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Bayan S, Bhattacharya D, Mitra RK, Ray SK. Two-dimensional graphitic carbon nitride nanosheets: a novel platform for flexible, robust and optically active triboelectric nanogenerators. NANOSCALE 2020; 12:21334-21343. [PMID: 33074267 DOI: 10.1039/d0nr03879b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We report on the characteristics of mechanically flexible, stable and photoactive triboelectric nanogenerators based on two-dimensional graphitic carbon nitride (g-C3N4) nanosheets. The performance of nanogenerator devices has been studied with varying frictional surfaces (such as polypropylene, aluminium oxide, Teflon and polyethylene terephthalate). Energy band diagrams have been used to explain the mechanism of triboelectric charge transfer in pristine and doped g-C3N4, with the former showing better characteristics. An optimized device has been found to be responsive to external stimuli to generate an output voltage of 10 V upon simple biomechanical impulses. To demonstrate the efficacy for practical applications of g-C3N4-based triboelectric nanogenerators, output voltages have been recorded for different common activities like walking, water showering, using as a writing/drawing pad, etc. Repetitive finger tapping on a device could charge a capacitor to as high as 55 V within ∼50 s, while that under UV illumination is found to be much faster (∼14 s) due to photoinduced carrier generations in g-C3N4. The exhibition of a superior photoresponsivity of ∼117 V W-1 under UV illumination demonstrates the dual functionality of g-C3N4-based triboelectric devices as a nanogenerator as well as an active flexible photosensor, which is hitherto unreported. Excellent mechanical flexibility, stability and photoinduced enhancement of output characteristics make g-C3N4 an attractive candidate for nanogenerator devices for future applications.
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Pomeranz Krummel DA, Nasti TH, Kaluzova M, Kallay L, Bhattacharya D, Melms JC, Izar B, Xu M, Burnham A, Ahmed T, Li G, Lawson D, Kowalski J, Cao Y, Switchenko JM, Ionascu D, Cook JM, Medvedovic M, Jenkins A, Khan MK, Sengupta S. Melanoma Cell Intrinsic GABA A Receptor Enhancement Potentiates Radiation and Immune Checkpoint Inhibitor Response by Promoting Direct and T Cell-Mediated Antitumor Activity. Int J Radiat Oncol Biol Phys 2020; 109:1040-1053. [PMID: 33289666 DOI: 10.1016/j.ijrobp.2020.10.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/17/2022]
Abstract
PURPOSE Most patients with metastatic melanoma show variable responses to radiation therapy and do not benefit from immune checkpoint inhibitors. Improved strategies for combination therapy that leverage potential benefits from radiation therapy and immune checkpoint inhibitors are critical. METHODS AND MATERIALS We analyzed metastatic melanoma tumors in the TCGA cohort for expression of genes coding for subunits of type A γ-aminobutyric acid (GABA) receptor (GABAAR), a chloride ion channel and major inhibitory neurotransmitter receptor. Electrophysiology was used to determine whether melanoma cells possess intrinsic GABAAR activity. Melanoma cell viability studies were conducted to test whether enhancing GABAAR mediated chloride transport using benzodiazepine-impaired viability. A syngeneic melanoma mouse model was used to assay the effect of benzodiazepine on tumor volume and its ability to potentiate radiation therapy or immunotherapy. Treated tumors were analyzed for changes in gene expression by RNA sequencing and presence of tumor-infiltrating lymphocytes by flow cytometry. RESULTS Genes coding for subunits of GABAARs express functional GABAARs in melanoma cells. By enhancing GABAAR-mediated anion transport, benzodiazepines depolarize melanoma cells and impair their viability. In vivo, benzodiazepine alone reduces tumor growth and potentiates radiation therapy and α-PD-L1 antitumor activity. The combination of benzodiazepine, radiation therapy, and α-PD-L1 results in near complete regression of treated tumors and a potent abscopal effect, mediated by increased infiltration of polyfunctional CD8+ T cells. Treated tumors show expression of cytokine-cytokine receptor interactions and overrepresentation of p53 signaling. CONCLUSIONS This study identifies an antitumor strategy combining radiation and/or an immune checkpoint inhibitor with modulation of GABAARs in melanoma using benzodiazepine.
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Patnaik S, Bhattacharya D, Chakrabarti K, Saravanan B, Bhatt AK, Verma MB. A Note on the Occurrence of Hydrothermal Anhydrite (CaSO4) in Kanchankayi area, Bhima Basin, Yadgir District, Karnataka. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2020. [DOI: 10.16943/ptinsa/2020/154985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Bayan S, Bhattacharya D, Mitra RK, Ray SK. Self-powered flexible photodetectors based on Ag nanoparticle-loaded g-C 3N 4 nanosheets and PVDF hybrids: role of plasmonic and piezoelectric effects. NANOTECHNOLOGY 2020; 31:365401. [PMID: 32428897 DOI: 10.1088/1361-6528/ab9470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Here we demonstrate novel self-powered photodetection using silver (Ag) nanoparticle-loaded two-dimensional graphitic carbon nitride (g-C3N4) nanosheets triggered by poly-vinylidene fluoride (PVDF)-based flexible piezoelectric nanogenerators. A self-poled PVDF-based nanogenerator has been obtained upon exploiting pristine g-C3N4 nanosheets as a filler material within the PVDF matrix. The fabricated nanogenerator devices are found to be highly efficient in generating the maximum voltage of ∼2.3 V and maximum power ∼110 μWatt/cm2, upon finger tapping. Further, the integration of an additional layer of plasmonic Ag nanoparticle-loaded g-C3N4 nanosheets, has led to a significant enhancement of photoresponse. The hybrid plasmonic nanogenerator (with a strain of ∼0.021%) has resulted in self-powered photodetection with a photo-to-dark current ratio of ∼60, as compared to the unstrained device (∼2.0). In contrast to the usual behaviour (positive photoresponse), the exposure of an ultraviolet light lowers the output current indicating a negative photoresponse reported for the first time in such a system. The origin of such negative photoresponse has been attributed to the screening of piezopotential of PVDF by photogenerated carriers of g-C3N4 nanosheets. On the other hand, visible light-induced positive photoresponse has originated from the increment in the current, indicating the useful role of Ag nanoparticles in plasmon-induced hot electron transfer process.
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Sengupta S, Nasti T, Kaluzova M, Kallay L, Melms J, Izar B, Xu M, Bhattacharya D, Burnham A, Li G, Ahmed T, Lawson D, Kowalski J, Cook J, Medvedovic M, Jenkins A, Khan M, Pomeranz Krummel D. 20. MELANOMA CELL INTRINSIC GABAA RECEPTOR ENHANCEMENT POTENTIATES RADIATION AND IMMUNE CHECKPOINT INHIBITOR RESPONSE BY PROMOTING DIRECT AND T CELL-MEDIATED ANTI-TUMOR ACTIVITY. Neurooncol Adv 2020. [PMCID: PMC7401396 DOI: 10.1093/noajnl/vdaa073.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Most metastatic melanoma patients exhibit poor and variable response to radiotherapy and targeted therapies, including immune checkpoint inhibitors. There is a need for therapeutics that can potentiate existing treatments to positively impact clinical outcomes of metastatic melanoma patients. We reanalyzed melanoma TCGA transcriptomes and identified, as linked to previously defined molecular subgroups, enhanced expression of genes coding for subunits of the Type A GABA receptor (GABAAR), a chloride ion channel and major inhibitory neurotransmitter receptor. Using whole-cell patch clamp electrophysiology, we find that melanoma cells possess GABAARs that control membrane permeability to anions. Select benzodiazepines, by enhancing GABAAR mediated anion transport, depolarize melanoma cell mitochondrial membrane potential and impair cell viability in vitro. Using a syngeneic melanoma mouse model, we find that a benzodiazepine promotes reduction in tumor volume when administered alone and potentiated radiation or immune checkpoint inhibitor α-PD-L1. When a benzodiazepine is combined with concurrent α-PD-L1 and a sub-lethal radiation dose, there is near complete loss of tumor, beyond what is observed for benzodiazepine with radiation or α-PD-L1. Mechanistically, benzodiazepine with radiation or α-PD-L1 results in ipsilateral and an abscopal tumor volume reduction commensurate with enhanced infiltration into the tumor milieu of polyfunctional CD8 T-cells. There is also an increased expression of genes with roles in the cytokine-cytokine receptor and p53 signaling pathways. This study provides evidence for melanoma cell GABAARs as a therapeutic vulnerability with benzodiazepines promoting both direct and immune-mediated anti-tumor activity.
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Bhattacharya D, Pomeroy SL, Pomeranz Krummel DA, Sengupta S. Epigenetics and survivorship in pediatric brain tumor patients. J Neurooncol 2020; 150:77-83. [PMID: 32451770 DOI: 10.1007/s11060-020-03535-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/12/2020] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Brain tumors make up over a quarter of pediatric malignancies. Depending on the age of presentation and treatment, pediatric brain tumor survivors experience varying degrees of treatment induced morbidity and sequelae. Epigenetic mechanisms play a critical role in silencing of tumor suppressor genes and activation of driver genes involved in oncogenesis in different types of brain tumors. Epigenetic modifications in pediatric brain tumor patients may influence long-term survival and may refine the molecular response to treatment induced morbidity and sequelae. However, there is a dearth of studies on how epigenetics of pediatric brain tumors is connected with neurocognition and other treatment related sequelae in survivors. METHODS/RESULTS In this review we explore epigenetic factors that may contribute to the survivorship and treatment of pediatric brain tumor patients. We focus on glioblastoma, medulloblastoma, and the neurocutaneous syndrome neurofibromatosis type-1 to highlight epigenetic biomarkers that can potentially serve not only as prognostic indicators of overall patient survival, but hopefully as indicators to the response to treatment neurocognitively and otherwise. CONCLUSIONS Future studies will hopefully soon bridge the gap in our knowledge on how epigenetic modifications are linked to treatment related sequelae in pediatric brain tumor patients.
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Maitra S, Bhattacharya D, Das S, Bhattacharya S. Melatonin and its anti-glioma functions: a comprehensive review. Rev Neurosci 2020; 30:527-541. [PMID: 30645197 DOI: 10.1515/revneuro-2018-0041] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/07/2018] [Indexed: 01/20/2023]
Abstract
Melatonin (N-acetyl-5-methoxytryptamine) is a naturally synthesized hormone secreted from the pineal gland in a variety of animals and is primarily involved in the regulation of the circadian rhythm, which is the natural cycle controlling sleep in organisms. Melatonin acts on specific receptors and has an important role in overall energy metabolism. This review encompasses several aspects of melatonin activity, such as synthesis, source, structure, distribution, function, signaling and its role in normal physiology. The review highlights the cellular signaling and messenger systems involved in melatonin's action on the body and their wider implications, the distribution and diverse action of different melatonin receptors in specific areas of the brain, and the pharmacological agonists and antagonists that have specific action on these melatonin receptors. This review also incorporates the antitumor effects of melatonin in considerable detail, emphasizing on melatonin's role as an adjuvant therapeutic agent in glioma treatment. We conclude that the diminishing levels of melatonin have significant debilitating effects on normal physiology and can also be associated with malignant conditions such as glioma. Based on the review of the available evidence, our study provides a broad platform for a better understanding of the specific roles of melatonin and serves as a starting point for further investigation into the therapeutic effect of melatonin in glioma as an adjuvant therapeutic agent.
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Alyethodi RR, Karthik S, Muniswamy K, Ravi SK, Perumal P, Bhattacharya D, Bala PA, De AK, Sujatha T, Sunder J, Kundu A. Assessment of Protein Profiles of RNAlater Stored and Fresh PBMC Cells Using Different Protein Extraction Buffers. Protein J 2020; 39:291-300. [DOI: 10.1007/s10930-020-09888-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Bhattacharya D, Krummel DP, Sengupta S. Pediatric cerebellar tumors: transcriptionally distinct but developmentally heterogeneous. Transl Cancer Res 2020; 9:1322-1325. [PMID: 35117480 PMCID: PMC8798252 DOI: 10.21037/tcr.2020.01.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/08/2020] [Indexed: 11/11/2022]
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De AK, George Z, Mondal S, Perumal P, Muniswamy K, Kundu A, Sunder J, Muthiyan R, Zamir Ahmed SK, Chakraborty G, Sujatha T, Bhattacharya D. Tracing the genetic root of Trinket cattle: an endangered cattle population of a small isolated island of Nicobar group of islands. J Genet 2020; 99:16. [PMID: 32366739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Trinket cattle are the inhabitant of a small island called Trinket, which is one of the picturesque islands of Andaman. This herd is thought to be of Danish leftover during their dynasty in Nicobar archipelago. When the island was abandoned by foreign invaders, indigenes utilized the animals for the purpose of meat. As a result, the cattle became semi-feral in nature. After the Great Sumatra earthquake and tsunami of Indian Ocean in 2004, Trinket island was left abandoned by indigenes and the cattle became totally feral in nature. To trace the genetic root of the cattle, this study has been undertaken based on the sequence information of the mitochondrial D-loop and cytochrome b gene. The genomic DNA was extracted from the blood samples of the Trinket cattle and was used for amplification of mitochondrial markers, and the sequence information was generated by Sanger sequencing. The analysis of sequence information revealed that the Trinket cattle belongs to Bos indicus (I) haplotype, sub-haplotype I2. The presence of I2 sub-haplotype in Trinket cattle may be due to the expansion of this I2 haplotype towards Southeast Asian countries. This is a novel input for the formulation of breeding strategy towards conservation of eco-friendly sustainable livestock in the isolated island ecosystem.
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Bhattacharya D, Zhu D, Osuka S, Kaluz S, Devi N, Van Meir E. PDTM-12. ADGRB3 IS EPIGENETICALLY SILENCED IN WNT-MEDULLOBLASTOMA AND ITS REACTIVATION HAS THERAPEUTIC BENEFITS. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Medulloblastoma (MB) are the most aggressive primary malignant brain tumors in children and are classified into four major molecular subgroups. WNT-MB is characterized by an activated WNT signature and has relatively better prognosis with treatment. However, young WNT-MB patients who survive after conventional treatment suffer from long-term irreversible neurocognitive and endocrine side effects leading to poor quality of life. ADGRB3 is a member of the ADGRB1-3 subfamily of adhesion GPCR transmembrane proteins, which are highly expressed in the cerebellum and hippocampal neurons. Our recent analysis of RNA-seq data from a published panel of MB tumor samples and RT-PCR experiments with tumor samples showed that ADGRB3 mRNA expression is selectively repressed in WNT-MB tumors compared to the other molecular subgroups and normal human cerebellum. We detected hypermethylation of the ADGRB3 promoter exclusively in WNT-MB samples. ChIP assays revealed enrichment of repressive methyl CpG binding MBD2 protein and trimethylated histone H3K9me3 in the ADGRB3 promoter region. We found that ATP dependent chromatin remodeler protein BRG-1 regulates ADGRB3 expression through epigenetic reprogramming at the gene promoter. Lentiviral reconstitution of ADGRB3 inhibited growth and WNT signaling in UW288-1, and PFSK-1 cells in culture. ADGRB3 reconstitution in UW288-1 MB cells causes a significant reduction in tumor growth and WNT target gene activation in orthotopic xenografts in nude mice. Furthermore, we found that ADGRB3 reactivation could be achieved using a blood brain barrier permeable MBD2 antagonist and an EZH2 inhibitor and this can significantly reduce cell growth and inhibit WNT signaling targets. Altogether, our findings define an epigenetic mechanism for ADGRB3 silencing in WNT-MB and demonstrated that reactivation of ADGRB3 can prevent WNT-MB tumor growth by suppressing WNT signaling. Our study supports translating epigenetic reactivation of ADGRB3 as a novel therapeutic intervention for children affected with WNT-MB.
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Adhikari A, Chhetri VS, Bhattacharya D, Cason C, Luu P, Suazo A. Effectiveness of daily rinsing of alfalfa sprouts with aqueous chlorine dioxide and ozonated water on the growth of Listeria monocytogenes during sprouting. Lett Appl Microbiol 2019; 69:252-257. [PMID: 31429475 DOI: 10.1111/lam.13209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022]
Abstract
Alfalfa sprouts have been implicated in multiple foodborne disease outbreaks. This study evaluated the growth of Listeria monocytogenes during sprouting of alfalfa seeds and the effectiveness of daily chlorine dioxide & ozone rinsing in controlling the growth. Alfalfa seeds inoculated with L. monocytogenes were sprouted for 5 days (25°C) with a daily aqueous ClO2 (3 ppm, 10 min) or ozone water (2 ppm, 5 min) rinse. Neither treatment significantly reduced the growth of L. monocytogenes on sprouting alfalfa seeds. The initial level of L. monocytogenes was 3·44 ± 0·27, which increased to c. 7·0 log CFU per g following 3 days of sprouting. There was no significant difference in the bacterial population between the treatment schemes. Bacterial distribution in roots (7·63 ± 0·511 log CFU per g), stems (7·51 ± 0·511 log CFU per g) and leaves (7·41 ± 0·511 log CFU per g) were similar after 5 days. Spent sanitizers had significantly lower levels of bacterial populations compared to the spent distilled water control. The results indicated that sprouting process provides a favourable condition for the growth of L. monocytogenes and the sanitizer treatment alone may not be able to reduce food safety risks. SIGNIFICANCE AND IMPACT OF THE STUDY: Sprouts are high-risk foods. Consumption of raw sprouts is frequently associated with foodborne disease outbreaks. Optimum sprouting procedure involves soaking seeds in water followed by daily water rinsing to maintain a moist environment that is also favourable for the growth of pathogenic micro-organisms. The present study emphasized the potential food safety risks during sprouting and the effect of applying daily sanitizer rinsing in the place of water rinsing to reduce those risks. The finding of this study may be useful in the development of pre-harvest and post-harvest risk management strategies.
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Bhattacharya D, Zhu D, Osuka S, Devi SN, Meir EGV. Abstract 3477: ADGRB3 is epigenetically silenced in WNT-medulloblastoma and inhibits WNT signaling. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Medulloblastoma (MB), is the most aggressive primary malignant brain tumor in children and are classified into four molecular subgroups. While some subtypes of MB show a favorable prognosis with treatment, still one third of patients succumb to this disease and the children who survive after therapy suffer from long-term neurocognitive and endocrine side effects of the conventional treatments. ADGRB3 (formerly called BAI3) is a member of the ADGRB1-3 subfamily of adhesion GPCR transmembrane proteins, which are highly expressed in the brain specially in cerebellum and hippocampal neurons. Our recent analysis of RNA-seq data from a published panel of medulloblastoma tumor samples and RT-PCR experiments with MB tumor samples showed that ADGRB3 mRNA expression was selectively repressed in WNT-MB tumor tissue compared to other three molecular subgroups and normal human cerebellar tissue. Using bisulfite sequencing and MS-PCR we have detected hypermethylation of the ADGRB3 promoter region exclusively in WNT-MB subgroup of MB tissues but not in the other three molecular subgroups and normal human cerebellar tissue. ChIP assays revealed enrichment of repressive methyl CpG binding protein MBD2 and the trimethylated histone H3K9me3 in the ADGRB3 promoter region of UW288-1 cells. Collectively, these indicates epigenetic silencing of ADGRB3 in WNT-MB via promoter hypermethylation and repressive histone modifications. We found that knockdown of ATP dependent chromatin remodeler protein Brg1 in MB cells can silence ADGRB3 expression through epigenetic reprogramming at the gene promoter. Lentiviral reconstitution of ADGRB3 in silent MB cells (UW288-1, PFSK-1) inhibited growth of these cells in culture and inhibited WNT signaling targets. ADGRB3 reconstituted UW288-1 MB cells when xenografted yielded significantly reduced tumor in immunocompromised mice compared to the parental cells. Pharmacological reactivation of ADGRB3 expression in silent WNT MB cells using our recently established MBD2 antagonist and an EZH2 inhibitor significantly reduced cell growth in vitro and inhibits some specific WNT signaling targets. We further identified a novel mechanism underlying ADGRB3 mediated regulation of WNT signaling by performing co-immunoprecipitation experiments. Altogether, our findings define an epigenetic mechanism for ADGRB3 silencing in WNT-MB and demonstrates a mechanism through which ADGRB3 restrains activation of WNT signaling involved in cerebellar transformation. Our findings highlight the potential of epigenetic reactivation of ADGRB3 as a less toxic therapeutic intervention for the children suffering from WNT-MB.
Citation Format: Debanjan Bhattacharya, Dan Zhu, Satoru Osuka, Saroja Narra Devi, Erwin G. Van Meir. ADGRB3 is epigenetically silenced in WNT-medulloblastoma and inhibits WNT signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3477.
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Sreevatsava V, De S, Bandyopadhyay S, Chaudhury P, Bera AK, Muthiyan R, De AK, Perumal P, Sunder J, Chakraborty G, Bhattacharya D. Variability of the EG95 antigen-coding gene of Echinococcus granulosus in animal and human origin: implications for vaccine development. J Genet 2019; 98:53. [PMID: 31204707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the present study, the genetic variability of the EG95 protein-coding gene in several animal and human isolates of Echinococcus granulosus was investigated. A total of 24 isolates collected from cattle, buffalo, sheep, goat, dog and man were amplified by Eg95-coding gene-specific primers. From the generated sequence information, a conceptual amino acid sequence was deduced. Phylogenetically, the Eg95 coding gene belongs to the Eg95-1/Eg95-2/Eg95-3/Eg95-4 cluster. Further confirmation on the maximum composite likelihood analysis revealed that the overall transition/transversion bias was 2.913. This finding indicated thatthere is bias towards transitional and transversional substitution. Using artificial neural networks, a B-cell epitope was predicted on primary sequence information. Stretches of amino acid residues varied between animal and human isolates when hydrophobicity was considered. Flexibility also varied between larval and adult stages of the organism. This observation is important to develop vaccines. However, cytotoxic T-lymphocyte epitopes on primary sequence data remained constant in all isolates. In this study, agretope identification started with hydrophobic amino acids. Amino acids with the same physico-chemical properties were present in the middle. The conformational propensity of the Eg95-coding gene of 156 amino acid residues had α-turns and β-turns, and α-amphipathic regions up to 129, 138-156 and 151-155 residues, respectively. The results indicated potential T-cell antigenic sites. The overall Tajima's D value was negative (-2.404165), indicative of negative selection pressure.
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Sreevatsava V, De S, Bandyopadhyay S, Chaudhury P, Bera AK, Muthiyan R, De AK, Perumal P, Sunder J, Chakraborty G, Bhattacharya D. Variability of the EG95 antigen-coding gene of Echinococcus granulosus in animal and human origin: implications for vaccine development. J Genet 2019. [DOI: 10.1007/s12041-019-1097-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Bhattacharya D, Van Meir EG. A simple genotyping method to detect small CRISPR-Cas9 induced indels by agarose gel electrophoresis. Sci Rep 2019; 9:4437. [PMID: 30872606 PMCID: PMC6418129 DOI: 10.1038/s41598-019-39950-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 01/25/2019] [Indexed: 01/22/2023] Open
Abstract
CRISPR gene editing creates indels in targeted genes that are detected by genotyping. Separating PCR products generated from wild-type versus mutant alleles with small indels based on size is beyond the resolution capacity of regular agarose gel electrophoresis. To overcome this limitation, we developed a simple genotyping method that exploits the differential electrophoretic mobility of homoduplex versus heteroduplex DNA hybrids in high concentration agarose gels. First, the CRISPR target region is PCR amplified and homo- and hetero-duplexed amplicons formed during the last annealing cycle are separated by 4–6% agarose gel electrophoresis. WT/mutant heteroduplexes migrate more slowly and are distinguished from WT or mutant homoduplexes. Heterozygous alleles are immediately identified as they produce two distinct bands, while homozygous wild-type or mutant alleles yield a single band. To discriminate the latter, equal amounts of PCR products of homozygous samples are mixed with wild-type control samples, subjected to one denaturation/renaturation cycle and products are electrophoresed again. Samples from homozygous mutant alleles now produce two bands, while those from wild-type alleles yield single bands. This method is simple, fast and inexpensive and can identify indels >2 bp. in size in founder pups and genotype offspring in established transgenic mice colonies.
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Das PP, Krishnan G, Doley J, Bhattacharya D, Deb SM, Chakravarty P, Das PJ. Establishing gene Amelogenin as sex-specific marker in yak by genomic approach. J Genet 2019; 98:7. [PMID: 30945688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Yak, an economically important bovine species considered as lifeline of the Himalaya. Indeed, this gigantic bovine is neglected because of the scientific intervention for its conservation as well as research documentation for a long time. Amelogenin is an essential protein for tooth enamel which eutherian mammals contain two copies in both X and Y chromosome each. In bovine, the deletion of a fragment of the nucleotide sequence in Y chromosome copy of exon 6 made Amelogenin an excellent sex-specific marker. Thus, an attempt was made to use the gene as an advanced molecular marker of sexing of the yak to improve breeding strategies and reproduction. The present study confirmed that the polymerase chain reaction amplification of the Amelogenin gene with a unique primer is useful in sex identification of the yak. The test is further refined with qPCR validation by quantifying the DNA copy number of the Amelogenin gene in male and female. We observed a high level of sequence polymorphisms of AMELX and AMELY in yak considered as novel identification. These tests can be further extended into several other specialized fields including forensics, meat production and processing, and quality control.
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Cenci U, Qiu H, Pillonel T, Cardol P, Remacle C, Colleoni C, Kadouche D, Chabi M, Greub G, Bhattacharya D, Ball SG. Host-pathogen biotic interactions shaped vitamin K metabolism in Archaeplastida. Sci Rep 2018; 8:15243. [PMID: 30323231 PMCID: PMC6189191 DOI: 10.1038/s41598-018-33663-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/03/2018] [Indexed: 02/01/2023] Open
Abstract
Menaquinone (vitamin K2) shuttles electrons between membrane-bound respiratory complexes under microaerophilic conditions. In photosynthetic eukaryotes and cyanobacteria, phylloquinone (vitamin K1) participates in photosystem I function. Here we elucidate the evolutionary history of vitamin K metabolism in algae and plants. We show that Chlamydiales intracellular pathogens made major genetic contributions to the synthesis of the naphthoyl ring core and the isoprenoid side-chain of these quinones. Production of the core in extremophilic red algae is under control of a menaquinone (Men) gene cluster consisting of 7 genes that putatively originated via lateral gene transfer (LGT) from a chlamydial donor to the plastid genome. In other green and red algae, functionally related nuclear genes also originated via LGT from a non-cyanobacterial, albeit unidentified source. In addition, we show that 3-4 of the 9 required steps for synthesis of the isoprenoid side chains are under control of genes of chlamydial origin. These results are discussed in the light of the hypoxic response experienced by the cyanobacterial endosymbiont when it gained access to the eukaryotic cytosol.
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Bhattacharya D, Zhu D, Devi N, Meir EGV. Abstract B17: ADGRB3 is a novel tumor suppressor epigenetically silenced in WNT medulloblastoma. Cancer Res 2018. [DOI: 10.1158/1538-7445.pedca17-b17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Medulloblastoma (MB) is the most aggressive primary malignant brain tumor in children and arises from neural progenitor cells in the developing cerebellum. Although some subtypes of MB show a favorable prognosis with treatment, still one third of patients succumb to this disease and the children who survive suffer from long-term side effects of the aggressive treatments. ADGRB3 (formerly called BAI3) is a member of the ADGRB1-3 subfamily of adhesion GPCR transmembrane proteins, which are highly expressed in the brain specially in cerebellum and hippocampal neurons. The ADGRB3 gene was recently found to undergo somatic mutations in several cancers, but nothing is known about the functional role of ADGRB3 in medulloblastoma. Our recent findings based on analysis of a published microarray dataset and RT-PCR experiments showed that ADGRB3 mRNA expression was selectively repressed in WNT-MB tumor tissue compared to other three molecular subgroups and normal human cerebellar tissue. Using bisulfite sequencing we have detected hypermethylation of the ADGRB3 promoter exclusively in WNT-MB subgroup of human MB tissue but not in the other three molecular subgroups and normal human cerebellar tissue. These results clearly indicate that ADGRB3 is epigenetically silenced in WNT-MB via promoter hypermethylation. In vitro experiments showed that restoration of ADGRB3 expression in ADGRB3-silenced MB cell lines slows cell growth and inhibits WNT signaling targets. We further analyzed whether methyl CpG binding proteins and histone modifications modulate transcriptional repression of ADGRB3 in WNT-MB. ChIP assays revealed enrichment of repressive MBD2 protein in the ADGRB3 promoter region. siRNA mediated knockdown of ADGRB3 in ADGRB3-silent MB cell line (UW288-1) was found to reactivate ADGRB3 expression. We found that in vitro treatment with KCC-07, a recently discovered MBD2 inhibitor, reactivates ADGRB3 mRNA expression in ADGRB3-silent but not expressing MB cells. We are currently investigating whether ADGRB3 can negatively regulate the WNT/beta-catenin pathway or acts via an independent pathway that synergizes with it to facilitate transformation. Altogether, our findings define an epigenetic mechanism for ADGRB3 silencing in WNT-MB and indicate a novel role of ADGRB3 as a potent suppressor of oncogenic cerebellar transformation. Our findings also highlight the potential of epigenetic reactivation of ADGRB3 as a less toxic therapeutic intervention for the children suffering from WNT-MB.
Citation Format: Debanjan Bhattacharya, Dan Zhu, Narra Devi, Erwin G. Van Meir. ADGRB3 is a novel tumor suppressor epigenetically silenced in WNT medulloblastoma [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr B17.
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Katangwe T, Kirkdale C, Bhattacharya D, Twigg M. The community pharmacy setting for delivering diabetes prevention programmes: A mixed methods study in people with ‘pre-diabetes’. Res Social Adm Pharm 2018. [DOI: 10.1016/j.sapharm.2018.05.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Warne RR, Carney OM, Wang G, Bhattacharya D, Chong WK, Aylett SE, Mankad K. The Bone Does Not Predict the Brain in Sturge-Weber Syndrome. AJNR Am J Neuroradiol 2018; 39:1543-1549. [PMID: 30026385 DOI: 10.3174/ajnr.a5722] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/18/2018] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE It has been hypothesized that skull marrow signal alteration may represent an early disease manifestation of Sturge-Weber syndrome before development of its intracranial manifestations. We alternatively hypothesized that intraosseous changes are associated with the overlying port-wine stain rather than the intracranial stigmata of Sturge-Weber syndrome and hence are not a predictor of brain involvement. MATERIALS AND METHODS MR imaging of children presenting with port-wine stain and/or Sturge-Weber syndrome between 1998 and 2017 was evaluated by 2 pediatric neuroradiologists for marrow signal abnormality and pial angioma and other Sturge-Weber syndrome features: ocular hemangioma, atrophy, and white matter changes (advanced myelination). Groups were divided into port-wine stain-only (without intracranial Sturge-Weber syndrome features) and Sturge-Weber syndrome (the presence of cerebral pial angioma). The χ2 test was performed to evaluate the association between port-wine stain and bone marrow changes and between osseous change and pial angioma. RESULTS We reviewed 139 cases: 40 with port-wine stain-only and 99 with Sturge-Weber syndrome with pial angioma. Fifteen of 99 cases of Sturge-Weber syndrome had no port-wine stain. In the port-wine stain-only cohort, 78% had ipsilateral bony changes and 17% had no intraosseous changes. In the Sturge-Weber syndrome cohort, 84/99 had associated port-wine stain, 91% (P < .01) had bony changes ipsilateral to the port-wine stain or had no bone changes in the absence of port-wine stain, and 77% (P = .27) had bony changes ipsilateral to a cerebral pial angioma. Eighty percent of patients with Sturge-Weber syndrome who lacked a port-wine stain also lacked marrow changes. Five patients with bilateral port-wine stain and bilateral marrow changes had only a unilateral pial angioma. CONCLUSIONS Intraosseous marrow changes are strongly associated with facial port-wine stain; no significant association was found between pial angioma and bone marrow changes.
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Katangwe T, Kirkdale C, Bhattacharya D, Twigg M. The community pharmacy setting for the delivery of diabetes prevention programmes: Views and perceptions of healthcare professionals. Res Social Adm Pharm 2018. [DOI: 10.1016/j.sapharm.2018.05.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zhu D, Osuka S, Zhang Z, Reichert ZR, Yang L, Kanemura Y, Jiang Y, You S, Zhang H, Devi NS, Bhattacharya D, Takano S, Gillespie GY, Macdonald T, Tan C, Nishikawa R, Nelson WG, Olson JJ, Van Meir EG. BAI1 Suppresses Medulloblastoma Formation by Protecting p53 from Mdm2-Mediated Degradation. Cancer Cell 2018; 33:1004-1016.e5. [PMID: 29894688 PMCID: PMC6002773 DOI: 10.1016/j.ccell.2018.05.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/29/2017] [Accepted: 05/11/2018] [Indexed: 01/20/2023]
Abstract
Adhesion G protein-coupled receptors (ADGRs) encompass 33 human transmembrane proteins with long N termini involved in cell-cell and cell-matrix interactions. We show the ADGRB1 gene, which encodes Brain-specific angiogenesis inhibitor 1 (BAI1), is epigenetically silenced in medulloblastomas (MBs) through a methyl-CpG binding protein MBD2-dependent mechanism. Knockout of Adgrb1 in mice augments proliferation of cerebellar granule neuron precursors, and leads to accelerated tumor growth in the Ptch1+/- transgenic MB mouse model. BAI1 prevents Mdm2-mediated p53 polyubiquitination, and its loss substantially reduces p53 levels. Reactivation of BAI1/p53 signaling axis by a brain-permeable MBD2 pathway inhibitor suppresses MB growth in vivo. Altogether, our data define BAI1's physiological role in tumorigenesis and directly couple an ADGR to cancer formation.
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Bhattacharya D, Ghosh D, Bhattacharya S, Sarkar S, Karmakar P, Koley H, Gachhui R. Antibacterial activity of polyphenolic fraction of Kombucha against Vibrio cholerae: targeting cell membrane. Lett Appl Microbiol 2018; 66:145-152. [PMID: 29193174 DOI: 10.1111/lam.12829] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/22/2017] [Accepted: 11/23/2017] [Indexed: 11/28/2022]
Abstract
The present study was undertaken to determine the mechanism of antibacterial activity of a polyphenolic fraction, composed of mainly catechin and isorhamnetin, previously isolated from Kombucha, a 14-day fermented beverage of sugared black tea, against the enteropathogen Vibrio cholerae N16961. Bacterial growth was found to be seriously impaired by the polyphenolic fraction in a dose-dependent manner. Scanning Electron Microscopy demonstrated morphological alterations in bacterial cells when exposed to the polyphenolic fraction in a concentration-dependent manner. Permeabilization assays confirmed that the fraction disrupted bacterial membrane integrity in both time- and dose-dependent manners, which were proportional to the production of intracellular reactive oxygen species (ROS). Furthermore, each of the polyphenols catechin and isorhamnetin showed the ability to permeate bacterial cell membranes by generating oxidative stress, thereby suggesting their role in the antibacterial potential of Kombucha. Thus, the basic mechanism of antibacterial activity of the Kombucha polyphenolic fraction against V. cholerae involved bacterial membrane permeabilization and morphological changes, which might be due to the generation of intracellular ROS. To the best of our knowledge, this is the first report on the investigation of antibacterial mechanism of Kombucha, which is mostly attributed to its polyphenolic content. SIGNIFICANCE AND IMPACT OF THE STUDY The emergence of multidrug-resistant Vibrio cholerae strains has hindered an efficient anti-Vibrio therapy. This study has demonstrated the membrane damage-mediated antibacterial mechanism of Kombucha, a popular fermented beverage of sugared tea, which is mostly attributed to its polyphenolic content. This study also implies the exploitation of Kombucha as a potential new source of bioactive polyphenols against V. cholerae.
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Allyn PR, O'Malley SM, Ferguson J, Tseng CH, Chew KW, Bhattacharya D. Attitudes and potential barriers towards hepatitis C treatment in patients with and without HIV coinfection. Int J STD AIDS 2018; 29:334-340. [PMID: 28820346 PMCID: PMC5670019 DOI: 10.1177/0956462417725462] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This study aimed to assess attitudes and potential barriers towards treatment in patients with hepatitis C virus (HCV) infection, comparing those with and without HIV coinfection. A cross-sectional survey of 82 HCV-infected adults with and without HIV was conducted in greater Los Angeles between November 2013 and July 2015. Overall, there were 53 (64.6%) with HIV coinfection, 20 (25.0%) with self-reported cirrhosis, and 22 (26.8%) with a history of prior HCV treatment. Of all, 93.2% wanted HCV treatment, but 45.9% were unwilling/unable to spend anything out of pocket, 29.4% were waiting for new therapies, and 23.5% were recommended to defer HCV treatment. HIV/HCV-coinfected patients were more likely to want treatment within one year (90.2% versus 68.2%, p = 0.02), more willing to join a clinical trial (74.5% versus 8.0%, p < 0.01), more willing to take medications twice daily (86.3% versus 61.5%, p = 0.01), and more likely to prefer hepatitis C treatment by an infectious diseases/HIV physician (36.7% versus 4.0%, p < 0.01). Of all, 77.1% of coinfected patients were willing to change antiretroviral therapy if necessary to treat HCV, but only 48.0% of patients were willing to take a medication if it had not been studied in HIV-positive patients. Treatment preferences differ between HIV/HCV-coinfected and HCV-monoinfected patients. Despite a strong willingness among the study cohort to start HCV treatment, other factors such as cost, access to medications, and provider reluctance may be delaying treatment initiation.
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