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Praharaj PP, Patra S, Singh A, Panigrahi DP, Lee HY, Kabir MF, Hossain MK, Patra SK, Patro BS, Patil S, Klionsky DJ, Chae HJ, Bhutia SK. CLU (clusterin) and PPARGC1A/PGC1α coordinately control mitophagy and mitochondrial biogenesis for oral cancer cell survival. Autophagy 2024:1-25. [PMID: 38447939 DOI: 10.1080/15548627.2024.2309904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024] Open
Abstract
Mitophagy involves the selective elimination of defective mitochondria during chemotherapeutic stress to maintain mitochondrial homeostasis and sustain cancer growth. Here, we showed that CLU (clusterin) is localized to mitochondria to induce mitophagy controlling mitochondrial damage in oral cancer cells. Moreover, overexpression and knockdown of CLU establish its mitophagy-specific role, where CLU acts as an adaptor protein that coordinately interacts with BAX and LC3 recruiting autophagic machinery around damaged mitochondria in response to cisplatin treatment. Interestingly, CLU triggers class III phosphatidylinositol 3-kinase (PtdIns3K) activity around damaged mitochondria, and inhibition of mitophagic flux causes the accumulation of excessive mitophagosomes resulting in reactive oxygen species (ROS)-dependent apoptosis during cisplatin treatment in oral cancer cells. In parallel, we determined that PPARGC1A/PGC1α (PPARG coactivator 1 alpha) activates mitochondrial biogenesis during CLU-induced mitophagy to maintain the mitochondrial pool. Intriguingly, PPARGC1A inhibition through small interfering RNA (siPPARGC1A) and pharmacological inhibitor (SR-18292) treatment counteracts CLU-dependent cytoprotection leading to mitophagy-associated cell death. Furthermore, co-treatment of SR-18292 with cisplatin synergistically suppresses tumor growth in oral cancer xenograft models. In conclusion, CLU and PPARGC1A are essential for sustained cancer cell growth by activating mitophagy and mitochondrial biogenesis, respectively, and their inhibition could provide better therapeutic benefits against oral cancer.
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Affiliation(s)
- Prakash P Praharaj
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Srimanta Patra
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Amruta Singh
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Debasna P Panigrahi
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Hwa Y Lee
- Department of Pharmacology, Jeonbuk National University Medical School, Jeonju, Jeonbuk, Republic of Korea
| | - Mohammad F Kabir
- Department of Pharmacology, School of Medicine, Institute of New Drug Development, Jeonbuk National University, Jeonju, Republic of Korea
| | - Muhammad K Hossain
- School of Pharmacy, Jeonbuk National University, Jeonju, Jeonbuk, Republic of Korea
| | - Samir K Patra
- Laboratory of epigenetics, Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Birija S Patro
- Bio-Organic Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UT, USA
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Han J Chae
- School of Pharmacy, Jeonbuk National University, Jeonju, Jeonbuk, Republic of Korea
- Non-Clinical Evaluation Center, Biomedical Research Institute, Jeonbuk National University Hospital, Jeonju, Jeonbuk, Republic of Korea
| | - Sujit K Bhutia
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India
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Mishra J, Chakraborty S, Niharika, Roy A, Manna S, Baral T, Nandi P, Patra SK. Mechanotransduction and epigenetic modulations of chromatin: Role of mechanical signals in gene regulation. J Cell Biochem 2024; 125:e30531. [PMID: 38345428 DOI: 10.1002/jcb.30531] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/08/2024] [Accepted: 01/26/2024] [Indexed: 03/12/2024]
Abstract
Mechanical forces may be generated within a cell due to tissue stiffness, cytoskeletal reorganization, and the changes (even subtle) in the cell's physical surroundings. These changes of forces impose a mechanical tension within the intracellular protein network (both cytosolic and nuclear). Mechanical tension could be released by a series of protein-protein interactions often facilitated by membrane lipids, lectins and sugar molecules and thus generate a type of signal to drive cellular processes, including cell differentiation, polarity, growth, adhesion, movement, and survival. Recent experimental data have accentuated the molecular mechanism of this mechanical signal transduction pathway, dubbed mechanotransduction. Mechanosensitive proteins in the cell's plasma membrane discern the physical forces and channel the information to the cell interior. Cells respond to the message by altering their cytoskeletal arrangement and directly transmitting the signal to the nucleus through the connection of the cytoskeleton and nucleoskeleton before the information despatched to the nucleus by biochemical signaling pathways. Nuclear transmission of the force leads to the activation of chromatin modifiers and modulation of the epigenetic landscape, inducing chromatin reorganization and gene expression regulation; by the time chemical messengers (transcription factors) arrive into the nucleus. While significant research has been done on the role of mechanotransduction in tumor development and cancer progression/metastasis, the mechanistic basis of force-activated carcinogenesis is still enigmatic. Here, in this review, we have discussed the various cues and molecular connections to better comprehend the cellular mechanotransduction pathway, and we also explored the detailed role of some of the multiple players (proteins and macromolecular complexes) involved in mechanotransduction. Thus, we have described an avenue: how mechanical stress directs the epigenetic modifiers to modulate the epigenome of the cells and how aberrant stress leads to the cancer phenotype.
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Affiliation(s)
- Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Samir K Patra
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
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Manna S, Mishra J, Baral T, Kirtana R, Nandi P, Roy A, Chakraborty S, Niharika, Patra SK. Epigenetic signaling and crosstalk in regulation of gene expression and disease progression. Epigenomics 2023; 15:723-740. [PMID: 37661861 DOI: 10.2217/epi-2023-0235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023] Open
Abstract
Chromatin modifications - including DNA methylation, modification of histones and recruitment of noncoding RNAs - are essential epigenetic events. Multiple sequential modifications converge into a complex epigenetic landscape. For example, promoter DNA methylation is recognized by MeCP2/methyl CpG binding domain proteins which further recruit SETDB1/SUV39 to attain a higher order chromatin structure by propagation of inactive epigenetic marks like H3K9me3. Many studies with new information on different epigenetic modifications and associated factors are available, but clear maps of interconnected pathways are also emerging. This review deals with the salient epigenetic crosstalk mechanisms that cells utilize for different cellular processes and how deregulation or aberrant gene expression leads to disease progression.
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Affiliation(s)
- Soumen Manna
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Jagdish Mishra
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Tirthankar Baral
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - R Kirtana
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Piyasa Nandi
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Ankan Roy
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Subhajit Chakraborty
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Niharika
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Samir K Patra
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
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Patra S, Mishra SR, Behera BP, Mahapatra KK, Panigrahi DP, Bhol CS, Praharaj PP, Sethi G, Patra SK, Bhutia SK. Autophagy-modulating phytochemicals in cancer therapeutics: Current evidences and future perspectives. Semin Cancer Biol 2020; 80:205-217. [PMID: 32450139 DOI: 10.1016/j.semcancer.2020.05.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 02/08/2023]
Abstract
Autophagy is an intracellular catabolic self-cannibalism that eliminates dysfunctional cytoplasmic cargos by the fusion of cargo-containing autophagosomes with lysosomes to maintain cyto-homeostasis. Autophagy sustains a dynamic interlink between cytoprotective and cytostatic function during malignant transformation in a context-dependent manner. The antioxidant and immunomodulatory phyto-products govern autophagy and autophagy-associated signaling pathways to combat cellular incompetence during malignant transformation. Moreover, in a close cellular signaling circuit, autophagy regulates aberrant epigenetic modulation and inflammation, which limits tumor metastasis. Thus, manipulating autophagy for induction of cell death and associated regulatory phenomena will embark on a new strategy for tumor suppression with wide therapeutic implications. Despite the prodigious availability of lead pharmacophores in nature, the central autophagy regulating entities, their explicit target, as well as pre-clinical and clinical assessment remains a major question to be answered. In addition to this, the stage-specific regulation of autophagy and mode of action with natural products in regulating the key autophagic molecules, control of tumor-specific pathways in relation to modulation of autophagic network specify therapeutic target in caner. Moreover, the molecular pathway specificity and enhanced efficacy of the pre-existing chemotherapeutic agents in co-treatment with these phytochemicals hold high prevalence for target specific cancer therapeutics. Hence, the multi-specific role of phytochemicals in a cellular and tumor context dependent manner raises immense curiosity for investigating of novel therapeutic avenues. In this perspective, this review discusses about diverse implicit mechanisms deployed by the bioactive compounds in diagnosis and therapeutics approach during cancer progression with special insight into autophagic regulation.
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Affiliation(s)
- Srimanta Patra
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Soumya R Mishra
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Bishnu P Behera
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Kewal K Mahapatra
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Debasna P Panigrahi
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Chandra S Bhol
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Prakash P Praharaj
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
| | - Samir K Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Sujit K Bhutia
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India.
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Dey S, Raman VS, Patra SK, Chand K. Common cloaca: An uncommon entity posing diagnostic and management challenges: Our experience with nine cases. Med J Armed Forces India 2020; 77:165-169. [PMID: 33867632 DOI: 10.1016/j.mjafi.2020.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/10/2020] [Indexed: 11/15/2022] Open
Abstract
Background Cloacal anomalies are the severest and most complex of all anorectal malformations (ARMs). They require careful evaluation and meticulous surgery tailored to suit each variant. We present our experience in a series of nine cases. Methods This includes a retrospective review of 9 cases of cloaca managed at a tertiary care centre between 2015 and 2019. Results Associated anomalies were seen in 44% cases. The definitive surgery was performed at a mean age of 15.2 months (10 months-19 months), the definitive surgery being rectal separation with total urogenital mobilisation. The common channel as measured during panendoscopy was up to 3 cm in 7 patients (78%), and only 2 patients had a common channel of more than 3 cm (22%). Of the 34 procedures that these nine patients underwent, there were four complications (12%). The median follow-up period after stoma closure was 18 months (5-32 months), and the mean age at last follow-up was 38 months (22-48 months). Five children (63%) had spontaneous voiding and remained dry in the intervening period. Three patients (37%) had poor urinary stream with dribbling and high postvoid residue requiring clean intermittent catheterisation. Six patients had faecal soiling (66%); four had daily soiling; and two had occasional soiling. Four patients had constipation (44%). Seven patients (77%) required daily enemas for bowel evacuation and to remain dry. Conclusion Cloacal anomalies are rare and complex ARMs. Satisfactory urinary and bowel continence rates can be achieved even in these complex anomalies.
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Affiliation(s)
- Santosh Dey
- Classified Specialist (Surgery) and Pediatric Surgeon, Command Hospital (Southern Command), Pune, 411040, India
| | - V Shankar Raman
- Senior Advisor (Surgery) and Pediatric Surgeon, Command Hospital (Southern Command), Pune, 411040, India
| | - S K Patra
- Resident, Department of Surgery, Armed Forces Medical College, Pune, 411040, India
| | - Karunesh Chand
- Senior Advisor (Surgery) and Pediatric Surgeon, Army Hospital (R&R), Delhi Cantt, 110010, India
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Roble AA, Patra SK, Massabuau F, Frentrup M, Leontiadou MA, Dawson P, Kappers MJ, Oliver RA, Graham DM, Schulz S. Publisher Correction: Impact of alloy fluctuations and Coulomb effects on the electronic and optical properties of c-plane GaN/AlGaN quantum wells. Sci Rep 2020; 10:5667. [PMID: 32205854 PMCID: PMC7090005 DOI: 10.1038/s41598-020-62494-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- A A Roble
- Department of Physics and Astronomy, and Photon Science Institute, The University of Manchester, Manchester, M13 9PL, United Kingdom.
| | - S K Patra
- Tyndall National Institute, University College Cork, Cork, T12 R5CP, Ireland. .,Department of Electrical Engineering, University College Cork, Cork, T12 YN60, Ireland.
| | - F Massabuau
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge, CB3 0FS, United Kingdom
| | - M Frentrup
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge, CB3 0FS, United Kingdom
| | - M A Leontiadou
- Department of Physics and Astronomy, and Photon Science Institute, The University of Manchester, Manchester, M13 9PL, United Kingdom.,School of Science, Engineering and Environment, University of Salford, Salford, Greater Manchester, M5 4WT, United Kingdom
| | - P Dawson
- Department of Physics and Astronomy, and Photon Science Institute, The University of Manchester, Manchester, M13 9PL, United Kingdom
| | - M J Kappers
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge, CB3 0FS, United Kingdom
| | - R A Oliver
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge, CB3 0FS, United Kingdom
| | - D M Graham
- Department of Physics and Astronomy, and Photon Science Institute, The University of Manchester, Manchester, M13 9PL, United Kingdom
| | - S Schulz
- Tyndall National Institute, University College Cork, Cork, T12 R5CP, Ireland
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Mishra A, Behura A, Mawatwal S, Kumar A, Naik L, Mohanty SS, Manna D, Dokania P, Mishra A, Patra SK, Dhiman R. Structure-function and application of plant lectins in disease biology and immunity. Food Chem Toxicol 2019; 134:110827. [PMID: 31542433 PMCID: PMC7115788 DOI: 10.1016/j.fct.2019.110827] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/28/2019] [Accepted: 09/17/2019] [Indexed: 02/06/2023]
Abstract
Lectins are proteins with a high degree of stereospecificity to recognize various sugar structures and form reversible linkages upon interaction with glyco-conjugate complexes. These are abundantly found in plants, animals and many other species and are known to agglutinate various blood groups of erythrocytes. Further, due to the unique carbohydrate recognition property, lectins have been extensively used in many biological functions that make use of protein-carbohydrate recognition like detection, isolation and characterization of glycoconjugates, histochemistry of cells and tissues, tumor cell recognition and many more. In this review, we have summarized the immunomodulatory effects of plant lectins and their effects against diseases, including antimicrobial action. We found that many plant lectins mediate its microbicidal activity by triggering host immune responses that result in the release of several cytokines followed by activation of effector mechanism. Moreover, certain lectins also enhance the phagocytic activity of macrophages during microbial infections. Lectins along with heat killed microbes can act as vaccine to provide long term protection from deadly microbes. Hence, lectin based therapy can be used as a better substitute to fight microbial diseases efficiently in future.
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Affiliation(s)
- Abtar Mishra
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Assirbad Behura
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Shradha Mawatwal
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Ashish Kumar
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Lincoln Naik
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Subhashree Subhasmita Mohanty
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Debraj Manna
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Puja Dokania
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342011, India
| | - Samir K Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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Abstract
Infertility is a complex pathophysiological condition. It may caused by specific or multiple physical and physiological factors, including abnormalities in homeostasis, hormonal imbalances and genetic alterations. In recent times various studies implicated that, aberrant epigenetic mechanisms are associated with reproductive infertility. There might be transgenerational effects associated with epigenetic modifications of gametes and studies suggest the importance of alterations in epigenetic modification at early and late stages of gametogenesis. To determine the causes of infertility it is necessary to understand the altered epigenetic modifications of associated gene and mechanisms involved therein. This review is devoted to elucidate the recent mechanistic advances in regulation of genes by epigenetic modification and emphasizes their possible role related to reproductive infertility. It includes environmental, nutritional, hormonal and physiological factors and influence of internal structural architecture of chromatin nucleosomes affecting DNA and histone modifications in both male and female gametes, early embryogenesis and offspring. Finally, we would like to emphasize that research on human infertility by gene knock out of epigenetic modifiers genes must be relied upon animal models.
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Affiliation(s)
- Laxmidhar Das
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Sabnam Parbin
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Nibedita Pradhan
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Chahat Kausar
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Samir K Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India,
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Shilpi A, Bi Y, Jung S, Patra SK, Davuluri RV. Identification of Genetic and Epigenetic Variants Associated with Breast Cancer Prognosis by Integrative Bioinformatics Analysis. Cancer Inform 2017; 16:1-13. [PMID: 28096648 PMCID: PMC5224237 DOI: 10.4137/cin.s39783] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 09/05/2016] [Accepted: 09/09/2016] [Indexed: 01/06/2023] Open
Abstract
INTRODUCTION Breast cancer being a multifaceted disease constitutes a wide spectrum of histological and molecular variability in tumors. However, the task for the identification of these variances is complicated by the interplay between inherited genetic and epigenetic aberrations. Therefore, this study provides an extrapolate outlook to the sinister partnership between DNA methylation and single-nucleotide polymorphisms (SNPs) in relevance to the identification of prognostic markers in breast cancer. The effect of these SNPs on methylation is defined as methylation quantitative trait loci (meQTL). MATERIALS AND METHODS We developed a novel method to identify prognostic gene signatures for breast cancer by integrating genomic and epigenomic data. This is based on the hypothesis that multiple sources of evidence pointing to the same gene or pathway are likely to lead to reduced false positives. We also apply random resampling to reduce overfitting noise by dividing samples into training and testing data sets. Specifically, the common samples between Illumina 450 DNA methylation, Affymetrix SNP array, and clinical data sets obtained from the Cancer Genome Atlas (TCGA) for breast invasive carcinoma (BRCA) were randomly divided into training and test models. An intensive statistical analysis based on log-rank test and Cox proportional hazard model has established a significant association between differential methylation and the stratification of breast cancer patients into high- and low-risk groups, respectively. RESULTS The comprehensive assessment based on the conjoint effect of CpG–SNP pair has guided in delaminating the breast cancer patients into the high- and low-risk groups. In particular, the most significant association was found with respect to cg05370838–rs2230576, cg00956490–rs940453, and cg11340537–rs2640785 CpG–SNP pairs. These CpG–SNP pairs were strongly associated with differential expression of ADAM8, CREB5, and EXPH5 genes, respectively. Besides, the exclusive effect of SNPs such as rs10101376, rs140679, and rs1538146 also hold significant prognostic determinant. CONCLUSIONS Thus, the analysis based on DNA methylation and SNPs have resulted in the identification of novel susceptible loci that hold prognostic relevance in breast cancer.
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Affiliation(s)
- Arunima Shilpi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group Department of Life Science, National Institute of Technology Rourkela, Odisha, India
| | - Yingtao Bi
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Segun Jung
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Samir K Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group Department of Life Science, National Institute of Technology Rourkela, Odisha, India
| | - Ramana V Davuluri
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Bhutia SK, Behera B, Nandini Das D, Mukhopadhyay S, Sinha N, Panda PK, Naik PP, Patra SK, Mandal M, Sarkar S, Menezes ME, Talukdar S, Maiti TK, Das SK, Sarkar D, Fisher PB. Abrus agglutinin is a potent anti-proliferative and anti-angiogenic agent in human breast cancer. Int J Cancer 2016; 139:457-66. [PMID: 26914517 DOI: 10.1002/ijc.30055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 12/01/2014] [Accepted: 12/03/2014] [Indexed: 11/11/2022]
Abstract
Abrus agglutinin (AGG), a plant lectin isolated from the seeds of Abrus precatorius, has documented antitumor and immunostimulatory effects in murine models. To examine possible antitumor activity against breast cancer, we established human breast tumor xenografts in athymic nude mice and intraperitoneally administered AGG. AGG inhibited tumor growth and angiogenesis as confirmed by monitoring the expression of Ki-67 and CD-31, respectively. In addition, TUNEL positive cells increased in breast tumors treated with AGG suggesting that AGG mediates anti-tumorigenic activity through induction of apoptosis and inhibition of angiogenesis. On a molecular level, AGG caused extrinsic apoptosis through ROS generation that was AKT-dependent in breast cancer cells, without affecting primary mammary epithelial cells, suggesting potential cancer specificity of this natural compound. In addition, using HUVECs, AGG inhibited expression of the pro-angiogenic factor IGFBP-2 in an AKT-dependent manner, reducing angiogenic phenotypes both in vitro and in vivo. Overall, the present results establish that AGG promotes both apoptosis and anti-angiogenic activities in human breast tumor cells, which might be exploited for treatment of breast and other cancers.
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Affiliation(s)
- Sujit K Bhutia
- Department of Life Science, National Institute of Technology, Rourkela, India
| | - Birendra Behera
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Durgesh Nandini Das
- Department of Life Science, National Institute of Technology, Rourkela, India
| | | | - Niharika Sinha
- Department of Life Science, National Institute of Technology, Rourkela, India
| | | | | | - Samir K Patra
- Department of Life Science, National Institute of Technology, Rourkela, India
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, India
| | - Siddik Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | - Mitchell E Menezes
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | - Sarmistha Talukdar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | - Tapas K Maiti
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Swadesh K Das
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.,VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.,VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.,VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | - Paul B Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.,VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.,VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
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11
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Roy A, Ghosh T, Patra SK, Manna A. Anaerobic culture on growth efficient bi-layered culture plate in a modified candle jar using a rapid and slow combustion system: few comments. Indian J Med Microbiol 2014; 32:351-2. [PMID: 25008842 DOI: 10.4103/0255-0857.136614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
| | | | | | - A Manna
- Department of Microbiology, Malda Medical College, Malda, West Bengal, India
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Bhutia SK, Mukhopadhyay S, Sinha N, Das DN, Panda PK, Patra SK, Maiti TK, Mandal M, Dent P, Wang XY, Das SK, Sarkar D, Fisher PB. Autophagy: cancer's friend or foe? Adv Cancer Res 2013; 118:61-95. [PMID: 23768510 DOI: 10.1016/b978-0-12-407173-5.00003-0] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The functional relevance of autophagy in tumor formation and progression remains controversial. Autophagy can promote tumor suppression during cancer initiation and protect tumors during progression. Autophagy-associated cell death may act as a tumor suppressor, with several autophagy-related genes deleted in cancers. Loss of autophagy induces genomic instability and necrosis with inflammation in mouse tumor models. Conversely, autophagy enhances survival of tumor cells subjected to metabolic stress and may promote metastasis by enhancing tumor cell survival under environmental stress. Unraveling the complex molecular regulation and multiple diverse roles of autophagy is pivotal in guiding development of rational and novel cancer therapies.
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Affiliation(s)
- Sujit K Bhutia
- Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India.
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Dewangan KN, Rakheja S, Marcotte P, Shahmir A, Patra SK. Comparisons of apparent mass responses of human subjects seated on rigid and elastic seats under vertical vibration. Ergonomics 2013; 56:1806-1822. [PMID: 24088118 DOI: 10.1080/00140139.2013.842656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The apparent mass (AM) responses of human body seated on elastic seat, without and with a vertical back support, are measured using a seat pressure sensing mat under three levels of vertical vibration (0.25, 0.50 and 0.75 m/s(2) rms acceleration) in 0.50-20 Hz frequency range. The responses were also measured with a rigid seat using the pressure mat and a force plate in order to examine the validity of the pressure mat. The pressure mat resulted in considerably lower AM magnitudes compared to the force plate. A correction function was proposed and applied, which resulted in comparable AM from both measurement systems for the rigid seat. The correction function was subsequently applied to derive AM of subjects seated on elastic seat. The responses revealed lower peak magnitude and corresponding frequency compared to those measured with rigid seat, irrespective of back support and excitation considered.
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Affiliation(s)
- K N Dewangan
- a CONCAVE Research Centre, Concordia University , Montreal , Canada
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14
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Tayal D, Goswami B, Patra SK, Tripathi R, Khaneja A. Association of inflammatory cytokines, lipid peroxidation end products and nitric oxide with the clinical severity and fetal outcome in preeclampsia in Indian women. Indian J Clin Biochem 2013; 29:139-44. [PMID: 24757293 DOI: 10.1007/s12291-013-0320-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/24/2013] [Indexed: 11/25/2022]
Abstract
Preeclampsia is a multisystem disorder associated with maternal hypertension, placental abnormalities and adverse fetal outcomes. The various pathways involved in its etiology include endothelial dysfunction, inflammatory milieu, lipid peroxidation and immunological imbalance. The present study was conducted to evaluate the causative and predictive role of nitric oxide, lipid peroxidation end products (MDA) and inflammatory cytokines (IL-6, TNF-α) in clinical presentation, severity and fetal outcome in preeclampsia. The study population was divided into 3 groups- Non- pregnant females comprising the control population; G1 and G2 groups included normal pregnant and pregnant females with preeclampsia with 50 patients in each group. Nitric Oxide and MDA levels were found to be highest in the preeclamptic patients as compared to other two groups. ROC curve analysis shows the superiority of the inflammatory markers as determinants of severity of preeclampsia which suggests the emerging role of pro inflammatory markers in the various pathological changes in preeclampsia. TNF-α emerged as the best marker in multivariate analysis and thus, has the potential for being used as a marker for PIH. Our study illustrates the multifactorial etiology of preeclampsia involving oxidative stress, proinflammatory milieu and endothelial dysfunction.
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Affiliation(s)
- Devika Tayal
- Department of Biochemistry, Lala Ram Swaroop Institute, New Delhi, India
| | - Binita Goswami
- Department of Biochemistry, Lady Hardinge Medical College, New Delhi, India
| | - S K Patra
- Department of Biochemistry, Lady Hardinge Medical College, New Delhi, India
| | - Reva Tripathi
- Department of Obstetrics & Gynaecology, Maulana Azad Medical College & Associated LN Hospital, New Delhi, India
| | - Alka Khaneja
- Department of Biochemistry, Maulana Azad Medical College & Associated LN Hospital, New Delhi, India
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15
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Goswami B, Rajappa M, Chakraborty B, Patra SK, Kumar S, Mallika V. Comparison of the various lipid ratios and indices for risk assessment in patients of myocardial infarction. Clin Biochem 2012; 45:445-9. [PMID: 22318009 DOI: 10.1016/j.clinbiochem.2012.01.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 01/20/2012] [Accepted: 01/21/2012] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Coronary artery disease (CAD) has emerged as the major cause of morbidity and mortality among Asian Indians in the recent past. The following study was undertaken to assess the predictive value of novel biomarkers of dyslipidemia for risk assessment for CAD in the Indian population. DESIGN AND METHODS The study group comprised of 100 clinically assessed patients of myocardial infarction and 100 age and sex matched healthy controls. Apolipoprotein-A (Apo-AI) and Apolipoprotein-B (Apo-B) were estimated and small dense LDL was derived mathematically. RESULTS The cases showed significantly high levels of total serum cholesterol, triglycerides, LDL cholesterol, Apo-B, sdLDL, and non-HDL cholesterol. On carrying out multivariate regression analysis, Lp(a)/HDL ratio emerged as the best determinant of CAD risk CONCLUSION The above data clearly underlines the role of these novel biomarkers in the risk assessment for CAD in the Indian context.
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Affiliation(s)
- Binita Goswami
- Department of Biochemistry, Lady Hardinge Medical College & Associated hospitals, New Delhi-110001, India.
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16
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Abstract
DNA (cytosine-5-carbon) methylation is one of the hallmarks of mammalian chromatin modifications. Distinct methylation pattern can generate synergistic or antagonistic interaction affinities for CpG-islands associated with methylated or unmethylated cytosine binding proteins, which also may dictate histone modifications and dynamic transition between transcriptionally silent or transcriptionally active chromatin states. The enzymes and cofactors associated with DNA-methylation reactions are convincing in terms of chemistry and chemical thermodynamics. The mechanism of demethylation, the candidate enzyme(s) exhibiting direct demethylase activity, and associated cofactors are not firmly established. Use of azanucleosides, such as 5-azacytidine and 5-aza-2'-deoxycytidine (AzadC), in cell culture produces re-expression of certain genes, which otherwise were repressed in association with hypermethylated CpG-rich promoters. Hence the notion developed that AzadC is a demethylating agent. Here we discuss the broad global pictures with the following points: first, chemical definition and recent advances regarding the mechanism of DNA (cytosine-5-carbon) methylation ((Me)CpG-DNA or (Me)CpNpG-DNA formation) and (Me)CpG/(Me)CpNpG-DNA-demethylation, and then with the mechanistic basis of inactivation of DNA-methyltransferase 1 by AzadC. This will clarify that: (i) AzadC has nothing to do with DNA-demethylation; (ii) it cannot prevent even de novo methylation in non-replicating cells; (iii) it can only prevent replication coupled maintenance as well as de novo methylations. Finally, we would like to suggest that terming/designating AzadC as DNA-demethylating agent is a serious misuse of chemistry and chemical terminology.
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Affiliation(s)
- S K Patra
- Division of Biochemistry, Department of Experimental Medicine, University of Parma, Parma, Italy.
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17
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Patra SK, Rizzi F, Silva A, Rugina DO, Bettuzzi S. Molecular targets of (-)-epigallocatechin-3-gallate (EGCG): specificity and interaction with membrane lipid rafts. J Physiol Pharmacol 2008; 59 Suppl 9:217-235. [PMID: 19261982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 12/20/2008] [Indexed: 05/27/2023]
Abstract
Proteomic studies on anticancer activity of Green Tea Catechins (specifically EGCG) are suggesting a large set of protein targets that may directly interact with EGCG and alter the physiology of diseased cells, including cancer. Of notice, benign cells are usually left untouched. Lipid rafts have been recently recognized as signal processing hubs and suggested to be involved in drug uptake by means of endocytosis. These findings are suggesting new insights on the molecular mechanisms of anticancer drugs action. In the membrane, EGCG is hijacked by the laminin receptor (LamR), a lipid raft protein. Similar to aplidin and edelfosin, EGCG alters membrane domains composition also preventing EGF binding to EGFR, imerization of EGFR and relocation of phosphorylated EGFR to lipid rafts. In vitro studies have recently shown that EGCG also binds both DNA and RNA in GpC-rich regions. This event may importantly affect genes function. Moreover, EGCG was shown to inhibit telomerase, topoisomerase II and DNA methyltransferase 1 (DNMT1), thus ultimately affecting chromatin maintenance and remodeling. But another important alternative pathway besides interaction with specific proteins may play an important role in EGCG action: direct targeting of bioactive membrane platforms, lipid rafts. Structural alteration of the platforms deeply impact (and often inactivates) important pathways involving MAP kinases. The key issue is that, important and specific differences in lipid rafts composition have been found in transformed versus benign cells and apoptotic versus non-apoptotic cells. We suggest here that the anticancer activity of Green Tea Catechins against different kind of cancers may find an explanation in direct targeting of lipid rafts by EGCG.
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Affiliation(s)
- S K Patra
- Department of Experimental Medicine, University of Parma, Parma, Italy
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18
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Patra SK, Alonso A, Arrondo JLR, Goñi FM. Liposomes Containing Sphingomyelin and Cholesterol: Detergent Solubilisation and Infrared Spectroscopic Studies. J Liposome Res 2008. [DOI: 10.3109/08982109909024788] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Abstract
Cytosine methylation at the 5-carbon position is the only known stable base modification found in the mammalian genome. The organization and modification of chromatin is a key factor in programming gene expression patterns. Recent findings suggest that DNA methylation at the junction of transcription initiation and elongation plays a critical role in suppression of transcription. This effect is mechanistically mediated by the state of chromatin modification. DNA methylation attracts binding of methyl-CpG-binding domain proteins that trigger repression of transcription, whereas DNA demethylation facilitates transcription activation. Understanding the rules that guide differential gene expression, as well as transcription dynamics and transcript abundance, has proven to be a taxing problem for molecular biologists and oncologists alike. The use of novel molecular modeling methods is providing exciting insights into the challenging problem of how methylation mediates chromatin dynamics. New data implicate lipid rafts as the coordinators of signals emanating from the cell membrane and are converging on the mechanisms linking DNA methylation and chromatin dynamics. This review focuses on some of these recent advances and uses lipid-raft-facilitated Ras signaling as a paradigm for understanding DNA methylation, chromatin dynamics and apoptosis.
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Patra SK, Bettuzzi S. Epigenetic DNA-methylation regulation of genes coding for lipid raft-associated components: a role for raft proteins in cell transformation and cancer progression (review). Oncol Rep 2007; 17:1279-90. [PMID: 17487380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
Metastatic progression is the cause of most cancer deaths. Host tumour cell separation (fission) is accompanied by simultaneous acquisition of migrating capability of cancer cells, remodeling of cellular architecture and effective 'homing' in body host environment. Cell remodeling involves cytoskeletal protein-protein and lipid-protein interaction together with altered signaling. Alteration of signaling in tumour cells may affect expression of many genes also by DNA-methylation/demethylation. This would alter the steady-state intracellular level of structural proteins or metabolic enzymes, and notably enzymes involved in the biosynthesis of lipids, affecting the composition of membranes. Lipid rafts are small, heterogeneous, highly dynamic, sterol- and sphingolipid-enriched domains that compartmentalize cellular processes. Small rafts can be stabilized to form larger platforms through protein-protein and protein-lipid interactions. Lipid rafts play an important role in intracellular protein transport, membrane fusion and trans-cytosis, also being platforms for cell surface antigens and adhesion molecules which are crucial for cell activation, polarization and signaling. Detachment of individual tumour cells from the host tumour lump requires lipid-protein-lipid raft (LPLR) reordering. Lipid rafts are also involved in angiogenesis and local invasion, which occurs within the host tumour vicinity by exchange of enzymes, cytokines and motility factors that modify the surrounding extracellular matrix (ECM). Many cell surface adhesion, ECM, and signaling proteins (such as E-cadherin, catenin, CD44, MMP-9 and caveolin-1) are known to be absent or reduced following gene promoter-CpG-island hypermethylation in mid-stage growing tumours, but re-expressed (by gene promoter-mCpG-DNA demethylation) in carcinomas such as metastasized lung, prostate and sarcomas. The recent research acquisitions on lipid rafts have tremendous implications in understanding the genetic and biochemical bases of metastatic diffusion of cancer.
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Affiliation(s)
- Samir K Patra
- Department of Medicina Sperimentale, University of Parma, I-43100 Parma, Italy.
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Patra SK, Patra A, Zhao H, Carroll P, Dahiya R. Methyl-CpG-DNA binding proteins in human prostate cancer: expression of CXXC sequence containing MBD1 and repression of MBD2 and MeCP2. Biochem Biophys Res Commun 2003; 302:759-66. [PMID: 12646234 DOI: 10.1016/s0006-291x(03)00253-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We analyzed gene expression of MBD1, MBD2, MBD3, MBD4, and MeCP2 and protein expression of MBD1, MBD2, and MeCP2 in prostate cancer cell lines, benign prostate epithelium (BPH-1) cell line, 49 BPH tissues, and 46 prostate cancer tissues. The results of this study demonstrate that MBD2 gene is expressed in all samples and MeCP2 gene is expressed in all cancer cell lines but not in BPH-1 cell line. However, there was no protein expression for MBD2 and MeCP2 in cancer cell lines and cancer tissues. For CXXC sequence containing MBD1, both protein and mRNA were expressed in cancer cell lines, cancer tissues, BPH-1 cell line, and BPH tissues. We observed that, in BPH tissues and low-grade cancer tissues, MBD1 protein expression was very high and gradually decreased with increase of cancer grade. Treatment of cancer cell lines with proteasome inhibitor (MG-132) did not restore expression of MBD2 and MeCP2 proteins. When prostate cancer cell lines were treated with hypomethylating agent, 5-aza-2(')-deoxycytidine (DNMT inhibitor), HDAC1 and HDAC2 expression was decreased. This is the first report demonstrating that CXXC sequence containing MBD1 is overexpressed and can be the major factor of hypermethylated chromatin segments through HDAC1/2 translocation and histone deacetylation in human prostate cancer.
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Affiliation(s)
- Samir K Patra
- Department of Urology, Urology Research Center (112F), University of California at San Francisco and Veterans Affairs Medical Center, 4150 Clement Street, San Francisco, CA 94121, USA
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22
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Abstract
Recent studies have shown that cytosine-5 methylation at CpG islands in the regulatory sequence of a gene is one of the key mechanisms of inactivation. The enzymes responsible for CpG methylation are DNA methyltransferase (DNMT) 1, DNMT3a, and DNMT3b, and the enzyme responsible for demethylation is DNA demethylase (MBD2). Studies on methylation-demethylation enzymes are lacking in human prostate cancer. We hypothesize that MBD2 enzyme activity is repressed and that DNMT1 enzyme activity is elevated in human prostate cancer. To test this hypothesis, we analyzed enzyme activities, mRNA, and protein levels of MBD2 and DNMT1, DNMT3a, and DNMT3b in human prostate cancer cell lines and tissues. The enzyme activities of DNMTs and MBD2 were analyzed by biochemical assay. The mRNA expression was analyzed by reverse transcriptase-polymerase chain reaction and by Northern blotting. The protein expression was measured by immunohistochemistry with specific antibodies. The results of these experiments demonstrated that (1) the activity of DNMTs was twofold to threefold higher in cancer cell lines and cancer tissues, as compared with a benign prostate epithelium cell line (BPH-1) and benign prostatic hyperplasia (BPH) tissues; (2) MBD2 activity was lacking in prostate cancer cell lines but present in BPH-1 cells; (3) immunohistochemical analyses exhibited higher expression of DNMT1 in all prostate cancer cell lines and cancer tissues, as compared with BPH-1 cell lines and BPH tissues; (4) MBD2 protein expression was significantly higher in BPH-1 cells and lacking in prostate cancer cell lines and, in BPH tissues, MBD2 protein expression was poorly observed, as compared with no expression in prostate cancer tissues; and (5) mRNA expression for DNMT1 was upregulated in prostate cancer, as compared with BPH-1, and mRNA expression for MBD2 was found to be significantly expressed in all cases. The results of these studies clearly demonstrate that DNMT1 activity is upregulated, whereas MBD2 is repressed at the level of translation in human prostate cancer. These results may demonstrate molecular mechanisms of CpG hypermethylation of various genes in prostate cancer.
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Affiliation(s)
- Samir K Patra
- Department of Urology, University of California San Francisco and Veterans Affairs Medical Center, San Francisco, California 94121, USA
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23
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Abstract
CpG island hypermethylation and chromatin remodeling play important roles in repression of various genes during malignant transformation. We hypothesized that histone deacetylases (HDACs) and DNA methyltransferases (DNMTase) are associated with prostate cancer and we examined the enzyme activity, gene, and protein expression of HDAC1 and DNMT1 in cell lines and tissues. We found that DNMTase and HDACs activities were two- to threefold higher in cell lines compared to benign prostatic hyperplasia (BPH-1) cell line. Treatment of cells with 5-aza-2'-deoxycytidine decreased the activity of HDAC and DNMTase. The mRNA expression of these genes in BPH-1 cells and BPH tissues was lower than that in prostate cancer cells and tissues. HDAC1 and DNMT1 protein expression was higher in prostate cancer compared to BPH. This is the first report to demonstrate that DNMT1 and HDAC1 levels are up-regulated in prostate cancer compared to BPH, suggesting their roles in inactivation of various genes, by DNA-methylation-induced chromatin-remodeling, in prostate cancer.
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Affiliation(s)
- S K Patra
- Department of Urology, University of California at San Francisco, San Francisco, California 94121, USA
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Abstract
Effect of chronic oral exposure (10 and 20 mg kg(-1) body wt. for 7, 15 and 30 days) to hexachlorocyclohexane (HCH) on open-field behaviour and activities of cerebral Na+,K+-ATPase, Mg2+-ATPase and acetylcholinesterase (AChE) of rat was evaluated. Motor and grooming activities were altered, whereas vertical exploratory activity was unaffected by HCH. Activities of Na+,K+-ATPase, Mg2+-ATPase and AChE were inhibited significantly by the pesticide. The results suggest that HCH induces impairment of the enzymes involved in synaptic activity, resulting in behavioural alterations.
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Affiliation(s)
- A Sahoo
- Department of Zoology, S.V.M. College, Jagatsinghpur, Orissa, India
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Patra SK, Alonso A, Goñi FM. Detergent solubilisation of phospholipid bilayers in the gel state: the role of polar and hydrophobic forces. Biochim Biophys Acta 1998; 1373:112-8. [PMID: 9733939 DOI: 10.1016/s0005-2736(98)00095-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Testing the solubilisation of phosphatidylcholine (PC) bilayers by Triton X-100 reveals that in the gel state, but not in the fluid state, the amount of detergent required to solubilise the phospholipid is highly dependent on the chain length. Saturated C16 and C18 PC are virtually insoluble at 4 degreesC. However, addition of water-soluble reagents that perturb hydrogen bonding, e.g. urea, or of small proportions of non-bilayer lipids, make the bilayers amenable to detergent solubilisation, even at low temperatures. These results are relevant in the explanation of the origin of detergent-resistant membrane fragments as found, e.g. in caveolae or 'rafts'.
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Affiliation(s)
- S K Patra
- Grupo Biomembranas (Unidad Asociada al CSIC), Departamento de Bioquímica, Universidad del País Vasco, Aptdo. 644, 48080 Bilbao, Spain
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Patra SK, Pal MK. Red edge excitation shift emission spectroscopic investigation of serum albumins and serum albumin-bilirubin complexes. Spectrochim Acta A Mol Biomol Spectrosc 1997; 53A:1609-1614. [PMID: 9358651 DOI: 10.1016/s1386-1425(97)00098-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The microenvironments around the intrinsic and extrinsic fluorophores in bovine and human serum albumins as well as their complexes with bilirubin have been visualized by red edge excitation shift (REES) emission spectroscopic investigation. The two albumins and their bilirubin complexes in aqueous buffered solutions (pH 7.5) do not exhibit any appreciable shift in their emission maxima, upon gradual change in excitation wavelength towards the red edge of their respective absorption band. The addition of Triton X-100 triggers REES emission in both the fluorophores. The observations suggest that the microenvironment around the flurophores are not so rigid, and even the extrinsic flurophore bilirubin having two carboxylic acid groups acts as a hydrophobic non-polar molecule when bound to albumins. The ligand binding domains (receptor sites) are large enough and incorporation of Triton X-100 makes the fluorophore environments rigid and subtle polarity may also be induced. Whereas small polar molecules like CHCl3, ANS and L-trp fail to induce REES emission in either of the fluorophores.
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Affiliation(s)
- S K Patra
- Department of Biochemistry and Biophysics, University of Kalyani, West Bengal, India
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27
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Patra SK, Pal MK. Spectroscopic probes of the individual and combined effects of Triton X-100 and chloroform on serum albumins and serum-albumin.bilirubin complexes. Eur J Biochem 1997; 246:658-64. [PMID: 9219523 DOI: 10.1111/j.1432-1033.1997.t01-1-00658.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The effects of the non-ionic surfactant Triton X-100 on the biphasic induced CD spectra of bilirubin complexes of human and bovine serum albumins (HSA and BSA) are divergent. While Triton X-100 inverts the induced CD spectrum of HSA.bilirubin, this surfactant enhances the ellipticity values of induced CD of BSA.bilirubin without inversion. The effect of Triton X-100 on the characteristic ultraviolet-CD spectra of the albumins are similar; both the albumins are denatured from their native globular structures. The anionic surfactant SDS, unlike non-ionic Triton X-100, dislodges the ligand from its protein complexes, indicating that both electrostatic and hydrophobic forces are involved in binding of bilirubin to the albumins. The aprotic solvent chloroform inverts the biphasic induced CD spectra of HSA.bilirubin and BSA.bilirubin, whereas CHCl3 has relatively little effect on the ultraviolet CD spectra of the albumins. The combined effect of Triton X-100 and CHCl3 shows that the effect of CHCl3 predominates over that of Triton X-100. The perturbing effects of Triton X-100 and CHCl3 on the CD or induced CD spectra of the proteins or their bilirubin complexes are reversible, and independent of the order in which components were added. The observations suggest that the denaturation of the albumins by Triton X-100 or solvation of CHCl3 within albumins markedly alter the internal topography or dynamics of the receptor sites, triggering alterations of the chirality of the bound pigment in sign and/or magnitude.
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Affiliation(s)
- S K Patra
- Department of Biochemistry and Biophysics, University of Kalyani, India
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Takigawa N, Yoshida S, Hagino K, Patra SK, Praharaj CR. Reply to "Comment on 'Shape and superdeformed structure in Hg isotopes in relativistic mean field model' and 'Structure of neutron-deficient Pt, Hg, and Pb isotopes' ". Phys Rev C Nucl Phys 1996; 53:1038-1040. [PMID: 9971032 DOI: 10.1103/physrevc.53.1038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Abstract
In this study we examined a possible contribution of serotonin (5-hydroxytryptamine, 5-HT) to spatial memory performance in the rat. Rats were trained to run in a radial maze in a manner that involved two kinds of memory function, i.e. working memory and reference memory. They received intrahippocampal microinjections of a 5-HT1A [8-hydroxy-2-(di-n-propylamino)tetralin or 8-OH-DPAT], or a 5-HT1B [3-(1,2,5,6-tetrahydropyrid-4-yl)pyrrolo[3,2-b]pyrid-5-one or CP-93,129] receptor agonist, and a muscarinic receptor antagonist (scopolamine). 8-OH-DPAT (5 micrograms/microliters), like injections of saline, induced no change in performance levels. In contrast, rats suffered an impairment in both reference and working memory following injection of scopolamine (10 micrograms/microliters). CP-93,129 induced a higher frequency of reference memory errors than of working memory errors at the intermediate (10 micrograms/microliters) and higher doses (16 micrograms/microliters). Thus, the stimulation of 5-HT1B receptors in the CA1 field of the dorsal hippocampus impairs the performance of rats in a spatial learning task.
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Affiliation(s)
- M C Buhot
- Centre National de la Recherche Scientifique, Laboratoire de Neurosciences Comportementales et Cognitives, C.N.R.S. URA 339, Université de Bordeaux I, Talence, France
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Yoshida S, Patra SK, Takigawa N, Praharaj CR. Surface properties of Cs isotopes. Phys Rev C Nucl Phys 1995; 52:157-163. [PMID: 9970493 DOI: 10.1103/physrevc.52.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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31
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Patra SK, Yoshida S, Takigawa N, Praharaj CR, Rath AK. Hexadecapole shape change in ytterbium isotopes. Phys Rev C Nucl Phys 1995; 51:2248-2251. [PMID: 9970300 DOI: 10.1103/physrevc.51.2248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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32
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Patra SK, Yoshida S, Takigawa N, Praharaj CR. Shape and superdeformed structure in Hg isotopes in relativistic mean field model. Phys Rev C Nucl Phys 1994; 50:1924-1931. [PMID: 9969868 DOI: 10.1103/physrevc.50.1924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Yoshida S, Patra SK, Takigawa N, Praharaj CR. Structure of neutron-deficient Pt, Hg, and Pb isotopes. Phys Rev C Nucl Phys 1994; 50:1398-1403. [PMID: 9969801 DOI: 10.1103/physrevc.50.1398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Pal MK, Patra SK. Fluorimetric probes of the individual and competitive binding of 1-anilinonaphthalene-8-sulfonate, eosine and fluorescene to bovine serum albumin. Indian J Biochem Biophys 1994; 31:109-14. [PMID: 7523280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Fluorescence of 1-anilinonaphthalene-8-sulfonate (ANS) is greatly enhanced on its binding to bovine serum albumin (BSA). Fluorimetric titration shows that three ANS molecules bind per BSA molecule. The enhanced fluorescence of BSA-ANS is quenched by eosine (EOS); and one EOS physically displaces one ANS bound to BSA. The enhanced fluorescence of free ANS in the hydrophobic environment of the nonionic surfactant Triton X 100 is also quenched by EOS but by an energy transfer mechanism. The dye fluorescene (FLSN) also quenches the fluorescence of BSA-bound ANS, but by the energy transfer mechanism. The binding region of ANS in BSA has been speculated.
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Affiliation(s)
- M K Pal
- Department of Biochemistry & Biophysics, University of Kalyani, West Bengal, India
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Patra SK. Effects of pairing correlation in light nuclei. Phys Rev C Nucl Phys 1993; 48:1449-1451. [PMID: 9968979 DOI: 10.1103/physrevc.48.1449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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36
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Patra SK, Praharaj CR. Shapes of exotic nuclei in the mass A=70 region. Phys Rev C Nucl Phys 1993; 47:2978-2981. [PMID: 9968775 DOI: 10.1103/physrevc.47.2978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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37
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Patra SK, Panda PK. Systematic study of neutron-deficient Ho isotopes in a relativistic mean field theory. Phys Rev C Nucl Phys 1993; 47:1514-1518. [PMID: 9968597 DOI: 10.1103/physrevc.47.1514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Patra SK, Praharaj CR. Relativistic mean field study of light medium nuclei away from beta stability. Phys Rev C Nucl Phys 1991; 44:2552-2565. [PMID: 9967691 DOI: 10.1103/physrevc.44.2552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Chakraborti S, Michael JR, Patra SK. Protein kinase C dependent and independent activation of phospholipase A2 under calcium ionophore (A23187) exposure in rabbit pulmonary arterial smooth muscle cells. FEBS Lett 1991; 285:104-7. [PMID: 1906011 DOI: 10.1016/0014-5793(91)80735-l] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Exposure of rabbit pulmonary arterial smooth muscle cells to the calcium ionophore A23187, dose-dependently stimulates arachidonic acid (AA) release and phospholipase A2 (PLA2) activity. The protein kinase C (PKC) inhibitor, sphingosine does not prevents AA release and PLA2 activity caused by low doses of A23187. In contrast, sphingosine markedly prevents AA release and PLA2 activity caused by higher doses of A23187. PKC activity profile indicates that treatment of the cells with low doses of A23187 does not cause significant alteration of PKC translocation from cytosol to membrane whereas higher concentrations of the ionophore dose-dependently enhance PKC translocation from cytosol to membrane in the smooth muscle cells.
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Affiliation(s)
- S Chakraborti
- Department of Biochemistry and Biophysics, University of Kalyani, India
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Dandapat MC, Mohapatra SK, Patra SK. Adjuvant combination immunotherapy (BCG and levamisole) in malignant melanoma. Indian J Cancer 1985; 22:100-7. [PMID: 3842124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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