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Mikheeva SA, Funk CC, Horner PJ, Rostomily RC, Mikheev AM. Novel TCF4:TCF12 heterodimer inhibits glioblastoma growth. Mol Oncol 2024; 18:517-527. [PMID: 37507199 PMCID: PMC10920085 DOI: 10.1002/1878-0261.13496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/15/2023] [Accepted: 07/24/2023] [Indexed: 07/30/2023] Open
Abstract
TWIST1 (TW) is a pro-oncogenic basic helix-loop-helix (bHLH) transcription factor and promotes the hallmark features of malignancy (e.g., cell invasion, cancer cell stemness, and treatment resistance), which contribute to poor prognoses of glioblastoma (GBM). We previously reported that specific TW dimerization motifs regulate unique cellular phenotypes in GBM. For example, the TW:E12 heterodimer increases periostin (POSTN) expression and promotes cell invasion. TW dimer-specific transcriptional regulation requires binding to the regulatory E-box consensus sequences, but alternative bHLH dimers that balance TW dimer activity in regulating pro-oncogenic TW target genes are unknown. We leveraged the ENCODE DNase I hypersensitivity data to identify E-box sites and tethered TW:E12 and TW:TW proteins to validate dimer binding to E-boxes in vitro. Subsequently, TW knockdown revealed a novel TCF4:TCF12 bHLH dimer occupying the same TW E-box site that, when expressed as a tethered TCF4:TCF12 dimer, markedly repressed POSTN expression and extended animal survival. These observations support TCF4:TCF12 as a novel dimer with tumor-suppressor activity in GBM that functions in part through displacement of and/or competitive inhibition of pro-oncogenic TW dimers at E-box sites.
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Affiliation(s)
- Svetlana A. Mikheeva
- Department of Neurosurgery, Center for NeuroregenerationHouston Methodist Research InstituteTexasUSA
| | - Cory C. Funk
- Institute for Systems BiologySeattleWashingtonUSA
| | - Philip J. Horner
- Department of Neurosurgery, Center for NeuroregenerationHouston Methodist Research InstituteTexasUSA
- Department of NeurosurgeryUniversity of WashingtonSeattleWashingtonUSA
- Institute for Stem Cell and Regenerative MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Robert C. Rostomily
- Department of Neurosurgery, Center for NeuroregenerationHouston Methodist Research InstituteTexasUSA
- Department of NeurosurgeryUniversity of WashingtonSeattleWashingtonUSA
- Institute for Stem Cell and Regenerative MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Andrei M. Mikheev
- Department of Neurosurgery, Center for NeuroregenerationHouston Methodist Research InstituteTexasUSA
- Department of NeurosurgeryUniversity of WashingtonSeattleWashingtonUSA
- Institute for Stem Cell and Regenerative MedicineUniversity of WashingtonSeattleWashingtonUSA
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2
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Huang L, Xing Y, Ning X, Yu Z, Bai X, Liu L, Sun S. Roles of Twist1 in lipid and glucose metabolism. Cell Commun Signal 2023; 21:270. [PMID: 37784111 PMCID: PMC10544448 DOI: 10.1186/s12964-023-01262-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/09/2023] [Indexed: 10/04/2023] Open
Abstract
The abnormal lipid and glucose metabolisms are linked to the metabolic disorders, tumorigenesis, and fibrotic diseases, which attracts the increasing attention to find out the key molecules involved in the lipid and glucose metabolism as the possible therapeutic targets on these diseases. A transcriptional factor Twist1 has been associated with not only the embryonic development, cancer, and fibrotic diseases, but also the regulation of lipid and glucose metabolism. In this review, we will discuss the roles and mechanisms of Twist1 in the obesity-associated white adipose tissue inflammation and insulin resistance, brown adipose tissue metabolism, fatty acid oxidation, and glucose metabolism in skeletal muscle to provide a rational perspective to consider Twist1 as a potential treatment target in clinic. Video Abstract.
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Affiliation(s)
- Liuyifei Huang
- Department of Nephrology, Xijing Hospital, The Fourth Military Medical University, Changle Road, No. 127 Changle West Road, Xi'an, Shaanxi, China
| | - Yan Xing
- Department of Nephrology, Xijing Hospital, The Fourth Military Medical University, Changle Road, No. 127 Changle West Road, Xi'an, Shaanxi, China
| | - Xiaoxuan Ning
- Department of Geriatrics, Xijing Hospital, The Fourth Military Medical University, Changle Road, No. 127 Changle West Road, Xi'an, Shaanxi, China
| | - Zhixiang Yu
- Department of Nephrology, Xijing Hospital, The Fourth Military Medical University, Changle Road, No. 127 Changle West Road, Xi'an, Shaanxi, China
| | - Xiao Bai
- Department of Nephrology, Xijing Hospital, The Fourth Military Medical University, Changle Road, No. 127 Changle West Road, Xi'an, Shaanxi, China
| | - Limin Liu
- School of Medicine, Northwest University, 229 Taibai North Road, Xi'an, 710032, Shaanxi, China.
| | - Shiren Sun
- Department of Nephrology, Xijing Hospital, The Fourth Military Medical University, Changle Road, No. 127 Changle West Road, Xi'an, Shaanxi, China.
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3
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Admoni-Elisha L, Elbaz T, Chopra A, Shapira G, Bedford M, Fry C, Shomron N, Biggar K, Feldman M, Levy D. TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in glioma. Nucleic Acids Res 2022; 50:6903-6918. [PMID: 35694846 PMCID: PMC9262621 DOI: 10.1093/nar/gkac485] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 05/16/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
Gliomas are one of the most common and lethal brain tumors among adults. One process that contributes to glioma progression and recurrence is the epithelial to mesenchymal transition (EMT). EMT is regulated by a set of defined transcription factors which tightly regulate this process, among them is the basic helix-loop-helix family member, TWIST1. Here we show that TWIST1 is methylated on lysine-33 at chromatin by SETD6, a methyltransferase with expression levels correlating with poor survival in glioma patients. RNA-seq analysis in U251 glioma cells suggested that both SETD6 and TWIST1 regulate cell adhesion and migration processes. We further show that TWIST1 methylation attenuates the expression of the long-non-coding RNA, LINC-PINT, thereby promoting EMT in glioma. Mechanistically, TWIST1 methylation represses the transcription of LINC-PINT by increasing the occupancy of EZH2 and the catalysis of the repressive H3K27me3 mark at the LINC-PINT locus. Under un-methylated conditions, TWIST1 dissociates from the LINC-PINT locus, allowing the expression of LINC-PINT which leads to increased cell adhesion and decreased cell migration. Together, our findings unravel a new mechanistic dimension for selective expression of LINC-PINT mediated by TWIST1 methylation.
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Affiliation(s)
- Lee Admoni-Elisha
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er-Sheva, Israel,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be’er-Sheva 84105, Israel
| | - Tzofit Elbaz
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er-Sheva, Israel,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be’er-Sheva 84105, Israel
| | - Anand Chopra
- Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Guy Shapira
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Mark T Bedford
- Department of Carcinogenesis, M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Kyle Biggar
- Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er-Sheva, Israel,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be’er-Sheva 84105, Israel
| | - Dan Levy
- To whom correspondence should be addressed. Tel: +972 8 647 7251;
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Ardalan Khales S, Abbaszadegan MR, Hosseini SE, Forghanifard MM. Contribution of TWIST1-EVX1 Axis in Invasiveness of Esophageal Squamous Cell Carcinoma; a Functional Study. IRANIAN JOURNAL OF BIOTECHNOLOGY 2022; 20:e2733. [PMID: 36337061 PMCID: PMC9583822 DOI: 10.30498/ijb.2022.224786.2733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND Epithelial-mesenchymal transition (EMT) is a biological process in embryonic development and cancer progression, and different gene families, such as HOX genes, are closely related to this process. OBJECTIVES Our aim in this study was to investigate the correlation between TWIST1 and EVX1 mRNA expression in ESCC patients and also examine the probable regulatory function of TWIST1 on EVX1 expression in human ESCC cell line. MATERIALS AND METHODS TWIST1 and EVX1 gene expression patterns were assessed in ESCC patients by relative comparative Real-time PCR then correlated with their clinical characteristics. In silico analysis of the EVX1 gene was conducted. KYSE-30 cells were transduced by a retroviral system to ectopically express TWIST1, followed by qRT-PCR to reveal the correlation between TWIST1 and EVX1 gene expression. RESULTS The expression of TWIST1 and EVX1 was correlated to each other significantly (p=0.005) in ESCC. Of 28 patients with under/normal expression of TWIST1, 22 samples (78.57%) had over/normal expression of EVX1. TWIST1 overexpression was correlated with advanced stages of the tumor (III, IV) (P = 0.019) and lymph node metastasis. However, EVX1 under expression was associated with lymph node metastasis (p = 0.027) and invasiveness of the disease (P = 0.037) in ESCC. Furthermore, retroviral transduction enforced significant overexpression of TWIST1 in GFP-hTWIST-1 approximately 9-fold compared to GFP control cells, causing a - 8.83- fold reduction in EVX1 mRNA expression significantly. CONCLUSIONS Our results indicated the repressive role of TWIST1 on EVX1 gene expression in ESCC. Therefore, our findings can help dissect the molecular mechanism of ESCC tumorigenesis and discover novel therapeutic targets for ESCC invasion and metastasis.
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Affiliation(s)
| | | | - Seyed Ebrahim Hosseini
- Department of Biology, Faculty of Sciences, Zand Institute of Higher Education, Shiraz, Iran
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Mechanisms of Binding Specificity among bHLH Transcription Factors. Int J Mol Sci 2021; 22:ijms22179150. [PMID: 34502060 PMCID: PMC8431614 DOI: 10.3390/ijms22179150] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 12/25/2022] Open
Abstract
The transcriptome of every cell is orchestrated by the complex network of interaction between transcription factors (TFs) and their binding sites on DNA. Disruption of this network can result in many forms of organism malfunction but also can be the substrate of positive natural selection. However, understanding the specific determinants of each of these individual TF-DNA interactions is a challenging task as it requires integrating the multiple possible mechanisms by which a given TF ends up interacting with a specific genomic region. These mechanisms include DNA motif preferences, which can be determined by nucleotide sequence but also by DNA’s shape; post-translational modifications of the TF, such as phosphorylation; and dimerization partners and co-factors, which can mediate multiple forms of direct or indirect cooperative binding. Binding can also be affected by epigenetic modifications of putative target regions, including DNA methylation and nucleosome occupancy. In this review, we describe how all these mechanisms have a role and crosstalk in one specific family of TFs, the basic helix-loop-helix (bHLH), with a very conserved DNA binding domain and a similar DNA preferred motif, the E-box. Here, we compile and discuss a rich catalog of strategies used by bHLH to acquire TF-specific genome-wide landscapes of binding sites.
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6
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Španinger E, Potočnik U, Bren U. Molecular Dynamics Simulations Predict That rSNP Located in the HNF‑1α Gene Promotor Region Linked with MODY3 and Hepatocellular Carcinoma Promotes Stronger Binding of the HNF‑4α Transcription Factor. Biomolecules 2020; 10:biom10121700. [PMID: 33371430 PMCID: PMC7767403 DOI: 10.3390/biom10121700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/06/2020] [Accepted: 12/18/2020] [Indexed: 12/24/2022] Open
Abstract
Our study aims to investigate the impact of the Maturity-onset diabetes of the young 3 disease-linked rSNP rs35126805 located in the HNF-1α gene promotor on the binding of the transcription factor HNF-4α and consequently on the regulation of HNF-1α gene expression. Our focus is to calculate the change in the binding affinity of the transcription factor HNF-4α to the DNA, caused by the regulatory single nucleotide polymorphism (rSNP) through molecular dynamics simulations and thermodynamic analysis of acquired results. Both root-mean-square difference (RMSD) and the relative binding free energy ΔΔGbind reveal that the HNF-4α binds slightly more strongly to the DNA containing the mutation (rSNP) making the complex more stable/rigid, and thereby influencing the expression of the HNF-1α gene. The resulting disruption of the HNF-4α/HNF-1α pathway is also linked to hepatocellular carcinoma metastasis and enhanced apoptosis in pancreatic cancer cells. To the best of our knowledge, this represents the first study where thermodynamic analysis of the results obtained from molecular dynamics simulations is performed to uncover the influence of rSNP on the protein binding to DNA. Therefore, our approach can be generally applied for studying the impact of regulatory single nucleotide polymorphisms on the binding of transcription factors to the DNA.
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Affiliation(s)
- Eva Španinger
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia; (E.Š.); (U.P.)
| | - Uroš Potočnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia; (E.Š.); (U.P.)
- Faculty of Medicine, University of Maribor, Taborska 8, SI-2000 Maribor, Slovenia
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia; (E.Š.); (U.P.)
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
- Correspondence: ; Tel.: +386-2-2294-421
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7
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Luo Y, Chen J, Liu M, Chen S, Su X, Su J, Zhao C, Han Z, Shi M, Ma X, Huang H. Twist1 promotes dendritic cell-mediated antitumor immunity. Exp Cell Res 2020; 392:112003. [PMID: 32278689 DOI: 10.1016/j.yexcr.2020.112003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 01/27/2023]
Abstract
Dendritic cells (DCs) play a central role in autoimmunity, immune homeostasis, and presentation of tumor antigens to T cells in order to prime antitumor responses. The number of tumor-infiltrating DCs is associated with survival and prognosis in cancer. Twist1 is a well-known regulator of tumor initiation and promotion, but whether and how DC-derived Twist1 regulates antitumor responses remains poorly understood. Here, we generated a mouse line with Twist1 conditionally depleted in DCs and found that Twist1-deficiency in DCs did not affect the DCs and T cell homeostasis under steady-state conditions; however, in melanoma models, the proportion of conventional DCs (cDCs) in draining lymph nodes (DLNs) was significantly decreased. Accordingly, a decreased ratio and number of tumor-infiltrating cDCs were observed, which reduced the recruitment of tumor-infiltrating T cells. Furthermore, production of IFN-γ, a crucial antitumor factor, by T cells, was dramatically decreased, which can further dampen the T cell antitumor functions. Collectively, our data indicate that Twist1 in DCs regulates antitumor functions by maintain the number of tumor-infiltrating DCs and T cells, and their antitumor activity.
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Affiliation(s)
- Yuechen Luo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Disease, Institute of Hematology & Hospital of Blood Disease, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jiadi Chen
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Maolan Liu
- Department of Hematology, The First Affiliated Hospital of Kunming Medical University, Hematology Research Center of Yunnan Province, Kunming, 650032, China
| | - Song Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Disease, Institute of Hematology & Hospital of Blood Disease, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Xiuhua Su
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Disease, Institute of Hematology & Hospital of Blood Disease, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jing Su
- Department of Hematology, The First Affiliated Hospital of Kunming Medical University, Hematology Research Center of Yunnan Province, Kunming, 650032, China
| | - Chunxiao Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Disease, Institute of Hematology & Hospital of Blood Disease, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Zhongchao Han
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Disease, Institute of Hematology & Hospital of Blood Disease, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Mingxia Shi
- Department of Hematology, The First Affiliated Hospital of Kunming Medical University, Hematology Research Center of Yunnan Province, Kunming, 650032, China.
| | - Xiaotong Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Disease, Institute of Hematology & Hospital of Blood Disease, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
| | - Huifang Huang
- Central Laboratory, Fujian Medical University Union Hospital, Fuzhou, China.
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8
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An ENU-induced mutation in Twist1 transactivation domain causes hindlimb polydactyly with complete penetrance and dominant-negatively impairs E2A-dependent transcription. Sci Rep 2020; 10:2501. [PMID: 32051525 PMCID: PMC7016005 DOI: 10.1038/s41598-020-59455-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 01/29/2020] [Indexed: 11/08/2022] Open
Abstract
Twist1 encodes a basic helix-loop-helix transcription factor (TF), which forms homodimer or heterodimer with other TFs, like E2A, to regulate target genes' expression. Mutations in TWIST1 are associated with Saethre-Chotzen syndrome (SCS), a rare congenital disorder characterized with osteogenesis abnormalities. However, how dysfunction of TWIST1 leads to SCS is still largely unknown. Here, using an unbiased ENU-induced mutagenesis screening, we identified a novel Twist1 mutation and the mutant mouse phenocopies some features of SCS in a dominant manner. Physically, our mutation p.F191S lies at the edge of a predicted α-helix in Twist1 transactivation (TA) domain. Adjacent to F191, a consecutive three-residue (AFS) has been hit by 3 human and 2 mouse disease-associated mutations, including ours. Unlike previously reported mouse null and p.S192P alleles that lead to hindlimb polydactyly with incomplete penetrance but a severe craniofacial malformation, our p.F191S causes the polydactyly (84.2% bilateral and 15.8% unilateral) with complete penetrance but a mild craniofacial malformation. Consistent with the higher penetrance, p.F191S has stronger impairment on E2A-dependent transcription than p.S192P. Although human p.A186T and mouse p.S192P disease mutations are adjacent to ours, these three mutations function differently to impair the E2A-dependent transcription. Unlike p.A186T and p.S192S that disturb local protein conformation and unstabilize the mutant proteins, p.F191S keeps the mutant protein stable and its interaction with E2A entire. Therefore, we argue that p.F191S we identified acts in a dominant-negative manner to impair E2A-dependent transcription and to cause the biological consequences. In addition, the mutant mouse we provided here could be an additional and valuable model for better understanding the disease mechanisms underlying SCS caused by TWIST1 dysfunction.
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9
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Tarczewska A, Greb-Markiewicz B. The Significance of the Intrinsically Disordered Regions for the Functions of the bHLH Transcription Factors. Int J Mol Sci 2019; 20:E5306. [PMID: 31653121 PMCID: PMC6862971 DOI: 10.3390/ijms20215306] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 11/17/2022] Open
Abstract
The bHLH proteins are a family of eukaryotic transcription factors regulating expression of a wide range of genes involved in cell differentiation and development. They contain the Helix-Loop-Helix (HLH) domain, preceded by a stretch of basic residues, which are responsible for dimerization and binding to E-box sequences. In addition to the well-preserved DNA-binding bHLH domain, these proteins may contain various additional domains determining the specificity of performed transcriptional regulation. According to this, the family has been divided into distinct classes. Our aim was to emphasize the significance of existing disordered regions within the bHLH transcription factors for their functionality. Flexible, intrinsically disordered regions containing various motives and specific sequences allow for multiple interactions with transcription co-regulators. Also, based on in silico analysis and previous studies, we hypothesize that the bHLH proteins have a general ability to undergo spontaneous phase separation, forming or participating into liquid condensates which constitute functional centers involved in transcription regulation. We shortly introduce recent findings on the crucial role of the thermodynamically liquid-liquid driven phase separation in transcription regulation by disordered regions of regulatory proteins. We believe that further experimental studies should be performed in this field for better understanding of the mechanism of gene expression regulation (among others regarding oncogenes) by important and linked to many diseases the bHLH transcription factors.
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Affiliation(s)
- Aneta Tarczewska
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
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10
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Yang J, Zhang X, Blumenthal RM, Cheng X. Detection of DNA Modifications by Sequence-Specific Transcription Factors. J Mol Biol 2019:S0022-2836(19)30568-6. [PMID: 31626807 DOI: 10.1016/j.jmb.2019.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/16/2022]
Abstract
The establishment, detection, and alteration or elimination of epigenetic DNA modifications are essential to controlling gene expression ranging from bacteria to mammals. The DNA methylations occurring at cytosine and adenine are carried out by SAM-dependent methyltransferases. Successive oxidations of 5-methylcytosine (5mC) by Tet dioxygenases generate 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC) derivatives; thus, DNA elements with multiple methylation sites can have a wide range of modification states. In contrast, oxidation of N6-methyladenine by homologs of Escherichia coli AlkB removes the methyl group directly. Both Tet and AlkB enzymes are 2-oxoglutarate- and Fe(II)-dependent dioxygenases. DNA-binding proteins decode the modification status of specific genomic regions. This article centers on two families of sequence-specific transcription factors: bZIP (basic leucine-zipper) proteins, exemplified by the AP-1 and CEBPβ recognition of 5mC; and bHLH (basic helix-loop-helix) proteins, exemplified by MAX and TCF4 recognition of 5caC. We discuss the impact of template strand DNA modification on the activities of DNA and RNA polymerases, and the varied tendencies of modifications to alter base pairing and their interactions with DNA repair enzymes.
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Affiliation(s)
- Jie Yang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Sinha S, Pattnaik S, Aradhyam GK. Molecular evolution guided functional analyses reveals Nucleobindin-1 as a canonical E-box binding protein promoting Epithelial-to-Mesenchymal transition (EMT). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:765-775. [DOI: 10.1016/j.bbapap.2019.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/15/2019] [Accepted: 05/31/2019] [Indexed: 01/18/2023]
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12
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Pan Y, Zhu Y, Yang W, Tycksen E, Liu S, Palucki J, Zhu L, Sasaki Y, Sharma MK, Kim AH, Zhang B, Yano H. The role of Twist1 in mutant huntingtin-induced transcriptional alterations and neurotoxicity. J Biol Chem 2018; 293:11850-11866. [PMID: 29891550 DOI: 10.1074/jbc.ra117.001211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/14/2018] [Indexed: 01/12/2023] Open
Abstract
Huntington's disease (HD) is a fatal neurodegenerative disorder caused by an abnormal expansion of polyglutamine repeats in the huntingtin protein (Htt). Transcriptional dysregulation is an early event in the course of HD progression and is thought to contribute to disease pathogenesis, but how mutant Htt causes transcriptional alterations and subsequent cell death in neurons is not well understood. RNA-Seq analysis revealed that expression of a mutant Htt fragment in primary cortical neurons leads to robust gene expression changes before neuronal death. Basic helix-loop-helix transcription factor Twist1, which is essential for embryogenesis and is normally expressed at low levels in mature neurons, was substantially up-regulated in mutant Htt-expressing neurons in culture and in the brains of HD mouse models. Knockdown of Twist1 by RNAi in mutant Htt-expressing primary cortical neurons reversed the altered expression of a subset of genes involved in neuronal function and, importantly, abrogated neurotoxicity. Using brain-derived neurotrophic factor (Bdnf), which is known to be involved in HD pathogenesis, as a model gene, we found that Twist1 knockdown could reverse mutant Htt-induced DNA hypermethylation at the Bdnf regulatory region and reactivate Bdnf expression. Together, these results suggest that Twist1 is an important upstream mediator of mutant Htt-induced neuronal death and may in part operate through epigenetic mechanisms.
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Affiliation(s)
| | - Ying Zhu
- From the Department of Neurological Surgery
| | - Wei Yang
- Genome Technology Access Center.,Department of Genetics
| | | | | | | | | | | | | | - Albert H Kim
- From the Department of Neurological Surgery.,Department of Genetics.,Department of Developmental Biology.,Center of Regenerative Medicine.,Department of Neurology, and.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Bo Zhang
- Department of Developmental Biology.,Center of Regenerative Medicine
| | - Hiroko Yano
- From the Department of Neurological Surgery, .,Department of Genetics.,Center of Regenerative Medicine.,Department of Neurology, and.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110
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Shao T, Song P, Hua H, Zhang H, Sun X, Kong Q, Wang J, Luo T, Jiang Y. Gamma synuclein is a novel Twist1 target that promotes TGF-β-induced cancer cell migration and invasion. Cell Death Dis 2018; 9:625. [PMID: 29795373 PMCID: PMC5967338 DOI: 10.1038/s41419-018-0657-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/19/2018] [Accepted: 05/02/2018] [Indexed: 02/05/2023]
Abstract
Transforming growth factor β (TGF-β) is critical for embryonic development, adult tissue homeostasis, and tumor progression. TGF-β suppresses tumors at early stage, but promotes metastasis at later stage through oncogenes such as Twist1. Gamma-synuclein (SNCG) is overexpressed in a variety of invasive and metastatic cancer. Here, we show that TGF-β induces SNCG expression by Smad-Twist1 axis, thus promoting TGF-β- and Twist1-induced cancer cell migration and invasion. We identify multiple Twist1-binding sites (E-boxes) in SNCG promoter. Chromatin immunoprecipitation and luciferase assays confirm the binding of Twist1 to the E-boxes of SNCG promoter sequence (−129/−1026 bp). Importantly, the Twist1-binding site close to the transcription initiation site is critical for the upregulation of SNCG expression by TGF-β and Twist1. Mutations of Twist1 motif on the SNCG promoter constructs markedly reduces the promoter activity. We further show that TGF-β induces Twist1 expression through Smad thereby enhancing the binding of Twist1 to SNCG promoter, upregulating SNCG promoter activity and increasing SNCG expression. SNCG knockdown abrogates TGF-β- or Twist1-induced cancer cell migration and invasion. Finally, SNCG knockdown inhibits the promotion of cancer metastasis by Twist1. Together, our data demonstrate that SNCG is a novel target of TGF-β-Smad-Twist1 axis and a mediator of Twist1-induced cancer metastasis.
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Affiliation(s)
- Ting Shao
- State Key Laboratory of Biotherapy, Section of Oncogene, Cancer Center, West China Hospital, Sichuan University and Collaboratory Inovation Center for Biotherapy, Chengdu, China
| | - Peiying Song
- State Key Laboratory of Biotherapy, Section of Oncogene, Cancer Center, West China Hospital, Sichuan University and Collaboratory Inovation Center for Biotherapy, Chengdu, China
| | - Hui Hua
- Laboratory of Stem Cell Biology, West China Hospital, Sichuan University, Chengdu, China
| | - Hongying Zhang
- State Key Laboratory of Biotherapy, Section of Oncogene, Cancer Center, West China Hospital, Sichuan University and Collaboratory Inovation Center for Biotherapy, Chengdu, China
| | - Xiangmin Sun
- State Key Laboratory of Biotherapy, Section of Oncogene, Cancer Center, West China Hospital, Sichuan University and Collaboratory Inovation Center for Biotherapy, Chengdu, China
| | - Qingbin Kong
- State Key Laboratory of Biotherapy, Section of Oncogene, Cancer Center, West China Hospital, Sichuan University and Collaboratory Inovation Center for Biotherapy, Chengdu, China
| | - Jiao Wang
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ting Luo
- Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yangfu Jiang
- State Key Laboratory of Biotherapy, Section of Oncogene, Cancer Center, West China Hospital, Sichuan University and Collaboratory Inovation Center for Biotherapy, Chengdu, China.
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Raghuraman P, Sudandiradoss C. R516Q mutation in Melanoma differentiation-associated protein 5 (MDA5) and its pathogenic role towards rare Singleton-Merten syndrome; a signature associated molecular dynamics study. J Biomol Struct Dyn 2018; 37:750-765. [DOI: 10.1080/07391102.2018.1439770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- P. Raghuraman
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore 632014, India
| | - C. Sudandiradoss
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore 632014, India
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Raghuraman P, Jesu Jaya Sudan R, Lesitha Jeeva Kumari J, Sudandiradoss C. Systematic prioritization of functional hotspot in RIG-1 domains using pattern based conventional molecular dynamic simulation. Life Sci 2017; 184:58-70. [PMID: 28705469 DOI: 10.1016/j.lfs.2017.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/29/2017] [Accepted: 07/09/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Retinoic acid inducible gene 1 (RIG-1), multi-domain protein has a role-play in detecting viral nucleic acids and stimulates the antiviral response. Dysfunction of this protein due to mutations makes the route vulnerable to viral diseases. AIM Identification of functional hotspots that maintains conformational stability in RIG-1 domains. METHODS In this study, we employed a systematic in silico strategy on RIG-1 protein to understand the mechanism of structural changes upon mutation. We computationally investigated the protein sequence signature for all the three domains of RIG-1 protein that encloses the mutation within the motif. Further, we carried out a structural comparison between RIG-1 domains with their respective distant orthologs which revealed the minimal number of interactions required to maintain its structural fold. This intra-protein network paved the way to infer hotspot residues crucial for the maintenance of the structural architecture and folding pattern. KEY FINDINGS Our analysis revealed about 40 hotspot residues that determine the folding pattern of the RIG-1 domains. Also, conventional molecular dynamic simulation coupled with essential dynamics provides conformational transitions of hot spot residues among native and mutant structures. Structural variations owing to hotspot residues in mutants again confirm the significance of these residues in structural characterization of RIG-1 domains. We believe our results will help the researchers to better comprehend towards regulatory regions and target-binding sites for therapeutic design within the pattern recognition receptor proteins. SIGNIFICANCE Our protocol employed in this work describes a novel approach in identifying signature residues that would provide structural insights in protein folding.
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Affiliation(s)
- P Raghuraman
- Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore 632014, India
| | - R Jesu Jaya Sudan
- Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore 632014, India
| | - J Lesitha Jeeva Kumari
- Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore 632014, India
| | - C Sudandiradoss
- Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore 632014, India.
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16
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Bouard C, Terreux R, Tissier A, Jacqueroud L, Vigneron A, Ansieau S, Puisieux A, Payen L. Destabilization of the TWIST1/E12 complex dimerization following the R154P point-mutation of TWIST1: an in silico approach. BMC STRUCTURAL BIOLOGY 2017; 17:6. [PMID: 28521820 PMCID: PMC5437649 DOI: 10.1186/s12900-017-0076-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/02/2017] [Indexed: 11/24/2022]
Abstract
Background The bHLH transcription factor TWIST1 plays a key role in the embryonic development and in tumorigenesis. Some loss-of-function mutations of the TWIST1 gene have been shown to cause an autosomal dominant craniosynostosis, known as the Saethre-Chotzen syndrome (SCS). Although the functional impacts of many TWIST1 mutations have been experimentally reported, little is known on the molecular mechanisms underlying their loss-of-function. In a previous study, we highlighted the predictive value of in silico molecular dynamics (MD) simulations in deciphering the molecular function of TWIST1 residues. Results Here, since the substitution of the arginine 154 amino acid by a glycine residue (R154G) is responsible for the SCS phenotype and the substitution of arginine 154 by a proline experimentally decreases the dimerizing ability of TWIST1, we investigated the molecular impact of this point mutation using MD approaches. Consistently, MD simulations highlighted a clear decrease in the stability of the α-helix during the dimerization of the mutated R154P TWIST1/E12 dimer compared to the wild-type TE complex, which was further confirmed in vitro using immunoassays. Conclusions Our study demonstrates that MD simulations provide a structural explanation for the loss-of-function associated with the SCS TWIST1 mutation and provides a proof of concept of the predictive value of these MD simulations. This in silico methodology could be used to determine reliable pharmacophore sites, leading to the application of docking approaches in order to identify specific inhibitors of TWIST1 complexes. Electronic supplementary material The online version of this article (doi:10.1186/s12900-017-0076-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Charlotte Bouard
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,LabEX DEVweCAN, Lyon, France.,UNIV UMR1052, Lyon, 69008, France.,Centre Léon Bérard, Lyon, 69373, France
| | - Raphael Terreux
- Université de Lyon1, ISPB, Lyon, 69008, France.,Pole Rhône-Alpes de Bioinformatique - Lyon Gerland (PRABI-LG), Lyon, 69007, France.,CNRS UMR 5305, Lyon, France
| | - Agnès Tissier
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,LabEX DEVweCAN, Lyon, France.,UNIV UMR1052, Lyon, 69008, France.,Centre Léon Bérard, Lyon, 69373, France
| | - Laurent Jacqueroud
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,LabEX DEVweCAN, Lyon, France.,UNIV UMR1052, Lyon, 69008, France.,Centre Léon Bérard, Lyon, 69373, France
| | - Arnaud Vigneron
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,LabEX DEVweCAN, Lyon, France.,UNIV UMR1052, Lyon, 69008, France.,Centre Léon Bérard, Lyon, 69373, France
| | - Stéphane Ansieau
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,LabEX DEVweCAN, Lyon, France.,UNIV UMR1052, Lyon, 69008, France.,Centre Léon Bérard, Lyon, 69373, France
| | - Alain Puisieux
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.,LabEX DEVweCAN, Lyon, France.,UNIV UMR1052, Lyon, 69008, France.,Centre Léon Bérard, Lyon, 69373, France.,Université de Lyon1, ISPB, Lyon, 69008, France.,Institut Universitaire de France, Paris, 75231, France
| | - Léa Payen
- Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France. .,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France. .,LabEX DEVweCAN, Lyon, France. .,UNIV UMR1052, Lyon, 69008, France. .,Centre Léon Bérard, Lyon, 69373, France. .,Université de Lyon1, ISPB, Lyon, 69008, France. .,Laboratoire de Biochimie et Biologie Moléculaire (CHLS), Hospices Civils de Lyon, Lyon, 69003, France.
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Raghuraman P, Jesu Jaya Sudan R, Lesitha Jeeva Kumari J, Sudandiradoss C. Casting the critical regions in nucleotide binding oligomerization domain 2 protein: a signature mediated structural dynamics approach. J Biomol Struct Dyn 2016; 35:3297-3315. [PMID: 27790943 DOI: 10.1080/07391102.2016.1254116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleotide binding oligomerization domain 2 (NOD2), a protein involved in the first line defence mechanism has a pivotal role in innate immunity. Impaired function of this protein is implicated in disorders such as Blau syndrome and Crohn's disease. Since an altered function is linked to protein's structure, we framed a systematic strategy to interpret the structure-function relationship of the protein. Initiated with mutation-based pattern prediction and identified a distant ortholog (DO) of NOD2 from which the intra-residue interaction network was elucidated. The network was used to identify hotspots that serve as critical points to maintain the stable architecture of the protein. Structural comparison of NOD2 domains with a DO revealed the minimal number of intra-protein interactions required by the protein to maintain the structural fold. In addition, the conventional molecular dynamics simulation emphasized the conformational transitions at hot spot residues between native NOD2 domains and its respective mutants (G116R, R42W and R54A) structures. The analysis of intra-protein interactions globally and the displacement of residues locally around the mutational site revealed loss of several critical bonds and residues vital for the protein's function. Conclusively we report, about 10 residues in leucine-rich repeat, 13 residues in NOD and 6 residues in CARD domain are required by the NOD2 to maintain its function. This protocol will help the researchers to achieve for more prospective studies to attest druggable site utility in discovering novel drug candidates.
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Affiliation(s)
- P Raghuraman
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
| | - R Jesu Jaya Sudan
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
| | - J Lesitha Jeeva Kumari
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
| | - C Sudandiradoss
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
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