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Dey M. Enabling inclusion and looking ahead. Cell Chem Biol 2023; 30:1323. [PMID: 37977123 DOI: 10.1016/j.chembiol.2023.10.020] [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] [Received: 10/27/2023] [Indexed: 11/19/2023]
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Nandi S, Dey M. Identification of residues involved in allosteric signal transmission from amino acid binding site of pyruvate kinase muscle isoform 2. PLoS One 2023; 18:e0282508. [PMID: 36897854 PMCID: PMC10004559 DOI: 10.1371/journal.pone.0282508] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/16/2023] [Indexed: 03/11/2023] Open
Abstract
PKM2 is a rate-limiting enzyme in the glycolytic process and is involved in regulating tumor proliferation. Several amino acids (AAs) such as Asn, Asp, Val, and Cys have been shown to bind to the AA binding pocket of PKM2 and modulate its oligomeric state, substrate binding affinity, and activity. Although previous studies have attributed that the main chain and side chain of bound AAs are responsible for initiating signal to regulate PKM2, the signal transduction pathway remains elusive. To identify the residues involved in signal transfer process, N70 and N75 located at two ends of a β strand connecting the active site and AA binding pocket were altered. Biochemical studies of these variants with various AA ligands (Asn, Asp, Val, and Cys), illustrate that N70 and N75, along with β1 connecting these residues are part of the signal transduction pathway between the AA binding pocket and the active site. The results demonstrate that mutation of N70 to D prevents the transfer of the inhibitory signal mediated by Val and Cys, whereas N75 to L alteration blocks the activating signal initiated by Asn and Asp. Taken together, this study confirms that N70 is one of the residues responsible for transmitting the inhibitory signal and N75 is involved in the activation signal flow.
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Affiliation(s)
- Suparno Nandi
- Department of Chemistry, The University of Iowa, Iowa City, IA, United States of America
| | - Mishtu Dey
- Department of Chemistry, The University of Iowa, Iowa City, IA, United States of America
- * E-mail: ,
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Dey M, Bukhari M. Cluster analysis demonstrates co-existing sites of fragility fracture and associated comorbidities. Osteoporos Int 2022; 33:1613-1618. [PMID: 35312823 DOI: 10.1007/s00198-022-06377-z] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/11/2022] [Indexed: 10/18/2022]
Abstract
UNLABELLED We undertook cluster analysis in 11,003 patients who had sustained ≥ 1 fragility fracture, to find associations between fracture sites and comorbidities. We identified three distinct groups of fracture sites and four clusters of fractures and comorbidities. Knowledge of factors associated with fracture sites will aid prophylaxis in at-risk patients. INTRODUCTION Fragility fracture (FF) prevalence is increasing. Subsequent fractures lead to greater morbidity and mortality. Few data are available on the association between FF sites and comorbidities. OBJECTIVES 1. Establish the most common sites of FF and clusters within patients. 2. Identify patterns of co-existing FF and associated comorbidities. METHODS We retrospectively reviewed clinical records of patients undergoing bone mineral density estimation at a district hospital in North-West England, 2004-2016, identifying those who had sustained ≥ 1 FF. Demographics, FF site(s), comorbidities, and medications were recorded. Cluster analysis was performed on fracture sites alone, and sites and comorbidities, using Jaccard similarity coefficient. Results were plotted on a dendrogram and divided into clusters. RESULTS Of 28,868 patients, 11,003 had sustained ≥ 1 FF, 84.6% female, with overall mean age 67.5 years and median T-score - 1.12 SD. FF of the forearm was more frequent (n = 5045), most commonly co-existing with tibia/fibula fractures. Three FF site clusters were identified: ankle and elbow; forearm, tibia/fibula, ribs and spine; and pelvis, femur and humerus. When including comorbidities, four clusters were identified: forearm, tibia/fibula, spine, associated with family history of FF, smoking, corticosteroids and bisphosphonates; pelvis associated with hyperparathyroidism, PMR, coeliac disease and HRT; femur and humerus associated with IBD and RA; and ribs associated with alcohol and hyperthyroidism. CONCLUSION Cluster analysis demonstrated three fracture site clusters, and four subgroups of FF sites and comorbidities. Cluster analysis is a novel method to evaluate comorbidities associated with FF sites. Knowledge of factors associated with FF sites will aid prophylaxis in at-risk patients.
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Affiliation(s)
- M Dey
- Institute of Life Course and Medical Sciences, University of Liverpool, Brownlow Hill, Liverpool, L69 3BX, UK.
- Department of Rheumatology, Countess of Chester Hospital NHS Foundation Trust, Liverpool Road, Chester, CH2 1UL, UK.
| | - M Bukhari
- Department of Rheumatology, Royal Lancaster Infirmary, University Hospitals of Morecambe Bay, Lancaster, LA1 4RP, UK
- Lancaster University Medical School, Lancaster University, Lancaster, LA1 4YW, UK
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Fragoulis GE, Dey M, Zhao SS, Courvoisier D, Galloway J, Hyrich K, Nikiphorou E. POS1179 SYSTEMATIC LITERATURE REVIEW ON THE SCREENING AND PROPHYLAXIS OF CHRONIC AND OPPORTUNISTIC INFECTIONS. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.1712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BackgroundOpportunistic and chronic infections can arise in the context of treatment used for Autoimmune Rheumatic Diseases (ARDs). Although it is recognized that screening procedures and prophylactic measures must be followed, clinical practice is largely heterogeneous, with relevant recommendations not currently developed or disparately located across the literature.ObjectivesTo conduct a systematic literature review (SLR) focusing on the screening and prophylaxis of opportunistic and chronic infections in ARDs. This is preparatory work done by members of the respective EULAR task force (TF).MethodsFollowing the EULAR standardised operating procedures, we conducted an SLR with the following 5 search domains; 1) Infection: infectious agents identifed by a scoping review and expert opinion (TF members), 2) Rheumatic Diseases: all ARDs, 3) Immunosuppression: all immunosuppressives/immunomodulators used in rheumatology, 4) Screening: general and specific (e.g mantoux test) terms, 5) Prophylaxis: general and specific (e.g trimethoprim) terms. Articles were retrieved having the terms from domains 1 AND 2 AND 3, plus terms from domains 4 OR 5. Databases searched: Pubmed, Embase, Cochrane. Exclusion criteria: post-operative infections, pediatric ARDs, not ARDs (e.g septic arthritis), not concerning screening or prophylaxis, Covid-19 studies, articles concerning vaccinations and non-Εnglish literature. Quality of studies included was assessed as follows: Newcastle Ottawa scale for non-randomized controlled trials (RCTs), RoB-Cochrane tool for RCTs, AMSTAR2 for SLRs.Results5641 studies were initially retrieved (Figure 1). After title and abstract screening and removal of duplicates, 568 full-text articles were assessed for eligibility. Finally, 293 articles were included in the SLR. Most studies were of medium quality. Reasons for exclusion are shown in Figure 1. Results categorized as per type of microbe, are as follows: For Tuberculosis; evidence suggests that tuberculin skin test (TST) is affected by treatment with glucocorticoids and conventional synthetic DMARDs (csDMARDs) and its performance is inferior to interferon gamma release assay (IGRA). Agreement between TST and IGRA is moderate to low. Conversion of TST/IGRA occurs in about 10-15% of patients treated with biologic DMARDs (bDMARDs). Various prophylactic schemes have been used for latent TB, including isoniazide for 9 months, rifampicin for 4 months, isoniazide/rifampicin for 3-4 months. For hepatitis B (HBV): there is evidence that risk of reactivation is increased in patients positive for hepatitis B surface antigen. These patients should be referred for HBV treatment. Patients who are positive for anti-HBcore antibodies, are at low risk for reactivation when treated with glucocorticoids, cDMARDs and bDMARDs but should be monitored periodically with liver function tests and HBV-viral load. Patients treated with rituximab display higher risk for HBV reactivation especially when anti-HBs titers are low. Risk for reactivation in hepatitis C RNA positive patients, treated with bDMARDs is low. However, all patients should be referred for antiviral treatment and monitored periodically. For pneumocystis jirovecii: prophylaxis with trimethoprim/sulfamethoxazole (alternatively with atovaquone or pentamidine) should be considered in patients treated with prednisolone: 15-30mg/day for more than 4 weeks. Few data exist for screening and prophylaxis from viruses like EBV, CMV and Varicella Zoster Virus. Expert opinion supports the screening of rare bugs like histoplasma and trypanosoma in patients considered to be at high risk (e.g living in endemic areas).Figure 1.SLR flowchartConclusionThe risk of chronic and opportunistic infections should be considered in all patients prior to treatment with immunosuppressives/immunomodulators. Different screening and prophylaxis approaches are described in the literature, partly determined by individual patient and disease characteristics. Collaboration between different disciplines is important.AcknowledgementsWe would like to thank all members of the EULAR Task Force for the screening and prophylaxis of chronic and opportunistic infections in Autoimmune Rheumatic Diseases.Disclosure of InterestsNone declared
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Hng M, Dey M, Moots R. POS1461 GIANT CELL ARTERITIS-RELATED STROKE IN A MAN WITH ELDERLY-ONSET RHEUMATOID ARTHRITIS. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BackgroundGiant cell arteritis-related stroke is rare, with high early mortality and major morbidity in survivors.ObjectivesTo increase the awareness of coexistence of giant cell arteritis-related stroke and rheumatoid arthritis.MethodsA case report and discussion.ResultsA 73 year-old man with seronegative elderly-onset rheumatoid arthritis (EORA) presented to the emergency department (ED) with a one week history of frontal headache, vomiting and dizziness. He had multiple cardiovascular comorbidities and took multiple medications, including methotrexate and sulfasalazine. He also had long-standing history of thrombocytopenia without requiring any treatment. Neurological examination performed in the ED was unremarkable. His C-reactive protein (CRP) was 69mg/L and erythrocyte sedimentation rate (ESR) 82mm/hour. Computed tomography (CT) of the brain was normal. The headache settled with analgesia. A diagnosis of probable tension-type headache, with underlying active EORA, was made.One month later, he presented to an ophthalmologist with recurrence of headache associated with visual disturbance and was diagnosed with giant cell arteritis (GCA). Both CRP (77mg/L) and ESR (85mm/hour) remained raised. Neither temporal artery biopsy nor temporal artery ultrasound were possible due to the coronavirus disease 2019 (COVID-19) pandemic. The headache and visual symptoms resolved completely a week after prednisolone 60mg daily was prescribed. In parallel, the CRP dropped to 2mg/L and ESR 16mm/hour. The patient’s glucocorticoid dose was then tapered. While on prednisolone 20mg daily, about 3 weeks later, he developed slurred speech and generalized weakness. Examination showed cerebellar signs and MRI brain showed acute cerebellar infarct. He was treated pragmatically as an atherosclerotic stroke with clopidogrel, and the steroid was rapidly tapered in view of absence of headache and normalization of inflammatory markers.Four weeks later, he was noted to have persistent confusion and unsteadiness of gait. CRP was elevated at 92mg/L. An urgent positron emission tomography-CT (PET-CT) scan showed inflammation in the vertebral arteries [Figure 1] and cerebellar stroke. Prednisolone 40mg daily was restarted which led to a rapid improvement in his symptoms and normalization of inflammatory markers. The glucocorticoids were tapered in a slower manner this time.Figure 1.Fused axial image of a PET-CT scan demonstrating increased uptake in the region of the left vertebral artery within the vertebral foramen.A diagnosis of GCA-related cerebellar stroke with vertebral vasculitis was made and, with glucocorticoids, the patient made a good clinical recovery. His inflammatory joints pain also improved in parallel.ConclusionStroke or transient ischemic stroke are rare complications, reported in 2.8-16% of patients with active GCA. Most studies report strokes as occurring between the onset of GCA symptoms and 4 weeks after commencement of glucocorticoids1-3.Vertebrobasilar territory is involved in 60–88% of cases of GCA-related stroke1-3. In contrast, the vertebrobasilar territory is affected only in 15-20% of atherosclerotic strokes1,2. One study reported fatal outcomes in 11 out of 40 patients (28%) with GCA-related stroke, 7 within 2-13 days of stroke2.To conclude, this case demonstrates that high-dose glucocorticoids with slower tapering were able to control GCA-related stroke due to vertebral vasculitis in patient with EORA on background methotrexate and sulfasalazine.References[1]Gonzalez-Gay MA, Vazquez-Rodriguez TR, Gomez-Acebo I, et al. Strokes at time of disease diagnosis in a series of 287 patients with biopsy-proven giant cell arteritis. Medicine. 2009;88(4):227-35.[2]de Boysson H, Liozon E, Larivière D, et al. Giant cell arteritis–related stroke: a retrospective multicenter case-control study. 2017;44(3):297-303.[3]Pariente A, Guédon A, Alamowitch S, et al. Ischemic stroke in giant-cell arteritis: French retrospective study. 2019;99:48.AcknowledgementsWe would like to thank Dr Lenetta Boyce for providing the PET-CT images.Disclosure of InterestsNone declared
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Wagner BK, Dey M. Chemical strategies to understand and manipulate host-pathogen interactions. Cell Chem Biol 2022; 29:711-712. [PMID: 35594847 DOI: 10.1016/j.chembiol.2022.05.001] [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: 11/03/2022]
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Dey M. Using chemical biology for targeting cancer. Cell Chem Biol 2022; 29:351-352. [PMID: 35303438 DOI: 10.1016/j.chembiol.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Mitchell D, Kwon HJ, Kubica PA, Huff WX, O’Regan R, Dey M. Brain metastases: An update on the multi-disciplinary approach of clinical management. Neurochirurgie 2022; 68:69-85. [PMID: 33864773 PMCID: PMC8514593 DOI: 10.1016/j.neuchi.2021.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/16/2021] [Accepted: 04/03/2021] [Indexed: 01/03/2023]
Abstract
IMPORTANCE Brain metastasis (BM) is the most common malignant intracranial neoplasm in adults with over 100,000 new cases annually in the United States and outnumbering primary brain tumors 10:1. OBSERVATIONS The incidence of BM in adult cancer patients ranges from 10-40%, and is increasing with improved surveillance, effective systemic therapy, and an aging population. The overall prognosis of cancer patients is largely dependent on the presence or absence of brain metastasis, and therefore, a timely and accurate diagnosis is crucial for improving long-term outcomes, especially in the current era of significantly improved systemic therapy for many common cancers. BM should be suspected in any cancer patient who develops new neurological deficits or behavioral abnormalities. Gadolinium enhanced MRI is the preferred imaging technique and BM must be distinguished from other pathologies. Large, symptomatic lesion(s) in patients with good functional status are best treated with surgery and stereotactic radiosurgery (SRS). Due to neurocognitive side effects and improved overall survival of cancer patients, whole brain radiotherapy (WBRT) is reserved as salvage therapy for patients with multiple lesions or as palliation. Newer approaches including multi-lesion stereotactic surgery, targeted therapy, and immunotherapy are also being investigated to improve outcomes while preserving quality of life. CONCLUSION With the significant advancements in the systemic treatment for cancer patients, addressing BM effectively is critical for overall survival. In addition to patient's performance status, therapeutic approach should be based on the type of primary tumor and associated molecular profile as well as the size, number, and location of metastatic lesion(s).
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Affiliation(s)
- D Mitchell
- Department of Neurosurgery, Indiana University School of Medicine, Indiana University Purdue University Indianapolis, IN, USA
| | - HJ Kwon
- Department of Neurosurgery, Indiana University School of Medicine, Indiana University Purdue University Indianapolis, IN, USA
| | - PA Kubica
- Department of Neurosurgery, University of Wisconsin School of Medicine & Public Health, UW Carbone Cancer Center, Madison, WI, USA
| | - WX Huff
- Department of Neurosurgery, Indiana University School of Medicine, Indiana University Purdue University Indianapolis, IN, USA
| | - R O’Regan
- Department of Medicine/Hematology Oncology, University of Wisconsin School of Medicine & Public Health, UW Carbone Cancer Center, Madison, WI, USA
| | - M Dey
- Department of Neurosurgery, University of Wisconsin School of Medicine & Public Health, UW Carbone Cancer Center, Madison, WI, USA,Correspondence Should Be Addressed To: Mahua Dey, MD, University of Wisconsin School of Medicine & Public Health, 600 Highland Ave, Madison, WI 53792; Tel: 317-274-2601;
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Dey M. Cell Chemical Biology announces changes to the editorial team. Cell Chem Biol 2021; 28:1389. [PMID: 34678165 DOI: 10.1016/j.chembiol.2021.10.009] [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: 10/20/2022]
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Affiliation(s)
| | - Mishtu Dey
- Senior Scientific Editor, Cell Chemical Biology
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Dey M, Bechman K, Smith C, Cope A, Nikiphorou E, Galloway J. AB0649 INFECTION PROFILE OF IMMUNE-MODULATORY DRUGS USED IN AUTOIMMUNE DISEASES: ANALYSIS OF SUMMARY OF PRODUCT CHARACTERISTIC DATA. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.2207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:The number of immune-modulatory drugs used to treat immune-mediated inflammatory diseases (IMIDs) has exponentially increased in recent decades. While effective in controlling disease, serious infection remains a concern.Accurate information on immune-modulatory drugs, including infections, is required to guide prescribing decisions. The “summary of product characteristics” (SmPC) by the European Medicines Agency (EMA) provides a useful repository of information on adverse events e.g. infections, from clinical trials and post-marketing pharmacovigilance (1).To date, no comparison has been undertaken on reported infection frequencies across SmPCs for immune-modulators.Objectives:To compare infection frequency, site and type across the most commonly-prescribed immune-modulatory drugs used to treat IMIDs, using information provided by SmPCs.Methods:A drug was included if licensed in Europe for treatment of one of the following: rheumatoid arthritis, axial spondyloarthritis, connective tissue disease, autoimmune vasculitis, autoinflammatory syndromes, inflammatory bowel disease (Crohn’s and ulcerative colitis), psoriasis, multiple sclerosis and other rarer conditions.The Electronic Medicines Compendium (EMC) was searched for commonly prescribed immune-modulatory drugs used for the above indications. SmPC documents were manually searched for information on infection frequency, extracted from sections 4.4 and 4.8. Infection frequency was recorded as per convention in the SmPC: very common (≥1/10); common (≥1/100 to <1/10); uncommon (≥1/1,000 to <1/100); rare (≥1/10,000 to <1/1,000); very rare (<1/10,000) (1), for each drug. Information was further extracted on infection site (e.g. respiratory, skin etc), type (e.g. bacterial, viral etc) and individual pathogenic organisms.25% of included SmPCs were screened and extracted by a second reviewer. Disagreements were resolved with input from a third reviewer.Results:In total, 39 drugs were included, used across 20 indications: nine conventional synthetic disease-modifying anti-rheumatic drugs (csDMARDs), six targeted synthetic DMARDs (tsDMARDs; four Janus kinase [JAK] inhibitors, two sphingosine 1-phosphate receptor modulators) and 24 biologic DMARDs (17 cytokine-targeted; seven cell-targeted).Twelve sites of infection were recorded. Minimal or no site information was available for most csDMARDs and siponimod, certolizumab pegol and rituximab. The most common sites of infection are listed by drug group in Figure 1. Upper respiratory tract was the most common site, especially with bDMARDs. Lower respiratory, ear/nose/throat (including sinusitis) and urinary tract infections were moderately common, with clustering within drug groups. No drugs reported risk of cardiac infections; the eye, musculoskeletal, neurological, oral and reproductive sites were the least commonly-reported sites of infection.Infection data for 27 distinct pathogens were recorded, the majority viruses, especially with bDMARD use. Herpes simplex and zoster were the most frequently listed (mainly with bDMARDs and tsDMARDs), followed by influenza. Common non-viral causes of infection were candida and tinea species.Variable or absent reporting was noted for opportunistic infections (e.g. tuberculosis and fungi) and certain high-prevalence viruses e.g. Epstein-Barr.Conclusion:The SmPC literature reports differences in infection risk, by site and pathogen, between immune-modulatory drugs. The findings can be used to visualise differences and aid treatment decisions. However, some of the patterns we have shown lack face-validity to clinicians familiar with real-world safety data. The data fail to capture risk of rare infections, are likely skewed by trial selection criteria, varying number of trials per drug and quirks of individual study-reporting methodologies.The findings highlight the need for robust post-marketing pharmacovigilance studies.References:[1]A Guideline on Summary of Product Characteristics Module 1.3. 2008.Disclosure of Interests:None declared.
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Nandi S, Razzaghi M, Srivastava D, Dey M. Structural basis for allosteric regulation of pyruvate kinase M2 by phosphorylation and acetylation. J Biol Chem 2021; 295:17425-17440. [PMID: 33453989 DOI: 10.1074/jbc.ra120.015800] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/18/2020] [Indexed: 01/01/2023] Open
Abstract
Pyruvate kinase muscle isoform 2 (PKM2) is a key glycolytic enzyme and transcriptional coactivator and is critical for tumor metabolism. In cancer cells, native tetrameric PKM2 is phosphorylated or acetylated, which initiates a switch to a dimeric/monomeric form that translocates into the nucleus, causing oncogene transcription. However, it is not known how these post-translational modifications (PTMs) disrupt the oligomeric state of PKM2. We explored this question via crystallographic and biophysical analyses of PKM2 mutants containing residues that mimic phosphorylation and acetylation. We find that the PTMs elicit major structural reorganization of the fructose 1,6-bisphosphate (FBP), an allosteric activator, binding site, impacting the interaction with FBP and causing a disruption in oligomerization. To gain insight into how these modifications might cause unique outcomes in cancer cells, we examined the impact of increasing the intracellular pH (pHi) from ∼7.1 (in normal cells) to ∼7.5 (in cancer cells). Biochemical studies of WT PKM2 (wtPKM2) and the two mimetic variants demonstrated that the activity decreases as the pH is increased from 7.0 to 8.0, and wtPKM2 is optimally active and amenable to FBP-mediated allosteric regulation at pHi 7.5. However, the PTM mimetics exist as a mixture of tetramer and dimer, indicating that physiologically dimeric fraction is important and might be necessary for the modified PKM2 to translocate into the nucleus. Thus, our findings provide insight into how PTMs and pH regulate PKM2 and offer a broader understanding of its intricate allosteric regulation mechanism by phosphorylation or acetylation.
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Affiliation(s)
- Suparno Nandi
- Department of Chemistry, University of Iowa, Iowa City, Iowa, USA
| | | | | | - Mishtu Dey
- Department of Chemistry, University of Iowa, Iowa City, Iowa, USA.
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Wagner BK, Dey M. Phenotypic approaches to small-molecule discovery in chemical biology. Cell Chem Biol 2021; 28:245. [PMID: 33740431 DOI: 10.1016/j.chembiol.2021.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Dey M, Weerapana E. Chemical Tools in Biological Discovery. Cell Chem Biol 2020; 27:889-890. [PMID: 32822618 PMCID: PMC7439815 DOI: 10.1016/j.chembiol.2020.08.004] [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: 11/06/2022]
Affiliation(s)
- Mishtu Dey
- Senior Scientific Editor, Cell Chemical Biology.
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Dey M, Bukhari M. OP0294 DIFFERENTIAL INFLUENCE OF CO-MORBIDITIES ON SITE OF FRAGILITY FRACTURES. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:Fragility fractures (FF) can occur at various sites of the skeleton, and are associated with multiple risk factors [1]. The prevalence of FF markedly increases with age. As the longevity of the population increases, so will the incidence of FF, and that of associated co-morbidities and risk factors. There are few data on co-morbidities associated with fractures at each site.Objectives:Identify associations of co-morbidities with sites of FF, by applying cluster analysis.Methods:We reviewed 28868 patients presenting for BMD estimation at a district general hospital in North West England, 2004-2016. We identified patients who had sustained one or more FF at time of presentation. Site(s) of FF were recorded for each patient, including femur, forearm, humerus, pelvis, ribs, spine, tibia or fibula. The following co-morbidities or treatments were recorded: excess alcohol consumption (previous or current); bisphosphonates; coeliac disease; family history of FF; hormone replacement therapy; hyperparathyroidism; hyperthyroidism; inflammatory bowel disease; polymyalgia rheumatica; rheumatoid arthritis; smoking (previous or current); corticosteroids (previous or current). Cluster analysis was performed on fracture sites and co-morbidities, using Jaccard similarity coefficient, and plotted on a dendrogram. Results were divided into an optimal number of clusters, derived using the elbow and silhouette methods.Results:11003 of 28868 patients had sustained one or more FF at time of BMD estimation. Overall, 84.6% patients were female, mean age 67.5years, and median T-score -1.12 SD. Cluster analysis was performed for FF sites and co-morbidities, with Jaccard similarity coefficients calculated. 4 clusters were identified (Figure 1): FF of forearm (n=5054), tibia/fibula (n=2617), spine (n=2352), associated with family history of FF, smoking, corticosteroids, and bisphosphonate treatment; FF of pelvis (n=300) associated with hyperparathyroidism, PMR, coeliac disease, and HRT; FF of femur (n=1181) and humerus (n=1131) associated with IBD and RA; FF of ribs (n=1022) associated with alcohol and hyperthyroidism.Conclusion:Cluster analysis demonstrated 4 distinct subgroups of FF sites and associated co-morbidities. To our knowledge, this is the first study applying cluster analysis to evaluate co-morbidities associated with FF sites. Risk factors may influence trabecular more than cortical bone, accounting for the difference in clusters. Knowledge of risk factors associated with FF site subgroups will aid prophylaxis and management in at-risk patients.References:[1]Kanis JA. Diagnosis of osteoporosis and assessment of fracture risk. Lancet (London, England). 2002 Jun 1;359(9321):1929–36Disclosure of Interests:Mrinalini Dey: None declared, Marwan Bukhari Speakers bureau: Bristol-Myers Squib, UCB celltech, Roche/Chugai, Pfizer, Abbvie, Merck, Mennarini, Sanofi-aventis, Eli-Lilly, Janssen, Amgen and Novartis.
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Dey M, Bukhari M. OP0324 CLUSTERING OF FRAGILITY FRACTURES BY SITE IN PATIENTS REFERRED FOR BONE MINERAL DENSITY ESTIMATION: AN OBSERVATIONAL STUDY. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:Fragility fractures (FF) are those resulting from mechanical forces equivalent to a fall from standing height or less [1]. They most commonly occur in the spine (vertebrae), forearm, and femur, but also occur at other sites. Prevalence markedly increases with age, due to age-related and menopause-related bone loss. FF cause substantial pain and disability, and are associated with decreased life expectancy. While many studies have investigated risk factors associated with FF, there are few data on the association between FF sites in at-risk patients.Objectives:1. Establish the most common sites of FF in patients presenting for bone mineral density (BMD) estimation.2. Identify patterns of co-existing FF in the above cohort by applying cluster analysis.Methods:We retrospectively reviewed the clinical records of 28868 patients presenting for BMD estimation at a district general hospital in North West England, 2004-2016, identifying those who had sustained one or more FF. Site(s) of FF were recorded for each patient, categorised as: ankle, elbow, femur, forearm, humerus, pelvis, ribs, spine, tibia or fibula (recorded as “tibfib”). Cluster analysis was performed on fracture sites, using Jaccard similarity coefficient. Results were plotted on a dendrogram and divided into clusters, as per results derived from elbow and silhouette cluster methods.Results:Out of 28868 patients presenting for BMD estimation, 11003 were identified as having sustained one or more FF. 84.6% patients were female, with overall mean age 67.5years and median T-score -1.12 SD. The most common site of FF was the forearm (n=5045), most commonly co-existing with fractures of the tibia or fibula. Frequencies of the most common and co-existing FF sites are shown in Figure 1 (top). Cluster analysis identified 3 clusters: ankle and elbow; forearm, tibia/fibula, ribs, and spine; pelvis, femur, and humerus. The second half of Figure 1 displays the dendrogram of cluster analysis results, with Jaccard similarity measure.Conclusion:We applied cluster analysis to a large cohort of patients presenting for BMD estimation. Our results are in keeping with previous studies demonstrating the FF to most commonly occur in the forearm, and in those with osteopenia (T-score -2.5 < -1 SD) [2]. To our knowledge, this is the first study to apply cluster analysis to sites of FF. Results may be due to differences in cortical and trabecular bone structure, and have potential to aid prevention, monitoring, and management in at-risk patients.References:[1]National Institute for Health and Care Excellence (NICE). Osteoporosis: assessing the risk of fragility fracture - Clinical Guideline (CG146). 2012;(August):1–14.[2]Siris ES et al. Bone mineral density thresholds for pharmacological intervention to prevent fractures. Arch Intern Med. 2004 May 24;164(10):1108–12.Disclosure of Interests:Mrinalini Dey: None declared, Marwan Bukhari Speakers bureau: Bristol-Myers Squib, UCB celltech, Roche/Chugai, Pfizer, Abbvie, Merck, Mennarini, Sanofi-aventis, Eli-Lilly, Janssen, Amgen and Novartis.
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Dey M, Al-Attar M, Peruffo L, Wilson I, Zhao SS, Duffield S, Goodson N. AB0940 BIOMARKERS IN THE DIAGNOSIS OF ACUTE HOT JOINTS: AN EVALUATION OF RESEARCH INTEREST 1960-2018. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:The acute hot joint presentation is a common clinical emergency, often the result of crystal arthritis or trauma. However, all diagnoses can mimic septic arthritis, which should be excluded promptly due to the potential for rapid joint destruction and significant morbidity. The gold-standard test for septic arthritis is synovial fluid culture, which can take several days to perform. Meanwhile, patients are often admitted and given antimicrobials. Other specialties have made use of rapid biomarkers to exclude infection, for example, exclusion of empyema using pleural fluid pH and glucose [1]. Such biomarkers could reduce the need for lengthy hospital admissions and inappropriate antibiotic use in the acute hot joint presentation.Objectives:1.Evaluate research interest over time, on the use of diagnostic biomarkers in the acute hot joint presentation.2.Compare research interest in the use of diagnostic biomarkers in acute hot native versus acute hot prosthetic joints.Methods:We performed a review of the number of publications reporting the use and diagnostic accuracy of biomarkers to exclude infection in the acute hot joint presentations. The database,Scopus, was searched for English-language studies (1946-2018) using search terms relating to septic arthritis, crystal arthritis, and diagnostic markers derived from synovial fluid/aspirate. The number of papers published per year on prosthetic joints only was also calculated. Therefore, the following were recorded for each year 1946-2018: total number of studies; prosthetic joints only; native joints only. Values were plotted, with polynomial trend-lines and R2calculated.Results:Our search yielded 2279 relevant studies in total (561 on prosthetic joints), published 1946-2018. Only 1 study was identified for the year 1946; the next recorded publication was in 1960. Therefore, this single study was excluded as an outlier. Results are presented in Figure 1. The number of studies on diagnostic biomarkers for acute hot joints continued to increase after 1960. From 2016, the number of studies conducted in prosthetic joints outnumbered those done in native joints. Polynomial trend-lines applied to the results showed studies on native acute hot joints are predicted to decline, while those in prosthetic joints will continue to increase.Conclusion:Reasons for an increasing number of studies on prosthetic compared to native acute hot joints include a narrower differential diagnosis in prosthetic joints, i.e. septic vs aseptic. In contrast, native acute hot joints may be the result of various causes including crystal arthritis, inflammatory arthritis, and trauma. Having a narrower differential diagnosis may facilitate diagnostic research in prosthetic joint presentations. Furthermore, incidence of prosthetic joint infection is also greater than that of native joint infection [2]. Nonetheless, the incidence of native joint infection is increasing [3]. This, and the lack of methods by which to rapidly distinguish native joint septic arthritis from non-infective causes, indicates that more research is required in this area.References:[1]Heffner JE et al. Pleural fluid chemical analysis in parapneumonic effusions. A meta-analysis. Am J Respir Crit Care Med. 1995 Jun;151(6):1700–8.[2]Roerdink RL et al. The difference between native septic arthritis and prosthetic joint infections: A review of literature. J Orthop Surg (Hong Kong).[3]Rutherford AI et al. A population study of the reported incidence of native joint septic arthritis in the United Kingdom between 1998 and 2013. Rheumatol (United Kingdom). 2016;55(12):2176–80.Disclosure of Interests:None declared
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Nandi S, Dey M. Biochemical and structural insights into how amino acids regulate pyruvate kinase muscle isoform 2. J Biol Chem 2020; 295:5390-5403. [PMID: 32144209 PMCID: PMC7170521 DOI: 10.1074/jbc.ra120.013030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/03/2020] [Indexed: 12/12/2022] Open
Abstract
Pyruvate kinase muscle isoform 2 (PKM2) is a key glycolytic enzyme involved in ATP generation and critical for cancer metabolism. PKM2 is expressed in many human cancers and is regulated by complex mechanisms that promote tumor growth and proliferation. Therefore, it is considered an attractive therapeutic target for modulating tumor metabolism. Various stimuli allosterically regulate PKM2 by cycling it between highly active and less active states. Several small molecules activate PKM2 by binding to its intersubunit interface. Serine and cysteine serve as an activator and inhibitor of PKM2, respectively, by binding to its amino acid (AA)-binding pocket, which therefore represents a potential druggable site. Despite binding similarly to PKM2, how cysteine and serine differentially regulate this enzyme remains elusive. Using kinetic analyses, fluorescence binding, X-ray crystallography, and gel filtration experiments with asparagine, aspartate, and valine as PKM2 ligands, we examined whether the differences in the side-chain polarity of these AAs trigger distinct allosteric responses in PKM2. We found that Asn (polar) and Asp (charged) activate PKM2 and that Val (hydrophobic) inhibits it. The results also indicate that both Asn and Asp can restore the activity of Val-inhibited PKM2. AA-bound crystal structures of PKM2 displayed distinctive interactions within the binding pocket, causing unique allosteric effects in the enzyme. These structure-function analyses of AA-mediated PKM2 regulation shed light on the chemical requirements in the development of mechanism-based small-molecule modulators targeting the AA-binding pocket of PKM2 and provide broader insights into the regulatory mechanisms of complex allosteric enzymes.
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Affiliation(s)
- Suparno Nandi
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242
| | - Mishtu Dey
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242.
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Dey M, Wagner B. The Role of Chemical Biology in the Discovery and Understanding of Ferroptosis. Cell Chem Biol 2020; 27:363-364. [PMID: 32302581 PMCID: PMC7161471 DOI: 10.1016/j.chembiol.2020.03.017] [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: 12/05/2022]
Affiliation(s)
- Mishtu Dey
- Scientific Editor, Cell Chemical Biology.
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Wang J, Dey M, Soldati L, Weiss M, Gmel G, Mohler-Kuo M. Psychiatric disorders, suicidality, and personality among young men by sexual orientation. Eur Psychiatry 2020; 29:514-22. [DOI: 10.1016/j.eurpsy.2014.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 05/05/2014] [Accepted: 05/10/2014] [Indexed: 11/15/2022] Open
Abstract
AbstractPersonality and its potential role in mediating risk of psychiatric disorders and suicidality are assessed by sexual orientation, using data collected among young Swiss men (n = 5875) recruited while presenting for mandatory military conscription. Mental health outcomes were analyzed by sexual attraction using logistic regression, controlling for five-factor model personality traits and socio-demographics. Homo/bisexual men demonstrated the highest scores for neuroticism-anxiety but the lowest for sociability and sensation seeking, with no differences for aggression-hostility. Among homo/bisexual men, 10.2% fulfilled diagnostic criteria for major depression in the past 2 weeks, 10.8% for ADHD in the past 12 months, 13.8% for lifetime anti-social personality disorder (ASPD), and 6.0% attempted suicide in the past 12 months. Upon adjusting (AOR) for personality traits, their odds ratios (OR) for major depression (OR = 4.78, 95% CI 2.81–8.14; AOR = 1.46, 95% CI 0.80–2.65) and ADHD (OR = 2.17, 95% CI = 1.31–3.58; AOR = 1.00, 95% CI 0.58–1.75) lost statistical significance, and the odds ratio for suicide attempt was halved (OR = 5.10, 95% CI 2.57–10.1; AOR = 2.42, 95% CI 1.16–5.02). There are noteworthy differences in personality traits by sexual orientation, and much of the increased mental morbidity appears to be accounted for by such underlying differences, with important implications for etiology and treatment.
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Dey M, Paz Castro R, Haug S, Schaub MP. Quality of life of parents of mentally-ill children: a systematic review and meta-analysis. Epidemiol Psychiatr Sci 2019; 28:563-577. [PMID: 30078381 PMCID: PMC6999041 DOI: 10.1017/s2045796018000409] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/24/2018] [Accepted: 07/06/2018] [Indexed: 12/27/2022] Open
Abstract
AIMS To examine the quality of life (QOL) of parents of children with a specific mental disorder (any age). METHODS Relevant articles were searched using different databases. Articles were included that compared the QOL of parents with mentally-ill children to parents of healthy controls or norm values or provided the required data for this comparison. A meta-analysis was conducted to obtain an overall mean effect size estimate. Additional analyses were performed to assess publication bias and moderation. RESULTS Twenty-six out of 10 548 articles met the pre-defined inclusion criteria. Most of these studies focused on attention-deficit/hyperactivity disorder or autism spectrum disorder, used clinical samples that mainly included males and young children and studied the QOL of mothers. The meta-analysis revealed that parents of mentally-ill children are experiencing a clinically relevant reduction in their QOL relative to parents of healthy children and norm values (g = -0.66). CONCLUSIONS The compromised QOL of parents of mentally-ill children needs to be considered and addressed by health professionals who are in contact with them. The paper provides insights into existing research gaps and suggests improvements for subsequent work.
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Affiliation(s)
- M. Dey
- Swiss Research Institute for Public Health and Addiction, University of Zurich, Zurich, Switzerland
| | - R. Paz Castro
- Swiss Research Institute for Public Health and Addiction, University of Zurich, Zurich, Switzerland
| | - S. Haug
- Swiss Research Institute for Public Health and Addiction, University of Zurich, Zurich, Switzerland
| | - M. P. Schaub
- Swiss Research Institute for Public Health and Addiction, University of Zurich, Zurich, Switzerland
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Abstract
Cancer cells regulate key enzymes in the glycolytic pathway to control the glycolytic flux, which is necessary for their growth and proliferation. One of the enzymes is pyruvate kinase muscle isoform 2 (PKM2), which is allosterically regulated by various small molecules. Using detailed biochemical and kinetic studies, we demonstrate that cysteine inhibits wild-type (wt) PKM2 by shifting from an active tetramer to a mixture of a tetramer and a less active dimer/monomer equilibrium and that the inhibition is dependent on cysteine concentration. The cysteine-mediated PKM2 inhibition is reversed by fructose 1,6-bisphosphate, an allosteric activator of PKM2. Furthermore, kinetic studies using two dimeric PKM2 variants, S437Y PKM2 and G415R PKM2, show that the reversal is caused by the tetramerization of wtPKM2. The crystal structure of the wtPKM2-Cys complex was determined at 2.25 Å, which showed that cysteine is held to the amino acid binding site via its main chain groups, similar to that observed for phenylalanine, alanine, serine, and tryptophan. Notably, ligand binding studies using fluorescence and isothermal titration calorimetry show that the presence of phosphoenolpyruvate alters the binding affinities of amino acids for wtPKM2 and vice versa, thereby unravelling the existence of a functionally bidirectional coupling between the amino acid binding site and the active site of wtPKM2.
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Affiliation(s)
- Dhiraj Srivastava
- Department of Chemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
| | - Suparno Nandi
- Department of Chemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
| | - Mishtu Dey
- Department of Chemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
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Nandi S, Dey M. Biochemical and structural investigation of the dynamic regulation mechanism of pyruvate kinase muscle isoform 2 using amino acids. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s010876731909603x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Dey M, Marti L, Jorm A. The Swiss Youth Mental Health Literacy and Stigma Survey: Study methodology, survey questions/vignettes, and lessons learned. The European Journal of Psychiatry 2019. [DOI: 10.1016/j.ejpsy.2018.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Shahi M, Dey M, Chowdhury A. A study on possibility of high sensitivity C - reactive protein (hs-CRP) and circulating interluekin-6 (IL-6) as biomarker in breast cancer patients. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy426.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
Objectives Bone loss in systemic lupus erythematosus is multifactorial. Recent studies demonstrate corticosteroids, previous fractures and increasing age decrease bone mineral density. The effect of body mass index and fat mass are less well characterized. We sought to determine fracture risk factors in patients undergoing dual-energy X-ray absorptiometry scanning at a district hospital in 2004-2015. Methods Standard dual-energy X-ray absorptiometry parameters were recorded, plus rheumatoid arthritis diagnosis, smoking status, alcohol consumption, family history of fractures, history of secondary operation and corticosteroid use. Data were analyzed using Fisher's exact test for categorical data and logistic regression for continuous data. Results One hundred and fifty patients (141 women, nine men) with SLE were included; 52 (34.6%) had sustained at least one fracture. Fracture risk increased with increased age, body mass index, fat mass and average tissue thickness, and decreased lean mass (adjusted for steroid use), as well as with smoking and rheumatoid arthritis. Increased femoral and vertebral bone mineral density conversely decreased fracture risk. Conclusion Our study suggests increased age, body mass index, fat mass, smoking and/or rheumatoid arthritis increase fracture risk in SLE patients. To our knowledge, this is the first demonstration of a correlation between increased fat mass, adjusted for steroid use and fracture risk, in adults, potentially indicating a differential effect of fat on bone metabolism and lessening of lean body mass.
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Affiliation(s)
- M Dey
- University Hospitals of Morecambe Bay NHS Foundation Trust, Royal Lancaster Infirmary, Lancaster, UK
| | - M Bukhari
- University Hospitals of Morecambe Bay NHS Foundation Trust, Royal Lancaster Infirmary, Lancaster, UK
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Abstract
Pyruvate kinase muscle isoform 2 (PKM2) catalyzes the terminal step in glycolysis, transferring a phosphoryl group from phosphoenolpyruvate to ADP, to produce pyruvate and ATP. PKM2 activity is allosterically regulated by fructose 1,6-bisphosphate (FBP), an upstream glycolytic intermediate. FBP stabilizes the tetrameric form of the enzyme. In its absence, the PKM2 tetramers dissociate, yielding a dimer-monomer mixture having lower enzymatic activity. The S437Y variant of PKM2 is incapable of binding FBP. Consistent with that defect, we find that S437Y exists in a monomer-dimer equilibrium in solution, with a Kd of ∼20 μM. Interestingly, however, the protein crystallizes as a tetramer, providing insight into the structural basis for impaired FBP binding of S437Y.
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Affiliation(s)
- Dhiraj Srivastava
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Mortezaali Razzaghi
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Michael T Henzl
- Department of Biochemistry, University of Missouri-Columbia , Columbia, Missouri 65211, United States
| | - Mishtu Dey
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
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Schnicker NJ, Razzaghi M, Guha Thakurta S, Chakravarthy S, Dey M. Bacillus anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu. Biochemistry 2017; 56:5771-5785. [PMID: 28981257 DOI: 10.1021/acs.biochem.7b00601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prolyl hydroxylation is a very common post-translational modification and plays many roles in eukaryotes such as collagen stabilization, hypoxia sensing, and controlling protein transcription and translation. There is a growing body of evidence that suggests that prokaryotes contain prolyl 4-hydroxylases (P4Hs) homologous to the hypoxia-inducible factor (HIF) prolyl hydroxylase domain (PHD) enzymes that act on elongation factor Tu (EFTu) and are likely involved in the regulation of bacterial translation. Recent biochemical and structural studies with a PHD from Pseudomonas putida (PPHD) determined that it forms a complex with EFTu and hydroxylates a prolyl residue of EFTu. Moreover, while animal, plant, and viral P4Hs act on peptidyl proline, most prokaryotic P4Hs have been known to target free l-proline; the exceptions include PPHD and a P4H from Bacillus anthracis (BaP4H) that modifies collagen-like proline-rich peptides. Here we use biophysical and mass spectrometric methods to demonstrate that BaP4H recognizes full-length BaEFTu and a BaEFTu 9-mer peptide for site-specific proline hydroxylation. Using size-exclusion chromatography coupled small-angle X-ray scattering (SEC-SAXS) and binding studies, we determined that BaP4H forms a 1:1 heterodimeric complex with BaEFTu. The SEC-SAXS studies reveal dissociation of BaP4H dimeric subunits upon interaction with BaEFTu. While BaP4H is unusual within bacteria in that it is structurally and functionally similar to the animal PHDs and collagen P4Hs, respectively, this work provides further evidence of its promiscuous substrate recognition. It is possible that the enzyme might have evolved to hydroxylate a universally conserved protein in prokaryotes, similar to the PHDs, and implies a functional role in B. anthracis.
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Affiliation(s)
- Nicholas J Schnicker
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Mortezaali Razzaghi
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Sanjukta Guha Thakurta
- Department of Cell Biology, Harvard Medical School , 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Mishtu Dey
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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Schnicker NJ, De Silva SM, Todd JD, Dey M. Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter. Biochemistry 2017; 56:2873-2885. [DOI: 10.1021/acs.biochem.7b00099] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Nicholas J. Schnicker
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Saumya M. De Silva
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Jonathan D. Todd
- School
of Biological Sciences, University of East Anglia, Norwich Research
Park, Norwich NR4 7TJ, United Kingdom
| | - Mishtu Dey
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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Lal H, Yadav P, Dey M, Kumar N. Postrenal transplant metastatic colonic neoplasm: Posttransplant lymphoproliferative disorder or adenocarcinoma? Indian J Nephrol 2017; 27:218-221. [PMID: 28553044 PMCID: PMC5434690 DOI: 10.4103/0971-4065.200519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Transplant recipients are vulnerable to a horde of infections and neoplastic conditions due to immunosuppression. Posttransplant lymphoproliferative disorder (PTLD) is a condition unique to the transplant recipient occurring due to monoclonal lymphocytic proliferation. It may affect any organ system with reportedly highest incidence in the gastrointestinal tract. The incidence of adenocarcinoma of the colon, however, has not been shown to be uniformly higher in transplant recipients. We report here an unusual case of adenocarcinoma of the ascending colon presenting with liver, lymph node and skin metastasis in a transplant recipient, which simulated PTLD both clinically and radiologically. For any gastrointestinal lesion in transplant recipient, the possibility of carcinoma must be considered. However, a high index of suspicion for PTLD facilitates early diagnosis since the treatment of the two conditions is starkly different.
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Brummett AE, Dey M. New Mechanistic Insight from Substrate- and Product-Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase DddQ. Biochemistry 2016; 55:6162-6174. [PMID: 27755868 DOI: 10.1021/acs.biochem.6b00585] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The marine microbial catabolism of dimethylsulfoniopropionate (DMSP) by the lyase pathway liberates ∼300 million tons of dimethyl sulfide (DMS) per year, which plays a major role in the biogeochemical cycling of sulfur. Recent biochemical and structural studies of some DMSP lyases, including DddQ, reveal the importance of divalent transition metal ions in assisting DMSP cleavage. While DddQ is believed to be zinc-dependent primarily on the basis of structural studies, excess zinc inhibits the enzyme. We examine the importance of iron in regulating the DMSP β-elimination reaction catalyzed by DddQ as our as-isolated purple-colored enzyme possesses ∼0.5 Fe/subunit. The UV-visible spectrum exhibited a feature at 550 nm, consistent with a tyrosinate-Fe(III) ligand-to-metal charge transfer transition. Incubation of as-isolated DddQ with added iron increases the intensity of the 550 nm peak, whereas addition of dithionite causes a bleaching as Fe(III) is reduced. Both the Fe(III) oxidized and Fe(II) reduced species are active, with similar kcat values and 2-fold differences in their Km values for DMSP. The slow turnover of Fe(III)-bound DddQ allowed us to capture a substrate-bound form of the enzyme. Our DMSP-Fe(III)-DddQ structure reveals conformational changes associated with substrate binding and shows that DMSP is positioned optimally to bind iron and is in the proximity of Tyr 120 that acts as a Lewis base to initiate catalysis. The structures of Tris-, DMSP-, and acrylate-bound forms of Fe(III)-DddQ reported here illustrate various states of the enzyme along the reaction pathway. These results provide new insights into DMSP lyase catalysis and have broader significance for understanding the mechanism of oceanic DMS production.
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Affiliation(s)
- Adam E Brummett
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Mishtu Dey
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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Schnicker NJ, Dey M. Structural analysis of cofactor binding for a prolyl 4-hydroxylase from the pathogenic bacteriumBacillus anthracis. Acta Crystallogr D Struct Biol 2016; 72:675-81. [DOI: 10.1107/s2059798316004198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/11/2016] [Indexed: 11/11/2022]
Abstract
The prolyl 4-hydroxylases (P4Hs) are mononuclear nonheme iron enzymes that catalyze the formation of 4R-hydroxyproline from many different substrates, with various biological implications. P4H is a key player in collagen accumulation, which has implications in fibrotic disorders. The stabilization of collagen triple-helical structureviaprolyl hydroxylation is the rate-limiting step in collagen biosynthesis, and therefore P4H has been extensively investigated as a potential therapeutic target of fibrotic disease. Understanding how these enzymes recognize cofactors and substrates is important and will aid in the future design of inhibitors of P4H. In this article, X-ray crystal structures of a metallocofactor- and α-ketoglutarate (αKG)-bound form of P4H fromBacillus anthracis(BaP4H) are reported. Structures of BaP4H were solved at 1.63 and 2.35 Å resolution and contained a cadmium ion and αKG bound in the active site. The αKG–Cd–BaP4H ternary complex reveals conformational changes of conserved residues upon the binding of metal ion and αKG, resulting in a closed active-site configuration required for dioxygen, substrate binding and catalysis.
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Schnicker NJ, Dey M. Bacillus anthracis Prolyl 4-Hydroxylase Modifies Collagen-like Substrates in Asymmetric Patterns. J Biol Chem 2016; 291:13360-74. [PMID: 27129244 DOI: 10.1074/jbc.m116.725432] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 03/08/2016] [Indexed: 11/06/2022] Open
Abstract
Proline hydroxylation is the most prevalent post-translational modification in collagen. The resulting product trans-4-hydroxyproline (Hyp) is of critical importance for the stability and thus function of collagen, with defects leading to several diseases. Prolyl 4-hydroxylases (P4Hs) are mononuclear non-heme iron α-ketoglutarate (αKG)-dependent dioxygenases that catalyze Hyp formation. Although animal and plant P4Hs target peptidyl proline, prokaryotes have been known to use free l-proline as a precursor to form Hyp. The P4H from Bacillus anthracis (BaP4H) has been postulated to act on peptidyl proline in collagen peptides, making it unusual within the bacterial clade, but its true physiological substrate remains enigmatic. Here we use mass spectrometry, fluorescence binding, x-ray crystallography, and docking experiments to confirm that BaP4H recognizes and acts on peptidyl substrates but not free l-proline, using elements characteristic of an Fe(II)/αKG-dependent dioxygenases. We further show that BaP4H can hydroxylate unique peptidyl proline sites in collagen-derived peptides with asymmetric hydroxylation patterns. The cofactor-bound crystal structures of BaP4H reveal active site conformational changes that define open and closed forms and mimic "ready" and "product-released" states of the enzyme in the catalytic cycle. These results help to clarify the role of BaP4H as well as provide broader insights into human collagen P4H and proteins with poly-l-proline type II helices.
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Affiliation(s)
- Nicholas J Schnicker
- From the Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1727
| | - Mishtu Dey
- From the Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1727
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Brummett AE, Schnicker NJ, Crider A, Todd JD, Dey M. Biochemical, Kinetic, and Spectroscopic Characterization of Ruegeria pomeroyi DddW--A Mononuclear Iron-Dependent DMSP Lyase. PLoS One 2015; 10:e0127288. [PMID: 25993446 PMCID: PMC4437653 DOI: 10.1371/journal.pone.0127288] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/13/2015] [Indexed: 11/19/2022] Open
Abstract
The osmolyte dimethylsulfoniopropionate (DMSP) is a key nutrient in marine environments and its catabolism by bacteria through enzymes known as DMSP lyases generates dimethylsulfide (DMS), a gas of importance in climate regulation, the sulfur cycle, and signaling to higher organisms. Despite the environmental significance of DMSP lyases, little is known about how they function at the mechanistic level. In this study we biochemically characterize DddW, a DMSP lyase from the model roseobacter Ruegeria pomeroyi DSS-3. DddW is a 16.9 kDa enzyme that contains a C-terminal cupin domain and liberates acrylate, a proton, and DMS from the DMSP substrate. Our studies show that as-purified DddW is a metalloenzyme, like the DddQ and DddP DMSP lyases, but contains an iron cofactor. The metal cofactor is essential for DddW DMSP lyase activity since addition of the metal chelator EDTA abolishes its enzymatic activity, as do substitution mutations of key metal-binding residues in the cupin motif (His81, His83, Glu87, and His121). Measurements of metal binding affinity and catalytic activity indicate that Fe(II) is most likely the preferred catalytic metal ion with a nanomolar binding affinity. Stoichiometry studies suggest DddW requires one Fe(II) per monomer. Electronic absorption and electron paramagnetic resonance (EPR) studies show an interaction between NO and Fe(II)-DddW, with NO binding to the EPR silent Fe(II) site giving rise to an EPR active species (g = 4.29, 3.95, 2.00). The change in the rhombicity of the EPR signal is observed in the presence of DMSP, indicating that substrate binds to the iron site without displacing bound NO. This work provides insight into the mechanism of DMSP cleavage catalyzed by DddW.
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Affiliation(s)
- Adam E. Brummett
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Nicholas J. Schnicker
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Alexander Crider
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
| | - Mishtu Dey
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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Bewley KD, Dey M, Bjork RE, Mitra S, Chobot SE, Drennan CL, Elliott SJ. Rheostat re-wired: alternative hypotheses for the control of thioredoxin reduction potentials. PLoS One 2015; 10:e0122466. [PMID: 25874934 PMCID: PMC4395160 DOI: 10.1371/journal.pone.0122466] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 02/11/2015] [Indexed: 11/19/2022] Open
Abstract
Thioredoxins are small soluble proteins that contain a redox-active disulfide (CXXC). These disulfides are tuned to oxidizing or reducing potentials depending on the function of the thioredoxin within the cell. The mechanism by which the potential is tuned has been controversial, with two main hypotheses: first, that redox potential (Em) is specifically governed by a molecular 'rheostat'-the XX amino acids, which influence the Cys pKa values, and thereby, Em; and second, the overall thermodynamics of protein folding stability regulates the potential. Here, we use protein film voltammetry (PFV) to measure the pH dependence of the redox potentials of a series of wild-type and mutant archaeal Trxs, PFV and glutathionine-equilibrium to corroborate the measured potentials, the fluorescence probe BADAN to measure pKa values, guanidinium-based denaturation to measure protein unfolding, and X-ray crystallography to provide a structural basis for our functional analyses. We find that when these archaeal thioredoxins are probed directly using PFV, both the high and low potential thioredoxins display consistent 2H+:2e- coupling over a physiological pH range, in conflict with the conventional 'rheostat' model. Instead, folding measurements reveals an excellent correlation to reduction potentials, supporting the second hypothesis and revealing the molecular mechanism of reduction potential control in the ubiquitous Trx family.
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Affiliation(s)
- Kathryn D. Bewley
- Department of Chemistry, Boston University, Boston, Massachusetts, United States of America
| | - Mishtu Dey
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rebekah E. Bjork
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Sangha Mitra
- Department of Chemistry, Boston University, Boston, Massachusetts, United States of America
| | - Sarah E. Chobot
- Department of Chemistry, Boston University, Boston, Massachusetts, United States of America
| | - Catherine L. Drennan
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Sean J. Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts, United States of America
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Wang J, Dey M, Soldati L, Weiss M, Gmel G, Mohler-Kuo M. Erratum to “Psychiatric disorders, suicidality, and personality among young men by sexual orientation” [Eur. Psych. 29 (2014) 514–22]. Eur Psychiatry 2015. [DOI: 10.1016/j.eurpsy.2014.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Dey M, Chang A, Wainwright D, Ahmed A, Han Y, Lesniak M. IT-07 * COMPARATIVE EVALUATION OF pDCs AND mDCs FOR DENDRITIC CELL BASED VACCINE STRATEGY FOR MALIGNANT GLIOMA. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou258.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Auffinger B, Tobias A, Han Y, Lee G, Guo D, Dey M, Lesniak M, Ahmed A. SC-02 * CONVERSION OF DIFFERENTIATED CANCER CELLS INTO CANCER STEM-LIKE CELLS IN A GLIOBLASTOMA MODEL AFTER PRIMARY CHEMOTHERAPY. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou275.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Qiao J, Dey M, Chang A, Woongki K, Han Y, Zhang L, Lesniak M. IT-27 * ONCOLYTIC ADENOVIRUSES-MEDIATED IMMUNE RESPONSES IN SYNGENEIC MURINE GLIOMA MODEL. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou258.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Balyasnikova I, Dey M, Tobias A, Kanojia D, Lee G, Han Y, Zhang L, Ahmed A, Aboody K, Lesniak M. ET-05 * INTRANASAL DELIVERY OF NEURAL STEM CELLS LOADED WITH ONCOLYTIC ADENOVIRUS EXTENDS SURVIVAL OF MICE WITH INTRACRANIAL GLIOMA. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou255.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Auffinger B, Tobias AL, Han Y, Lee G, Guo D, Dey M, Lesniak MS, Ahmed AU. Conversion of differentiated cancer cells into cancer stem-like cells in a glioblastoma model after primary chemotherapy. Cell Death Differ 2014; 21:1119-31. [PMID: 24608791 DOI: 10.1038/cdd.2014.31] [Citation(s) in RCA: 244] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 02/03/2014] [Accepted: 02/03/2014] [Indexed: 12/28/2022] Open
Abstract
Glioblastoma multiforme patients have a poor prognosis due to therapeutic resistance and tumor relapse. It has been suggested that gliomas are driven by a rare subset of tumor cells known as glioma stem cells (GSCs). This hypothesis states that only a few GSCs are able to divide, differentiate, and initiate a new tumor. It has also been shown that this subpopulation is more resistant to conventional therapies than its differentiated counterpart. In order to understand glioma recurrence post therapy, we investigated the behavior of GSCs after primary chemotherapy. We first show that exposure of patient-derived as well as established glioma cell lines to therapeutic doses of temozolomide (TMZ), the most commonly used antiglioma chemotherapy, consistently increases the GSC pool over time both in vitro and in vivo. Secondly, lineage-tracing analysis of the expanded GSC pool suggests that such amplification is a result of a phenotypic shift in the non-GSC population to a GSC-like state in the presence of TMZ. The newly converted GSC population expresses markers associated with pluripotency and stemness, such as CD133, SOX2, Oct4, and Nestin. Furthermore, we show that intracranial implantation of the newly converted GSCs in nude mice results in a more efficient grafting and invasive phenotype. Taken together, these findings provide the first evidence that glioma cells exposed to chemotherapeutic agents are able to interconvert between non-GSCs and GSCs, thereby replenishing the original tumor population, leading to a more infiltrative phenotype and enhanced chemoresistance. This may represent a potential mechanism for therapeutic relapse.
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Affiliation(s)
- B Auffinger
- The Brain Tumor Center, The University of Chicago, Chicago, IL, USA
| | - A L Tobias
- The Brain Tumor Center, The University of Chicago, Chicago, IL, USA
| | - Y Han
- The Brain Tumor Center, The University of Chicago, Chicago, IL, USA
| | - G Lee
- The Brain Tumor Center, The University of Chicago, Chicago, IL, USA
| | - D Guo
- The Brain Tumor Center, The University of Chicago, Chicago, IL, USA
| | - M Dey
- The Brain Tumor Center, The University of Chicago, Chicago, IL, USA
| | - M S Lesniak
- 1] The Brain Tumor Center, The University of Chicago, Chicago, IL, USA [2] Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - A U Ahmed
- 1] The Brain Tumor Center, The University of Chicago, Chicago, IL, USA [2] Department of Surgery, The University of Chicago, Chicago, IL, USA
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Affiliation(s)
- M. Dey
- South Dakota State University, Brookings, SD, U.S.A
- Corresponding author. Health and Nutritional Sciences, Box 2203, South Dakota State University, Brookings, SD 57007, U.S.A.Tel: +1.605.688.4050; Fax: +1.605.688.5603
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Barish M, Weng L, D'Apuzzo M, Forman S, Brown C, Ben Horin I, Volovitz I, Ram Z, Chang A, Wainwright D, Dey M, Han Y, Lesniak M, Chow K, Yi J, Shaffer D, Gottschalk S, Clark A, Safaee M, Oh T, Ivan M, Kaur R, Sun M, Lu YJ, Ozawa T, James CD, Bloch O, Parsa A, Debinski W, Choi YA, Gibo DM, Dey M, Wainwright D, Chang A, Han Y, Lesniak M, Herold-Mende C, Mossemann J, Jungk C, Ahmadi R, Capper D, von Deimling A, Unterberg A, Beckhove P, Jiang H, Klein SR, Piya S, Vence L, Yung WKA, Sawaya R, Heimberger A, Conrad C, Lang F, Gomez-Manzano C, Fueyo J, Jung TY, Choi YD, Kim YH, Lee JJ, Kim HS, Kim JS, Kim SK, Jung S, Cho D, Kosaka A, Ohkuri T, Okada H, Erickson K, Malone C, Ha E, Soto H, Hickey M, Owens G, Liau L, Prins R, Minev B, Kruse C, Lee J, Dang X, Borboa A, Coimbra R, Baird A, Eliceiri B, Mathios D, Lim M, Ruzevick J, Nicholas S, Polanczyk M, Jackson C, Taube J, Burger P, Martin A, Xu H, Ochs K, Sahm F, Opitz CA, Lanz TV, Oezen I, Couraud PO, von Deimling A, Wick W, Platten M, Ohkuri T, Ghosh A, Kosaka A, Zhu J, Ikeura M, Watkins S, Sarkar S, Okada H, Pellegatta S, Pessina S, Cantini G, Kapetis D, Finocchiaro G, Avril T, Vauleon E, Hamlat A, Mosser J, Quillien V, Raychaudhuri B, Rayman P, Huang P, Grabowski M, Hamburdzumyan D, Finke J, Vogelbaum M, Renner D, Litterman A, Balgeman A, Jin F, Hanson L, Gamez J, Carlson B, Sarkaria J, Parney I, Ohlfest J, Pirko I, Pavelko K, Johnson A, Sims J, Grinshpun B, Feng Y, Amendolara B, Shen Y, Canoll P, Sims P, Bruce J, Lee SX, Wong E, Swanson K, Wainwright D, Chang A, Dey M, Balyasnikova I, Cheng Y, Han Y, Lesniak M, Wang F, Wei J, Xu S, Ling X, Yaghi N, Kong LY, Doucette T, Weinberg J, DeMonte F, Lang F, Prabhu S, Heimberger A, Wiencke J, Accomando W, Houseman EA, Nelson H, Wrensch M, Wiemels J, Zheng S, Hsuang G, Bracci P, Kelsey K. IMMUNOLOGY RESEARCH. Neuro Oncol 2013. [DOI: 10.1093/neuonc/not177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Campian J, Gladstone D, Ambady P, Ye X, King K, Borrello I, Petrik S, Golightly M, Holdhoff M, Grossman S, Bhardwaj R, Chakravadhanula M, Ozols V, Georges J, Carlson E, Hampton C, Decker W, Chiba Y, Hashimoto N, Kagawa N, Hirayama R, Tsuboi A, Oji Y, Oka Y, Sugiyama H, Yoshimine T, Choi B, Gedeon P, Herndon J, Sanchez-Perez L, Mitchell D, Bigner D, Sampson J, Choi YA, Pandya H, Gibo DM, Debinski W, Cloughesy TF, Liau LM, Chiocca EA, Jolly DJ, Robbins JM, Ostertag D, Ibanez CE, Gruber HE, Kasahara N, Vogelbaum MA, Kesari S, Mikkelsen T, Kalkanis S, Landolfi J, Bloomfield S, Foltz G, Pertschuk D, Everson R, Jin R, Safaee M, Lisiero D, Odesa S, Liau L, Prins R, Gholamin S, Mitra SS, Richard CE, Achrol A, Kahn SA, Volkmer AK, Volkmer JP, Willingham S, Kong D, Shin JJ, Monje-Deisseroth M, Cho YJ, Weissman I, Cheshier SH, Kanemura Y, Sumida M, Yoshioka E, Yamamoto A, Kanematsu D, Takada A, Nonaka M, Nakajima S, Goto S, Kamigaki T, Takahara M, Maekawa R, Shofuda T, Moriuchi S, Yamasaki M, Kebudi R, Cakir FB, Gorgun O, Agaoglu FY, Darendeliler E, Lin Y, Wang Y, Qiu X, Jiang T, Lin Y, Wang Y, Jiang T, Zhang G, Wang J, Okada H, Butterfield L, Hamilton R, Drappatz J, Engh J, Amankulor N, Lively M, Chan M, Salazar A, Potter D, Shaw E, Lieberman F, Pandya H, Choi Y, Park J, Phuphanich S, Wheeler C, Rudnick J, Hu J, Mazer M, Wang H, Nuno M, Guevarra A, Sanchez C, Fan X, Ji J, Chu R, Bender J, Hawkins E, Black K, Yu J, Reap E, Archer G, Sanchez-Perez L, Norberg P, Schmittling R, Nair S, Cui X, Snyder D, Chandramohan V, Choi B, Kuan CT, Mitchell D, Bigner D, Yan H, Sampson J, Reardon D, Li G, Recht L, Fink K, Nabors L, Tran D, Desjardins A, Chandramouli N, Duic JP, Groves M, Clarke A, Hawthorne T, Green J, Yellin M, Sampson J, Rigakos G, Spyri O, Nomikos P, Stavridi F, Grossi I, Theodorakopoulou I, Assi A, Kouvatseas G, Papadopoulou E, Nasioulas G, Labropoulos S, Razis E, Rudnick J, Ravi A, Sanchez C, Tang DN, Hu J, Yu J, Sharma P, Black K, Sengupta S, Sampath P, Soto H, Erickson K, Malone C, Hickey M, Ha E, Young E, Ellingson B, Prins R, Liau L, Kruse C, Sul J, Hilf N, Kutscher S, Schoor O, Lindner J, Reinhardt C, Kreisl T, Iwamoto F, Fine H, Singh-Jasuja H, Teijeira L, Gil-Arnaiz I, Hernandez-Marin B, Martinez-Aguillo M, Sanchez SDLC, Viudez A, Hernandez-Garcia I, Lecumberri MJ, Grandez R, de Lascoiti AF, Garcia RV, Thomas A, Fisher J, Baron U, Olek S, Rhodes H, Gui J, Hampton T, Tafe L, Tsongalis G, Lefferts J, Wishart H, Kleen J, Miller M, Ernstoff M, Fadul C, Vlahovic G, Desjardins A, Peters K, Ranjan T, Herndon J, Friedman A, Friedman H, Bigner D, Archer G, Lally-Goss D, Sampson J, Wainwright D, Dey M, Chang A, Cheng Y, Han Y, Lesniak M, Weller M, Kaulich K, Hentschel B, Felsberg J, Gramatzki D, Pietsch T, Simon M, Westphal M, Schackert G, Tonn JC, Loeffler M, Reifenberger G, Yu J, Rudnick J, Hu J, Phuphanich S, Mazer M, Wang H, Xu M, Nuno M, Patil C, Chu R, Black K, Wheeler C. IMMUNOTHERAPY/BIOLOGICAL THERAPIES. Neuro Oncol 2013; 15:iii68-iii74. [PMCID: PMC3823893 DOI: 10.1093/neuonc/not178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023] Open
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Maheshwari R, Sukul RR, Gupta Y, Gupta M, Phougat A, Dey M, Jain R, Srivastava G, Bhardwaj U, Dikshit S. Accommodation: its relation to refractive errors, amblyopia and biometric parameters. Nepal J Ophthalmol 2011; 3:146-50. [PMID: 21876588 DOI: 10.3126/nepjoph.v3i2.5267] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
AIM To study accommodation in relation to different refractive errors, amblyopia and to measure the anatomical changes in the accommodating eye MATERIALS AND METHODS We studied the amplitude of accommodation (AA) in 150 patients in the age group 11 ± 30 years which included emmetropes, myopes, hypermetropes and hypermetropic amblyopes using the Royal Air Force (RAF) rule. The anterior chamber depth (ACD), axial length (AxL) and lens thickness (LT) changes during accommodation were measured using an A-scan. Myopes and hypermetropes were further divided based on the amount of refractive error : less than 2D, 2 -4D and greater than 4D. RESULTS Corrected low myopes had the highest accommodation amplitude (p less than 0.05) followed by emmetropes. Corrected hypermetropes were found to have the lowest amplitude of accommodation (p less than 0.05). The amblyopic eye had a significantly low AA compared to the non-amblyopic eye (p less than 0.05). ACD decreased (p less than 0.05) and LT increased (p less than 0.05) during accommodation. The AxL increase was maximum in myopes (p less than 0.05) followed by hypermetropes but the change was not significant in hypermetropes (p greater than 0.05). CONCLUSION The amblyopic eye has low amplitudes of accommodation proving the benefit of near adds in amblyopic patients. Prolonged near work might induce myopia in susceptible eyes by increasing the axial length.
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Affiliation(s)
- R Maheshwari
- Department of Physiology, Aligarh Muslim University, Aligarh, India
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Abstract
AIM To study the various ocular anatomical and physiological parameters in presbyopia. MATERIALS AND METHODS We studied the various ocular anatomical and physiological parameters like corneal curvature (keratometry readings: K1 and K2), central corneal thickness (CCT), anterior chamber depth (ACD), lens thickness (LT) and axial length (AL) in 100 presbyopic patients between 35 - 55 years of age. The patients were divided into two age groups: I (35 ± 44 years) and II (45-55 yrs). ACD, AL and LT were measured using an Ascan. CCT was measured with ultrasonic pachymetry. RESULTS The CCT decreased (BE), LT increased and ACD decreased (RE) significantly with increasing age (p less than 0.05). There was no significant difference in males and females. Nearly 3/4th of the total increase in lens thickness was responsible for the decrease in the anterior chamber depth and the rest, 1/4th , goes posteriorly. Corneal curvature and AL showed no significant change with age. CONCLUSIONS The mean of CCT decreased significantly with advancing age. As age increased, the mean value of lens thickness increased and anterior chamber depth decreased. Nearly 3/4th of total increase in LT was anteriorly, decreasing the ACD. Corneal curvature and AL has no relation with age.
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Affiliation(s)
- M Gupta
- Department of Physiology, Aligarh Muslim University, Aligarh, India.
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Yun D, Dey M, Higgins LJ, Yan F, Liu HW, Drennan CL. Structural basis of regiospecificity of a mononuclear iron enzyme in antibiotic fosfomycin biosynthesis. J Am Chem Soc 2011; 133:11262-9. [PMID: 21682308 PMCID: PMC3140168 DOI: 10.1021/ja2025728] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroxypropylphosphonic acid epoxidase (HppE) is an unusual mononuclear iron enzyme that uses dioxygen to catalyze the oxidative epoxidation of (S)-2-hydroxypropylphosphonic acid (S-HPP) in the biosynthesis of the antibiotic fosfomycin. Additionally, the enzyme converts the R-enantiomer of the substrate (R-HPP) to 2-oxo-propylphosphonic acid. To probe the mechanism of HppE regiospecificity, we determined three X-ray structures: R-HPP with inert cobalt-containing enzyme (Co(II)-HppE) at 2.1 Å resolution; R-HPP with active iron-containing enzyme (Fe(II)-HppE) at 3.0 Å resolution; and S-HPP-Fe(II)-HppE in complex with dioxygen mimic NO at 2.9 Å resolution. These structures, along with previously determined structures of S-HPP-HppE, identify the dioxygen binding site on iron and elegantly illustrate how HppE is able to recognize both substrate enantiomers to catalyze two completely distinct reactions.
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Affiliation(s)
- Danny Yun
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Cedervall PE, Dey M, Li X, Sarangi R, Hedman B, Ragsdale SW, Wilmot CM. Structural analysis of a Ni-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis. J Am Chem Soc 2011; 133:5626-8. [PMID: 21438550 DOI: 10.1021/ja110492p] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present the 1.2 Å resolution X-ray crystal structure of a Ni-methyl species that is a proposed catalytic intermediate in methyl-coenzyme M reductase (MCR), the enzyme that catalyzes the biological formation of methane. The methyl group is situated 2.1 Å proximal of the Ni atom of the MCR coenzyme F(430). A rearrangement of the substrate channel has been posited to bring together substrate species, but Ni(III)-methyl formation alone does not lead to any observable structural changes in the channel.
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Affiliation(s)
- Peder E Cedervall
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Dey M, Sengupta R, Bunkheila A, Roberts D, Bonduelle M. Selective arterial embolisation: life-saving intervention in the management of retroperitoneal haematoma in obstetrics. J OBSTET GYNAECOL 2011; 31:266-7. [PMID: 21417659 DOI: 10.3109/01443615.2010.547953] [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: 11/13/2022]
Affiliation(s)
- M Dey
- Department of Obstetrics and Gynaecology, Singleton Hospital, Sketty Lane, Swansea SA2 8QA, UK.
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Dey M, Li X, Kunz RC, Ragsdale SW. Detection of Organometallic and Radical Intermediates in the Catalytic Mechanism of Methyl-Coenzyme M Reductase Using the Natural Substrate Methyl-Coenzyme M and a Coenzyme B Substrate Analogue. Biochemistry 2010; 49:10902-11. [DOI: 10.1021/bi101562m] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mishtu Dey
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Xianghui Li
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ryan C. Kunz
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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