusetts, USA
- Atlas Venture, Cambridge, Massachusetts, USA
| | - Cecilia Cotta-Ramusino
- Editas Medicine, Cambridge, Massachusetts, USA
- Tessera Therapeutic, Cambridge, Massachusetts, USA
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Ovalle W, Viswanathan R. Sustaining Sugarcane Production in Guatemala and Nicaragua Through Efficient Disease Management Approaches. Sugar Tech 2020. [DOI: 10.1007/s12355-020-00801-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Viswanathan R, Cheruba E, Cheow LF. DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells. Nucleic Acids Res 2019; 47:e122. [PMID: 31418018 PMCID: PMC6821369 DOI: 10.1093/nar/gkz717] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/21/2019] [Accepted: 08/13/2019] [Indexed: 12/11/2022] Open
Abstract
Genome-wide profiling of copy number alterations and DNA methylation in single cells could enable detailed investigation into the genomic and epigenomic heterogeneity of complex cell populations. However, current methods to do this require complex sample processing and cleanup steps, lack consistency, or are biased in their genomic representation. Here, we describe a novel single-tube enzymatic method, DNA Analysis by Restriction Enzyme (DARE), to perform deterministic whole genome amplification while preserving DNA methylation information. This method was evaluated on low amounts of DNA and single cells, and provides accurate copy number aberration calling and representative DNA methylation measurement across the whole genome. Single-cell DARE is an attractive and scalable approach for concurrent genomic and epigenomic characterization of cells in a heterogeneous population.
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Affiliation(s)
- Ramya Viswanathan
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore 117583, Singapore
| | - Elsie Cheruba
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore 117583, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore 117583, Singapore
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Heiss G, Ploetz E, Voith von Voithenberg L, Viswanathan R, Glaser S, Schluesche P, Madhira S, Meisterernst M, Auble DT, Lamb DC. Conformational changes and catalytic inefficiency associated with Mot1-mediated TBP-DNA dissociation. Nucleic Acids Res 2019; 47:2793-2806. [PMID: 30649478 PMCID: PMC6451094 DOI: 10.1093/nar/gky1322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 12/21/2018] [Accepted: 01/07/2019] [Indexed: 11/12/2022] Open
Abstract
The TATA-box Binding Protein (TBP) plays a central role in regulating gene expression and is the first step in the process of pre-initiation complex (PIC) formation on promoter DNA. The lifetime of TBP at the promoter site is controlled by several cofactors including the Modifier of transcription 1 (Mot1), an essential TBP-associated ATPase. Based on ensemble measurements, Mot1 can use adenosine triphosphate (ATP) hydrolysis to displace TBP from DNA and various models for how this activity is coupled to transcriptional regulation have been proposed. However, the underlying molecular mechanism of Mot1 action is not well understood. In this work, the interaction of Mot1 with the DNA/TBP complex was investigated by single-pair Förster resonance energy transfer (spFRET). Upon Mot1 binding to the DNA/TBP complex, a transition in the DNA/TBP conformation was observed. Hydrolysis of ATP by Mot1 led to a conformational change but was not sufficient to efficiently disrupt the complex. SpFRET measurements of dual-labeled DNA suggest that Mot1's ATPase activity primes incorrectly oriented TBP for dissociation from DNA and additional Mot1 in solution is necessary for TBP unbinding. These findings provide a framework for understanding how the efficiency of Mot1's catalytic activity is tuned to establish a dynamic pool of TBP without interfering with stable and functional TBP-containing complexes.
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Affiliation(s)
- Gregor Heiss
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
| | - Evelyn Ploetz
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
| | - Lena Voith von Voithenberg
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
| | - Ramya Viswanathan
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Samson Glaser
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
| | - Peter Schluesche
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
| | - Sushi Madhira
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
| | - Michael Meisterernst
- Institut für Molekulare Tumorbiologie, Westfälische Wilhelms-Universität, Münster 48149, Germany
| | - David T Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Don C Lamb
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
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Nandakumar M, Malathi P, Sundar AR, Viswanathan R. Use of Green Fluorescent Protein Expressing Colletotrichum falcatum, the Red Rot Pathogen for Precise Host–Pathogen Interaction Studies in Sugarcane. Sugar Tech 2019. [DOI: 10.1007/s12355-019-00751-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Viswanathan R, Bingham A, Raghav S, Arjunan SP, Jelfs B, Kempster P, Kumar DK. Normalized Mutual Information of phonetic sound to distinguish the speech of Parkinson's disease. Annu Int Conf IEEE Eng Med Biol Soc 2019; 2019:3523-3526. [PMID: 31946638 DOI: 10.1109/embc.2019.8857112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This study has investigated the use of inter-personnel mutual information computed from the phonetic sound recordings to differentiate between Parkinson's disease (PD) and control subjects. The normalized mutual information (NMI) denotes the amount of information shared between the voice recordings of people within the same group: PD and Control. The hypothesis of this study was that within group NMI will be significantly different when compared with inter- group NMI. For each phonetic sound, the NMI was computed for every pairing of recordings for both the PD and control groups. Pearson correlation coefficient analysis was used to determine the association of NMI with clinical parameters including Unified Parkinson's Disease Rating Scale (UPDRS), Montreal cognitive assessment (MoCA) and disease duration. ANOVA test for the three phonetic sounds of control and PD subjects showed that there is significant difference between the intra-group mean NMI for the two groups (p <; 0.003) and also showed significant association with the UPDRS motor examination score, MoCA and disease duration.
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Malathi P, Viswanathan R, Jothi R. Specific adaptation of colletotrichum falcatum pathotypes to sugarcane cultivars. Sugar Tech 2018. [DOI: 10.1007/bf02943742] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Anandakumar L, Bagyalakshmi K, Nithya K, Parameswari B, Viswanathan R. Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Assay for Rapid Diagnosis of Sugarcane yellow leaf virus in Sugarcane. Sugar Tech 2018. [DOI: 10.1007/s12355-018-0606-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Arun Prakash VR, Viswanathan R. Microwave-shielding behavior of silanized Cu and Cu–Fe3O4 compound particle-reinforced epoxy resin composite in E-, F-, I-, and J-band frequencies. Polym Bull (Berl) 2018. [DOI: 10.1007/s00289-017-2262-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Clapier CR, Kasten MM, Parnell TJ, Viswanathan R, Szerlong H, Sirinakis G, Zhang Y, Cairns BR. Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection. Mol Cell 2017; 62:453-461. [PMID: 27153540 DOI: 10.1016/j.molcel.2016.03.032] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 01/29/2016] [Accepted: 03/30/2016] [Indexed: 11/30/2022]
Abstract
The RSC chromatin remodeler slides and ejects nucleosomes, utilizing a catalytic subunit (Sth1) with DNA translocation activity, which can pump DNA around the nucleosome. A central question is whether and how DNA translocation is regulated to achieve sliding versus ejection. Here, we report the regulation of DNA translocation efficiency by two domains residing on Sth1 (Post-HSA and Protrusion 1) and by actin-related proteins (ARPs) that bind Sth1. ARPs facilitated sliding and ejection by improving "coupling"-the amount of DNA translocation by Sth1 relative to ATP hydrolysis. We also identified and characterized Protrusion 1 mutations that promote "coupling," and Post-HSA mutations that improve ATP hydrolysis; notably, the strongest mutations conferred efficient nucleosome ejection without ARPs. Taken together, sliding-to-ejection involves a continuum of DNA translocation efficiency, consistent with higher magnitudes of ATPase and coupling activities (involving ARPs and Sth1 domains), enabling the simultaneous rupture of multiple histone-DNA contacts facilitating ejection.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Margaret M Kasten
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Timothy J Parnell
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Ramya Viswanathan
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Heather Szerlong
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - George Sirinakis
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Bradley R Cairns
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Ashwin NMR, Barnabas L, Ramesh Sundar A, Malathi P, Viswanathan R, Masi A, Agrawal GK, Rakwal R. Advances in proteomic technologies and their scope of application in understanding plant–pathogen interactions. J Plant Biochem Biotechnol 2017. [DOI: 10.1007/s13562-017-0402-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Kaverinathan K, Scindiya M, Malathi P, Viswanathan R, Ramesh Sundar A. Role of Melanin in Colletotrichum falcatum Pathogenesis Causing Sugarcane Red Rot. Sugar Tech 2017. [DOI: 10.1007/s12355-017-0519-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Barnabas L, Ashwin NMR, Kaverinathan K, Trentin AR, Pivato M, Sundar AR, Malathi P, Viswanathan R, Rosana OB, Neethukrishna K, Carletti P, Arrigoni G, Masi A, Agrawal GK, Rakwal R. Proteomic analysis of a compatible interaction between sugarcane and Sporisorium scitamineum. Proteomics 2016; 16:1111-22. [PMID: 26857420 DOI: 10.1002/pmic.201500245] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 01/05/2016] [Accepted: 02/02/2016] [Indexed: 02/05/2023]
Abstract
Smut caused by Sporisorium scitamineum is one of the important diseases of sugarcane with global significance. Despite the intriguing nature of sugarcane, S. scitamineum interaction, several pertinent aspects remain unexplored. This study investigates the proteome level alterations occurring in the meristem of a S. scitamineum infected susceptible sugarcane cultivar at whip emergence stage. Differentially abundant proteins were identified by 2DE coupled with MALDI-TOF/TOF-MS. Comprehensively, 53 sugarcane proteins identified were related to defence, stress, metabolism, protein folding, energy, and cell division; in addition, a putative effector of S. scitamineum, chorismate mutase, was identified. Transcript expression vis-à-vis the activity of phenylalanine ammonia lyase was relatively higher in the infected meristem. Abundance of seven candidate proteins in 2D gel profiles was in correlation with its corresponding transcript expression levels as validated by qRT-PCR. Furthermore, this study has opened up new perspectives on the interaction between sugarcane and S. scitamineum.
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Affiliation(s)
- Leonard Barnabas
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - N M R Ashwin
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - K Kaverinathan
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - Anna Rita Trentin
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Micaela Pivato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - A Ramesh Sundar
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - P Malathi
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - R Viswanathan
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - O B Rosana
- Bioinformatics Center, ICAR-Indian Institute of Spices Research, Kozhikode, India
| | - K Neethukrishna
- Bioinformatics Center, ICAR-Indian Institute of Spices Research, Kozhikode, India
| | - Paolo Carletti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Giorgio Arrigoni
- Proteomics Center of Padova University, Padova, Italy.,Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.,GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.,GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal.,Tsukuba International Academy for Sport Studies (TIAS) and Faculty of Health and Sport Sciences, University of Tsukuba, Ibaraki, Japan
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48
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Viswanathan R, True JD, Auble DT. Molecular Mechanism of Mot1, a TATA-binding Protein (TBP)-DNA Dissociating Enzyme. J Biol Chem 2016; 291:15714-26. [PMID: 27255709 DOI: 10.1074/jbc.m116.730366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 11/06/2022] Open
Abstract
The essential Saccharomyces cerevisiae ATPase Mot1 globally regulates transcription by impacting the genomic distribution and activity of the TATA-binding protein (TBP). In vitro, Mot1 forms a ternary complex with TBP and DNA and can use ATP hydrolysis to dissociate the TBP-DNA complex. Prior work suggested an interaction between the ATPase domain and a functionally important segment of DNA flanking the TATA sequence. However, how ATP hydrolysis facilitates removal of TBP from DNA is not well understood, and several models have been proposed. To gain insight into the Mot1 mechanism, we dissected the role of the flanking DNA segment by biochemical analysis of complexes formed using DNAs with short single-stranded gaps. In parallel, we used a DNA tethered cleavage approach to map regions of Mot1 in proximity to the DNA under different conditions. Our results define non-equivalent roles for bases within a broad segment of flanking DNA required for Mot1 action. Moreover, we present biochemical evidence for two distinct conformations of the Mot1 ATPase, the detection of which can be modulated by ATP analogs as well as DNA sequence flanking the TATA sequence. We also show using purified complexes that Mot1 dissociation of a stable, high affinity TBP-DNA interaction is surprisingly inefficient, suggesting how other transcription factors that bind to TBP may compete with Mot1. Taken together, these results suggest that TBP-DNA affinity as well as other aspects of promoter sequence influence Mot1 function in vivo.
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Affiliation(s)
- Ramya Viswanathan
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - Jason D True
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - David T Auble
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
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Viswanathan R. Pathogen Virulence in Sugarcane Red Rot Pathogen Versus Varieties in Cultivation: Classical Case of Loss in Virulence in the Pathotype CF06 (Cf671). Sugar Tech 2016. [DOI: 10.1007/s12355-016-0458-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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50
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Chhabra ML, Parameswari B, Viswanathan R. Pathogenic behaviour pattern of Colletotrichum falcatum isolates of sugarcane in sub-tropical India. ACTA ACUST UNITED AC 2016. [DOI: 10.5958/2229-4473.2016.00103.8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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