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Leclercq N, Marshall L, Weekers T, Basu P, Benda D, Bevk D, Bhattacharya R, Bogusch P, Bontšutšnaja A, Bortolotti L, Cabirol N, Calderón-Uraga E, Carvalho R, Castro S, Chatterjee S, De La Cruz Alquicira M, de Miranda JR, Dirilgen T, Dorchin A, Dorji K, Drepper B, Flaminio S, Gailis J, Galloni M, Gaspar H, Gikungu MW, Hatteland BA, Hinojosa-Diaz I, Hostinská L, Howlett BG, Hung KLJ, Hutchinson L, Jesus RO, Karklina N, Khan MS, Loureiro J, Men X, Molenberg JM, Mudri-Stojnić S, Nikolic P, Normandin E, Osterman J, Ouyang F, Oygarden AS, Ozolina-Pole L, Ozols N, Parra Saldivar A, Paxton RJ, Pitts-Singer T, Poveda K, Prendergast K, Quaranta M, Read SFJ, Reinhardt S, Rojas-Oropeza M, Ruiz C, Rundlöf M, Sade A, Sandberg C, Sgolastra F, Shah SF, Shebl MA, Soon V, Stanley DA, Straka J, Theodorou P, Tobajas E, Vaca-Uribe JL, Vera A, Villagra CA, Williams MK, Wolowski M, Wood TJ, Yan Z, Zhang Q, Vereecken NJ. Global taxonomic, functional, and phylogenetic diversity of bees in apple orchards. Sci Total Environ 2023; 901:165933. [PMID: 37536603 DOI: 10.1016/j.scitotenv.2023.165933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 07/27/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
An essential prerequisite to safeguard pollinator species is characterisation of the multifaceted diversity of crop pollinators and identification of the drivers of pollinator community changes across biogeographical gradients. The extent to which intensive agriculture is associated with the homogenisation of biological communities at large spatial scales remains poorly understood. In this study, we investigated diversity drivers for 644 bee species/morphospecies in 177 commercial apple orchards across 33 countries and four global biogeographical biomes. Our findings reveal significant taxonomic dissimilarity among biogeographical zones. Interestingly, despite this dissimilarity, species from different zones share similar higher-level phylogenetic groups and similar ecological and behavioural traits (i.e. functional traits), likely due to habitat filtering caused by perennial monoculture systems managed intensively for crop production. Honey bee species dominated orchard communities, while other managed/manageable and wild species were collected in lower numbers. Moreover, the presence of herbaceous, uncultivated open areas and organic management practices were associated with increased wild bee diversity. Overall, our study sheds light on the importance of large-scale analyses contributing to the emerging fields of functional and phylogenetic diversity, which can be related to ecosystem function to promote biodiversity as a key asset in agroecosystems in the face of global change pressures.
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Affiliation(s)
- N Leclercq
- Agroecology Lab, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/02, B-1050 Brussels, Belgium.
| | - L Marshall
- Agroecology Lab, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/02, B-1050 Brussels, Belgium; Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, Netherlands
| | - T Weekers
- Agroecology Lab, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/02, B-1050 Brussels, Belgium
| | - P Basu
- Centre for Pollination Studies, University of Calcutta, Kolkata, India
| | - D Benda
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic; Department of Entomology, National Museum, Prague, Czech Republic
| | - D Bevk
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
| | - R Bhattacharya
- Centre for Pollination Studies, University of Calcutta, Kolkata, India
| | - P Bogusch
- Department of Biology, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - A Bontšutšnaja
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - L Bortolotti
- CREA Research Centre for Agriculture and Environment, Bologna, Italy
| | - N Cabirol
- Department of Ecology and Natural Resources, Faculty of Science, UNAM, México City, Mexico
| | - E Calderón-Uraga
- Department of Ecology and Natural Resources, Faculty of Science, UNAM, México City, Mexico
| | - R Carvalho
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - S Castro
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - S Chatterjee
- Centre for Pollination Studies, University of Calcutta, Kolkata, India
| | - M De La Cruz Alquicira
- Department of Ecology and Natural Resources, Faculty of Science, UNAM, México City, Mexico
| | - J R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, 750 05, Sweden
| | - T Dirilgen
- School of Agriculture and Food Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - A Dorchin
- Laboratory of Zoology, Université de Mons, Mons, Belgium; The Steinhardt Museum of Natural History, Tel Aviv University, 69978 Tel Aviv, Israel; Department of Entomology, Royal Museum for Central Africa, Tervuren, Belgium
| | - K Dorji
- College of Natural Resources, Royal University of Bhutan, Punakha, Bhutan
| | - B Drepper
- Division of Forest, Nature and Landscape, University of Leuven, Leuven, Belgium
| | - S Flaminio
- CREA Research Centre for Agriculture and Environment, Bologna, Italy; Laboratory of Zoology, Université de Mons, Mons, Belgium
| | - J Gailis
- Institute for Plant Protection Research Agrihorts, Latvia University of Life Sciences and Technologies, Jelgava, Latvia
| | - M Galloni
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - H Gaspar
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - M W Gikungu
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - B A Hatteland
- Division for Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Aas, Norway; Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - I Hinojosa-Diaz
- Department of Zoology, Institute of Biology, UNAM, México City, Mexico
| | - L Hostinská
- Department of Biology, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - B G Howlett
- The New Zealand Institute for Plant & Food Research Limited, Lincoln, Canterbury, New Zealand
| | - K-L J Hung
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; Oklahoma Biological Survey, University of Oklahoma, Norman, OK 73019, USA
| | - L Hutchinson
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - R O Jesus
- Graduate Program in Ecology, State University of Campinas, Campinas, São Paulo, Brazil
| | - N Karklina
- Institute for Plant Protection Research Agrihorts, Latvia University of Life Sciences and Technologies, Jelgava, Latvia
| | - M S Khan
- Department of Entomology, University of Agriculture, Peshawar, Pakistan
| | - J Loureiro
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - X Men
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Plant Virology,Jinan 250100, China
| | - J-M Molenberg
- Agroecology Lab, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/02, B-1050 Brussels, Belgium
| | - S Mudri-Stojnić
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - P Nikolic
- Faculty of Agriculture, University of Banja Luka, Banja Luka, Bosnia and Herzegovina
| | - E Normandin
- Centre sur la biodiversité, Département des sciences biologiques, Université de Montréal, QC, Québec H1X 2B2, Canada
| | - J Osterman
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany; Nature Conservation and Landscape Ecology, University of Freiburg, Tennenbacherstrasse 4, 79106, Freiburg im Breisgau, Germany
| | - F Ouyang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - A S Oygarden
- Department of Natural Sciences and Environmental Health, University of South-Eastern Norway, Bø, Norway
| | - L Ozolina-Pole
- Institute for Plant Protection Research Agrihorts, Latvia University of Life Sciences and Technologies, Jelgava, Latvia
| | - N Ozols
- Institute for Plant Protection Research Agrihorts, Latvia University of Life Sciences and Technologies, Jelgava, Latvia
| | - A Parra Saldivar
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación (UMCE), Santiago, Chile
| | - R J Paxton
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
| | - T Pitts-Singer
- USDA Agricultural Research Service, Pollinating Insects Research Unit, Logan, UT 84322, USA
| | - K Poveda
- Department of Entomology, Cornell University, 4126 Comstock Hall, Ithaca, NY 14853, USA
| | - K Prendergast
- Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - M Quaranta
- CREA Research Centre for Agriculture and Environment, Bologna, Italy
| | - S F J Read
- The New Zealand Institute for Plant & Food Research Limited, Lincoln, Canterbury, New Zealand
| | - S Reinhardt
- Department of Natural Sciences and Environmental Health, University of South-Eastern Norway, Bø, Norway
| | - M Rojas-Oropeza
- Department of Ecology and Natural Resources, Faculty of Science, UNAM, México City, Mexico
| | - C Ruiz
- Departamento Biología Animal, Edafología y Geología, Facultad de Ciencias, Universidad de La Laguna, La Laguna, 38206, Tenerife, Spain
| | - M Rundlöf
- Department of Biology, Lund University, Lund, Sweden
| | - A Sade
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905 Haifa, Israel
| | - C Sandberg
- Department of Biology, Lund University, Lund, Sweden; Calluna AB, Husargatan 3, Malmö, 211 28, Sweden
| | - F Sgolastra
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - S F Shah
- Department of Entomology, University of Agriculture, Peshawar, Pakistan
| | - M A Shebl
- Department of Plant Protection, Faculty of Agriculture, Suez Canal University, Ismailia 41522, Egypt
| | - V Soon
- Natural History Museum and Botanical Garden, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - D A Stanley
- School of Agriculture and Food Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - J Straka
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - P Theodorou
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
| | - E Tobajas
- Department of Biology, Lund University, Lund, Sweden; Department of Animal Biology, University of Salamanca, Campus Miguel de Unamuno, Salamanca, 37007, Spain
| | - J L Vaca-Uribe
- Laboratorio de Investigaciones en Abejas LABUN, Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá,111321, Colombia
| | - A Vera
- Departamento de Biología, Universidad Metropolitana de Ciencias de la Educación (UMCE), Santiago, Chile
| | - C A Villagra
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación (UMCE), Santiago, Chile
| | - M-K Williams
- Department of Biology, Utah State University, Logan, UT 84322, USA
| | - M Wolowski
- Institute of Natural Sciences, Federal University of Alfenas, Alfenas, Minas Gerais, Brazil
| | - T J Wood
- Laboratory of Zoology, Université de Mons, Mons, Belgium
| | - Z Yan
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Q Zhang
- Beijing Biodiversity Conservation Research Center/Beijing Milu Ecological Research Center, Beijing 100076, China
| | - N J Vereecken
- Agroecology Lab, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/02, B-1050 Brussels, Belgium
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Yadav R, Parikh S, Panchal H, Patel A, Garg A, Shah K, Basu P, Patel V, Ganta S, Ravichandran S, Banerjee D. 34P Efficacy and toxicity analysis of imatinib in newly diagnosed patients of chronic myeloid leukaemia: 18-years’ experience at a single large-volume centre. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.01.043] [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: 11/26/2022] Open
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Chargari C, Arbyn M, Leary A, Abu-Rustum NR, Basu P, Bray F, Chopra S, Nout R, Tanderup K, Viswanathan AN, Zacharopoulou C, Soria JC, Deutsch E, Gouy S, Morice P. Increasing global accessibility to high-level treatments for cervical cancers. Gynecol Oncol 2022; 164:231-241. [PMID: 34716024 PMCID: PMC9496636 DOI: 10.1016/j.ygyno.2021.10.073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/04/2021] [Accepted: 10/11/2021] [Indexed: 01/03/2023]
Abstract
Human papillomaviruses (HPV)-related gynecological cancers are a major health care issue, and a leading cause of cancer death in low- and middle-income countries (LMIC). In 2020, the World Health Organization launched a program aimed at cervical cancer elimination, by screening and vaccination strategies. Offering the best possible care to women diagnosed with invasive cancer is a complementary objective. Treatment of cervical cancer as per modern standards is complex and multimodal, mainly relying on surgery, external-beam radiotherapy (+/-chemotherapy) and brachytherapy. In parallel with the pivotal role of multidisciplinary discussion, international societies provide guidance to define the most effective and least toxic anti-cancer strategy, homogenize treatment protocols and provide benchmark quality indicators as a basis for accreditation processes. The challenge is to offer the appropriate diagnostic workup and treatment upfront and to avoid non- evidence-based treatment that consumes resources, impairs quality of life (QoL), and compromises oncological outcome. Various strategies may be applied for improving treatment quality: development of surgical mentorship, companion-training programs and international cooperation. The lack of radiotherapy/brachytherapy facilities is a major concern in LMIC. Reinforcing international support in terms of education, training, research and development and technical cooperation with national projects is required to increase access to minimum requirements but also introduce modern techniques, upgrade radiotherapy/brachytherapy services, and expand access to modern systemic treatments. In countries with robust economies, compliance to standards should also be increased. Integrative cancer care and multidisciplinary approaches are needed to tackle the dual challenge of increasing cure rates while minimizing QoL impairment. Appropriate dimensioning of the resources to avoid harmful treatment delays and access to expert referral centers is also a priority.
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Affiliation(s)
- C Chargari
- Radiation Oncology, Gustave Roussy Cancer Campus, Villejuif, France; Inserm U-1030, Université Paris-Saclay, Le Kremlin-Bicêtre, France.
| | - M Arbyn
- Unit Cancer Epidemiology - Belgian Cancer Centre, Brussels, Belgium
| | - A Leary
- Medical Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - N R Abu-Rustum
- Surgical Oncology, Memorial Sloan Kettering Cancer Center, New York, United States; European Society of Gynecological Oncology, Geneva, Switzerland
| | - P Basu
- Early Detection, Prevention & Infection Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - F Bray
- Cancer Surveillance Branch, International Agency for Research on Cancer, UK
| | - S Chopra
- Radiation Oncology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Homi Bhabha National Institute, Maharashtra, India
| | - R Nout
- Radiotherapy, Erasmus MC Cancer Institute, University Medical Center Rotterdam, the Netherlands
| | - K Tanderup
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - A N Viswanathan
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins Medicine, Baltimore, MD, United States
| | - C Zacharopoulou
- European Parliament, Committee on the Environment, Public Health and Food Safety, France
| | - J C Soria
- Governance, Gustave Roussy Cancer Campus, Villejuif, France; Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - E Deutsch
- Radiation Oncology, Gustave Roussy Cancer Campus, Villejuif, France; Inserm U-1030, Université Paris-Saclay, Le Kremlin-Bicêtre, France; Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - S Gouy
- Inserm U-1030, Université Paris-Saclay, Le Kremlin-Bicêtre, France; Université Paris-Saclay, Le Kremlin-Bicêtre, France; Surgical Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - P Morice
- Inserm U-1030, Université Paris-Saclay, Le Kremlin-Bicêtre, France; European Society of Gynecological Oncology, Geneva, Switzerland; Université Paris-Saclay, Le Kremlin-Bicêtre, France; Surgical Oncology, Gustave Roussy Cancer Campus, Villejuif, France
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Ortmann O, Torode J, Schmiegel W, Thomssen C, Hakama M, Basu P, Ringborg U, Helbig U. Correction to: Knowledge transfer as a tool towards improvement of cancer care in low- and middle-income countries. 6th European Roundtable Meeting (ERTM), June 14th, 2019, Berlin, Germany. J Cancer Res Clin Oncol 2021; 147:3773. [PMID: 34213663 PMCID: PMC8557141 DOI: 10.1007/s00432-021-03709-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- O Ortmann
- German Cancer Society, Berlin, Germany.
- Department of Gynecology and Obstetrics, University Medical Center Regensburg, Landshuter Straße 65, 93053, Regensburg, Germany.
| | - J Torode
- Union for International Cancer Control (UICC), Geneva, Switzerland
| | - W Schmiegel
- University Clinic at the University Hospital Knappschaftskrankenhaus Bochum, Bochum, Germany
| | - C Thomssen
- University Clinic and Polyclinic for Gynaecology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - M Hakama
- The Finnish Cancer Registry, Helsinki, Finland
| | - P Basu
- International Agency for Research On Cancer, World Health Organisation, Lyon, France
| | - U Ringborg
- EUROCAN Platform, Cancer Center Karolinska, Stockholm, Sweden
| | - U Helbig
- German Cancer Society, Berlin, Germany
- Deutsche Krebshilfe, Berlin, Germany
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Chatterjee A, Basu A, Das K, Singh P, Mondal D, Bhattacharya B, Roychoudhury S, Majumder PP, Chowdhury A, Basu P. Hepatic transcriptome signature correlated with HOMA-IR explains early nonalcoholic fatty liver disease pathogenesis. Ann Hepatol 2021; 19:472-481. [PMID: 32682086 DOI: 10.1016/j.aohep.2020.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 02/04/2023]
Abstract
INTRODUCTION AND OBJECTIVES Non-alcoholic fatty liver disease (NAFLD) is multistage with heterogeneous outcomes. We studied the influence of insulin resistance (IR) on the hepatic transcriptome of early NAFLD stages, to understand disease development. MATERIALS AND METHODS In this cross-sectional study, possible clinicopathological risk factors were compared between mild-NAFL (N = 72) and non-alcoholic steatohepatitis (NASH; N = 51) patients. Liver tissue-transcriptome difference was studied between a subset of 25 mild-NAFL and 20 NASH biopsies and validated on another subset of 12 mild-NAFL and 13 NASH biopsies, using RT-PCR. The relationship between IR driven gene expression changes with fibrosis in NASH was investigated. RESULTS Significantly higher weight (p = 0.005) and elevated levels of HbA1c (p = 0.009), FBG (p = 0.03) and HOMA-IR (p = 0.009) were found in NASH patients. Five differentially expressed genes (DEGs, fold change > 1.5) were identified in NASH-FABP4, FABP5L2, CD24, PRAP1, and SPP1. The DEGs were positively associated with disease severity and HOMA-IR, and were found to be efficient classifiers of mild-NAFL and NASH. Additional 1218 genes identified related to IR (IrCGs), which can classify NASH-with-fibrosis patients separately from mild-NAFL and NASH patients. IrCGs can promote intra-hepatic fat accumulation, dysregulation of the lipid metabolism, lipotoxicity, and activation of cell survival pathways including activation of cell proliferation and differentiation pathways. CONCLUSIONS Hepatic expression of genes associated with insulin resistance may drive NAFLD development and progression.
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Affiliation(s)
- Ankita Chatterjee
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Kausik Das
- Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | - Pankaj Singh
- Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | - Dipankar Mondal
- Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | | | | | - Partha P Majumder
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Abhijit Chowdhury
- Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | - Priyadarshi Basu
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India.
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Basu P, Das A, Mandal P, Bandyopadhyay A. Contribution of plasma protein PGLYRP2 in the inflammatory pathway in atherosclerosis. Atherosclerosis 2021. [DOI: 10.1016/j.atherosclerosis.2021.06.246] [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: 11/25/2022]
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Chatterjee A, Basu A, Das K, Chowdhury A, Basu P. Exome-wide scan identifies significant association of rs4788084 in IL27 promoter with increase in hepatic fat content among Indians. Gene 2021; 775:145431. [PMID: 33444683 DOI: 10.1016/j.gene.2021.145431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/23/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is a global epidemic that often progresses to liver cirrhosis and hepatocellular carcinoma. In contrast to most world populations where NAFLD is mostly prevalent among obese, NAFLD among Indians and generally among South and South-East Asians is unique and highly prevalent among individuals who are lean. Genetics of NAFLD in Indian populations is understudied. In this study, we have used an exome-wide approach to identify genetic determinants of hepatic fat content (HFC) in India. METHODS HFC was measured in 244 participants using Proton magnetic resonance spectroscopy (H1-MRS). Quantitative trait loci (QTL) mapping was done exome-wide, to identify SNPs associated with HFC. The effects of the interaction between adiposity and QTLs on HFC were studied using a regression model. Association of the significant loci with disease severity was studied in 146 NAFLD patients among 244 participants, who underwent liver biopsy. RESULTS Our study identified 4 significantly associated SNPs (rs738409 and rs2281135 (PNPLA3), rs3761472 (SAMM50), rs17513722 (FAM161A) and rs4788084), with HFC after adjusting for the effects of covariates (p-value < 0.0005). rs738409, rs2281135 (PNPLA3), and rs3761472 (SAMM50) were associated with hepatocyte ballooning, lobular and portal inflammation and non-alcoholic steatohepatitis (NASH) (p-value < 0.05). rs4788048 is an eQTL for IL27 and SULT1A2 genes, both of which are highly expressed in healthy livers and are likely to be involved in NAFLD pathogenesis. CONCLUSIONS Our study identified the novel association of rs4788084 with HFC, which regulates the expression of IL-27, an immune regulatory gene. We further showed that adiposity affected the HFC, irrespective of the genetic predisposition.
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Affiliation(s)
- Ankita Chatterjee
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Kausik Das
- Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | - Abhijit Chowdhury
- Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | - Priyadarshi Basu
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India.
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Teo K, Abeysekera KWM, Adams L, Aigner E, Anstee QM, Banales JM, Banerjee R, Basu P, Berg T, Bhatnagar P, Buch S, Canbay A, Caprio S, Chatterjee A, Ida Chen YD, Chowdhury A, Daly AK, Datz C, de Gracia Hahn D, DiStefano JK, Dong J, Duret A, Emdin C, Fairey M, Gerhard GS, Guo X, Hampe J, Hickman M, Heintz L, Hudert C, Hunter H, Kelly M, Kozlitina J, Krawczyk M, Lammert F, Langenberg C, Lavine J, Li L, Lim HK, Loomba R, Luukkonen PK, Melton PE, Mori TA, Palmer ND, Parisinos CA, Pillai SG, Qayyum F, Reichert MC, Romeo S, Rotter JI, Im YR, Santoro N, Schafmayer C, Speliotes EK, Stender S, Stickel F, Still CD, Strnad P, Taylor KD, Tybjærg-Hansen A, Umano GR, Utukuri M, Valenti L, Wagenknecht LE, Wareham NJ, Watanabe RM, Wattacheril J, Yaghootkar H, Yki-Järvinen H, Young KA, Mann JP. rs641738C>T near MBOAT7 is associated with liver fat, ALT and fibrosis in NAFLD: A meta-analysis. J Hepatol 2021; 74:20-30. [PMID: 32882372 PMCID: PMC7755037 DOI: 10.1016/j.jhep.2020.08.027] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/29/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS A common genetic variant near MBOAT7 (rs641738C>T) has been previously associated with hepatic fat and advanced histology in NAFLD; however, these findings have not been consistently replicated in the literature. We aimed to establish whether rs641738C>T is a risk factor across the spectrum of NAFLD and to characterise its role in the regulation of related metabolic phenotypes through a meta-analysis. METHODS We performed a meta-analysis of studies with data on the association between rs641738C>T genotype and liver fat, NAFLD histology, and serum alanine aminotransferase (ALT), lipids or insulin. These included directly genotyped studies and population-level data from genome-wide association studies (GWAS). We performed a random effects meta-analysis using recessive, additive and dominant genetic models. RESULTS Data from 1,066,175 participants (9,688 with liver biopsies) across 42 studies were included in the meta-analysis. rs641738C>T was associated with higher liver fat on CT/MRI (+0.03 standard deviations [95% CI 0.02-0.05], pz = 4.8×10-5) and diagnosis of NAFLD (odds ratio [OR] 1.17 [95% CI 1.05-1.3], pz = 0.003) in Caucasian adults. The variant was also positively associated with presence of advanced fibrosis (OR 1.22 [95% CI 1.03-1.45], pz = 0.021) in Caucasian adults using a recessive model of inheritance (CC + CT vs. TT). Meta-analysis of data from previous GWAS found the variant to be associated with higher ALT (pz = 0.002) and lower serum triglycerides (pz = 1.5×10-4). rs641738C>T was not associated with fasting insulin and no effect was observed in children with NAFLD. CONCLUSIONS Our study validates rs641738C>T near MBOAT7 as a risk factor for the presence and severity of NAFLD in individuals of European descent. LAY SUMMARY Fatty liver disease is a common condition where fat builds up in the liver, which can cause liver inflammation and scarring (including 'cirrhosis'). It is closely linked to obesity and diabetes, but some genes are also thought to be important. We did this study to see whether one specific change ('variant') in one gene ('MBOAT7') was linked to fatty liver disease. We took data from over 40 published studies and found that this variant near MBOAT7 is linked to more severe fatty liver disease. This means that drugs designed to work on MBOAT7 could be useful for treating fatty liver disease.
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Affiliation(s)
- Kevin Teo
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Leon Adams
- Medical School, Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, Australia; Department of Hepatology, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Elmar Aigner
- First Department of Medicine, Paracelsus Medical University Salzburg, Austria
| | - Quentin M Anstee
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Jesus M Banales
- Department on Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, Ikerbasque, San Sebastian, Spain
| | | | | | - Thomas Berg
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | | | - Stephan Buch
- Medical Department 1, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Ali Canbay
- Gastroenterology, Hepatology and Infectiology, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Sonia Caprio
- Yale University, Department of Pediatrics, New Haven, CT, USA
| | | | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Abhijit Chowdhury
- Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Ann K Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Christian Datz
- Department of Internal Medicine, General Hospital Oberndorf, Teaching Hospital of the Paracelsus Medical University Salzburg, Oberndorf, Austria
| | | | - Johanna K DiStefano
- Diabetes and Fibrotic Disease Unit Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Jiawen Dong
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Amedine Duret
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Connor Emdin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Boston, MA, USA
| | - Madison Fairey
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Glenn S Gerhard
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Matthew Hickman
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
| | - Lena Heintz
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany
| | - Christian Hudert
- Department of Pediatric Gastroenterology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Harriet Hunter
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Julia Kozlitina
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Marcin Krawczyk
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany; Laboratory of Metabolic Liver Diseases, Department of General, Transplant and Liver Surgery, Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Frank Lammert
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Joel Lavine
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Lin Li
- BioStat Solutions LLC, Frederick, MD, USA
| | - Hong Kai Lim
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Rohit Loomba
- NAFLD Research Center, Division of Gastroenterology and Epidemiology, University of California at San Diego, La Jolla, CA, USA
| | - Panu K Luukkonen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland; Department of Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Yale University School of Medicine, New Haven, CT, USA
| | - Phillip E Melton
- School of Global Population Health, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, WA, Australia; School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, WA, Australia; Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Australia
| | - Trevor A Mori
- Medical School, Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, Australia
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Constantinos A Parisinos
- Institute of Health Informatics, Faculty of Population Health Sciences, University College London, London, UK
| | | | - Faiza Qayyum
- Department of Clinical Biochemistry, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - Matthias C Reichert
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany
| | - Stefano Romeo
- Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden; Cardiology Department, Sahlgrenska University Hospital, Gothenburg, Sweden; Clinical Nutrition Unit, Department of Medical and Surgical Sciences, University Magna Graecia, Catanzaro, Italy
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yu Ri Im
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Nicola Santoro
- Yale University, Department of Pediatrics, New Haven, CT, USA; Department of Medicine and Health Sciences 'V. Tiberio' University of Molise, Campobasso, Italy
| | - Clemens Schafmayer
- Department of Visceral and Thoracic Surgery, Kiel University, Kiel, Germany
| | - Elizabeth K Speliotes
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Michigan Health System, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stefan Stender
- Department of Clinical Biochemistry, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - Felix Stickel
- Department of Gastroenterology and Hepatology, University Hospital of Zurich, Zurich, Switzerland
| | | | - Pavel Strnad
- Medical Clinic III, University Hospital RWTH Aachen, Aachen, Germany
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Anne Tybjærg-Hansen
- Department of Clinical Biochemistry, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - Giuseppina Rosaria Umano
- Yale University, Department of Pediatrics, New Haven, CT, USA; Department of the Woman, the Child, of General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Mrudula Utukuri
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy; Translational Medicine, Department of Transfusion Medicine and Hematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, Milan, Italy
| | - Lynne E Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Richard M Watanabe
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Julia Wattacheril
- Department of Medicine, Center for Liver Disease and Transplantation, Columbia University College of Physicians and Surgeons, New York Presbyterian Hospital, New York, NY, USA
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Hannele Yki-Järvinen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland; Department of Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kendra A Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Jake P Mann
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
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Das A, Basu P, Mandal P, Bandyopadhyay A. Plasma proteomic analyses of NSTEMI patients reveal involvement of DECTIN1 in NF-KB mediated activation of inflammation in atherosclerosis through DECTIN1-GALECTIN3 interaction. Atherosclerosis 2020. [DOI: 10.1016/j.atherosclerosis.2020.10.185] [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: 11/30/2022]
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10
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Roy A, Mondal B, Banerjee R, Choudhury S, Chatterjee K, Basu P, Dey S, Kumar H. Interplay of cytokines and nerve-growth factor in patients with Parkinson's Disease: A study in Eastern Indian population. Parkinsonism Relat Disord 2020. [DOI: 10.1016/j.parkreldis.2020.06.305] [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: 10/22/2022]
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Basu P, Choudhury S, Roy A, Baker M, Baker S, Kumar H. Motor response inhibition - A potential tool to determine optimum STN-DBS parameters. Parkinsonism Relat Disord 2020. [DOI: 10.1016/j.parkreldis.2020.06.176] [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: 10/22/2022]
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Affiliation(s)
- P. Basu
- School of Medicine University of California San Diego San Diego CA USA
| | - Y. Tong
- Department of Dermatology University of California San Diego San Diego CA USA
| | - B.R. Hinds
- Department of Dermatology University of California San Diego San Diego CA USA
| | - J.A. Schneider
- Department of Dermatology University of California San Diego San Diego CA USA
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Ortmann O, Torode J, Schmiegel W, Thomssen C, Hakama M, Basu P, Ringborg U, Helbig U. Knowledge transfer as a tool towards improvement of cancer care in low- and middle-income countries. 6th European Roundtable Meeting (ERTM), June 14th, 2019, Berlin, Germany. J Cancer Res Clin Oncol 2020; 146:1813-1818. [PMID: 32270287 PMCID: PMC8253705 DOI: 10.1007/s00432-020-03209-7] [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] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 11/30/2022]
Abstract
PURPOSE To identify key factors for the best practice of knowledge transfer from high-income settings to low- and middle-income settings. RESULTS Interactive sessions led to the identification of European learnings that can and should be shared beyond Europe. Furthermore, methods were characterised which may lead to successful knowledge transfer with subsequent quality improvement. CONCLUSION To ensure successful implementation of knowledge and new methods, political support is extremely important. A strong focus should be an improvement of collaboration and network development. Rehabilitation, early and late pallative care, cost effectiveness and long-term follow-up are priorities. Limitations are budget constraints which limit the execution of NCCPs.
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Affiliation(s)
- O Ortmann
- German Cancer Society, Berlin, Germany.
- Department of Gynecology and Obstetrics, University Medical Center Regensburg, Landshuter Straße 65, 93053, Regensburg, Germany.
| | - J Torode
- Union for International Cancer Control (UICC), Geneva, Switzerland
| | - W Schmiegel
- University Clinic at the University Hospital Knappschaftskrankenhaus Bochum, Bochum, Germany
| | - C Thomssen
- University Clinic and Polyclinic for Gynaecology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - M Hakama
- The Finnish Cancer Registry, Helsinki, Finland
| | - P Basu
- International Agency for Research On Cancer, World Health Organisation, Lyon, France
| | - U Ringborg
- EUROCAN Platform, Cancer Center Karolinska, Stockholm, Sweden
| | - U Helbig
- German Cancer Society, Berlin, Germany
- Deutsche Krebshilfe, Berlin, Germany
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14
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Basu P, Beckles A, Porter M, Olbricht S. LB1074 Predicting treatment decisions in elderly patients with non-melanoma skin cancers. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.06.035] [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: 10/26/2022]
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15
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Pinder L, Basu P, Prendiville W, Muwonge R, Lucas E, Parham G. Safety, acceptability and efficacy of a new thermal ablation technique to prevent cervical cancer in low- and middle-income countries – preliminary results. Gynecol Oncol 2019. [DOI: 10.1016/j.ygyno.2019.04.098] [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: 10/26/2022]
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16
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Mittal S, Basu P, Mandal R, Ghosh I, Banerjee D, Panda C, Biswas J. Enablers and Barriers of Follow-Up Care: An Experience From an HPV DNA Detection–Based Cervical Cancer Screening Program in Rural India. J Glob Oncol 2018. [DOI: 10.1200/jgo.18.24200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Success of a cervical cancer screening program is intrinsically linked with appropriate management of women detected positive on screening tests. While routine screening can be done in any setting, the follow-up care of screen positive women is linked with settings that are equipped with diagnostic and treatment facilities, and trained medical providers. In low resource settings, the major obstacles to deliver follow-up care are lack of adequate healthcare infrastructure and trained service providers at district or subdistrict levels. Aim: To assess feasibility of implementing community based interventions to increase uptake of follow-up care of screen positive women in a HPV detection based screening program conducted by Chittaranjan National Cancer Institute (CNCI), Kolkata. Strategy: A network of key stakeholders including government authorities and civil society organizations was developed to deliver continuum of care at the doorsteps of screen positive women. The infrastructure of government's primary health care delivery system was used to set up temporary clinics at district and subdistrict levels. The clinics were organized on prescheduled dates and times that were convenient to the women. Community health workers (CHWs) were trained in community mobilization strategies to increase uptake of follow-up services. All instruments, equipment and consumables required for providing follow-up services were carried to the clinics in a vehicle. Program: The CHWs played a key role in counseling and recalling the screen positive women. The temporary clinics were arranged in the government primary health centers. A team of trained doctors and paramedics provided the diagnostic and treatment services. Colposcopy was performed on all screen positive women using portable colposcopes and guided biopsies were taken as indicated. Women who were eligible for ablative treatment were counseled and treated in the same sitting. All women were advised yearly follow-up. Outcomes: A total of 43,325 women were screened by HC2 test during July 2010 to March 2015, and 2045 (4.7%) women were detected to be high-risk HPV positive. Compliance to first recall was good with 78.6% (1608/2045) of women undergoing diagnostic evaluation at field clinics. But overall compliance to at least one follow-up visit after 1 year was poor (23.2%). Follow-up compliance rate was higher in women who were diagnosed with CIN1 as compared with those with normal diagnosis ( P < 0.001). What was learned: Diagnostic and treatment services could be effectively organized in the community in convergence with existing healthcare delivery system. High compliance to initial diagnostic evaluation and treatment was achieved by making the services available close to the doorsteps of the women. The reasons for low compliance to yearly follow-up were lack of understanding of future cancer risk, unwilling to undergo speculum examination again, and lack of cooperation of spouse/family.
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Affiliation(s)
- S. Mittal
- Chittaranjan National Cancer Institute, Gynecologic Oncology, Kolkata, India
| | - P. Basu
- International Agency for Research on Cancer, Screening Group, Lyon, France
| | - R. Mandal
- Chittaranjan National Cancer Institute, Gynecologic Oncology, Kolkata, India
| | - I. Ghosh
- Chittaranjan National Cancer Institute, Gynecologic Oncology, Kolkata, India
| | - D. Banerjee
- Chittaranjan National Cancer Institute, Gynecologic Oncology, Kolkata, India
| | - C. Panda
- Chittaranjan National Cancer Institute, Oncogene Regulation, Kolkata, India
| | - J. Biswas
- Chittaranjan National Cancer Institute, Surgical Oncology, Kolkata, India
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Chatterjee S, Basu P. Food preferences determine habitat selection at multiple scales: implication for bird conservation in tropical forests. Anim Conserv 2018. [DOI: 10.1111/acv.12397] [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: 10/18/2022]
Affiliation(s)
- S. Chatterjee
- Ecology Research Unit; Department of Zoology; University of Calcutta; Kolkata India
- Centre for Pollination Studies; Department of Zoology; University of Calcutta; Kolkata India
| | - P. Basu
- Ecology Research Unit; Department of Zoology; University of Calcutta; Kolkata India
- Centre for Pollination Studies; Department of Zoology; University of Calcutta; Kolkata India
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Mukherjee A, Biswas P, Shaikh MM, Roy S, Goswami A, Pradhan M, Basu P, Santra S, Pandit S, Mahata K, Shrivastava A. Study of Quasielastic scattering for 7Li+ 159Tb at around- barrier energies. EPJ Web Conf 2017. [DOI: 10.1051/epjconf/201716300039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Roy N, Dasgupta D, Mukhopadhyay I, Chatterjee A, Das K, Bhowmik P, Das S, Basu P, Santra AK, Datta S, Dhali GK, Chowdhury A, Banerjee S. Genetic Association and Gene-Gene Interaction Reveal Genetic Variations in ADH1B, GSTM1 and MnSOD Independently Confer Risk to Alcoholic Liver Diseases in India. PLoS One 2016; 11:e0149843. [PMID: 26937962 PMCID: PMC4777485 DOI: 10.1371/journal.pone.0149843] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/05/2016] [Indexed: 02/07/2023] Open
Abstract
Genetic susceptibility is an important modifier of clinical outcome and natural history of progression in Alcoholic liver disease (ALD). While the significance of ethnicity in this evolution is very clear, subtle inter-individual genetic variant(s) might be important and thus we investigated those in an Indian population. Fourteen markers were genotyped within two alcohol metabolism genes [Alcohol dehydrogenase (ADH) gene clusters (ADH1B and ADH1C) and Aldehyde dehydrogenase (ALDH2)], one microsomal ethanol oxidizing enzyme cytochrome p450 (CYP2E1) and three oxidative stress response (OSR) genes (MnSOD, GSTT1 and GSTM1) among 490 Bengali individuals (322 ALD and 168 control) from Eastern and North-Eastern India and validation was performed in a new cohort of 150 Bengali patients including 100 ALD and 50 advanced non-alcoholic steatohepatitis (NASH). Out of 14 genetic variants, carriage of 5 genotypes (rs2066701CC in ADH1B, rs1693425TT in ADH1C, rs4880TT in MnSOD and GSTT1/GSTM1 null, p-value <0.05) were noted significantly higher among ALD patients while inter or intra group gene-gene interaction analysis revealed that addition of risk genotype of any OSR gene enhanced the possibility of ALD synergistically. Multiple logistic regression analysis showed independent association of rs2066701CC, rs4880TT and GSTM1 null genotype with ALD while lower frequencies of those genotypes in advanced NASH patients further confirmed their causal relation to ALD. Thus these findings suggest that the three variants of ADH1C, MnSOD and GSTM1 can be used to identify individuals who are at high risk to develop ALD and may be helpful in proper management of Indian alcoholics.
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Affiliation(s)
- Neelanjana Roy
- Center for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | - Debanjali Dasgupta
- Center for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | | | | | - Kausik Das
- Department of Hepatology, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | - Pradip Bhowmik
- Agartala Government Medical College, Agartala, Tripura, India
| | - Soumyajit Das
- Center for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | | | - Amal K. Santra
- Center for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | - Simanti Datta
- Center for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | - Gopal Krishna Dhali
- Department of Gastroenterology, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Abhijit Chowdhury
- Department of Hepatology, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
| | - Soma Banerjee
- Center for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, West Bengal, India
- * E-mail:
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20
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Chatterjee A, Basu A, Chowdhury A, Das K, Sarkar-Roy N, Majumder PP, Basu P. Comparative analyses of genetic risk prediction methods reveal extreme diversity of genetic predisposition to nonalcoholic fatty liver disease (NAFLD) among ethnic populations of India. J Genet 2016; 94:105-13. [PMID: 25846882 DOI: 10.1007/s12041-015-0494-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a distinct pathologic condition characterized by a disease spectrum ranging from simple steatosis to steato-hepatitis, cirrhosis and hepatocellular carcinoma. Prevalence of NAFLD varies in different ethnic groups, ranging from 12% in Chinese to 45% in Hispanics. Among Indian populations, the diversity in prevalence is high, ranging from 9% in rural populations to 32% in urban populations, with geographic differences as well. Here, we wished to find out if this difference is reflected in their genetic makeup. To date, several candidate genes and a few genomewide association studies (GWAS) have been carried out, and many associations between single nucleotide polymorphisms (SNPs) and NAFLD have been observed. In this study, the risk allele frequencies (RAFs) of NAFLD-associated SNPs in 20 Indian ethnic populations (376 individuals) were analysed. We used two different measures for calculating genetic risk scores and compared their performance. The correlation of additive risk scores of NAFLD for three Hapmap populations with their weighted mean prevalence was found to be high (R(2) = 0.93). Later we used this method to compare NAFLD risk among ethnic Indian populations. Based on our observation, the Indian caste populations have high risk scores compared to Caucasians, who are often used as surrogate and similar to Indian caste population in disease gene association studies, and is significantly higher than the Indian tribal populations.
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Affiliation(s)
- Ankita Chatterjee
- National Institute of Biomedical Genomics, Netaji Subhas Sanatorium (T. B. Hospital), Kalyani 741 251, India.
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Moin Shaikh M, Roy S, Rajbanshi S, Mukherjee A, Pradhan MK, Basu P, Pal S, Nanal V, Shrivastava A, Saha S, Pillay RG. Measurement of fusion excitation function for 7Li+ 64Ni near the barrier. EPJ Web of Conferences 2016. [DOI: 10.1051/epjconf/201611708020] [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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Shaikh MM, Roy S, Rajbanshi S, Pradhan MK, Mukherjee A, Basu P, Pal S, Nanal V, Pillay RG, Shrivastav A. Fusion excitation function measurement for 6Li+ 64Ni at near-barrier energies. EPJ Web of Conferences 2015. [DOI: 10.1051/epjconf/20158600044] [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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Sengupta R, Bapiraju S, Basu P, Melcher D. Accounting for subjective time expansion based on a decision, rather than perceptual, mechanism. J Vis 2014. [DOI: 10.1167/14.10.1150] [Citation(s) in RCA: 2] [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: 11/24/2022] Open
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Sarkar B, Nandy M, Manikandan A, Basu P, Sujatha N, Ray DK, Senthilkumar P, Ray S, Roy SS, Ray A, Basu S, Bhattacharya K. SU-E-T-57: Estimation of Uncertainty in Dose Delivery Due to MLC Position Inaccuracies by Inverse Derivative Method during Volumetric Modulated Arc Therapy Delivery by Elekta Beam Modulator. Med Phys 2012. [DOI: 10.1118/1.4735113] [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: 11/07/2022] Open
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Sinha M, Roy S, Basu P, Majumdar H, Santra S, Parkar V, Golda K, Kailas S. Coupled channel effect in elastic scattering and fusion for 6,7Li+ 28Si. EPJ Web of Conferences 2011. [DOI: 10.1051/epjconf/20111703004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [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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Meng H, Joyce AR, Adkins DE, Basu P, Jia Y, Li G, Sengupta TK, Zedler BK, Murrelle EL, van den Oord EJCG. A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling. BMC Bioinformatics 2010; 11:227. [PMID: 20441598 PMCID: PMC2876131 DOI: 10.1186/1471-2105-11-227] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Accepted: 05/05/2010] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND High-throughput DNA methylation arrays are likely to accelerate the pace of methylation biomarker discovery for a wide variety of diseases. A potential problem with a standard set of probes measuring the methylation status of CpG sites across the whole genome is that many sites may not show inter-individual methylation variation among the biosamples for the disease outcome being studied. Inclusion of these so-called "non-variable sites" will increase the risk of false discoveries and reduce statistical power to detect biologically relevant methylation markers. RESULTS We propose a method to estimate the proportion of non-variable CpG sites and eliminate those sites from further analyses. Our method is illustrated using data obtained by hybridizing DNA extracted from the peripheral blood mononuclear cells of 311 samples to an array assaying 1505 CpG sites. Results showed that a large proportion of the CpG sites did not show inter-individual variation in methylation. CONCLUSIONS Our method resulted in a substantial improvement in association signals between methylation sites and outcome variables while controlling the false discovery rate at the same level.
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Affiliation(s)
- Hailong Meng
- Altria Client Services, Research Development & Engineering, Richmond, VA 23219, USA.
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Basu P, De P, Mandal S, Ray K, Biswas J. Study of 'patterns of care' of ovarian cancer patients in a specialized cancer institute in Kolkata, eastern India. Indian J Cancer 2009; 46:28-33. [PMID: 19282563 DOI: 10.4103/0019-509x.48592] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Ovarian cancer is one of the leading cancers in Indian women. The current standard of care is a combination of surgical staging, maximal surgical effort to achieve cytoreduction, and judicious use of chemotherapy. Multimodality therapy can reduce mortality, but the practice and uptake of such therapy in Indian Institutions are not up to the desired level. OBJECTIVES To study the protocol adherence for ovarian cancer management along with patient compliance and evaluate their effects on survival. MATERIALS AND METHODS The retrospective study obtained and analyzed data from records of patients operated for ovarian cancer at a Regional Cancer Center in eastern India between January 2002 and December 2006. RESULTS The records of 202 patients were evaluable. None of the patients who had primary surgery outside the institute had staging information. A substantial number of patients operated at the institute had incomplete surgical staging, inadequate information on residual disease after surgery, and incomplete histology report. Only 20.3% patients could have optimal cytoreduction after surgery. Compliance to chemotherapy was poor. The median overall survival time and disease-free survival time were 24 months and 5 months, respectively. The residual disease after surgery significantly affected the overall survival, but not the disease-free survival. Incomplete chemotherapy was found to adversely affect survival after adjusting for advanced stage and bulky residual disease. CONCLUSION Management of ovarian cancer is suboptimal even in the specialized cancer institute. Poor patient compliance to chemotherapy is one of the major factors adversely affecting survival from advanced ovarian cancer.
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Affiliation(s)
- P Basu
- Department of Gynecologic Oncology, Chittaranjan National Cancer Institute, 37, S. P. Mukherjee Road, Kolkata, India.
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Verma P, Gautam S, Pal S, Kumar P, Chaturvedi P, Rawat J, Chaudhary P, Harsh D, Basu P, Bhatanagar P. Carbon Nanotube-based Cold Cathode for High Power MicrowaveVacuum Electronic Devices: A Potential Field Emitter. DEFENCE SCI J 2008. [DOI: 10.14429/dsj.58.1688] [Citation(s) in RCA: 3] [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]
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Basu P, Lung TK, Lemsaddek W, Sargent TG, Williams DC, Basu M, Redmond LC, Lingrel JB, Haar JL, Lloyd JA. EKLF and KLF2 have compensatory roles in embryonic beta-globin gene expression and primitive erythropoiesis. Blood 2007; 110:3417-25. [PMID: 17675555 PMCID: PMC2200909 DOI: 10.1182/blood-2006-11-057307] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The Krüppel-like C2/H2 zinc finger transcription factors (KLFs) control development and differentiation. Erythroid Krüppel-like factor (EKLF or KLF1) regulates adult beta-globin gene expression and is necessary for normal definitive erythropoiesis. KLF2 is required for normal embryonic Ey- and betah1-, but not adult betaglobin, gene expression in mice. Both EKLF and KLF2 play roles in primitive erythroid cell development. To investigate potential interactions between these genes, EKLF/KLF2 double-mutant embryos were analyzed. EKLF(-/-)KLF2(-/-) mice appear anemic at embryonic day 10.5 (E10.5) and die before E11.5, whereas single-knockout EKLF(-/-) or KLF2(-/-) embryos are grossly normal at E10.5 and die later than EKLF(-/-)KLF2(-/-) embryos. At E10.5, Ey- and betah1-globin mRNA is greatly reduced in EKLF(-/-)KLF2(-/-), compared with EKLF(-/-) or KLF2(-/-) embryos, consistent with the observed anemia. Light and electron microscopic analyses of E9.5 EKLF(-/-)KLF2(-/-) yolk sacs, and cytospins, indicate that erythroid and endothelial cells are morphologically more abnormal than in either single knockout. EKLF(-/-)KLF2(-/-) erythroid cells are markedly irregularly shaped, suggesting membrane abnormalities. EKLF and KLF2 may have coordinate roles in a common progenitor to erythroid and endothelial cells. The data indicate that EKLF and KLF2 have redundant functions in embryonic beta-like globin gene expression, primitive erythropoiesis, and endothelial development.
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Affiliation(s)
- Priyadarshi Basu
- Department of Human Genetics, and Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, VA 23298, USA
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Chervenak AP, Basu P, Shin M, Redmond LC, Sheng G, Lloyd JA. Identification, characterization, and expression pattern of the chicken EKLF gene. Dev Dyn 2006; 235:1933-40. [PMID: 16680725 DOI: 10.1002/dvdy.20829] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
EKLF/KLF1 was the first of the Krüppel-like factors (KLFs) to be identified in mammals and plays an important role in primitive and definitive erythropoiesis. Here, we identify and characterize EKLF in the chicken (cEKLF). The predicted amino acid sequence of the zinc finger region of cEKLF is at least 87.7% similar to mammalian EKLF proteins and is 98.8% and 95% similar to the EKLF orthologues in Xenopus and zebrafish, respectively. During early embryonic development, cEKLF expression is seen in the posterior primitive streak, which gives rise to hematopoietic cells, and then in the blood islands and in circulating blood cells. cEKLF mRNA is expressed in blood cells but not in brain later in chicken embryonic development. cEKLF mRNA is increased in definitive compared with primitive erythropoiesis. The conserved sequence and expression pattern of cEKLF suggests that its function is similar to its orthologues in mammals, Xenopus, and zebrafish.
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Affiliation(s)
- Andrew P Chervenak
- Department of Human Genetics, Virginia Commonwealth University, Richmond, Virginia 23298-0033, USA
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Redmond LC, Haar JL, Giebel ML, Dumur CI, Basu P, Ware JL, Lloyd JA. Isolation of erythroid cells from the mouse embryonic yolk sac by laser capture microdissection and subsequent microarray hybridization. Blood Cells Mol Dis 2006; 37:27-32. [PMID: 16697667 DOI: 10.1016/j.bcmd.2006.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Revised: 01/17/2006] [Indexed: 11/21/2022]
Abstract
Erythropoietic tissues are complex, containing both erythroid and other cells. The embryonic yolk sac in particular contains primitive erythroid cells in low abundance. Laser capture microdissection (LCM) was performed to isolate erythroid cells, and epithelial cells, from mouse embryonic day 10 (E10) yolk sac. Quantitative RT-PCR was performed to confirm that enriched cell populations were obtained. epsilony- and betaH1-globin mRNAs were enriched in the erythroid compared to the epithelial fraction, and villin mRNA was enriched in the epithelial compared to the erythroid fraction. RNA isolated from the microdissected erythroid cells was of high quality as indicated by capillary electrophoresis. The RNA from the LCM erythroid fraction was linearly amplified with T7 RNA polymerase and hybridized to a Mouse 430A 2.0 Affymetrix array. Forty-eight percent of genes were present in the microarray assays, including low abundance transcripts such as erythroid transcription factors and enzymes involved in heme synthesis. With the LCM/microarray strategy, it will be possible to identify genes that are differentially regulated in native primitive and definitive erythroid cells.
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Affiliation(s)
- Latasha C Redmond
- Department of Human Genetics, Virginia Commonwealth University, Richmond, Richmond, VA 23298, USA
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Haar JL, Redmond LC, Dumur CI, Archer KJ, Basu P, Lloyd JA. Comparing the genetic profiles of E9 mouse yolk sac erythroid and epithelial cells isolated by microdissection. FASEB J 2006. [DOI: 10.1096/fasebj.20.5.lb3-b] [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: 11/11/2022]
Affiliation(s)
| | | | | | - Kelly J. Archer
- BiostatisticsVirginia Commonwealth Univ.1101 E. Marshall StRichmondVirginia23298
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Basu P, Biswas J, Mandal R, Choudhury P. Is interferon-α and retinoic acid combination along with radiation superior to chemo-radiation in the treatment of advanced carcinoma of cervix? Indian J Cancer 2006; 43:54-9. [PMID: 16790941 DOI: 10.4103/0019-509x.25885] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Locally advanced cervical cancers comprise a large majority of the gynecologic cancers in India and other developing countries. Concurrent chemo-radiation has improved the survival of high risk stage I and stage II cervical cancers. There is no evidence that the same survival benefit has been achieved with chemo-radiation in stage III and stage IV disease. Interferon-alpha and Retinoic acid have synergistic anti-proliferative activity. In combination with radiation, they substantially enhance the sensitivity of the squamous carcinoma cells to radiation. Based on these observations from the in vitro studies, a few clinical trials have evaluated the combination of interferon-alpha and Retinoic acid, concomitant with radiation, to treat cervical cancers. The results from these early trials were encouraging and the combination had minimal toxicities. However, till date, no phase III randomized controlled trial has been done to evaluate this therapeutic modality.
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Affiliation(s)
- P Basu
- Department of Gynecologic Oncology, Chittaranjan National Cancer Institute, 37, S. P. Mukherjee Road, Kolkata, India.
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Zhang P, Basu P, Redmond LC, Morris PE, Rupon JW, Ginder GD, Lloyd JA. A functional screen for Krüppel-like factors that regulate the human γ-globin gene through the CACCC promoter element. Blood Cells Mol Dis 2005; 35:227-35. [PMID: 16023392 DOI: 10.1016/j.bcmd.2005.04.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [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: 12/16/2004] [Accepted: 04/14/2005] [Indexed: 10/25/2022]
Abstract
Krüppel-like factors (KLFs) have been systematically screened as potential candidates to regulate human gamma-globin gene expression through its CACCC element. Initially, 21 human proteins that have close sequence similarity to EKLF/KLF1, a known regulator of the human beta-globin gene, were identified. The phylogenetic relationship of these 22 KLF/Sp1 proteins was determined. KLF2/LKLF, KLF3/BKLF, KLF4/GKLF, KLF5/IKLF, KLF8/BKLF3, KLF11/FKLF, KLF12/AP-2rep and KLF13/FKLF2 were chosen for functional screening. Semi-quantitative RT-PCR demonstrated that all eight of these candidates are present in human erythroid cell lines, and that the expression of the KLF2, 4, 5 and 12 mRNAs changed significantly upon erythroid differentiation. Each of the eight KLF mRNAs is expressed in mouse erythroid tissues, throughout development. UV cross-linking assays suggest that multiple erythroid proteins from human cell lines and chicken primary cells interact with the gamma-globin CACCC element. In co-transfection assays in K562 cells, it was demonstrated that KLF2, 5 and 13 positively regulate, and KLF8 negatively regulates, the gamma-globin gene through the CACCC promoter element. The data collectively suggest that multiple KLFs may participate in the regulation of gamma-globin gene expression and that KLF2, 5, 8 and 13 are prime candidates for further study.
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Affiliation(s)
- Ping Zhang
- Department of Human Genetics, Virginia Commonwealth University, PO Box 980033, 1101 E. Marshall Street, Richmond, VA 23298-0033, USA
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Basu P, Morris PE, Haar JL, Wani MA, Lingrel JB, Gaensler KML, Lloyd JA. KLF2 is essential for primitive erythropoiesis and regulates the human and murine embryonic beta-like globin genes in vivo. Blood 2005; 106:2566-71. [PMID: 15947087 PMCID: PMC1895257 DOI: 10.1182/blood-2005-02-0674] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Krüppel-like factors (KLFs) are a family of C2/H2 zinc finger DNA-binding proteins that are important in controlling developmental programs. Erythroid Krüppel-like factor (EKLF or KLF1) positively regulates the beta-globin gene in definitive erythroid cells. KLF2 (LKLF) is closely related to EKLF and is expressed in erythroid cells. KLF2-/- mice die between embryonic day 12.5 (E12.5) and E14.5, because of severe intraembryonic hemorrhaging. They also display growth retardation and anemia. We investigated the expression of the beta-like globin genes in KLF2 knockout mice. Our results show that KLF2-/- mice have a significant reduction of murine embryonic Ey- and beta h1-globin but not zeta-globin gene expression in the E10.5 yolk sac, compared with wild-type mice. The expression of the adult beta(maj)- and beta(min)-globin genes is unaffected in the fetal livers of E12.5 embryos. In mice carrying the entire human globin locus, KLF2 also regulates the expression of the human embryonic epsilon-globin gene but not the adult beta-globin gene, suggesting that this developmental-stage-specific role is evolutionarily conserved. KLF2 also plays a role in the maturation and/or stability of erythroid cells in the yolk sac. KLF2-/- embryos have a significantly increased number of primitive erythroid cells undergoing apoptotic cell death.
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Affiliation(s)
- Priyadarshi Basu
- Department of Human Genetics, Virginia Commonwealth University, PO Box 980033, Richmond, VA 23298-0033, USA
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Basu P, Sargent TG, Redmond LC, Aisenberg JC, Kransdorf EP, Wang SZ, Ginder GD, Lloyd JA. Evolutionary conservation of KLF transcription factors and functional conservation of human γ-globin gene regulation in chicken☆. Genomics 2004; 84:311-9. [PMID: 15233995 DOI: 10.1016/j.ygeno.2004.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [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: 11/25/2003] [Accepted: 02/18/2004] [Indexed: 11/17/2022]
Abstract
The Krüppel-like factors (KLFs) are a family of Cys2His2 zinc-finger DNA binding proteins with homology to Drosophila Krüppel. KLFs can bind to CACCC elements, which are important in controlling developmental programs. The CACCC promoter element is critical for the developmental regulation of the human gamma-globin gene. In the present study, chicken homologues of the human KLF2, 3, 4, 5, 9, 11, 12, 13, and 15 genes were identified. Phylogenetic analysis confirms that these genes are more closely related to their human homologues than they are to other chicken KLFs. This work also represents the first systematic study of the expression patterns of KLFs during erythroid development. In addition, transient transfections of human globin constructs into 5-day (primitive) chicken red blood cells show that human gamma-globin expression is regulated via its CACCC promoter element. This indicates that a CACCC-binding factor(s) important for gamma-globin expression functions in 5-day chicken red cells.
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Affiliation(s)
- Priyadarshi Basu
- Department of Human Genetics, Virginia Commonwealth University, P.O. Box 980033, 1101 E. Marshall Street, Richmond, VA 23298-0033, USA
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Dasbaksi K, Mukherjee P, Roy B, Mitra H, Basu P, Krishna A. Thoracoscopic surgery-minimally invasive approach in thoracic diseases. Indian J Thorac Cardiovasc Surg 2004. [DOI: 10.1007/s12055-004-0466-0] [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: 10/22/2022] Open
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Mukherjee P, Dasbaksi K, Roy B, Mitra H, Basu P. Our experience with transhiatal oesophagectomy for cancer oesophagus. Indian J Thorac Cardiovasc Surg 2004. [DOI: 10.1007/s12055-004-0449-1] [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: 11/30/2022] Open
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Chattopadhyay B, Basu P, Gangopadhyay PK, Mukherjee SC, Sinha KK, Chakraborty A, Roy T, Roychoudhury S, Majumder PP, Bhattacharyya NP. Variation of CAG repeats and two intragenic polymorphisms at SCA3 locus among Machado-Joseph disease/SCA3 patients and diverse normal populations from eastern India. Acta Neurol Scand 2003; 108:407-14. [PMID: 14616293 DOI: 10.1034/j.1600-0404.2003.00167.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVES MJD1/SCA3 is the most common type of spinocerebellar ataxia (SCA) worldwide. To explain the low prevalence of the disease among SCA patients from eastern India, we analysed CAG repeats and two bi-allelic intragenic markers at SCA3 locus among 412 normal individuals and 10 patients. MATERIALS AND METHODS For CAG repeat analysis, PCR amplified fragments were run on polyacrylamide gel, transferred to a membrane, probed with (CAG)10 and detected on an autoradiograph. Bi-allelic markers were analysed using allele specific PCR amplification. RESULTS Large normal alleles (>33 CAG repeats) were 0.015 in pooled populations. All the patients had the common haplotype C-A as observed worldwide. Frequency of C-A haplotype among large normal alleles was 0.75. CONCLUSIONS Observed low prevalence of SCA3 could be because of the low prevalence of large normal alleles that might act as the reservoir for the expanded alleles. SCA3 mutation in Indian populations had the same origin as found worldwide.
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Affiliation(s)
- B Chattopadhyay
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
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Sankaranarayanan R, Nene BM, Dinshaw K, Rajkumar R, Shastri S, Wesley R, Basu P, Sharma R, Thara S, Budukh A, Parkin DM. Early detection of cervical cancer with visual inspection methods: a summary of completed and on-going studies in India. Salud pública Méx 2003; 45 Suppl 3:S399-407. [PMID: 14746033 DOI: 10.1590/s0036-36342003000900014] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
India is a high-risk country for cervical cancer which accounts a quarter (126,000 new cases, 71,000 deaths around 2,000) of the world burden. The age-standardized incidence rates range from 16-55 per 100,000 women in different regions with particularly high rates in rural areas. Control of cervical cancer by early detection and treatment is a priority of the National Cancer Control Programme of India. There are no organized cytology screening programmes in the country. The technical and financial constraints to organize cytology screening have encouraged the evaluation of visual inspection approaches as potential alternatives to cervical cytology in India. Four types of visual detection approaches for cervical neoplasia are investigated in India: a) naked eye inspection without acetic acid application, widely known as 'downstaging'; b) naked eye inspection after application of 3-5% acetic acid (VIA); c) VIA using magnification devices (VIAM); d) visual inspection after the application of Lugol's iodine (VILI). Downstaging has been shown to be poorly sensitive and specific to detect cervical neoplasia and is no longer considered as a suitable screening test for cervical cancer. VIA, VIAM and VILI are currently being investigated in multicentre cross-sectional studies (without verification bias), in which cytology and HPV testing are also simultaneously evaluated, and the results of these investigations will be available in 2003. These studies will provide valuable information on the average, comparative test performances in detecting high-grade cervical cancer precursors and cancer. Results from pooled analysis of data from two completed studies indicated an approximate sensitivity of 93.4% and specificity of 85.1% for VIA to detect CIN 2 or worse lesions; the corresponding figures for cytology were 72.1% and 91.6%. The efficacy of VIA in reducing incidence of an mortality from cervical cancer and its cost-effectiveness is currently being investigated in two cluster randomized controlled intervention trials in India. One of these studies is a 4-arm trial addressing the comparative efficacy of VIA, cytology and primary screening with HPV DNA testing. This trial will provide valuable information on comparative detection rates of CIN 2-3 lesions by the middle of 2003. The expected outcomes from the Indian studies will contribute valuable information for guiding the development of public health policies on cervical cancer prevention in countries with different levels of socio-economic and health services development and open up new avenues of research. This paper is available too at: http//www.insp.mx/salud/index.html.
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Affiliation(s)
- R Sankaranarayanan
- International Agency for Research on Cancer, 150 Cours Albert Thomas, Lyon 69008, France.
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Abstract
Microbial activity is responsible for the transformation of at least one third of the elements in the periodic table. These transformations are the result of assimilatory, dissimilatory, or detoxification processes and form the cornerstones of many biogeochemical cycles. Arsenic and selenium are two elements whose roles in microbial ecology have only recently been recognized. Known as "essential toxins", they are required in trace amounts for growth and metabolism but are toxic at elevated concentrations. Arsenic is used as an osmolite in some marine organisms while selenium is required as selenocysteine (i.e. the twenty-first amino acid) or as a ligand to metal in some enzymes (e.g. FeNiSe hydrogenase). Arsenic resistance involves a small-molecular-weight arsenate reductase (ArsC). The use of arsenic and selenium oxyanions for energy is widespread in prokaryotes with representative organisms from the Crenarchaeota, thermophilic bacteria, low and high G+C gram-positive bacteria, and Proteobacteria. Recent studies have shown that both elements are actively cycled and play a significant role in carbon mineralization in certain environments. The occurrence of multiple mechanisms involving different enzymes for arsenic and selenium transformation indicates several different evolutionary pathways (e.g. convergence and lateral gene transfer) and underscores the environmental significance and selective impact in microbial evolution of these two elements.
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Affiliation(s)
- J F Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA.
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Basu P, Yates JT. Carbon-hydrogen bond lability in adsorbed hydrocarbon layers: butadiene-derived species on rhodium/alumina. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100353a032] [Citation(s) in RCA: 4] [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: 11/29/2022]
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Basu P, Panayotov D, Yates JT. Spectroscopic evidence for the involvement of hydroxyl groups in the formation of dicarbonylrhodium(I) on metal oxide supports. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100296a007] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Basu P, Panayotov D, Yates JT. Rhodium-carbon monoxide surface chemistry: the involvement of surface hydroxyl groups on alumina and silica supports. J Am Chem Soc 2002. [DOI: 10.1021/ja00215a010] [Citation(s) in RCA: 192] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Chen JG, Crowell JE, Ng L, Basu P, Yates JT. Dissociative chemisorption of carbon monoxide on nickel films promoted by aluminum: detection of a precursor state to carbon monoxide dissociation by Electron Energy Loss Spectroscopy. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100320a035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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