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Fink JL, Fernicola P, Chandran R, Parastatidis S, Wade A, Naim O, Quinn GB, Bourne PE. Word add-in for ontology recognition: semantic enrichment of scientific literature. BMC Bioinformatics 2010; 11:103. [PMID: 20181245 PMCID: PMC2837026 DOI: 10.1186/1471-2105-11-103] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 02/24/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the current era of scientific research, efficient communication of information is paramount. As such, the nature of scholarly and scientific communication is changing; cyberinfrastructure is now absolutely necessary and new media are allowing information and knowledge to be more interactive and immediate. One approach to making knowledge more accessible is the addition of machine-readable semantic data to scholarly articles. RESULTS The Word add-in presented here will assist authors in this effort by automatically recognizing and highlighting words or phrases that are likely information-rich, allowing authors to associate semantic data with those words or phrases, and to embed that data in the document as XML. The add-in and source code are publicly available at http://www.codeplex.com/UCSDBioLit. CONCLUSIONS The Word add-in for ontology term recognition makes it possible for an author to add semantic data to a document as it is being written and it encodes these data using XML tags that are effectively a standard in life sciences literature. Allowing authors to mark-up their own work will help increase the amount and quality of machine-readable literature metadata.
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Affiliation(s)
- J Lynn Fink
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093-0444 USA
| | - Pablo Fernicola
- External Research, MS 99/4618, Microsoft Corporation, 1 Microsoft Way, Redmond, WA, 98052 USA
| | - Rahul Chandran
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093-0444 USA
| | - Savas Parastatidis
- External Research, MS 99/4618, Microsoft Corporation, 1 Microsoft Way, Redmond, WA, 98052 USA
| | - Alex Wade
- External Research, MS 99/4618, Microsoft Corporation, 1 Microsoft Way, Redmond, WA, 98052 USA
| | - Oscar Naim
- External Research, MS 99/4618, Microsoft Corporation, 1 Microsoft Way, Redmond, WA, 98052 USA
| | - Gregory B Quinn
- San Diego Supercomputer Center, 10100 Hopkins Dr., San Diego, CA, 92093-0743 USA
| | - Philip E Bourne
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093-0444 USA
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Lin A, Kadam JS, Bodenheimer HC, Leonard J, Joyce MA, Lake-Bakaar G. Concomitant diffuse large B-cell lymphoma and hepatocellular carcinoma in chronic hepatitis C virus liver disease: A study of two cases. J Med Virol 2008; 80:1350-3. [DOI: 10.1002/jmv.21109] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Abstract
HCV chronic infection leads to liver diseases and also to a wide range of extrahepatic disorders including benign, but pre-lymphomatous forms (mixed cryoglobulinemia) to frank hematological neoplasia (non-Hodgkin's lymphoma). Recent data showed the involvement of p53 superfamily members in the pathogenesis of different lymphatic malignancies. In fact, tymomas and a subset of non-Hodgkin's lymphomas (NHLs) express high levels of p63. Thus, we analyzed whether alterations in p53 superfamily gene expression are observable in B lymphocytes isolated from HCV-infected patients with and without lymphoproliferative disorders. We showed, by real-time PCR, a significant induction of DNp63 mRNAs in B lymphocytes obtained from HCV-positive low grade non-Hodgkin's lymphoma patients. Since our current understanding of HCV proteins emphasizes the ability of the HCV core protein to deregulate the expression and activity of p53-related proteins, we established different B lymphocyte cell lines (Wil2-ns, Daudi and Ramos) stably expressing HCV core protein, in order to investigate the possible involvement of the viral protein in the upregulation of DNp63 in B lymphocytes. The analysis of p63 family transcripts showed no transcriptional changes for the p63 TA isoforms, whereas an increase (>5 times) of DNp63 mRNA occurred. In all cell lines, this abnormal expression was associated with a significant increase of cell proliferation that was specifically inhibited by silencing DNp63 mRNA. These findings suggest a pathogenetic role of the HCV core in HCV-related lymphomagenesis, through the induction of DNp63's pro-proliferative effects.
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Alisi A, Giannini C, Spaziani A, Caini P, Zignego AL, Balsano C. Involvement of PI3K in HCV-related lymphoproliferative disorders. J Cell Physiol 2007; 214:396-404. [PMID: 17654494 DOI: 10.1002/jcp.21211] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Hepatitis C virus (HCV) core protein has been shown to deregulate cell growth and programmed cell death in hepatoma cells, but only minimal informations are available about its possible role on B-lymphoproliferative disorders (LPDs). The aim of our work was to analyze the biological activity of HCV core protein on B-cell proliferation. We established Wil2-ns and Ramos B-cell lines that stably expressed the HCV core protein. Growth curve, thymidine incorporation analysis, as well as the expression of PCNA and activated-ERKs demonstrated that HCV core protein induced an increased growth in both cell lines. Interestingly, the HCV core protein expression determined, in our model, a downregulation of DNp73 and an upregulation of DNp63, which was essential for the maintenance of viral-dependent effects on cell growth. Finally, we have identified phosphoinositide 3-kinase (PI3K) as mediator of HCV core-dependent transcriptional increase of DNp63, which in turn correlated with the increasing of lymphocyte proliferation. In primary B-lymphocytes, derived from HCV-related low-grade non-Hodgkin's lymphoma patients, consistent results were obtained. These findings provide evidence for a possible pathogenetic role played by HCV core protein in HCV-related lymphomagenesis; it could occur through the deregulation of PI3K activity, consequent activation of Akt and overexpression of DNp63.
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Affiliation(s)
- Anna Alisi
- Laboratory of Molecular Virology and Oncology, Fondazione A. Cesalpino, University of Rome La Sapienza, Rome, Italy
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Coban S, Palabiyikoğlu M, Ensari A, Idilman R, Köklü S, Yolcu OF, Ormeci N. Intestinal B cell lymphoma associated with chronic hepatitis C and celiac disease. Dig Dis Sci 2005; 50:2359-61. [PMID: 16416190 DOI: 10.1007/s10620-005-3063-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Accepted: 11/03/2004] [Indexed: 12/20/2022]
MESH Headings
- Abdomen, Acute/diagnosis
- Abdomen, Acute/surgery
- Aged
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biopsy, Needle
- Celiac Disease/complications
- Celiac Disease/diagnosis
- Celiac Disease/therapy
- Colonic Diseases/complications
- Colonic Diseases/diagnosis
- Colonic Diseases/surgery
- Follow-Up Studies
- Hepatitis C, Chronic/complications
- Hepatitis C, Chronic/diagnosis
- Hepatitis C, Chronic/drug therapy
- Humans
- Immunohistochemistry
- Laparotomy
- Lymphoma, B-Cell/complications
- Lymphoma, B-Cell/diagnosis
- Lymphoma, B-Cell/drug therapy
- Lymphoma, Non-Hodgkin/complications
- Lymphoma, Non-Hodgkin/diagnosis
- Lymphoma, Non-Hodgkin/drug therapy
- Male
- Risk Assessment
- Severity of Illness Index
- Treatment Outcome
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Affiliation(s)
- Sahin Coban
- Department of Gastroenterology, Ankara University Medical School, Ankara, Turkey.
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Abstract
Chronic hepatitis C virus (HCV) infection is associated with the development of lymphoproliferative disorders (LPDs). The aim of this investigation was to determine the prevalence and characterization of monoclonal gammopathy and benign and malignant LPDs in individuals with chronic hepatitis C. A total of 233 subjects diagnosed with chronic hepatitis C (male/female ratio: 131/102, median age; 49 years) were studied. Serum and urine were examined for the presence of a monoclonal gammopathy. A bone marrow aspirate and biopsy was obtained in individuals with a monoclonal gammopathy. Thirty-two patients (13.7%, 32 of 233) had a monoclonal gammopathy; 75% of them were benign and were not associated with malignant disorders (24 of 32) while 25% were associated with malignant LPDs or a plasma cell disorder (eight of 32). Two additional subjects without monoclonal gammopathy were diagnosed as having a malignant LPDs. The prevalence of malignant LPDs/plasma cell disorder in individuals with HCV-induced chronic liver disease was 4.3%. No difference was found in terms of disease duration, HCV genotype, viral load, alanine aminotransferase level or histopathologic score between the subjects with or without a monoclonal gammopathy. The presence of mixed cryoglobulinaemia was strongly associated with the presence of an underlying malignant disorder. Hence a monoclonal gammopathy is found in 14% of patients with chronic hepatitis C and is associated with malignant B-cell LPD in more than a quarter of such patients. The prevalence of LPDs in individuals with HCV-induced chronic liver disease is greater than that of the normal healthy population.
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Affiliation(s)
- R Idilman
- Department of Medicine, Division of Gastroenterology and Liver Transplantation, Loyola University Medical Center, Maywood, IL, USA.
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Galli-Stampino L, Pasqualini A, Pozzato G, Bonino F, Filipponi F, Mosca M, Masciopinto F, Abrignani S, Uematsu Y. Molecular analysis of V(H)I+ B lymphocytes in hepatitis C patients. Dig Liver Dis 2003; 35:788-94. [PMID: 14674669 DOI: 10.1016/s1590-8658(03)00452-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Hepatitis C virus infection is often associated with lymphoproliferative disorders such as essential mixed cryoglobulinemia and B-cell non-Hodgkin lymphoma, which show preferential expression of VHI family products. By analyzing immunoglobulin heavy chain usage, we addressed the question of whether or not clonal B-cell expansion occurrs in patients free of essential mixed cryoglobulinemia or non-Hodgkin lymphoma. PATIENTS AND METHODS Four hepatitis C virus-positive patients, all undergoing liver transplantation, were studied. Peripheral blood, intra-hepatic, and lymph node lymphocytes were used as a source of B cells. A patient with hepatocellular carcinoma and fresh blood from four healthy donors were used as negative controls. VHI family sequences were cloned and analyzed by reverse transcription-polymerase chain reaction. RESULTS Immunoglobulin heavy chain sequences from clonally expanded B lymphocytes were identified in three out of four hepatitis C virus-infected patients. The clonally expanded B lymphocyte populations showed a broad spectra of immunoglobulin heavy chain gene usage. CONCLUSIONS HCV infection can induce B-cell expansion with larger clonal variation. The restricted V gene usage in hepatitis C virus-associated non-Hodgkin lymphoma suggests that there may be selection mechanisms to develop non-Hodgkin lymphoma from non-malignant, clonally expanded B-cell populations in hepatitis C virus-infected patients.
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Affiliation(s)
- L Galli-Stampino
- Department of Immunology, IRIS, Chiron S.r.l., Via Fiorentina, 1, 1-53100 Siena, Italy
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Keresztes K, Takács M, Horányi M, Miltényi Z, Illés A. HCV and HGV infection in Hodgkin's disease. Pathol Oncol Res 2003; 9:222-5. [PMID: 14688827 DOI: 10.1007/bf02893381] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2003] [Accepted: 11/12/2003] [Indexed: 11/28/2022]
Abstract
Numerous observations imply that the pathogenesis of malignant lymphomas is multifactorial and that viruses probably play an important etiologic role. Besides Epstein-Barr virus, there might be other viruses among the causes of Hodgkin's disease. A total of 111 randomly selected patients with Hodgkin's disease were included in this study, and hepatitis C and G viruses were tested with polymerase chain reaction. The results were compared to hepatitis C and G virus infection ratios assessed by polymerase chain reaction in the Hungarian blood bank. Hepatitis C virus was diagnosed in 10 (9%) patients, and hepatitis G virus in 9 (8,1%), which is a 12-fold and a 1,5-fold infection rate as compared to that of the Hungarian blood bank, respectively. There was no significant difference between hepatitis positive and negative patients concerning mean age at the time of diagnosis, sex, disease stage, histology type, treatment applied, risk factors in the history of the infection and liver enzymes. Hepatitis C virus positivity in patients with Hodgkin's disease differs significantly from that in blood donors. Based on these results and data in the literature, no definite statement can be made on the etiological role of viruses, but further studies are needed.
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Affiliation(s)
- Katalin Keresztes
- 3rd Department of Medicine, Medical and Health Science Center, University of Debrecen, Debrecen, H-4004, Hungary.
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Musto P. Hepatitis C virus infection and B-cell non-Hodgkin's lymphomas: more than a simple association. CLINICAL LYMPHOMA 2002; 3:150-60. [PMID: 12521391 DOI: 10.3816/clm.2002.n.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Several studies have reported that the prevalence of the hepatitis C virus (HCV) infection is significantly overrepresented in patients affected by non-Hodgkin's lymphoma (NHL), thus suggesting that besides the well-established link with essential mixed cryoglobulinemia, a possible role for HCV is determining the development of at least some types of B-cell NHL. Such an association, however, seems to be limited to geographic areas where the presence of HCV is more relevant or endemic. According to a multistep pathogenetic model based on a large series of clinical, immunological, histological, and molecular evidences, an HCV antigen-driven polyclonal B-cell lymphoproliferation could be the initial phase of a process leading, in a variable time, into a true clonal disease. Particular genetic and environmental backgrounds could play a role in the development of a malignant phenotype, while specific HCV genotypes do not seem to be relevant in this setting. Hepatitis C virus correlated with NHL often shows some distinctive clinicopathological features, such as older age, liver damage, presence of monoclonal gammopathy (often with no clinically relevant cryoglobulinemic and/or rheumatoid activity), increased rate of autoimmune disorders, extranodal localizations, and restricted histological subtypes. Overall, the clinical outcome of HCV-positive NHL does not seem to be different from that of NHL patients without HCV infection. However, the evidence of a significant hepatic injury may predict a worse prognosis in these subjects.
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Affiliation(s)
- Pellegrino Musto
- Unit of Hematology and Stem Cell Transplantation, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy.
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Bates I, Bedu-Addo G, Jarrett RF, Schulz T, Wallace S, Armstrong A, Sheldon J, Rutherford T. B-lymphotropic viruses in a novel tropical splenic lymphoma. Br J Haematol 2001; 112:161-6. [PMID: 11167797 DOI: 10.1046/j.1365-2141.2001.02517.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Peripheral blood from patients with a novel tropical splenic lymphoma, characterized by splenomegaly and circulating naïve CD5-negative villous B lymphocytes, has been screened for evidence of an association with the B-lymphotropic viruses, Epstein--Barr virus (EBV), hepatitis C virus (HCV) and human herpesvirus 8 (HHV8). No increased prevalence of EBV, HCV and HHV8 was demonstrated using serological and molecular techniques, compared with a geographical, age-matched control group. However, lymphoma patients had markedly raised EBV antibody levels without a concomitant increase in the rate of detection of viral genomes in the peripheral blood. This phenomenon also occurred in patients with hyper-reactive malarial splenomegaly, a condition that occurs in the same geographical area and that is clinically indistinguishable from tropical splenic lymphoma, adding further weight to the suggestion that there may be an aetiological association between these two disorders.
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Affiliation(s)
- I Bates
- Liverpool School of Tropical Medicine, UK.
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11
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García-Carrasco M, Ramos-Casals M, Cervera R, Font J. [Primary Sjögren's syndrome and lymphatic proliferation]. Med Clin (Barc) 2000; 114:740-6. [PMID: 10919130 DOI: 10.1016/s0025-7753(00)71420-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- M García-Carrasco
- Unitat de Malalties Autoimmunes Sistèmiques, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona
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Chassagne-Clément C, Philip T. [Epidemiology of malignant non-Hodgkin's lymphoma: current data]. Rev Med Interne 1998; 19 Suppl 1:9S-11S. [PMID: 9789520 DOI: 10.1016/s0248-8663(98)80002-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Abstract
A pathogenetic role of the hepatitis C virus (HCV) has been hypothesized for a subset of B-cell non-Hodgkin's lymphomas (NHLs). However, the preliminary characterization of B-cell NHLs in HCV-infected individuals has been poorly addressed. In the present study, we report detailed information on 35 consecutive patients with overt B-cell NHL of recent onset and HCV infection; all patients referred to a single oncological center in Northeast Italy. Histopathologic evaluation was performed by a single reference hemopathologist, and the link with the two relevant autoimmune diseases predisposing to B-cell NHL and in which HCV has been implied, ie, “essential” mixed cryoglobulinemia (EMC) and Sjögren's syndrome, was investigated. Control groups included 122 consecutive HCV-negative patients with B-cell NHL and 464 consecutive histopathologic cases of B-cell NHL referred to the same center, as well as 127 consecutive patients with HCV infection and without lymphoma referred to a different center in the same geographical area. B-cell NHLs in HCV-infected patients frequently presented at onset (1) an extranodal localization with peculiar target organs of HCV infection (ie, the liver and major salivary glands) being significantly overrepresented; (2) a diffuse large cell histotype without any prior history of low-grade B-cell malignancy or bone marrow involvement; and (3) a weak association with a full-blown predisposing autoimmune disease, although serum autoimmune features were common and cryoglobulins were always present. Therefore, the HCV-related B-cell NHLs in this oncological series presented distinctive features compared with B-cell NHLs in HCV-negative patients, and they differed from bone marrow low-grade NHLs frequently diagnosed in HCV-positive patients with EMC. Such novel information may be relevant for future research aimed at clarifying the possible link between HCV infection, autoimmunity, nonmalignant B-cell lymphoproliferation, and overt B-cell malignancy.
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Abstract
Abstract
A pathogenetic role of the hepatitis C virus (HCV) has been hypothesized for a subset of B-cell non-Hodgkin's lymphomas (NHLs). However, the preliminary characterization of B-cell NHLs in HCV-infected individuals has been poorly addressed. In the present study, we report detailed information on 35 consecutive patients with overt B-cell NHL of recent onset and HCV infection; all patients referred to a single oncological center in Northeast Italy. Histopathologic evaluation was performed by a single reference hemopathologist, and the link with the two relevant autoimmune diseases predisposing to B-cell NHL and in which HCV has been implied, ie, “essential” mixed cryoglobulinemia (EMC) and Sjögren's syndrome, was investigated. Control groups included 122 consecutive HCV-negative patients with B-cell NHL and 464 consecutive histopathologic cases of B-cell NHL referred to the same center, as well as 127 consecutive patients with HCV infection and without lymphoma referred to a different center in the same geographical area. B-cell NHLs in HCV-infected patients frequently presented at onset (1) an extranodal localization with peculiar target organs of HCV infection (ie, the liver and major salivary glands) being significantly overrepresented; (2) a diffuse large cell histotype without any prior history of low-grade B-cell malignancy or bone marrow involvement; and (3) a weak association with a full-blown predisposing autoimmune disease, although serum autoimmune features were common and cryoglobulins were always present. Therefore, the HCV-related B-cell NHLs in this oncological series presented distinctive features compared with B-cell NHLs in HCV-negative patients, and they differed from bone marrow low-grade NHLs frequently diagnosed in HCV-positive patients with EMC. Such novel information may be relevant for future research aimed at clarifying the possible link between HCV infection, autoimmunity, nonmalignant B-cell lymphoproliferation, and overt B-cell malignancy.
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